python-cobra →
0.14.2-2 →
armhf → 2020-02-24 11:28:50
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| python-cobra 0.14.2-2 (armhf) Mon, 24 Feb 2020 10:59:03 +0000 |
+==============================================================================+
Package: python-cobra
Version: 0.14.2-2
Source Version: 0.14.2-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-1662a47c-758b-4c86-9f1e-82ecb874eb22' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.6 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.3 MB in 33s (734 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'python-cobra' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/python-cobra.git
Please use:
git clone https://salsa.debian.org/med-team/python-cobra.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1779 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main python-cobra 0.14.2-2 (dsc) [2608 B]
Get:2 http://172.17.0.1/private bullseye-staging/main python-cobra 0.14.2-2 (tar) [1769 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main python-cobra 0.14.2-2 (diff) [7368 B]
Fetched 1779 kB in 1s (2021 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-cobra-Aa5O4s/python-cobra-0.14.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-cobra-Aa5O4s' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-J1VyWc/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-J1VyWc/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-J1VyWc/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-J1VyWc/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-J1VyWc/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-J1VyWc/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-J1VyWc/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-J1VyWc/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2690 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 27 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-J1VyWc/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12236 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 12~), dh-python, libglpk-dev, python3-all, python3-all-dev, python3-setuptools, python3-depinfo, python3-future, python3-numpy, python3-optlang, python3-ruamel.yaml, python3-pandas (>= 0.17.0), python3-pip, python3-pipdeptree, python3-requests, python3-swiglpk, python3-tabulate, python3-sbml, python3-simplejson, cython3, python3-pytest, python3-pytest-benchmark, python3-jsonschema (>> 2.5.0)
Filtered Build-Depends: debhelper (>= 12~), dh-python, libglpk-dev, python3-all, python3-all-dev, python3-setuptools, python3-depinfo, python3-future, python3-numpy, python3-optlang, python3-ruamel.yaml, python3-pandas (>= 0.17.0), python3-pip, python3-pipdeptree, python3-requests, python3-swiglpk, python3-tabulate, python3-sbml, python3-simplejson, cython3, python3-pytest, python3-pytest-benchmark, python3-jsonschema (>> 2.5.0)
dpkg-deb: building package 'sbuild-build-depends-python-cobra-dummy' in '/<<BUILDDIR>>/resolver-J1VyWc/apt_archive/sbuild-build-depends-python-cobra-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-python-cobra-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-J1VyWc/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-J1VyWc/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-J1VyWc/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-J1VyWc/apt_archive ./ Sources [647 B]
Get:5 copy:/<<BUILDDIR>>/resolver-J1VyWc/apt_archive ./ Packages [729 B]
Fetched 2709 B in 1s (3425 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install python-cobra build dependencies (apt-based resolver)
------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils ca-certificates
cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file
gettext gettext-base groff-base intltool-debian libamd2 libarchive-zip-perl
libblas-dev libblas3 libbsd0 libbtf1 libcamd2 libccolamd2 libcholmod3
libcolamd2 libcroco3 libcxsparse3 libdebhelper-perl libelf1 libexpat1
libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0
libglpk-dev libglpk40 libgmp-dev libgmpxx4ldbl libgraphblas3 libicu63
libklu1 liblapack-dev liblapack3 libldl2 libltdl7 libmagic-mgc libmagic1
libmetis5 libmongoose2 libmpdec2 libpipeline1 libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev
libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev
libpython3.8-minimal libpython3.8-stdlib librbio2 libsigsegv2 libspqr2
libssl1.1 libsub-override-perl libsuitesparse-dev libsuitesparseconfig5
libtinfo5 libtool libuchardet0 libumfpack5 libxml2 m4 man-db mime-support
openssl po-debconf python-pip-whl python3 python3-all python3-all-dev
python3-atomicwrites python3-attr python3-certifi python3-chardet
python3-cpuinfo python3-dateutil python3-depinfo python3-dev
python3-distutils python3-future python3-idna python3-importlib-metadata
python3-jsonschema python3-lib2to3 python3-minimal python3-more-itertools
python3-mpmath python3-numpy python3-optlang python3-packaging
python3-pandas python3-pandas-lib python3-pip python3-pipdeptree
python3-pkg-resources python3-pluggy python3-py python3-pyparsing
python3-pyrsistent python3-pytest python3-pytest-benchmark python3-requests
python3-ruamel.yaml python3-sbml5 python3-setuptools python3-simplejson
python3-six python3-swiglpk python3-sympy python3-tabulate python3-tz
python3-urllib3 python3-wcwidth python3-zipp python3.7 python3.7-dev
python3.7-minimal python3.8 python3.8-dev python3.8-minimal sensible-utils
swig swig3.0 zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev
groff liblapack-doc libiodbc2-dev default-libmysqlclient-dev gmp-doc
libgmp10-doc libmpfr-dev libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk
python3-venv python-attr-doc python-future-doc python-jsonschema-doc
python3-gmpy2 python3-matplotlib python-mpmath-doc gfortran python-numpy-doc
python3-numpy-dbg python-pandas-doc python3-statsmodels subversion
python-pyparsing-doc python3-cryptography python3-openssl python3-socks
python-setuptools-doc texlive-fonts-extra dvipng python-sympy-doc
python3.7-venv python3.7-doc binfmt-support python3.8-venv python3.8-doc
swig-doc swig-examples swig3.0-examples swig3.0-doc
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl python3-scipy
python3-matplotlib python3-numexpr python3-tables python3-xlrd
python3-openpyxl python3-xlwt python3-bs4 python3-html5lib python3-lxml
python3-wheel python3-elasticsearch python3-freezegun python3-pygal
python3-pil ipython3
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils ca-certificates
cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file
gettext gettext-base groff-base intltool-debian libamd2 libarchive-zip-perl
libblas-dev libblas3 libbsd0 libbtf1 libcamd2 libccolamd2 libcholmod3
libcolamd2 libcroco3 libcxsparse3 libdebhelper-perl libelf1 libexpat1
libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0
libglpk-dev libglpk40 libgmp-dev libgmpxx4ldbl libgraphblas3 libicu63
libklu1 liblapack-dev liblapack3 libldl2 libltdl7 libmagic-mgc libmagic1
libmetis5 libmongoose2 libmpdec2 libpipeline1 libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev
libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev
libpython3.8-minimal libpython3.8-stdlib librbio2 libsigsegv2 libspqr2
libssl1.1 libsub-override-perl libsuitesparse-dev libsuitesparseconfig5
libtinfo5 libtool libuchardet0 libumfpack5 libxml2 m4 man-db mime-support
openssl po-debconf python-pip-whl python3 python3-all python3-all-dev
python3-atomicwrites python3-attr python3-certifi python3-chardet
python3-cpuinfo python3-dateutil python3-depinfo python3-dev
python3-distutils python3-future python3-idna python3-importlib-metadata
python3-jsonschema python3-lib2to3 python3-minimal python3-more-itertools
python3-mpmath python3-numpy python3-optlang python3-packaging
python3-pandas python3-pandas-lib python3-pip python3-pipdeptree
python3-pkg-resources python3-pluggy python3-py python3-pyparsing
python3-pyrsistent python3-pytest python3-pytest-benchmark python3-requests
python3-ruamel.yaml python3-sbml5 python3-setuptools python3-simplejson
python3-six python3-swiglpk python3-sympy python3-tabulate python3-tz
python3-urllib3 python3-wcwidth python3-zipp python3.7 python3.7-dev
python3.7-minimal python3.8 python3.8-dev python3.8-minimal
sbuild-build-depends-python-cobra-dummy sensible-utils swig swig3.0
zlib1g-dev
The following packages will be upgraded:
zlib1g
1 upgraded, 140 newly installed, 0 to remove and 26 not upgraded.
Need to get 160 MB of archives.
After this operation, 535 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-J1VyWc/apt_archive ./ sbuild-build-depends-python-cobra-dummy 0.invalid.0 [1016 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf zlib1g armhf 1:1.2.11.dfsg-1.2 [84.6 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.6-1+b1 [585 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.6-1+b1 [1525 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-3 [36.8 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.6-1+b1 [1669 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.6-1+b1 [351 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-3 [20.2 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-3 [62.1 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.2~rc2-2 [743 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.2~rc2-2 [1625 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-4 [262 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1d-2 [806 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20190110 [157 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf cython3 armhf 0.29.14-0.1 [1375 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-13 [513 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.9 [183 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-2 [14.7 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-2 [1138 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.9 [994 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.8.0-1 [78.3 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.8.0-1 [145 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20191017 [94.4 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libsuitesparseconfig5 armhf 1:5.6.0+dfsg-2 [21.7 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libamd2 armhf 1:5.6.0+dfsg-2 [28.3 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-1 [108 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-1 [113 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libbtf1 armhf 1:5.6.0+dfsg-2 [22.3 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libcamd2 armhf 1:5.6.0+dfsg-2 [28.9 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libccolamd2 armhf 1:5.6.0+dfsg-2 [29.6 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libcolamd2 armhf 1:5.6.0+dfsg-2 [26.4 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.2.1-25+rpi1 [231 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-1 [1597 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libmetis5 armhf 5.1.0.dfsg-5 [131 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libcholmod3 armhf 1:5.6.0+dfsg-2 [212 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libcxsparse3 armhf 1:5.6.0+dfsg-2 [50.8 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libexpat1-dev armhf 2.2.9-1 [119 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-13 [388 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libglpk40 armhf 4.65-2 [339 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libgmpxx4ldbl armhf 2:6.1.2+dfsg-4 [21.8 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libgmp-dev armhf 2:6.1.2+dfsg-4 [570 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1.2 [203 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libgraphblas3 armhf 1:5.6.0+dfsg-2 [1930 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libklu1 armhf 1:5.6.0+dfsg-2 [50.1 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libldl2 armhf 1:5.6.0+dfsg-2 [22.1 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libmongoose2 armhf 1:5.6.0+dfsg-2 [42.3 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libumfpack5 armhf 1:5.6.0+dfsg-2 [126 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf librbio2 armhf 1:5.6.0+dfsg-2 [30.9 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libspqr2 armhf 1:5.6.0+dfsg-2 [67.8 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-1 [2981 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libsuitesparse-dev armhf 1:5.6.0+dfsg-2 [2262 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libglpk-dev armhf 4.65-2 [379 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7 armhf 3.7.6-1+b1 [1256 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-dev armhf 3.7.6-1+b1 [40.2 MB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libpython3-dev armhf 3.7.5-3 [20.3 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.2~rc2-2 [1598 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8 armhf 3.8.2~rc2-2 [1365 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-dev armhf 3.8.2~rc2-2 [46.0 MB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libpython3-all-dev armhf 3.7.5-3 [1072 B]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf python-pip-whl all 18.1-5 [1591 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.2~rc2-2 [409 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf python3-all armhf 3.7.5-3 [1060 B]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf python3.7-dev armhf 3.7.6-1+b1 [518 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf python3-dev armhf 3.7.5-3 [1260 B]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf python3.8-dev armhf 3.8.2~rc2-2 [519 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf python3-all-dev armhf 3.7.5-3 [1076 B]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf python3-atomicwrites all 1.1.5-2 [6892 B]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf python3-attr all 19.3.0-1 [43.1 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf python3-certifi all 2019.11.28-1 [149 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 44.0.0-1 [155 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf python3-chardet all 3.0.4-4 [80.8 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf python3-cpuinfo all 5.0.0-2 [19.0 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf python3-six all 1.14.0-2 [16.7 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf python3-dateutil all 2.7.3-3 [64.5 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf python3-pip all 18.1-5 [171 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf python3-pipdeptree armhf 0.13.2-1 [15.5 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf python3-depinfo armhf 1.5.1-1 [5528 B]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf python3-future all 0.18.2-1 [348 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf python3-idna all 2.6-2 [34.4 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf python3-more-itertools all 4.2.0-1 [42.2 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf python3-zipp all 1.0.0-1 [5944 B]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf python3-importlib-metadata all 1.5.0-1 [9956 B]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf python3-setuptools all 44.0.0-1 [313 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf python3-pyrsistent armhf 0.15.5-1 [55.5 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf python3-jsonschema all 3.0.2-4 [44.9 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf python3-mpmath all 1.1.0-1 [416 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf python3-numpy armhf 1:1.17.4-5+b1 [4484 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf python3-swiglpk armhf 4.65.0-2 [52.8 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf python3-sympy all 1.4-1 [3604 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf python3-optlang all 1.4.4-2 [67.7 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf python3-pyparsing all 2.4.6-1 [109 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf python3-packaging all 19.1-2 [23.9 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf python3-tz all 2019.3-1 [27.2 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf python3-pandas-lib armhf 0.25.3+dfsg-4+b1 [7002 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf python3-pandas all 0.25.3+dfsg-4 [1983 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf python3-pluggy all 0.13.0-2 [21.9 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf python3-py all 1.8.1-1 [86.8 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf python3-wcwidth all 0.1.8+dfsg1-3 [17.4 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf python3-pytest all 4.6.9-1 [267 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf python3-pytest-benchmark all 3.2.2-2 [46.4 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf python3-urllib3 all 1.25.8-1 [104 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf python3-requests all 2.22.0-2 [67.0 kB]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf python3-ruamel.yaml armhf 0.15.89-3 [216 kB]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf swig3.0 armhf 3.0.12-2.2 [1242 kB]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf swig armhf 3.0.12-2.2 [310 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf python3-sbml5 armhf 5.18.0+dfsg-1 [2870 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf python3-simplejson armhf 3.16.0-2 [58.0 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf python3-tabulate all 0.8.2-1.1 [32.2 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libglpk-dev:armhf (4.65-2) ...
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Unpacking python3-mpmath (1.1.0-1) ...
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Unpacking python3-numpy (1:1.17.4-5+b1) ...
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Unpacking python3-sympy (1.4-1) ...
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Unpacking python3-packaging (19.1-2) ...
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Unpacking python3-tz (2019.3-1) ...
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Unpacking python3-py (1.8.1-1) ...
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Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up libgraphblas3:armhf (1:5.6.0+dfsg-2) ...
Setting up libpython3.8-minimal:armhf (3.8.2~rc2-2) ...
Setting up mime-support (3.64) ...
Setting up libmagic-mgc (1:5.38-4) ...
Setting up libarchive-zip-perl (1.67-1) ...
Setting up libglib2.0-0:armhf (2.62.4-2) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (12.9) ...
Setting up libldl2:armhf (1:5.6.0+dfsg-2) ...
Setting up libmagic1:armhf (1:5.38-4) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up libmetis5:armhf (5.1.0.dfsg-5) ...
Setting up file (1:5.38-4) ...
Setting up libbtf1:armhf (1:5.6.0+dfsg-2) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up libblas3:armhf (3.9.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libgmpxx4ldbl:armhf (2:6.1.2+dfsg-4) ...
Setting up libexpat1-dev:armhf (2.2.9-1) ...
Setting up swig3.0 (3.0.12-2.2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libltdl7:armhf (2.4.6-13) ...
Setting up libgfortran5:armhf (9.2.1-25+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1.2) ...
Setting up python3.8-minimal (3.8.2~rc2-2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libcxsparse3:armhf (1:5.6.0+dfsg-2) ...
Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up libpython3.8-stdlib:armhf (3.8.2~rc2-2) ...
Setting up python3.8 (3.8.2~rc2-2) ...
Setting up openssl (1.1.1d-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up libsuitesparseconfig5:armhf (1:5.6.0+dfsg-2) ...
Setting up libblas-dev:armhf (3.9.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up librbio2:armhf (1:5.6.0+dfsg-2) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-2) ...
Setting up libamd2:armhf (1:5.6.0+dfsg-2) ...
Setting up libpython3.7-stdlib:armhf (3.7.6-1+b1) ...
Setting up liblapack3:armhf (3.9.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up swig (3.0.12-2.2) ...
Setting up libgmp-dev:armhf (2:6.1.2+dfsg-4) ...
Setting up libcolamd2:armhf (1:5.6.0+dfsg-2) ...
Setting up libpython3.7:armhf (3.7.6-1+b1) ...
Setting up libtool (2.4.6-13) ...
Setting up libpython3.7-dev:armhf (3.7.6-1+b1) ...
Setting up m4 (1.4.18-4) ...
Setting up ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
128 added, 0 removed; done.
Setting up libcamd2:armhf (1:5.6.0+dfsg-2) ...
Setting up libmongoose2:armhf (1:5.6.0+dfsg-2) ...
Setting up libglpk40:armhf (4.65-2) ...
Setting up libpython3.8:armhf (3.8.2~rc2-2) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up liblapack-dev:armhf (3.9.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.6.3-2) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up libklu1:armhf (1:5.6.0+dfsg-2) ...
Setting up libccolamd2:armhf (1:5.6.0+dfsg-2) ...
Setting up python-pip-whl (18.1-5) ...
Setting up libcholmod3:armhf (1:5.6.0+dfsg-2) ...
Setting up libpython3-stdlib:armhf (3.7.5-3) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libspqr2:armhf (1:5.6.0+dfsg-2) ...
Setting up python3.7 (3.7.6-1+b1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libpython3-dev:armhf (3.7.5-3) ...
Setting up python3 (3.7.5-3) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python3.7-dev (3.7.6-1+b1) ...
Setting up python3-sbml5 (5.18.0+dfsg-1) ...
Setting up python3-tz (2019.3-1) ...
Setting up python3-atomicwrites (1.1.5-2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up python3-six (1.14.0-2) ...
Setting up python3-simplejson (3.16.0-2) ...
Setting up libumfpack5:armhf (1:5.6.0+dfsg-2) ...
Setting up python3-wcwidth (0.1.8+dfsg1-3) ...
Setting up python3-pyparsing (2.4.6-1) ...
Setting up python3-certifi (2019.11.28-1) ...
Setting up libpython3.8-dev:armhf (3.8.2~rc2-2) ...
Setting up libpython3-all-dev:armhf (3.7.5-3) ...
Setting up python3-idna (2.6-2) ...
Setting up cython3 (0.29.14-0.1) ...
Setting up python3-cpuinfo (5.0.0-2) ...
Setting up python3-urllib3 (1.25.8-1) ...
Setting up python3.8-dev (3.8.2~rc2-2) ...
Setting up python3-ruamel.yaml (0.15.89-3) ...
Setting up python3-pyrsistent:armhf (0.15.5-1) ...
Setting up python3-dateutil (2.7.3-3) ...
Setting up python3-mpmath (1.1.0-1) ...
/usr/lib/python3/dist-packages/mpmath/ctx_mp_python.py:892: SyntaxWarning: "is" with a literal. Did you mean "=="?
if other is 0:
/usr/lib/python3/dist-packages/mpmath/ctx_mp_python.py:986: SyntaxWarning: "is" with a literal. Did you mean "=="?
if other is 0:
Setting up python3-lib2to3 (3.8.0-1) ...
Setting up python3-swiglpk (4.65.0-2) ...
Setting up python3-pkg-resources (44.0.0-1) ...
Setting up python3-distutils (3.8.0-1) ...
Setting up dh-python (4.20191017) ...
Setting up python3-more-itertools (4.2.0-1) ...
Setting up python3-sympy (1.4-1) ...
/usr/lib/python3/dist-packages/sympy/core/tests/test_containers.py:55: SyntaxWarning: "is not" with a literal. Did you mean "!="?
assert Tuple(1, 2) is not (1, 2)
/usr/lib/python3/dist-packages/sympy/geometry/tests/test_plane.py:190: SyntaxWarning: "is" with a literal. Did you mean "=="?
assert len(pl8.intersection(Ray3D(Point3D(0, 2, 3), Point3D(1, 0, 3)))) is 0
/usr/lib/python3/dist-packages/sympy/physics/vector/printing.py:155: SyntaxWarning: "is not" with a literal. Did you mean "!="?
if len(base_split) is not 1:
/usr/lib/python3/dist-packages/sympy/plotting/plot.py:509: SyntaxWarning: "is" with a literal. Did you mean "=="?
if self.xscale is 'log':
/usr/lib/python3/dist-packages/sympy/plotting/plot.py:529: SyntaxWarning: "is" with a literal. Did you mean "=="?
if self.xscale is 'log':
/usr/lib/python3/dist-packages/sympy/plotting/plot.py:542: SyntaxWarning: "is" with a literal. Did you mean "=="?
if self.xscale is 'log':
/usr/lib/python3/dist-packages/sympy/plotting/plot.py:549: SyntaxWarning: "is" with a literal. Did you mean "=="?
if self.xscale is 'log':
/usr/lib/python3/dist-packages/sympy/polys/agca/modules.py:360: SyntaxWarning: "is" with a literal. Did you mean "=="?
elif elem is 0:
/usr/lib/python3/dist-packages/sympy/solvers/diophantine.py:3186: SyntaxWarning: "is" with a literal. Did you mean "=="?
if feasible is 1: # it's prime and k == 2
/usr/lib/python3/dist-packages/sympy/vector/coordsysrect.py:170: SyntaxWarning: "is" with a literal. Did you mean "=="?
if transformation.name is 'spherical':
/usr/lib/python3/dist-packages/sympy/vector/coordsysrect.py:172: SyntaxWarning: "is" with a literal. Did you mean "=="?
elif transformation.name is 'cylindrical':
Setting up python3-attr (19.3.0-1) ...
Setting up python3-setuptools (44.0.0-1) ...
Setting up python3-py (1.8.1-1) ...
Setting up libsuitesparse-dev:armhf (1:5.6.0+dfsg-2) ...
Setting up po-debconf (1.0.21) ...
Setting up python3-tabulate (0.8.2-1.1) ...
Setting up python3-all (3.7.5-3) ...
Setting up python3-zipp (1.0.0-1) ...
Setting up python3-packaging (19.1-2) ...
Setting up python3-chardet (3.0.4-4) ...
Setting up python3-jsonschema (3.0.2-4) ...
Setting up libglpk-dev:armhf (4.65-2) ...
Setting up python3-dev (3.7.5-3) ...
Setting up python3-requests (2.22.0-2) ...
Setting up python3-pip (18.1-5) ...
Setting up python3-numpy (1:1.17.4-5+b1) ...
Setting up python3-future (0.18.2-1) ...
update-alternatives: using /usr/bin/python3-futurize to provide /usr/bin/futurize (futurize) in auto mode
update-alternatives: using /usr/bin/python3-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode
Setting up python3-pipdeptree (0.13.2-1) ...
Setting up python3-optlang (1.4.4-2) ...
/usr/lib/python3/dist-packages/slow_tests/test_miplib_cplex_interface.py:65: SyntaxWarning: "is not" with a literal. Did you mean "!="?
if status is not "time_limit":
/usr/lib/python3/dist-packages/slow_tests/test_miplib_cplex_interface.py:68: SyntaxWarning: "is" with a literal. Did you mean "=="?
if status is "optimal":
/usr/lib/python3/dist-packages/slow_tests/test_miplib_glpk_interface.py:58: SyntaxWarning: "is not" with a literal. Did you mean "!="?
if status is not "time_limit":
/usr/lib/python3/dist-packages/slow_tests/test_miplib_glpk_interface.py:61: SyntaxWarning: "is" with a literal. Did you mean "=="?
if status is "optimal":
/usr/lib/python3/dist-packages/slow_tests/test_miplib_gurobi_interface.py:65: SyntaxWarning: "is not" with a literal. Did you mean "!="?
if status is not "time_limit":
/usr/lib/python3/dist-packages/slow_tests/test_miplib_gurobi_interface.py:68: SyntaxWarning: "is" with a literal. Did you mean "=="?
if status is "optimal":
Setting up python3-all-dev (3.7.5-3) ...
Setting up python3-importlib-metadata (1.5.0-1) ...
Setting up python3-pandas-lib (0.25.3+dfsg-4+b1) ...
Setting up python3-pandas (0.25.3+dfsg-4) ...
/usr/lib/python3/dist-packages/pandas/tests/frame/test_alter_axes.py:241: SyntaxWarning: "is" with a literal. Did you mean "=="?
False if (keys[0] is "A" and keys[1] is "A") else drop # noqa: F632
/usr/lib/python3/dist-packages/pandas/tests/frame/test_alter_axes.py:241: SyntaxWarning: "is" with a literal. Did you mean "=="?
False if (keys[0] is "A" and keys[1] is "A") else drop # noqa: F632
Setting up python3-depinfo (1.5.1-1) ...
Setting up python3-pluggy (0.13.0-2) ...
Setting up python3-pytest (4.6.9-1) ...
Setting up python3-pytest-benchmark (3.2.2-2) ...
Setting up debhelper (12.9) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-python-cobra-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-9+rpi1) ...
Processing triggers for ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.33.90.20200122-2+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-25+rpi1 gcc-9_9.2.1-25+rpi1 libc6-dev_2.29-9+rpi1 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-5 binutils_2.33.90.20200122-2+rpi1 binutils-arm-linux-gnueabihf_2.33.90.20200122-2+rpi1 binutils-common_2.33.90.20200122-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 ca-certificates_20190110 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-25+rpi1 cython3_0.29.14-0.1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20191017 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dirmngr_2.2.19-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-25+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-25+rpi1 gcc-9-base_9.2.1-25+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.19-1 gnupg-l10n_2.2.19-1 gnupg-utils_2.2.19-1 gpg_2.2.19-1 gpg-agent_2.2.19-1 gpg-wks-client_2.2.19-1 gpg-wks-server_2.2.19-1 gpgconf_2.2.19-1 gpgsm_2.2.19-1 gpgv_2.2.19-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.9-3 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-5 libamd2_1:5.6.0+dfsg-2 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-25+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-25+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.90.20200122-2+rpi1 libblas-dev_3.9.0-1 libblas3_3.9.0-1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbtf1_1:5.6.0+dfsg-2 libbz2-1.0_1.0.8-2 libc-bin_2.29-9+rpi1 libc-dev-bin_2.29-9+rpi1 libc6_2.29-9+rpi1 libc6-dev_2.29-9+rpi1 libcamd2_1:5.6.0+dfsg-2 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-25+rpi1 libccolamd2_1:5.6.0+dfsg-2 libcholmod3_1:5.6.0+dfsg-2 libcolamd2_1:5.6.0+dfsg-2 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libctf-nobfd0_2.33.90.20200122-2+rpi1 libctf0_2.33.90.20200122-2+rpi1 libcxsparse3_1:5.6.0+dfsg-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.9 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libexpat1-dev_2.2.9-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libgcc-9-dev_9.2.1-25+rpi1 libgcc1_1:9.2.1-25+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_9.2.1-25+rpi1 libglib2.0-0_2.62.4-2 libglpk-dev_4.65-2 libglpk40_4.65-2 libgmp-dev_2:6.1.2+dfsg-4 libgmp10_2:6.1.2+dfsg-4 libgmpxx4ldbl_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-25+rpi1 libgpg-error0_1.36-7 libgraphblas3_1:5.6.0+dfsg-2 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libklu1_1:5.6.0+dfsg-2 libksba8_1.3.5-2 liblapack-dev_3.9.0-1 liblapack3_3.9.0-1 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 libldl2_1:5.6.0+dfsg-2 libltdl7_2.4.6-13 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmetis5_5.1.0.dfsg-5 libmongoose2_1:5.6.0+dfsg-2 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2+b1 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpython3-all-dev_3.7.5-3 libpython3-dev_3.7.5-3 libpython3-stdlib_3.7.5-3 libpython3.7_3.7.6-1+b1 libpython3.7-dev_3.7.6-1+b1 libpython3.7-minimal_3.7.6-1+b1 libpython3.7-stdlib_3.7.6-1+b1 libpython3.8_3.8.2~rc2-2 libpython3.8-dev_3.8.2~rc2-2 libpython3.8-minimal_3.8.2~rc2-2 libpython3.8-stdlib_3.8.2~rc2-2 librbio2_1:5.6.0+dfsg-2 libreadline7_7.0-5 libreadline8_8.0-3 librust-rand-core-dev_0.5.1-1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libspqr2_1:5.6.0+dfsg-2 libsqlite3-0_3.31.0+really3.30.1+fossil191229-1 libss2_1.45.5-2 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 libsub-override-perl_0.09-2 libsuitesparse-dev_1:5.6.0+dfsg-2 libsuitesparseconfig5_1:5.6.0+dfsg-2 libsystemd0_244.1-1+rpi1 libtasn1-6_4.15.0-2 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-13 libubsan1_9.2.1-25+rpi1 libuchardet0_0.0.6-3 libudev1_244.1-1+rpi1 libumfpack5_1:5.6.0+dfsg-2 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8-1 logsave_1.45.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.4.20200120-1 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_6.0 openssl_1.1.1d-2 passwd_1:4.8-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 python-pip-whl_18.1-5 python3_3.7.5-3 python3-all_3.7.5-3 python3-all-dev_3.7.5-3 python3-atomicwrites_1.1.5-2 python3-attr_19.3.0-1 python3-certifi_2019.11.28-1 python3-chardet_3.0.4-4 python3-cpuinfo_5.0.0-2 python3-dateutil_2.7.3-3 python3-depinfo_1.5.1-1 python3-dev_3.7.5-3 python3-distutils_3.8.0-1 python3-future_0.18.2-1 python3-idna_2.6-2 python3-importlib-metadata_1.5.0-1 python3-jsonschema_3.0.2-4 python3-lib2to3_3.8.0-1 python3-minimal_3.7.5-3 python3-more-itertools_4.2.0-1 python3-mpmath_1.1.0-1 python3-numpy_1:1.17.4-5+b1 python3-optlang_1.4.4-2 python3-packaging_19.1-2 python3-pandas_0.25.3+dfsg-4 python3-pandas-lib_0.25.3+dfsg-4+b1 python3-pip_18.1-5 python3-pipdeptree_0.13.2-1 python3-pkg-resources_44.0.0-1 python3-pluggy_0.13.0-2 python3-py_1.8.1-1 python3-pyparsing_2.4.6-1 python3-pyrsistent_0.15.5-1 python3-pytest_4.6.9-1 python3-pytest-benchmark_3.2.2-2 python3-requests_2.22.0-2 python3-ruamel.yaml_0.15.89-3 python3-sbml5_5.18.0+dfsg-1 python3-setuptools_44.0.0-1 python3-simplejson_3.16.0-2 python3-six_1.14.0-2 python3-swiglpk_4.65.0-2 python3-sympy_1.4-1 python3-tabulate_0.8.2-1.1 python3-tz_2019.3-1 python3-urllib3_1.25.8-1 python3-wcwidth_0.1.8+dfsg1-3 python3-zipp_1.0.0-1 python3.7_3.7.6-1+b1 python3.7-dev_3.7.6-1+b1 python3.7-minimal_3.7.6-1+b1 python3.8_3.8.2~rc2-2 python3.8-dev_3.8.2~rc2-2 python3.8-minimal_3.8.2~rc2-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-cobra-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 swig_3.0.12-2.2 swig3.0_3.0.12-2.2 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1.2 zlib1g-dev_1:1.2.11.dfsg-1.2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Mar 2 06:26:37 2019 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-cobra_0.14.2-2.dsc
dpkg-source: info: extracting python-cobra in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking python-cobra_0.14.2.orig.tar.gz
dpkg-source: info: unpacking python-cobra_0.14.2-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying mathjax.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-1662a47c-758b-4c86-9f1e-82ecb874eb22
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package python-cobra
dpkg-buildpackage: info: source version 0.14.2-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
I: pybuild base:217: python3.8 setup.py clean
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.8' does not exist -- can't clean it
I: pybuild base:217: python3.7 setup.py clean
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.7' does not exist -- can't clean it
rm -f cobra/solvers/cglpk.c
rm -rf .pytest_cache
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules build-arch
dh build-arch --with python3 --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_autoreconf -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:217: python3.8 setup.py config
running config
I: pybuild base:217: python3.7 setup.py config
running config
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:217: /usr/bin/python3.8 setup.py build
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra
copying cobra/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra
copying cobra/exceptions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
copying cobra/core/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
copying cobra/core/configuration.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
copying cobra/core/dictlist.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
copying cobra/core/formula.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
copying cobra/core/gene.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
copying cobra/core/metabolite.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
copying cobra/core/model.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
copying cobra/core/object.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
copying cobra/core/reaction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
copying cobra/core/singleton.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
copying cobra/core/solution.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
copying cobra/core/species.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/deletion.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/gapfilling.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/geometric.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/loopless.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/moma.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/parsimonious.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/phenotype_phase_plane.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/reaction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/room.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/sampling.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/summary.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/variability.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
copying cobra/io/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
copying cobra/io/dict.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
copying cobra/io/json.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
copying cobra/io/mat.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
copying cobra/io/sbml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
copying cobra/io/sbml3.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
copying cobra/io/yaml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/manipulation
copying cobra/manipulation/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/manipulation
copying cobra/manipulation/annotate.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/manipulation
copying cobra/manipulation/delete.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/manipulation
copying cobra/manipulation/modify.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/manipulation
copying cobra/manipulation/validate.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/manipulation
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/medium
copying cobra/medium/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/medium
copying cobra/medium/annotations.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/medium
copying cobra/medium/boundary_types.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/medium
copying cobra/medium/minimal_medium.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/medium
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test
copying cobra/test/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test
copying cobra/test/conftest.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test
copying cobra/test/test_manipulation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test
copying cobra/test/test_medium.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/util
copying cobra/util/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/util
copying cobra/util/array.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/util
copying cobra/util/context.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/util
copying cobra/util/solver.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/util
copying cobra/util/util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/util
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
copying cobra/test/test_io/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
copying cobra/test/test_io/conftest.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_io_order.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_json.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_mat.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_pickle.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_sbml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_sbml3.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_yaml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/iJO1366.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/iJO1366.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/invalid0.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/invalid1.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/invalid2.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/mini.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/mini.mat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/mini.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/mini.yml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/mini_cobra.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/mini_fbc1.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/mini_fbc2.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/mini_fbc2.xml.bz2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/mini_fbc2.xml.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/raven.mat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/raven.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/salmonella.genes -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/salmonella.media -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/salmonella.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/salmonella.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/textbook.xml.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/textbook_fva.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/textbook_pfba_fva.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/textbook_solution.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
copying cobra/test/data/update_pickles.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
I: pybuild base:217: /usr/bin/python3 setup.py build
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra
copying cobra/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra
copying cobra/exceptions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
copying cobra/core/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
copying cobra/core/configuration.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
copying cobra/core/dictlist.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
copying cobra/core/formula.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
copying cobra/core/gene.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
copying cobra/core/metabolite.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
copying cobra/core/model.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
copying cobra/core/object.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
copying cobra/core/reaction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
copying cobra/core/singleton.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
copying cobra/core/solution.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
copying cobra/core/species.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/deletion.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/gapfilling.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/geometric.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/loopless.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/moma.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/parsimonious.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/phenotype_phase_plane.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/reaction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/room.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/sampling.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/summary.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
copying cobra/flux_analysis/variability.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
copying cobra/io/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
copying cobra/io/dict.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
copying cobra/io/json.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
copying cobra/io/mat.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
copying cobra/io/sbml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
copying cobra/io/sbml3.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
copying cobra/io/yaml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation
copying cobra/manipulation/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation
copying cobra/manipulation/annotate.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation
copying cobra/manipulation/delete.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation
copying cobra/manipulation/modify.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation
copying cobra/manipulation/validate.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/medium
copying cobra/medium/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/medium
copying cobra/medium/annotations.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/medium
copying cobra/medium/boundary_types.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/medium
copying cobra/medium/minimal_medium.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/medium
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test
copying cobra/test/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test
copying cobra/test/conftest.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test
copying cobra/test/test_manipulation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test
copying cobra/test/test_medium.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/util
copying cobra/util/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/util
copying cobra/util/array.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/util
copying cobra/util/context.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/util
copying cobra/util/solver.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/util
copying cobra/util/util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/util
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
copying cobra/test/test_io/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
copying cobra/test/test_io/conftest.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_io_order.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_json.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_mat.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_pickle.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_sbml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_sbml3.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
copying cobra/test/test_io/test_yaml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/iJO1366.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/iJO1366.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/invalid0.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/invalid1.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/invalid2.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/mini.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/mini.mat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/mini.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/mini.yml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/mini_cobra.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/mini_fbc1.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/mini_fbc2.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/mini_fbc2.xml.bz2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/mini_fbc2.xml.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/raven.mat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/raven.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/salmonella.genes -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/salmonella.media -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/salmonella.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/salmonella.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/textbook.xml.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/textbook_fva.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/textbook_pfba_fva.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/textbook_solution.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
copying cobra/test/data/update_pickles.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:217: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build; python3.8 -m pytest
============================= test session starts ==============================
platform linux -- Python 3.8.2rc2, pytest-4.6.9, py-1.8.1, pluggy-0.13.0
benchmark: 3.2.2 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /<<PKGBUILDDIR>>, inifile: setup.cfg
plugins: benchmark-3.2.2
No solvers were available and/or loadable.
collected 79 items
cobra/test/test_manipulation.py EEEFEEEEEEE [ 13%]
cobra/test/test_medium.py EEEEEEEEEEEEEEEEE [ 35%]
cobra/test/test_io/test_io_order.py EEEEEEEEEEEEEEEEEEEEEEEEEEE [ 69%]
cobra/test/test_io/test_json.py xEx [ 73%]
cobra/test/test_io/test_mat.py ss [ 75%]
cobra/test/test_io/test_pickle.py EEEE [ 81%]
cobra/test/test_io/test_sbml.py sss [ 84%]
cobra/test/test_io/test_sbml3.py FE.FEEEEEE [ 97%]
cobra/test/test_io/test_yaml.py Ex [100%]
==================================== ERRORS ====================================
______________ ERROR at setup of TestManipulation.test_escape_ids ______________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
@pytest.fixture(scope="session")
def small_model():
> return create_test_model("textbook")
cobra/test/conftest.py:49:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_____________ ERROR at setup of TestManipulation.test_rename_gene ______________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
______ ERROR at setup of TestManipulation.test_gene_knockout_computation _______
def swig_import_helper():
import importlib
pkg = __name__.rpartition('.')[0]
mname = '.'.join((pkg, '_swiglpk')).lstrip('.')
try:
> return importlib.import_module(mname)
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:14:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
/usr/lib/python3.8/importlib/__init__.py:127:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None, level = 0
> ???
<frozen importlib._bootstrap>:1014:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
<frozen importlib._bootstrap>:991:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
E ModuleNotFoundError: No module named 'swiglpk._swiglpk'
<frozen importlib._bootstrap>:973: ModuleNotFoundError
During handling of the above exception, another exception occurred:
@pytest.fixture(scope="session")
def medium_model():
> return create_test_model("salmonella")
cobra/test/conftest.py:69:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/__init__.py:45: in create_test_model
return _load(infile)
/usr/lib/python3/dist-packages/optlang/glpk_interface.py:41: in <module>
from swiglpk import glp_find_col, glp_get_col_prim, glp_get_col_dual, GLP_CV, GLP_IV, GLP_BV, GLP_UNDEF, GLP_FEAS, \
/usr/lib/python3/dist-packages/swiglpk/__init__.py:1: in <module>
from .swiglpk import *
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:17: in <module>
_swiglpk = swig_import_helper()
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:16: in swig_import_helper
return importlib.import_module('_swiglpk')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = '_swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
E ModuleNotFoundError: No module named '_swiglpk'
/usr/lib/python3.8/importlib/__init__.py:127: ModuleNotFoundError
____________ ERROR at setup of TestManipulation.test_sbo_annotation ____________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_____ ERROR at setup of TestManipulation.test_validate_formula_compartment _____
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
________ ERROR at setup of TestManipulation.test_validate_mass_balance _________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
____ ERROR at setup of TestManipulation.test_prune_unused_mets_output_type _____
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
___ ERROR at setup of TestManipulation.test_prune_unused_mets_functionality ____
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
____ ERROR at setup of TestManipulation.test_prune_unused_rxns_output_type _____
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
___ ERROR at setup of TestManipulation.test_prune_unused_rxns_functionality ____
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_____________ ERROR at setup of TestModelMedium.test_model_medium ______________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
________ ERROR at setup of TestTypeDetection.test_external_compartment _________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
___________ ERROR at setup of TestTypeDetection.test_multi_external ____________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
______________ ERROR at setup of TestTypeDetection.test_exchange _______________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_______________ ERROR at setup of TestTypeDetection.test_demand ________________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
________________ ERROR at setup of TestTypeDetection.test_sink _________________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
______________ ERROR at setup of TestTypeDetection.test_sbo_terms ______________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
____________ ERROR at setup of TestMinimalMedia.test_medium_linear _____________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
______________ ERROR at setup of TestMinimalMedia.test_medium_mip ______________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
________ ERROR at setup of TestMinimalMedia.test_medium_alternative_mip ________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_______ ERROR at setup of TestMinimalMedia.test_benchmark_medium_linear ________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_________ ERROR at setup of TestMinimalMedia.test_benchmark_medium_mip _________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
____________ ERROR at setup of TestMinimalMedia.test_medium_exports ____________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
____________ ERROR at setup of TestMinimalMedia.test_open_exchanges ____________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_____ ERROR at setup of TestErrorsAndExceptions.test_no_boundary_reactions _____
@pytest.fixture(scope="session")
def empty_once():
> return Model()
cobra/test/conftest.py:39:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model None at 0xb1b63f58>, id_or_model = None, name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
_ ERROR at setup of TestErrorsAndExceptions.test_no_names_or_boundary_reactions _
tp = <class 'AttributeError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:39: in empty_once
return Model()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model None at 0xb1b63f58>, id_or_model = None, name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
_________ ERROR at setup of TestErrorsAndExceptions.test_bad_exchange __________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[metabolites-minimized_shuffle-read_sbml_model-write_sbml_model-.xml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[metabolites-minimized_shuffle-load_json_model-save_json_model-.json] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[metabolites-minimized_shuffle-load_yaml_model-save_yaml_model-.yml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[metabolites-minimized_reverse-read_sbml_model-write_sbml_model-.xml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[metabolites-minimized_reverse-load_json_model-save_json_model-.json] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[metabolites-minimized_reverse-load_yaml_model-save_yaml_model-.yml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[reactions-minimized_reverse-read_sbml_model-write_sbml_model-.xml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[reactions-minimized_reverse-load_json_model-save_json_model-.json] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[reactions-minimized_reverse-load_yaml_model-save_yaml_model-.yml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[reactions-minimized_shuffle-read_sbml_model-write_sbml_model-.xml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[reactions-minimized_shuffle-load_json_model-save_json_model-.json] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[reactions-minimized_shuffle-load_yaml_model-save_yaml_model-.yml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[reactions-minimized_sorted-read_sbml_model-write_sbml_model-.xml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[reactions-minimized_sorted-load_json_model-save_json_model-.json] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[reactions-minimized_sorted-load_yaml_model-save_yaml_model-.yml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[metabolites-minimized_sorted-read_sbml_model-write_sbml_model-.xml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[metabolites-minimized_sorted-load_json_model-save_json_model-.json] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[metabolites-minimized_sorted-load_yaml_model-save_yaml_model-.yml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[genes-minimized_sorted-read_sbml_model-write_sbml_model-.xml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[genes-minimized_sorted-load_json_model-save_json_model-.json] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[genes-minimized_sorted-load_yaml_model-save_yaml_model-.yml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[genes-minimized_reverse-read_sbml_model-write_sbml_model-.xml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[genes-minimized_reverse-load_json_model-save_json_model-.json] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[genes-minimized_reverse-load_yaml_model-save_yaml_model-.yml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[genes-minimized_shuffle-read_sbml_model-write_sbml_model-.xml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[genes-minimized_shuffle-load_json_model-save_json_model-.json] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_ ERROR at setup of test_io_order[genes-minimized_shuffle-load_yaml_model-save_yaml_model-.yml] _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
____________________ ERROR at setup of test_load_json_model ____________________
def swig_import_helper():
import importlib
pkg = __name__.rpartition('.')[0]
mname = '.'.join((pkg, '_swiglpk')).lstrip('.')
try:
> return importlib.import_module(mname)
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:14:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
/usr/lib/python3.8/importlib/__init__.py:127:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None, level = 0
> ???
<frozen importlib._bootstrap>:1014:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
<frozen importlib._bootstrap>:991:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
E ModuleNotFoundError: No module named 'swiglpk._swiglpk'
<frozen importlib._bootstrap>:973: ModuleNotFoundError
During handling of the above exception, another exception occurred:
data_directory = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/'
@pytest.fixture(scope="module")
def mini_model(data_directory):
"""Fixture for mini model."""
with open(join(data_directory, "mini.pickle"), "rb") as infile:
> return load(infile)
cobra/test/test_io/conftest.py:17:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3/dist-packages/optlang/glpk_interface.py:41: in <module>
from swiglpk import glp_find_col, glp_get_col_prim, glp_get_col_dual, GLP_CV, GLP_IV, GLP_BV, GLP_UNDEF, GLP_FEAS, \
/usr/lib/python3/dist-packages/swiglpk/__init__.py:1: in <module>
from .swiglpk import *
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:17: in <module>
_swiglpk = swig_import_helper()
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:16: in swig_import_helper
return importlib.import_module('_swiglpk')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = '_swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
E ModuleNotFoundError: No module named '_swiglpk'
/usr/lib/python3.8/importlib/__init__.py:127: ModuleNotFoundError
______________ ERROR at setup of test_read_pickle[load_function0] ______________
def swig_import_helper():
import importlib
pkg = __name__.rpartition('.')[0]
mname = '.'.join((pkg, '_swiglpk')).lstrip('.')
try:
> return importlib.import_module(mname)
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:14:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
/usr/lib/python3.8/importlib/__init__.py:127:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None, level = 0
> ???
<frozen importlib._bootstrap>:1014:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
<frozen importlib._bootstrap>:991:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
E ModuleNotFoundError: No module named 'swiglpk._swiglpk'
<frozen importlib._bootstrap>:973: ModuleNotFoundError
During handling of the above exception, another exception occurred:
data_directory = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/'
@pytest.fixture(scope="module")
def mini_model(data_directory):
"""Fixture for mini model."""
with open(join(data_directory, "mini.pickle"), "rb") as infile:
> return load(infile)
cobra/test/test_io/conftest.py:17:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3/dist-packages/optlang/glpk_interface.py:41: in <module>
from swiglpk import glp_find_col, glp_get_col_prim, glp_get_col_dual, GLP_CV, GLP_IV, GLP_BV, GLP_UNDEF, GLP_FEAS, \
/usr/lib/python3/dist-packages/swiglpk/__init__.py:1: in <module>
from .swiglpk import *
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:17: in <module>
_swiglpk = swig_import_helper()
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:16: in swig_import_helper
return importlib.import_module('_swiglpk')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = '_swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
E ModuleNotFoundError: No module named '_swiglpk'
/usr/lib/python3.8/importlib/__init__.py:127: ModuleNotFoundError
___________________ ERROR at setup of test_read_pickle[None] ___________________
def swig_import_helper():
import importlib
pkg = __name__.rpartition('.')[0]
mname = '.'.join((pkg, '_swiglpk')).lstrip('.')
try:
> return importlib.import_module(mname)
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:14:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
/usr/lib/python3.8/importlib/__init__.py:127:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None, level = 0
> ???
<frozen importlib._bootstrap>:1014:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
<frozen importlib._bootstrap>:991:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
E ModuleNotFoundError: No module named 'swiglpk._swiglpk'
<frozen importlib._bootstrap>:973: ModuleNotFoundError
During handling of the above exception, another exception occurred:
tp = <class 'ModuleNotFoundError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/test_io/conftest.py:17: in mini_model
return load(infile)
/usr/lib/python3/dist-packages/optlang/glpk_interface.py:41: in <module>
from swiglpk import glp_find_col, glp_get_col_prim, glp_get_col_dual, GLP_CV, GLP_IV, GLP_BV, GLP_UNDEF, GLP_FEAS, \
/usr/lib/python3/dist-packages/swiglpk/__init__.py:1: in <module>
from .swiglpk import *
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:17: in <module>
_swiglpk = swig_import_helper()
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:16: in swig_import_helper
return importlib.import_module('_swiglpk')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = '_swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
E ModuleNotFoundError: No module named '_swiglpk'
/usr/lib/python3.8/importlib/__init__.py:127: ModuleNotFoundError
_____________ ERROR at setup of test_write_pickle[dump_function0] ______________
def swig_import_helper():
import importlib
pkg = __name__.rpartition('.')[0]
mname = '.'.join((pkg, '_swiglpk')).lstrip('.')
try:
> return importlib.import_module(mname)
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:14:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
/usr/lib/python3.8/importlib/__init__.py:127:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None, level = 0
> ???
<frozen importlib._bootstrap>:1014:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
<frozen importlib._bootstrap>:991:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
E ModuleNotFoundError: No module named 'swiglpk._swiglpk'
<frozen importlib._bootstrap>:973: ModuleNotFoundError
During handling of the above exception, another exception occurred:
tp = <class 'ModuleNotFoundError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/test_io/conftest.py:17: in mini_model
return load(infile)
/usr/lib/python3/dist-packages/optlang/glpk_interface.py:41: in <module>
from swiglpk import glp_find_col, glp_get_col_prim, glp_get_col_dual, GLP_CV, GLP_IV, GLP_BV, GLP_UNDEF, GLP_FEAS, \
/usr/lib/python3/dist-packages/swiglpk/__init__.py:1: in <module>
from .swiglpk import *
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:17: in <module>
_swiglpk = swig_import_helper()
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:16: in swig_import_helper
return importlib.import_module('_swiglpk')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = '_swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
E ModuleNotFoundError: No module named '_swiglpk'
/usr/lib/python3.8/importlib/__init__.py:127: ModuleNotFoundError
__________________ ERROR at setup of test_write_pickle[None] ___________________
def swig_import_helper():
import importlib
pkg = __name__.rpartition('.')[0]
mname = '.'.join((pkg, '_swiglpk')).lstrip('.')
try:
> return importlib.import_module(mname)
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:14:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
/usr/lib/python3.8/importlib/__init__.py:127:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None, level = 0
> ???
<frozen importlib._bootstrap>:1014:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
<frozen importlib._bootstrap>:991:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
E ModuleNotFoundError: No module named 'swiglpk._swiglpk'
<frozen importlib._bootstrap>:973: ModuleNotFoundError
During handling of the above exception, another exception occurred:
tp = <class 'ModuleNotFoundError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/test_io/conftest.py:17: in mini_model
return load(infile)
/usr/lib/python3/dist-packages/optlang/glpk_interface.py:41: in <module>
from swiglpk import glp_find_col, glp_get_col_prim, glp_get_col_dual, GLP_CV, GLP_IV, GLP_BV, GLP_UNDEF, GLP_FEAS, \
/usr/lib/python3/dist-packages/swiglpk/__init__.py:1: in <module>
from .swiglpk import *
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:17: in <module>
_swiglpk = swig_import_helper()
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:16: in swig_import_helper
return importlib.import_module('_swiglpk')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = '_swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
E ModuleNotFoundError: No module named '_swiglpk'
/usr/lib/python3.8/importlib/__init__.py:127: ModuleNotFoundError
____________________ ERROR at setup of test_benchmark_write ____________________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model e_coli_core at 0xb1c6f550>, id_or_model = 'e_coli_core'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
tp = <class 'cobra.io.sbml3.CobraSBMLError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/conftest.py:49: in small_model
return create_test_model("textbook")
cobra/test/__init__.py:37: in create_test_model
return read_sbml_model(textbook_sbml)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/textbook.xml.gz'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb2037da8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb235e0a0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
____________ ERROR at setup of test_read_sbml_model[mini_fbc2.xml] _____________
def swig_import_helper():
import importlib
pkg = __name__.rpartition('.')[0]
mname = '.'.join((pkg, '_swiglpk')).lstrip('.')
try:
> return importlib.import_module(mname)
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:14:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
/usr/lib/python3.8/importlib/__init__.py:127:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None, level = 0
> ???
<frozen importlib._bootstrap>:1014:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
<frozen importlib._bootstrap>:991:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
E ModuleNotFoundError: No module named 'swiglpk._swiglpk'
<frozen importlib._bootstrap>:973: ModuleNotFoundError
During handling of the above exception, another exception occurred:
data_directory = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/'
@pytest.fixture(scope="module")
def mini_model(data_directory):
"""Fixture for mini model."""
with open(join(data_directory, "mini.pickle"), "rb") as infile:
> return load(infile)
cobra/test/test_io/conftest.py:17:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3/dist-packages/optlang/glpk_interface.py:41: in <module>
from swiglpk import glp_find_col, glp_get_col_prim, glp_get_col_dual, GLP_CV, GLP_IV, GLP_BV, GLP_UNDEF, GLP_FEAS, \
/usr/lib/python3/dist-packages/swiglpk/__init__.py:1: in <module>
from .swiglpk import *
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:17: in <module>
_swiglpk = swig_import_helper()
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:16: in swig_import_helper
return importlib.import_module('_swiglpk')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = '_swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
E ModuleNotFoundError: No module named '_swiglpk'
/usr/lib/python3.8/importlib/__init__.py:127: ModuleNotFoundError
___________ ERROR at setup of test_read_sbml_model[mini_fbc2.xml.gz] ___________
def swig_import_helper():
import importlib
pkg = __name__.rpartition('.')[0]
mname = '.'.join((pkg, '_swiglpk')).lstrip('.')
try:
> return importlib.import_module(mname)
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:14:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
/usr/lib/python3.8/importlib/__init__.py:127:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None, level = 0
> ???
<frozen importlib._bootstrap>:1014:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
<frozen importlib._bootstrap>:991:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
E ModuleNotFoundError: No module named 'swiglpk._swiglpk'
<frozen importlib._bootstrap>:973: ModuleNotFoundError
During handling of the above exception, another exception occurred:
tp = <class 'ModuleNotFoundError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/test_io/conftest.py:17: in mini_model
return load(infile)
/usr/lib/python3/dist-packages/optlang/glpk_interface.py:41: in <module>
from swiglpk import glp_find_col, glp_get_col_prim, glp_get_col_dual, GLP_CV, GLP_IV, GLP_BV, GLP_UNDEF, GLP_FEAS, \
/usr/lib/python3/dist-packages/swiglpk/__init__.py:1: in <module>
from .swiglpk import *
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:17: in <module>
_swiglpk = swig_import_helper()
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:16: in swig_import_helper
return importlib.import_module('_swiglpk')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = '_swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
E ModuleNotFoundError: No module named '_swiglpk'
/usr/lib/python3.8/importlib/__init__.py:127: ModuleNotFoundError
__________ ERROR at setup of test_read_sbml_model[mini_fbc2.xml.bz2] ___________
def swig_import_helper():
import importlib
pkg = __name__.rpartition('.')[0]
mname = '.'.join((pkg, '_swiglpk')).lstrip('.')
try:
> return importlib.import_module(mname)
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:14:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
/usr/lib/python3.8/importlib/__init__.py:127:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None, level = 0
> ???
<frozen importlib._bootstrap>:1014:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
<frozen importlib._bootstrap>:991:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
E ModuleNotFoundError: No module named 'swiglpk._swiglpk'
<frozen importlib._bootstrap>:973: ModuleNotFoundError
During handling of the above exception, another exception occurred:
tp = <class 'ModuleNotFoundError'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/lib/python3/dist-packages/six.py:702:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/test/test_io/conftest.py:17: in mini_model
return load(infile)
/usr/lib/python3/dist-packages/optlang/glpk_interface.py:41: in <module>
from swiglpk import glp_find_col, glp_get_col_prim, glp_get_col_dual, GLP_CV, GLP_IV, GLP_BV, GLP_UNDEF, GLP_FEAS, \
/usr/lib/python3/dist-packages/swiglpk/__init__.py:1: in <module>
from .swiglpk import *
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:17: in <module>
_swiglpk = swig_import_helper()
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:16: in swig_import_helper
return importlib.import_module('_swiglpk')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = '_swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
E ModuleNotFoundError: No module named '_swiglpk'
/usr/lib/python3.8/importlib/__init__.py:127: ModuleNotFoundError
________________ ERROR at setup of test_write_sbml_model[.xml] _________________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/mini_fbc2.xml'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb1b281a8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb1962b18>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb1962b18>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model mini_textbook at 0xb1b28220>, id_or_model = 'mini_textbook'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
data_directory = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/'
@pytest.fixture(scope="function")
def mini_fbc2_model(data_directory):
"""Return mini_fbc2 model."""
> return io.sbml3.read_sbml_model(join(data_directory, "mini_fbc2.xml"))
cobra/test/test_io/test_sbml3.py:19:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/mini_fbc2.xml'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb1b281a8>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb1962b18>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
_______________ ERROR at setup of test_write_sbml_model[.xml.gz] _______________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/mini_fbc2.xml'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb1afd760>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb191d3c0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb191d3c0>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model mini_textbook at 0xb1afdd90>, id_or_model = 'mini_textbook'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
data_directory = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/'
@pytest.fixture(scope="function")
def mini_fbc2_model(data_directory):
"""Return mini_fbc2 model."""
> return io.sbml3.read_sbml_model(join(data_directory, "mini_fbc2.xml"))
cobra/test/test_io/test_sbml3.py:19:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/mini_fbc2.xml'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb1afd760>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb191d3c0>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
______________ ERROR at setup of test_write_sbml_model[.xml.bz2] _______________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/mini_fbc2.xml'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb1811868>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb195ee88>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb195ee88>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model mini_textbook at 0xb1811040>, id_or_model = 'mini_textbook'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
data_directory = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/'
@pytest.fixture(scope="function")
def mini_fbc2_model(data_directory):
"""Return mini_fbc2 model."""
> return io.sbml3.read_sbml_model(join(data_directory, "mini_fbc2.xml"))
cobra/test/test_io/test_sbml3.py:19:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/mini_fbc2.xml'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb1811868>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb195ee88>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
____________________ ERROR at setup of test_load_yaml_model ____________________
def swig_import_helper():
import importlib
pkg = __name__.rpartition('.')[0]
mname = '.'.join((pkg, '_swiglpk')).lstrip('.')
try:
> return importlib.import_module(mname)
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:14:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
/usr/lib/python3.8/importlib/__init__.py:127:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', package = None, level = 0
> ???
<frozen importlib._bootstrap>:1014:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
<frozen importlib._bootstrap>:991:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = 'swiglpk._swiglpk', import_ = <function _gcd_import at 0xb6c38d60>
> ???
E ModuleNotFoundError: No module named 'swiglpk._swiglpk'
<frozen importlib._bootstrap>:973: ModuleNotFoundError
During handling of the above exception, another exception occurred:
data_directory = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/'
@pytest.fixture(scope="module")
def mini_model(data_directory):
"""Fixture for mini model."""
with open(join(data_directory, "mini.pickle"), "rb") as infile:
> return load(infile)
cobra/test/test_io/conftest.py:17:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3/dist-packages/optlang/glpk_interface.py:41: in <module>
from swiglpk import glp_find_col, glp_get_col_prim, glp_get_col_dual, GLP_CV, GLP_IV, GLP_BV, GLP_UNDEF, GLP_FEAS, \
/usr/lib/python3/dist-packages/swiglpk/__init__.py:1: in <module>
from .swiglpk import *
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:17: in <module>
_swiglpk = swig_import_helper()
/usr/lib/python3/dist-packages/swiglpk/swiglpk.py:16: in swig_import_helper
return importlib.import_module('_swiglpk')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
name = '_swiglpk', package = None
def import_module(name, package=None):
"""Import a module.
The 'package' argument is required when performing a relative import. It
specifies the package to use as the anchor point from which to resolve the
relative import to an absolute import.
"""
level = 0
if name.startswith('.'):
if not package:
msg = ("the 'package' argument is required to perform a relative "
"import for {!r}")
raise TypeError(msg.format(name))
for character in name:
if character != '.':
break
level += 1
> return _bootstrap._gcd_import(name[level:], package, level)
E ModuleNotFoundError: No module named '_swiglpk'
/usr/lib/python3.8/importlib/__init__.py:127: ModuleNotFoundError
=================================== FAILURES ===================================
______________________ TestManipulation.test_remove_genes ______________________
self = <cobra.test.test_manipulation.TestManipulation object at 0xb1e15730>
def test_remove_genes(self):
> m = Model("test")
cobra/test/test_manipulation.py:118:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model test at 0xb1e15328>, id_or_model = 'test', name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
_____________________________ test_benchmark_read ______________________________
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/mini_fbc2.xml'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb172f6d0>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb16bec80>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
> return parse_xml_into_model(xml, number=number)
cobra/io/sbml3.py:587:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb16bec80>
number = <class 'float'>
def parse_xml_into_model(xml, number=float):
xml_model = xml.find(ns("sbml:model"))
if get_attrib(xml_model, "fbc:strict") != "true":
warn('loading SBML model without fbc:strict="true"')
model_id = get_attrib(xml_model, "id")
> model = Model(model_id)
cobra/io/sbml3.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Model mini_textbook at 0xb172f490>, id_or_model = 'mini_textbook'
name = None
def __init__(self, id_or_model=None, name=None):
if isinstance(id_or_model, Model):
Object.__init__(self, name=name)
self.__setstate__(id_or_model.__dict__)
if not hasattr(self, "name"):
self.name = None
self._solver = id_or_model.solver
else:
Object.__init__(self, id_or_model, name=name)
self._trimmed = False
self._trimmed_genes = []
self._trimmed_reactions = {}
self.genes = DictList()
self.reactions = DictList() # A list of cobra.Reactions
self.metabolites = DictList() # A list of cobra.Metabolites
# genes based on their ids {Gene.id: Gene}
self._compartments = {}
self._contexts = []
# from cameo ...
# if not hasattr(self, '_solver'): # backwards compatibility
# with older cobrapy pickles?
interface = CONFIGURATION.solver
> self._solver = interface.Model()
E AttributeError: 'NoneType' object has no attribute 'Model'
cobra/core/model.py:105: AttributeError
During handling of the above exception, another exception occurred:
data_directory = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/'
benchmark = <pytest_benchmark.fixture.BenchmarkFixture object at 0xb172f388>
def test_benchmark_read(data_directory, benchmark):
"""Benchmark SBML read."""
> benchmark(io.sbml3.read_sbml_model, join(data_directory, "mini_fbc2.xml"))
cobra/test/test_io/test_sbml3.py:25:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3/dist-packages/pytest_benchmark/fixture.py:126: in __call__
return self._raw(function_to_benchmark, *args, **kwargs)
/usr/lib/python3/dist-packages/pytest_benchmark/fixture.py:148: in _raw
duration, iterations, loops_range = self._calibrate_timer(runner)
/usr/lib/python3/dist-packages/pytest_benchmark/fixture.py:276: in _calibrate_timer
duration = runner(loops_range)
/usr/lib/python3/dist-packages/pytest_benchmark/fixture.py:91: in runner
function_to_benchmark(*args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/mini_fbc2.xml'
number = <class 'float'>, kwargs = {}
xmlfile = <xml.etree.ElementTree.ElementTree object at 0xb172f6d0>
xml = <Element '{http://www.sbml.org/sbml/level3/version1/core}sbml' at 0xb16bec80>
use_libsbml = False
def read_sbml_model(filename, number=float, **kwargs):
if not _with_lxml:
warn("Install lxml for faster SBML I/O", ImportWarning)
xmlfile = parse_stream(filename)
xml = xmlfile.getroot()
# use libsbml if not l3v1 with fbc v2
use_libsbml = (xml.get("level") != "3" or xml.get("version") != "1" or
get_attrib(xml, "fbc:required") is None)
if use_libsbml:
if libsbml is None:
raise ImportError("libSBML required for fbc < 2")
# libsbml needs a file string, so write to temp file if a file handle
if hasattr(filename, "read"):
with NamedTemporaryFile(suffix=".xml", delete=False) as outfile:
xmlfile.write(outfile, encoding="UTF-8", xml_declaration=True)
filename = outfile.name
return read_sbml2(filename, **kwargs)
try:
return parse_xml_into_model(xml, number=number)
except Exception:
> raise CobraSBMLError(
"Something went wrong reading the model. You can get a detailed "
"report using the `cobra.io.sbml3.validate_sbml_model` function "
"or using the online validator at http://sbml.org/validator")
E cobra.io.sbml3.CobraSBMLError: Something went wrong reading the model. You can get a detailed report using the `cobra.io.sbml3.validate_sbml_model` function or using the online validator at http://sbml.org/validator
cobra/io/sbml3.py:589: CobraSBMLError
___________________________ test_validate_sbml_model ___________________________
data_directory = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data/'
def test_validate_sbml_model(data_directory):
"""Test validation of SBML."""
# invalid SBML
for i in range(3):
filename = join(data_directory, "invalid{}.xml".format(i))
_, errors = io.sbml3.validate_sbml_model(filename)
assert all(len(v) >= 1 for v in itervalues(errors)) is False
# valid SBML
filename = join(data_directory, "mini_fbc2.xml")
_, errors = io.sbml3.validate_sbml_model(filename)
> assert all(len(v) == 0 for v in itervalues(errors))
E assert False
E + where False = all(<generator object test_validate_sbml_model.<locals>.<genexpr> at 0xb2cf12c8>)
cobra/test/test_io/test_sbml3.py:52: AssertionError
=============================== warnings summary ===============================
/usr/share/python-wheels/colorama-0.3.7-py2.py3-none-any.whl/colorama/ansitowin32.py:49
/usr/share/python-wheels/colorama-0.3.7-py2.py3-none-any.whl/colorama/ansitowin32.py:49
/usr/share/python-wheels/colorama-0.3.7-py2.py3-none-any.whl/colorama/ansitowin32.py:49 [1;31mDeprecationWarning[0m: invalid escape sequence \[
/usr/share/python-wheels/colorama-0.3.7-py2.py3-none-any.whl/colorama/ansitowin32.py:50
/usr/share/python-wheels/colorama-0.3.7-py2.py3-none-any.whl/colorama/ansitowin32.py:50
/usr/share/python-wheels/colorama-0.3.7-py2.py3-none-any.whl/colorama/ansitowin32.py:50 [1;31mDeprecationWarning[0m: invalid escape sequence \]
/usr/share/python-wheels/html5lib-1.0.1-py2.py3-none-any.whl/html5lib/_trie/_base.py:3
/usr/share/python-wheels/html5lib-1.0.1-py2.py3-none-any.whl/html5lib/_trie/_base.py:3 [1;31mDeprecationWarning[0m: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.9 it will stop working
/usr/share/python-wheels/pyparsing-2.2.0-py2.py3-none-any.whl/pyparsing.py:943
/usr/share/python-wheels/pyparsing-2.2.0-py2.py3-none-any.whl/pyparsing.py:943 [1;31mDeprecationWarning[0m: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.9 it will stop working
/usr/share/python-wheels/pyparsing-2.2.0-py2.py3-none-any.whl/pyparsing.py:3245
/usr/share/python-wheels/pyparsing-2.2.0-py2.py3-none-any.whl/pyparsing.py:3245 [1;31mDeprecationWarning[0m: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.9 it will stop working
cobra/core/dictlist.py:213
cobra/core/dictlist.py:213 [1;31mSyntaxWarning[0m: "is" with a literal. Did you mean "=="?
cobra/core/gene.py:249
cobra/core/gene.py:249 [1;31mDeprecationWarning[0m: invalid escape sequence \(
cobra/core/gene.py:263
cobra/core/gene.py:263 [1;31mDeprecationWarning[0m: invalid escape sequence \(
cobra/core/reaction.py:38
cobra/core/reaction.py:38 [1;31mDeprecationWarning[0m: invalid escape sequence \s
cobra/flux_analysis/gapfilling.py:13
cobra/flux_analysis/gapfilling.py:13 [1;31mDeprecationWarning[0m: invalid escape sequence \s
-- Docs: https://docs.pytest.org/en/latest/warnings.html
= 3 failed, 1 passed, 5 skipped, 3 xfailed, 12 warnings, 67 error in 96.33 seconds =
E: pybuild pybuild:341: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build; python3.8 -m pytest
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.8 3.7" returned exit code 13
make: *** [debian/rules:10: build-arch] Error 25
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2020-02-24T11:28:44Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 0
Build-Time: 132
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 1587
Job: python-cobra_0.14.2-2
Machine Architecture: armhf
Package: python-cobra
Package-Time: 1781
Source-Version: 0.14.2-2
Space: 0
Status: failed
Version: 0.14.2-2
--------------------------------------------------------------------------------
Finished at 2020-02-24T11:28:44Z
Build needed 00:00:00, 0k disc space