Created
October 16, 2023 15:07
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/molsys/AstroVascPy/-/pipelines/161829 (:no_entry:) running on GitHub PR BlueBrain/AstroVascPy#5.
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[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
[0K on BB5 map runner pnPo3yJy[0;m | |
section_start:1697468353:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
section_end:1697468353:resolve_secrets [0Ksection_start:1697468353:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor1787680537, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
Runner ID 29, project root molsys, project name AstroVascPy | |
Pipeline ID 161829, build ref , job ID 965618 | |
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J965618, optional exclusive flag , optional cpus per task flag --cpus-per-task=6, optional qos flag , optional reservation flag | |
A slurm job will be created with name GL_J965618_PROD_P2342_CP0_C24 | |
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcimolsys partition=prod qos= reservation= | |
Not executing the chown -R | |
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
Submitted batch job 1841409 | |
job state: R | |
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J965618_PROD_P2342_CP0_C24 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J965618 --time=1:00:00 --wrap="sleep infinity" | |
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J965618 --ntasks=1 --jobid=1841409 --cpus-per-task=6 --mem=30750M | |
section_end:1697468354:prepare_executor [0Ksection_start:1697468354:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
Using git from spack modules | |
Running on r1i4n24 via bbpv1.epfl.ch... | |
section_end:1697468358:prepare_script [0Ksection_start:1697468358:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
Using git from spack modules | |
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
[32;1mFetching changes with git depth set to 20...[0;m | |
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965618/molsys/AstroVascPy/.git/ | |
[32;1mCreated fresh repository.[0;m | |
[32;1mChecking out 2fa9a3c1 as nicola/petsc_improvement...[0;m | |
Skipping object checkout, Git LFS is not installed. | |
[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m | |
section_end:1697468361:get_sources [0Ksection_start:1697468361:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
Using git from spack modules | |
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
[32;1m$ module purge[0;m | |
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
[32;1m$ module load archive/2020-12 python/3.7.4[0;m | |
[32;1m$ module unload archive/2020-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.7.4 | |
[32;1m$ module load archive/2021-12 python/3.8.3[0;m | |
[32;1m$ module unload archive/2021-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.8.3 | |
[32;1m$ module load archive/2023-02 python/3.9.7[0;m | |
[32;1m$ module unload archive/2023-02[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.9.7 | |
[32;1m$ module load unstable python[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.10.8 | |
[32;1m$ load-modules() { # collapsed multi-line command[0;m | |
[32;1m$ load-modules $SYSTEM_MODULES[0;m | |
Loaded module git from unstable | |
Loaded module cmake from unstable | |
Loaded module graphviz from unstable | |
[32;1m$ load-modules $EXTRA_MODULES[0;m | |
Loaded module gcc from unstable | |
Loaded module hpe-mpi from unstable | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module petsc from unstable | |
Autoloading python/3.10.8 | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module py-petsc4py from unstable | |
[32;1m$ module list -t[0;m | |
Currently Loaded Modulefiles: | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4 | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/python/3.10.8 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/git/2.38.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/cmake/3.24.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/graphviz/2.49.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/compilers/linux-rhel7-haswell/gcc/12.2.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/petsc/3.18.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/py-petsc4py/3.18.1 | |
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
[32;1m$ print_var XDG_CONFIG_HOME[0;m | |
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965618/molsys/AstroVascPy/local_config[0m | |
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
insteadOf = https://bbpgitlab.epfl.ch/ | |
insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
insteadOf = git@bbpgitlab.epfl.ch: | |
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
[0Ksection_start:1697468363:section_venv[collapsed=true] [0KSetting up the virtual env | |
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
[32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
[32;1m$ rm -rf "$CI_VENV"[0;m | |
[32;1m$ python -mvenv "$CI_VENV"[0;m | |
[32;1m$ source "$CI_VENV/bin/activate"[0;m | |
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (22.2.2) | |
Collecting pip | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/bc3/8bb52bc286514/pip-23.3-py3-none-any.whl (2.1 MB) | |
ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 75.7 MB/s eta 0:00:00 | |
Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages (63.0.0) | |
Collecting setuptools | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b45/4a35605876da6/setuptools-68.2.2-py3-none-any.whl (807 kB) | |
âââââââââââââââââââââââââââââââââââââ 807.9/807.9 kB 245.8 MB/s eta 0:00:00 | |
Collecting wheel | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/759/09db2664838d0/wheel-0.41.2-py3-none-any.whl (64 kB) | |
âââââââââââââââââââââââââââââââââââââââ 64.8/64.8 kB 206.2 MB/s eta 0:00:00 | |
Installing collected packages: wheel, setuptools, pip | |
Attempting uninstall: setuptools | |
Found existing installation: setuptools 63.0.0 | |
Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965618/molsys/AstroVascPy/venv | |
Can't uninstall 'setuptools'. No files were found to uninstall. | |
Attempting uninstall: pip | |
Found existing installation: pip 22.2.2 | |
Uninstalling pip-22.2.2: | |
Successfully uninstalled pip-22.2.2 | |
Successfully installed pip-23.3 setuptools-68.2.2 wheel-0.41.2 | |
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Collecting tox | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/599/af5e5bb0cad01/tox-4.11.3-py3-none-any.whl (153 kB) | |
ââââââââââââââââââââââââââââââââââââââ 153.8/153.8 kB 20.0 MB/s eta 0:00:00 | |
Collecting cachetools>=5.3.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/95e/f631eeaea14ba/cachetools-5.3.1-py3-none-any.whl (9.3 kB) | |
Collecting chardet>=5.2 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 61.4 MB/s eta 0:00:00 | |
Collecting colorama>=0.4.6 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
Collecting filelock>=3.12.3 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/08c/21d87ded6e2b9/filelock-3.12.4-py3-none-any.whl (11 kB) | |
Collecting packaging>=23.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/8c4/91190033a9af7/packaging-23.2-py3-none-any.whl (53 kB) | |
âââââââââââââââââââââââââââââââââââââââ 53.0/53.0 kB 194.6 MB/s eta 0:00:00 | |
Collecting platformdirs>=3.10 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e9d/171d00af68be5/platformdirs-3.11.0-py3-none-any.whl (17 kB) | |
Collecting pluggy>=1.3 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/d89/c696a773f8bd3/pluggy-1.3.0-py3-none-any.whl (18 kB) | |
Collecting pyproject-api>=1.6.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
Collecting tomli>=2.0.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/939/de3e7a6161af0/tomli-2.0.1-py3-none-any.whl (12 kB) | |
Collecting virtualenv>=20.24.3 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b80/039f280f4919c/virtualenv-20.24.5-py3-none-any.whl (3.7 MB) | |
ââââââââââââââââââââââââââââââââââââââââ 3.7/3.7 MB 177.4 MB/s eta 0:00:00 | |
Collecting distlib<1,>=0.3.7 (from virtualenv>=20.24.3->tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2e2/4928bc811348f/distlib-0.3.7-py2.py3-none-any.whl (468 kB) | |
âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 240.4 MB/s eta 0:00:00 | |
Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
Successfully installed cachetools-5.3.1 chardet-5.2.0 colorama-0.4.6 distlib-0.3.7 filelock-3.12.4 packaging-23.2 platformdirs-3.11.0 pluggy-1.3.0 pyproject-api-1.6.1 tomli-2.0.1 tox-4.11.3 virtualenv-20.24.5 | |
[32;1m$ section_end section_venv[0;m | |
[0Ksection_end:1697468379:section_venv [0K | |
[32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
[36mPRE_BUILD_COMMAND=[0m | |
[32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
[32;1m$ section_start section_tox "Running Tox"[0;m | |
[0Ksection_start:1697468379:section_tox [0KRunning Tox | |
[32;1m$ python -mtox $TOX_OPTIONS[0;m | |
check-packaging: install_deps> python -I -m pip install build twine | |
check-packaging: freeze> python -m pip freeze --all | |
check-packaging: build==1.0.3,certifi==2023.7.22,cffi==1.16.0,charset-normalizer==3.3.0,cryptography==41.0.4,docutils==0.20.1,idna==3.4,importlib-metadata==6.8.0,jaraco.classes==3.3.0,jeepney==0.8.0,keyring==24.2.0,markdown-it-py==3.0.0,mdurl==0.1.2,more-itertools==10.1.0,mpi4py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mpi4py-3.1.4-glx4cfnu5cionch2hbeyzns5ol3vexp7/spack-src,nh3==0.2.14,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging==23.2,petsc4py @ file:///nvme/bbpcihpcdeploy/1644090/spack-stage/spack-stage-py-petsc4py-3.18.1-7rysecnje3dndrjv36w723cz6tfioxhe/spack-src,pip==23.2.1,pkginfo==1.9.6,pycparser==2.21,Pygments==2.16.1,pyproject_hooks==1.0.0,readme-renderer==42.0,requests==2.31.0,requests-toolbelt==1.0.0,rfc3986==2.0.0,rich==13.6.0,SecretStorage==3.3.3,setuptools @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-setuptools-63.0.0-c6hdpvjjddmcm3xf5begyfpkjkzj2oke/spack-src/setuptools-63.0.0-py3-none-any.whl,tomli==2.0.1,twine==4.0.2,urllib3==2.0.6,wheel==0.41.2,zipp==3.17.0 | |
check-packaging: commands[0]> python -m build -o /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965618/molsys/AstroVascPy/.tox/check-packaging/tmp/dist | |
* Creating venv isolated environment... | |
* Installing packages in isolated environment... (setuptools>=42, setuptools_scm[toml]>=3.4, wheel) | |
* Getting build dependencies for sdist... | |
running egg_info | |
creating AstroVascPy.egg-info | |
writing AstroVascPy.egg-info/PKG-INFO | |
writing dependency_links to AstroVascPy.egg-info/dependency_links.txt | |
writing entry points to AstroVascPy.egg-info/entry_points.txt | |
writing requirements to AstroVascPy.egg-info/requires.txt | |
writing top-level names to AstroVascPy.egg-info/top_level.txt | |
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
reading manifest template 'MANIFEST.in' | |
warning: no previously-included files matching '*.py[co]' found anywhere in distribution | |
warning: no previously-included files matching '.DS_Store' found anywhere in distribution | |
adding license file 'LICENSE.txt' | |
adding license file 'AUTHORS.txt' | |
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
* Building sdist... | |
running sdist | |
running egg_info | |
writing AstroVascPy.egg-info/PKG-INFO | |
writing dependency_links to AstroVascPy.egg-info/dependency_links.txt | |
writing entry points to AstroVascPy.egg-info/entry_points.txt | |
writing requirements to AstroVascPy.egg-info/requires.txt | |
writing top-level names to AstroVascPy.egg-info/top_level.txt | |
reading manifest template 'MANIFEST.in' | |
warning: no previously-included files matching '*.py[co]' found anywhere in distribution | |
warning: no previously-included files matching '.DS_Store' found anywhere in distribution | |
adding license file 'LICENSE.txt' | |
adding license file 'AUTHORS.txt' | |
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
running check | |
creating AstroVascPy-0.0.1 | |
creating AstroVascPy-0.0.1/AstroVascPy.egg-info | |
creating AstroVascPy-0.0.1/astrovascpy | |
creating AstroVascPy-0.0.1/docs | |
creating AstroVascPy-0.0.1/docs/source | |
creating AstroVascPy-0.0.1/docs/source/logo | |
creating AstroVascPy-0.0.1/examples | |
creating AstroVascPy-0.0.1/examples/data | |
creating AstroVascPy-0.0.1/examples/data/graphs_folder | |
creating AstroVascPy-0.0.1/tests | |
creating AstroVascPy-0.0.1/tests/data | |
creating AstroVascPy-0.0.1/tests/data/input_flow | |
creating AstroVascPy-0.0.1/tests/data/reporting | |
copying files to AstroVascPy-0.0.1... | |
copying .auto-changelog -> AstroVascPy-0.0.1 | |
copying .auto-changelog-template.hbs -> AstroVascPy-0.0.1 | |
copying .codespellignorelines -> AstroVascPy-0.0.1 | |
copying .codespellrc -> AstroVascPy-0.0.1 | |
copying .copier-answers.yml -> AstroVascPy-0.0.1 | |
copying .flake8 -> AstroVascPy-0.0.1 | |
copying .gitattributes -> AstroVascPy-0.0.1 | |
copying .gitignore -> AstroVascPy-0.0.1 | |
copying .gitlab-ci.yml -> AstroVascPy-0.0.1 | |
copying .gitreview -> AstroVascPy-0.0.1 | |
copying .pre-commit-config.yaml -> AstroVascPy-0.0.1 | |
copying .pylintrc -> AstroVascPy-0.0.1 | |
copying AUTHORS.txt -> AstroVascPy-0.0.1 | |
copying CHANGELOG.md -> AstroVascPy-0.0.1 | |
copying CONTRIBUTING.md -> AstroVascPy-0.0.1 | |
copying LICENSE.txt -> AstroVascPy-0.0.1 | |
copying MANIFEST.in -> AstroVascPy-0.0.1 | |
copying README.md -> AstroVascPy-0.0.1 | |
copying commitlint.config.js -> AstroVascPy-0.0.1 | |
copying package.json -> AstroVascPy-0.0.1 | |
copying pyproject.toml -> AstroVascPy-0.0.1 | |
copying setup.py -> AstroVascPy-0.0.1 | |
copying setup.sh -> AstroVascPy-0.0.1 | |
copying tox.ini -> AstroVascPy-0.0.1 | |
copying AstroVascPy.egg-info/PKG-INFO -> AstroVascPy-0.0.1/AstroVascPy.egg-info | |
copying AstroVascPy.egg-info/SOURCES.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info | |
copying AstroVascPy.egg-info/dependency_links.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info | |
copying AstroVascPy.egg-info/entry_points.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info | |
copying AstroVascPy.egg-info/requires.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info | |
copying AstroVascPy.egg-info/top_level.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info | |
copying astrovascpy/PetscBinaryIO.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/__init__.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/bloodflow.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/exceptions.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/io.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/ou.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/plotting.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/report_reader.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/report_writer.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/scipy_petsc_conversions.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/utils.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/version.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/vtk_io.py -> AstroVascPy-0.0.1/astrovascpy | |
copying docs/Makefile -> AstroVascPy-0.0.1/docs | |
copying docs/source/api_ref.rst -> AstroVascPy-0.0.1/docs/source | |
copying docs/source/changelog.rst -> AstroVascPy-0.0.1/docs/source | |
copying docs/source/conf.py -> AstroVascPy-0.0.1/docs/source | |
copying docs/source/index.rst -> AstroVascPy-0.0.1/docs/source | |
copying docs/source/logo/BPP-AstroVascPy-Github.jpg -> AstroVascPy-0.0.1/docs/source/logo | |
copying examples/compute_static_flow_pressure.py -> AstroVascPy-0.0.1/examples | |
copying examples/job_script.sbatch -> AstroVascPy-0.0.1/examples | |
copying examples/run_ou.sbatch -> AstroVascPy-0.0.1/examples | |
copying examples/simulate_OU_process.py -> AstroVascPy-0.0.1/examples | |
copying examples/data/params.yaml -> AstroVascPy-0.0.1/examples/data | |
copying examples/data/graphs_folder/edge_dataset.csv -> AstroVascPy-0.0.1/examples/data/graphs_folder | |
copying examples/data/graphs_folder/node_dataset.csv -> AstroVascPy-0.0.1/examples/data/graphs_folder | |
copying examples/data/graphs_folder/toy_graph.bin -> AstroVascPy-0.0.1/examples/data/graphs_folder | |
copying examples/data/graphs_folder/toy_graph.h5 -> AstroVascPy-0.0.1/examples/data/graphs_folder | |
copying tests/__init__.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_bloodflow.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_graphs.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_io.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_mpi.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_ou.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_report_reader.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_report_writer.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_utils.py -> AstroVascPy-0.0.1/tests | |
copying tests/data/dataset.h5 -> AstroVascPy-0.0.1/tests/data | |
copying tests/data/edge_dataset.csv -> AstroVascPy-0.0.1/tests/data | |
copying tests/data/node_dataset.csv -> AstroVascPy-0.0.1/tests/data | |
copying tests/data/toy_graph.bin -> AstroVascPy-0.0.1/tests/data | |
copying tests/data/toy_graph.h5 -> AstroVascPy-0.0.1/tests/data | |
copying tests/data/input_flow/sine.csv -> AstroVascPy-0.0.1/tests/data/input_flow | |
copying tests/data/reporting/compartment_report.h5 -> AstroVascPy-0.0.1/tests/data/reporting | |
copying tests/data/reporting/create_reports.py -> AstroVascPy-0.0.1/tests/data/reporting | |
copying tests/data/reporting/diff_unit_compartment_report.h5 -> AstroVascPy-0.0.1/tests/data/reporting | |
Writing AstroVascPy-0.0.1/setup.cfg | |
Creating tar archive | |
removing 'AstroVascPy-0.0.1' (and everything under it) | |
* Building wheel from sdist | |
* Creating venv isolated environment... | |
* Installing packages in isolated environment... (setuptools>=42, setuptools_scm[toml]>=3.4, wheel) | |
* Getting build dependencies for wheel... | |
running egg_info | |
writing AstroVascPy.egg-info/PKG-INFO | |
writing dependency_links to AstroVascPy.egg-info/dependency_links.txt | |
writing entry points to AstroVascPy.egg-info/entry_points.txt | |
writing requirements to AstroVascPy.egg-info/requires.txt | |
writing top-level names to AstroVascPy.egg-info/top_level.txt | |
ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any | |
reading manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
reading manifest template 'MANIFEST.in' | |
warning: no previously-included files matching '*.py[co]' found anywhere in distribution | |
warning: no previously-included files matching '.DS_Store' found anywhere in distribution | |
adding license file 'LICENSE.txt' | |
adding license file 'AUTHORS.txt' | |
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
* Installing packages in isolated environment... (wheel) | |
* Building wheel... | |
running bdist_wheel | |
running build | |
running build_py | |
creating build | |
creating build/lib | |
creating build/lib/astrovascpy | |
copying astrovascpy/report_reader.py -> build/lib/astrovascpy | |
copying astrovascpy/PetscBinaryIO.py -> build/lib/astrovascpy | |
copying astrovascpy/version.py -> build/lib/astrovascpy | |
copying astrovascpy/exceptions.py -> build/lib/astrovascpy | |
copying astrovascpy/io.py -> build/lib/astrovascpy | |
copying astrovascpy/vtk_io.py -> build/lib/astrovascpy | |
copying astrovascpy/report_writer.py -> build/lib/astrovascpy | |
copying astrovascpy/scipy_petsc_conversions.py -> build/lib/astrovascpy | |
copying astrovascpy/plotting.py -> build/lib/astrovascpy | |
copying astrovascpy/ou.py -> build/lib/astrovascpy | |
copying astrovascpy/utils.py -> build/lib/astrovascpy | |
copying astrovascpy/bloodflow.py -> build/lib/astrovascpy | |
copying astrovascpy/__init__.py -> build/lib/astrovascpy | |
running egg_info | |
writing AstroVascPy.egg-info/PKG-INFO | |
writing dependency_links to AstroVascPy.egg-info/dependency_links.txt | |
writing entry points to AstroVascPy.egg-info/entry_points.txt | |
writing requirements to AstroVascPy.egg-info/requires.txt | |
writing top-level names to AstroVascPy.egg-info/top_level.txt | |
ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any | |
reading manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
reading manifest template 'MANIFEST.in' | |
warning: no previously-included files matching '*.py[co]' found anywhere in distribution | |
warning: no previously-included files matching '.DS_Store' found anywhere in distribution | |
adding license file 'LICENSE.txt' | |
adding license file 'AUTHORS.txt' | |
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
installing to build/bdist.linux-x86_64/wheel | |
running install | |
running install_lib | |
creating build/bdist.linux-x86_64 | |
creating build/bdist.linux-x86_64/wheel | |
creating build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/report_reader.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/PetscBinaryIO.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/version.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/exceptions.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/io.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/vtk_io.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/report_writer.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/scipy_petsc_conversions.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/plotting.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/ou.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/utils.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/bloodflow.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/__init__.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
running install_egg_info | |
Copying AstroVascPy.egg-info to build/bdist.linux-x86_64/wheel/AstroVascPy-0.0.1-py3.10.egg-info | |
running install_scripts | |
creating build/bdist.linux-x86_64/wheel/AstroVascPy-0.0.1.dist-info/WHEEL | |
creating '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965618/molsys/AstroVascPy/.tox/check-packaging/tmp/dist/tmpary0z084/AstroVascPy-0.0.1-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it | |
adding 'astrovascpy/PetscBinaryIO.py' | |
adding 'astrovascpy/__init__.py' | |
adding 'astrovascpy/bloodflow.py' | |
adding 'astrovascpy/exceptions.py' | |
adding 'astrovascpy/io.py' | |
adding 'astrovascpy/ou.py' | |
adding 'astrovascpy/plotting.py' | |
adding 'astrovascpy/report_reader.py' | |
adding 'astrovascpy/report_writer.py' | |
adding 'astrovascpy/scipy_petsc_conversions.py' | |
adding 'astrovascpy/utils.py' | |
adding 'astrovascpy/version.py' | |
adding 'astrovascpy/vtk_io.py' | |
adding 'AstroVascPy-0.0.1.dist-info/AUTHORS.txt' | |
adding 'AstroVascPy-0.0.1.dist-info/LICENSE.txt' | |
adding 'AstroVascPy-0.0.1.dist-info/METADATA' | |
adding 'AstroVascPy-0.0.1.dist-info/WHEEL' | |
adding 'AstroVascPy-0.0.1.dist-info/entry_points.txt' | |
adding 'AstroVascPy-0.0.1.dist-info/top_level.txt' | |
adding 'AstroVascPy-0.0.1.dist-info/RECORD' | |
removing build/bdist.linux-x86_64/wheel | |
Successfully built AstroVascPy-0.0.1.tar.gz and AstroVascPy-0.0.1-py3-none-any.whl | |
check-packaging: commands[1]> twine check '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965618/molsys/AstroVascPy/.tox/check-packaging/tmp/dist/*' | |
Checking | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965618/molsys/AstroVascPy/.to | |
x/check-packaging/tmp/dist/AstroVascPy-0.0.1-py3-none-any.whl: [32mPASSED[0m | |
Checking | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965618/molsys/AstroVascPy/.to | |
x/check-packaging/tmp/dist/AstroVascPy-0.0.1.tar.gz: [32mPASSED[0m | |
check-packaging: OK (52.59=setup[24.57]+cmd[26.19,1.84] seconds) | |
congratulations :) (53.04 seconds) | |
[32;1m$ section_end section_tox[0;m | |
[0Ksection_end:1697468432:section_tox [0K | |
section_end:1697468432:step_script [0Ksection_start:1697468432:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
Using git from spack modules | |
section_end:1697468433:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
[0K on BB5 map runner pnPo3yJy[0;m | |
section_start:1697468354:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
section_end:1697468354:resolve_secrets [0Ksection_start:1697468354:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor793818897, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
Runner ID 29, project root molsys, project name AstroVascPy | |
Pipeline ID 161829, build ref , job ID 965620 | |
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J965620, optional exclusive flag , optional cpus per task flag --cpus-per-task=6, optional qos flag , optional reservation flag | |
A slurm job will be created with name GL_J965620_PROD_P2342_CP2_C26 | |
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcimolsys partition=prod qos= reservation= | |
Not executing the chown -R | |
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
Submitted batch job 1841411 | |
job state: PD | |
job state: PD | |
job state: R | |
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J965620_PROD_P2342_CP2_C26 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J965620 --time=1:00:00 --wrap="sleep infinity" | |
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J965620 --ntasks=1 --jobid=1841411 --cpus-per-task=6 --mem=30750M | |
section_end:1697468357:prepare_executor [0Ksection_start:1697468357:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
Using git from spack modules | |
Running on r1i4n24 via bbpv1.epfl.ch... | |
section_end:1697468358:prepare_script [0Ksection_start:1697468358:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
Using git from spack modules | |
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
[32;1mFetching changes with git depth set to 20...[0;m | |
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.git/ | |
[32;1mCreated fresh repository.[0;m | |
[32;1mChecking out 2fa9a3c1 as nicola/petsc_improvement...[0;m | |
Skipping object checkout, Git LFS is not installed. | |
[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m | |
section_end:1697468361:get_sources [0Ksection_start:1697468361:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
Using git from spack modules | |
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
[32;1m$ module purge[0;m | |
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
[32;1m$ module load archive/2020-12 python/3.7.4[0;m | |
[32;1m$ module unload archive/2020-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.7.4 | |
[32;1m$ module load archive/2021-12 python/3.8.3[0;m | |
[32;1m$ module unload archive/2021-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.8.3 | |
[32;1m$ module load archive/2023-02 python/3.9.7[0;m | |
[32;1m$ module unload archive/2023-02[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.9.7 | |
[32;1m$ module load unstable python[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.10.8 | |
[32;1m$ load-modules() { # collapsed multi-line command[0;m | |
[32;1m$ load-modules $SYSTEM_MODULES[0;m | |
Loaded module git from unstable | |
Loaded module cmake from unstable | |
Loaded module graphviz from unstable | |
[32;1m$ load-modules $EXTRA_MODULES[0;m | |
Loaded module gcc from unstable | |
Loaded module hpe-mpi from unstable | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module petsc from unstable | |
Autoloading python/3.10.8 | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module py-petsc4py from unstable | |
[32;1m$ module list -t[0;m | |
Currently Loaded Modulefiles: | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4 | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/python/3.10.8 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/git/2.38.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/cmake/3.24.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/graphviz/2.49.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/compilers/linux-rhel7-haswell/gcc/12.2.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/petsc/3.18.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/py-petsc4py/3.18.1 | |
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
[32;1m$ print_var XDG_CONFIG_HOME[0;m | |
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/local_config[0m | |
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
insteadOf = https://bbpgitlab.epfl.ch/ | |
insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
insteadOf = git@bbpgitlab.epfl.ch: | |
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
[0Ksection_start:1697468363:section_venv[collapsed=true] [0KSetting up the virtual env | |
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
[32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
[32;1m$ rm -rf "$CI_VENV"[0;m | |
[32;1m$ python -mvenv "$CI_VENV"[0;m | |
[32;1m$ source "$CI_VENV/bin/activate"[0;m | |
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Installing collected packages: wheel, setuptools, pip | |
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Found existing installation: setuptools 63.0.0 | |
Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/venv | |
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Attempting uninstall: pip | |
Found existing installation: pip 22.2.2 | |
Uninstalling pip-22.2.2: | |
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Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
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[32;1m$ section_end section_venv[0;m | |
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[0Ksection_start:1697468379:section_tox [0KRunning Tox | |
[32;1m$ python -mtox $TOX_OPTIONS[0;m | |
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel | |
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: get_requires_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: install_requires_for_build_wheel> python -I -m pip install wheel | |
.pkg: freeze> python -m pip freeze --all | |
.pkg: packaging==23.2,pip==23.2.1,setuptools==68.2.0,setuptools-scm==8.0.4,tomli==2.0.1,typing_extensions==4.8.0,wheel==0.41.2 | |
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
docs: install_package_deps> python -I -m pip install cached-property click coverage cython h5py libsonata m2r2 matplotlib morphio mpi4py networkx numpy 'pandas<2.0.0' psutil pytest pyyaml scipy seaborn sphinx sphinx-bluebrain-theme sphinx-click tables tqdm trimesh vascpy vtk | |
docs: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz | |
docs: freeze> python -m pip freeze --all | |
docs: alabaster==0.7.13,AstroVascPy @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz#sha256=7a517c32a5754e4bd6b7ab3f6ff9dc4c977bbe4dba727701914791d5046ed93f,Babel==2.13.0,blosc2==2.2.9,cached-property==1.5.2,certifi==2023.7.22,charset-normalizer==3.3.0,click==8.1.7,contourpy==1.1.1,coverage==7.3.2,cycler==0.12.1,Cython==3.0.3,docutils==0.20.1,exceptiongroup==1.1.3,fonttools==4.43.1,h5py==3.10.0,idna==3.4,imagesize==1.4.1,iniconfig==2.0.0,Jinja2==3.0.3,kiwisolver==1.4.5,libsonata==0.1.24,m2r2==0.3.3.post2,MarkupSafe==2.1.3,matplotlib==3.8.0,mistune==0.8.4,MorphIO==3.3.6,mpi4py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mpi4py-3.1.4-glx4cfnu5cionch2hbeyzns5ol3vexp7/spack-src,msgpack==1.0.7,ndindex==1.7,networkx==3.1,numexpr==2.8.7,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging==23.2,pandas==1.5.3,petsc4py @ file:///nvme/bbpcihpcdeploy/1644090/spack-stage/spack-stage-py-petsc4py-3.18.1-7rysecnje3dndrjv36w723cz6tfioxhe/spack-src,Pillow==10.1.0,pip==23.2.1,pluggy==1.3.0,psutil==5.9.6,py-cpuinfo==9.0.0,Pygments==2.16.1,pyparsing==3.1.1,pytest==7.4.2,python-dateutil==2.8.2,pytz==2023.3.post1,PyYAML==6.0.1,requests==2.31.0,scipy==1.11.3,seaborn==0.13.0,setuptools @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-setuptools-63.0.0-c6hdpvjjddmcm3xf5begyfpkjkzj2oke/spack-src/setuptools-63.0.0-py3-none-any.whl,six==1.16.0,snowballstemmer==2.2.0,Sphinx==7.2.6,sphinx-bluebrain-theme==0.4.2,sphinx-click==5.0.1,sphinxcontrib-applehelp==1.0.7,sphinxcontrib-devhelp==1.0.5,sphinxcontrib-htmlhelp==2.0.4,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==1.0.6,sphinxcontrib-serializinghtml==1.1.9,tables==3.9.1,tomli==2.0.1,tqdm==4.66.1,trimesh==4.0.0,urllib3==2.0.6,vascpy==0.1.1,vtk==9.2.6,wheel==0.41.2 | |
docs: commands[0] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs> make html | |
# Generate the documentation | |
Running Sphinx v7.2.6 | |
making output directory... done | |
[autosummary] generating autosummary for: api_ref.rst, changelog.rst, index.rst | |
[autosummary] generating autosummary for: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/generated/astrovascpy.PetscBinaryIO.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/generated/astrovascpy.bloodflow.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/generated/astrovascpy.exceptions.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/generated/astrovascpy.io.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/generated/astrovascpy.ou.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/generated/astrovascpy.plotting.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/generated/astrovascpy.report_reader.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/generated/astrovascpy.report_writer.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/generated/astrovascpy.scipy_petsc_conversions.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/generated/astrovascpy.utils.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/generated/astrovascpy.vtk_io.rst | |
loading intersphinx inventory from https://docs.python.org/3/objects.inv... | |
building [mo]: targets for 0 po files that are out of date | |
writing output... | |
building [html]: targets for 3 source files that are out of date | |
updating environment: [new config] 14 added, 0 changed, 0 removed | |
[2Kreading sources... [ 7%] api_ref [2Kreading sources... [ 14%] changelog [2Kreading sources... [ 21%] generated/astrovascpy.PetscBinaryIO [2Kreading sources... [ 29%] generated/astrovascpy.bloodflow [2Kreading sources... [ 36%] generated/astrovascpy.exceptions [2Kreading sources... [ 43%] generated/astrovascpy.io [2Kreading sources... [ 50%] generated/astrovascpy.ou [2Kreading sources... [ 57%] generated/astrovascpy.plotting [2Kreading sources... [ 64%] generated/astrovascpy.report_reader [2Kreading sources... [ 71%] generated/astrovascpy.report_writer [2Kreading sources... [ 79%] generated/astrovascpy.scipy_petsc_conversions [2Kreading sources... [ 86%] generated/astrovascpy.utils [2Kreading sources... [ 93%] generated/astrovascpy.vtk_io [2Kreading sources... [100%] index | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:15: WARNING: Title underline too short. | |
COPIED FROM PETSC Library -> $PETSC_DIR/lib/petsc/bin (along with get_conf function) | |
=============== | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:15: WARNING: Title underline too short. | |
COPIED FROM PETSC Library -> $PETSC_DIR/lib/petsc/bin (along with get_conf function) | |
=============== | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:21: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:23: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:33: WARNING: Definition list ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.readBinaryFile:3: WARNING: Inline strong start-string without end-string. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.readIS:3: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.readMatDense:3: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.readVec:3: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.writeBinaryFile:8: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.writeIS:3: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.writeMatSparse:3: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.writeVec:3: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/bloodflow.py:docstring of astrovascpy.bloodflow:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/bloodflow.py:docstring of astrovascpy.bloodflow:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/exceptions.py:docstring of astrovascpy.exceptions:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/exceptions.py:docstring of astrovascpy.exceptions:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/io.py:docstring of astrovascpy.io:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/io.py:docstring of astrovascpy.io:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/ou.py:docstring of astrovascpy.ou:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/ou.py:docstring of astrovascpy.ou:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/ou.py:docstring of astrovascpy.ou.expected_time:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/ou.py:docstring of astrovascpy.ou.expected_time:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/ou.py:docstring of astrovascpy.ou.ornstein_uhlenbeck_process:7: WARNING: Definition list ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/plotting.py:docstring of astrovascpy.plotting:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/plotting.py:docstring of astrovascpy.plotting:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/report_reader.py:docstring of astrovascpy.report_reader:11: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/report_reader.py:docstring of astrovascpy.report_reader:12: WARNING: Block quote ends without a blank line; unexpected unindent. | |
looking for now-outdated files... none found | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/report_writer.py:docstring of astrovascpy.report_writer:6: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/report_writer.py:docstring of astrovascpy.report_writer:7: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/scipy_petsc_conversions.py:docstring of astrovascpy.scipy_petsc_conversions:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/scipy_petsc_conversions.py:docstring of astrovascpy.scipy_petsc_conversions:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/utils.py:docstring of astrovascpy.utils:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/utils.py:docstring of astrovascpy.utils:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/vtk_io.py:docstring of astrovascpy.vtk_io:6: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/vtk_io.py:docstring of astrovascpy.vtk_io:7: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/index.rst:8: WARNING: toctree contains reference to nonexisting document 'installation' | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/README.md:: WARNING: image file not readable: docs/source/logo/BPP-AstroVascPy-Github.jpg | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/index.rst:4: WARNING: image file not readable: logo/BBP-AstroVascPy-Github.jpg | |
pickling environment... done | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/api_ref.rst: WARNING: document isn't included in any toctree | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/docs/source/changelog.rst: WARNING: document isn't included in any toctree | |
checking consistency... done | |
preparing documents... done | |
copying assets... copying static files... done | |
copying extra files... done | |
done | |
[2Kwriting output... [ 7%] api_ref [2Kwriting output... [ 14%] changelog [2Kwriting output... [ 21%] generated/astrovascpy.PetscBinaryIO [2Kwriting output... [ 29%] generated/astrovascpy.bloodflow [2Kwriting output... [ 36%] generated/astrovascpy.exceptions [2Kwriting output... [ 43%] generated/astrovascpy.io [2Kwriting output... [ 50%] generated/astrovascpy.ou [2Kwriting output... [ 57%] generated/astrovascpy.plotting [2Kwriting output... [ 64%] generated/astrovascpy.report_reader [2Kwriting output... [ 71%] generated/astrovascpy.report_writer [2Kwriting output... [ 79%] generated/astrovascpy.scipy_petsc_conversions [2Kwriting output... [ 86%] generated/astrovascpy.utils [2Kwriting output... [ 93%] generated/astrovascpy.vtk_io [2Kwriting output... [100%] index | |
generating indices... genindex py-modindex done | |
writing additional pages... search done | |
dumping search index in English (code: en)... done | |
dumping object inventory... done | |
build succeeded, 43 warnings. | |
The HTML pages are in build/html. | |
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
docs: OK (323.42=setup[314.35]+cmd[9.07] seconds) | |
congratulations :) (323.73 seconds) | |
[32;1m$ section_end section_tox[0;m | |
[0Ksection_end:1697468703:section_tox [0K | |
section_end:1697468703:step_script [0Ksection_start:1697468703:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m[0;m | |
Using git from spack modules | |
[32;1mUploading artifacts...[0;m | |
Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=212664 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
[0;33mWARNING: ./doc/build/: no matching files [0;m | |
./docs/build/: found 167 matching files and directories[0;m | |
Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=965620 responseStatus[0;m=201 Created token[0;m=64_yhY6y | |
section_end:1697468705:upload_artifacts_on_success [0Ksection_start:1697468705:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
Using git from spack modules | |
section_end:1697468705:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
[0K on BB5 map runner pnPo3yJy[0;m | |
section_start:1697468353:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
section_end:1697468353:resolve_secrets [0Ksection_start:1697468353:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor3917486544, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
Runner ID 29, project root molsys, project name AstroVascPy | |
Pipeline ID 161829, build ref , job ID 965619 | |
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J965619, optional exclusive flag , optional cpus per task flag --cpus-per-task=6, optional qos flag , optional reservation flag | |
A slurm job will be created with name GL_J965619_PROD_P2342_CP1_C25 | |
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcimolsys partition=prod qos= reservation= | |
Not executing the chown -R | |
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
Submitted batch job 1841410 | |
job state: PD | |
job state: PD | |
job state: R | |
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J965619_PROD_P2342_CP1_C25 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J965619 --time=1:00:00 --wrap="sleep infinity" | |
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J965619 --ntasks=1 --jobid=1841410 --cpus-per-task=6 --mem=30750M | |
section_end:1697468357:prepare_executor [0Ksection_start:1697468357:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
Using git from spack modules | |
Running on r1i4n24 via bbpv1.epfl.ch... | |
section_end:1697468364:prepare_script [0Ksection_start:1697468364:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
Using git from spack modules | |
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
[32;1mFetching changes with git depth set to 20...[0;m | |
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy/.git/ | |
[32;1mCreated fresh repository.[0;m | |
[32;1mChecking out 2fa9a3c1 as nicola/petsc_improvement...[0;m | |
Skipping object checkout, Git LFS is not installed. | |
[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m | |
section_end:1697468367:get_sources [0Ksection_start:1697468367:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
Using git from spack modules | |
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
[32;1m$ module purge[0;m | |
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
[32;1m$ module load archive/2020-12 python/3.7.4[0;m | |
[32;1m$ module unload archive/2020-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.7.4 | |
[32;1m$ module load archive/2021-12 python/3.8.3[0;m | |
[32;1m$ module unload archive/2021-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.8.3 | |
[32;1m$ module load archive/2023-02 python/3.9.7[0;m | |
[32;1m$ module unload archive/2023-02[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.9.7 | |
[32;1m$ module load unstable python[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.10.8 | |
[32;1m$ load-modules() { # collapsed multi-line command[0;m | |
[32;1m$ load-modules $SYSTEM_MODULES[0;m | |
Loaded module git from unstable | |
Loaded module cmake from unstable | |
Loaded module graphviz from unstable | |
[32;1m$ load-modules $EXTRA_MODULES[0;m | |
Loaded module gcc from unstable | |
Loaded module hpe-mpi from unstable | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module petsc from unstable | |
Autoloading python/3.10.8 | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module py-petsc4py from unstable | |
[32;1m$ module list -t[0;m | |
Currently Loaded Modulefiles: | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4 | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/python/3.10.8 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/git/2.38.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/cmake/3.24.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/graphviz/2.49.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/compilers/linux-rhel7-haswell/gcc/12.2.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/petsc/3.18.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/py-petsc4py/3.18.1 | |
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
[32;1m$ print_var XDG_CONFIG_HOME[0;m | |
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy/local_config[0m | |
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
insteadOf = https://bbpgitlab.epfl.ch/ | |
insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
insteadOf = git@bbpgitlab.epfl.ch: | |
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
[0Ksection_start:1697468369:section_venv[collapsed=true] [0KSetting up the virtual env | |
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
[32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
[32;1m$ rm -rf "$CI_VENV"[0;m | |
[32;1m$ python -mvenv "$CI_VENV"[0;m | |
[32;1m$ source "$CI_VENV/bin/activate"[0;m | |
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (22.2.2) | |
Collecting pip | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/bc3/8bb52bc286514/pip-23.3-py3-none-any.whl (2.1 MB) | |
ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 74.5 MB/s eta 0:00:00 | |
Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages (63.0.0) | |
Collecting setuptools | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b45/4a35605876da6/setuptools-68.2.2-py3-none-any.whl (807 kB) | |
âââââââââââââââââââââââââââââââââââââ 807.9/807.9 kB 171.2 MB/s eta 0:00:00 | |
Collecting wheel | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/759/09db2664838d0/wheel-0.41.2-py3-none-any.whl (64 kB) | |
âââââââââââââââââââââââââââââââââââââââ 64.8/64.8 kB 204.5 MB/s eta 0:00:00 | |
Installing collected packages: wheel, setuptools, pip | |
Attempting uninstall: setuptools | |
Found existing installation: setuptools 63.0.0 | |
Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy/venv | |
Can't uninstall 'setuptools'. No files were found to uninstall. | |
Attempting uninstall: pip | |
Found existing installation: pip 22.2.2 | |
Uninstalling pip-22.2.2: | |
Successfully uninstalled pip-22.2.2 | |
Successfully installed pip-23.3 setuptools-68.2.2 wheel-0.41.2 | |
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Collecting tox | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/599/af5e5bb0cad01/tox-4.11.3-py3-none-any.whl (153 kB) | |
ââââââââââââââââââââââââââââââââââââââ 153.8/153.8 kB 15.7 MB/s eta 0:00:00 | |
Collecting cachetools>=5.3.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/95e/f631eeaea14ba/cachetools-5.3.1-py3-none-any.whl (9.3 kB) | |
Collecting chardet>=5.2 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 60.4 MB/s eta 0:00:00 | |
Collecting colorama>=0.4.6 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
Collecting filelock>=3.12.3 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/08c/21d87ded6e2b9/filelock-3.12.4-py3-none-any.whl (11 kB) | |
Collecting packaging>=23.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/8c4/91190033a9af7/packaging-23.2-py3-none-any.whl (53 kB) | |
âââââââââââââââââââââââââââââââââââââââ 53.0/53.0 kB 193.6 MB/s eta 0:00:00 | |
Collecting platformdirs>=3.10 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e9d/171d00af68be5/platformdirs-3.11.0-py3-none-any.whl (17 kB) | |
Collecting pluggy>=1.3 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/d89/c696a773f8bd3/pluggy-1.3.0-py3-none-any.whl (18 kB) | |
Collecting pyproject-api>=1.6.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
Collecting tomli>=2.0.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/939/de3e7a6161af0/tomli-2.0.1-py3-none-any.whl (12 kB) | |
Collecting virtualenv>=20.24.3 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b80/039f280f4919c/virtualenv-20.24.5-py3-none-any.whl (3.7 MB) | |
ââââââââââââââââââââââââââââââââââââââââ 3.7/3.7 MB 190.0 MB/s eta 0:00:00 | |
Collecting distlib<1,>=0.3.7 (from virtualenv>=20.24.3->tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2e2/4928bc811348f/distlib-0.3.7-py2.py3-none-any.whl (468 kB) | |
âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 244.9 MB/s eta 0:00:00 | |
Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
Successfully installed cachetools-5.3.1 chardet-5.2.0 colorama-0.4.6 distlib-0.3.7 filelock-3.12.4 packaging-23.2 platformdirs-3.11.0 pluggy-1.3.0 pyproject-api-1.6.1 tomli-2.0.1 tox-4.11.3 virtualenv-20.24.5 | |
[32;1m$ section_end section_venv[0;m | |
[0Ksection_end:1697468390:section_venv [0K | |
[32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
[36mPRE_BUILD_COMMAND=[0m | |
[32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
[32;1m$ section_start section_tox "Running Tox"[0;m | |
[0Ksection_start:1697468390:section_tox [0KRunning Tox | |
[32;1m$ python -mtox $TOX_OPTIONS[0;m | |
lint: install_deps> python -I -m pip install pre-commit pylint pylint-exit | |
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel | |
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: get_requires_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: install_requires_for_build_wheel> python -I -m pip install wheel | |
.pkg: freeze> python -m pip freeze --all | |
.pkg: packaging==23.2,pip==23.2.1,setuptools==68.2.0,setuptools-scm==8.0.4,tomli==2.0.1,typing_extensions==4.8.0,wheel==0.41.2 | |
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
lint: install_package_deps> python -I -m pip install cached-property click coverage cython h5py libsonata matplotlib mock morphio mpi4py networkx numpy 'pandas<2.0.0' psutil pytest pytest-click pytest-cov pytest-html pyyaml scipy seaborn tables tqdm trimesh vascpy vtk | |
lint: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz | |
lint: freeze> python -m pip freeze --all | |
lint: astroid==3.0.1,AstroVascPy @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz#sha256=61f3af103370421ffbd95927fc821dd24d87bdbb9f857784450bccf4e1095d81,blosc2==2.2.9,cached-property==1.5.2,cfgv==3.4.0,click==8.1.7,contourpy==1.1.1,coverage==7.3.2,cycler==0.12.1,Cython==3.0.3,dill==0.3.7,distlib==0.3.7,exceptiongroup==1.1.3,filelock==3.12.4,fonttools==4.43.1,h5py==3.10.0,identify==2.5.30,iniconfig==2.0.0,isort==5.12.0,Jinja2==3.1.2,kiwisolver==1.4.5,libsonata==0.1.24,MarkupSafe==2.1.3,matplotlib==3.8.0,mccabe==0.7.0,mock==5.1.0,MorphIO==3.3.6,mpi4py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mpi4py-3.1.4-glx4cfnu5cionch2hbeyzns5ol3vexp7/spack-src,msgpack==1.0.7,ndindex==1.7,networkx==3.1,nodeenv==1.8.0,numexpr==2.8.7,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging==23.2,pandas==1.5.3,petsc4py @ file:///nvme/bbpcihpcdeploy/1644090/spack-stage/spack-stage-py-petsc4py-3.18.1-7rysecnje3dndrjv36w723cz6tfioxhe/spack-src,Pillow==10.1.0,pip==23.2.1,platformdirs==3.11.0,pluggy==1.3.0,pre-commit==3.5.0,psutil==5.9.6,py-cpuinfo==9.0.0,pylint==3.0.1,pylint-exit==1.2.0,pyparsing==3.1.1,pytest==7.4.2,pytest-click==1.1.0,pytest-cov==4.1.0,pytest-html==4.0.2,pytest-metadata==3.0.0,python-dateutil==2.8.2,pytz==2023.3.post1,PyYAML==6.0.1,scipy==1.11.3,seaborn==0.13.0,setuptools @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-setuptools-63.0.0-c6hdpvjjddmcm3xf5begyfpkjkzj2oke/spack-src/setuptools-63.0.0-py3-none-any.whl,six==1.16.0,tables==3.9.1,tomli==2.0.1,tomlkit==0.12.1,tqdm==4.66.1,trimesh==4.0.0,typing_extensions==4.8.0,vascpy==0.1.1,virtualenv==20.24.5,vtk==9.2.6,wheel==0.41.2 | |
lint: commands[0]> pre-commit run --all-files --show-diff-on-failure | |
[INFO] Initializing environment for https://github.com/pre-commit/pre-commit-hooks. | |
[INFO] Initializing environment for https://github.com/alessandrojcm/commitlint-pre-commit-hook. | |
[INFO] Initializing environment for https://github.com/alessandrojcm/commitlint-pre-commit-hook:conventional-changelog-conventionalcommits. | |
[INFO] Initializing environment for https://github.com/pycqa/isort. | |
[INFO] Initializing environment for https://github.com/psf/black. | |
[INFO] Initializing environment for https://github.com/codespell-project/codespell. | |
[INFO] Initializing environment for https://github.com/PyCQA/flake8. | |
[INFO] Installing environment for https://github.com/pre-commit/pre-commit-hooks. | |
[INFO] Once installed this environment will be reused. | |
[INFO] This may take a few minutes... | |
[INFO] Installing environment for https://github.com/pycqa/isort. | |
[INFO] Once installed this environment will be reused. | |
[INFO] This may take a few minutes... | |
[INFO] Installing environment for https://github.com/psf/black. | |
[INFO] Once installed this environment will be reused. | |
[INFO] This may take a few minutes... | |
[INFO] Installing environment for https://github.com/codespell-project/codespell. | |
[INFO] Once installed this environment will be reused. | |
[INFO] This may take a few minutes... | |
[INFO] Installing environment for https://github.com/PyCQA/flake8. | |
[INFO] Once installed this environment will be reused. | |
[INFO] This may take a few minutes... | |
check for added large files..............................................Passed | |
check for case conflicts.................................................Passed | |
check for merge conflicts................................................Passed | |
check for broken symlinks............................(no files to check)Skipped | |
check yaml...............................................................Passed | |
debug statements (python)................................................Passed | |
fix end of files.........................................................Passed | |
trim trailing whitespace.................................................Failed | |
- hook id: trailing-whitespace | |
- exit code: 1 | |
- files were modified by this hook | |
Fixing tox.ini | |
isort....................................................................Passed | |
black....................................................................Passed | |
codespell................................................................Passed | |
flake8...................................................................Passed | |
pre-commit hook(s) made changes. | |
If you are seeing this message in CI, reproduce locally with: `pre-commit run --all-files`. | |
To run `pre-commit` as part of git workflow, use `pre-commit install`. | |
All changes made by hooks: | |
diff --git a/tox.ini b/tox.ini | |
index 6afdd18..bc03dea 100644 | |
--- a/tox.ini | |
+++ b/tox.ini | |
@@ -35,7 +35,7 @@ commands = pytest \ | |
{posargs} | |
mpirun -n 4 pytest --with-mpi {toxinidir}/tests/test_mpi.py | |
coverage report | |
- | |
+ | |
[testenv:check-packaging] | |
skip_install = true | |
deps = | |
lint: exit 1 (40.86 seconds) /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy> pre-commit run --all-files --show-diff-on-failure pid=210638 | |
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
lint: FAIL code 1 (341.28=setup[300.42]+cmd[40.86] seconds) | |
evaluation failed :( (341.62 seconds) | |
srun: error: r1i4n24: task 0: Exited with exit code 1 | |
section_end:1697468732:step_script [0Ksection_start:1697468732:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
Using git from spack modules | |
section_end:1697468733:cleanup_file_variables [0K[31;1mERROR: Job failed: exit status 1 | |
[0;m |
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[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
[0K on BB5 map runner pnPo3yJy[0;m | |
section_start:1697468354:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
section_end:1697468354:resolve_secrets [0Ksection_start:1697468354:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor1431981264, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
Runner ID 29, project root molsys, project name AstroVascPy | |
Pipeline ID 161829, build ref , job ID 965621 | |
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J965621, optional exclusive flag , optional cpus per task flag --cpus-per-task=6, optional qos flag , optional reservation flag | |
A slurm job will be created with name GL_J965621_PROD_P2342_CP3_C27 | |
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcimolsys partition=prod qos= reservation= | |
Not executing the chown -R | |
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
Submitted batch job 1841412 | |
job state: PD | |
job state: R | |
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J965621_PROD_P2342_CP3_C27 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J965621 --time=1:00:00 --wrap="sleep infinity" | |
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J965621 --ntasks=1 --jobid=1841412 --cpus-per-task=6 --mem=30750M | |
section_end:1697468357:prepare_executor [0Ksection_start:1697468357:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
Using git from spack modules | |
Running on r1i4n24 via bbpv1.epfl.ch... | |
section_end:1697468364:prepare_script [0Ksection_start:1697468364:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
Using git from spack modules | |
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
[32;1mFetching changes with git depth set to 20...[0;m | |
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/.git/ | |
[32;1mCreated fresh repository.[0;m | |
[32;1mChecking out 2fa9a3c1 as nicola/petsc_improvement...[0;m | |
Skipping object checkout, Git LFS is not installed. | |
[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m | |
section_end:1697468367:get_sources [0Ksection_start:1697468367:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
Using git from spack modules | |
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
[32;1m$ module purge[0;m | |
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
[32;1m$ module load archive/2020-12 python/3.7.4[0;m | |
[32;1m$ module unload archive/2020-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.7.4 | |
[32;1m$ module load archive/2021-12 python/3.8.3[0;m | |
[32;1m$ module unload archive/2021-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.8.3 | |
[32;1m$ module load archive/2023-02 python/3.9.7[0;m | |
[32;1m$ module unload archive/2023-02[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.9.7 | |
[32;1m$ module load unstable python[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.10.8 | |
[32;1m$ load-modules() { # collapsed multi-line command[0;m | |
[32;1m$ load-modules $SYSTEM_MODULES[0;m | |
Loaded module git from unstable | |
Loaded module cmake from unstable | |
Loaded module graphviz from unstable | |
[32;1m$ load-modules $EXTRA_MODULES[0;m | |
Loaded module gcc from unstable | |
Loaded module hpe-mpi from unstable | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module petsc from unstable | |
Autoloading python/3.10.8 | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module py-petsc4py from unstable | |
[32;1m$ module list -t[0;m | |
Currently Loaded Modulefiles: | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4 | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/python/3.10.8 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/git/2.38.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/cmake/3.24.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/graphviz/2.49.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/compilers/linux-rhel7-haswell/gcc/12.2.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/petsc/3.18.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/py-petsc4py/3.18.1 | |
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
[32;1m$ print_var XDG_CONFIG_HOME[0;m | |
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/local_config[0m | |
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
insteadOf = https://bbpgitlab.epfl.ch/ | |
insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
insteadOf = git@bbpgitlab.epfl.ch: | |
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
[0Ksection_start:1697468369:section_venv[collapsed=true] [0KSetting up the virtual env | |
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
[32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
[32;1m$ rm -rf "$CI_VENV"[0;m | |
[32;1m$ python -mvenv "$CI_VENV"[0;m | |
[32;1m$ source "$CI_VENV/bin/activate"[0;m | |
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (22.2.2) | |
Collecting pip | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/bc3/8bb52bc286514/pip-23.3-py3-none-any.whl (2.1 MB) | |
ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 75.6 MB/s eta 0:00:00 | |
Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages (63.0.0) | |
Collecting setuptools | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b45/4a35605876da6/setuptools-68.2.2-py3-none-any.whl (807 kB) | |
âââââââââââââââââââââââââââââââââââââ 807.9/807.9 kB 191.5 MB/s eta 0:00:00 | |
Collecting wheel | |
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Installing collected packages: wheel, setuptools, pip | |
Attempting uninstall: setuptools | |
Found existing installation: setuptools 63.0.0 | |
Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/venv | |
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Attempting uninstall: pip | |
Found existing installation: pip 22.2.2 | |
Uninstalling pip-22.2.2: | |
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Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
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[32;1m$ section_end section_venv[0;m | |
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[32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
[36mPRE_BUILD_COMMAND=[0m | |
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[32;1m$ section_start section_tox "Running Tox"[0;m | |
[0Ksection_start:1697468389:section_tox [0KRunning Tox | |
[32;1m$ python -mtox $TOX_OPTIONS[0;m | |
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel | |
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: get_requires_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: install_requires_for_build_wheel> python -I -m pip install wheel | |
.pkg: freeze> python -m pip freeze --all | |
.pkg: packaging==23.2,pip==23.2.1,setuptools==68.2.0,setuptools-scm==8.0.4,tomli==2.0.1,typing_extensions==4.8.0,wheel==0.41.2 | |
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
py310: install_package_deps> python -I -m pip install cached-property click coverage cython h5py libsonata matplotlib mock morphio mpi4py networkx numpy 'pandas<2.0.0' psutil pytest pytest-click pytest-cov pytest-html pyyaml scipy seaborn tables tqdm trimesh vascpy vtk | |
py310: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz | |
py310: freeze> python -m pip freeze --all | |
py310: AstroVascPy @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz#sha256=caf2b2a229f9e4c637c72f2f8b40f69a6d29a168594b677dea23cf0c257fb947,blosc2==2.2.9,cached-property==1.5.2,click==8.1.7,contourpy==1.1.1,coverage==7.3.2,cycler==0.12.1,Cython==3.0.3,exceptiongroup==1.1.3,fonttools==4.43.1,h5py==3.10.0,iniconfig==2.0.0,Jinja2==3.1.2,kiwisolver==1.4.5,libsonata==0.1.24,MarkupSafe==2.1.3,matplotlib==3.8.0,mock==5.1.0,MorphIO==3.3.6,mpi4py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mpi4py-3.1.4-glx4cfnu5cionch2hbeyzns5ol3vexp7/spack-src,msgpack==1.0.7,ndindex==1.7,networkx==3.1,numexpr==2.8.7,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging==23.2,pandas==1.5.3,petsc4py @ file:///nvme/bbpcihpcdeploy/1644090/spack-stage/spack-stage-py-petsc4py-3.18.1-7rysecnje3dndrjv36w723cz6tfioxhe/spack-src,Pillow==10.1.0,pip==23.2.1,pluggy==1.3.0,psutil==5.9.6,py-cpuinfo==9.0.0,pyparsing==3.1.1,pytest==7.4.2,pytest-click==1.1.0,pytest-cov==4.1.0,pytest-html==4.0.2,pytest-metadata==3.0.0,python-dateutil==2.8.2,pytz==2023.3.post1,PyYAML==6.0.1,scipy==1.11.3,seaborn==0.13.0,setuptools @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-setuptools-63.0.0-c6hdpvjjddmcm3xf5begyfpkjkzj2oke/spack-src/setuptools-63.0.0-py3-none-any.whl,six==1.16.0,tables==3.9.1,tomli==2.0.1,tqdm==4.66.1,trimesh==4.0.0,vascpy==0.1.1,vtk==9.2.6,wheel==0.41.2 | |
py310: commands[0]> pytest --basetemp=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/.tox/py310/tmp --cov=astrovascpy --cov-branch --cov-fail-under=50 --no-cov-on-fail --cov-report term-missing --cov-report html:reports/coverage-py310 --cov-report xml:reports/coverage-py310.xml --html reports/pytest-py310.html --junit-xml=reports/pytest-py310.xml --self-contained-html --verbose | |
============================= test session starts ============================== | |
platform linux -- Python 3.10.8, pytest-7.4.2, pluggy-1.3.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/.tox/py310/bin/python | |
cachedir: .tox/py310/.pytest_cache | |
metadata: {'Python': '3.10.8', 'Platform': 'Linux-3.10.0-1160.42.2.el7.x86_64-x86_64-with-glibc2.17', 'Packages': {'pytest': '7.4.2', 'pluggy': '1.3.0'}, 'Plugins': {'metadata': '3.0.0', 'html': '4.0.2', 'cov': '4.1.0', 'click': '1.1.0'}, 'CI': 'true', 'CI_COMMIT_REF_NAME': 'nicola/petsc_improvement', 'CI_COMMIT_REF_SLUG': 'nicola-petsc-improvement', 'CI_COMMIT_SHA': '2fa9a3c1b16861319b840d6a8cd4b1354bb89ae0', 'CI_JOB_ID': '965621', 'CI_JOB_NAME': 'py310', 'CI_JOB_STAGE': 'test', 'CI_RUNNER_DESCRIPTION': 'BB5 map runner', 'CI_RUNNER_ID': '29', 'CI_RUNNER_TAGS': '["bb5_map"]', 'CI_PIPELINE_ID': '161829', 'CI_PROJECT_DIR': '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy', 'CI_PROJECT_ID': '2342', 'CI_PROJECT_NAME': 'AstroVascPy', 'CI_PROJECT_NAMESPACE': 'molsys', 'CI_PROJECT_PATH': 'molsys/AstroVascPy', 'CI_PROJECT_URL': 'https://bbpgitlab.epfl.ch/molsys/AstroVascPy', 'CI_REGISTRY': 'bbpgitlab.epfl.ch:5050', 'CI_REGISTRY_IMAGE': 'bbpgitlab.epfl.ch:5050/molsys/astrovascpy', 'CI_REGISTRY_USER': 'gitlab-ci-token', 'CI_SERVER': 'yes', 'CI_SERVER_NAME': 'GitLab', 'CI_SERVER_REVISION': '40d6bde8c59', 'CI_SERVER_VERSION': '16.3.5-ee', 'GITLAB_CI': 'true', 'GITLAB_USER_ID': '17', 'GITLAB_USER_EMAIL': 'tristan.carel@epfl.ch'} | |
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy | |
configfile: pyproject.toml | |
testpaths: tests | |
plugins: metadata-3.0.0, html-4.0.2, cov-4.1.0, click-1.1.0 | |
collecting ... collected 56 items | |
tests/test_bloodflow.py::test_compute_edge_resistances PASSED [ 1%] | |
tests/test_bloodflow.py::test_set_edge_resistances PASSED [ 3%] | |
tests/test_bloodflow.py::test_set_endfeet_ids PASSED [ 5%] | |
tests/test_bloodflow.py::test_get_radii_at_endfeet PASSED [ 7%] | |
tests/test_bloodflow.py::test_get_radius_at_endfoot PASSED [ 8%] | |
tests/test_bloodflow.py::test_set_radii_at_endfeet PASSED [ 10%] | |
tests/test_bloodflow.py::test_set_radius_at_endfoot PASSED [ 12%] | |
tests/test_bloodflow.py::test_set_endfoot_id PASSED [ 14%] | |
tests/test_bloodflow.py::test_get_closest_edges PASSED [ 16%] | |
tests/test_bloodflow.py::test_simulate_vasodilation_ou_process PASSED [ 17%] | |
tests/test_bloodflow.py::test_simulate_ou_process PASSED [ 19%] | |
tests/test_bloodflow.py::test_depth_first_search PASSED [ 21%] | |
tests/test_bloodflow.py::test_compute_static_laplacian PASSED [ 23%] | |
tests/test_bloodflow.py::test_update_static_flow_pressure PASSED [ 25%] | |
tests/test_bloodflow.py::test_total_flow_conservation_in_graph PASSED [ 26%] | |
tests/test_bloodflow.py::test_conservation_flow PASSED [ 28%] | |
tests/test_bloodflow.py::test_static_construct_incidence_matrix PASSED [ 30%] | |
tests/test_bloodflow.py::test_solve_linear PASSED [ 32%] | |
tests/test_bloodflow.py::test_boundary_flows_A_based PASSED [ 33%] | |
tests/test_graphs.py::test_simple_graph PASSED [ 35%] | |
tests/test_graphs.py::test_bifurcation PASSED [ 37%] | |
tests/test_graphs.py::test_loop PASSED [ 39%] | |
tests/test_io.py::test_petsc_installation PASSED [ 41%] | |
tests/test_io.py::test_load_graph PASSED [ 42%] | |
tests/test_io.py::test_load_graph_from_h5 PASSED [ 44%] | |
tests/test_io.py::test_load_graph_from_csv PASSED [ 46%] | |
tests/test_io.py::test_load_graph_from_bin PASSED [ 48%] | |
tests/test_mpi.py::test_numpy_array2petsc PASSED [ 50%] | |
tests/test_mpi.py::test_scipy_coo2petsc PASSED [ 51%] | |
tests/test_mpi.py::test_coomatrix2PETScMat PASSED [ 53%] | |
tests/test_ou.py::test_OU_calibration PASSED [ 55%] | |
tests/test_report_reader.py::TestBloodflowReport::test_time_units PASSED [ 57%] | |
tests/test_report_reader.py::TestBloodflowReport::test_data_units PASSED [ 58%] | |
tests/test_report_reader.py::TestBloodflowReport::test_population_names PASSED [ 60%] | |
tests/test_report_reader.py::TestBloodflowReport::test_get_population PASSED [ 62%] | |
tests/test_report_reader.py::TestBloodflowReport::test_iter PASSED [ 64%] | |
tests/test_report_reader.py::TestBloodflowReport::test_filter PASSED [ 66%] | |
tests/test_report_reader.py::TestPopulationBloodflowReport::test_name PASSED [ 67%] | |
tests/test_report_reader.py::TestPopulationBloodflowReport::test_get PASSED [ 69%] | |
tests/test_report_reader.py::TestPopulationBloodflowReport::test_node_ids PASSED [ 71%] | |
tests/test_report_reader.py::test_overriden_function PASSED [ 73%] | |
tests/test_report_writer.py::test_write_simulation_report PASSED [ 75%] | |
tests/test_utils.py::test_find_neighbors PASSED [ 76%] | |
tests/test_utils.py::test_find_degrees_of_neighbors PASSED [ 78%] | |
tests/test_utils.py::test_create_entry_largest_nodes PASSED [ 80%] | |
tests/test_utils.py::test_get_largest_nodes PASSED [ 82%] | |
tests/test_utils.py::test_get_large_nodes PASSED [ 83%] | |
tests/test_utils.py::test_compute_edge_data PASSED [ 85%] | |
tests/test_utils.py::test_set_edge_data PASSED [ 87%] | |
tests/test_utils.py::test_is_iterable PASSED [ 89%] | |
tests/test_utils.py::test_ensure_list PASSED [ 91%] | |
tests/test_utils.py::test_ensure_ids PASSED [ 92%] | |
tests/test_utils.py::test_create_input_speed PASSED [ 94%] | |
tests/test_utils.py::test_sine_estimation[None] PASSED [ 96%] | |
tests/test_utils.py::test_sine_estimation[15] PASSED [ 98%] | |
tests/test_utils.py::test_sine_estimation[30] PASSED [100%] | |
=============================== warnings summary =============================== | |
tests/test_mpi.py:22 | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/tests/test_mpi.py:22: PytestUnknownMarkWarning: Unknown pytest.mark.mpi - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html | |
@pytest.mark.mpi(min_size=2) | |
tests/test_mpi.py:50 | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/tests/test_mpi.py:50: PytestUnknownMarkWarning: Unknown pytest.mark.mpi - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html | |
@pytest.mark.mpi(min_size=2) | |
tests/test_mpi.py:106 | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/tests/test_mpi.py:106: PytestUnknownMarkWarning: Unknown pytest.mark.mpi - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html | |
@pytest.mark.mpi(min_size=2) | |
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
- generated xml file: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/reports/pytest-py310.xml - | |
---------- coverage: platform linux, python 3.10.8-final-0 ----------- | |
Name Stmts Miss Branch BrPart Cover Missing | |
------------------------------------------------------------------------------------ | |
astrovascpy/PetscBinaryIO.py 309 167 96 22 43% 63-76, 83-104, 108-110, 120-122, 128, 131, 132->134, 144->149, 184, 191, 198, 201, 206-209, 255, 284->304, 286->292, 288, 292->298, 294, 298->304, 300, 313, 316, 318, 323-324, 334-341, 366-381, 387-399, 405-425, 429-430, 434-441, 452-459, 465-471, 477-480, 501-536, 550->554, 557-571, 572->574 | |
astrovascpy/__init__.py 0 0 0 0 100% | |
astrovascpy/bloodflow.py 315 56 122 33 75% 96->106, 102, 116->exit, 152->155, 199-211, 388, 420->440, 428-429, 434-435, 442->444, 447, 449->454, 474-476, 490->493, 492, 495, 498->502, 503-508, 542->547, 555->560, 561->565, 565->571, 573->576, 579, 586->571, 594, 628, 632, 639-658, 661, 683, 701->705, 703, 706->708, 711-713, 717->725 | |
astrovascpy/exceptions.py 1 0 0 0 100% | |
astrovascpy/io.py 57 8 24 11 77% 49, 67->71, 70, 73, 91->95, 94, 97, 121, 124->127, 128, 132 | |
astrovascpy/ou.py 14 1 2 1 88% 135 | |
astrovascpy/plotting.py 17 17 6 0 0% 13-205 | |
astrovascpy/report_reader.py 90 0 18 0 100% | |
astrovascpy/report_writer.py 27 0 4 0 100% | |
astrovascpy/scipy_petsc_conversions.py 223 92 52 12 56% 51-73, 90->98, 101->108, 121-138, 176-181, 208, 220->224, 251-310, 319-331, 350, 366, 370, 401, 405, 410, 456 | |
astrovascpy/utils.py 300 117 74 6 60% 138-146, 160-163, 168-189, 251, 253, 267, 269-270, 274, 317-318, 437-455, 512-562, 584-631 | |
astrovascpy/version.py 2 2 0 0 0% 14-15 | |
astrovascpy/vtk_io.py 5 5 0 0 0% 14-20 | |
------------------------------------------------------------------------------------ | |
TOTAL 1360 465 398 85 62% | |
Coverage HTML written to dir reports/coverage-py310 | |
Coverage XML written to file reports/coverage-py310.xml | |
Required test coverage of 50% reached. Total coverage: 62.46% | |
- Generated html report: file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/reports/pytest-py310.html - | |
======================= 56 passed, 3 warnings in 12.86s ======================== | |
py310: commands[1]> mpirun -n 4 pytest --with-mpi /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/tests/test_mpi.py | |
ERROR: usage: pytest [options] [file_or_dir] [file_or_dir] [...] | |
pytest: error: unrecognized arguments: --with-mpi | |
inifile: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/pyproject.toml | |
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy | |
MPT ERROR: could not run executable. | |
(HPE HMPT 2.25 10/22/21 03:19:55) | |
py310: exit 255 (91.64 seconds) /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy> mpirun -n 4 pytest --with-mpi /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/tests/test_mpi.py pid=212361 | |
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
py310: FAIL code 255 (401.70=setup[296.20]+cmd[13.86,91.64] seconds) | |
evaluation failed :( (402.00 seconds) | |
srun: error: r1i4n24: task 0: Exited with exit code 1 | |
section_end:1697468792:step_script [0Ksection_start:1697468792:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
Using git from spack modules | |
section_end:1697468793:cleanup_file_variables [0K[31;1mERROR: Job failed: exit status 1 | |
[0;m |
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