Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/molsys/AstroVascPy/-/pipelines/161829 (:no_entry:) running on GitHub PR BlueBrain/AstroVascPy#5.

check-packaging.txt

Running with gitlab-runner 15.5.0 (0d4137b8)
  on BB5 map runner pnPo3yJy
section_start:1697468353:resolve_secrets
Resolving secrets
section_end:1697468353:resolve_secrets
section_start:1697468353:prepare_executor
Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
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
section_start:1697468354:prepare_script
Preparing environment
Using git from spack modules
Running on r1i4n24 via bbpv1.epfl.ch...
section_end:1697468358:prepare_script
section_start:1697468358:get_sources
Getting source from Git repository
Using git from spack modules
$ 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 '*'
Fetching changes with git depth set to 20...
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965618/molsys/AstroVascPy/.git/
Created fresh repository.
Checking out 2fa9a3c1 as nicola/petsc_improvement...
Skipping object checkout, Git LFS is not installed.

Updating/initializing submodules recursively with git depth set to 20...
section_end:1697468361:get_sources
section_start:1697468361:step_script
Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi
$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }
$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }
$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }
$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }
$ module purge
$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')
$ module load archive/2020-12 python/3.7.4
$ module unload archive/2020-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.7.4
$ module load archive/2021-12 python/3.8.3
$ module unload archive/2021-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.8.3
$ module load archive/2023-02 python/3.9.7
$ module unload archive/2023-02
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.9.7
$ module load unstable python
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.10.8
$ load-modules() { # collapsed multi-line command
$ load-modules $SYSTEM_MODULES
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
$ load-modules $EXTRA_MODULES
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
$ module list -t
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
$ export XDG_CONFIG_HOME=${PWD}/local_config
$ print_var XDG_CONFIG_HOME
XDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965618/molsys/AstroVascPy/local_config
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command
$ cat "${XDG_CONFIG_HOME}/git/config"
[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:
$ section_start section_venv[collapsed=true] "Setting up the virtual env"
section_start:1697468363:section_venv[collapsed=true]
Setting up the virtual env
$ cd "${PYTHON_PROJECT_DIR}"
$ CI_VENV="$(pwd)/venv"
$ rm -rf "$CI_VENV"
$ python -mvenv "$CI_VENV"
$ source "$CI_VENV/bin/activate"
$ python -mpip install --upgrade pip setuptools wheel
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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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
$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi
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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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
$ section_end section_venv
section_end:1697468379:section_venv

$ print_var PRE_BUILD_COMMAND
PRE_BUILD_COMMAND=
$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi
$ section_start section_tox "Running Tox"
section_start:1697468379:section_tox
Running Tox
$ python -mtox $TOX_OPTIONS
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: PASSED
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: PASSED
  check-packaging: OK (52.59=setup[24.57]+cmd[26.19,1.84] seconds)
  congratulations :) (53.04 seconds)
$ section_end section_tox
section_end:1697468432:section_tox

section_end:1697468432:step_script
section_start:1697468432:cleanup_file_variables
Cleaning up project directory and file based variables
Using git from spack modules
section_end:1697468433:cleanup_file_variables
Job succeeded

docs.txt

Running with gitlab-runner 15.5.0 (0d4137b8)
  on BB5 map runner pnPo3yJy
section_start:1697468354:resolve_secrets
Resolving secrets
section_end:1697468354:resolve_secrets
section_start:1697468354:prepare_executor
Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
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
section_start:1697468357:prepare_script
Preparing environment
Using git from spack modules
Running on r1i4n24 via bbpv1.epfl.ch...
section_end:1697468358:prepare_script
section_start:1697468358:get_sources
Getting source from Git repository
Using git from spack modules
$ 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 '*'
Fetching changes with git depth set to 20...
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/.git/
Created fresh repository.
Checking out 2fa9a3c1 as nicola/petsc_improvement...
Skipping object checkout, Git LFS is not installed.

Updating/initializing submodules recursively with git depth set to 20...
section_end:1697468361:get_sources
section_start:1697468361:step_script
Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi
$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }
$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }
$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }
$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }
$ module purge
$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')
$ module load archive/2020-12 python/3.7.4
$ module unload archive/2020-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.7.4
$ module load archive/2021-12 python/3.8.3
$ module unload archive/2021-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.8.3
$ module load archive/2023-02 python/3.9.7
$ module unload archive/2023-02
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.9.7
$ module load unstable python
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.10.8
$ load-modules() { # collapsed multi-line command
$ load-modules $SYSTEM_MODULES
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
$ load-modules $EXTRA_MODULES
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
$ module list -t
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
$ export XDG_CONFIG_HOME=${PWD}/local_config
$ print_var XDG_CONFIG_HOME
XDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965620/molsys/AstroVascPy/local_config
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command
$ cat "${XDG_CONFIG_HOME}/git/config"
[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:
$ section_start section_venv[collapsed=true] "Setting up the virtual env"
section_start:1697468363:section_venv[collapsed=true]
Setting up the virtual env
$ cd "${PYTHON_PROJECT_DIR}"
$ CI_VENV="$(pwd)/venv"
$ rm -rf "$CI_VENV"
$ python -mvenv "$CI_VENV"
$ source "$CI_VENV/bin/activate"
$ python -mpip install --upgrade pip setuptools wheel
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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 76.6 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 807.9/807.9 kB 249.6 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 64.8/64.8 kB 213.6 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/J965620/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
$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi
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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 153.8/153.8 kB 19.3 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 199.4/199.4 kB 60.1 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.0/53.0 kB 189.7 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.7/3.7 MB 181.0 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 468.9/468.9 kB 242.4 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
$ section_end section_venv
section_end:1697468379:section_venv

$ print_var PRE_BUILD_COMMAND
PRE_BUILD_COMMAND=
$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi
$ section_start section_tox "Running Tox"
section_start:1697468379:section_tox
Running Tox
$ python -mtox $TOX_OPTIONS
.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
reading sources... [  7%] api_ref
reading sources... [ 14%] changelog
reading sources... [ 21%] generated/astrovascpy.PetscBinaryIO
reading sources... [ 29%] generated/astrovascpy.bloodflow
reading sources... [ 36%] generated/astrovascpy.exceptions
reading sources... [ 43%] generated/astrovascpy.io
reading sources... [ 50%] generated/astrovascpy.ou
reading sources... [ 57%] generated/astrovascpy.plotting
reading sources... [ 64%] generated/astrovascpy.report_reader
reading sources... [ 71%] generated/astrovascpy.report_writer
reading sources... [ 79%] generated/astrovascpy.scipy_petsc_conversions
reading sources... [ 86%] generated/astrovascpy.utils
reading sources... [ 93%] generated/astrovascpy.vtk_io
reading 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
writing output... [  7%] api_ref
writing output... [ 14%] changelog
writing output... [ 21%] generated/astrovascpy.PetscBinaryIO
writing output... [ 29%] generated/astrovascpy.bloodflow
writing output... [ 36%] generated/astrovascpy.exceptions
writing output... [ 43%] generated/astrovascpy.io
writing output... [ 50%] generated/astrovascpy.ou
writing output... [ 57%] generated/astrovascpy.plotting
writing output... [ 64%] generated/astrovascpy.report_reader
writing output... [ 71%] generated/astrovascpy.report_writer
writing output... [ 79%] generated/astrovascpy.scipy_petsc_conversions
writing output... [ 86%] generated/astrovascpy.utils
writing output... [ 93%] generated/astrovascpy.vtk_io
writing 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)
$ section_end section_tox
section_end:1697468703:section_tox

section_end:1697468703:step_script
section_start:1697468703:upload_artifacts_on_success
Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform                                    arch=amd64 os=linux pid=212664 revision=58ba2b95 version=14.2.0
WARNING: ./doc/build/: no matching files           
./docs/build/: found 167 matching files and directories 
Uploading artifacts as "archive" to coordinator... ok  id=965620 responseStatus=201 Created token=64_yhY6y
section_end:1697468705:upload_artifacts_on_success
section_start:1697468705:cleanup_file_variables
Cleaning up project directory and file based variables
Using git from spack modules
section_end:1697468705:cleanup_file_variables
Job succeeded

GitLab logs for bluebrain-astrovascpy#5

!

lint.txt

Running with gitlab-runner 15.5.0 (0d4137b8)
  on BB5 map runner pnPo3yJy
section_start:1697468353:resolve_secrets
Resolving secrets
section_end:1697468353:resolve_secrets
section_start:1697468353:prepare_executor
Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
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
section_start:1697468357:prepare_script
Preparing environment
Using git from spack modules
Running on r1i4n24 via bbpv1.epfl.ch...
section_end:1697468364:prepare_script
section_start:1697468364:get_sources
Getting source from Git repository
Using git from spack modules
$ 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 '*'
Fetching changes with git depth set to 20...
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy/.git/
Created fresh repository.
Checking out 2fa9a3c1 as nicola/petsc_improvement...
Skipping object checkout, Git LFS is not installed.

Updating/initializing submodules recursively with git depth set to 20...
section_end:1697468367:get_sources
section_start:1697468367:step_script
Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi
$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }
$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }
$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }
$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }
$ module purge
$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')
$ module load archive/2020-12 python/3.7.4
$ module unload archive/2020-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.7.4
$ module load archive/2021-12 python/3.8.3
$ module unload archive/2021-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.8.3
$ module load archive/2023-02 python/3.9.7
$ module unload archive/2023-02
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.9.7
$ module load unstable python
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.10.8
$ load-modules() { # collapsed multi-line command
$ load-modules $SYSTEM_MODULES
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
$ load-modules $EXTRA_MODULES
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
$ module list -t
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
$ export XDG_CONFIG_HOME=${PWD}/local_config
$ print_var XDG_CONFIG_HOME
XDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965619/molsys/AstroVascPy/local_config
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command
$ cat "${XDG_CONFIG_HOME}/git/config"
[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:
$ section_start section_venv[collapsed=true] "Setting up the virtual env"
section_start:1697468369:section_venv[collapsed=true]
Setting up the virtual env
$ cd "${PYTHON_PROJECT_DIR}"
$ CI_VENV="$(pwd)/venv"
$ rm -rf "$CI_VENV"
$ python -mvenv "$CI_VENV"
$ source "$CI_VENV/bin/activate"
$ python -mpip install --upgrade pip setuptools wheel
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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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
$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi
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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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
$ section_end section_venv
section_end:1697468390:section_venv

$ print_var PRE_BUILD_COMMAND
PRE_BUILD_COMMAND=
$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi
$ section_start section_tox "Running Tox"
section_start:1697468390:section_tox
Running Tox
$ python -mtox $TOX_OPTIONS
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
section_start:1697468732:cleanup_file_variables
Cleaning up project directory and file based variables
Using git from spack modules
section_end:1697468733:cleanup_file_variables
ERROR: Job failed: exit status 1


py310.txt

Running with gitlab-runner 15.5.0 (0d4137b8)
  on BB5 map runner pnPo3yJy
section_start:1697468354:resolve_secrets
Resolving secrets
section_end:1697468354:resolve_secrets
section_start:1697468354:prepare_executor
Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
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
section_start:1697468357:prepare_script
Preparing environment
Using git from spack modules
Running on r1i4n24 via bbpv1.epfl.ch...
section_end:1697468364:prepare_script
section_start:1697468364:get_sources
Getting source from Git repository
Using git from spack modules
$ 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 '*'
Fetching changes with git depth set to 20...
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/.git/
Created fresh repository.
Checking out 2fa9a3c1 as nicola/petsc_improvement...
Skipping object checkout, Git LFS is not installed.

Updating/initializing submodules recursively with git depth set to 20...
section_end:1697468367:get_sources
section_start:1697468367:step_script
Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi
$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }
$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }
$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }
$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }
$ module purge
$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')
$ module load archive/2020-12 python/3.7.4
$ module unload archive/2020-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.7.4
$ module load archive/2021-12 python/3.8.3
$ module unload archive/2021-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.8.3
$ module load archive/2023-02 python/3.9.7
$ module unload archive/2023-02
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.9.7
$ module load unstable python
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.10.8
$ load-modules() { # collapsed multi-line command
$ load-modules $SYSTEM_MODULES
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
$ load-modules $EXTRA_MODULES
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
$ module list -t
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
$ export XDG_CONFIG_HOME=${PWD}/local_config
$ print_var XDG_CONFIG_HOME
XDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J965621/molsys/AstroVascPy/local_config
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command
$ cat "${XDG_CONFIG_HOME}/git/config"
[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:
$ section_start section_venv[collapsed=true] "Setting up the virtual env"
section_start:1697468369:section_venv[collapsed=true]
Setting up the virtual env
$ cd "${PYTHON_PROJECT_DIR}"
$ CI_VENV="$(pwd)/venv"
$ rm -rf "$CI_VENV"
$ python -mvenv "$CI_VENV"
$ source "$CI_VENV/bin/activate"
$ python -mpip install --upgrade pip setuptools wheel
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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 807.9/807.9 kB 191.5 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 64.8/64.8 kB 216.0 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/J965621/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
$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi
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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 153.8/153.8 kB 12.3 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 199.4/199.4 kB 56.4 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.0/53.0 kB 185.3 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.7/3.7 MB 196.7 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 468.9/468.9 kB 235.8 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
$ section_end section_venv
section_end:1697468389:section_venv

$ print_var PRE_BUILD_COMMAND
PRE_BUILD_COMMAND=
$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi
$ section_start section_tox "Running Tox"
section_start:1697468389:section_tox
Running Tox
$ python -mtox $TOX_OPTIONS
.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
section_start:1697468792:cleanup_file_variables
Cleaning up project directory and file based variables
Using git from spack modules
section_end:1697468793:cleanup_file_variables
ERROR: Job failed: exit status 1