bbpbuildbot/GitLab logs for bluebrain-astrovascpy#20 Secret

## check-packaging.txt
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
[0K  on BB5 map runner pnPo3yJy[0;m
section_start:1702976018:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1702976018:resolve_secrets
[0Ksection_start:1702976018:prepare_executor
[0K[0K[36;1mPreparing the "custom" executor[0;m[0;m
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor3795881504, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root molsys, project name AstroVascPy
Pipeline ID 181495, build ref , job ID 1089692
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089692, 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_J1089692_PROD_P2342_CP0_C1
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 1950770
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J1089692_PROD_P2342_CP0_C1 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089692 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089692 --ntasks=1 --jobid=1950770 --cpus-per-task=6 --mem=30750M
section_end:1702976020:prepare_executor
[0Ksection_start:1702976020:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i7n22 via bbpv1.epfl.ch...
section_end:1702976024:prepare_script
[0Ksection_start:1702976024:get_sources
[0K[0K[36;1mGetting source from Git repository[0;m[0;m
Using git from spack modules
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m
[32;1mFetching changes with git depth set to 20...[0;m
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089692/molsys/AstroVascPy/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 8758d502 as nicola/scipy_petsc_bug...[0;m
Skipping object checkout, Git LFS is not installed.

[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m
section_end:1702976027:get_sources
[0Ksection_start:1702976027:step_script
[0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m
Using git from spack modules
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m
[32;1m$ module purge[0;m
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m
[32;1m$ module load archive/2020-12 python/3.7.4[0;m
[32;1m$ module unload archive/2020-12[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.7.4
[32;1m$ module load archive/2021-12 python/3.8.3[0;m
[32;1m$ module unload archive/2021-12[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.8.3
[32;1m$ module load archive/2023-02 python/3.9.7[0;m
[32;1m$ module unload archive/2023-02[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.9.7
[32;1m$ module load unstable python[0;m
[32;1m$ module unload unstable[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.10.8
[32;1m$ load-modules() { # collapsed multi-line command[0;m
[32;1m$ load-modules $SYSTEM_MODULES[0;m
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
[32;1m$ load-modules $EXTRA_MODULES[0;m
Loaded module gcc from unstable
Loaded module hpe-mpi from unstable
Autoloading python/3.10.8
Autoloading hpe-mpi/2.25.hmpt
Loaded module py-mpi4py from unstable
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
Loaded module petsc from unstable
Autoloading python/3.10.8
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
Loaded module py-petsc4py from unstable
[32;1m$ module list -t[0;m
Currently Loaded Modulefiles:
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/python/3.10.8
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/git/2.38.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/cmake/3.24.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/graphviz/2.49.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/compilers/linux-rhel7-haswell/gcc/12.2.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-mpi4py/3.1.4
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/petsc/3.18.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-petsc4py/3.18.1
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m
[32;1m$ print_var XDG_CONFIG_HOME[0;m
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089692/molsys/AstroVascPy/local_config[0m
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
  insteadOf = https://bbpgitlab.epfl.ch/
  insteadOf = ssh://git@bbpgitlab.epfl.ch/
  insteadOf = git@bbpgitlab.epfl.ch:
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m
[0Ksection_start:1702976029:section_venv[collapsed=true]
[0KSetting up the virtual env
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m
[32;1m$ CI_VENV="$(pwd)/venv"[0;m
[32;1m$ rm -rf "$CI_VENV"[0;m
[32;1m$ python -mvenv "$CI_VENV"[0;m
[32;1m$ source "$CI_VENV/bin/activate"[0;m
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (22.2.2)
Collecting pip
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/505/2d7889c1f9d05/pip-23.3.2-py3-none-any.whl (2.1 MB)
     ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 76.1 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/1e8/fdff6797d3865/setuptools-69.0.2-py3-none-any.whl (819 kB)
     âââââââââââââââââââââââââââââââââââââ 819.5/819.5 kB 266.1 MB/s eta 0:00:00
Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/177/f9c9b0d45c478/wheel-0.42.0-py3-none-any.whl (65 kB)
     âââââââââââââââââââââââââââââââââââââââ 65.4/65.4 kB 215.3 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/J1089692/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-23.3.2 setuptools-69.0.2 wheel-0.42.0
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Collecting tox
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2ad/b83d68f271168/tox-4.11.4-py3-none-any.whl (153 kB)
     ââââââââââââââââââââââââââââââââââââââ 154.0/154.0 kB 19.1 MB/s eta 0:00:00
Collecting cachetools>=5.3.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/861/f35a13a451f94/cachetools-5.3.2-py3-none-any.whl (9.3 kB)
Collecting chardet>=5.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB)
     ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 55.6 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/57d/bda9b35157b05/filelock-3.13.1-py3-none-any.whl (11 kB)
Collecting packaging>=23.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/8c4/91190033a9af7/packaging-23.2-py3-none-any.whl (53 kB)
     âââââââââââââââââââââââââââââââââââââââ 53.0/53.0 kB 218.3 MB/s eta 0:00:00
Collecting platformdirs>=3.10 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/11c/8f37bcca40db9/platformdirs-4.1.0-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/423/8949c5ffe6876/virtualenv-20.25.0-py3-none-any.whl (3.8 MB)
     ââââââââââââââââââââââââââââââââââââââââ 3.8/3.8 MB 178.3 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/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB)
     âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 256.7 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-5.3.2 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-23.2 platformdirs-4.1.0 pluggy-1.3.0 pyproject-api-1.6.1 tomli-2.0.1 tox-4.11.4 virtualenv-20.25.0
[32;1m$ section_end section_venv[0;m
[0Ksection_end:1702976045:section_venv
[0K
[32;1m$ print_var PRE_BUILD_COMMAND[0;m
[36mPRE_BUILD_COMMAND=[0m
[32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m
[32;1m$ section_start section_tox "Running Tox"[0;m
[0Ksection_start:1702976045:section_tox
[0KRunning Tox
[32;1m$ python -mtox $TOX_OPTIONS[0;m
check-packaging: install_deps> python -I -m pip install build twine
check-packaging: freeze> python -m pip freeze --all
check-packaging: build==1.0.3,certifi==2023.11.17,cffi==1.16.0,charset-normalizer==3.3.2,cryptography==41.0.7,docutils==0.20.1,idna==3.6,importlib-metadata==7.0.0,jaraco.classes==3.3.0,jeepney==0.8.0,keyring==24.3.0,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==0.2.15,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging==23.2,petsc4py @ file:///nvme/bbpcihpcdeploy/1912700/spack-stage/spack-stage-py-petsc4py-3.18.1-k6k4ybhubjpjanttcmmql5ditq2bxn32/spack-src,pip==23.3.1,pkginfo==1.9.6,pycparser==2.21,Pygments==2.17.2,pyproject_hooks==1.0.0,readme-renderer==42.0,requests==2.31.0,requests-toolbelt==1.0.0,rfc3986==2.0.0,rich==13.7.0,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==2.1.0,wheel==0.42.0,zipp==3.17.0
check-packaging: commands[0]> python -m build -o /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089692/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/typing.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/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/io.py -> build/lib/astrovascpy
copying astrovascpy/typing.py -> build/lib/astrovascpy
copying astrovascpy/report_writer.py -> build/lib/astrovascpy
copying astrovascpy/vtk_io.py -> build/lib/astrovascpy
copying astrovascpy/plotting.py -> build/lib/astrovascpy
copying astrovascpy/report_reader.py -> build/lib/astrovascpy
copying astrovascpy/version.py -> build/lib/astrovascpy
copying astrovascpy/ou.py -> build/lib/astrovascpy
copying astrovascpy/PetscBinaryIO.py -> build/lib/astrovascpy
copying astrovascpy/utils.py -> build/lib/astrovascpy
copying astrovascpy/exceptions.py -> build/lib/astrovascpy
copying astrovascpy/scipy_petsc_conversions.py -> build/lib/astrovascpy
copying astrovascpy/__init__.py -> build/lib/astrovascpy
copying astrovascpy/bloodflow.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/io.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/typing.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/vtk_io.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/report_reader.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/ou.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/utils.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/scipy_petsc_conversions.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/__init__.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/bloodflow.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/J1089692/molsys/AstroVascPy/.tox/check-packaging/tmp/dist/tmpgohyfnbv/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/typing.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/J1089692/molsys/AstroVascPy/.tox/check-packaging/tmp/dist/*'
Checking
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089692/molsys/AstroVascPy/.t
ox/check-packaging/tmp/dist/AstroVascPy-0.0.1-py3-none-any.whl: [32mPASSED[0m
Checking
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089692/molsys/AstroVascPy/.t
ox/check-packaging/tmp/dist/AstroVascPy-0.0.1.tar.gz: [32mPASSED[0m
  check-packaging: OK (28.48=setup[13.45]+cmd[14.62,0.41] seconds)
  congratulations :) (28.92 seconds)
[32;1m$ section_end section_tox[0;m
[0Ksection_end:1702976074:section_tox
[0K
section_end:1702976074:step_script
[0Ksection_start:1702976074:cleanup_file_variables
[0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m
Using git from spack modules
section_end:1702976075:cleanup_file_variables
[0K[32;1mJob succeeded[0;m

## docs.txt
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
[0K  on BB5 map runner pnPo3yJy[0;m
section_start:1702976019:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1702976019:resolve_secrets
[0Ksection_start:1702976019:prepare_executor
[0K[0K[36;1mPreparing the "custom" executor[0;m[0;m
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor4031834543, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root molsys, project name AstroVascPy
Pipeline ID 181495, build ref , job ID 1089694
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089694, 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_J1089694_PROD_P2342_CP2_C3
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 1950772
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J1089694_PROD_P2342_CP2_C3 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089694 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089694 --ntasks=1 --jobid=1950772 --cpus-per-task=6 --mem=30750M
section_end:1702976021:prepare_executor
[0Ksection_start:1702976021:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i7n22 via bbpv1.epfl.ch...
section_end:1702976028:prepare_script
[0Ksection_start:1702976028:get_sources
[0K[0K[36;1mGetting source from Git repository[0;m[0;m
Using git from spack modules
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m
[32;1mFetching changes with git depth set to 20...[0;m
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 8758d502 as nicola/scipy_petsc_bug...[0;m
Skipping object checkout, Git LFS is not installed.

[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m
section_end:1702976031:get_sources
[0Ksection_start:1702976031:step_script
[0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m
Using git from spack modules
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m
[32;1m$ module purge[0;m
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m
[32;1m$ module load archive/2020-12 python/3.7.4[0;m
[32;1m$ module unload archive/2020-12[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.7.4
[32;1m$ module load archive/2021-12 python/3.8.3[0;m
[32;1m$ module unload archive/2021-12[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.8.3
[32;1m$ module load archive/2023-02 python/3.9.7[0;m
[32;1m$ module unload archive/2023-02[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.9.7
[32;1m$ module load unstable python[0;m
[32;1m$ module unload unstable[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.10.8
[32;1m$ load-modules() { # collapsed multi-line command[0;m
[32;1m$ load-modules $SYSTEM_MODULES[0;m
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
[32;1m$ load-modules $EXTRA_MODULES[0;m
Loaded module gcc from unstable
Loaded module hpe-mpi from unstable
Autoloading python/3.10.8
Autoloading hpe-mpi/2.25.hmpt
Loaded module py-mpi4py from unstable
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
Loaded module petsc from unstable
Autoloading python/3.10.8
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
Loaded module py-petsc4py from unstable
[32;1m$ module list -t[0;m
Currently Loaded Modulefiles:
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/python/3.10.8
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/git/2.38.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/cmake/3.24.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/graphviz/2.49.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/compilers/linux-rhel7-haswell/gcc/12.2.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-mpi4py/3.1.4
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/petsc/3.18.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-petsc4py/3.18.1
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m
[32;1m$ print_var XDG_CONFIG_HOME[0;m
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/local_config[0m
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
  insteadOf = https://bbpgitlab.epfl.ch/
  insteadOf = ssh://git@bbpgitlab.epfl.ch/
  insteadOf = git@bbpgitlab.epfl.ch:
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m
[0Ksection_start:1702976033:section_venv[collapsed=true]
[0KSetting up the virtual env
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m
[32;1m$ CI_VENV="$(pwd)/venv"[0;m
[32;1m$ rm -rf "$CI_VENV"[0;m
[32;1m$ python -mvenv "$CI_VENV"[0;m
[32;1m$ source "$CI_VENV/bin/activate"[0;m
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (22.2.2)
Collecting pip
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/505/2d7889c1f9d05/pip-23.3.2-py3-none-any.whl (2.1 MB)
     ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 75.1 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/1e8/fdff6797d3865/setuptools-69.0.2-py3-none-any.whl (819 kB)
     âââââââââââââââââââââââââââââââââââââ 819.5/819.5 kB 270.4 MB/s eta 0:00:00
Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/177/f9c9b0d45c478/wheel-0.42.0-py3-none-any.whl (65 kB)
     âââââââââââââââââââââââââââââââââââââââ 65.4/65.4 kB 222.6 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/J1089694/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-23.3.2 setuptools-69.0.2 wheel-0.42.0
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Collecting tox
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Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox
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[32;1m$ section_end section_venv[0;m
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[32;1m$ section_start section_tox "Running Tox"[0;m
[0Ksection_start:1702976049:section_tox
[0KRunning Tox
[32;1m$ python -mtox $TOX_OPTIONS[0;m
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/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/J1089694/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/J1089694/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==23.3.1,setuptools==69.0.2,setuptools-scm==8.0.4,tomli==2.0.1,typing_extensions==4.9.0,wheel==0.42.0
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/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/J1089694/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 networkx numpy 'pandas<2.0.0' psutil pyyaml scipy seaborn sphinx sphinx-bluebrain-theme sphinx-click tables tqdm trimesh vascpy
docs: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/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/J1089694/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz#sha256=1835035a4af0fa5dffa69c1da40c1881b14bb32357f600e62cfa6bfde687fc07,Babel==2.14.0,blosc2==2.3.2,cached-property==1.5.2,certifi==2023.11.17,charset-normalizer==3.3.2,click==8.1.7,contourpy==1.2.0,coverage==7.3.3,cycler==0.12.1,Cython==3.0.6,docutils==0.20.1,fonttools==4.47.0,h5py==3.10.0,idna==3.6,imagesize==1.4.1,Jinja2==3.0.3,kiwisolver==1.4.5,libsonata==0.1.24,m2r2==0.3.3.post2,MarkupSafe==2.1.3,matplotlib==3.8.2,mistune==0.8.4,MorphIO==3.3.7,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==3.2.1,numexpr==2.8.8,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/1912700/spack-stage/spack-stage-py-petsc4py-3.18.1-k6k4ybhubjpjanttcmmql5ditq2bxn32/spack-src,Pillow==10.1.0,pip==23.3.1,psutil==5.9.7,py-cpuinfo==9.0.0,Pygments==2.17.2,pyparsing==3.1.1,python-dateutil==2.8.2,pytz==2023.3.post1,PyYAML==6.0.1,requests==2.31.0,scipy==1.11.4,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==5.1.0,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==3.9.2,tqdm==4.66.1,trimesh==4.0.6,urllib3==2.1.0,vascpy==0.1.1,wheel==0.42.0
docs: commands[0] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/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
WARNING: [autosummary] failed to import astrovascpy.vtk_io.
Possible hints:
* ModuleNotFoundError: No module named 'vtk'
* ImportError:
* AttributeError: module 'astrovascpy' has no attribute 'vtk_io'
[autosummary] generating autosummary for: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.PetscBinaryIO.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.bloodflow.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.exceptions.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.io.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.ou.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.plotting.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.report_reader.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.report_writer.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.scipy_petsc_conversions.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.utils.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] 13 added, 0 changed, 0 removed
[2Kreading sources... [  8%] api_ref
[2Kreading sources... [ 15%] changelog
[2Kreading sources... [ 23%] generated/astrovascpy.PetscBinaryIO
[2Kreading sources... [ 31%] generated/astrovascpy.bloodflow
[2Kreading sources... [ 38%] generated/astrovascpy.exceptions
[2Kreading sources... [ 46%] generated/astrovascpy.io
[2Kreading sources... [ 54%] generated/astrovascpy.ou
[2Kreading sources... [ 62%] generated/astrovascpy.plotting
[2Kreading sources... [ 69%] generated/astrovascpy.report_reader
[2Kreading sources... [ 77%] generated/astrovascpy.report_writer
[2Kreading sources... [ 85%] generated/astrovascpy.scipy_petsc_conversions
[2Kreading sources... [ 92%] generated/astrovascpy.utils
[2Kreading sources... [100%] index
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/api_ref.rst:6: WARNING: autosummary: failed to import astrovascpy.vtk_io.
Possible hints:
* ModuleNotFoundError: No module named 'vtk'
* ImportError:
* AttributeError: module 'astrovascpy' has no attribute 'vtk_io'
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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/J1089694/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.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/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/J1089694/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/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/scipy_petsc_conversions.py:docstring of astrovascpy.scipy_petsc_conversions:5: ERROR: Unexpected indentation.
looking for now-outdated files... none found
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/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/J1089694/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/J1089694/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/J1089694/molsys/AstroVascPy/docs/source/index.rst:8: WARNING: toctree contains reference to nonexisting document 'installation'
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/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/J1089694/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/J1089694/molsys/AstroVascPy/docs/source/api_ref.rst: WARNING: document isn't included in any toctree
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/changelog.rst: WARNING: document isn't included in any toctree
checking consistency... done
preparing documents... done
copying assets... copying static files... done
copying extra files... done
done
[2Kwriting output... [  8%] api_ref
[2Kwriting output... [ 15%] changelog
[2Kwriting output... [ 23%] generated/astrovascpy.PetscBinaryIO
[2Kwriting output... [ 31%] generated/astrovascpy.bloodflow
[2Kwriting output... [ 38%] generated/astrovascpy.exceptions
[2Kwriting output... [ 46%] generated/astrovascpy.io
[2Kwriting output... [ 54%] generated/astrovascpy.ou
[2Kwriting output... [ 62%] generated/astrovascpy.plotting
[2Kwriting output... [ 69%] generated/astrovascpy.report_reader
[2Kwriting output... [ 77%] generated/astrovascpy.report_writer
[2Kwriting output... [ 85%] generated/astrovascpy.scipy_petsc_conversions
[2Kwriting output... [ 92%] generated/astrovascpy.utils
[2Kwriting output... [100%] index
generating indices... genindex py-modindex done
writing additional pages... search done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 43 warnings.

The HTML pages are in build/html.
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
  docs: OK (85.72=setup[76.88]+cmd[8.84] seconds)
  congratulations :) (86.01 seconds)
[32;1m$ section_end section_tox[0;m
[0Ksection_end:1702976136:section_tox
[0K
section_end:1702976136:step_script
[0Ksection_start:1702976136:upload_artifacts_on_success
[0K[0K[36;1mUploading artifacts for successful job[0;m[0;m
Using git from spack modules
[32;1mUploading artifacts...[0;m
Runtime platform                                  [0;m  arch[0;m=amd64 os[0;m=linux pid[0;m=86972 revision[0;m=58ba2b95 version[0;m=14.2.0
[0;33mWARNING: ./doc/build/: no matching files          [0;m
./docs/build/: found 164 matching files and directories[0;m
Uploading artifacts as "archive" to coordinator... ok[0;m  id[0;m=1089694 responseStatus[0;m=201 Created token[0;m=64_VJRz2
section_end:1702976137:upload_artifacts_on_success
[0Ksection_start:1702976137:cleanup_file_variables
[0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m
Using git from spack modules
section_end:1702976138:cleanup_file_variables
[0K[32;1mJob succeeded[0;m

## GitLab logs for bluebrain-astrovascpy#20
!

## lint.txt
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
[0K  on BB5 map runner pnPo3yJy[0;m
section_start:1702976019:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1702976019:resolve_secrets
[0Ksection_start:1702976019:prepare_executor
[0K[0K[36;1mPreparing the "custom" executor[0;m[0;m
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor4068472163, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root molsys, project name AstroVascPy
Pipeline ID 181495, build ref , job ID 1089693
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089693, 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_J1089693_PROD_P2342_CP1_C2
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 1950771
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J1089693_PROD_P2342_CP1_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089693 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089693 --ntasks=1 --jobid=1950771 --cpus-per-task=6 --mem=30750M
section_end:1702976020:prepare_executor
[0Ksection_start:1702976020:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i7n22 via bbpv1.epfl.ch...
section_end:1702976027:prepare_script
[0Ksection_start:1702976027:get_sources
[0K[0K[36;1mGetting source from Git repository[0;m[0;m
Using git from spack modules
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m
[32;1mFetching changes with git depth set to 20...[0;m
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 8758d502 as nicola/scipy_petsc_bug...[0;m
Skipping object checkout, Git LFS is not installed.

[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m
section_end:1702976030:get_sources
[0Ksection_start:1702976030:step_script
[0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m
Using git from spack modules
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m
[32;1m$ module purge[0;m
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m
[32;1m$ module load archive/2020-12 python/3.7.4[0;m
[32;1m$ module unload archive/2020-12[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.7.4
[32;1m$ module load archive/2021-12 python/3.8.3[0;m
[32;1m$ module unload archive/2021-12[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.8.3
[32;1m$ module load archive/2023-02 python/3.9.7[0;m
[32;1m$ module unload archive/2023-02[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.9.7
[32;1m$ module load unstable python[0;m
[32;1m$ module unload unstable[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.10.8
[32;1m$ load-modules() { # collapsed multi-line command[0;m
[32;1m$ load-modules $SYSTEM_MODULES[0;m
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
[32;1m$ load-modules $EXTRA_MODULES[0;m
Loaded module gcc from unstable
Loaded module hpe-mpi from unstable
Autoloading python/3.10.8
Autoloading hpe-mpi/2.25.hmpt
Loaded module py-mpi4py from unstable
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
Loaded module petsc from unstable
Autoloading python/3.10.8
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
Loaded module py-petsc4py from unstable
[32;1m$ module list -t[0;m
Currently Loaded Modulefiles:
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/python/3.10.8
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/git/2.38.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/cmake/3.24.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/graphviz/2.49.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/compilers/linux-rhel7-haswell/gcc/12.2.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-mpi4py/3.1.4
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/petsc/3.18.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-petsc4py/3.18.1
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m
[32;1m$ print_var XDG_CONFIG_HOME[0;m
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/local_config[0m
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
  insteadOf = https://bbpgitlab.epfl.ch/
  insteadOf = ssh://git@bbpgitlab.epfl.ch/
  insteadOf = git@bbpgitlab.epfl.ch:
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m
[0Ksection_start:1702976032:section_venv[collapsed=true]
[0KSetting up the virtual env
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m
[32;1m$ CI_VENV="$(pwd)/venv"[0;m
[32;1m$ rm -rf "$CI_VENV"[0;m
[32;1m$ python -mvenv "$CI_VENV"[0;m
[32;1m$ source "$CI_VENV/bin/activate"[0;m
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (22.2.2)
Collecting pip
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/505/2d7889c1f9d05/pip-23.3.2-py3-none-any.whl (2.1 MB)
     ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 74.1 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/1e8/fdff6797d3865/setuptools-69.0.2-py3-none-any.whl (819 kB)
     âââââââââââââââââââââââââââââââââââââ 819.5/819.5 kB 271.4 MB/s eta 0:00:00
Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/177/f9c9b0d45c478/wheel-0.42.0-py3-none-any.whl (65 kB)
     âââââââââââââââââââââââââââââââââââââââ 65.4/65.4 kB 209.0 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/J1089693/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-23.3.2 setuptools-69.0.2 wheel-0.42.0
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Collecting tox
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2ad/b83d68f271168/tox-4.11.4-py3-none-any.whl (153 kB)
     ââââââââââââââââââââââââââââââââââââââ 154.0/154.0 kB 18.6 MB/s eta 0:00:00
Collecting cachetools>=5.3.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/861/f35a13a451f94/cachetools-5.3.2-py3-none-any.whl (9.3 kB)
Collecting chardet>=5.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB)
     ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 55.3 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/57d/bda9b35157b05/filelock-3.13.1-py3-none-any.whl (11 kB)
Collecting packaging>=23.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/8c4/91190033a9af7/packaging-23.2-py3-none-any.whl (53 kB)
     âââââââââââââââââââââââââââââââââââââââ 53.0/53.0 kB 209.2 MB/s eta 0:00:00
Collecting platformdirs>=3.10 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/11c/8f37bcca40db9/platformdirs-4.1.0-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/423/8949c5ffe6876/virtualenv-20.25.0-py3-none-any.whl (3.8 MB)
     ââââââââââââââââââââââââââââââââââââââââ 3.8/3.8 MB 177.6 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/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB)
     âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 270.0 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-5.3.2 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-23.2 platformdirs-4.1.0 pluggy-1.3.0 pyproject-api-1.6.1 tomli-2.0.1 tox-4.11.4 virtualenv-20.25.0
[32;1m$ section_end section_venv[0;m
[0Ksection_end:1702976049:section_venv
[0K
[32;1m$ print_var PRE_BUILD_COMMAND[0;m
[36mPRE_BUILD_COMMAND=[0m
[32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m
[32;1m$ section_start section_tox "Running Tox"[0;m
[0Ksection_start:1702976049:section_tox
[0KRunning Tox
[32;1m$ python -mtox $TOX_OPTIONS[0;m
lint: install_deps> python -I -m pip install pre-commit pylint pylint-exit
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/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/J1089693/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/J1089693/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==23.3.1,setuptools==69.0.2,setuptools-scm==8.0.4,tomli==2.0.1,typing_extensions==4.9.0,wheel==0.42.0
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/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/J1089693/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 morphio networkx numpy 'pandas<2.0.0' psutil pytest pytest-mpi pyyaml scipy seaborn tables tqdm trimesh vascpy
lint: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz
lint: freeze> python -m pip freeze --all
lint: astroid==3.0.2,AstroVascPy @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz#sha256=19e8cb9814bd98f0088dba42bc107d8291378c2cb81d2262b04eceeb4b7e6411,blosc2==2.3.2,cached-property==1.5.2,cfgv==3.4.0,click==8.1.7,contourpy==1.2.0,coverage==7.3.3,cycler==0.12.1,Cython==3.0.6,dill==0.3.7,distlib==0.3.8,exceptiongroup==1.2.0,filelock==3.13.1,fonttools==4.47.0,h5py==3.10.0,identify==2.5.33,iniconfig==2.0.0,isort==5.13.2,kiwisolver==1.4.5,libsonata==0.1.24,matplotlib==3.8.2,mccabe==0.7.0,MorphIO==3.3.7,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==3.2.1,nodeenv==1.8.0,numexpr==2.8.8,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/1912700/spack-stage/spack-stage-py-petsc4py-3.18.1-k6k4ybhubjpjanttcmmql5ditq2bxn32/spack-src,Pillow==10.1.0,pip==23.3.1,platformdirs==4.1.0,pluggy==1.3.0,pre-commit==3.6.0,psutil==5.9.7,py-cpuinfo==9.0.0,pylint==3.0.3,pylint-exit==1.2.0,pyparsing==3.1.1,pytest==7.4.3,pytest-mpi==0.6,python-dateutil==2.8.2,pytz==2023.3.post1,PyYAML==6.0.1,scipy==1.11.4,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==3.9.2,tomli==2.0.1,tomlkit==0.12.3,tqdm==4.66.1,trimesh==4.0.6,typing_extensions==4.9.0,vascpy==0.1.1,virtualenv==20.25.0,wheel==0.42.0
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.................................................Passed
isort....................................................................Passed
black....................................................................Passed
codespell................................................................Passed
flake8...................................................................Passed
lint: commands[1]> bash -c 'pylint -j 1 astrovascpy docs/source/conf.py setup.py || pylint-exit $?'
************* Module astrovascpy.io
astrovascpy/io.py:64:26: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
astrovascpy/io.py:51:34: W0613: Unused argument 'is_cc' (unused-argument)
astrovascpy/io.py:74:33: W0613: Unused argument 'is_cc' (unused-argument)
astrovascpy/io.py:96:54: W0613: Unused argument 'is_cc' (unused-argument)
************* Module astrovascpy.utils
astrovascpy/utils.py:67:19: W0212: Access to a protected member _node_properties of a client class (protected-access)
astrovascpy/utils.py:67:55: W0212: Access to a protected member _edge_properties of a client class (protected-access)
astrovascpy/utils.py:542:15: R1735: Consider using '{}' instead of a call to 'dict'. (use-dict-literal)
astrovascpy/utils.py:545:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/utils.py:545:4: E0213: Method 'region' should have "self" as first argument (no-self-argument)
astrovascpy/utils.py:556:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/utils.py:588:8: C0206: Consider iterating with .items() (consider-using-dict-items)
astrovascpy/utils.py:613:11: R1735: Consider using '{}' instead of a call to 'dict'. (use-dict-literal)
astrovascpy/utils.py:616:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/utils.py:616:4: E0213: Method 'region' should have "self" as first argument (no-self-argument)
astrovascpy/utils.py:628:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/utils.py:658:8: C0206: Consider iterating with .items() (consider-using-dict-items)
astrovascpy/utils.py:733:8: W0621: Redefining name 'time' from outer scope (line 15) (redefined-outer-name)
************* Module astrovascpy.scipy_petsc_conversions
astrovascpy/scipy_petsc_conversions.py:35:15: W0212: Access to a protected member _typedict of a client class (protected-access)
astrovascpy/scipy_petsc_conversions.py:130:8: W0632: Possible unbalanced tuple unpacking with sequence defined at line 537 of astrovascpy.PetscBinaryIO: left side has 1 label, right side has 0 values (unbalanced-tuple-unpacking)
************* Module astrovascpy.PetscBinaryIO
astrovascpy/PetscBinaryIO.py:72:20: W0707: Consider explicitly re-raising using 'except Exception as exc' and 'raise importlib.metadata.PackageNotFoundError from exc' (raise-missing-from)
astrovascpy/PetscBinaryIO.py:77:27: W0212: Access to a protected member _path of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:108:14: W1514: Using open without explicitly specifying an encoding (unspecified-encoding)
astrovascpy/PetscBinaryIO.py:108:14: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
astrovascpy/PetscBinaryIO.py:120:14: W1514: Using open without explicitly specifying an encoding (unspecified-encoding)
astrovascpy/PetscBinaryIO.py:45:0: R0912: Too many branches (23/12) (too-many-branches)
astrovascpy/PetscBinaryIO.py:45:0: R0915: Too many statements (55/50) (too-many-statements)
astrovascpy/PetscBinaryIO.py:120:14: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
astrovascpy/PetscBinaryIO.py:202:12: W0212: Access to a protected member _update_dtypes of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:210:12: W0212: Access to a protected member _update_dtypes of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:217:0: C0115: Missing class docstring (missing-class-docstring)
astrovascpy/PetscBinaryIO.py:256:15: C0209: Formatting a regular string which could be an f-string (consider-using-f-string)
astrovascpy/PetscBinaryIO.py:256:33: R1725: Consider using Python 3 style super() without arguments (super-with-arguments)
astrovascpy/PetscBinaryIO.py:271:0: R0205: Class 'PetscBinaryIO' inherits from object, can be safely removed from bases in python3 (useless-object-inheritance)
astrovascpy/PetscBinaryIO.py:329:27: C0209: Formatting a regular string which could be an f-string (consider-using-f-string)
astrovascpy/PetscBinaryIO.py:339:12: W0707: Consider explicitly re-raising using 'except MemoryError as exc' and 'raise IOError('Inconsistent or invalid Vec data in file') from exc' (raise-missing-from)
astrovascpy/PetscBinaryIO.py:348:29: W0212: Access to a protected member _classid of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:345:4: R1711: Useless return at end of function or method (useless-return)
astrovascpy/PetscBinaryIO.py:380:12: W0707: Consider explicitly re-raising using 'except (AssertionError, MemoryError, IndexError) as exc' and 'raise IOError('Inconsistent or invalid Mat data in file') from exc' (raise-missing-from)
astrovascpy/PetscBinaryIO.py:389:29: W0212: Access to a protected member _classid of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:385:4: R1711: Useless return at end of function or method (useless-return)
astrovascpy/PetscBinaryIO.py:420:12: W0707: Consider explicitly re-raising using 'except (AssertionError, MemoryError, IndexError) as exc' and 'raise IOError('Inconsistent or invalid Mat data in file') from exc' (raise-missing-from)
astrovascpy/PetscBinaryIO.py:429:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/PetscBinaryIO.py:434:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/PetscBinaryIO.py:438:8: W0612: Unused variable 'V' (unused-variable)
astrovascpy/PetscBinaryIO.py:439:8: W0612: Unused variable 'M' (unused-variable)
astrovascpy/PetscBinaryIO.py:439:11: W0612: Unused variable 'N' (unused-variable)
astrovascpy/PetscBinaryIO.py:440:8: W0612: Unused variable 'J' (unused-variable)
astrovascpy/PetscBinaryIO.py:441:8: W0612: Unused variable 'I' (unused-variable)
astrovascpy/PetscBinaryIO.py:471:12: W0707: Consider explicitly re-raising using 'except (MemoryError, IndexError) as exc' and 'raise IOError('Inconsistent or invalid IS data in file') from exc' (raise-missing-from)
astrovascpy/PetscBinaryIO.py:478:29: W0212: Access to a protected member _classid of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:475:4: R1711: Useless return at end of function or method (useless-return)
astrovascpy/PetscBinaryIO.py:515:20: W0707: Consider explicitly re-raising using 'except (MemoryError, IndexError) as exc' and 'raise DoneWithFile from exc' (raise-missing-from)
astrovascpy/PetscBinaryIO.py:519:20: W0707: Consider explicitly re-raising using 'except KeyError as exc' and 'raise IOError('Invalid PetscObject CLASSID or object not implemented for python') from exc' (raise-missing-from)
astrovascpy/PetscBinaryIO.py:505:18: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
astrovascpy/PetscBinaryIO.py:572:20: W0707: Consider explicitly re-raising using 'except AssertionError as exc' and 'raise TypeError('Object %s is not a valid PETSc object' % petscobj.__repr__()) from exc' (raise-missing-from)
astrovascpy/PetscBinaryIO.py:572:36: C0209: Formatting a regular string which could be an f-string (consider-using-f-string)
astrovascpy/PetscBinaryIO.py:572:79: C2801: Unnecessarily calls dunder method __repr__. Use repr built-in function. (unnecessary-dunder-call)
astrovascpy/PetscBinaryIO.py:540:4: R1711: Useless return at end of function or method (useless-return)
astrovascpy/PetscBinaryIO.py:552:18: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
************* Module astrovascpy.bloodflow
astrovascpy/bloodflow.py:44:0: W0622: Redefining built-in 'print' (redefined-builtin)
astrovascpy/bloodflow.py:418:0: R0914: Too many local variables (36/25) (too-many-locals)
astrovascpy/bloodflow.py:418:0: R0912: Too many branches (17/12) (too-many-branches)
astrovascpy/bloodflow.py:418:0: R0915: Too many statements (72/50) (too-many-statements)
astrovascpy/bloodflow.py:684:34: C0209: Formatting a regular string which could be an f-string (consider-using-f-string)
astrovascpy/bloodflow.py:644:0: R0912: Too many branches (15/12) (too-many-branches)
astrovascpy/bloodflow.py:644:0: R0915: Too many statements (66/50) (too-many-statements)
************* Module astrovascpy.typing
astrovascpy/typing.py:9:0: C0115: Missing class docstring (missing-class-docstring)
astrovascpy/typing.py:15:0: C0115: Missing class docstring (missing-class-docstring)

-----------------------------------
Your code has been rated at 9.48/10

The following messages were raised:

  - error message issued
  - warning message issued
  - refactor message issued
  - convention message issued

No fatal messages detected.  Exiting gracefully...
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
  lint: OK (142.19=setup[65.75]+cmd[42.10,34.33] seconds)
  congratulations :) (142.46 seconds)
[32;1m$ section_end section_tox[0;m
[0Ksection_end:1702976192:section_tox
[0K
section_end:1702976192:step_script
[0Ksection_start:1702976192:cleanup_file_variables
[0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m
Using git from spack modules
section_end:1702976193:cleanup_file_variables
[0K[32;1mJob succeeded[0;m

## py310.txt
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
[0K  on BB5 map runner pnPo3yJy[0;m
section_start:1702976020:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1702976020:resolve_secrets
[0Ksection_start:1702976020:prepare_executor
[0K[0K[36;1mPreparing the "custom" executor[0;m[0;m
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor401415700, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root molsys, project name AstroVascPy
Pipeline ID 181495, build ref , job ID 1089695
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089695, 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_J1089695_PROD_P2342_CP3_C4
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 1950773
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_J1089695_PROD_P2342_CP3_C4 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089695 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089695 --ntasks=1 --jobid=1950773 --cpus-per-task=6 --mem=30750M
section_end:1702976023:prepare_executor
[0Ksection_start:1702976023:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i7n22 via bbpv1.epfl.ch...
section_end:1702976025:prepare_script
[0Ksection_start:1702976025:get_sources
[0K[0K[36;1mGetting source from Git repository[0;m[0;m
Using git from spack modules
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m
[32;1mFetching changes with git depth set to 20...[0;m
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 8758d502 as nicola/scipy_petsc_bug...[0;m
Skipping object checkout, Git LFS is not installed.

[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m
section_end:1702976028:get_sources
[0Ksection_start:1702976028:step_script
[0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m
Using git from spack modules
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m
[32;1m$ module purge[0;m
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m
[32;1m$ module load archive/2020-12 python/3.7.4[0;m
[32;1m$ module unload archive/2020-12[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.7.4
[32;1m$ module load archive/2021-12 python/3.8.3[0;m
[32;1m$ module unload archive/2021-12[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.8.3
[32;1m$ module load archive/2023-02 python/3.9.7[0;m
[32;1m$ module unload archive/2023-02[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.9.7
[32;1m$ module load unstable python[0;m
[32;1m$ module unload unstable[0;m
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m
[32;1m$ echo "Loaded $(python -V)"[0;m
Loaded Python 3.10.8
[32;1m$ load-modules() { # collapsed multi-line command[0;m
[32;1m$ load-modules $SYSTEM_MODULES[0;m
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
[32;1m$ load-modules $EXTRA_MODULES[0;m
Loaded module gcc from unstable
Loaded module hpe-mpi from unstable
Autoloading python/3.10.8
Autoloading hpe-mpi/2.25.hmpt
Loaded module py-mpi4py from unstable
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
Loaded module petsc from unstable
Autoloading python/3.10.8
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
Loaded module py-petsc4py from unstable
[32;1m$ module list -t[0;m
Currently Loaded Modulefiles:
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/python/3.10.8
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/git/2.38.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/cmake/3.24.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/graphviz/2.49.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/compilers/linux-rhel7-haswell/gcc/12.2.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-mpi4py/3.1.4
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/petsc/3.18.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-petsc4py/3.18.1
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m
[32;1m$ print_var XDG_CONFIG_HOME[0;m
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/local_config[0m
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
  insteadOf = https://bbpgitlab.epfl.ch/
  insteadOf = ssh://git@bbpgitlab.epfl.ch/
  insteadOf = git@bbpgitlab.epfl.ch:
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m
[0Ksection_start:1702976030:section_venv[collapsed=true]
[0KSetting up the virtual env
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m
[32;1m$ CI_VENV="$(pwd)/venv"[0;m
[32;1m$ rm -rf "$CI_VENV"[0;m
[32;1m$ python -mvenv "$CI_VENV"[0;m
[32;1m$ source "$CI_VENV/bin/activate"[0;m
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (22.2.2)
Collecting pip
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/505/2d7889c1f9d05/pip-23.3.2-py3-none-any.whl (2.1 MB)
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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/1e8/fdff6797d3865/setuptools-69.0.2-py3-none-any.whl (819 kB)
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Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/177/f9c9b0d45c478/wheel-0.42.0-py3-none-any.whl (65 kB)
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Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 63.0.0
    Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/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-23.3.2 setuptools-69.0.2 wheel-0.42.0
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Collecting tox
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2ad/b83d68f271168/tox-4.11.4-py3-none-any.whl (153 kB)
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Collecting cachetools>=5.3.1 (from tox)
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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)
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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/57d/bda9b35157b05/filelock-3.13.1-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)
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Collecting platformdirs>=3.10 (from tox)
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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/423/8949c5ffe6876/virtualenv-20.25.0-py3-none-any.whl (3.8 MB)
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Collecting distlib<1,>=0.3.7 (from virtualenv>=20.24.3->tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB)
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Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox
Successfully installed cachetools-5.3.2 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-23.2 platformdirs-4.1.0 pluggy-1.3.0 pyproject-api-1.6.1 tomli-2.0.1 tox-4.11.4 virtualenv-20.25.0
[32;1m$ section_end section_venv[0;m
[0Ksection_end:1702976046:section_venv
[0K
[32;1m$ print_var PRE_BUILD_COMMAND[0;m
[36mPRE_BUILD_COMMAND=[0m
[32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m
[32;1m$ section_start section_tox "Running Tox"[0;m
[0Ksection_start:1702976046:section_tox
[0KRunning Tox
[32;1m$ python -mtox $TOX_OPTIONS[0;m
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/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/J1089695/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/J1089695/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==23.3.1,setuptools==69.0.2,setuptools-scm==8.0.4,tomli==2.0.1,typing_extensions==4.9.0,wheel==0.42.0
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/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/J1089695/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 morphio networkx numpy 'pandas<2.0.0' psutil pytest pytest-mpi pyyaml scipy seaborn tables tqdm trimesh vascpy
py310: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/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/J1089695/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz#sha256=6c0ee13d2362e3b66656824fc44e960be06486fdf444537aa6a87e85ed174b00,blosc2==2.3.2,cached-property==1.5.2,click==8.1.7,contourpy==1.2.0,coverage==7.3.3,cycler==0.12.1,Cython==3.0.6,exceptiongroup==1.2.0,fonttools==4.47.0,h5py==3.10.0,iniconfig==2.0.0,kiwisolver==1.4.5,libsonata==0.1.24,matplotlib==3.8.2,MorphIO==3.3.7,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==3.2.1,numexpr==2.8.8,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/1912700/spack-stage/spack-stage-py-petsc4py-3.18.1-k6k4ybhubjpjanttcmmql5ditq2bxn32/spack-src,Pillow==10.1.0,pip==23.3.1,pluggy==1.3.0,psutil==5.9.7,py-cpuinfo==9.0.0,pyparsing==3.1.1,pytest==7.4.3,pytest-mpi==0.6,python-dateutil==2.8.2,pytz==2023.3.post1,PyYAML==6.0.1,scipy==1.11.4,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==3.9.2,tomli==2.0.1,tqdm==4.66.1,trimesh==4.0.6,vascpy==0.1.1,wheel==0.42.0
py310: commands[0]> coverage run --branch --source=astrovascpy -m pytest --basetemp=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/.tox/py310/tmp --verbose --junit-xml=reports/pytest-py310.xml
============================= test session starts ==============================
platform linux -- Python 3.10.8, pytest-7.4.3, pluggy-1.3.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/.tox/py310/bin/python
cachedir: .tox/py310/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy
configfile: pyproject.toml
testpaths: tests
plugins: mpi-0.6
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 SKIPPED (need --with-mpi o...) [ 50%]
tests/test_mpi.py::test_scipy2petsc_conversion SKIPPED (need --with-...) [ 51%]
tests/test_mpi.py::test_coomatrix2PETScMat SKIPPED (need --with-mpi ...) [ 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%]

- generated xml file: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/reports/pytest-py310.xml -
======================== 53 passed, 3 skipped in 9.89s =========================
py310: commands[1]> mpirun -n 4 coverage run --branch --parallel-mode --source=astrovascpy -m pytest --with-mpi /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/tests/test_mpi.py
============================= test session starts ==============================
platform linux -- Python 3.10.8, pytest-7.4.3, pluggy-1.3.0
cachedir: .tox/py310/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy
configfile: pyproject.toml
plugins: mpi-0.6
collected 3 items

tests/test_mpi.py ============================= test session starts ==============================
platform linux -- Python 3.10.8, pytest-7.4.3, pluggy-1.3.0
cachedir: .tox/py310/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy
configfile: pyproject.toml
plugins: mpi-0.6
collected 3 items

tests/test_mpi.py ============================= test session starts ==============================
platform linux -- Python 3.10.8, pytest-7.4.3, pluggy-1.3.0
cachedir: .tox/py310/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy
configfile: pyproject.toml
plugins: mpi-0.6
collected 3 items

tests/test_mpi.py ============================= test session starts ==============================
platform linux -- Python 3.10.8, pytest-7.4.3, pluggy-1.3.0
cachedir: .tox/py310/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy
configfile: pyproject.toml
plugins: mpi-0.6
collected 3 items

tests/test_mpi.py ............                                                    [100%]                                                    [100%]                                                    [100%]                                                    [100%]
=============================== MPI Information ================================
rank: 1
size: 4
MPI version: 3.1
MPI library version: HPE HMPT 2.25  10/22/21 03:18:39
MPI vendor: unknown 0.0.0
mpi4py rc:
mpi4py config:
 mpicc: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicc
 mpicxx: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicxx
 mpif90: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif90
 mpif77: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif77

============================== 3 passed in 0.96s ===============================

=============================== MPI Information ================================
rank: 2
size: 4
MPI version: 3.1
MPI library version: HPE HMPT 2.25  10/22/21 03:18:39
MPI vendor: unknown 0.0.0
mpi4py rc:
mpi4py config:
 mpicc: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicc
 mpicxx: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicxx
 mpif90: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif90
 mpif77: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif77

============================== 3 passed in 0.96s ===============================

=============================== MPI Information ================================
rank: 0
size: 4
MPI version: 3.1
MPI library version: HPE HMPT 2.25  10/22/21 03:18:39
MPI vendor: unknown 0.0.0
mpi4py rc:
mpi4py config:
 mpicc: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicc
 mpicxx: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicxx
 mpif90: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif90
 mpif77: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif77

============================== 3 passed in 0.96s ===============================

=============================== MPI Information ================================
rank: 3
size: 4
MPI version: 3.1
MPI library version: HPE HMPT 2.25  10/22/21 03:18:39
MPI vendor: unknown 0.0.0
mpi4py rc:
mpi4py config:
 mpicc: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicc
 mpicxx: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicxx
 mpif90: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif90
 mpif77: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif77

============================== 3 passed in 0.96s ===============================
py310: commands[2]> coverage combine --append
Combined data file .coverage-py310.r1i7n22.86070.XuSvcLdx
Combined data file .coverage-py310.r1i7n22.86067.XArcBlqx
Skipping duplicate data .coverage-py310.r1i7n22.86068.Xoozhjex
Skipping duplicate data .coverage-py310.r1i7n22.86069.XuInyjEx
py310: commands[3]> coverage report --fail-under=50
Name                                     Stmts   Miss Branch BrPart  Cover
--------------------------------------------------------------------------
astrovascpy/PetscBinaryIO.py               310    167     96     22    44%
astrovascpy/__init__.py                      0      0      0      0   100%
astrovascpy/bloodflow.py                   332     58    126     35    75%
astrovascpy/exceptions.py                    1      0      0      0   100%
astrovascpy/io.py                           50      7     16      7    79%
astrovascpy/ou.py                           14      1      2      1    88%
astrovascpy/plotting.py                     17     17      6      0     0%
astrovascpy/report_reader.py                90      0     18      0   100%
astrovascpy/report_writer.py                27      0      4      0   100%
astrovascpy/scipy_petsc_conversions.py     172     28     44      2    82%
astrovascpy/typing.py                       10      0      0      0   100%
astrovascpy/utils.py                       321    125     80      7    60%
astrovascpy/version.py                       2      2      0      0     0%
astrovascpy/vtk_io.py                        5      5      0      0     0%
--------------------------------------------------------------------------
TOTAL                                     1351    410    392     74    66%
py310: commands[4]> coverage html --directory=reports
Wrote HTML report to reports/index.html
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
  py310: OK (81.25=setup[66.55]+cmd[10.73,2.54,0.23,0.42,0.79] seconds)
  congratulations :) (81.57 seconds)
[32;1m$ section_end section_tox[0;m
[0Ksection_end:1702976128:section_tox
[0K
section_end:1702976128:step_script
[0Ksection_start:1702976128:cleanup_file_variables
[0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m
Using git from spack modules
section_end:1702976129:cleanup_file_variables
[0K[32;1mJob succeeded[0;m