bbpbuildbot/GitLab logs for bluebrain-astrovascpy#5 Secret

## check-packaging.txt
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
[0K  on BB5 map runner pnPo3yJy[0;m
section_start:1698010814:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1698010814:resolve_secrets
[0Ksection_start:1698010814: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-executor3455236079, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root molsys, project name AstroVascPy
Pipeline ID 163955, build ref , job ID 980658
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J980658, 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_J980658_PROD_P2342_CP0_C0
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 1856061
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J980658_PROD_P2342_CP0_C0 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J980658 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J980658 --ntasks=1 --jobid=1856061 --cpus-per-task=6 --mem=30750M
section_end:1698010816:prepare_executor
[0Ksection_start:1698010816:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i4n17 via bbpv1.epfl.ch...
section_end:1698010819:prepare_script
[0Ksection_start:1698010819: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/J980658/molsys/AstroVascPy/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 3afb4f3a as nicola/petsc_improvement...[0;m
Skipping object checkout, Git LFS is not installed.

[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m
section_end:1698010821:get_sources
[0Ksection_start:1698010821: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/2023-10/externals/linux-rhel7-skylake/python/3.10.8
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/git/2.38.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/cmake/3.24.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/graphviz/2.49.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/compilers/linux-rhel7-haswell/gcc/12.2.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/py-mpi4py/3.1.4
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/petsc/3.18.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/py-petsc4py/3.18.1
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m
[32;1m$ print_var XDG_CONFIG_HOME[0;m
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980658/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:1698010823: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/55e/b67bb6171d374/pip-23.3.1-py3-none-any.whl (2.1 MB)
     ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 73.0 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages (63.0.0)
Collecting setuptools
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b45/4a35605876da6/setuptools-68.2.2-py3-none-any.whl (807 kB)
     âââââââââââââââââââââââââââââââââââââ 807.9/807.9 kB 257.0 MB/s eta 0:00:00
Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/759/09db2664838d0/wheel-0.41.2-py3-none-any.whl (64 kB)
     âââââââââââââââââââââââââââââââââââââââ 64.8/64.8 kB 208.7 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/J980658/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-23.3.1 setuptools-68.2.2 wheel-0.41.2
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Collecting tox
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/599/af5e5bb0cad01/tox-4.11.3-py3-none-any.whl (153 kB)
     ââââââââââââââââââââââââââââââââââââââ 153.8/153.8 kB 19.8 MB/s eta 0:00:00
Collecting cachetools>=5.3.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/95e/f631eeaea14ba/cachetools-5.3.1-py3-none-any.whl (9.3 kB)
Collecting chardet>=5.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB)
     ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 63.7 MB/s eta 0:00:00
Collecting colorama>=0.4.6 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting filelock>=3.12.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/08c/21d87ded6e2b9/filelock-3.12.4-py3-none-any.whl (11 kB)
Collecting packaging>=23.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/8c4/91190033a9af7/packaging-23.2-py3-none-any.whl (53 kB)
     âââââââââââââââââââââââââââââââââââââââ 53.0/53.0 kB 179.5 MB/s eta 0:00:00
Collecting platformdirs>=3.10 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e9d/171d00af68be5/platformdirs-3.11.0-py3-none-any.whl (17 kB)
Collecting pluggy>=1.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/d89/c696a773f8bd3/pluggy-1.3.0-py3-none-any.whl (18 kB)
Collecting pyproject-api>=1.6.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB)
Collecting tomli>=2.0.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/939/de3e7a6161af0/tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting virtualenv>=20.24.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b80/039f280f4919c/virtualenv-20.24.5-py3-none-any.whl (3.7 MB)
     ââââââââââââââââââââââââââââââââââââââââ 3.7/3.7 MB 163.3 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/2e2/4928bc811348f/distlib-0.3.7-py2.py3-none-any.whl (468 kB)
     âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 249.7 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-5.3.1 chardet-5.2.0 colorama-0.4.6 distlib-0.3.7 filelock-3.12.4 packaging-23.2 platformdirs-3.11.0 pluggy-1.3.0 pyproject-api-1.6.1 tomli-2.0.1 tox-4.11.3 virtualenv-20.24.5
[32;1m$ section_end section_venv[0;m
[0Ksection_end:1698010837: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:1698010837:section_tox
[0KRunning Tox
[32;1m$ python -mtox $TOX_OPTIONS[0;m
check-packaging: install_deps> python -I -m pip install build twine
check-packaging: freeze> python -m pip freeze --all
check-packaging: build==1.0.3,certifi==2023.7.22,cffi==1.16.0,charset-normalizer==3.3.1,cryptography==41.0.4,docutils==0.20.1,idna==3.4,importlib-metadata==6.8.0,jaraco.classes==3.3.0,jeepney==0.8.0,keyring==24.2.0,markdown-it-py==3.0.0,mdurl==0.1.2,more-itertools==10.1.0,mpi4py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mpi4py-3.1.4-glx4cfnu5cionch2hbeyzns5ol3vexp7/spack-src,nh3==0.2.14,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging==23.2,petsc4py @ file:///nvme/bbpcihpcdeploy/1644090/spack-stage/spack-stage-py-petsc4py-3.18.1-7rysecnje3dndrjv36w723cz6tfioxhe/spack-src,pip==23.2.1,pkginfo==1.9.6,pycparser==2.21,Pygments==2.16.1,pyproject_hooks==1.0.0,readme-renderer==42.0,requests==2.31.0,requests-toolbelt==1.0.0,rfc3986==2.0.0,rich==13.6.0,SecretStorage==3.3.3,setuptools @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-setuptools-63.0.0-c6hdpvjjddmcm3xf5begyfpkjkzj2oke/spack-src/setuptools-63.0.0-py3-none-any.whl,tomli==2.0.1,twine==4.0.2,urllib3==2.0.7,wheel==0.41.2,zipp==3.17.0
check-packaging: commands[0]> python -m build -o /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980658/molsys/AstroVascPy/.tox/check-packaging/tmp/dist
* Creating venv isolated environment...
* Installing packages in isolated environment... (setuptools>=42, setuptools_scm[toml]>=3.4, wheel)
* Getting build dependencies for sdist...
running egg_info
creating AstroVascPy.egg-info
writing AstroVascPy.egg-info/PKG-INFO
writing dependency_links to AstroVascPy.egg-info/dependency_links.txt
writing entry points to AstroVascPy.egg-info/entry_points.txt
writing requirements to AstroVascPy.egg-info/requires.txt
writing top-level names to AstroVascPy.egg-info/top_level.txt
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.py[co]' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
adding license file 'LICENSE.txt'
adding license file 'AUTHORS.txt'
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt'
* Building sdist...
running sdist
running egg_info
writing AstroVascPy.egg-info/PKG-INFO
writing dependency_links to AstroVascPy.egg-info/dependency_links.txt
writing entry points to AstroVascPy.egg-info/entry_points.txt
writing requirements to AstroVascPy.egg-info/requires.txt
writing top-level names to AstroVascPy.egg-info/top_level.txt
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.py[co]' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
adding license file 'LICENSE.txt'
adding license file 'AUTHORS.txt'
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt'
running check
creating AstroVascPy-0.0.1
creating AstroVascPy-0.0.1/AstroVascPy.egg-info
creating AstroVascPy-0.0.1/astrovascpy
creating AstroVascPy-0.0.1/docs
creating AstroVascPy-0.0.1/docs/source
creating AstroVascPy-0.0.1/docs/source/logo
creating AstroVascPy-0.0.1/examples
creating AstroVascPy-0.0.1/examples/data
creating AstroVascPy-0.0.1/examples/data/graphs_folder
creating AstroVascPy-0.0.1/tests
creating AstroVascPy-0.0.1/tests/data
creating AstroVascPy-0.0.1/tests/data/input_flow
creating AstroVascPy-0.0.1/tests/data/reporting
copying files to AstroVascPy-0.0.1...
copying .auto-changelog -> AstroVascPy-0.0.1
copying .auto-changelog-template.hbs -> AstroVascPy-0.0.1
copying .codespellignorelines -> AstroVascPy-0.0.1
copying .codespellrc -> AstroVascPy-0.0.1
copying .copier-answers.yml -> AstroVascPy-0.0.1
copying .flake8 -> AstroVascPy-0.0.1
copying .gitattributes -> AstroVascPy-0.0.1
copying .gitignore -> AstroVascPy-0.0.1
copying .gitlab-ci.yml -> AstroVascPy-0.0.1
copying .gitreview -> AstroVascPy-0.0.1
copying .pre-commit-config.yaml -> AstroVascPy-0.0.1
copying .pylintrc -> AstroVascPy-0.0.1
copying AUTHORS.txt -> AstroVascPy-0.0.1
copying CHANGELOG.md -> AstroVascPy-0.0.1
copying CONTRIBUTING.md -> AstroVascPy-0.0.1
copying LICENSE.txt -> AstroVascPy-0.0.1
copying MANIFEST.in -> AstroVascPy-0.0.1
copying README.md -> AstroVascPy-0.0.1
copying commitlint.config.js -> AstroVascPy-0.0.1
copying package.json -> AstroVascPy-0.0.1
copying pyproject.toml -> AstroVascPy-0.0.1
copying setup.py -> AstroVascPy-0.0.1
copying setup.sh -> AstroVascPy-0.0.1
copying tox.ini -> AstroVascPy-0.0.1
copying AstroVascPy.egg-info/PKG-INFO -> AstroVascPy-0.0.1/AstroVascPy.egg-info
copying AstroVascPy.egg-info/SOURCES.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info
copying AstroVascPy.egg-info/dependency_links.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info
copying AstroVascPy.egg-info/entry_points.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info
copying AstroVascPy.egg-info/requires.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info
copying AstroVascPy.egg-info/top_level.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info
copying astrovascpy/PetscBinaryIO.py -> AstroVascPy-0.0.1/astrovascpy
copying astrovascpy/__init__.py -> AstroVascPy-0.0.1/astrovascpy
copying astrovascpy/bloodflow.py -> AstroVascPy-0.0.1/astrovascpy
copying astrovascpy/exceptions.py -> AstroVascPy-0.0.1/astrovascpy
copying astrovascpy/io.py -> AstroVascPy-0.0.1/astrovascpy
copying astrovascpy/ou.py -> AstroVascPy-0.0.1/astrovascpy
copying astrovascpy/plotting.py -> AstroVascPy-0.0.1/astrovascpy
copying astrovascpy/report_reader.py -> AstroVascPy-0.0.1/astrovascpy
copying astrovascpy/report_writer.py -> AstroVascPy-0.0.1/astrovascpy
copying astrovascpy/scipy_petsc_conversions.py -> AstroVascPy-0.0.1/astrovascpy
copying astrovascpy/utils.py -> AstroVascPy-0.0.1/astrovascpy
copying astrovascpy/version.py -> AstroVascPy-0.0.1/astrovascpy
copying astrovascpy/vtk_io.py -> AstroVascPy-0.0.1/astrovascpy
copying docs/Makefile -> AstroVascPy-0.0.1/docs
copying docs/source/api_ref.rst -> AstroVascPy-0.0.1/docs/source
copying docs/source/changelog.rst -> AstroVascPy-0.0.1/docs/source
copying docs/source/conf.py -> AstroVascPy-0.0.1/docs/source
copying docs/source/index.rst -> AstroVascPy-0.0.1/docs/source
copying docs/source/logo/BPP-AstroVascPy-Github.jpg -> AstroVascPy-0.0.1/docs/source/logo
copying examples/compute_static_flow_pressure.py -> AstroVascPy-0.0.1/examples
copying examples/job_script.sbatch -> AstroVascPy-0.0.1/examples
copying examples/run_ou.sbatch -> AstroVascPy-0.0.1/examples
copying examples/simulate_OU_process.py -> AstroVascPy-0.0.1/examples
copying examples/data/params.yaml -> AstroVascPy-0.0.1/examples/data
copying examples/data/graphs_folder/edge_dataset.csv -> AstroVascPy-0.0.1/examples/data/graphs_folder
copying examples/data/graphs_folder/node_dataset.csv -> AstroVascPy-0.0.1/examples/data/graphs_folder
copying examples/data/graphs_folder/toy_graph.bin -> AstroVascPy-0.0.1/examples/data/graphs_folder
copying examples/data/graphs_folder/toy_graph.h5 -> AstroVascPy-0.0.1/examples/data/graphs_folder
copying tests/__init__.py -> AstroVascPy-0.0.1/tests
copying tests/test_bloodflow.py -> AstroVascPy-0.0.1/tests
copying tests/test_graphs.py -> AstroVascPy-0.0.1/tests
copying tests/test_io.py -> AstroVascPy-0.0.1/tests
copying tests/test_mpi.py -> AstroVascPy-0.0.1/tests
copying tests/test_ou.py -> AstroVascPy-0.0.1/tests
copying tests/test_report_reader.py -> AstroVascPy-0.0.1/tests
copying tests/test_report_writer.py -> AstroVascPy-0.0.1/tests
copying tests/test_utils.py -> AstroVascPy-0.0.1/tests
copying tests/data/dataset.h5 -> AstroVascPy-0.0.1/tests/data
copying tests/data/edge_dataset.csv -> AstroVascPy-0.0.1/tests/data
copying tests/data/node_dataset.csv -> AstroVascPy-0.0.1/tests/data
copying tests/data/toy_graph.bin -> AstroVascPy-0.0.1/tests/data
copying tests/data/toy_graph.h5 -> AstroVascPy-0.0.1/tests/data
copying tests/data/input_flow/sine.csv -> AstroVascPy-0.0.1/tests/data/input_flow
copying tests/data/reporting/compartment_report.h5 -> AstroVascPy-0.0.1/tests/data/reporting
copying tests/data/reporting/create_reports.py -> AstroVascPy-0.0.1/tests/data/reporting
copying tests/data/reporting/diff_unit_compartment_report.h5 -> AstroVascPy-0.0.1/tests/data/reporting
Writing AstroVascPy-0.0.1/setup.cfg
Creating tar archive
removing 'AstroVascPy-0.0.1' (and everything under it)
* Building wheel from sdist
* Creating venv isolated environment...
* Installing packages in isolated environment... (setuptools>=42, setuptools_scm[toml]>=3.4, wheel)
* Getting build dependencies for wheel...
running egg_info
writing AstroVascPy.egg-info/PKG-INFO
writing dependency_links to AstroVascPy.egg-info/dependency_links.txt
writing entry points to AstroVascPy.egg-info/entry_points.txt
writing requirements to AstroVascPy.egg-info/requires.txt
writing top-level names to AstroVascPy.egg-info/top_level.txt
ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
reading manifest file 'AstroVascPy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.py[co]' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
adding license file 'LICENSE.txt'
adding license file 'AUTHORS.txt'
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt'
* Installing packages in isolated environment... (wheel)
* Building wheel...
running bdist_wheel
running build
running build_py
creating build
creating build/lib
creating build/lib/astrovascpy
copying astrovascpy/__init__.py -> build/lib/astrovascpy
copying astrovascpy/vtk_io.py -> build/lib/astrovascpy
copying astrovascpy/PetscBinaryIO.py -> build/lib/astrovascpy
copying astrovascpy/report_writer.py -> build/lib/astrovascpy
copying astrovascpy/scipy_petsc_conversions.py -> build/lib/astrovascpy
copying astrovascpy/plotting.py -> build/lib/astrovascpy
copying astrovascpy/io.py -> build/lib/astrovascpy
copying astrovascpy/utils.py -> build/lib/astrovascpy
copying astrovascpy/report_reader.py -> build/lib/astrovascpy
copying astrovascpy/bloodflow.py -> build/lib/astrovascpy
copying astrovascpy/version.py -> build/lib/astrovascpy
copying astrovascpy/exceptions.py -> build/lib/astrovascpy
copying astrovascpy/ou.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/__init__.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/PetscBinaryIO.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/report_writer.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/scipy_petsc_conversions.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/plotting.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/io.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/report_reader.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/bloodflow.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/version.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/exceptions.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/ou.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/J980658/molsys/AstroVascPy/.tox/check-packaging/tmp/dist/tmp9pixvuh8/AstroVascPy-0.0.1-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'astrovascpy/PetscBinaryIO.py'
adding 'astrovascpy/__init__.py'
adding 'astrovascpy/bloodflow.py'
adding 'astrovascpy/exceptions.py'
adding 'astrovascpy/io.py'
adding 'astrovascpy/ou.py'
adding 'astrovascpy/plotting.py'
adding 'astrovascpy/report_reader.py'
adding 'astrovascpy/report_writer.py'
adding 'astrovascpy/scipy_petsc_conversions.py'
adding 'astrovascpy/utils.py'
adding 'astrovascpy/version.py'
adding 'astrovascpy/vtk_io.py'
adding 'AstroVascPy-0.0.1.dist-info/AUTHORS.txt'
adding 'AstroVascPy-0.0.1.dist-info/LICENSE.txt'
adding 'AstroVascPy-0.0.1.dist-info/METADATA'
adding 'AstroVascPy-0.0.1.dist-info/WHEEL'
adding 'AstroVascPy-0.0.1.dist-info/entry_points.txt'
adding 'AstroVascPy-0.0.1.dist-info/top_level.txt'
adding 'AstroVascPy-0.0.1.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built AstroVascPy-0.0.1.tar.gz and AstroVascPy-0.0.1-py3-none-any.whl
check-packaging: commands[1]> twine check '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980658/molsys/AstroVascPy/.tox/check-packaging/tmp/dist/*'
Checking
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980658/molsys/AstroVascPy/.to
x/check-packaging/tmp/dist/AstroVascPy-0.0.1-py3-none-any.whl: [32mPASSED[0m
Checking
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980658/molsys/AstroVascPy/.to
x/check-packaging/tmp/dist/AstroVascPy-0.0.1.tar.gz: [32mPASSED[0m
  check-packaging: OK (32.01=setup[15.95]+cmd[15.67,0.40] seconds)
  congratulations :) (32.54 seconds)
[32;1m$ section_end section_tox[0;m
[0Ksection_end:1698010870:section_tox
[0K
section_end:1698010870:step_script
[0Ksection_start:1698010870: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:1698010871: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:1698010815:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1698010815:resolve_secrets
[0Ksection_start:1698010815: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-executor3466989561, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root molsys, project name AstroVascPy
Pipeline ID 163955, build ref , job ID 980660
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J980660, 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_J980660_PROD_P2342_CP2_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 1856063
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_J980660_PROD_P2342_CP2_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J980660 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J980660 --ntasks=1 --jobid=1856063 --cpus-per-task=6 --mem=30750M
section_end:1698010819:prepare_executor
[0Ksection_start:1698010819:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i4n17 via bbpv1.epfl.ch...
section_end:1698010825:prepare_script
[0Ksection_start:1698010825: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/J980660/molsys/AstroVascPy/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 3afb4f3a as nicola/petsc_improvement...[0;m
Skipping object checkout, Git LFS is not installed.

[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m
section_end:1698010827:get_sources
[0Ksection_start:1698010827: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/2023-10/externals/linux-rhel7-skylake/python/3.10.8
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/git/2.38.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/cmake/3.24.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/graphviz/2.49.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/compilers/linux-rhel7-haswell/gcc/12.2.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/py-mpi4py/3.1.4
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/petsc/3.18.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/py-petsc4py/3.18.1
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m
[32;1m$ print_var XDG_CONFIG_HOME[0;m
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/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:1698010829: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/55e/b67bb6171d374/pip-23.3.1-py3-none-any.whl (2.1 MB)
     ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 75.6 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages (63.0.0)
Collecting setuptools
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b45/4a35605876da6/setuptools-68.2.2-py3-none-any.whl (807 kB)
     âââââââââââââââââââââââââââââââââââââ 807.9/807.9 kB 264.8 MB/s eta 0:00:00
Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/759/09db2664838d0/wheel-0.41.2-py3-none-any.whl (64 kB)
     âââââââââââââââââââââââââââââââââââââââ 64.8/64.8 kB 221.5 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 63.0.0
    Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/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-23.3.1 setuptools-68.2.2 wheel-0.41.2
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
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Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox
Successfully installed cachetools-5.3.1 chardet-5.2.0 colorama-0.4.6 distlib-0.3.7 filelock-3.12.4 packaging-23.2 platformdirs-3.11.0 pluggy-1.3.0 pyproject-api-1.6.1 tomli-2.0.1 tox-4.11.3 virtualenv-20.24.5
[32;1m$ section_end section_venv[0;m
[0Ksection_end:1698010844: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:1698010844: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/J980660/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/J980660/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/J980660/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: install_requires_for_build_wheel> python -I -m pip install wheel
.pkg: freeze> python -m pip freeze --all
.pkg: packaging==23.2,pip==23.2.1,setuptools==68.2.0,setuptools-scm==8.0.4,tomli==2.0.1,typing_extensions==4.8.0,wheel==0.41.2
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/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/J980660/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 pytest pyyaml scipy seaborn sphinx sphinx-bluebrain-theme sphinx-click tables tqdm trimesh vascpy vtk
docs: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/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/J980660/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz#sha256=fcc0e2ef88bada6afddc6057a9ebbe511a79ae8617695c587106d71fba7bcc2c,Babel==2.13.0,blosc2==2.2.9,cached-property==1.5.2,certifi==2023.7.22,charset-normalizer==3.3.1,click==8.1.7,contourpy==1.1.1,coverage==7.3.2,cycler==0.12.1,Cython==3.0.4,docutils==0.20.1,exceptiongroup==1.1.3,fonttools==4.43.1,h5py==3.10.0,idna==3.4,imagesize==1.4.1,iniconfig==2.0.0,Jinja2==3.0.3,kiwisolver==1.4.5,libsonata==0.1.24,m2r2==0.3.3.post2,MarkupSafe==2.1.3,matplotlib==3.8.0,mistune==0.8.4,MorphIO==3.3.6,mpi4py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mpi4py-3.1.4-glx4cfnu5cionch2hbeyzns5ol3vexp7/spack-src,msgpack==1.0.7,ndindex==1.7,networkx==3.2,numexpr==2.8.7,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging==23.2,pandas==1.5.3,petsc4py @ file:///nvme/bbpcihpcdeploy/1644090/spack-stage/spack-stage-py-petsc4py-3.18.1-7rysecnje3dndrjv36w723cz6tfioxhe/spack-src,Pillow==10.1.0,pip==23.2.1,pluggy==1.3.0,psutil==5.9.6,py-cpuinfo==9.0.0,Pygments==2.16.1,pyparsing==3.1.1,pytest==7.4.2,python-dateutil==2.8.2,pytz==2023.3.post1,PyYAML==6.0.1,requests==2.31.0,scipy==1.11.3,seaborn==0.13.0,setuptools @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-setuptools-63.0.0-c6hdpvjjddmcm3xf5begyfpkjkzj2oke/spack-src/setuptools-63.0.0-py3-none-any.whl,six==1.16.0,snowballstemmer==2.2.0,Sphinx==7.2.6,sphinx-bluebrain-theme==0.4.2,sphinx-click==5.0.1,sphinxcontrib-applehelp==1.0.7,sphinxcontrib-devhelp==1.0.5,sphinxcontrib-htmlhelp==2.0.4,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==1.0.6,sphinxcontrib-serializinghtml==1.1.9,tables==3.9.1,tomli==2.0.1,tqdm==4.66.1,trimesh==4.0.0,urllib3==2.0.7,vascpy==0.1.1,vtk==9.2.6,wheel==0.41.2
docs: commands[0] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs> make html
# Generate the documentation
Running Sphinx v7.2.6
making output directory... done
[autosummary] generating autosummary for: api_ref.rst, changelog.rst, index.rst
[autosummary] generating autosummary for: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs/source/generated/astrovascpy.PetscBinaryIO.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs/source/generated/astrovascpy.bloodflow.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs/source/generated/astrovascpy.exceptions.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs/source/generated/astrovascpy.io.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs/source/generated/astrovascpy.ou.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs/source/generated/astrovascpy.plotting.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs/source/generated/astrovascpy.report_reader.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs/source/generated/astrovascpy.report_writer.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs/source/generated/astrovascpy.scipy_petsc_conversions.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs/source/generated/astrovascpy.utils.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs/source/generated/astrovascpy.vtk_io.rst
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 3 source files that are out of date
updating environment: [new config] 14 added, 0 changed, 0 removed
[2Kreading sources... [  7%] api_ref
[2Kreading sources... [ 14%] changelog
[2Kreading sources... [ 21%] generated/astrovascpy.PetscBinaryIO
[2Kreading sources... [ 29%] generated/astrovascpy.bloodflow
[2Kreading sources... [ 36%] generated/astrovascpy.exceptions
[2Kreading sources... [ 43%] generated/astrovascpy.io
[2Kreading sources... [ 50%] generated/astrovascpy.ou
[2Kreading sources... [ 57%] generated/astrovascpy.plotting
[2Kreading sources... [ 64%] generated/astrovascpy.report_reader
[2Kreading sources... [ 71%] generated/astrovascpy.report_writer
[2Kreading sources... [ 79%] generated/astrovascpy.scipy_petsc_conversions
[2Kreading sources... [ 86%] generated/astrovascpy.utils
[2Kreading sources... [ 93%] generated/astrovascpy.vtk_io
[2Kreading sources... [100%] index
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/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/J980660/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/report_reader.py:docstring of astrovascpy.report_reader:12: WARNING: Block quote ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/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/J980660/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/J980660/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/scipy_petsc_conversions.py:docstring of astrovascpy.scipy_petsc_conversions:5: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/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/J980660/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/J980660/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/J980660/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/vtk_io.py:docstring of astrovascpy.vtk_io:6: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/vtk_io.py:docstring of astrovascpy.vtk_io:7: WARNING: Block quote ends without a blank line; unexpected unindent.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs/source/index.rst:8: WARNING: toctree contains reference to nonexisting document 'installation'
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/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/J980660/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/J980660/molsys/AstroVascPy/docs/source/api_ref.rst: WARNING: document isn't included in any toctree
checking consistency... done
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/docs/source/changelog.rst: WARNING: document isn't included in any toctree
preparing documents... done
copying assets... copying static files... done
copying extra files... done
done
[2Kwriting output... [  7%] api_ref
[2Kwriting output... [ 14%] changelog
[2Kwriting output... [ 21%] generated/astrovascpy.PetscBinaryIO
[2Kwriting output... [ 29%] generated/astrovascpy.bloodflow
[2Kwriting output... [ 36%] generated/astrovascpy.exceptions
[2Kwriting output... [ 43%] generated/astrovascpy.io
[2Kwriting output... [ 50%] generated/astrovascpy.ou
[2Kwriting output... [ 57%] generated/astrovascpy.plotting
[2Kwriting output... [ 64%] generated/astrovascpy.report_reader
[2Kwriting output... [ 71%] generated/astrovascpy.report_writer
[2Kwriting output... [ 79%] generated/astrovascpy.scipy_petsc_conversions
[2Kwriting output... [ 86%] generated/astrovascpy.utils
[2Kwriting output... [ 93%] generated/astrovascpy.vtk_io
[2Kwriting output... [100%] index
generating indices... genindex py-modindex done
writing additional pages... search done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 43 warnings.

The HTML pages are in build/html.
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980660/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
  docs: OK (92.08=setup[83.50]+cmd[8.58] seconds)
  congratulations :) (92.33 seconds)
[32;1m$ section_end section_tox[0;m
[0Ksection_end:1698010936:section_tox
[0K
section_end:1698010936:step_script
[0Ksection_start:1698010936: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=121016 revision[0;m=58ba2b95 version[0;m=14.2.0
[0;33mWARNING: ./doc/build/: no matching files          [0;m
./docs/build/: found 167 matching files and directories[0;m
Uploading artifacts as "archive" to coordinator... ok[0;m  id[0;m=980660 responseStatus[0;m=201 Created token[0;m=64_RBqsx
section_end:1698010937:upload_artifacts_on_success
[0Ksection_start:1698010937: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:1698010938:cleanup_file_variables
[0K[32;1mJob succeeded[0;m

## GitLab logs for bluebrain-astrovascpy#5
!

## lint.txt
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
[0K  on BB5 map runner pnPo3yJy[0;m
section_start:1698010815:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1698010815:resolve_secrets
[0Ksection_start:1698010815: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-executor1864244141, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root molsys, project name AstroVascPy
Pipeline ID 163955, build ref , job ID 980659
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J980659, 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_J980659_PROD_P2342_CP1_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 1856062
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_J980659_PROD_P2342_CP1_C1 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J980659 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J980659 --ntasks=1 --jobid=1856062 --cpus-per-task=6 --mem=30750M
section_end:1698010818:prepare_executor
[0Ksection_start:1698010818:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i4n17 via bbpv1.epfl.ch...
section_end:1698010826:prepare_script
[0Ksection_start:1698010826: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/J980659/molsys/AstroVascPy/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 3afb4f3a as nicola/petsc_improvement...[0;m
Skipping object checkout, Git LFS is not installed.

[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m
section_end:1698010828:get_sources
[0Ksection_start:1698010828: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/2023-10/externals/linux-rhel7-skylake/python/3.10.8
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/git/2.38.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/cmake/3.24.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/graphviz/2.49.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/compilers/linux-rhel7-haswell/gcc/12.2.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/py-mpi4py/3.1.4
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/petsc/3.18.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/py-petsc4py/3.18.1
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m
[32;1m$ print_var XDG_CONFIG_HOME[0;m
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980659/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:1698010830: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/55e/b67bb6171d374/pip-23.3.1-py3-none-any.whl (2.1 MB)
     ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 76.6 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages (63.0.0)
Collecting setuptools
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b45/4a35605876da6/setuptools-68.2.2-py3-none-any.whl (807 kB)
     âââââââââââââââââââââââââââââââââââââ 807.9/807.9 kB 268.7 MB/s eta 0:00:00
Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/759/09db2664838d0/wheel-0.41.2-py3-none-any.whl (64 kB)
     âââââââââââââââââââââââââââââââââââââââ 64.8/64.8 kB 221.8 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/J980659/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-23.3.1 setuptools-68.2.2 wheel-0.41.2
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Collecting tox
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/599/af5e5bb0cad01/tox-4.11.3-py3-none-any.whl (153 kB)
     ââââââââââââââââââââââââââââââââââââââ 153.8/153.8 kB 18.4 MB/s eta 0:00:00
Collecting cachetools>=5.3.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/95e/f631eeaea14ba/cachetools-5.3.1-py3-none-any.whl (9.3 kB)
Collecting chardet>=5.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB)
     ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 54.9 MB/s eta 0:00:00
Collecting colorama>=0.4.6 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting filelock>=3.12.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/08c/21d87ded6e2b9/filelock-3.12.4-py3-none-any.whl (11 kB)
Collecting packaging>=23.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/8c4/91190033a9af7/packaging-23.2-py3-none-any.whl (53 kB)
     âââââââââââââââââââââââââââââââââââââââ 53.0/53.0 kB 207.7 MB/s eta 0:00:00
Collecting platformdirs>=3.10 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e9d/171d00af68be5/platformdirs-3.11.0-py3-none-any.whl (17 kB)
Collecting pluggy>=1.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/d89/c696a773f8bd3/pluggy-1.3.0-py3-none-any.whl (18 kB)
Collecting pyproject-api>=1.6.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB)
Collecting tomli>=2.0.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/939/de3e7a6161af0/tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting virtualenv>=20.24.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b80/039f280f4919c/virtualenv-20.24.5-py3-none-any.whl (3.7 MB)
     ââââââââââââââââââââââââââââââââââââââââ 3.7/3.7 MB 188.7 MB/s eta 0:00:00
Collecting distlib<1,>=0.3.7 (from virtualenv>=20.24.3->tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2e2/4928bc811348f/distlib-0.3.7-py2.py3-none-any.whl (468 kB)
     âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 274.9 MB/s eta 0:00:00
Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox
Successfully installed cachetools-5.3.1 chardet-5.2.0 colorama-0.4.6 distlib-0.3.7 filelock-3.12.4 packaging-23.2 platformdirs-3.11.0 pluggy-1.3.0 pyproject-api-1.6.1 tomli-2.0.1 tox-4.11.3 virtualenv-20.24.5
[32;1m$ section_end section_venv[0;m
[0Ksection_end:1698010844: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:1698010844: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/J980659/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/J980659/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/J980659/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: install_requires_for_build_wheel> python -I -m pip install wheel
.pkg: freeze> python -m pip freeze --all
.pkg: packaging==23.2,pip==23.2.1,setuptools==68.2.0,setuptools-scm==8.0.4,tomli==2.0.1,typing_extensions==4.8.0,wheel==0.41.2
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980659/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/J980659/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 vtk
lint: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980659/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz
lint: freeze> python -m pip freeze --all
lint: astroid==3.0.1,AstroVascPy @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980659/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz#sha256=7a8e09cf310f5efee0236d4a492a0aa8614773d122dc9ba65befcaa380d689d8,blosc2==2.2.9,cached-property==1.5.2,cfgv==3.4.0,click==8.1.7,contourpy==1.1.1,coverage==7.3.2,cycler==0.12.1,Cython==3.0.4,dill==0.3.7,distlib==0.3.7,exceptiongroup==1.1.3,filelock==3.12.4,fonttools==4.43.1,h5py==3.10.0,identify==2.5.30,iniconfig==2.0.0,isort==5.12.0,kiwisolver==1.4.5,libsonata==0.1.24,matplotlib==3.8.0,mccabe==0.7.0,MorphIO==3.3.6,mpi4py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mpi4py-3.1.4-glx4cfnu5cionch2hbeyzns5ol3vexp7/spack-src,msgpack==1.0.7,ndindex==1.7,networkx==3.2,nodeenv==1.8.0,numexpr==2.8.7,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging==23.2,pandas==1.5.3,petsc4py @ file:///nvme/bbpcihpcdeploy/1644090/spack-stage/spack-stage-py-petsc4py-3.18.1-7rysecnje3dndrjv36w723cz6tfioxhe/spack-src,Pillow==10.1.0,pip==23.2.1,platformdirs==3.11.0,pluggy==1.3.0,pre-commit==3.5.0,psutil==5.9.6,py-cpuinfo==9.0.0,pylint==3.0.2,pylint-exit==1.2.0,pyparsing==3.1.1,pytest==7.4.2,pytest-mpi==0.6,python-dateutil==2.8.2,pytz==2023.3.post1,PyYAML==6.0.1,scipy==1.11.3,seaborn==0.13.0,setuptools @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-setuptools-63.0.0-c6hdpvjjddmcm3xf5begyfpkjkzj2oke/spack-src/setuptools-63.0.0-py3-none-any.whl,six==1.16.0,tables==3.9.1,tomli==2.0.1,tomlkit==0.12.1,tqdm==4.66.1,trimesh==4.0.0,typing_extensions==4.8.0,vascpy==0.1.1,virtualenv==20.24.5,vtk==9.2.6,wheel==0.41.2
lint: commands[0]> pre-commit run --all-files --show-diff-on-failure
[INFO] Initializing environment for https://github.com/pre-commit/pre-commit-hooks.
[INFO] Initializing environment for https://github.com/alessandrojcm/commitlint-pre-commit-hook.
[INFO] Initializing environment for https://github.com/alessandrojcm/commitlint-pre-commit-hook:conventional-changelog-conventionalcommits.
[INFO] Initializing environment for https://github.com/pycqa/isort.
[INFO] Initializing environment for https://github.com/psf/black.
[INFO] Initializing environment for https://github.com/codespell-project/codespell.
[INFO] Initializing environment for https://github.com/PyCQA/flake8.
[INFO] Installing environment for https://github.com/pre-commit/pre-commit-hooks.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/pycqa/isort.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/psf/black.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/codespell-project/codespell.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/PyCQA/flake8.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
check for added large files..............................................Passed
check for case conflicts.................................................Passed
check for merge conflicts................................................Passed
check for broken symlinks............................(no files to check)Skipped
check yaml...............................................................Passed
debug statements (python)................................................Passed
fix end of files.........................................................Passed
trim trailing whitespace.................................................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:65:26: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
************* Module astrovascpy.utils
astrovascpy/utils.py:497:15: R1735: Consider using '{}' instead of a call to 'dict'. (use-dict-literal)
astrovascpy/utils.py:500:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/utils.py:500:4: E0213: Method 'region' should have "self" as first argument (no-self-argument)
astrovascpy/utils.py:511:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/utils.py:543:8: C0206: Consider iterating with .items() (consider-using-dict-items)
astrovascpy/utils.py:568:11: R1735: Consider using '{}' instead of a call to 'dict'. (use-dict-literal)
astrovascpy/utils.py:571:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/utils.py:571:4: E0213: Method 'region' should have "self" as first argument (no-self-argument)
astrovascpy/utils.py:583:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/utils.py:613:8: C0206: Consider iterating with .items() (consider-using-dict-items)
astrovascpy/utils.py:688:8: 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 536 of astrovascpy.PetscBinaryIO: left side has 1 label, right side has 0 values (unbalanced-tuple-unpacking)
astrovascpy/scipy_petsc_conversions.py:314:45: W0621: Redefining name 'dtype' from outer scope (line 19) (redefined-outer-name)
************* Module astrovascpy.PetscBinaryIO
astrovascpy/PetscBinaryIO.py:71:20: W0707: Consider explicitly re-raising using 'except Exception as exc' and 'raise importlib.metadata.PackageNotFoundError from exc' (raise-missing-from)
astrovascpy/PetscBinaryIO.py:76:27: W0212: Access to a protected member _path of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:107:14: W1514: Using open without explicitly specifying an encoding (unspecified-encoding)
astrovascpy/PetscBinaryIO.py:107:14: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
astrovascpy/PetscBinaryIO.py:119:14: 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 (54/50) (too-many-statements)
astrovascpy/PetscBinaryIO.py:119:14: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
astrovascpy/PetscBinaryIO.py:201:12: W0212: Access to a protected member _update_dtypes of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:209:12: W0212: Access to a protected member _update_dtypes of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:216:0: C0115: Missing class docstring (missing-class-docstring)
astrovascpy/PetscBinaryIO.py:255:15: C0209: Formatting a regular string which could be an f-string (consider-using-f-string)
astrovascpy/PetscBinaryIO.py:255:33: R1725: Consider using Python 3 style super() without arguments (super-with-arguments)
astrovascpy/PetscBinaryIO.py:270:0: R0205: Class 'PetscBinaryIO' inherits from object, can be safely removed from bases in python3 (useless-object-inheritance)
astrovascpy/PetscBinaryIO.py:328:27: C0209: Formatting a regular string which could be an f-string (consider-using-f-string)
astrovascpy/PetscBinaryIO.py:338:12: 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:347:29: W0212: Access to a protected member _classid of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:344:4: R1711: Useless return at end of function or method (useless-return)
astrovascpy/PetscBinaryIO.py:379:12: 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:388:29: W0212: Access to a protected member _classid of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:384:4: R1711: Useless return at end of function or method (useless-return)
astrovascpy/PetscBinaryIO.py:419:12: 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:428:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/PetscBinaryIO.py:433:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/PetscBinaryIO.py:437:8: W0612: Unused variable 'V' (unused-variable)
astrovascpy/PetscBinaryIO.py:438:8: W0612: Unused variable 'M' (unused-variable)
astrovascpy/PetscBinaryIO.py:438:11: W0612: Unused variable 'N' (unused-variable)
astrovascpy/PetscBinaryIO.py:439:8: W0612: Unused variable 'J' (unused-variable)
astrovascpy/PetscBinaryIO.py:440:8: W0612: Unused variable 'I' (unused-variable)
astrovascpy/PetscBinaryIO.py:470:12: 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:477:29: W0212: Access to a protected member _classid of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:474:4: R1711: Useless return at end of function or method (useless-return)
astrovascpy/PetscBinaryIO.py:514:20: W0707: Consider explicitly re-raising using 'except (MemoryError, IndexError) as exc' and 'raise DoneWithFile from exc' (raise-missing-from)
astrovascpy/PetscBinaryIO.py:518:20: 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:504:18: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
astrovascpy/PetscBinaryIO.py:571:20: 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:571:36: C0209: Formatting a regular string which could be an f-string (consider-using-f-string)
astrovascpy/PetscBinaryIO.py:571:79: C2801: Unnecessarily calls dunder method __repr__. Use repr built-in function. (unnecessary-dunder-call)
astrovascpy/PetscBinaryIO.py:539:4: R1711: Useless return at end of function or method (useless-return)
astrovascpy/PetscBinaryIO.py:551:18: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
************* Module astrovascpy.bloodflow
astrovascpy/bloodflow.py:42:0: W0622: Redefining built-in 'print' (redefined-builtin)
astrovascpy/bloodflow.py:391:0: R0914: Too many local variables (36/25) (too-many-locals)
astrovascpy/bloodflow.py:391:0: R0912: Too many branches (17/12) (too-many-branches)
astrovascpy/bloodflow.py:391:0: R0915: Too many statements (71/50) (too-many-statements)
astrovascpy/bloodflow.py:655:34: C0209: Formatting a regular string which could be an f-string (consider-using-f-string)
astrovascpy/bloodflow.py:615:0: R0912: Too many branches (15/12) (too-many-branches)
astrovascpy/bloodflow.py:615:0: R0915: Too many statements (66/50) (too-many-statements)

-----------------------------------
Your code has been rated at 9.53/10

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/J980659/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
  lint: OK (144.23=setup[70.80]+cmd[39.56,33.87] seconds)
  congratulations :) (144.51 seconds)
[32;1m$ section_end section_tox[0;m
[0Ksection_end:1698010989:section_tox
[0K
section_end:1698010989:step_script
[0Ksection_start:1698010989: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:1698010997: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:1698010816:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1698010816:resolve_secrets
[0Ksection_start:1698010816: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-executor429257639, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root molsys, project name AstroVascPy
Pipeline ID 163955, build ref , job ID 980661
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J980661, 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_J980661_PROD_P2342_CP3_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 1856064
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J980661_PROD_P2342_CP3_C3 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J980661 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J980661 --ntasks=1 --jobid=1856064 --cpus-per-task=6 --mem=30750M
section_end:1698010818:prepare_executor
[0Ksection_start:1698010818:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i4n17 via bbpv1.epfl.ch...
section_end:1698010825:prepare_script
[0Ksection_start:1698010825: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/J980661/molsys/AstroVascPy/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 3afb4f3a as nicola/petsc_improvement...[0;m
Skipping object checkout, Git LFS is not installed.

[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m
section_end:1698010827:get_sources
[0Ksection_start:1698010827: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/2023-10/externals/linux-rhel7-skylake/python/3.10.8
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/git/2.38.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/cmake/3.24.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/graphviz/2.49.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/compilers/linux-rhel7-haswell/gcc/12.2.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/py-mpi4py/3.1.4
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/petsc/3.18.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-10/applications/linux-rhel7-skylake/py-petsc4py/3.18.1
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m
[32;1m$ print_var XDG_CONFIG_HOME[0;m
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980661/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:1698010829: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/55e/b67bb6171d374/pip-23.3.1-py3-none-any.whl (2.1 MB)
     ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 75.2 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages (63.0.0)
Collecting setuptools
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b45/4a35605876da6/setuptools-68.2.2-py3-none-any.whl (807 kB)
     âââââââââââââââââââââââââââââââââââââ 807.9/807.9 kB 266.5 MB/s eta 0:00:00
Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/759/09db2664838d0/wheel-0.41.2-py3-none-any.whl (64 kB)
     âââââââââââââââââââââââââââââââââââââââ 64.8/64.8 kB 221.2 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 63.0.0
    Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980661/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-23.3.1 setuptools-68.2.2 wheel-0.41.2
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Collecting tox
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/599/af5e5bb0cad01/tox-4.11.3-py3-none-any.whl (153 kB)
     ââââââââââââââââââââââââââââââââââââââ 153.8/153.8 kB 19.4 MB/s eta 0:00:00
Collecting cachetools>=5.3.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/95e/f631eeaea14ba/cachetools-5.3.1-py3-none-any.whl (9.3 kB)
Collecting chardet>=5.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB)
     ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 56.0 MB/s eta 0:00:00
Collecting colorama>=0.4.6 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting filelock>=3.12.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/08c/21d87ded6e2b9/filelock-3.12.4-py3-none-any.whl (11 kB)
Collecting packaging>=23.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/8c4/91190033a9af7/packaging-23.2-py3-none-any.whl (53 kB)
     âââââââââââââââââââââââââââââââââââââââ 53.0/53.0 kB 216.5 MB/s eta 0:00:00
Collecting platformdirs>=3.10 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e9d/171d00af68be5/platformdirs-3.11.0-py3-none-any.whl (17 kB)
Collecting pluggy>=1.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/d89/c696a773f8bd3/pluggy-1.3.0-py3-none-any.whl (18 kB)
Collecting pyproject-api>=1.6.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB)
Collecting tomli>=2.0.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/939/de3e7a6161af0/tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting virtualenv>=20.24.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b80/039f280f4919c/virtualenv-20.24.5-py3-none-any.whl (3.7 MB)
     ââââââââââââââââââââââââââââââââââââââââ 3.7/3.7 MB 177.4 MB/s eta 0:00:00
Collecting distlib<1,>=0.3.7 (from virtualenv>=20.24.3->tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2e2/4928bc811348f/distlib-0.3.7-py2.py3-none-any.whl (468 kB)
     âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 267.0 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-5.3.1 chardet-5.2.0 colorama-0.4.6 distlib-0.3.7 filelock-3.12.4 packaging-23.2 platformdirs-3.11.0 pluggy-1.3.0 pyproject-api-1.6.1 tomli-2.0.1 tox-4.11.3 virtualenv-20.24.5
[32;1m$ section_end section_venv[0;m
[0Ksection_end:1698010844: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:1698010844: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/J980661/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/J980661/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/J980661/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: install_requires_for_build_wheel> python -I -m pip install wheel
.pkg: freeze> python -m pip freeze --all
.pkg: packaging==23.2,pip==23.2.1,setuptools==68.2.0,setuptools-scm==8.0.4,tomli==2.0.1,typing_extensions==4.8.0,wheel==0.41.2
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980661/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/J980661/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 vtk
py310: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980661/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/J980661/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz#sha256=430da36d621866405f5ad4f97d763e364eee6e4490853be16eed7800913f8610,blosc2==2.2.9,cached-property==1.5.2,click==8.1.7,contourpy==1.1.1,coverage==7.3.2,cycler==0.12.1,Cython==3.0.4,exceptiongroup==1.1.3,fonttools==4.43.1,h5py==3.10.0,iniconfig==2.0.0,kiwisolver==1.4.5,libsonata==0.1.24,matplotlib==3.8.0,MorphIO==3.3.6,mpi4py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mpi4py-3.1.4-glx4cfnu5cionch2hbeyzns5ol3vexp7/spack-src,msgpack==1.0.7,ndindex==1.7,networkx==3.2,numexpr==2.8.7,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging==23.2,pandas==1.5.3,petsc4py @ file:///nvme/bbpcihpcdeploy/1644090/spack-stage/spack-stage-py-petsc4py-3.18.1-7rysecnje3dndrjv36w723cz6tfioxhe/spack-src,Pillow==10.1.0,pip==23.2.1,pluggy==1.3.0,psutil==5.9.6,py-cpuinfo==9.0.0,pyparsing==3.1.1,pytest==7.4.2,pytest-mpi==0.6,python-dateutil==2.8.2,pytz==2023.3.post1,PyYAML==6.0.1,scipy==1.11.3,seaborn==0.13.0,setuptools @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-setuptools-63.0.0-c6hdpvjjddmcm3xf5begyfpkjkzj2oke/spack-src/setuptools-63.0.0-py3-none-any.whl,six==1.16.0,tables==3.9.1,tomli==2.0.1,tqdm==4.66.1,trimesh==4.0.0,vascpy==0.1.1,vtk==9.2.6,wheel==0.41.2
py310: commands[0]> coverage run --branch --source=astrovascpy -m pytest --basetemp=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980661/molsys/AstroVascPy/.tox/py310/tmp --verbose --junit-xml=reports/pytest-py310.xml
============================= test session starts ==============================
platform linux -- Python 3.10.8, pytest-7.4.2, pluggy-1.3.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980661/molsys/AstroVascPy/.tox/py310/bin/python
cachedir: .tox/py310/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980661/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/J980661/molsys/AstroVascPy/reports/pytest-py310.xml -
======================== 53 passed, 3 skipped in 10.74s ========================
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/J980661/molsys/AstroVascPy/tests/test_mpi.py
============================= test session starts ==============================
platform linux -- Python 3.10.8, pytest-7.4.2, pluggy-1.3.0
cachedir: .tox/py310/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980661/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-7.4.2, pluggy-1.3.0
cachedir: .tox/py310/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980661/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-7.4.2, pluggy-1.3.0
cachedir: .tox/py310/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980661/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-7.4.2, pluggy-1.3.0
cachedir: .tox/py310/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J980661/molsys/AstroVascPy
configfile: pyproject.toml
plugins: mpi-0.6
collected 3 items

tests/test_mpi.py ............                                                    [100%]                                                    [100%]                                                    [100%]                                                    [100%]
=============================== 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 0.60s ===============================

=============================== 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 0.60s ===============================

=============================== 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 0.60s ===============================

=============================== 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 0.60s ===============================
py310: commands[2]> coverage combine --append
Combined data file .coverage-py310.r1i4n17.120373.998640
Combined data file .coverage-py310.r1i4n17.120372.445266
Skipping duplicate data .coverage-py310.r1i4n17.120375.626854
Skipping duplicate data .coverage-py310.r1i4n17.120374.093608
py310: commands[3]> coverage report --fail-under=50
Name                                     Stmts   Miss Branch BrPart  Cover
--------------------------------------------------------------------------
astrovascpy/PetscBinaryIO.py               309    167     96     22    43%
astrovascpy/__init__.py                      0      0      0      0   100%
astrovascpy/bloodflow.py                   315     56    122     33    75%
astrovascpy/exceptions.py                    1      0      0      0   100%
astrovascpy/io.py                           57      8     24     11    77%
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/utils.py                       300    117     74      6    60%
astrovascpy/version.py                       2      2      0      0     0%
astrovascpy/vtk_io.py                        5      5      0      0     0%
--------------------------------------------------------------------------
TOTAL                                     1309    401    390     75    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/J980661/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
  py310: OK (85.45=setup[71.37]+cmd[11.54,1.29,0.18,0.38,0.69] seconds)
  congratulations :) (85.70 seconds)
[32;1m$ section_end section_tox[0;m
[0Ksection_end:1698010930:section_tox
[0K
section_end:1698010930:step_script
[0Ksection_start:1698010930: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:1698010935:cleanup_file_variables
[0K[32;1mJob succeeded[0;m