Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/molsys/AstroVascPy/-/pipelines/200493 (:no_entry:) running on GitHub PR BlueBrain/AstroVascPy#27.

build-wheels-py310.txt

Running with gitlab-runner 16.8.1 (a6097117)
  on kubernetes f34dUjJy, system ID: r_e79EgkF1seUj
section_start:1710424267:resolve_secrets
Resolving secrets
section_end:1710424267:resolve_secrets
section_start:1710424267:prepare_executor
Preparing the "kubernetes" executor
Using Kubernetes namespace: gitlab-runners
Using Kubernetes executor with image quay.io/pypa/manylinux2014_x86_64 ...
Using attach strategy to execute scripts...
section_end:1710424267:prepare_executor
section_start:1710424267:prepare_script
Preparing environment
Using FF_USE_POD_ACTIVE_DEADLINE_SECONDS, the Pod activeDeadlineSeconds will be set to the job timeout: 1h0m0s...
Waiting for pod gitlab-runners/runner-f34dujjy-project-2342-concurrent-0-4ihcte0r to be running, status is Pending
Running on runner-f34dujjy-project-2342-concurrent-0-4ihcte0r via cs-gitlab-runners-gitlab-runner-557b4c775c-dn88n...

section_end:1710424272:prepare_script
section_start:1710424272:get_sources
Getting source from Git repository
Fetching changes with git depth set to 20...
Initialized empty Git repository in /builds/molsys/AstroVascPy/.git/
Created fresh repository.
Checking out c48174de as detached HEAD (ref is tristan/mpi4py)...

Updating/initializing submodules recursively with git depth set to 20...
Updated submodules

section_end:1710424275:get_sources
section_start:1710424275:download_artifacts
Downloading artifacts
Downloading artifacts for docs (1209079)...
Downloading artifacts from coordinator... ok        host=bbpgitlab.epfl.ch id=1209079 responseStatus=200 OK token=64_7gVu5

section_end:1710424277:download_artifacts
section_start:1710424277:step_script
Executing "step_script" stage of the job script
$ declare -A PY_MAP=( [py38]=cp38-cp38 [py39]=cp39-cp39 [py310]=cp310-cp310 [py311]=cp311-cp311 [py312]=cp312-cp312 )
$ print_var() { echo -e "${TXT_CYAN}${1}=${!1}${TXT_CLEAR}"; }
$ set_and_print() { eval $1=$2; print_var $1; }
$ cd "${PYTHON_PROJECT_DIR}"
$ set_and_print PY_BIN_NAME "${PY_MAP[$PY_VERSION]}"
PY_BIN_NAME=cp310-cp310
$ set_and_print PY_BIN "/opt/python/${PY_BIN_NAME}/bin"
PY_BIN=/opt/python/cp310-cp310/bin
$ print_var SYS_PACKAGES
SYS_PACKAGES=
$ if [[ -n $SYS_PACKAGES ]]; then yum install -y $SYS_PACKAGES; fi
$ print_var PRE_BUILD_COMMAND
PRE_BUILD_COMMAND=
$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi
$ ${PY_BIN}/pip install --upgrade --no-cache-dir pip setuptools wheel
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Requirement already satisfied: pip in /opt/_internal/cpython-3.10.13/lib/python3.10/site-packages (24.0)
Requirement already satisfied: setuptools in /opt/_internal/cpython-3.10.13/lib/python3.10/site-packages (69.1.1)
Collecting setuptools
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c21/c49fb1042386d/setuptools-69.2.0-py3-none-any.whl (821 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 821.5/821.5 kB 117.9 MB/s eta 0:00:00
Requirement already satisfied: wheel in /opt/_internal/cpython-3.10.13/lib/python3.10/site-packages (0.43.0)
Installing collected packages: setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 69.1.1
    Uninstalling setuptools-69.1.1:
      Successfully uninstalled setuptools-69.1.1
Successfully installed setuptools-69.2.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
$ set_and_print WHEELS_DIR "${PYTHON_PROJECT_DIR}/wheelhouse"
WHEELS_DIR=./wheelhouse
$ rm -rf $WHEELS_DIR && mkdir -p $WHEELS_DIR
$ ${PY_BIN}/pip wheel . -w $WHEELS_DIR --no-deps
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Processing /builds/molsys/AstroVascPy
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: AstroVascPy
  Building wheel for AstroVascPy (pyproject.toml): started
  Building wheel for AstroVascPy (pyproject.toml): finished with status 'done'
  Created wheel for AstroVascPy: filename=AstroVascPy-0.1.4-py3-none-any.whl size=45236 sha256=faf9fde6e173004d26c75ab0cefca26bbbc30041466994350123493f846fc4d1
  Stored in directory: /tmp/pip-ephem-wheel-cache-rjqqpf1j/wheels/87/40/b2/858192df9193a18fc502074da3ae7b563b65bf229c2d77ff76
Successfully built AstroVascPy
$ if [[ "$TEST_RUN_TOX" != "true" ]]; then { echo -e "${TXT_CYAN}Skipping tests.${TXT_CLEAR}"; exit 0; } fi
Skipping tests.

section_end:1710424290:step_script
section_start:1710424290:upload_artifacts_on_success
Uploading artifacts for successful job
Uploading artifacts...
./wheelhouse/: found 2 matching artifact files and directories 
Uploading artifacts as "archive" to coordinator... 201 Created  id=1209081 responseStatus=201 Created token=64_7gVu5

section_end:1710424292:upload_artifacts_on_success
section_start:1710424292:cleanup_file_variables
Cleaning up project directory and file based variables

section_end:1710424293:cleanup_file_variables
Job succeeded

check-packaging.txt

Running with gitlab-runner 15.5.0 (0d4137b8)
  on BB5 map runner pnPo3yJy
section_start:1710424046:resolve_secrets
Resolving secrets
section_end:1710424046:resolve_secrets
section_start:1710424046:prepare_executor
Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user 
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor411116535, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root molsys, project name AstroVascPy
Pipeline ID 200493, build ref , job ID 1209077
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1209077, 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_J1209077_PROD_P2342_CP0_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 2083943
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J1209077_PROD_P2342_CP0_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1209077 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1209077 --ntasks=1 --jobid=2083943 --cpus-per-task=6 --mem=30750M     
section_end:1710424048:prepare_executor
section_start:1710424048:prepare_script
Preparing environment
Using git from spack modules
Running on r1i4n18 via bbpv1.epfl.ch...
section_end:1710424063:prepare_script
section_start:1710424063:get_sources
Getting source from Git repository
Using git from spack modules
$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'
Fetching changes with git depth set to 20...
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209077/molsys/AstroVascPy/.git/
Created fresh repository.
Checking out c48174de as tristan/mpi4py...
Skipping object checkout, Git LFS is not installed.

Updating/initializing submodules recursively with git depth set to 20...
section_end:1710424071:get_sources
section_start:1710424071:step_script
Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi
$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }
$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }
$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }
$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }
$ module purge
$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')
$ module load unstable python/3.12.0
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.12.0
$ module load unstable python/3.8.18
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.8.18
$ module load unstable python/3.9.18
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.9.18
$ module load unstable python/3.10.13
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.10.13
$ module load unstable python/3.11.6
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.11.6
$ load-modules() { # collapsed multi-line command
$ load-modules $SYSTEM_MODULES
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
$ load-modules $EXTRA_MODULES
Loaded module gcc from unstable
Loaded module hpe-mpi from unstable
Loaded module py-mpi4py from unstable
Loaded module petsc from unstable
Loaded module py-petsc4py from unstable
$ module list -t
Currently Loaded Modulefiles:
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.12.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.8.18
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.9.18
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.10.13
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.11.6
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/git/2.42.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/cmake/3.27.7
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/graphviz/8.0.5
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/compilers/linux-rhel7-haswell/gcc/12.3.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/py-mpi4py/3.1.4
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/petsc/3.20.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/py-petsc4py/3.20.1
$ export XDG_CONFIG_HOME=${PWD}/local_config
$ print_var XDG_CONFIG_HOME
XDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209077/molsys/AstroVascPy/local_config
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
  insteadOf = https://bbpgitlab.epfl.ch/
  insteadOf = ssh://git@bbpgitlab.epfl.ch/
  insteadOf = git@bbpgitlab.epfl.ch:
$ section_start section_venv[collapsed=true] "Setting up the virtual env"
section_start:1710424078:section_venv[collapsed=true]
Setting up the virtual env
$ cd "${PYTHON_PROJECT_DIR}"
$ CI_VENV="$(pwd)/venv"
$ rm -rf "$CI_VENV"
$ python -mvenv "$CI_VENV"
$ source "$CI_VENV/bin/activate"
$ python -mpip install --upgrade pip setuptools wheel
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1)
Collecting pip
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 75.6 MB/s eta 0:00:00
Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0)
Collecting setuptools
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c21/c49fb1042386d/setuptools-69.2.0-py3-none-any.whl (821 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 821.5/821.5 kB 163.2 MB/s eta 0:00:00
Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 65.8/65.8 kB 220.9 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 23.2.1
    Uninstalling pip-23.2.1:
      Successfully uninstalled pip-23.2.1
Successfully installed pip-24.0 setuptools-69.2.0 wheel-0.43.0
$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Collecting tox
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b03/754b6ee6dadc7/tox-4.14.1-py3-none-any.whl (155 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.3/155.3 kB 17.9 MB/s eta 0:00:00
Collecting cachetools>=5.3.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 kB)
Collecting chardet>=5.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 199.4/199.4 kB 56.8 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>=3.13.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/57d/bda9b35157b05/filelock-3.13.1-py3-none-any.whl (11 kB)
Collecting packaging>=23.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.5/53.5 kB 215.2 MB/s eta 0:00:00
Collecting platformdirs>=4.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/061/4df2a2f37e1a6/platformdirs-4.2.0-py3-none-any.whl (17 kB)
Collecting pluggy>=1.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7db/9f7b503d67d1c/pluggy-1.4.0-py3-none-any.whl (20 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 virtualenv>=20.25 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/961/c026ac520bac5/virtualenv-20.25.1-py3-none-any.whl (3.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.8/3.8 MB 153.4 MB/s eta 0:00:00
Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 468.9/468.9 kB 261.9 MB/s eta 0:00:00
Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox
Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-24.0 platformdirs-4.2.0 pluggy-1.4.0 pyproject-api-1.6.1 tox-4.14.1 virtualenv-20.25.1
$ section_end section_venv
section_end:1710424095:section_venv

$ print_var PRE_BUILD_COMMAND
PRE_BUILD_COMMAND=
$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi
$ section_start section_tox "Running Tox"
section_start:1710424095:section_tox
Running Tox
$ python -mtox $TOX_OPTIONS
check-packaging: install_deps> python -I -m pip install build twine
check-packaging: freeze> python -m pip freeze --all
check-packaging: build==1.1.1,certifi==2024.2.2,cffi==1.16.0,charset-normalizer==3.3.2,cryptography==42.0.5,docutils==0.20.1,idna==3.6,importlib_metadata==7.0.2,jaraco.classes==3.3.1,jeepney==0.8.0,keyring==24.3.1,markdown-it-py==3.0.0,mdurl==0.1.2,more-itertools==10.2.0,mpi4py @ file:///nvme/bbpcihpcdeploy/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,nh3==0.2.15,numpy @ file:///nvme/bbpcihpcdeploy/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,packaging==24.0,petsc4py @ file:///nvme/bbpcihpcdeploy/1998222/spack-stage/spack-stage-py-petsc4py-3.20.1-jootwwazqwscmwl7nyiqksdarrzdveu5/spack-src,pip==24.0,pkginfo==1.10.0,pycparser==2.21,Pygments==2.17.2,pyproject_hooks==1.0.0,readme_renderer==43.0,requests==2.31.0,requests-toolbelt==1.0.0,rfc3986==2.0.0,rich==13.7.1,SecretStorage==3.3.3,setuptools==69.1.0,twine==5.0.0,urllib3==2.2.1,wheel==0.42.0,zipp==3.18.0
check-packaging: commands[0]> python -m build -o /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209077/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-0.1.4
creating AstroVascPy-0.1.4/AstroVascPy.egg-info
creating AstroVascPy-0.1.4/astrovascpy
creating AstroVascPy-0.1.4/docs
creating AstroVascPy-0.1.4/docs/source
creating AstroVascPy-0.1.4/docs/source/logo
creating AstroVascPy-0.1.4/examples
creating AstroVascPy-0.1.4/examples/data
creating AstroVascPy-0.1.4/examples/data/graphs_folder
creating AstroVascPy-0.1.4/tests
creating AstroVascPy-0.1.4/tests/data
creating AstroVascPy-0.1.4/tests/data/input_flow
creating AstroVascPy-0.1.4/tests/data/reporting
copying files to AstroVascPy-0.1.4...
copying .auto-changelog -> AstroVascPy-0.1.4
copying .auto-changelog-template.hbs -> AstroVascPy-0.1.4
copying .codespellignorelines -> AstroVascPy-0.1.4
copying .codespellrc -> AstroVascPy-0.1.4
copying .copier-answers.yml -> AstroVascPy-0.1.4
copying .flake8 -> AstroVascPy-0.1.4
copying .gitattributes -> AstroVascPy-0.1.4
copying .gitignore -> AstroVascPy-0.1.4
copying .gitlab-ci.yml -> AstroVascPy-0.1.4
copying .gitreview -> AstroVascPy-0.1.4
copying .pre-commit-config.yaml -> AstroVascPy-0.1.4
copying .pylintrc -> AstroVascPy-0.1.4
copying AUTHORS.txt -> AstroVascPy-0.1.4
copying CHANGELOG.md -> AstroVascPy-0.1.4
copying CITATION.cff -> AstroVascPy-0.1.4
copying CONTRIBUTING.md -> AstroVascPy-0.1.4
copying LICENSE.txt -> AstroVascPy-0.1.4
copying MANIFEST.in -> AstroVascPy-0.1.4
copying README.md -> AstroVascPy-0.1.4
copying commitlint.config.js -> AstroVascPy-0.1.4
copying package.json -> AstroVascPy-0.1.4
copying pyproject.toml -> AstroVascPy-0.1.4
copying setup.py -> AstroVascPy-0.1.4
copying setup.sh -> AstroVascPy-0.1.4
copying tox.ini -> AstroVascPy-0.1.4
copying AstroVascPy.egg-info/PKG-INFO -> AstroVascPy-0.1.4/AstroVascPy.egg-info
copying AstroVascPy.egg-info/SOURCES.txt -> AstroVascPy-0.1.4/AstroVascPy.egg-info
copying AstroVascPy.egg-info/dependency_links.txt -> AstroVascPy-0.1.4/AstroVascPy.egg-info
copying AstroVascPy.egg-info/entry_points.txt -> AstroVascPy-0.1.4/AstroVascPy.egg-info
copying AstroVascPy.egg-info/requires.txt -> AstroVascPy-0.1.4/AstroVascPy.egg-info
copying AstroVascPy.egg-info/top_level.txt -> AstroVascPy-0.1.4/AstroVascPy.egg-info
copying astrovascpy/PetscBinaryIO.py -> AstroVascPy-0.1.4/astrovascpy
copying astrovascpy/__init__.py -> AstroVascPy-0.1.4/astrovascpy
copying astrovascpy/bloodflow.py -> AstroVascPy-0.1.4/astrovascpy
copying astrovascpy/exceptions.py -> AstroVascPy-0.1.4/astrovascpy
copying astrovascpy/io.py -> AstroVascPy-0.1.4/astrovascpy
copying astrovascpy/ou.py -> AstroVascPy-0.1.4/astrovascpy
copying astrovascpy/plotting.py -> AstroVascPy-0.1.4/astrovascpy
copying astrovascpy/report_reader.py -> AstroVascPy-0.1.4/astrovascpy
copying astrovascpy/report_writer.py -> AstroVascPy-0.1.4/astrovascpy
copying astrovascpy/scipy_petsc_conversions.py -> AstroVascPy-0.1.4/astrovascpy
copying astrovascpy/typing.py -> AstroVascPy-0.1.4/astrovascpy
copying astrovascpy/utils.py -> AstroVascPy-0.1.4/astrovascpy
copying astrovascpy/version.py -> AstroVascPy-0.1.4/astrovascpy
copying astrovascpy/vtk_io.py -> AstroVascPy-0.1.4/astrovascpy
copying docs/Makefile -> AstroVascPy-0.1.4/docs
copying docs/source/api_ref.rst -> AstroVascPy-0.1.4/docs/source
copying docs/source/changelog.rst -> AstroVascPy-0.1.4/docs/source
copying docs/source/conf.py -> AstroVascPy-0.1.4/docs/source
copying docs/source/index.rst -> AstroVascPy-0.1.4/docs/source
copying docs/source/logo/BPP-AstroVascPy-Github.jpg -> AstroVascPy-0.1.4/docs/source/logo
copying examples/compute_static_flow_pressure.py -> AstroVascPy-0.1.4/examples
copying examples/job_script.sbatch -> AstroVascPy-0.1.4/examples
copying examples/simulate_OU_process.py -> AstroVascPy-0.1.4/examples
copying examples/data/params.yaml -> AstroVascPy-0.1.4/examples/data
copying examples/data/graphs_folder/edge_dataset.csv -> AstroVascPy-0.1.4/examples/data/graphs_folder
copying examples/data/graphs_folder/node_dataset.csv -> AstroVascPy-0.1.4/examples/data/graphs_folder
copying examples/data/graphs_folder/toy_graph.bin -> AstroVascPy-0.1.4/examples/data/graphs_folder
copying examples/data/graphs_folder/toy_graph.h5 -> AstroVascPy-0.1.4/examples/data/graphs_folder
copying tests/__init__.py -> AstroVascPy-0.1.4/tests
copying tests/test_bloodflow.py -> AstroVascPy-0.1.4/tests
copying tests/test_graphs.py -> AstroVascPy-0.1.4/tests
copying tests/test_io.py -> AstroVascPy-0.1.4/tests
copying tests/test_mpi.py -> AstroVascPy-0.1.4/tests
copying tests/test_ou.py -> AstroVascPy-0.1.4/tests
copying tests/test_report_reader.py -> AstroVascPy-0.1.4/tests
copying tests/test_report_writer.py -> AstroVascPy-0.1.4/tests
copying tests/test_utils.py -> AstroVascPy-0.1.4/tests
copying tests/data/dataset.h5 -> AstroVascPy-0.1.4/tests/data
copying tests/data/edge_dataset.csv -> AstroVascPy-0.1.4/tests/data
copying tests/data/node_dataset.csv -> AstroVascPy-0.1.4/tests/data
copying tests/data/toy_graph.bin -> AstroVascPy-0.1.4/tests/data
copying tests/data/toy_graph.h5 -> AstroVascPy-0.1.4/tests/data
copying tests/data/input_flow/sine.csv -> AstroVascPy-0.1.4/tests/data/input_flow
copying tests/data/reporting/compartment_report.h5 -> AstroVascPy-0.1.4/tests/data/reporting
copying tests/data/reporting/create_reports.py -> AstroVascPy-0.1.4/tests/data/reporting
copying tests/data/reporting/diff_unit_compartment_report.h5 -> AstroVascPy-0.1.4/tests/data/reporting
Writing AstroVascPy-0.1.4/setup.cfg
Creating tar archive
removing 'AstroVascPy-0.1.4' (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/scipy_petsc_conversions.py -> build/lib/astrovascpy
copying astrovascpy/PetscBinaryIO.py -> build/lib/astrovascpy
copying astrovascpy/plotting.py -> build/lib/astrovascpy
copying astrovascpy/exceptions.py -> build/lib/astrovascpy
copying astrovascpy/ou.py -> build/lib/astrovascpy
copying astrovascpy/report_writer.py -> build/lib/astrovascpy
copying astrovascpy/io.py -> build/lib/astrovascpy
copying astrovascpy/vtk_io.py -> build/lib/astrovascpy
copying astrovascpy/typing.py -> build/lib/astrovascpy
copying astrovascpy/version.py -> build/lib/astrovascpy
copying astrovascpy/bloodflow.py -> build/lib/astrovascpy
copying astrovascpy/report_reader.py -> build/lib/astrovascpy
copying astrovascpy/__init__.py -> build/lib/astrovascpy
copying astrovascpy/utils.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/scipy_petsc_conversions.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/plotting.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
copying build/lib/astrovascpy/report_writer.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/io.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/vtk_io.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/typing.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/bloodflow.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/__init__.py -> build/bdist.linux-x86_64/wheel/astrovascpy
copying build/lib/astrovascpy/utils.py -> build/bdist.linux-x86_64/wheel/astrovascpy
running install_egg_info
Copying AstroVascPy.egg-info to build/bdist.linux-x86_64/wheel/AstroVascPy-0.1.4-py3.11.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/AstroVascPy-0.1.4.dist-info/WHEEL
creating '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209077/molsys/AstroVascPy/.tox/check-packaging/tmp/dist/.tmp-bq5jmuce/AstroVascPy-0.1.4-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'astrovascpy/PetscBinaryIO.py'
adding 'astrovascpy/__init__.py'
adding 'astrovascpy/bloodflow.py'
adding 'astrovascpy/exceptions.py'
adding 'astrovascpy/io.py'
adding 'astrovascpy/ou.py'
adding 'astrovascpy/plotting.py'
adding 'astrovascpy/report_reader.py'
adding 'astrovascpy/report_writer.py'
adding 'astrovascpy/scipy_petsc_conversions.py'
adding 'astrovascpy/typing.py'
adding 'astrovascpy/utils.py'
adding 'astrovascpy/version.py'
adding 'astrovascpy/vtk_io.py'
adding 'AstroVascPy-0.1.4.dist-info/AUTHORS.txt'
adding 'AstroVascPy-0.1.4.dist-info/LICENSE.txt'
adding 'AstroVascPy-0.1.4.dist-info/METADATA'
adding 'AstroVascPy-0.1.4.dist-info/WHEEL'
adding 'AstroVascPy-0.1.4.dist-info/entry_points.txt'
adding 'AstroVascPy-0.1.4.dist-info/top_level.txt'
adding 'AstroVascPy-0.1.4.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built AstroVascPy-0.1.4.tar.gz and AstroVascPy-0.1.4-py3-none-any.whl
check-packaging: commands[1]> twine check '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209077/molsys/AstroVascPy/.tox/check-packaging/tmp/dist/*'
Checking 
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209077/molsys/AstroVascPy/.t
ox/check-packaging/tmp/dist/AstroVascPy-0.1.4-py3-none-any.whl: PASSED
Checking 
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209077/molsys/AstroVascPy/.t
ox/check-packaging/tmp/dist/AstroVascPy-0.1.4.tar.gz: PASSED
  check-packaging: OK (32.82=setup[19.32]+cmd[13.07,0.43] seconds)
  congratulations :) (32.93 seconds)
$ section_end section_tox
section_end:1710424129:section_tox

section_end:1710424129:step_script
section_start:1710424129:cleanup_file_variables
Cleaning up project directory and file based variables
Using git from spack modules
section_end:1710424131:cleanup_file_variables
Job succeeded

docs.txt

Running with gitlab-runner 15.5.0 (0d4137b8)
  on BB5 map runner pnPo3yJy
section_start:1710424048:resolve_secrets
Resolving secrets
section_end:1710424048:resolve_secrets
section_start:1710424048:prepare_executor
Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user 
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor1959872125, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root molsys, project name AstroVascPy
Pipeline ID 200493, build ref , job ID 1209079
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1209079, 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_J1209079_PROD_P2342_CP2_C4
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcimolsys partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 2083945
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_J1209079_PROD_P2342_CP2_C4 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1209079 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1209079 --ntasks=1 --jobid=2083945 --cpus-per-task=6 --mem=30750M     
section_end:1710424051:prepare_executor
section_start:1710424051:prepare_script
Preparing environment
Using git from spack modules
Running on r1i4n18 via bbpv1.epfl.ch...
section_end:1710424060:prepare_script
section_start:1710424060:get_sources
Getting source from Git repository
Using git from spack modules
$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'
Fetching changes with git depth set to 20...
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.git/
Created fresh repository.
Checking out c48174de as tristan/mpi4py...
Skipping object checkout, Git LFS is not installed.

Updating/initializing submodules recursively with git depth set to 20...
section_end:1710424069:get_sources
section_start:1710424069:step_script
Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi
$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }
$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }
$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }
$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }
$ module purge
$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')
$ module load unstable python/3.12.0
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.12.0
$ module load unstable python/3.8.18
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.8.18
$ module load unstable python/3.9.18
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.9.18
$ module load unstable python/3.10.13
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.10.13
$ module load unstable python/3.11.6
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.11.6
$ load-modules() { # collapsed multi-line command
$ load-modules $SYSTEM_MODULES
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
$ load-modules $EXTRA_MODULES
Loaded module gcc from unstable
Loaded module hpe-mpi from unstable
Loaded module py-mpi4py from unstable
Loaded module petsc from unstable
Loaded module py-petsc4py from unstable
$ module list -t
Currently Loaded Modulefiles:
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.12.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.8.18
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.9.18
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.10.13
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.11.6
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/git/2.42.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/cmake/3.27.7
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/graphviz/8.0.5
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/compilers/linux-rhel7-haswell/gcc/12.3.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/py-mpi4py/3.1.4
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/petsc/3.20.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/py-petsc4py/3.20.1
$ export XDG_CONFIG_HOME=${PWD}/local_config
$ print_var XDG_CONFIG_HOME
XDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/local_config
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
  insteadOf = https://bbpgitlab.epfl.ch/
  insteadOf = ssh://git@bbpgitlab.epfl.ch/
  insteadOf = git@bbpgitlab.epfl.ch:
$ section_start section_venv[collapsed=true] "Setting up the virtual env"
section_start:1710424076:section_venv[collapsed=true]
Setting up the virtual env
$ cd "${PYTHON_PROJECT_DIR}"
$ CI_VENV="$(pwd)/venv"
$ rm -rf "$CI_VENV"
$ python -mvenv "$CI_VENV"
$ source "$CI_VENV/bin/activate"
$ python -mpip install --upgrade pip setuptools wheel
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1)
Collecting pip
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB)
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Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 23.2.1
    Uninstalling pip-23.2.1:
      Successfully uninstalled pip-23.2.1
Successfully installed pip-24.0 setuptools-69.2.0 wheel-0.43.0
$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Collecting tox
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Collecting chardet>=5.2 (from tox)
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Collecting filelock>=3.13.1 (from tox)
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Collecting packaging>=23.2 (from tox)
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Collecting pluggy>=1.3 (from tox)
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Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox
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$ section_end section_venv
section_end:1710424095:section_venv

$ print_var PRE_BUILD_COMMAND
PRE_BUILD_COMMAND=
$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi
$ section_start section_tox "Running Tox"
section_start:1710424095:section_tox
Running Tox
$ python -mtox $TOX_OPTIONS
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/venv/lib/python3.11/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/J1209079/molsys/AstroVascPy/venv/lib/python3.11/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/J1209079/molsys/AstroVascPy/venv/lib/python3.11/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==24.0,pip==24.0,setuptools==69.1.0,setuptools-scm==8.0.4,typing_extensions==4.10.0,wheel==0.42.0
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
docs: install_package_deps> python -I -m pip install cached-property click coverage cython h5py libsonata m2r2 matplotlib morphio networkx numpy 'pandas<2.0.0' psutil pyyaml scipy seaborn sphinx sphinx-bluebrain-theme sphinx-click tables tqdm trimesh vascpy
docs: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.1.4.tar.gz
docs: freeze> python -m pip freeze --all
docs: alabaster==0.7.16,AstroVascPy @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.1.4.tar.gz#sha256=045c3342538f81b93bd219fd94f3dde69f6747a9ec3dc58c924d14906e3be118,Babel==2.14.0,blosc2==2.5.1,cached-property==1.5.2,certifi==2024.2.2,charset-normalizer==3.3.2,click==8.1.7,contourpy==1.2.0,coverage==7.4.3,cycler==0.12.1,Cython==3.0.9,docutils==0.20.1,fonttools==4.49.0,h5py==3.10.0,idna==3.6,imagesize==1.4.1,Jinja2==3.1.3,kiwisolver==1.4.5,libsonata==0.1.25,m2r2==0.3.3.post2,MarkupSafe==2.1.5,matplotlib==3.8.3,mistune==0.8.4,MorphIO==3.3.7,mpi4py @ file:///nvme/bbpcihpcdeploy/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,msgpack==1.0.8,ndindex==1.8,networkx==3.2.1,numexpr==2.9.0,numpy @ file:///nvme/bbpcihpcdeploy/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,packaging==24.0,pandas==1.5.3,petsc4py @ file:///nvme/bbpcihpcdeploy/1998222/spack-stage/spack-stage-py-petsc4py-3.20.1-jootwwazqwscmwl7nyiqksdarrzdveu5/spack-src,pillow==10.2.0,pip==24.0,psutil==5.9.8,py-cpuinfo==9.0.0,Pygments==2.17.2,pyparsing==3.1.2,python-dateutil==2.9.0.post0,pytz==2024.1,PyYAML==6.0.1,requests==2.31.0,scipy==1.12.0,seaborn==0.13.2,setuptools==69.1.0,six==1.16.0,snowballstemmer==2.2.0,Sphinx==7.2.6,sphinx-bluebrain-theme==0.4.4,sphinx-click==5.1.0,sphinxcontrib-applehelp==1.0.8,sphinxcontrib-devhelp==1.0.6,sphinxcontrib-htmlhelp==2.0.5,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==1.0.7,sphinxcontrib-serializinghtml==1.1.10,tables==3.9.2,tqdm==4.66.2,trimesh==4.2.0,urllib3==2.2.1,vascpy==0.1.1,wheel==0.42.0
docs: commands[0] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/docs> make html
# Generate the documentation
Running Sphinx v7.2.6
making output directory... done
[autosummary] generating autosummary for: api_ref.rst, changelog.rst, index.rst
WARNING: [autosummary] failed to import astrovascpy.vtk_io.
Possible hints:
* AttributeError: module 'astrovascpy' has no attribute 'vtk_io'
* ModuleNotFoundError: No module named 'vtk'
* ImportError: 
[autosummary] generating autosummary for: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/docs/source/generated/astrovascpy.PetscBinaryIO.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/docs/source/generated/astrovascpy.bloodflow.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/docs/source/generated/astrovascpy.exceptions.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/docs/source/generated/astrovascpy.io.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/docs/source/generated/astrovascpy.ou.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/docs/source/generated/astrovascpy.plotting.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/docs/source/generated/astrovascpy.report_reader.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/docs/source/generated/astrovascpy.report_writer.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/docs/source/generated/astrovascpy.scipy_petsc_conversions.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/docs/source/generated/astrovascpy.utils.rst
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 3 source files that are out of date
updating environment: [new config] 13 added, 0 changed, 0 removed
reading sources... [  8%] api_ref
reading sources... [ 15%] changelog
reading sources... [ 23%] generated/astrovascpy.PetscBinaryIO
reading sources... [ 31%] generated/astrovascpy.bloodflow
reading sources... [ 38%] generated/astrovascpy.exceptions
reading sources... [ 46%] generated/astrovascpy.io
reading sources... [ 54%] generated/astrovascpy.ou
reading sources... [ 62%] generated/astrovascpy.plotting
reading sources... [ 69%] generated/astrovascpy.report_reader
reading sources... [ 77%] generated/astrovascpy.report_writer
reading sources... [ 85%] generated/astrovascpy.scipy_petsc_conversions
reading sources... [ 92%] generated/astrovascpy.utils
reading sources... [100%] index
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/docs/source/api_ref.rst:6: WARNING: autosummary: failed to import astrovascpy.vtk_io.
Possible hints:
* AttributeError: module 'astrovascpy' has no attribute 'vtk_io'
* ModuleNotFoundError: No module named 'vtk'
* ImportError: 
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:5: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:21: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.readIS:3: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.readMatDense:3: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.readVec:3: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.writeBinaryFile:8: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.writeIS:3: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.writeMatSparse:3: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.writeVec:3: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/bloodflow.py:docstring of astrovascpy.bloodflow:5: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/exceptions.py:docstring of astrovascpy.exceptions:5: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/io.py:docstring of astrovascpy.io:5: ERROR: Unexpected indentation.
looking for now-outdated files... none found
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/ou.py:docstring of astrovascpy.ou:5: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/ou.py:docstring of astrovascpy.ou.expected_time:5: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/plotting.py:docstring of astrovascpy.plotting:5: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/report_reader.py:docstring of astrovascpy.report_reader:11: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/report_reader.py:docstring of astrovascpy.report_reader:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/report_writer.py:docstring of astrovascpy.report_writer:6: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/site-packages/astrovascpy/utils.py:docstring of astrovascpy.utils:5: ERROR: Unexpected indentation.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.tox/docs/lib/python3.11/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/J1209079/molsys/AstroVascPy/docs/source/index.rst:8: WARNING: toctree contains reference to nonexisting document 'installation'
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/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/J1209079/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/J1209079/molsys/AstroVascPy/docs/source/api_ref.rst: WARNING: document isn't included in any toctree
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/docs/source/changelog.rst: WARNING: document isn't included in any toctree
checking consistency... done
preparing documents... done
copying assets... copying static files... done
copying extra files... done
done
writing output... [  8%] api_ref
writing output... [ 15%] changelog
writing output... [ 23%] generated/astrovascpy.PetscBinaryIO
writing output... [ 31%] generated/astrovascpy.bloodflow
writing output... [ 38%] generated/astrovascpy.exceptions
writing output... [ 46%] generated/astrovascpy.io
writing output... [ 54%] generated/astrovascpy.ou
writing output... [ 62%] generated/astrovascpy.plotting
writing output... [ 69%] generated/astrovascpy.report_reader
writing output... [ 77%] generated/astrovascpy.report_writer
writing output... [ 85%] generated/astrovascpy.scipy_petsc_conversions
writing output... [ 92%] generated/astrovascpy.utils
writing output... [100%] index
generating indices... genindex py-modindex done
writing additional pages... search done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 43 warnings.

The HTML pages are in build/html.
  docs: OK (101.79=setup[90.71]+cmd[11.08] seconds)
  congratulations :) (101.90 seconds)
$ section_end section_tox
section_end:1710424197:section_tox

section_end:1710424198:step_script
section_start:1710424198:upload_artifacts_on_success
Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform                                    arch=amd64 os=linux pid=31560 revision=58ba2b95 version=14.2.0
WARNING: ./doc/build/: no matching files           
./docs/build/: found 164 matching files and directories 
Uploading artifacts as "archive" to coordinator... ok  id=1209079 responseStatus=201 Created token=64_tLnCx
section_end:1710424200:upload_artifacts_on_success
section_start:1710424200:cleanup_file_variables
Cleaning up project directory and file based variables
Using git from spack modules
section_end:1710424202:cleanup_file_variables
Job succeeded

GitLab logs for bluebrain-astrovascpy#27

!

lint.txt

Running with gitlab-runner 15.5.0 (0d4137b8)
  on BB5 map runner pnPo3yJy
section_start:1710424047:resolve_secrets
Resolving secrets
section_end:1710424047:resolve_secrets
section_start:1710424047:prepare_executor
Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user 
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor2075428907, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root molsys, project name AstroVascPy
Pipeline ID 200493, build ref , job ID 1209078
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1209078, 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_J1209078_PROD_P2342_CP1_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 2083944
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J1209078_PROD_P2342_CP1_C3 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1209078 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1209078 --ntasks=1 --jobid=2083944 --cpus-per-task=6 --mem=30750M     
section_end:1710424048:prepare_executor
section_start:1710424048:prepare_script
Preparing environment
Using git from spack modules
Running on r1i4n18 via bbpv1.epfl.ch...
section_end:1710424064:prepare_script
section_start:1710424064:get_sources
Getting source from Git repository
Using git from spack modules
$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'
Fetching changes with git depth set to 20...
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209078/molsys/AstroVascPy/.git/
Created fresh repository.
Checking out c48174de as tristan/mpi4py...
Skipping object checkout, Git LFS is not installed.

Updating/initializing submodules recursively with git depth set to 20...
section_end:1710424071:get_sources
section_start:1710424071:step_script
Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi
$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }
$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }
$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }
$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }
$ module purge
$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')
$ module load unstable python/3.12.0
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.12.0
$ module load unstable python/3.8.18
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.8.18
$ module load unstable python/3.9.18
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.9.18
$ module load unstable python/3.10.13
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.10.13
$ module load unstable python/3.11.6
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.11.6
$ load-modules() { # collapsed multi-line command
$ load-modules $SYSTEM_MODULES
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
$ load-modules $EXTRA_MODULES
Loaded module gcc from unstable
Loaded module hpe-mpi from unstable
Loaded module py-mpi4py from unstable
Loaded module petsc from unstable
Loaded module py-petsc4py from unstable
$ module list -t
Currently Loaded Modulefiles:
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.12.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.8.18
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.9.18
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.10.13
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.11.6
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/git/2.42.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/cmake/3.27.7
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/graphviz/8.0.5
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/compilers/linux-rhel7-haswell/gcc/12.3.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/py-mpi4py/3.1.4
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/petsc/3.20.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/py-petsc4py/3.20.1
$ export XDG_CONFIG_HOME=${PWD}/local_config
$ print_var XDG_CONFIG_HOME
XDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209078/molsys/AstroVascPy/local_config
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
  insteadOf = https://bbpgitlab.epfl.ch/
  insteadOf = ssh://git@bbpgitlab.epfl.ch/
  insteadOf = git@bbpgitlab.epfl.ch:
$ section_start section_venv[collapsed=true] "Setting up the virtual env"
section_start:1710424079:section_venv[collapsed=true]
Setting up the virtual env
$ cd "${PYTHON_PROJECT_DIR}"
$ CI_VENV="$(pwd)/venv"
$ rm -rf "$CI_VENV"
$ python -mvenv "$CI_VENV"
$ source "$CI_VENV/bin/activate"
$ python -mpip install --upgrade pip setuptools wheel
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1)
Collecting pip
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 76.5 MB/s eta 0:00:00
Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0)
Collecting setuptools
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c21/c49fb1042386d/setuptools-69.2.0-py3-none-any.whl (821 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 821.5/821.5 kB 267.1 MB/s eta 0:00:00
Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 65.8/65.8 kB 223.3 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 23.2.1
    Uninstalling pip-23.2.1:
      Successfully uninstalled pip-23.2.1
Successfully installed pip-24.0 setuptools-69.2.0 wheel-0.43.0
$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Collecting tox
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b03/754b6ee6dadc7/tox-4.14.1-py3-none-any.whl (155 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.3/155.3 kB 18.8 MB/s eta 0:00:00
Collecting cachetools>=5.3.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 kB)
Collecting chardet>=5.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 199.4/199.4 kB 53.3 MB/s eta 0:00:00
Collecting colorama>=0.4.6 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting filelock>=3.13.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/57d/bda9b35157b05/filelock-3.13.1-py3-none-any.whl (11 kB)
Collecting packaging>=23.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.5/53.5 kB 235.1 MB/s eta 0:00:00
Collecting platformdirs>=4.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/061/4df2a2f37e1a6/platformdirs-4.2.0-py3-none-any.whl (17 kB)
Collecting pluggy>=1.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7db/9f7b503d67d1c/pluggy-1.4.0-py3-none-any.whl (20 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 virtualenv>=20.25 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/961/c026ac520bac5/virtualenv-20.25.1-py3-none-any.whl (3.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.8/3.8 MB 95.1 MB/s eta 0:00:00
Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 468.9/468.9 kB 270.9 MB/s eta 0:00:00
Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox
Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-24.0 platformdirs-4.2.0 pluggy-1.4.0 pyproject-api-1.6.1 tox-4.14.1 virtualenv-20.25.1
$ section_end section_venv
section_end:1710424095:section_venv

$ print_var PRE_BUILD_COMMAND
PRE_BUILD_COMMAND=
$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi
$ section_start section_tox "Running Tox"
section_start:1710424095:section_tox
Running Tox
$ python -mtox $TOX_OPTIONS
lint: install_deps> python -I -m pip install pre-commit pylint pylint-exit
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209078/molsys/AstroVascPy/venv/lib/python3.11/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/J1209078/molsys/AstroVascPy/venv/lib/python3.11/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/J1209078/molsys/AstroVascPy/venv/lib/python3.11/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==24.0,pip==24.0,setuptools==69.1.0,setuptools-scm==8.0.4,typing_extensions==4.10.0,wheel==0.42.0
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209078/molsys/AstroVascPy/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209078/molsys/AstroVascPy/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
lint: install_package_deps> python -I -m pip install cached-property click coverage cython h5py libsonata matplotlib morphio networkx numpy 'pandas<2.0.0' psutil pytest pytest-mpi pyyaml scipy seaborn tables tqdm trimesh vascpy
lint: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209078/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.1.4.tar.gz
lint: freeze> python -m pip freeze --all
lint: astroid==3.1.0,AstroVascPy @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209078/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.1.4.tar.gz#sha256=4af3c2ee0f834ce3d61292dac5688b731869e6c42621ce0fecb0ede249ebb0e2,blosc2==2.5.1,cached-property==1.5.2,cfgv==3.4.0,click==8.1.7,contourpy==1.2.0,coverage==7.4.3,cycler==0.12.1,Cython==3.0.9,dill==0.3.8,distlib==0.3.8,filelock==3.13.1,fonttools==4.49.0,h5py==3.10.0,identify==2.5.35,iniconfig==2.0.0,isort==5.13.2,kiwisolver==1.4.5,libsonata==0.1.25,matplotlib==3.8.3,mccabe==0.7.0,MorphIO==3.3.7,mpi4py @ file:///nvme/bbpcihpcdeploy/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,msgpack==1.0.8,ndindex==1.8,networkx==3.2.1,nodeenv==1.8.0,numexpr==2.9.0,numpy @ file:///nvme/bbpcihpcdeploy/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,packaging==24.0,pandas==1.5.3,petsc4py @ file:///nvme/bbpcihpcdeploy/1998222/spack-stage/spack-stage-py-petsc4py-3.20.1-jootwwazqwscmwl7nyiqksdarrzdveu5/spack-src,pillow==10.2.0,pip==24.0,platformdirs==4.2.0,pluggy==1.4.0,pre-commit==3.6.2,psutil==5.9.8,py-cpuinfo==9.0.0,pylint==3.1.0,pylint-exit==1.2.0,pyparsing==3.1.2,pytest==8.1.1,pytest-mpi==0.6,python-dateutil==2.9.0.post0,pytz==2024.1,PyYAML==6.0.1,scipy==1.12.0,seaborn==0.13.2,setuptools==69.1.0,six==1.16.0,tables==3.9.2,tomlkit==0.12.4,tqdm==4.66.2,trimesh==4.2.0,vascpy==0.1.1,virtualenv==20.25.1,wheel==0.42.0
lint: commands[0]> pre-commit run --all-files --show-diff-on-failure
[INFO] Initializing environment for https://github.com/pre-commit/pre-commit-hooks.
[INFO] Initializing environment for https://github.com/alessandrojcm/commitlint-pre-commit-hook.
[INFO] Initializing environment for https://github.com/alessandrojcm/commitlint-pre-commit-hook:conventional-changelog-conventionalcommits.
[INFO] Initializing environment for https://github.com/pycqa/isort.
[INFO] Initializing environment for https://github.com/psf/black.
[INFO] Initializing environment for https://github.com/codespell-project/codespell.
[INFO] Initializing environment for https://github.com/PyCQA/flake8.
[INFO] Installing environment for https://github.com/pre-commit/pre-commit-hooks.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/pycqa/isort.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/psf/black.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/codespell-project/codespell.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/PyCQA/flake8.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
check for added large files..............................................Passed
check for case conflicts.................................................Passed
check for merge conflicts................................................Passed
check for broken symlinks............................(no files to check)Skipped
check yaml...............................................................Passed
debug statements (python)................................................Passed
fix end of files.........................................................Passed
trim trailing whitespace.................................................Passed
isort....................................................................Passed
black....................................................................Passed
codespell................................................................Passed
flake8...................................................................Passed
lint: commands[1]> bash -c 'pylint -j 1 astrovascpy docs/source/conf.py setup.py || pylint-exit $?'
************* Module astrovascpy.io
astrovascpy/io.py:60:26: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
************* Module astrovascpy.utils
astrovascpy/utils.py:52:4: C0415: Import outside toplevel (mpi4py.MPI) (import-outside-toplevel)
astrovascpy/utils.py:114:20: W0212: Access to a protected member _node_properties of a client class (protected-access)
astrovascpy/utils.py:115:20: W0212: Access to a protected member _edge_properties of a client class (protected-access)
astrovascpy/utils.py:598:15: R1735: Consider using '{}' instead of a call to 'dict'. (use-dict-literal)
astrovascpy/utils.py:601:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/utils.py:601:4: E0213: Method 'region' should have "self" as first argument (no-self-argument)
astrovascpy/utils.py:612:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/utils.py:640:8: C0206: Consider iterating with .items() (consider-using-dict-items)
astrovascpy/utils.py:665:11: R1735: Consider using '{}' instead of a call to 'dict'. (use-dict-literal)
astrovascpy/utils.py:668:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/utils.py:668:4: E0213: Method 'region' should have "self" as first argument (no-self-argument)
astrovascpy/utils.py:680:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/utils.py:707:8: C0206: Consider iterating with .items() (consider-using-dict-items)
astrovascpy/utils.py:718:15: W0126: Using a conditional statement with potentially wrong function or method call due to missing parentheses (missing-parentheses-for-call-in-test)
astrovascpy/utils.py:718:15: W0125: Using a conditional statement with a constant value (using-constant-test)
astrovascpy/utils.py:723:11: W0126: Using a conditional statement with potentially wrong function or method call due to missing parentheses (missing-parentheses-for-call-in-test)
astrovascpy/utils.py:723:11: W0125: Using a conditional statement with a constant value (using-constant-test)
astrovascpy/utils.py:782:8: W0621: Redefining name 'time' from outer scope (line 17) (redefined-outer-name)
************* Module astrovascpy.scipy_petsc_conversions
astrovascpy/scipy_petsc_conversions.py:36:15: W0212: Access to a protected member _typedict of a client class (protected-access)
astrovascpy/scipy_petsc_conversions.py:131:8: W0632: Possible unbalanced tuple unpacking with sequence defined at line 538 of astrovascpy.PetscBinaryIO: left side has 1 label, right side has 0 values (unbalanced-tuple-unpacking)
************* Module astrovascpy.PetscBinaryIO
astrovascpy/PetscBinaryIO.py:73:20: W0707: Consider explicitly re-raising using 'except Exception as exc' and 'raise importlib.metadata.PackageNotFoundError from exc' (raise-missing-from)
astrovascpy/PetscBinaryIO.py:78:27: W0212: Access to a protected member _path of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:109:14: W1514: Using open without explicitly specifying an encoding (unspecified-encoding)
astrovascpy/PetscBinaryIO.py:109:14: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
astrovascpy/PetscBinaryIO.py:121:14: W1514: Using open without explicitly specifying an encoding (unspecified-encoding)
astrovascpy/PetscBinaryIO.py:46:0: R0912: Too many branches (23/12) (too-many-branches)
astrovascpy/PetscBinaryIO.py:46:0: R0915: Too many statements (55/50) (too-many-statements)
astrovascpy/PetscBinaryIO.py:121:14: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
astrovascpy/PetscBinaryIO.py:203:12: W0212: Access to a protected member _update_dtypes of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:211:12: W0212: Access to a protected member _update_dtypes of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:218:0: C0115: Missing class docstring (missing-class-docstring)
astrovascpy/PetscBinaryIO.py:257:15: C0209: Formatting a regular string which could be an f-string (consider-using-f-string)
astrovascpy/PetscBinaryIO.py:257:33: R1725: Consider using Python 3 style super() without arguments (super-with-arguments)
astrovascpy/PetscBinaryIO.py:272:0: R0205: Class 'PetscBinaryIO' inherits from object, can be safely removed from bases in python3 (useless-object-inheritance)
astrovascpy/PetscBinaryIO.py:330:27: C0209: Formatting a regular string which could be an f-string (consider-using-f-string)
astrovascpy/PetscBinaryIO.py:340:12: 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:349:29: W0212: Access to a protected member _classid of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:346:4: R1711: Useless return at end of function or method (useless-return)
astrovascpy/PetscBinaryIO.py:381:12: 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:390:29: W0212: Access to a protected member _classid of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:386:4: R1711: Useless return at end of function or method (useless-return)
astrovascpy/PetscBinaryIO.py:421:12: 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:430:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/PetscBinaryIO.py:435:4: C0116: Missing function or method docstring (missing-function-docstring)
astrovascpy/PetscBinaryIO.py:439:8: W0612: Unused variable 'V' (unused-variable)
astrovascpy/PetscBinaryIO.py:440:8: W0612: Unused variable 'M' (unused-variable)
astrovascpy/PetscBinaryIO.py:440:11: W0612: Unused variable 'N' (unused-variable)
astrovascpy/PetscBinaryIO.py:441:8: W0612: Unused variable 'J' (unused-variable)
astrovascpy/PetscBinaryIO.py:442:8: W0612: Unused variable 'I' (unused-variable)
astrovascpy/PetscBinaryIO.py:472:12: 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:479:29: W0212: Access to a protected member _classid of a client class (protected-access)
astrovascpy/PetscBinaryIO.py:476:4: R1711: Useless return at end of function or method (useless-return)
astrovascpy/PetscBinaryIO.py:516:20: W0707: Consider explicitly re-raising using 'except (MemoryError, IndexError) as exc' and 'raise DoneWithFile from exc' (raise-missing-from)
astrovascpy/PetscBinaryIO.py:520:20: 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:506:18: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
astrovascpy/PetscBinaryIO.py:573:20: 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:573:36: C0209: Formatting a regular string which could be an f-string (consider-using-f-string)
astrovascpy/PetscBinaryIO.py:573:79: C2801: Unnecessarily calls dunder method __repr__. Use repr built-in function. (unnecessary-dunder-call)
astrovascpy/PetscBinaryIO.py:541:4: R1711: Useless return at end of function or method (useless-return)
astrovascpy/PetscBinaryIO.py:553:18: R1732: Consider using 'with' for resource-allocating operations (consider-using-with)
************* Module astrovascpy.bloodflow
astrovascpy/bloodflow.py:50:0: W0622: Redefining built-in 'print' (redefined-builtin)
astrovascpy/bloodflow.py:426:0: R0914: Too many local variables (34/25) (too-many-locals)
astrovascpy/bloodflow.py:426:0: R0912: Too many branches (17/12) (too-many-branches)
astrovascpy/bloodflow.py:426:0: R0915: Too many statements (68/50) (too-many-statements)
astrovascpy/bloodflow.py:704:34: C0209: Formatting a regular string which could be an f-string (consider-using-f-string)
astrovascpy/bloodflow.py:771:12: W1203: Use lazy % formatting in logging functions (logging-fstring-interpolation)
astrovascpy/bloodflow.py:643:0: R0912: Too many branches (20/12) (too-many-branches)
astrovascpy/bloodflow.py:643:0: R0915: Too many statements (89/50) (too-many-statements)
************* Module astrovascpy.typing
astrovascpy/typing.py:20:0: C0115: Missing class docstring (missing-class-docstring)
astrovascpy/typing.py:26:0: C0115: Missing class docstring (missing-class-docstring)

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

The following messages were raised:

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

No fatal messages detected.  Exiting gracefully...
  lint: OK (162.76=setup[83.95]+cmd[45.37,33.45] seconds)
  congratulations :) (162.87 seconds)
$ section_end section_tox
section_end:1710424258:section_tox

section_end:1710424259:step_script
section_start:1710424259:cleanup_file_variables
Cleaning up project directory and file based variables
Using git from spack modules
section_end:1710424261:cleanup_file_variables
Job succeeded

py311.txt

Running with gitlab-runner 15.5.0 (0d4137b8)
  on BB5 map runner pnPo3yJy
section_start:1710424048:resolve_secrets
Resolving secrets
section_end:1710424048:resolve_secrets
section_start:1710424048:prepare_executor
Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user 
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor1454942258, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root molsys, project name AstroVascPy
Pipeline ID 200493, build ref , job ID 1209080
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1209080, 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_J1209080_PROD_P2342_CP3_C5
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 2083946
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_J1209080_PROD_P2342_CP3_C5 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1209080 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1209080 --ntasks=1 --jobid=2083946 --cpus-per-task=6 --mem=30750M     
section_end:1710424052:prepare_executor
section_start:1710424052:prepare_script
Preparing environment
Using git from spack modules
Running on r1i4n18 via bbpv1.epfl.ch...
section_end:1710424060:prepare_script
section_start:1710424060:get_sources
Getting source from Git repository
Using git from spack modules
$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'
Fetching changes with git depth set to 20...
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/.git/
Created fresh repository.
Checking out c48174de as tristan/mpi4py...
Skipping object checkout, Git LFS is not installed.

Updating/initializing submodules recursively with git depth set to 20...
section_end:1710424069:get_sources
section_start:1710424069:step_script
Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi
$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }
$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }
$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }
$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }
$ module purge
$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')
$ module load unstable python/3.12.0
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.12.0
$ module load unstable python/3.8.18
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.8.18
$ module load unstable python/3.9.18
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.9.18
$ module load unstable python/3.10.13
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.10.13
$ module load unstable python/3.11.6
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.11.6
$ load-modules() { # collapsed multi-line command
$ load-modules $SYSTEM_MODULES
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
$ load-modules $EXTRA_MODULES
Loaded module gcc from unstable
Loaded module hpe-mpi from unstable
Loaded module py-mpi4py from unstable
Loaded module petsc from unstable
Loaded module py-petsc4py from unstable
$ module list -t
Currently Loaded Modulefiles:
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.12.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.8.18
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.9.18
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.10.13
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.11.6
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/git/2.42.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/cmake/3.27.7
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/graphviz/8.0.5
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/compilers/linux-rhel7-haswell/gcc/12.3.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/py-mpi4py/3.1.4
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/petsc/3.20.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/py-petsc4py/3.20.1
$ export XDG_CONFIG_HOME=${PWD}/local_config
$ print_var XDG_CONFIG_HOME
XDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/local_config
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
  insteadOf = https://bbpgitlab.epfl.ch/
  insteadOf = ssh://git@bbpgitlab.epfl.ch/
  insteadOf = git@bbpgitlab.epfl.ch:
$ section_start section_venv[collapsed=true] "Setting up the virtual env"
section_start:1710424076:section_venv[collapsed=true]
Setting up the virtual env
$ cd "${PYTHON_PROJECT_DIR}"
$ CI_VENV="$(pwd)/venv"
$ rm -rf "$CI_VENV"
$ python -mvenv "$CI_VENV"
$ source "$CI_VENV/bin/activate"
$ python -mpip install --upgrade pip setuptools wheel
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1)
Collecting pip
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 74.8 MB/s eta 0:00:00
Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0)
Collecting setuptools
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c21/c49fb1042386d/setuptools-69.2.0-py3-none-any.whl (821 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 821.5/821.5 kB 79.9 MB/s eta 0:00:00
Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 65.8/65.8 kB 218.8 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
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      Successfully uninstalled setuptools-65.5.0
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    Uninstalling pip-23.2.1:
      Successfully uninstalled pip-23.2.1
Successfully installed pip-24.0 setuptools-69.2.0 wheel-0.43.0
$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
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$ section_end section_venv
section_end:1710424095:section_venv

$ print_var PRE_BUILD_COMMAND
PRE_BUILD_COMMAND=
$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi
$ section_start section_tox "Running Tox"
section_start:1710424095:section_tox
Running Tox
$ python -mtox $TOX_OPTIONS
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/venv/lib/python3.11/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/J1209080/molsys/AstroVascPy/venv/lib/python3.11/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/J1209080/molsys/AstroVascPy/venv/lib/python3.11/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==24.0,pip==24.0,setuptools==69.1.0,setuptools-scm==8.0.4,typing_extensions==4.10.0,wheel==0.42.0
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
py311: 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
py311: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.1.4.tar.gz
py311: freeze> python -m pip freeze --all
py311: AstroVascPy @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.1.4.tar.gz#sha256=d434b38593efeb806213ffe902194eb8b149ed9467aad0d11828eb7da6d59039,blosc2==2.5.1,cached-property==1.5.2,click==8.1.7,contourpy==1.2.0,coverage==7.4.3,cycler==0.12.1,Cython==3.0.9,fonttools==4.49.0,h5py==3.10.0,iniconfig==2.0.0,kiwisolver==1.4.5,libsonata==0.1.25,matplotlib==3.8.3,MorphIO==3.3.7,mpi4py @ file:///nvme/bbpcihpcdeploy/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,msgpack==1.0.8,ndindex==1.8,networkx==3.2.1,numexpr==2.9.0,numpy @ file:///nvme/bbpcihpcdeploy/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,packaging==24.0,pandas==1.5.3,petsc4py @ file:///nvme/bbpcihpcdeploy/1998222/spack-stage/spack-stage-py-petsc4py-3.20.1-jootwwazqwscmwl7nyiqksdarrzdveu5/spack-src,pillow==10.2.0,pip==24.0,pluggy==1.4.0,psutil==5.9.8,py-cpuinfo==9.0.0,pyparsing==3.1.2,pytest==8.1.1,pytest-mpi==0.6,python-dateutil==2.9.0.post0,pytz==2024.1,PyYAML==6.0.1,scipy==1.12.0,seaborn==0.13.2,setuptools==69.1.0,six==1.16.0,tables==3.9.2,tqdm==4.66.2,trimesh==4.2.0,vascpy==0.1.1,wheel==0.42.0
py311: commands[0]> coverage run --branch --source=astrovascpy -m pytest --basetemp=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/.tox/py311/tmp --verbose --junit-xml=reports/pytest-py311.xml
============================= test session starts ==============================
platform linux -- Python 3.11.6, pytest-8.1.1, pluggy-1.4.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/.tox/py311/bin/python
cachedir: .tox/py311/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy
configfile: pyproject.toml
testpaths: tests
plugins: mpi-0.6
collecting ... collected 57 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                   [ 15%]
tests/test_bloodflow.py::test_simulate_vasodilation_ou_process PASSED    [ 17%]
tests/test_bloodflow.py::test_simulate_ou_process FAILED                 [ 19%]
tests/test_bloodflow.py::test_depth_first_search PASSED                  [ 21%]
tests/test_bloodflow.py::test_compute_static_laplacian PASSED            [ 22%]
tests/test_bloodflow.py::test_update_static_flow_pressure FAILED         [ 24%]
tests/test_bloodflow.py::test_total_flow_conservation_in_graph FAILED    [ 26%]
tests/test_bloodflow.py::test_conservation_flow FAILED                   [ 28%]
tests/test_bloodflow.py::test_static_construct_incidence_matrix PASSED   [ 29%]
tests/test_bloodflow.py::test_solve_linear PASSED                        [ 31%]
tests/test_bloodflow.py::test_boundary_flows_A_based PASSED              [ 33%]
tests/test_graphs.py::test_simple_graph FAILED                           [ 35%]
tests/test_graphs.py::test_bifurcation FAILED                            [ 36%]
tests/test_graphs.py::test_loop FAILED                                   [ 38%]
tests/test_io.py::test_petsc_installation PASSED                         [ 40%]
tests/test_io.py::test_load_graph PASSED                                 [ 42%]
tests/test_io.py::test_load_graph_from_h5 PASSED                         [ 43%]
tests/test_io.py::test_load_graph_from_csv PASSED                        [ 45%]
tests/test_io.py::test_load_graph_from_bin PASSED                        [ 47%]
tests/test_mpi.py::test_distribute_array SKIPPED (need --with-mpi op...) [ 49%]
tests/test_mpi.py::test_numpy_array2petsc SKIPPED (need --with-mpi o...) [ 50%]
tests/test_mpi.py::test_scipy2petsc_conversion SKIPPED (need --with-...) [ 52%]
tests/test_mpi.py::test_coomatrix2PETScMat SKIPPED (need --with-mpi ...) [ 54%]
tests/test_ou.py::test_OU_calibration PASSED                             [ 56%]
tests/test_report_reader.py::TestBloodflowReport::test_time_units PASSED [ 57%]
tests/test_report_reader.py::TestBloodflowReport::test_data_units PASSED [ 59%]
tests/test_report_reader.py::TestBloodflowReport::test_population_names PASSED [ 61%]
tests/test_report_reader.py::TestBloodflowReport::test_get_population PASSED [ 63%]
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 [ 68%]
tests/test_report_reader.py::TestPopulationBloodflowReport::test_get PASSED [ 70%]
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                          [ 77%]
tests/test_utils.py::test_find_degrees_of_neighbors PASSED               [ 78%]
tests/test_utils.py::test_create_entry_largest_nodes FAILED              [ 80%]
tests/test_utils.py::test_get_largest_nodes PASSED                       [ 82%]
tests/test_utils.py::test_get_large_nodes PASSED                         [ 84%]
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%]

=================================== FAILURES ===================================
___________________________ test_simulate_ou_process ___________________________

point_properties =    x  y  z  diameter
0  0  0  2         1
1  0  1  1         3
2  0  2  0         2
edge_properties =                        start_node  end_node  ...  endfeet_id    volume
section_id segment_id                        ..... ...          -1  4.442883
           1                    1         2  ...           1  6.942005

[2 rows x 8 columns]
params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}

    def test_simulate_ou_process(point_properties, edge_properties, params):
        graph = utils.Graph(point_properties, edge_properties)
    
        dt = 0.01
        nb_iteration = 100
        entry_nodes = np.array([0])
        simulation_time = nb_iteration * dt
        relaxation_start = 1.0
        time_step = dt
        section_id = 0
        segment_id = 1
        endfoot_id = 1
        endfeet_length = 1.0
        entry_speed = [1] * nb_iteration
    
        tested.set_endfoot_id(graph, endfoot_id, section_id, segment_id, endfeet_length)
>       flows, pressures, radiii = tested.simulate_ou_process(
            graph, entry_nodes, simulation_time, relaxation_start, time_step, entry_speed, params
        )

tests/test_bloodflow.py:246: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
astrovascpy/bloodflow.py:612: in simulate_ou_process
    update_static_flow_pressure(graph, boundary_flow, params)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

graph = Graph(_node_properties=   x  y  z  diameter
0  0  0  2         1
1  0  1  1         3
2  0  2  0         2, _edge_prop......          -1  4.442883
           1                    1         2  ...           1  6.942005

[2 rows x 8 columns])
input_flow = array([ 3.14159265,  0.        , -3.14159265])
params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}
with_hematocrit = True

    def update_static_flow_pressure(
        graph: Graph,
        input_flow: npt.NDArray[np.float64],
        params: VasculatureParams,
        with_hematocrit: bool = True,
    ):
        """Compute the time-independent pressure and flow.
    
        Args:
            graph (utils.Graph): graph containing point vasculature skeleton.
            input_flow(numpy.array): input flow for each graph node.
            params (dict): general parameters for vasculature.
            with_hematocrit (bool): consider hematrocrit for resistance model
    
        Concerns: This function is part of the public API. Any change of signature
        or functional behavior may be done thoroughly.
    
        """
    
        if graph is not None:
            if not isinstance(graph, Graph):
                raise BloodFlowError("'graph' parameter must be an instance of Graph")
            for param in VasculatureParams.__annotations__:
                if param not in params:
>                   raise BloodFlowError(f"Missing parameter '{param}'")
E                   astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'

astrovascpy/bloodflow.py:107: BloodFlowError
----------------------------- Captured stdout call -----------------------------
-> simulate_vasodilation_ou_process
kappa for capillaries:  9.465822125149598
kappa for arteries:  None
----------------------------- Captured stderr call -----------------------------

  0%|          | 0/100 [00:00<?, ?it/s]
  0%|          | 0/100 [00:00<?, ?it/s]
_______________________ test_update_static_flow_pressure _______________________

params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}

    def test_update_static_flow_pressure(params):
        point_properties = pd.DataFrame(
            {
                "x": [0, 0, 0, 0, 0, 0, 0, 0],
                "y": [0, 0, 0, 1, 1, 1, 0, 0],
                "z": [0, 1, 2, 0, 1, 2, 3, 4],
                "diameter": [10, 11, 9, 11, 4, 10, 5, 56],
            }
        )
    
        edge_properties = pd.DataFrame(
            {
                "start_node": [0, 1, 2, 3, 3, 6],
                "end_node": [1, 2, 3, 4, 5, 7],
                "type": [0, 0, 0, 0, 0, 0],
            },
            index=pd.MultiIndex.from_tuples(
                ([0, 0], [0, 1], [1, 0], [1, 1], [0, 2], [1, 2]),
                names=["section_id", "segment_id"],
            ),
        )
        graph = utils.Graph(point_properties, edge_properties)
        entry_nodes = [0]
        input_flow = len(entry_nodes) * [1.0]
        boundary_flow = tested.boundary_flows_A_based(graph, entry_nodes, input_flow)
>       tested.update_static_flow_pressure(graph, boundary_flow, params, with_hematocrit=True)

tests/test_bloodflow.py:410: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

graph = Graph(_node_properties=   x  y  z  diameter
0  0  0  0        10
1  0  0  1        11
2  0  0  2         9
3  0  1  0 ...         -1  173.180295
1          2                    6         7  ...          -1  730.616642

[6 rows x 8 columns])
input_flow = array([ 1.        ,  0.        ,  0.        ,  0.        , -0.13793103,
       -0.86206897,  0.        ,  0.        ])
params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}
with_hematocrit = True

    def update_static_flow_pressure(
        graph: Graph,
        input_flow: npt.NDArray[np.float64],
        params: VasculatureParams,
        with_hematocrit: bool = True,
    ):
        """Compute the time-independent pressure and flow.
    
        Args:
            graph (utils.Graph): graph containing point vasculature skeleton.
            input_flow(numpy.array): input flow for each graph node.
            params (dict): general parameters for vasculature.
            with_hematocrit (bool): consider hematrocrit for resistance model
    
        Concerns: This function is part of the public API. Any change of signature
        or functional behavior may be done thoroughly.
    
        """
    
        if graph is not None:
            if not isinstance(graph, Graph):
                raise BloodFlowError("'graph' parameter must be an instance of Graph")
            for param in VasculatureParams.__annotations__:
                if param not in params:
>                   raise BloodFlowError(f"Missing parameter '{param}'")
E                   astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'

astrovascpy/bloodflow.py:107: BloodFlowError
____________________ test_total_flow_conservation_in_graph _____________________

params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}

    def test_total_flow_conservation_in_graph(params):
        """Check the total conservation of the flow in a connected graph.
        Here we compute the boundary flows using the area based method.
        """
    
        TEST_DIR = Path(__file__).resolve().parent.parent
        graph_path_cc = TEST_DIR / "examples/data/graphs_folder/toy_graph.bin"
        filehandler = open(graph_path_cc, "rb")
        pv = pickle.load(filehandler)
        graph = utils.Graph.from_point_vasculature(pv)
    
        entry_nodes = [123, 144, 499]
        input_flows = [1] * len(entry_nodes)
    
        dropped_graph = graph.edge_properties.drop(columns=["section_id", "segment_id"]).reset_index()
        df_entry_nodes = dropped_graph[
            (dropped_graph["start_node"].isin(entry_nodes))
            | (dropped_graph["end_node"].isin(entry_nodes))
        ]
    
        transp_incidence = tested.construct_static_incidence_matrix(graph)
        incidence = transp_incidence.T
    
        boundary_flows = tested.boundary_flows_A_based(graph, entry_nodes, input_flows)
    
        npt.assert_allclose(
            np.sum(boundary_flows),
            0.0,
            rtol=1e-2,
            atol=1e-2,
        )
    
>       tested.update_static_flow_pressure(graph, boundary_flows, params, with_hematocrit=True)

tests/test_bloodflow.py:451: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

graph = Graph(_node_properties=        x     y     z  diameter
0    30.0  20.0  20.0  7.454232
1    25.0  25.0  25.0  5.932791...     -1  218.85156
583         523       584     1  ...       2.651218          -1  191.23671

[584 rows x 10 columns])
input_flow = array([-0.00896778,  0.        ,  0.        ,  0.        ,  0.        ,
        0.        , -0.00755749, -0.00517843, ...860054, -0.00542753, -0.00662743, -0.00854959,
       -0.0049437 , -0.0049061 , -0.00639652, -0.00573718, -0.00440165])
params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}
with_hematocrit = True

    def update_static_flow_pressure(
        graph: Graph,
        input_flow: npt.NDArray[np.float64],
        params: VasculatureParams,
        with_hematocrit: bool = True,
    ):
        """Compute the time-independent pressure and flow.
    
        Args:
            graph (utils.Graph): graph containing point vasculature skeleton.
            input_flow(numpy.array): input flow for each graph node.
            params (dict): general parameters for vasculature.
            with_hematocrit (bool): consider hematrocrit for resistance model
    
        Concerns: This function is part of the public API. Any change of signature
        or functional behavior may be done thoroughly.
    
        """
    
        if graph is not None:
            if not isinstance(graph, Graph):
                raise BloodFlowError("'graph' parameter must be an instance of Graph")
            for param in VasculatureParams.__annotations__:
                if param not in params:
>                   raise BloodFlowError(f"Missing parameter '{param}'")
E                   astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'

astrovascpy/bloodflow.py:107: BloodFlowError
____________________________ test_conservation_flow ____________________________

params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}

    def test_conservation_flow(params):
        point_properties = pd.DataFrame(
            {
                "x": [0, 0, 0, 0],
                "y": [0, 1, 2, 2],
                "z": [1, 1, 0, 2],
                "diameter": [7.0, 3.0, 10.0, 5.0],
            }
        )
    
        edge_properties = pd.DataFrame(
            {
                "start_node": [0, 1, 1],
                "end_node": [1, 2, 3],
                "type": [0, 0, 0],
            },
            index=pd.MultiIndex.from_tuples(
                ([0, 0], [1, 0], [2, 0]),
                names=["section_id", "segment_id"],
            ),
        )
        graph = utils.Graph(point_properties, edge_properties)
    
        entry_nodes = [0]
        input_flow = len(entry_nodes) * [1.0]
    
        boundary_flow = tested.boundary_flows_A_based(graph, entry_nodes, input_flow)
    
>       tested.update_static_flow_pressure(graph, boundary_flow, params)

tests/test_bloodflow.py:514: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

graph = Graph(_node_properties=   x  y  z  diameter
0  0  0  1       7.0
1  0  1  1       3.0
2  0  2  0      10.0
3  0  2  2 ....          -1  46.927951
2          0                    1         3  ...          -1  17.771532

[3 rows x 8 columns])
input_flow = array([ 1. ,  0. , -0.8, -0.2])
params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}
with_hematocrit = True

    def update_static_flow_pressure(
        graph: Graph,
        input_flow: npt.NDArray[np.float64],
        params: VasculatureParams,
        with_hematocrit: bool = True,
    ):
        """Compute the time-independent pressure and flow.
    
        Args:
            graph (utils.Graph): graph containing point vasculature skeleton.
            input_flow(numpy.array): input flow for each graph node.
            params (dict): general parameters for vasculature.
            with_hematocrit (bool): consider hematrocrit for resistance model
    
        Concerns: This function is part of the public API. Any change of signature
        or functional behavior may be done thoroughly.
    
        """
    
        if graph is not None:
            if not isinstance(graph, Graph):
                raise BloodFlowError("'graph' parameter must be an instance of Graph")
            for param in VasculatureParams.__annotations__:
                if param not in params:
>                   raise BloodFlowError(f"Missing parameter '{param}'")
E                   astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'

astrovascpy/bloodflow.py:107: BloodFlowError
______________________________ test_simple_graph _______________________________

params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}

    def test_simple_graph(params):
        point_properties = pd.DataFrame(
            {
                "x": [0, 0, 0, 0, 0],
                "y": [0, 1, 2, 3, 4],
                "z": [0, 0, 0, 0, 0],
                "diameter": [10, 9, 9, 8, 7],
            }
        )
        edge_properties = pd.DataFrame(
            {
                "start_node": [0, 1, 2, 3],
                "end_node": [1, 2, 3, 4],
                "type": [0, 0, 0, 0],
            },
            index=pd.MultiIndex.from_tuples(
                ([0, 0], [0, 1], [0, 2], [0, 3]),
                names=["section_id", "segment_id"],
            ),
        )
        graph = Graph(point_properties, edge_properties)
        entry_nodes = [0]
        input_flow = [1.0]
        boundary_flow = tested.boundary_flows_A_based(graph, entry_nodes, input_flow)
>       tested.update_static_flow_pressure(graph, boundary_flow, params)

tests/test_graphs.py:53: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

graph = Graph(_node_properties=   x  y  z  diameter
0  0  0  0        10
1  0  1  0         9
2  0  2  0         9
3  0  3  0 ....          -1  56.745017
           3                    3         4  ...          -1  44.178647

[4 rows x 8 columns])
input_flow = array([ 1.,  0.,  0.,  0., -1.])
params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}
with_hematocrit = True

    def update_static_flow_pressure(
        graph: Graph,
        input_flow: npt.NDArray[np.float64],
        params: VasculatureParams,
        with_hematocrit: bool = True,
    ):
        """Compute the time-independent pressure and flow.
    
        Args:
            graph (utils.Graph): graph containing point vasculature skeleton.
            input_flow(numpy.array): input flow for each graph node.
            params (dict): general parameters for vasculature.
            with_hematocrit (bool): consider hematrocrit for resistance model
    
        Concerns: This function is part of the public API. Any change of signature
        or functional behavior may be done thoroughly.
    
        """
    
        if graph is not None:
            if not isinstance(graph, Graph):
                raise BloodFlowError("'graph' parameter must be an instance of Graph")
            for param in VasculatureParams.__annotations__:
                if param not in params:
>                   raise BloodFlowError(f"Missing parameter '{param}'")
E                   astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'

astrovascpy/bloodflow.py:107: BloodFlowError
_______________________________ test_bifurcation _______________________________

params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}

    def test_bifurcation(params):
        point_properties = pd.DataFrame(
            {
                "x": [0, 0, 0, 0],
                "y": [0, 1, 2, 2],
                "z": [1, 1, 0, 2],
                "diameter": [12, 6, 10, 8],
            }
        )
    
        edge_properties = pd.DataFrame(
            {
                "start_node": [0, 1, 1],
                "end_node": [1, 2, 3],
                "type": [0, 0, 0],
            },
            index=pd.MultiIndex.from_tuples(
                ([0, 0], [0, 1], [0, 2]),
                names=["section_id", "segment_id"],
            ),
        )
        graph = Graph(point_properties, edge_properties)
        entry_nodes = [0]
        input_flow = [1.0]
        boundary_flow = tested.boundary_flows_A_based(graph, entry_nodes, input_flow)
>       tested.update_static_flow_pressure(graph, boundary_flow, params)

tests/test_graphs.py:125: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

graph = Graph(_node_properties=   x  y  z  diameter
0  0  0  1        12
1  0  1  1         6
2  0  2  0        10
3  0  2  2 ....          -1  71.086127
           2                    1         3  ...          -1  54.425316

[3 rows x 8 columns])
input_flow = array([ 1.       ,  0.       , -0.6097561, -0.3902439])
params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}
with_hematocrit = True

    def update_static_flow_pressure(
        graph: Graph,
        input_flow: npt.NDArray[np.float64],
        params: VasculatureParams,
        with_hematocrit: bool = True,
    ):
        """Compute the time-independent pressure and flow.
    
        Args:
            graph (utils.Graph): graph containing point vasculature skeleton.
            input_flow(numpy.array): input flow for each graph node.
            params (dict): general parameters for vasculature.
            with_hematocrit (bool): consider hematrocrit for resistance model
    
        Concerns: This function is part of the public API. Any change of signature
        or functional behavior may be done thoroughly.
    
        """
    
        if graph is not None:
            if not isinstance(graph, Graph):
                raise BloodFlowError("'graph' parameter must be an instance of Graph")
            for param in VasculatureParams.__annotations__:
                if param not in params:
>                   raise BloodFlowError(f"Missing parameter '{param}'")
E                   astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'

astrovascpy/bloodflow.py:107: BloodFlowError
__________________________________ test_loop ___________________________________

params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}

    def test_loop(params):
        """This example is from F. Schmidt Phd thesis, figure 9.1A"""
        point_properties = pd.DataFrame(
            {
                "x": [0, 1, 2, 3, 2, 3, 4, 5],
                "y": [0, 0, 1, 1, -1, -1, 0, 0],
                "z": [0, 0, 0, 0, 0, 0, 0, 0],
                "diameter": [1, 1, 1, 1, 1, 1, 1, 1],
            }
        )
    
        edge_properties = pd.DataFrame(
            {
                "start_node": [0, 1, 2, 3, 1, 4, 5, 6],
                "end_node": [1, 2, 3, 6, 4, 5, 6, 7],
                "type": [0, 0, 0, 0, 0, 0, 0, 0],
            },
            index=pd.MultiIndex.from_tuples(
                ([0, 0], [1, 0], [1, 1], [1, 2], [2, 0], [2, 1], [2, 2], [3, 0]),
                names=["section_id", "segment_id"],
            ),
        )
    
        graph = Graph(point_properties, edge_properties)
        entry_nodes = [0]
        input_flow = [1.0]
        boundary_flow = tested.boundary_flows_A_based(graph, entry_nodes, input_flow)
>       tested.update_static_flow_pressure(graph, boundary_flow, params)

tests/test_graphs.py:182: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

graph = Graph(_node_properties=   x  y  z  diameter
0  0  0  0         1
1  1  0  0         1
2  2  1  0         1
3  3  1  0 ......          -1  1.110721
3          0                    6         7  ...          -1  0.785398

[8 rows x 8 columns])
input_flow = array([ 1.,  0.,  0.,  0.,  0.,  0.,  0., -1.])
params = {'blood_viscosity': 0.1, 'depth_ratio': 0.05, 'max_nb_inputs': 3, 'max_r_artery': 1.23, ...}
with_hematocrit = True

    def update_static_flow_pressure(
        graph: Graph,
        input_flow: npt.NDArray[np.float64],
        params: VasculatureParams,
        with_hematocrit: bool = True,
    ):
        """Compute the time-independent pressure and flow.
    
        Args:
            graph (utils.Graph): graph containing point vasculature skeleton.
            input_flow(numpy.array): input flow for each graph node.
            params (dict): general parameters for vasculature.
            with_hematocrit (bool): consider hematrocrit for resistance model
    
        Concerns: This function is part of the public API. Any change of signature
        or functional behavior may be done thoroughly.
    
        """
    
        if graph is not None:
            if not isinstance(graph, Graph):
                raise BloodFlowError("'graph' parameter must be an instance of Graph")
            for param in VasculatureParams.__annotations__:
                if param not in params:
>                   raise BloodFlowError(f"Missing parameter '{param}'")
E                   astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'

astrovascpy/bloodflow.py:107: BloodFlowError
_______________________ test_create_entry_largest_nodes ________________________

point_properties =    x  y  z  diameter
0  0  0  2         1
1  0  1  1         3
2  0  2  0         2
edge_properties =                        start_node  end_node  ...  endfeet_id    volume
section_id segment_id                        ..... ...          -1  4.442883
           1                    1         2  ...          -1  6.942005

[2 rows x 8 columns]
caplog = <_pytest.logging.LogCaptureFixture object at 0x2acadd804c90>

    def test_create_entry_largest_nodes(point_properties, edge_properties, caplog):
        graph = test_module.Graph(point_properties, edge_properties)
    
        with pytest.raises(BloodFlowError):
            test_module.create_entry_largest_nodes(graph, params={"max_nb_inputs": -1.0})
        with pytest.raises(BloodFlowError):
            test_module.create_entry_largest_nodes(graph, params={"depth_ratio": -1.0})
        with pytest.raises(BloodFlowError):
            test_module.create_entry_largest_nodes(graph, params={"vasc_axis": -1.0})
    
        with caplog.at_level(logging.WARNING):
>           assert (
                test_module.create_entry_largest_nodes(
                    graph,
                    params={
                        "max_nb_inputs": 1,
                        "depth_ratio": 10,
                        "vasc_axis": 1,
                        "blood_viscosity": 0.1,
                        "p_base": 1.33e-3,
                    },
                )
                == np.array([2])
            ).all()

tests/test_utils.py:72: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

graph = Graph(_node_properties=   x  y  z  diameter
0  0  0  2         1
1  0  1  1         3
2  0  2  0         2, _edge_prop......          -1  4.442883
           1                    1         2  ...          -1  6.942005

[2 rows x 8 columns])
params = {'blood_viscosity': 0.1, 'depth_ratio': 10, 'max_nb_inputs': 1, 'p_base': 0.00133, ...}

    def create_entry_largest_nodes(graph: Graph, params: VasculatureParams):
        """Get the largest nodes of degree 1 for input in the largest connected components.
    
        Args:
            graph (Graph): graph containing point vasculature skeleton.
            params (dict): general parameters for vasculature.
    
        Returns:
            numpy.array: (1,) Ids of the largest nodes.
    
        Raises:
            BloodFlowError: if n_nodes <= 0 or if vasc_axis is not 0, 1 or 2.
    
        Concerns: This function is part of the public API. Any change of signature
        or functional behavior may be done thoroughly.
        """
        if graph is not None:
            if not isinstance(graph, Graph):
                raise BloodFlowError("'graph' parameter must be an instance of Graph")
            for param in VasculatureParams.__annotations__:
                if param not in params:
>                   raise BloodFlowError(f"Missing parameter '{param}'")
E                   astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'

astrovascpy/utils.py:341: BloodFlowError
=============================== warnings summary ===============================
tests/test_bloodflow.py::test_get_radii_at_endfeet
  /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/.tox/py311/lib/python3.11/site-packages/pandas/core/dtypes/cast.py:1641: DeprecationWarning: np.find_common_type is deprecated.  Please use `np.result_type` or `np.promote_types`.
  See https://numpy.org/devdocs/release/1.25.0-notes.html and the docs for more information.  (Deprecated NumPy 1.25)
    return np.find_common_type(types, [])

tests/test_bloodflow.py::test_total_flow_conservation_in_graph
tests/test_bloodflow.py::test_total_flow_conservation_in_graph
  /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/.tox/py311/lib/python3.11/site-packages/pandas/core/algorithms.py:522: DeprecationWarning: np.find_common_type is deprecated.  Please use `np.result_type` or `np.promote_types`.
  See https://numpy.org/devdocs/release/1.25.0-notes.html and the docs for more information.  (Deprecated NumPy 1.25)
    common = np.find_common_type([values.dtype, comps_array.dtype], [])

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
- generated xml file: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/reports/pytest-py311.xml -
=========================== short test summary info ============================
FAILED tests/test_bloodflow.py::test_simulate_ou_process - astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'
FAILED tests/test_bloodflow.py::test_update_static_flow_pressure - astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'
FAILED tests/test_bloodflow.py::test_total_flow_conservation_in_graph - astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'
FAILED tests/test_bloodflow.py::test_conservation_flow - astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'
FAILED tests/test_graphs.py::test_simple_graph - astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'
FAILED tests/test_graphs.py::test_bifurcation - astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'
FAILED tests/test_graphs.py::test_loop - astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'
FAILED tests/test_utils.py::test_create_entry_largest_nodes - astrovascpy.exceptions.BloodFlowError: Missing parameter 'base_pressure'
============= 8 failed, 45 passed, 4 skipped, 3 warnings in 6.97s ==============
WARNING! There are options you set that were not used!
WARNING! could be spelling mistake, etc!
There are 2 unused database options. They are:
Option left: name:-pc_factor_shift_amount value: -1 source: code
Option left: name:-pc_factor_shift_type value: NONZERO source: code
py311: exit 1 (7.76 seconds) /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy> coverage run --branch --source=astrovascpy -m pytest --basetemp=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/.tox/py311/tmp --verbose --junit-xml=reports/pytest-py311.xml pid=30276
  py311: FAIL code 1 (91.74=setup[83.98]+cmd[7.76] seconds)
  evaluation failed :( (91.87 seconds)
srun: error: r1i4n18: task 0: Exited with exit code 1
section_end:1710424188:step_script
section_start:1710424188:cleanup_file_variables
Cleaning up project directory and file based variables
Using git from spack modules
section_end:1710424190:cleanup_file_variables
ERROR: Job failed: exit status 1