Created
March 14, 2024 13:52
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/molsys/AstroVascPy/-/pipelines/200493 (:no_entry:) running on GitHub PR BlueBrain/AstroVascPy#27.
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[0KRunning with gitlab-runner 16.8.1 (a6097117)[0;m | |
[0K on kubernetes f34dUjJy, system ID: r_e79EgkF1seUj[0;m | |
section_start:1710424267:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
section_end:1710424267:resolve_secrets [0Ksection_start:1710424267:prepare_executor [0K[0K[36;1mPreparing the "kubernetes" executor[0;m[0;m | |
[0KUsing Kubernetes namespace: gitlab-runners[0;m | |
[0KUsing Kubernetes executor with image quay.io/pypa/manylinux2014_x86_64 ...[0;m | |
[0KUsing attach strategy to execute scripts...[0;m | |
section_end:1710424267:prepare_executor [0Ksection_start:1710424267:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
[0KUsing FF_USE_POD_ACTIVE_DEADLINE_SECONDS, the Pod activeDeadlineSeconds will be set to the job timeout: 1h0m0s...[0;m | |
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 [0Ksection_start:1710424272:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
[32;1mFetching changes with git depth set to 20...[0;m | |
Initialized empty Git repository in /builds/molsys/AstroVascPy/.git/ | |
[32;1mCreated fresh repository.[0;m | |
[32;1mChecking out c48174de as detached HEAD (ref is tristan/mpi4py)...[0;m | |
[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m | |
[32;1mUpdated submodules[0;m | |
section_end:1710424275:get_sources [0Ksection_start:1710424275:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
[32;1mDownloading artifacts for docs (1209079)...[0;m | |
Downloading artifacts from coordinator... ok [0;m host[0;m=bbpgitlab.epfl.ch id[0;m=1209079 responseStatus[0;m=200 OK token[0;m=64_7gVu5 | |
section_end:1710424277:download_artifacts [0Ksection_start:1710424277:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
[32;1m$ declare -A PY_MAP=( [py38]=cp38-cp38 [py39]=cp39-cp39 [py310]=cp310-cp310 [py311]=cp311-cp311 [py312]=cp312-cp312 )[0;m | |
[32;1m$ print_var() { echo -e "${TXT_CYAN}${1}=${!1}${TXT_CLEAR}"; }[0;m | |
[32;1m$ set_and_print() { eval $1=$2; print_var $1; }[0;m | |
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
[32;1m$ set_and_print PY_BIN_NAME "${PY_MAP[$PY_VERSION]}"[0;m | |
[36mPY_BIN_NAME=cp310-cp310[0m | |
[32;1m$ set_and_print PY_BIN "/opt/python/${PY_BIN_NAME}/bin"[0;m | |
[36mPY_BIN=/opt/python/cp310-cp310/bin[0m | |
[32;1m$ print_var SYS_PACKAGES[0;m | |
[36mSYS_PACKAGES=[0m | |
[32;1m$ if [[ -n $SYS_PACKAGES ]]; then yum install -y $SYS_PACKAGES; fi[0;m | |
[32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
[36mPRE_BUILD_COMMAND=[0m | |
[32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
[32;1m$ ${PY_BIN}/pip install --upgrade --no-cache-dir pip setuptools wheel[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Requirement already satisfied: pip in /opt/_internal/cpython-3.10.13/lib/python3.10/site-packages (24.0) | |
Requirement already satisfied: setuptools in /opt/_internal/cpython-3.10.13/lib/python3.10/site-packages (69.1.1) | |
Collecting setuptools | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c21/c49fb1042386d/setuptools-69.2.0-py3-none-any.whl (821 kB) | |
âââââââââââââââââââââââââââââââââââââ 821.5/821.5 kB 117.9 MB/s eta 0:00:00 | |
Requirement already satisfied: wheel in /opt/_internal/cpython-3.10.13/lib/python3.10/site-packages (0.43.0) | |
Installing collected packages: setuptools | |
Attempting uninstall: setuptools | |
Found existing installation: setuptools 69.1.1 | |
Uninstalling setuptools-69.1.1: | |
Successfully uninstalled setuptools-69.1.1 | |
Successfully installed setuptools-69.2.0 | |
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv | |
[32;1m$ set_and_print WHEELS_DIR "${PYTHON_PROJECT_DIR}/wheelhouse"[0;m | |
[36mWHEELS_DIR=./wheelhouse[0m | |
[32;1m$ rm -rf $WHEELS_DIR && mkdir -p $WHEELS_DIR[0;m | |
[32;1m$ ${PY_BIN}/pip wheel . -w $WHEELS_DIR --no-deps[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Processing /builds/molsys/AstroVascPy | |
Installing build dependencies: started | |
Installing build dependencies: finished with status 'done' | |
Getting requirements to build wheel: started | |
Getting requirements to build wheel: finished with status 'done' | |
Preparing metadata (pyproject.toml): started | |
Preparing metadata (pyproject.toml): finished with status 'done' | |
Building wheels for collected packages: AstroVascPy | |
Building wheel for AstroVascPy (pyproject.toml): started | |
Building wheel for AstroVascPy (pyproject.toml): finished with status 'done' | |
Created wheel for AstroVascPy: filename=AstroVascPy-0.1.4-py3-none-any.whl size=45236 sha256=faf9fde6e173004d26c75ab0cefca26bbbc30041466994350123493f846fc4d1 | |
Stored in directory: /tmp/pip-ephem-wheel-cache-rjqqpf1j/wheels/87/40/b2/858192df9193a18fc502074da3ae7b563b65bf229c2d77ff76 | |
Successfully built AstroVascPy | |
[32;1m$ if [[ "$TEST_RUN_TOX" != "true" ]]; then { echo -e "${TXT_CYAN}Skipping tests.${TXT_CLEAR}"; exit 0; } fi[0;m | |
[36mSkipping tests.[0m | |
section_end:1710424290:step_script [0Ksection_start:1710424290:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m[0;m | |
[32;1mUploading artifacts...[0;m | |
./wheelhouse/: found 2 matching artifact files and directories[0;m | |
Uploading artifacts as "archive" to coordinator... 201 Created[0;m id[0;m=1209081 responseStatus[0;m=201 Created token[0;m=64_7gVu5 | |
section_end:1710424292:upload_artifacts_on_success [0Ksection_start:1710424292:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
section_end:1710424293:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
[0K on BB5 map runner pnPo3yJy[0;m | |
section_start:1710424046:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
section_end:1710424046:resolve_secrets [0Ksection_start:1710424046:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-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 [0Ksection_start:1710424048:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
Using git from spack modules | |
Running on r1i4n18 via bbpv1.epfl.ch... | |
section_end:1710424063:prepare_script [0Ksection_start:1710424063:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
Using git from spack modules | |
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
[32;1mFetching changes with git depth set to 20...[0;m | |
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209077/molsys/AstroVascPy/.git/ | |
[32;1mCreated fresh repository.[0;m | |
[32;1mChecking out c48174de as tristan/mpi4py...[0;m | |
Skipping object checkout, Git LFS is not installed. | |
[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m | |
section_end:1710424071:get_sources [0Ksection_start:1710424071:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
Using git from spack modules | |
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
[32;1m$ module purge[0;m | |
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
[32;1m$ module load unstable python/3.12.0[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.12.0 | |
[32;1m$ module load unstable python/3.8.18[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.8.18 | |
[32;1m$ module load unstable python/3.9.18[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.9.18 | |
[32;1m$ module load unstable python/3.10.13[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.10.13 | |
[32;1m$ module load unstable python/3.11.6[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.11.6 | |
[32;1m$ load-modules() { # collapsed multi-line command[0;m | |
[32;1m$ load-modules $SYSTEM_MODULES[0;m | |
Loaded module git from unstable | |
Loaded module cmake from unstable | |
Loaded module graphviz from unstable | |
[32;1m$ load-modules $EXTRA_MODULES[0;m | |
Loaded module gcc from unstable | |
Loaded module hpe-mpi from unstable | |
Loaded module py-mpi4py from unstable | |
Loaded module petsc from unstable | |
Loaded module py-petsc4py from unstable | |
[32;1m$ module list -t[0;m | |
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 | |
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
[32;1m$ print_var XDG_CONFIG_HOME[0;m | |
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209077/molsys/AstroVascPy/local_config[0m | |
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
insteadOf = https://bbpgitlab.epfl.ch/ | |
insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
insteadOf = git@bbpgitlab.epfl.ch: | |
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
[0Ksection_start:1710424078:section_venv[collapsed=true] [0KSetting up the virtual env | |
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
[32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
[32;1m$ rm -rf "$CI_VENV"[0;m | |
[32;1m$ python -mvenv "$CI_VENV"[0;m | |
[32;1m$ source "$CI_VENV/bin/activate"[0;m | |
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Requirement already satisfied: pip in ./venv/lib/python3.11/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) | |
ââââââââââââââââââââââââââââââââââââââââ 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) | |
âââââââââââââââââââââââââââââââââââââ 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) | |
âââââââââââââââââââââââââââââââââââââââ 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 | |
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Collecting tox | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b03/754b6ee6dadc7/tox-4.14.1-py3-none-any.whl (155 kB) | |
ââââââââââââââââââââââââââââââââââââââ 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) | |
ââââââââââââââââââââââââââââââââââââââ 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) | |
âââââââââââââââââââââââââââââââââââââââ 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) | |
ââââââââââââââââââââââââââââââââââââââââ 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) | |
âââââââââââââââââââââââââââââââââââââ 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 | |
[32;1m$ section_end section_venv[0;m | |
[0Ksection_end:1710424095:section_venv [0K | |
[32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
[36mPRE_BUILD_COMMAND=[0m | |
[32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
[32;1m$ section_start section_tox "Running Tox"[0;m | |
[0Ksection_start:1710424095:section_tox [0KRunning Tox | |
[32;1m$ python -mtox $TOX_OPTIONS[0;m | |
check-packaging: install_deps> python -I -m pip install build twine | |
check-packaging: freeze> python -m pip freeze --all | |
check-packaging: build==1.1.1,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: [32mPASSED[0m | |
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: [32mPASSED[0m | |
check-packaging: OK (32.82=setup[19.32]+cmd[13.07,0.43] seconds) | |
congratulations :) (32.93 seconds) | |
[32;1m$ section_end section_tox[0;m | |
[0Ksection_end:1710424129:section_tox [0K | |
section_end:1710424129:step_script [0Ksection_start:1710424129:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
Using git from spack modules | |
section_end:1710424131:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
[0K on BB5 map runner pnPo3yJy[0;m | |
section_start:1710424048:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
section_end:1710424048:resolve_secrets [0Ksection_start:1710424048:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-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 [0Ksection_start:1710424051:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
Using git from spack modules | |
Running on r1i4n18 via bbpv1.epfl.ch... | |
section_end:1710424060:prepare_script [0Ksection_start:1710424060:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
Using git from spack modules | |
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
[32;1mFetching changes with git depth set to 20...[0;m | |
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/.git/ | |
[32;1mCreated fresh repository.[0;m | |
[32;1mChecking out c48174de as tristan/mpi4py...[0;m | |
Skipping object checkout, Git LFS is not installed. | |
[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m | |
section_end:1710424069:get_sources [0Ksection_start:1710424069:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
Using git from spack modules | |
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
[32;1m$ module purge[0;m | |
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
[32;1m$ module load unstable python/3.12.0[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.12.0 | |
[32;1m$ module load unstable python/3.8.18[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.8.18 | |
[32;1m$ module load unstable python/3.9.18[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.9.18 | |
[32;1m$ module load unstable python/3.10.13[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.10.13 | |
[32;1m$ module load unstable python/3.11.6[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.11.6 | |
[32;1m$ load-modules() { # collapsed multi-line command[0;m | |
[32;1m$ load-modules $SYSTEM_MODULES[0;m | |
Loaded module git from unstable | |
Loaded module cmake from unstable | |
Loaded module graphviz from unstable | |
[32;1m$ load-modules $EXTRA_MODULES[0;m | |
Loaded module gcc from unstable | |
Loaded module hpe-mpi from unstable | |
Loaded module py-mpi4py from unstable | |
Loaded module petsc from unstable | |
Loaded module py-petsc4py from unstable | |
[32;1m$ module list -t[0;m | |
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 | |
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
[32;1m$ print_var XDG_CONFIG_HOME[0;m | |
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209079/molsys/AstroVascPy/local_config[0m | |
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
insteadOf = https://bbpgitlab.epfl.ch/ | |
insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
insteadOf = git@bbpgitlab.epfl.ch: | |
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
[0Ksection_start:1710424076:section_venv[collapsed=true] [0KSetting up the virtual env | |
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
[32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
[32;1m$ rm -rf "$CI_VENV"[0;m | |
[32;1m$ python -mvenv "$CI_VENV"[0;m | |
[32;1m$ source "$CI_VENV/bin/activate"[0;m | |
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Requirement already satisfied: pip in ./venv/lib/python3.11/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) | |
ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 77.1 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) | |
âââââââââââââââââââââââââââââââââââââ 821.5/821.5 kB 147.3 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) | |
âââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 224.7 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 | |
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Collecting tox | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b03/754b6ee6dadc7/tox-4.14.1-py3-none-any.whl (155 kB) | |
ââââââââââââââââââââââââââââââââââââââ 155.3/155.3 kB 16.3 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) | |
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Collecting colorama>=0.4.6 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
Collecting filelock>=3.13.1 (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) | |
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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) | |
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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) | |
âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 278.0 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 | |
[32;1m$ section_end section_venv[0;m | |
[0Ksection_end:1710424095:section_venv [0K | |
[32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
[36mPRE_BUILD_COMMAND=[0m | |
[32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
[32;1m$ section_start section_tox "Running Tox"[0;m | |
[0Ksection_start:1710424095:section_tox [0KRunning Tox | |
[32;1m$ python -mtox $TOX_OPTIONS[0;m | |
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel | |
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/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 | |
[2Kreading sources... [ 8%] api_ref [2Kreading sources... [ 15%] changelog [2Kreading sources... [ 23%] generated/astrovascpy.PetscBinaryIO [2Kreading sources... [ 31%] generated/astrovascpy.bloodflow [2Kreading sources... [ 38%] generated/astrovascpy.exceptions [2Kreading sources... [ 46%] generated/astrovascpy.io [2Kreading sources... [ 54%] generated/astrovascpy.ou [2Kreading sources... [ 62%] generated/astrovascpy.plotting [2Kreading sources... [ 69%] generated/astrovascpy.report_reader [2Kreading sources... [ 77%] generated/astrovascpy.report_writer [2Kreading sources... [ 85%] generated/astrovascpy.scipy_petsc_conversions [2Kreading sources... [ 92%] generated/astrovascpy.utils [2Kreading sources... [100%] index | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/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 | |
[2Kwriting output... [ 8%] api_ref [2Kwriting output... [ 15%] changelog [2Kwriting output... [ 23%] generated/astrovascpy.PetscBinaryIO [2Kwriting output... [ 31%] generated/astrovascpy.bloodflow [2Kwriting output... [ 38%] generated/astrovascpy.exceptions [2Kwriting output... [ 46%] generated/astrovascpy.io [2Kwriting output... [ 54%] generated/astrovascpy.ou [2Kwriting output... [ 62%] generated/astrovascpy.plotting [2Kwriting output... [ 69%] generated/astrovascpy.report_reader [2Kwriting output... [ 77%] generated/astrovascpy.report_writer [2Kwriting output... [ 85%] generated/astrovascpy.scipy_petsc_conversions [2Kwriting output... [ 92%] generated/astrovascpy.utils [2Kwriting output... [100%] index | |
generating indices... genindex py-modindex done | |
writing additional pages... search done | |
dumping search index in English (code: en)... done | |
dumping object inventory... done | |
build succeeded, 43 warnings. | |
The HTML pages are in build/html. | |
docs: OK (101.79=setup[90.71]+cmd[11.08] seconds) | |
congratulations :) (101.90 seconds) | |
[32;1m$ section_end section_tox[0;m | |
[0Ksection_end:1710424197:section_tox [0K | |
section_end:1710424198:step_script [0Ksection_start:1710424198:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m[0;m | |
Using git from spack modules | |
[32;1mUploading artifacts...[0;m | |
Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=31560 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
[0;33mWARNING: ./doc/build/: no matching files [0;m | |
./docs/build/: found 164 matching files and directories[0;m | |
Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=1209079 responseStatus[0;m=201 Created token[0;m=64_tLnCx | |
section_end:1710424200:upload_artifacts_on_success [0Ksection_start:1710424200:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
Using git from spack modules | |
section_end:1710424202:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
[0K on BB5 map runner pnPo3yJy[0;m | |
section_start:1710424047:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
section_end:1710424047:resolve_secrets [0Ksection_start:1710424047:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-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 [0Ksection_start:1710424048:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
Using git from spack modules | |
Running on r1i4n18 via bbpv1.epfl.ch... | |
section_end:1710424064:prepare_script [0Ksection_start:1710424064:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
Using git from spack modules | |
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
[32;1mFetching changes with git depth set to 20...[0;m | |
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209078/molsys/AstroVascPy/.git/ | |
[32;1mCreated fresh repository.[0;m | |
[32;1mChecking out c48174de as tristan/mpi4py...[0;m | |
Skipping object checkout, Git LFS is not installed. | |
[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m | |
section_end:1710424071:get_sources [0Ksection_start:1710424071:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
Using git from spack modules | |
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
[32;1m$ module purge[0;m | |
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
[32;1m$ module load unstable python/3.12.0[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.12.0 | |
[32;1m$ module load unstable python/3.8.18[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.8.18 | |
[32;1m$ module load unstable python/3.9.18[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.9.18 | |
[32;1m$ module load unstable python/3.10.13[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.10.13 | |
[32;1m$ module load unstable python/3.11.6[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.11.6 | |
[32;1m$ load-modules() { # collapsed multi-line command[0;m | |
[32;1m$ load-modules $SYSTEM_MODULES[0;m | |
Loaded module git from unstable | |
Loaded module cmake from unstable | |
Loaded module graphviz from unstable | |
[32;1m$ load-modules $EXTRA_MODULES[0;m | |
Loaded module gcc from unstable | |
Loaded module hpe-mpi from unstable | |
Loaded module py-mpi4py from unstable | |
Loaded module petsc from unstable | |
Loaded module py-petsc4py from unstable | |
[32;1m$ module list -t[0;m | |
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 | |
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
[32;1m$ print_var XDG_CONFIG_HOME[0;m | |
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209078/molsys/AstroVascPy/local_config[0m | |
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
insteadOf = https://bbpgitlab.epfl.ch/ | |
insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
insteadOf = git@bbpgitlab.epfl.ch: | |
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
[0Ksection_start:1710424079:section_venv[collapsed=true] [0KSetting up the virtual env | |
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
[32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
[32;1m$ rm -rf "$CI_VENV"[0;m | |
[32;1m$ python -mvenv "$CI_VENV"[0;m | |
[32;1m$ source "$CI_VENV/bin/activate"[0;m | |
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
Collecting pip | |
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Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
Collecting setuptools | |
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Collecting wheel | |
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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 | |
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Collecting tox | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b03/754b6ee6dadc7/tox-4.14.1-py3-none-any.whl (155 kB) | |
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Collecting cachetools>=5.3.2 (from tox) | |
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Collecting chardet>=5.2 (from tox) | |
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Collecting colorama>=0.4.6 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
Collecting filelock>=3.13.1 (from tox) | |
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Collecting packaging>=23.2 (from tox) | |
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Collecting platformdirs>=4.1 (from tox) | |
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Collecting pluggy>=1.3 (from tox) | |
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Collecting virtualenv>=20.25 (from tox) | |
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Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox) | |
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Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-24.0 platformdirs-4.2.0 pluggy-1.4.0 pyproject-api-1.6.1 tox-4.14.1 virtualenv-20.25.1 | |
[32;1m$ section_end section_venv[0;m | |
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[32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
[36mPRE_BUILD_COMMAND=[0m | |
[32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
[32;1m$ section_start section_tox "Running Tox"[0;m | |
[0Ksection_start:1710424095:section_tox [0KRunning Tox | |
[32;1m$ python -mtox $TOX_OPTIONS[0;m | |
lint: install_deps> python -I -m pip install pre-commit pylint pylint-exit | |
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel | |
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/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) | |
[32;1m$ section_end section_tox[0;m | |
[0Ksection_end:1710424258:section_tox [0K | |
section_end:1710424259:step_script [0Ksection_start:1710424259:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
Using git from spack modules | |
section_end:1710424261:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
[0K on BB5 map runner pnPo3yJy[0;m | |
section_start:1710424048:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
section_end:1710424048:resolve_secrets [0Ksection_start:1710424048:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-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 [0Ksection_start:1710424052:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
Using git from spack modules | |
Running on r1i4n18 via bbpv1.epfl.ch... | |
section_end:1710424060:prepare_script [0Ksection_start:1710424060:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
Using git from spack modules | |
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
[32;1mFetching changes with git depth set to 20...[0;m | |
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/.git/ | |
[32;1mCreated fresh repository.[0;m | |
[32;1mChecking out c48174de as tristan/mpi4py...[0;m | |
Skipping object checkout, Git LFS is not installed. | |
[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m | |
section_end:1710424069:get_sources [0Ksection_start:1710424069:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
Using git from spack modules | |
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
[32;1m$ module purge[0;m | |
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
[32;1m$ module load unstable python/3.12.0[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.12.0 | |
[32;1m$ module load unstable python/3.8.18[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.8.18 | |
[32;1m$ module load unstable python/3.9.18[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.9.18 | |
[32;1m$ module load unstable python/3.10.13[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.10.13 | |
[32;1m$ module load unstable python/3.11.6[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.11.6 | |
[32;1m$ load-modules() { # collapsed multi-line command[0;m | |
[32;1m$ load-modules $SYSTEM_MODULES[0;m | |
Loaded module git from unstable | |
Loaded module cmake from unstable | |
Loaded module graphviz from unstable | |
[32;1m$ load-modules $EXTRA_MODULES[0;m | |
Loaded module gcc from unstable | |
Loaded module hpe-mpi from unstable | |
Loaded module py-mpi4py from unstable | |
Loaded module petsc from unstable | |
Loaded module py-petsc4py from unstable | |
[32;1m$ module list -t[0;m | |
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 | |
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
[32;1m$ print_var XDG_CONFIG_HOME[0;m | |
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1209080/molsys/AstroVascPy/local_config[0m | |
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
insteadOf = https://bbpgitlab.epfl.ch/ | |
insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
insteadOf = git@bbpgitlab.epfl.ch: | |
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
[0Ksection_start:1710424076:section_venv[collapsed=true] [0KSetting up the virtual env | |
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
[32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
[32;1m$ rm -rf "$CI_VENV"[0;m | |
[32;1m$ python -mvenv "$CI_VENV"[0;m | |
[32;1m$ source "$CI_VENV/bin/activate"[0;m | |
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Requirement already satisfied: pip in ./venv/lib/python3.11/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) | |
ââââââââââââââââââââââââââââââââââââââââ 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) | |
ââââââââââââââââââââââââââââââââââââââ 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) | |
âââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 218.8 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 | |
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Collecting tox | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b03/754b6ee6dadc7/tox-4.14.1-py3-none-any.whl (155 kB) | |
ââââââââââââââââââââââââââââââââââââââ 155.3/155.3 kB 18.9 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) | |
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Collecting colorama>=0.4.6 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
Collecting filelock>=3.13.1 (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) | |
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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) | |
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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) | |
âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 266.3 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 | |
[32;1m$ section_end section_venv[0;m | |
[0Ksection_end:1710424095:section_venv [0K | |
[32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
[36mPRE_BUILD_COMMAND=[0m | |
[32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
[32;1m$ section_start section_tox "Running Tox"[0;m | |
[0Ksection_start:1710424095:section_tox [0KRunning Tox | |
[32;1m$ python -mtox $TOX_OPTIONS[0;m | |
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel | |
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/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%] | |
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=================================== 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 [0Ksection_start:1710424188:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
Using git from spack modules | |
section_end:1710424190:cleanup_file_variables [0K[31;1mERROR: Job failed: exit status 1 | |
[0;m |
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