Created
December 19, 2023 08:57
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/molsys/AstroVascPy/-/pipelines/181495 (:white_check_mark:) running on GitHub PR BlueBrain/AstroVascPy#20.
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[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
[0K on BB5 map runner pnPo3yJy[0;m | |
section_start:1702976018:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
section_end:1702976018:resolve_secrets [0Ksection_start:1702976018:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor3795881504, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
Runner ID 29, project root molsys, project name AstroVascPy | |
Pipeline ID 181495, build ref , job ID 1089692 | |
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089692, optional exclusive flag , optional cpus per task flag --cpus-per-task=6, optional qos flag , optional reservation flag | |
A slurm job will be created with name GL_J1089692_PROD_P2342_CP0_C1 | |
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcimolsys partition=prod qos= reservation= | |
Not executing the chown -R | |
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
Submitted batch job 1950770 | |
job state: R | |
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1089692_PROD_P2342_CP0_C1 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089692 --time=1:00:00 --wrap="sleep infinity" | |
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089692 --ntasks=1 --jobid=1950770 --cpus-per-task=6 --mem=30750M | |
section_end:1702976020:prepare_executor [0Ksection_start:1702976020:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
Using git from spack modules | |
Running on r1i7n22 via bbpv1.epfl.ch... | |
section_end:1702976024:prepare_script [0Ksection_start:1702976024:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
Using git from spack modules | |
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
[32;1mFetching changes with git depth set to 20...[0;m | |
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089692/molsys/AstroVascPy/.git/ | |
[32;1mCreated fresh repository.[0;m | |
[32;1mChecking out 8758d502 as nicola/scipy_petsc_bug...[0;m | |
Skipping object checkout, Git LFS is not installed. | |
[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m | |
section_end:1702976027:get_sources [0Ksection_start:1702976027:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
Using git from spack modules | |
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
[32;1m$ module purge[0;m | |
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
[32;1m$ module load archive/2020-12 python/3.7.4[0;m | |
[32;1m$ module unload archive/2020-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.7.4 | |
[32;1m$ module load archive/2021-12 python/3.8.3[0;m | |
[32;1m$ module unload archive/2021-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.8.3 | |
[32;1m$ module load archive/2023-02 python/3.9.7[0;m | |
[32;1m$ module unload archive/2023-02[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.9.7 | |
[32;1m$ module load unstable python[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.10.8 | |
[32;1m$ load-modules() { # collapsed multi-line command[0;m | |
[32;1m$ load-modules $SYSTEM_MODULES[0;m | |
Loaded module git from unstable | |
Loaded module cmake from unstable | |
Loaded module graphviz from unstable | |
[32;1m$ load-modules $EXTRA_MODULES[0;m | |
Loaded module gcc from unstable | |
Loaded module hpe-mpi from unstable | |
Autoloading python/3.10.8 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module py-mpi4py from unstable | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module petsc from unstable | |
Autoloading python/3.10.8 | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module py-petsc4py from unstable | |
[32;1m$ module list -t[0;m | |
Currently Loaded Modulefiles: | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4 | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/python/3.10.8 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/git/2.38.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/cmake/3.24.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/graphviz/2.49.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/compilers/linux-rhel7-haswell/gcc/12.2.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-mpi4py/3.1.4 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/petsc/3.18.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-petsc4py/3.18.1 | |
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
[32;1m$ print_var XDG_CONFIG_HOME[0;m | |
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089692/molsys/AstroVascPy/local_config[0m | |
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
insteadOf = https://bbpgitlab.epfl.ch/ | |
insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
insteadOf = git@bbpgitlab.epfl.ch: | |
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
[0Ksection_start:1702976029:section_venv[collapsed=true] [0KSetting up the virtual env | |
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
[32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
[32;1m$ rm -rf "$CI_VENV"[0;m | |
[32;1m$ python -mvenv "$CI_VENV"[0;m | |
[32;1m$ source "$CI_VENV/bin/activate"[0;m | |
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (22.2.2) | |
Collecting pip | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/505/2d7889c1f9d05/pip-23.3.2-py3-none-any.whl (2.1 MB) | |
ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 76.1 MB/s eta 0:00:00 | |
Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages (63.0.0) | |
Collecting setuptools | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/1e8/fdff6797d3865/setuptools-69.0.2-py3-none-any.whl (819 kB) | |
âââââââââââââââââââââââââââââââââââââ 819.5/819.5 kB 266.1 MB/s eta 0:00:00 | |
Collecting wheel | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/177/f9c9b0d45c478/wheel-0.42.0-py3-none-any.whl (65 kB) | |
âââââââââââââââââââââââââââââââââââââââ 65.4/65.4 kB 215.3 MB/s eta 0:00:00 | |
Installing collected packages: wheel, setuptools, pip | |
Attempting uninstall: setuptools | |
Found existing installation: setuptools 63.0.0 | |
Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089692/molsys/AstroVascPy/venv | |
Can't uninstall 'setuptools'. No files were found to uninstall. | |
Attempting uninstall: pip | |
Found existing installation: pip 22.2.2 | |
Uninstalling pip-22.2.2: | |
Successfully uninstalled pip-22.2.2 | |
Successfully installed pip-23.3.2 setuptools-69.0.2 wheel-0.42.0 | |
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Collecting tox | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2ad/b83d68f271168/tox-4.11.4-py3-none-any.whl (153 kB) | |
ââââââââââââââââââââââââââââââââââââââ 154.0/154.0 kB 19.1 MB/s eta 0:00:00 | |
Collecting cachetools>=5.3.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/861/f35a13a451f94/cachetools-5.3.2-py3-none-any.whl (9.3 kB) | |
Collecting chardet>=5.2 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 55.6 MB/s eta 0:00:00 | |
Collecting colorama>=0.4.6 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
Collecting filelock>=3.12.3 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/57d/bda9b35157b05/filelock-3.13.1-py3-none-any.whl (11 kB) | |
Collecting packaging>=23.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/8c4/91190033a9af7/packaging-23.2-py3-none-any.whl (53 kB) | |
âââââââââââââââââââââââââââââââââââââââ 53.0/53.0 kB 218.3 MB/s eta 0:00:00 | |
Collecting platformdirs>=3.10 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/11c/8f37bcca40db9/platformdirs-4.1.0-py3-none-any.whl (17 kB) | |
Collecting pluggy>=1.3 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/d89/c696a773f8bd3/pluggy-1.3.0-py3-none-any.whl (18 kB) | |
Collecting pyproject-api>=1.6.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
Collecting tomli>=2.0.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/939/de3e7a6161af0/tomli-2.0.1-py3-none-any.whl (12 kB) | |
Collecting virtualenv>=20.24.3 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/423/8949c5ffe6876/virtualenv-20.25.0-py3-none-any.whl (3.8 MB) | |
ââââââââââââââââââââââââââââââââââââââââ 3.8/3.8 MB 178.3 MB/s eta 0:00:00 | |
Collecting distlib<1,>=0.3.7 (from virtualenv>=20.24.3->tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 256.7 MB/s eta 0:00:00 | |
Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
Successfully installed cachetools-5.3.2 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-23.2 platformdirs-4.1.0 pluggy-1.3.0 pyproject-api-1.6.1 tomli-2.0.1 tox-4.11.4 virtualenv-20.25.0 | |
[32;1m$ section_end section_venv[0;m | |
[0Ksection_end:1702976045:section_venv [0K | |
[32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
[36mPRE_BUILD_COMMAND=[0m | |
[32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
[32;1m$ section_start section_tox "Running Tox"[0;m | |
[0Ksection_start:1702976045:section_tox [0KRunning Tox | |
[32;1m$ python -mtox $TOX_OPTIONS[0;m | |
check-packaging: install_deps> python -I -m pip install build twine | |
check-packaging: freeze> python -m pip freeze --all | |
check-packaging: build==1.0.3,certifi==2023.11.17,cffi==1.16.0,charset-normalizer==3.3.2,cryptography==41.0.7,docutils==0.20.1,idna==3.6,importlib-metadata==7.0.0,jaraco.classes==3.3.0,jeepney==0.8.0,keyring==24.3.0,markdown-it-py==3.0.0,mdurl==0.1.2,more-itertools==10.1.0,mpi4py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mpi4py-3.1.4-glx4cfnu5cionch2hbeyzns5ol3vexp7/spack-src,nh3==0.2.15,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging==23.2,petsc4py @ file:///nvme/bbpcihpcdeploy/1912700/spack-stage/spack-stage-py-petsc4py-3.18.1-k6k4ybhubjpjanttcmmql5ditq2bxn32/spack-src,pip==23.3.1,pkginfo==1.9.6,pycparser==2.21,Pygments==2.17.2,pyproject_hooks==1.0.0,readme-renderer==42.0,requests==2.31.0,requests-toolbelt==1.0.0,rfc3986==2.0.0,rich==13.7.0,SecretStorage==3.3.3,setuptools @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-setuptools-63.0.0-c6hdpvjjddmcm3xf5begyfpkjkzj2oke/spack-src/setuptools-63.0.0-py3-none-any.whl,tomli==2.0.1,twine==4.0.2,urllib3==2.1.0,wheel==0.42.0,zipp==3.17.0 | |
check-packaging: commands[0]> python -m build -o /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089692/molsys/AstroVascPy/.tox/check-packaging/tmp/dist | |
* Creating venv isolated environment... | |
* Installing packages in isolated environment... (setuptools>=42, setuptools_scm[toml]>=3.4, wheel) | |
* Getting build dependencies for sdist... | |
running egg_info | |
creating AstroVascPy.egg-info | |
writing AstroVascPy.egg-info/PKG-INFO | |
writing dependency_links to AstroVascPy.egg-info/dependency_links.txt | |
writing entry points to AstroVascPy.egg-info/entry_points.txt | |
writing requirements to AstroVascPy.egg-info/requires.txt | |
writing top-level names to AstroVascPy.egg-info/top_level.txt | |
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
reading manifest template 'MANIFEST.in' | |
warning: no previously-included files matching '*.py[co]' found anywhere in distribution | |
warning: no previously-included files matching '.DS_Store' found anywhere in distribution | |
adding license file 'LICENSE.txt' | |
adding license file 'AUTHORS.txt' | |
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
* Building sdist... | |
running sdist | |
running egg_info | |
writing AstroVascPy.egg-info/PKG-INFO | |
writing dependency_links to AstroVascPy.egg-info/dependency_links.txt | |
writing entry points to AstroVascPy.egg-info/entry_points.txt | |
writing requirements to AstroVascPy.egg-info/requires.txt | |
writing top-level names to AstroVascPy.egg-info/top_level.txt | |
reading manifest template 'MANIFEST.in' | |
warning: no previously-included files matching '*.py[co]' found anywhere in distribution | |
warning: no previously-included files matching '.DS_Store' found anywhere in distribution | |
adding license file 'LICENSE.txt' | |
adding license file 'AUTHORS.txt' | |
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
running check | |
creating AstroVascPy-0.0.1 | |
creating AstroVascPy-0.0.1/AstroVascPy.egg-info | |
creating AstroVascPy-0.0.1/astrovascpy | |
creating AstroVascPy-0.0.1/docs | |
creating AstroVascPy-0.0.1/docs/source | |
creating AstroVascPy-0.0.1/docs/source/logo | |
creating AstroVascPy-0.0.1/examples | |
creating AstroVascPy-0.0.1/examples/data | |
creating AstroVascPy-0.0.1/examples/data/graphs_folder | |
creating AstroVascPy-0.0.1/tests | |
creating AstroVascPy-0.0.1/tests/data | |
creating AstroVascPy-0.0.1/tests/data/input_flow | |
creating AstroVascPy-0.0.1/tests/data/reporting | |
copying files to AstroVascPy-0.0.1... | |
copying .auto-changelog -> AstroVascPy-0.0.1 | |
copying .auto-changelog-template.hbs -> AstroVascPy-0.0.1 | |
copying .codespellignorelines -> AstroVascPy-0.0.1 | |
copying .codespellrc -> AstroVascPy-0.0.1 | |
copying .copier-answers.yml -> AstroVascPy-0.0.1 | |
copying .flake8 -> AstroVascPy-0.0.1 | |
copying .gitattributes -> AstroVascPy-0.0.1 | |
copying .gitignore -> AstroVascPy-0.0.1 | |
copying .gitlab-ci.yml -> AstroVascPy-0.0.1 | |
copying .gitreview -> AstroVascPy-0.0.1 | |
copying .pre-commit-config.yaml -> AstroVascPy-0.0.1 | |
copying .pylintrc -> AstroVascPy-0.0.1 | |
copying AUTHORS.txt -> AstroVascPy-0.0.1 | |
copying CHANGELOG.md -> AstroVascPy-0.0.1 | |
copying CONTRIBUTING.md -> AstroVascPy-0.0.1 | |
copying LICENSE.txt -> AstroVascPy-0.0.1 | |
copying MANIFEST.in -> AstroVascPy-0.0.1 | |
copying README.md -> AstroVascPy-0.0.1 | |
copying commitlint.config.js -> AstroVascPy-0.0.1 | |
copying package.json -> AstroVascPy-0.0.1 | |
copying pyproject.toml -> AstroVascPy-0.0.1 | |
copying setup.py -> AstroVascPy-0.0.1 | |
copying setup.sh -> AstroVascPy-0.0.1 | |
copying tox.ini -> AstroVascPy-0.0.1 | |
copying AstroVascPy.egg-info/PKG-INFO -> AstroVascPy-0.0.1/AstroVascPy.egg-info | |
copying AstroVascPy.egg-info/SOURCES.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info | |
copying AstroVascPy.egg-info/dependency_links.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info | |
copying AstroVascPy.egg-info/entry_points.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info | |
copying AstroVascPy.egg-info/requires.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info | |
copying AstroVascPy.egg-info/top_level.txt -> AstroVascPy-0.0.1/AstroVascPy.egg-info | |
copying astrovascpy/PetscBinaryIO.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/__init__.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/bloodflow.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/exceptions.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/io.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/ou.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/plotting.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/report_reader.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/report_writer.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/scipy_petsc_conversions.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/typing.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/utils.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/version.py -> AstroVascPy-0.0.1/astrovascpy | |
copying astrovascpy/vtk_io.py -> AstroVascPy-0.0.1/astrovascpy | |
copying docs/Makefile -> AstroVascPy-0.0.1/docs | |
copying docs/source/api_ref.rst -> AstroVascPy-0.0.1/docs/source | |
copying docs/source/changelog.rst -> AstroVascPy-0.0.1/docs/source | |
copying docs/source/conf.py -> AstroVascPy-0.0.1/docs/source | |
copying docs/source/index.rst -> AstroVascPy-0.0.1/docs/source | |
copying docs/source/logo/BPP-AstroVascPy-Github.jpg -> AstroVascPy-0.0.1/docs/source/logo | |
copying examples/compute_static_flow_pressure.py -> AstroVascPy-0.0.1/examples | |
copying examples/job_script.sbatch -> AstroVascPy-0.0.1/examples | |
copying examples/simulate_OU_process.py -> AstroVascPy-0.0.1/examples | |
copying examples/data/params.yaml -> AstroVascPy-0.0.1/examples/data | |
copying examples/data/graphs_folder/edge_dataset.csv -> AstroVascPy-0.0.1/examples/data/graphs_folder | |
copying examples/data/graphs_folder/node_dataset.csv -> AstroVascPy-0.0.1/examples/data/graphs_folder | |
copying examples/data/graphs_folder/toy_graph.bin -> AstroVascPy-0.0.1/examples/data/graphs_folder | |
copying examples/data/graphs_folder/toy_graph.h5 -> AstroVascPy-0.0.1/examples/data/graphs_folder | |
copying tests/__init__.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_bloodflow.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_graphs.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_io.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_mpi.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_ou.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_report_reader.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_report_writer.py -> AstroVascPy-0.0.1/tests | |
copying tests/test_utils.py -> AstroVascPy-0.0.1/tests | |
copying tests/data/dataset.h5 -> AstroVascPy-0.0.1/tests/data | |
copying tests/data/edge_dataset.csv -> AstroVascPy-0.0.1/tests/data | |
copying tests/data/node_dataset.csv -> AstroVascPy-0.0.1/tests/data | |
copying tests/data/toy_graph.bin -> AstroVascPy-0.0.1/tests/data | |
copying tests/data/toy_graph.h5 -> AstroVascPy-0.0.1/tests/data | |
copying tests/data/input_flow/sine.csv -> AstroVascPy-0.0.1/tests/data/input_flow | |
copying tests/data/reporting/compartment_report.h5 -> AstroVascPy-0.0.1/tests/data/reporting | |
copying tests/data/reporting/create_reports.py -> AstroVascPy-0.0.1/tests/data/reporting | |
copying tests/data/reporting/diff_unit_compartment_report.h5 -> AstroVascPy-0.0.1/tests/data/reporting | |
Writing AstroVascPy-0.0.1/setup.cfg | |
Creating tar archive | |
removing 'AstroVascPy-0.0.1' (and everything under it) | |
* Building wheel from sdist | |
* Creating venv isolated environment... | |
* Installing packages in isolated environment... (setuptools>=42, setuptools_scm[toml]>=3.4, wheel) | |
* Getting build dependencies for wheel... | |
running egg_info | |
writing AstroVascPy.egg-info/PKG-INFO | |
writing dependency_links to AstroVascPy.egg-info/dependency_links.txt | |
writing entry points to AstroVascPy.egg-info/entry_points.txt | |
writing requirements to AstroVascPy.egg-info/requires.txt | |
writing top-level names to AstroVascPy.egg-info/top_level.txt | |
ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any | |
reading manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
reading manifest template 'MANIFEST.in' | |
warning: no previously-included files matching '*.py[co]' found anywhere in distribution | |
warning: no previously-included files matching '.DS_Store' found anywhere in distribution | |
adding license file 'LICENSE.txt' | |
adding license file 'AUTHORS.txt' | |
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
* Installing packages in isolated environment... (wheel) | |
* Building wheel... | |
running bdist_wheel | |
running build | |
running build_py | |
creating build | |
creating build/lib | |
creating build/lib/astrovascpy | |
copying astrovascpy/io.py -> build/lib/astrovascpy | |
copying astrovascpy/typing.py -> build/lib/astrovascpy | |
copying astrovascpy/report_writer.py -> build/lib/astrovascpy | |
copying astrovascpy/vtk_io.py -> build/lib/astrovascpy | |
copying astrovascpy/plotting.py -> build/lib/astrovascpy | |
copying astrovascpy/report_reader.py -> build/lib/astrovascpy | |
copying astrovascpy/version.py -> build/lib/astrovascpy | |
copying astrovascpy/ou.py -> build/lib/astrovascpy | |
copying astrovascpy/PetscBinaryIO.py -> build/lib/astrovascpy | |
copying astrovascpy/utils.py -> build/lib/astrovascpy | |
copying astrovascpy/exceptions.py -> build/lib/astrovascpy | |
copying astrovascpy/scipy_petsc_conversions.py -> build/lib/astrovascpy | |
copying astrovascpy/__init__.py -> build/lib/astrovascpy | |
copying astrovascpy/bloodflow.py -> build/lib/astrovascpy | |
running egg_info | |
writing AstroVascPy.egg-info/PKG-INFO | |
writing dependency_links to AstroVascPy.egg-info/dependency_links.txt | |
writing entry points to AstroVascPy.egg-info/entry_points.txt | |
writing requirements to AstroVascPy.egg-info/requires.txt | |
writing top-level names to AstroVascPy.egg-info/top_level.txt | |
ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any | |
reading manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
reading manifest template 'MANIFEST.in' | |
warning: no previously-included files matching '*.py[co]' found anywhere in distribution | |
warning: no previously-included files matching '.DS_Store' found anywhere in distribution | |
adding license file 'LICENSE.txt' | |
adding license file 'AUTHORS.txt' | |
writing manifest file 'AstroVascPy.egg-info/SOURCES.txt' | |
installing to build/bdist.linux-x86_64/wheel | |
running install | |
running install_lib | |
creating build/bdist.linux-x86_64 | |
creating build/bdist.linux-x86_64/wheel | |
creating build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/io.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/typing.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/report_writer.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/vtk_io.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/plotting.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/report_reader.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/version.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/ou.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/PetscBinaryIO.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/utils.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/exceptions.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/scipy_petsc_conversions.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/__init__.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
copying build/lib/astrovascpy/bloodflow.py -> build/bdist.linux-x86_64/wheel/astrovascpy | |
running install_egg_info | |
Copying AstroVascPy.egg-info to build/bdist.linux-x86_64/wheel/AstroVascPy-0.0.1-py3.10.egg-info | |
running install_scripts | |
creating build/bdist.linux-x86_64/wheel/AstroVascPy-0.0.1.dist-info/WHEEL | |
creating '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089692/molsys/AstroVascPy/.tox/check-packaging/tmp/dist/tmpgohyfnbv/AstroVascPy-0.0.1-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it | |
adding 'astrovascpy/PetscBinaryIO.py' | |
adding 'astrovascpy/__init__.py' | |
adding 'astrovascpy/bloodflow.py' | |
adding 'astrovascpy/exceptions.py' | |
adding 'astrovascpy/io.py' | |
adding 'astrovascpy/ou.py' | |
adding 'astrovascpy/plotting.py' | |
adding 'astrovascpy/report_reader.py' | |
adding 'astrovascpy/report_writer.py' | |
adding 'astrovascpy/scipy_petsc_conversions.py' | |
adding 'astrovascpy/typing.py' | |
adding 'astrovascpy/utils.py' | |
adding 'astrovascpy/version.py' | |
adding 'astrovascpy/vtk_io.py' | |
adding 'AstroVascPy-0.0.1.dist-info/AUTHORS.txt' | |
adding 'AstroVascPy-0.0.1.dist-info/LICENSE.txt' | |
adding 'AstroVascPy-0.0.1.dist-info/METADATA' | |
adding 'AstroVascPy-0.0.1.dist-info/WHEEL' | |
adding 'AstroVascPy-0.0.1.dist-info/entry_points.txt' | |
adding 'AstroVascPy-0.0.1.dist-info/top_level.txt' | |
adding 'AstroVascPy-0.0.1.dist-info/RECORD' | |
removing build/bdist.linux-x86_64/wheel | |
Successfully built AstroVascPy-0.0.1.tar.gz and AstroVascPy-0.0.1-py3-none-any.whl | |
check-packaging: commands[1]> twine check '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089692/molsys/AstroVascPy/.tox/check-packaging/tmp/dist/*' | |
Checking | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089692/molsys/AstroVascPy/.t | |
ox/check-packaging/tmp/dist/AstroVascPy-0.0.1-py3-none-any.whl: [32mPASSED[0m | |
Checking | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089692/molsys/AstroVascPy/.t | |
ox/check-packaging/tmp/dist/AstroVascPy-0.0.1.tar.gz: [32mPASSED[0m | |
check-packaging: OK (28.48=setup[13.45]+cmd[14.62,0.41] seconds) | |
congratulations :) (28.92 seconds) | |
[32;1m$ section_end section_tox[0;m | |
[0Ksection_end:1702976074:section_tox [0K | |
section_end:1702976074:step_script [0Ksection_start:1702976074:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
Using git from spack modules | |
section_end:1702976075:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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:1702976019:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
section_end:1702976019:resolve_secrets [0Ksection_start:1702976019:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor4031834543, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
Runner ID 29, project root molsys, project name AstroVascPy | |
Pipeline ID 181495, build ref , job ID 1089694 | |
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089694, optional exclusive flag , optional cpus per task flag --cpus-per-task=6, optional qos flag , optional reservation flag | |
A slurm job will be created with name GL_J1089694_PROD_P2342_CP2_C3 | |
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcimolsys partition=prod qos= reservation= | |
Not executing the chown -R | |
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
Submitted batch job 1950772 | |
job state: R | |
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1089694_PROD_P2342_CP2_C3 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089694 --time=1:00:00 --wrap="sleep infinity" | |
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089694 --ntasks=1 --jobid=1950772 --cpus-per-task=6 --mem=30750M | |
section_end:1702976021:prepare_executor [0Ksection_start:1702976021:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
Using git from spack modules | |
Running on r1i7n22 via bbpv1.epfl.ch... | |
section_end:1702976028:prepare_script [0Ksection_start:1702976028:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
Using git from spack modules | |
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
[32;1mFetching changes with git depth set to 20...[0;m | |
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.git/ | |
[32;1mCreated fresh repository.[0;m | |
[32;1mChecking out 8758d502 as nicola/scipy_petsc_bug...[0;m | |
Skipping object checkout, Git LFS is not installed. | |
[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m | |
section_end:1702976031:get_sources [0Ksection_start:1702976031:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
Using git from spack modules | |
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
[32;1m$ module purge[0;m | |
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
[32;1m$ module load archive/2020-12 python/3.7.4[0;m | |
[32;1m$ module unload archive/2020-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.7.4 | |
[32;1m$ module load archive/2021-12 python/3.8.3[0;m | |
[32;1m$ module unload archive/2021-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.8.3 | |
[32;1m$ module load archive/2023-02 python/3.9.7[0;m | |
[32;1m$ module unload archive/2023-02[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.9.7 | |
[32;1m$ module load unstable python[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.10.8 | |
[32;1m$ load-modules() { # collapsed multi-line command[0;m | |
[32;1m$ load-modules $SYSTEM_MODULES[0;m | |
Loaded module git from unstable | |
Loaded module cmake from unstable | |
Loaded module graphviz from unstable | |
[32;1m$ load-modules $EXTRA_MODULES[0;m | |
Loaded module gcc from unstable | |
Loaded module hpe-mpi from unstable | |
Autoloading python/3.10.8 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module py-mpi4py from unstable | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module petsc from unstable | |
Autoloading python/3.10.8 | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module py-petsc4py from unstable | |
[32;1m$ module list -t[0;m | |
Currently Loaded Modulefiles: | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4 | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/python/3.10.8 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/git/2.38.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/cmake/3.24.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/graphviz/2.49.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/compilers/linux-rhel7-haswell/gcc/12.2.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-mpi4py/3.1.4 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/petsc/3.18.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-petsc4py/3.18.1 | |
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
[32;1m$ print_var XDG_CONFIG_HOME[0;m | |
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/local_config[0m | |
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
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.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel | |
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: get_requires_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: install_requires_for_build_wheel> python -I -m pip install wheel | |
.pkg: freeze> python -m pip freeze --all | |
.pkg: packaging==23.2,pip==23.3.1,setuptools==69.0.2,setuptools-scm==8.0.4,tomli==2.0.1,typing_extensions==4.9.0,wheel==0.42.0 | |
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
docs: install_package_deps> python -I -m pip install cached-property click coverage cython h5py libsonata m2r2 matplotlib morphio networkx numpy 'pandas<2.0.0' psutil pyyaml scipy seaborn sphinx sphinx-bluebrain-theme sphinx-click tables tqdm trimesh vascpy | |
docs: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz | |
docs: freeze> python -m pip freeze --all | |
docs: alabaster==0.7.13,AstroVascPy @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz#sha256=1835035a4af0fa5dffa69c1da40c1881b14bb32357f600e62cfa6bfde687fc07,Babel==2.14.0,blosc2==2.3.2,cached-property==1.5.2,certifi==2023.11.17,charset-normalizer==3.3.2,click==8.1.7,contourpy==1.2.0,coverage==7.3.3,cycler==0.12.1,Cython==3.0.6,docutils==0.20.1,fonttools==4.47.0,h5py==3.10.0,idna==3.6,imagesize==1.4.1,Jinja2==3.0.3,kiwisolver==1.4.5,libsonata==0.1.24,m2r2==0.3.3.post2,MarkupSafe==2.1.3,matplotlib==3.8.2,mistune==0.8.4,MorphIO==3.3.7,mpi4py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mpi4py-3.1.4-glx4cfnu5cionch2hbeyzns5ol3vexp7/spack-src,msgpack==1.0.7,ndindex==1.7,networkx==3.2.1,numexpr==2.8.8,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging==23.2,pandas==1.5.3,petsc4py @ file:///nvme/bbpcihpcdeploy/1912700/spack-stage/spack-stage-py-petsc4py-3.18.1-k6k4ybhubjpjanttcmmql5ditq2bxn32/spack-src,Pillow==10.1.0,pip==23.3.1,psutil==5.9.7,py-cpuinfo==9.0.0,Pygments==2.17.2,pyparsing==3.1.1,python-dateutil==2.8.2,pytz==2023.3.post1,PyYAML==6.0.1,requests==2.31.0,scipy==1.11.4,seaborn==0.13.0,setuptools @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-setuptools-63.0.0-c6hdpvjjddmcm3xf5begyfpkjkzj2oke/spack-src/setuptools-63.0.0-py3-none-any.whl,six==1.16.0,snowballstemmer==2.2.0,Sphinx==7.2.6,sphinx-bluebrain-theme==0.4.2,sphinx-click==5.1.0,sphinxcontrib-applehelp==1.0.7,sphinxcontrib-devhelp==1.0.5,sphinxcontrib-htmlhelp==2.0.4,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==1.0.6,sphinxcontrib-serializinghtml==1.1.9,tables==3.9.2,tqdm==4.66.1,trimesh==4.0.6,urllib3==2.1.0,vascpy==0.1.1,wheel==0.42.0 | |
docs: commands[0] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs> make html | |
# Generate the documentation | |
Running Sphinx v7.2.6 | |
making output directory... done | |
[autosummary] generating autosummary for: api_ref.rst, changelog.rst, index.rst | |
WARNING: [autosummary] failed to import astrovascpy.vtk_io. | |
Possible hints: | |
* ModuleNotFoundError: No module named 'vtk' | |
* ImportError: | |
* AttributeError: module 'astrovascpy' has no attribute 'vtk_io' | |
[autosummary] generating autosummary for: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.PetscBinaryIO.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.bloodflow.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.exceptions.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.io.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.ou.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.plotting.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.report_reader.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.report_writer.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.scipy_petsc_conversions.rst, /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/generated/astrovascpy.utils.rst | |
loading intersphinx inventory from https://docs.python.org/3/objects.inv... | |
building [mo]: targets for 0 po files that are out of date | |
writing output... | |
building [html]: targets for 3 source files that are out of date | |
updating environment: [new config] 13 added, 0 changed, 0 removed | |
[2Kreading sources... [ 8%] api_ref [2Kreading sources... [ 15%] changelog [2Kreading sources... [ 23%] generated/astrovascpy.PetscBinaryIO [2Kreading sources... [ 31%] generated/astrovascpy.bloodflow [2Kreading sources... [ 38%] generated/astrovascpy.exceptions [2Kreading sources... [ 46%] generated/astrovascpy.io [2Kreading sources... [ 54%] generated/astrovascpy.ou [2Kreading sources... [ 62%] generated/astrovascpy.plotting [2Kreading sources... [ 69%] generated/astrovascpy.report_reader [2Kreading sources... [ 77%] generated/astrovascpy.report_writer [2Kreading sources... [ 85%] generated/astrovascpy.scipy_petsc_conversions [2Kreading sources... [ 92%] generated/astrovascpy.utils [2Kreading sources... [100%] index | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/api_ref.rst:6: WARNING: autosummary: failed to import astrovascpy.vtk_io. | |
Possible hints: | |
* ModuleNotFoundError: No module named 'vtk' | |
* ImportError: | |
* AttributeError: module 'astrovascpy' has no attribute 'vtk_io' | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:15: WARNING: Title underline too short. | |
COPIED FROM PETSC Library -> $PETSC_DIR/lib/petsc/bin (along with get_conf function) | |
=============== | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:15: WARNING: Title underline too short. | |
COPIED FROM PETSC Library -> $PETSC_DIR/lib/petsc/bin (along with get_conf function) | |
=============== | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:21: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:23: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO:33: WARNING: Definition list ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.readBinaryFile:3: WARNING: Inline strong start-string without end-string. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.readIS:3: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.readMatDense:3: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.readVec:3: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.writeBinaryFile:8: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.writeIS:3: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.writeMatSparse:3: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/PetscBinaryIO.py:docstring of astrovascpy.PetscBinaryIO.PetscBinaryIO.writeVec:3: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/bloodflow.py:docstring of astrovascpy.bloodflow:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/bloodflow.py:docstring of astrovascpy.bloodflow:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/exceptions.py:docstring of astrovascpy.exceptions:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/exceptions.py:docstring of astrovascpy.exceptions:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/io.py:docstring of astrovascpy.io:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/io.py:docstring of astrovascpy.io:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/ou.py:docstring of astrovascpy.ou:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/ou.py:docstring of astrovascpy.ou:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/ou.py:docstring of astrovascpy.ou.expected_time:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/ou.py:docstring of astrovascpy.ou.expected_time:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/ou.py:docstring of astrovascpy.ou.ornstein_uhlenbeck_process:7: WARNING: Definition list ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/plotting.py:docstring of astrovascpy.plotting:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/plotting.py:docstring of astrovascpy.plotting:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/report_reader.py:docstring of astrovascpy.report_reader:11: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/report_reader.py:docstring of astrovascpy.report_reader:12: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/report_writer.py:docstring of astrovascpy.report_writer:6: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/report_writer.py:docstring of astrovascpy.report_writer:7: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/scipy_petsc_conversions.py:docstring of astrovascpy.scipy_petsc_conversions:5: ERROR: Unexpected indentation. | |
looking for now-outdated files... none found | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/scipy_petsc_conversions.py:docstring of astrovascpy.scipy_petsc_conversions:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/utils.py:docstring of astrovascpy.utils:5: ERROR: Unexpected indentation. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/.tox/docs/lib/python3.10/site-packages/astrovascpy/utils.py:docstring of astrovascpy.utils:6: WARNING: Block quote ends without a blank line; unexpected unindent. | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/index.rst:8: WARNING: toctree contains reference to nonexisting document 'installation' | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/README.md:: WARNING: image file not readable: docs/source/logo/BPP-AstroVascPy-Github.jpg | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/index.rst:4: WARNING: image file not readable: logo/BBP-AstroVascPy-Github.jpg | |
pickling environment... done | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/api_ref.rst: WARNING: document isn't included in any toctree | |
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/docs/source/changelog.rst: WARNING: document isn't included in any toctree | |
checking consistency... done | |
preparing documents... done | |
copying assets... copying static files... done | |
copying extra files... done | |
done | |
[2Kwriting output... [ 8%] api_ref [2Kwriting output... [ 15%] changelog [2Kwriting output... [ 23%] generated/astrovascpy.PetscBinaryIO [2Kwriting output... [ 31%] generated/astrovascpy.bloodflow [2Kwriting output... [ 38%] generated/astrovascpy.exceptions [2Kwriting output... [ 46%] generated/astrovascpy.io [2Kwriting output... [ 54%] generated/astrovascpy.ou [2Kwriting output... [ 62%] generated/astrovascpy.plotting [2Kwriting output... [ 69%] generated/astrovascpy.report_reader [2Kwriting output... [ 77%] generated/astrovascpy.report_writer [2Kwriting output... [ 85%] generated/astrovascpy.scipy_petsc_conversions [2Kwriting output... [ 92%] generated/astrovascpy.utils [2Kwriting output... [100%] index | |
generating indices... genindex py-modindex done | |
writing additional pages... search done | |
dumping search index in English (code: en)... done | |
dumping object inventory... done | |
build succeeded, 43 warnings. | |
The HTML pages are in build/html. | |
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089694/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
docs: OK (85.72=setup[76.88]+cmd[8.84] seconds) | |
congratulations :) (86.01 seconds) | |
[32;1m$ section_end section_tox[0;m | |
[0Ksection_end:1702976136:section_tox [0K | |
section_end:1702976136:step_script [0Ksection_start:1702976136:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m[0;m | |
Using git from spack modules | |
[32;1mUploading artifacts...[0;m | |
Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=86972 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
[0;33mWARNING: ./doc/build/: no matching files [0;m | |
./docs/build/: found 164 matching files and directories[0;m | |
Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=1089694 responseStatus[0;m=201 Created token[0;m=64_VJRz2 | |
section_end:1702976137:upload_artifacts_on_success [0Ksection_start:1702976137:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
Using git from spack modules | |
section_end:1702976138:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
[0K on BB5 map runner pnPo3yJy[0;m | |
section_start:1702976019:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
section_end:1702976019:resolve_secrets [0Ksection_start:1702976019:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor4068472163, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
Runner ID 29, project root molsys, project name AstroVascPy | |
Pipeline ID 181495, build ref , job ID 1089693 | |
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089693, optional exclusive flag , optional cpus per task flag --cpus-per-task=6, optional qos flag , optional reservation flag | |
A slurm job will be created with name GL_J1089693_PROD_P2342_CP1_C2 | |
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcimolsys partition=prod qos= reservation= | |
Not executing the chown -R | |
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
Submitted batch job 1950771 | |
job state: R | |
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1089693_PROD_P2342_CP1_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089693 --time=1:00:00 --wrap="sleep infinity" | |
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089693 --ntasks=1 --jobid=1950771 --cpus-per-task=6 --mem=30750M | |
section_end:1702976020:prepare_executor [0Ksection_start:1702976020:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
Using git from spack modules | |
Running on r1i7n22 via bbpv1.epfl.ch... | |
section_end:1702976027:prepare_script [0Ksection_start:1702976027:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
Using git from spack modules | |
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
[32;1mFetching changes with git depth set to 20...[0;m | |
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/.git/ | |
[32;1mCreated fresh repository.[0;m | |
[32;1mChecking out 8758d502 as nicola/scipy_petsc_bug...[0;m | |
Skipping object checkout, Git LFS is not installed. | |
[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m | |
section_end:1702976030:get_sources [0Ksection_start:1702976030:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
Using git from spack modules | |
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
[32;1m$ module purge[0;m | |
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
[32;1m$ module load archive/2020-12 python/3.7.4[0;m | |
[32;1m$ module unload archive/2020-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.7.4 | |
[32;1m$ module load archive/2021-12 python/3.8.3[0;m | |
[32;1m$ module unload archive/2021-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.8.3 | |
[32;1m$ module load archive/2023-02 python/3.9.7[0;m | |
[32;1m$ module unload archive/2023-02[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.9.7 | |
[32;1m$ module load unstable python[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.10.8 | |
[32;1m$ load-modules() { # collapsed multi-line command[0;m | |
[32;1m$ load-modules $SYSTEM_MODULES[0;m | |
Loaded module git from unstable | |
Loaded module cmake from unstable | |
Loaded module graphviz from unstable | |
[32;1m$ load-modules $EXTRA_MODULES[0;m | |
Loaded module gcc from unstable | |
Loaded module hpe-mpi from unstable | |
Autoloading python/3.10.8 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module py-mpi4py from unstable | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module petsc from unstable | |
Autoloading python/3.10.8 | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module py-petsc4py from unstable | |
[32;1m$ module list -t[0;m | |
Currently Loaded Modulefiles: | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4 | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/python/3.10.8 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/git/2.38.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/cmake/3.24.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/graphviz/2.49.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/compilers/linux-rhel7-haswell/gcc/12.2.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-mpi4py/3.1.4 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/petsc/3.18.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-petsc4py/3.18.1 | |
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
[32;1m$ print_var XDG_CONFIG_HOME[0;m | |
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/local_config[0m | |
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
insteadOf = https://bbpgitlab.epfl.ch/ | |
insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
insteadOf = git@bbpgitlab.epfl.ch: | |
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
[0Ksection_start:1702976032:section_venv[collapsed=true] [0KSetting up the virtual env | |
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
[32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
[32;1m$ rm -rf "$CI_VENV"[0;m | |
[32;1m$ python -mvenv "$CI_VENV"[0;m | |
[32;1m$ source "$CI_VENV/bin/activate"[0;m | |
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (22.2.2) | |
Collecting pip | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/505/2d7889c1f9d05/pip-23.3.2-py3-none-any.whl (2.1 MB) | |
ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 74.1 MB/s eta 0:00:00 | |
Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages (63.0.0) | |
Collecting setuptools | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/1e8/fdff6797d3865/setuptools-69.0.2-py3-none-any.whl (819 kB) | |
âââââââââââââââââââââââââââââââââââââ 819.5/819.5 kB 271.4 MB/s eta 0:00:00 | |
Collecting wheel | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/177/f9c9b0d45c478/wheel-0.42.0-py3-none-any.whl (65 kB) | |
âââââââââââââââââââââââââââââââââââââââ 65.4/65.4 kB 209.0 MB/s eta 0:00:00 | |
Installing collected packages: wheel, setuptools, pip | |
Attempting uninstall: setuptools | |
Found existing installation: setuptools 63.0.0 | |
Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/venv | |
Can't uninstall 'setuptools'. No files were found to uninstall. | |
Attempting uninstall: pip | |
Found existing installation: pip 22.2.2 | |
Uninstalling pip-22.2.2: | |
Successfully uninstalled pip-22.2.2 | |
Successfully installed pip-23.3.2 setuptools-69.0.2 wheel-0.42.0 | |
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Collecting tox | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2ad/b83d68f271168/tox-4.11.4-py3-none-any.whl (153 kB) | |
ââââââââââââââââââââââââââââââââââââââ 154.0/154.0 kB 18.6 MB/s eta 0:00:00 | |
Collecting cachetools>=5.3.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/861/f35a13a451f94/cachetools-5.3.2-py3-none-any.whl (9.3 kB) | |
Collecting chardet>=5.2 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 55.3 MB/s eta 0:00:00 | |
Collecting colorama>=0.4.6 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
Collecting filelock>=3.12.3 (from tox) | |
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Collecting packaging>=23.1 (from tox) | |
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Collecting platformdirs>=3.10 (from tox) | |
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Collecting pluggy>=1.3 (from tox) | |
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Collecting tomli>=2.0.1 (from tox) | |
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Collecting virtualenv>=20.24.3 (from tox) | |
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Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
Successfully installed cachetools-5.3.2 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-23.2 platformdirs-4.1.0 pluggy-1.3.0 pyproject-api-1.6.1 tomli-2.0.1 tox-4.11.4 virtualenv-20.25.0 | |
[32;1m$ section_end section_venv[0;m | |
[0Ksection_end:1702976049:section_venv [0K | |
[32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
[36mPRE_BUILD_COMMAND=[0m | |
[32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
[32;1m$ section_start section_tox "Running Tox"[0;m | |
[0Ksection_start:1702976049:section_tox [0KRunning Tox | |
[32;1m$ python -mtox $TOX_OPTIONS[0;m | |
lint: install_deps> python -I -m pip install pre-commit pylint pylint-exit | |
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel | |
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: get_requires_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: install_requires_for_build_wheel> python -I -m pip install wheel | |
.pkg: freeze> python -m pip freeze --all | |
.pkg: packaging==23.2,pip==23.3.1,setuptools==69.0.2,setuptools-scm==8.0.4,tomli==2.0.1,typing_extensions==4.9.0,wheel==0.42.0 | |
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
lint: install_package_deps> python -I -m pip install cached-property click coverage cython h5py libsonata matplotlib morphio networkx numpy 'pandas<2.0.0' psutil pytest pytest-mpi pyyaml scipy seaborn tables tqdm trimesh vascpy | |
lint: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz | |
lint: freeze> python -m pip freeze --all | |
lint: astroid==3.0.2,AstroVascPy @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz#sha256=19e8cb9814bd98f0088dba42bc107d8291378c2cb81d2262b04eceeb4b7e6411,blosc2==2.3.2,cached-property==1.5.2,cfgv==3.4.0,click==8.1.7,contourpy==1.2.0,coverage==7.3.3,cycler==0.12.1,Cython==3.0.6,dill==0.3.7,distlib==0.3.8,exceptiongroup==1.2.0,filelock==3.13.1,fonttools==4.47.0,h5py==3.10.0,identify==2.5.33,iniconfig==2.0.0,isort==5.13.2,kiwisolver==1.4.5,libsonata==0.1.24,matplotlib==3.8.2,mccabe==0.7.0,MorphIO==3.3.7,mpi4py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mpi4py-3.1.4-glx4cfnu5cionch2hbeyzns5ol3vexp7/spack-src,msgpack==1.0.7,ndindex==1.7,networkx==3.2.1,nodeenv==1.8.0,numexpr==2.8.8,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging==23.2,pandas==1.5.3,petsc4py @ file:///nvme/bbpcihpcdeploy/1912700/spack-stage/spack-stage-py-petsc4py-3.18.1-k6k4ybhubjpjanttcmmql5ditq2bxn32/spack-src,Pillow==10.1.0,pip==23.3.1,platformdirs==4.1.0,pluggy==1.3.0,pre-commit==3.6.0,psutil==5.9.7,py-cpuinfo==9.0.0,pylint==3.0.3,pylint-exit==1.2.0,pyparsing==3.1.1,pytest==7.4.3,pytest-mpi==0.6,python-dateutil==2.8.2,pytz==2023.3.post1,PyYAML==6.0.1,scipy==1.11.4,seaborn==0.13.0,setuptools @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-setuptools-63.0.0-c6hdpvjjddmcm3xf5begyfpkjkzj2oke/spack-src/setuptools-63.0.0-py3-none-any.whl,six==1.16.0,tables==3.9.2,tomli==2.0.1,tomlkit==0.12.3,tqdm==4.66.1,trimesh==4.0.6,typing_extensions==4.9.0,vascpy==0.1.1,virtualenv==20.25.0,wheel==0.42.0 | |
lint: commands[0]> pre-commit run --all-files --show-diff-on-failure | |
[INFO] Initializing environment for https://github.com/pre-commit/pre-commit-hooks. | |
[INFO] Initializing environment for https://github.com/alessandrojcm/commitlint-pre-commit-hook. | |
[INFO] Initializing environment for https://github.com/alessandrojcm/commitlint-pre-commit-hook:conventional-changelog-conventionalcommits. | |
[INFO] Initializing environment for https://github.com/pycqa/isort. | |
[INFO] Initializing environment for https://github.com/psf/black. | |
[INFO] Initializing environment for https://github.com/codespell-project/codespell. | |
[INFO] Initializing environment for https://github.com/PyCQA/flake8. | |
[INFO] Installing environment for https://github.com/pre-commit/pre-commit-hooks. | |
[INFO] Once installed this environment will be reused. | |
[INFO] This may take a few minutes... | |
[INFO] Installing environment for https://github.com/pycqa/isort. | |
[INFO] Once installed this environment will be reused. | |
[INFO] This may take a few minutes... | |
[INFO] Installing environment for https://github.com/psf/black. | |
[INFO] Once installed this environment will be reused. | |
[INFO] This may take a few minutes... | |
[INFO] Installing environment for https://github.com/codespell-project/codespell. | |
[INFO] Once installed this environment will be reused. | |
[INFO] This may take a few minutes... | |
[INFO] Installing environment for https://github.com/PyCQA/flake8. | |
[INFO] Once installed this environment will be reused. | |
[INFO] This may take a few minutes... | |
check for added large files..............................................Passed | |
check for case conflicts.................................................Passed | |
check for merge conflicts................................................Passed | |
check for broken symlinks............................(no files to check)Skipped | |
check yaml...............................................................Passed | |
debug statements (python)................................................Passed | |
fix end of files.........................................................Passed | |
trim trailing whitespace.................................................Passed | |
isort....................................................................Passed | |
black....................................................................Passed | |
codespell................................................................Passed | |
flake8...................................................................Passed | |
lint: commands[1]> bash -c 'pylint -j 1 astrovascpy docs/source/conf.py setup.py || pylint-exit $?' | |
************* Module astrovascpy.io | |
astrovascpy/io.py:64:26: R1732: Consider using 'with' for resource-allocating operations (consider-using-with) | |
astrovascpy/io.py:51:34: W0613: Unused argument 'is_cc' (unused-argument) | |
astrovascpy/io.py:74:33: W0613: Unused argument 'is_cc' (unused-argument) | |
astrovascpy/io.py:96:54: W0613: Unused argument 'is_cc' (unused-argument) | |
************* Module astrovascpy.utils | |
astrovascpy/utils.py:67:19: W0212: Access to a protected member _node_properties of a client class (protected-access) | |
astrovascpy/utils.py:67:55: W0212: Access to a protected member _edge_properties of a client class (protected-access) | |
astrovascpy/utils.py:542:15: R1735: Consider using '{}' instead of a call to 'dict'. (use-dict-literal) | |
astrovascpy/utils.py:545:4: C0116: Missing function or method docstring (missing-function-docstring) | |
astrovascpy/utils.py:545:4: E0213: Method 'region' should have "self" as first argument (no-self-argument) | |
astrovascpy/utils.py:556:4: C0116: Missing function or method docstring (missing-function-docstring) | |
astrovascpy/utils.py:588:8: C0206: Consider iterating with .items() (consider-using-dict-items) | |
astrovascpy/utils.py:613:11: R1735: Consider using '{}' instead of a call to 'dict'. (use-dict-literal) | |
astrovascpy/utils.py:616:4: C0116: Missing function or method docstring (missing-function-docstring) | |
astrovascpy/utils.py:616:4: E0213: Method 'region' should have "self" as first argument (no-self-argument) | |
astrovascpy/utils.py:628:4: C0116: Missing function or method docstring (missing-function-docstring) | |
astrovascpy/utils.py:658:8: C0206: Consider iterating with .items() (consider-using-dict-items) | |
astrovascpy/utils.py:733:8: W0621: Redefining name 'time' from outer scope (line 15) (redefined-outer-name) | |
************* Module astrovascpy.scipy_petsc_conversions | |
astrovascpy/scipy_petsc_conversions.py:35:15: W0212: Access to a protected member _typedict of a client class (protected-access) | |
astrovascpy/scipy_petsc_conversions.py:130:8: W0632: Possible unbalanced tuple unpacking with sequence defined at line 537 of astrovascpy.PetscBinaryIO: left side has 1 label, right side has 0 values (unbalanced-tuple-unpacking) | |
************* Module astrovascpy.PetscBinaryIO | |
astrovascpy/PetscBinaryIO.py:72:20: W0707: Consider explicitly re-raising using 'except Exception as exc' and 'raise importlib.metadata.PackageNotFoundError from exc' (raise-missing-from) | |
astrovascpy/PetscBinaryIO.py:77:27: W0212: Access to a protected member _path of a client class (protected-access) | |
astrovascpy/PetscBinaryIO.py:108:14: W1514: Using open without explicitly specifying an encoding (unspecified-encoding) | |
astrovascpy/PetscBinaryIO.py:108:14: R1732: Consider using 'with' for resource-allocating operations (consider-using-with) | |
astrovascpy/PetscBinaryIO.py:120:14: W1514: Using open without explicitly specifying an encoding (unspecified-encoding) | |
astrovascpy/PetscBinaryIO.py:45:0: R0912: Too many branches (23/12) (too-many-branches) | |
astrovascpy/PetscBinaryIO.py:45:0: R0915: Too many statements (55/50) (too-many-statements) | |
astrovascpy/PetscBinaryIO.py:120:14: R1732: Consider using 'with' for resource-allocating operations (consider-using-with) | |
astrovascpy/PetscBinaryIO.py:202:12: W0212: Access to a protected member _update_dtypes of a client class (protected-access) | |
astrovascpy/PetscBinaryIO.py:210:12: W0212: Access to a protected member _update_dtypes of a client class (protected-access) | |
astrovascpy/PetscBinaryIO.py:217:0: C0115: Missing class docstring (missing-class-docstring) | |
astrovascpy/PetscBinaryIO.py:256:15: C0209: Formatting a regular string which could be an f-string (consider-using-f-string) | |
astrovascpy/PetscBinaryIO.py:256:33: R1725: Consider using Python 3 style super() without arguments (super-with-arguments) | |
astrovascpy/PetscBinaryIO.py:271:0: R0205: Class 'PetscBinaryIO' inherits from object, can be safely removed from bases in python3 (useless-object-inheritance) | |
astrovascpy/PetscBinaryIO.py:329:27: C0209: Formatting a regular string which could be an f-string (consider-using-f-string) | |
astrovascpy/PetscBinaryIO.py:339:12: W0707: Consider explicitly re-raising using 'except MemoryError as exc' and 'raise IOError('Inconsistent or invalid Vec data in file') from exc' (raise-missing-from) | |
astrovascpy/PetscBinaryIO.py:348:29: W0212: Access to a protected member _classid of a client class (protected-access) | |
astrovascpy/PetscBinaryIO.py:345:4: R1711: Useless return at end of function or method (useless-return) | |
astrovascpy/PetscBinaryIO.py:380:12: W0707: Consider explicitly re-raising using 'except (AssertionError, MemoryError, IndexError) as exc' and 'raise IOError('Inconsistent or invalid Mat data in file') from exc' (raise-missing-from) | |
astrovascpy/PetscBinaryIO.py:389:29: W0212: Access to a protected member _classid of a client class (protected-access) | |
astrovascpy/PetscBinaryIO.py:385:4: R1711: Useless return at end of function or method (useless-return) | |
astrovascpy/PetscBinaryIO.py:420:12: W0707: Consider explicitly re-raising using 'except (AssertionError, MemoryError, IndexError) as exc' and 'raise IOError('Inconsistent or invalid Mat data in file') from exc' (raise-missing-from) | |
astrovascpy/PetscBinaryIO.py:429:4: C0116: Missing function or method docstring (missing-function-docstring) | |
astrovascpy/PetscBinaryIO.py:434:4: C0116: Missing function or method docstring (missing-function-docstring) | |
astrovascpy/PetscBinaryIO.py:438:8: W0612: Unused variable 'V' (unused-variable) | |
astrovascpy/PetscBinaryIO.py:439:8: W0612: Unused variable 'M' (unused-variable) | |
astrovascpy/PetscBinaryIO.py:439:11: W0612: Unused variable 'N' (unused-variable) | |
astrovascpy/PetscBinaryIO.py:440:8: W0612: Unused variable 'J' (unused-variable) | |
astrovascpy/PetscBinaryIO.py:441:8: W0612: Unused variable 'I' (unused-variable) | |
astrovascpy/PetscBinaryIO.py:471:12: W0707: Consider explicitly re-raising using 'except (MemoryError, IndexError) as exc' and 'raise IOError('Inconsistent or invalid IS data in file') from exc' (raise-missing-from) | |
astrovascpy/PetscBinaryIO.py:478:29: W0212: Access to a protected member _classid of a client class (protected-access) | |
astrovascpy/PetscBinaryIO.py:475:4: R1711: Useless return at end of function or method (useless-return) | |
astrovascpy/PetscBinaryIO.py:515:20: W0707: Consider explicitly re-raising using 'except (MemoryError, IndexError) as exc' and 'raise DoneWithFile from exc' (raise-missing-from) | |
astrovascpy/PetscBinaryIO.py:519:20: W0707: Consider explicitly re-raising using 'except KeyError as exc' and 'raise IOError('Invalid PetscObject CLASSID or object not implemented for python') from exc' (raise-missing-from) | |
astrovascpy/PetscBinaryIO.py:505:18: R1732: Consider using 'with' for resource-allocating operations (consider-using-with) | |
astrovascpy/PetscBinaryIO.py:572:20: W0707: Consider explicitly re-raising using 'except AssertionError as exc' and 'raise TypeError('Object %s is not a valid PETSc object' % petscobj.__repr__()) from exc' (raise-missing-from) | |
astrovascpy/PetscBinaryIO.py:572:36: C0209: Formatting a regular string which could be an f-string (consider-using-f-string) | |
astrovascpy/PetscBinaryIO.py:572:79: C2801: Unnecessarily calls dunder method __repr__. Use repr built-in function. (unnecessary-dunder-call) | |
astrovascpy/PetscBinaryIO.py:540:4: R1711: Useless return at end of function or method (useless-return) | |
astrovascpy/PetscBinaryIO.py:552:18: R1732: Consider using 'with' for resource-allocating operations (consider-using-with) | |
************* Module astrovascpy.bloodflow | |
astrovascpy/bloodflow.py:44:0: W0622: Redefining built-in 'print' (redefined-builtin) | |
astrovascpy/bloodflow.py:418:0: R0914: Too many local variables (36/25) (too-many-locals) | |
astrovascpy/bloodflow.py:418:0: R0912: Too many branches (17/12) (too-many-branches) | |
astrovascpy/bloodflow.py:418:0: R0915: Too many statements (72/50) (too-many-statements) | |
astrovascpy/bloodflow.py:684:34: C0209: Formatting a regular string which could be an f-string (consider-using-f-string) | |
astrovascpy/bloodflow.py:644:0: R0912: Too many branches (15/12) (too-many-branches) | |
astrovascpy/bloodflow.py:644:0: R0915: Too many statements (66/50) (too-many-statements) | |
************* Module astrovascpy.typing | |
astrovascpy/typing.py:9:0: C0115: Missing class docstring (missing-class-docstring) | |
astrovascpy/typing.py:15:0: C0115: Missing class docstring (missing-class-docstring) | |
----------------------------------- | |
Your code has been rated at 9.48/10 | |
The following messages were raised: | |
- error message issued | |
- warning message issued | |
- refactor message issued | |
- convention message issued | |
No fatal messages detected. Exiting gracefully... | |
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089693/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
lint: OK (142.19=setup[65.75]+cmd[42.10,34.33] seconds) | |
congratulations :) (142.46 seconds) | |
[32;1m$ section_end section_tox[0;m | |
[0Ksection_end:1702976192:section_tox [0K | |
section_end:1702976192:step_script [0Ksection_start:1702976192:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
Using git from spack modules | |
section_end:1702976193:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
[0K on BB5 map runner pnPo3yJy[0;m | |
section_start:1702976020:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
section_end:1702976020:resolve_secrets [0Ksection_start:1702976020:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor401415700, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
Runner ID 29, project root molsys, project name AstroVascPy | |
Pipeline ID 181495, build ref , job ID 1089695 | |
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089695, optional exclusive flag , optional cpus per task flag --cpus-per-task=6, optional qos flag , optional reservation flag | |
A slurm job will be created with name GL_J1089695_PROD_P2342_CP3_C4 | |
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcimolsys partition=prod qos= reservation= | |
Not executing the chown -R | |
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
Submitted batch job 1950773 | |
job state: PD | |
job state: PD | |
job state: R | |
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1089695_PROD_P2342_CP3_C4 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089695 --time=1:00:00 --wrap="sleep infinity" | |
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcimolsys/J1089695 --ntasks=1 --jobid=1950773 --cpus-per-task=6 --mem=30750M | |
section_end:1702976023:prepare_executor [0Ksection_start:1702976023:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
Using git from spack modules | |
Running on r1i7n22 via bbpv1.epfl.ch... | |
section_end:1702976025:prepare_script [0Ksection_start:1702976025:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
Using git from spack modules | |
[32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
[32;1mFetching changes with git depth set to 20...[0;m | |
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/.git/ | |
[32;1mCreated fresh repository.[0;m | |
[32;1mChecking out 8758d502 as nicola/scipy_petsc_bug...[0;m | |
Skipping object checkout, Git LFS is not installed. | |
[32;1mUpdating/initializing submodules recursively with git depth set to 20...[0;m | |
section_end:1702976028:get_sources [0Ksection_start:1702976028:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
Using git from spack modules | |
[32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
[32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
[32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
[32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
[32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
[32;1m$ module purge[0;m | |
[32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
[32;1m$ module load archive/2020-12 python/3.7.4[0;m | |
[32;1m$ module unload archive/2020-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.7.4 | |
[32;1m$ module load archive/2021-12 python/3.8.3[0;m | |
[32;1m$ module unload archive/2021-12[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.8.3 | |
[32;1m$ module load archive/2023-02 python/3.9.7[0;m | |
[32;1m$ module unload archive/2023-02[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.9.7 | |
[32;1m$ module load unstable python[0;m | |
[32;1m$ module unload unstable[0;m | |
[32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
[32;1m$ echo "Loaded $(python -V)"[0;m | |
Loaded Python 3.10.8 | |
[32;1m$ load-modules() { # collapsed multi-line command[0;m | |
[32;1m$ load-modules $SYSTEM_MODULES[0;m | |
Loaded module git from unstable | |
Loaded module cmake from unstable | |
Loaded module graphviz from unstable | |
[32;1m$ load-modules $EXTRA_MODULES[0;m | |
Loaded module gcc from unstable | |
Loaded module hpe-mpi from unstable | |
Autoloading python/3.10.8 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module py-mpi4py from unstable | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module petsc from unstable | |
Autoloading python/3.10.8 | |
Autoloading intel-oneapi-mkl/2021.4.0 | |
Autoloading hpe-mpi/2.25.hmpt | |
Loaded module py-petsc4py from unstable | |
[32;1m$ module list -t[0;m | |
Currently Loaded Modulefiles: | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4 | |
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/python/3.10.8 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/git/2.38.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/cmake/3.24.3 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/graphviz/2.49.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/compilers/linux-rhel7-haswell/gcc/12.2.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-mpi4py/3.1.4 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/petsc/3.18.1 | |
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-12/applications/linux-rhel7-skylake/py-petsc4py/3.18.1 | |
[32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
[32;1m$ print_var XDG_CONFIG_HOME[0;m | |
[36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/local_config[0m | |
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
[32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
insteadOf = https://bbpgitlab.epfl.ch/ | |
insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
insteadOf = git@bbpgitlab.epfl.ch: | |
[32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
[0Ksection_start:1702976030:section_venv[collapsed=true] [0KSetting up the virtual env | |
[32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
[32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
[32;1m$ rm -rf "$CI_VENV"[0;m | |
[32;1m$ python -mvenv "$CI_VENV"[0;m | |
[32;1m$ source "$CI_VENV/bin/activate"[0;m | |
[32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (22.2.2) | |
Collecting pip | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/505/2d7889c1f9d05/pip-23.3.2-py3-none-any.whl (2.1 MB) | |
ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 74.4 MB/s eta 0:00:00 | |
Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages (63.0.0) | |
Collecting setuptools | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/1e8/fdff6797d3865/setuptools-69.0.2-py3-none-any.whl (819 kB) | |
âââââââââââââââââââââââââââââââââââââ 819.5/819.5 kB 225.6 MB/s eta 0:00:00 | |
Collecting wheel | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/177/f9c9b0d45c478/wheel-0.42.0-py3-none-any.whl (65 kB) | |
âââââââââââââââââââââââââââââââââââââââ 65.4/65.4 kB 202.1 MB/s eta 0:00:00 | |
Installing collected packages: wheel, setuptools, pip | |
Attempting uninstall: setuptools | |
Found existing installation: setuptools 63.0.0 | |
Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/venv | |
Can't uninstall 'setuptools'. No files were found to uninstall. | |
Attempting uninstall: pip | |
Found existing installation: pip 22.2.2 | |
Uninstalling pip-22.2.2: | |
Successfully uninstalled pip-22.2.2 | |
Successfully installed pip-23.3.2 setuptools-69.0.2 wheel-0.42.0 | |
[32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
Collecting tox | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2ad/b83d68f271168/tox-4.11.4-py3-none-any.whl (153 kB) | |
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Collecting cachetools>=5.3.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/861/f35a13a451f94/cachetools-5.3.2-py3-none-any.whl (9.3 kB) | |
Collecting chardet>=5.2 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
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Collecting colorama>=0.4.6 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
Collecting filelock>=3.12.3 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/57d/bda9b35157b05/filelock-3.13.1-py3-none-any.whl (11 kB) | |
Collecting packaging>=23.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/8c4/91190033a9af7/packaging-23.2-py3-none-any.whl (53 kB) | |
âââââââââââââââââââââââââââââââââââââââ 53.0/53.0 kB 211.3 MB/s eta 0:00:00 | |
Collecting platformdirs>=3.10 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/11c/8f37bcca40db9/platformdirs-4.1.0-py3-none-any.whl (17 kB) | |
Collecting pluggy>=1.3 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/d89/c696a773f8bd3/pluggy-1.3.0-py3-none-any.whl (18 kB) | |
Collecting pyproject-api>=1.6.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
Collecting tomli>=2.0.1 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/939/de3e7a6161af0/tomli-2.0.1-py3-none-any.whl (12 kB) | |
Collecting virtualenv>=20.24.3 (from tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/423/8949c5ffe6876/virtualenv-20.25.0-py3-none-any.whl (3.8 MB) | |
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Collecting distlib<1,>=0.3.7 (from virtualenv>=20.24.3->tox) | |
Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 256.0 MB/s eta 0:00:00 | |
Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
Successfully installed cachetools-5.3.2 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-23.2 platformdirs-4.1.0 pluggy-1.3.0 pyproject-api-1.6.1 tomli-2.0.1 tox-4.11.4 virtualenv-20.25.0 | |
[32;1m$ section_end section_venv[0;m | |
[0Ksection_end:1702976046:section_venv [0K | |
[32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
[36mPRE_BUILD_COMMAND=[0m | |
[32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
[32;1m$ section_start section_tox "Running Tox"[0;m | |
[0Ksection_start:1702976046:section_tox [0KRunning Tox | |
[32;1m$ python -mtox $TOX_OPTIONS[0;m | |
.pkg: install_requires> python -I -m pip install 'setuptools>=42' 'setuptools_scm[toml]>=3.4' wheel | |
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: get_requires_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: install_requires_for_build_wheel> python -I -m pip install wheel | |
.pkg: freeze> python -m pip freeze --all | |
.pkg: packaging==23.2,pip==23.3.1,setuptools==69.0.2,setuptools-scm==8.0.4,tomli==2.0.1,typing_extensions==4.9.0,wheel==0.42.0 | |
.pkg: prepare_metadata_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
py310: install_package_deps> python -I -m pip install cached-property click coverage cython h5py libsonata matplotlib morphio networkx numpy 'pandas<2.0.0' psutil pytest pytest-mpi pyyaml scipy seaborn tables tqdm trimesh vascpy | |
py310: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz | |
py310: freeze> python -m pip freeze --all | |
py310: AstroVascPy @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/.tox/.tmp/package/1/AstroVascPy-0.0.1.tar.gz#sha256=6c0ee13d2362e3b66656824fc44e960be06486fdf444537aa6a87e85ed174b00,blosc2==2.3.2,cached-property==1.5.2,click==8.1.7,contourpy==1.2.0,coverage==7.3.3,cycler==0.12.1,Cython==3.0.6,exceptiongroup==1.2.0,fonttools==4.47.0,h5py==3.10.0,iniconfig==2.0.0,kiwisolver==1.4.5,libsonata==0.1.24,matplotlib==3.8.2,MorphIO==3.3.7,mpi4py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mpi4py-3.1.4-glx4cfnu5cionch2hbeyzns5ol3vexp7/spack-src,msgpack==1.0.7,ndindex==1.7,networkx==3.2.1,numexpr==2.8.8,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging==23.2,pandas==1.5.3,petsc4py @ file:///nvme/bbpcihpcdeploy/1912700/spack-stage/spack-stage-py-petsc4py-3.18.1-k6k4ybhubjpjanttcmmql5ditq2bxn32/spack-src,Pillow==10.1.0,pip==23.3.1,pluggy==1.3.0,psutil==5.9.7,py-cpuinfo==9.0.0,pyparsing==3.1.1,pytest==7.4.3,pytest-mpi==0.6,python-dateutil==2.8.2,pytz==2023.3.post1,PyYAML==6.0.1,scipy==1.11.4,seaborn==0.13.0,setuptools @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-setuptools-63.0.0-c6hdpvjjddmcm3xf5begyfpkjkzj2oke/spack-src/setuptools-63.0.0-py3-none-any.whl,six==1.16.0,tables==3.9.2,tomli==2.0.1,tqdm==4.66.1,trimesh==4.0.6,vascpy==0.1.1,wheel==0.42.0 | |
py310: commands[0]> coverage run --branch --source=astrovascpy -m pytest --basetemp=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/.tox/py310/tmp --verbose --junit-xml=reports/pytest-py310.xml | |
============================= test session starts ============================== | |
platform linux -- Python 3.10.8, pytest-7.4.3, pluggy-1.3.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/.tox/py310/bin/python | |
cachedir: .tox/py310/.pytest_cache | |
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy | |
configfile: pyproject.toml | |
testpaths: tests | |
plugins: mpi-0.6 | |
collecting ... collected 56 items | |
tests/test_bloodflow.py::test_compute_edge_resistances PASSED [ 1%] | |
tests/test_bloodflow.py::test_set_edge_resistances PASSED [ 3%] | |
tests/test_bloodflow.py::test_set_endfeet_ids PASSED [ 5%] | |
tests/test_bloodflow.py::test_get_radii_at_endfeet PASSED [ 7%] | |
tests/test_bloodflow.py::test_get_radius_at_endfoot PASSED [ 8%] | |
tests/test_bloodflow.py::test_set_radii_at_endfeet PASSED [ 10%] | |
tests/test_bloodflow.py::test_set_radius_at_endfoot PASSED [ 12%] | |
tests/test_bloodflow.py::test_set_endfoot_id PASSED [ 14%] | |
tests/test_bloodflow.py::test_get_closest_edges PASSED [ 16%] | |
tests/test_bloodflow.py::test_simulate_vasodilation_ou_process PASSED [ 17%] | |
tests/test_bloodflow.py::test_simulate_ou_process PASSED [ 19%] | |
tests/test_bloodflow.py::test_depth_first_search PASSED [ 21%] | |
tests/test_bloodflow.py::test_compute_static_laplacian PASSED [ 23%] | |
tests/test_bloodflow.py::test_update_static_flow_pressure PASSED [ 25%] | |
tests/test_bloodflow.py::test_total_flow_conservation_in_graph PASSED [ 26%] | |
tests/test_bloodflow.py::test_conservation_flow PASSED [ 28%] | |
tests/test_bloodflow.py::test_static_construct_incidence_matrix PASSED [ 30%] | |
tests/test_bloodflow.py::test_solve_linear PASSED [ 32%] | |
tests/test_bloodflow.py::test_boundary_flows_A_based PASSED [ 33%] | |
tests/test_graphs.py::test_simple_graph PASSED [ 35%] | |
tests/test_graphs.py::test_bifurcation PASSED [ 37%] | |
tests/test_graphs.py::test_loop PASSED [ 39%] | |
tests/test_io.py::test_petsc_installation PASSED [ 41%] | |
tests/test_io.py::test_load_graph PASSED [ 42%] | |
tests/test_io.py::test_load_graph_from_h5 PASSED [ 44%] | |
tests/test_io.py::test_load_graph_from_csv PASSED [ 46%] | |
tests/test_io.py::test_load_graph_from_bin PASSED [ 48%] | |
tests/test_mpi.py::test_numpy_array2petsc SKIPPED (need --with-mpi o...) [ 50%] | |
tests/test_mpi.py::test_scipy2petsc_conversion SKIPPED (need --with-...) [ 51%] | |
tests/test_mpi.py::test_coomatrix2PETScMat SKIPPED (need --with-mpi ...) [ 53%] | |
tests/test_ou.py::test_OU_calibration PASSED [ 55%] | |
tests/test_report_reader.py::TestBloodflowReport::test_time_units PASSED [ 57%] | |
tests/test_report_reader.py::TestBloodflowReport::test_data_units PASSED [ 58%] | |
tests/test_report_reader.py::TestBloodflowReport::test_population_names PASSED [ 60%] | |
tests/test_report_reader.py::TestBloodflowReport::test_get_population PASSED [ 62%] | |
tests/test_report_reader.py::TestBloodflowReport::test_iter PASSED [ 64%] | |
tests/test_report_reader.py::TestBloodflowReport::test_filter PASSED [ 66%] | |
tests/test_report_reader.py::TestPopulationBloodflowReport::test_name PASSED [ 67%] | |
tests/test_report_reader.py::TestPopulationBloodflowReport::test_get PASSED [ 69%] | |
tests/test_report_reader.py::TestPopulationBloodflowReport::test_node_ids PASSED [ 71%] | |
tests/test_report_reader.py::test_overriden_function PASSED [ 73%] | |
tests/test_report_writer.py::test_write_simulation_report PASSED [ 75%] | |
tests/test_utils.py::test_find_neighbors PASSED [ 76%] | |
tests/test_utils.py::test_find_degrees_of_neighbors PASSED [ 78%] | |
tests/test_utils.py::test_create_entry_largest_nodes PASSED [ 80%] | |
tests/test_utils.py::test_get_largest_nodes PASSED [ 82%] | |
tests/test_utils.py::test_get_large_nodes PASSED [ 83%] | |
tests/test_utils.py::test_compute_edge_data PASSED [ 85%] | |
tests/test_utils.py::test_set_edge_data PASSED [ 87%] | |
tests/test_utils.py::test_is_iterable PASSED [ 89%] | |
tests/test_utils.py::test_ensure_list PASSED [ 91%] | |
tests/test_utils.py::test_ensure_ids PASSED [ 92%] | |
tests/test_utils.py::test_create_input_speed PASSED [ 94%] | |
tests/test_utils.py::test_sine_estimation[None] PASSED [ 96%] | |
tests/test_utils.py::test_sine_estimation[15] PASSED [ 98%] | |
tests/test_utils.py::test_sine_estimation[30] PASSED [100%] | |
- generated xml file: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/reports/pytest-py310.xml - | |
======================== 53 passed, 3 skipped in 9.89s ========================= | |
py310: commands[1]> mpirun -n 4 coverage run --branch --parallel-mode --source=astrovascpy -m pytest --with-mpi /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/tests/test_mpi.py | |
============================= test session starts ============================== | |
platform linux -- Python 3.10.8, pytest-7.4.3, pluggy-1.3.0 | |
cachedir: .tox/py310/.pytest_cache | |
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy | |
configfile: pyproject.toml | |
plugins: mpi-0.6 | |
collected 3 items | |
tests/test_mpi.py ============================= test session starts ============================== | |
platform linux -- Python 3.10.8, pytest-7.4.3, pluggy-1.3.0 | |
cachedir: .tox/py310/.pytest_cache | |
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy | |
configfile: pyproject.toml | |
plugins: mpi-0.6 | |
collected 3 items | |
tests/test_mpi.py ============================= test session starts ============================== | |
platform linux -- Python 3.10.8, pytest-7.4.3, pluggy-1.3.0 | |
cachedir: .tox/py310/.pytest_cache | |
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy | |
configfile: pyproject.toml | |
plugins: mpi-0.6 | |
collected 3 items | |
tests/test_mpi.py ============================= test session starts ============================== | |
platform linux -- Python 3.10.8, pytest-7.4.3, pluggy-1.3.0 | |
cachedir: .tox/py310/.pytest_cache | |
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy | |
configfile: pyproject.toml | |
plugins: mpi-0.6 | |
collected 3 items | |
tests/test_mpi.py ............ [100%] [100%] [100%] [100%] | |
=============================== MPI Information ================================ | |
rank: 1 | |
size: 4 | |
MPI version: 3.1 | |
MPI library version: HPE HMPT 2.25 10/22/21 03:18:39 | |
MPI vendor: unknown 0.0.0 | |
mpi4py rc: | |
mpi4py config: | |
mpicc: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicc | |
mpicxx: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicxx | |
mpif90: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif90 | |
mpif77: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif77 | |
============================== 3 passed in 0.96s =============================== | |
=============================== MPI Information ================================ | |
rank: 2 | |
size: 4 | |
MPI version: 3.1 | |
MPI library version: HPE HMPT 2.25 10/22/21 03:18:39 | |
MPI vendor: unknown 0.0.0 | |
mpi4py rc: | |
mpi4py config: | |
mpicc: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicc | |
mpicxx: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicxx | |
mpif90: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif90 | |
mpif77: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif77 | |
============================== 3 passed in 0.96s =============================== | |
=============================== MPI Information ================================ | |
rank: 0 | |
size: 4 | |
MPI version: 3.1 | |
MPI library version: HPE HMPT 2.25 10/22/21 03:18:39 | |
MPI vendor: unknown 0.0.0 | |
mpi4py rc: | |
mpi4py config: | |
mpicc: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicc | |
mpicxx: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicxx | |
mpif90: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif90 | |
mpif77: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif77 | |
============================== 3 passed in 0.96s =============================== | |
=============================== MPI Information ================================ | |
rank: 3 | |
size: 4 | |
MPI version: 3.1 | |
MPI library version: HPE HMPT 2.25 10/22/21 03:18:39 | |
MPI vendor: unknown 0.0.0 | |
mpi4py rc: | |
mpi4py config: | |
mpicc: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicc | |
mpicxx: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpicxx | |
mpif90: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif90 | |
mpif77: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/hpe-mpi-2.25.hmpt-bvghnw/bin/mpif77 | |
============================== 3 passed in 0.96s =============================== | |
py310: commands[2]> coverage combine --append | |
Combined data file .coverage-py310.r1i7n22.86070.XuSvcLdx | |
Combined data file .coverage-py310.r1i7n22.86067.XArcBlqx | |
Skipping duplicate data .coverage-py310.r1i7n22.86068.Xoozhjex | |
Skipping duplicate data .coverage-py310.r1i7n22.86069.XuInyjEx | |
py310: commands[3]> coverage report --fail-under=50 | |
Name Stmts Miss Branch BrPart Cover | |
-------------------------------------------------------------------------- | |
astrovascpy/PetscBinaryIO.py 310 167 96 22 44% | |
astrovascpy/__init__.py 0 0 0 0 100% | |
astrovascpy/bloodflow.py 332 58 126 35 75% | |
astrovascpy/exceptions.py 1 0 0 0 100% | |
astrovascpy/io.py 50 7 16 7 79% | |
astrovascpy/ou.py 14 1 2 1 88% | |
astrovascpy/plotting.py 17 17 6 0 0% | |
astrovascpy/report_reader.py 90 0 18 0 100% | |
astrovascpy/report_writer.py 27 0 4 0 100% | |
astrovascpy/scipy_petsc_conversions.py 172 28 44 2 82% | |
astrovascpy/typing.py 10 0 0 0 100% | |
astrovascpy/utils.py 321 125 80 7 60% | |
astrovascpy/version.py 2 2 0 0 0% | |
astrovascpy/vtk_io.py 5 5 0 0 0% | |
-------------------------------------------------------------------------- | |
TOTAL 1351 410 392 74 66% | |
py310: commands[4]> coverage html --directory=reports | |
Wrote HTML report to reports/index.html | |
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcimolsys/J1089695/molsys/AstroVascPy/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__ | |
py310: OK (81.25=setup[66.55]+cmd[10.73,2.54,0.23,0.42,0.79] seconds) | |
congratulations :) (81.57 seconds) | |
[32;1m$ section_end section_tox[0;m | |
[0Ksection_end:1702976128:section_tox [0K | |
section_end:1702976128:step_script [0Ksection_start:1702976128:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
Using git from spack modules | |
section_end:1702976129:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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