Freesurfer Anat Pipelines Tests #3
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| name: Freesurfer Anat Pipelines Tests | |
| on: | |
| schedule: | |
| - cron: 0 20 * * 2 # every tuesday at 8pm | |
| permissions: | |
| contents: read | |
| env: | |
| POETRY_VERSION: '1.6.1' | |
| PYTHON_VERSION: '3.10' | |
| jobs: | |
| test-pipelines-anat-freesurfer-MacOS: | |
| runs-on: | |
| - self-hosted | |
| - macOS | |
| timeout-minutes: 1440 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: snok/install-poetry@v1 | |
| - name: Run tests for anat pipelines using freesurfer | |
| run: | | |
| make env.conda | |
| source ~/miniconda3/etc/profile.d/conda.sh | |
| conda activate "${{ github.workspace }}"/env | |
| source "$(brew --prefix)/opt/modules/init/bash" | |
| module load clinica/freesurfer/6.0.0 | |
| make install | |
| cd test | |
| poetry run pytest --verbose \ | |
| --working_directory=/Volumes/data/working_dir_mac \ | |
| --input_data_directory=/Volumes/data_ci \ | |
| --basetemp=/Volumes/data/tmp \ | |
| --junitxml=./test-reports/non_regression_anat_t1_freesurfer_mac.xml \ | |
| --disable-warnings \ | |
| ./nonregression/pipelines/anat/test_t1_freesurfer.py | |
| test-pipelines-anat-freesurfer-Linux: | |
| runs-on: | |
| - self-hosted | |
| - Linux | |
| - test-runner | |
| timeout-minutes: 1440 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: snok/install-poetry@v1 | |
| with: | |
| version: ${{ env.POETRY_VERSION }} | |
| virtualenvs-create: false | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| cache: poetry | |
| - name: Run tests for anat pipelines using freesurfer | |
| run: | | |
| make env.conda | |
| source /builds/miniconda/etc/profile.d/conda.sh | |
| conda activate "${{ github.workspace }}"/env | |
| source /usr/local/Modules/init/profile.sh | |
| module load clinica/freesurfer/6.0.0 | |
| make install | |
| cd test | |
| poetry run pytest --verbose \ | |
| --working_directory=/mnt/data/ci/working_dir_linux \ | |
| --input_data_directory=/mnt/data_ci \ | |
| --basetemp=/mnt/data/ci/tmp \ | |
| --junitxml=./test-reports/non_regression_anat_t1_freesurfer_linux.xml \ | |
| --disable-warnings \ | |
| ./nonregression/pipelines/anat/test_t1_freesurfer.py |