Freesurfer Anat Pipelines Tests #35
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
| 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 |