test_pipelines_anat.yml

name: Anat Pipelines Tests

on:
  schedule:
    - cron: 0 20 * * 4 # every thursday at 8pm

permissions:
  contents: read

jobs:
  test-t1-linear-MacOS:
    runs-on:
      - self-hosted
      - macOS
    timeout-minutes: 120
    steps:
      - uses: actions/checkout@v4
      - name: Run tests for t1 linear pipelines
        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/ants/2.4.4
          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_linear_mac.xml \
          --disable-warnings \
          ./nonregression/pipelines/anat/test_t1_linear.py

  test-t1-volume-MacOS:
    runs-on:
      - self-hosted
      - macOS
    timeout-minutes: 720
    steps:
      - uses: actions/checkout@v4
      - name: Run tests for t1 volume pipelines
        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/matlab/2019b
          module load clinica/spm12/r7771
          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_volume_mac.xml \
          --disable-warnings \
          ./nonregression/pipelines/anat/test_t1_volume.py

  test-t1-linear-Linux:
    runs-on:
      - self-hosted
      - Linux
      - test-runner
    timeout-minutes: 120
    steps:
      - uses: actions/checkout@v4
      - name: Run tests for t1 linear pipelines
        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/ants/2.4.4
          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_linear_linux.xml \
          --disable-warnings \
          ./nonregression/pipelines/anat/test_t1_linear.py

  test-t1-volume-Linux:
    runs-on:
      - self-hosted
      - Linux
      - test-runner
    timeout-minutes: 720
    steps:
      - uses: actions/checkout@v4
      - name: Run tests for t1 volume pipelines
        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/matlab/2017a
          module load clinica/spm12/r7771
          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_volume_linux.xml \
          --disable-warnings \
          ./nonregression/pipelines/anat/test_t1_volume.py