Anat Pipelines Tests #12
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name: Anat Pipelines Tests | |
on: | |
schedule: | |
- cron: 0 20 * * 4 # every thursday at 8pm | |
permissions: | |
contents: read | |
env: | |
POETRY_VERSION: '1.6.1' | |
PYTHON_VERSION: '3.10' | |
jobs: | |
test-t1-linear-MacOS: | |
runs-on: | |
- self-hosted | |
- macOS | |
timeout-minutes: 120 | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: snok/install-poetry@v1 | |
- 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 | |
- uses: snok/install-poetry@v1 | |
- 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 | |
- uses: snok/install-poetry@v1 | |
with: | |
version: ${{ env.POETRY_VERSION }} | |
virtualenvs-create: false | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ env.PYTHON_VERSION }} | |
cache: poetry | |
- name: Run tests for t1 linear pipelines | |
run: | | |
make env.conda | |
source /builds/miniconda/etc/profile.d/conda.sh | |
conda activate "${{ 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 | |
- uses: snok/install-poetry@v1 | |
with: | |
version: ${{ env.POETRY_VERSION }} | |
virtualenvs-create: false | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ env.PYTHON_VERSION }} | |
cache: poetry | |
- name: Run tests for t1 volume pipelines | |
run: | | |
make env.conda | |
source /builds/miniconda/etc/profile.d/conda.sh | |
conda activate "${{ 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 |