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test_pipelines_anat.yml
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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