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test_pipelines_dwi_preprocessing.yml
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name: DWI Preprocessing Pipelines Tests
on:
schedule:
- cron: 0 20 * * 1 # every monday at 8pm
permissions:
contents: read
env:
POETRY_VERSION: '1.6.1'
PYTHON_VERSION: '3.10'
jobs:
test-dwi-preproc-t1-MacOS:
runs-on:
- self-hosted
- macOS
timeout-minutes: 720
steps:
- uses: actions/checkout@v4
- uses: snok/install-poetry@v1
- name: Run tests for dwi pre-processing using t1 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.all
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_dwi_preproc_using_t1_mac.xml \
--disable-warnings \
./nonregression/pipelines/dwi/preprocessing/test_t1.py
test-dwi-preproc-phasediff-MacOS:
runs-on:
- self-hosted
- macOS
timeout-minutes: 720
steps:
- uses: actions/checkout@v4
- uses: snok/install-poetry@v1
- name: Run tests for dwi pre-processing using phasediff 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.all
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_dwi_preproc_using_phasediff_mac.xml \
--disable-warnings \
./nonregression/pipelines/dwi/preprocessing/test_phase_diff.py
test-dwi-preproc-t1-Linux:
runs-on:
- self-hosted
- Linux
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: ${{ env.PYTHON_VERSION }}
cache: poetry
- name: Run tests for dwi pre-processing using t1 pipelines
run: |
make env.conda
source /builds/miniconda/etc/profile.d/conda.sh
conda activate "${{ github.workspace }}"/env
source /usr/local/Modules/init/profile.sh
module load clinica.all
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_dwi_preproc_using_t1_linux.xml \
--disable-warnings \
./nonregression/pipelines/dwi/preprocessing/test_t1.py
test-dwi-preproc-phasediff-Linux:
runs-on:
- self-hosted
- Linux
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: ${{ env.PYTHON_VERSION }}
cache: poetry
- name: Run tests for dwi pre-processing using phasediff pipelines
run: |
make env.conda
source /builds/miniconda/etc/profile.d/conda.sh
conda activate "${{ github.workspace }}"/env
source /usr/local/Modules/init/profile.sh
module load clinica.all
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_dwi_preproc_using_phasediff_linux.xml \
--disable-warnings \
./nonregression/pipelines/dwi/preprocessing/test_phase_diff.py