Freesurfer Anat Pipelines Tests #40

	name: Freesurfer Anat Pipelines Tests

	on:
	schedule:
	- cron: 0 20 * * 2 # every tuesday at 8pm

	permissions:
	contents: read

	jobs:
	test-pipelines-anat-freesurfer-MacOS:
	runs-on:
	- self-hosted
	- macOS
	timeout-minutes: 1440
	steps:
	- uses: actions/checkout@v4
	- 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
	- 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

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