[INFRA] Run anat non regression tests with GitHub actions (#987)

* refactor anat pipelines tests

* update jenkins files

* Add a ghaction workflow (runs on PR for now but will make it a cron)

* increase timeout and make cron

.github/workflows/test_pipelines_anat.yml

@@ -0,0 +1,59 @@
+name: Anat Pipelines Tests
+
+on:
+  schedule:
+    - cron: 0 20 * * 4 # every thursday at 8pm
+
+permissions:
+  contents: read
+
+jobs:
+  test-pipelines-anat-MacOS:
+    runs-on:
+      - self-hosted
+      - macOS
+    timeout-minutes: 720
+    steps:
+      - uses: actions/checkout@v4
+      - uses: snok/install-poetry@v1
+      - name: Run tests for anat 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_anat_mac.xml \
+          --disable-warnings \
+          ./nonregression/pipelines/anat
+
+  test-pipelines-anat-Linux:
+    runs-on:
+      - self-hosted
+      - Linux
+    timeout-minutes: 720
+    steps:
+      - uses: actions/checkout@v4
+      - uses: snok/install-poetry@v1
+      - name: Run tests for anat 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_anat_linux.xml \
+          --disable-warnings \
+          ./nonregression/pipelines/anat

.jenkins/nonregression_fast.Jenkinsfile

@@ -186,7 +186,7 @@ pipeline {
                     --disable-warnings \
                     --timeout=0 \
                     -m "not slow" \
-                    ./nonregression/pipelines/test_run_pipelines_anat.py
+                    ./nonregression/pipelines/anat
                 '''
               }
               post {
@@ -415,7 +415,7 @@ pipeline {
                     --timeout=0 \
                     -n 4 \
                     -m "not slow" \
-                    ./nonregression/pipelines/test_run_pipelines_anat.py
+                    ./nonregression/pipelines/anat
                 '''
               }
               post {

.jenkins/nonregression_slow.Jenkinsfile

@@ -193,7 +193,7 @@ pipeline {
                     --timeout=0 \
                     -n 4 \
                     -m "slow" \
-                    ./nonregression/pipelines/test_run_pipelines_anat.py
+                    ./nonregression/pipelines/anat
                 '''
                 }
               }
@@ -424,7 +424,7 @@ pipeline {
                     --timeout=0 \
                     -n 4 \
                     -m "slow" \
-                    ./nonregression/pipelines/test_run_pipelines_anat.py
+                    ./nonregression/pipelines/anat
                 '''
               }
               post {

test/nonregression/pipelines/anat/test_t1_freesurfer.py

@@ -0,0 +1,191 @@
+import shutil
+from os import fspath
+from pathlib import Path
+from test.nonregression.testing_tools import compare_folders, configure_paths
+
+import pytest
+
+
+@pytest.mark.slow
+def test_t1_freesurfer_cross_sectional(cmdopt, tmp_path):
+    base_dir = Path(cmdopt["input"])
+    working_dir = Path(cmdopt["wd"])
+    input_dir, tmp_dir, ref_dir = configure_paths(base_dir, tmp_path, "T1FreeSurfer")
+    run_t1_freesurfer_cross_sectional(input_dir, tmp_dir, ref_dir, working_dir)
+
+
+def run_t1_freesurfer_cross_sectional(
+    input_dir: Path, output_dir: Path, ref_dir: Path, working_dir: Path
+) -> None:
+    """Run the T1FreeSurfer pipeline on test data.
+
+    Notes
+    -----
+    Data for this functional test comes from https://openneuro.org/datasets/ds000204
+
+    We only check that folders are the same meaning that FreeSurfer finished without error.
+    surf/ folder is ignored because it contains symlinks that makes hard to check with ref data
+    (symlinks of ref data are ignored after rsync on CI machines).
+    """
+    from clinica.pipelines.t1_freesurfer.t1_freesurfer_pipeline import T1FreeSurfer
+
+    parameters = {"recon_all_args": "-qcache", "skip_question": False}
+
+    pipeline = T1FreeSurfer(
+        bids_directory=fspath(input_dir / "bids"),
+        caps_directory=fspath(output_dir / "caps"),
+        tsv_file=fspath(input_dir / "subjects.tsv"),
+        parameters=parameters,
+        base_dir=fspath(working_dir),
+    )
+    pipeline.run(bypass_check=True)
+
+    folder = _get_path_to_caps_freesurfer_cross_sectional("sub-01", "ses-2011")
+    compare_folders(
+        output_dir / folder / "regional_measures",
+        ref_dir / folder / "regional_measures",
+        output_dir,
+    )
+    for sub_folder in ("label", "mri", "stats"):
+        compare_folders(
+            output_dir / folder / "sub-01_ses-2011" / sub_folder,
+            ref_dir / folder / "sub-01_ses-2011" / sub_folder,
+            output_dir,
+        )
+
+
+def _get_path_to_caps_freesurfer_cross_sectional(part_id: str, session_id: str) -> Path:
+    return (
+        Path("caps")
+        / "subjects"
+        / part_id
+        / session_id
+        / "t1"
+        / "freesurfer_cross_sectional"
+    )
+
+
+@pytest.mark.slow
+def test_t1_freesurfer_template(cmdopt, tmp_path):
+    base_dir = Path(cmdopt["input"])
+    working_dir = Path(cmdopt["wd"])
+    input_dir, tmp_dir, ref_dir = configure_paths(
+        base_dir, tmp_path, "T1FreeSurferTemplate"
+    )
+    run_t1_freesurfer_template(input_dir, tmp_dir, ref_dir, working_dir)
+
+
+def run_t1_freesurfer_template(
+    input_dir: Path, output_dir: Path, ref_dir: Path, working_dir: Path
+) -> None:
+    """Run the T1FreeSurferTemplate pipeline on test data.
+
+    Notes
+    -----
+    Data for this functional test comes from https://openneuro.org/datasets/ds000204
+
+    sub-01 was duplicated into to sub-02 with one session in order to test the "one time point" case.
+
+    We only check that folders are the same meaning that FreeSurfer finished without error.
+    surf/ folder is ignored because it contains symlinks that makes hard to check with ref data
+    (symlinks of ref data are ignored after rsync on CI machines).
+    """
+    from clinica.pipelines.t1_freesurfer_longitudinal.t1_freesurfer_template_pipeline import (
+        T1FreeSurferTemplate,
+    )
+
+    shutil.copytree(input_dir / "caps", output_dir / "caps", copy_function=shutil.copy)
+
+    pipeline = T1FreeSurferTemplate(
+        caps_directory=fspath(output_dir / "caps"),
+        tsv_file=fspath(input_dir / "subjects.tsv"),
+        base_dir=fspath(working_dir),
+    )
+    pipeline.run(plugin="MultiProc", plugin_args={"n_procs": 2}, bypass_check=True)
+
+    for part_id, long_id in zip(["sub-01", "sub-02"], ["long-20112015", "long-2011"]):
+        folder = (
+            _get_path_to_caps_freesurfer_template(part_id, long_id)
+            / f"{part_id}_{long_id}"
+        )
+        for sub_folder in ("label", "mri", "stats"):
+            compare_folders(
+                output_dir / folder / sub_folder,
+                ref_dir / folder / sub_folder,
+                output_dir,
+            )
+
+
+def _get_path_to_caps_freesurfer_template(part_id: str, long_id: str) -> Path:
+    return (
+        Path("caps") / "subjects" / part_id / long_id / "freesurfer_unbiased_template"
+    )
+
+
+@pytest.mark.slow
+def test_t1_freesurfer_longitudinal_correction(cmdopt, tmp_path):
+    base_dir = Path(cmdopt["input"])
+    working_dir = Path(cmdopt["wd"])
+    input_dir, tmp_dir, ref_dir = configure_paths(
+        base_dir, tmp_path, "T1FreeSurferLongitudinalCorrection"
+    )
+    run_t1_freesurfer_longitudinal_correction(input_dir, tmp_dir, ref_dir, working_dir)
+
+
+def run_t1_freesurfer_longitudinal_correction(
+    input_dir: Path, output_dir: Path, ref_dir: Path, working_dir: Path
+) -> None:
+    """Run the T1FreeSurferLongitudinalCorrection pipeline on test data.
+
+    Notes
+    -----
+    Data for this functional test comes from https://openneuro.org/datasets/ds000204
+
+    We only check that folders are the same meaning that FreeSurfer finished without error.
+    surf/ folder is ignored because it contains symlinks that makes hard to check with ref data
+    (symlinks of ref data are ignored after rsync on CI machines).
+    """
+    from clinica.pipelines.t1_freesurfer_longitudinal.t1_freesurfer_longitudinal_correction_pipeline import (
+        T1FreeSurferLongitudinalCorrection,
+    )
+
+    shutil.copytree(input_dir / "caps", output_dir / "caps", copy_function=shutil.copy)
+
+    pipeline = T1FreeSurferLongitudinalCorrection(
+        caps_directory=fspath(output_dir / "caps"),
+        tsv_file=fspath(input_dir / "subjects.tsv"),
+        base_dir=fspath(working_dir),
+    )
+    pipeline.run(bypass_check=True)
+
+    folder = _get_path_to_caps_freesurfer_longitudinal(
+        "sub-01", "ses-2011", "long-20112015"
+    )
+    compare_folders(
+        output_dir / folder / "regional_measures",
+        ref_dir / folder / "regional_measures",
+        output_dir,
+    )
+    for sub_folder in ("label", "mri", "stats"):
+        compare_folders(
+            output_dir
+            / folder
+            / "sub-01_ses-2011.long.sub-01_long-20112015"
+            / sub_folder,
+            ref_dir / folder / "sub-01_ses-2011.long.sub-01_long-20112015" / sub_folder,
+            output_dir,
+        )
+
+
+def _get_path_to_caps_freesurfer_longitudinal(
+    part_id: str, session_id: str, long_id: str
+) -> Path:
+    return (
+        Path("caps")
+        / "subjects"
+        / part_id
+        / session_id
+        / "t1"
+        / long_id
+        / "freesurfer_longitudinal"
+    )

test/nonregression/pipelines/anat/test_t1_linear.py

@@ -0,0 +1,56 @@
+from os import fspath
+from pathlib import Path
+from test.nonregression.testing_tools import compare_folders, configure_paths
+
+import pytest
+
+
+@pytest.mark.fast
+def test_t1_linear(cmdopt, tmp_path):
+    base_dir = Path(cmdopt["input"])
+    working_dir = Path(cmdopt["wd"])
+    input_dir, tmp_dir, ref_dir = configure_paths(base_dir, tmp_path, "T1Linear")
+    run_t1_linear(input_dir, tmp_dir, ref_dir, working_dir)
+
+
+@pytest.mark.fast
+def test_flair_linear(cmdopt, tmp_path):
+    base_dir = Path(cmdopt["input"])
+    working_dir = Path(cmdopt["wd"])
+    input_dir, tmp_dir, ref_dir = configure_paths(base_dir, tmp_path, "FlairLinear")
+    run_flair_linear(input_dir, tmp_dir, ref_dir, working_dir)
+
+
+def run_t1_linear(
+    input_dir: Path, output_dir: Path, ref_dir: Path, working_dir: Path
+) -> None:
+    from clinica.pipelines.t1_linear.anat_linear_pipeline import AnatLinear
+
+    pipeline = AnatLinear(
+        bids_directory=fspath(input_dir / "bids"),
+        caps_directory=fspath(output_dir / "caps"),
+        tsv_file=fspath(input_dir / "subjects.tsv"),
+        base_dir=fspath(working_dir),
+        parameters={"uncropped_image": False},
+        name="t1-linear",
+    )
+    pipeline.run(plugin="MultiProc", plugin_args={"n_procs": 4}, bypass_check=True)
+
+    compare_folders(output_dir / "caps", ref_dir / "caps", output_dir)
+
+
+def run_flair_linear(
+    input_dir: Path, output_dir: Path, ref_dir: Path, working_dir: Path
+) -> None:
+    from clinica.pipelines.t1_linear.anat_linear_pipeline import AnatLinear
+
+    pipeline = AnatLinear(
+        bids_directory=fspath(input_dir / "bids"),
+        caps_directory=fspath(output_dir / "caps"),
+        base_dir=fspath(working_dir),
+        parameters={"uncropped_image": False},
+        name="flair-linear",
+    )
+    pipeline.run(plugin="MultiProc", plugin_args={"n_procs": 4}, bypass_check=True)
+
+    compare_folders(output_dir / "caps", ref_dir / "caps", output_dir)