WIP: Add integration testing and github actions

.circleci/config.yml

@@ -0,0 +1,30 @@
+version: 2.1
+
+orbs:
+  conda: circleci/[email protected]
+
+jobs:
+  tests:
+    executor:
+      name: conda/default
+    steps:
+      - checkout
+      - conda/update-env:
+          environment-file: env.yml
+          environment-name: petprep
+      - conda/run:
+          environment-name: petprep
+          command: |
+            pip install -e .[tests]
+            pytest -n auto --junitxml=test-results/junit.xml --cov=petprep --cov-report=xml
+      - store_test_results:
+          path: test-results
+      - store_artifacts:
+          path: coverage.xml
+          destination: coverage.xml
+
+workflows:
+  version: 2
+  test:
+    jobs:
+      - tests

.github/workflows/coverage.yml

@@ -13,14 +13,14 @@ jobs:
     runs-on: macos-latest
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Set up Conda
       uses: conda-incubator/setup-miniconda@v2
       with:
         miniconda-version: "latest"
         activate-environment: petprep
-        environment-file: environment.yml
+        environment-file: env.yml
         auto-activate-base: true
 
     - name: Install dependencies
@@ -42,13 +42,13 @@ jobs:
       shell: bash -l {0}
 
     - name: Upload coverage report
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name: coverage
         path: coverage.xml
 
     - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml
       env:

.github/workflows/tests.yml

@@ -0,0 +1,25 @@
+name: Tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - run: pip install -e .[tests]
+      - run: pytest -sv
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4

.gitignore

@@ -0,0 +1,31 @@
+# Python cache and bytecode files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Coverage reports
+.coverage
+.coverage.*
+htmlcov/
+coverage.xml
+
+# Build directories
+build/
+dist/
+.eggs/
+*.egg-info/
+*.egg
+# docs build
+/docs/_build/
+
+# Editor and OS artifacts
+.DS_Store
+*.swp
+*~
+.vscode/
+.idea/
+.env
+.envrc
+
+# Additional
+.ipynb_checkpoints/

NOTICE

@@ -0,0 +1,15 @@
+PETPrep
+Copyright The NiPreps Developers.
+
+This product includes software developed by
+the NiPreps Community (https://nipreps.org/).
+
+Portions of this software were developed at the Department of
+Psychology at Stanford University, Stanford, CA, US.
+
+This software is also distributed as a Docker container image.
+The bootstrapping file for the image ("Dockerfile") is licensed
+under the MIT License.
+
+This software may be distributed through an add-on package called
+"Docker Wrapper" that is under the BSD 3-clause License.

env.yml

@@ -13,35 +13,29 @@ dependencies:
   # git-annex for templateflow users with DataLad superdatasets
   - git-annex=*=alldep*
   # Base scientific python stack; required by FSL, so pinned here
-  - numpy=1.26
+  - numpy=2.2
   - scipy=1.15
-  - matplotlib=3.9
+  - matplotlib=3.10
   - pandas=2.2
   - h5py=3.13
   # Dependencies compiled against numpy, best to stick with conda
   - nitime=0.11
   - scikit-image=0.25
   - scikit-learn=1.6
   # Utilities
-  - graphviz=11.0
-  - pandoc=3.6
+  - graphviz=12.2
+  - pandoc=3.7
   # Workflow dependencies: ANTs
-  - ants=2.5
-  # 5.4.1 and 5.4.2 cause segfaults with ants
-  # Try to remove this ASAP
-  # https://github.com/conda-forge/ants-feedstock/issues/19
-  - libitk=5.4.0
-  # Workflow dependencies: Convert3d
-  - convert3d=1.4
+  - ants=2.6
   # Workflow dependencies: Connectome Workbench
   - connectome-workbench-cli=2.0
-  # Workflow dependencies: FSL (versions pinned in 6.0.7.13)
+  # Workflow dependencies: FSL (versions pinned in 6.0.7.17.20250415.fe1c582e)
   - fsl-bet2=2111.8
-  - fsl-flirt=2111.2
+  - fsl-flirt=2111.4
   - fsl-fast4=2111.3
   - fsl-fugue=2201.5
   - fsl-mcflirt=2111.0
-  - fsl-miscmaths=2203.2
+  - fsl-miscmaths=2412.4
   - fsl-topup=2203.5
   - pip
   - pip:

petprep/_version.py

@@ -17,5 +17,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '25.0.0.dev172+gf8fd378'
-__version_tuple__ = version_tuple = (25, 0, 0, 'dev172', 'gf8fd378')
+__version__ = version = '25.0.0.dev238+gac5d4f1.d20250605'
+__version_tuple__ = version_tuple = (25, 0, 0, 'dev238', 'gac5d4f1.d20250605')

petprep/cli/tests/test_parser.py

@@ -115,9 +115,9 @@ def _mock_check_latest(*args, **kwargs):
     captured = capsys.readouterr().err
 
     msg = f"""\
-You are using fMRIPrep-{current}, and a newer version of fMRIPrep is available: {latest}.
+You are using PETPrep-{current}, and a newer version of PETPrep is available: {latest}.
 Please check out our documentation about how and when to upgrade:
-https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading"""
+https://petprep.readthedocs.io/en/latest/faq.html#upgrading"""
 
     assert (msg in captured) is expectation
 
@@ -184,52 +184,6 @@ def test_bids_filter_file(tmp_path, capsys):
     _reset_config()
 
 
-@pytest.mark.parametrize('st_ref', (None, '0', '1', '0.5', 'start', 'middle'))  # noqa: PT007
-def test_slice_time_ref(tmp_path, st_ref):
-    bids_path = tmp_path / 'data'
-    out_path = tmp_path / 'out'
-    args = [str(bids_path), str(out_path), 'participant']
-    if st_ref:
-        args.extend(['--slice-time-ref', st_ref])
-    bids_path.mkdir()
-
-    parser = _build_parser()
-
-    parser.parse_args(args)
-    _reset_config()
-
-
-@pytest.mark.parametrize(
-    ('args', 'expectation'),
-    [
-        ([], False),
-        (['--use-syn-sdc'], 'error'),
-        (['--use-syn-sdc', 'error'], 'error'),
-        (['--use-syn-sdc', 'warn'], 'warn'),
-        (['--use-syn-sdc', 'other'], (SystemExit, ArgumentError)),
-    ],
-)
-def test_use_syn_sdc(tmp_path, args, expectation):
-    bids_path = tmp_path / 'data'
-    out_path = tmp_path / 'out'
-    args = [str(bids_path), str(out_path), 'participant'] + args
-    bids_path.mkdir()
-
-    parser = _build_parser()
-
-    cm = nullcontext()
-    if isinstance(expectation, tuple):
-        cm = pytest.raises(expectation)
-
-    with cm:
-        opts = parser.parse_args(args)
-
-    if not isinstance(expectation, tuple):
-        assert opts.use_syn_sdc == expectation
-
-    _reset_config()
-
-
 def test_derivatives(tmp_path):
     """Check the correct parsing of the derivatives argument."""
     bids_path = tmp_path / 'data'

petprep/data/io_spec.json

@@ -2,20 +2,20 @@
   "queries": {
     "baseline": {
       "hmc": {
-        "datatype": "func",
+        "datatype": "pet",
         "space": null,
         "desc": "hmc",
-        "suffix": "boldref",
+        "suffix": "petref",
         "extension": [
           ".nii.gz",
           ".nii"
         ]
       },
       "coreg": {
-        "datatype": "func",
+        "datatype": "pet",
         "space": null,
         "desc": "coreg",
-        "suffix": "boldref",
+        "suffix": "petref",
         "extension": [
           ".nii.gz",
           ".nii"
@@ -24,16 +24,16 @@
     },
     "transforms": {
       "hmc": {
-        "datatype": "func",
+        "datatype": "pet",
         "from": "orig",
-        "to": "boldref",
+        "to": "petref",
         "mode": "image",
         "suffix": "xfm",
         "extension": ".txt"
       },
-      "boldref2anat": {
-        "datatype": "func",
-        "from": "boldref",
+      "petref2anat": {
+        "datatype": "pet",
+        "from": "petref",
         "to": ["anat", "T1w", "T2w"],
         "mode": "image",
         "suffix": "xfm",
@@ -42,9 +42,9 @@
     }
   },
   "patterns": [
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_res-{res}][_label-{label}][_echo-{echo}][_space-{space}][_desc-{desc}]_{suffix<bold|boldref|dseg|mask>}.{extension<nii|nii.gz|json>|nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}.{extension<txt|h5>}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_part-{part}][_desc-{desc}]_{suffix<timeseries>}.{extension<tsv|json>}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_den-{den}][_hemi-{hemi}[_label-{label}][_desc-{desc}]_{suffix<|boldref|dseg|mask>}.{extension<dtseries.nii|dtseries.json>}"
+    "sub-{subject}[/ses-{session}]/{datatype<func|pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_res-{res}][_label-{label}][_echo-{echo}][_space-{space}][_desc-{desc}]_{suffix<bold|boldref|pet|petref|dseg|mask>}.{extension<nii|nii.gz|json>|nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<func|pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}.{extension<txt|h5>}",
+    "sub-{subject}[/ses-{session}]/{datatype<func|pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_part-{part}][_desc-{desc}]_{suffix<timeseries>}.{extension<tsv|json>}",
+    "sub-{subject}[/ses-{session}]/{datatype<func|pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_den-{den}][_hemi-{hemi}[_label-{label}][_desc-{desc}]_{suffix<|boldref|petref|dseg|mask>}.{extension<dtseries.nii|dtseries.json>}"
   ]
 }