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/tests.yml

@@ -0,0 +1,89 @@
+name: Stable tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+defaults:
+  run:
+    shell: bash
+
+env:
+  FORCE_COLOR: true
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ 'ubuntu-latest' ]
+        python-version: ['3.10', '3.11', '3.12', '3.13']
+        dependencies: ['latest', 'pre']
+        include:
+          - os: ubuntu-latest
+            python-version: '3.10'
+            dependencies: 'min'
+    env:
+      DEPENDS: ${{ matrix.dependencies }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - uses: actions/cache@v4
+        with:
+          path: ~/.cache/templateflow
+          key: templateflow-v1
+      - name: Install dependencies
+        run: |
+          sudo apt update
+          sudo apt install -y --no-install-recommends graphviz
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install tox
+        run: |
+          uv tool install --with=tox-uv --with=tox-gh-actions tox
+      - name: Show tox config
+        run: tox c
+      - name: Run tox
+        run: tox -v --exit-and-dump-after 1200
+      - uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+        if: ${{ always() }}
+
+  checks:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    strategy:
+      matrix:
+        check: ['style', 'spellcheck']
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install tox
+        run: uv tool install tox --with=tox-uv
+      - name: Show tox config
+        run: tox c -e ${{ matrix.check }}
+      - name: Run check
+        run: tox -e ${{ matrix.check }}

.gitignore

@@ -0,0 +1,34 @@
+# Python cache and bytecode files
+__pycache__/
+*.py[cod]
+*$py.class
+*.pyo
+*.pyd
+
+# 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/
+_version.py

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.

docs/faq.rst

@@ -321,26 +321,4 @@ finer control can be achieved of what files are visible to PETPrep.
 Note that any discrepancies between the pre-indexed database and
 the BIDS dataset complicate the provenance of PETPrep derivatives.
 If ``--bids-database-dir`` is used, the referenced directory should be
-preserved for the sake of reporting and reproducibility.
-
-Error in slice timing correction: *insufficient length of BOLD data after discarding nonsteady-states*
-------------------------------------------------------------------------------------------------------
-Typically, the scanner will be in a *nonsteady state* during a few initial time points of the acquisition,
-until it stabilizes.
-These *nonsteady states* (also called *dummy* scans) typically show greater T1 contrast and higher average
-intensity, and therefore potentially are detrimental if used in the interpolation of slice timing corrections.
-Hence, *nonsteady states* are discarded by the slice timing correction tool (in this case, AFNI's ``3dTShift``).
-However, ``3dTShift`` requires that at least five (5) time points are present in the target series, after
-dismissing the initial *nonsteady states*.
-
-*PETPrep* estimates the number of *nonsteady states* within the pipeline, unless the parameter is provided
-by the user with the argument ``--dummy-scans <num>``.
-Either way, if the number of *nonsteady states* is, say 4, then the length of the BOLD series must be greater
-than 8.
-If you encounter this error, first check that the number of *nonsteady states* is not suspiciously large
-(it typically ranges from zero to five).
-Next, if the number of *nonsteady states* is reasonable, consider why your BOLD time series are so short
-and whether slice timing correction is appropriate under these conditions.
-Finally, you can either skip the slice-timing correction with the argument ``--ignore slicetiming`` or
-enforce a number of *nonsteady states* lower than the maximum for your data with ``--dummy-scans <num>``.
-Please note that both strategies will apply to all tasks and runs that are to be processed.
+preserved for the sake of reporting and reproducibility.

docs/outputs.rst

@@ -363,25 +363,6 @@ Then the output will include::
 These may then be used independently with multi-echo tools, such as `tedana`_,
 to perform more advanced denoising or alternative combination strategies.
 
-.. danger::
-   Slice timing correction in *PETPrep* is referenced to the middle slice by default,
-   which leads to a time shift in the volume onsets by 0.5 TR (repetition time).
-   For example, assuming a TR of 2s, original onsets of 0, 2, and 4s would be shifted
-   to 1, 3, and 5s, respectively.
-   In case you did execute slice timing correction, you must check that subsequent
-   analyses (e.g., general linear modeling) consider the right onset shifts.
-   For example, when specifying a first-level model, you should set parameters in your
-   software package or first-level model function accordingly (e.g., select the middle
-   slice as reference).
-   Alternatively, you could manually adjust the volume onsets (e.g. as mentioned in
-   the example above from [0, 2, 4] to [1, 3, 5]) or the event onsets accordingly.
-   In contrast to volume onsets, event onsets need to be shifted *backward* by half a TR,
-   for example, from [5, 10, 15] to [4, 9, 14].
-
-   Further information on this issue is found at
-   `this blog post (with thanks to Russell Poldrack and Jeanette Mumford)
-   <https://reproducibility.stanford.edu/slice-timing-correction-in-petprep-and-linear-modeling/>`__.
-
 Confounds
 ---------
 The :abbr:`BOLD (blood-oxygen level dependent)` signal measured with fMRI is a mixture of fluctuations

docs/workflows.rst

@@ -5,9 +5,8 @@ Processing pipeline details
 ===========================
 *PETPrep* adapts its pipeline depending on what data and metadata are
 available and are used as the input.
-For example, slice timing correction will be
-performed only if the ``SliceTiming`` metadata field is found for the input
-dataset.
+Certain processing steps will run only when the required metadata is
+available in the input dataset.
 
 A (very) high-level view of the simplest pipeline (for a single-band dataset with only
 one task, single-run, with no slice-timing information nor fieldmap acquisitions)
@@ -571,7 +570,6 @@ Confounds estimation
         metadata={
             "FrameTimesStart": [0, 2, 4, 6],
             "FrameDuration": [2, 2, 2, 2],
-            "SliceTiming": [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9],
         },
         regressors_all_comps=False,
         regressors_dvars_th=1.5,

env.yml

@@ -1,4 +1,4 @@
-name: fmriprep
+name: petprep
 channels:
   - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
   - conda-forge
@@ -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: