ENH: Allow Jacobian correction to be toggled on/off #12
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| pull_request: | |
| schedule: | |
| - cron: 0 0 * * 0 | |
| # Allow job to be triggered manually from GitHub interface | |
| workflow_dispatch: | |
| # Force pytest to use color | |
| env: | |
| FORCE_COLOR: true | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| jobs: | |
| build-package: | |
| name: Build & inspect package | |
| runs-on: ubuntu-latest | |
| permissions: | |
| attestations: write | |
| id-token: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: hynek/build-and-inspect-python-package@v2 | |
| test: | |
| if: "!contains(github.event.head_commit.message, '[skip ci]' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name != 'nipreps/sdcflows'))" | |
| runs-on: ubuntu-latest | |
| env: | |
| TEST_DATA_HOME: /home/runner/sdcflows-tests | |
| FSLOUTPUTTYPE: NIFTI_GZ | |
| FSLMULTIFILEQUIT: TRUE | |
| AFNI_HOME: /opt/afni | |
| AFNI_MODELPATH: /opt/afni/models | |
| AFNI_IMSAVE_WARNINGS: NO | |
| AFNI_TTATLAS_DATASET: /opt/afni/atlases | |
| AFNI_PLUGINPATH: /opt/afni/plugins | |
| strategy: | |
| max-parallel: 6 | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| marks: ["not slow"] | |
| include: | |
| - python-version: "3.9" | |
| marks: "slow and not veryslow" | |
| - python-version: "3.12" | |
| marks: "veryslow" | |
| steps: | |
| - uses: actions/cache@v4 | |
| with: | |
| path: /var/lib/apt | |
| key: apt-cache-v3 | |
| restore-keys: | | |
| apt-cache-v3 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y --no-install-recommends \ | |
| curl bzip2 ca-certificates \ | |
| tcsh gsl-bin netpbm \ | |
| libjpeg62 xvfb xterm \ | |
| libglu1-mesa-dev libglw1-mesa \ | |
| libxm4 build-essential | |
| - uses: actions/cache@v4 | |
| with: | |
| path: /opt/afni | |
| key: afni-v1 | |
| restore-keys: | | |
| afni-v1 | |
| - name: Install AFNI | |
| run: | | |
| if [[ ! -d "${AFNI_HOME}" ]]; then | |
| curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries && \ | |
| tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir ${AFNI_HOME} | |
| fi | |
| - name: Git settings (pacify DataLad) | |
| run: | | |
| git config --global user.name 'NiPreps Bot' | |
| git config --global user.email '[email protected]' | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| auto-activate-base: true | |
| python-version: ${{ matrix.python-version }} | |
| channels: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/,conda-forge | |
| - uses: actions/cache@v4 | |
| id: conda | |
| env: | |
| CACHE_NUM: v5 | |
| with: | |
| path: | | |
| ~/conda_pkgs_dir | |
| /home/runner/.cache/pip | |
| key: python-${{ matrix.python-version }}-${{ env.CACHE_NUM }} | |
| restore-keys: | | |
| python-${{ matrix.python-version }}-${{ env.CACHE_NUM }} | |
| - name: Install DataLad | |
| run: | | |
| conda install git-annex=*=alldep* pip | |
| pip install datalad datalad-osf | |
| - name: Install fsl and ANTs | |
| run: | | |
| conda install fsl-fugue fsl-topup ants | |
| - uses: actions/checkout@v4 | |
| - name: Install dependencies | |
| timeout-minutes: 5 | |
| run: | | |
| pip install .[tests] | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/templateflow | |
| key: tf-cache-v1 | |
| restore-keys: | | |
| tf-cache- | |
| - name: Get TemplateFlow's required objects | |
| run: | | |
| python tools/cache_templateflow.py | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.TEST_DATA_HOME }} | |
| key: data-cache-v2 | |
| restore-keys: | | |
| data-cache- | |
| - name: Install test data | |
| run: | | |
| mkdir -p ${{ env.TEST_DATA_HOME }} | |
| cd ${{ env.TEST_DATA_HOME }} | |
| # ds001600 | |
| datalad install -r https://github.com/nipreps-data/ds001600.git | |
| datalad update -r --merge -d ds001600/ | |
| datalad get -r -J 2 -d ds001600/ ds001600/sub-1/ | |
| # HCP/sub-101006 | |
| datalad install -r https://github.com/nipreps-data/HCP101006.git | |
| datalad update -r --merge -d HCP101006/ | |
| datalad get -r -J 2 -d HCP101006 HCP101006/* | |
| # ds001771 | |
| datalad install -r https://github.com/nipreps-data/ds001771.git | |
| datalad update -r --merge -d ds001771/ | |
| datalad get -r -J 2 -d ds001771/ ds001771/sub-36/* | |
| datalad get -r -J 2 -d ds001771/derivatives ds001771/derivatives/openneuro/sub-36/* | |
| # ds000054 | |
| datalad install -r https://github.com/nipreps-data/ds000054.git | |
| datalad update --merge -d ds000054/ | |
| datalad get -r -d ds000054/ ds000054/sub-100185/* | |
| datalad get -r -J 2 -d ds000054/ ds000054/derivatives/smriprep-0.6/sub-100185/anat/ | |
| # ds000206 | |
| datalad install -r https://github.com/nipreps-data/ds000206.git | |
| datalad update -r --merge -d ds000206/ | |
| datalad get -r -J 2 -d ds000206/ ds000206/sub-05/ | |
| # Brain extraction tests | |
| datalad install -r https://gin.g-node.org/nipreps-data/brain-extraction-tests | |
| datalad update --merge -d brain-extraction-tests/ | |
| datalad get -r -J 2 -d brain-extraction-tests brain-extraction-tests/* | |
| # HCPH pilot | |
| datalad install -r https://github.com/nipreps-data/hcph-pilot_fieldmaps.git | |
| datalad update -r --merge -d hcph-pilot_fieldmaps/ | |
| datalad get -r -J 2 -d hcph-pilot_fieldmaps/ hcph-pilot_fieldmaps/* | |
| - name: Set FreeSurfer variables | |
| run: | | |
| echo "FREESURFER_HOME=$HOME/.cache/freesurfer" >> $GITHUB_ENV | |
| echo "FS_LICENSE=$HOME/.cache/freesurfer/license.txt" >> $GITHUB_ENV | |
| - name: Install FreeSurfer's mri_robust_template | |
| env: | |
| MRI_ROBUST_TEMPLATE: sx2n7/providers/osfstorage/5e825301d0e35400ebb481f2 | |
| run: | | |
| curl https://files.osf.io/v1/resources/$MRI_ROBUST_TEMPLATE?direct > mri_robust_template | |
| sudo install mri_robust_template /usr/local/bin | |
| mkdir -p $( dirname $FS_LICENSE ) | |
| echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" | base64 -d > $FS_LICENSE | |
| - name: Run pytest with coverage | |
| run: | | |
| export PATH=${AFNI_HOME}:$PATH | |
| export FSLDIR=${CONDA_PREFIX} | |
| pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules -n auto sdcflows \ | |
| --durations=20 --durations-min=10 -m "$MARKS" | |
| env: | |
| MARKS: ${{ matrix.marks }} | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| file: cov.xml | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| if: ${{ always() }} | |
| publish: | |
| name: Publish released package to pypi.org | |
| environment: release-pypi | |
| if: github.event.action == 'published' | |
| runs-on: ubuntu-latest | |
| needs: [build-package, test] | |
| permissions: | |
| attestations: write | |
| id-token: write | |
| steps: | |
| - name: Download packages built by build-and-inspect-python-package | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: Packages | |
| path: dist | |
| - name: Upload package to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 |