ENH: Fix caching-related warnings in GHA build-test-publish CI
#95
Workflow file for this run
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| name: CI | ||
| on: | ||
| push: | ||
| branches: | ||
| - master | ||
| - main | ||
| - maint/* | ||
| tags: | ||
| - '*' | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| - main | ||
| - maint/* | ||
| schedule: | ||
| # 9am EST / 10am EDT Mondays | ||
| - cron: 0 14 * * 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 | ||
| MARKS: ${{ matrix.marks }} | ||
| DEPENDS: ${{ matrix.dependencies }} | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] | ||
| dependencies: ["latest", "pre"] | ||
| marks: ["fast"] | ||
| include: | ||
| - python-version: "3.9" | ||
| dependencies: "min" | ||
| marks: "fast" | ||
| - python-version: "3.9" | ||
| dependencies: "latest" | ||
| marks: "slow" | ||
| - python-version: "3.12" | ||
| dependencies: "latest" | ||
| marks: "veryslow" | ||
| exclude: | ||
| - python-version: "3.9" | ||
| dependencies: "pre" | ||
| - python-version: "3.10" | ||
| dependencies: "pre" | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: actions/cache@v4 | ||
| with: | ||
| path: ${{ runner.temp }}/cache-linux | ||
| key: apt-cache-v3 | ||
| restore-keys: | | ||
| apt-cache-v3 | ||
| - name: Install dependencies | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y --no-install-recommends \ | ||
| curl bzip2 ca-certificates \ | ||
| tcsh gsl-bin netpbm \ | ||
| libjpeg62 xvfb xterm \ | ||
| libglu1-mesa-dev libglw1-mesa \ | ||
| libxm4 build-essential | ||
| - name: Restore cache for AFNI | ||
| id: cache-afni | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: /opt/afni | ||
| key: afni-v1-${{ python-version }}-${{ matrix.dependencies }}-${{ matrix.marks }} | ||
|
Check failure on line 110 in .github/workflows/build-test-publish.yml
|
||
| restore-keys: | | ||
| afni-v1- | ||
| - name: Install AFNI | ||
| if: steps.cache-afni.outputs.cache-hit != 'true' | ||
| 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 | ||
| ls -l ${AFNI_HOME} | ||
| echo "PATH=${AFNI_HOME}:$PATH" | tee -a $GITHUB_ENV | ||
| - name: Git settings (pacify DataLad) | ||
| run: | | ||
| git config --global user.name 'NiPreps Bot' | ||
| git config --global user.email '[email protected]' | ||
| - name: Install the latest version of uv | ||
| uses: astral-sh/setup-uv@v4 | ||
| - 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 }} | ||
| - name: Install DataLad | ||
| run: | | ||
| conda install git-annex=*=alldep* | ||
| uv tool install datalad --with=datalad-next --with=datalad-osf | ||
| uv tool install datalad-osf --with=datalad-next | ||
| - name: Install fsl and ANTs | ||
| run: | | ||
| conda install fsl-fugue fsl-topup ants | ||
| - uses: actions/cache@v4 | ||
| with: | ||
| path: ~/.cache/templateflow | ||
| key: tf-cache-v1 | ||
| restore-keys: | | ||
| tf-cache- | ||
| - name: Get TemplateFlow's required objects | ||
| run: | | ||
| uv run 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: Install tox | ||
| run: | | ||
| uv tool install tox --with=tox-uv --with=tox-gh-actions | ||
| - 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() }} | ||
| publish: | ||
| name: Publish released package to pypi.org | ||
| environment: release-pypi | ||
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | ||
| 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 | ||
