Edits to seedmap and fmriprep notebooks #134
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| on: | |
| push: | |
| branches: | |
| - main | |
| - maint/* | |
| tags: | |
| - "*" | |
| pull_request: | |
| branches: | |
| - main | |
| - maint/* | |
| workflow_dispatch: | |
| inputs: | |
| debug_enabled: | |
| type: boolean | |
| description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)' | |
| required: false | |
| default: false | |
| defaults: | |
| run: | |
| shell: bash | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| jobs: | |
| get-dataset: | |
| runs-on: ubuntu-latest | |
| name: Datalad install and get | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Get Submodule Hash | |
| id: get-smhash | |
| run: | | |
| echo "smhash=$(git submodule status contarg/test/data)" >> $GITHUB_OUTPUT | |
| - name: Cache Dataset | |
| id: restore-dataset | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: | | |
| ./contarg/test/data | |
| .git/modules/contarg/test/data | |
| key: ${{ runner.os }}-${{steps.get-smhash.outputs.smhash}} | |
| - name: Install datalad | |
| if: steps.restore-dataset.outputs.cache-hit != 'true' | |
| uses: datalad/datalad-action/install@main | |
| - name: Download Dataset | |
| if: steps.restore-dataset.outputs.cache-hit != 'true' | |
| run: | | |
| datalad get -r contarg/test/data/derivatives/contarg/seedmap/ \ | |
| contarg/test/data/derivatives/contarg/hierarchical/testing2subs/sub-*/func/*mask.nii.gz \ | |
| contarg/test/data/ds002330/*.json \ | |
| contarg/test/data/ds002330/*.tsv \ | |
| contarg/test/data/derivatives/fmriprep/*.json \ | |
| contarg/test/data/derivatives/fmriprep/sub-*/anat/sub-*_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5 \ | |
| contarg/test/data/derivatives/fmriprep/sub-*/anat/*preproc_T1w.* \ | |
| contarg/test/data/derivatives/fmriprep/sub-*/func/*preproc_bold.* \ | |
| contarg/test/data/derivatives/fmriprep/sub-*/func/*brain_mask.* \ | |
| contarg/test/data/derivatives/fmriprep/sub-*/func/*boldref.* \ | |
| contarg/test/data/derivatives/fmriprep/sub-*/func/*confounds_timeseries.* \ | |
| contarg/test/data/derivatives/contarg/hierarchical/testing*_ref/ \ | |
| contarg/test/data/derivatives/contarg/hierarchical/testing1sub/sub-*/func/*mask.nii.gz \ | |
| contarg/test/data/derivatives/contarg/cluster/ | |
| - name: Cache Dataset | |
| if: steps.restore-dataset.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@v3 | |
| with: | |
| path: | | |
| ./contarg/test/data | |
| .git/modules/contarg/test/data | |
| key: ${{ runner.os }}-${{steps.get-smhash.outputs.smhash}} | |
| - name: Setup tmate session | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled && (success() || failure())}} | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3 | |
| - run: pip install --upgrade build twine | |
| - name: Build sdist and wheel | |
| run: python -m build | |
| - run: twine check dist/* | |
| - name: Upload sdist and wheel artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/ | |
| - name: Build git archive | |
| run: mkdir archive && git archive -v -o archive/archive.tgz HEAD | |
| - name: Upload git archive artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: archive | |
| path: archive/ | |
| test-package: | |
| runs-on: ubuntu-latest | |
| needs: [get-dataset, build] | |
| strategy: | |
| matrix: | |
| package: ['wheel', 'sdist', 'archive'] | |
| steps: | |
| - name: Download sdist and wheel artifacts | |
| if: matrix.package != 'archive' | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/ | |
| - name: Download git archive artifact | |
| if: matrix.package == 'archive' | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: archive | |
| path: archive/ | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3 | |
| - name: Display Python version | |
| run: python -c "import sys; print(sys.version)" | |
| - name: Update pip | |
| run: pip install --upgrade pip | |
| - name: Install wheel | |
| if: matrix.package == 'wheel' | |
| run: pip install dist/*.whl | |
| - name: Install sdist | |
| if: matrix.package == 'sdist' | |
| run: pip install dist/*.tar.gz | |
| - name: Install archive | |
| if: matrix.package == 'archive' | |
| run: pip install archive/archive.tgz | |
| - name: Install test extras | |
| run: pip install contarg[test] | |
| - name: Restore Dataset | |
| id: restore-dataset | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: | | |
| ./contarg/test/data | |
| .git/modules/contarg/test/data | |
| key: ${{ runner.os }}-${{steps.get-smhash.outputs.smhash}} | |
| - name: Move data | |
| run: | | |
| contarg_path=$(which contarg) | |
| contarg_test_path=${contarg_path:0:-12}/lib/python*/site-packages/contarg/test | |
| mv contarg/test/data $contarg_test_path/ | |
| rm -rf $contarg_test_path/data/.git | |
| mv .git/modules/contarg/test/data .git/modules/contarg/test/.git | |
| mv .git/modules/contarg/test/.git $contarg_test_path/data/ | |
| - name: Run tests | |
| run: pytest --doctest-modules -v --pyargs contarg | |
| - name: Setup tmate session | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled && (success() || failure())}} | |
| publish: | |
| runs-on: ubuntu-latest | |
| needs: [test-package] | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/') | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/ | |
| - uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} |