update: bypass git dubious ownership issue in ci.yml #3195
Workflow file for this run
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| name: Run Tests | |
| on: | |
| push: | |
| paths: | |
| - 'junifer/**' | |
| - '.github/workflows/**' | |
| pull_request: | |
| paths: | |
| - 'junifer/**' | |
| - '.github/workflows/**' | |
| jobs: | |
| run-tests: | |
| runs-on: ubuntu-latest | |
| # Use custom docs CI image | |
| container: ghcr.io/juaml/junifer-ci:main | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.9', '3.10', '3.11', '3.12', '3.13'] | |
| steps: | |
| - name: Check ANTs | |
| if: matrix.python-version == 3.12 | |
| run: | | |
| echo "Using ANTs : $(antsRegistration --version)" | |
| - name: Check AFNI | |
| if: matrix.python-version == 3.12 | |
| run: | | |
| echo "Using AFNI : $(afni --version)" | |
| - name: Check FSL | |
| if: matrix.python-version == 3.12 | |
| run: | | |
| echo "Using FSL : $(flirt -version)" | |
| - name: Install system dependencies | |
| run: | | |
| # actions/checkout fails to identify Git as it's not in the CI image | |
| apt-get -qq update && \ | |
| apt-get -qq install -y \ | |
| git \ | |
| git-annex \ | |
| make \ | |
| jq | |
| # Copy xfms directory | |
| mkdir -p $HOME/junifer/data/xfms && \ | |
| cp -ar /root/junifer/data/xfms/. $HOME/junifer/data/xfms/ | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install tox tox-gh-actions | |
| - name: Configure Git for DataLad | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "GitHub Runner" | |
| - name: Test with tox | |
| run: | | |
| # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583 | |
| git config --system --add safe.directory $(pwd) | |
| tox | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| flags: junifer | |
| if: success() && matrix.python-version == 3.12 |