Add unwrap CLI #1284
Workflow file for this run
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| name: CI-Tests | |
| on: | |
| # Triggers the workflow on push or pull request events but only for the master branch | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| env: | |
| FSLOUTPUTTYPE: NIFTI_GZ | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: | |
| - 'macos-12' | |
| - 'macos-13' | |
| - 'ubuntu-22.04' | |
| - 'ubuntu-20.04' | |
| python-version: | |
| - '3.9' | |
| steps: | |
| - name: Get home directory | |
| run: | | |
| echo ~ | |
| echo $HOME | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Package installation | |
| run: | | |
| echo "shimming-toolbox installation" | |
| make install | |
| - name: Set path for Shimming Toolbox | |
| run: | | |
| echo "$HOME/shimming-toolbox/bin" >> $GITHUB_PATH | |
| - name: Spinal Cord Toolbox clone | |
| run: | | |
| cd ~/work | |
| git clone --depth 1 https://github.com/neuropoly/spinalcordtoolbox | |
| cd spinalcordtoolbox | |
| # Use HEAD commit hash as key for cache | |
| git rev-parse HEAD > $GITHUB_WORKSPACE/.sct_HEAD_hash | |
| cat $GITHUB_WORKSPACE/.sct_HEAD_hash | |
| - name: Cache SCT | |
| id: cache-sct | |
| uses: actions/cache@v2 | |
| with: | |
| path: ~/work/spinalcordtoolbox | |
| # Use commit hash file from previous step as key | |
| key: ${{ matrix.os }}-${{ hashFiles('**/.sct_HEAD_hash') }} | |
| - name: Spinal Cord Toolbox installation | |
| if: steps.cache-sct.outputs.cache-hit != 'true' | |
| run: | | |
| cd ../../spinalcordtoolbox | |
| ./install_sct -y | |
| - name: Set path for SCT | |
| run: echo "$HOME/work/spinalcordtoolbox/bin" >> $GITHUB_PATH | |
| - name: prelude macOS | |
| if: contains(matrix.os, 'macos') | |
| run: | | |
| echo "Download prelude for macOS" | |
| mkdir prelude | |
| curl -o prelude/prelude -JL https://github.com/shimming-toolbox/binaries/raw/master/prelude_macos | |
| sudo install prelude/prelude /usr/local/bin | |
| - name: prelude Ubuntu | |
| if: contains(matrix.os, 'ubuntu') | |
| run: | | |
| echo "Download prelude" | |
| st_download_data prelude | |
| sudo install prelude/prelude /usr/local/bin | |
| - name: Check dependencies | |
| run: st_check_dependencies | |
| - name: Run unit tests | |
| run: | | |
| source ~/shimming-toolbox/python/bin/activate # to be able to call conda | |
| py.test . -v --cov shimmingtoolbox/ --cov-report term-missing | |
| - name: macOS Shellcheck | |
| if: contains(matrix.os, 'macos') | |
| run: brew install shellcheck | |
| - name: Shellcheck | |
| run: | | |
| echo "Check Bash scripts" | |
| if [[ -n "$(ls examples/*.sh)" ]]; then shellcheck examples/*.sh; fi | |
| - name: Upload Coverage | |
| run: | | |
| pip3 install coveralls | |
| coveralls --service=github --rcfile=.coveragerc | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| COVERALLS_FLAG_NAME: ${{ matrix.os }}-Python-${{ matrix.python-version }} | |
| COVERALLS_PARALLEL: true | |
| coveralls: | |
| name: Finish Coveralls | |
| needs: test | |
| runs-on: 'ubuntu-22.04' | |
| steps: | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.7' | |
| - name: Finished | |
| run: | | |
| pip3 install --upgrade coveralls | |
| coveralls --finish --rcfile=.coveragerc | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |