update docs formatting #2839
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| name: pytest | |
| on: [push, pull_request] | |
| jobs: | |
| collect_references: | |
| name: collect_references | |
| outputs: | |
| MATLAB_REFS_HASH: ${{ steps.matlab-refs-hash.outputs.MATLAB_REFS_HASH }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| path: k-Wave-python | |
| # Calculate hash value that will be used as a cache key | |
| - name: Calculate matlab references hash | |
| id: matlab-refs-hash | |
| run: | | |
| MATLAB_REFS_HASH=$(find ./k-Wave-python/tests/matlab_test_data_collectors/matlab_collectors -type f | xargs sha1sum | sha1sum | awk '{ print $1 }'); | |
| echo "MATLAB_REFS_HASH=$MATLAB_REFS_HASH" >> $GITHUB_OUTPUT | |
| # Pull cache if exists, otherwise cache will be created at the specified path | |
| - name: Cache collected references | |
| uses: actions/cache@v3 | |
| id: matlab-refs-cache | |
| env: | |
| cache-name: cache-matlab-references | |
| with: | |
| key: ${{ steps.matlab-refs-hash.outputs.MATLAB_REFS_HASH }} | |
| path: ./collectedValues.tar.gz | |
| - name: Checkout reference k-Wave repo | |
| uses: actions/checkout@v4 | |
| if: ${{ steps.matlab-refs-cache.outputs.cache-hit != 'true' }} | |
| with: | |
| repository: ucl-bug/k-wave | |
| path: k-wave | |
| ref: v1.4.0 | |
| - name: setup MATLAB | |
| uses: matlab-actions/setup-matlab@v1 | |
| if: ${{ steps.matlab-refs-cache.outputs.cache-hit != 'true' }} | |
| - name: run reference generation | |
| uses: matlab-actions/run-command@v1 | |
| if: ${{ steps.matlab-refs-cache.outputs.cache-hit != 'true' }} | |
| with: | |
| command: | | |
| ls; | |
| pwd; | |
| if exist('k-wave/k-Wave'); ls 'k-wave/k-Wave'; end; | |
| addpath('k-Wave-python','k-wave/k-Wave'); | |
| cd k-Wave-python/tests/matlab_test_data_collectors; | |
| run_all_collectors; | |
| - name: Compress generated references | |
| uses: a7ul/[email protected] | |
| if: ${{ steps.matlab-refs-cache.outputs.cache-hit != 'true' }} | |
| with: | |
| command: c | |
| cwd: ./k-Wave-python/tests/matlab_test_data_collectors/matlab_collectors/ | |
| files: | | |
| ./collectedValues | |
| outPath: collectedValues.tar.gz | |
| - name: upload reference values artifact | |
| id: artifact-upload-step | |
| if: ${{ steps.matlab-refs-cache.outputs.cache-hit != 'true' }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: matlab_reference_test_values | |
| path: collectedValues.tar.gz | |
| # overwrite: true | |
| - name: Output artifact URL | |
| if: ${{ steps.matlab-refs-cache.outputs.cache-hit != 'true' }} | |
| run: echo 'Artifact URL is ${{ steps.artifact-upload-step.outputs.artifact-url }}' | |
| test: | |
| needs: collect_references | |
| strategy: | |
| matrix: | |
| os: [ "windows-latest", "ubuntu-latest" , "macos-latest"] | |
| python-version: [ "3.10", "3.11", "3.12", "3.13" ] | |
| runs-on: ${{matrix.os}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # Pull the cache based on the hash value | |
| - name: Cache collected references | |
| uses: actions/cache@v3 | |
| id: cache-matlab-refs | |
| env: | |
| cache-name: cache-matlab-references | |
| with: | |
| key: ${{ needs.collect_references.outputs.MATLAB_REFS_HASH }} | |
| path: ./collectedValues.tar.gz | |
| fail-on-cache-miss: true | |
| enableCrossOsArchive: true | |
| # Now we have the references archive available in this job, proceed by unpacking it | |
| - name: unpack collectedValues | |
| uses: a7ul/[email protected] | |
| with: | |
| command: x | |
| cwd: ./tests/matlab_test_data_collectors/python_testers/ | |
| files: ${{github.workspace}}/collectedValues.tar.gz | |
| - name: where are the files? | |
| run: | | |
| ls ./tests/matlab_test_data_collectors/python_testers/ | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| pip install '.[test]' | |
| - name: Test with pytest | |
| run: | | |
| coverage run | |
| - name: Create coverage report | |
| run: | | |
| coverage xml | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| env_vars: ${{matrix.os}},${{ matrix.python-version }} | |
| fail_ci_if_error: true | |
| flags: ${{matrix.os}},${{ matrix.python-version }} | |
| name: ${{matrix.os}},${{ matrix.python-version }} | |
| verbose: true | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |