ipython notebook test #330
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| """ | ||
| Dynamically creates a matrix for the GitHub Actions workflow that | ||
| runs the notebooks in the examples directory. | ||
| """ | ||
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| import os | ||
| import json | ||
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| # Dictionary to store custom timeouts for each notebook | ||
| notebook_timeouts = { | ||
| "ADCP_Delft3D_TRTS_example.ipynb": 1200, | ||
| "adcp_example.ipynb": 240, | ||
| "adv_example.ipynb": 180, | ||
| "cdip_example.ipynb": 180, | ||
| "Delft3D_example.ipynb": 180, | ||
| "directional_waves.ipynb": 180, | ||
| "environmental_contours_example.ipynb": 720, | ||
| "extreme_response_contour_example.ipynb": 360, | ||
| "extreme_response_full_sea_state_example.ipynb": 420, | ||
| "extreme_response_MLER_example.ipynb": 650, | ||
| "loads_example.ipynb": 180, | ||
| "metocean_example.ipynb": 240, | ||
| "mooring_example.ipynb": 300, | ||
| "PacWave_resource_characterization_example.ipynb": 780, | ||
| "power_example.ipynb": 180, | ||
| "qc_example.ipynb": 180, | ||
| "river_example.ipynb": 240, | ||
| "short_term_extremes_example.ipynb": 180, | ||
| "SWAN_example.ipynb": 180, | ||
| "tidal_example.ipynb": 240, | ||
| "tidal_performance_example.ipynb": 180, | ||
| "upcrossing_example.ipynb": 180, | ||
| "wave_example.ipynb": 180, | ||
| "wecsim_example.ipynb": 180, | ||
| "WPTO_hindcast_example.ipynb": 1200, | ||
| "default": 300, # Default timeout for other notebooks | ||
| } | ||
| notebooks = [] | ||
| for root, dirs, files in os.walk("examples"): | ||
| for file in files: | ||
| if file.endswith(".ipynb"): | ||
| notebooks.append(os.path.join(root, file)) | ||
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| # Generate the matrix configuration | ||
| matrix = {"include": []} | ||
| for notebook in notebooks: | ||
| timeout = notebook_timeouts.get( | ||
| os.path.basename(notebook), notebook_timeouts["default"] | ||
| ) | ||
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| matrix["include"].append({"notebook": notebook, "timeout": timeout}) | ||
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| # Print the matrix as a properly formatted JSON string | ||
| matrix_json = json.dumps(matrix) | ||
| print(f"matrix={matrix_json}") | ||
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|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| name: Py 3.10, 3.11 | Windows Mac Linux | ||
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| on: | ||
| push: | ||
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@@ -52,7 +52,7 @@ jobs: | |
| prepare-nonhindcast-cache: | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| PYTHON_VER: 3.11 | ||
| steps: | ||
| - name: Checkout code | ||
| uses: actions/checkout@v4 | ||
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@@ -95,7 +95,7 @@ jobs: | |
| needs: [check-changes] | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| PYTHON_VER: 3.11 | ||
| if: (needs.check-changes.outputs.should-run-hindcast == 'true') | ||
| steps: | ||
| - name: Checkout code | ||
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@@ -137,7 +137,7 @@ jobs: | |
| needs: [check-changes, prepare-wave-hindcast-cache] | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| PYTHON_VER: 3.11 | ||
| if: (needs.check-changes.outputs.should-run-hindcast == 'true') | ||
| steps: | ||
| - name: Checkout code | ||
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@@ -183,7 +183,7 @@ jobs: | |
| fail-fast: false | ||
| matrix: | ||
| os: ${{fromJson(needs.set-os.outputs.matrix_os)}} | ||
| python-version: ['3.10', '3.11'] | ||
| env: | ||
| PYTHON_VER: ${{ matrix.python-version }} | ||
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@@ -234,7 +234,7 @@ jobs: | |
| fail-fast: false | ||
| matrix: | ||
| os: ${{fromJson(needs.set-os.outputs.matrix_os)}} | ||
| python-version: ['3.10', '3.11'] | ||
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| steps: | ||
| - uses: conda-incubator/setup-miniconda@v3 | ||
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@@ -244,21 +244,6 @@ jobs: | |
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
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| - name: Set up Git repository | ||
| uses: actions/checkout@v4 | ||
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@@ -305,7 +290,7 @@ jobs: | |
| fail-fast: false | ||
| matrix: | ||
| os: ${{fromJson(needs.set-os.outputs.matrix_os)}} | ||
| python-version: ['3.10', '3.11'] | ||
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| steps: | ||
| - uses: actions/checkout@v4 | ||
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@@ -359,6 +344,104 @@ jobs: | |
| parallel: true | ||
| path-to-lcov: ./coverage.lcov | ||
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| notebook-matrix: | ||
| runs-on: ubuntu-latest | ||
| needs: | ||
| [ | ||
| check-changes, | ||
| prepare-nonhindcast-cache, | ||
| prepare-wave-hindcast-cache, | ||
| prepare-wind-hindcast-cache, | ||
| ] | ||
| if: | | ||
| always() && | ||
| ( | ||
| ( | ||
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There was a problem hiding this comment. "always() &&" seems redundant There was a problem hiding this comment. I agree, however, I have become accustomed to this syntax in actions and you will find it throughout our tests. There is discussion here agreeing that you should not need to but that you do: |
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| needs.prepare-nonhindcast-cache.result == 'success' && | ||
| needs.prepare-wave-hindcast-cache.result == 'skipped' && | ||
| needs.prepare-wind-hindcast-cache.result == 'skipped' && | ||
| needs.check-changes.outputs.should-run-hindcast == 'false' | ||
| ) || | ||
| ( | ||
| needs.prepare-nonhindcast-cache.result == 'success' && | ||
| needs.prepare-wave-hindcast-cache.result == 'success' && | ||
| needs.prepare-wind-hindcast-cache.result == 'success' && | ||
| needs.check-changes.outputs.should-run-hindcast == 'true' | ||
| ) | ||
| ) | ||
| outputs: | ||
| matrix: ${{ steps.set-matrix.outputs.matrix }} | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
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| - name: Set up Python | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: '3.11' | ||
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| - name: Generate matrix | ||
| id: set-matrix | ||
| run: | | ||
| matrix_json=$(python .github/workflows/generate_notebook_matrix.py) | ||
| echo "$matrix_json" >> $GITHUB_OUTPUT | ||
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There was a problem hiding this comment. What is the purpose of the There was a problem hiding this comment. In bash here we are setting a variable So the |
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| test-notebooks: | ||
| needs: | ||
| [ | ||
| notebook-matrix, | ||
| check-changes, | ||
| prepare-nonhindcast-cache, | ||
| prepare-wave-hindcast-cache, | ||
| prepare-wind-hindcast-cache, | ||
| ] | ||
| strategy: | ||
| matrix: ${{ fromJson(needs.notebook-matrix.outputs.matrix) }} | ||
| if: | | ||
| always() | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
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| - name: Set up Miniconda | ||
| uses: conda-incubator/setup-miniconda@v3 | ||
| with: | ||
| miniconda-version: 'latest' | ||
| auto-update-conda: true | ||
| python-version: '3.11' | ||
| activate-environment: TESTconda | ||
| use-only-tar-bz2: true | ||
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| - name: Install dependencies | ||
| shell: bash -l {0} | ||
| run: | | ||
| conda install numpy cython pip hdf5 libnetcdf cftime netcdf4 --strict-channel-priority | ||
| pip install -e . --force-reinstall | ||
| python -m pip install --upgrade pip wheel | ||
| pip install nbval jupyter | ||
| pip install utm folium | ||
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| - name: Ensure Conda environment is activated | ||
| shell: bash -l {0} | ||
| run: | | ||
| echo "source ~/miniconda3/etc/profile.d/conda.sh" >> ~/.bashrc | ||
| echo "conda activate TESTconda" >> ~/.bashrc | ||
| source ~/.bashrc | ||
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| - name: Run notebook | ||
| shell: bash -l {0} | ||
| run: | | ||
| if [[ "${{ matrix.notebook }}" == "examples/metocean_example.ipynb" || "${{ matrix.notebook }}" == "examples/WPTO_hindcast_example.ipynb" ]]; then | ||
| if [[ "${{ needs.check-changes.outputs.should-run-hindcast }}" == 'true' ]]; then | ||
| jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=${{ matrix.timeout }} "${{ matrix.notebook }}" | ||
| else | ||
|
There was a problem hiding this comment. Will "ExecutePreprocessor" fail each notebook test if it hits the timeout? There was a problem hiding this comment. Yes each notebook in the repo has a custom timeout specified. It will fail if you go overtime. You can see some of these failures on previous commits such as the commit before "Increase ADCP timeout". |
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| echo "Skipping ${{ matrix.notebook }}" | ||
| fi | ||
| else | ||
| jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=${{ matrix.timeout }} "${{ matrix.notebook }}" | ||
| fi | ||
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| coveralls: | ||
| name: Indicate completion to coveralls.io | ||
| needs: | ||
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Does the key "include" have to do with how Actions creates a testing matrix from the test variable?
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Yes.
The include key is a dummy key/ catch all for Actions because you can only have a single variable json at the top level.
So its called include to include all the keys I want to use.