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Merge pull request #418 from ahernank/417-fix-tests-after-year-change
Update cohorts version & expected frq col
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,44 +1,44 @@ | ||
| name: notebooks | ||
| on: | ||
| push: | ||
| branches: | ||
| - master | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| push: | ||
| branches: | ||
| - master | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| jobs: | ||
| notebooks: | ||
| strategy: | ||
| fail-fast: true | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout source | ||
| uses: actions/checkout@v3 | ||
| notebooks: | ||
| strategy: | ||
| fail-fast: true | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout source | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - name: Install poetry | ||
| run: pipx install poetry==1.4.2 | ||
| - name: Install poetry | ||
| run: pipx install poetry==1.4.2 | ||
|
|
||
| - name: Setup python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: '3.11' | ||
| cache: 'poetry' | ||
| - name: Setup python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.11" | ||
| cache: "poetry" | ||
|
|
||
| - name: Install dependencies | ||
| run: poetry install | ||
| - name: Install dependencies | ||
| run: poetry install | ||
|
|
||
| - name: Restore GCS cache | ||
| uses: actions/cache/restore@v3 | ||
| with: | ||
| path: gcs_cache | ||
| key: gcs_cache_notebooks_20230425 | ||
| - name: Restore GCS cache | ||
| uses: actions/cache/restore@v3 | ||
| with: | ||
| path: gcs_cache | ||
| key: gcs_cache_notebooks_20230811 | ||
|
|
||
| - name: Run notebooks | ||
| run: poetry run jupyter nbconvert --execute notebooks/* --inplace | ||
| - name: Run notebooks | ||
| run: poetry run jupyter nbconvert --execute notebooks/* --inplace | ||
|
|
||
| - name: Save GCS cache | ||
| uses: actions/cache/save@v3 | ||
| if: always() | ||
| with: | ||
| path: gcs_cache | ||
| key: gcs_cache_notebooks_20230425 | ||
| - name: Save GCS cache | ||
| uses: actions/cache/save@v3 | ||
| if: always() | ||
| with: | ||
| path: gcs_cache | ||
| key: gcs_cache_notebooks_20230811 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,51 +1,51 @@ | ||
| name: tests | ||
| on: | ||
| push: | ||
| branches: | ||
| - master | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| push: | ||
| branches: | ||
| - master | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| jobs: | ||
| tests: | ||
| strategy: | ||
| fail-fast: true | ||
| matrix: | ||
| python-version: ['3.8', '3.9', '3.10', '3.11'] | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout source | ||
| uses: actions/checkout@v3 | ||
| tests: | ||
| strategy: | ||
| fail-fast: true | ||
| matrix: | ||
| python-version: ["3.8", "3.9", "3.10", "3.11"] | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout source | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - name: Install poetry | ||
| run: pipx install poetry==1.4.2 | ||
| - name: Install poetry | ||
| run: pipx install poetry==1.4.2 | ||
|
|
||
| - name: Setup python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| cache: 'poetry' | ||
| - name: Setup python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| cache: "poetry" | ||
|
|
||
| - name: Install dependencies | ||
| run: poetry install | ||
| - name: Install dependencies | ||
| run: poetry install | ||
|
|
||
| # Run a subset of tests first which run quickly without accessing | ||
| # any remote data in order to fail fast where possible. | ||
| - name: Run fast unit tests | ||
| run: poetry run pytest -v tests/anoph --typeguard-packages=malariagen_data,malariagen_data.anoph | ||
| # Run a subset of tests first which run quickly without accessing | ||
| # any remote data in order to fail fast where possible. | ||
| - name: Run fast unit tests | ||
| run: poetry run pytest -v tests/anoph --typeguard-packages=malariagen_data,malariagen_data.anoph | ||
|
|
||
| - name: Restore GCS cache | ||
| uses: actions/cache/restore@v3 | ||
| with: | ||
| path: gcs_cache | ||
| key: gcs_cache_tests_20230420 | ||
| - name: Restore GCS cache | ||
| uses: actions/cache/restore@v3 | ||
| with: | ||
| path: gcs_cache | ||
| key: gcs_cache_tests_20230811 | ||
|
|
||
| - name: Run full test suite | ||
| run: poetry run pytest -v tests | ||
| - name: Run full test suite | ||
| run: poetry run pytest -v tests | ||
|
|
||
| - name: Save GCS cache | ||
| uses: actions/cache/save@v3 | ||
| if: always() | ||
| with: | ||
| path: gcs_cache | ||
| key: gcs_cache_tests_20230420 | ||
| - name: Save GCS cache | ||
| uses: actions/cache/save@v3 | ||
| if: always() | ||
| with: | ||
| path: gcs_cache | ||
| key: gcs_cache_tests_20230811 |
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