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Better handling and documentation of dependencies (#1589)
* Rename and add environments * Thin out requirements in setup.cfg, add note * Remove improver_tests tests from built package The previous exclude was not effective - it excluded the top level directory, but not the subdirectories containing all the test source code files. * Skip checksum sorted test if file not available * Pytest skips for stratify * Move stratify import inside function * Remove duplicated statsmodels * Better explanation for latest environment * Add sphinx typehints to conda-forge tests section * Run security checks on all environments * Separate coverage and no-coverage environments * Add detailed pinning to A/B environments * Pin numpy/cartopy in latest environment Unit test failures occur with older versions * Start documentation * Remove dateutil dependency * More documentation * Remove timezone database dependence in unit test * Fix duplicated name in conda-forge environment * Add note that not all CLIs are available with environment_b * Remove leftover expected data from test_process * Fix flake8 * Remove not-really-working install_requires section * Clarify conda-forge environment comment * Move latest environment tests to schedule * Fix actions YAML * Reschedule * Fix scheduling, add manual running, metoppv-only * Add timezone mask test on europe lat/lon domain
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,137 @@ | ||
| name: Scheduled Tests | ||
|
|
||
| on: | ||
| schedule: | ||
| - cron: '7 4 * * *' | ||
| workflow_dispatch: | ||
| jobs: | ||
| Sphinx-Pytest-Coverage: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| env: [latest] | ||
| if: github.repository_owner == 'metoppv' | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - uses: actions/cache@v2 | ||
| id: cache | ||
| env: | ||
| # Increase this value to reset cache | ||
| CACHE_NUMBER: 2 | ||
| with: | ||
| path: /usr/share/miniconda/envs/im${{ matrix.env }} | ||
| key: ${{ format('{0}-conda-improver-{1}-{2}-{3}', runner.os, env.CACHE_NUMBER, matrix.env, hashFiles(format('envs/{0}.yml', matrix.env))) }} | ||
| - name: conda env update | ||
| if: steps.cache.outputs.cache-hit != 'true' | ||
| run: | | ||
| source '/usr/share/miniconda/etc/profile.d/conda.sh' | ||
| conda install -c conda-forge mamba | ||
| mamba env update -q --file envs/${{ matrix.env }}.yml --name im${{ matrix.env }} | ||
| - name: conda info | ||
| run: | | ||
| source '/usr/share/miniconda/etc/profile.d/conda.sh' | ||
| conda activate im${{ matrix.env }} | ||
| conda info | ||
| conda list | ||
| - name: sphinx documentation | ||
| run: | | ||
| source '/usr/share/miniconda/etc/profile.d/conda.sh' | ||
| conda activate im${{ matrix.env }} | ||
| make -C doc html SPHINXOPTS="-W --keep-going" | ||
| - name: pytest without coverage | ||
| if: matrix.env != 'environment_a' | ||
| run: | | ||
| source '/usr/share/miniconda/etc/profile.d/conda.sh' | ||
| conda activate im${{ matrix.env }} | ||
| pytest | ||
| - name: pytest with coverage | ||
| if: matrix.env == 'environment_a' | ||
| run: | | ||
| source '/usr/share/miniconda/etc/profile.d/conda.sh' | ||
| conda activate im${{ matrix.env }} | ||
| pytest --cov=improver --cov-report xml:coverage.xml | ||
| - name: codacy upload | ||
| if: env.CODACY_PROJECT_TOKEN && matrix.env == 'environment_a' | ||
| run: | | ||
| source '/usr/share/miniconda/etc/profile.d/conda.sh' | ||
| conda activate im${{ matrix.env }} | ||
| python-codacy-coverage -v -r coverage.xml | ||
| env: | ||
| CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }} | ||
| - name: codecov upload | ||
| uses: codecov/codecov-action@v1 | ||
| if: matrix.env == 'environment_a' | ||
| Safety-Bandit: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| env: [latest] | ||
| if: github.repository_owner == 'metoppv' | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - uses: actions/cache@v2 | ||
| id: cache | ||
| env: | ||
| # Increase this value to reset cache | ||
| CACHE_NUMBER: 2 | ||
| with: | ||
| path: /usr/share/miniconda/envs/im${{ matrix.env }} | ||
| key: ${{ format('{0}-conda-improver-{1}-{2}-{3}', runner.os, env.CACHE_NUMBER, matrix.env, hashFiles(format('envs/{0}.yml', matrix.env))) }} | ||
| - name: conda env update | ||
| if: steps.cache.outputs.cache-hit != 'true' | ||
| run: | | ||
| source '/usr/share/miniconda/etc/profile.d/conda.sh' | ||
| conda install -c conda-forge mamba | ||
| mamba env update -q --file envs/${{ matrix.env }}.yml --name im${{ matrix.env }} | ||
| - name: conda info | ||
| run: | | ||
| source '/usr/share/miniconda/etc/profile.d/conda.sh' | ||
| conda activate im${{ matrix.env }} | ||
| conda info | ||
| conda list | ||
| - name: safety | ||
| run: | | ||
| source '/usr/share/miniconda/etc/profile.d/conda.sh' | ||
| conda activate im${{ matrix.env }} | ||
| safety check || true | ||
| - name: bandit | ||
| run: | | ||
| source '/usr/share/miniconda/etc/profile.d/conda.sh' | ||
| conda activate im${{ matrix.env }} | ||
| bandit -r improver | ||
| Type-checking: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| env: [latest] | ||
| if: github.repository_owner == 'metoppv' | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - uses: actions/cache@v2 | ||
| id: cache | ||
| env: | ||
| # Increase this value to reset cache | ||
| CACHE_NUMBER: 2 | ||
| with: | ||
| path: /usr/share/miniconda/envs/im${{ matrix.env }} | ||
| key: ${{ format('{0}-conda-improver-{1}-{2}-{3}', runner.os, env.CACHE_NUMBER, matrix.env, hashFiles(format('envs/{0}.yml', matrix.env))) }} | ||
| - name: conda env update | ||
| if: steps.cache.outputs.cache-hit != 'true' | ||
| run: | | ||
| source '/usr/share/miniconda/etc/profile.d/conda.sh' | ||
| conda install -c conda-forge mamba | ||
| mamba env update -q --file envs/${{ matrix.env }}.yml --name im${{ matrix.env }} | ||
| - name: conda info | ||
| run: | | ||
| source '/usr/share/miniconda/etc/profile.d/conda.sh' | ||
| conda activate im${{ matrix.env }} | ||
| conda info | ||
| conda list | ||
| - name: mypy | ||
| run: | | ||
| source '/usr/share/miniconda/etc/profile.d/conda.sh' | ||
| conda activate im${{ matrix.env }} | ||
| mypy improver || true |
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