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Adding TargetValue and MolecularWeight Sampler (#172)
This PR supersedes #165 and #170 and resolves #168. #165 implemented a sampler which would divide molecules based on their molecular weight (either ascending or descending), and #170 added basically the same thing but for arbitrary target values. This PR just refactors #170 as if #165 where already implemented, reducing code duplication quite a bit. There is also some small internal cleanup, namely 00eeca6, 98b3efd, and 3b8bca1 (as well as some long-overdue CI updates).
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| name: Continuous Integration | ||
| on: | ||
| schedule: | ||
| - cron: "0 8 * * 1-5" | ||
| push: | ||
| branches: [main] | ||
| pull_request: | ||
| branches: [main] | ||
| workflow_dispatch: | ||
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| concurrency: | ||
| group: actions-id-${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
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| jobs: | ||
| check-formatting: | ||
| name: Check Build and Formatting Errors | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Install Dependencies | ||
| run: | | ||
| python -m pip install pycodestyle isort | ||
| - name: Check Build | ||
| run: | | ||
| python -m pip install . | ||
| - name: Run pycodestyle | ||
| run: | | ||
| pycodestyle --statistics --count --max-line-length=150 --show-source --ignore=E203 . | ||
| - name: Check Import Ordering Errors | ||
| run: | | ||
| isort --check-only --verbose . | ||
| build-and-test: | ||
| needs: check-formatting | ||
| continue-on-error: true | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | ||
| os: [ubuntu-latest, windows-latest, macos-latest] | ||
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| runs-on: ${{ matrix.os }} | ||
| defaults: | ||
| run: | ||
| shell: bash -el {0} | ||
| name: ${{ matrix.os }} Python ${{ matrix.python-version }} Subtest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: mamba-org/setup-micromamba@main | ||
| with: | ||
| environment-name: temp | ||
| condarc: | | ||
| channels: | ||
| - defaults | ||
| - conda-forge | ||
| channel_priority: flexible | ||
| create-args: | | ||
| python=${{ matrix.python-version }} | ||
| - name: Install Dependencies | ||
| run: | | ||
| python -m pip install -e .[molecules] | ||
| python -m pip install coverage pytest | ||
| - name: Run Tests | ||
| run: | | ||
| coverage run --source=. --omit=astartes/__init__.py,setup.py,test/* -m pytest -v | ||
| - name: Show Coverage | ||
| run: | | ||
| coverage report -m | ||
| ipynb-ci: | ||
| needs: check-formatting | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| nb-file: | ||
| ["barrier_prediction_with_RDB7/RDB7_barrier_prediction_example", "train_val_test_split_sklearn_example/train_val_test_split_example", "split_comparisons/split_comparisons", "mlpds_2023_astartes_demonstration/mlpds_2023_demo"] | ||
| runs-on: ubuntu-latest | ||
| defaults: | ||
| run: | ||
| shell: bash -el {0} | ||
| name: Check ${{ matrix.nb-file }} Notebook Execution | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: mamba-org/setup-micromamba@main | ||
| with: | ||
| environment-name: temp | ||
| condarc: | | ||
| channels: | ||
| - defaults | ||
| - conda-forge | ||
| channel_priority: flexible | ||
| create-args: | | ||
| python=3.11 | ||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install -e .[molecules,demos] | ||
| python -m pip install notebook | ||
| - name: Test Execution | ||
| run: | | ||
| cd examples/$(dirname ${{ matrix.nb-file }}) | ||
| jupyter nbconvert --to script $(basename ${{ matrix.nb-file }}).ipynb | ||
| ipython $(basename ${{ matrix.nb-file }}).py | ||
| coverage-check: | ||
| if: contains(github.event.pull_request.labels.*.name, 'PR Ready for Review') | ||
| needs: [build-and-test, ipynb-ci] | ||
| runs-on: ubuntu-latest | ||
| defaults: | ||
| run: | ||
| shell: bash -el {0} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| auto-update-conda: true | ||
| python-version: "3.10" | ||
| - name: Install Dependencies | ||
| run: | | ||
| python -m pip install -e .[molecules] | ||
| python -m pip install coverage | ||
| - name: Run Tests | ||
| run: | | ||
| coverage run --source=. --omit=astartes/__init__.py,setup.py,test/*,astartes/samplers/sampler.py -m unittest discover -v | ||
| - name: Show Coverage | ||
| run: | | ||
| coverage report -m > temp.txt | ||
| cat temp.txt | ||
| python .github/workflows/coverage_helper.py | ||
| echo "COVERAGE_PERCENT=$(cat temp2.txt)" >> $GITHUB_ENV | ||
| - name: Request Changes via Review | ||
| if: ${{ env.COVERAGE_PERCENT < 90 }} | ||
| uses: andrewmusgrave/[email protected] | ||
| with: | ||
| repo-token: ${{ secrets.GITHUB_TOKEN }} | ||
| event: REQUEST_CHANGES | ||
| body: "Increase test coverage from ${{ env.COVERAGE_PERCENT }}% to at least 90% before merging." | ||
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| - name: Approve PR if Coverage Sufficient | ||
| if: ${{ env.COVERAGE_PERCENT > 89 }} | ||
| uses: andrewmusgrave/[email protected] | ||
| with: | ||
| repo-token: ${{ secrets.GITHUB_TOKEN }} | ||
| event: APPROVE | ||
| body: "Test coverage meets or exceeds 90% threshold (currently ${{ env.COVERAGE_PERCENT }}%)." | ||
|
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| ci-report-status: | ||
| name: report CI status | ||
| needs: [build-and-test, ipynb-ci] | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - run: | | ||
| result_1="${{ needs.build-and-test.result }}" | ||
| result_2="${{ needs.ipynb-ci.result }}" | ||
| if test $result_1 == "success" && test $result_2 == "success"; then | ||
| exit 0 | ||
| else | ||
| exit 1 | ||
| fi | ||
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