Update to latest matchms, gensim and poetry buildsystem #249
Workflow file for this run
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| name: CI Build | |
| on: | |
| push: | |
| pull_request: | |
| types: [opened, reopened] | |
| jobs: | |
| first_check: | |
| name: first code check / python-3.9 / ubuntu-latest | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.9 | |
| - name: Python info | |
| run: | | |
| which python | |
| python --version | |
| - name: Build package and create dev environment | |
| run: | | |
| python -m pip install --upgrade pip poetry | |
| poetry install | |
| - name: Show pip list | |
| run: | | |
| pip list | |
| - name: Test with coverage | |
| run: | | |
| poetry run pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml | |
| - name: Correct coverage paths | |
| run: sed -i "s+$PWD/++g" coverage.xml | |
| - name: Check style against standards using prospector | |
| shell: bash -l {0} | |
| run: poetry run prospector -o grouped -o pylint:pylint-report.txt | |
| - name: Check whether import statements are used consistently | |
| shell: bash -l {0} | |
| run: poetry run isort --check-only --diff --conda-env spec2vec-dev . | |
| - name: SonarCloud Scan | |
| if: github.repository == 'iomega/spec2vec' | |
| uses: sonarsource/sonarcloud-github-action@master | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} | |
| build_pypi: | |
| name: Pypi and documentation build / python-${{ matrix.python-version }} / ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| needs: first_check | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ['ubuntu-latest', 'macos-latest', 'windows-latest'] | |
| python-version: ['3.9'] | |
| exclude: | |
| # already tested in first_check job | |
| - python-version: 3.9 | |
| os: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Python info | |
| run: | | |
| which python | |
| python --version | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip poetry | |
| - name: Build package | |
| run: | | |
| poetry build | |
| - name: Test package | |
| run: | | |
| poetry install --only dev | |
| python -m twine check dist/* | |
| - name: Show pip list | |
| run: | | |
| pip list | |
| - name: Install development dependencies | |
| run: | | |
| poetry install | |
| - name: Test | |
| run: | | |
| poetry run pytest | |
| - name: Show environment variables | |
| shell: bash -l {0} | |
| run: | | |
| env | sort | |
| - name: Build documentation | |
| shell: bash -l {0} | |
| run: | | |
| cd readthedocs | |
| make coverage doctest html | |
| working-directory: readthedocs/ | |
| env: | |
| SPHINXOPTS: "-n" # enable nit-picky mode | |
| - name: Check documentation coverage threshold | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| cat readthedocs/_build/coverage/python.txt | |
| UNCOVERED_MEMBERS=$(grep '*' readthedocs/_build/coverage/python.txt | wc -l) | |
| UNCOVERED_MEMBERS_ALLOWED=5 | |
| if (( $UNCOVERED_MEMBERS > $UNCOVERED_MEMBERS_ALLOWED )) ; then echo "There are currently ${UNCOVERED_MEMBERS} uncovered members in the documentation, which is more than the ${UNCOVERED_MEMBERS_ALLOWED} allowed." && exit 1;fi | |
| echo "The code is sufficiently documented with ${UNCOVERED_MEMBERS} uncovered members out of ${UNCOVERED_MEMBERS_ALLOWED} allowed."; | |
| anaconda_build: | |
| name: Anaconda build / python-3.9 / ubuntu-latest | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| needs: first_check | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: "0" | |
| - name: Create spec2vec-build environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: spec2vec-build | |
| auto-update-conda: true | |
| environment-file: conda/environment-build.yml | |
| python-version: 3.9 | |
| - name: Show conda config | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| conda config --show-sources | |
| conda config --show | |
| conda env list | |
| - name: Python info | |
| shell: bash -l {0} | |
| run: | | |
| which python | |
| python --version | |
| - name: Show environment variables | |
| shell: bash -l {0} | |
| run: | | |
| env | sort | |
| - name: Build the conda package | |
| shell: bash -l {0} | |
| run: | | |
| export BUILDDIR=$RUNNER_TEMP/spec2vec/_build | |
| [ "$RUNNING_OS" = "Windows" ] && export BUILDDIR=$RUNNER_TEMP\\spec2vec\\_build\\ | |
| conda config --set anaconda_upload no | |
| conda build --no-include-recipe \ | |
| --channel bioconda --channel conda-forge \ | |
| --croot ${BUILDDIR} \ | |
| ./conda | |
| - name: Upload package artifact from build | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: conda-package-artifact | |
| path: ${{ runner.temp }}/spec2vec/_build |