CI_build.yml

name: CI Build

on:
  push:
  pull_request:
    types: [opened, reopened]

jobs:

  first_check:
    name: first code check / python-3.10 / ubuntu-latest
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.10"
      - 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: ['3.10']
        exclude:
          # already tested in first_check job
          - python-version: "3.10"
            os: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
      - name: Python info
        run: |
          which python
          python --version
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip poetry
      - name: Build package
        run: |
          poetry build
      - name: Test package
        run: |
          pip install twine
          python -m twine check dist/*
      - name: Show pip list
        run: |
          pip list
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip poetry
          poetry install
      - name: Test
        run: |
          poetry run pytest
      - name: Show environment variables
        shell: bash -l {0}
        run: |
          env | sort
      - name: Build documentation
        shell: bash -l {0}
        run: |
          cd readthedocs
          make coverage doctest html
        working-directory: readthedocs/
        env:
          SPHINXOPTS: "-n"  # enable nit-picky mode
      - name: Check documentation coverage threshold
        if: matrix.os == 'ubuntu-latest'
        run: |
          cat readthedocs/_build/coverage/python.txt
          UNCOVERED_MEMBERS=$(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-3.10 / 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: "3.10"
      - 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