linting_and_testing.yml

name: tests

on:
  # workflow_dispatch
  push:
    branches: [ master ]
    paths-ignore:
      - '.gitignore'
      - '.readthedocs.yaml'
      - 'LICENSE'
      - 'setup.py'
      - 'README.md'
      - 'CITATION.cff'
      - 'references.jsonld'
      - '**/docs/**'
      - '**/json_schemas/**'

jobs:
  # Name of the Job
  lint_and_test:
    strategy:
      matrix:
        os: [self-hosted]
        python-version: ["3.9", "3.10", "3.11", "3.12"]
    runs-on: ${{ matrix.os }}
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4

      - run: echo "Repository -> ${{ github.repository }}"
      - run: echo "Branch -> ${{ github.ref }}"
      - run: echo "Trigger event -> ${{ github.event_name }}"
      - run: echo "Runner OS -> ${{ runner.os }}"


      - name: List files in the repository
        run: |
          ls ${{ github.workspace }}

      - name: Remove all micromamba installations
        run: |
          rm -rf /home/user/.bash_profile /home/user/.conda /home/user/micromamba /home/user/micromamba-bin 2>/dev/null
          touch /home/user/.bash_profile

      - name: setup-micromamba
        uses: mamba-org/setup-micromamba@v2.0.0
        with:
          generate-run-shell: true
          micromamba-version: '2.0.2-2'
          post-cleanup: 'all'
          init-shell: bash
          environment-file: .github/env.yaml
          create-args: >-
            python=${{ matrix.python-version }}
            pytest
            pytest-cov
            pytest-html
            flake8
            pip

      - name: Install genbadge from pip
        shell: bash -l {0}
        run: pip install genbadge[all]

      - name: List installed package versions
        shell: bash -l {0}
        run: micromamba list

      - name: Lint with flake8
        shell: bash -l {0}
        run: |
          # F Codes: https://flake8.pycqa.org/en/latest/user/error-codes.html
          # E Code: https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes

          # Workflow fails: Stop the build if there are Python syntax errors or undefined names
          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics

          # Create directory for flake8 reports
          mkdir -p ./reports/flake8

          # Exit-zero treats all errors as warnings, workflow will not fail:
          flake8 . --exclude=docs --ignore=C901,E226 --count --exit-zero --max-complexity=10 --max-line-length=9999 --statistics --format=html --htmldir=./reports/flake8/ --tee --output-file=./reports/flake8/flake8stats.txt

      - name: Generate Flake8 badge
        shell: bash -l {0}
        run: |
          genbadge flake8 --name "Flake8" --input-file ./reports/flake8/flake8stats.txt  --output-file ./reports/flake8/flake8badge.svg

      - name: Checkout biobb_common
        uses: actions/checkout@v4
        with:
          repository: bioexcel/biobb_common
          path: './biobb_common'

      - name: Run tests
        shell: bash -l {0}
        run: |
          # Ignoring docker and singularity tests
          export PYTHONPATH=.:./biobb_common:$PYTHONPATH

          # copying .curvesplus data
          mkdir -p $CONDA_PREFIX/.curvesplus
          cp biobb_dna/curvesplus/.curvesplus/* $CONDA_PREFIX/.curvesplus

          # Copying .cdi file for canion
          wget https://mmb.irbbarcelona.org/biobb-api/rest/v1/sample/biobb_dna/biobb_canion/input_cdi_path -O biobb_dna/test/data/curvesplus/THGA_K.cdi

          # Create directory for tests reports
          mkdir -p ./reports/junit

          # Production one
          pytest biobb_dna/test/unitests/ --cov=biobb_dna/ --cov-report=xml --junit-xml=./reports/junit/junit.xml --html=./reports/junit/report.html

      - name: Generate Tests badge
        shell: bash -l {0}
        run: |
          genbadge tests --name "Tests" --input-file ./reports/junit/junit.xml  --output-file ./reports/junit/testsbadge.svg

      - name: Generate Coverage badge
        shell: bash -l {0}
        run: |
          # Create directory for flake8 reports
          mkdir -p ./reports/coverage

          coverage xml -o ./reports/coverage/coverage.xml
          coverage html -d ./reports/coverage/

          genbadge coverage --name "Coverage" --input-file ./reports/coverage/coverage.xml  --output-file ./reports/coverage/coveragebadge.svg

      - name: Publish coverage report to GitHub Pages
        uses: JamesIves/github-pages-deploy-action@v4
        with:
          folder: ./reports

      # - name: Restore .bash_profile
      #   run: cp ~/.bash_profile_orig ~/.bash_profile