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/**'
      - '.github/workflows/pr-tests.yml'
      - '**/test/data/**'
      - '**/test/references/**'
      - '.github/workflows/test_containers.yml'

jobs:
  # Name of the Job
  lint_and_test:
    strategy:
      matrix:
        os: [mmbswarm]
        python-version: ["3.10", "3.11", "3.12"]
    runs-on: ${{ matrix.os }}
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - 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: Detect changed files and set test paths
        id: changes
        shell: bash
        run: |
          BEFORE="${{ github.event.before }}"
          AFTER="${{ github.sha }}"

          if [ "$BEFORE" = "0000000000000000000000000000000000000000" ]; then
            echo "New branch detected – running full test suite"
            echo "test_paths=" >> "$GITHUB_OUTPUT"
            exit 0
          fi

          CHANGED_FILES=$(git diff --name-only "$BEFORE" "$AFTER" 2>/dev/null || echo "")
          echo "Changed files:"
          echo "${CHANGED_FILES:-(none)}"

          TESTS=""
          while IFS= read -r FILE; do
            [ -z "$FILE" ] && continue
            if [[ "$FILE" =~ ^${{ github.event.repository.name }}/test/unitests/test_[^/]+/test_[^/]+\.py$ ]]; then
              # Direct test file change – run only this file (skip container tests)
              if [[ "$FILE" != *_container.py ]]; then
                [ -f "$FILE" ] && TESTS+=$'\n'"$FILE"
              fi
            elif [[ "$FILE" =~ ^${{ github.event.repository.name }}/([a-z][^/]+)/([^/]+)\.py$ ]]; then
              TOOL="${BASH_REMATCH[1]}"
              BASE="${BASH_REMATCH[2]}"
              if [[ "$BASE" == "__init__" || "$BASE" == "common" ]]; then
                # Run all tests for this tool
                TEST_DIR="${{ github.event.repository.name }}/test/unitests/test_${TOOL}"
                [ -d "$TEST_DIR" ] && TESTS+=$'\n'"$TEST_DIR"
              else
                # Run the matching test file for this source file
                TEST_FILE="${{ github.event.repository.name }}/test/unitests/test_${TOOL}/test_${BASE}.py"
                if [ -f "$TEST_FILE" ]; then
                  TESTS+=$'\n'"$TEST_FILE"
                else
                  TEST_DIR="${{ github.event.repository.name }}/test/unitests/test_${TOOL}"
                  [ -d "$TEST_DIR" ] && TESTS+=$'\n'"$TEST_DIR"
                fi
              fi
            fi
          done <<< "$CHANGED_FILES"

          TESTS=$(echo "$TESTS" | grep -v '^$' | sort -u | tr '\n' ' ' | xargs || echo "")
          echo "Test paths: ${TESTS:-(none detected – will run full suite)}"
          echo "test_paths=$TESTS" >> "$GITHUB_OUTPUT"

      - name: Remove all micromamba installations
        run: |
          rm -rf $HOME/.bash_profile $HOME/.conda $HOME/micromamba $HOME/micromamba-bin 2>/dev/null
          touch $HOME/.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: Run tests
        shell: bash -l {0}
        run: |
          # Ignoring docker and singularity tests
          export PYTHONPATH=.:$PYTHONPATH

          # copying cp2k_aux data
          mkdir -p $CONDA_PREFIX/cp2k_aux
          cp -r biobb_cp2k/cp2k/cp2k_in $CONDA_PREFIX/cp2k_aux
          cp -r biobb_cp2k/cp2k/cp2k_data $CONDA_PREFIX/cp2k_aux

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

          # Run only tests for modified tools, fall back to full suite when nothing specific detected
          TEST_PATHS="${{ steps.changes.outputs.test_paths }}"
          if [ -z "$TEST_PATHS" ]; then
            TEST_PATHS="${{ github.event.repository.name }}/test/unitests/"
          fi

          pytest $TEST_PATHS --cov=${{ github.event.repository.name }}/ --cov-report=xml --ignore-glob=*container.py --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