tests.yml

name: Tests

on:
  push:
    branches:
      - main
      - master
    paths:
      - "**.py"
      - "**/Dockerfile"
      - ".github/workflows/*.yml"
      - poetry.lock
      - pyproject.toml

  pull_request:
    branches:
      - main
      - master
    paths:
      - "**.py"
      - "**/Dockerfile"
      - ".github/workflows/*.yml"
      - poetry.lock
      - pyproject.toml

jobs:
  tests:
    name: ${{ matrix.session }} ${{ matrix.python }} / ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        include:
          - { python: "3.10", os: "ubuntu-latest", session: "pre-commit" }
          - { python: "3.10", os: "ubuntu-latest", session: "safety" }
          - { python: "3.10", os: "ubuntu-latest", session: "mypy" }
          - { python: "3.9", os: "ubuntu-latest", session: "mypy" }
          - { python: "3.10", os: "ubuntu-latest", session: "tests" }
          - { python: "3.9", os: "ubuntu-latest", session: "tests" }
          - { python: "3.10", os: "macos-latest", session: "tests" }
          - { python: "3.9", os: "macos-latest", session: "tests" }
          - { python: "3.10", os: "ubuntu-latest", session: "docs-build" }

    env:
      NOXSESSION: ${{ matrix.session }}
      FORCE_COLOR: "1"
      PRE_COMMIT_COLOR: "always"

    steps:
      - name: Check out the repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 1

      - name: Cache pip packages
        uses: actions/cache@v3
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ matrix.python }}-${{ hashFiles('**/requirements.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-${{ matrix.python }}-
            ${{ runner.os }}-pip-

      - name: Cache Poetry virtual environment
        uses: actions/cache@v3
        with:
          path: .venv
          key: ${{ runner.os }}-poetry-${{ matrix.python }}-${{ hashFiles('pyproject.toml') }}
          restore-keys: |
            ${{ runner.os }}-poetry-${{ matrix.python }}-
            ${{ runner.os }}-poetry-

      - name: Set up Python ${{ matrix.python }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python }}

      - name: Upgrade pip
        run: |
          pip install --constraint=.github/workflows/constraints.txt pip
          pip --version

      - name: Upgrade pip in virtual environments
        shell: python
        run: |
          import os
          import pip

          with open(os.environ["GITHUB_ENV"], mode="a") as io:
              print(f"VIRTUALENV_PIP={pip.__version__}", file=io)

      - name: Install Dependencies
        if: matrix.os == 'ubuntu-latest'
        run: |
          sudo apt-get update
          sudo apt-get install -q --no-install-recommends --no-install-suggests libhts-dev  libssl-dev

      - name: Cache macOS dependencies
        if: matrix.os == 'macos-latest'
        uses: actions/cache@v3
        with:
          path: ~/brew-cache
          key: macos-brew-${{ hashFiles('**/Dockerfile') }}
          restore-keys: |
            macos-brew-

      - name: Configure Homebrew
        if: matrix.os == 'macos-latest'
        uses: Homebrew/actions/setup-homebrew@master

      - name: Install Dependencies
        if: matrix.os == 'macos-latest'
        env:
          HOMEBREW_NO_AUTO_UPDATE: 1
          HOMEBREW_NO_INSTALL_CLEANUP: 1 # Do not run brew cleanup automatically.
          HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: 1 # Do not automatically update packages.

        run: |
          brew install htslib
          brew install openssl@3
          ln -sf  $(brew --prefix openssl)/include/openssl /usr/local/include/openssl
          ln -sf  $(brew --prefix openssl)/lib/*a /usr/local/lib/
          ln -sf  $(brew --prefix openssl)/lib/*dylib /usr/local/lib/

      - name: Install Poetry
        run: |
          pipx install --pip-args=--constraint=.github/workflows/constraints.txt poetry
          poetry --version

      - name: debug
        if: matrix.os == 'macos-latest'
        run: |
          which python

      - name: Install Nox
        run: |
          pipx install --pip-args=--constraint=.github/workflows/constraints.txt nox
          pipx inject --pip-args=--constraint=.github/workflows/constraints.txt nox nox-poetry
          nox --version

      - name: Compute pre-commit cache key
        if: matrix.session == 'pre-commit'
        id: pre-commit-cache
        shell: python
        run: |
          import hashlib
          import sys

          python = "py{}.{}".format(*sys.version_info[:2])
          payload = sys.version.encode() + sys.executable.encode()
          digest = hashlib.sha256(payload).hexdigest()
          result = "${{ runner.os }}-{}-{}-pre-commit".format(python, digest[:8])

          print("::set-output name=result::{}".format(result))

      - name: Restore pre-commit cache
        uses: actions/cache@v3
        if: matrix.session == 'pre-commit'
        with:
          path: ~/.cache/pre-commit
          key: ${{ steps.pre-commit-cache.outputs.result }}-${{ hashFiles('.pre-commit-config.yaml') }}
          restore-keys: |
            ${{ steps.pre-commit-cache.outputs.result }}-

      - name: Run Nox
        run: |
          nox --force-color --python=${{ matrix.python }}

      - name: Upload coverage data
        if: always() && matrix.session == 'tests'
        uses: "actions/upload-artifact@v3"
        with:
          name: coverage-data
          path: ".coverage.*"

      - name: Upload documentation
        if: matrix.session == 'docs-build'
        uses: actions/upload-artifact@v3
        with:
          name: docs
          path: docs/_build

  coverage:
    runs-on: ubuntu-latest
    needs: tests
    steps:
      - name: Check out the repository
        uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.10"

      - name: Upgrade pip
        run: |
          pip install --constraint=.github/workflows/constraints.txt pip
          pip --version

      - name: Install Poetry
        run: |
          pipx install --pip-args=--constraint=.github/workflows/constraints.txt poetry
          poetry --version

      - name: Install Nox
        run: |
          pipx install --pip-args=--constraint=.github/workflows/constraints.txt nox
          pipx inject --pip-args=--constraint=.github/workflows/constraints.txt nox nox-poetry
          nox --version

      - name: Download coverage data
        uses: actions/download-artifact@v3.0.2
        with:
          name: coverage-data

      - name: Combine coverage data and display human readable report
        run: |
          nox --force-color --session=coverage -v

      - name: Create coverage report
        run: |
          nox --force-color --session=coverage -- xml

      - name: Upload coverage report
        uses: codecov/codecov-action@v3