ci.yml

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: CI

# define when this workflow is triggered
on:
  workflow_dispatch:
  pull_request:
  push:
    branches:
      - main

# cancel any currently running workflows in this same PR
concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

# Use bash by default in all jobs
defaults:
  run:
    shell: bash -el {0}

jobs:
  # run pre-commit which includes many formatting and linting tools
  pre-commit:
    name: Format
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - uses: actions/setup-python@v5
        with:
          python-version: "3.x"
      - uses: pre-commit/action@v3.0.1
        with:
          extra_args: --hook-stage manual --all-files
      - name: Run PyLint
        run: pipx run nox -s pylint -- --output-format=github

  # Run tests and upload to codecov
  test:
    name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
    runs-on: ${{ matrix.runs-on }}
    if: |
      ${{!startsWith(github.event.head_commit.message, 'docs:') }} ||
      ${{!startsWith(github.event.head_commit.message, 'style:') }}
    needs: [pre-commit]
    strategy:
      # Otherwise, the workflow would stop if a single job fails. We want to
      # run all of them to catch failures in different combinations.
      fail-fast: false
      matrix:
        python-version: ["3.9", "3.10", "3.11", "3.12"]
        runs-on: [ubuntu-latest, macos-latest, windows-latest]
    env:
      FORCE_COLOR: 3
      NUMBA_DISABLE_JIT: "1"
    timeout-minutes: 30
    steps:
      # Checkout current git repository
      - name: Checkout
        uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Switch to Current Branch
        run: git checkout ${{ env.BRANCH }}

      - name: Get current week number of year
        id: date
        run: echo "date=$(date +%Y-W%W)" >> $GITHUB_OUTPUT # e.g., 2024-W19

      # Install Micromamba with conda-forge dependencies
      - name: Setup Micromamba
        uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: env/testing_env.yml
          create-args: >-
            python=${{ matrix.python-version }}
          post-cleanup: "all"
          cache-downloads: false
          # environment cache is persistent for one week.
          cache-environment-key:
            micromamba-environment-${{ steps.date.outputs.date }}

      # Install the package that we want to test
      - name: Install the package
        run: pip install --no-deps -e .

      - name: Run the tests
        run: >-
          pytest -m "not fetch and not issue" -ra --cov --cov-report=xml
          --cov-report=term --durations=20

      - name: Upload coverage report
        uses: codecov/codecov-action@v4.3.1
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}