test_and_deploy.yml

# This workflows will upload a Python Package using Twine when a release is created
# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries

name: tests

on:
  push:
    branches:
      - main
      - npe2
    tags:
      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
  pull_request:
    branches:
      - main
      - npe2
  workflow_dispatch:

jobs:
  test:
    name: ${{ matrix.platform }} py${{ matrix.python-version }}
    runs-on: ${{ matrix.platform }}
    timeout-minutes: 30
    strategy:
      matrix:
        platform: [ubuntu-latest, macos-latest]
        python-version: ["3.11", "3.12"]

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      # these libraries enable testing on Qt on linux
      - uses: tlambert03/setup-qt-libs@v1

      # note: if you need dependencies from conda, considering using
      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
      # and
      # tox-conda: https://github.com/tox-dev/tox-conda
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          python -m pip install setuptools tox tox-gh-actions scikit-learn-extra
          
      - name: Pip cache
        uses: actions/cache@v4
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml', 'tox.ini') }}
          restore-keys: |
            ${{ runner.os }}-pip-

      - name: Remove .tox cache
        run: rm -rf .tox

      - name: Free up disk space (Linux)
        if: runner.os == 'Linux'
        run: |
          # Remove unnecessary tools and packages to free up disk space
          sudo rm -rf /usr/share/dotnet
          sudo rm -rf /usr/local/lib/android
          sudo rm -rf /opt/ghc
          sudo rm -rf /opt/hostedtoolcache/CodeQL
          sudo docker image prune --all --force
          df -h

      - name: Upgrade critical dependencies
        run: |
          python -m pip install --upgrade numpy psygnal pytest
          python -m pip install --upgrade pip setuptools wheel

      - name: Install system dependencies (Linux)
        if: runner.os == 'Linux'
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            libgl1-mesa-dev \
            libglib2.0-0 \
            libsm6 \
            libxext6 \
            libxrender1 \
            libgomp1

      # this runs the platform-specific tests declared in tox.ini
      - name: Test with tox
        uses: aganders3/headless-gui@v2
        with:
          run: python -m tox -r -- -m "not slow"
        env:
          PLATFORM: ${{ matrix.platform }}
          QT_QPA_PLATFORM: offscreen
          MPLBACKEND: Agg
          PYTHONUNBUFFERED: 1
          PYTHONDONTWRITEBYTECODE: 1

      - name: Show pytest summary (if available)
        if: always()
        shell: bash
        run: |
          set -euo pipefail
          echo "Checking for coverage.xml..."
          FOUND=0
          if [ -f coverage.xml ]; then
            echo "Found coverage.xml at repo root"; FOUND=1
          fi
          # Glob inside .tox envs (quiet if none)
          if ls .tox/*/coverage.xml >/dev/null 2>&1; then
            echo "Found coverage.xml inside .tox environment"; FOUND=1
          fi
          if [ "$FOUND" -eq 0 ]; then
            echo "No coverage.xml found (this may be fine if tests were skipped).";
            ls -al . | sed -n '1,120p'
          fi

      - name: Coverage
        uses: codecov/codecov-action@v3

  deploy:
    # this will run when you have tagged a commit, starting with "v*"
    # and requires that you have put your twine API key in your
    # github secrets (see readme for details)
    needs: [test]
    runs-on: ubuntu-latest
    if: contains(github.ref, 'tags')
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.x"
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -U setuptools setuptools_scm wheel twine build
      - name: Build and publish
        env:
          TWINE_USERNAME: __token__
          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
        run: |
          git tag
          python -m build .
          twine upload dist/*