python-package-conda.yml

name: Conda

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main
  release:
  workflow_dispatch:
    inputs:
      reason:
        description: Reason for the workflow dispatch.
        required: true

jobs:
  build:
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -l {0}
    strategy:
      matrix:
        os: ["ubuntu-latest", "windows-latest"]
      max-parallel: 5
    env:
      FAKE_HISEQ: 1

    steps:
      - uses: actions/checkout@v2

      - name: Cache conda
        uses: actions/cache@v2
        env:
          # Increase this value to reset cache if etc/example-environment.yml has not changed
          CACHE_NUMBER: 0
        with:
          path: ~/conda_pkgs_dir
          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/ci_env.yml') }}-${{ hashFiles('conda-lock.yml') }}

      - uses: conda-incubator/setup-miniconda@v2
        with:
          miniforge-version: latest
          environment-file: .github/ci_env.yml
          activate-environment: pyseq
          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!

      - name: Update env with conda
        run: |
          conda-lock install -n pyseq conda-lock.yml
          conda env update -f environment-web.yml

      - name: Install with pip
        run: |
          pip install .

      # - name: Type check with Pyright
      #   run: |
      #     npm i -g pyright
      #     pyright pyseq2

      - name: Test with Pytest
        run: |
          pytest -rP
      #       - name: Debug with tmate
      #         uses: mxschmitt/action-tmate@v3

      - name: Build docs
        if: ${{ matrix.os == 'ubuntu-latest'}}
        run: |
          conda install mkdocs mkdocs-material
          pip install mkdocstrings[python] mkdocs-git-revision-date-localized-plugin
          mkdocs build

      - name: Deploy docs
        uses: peaceiris/actions-gh-pages@v3
        if: ${{ github.ref == 'refs/heads/main' && matrix.os == 'ubuntu-latest'}}
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          publish_dir: ./site

  # tox:
  #   runs-on: ${{ matrix.os }}
  #   defaults:
  #     run:
  #       shell: bash -l {0}
  #   strategy:
  #     matrix:
  #       os: ["ubuntu-latest", "windows-latest"]
  #     max-parallel: 5
  #   env:
  #     FAKE_HISEQ: 1

  #   steps:
  #     - uses: actions/checkout@v2

  #     - name: Cache conda
  #       uses: actions/cache@v2
  #       env:
  #         # Increase this value to reset cache if etc/example-environment.yml has not changed
  #         CACHE_NUMBER: 0
  #       with:
  #         path: ~/conda_pkgs_dir
  #         key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
  #           hashFiles('.github/ci_env.yml') }}

  #     - uses: conda-incubator/setup-miniconda@v2
  #       with:
  #         miniforge-version: latest
  #         environment-file: .github/ci_env.yml
  #         activate-environment: pyseq
  #         use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!

  #     - name: Test with Tox
  #       run: |
  #         tox -vv