publish.yaml

# Based on https://github.com/prettier/prettier/blob/master/.github/workflows/dev-test.yml
name: Publish to PyPi

on:
  workflow_dispatch:
    inputs:
      randomlyseed:
        description: 'Pytest Randomly Seed'
        required: false
        default: ''
      dry_run:
        description: 'Do a dry run and do not publish'
        required: false
        default: '0'
  push:
    branches:
      - main

jobs:
  test:
    strategy:
      fail-fast: false
      matrix:
        os:
          - "ubuntu-18.04"
          - "ubuntu-20.04"
          - "windows-2019"
          - "macos-10.15"
          # - "macos-11.0"
        python-version:
            - 3.7
            - 3.8
            - 3.9
        include:
          # only enable coverage on the fastest job
          - os: "ubuntu-20.04"
            python-version: "3.9"
            IS_FASTEST_JOB: true

    name: Test code before publishing in Python ${{ matrix.python-version }} on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    steps:
      - name: Checkout
        uses: actions/checkout@v2
        with:
          fetch-depth: 1

      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - name: Display Python version
        run: |
          python -c "import sys; print(sys.version)"
          python -m venv venv

      - name: Extract version number # Adapted from: https://stackoverflow.com/questions/58033366/how-to-get-current-branch-within-github-actions
        shell: bash
        run: echo '##[set-output name=package-version;]$(echo $(python .github/workflows/extract_package_info.py package_version))'
        id: extract_version

      - name: Display extracted version number
        shell: bash
        run: |
          echo "Version: ${{ steps.extract_version.outputs.package-version }}"

      - name: Confirming tag not already present on remote (if publishing)
        if: github.event.inputs.dry_run != '1' && matrix.IS_FASTEST_JOB == true
        run: if [$(git ls-remote --tags origin | grep v${{ steps.extract_version.outputs.package-version }}) = '']; then echo Tag does not exist on remote; else echo Tag already exists on remote && exit 1; fi

      - name: Cache Pre-commit hooks
        uses: actions/cache@v2.1.4
        env:
          cache-name: cache-pre-commit-hooks
        if: matrix.IS_FASTEST_JOB == true
        with:
          path: ./.precommit_cache
          key: ${{ matrix.os }}-${{ matrix.python-version }}-build-${{ env.cache-name }}-${{ hashFiles('**/.pre-commit-config.yaml') }}
          restore-keys: |
            ${{ matrix.os }}-${{ matrix.python-version }}-build-${{ env.cache-name }}-

      - name: Extract branch name # Adapted from: https://stackoverflow.com/questions/58033366/how-to-get-current-branch-within-github-actions
        if: runner.os == 'Linux'
        shell: bash
        run: |
          git branch -av
          echo '##[set-output name=sha-of-main-branch;]$(echo $(git branch -av | grep remotes/origin/main | grep -oP "main\s+\K\w+"))'
          echo '##[set-output name=sha-of-development-branch;]$(echo $(git branch -av | grep remotes/origin/development | grep -oP "development\s+\K\w+"))'
          echo '##[set-output name=sha-of-current-branch;]$(echo $(git branch -av | grep "*" | grep -oP " \s+\K\w+"))'
        id: extract_branch

      - name: Display extracted branch information
        if: runner.os == 'Linux'
        run: |
          echo "SHA of current branch: ${{ steps.extract_branch.outputs.sha-of-current-branch }}"
          echo "SHA of main branch: ${{ steps.extract_branch.outputs.sha-of-main-branch }}"
          echo "SHA of development branch: ${{ steps.extract_branch.outputs.sha-of-development-branch }}"

      - name: Is this running on development branch?
        if: runner.os == 'Linux'
        run: if [ "${{ steps.extract_branch.outputs.sha-of-current-branch}}" = "${{ steps.extract_branch.outputs.sha-of-development-branch}}" ] ; then echo "Running on development branch."; else echo "Not running on development branch."; fi

      - name: Is this running on main branch?
        if: runner.os == 'Linux'
        run: if [ "${{ steps.extract_branch.outputs.sha-of-current-branch}}" = "${{ steps.extract_branch.outputs.sha-of-main-branch}}" ] ; then echo "Running on main branch."; else echo "Not running on main branch."; fi

      - name: Fail if attempting to publish from a branch other than main
        if: runner.os == 'Linux' && github.event.inputs.dry_run != '1'
        run: if [ "${{ steps.extract_branch.outputs.sha-of-current-branch}}" = "${{ steps.extract_branch.outputs.sha-of-main-branch}}" ] ; then echo "Running on main branch, can proceed to publish."; else exit 1; fi

      - name: Activate virtual environment (Linux/MacOS)
        if: runner.os == 'Linux' || runner.os == 'macOS'
        run: . venv/bin/activate

      - name: Activate virtual environment (Windows)
        if: runner.os == 'Windows'
        run: venv\Scripts\Activate.ps1

      - name: Display Pip Version and confirm environment empty
        run: |
          pip -V
          pip freeze
      - name: Install Dev Dependencies
        run: |
          pip install -r requirements-dev.txt
          pip install -r docs/requirements.txt

      - name: Install Main Package
        run: pip install -e .
      - name: Log full installed packages
        run: pip freeze

      - name: Run pre-commit hooks
        if: matrix.IS_FASTEST_JOB == true
        run: |
          pre-commit install
          pre-commit run -a

      - name: Run Tests with randomly generated seed
        if: github.event.inputs.randomlyseed == ''
        run: pytest -xsvv --cov-report=xml --full-ci --include-slow-tests -n auto

      - name: Run Tests with supplied pytest-randomly seed
        if: github.event.inputs.randomlyseed != ''
        run: pytest -xsvv --cov-report=xml --full-ci --include-slow-tests -n auto --randomly-seed=${{ github.event.inputs.randomlyseed }}

      - name: Confirm Sphinx Docs build correctly
        # only check Sphinx docs build on the fastest job
        if: matrix.IS_FASTEST_JOB == true
        run: SPHINXOPTS="-W" make --directory=docs html # the -W flag treats warnings as errors to cause build failures

      - name: Run prerelease to check packaging compatibilty
        run: prerelease --no-input

      - name: Build wheel for release
        run: python setup.py bdist_wheel

      # IMPORTANT! If a platform-specific wheel is generated, sometimes they may need to be renamed or there can be unexplained (Eli 2/25/21) issues getting the to install. See example: https://github.com/CuriBio/mantarray-waveform-analysis/blob/b4ef677f20c16e14156f941c6581b50802773010/.github/workflows/publish.yaml#L158

      - name: Build sdist for release (Linux)
        if: matrix.IS_FASTEST_JOB == true
        run: python setup.py sdist

      - name: Confirm no modifications to the repository files occurred when running the test suite
        if: matrix.IS_FASTEST_JOB == true # only enable pre-commit on the fastest job
        env:
          PRE_COMMIT_HOME: ./.precommit_cache
        run: pre-commit run git-dirty -a

      - name: Upload build artifact
        uses: actions/upload-artifact@v2
        with:
          name: dist--${{ matrix.os }}--${{ matrix.python-version }}
          path: dist/*


  publish_to_test_pypi:
    needs: [test]
    strategy:
      fail-fast: false
      matrix: # if publishing pure python code, then disable all except one os and python version combination. But if publishing code that uses Cython then likely all combinations will be needed
        os:
          - "ubuntu-20.04"
          - "windows-2019"
          - "macos-10.15"
          # - "macos-11.0"
        python-version:
            - 3.7
            - 3.8
            - 3.9
    name: Publish to Test PyPI for Python ${{ matrix.python-version }} on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    steps:
      - name: Checkout
        uses: actions/checkout@v2
        with:
          fetch-depth: 1

      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - name: Display Python version
        run: |
          python -c "import sys; print(sys.version)"
          python -m venv venv

      - name: Activate virtual environment (Linux/MacOS)
        if: runner.os == 'Linux' || runner.os == 'macOS'
        run: . venv/bin/activate

      - name: Activate virtual environment (Windows)
        if: runner.os == 'Windows'
        run: venv\Scripts\Activate.ps1

      - name: Display Pip Version and confirm environment empty
        run: |
          pip -V
          pip freeze
      - name: Install Dev Dependencies
        run: pip install -r requirements-dev.txt

      - name: Log full installed packages
        run: pip freeze

      - name: Download built dist folder from previous step
        uses: actions/download-artifact@v2
        with:
          name: dist--${{ matrix.os }}--${{ matrix.python-version }}
          path: dist

      - name: Uploading to Test PyPI
        if: github.event.inputs.dry_run != '1'
        env:
          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}

        run: twine upload --repository testpypi dist/*

      - name: Sleep for 360 seconds to allow Test PyPI Index to update before proceeding to the next step
        if: github.event.inputs.dry_run != '1'
        uses: juliangruber/sleep-action@v1
        with:
          time: 360s

  install_from_test_pypi:
    needs: [publish_to_test_pypi]
    strategy:
      fail-fast: false
      matrix:
        os:
          - "ubuntu-18.04"
          - "ubuntu-20.04"
          - "windows-2019"
          - "macos-10.15"
          # - "macos-11.0"
        python-version:
            - 3.7
            - 3.8
            - 3.9
    name: Install from Test PyPI and run tests on Python ${{ matrix.python-version }} on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    steps:
      - name: Checkout
        uses: actions/checkout@v2
        with:
          fetch-depth: 1

      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - name: Display Python version
        run: |
          python -c "import sys; print(sys.version)"
          python -m venv venv

      - name: Activate virtual environment (Linux/MacOS)
        if: runner.os == 'Linux' || runner.os == 'macOS'
        run: . venv/bin/activate

      - name: Activate virtual environment (Windows)
        if: runner.os == 'Windows'
        run: venv\Scripts\Activate.ps1

      - name: Display Pip Version and confirm environment empty
        run: |
          pip -V
          pip freeze

      - name: Download built dist folder from previous step
        uses: actions/download-artifact@v2
        with:
          name: dist--${{ matrix.os }}--${{ matrix.python-version }}
          path: dist

      - name: Extract package info # Adapted from: https://stackoverflow.com/questions/58033366/how-to-get-current-branch-within-github-actions
        shell: bash
        run: |
          echo '##[set-output name=package-name;]$(echo $(python .github/workflows/extract_package_info.py package_name))'
          echo '##[set-output name=package-version;]$(echo $(python .github/workflows/extract_package_info.py package_version))'
        id: extract_package_info

      - name: Install Main Package From Test PyPI
        if: github.event.inputs.dry_run != '1'
        run: python .github/workflows/extract_package_info.py install_from_test_pypi

      - name: Install Main Package From built wheel file as test since not publishing to PyPI
        if: github.event.inputs.dry_run == '1'
        run: python .github/workflows/extract_package_info.py install_from_dist

      - name: Confirm no import errors when opening package
        run: python -c "import ${{ steps.extract_package_info.outputs.package-name }}"

      - name: Install Dev Dependencies
        run: pip install -r requirements-dev.txt

      - name: Log full installed packages
        run: pip freeze

      - name: Run Tests with randomly generated seed
        if: github.event.inputs.randomlyseed == ''
        run: pytest -xsvv --full-ci --include-slow-tests -n auto

      - name: Run Tests with supplied pytest-randomly seed
        if: github.event.inputs.randomlyseed != ''
        run: pytest -xsvv --full-ci --include-slow-tests -n auto --randomly-seed=${{ github.event.inputs.randomlyseed }}

  publish_to_pypi:
    needs: [install_from_test_pypi]
    strategy:
      fail-fast: false
      matrix: # if publishing pure python code, then disable all except one os and python version combination. But if publishing code that uses Cython then likely all combinations will be needed
        os:
          - "ubuntu-20.04"
          - "windows-2019"
          - "macos-10.15"
          # - "macos-11.0"
        python-version:
            - 3.7
            - 3.8
            - 3.9
    name: Publish to PyPI for Python ${{ matrix.python-version }} on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    steps:
      - name: Checkout
        uses: actions/checkout@v2
        with:
          fetch-depth: 1

      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - name: Display Python version
        run: |
          python -c "import sys; print(sys.version)"
          python -m venv venv

      - name: Activate virtual environment (Linux/MacOS)
        if: runner.os == 'Linux' || runner.os == 'macOS'
        run: . venv/bin/activate

      - name: Activate virtual environment (Windows)
        if: runner.os == 'Windows'
        run: venv\Scripts\Activate.ps1

      - name: Display Pip Version and confirm environment empty
        run: |
          pip -V
          pip freeze
      - name: Install Dev Dependencies
        run: pip install -r requirements-dev.txt

      - name: Log full installed packages
        run: pip freeze

      - name: Download built dist folder from previous step
        uses: actions/download-artifact@v2
        with:
          name: dist--${{ matrix.os }}--${{ matrix.python-version }}
          path: dist

      - name: Uploading to PyPi
        if: github.event.inputs.dry_run != '1'
        env:
          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}

        run: twine upload dist/*

      - name: Sleep for 360 seconds to allow PyPI Index to update before proceeding to the next step
        if: github.event.inputs.dry_run != '1'
        uses: juliangruber/sleep-action@v1
        with:
          time: 360s


  install_from_pypi:
    needs: [publish_to_pypi]
    strategy:
      fail-fast: false
      matrix:
        os:
          - "ubuntu-18.04"
          - "ubuntu-20.04"
          - "windows-2019"
          - "macos-10.15"
          # - "macos-11.0"
        python-version:
            - 3.7
            - 3.8
            - 3.9
    name: Test installation from PyPI for Python ${{ matrix.python-version }} on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    steps:
      - name: Checkout
        uses: actions/checkout@v2
        with:
          fetch-depth: 1

      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - name: Display Python version
        run: |
          python -c "import sys; print(sys.version)"
          python -m venv venv

      - name: Activate virtual environment (Linux/MacOS)
        if: runner.os == 'Linux' || runner.os == 'macOS'
        run: . venv/bin/activate

      - name: Activate virtual environment (Windows)
        if: runner.os == 'Windows'
        run: venv\Scripts\Activate.ps1

      - name: Display Pip Version and confirm environment empty
        run: |
          pip -V
          pip freeze

      - name: Download built dist folder from previous step
        uses: actions/download-artifact@v2
        with:
          name: dist--${{ matrix.os }}--${{ matrix.python-version }}
          path: dist

      - name: Extract package info # Adapted from: https://stackoverflow.com/questions/58033366/how-to-get-current-branch-within-github-actions
        shell: bash
        run: |
          echo '##[set-output name=package-name;]$(echo $(python .github/workflows/extract_package_info.py package_name))'
          echo '##[set-output name=package-version;]$(echo $(python .github/workflows/extract_package_info.py package_version))'
        id: extract_package_info

      - name: Install Main Package From PyPI
        if: github.event.inputs.dry_run != '1'
        run: python .github/workflows/extract_package_info.py install_from_pypi

      - name: Install Main Package From built wheel file as test since not publishing to PyPI
        if: github.event.inputs.dry_run == '1'
        run: python .github/workflows/extract_package_info.py install_from_dist

      - name: Confirm no import errors when opening package
        run: python -c "import ${{ steps.extract_package_info.outputs.package-name }}"

      - name: Install Dev Dependencies
        run: pip install -r requirements-dev.txt

      - name: Log full installed packages
        run: pip freeze

      - name: Run Tests with randomly generated seed
        if: github.event.inputs.randomlyseed == ''
        run: pytest -xsvv --full-ci --include-slow-tests -n auto

      - name: Run Tests with supplied pytest-randomly seed
        if: github.event.inputs.randomlyseed != ''
        run: pytest -xsvv --full-ci --include-slow-tests -n auto --randomly-seed=${{ github.event.inputs.randomlyseed }}

  create_tag:
    needs: [install_from_pypi]
    strategy:
      fail-fast: false
      matrix:
        os:
          - "ubuntu-20.04"
    name: Creating tag on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    steps:
      - name: Checkout
        uses: actions/checkout@v2
        with:
          fetch-depth: 1

      - name: Extract version number # Adapted from: https://stackoverflow.com/questions/58033366/how-to-get-current-branch-within-github-actions
        shell: bash
        run: echo '##[set-output name=package-version;]$(echo $(grep -Po "(?<=    version=\")[0-9.]+" setup.py))'
        id: extract_version

      - name: Tagging commit
        run: |
          echo "About to tag with: v${{ steps.extract_version.outputs.package-version }}"
          git tag "v${{ steps.extract_version.outputs.package-version }}"

      - name: Listing all local tags (including new tag)
        run: git tag -l

      - name: Pushing Tag
        if: github.event.inputs.dry_run != '1'
        run: git push --tags