library.yml

name: Library

on:
  push:
    branches:
      - main
  pull_request:
  release:
    types:
      - created

jobs:
  # =============================================================================

  PreCommit:
    # if: false

    runs-on: ubuntu-latest
    timeout-minutes: 60

    steps:
      - uses: actions/checkout@v2
        with:
          persist-credentials: false
          fetch-depth: 0
      - name: Set up Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - uses: actions/cache@v2
        with:
          path: ~/.cache/pre-commit
          key: pre-commit-cache

      - name: Run Pre-Commit
        run: |
          pip install pre-commit
          pre-commit run --all-files
      - name: Fix any issues
        if: failure()
        run: |
          git config --local user.email "pre-commit-bot@pymedphys.com"
          git config --local user.name "PyMedPhys Pre-Commit Bot"
          git add -A
          git stash
          git checkout $GITHUB_HEAD_REF
          git pull
          pre-commit run --all-files || true
          git commit -m "Fix pre-commit failures" -a

          echo "##[set-output name=complete;]$(echo 1)"

        id: fix_issues

      - name: Push changes
        if: failure() && steps.fix_issues.outputs.complete
        uses: ad-m/github-push-action@057a6ba835d986bfe495dd476a6c4db1d5f9503c
        with:
          github_token: ${{ secrets.PYMEDPHYS_BOT_TOKEN }}
          branch: ${{ github.event.pull_request.head.ref }}

  # =============================================================================

  Tests:
    strategy:
      fail-fast: true
      matrix:
        os: ["ubuntu", "macos", "windows"]
        task:
          [
            "tests",
            "docs",
            "stackoverflow",
            "updates",
            "cypress",
            "slow",
            "build",
            "pyright",
            "propagate",
          ]

        exclude:
          - os: "windows"
            task: "stackoverflow"
          - os: "windows"
            task: "updates"
          - os: "windows"
            task: "slow"
          - os: "windows"
            task: "pyright"
          - os: "windows"
            task: "propagate"
          - os: "windows"
            task: "cypress"

          - os: "macos"
            task: "stackoverflow"
          - os: "macos"
            task: "updates"
          - os: "macos"
            task: "cypress"
          - os: "macos"
            task: "slow"
          - os: "macos"
            task: "pyright"
          - os: "macos"
            task: "propagate"

        include:
          # Version numbers under support currently are versions 3.8, 3.9, and
          # 3.10. Instead of doing a full OS python version matrix, instead
          # just one version is chosen per OS in the hope that that offers a
          # reasonable trade off between test coverage and CI minutes utilised.
          # Windows is chosen to be the one using 3.10 since that is known to
          # work for the docs build. 3.9 and 3.8 are divied up between Ubuntu
          # and macOS arbitrarily.
          - os: "ubuntu"
            python-version: "3.9"
          - os: "windows"
            python-version: "3.10"
          - os: "macos"
            python-version: "3.8"

    runs-on: ${{ matrix.os }}-latest
    timeout-minutes: 60

    steps:
      - uses: actions/checkout@v2
        if: matrix.task != 'propagate'

      - uses: actions/checkout@v2
        if: matrix.task == 'propagate'
        with:
          persist-credentials: false
          fetch-depth: 0

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}

      - name: Get full Python version
        id: full-python-version
        shell: bash
        run: |
          echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")

      # -----------------------------------------------------------------------------

      # Set up pip

      - name: Get pip cache dir
        id: pip-cache
        run: |
          python -m pip install -U pip # to ensure version > 20 to have cache dir
          echo "::set-output name=dir::$(pip cache dir)"

      - name: Pip Cache
        uses: actions/cache@v2
        with:
          path: ${{ steps.pip-cache.outputs.dir }}
          key: pip-${{ matrix.task }}-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}

      # -----------------------------------------------------------------------------

      # Upgrade pip and setuptools, and install poetry

      - name: Upgrade pip and setuptools
        run: |
          pip install --upgrade pip setuptools

      - name: Install Poetry
        uses: snok/install-poetry@v1
        with:
          version: 1.2.1
          virtualenvs-create: true

      - name: Update PATH in Windows
        if: matrix.os == 'windows'
        run: |
          Add-Content -Path $env:GITHUB_PATH -Value "$env:USERPROFILE\.poetry\bin"
          Get-Content -Path $env:GITHUB_PATH

      - name: Configure Poetry to not use experimental installer
        run: |
          poetry config experimental.new-installer false

      # -----------------------------------------------------------------------------

      # No import and run CLI with no dependencies

      - name: Build wheel
        if: matrix.task == 'tests'
        run: |
          poetry build --format wheel

      - name: Install wheel
        if: matrix.task == 'tests' && matrix.os == 'windows'
        run: |
          python -m pip install (Get-Item .\dist\*.whl)

      - name: Install wheel
        if: matrix.task == 'tests' && matrix.os != 'windows'
        run: |
          python -m pip install ./dist/*.whl

      - name: Run clean tests
        if: matrix.task == 'tests'
        run: |
          pymedphys --help
          python -c "import pymedphys"
          python -c "import pymedphys.beta"
          python -c "import pymedphys.experimental"

      # Remove confusion for tests down the line
      - name: Remove base install of pymedphys
        if: matrix.task == 'tests'
        run: |
          pip uninstall -y pymedphys

      # -----------------------------------------------------------------------------

      # Set up Poetry

      - name: Configure poetry
        run: |
          poetry config virtualenvs.in-project true

      - name: Poetry Cache
        uses: actions/cache@v2
        id: poetry-cache
        with:
          path: .venv
          key: venv-${{ matrix.task }}-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}

      # This is from <https://github.com/python-poetry/poetry/blob/639d5e057/.github/workflows/main.yml#L57-L60>
      - name: Ensure cache is healthy
        if: steps.poetry-cache.outputs.cache-hit == 'true'
        shell: bash
        run: |
          timeout 10s poetry run pip --version || rm -rf .venv

      # Install Node

      - uses: actions/setup-node@v3
        if: matrix.task == 'cypress' || matrix.task == 'pyright' || matrix.task == 'build'
        with:
          node-version: "14"
          # cache: "yarn"  # TODO: Sort out this cache parameter

      # -----------------------------------------------------------------------------

      # System installs

      - name: Install Pandoc on Ubuntu
        if: ( matrix.task == 'docs' || matrix.task == 'updates' ) && matrix.os == 'ubuntu'
        run: |
          sudo apt-get install -y pandoc

      - name: Install Pandoc on MacOS
        if: matrix.task == 'docs' && matrix.os == 'macos'
        run: |
          brew install pandoc

      - name: Install Pandoc on Windows
        if: matrix.task == 'docs' && matrix.os == 'windows'
        run: |
          choco install pandoc

      ## Plain install

      - name: Install a plain environment
        if: matrix.task == 'stackoverflow'
        run: |
          poetry install -E user

      ## Install with Documentation Environment

      - name: Install a docs environment
        if: matrix.task == 'docs'
        run: |
          poetry install -E docs

      ## Install with Tests Environment
      # TODO: Redesign CI to be more efficient once this issue lands python-poetry/poetry#4842

      - name: Install a tests/doctests environment
        if: matrix.task == 'tests' || matrix.task == 'cypress' || matrix.task == 'slow' || matrix.task == 'pyright'
        run: |
          poetry install -E user -E tests -E doctests

      ## Install remaining packages for pyright

      - name: Install a propagate environment
        if: matrix.task == 'pyright' || matrix.task == 'propagate'
        run: |
          poetry install -E propagate || poetry lock --no-update && poetry install -E propagate

      ## Install with Binary Build Environment

      - name: Install a binary build environment
        if: matrix.task == 'build'
        run: |
          poetry install -E build -E cli

      ## Update all packages and then install with tests environment

      - name: Update all packages then install with tests and user environment
        if: matrix.task == 'updates'
        run: |
          poetry install -E user -E tests -E docs
          poetry update
          poetry install -E user -E tests -E docs

      # -----------------------------------------------------------------------------

      # PyMedPhys Data Cache

      - name: Get PyMedPhys cache directory
        id: pymedphys-cache-location
        if: matrix.task != 'build' && matrix.task != 'pyright'
        run: |
          echo "::set-output name=dir::$(poetry run python -c 'import pymedphys._config as cf; print(str(cf.get_config_dir()))')"

      - name: PyMedPhys Cache
        id: pymedphys-cache
        if: matrix.task != 'build' && matrix.task != 'pyright'
        uses: actions/cache@v2
        with:
          path: ${{ steps.pymedphys-cache-location.outputs.dir }}
          key: pymedphys-${{ matrix.task }}-${{ runner.os }}-${{ hashFiles('**/hashes.json') }}

      # -----------------------------------------------------------------------------

      # Binary building

      - name: Build Binary
        if: matrix.task == 'build'
        run: |
          poetry run pymedphys dev build --install

      - uses: actions/upload-artifact@v3
        if: matrix.task == 'build'
        with:
          name: PyMedPhysApp-${{ runner.os }}
          path: |
            js/app/dist/*.dmg
            js/app/dist/*.exe
            js/app/dist/*.snap
            js/app/dist/*.AppImage
            !js/app/dist/*unpacked/

      # TODO:
      # - name: Test Binary
      #   if: matrix.task == 'build'
      #   run: |

      # -----------------------------------------------------------------------------

      # TESTS

      ## Propagate
      - name: See if propagate is needed
        if: matrix.task == 'propagate'
        id: propagate-test
        run: |
          echo "::set-output name=status::before"
          poetry run pymedphys dev propagate

          git config --local user.email "propagate-bot@pymedphys.com"
          git config --local user.name "PyMedPhys Propagate Bot"

          git add poetry.lock
          git commit -m "commit changes to poetry.lock" || true

          git status
          git diff-index --quiet HEAD --

      ## Pyright

      - name: Install and run pyright
        if: matrix.task == 'pyright'
        run: |
          npm install -g pyright
          poetry run pyright

      ## Pytest

      - name: Run basic pytest tests
        if: matrix.task == 'tests' || matrix.task == 'updates'
        run: |
          poetry run pymedphys dev tests -v

      ## Doctest

      - name: Run doctest tests
        if: matrix.os == 'ubuntu' && matrix.task == 'tests'
        run: |
          poetry run pymedphys dev doctests -v

      ## Pylint

      - name: Run pylint tests
        if: matrix.os == 'ubuntu' && ( matrix.task == 'tests' || matrix.task == 'updates' )
        run: |
          poetry run pymedphys dev lint

      ## Slow

      - name: Run slow tests
        if: matrix.task == 'slow'
        run: |
          poetry run pymedphys dev tests -v --slow

      ## Docs

      - name: Download docs files
        if: matrix.task == 'docs' && matrix.os == 'ubuntu'
        run: |
          poetry run python -c "import pymedphys; pymedphys.data_path('original_dose_beam_4.dcm'); pymedphys.data_path('logfile_dose_beam_4.dcm');"

      - name: Build docs
        if: matrix.task == 'docs' || matrix.task == 'updates'
        run: |
          poetry run pymedphys dev docs

      - name: Add GitHub Pages Config Files
        if: matrix.task == 'docs' && matrix.os == 'ubuntu' && github.event_name == 'push'
        run: |
          echo docs.pymedphys.com > lib/pymedphys/docs/_build/html/CNAME
          touch lib/pymedphys/docs/_build/html/.nojekyll

      - name: Deploy docs
        if: matrix.task == 'docs' && matrix.os == 'ubuntu' && github.event_name == 'push'
        uses: JamesIves/github-pages-deploy-action@4.1.3
        with:
          branch: docs
          folder: lib/pymedphys/docs/_build/html
          ssh-key: ${{ secrets.DEPLOY_KEY }}

      ## Stackoverflow

      - name: Run stackoverflow example(s)
        if: matrix.task == 'stackoverflow'
        run: |
          poetry run python ./examples/stackoverflow/gamma.py

      ## Cypress
      - name: Run Cypress tests
        if: matrix.task == 'cypress'
        run: |
          poetry run pymedphys dev tests --cypress

      - uses: actions/upload-artifact@v2
        if: failure() && matrix.task == 'cypress'
        with:
          name: cypress-videos
          path: pymedphys/tests/e2e/cypress/videos

  # --------------------------------------------------------------------------- #
  #                                  DEPLOYMENT                                 #
  # --------------------------------------------------------------------------- #

  ValidateVersionReleaseMatch:
    if: false # Skip for now
    # if: github.event_name == 'release' && github.event.action == 'created'
    runs-on: ubuntu-latest
    timeout-minutes: 60

    steps:
      - name: Get the tag version number
        # https://github.community/t/how-to-get-just-the-tag-name/16241/7
        id: tag_version
        run: echo ::set-output name=VERSION::${GITHUB_REF/refs\/tags\/v/}

      - uses: actions/checkout@v2
      - name: Set up Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8
      - name: Install base PyMedPhys
        run: |
          pip install .
      - name: Verify that version matches
        run: |
          python -c "import pymedphys; assert pymedphys.__version__ == '${{ steps.tag_version.outputs.VERSION }}'"

  PyPI:
    if: false # Skip for now
    needs:
      - ValidateVersionReleaseMatch
      # - PreCommit
      # - Tests
    runs-on: ubuntu-latest
    timeout-minutes: 60

    steps:
      - uses: actions/checkout@v2
      - name: Set up Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8
      - name: Install Poetry
        uses: snok/install-poetry@v1.1.1
      - name: Build and publish
        run: |
          poetry build

          # poetry config repositories.test-pypi https://test.pypi.org/legacy/
          # poetry config pypi-token.test-pypi ${{ secrets.TEST_PYPI_API_TOKEN }}
          # poetry publish -r test-pypi

          poetry config pypi-token.pypi ${{ secrets.PYPI_API_TOKEN }}
          poetry publish

  OfflineInstallBundles:
    if: false # Skip for now
    # needs:
    # - PyPI
    # - ValidateVersionReleaseMatch
    runs-on: ${{ matrix.os }}-latest
    strategy:
      fail-fast: true
      matrix:
        os: ["ubuntu", "macos", "windows"]
        python-version: [3.8, 3.9, 3.10]
    steps:
      - uses: actions/checkout@v2
      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}

      # - name: Get pip cache dir
      #   id: pip-cache
      #   run: |
      #     python -m pip install -U pip # to ensure version > 20 to have cache dir
      #     echo "::set-output name=dir::$(pip cache dir)"
      # - name: Pip Cache
      #   uses: actions/cache@v2
      #   with:
      #     path: ${{ steps.pip-cache.outputs.dir }}
      #     key: pip-offline-install-bundles-${{ runner.os }}-${{ matrix.python-version }}-${{ steps.full-python-version.outputs.version }}

      - name: Download Source Files and Build PyMedPhys Wheel
        run: |
          pip install wheel
          pip wheel . -w offline --no-deps
          pip download -r requirements-dev.txt -d offline
      - name: Get Wheel Types
        id: wheel_label
        run: |
          python -c "import pathlib; path = str(next(pathlib.Path('offline').glob('pyarrow*.whl'))); print(f\"::set-output name=NAMING::{'-'.join(path.split('-')[2::])[:-4]}\")"
        shell: bash
      - uses: actions/upload-artifact@v2
        with:
          name: offline-install-bundle-${{ steps.wheel_label.outputs.NAMING }}
          path: offline/*

  UpdateRelease:
    if: false # Skip for now
    needs:
      # - Tests
      - OfflineInstallBundles
      # - ValidateVersionReleaseMatch
    runs-on: ubuntu-latest
    timeout-minutes: 60

    steps:
      - name: Hello World
        run: |
          echo Hello World