ci-cd.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: CI/CD

on:
  push:
    branches: [ main, develop ]
    tags: [ '*' ]
  pull_request:
    branches: [ main, develop ]
  release:
    types: [published]
  workflow_dispatch:  # Allow manual triggering by a user with write access to this repo

defaults:
  run:
    shell: bash

env:
  PYPI_URL: https://pypi.org/simple
  
jobs:

  build-docs:
    runs-on: ubuntu-20.04
    steps:
      - name: Checkout repository
        uses: actions/checkout@v2
        with:
          submodules: recursive  # Fetch Hugo themes (true OR recursive)
          fetch-depth: 1    # Fetch all history for .GitInfo and .Lastmod
      # TODO: Need a unique key we can pass, but as we're targeting
      #
      # - name: Cache dependencies
      #   uses: actions/cache@v1
      #   with:
      #     path: ~/.local/lib
      #     key: ${{ runner.os }}-python-${{ hashFiles('**/package-lock.json') }}
      #     restore-keys: |
      #       ${{ runner.os }}-python-
      - name: Setup Python
        uses: actions/setup-python@v2
        with:
          python-version: '3.11' # Version range or exact version of a Python version to use, using SemVer'
      - name: Install python dependencies
        run: pip install -r ./requirements.txt
      - name: Generate pipeline docs
        run: pydra2app make-docs specs/australian-imaging-service-community docs/pipelines --flatten --default-data-space common:Clinical
      - uses: actions/upload-artifact@v3
        with:
          name: built-docs
          path: docs/build/html

  python:
    needs: ["build-docs"]
    strategy:
      matrix:
        subpackage:
        - au.edu.sydney.sydneyimaging
      fail-fast: false
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}
    steps:
    - name: Checkout
      uses: actions/checkout@v2
    - name: Unset header
      # checkout@v2 adds a header that makes branch protection report errors
      # because the Github action bot is not a collaborator on the repo
      run: git config --local --unset http.https://github.com/.extraheader
    - name: Fetch tags
      run: git fetch --prune --unshallow
    - name: Disable etelemetry
      run:  echo "NO_ET=TRUE" >> $GITHUB_ENV
    - name: Set up Python
      uses: actions/setup-python@v2
      with:
        python-version: "3.12"
    - name: Update build tools
      run: python3 -m pip install --upgrade pip
    - name: Install Package
      run: python3 -m pip install -e ./src/${{ matrix.subpackage }}[test]
    - name: Pytest
      run: >
        pytest -vvs --cov australianimagingservice.community.${{ matrix.subpackage }}
        --cov-config .coveragerc --cov-report xml ./src/${{ matrix.subpackage }}
    - name: Install build tools
      run: python3 -m pip install build twine
    - name: Build source and wheel distributions
      run: python3 -m build ./src/${{ matrix.subpackage }}
    - name: Check distributions
      run: twine check ./src/${{ matrix.subpackage }}/dist/*
    - name: Extract package name and versions
      run: |
        PKG=$(ls ./src/${{ matrix.subpackage }}/dist | grep -e '.tar.gz')
        PKG=${PKG%.tar.gz}
        echo "PKG_NAME=${PKG%%-*}" >> $GITHUB_ENV
        echo "PKG_VERSION=${PKG##*-}" >> $GITHUB_ENV
        echo "PYPI_VERSION=$(curl -s "${PYPI_URL}/${PKG_NAME}/" | grep -oP "${PKG_NAME}-\K[0-9]+\.[0-9]+\.[0-9]+(?=\.tar\.gz)" | sort -V | tail -n 1)" >> $GITHUB_ENV
    - name: Check for PyPI token on tag
      id: deployable
      if: github.event_name == 'release'
      env:
        PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
      run: if [ -n "$PYPI_API_TOKEN" ] && [ "$PKG_VERSION" != "$PYPI_VERSION" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
    - name: Upload to PyPI
      if: steps.deployable.outputs.DEPLOY
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        user: __token__
        password: ${{ secrets.PYPI_API_TOKEN }}
    - name: Wait for package to mirror
      if: steps.deployable.outputs.DEPLOY
      run: |
        MAX_ATTEMPTS=60  # Adjust the maximum number of attempts as needed
        SLEEP_INTERVAL=5  # Adjust the sleep interval (in seconds) as needed
        for ((attempt = 1; attempt <= MAX_ATTEMPTS; attempt++)); do
          LATEST_VERSION=$(curl -s "${PYPI_URL}/${PKG_NAME}/" | grep -oP "${PKG_NAME}-\K[0-9]+\.[0-9]+\.[0-9]+(?=\.tar\.gz)" | sort -V | tail -n 1)
          if [ "$PKG_VERSION" == "$LATEST_VERSION" ]; then
            echo "Updated package version ${PKG_VERSION} is now available on PyPI. Exiting..."
            exit 0
          else
            echo "Package version ${PKG_VERSION} not yet available on PyPI (latest found = $LATEST_VERSION). Waiting..."
            sleep $SLEEP_INTERVAL
          fi
        done
        echo "Timeout reached. Exiting..."
        exit 1
            
  pipelines:
    needs: [python]
    runs-on: ubuntu-latest
    steps:
    - name: Remove unnecessary tools to free space
      run: |
        sudo rm -rf /usr/share/dotnet
        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
    - name: Checkout
      uses: actions/checkout@v2
    - name: Get release tag
      run: |
        git fetch --prune --unshallow
        echo "VERSION=`echo $(git describe --tags --abbrev=0)`" >> $GITHUB_ENV
    - name: Unset header
      # checkout@v2 adds a header that makes branch protection report errors
      # because the Github action bot is not a collaborator on the repo
      run: git config --local --unset http.https://github.com/.extraheader
    - name: Set up Python
      uses: actions/setup-python@v2
      with:
        python-version: '3.11'
    - name: Update build tools
      run: python -m pip install --upgrade pip
    - name: Install dependencies
      run: pip install -r requirements.txt
    - uses: docker/login-action@v2
      with:
        registry: ghcr.io
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }} # - must be in GitHub Secrets!
    - name: Check for tagged release
      if: github.event_name == 'release'
      run: echo "RELEASE=1" >> $GITHUB_ENV
    - name: Build and push container images
      run: |
        if [ -z "$RELEASE" ]; then
          OPTIONS=--push
        else
          OPTIONS=--use-local-packages
          for pkg in ./src/*; do 
            pip install -e ./src/$pkg
          done
        fi
        pydra2app make xnat specs/australian-imaging-service-community \
        --registry ghcr.io --check-registry --clean-up --tag-latest --loglevel info \
        --release pipelines-community-metapackage $VERSION $OPTIONS

  deploy-docs:
    needs: [build-docs, pipelines]
    runs-on: ubuntu-latest
    steps:
    - name: Download built docs
      uses: actions/download-artifact@v3
      with:
        name: built-docs
        path: docs/build/html
    - name: Remove /docs/pipelines/ from .gitignore
      run: sed -i 's%^/docs/pipelines/\*$%%' .gitignore            
    - name: Check for GHPAGES_DEPLOY_KEY token on tag
      id: deployable
      if: github.event_name == 'release'
      env:
        GHPAGES_DEPLOY_KEY: "${{ secrets.GHPAGES_DEPLOY_KEY }}"
      run: if [ -n "$GHPAGES_DEPLOY_KEY" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
    - name: Deploy docs
      uses: peaceiris/actions-gh-pages@v3
      if: steps.deployable.outputs.DEPLOY
      with:
        github_token: ${{ secrets.GITHUB_TOKEN }}
        publish_dir: .
        publish_branch: docs
        enable_jekyll: true  # This branch isn't actually fed to GH pages
    # It's possible, likely even, that we'll trigger unnecessary docs
    # rebuilds with this. Running this properly as a separate workflow
    # only when real docs changes occur would require using a PAT.
    - name: Trigger rebuild of docs
      uses: peter-evans/repository-dispatch@v1
      if: steps.deployable.outputs.DEPLOY
      with:
        token: ${{ secrets.GITHUBPAGES_KEY }}
        repository: Australian-Imaging-Service/Australian-Imaging-Service.github.io
        event-type: Rebuild docs