ci-cd.yml

name: CI/CD

on:
  push:
    branches: [ main, develop ]
  pull_request:
    branches: [ main, develop ]
  release:
    types: [published]

defaults:
  run:
    shell: bash

jobs:
  test:
    strategy:
      matrix:
        os: [ubuntu-latest]
        python-version: ["3.8", "3.12"]
      fail-fast: false
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -l {0}
    env:
      PIP_BREAK_SYSTEM_PACKAGES: 1
    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: Install Dcm2niix
      run: |
        curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_lnx.zip
        unzip dcm2niix_lnx.zip
        mv dcm2niix /usr/local/bin
    - name: Install Minconda
      uses: conda-incubator/setup-miniconda@v2
      with:
        auto-activate-base: true
        activate-environment: ""
    - name: Install MRtrix via Conda
      run: |
        conda install -c mrtrix3 mrtrix3
        mrconvert --version
    - name: Disable etelemetry
      run:  echo "NO_ET=TRUE" >> $GITHUB_ENV
    - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Update build tools
      run: python3 -m pip install --upgrade pip
    - name: Install Package
      run: python3 -m pip install .[test] ./extras[test]
    - name: MyPy
      run: mypy --install-types --non-interactive  --no-warn-unused-ignores .
    - name: Pytest
      run: |
        mkdir work-dir
        cd work-dir
        pytest -vvs --cov fileformats --cov-config .coveragerc --cov-report xml ..
    - name: Upload coverage to Codecov
      uses: codecov/codecov-action@v2
      with:
        fail_ci_if_error: true
        token: ${{ secrets.CODECOV_TOKEN }}

  build:
    needs: [test]
    runs-on: ubuntu-latest
    strategy:
      matrix:
        pkg:
          - ["main", "."]
          - ["extras", "./extras"]
    steps:
    - uses: actions/checkout@v3
      with:
        submodules: recursive
        fetch-depth: 0
    - 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@v4
      with:
        python-version: '3.12'
    - name: Install build tools
      run: python3 -m pip install build twine
    - name: Build source and wheel distributions
      run: python3 -m build ${{ matrix.pkg[1] }}
    - name: Check distributions
      run: twine check ${{ matrix.pkg[1] }}/dist/*
    - uses: actions/upload-artifact@v3
      with:
        name: built-${{ matrix.pkg[0] }}
        path: ${{ matrix.pkg[1] }}/dist

  deploy:
    needs: [build]
    runs-on: ubuntu-latest
    steps:
    - name: Download build
      uses: actions/download-artifact@v3
      with:
        name: built-main
        path: dist
    - 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" ]; 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 }}

  deploy-extras:
    needs: [build, deploy]
    runs-on: ubuntu-latest
    steps:
    - name: Download build
      uses: actions/download-artifact@v3
      with:
        name: built-extras
        path: dist
    - name: Check for PyPI token on tag
      id: deployable
      if: github.event_name == 'release'
      env:
        EXTRAS_PYPI_API_TOKEN: "${{ secrets.EXTRAS_PYPI_API_TOKEN }}"
      run: if [ -n "$EXTRAS_PYPI_API_TOKEN" ]; 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.EXTRAS_PYPI_API_TOKEN }}

# Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
# Secrets are not accessible in the if: condition [0], so set an output variable [1]
# [0] https://github.community/t/16928
# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter