ci.yml

name: ci

on:
  pull_request:
    branches:
     - dev
  push:
    branches:
      - '*'
 
jobs:

  static-code-analysis:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}

    steps:
      - name: Check out repository
        uses: actions/checkout@v4
         
      - name: Setup Conda/Mamba
        uses: conda-incubator/setup-miniconda@v2
        with:
          mamba-version: "*"
          auto-update-conda: true
          activate-environment: scrnasim-toolz
          environment-file: environment.yml
          auto-activate-base: false
      
      - name: Update scrnasim-toolz env with dev packages
        run: mamba env update -n scrnasim-toolz -f environment-dev.yml
      
      - name: Display environment info
        run: |
          conda info -a
          conda list

      - name: flake8
        run: flake8

      - name: pylint
        run: pylint --rcfile pylint.cfg setup.py scRNAsim_toolz/

      - name: mypy
        run: mypy scRNAsim_toolz

  unit-testing:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}

    steps:
    
      - name: Checkout repository
        uses: actions/checkout@v4
         
      - name: Setup Conda/Mamba
        uses: conda-incubator/setup-miniconda@v2
        with:
          mamba-version: "*"
          auto-update-conda: true
          activate-environment: scrnasim-toolz
          environment-file: environment.yml
          auto-activate-base: false
      
      - name: Update scrnasim-toolz env with dev packages
        run: mamba env update -n scrnasim-toolz -f environment-dev.yml
      
      - name: Display environment info
        run: |
          conda info -a
          conda list
      
      - name: Run unit tests
        run: |
          coverage run --source scRNAsim_toolz -m pytest
          coverage xml

      - name: Submit coverage report
        uses: codecov/codecov-action@v2
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          files: ./coverage.xml
          verbose: true
          fail_ci_if_error: false

  publish:
    name: build and publish app image
    runs-on: ubuntu-latest
    if: |
      github.event_name == 'push' && 
      github.ref == format('refs/heads/{0}', github.event.repository.default_branch)

    steps:

      - name: Check out repository
        uses: actions/checkout@v4

      - name: Generate tag
        run: |
          echo "TAG=$(date '+%Y%m%d')" >> $GITHUB_ENV

      - name: Build and publish image
        id: docker
        uses: philips-software/docker-ci-scripts@v5.1.0
        with:
          dockerfile: .
          image-name: "scrnasim-toolz"
          tags: "latest ${{ env.TAG }}"
          push-branches: "${{ github.event.repository.default_branch }}"
        env:
          REGISTRY_USERNAME: ${{ secrets.DOCKERHUB_LOGIN }}
          REGISTRY_TOKEN: "${{ secrets.DOCKERHUB_TOKEN }}"
          DOCKER_ORGANIZATION: ${{ secrets.DOCKERHUB_ORG }}
          GITHUB_ORGANIZATION: ${{ github.repository_owner }}

      - name: Verify that image was pushed
        run: |
          echo "Push indicator: ${{ steps.docker.outputs.push-indicator }}"
          echo "# Set to 'true' if image was pushed, empty string otherwise"
          test "${{ steps.docker.outputs.push-indicator }}" == "true"