build_and_test_cli.yml

# Workflow to build nii2dcm, run unit tests and then execute command line interface (CLI) end-to-end

name: Build nii2dcm

on:
  pull_request:

jobs:
  build-and-test:
    name: Build, Unit Tests & E2E

    runs-on: ${{ matrix.os }}

    strategy:
      fail-fast: false
      matrix:
        os: [ ubuntu-latest ]
        python-version: [ '3.9' ]

    steps:
    - uses: actions/checkout@v3
      with:
        fetch-depth: 0

    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install Python packages
      run: |
        python -m pip install --upgrade pip
        pip install setuptools wheel
        pip install flake8 pytest pytest-cov
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi

    - name: Display installed pip packages
      run: |
        pip list

    - name: Setup flake8 annotations
      uses: rbialon/flake8-annotations@v1

    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

    - name: Build nii2dcm
      run: |
        pip install .

    - name: Test nii2dcm install
      run: |
        nii2dcm -h
        nii2dcm -v

    - name: Run unit tests
      run: |
        pytest tests/

    - name: Test DicomMRISVR creation
      run: |
        # run nii2dcm
        mkdir output
        nii2dcm tests/data/DicomMRISVR/t2-svr-atlas-35wk.nii.gz ./output -d SVR
        ls ./output
        # assert DICOM files exist
        [ -f "./output/IM_0001.dcm" ] && echo "Output DICOM file exists" || exit 1

    - name: Build pytest coverage file
      run: |
        pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=nii2dcm tests/ | tee pytest-coverage.txt ; echo $?

    - name: Pytest coverage comment
      id: coverageComment
      uses: MishaKav/pytest-coverage-comment@main
      with:
        pytest-coverage-path: ./pytest-coverage.txt
        junitxml-path: ./pytest.xml
        default-branch: unit-tests

    - name: Update Coverage Badge
      uses: schneegans/dynamic-badges-action@v1.7.0
      with:
        auth: ${{ secrets.PYTEST_COVERAGE_COMMENT }}
        gistID: 57ef8057d04f67dbe6e64df410b83079
        filename: nii2dcm-pytest-coverage-comment.json
        label: Coverage Report
        message: ${{ steps.coverageComment.outputs.coverage }}
        color: ${{ steps.coverageComment.outputs.color }}
        namedLogo: python

  container-build-and-test:
    name: Container Build & Test

    runs-on: ${{ matrix.os }}

    strategy:
      fail-fast: false
      matrix:
        os: [ ubuntu-latest ]
        python-version: [ '3.9' ]

    steps:
      - uses: actions/checkout@v3
        with:
          fetch-depth: 0

      - name: Build container
        run: |
          docker build -t nii2dcm --progress=plain --no-cache .
          docker ps

      - name: Test nii2dcm container
        run: |
          docker run nii2dcm -h
          echo "nii2dcm version:"
          docker run nii2dcm -v