ci-pytest.yml

name: ci-pytest

on:
  push:
    branches:
      - master
  pull_request:
    branches:
      - master
  workflow_dispatch:

env:
  # Updates or changes to this, or the runner OS or arch will invalidate the cache
  python_version: '3.10' # Python version to use for testing - update when needed

jobs:
  test:
    runs-on: ubuntu-20.04
    # Default shell needs to be bash for conda
    # https://github.com/conda-incubator/setup-miniconda?tab=readme-ov-file#important
    defaults:
        run:
          shell: bash -el {0}
    steps:
    - name: Setup Miniconda
      uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # v3.0.3, devs recommend using hash
      with:
        miniconda-version: "latest"
        python-version: ${{ env.python_version }}
        auto-update-conda: true
        activate-environment: "test-env"

    - name: Configure Conda to use only .tar.bz2
      run: |
        conda config --set use_only_tar_bz2 true

    - name: Checkout code
      uses: actions/checkout@v4 # Checkout PR code to 'antspy-pr'
      with:
        path: antspy-pr

    - name: Load conda environment from cache if available
      id: cache-env
      uses: actions/cache@v4
      with:
        path: ~/conda-env.tar.bz2
        key: >-
            ${{ runner.os }}-conda-${{ env.python_version }}-${{ hashFiles('antspy-pr/ants/environment.yml',
            'antspy-pr/ants/requirements.txt', 'antspy-pr/ants/setup.py', 'antspy-pr/scripts/configure_ITK.sh',
            'antspy-pr/scripts/configure_ANTsPy.sh', 'antspy-pr/ants/lib/*') }}

    - name: Unpack cached environment
      if: steps.cache-env.outputs.cache-hit == 'true'
      run: |
        mkdir -p ${CONDA}/envs/antspy-env
        tar -xjf ~/conda-env.tar.bz2 -C ${CONDA}/envs/antspy-env
        conda activate antspy-env
        conda-unpack

    - name: Install dependencies and ANTsPy from PR
      if: steps.cache-env.outputs.cache-hit != 'true'
      run: |
        conda create -n antspy-env python=${{ env.python_version }} -y
        conda activate antspy-env
        conda install -c conda-forge conda-pack coverage
        conda info
        pip install ./antspy-pr
        conda list
        antspy-pr/tests/run_tests.sh -c
        conda pack -n antspy-env -o ~/conda-env.tar.bz2

    - name: Cache Conda environment
      if: steps.cache-env.outputs.cache-hit != 'true'
      uses: actions/cache@v4
      with:
        path: ~/conda-env.tar.bz2
        key: >-
            ${{ runner.os }}-conda-${{ env.python_version }}-${{ hashFiles('antspy-pr/ants/environment.yml',
            'antspy-pr/ants/requirements.txt', 'antspy-pr/ants/setup.py', 'antspy-pr/scripts/configure_ITK.sh',
            'antspy-pr/scripts/configure_ANTsPy.sh', 'antspy-pr/ants/lib/*') }}) }}

    - name: Replace installed ANTsPy with PR code
      if: steps.cache-env.outputs.cache-hit == 'true'
      run: |
        conda activate antspy-env
        ANTS_SITE_PACKAGES="${CONDA}/envs/antspy-env/lib/python${{ env.python_version }}/site-packages/ants"
        for d in contrib core learn registration segmentation utils viz; do
          rm -rf $ANTS_SITE_PACKAGES/$d;
          cp -r antspy-pr/ants/$d $ANTS_SITE_PACKAGES/$d;
          done
        find $ANTS_SITE_PACKAGES -name '__pycache__' -exec rm -rf {} +

    - name: Run tests
      if: steps.cache-env.outputs.cache-hit == 'true'
      run: |
        conda activate antspy-env
        bash antspy-pr/tests/run_tests.sh -c

    - name: Coveralls
      uses: coverallsapp/github-action@v2
      with:
        files: antspy-pr/tests/coverage.xml