continous-integration.yml

##################################################################################################
# @Date:      May 9th 2024
# @Author:    Patrick 
# @Email:     pinyuan.li@emory.edu 
# @Description: This workflow will automatically run pytest
##################################################################################################

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

name: Python application

on: [push, pull_request]

permissions:
  contents: read

jobs:
  build:
    runs-on: macos-latest
    steps:
      - uses: actions/checkout@v3

      - name: Set up Miniconda
        uses: conda-incubator/setup-miniconda@v2
        with:
          auto-update-conda: true
          miniconda-version: "latest"
          channels: anaconda
          channel-priority: true

      - name: Create conda environment
        run: conda env create -f devtools/conda-envs/environment.yml

      - name: Activate conda environment
        shell: bash -l {0}
        run: conda activate autosolvate

      - name: Install additional dependencies if needed
        run: conda install --yes flake8 pytest

      - name: Create test reports directory
        run: mkdir -p test-reports

      - name: Test with pytest
        run: conda run -n autosolvate pytest --junitxml=test-reports/results.xml

      - name: Show test-reports directory contents
        run: |
          echo "Content of test-reports directory:"
          ls -la test-reports/

      - name: Show pytest results
        run: |
          if [ -f test-reports/results.xml ]; then
            cat test-reports/results.xml
          else
            echo "results.xml not found"
          fi

      - name: Upload Test Reports
        uses: actions/upload-artifact@v3
        with:
          name: test-reports
          path: test-reports/results.xml