test-mamba.yml

name: mamba environment testing

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main ]

jobs:
  build-linux:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: 'true'

      - name: Set up Miniconda
        uses: conda-incubator/setup-miniconda@v3
        with:
          activate-environment: AodnCloudOptimised
          environment-file: environment.yml
          auto-activate-base: false  # Prevent activating base env

      - name: Install dependencies
        shell: bash -el {0}
        run: |
          conda install --yes mamba
          mamba env create --name AodnCloudOptimised --file environment.yml || true  # Create only if not exists
          conda activate AodnCloudOptimised
          mamba env update --name AodnCloudOptimised --file environment.yml

      - name: Activate Conda environment
        shell: bash -el {0}
        run: |
          conda init
          conda activate AodnCloudOptimised
          poetry install --no-interaction

      - name: Run pytest and coverage
        run: |
          coverage run -m pytest
          coverage report --fail-under=60
          coverage xml -o coverage.xml

#      - name: Upload coverage report
        #uses: actions/upload-artifact@v2
        #with:
          #name: coverage-report
#          path: coverage.xml
      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v4.0.1
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          path: coverage.xml