conda-env-create-run-pytest.yml

name: conda-env-create-run-pytest

on: [pull_request]

jobs:
  build-linux:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python 3.10
      uses: actions/setup-python@v5
      with:
        python-version: '3.10'

    - name: Add conda to system path
      run: |
        # $CONDA is an environment variable pointing to the root of the miniconda directory
        echo $CONDA/bin >> $GITHUB_PATH

    - name: Create catalogbuilder conda environment
      run: |
        # create environment catalogbuilder will be installed into
        conda env create -f environment.yml --name catalogbuilder
        # put conda env binaries in GITHUB_PATH
        echo $CONDA/envs/catalogbuilder/bin >> $GITHUB_PATH
        # install catalogbuilder to conda env directories
        $CONDA/envs/catalogbuilder/bin/python -m pip install --prefix $CONDA/envs/catalogbuilder .

    - name: Make sample data
      run: |
        which python
        python catalogbuilder/tests/make_sample_data.py

    - name: Generate catalog
      run: |
        which python
        python catalogbuilder/scripts/gen_intake_gfdl.py archive/am5/am5/am5f3b1r0/c96L65_am5f3b1r0_pdclim1850F/gfdl.ncrc5-deploy-prod-openmp/pp gfdl_autotest

    - name: Generate catalog with yaml
      run: |
        which python
        python catalogbuilder/scripts/gen_intake_gfdl.py --config catalogbuilder/tests/test_config.yaml
  
    - name: upload-artifacts
      uses: actions/upload-artifact@v4
      with:
          name: workflow-artifacts1 
          path: |
            catalogbuilder/cats/gfdl_autotest_from_yaml.json
            catalogbuilder/cats/gfdl_autotest_from_yaml.csv 
    - name: Download all workflow run artifacts
      uses: actions/download-artifact@v4

    - name: Run pytest with downloaded artifacts
      run: |
        $CONDA/envs/catalogbuilder/bin/pytest -v --runxfail catalogbuilder

    - name: Test for completeness
      run: | 
        which python
        python catalogbuilder/scripts/test_catalog.py -tf gfdl_autotest.json catalogbuilder/cats/gfdl_template.json
        python catalogbuilder/scripts/test_catalog.py -tf catalogbuilder/cats/gfdl_autotest_from_yaml.json