tests_and_cleanup.yml

name: Ersilia tests, installation checks, and cleanup of model request template

on:
  pull_request:
    branches: [ master ]
  push:
    branches: [ master ]
  workflow_dispatch:

jobs:
  install-ersilia:
    strategy:
      matrix:
        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
    runs-on: ubuntu-22.04

    steps:
    - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install Ersilia
      run: |
        python -m pip install git+https://github.com/ersilia-os/bentoml-ersilia.git
        python -m pip install -e .
    - name: Test help command
      run: |
        ersilia --help
        ersilia --version

  test-docker:
    strategy:
      matrix:
        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
    runs-on: ubuntu-22.04
    steps:
    - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install Ersilia without pre-installing BentoML
      run: |
        python -m pip install -e .
    - name: Test help command again
      run: |
        ersilia --help
        ersilia --version
    - name: Fetch molecular weight model from DockerHub
      run: |
        ersilia -v fetch molecular-weight --from_dockerhub

  test-os:
    strategy:
      matrix:
        platform: [ubuntu-22.04, macos-latest]
    runs-on: ${{ matrix.platform }}
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # pin@v3.5.3
      - uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          python-version: "3.10.10"

      - name: Install dependencies
        run: |
          conda install git-lfs -c conda-forge
          git-lfs install
          conda install gh -c conda-forge

      - name: Install ersilia from source
        run: |
          python --version
          python -m pip install -e .

      - name: Ersilia help
        run: |
          ersilia --help

  run-pytest:
    runs-on: ubuntu-22.04
    steps:
      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # pin@v3.5.3

      - name: Add conda to system path
        run: echo $CONDA/bin >> $GITHUB_PATH

      - name: Source conda
        run: source $CONDA/etc/profile.d/conda.sh
        
      - name: Set Python to 3.10.10
        run:
         conda install -y python=3.10.10  

      - name: Install dependencies
        run: |
          source activate
          conda init
          conda install git-lfs -c conda-forge
          git-lfs install
          conda install gh -c conda-forge

      - name: Install ersilia
        run: |
          source activate
          python --version
          echo "After conda init"
          conda init
          python -m pip install -e .[test]

      - name: Run pytest
        run: |
          source activate          
          pip install pytest pytest-benchmark pytest-asyncio
          pytest

  test-colab-notebook:
    runs-on: ubuntu-22.04
    steps:
      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # pin@v3.5.3
      - name: Add conda to system path
        run: echo $CONDA/bin >> $GITHUB_PATH

      - name: Source conda
        run: source $CONDA/etc/profile.d/conda.sh

      - name: Set Python to 3.10.10
        run:
         conda install -y python=3.10.10 

      - name: Install dependencies
        run: |
          source activate
          conda init
          conda install google-colab -c conda-forge
          jupyter --version
          pip install --upgrade nbconvert nbformat jsonschema pandas

      - name: Test Google Colab Notebook with CLI shell commands
        run: |
          jupyter nbconvert --to notebook --execute notebooks/test-colab-notebook-cli.ipynb --output=output-cli.ipynb --ExecutePreprocessor.timeout=-1

      - name: Test Google Colab Notebook with Python API commands
        run: |
          echo "Skipping Python API notebook due to unresolved issue"
          #jupyter nbconvert --to notebook --execute notebooks/test-colab-notebook-python-api.ipynb --output=output-python-api.ipynb --ExecutePreprocessor.timeout=-1

      - name: Upload Output of the Google Colab Notebook CLI
        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # pin@v4.4.0
        with:
          name: output-cli.ipynb
          path: notebooks/output-cli.ipynb
          retention-days: 7

  update-model-request_template:
    runs-on: ubuntu-22.04
    steps:
      - uses: actions/checkout@v4
      
      - name: Path Filter
        id: filter
        uses: dorny/paths-filter@v3
        with:
          filters: |
            tag-file:
              - 'ersilia/hub/content/metadata/tag.txt'

      - name: Set up Python
        if: steps.filter.outputs.tag-file == 'true'
        uses: actions/setup-python@v5
        with:
          python-version: '3.10'

      - name: Install dependencies
        if: steps.filter.outputs.tag-file == 'true'
        run: |
          python -m pip install --upgrade pip
          pip install pyyaml

      - name: Run update_model_request_template.py
        if: steps.filter.outputs.tag-file == 'true'
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        run: python .github/scripts/update_model_request_template.py

      - name: Commit and push changes
        if: steps.filter.outputs.tag-file == 'true'
        uses: actions-js/push@5a7cbd780d82c0c937b5977586e641b2fd94acc5 # pin@v1.5
        with:
          author_name: "ersilia-bot"
          author_email: "ersilia-bot@users.noreply.github.com"
          message: "Update model request template [skip ci]"
          repository: "ersilia-os/ersilia"
          github_token: ${{ secrets.GITHUB_TOKEN }}
          force: true
          branch: "master"