ci.yaml

name: Run unit tests, integration tests, and publish package if tagged
on:
  push:
    branches: [main, dev]
  pull_request:
    branches: [main, dev]
  release:
    types: [published]
  schedule:
    - cron: '0 2 * * 3,6'
jobs:
  run-unit-and-integration-tests-with-conda-install:
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -el {0}
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest",
             #"macos-13",
             # "windows-latest" # rrcovNA cannot be build from source on windows-server
             ]
        python-version: ["3.8", "3.9", "3.10"]
    steps:
    - name: Checkout
      uses: actions/checkout@v4
    - name: Set up Miniconda
      uses: conda-incubator/setup-miniconda@v3
      with: 
        # miniforge-variant: Mambaforge
        # miniforge-version: latest
        # conda-solver: libmamba
        # use-mamba: true
        # channels: conda-forge,defaults
        python-version: ${{ matrix.python-version }}
        # mamba-version: "*" 
        # channels: conda-forge,defaults
        channel-priority: strict
        environment-file: snakemake_env.yml
        activate-environment: snakemake
        auto-activate-base: true
        auto-update-conda: true
    # - uses: mamba-org/setup-micromamba@v1
    #   with:
    #     micromamba-version: 'latest' # any version from https://github.com/mamba-org/micromamba-releases
    #     environment-file: snakemake_env.yml
    #     create-args: >-
    #       python=${{ matrix.python-version }} 
    #     init-shell: >-
    #       bash
    #     cache-environment: false
    #     post-cleanup: 'none'
    # - name: inspect-conda-environment
    #   run: |
    #     conda info
    #     conda list
    #     conda env export --from-history --no-builds > environment.yml
    #     conda env export --no-builds
    #     conda env export --no-builds > environment_w_versions.yml
    # - name: test-r-kernel-imports
    #   run: |
    #     Rscript -e "library(stringi)"
    #     Rscript -e "library(stringr)"
    #     Rscript -e "library(reshape2)"
    - name: Dry-Run demo workflow (integration test)
      run: | 
       cd project
       snakemake -p -c1 --configfile config/single_dev_dataset/example/config.yaml --use-conda -n
    - name: Run demo workflow (integration test)
      continue-on-error: true
      run: | 
       cd project
       snakemake -p -c4 -k --configfile config/single_dev_dataset/example/config.yaml --use-conda
    - name: Show current files in conda snakemake folder
      run: ls -l project/.snakemake/conda/
    - name: Run demo workflow again (in case of installation issues)
      continue-on-error: true
      run: | 
        cd project
        snakemake -p -c4 -k --configfile config/single_dev_dataset/example/config.yaml --use-conda
    - name: Run demo workflow again (in case of installation issues) - one thread
      run: | 
        cd project
        snakemake -p -c1 --configfile config/single_dev_dataset/example/config.yaml --use-conda
    - name: Archive results
    # https://github.com/actions/upload-artifact
      uses: actions/upload-artifact@v4
      with:
        name: ${{ matrix.os }}-${{ matrix.python-version }}-example-workflow-results
        path: |
          project/runs/example/
          environment.yml
          environment_w_versions.yml

  run-unit-local-pip-installation:
    runs-on: ${{ matrix.os }}
    name: test-pip-installation
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest",]
        # "macos-latest", "windows-latest"]
        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
    steps:
      - uses: actions/checkout@v4

      # - uses: actions/setup-python@v5
      #   with:
      #     python-version: ${{ matrix.python-version }}

      - uses: conda-incubator/setup-miniconda@v3
        with:
          python-version: ${{ matrix.python-version }}
          auto-activate-base: true
          auto-update-conda: true

      
      - name: Install build dependencies explicitly
        run: |
          pip install setuptools_scm
          conda list


      - name: install pimms
        run: pip install .
      
      - name: Install pytest
        run: pip install pytest pytest-cov
      
      - name: Run pytest
        run: pytest .

      - name: Install papermill
        run: pip install papermill ipykernel
      
      - name: View papermill help message for notebooks (as scripts)
        run: |
          cd project
          papermill 01_0_split_data.ipynb --help-notebook
          papermill 01_1_train_VAE.ipynb --help-notebook
          papermill 01_1_train_DAE.ipynb --help-notebook
          papermill 01_1_train_CF.ipynb --help-notebook
      - name: Run tutorial notebooks
        run: |
          cd project
          mkdir runs
          papermill 04_1_train_pimms_models.ipynb runs/04_1_train_pimms_models.ipynb
          papermill 04_1_train_pimms_models.ipynb runs/04_1_train_pimms_models_no_val.ipynb -p sample_splits False

  publish:
    name: Publish package
    if: startsWith(github.ref, 'refs/tags')
    needs:
      - run-unit-and-integration-tests-with-conda-install
      - run-unit-local-pip-installation
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
  
      - uses: actions/setup-python@v5
        with:
          python-version: "3.8"
      - name: Install twine and build
        run: python -m pip install --upgrade twine build
      - name: Build
        run: python -m build

      - uses: pypa/gh-action-pypi-publish@release/v1
        with:
          user: __token__
          password: ${{ secrets.PYPI_API_TOKEN }}