python-package-conda.yml

---  # yamllint disable-line rule:new-lines

name: SACCHARIS Conda Test Suite

on:  # yamllint disable-line rule:truthy
  push:
    branches:
      - main
      - test
  pull_request:
    branches:
      - main
      - test
  workflow_dispatch:


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

    steps:
      - uses: actions/checkout@v3
      - name: Install system dependencies
        run: |
          sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev
      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.3.1'
      - name: Install rsaccharis and dependencies
        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
        run: >
          Rscript -e 'install.packages("BiocManager", repos = "http://cran.us.r-project.org")'
          -e 'if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager");BiocManager::install()'
          -e 'BiocManager::install(c("remotes", "saccharis/rsaccharis"), dependencies=TRUE)'
      - name: Set up Python 3.11
        uses: actions/setup-python@v3
        with:
          python-version: '3.11'     
      - name: Set up conda/mamba
        uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          python-version: ${{ matrix.python-version }}
          mamba-version: "*"
          channel-priority: true
          channels: conda-forge,bioconda,defaults
          environment-file: environment.yml
      - 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: Install conda dependencies
      #   run: conda env update --file environment.yml --name base
      - name: Build and install SACCHARIS
        run: |
          conda install conda-build
          conda build .
          conda install --use-local saccharis
      - name: Lint with flake8
        run: |
          conda install flake8
          # stop the build if there are Python syntax errors or undefined names
          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
      - name: Test with pytest
        run: |
          conda install pytest
          pytest tests_package
      - name: Zip build artifact
        if: ${{ failure() }}
        run: zip -r artifact.zip /home/runner/work/
      - name: Upload build artifact
        uses: actions/upload-artifact@v3
        if: ${{ failure() }}
        with:
          name: artifact-all
          path: artifact.zip
          retention-days: 5