upload-package-anaconda.yml

name: Upload MAESTRO Package to anaconda

on:
  release:
    types: [created]
jobs:
  upload-linux:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5
    defaults:
      run:
        shell: bash
    steps:
    - uses: actions/checkout@v2
    - name: Set up Python 3.8
      uses: actions/setup-python@v2
      with:
        python-version: 3.8
    - 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: Cache conda pkgs
    #  uses: actions/cache@v2
    #  with:
    #    path: |
    #      /usr/share/miniconda/pkgs
    #      /home/runner/.conda/pkgs
    - name: Install dependencies
      run: |
        conda config --set always_yes yes --set changeps1 no
        # need conda-build/verify to test building conda package
        conda install -q conda-build
        conda install -q conda-verify
        conda update -q conda
        # Useful for debugging any issues with conda
        conda info -a
        # configure the channels
        conda config --add channels defaults
        conda config --add channels liulab-dfci
        conda config --add channels bioconda
        conda config --add channels conda-forge
        conda install -q mamba -c conda-forge
    - name: Build package
      run: |
        mkdir bld-dir
        conda build -q conda/MAESTRO --python=3.8 --output-folder bld-dir
    - name: Test installing package
      run: |
        # Now add this folder as a highest priority channel
        conda config --add channels "file://`pwd`/bld-dir"
        # install MAESTRO from local repo
        mamba create -q -n MAESTRO maestro
        # Activate this environment
        source /usr/share/miniconda/etc/profile.d/conda.sh
        conda activate MAESTRO
        # list conda env packages for reference
        conda list
    - name: Test installed MAESTRO package (cmdline)
      run: |
        source /usr/share/miniconda/etc/profile.d/conda.sh
        conda activate MAESTRO
        giggle search
        sinto -h
        lisa
        MAESTRO -v
        MAESTRO scrna-init -h
        MAESTRO scatac-init -h
        MAESTRO samples-init -h
        R -e "library(MAESTRO);library(Seurat)"
        R -e "library(org.Hs.eg.db);library(org.Mm.eg.db)"
    - name: Test installed MAESTRO package (other)
      run: |
        source /usr/share/miniconda/etc/profile.d/conda.sh
        conda activate MAESTRO
        # test python utility scripts
        cd test
        bash test.sh
        cd ..
    - name: Publish
      env:
        ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
      run: |
        mamba install anaconda-client
        anaconda upload bld-dir/**/maestro-*.tar.bz2