action.yml

# adapted from https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

name: Build msyd
description: "Checks out, installs dependencies and builds the msyd package. Formulated as a composite action to reduce code duplication in testing. Composite workflows cannot perserve state. Currently broken b/c of a version bound in the SyRI conda package."

#inputs:
#  python-version:
#    description: 'Python version to use'
#    required: true
#    default: '3.12'

runs:
  using: composite
  steps:
  - name: Checkout repo
    uses: actions/checkout@v4
  - name: Set up Python ${{ inputs.python-version }}
    uses: actions/setup-python@v5
    with:
      python-version: '3.10'
      cache: pip
    #  - name: Update pip
    #    run: python -m pip install --upgrade pip setuptools
    #    shell: bash
    #  - name: Install SyRI manually
    #    run: |
    #      # manually install syris dependencies
    #      # the python version spoofing requires the --no-deps flag, so this is necessary
    #      pip install Cython numpy pandas scipy psutil igraph longestrunsubsequence pysam pulp
    #      # manually use pip to install syri from github, as it isn't on pypi
    #      # spoof python version to get around bounds check
    #      pip install 'git+https://github.com/schneebergerlab/syri.git' --python-version '3.10' --no-deps --no-warn-conflicts --target $(python -m site --user-site)
    #    shell: bash
    #  - name: Install other dependencies
    #    run: pip install -r requirements.txt
    #    shell: bash
  - name: Setup conda env, install msyd
    run: |
      #$CONDA/bin/conda init
      #source ~/.bashrc
      #$CONDA/bin/conda env create -n msyd --file ./environment.yml
      #$CONDA/bin/conda activate msyd
      conda env update -n base --file ./environment.yml
    shell: bash
    # python -m pip install mappy
  - name: Build msyd
    run: pip install .
    shell: bash