build.yml

name: Build and Test

on:
  push:
    branches: [ main, dev ]
  pull_request:
    branches: [ main, dev ]

jobs:
  docker:
    runs-on: ubuntu-latest
    env:
      ACTIONS_ALLOW_UNSECURE_COMMANDS: true
    steps:
    - uses: actions/checkout@v3
    - name: Checkout tags
      run: git fetch --unshallow origin +refs/tags/*:refs/tags/*
    - name: Set git branch variable
      run: echo ::set-env name=BRANCH::$(git branch --show-current)
    - name: Set git tag variable
      run: if [ $BRANCH == "main" ];then echo ::set-env name=TAG::$(git describe --tags);else echo ::set-env name=TAG::$BRANCH;fi
    - name: Checkout submodules
      shell: bash
      run: |
        auth_header="$(git config --local --get http.https://github.com/.extraheader)"
        git submodule sync --recursive
        git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
    - name: Build the Docker image
      run: docker build . -t quay.io/matsengrp/partis:$TAG
    # - name: Run tests in the Docker image  # eh, would need to install simulation stuff to do this, and not worth it at the moment (the quick test is run at the end of the docker build above)
    #   run: docker run quay.io/matsengrp/partis:$TAG /bin/bash -c "/partis/test/test.py --run-all"

  test:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-15-intel] # this is the last intel build, will be deprecated dec 2027, and atm we can't run on non-intel macs: https://github.com/psathyrella/partis/issues/330
        python-version: ['3.12']
        install-method: ['pip', 'pipx']
      fail-fast: false

    env:
      TERM: xterm

    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0
    
    - name: Checkout ham submodule
      if: matrix.install-method == 'pip'
      run: |
        git submodule update --init packages/ham

    - name: Checkout ig-sw submodule
      if: matrix.install-method == 'pip'
      run: |
        git submodule update --init packages/ig-sw

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install system dependencies (Ubuntu)
      if: matrix.os == 'ubuntu-latest'
      run: |
        sudo apt update
        sudo apt install -y python3 python3-pip python-is-python3 pipx build-essential cmake libgsl-dev libyaml-cpp-dev scons mafft ncurses-base ncurses-bin r-base
        # sudo apt install libbpp-core libbpp-seq  # which packages do i actually have to write here?

    - name: Install system dependencies (macOS)
      if: startsWith(matrix.os, 'macos')
      run: |
        brew install gsl yaml-cpp scons mafft r
        # brew tap jydu/homebrew-biopp
        # brew install libbpp-core bppsuite  # which packages do i actually have to write here?
        brew install --cask font-lato
        
    # - name: Set Homebrew paths for ARM64 Mac  # not used atm, but we'll want these if we manage to fix the emmintrin.h/SSE2 issue, so leaving in
    #   if: matrix.os == 'macos-14'
    #   run: |
    #     echo "CPPFLAGS=-I/opt/homebrew/include" >> $GITHUB_ENV
    #     echo "LDFLAGS=-L/opt/homebrew/lib" >> $GITHUB_ENV

    # - name: Install R tree generation packages  # could turn this back on, but it's really slow and not super important (and is unnecessary with --no-tree-gen arg below), although note we're still installing R above
    #   run: |
    #     R --slave -e 'dir.create(c(Sys.getenv("R_LIBS_USER")), recursive=TRUE); install.packages(c("TreeSim", "TreeSimGM", "geiger", "MASS"), repos="http://cran.rstudio.com/", dependencies=TRUE, lib=c(Sys.getenv("R_LIBS_USER")))'

    - name: Install with pip
      if: matrix.install-method == 'pip'
      run: |
        python -m pip install --upgrade pip
        python -m pip install -e . -v

    - name: Install with pipx
      if: matrix.install-method == 'pipx'
      run: |
        pipx install partis-bcr

    - name: Test partis help
      run: |
        partis --help

    - name: Test scripts work
      run: |
        split-loci.py --help

    - name: Run quick test
      run: |
        partis-test.py --quick

    - name: Run full test
      run: |
        # if [[ "${{ matrix.install-method }}" == "pipx" || "${{ matrix.os }}" == macos* ]]; then
        if [[ "${{ matrix.os }}" == macos* ]]; then
          partis-test.py --no-simu
          partis-test.py --paired --no-simu
        else
          partis-test.py --no-per-base-mutation --no-tree-gen
          partis-test.py --paired --no-per-base-mutation --no-tree-gen
        fi

    - name: Build and publish to PyPI
      if: matrix.install-method == 'pip' && github.event_name == 'push'  #  && github.ref == 'refs/heads/main'  #  && matrix.os == 'ubuntu-latest'
      run: |
        python -m pip install build twine
        if [ "${{ matrix.os }}" = "ubuntu-latest" ]; then
          python setup.py bdist_wheel --plat-name manylinux1_x86_64
          python -m build --sdist 2>&1 | grep -v 'adding .test/\|adding .data/\|creating partis_bcr.*/test/\|copying docs/\|copying data/\|copying packages/\|copying python/.*/test/\|copying build/.*/test/'
          python -m twine check dist/*
          python -m twine upload dist/*
        else
          python -m build --wheel 2>&1 | grep -v 'adding .test/\|adding .data/\|creating partis_bcr.*/test/\|copying docs/\|copying data/\|copying packages/\|copying python/.*/test/\|copying build/.*/test/'
          python -m twine check dist/*.whl
          python -m twine upload dist/*.whl
        fi
      env:
        TWINE_USERNAME: __token__
        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}