github_build.yml

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: build

on:
  push:
    branches:
      - master
      - 0.1.0
    tags:
      - '*'
  pull_request:
    branches: [ master ]

jobs:
  build:
    runs-on: ubuntu-22.04
    strategy:
      matrix:
        python-version: [3.12]
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install metaeuk
      run: |
        wget https://mmseqs.com/metaeuk/metaeuk-linux-avx2.tar.gz
        tar -xzf metaeuk-linux-avx2.tar.gz
        sudo install -m 755 metaeuk/bin/metaeuk /usr/local/bin/metaeuk
    - name: Install miniprot
      run: |
        git clone --depth 1 https://github.com/lh3/miniprot
        make -C miniprot
        sudo install -m 755 miniprot/miniprot /usr/local/bin/miniprot
    - name: Install augustus
      run: |
        sudo apt-get update
        sudo apt-get install -y \
          build-essential \
          zlib1g-dev \
          libgsl-dev \
          libboost-all-dev \
          liblpsolve55-dev \
          libmysql++-dev \
          libmysqlclient-dev \
          libbamtools-dev \
          libhts-dev
        git clone --depth 1 https://github.com/Gaius-Augustus/Augustus.git
        make -C Augustus clean
        make -C Augustus \
          MYSQL=0 \
          SQLITE=0 \
          COMPGENEPRED=1
        sudo make -C Augustus install
        echo "$GITHUB_WORKSPACE/Augustus/scripts" >> $GITHUB_PATH
    - name: Install python dependencies
      run: |
        python -m pip install --upgrade pip
        python -m pip install flake8 pytest wheel
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --exclude=Augustus --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --exclude=Augustus --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
    - name: Test
      run: |
        pwd
        python -m pip install .
        sudo apt-get update
        path=$(fdog.setup -d ./ --getSourcepath); xargs -a $path/data/dependencies.txt sudo apt-get install -y -qq
        echo "######### current dir #########"
        pwd
        ls
        bash scripts/run_tests.sh
  conda-test:
    runs-on: ubuntu-22.04
    steps:
      - uses: actions/checkout@v4
      - name: Setup micromamba
        uses: mamba-org/setup-micromamba@v3
        with:
          environment-name: fdog-env
          create-args: >-
            python=3.12 pip
          cache-environment: true
          cache-downloads: true
          init-shell: bash
      - name: Run tests (conda env)
        shell: bash -l {0}
        run: |
          python -m pip install .
          bash scripts/run_tests.sh
  deploy:
    needs: [build, conda-test]
    runs-on: ubuntu-22.04
    if: startsWith(github.event.ref, 'refs/tags')
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.12"
      - name: Install build tools
        run: |
          python -m pip install --upgrade pip
          python -m pip install build
      - name: Build distribution packages
        run: python -m build
      - name: Publish to PyPI
        uses: pypa/gh-action-pypi-publish@release/v1
        with:
          password: ${{ secrets.pypi }}