CI.yaml

name: CI

on:
  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
  # Existing codes likely still have "master" as the primary branch
  # Both are tracked here to keep legacy and new codes working
  push:
    branches:
      - "main"
  pull_request:
    branches:
      - "main"
  # schedule:
    # Nightly tests run on master by default:
    #   Scheduled workflows run on the latest commit on the default or base branch.
    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
    # - cron: "0 0 * * *"

jobs:
  test:
    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
    runs-on: ${{ matrix.os }}
    strategy:
      max-parallel: 1
      matrix:
        #os: [macOS-latest, ubuntu-latest, windows-latest]
        #python-version: [3.8, 3.9, "3.10"]
        os: [ubuntu-latest]
        python-version: [3.8, 3.9, "3.10", "3.11"]
    steps:
    - uses: actions/checkout@v1

    - name: Additional info about the build
      shell: bash
      run: |
        uname -a
        df -h
        ulimit -a

    - name: Install hmmer
      run: |
       wget http://eddylab.org/software/hmmer/hmmer-3.3.2.tar.gz
       tar zxf hmmer-3.3.2.tar.gz
       cd hmmer-3.3.2
       ./configure
       make
       make check
       sudo make install
       cd ..  

    - name: checkout source
      uses: actions/checkout@v2
#      with:
#        path: main
    
    # - name: Generate lfs file list
    #   run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id
    
    # - name: Restore lfs cache
    #   uses: actions/cache@v2
    #   id: lfs-cache
    #   with:
    #     path: .git/lfs
    #     key: ${{ runner.os }}-lfs-${{ hashFiles('.lfs-assets-id') }}-v1
    
    # - name: Pull lfs files
    #   run: git lfs pull
    
    
#    - name: Change to main directory
#      run: |
#        cd main
#        pwd

    # More info on options: https://github.com/conda-incubator/setup-miniconda
    - uses: conda-incubator/setup-miniconda@v2
      with:
        python-version: ${{ matrix.python-version }}
        environment-file: devtools/conda-envs/test_env.yaml

        channels: conda-forge, defaults, bioconda

        activate-environment: test
        auto-update-conda: false
        auto-activate-base: false
        show-channel-urls: true

#    - name: Change to root directory
#      run: |
#        cd main
#        pwd
    
    #Install numpy first
    - name: Install numpy
      run: conda install "numpy<2"

    #Install pydca
    - name: Check out pydca
      uses: actions/checkout@v3
      with:
        repository: cabb99/pydca
        path: pydca_dir
    - name: Install pydca
      run: |
        cd pydca_dir
        echo "numpy<2" > constraints.txt
        pip install -r requirements.txt -c constraints.txt
        python -m pip install . --no-deps
        conda list
        cd ..
        pwd
    
    - name: Install package

      # conda setup requires this special shell
      shell: bash -l {0}
      run: |
        conda install -c conda-forge --file requirements.txt
        python -m pip install . --no-deps
        conda list

    - name: Install pdbfixer

      # conda setup requires this special shell
      shell: bash -l {0}
      run: |
        conda install -c conda-forge pdbfixer

    - name: Run tests

      # conda setup requires this special shell
      shell: bash -l {0}

      run: |
        pytest -v --cov=frustratometer --cov-report=xml --color=yes tests/

    - name: CodeCov
      uses: codecov/codecov-action@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml
        flags: unittests
        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}