main.yml

name: microsetta-interface CI

on:
  pull_request:
  push:
    branches:
      - master

jobs:
  lint:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - name: set up python 3.7
      uses: actions/setup-python@v1
      with:
        python-version: 3.7
    - name: lint it
      run: python -m pip install --upgrade pip
    - name: lint
      run: |
        pip install -q flake8
        flake8 microsetta_interface
  test:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2

    - name: Setup for conda
      uses: conda-incubator/setup-miniconda@v2
      with:        
        auto-update-conda: true
        python-version: 3.7
      
    - name: Install
      shell: bash -l {0}
      run: |
        conda create --yes -n test-microsetta-interface python=3.7
        conda activate test-microsetta-interface
        conda install --yes --file ci/conda_requirements.txt
        pip install -r ci/pip_requirements.txt
        pip install -e . --no-deps 

    - name: Test
      shell: bash -l {0}
      run: |
        conda activate test-microsetta-interface
        pytest
  integration:
    runs-on: ubuntu-latest
      
    # Service containers to run with `runner-job`
    services:
      # Label used to access the service container
      postgres:
        # Docker Hub image
        image: postgres:13.4
        env:
          POSTGRES_DB: ag_test  
          POSTGRES_USER: postgres  
          POSTGRES_PASSWORD: postgres
          
        # Set health checks to wait until postgres has started
        options: >-
          --health-cmd pg_isready
          --health-interval 10s
          --health-timeout 5s
          --health-retries 5
        ports:
          # based on https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml#L44-L72
          - 5432/tcp

    steps:
    # Downloads a copy of the code in your repository before running CI tests
    - name: Check out repository code
      uses: actions/checkout@v2

    - name: Setup for conda
      uses: conda-incubator/setup-miniconda@v2
      with:        
        auto-update-conda: true
        python-version: 3.7 
    
    - name: Install
      env:
        BRANCH: ${{ github.base_ref == 'master-overhaul' && 'master-overhaul' || 'master' }}
      shell: bash -l {0}
      run: |
        echo Branch: $BRANCH
        conda create --yes -n microsetta-interface python=3.7
        conda activate microsetta-interface
        conda install --yes --file ci/conda_requirements.txt
        pip install -r ci/pip_requirements.txt
        python setup.py compile_catalog
        pip install -e . --no-deps
        
        git clone -b $BRANCH --single-branch https://github.com/biocore/microsetta-private-api.git
        pushd microsetta-private-api
        pgport=${{ job.services.postgres.ports[5432] }}
        sed -i "s/self.port = 5432/self.port = $pgport/" microsetta_private_api/config_manager.py
        
        # PGPASSWORD is read by pg_restore, which is called by the build_db process. 
        export PGPASSWORD=postgres
        
        conda create --yes -n microsetta-private-api python=3.7
        conda activate microsetta-private-api
        conda install --yes --file ci/conda_requirements.txt
        pip install -r ci/pip_requirements.txt
        pip install -e . --no-deps 
        
        # establish database state
        python microsetta_private_api/LEGACY/build_db.py
        popd
    - name: Run integration tests
      shell: bash -l {0}
      run: |
        conda activate microsetta-private-api
        pushd microsetta-private-api
        sed -i 's/"debug": true,/"debug": true, "disable_authentication": true,/' microsetta_private_api/server_config.json
        python microsetta_private_api/server.py &
        sleep 10 # give time to start up
        popd

        conda activate microsetta-interface
        redis-server --daemonize yes
        source keys_for_testing.sh
        python microsetta_interface/tests/test_integration.py 2> >(tee -a stderr.log >&2)
        
        # make sure we did not skip tests, which would indicate a failure in
        # the harness. this test will produce an exit status of 1 if the
        # test suite reports skipped tests
        [[ $(tail -n 1 stderr.log | grep skipped) == "" ]];