python-package-conda.yml

name: Run Test Suite

on: [pull_request, workflow_dispatch]

jobs:
  build-linux:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5

    steps:
    - uses: actions/checkout@v2

    # Necessary to prevent permission issues with tar when unpacking the cache
    # into the /usr/share/miniconda/ directory
    - name: Set cached directory permissions
      run: |
        sudo chown -R $(whoami):$(id -ng) /usr/share/miniconda/

    # Modified from:
    # https://github.com/marketplace/actions/setup-miniconda#caching
    - name: Set or unpack cached conda packages
      uses: actions/cache@v2
      env:
        # Increase this value to reset cache if environment.yml has not changed
        CACHE_NUMBER: 0
      with:
        path: /usr/share/miniconda
        key:
          ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
            hashFiles('environment.yml') }}-${{
            hashFiles('environment-synthetic-data.yml') }}

    - name: Add conda to system path
      run: |
        # $CONDA is an environment variable pointing to the root of the
        # miniconda directory
        echo $CONDA/bin >> $GITHUB_PATH

    - name: Install bids-validator for test suite
      run: |
        sudo npm install -g bids-validator@1.7.3

    - name: Install conda environment
      run: |
        conda install -y -c defaults -c conda-forge awscli bcrypt boto3 dcm2niix flake8 indexed_gzip jupyter mypy nibabel nilearn nodejs pip pydicom pytest python=3.8 requests rpyc scipy toml tornado websocket-client
        pip install inotify pybids watchdog wsaccel 
        # conda list
        # conda env update --file environment.yml --name base
        # conda env update --file environment-synthetic-data.yml --name base

    - name: Lint with flake8
      run: |
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings.
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=80 --statistics

    - name: Setup certificates directory for running tests
      run: |
        mkdir certs
        openssl genrsa -out certs/rtcloud_private.key 2048
        bash scripts/make-sslcert.sh -ip `hostname -i`

#     - name: Test with pytest
#       run: |
#         python -m pytest tests/