build-main.yaml

---
name: build main

# Actions that take place after every commit the master/main branch.
# Here every commit is built and tested.
#
# Actions also run if the repository is tagged.
#
# Actions also run on a schedule.

# ---------------
# Control secrets
# ---------------
#
# At the GitHub 'organisation' or 'project' level you are expected to
# have the following GitHub 'Repository Secrets' defined
# (i.e. via 'Settings -> Secrets'): -
#
# (none)
#
# -----------
# Environment (GitHub Environments)
# -----------
#
# (none)

on:
  push:
    branches:
    - 'master'
    - 'main'
    tags:
    - '**'
  pull_request:
    branches:
    - 'master'
    - 'main'
    tags:
    - '**'
  schedule:  
  # Build every Sunday (0) at 3:45pm
  - cron: '45 15 * * 0'

env:
  CONDA_ORIGIN: http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh

jobs:
  build:
    runs-on: ubuntu-latest
    steps:
    - name: Checkout
      uses: actions/checkout@v2
    - name: Setup python
      uses: actions/setup-python@v2
      with:
        python-version: 3.7.10
    - name: Install conda
      run: |
        # Install Miniconda.
        # This will be installed in /home/runner/miniconda2
        wget $CONDA_ORIGIN -O miniconda.sh
        chmod +x miniconda.sh
        ./miniconda.sh -b
        export PATH=/home/runner/miniconda2/bin:$PATH

        # Echo (for reference) the installed conda.
        # When last observed this was '4.0.5'.
        conda -V

        # Update conda (otherwise conda can't be found)
        conda update conda -y

        # Set up a conda environment with the right Python version.
        conda create -y -n action_env python=3.7.10

        # Move to the environment
        source activate action_env

        # Install the requirements from the environment file
        # - conda install -c schrodinger pymol -y
        # Required...
        git clone https://github.com/xchem/gemmi_pandda.git
        cd ./gemmi_pandda
        pip install --force-reinstall .
        cd ..

        # Also Required
        git clone https://github.com/xchem/pandda_gemmi.git
        cd ./pandda_gemmi
        pip install -e .
        cd ..
        conda install -c rdkit rdkit -y

        # Install additional dependencies used only for testing
        conda install -y pytest codecov

        # You can also install some dependencies with pip if not available in conda
        pip install -e .

        # Run tests and coverage report
        coverage run -m py.test
        coverage report --omit="pandda_gemmi/*,gemmi_pandda/*,tests/*" -m