debug.yml

name: debug

# Only run this when the master branch changes
on: [workflow_dispatch]
#on:
#  push:
#    branches:
#    - master

# This job installs dependencies, build the book, and pushes it to `gh-pages`
jobs:
  deploy-book:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2

    # Install dependencies
    - name: Set up Python 3.7
      uses: actions/setup-python@v1
      with:
        python-version: 3.7

    # Install conda dependencies
    - name: Install dependencies
      run: |
        # $CONDA is an environment variable pointing to the root of the miniconda directory
        $CONDA/bin/conda env update --file environment.yml --name base
    
    # Install pip dependencies
    - name: Install dependencies
      run: |
        $CONDA/bin/pip install -r requirements.txt

    # Show packages
    - name: Show packages
      run: |
        $CONDA/bin/conda list

    # Compile the docs
    - name: Compile sphinx
      run: |
        $CONDA/bin/sphinx-apidoc -o docs/source morphodynamics/

    # Copy the dataset where necessary
    - name: Copy files
      run: |
        mkdir -p synthetic/data/Results_cellpose
        mkdir -p synthetic/data/Results_step
        cp -R synthetic/data/Results_ilastik/segmented synthetic/data/Results_cellpose
        cp -R synthetic/data/Results_ilastik/segmented synthetic/data/Results_step

    # debug using tmate
    - name: Setup tmate session
      uses: mxschmitt/action-tmate@v3