AlphaPulldown/manuals/Developing.md

1. Clone the GitHub repo

   git clone --recurse-submodules git@github.com:KosinskiLab/AlphaPulldown.git
   cd AlphaPulldown 
   git submodule init
   git submodule update 
   

2. Create the Conda environment as described in https://github.com/KosinskiLab/AlphaPulldown/blob/installation-intro-update/README.md#create-anaconda-environment
3. Add AlphaPulldown package and its submodules to the Conda environment

   source activate AlphaPulldown
   cd AlphaPulldown
   pip install .
   pip install -e alphapulldown/ColabFold --no-deps
   pip install -e alphafold --no-deps
   

   You need to do it only once.
4. When you want to develop, activate the environment, modify files, and the changes should be automatically recognized.
5. Test your package during development using tests in test/, e.g.:

   pip install pytest
   pytest -s test/
   pytest -s test/test_predictions_slurm.py
   pytest -s test/test_features_with_templates.py::TestCreateIndividualFeaturesWithTemplates::test_1a_run_features_generation
   

6. Before pushing to the remote or submitting pull request

   pip install .
   pytest -s test/
   

   to install the package and test. Pytest for predictions only work if slurm is available. Check the created log files in your current directory.