development.md

description	Development notes regarding Metacity package

Development notes

After uploading any code to the Metacity GitHub repo, the actions specified in ci.yaml are executed. Generally, it involves

1. Building the C++ parts of the code
2. Running tests with pytest - see Testing

Local compilation

Metacity is written in Python and C++ using pybind11. If you want to edit the package code yourself, we recommend following these steps first:

Clone the repository:

git clone git@github.com:MetacitySuite/Metacity.git

(Optional but strongly recommended) Initialize local Python virtual environment

cd Metacity
python -m venv env
. ./env/bin/activate

Any time you make a change to the C++ or Python code, you can build it with:

pip install .

{% hint style="info" %} Up to version 0.5.3 there was a bug in the setup, which caused pollution of the python environment folder with files unrelated to the installation. This has been fixed. {% endhint %}

Debugging

If you encounter any problems, ensure you:

• have CMake installed
• have a C++ compiler supporting C++14 installed

Testing

Metacity comes with a few testing datasets and uses pytest. To run the tests locally, with coverage analysis, run:

python -m pytest tests/* --cov=metacity --cov-report term-missing

If you need to see the output of the tested code, run the command above with an extra flag -s

The tests are located inside the tests directory:

• tests/conftest.py contains fixtures providing the testing data.
• tests/test_module.py contains individual tests, the module placeholder in the filename is usually replaced with the name of the tested Python module (not required)

Always test your code!

Release

Everything merged into the branch release gets released. Before you publish a new version:

• make sure the version number in your code is set up correctly

Branches

Branch	Status	Description
release		for production
dev		merged PRs auto tested, for development