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CONTRIBUTING.md

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Contributing to mdlearn

If you are interested in contributing to mdearn, your contributions will fall into two categories:

  1. You want to implement a new feature:
    • In general, we accept any features as long as they fit the scope of this package. If you are unsure about this or need help on the design/implementation of your feature, post about it in an issue.
  2. You want to fix a bug:
    • Please post an issue using the Bug template which provides a clear and concise description of what the bug was.

Once you finish implementing a feature or bug-fix, please send a Pull Request to https://github.com/ramanathanlab/mdlearn.

Developing mdlearn

To develop mdlearn on your machine, please follow these instructions:

  1. Clone a copy of mdlearn from source:
git clone https://github.com/ramanathanlab/mdlearn.git
cd mdlearn
  1. If you already have a mdlearn from source, update it:
git pull
  1. Install mdlearn in develop mode:

For development, it is recommended to use a virtual environment. The following commands will create a virtual environment, install the package in editable mode, and install the pre-commit hooks.

python -m venv venv
source venv/bin/activate
pip install -U pip setuptools wheel
pip install -e '.[dev,docs,torch]'
pre-commit install

Unit Testing

To run the test suite:

First, Build and install mdlearn from source.

To test the code, run the following command:

pre-commit run --all-files
tox -e py312

If contributing, please add a test_<module_name>.py in the test/ directory in a subdirectory that matches the mdlearn package directory structure. Inside, test_<module_name>.py implement test functions using pytest.

Building Documentation

To build the documentation:

  1. Build and install mdlearn from source.
  2. Generate the documentation file via:
cd docs
make html

The docs are located in build/html/index.html.

To view the docs run: open build/html/index.html.

Releasing to PyPI

To release a new version of mdlearn to PyPI:

  1. Merge the develop branch into the main branch with an updated version number in pyproject.toml.
  2. Make a new release on GitHub with the tag and name equal to the version number.
  3. Build and install mdlearn from source.
  4. Run the following commands:
cd docs
make html
cd ..
rm -r dist
python3 -m build
twine upload dist/*