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Contributing to pymc_bart

This document outlines only the most common contributions. More information coming soon. We welcome a wide range of contributions, not only code!

Reporting issues

If you encounter any bug or incorrect behaviour while using pymc_bart, please report an issue to our issue tracker. Please include any supporting information, in particular the version of pymc_bart that you are using. The issue tracker has several templates available to help in writing the issue and including useful supporting information.

Contributing code

Thanks for your interest in contributing code to pymc_bart!

If this is your first time contributing to a project on GitHub, please read through our step by step guide to contributing to pymc_bart

Local Development

  1. Create a virtual environment (optional, but strongly recommended)

  2. Install the library in editable mode

pip install -e .

Feature Branch

  1. From the fork of the pymc_bart repository, create a new branch for your feature.
git checkout -b feature_branch_name
  1. Make your changes to the code base.

3.Add and commit your changes.

git add my_modified_file.py
git commit -m "Added a new feature"
  1. Push your changes to your fork of the pymc_bart repository.
git push origin feature_branch_name

Code Style

The repository has some code style checks in place. This will happen on every commit of a pull request. If you want to run the checks locally, you can do so by running the following command from the root of the repository:

  1. Install pre-commit
pip install pre-commit
  1. Set up pre-commit
pre-commit install
  1. Run the complete pre-commit hook to check specific files:
pre-commit run --files pymc_bart/tree.py

or all files:

pre-commit run --all-files

Once you commit something the pre-commit hook will run all the checks!

In particular, if the commited changed have linting errors, the commit will try to fix them. If successful,you need to add the changes again (for example, git add -u) and commit again. If not successful, you need to fix the errors manually and commit again.

You can skip this (for example when is WIP) by adding a flag (-n means no-verify)

git commit -m"my message" -n

Pre-Commit Components

One can, of course, install ruff in the Python environment to enable auto-format (for example in VS Code), but this is not strictly necessary. The specific versions of ruff and mypy must be only specified in .pre-commit-config.yaml. It should be the only source of truth! Hence, if you want to install them locally make sure you use the same versions (revisions rev in the config file) as in the config file.

Ruff

Once installed locally as

pip install ruff==<VERSION>

You can check the lint as

ruff . --no-fix

You can allow ruff to fix the code by using the flag:

ruff . --fix

MyPy

We use mypy to check the type annotations. Once installed locally as

pip install mypy==<VERSION>

You also need the pandas-stubs library with the version specified in the .pre-commit-config.yaml file.

pip install pandas-stubs==<VERSION>

Now, you can check the type annotations as

mypy pymc_bart/.

Adding new features

If you are interested in adding a new feature to pymc_bart, first submit an issue using the "Feature Request" label for the community to discuss its place and implementation within pymc_bart.