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CONTRIBUTING.md

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Contributing to Biofit

Biofit is an open source project, so all contributions and suggestions are welcome.

You can contribute in many different ways: giving ideas, answering questions, reporting bugs, proposing enhancements, improving the documentation, fixing bugs, and more.

Many thanks in advance to every contributor.

How to Work on an Open Issue?

You have the list of open Issues at: Biofit Issues

How to Create a Pull Request?

If you want to contribute to the codebase, follow these steps:

  1. Clone the Repository:

    Clone the dev branch of the repository to your local disk:

    git clone [email protected]:psmyth94/biofit
cd biofit

  2. Create a New Branch:

    Create a new branch to hold your development changes:

    git checkout -b a-descriptive-name-for-my-changes

    Do not work on the main branch directly.

  3. Set Up a Development Environment:

    Set up a development environment by running the following command:

    mamba env create -n biofit-local python=3.10
mamba activate biofit-local
pip install -e ".[test]"

    (If Biofit was already installed in the virtual environment, remove it with pip uninstall biofit before reinstalling it in editable mode with the -e flag.)

  4. Develop the Features on Your Branch:

    Make your changes to the code.

  5. Format Your Code:

    Format your code. Run ruff so that your newly added files look nice with the following command:

    ruff check . --fix

  6. (Optional) Use Pre-commit Hooks:

    You can also use pre-commit to format your code automatically each time you run git commit, instead of running ruff manually. To do this, install pre-commit via pip install pre-commit and then run pre-commit install in the project's root directory to set up the hooks. Note that if any files were formatted by pre-commit hooks during committing, you have to run git commit again.

  7. Commit Your Changes:

    Once you're happy with your contribution, add your changed files and make a commit to record your changes locally:

    git add -u
git commit -m "Your commit message"

  8. Sync with the Original Repository:

    It is a good idea to sync your copy of the code with the original repository regularly. This way you can quickly account for changes:

    git fetch upstream
git rebase upstream main

  9. Push the Changes:

    Once you are satisfied, push the changes to the remote repository using:

    git push origin a-descriptive-name-for-my-changes

  10. Create a Pull Request:

    Go to the webpage of the repository on GitHub. Click on "Pull request" to send your changes to the project maintainers for review.

Code of Conduct

This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to abide by this code.