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Contributing to bsedic

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and here's what you need to know:

Contribution Agreement

Review the Contributor License Agreement (CLA). Whenever you submit a contribution to sed, you are agreeing to the CLA, which grants us rights to use your contribution. You don't need to do anything special to "sign" the CLA. Instead, opening a pull request indicates your agreement to the CLA.

Code of Conduct

We expect kindness and respect in all interactions with the BioSimulators community. Harassing or insulting behavior is not welcome and will result in enforcement actions. Please review our code of conduct, which describes our expectations and enforcement actions in more detail.

Contacting Us

To contact the maintainers privately (for example to report a violation of our code of conduct or to notify us of a security issue), you can use the contact information in the AUTHORS.md file.

Types of Contributions

You can contribute in many ways:

Report Bugs

Report bugs at https://github.com/biosimulators/sed/issues

If you are reporting a bug, please include:

  • Your operating system name and version.
  • Any details about your local setup that might be helpful in troubleshooting.
  • Detailed steps to reproduce the bug.

Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with "bug" and "help wanted" is open to whoever wants to implement a fix for it.

Implement Features

Look through the GitHub issues for features. Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it.

Write Documentation

sed could always use more documentation, whether as part of the official docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback

The best way to send feedback is to file an issue at https://github.com/biosimulators/sed/issues.

If you are proposing a new feature:

  • Explain in detail how it would work.
  • Keep the scope as narrow as possible, to make it easier to implement.
  • Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started!

Ready to contribute? Here's how to set up sed for local development. Please note this documentation assumes you already have uv and Git installed and ready to go.

  1. Fork the sed repo on GitHub.

  2. Clone your fork locally:

cd <directory_in_which_repo_should_be_created>
git clone git@github.com:YOUR_NAME/sed.git
  1. Now we need to install the environment. Navigate into the directory
cd sed

Then, install and activate the environment with:

uv sync
  1. Install pre-commit to run linters/formatters at commit time:
uv run pre-commit install
  1. Create a branch for local development:
git checkout -b name-of-your-bugfix-or-feature

Now you can make your changes locally.

  1. Don't forget to add test cases for your added functionality to the tests directory.

  2. When you're done making changes, check that your changes pass the formatting tests.

make check

Now, validate that all unit tests are passing:

make test
  1. Before raising a pull request you should also run tox. This will run the tests across different versions of Python:
tox

This requires you to have multiple versions of python installed. This step is also triggered in the CI/CD pipeline, so you could also choose to skip this step locally.

  1. Commit your changes and push your branch to GitHub:
git add .
git commit -m "Your detailed description of your changes."
git push origin name-of-your-bugfix-or-feature
  1. Submit a pull request through the GitHub website. Before you submit a pull request, check that it meets these guidelines:
  • The pull request should include tests.
  • If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.md.