Contributing

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

You can contribute in many ways:

Allen Institute Contribution Agreement

This document describes the terms under which you may make “Contributions” — which may include without limitation, software additions, revisions, bug fixes, configuration changes, documentation, or any other materials — to any of the projects owned or managed by the Allen Institute. If you have questions about these terms, please contact us at terms@alleninstitute.org.

You certify that:

  • Your Contributions are either:
  1. Created in whole or in part by you and you have the right to submit them under the designated license (described below); or
  2. Based upon previous work that, to the best of your knowledge, is covered under an appropriate open source license and you have the right under that license to submit that work with modifications, whether created in whole or in part by you, under the designated license; or
  3. Provided directly to you by some other person who certified (1) or (2) and you have not modified them.
  • You are granting your Contributions to the Allen Institute under the terms of the [2-Clause BSD license](https://opensource.org/licenses/BSD-2-Clause) (the “designated license”).
  • You understand and agree that the Allen Institute projects and your Contributions are public and that a record of the Contributions (including all metadata and personal information you submit with them) is maintained indefinitely and may be redistributed consistent with the Allen Institute’s mission and the 2-Clause BSD license.

Types of Contributions

Report Bugs

Report bugs at https://github.com/AllenCellModeling/brightfield2fish/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 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

brightfield2fish could always use more documentation, whether as part of the official brightfield2fish 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/AllenCellModeling/brightfield2fish/issues.

If you are proposing a 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 brightfield2fish for local development.

  1. Fork the brightfield2fish repo on GitHub.

  2. Clone your fork locally:

    $ git clone git@github.com:your_name_here/brightfield2fish.git

  3. Install your local copy into an anaconda environment (or virtualenv). Assuming you have anaconda installed, this is how you set up your fork for local development:

    $ conda create --name brightfield2fish python=3.6
$ conda activate brightfield2fish
$ cd brightfield2fish/
$ pip install -e .[test]
$ pip install -e .[dev]
$ pre-commit install

  4. Create a branch for local development:

    $ git checkout -b name-of-your-bugfix-or-feature

    Now you can make your changes locally.

  5. When you’re done making changes, check that your changes pass the tests, including testing other Python versions with tox:

    $ make test-all

  6. Commit your changes and push your branch to GitHub:

    $ git add .
$ git commit -m "Resolves gh-###. Your detailed description of your changes."
$ git push origin name-of-your-bugfix-or-feature

    black (a formatter) and flake8 (a linter) should run as pre-commit hooks, and will prevent the code from being commited until it passes these standards. You may need to edit you code and git add it again until it passes and the commit is logged.

  7. Submit a pull request through the GitHub website.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

  1. The pull request should include tests.
  2. 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.rst.
  3. The pull request should work for Python 3.6 and 3.7, and for PyPy. Check https://travis-ci.org/AllenCellModeling/brightfield2fish/pull_requests and make sure that the tests pass for all supported Python versions.

Tips

To run a subset of tests:

$ py.test tests.test_brightfield2fish

Deploying

A reminder for the maintainers on how to deploy. Make sure all your changes are committed (including an entry in HISTORY.rst). Then run:

$ bumpversion patch # possible: major / minor / patch
$ git push
$ git push --tags

Travis will then deploy to PyPI if tests pass.