Welcome to gloria_soria_ddRAD_2015’s documentation!

Contents:

Overview

gloria_soria_ddRAD_2015

Code supporting the Gloria-Soria et al 2015 paper on tsetse population genomics using ddRAD seq.

  • Free software: BSD license

Installation

pip install git+https://github.com/CacconeLabYale/gloria_soria_ddRAD_2015.git

Installation

At the command line:

pip install git+https://github.com/CacconeLabYale/gloria_soria_ddRAD_2015.git

Usage

To use gloria_soria_ddRAD_2015 in a project:

import gs_ddRAD2015

To use gloria_soria_ddRAD_2015 from the command line:

$ gs_ddRAD2015 --help

This will yield the help text:

$ gs_ddRAD2015 --help
Usage: gs_ddRAD2015 [OPTIONS] COMMAND [ARGS]...

  Command interface to the paper's LD analysis.

  For command specific help text, call the specific command followed by the
  --help option.

Options:
  --config FILENAME  Path to optional config.yaml
  --help             Show this message and exit.

Commands:
  ld_figures       Generates LD figures.
  process_ld_data  Performs the LD analysis.

Reference

gs_ddRAD2015

Contributing

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

Bug reports

When 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.

Documentation improvements

gloria_soria_ddRAD_2015 could always use more documentation, whether as part of the official gloria_soria_ddRAD_2015 docs, in docstrings, or even on the web in blog posts, articles, and such.

Feature requests and feedback

The best way to send feedback is to file an issue at https://github.com/CacconeLabYale/gloria_soria_ddRAD_2015/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 :)

Development

To set up gloria_soria_ddRAD_2015 for local development:

  1. Fork gloria_soria_ddRAD_2015 on GitHub.

  2. Clone your fork locally:

    git clone git@github.com:your_name_here/gloria_soria_ddRAD_2015.git

  3. Create a branch for local development:

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

    Now you can make your changes locally.

  4. When you’re done making changes, run all the checks, doc builder and spell checker with tox one command:

    tox

  5. 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

  6. Submit a pull request through the GitHub website.

Pull Request Guidelines

If you need some code review or feedback while you’re developing the code just make the pull request.

For merging, you should:

  1. Include passing tests (run tox) [1].
  2. Update documentation when there’s new API, functionality etc.
  3. Add a note to CHANGELOG.rst about the changes.
  4. Add yourself to AUTHORS.rst.
[1]

If you don’t have all the necessary python versions available locally you can rely on Travis - it will run the tests for each change you add in the pull request.

It will be slower though ...

Tips

To run a subset of tests:

tox -e envname -- py.test -k test_myfeature

To run all the test environments in parallel (you need to pip install detox):

detox

Changelog

0.1.0 (2015-02-04)

  • First release on PyPI.

Indices and tables