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:

Types of Contributions¶

Report Bugs¶

Report bugs at https://bitbucket.org/scilifelab-lts/lts-workflows-sm-scrnaseq/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 Bitbucket issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.

Implement Features¶

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

Write Documentation¶

lts_workflows_sm_scrnaseq could always use more documentation, whether as part of the official lts_workflows_sm_scrnaseq 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://bitbucket.org/scilifelab-lts/lts-workflows-sm-scrnaseq/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 lts_workflows_sm_scrnaseq for local development.

Fork the lts_workflows_sm_scrnaseq repo on Bitbucket.

Clone your fork locally:

.. code-block:: console

   $ git clone git@bitbucket.org:your_name_here/lts-workflows-sm-scrnaseq.git

Follow the instructions in Development to install a conda development environment and the package.

Create a branch for local development:

.. code-block:: console

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

Now you can make your changes locally.

When you’re done making changes, check that your changes pass flake8 and the tests:
```
$ make lint
$ pytest -v -s -rs
```

Commit your changes and push your branch to Bitbucket:

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

Submit a pull request through the Bitbucket website.

Pull Request Guidelines¶

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

The pull request should include tests (optional).
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 HISTORY.rst.
Check https://bitbucket.org/scilifelab-lts/lts-workflows-sm-scrnaseq/addon/pipelines/home and make sure that the CI tests pass.