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://github.com/kircherlab/MPRAsnakeflow/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. If you want to start working on a bug, please write a short message on the issue tracker to prevent duplicate work.

Implement Features

Look through the GitHub issues for feature requests. If you want to start working on an issue, please write a short message on the issue tracker to prevent duplicate work.

Write Documentation

MPRAsnakeflow could always use more documentation, including on the web in blog posts, articles, and similar formats.

MPRAsnakeflow uses Sphinx for the user documentation (that you are currently reading). See doc_guidelines for how the documentation reStructuredText is used. See doc_setup for creating a local setup for building the documentation.

Submit Feedback

The best way to send feedback is to file an issue at https://github.com/kircherlab/MPRAsnakeflow/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 contributions are welcome :)

Documentation Guidelines

For the documentation, please adhere to the following guidelines:

Put each sentence on its own line. This makes tracking changes through Git SCM easier.
Provide hyperlink targets, at least for the first two section levels.
Use the section structure from below.

.. heading_1:

=========
Heading 1
=========

.. heading_2:

---------
Heading 2
---------

.. heading_3:

Heading 3
=========

.. heading_4:

Heading 4
---------

.. heading_5:

Heading 5
~~~~~~~~~

.. heading_6:

Heading 6
:::::::::

Documentation Setup

For building the documentation, you have to install the Python program Sphinx. This is best done in a virtual environment. We created a conda environment to work with the actual documentation.

Use the following steps for installing Sphinx and the dependencies for building the MPRAsnakeflow documentation:

cd MPRAsnakeflow/docs
conda env create -f environment.yml -n sphinx
conda activate sphinx

Use the following commands for building the documentation. The first two lines are only required for loading the virtual environment. Afterwards, you can always use make html for building.

cd MPRAsnakeflow/docs
conda activate sphinx
make html  # rebuild for changed files only
make clean && make html  # force rebuild

Get Started!

Ready to contribute? First, create your development setup.

Fork the MPRAsnakeflow repo on GitHub (master branch).

Clone your fork locally:

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

Create a branch for local development:
```
git checkout -b name-of-your-bugfix-or-feature
```
Now you can make your changes locally.
When you’re done making your changes, make sure that Snakemake runs properly by using a dry-run. For Snakemake:
```
snakemake --sdm conda --configfile config.yml -p -n
```
For documentation:
```
cd docs
make clean && make html
```

Commit your changes and push your branch to GitHub:

git add <your_new_file>  # or git stage <your_edited_file>
git commit -m "Your detailed description of your changes."
git push origin name-of-your-bugfix-or-feature

Submit a pull request through the GitHub website.

Pull Request Guidelines

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 documentation should be updated.
The pull request should pass all tests and checks.
Include a clear description of what the pull request does and why it is needed.