.. _contributing:

============
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 then please write short message on the issue tracker to prevent duplicate work.


Implement Features
==================

Look through the Github issues for features.
If you want to start working on an issue then please write short message on the issue tracker to prevent duplicate work.


Write Documentation
===================

MPRAsnakeflow could always use more documentation, even on the web in blog posts, articles, and such.

MPRAsnakeflow uses `Sphinx <https://www.sphinx-doc.org>`_ for the user documentation (that you are currently reading).
See `doc_guidelines` on how the documentation reStructuredText is used.
See `doc_setup` on 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 that contributions are welcome :)


.. _doc_guidelines:

------------------------
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
    :::::::::


.. _doc_setup:

-------------------
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:

.. code-block:: bash

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

Use the following for building the documentation.
The first two lines is only required for loading the virtualenv.
Afterwards, you can always use ``make html`` for building.

.. code-block:: bash

    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 Documentation development setup.

1. Fork the `MPRAsnakeflow` repo on GitHub (master branch).
2. Clone your fork locally::

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

3. 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 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

6. 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

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.