DOC add contribution guidelines (#49)

add contribution guidelines

docs/source/usage/contributing.rst

@@ -1,5 +1,175 @@
 Contributing
 ------------
 
-PyDESeq2 is a living project and any contributions are welcome! The project is hosted on `Github <https://github.com/owkin/PyDESeq2>`_.
-Feel free to come and open new PRs or issues.
+PyDESeq2 is a living project and any contributions are welcome!
+The project is hosted on `Github <https://github.com/owkin/PyDESeq2>`_.
+
+You can help us by adding a star to the `PyDESeq2 repository <https://github.com/owkin/PyDESeq2>`_ on github or talk about
+our repository on the social media or on your blog or article.
+
+We also kindly ask you to follow the `Python code of conduct <https://www.python.org/psf/codeofconduct/>`_.
+
+If you find any bugs in the code please report them to the
+`issue tracker <https://github.com/owkin/PyDESeq2/issues>`_.
+
+How can I contribute?
+=====================
+- :ref:`bug`
+- :ref:`code_contrib`
+- :ref:`doc_contrib`
+- :ref:`answers`
+
+.. _bug:
+
+Submitting a bug or asking for a new feature
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+First, check if the issue which you are facing or the feature you would like to
+have added is not already described in the
+`issue tracker <https://github.com/owkin/PyDESeq2/issues>`_.
+If this is the case you can give a thumb up to that
+issue / feature. If there are multiple thumbs ups to a given issue it makes us
+prioritize it higher. You can also add a comment if you think there is something
+you would like to add to what have been said.
+
+If the issue / feature is not yet described make sure to give precise details on
+how you reached that issue (if possible giving code snippets) or precisely
+describe how the new feature should function. If it's an issue you should also
+mention which version of `pydeseq2` you are using. You can check this by running the following python code:
+
+.. code-block:: python
+
+    import pydeseq2
+    pydeseq2.__version__
+
+.. _code_contrib:
+
+Contributing to the code
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+Thanks for willing to help us out with the `pydeseq2` development.
+
+If you are contributing to an existing issue, add in the comment of that issue
+that you plan to contribute on it to avoid duplicate work. Once you start
+working on your pull request, link it to the issue by adding `#issue_number`
+
+1. To contribute, you will first need to fork the `Github <https://github.com/owkin/PyDESeq2>`_
+repository using the fork button in github. This will create a copy of
+`pydeseq2` on your github account (you must be logged in to github).
+
+1. clone the `pydeseq2` version from your account:
+
+.. code-block:: python
+
+    git clone git@github.com:<your-github-username>/pydeseq2.git
+    cd pydeseq2
+
+We recommend using conda environment, run:
+
+.. code-block:: bash
+
+    conda env create -n pydeseq2-dev python=3.8
+    conda activate pydeseq2-dev
+
+and then install `pydeseq2` in the development mode. This will also install all
+the required dependencies.
+
+.. code-block:: bash
+
+    pip install -e ."[dev]"
+    pre-commit install
+
+The pre-commit tool will automatically run `black` and `isort`, and check `flake8`
+compatibility
+
+3. Add the upstream remote:
+
+.. code-block:: bash
+
+    git remote add upstream [email protected]:owkin/pydeseq2.git
+
+4. Ensure that the origin and upstream are configured correctly by running:
+
+.. code-block:: bash
+
+    git remote -v
+
+you should see someting like this:
+
+.. code-block:: bash
+
+    origin  [email protected]:<your-github-username>/pydeseq2.git (fetch)
+    origin  [email protected]:<your-github-username>/pydeseq2.git (push)
+    upstream        [email protected]:owkin/pydeseq2.git (fetch)
+    upstream        [email protected]:owkin/pydeseq2.git (push)
+
+You are now all set and ready to start on your pull request (PR).
+
+5. Synchronize your branch with the upstream repository:
+
+.. code-block:: bash
+
+    git checkout main
+    git fetch upstream
+    git merge upstream/main --rebase
+
+6. Create a new branch where you will add your contributions:
+
+.. code-block:: bash
+
+    git checkout -b my_new_branch
+
+You can now make the changes commiting to your new branch. Each time you commit,
+the pre-commit will check for style in your code.
+
+7. Once you are ready to submit your PR, first make sure that all the changes
+   you have made are pushed into your github account:
+
+.. code-block:: bash
+
+    git push -u origin my_feature
+
+8. Now create a pull request from your fork by following those
+   `guidelines <https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request-from-a-fork>`_.
+   Ensure that the description of your PR is sufficient to understand what you
+   are doing in the code.
+   The core developers of `pydeseq2` will receive a message that your PR is
+   ready for reviews.
+
+9. You will need to respond to all the comments before your PR can be merged.
+   Thanks for your contribution.
+
+.. _doc_contrib:
+
+Improving the documentation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you wish to contribute to the documentation you need to follow the same
+guidelines as for the code PR (:ref:`code_contrib`) and additionally install the
+dependencies required for building the documentation.
+Once you have your environment for development ready, navigate to docs directory
+and install required libraries
+
+.. code-block:: bash
+
+    cd docs
+    pip install -r requirements.txt
+
+After you make the changes in the documentation you can check if it builds
+correctly by running (in the docs directory):
+
+.. code-block:: bash
+
+    make clean html
+
+If the build was correct you can now view the new document in the
+`docs/build/html` directory.
+
+.. _answers:
+
+PR reviews and answering questions on issues
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+You can also help us by reviewing an existing PR or by answering questions posed
+on the issue borad `issue tracker <https://github.com/owkin/PyDESeq2/issues>`_.
+
+Thanks again and happy contributing!