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Contributing to POT
===================
First off, thank you for considering contributing to POT.
How to contribute
-----------------
The preferred workflow for contributing to POT is to fork the
[main repository](https://github.com/rflamary/POT) on
GitHub, clone, and develop on a branch. Steps:
1. Fork the [project repository](https://github.com/rflamary/POT)
by clicking on the 'Fork' button near the top right of the page. This creates
a copy of the code under your GitHub user account. For more details on
how to fork a repository see [this guide](https://help.github.com/articles/fork-a-repo/).
2. Clone your fork of the POT repo from your GitHub account to your local disk:
```bash
$ git clone git@github.com:YourLogin/POT.git
$ cd POT
```
3. Create a ``feature`` branch to hold your development changes:
```bash
$ git checkout -b my-feature
```
Always use a ``feature`` branch. It's good practice to never work on the ``master`` branch!
4. Develop the feature on your feature branch. Add changed files using ``git add`` and then ``git commit`` files:
```bash
$ git add modified_files
$ git commit
```
to record your changes in Git, then push the changes to your GitHub account with:
```bash
$ git push -u origin my-feature
```
5. Follow [these instructions](https://help.github.com/articles/creating-a-pull-request-from-a-fork)
to create a pull request from your fork. This will send an email to the committers.
(If any of the above seems like magic to you, please look up the
[Git documentation](https://git-scm.com/documentation) on the web, or ask a friend or another contributor for help.)
Pull Request Checklist
----------------------
We recommended that your contribution complies with the
following rules before you submit a pull request:
- Follow the PEP8 Guidelines.
- If your pull request addresses an issue, please use the pull request title
to describe the issue and mention the issue number in the pull request description. This will make sure a link back to the original issue is
created.
- All public methods should have informative docstrings with sample
usage presented as doctests when appropriate.
- Please prefix the title of your pull request with `[MRG]` (Ready for
Merge), if the contribution is complete and ready for a detailed review.
Two core developers will review your code and change the prefix of the pull
request to `[MRG + 1]` and `[MRG + 2]` on approval, making it eligible
for merging. An incomplete contribution -- where you expect to do more work before
receiving a full review -- should be prefixed `[WIP]` (to indicate a work
in progress) and changed to `[MRG]` when it matures. WIPs may be useful
to: indicate you are working on something to avoid duplicated work,
request broad review of functionality or API, or seek collaborators.
WIPs often benefit from the inclusion of a
[task list](https://github.com/blog/1375-task-lists-in-gfm-issues-pulls-comments)
in the PR description.
- When adding additional functionality, provide at least one
example script in the ``examples/`` folder. Have a look at other
examples for reference. Examples should demonstrate why the new
functionality is useful in practice and, if possible, compare it
to other methods available in POT.
- Documentation and high-coverage tests are necessary for enhancements to be
accepted. Bug-fixes or new features should be provided with
[non-regression tests](https://en.wikipedia.org/wiki/Non-regression_testing).
These tests verify the correct behavior of the fix or feature. In this
manner, further modifications on the code base are granted to be consistent
with the desired behavior.
For the Bug-fixes case, at the time of the PR, this tests should fail for
the code base in master and pass for the PR code.
- At least one paragraph of narrative documentation with links to
references in the literature (with PDF links when possible) and
the example.
You can also check for common programming errors with the following
tools:
- No pyflakes warnings, check with:
```bash
$ pip install pyflakes
$ pyflakes path/to/module.py
```
- No PEP8 warnings, check with:
```bash
$ pip install pep8
$ pep8 path/to/module.py
```
- AutoPEP8 can help you fix some of the easy redundant errors:
```bash
$ pip install autopep8
$ autopep8 path/to/pep8.py
```
Bonus points for contributions that include a performance analysis with
a benchmark script and profiling output (please report on the mailing
list or on the GitHub issue).
Filing bugs
-----------
We use Github issues to track all bugs and feature requests; feel free to
open an issue if you have found a bug or wish to see a feature implemented.
It is recommended to check that your issue complies with the
following rules before submitting:
- Verify that your issue is not being currently addressed by other
[issues](https://github.com/rflamary/POT/issues?q=)
or [pull requests](https://github.com/rflamary/POT/pulls?q=).
- Please ensure all code snippets and error messages are formatted in
appropriate code blocks.
See [Creating and highlighting code blocks](https://help.github.com/articles/creating-and-highlighting-code-blocks).
- Please include your operating system type and version number, as well
as your Python, POT, numpy, and scipy versions. This information
can be found by running the following code snippet:
```python
import platform; print(platform.platform())
import sys; print("Python", sys.version)
import numpy; print("NumPy", numpy.__version__)
import scipy; print("SciPy", scipy.__version__)
import ot; print("POT", ot.__version__)
```
- Please be specific about what estimators and/or functions are involved
and the shape of the data, as appropriate; please include a
[reproducible](http://stackoverflow.com/help/mcve) code snippet
or link to a [gist](https://gist.github.com). If an exception is raised,
please provide the traceback.
New contributor tips
--------------------
A great way to start contributing to POT is to pick an item
from the list of [Easy issues](https://github.com/rflamary/POT/issues?labels=Easy)
in the issue tracker. Resolving these issues allow you to start
contributing to the project without much prior knowledge. Your
assistance in this area will be greatly appreciated by the more
experienced developers as it helps free up their time to concentrate on
other issues.
Documentation
-------------
We are glad to accept any sort of documentation: function docstrings,
reStructuredText documents (like this one), tutorials, etc.
reStructuredText documents live in the source code repository under the
doc/ directory.
You can edit the documentation using any text editor and then generate
the HTML output by typing ``make html`` from the doc/ directory.
Alternatively, ``make`` can be used to quickly generate the
documentation without the example gallery. The resulting HTML files will
be placed in ``_build/html/`` and are viewable in a web browser. See the
``README`` file in the ``doc/`` directory for more information.
For building the documentation, you will need
[sphinx](http://sphinx.pocoo.org/),
[matplotlib](http://matplotlib.org/), and
[pillow](http://pillow.readthedocs.io/en/latest/).
When you are writing documentation, it is important to keep a good
compromise between mathematical and algorithmic details, and give
intuition to the reader on what the algorithm does. It is best to always
start with a small paragraph with a hand-waving explanation of what the
method does to the data and a figure (coming from an example)
illustrating it.
This Contribution guide is strongly inpired by the one of the [scikit-learn](https://github.com/scikit-learn/scikit-learn) team.
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