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Contributing to SciPy
=====================
This document aims to give an overview of how to contribute to SciPy. It
tries to answer commonly asked questions, and provide some insight into how the
community process works in practice. Readers who are familiar with the SciPy
community and are experienced Python coders may want to jump straight to the
`git workflow`_ documentation.
Contributing new code
---------------------
If you have been working with the scientific Python toolstack for a while, you
probably have some code lying around of which you think "this could be useful
for others too". Perhaps it's a good idea then to contribute it to SciPy or
another open source project. The first question to ask is then, where does
this code belong? That question is hard to answer here, so we start with a
more specific one: *what code is suitable for putting into SciPy?*
Almost all of the new code added to scipy has in common that it's potentially
useful in multiple scientific domains and it fits in the scope of existing
scipy submodules. In principle new submodules can be added too, but this is
far less common. For code that is specific to a single application, there may
be an existing project that can use the code. Some scikits (`scikit-learn`_,
`scikits-image`_, `statsmodels`_, etc.) are good examples here; they have a
narrower focus and because of that more domain-specific code than SciPy.
Now if you have code that you would like to see included in SciPy, how do you
go about it? After checking that your code can be distributed in SciPy under a
compatible license (see FAQ for details), the first step is to discuss on the
scipy-dev mailing list. All new features, as well as changes to existing code,
are discussed and decided on there. You can, and probably should, already
start this discussion before your code is finished.
Assuming the outcome of the discussion on the mailing list is positive and you
have a function or piece of code that does what you need it to do, what next?
Before code is added to SciPy, it at least has to have good documentation, unit
tests and correct code style.
1. Unit tests
In principle you should aim to create unit tests that exercise all the code
that you are adding. This gives some degree of confidence that your code
runs correctly, also on Python versions and hardware or OSes that you don't
have available yourself. An extensive description of how to write unit
tests is given in the NumPy `testing guidelines`_.
2. Documentation
Clear and complete documentation is essential in order for users to be able
to find and understand the code. Documentation for individual functions
and classes -- which includes at least a basic description, type and
meaning of all parameters and returns values, and usage examples in
`doctest`_ format -- is put in docstrings. Those docstrings can be read
within the interpreter, and are compiled into a reference guide in html and
pdf format. Higher-level documentation for key (areas of) functionality is
provided in tutorial format and/or in module docstrings. A guide on how to
write documentation is given in `how to document`_.
3. Code style
Uniformity of style in which code is written is important to others trying
to understand the code. SciPy follows the standard Python guidelines for
code style, `PEP8`_. In order to check that your code conforms to PEP8,
you can use the `pep8 package`_ style checker. Most IDEs and text editors
have settings that can help you follow PEP8, for example by translating
tabs by four spaces. Using `pyflakes`_ to check your code is also a good
idea.
At the end of this document a checklist is given that may help to check if your
code fulfills all requirements for inclusion in SciPy.
Another question you may have is: *where exactly do I put my code*? To answer
this, it is useful to understand how the SciPy public API (application
programming interface) is defined. For most modules the API is two levels
deep, which means your new function should appear as
``scipy.submodule.my_new_func``. ``my_new_func`` can be put in an existing or
new file under ``/scipy/<submodule>/``, its name is added to the ``__all__``
dict in that file (which lists all public functions in the file), and those
public functions are then imported in ``/scipy/<submodule>/__init__.py``. Any
private functions/classes should have a leading underscore (``_``) in their
name. A more detailed description of what the public API of SciPy is, is given
in `SciPy API`_.
Once you think your code is ready for inclusion in SciPy, you can send a pull
request (PR) on Github. We won't go into the details of how to work with git
here, this is described well in the `git workflow`_ section of the NumPy
documentation and in the Github help pages. When you send the PR for a new
feature, be sure to also mention this on the scipy-dev mailing list. This can
prompt interested people to help review your PR. Assuming that you already got
positive feedback before on the general idea of your code/feature, the purpose
of the code review is to ensure that the code is correct, efficient and meets
the requirements outlined above. In many cases the code review happens
relatively quickly, but it's possible that it stalls. If you have addressed
all feedback already given, it's perfectly fine to ask on the mailing list
again for review (after a reasonable amount of time, say a couple of weeks, has
passed). Once the review is completed, the PR is merged into the "master"
branch of SciPy.
The above describes the requirements and process for adding code to SciPy. It
doesn't yet answer the question though how decisions are made exactly. The
basic answer is: decisions are made by consensus, by everyone who chooses to
participate in the discussion on the mailing list. This includes developers,
other users and yourself. Aiming for consensus in the discussion is important
-- SciPy is a project by and for the scientific Python community. In those
rare cases that agreement cannot be reached, the `maintainers`_ of the module
in question can decide the issue.
Contributing by helping maintain existing code
----------------------------------------------
The previous section talked specifically about adding new functionality to
SciPy. A large part of that discussion also applies to maintenance of existing
code. Maintenance means fixing bugs, improving code quality or style,
documenting existing functionality better, adding missing unit tests, keeping
build scripts up-to-date, etc. The SciPy `Trac`_ bug tracker contains all
reported bugs, build/documentation issues, etc. Fixing issues described in
Trac tickets helps improve the overall quality of SciPy, and is also a good way
of getting familiar with the project. You may also want to fix a bug because
you ran into it and need the function in question to work correctly.
The discussion on code style and unit testing above applies equally to bug
fixes. It is usually best to start by writing a unit test that shows the
problem, i.e. it should pass but doesn't. Once you have that, you can fix the
code so that the test does pass. That should be enough to send a PR for this
issue. Unlike when adding new code, discussing this on the mailing list may
not be necessary - if the old behavior of the code is clearly incorrect, no one
will object to having it fixed. It may be necessary to add some warning or
deprecation message for the changed behavior. This should be part of the
review process.
Other ways to contribute
------------------------
There are many ways to contribute other than contributing code. Participating
in discussions on the scipy-user and scipy-dev *mailing lists* is a contribution
in itself. The `scipy.org`_ *website* contains a lot of information on the
SciPy community and can always use a new pair of hands. A redesign of this
website is ongoing, see `scipy.github.com`_. The redesigned website is a
static site based on Sphinx, the sources for it are
also on Github at `scipy.org-new`_.
The SciPy *documentation* is constantly being improved by many developers and
users. You can contribute by sending a PR on Github that improves the
documentation, but there's also a `documentation wiki`_ that is very convenient
for making edits to docstrings (and doesn't require git knowledge). Anyone can
register a username on that wiki, ask on the scipy-dev mailing list for edit
rights and make edits. The documentation there is updated every day with the
latest changes in the SciPy master branch, and wiki edits are regularly
reviewed and merged into master. Another advantage of the documentation wiki
is that you can immediately see how the reStructuredText (reST) of docstrings
and other docs is rendered as html, so you can easily catch formatting errors.
Code that doesn't belong in SciPy itself or in another package but helps users
accomplish a certain task is valuable. `SciPy Central`_ is the place to share
this type of code (snippets, examples, plotting code, etc.).
Useful links, FAQ, checklist
----------------------------
Checklist before submitting a PR
````````````````````````````````
- Are there unit tests with good code coverage?
- Do all public function have docstrings including examples?
- Is the code style correct (PEP8, pyflakes)
- Is the new functionality tagged with ``.. versionadded:: X.Y.Z`` (with
X.Y.Z the version number of the next release - can be found in setup.py)?
- Is the new functionality mentioned in the release notes of the next
release?
- Is the new functionality added to the reference guide?
- In case of larger additions, is there a tutorial or more extensive
module-level description?
- In case compiled code is added, is it integrated correctly via setup.py
(and preferably also Bento/Numscons configuration files)?
- If you are a first-time contributor, did you add yourself to THANKS.txt?
Please note that this is perfectly normal and desirable - the aim is to
give every single contributor credit, and if you don't add yourself it's
simply extra work for the reviewer (or worse, the reviewer may forget).
- Did you check that the code can be distributed under a BSD license?
Useful SciPy documents
``````````````````````
- The `how to document`_ guidelines
- NumPy/SciPy `testing guidelines`_
- `SciPy API`_
- SciPy `maintainers`_
- NumPy/SciPy `git workflow`_
FAQ
```
*I based my code on existing Matlab/R/... code I found online, is this OK?*
It depends. SciPy is distributed under a BSD license, so if the code that you
based your code on is also BSD licensed or has a BSD-compatible license (MIT,
Apache, ...) then it's OK. Code which is GPL-licensed, has no clear license,
requires citation or is free for academic use only can't be included in SciPy.
Therefore if you copied existing code with such a license or made a direct
translation to Python of it, your code can't be included. See also `license
compatibility`_.
*How do I set up SciPy so I can edit files, run the tests and make commits?*
The simplest method is setting up an in-place build. To create your local git
repo and do the in-place build::
$ git clone https://github.com/scipy/scipy.git scipy
$ cd scipy
$ python setup.py build_ext -i
Then you need to either set up a symlink in your site-packages or add this
directory to your PYTHONPATH environment variable, so Python can find it. Some
IDEs (Spyder for example) have utilities to manage PYTHONPATH. On Linux and OS
X, you can for example edit your .bash_login file to automatically add this dir
on startup of your terminal. Add the line::
export PYTHONPATH="$HOME/scipy:${PYTHONPATH}"
Alternatively, to set up the symlink, use (prefix only necessary if you want to
use your local instead of global site-packages dir)::
$ python setupegg.py develop --prefix=${HOME}
To test that everything works, start the interpreter (not inside the scipy/
source dir) and run the tests::
$ python
>>> import scipy as sp
>>> sp.test()
Now editing a Python source file in SciPy allows you to immediately test and
use your changes, by simply restarting the interpreter.
Note that while the above procedure is the most straightforward way to get
started, you may want to look into using Bento or numscons for faster and more
flexible building, or virtualenv to maintain development environments for
multiple Python versions.
*How do I set up a development version of SciPy in parallel to a released
version that I use to do my job/research?*
One simple way to achieve this is to install the released version in
site-packages, by using a binary installer or pip for example, and set up the
development version with an in-place build in a virtualenv. First install
`virtualenv`_ and `virtualenvwrapper`_, then create your virtualenv (named
scipy-dev here) with::
$ mkvirtualenv scipy-dev
Now, whenever you want to switch to the virtual environment, you can use the
command ``workon scipy-dev``, while the command ``deactivate`` exits from the
virtual environment and brings back your previous shell. With scipy-dev
activated, follow the in-place build with the symlink install above to actually
install your development version of SciPy.
*Can I use a programming language other than Python to speed up my code?*
Yes. The languages used in SciPy are Python, Cython, C, C++ and Fortran. All
of these have their pros and cons. If Python really doesn't offer enough
performance, one of those languages can be used. Important concerns when
using compiled languages are maintainability and portability. For
maintainability, Cython is clearly preferred over C/C++/Fortran. Cython and C
are more portable than C++/Fortran. A lot of the existing C and Fortran code
in SciPy is older, battle-tested code that was only wrapped in (but not
specifically written for) Python/SciPy. Therefore the basic advice is: use
Cython. If there's specific reasons why C/C++/Fortran should be preferred,
please discuss those reasons first.
*There's overlap between Trac and Github, which do I use for what?*
Trac_ is the bug tracker, Github_ the code repository. Before the SciPy code
repository moved to Github, the preferred way to contribute code was to create
a patch and attach it to a Trac ticket. The overhead of this approach is much
larger than sending a PR on Github, so please don't do this anymore. Use Trac
for bug reports, Github for patches.
.. _scikit-learn: http://scikit-learn.org
.. _scikits-image: http://scikits-image.org/
.. _statsmodels: http://statsmodels.sourceforge.net/
.. _testing guidelines: https://github.com/numpy/numpy/blob/master/doc/TESTS.rst.txt
.. _how to document: https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt
.. _PEP8: http://www.python.org/dev/peps/pep-0008/
.. _pep8 package: http://pypi.python.org/pypi/pep8
.. _pyflakes: http://pypi.python.org/pypi/pyflakes
.. _SciPy API: http://docs.scipy.org/doc/scipy/reference/api.html
.. _git workflow: http://docs.scipy.org/doc/numpy/dev/gitwash/index.html
.. _maintainers: https://github.com/scipy/scipy/blob/master/doc/MAINTAINERS.rst.txt
.. _Trac: http://projects.scipy.org/scipy/timeline
.. _Github: https://github.com/scipy/scipy
.. _scipy.org: http://scipy.org/
.. _scipy.github.com: http://scipy.github.com/
.. _scipy.org-new: https://github.com/scipy/scipy.org-new
.. _documentation wiki: http://docs.scipy.org/scipy/Front%20Page/
.. _SciPy Central: http://scipy-central.org/
.. _license compatibility: http://www.scipy.org/License_Compatibility
.. _doctest: http://www.doughellmann.com/PyMOTW/doctest/
.. _virtualenv: http://www.virtualenv.org/
.. _virtualenvwrapper: http://www.doughellmann.com/projects/virtualenvwrapper/