Developers’ guide

These instructions are for developing on a Unix-like platform, e.g. Linux or Mac OS X, with the bash shell. If you develop on Windows, please get in touch.

Mailing lists

General discussion of Elephant development takes place in the NeuralEnsemble Google group.

Discussion of issues specific to a particular ticket in the issue tracker should take place on the tracker.

Using the issue tracker

If you find a bug in Elephant, please create a new ticket on the issue tracker, setting the type to “defect”. Choose a name that is as specific as possible to the problem you’ve found, and in the description give as much information as you think is necessary to recreate the problem. The best way to do this is to create the shortest possible Python script that demonstrates the problem, and attach the file to the ticket.

If you have an idea for an improvement to Elephant, create a ticket with type “enhancement”. If you already have an implementation of the idea, open a pull request.

Requirements

See Prerequisites / Installation. We strongly recommend using virtualenv or similar.

Getting the source code

We use the Git version control system. The best way to contribute is through GitHub. You will first need a GitHub account, and you should then fork the repository at https://github.com/NeuralEnsemble/elephant (see http://help.github.com/fork-a-repo/).

To get a local copy of the repository:

$ cd /some/directory
$ git clone git@github.com:<username>/elephant.git

Now you need to make sure that the elephant package is on your PYTHONPATH. You can do this by installing Elephant:

$ cd elephant
$ python setup.py install
$ python3 setup.py install

but if you do this, you will have to re-run setup.py install any time you make changes to the code. A better solution is to install Elephant with the develop option, this avoids reinstalling when there are changes in the code:

$ python setup.py develop

or:

$ pip install -e .

To update to the latest version from the repository:

$ git pull

Running the test suite

Before you make any changes, run the test suite to make sure all the tests pass on your system:

$ cd elephant/test

With Python 2.7 or 3.x:

$ python -m unittest discover
$ python3 -m unittest discover

If you have nose installed:

$ nosetests

At the end, if you see “OK”, then all the tests passed (or were skipped because certain dependencies are not installed), otherwise it will report on tests that failed or produced errors.

Writing tests

You should try to write automated tests for any new code that you add. If you have found a bug and want to fix it, first write a test that isolates the bug (and that therefore fails with the existing codebase). Then apply your fix and check that the test now passes.

To see how well the tests cover the code base, run:

$ nosetests --with-coverage --cover-package=elephant --cover-erase

Working on the documentation

The documentation is written in reStructuredText, using the Sphinx documentation system. To build the documentation:

$ cd elephant/doc
$ make html

Then open some/directory/elephant/doc/_build/html/index.html in your browser. Docstrings should conform to the NumPy docstring standard.

To check that all example code in the documentation is correct, run:

$ make doctest

To check that all URLs in the documentation are correct, run:

$ make linkcheck

Committing your changes

Once you are happy with your changes, run the test suite again to check that you have not introduced any new bugs. Then you can commit them to your local repository:

$ git commit -m 'informative commit message'

If this is your first commit to the project, please add your name and affiliation/employer to doc/source/authors.rst

You can then push your changes to your online repository on GitHub:

$ git push

Once you think your changes are ready to be included in the main Elephant repository, open a pull request on GitHub (see https://help.github.com/articles/using-pull-requests).

Python 3

Elephant should work with Python 2.7 and Python 3.

So far, we have managed to write code that works with both Python 2 and 3. Mainly this involves avoiding the print statement (use logging.info instead), and putting from __future__ import division at the beginning of any file that uses division.

If in doubt, Porting to Python 3 by Lennart Regebro is an excellent resource.

The most important thing to remember is to run tests with at least one version of Python 2 and at least one version of Python 3. There is generally no problem in having multiple versions of Python installed on your computer at once: e.g., on Ubuntu Python 2 is available as python and Python 3 as python3, while on Arch Linux Python 2 is python2 and Python 3 python. See PEP394 for more on this.

Coding standards and style

All code should conform as much as possible to PEP 8, and should run with Python 2.7 and 3.2-3.5.

Making a release

First check that the version string (in elephant/__init__.py, setup.py, doc/conf.py and doc/install.rst) is correct.

To build a source package:

$ python setup.py sdist

To upload the package to PyPI (if you have the necessary permissions):

$ python setup.py sdist upload

Finally, tag the release in the Git repository and push it:

$ git tag <version>
$ git push --tags upstream