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.
General discussion of Neo 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.
If you find a bug in Neo, 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 Neo, create a ticket with type “enhancement”. If you already have an implementation of the idea, create a patch (see below) and attach it to the ticket.
To keep track of changes to the code and to tickets, you can follow the RSS feed.
- Python 2.6, 2.7, 3.1 or 3.2
- numpy >= 1.3.0
- quantities >= 0.9.0
- nose >= 0.11.1
- if using Python 2.6 or 3.1, unittest2 >= 0.5.1
- Distribute >= 0.6
- Sphinx >= 0.6.4
- (optional) tox >= 0.9 (makes it easier to test with multiple Python versions)
- (optional) coverage >= 2.85 (for measuring test coverage)
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/python-neo (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>/python-neo.git
Now you need to make sure that the neo package is on your PYTHONPATH. You can do this either by installing Neo:
$ cd python-neo
$ python setup.py install
$ python3 setup.py install
(if you do this, you will have to re-run setup.py install any time you make changes to the code) or by creating symbolic links from somewhere on your PYTHONPATH, for example:
$ ln -s python-neo/neo
$ export PYTHONPATH=/some/directory:${PYTHONPATH}
An alternate solution is to install Neo with the develop option, this avoids reinstalling when there are changes in the code:
$ sudo python setup.py develop
To update to the latest version from the repository:
$ git pull
Before you make any changes, run the test suite to make sure all the tests pass on your system:
$ cd neo/test
With Python 2.7 or 3.2:
$ 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.
To run tests from an individual file:
$ python test_analogsignal.py
$ python3 test_analogsignal.py
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=neo --cover-erase
The documentation is written in reStructuredText, using the Sphinx documentation system. To build the documentation:
$ cd python-neo/doc
$ make html
Then open some/directory/neo_trunk/doc/build/html/index.html in your browser.
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 Neo repository, open a pull request on GitHub (see https://help.github.com/articles/using-pull-requests).
Neo core should work with both recent versions of Python 2 (versions 2.6 and 2.7) and Python 3. Neo IO modules should ideally work with both Python 2 and 3, but certain modules may only work with one or the other (see :doc:install).
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.
All code should conform as much as possible to PEP 8, and should run with Python 2.6, 2.7, 3.1 and 3.2.
First check that the version string (in neo/version.py, setup.py and doc/conf.py) is correct.
To build a source package:
$ python setup.py sdist
To upload the package to PyPI (currently Samuel Garcia and Andrew Davison have the necessary permissions to do this):
$ python setup.py sdist upload
$ python setup.py upload_docs --upload-dir=doc/build/html
Finally, tag the release in the Git repository:
$ git tag <version>
See IO developers’ guide for implementation of a new IO.