Coding conventions

General recommendations

Syntax is chosen as much as possible from the user point of view, to reflect the concepts as directly as possible. Ideally, a Brian script should be readable by someone who doesn’t know Python or Brian, although this isn’t always possible. Function, class and keyword argument names should be explicit rather than abbreviated and consistent across Brian. See Romain’s paper On the design of script languages for neural simulators for a discussion.

We use the PEP-8 coding conventions for our code. This in particular includes the following conventions:

  • Use 4 spaces instead of tabs per indentation level

  • Use spaces after commas and around the following binary operators: assignment (=), augmented assignment (+=, -= etc.), comparisons (==, <, >, !=, <>, <=, >=, in, not in, is, is not), Booleans (and, or, not).

  • Do not use spaces around the equals sign in keyword arguments or when specifying default values. Neither put spaces immediately inside parentheses, brackets or braces, immediately before the open parenthesis that starts the argument list of a function call, or immediately before the open parenthesis that starts an indexing or slicing.

  • Avoid using a backslash for continuing lines whenever possible, instead use Python’s implicit line joining inside parentheses, brackets and braces.

  • The core code should only contain ASCII characters, no encoding has to be declared

  • imports should be on different lines (e.g. do not use import sys, os) and should be grouped in the following order, using blank lines between each group:

    1. standard library imports
    2. third-party library imports (e.g. numpy, scipy, sympy, …)
    3. brian imports
  • Use absolute imports for everything outside of “your” package, e.g. if you are working in brian2.equations, import functions from the stringtools modules via from brian2.utils.stringtools import .... Use the full path when importing, e.g. do from brian2.units.fundamentalunits import seconds instead of from brian2 import seconds.

  • Use “new-style” relative imports for everything in “your” package, e.g. in import the Function class as from .specifiers import Function.

  • Do not use wildcard imports (from brian2 import *), instead import only the identifiers you need, e.g. from brian2 import NeuronGroup, Synapses. For packages like numpy that are used a lot, use import numpy as np. But note that the user should still be able to do something like from brian2 import * (and this style can also be freely used in examples and tests, for example). Modules always have to use the __all__ mechanism to specify what is being made available with a wildcard import. As an exception from this rule, the main brian2/ may use wildcard imports.

Python 2 vs. Python 3

Brian is written in Python 2 but runs on Python 3 using the 2to3 conversion tool (which is automatically applied if Brian is installed using the standard python install mechanism). To make this possible without too much effort, Brian no longer supports Python 2.5 and can therefore make use of a couple of forward-compatible (but backward-incompatible) idioms introduced in Python 2.6. The Porting to Python 3 book is available online and has a lot of information on these topics. Here are some things to keep in mind when developing Brian:

  • If you are working with integers and using division, consider using // for flooring division (default behaviour for / in python 2) and switch the behaviour of / to floating point division by using from __future__ import division .
  • If importing modules from the standard library (which have changed quite a bit from Python 2 to Python 3), only use simple import statements like import itertools instead of from itertools import izip2to3 is otherwise unable to make the correct conversion.
  • If you are using the print statement (which should only occur in tests, in particular doctests – always use the Logging framework if you want to present messages to the user otherwise), try “cheating” and use the functional style in Python 2, i.e. write print('some text') instead of print 'some text'. More complicated print statements should be avoided, e.g instead of print >>sys.stderr, 'Error message use sys.stderr.write('Error message\n') (or, again, use logging).
  • Exception stacktraces look a bit different in Python 2 and 3: For non-standard exceptions, Python 2 only prints the Exception class name (e.g. DimensionMismatchError) whereas Python 3 prints the name including the module name (e.g. brian2.units.fundamentalunits.DimensionMismatchError). This will make doctests fail that match the exception message. In this case, write the doctest in the style of Python 2 but add the doctest directive #doctest: +IGNORE_EXCEPTION_DETAIL to the statement leading to the exception. This unfortunately has the side effect of also ignoring the text of the exception, but it will still fail for an incorrect exception type.
  • If you write code reading and writing strings to files, make sure you make the distinction between bytes and unicode (see “separate binary data and strings” ) In general, strings within Brian are unicode strings and only converted to bytes when reading from or writing to a file (or something like a network stream, for example).
  • If you are sorting lists or dictionaries, have a look at “when sorting, use key instead of cmp”
  • Make sure to define a __hash__ function for objects that define an __eq__ function (and to define it consistently). Python 3 is more strict about this, an object with __eq__ but without __hash__ is unhashable.