Coding Guidelines for Topographica

This section covers general issues of how to write code to be included in Topographica. It includes general info on writing in Python and Python-specific conventions, plus Topographica-specific conventions such as guidelines for naming, comments, documentation, parameters, numerical units, and file extensions.

Coding in Python

If you are familiar with other programming languages, but not Python, the best place to start is to run the Python tutorial on the web site. On the first pass, don’t try to memorize anything, just try to get a feel for the overall syntax and workings of Python. Then try looking at the Topographica code. After working with Topographica a while, it is then a good idea to revisit the Python tutorial and go over it in more detail, trying to figure everything out and remember it now that the basic concepts are there.

For those with experience with functional programming languages like ML, Haskell, Scheme, or Lisp, you will be pleased to find features such as map, apply, reduce, filter, zip, and list comprehensions. For those who aren’t familiar with any of those, it is very important to study the “Functional Programming Tools” and “List Comprehensions” sections of the tutorial, because we often use those features to write concise functions that may be hard to understand at first glance. Lisp programmers should probably check out Python for Lisp Programmers for details of differences.

For those with experience in Java or C++, a good (opinionated) introduction is Python is not Java, and the Python and Java Side-by-side comparison may also be useful. For those without prior experience in any programming language, you are probably really a user, not a Topographica developer :-), but feel free to get started by learning Python.

General conventions

By default, the project uses the standard set of Python coding conventions written by Guido van Rossum, Python’s author.

These need not be followed to the letter; they simply help resolve differences between Topographica authors if there are disagreements.

One particular guideline of these that Jim does not always follow is that he likes to use lines much longer than 80 characters, e.g. for a string. Other differences are listed elsewhere in this file, such as in the revision control section.

To keep things simple and consistent, we try to use what seems to be the most common Python names for the following concepts (as opposed to those from C++ or Java):

(not ‘member function’ or ‘virtual function’)
(although ‘derived class’ is also ok)
(although ‘base class’ is also ok)

Typically, classes are named with InitialCapitalLetters, functions, methods, attributes, and parameters are lower_case_with_underscores, and filenames are

For whitespace, the convention is to use no more than one blank line within a function or method, two blank lines between methods, and three between classes. The goal is to have the code making up a function or method group visually into a single unit, and then to have all methods and data in one class group visually into a higher level unit. See the files in topo/base/ for examples.

All variable names, documentation, and comments should be in English, using American spelling for consistency.

Using consistent names

Where there are already classes defined, please use the existing names when writing new code, documentation, variable names, user messages, window names, and comments. (Or else change all of the old ones to match your new version!) For instance, Topographica is based on Sheets, so everything should call a Sheet a Sheet, not a Region, Area, or Layer.

In particular, when writing user interface code, think about what you are letting the user plot or manipulate, and ask whether that’s one of the concepts for which we have (laboriously!) worked out a specific term. Examples of acceptable, well-defined terms:


Examples of confusing, ambiguous terms to be avoided:

(Sheets only sometimes correspond to neural regions like V1)
(Same problem as Region)
(Used in too many different senses)
(Biology and neural-network people use it very differently)
(Implies a specific stimulus, which is not always true)
receptive field
(Only valid if plotted with reference to the external world)

As discussed elsewhere under general principles of object-oriented design, such undefined terms can be used in examples that bring in concepts from the world outside of Topographica, but they are not appropriate for variable or class names, documentation, or comments making up the Topographica simulator itself.

Communication: code, documentation, and comments

Writing Python code is similar to writing anything else: to do it well, you need to keep your intended audience in mind. There are three different audiences for the different types of material in a Python source file, and thus the guidelines for each category are different:

Program code: Communicating with the computer and the human reader

Program code tells the computer what to do, and needs to be written so that it is obvious to a human being what the computer is being told to do. This means using class, variable, function, and function argument names that say exactly what they are, and favoring short, clear bits of code rather than long, convoluted logic. For instance, any function longer than about a screenful should be broken up into more meaningful chunks that a human can understand.

Docstrings: Communicating with the user

Every file, class, function, and Parameter should have an appropriate docstring that says what that object does. The first line of the docstring should be a brief summary that fits into 80 columns. If there are additional lines, there should be an intervening blank line, followed by this more detailed discussion. For functions, the summary line should use the imperative voice, as in """Return the sum of all arguments.""". Such documentation is collected automatically for the online help and for the Reference manual, and must be written from the user’s perspective. I.e., the docstring must say how someone calling this function, class, etc. can use it, rather than having details about how it was implemented or its implementation history. These strings are used to create the reference manual, and are thus extremely important.

If you want to include structured text in your docstrings such as italics, bold, bulleted or numbered lists, hyperlinks, etc., please use the ReStructuredText format. That way the strings will be interpreted correctly when we generate the reference manual.

Comments: Communicating with the human reader

Comments (lines starting with #) are not processed by the computer, and are not visible to the user. Thus comments should consist of things that you want to be visible to someone reading the file to really understand how something is implemented. Usually such a person will either be (a) trying to fix a bug, or (b) trying to add a new feature. Thus the comments should be focused on what is needed for such readers. Please do not add redundant comments that simply describe what each statement does; the code itself documents that already. Redundant comments add more work for the reader, because they are usually out of date, and not necessarily accurate. Instead, please use comments for things that are not obvious, such as the reason a particular approach was chosen, descriptions of things that would be nice to add but haven’t been done yet, high-level explanations of a long section of low-level code, etc. Do not include information relevant to the user; such things go into docstrings.

To summarize, please use code, docstrings, and comments appropriately. Any bit of information you add to a file should go into the correct one of those three categories, and all files should be written to be usable by all three of the different intended audiences.

Parameters and bounds

When writing user-visible classes, attributes that are meant to be user-modifiable should be of class Parameter, so that they will be visible in the various user interfaces.

Parameters should have the narrowest type and tightest bounds that would be meaningful. For instance, a parameter that can be either true or false should be of type param.Boolean, while one that can only have a value from 0 to 0.5 should be of type param.Number with a hard bound of 0 to 0.5. Using the right types and bounds greatly simplifies life for the programmer, who can reason about the code knowing the full allowable range of the parameter, and for the user, who can tell what values make sense to use.

For Parameters that might show up in a GUI, soft bounds should also be included wherever appropriate. These bounds set the range of sliders, etc., and are a suggested range for the Parameter. If there are hard bounds at both ends, soft bounds are not usually needed, but can be useful if the reasonable range of the Parameter is much smaller than the legal range.

Parameters should each be documented with an appropriate docstring passed to the constructor. The documentation should be written from the user perspective, not the programmer’s, because it will appear in various online and other forms of user documentation.

Numerical units in the user interface

All quantities visible to the user, such as GUI labels, parameters, etc. must be in appropriate units that are independent of simulation or implementation details. For instance, all coordinates and subregions of Sheets must be in Sheet coordinates, not e.g. exposing the row and column in the underlying matrix. Similarly, unit specifiers should be in Sheet coordinates, selecting the nearest appropriate unit, not row and column.

Appropriate units for most parameters can be determined by considering the continuous plane underlying the discrete units forming the model sheet, and the continuous logical timeline behind the discrete timesteps in the model. Some parameters should be expressed in terms of lengths in that plane, some in terms of areas, and some in terms of volumes, rather than numbers of units, etc. Others are expressed in terms of lengths of time, rather than number of time steps. More information is available in Bednar et al, Neuroinformatics, 2004. There is usually only one correct answer for how to specify a particular parameter, so please discuss it with all, or at least with Jim, before picking a unit arbitrarily.

User-level and simulator code file extensions

By convention, we use a file extension of .py for the Python code making up the simulator, in the topo/ subdirectory. Models and other user-level code such as scripts and examples should use an extension of .ty, indicating that it is a file for use with Topographica. (Many of the .py files are general purpose, and could be used with any Python program, but the .ty files typically require all or most of Topographica.)

All .ty files should use only the publicly available classes and functions in topo/, i.e. they should respect the (as-yet-only-loosely-defined) Topographica API.

Typically, files organized around one main class will be named with the lowercase version of that main class. E.g. contains class Sheet and some associated functions. Often files will include not just one class but a superclass and several subclasses; such files are named after the superclass. Other files contain a number of thematically linked functions or classes, not necessarily a class hierarchy; these should be named for the principle or theme that relates them (as in

Accessing files and handling paths

There are two points to consider when referring to files or paths on the filesystem (which you would do, for instance, to open a file). The first is how relative paths are processed, and the second is differences in schemes for referring to paths on different operating systems.

Relative paths

While programming Topographica, you might wish to refer to a file somewhere within the Topographica distribution. For instance, the Topographica window icon is topo/tkgui/icons/topo.xbm. This path is relative to the topographica base path, so open('topo/tkgui/icons/topo.xbm') will successfully open the file only when the topographica base path is the operating system’s current working directory (e.g. when topographica was started from within its own directory, and the current working directory has not subsequently been changed).

To avoid this problem, simply use the functions param.resolve_path() (to locate an existing file) or param.normalize_path() (to prepare a path for writing). The example above would become open(resolve_path('topo/tkgui/icons/topo.xbm')); to create a file for writing, one could write open(normalize_path('topo/new_file.txt')). See the documentation for the two functions for more information.

Operating system differences

Topographica is used on various platforms, and one of these is Windows, which uses a different scheme for paths from the one used by linux and OS X. For instance, the path topo/tkgui/ is topo\tkgui\ on Windows. To ensure that Topographica runs on all platforms:

  1. Do not attempt to perform operations such as open on ‘raw’ linux-style paths. Instead, use one of the functions param.normalize_path() or param.resolve_path() (as described above).
  2. (For Windows developers) Never use Windows-style paths within the code: always specify paths in linux format. The above-mentioned functions correctly convert paths from linux to Windows, but do not handle the inverse conversion (in common with Python’s own path-handling functions).

Python itself provides a number of functions for dealing with paths in its os.path module. The functions above are based on those, but facilitate the use of ‘search paths’, allowing users to specify prefixes to search for relative paths.