Topographica is under very active development, but there are always more features that we have not yet been able to implement or bugs that we have not been able to address. These will be listed in our GitHub Issues list, or or in the issues for a specific subproject if appropriate. Feel free to add suggestions of your own to those lists, or to tackle one of the existing problems listed if you need that feature for your work. In particular, we are always happy to receive your (well-written) pull requests! Other general, ongoing tasks include:
There are a large number of relatively small problems noted in the source code for the simulator; these are marked with comments containing the string ALERT. These comments help clarify how the code should look when it is fully polished, and act as our to-do list. They also help prevent poor programming style from being propagated to other parts of the code before we have a chance to correct it. We are slowly working to correct these issues.
The reference manual is generated automatically from the source code, and needs significant attention to ensure that it is readable and consistent. For instance, not all parameters are documented yet, but all will need to be.
Topographica has a fairly complete test library, but there are still classes and functions without corresponding tests. Eventually, there should be tests for everything.
Topographica code is automatically checked using pyflakes, but more stringent tests can be performed by the pycheck and pylint programs. It would be very useful to fix any suspicious items reported by those programs, and to disable the remaining warnings. That way, new code could be automatically checked with those programs and the warnings would be likely to be meaningful. (Right now, the real issues detected by those programs are buried in a sea of spurious warnings.)
Much of the neural-specific code in Topographica was designed with visual areas in mind, but it is written generally so that it applies to any topographically organized region. Examples are provided for somatosensory inputs (e.g. rodent whisker barrels), auditory inputs, and motor outputs (for controlling eye movements) that show how to work with those modalities, but additional contributions for other types of sensory inputs or motor outputs would be very welcome from Topographica users with experience in these domains.
Topographica currently includes examples of each type of library component, such as Sheets, Projections, TransferFns, ResponseFunctions, LearningFunctions, and PatternGenerators. However, many other types are used in the literature, and as these are implemented in Topographica they will be added to the library. Again, user contributions are very welcome!
Topographica currently includes a number of example models, mostly from the visual system but also from somatosensory, auditory, and motor areas. As additional models are implemented, they will be added as examples and starting points. Again, user contributions are very welcome!