Reporting specific problems with TopographicaΒΆ

Topographica is used actively in research, and is thus continuously changing, which inevitably adds new problems as old ones are fixed and new features are added. When you have found what appears to be a problem with Topographica itself (whether a bug or a missing feature), please try the following:

  1. If you are using a version that is more than a few weeks old, consider trying the most up to date (“bleeding-edge”) version via Git. The code is updated nearly every day, so by the end of a few weeks many changes will have accumulated. Often, bugs will have been fixed and new features will have been added already in the Git repository, even though they are not yet released officially.

  2. If the problem is still present in the current version, you can search the list of issues on our project pages at GitHub to see if we already know about the problem. Issues are stored separately for each subproject (Param, ParamTk, ImaGen (aliased to topo.pattern in Topographica), or FeatureMapper). If you find your issue has already been reported, please feel free to add additional comments to the report.

  3. If you can locate where in the code there might be a problem (e.g. by going to the line numbers mentioned in a Python exception), you will often find a comment with the keyword “ALERT” beside the code. These notes are used to mark problems of which we are aware but have not yet been able to address. If so, please let us know that fixing the problem is urgent, and/or suggest fixes for the offending code.

  4. If you can can suggest specfic code to fix the problem you found, we are happy to receive GitHub pull requests. Simple fixes can then be applied very quickly, and you’ll be marked as having contributed the fix! You can also submit new features this way, and after we verify that the code fits our guidelines we can incorporate it into the official repositories.

  5. Otherwise, please create a new issue at the appropriate project site (defaulting to Topographica if you aren’t sure where the problem arises). If possible, please include:

    • the full error message, if any

    • if you are not using Git (i.e. you downloaded a released version), please include the Topographica release number (you can obtain this by starting Topographica and typing topo.release)

    • if you are using Git, please include the output of git diff, git status, and git describe; you can create a single file (report) containing this information with the following command:

      git describe > report; git status >> report; git diff >> report
    • which operating system (OS) you are using (Linux, Mac, or Windows) and which OS version

    • any additional file needed to replicate the problem (e.g. a script you’re using)

    • a specific recipe (list of steps) that can reproduce the problem

    To maximize the speed of resolution, please make sure that your problem can be replicated using an unmodified copy of Topographica (either released or from Git), and try to have a small, clear, quick-to-run example of the problem. Any bug report is better than none, so in any case please do send it in even if you can’t satisfy the above requests. In any case, the clearer and simpler it is, the more likely (and more quickly) we will be able to address the problem.

  6. If you get no reply after a few days, you can try emailing Jim directly, in case there was some problem with the email notification from the issue tracking system. But it’s much more effective to use the issue tracking, which automatically delivers the appropriate messages to the appropriate developers.