DateFebruary 15, 2012

Neuronvisio 0.8.0 out in the wild

pyramidal_3D_change_voltage

A Pyramidal Neuron model visualized with Neuronvisio

We have just released a new version of Neuronvisio, which depends on Mayavi 4.1.x. All the goodies are described in the docs, but I want to highlight an aspect of this release which is pretty important.

When we have ported Neuronvisio, from Mayavi 3.4 to Mayavi 4.1.0, two regression bugs popped out: Issues #32 and Issue #34 .

The good thing about issue #34 was that it was gone in the 4.1.1.dev version of traitsui, therefore we had just to depend on the development snapshot, however the story was different for #32. The bug was difficult to replicate, and it seems to not be deterministic. After investigating the problem, I’ve managed to isolate and set up a Pull Request which actually fixes it https://github.com/enthought/mayavi/pull/23.

While the Pull Request was still to be accepted in the main tree of Mayavi, we wanted to distribute it out there, because Neuronvisio paper is under reviewing, and the Reviewers had several trouble to install the version 0.7.3, which depends on Mayavi 3.4. We managed to package both traitsui and Mayavi and make them as required dependencies of the new Neuronvisio, and using the special version requirement in the pavement, we could make the installation as automatic as possible.

All in all, to install the latest version of Neuronvisio, depending on the latest version of Traitsui and the patched version of Mayavi 4.1.1.dev a user has to run

pip install -U --extra-index-url=http://www.ebi.ac.uk/~mattioni/snapshots/ neuronvisio

which I think it’s pretty neat.

With the new version out, we didn’t want to remove the old docs, ’cause the version are quite different and same information applying to one version in particular. Some of our user may don’t want to update to the latest version, so we have now Neuronvisio docs hosted to the beautiful Read The Docs, at http://readthedocs.org/projects/neuronvisio/ where you can choose the docs according to the version.

How to fix github-tools when it doesn’t update the docs

Note to memory: when github-tools explodes and doesn’t work anymore, just double check the submodule in .gitsubmodule.

Remove it and recreate it.

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