See mne-tools/mne-python#6262 (comment) :

seeing this in a example I would suggest to add a method Covariance.plot_topomap(info) to display the topomap of diagonal. this would simplify this example a lot

This will hopefully just require some short function in mne/viz/topomap.py. Even using the EvokedArray approach seems okay since it's pretty straigh

Dollar signs entered into Builder loop nReps fields are being compiled to JS in the TrialHandler nReps parameter, causing a reference error in browsers, e.g., see Discourse post

Following what pytest-xdist does I think it would look nice to include a badge of Python versions. This is what ours looks like at the moment, and would appear both on PyPi and on the GitHub README:

https://img.shields.io/pypi/pyversions/nengo.svg

Reference:

A biexponential synapse, as per the Brian 2 documentation, should implement a current/conductance as g(t)=(tau2/(tau2-tau1))*(exp(-t/tau1)-exp(-t/tau2)).

When playing around with the biexponential synapse concept, I found that maybe the above description might need to be updated. Consider

import matplotlib as mpl
mpl.use('Agg')
import pylab as pl

import numpy as np
from b

Reported by @britta-wstnr by e-mail:

Documenting and taking it from here

1. we just came across some unexpected behavior (helping a student today) with ft_prepare_sourcemodel(). If we warp an MNI template, inwardshift has no effect - is that because that would shift grid points to the wrong positions after warping?

2. We often see problems with not inwardshifted sources when using the ope

From this paper

Wang, Lei, et al. "Beyond covariance: Feature representation with nonlinear kernel matrices." Proceedings of the IEEE International Conference on Computer Vision. 2015.

we can replace covariance by a kernel matrix. In our case, we could apply a kernel functi

There currently isn't any documentation or examples on how to use the the Fluorescence plugin for the PBRT rendering engine. Providing some example code / configurations using a neuron mesh exported from NeuroMorphoVis would be very useful.

I am currently writing a python pipeline that uses swc files from neurons generated in simulated neurite outgrowth generated by the DeNSE [https://github.co

Some is already in .gitignore, but some is not. We should check all examples.

ATM it seems I just need to point to this repository, which is IMHO suboptimal. Would be nice if there was at least some at least minimal website (e.g. on readthedocs) with rendered examples etc

Client libraries that wrap or heavily use DVID endpoints should mention (in their own documentation) which DVID endpoints they are wrapping/using. To that end, it would be nice if they could include links to the DVID documentation for various endpoints.

The DVID API is extensively documented via .../api/help, but there are couple of issues with the current scheme:

1. At the moment, the dv

Documentation needs care. Apart from issue #46, I spotted some minor corrections to make:

• In API, SSVEPExo() appears in MI datasets which is not correct. It is also correctly listed in SSVEP datasets
• Paradigms in API list only Motor Imagery, no ERP

His website is probably the best comp neuro resource outside of NIF. Should communicate with him and add everything he's found over the years to the list.

Add departments column and values for PIs at Stanford University

Right now, the logger sorts variables (columns) alphabetically. Some people prefer to have them sorted by the moment of their appearance instead, which practically speaking simply means to not sort them.

Currently BMTK will delete all files & subfolders in the output_dir as specified of a Sonata file:

 "output":{ 
    "output_dir": "$OUTPUT_DIR",
   ...
  }

including presumably the user's home directory if they specify that...

https://github.com/AllenInstitute/bmtk/blob/develop/bmtk/simulator/core/io_tools.py#L73

It would be better to only delete the files BMTK expects to gene

Dear ERPLAB developers,

I’ve got a question on erplab_shiftEventCodes and its documentation. In the documentation it says that the timeshift argument should contain in milliseconds how I want to shift my event code. So shifting it to 15 ms later, I should use 15 as the value. In the example in the documentation, however, the value for timeshift is given as 0.015 and the comment says that this s

Needs to allow for:

• hoc code should be read from string (See #143). hoc_path is not necessary anymore. Should be first argument after name.
• we need a morph_dir argument to specify morphology directory. when this is specified morph filename in hoc can be used.
• morph_filename, overwrite morph_filename specified in hoc
• hoc code should not have full path to morpho anymore (only morph_filename

• Documentation on how to build and view the sphinx docs
• More modular make clean-* recipes so that individual build targets can be cleaned before build (to prevent obsolete files hanging around)
• make recipes for file watching (install watchdog, watchmedo -R -D -p '*.rst' -c '$(MAKE) html'), and possibly file serving for development
  • If files are served, expose the por