Tom Chartrand

mergetool fails to save or download

2

Using nbdime 1.0.7 Seems related to issue #404 When I try to download or close the tool I get the warning "There are conflicts remaining. Do you still want to...

save_nodes fails to overwrite (nodes file already open)

1

When trying to modify and re-run a network interactively in ipython/jupyter, NetworkBuilder.save_nodes fails with the message (from h5py): ``IOError: Unable to create file (unable to truncate a file which is...

Should support setting dynamics_params for individual nodes, both at network building (saving to h5) and simulation instantiation (loading from h5).

The neuron VecStim definition, from vecevent.mod, is required to run a network with artificial cells created by bmtk - it would be great if it could be compiled and added...

[Feature]: method to report currently loaded namespace versions

1

### What would you like to see added to PyNWB? It would be great to have an easy method to report the currently active namespaces and their versions. Tracking down...

I think the install instructions are missing installing WGCNA from bioconductor? They say "several dependencies, including two from BioConductor and one from Github", but only list limma from bioconductor, and...

upgrade vitessce version?

3

I'm hoping that the pinned version of the core vitessce.js dependency can be updated sometime soon? In particular, this is because of the newer Anndata support (https://github.com/vitessce/vitessce/pull/1319), but in general...

Split core modules into new repository with minimal dependencies

2

**Describe the use case that is addressed by this feature.** It's currently impossible to simply PIP install IPFX due to complex dependency conflicts between IPFX and AllenSDK. The actual portions...

Change allow_hidden config default for easier hidden files access

1

### Problem It's still needlessly involved as a user to enable viewing hidden files from jupyter/jupyterlab, leading to issues like https://github.com/jupyterlab/jupyterlab/issues/13108. Since there is a UI setting to enable the...

Just noticed that the tutorial at https://taxonomy.shinyapps.io/scrattch_tutorial/ can't be run since it uses the old column names for tasic2016data, before the change https://github.com/AllenInstitute/tasic2016data/commit/17098ed8f1e2e22c74b6f32cfe764f4cf6a499ff