Robert A McDougal

rxd reaction compilation fails with Anaconda on Windows if User Name has a space

17

## Context ### Overview of the issue I have access to a windows machine where my username has a space in it. When attempting to run an rxd simulation with...

Meaningful Python types

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We want `h.Vector()` to return an object with a different data type than `h.Deck()`. In current NEURON, they both are of type `hoc.HocObject`. Likewise for all other built-in NEURON classes....

NEURON documentation plan

2

Everything here is subject to discussion, but here's an attempt at identifying documentation TODOs both in general and to migrate the key content onto the readthedocs site. There are many...

basic NetCon graph in ModelView

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Selecting the "### NetCon objects" in a ModelView shows a graph of the pre/post NetCon relationships by cell. e.g. for the model of Short et al., 2016 (http://modeldb.yale.edu/183300) This works...

In particular, https://nrn.readthedocs.io/en/latest/hoc/modelspec/programmatic/mechanisms/nmodl.html uses the assign to the thing on the right syntax h.setpointer(axon(1)._ref_v, 'vpre', syn) Instead of the shorter: syn._ref_vpre = axon(1)._ref_v We need to keep documentation of `setpointer`...

GH issue template: documentation

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## Overview of the feature We should add a template for suggesting documentation requests. This could include an overview, the location of the page(s) involved, information on how the changes...

nrnivmodl allows unclosed safe CURIEs

1

nrnivmodl correctly compiles each of - `USEION na READ ena WRITE ina REPRESENTS [CHEBI:29101]` - `USEION na READ ena WRITE ina REPRESENTS CHEBI:29101` correctly only looks for ONTOLOGY_IDs after a...

NEURON provides its own home-brewed units submodule which consists solely of scale factors. This was added primarily for rxd, but is useful for e.g. `h.continuerun(50 * ms)`. It might be...

annotation of signatures in documentation

2

Parts of the Vector class updated to include the signatures in the header and a smaller part updated to use `:param:` etc. Also moved the order of some of the...

Sometimes on a Mac with e.g. Anaconda installed which pip and which python might point to different Pythons (e.g. pip might use the frameworks build, and python might use anaconda)....