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NeuronConnector class for connectivity of TreeNeurons #119

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wants to merge 33 commits into from
Closed

NeuronConnector class for connectivity of TreeNeurons #119

wants to merge 33 commits into from

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clbarnes
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@clbarnes clbarnes commented Jun 8, 2023

For converting a bag of neurons with possibly-intersecting connector nodes into a graph or adjacency matrix.

@schlegelp
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This looks useful! I guess the main use case are CATMAID neurons for now? Given that it requires meaningful connector IDs I would suggest making a note in the docstring. Perhaps even a sanity check that throws a warning if a neuron is added with sequential connector IDs?

I'd also add the NeuronConnector class to the API page.

@clbarnes
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Docs added, including documenting the fact that connector IDs need to be consistent between neurons, and raising a warning every time a connector ID seems to have more than one input. Needs some test data, though, I think.

@clbarnes clbarnes marked this pull request as ready for review July 28, 2023 11:40
@schlegelp
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Hi Chris. Sorry, I lost track of this. Happy to merge if ready?

schlegelp and others added 20 commits October 23, 2023 16:02
@schlegelp @clbarnes
docs: small updates
3a7ff88
@schlegelp @clbarnes
TraversalModel: avoid changing source/target data type
c311be3 
- the old implementation led to a int->float->int conversion which caused
  64bit integer IDs to be mangled
- also add warning about non-numeric source/target IDs
@schlegelp @clbarnes
MeshNeuron: fix docstring
7e161fa
@schlegelp @clbarnes
new TreeNeuron property: .surface_area
2790292
@schlegelp @clbarnes
improve pointlabels_to_meshes:
d925fc9 
- fix bug that prevent it from running
- add second method "majority"
@schlegelp @clbarnes
insect brain db interface: fix brain mesh download and use ThreadPool
78751c4
@schlegelp @clbarnes
neuron CompartmentModel: speed up adding recordings by ...
d8a2b2c 
... looking up all segments at once
@schlegelp @clbarnes
readthedocs: drop system_packages and bump build version 3.8->3.10
e8d7c8b
@schlegelp @clbarnes
readthedocs: drop redundant config file
624d5a2
@schlegelp @clbarnes
fix readthedoc config
a591dc2
@schlegelp @clbarnes
subset_neuron: fix bug with dropping connectors if subset is mask
da32100
@schlegelp @clbarnes
bump setuptools minimum version because of known security vulnerability
c7e4bd2
@schlegelp @clbarnes
docs: fix Zenodo badge
a080156
@schlegelp @clbarnes
README: add some example references
ccf8791
@schlegelp @clbarnes
Create CODE_OF_CONDUCT.md
8794995
@schlegelp @clbarnes
first pass at parquet format specifications
2e73f2f
@schlegelp @clbarnes
first pass at I/O using parquet files
8e6124a
@schlegelp @clbarnes
Update issue templates
98adc93
@schlegelp @clbarnes
Update issue templates
5a19736
@stuarteberg @clbarnes
neuprint: Support single-resolution neuroglancer precomputed meshes
d1cbd03
stuarteberg and others added 7 commits October 23, 2023 16:03
@stuarteberg @clbarnes
neuprint: If the segmentation layer has multiple sources, assume we w…
2b16dfc 
…ant the first one.
@schlegelp @clbarnes
Github actions: install pyarrow for tests
5c9ca5c
@schlegelp @clbarnes
write_parquet: skip doctest for scan_parquet results
5470fc9
@floesche @clbarnes
empty plot for empty TreeNeuron instead of error
c66c04b 
Plotting an empty TreeNeuron previously threw an `AttributeError`:

```
empty_skel = navis.TreeNeuron(None)
navis.plot3d(empty_skel)
```
@floesche @clbarnes
empty plot for empty TreeNeuron instead of AttributeError
2c32c29 
Plotting an empty TreeNeuron previously threw an `AttributeError`:

```
empty_skel = navis.TreeNeuron(None)
navis.plot3d(empty_skel)
```
@clbarnes
Add integration test for NeuronConnector
1100f3b
@clbarnes
Fix modern typing usage
149a95b
@clbarnes
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I've added an integration test so I'm happy that it works now. The merge log looks pretty whacky, though, it's claiming responsibility for a bunch of older commits, possibly because of a rebase.

@clbarnes clbarnes mentioned this pull request Nov 14, 2023
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@clbarnes
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Superceded by #133

@clbarnes clbarnes closed this Nov 14, 2023
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4 participants
@clbarnes @schlegelp @stuarteberg @floesche