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NeuronConnector class for connectivity of TreeNeurons #119

Closed
wants to merge 33 commits into from
Closed

NeuronConnector class for connectivity of TreeNeurons #119

wants to merge 33 commits into from

Commits on Jul 28, 2023

  1. NeuronConnector class for connectivity of TreeNeurons

    @clbarnes
    clbarnes committed Jul 28, 2023
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  2. NeuronConnector: document need for consistent conn IDs

    @clbarnes
    clbarnes committed Jul 28, 2023
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  3. Docs: document NeuronConnector

    @clbarnes
    clbarnes committed Jul 28, 2023
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  4. test and fix NeuronConnector

    @clbarnes
    clbarnes committed Jul 28, 2023
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  5. Use old typing names

    @clbarnes
    clbarnes committed Jul 28, 2023
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Commits on Oct 23, 2023

  1. docs: small updates

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  2. TraversalModel: avoid changing source/target data type 

    - 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
    schlegelp authored and clbarnes committed Oct 23, 2023
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  3. MeshNeuron: fix docstring

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  4. new TreeNeuron property: .surface_area

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  5. improve pointlabels_to_meshes: 

    - fix bug that prevent it from running
- add second method "majority"
    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  6. insect brain db interface: fix brain mesh download and use ThreadPool

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  7. neuron CompartmentModel: speed up adding recordings by ... 

    ... looking up all segments at once
    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  8. readthedocs: drop system_packages and bump build version 3.8->3.10

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  9. readthedocs: drop redundant config file

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  10. fix readthedoc config

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  11. subset_neuron: fix bug with dropping connectors if subset is mask

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  12. bump setuptools minimum version because of known security vulnerability

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  13. docs: fix Zenodo badge

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  14. README: add some example references

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  15. Create CODE_OF_CONDUCT.md

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  16. first pass at parquet format specifications

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  17. first pass at I/O using parquet files

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  18. Update issue templates

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  19. Update issue templates

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  20. neuprint: Support single-resolution neuroglancer precomputed meshes

    @stuarteberg @clbarnes
    stuarteberg authored and clbarnes committed Oct 23, 2023
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  21. neuprint: If the segmentation layer has multiple sources, assume we w… 

    …ant the first one.
    @stuarteberg @clbarnes
    stuarteberg authored and clbarnes committed Oct 23, 2023
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  22. Github actions: install pyarrow for tests

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  23. write_parquet: skip doctest for scan_parquet results

    @schlegelp @clbarnes
    schlegelp authored and clbarnes committed Oct 23, 2023
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  24. empty plot for empty TreeNeuron instead of error 

    Plotting an empty TreeNeuron previously threw an `AttributeError`:

```
empty_skel = navis.TreeNeuron(None)
navis.plot3d(empty_skel)
```
    @floesche @clbarnes
    floesche authored and clbarnes committed Oct 23, 2023
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  25. empty plot for empty TreeNeuron instead of AttributeError 

    Plotting an empty TreeNeuron previously threw an `AttributeError`:

```
empty_skel = navis.TreeNeuron(None)
navis.plot3d(empty_skel)
```
    @floesche @clbarnes
    floesche authored and clbarnes committed Oct 23, 2023
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  26. Add integration test for NeuronConnector

    @clbarnes
    clbarnes committed Oct 23, 2023
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  27. Fix modern typing usage

    @clbarnes
    clbarnes committed Oct 23, 2023
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  28. NeuronConnector: update dir name in tests

    @clbarnes
    clbarnes committed Oct 23, 2023
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