Navis

Breaking
- with this release we've dropped support for Python 3.8 as per [NEP 29](https://numpy.org/neps/nep-0029-deprecation_policy.html>)
- `navis.write_swc` no longer writes `Dotprops`

New Features
- `navis.read_parquet` and `navis.write_parquet` let you read/write large set of skeletons or dotprops; note: these are experimental and the format specs might still change but feel free to take it for a spin
- new `navis.NeuronConnector` class for creating connectivity graphs from groups of neurons with consistent connector IDs (e.g. from `pymaid` neurons)

Improvements
- improved logic for splitting NBLASTs across multiple cores
- i/o functions can now read directly from `.tar` or `.tar.gz` files (`.zip` was already supported)

Fixes
* fixes to the neuPrint interface by stuarteberg
* plotting empty TreeNeurons no longer breaks things thanks to floesche
* reading large files (i.e. mostly meshes) directly from a URL should not break anymore

New Contributors
* stuarteberg made their first contribution in https://github.com/navis-org/navis/pull/124
* floesche made their first contribution in https://github.com/navis-org/navis/pull/125

**Full Changelog**: https://navis.readthedocs.io/en/latest/source/whats_new.html
**Commit history**: https://github.com/navis-org/navis/compare/v1.5.0...v1.6.0

Changes:
- BREAKING: dropped support for Python 3.7
- new function: [navis.pop3d()](https://navis.readthedocs.io/en/latest/source/generated/navis.pop3d.html#navis.pop3d) removes the most recently added object from the vispy 3d viewer
- new experimental functions for (pairwise) alignment of neurons using the pycpd package: [navis.nblast_align()](https://navis.readthedocs.io/en/latest/source/generated/navis.nblast_align.html#navis.nblast_align), `navis.align.align_deform()`, `navis.align.align_rigid()`, `navis.align.align_pca()`, `navis.align.align_pairwise()`
- [navis.xform_brain()](https://navis.readthedocs.io/en/latest/source/generated/navis.xform_brain.html#navis.xform_brain) now recognizes the target template’s units if available
- new NeuronList method: `navis.NeuronList.set_neuron_attributes()`
- new utility functions: [navis.nbl.compress_scores()](https://navis.readthedocs.io/en/latest/source/generated/navis.nbl.compress_scores.html#navis.nbl.compress_scores), `navis.nbl.nblast_prime()`
- improved persistence functions: [navis.persistence_distances()](https://navis.readthedocs.io/en/latest/source/generated/navis.persistence_distances.html#navis.persistence_distances), `navis.persistence_vector()`, `navis.persistence_diagram()`
- [navis.longest_neurite()](https://navis.readthedocs.io/en/latest/source/generated/navis.longest_neurite.html#navis.longest_neurite) and [navis.cell_body_fiber()](https://navis.readthedocs.io/en/latest/source/generated/navis.cell_body_fiber.html#navis.cell_body_fiber) now also allow removing the longest neurite and CBF, respectively
- [navis.heal_skeleton()](https://navis.readthedocs.io/en/latest/source/generated/navis.heal_skeleton.html#navis.heal_skeleton) now accepts a mask parameter that allows restricting where fragments are stitched
- various other bugfixes

This is release contains various improvements and fixes. Importantly, it fixes a couple incompatibilities with `numpy` `1.24.0`.

Even though this is not a new major version there is one breaking change:

`navis.flow_centrality` was renamed to `navis.synapse_flow_centrality` and a new non-synaptic `navis.flow_centrality` function was added. This also impacts the `method` parameter in `navis.split_axon_dendrite`!

Please see the [change log](https://navis.readthedocs.io/en/latest/source/whats_new.html) for other changes.

This is a small release containing 2 fixes:
1. Fixes a bug with the most recent version of `dill` which impact parallel processing.
2. In Jupyter, NBLAST now uses classic progress bars. This is not ideal and all progress bars are printed on top of another but the widgets seem to be entirely broken with the most recent version of `tqdm`.

- as of this version `pip install navis` won't install a vispy backend (see [install instructions](https://navis.readthedocs.io/en/latest/source/install.html) for details)
- new interface to fetch data from Virtual Fly Brain: `navis.interfaces.vfb`
- tools to build custom NBLAST score matrices (big thanks to clbarnes): see the new [tutorial](https://navis.readthedocs.io/en/latest/source/tutorials/smat.html)
- Bayesian implementation of the network traversal model: `navis.models.network_models.BayesianTraversalModel` (big thanks to aschampion)
- NBLASTs: new `approx_nn` parameter (sacrifices precision for speed)
- example neurons now come with some meta data
- new morphometrics functions: `navis.segment_analysis` &`navis.form_factor`
- new function to write meshes: `navis.write_mesh`
- lots of fixes and improvements in particular for i/o-related functions

Small fix for `split_axon_dendrite`.