navis-fastcore 0.0.1

NAVis core functions reimplemented in Rust.

fastcore-rs [WIP]

Rust re-implementation of navis core functions. This is an experiment to test replacing Cython with Rust for navis-fastcore to enable cross-platform usage of the library.

Notes

• internally, we use i32 to represent node indices which means we can't process neurons with more than 2,147,483,647 nodes (should be fine though)

TO-DOs

• geodesic distances
• generation of segments
• nearest-neighbor lookup (via bosque)
• synapse flow centrality
• flow centrality
• NBLAST
• shortest paths
• classify nodes
• cater for i32 node IDs which are currently cast up to i64
• faster version of segments_to_coords
• faster version of connectected_subgraph

Build

1. cd into directory
2. Activate virtual environment: source .venv/bin/activate
3. Run maturin develop --release (use maturin build --release to build wheel)

Test

First make sure pytest is installed:

pip install pytest -U

Then run the test-suite like so:

pytest --verbose -s

Note that unless you compiled with maturin develop --release the timings will be much slower (up to 10x) than in a release build.