navis-fastcore 0.0.3

NAVis core functions reimplemented in Rust.

fastcore-rs

Rust re-implementation of navis core functions. Check out the documentation for details.

TO-DOs

• geodesic distances
• connected components
• generation of linear segments
• synapse flow centrality
• Strahler index
• classify nodes
• flow centrality
• CI tests
• NBLAST (started a prototype)
• shortest paths
• cater for i32 node IDs which are currently cast up to i64
• faster version of navis.connected_subgraph

Additional 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)

Install

We provide precompiled binaries for all major Python versions, CPU architectures and operating systems.

From PyPI:

pip install navis-fastcore

If that fails, try building from source (see below).

Usage

navis will automatically use fastcore if it is available. The integration is still work in progress, so for now you should install navis from Github to make sure you have the latest version.

Build

1. Install rust
2. Clone this repository
3. cd into fastcore-rs directory
4. Create a virtual environment: python3 -m venv .venv
5. Activate virtual environment: source .venv/bin/activate
6. Compile via either:
   • maturin develop --release which will compile the extension into the fastcore/ directory
   • maturin build --release to build wheel in /target/wheels
7. To install the Python package either do:

• pip install -e . to install in editable mode
• pip install targets/wheels/navis_fastcore....whl

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

Test

First make sure pytest is installed:

pip install pytest -U

Then run the test-suite like so:

pytest --verbose -s