fa2rs 0.3.2

Bindings to full Rust ForceAtlas2 implementation

ForceAtlas2 Python bindings from Rust

Python 3 bindings for Rust forceatlas2 crate: fast force-based graph spacialization layout, with optional multithread and SIMD.

Note: Cross-compiling with PyO3 is hard, so the distributed binary only works for GNU/Linux with latest versions of glibc (typically not Debian). Any help with cross-compilation or static glibc linking is welcome. :)

Example

import fa2rs

edges = [(0,1), (1,2), (2,0), (2,3)]
layout = fa2rs.Layout.from_graph(edges, fa2rs.Settings(ka=0.1, kg=0.1, kr=0.1), nb_nodes=4)

for i in range(100):
    layout.iteration()

print(layout.points)

You may need to tweak the settings to fit your data. The most important parameter is the ratio between ka and kr. If the ratio has too low or high values, the graph will collapse or explode (resulting in zero or infinite values).

• ka: attraction coefficient (all neighbor nodes attract each other)
• kg: gravity coefficient (all nodes are attracted to the origin) (can be set to 0)
• kr: repulsion coefficient (all nodes repulse each other)
• chunk_size: decrease to use more threads, increase to use fewer threads. Tune it to minimize both thread management time and unparallelized time. Set to None to disable parallelization.

Build & install

Build:

sh build_wheel.sh

Install:

pip3 install target/wheel/dist/fa2rs-0.2.1-py3-none-any.whl --upgrade

More information about optimizations on the Rust repository.

Layout and Settings are aliases for Layout32 and Settings32. The 32 and 64 versions refer to the size of the floats. 64-bit floats are more precise, but when SIMD is available, the layout is approximately twice slower than with 32-bit floats.

SIMD is only available on x86 and x86_64 with avx2 feature. (check with grep avx2 /proc/cpuinfo)

License

GNU AGPL v3, CopyLeft 2020-2021 Pascal Engélibert
The ForceAtlas2 paper was released under CC BY, Copyright 2014 Jacomy et al.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, version 3 of the License.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see https://www.gnu.org/licenses/.