sc-cluster-libreville
Seeded, deterministic, parallel Leiden community detection (modularity), written in Rust. The same seed gives the same labels at any number of threads, so results are reproducible on a laptop and on a 64-core server. The parallel design follows GVE-Leiden (Sahu et al. 2024, arXiv:2312.13936), with synchronous, order-independent moves instead of asynchronous ones.
pip install sc-cluster-libreville # import cluster_libreville
import cluster_libreville as cl
import numpy as np
# a symmetric scipy sparse matrix, e.g. scanpy's kNN connectivities
graph = adata.obsp["connectivities"]
labels = cl.leiden(graph, resolution=1.0, seed=0) # int32, 0 = largest
cl.modularity(graph, labels) # of any labels on the graph, e.g. to compare partitions
# scanpy-style: writes adata.obs["leiden"] (categorical) like sc.tl.leiden
cl.tl.leiden(adata, resolution=1.0, random_state=0)
# an undirected edge list: polars / pandas / pyarrow / numpy columns
labels = cl.leiden_edges(df["src"], df["dst"], df["weight"], seed=0)
# experimental, the API may change. Pick the resolution (CHAMP): Leiden over resolutions x seeds, keep the partitions that are best somewhere
c = cl.champ(graph, np.logspace(-1, 1, 20), seeds=np.arange(5)) # metric="nvi" (default) or "ami"
cl.ecs(c.labels[0], c.labels[1]) # per-cell element-centric similarity: which cells move between two partitions
c.labels[c.best] # the widest resolution range; c.to_seeds near 0 = stable across seeds
cl.tl.champ(adata) # scanpy-style: adata.obs["champ"], adata.uns["champ"]["domains"]
Options: resolution, seed, n_iterations (-1: until an iteration changes nothing),
theta (refinement randomness), min_gain (optional early stop), threads (default: all
cores; never changes the result).
License: MIT.
1 maintainer
Metadata
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Release files for sc-cluster-libreville 0.1.0
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Built distributions (wheels)
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| sc_cluster_libreville-0.1.0-cp310-abi3-win_amd64.whl | CPython 3.10 | abi3 | Windows x86-64 | Details |
| sc_cluster_libreville-0.1.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.10 | abi3 | Linux glibc 2.17+ x86-64 | Details |
| sc_cluster_libreville-0.1.0-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl | CPython 3.10 | abi3 | Linux glibc 2.17+ ARM64 | Details |
| sc_cluster_libreville-0.1.0-cp310-abi3-macosx_11_0_arm64.whl | CPython 3.10 | abi3 | macOS 11.0+ ARM64 | Details |
| sc_cluster_libreville-0.1.0-cp310-abi3-macosx_10_12_x86_64.whl | CPython 3.10 | abi3 | macOS 10.12+ x86-64 | Details |
Total release size: 2.6 MB
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