pylmcf 1.0.0

Python bindings for Network Simplex algorithm from LEMON library

pylmcf: Python bindings for Min Cost Flow solvers from the LEMON graph library

Overview

pylmcf provides Python bindings for the min-cost flow solvers implemented in the LEMON graph library. It enables efficient network flow optimization in Python applications. It is used by wnet (a Python package enabling the efficient computation of Wasserstein and Truncated Wasserstein distance between multidimensional distributions) and wnetalign (a Python package enabling efficient alignment of MS or NMR spectra).

Features

• Fast min-cost flow computation using C++ backend (LEMON's Network Simplex by default)
• Multiple solver variants: Network Simplex, Cycle Canceling, Cost Scaling, Capacity Scaling
• Supports capacities, costs, supplies/demands, and per-edge lower bounds (minimum flow)
• NetworkX integration: construct from nx.DiGraph or convert results back for visualization
• C++ headers exposed for downstream packages that want to call the solver directly

Installation

pip install pylmcf

Optional extras for NetworkX support and visualization:

pip install pylmcf[extras]

Usage

Basic usage

import numpy as np
import pylmcf

# 3-node graph with edges 0→1, 0→2, 1→2
# Edges must be sorted by (start, end)
G = pylmcf.Graph(3,
    edge_starts=np.array([0, 0, 1]),
    edge_ends=np.array([1, 2, 2]))

G.set_node_supply(np.array([5, 0, -5]))   # node 0 supplies 5, node 2 demands 5
G.set_edge_costs(np.array([1, 3, 5]))
G.set_edge_capacities(np.array([3, 3, 5]))

G.solve()

G.result()      # np.array([2, 3, 2])  — flow on each edge
G.total_cost()  # 21

Per-edge lower bounds (minimum flow)

G.set_edge_minimums(np.array([3, 0, 0]))  # edge 0→1 must carry at least 3 units
G.solve()
G.result()      # np.array([3, 2, 3])
G.total_cost()  # 24

Constructing from a NetworkX graph

Note: Graph.FromNX() iterates over graph elements in Python and is significantly slower than constructing Graph directly from numpy arrays. Prefer the direct API for performance-sensitive code.

import networkx as nx

G_nx = nx.DiGraph()
G_nx.add_edge(0, 1, weight=1, capacity=3)
G_nx.add_edge(0, 2, weight=3, capacity=3)
G_nx.add_edge(1, 2, weight=5, capacity=5)
G_nx.nodes[0]["demand"] = -5
G_nx.nodes[2]["demand"] = 5

G = pylmcf.Graph.FromNX(G_nx)
G.solve()
G.result()      # np.array([2, 3, 2])

Alternative solvers

The default solver is LEMON's Network Simplex. Three alternatives are available via the low-level functional API:

from pylmcf import pylmcf_cpp
import numpy as np

a = lambda x: np.array(x, dtype=np.int64)
supply = a([5, 0, -5])
starts = a([0, 0, 1])
ends   = a([1, 2, 2])
caps   = a([3, 3, 5])
costs  = a([1, 3, 5])

flows = pylmcf_cpp.lmcf(supply, starts, ends, caps, costs)               # Network Simplex (default)
flows = pylmcf_cpp.lmcf_cycle_canceling(supply, starts, ends, caps, costs)
flows = pylmcf_cpp.lmcf_cost_scaling(supply, starts, ends, caps, costs)   # int32/int64 only
flows = pylmcf_cpp.lmcf_capacity_scaling(supply, starts, ends, caps, costs)  # int32/int64 only

Visualization

G.show()               # display with matplotlib
G.show("graph.png")    # save to file

C++ include path

If you want to call the LEMON solver from your own C++ extension:

python -m pylmcf --include

Requirements

• Python 3.9+

Licence

pylmcf is published under the Boost Software Licence. LEMON (which resides in src/pylmcf/cpp/lemon) is also covered by the Boost Software Licence.

Citation

If you use this software, please cite:

Król J, Bochenek M, Jopa S, Kazimierczuk K, Gambin A, Startek MP (2026). WNetAlign: fast and accurate spectra alignment using truncated Wasserstein distance and network simplex. Briefings in Bioinformatics, 27(3), bbag247. https://doi.org/10.1093/bib/bbag247

@article{krol2026wnetalign,
  title   = {WNetAlign: fast and accurate spectra alignment using truncated Wasserstein distance and network simplex},
  author  = {Kr{\'o}l, Justyna and Bochenek, Maria and Jopa, Sylwia and Kazimierczuk, Krzysztof and Gambin, Anna and Startek, Micha{\l} Piotr},
  journal = {Briefings in Bioinformatics},
  volume  = {27},
  number  = {3},
  pages   = {bbag247},
  year    = {2026},
  doi     = {10.1093/bib/bbag247}
}

References

• LEMON Graph Library
• wnet package
• wnetalign package
• Min Cost Flow Problem