helios-network 0.10.1

Helios Network Python bindings

Helios Network (Python)

Python bindings for the Helios Network C core.

Quick start

from helios_network import AttributeScope, AttributeType, Network

network = Network(directed=False)
node_ids = network.add_nodes(3)
network.add_edges([(node_ids[0], node_ids[1])])

network.define_attribute(AttributeScope.Node, "weight", AttributeType.Double, 1)
network.nodes["weight"] = 1.0

# Auto-define attributes on assignment
network.nodes["score"] = 2.5

network.define_attribute(AttributeScope.Network, "title", AttributeType.String, 1)
network.network["title"] = "demo"
print(network.graph["title"])
network["title"] = "demo2"

# Node access
print(network.nodes[node_ids[0]]["weight"])
network.nodes[[node_ids[0], node_ids[1]]]["weight"] = [2.0, 3.0]

for node in network.nodes:
    node["weight"] = 4.0

Selectors

• network.nodes[id] returns a node view
• network.nodes[[id1, id2]] returns a selector for active nodes
• network.nodes["attr"] returns a list of attribute values for active nodes
• network.nodes["attr"] = value assigns a constant to all active nodes
• network.nodes[[id1, id2]]["attr"] = [v1, v2] assigns per-node values

Edge access mirrors node access via network.edges, with network.edges.pairs() yielding (source, target) tuples.

For large generated graphs, avoid materializing Python (source, target) tuples:

from array import array

network.add_nodes(1_000_000)
network.add_edges_from_arrays(
    array("I", sources),
    array("I", targets),
)

Network Generators

The Python package exposes native generators as module-level constructors:

from helios_network import generate_watts_strogatz

network = generate_watts_strogatz(
    5_000,
    neighbor_level=2,
    rewiring_probability=0.01,
    seed=1,
)

Available generators include generate_stochastic_block_model, generate_barabasi_albert, generate_watts_strogatz, generate_random_geometric, generate_waxman, generate_configuration_model, and generate_lattice_2d.

Edge indices

for edge_id, (source, target) in network.edges.with_indices():
    print(edge_id, source, target)

Measurements and Community Detection

The Python wrapper exposes the native measurement APIs:

degree = network.measure_degree(direction="both")
components = network.measure_connected_components(mode="weak")
leiden = network.leiden_modularity(
    resolution=1.0,
    seed=42,
    out_node_community_attribute="community",
)

leiden_modularity(...) is an alias for measure_leiden_modularity(...). It writes an unsigned-integer node attribute and returns community_count, modularity, and values_by_node.

To label only major components for filtering or visualization:

major = network.label_major_components(
    mode="weak",
    max_components=3,
    min_size=100,
    out_node_component_attribute="major_component",
)

Selected components receive rank labels 1..N by decreasing size. Other nodes receive 0 by default.

The Leiden comparison harness in research/benchmarks/leiden_compare/ uses a conda environment file:

conda env create -f research/benchmarks/leiden_compare/environment.yml
conda run -n helios-leiden-compare python -m pip install -e python --no-build-isolation
conda run -n helios-leiden-compare python research/benchmarks/leiden_compare/compare_leiden.py

Installation

Standard install:

python -m pip install ./python --upgrade

Editable install (recommended during development):

python -m pip install -e python --no-build-isolation

mesonpy editable builds require --no-build-isolation.

If editable install fails, install build tools in the active environment:

python -m pip install meson ninja meson-python
python -m pip install -e python --no-build-isolation

Optional conversions

NetworkX and igraph conversions are optional. Install when needed:

python -m pip install networkx
python -m pip install igraph

UMAP export

Install the optional UMAP stack when you want a Helios-ready fuzzy graph or kNN graph export:

python -m pip install ./python[umap]

from helios_network import HeliosUMAP

umap_export = HeliosUMAP(
    n_neighbors=15,
    min_dist=0.1,
    build_knn_network=True,
)

network = umap_export.fit_network(X)
network.save_bxnet("embedding.bxnet")

# Optional directed kNN export
umap_export.knn_network_.save_zxnet("embedding-knn.zxnet")

If you want only the UMAP graph construction output for helios-web-next to lay out from scratch, use the graph-only export path instead:

graph_network = umap_export.fit_graph_network(X)
graph_network.save_zxnet("umap-graph.zxnet")

The fit graph export writes:

• node attributes: umap_embedding, _helios_visuals_position, umap_mass
• edge attribute: umap_weight
• network attributes that let helios-web-next auto-enable UMAP force mode on import

The graph-only export writes the same UMAP edge weights and graph metadata, but omits umap_embedding and _helios_visuals_position so helios-web-next can start its own realtime UMAP-like layout from scratch.

Examples

From python/:

python examples/basic_usage.py
python examples/toroidal_dimensions_table.py
python examples/toroidal_dimensions_plot.py --skip-plot
python examples/toroidal_dimensions_plot.py
python examples/toroidal_dimensions_plot.py --large --skip-plot
python examples/generate_umap_example_networks.py --sizes 200 2000 20000

toroidal_dimensions_plot.py uses matplotlib for plotting local dimension curves. Install it with:

python -m pip install matplotlib

Vector attributes

Attributes with dimension > 1 accept vector assignments:

network.define_attribute(AttributeScope.Node, "i3", AttributeType.Integer, 3)
network.nodes["i3"] = [1, 2, 3]  # broadcast to all nodes
network.nodes[[0, 1]]["i3"] = [[4, 5, 6], [7, 8, 9]]