opencode-skills-collection 4.1.14 → 4.1.16

package/bundled-skills/networkx/references/algorithms.md

@@ -0,0 +1,383 @@
+# NetworkX Graph Algorithms
+
+## Shortest Paths
+
+### Single Source Shortest Paths
+```python
+# Dijkstra's algorithm (weighted graphs)
+path = nx.shortest_path(G, source=1, target=5, weight='weight')
+length = nx.shortest_path_length(G, source=1, target=5, weight='weight')
+
+# All shortest paths from source
+paths = nx.single_source_shortest_path(G, source=1)
+lengths = nx.single_source_shortest_path_length(G, source=1)
+
+# Bellman-Ford (handles negative weights)
+path = nx.bellman_ford_path(G, source=1, target=5, weight='weight')
+```
+
+### All Pairs Shortest Paths
+```python
+# All pairs (returns iterator)
+for source, paths in nx.all_pairs_shortest_path(G):
+    print(f"From {source}: {paths}")
+
+# Floyd-Warshall algorithm
+lengths = dict(nx.all_pairs_shortest_path_length(G))
+```
+
+### Specialized Shortest Path Algorithms
+```python
+# A* algorithm (with heuristic)
+def heuristic(u, v):
+    # Custom heuristic function
+    return abs(u - v)
+
+path = nx.astar_path(G, source=1, target=5, heuristic=heuristic, weight='weight')
+
+# Average shortest path length
+avg_length = nx.average_shortest_path_length(G)
+```
+
+## Connectivity
+
+### Connected Components (Undirected)
+```python
+# Check if connected
+is_connected = nx.is_connected(G)
+
+# Number of components
+num_components = nx.number_connected_components(G)
+
+# Get all components (returns iterator of sets)
+components = list(nx.connected_components(G))
+largest_component = max(components, key=len)
+
+# Get component containing specific node
+component = nx.node_connected_component(G, node=1)
+```
+
+### Strong/Weak Connectivity (Directed)
+```python
+# Strong connectivity (mutually reachable)
+is_strongly_connected = nx.is_strongly_connected(G)
+strong_components = list(nx.strongly_connected_components(G))
+largest_scc = max(strong_components, key=len)
+
+# Weak connectivity (ignoring direction)
+is_weakly_connected = nx.is_weakly_connected(G)
+weak_components = list(nx.weakly_connected_components(G))
+
+# Condensation (DAG of strongly connected components)
+condensed = nx.condensation(G)
+```
+
+### Cuts and Connectivity
+```python
+# Minimum node/edge cut
+min_node_cut = nx.minimum_node_cut(G, s=1, t=5)
+min_edge_cut = nx.minimum_edge_cut(G, s=1, t=5)
+
+# Node/edge connectivity
+node_connectivity = nx.node_connectivity(G)
+edge_connectivity = nx.edge_connectivity(G)
+```
+
+## Centrality Measures
+
+### Degree Centrality
+```python
+# Fraction of nodes each node is connected to
+degree_cent = nx.degree_centrality(G)
+
+# For directed graphs
+in_degree_cent = nx.in_degree_centrality(G)
+out_degree_cent = nx.out_degree_centrality(G)
+```
+
+### Betweenness Centrality
+```python
+# Fraction of shortest paths passing through node
+betweenness = nx.betweenness_centrality(G, weight='weight')
+
+# Edge betweenness
+edge_betweenness = nx.edge_betweenness_centrality(G, weight='weight')
+
+# Approximate for large graphs
+approx_betweenness = nx.betweenness_centrality(G, k=100)  # Sample 100 nodes
+```
+
+### Closeness Centrality
+```python
+# Reciprocal of average shortest path length
+closeness = nx.closeness_centrality(G)
+
+# For disconnected graphs
+closeness = nx.closeness_centrality(G, wf_improved=True)
+```
+
+### Eigenvector Centrality
+```python
+# Centrality based on connections to high-centrality nodes
+eigenvector = nx.eigenvector_centrality(G, max_iter=1000)
+
+# Katz centrality (variant with attenuation factor)
+katz = nx.katz_centrality(G, alpha=0.1, beta=1.0)
+```
+
+### PageRank
+```python
+# Google's PageRank algorithm
+pagerank = nx.pagerank(G, alpha=0.85)
+
+# Personalized PageRank
+personalization = {node: 1.0 if node in [1, 2] else 0.0 for node in G}
+ppr = nx.pagerank(G, personalization=personalization)
+```
+
+## Clustering
+
+### Clustering Coefficients
+```python
+# Clustering coefficient for each node
+clustering = nx.clustering(G)
+
+# Average clustering coefficient
+avg_clustering = nx.average_clustering(G)
+
+# Weighted clustering
+weighted_clustering = nx.clustering(G, weight='weight')
+```
+
+### Transitivity
+```python
+# Overall clustering (ratio of triangles to triads)
+transitivity = nx.transitivity(G)
+```
+
+### Triangles
+```python
+# Count triangles per node
+triangles = nx.triangles(G)
+
+# Total number of triangles
+total_triangles = sum(triangles.values()) // 3
+```
+
+## Community Detection
+
+### Modularity-Based
+```python
+from networkx.algorithms import community
+
+# Greedy modularity maximization
+communities = community.greedy_modularity_communities(G)
+
+# Compute modularity
+modularity = community.modularity(G, communities)
+```
+
+### Label Propagation
+```python
+# Fast community detection
+communities = community.label_propagation_communities(G)
+```
+
+### Girvan-Newman
+```python
+# Hierarchical community detection via edge betweenness
+comp = community.girvan_newman(G)
+limited = itertools.takewhile(lambda c: len(c) <= 10, comp)
+for communities in limited:
+    print(tuple(sorted(c) for c in communities))
+```
+
+## Matching and Covering
+
+### Maximum Matching
+```python
+# Maximum cardinality matching
+matching = nx.max_weight_matching(G)
+
+# Check if matching is valid
+is_matching = nx.is_matching(G, matching)
+is_perfect = nx.is_perfect_matching(G, matching)
+```
+
+### Minimum Vertex/Edge Cover
+```python
+# Minimum set of nodes covering all edges
+min_vertex_cover = nx.approximation.min_weighted_vertex_cover(G)
+
+# Minimum edge dominating set
+min_edge_dom = nx.approximation.min_edge_dominating_set(G)
+```
+
+## Tree Algorithms
+
+### Minimum Spanning Tree
+```python
+# Kruskal's or Prim's algorithm
+mst = nx.minimum_spanning_tree(G, weight='weight')
+
+# Maximum spanning tree
+mst_max = nx.maximum_spanning_tree(G, weight='weight')
+
+# Enumerate all spanning trees
+all_spanning = nx.all_spanning_trees(G)
+```
+
+### Tree Properties
+```python
+# Check if graph is tree
+is_tree = nx.is_tree(G)
+is_forest = nx.is_forest(G)
+
+# For directed graphs
+is_arborescence = nx.is_arborescence(G)
+```
+
+## Flow and Capacity
+
+### Maximum Flow
+```python
+# Maximum flow value
+flow_value = nx.maximum_flow_value(G, s=1, t=5, capacity='capacity')
+
+# Maximum flow with flow dict
+flow_value, flow_dict = nx.maximum_flow(G, s=1, t=5, capacity='capacity')
+
+# Minimum cut
+cut_value, partition = nx.minimum_cut(G, s=1, t=5, capacity='capacity')
+```
+
+### Cost Flow
+```python
+# Minimum cost flow
+flow_dict = nx.min_cost_flow(G, demand='demand', capacity='capacity', weight='weight')
+cost = nx.cost_of_flow(G, flow_dict, weight='weight')
+```
+
+## Cycles
+
+### Finding Cycles
+```python
+# Simple cycles (for directed graphs)
+cycles = list(nx.simple_cycles(G))
+
+# Cycle basis (for undirected graphs)
+basis = nx.cycle_basis(G)
+
+# Check if acyclic
+is_dag = nx.is_directed_acyclic_graph(G)
+```
+
+### Topological Sorting
+```python
+# Only for DAGs
+try:
+    topo_order = list(nx.topological_sort(G))
+except nx.NetworkXError:
+    print("Graph has cycles")
+
+# All topological sorts
+all_topo = nx.all_topological_sorts(G)
+```
+
+## Cliques
+
+### Finding Cliques
+```python
+# All maximal cliques
+cliques = list(nx.find_cliques(G))
+
+# Maximum clique (NP-complete, approximate)
+max_clique = nx.approximation.max_clique(G)
+
+# Clique number
+clique_number = nx.graph_clique_number(G)
+
+# Number of maximal cliques containing each node
+clique_counts = nx.node_clique_number(G)
+```
+
+## Graph Coloring
+
+### Node Coloring
+```python
+# Greedy coloring
+coloring = nx.greedy_color(G, strategy='largest_first')
+
+# Different strategies: 'largest_first', 'smallest_last', 'random_sequential'
+coloring = nx.greedy_color(G, strategy='smallest_last')
+```
+
+## Isomorphism
+
+### Graph Isomorphism
+```python
+# Check if graphs are isomorphic
+is_isomorphic = nx.is_isomorphic(G1, G2)
+
+# Get isomorphism mapping
+from networkx.algorithms import isomorphism
+GM = isomorphism.GraphMatcher(G1, G2)
+if GM.is_isomorphic():
+    mapping = GM.mapping
+```
+
+### Subgraph Isomorphism
+```python
+# Check if G1 is subgraph isomorphic to G2
+is_subgraph_iso = nx.is_isomorphic(G1, G2.subgraph(nodes))
+```
+
+## Traversal Algorithms
+
+### Depth-First Search (DFS)
+```python
+# DFS edges
+dfs_edges = list(nx.dfs_edges(G, source=1))
+
+# DFS tree
+dfs_tree = nx.dfs_tree(G, source=1)
+
+# DFS predecessors
+dfs_pred = nx.dfs_predecessors(G, source=1)
+
+# Preorder and postorder
+preorder = list(nx.dfs_preorder_nodes(G, source=1))
+postorder = list(nx.dfs_postorder_nodes(G, source=1))
+```
+
+### Breadth-First Search (BFS)
+```python
+# BFS edges
+bfs_edges = list(nx.bfs_edges(G, source=1))
+
+# BFS tree
+bfs_tree = nx.bfs_tree(G, source=1)
+
+# BFS predecessors and successors
+bfs_pred = nx.bfs_predecessors(G, source=1)
+bfs_succ = nx.bfs_successors(G, source=1)
+```
+
+## Efficiency Considerations
+
+### Algorithm Complexity
+- Many algorithms have parameters to control computation time
+- For large graphs, consider approximate algorithms
+- Use `k` parameter to sample nodes in centrality calculations
+- Set `max_iter` for iterative algorithms
+
+### Memory Usage
+- Iterator-based functions (e.g., `nx.simple_cycles()`) save memory
+- Convert to list only when necessary
+- Use generators for large result sets
+
+### Numerical Precision
+When using weighted algorithms with floating-point numbers, results are approximate. Consider:
+- Using integer weights when possible
+- Setting appropriate tolerance parameters
+- Being aware of accumulated rounding errors in iterative algorithms