Merge pull request #29 from elecbug/v0.8

Update v0.8.1

Author: elecbug

.github/workflows/go.yml

@@ -25,4 +25,4 @@ jobs:
       run: go build -v ./...
 
     - name: Test
-      run: go test -v ./...
+      run: go test ./...

graph/algorithm/betweenness_centrality.go

@@ -5,16 +5,15 @@ import (
 	"sync"
 
 	"github.com/elecbug/netkit/graph"
-	"github.com/elecbug/netkit/graph/node"
 )
 
 // BetweennessCentrality computes betweenness centrality using cached all shortest paths.
 // - Uses AllShortestPaths(g, cfg) (assumed cached/fast) to enumerate all shortest paths.
 // - For each pair (s,t), each interior node on a shortest path gets 1/|SP(s,t)| credit.
 // - Undirected graphs enqueue only i<j pairs (no double counting).
 // - Normalization matches NetworkX: undirected => 2/((n-1)(n-2)), directed => 1/((n-1)(n-2)).
-func BetweennessCentrality(g *graph.Graph, cfg *Config) map[node.ID]float64 {
-	res := make(map[node.ID]float64)
+func BetweennessCentrality(g *graph.Graph, cfg *Config) map[graph.NodeID]float64 {
+	res := make(map[graph.NodeID]float64)
 	if g == nil {
 		return res
 	}
@@ -46,30 +45,30 @@ func BetweennessCentrality(g *graph.Graph, cfg *Config) map[node.ID]float64 {
 	}
 
 	// Use cached all-pairs shortest paths.
-	// Type: map[node.ID]map[node.ID][]path.Path
+	// Type: map[graph.NodeID]map[graph.NodeID][]path.Path
 	all := AllShortestPaths(g, cfg)
 
 	// Build an index for stable iteration and pair generation.
-	idxOf := make(map[node.ID]int, n)
+	idxOf := make(map[graph.NodeID]int, n)
 	for i, u := range ids {
 		idxOf[u] = i
 	}
 
-	type pair struct{ s, t node.ID }
+	type pair struct{ s, t graph.NodeID }
 	isUndirected := g.IsBidirectional()
 
 	// Generate all (s,t) jobs.
 	jobs := make(chan pair, n)
 	var wg sync.WaitGroup
 
 	// Global accumulator with lock; each worker keeps a local map to minimize contention.
-	global := make(map[node.ID]float64, n)
+	global := make(map[graph.NodeID]float64, n)
 	var mu sync.Mutex
 
 	// Worker: consume pairs and accumulate contributions into a local map, then merge.
 	workerFn := func() {
 		defer wg.Done()
-		local := make(map[node.ID]float64, n)
+		local := make(map[graph.NodeID]float64, n)
 
 		for job := range jobs {
 			row, ok := all[job.s]
@@ -84,7 +83,7 @@ func BetweennessCentrality(g *graph.Graph, cfg *Config) map[node.ID]float64 {
 
 			// For each shortest path s->...->t, every interior node gets 1/den.
 			for _, pth := range pathsST {
-				seq := pth.Nodes() // []node.ID; interior nodes are [1 : len-1)
+				seq := pth.Nodes() // []graph.NodeID; interior nodes are [1 : len-1)
 				if len(seq) <= 2 {
 					continue // no interior node
 				}

graph/algorithm/cache.go

@@ -2,18 +2,30 @@ package algorithm
 
 import (
 	"sync"
+	"time"
 
-	"github.com/elecbug/netkit/graph/path"
+	"github.com/elecbug/netkit/graph"
 )
 
-var cachedAllShortestPaths = make(map[string]path.GraphPaths)
-var cachedAllShortestPathLengths = make(map[string]path.PathLength)
+var cachedAllShortestPaths = make(map[string]graph.Paths)
+var cachedAllShortestPathLengths = make(map[string]graph.PathLength)
 var cacheMu sync.RWMutex
 
 // CacheClear clears the cached shortest paths and their lengths.
 func CacheClear() {
 	cacheMu.Lock()
 	defer cacheMu.Unlock()
-	cachedAllShortestPaths = make(map[string]path.GraphPaths)
-	cachedAllShortestPathLengths = make(map[string]path.PathLength)
+	cachedAllShortestPaths = make(map[string]graph.Paths)
+	cachedAllShortestPathLengths = make(map[string]graph.PathLength)
+}
+
+// AutoCacheClear starts a goroutine that clears the cache at regular intervals defined by tick.
+func AutoCacheClear(tick time.Duration) {
+	go func() {
+		for {
+			time.Sleep(tick)
+
+			CacheClear()
+		}
+	}()
 }

graph/algorithm/closeness_centrality.go

@@ -2,7 +2,6 @@ package algorithm
 
 import (
 	"github.com/elecbug/netkit/graph"
-	"github.com/elecbug/netkit/graph/node"
 )
 
 // ClosenessCentrality computes NetworkX-compatible closeness centrality.
@@ -17,8 +16,8 @@ import (
 // Requirements:
 // - AllShortestPaths(g, cfg) must respect directedness of g.
 // - cfg.Closeness.WfImproved follows NetworkX default (true) unless overridden.
-func ClosenessCentrality(g *graph.Graph, cfg *Config) map[node.ID]float64 {
-	out := make(map[node.ID]float64)
+func ClosenessCentrality(g *graph.Graph, cfg *Config) map[graph.NodeID]float64 {
+	out := make(map[graph.NodeID]float64)
 	if g == nil {
 		return out
 	}

graph/algorithm/clustering_coefficient.go

@@ -5,15 +5,14 @@ import (
 	"sync"
 
 	"github.com/elecbug/netkit/graph"
-	"github.com/elecbug/netkit/graph/node"
 )
 
 // ClusteringCoefficientAll computes local clustering coefficients for all nodes.
 // - If g.IsBidirectional()==false (directed): Fagiolo (2007) directed clustering (matches NetworkX).
 // - If g.IsBidirectional()==true (undirected): standard undirected clustering.
-// Returns map[node.ID]float64 with a value for every node in g.
-func ClusteringCoefficient(g *graph.Graph, cfg *Config) map[node.ID]float64 {
-	res := make(map[node.ID]float64)
+// Returns map[graph.NodeID]float64 with a value for every node in g.
+func ClusteringCoefficient(g *graph.Graph, cfg *Config) map[graph.NodeID]float64 {
+	res := make(map[graph.NodeID]float64)
 	if g == nil {
 		return res
 	}
@@ -35,10 +34,10 @@ func ClusteringCoefficient(g *graph.Graph, cfg *Config) map[node.ID]float64 {
 	// Build helper structures
 	// outNeighbors[v] = slice of out-neighbors of v (exclude self)
 	// inNeighbors[v]  = slice of in-neighbors of v (exclude self) - only needed for directed
-	outNeighbors := make(map[node.ID][]node.ID, n)
+	outNeighbors := make(map[graph.NodeID][]graph.NodeID, n)
 	for _, v := range nodes {
 		ns := g.Neighbors(v)
-		buf := make([]node.ID, 0, len(ns))
+		buf := make([]graph.NodeID, 0, len(ns))
 		for _, w := range ns {
 			if w != v {
 				buf = append(buf, w)
@@ -48,9 +47,9 @@ func ClusteringCoefficient(g *graph.Graph, cfg *Config) map[node.ID]float64 {
 	}
 
 	isDirected := !g.IsBidirectional()
-	var inNeighbors map[node.ID][]node.ID
+	var inNeighbors map[graph.NodeID][]graph.NodeID
 	if isDirected {
-		inNeighbors = make(map[node.ID][]node.ID, n)
+		inNeighbors = make(map[graph.NodeID][]graph.NodeID, n)
 		for _, u := range nodes {
 			for _, w := range outNeighbors[u] {
 				// u -> w, so u is in-neighbor of w
@@ -59,13 +58,13 @@ func ClusteringCoefficient(g *graph.Graph, cfg *Config) map[node.ID]float64 {
 		}
 	}
 
-	type job struct{ v node.ID }
+	type job struct{ v graph.NodeID }
 	jobs := make(chan job, workers*2)
 	var wg sync.WaitGroup
 	var mu sync.Mutex // protects res map
 
 	// Edge multiplicity for Fagiolo: b(u,v) = a_uv + a_vu ∈ {0,1,2}
-	b := func(u, v node.ID) int {
+	b := func(u, v graph.NodeID) int {
 		sum := 0
 
 		if g.HasEdge(u, v) {
@@ -98,7 +97,7 @@ func ClusteringCoefficient(g *graph.Graph, cfg *Config) map[node.ID]float64 {
 					mu.Unlock()
 					continue
 				}
-				outSet := make(map[node.ID]struct{}, kOut)
+				outSet := make(map[graph.NodeID]struct{}, kOut)
 				for _, w := range outNeighbors[v] {
 					outSet[w] = struct{}{}
 				}
@@ -119,15 +118,15 @@ func ClusteringCoefficient(g *graph.Graph, cfg *Config) map[node.ID]float64 {
 
 				// T_v = sum_{j != k} b(v,j) * b(j,k) * b(k,v)
 				// with j,k in tot = in(v) ∪ out(v)
-				totSet := make(map[node.ID]struct{}, kTot) // upper bound
+				totSet := make(map[graph.NodeID]struct{}, kTot) // upper bound
 				for _, u := range outNeighbors[v] {
 					totSet[u] = struct{}{}
 				}
 				for _, u := range inNeighbors[v] {
 					totSet[u] = struct{}{}
 				}
 				// Make a slice to iterate
-				tot := make([]node.ID, 0, len(totSet))
+				tot := make([]graph.NodeID, 0, len(totSet))
 				for u := range totSet {
 					if u != v { // guard (shouldn't be in set anyway)
 						tot = append(tot, u)

graph/algorithm/degree_assortativity_coefficient.go

@@ -6,7 +6,6 @@ import (
 	"math"
 
 	"github.com/elecbug/netkit/graph"
-	"github.com/elecbug/netkit/graph/node"
 )
 
 // DegreeAssortativityCoefficient computes Newman's degree assortativity coefficient (Pearson correlation)
@@ -54,16 +53,16 @@ func DegreeAssortativityCoefficient(g *graph.Graph, cfg *Config) float64 {
 	}
 
 	// Build an index for upper-triangle filtering on undirected graphs.
-	idxOf := make(map[node.ID]int, n)
+	idxOf := make(map[graph.NodeID]int, n)
 	for i, u := range ids {
 		idxOf[u] = i
 	}
 
 	// Degree caches
 	// NOTE: Replace the neighbor getters with your graph API if needed.
-	outDeg := make(map[node.ID]int, n)
-	inDeg := make(map[node.ID]int, n)
-	undeg := make(map[node.ID]int, n)
+	outDeg := make(map[graph.NodeID]int, n)
+	inDeg := make(map[graph.NodeID]int, n)
+	undeg := make(map[graph.NodeID]int, n)
 
 	if isUndirected {
 		for _, u := range ids {

graph/algorithm/degree_centrality.go

@@ -5,7 +5,6 @@ import (
 	"sync"
 
 	"github.com/elecbug/netkit/graph"
-	"github.com/elecbug/netkit/graph/node"
 )
 
 // DegreeCentralityConfig (suggested to be added inside your config package)
@@ -32,8 +31,8 @@ import (
 // - Undirected: deg(u)/(n-1).
 // - Directed (default "total"): (in(u)+out(u))/(n-1). Use "in"/"out" for the specific variants.
 // Self-loops are ignored for centrality.
-func DegreeCentrality(g *graph.Graph, cfg *Config) map[node.ID]float64 {
-	res := make(map[node.ID]float64)
+func DegreeCentrality(g *graph.Graph, cfg *Config) map[graph.NodeID]float64 {
+	res := make(map[graph.NodeID]float64)
 	if g == nil {
 		return res
 	}
@@ -55,7 +54,7 @@ func DegreeCentrality(g *graph.Graph, cfg *Config) map[node.ID]float64 {
 	}
 
 	// --- indexing ---
-	idxOf := make(map[node.ID]int, n)
+	idxOf := make(map[graph.NodeID]int, n)
 	for i, u := range ids {
 		idxOf[u] = i
 	}

graph/algorithm/edge_betweenness_centrality.go

@@ -5,10 +5,9 @@ import (
 	"sync"
 
 	"github.com/elecbug/netkit/graph"
-	"github.com/elecbug/netkit/graph/node"
 )
 
-func makeEdgeKey(u, v node.ID, undirected bool) (node.ID, node.ID) {
+func makeEdgeKey(u, v graph.NodeID, undirected bool) (graph.NodeID, graph.NodeID) {
 	if undirected && v < u {
 		u, v = v, u
 	}
@@ -34,11 +33,11 @@ func makeEdgeKey(u, v node.ID, undirected bool) (node.ID, node.ID) {
 // in Brandes accumulation (same practice as NetworkX).
 //
 // Returns:
-//   - map[node.ID]map[node.ID]float64 where:
+//   - map[graph.NodeID]map[graph.NodeID]float64 where:
 //   - Undirected: key is canonical [min(u,v), max(u,v)]
 //   - Directed:   key is (u,v) ordered
-func EdgeBetweennessCentrality(g *graph.Graph, cfg *Config) map[node.ID]map[node.ID]float64 {
-	out := make(map[node.ID]map[node.ID]float64)
+func EdgeBetweennessCentrality(g *graph.Graph, cfg *Config) map[graph.NodeID]map[graph.NodeID]float64 {
+	out := make(map[graph.NodeID]map[graph.NodeID]float64)
 	if g == nil {
 		return out
 	}
@@ -79,15 +78,15 @@ func EdgeBetweennessCentrality(g *graph.Graph, cfg *Config) map[node.ID]map[node
 			u, v := makeEdgeKey(u, v, isUndirected)
 
 			if out[u] == nil {
-				out[u] = make(map[node.ID]float64)
+				out[u] = make(map[graph.NodeID]float64)
 			}
 
 			out[u][v] = 0.0
 		}
 	}
 
 	// ----- worker pool over source nodes -----
-	type job struct{ s node.ID }
+	type job struct{ s graph.NodeID }
 	jobs := make(chan job, n)
 
 	var mu sync.Mutex
@@ -97,16 +96,16 @@ func EdgeBetweennessCentrality(g *graph.Graph, cfg *Config) map[node.ID]map[node
 		defer wg.Done()
 
 		// Local accumulator to reduce lock contention
-		local := make(map[node.ID]map[node.ID]float64, 64)
+		local := make(map[graph.NodeID]map[graph.NodeID]float64, 64)
 
 		for jb := range jobs {
 			s := jb.s
 
 			// Brandes data structures
-			stack := make([]node.ID, 0, n)
-			preds := make(map[node.ID][]node.ID, n)
-			sigma := make(map[node.ID]float64, n)
-			dist := make(map[node.ID]int, n)
+			stack := make([]graph.NodeID, 0, n)
+			preds := make(map[graph.NodeID][]graph.NodeID, n)
+			sigma := make(map[graph.NodeID]float64, n)
+			dist := make(map[graph.NodeID]int, n)
 
 			for _, v := range ids {
 				dist[v] = -1
@@ -115,7 +114,7 @@ func EdgeBetweennessCentrality(g *graph.Graph, cfg *Config) map[node.ID]map[node
 			dist[s] = 0
 
 			// BFS (unweighted)
-			q := []node.ID{s}
+			q := []graph.NodeID{s}
 			for len(q) > 0 {
 				v := q[0]
 				q = q[1:]
@@ -136,7 +135,7 @@ func EdgeBetweennessCentrality(g *graph.Graph, cfg *Config) map[node.ID]map[node
 			}
 
 			// Dependency accumulation
-			delta := make(map[node.ID]float64, n)
+			delta := make(map[graph.NodeID]float64, n)
 			for len(stack) > 0 {
 				w := stack[len(stack)-1]
 				stack = stack[:len(stack)-1]
@@ -150,7 +149,7 @@ func EdgeBetweennessCentrality(g *graph.Graph, cfg *Config) map[node.ID]map[node
 					eu, ev := makeEdgeKey(v, w, isUndirected)
 
 					if local[eu] == nil {
-						local[eu] = make(map[node.ID]float64)
+						local[eu] = make(map[graph.NodeID]float64)
 					}
 
 					local[eu][ev] += c

graph/algorithm/eigenvector_centrality.go

@@ -6,7 +6,6 @@ import (
 	"sync"
 
 	"github.com/elecbug/netkit/graph"
-	"github.com/elecbug/netkit/graph/node"
 )
 
 // EigenvectorCentrality computes eigenvector centrality using parallel power iteration.
@@ -16,8 +15,8 @@ import (
 //     Set Reverse=true to use successors/out-edges (right eigenvector).
 //
 // Unweighted edges are assumed. The result vector is L2-normalized (sum of squares == 1).
-func EigenvectorCentrality(g *graph.Graph, cfg *Config) map[node.ID]float64 {
-	out := make(map[node.ID]float64)
+func EigenvectorCentrality(g *graph.Graph, cfg *Config) map[graph.NodeID]float64 {
+	out := make(map[graph.NodeID]float64)
 	if g == nil {
 		return out
 	}
@@ -26,7 +25,7 @@ func EigenvectorCentrality(g *graph.Graph, cfg *Config) map[node.ID]float64 {
 	maxIter := 100
 	tol := 1e-6
 	reverse := false
-	var nstart *map[node.ID]float64
+	var nstart *map[graph.NodeID]float64
 	workers := runtime.NumCPU()
 
 	if cfg != nil {
@@ -54,7 +53,7 @@ func EigenvectorCentrality(g *graph.Graph, cfg *Config) map[node.ID]float64 {
 	if n == 0 {
 		return out
 	}
-	idxOf := make(map[node.ID]int, n)
+	idxOf := make(map[graph.NodeID]int, n)
 	for i, u := range ids {
 		idxOf[u] = i
 	}