add README

README.md

@@ -0,0 +1,25 @@
+# gv2adj
+gv2adj computes adjacency matrices (either weighted or unweighted) for Graphviz
+graphs (both directed and undirected).
+
+## Usage
+To get the adjacency matrix of a graph in `graph.gv`:
+```
+gv2adj -f graph.gv
+```
+
+To get the matrix, but using the values stored in the `len` attribute as edge weights:
+```
+gv2adj -f graph.gv --weight-attr len
+```
+
+Say the nodes in the graph are named `foo`, `bar`, and `baz`. To order the rows and columns of the matrix so they correspond to `bar`, `baz`, `foo`:
+```
+gv2adj -f graph.gv --order bar,baz,foo
+```
+
+## Quirks
+* If the `--weight-attr` flag is supplied, but an edge does not have the given
+  attribute, NaN will be output for that edge.
+* If there are multiple edges going from node `a` to node `b`, the matrix entry
+  will be the sum of the two.

cmd/internal/graph/common.go

@@ -18,19 +18,23 @@ package graph
 
 import (
 	"gonum.org/v1/gonum/graph"
+	"gonum.org/v1/gonum/graph/multi"
+	"gonum.org/v1/gonum/graph/simple"
 	"gonum.org/v1/gonum/mat"
 )
 
+// WeightedGraph is an interface so we can construct adjacency matrices for
+// both directed and undirected graphs.
 type WeightedGraph interface {
 	graph.Weighted
 	graph.WeightedMultigraph
 	graph.WeightedMultigraphBuilder
 
 	WeightedEdges() graph.WeightedEdges
-
-	AdjacencyMatrix() *mat.Dense
 }
 
+// WeightedMatrix is an interface to handle the construction of both directed
+// and undirected adjacency matrices.
 type WeightedMatrix interface {
 	graph.Weighted
 
@@ -38,10 +42,25 @@ type WeightedMatrix interface {
 	Matrix() mat.Matrix
 }
 
+// AdjacencyMatrix returns the graph's adjacency matrix.
+func AdjacencyMatrix(g WeightedGraph) *mat.Dense {
+	var adj WeightedMatrix
+	switch g.(type) {
+	case *multi.WeightedDirectedGraph:
+		adj = simple.NewDirectedMatrix(g.Nodes().Len(), 0, 0, 0)
+	case *multi.WeightedUndirectedGraph:
+		adj = simple.NewUndirectedMatrix(g.Nodes().Len(), 0, 0, 0)
+	default:
+		panic("not a graph type we handle")
+	}
+
+	matrix := toAdjMatrix(g, adj)
+	return matrix
+}
+
 func toAdjMatrix(g WeightedGraph, adj WeightedMatrix) *mat.Dense {
 	copyEdges(g, adj)
-	matrix := mat.DenseCopyOf(adj.Matrix())
+	matrix := addSelfEdges(g, adj)
-	addSelfEdges(g, matrix)
 
 	return matrix
 }
@@ -50,6 +69,7 @@ func copyEdges(g WeightedGraph, adj WeightedMatrix) {
 	for edges := g.WeightedEdges(); edges.Next(); {
 		e := edges.WeightedEdge()
 		if e.From() == e.To() {
+			// the simple Matrix classes don't handle self loops
 			continue
 		}
 
@@ -57,14 +77,19 @@ func copyEdges(g WeightedGraph, adj WeightedMatrix) {
 	}
 }
 
-func addSelfEdges(g WeightedGraph, matrix mat.Mutable) {
+func addSelfEdges(g WeightedGraph, adj WeightedMatrix) *mat.Dense {
-	nodes := g.Nodes()
+	matrix := mat.DenseCopyOf(adj.Matrix())
+
+	nodes := adj.Nodes()
 	for i := 0; nodes.Next(); i++ {
-		u := nodes.Node()
+		id := nodes.Node().ID()
+		u := g.Node(id)
 
 		e := g.WeightedEdge(u.ID(), u.ID())
 		if e != nil {
 			matrix.Set(i, i, e.Weight())
 		}
 	}
+
+	return matrix
 }

cmd/internal/graph/directed.go

@@ -1,41 +0,0 @@
-/*
-Copyright © 2025 filifa
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-*/
-package graph
-
-import (
-	"gonum.org/v1/gonum/graph/multi"
-	"gonum.org/v1/gonum/graph/simple"
-	"gonum.org/v1/gonum/mat"
-)
-
-// DirectedGraph embeds a multi.WeightedDirectedGraph (as opposed to
-// simple.WeightedDirectedGraph) to handle self loops.
-type DirectedGraph struct {
-	*multi.WeightedDirectedGraph
-}
-
-// NewDirectedGraph returns a graph with no nodes or edges.
-func NewDirectedGraph() *DirectedGraph {
-	return &DirectedGraph{WeightedDirectedGraph: multi.NewWeightedDirectedGraph()}
-}
-
-// AdjacencyMatrix returns the graph's adjacency matrix.
-func (g *DirectedGraph) AdjacencyMatrix() *mat.Dense {
-	adj := simple.NewDirectedMatrix(g.Nodes().Len(), 0, 0, 0)
-	matrix := toAdjMatrix(g, adj)
-	return matrix
-}

cmd/internal/graph/dot/graph.go

@@ -25,7 +25,7 @@ import (
 	"gonum.org/v1/gonum/graph/multi"
 )
 
-// DOTWeightedGraph is a graph to unmarshal DOT graphs.
+// DOTWeightedGraph is a struct to unmarshal DOT graphs.
 type DOTWeightedGraph struct {
 	igraph.WeightedGraph
 	WeightAttribute string
@@ -33,11 +33,12 @@ type DOTWeightedGraph struct {
 
 // NewDOTDirectedGraph returns a graph with no nodes or edges.
 func NewDOTDirectedGraph(weightAttr string) DOTWeightedGraph {
-	return DOTWeightedGraph{WeightedGraph: igraph.NewDirectedGraph(), WeightAttribute: weightAttr}
+	return DOTWeightedGraph{WeightedGraph: multi.NewWeightedDirectedGraph(), WeightAttribute: weightAttr}
 }
 
+// NewDOTUndirectedGraph returns a graph with no nodes or edges.
 func NewDOTUndirectedGraph(weightAttr string) DOTWeightedGraph {
-	return DOTWeightedGraph{WeightedGraph: igraph.NewUndirectedGraph(), WeightAttribute: weightAttr}
+	return DOTWeightedGraph{WeightedGraph: multi.NewWeightedUndirectedGraph(), WeightAttribute: weightAttr}
 }