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}
 }
 
 // NewLine returns a DOT-aware weighted line.

cmd/internal/graph/dot/nodes_edges.go

@@ -48,8 +48,8 @@ type weightedLine struct {
 	weightAttribute string
 }
 
-// SetAttribute enables storing the weight read from a DOT file. It errors if
+// SetAttribute enables storing the weight read from a DOT file. It only errors
-// an attribute is read that can't be stored in a weightedLine.
+// if the weight can't be parsed as a float.
 func (e *weightedLine) SetAttribute(attr encoding.Attribute) error {
 	var err error
 

cmd/internal/graph/undirected.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"
-)
-
-// UndirectedGraph embeds a multi.WeightedUndirectedGraph (as opposed to
-// simple.WeightedUndirectedGraph) to handle self loops.
-type UndirectedGraph struct {
-	*multi.WeightedUndirectedGraph
-}
-
-// NewUndirectedGraph returns a graph with no nodes or edges.
-func NewUndirectedGraph() *UndirectedGraph {
-	return &UndirectedGraph{WeightedUndirectedGraph: multi.NewWeightedUndirectedGraph()}
-}
-
-// AdjacencyMatrix returns the graph's adjacency matrix.
-func (g *UndirectedGraph) AdjacencyMatrix() *mat.Dense {
-	adj := simple.NewUndirectedMatrix(g.Nodes().Len(), 0, 0, 0)
-	matrix := toAdjMatrix(g, adj)
-	return matrix
-}

cmd/root.go

@@ -21,6 +21,7 @@ import (
 	"fmt"
 	"os"
 
+	igraph "scm.dairydemon.net/filifa/gv2adj/cmd/internal/graph"
 	idot "scm.dairydemon.net/filifa/gv2adj/cmd/internal/graph/dot"
 
 	"github.com/spf13/cobra"
@@ -43,27 +44,29 @@ var nodeOrder []string
 // rootCmd represents the base command when called without any subcommands
 var rootCmd = &cobra.Command{
 	Use:   "gv2adj",
-	Short: "A brief description of your application",
+	Short: "Compute adjacency matrices for Graphviz graphs",
-	Long: `A longer description that spans multiple lines and likely contains
+	Long: `Compute adjacency matrices (either weighted or unweighted) for Graphviz graphs (both directed and undirected).
-examples and usage of using your application. For example:
 
-Cobra is a CLI library for Go that empowers applications.
+Compute an unweighted adjacency matrix:
-This application is a tool to generate the needed files
+gv2adj -f <dot file>
-to quickly create a Cobra application.`,
+
+Compute a weighted adjacency matrix, where weights are stored in the 'len' attribute of each edge:
+gv2adj -f <dot file> --weight-attr len
+	`,
 	// Uncomment the following line if your bare application
 	// has an action associated with it:
-	Run: parse,
+	RunE: parse,
 }
 
-func parse(cmd *cobra.Command, args []string) {
+func parse(cmd *cobra.Command, args []string) error {
 	data, err := os.ReadFile(file)
 	if err != nil {
-		panic(err)
+		return err
 	}
 
 	ast, err := dotfmt.ParseBytes(data)
 	if err != nil {
-		panic(err)
+		return err
 	}
 
 	first := ast.Graphs[0]
@@ -76,19 +79,20 @@ func parse(cmd *cobra.Command, args []string) {
 
 	err = dot.UnmarshalMulti(data, graph)
 	if err != nil {
-		panic(err)
+		return err
 	}
 
-	matrix, err := orderedAdjMatrix(graph)
+	matrix, err := orderedAdjMatrix(graph.WeightedGraph)
 	if err != nil {
-		panic(err)
+		return err
 	}
 
 	outputMatrix(matrix)
+	return nil
 }
 
-func orderedAdjMatrix(g idot.DOTWeightedGraph) (*mat.Dense, error) {
+func orderedAdjMatrix(g igraph.WeightedGraph) (*mat.Dense, error) {
-	matrix := g.AdjacencyMatrix()
+	matrix := igraph.AdjacencyMatrix(g)
 	if len(nodeOrder) == 0 {
 		return matrix, nil
 	}
@@ -107,7 +111,7 @@ func orderedAdjMatrix(g idot.DOTWeightedGraph) (*mat.Dense, error) {
 		var ok bool
 		newOrder[node.ID()], ok = nodeIndexes[id]
 		if !ok {
-			return nil, errors.New("node '" + id + "' not in given order")
+			return nil, errors.New("node '" + id + "' not found in given order")
 		}
 	}
 
@@ -130,9 +134,9 @@ func outputMatrix(matrix mat.Matrix) {
 	// for matlab and python formats, %#v outputs as matrix and %v is
 	// oneline, but for standard format, it's the opposite, so we xor
 	if (matlabFmt || pythonFmt) != oneline {
-		fmt.Printf("%#v\n", out)
+		fmt.Printf("%#.6v\n", out)
 	} else {
-		fmt.Printf("%v\n", out)
+		fmt.Printf("%.6v\n", out)
 	}
 }
 
@@ -146,14 +150,6 @@ func Execute() {
 }
 
 func init() {
-	// Here you will define your flags and configuration settings.
-	// Cobra supports persistent flags, which, if defined here,
-	// will be global for your application.
-
-	// rootCmd.PersistentFlags().StringVar(&cfgFile, "config", "", "config file (default is $HOME/.gv2adj.yaml)")
-
-	// Cobra also supports local flags, which will only run
-	// when this action is called directly.
 	rootCmd.Flags().StringVarP(&file, "file", "f", "", "dot file")
 	rootCmd.MarkFlagRequired("file")
 
@@ -163,7 +159,7 @@ func init() {
 
 	rootCmd.Flags().BoolVar(&oneline, "oneline", false, "output on one line")
 
-	rootCmd.Flags().StringVar(&weightAttr, "weight-attr", "", "edge attribute to use as weight")
+	rootCmd.Flags().StringVarP(&weightAttr, "weight-attr", "w", "", "edge attribute to use as weight")
 
-	rootCmd.Flags().StringSliceVarP(&nodeOrder, "order", "o", nil, "order of nodes in rows/columns of output")
+	rootCmd.Flags().StringSliceVarP(&nodeOrder, "order", "o", nil, "list the graph node names in the order they should be placed in the matrix")
 }