README.md

@@ -1,25 +0,0 @@
-# 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

@@ -18,23 +18,19 @@ 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
 
@@ -42,25 +38,10 @@ 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 := addSelfEdges(g, adj)
+	matrix := mat.DenseCopyOf(adj.Matrix())
+	addSelfEdges(g, matrix)
 
 	return matrix
 }
@@ -69,7 +50,6 @@ 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
 		}
 
@@ -77,19 +57,14 @@ func copyEdges(g WeightedGraph, adj WeightedMatrix) {
 	}
 }
 
-func addSelfEdges(g WeightedGraph, adj WeightedMatrix) *mat.Dense {
+func addSelfEdges(g WeightedGraph, matrix mat.Mutable) {
-	matrix := mat.DenseCopyOf(adj.Matrix())
+	nodes := g.Nodes()
-
-	nodes := adj.Nodes()
 	for i := 0; nodes.Next(); i++ {
-		id := nodes.Node().ID()
+		u := nodes.Node()
-		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

@@ -0,0 +1,41 @@
+/*
+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 struct to unmarshal DOT graphs.
+// DOTWeightedGraph is a graph to unmarshal DOT graphs.
 type DOTWeightedGraph struct {
 	igraph.WeightedGraph
 	WeightAttribute string
@@ -33,12 +33,11 @@ type DOTWeightedGraph struct {
 
 // NewDOTDirectedGraph returns a graph with no nodes or edges.
 func NewDOTDirectedGraph(weightAttr string) DOTWeightedGraph {
-	return DOTWeightedGraph{WeightedGraph: multi.NewWeightedDirectedGraph(), WeightAttribute: weightAttr}
+	return DOTWeightedGraph{WeightedGraph: igraph.NewDirectedGraph(), WeightAttribute: weightAttr}
 }
 
-// NewDOTUndirectedGraph returns a graph with no nodes or edges.
 func NewDOTUndirectedGraph(weightAttr string) DOTWeightedGraph {
-	return DOTWeightedGraph{WeightedGraph: multi.NewWeightedUndirectedGraph(), WeightAttribute: weightAttr}
+	return DOTWeightedGraph{WeightedGraph: igraph.NewUndirectedGraph(), 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 only errors
+// SetAttribute enables storing the weight read from a DOT file. It errors if
-// if the weight can't be parsed as a float.
+// an attribute is read that can't be stored in a weightedLine.
 func (e *weightedLine) SetAttribute(attr encoding.Attribute) error {
 	var err error
 

cmd/internal/graph/undirected.go

@@ -0,0 +1,41 @@
+/*
+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

@@ -21,7 +21,6 @@ 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"
@@ -44,29 +43,27 @@ var nodeOrder []string
 // rootCmd represents the base command when called without any subcommands
 var rootCmd = &cobra.Command{
 	Use:   "gv2adj",
-	Short: "Compute adjacency matrices for Graphviz graphs",
+	Short: "A brief description of your application",
-	Long: `Compute adjacency matrices (either weighted or unweighted) for Graphviz graphs (both directed and undirected).
+	Long: `A longer description that spans multiple lines and likely contains
+examples and usage of using your application. For example:
 
-Compute an unweighted adjacency matrix:
+Cobra is a CLI library for Go that empowers applications.
-gv2adj -f <dot file>
+This application is a tool to generate the needed files
-
+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:
-	RunE: parse,
+	Run: parse,
 }
 
-func parse(cmd *cobra.Command, args []string) error {
+func parse(cmd *cobra.Command, args []string) {
 	data, err := os.ReadFile(file)
 	if err != nil {
-		return err
+		panic(err)
 	}
 
 	ast, err := dotfmt.ParseBytes(data)
 	if err != nil {
-		return err
+		panic(err)
 	}
 
 	first := ast.Graphs[0]
@@ -79,20 +76,19 @@ func parse(cmd *cobra.Command, args []string) error {
 
 	err = dot.UnmarshalMulti(data, graph)
 	if err != nil {
-		return err
+		panic(err)
 	}
 
-	matrix, err := orderedAdjMatrix(graph.WeightedGraph)
+	matrix, err := orderedAdjMatrix(graph)
 	if err != nil {
-		return err
+		panic(err)
 	}
 
 	outputMatrix(matrix)
-	return nil
 }
 
-func orderedAdjMatrix(g igraph.WeightedGraph) (*mat.Dense, error) {
+func orderedAdjMatrix(g idot.DOTWeightedGraph) (*mat.Dense, error) {
-	matrix := igraph.AdjacencyMatrix(g)
+	matrix := g.AdjacencyMatrix()
 	if len(nodeOrder) == 0 {
 		return matrix, nil
 	}
@@ -111,7 +107,7 @@ func orderedAdjMatrix(g igraph.WeightedGraph) (*mat.Dense, error) {
 		var ok bool
 		newOrder[node.ID()], ok = nodeIndexes[id]
 		if !ok {
-			return nil, errors.New("node '" + id + "' not found in given order")
+			return nil, errors.New("node '" + id + "' not in given order")
 		}
 	}
 
@@ -134,9 +130,9 @@ 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("%#.6v\n", out)
+		fmt.Printf("%#v\n", out)
 	} else {
-		fmt.Printf("%.6v\n", out)
+		fmt.Printf("%v\n", out)
 	}
 }
 
@@ -150,6 +146,14 @@ 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")
 
@@ -159,7 +163,7 @@ func init() {
 
 	rootCmd.Flags().BoolVar(&oneline, "oneline", false, "output on one line")
 
-	rootCmd.Flags().StringVarP(&weightAttr, "weight-attr", "w", "", "edge attribute to use as weight")
+	rootCmd.Flags().StringVar(&weightAttr, "weight-attr", "", "edge attribute to use as weight")
 
-	rootCmd.Flags().StringSliceVarP(&nodeOrder, "order", "o", nil, "list the graph node names in the order they should be placed in the matrix")
+	rootCmd.Flags().StringSliceVarP(&nodeOrder, "order", "o", nil, "order of nodes in rows/columns of output")
 }