Issue89 eaps 5100 upgrade Step 1

examples/express/write_tests.py

@@ -30,3 +30,6 @@
 planarity.write(edgelist, "stdout", planarity.WRITE_G6)
 print("\n")
 
+print("GraphML: ")
+planarity.write(edgelist, "stdout", planarity.WRITE_GRAPHML)
+print("\n")

examples/full/demo_specific_graph.py

@@ -31,6 +31,7 @@ def specific_graph(
     WRITE_ADJLIST,
     WRITE_ADJMATRIX,
     WRITE_G6,
+    WRITE_GRAPHML,
     Graph,
 )
 
@@ -65,7 +66,7 @@ def specific_graph(
         outdir: parent directory under which to make output directory
         command: algorithm command specifier
         output_mode: the desired output format, i.e., WRITE_ADJLIST,
-            WRITE_ADJMATRIX, or WRITE_G6
+            WRITE_ADJMATRIX, WRITE_G6, or WRITE_GRAPHML
 
     Returns:
         OK, NONEMBEDDABLE, or NOTOK based on the embed_result
@@ -78,7 +79,7 @@ def specific_graph(
     """
     gp_SetQuietMode(QUIETMODE_NONE)
 
-    if output_mode not in (WRITE_ADJLIST, WRITE_ADJMATRIX, WRITE_G6):
+    if output_mode not in (WRITE_ADJLIST, WRITE_ADJMATRIX, WRITE_G6, WRITE_GRAPHML):
         raise ValueError(
             f"Invalid output_mode = {output_mode}"
         )
@@ -232,8 +233,8 @@ def print_embed_result(command: str, embed_result: int) -> None:
         type=str,
         required=False,
         default="a",
-        help="Desired graph output format: .g6 (g), Adjacency List (a), or "
-            "Adjacency Matrix (m). Defaults to 'a'\n",
+        help="Desired graph output format: .g6 (g), .graphml (x), "
+            "Adjacency List (a), or Adjacency Matrix (m). Defaults to 'a'\n",
     )
 
     args = parser.parse_args()
@@ -245,14 +246,15 @@ def print_embed_result(command: str, embed_result: int) -> None:
     ] if args.commands else PLANARITY_ALGORITHM_SPECIFIERS()
 
     output_mode = (WRITE_ADJLIST if args.mode == "a"
-                         else (WRITE_ADJMATRIX if args.mode == "m" 
+                         else (WRITE_ADJMATRIX if args.mode == "m"
                                else (WRITE_G6 if args.mode == "g"
-                                     else None)))
+                                     else (WRITE_GRAPHML if args.mode == "x"
+                                        else None))))
 
     if not output_mode:
         raise ValueError(
-            f"Invalid argument for mode = {args.mode}; only accepted values "
-            "are g (.g6), a (Adjacency List), or m (Adjacency Matrix)"
+            f"Invalid argument for mode = {args.mode}; only accepted values are "
+            "g (.g6), x (.graphml), a (Adjacency List), or m (Adjacency Matrix)"
         )
 
     for command in commands:

examples/full/sample_files/one_edge.graphml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
+     http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
+  <graph id="G1" edgedefault="undirected"
+         parse.nodes="2" parse.edges="1"
+         parse.nodeids="canonical" parse.edgeids="canonical"
+         parse.order="nodesfirst">
+    <node id="n0"/>
+    <node id="n1"/>
+    <edge id="e0" source="n0" target="n1"/>
+  </graph>
+</graphml>

examples/full/sample_files/one_edge.txt

@@ -0,0 +1,3 @@
+N=2
+1: 2 0
+2: 1 0

planarity/__init__.py

@@ -53,6 +53,7 @@
     WRITE_ADJLIST,
     WRITE_ADJMATRIX,
     WRITE_G6,
+    WRITE_GRAPHML,
     GRAPHFLAGS_ZEROBASEDIO,
 )
 # Surfaced from planarity/c/graphLib/planarityRelated/graphPlanarity.h

planarity/c/LICENSE.TXT

@@ -1,26 +1,4 @@
-The Edge Addition Planarity Suite
 Copyright (c) 1997-2026, John M. Boyer
-All rights reserved. Includes a reference implementation of the following:
-
-* John M. Boyer. "Subgraph Homeomorphism via the Edge Addition Planarity Algorithm".
-  Journal of Graph Algorithms and Applications, Vol. 16, no. 2, pp. 381-410, 2012.
-  http://dx.doi.org/10.7155/jgaa.00268
-
-* John M. Boyer. "A New Method for Efficiently Generating Planar Graph
-  Visibility Representations". In P. Eades and P. Healy, editors,
-  Proceedings of the 13th International Conference on Graph Drawing 2005,
-  Lecture Notes Comput. Sci., Volume 3843, pp. 508-511, Springer-Verlag, 2006.
-  http://dx.doi.org/10.1007/11618058_47
-
-* John M. Boyer and Wendy J. Myrvold. "On the Cutting Edge: Simplified O(n)
-  Planarity by Edge Addition". Journal of Graph Algorithms and Applications,
-  Vol. 8, No. 3, pp. 241-273, 2004.
-  http://dx.doi.org/10.7155/jgaa.00091
-
-* John M. Boyer. "Simplified O(n) Algorithms for Planar Graph Embedding,
-  Kuratowski Subgraph Isolation, and Related Problems". Ph.D. Dissertation,
-  University of Victoria, 2001.
-  https://dspace.library.uvic.ca/handle/1828/9918
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

planarity/c/graphLib/extensionSystem/graphExtensions.c

@@ -8,6 +8,7 @@ See the LICENSE.TXT file for licensing information.
 #include <string.h>
 
 #include "../lowLevelUtils/appconst.h"
+#include "../graph.private.h"
 
 #include "graphExtensions.private.h"
 #include "graphExtensions.h"
@@ -95,15 +96,11 @@ static int moduleIDGenerator = 0;
      if your feature is attached but not active or if your feature
      augments the base behavior rather than replacing it.
 
-     a) If extra data must be maintained at the graph, vertex or edge 
-        levels, then fpEnsureVertexCapacity(), fpEnsureEdgeCapacity(), 
-        and fpResetGraphStorage() must be overloaded.
+     a) If extra data must be maintained at the graph, vertex or edge
+        levels, then fpEnsureVertexCapacity(), fpEnsureEdgeCapacity(),
+        fpDeleteEdge(), and fpResetGraphStorage() must be overloaded.
 
-     b) For a parallel array of edge data, the extension must currently
-        provides its own _Feature_DeleteEdge() that initializes its edge
-        extension data along with calling gp_DeleteEdge().
-
-     c) If any data must be persisted in the file format, then overloads
+     b) If any data must be persisted in the file format, then overloads
         of fpReadPostprocess() and fpWritePostprocess() are needed.
 
   7) Define internal functions for _Feature_ClearStructures(),
@@ -182,7 +179,12 @@ int gp_AddExtension(graphP theGraph,
 
     if (theGraph == NULL || pModuleID == NULL ||
         context == NULL || copyData == NULL || freeContext == NULL ||
-        functions == NULL)
+        functions == NULL || theGraph->extensionLookupTable == NULL)
+    {
+        return NOTOK;
+    }
+
+    if (*pModuleID < 0 || *pModuleID > MAXNUMSUPPORTEDEXTENSIONS)
     {
         return NOTOK;
     }
@@ -196,6 +198,10 @@ int gp_AddExtension(graphP theGraph,
     // Assign a unique ID to the extension if it does not already have one
     if (*pModuleID == 0)
     {
+        if (moduleIDGenerator >= MAXNUMSUPPORTEDEXTENSIONS)
+        {
+            return NOTOK;
+        }
         *pModuleID = ++moduleIDGenerator;
     }
 
@@ -218,6 +224,7 @@ int gp_AddExtension(graphP theGraph,
     // Make the new linkages
     newExtension->next = (struct graphExtensionStruct *)theGraph->extensions;
     theGraph->extensions = newExtension;
+    theGraph->extensionLookupTable[newExtension->moduleID] = newExtension;
 
     // The new extension was successfully added
     return OK;
@@ -273,32 +280,28 @@ void _OverloadFunctions(graphP theGraph, graphFunctionTableP functions)
 
 int gp_FindExtension(graphP theGraph, int moduleID, void **pContext)
 {
-    graphExtensionP first = NULL, next = NULL;
+    graphExtensionP extension = NULL;
 
     if (pContext != NULL)
     {
         *pContext = NULL;
     }
 
-    if (theGraph == NULL || moduleID == 0)
+    if (theGraph == NULL || moduleID <= 0 ||
+        moduleID > MAXNUMSUPPORTEDEXTENSIONS ||
+        theGraph->extensionLookupTable == NULL)
     {
         return FALSE;
     }
 
-    first = theGraph->extensions;
-
-    while (first != NULL)
+    extension = theGraph->extensionLookupTable[moduleID];
+    if (extension != NULL)
     {
-        next = (graphExtensionP)first->next;
-        if (first->moduleID == moduleID)
+        if (pContext != NULL)
         {
-            if (pContext != NULL)
-            {
-                *pContext = first->context;
-            }
-            return TRUE;
+            *pContext = extension->context;
         }
-        first = next;
+        return TRUE;
     }
 
     return FALSE;
@@ -342,7 +345,9 @@ int gp_RemoveExtension(graphP theGraph, int moduleID)
 {
     graphExtensionP prev = NULL, curr = NULL, next = NULL;
 
-    if (theGraph == NULL || moduleID == 0)
+    if (theGraph == NULL || moduleID <= 0 ||
+        moduleID > MAXNUMSUPPORTEDEXTENSIONS ||
+        theGraph->extensionLookupTable == NULL)
         return NOTOK;
 
     curr = theGraph->extensions;
@@ -372,6 +377,7 @@ int gp_RemoveExtension(graphP theGraph, int moduleID)
             theGraph->extensions = next;
 
         // Free the curr extension
+        theGraph->extensionLookupTable[curr->moduleID] = NULL;
         _FreeExtension(curr);
     }
 
@@ -448,7 +454,8 @@ int gp_DupExtensions(graphP dstGraph, graphP srcGraph)
 {
     graphExtensionP next = NULL, newNext = NULL, newLast = NULL;
 
-    if (srcGraph == NULL || dstGraph == NULL)
+    if (srcGraph == NULL || dstGraph == NULL ||
+        dstGraph->extensionLookupTable == NULL)
         return NOTOK;
 
     gp_FreeExtensions(dstGraph);
@@ -457,6 +464,12 @@ int gp_DupExtensions(graphP dstGraph, graphP srcGraph)
 
     while (next != NULL)
     {
+        if (next->moduleID <= 0 || next->moduleID > MAXNUMSUPPORTEDEXTENSIONS)
+        {
+            gp_FreeExtensions(dstGraph);
+            return NOTOK;
+        }
+
         if ((newNext = (graphExtensionP)malloc(sizeof(graphExtensionStruct))) == NULL)
         {
             gp_FreeExtensions(dstGraph);
@@ -471,6 +484,10 @@ int gp_DupExtensions(graphP dstGraph, graphP srcGraph)
         newNext->functions = next->functions;
         newNext->next = NULL;
 
+        // Add the new extension to the dstGraph extension lookup table
+        dstGraph->extensionLookupTable[newNext->moduleID] = newNext;
+
+        // Add the new extension to the dstGraph extensions linked list
         if (newLast != NULL)
             newLast->next = (struct graphExtensionStruct *)newNext;
         else
@@ -488,38 +505,18 @@ int gp_DupExtensions(graphP dstGraph, graphP srcGraph)
  gp_CopyExtensions()
  ********************************************************************/
 
-// This number can just be made bigger if ever needed
-#define MAXNUMSUPPORTEDEXTENSIONS 32
-
 int gp_CopyExtensions(graphP dstGraph, graphP srcGraph)
 {
     graphExtensionP dstExtension = NULL, srcExtension = NULL;
-    graphExtensionP srcExtensionIDMap[MAXNUMSUPPORTEDEXTENSIONS+1];
 
-    if (srcGraph == NULL || dstGraph == NULL)
+    if (srcGraph == NULL || dstGraph == NULL ||
+        srcGraph->extensionLookupTable == NULL ||
+        dstGraph->extensionLookupTable == NULL)
         return NOTOK;
 
     if (gp_GetN(dstGraph) != gp_GetN(srcGraph) || gp_GetN(dstGraph) == 0)
         return NOTOK;
 
-    // NULL out the pointers in the srcExtensionIDMap
-    memset(srcExtensionIDMap, 0, (MAXNUMSUPPORTEDEXTENSIONS+1)*sizeof(graphExtensionP));
-
-    // Run through the srcGraph extensions linked list and put the pointer to 
-    // each extension in the srcExtensionIDMap at the index location indicated
-    // by the extension module ID. This mapping is needed because the srcGraph
-    // may have been extended with the extensions in a different order than the
-    // dstGraph, but the moduleID for each extension is the same across graphs. 
-    srcExtension = srcGraph->extensions;
-    while (srcExtension != NULL)
-    {
-        if (srcExtension->moduleID < 0 || srcExtension->moduleID > MAXNUMSUPPORTEDEXTENSIONS)
-            return NOTOK;
-
-        srcExtensionIDMap[srcExtension->moduleID] = srcExtension;
-        srcExtension = (graphExtensionP)srcExtension->next;        
-    }
-
     // For each extension in the dstGraph, if the srcGraph has the same extension,
     // then we invoke the extension's copyData to copy from srcGraph to dstGraph.
     // If the dstGraph has an extension that the srcGraph does not have, then
@@ -528,7 +525,11 @@ int gp_CopyExtensions(graphP dstGraph, graphP srcGraph)
     dstExtension = dstGraph->extensions;
     while (dstExtension != NULL)
     {
-        srcExtension = srcExtensionIDMap[dstExtension->moduleID];
+        if (dstExtension->moduleID <= 0 ||
+            dstExtension->moduleID > MAXNUMSUPPORTEDEXTENSIONS)
+            return NOTOK;
+
+        srcExtension = srcGraph->extensionLookupTable[dstExtension->moduleID];
         if (dstExtension->copyData(dstExtension->context, srcExtension ? srcExtension->context : NULL) != OK)
             return NOTOK;
 
@@ -562,6 +563,10 @@ void gp_FreeExtensions(graphP theGraph)
         }
 
         theGraph->extensions = NULL;
+        if (theGraph->extensionLookupTable != NULL)
+        {
+            memset(theGraph->extensionLookupTable, 0, (MAXNUMSUPPORTEDEXTENSIONS+1)*sizeof(graphExtensionP));
+        }
         _InitFunctionTable(theGraph);
     }
 }

planarity/c/graphLib/extensionSystem/graphExtensions.h

@@ -17,9 +17,9 @@ extern "C"
     int gp_AddExtension(graphP theGraph,
                         int *pModuleID,
                         void *context,
-                        void *(*dupContext)(void *, void *),
-                        int  (*copyData)(void *, void *),
-                        void (*freeContext)(void *),
+                        void *(*dupContext)(void *pContext, void *theGraph),
+                        int  (*copyData)(void *dstContext, void *srcContext),
+                        void (*freeContext)(void *pContext),
                         graphFunctionTableP overloadTable);
 
     int gp_FindExtension(graphP theGraph, int moduleID, void **pContext);

planarity/c/graphLib/extensionSystem/graphExtensions.private.h

@@ -18,9 +18,9 @@ extern "C"
     {
         int moduleID;
         void *context;
-        void *(*dupContext)(void *, void *);
-        int  (*copyData)(void *, void *);
-        void (*freeContext)(void *);
+        void *(*dupContext)(void *pContext, void *theGraph);
+        int  (*copyData)(void *dstContext, void *srcContext);
+        void (*freeContext)(void *pContext);
 
         graphFunctionTableP functions;