Fixes read/write_gml with nan/inf attributes (#4497)

* handle nan/inf for gml files

* handle nan/inf for gml files

* ran black

* Better fix for nan/inf.

* add tests for special floats in gml.py

Co-authored-by: Dan Schult <dschult@colgate.edu>

2 files changed, 124 insertions, 7 deletions

diff --git a/networkx/readwrite/gml.py b/networkx/readwrite/gml.py
index bc3ef710..d84f9260 100644
--- a/networkx/readwrite/gml.py
+++ b/networkx/readwrite/gml.py
@@ -288,7 +288,7 @@ def parse_gml_lines(lines, label, destringizer):
         patterns = [
             r"[A-Za-z][0-9A-Za-z_]*\b",  # keys
             # reals
-            r"[+-]?(?:[0-9]*\.[0-9]+|[0-9]+\.[0-9]*)(?:[Ee][+-]?[0-9]+)?",
+            r"[+-]?(?:[0-9]*\.[0-9]+|[0-9]+\.[0-9]*|INF)(?:[Ee][+-]?[0-9]+)?",
             r"[+-]?[0-9]+",  # ints
             r'".*?"',  # strings
             r"\[",  # dict start
@@ -370,6 +370,15 @@ def parse_gml_lines(lines, label, destringizer):
                             + " convertable ASCII value for node id or label"
                         )
                         unexpected(curr_token, msg)
+                # Special handling for nan and infinity.  Since the gml language
+                # defines unquoted strings as keys, the numeric and string branches
+                # are skipped and we end up in this special branch, so we need to
+                # convert the current token value to a float for NAN and plain INF.
+                # +/-INF are handled in the pattern for 'reals' in tokenize().  This
+                # allows labels and values to be nan or infinity, but not keys.
+                elif curr_token.value in {"NAN", "INF"}:
+                    value = float(curr_token.value)
+                    curr_token = next(tokens)
                 else:  # Otherwise error out
                     unexpected(curr_token, "an int, float, string or '['")
             dct[key].append(value)
@@ -680,12 +689,17 @@ def generate_gml(G, stringizer=None):
                     yield indent + key + " " + str(value)
             elif isinstance(value, float):
                 text = repr(value).upper()
-                # GML requires that a real literal contain a decimal point, but
-                # repr may not output a decimal point when the mantissa is
-                # integral and hence needs fixing.
-                epos = text.rfind("E")
-                if epos != -1 and text.find(".", 0, epos) == -1:
-                    text = text[:epos] + "." + text[epos:]
+                # GML matches INF to keys, so prepend + to INF. Use repr(float(*))
+                # instead of string literal to future proof against changes to repr.
+                if text == repr(float("inf")).upper():
+                    text = "+" + text
+                else:
+                    # GML requires that a real literal contain a decimal point, but
+                    # repr may not output a decimal point when the mantissa is
+                    # integral and hence needs fixing.
+                    epos = text.rfind("E")
+                    if epos != -1 and text.find(".", 0, epos) == -1:
+                        text = text[:epos] + "." + text[epos:]
                 if key == "label":
                     yield indent + key + ' "' + text + '"'
                 else:
diff --git a/networkx/readwrite/tests/test_gml.py b/networkx/readwrite/tests/test_gml.py
index 7511c233..51c08c4f 100644
--- a/networkx/readwrite/tests/test_gml.py
+++ b/networkx/readwrite/tests/test_gml.py
@@ -2,6 +2,7 @@ from ast import literal_eval
 import codecs
 from contextlib import contextmanager
 import io
+import math
 import pytest
 import networkx as nx
 from networkx.readwrite.gml import literal_stringizer, literal_destringizer
@@ -287,6 +288,108 @@ graph
 ]"""
         assert data == answer
 
+    def test_float_label(self):
+        special_floats = [float("nan"), float("+inf"), float("-inf")]
+        try:
+            import numpy as np
+
+            special_floats += [np.nan, np.inf, np.inf * -1]
+        except ImportError:
+            special_floats += special_floats
+
+        G = nx.cycle_graph(len(special_floats))
+        attrs = dict(enumerate(special_floats))
+        nx.set_node_attributes(G, attrs, "nodefloat")
+        edges = list(G.edges)
+        attrs = {edges[i]: value for i, value in enumerate(special_floats)}
+        nx.set_edge_attributes(G, attrs, "edgefloat")
+
+        fobj = tempfile.NamedTemporaryFile()
+        nx.write_gml(G, fobj)
+        fobj.seek(0)
+        # Should be bytes in 2.x and 3.x
+        data = fobj.read().strip().decode("ascii")
+        answer = """graph [
+  node [
+    id 0
+    label "0"
+    nodefloat NAN
+  ]
+  node [
+    id 1
+    label "1"
+    nodefloat +INF
+  ]
+  node [
+    id 2
+    label "2"
+    nodefloat -INF
+  ]
+  node [
+    id 3
+    label "3"
+    nodefloat NAN
+  ]
+  node [
+    id 4
+    label "4"
+    nodefloat +INF
+  ]
+  node [
+    id 5
+    label "5"
+    nodefloat -INF
+  ]
+  edge [
+    source 0
+    target 1
+    edgefloat NAN
+  ]
+  edge [
+    source 0
+    target 5
+    edgefloat +INF
+  ]
+  edge [
+    source 1
+    target 2
+    edgefloat -INF
+  ]
+  edge [
+    source 2
+    target 3
+    edgefloat NAN
+  ]
+  edge [
+    source 3
+    target 4
+    edgefloat +INF
+  ]
+  edge [
+    source 4
+    target 5
+    edgefloat -INF
+  ]
+]"""
+        assert data == answer
+
+        fobj.seek(0)
+        graph = nx.read_gml(fobj)
+        for indx, value in enumerate(special_floats):
+            node_value = graph.nodes[str(indx)]["nodefloat"]
+            if math.isnan(value):
+                assert math.isnan(node_value)
+            else:
+                assert node_value == value
+
+            edge = edges[indx]
+            string_edge = (str(edge[0]), str(edge[1]))
+            edge_value = graph.edges[string_edge]["edgefloat"]
+            if math.isnan(value):
+                assert math.isnan(edge_value)
+            else:
+                assert edge_value == value
+
     def test_name(self):
         G = nx.parse_gml('graph [ name "x" node [ id 0 label "x" ] ]')
         assert "x" == G.graph["name"]