Add several bug fix patches.

- Add -doc patch to fix building the gallery of examples.
- Add -is patch to reduce noise in sagemath.
- Add upstream bug fix patches: -source-target, -union-find, -cb-iterable,
  -iterable, and -dict-iteration.

python-networkx-cb-iterable.patch

@@ -0,0 +1,60 @@
+https://github.com/networkx/networkx/commit/eb3a675c5b2b15e33b0a4a35bcee34d6b81ed94d
+Replace cb.iterable with np.iterable (#3458)
+
+`matplotlib.cbook.iterable` is deprecated in matplotlib 3.1
+https://matplotlib.org/3.1.0/api/cbook_api.html#matplotlib.cbook.iterable
+
+Fixes https://github.com/networkx/networkx/issues/3466
+
+--- networkx/drawing/nx_pylab.py.orig	2019-04-11 14:52:34.000000000 -0600
++++ networkx/drawing/nx_pylab.py	2019-09-11 10:14:12.380878784 -0600
+@@ -550,7 +550,6 @@ def draw_networkx_edges(G, pos,
+     try:
+         import matplotlib
+         import matplotlib.pyplot as plt
+-        import matplotlib.cbook as cb
+         from matplotlib.colors import colorConverter, Colormap, Normalize
+         from matplotlib.collections import LineCollection
+         from matplotlib.patches import FancyArrowPatch
+@@ -576,13 +575,13 @@ def draw_networkx_edges(G, pos,
+     # set edge positions
+     edge_pos = np.asarray([(pos[e[0]], pos[e[1]]) for e in edgelist])
+ 
+-    if not cb.iterable(width):
++    if not np.iterable(width):
+         lw = (width,)
+     else:
+         lw = width
+ 
+     if not is_string_like(edge_color) \
+-            and cb.iterable(edge_color) \
++            and np.iterable(edge_color) \
+             and len(edge_color) == len(edge_pos):
+         if np.alltrue([is_string_like(c) for c in edge_color]):
+             # (should check ALL elements)
+@@ -591,7 +590,7 @@ def draw_networkx_edges(G, pos,
+                                  for c in edge_color])
+         elif np.alltrue([not is_string_like(c) for c in edge_color]):
+             # If color specs are given as (rgb) or (rgba) tuples, we're OK
+-            if np.alltrue([cb.iterable(c) and len(c) in (3, 4)
++            if np.alltrue([np.iterable(c) and len(c) in (3, 4)
+                            for c in edge_color]):
+                 edge_colors = tuple(edge_color)
+             else:
+@@ -673,7 +672,7 @@ def draw_networkx_edges(G, pos,
+             line_width = None
+             shrink_source = 0  # space from source to tail
+             shrink_target = 0  # space from  head to target
+-            if cb.iterable(node_size):  # many node sizes
++            if np.iterable(node_size):  # many node sizes
+                 src_node, dst_node = edgelist[i][:2]
+                 index_node = nodelist.index(dst_node)
+                 marker_size = node_size[index_node]
+@@ -797,7 +796,6 @@ def draw_networkx_labels(G, pos,
+     """
+     try:
+         import matplotlib.pyplot as plt
+-        import matplotlib.cbook as cb
+     except ImportError:
+         raise ImportError("Matplotlib required for draw()")
+     except RuntimeError:

python-networkx-dict-iteration.patch

@@ -0,0 +1,17 @@
+https://github.com/networkx/networkx/commit/52e7b5d8732c84512f5423661f234790ce7b1b5f
+Fix dict iteration for Py3.8
+
+Python 3.8 tracks if any key names change while iterating.
+https://github.com/python/cpython/pull/12596
+
+--- networkx/classes/reportviews.py.orig	2019-04-11 14:52:34.000000000 -0600
++++ networkx/classes/reportviews.py	2019-09-11 09:36:56.783002687 -0600
+@@ -1025,7 +1025,7 @@ class EdgeView(OutEdgeView):
+     def __iter__(self):
+         seen = {}
+         for n, nbrs in self._nodes_nbrs():
+-            for nbr in nbrs:
++            for nbr in list(nbrs):
+                 if nbr not in seen:
+                     yield (n, nbr)
+             seen[n] = 1

python-networkx-doc.patch

@@ -0,0 +1,12 @@
+--- doc/conf.py.orig	2019-04-11 14:52:34.000000000 -0600
++++ doc/conf.py	2019-09-11 12:27:51.389122126 -0600
+@@ -72,7 +72,8 @@ sphinx_gallery_conf = {
+     # path where to save gallery generated examples
+     'gallery_dirs': 'auto_examples',
+     'backreferences_dir': 'modules/generated',
+-    'expected_failing_examples': ['../examples/advanced/plot_parallel_betweenness.py']
++    'filename_pattern': '/plot_(?!parallel_betweenness)',
++    'expected_failing_examples': ['../examples/graph/plot_football.py']
+ }
+ 
+ # generate autosummary pages

python-networkx-is.patch

@@ -0,0 +1,22 @@
+--- networkx/convert_matrix.py.orig	2019-04-11 14:52:34.000000000 -0600
++++ networkx/convert_matrix.py	2019-09-11 09:40:18.967671622 -0600
+@@ -560,7 +560,7 @@ def from_numpy_matrix(A, parallel_edges=
+     edges = map(lambda e: (int(e[0]), int(e[1])),
+                 zip(*(np.asarray(A).nonzero())))
+     # handle numpy constructed data type
+-    if python_type is 'void':
++    if python_type == 'void':
+         # Sort the fields by their offset, then by dtype, then by name.
+         fields = sorted((offset, dtype, name) for name, (dtype, offset) in
+                         A.dtype.fields.items())
+--- networkx/drawing/nx_pydot.py.orig	2019-04-11 14:52:34.000000000 -0600
++++ networkx/drawing/nx_pydot.py	2019-09-11 09:40:50.592150597 -0600
+@@ -199,7 +199,7 @@ def to_pydot(N):
+ 
+     name = N.name
+     graph_defaults = N.graph.get('graph', {})
+-    if name is '':
++    if name == '':
+         P = pydot.Dot('', graph_type=graph_type, strict=strict,
+                       **graph_defaults)
+     else:

python-networkx-iterable.patch

@@ -0,0 +1,27 @@
+https://github.com/networkx/networkx/commit/d27930ce099d6f0edca8d5d91d5f3a8d9dc90c9d
+
+Fix deprecation warning with Python 3.7 (#3487)
+
+Replace collections.Iterable with collections.abc.Iterable to fix deprecation warning with Python 3.7:
+"DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working"
+
+--- networkx/drawing/nx_pylab.py.orig	2019-09-11 10:14:12.380878784 -0600
++++ networkx/drawing/nx_pylab.py	2019-09-11 10:14:26.196649773 -0600
+@@ -373,7 +373,7 @@ def draw_networkx_nodes(G, pos,
+     draw_networkx_labels()
+     draw_networkx_edge_labels()
+     """
+-    import collections
++    from collections.abc import Iterable
+     try:
+         import matplotlib.pyplot as plt
+         import numpy as np
+@@ -399,7 +399,7 @@ def draw_networkx_nodes(G, pos,
+     except ValueError:
+         raise nx.NetworkXError('Bad value in node positions.')
+ 
+-    if isinstance(alpha, collections.Iterable):
++    if isinstance(alpha, Iterable):
+         node_color = apply_alpha(node_color, alpha, nodelist, cmap, vmin, vmax)
+         alpha = None
+ 

python-networkx-source-target.patch

@@ -0,0 +1,34 @@
+https://github.com/networkx/networkx/commit/ea2c8db07e0047daa649d484c4cf68ec2d9035f7
+typo: swap source and target
+
+--- networkx/algorithms/shortest_paths/astar.py.orig	2019-04-11 14:52:34.000000000 -0600
++++ networkx/algorithms/shortest_paths/astar.py	2019-09-11 09:22:19.922448001 -0600
+@@ -131,7 +131,7 @@ def astar_path(G, source, target, heuris
+             enqueued[neighbor] = ncost, h
+             push(queue, (ncost + h, next(c), neighbor, ncost, curnode))
+ 
+-    raise nx.NetworkXNoPath("Node %s not reachable from %s" % (source, target))
++    raise nx.NetworkXNoPath("Node %s not reachable from %s" % (target, source))
+ 
+ 
+ def astar_path_length(G, source, target, heuristic=None, weight='weight'):
+--- networkx/algorithms/shortest_paths/weighted.py.orig	2019-04-11 14:52:34.000000000 -0600
++++ networkx/algorithms/shortest_paths/weighted.py	2019-09-11 09:22:46.694007187 -0600
+@@ -1422,7 +1422,7 @@ def bellman_ford_path_length(G, source,
+         return length[target]
+     except KeyError:
+         raise nx.NetworkXNoPath(
+-            "node %s not reachable from %s" % (source, target))
++            "node %s not reachable from %s" % (target, source))
+ 
+ 
+ def single_source_bellman_ford_path(G, source, weight='weight'):
+@@ -1597,7 +1597,7 @@ def single_source_bellman_ford(G, source
+     try:
+         return (dist[target], paths[target])
+     except KeyError:
+-        msg = "Node %s not reachable from %s" % (source, target)
++        msg = "Node %s not reachable from %s" % (target, source)
+         raise nx.NetworkXNoPath(msg)
+ 
+ 

python-networkx-union-find.patch

@@ -0,0 +1,33 @@
+https://github.com/networkx/networkx/commit/1203164760f7be90d5c3a50ab7ab99f04453af8f
+Fix UnionFind set extraction (#3224)
+
+Paths are not guaranteed to be fully pruned by the current
+implementation if subtrees are unioned, e.g.:
+> uf = UnionFind()
+> uf.union(1, 2)
+> uf.union(3, 4)
+> uf.union(4, 5)
+> uf.union(1, 5)
+
+In the current implementation, parents[1]=3 and parents[2]=1.
+Thus, the mere call of networkx.utils.groups(parents) will yield a
+wrong result:
+[set([2]), set([1, 3, 4, 5])]
+
+This patch fixes this behavior by simply doing a "find" operation
+(which, in turn, does full path pruning) on every key before calling
+groups.
+
+--- networkx/utils/union_find.py.orig	2019-04-11 14:52:34.000000000 -0600
++++ networkx/utils/union_find.py	2019-09-11 09:27:32.240303742 -0600
+@@ -90,6 +90,10 @@ class UnionFind:
+             [['x', 'y'], ['z']]
+ 
+         """
++        # Ensure fully pruned paths
++        for x in self.parents.keys():
++            _ = self[x] # Evaluated for side-effect only
++
+         # TODO In Python 3.3+, this should be `yield from ...`.
+         for block in groups(self.parents).values():
+             yield block

python-networkx.spec

@@ -2,11 +2,33 @@
 
 Name:           python-%{srcname}
 Version:        2.3
-Release:        4%{?dist}
+Release:        5%{?dist}
 Summary:        Creates and Manipulates Graphs and Networks
 License:        BSD
 URL:            http://networkx.github.io/
 Source0:        https://github.com/networkx/networkx/archive/%{srcname}-%{version}.tar.gz
+# The football example requires network access, so expect it to fail.
+# The parallel betweenness example hangs when executed, possibly due to a
+# function that cannot be pickled.  In any case, skip it.
+Patch0:         %{name}-doc.patch
+# Fix incorrect uses of the 'is' keyword
+Patch1:         %{name}-is.patch
+# Fix swapped source and target arguments
+# https://github.com/networkx/networkx/commit/ea2c8db07e0047daa649d484c4cf68ec2d9035f7
+Patch2:         %{name}-source-target.patch
+# Fix UnionFind set extraction
+# https://github.com/networkx/networkx/commit/1203164760f7be90d5c3a50ab7ab99f04453af8f
+Patch3:         %{name}-union-find.patch
+# Replace use of deprecated matplotlib.cbook.iterable with np.iterable
+# https://github.com/networkx/networkx/commit/eb3a675c5b2b15e33b0a4a35bcee34d6b81ed94d
+Patch4:         %{name}-cb-iterable.patch
+# Fix the import of Iterable for python 3
+# https://github.com/networkx/networkx/commit/d27930ce099d6f0edca8d5d91d5f3a8d9dc90c9d
+Patch5:         %{name}-iterable.patch
+# Fix iterating over a dictionary when the key names may change
+# https://github.com/networkx/networkx/commit/52e7b5d8732c84512f5423661f234790ce7b1b5f
+Patch6:         %{name}-dict-iteration.patch
+
 BuildArch:      noarch
 
 BuildRequires:  python3-devel
@@ -100,15 +122,11 @@ for f in $(grep -FRl %{_bindir}/env .); do
   rm $f.orig
 done
 
-# The football example requires network access, and the parallel betweenness
-# example has a function that cannot be pickled.
-sed -i "/expected_failing_examples/s|]|,'../examples/advanced/plot_parallel_betweenness.py','../examples/graph/plot_football.py'&|" doc/conf.py
-
 %build
 %py3_build
 
 # Build the documentation
-PYTHONPATH=$PWD/build/lib sphinx-build-3 -C doc html
+PYTHONPATH=$PWD/build/lib make -C doc html
 
 %install
 %py3_install
@@ -141,9 +159,15 @@ grep -rlZ '^#!' %{buildroot}%{python3_sitelib}/networkx | xargs -0 chmod a+x
 %{python3_sitelib}/networkx*
 
 %files doc
-%doc html/*
+%doc doc/build/html/*
 
 %changelog
+* Wed Sep 11 2019 Jerry James <loganjerry@gmail.com> - 2.3-5
+- Add -doc patch to fix building the gallery of examples
+- Add -is patch to reduce noise in sagemath
+- Add upstream bug fix patches: -source-target, -union-find, -cb-iterable,
+  -iterable, and -dict-iteration
+
 * Mon Aug 19 2019 Miro Hrončok <mhroncok@redhat.com> - 2.3-4
 - Rebuilt for Python 3.8