From f6852e8613efb159d3c36e345830dc0ab064d3b6 Mon Sep 17 00:00:00 2001 From: Jerry James Date: Wed, 11 Sep 2019 13:16:07 -0600 Subject: [PATCH] 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 | 60 ++++++++++++++++++++++++++++ python-networkx-dict-iteration.patch | 17 ++++++++ python-networkx-doc.patch | 12 ++++++ python-networkx-is.patch | 22 ++++++++++ python-networkx-iterable.patch | 27 +++++++++++++ python-networkx-source-target.patch | 34 ++++++++++++++++ python-networkx-union-find.patch | 33 +++++++++++++++ python-networkx.spec | 38 ++++++++++++++---- 8 files changed, 236 insertions(+), 7 deletions(-) create mode 100644 python-networkx-cb-iterable.patch create mode 100644 python-networkx-dict-iteration.patch create mode 100644 python-networkx-doc.patch create mode 100644 python-networkx-is.patch create mode 100644 python-networkx-iterable.patch create mode 100644 python-networkx-source-target.patch create mode 100644 python-networkx-union-find.patch diff --git a/python-networkx-cb-iterable.patch b/python-networkx-cb-iterable.patch new file mode 100644 index 0000000..b0edd7d --- /dev/null +++ b/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: diff --git a/python-networkx-dict-iteration.patch b/python-networkx-dict-iteration.patch new file mode 100644 index 0000000..5ef9477 --- /dev/null +++ b/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 diff --git a/python-networkx-doc.patch b/python-networkx-doc.patch new file mode 100644 index 0000000..116d91b --- /dev/null +++ b/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 diff --git a/python-networkx-is.patch b/python-networkx-is.patch new file mode 100644 index 0000000..273dab5 --- /dev/null +++ b/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: diff --git a/python-networkx-iterable.patch b/python-networkx-iterable.patch new file mode 100644 index 0000000..5d9599e --- /dev/null +++ b/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 + diff --git a/python-networkx-source-target.patch b/python-networkx-source-target.patch new file mode 100644 index 0000000..c43edf2 --- /dev/null +++ b/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) + + diff --git a/python-networkx-union-find.patch b/python-networkx-union-find.patch new file mode 100644 index 0000000..3be645d --- /dev/null +++ b/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 diff --git a/python-networkx.spec b/python-networkx.spec index 68eadf5..ca4ecfe 100644 --- a/python-networkx.spec +++ b/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 - 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 - 2.3-4 - Rebuilt for Python 3.8