#7608: upgrade NetworkX to version 1.0.1
-------------------------------------------+--------------------------------
Reporter: ylchapuy | Owner: jason
Type: enhancement | Status: needs_work
Priority: major | Milestone: sage-4.4
Component: graph theory | Keywords:
Author: Gregory McWhirter | Upstream: N/A
Reviewer: Minh Van Nguyen, Rob Beezer | Merged:
Work_issues: |
-------------------------------------------+--------------------------------
Changes (by jason):
* status: needs_review => needs_work
Comment:
I get a number of failures for "make ptestlong" on sage 4.3.5. It seems
that there are maybe 5-6 real issues. The files that don't pass doctests
are:
{{{
The following tests failed:
sage -t -long
4.3.5/devel/sage/doc/en/bordeaux_2008/elliptic_curves.rst # 8 doctests
failed
sage -t -long 4.3.5/devel/sage/sage/combinat/graph_path.py # 59
doctests failed
sage -t -long 4.3.5/devel/sage/sage/combinat/posets/lattices.py #
67 doctests failed
sage -t -long 4.3.5/devel/sage/sage/combinat/posets/elements.py #
57 doctests failed
sage -t -long
4.3.5/devel/sage/sage/combinat/posets/hasse_diagram.py # 79 doctests
failed
sage -t -long
4.3.5/devel/sage/sage/combinat/posets/poset_examples.py # 44 doctests
failed
sage -t -long 4.3.5/devel/sage/sage/graphs/linearextensions.py #
1 doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/chrompoly.pyx # 10
doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/planarity.pyx # 2
doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/graph_coloring.py # 11
doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/graph_list.py # 25
doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/graph_editor.py # 5
doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/bipartite_graph.py #
22 doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/graph_bundle.py # 2
doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/digraph_generators.py
# 9 doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/graph_latex.py # 17
doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/graph.py # 109
doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/schnyder.py # 23
doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/generic_graph_pyx.pyx
# 6 doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/graph_plot.py # 11
doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/base/dense_graph.pyx #
1 doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/base/c_graph.pyx # 3
doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/base/sparse_graph.pyx
# 1 doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/base/graph_backends.py
# 58 doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/digraph.py # 44
doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/graph_generators.py #
230 doctests failed
sage -t -long 4.3.5/devel/sage/sage/graphs/generic_graph.py # 566
doctests failed
sage -t -long
4.3.5/devel/sage/sage/categories/finite_coxeter_groups.py # 18 doctests
failed
sage -t -long 4.3.5/devel/sage/sage/categories/category.py # 1
doctests failed
sage -t -long 4.3.5/devel/sage/sage/geometry/polyhedra.py # 4
doctests failed
sage -t -long 4.3.5/devel/sage/sage/categories/coxeter_groups.py
# 7 doctests failed
sage -t -long
4.3.5/devel/sage/sage/groups/perm_gps/partn_ref/refinement_graphs.pyx # 1
doctests failed
sage -t -long
4.3.5/devel/sage/sage/homology/simplicial_complex.py # 9 doctests failed
sage -t -long 4.3.5/devel/sage/sage/homology/delta_complex.py # 2
doctests failed
sage -t -long 4.3.5/devel/sage/sage/homology/cell_complex.py # 3
doctests failed
sage -t -long
4.3.5/devel/sage/sage/schemes/elliptic_curves/descent_two_isogeny.pyx # 1
doctests failed
sage -t -long
4.3.5/devel/sage/sage/schemes/elliptic_curves/lseries_ell.py # 10 doctests
failed
sage -t -long
4.3.5/devel/sage/sage/schemes/elliptic_curves/ell_modular_symbols.py # 66
doctests failed
sage -t -long
4.3.5/devel/sage/sage/schemes/elliptic_curves/heegner.py # 10 doctests
failed
sage -t -long
4.3.5/devel/sage/sage/schemes/elliptic_curves/padics.py # 25 doctests
failed
sage -t -long
4.3.5/devel/sage/sage/schemes/elliptic_curves/BSD.py # 9 doctests failed
sage -t -long
4.3.5/devel/sage/sage/schemes/elliptic_curves/sha_tate.py # 48 doctests
failed
sage -t -long
4.3.5/devel/sage/sage/schemes/elliptic_curves/padic_lseries.py # 102
doctests failed
sage -t -long
4.3.5/devel/sage/sage/schemes/elliptic_curves/ell_rational_field.py # 21
doctests failed
sage -t -long 4.3.5/devel/sage/sage/combinat/posets/posets.py #
240 doctests failed
}}}
Here is a sampling of the issues:
{{{
**********************************************************************
File "/home/grout/sage-4.3.5/devel/sage-main/sage/categories/category.py",
line 518:
sage: G.is_directed_acyclic()
Expected:
True
Got:
False
**********************************************************************
1 items had failures:
1 of 6 in __main__.example_12
***Test Failed*** 1 failures.
**********************************************************************
File "/home/grout/sage-4.3.5/devel/sage-
main/sage/graphs/generic_graph.py", line 5453:
sage: G = graphs.TetrahedralGraph()
Exception raised:
Traceback (most recent call last):
File "/home/grout/sage/local/bin/ncadoctest.py", line 1231, in
run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/home/grout/sage/local/bin/sagedoctest.py", line 38, in
run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/home/grout/sage/local/bin/ncadoctest.py", line 1172, in
run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_98[5]>", line 1, in <module>
G = graphs.TetrahedralGraph()###line 5453:
sage: G = graphs.TetrahedralGraph()
File "/home/grout/sage/local/lib/python/site-
packages/sage/graphs/graph_generators.py", line 1651, in TetrahedralGraph
return graph.Graph(G, name="Tetrahedron")
File "/home/grout/sage/local/lib/python/site-
packages/sage/graphs/graph.py", line 832, in __init__
if isinstance(data, (networkx.DiGraph,
networkx.classes.MultiDiGraph)):
AttributeError: 'module' object has no attribute 'classes'
**********************************************************************
**********************************************************************
File "/home/grout/sage-4.3.5/devel/sage-
main/sage/graphs/generic_graph.py", line 10036:
sage: G.get_vertices()
Expected:
{0: 'before', 1: 'after', 2: None, 3: None}
Got:
{0: 'before', 1: 'after', 2: None, 3: None, 4: None, 5: None, 6: None}
**********************************************************************
**********************************************************************
File "/home/grout/sage-4.3.5/devel/sage-
main/sage/graphs/generic_graph.py", line 481:
sage: h._pos is g._pos
Expected:
False
Got:
True
**********************************************************************
**********************************************************************
File "/home/grout/sage-4.3.5/devel/sage-
main/sage/graphs/generic_graph.py", line 7664:
sage: G.shortest_path_lengths(0, by_weight=True)
Exception raised:
Traceback (most recent call last):
File "/home/grout/sage/local/bin/ncadoctest.py", line 1231, in
run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/home/grout/sage/local/bin/sagedoctest.py", line 38, in
run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/home/grout/sage/local/bin/ncadoctest.py", line 1172, in
run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_139[6]>", line 1, in <module>
G.shortest_path_lengths(Integer(0), by_weight=True)###line 7664:
sage: G.shortest_path_lengths(0, by_weight=True)
File "/home/grout/sage/local/lib/python/site-
packages/sage/graphs/generic_graph.py", line 7669, in
shortest_path_lengths
paths = self.shortest_paths(u, by_weight)
File "/home/grout/sage/local/lib/python/site-
packages/sage/graphs/generic_graph.py", line 7632, in shortest_paths
return
networkx.single_source_dijkstra_path(self.networkx_graph(copy=False), u)
File "/home/grout/sage/local/lib/python/site-
packages/sage/graphs/generic_graph.py", line 569, in networkx_graph
name=self.name())
TypeError: __init__() got an unexpected keyword argument 'selfloops'
**********************************************************************
}}}
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/7608#comment:51>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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