#5934: [with spkg; needs review] networkx -- fix bad spkg
--------------------------+-------------------------------------------------
Reporter: was | Owner: rlm
Type: defect | Status: new
Priority: blocker | Milestone: sage-4.0
Component: graph theory | Keywords:
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Comment(by mvngu):
REFEREE REPORT
[[BR]][[BR]]
The results of #4860 were due to bad refereeing on my part.
[[BR]][[BR]]
The current version of NetworkX in Sage 3.4.2 is, as stated, actually
version 0.36 instead of 0.99 as claimed by the spkg name in
SAGE_ROOT/spkg/standard. Version 0.35.1 has a demo/toy/testing
implementation of {{{edge_betweenness}}}, whereas version 0.36 has an
actual working implementation. Furthermore, version 0.36 doesn't have the
module {{{networkx/matching.py}}}, which was introduced in 0.37. Also,
0.99 has a lot of stuff under {{{networkx/algorithms}}}, whereas 0.36
doesn't even have such a directory. So with the current actual version
0.36 as shipped with Sage 3.4.2, the following is expected:
{{{
sage: # version 0.36 has a working edge_centrality for the first time
sage: from networkx import *
sage: G = Graph()
sage: G.add_node(1)
sage: G.add_nodes_from([2,3])
sage: H=path_graph(10)
sage: G.add_nodes_from(H)
sage: G.add_node(H)
sage: G.add_edge( (1,2) )
sage: G.add_edges_from([(1,2),(1,3)])
sage: G.add_edges_from(H.edges())
sage: networkx.centrality.edge_betweenness(G)
{(0, 1): 0.25,
(1, 2): 0.055555555555555552,
(1, 3): 0.38888888888888884,
(2, 3): 0.19444444444444442,
(3, 4): 0.66666666666666663,
(4, 5): 0.69444444444444442,
(5, 6): 0.66666666666666663,
(6, 7): 0.58333333333333326,
(7, 8): 0.44444444444444442,
(8, 9): 0.25}
sage:
sage: # networkx.algorithms.* not in version 0.36, but appears in version
0.99
sage: from networkx.algorithms.isomorphism.isomorph import
graph_could_be_isomorphic as isomorphic
---------------------------------------------------------------------------
ImportError Traceback (most recent call
last)
/home/mvngu/.sage/temp/sage.math.washington.edu/8026/_home_mvngu__sage_init_sage_0.py
in <module>()
ImportError: No module named algorithms.isomorphism.isomorph
sage:
sage: # version 0.36 doesn't have networkx.matching, which appears for the
first time in 0.37
sage: import networkx.matching
---------------------------------------------------------------------------
ImportError Traceback (most recent call
last)
/home/mvngu/.sage/temp/sage.math.washington.edu/8026/_home_mvngu__sage_init_sage_0.py
in <module>()
ImportError: No module named matching
}}}
[[BR]]
After installing the fake spkg {{{0.99.p1}}} with
[[BR]][[BR]]
sage -i
http://wstein.org/home/wstein/patches/networkx-0.99.p1-fake_really-0.36.spkg
[[BR]][[BR]]
and rebuilding with {{{sage -b}}}, I ran all tests on {{{sage/graphs}}}
with the options {{{-t -long}}} and the tests passed. Running the same
commands as above that use NetworkX returned similar results:
{{{
# version 0.36 has a working edge_centrality for the first time
sage: from networkx import *
sage: G = Graph()
sage: G.add_node(1)
sage: G.add_nodes_from([2,3])
sage: H=path_graph(10)
sage: G.add_nodes_from(H)
sage: G.add_node(H)
sage: G.add_edge( (1,2) )
sage: G.add_edges_from([(1,2),(1,3)])
sage: G.add_edges_from(H.edges())
sage: networkx.centrality.edge_betweenness(G)
{(0, 1): 0.25,
(1, 2): 0.055555555555555552,
(1, 3): 0.38888888888888884,
(2, 3): 0.19444444444444442,
(3, 4): 0.66666666666666663,
(4, 5): 0.69444444444444442,
(5, 6): 0.66666666666666663,
(6, 7): 0.58333333333333326,
(7, 8): 0.44444444444444442,
(8, 9): 0.25}
sage:
sage: # networkx.algorithms.* not in version 0.36, but appears in version
0.99
sage: from networkx.algorithms.isomorphism.isomorph import
graph_could_be_isomorphic as isomorphic
---------------------------------------------------------------------------
ImportError Traceback (most recent call
last)
/home/mvngu/.sage/temp/sage.math.washington.edu/22888/_home_mvngu__sage_init_sage_0.py
in <module>()
ImportError: No module named algorithms.isomorphism.isomorph
sage:
sage: # version 0.36 doesn't have networkx.matching, which appears for the
first time in 0.37
sage: import networkx.matching
---------------------------------------------------------------------------
ImportError Traceback (most recent call
last)
/home/mvngu/.sage/temp/sage.math.washington.edu/22888/_home_mvngu__sage_init_sage_0.py
in <module>()
ImportError: No module named matching
}}}
So on the one hand, the fake {{{0.99.p1}}} installs OK against Sage 3.4.2
and all tests passed even with the option {{{-long}}}. On the other hand,
it is precisely (fingers crossed) version 0.36 of NetworkX as argued
above. I hope I've redeemed myself.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/5934#comment:1>
Sage <http://sagemath.org/>
Sage - Open Source Mathematical Software: Building the Car Instead of
Reinventing the Wheel
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