On Tue, 03 Apr 2012 23:38:32 Daniel Krenn wrote: > Am 2012-04-01 12:25, schrieb Daniel Krenn: > > Am 2012-03-31 19:36, schrieb Dima Pasechnik: > >> On 2012-03-31, Daniel Krenn <kr...@aon.at> wrote: > >>> At the moment networkx-1.2.p2.spkg is included in Sage. Networkx 1.2 > >>> is > >>> now over 20 month old and networkx 1.6 is available. Does anyone > >>> plan > >>> upgrading this? > >> > >> Why wouldn't you try to do the upgrade? :-) > >> This looks relatively straightforward - the biggest issue is to figure > >> out what to do with two Sage patches that the spkg applies now. > >> The patches are for > >> readwrite/gml.py > >> and > >> readwrite/tests/test_gml.py > >> (to provide some kind of matplotlib interface) > > > > Ok, maybe it is easier than I thought. I'll give it a try. > > I upgraded the package, available at [1]. The upgrading was really easy; > all patches were already included into 1.6, so obsolete. > > > But now some doctests in graphs are failing, see output below. It seems > that sometimes the output-format has changed (more or less output is > given), but sometimes also the values changed... > > Daniel > > [1] http://www.math.tugraz.at/~krenn/whatever/networkx-1.6.spkg > > > Parts of the doctest on sage.graphs: > > ********************************************************************** > File > "/local/data/krenn/sage-dev/Sage-4.8-amd64-clean/devel/sage-main/sage/graphs > /digraph.py", line 2355: > sage: networkx.topological_sort_recursive(N) is None > Expected: > True > Got: > False > > ********************************************************************** > File > "/local/data/krenn/sage-dev/Sage-4.8-amd64-clean/devel/sage-main/sage/graphs > /graph.py", line 3106: > sage: (graphs.ChvatalGraph()).centrality_betweenness() > Expected: > {0: 0.069696969696969688, 1: 0.069696969696969688, 2: > 0.060606060606060601, 3: 0.060606060606060601, 4: 0.069696969696969688, > 5: 0.069696969696969688, 6: > 0.060606060606060601, 7: 0.060606060606060601, 8: 0.060606060606060601, > 9: 0.060606060606060601, 10: 0.060606060606060601, 11: 0.060606060606060601} > Got: > {0: 0.0, 1: 0.0, 2: 0.19999999999999998, 3: 0.0, 4: > 0.19999999999999998, 5: 0.0, 6: 0.0, 7: 0.14545454545454545, 8: 0.0, 9: > 0.21818181818181817, 10: 0.0, 11: 0.0} > > ********************************************************************** > File > "/local/data/krenn/sage-dev/Sage-4.8-amd64-clean/devel/sage-main/sage/graphs > /graph.py", line 3108: > sage: (graphs.ChvatalGraph()).centrality_betweenness(normalized=False) > Exception raised: > Traceback (most recent call last): > File > "/local/data/krenn/sage-dev/Sage-4.8-amd64-clean/local/bin/ncadoctest.py", > line 1231, in run_one_test > self.run_one_example(test, example, filename, compileflags) > File > "/local/data/krenn/sage-dev/Sage-4.8-amd64-clean/local/bin/sagedoctest.py", > line 38, in run_one_example > OrigDocTestRunner.run_one_example(self, test, example, filename, > compileflags) > File > "/local/data/krenn/sage-dev/Sage-4.8-amd64-clean/local/bin/ncadoctest.py", > line 1172, in run_one_example > compileflags, 1) in test.globs > File "<doctest __main__.example_27[3]>", line 1, in <module> > > (graphs.ChvatalGraph()).centrality_betweenness(normalized=False)###line > 3108: > sage: (graphs.ChvatalGraph()).centrality_betweenness(normalized=False) > File > "/local/data/krenn/sage-dev/Sage-4.8-amd64-clean/local/lib/python/site-packa > ges/sage/graphs/graph.py", line 3118, in centrality_betweenness > return > networkx.betweenness_centrality(self.networkx_graph(copy=False), normalized) > File > "/local/data/krenn/sage-dev/Sage-4.8-amd64-clean/local/lib/python2.6/network > x/algorithms/centrality/betweenness.py", line 118, in betweenness_centrality > k=k) > File > "/local/data/krenn/sage-dev/Sage-4.8-amd64-clean/local/lib/python2.6/network > x/algorithms/centrality/betweenness.py", line 315, in _rescale > scale=scale*n/k > ZeroDivisionError: float division > > ********************************************************************** > File > "/local/data/krenn/sage-dev/Sage-4.8-amd64-clean/devel/sage-main/sage/graphs > /graph.py", line 3114: > sage: D.centrality_betweenness() > Expected: > {0: 0.16666666666666666, 1: 0.16666666666666666, 2: 0.0, 3: 0.0} > Got: > {0: 0.33333333333333331, 1: 0.33333333333333331, 2: 0.0, 3: 0.0} > > ********************************************************************** > File > "/local/data/krenn/sage-dev/Sage-4.8-amd64-clean/devel/sage-main/sage/graphs > /generic_graph.py", line 10294: > sage: (graphs.FruchtGraph()).clustering_coeff(weights=True) > Expected: > ({0: 0.33333333333333331, 1: 0.33333333333333331, 2: 0.0, 3: > 0.33333333333333331, 4: 0.33333333333333331, 5: 0.33333333333333331, 6: > 0.33333333333333331, 7: 0.33333333333333331, 8: 0.0, 9: > 0.33333333333333331, 10: 0.33333333333333331, 11: 0.0}, {0: > 0.083333333333333329, 1: 0.083333333333333329, 2: 0.083333333333333329, > 3: 0.083333333333333329, 4: 0.083333333333333329, 5: > 0.083333333333333329, 6: 0.083333333333333329, 7: 0.083333333333333329, > 8: 0.083333333333333329, 9: 0.083333333333333329, 10: > 0.083333333333333329, 11: 0.083333333333333329}) > Got: > {0: 0.33333333333333331, 1: 0.33333333333333331, 2: 0.0, 3: > 0.33333333333333331, 4: 0.33333333333333331, 5: 0.33333333333333331, 6: > 0.33333333333333331, 7: 0.33333333333333331, 8: 0.0, 9: > 0.33333333333333331, 10: 0.33333333333333331, 11: 0.0} > > ********************************************************************** > File > "/local/data/krenn/sage-dev/Sage-4.8-amd64-clean/devel/sage-main/sage/graphs > /generic_graph.py", line 10298: > sage: > (graphs.FruchtGraph()).clustering_coeff(nbunch=[0,1,2],weights=True) > Expected: > ({0: 0.33333333333333331, 1: 0.33333333333333331, 2: 0.0}, {0: > 0.33333333333333331, 1: 0.33333333333333331, 2: 0.33333333333333331}) > Got: > {0: 0.33333333333333331, 1: 0.33333333333333331, 2: 0.0} > > ********************************************************************** > sage -t devel/sage/sage/graphs/graph_generators.py > *** *** Error: TIMED OUT! PROCESS KILLED! *** ***
There is a lot of stuff there. In sage-on-gentoo I remember we had to lock networkx to 1.2 because in 1.3+ they had changed some interface that was breaking some doctests. In 1.3 this broke doctests: API Changes minimum_spanning_tree() now returns a NetworkX Graph (a tree or forest) But I cannot associate with any of the failing doctests you mention. However I think the API changes introduced in 1.5 are spot on with some of your doctest: http://networkx.lanl.gov/reference/api_1.5.html I think some may be from the changes in 1.6: http://networkx.lanl.gov/reference/api_1.6.html The changes from 1.3 and 1.4 are on this page http://networkx.lanl.gov/reference/news.html But not as many details. In short because of all the changes we will need to do a certain amount of patching in sage before we can ship 1.6 Francois -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
