On 2012-04-03, François Bissey <francois.bis...@canterbury.ac.nz> wrote: > 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.
Please open a track ticket on this. Thanks, Dima >> >> >> 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
