Thanks for the rely. I tried that with boh Graph and Poset (since
graph failed as well) under networkx-0.36 and networkx-1.0.1 both un
un-patched 4.3.1 and patched to account for 1.0.1.
However, everything went through without a hitch.
Un tar-ing the pickle_jar and load
("_class__sage_graphs_graph_Graph__.sobj") or load
("_class__sage_combinat_posets_posets_FinitePoset__.sobj") gives the
error of "ImportError: No module named xgraph" or "ImportError: No
module named xdigraph" respectively (these modules held the classes
removed between 0.36 and 1.0.1). I don't know where these are getting
called if the lines output by explain(dumps(P)) all work?
- Greg
On Jan 29, 1:27 am, "Nicolas M. Thiery" <nicolas.thi...@u-psud.fr>
wrote:
> Hi Greg!
>
> On Thu, Jan 28, 2010 at 08:27:30PM -0800, Greg McWhirter wrote:
> > I've been working on upgrading networkx to 1.0.1 for the past couple
> > days and have things passing almost all the tests (modulo some answer
> > correction for changed format of networkx representations)
>
> Thanks for your work: +1 on staying synchronized with networkx!
>
> > The other big block of tests that don't pass are unpickling tests from
> > sage/structure/sage_object.pyx
> > I am wondering how big a problem this really is?
>
> > Looking at some of the classes for some of the things it fails on
> > (detailed at the bottom), it seems they use a graph object somewhere
> > in the internals. I am guessing that since networkx removed the XGraph
> > and XDiGraph objects somewhere between 0.36 (which is the version
> > currently shipping with sage) and 1.0.1, the pickled objects can't
> > find those classes and fail to unpickle. However, I don't know how to
> > test that exactly, nor what to do about it (possibly patching networkx
> > to do something when asked for those classes, loading up the up-to-
> > date ones instead?)
>
> A confirmation: dynkin diagrams inherit from DiGraph, and all crystals
> point to a dynkin diagram. Similarly for posets. So if some type of
> graphs don't unpickle, I am not surprised for all of this to fail.
>
> The following command (to be run with Sage with the old networkx)
> tells you what will happens upon later unpickling, say, a poset:
>
> sage: P = Poset()
> sage: explain_pickle(dumps(P))
> pg_FinitePoset = unpickle_global('sage.combinat.posets.posets',
> 'FinitePoset')
> si1 = unpickle_newobj(pg_FinitePoset, ())
> pg_HasseDiagram = unpickle_global('sage.combinat.posets.hasse_diagram',
> 'HasseDiagram')
> si2 = unpickle_newobj(pg_HasseDiagram, ())
> pg_SparseGraphBackend = unpickle_global('sage.graphs.base.sparse_graph',
> 'SparseGraphBackend')
> si3 = unpickle_newobj(pg_SparseGraphBackend, ())
> pg_SparseGraph = unpickle_global('sage.graphs.base.sparse_graph',
> 'SparseGraph')
> unpickle_build(si3, {'_cg_rev':pg_SparseGraph(0r, 16r, 10r, [], []),
> 'directed':True, 'vertex_labels':{}, '_multiple_edges':False,
> '_directed':True, '_name':'', 'vertex_ints':{}, '_loops':False,
> 'edge_labels':{0r:None}, '_cg':pg_SparseGraph(0r, 16r, 10r, [], [])})
> unpickle_build(si2, {'_weighted':False, '_pos':None, '_boundary':[],
> '_latex_opts':None, '_backend':si3})
> unpickle_build(si1, {'_hasse_diagram':si2, '_embedding':None,
> '_convert_method_name':None, '_cdata':None, '_category':None, '_names':None,
> '_generators':None, '_elements':[], '_hash':None, '_pickle_version':1r,
> '_element_constructor':None, '_initial_convert_list':[],
> '_element_init_pass_parent':False, '_initial_action_list':[],
> '_initial_coerce_list':[], '_base':None})
> si1
>
> Then, you can just copy paste the commands in a Sage with the new
> networkx, and see what breaks. Most likely it is the
> SparseGraphBackend thing. If it's just a question of renamed class,
> then you can add something along the following lines somewhere in the
> graph code:
>
> from sage.structure.sage_object import register_unpickle_override
>
> register_unpickle_override('sage.graphs.base.sparse_graph','SparseGraphBack
> end',
> <some function or class that will emulate
> the previous thing>)
>
> Cheers,
> Nicolas
> --
> Nicolas M. Thi ry "Isil" <nthi...@users.sf.net>http://Nicolas.Thiery.name/
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