#9567 closed enhancement (fixed)
Networkx-1.2 spkg
Reported by: | bedwards | Owned by: | jason, ncohen, rlm |
---|---|---|---|
Priority: | minor | Milestone: | sage-4.5.3 |
Component: | graph theory | Keywords: | networkx spkg graph theory |
Cc: | ncohen | Merged in: | sage-4.5.3.alpha1 |
Authors: | Ben Edwards, Nathann Cohen | Reviewers: | Ben Edwards, Nathann Cohen, Robert Miller |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description
This is the updated networkx package. It includes new features, bug fixes, and a couple of API changes. More information can be found here:
http://networkx.lanl.gov/reference/news.html
Package:
http://spkg-upload.googlecode.com/files/networkx-1.1.spkg
MD5 Sum
http://spkg-upload.googlecode.com/files/networkx-1.1.spkg.md5
Attachments (4)
Change History (36)
comment:1 Changed 12 years ago by
comment:2 Changed 12 years ago by
Three files with doctest failures, most look pretty harmless, different number of arguments, etc.:
The failures were
---------------------------------------------------------------------- The following tests failed: sage -t --long devel/sage-main/sage/graphs/graph_generators.py # 1 doctests failed sage -t --long devel/sage-main/sage/graphs/generic_graph.py # 8 doctests failed sage -t --long devel/sage-main/sage/graphs/graph.py # 19 doctests failed ----------------------------------------------------------------------
comment:3 Changed 12 years ago by
The graph_generators.py
failure looks like a new NX bug:
sage: networkx.random_powerlaw_tree(10, 2) --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /scratch/rlmill/sage-4.5-linux-64bit-ubuntu_8.04.4_lts-x86_64-Linux/<ipython console> in <module>() /scratch/rlmill/sage-4.5-linux-64bit-ubuntu_8.04.4_lts-x86_64-Linux/local/lib/python/networkx/generators/random_graphs.pyc in random_powerlaw_tree(n, gamma, create_using, seed, tries) 930 931 """ --> 932 from nx.generators.degree_seq import degree_sequence_tree 933 try: 934 s=random_powerlaw_tree_sequence(n, ImportError: No module named nx.generators.degree_seq
comment:4 Changed 12 years ago by
- Milestone set to sage-4.5.2
- Report Upstream changed from Reported upstream. Little or no feedback. to N/A
Several API changes:
sage: networkx.triangles? Type: function Base Class: <type 'function'> String Form: <function triangles at 0x4899b18> Namespace: Interactive File: /scratch/rlmill/sage-4.5-linux-64bit-ubuntu_8.04.4_lts-x86_64-Linux/local/lib/python/networkx/algorithms/cluster.py Definition: networkx.triangles(G, nbunch=None) Docstring: <no docstring>
(triangles used to take another argument) -- cluster_triangles()
in Sage will need to be updated to reflect this.
sage: networkx.clustering? Type: function Base Class: <type 'function'> String Form: <function clustering at 0x4899c80> Namespace: Interactive File: /scratch/rlmill/sage-4.5-linux-64bit-ubuntu_8.04.4_lts-x86_64-Linux/local/lib/python/networkx/algorithms/cluster.py Definition: networkx.clustering(G, nbunch=None, weights=False) Docstring: <no docstring>
this is Sage's clustering_coeff()
These are both coming from the argument with_weights
disappearing in NX.
comment:5 Changed 12 years ago by
No idea here:
********************************************************************** File "/scratch/rlmill/sage-4.5-linux-64bit-ubuntu_8.04.4_lts-x86_64-Linux/devel/sage-main/sage/graphs/graph.py", line 2411: sage: (graphs.ChvatalGraph()).centrality_betweenness(normalized=False) Expected: {0: 7.6666666666666661, 1: 7.6666666666666661, 2: 6.6666666666666661, 3: 6.6666666666666661, 4: 7.6666666666666661, 5: 7.6666666666666661, 6: 6.6666666666666661, 7: 6.6666666666666661, 8: 6.6666666666666661, 9: 6.6666666666666661, 10: 6.6666666666666661, 11: 6.6666666666666661} Got: {0: 3.833333333333333, 1: 3.833333333333333, 2: 3.333333333333333, 3: 3.333333333333333, 4: 3.833333333333333, 5: 3.833333333333333, 6: 3.333333333333333, 7: 3.333333333333333, 8: 3.333333333333333, 9: 3.333333333333333, 10: 3.333333333333333, 11: 3.333333333333333} **********************************************************************
comment:6 Changed 12 years ago by
This function no longer takes a vertex as input:
sage: networkx.degree_centrality? Type: function Base Class: <type 'function'> String Form: <function degree_centrality at 0x87e9b0> Namespace: Interactive File: /scratch/rlmill/sage-4.5-linux-64bit-ubuntu_8.04.4_lts-x86_64-Linux/local/lib/python/networkx/algorithms/centrality/degree.py Definition: networkx.degree_centrality(G) Docstring: <no docstring>
comment:7 Changed 12 years ago by
- Cc ncohen added
- Status changed from new to needs_work
There are also some failures related to changes in the API of cliques functionality, but since we ship cliquer standard, which is an optimized C library for just this purpose, it seems we should be using that instead anyway.
All in all, these don't look bad at all. Not nearly as bad as upgrading to 1.0.
Ben -- If you want to submit a patch, I'd be glad to review it.
comment:8 follow-up: ↓ 11 Changed 12 years ago by
The betweenness centrality test is a little concerning, and at a glance I am unsure about the bug in the random_powerlaw_tree, it seems that should work just fine... I'll start working on a patch. The API changes are improvements in the package, imho, returning dictionaries instead of lists, do we change the tests or is that a whole other process? Sorry, I'm new at this.
comment:9 Changed 12 years ago by
comment:10 Changed 12 years ago by
Ok, what I just did sounds stupid. It will be way easier to solve all the bugs and expose methods in the same patch. Let's talk discuss it through emails :-)
Nathann
comment:11 in reply to: ↑ 8 Changed 12 years ago by
Replying to bedwards:
The API changes are improvements in the package, imho, returning dictionaries instead of lists, do we change the tests or is that a whole other process? Sorry, I'm new at this.
We should change everything to support the new syntax, especially since it is so easy. If the pickle jar were having problems, it might mean we would have more work to do, but it seems that 1.0->1.1 involves very minimal changes.
comment:12 Changed 12 years ago by
Started working on this a bit. I think the bug is in the test for the betweenness centrality, I tested it using igraph in R, and it returns the same betweenness centrality as networkx-1.1. Also this was noted as a bug fix in the networkx change log.
comment:13 Changed 12 years ago by
I've completed the patch, and the new version of the package. I've installed this on sage 4.5.1. Adding the spkg, and applying the patch should result in passing tests!
http://groups.google.com/group/sage-devel/attach/8cb10fd6e32e6380/networkx-1.1.p1.spkg?part=4
http://groups.google.com/group/sage-devel/attach/8cb10fd6e32e6380/networkx-1.1.p1.spkg.md5?part=5
http://groups.google.com/group/sage-devel/attach/8cb10fd6e32e6380/14602.patch?part=6
http://groups.google.com/group/sage-devel/attach/15cfd72f79082382/14602.patch.md5?part=4
comment:14 Changed 12 years ago by
Ben,
Can you simply attach the patch to the ticket? Hit the attach button towards the top of the page :)
comment:15 Changed 12 years ago by
No, problem, wasn't quite sure of the protocol, here you go.
Changed 12 years ago by
Changed 12 years ago by
comment:16 Changed 12 years ago by
- Status changed from needs_work to needs_review
comment:17 Changed 12 years ago by
networkx develops fast. Here is a new package for version 1.2. With the patch already attached above this should pass all the graphs/ tests with sage 4.5.1.
http://groups.google.com/group/sage-devel/attach/9521dbae9b6b22db/networkx-1.2.spkg?part=5
http://groups.google.com/group/sage-devel/attach/9521dbae9b6b22db/networkx-1.2.spkg.md5?part=4
comment:18 Changed 12 years ago by
Hello Ben !!!
I added a small patch containing the method cycle_basis (with a long doctest), that just calls NetworkX's. I haven't been able to properly write a cycle_space method (see http://groups.google.com/group/sage-support/browse_thread/thread/f99b59eaabf679a5/8bf34d54c183ab6b?lnk=gst&q=labelled#8bf34d54c183ab6b), so I tried to give a satisfying example in this docstring.
I give a positive review to your own patch for your patch/spkg, short of these two details :
- I fixed some occurences of "dictionary" in my own patch
- Your NetworkX SPKG has "uncommitted changes". Could you do a "hg commit", then upload the new version ? ( You can notice this when using the "sage -pkg" command to build spkg).
Nathann
comment:19 Changed 12 years ago by
Sorry forgot to commit, last time I built the package. Here is the newest one. Sorry about my bad spelling...
comment:20 Changed 12 years ago by
comment:21 Changed 12 years ago by
Well, then if you can review my patch and find everything to your taste, you can set this whole ticket as having received a positive review :-)
Nathann
comment:22 Changed 12 years ago by
On google code, in case they disappear
http://spkg-upload.googlecode.com/files/networkx-1.2.spkg.md5
comment:23 Changed 12 years ago by
- Status changed from needs_review to positive_review
Nathan, you're patch looks great, and I learned a little about cycle basis! Thanks again for correcting my spelling. This one is ready.
comment:24 Changed 12 years ago by
- Status changed from positive_review to needs_work
Should I apply exactly
- http://spkg-upload.googlecode.com/files/networkx-1.2.spkg
- 14602.patch
- trac_9567-cycle_basis.patch
to merge this ticket?
I'm changing the status to 'needs_work' for this: The first patch is missing the ticket number in the first line of its commit string. The first line itself should also be short (< 80 characters) but stand on its own, in order to keep hg log
listings succinct and informative. Of course, there's no problem with extra lines that describe the changes in detail.
The second patch's commit string should perhaps be a bit more descriptive.
Also, please update the Author(s) and Reviewer(s) fields.
comment:25 Changed 12 years ago by
- Reviewers set to Ben Edwards, Nathann Cohen, Robert Miller
The ordering is correct...
Ben : could you update your patch ? I can not overwrite it, and that's the only thing left to do.
Nathann
comment:26 Changed 12 years ago by
Sorry, I was out of town for the weekend. Saw that sage-4.5.2 came out over the weekend, rebuilt the patch for that version, fixing my spelling as well. The appropriate order would be to merge:
http://spkg-upload.googlecode.com/files/networkx-1.2.spkg trac_9567-network-1.2.patch trac_9567-cycle_basis.patch
Nathann, maybe update yours for sage 4.5.2?
Changed 12 years ago by
comment:27 Changed 12 years ago by
Here is a new patched networkx-1.2 spkg that patches networkx to make it compatible with matplotlib.pyparsing.
http://spkg-upload.googlecode.com/files/networkx-1.2.p1.spkg
http://spkg-upload.googlecode.com/files/networkx-1.2.p1.spkg.md5
comment:28 Changed 12 years ago by
Updated !
Nathann
Changed 12 years ago by
comment:29 Changed 12 years ago by
- Status changed from needs_work to positive_review
And back to positive review, as the fiels/descriptions have been filled :-)
Nathann
comment:30 Changed 12 years ago by
- Merged in set to sage-4.5.3.alpha0
- Resolution set to fixed
- Status changed from positive_review to closed
comment:31 Changed 12 years ago by
- Merged in changed from sage-4.5.3.alpha0 to sage-4.5.3.alpha1
comment:32 Changed 12 years ago by
- Summary changed from Networkx-1.1 spkg to Networkx-1.2 spkg
Is this ready for review?