Opened 11 years ago
Closed 11 years ago
#8329 closed defect (fixed)
Missing copy() method in BipartiteGraph
Reported by: | rhinton | Owned by: | rhinton |
---|---|---|---|
Priority: | major | Milestone: | sage-4.4 |
Component: | graph theory | Keywords: | BipartiteGraph, copy |
Cc: | rlm, jason | Merged in: | sage-4.4.alpha0 |
Authors: | Ryan Hinton | Reviewers: | Robert Miller |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description
BipartiteGraph? is missing a copy() method.
sage: bg = BipartiteGraph(graphs.CycleGraph(4)) sage: type(bg) <class 'sage.graphs.bipartite_graph.BipartiteGraph'> sage: bg2 = bg.copy() sage: type(bg2) <class 'sage.graphs.graph.Graph'>
The result is not horrendous because the base Graph class has a copy() method. But the result is unexpected: copy() a BipartiteGraph? and you get a Graph?
Attachments (2)
Change History (20)
comment:1 Changed 11 years ago by
- Status changed from new to needs_review
comment:2 Changed 11 years ago by
- Cc jason added; jgrout removed
comment:3 Changed 11 years ago by
- Status changed from needs_review to needs_work
comment:4 Changed 11 years ago by
- Status changed from needs_work to needs_review
New patch (replaced old) should work, including fixed doctest.
comment:5 follow-up: ↓ 6 Changed 11 years ago by
This is item 9 on trac #1941.
comment:6 in reply to: ↑ 5 ; follow-up: ↓ 7 Changed 11 years ago by
Right, I had forgotten about this. Obviously I'm fixing methods as I need them. I don't have time right now for the complete overhaul. Is the piecemeal approach OK?
Incidentally, I think I have a decent approach for add_vertex. I was planning on opening another ticket.... :-)
comment:7 in reply to: ↑ 6 ; follow-up: ↓ 9 Changed 11 years ago by
Replying to rhinton:
Right, I had forgotten about this. Obviously I'm fixing methods as I need them. I don't have time right now for the complete overhaul. Is the piecemeal approach OK?
I was just linking the tickets to each other. Adding edges to trac I guess... Any way you want to improve bipartite graphs I'll gladly review once I get the time, I just wanted to make sure you were aware of that ticket.
Incidentally, I think I have a decent approach for add_vertex. I was planning on opening another ticket.... :-)
Go for it!
comment:8 Changed 11 years ago by
Note for someone who is more knowledgeable: the new BipartiteGraph?.copy() method doesn't try to do anything tricky with vertex associations, boundaries, positions, etc. It just tries the Graph constructor. I haven't figured out a way to copy() the Graph part and get out a BipartiteGraph? instance. This way works for me, but I'm not sure if it does all the special stuff that Graph.copy() does.
comment:9 in reply to: ↑ 7 Changed 11 years ago by
I get it ... adding edges. :-)
Replying to rlm:
Replying to rhinton:
Right, I had forgotten about this. Obviously I'm fixing methods as I need them. I don't have time right now for the complete overhaul. Is the piecemeal approach OK?
I was just linking the tickets to each other. Adding edges to trac I guess... Any way you want to improve bipartite graphs I'll gladly review once I get the time, I just wanted to make sure you were aware of that ticket.
comment:10 Changed 11 years ago by
- Cc ncohen added
- Keywords copy added
The new patch to GenericGraph?.copy() always creates a new object of the same class as the original object -- no special case code for Graph, DiGraph?, or BipartiteGraph?. Any future subclasses will work as well assuming they can handle the same initializer arguments (by passing them to the superclass initializer).
comment:11 Changed 11 years ago by
This patch exposes a bug in another seldom used extension of the Graph
class, GraphBundle
.
File "/Users/rlmill/sage-4.3.3/devel/sage-main/sage/graphs/graph_bundle.py", line 163: sage: B.plot() Exception raised: Traceback (most recent call last): File "/Users/rlmill/sage-4.3.3/local/bin/ncadoctest.py", line 1231, in run_one_test self.run_one_example(test, example, filename, compileflags) File "/Users/rlmill/sage-4.3.3/local/bin/sagedoctest.py", line 38, in run_one_example OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags) File "/Users/rlmill/sage-4.3.3/local/bin/ncadoctest.py", line 1172, in run_one_example compileflags, 1) in test.globs File "<doctest __main__.example_5[5]>", line 1, in <module> B.plot()###line 163: sage: B.plot() File "/Users/rlmill/sage-4.3.3/local/lib/python/site-packages/sage/graphs/graph_bundle.py", line 173, in plot total_pos = generic_graph_pyx.spring_layout_fast(self, iterations=iters) File "generic_graph_pyx.pyx", line 86, in sage.graphs.generic_graph_pyx.spring_layout_fast (sage/graphs/generic_graph_pyx.c:1361) File "/Users/rlmill/sage-4.3.3/local/lib/python/site-packages/sage/graphs/graph.py", line 2061, in to_undirected return copy(self) File "/Users/rlmill/sage-4.3.3/local/lib/python2.6/copy.py", line 79, in copy return copier(x) File "/Users/rlmill/sage-4.3.3/local/lib/python/site-packages/sage/graphs/generic_graph.py", line 483, in __copy__ G = self.__class__(self, name=self.name(), pos=copy(self._pos), boundary=copy(self._boundary), implementation=implementation, sparse=sparse) File "/Users/rlmill/sage-4.3.3/local/lib/python/site-packages/sage/graphs/graph_bundle.py", line 73, in __init__ if isinstance(args[0], (list, tuple)): IndexError: tuple index out of range
comment:12 Changed 11 years ago by
I will offer the suggestion to disable the failing doctest, for discussion. I don't know of anyone who uses graph bundles in Sage. I've emailed Chris Godsil to see if he ever uses it.
comment:13 Changed 11 years ago by
Sounds great to me. The new patch disables the "plot" doctest that was failing and adds a "known bugs" warning to the beginning of the graph_bundle.py.
comment:14 Changed 11 years ago by
- Reviewers set to Robert Miller
- Status changed from needs_review to positive_review
Anyone queasy about the GraphBundle
doctest, Godsil tells me he has a student who is working on a bundle package, which I am assuming actually does something (unlike bundles in Sage). Look for this to appear in Sage at some point soon!
comment:15 Changed 11 years ago by
- Cc ncohen removed
- Status changed from positive_review to needs_work
Found a failing doctest in combinat/posets/posets.py due to this change. Additional patch coming soon.
comment:16 Changed 11 years ago by
- Status changed from needs_work to needs_review
New patch fixes posets doctest failure. Apply both patches; order does not matter.
comment:17 Changed 11 years ago by
- Status changed from needs_review to positive_review
Good patch ! Applies fine, does its job.. :-)
Nathann
comment:18 Changed 11 years ago by
- Merged in set to sage-4.4.alpha0
- Resolution set to fixed
- Status changed from positive_review to closed
Merged in 4.4.alpha0:
- trac_8329-bipartite-graph-copy.patch
- trac_8329-posets-repr.patch
Oops, bug in doctest, the patch doesn't work at all.