faster matroid 3 connectivity

[b4a46f46-8d8a-415c-ad35-64549def2993]

Implement the efficient 3 connectivity algorithm.

R. E. Bixby, W. H. Cunningham, Matroids, Graphs, and 3-Connectivity. In Graph theory and related topics (Proc. Conf., Univ. Waterloo, Waterloo, ON, 1977), 91-103

Depends on #18448

CC: @sagetrac-Stefan @sagetrac-yomcat @sagetrac-Rudi

Component: matroid theory

Author: Chao Xu

Branch/Commit: 482ce85

Reviewer: Michael Welsh, Rudi Pendavingh

Issue created by migration from https://trac.sagemath.org/ticket/18539

[b4a46f46-8d8a-415c-ad35-64549def2993]

comment:40

Good point. updated.

[35e1b81c-f27a-4274-bfe3-67d727b6c772]

Reviewer: Michael Welsh

[35e1b81c-f27a-4274-bfe3-67d727b6c772]

comment:41

I'm happy with it now. I'll wait for Stefan/Rudi to give the final sign off. And patchbot should get involved.

[156bf7a1-cdbf-4d2b-a578-797e3af0730c]

comment:42

Hi Chao,

I think the code as such looks great and works great. Repair these last few issues and I'll give a positive review:

The docstring of is_3connected only mentions BC under ..ALGORITHM:. Please also describe the other method.

When _is_3connected_BC throws NotImplementedError, give a description of the problem , e.g. NotImplementedError("The Bixby-Cunningham algorithm does not return a separation")

In the docstring of _is_3connected_CE and _is_3connected_BC, there are several X and one T that need to have single accolades (now double). You can check the appearance of the docstring in the notebook by entering M._is_3connected_BC? on a matroid M.

Finally, I don't believe keeping&depricating the option separation is necessary in this case. This option was introduced in 6.8 beta and so never saw an official release. So if we make sure it's gone before 6.8 is released we should be fine.

If the others agree you can perhaps still change this. Otherwise I'll give the positive review after you settled the above 3 issues.

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Branch pushed to git repo; I updated commit sha1. New commits:

183b216

updated docs

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Changed commit from 6a3484d to 183b216

[156bf7a1-cdbf-4d2b-a578-797e3af0730c]

comment:44

Error building the documentation.
Traceback (most recent call last):
  File "/Users/rudi/Documents/Development/sage-6.7/src/doc/common/builder.py", line 1626, in <module>
    getattr(get_builder(name), type)()
  File "/Users/rudi/Documents/Development/sage-6.7/src/doc/common/builder.py", line 292, in _wrapper
    getattr(get_builder(document), 'inventory')(*args, **kwds)
  File "/Users/rudi/Documents/Development/sage-6.7/src/doc/common/builder.py", line 503, in _wrapper
    x.get(99999)
  File "/Users/rudi/Documents/Development/sage-6.7/local/lib/python/multiprocessing/pool.py", line 558, in get
    raise self._value
OSError: [matroids ] docstring of sage.matroids.matroid.Matroid.is_3connected:33: WARNING: Bullet list ends without a blank line; unexpected unindent.

[156bf7a1-cdbf-4d2b-a578-797e3af0730c]

Changed reviewer from Michael Welsh to Michael Welsh, Rudi Pendavingh

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Changed commit from 183b216 to 2372476

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Branch pushed to git repo; I updated commit sha1. New commits:

2372476

indent problem

[156bf7a1-cdbf-4d2b-a578-797e3af0730c]

comment:46

Code compiles, tests succeed, docs build.

Positive review!

[vbraun]

comment:47

merge conflict, probably #18448

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Changed commit from 2372476 to 34be00b

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Branch pushed to git repo; I updated commit sha1. New commits:

34be00b

Merge branch 'develop' into t/18539/faster_matroid_3_connectivity

[b4a46f46-8d8a-415c-ad35-64549def2993]

comment:50

What can I do at this point to resolve the merge conflict?

[156bf7a1-cdbf-4d2b-a578-797e3af0730c]

comment:51

Hi Chao,

I am also still learning git so perhaps I'm not the right person to give expert advice. But take a look at the way a merge conflict is resolved in this recent ticket #17492. The way to go seems to be to merge the conflicting ticket #18448 into your code. You can do so by a git trac pull 18448 while working on your ticket (this is destructive so if you want to be safe, perform a merge of the two patches in a separate branch). The automatic merge will partially fail and you have to repair some of the source (probably matroid.pyx). Places where the automerger could not decide what to do will be indicated in the source with <<< and >>>.

I doubt that the manual merge will be very difficult in this case, the issue is probably that the new code in both tickets are more or less in the same location. If you want, I will attempt the merge for you.

Just merging develop into your branch as you just did may not suffice, since 18448 is not yet part of develop.

Cheers, Rudi

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

edaf4c7	Improved docstrings, added .is_binary() for BinaryMatroid and RegularMatroid
7ad1f5b	Docstring improvements
503b1e7	Finishing touch docstrings
63767a1	One more ALGORITHM block
8967234	Fixed latex in docstring
29e84da	Merge branch 'u/Rudi/add_test_if_a_matroid_is_binary' of trac.sagemath.org:sage into u/Rudi/add_test_if_a_matroid_is_binary
ada6742	Some changes, tweaks, and made a method public.
b9c3268	Added method .binary_matroid() for Matroid, BinaryMatroid, RegularMatroid
fab68cc	deleted a white space that messed up unindent in docs
482ce85	Merge branch 'u/Rudi/binary_matroid-18448' of git://git.sagemath.org/sage into t/18539/faster_matroid_3_connectivity

[7ed8c4ca-6d56-4ae9-953a-41e42b4ed313]

Changed commit from 34be00b to 482ce85

[b4a46f46-8d8a-415c-ad35-64549def2993]

comment:53

Thanks Rudi, I followed your steps. Hopefully this solves all the conflicts.

[156bf7a1-cdbf-4d2b-a578-797e3af0730c]

comment:54

Yes, that should do it. Positive review again.

[156bf7a1-cdbf-4d2b-a578-797e3af0730c]

Dependencies: 18448

[vbraun]

Changed branch from u/chaoxu/faster_matroid_3_connectivity to 482ce85