Boring paperwork in the graph/ files

[nathanncohen]

This patch does absolutely nothing.

It removes functions that appeared twice in the code by importing them, which should have been done since the beginning. It also updates deprecation warnings.

Nathann

Depends on #13073

CC: @dcoudert

Component: graph theory

Author: Nathann Cohen

Reviewer: Travis Scrimshaw

Merged: sage-5.5.beta0

Issue created by migration from https://trac.sagemath.org/ticket/13188

[sagetrac-jlopez]

comment:3

Hi Nathan,

the patch fails to apply against sage 5.1rc1 (which barring unexpected failures should be released as 5.1 shortly). You probably want to rebase it.

[sagetrac-jlopez]

Work Issues: Patch fails to apply

[nathanncohen]

comment:4

Rebased ! (I leave tomorrow for 2 months :-p)

Nathann

[tscrim]

comment:5

This fails to apply for me on Sage 5.4.beta1. Additionally the deprecations changed in 5.2 and so sage fails to start properly. Also for line 120 in cliquer.py:

sage: C = Graph('DJ{')

is that brace { suppose to be there?

[nathanncohen]

comment:6

Here it is ! Patch rebased ! And yes, this { is supposed to be there... I mean, it's just how the graph is encoded :-)

sage: Graph('DJ{').size()
7
sage: Graph('DJ').size() 
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)

/home/ncohen/.Sage/devel/sage-2/sage/graphs/<ipython console> in <module>()

/home/ncohen/.Sage/local/lib/python2.7/site-packages/sage/graphs/graph.pyc in __init__(self, data, pos, loops, format, boundary, weighted, implementation, sparse, vertex_labels, name, multiedges, convert_empty_dict_labels_to_None)
   1162                 raise RuntimeError("The string (%s) seems corrupt: for n = %d, the string is too long."%(ss,n))
   1163             elif len(m) < expected:
-> 1164                 raise RuntimeError("The string (%s) seems corrupt: for n = %d, the string is too short."%(ss,n))
   1165             num_verts = n
   1166         elif format == 'sparse6':

RuntimeError: The string (DJ) seems corrupt: for n = 5, the string is too short.

Nathann

[tscrim]

comment:7

I couldn't run the doctest and it seemed out of place. Now the patch applies and functions, however I get new docstring errors/warnings:

docstring of sage.graphs.cliquer.all_max_clique:18: WARNING: duplicate citation NisOst2003, other instance in /home/travis/sage-5.4.beta1/devel/sage/doc/en/reference/sage/graphs/graph.rst
/home/travis/sage-5.4.beta1/local/lib/python2.7/site-packages/sage/graphs/graph.py:docstring of sage.graphs.graph:2: ERROR: Unexpected indentation.
/home/travis/sage-5.4.beta1/local/lib/python2.7/site-packages/sage/graphs/graph.py:docstring of sage.graphs.graph:4: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/travis/sage-5.4.beta1/local/lib/python2.7/site-packages/sage/graphs/graph.py:docstring of sage.graphs.graph.Graph.cliques_maximum:18: WARNING: duplicate citation NisOst2003, other instance in /home/travis/sage-5.4.beta1/devel/sage/doc/en/reference/sage/graphs/cliquer.rst
/home/travis/sage-5.4.beta1/local/lib/python2.7/site-packages/sage/graphs/graph.py:docstring of sage.graphs.graph.Graph.matching_polynomial:162: WARNING: duplicate citation Godsil93, other instance in /home/travis/sage-5.4.beta1/devel/sage/doc/en/reference/sage/graphs/matchpoly.rst
docstring of sage.graphs.matchpoly.matching_polynomial:162: WARNING: duplicate citation Godsil93, other instance in /home/travis/sage-5.4.beta1/devel/sage/doc/en/reference/sage/graphs/graph.rst

The error seems to be in chromatic_polynomial(), but I don't know where the bullet list warning is.

[tscrim]

Changed work issues from Patch fails to apply to docstrings

[nathanncohen]

comment:8

Hellooooooooooooo !!

Could you try to see if this patch works better ? There's still a duplicate reference on my computer but I wonder whether it could be some Sphinx cache problem... So it may work on "any machine different from mine" :-)

Nathann

[tscrim]

comment:9

Attachment: trac_13188.patch.gz

It is good now. I ran build the first time, got the duplicate reference. Popped the patch off, recompiled sage, pushed the patch, recompiled, then rebuilt the docstrings and it was clean.

Travis

[tscrim]

Changed work issues from docstrings to none

[tscrim]

Reviewer: Travis Scrimshaw

[jdemeyer]

Merged: sage-5.5.beta0