Opened 8 years ago
Closed 7 years ago
#17462 closed defect (fixed)
Remove the (deprecated) _boundary parameter
Reported by:  Nathann Cohen  Owned by:  

Priority:  major  Milestone:  sage6.9 
Component:  graph theory  Keywords:  
Cc:  Merged in:  
Authors:  Nathann Cohen  Reviewers:  David Coudert 
Report Upstream:  N/A  Work issues:  
Branch:  43cf74a (Commits, GitHub, GitLab)  Commit:  43cf74ac4b0bb2729ffe7288d8d1ab4ed8e76a8d 
Dependencies:  Stopgaps: 
Description (last modified by )
The _boundary attribute has been deprecated since Sage 6.3 in #15494. This ticket totally removes it fro the graph class.
The branch fixes a small problem that went probably unnoticed in #15494: the function Graph.genus was using this attribute (and so has been raising warnings for one year) but there was no other way to give a list of vertices to the function. Consequently, this branch turns one of its boolean arguments into a list, so that this function can be used properly, i.e. without global variables.
Change History (20)
comment:1 Changed 8 years ago by
Branch:  → u/ncohen/17462 

Description:  modified (diff) 
Status:  new → needs_review 
comment:2 Changed 8 years ago by
Commit:  → 55b2fdd77f0eb3de5aa789801f26f5f79ffef267 

comment:3 Changed 8 years ago by
Description:  modified (diff) 

Milestone:  sage6.5 → sagepending 
comment:4 Changed 8 years ago by
Description:  modified (diff) 

Milestone:  sagepending → sage6.5 
Please do not add such a message on the ticket without explaining why. The developper's manual says that the deprecation should hold for at least a year, and this deprecation is from more than one year.
http://www.sagemath.org/doc/developer/coding_in_python.html#deprecation
Nathann
comment:5 followup: 6 Changed 8 years ago by
Description:  modified (diff) 

Milestone:  sage6.5 → sagepending 
I think the "one year" rule should be interpreted since a stable Sage release, not just since the opening of the ticket. The idea is to give users a one year warning that whatever they are using is deprecated.
It's very unreasonable to expect users to read all trac tickets for deprecations.
comment:6 followup: 7 Changed 8 years ago by
Really Jeroen, I do not think that you are achieving anything besides being unpleasant. Coming on somebody else's ticket to discuss whether the date to take into account for deprecation is the day it was merged or the stable release that followed, really....
You take into account the 'first stable release' as the first date on which the deprecation appears, and you add a message here saying that 'no beta release' should be made that contains this branch. Stable on one hand, beta on the other, and all for nothing.
Anyway. Not even worth fighting for, it is just unpleasant and pointless.
Nathann
comment:7 Changed 8 years ago by
Replying to ncohen:
Coming on somebody else's ticket to discuss whether the date to take into account for deprecation is the day it was merged or the stable release that followed, really....
For this ticket, it was merged in the git repo 20150606, which is only half a year ago.
comment:9 Changed 8 years ago by
Commit:  55b2fdd77f0eb3de5aa789801f26f5f79ffef267 → 084df3f59d4f5a3b1cc4614de742d846d7f8da96 

Branch pushed to git repo; I updated commit sha1. New commits:
084df3f  trac #17462: Merged with 6.7.beta4

comment:10 Changed 7 years ago by
Description:  modified (diff) 

comment:11 Changed 7 years ago by
Commit:  084df3f59d4f5a3b1cc4614de742d846d7f8da96 → 41943ff9a08e086a14f2bf4d897bac60321288c1 

Branch pushed to git repo; I updated commit sha1. New commits:
41943ff  trac #17462: Merged with 6.9.beta0

comment:12 Changed 7 years ago by
Long tests ok for graph.py
, digraph.py
and graph_plot.py
, but not for generic_graph.py
.
sage t long src/sage/graphs/generic_graph.py ********************************************************************** File "src/sage/graphs/generic_graph.py", line 1999, in sage.graphs.generic_graph.GenericGraph.get_embedding Failed example: G.genus() Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.get_embedding[1]>", line 1, in <module> G.genus() File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 4362, in genus raise ValueError("'circular' is expected to be a list") ValueError: 'circular' is expected to be a list ********************************************************************** File "src/sage/graphs/generic_graph.py", line 2001, in sage.graphs.generic_graph.GenericGraph.get_embedding Failed example: G.get_embedding() Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.get_embedding[2]>", line 1, in <module> G.get_embedding() File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 2007, in get_embedding raise ValueError('%s has been modified and the embedding is no longer valid'%self) ValueError: Petersen graph has been modified and the embedding is no longer valid ********************************************************************** File "src/sage/graphs/generic_graph.py", line 3823, in sage.graphs.generic_graph.GenericGraph.is_planar Failed example: g.is_planar(on_embedding=emb) Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.is_planar[26]>", line 1, in <module> g.is_planar(on_embedding=emb) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 3834, in is_planar return (0 == self.genus(minimal=False,set_embedding=False,on_embedding=on_embedding)) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 4362, in genus raise ValueError("'circular' is expected to be a list") ValueError: 'circular' is expected to be a list ********************************************************************** File "src/sage/graphs/generic_graph.py", line 4280, in sage.graphs.generic_graph.GenericGraph.genus Failed example: g.genus() # tests for minimal genus by default Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.genus[1]>", line 1, in <module> g.genus() # tests for minimal genus by default File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 4362, in genus raise ValueError("'circular' is expected to be a list") ValueError: 'circular' is expected to be a list ********************************************************************** File "src/sage/graphs/generic_graph.py", line 4282, in sage.graphs.generic_graph.GenericGraph.genus Failed example: g.genus(on_embedding=True, maximal=True) # on_embedding overrides minimal and maximal arguments Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.genus[2]>", line 1, in <module> g.genus(on_embedding=True, maximal=True) # on_embedding overrides minimal and maximal arguments File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 4362, in genus raise ValueError("'circular' is expected to be a list") ValueError: 'circular' is expected to be a list ********************************************************************** File "src/sage/graphs/generic_graph.py", line 4284, in sage.graphs.generic_graph.GenericGraph.genus Failed example: g.genus(maximal=True) # setting maximal to True overrides default minimal=True Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.genus[3]>", line 1, in <module> g.genus(maximal=True) # setting maximal to True overrides default minimal=True File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 4362, in genus raise ValueError("'circular' is expected to be a list") ValueError: 'circular' is expected to be a list ********************************************************************** File "src/sage/graphs/generic_graph.py", line 4286, in sage.graphs.generic_graph.GenericGraph.genus Failed example: g.genus(on_embedding=g.get_embedding()) # can also send a valid combinatorial embedding dict Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.genus[4]>", line 1, in <module> g.genus(on_embedding=g.get_embedding()) # can also send a valid combinatorial embedding dict File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 2007, in get_embedding raise ValueError('%s has been modified and the embedding is no longer valid'%self) ValueError: Petersen graph has been modified and the embedding is no longer valid ********************************************************************** File "src/sage/graphs/generic_graph.py", line 4288, in sage.graphs.generic_graph.GenericGraph.genus Failed example: (graphs.CubeGraph(3)).genus() Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.genus[5]>", line 1, in <module> (graphs.CubeGraph(Integer(3))).genus() File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 4362, in genus raise ValueError("'circular' is expected to be a list") ValueError: 'circular' is expected to be a list ********************************************************************** File "src/sage/graphs/generic_graph.py", line 4291, in sage.graphs.generic_graph.GenericGraph.genus Failed example: K23.genus() Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.genus[7]>", line 1, in <module> K23.genus() File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 4362, in genus raise ValueError("'circular' is expected to be a list") ValueError: 'circular' is expected to be a list ********************************************************************** File "src/sage/graphs/generic_graph.py", line 4294, in sage.graphs.generic_graph.GenericGraph.genus Failed example: K33.genus() Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.genus[9]>", line 1, in <module> K33.genus() File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 4362, in genus raise ValueError("'circular' is expected to be a list") ValueError: 'circular' is expected to be a list ********************************************************************** File "src/sage/graphs/generic_graph.py", line 4321, in sage.graphs.generic_graph.GenericGraph.genus Failed example: G.genus() Expected: Traceback (most recent call last): ... NotImplementedError: Can't work with embeddings of nonsimple graphs Got: <BLANKLINE> Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.genus[17]>", line 1, in <module> G.genus() File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 4362, in genus raise ValueError("'circular' is expected to be a list") ValueError: 'circular' is expected to be a list ********************************************************************** File "src/sage/graphs/generic_graph.py", line 4325, in sage.graphs.generic_graph.GenericGraph.genus Failed example: G.to_simple().genus() Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.genus[18]>", line 1, in <module> G.to_simple().genus() File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 4362, in genus raise ValueError("'circular' is expected to be a list") ValueError: 'circular' is expected to be a list ********************************************************************** File "src/sage/graphs/generic_graph.py", line 4327, in sage.graphs.generic_graph.GenericGraph.genus Failed example: G.genus(set_embedding=False) Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.genus[19]>", line 1, in <module> G.genus(set_embedding=False) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 4362, in genus raise ValueError("'circular' is expected to be a list") ValueError: 'circular' is expected to be a list ********************************************************************** File "src/sage/graphs/generic_graph.py", line 4329, in sage.graphs.generic_graph.GenericGraph.genus Failed example: G.genus(maximal=True, set_embedding=False) Expected: Traceback (most recent call last): ... NotImplementedError: Can't compute the maximal genus of a graph with loops or multiple edges Got: <BLANKLINE> Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.genus[20]>", line 1, in <module> G.genus(maximal=True, set_embedding=False) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 4362, in genus raise ValueError("'circular' is expected to be a list") ValueError: 'circular' is expected to be a list ********************************************************************** File "src/sage/graphs/generic_graph.py", line 4346, in sage.graphs.generic_graph.GenericGraph.genus Failed example: G.genus() Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 496, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 858, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.generic_graph.GenericGraph.genus[25]>", line 1, in <module> G.genus() File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/graphs/generic_graph.py", line 4362, in genus raise ValueError("'circular' is expected to be a list") ValueError: 'circular' is expected to be a list ********************************************************************** 3 items had failures: 12 of 27 in sage.graphs.generic_graph.GenericGraph.genus 2 of 4 in sage.graphs.generic_graph.GenericGraph.get_embedding 1 of 28 in sage.graphs.generic_graph.GenericGraph.is_planar [2690 tests, 15 failures, 63.86 s]  sage t long src/sage/graphs/generic_graph.py # 15 doctests failed  Total time for all tests: 64.4 seconds cpu time: 45.2 seconds cumulative wall time: 63.9 seconds
comment:13 Changed 7 years ago by
Commit:  41943ff9a08e086a14f2bf4d897bac60321288c1 → 43bb53f2d5e98c58d571695dd797f858ad2f96ae 

Branch pushed to git repo; I updated commit sha1. New commits:
43bb53f  trac #17462: Change the default value of 'circular' in GenericGraph.genus

comment:14 Changed 7 years ago by
Sorry for that. The default value was clearly wrong, so I changed it ^^;
Nathann
comment:15 Changed 7 years ago by
Branch:  u/ncohen/17462 → u/dcoudert/17462 

comment:16 Changed 7 years ago by
Commit:  43bb53f2d5e98c58d571695dd797f858ad2f96ae → 43cf74ac4b0bb2729ffe7288d8d1ab4ed8e76a8d 

Hello,
I did small modifications, but I'm not good for pushing commits and so all is in a new branch. Sorry for that.
I did only the following modifications:
 in both files
graph.py
anddigraph.py
, remove in the description of the class parameters ``boundary``  a list of boundary vertices, if empty, digraph is considered as a 'graph without boundary'
 and remove
boundary=None
indef __init__(self, data=None, pos=None, loops=None, format=None, boundary=None, weighted=None, implementation='c_graph', data_structure="sparse", vertex_labels=True, name=None, multiedges=None, convert_empty_dict_labels_to_None=None, sparse=True, immutable=False):
 In file
generic_graph.py
, remove wordboundary
from the method description:meth:`~GenericGraph.clear`  Empty the graph of vertices and edges and removes name, boundary, associated objects, and position information.
 and in
def clear(self): """ Empties the graph of vertices and edges and removes name, boundary, associated objects, and position information.
If you agree, you can set the ticket to positive review.
David.
New commits:
e1c00eb  trac #17462: remove useless doc and parameter in graph.py and digraph.py

43cf74a  trac #17462: clean doc in generic_graph.py

comment:17 Changed 7 years ago by
Status:  needs_review → positive_review 

:/
Thank you very much. My branch was clearly careless :/
Thanks.
Nathann
comment:18 Changed 7 years ago by
Reviewers:  → David Coudert 

should we set the milestone to 6.9 or is it too early ?
comment:19 Changed 7 years ago by
Milestone:  sagepending → sage6.9 

Nono it's fine. I don't see a stable version released before 5 days :P
comment:20 Changed 7 years ago by
Branch:  u/dcoudert/17462 → 43cf74ac4b0bb2729ffe7288d8d1ab4ed8e76a8d 

Resolution:  → fixed 
Status:  positive_review → closed 
Branch pushed to git repo; I updated commit sha1. New commits:
trac #17462: Removed the _boundary flag, deprecated in #15494 on 20131208