Opened 6 years ago
Closed 2 weeks ago
#22349 closed enhancement (fixed)
Deprecate sorting of Graph vertices and edges by default
Reported by:  jdemeyer  Owned by:  

Priority:  critical  Milestone:  sage9.7 
Component:  graph theory  Keywords:  python3, richcmp 
Cc:  Stefan, jmantysalo, jhpalmieri  Merged in:  
Authors:  John Palmieri, David Coudert  Reviewers:  David Coudert, John Palmieri 
Report Upstream:  N/A  Work issues:  
Branch:  fe93716 (Commits, GitHub, GitLab)  Commit:  fe93716223af144c0c07fad94eea920e10f139bb 
Dependencies:  Stopgaps: 
Description (last modified by )
Why does Graph.vertices()
need to sort the list of vertices? If the user wants a sorted list, they can always call sorted()
anyway. The same for Graph.edges()
.
Sorting is broken badly now that #22029 is merged.
Change History (83)
comment:1 Changed 6 years ago by
 Description modified (diff)
comment:2 Changed 6 years ago by
 Description modified (diff)
comment:3 Changed 6 years ago by
 Summary changed from Graph.vertices() should not sort by default to Graph.vertices() should not be sorted
comment:4 Changed 6 years ago by
 Summary changed from Graph.vertices() should not be sorted to Deprecate sorting of Graph.vertices()
comment:5 Changed 6 years ago by
 Description modified (diff)
 Summary changed from Deprecate sorting of Graph.vertices() to Deprecate sorting of Graph vertices and edges
comment:6 Changed 6 years ago by
 Summary changed from Deprecate sorting of Graph vertices and edges to Deprecate sorting of Graph vertices and edges by default
comment:7 Changed 6 years ago by
 Branch set to u/jdemeyer/graph_vertices___should_not_be_sorted
comment:8 Changed 6 years ago by
 Commit set to 1c3a584d5f578ab4ff71969b79904ed1220ca4a1
comment:9 followup: ↓ 10 Changed 6 years ago by
What you propose to do is not an easy task. I suspect that many algorithms assume that the vertices are sorted. For sure, many algorithms assume that the ordering is always the same when calling vertices()
and vertex_iterator()
, so I hope that what you propose preserves this strong assumption.
Is your long term plan to remove parameter sort
from the methods or just to set its default value to false ?
I don't know the potential problems of sorting with Python 3, so I'm not sure of the motivation.
Many many tests are broken
sage t src/sage/graphs/generic_graph.py # 45 doctests failed sage t src/sage/graphs/generators/smallgraphs.py # 4 doctests failed sage t src/sage/graphs/strongly_regular_db.pyx # 1 doctest failed sage t src/sage/graphs/graph.py # 11 doctests failed sage t src/sage/graphs/base/static_sparse_graph.pyx # 1 doctest failed sage t src/sage/graphs/generators/families.py # 3 doctests failed sage t src/sage/graphs/digraph.py # 10 doctests failed sage t src/sage/graphs/digraph_generators.py # 3 doctests failed sage t src/sage/graphs/base/graph_backends.pyx # 2 doctests failed sage t src/sage/graphs/generic_graph_pyx.pyx # 3 doctests failed sage t src/sage/graphs/comparability.pyx # 1 doctest failed sage t src/sage/graphs/bipartite_graph.py # 3 doctests failed sage t src/sage/graphs/base/c_graph.pyx # 1 doctest failed sage t src/sage/graphs/graph_decompositions/vertex_separation.pyx # 4 doctests failed sage t src/sage/graphs/schnyder.py # 1 doctest failed sage t src/sage/graphs/line_graph.py # 3 doctests failed sage t src/sage/graphs/isgci.py # 1 doctest failed sage t src/sage/graphs/graph_decompositions/graph_products.pyx # 1 doctest failed sage t src/sage/quivers/path_semigroup.py # 3 doctests failed sage t src/sage/groups/perm_gps/partn_ref/refinement_graphs.pyx # 1 doctest failed
for instance (random copy/paste)
File "src/sage/graphs/line_graph.py", line 466, in sage.graphs.line_graph.root_graph Failed example: root_graph(graphs.DiamondGraph()) Expected: (Graph on 4 vertices, {0: (0, 3), 1: (0, 1), 2: (0, 2), 3: (1, 2)}) Got: (Graph on 4 vertices, {0: (1, 2), 1: (0, 1), 2: (0, 2), 3: (0, 3)}) ********************************************************************** File "src/sage/graphs/base/graph_backends.pyx", line 802, in sage.graphs.base.graph_backends.NetworkXGraphDeprecated.mutate Failed example: G.edges(sort=False) Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 498, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 861, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.base.graph_backends.NetworkXGraphDeprecated.mutate[5]>", line 1, in <module> G.edges(sort=False) TypeError: edges() got an unexpected keyword argument 'sort' ********************************************************************** File "src/sage/graphs/digraph.py", line 3424, in sage.graphs.digraph.DiGraph.flow_polytope Failed example: fl.vertices(sort=False) Exception raised: Traceback (most recent call last): File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 498, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dcoudert/sage/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 861, in compile_and_execute exec(compiled, globs) File "<doctest sage.graphs.digraph.DiGraph.flow_polytope[19]>", line 1, in <module> fl.vertices(sort=False) TypeError: __call__() got an unexpected keyword argument 'sort' ********************************************************************** File "src/sage/graphs/generic_graph.py", line 20558, in sage.graphs.generic_graph.GenericGraph.? Failed example: d.automorphism_group(algorithm='sage') Expected: Permutation Group with generators [('01','02')('10','20')('11','22')('12','21')] Got: Permutation Group with generators [()] ********************************************************************** File "src/sage/graphs/generic_graph.py", line 20197, in sage.graphs.generic_graph.GenericGraph.degree_to_cell Failed example: G.degree_to_cell('111', cell) Expected: 0 Got: 1
comment:10 in reply to: ↑ 9 Changed 6 years ago by
Replying to dcoudert:
What you propose to do is not an easy task.
I never claimed that it was easy. But it has to be done in order to support Python 3.
For sure, many algorithms assume that the ordering is always the same when calling
vertices()
andvertex_iterator()
, so I hope that what you propose preserves this strong assumption.
It should remain the same, yes.
Is your long term plan to remove parameter
sort
from the methods or just to set its default value to false ?
I don't care much. I guess once the default is False
, there will be little reason left to keep the sort
keyword.
I don't know the potential problems of sorting with Python 3, so I'm not sure of the motivation.
The problem is that you cannot sort arbitrary things in Python 3. For example:
>>> sorted([1, "hello"]) Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: unorderable types: str() < int()
comment:11 followups: ↓ 12 ↓ 17 Changed 6 years ago by
Now I understand the need for this big change.
Is there a way to sort arbitrary things in Python 3 ? some trick ?
comment:12 in reply to: ↑ 11 Changed 6 years ago by
Replying to dcoudert:
Is there a way to sort arbitrary things in Python 3 ?
Of course there is. The question is: what would you expect from such "arbitrary" sorting?
And if it's arbitrary anyway: why would you want to "sort" in the first place?
comment:13 followup: ↓ 18 Changed 6 years ago by
As far as I understand, there are at least two different issues here:
 some algorithms want a consistent and easy to test order on the vertices, typically (but probably not only) to loop over the unordered pairs of vertices normalized by putting the smalled vertex first;
 in interactive use, when there is a natural order on the vertices (in practice, mostly when they are integers, strings, or possibly nested tuples of such things), people want to see the vertices, edges, etc. listed in an order that makes the output easy to read, and it would be a significant regression to take that away from them.
Additionally, it may well be the case that some algorithms also rely on vertices of a certain type (say tuples of integers) automatically coming out sorted in a particular order, I'm not sure.
comment:14 Changed 6 years ago by
 Dependencies set to #22383
comment:15 Changed 6 years ago by
 Commit changed from 1c3a584d5f578ab4ff71969b79904ed1220ca4a1 to aa0691f9fa7b03f9130b398923d92de3fb5fcf36
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
aa0691f  Deprecate default sorting of Graph vertices and edges

comment:16 Changed 5 years ago by
 Cc Stefan added
comment:17 in reply to: ↑ 11 ; followups: ↓ 19 ↓ 20 Changed 5 years ago by
Replying to dcoudert:
Now I understand the need for this big change.
Is there a way to sort arbitrary things in Python 3 ? some trick ?
one way is
sorted( ..., key=str )
You could of course use another key function that uses some sorting heuristic (something like the key function used by https://pypi.python.org/pypi/natsort)
Display functions in IPython have hooks for nice sorting (used for dicts and sets), so if graphs need to display their keys and edges in a nice way, that's probably the hook to go for.
Algorithms that need their edges sorted should either insist on sortable labels or sort by index tuples or something like that (something that is guaranteed to be sortable regardless of what the user decides to use as labels).
comment:18 in reply to: ↑ 13 Changed 5 years ago by
Replying to mmezzarobba:
 in interactive use, when there is a natural order on the vertices (in practice, mostly when they are integers, strings, or possibly nested tuples of such things), people want to see the vertices, edges, etc. listed in an order that makes the output easy to read, and it would be a significant regression to take that away from them.
In that case, the best solution is probably to use a custom class for this. It would behave exactly like a Python list
(or tuple
) in all possible ways, except that it would be sorted on display.
comment:19 in reply to: ↑ 17 Changed 5 years ago by
Replying to nbruin:
Display functions in IPython have hooks for nice sorting (used for dicts and sets), so if graphs need to display their keys and edges in a nice way, that's probably the hook to go for.
Nils, I only just saw your comment now. But yes, this was exactly my point too.
comment:20 in reply to: ↑ 17 ; followup: ↓ 21 Changed 5 years ago by
Replying to nbruin:
Algorithms that need their edges sorted should either insist on sortable labels or sort by index tuples or something like that (something that is guaranteed to be sortable regardless of what the user decides to use as labels).
They could simply sort by id()
, provided that the same label is not represented by several physically distinct objects that compare equal. Unfortunately, this probably does happen (see #22374).
comment:21 in reply to: ↑ 20 ; followup: ↓ 22 Changed 5 years ago by
Replying to mmezzarobba:
They could simply sort by
id()
If you want to sort by id()
, what is the purpose of sorting at all? I mean, it's not sorting, it's putting in a deterministic (but otherwise arbitrary) order. Assuming that methods like vertices()
return the vertices in a deterministic order, I don't see the point.
comment:22 in reply to: ↑ 21 Changed 5 years ago by
Replying to jdemeyer:
Replying to mmezzarobba:
They could simply sort by
id()
If you want to sort by
id()
, what is the purpose of sorting at all? I mean, it's not sorting, it's putting in a deterministic (but otherwise arbitrary) order. Assuming that methods likevertices()
return the vertices in a deterministic order, I don't see the point.
All I'm saying is that some algorithms do want to access the vertices in some arbitrary deterministic order, typically in order to iterate over the unordered pairs {v,v'}, and, as far as I remember, currently rely on the output of vertices()
etc. being sorted to do that. If all the methods these algorithms use to access the vertices return them in the same deterministic order, then indeed, there is no need to do anything, otherwise, sorting by id()
may be a better option than requiring the labels to be ordered.
comment:23 Changed 4 years ago by
 Keywords richcmp added
 Milestone changed from sage7.6 to sage8.2
comment:24 Changed 4 years ago by
 Keywords python3 added
comment:25 Changed 4 years ago by
 Work issues set to merge conflicts
comment:26 Changed 4 years ago by
 Work issues merge conflicts deleted
comment:27 Changed 4 years ago by
 Dependencies #22383 deleted
comment:28 Changed 4 years ago by
 Milestone changed from sage8.2 to sage8.4
comment:29 Changed 4 years ago by
 Cc jmantysalo added
comment:30 Changed 4 years ago by
 Cc jhpalmieri added
comment:31 Changed 4 years ago by
Apart from the need for ensuring that the internal order of vertices/edges during iterations is always the same (many algorithms assume that we have such a fixed order, whatever it is) and doing our best to preserve a nice display for interactive use, I think we have another issue:
 For an edge
(u, v, label)
in an undirected graph, we usually haveu <= v
. So somehow we have a sorting here and many algorithms assume that vertices are ordered (not all). If I understand well, it is a problem with Python3 if vertex labels are of different types. We must find a solution for that.  In many algorithms, we have tests like
if u < v
. Again a big problem.
So what can we do ?
The only good news here is that vertices must be immutable.
comment:32 Changed 4 years ago by
#26169 Trial for not sorting multiple edges
comment:33 Changed 4 years ago by
Do we already have a plan for this ticket? I know that there have many graphrelated Python 3 tickets, but I'm a bit lost on the overall plan.
comment:34 Changed 4 years ago by
I am asking because there are now only a handful of doctest failures remaining in #22029 and they are almost all due to sorting in graphs.
comment:35 Changed 4 years ago by
There are 3 different points here: 1) sorting the list of vertices, 2) sorting the list of edges, and 3) sorting the vertices of an edge.
For 1), we made huge progresses in reducing the dependency of methods to .vertices()
. I'm not sure how many methods still rely on it. Most of them now use the ordering given by list(G)
without making specific assumption on that order. We create a mapping when needed, and pass it to some methods. We can certainly completely avoid that dependency, but can we do that without deprecation ?
For 2), similarly, we have reduced the number of methods relying on .edges()
, plus we can use sort=False
parameter. We can try and see...
3) is more tricky and I don't know how to do that yet.
comment:36 Changed 4 years ago by
For 1) there is still an issue with relabel()
: #27027
comment:37 Changed 4 years ago by
And one more with graph_isom_equivalent_non_edge_labeled_graph()
: #27029
comment:38 Changed 3 years ago by
 Description modified (diff)
 Milestone changed from sage8.4 to sage8.7
comment:39 Changed 3 years ago by
We have now drastically reduced the dependency to .vertices()
and .edges()
in the graph module (except in doctests, but we can specify sort=True
or just change the expected output).
We must now identify the remaining tasks to do and schedule the work. I propose to do that in #26640 to get a full picture.
comment:40 Changed 3 years ago by
Here is a concrete proposal for this ticket:
 If no
sort
option is given (the default), give a deprecation and try to sort but fail gracefully if the input is not sortable.
 If a
sort
option is given, do as before.
comment:41 Changed 3 years ago by
I also like the idea that somebody posted on sagedevel (I don't remember who) that .vertices()
and .edges()
should return a "view" which could have various operations on it.
comment:42 Changed 3 years ago by
It's Thierry (this message). I also like this idea. Should we do that here, before in another ticket, or later ?
Networkx now also use views networkx.Graph.edges.
comment:43 Changed 3 years ago by
A proposal for an EdgeView
in #27408.
comment:44 Changed 3 years ago by
 Milestone changed from sage8.7 to sage8.8
Ticket retargeted after milestone closed (if you don't believe this ticket is appropriate for the Sage 8.8 release please retarget manually)
comment:45 Changed 3 years ago by
 Milestone sage8.8 deleted
As the Sage8.8 release milestone is pending, we should delete the sage8.8 milestone for tickets that are not actively being worked on or that still require significant work to move forward. If you feel that this ticket should be included in the next Sage release at the soonest please set its milestone to the next release milestone (sage8.9).
comment:46 Changed 2 years ago by
 Milestone set to sage9.2
Now that we have EdgesView? #27408 and Python3, we have few remaining methods methods effectively relying on the order of the vertices and/or edges. So we should restart working on this ticket for 9.2.
comment:47 Changed 2 years ago by
With #30145, we propose to deprecate edge_iterator
, thus generalizing the use of .edges
method and so of EdgesView
. After that, it should be easier to deprecate sorting edges by default.
comment:48 Changed 2 years ago by
 Milestone changed from sage9.2 to sage9.3
comment:49 Changed 18 months ago by
 Milestone changed from sage9.3 to sage9.4
Setting new milestone based on a cursory review of ticket status, priority, and last modification date.
comment:50 Changed 13 months ago by
 Milestone changed from sage9.4 to sage9.5
comment:51 Changed 8 months ago by
 Milestone changed from sage9.5 to sage9.6
comment:52 followup: ↓ 54 Changed 5 months ago by
Actually, #27408 has silently (not mentioned in the ticket) introduced a deprecation warning for sorting edges by default, but it is used in method .edges(...)
only when sort is None
and the default value of sort
is True
. So I think noone is aware of it.
I'm not sure how to make this deprecation warning visible without breaking numerous doctests.
comment:53 Changed 5 months ago by
 Milestone changed from sage9.6 to sage9.7
comment:54 in reply to: ↑ 52 Changed 7 weeks ago by
Replying to dcoudert:
Actually, #27408 has silently (not mentioned in the ticket) introduced a deprecation warning for sorting edges by default, but it is used in method
.edges(...)
only whensort is None
and the default value ofsort
isTrue
. So I think noone is aware of it.I'm not sure how to make this deprecation warning visible without breaking numerous doctests.
I'd be interested in seeing this ticket resolved, perhaps you could ask about how to go about this deprecation on sagedevel? Or I am happy to follow this up if you'd prefer.
comment:55 Changed 7 weeks ago by
The difficulty is that we still have some methods relying on .vertices()
, and I don't know how to avoid that.
For instance in graph.py
: effective_resistance_matrix
, common_neighbors_matrix
, orientations
(but this one can be avoided easily), chromatic_quasisymmetric_function
, twograph
, write_to_eps
. And there might be other modules using graphs and relying on the ordering of the vertices given by .vertices()
(e.g., combinat
, geometry
, groups
, matroids
, schemes
, topology
, etc..
So the first step might be to identify methods/modules relying on .vertices()
and try to modify them. Once done, we will be able to safely deprecate sorting by default.
comment:56 Changed 7 weeks ago by
The .vertices()
method is probably used lots of times, but one fix could be:
 every time it's used, add the argument
sort=False
orsort=True
as necessary,  and then change the default to
sort=False
.
Maybe it's easier with edges: add the explicit argument everywhere and then change the default to None
.
Or is that too naïve? I tried this change:

src/sage/graphs/graph.py
diff git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py index 1579f23ad8..5dbb937b6b 100644
a b class Graph(GenericGraph): 3480 3480 name = 'An orientation of ' + name 3481 3481 3482 3482 if not self.size(): 3483 D = DiGraph(data=[self.vertices( ), []],3483 D = DiGraph(data=[self.vertices(sort=False), []], 3484 3484 format='vertices_and_edges', 3485 3485 name=name, 3486 3486 pos=self._pos, … … class Graph(GenericGraph): 3494 3494 3495 3495 E = [[(u,v,label), (v,u,label)] if u != v else [(u,v,label)] 3496 3496 for u,v,label in self.edge_iterator()] 3497 verts = self.vertices( )3497 verts = self.vertices(sort=False) 3498 3498 for edges in itertools.product(*E): 3499 3499 D = DiGraph(data=[verts, edges], 3500 3500 format='vertices_and_edges', … … class Graph(GenericGraph): 4009 4009 R = t.parent() 4010 4010 M = QuasiSymmetricFunctions(R).M() 4011 4011 ret = M.zero() 4012 V = self.vertices( )4012 V = self.vertices(sort=False) 4013 4013 4014 4014 def asc(sigma): 4015 4015 stat = 0 … … class Graph(GenericGraph): 6185 6185 T.append([x, y, z]) 6186 6186 6187 6187 T = TwoGraph(T) 6188 T.relabel({i: v for i,v in enumerate(self.vertices( ))})6188 T.relabel({i: v for i,v in enumerate(self.vertices(sort=False))}) 6189 6189 6190 6190 return T 6191 6191 … … class Graph(GenericGraph): 6221 6221 if filename[4:] != '.eps': 6222 6222 filename += '.eps' 6223 6223 f = open(filename, 'w') 6224 f.write( print_graph_eps(self.vertices( ), self.edge_iterator(), pos) )6224 f.write( print_graph_eps(self.vertices(sort=False), self.edge_iterator(), pos) ) 6225 6225 f.close() 6226 6226 6227 6227 @doc_index("Algorithmically hard stuff") … … class Graph(GenericGraph): 7940 7940 D = None 7941 7941 elif self.order() == 1: 7942 7942 D = create_prime_node() 7943 D.children.append(create_normal_node(self.vertices( )[0]))7943 D.children.append(create_normal_node(self.vertices(sort=False)[0])) 7944 7944 else: 7945 7945 D = habib_maurer_algorithm(self) 7946 7946 … … class Graph(GenericGraph): 9225 9225 if not n: 9226 9226 raise ValueError('unable to compute effective resistance for an empty Graph object') 9227 9227 if vertices is None: 9228 vertices = self.vertices( )9228 vertices = self.vertices(sort=False) 9229 9229 self._scream_if_not_simple() 9230 9230 if not self.is_connected(): 9231 9231 raise ValueError('the Graph is not a connected graph') … … class Graph(GenericGraph): 9458 9458 """ 9459 9459 self._scream_if_not_simple() 9460 9460 if vertices is None: 9461 vertices = self.vertices( )9461 vertices = self.vertices(sort=False) 9462 9462 set_immutable = kwds.pop('immutable', False) 9463 9463 A = self.adjacency_matrix(vertices=vertices, base_ring=base_ring, immutable=True, **kwds) 9464 9464 M = A**2
and all tests in the graphs directory still passed.
comment:57 followup: ↓ 58 Changed 7 weeks ago by
We cannot blindly use .vertices(sort=False)
. It will clearly break badly some methods, for instance methods building adjacency or laplacian matrices, etc.
We already pave the way by reducing the number of situations in which we call .vertices()
, but we still have work to do to reduce the dependency. We did the same for .edges()
.
The safe way is to use only .vertices(sort=True)
, and whenever possible, avoid calls to .vertices()
. For instance, I see in generic_graph.py
a call to self.vertices(sort=False)[0]
while we have self.order() == 1
. So we can avoid this call.
Then, we can set the default to None
with a deprecation warning that the default will be changed to False
.
comment:58 in reply to: ↑ 57 Changed 7 weeks ago by
Replying to dcoudert:
We cannot blindly use
.vertices(sort=False)
.
That's not what I suggested. Please reread the first bullet point.
comment:59 Changed 7 weeks ago by
Right, I missed some parts. I agree with your proposal, but we need an appropriate deprecation warning to inform users of the change. It's a big change.
comment:60 Changed 5 weeks ago by
The best I can think of right now is:
 Make the default
sort=None
and raise a deprecation warning if this default gets used, thereby requiring an explicit argument everywhere in the Sage library.
 So use
sort=False
orsort=True
as appropriate in the library.
Then later we can change the default to sort=False
.
comment:61 Changed 5 weeks ago by
 Branch changed from u/jdemeyer/graph_vertices___should_not_be_sorted to u/jhpalmieri/graph_vertices___should_not_be_sorted
comment:62 Changed 5 weeks ago by
 Commit changed from aa0691f9fa7b03f9130b398923d92de3fb5fcf36 to b6b6c34d8647620f41b1b392c5755e4bcbfe4779
Here is a start. This does what I proposed in comment:60, and all tests pass. I was not that careful in choosing sort=True
or sort=False
, and so I would not surprised if we could use sort=False
in more places. Feel free to modify the branch.
New commits:
27a6483  trac 22349: vertex sorting

b6b6c34  trac 22349: edge sorting

comment:63 Changed 5 weeks ago by
The key changes are in graphs/generic_graph.py
:
@@ 10972,15 +10974,20 @@ class GenericGraph(GenericGraph_pyx): for u in self._backend.iterator_nbrs(vertex): yield u  def vertices(self, sort=True, key=None, degree=None, vertex_property=None): + def vertices(self, sort=None, key=None, degree=None, vertex_property=None): r""" Return a list of the vertices. INPUT:   ``sort``  boolean (default: ``True``); if ``True``, vertices are +  ``sort``  boolean (default: ``None``); if ``True``, vertices are sorted according to the default ordering + As of :trac:`22349`, this argument must be explicitly + specified (unless a ``key`` is given); otherwise a warning + is printed and ``sort=True`` is used. The default will + eventually be changed to ``False``. +  ``key``  a function (default: ``None``); a function that takes a vertex as its one argument and returns a value that can be used for comparisons in the sorting algorithm (we must have ``sort=True``)
and
@@ 11065,9 +11072,23 @@ class GenericGraph(GenericGraph_pyx): Traceback (most recent call last): ... ValueError: sort keyword is False, yet a key function is given + + Deprecation warning for ``sort=None`` (:trac:`22349`):: + + sage: G = graphs.HouseGraph() + sage: G.vertices() + doctest:...: DeprecationWarning: parameter 'sort' will be set to False by default in the future + See http://trac.sagemath.org/22349 for details. + [0, 1, 2, 3, 4] """ + if sort is None: + if key is None: + deprecation(22349, "parameter 'sort' will be set to False by default in the future") + sort = True + if (not sort) and key: raise ValueError('sort keyword is False, yet a key function is given') + if sort: return sorted(self.vertex_iterator(degree=degree, vertex_property=vertex_property), key=key) return list(self.vertex_iterator(degree=degree, vertex_property=vertex_property))
and similar for edges
(although edges
already printed a warning if None
was used, but None
was not the default, so it had to be called explicitly as g.edges(sort=None)
to trigger the warning before).
comment:64 Changed 5 weeks ago by
I'm impressed !
I'm currently doing some tests and will push later some corrections.
comment:65 Changed 5 weeks ago by
 Branch changed from u/jhpalmieri/graph_vertices___should_not_be_sorted to public/graphs/22349_deprecate_sorting_vertices_and_edges
 Commit changed from b6b6c34d8647620f41b1b392c5755e4bcbfe4779 to fee74b61393ff08220faccfb5bf29c62a07ecb64
I did a few changes in graphs and many tests. I have not detected any problem yet, but others may raise some issues.
This ticket highlights many places were the usage of graphs must be improved. I did some (minor) corrections in src/sage/schemes/curves/zariski_vankampen.py
as example, but more can be done in this file.
Typically, it is better to use for u in G:
than for u in G.vertices(sort=False):
. The ordering of the vertices is the same, but we avoid building the list of vertices. Tests like u in G.vertices(sort=False)
should be replaced by u in G
. etc.
In future tickets, we should address (very bad) code like this in src/sage/geometry/hyperplane_arrangement/library.py
 for e in G.edges():  i = G.vertices().index(e[0])  j = G.vertices().index(e[1]) + for e in G.edges(sort=True): + i = G.vertices(sort=True).index(e[0]) + j = G.vertices(sort=True).index(e[1])
Clearly, we need to define a mapping from vertices to index.
New commits:
fee74b6  trac #22349: some corrections

comment:66 Changed 5 weeks ago by
 Status changed from new to needs_review
comment:67 Changed 5 weeks ago by
 Priority changed from major to critical
Great! I'm happy with your changes. We can try to get it merged soon, although with this many files affected, there might very well be merge conflicts.
comment:68 Changed 5 weeks ago by
 Reviewers set to David Coudert, John Palmieri
Positive review from me for your contributions.
comment:69 Changed 5 weeks ago by
 Status changed from needs_review to positive_review
We will certainly get merge conflicts (due to the many tickets improving the coding style for instance), but let's try.
Positive review from me too.
comment:70 Changed 4 weeks ago by
 Status changed from positive_review to needs_work
Merge failure on top of:
83a3df1c99 Trac #34131: some doc polishing in symbolic
dee5229b00 Trac #34130: some doc polishing in groups
fd80fa111f Trac #34126: some doc polishing in categories
718d356f1c Trac #34125: some doc polishing in modular
49390d8bcf Trac #34124: some doc polishing in combinat
af94c25b54 Trac #34096: Fix typo: enviroment > environment
d04c189c8e Trac #34050: add some space around == in paths and rational
1634bb6946 Trac #34047: Typo in _repr_Expression in symbolic/expression.pyx
dc8086fd57 Trac #34154: Fix repeated word typos
17b1c177aa Trac #34148: fix and activate pycodestyle E306
785bdbd0ec Trac #34136: modernize super() in rings (part one)
9882001355 Trac #34129: Dummy packages should write proper log files
dbc6b9e161 Trac #34109: pep8 for sagedoc.py
5e6a3318c8 Trac #34103: randomize infinite recursion
17ba76f00b Trac #34093: Wrong evaluation of elements of CBF[x] on polynomials from other rings
4657052737 Trac #34122: Bug in is_planar() method for directed graphs
c9cfb5395f Trac #34087: inverse reciprocal trig functions not (back)translated to/from Mathematica
1d6d055563 Trac #34076: pycodestyle cleanup in src/sage/graphs/genus.pyx
043d862b5d Trac #34071: pycodestyle cleanup in asteroidal_triples.pyx, chrompoly.pyx, cliquer.pyx, convexity_properties.pyx
b9b25dc735 Trac #34070: pycodestyle cleanup in src/sage/graphs/centrality.pyx
4ef2c6597d Trac #34069: pycodestyle cleanup in src/sage/graphs/comparability.pyx
5b1146766b Trac #34066: Tachyon help message
798adaa5a3 Trac #34065: pycodestyle cleanup in src/sage/graphs/bliss.pyx
ce62be23a2 Trac #34063: pycodestyle cleanup in src/sage/graphs/base/
a0eadb3e40 Trac #34059: Fix trivial case in conversion of list to number field element
fea0ac50a6 Trac #34057: changes about avoiding double dieses
9eefd5c27e Trac #34145: modernize super in geometry/
01e117dfd8 Trac #34137: modernize super in categories/
6c79334402 Trac #33819: build.yml: In workflow_dispatch, make container and base tag selectable; add doc
6a64ab8d00 Trac #33760: do not update _pos, _pos3d, _embedding on vertex/edge deletions
dbf091dbbb Trac #34139: fix the linter
625ac58151 Updated SageMath version to 9.7.beta5
merge was not clean: conflicts in src/sage/groups/perm_gps/partn_ref/refinement_graphs.pyx
comment:71 Changed 4 weeks ago by
 Commit changed from fee74b61393ff08220faccfb5bf29c62a07ecb64 to 1e1ea2425398d1481f8fb4954600e934f92daa0c
comment:72 Changed 4 weeks ago by
 Status changed from needs_work to positive_review
Rebased over #34130.
comment:73 Changed 3 weeks ago by
 Status changed from positive_review to needs_work
Merge failure on top of:
7f7149489c Updated SageMath version to 9.7.beta6
merge was not clean: conflicts in src/sage/combinat/yang_baxter_graph.py
comment:74 Changed 3 weeks ago by
 Commit changed from 1e1ea2425398d1481f8fb4954600e934f92daa0c to 4362cae77922139d9f1a7c97b7ae32469f60cedd
Branch pushed to git repo; I updated commit sha1. New commits:
4362cae  Merge branch 'develop' into t/22349/public/graphs/22349_deprecate_sorting_vertices_and_edges

comment:75 Changed 3 weeks ago by
 Status changed from needs_work to positive_review
Merged 9.7.beta6.
comment:76 Changed 3 weeks ago by
Let's hope this one can be merged soon to avoid new conflicts.
comment:77 followup: ↓ 78 Changed 3 weeks ago by
 Status changed from positive_review to needs_work
see patchbot
comment:78 in reply to: ↑ 77 Changed 3 weeks ago by
 Status changed from needs_work to positive_review
Replying to vbraun:
see patchbot
Which part? I believe the "deprecation number" warning is from this change:
@@ 12229,7 +12255,8 @@ class GenericGraph(GenericGraph_pyx): [(0, 1, None), (0, 2, None), (1, 3, None), (2, 3, None), (2, 4, None), (3, 4, None)] """ if sort is None:  deprecation(27408, "parameter 'sort' will be set to False by default in the future") + if key is None: + deprecation(27408, "parameter 'sort' will be set to False by default in the future") sort = True if vertices is not None and vertices in self:
and that seems appropriate: no reason to change the ticket number. (That's the only match for "27408" in the changes for this ticket.)
The pyflakes
warnings are not related to this ticket: they are in files touched by this ticket but not where we've modified them. (In addition, I don't understand the warning about simplicial_complex.py
)
comment:79 Changed 3 weeks ago by
It is more fundamental: there is a test failing for src/sage/graphs/edge_connectivity.pyx
.
comment:80 Changed 3 weeks ago by
 Status changed from positive_review to needs_work
comment:81 Changed 3 weeks ago by
 Commit changed from 4362cae77922139d9f1a7c97b7ae32469f60cedd to fe93716223af144c0c07fad94eea920e10f139bb
Branch pushed to git repo; I updated commit sha1. New commits:
fe93716  trac 22349: fix one more doctest

comment:83 Changed 2 weeks ago by
 Branch changed from public/graphs/22349_deprecate_sorting_vertices_and_edges to fe93716223af144c0c07fad94eea920e10f139bb
 Resolution set to fixed
 Status changed from positive_review to closed
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
Deprecate default sorting of Graph vertices and edges