Opened 5 years ago
Closed 5 years ago
#20499 closed defect (fixed)
Graphs: docstring of _add_ conflicts with function
Reported by:  jmantysalo  Owned by:  

Priority:  major  Milestone:  sage7.2 
Component:  graph theory  Keywords:  
Cc:  dcoudert, mcognetta  Merged in:  
Authors:  Jori Mäntysalo  Reviewers:  David Coudert 
Report Upstream:  N/A  Work issues:  
Branch:  2efa40a (Commits)  Commit:  2efa40a0db33ddc50ab076a86a22ead8680eec09 
Dependencies:  Stopgaps: 
Description
(Graph({'a': []})+Graph({'b': []})).vertices()
gives [0, 1]
, but docstring of __add__
says "If there are common vertices to both, they will be renamed." I do not know which way it should be.
Also there is no error checking, so Graph({0:[]})+'junk'
does and returns nothing.
Change History (20)
comment:1 Changed 5 years ago by
 Cc dcoudert added
 Status changed from new to needs_info
comment:2 followup: ↓ 7 Changed 5 years ago by
The current implementation of the add
method is
if isinstance(other_graph, GenericGraph): return self.disjoint_union(other_graph, labels='integers')
So it forces to relabel vertices as integer in [0..n1]
.
At the least, we should raise an error for cases such as Graph({0:[]})+'junk'
. Indeed, the other ordering raises an error
sage: 'junk'+Graph({0:[]})  TypeError Traceback (most recent call last) <ipythoninput992e66a308aaff> in <module>() > 1 'junk'+Graph({Integer(0):[]}) TypeError: cannot concatenate 'str' and 'Graph' objects
Now, the semantic of +
is the disjoint union, and I believe this is the right choice.
We should however ensure that the doc of __add__
, disjoint_union
, union
, __mul__
and may be join
, are clear enough and without ambiguity for users.
Concerning the relabel to integers part, I agree that this is often painful. We could propose and intermediate behavior like: relabel only if some vertices have same label. But again some people will complain.
David.
comment:3 Changed 5 years ago by
It seems that example given uses consecutive integeres. But yes, your suggestions sounds reasonable. But now I see this:
sage: G = Graph({'a': ['b']}) sage: G Graph on 2 vertices sage: G+G disjoint_union : Graph on 4 vertices sage: H = graphs.CycleGraph(3) sage: H Cycle graph: Graph on 3 vertices sage: H+H Cycle graph disjoint_union Cycle graph: Graph on 6 vertices
Maybe the __str__
needs modification also.
comment:4 Changed 5 years ago by
Right, we could improve the naming part of disjoint_union
. Currently it is:
G._name = '%s disjoint_union %s'%(self.name(), other.name())
I just saw that there is a deprecation warning in disjoint_union
. See #17053.
So some decisions have already been taken on how to relabel vertices.
comment:5 Changed 5 years ago by
Should I open a discussion about this in sagedevel?
comment:6 Changed 5 years ago by
That's a good idea. At least, interested people could add comments here.
comment:7 in reply to: ↑ 2 ; followup: ↓ 9 Changed 5 years ago by
Replying to dcoudert:
The current implementation of the
add
method isif isinstance(other_graph, GenericGraph): return self.disjoint_union(other_graph, labels='integers')So it forces to relabel vertices as integer in
[0..n1]
.At the least, we should raise an error for cases such as
Graph({0:[]})+'junk'
. Indeed, the other ordering raises an errorsage: 'junk'+Graph({0:[]})  TypeError Traceback (most recent call last) <ipythoninput992e66a308aaff> in <module>() > 1 'junk'+Graph({Integer(0):[]}) TypeError: cannot concatenate 'str' and 'Graph' objectsNow, the semantic of
+
is the disjoint union, and I believe this is the right choice. We should however ensure that the doc of__add__
,disjoint_union
,union
,__mul__
and may bejoin
, are clear enough and without ambiguity for users.Concerning the relabel to integers part, I agree that this is often painful. We could propose and intermediate behavior like: relabel only if some vertices have same label. But again some people will complain.
David.
I like the idea of only relabeling (the entire graph) if there are common vertices. NetworkX automatically relabels everything to integers when adding graphs and they get along fine without people complaining. We could possibly think about doing something with recording the previously named values when relabeling them. That way people could choose to invert the labeling if it was really necessary. Our add function could pass in a dictionary of the previous labels as an attribute in the newly created graph. In the end, I think that relabeling to integers is best. If people know they need to preserve vertex names, they can take precautions beforehand.
comment:8 Changed 5 years ago by
 Cc mcognetta added
comment:9 in reply to: ↑ 7 Changed 5 years ago by
Replying to mcognetta:
In the end, I think that relabeling to integers is best. If people know they need to preserve vertex names, they can take precautions beforehand.
OK for me. Then it would be like .disjoint_union(other, labels=’integers’)
. Current behaviour would be maintained, so there is no need for a deprecation. Should disjoint_union
have an option to get really direct union (and raise an exception it graphs have common vertices)? If not, I will add an example like we now have for disjoint union of posets.
And then there is the naming thing.
But first I will wait for three days to see if there will be opinions against this.
comment:10 Changed 5 years ago by
 Branch set to u/jmantysalo/graphs__docstring_of__add__conflicts_with_function
comment:11 Changed 5 years ago by
 Commit set to f05cd3f63f07dc35f913444d0e60cd3546321191
 Status changed from needs_info to needs_review
comment:12 Changed 5 years ago by
comment:13 followup: ↓ 15 Changed 5 years ago by
 Reviewers set to David Coudert
 Status changed from needs_review to needs_work
 "Labels of the resultin" > "Labels of the resulting"
 a doctest is needed for the
TypeError
case of the__add__
method.  the error message could be improved, for instance to something similar to
sage: 1+'a'  TypeError Traceback (most recent call last) ... TypeError: unsupported operand parent(s) for '+': 'Integer Ring' and '<type 'str'>'
We could using something like that, which is valid for both Graph
and DiGraph
.
raise TypeError("adding a '{}' and a '{}' is not defined".format(typeof(self),typeof(other))
 I'm not fully aware of python3 syntax, but I suggest to avoid using
G._name = '%s disjoint_union %s'%(a, b)
and to preferG._name = '{} disjoint_union {}'.format(a, b)
. Well actually this is certainly more robust:G.name('{} disjoint_union {}'.format(a, b))
.
comment:14 Changed 5 years ago by
 Commit changed from f05cd3f63f07dc35f913444d0e60cd3546321191 to 44e539e9c85793a3cfefaa8929a370ef28da5789
Branch pushed to git repo; I updated commit sha1. New commits:
44e539e  Added tests etc.

comment:15 in reply to: ↑ 13 Changed 5 years ago by
 Status changed from needs_work to needs_review
Replying to dcoudert:
I didi three changes as you suggested.
 I'm not fully aware of python3 syntax, but I suggest to avoid using
G._name = '%s disjoint_union %s'%(a, b)
and to preferG._name = '{} disjoint_union {}'.format(a, b)
. Well actually this is certainly more robust:G.name('{} disjoint_union {}'.format(a, b))
.
This will give an error: immutable graph can not change name. I suggest we keep this as it is now and think about this later.
comment:16 Changed 5 years ago by
The error message is confusing since the order of types is the reverse of the one used in the operation.
+ sage: G+42 + Traceback (most recent call last): + ... + TypeError: adding a <type 'sage.rings.integer.Integer'> to a <class 'sage.graphs.graph.Graph'> is not defined
I was not aware of the problem with immutable graphs. So ok to assign directly to G._name
.
However, you should replace G._name = '%s disjoint_union %s'%(a, b)
with G._name = '{} disjoint_union {}'.format(a, b)
.
Some people are actively working on making sage python3 compliant. No need to add extra work.
comment:17 Changed 5 years ago by
 Commit changed from 44e539e9c85793a3cfefaa8929a370ef28da5789 to 2efa40a0db33ddc50ab076a86a22ead8680eec09
Branch pushed to git repo; I updated commit sha1. New commits:
2efa40a  Python3 compliance.

comment:18 Changed 5 years ago by
OK, done that.
(But I think that naming question should be considered later. Maybe the design can be made better.)
comment:19 Changed 5 years ago by
 Status changed from needs_review to positive_review
The patch is good to go. Thanks, David.
comment:20 Changed 5 years ago by
 Branch changed from u/jmantysalo/graphs__docstring_of__add__conflicts_with_function to 2efa40a0db33ddc50ab076a86a22ead8680eec09
 Resolution set to fixed
 Status changed from positive_review to closed
David, a question. How should this function work?
union()
does.