Opened 6 years ago
Closed 6 years ago
#18828 closed enhancement (fixed)
Export graph to file
Reported by:  ncohen  Owned by:  

Priority:  major  Milestone:  sage6.8 
Component:  graph theory  Keywords:  
Cc:  dimpase, dcoudert, borassi  Merged in:  
Authors:  Nathann Cohen  Reviewers:  David Coudert 
Report Upstream:  N/A  Work issues:  
Branch:  254b36c (Commits, GitHub, GitLab)  Commit:  254b36c7132562b01b8802a0f3da49c90f6487d5 
Dependencies:  Stopgaps: 
Description
I feel rather guilty, as all that this branch does is steal networkx functions. With it we can export graphs to several file formats, using the networkx.write_*
functions.
Nathann
Change History (22)
comment:1 Changed 6 years ago by
 Branch set to u/ncohen/18828
 Commit set to 1bd29e566d28ac731e920d8aa6c70913ede27cb0
 Status changed from new to needs_review
comment:2 Changed 6 years ago by
 Cc dcoudert borassi added
comment:3 followup: ↓ 5 Changed 6 years ago by
 Status changed from needs_review to needs_work
Hello,
The patchbot reports compilation errors associated with ticket #18746. I don't know why... Actually I have the same issue when I try to compile my develop branch, and so I'm currently unable to test this patch.
Concerning this ticket. Don't feel guilty to steal networkx. It is very useful and we will certainly also have to do the same for reading graphs from file.
I suggest to change the way you guess the file format with something like:
for ext in formats: if filename.endswith('.'+ext): break finally: raise ...
With networkx it is possible to give extension like .edgelist.gz
in which case the file should be compressed (at least with version 1.9.1, but we only have 1.8.1). See https://networkx.github.io/documentation/latest/reference/generated/networkx.readwrite.edgelist.write_edgelist.html
David.
comment:4 followup: ↓ 6 Changed 6 years ago by
Hellooooo!
I have a little trouble understanding the goal of this ticket: would you like to have only one standard function to save graphs, instead of calling different NetworkX functions, right? Because, for instance, if I want to save a file in adjlist format I can simply type:
import networkx networkx.write_adjlist(G, path)
instead of using this new function.
In any case, I have tried to compile this code, both with make
and with make distclean && make
, and it works! Some small suggestions:
 could you make a test that checks if the output is correct?
 "the format is ‘guessed’ from the extension ..." maybe it is better to say "the format is the extension", because you do not guess, you simply use the extension.
 I would add a link to the NetworkX manual (http://networkx.lanl.gov/reference/readwrite.html), where the different file formats are detailed.
comment:5 in reply to: ↑ 3 Changed 6 years ago by
Hello,
The patchbot reports compilation errors associated with ticket #18746. I don't know why... Actually I have the same issue when I try to compile my develop branch, and so I'm currently unable to test this patch.
I had the same problem. Can be solved by removing all the cython cached files that you can find:
./src/build/temp.linuxx86_642.7/sage/graphs/graph_decompositions ./src/build/temp.linuxx86_642.7/home/ncohen/.Sage/src/build/cythonized/sage/graphs/graph_decompositions ./src/build/cythonized/sage/graphs/graph_decompositions ./src/build/cython_debug/cython_debug_info_sage.graphs.graph_decompositions* ./src/build/lib.linuxx86_642.7/sage/graphs/graph_decompositions ./local/lib/python2.7/sitepackages/sage/graphs/graph_decompositions
And then it works. That's trouble for the patchbots, though.
Concerning this ticket. Don't feel guilty to steal networkx. It is very useful and we will certainly also have to do the same for reading graphs from file.
Yep.
I suggest to change the way you guess the file format with something like:
for ext in formats: if filename.endswith('.'+ext): break finally: raise ...
Why? It is longer, and does the same. None of the extensions contains a point.
With networkx it is possible to give extension like
.edgelist.gz
in which case the file should be compressed (at least with version 1.9.1, but we only have 1.8.1). See https://networkx.github.io/documentation/latest/reference/generated/networkx.readwrite.edgelist.write_edgelist.html
So you want to add all combinations of .edgelist.gz, edgelist.tgz,..
for all possible combinations to the dictionary of extensions? O_o
Nathann
comment:6 in reply to: ↑ 4 ; followup: ↓ 9 Changed 6 years ago by
Hello,
I have a little trouble understanding the goal of this ticket: would you like to have only one standard function to save graphs, instead of calling different NetworkX functions, right?
Yes
Because, for instance, if I want to save a file in adjlist format I can simply type:
That's what the branch does, too. Only you may not know that those functions can be found in networkx.
In any case, I have tried to compile this code, both with
make
and withmake distclean && make
, and it works! Some small suggestions:
 could you make a test that checks if the output is correct?
I added one check, but it is unpleasant in many ways. First, the (integer) vertices become strings, and then each edge gets a label encoding a weight. Well, that's networkx...
 "the format is ‘guessed’ from the extension ..." maybe it is better to say "the format is the extension", because you do not guess, you simply use the extension.
How is that not a guess? Anyway, udpated.
 I would add a link to the NetworkX manual (http://networkx.lanl.gov/reference/readwrite.html), where the different file formats are detailed.
Done.
Nathann
comment:7 Changed 6 years ago by
 Commit changed from 1bd29e566d28ac731e920d8aa6c70913ede27cb0 to f7c4a18508cf66a958ffe3110754916d406c0ee3
Branch pushed to git repo; I updated commit sha1. New commits:
f7c4a18  trac #18828: Reviewer's remarks

comment:8 Changed 6 years ago by
 Status changed from needs_work to needs_review
comment:9 in reply to: ↑ 6 ; followup: ↓ 10 Changed 6 years ago by
This method is clearly useful. It is too boring to import networkx each time you want to read/write a graph from/to a file.
 could you make a test that checks if the output is correct?
I added one check, but it is unpleasant in many ways. First, the (integer) vertices become strings, and then each edge gets a label encoding a weight. Well, that's networkx...
By default method networx.write_edgelist
sets parameter data=True
. So your method produce a weighted edgelist instead of an edgelist
0 1 {}
instead of
0 1
I understand that you prefer short and fast code, but since writing to a file is slow anyway, we could spend some computation time to refine the behavior of the method.
David
comment:10 in reply to: ↑ 9 ; followup: ↓ 11 Changed 6 years ago by
I understand that you prefer short and fast code, but since writing to a file is slow anyway, we could spend some computation time to refine the behavior of the method.
Would it do the trick for you if we replaced 'networkx.write_edgelist' with 'lambda x:networkx.write_edgelist(x,data=False)'?
Nathann
comment:11 in reply to: ↑ 10 ; followup: ↓ 13 Changed 6 years ago by
Replying to ncohen:
I understand that you prefer short and fast code, but since writing to a file is slow anyway, we could spend some computation time to refine the behavior of the method.
Would it do the trick for you if we replaced 'networkx.write_edgelist' with 'lambda x:networkx.write_edgelist(x,data=False)'?
Nice trick. Furthermore, in case we want to write the labels, we can have another parameter to set data=True.
comment:12 Changed 6 years ago by
 Commit changed from f7c4a18508cf66a958ffe3110754916d406c0ee3 to c019634f9a18798786f80c2c3254b2263f58f7d8
Branch pushed to git repo; I updated commit sha1. New commits:
c019634  trac #18828: Expose all options from networkx

comment:13 in reply to: ↑ 11 Changed 6 years ago by
Nice trick. Furthermore, in case we want to write the labels, we can have another parameter to set data=True.
Some functions have this 'data' flag, others do not. To make everything simpler I updated the code to make it possible to forward any other flag to networkx. This way, we can pick whatever we want.
Nathann
comment:14 Changed 6 years ago by
I propose to add extend the tests in the following way. Let me know if you agree before I push a commit.
sage: g = graphs.PetersenGraph() sage: filename = tmp_filename(ext=".pajek") sage: g.export_to_file(filename) sage: import networkx sage: h = Graph( networkx.read_pajek(filename) sage: g.is_isomorphic(h) True sage: filename = tmp_filename(ext=".edgelist") sage: g.export_to_file(filename, data=False) sage: h = Graph( networkx.read_edgelist(filename) sage: g.is_isomorphic(h) True
Relying on vertex names is unfortunately not possible yet since the read method turns vertex id like 13
to u'13'
.
comment:15 Changed 6 years ago by
No problem no problem. Or perhaps we could relabel the graph with the function 'int' ? This should turn the u'13' into a proper 13.
Nathann
comment:16 Changed 6 years ago by
 Branch changed from u/ncohen/18828 to u/dcoudert/18828
comment:17 Changed 6 years ago by
 Commit changed from c019634f9a18798786f80c2c3254b2263f58f7d8 to 254b36c7132562b01b8802a0f3da49c90f6487d5
I have pushed a small edit on the example. Hope it helps.
For the unicode problem, I have once used the following trick. Certainly not the best way to do it.
import string if all(isinstance(u, unicode) for u in G): myaction = string.atoi elif all(isinstance(u, str) for u in G): myaction = ZZ else: myaction = lambda x:x try: L = {u:myaction(u) for u in G} except: L = {u:str(u) for u in G} G.relabel(perm=L, inplace=True)
New commits:
fed2fd7  trac #18828: Merged with 6.8.beta7

254b36c  trac #18828: fix and improve test/examples

comment:18 Changed 6 years ago by
Works for me !
comment:19 followup: ↓ 20 Changed 6 years ago by
 Reviewers set to David Coudert
 Status changed from needs_review to positive_review
So then good to go.
It would be nice to have a method for importing a graph from file, but I don't know where to put it: as a method of class Generic_Graph
? as a method of (di)graphs generators?
comment:20 in reply to: ↑ 19 ; followup: ↓ 21 Changed 6 years ago by
It would be nice to have a method for importing a graph from file, but I don't know where to put it: as a method of class
Generic_Graph
? as a method of (di)graphs generators?
The 'classiest way' would probably be something like Graph(filename)
. But adding formats to the current list scares me :P
Nathann
comment:21 in reply to: ↑ 20 Changed 6 years ago by
The 'classiest way' would probably be something like
Graph(filename)
. But adding formats to the current list scares me:P
I understand. Although you did an impressive cleaning, it's still hard. Well, we will think to something.
comment:22 Changed 6 years ago by
 Branch changed from u/dcoudert/18828 to 254b36c7132562b01b8802a0f3da49c90f6487d5
 Resolution set to fixed
 Status changed from positive_review to closed
New commits:
trac #18828: Export graph to file