Export graph to file #18828

nathanncohen · 2015-06-30T14:58:53Z

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

CC: @dimpase @dcoudert @sagetrac-borassi

Component: graph theory

Author: Nathann Cohen

Branch/Commit: 254b36c

Reviewer: David Coudert

Issue created by migration from https://trac.sagemath.org/ticket/18828

The text was updated successfully, but these errors were encountered:

nathanncohen · 2015-06-30T15:14:05Z

Commit: 1bd29e5

nathanncohen · 2015-06-30T15:14:05Z

Branch: u/ncohen/18828

nathanncohen · 2015-06-30T15:14:05Z

New commits:

`1bd29e5`	`trac #18828: Export graph to file`

dcoudert · 2015-06-30T18:11:26Z

comment:3

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.

sagetrac-borassi · 2015-07-01T09:20:50Z

comment:4

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.

nathanncohen · 2015-07-01T10:15:58Z

comment:5

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.linux-x86_64-2.7/sage/graphs/graph_decompositions
./src/build/temp.linux-x86_64-2.7/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.linux-x86_64-2.7/sage/graphs/graph_decompositions
./local/lib/python2.7/site-packages/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

nathanncohen · 2015-07-01T10:25:31Z

comment:6

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 with make 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

sagetrac-git · 2015-07-01T10:26:14Z

Changed commit from 1bd29e5 to f7c4a18

sagetrac-git · 2015-07-01T10:26:14Z

Branch pushed to git repo; I updated commit sha1. New commits:

`f7c4a18`	`trac #18828: Reviewer's remarks`

dcoudert · 2015-07-01T18:29:18Z

comment:9

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

nathanncohen · 2015-07-01T18:31:26Z

comment:10

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

dcoudert · 2015-07-01T18:51:52Z

comment:11

Replying to @nathanncohen:

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.

sagetrac-git · 2015-07-01T19:49:34Z

Branch pushed to git repo; I updated commit sha1. New commits:

`c019634`	`trac #18828: Expose all options from networkx`

sagetrac-git · 2015-07-01T19:49:34Z

Changed commit from f7c4a18 to c019634

nathanncohen · 2015-07-01T19:50:45Z

comment:13

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

dcoudert · 2015-07-02T10:42:12Z

comment:14

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'.

nathanncohen · 2015-07-02T10:44:00Z

comment:15

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

dcoudert · 2015-07-03T15:35:48Z

Changed branch from u/ncohen/18828 to u/dcoudert/18828

dcoudert · 2015-07-03T15:38:28Z

comment:17

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`

dcoudert · 2015-07-03T15:38:28Z

Changed commit from c019634 to 254b36c

nathanncohen · 2015-07-03T15:47:51Z

comment:18

Works for me !

dcoudert · 2015-07-03T16:00:17Z

comment:19

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?

dcoudert · 2015-07-03T16:00:17Z

Reviewer: David Coudert

nathanncohen · 2015-07-03T17:09:22Z

comment:20

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

dcoudert · 2015-07-03T17:10:50Z

comment:21

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.

vbraun · 2015-07-03T22:14:22Z

Changed branch from u/dcoudert/18828 to 254b36c

nathanncohen mannequin added this to the sage-6.8 milestone Jun 30, 2015

nathanncohen mannequin added c: graph theory labels Jun 30, 2015

nathanncohen mannequin added the s: needs review label Jun 30, 2015

dcoudert added s: needs work and removed s: needs review labels Jun 30, 2015

nathanncohen mannequin added s: needs review and removed s: needs work labels Jul 1, 2015

dcoudert added s: positive review and removed s: needs review labels Jul 3, 2015

vbraun removed the s: positive review label Jul 3, 2015

vbraun closed this as completed in 5017538 Jul 3, 2015

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Export graph to file #18828

Export graph to file #18828

nathanncohen mannequin commented Jun 30, 2015

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Export graph to file #18828

Export graph to file #18828

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nathanncohen mannequin commented Jun 30, 2015

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