KeyError raised by GraphLatex.dot2tex_picture when edge_labels=True #13624

seblabbe · 2012-10-19T09:03:36Z

The following is ok :

sage: G = DiGraph()
sage: G.add_edge(3333, 88, 'my_label')
sage: G.set_latex_options(format='dot2tex')
sage: view(G)

but with edges_labels=True a KeyError is raised :

sage: G.set_latex_options(edge_labels=True)
sage: view(G)
ERROR    Failed to process input
Traceback (most recent call last):
  File "/Users/slabbe/Applications/sage-5.2/local/lib/python2.7/site-packages/dot2tex/dot2tex.py", line 2939, in main
    s =  conv.convert(dotdata)
  File "/Users/slabbe/Applications/sage-5.2/local/lib/python2.7/site-packages/dot2tex/dot2tex.py", line 794, in convert
    return self.do_preview_preproc()
  File "/Users/slabbe/Applications/sage-5.2/local/lib/python2.7/site-packages/dot2tex/dot2tex.py", line 1167, in do_preview_preproc
    hp,dp,wt = pp.texdims[name]
KeyError: '3333880'

The error is also raised by dot2tex_picture method:

sage: G = DiGraph()
sage: G.add_edge(0, 1, 'p0')
sage: G.latex_options().dot2tex_picture()
'\n\\begin{tikzpicture}[>=latex,line join=bevel,]\n%%\n\\node (1) at (6bp,7bp) [draw,draw=none] {$1$};\n  \\node (0) at (6bp,57bp) [draw,draw=none] {$0$};\n  \\draw [black,->] (0) ..controls (6bp,44.053bp) and (6bp,33.103bp)  .. (1);\n%\n\\end{tikzpicture}\n'
.dot2tex_picture()
sage: G.set_latex_options(edge_labels=True)
sage: G.latex_options().dot2tex_picture()
ERROR    Failed to process input
Traceback (most recent call last):
  File "/Users/slabbe/Applications/sage-5.2/local/lib/python2.7/site-packages/dot2tex/dot2tex.py", line 2939, in main
    s =  conv.convert(dotdata)
  File "/Users/slabbe/Applications/sage-5.2/local/lib/python2.7/site-packages/dot2tex/dot2tex.py", line 794, in convert
    return self.do_preview_preproc()
  File "/Users/slabbe/Applications/sage-5.2/local/lib/python2.7/site-packages/dot2tex/dot2tex.py", line 1167, in do_preview_preproc
    hp,dp,wt = pp.texdims[name]
KeyError: '010'
''

This is due to dot2tex currently not supporting '\verb' properly.

The attached patch works around this by replacing \verb by \text, and stripping out tricky characters like ^ and _.

CC: @stumpc5 @nathanncohen

Component: packages: optional

Keywords: dot2tex, graph drawing

Author: Sébastien Labbé

Branch/Commit: 2634500

Reviewer: Christian Stump

Issue created by migration from https://trac.sagemath.org/ticket/13624

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

seblabbe · 2012-11-13T01:38:29Z

comment:2

I managed to fix the bug with the following hack :

diff --git a/src/dot2tex/dot2tex.py b/src/dot2tex/dot2tex.py
--- a/src/dot2tex/dot2tex.py
+++ b/src/dot2tex/dot2tex.py
@@ -1153,6 +1153,20 @@ To see what happened, run dot2tex with t
         for name,item in usededges.items():
 
             edge = item
+            break
             hp,dp,wt = pp.texdims[name]
             xmargin, ymargin = self.get_margins(edge)
             labelcode = '<<<table border="0" cellborder="0" cellpadding="0">'\

but I still don't know what was this loop for... because the output is OK (with edge labels).

seblabbe · 2012-11-16T18:16:50Z

comment:3

I just created an issue on the dot2tex google code project :

http://code.google.com/p/dot2tex/issues/detail?id=32

nthiery · 2013-03-11T18:11:44Z

comment:5

Hi Sébastien,

I had not noticed this ticket. A quick and dirty workaround has been in the Sage-Combinat queue for some time. I did some further cleanup, but it's still nothing but a workaround. Shall we get it into Sage? If you think the patch could use more work, do you mind taking it over?

Cheers,
Nicolas

nthiery · 2013-03-11T18:18:54Z

comment:6

While I was at it, I folded in a couple tests I had put in a later patch in the Sage-Combinat queue.

nthiery · 2013-03-11T19:37:41Z

comment:9

The change verb -> text in sage.misc.latex was breaking quite a few doctests. I made it a separate ticket: #14256. This one should not depend on it.

On the other hand, I added three tiny things that were in a later patch in the queue:

shape=plain text whenever there are labels on the vertices (latex or not)
trim "." from keys (I guess I must have had a problem with them at some point)
a doctest fix.

jdemeyer · 2013-03-13T14:38:53Z

comment:10

Please add your name as Author.

nthiery · 2013-03-13T14:47:54Z

Author: Nicolas M. Thiéry

nthiery · 2013-03-13T14:47:54Z

Changed keywords from dot2tex to dot2tex, graph drawing

nthiery · 2013-04-02T02:39:57Z

comment:12

Hi Nathann!

Would you have time to review this one?

Thanks!
Nicolas

nathanncohen · 2013-04-02T08:25:35Z

comment:13

This is what happens when I install graphviz

[...]
make[3]: *** No rule to make target `../../plugin/pango/libgvplugin_pango.la', needed by `dot_builtins'.  Stop.
make[3]: *** Waiting for unfinished jobs....
mv -f .deps/no_demand_loading.Tpo .deps/no_demand_loading.Po
mv -f .deps/dot_builtins.Tpo .deps/dot_builtins.Po
mv -f .deps/dot.Tpo .deps/dot.Po
make[3]: Leaving directory `/home/ncohen/.Sage/spkg/build/graphviz-2.16.1.p0/src/cmd/dot'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/ncohen/.Sage/spkg/build/graphviz-2.16.1.p0/src/cmd'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/ncohen/.Sage/spkg/build/graphviz-2.16.1.p0/src'
make: *** [all] Error 2
Error building Graphviz

real	0m53.650s
user	0m45.475s
sys	0m8.313s
************************************************************************
Error installing package graphviz-2.16.1.p0
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
  /home/ncohen/.Sage/spkg/logs/graphviz-2.16.1.p0.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/home/ncohen/.Sage/spkg/build/graphviz-2.16.1.p0 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
  (cd '/home/ncohen/.Sage/spkg/build/graphviz-2.16.1.p0' && '/home/ncohen/.Sage/sage' -sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************

Nathann

nthiery · 2013-04-02T12:03:46Z

comment:14

Hi!

Yes, the graphviz spkg is broken (and as far as I can remember has always been). But most linux distro have a graphviz package, so that's not too bad. The doc already says to install graphviz out of Sage.

We should probably remove this broken spkg from "experimental" ...

Cheers,
Nicolas

nathanncohen · 2013-04-02T12:07:37Z

comment:15

Yes, the graphviz spkg is broken (and as far as I can remember has always been). But most linux distro have a graphviz package, so that's not too bad. The doc already says to install graphviz out of Sage.

......

who the hell put that in the doc without removing the package ?...

Nathann

nathanncohen · 2013-04-02T12:17:38Z

comment:16

We should probably remove this broken spkg from "experimental" ...

Indeed. The only thing to do is update the doc to remove any mention of this graphviz package, and ask Jeroen in a ticket to remove it from experimental.

And it will be quickly reviewed, I swear.

Nathann

nthiery · 2013-04-02T13:14:29Z

comment:17

Replying to @nathanncohen:

We should probably remove this broken spkg from "experimental" ...

Indeed. The only thing to do is update the doc to remove any mention of this graphviz package, and ask Jeroen in a ticket to remove it from experimental.

I was already careful not to mention the spkg in the doc (but if you see how to improve the graphviz installation instructions, please go ahead in a separate ticket; I'll review it).

As for removing the spkg, this is now: #14398.

nathanncohen · 2013-04-02T13:22:05Z

comment:18

I was already careful not to mention the spkg in the doc (but if you see how to improve the graphviz installation instructions, please go ahead in a separate ticket; I'll review it).

Is written explicitly anywhere that there is no spkg and that the users should install it by themselves ?

Nathann

jdemeyer · 2013-04-02T13:31:09Z

comment:19

# optional - requires dot2tex and graphviz

should be

# optional - dot2tex graphviz

nathanncohen · 2013-04-02T13:32:13Z

comment:20

(and while you're editing the patch, you included a http link which Sphinx does not understand as one)

Nathann

nathanncohen · 2013-04-02T13:34:46Z

comment:21

5 doctests fail on my machine. The error message do not seem to say that there is something wrong with my install (dot or graphviz which I installed through my distro).

sage -t --long dot2tex_utils.py
**********************************************************************
File "dot2tex_utils.py", line 11, in sage.graphs.dot2tex_utils
Failed example:
    output = dot2tex.dot2tex(graph, format="positions", prog="neato") # optional - requires dot2tex and graphviz
Expected nothing
Got:
    ERROR    Failed to process input
    Traceback (most recent call last):
      File "/home/ncohen/.Sage/local/lib/python2.7/site-packages/dot2tex/dot2tex.py", line 2928, in main
        s =  conv.convert(dotdata)
      File "/home/ncohen/.Sage/local/lib/python2.7/site-packages/dot2tex/dot2tex.py", line 848, in convert
        return self.output()
      File "/home/ncohen/.Sage/local/lib/python2.7/site-packages/dot2tex/dot2tex.py", line 2566, in output
        positions[node.name] = map(int, pos.split(','))
    ValueError: invalid literal for int() with base 10: '87.137'
**********************************************************************

Nathann

nthiery · 2013-04-02T13:36:39Z

comment:22

Replying to @nathanncohen:

I was already careful not to mention the spkg in the doc (but if you see how to improve the graphviz installation instructions, please go ahead in a separate ticket; I'll review it).

Is written explicitly anywhere that there is no spkg and that the users should install it by themselves ?

It's written that the soft can be downloaded from the graphviz website. This seems explicit enough to me, but if you want to improve that, go ahead (but I would not speak of spkg at all).

nathanncohen · 2013-04-02T13:40:52Z

comment:23

It's written that the soft can be downloaded from the graphviz website.

Where ?

Nathann

seblabbe · 2013-04-02T22:35:40Z

comment:42

Ils sont fous ces romains...

Replying to @nthiery:

Have you installed the new spkg as I pointed out in my previous comment?

I think it is better not to update the old ticket #7004. Here is the link to the new spkg:

sage -f http://sage.math.washington.edu/home/nthiery/dot2tex-2.8.7-dev.spkg

seblabbe · 2013-04-03T14:42:48Z

comment:43

I just added a patch which fixes the broken doctests seen by the patchbot. I also added a doctest that make sure the issue of this ticket is solved. I also fixed an # optional - dot2tex, graphviz which was not up to date.

Finally I realize that some optional test are broken. Like this one that we can see in the doc of layout_graphviz. This may be considered in another ticket.

sage: g = digraphs.ButterflyGraph(2)
sage: g.plot(layout = "graphviz", prog = "neato") # optional - dot2tex, graphviz
Traceback (most recent call last): 
...
ValueError: invalid literal for int() with base 10: '67.297'

nthiery · 2013-04-03T15:01:43Z

comment:44

Replying to @seblabbe:

I just added a patch which fixes the broken doctests seen by the patchbot. I also added a doctest that make sure the issue of this ticket is solved. I also fixed an # optional - dot2tex, graphviz which was not up to date.

Thanks Sébastien! I looked at your reviewer patch, and it looks good to me. Let's see what the patchbot says. Back to needs review for the first patch.

Finally I realize that some optional test are broken. Like this one that we can see in the doc of layout_graphviz. This may be considered in another ticket.
sage: g = digraphs.ButterflyGraph(2)
sage: g.plot(layout = "graphviz", prog = "neato") # optional - dot2tex, graphviz
Traceback (most recent call last): 
...
ValueError: invalid literal for int() with base 10: '67.297'

+1 since the tests were already failing before this ticket. This is
now #14408 which is about updating the dot2tex spkg.

novoselt · 2013-04-17T20:53:28Z

comment:45

For the record, current installation instructions for dot2tex are outdated (I tried the example from the description and it failed at first).

With the current patch at #14382, the example from the description does not give errors.

seblabbe · 2013-06-03T08:29:29Z

Adding a doctest to make sure the initial issue is fixed

seblabbe · 2013-06-03T08:34:29Z

comment:46

Attachment: trac_13624-review-sl.patch.gz

I just updated my patch which adds a doctest. Even if #14382 finally fix the problem, I think it could be merged anyway.

I removed the part that was fixing dot2tex optional doctests errors. I will move this part in another patch that I am going to post on #14408 where similar issues were discussed.

novoselt · 2013-06-03T14:28:08Z

comment:47

Replying to @seblabbe:

Even if #14382 finally fix the problem,

Feel free to give it a try and set to positive review - it is not big ;-)

tscrim · 2014-04-26T12:28:58Z

comment:50

Currently in 6.2.rc0, the example given in the description works (probably from #14382):

sage: G = DiGraph()
sage: G.add_edge(333, 88, "my_label")
sage: G.set_latex_options(format="dot2tex", edge_labels=True)
sage: latex(G)

\begin{tikzpicture}[>=latex,line join=bevel,]
%%
\node (node_1) at (11.000000bp,79.000000bp) [draw,draw=none] {$333$};
  \node (node_0) at (11.000000bp,7.000000bp) [draw,draw=none] {$88$};
  \draw [black,->] (node_1) ..controls (11.000000bp,61.481000bp) and (11.000000bp,39.548000bp)  .. (node_0);
  \definecolor{strokecol}{rgb}{0.0,0.0,0.0};
  \pgfsetstrokecolor{strokecol}
  \draw (38.000000bp,43.000000bp) node {$\text{\texttt{my{\char`\_}label}}$};
%
\end{tikzpicture}

So how much of this ticket should we keep or should we just close as a "works-for-me"?

seblabbe · 2014-04-27T21:41:21Z

comment:51

So how much of this ticket should we keep or should we just close as a "works-for-me"?

As I suggested in a previous comment, I think we could merge the patch trac_13624-review-sl.patch which simply adds a doctest.

Sébastien

seblabbe · 2014-04-30T09:46:42Z

Commit: 2634500

seblabbe · 2014-04-30T09:46:42Z

comment:52

I just converted my old hg patch to a git branch. It should be easy to review as it only adds a doctest since the problem was fixed by #14382.

New commits:

`2634500`	`adding a doctest to make sure 13624 is fixed`

seblabbe · 2014-04-30T09:46:42Z

Branch: u/slabbe/13624

seblabbe · 2014-04-30T09:46:42Z

Changed author from Nicolas M. Thiéry to Sébastien Labbé

stumpc5 · 2014-04-30T09:50:14Z

Reviewer: Christian Stump

vbraun · 2014-05-01T10:18:33Z

Changed branch from u/slabbe/13624 to 2634500

seblabbe added this to the sage-5.11 milestone Oct 19, 2012

seblabbe added c: packages: optional labels Oct 19, 2012

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jdemeyer added s: needs work and removed s: needs review labels Apr 2, 2013

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jdemeyer modified the milestones: sage-5.11, sage-5.12 Aug 13, 2013

sagetrac-vbraun-spam mannequin modified the milestones: sage-6.1, sage-6.2 Jan 30, 2014

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vbraun closed this as completed in ca10fd5 May 1, 2014

seblabbe mentioned this issue May 21, 2013

Make dot2tex work with matplotlib 1.2.x (as well as older versions) #14594

Closed

KeyError raised by GraphLatex.dot2tex_picture when edge_labels=True #13624

KeyError raised by GraphLatex.dot2tex_picture when edge_labels=True #13624

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