from gap to libgap in strongly_regular_db #28818

dimpase · 2019-11-28T23:49:07Z

remove the last use of GAP pexpect in that file;

remove no longer needed #optional tags in some tests

CC: @fchapoton @dcoudert

Component: graph theory

Author: Dima Pasechnik

Branch/Commit: 6489a18

Reviewer: David Coudert

Issue created by migration from https://trac.sagemath.org/ticket/28818

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

dimpase · 2019-11-28T23:50:08Z

comment:1

this should make this a bit more robust and quick

dimpase · 2019-11-28T23:50:08Z

Reviewer: dcoudert

sagetrac-git · 2019-11-29T11:06:12Z

Changed commit from 249d582 to 23d6a45

sagetrac-git · 2019-11-29T11:06:12Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`23d6a45`	`use libgap instead of gap, remove no longer needed #optional`

dimpase · 2019-11-29T11:07:32Z

comment:4

a bit of cleanup in the updated commit

sagetrac-git · 2019-11-29T12:15:14Z

Changed commit from 23d6a45 to 82ec1c3

sagetrac-git · 2019-11-29T12:15:14Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`82ec1c3`	`use libgap instead of gap, remove no longer needed #optional`

sagetrac-git · 2019-11-29T12:47:25Z

Changed commit from 82ec1c3 to b3183e8

sagetrac-git · 2019-11-29T12:47:25Z

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

`b3183e8`	`use libgap to compute orbit lengths on edges/arcs`

dimpase · 2019-12-01T12:15:08Z

Changed reviewer from dcoudert to none

dcoudert · 2019-12-01T13:14:41Z

comment:8

after git trac try 28818 and sage -b, I did:

confetti:sage dcoudert$ ./sage -tp --long --optional=sage,optional,external src/sage/graphs/
too few successful tests, not using stored timings
Running doctests with ID 2019-12-01-14-02-49-49bed4c1.
Git branch: HEAD
Using --optional=benzene,bliss,cbc,csdp,dot2tex,external,gap_packages,gfortran,igraph,libsemigroups,mcqd,mpir,plantri,python_igraph,sage,sagenb,tdlib
External software to be detected: cplex,ffmpeg,graphviz,gurobi,imagemagick,internet,latex,macaulay2,magma,maple,mathematica,matlab,octave,pandoc,scilab
Sorting sources by runtime so that slower doctests are run first....
Doctesting 100 files using 4 threads.
sage -t --long src/sage/graphs/chrompoly.pyx
    [20 tests, 37.29 s]
sage -t --long src/sage/graphs/generators/smallgraphs.py
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 3506, in sage.graphs.generators.smallgraphs.LivingstoneGraph
Failed example:
    g = graphs.LivingstoneGraph() # optional - gap_packages internet
Exception raised:
    Traceback (most recent call last):
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.graphs.generators.smallgraphs.LivingstoneGraph[0]>", line 1, in <module>
        g = graphs.LivingstoneGraph() # optional - gap_packages internet
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/graphs/generators/smallgraphs.py", line 3522, in LivingstoneGraph
        return Graph(edges, name="Livingstone Graph")
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/graphs/graph.py", line 1120, in __init__
        raise ValueError("This input cannot be turned into a graph")
    ValueError: This input cannot be turned into a graph
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 3507, in sage.graphs.generators.smallgraphs.LivingstoneGraph
Failed example:
    g.order()                     # optional - gap_packages internet
Exception raised:
    Traceback (most recent call last):
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.graphs.generators.smallgraphs.LivingstoneGraph[1]>", line 1, in <module>
        g.order()                     # optional - gap_packages internet
    NameError: name 'g' is not defined
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 3509, in sage.graphs.generators.smallgraphs.LivingstoneGraph
Failed example:
    g.size()                      # optional - gap_packages internet
Exception raised:
    Traceback (most recent call last):
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.graphs.generators.smallgraphs.LivingstoneGraph[2]>", line 1, in <module>
        g.size()                      # optional - gap_packages internet
    NameError: name 'g' is not defined
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 3511, in sage.graphs.generators.smallgraphs.LivingstoneGraph
Failed example:
    g.girth()                     # optional - gap_packages internet
Exception raised:
    Traceback (most recent call last):
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.graphs.generators.smallgraphs.LivingstoneGraph[3]>", line 1, in <module>
        g.girth()                     # optional - gap_packages internet
    NameError: name 'g' is not defined
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 3513, in sage.graphs.generators.smallgraphs.LivingstoneGraph
Failed example:
    g.is_vertex_transitive()      # optional - gap_packages internet
Exception raised:
    Traceback (most recent call last):
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.graphs.generators.smallgraphs.LivingstoneGraph[4]>", line 1, in <module>
        g.is_vertex_transitive()      # optional - gap_packages internet
    NameError: name 'g' is not defined
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 3515, in sage.graphs.generators.smallgraphs.LivingstoneGraph
Failed example:
    g.is_distance_regular()       # optional - gap_packages internet
Exception raised:
    Traceback (most recent call last):
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/dcoudert/sage3/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.graphs.generators.smallgraphs.LivingstoneGraph[5]>", line 1, in <module>
        g.is_distance_regular()       # optional - gap_packages internet
    NameError: name 'g' is not defined
**********************************************************************
1 item had failures:
   6 of   7 in sage.graphs.generators.smallgraphs.LivingstoneGraph
    [582 tests, 6 failures, 72.94 s]
...
sage -t --long src/sage/graphs/strongly_regular_db.pyx
    [335 tests, 87.45 s]
...
sage -t --long src/sage/graphs/graph_latex.py
**********************************************************************
File "src/sage/graphs/graph_latex.py", line 1333, in sage.graphs.graph_latex.GraphLatex.dot2tex_picture
Failed example:
    print(g.latex_options().dot2tex_picture())  # optional - dot2tex graphviz
Expected:
    \begin{tikzpicture}[>=latex,line join=bevel,]
    %%
      \node (node_3) at (...bp,...bp) [draw,draw=none] {$\left(0, 1\right)$};
      \node (node_2) at (...bp,...bp) [draw,draw=none] {$\left(1, 0\right)$};
      \node (node_1) at (...bp,...bp) [draw,draw=none] {$\left(0, 0\right)$};
      \node (node_0) at (...bp,...bp) [draw,draw=none] {$\left(1, 1\right)$};
      \draw [black,->] (node_1) ..controls (...bp,...bp) and (...bp,...bp)  .. (node_3);
      \draw [black,->] (node_2) ..controls (...bp,...bp) and (...bp,...bp)  .. (node_3);
      \draw [black,->] (node_2) ..controls (...bp,...bp) and (...bp,...bp)  .. (node_0);
      \draw [black,->] (node_1) ..controls (...bp,...bp) and (...bp,...bp)  .. (node_0);
    %
    \end{tikzpicture}
Got:
    \begin{tikzpicture}[>=latex,line join=bevel,]
    %%
    \node (node_0) at (14.5bp,61.5bp) [draw,draw=none] {$\left(0, 0\right)$};
      \node (node_1) at (14.5bp,8.5bp) [draw,draw=none] {$\left(1, 1\right)$};
      \node (node_2) at (61.5bp,8.5bp) [draw,draw=none] {$\left(0, 1\right)$};
      \node (node_3) at (61.5bp,61.5bp) [draw,draw=none] {$\left(1, 0\right)$};
      \draw [black,->] (node_0) ..controls (14.5bp,45.802bp) and (14.5bp,35.845bp)  .. (node_1);
      \draw [black,->] (node_0) ..controls (28.968bp,45.185bp) and (38.841bp,34.051bp)  .. (node_2);
      \draw [black,->] (node_3) ..controls (47.032bp,45.185bp) and (37.159bp,34.051bp)  .. (node_1);
      \draw [black,->] (node_3) ..controls (61.5bp,45.802bp) and (61.5bp,35.845bp)  .. (node_2);
    %
    \end{tikzpicture}
**********************************************************************
File "src/sage/graphs/graph_latex.py", line 1352, in sage.graphs.graph_latex.GraphLatex.dot2tex_picture
Failed example:
    print(G.latex_options().dot2tex_picture()) # optional - dot2tex graphviz
Expected:
    \begin{tikzpicture}[>=latex,line join=bevel,]
    %%
    \node (node_1) at (...bp,...bp) [draw,draw=none] {$3333$};
      \node (node_0) at (...bp,...bp) [draw,draw=none] {$88$};
      \draw [black,->] (node_1) ..controls (...bp,...bp) and (...bp,...bp)  .. (node_0);
      \definecolor{strokecol}{rgb}{0.0,0.0,0.0};
      \pgfsetstrokecolor{strokecol}
      \draw (...bp,...bp) node {$\text{\texttt{my{\char`\_}label}}$};
    %
    \end{tikzpicture}
Got:
    \begin{tikzpicture}[>=latex,line join=bevel,]
    %%
    \node (node_0) at (13.5bp,75.5bp) [draw,draw=none] {$3333$};
      \node (node_1) at (13.5bp,6.5bp) [draw,draw=none] {$88$};
      \draw [black,->] (node_0) ..controls (13.5bp,58.557bp) and (13.5bp,38.274bp)  .. (node_1);
      \definecolor{strokecol}{rgb}{0.0,0.0,0.0};
      \pgfsetstrokecolor{strokecol}
      \draw (40.0bp,41.0bp) node {$\text{\texttt{my{\char`\_}label}}$};
    %
    \end{tikzpicture}
**********************************************************************
1 item had failures:
   2 of  12 in sage.graphs.graph_latex.GraphLatex.dot2tex_picture
    [199 tests, 2 failures, 8.30 s]
----------------------------------------------------------------------
sage -t --long src/sage/graphs/generators/smallgraphs.py  # 6 doctests failed
sage -t --long src/sage/graphs/graph_latex.py  # 2 doctests failed
----------------------------------------------------------------------

the failures graph_latex.py are independent (and may be already fixed in another ticket).

dimpase · 2019-12-01T13:54:22Z

comment:9

The error

File "src/sage/graphs/generators/smallgraphs.py", line 3506, in sage.graphs.generators.smallgraphs.LivingstoneGraph
Failed example:
    g = graphs.LivingstoneGraph() # optional - gap_packages internet
...

has not arisen from this branch, it's there without it. I guess noone tests with internet on :-)

OK, let me see if I can fix it quickly.

dcoudert · 2019-12-01T17:08:41Z

comment:10

Right. Let me know if you have a fix, or if we let these doctests for another ticket.

sagetrac-git · 2019-12-01T19:10:23Z

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

`1bf4fac`	`fix for outdated code, tests for LivinstoneGraph`

sagetrac-git · 2019-12-01T19:10:23Z

Changed commit from b3183e8 to 1bf4fac

dimpase · 2019-12-01T19:11:18Z

comment:12

OK, there was a failure in Graph's understanding that edges are edges.

dcoudert · 2019-12-01T20:02:05Z

Reviewer: David Coudert

dcoudert · 2019-12-01T20:02:05Z

comment:13

In strongly_regular_db.pyx, you changed

-        sage: g.is_strongly_regular(parameters=True) # long time # optional - gap_packages
+        sage: g=SRG_280_135_70_60()                  # long time

but this test needs libgap, right ? I have not followed the recent changes with gap. Is it now part of the standard distribution ? Otherwise, how can we prevent to run this test if we don't have lib gap ?

dimpase · 2019-12-01T20:29:30Z

comment:14

libgap is a standard package since I don't recall when. We're converting the whole sagelib to use libgap instead of gap.

dcoudert · 2019-12-01T21:59:54Z

comment:15

didn't know that. thanks.

LGTM

vbraun · 2019-12-03T23:19:46Z

comment:16

I'm getting timeouts at

sage: gg = graphs.HallJankoGraph(from_string=False) # long time ## line 683 ##

and

sage: g=SRG_280_135_70_60()                  # long time ## line 2243 ##

resulting in

sage -t --long src/sage/graphs/generators/smallgraphs.py  # Timed out
sage -t --long src/sage/graphs/strongly_regular_db.pyx  # Timed out

Several buildbots time out at the same test so its reproducable...

dimpase · 2019-12-03T23:36:41Z

comment:17

these tests need internet connection to cache data via GAP's AtlasRep package.
One can tag them # optional - internet

vbraun · 2019-12-04T08:09:27Z

comment:18

please do!

sagetrac-git · 2019-12-04T10:02:07Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`5fed72f`	`use libgap instead of gap, remove no longer needed #optional`
`2b08c1a`	`use libgap to compute orbit lengths on edges/arcs`
`70f67e5`	`fix for outdated code, tests for LivinstoneGraph`
`6489a18`	`# optional - internet tags for AtlasRep uses`

sagetrac-git · 2019-12-04T10:02:07Z

Changed commit from 1bf4fac to 6489a18

dimpase · 2019-12-04T10:04:11Z

comment:20

rebased over latest beta, added commit 6489a18 (with # optional - internet tags)

off to bots again.

dcoudert · 2019-12-04T10:54:48Z

comment:21

I have the same errors when I try ./sage -tp --long --optional=sage,optional,external src/sage/graphs/ but not when I try ./sage -tp --long src/sage/graphs/. So added flags are working well.

LGTM.

vbraun · 2019-12-08T21:19:37Z

Changed branch from u/dimpase/graphs/srgupd to 6489a18

dimpase added this to the sage-8.9 milestone Nov 28, 2019

dimpase added c: graph theory labels Nov 28, 2019

dimpase added the s: needs review label Nov 28, 2019

dimpase modified the milestones: sage-8.9, sage-9.0 Nov 28, 2019

dimpase added t: bug and removed t: enhancement labels Dec 1, 2019

dcoudert removed the s: needs review label Dec 1, 2019

dcoudert added the s: positive review label Dec 1, 2019

vbraun added s: needs work and removed s: positive review labels Dec 3, 2019

dimpase added s: positive review and removed s: needs work labels Dec 4, 2019

vbraun removed the s: positive review label Dec 8, 2019

vbraun closed this as completed in d3e64db Dec 8, 2019

dimpase mentioned this issue Mar 2, 2023

convert all of Sage library code to libgap #26902

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from gap to libgap in strongly_regular_db #28818

from gap to libgap in strongly_regular_db #28818

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from gap to libgap in strongly_regular_db #28818

from gap to libgap in strongly_regular_db #28818

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