graph canonical labels and doctest failures in databases/sql_db.py #26994

videlec · 2019-01-02T07:33:26Z

Starting from somewhere around 8.5.beta the canonical labels given by Sage and bliss are different on some instances

sage: G1 = Graph("Cr")
sage: G2 = Graph("C]")
sage: G1 == G2
False
sage: G1.is_isomorphic(G2) and G2.is_isomorphic(G1)
True
sage: G1.canonical_label(algorithm='bliss') == G1
True
sage: G1.canonical_label(algorithm='sage') == G2
True

That is Cr is canonical for bliss while C] is canonical for Sage... More examples:

4 vertices: C` vs CK, CR vs CL and Cr vs C]
5 vertices: DGC vs D@O, DAK vs D@S, DC[ vs D@s, DIK vs DBW, DD[ vs DBk, DDW vs DBg, D`{ vs DK{, DqK vs DLo, DMk vs Dbk, DR{ vs DL{, DR[ vs DJk, Dr{ vs D]{

As a consequence, when bliss is installed, we have the two following doctest failures in databases/sql_db.py.

sage -t --long src/sage/databases/sql_db.py
**********************************************************************
File "src/sage/databases/sql_db.py", line 956, in
sage.databases.sql_db.SQLDatabase.__init__
Failed example:
    D.show('simon')
Expected:
    graph6               vertices             edges
    ------------------------------------------------------------
    ?                    0                    0
    @                    1                    0
    A?                   2                    0
    A_                   2                    1
    B?                   3                    0
    BG                   3                    1
    BW                   3                    2
    Bw                   3                    3
    C?                   4                    0
    C@                   4                    1
    CB                   4                    2
    CF                   4                    3
    CJ                   4                    3
    CK                   4                    2
    CL                   4                    3
    CN                   4                    4
    C]                   4                    4
    C^                   4                    5
    C~                   4                    6
Got:
    graph6               vertices             edges
    ------------------------------------------------------------
    ?                    0                    0
    @                    1                    0
    A?                   2                    0
    A_                   2                    1
    B?                   3                    0
    BG                   3                    1
    BW                   3                    2
    Bw                   3                    3
    C?                   4                    0
    C@                   4                    1
    CB                   4                    2
    CF                   4                    3
    CJ                   4                    3
    C`                   4                    2
    CR                   4                    3
    CN                   4                    4
    Cr                   4                    4
    C^                   4                    5
    C~                   4                    6
**********************************************************************
File "src/sage/databases/sql_db.py", line 1004, in
sage.databases.sql_db.SQLDatabase.__init__
Failed example:
    E.show('simon')
Expected:
    graph6               vertices             edges
    ------------------------------------------------------------
    ?                    0                    0
    @                    1                    0
    A?                   2                    0
    A_                   2                    1
    B?                   3                    0
    BG                   3                    1
    BW                   3                    2
    Bw                   3                    3
    C?                   4                    0
    C@                   4                    1
    CB                   4                    2
    CF                   4                    3
    CJ                   4                    3
    CK                   4                    2
    CL                   4                    3
    CN                   4                    4
    C]                   4                    4
    C^                   4                    5
    C~                   4                    6
Got:
    graph6               vertices             edges
    ------------------------------------------------------------
    ?                    0                    0
    @                    1                    0
    A?                   2                    0
    A_                   2                    1
    B?                   3                    0
    BG                   3                    1
    BW                   3                    2
    Bw                   3                    3
    C?                   4                    0
    C@                   4                    1
    CB                   4                    2
    CF                   4                    3
    CJ                   4                    3
    C`                   4                    2
    CR                   4                    3
    CN                   4                    4
    Cr                   4                    4
    C^                   4                    5
    C~                   4                    6
**********************************************************************
1 item had failures:
   2 of  26 in sage.databases.sql_db.SQLDatabase.__init__
    [288 tests, 2 failures, 1.59 s]

CC: @kiwifb @dcoudert

Component: documentation

Author: David Coudert

Branch/Commit: a1a96fa

Reviewer: Volker Braun

Issue created by migration from https://trac.sagemath.org/ticket/26994

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

videlec · 2019-01-02T07:41:03Z

comment:1

The graph6 strings Cr and C] indeed corresponds to graphs on 4 vertices (isomorphic but not equal)

sage: G1 = Graph("Cr")
sage: G2 = Graph("C]")
sage: G1 == G2
False
sage: G1.is_isomorphic(G2) and G2.is_isomorphic(G1)
True

Still on SageMath 8.6.beta0 the canonical labeling is Cr

sage: G1.canonical_label() == G1 and G2.canonical_label() == G1
True

Hence the code in the doctest should have been added Cr in the database and not C] as it is currently written.

fchapoton · 2019-01-02T08:07:35Z

comment:4

see #26800

seblabbe · 2019-01-02T10:04:06Z

comment:5

This ticket is a duplicate of #26920 which I open about 2 weeks ago. I suggest to close #26920 since the one here seems more alive.

seblabbe · 2019-01-02T10:07:14Z

comment:6

See #25399 for another recent ticket fixing doctests failures related to bliss.

videlec · 2019-01-02T12:48:57Z

comment:7

Replying to @fchapoton:

see #26800

The failure in this ticket is not Python 3 related. Both Sage and bliss provides canonical labelings but different ones.

embray · 2019-01-02T15:43:43Z

comment:9

Being that bliss is an optional package, should this be a blocker? I'm not sure what the latest consensus is on that (being that there is an unfortunate lack--for some reason--of buildbots that test optional packages). It doesn't seem to be a particularly substantive failure either.

dcoudert · 2019-01-02T18:07:12Z

Author: David Coudert

dcoudert · 2019-01-02T18:07:12Z

Commit: a1a96fa

dcoudert · 2019-01-02T18:07:12Z

Branch: public/26994_sql_db

dcoudert · 2019-01-02T18:07:12Z

comment:10

The canonical label of a graph depends on the algorithm used to compute it. See the note in the documentation of canonical_label: Make sure you always compare canonical forms obtained by the same algorithm.

So a simple fix is to force algorithm='sage' in the doctest.

New commits:

`a1a96fa`	`trac #26994: fix doctest in sql_db`

vbraun · 2019-01-02T19:12:19Z

Reviewer: Volker Braun

vbraun · 2019-01-03T09:33:57Z

Changed branch from public/26994_sql_db to a1a96fa

SageMath version 8.6, Release Date: 2019-01-15 * tag '8.6': (15673 commits) Updated SageMath version to 8.6 Updated SageMath version to 8.6.rc1 maxint -> maxsize, for py2/3 compatibility sagemath#26326 : 32-bit vs 64-bit doctests sagemath#26326 : reorder creation of random graphs to avoid creating an empty one by bad luck on 32-bit systems. Updated SageMath version to 8.6.rc0 trac sagemath#26994: fix doctest in sql_db trivial cleanup force a UTF-8 locale on GAP in these tests allow setting additional environment variables when starting a Gap interface instance p_group_cohomology: Avoid conflict with a new global variable name in Gap Updated SageMath version to 8.6.beta1 25501: adding missing optional tags Fix tox testsuite for sage_bootstrap trac 26980 fix script for python3 trac 26978 remove module finite_class from doc a little firework of typos remove FiniteCombinatorialClass after sagemath#13552 remove some deprecated thing in combinat/partition remove deprecated things in combinat/integer_vector ...

videlec added this to the sage-8.6 milestone Jan 2, 2019

videlec added c: documentation labels Jan 2, 2019

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videlec changed the title ~~doctest failures in databases/sql_db.py~~ graph canonical labels and doctest failures in databases/sql_db.py Jan 2, 2019

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dcoudert added c: graph theory labels Jan 2, 2019

vbraun added s: positive review and removed s: needs review labels Jan 2, 2019

vbraun removed the s: positive review label Jan 3, 2019

vbraun closed this as completed in bc5178a Jan 3, 2019

seblabbe mentioned this issue Oct 21, 2022

meta-ticket: failing internet/optional doctests #25536

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graph canonical labels and doctest failures in databases/sql_db.py #26994

graph canonical labels and doctest failures in databases/sql_db.py #26994

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graph canonical labels and doctest failures in databases/sql_db.py #26994

graph canonical labels and doctest failures in databases/sql_db.py #26994

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