Failing doctest in poset_examples #26586

jdemeyer · 2018-10-28T22:57:08Z

With --gc=never, this doctest fails consistently:

./sage -t --gc=never src/sage/combinat/posets/poset_examples.py
too many failed tests, not using stored timings
Running doctests with ID 2018-10-28-23-55-00-fb2259d6.
Git branch: t/24593/upgrade_from_thebe_to_thebelab_for_live_documentation_support
Using --optional=dochtml,meataxe,memlimit,mpir,python2,sage
Doctesting 1 file.
sage -t src/sage/combinat/posets/poset_examples.py
**********************************************************************
File "src/sage/combinat/posets/poset_examples.py", line 1400, in sage.combinat.posets.poset_examples.Posets.YoungDiagramPoset
Failed example:
    P.cover_relations()
Expected:
    [[(0, 0), (0, 1)], [(0, 0), (1, 0)], [(0, 1), (1, 1)], [(1, 0),
    (1, 1)]]
Got:
    [[(0, 0), (1, 0)], [(0, 0), (0, 1)], [(1, 0), (1, 1)], [(0, 1), (1, 1)]]
**********************************************************************
1 item had failures:
   1 of   3 in sage.combinat.posets.poset_examples.Posets.YoungDiagramPoset
    [159 tests, 1 failure, 11.36 s]
----------------------------------------------------------------------
sage -t src/sage/combinat/posets/poset_examples.py  # 1 doctest failed
----------------------------------------------------------------------

Component: combinatorics

Author: Jeroen Demeyer

Branch/Commit: dc77918

Reviewer: Volker Braun, Frédéric Chapoton

Issue created by migration from https://trac.sagemath.org/ticket/26586

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

fchapoton · 2018-10-29T09:26:28Z

comment:1

It seems that adding sorted() to the doctest does not sort, hence does not fix the issue

chapoton@pc-chapoton:~/sage$ ./sage -t --gc=never src/sage/combinat/posets/poset_examples.py
too few successful tests, not using stored timings
Running doctests with ID 2018-10-29-10-25-27-f966edb9.
Git branch: poset
Using --optional=4ti2,ccache,dochtml,dot2tex,fricas,gfortran,latte_int,lidia,lrslib,memlimit,mpir,python2,sage
Doctesting 1 file.
sage -t src/sage/combinat/posets/poset_examples.py
**********************************************************************
File "src/sage/combinat/posets/poset_examples.py", line 1400, in sage.combinat.posets.poset_examples.Posets.YoungDiagramPoset
Failed example:
    sorted(P.cover_relations())
Expected:
    [[(0, 0), (0, 1)], [(0, 0), (1, 0)], [(0, 1), (1, 1)], [(1, 0),
    (1, 1)]]
Got:
    [[(0, 0), (1, 0)], [(0, 0), (0, 1)], [(1, 0), (1, 1)], [(0, 1), (1, 1)]]
**********************************************************************
1 item had failures:
   1 of   3 in sage.combinat.posets.poset_examples.Posets.YoungDiagramPoset
    [159 tests, 1 failure, 1.79 s]
----------------------------------------------------------------------
sage -t src/sage/combinat/posets/poset_examples.py  # 1 doctest failed

mantepse · 2018-11-21T06:29:23Z

comment:2

A difference also happens with respect to --long on the same file (on linux-ubuntu):

martin@convex63:~/sage-develop$ ./sage -t --long --optional=sage src/sage/combinat/posets/poset_examples.py                                          
too many failed tests, not using stored timings                                                                                                       
Running doctests with ID 2018-11-21-07-24-59-6ea730c0.                                                                                                
Git branch: develop                                                                                                                                   
Using --optional=memlimit,sage                                                                                                                        
Doctesting 1 file.                                                                                                                                    
sage -t --long src/sage/combinat/posets/poset_examples.py                                                                                             
    [160 tests, 2.88 s]                                                                                                                               
----------------------------------------------------------------------                                                                                
All tests passed!                                                                                                                                     
----------------------------------------------------------------------                                                                                
Total time for all tests: 3.0 seconds                                                                                                                 
    cpu time: 2.8 seconds                                                                                                                             
    cumulative wall time: 2.9 seconds
                                                                                                                 
martin@convex63:~/sage-develop$ ./sage -t --optional=sage src/sage/combinat/posets/poset_examples.py 
too many failed tests, not using stored timings                                                                                                       
Running doctests with ID 2018-11-21-07-25-08-142907c8.                                                                                                
Git branch: develop                                                                                                                                   
Using --optional=memlimit,sage                                                                                                                        
Doctesting 1 file.                                                                                                                                    
sage -t src/sage/combinat/posets/poset_examples.py                                                                                                    
**********************************************************************                                                                                
File "src/sage/combinat/posets/poset_examples.py", line 1400, in sage.combinat.posets.poset_examples.Posets.YoungDiagramPoset                         
Failed example:                                                                                                                                       
    P.cover_relations()                                                                                                                               
Expected:                                                                                                                                             
    [[(0, 0), (0, 1)], [(0, 0), (1, 0)], [(0, 1), (1, 1)], [(1, 0),                                                                                   
    (1, 1)]]                                                                                                                                          
Got:                                                                                                                                                  
    [[(0, 0), (1, 0)], [(0, 0), (0, 1)], [(1, 0), (1, 1)], [(0, 1), (1, 1)]]                                                                          
**********************************************************************                                                                                
1 item had failures:                                                                                                                                  
   1 of   3 in sage.combinat.posets.poset_examples.Posets.YoungDiagramPoset                                                                           
    [159 tests, 1 failure, 2.09 s]                                                                                                                    
----------------------------------------------------------------------                                                                                
sage -t src/sage/combinat/posets/poset_examples.py  # 1 doctest failed 
----------------------------------------------------------------------                                                                                
Total time for all tests: 2.2 seconds                                                                                                                 
    cpu time: 2.0 seconds                                                                                                                             
    cumulative wall time: 2.1 seconds

Moreover, removing the only # long marker from this file (in line 963), the problem is not visible anymore!

martin@convex63:~/sage-develop$ ./sage -t --long --optional=sage src/sage/combinat/posets/poset_examples.py                                          
too many failed tests, not using stored timings                                                                                                       
Running doctests with ID 2018-11-21-07-25-28-653967b1.                                                                                                
Git branch: develop                                                                                                                                   
Using --optional=memlimit,sage                                                                                                                        
Doctesting 1 file.                                                                                                                                    
sage -t --long src/sage/combinat/posets/poset_examples.py                                                                                             
    [160 tests, 2.88 s]                                                                                                                               
----------------------------------------------------------------------                                                                                
All tests passed!                                                                                                                                     
----------------------------------------------------------------------                                                                                
Total time for all tests: 2.9 seconds                                                                                                                 
    cpu time: 2.8 seconds                                                                                                                             
    cumulative wall time: 2.9 seconds                                                                                                                 

martin@convex63:~/sage-develop$ ./sage -t --optional=sage src/sage/combinat/posets/poset_examples.py                                          
too many failed tests, not using stored timings                                                                                                       
Running doctests with ID 2018-11-21-07-25-36-4df51548.                                                                                                
Git branch: develop                                                                                                                                   
Using --optional=memlimit,sage                                                                                                                        
Doctesting 1 file.                                                                                                                                    
sage -t src/sage/combinat/posets/poset_examples.py                                                                                                    
    [160 tests, 2.88 s]                                                                                                                               
----------------------------------------------------------------------                                                                                
All tests passed!                                                                                                                                     
----------------------------------------------------------------------                                                                                
Total time for all tests: 2.9 seconds                                                                                                                 
    cpu time: 2.8 seconds                                                                                                                             
    cumulative wall time: 2.9 seconds

mantepse · 2018-11-21T06:43:12Z

comment:3

Finally, when running the offending test on its own in a session, there is no mismatch:

martin@convex63:~/sage-develop$ ./sage                                                                                                                
┌────────────────────────────────────────────────────────────────────┐                                                                                
│ SageMath version 8.5.beta4, Release Date: 2018-11-18               │                                                                                
│ Using Python 2.7.15. Type "help()" for help.                       │                                                                                
└────────────────────────────────────────────────────────────────────┘                                                                                
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓                                                                                
┃ Warning: this is a prerelease version, and it may be unstable.     ┃                                                                                
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛                                                                                
sage: P = posets.YoungDiagramPoset(Partition([2,2])); P                                                                                               
Finite meet-semilattice containing 4 elements                                                                                                         
sage: P.cover_relations()                                                                                                                             
[[(0, 0), (0, 1)], [(0, 0), (1, 0)], [(0, 1), (1, 1)], [(1, 0), (1, 1)]]

Adding

            sage: import gc                                                                                                                           
            sage: gc.collect() # random

just before the test in line 1400 "fixes" it.

mantepse · 2018-11-21T13:42:55Z

comment:4

Here is a minimal example for my computer. Could you please check whether this yields a failure when run without --long and no failure when run with --long?

def A():
    """
    sage: posets.ProductOfChains([2, 2]).linear_extension()
    [(0, 0), (1, 0), (0, 1), (1, 1)]
    
    sage: posets.SSTPoset([3,2]).bottom()  # long time
    [[1, 1, 1], [2, 2]]
    """

def B():
    """
    sage: posets.YoungDiagramPoset(Partition([2,2])).cover_relations()
    [[(0, 0), (0, 1)], [(0, 0), (1, 0)], [(0, 1), (1, 1)], [(1, 0), (1, 1)]]
    """

simon-king-jena · 2018-11-21T19:52:08Z

comment:5

Apparently it has nothing to do with the doctest framework, i.e., your example can be easily reproduced in an interactive session:

sage: posets.ProductOfChains([2, 2]).linear_extension()
[(0, 0), (1, 0), (0, 1), (1, 1)]
sage: posets.SSTPoset([3,2]).bottom()
[[1, 1, 1], [2, 2]]
sage: posets.YoungDiagramPoset(Partition([2,2])).cover_relations()
[[(0, 0), (0, 1)], [(0, 0), (1, 0)], [(0, 1), (1, 1)], [(1, 0), (1, 1)]]

then restart Sage, then

sage: posets.ProductOfChains([2, 2]).linear_extension()
[(0, 0), (1, 0), (0, 1), (1, 1)]
sage: posets.YoungDiagramPoset(Partition([2,2])).cover_relations()
[[(0, 0), (1, 0)], [(0, 0), (0, 1)], [(1, 0), (1, 1)], [(0, 1), (1, 1)]]

Very likely some kind of caching is causing the inconsistency, but I am not familiar with the code and therefore have no clue where that cache can be found.

What I find odd: Even when sorting the output, the two results are different. Is sorting not properly implemented for sage.sets.cartesian_product.CartesianProduct_with_category.element_class?

mantepse · 2018-11-21T20:22:50Z

comment:6

But shouldn't doctests in each function start with a fresh environment?

simon-king-jena · 2018-11-21T20:28:31Z

comment:7

Replying to @mantepse:

But shouldn't doctests in each function start with a fresh environment?

No.

I could be mistaken, but when I write doctests, I always assume:

The tests of individual functions within a single file are ALL executed in the same environment.
The tests of the individual functions within a single file are executed in random order.

vbraun · 2018-11-21T20:32:33Z

comment:8

Its in the nature of posets that there is usually no canonical total order, so trying to make the output canonical is probably not going to happen in all cases.

Without looking at the code I'm guessing that you are somewhere iterating over an associative container, which ends up being random because the elements can't be ordered.

You probably want to rewrite the test as X == Y instead of looking at the output

simon-king-jena · 2018-11-21T20:36:53Z

comment:9

The output is a python list of python lists of elements. So, testing equality won't work. But perhaps one can turn the lists into sets and compare them?

mantepse · 2018-11-22T05:55:42Z

comment:10

We could do

sage: sorted(map(tuple, P.cover_relations()), key=lambda c: map(tuple, c))
[((0, 0), (0, 1)), ((0, 0), (1, 0)), ((0, 1), (1, 1)), ((1, 0), (1, 1))]

if we do not want to have sorting for cartesian products.

jm58660 · 2018-11-22T07:23:08Z

comment:11

Is it easier to just say sorted(sorted(x) for x in posets.YoungDiagramPoset(Partition([2,2])).cover_relations())? I think I have seen that structure in some other parts of Sage.

mantepse · 2018-11-22T13:02:37Z

comment:12

Wouldn't it be better to have cartesian product export sorting? (lexicographic)

mantepse · 2018-11-22T13:03:10Z

comment:13

Besides, shouldn't upper and lower covers be tuples, not lists?

vbraun · 2018-12-13T14:47:30Z

comment:14

Unless something happens real soon this will not be fixed in Sage 8.5

fchapoton · 2018-12-13T15:53:38Z

Branch: u/chapoton/26586

fchapoton · 2018-12-13T15:53:38Z

Commit: 3e8ef3b

fchapoton · 2018-12-13T15:53:38Z

Author: Frédéric Chapoton

fchapoton · 2018-12-13T15:53:38Z

comment:15

ok, here it is

New commits:

`3e8ef3b`	`trac 26586 fix the doctest in poset for -gc=never by sorting`

jdemeyer · 2018-12-13T16:22:17Z

comment:16

Why not use a plain sorted()?

fchapoton · 2018-12-13T16:23:31Z

comment:17

Because this does not work. See comment:1

vbraun · 2018-12-13T17:22:12Z

Reviewer: Volker Braun

jdemeyer · 2018-12-13T18:21:35Z

comment:19

I understand that you want to get rid of this blocker, but this is not a right fix.

jdemeyer · 2018-12-13T18:23:33Z

Changed branch from u/chapoton/26586 to u/jdemeyer/26586

jdemeyer · 2018-12-13T18:24:21Z

Changed author from Frédéric Chapoton to Frédéric Chapoton, Jeroen Demeyer

jdemeyer · 2018-12-13T18:24:21Z

Changed commit from 3e8ef3b to dc77918

jdemeyer · 2018-12-13T18:24:21Z

comment:21

Don't hide bugs, at least mark it as # known bug

New commits:

`dc77918`	`Mark doctest as known bug`

jdemeyer · 2018-12-13T18:24:44Z

comment:22

Replying to @mantepse:

Wouldn't it be better to have cartesian product export sorting? (lexicographic)

Yes obviously. I opened #26890 for that.

fchapoton · 2018-12-13T18:51:57Z

Changed author from Frédéric Chapoton, Jeroen Demeyer to Jeroen Demeyer

fchapoton · 2018-12-13T18:51:57Z

Changed reviewer from Volker Braun to Volker Braun, Frédéric Chapoton

fchapoton · 2018-12-13T18:51:57Z

comment:23

right. ok for me

vbraun · 2018-12-15T19:25:38Z

Changed branch from u/jdemeyer/26586 to dc77918

jdemeyer added this to the sage-8.5 milestone Oct 28, 2018

jdemeyer added c: combinatorics labels Oct 28, 2018

fchapoton added the s: needs review label Dec 13, 2018

vbraun added s: positive review and removed s: needs review labels Dec 13, 2018

jdemeyer removed the s: positive review label Dec 13, 2018

jdemeyer added the s: needs work label Dec 13, 2018

jdemeyer added s: needs review and removed s: needs work labels Dec 13, 2018

fchapoton added s: positive review and removed s: needs review labels Dec 13, 2018

vbraun removed the s: positive review label Dec 15, 2018

vbraun closed this as completed in 0f3e55e Dec 15, 2018

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Failing doctest in poset_examples #26586

Failing doctest in poset_examples #26586

jdemeyer commented Oct 28, 2018

fchapoton commented Oct 29, 2018

mantepse commented Nov 21, 2018

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vbraun commented Dec 15, 2018

Failing doctest in poset_examples #26586

Failing doctest in poset_examples #26586

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