Unstable doctests in equivariant Ehrhart methods

[mkoeppe]

From https://groups.google.com/g/sage-release/c/GOGWk66zaCQ/m/ToJcX-bxAAAJ:

On Ubuntu with a bunch of optional packages installed, I am getting the following failures due to pynormaliz:

Using --optional=bliss,coxeter3,database_knotinfo,debian,dot2tex,e_antic,fricas,gap_packages,kenzo,libsemigroups,lidia,meataxe,normaliz,pip,pynormaliz,sage,sage_spkg,sirocco,tides
Features to be detected: 4ti2,benzene,bliss,buckygen,conway_polynomials,csdp,database_cremona_ellcurve,database_cremona_mini_ellcurve,database_jones_numfield,database_knotinfo,dvipng,gfan,graphviz,imagemagick,jupymake,kenzo,latte_int,lrslib,mcqd,meataxe,nauty,palp,pandoc,pdf2svg,pdftocairo,plantri,polytopes_db,polytopes_db_4d,pynormaliz,python_igraph,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.plot,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.symbolic,sage_numerical_backends_coin,sagemath_doc_html,sphinx,tdlib

sage -t --warn-long 40.4 --random-seed=39360907713219164614940484824980321981 src/sage/geometry/polyhedron/base_QQ.py  # 8 doctests failed
sage -t --warn-long 40.4 --random-seed=39360907713219164614940484824980321981 src/sage/geometry/polyhedron/backend_normaliz.py  # 7 doctests failed

CC: @tscrim @braunmath @sophiasage @jplab @yuan-zhou

Component: geometry

Author: Sophia Elia

Branch/Commit: 938a6b4

Reviewer: Matthias Koeppe

Issue created by migration from https://trac.sagemath.org/ticket/33850

[mkoeppe]

comment:1

I also see these failures on macOS with homebrew

[sophiasage]

comment:2

I am seeing if I can get the doctest failures - building develop on macOS.

[sophiasage]

Branch: public/33850

[sophiasage]

New commits:

39cf556

first changes. simplified rational example in fixed_subpolytopes.

[sophiasage]

Commit: 39cf556

[sophiasage]

comment:4

I'm beginning to work on fixing these failures. My major mistake is that a polytope's restricted_automorphism_group doesn't have a consistent generators or order of elements.

[sagetrac-tmonteil]

comment:5

If it can help, i got such failure on Debian GNU/Linux too, with Sage 9.6, here is the whole log:

$ ./sage -t --long --random-seed=306453312432639962747126026414206033489 src/sage/geometry/polyhedron/backend_normaliz.py
Running doctests with ID 2022-05-24-04-51-23-f308a720.
Git branch: develop
Using --optional=4ti2,barvinok,benzene,bliss,buckygen,cbc,ccache,coxeter3,cryptominisat,csdp,cunningham_tables,cylp,d3js,debian,debugpy,dot2tex,e_antic,fricas,frobby,gap_jupyter,gap_packages,glucose,igraph,info,isl,kenzo,latte_int,libogg,libsemigroups,lidia,lrslib,mathics,mathics_scanner,mcqd,meataxe,mpfrcx,ninja_build,normaliz,notedown,palettable,pandoc_attributes,pari_elldata,pari_galpol,pari_jupyter,pari_nftables,pari_seadata,perl_term_readline_gnu,pint,pip,plantri,polylib,pycosat,pycryptosat,pynormaliz,pysingular,python_igraph,rubiks,saclib,sage,sage_numerical_backends_coin,sage_spkg,singular_jupyter,sip,sirocco,symengine,symengine_py,tdlib,texttable,tides,topcom
Features to be detected: 4ti2,benzene,bliss,buckygen,conway_polynomials,csdp,database_cremona_ellcurve,database_cremona_mini_ellcurve,database_jones_numfield,database_knotinfo,dvipng,gfan,graphviz,imagemagick,jupymake,kenzo,latte_int,lrslib,mcqd,meataxe,nauty,palp,pandoc,pdf2svg,pdftocairo,phitigra,plantri,polytopes_db,polytopes_db_4d,pynormaliz,python_igraph,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.plot,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.symbolic,sage_numerical_backends_coin,sagemath_doc_html,sphinx,tdlib
Doctesting 1 file.
sage -t --long --warn-long 57.8 --random-seed=306453312432639962747126026414206033489 src/sage/geometry/polyhedron/backend_normaliz.py
**********************************************************************
File "src/sage/geometry/polyhedron/backend_normaliz.py", line 2299, in sage.geometry.polyhedron.backend_normaliz.Polyhedron_QQ_normaliz._Hstar_function_normaliz
Failed example:
    G = K.subgroup(gens = [K[6]]); G                                      # optional - pynormaliz
Expected:
    Subgroup generated by [(0,2)(1,3)(4,6)(5,7)] of (Permutation Group with generators [(2,4)(3,5), (1,2)(5,6), (0,1)(2,3)(4,5)(6,7), (0,7)(1,3)(2,5)(4,6)])
Got:
    Subgroup generated by [(0,4)(1,5)(2,6)(3,7)] of (Permutation Group with generators [(2,4)(3,5), (1,2)(5,6), (0,1)(2,3)(4,5)(6,7)])
**********************************************************************
File "src/sage/geometry/polyhedron/backend_normaliz.py", line 2303, in sage.geometry.polyhedron.backend_normaliz.Polyhedron_QQ_normaliz._Hstar_function_normaliz
Failed example:
    list(Dict.keys())[0]                                                  # optional - pynormaliz
Expected:
    (0,2)(1,3)(4,6)(5,7)
Got:
    (0,4)(1,5)(2,6)(3,7)
**********************************************************************
File "src/sage/geometry/polyhedron/backend_normaliz.py", line 2305, in sage.geometry.polyhedron.backend_normaliz.Polyhedron_QQ_normaliz._Hstar_function_normaliz
Failed example:
    list(Dict.values())[0]                                                # optional - pynormaliz
Expected:
    [-1  0  1  0]
    [ 0  1  0  0]
    [ 0  0  1  0]
    [ 0  0  0  1]
Got:
    [ 1  0 -1  0]
    [ 0  1 -1  0]
    [ 0  0 -1  0]
    [ 0  0  0  1]
**********************************************************************
File "src/sage/geometry/polyhedron/backend_normaliz.py", line 2508, in sage.geometry.polyhedron.backend_normaliz.Polyhedron_QQ_normaliz._is_effective_normaliz
Failed example:
    H = G.subgroup(gens=[G.gens()[1],G.gens()[2]])             # optional - pynormaliz
Exception raised:
    Traceback (most recent call last):
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.geometry.polyhedron.backend_normaliz.Polyhedron_QQ_normaliz._is_effective_normaliz[2]>", line 1, in <module>
        H = G.subgroup(gens=[G.gens()[Integer(1)],G.gens()[Integer(2)]])             # optional - pynormaliz
    IndexError: list index out of range
**********************************************************************
File "src/sage/geometry/polyhedron/backend_normaliz.py", line 2509, in sage.geometry.polyhedron.backend_normaliz.Polyhedron_QQ_normaliz._is_effective_normaliz
Failed example:
    H.order()                                                  # optional - pynormaliz
Exception raised:
    Traceback (most recent call last):
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.geometry.polyhedron.backend_normaliz.Polyhedron_QQ_normaliz._is_effective_normaliz[3]>", line 1, in <module>
        H.order()                                                  # optional - pynormaliz
    NameError: name 'H' is not defined
**********************************************************************
File "src/sage/geometry/polyhedron/backend_normaliz.py", line 2511, in sage.geometry.polyhedron.backend_normaliz.Polyhedron_QQ_normaliz._is_effective_normaliz
Failed example:
    [Hstar, Hlin] = [p2.Hstar_function(H), p2.Hstar_function(H, output = 'Hstar_as_lin_comb')] # optional - pynormaliz
Exception raised:
    Traceback (most recent call last):
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.geometry.polyhedron.backend_normaliz.Polyhedron_QQ_normaliz._is_effective_normaliz[4]>", line 1, in <module>
        [Hstar, Hlin] = [p2.Hstar_function(H), p2.Hstar_function(H, output = 'Hstar_as_lin_comb')] # optional - pynormaliz
    NameError: name 'H' is not defined
**********************************************************************
File "src/sage/geometry/polyhedron/backend_normaliz.py", line 2512, in sage.geometry.polyhedron.backend_normaliz.Polyhedron_QQ_normaliz._is_effective_normaliz
Failed example:
    p2._is_effective_normaliz(Hstar,Hlin)                # optional - pynormaliz
Exception raised:
    Traceback (most recent call last):
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.geometry.polyhedron.backend_normaliz.Polyhedron_QQ_normaliz._is_effective_normaliz[5]>", line 1, in <module>
        p2._is_effective_normaliz(Hstar,Hlin)                # optional - pynormaliz
    NameError: name 'Hstar' is not defined
**********************************************************************
2 items had failures:
   3 of  17 in sage.geometry.polyhedron.backend_normaliz.Polyhedron_QQ_normaliz._Hstar_function_normaliz
   4 of  13 in sage.geometry.polyhedron.backend_normaliz.Polyhedron_QQ_normaliz._is_effective_normaliz
    [405 tests, 7 failures, 8.58 s]
----------------------------------------------------------------------
sage -t --long --warn-long 57.8 --random-seed=306453312432639962747126026414206033489 src/sage/geometry/polyhedron/backend_normaliz.py  # 7 doctests failed
----------------------------------------------------------------------
Total time for all tests: 8.8 seconds
    cpu time: 9.9 seconds
    cumulative wall time: 8.6 seconds
Features detected for doctesting: palp,sage.plot,sage.rings.number_field

and

$ ./pynormaliz sage -t --long --random-seed=306453312432639962747126026414206033489 src/sage/geometry/polyhedron/base_QQ.py
bash: ./pynormaliz: No such file or directory
sagemath@debian:/opt/sagemath/sage-9.6$ ./sage -t --long --random-seed=306453312432639962747126026414206033489 src/sage/geometry/polyhedron/base_QQ.py
Running doctests with ID 2022-05-24-05-19-07-df42a70d.
Git branch: develop
Using --optional=4ti2,barvinok,benzene,bliss,buckygen,cbc,ccache,coxeter3,cryptominisat,csdp,cunningham_tables,cylp,d3js,debian,debugpy,dot2tex,e_antic,fricas,frobby,gap_jupyter,gap_packages,glucose,igraph,info,isl,kenzo,latte_int,libogg,libsemigroups,lidia,lrslib,mathics,mathics_scanner,mcqd,meataxe,mpfrcx,ninja_build,normaliz,notedown,palettable,pandoc_attributes,pari_elldata,pari_galpol,pari_jupyter,pari_nftables,pari_seadata,perl_term_readline_gnu,pint,pip,plantri,polylib,pycosat,pycryptosat,pynormaliz,pysingular,python_igraph,rubiks,saclib,sage,sage_numerical_backends_coin,sage_spkg,singular_jupyter,sip,sirocco,symengine,symengine_py,tdlib,texttable,tides,topcom
Features to be detected: 4ti2,benzene,bliss,buckygen,conway_polynomials,csdp,database_cremona_ellcurve,database_cremona_mini_ellcurve,database_jones_numfield,database_knotinfo,dvipng,gfan,graphviz,imagemagick,jupymake,kenzo,latte_int,lrslib,mcqd,meataxe,nauty,palp,pandoc,pdf2svg,pdftocairo,phitigra,plantri,polytopes_db,polytopes_db_4d,pynormaliz,python_igraph,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.plot,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.symbolic,sage_numerical_backends_coin,sagemath_doc_html,sphinx,tdlib
Doctesting 1 file.
sage -t --long --warn-long 57.8 --random-seed=306453312432639962747126026414206033489 src/sage/geometry/polyhedron/base_QQ.py
**********************************************************************
File "src/sage/geometry/polyhedron/base_QQ.py", line 869, in sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.fixed_subpolytope
Failed example:
    G = P.restricted_automorphism_group(output = 'permutation');G  # optional - pynormaliz
Expected:
    Permutation Group with generators [(1,2), (0,1)(2,3), (0,3)]
Got:
    Permutation Group with generators [(1,2), (0,1)(2,3)]
**********************************************************************
File "src/sage/geometry/polyhedron/base_QQ.py", line 1049, in sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.Hstar_function
Failed example:
    G = K.subgroup(gens = [K[6]]); G                                       # optional - pynormaliz
Expected:
    Subgroup generated by [(0,2)(1,3)(4,6)(5,7)] of (Permutation Group with generators [(2,4)(3,5), (1,2)(5,6), (0,1)(2,3)(4,5)(6,7), (0,7)(1,3)(2,5)(4,6)])
Got:
    Subgroup generated by [(0,4)(1,5)(2,6)(3,7)] of (Permutation Group with generators [(2,4)(3,5), (1,2)(5,6), (0,1)(2,3)(4,5)(6,7)])
**********************************************************************
File "src/sage/geometry/polyhedron/base_QQ.py", line 1053, in sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.Hstar_function
Failed example:
    list(Dict.keys())[0]                                                   # optional - pynormaliz
Expected:
    (0,2)(1,3)(4,6)(5,7)
Got:
    (0,4)(1,5)(2,6)(3,7)
**********************************************************************
File "src/sage/geometry/polyhedron/base_QQ.py", line 1055, in sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.Hstar_function
Failed example:
    list(Dict.values())[0]                                                 # optional - pynormaliz
Expected:
    [-1  0  1  0]
    [ 0  1  0  0]
    [ 0  0  1  0]
    [ 0  0  0  1]
Got:
    [ 1  0 -1  0]
    [ 0  1 -1  0]
    [ 0  0 -1  0]
    [ 0  0  0  1]
**********************************************************************
File "src/sage/geometry/polyhedron/base_QQ.py", line 1171, in sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.is_effective
Failed example:
    H = G.subgroup(gens=[G.gens()[1],G.gens()[2]])             # optional - pynormaliz
Exception raised:
    Traceback (most recent call last):
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.is_effective[2]>", line 1, in <module>
        H = G.subgroup(gens=[G.gens()[Integer(1)],G.gens()[Integer(2)]])             # optional - pynormaliz
    IndexError: list index out of range
**********************************************************************
File "src/sage/geometry/polyhedron/base_QQ.py", line 1172, in sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.is_effective
Failed example:
    H.order()                                                  # optional - pynormaliz
Exception raised:
    Traceback (most recent call last):
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.is_effective[3]>", line 1, in <module>
        H.order()                                                  # optional - pynormaliz
    NameError: name 'H' is not defined
**********************************************************************
File "src/sage/geometry/polyhedron/base_QQ.py", line 1174, in sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.is_effective
Failed example:
    [Hstar, Hlin] = [p2.Hstar_function(H), p2.Hstar_function(H, output = 'Hstar_as_lin_comb')] # optional - pynormaliz
Exception raised:
    Traceback (most recent call last):
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.is_effective[4]>", line 1, in <module>
        [Hstar, Hlin] = [p2.Hstar_function(H), p2.Hstar_function(H, output = 'Hstar_as_lin_comb')] # optional - pynormaliz
    NameError: name 'H' is not defined
**********************************************************************
File "src/sage/geometry/polyhedron/base_QQ.py", line 1175, in sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.is_effective
Failed example:
    p2.is_effective(Hstar,Hlin)   # optional - pynormaliz
Exception raised:
    Traceback (most recent call last):
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/opt/sagemath/sage-9.6/local/var/lib/sage/venv-python3.10.3/lib/python3.10/site-packages/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.is_effective[5]>", line 1, in <module>
        p2.is_effective(Hstar,Hlin)   # optional - pynormaliz
    NameError: name 'Hstar' is not defined
**********************************************************************
3 items had failures:
   3 of  17 in sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.Hstar_function
   1 of  18 in sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.fixed_subpolytope
   4 of  13 in sage.geometry.polyhedron.base_QQ.Polyhedron_QQ.is_effective
    [181 tests, 8 failures, 2.34 s]
----------------------------------------------------------------------
sage -t --long --warn-long 57.8 --random-seed=306453312432639962747126026414206033489 src/sage/geometry/polyhedron/base_QQ.py  # 8 doctests failed
----------------------------------------------------------------------
Total time for all tests: 2.5 seconds
    cpu time: 2.2 seconds
    cumulative wall time: 2.3 seconds
Features detected for doctesting: 

[sagetrac-git]

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

e2b9b0f

fixing doctests in baseQQ and backendnormaliz

[sagetrac-git]

Changed commit from 39cf556 to e2b9b0f

[sagetrac-git]

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

938a6b4

rewrote tests that were dependent on ording of conjugacy classes representatives

[sagetrac-git]

Changed commit from e2b9b0f to 938a6b4

[sophiasage]

comment:8

I think that I've addressed the failures now. To test, I have been running
sage -t --optional=all the_file.py. Is there anything else I should do to test?

[mkoeppe]

comment:9

Tests also pass here, on macOS with python3.8

[tscrim]

comment:12

Since tests pass and this is now in needs review, should this be positive review?