py3: make all tests pass

[chapoton]

This ticket is used to keep track of the progress towards python3.

release	files having failing doctests	more than 100	from 10 to 100	from 1 to 10	failing doctests
8.4.b3	915	42	251	622	17972
8.4.b4	803	23	175	605	10921
8.4.b5	657	17	145	495	8509
8.4.b6	594	17	127	450	7706
8.4.b7	587	17	128	442	7678
8.4.rc0	524	16	119	389	6976
8.5.b0	461	6	94	361	4206
8.5.b1	414	3	76	335	3206
8.5.b2	370	1	66	303	2465
8.5.b3	339	1	62	276	2245
8.5.b4	312	0	58	254	1947
8.5.b5	295	0	51	244	1741
8.5.b6	264	0	43	221	1514
8.5.rc0	252	0	39	213	1393
8.6.b0	234	0	30	204	1163
8.6.b1	231	0	30	201	1146
8.6.rc0	232	0	28	204	1124
8.6.rc1	236	0	30	206	1136
8.7.b0	240	1	38	201	1605
8.7.b1	200	0	23	177	866
8.7.b2	198	0	24	174	863
8.7.b3	166	0	20	146	717
8.7.b4	165	0	19	146	703
8.7.b5	143	0	12	131	562
8.7.b6	137	0	8	129	464
8.7.b7	122	0	8	114	447
8.7.rc0	105	0	7	98	384
8.8.b0	102	0	7	95	370

Now with python 3.7.3:

release	files having failing doctests	more than 100	from 10 to 100	from 1 to 10	failing doctests
8.8.b1	105	0	6	99	382
8.8.b2	94	0	6	88	324
8.8.b3	82	0	6	76	282
8.8.b4	77	0	2	75	246
8.8.b5	56	0	2	54	173

Folders where all tests pass

• algebras #26316 #26399 #26279 #26646 #26688 #26766 #27414 #27415 (final)
• algebras/steenrod ✔ #26219 and #26220
• arith #26208 ✔
• calculus #26751 #26988 (final)
• categories #26545 #26780 #27349 #27541 #27732 (remains 8) #27757 (final?)
• coding #26026 #26765 (final)
• combinat/designs #26430, #26837 (regression)
• combinat/posets #26998 (final)
• combinat/rigged_configurations #26805
• combinat/sf (#26220 +) #26215
• combinat/species #26328, #26610, #27072 (final)
• combinat/words #26362, #26458, #26473, #26590
• crypto #26398 #27580 (final)
• databases #26702 #26704
• data_structures #24852 #27433 #27439 (final)
• docs ✔ #26310
• doc/en #26346 #27698 #27758 (final)
• features ✔
• finance #26213 ✔
• games ✔
• game_theory #26429 #26738 (final)
• groups/lie_gps #26518
• groups/matrix_gps #26400 (regression) #27459 (final again)
• homology #27452 (final)
• interacts #27117, #27157
• knots ✔
• libs/gsl
• lfunctions ✔
• logic #26214 ✔
• manifolds #26475
• matrix/ #26236 #26716, #27585, #27615 (final)
• media ✔
• modular #26382, #26611, #26967 #25301 #27145 #27313 (final)
• modular/modsym #26673 #27177
• modules #26276 #27115, #27466 (final)
• monoids ✔ #26294
• parallel ✔
• plot #26210 #26299 #26301 #26321, #27126 (final)
• probability #26216 ✔
• quadratic_forms/ #26224 ✔
• quivers #26211 ✔
• rings/asymptotic #26146
• rings/number_field #26263, #26619
• rings/function_field #26721 #26764 (final)
• rings/padics #27612 (final)
• sandpiles #26016 #26628 #26722
• sat #26543 ✔
• schemes #27049 #27449 #27471 #27619 (final)
• schemes/toric #26664
• schemes/curves
• schemes/product_projective
• schemes/elliptic_curves #26536, #26529, #26570, #26594 #26913 #26914 #27432 #27520 #27539
• server ✔
• sets #26659 #27456 #27794 (final)
• stats #26401 ✔
• structure #25694 #26768
• tensor #26295, #26601
• typeset ✔
• sage_setup #27075, #27073

Fragile folders (still fails sometimes)

• repl #26881 (fragile in src/sage/repl/attach.py)
• numerical/backends #24740 (for char * arguments management), #24741, #26631 (fragile in src/sage/numerical/backends/generic_backend.pyx), #27773 and #27774 (cplex_backend.pyx)
• numerical #27342 #27614
• libs/singular (in src/sage/libs/singular/function.pyx)

Folders with work in progress

• combinat/cluster_algebra_quiver #27517 (remains 3)
• combinat/crystals (remains 2)
• combinat/finite_state_machine #26147, #26468, #26737, #27667 #27679 (remains 1)
• combinat/root_system #26649 #27654 (remains 4)
• combinat/subset #26510 #27727
• combinat #26535 #26671 #26719 #26778 #26781 #26917 #26918 #27013 #26592 #27710 #27777
• cpython #26855 (remains 2, needs an upgrade of cython)
• doctest #27775 (remains 1)
• dynamics #27453 #26982 (remains 2)
• dynamics/arithmetic_dynamics #27779 (remains 1)
• ext #27776 (remains 1)
• functions #24758, #26591 #26865 #26770 #25979 #27812 (remains 1)
• geometry #26726 (remains 2)
• graphs #26431 #26447 #26527 #26640 #26645 #26846 #27125 (remains 3)
• groups #26799 (remains 2)
• interfaces #26314 (remains 1)
• libs #26665 #27275 #27383 #27360 #27465 #27588 #27630 (remains 2)
• matroids #26767, #27378, #27771 (remains 7)
• misc #26312, #26390 #26674 #26720 #27001 #27065 #27301 #27390 #27431 #27691 #27692 #27693 (remains 4)
• rings #26697 #27048 #27440 #27650 #27767
• rings (power series) #26539
• rings/polynomial #26670 #26760 #26909 #26792 #27674 #27768 #27791
• rings/valuation (remains 1)
• symbolic #27457 (remains 1)
• tests #27440 (remains 1)
• tests/french_book #26495 #23572 #27574 #27651 #27668 #27727 (remains 2)

[embray]

Hadn't even seen this ticket; very nice.

[chapoton]

good progress on 8.5.b0

[chapoton]

The six remaining files with many failures are

['sage -t --long src/sage/combinat/finite_state_machine.py  # 189 doctests failed',
 'sage -t --long src/sage/dynamics/arithmetic_dynamics/projective_ds.py  # 105 doctests failed',
 'sage -t --long src/sage/graphs/generic_graph.py  # 110 doctests failed',
 'sage -t --long src/sage/groups/lie_gps/nilpotent_lie_group.py  # 143 doctests failed',
 'sage -t --long src/sage/rings/padics/padic_lattice_element.py  # 167 doctests failed',
 'sage -t --long src/sage/rings/valuation/limit_valuation.py  # 106 doctests failed']

[jhpalmieri]

For whoever wants to work on it, regarding

sage -t --long src/sage/combinat/finite_state_machine.py  # 189 doctests failed

about 150 of the failures can be cured by replacing 'iteritems' by 'items' in lines like

        elif hasattr(data, 'iteritems'):
            # data is a dict (or something similar),

I don't know if 'items' is the right attribute to check, or if it would actually be better to change to isinstance(data, dict). What other data structures are mean to be acceptable? What is "something similar" to a dict?

[vklein]

Replying to jhpalmieri:

For whoever wants to work on it, regarding ... I don't know if 'items' is the right attribute to check, or if it would actually be better to change to isinstance(data, dict). What other data structures are mean to be acceptable? What is "something similar" to a dict?

There is some custom "Mapping types" in sage like FreeModuleElement_generic_sparse, which implements items and iteritems but doesn't inherit from dict.

[chapoton]

tool to extract the data from patchbot log

[chapoton]

There was a regression in the manifolds folder (sigh)..

The 3 remaining files with more than 100 failing doctests are

['sage -t --long src/sage/combinat/finite_state_machine.py  # 182 doctests failed',
 'sage -t --long src/sage/graphs/generic_graph.py  # 109 doctests failed',
 'sage -t --long src/sage/rings/padics/padic_lattice_element.py  # 167 doctests failed']

The first one is already tackled in #26147 at least partially.

[jhpalmieri]

Regarding

'sage -t --long src/sage/rings/padics/padic_lattice_element.py  # 167 doctests failed'

I can reproduce those failures when I run ./sage -t ..., but (at least for the first few) not when I run Sage interactively. Odd.

[chapoton]

Top ten bad files in 8.5.b2 are

['sage -t --long src/sage/numerical/backends/cvxopt_sdp_backend.pyx  # 39 doctests failed',
 'sage -t --long src/sage/algebras/iwahori_hecke_algebra.py  # 40 doctests failed',
 'sage -t --long src/sage/numerical/mip.pyx  # 47 doctests failed',
 'sage -t --long src/doc/en/thematic_tutorials/sandpile.rst  # 49 doctests failed',
 'sage -t --long src/sage/rings/function_field/ideal.py  # 56 doctests failed',
 'sage -t --long src/sage/graphs/graph.py  # 59 doctests failed',
 'sage -t --long src/sage/graphs/connectivity.pyx  # 60 doctests failed',
 'sage -t --long src/sage/misc/explain_pickle.py  # 70 doctests failed',
 'sage -t --long src/sage/numerical/sdp.pyx  # 75 doctests failed',
 'sage -t --long src/sage/graphs/generic_graph.py  # 109 doctests failed']

[chapoton]

The top ten worse files in 8.5.b3 are

['sage -t --long src/sage/combinat/finite_state_machine.py  # 31 doctests failed',
 'sage -t --long src/sage/schemes/riemann_surfaces/riemann_surface.py  # 36 doctests failed',
 'sage -t --long src/sage/numerical/mip.pyx  # 47 doctests failed',
 'sage -t --long src/doc/en/thematic_tutorials/sandpile.rst  # 49 doctests failed',
 'sage -t --long src/sage/rings/function_field/ideal.py  # 56 doctests failed',
 'sage -t --long src/sage/graphs/graph.py  # 58 doctests failed',
 'sage -t --long src/sage/graphs/connectivity.pyx  # 59 doctests failed',
 'sage -t --long src/sage/rings/tate_algebra_element.pyx  # 63 doctests failed',
 'sage -t --long src/sage/misc/explain_pickle.py  # 70 doctests failed',
 'sage -t --long src/sage/graphs/generic_graph.py  # 115 doctests failed']

[chapoton]

Top ten worst files in 8.5.b4 are:

src/sage/graphs/graph.py  # 30 doctests failed
src/sage/numerical/linear_functions.pyx  # 30 doctests failed
src/sage/combinat/finite_state_machine.py  # 31 doctests failed
src/sage/schemes/riemann_surfaces/riemann_surface.py  # 36 doctests failed
src/sage/numerical/mip.pyx  # 47 doctests failed
src/doc/en/thematic_tutorials/sandpile.rst  # 49 doctests failed
src/sage/graphs/connectivity.pyx  # 50 doctests failed
src/sage/rings/function_field/ideal.py  # 56 doctests failed
src/sage/misc/explain_pickle.py  # 70 doctests failed
src/sage/graphs/generic_graph.py  # 77 doctests failed

[chapoton]

Number of failing doctests in 8.5.beta4 by components

'en': 56, 'coding': 28, 'data_structures': 5, 'symbolic': 24, 'libs': 34,
 'schemes': 102, 'combinat': 292, 'dynamics': 39, 'interacts': 6, 'homology': 29,
 'plot': 5, 'functions': 5, 'matrix': 16, 'rings': 209, 'categories': 34,
 'docbuild': 2, 'algebras': 21, 'common': 1, 'calculus': 5, 'tests': 40,
 'matroids': 75, 'misc': 172, 'interfaces': 1, 'numerical': 206, 'modular': 82,
 'repl': 13, 'groups': 14, 'sandpiles': 22, 'game_theory': 11, 'structure': 6,
 'cpython': 7, 'sets': 6, 'geometry': 32, 'modules': 3, 'crypto': 13,
 'graphs': 292, 'ext': 8, 'doctest': 8, 'databases': 16

[chapoton]

Worst 15 files in 8.5.b5:

[' src/sage/homology/simplicial_complex.py  # 23 doctests failed',
 ' src/sage/numerical/linear_tensor_element.pyx  # 23 doctests failed',
 ' src/sage/matroids/matroid.pyx  # 24 doctests failed',
 ' src/sage/rings/integer.pyx  # 24 doctests failed',
 ' src/sage/misc/decorators.py  # 28 doctests failed',
 ' src/sage/numerical/linear_tensor_constraints.py  # 28 doctests failed',
 ' src/sage/combinat/rigged_configurations/kr_tableaux.py  # 30 doctests failed',
 ' src/sage/graphs/graph.py  # 30 doctests failed',
 ' src/sage/numerical/linear_functions.pyx  # 30 doctests failed',
 ' src/sage/schemes/riemann_surfaces/riemann_surface.py  # 36 doctests failed',
 ' src/sage/numerical/mip.pyx  # 47 doctests failed',
 ' src/doc/en/thematic_tutorials/sandpile.rst  # 49 doctests failed',
 ' src/sage/graphs/connectivity.pyx  # 49 doctests failed',
 ' src/sage/misc/explain_pickle.py  # 70 doctests failed',
 ' src/sage/graphs/generic_graph.py  # 79 doctests failed']

[chapoton]

and by components:

[('common', 1), ('interfaces', 1), ('docbuild', 2), ('coding', 2), ('modules', 4), 
('functions', 5), ('calculus', 5), ('plot', 5), ('data_structures', 5), ('structure',
 6), ('interacts', 6), ('sets', 6), ('cpython', 7), ('doctest', 8), ('ext', 8), 
('crypto', 13), ('geometry', 13), ('repl', 13), ('groups', 15), ('algebras', 16),
 ('matrix', 17), ('sandpiles', 22), ('symbolic', 26), ('homology', 30), ('libs', 34),
 ('categories', 35), ('tests', 40), ('dynamics', 40), ('en', 56), ('matroids', 73),
 ('schemes', 80), ('modular', 82), ('rings', 141), ('misc', 171), ('numerical', 206), 
('combinat', 240), ('graphs', 300)]

[chapoton]

worst 20 files in 8.5.b6:

['/sage/matroids/matroid.pyx  # 18 doctests failed',
 '/sage/combinat/finite_state_machine.py  # 20 doctests failed',
 '/sage/misc/classcall_metaclass.pyx  # 20 doctests failed',
 '/sage/numerical/linear_tensor.py  # 20 doctests failed',
 '/sage/dynamics/arithmetic_dynamics/wehlerK3.py  # 21 doctests failed',
 '/sage/rings/polynomial/multi_polynomial_ideal.py  # 21 doctests failed',
 '/sage/homology/simplicial_complex.py  # 22 doctests failed',
 '/sage/sandpiles/sandpile.py  # 22 doctests failed',
 '/sage/numerical/linear_tensor_element.pyx  # 23 doctests failed',
 '/sage/rings/integer.pyx  # 24 doctests failed',
 '/sage/misc/decorators.py  # 28 doctests failed',
 '/sage/numerical/linear_tensor_constraints.py  # 28 doctests failed',
 '/sage/graphs/graph.py  # 30 doctests failed',
 '/sage/numerical/linear_functions.pyx  # 30 doctests failed',
 '/sage/schemes/riemann_surfaces/riemann_surface.py  # 36 doctests failed',
 '/sage/numerical/mip.pyx  # 47 doctests failed',
 '/doc/en/thematic_tutorials/sandpile.rst  # 49 doctests failed',
 '/sage/graphs/connectivity.pyx  # 49 doctests failed',
 '/sage/misc/explain_pickle.py  # 70 doctests failed',
 '/sage/graphs/generic_graph.py  # 78 doctests failed']

[chapoton]

15 worst offenders in 8.5.rc0:

['src/sage/dynamics/arithmetic_dynamics/wehlerK3.py  # 21 doctests failed',
 'src/sage/matroids/matroid.pyx  # 21 doctests failed',
 'src/sage/rings/polynomial/multi_polynomial_ideal.py  # 21 doctests failed',
 'src/sage/homology/simplicial_complex.py  # 22 doctests failed',
 'src/sage/sandpiles/sandpile.py  # 22 doctests failed',
 'src/sage/numerical/linear_tensor_element.pyx  # 23 doctests failed',
 'src/sage/misc/decorators.py  # 28 doctests failed',
 'src/sage/numerical/linear_tensor_constraints.py  # 28 doctests failed',
 'src/sage/graphs/graph.py  # 30 doctests failed',
 'src/sage/numerical/linear_functions.pyx  # 30 doctests failed',
 'src/sage/schemes/riemann_surfaces/riemann_surface.py  # 36 doctests failed',
 'src/sage/numerical/mip.pyx  # 47 doctests failed',
 'src/doc/en/thematic_tutorials/sandpile.rst  # 49 doctests failed',
 'src/sage/misc/explain_pickle.py  # 70 doctests failed',
 'src/sage/graphs/generic_graph.py  # 74 doctests failed']

[chapoton]

15 worst offenders in 8.6.b0:

['src/sage/categories/finite_posets.py  # 15 doctests failed',
 'src/sage/combinat/matrices/hadamard_matrix.py  # 15 doctests failed',
 'src/sage/combinat/finite_state_machine.py  # 19 doctests failed',
 'src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed',
 'src/sage/dynamics/arithmetic_dynamics/wehlerK3.py  # 21 doctests failed',
 'src/sage/rings/polynomial/multi_polynomial_ideal.py  # 21 doctests failed',
 'src/sage/sandpiles/sandpile.py  # 22 doctests failed',
 'src/sage/matroids/matroid.pyx  # 23 doctests failed',
 'src/sage/homology/simplicial_complex.py  # 24 doctests failed',
 'src/sage/graphs/graph.py  # 28 doctests failed',
 'src/sage/misc/decorators.py  # 28 doctests failed',
 'src/sage/schemes/riemann_surfaces/riemann_surface.py  # 36 doctests failed',
 'src/doc/en/thematic_tutorials/sandpile.rst  # 49 doctests failed',
 'src/sage/graphs/generic_graph.py  # 68 doctests failed',
 'src/sage/misc/explain_pickle.py  # 70 doctests failed']

[chapoton]

maybe due to the upgrade of gap, there is a regression:

sage -t --long src/sage/groups/matrix_gps/finitely_generated.py
  # 3 doctests failed

[chapoton]

worst 15 files in 8.6.b1:

['src/sage/categories/finite_posets.py  # 15 doctests failed',
 'src/sage/combinat/matrices/hadamard_matrix.py  # 15 doctests failed',
 'src/sage/matroids/matroid.pyx  # 17 doctests failed',
 'src/sage/combinat/finite_state_machine.py  # 19 doctests failed',
 'src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed',
 'src/sage/dynamics/arithmetic_dynamics/wehlerK3.py  # 21 doctests failed',
 'src/sage/rings/polynomial/multi_polynomial_ideal.py  # 21 doctests failed',
 'src/sage/sandpiles/sandpile.py  # 22 doctests failed',
 'src/sage/homology/simplicial_complex.py  # 23 doctests failed',
 'src/sage/graphs/graph.py  # 28 doctests failed',
 'src/sage/misc/decorators.py  # 28 doctests failed',
 'src/sage/schemes/riemann_surfaces/riemann_surface.py  # 36 doctests failed',
 'src/doc/en/thematic_tutorials/sandpile.rst  # 49 doctests failed',
 'src/sage/graphs/generic_graph.py  # 63 doctests failed',
 'src/sage/misc/explain_pickle.py  # 70 doctests failed']

[chapoton]

files where failing doctests have re-appeared (regressions):

['src/sage/categories/crystals.py',
 'src/sage/matroids/circuit_closures_matroid.pyx',
 'src/sage/matroids/dual_matroid.py']

file where failing doctests have disappeared (progress):

['src/sage/misc/decorators.py',
 'src/sage/rings/polynomial/laurent_polynomial.pyx']

so this is a net loss of 1 file

[chapoton]

Getting worse again! Damn!

[chapoton]

regressions in

 'sage -t --long src/sage/combinat/multiset_partition_into_sets_ordered.py',
 'sage -t --long src/sage/combinat/set_partition.py',
 'sage -t --long src/sage/dynamics/arithmetic_dynamics/endPN_automorphism_group.py',
 'sage -t --long src/sage/graphs/spanning_tree.pyx',
 'sage -t --long src/sage/modules/multi_filtered_vector_space.py',
 'sage -t --long src/sage/rings/invariants/invariant_theory.py'

and progress in

 'sage -t --long src/sage/matrix/compute_J_ideal.py',
 'sage -t --long src/sage/matroids/circuit_closures_matroid.pyx'}

so this a net loss of 4 files

[dcoudert]

I don't have any doctest error with py3 for sage -t --long src/sage/graphs/spanning_tree.pyx. Can you share what you get. Thanks.

[chapoton]

This and other failures can be seen in the unique patchbot report running python3 on ticket 0:

​https://patchbot.sagemath.org/ticket/0/

sage -t --long src/sage/graphs/spanning_tree.pyx
**********************************************************************
File "src/sage/graphs/spanning_tree.pyx", line 188, in sage.graphs.spanning_tree.kruskal
Failed example:
    sorted(kruskal(G, check=True))
Expected:
    [('a', 'b', 4), ('a', 'h', 8), ('c', 'd', 7), ('c', 'f', 4), ('c', 'i', 2), ('d', 'e', 9), ('f', 'g', 2), ('g', 'h', 1)]
Got:
    [('a', 'b', 4),
     ('b', 'c', 8),
     ('c', 'd', 7),
     ('c', 'f', 4),
     ('c', 'i', 2),
     ('d', 'e', 9),
     ('f', 'g', 2),
     ('g', 'h', 1)]
**********************************************************************
1 item had failures:
   1 of  45 in sage.graphs.spanning_tree.kruskal
    [83 tests, 1 failure, 0.60 s]

[dcoudert]

See #27059 for of fix of the issue of ​#comment:184

[chapoton]

massive regression in 8.7.beta0, in particular here:

sage -t --long src/sage/schemes/elliptic_curves/BSD.py # 17 doctests failed
sage -t --long src/sage/schemes/elliptic_curves/gal_reps.py  # 20 doctests failed
sage -t --long src/sage/schemes/elliptic_curves/isogeny_small_degree.py  # 72 doctests failed
sage -t --long src/sage/schemes/elliptic_curves/ell_curve_isogeny.py  # 204 doctests failed

[chapoton]

Worst 15 files in 8.7.beta0 (once the large regression in isogenies is fixed):

 'sage -t --long src/sage/rings/polynomial/multi_polynomial_sequence.py  # 12 doctests failed',
 'sage -t --long src/sage/symbolic/constants.py  # 12 doctests failed',
 'sage -t --long src/sage/tests/french_book/mpoly.py  # 13 doctests failed',
 'sage -t --long src/sage/graphs/digraph.py  # 14 doctests failed',
 'sage -t --long src/sage/categories/finite_posets.py  # 15 doctests failed',
 'sage -t --long src/sage/combinat/finite_state_machine.py  # 19 doctests failed',
 'sage -t --long src/sage/matroids/matroid.pyx  # 19 doctests failed',
 'sage -t --long src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed',
 'sage -t --long src/sage/dynamics/arithmetic_dynamics/wehlerK3.py  # 21 doctests failed',
 'sage -t --long src/sage/rings/polynomial/multi_polynomial_ideal.py  # 21 doctests failed',
 'sage -t --long src/sage/sandpiles/sandpile.py  # 22 doctests failed',
 'sage -t --long src/sage/schemes/riemann_surfaces/riemann_surface.py  # 36 doctests failed',
 'sage -t --long src/doc/en/thematic_tutorials/sandpile.rst  # 49 doctests failed',
 'sage -t --long src/sage/graphs/generic_graph.py  # 51 doctests failed',
 'sage -t --long src/sage/misc/explain_pickle.py  # 70 doctests failed'

[chapoton]

good progress, no ? :-)

[chapoton]

worst 15 files in 8.7.b1:

 'src/sage/matroids/graphic_matroid.py  # 11 doctests failed',
 'src/sage/schemes/product_projective/point.py  # 11 doctests failed',
 'src/sage/symbolic/expression.pyx  # 11 doctests failed',
 'src/sage/rings/polynomial/multi_polynomial_sequence.py  # 12 doctests failed',
 'src/sage/symbolic/constants.py  # 12 doctests failed',
 'src/sage/modular/modform/element.py  # 13 doctests failed',
 'src/sage/tests/french_book/mpoly.py  # 13 doctests failed',
 'src/sage/categories/finite_posets.py  # 15 doctests failed',
 'src/sage/combinat/finite_state_machine.py  # 19 doctests failed',
 'src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed',
 'src/sage/rings/polynomial/multi_polynomial_ideal.py  # 20 doctests failed',
 'src/sage/dynamics/arithmetic_dynamics/wehlerK3.py  # 21 doctests failed',
 'src/sage/matroids/matroid.pyx  # 21 doctests failed',
 'src/sage/graphs/generic_graph.py  # 50 doctests failed',
 'src/sage/misc/explain_pickle.py  # 70 doctests failed'

[gh-timokau]

That is some impressive progress! Good work.

[chapoton]

some progress again

[chapoton]

Worst 15 files in 8.7.b3:

['src/sage/tests/french_book/programmation_doctest.py  # 10 doctests failed',
 'src/sage/matroids/graphic_matroid.py  # 11 doctests failed',
 'src/sage/schemes/product_projective/point.py  # 11 doctests failed',
 'src/sage/rings/polynomial/multi_polynomial_sequence.py  # 12 doctests failed',
 'src/sage/symbolic/constants.py  # 12 doctests failed',
 'src/sage/tests/french_book/mpoly.py  # 13 doctests failed',
 'src/sage/graphs/digraph.py  # 14 doctests failed',
 'src/sage/categories/finite_posets.py  # 15 doctests failed',
 'src/sage/combinat/finite_state_machine.py  # 19 doctests failed',
 'src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed',
 'src/sage/dynamics/arithmetic_dynamics/wehlerK3.py  # 21 doctests failed',
 'src/sage/matroids/matroid.pyx  # 21 doctests failed',
 'src/sage/rings/polynomial/multi_polynomial_ideal.py  # 21 doctests failed',
 'src/sage/graphs/generic_graph.py  # 30 doctests failed',
 'src/sage/misc/explain_pickle.py  # 70 doctests failed']

[chapoton]

Worst 15 files in 8.7.b4:

'src/sage/symbolic/expression.pyx  # 10 doctests failed',
 'src/sage/matroids/graphic_matroid.py  # 11 doctests failed',
 'src/sage/schemes/product_projective/point.py  # 11 doctests failed',
 'src/sage/rings/polynomial/multi_polynomial_sequence.py  # 12 doctests failed',
 'src/sage/symbolic/constants.py  # 12 doctests failed',
 'src/sage/matrix/matrix_polynomial_dense.pyx  # 14 doctests failed',
 'src/sage/tests/books/computational-mathematics-with-sagemath/mpoly_doctest.py  # 14 doctests failed',
 'src/sage/categories/finite_posets.py  # 15 doctests failed',
 'src/sage/graphs/generic_graph.py  # 18 doctests failed',
 'src/sage/combinat/finite_state_machine.py  # 19 doctests failed',
 'src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed',
 'src/sage/dynamics/arithmetic_dynamics/wehlerK3.py  # 21 doctests failed',
 'src/sage/matroids/matroid.pyx  # 21 doctests failed',
 'src/sage/rings/polynomial/multi_polynomial_ideal.py  # 21 doctests failed',
 'src/sage/misc/explain_pickle.py  # 70 doctests failed'

[jhpalmieri]

Re

 'src/sage/symbolic/constants.py  # 12 doctests failed',

I only see 6 failed doctests (this is on OS X; is it platform dependent?).

[dcoudert]

There are certainly some differences between plateforms and other factors. For instance, I see this, which is not in the reported worst 15:

sage -t --long src/sage/graphs/digraph.py  # 14 doctests failed

I had 14 with 8.7.beta1, only 7 with beta2 and beta3, and now 14 again. All these failed doctests are related to the order of items in the output. See #27170.

[chapoton]

worst 15 in 8.7.b5:

['src/sage/numerical/backends/cvxopt_backend.pyx  # 9 doctests failed',
 'src/sage/rings/integer.pyx  # 9 doctests failed',
 'src/sage/symbolic/expression.pyx  # 9 doctests failed',
 'src/sage/crypto/lwe.py  # 10 doctests failed',
 'src/sage/misc/test_class_pickling.py  # 10 doctests failed',
 'src/sage/numerical/sdp.pyx  # 10 doctests failed',
 'src/sage/matroids/graphic_matroid.py  # 11 doctests failed',
 'src/sage/schemes/product_projective/point.py  # 11 doctests failed',
 'src/sage/symbolic/constants.py  # 12 doctests failed',
 'src/sage/categories/finite_posets.py  # 15 doctests failed',
 'src/sage/graphs/generic_graph.py  # 18 doctests failed',
 'src/sage/matroids/matroid.pyx  # 18 doctests failed',
 'src/sage/combinat/finite_state_machine.py  # 19 doctests failed',
 'src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed',
 'src/sage/misc/explain_pickle.py  # 70 doctests failed']

[jdemeyer]

Is there an easy place where we can find a full log of all Python 3 test failures?

[vklein]

Yes ​https://patchbot.sagemath.org/log/0/Ubuntu/16.04/x86_64/4.4.0-141-generic/atlas/2019-02-24%2011:31:45.

[chapoton]

in 8.7.b6:

less than 1 : 55
less than 2 : 78
less than 4 : 106
less than 8 : 124
less than 16 : 134

and the worst 15 are:

['src/sage/libs/eclib/interface.py  # 8 doctests failed',
 'src/sage/libs/ntl/ntl_ZZ_pX.pyx  # 8 doctests failed',
 'src/sage/libs/ppl.pyx  # 9 doctests failed',
 'src/sage/misc/nested_class.pyx  # 9 doctests failed',
 'src/sage/numerical/backends/cvxopt_backend.pyx  # 9 doctests failed',
 'src/sage/rings/integer.pyx  # 9 doctests failed',
 'src/sage/symbolic/expression.pyx  # 9 doctests failed',
 'src/sage/crypto/lwe.py  # 10 doctests failed',
 'src/sage/misc/test_class_pickling.py  # 10 doctests failed',
 'src/sage/numerical/sdp.pyx  # 10 doctests failed',
 'src/sage/schemes/product_projective/point.py  # 11 doctests failed',
 'src/sage/symbolic/constants.py  # 12 doctests failed',
 'src/sage/combinat/finite_state_machine.py  # 19 doctests failed',
 'src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed',
 'src/sage/matroids/matroid.pyx  # 22 doctests failed']

[jhpalmieri]

When the next beta comes out, I think it will merge all of the algebra branches, and then we can move that out of the "in progress" list.

[chapoton]

on 8.7.b7:

less than 1 : 44
less than 2 : 64
less than 4 : 93
less than 8 : 111
less than 16 : 118

and the 15 worse are

['src/sage/libs/ntl/ntl_ZZ_pX.pyx  # 8 doctests failed',
 'src/sage/numerical/backends/cvxopt_backend.pyx  # 8 doctests failed',
 'src/sage/numerical/sdp.pyx  # 8 doctests failed',
 'src/sage/symbolic/expression.pyx  # 8 doctests failed',
 'src/sage/libs/ppl.pyx  # 9 doctests failed',
 'src/sage/misc/nested_class.pyx  # 9 doctests failed',
 'src/sage/rings/integer.pyx  # 9 doctests failed',
 'src/sage/crypto/lwe.py  # 10 doctests failed',
 'src/sage/schemes/product_projective/point.py  # 11 doctests failed',
 'src/sage/symbolic/constants.py  # 12 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/quiver.py  # 13 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/cluster_seed.py  # 18 doctests failed',
 'src/sage/matroids/matroid.pyx  # 18 doctests failed',
 'src/sage/combinat/finite_state_machine.py  # 19 doctests failed',
 'src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed']

[chapoton]

in 8.7.rc0: worst 15 are

['src/sage/groups/perm_gps/permgroup.py  # 7 doctests failed',
 'src/sage/graphs/generic_graph.py  # 8 doctests failed',
 'src/sage/libs/ntl/ntl_ZZ_pX.pyx  # 8 doctests failed',
 'src/sage/numerical/backends/cvxopt_backend.pyx  # 8 doctests failed',
 'src/sage/numerical/sdp.pyx  # 8 doctests failed',
 'src/sage/libs/ppl.pyx  # 9 doctests failed',
 'src/sage/misc/nested_class.pyx  # 9 doctests failed',
 'src/sage/rings/integer.pyx  # 9 doctests failed',
 'src/sage/symbolic/expression.pyx  # 10 doctests failed',
 'src/sage/symbolic/constants.py  # 12 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/quiver.py  # 14 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/cluster_seed.py  # 18 doctests failed',
 'src/sage/matroids/matroid.pyx  # 18 doctests failed',
 'src/sage/combinat/finite_state_machine.py  # 19 doctests failed',
 'src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed']

and there remains

less than 1 : 35
less than 2 : 56
less than 4 : 83
less than 8 : 95
less than 16 : 101
less than 64 : 105
less than 128 : 105
less than 256 : 105

[jhpalmieri]

Is there a followup ticket to modify src/ext/doctest/python3-known-passing.txt? Should that happen for every beta, or just every actual release? Anyway, we should add algebras, data_structures, homology, modular, modules, schemes/curves, schemes/product_projective. What am I missing?

[chapoton]

yes, this should be done from time to time. If you want to do that, please do! Now would be a good time. Here is my most recent list of good modules:

good = ["algebras", "algebras/steenrod", "arith", "coding",
        "calculus", "combinat/designs", "combinat/posets",
        "combinat/species", "combinat/rigged_configurations",
        "combinat/sf", "combinat/words", "databases",
        "data_structures", "docs", "features", "finance", "games",
        "game_theory", "groups/lie_gps", "groups/matrix_gps",
        "homology", "interacts", "knots", "libs/gsl", "lfunctions",
        "logic", "manifolds", "media", "modular/modsym", "modular",
        "modules", "monoids", "parallel", "plot", "probability",
        "quadratic_forms", "quivers", "rings/asymptotic",
        "rings/function_field", "rings/number_field", "sandpiles",
        "sat", "schemes/toric", "schemes/curves",
        "schemes/product_projective", "server", "stats", "structure",
        "tensor", "typeset", 'sage_setup']

[jhpalmieri]

See #27519. I'll post a branch there once I've finished testing.

[chapoton]

In 8.8.b0:

less than 1 : 33
less than 2 : 54
less than 4 : 80
less than 8 : 92
less than 16 : 99
less than 64 : 102

and the worst 15 are

['src/sage/combinat/root_system/weyl_group.py  # 7 doctests failed',
 'src/sage/groups/perm_gps/permgroup.py  # 7 doctests failed',
 'src/sage/libs/ntl/ntl_ZZ_pX.pyx  # 8 doctests failed',
 'src/sage/numerical/backends/cvxopt_backend.pyx  # 8 doctests failed',
 'src/sage/numerical/sdp.pyx  # 8 doctests failed',
 'src/sage/misc/nested_class.pyx  # 9 doctests failed',
 'src/sage/rings/integer.pyx  # 9 doctests failed',
 'src/sage/symbolic/expression.pyx  # 9 doctests failed',
 'src/sage/graphs/generic_graph.py  # 10 doctests failed',
 'src/sage/symbolic/constants.py  # 12 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/cluster_seed.py  # 13 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/quiver.py  # 13 doctests failed',
 'src/sage/matroids/matroid.pyx  # 18 doctests failed',
 'src/sage/combinat/finite_state_machine.py  # 19 doctests failed',
 'src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed']

[chapoton]

Little regression after passing to python 3.7.3:

less than 1 : 36
less than 2 : 56
less than 4 : 84
less than 8 : 94
less than 16 : 102
less than 64 : 105

In the 15 worst files, 178 broken doctests:

['src/sage/groups/perm_gps/permgroup.py  # 7 doctests failed',
 'src/sage/graphs/generic_graph.py  # 8 doctests failed',
 'src/sage/libs/ntl/ntl_ZZ_pX.pyx  # 8 doctests failed',
 'src/sage/numerical/backends/cvxopt_backend.pyx  # 8 doctests failed',
 'src/sage/doctest/sources.py  # 9 doctests failed',
 'src/sage/misc/nested_class.pyx  # 9 doctests failed',
 'src/sage/numerical/sdp.pyx  # 9 doctests failed',
 'src/sage/rings/integer.pyx  # 9 doctests failed',
 'src/sage/symbolic/expression.pyx  # 9 doctests failed',
 'src/sage/symbolic/constants.py  # 12 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/cluster_seed.py  # 13 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/quiver.py  # 14 doctests failed',
 'src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed',
 'src/sage/matroids/matroid.pyx  # 21 doctests failed',
 'src/sage/combinat/finite_state_machine.py  # 22 doctests failed']

[chapoton]

Some progress in 8.8.b2:

less than 1 : 34
less than 2 : 54
less than 4 : 77
less than 8 : 86
less than 16 : 91
less than 64 : 94

In the 15 worst files, 163 broken doctests:

['src/sage/tests/books/computational-mathematics-with-sagemath/graphtheory_doctest.py  # 5 doctests failed',
 'src/sage/ext/fast_callable.pyx  # 6 doctests failed',
 'src/sage/groups/perm_gps/permgroup.py  # 6 doctests failed',
 'src/sage/rings/polynomial/multi_polynomial.pyx  # 6 doctests failed',
 'src/sage/combinat/root_system/weyl_group.py  # 7 doctests failed',
 'src/sage/graphs/generic_graph.py  # 8 doctests failed',
 'src/sage/libs/ntl/ntl_ZZ_pX.pyx  # 8 doctests failed',
 'src/sage/misc/nested_class.pyx  # 9 doctests failed',
 'src/sage/rings/integer.pyx  # 9 doctests failed',
 'src/sage/symbolic/expression.pyx  # 12 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/cluster_seed.py  # 13 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/quiver.py  # 13 doctests failed',
 'src/sage/matroids/matroid.pyx  # 19 doctests failed',
 'src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed',
 'src/sage/combinat/finite_state_machine.py  # 22 doctests failed']

[chapoton]

on 8.8.b3:

less than 1 : 32
less than 2 : 48
less than 4 : 67
less than 8 : 74
less than 16 : 80
less than 64 : 82

In the 15 worst files, 153 broken doctests:

['src/sage/rings/polynomial/binary_form_reduce.py  # 5 doctests failed',
 'src/sage/ext/fast_callable.pyx  # 6 doctests failed',
 'src/sage/groups/perm_gps/permgroup.py  # 6 doctests failed',
 'src/sage/rings/polynomial/multi_polynomial.pyx  # 6 doctests failed',
 'src/sage/combinat/root_system/weyl_group.py  # 7 doctests failed',
 'src/sage/graphs/generic_graph.py  # 8 doctests failed',
 'src/sage/libs/ntl/ntl_ZZ_pX.pyx  # 8 doctests failed',
 'src/sage/misc/nested_class.pyx  # 9 doctests failed',
 'src/sage/rings/integer.pyx  # 9 doctests failed',
 'src/sage/symbolic/expression.pyx  # 10 doctests failed',
 'src/sage/combinat/finite_state_machine.py  # 11 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/cluster_seed.py  # 13 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/quiver.py  # 14 doctests failed',
 'src/sage/misc/classcall_metaclass.pyx  # 20 doctests failed',
 'src/sage/matroids/matroid.pyx  # 21 doctests failed']

[chapoton]

In the 15 worst files, 125 broken doctests:

['src/sage/combinat/set_partition.py  # 5 doctests failed',
 'src/sage/dynamics/arithmetic_dynamics/projective_ds.py  # 5 doctests failed',
 'src/sage/rings/polynomial/binary_form_reduce.py  # 5 doctests failed',
 'src/sage/ext/fast_callable.pyx  # 6 doctests failed',
 'src/sage/groups/perm_gps/permgroup.py  # 6 doctests failed',
 'src/sage/rings/polynomial/multi_polynomial.pyx  # 6 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/cluster_seed.py  # 7 doctests failed',
 'src/sage/combinat/root_system/weyl_group.py  # 7 doctests failed',
 'src/sage/graphs/generic_graph.py  # 8 doctests failed',
 'src/sage/libs/ntl/ntl_ZZ_pX.pyx  # 8 doctests failed',
 'src/sage/misc/nested_class.pyx  # 9 doctests failed',
 'src/sage/rings/integer.pyx  # 9 doctests failed',
 'src/sage/rings/qqbar.py  # 9 doctests failed',
 'src/sage/symbolic/expression.pyx  # 12 doctests failed',
 'src/sage/matroids/matroid.pyx  # 23 doctests failed']

One can note a large regression in qqbar, and that matroids still get worse too.

[jhpalmieri]

Regarding matroids: there is some piece of underlying data which is intrinsically unordered, and it is causing all sorts of failures. I don't know if it's best to mark them all # py3 random or to sort the data so this doesn't happen. Is there an active Sage developer who knows enough about matroids to help make this decision?

[chapoton]

With 8.8.b5:

less than 1 : 22
less than 2 : 30
less than 4 : 48
less than 8 : 52
less than 16 : 55
less than 64 : 56

In the 15 worst files, 102 broken doctests:

['src/sage/combinat/root_system/integrable_representations.py  # 4 doctests failed',
 'src/sage/combinat/set_partition.py  # 4 doctests failed',
 'src/sage/doctest/test.py  # 4 doctests failed',
 'src/sage/matroids/graphic_matroid.py  # 4 doctests failed',
 'src/sage/misc/functional.py  # 4 doctests failed',
 'src/sage/repl/attach.py  # 4 doctests failed',
 'src/sage/rings/polynomial/toy_buchberger.py  # 4 doctests failed',
 'src/sage/groups/perm_gps/permgroup.py  # 6 doctests failed',
 'src/sage/combinat/cluster_algebra_quiver/cluster_seed.py  # 7 doctests failed',
 'src/sage/combinat/root_system/weyl_group.py  # 7 doctests failed',
 'src/sage/graphs/generic_graph.py  # 8 doctests failed',
 'src/sage/misc/nested_class.pyx  # 9 doctests failed',
 'src/sage/rings/integer.pyx  # 9 doctests failed',
 'src/sage/symbolic/expression.pyx  # 10 doctests failed',
 'src/sage/matroids/matroid.pyx  # 18 doctests failed']

[dcoudert]

#27773 and #27774 fix various issues in Python 3 with src/sage/numerical/backends/cplex_backend.pyx and 1 in gurobi_backend.pyx. Cplex <= 12.8 is needed to test these tickets. Cplex >= 12.9 cannot be used yet (see #27790).