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sage.graphs
, sage.combinat.{designs,posets}
, sage.sandpiles
: Update # needs
#36273
sage.graphs
, sage.combinat.{designs,posets}
, sage.sandpiles
: Update # needs
#36273
Conversation
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These changes introduce new doctests warnings. For instance In graphs (many more in combinat):
sage -t --long --warn-long 32.7 --random-seed=56484082308499901277842533432351053437 src/sage/graphs/graph.py
**********************************************************************
File "src/sage/graphs/graph.py", line 5855, in sage.graphs.graph.Graph.distance_graph
Warning: Variable 'degrees' referenced here was set only in doctest marked '# long time, needs sage.symbolic'
degrees.append(2^8)
**********************************************************************
File "src/sage/graphs/graph.py", line 5856, in sage.graphs.graph.Graph.distance_graph
Warning: Variable 'degrees' referenced here was set only in doctest marked '# long time, needs sage.symbolic'
degrees == H.degree_histogram()
[1325 tests, 13.41 s]
sage -t --long --warn-long 32.7 --random-seed=56484082308499901277842533432351053437 src/sage/graphs/distances_all_pairs.pyx
**********************************************************************
File "src/sage/graphs/distances_all_pairs.pyx", line 2301, in sage.graphs.distances_all_pairs.szeged_index
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs networkx'
a = szeged_index(G, algorithm='low')
**********************************************************************
File "src/sage/graphs/distances_all_pairs.pyx", line 2302, in sage.graphs.distances_all_pairs.szeged_index
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs networkx'
b = szeged_index(G, algorithm='high')
[180 tests, 1.06 s]
sage -t --long --warn-long 32.7 --random-seed=56484082308499901277842533432351053437 src/sage/graphs/strongly_regular_db.pyx
**********************************************************************
File "src/sage/graphs/strongly_regular_db.pyx", line 1926, in sage.graphs.strongly_regular_db.SRG_100_44_18_20
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs sage.groups'
G.is_strongly_regular(parameters=True) # long time
**********************************************************************
File "src/sage/graphs/strongly_regular_db.pyx", line 1948, in sage.graphs.strongly_regular_db.SRG_100_45_20_20
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs sage.groups'
G.is_strongly_regular(parameters=True) # long time
**********************************************************************
File "src/sage/graphs/strongly_regular_db.pyx", line 2620, in sage.graphs.strongly_regular_db.SRG_630_85_20_10
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs sage.groups'
G.is_strongly_regular(parameters=True) # long time
[344 tests, 10.40 s]
sage -t --long --warn-long 32.7 --random-seed=56484082308499901277842533432351053437 src/sage/graphs/generators/distance_regular.pyx
**********************************************************************
File "src/sage/graphs/generators/distance_regular.pyx", line 363, in sage.graphs.generators.distance_regular.TruncatedWittGraph
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs sage.libs.pari sage.modules'
G.is_distance_regular(True) # long time (due to above) # needs sage.modules
[207 tests, 59.56 s]
sage -t --long --warn-long 32.7 --random-seed=56484082308499901277842533432351053437 src/sage/graphs/generators/smallgraphs.py
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 460, in sage.graphs.generators.smallgraphs.Cell600
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.rings.number_field'
g.size()
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 462, in sage.graphs.generators.smallgraphs.Cell600
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.rings.number_field'
g.is_regular(12)
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 464, in sage.graphs.generators.smallgraphs.Cell600
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.rings.number_field'
g.is_vertex_transitive()
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 536, in sage.graphs.generators.smallgraphs.Cell120
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.rings.number_field'
g.size()
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 538, in sage.graphs.generators.smallgraphs.Cell120
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.rings.number_field'
g.is_regular(4)
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 540, in sage.graphs.generators.smallgraphs.Cell120
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.rings.number_field'
g.is_vertex_transitive()
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 4759, in sage.graphs.generators.smallgraphs.MathonStronglyRegularGraph
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs sage.libs.gap'
G.is_strongly_regular(parameters=True) # long time
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 4766, in sage.graphs.generators.smallgraphs.MathonStronglyRegularGraph
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs sage.libs.gap'
G.is_strongly_regular(parameters=True)
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 4769, in sage.graphs.generators.smallgraphs.MathonStronglyRegularGraph
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs sage.libs.gap'
G.is_strongly_regular(parameters=True)
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 4793, in sage.graphs.generators.smallgraphs.JankoKharaghaniGraph
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.libs.pari'
g.is_strongly_regular(parameters=True) # long time
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 4885, in sage.graphs.generators.smallgraphs.JankoKharaghaniTonchevGraph
Warning: Variable 'Gamma' referenced here was set only in doctest marked '# long time, needs sage.libs.gap'
Gamma.is_strongly_regular(parameters=True) # long time
[574 tests, 26.23 s]
sage -t --long --warn-long 32.7 --random-seed=56484082308499901277842533432351053437 src/sage/graphs/generators/families.py
**********************************************************************
File "src/sage/graphs/generators/families.py", line 3845, in sage.graphs.generators.families.MathonPseudocyclicMergingGraph
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs sage.libs.gap'
G.is_strongly_regular(parameters=True) # long time
**********************************************************************
File "src/sage/graphs/generators/families.py", line 3848, in sage.graphs.generators.families.MathonPseudocyclicMergingGraph
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs sage.libs.gap'
G.is_strongly_regular(parameters=True) # long time
**********************************************************************
File "src/sage/graphs/generators/families.py", line 3851, in sage.graphs.generators.families.MathonPseudocyclicMergingGraph
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs sage.libs.gap'
G.is_strongly_regular(parameters=True) # long time
[482 tests, 12.80 s]
and a doctest error in sandpiles
sage -t --long --warn-long 32.8 --random-seed=321572006474589592224501753422986174817 src/sage/sandpiles/sandpile.py
**********************************************************************
File "src/sage/sandpiles/sandpile.py", line 2754, in sage.sandpiles.sandpile.Sandpile.solve
Failed example:
Z = S.solve() # needs sage.libs.singular
Expected:
[[-0.707107000000000 + 0.707107000000000*I,
0.707107000000000 - 0.707107000000000*I],
[-0.707107000000000 - 0.707107000000000*I,
0.707107000000000 + 0.707107000000000*I],
[-I, -I],
[I, I],
[0.707107000000000 + 0.707107000000000*I,
-0.707107000000000 - 0.707107000000000*I],
[0.707107000000000 - 0.707107000000000*I,
-0.707107000000000 + 0.707107000000000*I],
[1, 1],
[-1, -1]]
Got:
<BLANKLINE>
**********************************************************************
1 item had failures:
1 of 5 in sage.sandpiles.sandpile.Sandpile.solve
[935 tests, 1 failure, 26.22 s]
@@ -24014,7 +24016,7 @@ class by some canonization function `c`. If `G` and `H` are graphs, | |||
....: [(0,1), (0,2), (1,2)], | |||
....: [(0,1), (0,2), (0,3)]] | |||
sage: algos = ['sage'] | |||
sage: algos.append('bliss') # optional - bliss | |||
sage: import sage.graphs.bliss; algos.append('bliss') # optional - bliss |
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Why is this import necessary ?
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It makes this line immune to tag probing (sage --fixdoctests --probe all
):
Without this change, the line algos.append('bliss')
can be run whether bliss is available are not, so probing would remove this tag, leading to an error later.
…modules]' --overwrite src/sage/graphs
92c3fde
to
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I see other warnings such as:
sage -t --long --warn-long 33.8 --random-seed=61144299382637325659043318932957598596 src/sage/combinat/species/generating_series.py
**********************************************************************
File "src/sage/combinat/species/generating_series.py", line 548, in sage.combinat.species.generating_series.CycleIndexSeriesRing
Warning: Variable 'R' referenced here was set only in doctest marked '# needs sage.modules'
R is CycleIndexSeriesRing(QQ)
[130 tests, 1.44 s]
sage -t --long --warn-long 33.8 --random-seed=61144299382637325659043318932957598596 src/sage/combinat/words/word_generators.py
**********************************************************************
File "src/sage/combinat/words/word_generators.py", line 856, in sage.combinat.words.word_generators.WordGenerator.CharacteristicSturmianWord
Warning: Consider using a block-scoped tag by inserting the line 'sage: # needs sage.symbolic' just before this line to avoid repeating the tag 4 times
a = words.LowerMechanicalWord(1/pi)[1:] # optional - sage.symbolic
**********************************************************************
File "src/sage/combinat/words/word_generators.py", line 938, in sage.combinat.words.word_generators.WordGenerator._CharacteristicSturmianWord_LetterIterator
Warning: Consider using a block-scoped tag by inserting the line 'sage: # needs sage.symbolic' just before this line to avoid repeating the tag 4 times
alpha = (sqrt(3)-1)/2 # optional - sage.symbolic
[301 tests, 1.09 s]
sage -t --long --warn-long 33.8 --random-seed=61144299382637325659043318932957598596 src/sage/combinat/words/morphism.py
**********************************************************************
File "src/sage/combinat/words/morphism.py", line 2889, in sage.combinat.words.morphism.WordMorphism.?
Warning: Variable 'V' referenced here was set only in doctest marked '# needs sage.modules'
S = set(map(tuple, [i*V[0] + j*V[1]
for i in [-1,0,1] for j in [-1,0,1]]))
**********************************************************************
File "src/sage/combinat/words/morphism.py", line 3332, in sage.combinat.words.morphism.WordMorphism.abelian_rotation_subspace
Warning: Consider using a block-scoped tag by inserting the line 'sage: # needs sage.modules' just before this line to avoid repeating the tag 5 times
WordMorphism('0->1,1->0').abelian_rotation_subspace() # optional - sage.modules
[610 tests, 1.40 s]
@@ -456,7 +456,7 @@ def Cell600(embedding=1): | |||
EXAMPLES:: | |||
|
|||
sage: # long time | |||
sage: g = graphs.Cell600() | |||
sage: g = graphs.Cell600() # needs sage.rings.number_field |
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Remaining doctest warnings in src/sage/graphs/generators/smallgraphs.py
, introduced in this PR:
sage -t --long --warn-long 34.0 --random-seed=75874225553897883545888612139197852719 src/sage/graphs/generators/smallgraphs.py
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 460, in sage.graphs.generators.smallgraphs.Cell600
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.rings.number_field'
g.size()
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 462, in sage.graphs.generators.smallgraphs.Cell600
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.rings.number_field'
g.is_regular(12)
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 464, in sage.graphs.generators.smallgraphs.Cell600
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.rings.number_field'
g.is_vertex_transitive()
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 536, in sage.graphs.generators.smallgraphs.Cell120
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.rings.number_field'
g.size()
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 538, in sage.graphs.generators.smallgraphs.Cell120
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.rings.number_field'
g.is_regular(4)
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 540, in sage.graphs.generators.smallgraphs.Cell120
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.rings.number_field'
g.is_vertex_transitive()
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 4759, in sage.graphs.generators.smallgraphs.MathonStronglyRegularGraph
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs sage.libs.gap'
G.is_strongly_regular(parameters=True) # long time
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 4766, in sage.graphs.generators.smallgraphs.MathonStronglyRegularGraph
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs sage.libs.gap'
G.is_strongly_regular(parameters=True)
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 4769, in sage.graphs.generators.smallgraphs.MathonStronglyRegularGraph
Warning: Variable 'G' referenced here was set only in doctest marked '# long time, needs sage.libs.gap'
G.is_strongly_regular(parameters=True)
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 4793, in sage.graphs.generators.smallgraphs.JankoKharaghaniGraph
Warning: Variable 'g' referenced here was set only in doctest marked '# long time, needs sage.libs.pari'
g.is_strongly_regular(parameters=True) # long time
**********************************************************************
File "src/sage/graphs/generators/smallgraphs.py", line 4885, in sage.graphs.generators.smallgraphs.JankoKharaghaniTonchevGraph
Warning: Variable 'Gamma' referenced here was set only in doctest marked '# long time, needs sage.libs.gap'
Gamma.is_strongly_regular(parameters=True) # long time
[574 tests, 12.13 s]
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Thanks! Fixed in e110826
@@ -1,4 +1,4 @@ | |||
# optional - sage.combinat sage.groups | |||
# sage.doctest: needs sage.combinat sage.groups | |||
r""" |
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Remaining doctest warnings in this file:
sage -t --long --warn-long 33.8 --random-seed=61144299382637325659043318932957598596 src/sage/combinat/integer_vectors_mod_permgroup.py
**********************************************************************
File "src/sage/combinat/integer_vectors_mod_permgroup.py", line 190, in sage.combinat.integer_vectors_mod_permgroup.IntegerVectorsModPermutationGroup
Warning: Consider using a block-scoped tag by inserting the line 'sage: # long time' just before this line to avoid repeating the tag 4 times
G = PermutationGroup([[(6,)]]) # long time
[171 tests, 0.58 s]
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Done in 82fb0f5
@@ -1924,8 +1924,8 @@ def is_resolvable(self, certificate=False, solver=None, verbose=0, check=True, | |||
sage: TD.is_resolvable() |
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Remaining doctest warnings in this file:
sage -t --long --warn-long 33.8 --random-seed=61144299382637325659043318932957598596 src/sage/combinat/designs/incidence_structures.py
**********************************************************************
File "src/sage/combinat/designs/incidence_structures.py", line 1541, in sage.combinat.designs.incidence_structures.IncidenceStructure.is_t_design
Warning: Consider using a block-scoped tag by inserting the line 'sage: # optional - gap_package_design' just before this line to avoid repeating the tag 5 times
BD = designs.WittDesign(9) # optional - gap_package_design
[344 tests, 2.08 s]
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Fixed in 67eb2e1
@@ -1,4 +1,4 @@ | |||
# -*- coding: utf-8 -*- | |||
# sage.doctest: needs sage.combinat sage.modules | |||
r""" |
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remaining warnings in this file:
sage -t --long --warn-long 33.8 --random-seed=61144299382637325659043318932957598596 src/sage/combinat/words/paths.py
**********************************************************************
File "src/sage/combinat/words/paths.py", line 1648, in sage.combinat.words.paths.FiniteWordPath_2d.animate
Warning: Consider using a block-scoped tag by inserting the line 'sage: # needs sage.plot' just before this line to avoid repeating the tag 6 times
a = words.fibonacci_tile(0).animate() # optional - sage.plot
[531 tests, 29.82 s]
@@ -1,4 +1,4 @@ | |||
# -*- coding: utf-8 -*- | |||
# sage.doctest: needs sage.combinat sage.modules | |||
r""" |
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remaining warnings:
sage -t --long --warn-long 33.8 --random-seed=61144299382637325659043318932957598596 src/sage/combinat/diagram_algebras.py
**********************************************************************
File "src/sage/combinat/diagram_algebras.py", line 2416, in sage.combinat.diagram_algebras.PartitionAlgebra
Warning: Consider using a block-scoped tag by inserting the line 'sage: # needs sage.symbolic' just before this line to avoid repeating the tag 4 times
q = var('q') # optional - sage.symbolic
**********************************************************************
File "src/sage/combinat/diagram_algebras.py", line 2428, in sage.combinat.diagram_algebras.PartitionAlgebra
Warning: Consider using a block-scoped tag by inserting the line 'sage: # needs sage.symbolic' just before this line to avoid repeating the tag 4 times
P = PA.basis().list() # optional - sage.symbolic
**********************************************************************
File "src/sage/combinat/diagram_algebras.py", line 2458, in sage.combinat.diagram_algebras.PartitionAlgebra
Warning: Consider using a block-scoped tag by inserting the line 'sage: # needs sage.symbolic' just before this line to avoid repeating the tag 6 times
S = SymmetricGroupAlgebra(SR, 2) # optional - sage.symbolic
**********************************************************************
File "src/sage/combinat/diagram_algebras.py", line 3839, in sage.combinat.diagram_algebras.BrauerAlgebra.jucys_murphy
Warning: Consider using a block-scoped tag by inserting the line 'sage: # needs sage.symbolic' just before this line to avoid repeating the tag 4 times
z = var('z') # optional - sage.symbolic
[953 tests, 16.68 s]
…raphs_sage_combinat_designs_sage_combinat_posets_sage_sandpiles
…gs, docstring cosmetics
I'll take care of the other files (outside of |
Documentation preview for this PR (built with commit 67eb2e1; changes) is ready! 🎉 |
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LGTM.
Further PRs are needed to complete the task in combinat
.
Thank you! |
sagemathgh-36273: `sage.graphs`, `sage.combinat.{designs,posets}`, `sage.sandpiles`: Update # needs <!-- ^^^^^ Please provide a concise, informative and self-explanatory title. Don't put issue numbers in there, do this in the PR body below. For example, instead of "Fixes sagemath#1234" use "Introduce new method to calculate 1+1" --> <!-- Describe your changes here in detail --> Also file-level `# needs` in the rest of `sage.combinat`. <!-- Why is this change required? What problem does it solve? --> <!-- If this PR resolves an open issue, please link to it here. For example "Fixes sagemath#12345". --> - Part of: sagemath#29705 - Cherry-picked from: sagemath#35095 <!-- If your change requires a documentation PR, please link it appropriately. --> ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> <!-- If your change requires a documentation PR, please link it appropriately --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> <!-- Feel free to remove irrelevant items. --> - [x] The title is concise, informative, and self-explanatory. - [ ] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies <!-- List all open PRs that this PR logically depends on - sagemath#12345: short description why this is a dependency - sagemath#34567: ... --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> URL: sagemath#36273 Reported by: Matthias Köppe Reviewer(s): David Coudert, Matthias Köppe
Also file-level
# needs
in the rest ofsage.combinat
.📝 Checklist
⌛ Dependencies