#5386: [with patch, needs review] simplicial complexes and their homology
-------------------------+--------------------------------------------------
Reporter: jhpalmieri | Owner: jhpalmieri
Type: enhancement | Status: new
Priority: major | Milestone: sage-3.4.2
Component: misc | Keywords:
-------------------------+--------------------------------------------------
Comment(by was):
Some things changed in sage-3.4.1.rc2, so this needs to be fixed (this is
purely due to bitrot, not your fault):
{{{
wst...@sage:~/build/sage-3.4.1.rc2-ref2$ ./sage -t
devel/sage/sage/homology/simplicial_complex.py
sage -t "devel/sage/sage/homology/simplicial_complex.py"
**********************************************************************
File
"/scratch/wstein/build/sage-3.4.1.rc2-ref2/devel/sage/sage/homology/simplicial_complex.py",
line 863:
sage: Z = SimplicialComplex(S, S.subsets())
Exception raised:
Traceback (most recent call last):
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File
"/scratch/wstein/build/sage-3.4.1.rc2/local/bin/sagedoctest.py", line 38,
in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_28[3]>", line 1, in <module>
Z = SimplicialComplex(S, S.subsets())###line 863:
sage: Z = SimplicialComplex(S, S.subsets())
File "/scratch/wstein/build/sage-3.4.1.rc2-ref2/local/lib/python2.5
/site-packages/sage/homology/simplicial_complex.py", line 693, in __init__
if len(maximal_faces) == 0:
File "/scratch/wstein/build/sage-3.4.1.rc2-ref2/local/lib/python2.5
/site-packages/sage/combinat/combinat.py", line 869, in __len__
raise AttributeError, "__len__ has been removed; use
.cardinality() instead"
AttributeError: __len__ has been removed; use .cardinality() instead
**********************************************************************
File
"/scratch/wstein/build/sage-3.4.1.rc2-ref2/devel/sage/sage/homology/simplicial_complex.py",
line 864:
sage: Z
Exception raised:
Traceback (most recent call last):
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File
"/scratch/wstein/build/sage-3.4.1.rc2/local/bin/sagedoctest.py", line 38,
in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_28[4]>", line 1, in <module>
Z###line 864:
sage: Z
NameError: name 'Z' is not defined
**********************************************************************
File
"/scratch/wstein/build/sage-3.4.1.rc2-ref2/devel/sage/sage/homology/simplicial_complex.py",
line 866:
sage: Z.n_faces(2)
Exception raised:
Traceback (most recent call last):
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File
"/scratch/wstein/build/sage-3.4.1.rc2/local/bin/sagedoctest.py", line 38,
in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_28[5]>", line 1, in <module>
Z.n_faces(Integer(2))###line 866:
sage: Z.n_faces(2)
NameError: name 'Z' is not defined
**********************************************************************
File
"/scratch/wstein/build/sage-3.4.1.rc2-ref2/devel/sage/sage/homology/simplicial_complex.py",
line 869:
sage: Z.n_faces(2, subcomplex=K)
Exception raised:
Traceback (most recent call last):
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File
"/scratch/wstein/build/sage-3.4.1.rc2/local/bin/sagedoctest.py", line 38,
in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_28[7]>", line 1, in <module>
Z.n_faces(Integer(2), subcomplex=K)###line 869:
sage: Z.n_faces(2, subcomplex=K)
NameError: name 'Z' is not defined
**********************************************************************
File
"/scratch/wstein/build/sage-3.4.1.rc2-ref2/devel/sage/sage/homology/simplicial_complex.py",
line 887:
sage: Z = SimplicialComplex(S, S.subsets()); Z
Exception raised:
Traceback (most recent call last):
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File
"/scratch/wstein/build/sage-3.4.1.rc2/local/bin/sagedoctest.py", line 38,
in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_29[3]>", line 1, in <module>
Z = SimplicialComplex(S, S.subsets()); Z###line 887:
sage: Z = SimplicialComplex(S, S.subsets()); Z
File "/scratch/wstein/build/sage-3.4.1.rc2-ref2/local/lib/python2.5
/site-packages/sage/homology/simplicial_complex.py", line 693, in __init__
if len(maximal_faces) == 0:
File "/scratch/wstein/build/sage-3.4.1.rc2-ref2/local/lib/python2.5
/site-packages/sage/combinat/combinat.py", line 869, in __len__
raise AttributeError, "__len__ has been removed; use
.cardinality() instead"
AttributeError: __len__ has been removed; use .cardinality() instead
**********************************************************************
File
"/scratch/wstein/build/sage-3.4.1.rc2-ref2/devel/sage/sage/homology/simplicial_complex.py",
line 889:
sage: Z.f_vector()
Exception raised:
Traceback (most recent call last):
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File
"/scratch/wstein/build/sage-3.4.1.rc2/local/bin/sagedoctest.py", line 38,
in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_29[4]>", line 1, in <module>
Z.f_vector()###line 889:
sage: Z.f_vector()
NameError: name 'Z' is not defined
**********************************************************************
File
"/scratch/wstein/build/sage-3.4.1.rc2-ref2/devel/sage/sage/homology/simplicial_complex.py",
line 905:
sage: Z = SimplicialComplex(S, S.subsets()); Z
Exception raised:
Traceback (most recent call last):
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File
"/scratch/wstein/build/sage-3.4.1.rc2/local/bin/sagedoctest.py", line 38,
in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_30[3]>", line 1, in <module>
Z = SimplicialComplex(S, S.subsets()); Z###line 905:
sage: Z = SimplicialComplex(S, S.subsets()); Z
File "/scratch/wstein/build/sage-3.4.1.rc2-ref2/local/lib/python2.5
/site-packages/sage/homology/simplicial_complex.py", line 693, in __init__
if len(maximal_faces) == 0:
File "/scratch/wstein/build/sage-3.4.1.rc2-ref2/local/lib/python2.5
/site-packages/sage/combinat/combinat.py", line 869, in __len__
raise AttributeError, "__len__ has been removed; use
.cardinality() instead"
AttributeError: __len__ has been removed; use .cardinality() instead
**********************************************************************
File
"/scratch/wstein/build/sage-3.4.1.rc2-ref2/devel/sage/sage/homology/simplicial_complex.py",
line 907:
sage: [Z._f_dict()[n] for n in range(-1, 4)]
Exception raised:
Traceback (most recent call last):
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File
"/scratch/wstein/build/sage-3.4.1.rc2/local/bin/sagedoctest.py", line 38,
in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/scratch/wstein/build/sage-3.4.1.rc2/local/bin/ncadoctest.py",
line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_30[4]>", line 1, in <module>
[Z._f_dict()[n] for n in range(-Integer(1), Integer(4))]###line
907:
sage: [Z._f_dict()[n] for n in range(-1, 4)]
NameError: name 'Z' is not defined
**********************************************************************
3 items had failures:
4 of 8 in __main__.example_28
2 of 7 in __main__.example_29
2 of 7 in __main__.example_30
***Test Failed*** 8 failures.
For whitespace errors, see the file
/scratch/wstein/build/sage-3.4.1.rc2-ref2/tmp/.doctest_simplicial_complex.py
[3.0 s]
exit code: 1024
----------------------------------------------------------------------
The following tests failed:
sage -t "devel/sage/sage/homology/simplicial_complex.py"
Total time for all tests: 3.0 seconds
}}}
I think there is a bug in stanly_reisener_ring:
{{{
sage: S = SimplicialComplex(['a', 'b', 'c'], (('a', 'b'), ('a', 'c'),
('b', 'c')))
sage: S.stanley_reisner_ring()
Quotient of Multivariate Polynomial Ring in a, c, b over Integer Ring by
the ideal (a*c*b)
sage: S.product(S).stanley_reisner_ring()
...
ValueError: variable names must be alphanumeric, but one is '('b', 'c')'
which is not.
}}}
* It should be easier to get at all the standard examples of complexes,
e.g., like with graphs if you do {{{graphs.<tab>}}} you get a bunch of
graphs. Could you make it so there is something like
{{{complexes.<tab>}}} or something like that (which makes senses) and
gives examples?
Please ping me once you fix the above, so I can give this ''amazing
patch'' (!) a positive review.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/5386#comment:1>
Sage <http://sagemath.org/>
Sage - Open Source Mathematical Software: Building the Car Instead of
Reinventing the Wheel
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