Moving lyndon_word.py in sage.combinat.words

[nadialafreniere]

Someone told me that there was a Lyndon word file in sage.combinat that was outside of sage.combinat.words. We moved it.

[git]

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

​82cb74f

Minor corrections to importations in lyndon_word.py

[jdemeyer]

The old import location should be deprecated: ​http://doc.sagemath.org/html/en/developer/coding_in_python.html#deprecation

[git]

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

​0edf846	Added depeciation of sage/combinat/Lyndon_word.py
​ef3627d	deprecation of the old file

[jdemeyer]

I think you misunderstand how deprecation works. There should be a deprecation in the file src/sage/combinat/lyndon_word.py. Since you moved that, just create a new file with this name containing only the deprecation and a doctest. The doctest should show that

sage: from sage.combinat.lyndon_word import LyndonWord

still works.

[nadialafreniere]

I think I've done the deprecation in a proper way, though I'm not so sure... The developer's guide is not so clear about it for someone who never did it.

I started a new branch since I changed the version of sage I had on my computer in between. It's now based on 6.9beta5.

---

New commits:

​3d3d135	Modified location of Lyndon word, added deprecation
​b2ee0a8	trying to fix deprecation
​efb4873	deprecation fixed

[jdemeyer]

1. You cannot just put docstrings in arbitrary places. So in src/sage/combinat/lyndon_word.py, you should replace

   """
   docstring
   """
   
   code
   
   """
   doctests
   """
   

by

"""
docstring

doctests
"""

code

2. The indentation of the docstring is wrong:

   TESTS::
   
   sage: ...
   

should become

TESTS::

    sage: ...

3. Instead of testing import *, I would prefer to see a more concrete import (say LyndonWord)

[jdemeyer]

One more thing: you should also edit src/doc/en/reference/combinat/module_list.rst

[git]

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

​a4c5eff

Moving doctests in lyndon_word.py + editing the list of modules for documentation (reviewer's suggestions)

[nadialafreniere]

I've modified the patch in accordance with comments 11 and 12. Thanks for these suggestions.

[jdemeyer]

The file src/sage/combinat/enumerated_sets.py still has a reference to the old file:

Words
-----

- :class:`Words`
- :ref:`sage.combinat.subword`
- :ref:`sage.combinat.necklace`
- :ref:`sage.combinat.lyndon_word`
- :ref:`sage.combinat.dyck_word`
- :ref:`sage.combinat.debruijn_sequence`
- :ref:`sage.combinat.shuffle`

[git]

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

​266ec7f

Change the reference to Lyndon Words in enumerated_sets.py

[nadialafreniere]

Replying to jdemeyer:

The file src/sage/combinat/enumerated_sets.py still has a reference to the old file:

Words
-----

- :class:`Words`
- :ref:`sage.combinat.subword`
- :ref:`sage.combinat.necklace`
- :ref:`sage.combinat.lyndon_word`
- :ref:`sage.combinat.dyck_word`
- :ref:`sage.combinat.debruijn_sequence`
- :ref:`sage.combinat.shuffle`

I changed it. It doesn't seem to appear anywhere else, at least not in sage-combinat.

[jdemeyer]

There is a doctest failure (don't ask me exactly why):

sage -t --long src/sage/structure/sage_object.pyx
**********************************************************************
File "src/sage/structure/sage_object.pyx", line 1451, in sage.structure.sage_object.unpickle_all
Failed example:
    sage.structure.sage_object.unpickle_all()  # (4s on sage.math, 2011)
Expected:
    doctest:... DeprecationWarning: ...
    See http://trac.sagemath.org/... for details.
    Successfully unpickled ... objects.
    Failed to unpickle 0 objects.
Got:
    doctest:858: DeprecationWarning: You unpickled an object which relies on an old data structure. Save it again to update it, for it may break in the future.
    See http://trac.sagemath.org/18375 for details.
    doctest:1: DeprecationWarning: You unpickled an object which relies on an old data structure. Save it again to update it, for it may break in the future.
    See http://trac.sagemath.org/1000 for details.
     * unpickle failure: load('/home/jdemeyer/.sage/temp/tamiyo/21030/dir_pG8nxg//pickle_jar/_class__sage_combinat_lyndon_word_LyndonWords_evaluation__.sobj')
    Traceback (most recent call last):
      File "sage/structure/sage_object.pyx", line 1543, in sage.structure.sage_object.unpickle_all (build/cythonized/sage/structure/sage_object.c:15114)
        object = load(os.path.join(dir,A))
      File "sage/structure/sage_object.pyx", line 987, in sage.structure.sage_object.load (build/cythonized/sage/structure/sage_object.c:11494)
        X = loads(open(filename).read(), compress=compress)
      File "sage/structure/sage_object.pyx", line 1341, in sage.structure.sage_object.loads (build/cythonized/sage/structure/sage_object.c:13583)
        return unpickler.load()
    UnpicklingError: NEWOBJ class argument isn't a type object
     * unpickle failure: load('/home/jdemeyer/.sage/temp/tamiyo/21030/dir_pG8nxg//pickle_jar/_class__sage_combinat_lyndon_word_LyndonWords_nk__.sobj')
    Traceback (most recent call last):
      File "sage/structure/sage_object.pyx", line 1543, in sage.structure.sage_object.unpickle_all (build/cythonized/sage/structure/sage_object.c:15114)
        object = load(os.path.join(dir,A))
      File "sage/structure/sage_object.pyx", line 987, in sage.structure.sage_object.load (build/cythonized/sage/structure/sage_object.c:11494)
        X = loads(open(filename).read(), compress=compress)
      File "sage/structure/sage_object.pyx", line 1341, in sage.structure.sage_object.loads (build/cythonized/sage/structure/sage_object.c:13583)
        return unpickler.load()
    UnpicklingError: NEWOBJ class argument isn't a type object
     * unpickle failure: load('/home/jdemeyer/.sage/temp/tamiyo/21030/dir_pG8nxg//pickle_jar/_class__sage_combinat_lyndon_word_StandardBracketedLyndonWords_nk__.sobj')
    Traceback (most recent call last):
      File "sage/structure/sage_object.pyx", line 1543, in sage.structure.sage_object.unpickle_all (build/cythonized/sage/structure/sage_object.c:15114)
        object = load(os.path.join(dir,A))
      File "sage/structure/sage_object.pyx", line 987, in sage.structure.sage_object.load (build/cythonized/sage/structure/sage_object.c:11494)
        X = loads(open(filename).read(), compress=compress)
      File "sage/structure/sage_object.pyx", line 1341, in sage.structure.sage_object.loads (build/cythonized/sage/structure/sage_object.c:13583)
        return unpickler.load()
    UnpicklingError: NEWOBJ class argument isn't a type object
    doctest:1: DeprecationWarning: This function is only used to unpickle invalid objects
    See http://trac.sagemath.org/18848 for details.
    doctest:1: DeprecationWarning: OrderedAlphabet is deprecated; use Alphabet instead.
    See http://trac.sagemath.org/8920 for details.
    doctest:1: DeprecationWarning: gen_py.pari is deprecated, use sage.libs.pari.all.pari instead
    See http://trac.sagemath.org/17451 for details.
    doctest:632: DeprecationWarning: The "pari_mod" finite field implementation is deprecated
    See http://trac.sagemath.org/17297 for details.
    doctest:1: DeprecationWarning: MatrixSpace_ZZ_2x2 is deprecated. Please use MatrixSpace(ZZ,2) instead
    See http://trac.sagemath.org/17824 for details.
    Failed:
    _class__sage_combinat_lyndon_word_LyndonWords_evaluation__.sobj
    _class__sage_combinat_lyndon_word_LyndonWords_nk__.sobj
    _class__sage_combinat_lyndon_word_StandardBracketedLyndonWords_nk__.sobj
    ----------------------------------------------------------------------
    ** This error is probably due to an old pickle failing to unpickle.
    ** See sage.structure.sage_object.register_unpickle_override for
    ** how to override the default unpickling methods for (old) pickles.
    ** NOTE: pickles should never be removed from the pickle_jar! 
    ----------------------------------------------------------------------
    Successfully unpickled 583 objects.
    Failed to unpickle 3 objects.
**********************************************************************
File "src/sage/structure/sage_object.pyx", line 1459, in sage.structure.sage_object.unpickle_all
Failed example:
    sage.structure.sage_object.unpickle_all()
Expected:
    Successfully unpickled ... objects.
    Failed to unpickle 0 objects.
Got:
     * unpickle failure: load('/home/jdemeyer/.sage/temp/tamiyo/21030/dir_PjMOnq//pickle_jar/_class__sage_combinat_lyndon_word_LyndonWords_evaluation__.sobj')
    Traceback (most recent call last):
      File "sage/structure/sage_object.pyx", line 1543, in sage.structure.sage_object.unpickle_all (build/cythonized/sage/structure/sage_object.c:15114)
        object = load(os.path.join(dir,A))
      File "sage/structure/sage_object.pyx", line 987, in sage.structure.sage_object.load (build/cythonized/sage/structure/sage_object.c:11494)
        X = loads(open(filename).read(), compress=compress)
      File "sage/structure/sage_object.pyx", line 1341, in sage.structure.sage_object.loads (build/cythonized/sage/structure/sage_object.c:13583)
        return unpickler.load()
    UnpicklingError: NEWOBJ class argument isn't a type object
     * unpickle failure: load('/home/jdemeyer/.sage/temp/tamiyo/21030/dir_PjMOnq//pickle_jar/_class__sage_combinat_lyndon_word_LyndonWords_nk__.sobj')
    Traceback (most recent call last):
      File "sage/structure/sage_object.pyx", line 1543, in sage.structure.sage_object.unpickle_all (build/cythonized/sage/structure/sage_object.c:15114)
        object = load(os.path.join(dir,A))
      File "sage/structure/sage_object.pyx", line 987, in sage.structure.sage_object.load (build/cythonized/sage/structure/sage_object.c:11494)
        X = loads(open(filename).read(), compress=compress)
      File "sage/structure/sage_object.pyx", line 1341, in sage.structure.sage_object.loads (build/cythonized/sage/structure/sage_object.c:13583)
        return unpickler.load()
    UnpicklingError: NEWOBJ class argument isn't a type object
     * unpickle failure: load('/home/jdemeyer/.sage/temp/tamiyo/21030/dir_PjMOnq//pickle_jar/_class__sage_combinat_lyndon_word_StandardBracketedLyndonWords_nk__.sobj')
    Traceback (most recent call last):
      File "sage/structure/sage_object.pyx", line 1543, in sage.structure.sage_object.unpickle_all (build/cythonized/sage/structure/sage_object.c:15114)
        object = load(os.path.join(dir,A))
      File "sage/structure/sage_object.pyx", line 987, in sage.structure.sage_object.load (build/cythonized/sage/structure/sage_object.c:11494)
        X = loads(open(filename).read(), compress=compress)
      File "sage/structure/sage_object.pyx", line 1341, in sage.structure.sage_object.loads (build/cythonized/sage/structure/sage_object.c:13583)
        return unpickler.load()
    UnpicklingError: NEWOBJ class argument isn't a type object
    Failed:
    _class__sage_combinat_lyndon_word_LyndonWords_evaluation__.sobj
    _class__sage_combinat_lyndon_word_LyndonWords_nk__.sobj
    _class__sage_combinat_lyndon_word_StandardBracketedLyndonWords_nk__.sobj
    ----------------------------------------------------------------------
    ** This error is probably due to an old pickle failing to unpickle.
    ** See sage.structure.sage_object.register_unpickle_override for
    ** how to override the default unpickling methods for (old) pickles.
    ** NOTE: pickles should never be removed from the pickle_jar! 
    ----------------------------------------------------------------------
    Successfully unpickled 583 objects.
    Failed to unpickle 3 objects.
**********************************************************************