Moving lyndon_word.py in sage.combinat.words #19150

nadialafreniere · 2015-09-06T18:11:23Z

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

CC: @egunawan @sagetrac-mlapointe @sagetrac-sschanck @tscrim @sagetrac-tmonteil

Component: combinatorics

Keywords: Lyndon words, days69, fpsac2019

Author: Nadia Lafrenière

Branch/Commit: cb47f9d

Reviewer: Travis Scrimshaw

Issue created by migration from https://trac.sagemath.org/ticket/19150

The text was updated successfully, but these errors were encountered:

nadialafreniere · 2015-09-06T18:12:36Z

Branch: u/nadialafreniere/lyndon

sagetrac-git · 2015-09-06T18:27:35Z

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

`82cb74f`	`Minor corrections to importations in lyndon_word.py`

sagetrac-git · 2015-09-06T18:27:35Z

Commit: 82cb74f

nadialafreniere · 2015-09-07T17:33:06Z

Changed keywords from Lyndon words to Lyndon words, days69

jdemeyer · 2015-09-07T19:58:01Z

comment:4

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

sagetrac-git · 2015-09-07T22:37:17Z

Changed commit from 82cb74f to ef3627d

sagetrac-git · 2015-09-07T22:37:17Z

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 · 2015-09-08T06:27:40Z

comment:7

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 · 2015-09-08T23:16:32Z

Changed branch from u/nadialafreniere/lyndon to none

nadialafreniere · 2015-09-08T23:16:32Z

Changed commit from ef3627d to none

nadialafreniere · 2015-09-10T13:32:56Z

Branch: u/nadialafreniere/moved_lyndon

nadialafreniere · 2015-09-10T13:38:08Z

comment:10

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`

nadialafreniere · 2015-09-10T13:38:08Z

Commit: efb4873

jdemeyer · 2015-09-10T21:07:24Z

comment:11

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

The indentation of the docstring is wrong:

TESTS::

sage: ...

should become

TESTS::

    sage: ...

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

jdemeyer · 2015-09-11T10:00:56Z

comment:12

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

sagetrac-git · 2015-09-12T02:07:59Z

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)`

sagetrac-git · 2015-09-12T02:07:59Z

Changed commit from efb4873 to a4c5eff

nadialafreniere · 2015-09-12T02:11:08Z

comment:14

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

jdemeyer · 2015-09-14T11:24:27Z

comment:15

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`

sagetrac-git · 2015-09-14T13:24:11Z

Changed commit from a4c5eff to 266ec7f

sagetrac-git · 2015-09-14T13:24:11Z

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

`266ec7f`	`Change the reference to Lyndon Words in enumerated_sets.py`

nadialafreniere · 2015-09-14T13:37:34Z

comment:17

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 · 2015-09-17T15:15:10Z

comment:18

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.
**********************************************************************

fchapoton · 2019-07-07T10:26:14Z

Changed commit from 266ec7f to cb47f9d

fchapoton · 2019-07-07T10:26:14Z

Changed branch from u/nadialafreniere/moved_lyndon to public/ticket/19150

fchapoton · 2019-07-07T10:26:14Z

comment:21

fresh new branch

New commits:

`cb47f9d`	`trac 19150 moving lyndon words into words`

tscrim · 2019-07-08T12:05:12Z

Reviewer: Travis Scrimshaw

tscrim · 2019-07-08T12:05:12Z

comment:22

LGTM.

tscrim · 2019-07-08T13:02:13Z

Changed keywords from Lyndon words, days69 to Lyndon words, days69, fpsac2019

vbraun · 2019-07-09T12:58:42Z

Changed branch from public/ticket/19150 to cb47f9d

nadialafreniere added this to the sage-6.9 milestone Sep 6, 2015

nadialafreniere added c: combinatorics labels Sep 6, 2015

nadialafreniere added the s: needs review label Sep 7, 2015

jdemeyer added s: needs work and removed s: needs review labels Sep 7, 2015

nadialafreniere added s: needs review and removed s: needs work labels Sep 10, 2015

jdemeyer added s: needs work and removed s: needs review labels Sep 10, 2015

nadialafreniere removed the s: needs work label Sep 12, 2015

nadialafreniere added the s: needs review label Sep 12, 2015

jdemeyer added s: needs work and removed s: needs review labels Sep 14, 2015

nadialafreniere added s: needs review and removed s: needs work labels Sep 14, 2015

jdemeyer added s: needs work and removed s: needs review labels Sep 17, 2015

fchapoton added s: needs review and removed s: needs work labels Jul 7, 2019

tscrim modified the milestones: sage-6.9, sage-8.9 Jul 8, 2019

tscrim added s: positive review and removed s: needs review labels Jul 8, 2019

vbraun removed the s: positive review label Jul 9, 2019

vbraun closed this as completed in 6d36083 Jul 9, 2019

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Moving lyndon_word.py in sage.combinat.words #19150

Moving lyndon_word.py in sage.combinat.words #19150

nadialafreniere commented Sep 6, 2015

nadialafreniere commented Sep 6, 2015

sagetrac-git mannequin commented Sep 6, 2015

sagetrac-git mannequin commented Sep 6, 2015

nadialafreniere commented Sep 7, 2015

jdemeyer commented Sep 7, 2015

sagetrac-git mannequin commented Sep 7, 2015

sagetrac-git mannequin commented Sep 7, 2015

jdemeyer commented Sep 8, 2015

nadialafreniere commented Sep 8, 2015

nadialafreniere commented Sep 8, 2015

nadialafreniere commented Sep 10, 2015

nadialafreniere commented Sep 10, 2015

nadialafreniere commented Sep 10, 2015

jdemeyer commented Sep 10, 2015

jdemeyer commented Sep 11, 2015

sagetrac-git mannequin commented Sep 12, 2015

sagetrac-git mannequin commented Sep 12, 2015

nadialafreniere commented Sep 12, 2015

jdemeyer commented Sep 14, 2015

sagetrac-git mannequin commented Sep 14, 2015

sagetrac-git mannequin commented Sep 14, 2015

nadialafreniere commented Sep 14, 2015

jdemeyer commented Sep 17, 2015

fchapoton commented Jul 7, 2019

fchapoton commented Jul 7, 2019

fchapoton commented Jul 7, 2019

tscrim commented Jul 8, 2019

tscrim commented Jul 8, 2019

tscrim commented Jul 8, 2019

vbraun commented Jul 9, 2019

Moving lyndon_word.py in sage.combinat.words #19150

Moving lyndon_word.py in sage.combinat.words #19150

Comments

nadialafreniere commented Sep 6, 2015

nadialafreniere commented Sep 6, 2015

sagetrac-git mannequin commented Sep 6, 2015

sagetrac-git mannequin commented Sep 6, 2015

nadialafreniere commented Sep 7, 2015

jdemeyer commented Sep 7, 2015

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jdemeyer commented Sep 11, 2015

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jdemeyer commented Sep 14, 2015

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nadialafreniere commented Sep 14, 2015

jdemeyer commented Sep 17, 2015

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