remove expired deprecations in sage/combinat

[zabrocki]

A grep of the word deprecation in the source code of sage/combinat indicates that there are many functions which have expired. All warnings which were placed there with the intention of eventually removing them. We will clean up some of this code and remove deprecations which have been in Sage for at least one year (the focus will be on those that have been merged since two years).

Code deprecated from:

• merged in sage-5.X: Factor code between words's alphabets and sets/enumerated sets/ordered sets #8920 (5.8.beta2), Reorganization of set partitions #14140 (5.9.beta3), Remove CombinatorialClass from skew* #14101 (5.12.beta4), unify the three implementations of gaussian q-binomial coefficients #14496 (5.10.beta2), turn crystalographic into crystallographic #14673 (5.10.rc1), Remove CombinatorialClass from Permutations #14772 (5.12.beta3), Remove CombinatorialClass from DyckWords #14875 (5.13.beta0), Changes to RSK #15142 (5.13.beta0), More minor tableau and skew_tableau optimizations, and moving out attacking_pairs #15327 (5.13.beta3)
• merged in sage-6.X: Non-exceptional rigged configuration bijections #13872 (6.1.beta?), Minor fixes to symmetric functions #15473 (6.1.beta?), Implement a catalog for crystals #15882 (sage-6.2.beta?), standardize the interface to TransitiveIdeal and friends #6637 (6.3.beta?), BalancedIncompleteBlockDesign -> balanced_incomplete_block_design #16446 (6.3.beta?), get rid of PermutationsNK #16472 (sage-6.3.beta?), Clean IncidenceStructure #16553 (sage-6.3.beta?), Remove deprecated code #16933 (sage-6.4.beta?)

CC: @sagetrac-fwclarke @AndrewAtLarge @anneschilling @darijgr @VivianePons @hivert @fchapoton @sagetrac-chrisjamesberg @saliola @ghseeli @sagetrac-sage-combinat @zabrocki @nthiery @sagetrac-alubovsky @tscrim @simon-king-jena @bsalisbury1 @videlec @staroste @nathanncohen @brettpim

Component: combinatorics

Keywords: deprecate

Author: Mike Zabrocki

Branch/Commit: a97a800

Reviewer: Vincent Delecroix

Issue created by migration from https://trac.sagemath.org/ticket/19513

[jdemeyer]

comment:1

-1 to this ticket. There is no reason to just remove all deprecations like that. Those deprecations may be removed, that's true. But does this imply that it's the right thing to do? Not always. I doubt that any one person really understands all the deprecated code in Sage and you obviously should not remove deprecations that you don't understand.

Besides that, this ticket is simply too broad. If you want to remove specific deprecations, just remove those. But not all at once.

[zabrocki]

comment:2

Fair enough. At least sage/combinat merits a bit of cleanup and I do know something about those deprecations.

[jm58660]

comment:3

meet_matrix() and join_matrix() on posets.py were badly deprecated, see #17356. Anyway, there have been so much time that they can be be deleted. (They are of course available, but on (semi)lattices, not on posets.)

[zabrocki]

comment:4

Replying to @jm58660:

meet_matrix() and join_matrix() on posets.py were badly deprecated, see #17356. Anyway, there have been so much time that they can be be deleted. (They are of course available, but on (semi)lattices, not on posets.)

6.5 was released less than a year ago so those can stay a bit longer.

[zabrocki]

Branch: public/ticket/19513

[zabrocki]

Changed keywords from none to deprecate

[zabrocki]

Commit: 18dd976

[zabrocki]

comment:5

I'll give a full list of relevant tickets soon. I'll also add to the cc list to ensure that everyone is aware that these functions are disappearing. I decided my rule was not to touch anything that was deprecated in sage 6.4 or later. There is enough here for the moment.

---

Last 10 new commits:

4cf2094	remove from_row_and_column_length from skew_partition.py #14101
2ac8494	remove inf,sup,standard_form,less from set_partition.py #14140
bf1c7ba	remove deprecations from permutation.py #14772
1682451	remove permutation_nk.py #16472, RobinsonSchenstedKnuth* from rsk.py #15142
e327256	remove q_bin in sf/kfpoly.py #14496
c85c5af	remove SymmetricFunctionAlgebra from sfa.py #15473
2765365	crystalographic in root_system/cartan_type.py #14673 plus import statements from RSK
17e58fb	remove HighestWeight* from rigged_configurations/* #13872
cbd98cf	remove rigged_configurations/all.py lazy_import statements #15882
18dd976	remove OrderedAlphabet* from designs/alphabet.py #8920 and functions from designs/incidence_structures.py #16553

[zabrocki]

Author: Mike Zabrocki

[zabrocki]

comment:6

I will still have to go through the documentation and ensure that removed code does not appear there (this was just a first pass).

I just added a large number of people to the cc list hoping that they will all check that the code that they are responsible for deprecating really should be removed.

split_nk.py and choose_nk.py are in ticket #18674

[tscrim]

comment:7

I can vouch for everything except that in designs. Nathann, Vincent, I think those are more in your area.

[jdemeyer]

comment:8

NOTE: whenever deprecated_callable_import() is used (as opposed to other kinds of deprecation), you should only remove the functionality from the global namespace but not remove it completely.

For example, TransitiveIdeal itself is not deprecated, it's just deprecated within src/sage/combinat/all.py. Especially since the deprecation warning says "This class soon will not be available in that way anymore", nothing indicates that the whole class will be removed.

[zabrocki]

comment:9

nothing indicates that the whole class will be removed.

I can restore it if you (or Nicolas or Florent) think that it should remain, however I was following the instruction:

-- Once the deprecation has been there for enough time: delete
-  ``TransitiveIdeal`` and ``TransitiveIealGraded``.

that was in the file. Note that I did not delete SearchForest for that reason.

[tscrim]

comment:10

These classes were deprecated in favor of RecursivelyEnumeratedSet in #6637; so we are okay to remove them. (Just for reference, SearchForest is waiting on #16351.)

[jdemeyer]

comment:11

Replying to @tscrim:

These classes were deprecated in favor of RecursivelyEnumeratedSet in #6637

No, they were not. From #6637 (emphasis mine):

2. Deprecate TransitiveIdeal, TransitiveIdealGraded and SearchForest as entry point.

B. TransitiveIdeal and TransitiveIealGraded are used in the code of sage/combinat, sage/categories and sage/groups at least. These should be updated to use RecursivelyEnumeratedSet for speed improvements and also to avoid issues explained in C below. See #16352.

Those classes should have been deprecated in #16352, but they weren't.

[sagetrac-git]

Changed commit from 18dd976 to 946267b

[sagetrac-git]

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

946267b

restore TransitiveIdeal and TransitiveIdealGraded

[zabrocki]

comment:27

I am not convinced that the code in combinat/words from #16553 was meant to be removed and I am leaving it. I've done a search through the documentation and it seems all is removed and all tests pass now.

[sagetrac-git]

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

6800765

restore RestrictedPartitions, keep because the parts_in does not yet work with restricted length

[sagetrac-git]

Changed commit from 9396e3f to 6800765

[sagetrac-git]

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

9f85070

minimize changes to partition.py

[sagetrac-git]

Changed commit from 6800765 to 9f85070

[zabrocki]

comment:30

I had forgotten that I had not restored the RestrictedPartitions in combinat/partitions.py. Additional functionality needs to be added to Partitions before this can be removed.

[videlec]

comment:31

Apparently, you removed a global import and it causes trouble

**********************************************************************
6 items had failures:
   4 of   5 in sage.combinat.partition.RestrictedPartitions
   4 of   5 in sage.combinat.partition.RestrictedPartitions_nsk.__contains__
   1 of   3 in sage.combinat.partition.RestrictedPartitions_nsk.__init__
   1 of   2 in sage.combinat.partition.RestrictedPartitions_nsk._repr_
   2 of   3 in sage.combinat.partition.RestrictedPartitions_nsk.cardinality
   2 of   3 in sage.combinat.partition.RestrictedPartitions_nsk.list
    [1142 tests, 14 failures, 26.59 s]
----------------------------------------------------------------------
sage -t --long src/sage/combinat/partition.py  # 14 doctests failed
----------------------------------------------------------------------

[sagetrac-git]

Changed commit from 9f85070 to a97a800

[sagetrac-git]

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

a97a800

add import statments in doc-tests

[videlec]

comment:34

You removed some deprecation released in sage-6.4 (from 04/14/15)... One year deprecation implies that this should not be merged until 04/14/16 which is in 6 months. This concerns this modification

-        if compact is not None:
-            from sage.misc.superseded import deprecation
-            deprecation(16933, 'compact argument is deprecated.')

[jdemeyer]

comment:35

Sage 6.4 was released 14 november 2014, so it's more than 1 year ago.

[jdemeyer]

comment:36

See http://www.sagemath.org/changelogs/sage-6.4.txt

[jdemeyer]

comment:37

14 april 2015 is the release date of Sage 6.6

[videlec]

comment:38

Thanks Jeroen for the corrections! I used the dates from trac milestones that were obviously wrong. I fixed them. And I can set this ticket to positive review!

[videlec]

Reviewer: Vincent Delecroix

[vbraun]

Changed branch from public/ticket/19513 to a97a800