Opened 11 years ago

Last modified 8 years ago

#5457 closed enhancement

Refactor symmetric functions and k-bounded subspace — at Version 52

Reported by: nthiery Owned by: mhansen
Priority: major Milestone: sage-5.4
Component: combinatorics Keywords: symmetric functions, days38, sd40
Cc: sage-combinat, saliola, bump, chrisjamesberg, zabrocki, SimonKing Merged in:
Authors: Mike Zabrocki, Anne Schilling, Jason Bandlow Reviewers: Dan Bump, Nicolas M. Thiéry
Report Upstream: N/A Work issues:
Branch: Commit:
Dependencies: #11563, #13109, #12969 Stopgaps:

Description (last modified by zabrocki)

This patch restructures the implementation of symmetric functions in sage

The new implementation makes use of multiple realizations and the category framework. The new access to symmetric functions is via

sage: Sym = SymmetricFunctions(QQ)

Further new features that are implemented:

  • The ring of symmetric functions is now endowed with a Hopf algebra structure. The coproduct and antipode are implemented (which were missing before).
  • A tutorial on how to use symmetric functions in sage is included at the beginning of sf.py which is also accessible via
    sage: SymmetricFunctions??
    
  • Symmetric functions should now work a lot better with respect to specializing parameters like q and t for Hall-Littlewood, Jack and Macdonald symmetric functions. Certain functionalities before this change were broken or not possible.
  • Documentation was added to LLT polynomials (which had very sparse documentation previously).
  • The k-bounded subspace of the ring of symmetric function was implemented. The k-Schur functions now live in the k-bounded subspace rather than in the ring of symmetric functions as before.

This patch gained tremendously by the tutorial on symmetric functions written by Jason Bandlow, a draft on the k-bounded subspace by Jason Bandlow, and code multiple realizations written by Franco Saliola.

See also http://groups.google.com/group/sage-devel/msg/a49f3288fca1b75c

Apply

Change History (52)

comment:1 Changed 11 years ago by nthiery

  • Description modified (diff)

comment:2 Changed 11 years ago by nthiery

  • Cc sage-combinat added

comment:3 Changed 8 years ago by aschilling

  • Dependencies set to 13109
  • Report Upstream set to N/A

comment:4 Changed 8 years ago by aschilling

  • Dependencies 13109 deleted

comment:5 Changed 8 years ago by aschilling

  • Authors set to Mike Zabrocki, Anne Schilling
  • Description modified (diff)
  • Keywords symmetric functions sd38 sd40 added
  • Reviewers set to Dan Bump, Franco Saliola
  • Summary changed from Refactor symmetric functions to Refactor symmetric functions and k-bounded subspace

comment:6 Changed 8 years ago by aschilling

  • Cc saliola bump chrisjamesberg added

comment:7 Changed 8 years ago by aschilling

  • Cc zabrocki added

comment:8 Changed 8 years ago by aschilling

  • Status changed from new to needs_review

comment:9 Changed 8 years ago by aschilling

  • Status changed from needs_review to needs_work

comment:10 Changed 8 years ago by aschilling

Hi Mike,

I finished the doctests for the following files:

  • schur.py
  • homogeneous.py
  • elementrary.py
  • powersum.py
  • monomial.py
  • classical.py
  • dual.py
  • multiplicative.py
  • orthotriang.py
  • sf.py

In particular, at the beginning of sf.py I incorporated the tutorial that Jason and Nicolas wrote (which was further down the queue) and updated it. I marked them there as coauthors in that file.

This leaves the doctests for

  • hall_littlewood.py
  • jack.py
  • llt.py
  • macdonald.py
  • ns_macdonald.py
  • sfa.py

which I suppose you will do in the next couple of days? In particular, in the sfa.py the deprecation warnings need to be activated which I have not yet done.

Best,

Anne

comment:11 Changed 8 years ago by aschilling

  • Authors changed from Mike Zabrocki, Anne Schilling to Mike Zabrocki, Anne Schilling, Jason Bandlow

comment:12 Changed 8 years ago by vbraun

  • Dependencies set to #11563

comment:13 Changed 8 years ago by vbraun

  • Dependencies changed from #11563 to #11563, #13109

comment:14 follow-up: Changed 8 years ago by aschilling

  • Description modified (diff)

comment:15 in reply to: ↑ 14 ; follow-up: Changed 8 years ago by aschilling

Hi Mike,

I completed the doctests for sfa.py and also rebased everything on top of 13109. Please put your changes to

  • hall_littlewood.py
  • jack.py
  • llt.py
  • macdonald.py

on top of the current patch trac_5457-symmetric_functions-mz.patch. Unfortunately we need to abandon the sage-combinat queue for the moment since it would be very cumbersome to keep it backward compatible with 13109. I will send you a separate e-mail on how to proceed.

Cheers,

Anne

comment:16 in reply to: ↑ 15 Changed 8 years ago by aschilling

Ok, patch is ready for review! It should apply and run cleanly on sage.5.2.rc0!

Anne

comment:17 Changed 8 years ago by aschilling

  • Status changed from needs_work to needs_review

comment:19 Changed 8 years ago by SimonKing

  • Cc SimonKing added

comment:20 follow-up: Changed 8 years ago by aschilling

Hi Dan!

Thank you very much for your comments on the failing doctests in

  • devel/sage/sage/algebras/nil_coxeter_algebra.py
  • devel/sage/sage/categories/realizations.py

They are fixed in the updated version of the patch. I do not get failures for

  • devel/sage/sage/sandpiles/sandpile.py

on my machine.

lolita-4:sandpiles anne$ sage -t sandpile.py sage -t "devel/sage-sf/sage/sandpiles/sandpile.py"

[19.0 s]


All tests passed! Total time for all tests: 19.0 seconds

Anne

comment:21 in reply to: ↑ 20 Changed 8 years ago by bump

Replying to aschilling:

Hi Dan!

Thank you very much for your comments on the failing doctests in

  • devel/sage/sage/algebras/nil_coxeter_algebra.py
  • devel/sage/sage/categories/realizations.py

They are fixed in the updated version of the patch. I do not get failures for

  • devel/sage/sage/sandpiles/sandpile.py

on my machine.

I also get a doctest failure in sandpile.py with unpatched sage-5.2.rc0 so this failure is not caused by the patch.

Last edited 8 years ago by bump (previous) (diff)

comment:22 Changed 8 years ago by bump

Applies cleanly to sage-5.2 and passes all tests.

comment:23 follow-up: Changed 8 years ago by aschilling

  • Description modified (diff)

comment:24 in reply to: ↑ 23 Changed 8 years ago by aschilling

The attached review patch trac_5457-review-as.patch incorporates most of the comments that Dan Bump raised in e-mail conversations.

Anne

comment:25 follow-up: Changed 8 years ago by bump

  • Description modified (diff)
  • Status changed from needs_review to positive_review

This patch is a huge step forward for symmetric functions.

In addition to normal testing I spent quite a bit of time and privately sent comments (mainly on documentation) that have been taken into account in trac_5457-review-as.patch. I'm changing the status to positive review.

comment:26 in reply to: ↑ 25 Changed 8 years ago by aschilling

Replying to bump:

This patch is a huge step forward for symmetric functions.

In addition to normal testing I spent quite a bit of time and privately sent comments (mainly on documentation) that have been taken into account in trac_5457-review-as.patch. I'm changing the status to positive review.

Dear Dan, Thank you so much for your thorough and quick review of this huge patch! Mike and I just finished the review patch. Tests pass on both of our machines.

Anne

comment:27 follow-up: Changed 8 years ago by bump

I have reviewed the latest version of the patch and it still has positive review.

comment:28 in reply to: ↑ 27 Changed 8 years ago by aschilling

Since http://trac.sagemath.org/sage_trac/ticket/12969 just got merged into sage-5.3.beta0, please also apply the attachment trac12969_rel_5457.patch on the ticket 12969 to this patch. Otherwise there will be doctest failures.

Thanks,

Anne

comment:29 Changed 8 years ago by aschilling

  • Dependencies changed from #11563, #13109 to #11563, #13109, #12969

comment:30 Changed 8 years ago by aschilling

  • Description modified (diff)

comment:31 Changed 8 years ago by jdemeyer

This needs to be rebased to sage-5.3.beta0 (not yet released):

patching file sage/categories/realizations.py
Hunk #1 FAILED at 74
1 out of 1 hunks FAILED -- saving rejects to file sage/categories/realizations.py.rej
patching file sage/combinat/sf/classical.py
Hunk #3 FAILED at 88
1 out of 9 hunks FAILED -- saving rejects to file sage/combinat/sf/classical.py.rej
patching file sage/combinat/sf/sfa.py
Hunk #61 FAILED at 2589
1 out of 63 hunks FAILED -- saving rejects to file sage/combinat/sf/sfa.py.rej
abort: patch failed to apply

comment:32 Changed 8 years ago by jdemeyer

  • Status changed from positive_review to needs_work

comment:33 follow-up: Changed 8 years ago by aschilling

  • Description modified (diff)

comment:34 in reply to: ↑ 33 Changed 8 years ago by aschilling

I rebased and folded the three patches with respect to sage-5.3.beta0 from yesterday. It should apply cleanly now.

Mike and I are still going to fix one math bug that someone at FPSAC found.

Anne

comment:35 Changed 8 years ago by aschilling

Hi Dan,

Our new rebased patch is attached. You only need to apply trac_5457-symmetric_functions-mz.patch. Note that we did not fix apply_linear_morphism in /category/module_with_basis.py yet since Nicolas seems to have a review patch for this, but unfortunately his tests did not pass. Either he needs to fix his review patch or we will add your suggestion from the e-mail.

Anne

comment:36 Changed 8 years ago by aschilling

  • Status changed from needs_work to needs_review

comment:37 follow-up: Changed 8 years ago by nthiery

Note: I inserted in the queue the latest patch rebased for 5.3 beta0 from here. My review patch is also there, ready to be folded if you are happy with it.

comment:38 in reply to: ↑ 37 Changed 8 years ago by aschilling

Dear Dan and Nicolas,

Thank you so much for your reviews and work on this patch! I incorporated the changes that Dan suggested by e-mail and folded Nicolas' review patch. In addition, Mike had some minor improvements in the documentation of llt.py which are incorporated.

The new patch should apply cleanly on sage-5.3.beta0.

Anne

comment:39 Changed 8 years ago by aschilling

  • Reviewers changed from Dan Bump, Franco Saliola to Dan Bump, Nicolas M. Thiery

comment:40 Changed 8 years ago by bump

All tests pass with sage-5.3.beta0. The changes discussed over the last few days have all been incorporated. I think this is ready to go.

comment:41 Changed 8 years ago by bump

  • Status changed from needs_review to positive_review

comment:42 Changed 8 years ago by nthiery

  • Description modified (diff)

comment:43 Changed 8 years ago by jdemeyer

  • Status changed from positive_review to needs_work

This fails on arando (32-bit i386 Linux):

sage -t --long "devel/sage/sage/combinat/sf/llt.py"
**********************************************************************
File "/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.3.beta1/devel/sage/sage/combinat/sf/llt.py", line 329:
    sage: cmp(L3Q, L3Z)
Expected:
    -1
Got:
    1
**********************************************************************

comment:44 follow-up: Changed 8 years ago by aschilling

  • Description modified (diff)
  • Status changed from needs_work to needs_review

comment:45 in reply to: ↑ 44 Changed 8 years ago by aschilling

Hi Jeroen,

Hmm, this is hard for us to check since we are not running our code on that operating system. We attached a patch which will hopefully fix the problem

Apply

Thanks,

Anne

comment:46 Changed 8 years ago by aschilling

  • Status changed from needs_review to positive_review

comment:47 Changed 8 years ago by jdemeyer

  • Reviewers changed from Dan Bump, Nicolas M. Thiery to Dan Bump, Nicolas M. Thiéry
  • Status changed from positive_review to needs_work

comment:48 Changed 8 years ago by jdemeyer

  • Status changed from needs_work to needs_review

I think one of the original reviewers should review this additional patch.

comment:49 Changed 8 years ago by bump

  • Status changed from needs_review to positive_review

I think one of the original reviewers should review this additional patch.

This adds a cmp method for SymmetricFunctions?, which was missing, and that was uncovered by the test in llt.py. Two SymmetricFunctions? instances are compared equal if and only if they have the same base ring, which is as it should be.

Unless I'm missing something the patch is obviously correct. I ran --testall --long in the sf directory and all tests passed.

comment:50 Changed 8 years ago by nthiery

There is no compelling reason to have a cmp function for symmetric functions (nor its bases). The order has no meaning, and equality testing should be taken care of by UniqueRepresentation?.

So altogether, I'd rather not add a cmp function, and instead would rather replace the failing test by:

sage: cmp(L3Q, L3Z) != 0

which is platform independent, and is all we care about. We could even just discard this test.

Now, I don't want to slow down the integration of this patch, so I am happy leaving this issue for a latter ticket, at the author's choice.

Cheers,

Nicolas

comment:51 Changed 8 years ago by zabrocki

  • Status changed from positive_review to needs_work

As per Nicolas' suggestion, we are deleting the cmp function from llt and moving and modifying the doctests elsewhere in the llt.py file.

comment:52 Changed 8 years ago by zabrocki

  • Description modified (diff)
  • Status changed from needs_work to needs_review

This new patch deletes the function cmp from llt.py and inserts doctests into init in llt.py

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