Opened 9 years ago
Closed 4 years ago
#10519 closed enhancement (fixed)
analytic combinatorics: new code for computing asymptotics for multivariate generating functions
Reported by:  araichev  Owned by:  sagecombinat 

Priority:  major  Milestone:  sage7.1 
Component:  combinatorics  Keywords:  analytic combinatorics, multivariate generating functions, asymptotics 
Cc:  cyril.banderier, zaf, tmonteil, dkrenn, behackl  Merged in:  
Authors:  Daniel Krenn, Alex Raichev  Reviewers:  Daniel Krenn, David Loeffler, Travis Scrimshaw 
Report Upstream:  N/A  Work issues:  
Branch:  a951f08 (Commits)  Commit:  a951f08123d038f97b809095208bb04c22671a5e 
Dependencies:  Stopgaps: 
Description (last modified by )
This code is a collection of functions designed to compute asymptotics of Maclaurin coefficients of certain classes of multivariate generating functions.
The main function asymptotics() returns the first N
terms of
the asymptotic expansion of the Maclaurin coefficients F_{n\alpha}
of the multivariate meromorphic function F=G/H
as n\to\infty
.
It assumes that F
is holomorphic in a neighborhood of the origin,
that H
is a polynomial, and that asymptotics in the direction of
\alpha
(a tuple of positive integers) are controlled by smooth
or multiple points.
Attachments (12)
Change History (153)
Changed 9 years ago by
comment:1 Changed 9 years ago by
 Milestone changed from sage4.6.2 to sage4.6.1
comment:2 Changed 9 years ago by
comment:3 Changed 9 years ago by
 Status changed from new to needs_work
Question for you experienced Sage developers: how can i better package my code?
I think it makes sense to move the major functions such as 'asymptotics' to methods in the class /Applications/sage/devel/sage/sage/rings/polynomial/multi_polynomial.pyx, but what about the subsidiary functions that don't concern polynomials in particular such as 'diff_prod' which calculates derivatives of products and solves equations?
comment:4 Changed 9 years ago by
Question for you experienced Sage developers: how can i better package my code?
Hi, I am currently at Sage Days 28. Right now, there is a discussion about Analytic combinatorics in Sage and your code was mentionned in the discussion. I am not an expert of the domain, but I am coding oriented object Python since some time now. So below are just some of my thoughts to, I hope, help you turn your set of functions into an oriented object structure.
How to structure a bunch of functions into classes? How to find which objects
(python classes) you need? Here is the trick I personaly use. Consider each of
your functions as a question you ask. Then, ask yourself to who are you asking
each of your questions? Answers often gives you a good hint about the objects
you need to implement. EXAMPLE. Suppose I code the function determinant
.
Question :
To who do I ask the determinant?
. Answer:
To a matrix
.
Hence,
matrix
might be a good object (a python class) to implement.
You are the best person to answer to these questions. You might have 30 functions in you file, but only two or three different answers to the above question. Regroup the similar functions together: they will become the methods of a same class.
The sage file you uploaded starts with :
> This code relates to analytic combinatorics. > More specifically, it is a collection of functions designed > to compute asymptotics of Maclaurin coefficients of certain classes of > multivariate generating functions. > The main function asymptotics() returns the first `N` terms of > the asymptotic expansion of the Maclaurin coefficients `F_{n\alpha}` > of the multivariate meromorphic function `F=G/H` as `n\to\infty`. > It assumes that `F` is holomorphic in a neighborhood of the origin, > that `H` is a polynomial, and that asymptotics in the direction of > `\alpha` (a tuple of positive integers) are controlled by smooth > or multiple points.
Reading only these lines, I imagine the following structure:
class HolomorphicMultivariateMeromorphicFunction(object): # Constructor of the object def __init__(self, F, G): #stores important information on the object as attributes of self self._F = F self._G = G def maclaurin_coefficients(self, n, alpha): r""" Return the maclaurin coefficients of self. INPUT:  ``alpha``  tuple of positive integers OUTPUT: a python list of the first terms OR maybe an object of a class you implement if there exists pertinent questions to ask to it. """ #Do some computations based (I guess) on self._F and self._G intermediate_result1 = self.some_intermediate_computations_1() #Do more computations return something def asymptotics(self, N, alpha): r""" Returns the asymptotics of Maclaurin coefficients. """ #Do some computations based (I guess) on self._F and self._G intermediate_result2 = self.some_intermediate_computations_2() intermediate_result3 = self.some_intermediate_computations_3() return something #put here all the others functions needed to compute the asymptotics def some_intermediate_computations_1(self): pass def some_intermediate_computations_2(self): pass def some_intermediate_computations_3(self): pass ...
It also looks like you need some robustness somehow. But I need to know more information about what means
that asymptotics in the direction of
\alpha
(a tuple of positive integers) are controlled by smooth or multiple points.
to decide whether this is checked at the creation of the object or before returning the asymptotics. But these hypothesis should be checked somewhere.
Hope this helps.
Cheers,
Sébastien Labbé, Montréal, (but currently at Sage Days 28, Orsay, France)
comment:5 Changed 9 years ago by
 Cc cyril.banderier added
comment:6 followup: ↓ 7 Changed 9 years ago by
Hi Sebastien:
Thanks very much for your helpful comments. I've been working on rewriting my code in an objectoriented way and will incorporate your suggestions. Some functions in mgf.sage, such as deciding whether a list of polynomials is algebraically dependent, are general purpose, and so i'm trying to put them into existing Sage classes. The others are more specific to asymptotics and deserve their own class similar to the one you outlined above. Robustness is also something i need to improve upon.
I'll post my modifications here after i write and test them more.
Thanks again.
Alex
comment:7 in reply to: ↑ 6 Changed 9 years ago by
Hi Sebastien et al:
I rewrote my code in objectoriented style. Please have a look if you have the time. Do i need to make the file into a patch, or is it useable as is?
Thanks for your help. Alex
comment:8 Changed 9 years ago by
 Status changed from needs_work to needs_review
comment:9 followup: ↓ 10 Changed 9 years ago by
 Status changed from needs_review to needs_work
Cool. I now see that a lot of the functions are now inside a class, which looks better. So, as I said earlier, this is not really my field of study, so I don't know how far I can go on that review. But, I can suggest at least two things:
 It would be better if you post a Mercurial patch instead of a Sage file so that people can apply it and test it. Are you able to do this? Take a look at the Sage Developper's Guide, where it should be explain how to create a patch.
To add your file to the documentation, you might want to look here.
This winter, I gave a presentation on How to Contribute to Sage. This may helps you to start with Mercurial for instance.
Also, right now, I am working on #11379 where I am adding a new file to Sage. You might find it helpfull to see how I proceed.
 Some the Python convention are not always followed. See also pep0008. Especially for spaces :
Yes: i = i + 1 No: i= i+1
comment:10 in reply to: ↑ 9 Changed 9 years ago by
To add a file to a patch, you must do:
sage hg add your_file.py
I was not able to find this information anywhere which is strange...
Tell me if you have questions.
Sébastien
comment:11 followups: ↓ 12 ↓ 13 Changed 9 years ago by
Thanks for your help, Se'bastien. I'm trying to put my Sage file into a patch by following your presentation slides, but am running into difficulties. I cloned Sage and copied my Sage file as 'amgf.sage' into
/Applications/sage/devel/sagearaichev/sage/combinat/
I rebuilt Sage etc. and made it to step 10 "Test the changes" of your slides. But when i run Sage and test a few commands, Sage doesn't seem to see the QuasiRationalExpression? class i created in /Applications/sage/devel/sagearaichev/sage/combinat/amgf.sage.
I thought this might be because amgf.sage is a Sage file and not a Python file. So i renamed it amgf.py instead and got syntax errors. What's up with that? Do i have to rewrite all my code in Python instead of Sage?
Thanks for your attention. Alex
comment:12 in reply to: ↑ 11 Changed 9 years ago by
Hi Alex,
I thought this might be because amgf.sage is a Sage file and not a Python file. So i renamed it amgf.py instead and got syntax errors. What's up with that? Do i have to rewrite all my code in Python instead of Sage?
The basic answer is yes, but Rewriting is a big word for what is really needed. There is little work to do since Sage mostly follows Python syntax. The two main difference are handling of integer (see http://www.sagemath.org/doc/tutorial/afterword.html), and the necessity to import what you need.
Handling of integer
 Notation for exponentiation: In Python
**
means exponentiation and^
means “xor”.
 If you need to return an integer for the user, write it return
Integer(1)
instead of return 1. In Python 1 is a machine integerint
(32 or 64 bits depending on your machine) andInteger(1)
is a Sage/Gmp? arbitrary precision integer. AlsoInteger
are much more powerful thanint
, for example they know about prime and factorization.
Importing stuff
The second big change is the necessity to import all what you need. More
precisely, each time you use some Sage function, you need to import it at the
beginning of the file. for example if you want to you PolynomialRing
,
you need to write
from sage.rings.polynomial.polynomial_ring_constructor import PolynomialRing
You can ask Sage where to find PolynomialRing? using:
sage: PolynomialRing.__module__ 'sage.rings.polynomial.polynomial_ring_constructor'
This also correspond to the path starting after sitepackages
given when you are asking Sage for
PolynomialRing
help:
sage: PolynomialRing? Type: function [...] File: /home/florent/src/Sage/sage/local/lib/python2.6/sitepackages/sage/rings/polynomial/polynomial_ring_constructor.py [...]
I hope this helps,
Florent
comment:13 in reply to: ↑ 11 Changed 9 years ago by
Just answering as a complement to Florent's answer.
But when i run Sage and test a few commands, Sage doesn't seem to see the QuasiRationalExpression? class i created in /Applications/sage/devel/sagearaichev/sage/combinat/amgf.sage.
To test your code in a Sage session, you will first need to import the good class (or function). For instance :
sage: from sage.combinat.amgf import QuasiRationalExpression
If you would like QuasiRationalExpression
to be already imported once Sage is started, you must add the line from sage.combinat.amgf import QuasiRationalExpression
to the file sage/combinat/all.py
. Note that it is not "à la mode" to add new stuff to all.py files because Sage is very slow to start because of all the things that are imported. If you think a lot of people will use the code, then it might be defendable.
Sébastien
comment:14 Changed 9 years ago by
Thanks for the tips, Florent and Se'bastien. I'll get to work on converting amgf.sage to amgf.py.
Alex
comment:15 Changed 9 years ago by
Hang on, can i somehow use the Sage preparser to automatically convert amgf.sage to amgf.py?
Alex
comment:16 Changed 9 years ago by
Aha! The command 'sage amgf.sage' preparses amgf.sage and saves it as amgf.py. Thank you ask.sagemath.org!
Alex
comment:17 Changed 9 years ago by
 Status changed from needs_work to needs_review
comment:18 Changed 9 years ago by
The patch is empty. I hope you did not lose anything?
Sébastien
Changed 9 years ago by
comment:19 Changed 9 years ago by
Hmm, i couldn't figure out how to add the code to the patch. I tried 'sage hg add amgf.py' as you suggested, Se'bastien, but that didn't work. So i finally copied and pasted it in. I hope that works. Let me know the proper way, yo.
Sorry for the delay.
Alex
comment:20 Changed 9 years ago by
 Cc zaf added
comment:21 Changed 8 years ago by
 Cc tmonteil added
comment:22 Changed 8 years ago by
 Reviewers set to David Loeffler
 Status changed from needs_review to needs_work
Apply trac_10519fixed.patch
(for the patchbot).
Alex's last "patch" wasn't a patch at all, just a Mercurial header with some Python code arbitrarily pasted into it. I've just uploaded a nonbroken version of the patch. I also added the necessary import statements  a file that's supposed to be part of the Sage library can't import the Sage library (with from all_cmdline import *
), since that would lead to an infinite loop, so the necessary imports have to be done onebyone.
The patch now passes doctests on my machine, but there are some worrying errors that came up when I ran a syntax checker on the new file: {{{amgf.py:908: local variable 'R' is assigned to but never used amgf.py:909: local variable 'd' is assigned to but never used amgf.py:1070: local variable 'Ht' is assigned to but never used amgf.py:1251: local variable 'Ht' is assigned to but never used amgf.py:1591: undefined name 'n' amgf.py:2199: local variable 'H' is assigned to but never used amgf.py:2242: undefined name 'verdict' }}} The "undefined name" errors tend to suggest that some cases have bugs in them, *and* those cases are not checked in any doctest, which is a double whammy. Hence "needs work".
comment:23 Changed 8 years ago by
Sorry, that list got mangled. It should be
amgf.py:908: local variable 'R' is assigned to but never used amgf.py:909: local variable 'd' is assigned to but never used amgf.py:1070: local variable 'Ht' is assigned to but never used amgf.py:1251: local variable 'Ht' is assigned to but never used amgf.py:1591: undefined name 'n' amgf.py:2199: local variable 'H' is assigned to but never used amgf.py:2242: undefined name 'verdict'
comment:24 Changed 8 years ago by
Thanks for your review, David. This patch was my first on Sage Trac and i've since learned a lot, thanks to the constructive feedback of fellow Sagers such as yourself.
Since amgf.py was somewhat of a code bomb, i decided to split it up into simpler pieces, submit those pieces, and, once they get accepted, recombine them. If you or anyone else would like to help me in this endeavor, check out the latest amgf piece at http://trac.sagemath.org/sage_trac/ticket/12417.
Thanks!
I'll keep you all updated on the progress of amgf with these comments.
comment:25 Changed 7 years ago by
 Status changed from needs_work to needs_review
comment:26 Changed 7 years ago by
Apply only trac_10519.2.patch
comment:27 Changed 7 years ago by
 Status changed from needs_review to needs_work
 Work issues set to coverage, trailing whitespace
 Please ensure that every function is doctested
 Please remove all trailing whitespaces
Changed 7 years ago by
comment:28 Changed 7 years ago by
 Description modified (diff)
I have removed all whitespaces in the new patch. All test pass.
BUT there remains 6 procedures with no doctest. Remember that it is neccesary to have 100% doctesting.
Also the name amgf is not good. It should be changed to something more descriptive.
comment:29 Changed 7 years ago by
 Work issues changed from coverage, trailing whitespace to coverage
comment:30 Changed 7 years ago by
Thanks, folks. I'll document those outstanding 6 procedures within a week.
comment:31 Changed 7 years ago by
Hmm, i might take longer, because now that i've upgraded to Sage 5.3, i can't create a Sage clone :( See http://ask.sagemath.org/question/1821/cantcreatesagecloneagain.
comment:32 Changed 7 years ago by
Still can't create a Sage clone. In the meantime, here's my patch as a Python file (which i tested on Sage 5.3 with sage t long) for anyone who wants to review it: https://www.dropbox.com/s/fcxsbuw119qclxt/trac_10519v4.py.
Changed 7 years ago by
comment:33 Changed 7 years ago by
 Status changed from needs_work to needs_review
comment:35 Changed 7 years ago by
 Status changed from needs_review to needs_work
 Work issues changed from coverage to failing tests, trailing whitespaces
please remove all trailing whitespaces
please correct the failing doctests
comment:36 Changed 7 years ago by
 Description modified (diff)
 Status changed from needs_work to needs_review
apply trac_10519v5.patch
Changed 7 years ago by
comment:37 Changed 7 years ago by
apply trac_10519v5.patch
Changed 7 years ago by
comment:38 Changed 7 years ago by
Hmm, i don't understand why i didn't get any test errors when i submitted v4. Anyway, fixed the errors.
comment:39 Changed 7 years ago by
 Work issues failing tests, trailing whitespaces deleted
comment:41 Changed 7 years ago by
well, now version V5 works and version V6 does not pass the tests.
I had already made all the necessary corrections in version V5.
Can we just forget version V6 ?
comment:42 Changed 7 years ago by
OK, let's forget V6. I bet the problem is one or two docstring lines that output a dictionary. The random order of the keys is causing a test failure when it doesn't match up with the docstring key order. We can fix that by sorting the keys before printing them.
comment:44 Changed 7 years ago by
 Cc dkrenn added
comment:45 Changed 7 years ago by
Hi folks, is this patch ready to be added to Sage? If not, what's the next step?
comment:46 Changed 7 years ago by
The next step would be that somebody interested does a real review of this patch. This means looking seriously at the code, using the functions, trying to find bugs, and so on. I am not candidate, sorry.
comment:47 Changed 7 years ago by
Here is the report of pyflakes : some things that need to be corrected
sage/combinat/asymptotics_multivariate_generating_functions.py:147: 'UniqueFactorizationDomains' imported but unused sage/combinat/asymptotics_multivariate_generating_functions.py:156: 'CartesianProduct' imported but unused sage/combinat/asymptotics_multivariate_generating_functions.py:171: 'ZZ' imported but unused sage/combinat/asymptotics_multivariate_generating_functions.py:172: redefinition of unused 'PolynomialRing' from line 148 sage/combinat/asymptotics_multivariate_generating_functions.py:175: 'SageObject' imported but unused sage/combinat/asymptotics_multivariate_generating_functions.py:1719: local variable 'Ht' is assigned to but never used sage/combinat/asymptotics_multivariate_generating_functions.py:2097: local variable 'Ht' is assigned to but never used sage/combinat/asymptotics_multivariate_generating_functions.py:2992: local variable 'X' is assigned to but never used sage/combinat/asymptotics_multivariate_generating_functions.py:3083: undefined name 'Subsets'
comment:48 Changed 7 years ago by
 Status changed from needs_review to needs_work
 Work issues set to pyflakes report
Changed 7 years ago by
comment:49 Changed 7 years ago by
Thanks. Fixed.
comment:50 Changed 7 years ago by
 Status changed from needs_work to needs_review
comment:51 Changed 7 years ago by
 Description modified (diff)
 Work issues pyflakes report deleted
for the bot
Apply trac_10519v7.patch
comment:52 Changed 6 years ago by
 Milestone changed from sage5.11 to sage5.12
comment:53 followup: ↓ 54 Changed 6 years ago by
It does not seems to be properly integrated into sage:
sage: from sage.combinat.asymptotics_multivariate_generating_functions import *  ImportError Traceback (most recent call last) <ipythoninput13a279f9ff0e0> in <module>() > 1 from sage.combinat.asymptotics_multivariate_generating_functions import * ImportError: No module named asymptotics_multivariate_generating_functions sage:
and indeed, you can see that the patch should be for 'sage/combinat' directory, not for './'. Unless this is meant to go to the "combinat queue"  and I have no clue how such reviews are meant to happen and how the corresponding code "admin" should look like.
Question: how much of this is dependent upon the "combinat queue"?
comment:54 in reply to: ↑ 53 ; followup: ↓ 55 Changed 6 years ago by
Replying to dimpase:
Yes, the patch should be for sage/combinat
. Feel free to change that, if you'd like to review the patch now. Otherwise, i'll change it when i get some time in the next week.
It does not seems to be properly integrated into sage:
sage: from sage.combinat.asymptotics_multivariate_generating_functions import *  ImportError Traceback (most recent call last) <ipythoninput13a279f9ff0e0> in <module>() > 1 from sage.combinat.asymptotics_multivariate_generating_functions import * ImportError: No module named asymptotics_multivariate_generating_functions sage:and indeed, you can see that the patch should be for 'sage/combinat' directory, not for './'. Unless this is meant to go to the "combinat queue"  and I have no clue how such reviews are meant to happen and how the corresponding code "admin" should look like.
Question: how much of this is dependent upon the "combinat queue"?
comment:55 in reply to: ↑ 54 Changed 6 years ago by
Replying to araichev:
Replying to dimpase:
Yes, the patch should be for
sage/combinat
. Feel free to change that, if you'd like to review the patch now. Otherwise, i'll change it when i get some time in the next week.
One should use lazy_import
in sage/combinat/all.py
to import the stuff in this patch, rather than
forcing the user to do the explicit import
Question: how much of this is dependent upon the "combinat queue"?
So, how much, if anything at all?
comment:56 Changed 6 years ago by
 Milestone changed from sage6.1 to sage6.2
comment:57 followups: ↓ 58 ↓ 60 Changed 6 years ago by
 Branch set to public/combinat/analytic10519
 Commit set to 60b93376cbb072a1aab99646806555830799468f
Here's a git branch version along with some extensive review changes to the documentation. I made some internal methods private to cleanup the namespace (i.e. what you get with tab completion). I also made stuff python 3 compatible. Unfortunately I also cannot really give a good review to the mathematics behind this.
@Dima, I think you've misunderstood what the combinat queue is. However it's moot because we are no longer using hg.
New commits:
b01625d  10519: Removed unused modules and variables

443ab74  Work on cleaning up documentation.

7f9b89e  Merge branch 'develop' into public/combinat/analytic10519

40dacc9  Review changes and added new file to documentation.

60b9337  Tweaked print statements and list().

comment:58 in reply to: ↑ 57 Changed 6 years ago by
Hooray! Thanks heaps, @tscrim.
Replying to tscrim:
Here's a git branch version along with some extensive review changes to the documentation. I made some internal methods private to cleanup the namespace (i.e. what you get with tab completion). I also made stuff python 3 compatible. Unfortunately I also cannot really give a good review to the mathematics behind this.
@Dima, I think you've misunderstood what the combinat queue is. However it's moot because we are no longer using hg.
New commits:
b01625d 10519: Removed unused modules and variables
443ab74 Work on cleaning up documentation.
7f9b89e Merge branch 'develop' into public/combinat/analytic10519
40dacc9 Review changes and added new file to documentation.
60b9337 Tweaked print statements and list().
comment:59 Changed 6 years ago by
Why does one need these FFPD and FFPDSum classes? Are Sage's multivariate rational functions not good enough? One should have an interface between these FFPD and FFPDSum and "normal" Sage's rational functions, anyway.
Also, I think that the part that computes decomposition(s) of rational functions must be factored out (and put on another ticket, and they should not be in combinat/, as this has noting to do with combinatorics). It has independent uses, which need not have anything to do with the stated purpose of this ticket.
comment:60 in reply to: ↑ 57 ; followup: ↓ 61 Changed 6 years ago by
Replying to tscrim:
@Dima, I think you've misunderstood what the combinat queue is. However it's moot because we are no longer using hg.
Travis, I think already in 2010 I knew what the combinat queue is ;)
Somehow, when reading the code, something made me wonder if this code depends on some features from (what was formerly known as?) combinat queue. I'm happy to know that it's not the case.
comment:61 in reply to: ↑ 60 Changed 6 years ago by
Replying to dimpase:
Replying to tscrim:
@Dima, I think you've misunderstood what the combinat queue is. However it's moot because we are no longer using hg.
Travis, I think already in 2010 I knew what the combinat queue is ;)
Somehow, when reading the code, something made me wonder if this code depends on some features from (what was formerly known as?) combinat queue. I'm happy to know that it's not the case.
Ah sorry, it seemed to me from comment:53 like there was a misunderstanding. I'm also happy there's no dependence on any patches that are in the (now unused) queue that we might have to untangle.
comment:62 Changed 6 years ago by
 Milestone changed from sage6.2 to sage6.3
comment:63 Changed 6 years ago by
 Status changed from needs_review to needs_work
 Work issues set to rebase
comment:64 Changed 6 years ago by
 Commit changed from 60b93376cbb072a1aab99646806555830799468f to 7511d1454940e11462bf07452c745638fd48d95a
Branch pushed to git repo; I updated commit sha1. New commits:
7511d14  Merge branch 'public/combinat/analytic10519' of ssh://trac.sagemath.org:22/sage into 10519

comment:65 Changed 6 years ago by
 Status changed from needs_work to needs_review
comment:66 followup: ↓ 93 Changed 6 years ago by
Hi,
Just read the code and glance some remarks. The code looks very interesting but I have some advices/questions.
 as a matter of uniformization class name are better expanded (
FractionWithFactoredPolynomialDenominator
instead ofFFPD
) cartesian_product_iterator
will be very soonly deprecated, so useproduct
from the Pythonitertools
module instead. it is generally bad practice to have such a big import list at the begining of the file (because of potential circular import). Moreover some of them can be completely avoided:
L = FractionField(PolynomialRing(K, indets))
can bePolynomialRing(K, indets).fraction_field()
.
More seriously:
 I do not understand the specifications. It is said that the numerator must be an element p of a 0 or 1 variate factorial polynomial ring R but you have examples involving
cos(x)
. What is the underlying polynomial ring in that case?  repeating comment:59, Why there is a need for the class
FFDP
? Why isn't it directly implemented as the level of fractions of polynomials? It would makes sense to cache the factorization of the denominator if it is required in several places, but I do not see the point of theFFDP
class.  Some of the method needs definition:
critical_cone
,is_convenient_multiple_point
, ...  Some of the method would better be hidden:
combine_like_terms
, ...
Best Vincent
comment:67 followup: ↓ 68 Changed 6 years ago by
Hi folks, because of my new work and responsibilities outside the realm of analytic combinatorics and Sage, i've needed to put this project on hold indefinitely. Please feel free to change the code as you like. I hope i've documented it well enough with comments and references so that others can carry it to fruition.
comment:68 in reply to: ↑ 67 ; followup: ↓ 69 Changed 6 years ago by
Replying to araichev:
Hi folks, because of my new work and responsibilities outside the realm of analytic combinatorics and Sage, i've needed to put this project on hold indefinitely. Please feel free to change the code as you like. I hope i've documented it well enough with comments and references so that others can carry it to fruition.
Hey Alexei,
Good luck with your new work. I will read it carefully and see what I can do. It is definitely a good piece of work.
Vincent
comment:69 in reply to: ↑ 68 ; followup: ↓ 70 Changed 6 years ago by
Replying to vdelecroix:
Replying to araichev:
Hi folks, because of my new work and responsibilities outside the realm of analytic combinatorics and Sage, i've needed to put this project on hold indefinitely. Please feel free to change the code as you like. I hope i've documented it well enough with comments and references so that others can carry it to fruition.
Hey Alexei,
Good luck with your new work.
Yes, good luck with your new work.
I will read it carefully and see what I can do. It is definitely a good piece of work.
Vincent (or Dima), will you be able to check the math for this ticket? If not, I think I could go through it mathwise.
On the code front:
 Since there are only two classes, I agree with you that we should spell it out.
 Similar for changing to the builtin python tools.
 However I think the big import statement is okay since this is going to be a leaf (or at least on a short branch) of the import tree/poset/digraph.
 What methods do you think should be private?
 What can I do codewise to help get this in?
comment:70 in reply to: ↑ 69 ; followup: ↓ 76 Changed 6 years ago by
Replying to tscrim:
Replying to vdelecroix:
Replying to araichev:
Hi folks, because of my new work and responsibilities outside the realm of analytic combinatorics and Sage, i've needed to put this project on hold indefinitely. Please feel free to change the code as you like. I hope i've documented it well enough with comments and references so that others can carry it to fruition.
Hey Alexei,
Good luck with your new work.
Yes, good luck with your new work.
I will read it carefully and see what I can do. It is definitely a good piece of work.
Vincent (or Dima), will you be able to check the math for this ticket? If not, I think I could go through it mathwise.
please see my #comment:59
IMHO refactoring and interfacing with Sage's facilities for rational functions is due, before this can be merged.
comment:71 Changed 5 years ago by
 Milestone changed from sage6.3 to sage6.4
comment:72 Changed 5 years ago by
 Branch changed from public/combinat/analytic10519 to public/combinat/analytic10519on6.3
comment:73 Changed 5 years ago by
 Commit changed from 7511d1454940e11462bf07452c745638fd48d95a to 28057320fe66a23041b55a7769e4607ca4d8abbd
comment:74 followup: ↓ 79 Changed 5 years ago by
 Dependencies set to #16848
There is a doctest (and the doctest using the result below) failing:
sage t src/sage/combinat/asymptotics_multivariate_generating_functions.py ********************************************************************** File "src/sage/combinat/asymptotics_multivariate_generating_functions.py", line 90, in sage.combinat.asymptotics_multivariate_generating_functions Failed example: s Expected: [{x: 1, y: 1}] Got: []
This is now #16848.
comment:75 Changed 5 years ago by
 Reviewers changed from David Loeffler to Daniel Krenn, David Loeffler
comment:76 in reply to: ↑ 70 Changed 5 years ago by
Replying to dimpase:
Replying to tscrim:
Vincent (or Dima), will you be able to check the math for this ticket? If not, I think I could go through it mathwise.
At least, I started checking the math.
IMHO refactoring and interfacing with Sage's facilities for rational functions is due, before this can be merged.
Yes, this should be definitely done.
comment:77 Changed 5 years ago by
 Work issues rebase deleted
comment:78 Changed 5 years ago by
 Commit changed from 28057320fe66a23041b55a7769e4607ca4d8abbd to 8bc997179b09a47eb0b23fc3c623ec8b92391e8f
Branch pushed to git repo; I updated commit sha1. New commits:
8bc9971  fixed broken doctest

comment:79 in reply to: ↑ 74 Changed 5 years ago by
Replying to dkrenn:
There is a doctest (and the doctest using the result below) failing:
sage t src/sage/combinat/asymptotics_multivariate_generating_functions.py ********************************************************************** File "src/sage/combinat/asymptotics_multivariate_generating_functions.py", line 90, in sage.combinat.asymptotics_multivariate_generating_functions Failed example: s Expected: [{x: 1, y: 1}] Got: []This is now #16848.
This works now (by a workaround).
comment:80 Changed 5 years ago by
 Dependencies #16848 deleted
 Status changed from needs_review to needs_work
comment:81 Changed 5 years ago by
 Commit changed from 8bc997179b09a47eb0b23fc3c623ec8b92391e8f to 4a71e9c6c447323c20b7b0904e62084abad15c98
Branch pushed to git repo; I updated commit sha1. New commits:
4a71e9c  Merge branch 'public/combinat/analytic10519on6.3' of ssh://trac.sagemath.org:22/sage into 6.5.b4

comment:82 Changed 5 years ago by
I'm currently porting the code to Sage's parent/element framework.
comment:83 followup: ↓ 86 Changed 5 years ago by
My pep8 compliant branch is now available at "u/chapoton/10519".
I am not sure it will be easy to merge it with your other changes. Maybe it is not worth the trouble.
comment:84 Changed 5 years ago by
 Branch changed from public/combinat/analytic10519on6.3 to public/combinat/10519
comment:85 Changed 5 years ago by
 Commit changed from 4a71e9c6c447323c20b7b0904e62084abad15c98 to a54855dfb4c9855d2facb682542c5058534a276c
Last 10 new commits:
94d860d  implement equality testing (using coercion model)

38b0f7e  coercion from other FFPD rings implemented

c37addd  trac #10519 pep8 fully compliant

79e88d1  moved code like in "9914678  moved static methods to parent" to allow merging

53d60ea  Merge branch 'u/chapoton/10519' into t/10519on6.5.beta4

6a326a2  fixed doctests (ordering of dicts has changed)

494cd16  fixed doctests (x and y are ordered as y, x)

8dc6311  clauses for "R is None" removed

9654c94  restructure import of libraries

a54855d  update authors, copyright; new reference; some empty lines inserted

comment:86 in reply to: ↑ 83 ; followup: ↓ 88 Changed 5 years ago by
I've uploaded what I have up to now. There is one major change, namely transitioning to Sage's parent/element framework. There are a couple of minor issues to fix left and some doctests are still failing (this is due to using a wrong base ring...)
Replying to chapoton:
My pep8 compliant branch is now available at "u/chapoton/10519". I am not sure it will be easy to merge it with your other changes. Maybe it is not worth the trouble.
I've merged your changes/branch (most of them manually; I think I've got all but please check if in doubt).
In "u/chapoton/10519" Sage 6.5.beta4 was merged, which made some doctests failing. I've created a commit fixing most of them, but there is one annoying issue: The doctest in line 3672
DD = FFDR._diff_op(A, B, AB_derivs, T, M, 1, 2)
takes now forever (over 45 seconds compared to 1.78 seconds before). Does someone has an idea what between 6.3 and 6.5.beta4 could trigger this?
comment:87 Changed 5 years ago by
 Commit changed from a54855dfb4c9855d2facb682542c5058534a276c to 301843b542aa2a6d326e394853ea3b1de0af2e6e
Branch pushed to git repo; I updated commit sha1. New commits:
301843b  fixed long doctest (introduced in c37addd  trac #10519 pep8 fully compliant)

comment:88 in reply to: ↑ 86 Changed 5 years ago by
Replying to dkrenn:
Replying to chapoton:
My pep8 compliant branch is now available at "u/chapoton/10519".
In "u/chapoton/10519" [...] The doctest in line 3672
DD = FFDR._diff_op(A, B, AB_derivs, T, M, 1, 2)takes now forever (over 45 seconds compared to 1.78 seconds before). Does someone has an idea what between 6.3 and 6.5.beta4 could trigger this?
Finally found the problem; wasn't the Sage upgrade, but commit c37addd "trac #10519 pep8 fully compliant", which simplified
if something != Integer(0):
to
if something:
which made this test slow (don't know why...). Anyhow, pushed a commit which fixes this.
comment:89 Changed 5 years ago by
Oops, sorry for this. I thought it was simpler. I do not understand why is is much slower. Anyway, sorry again for the trouble.
comment:90 Changed 5 years ago by
 Commit changed from 301843b542aa2a6d326e394853ea3b1de0af2e6e to 898a1c63ed95aa3c1250727c1c4c9e637f71f26a
comment:91 Changed 5 years ago by
 Commit changed from 898a1c63ed95aa3c1250727c1c4c9e637f71f26a to b0b5c3f303c913687a26f6cacd9c1691b0135f96
Branch pushed to git repo; I updated commit sha1. New commits:
5e77b11  short code simplification (FractionField) (comment:66 of #10519)

438bd66  make combine_like_terms private (comment:66 of #10519)

c2b0dab  allow coercion from fraction field of polynomial rings

41e9956  rename FFPDElement and FFPDSum

b0b5c3f  repr of FractionWithFactoredDenominatorSum returns + between terms

comment:92 Changed 5 years ago by
 Commit changed from b0b5c3f303c913687a26f6cacd9c1691b0135f96 to 974d997af25eb9239d016da2667e38d47b7baa8c
Branch pushed to git repo; I updated commit sha1. New commits:
a7da403  remove .list, since not needed any may lead to confusion

a3bc051  some small changes in code during review

edd992f  add doc (so that it is built automatically)

605e62d  changes in docstrings during review

974d997  make coerce_point private

comment:93 in reply to: ↑ 66 Changed 5 years ago by
During review I've worked over the code and ported it to Sage's parent/element framework.
Here are comments to the comments above:
Replying to vdelecroix:
 as a matter of uniformization class name are better expanded (
FractionWithFactoredPolynomialDenominator
instead ofFFPD
)
Renaming done.
cartesian_product_iterator
will be very soonly deprecated, so useproduct
from the Pythonitertools
module instead.
itertools
are now used here.
 it is generally bad practice to have such a big import list at the begining of the file (because of potential circular import). Moreover some of them can be completely avoided:
L = FractionField(PolynomialRing(K, indets))
can bePolynomialRing(K, indets).fraction_field()
.
Moved imports to functions. Only a very few global (in the module) imports are left.
More seriously:
 I do not understand the specifications. It is said that the numerator must be an element p of a 0 or 1 variate factorial polynomial ring R but you have examples involving
cos(x)
. What is the underlying polynomial ring in that case? repeating comment:59, Why there is a need for the class
FFDP
? Why isn't it directly implemented as the level of fractions of polynomials? It would makes sense to cache the factorization of the denominator if it is required in several places, but I do not see the point of theFFDP
class.
The numerator can be any element from a ring into which the denominator coerces in. E.g. the denominator is a polynomial ring, but numerator is allowed to be out of the symbolic ring.
 Some of the method needs definition:
critical_cone
,is_convenient_multiple_point
, ...
Tried a bit of rephrasing, but they are defined in the cited works.
 Some of the method would better be hidden:
combine_like_terms
, ...
Done. (also some other functions/methods were made private).
Concerning the review:
 I've did a basic check on the mathematics: seems to be ok.
 I've read the docstrings and modified some of them either to make them clearer or to fit the guidelines in the developer guide (e.g. INPUT/OUTPUT blocks and so on). This is fine for me here (but documentation can, of course, always be improved ;) ).
 Documentation builds.
 All doctests pass.
 I'm towards a positive review, but, of course, someone has to cross review my transition of the code to parent/element framework.
Therefore: needs crossreview '''
comment:94 Changed 5 years ago by
 Status changed from needs_work to needs_review
comment:95 followups: ↓ 96 ↓ 103 ↓ 107 Changed 5 years ago by
Just two minor comments:
 If
FractionWithFactoredDenominatorRing
is intended to actually be a ring, shouldn't the numerators also be restricted to some given parent? (i.e., shouldn't there be anumerator_ring
and adenominator_ring
, or something like that, instead of just aring
?)  Isn't at least some of the code generalpurpose enough that it could live in
rings/
orsymbolic/
rather thancombinat/
? If not, perhaps it would be worth at least linking to it from the documentation of related objects.
comment:96 in reply to: ↑ 95 ; followup: ↓ 106 Changed 5 years ago by
Replying to mmezzarobba:
 Isn't at least some of the code generalpurpose enough that it could live in
rings/
orsymbolic/
rather thancombinat/
? If not, perhaps it would be worth at least linking to it from the documentation of related objects.
I have mentioned that in an old comment; IMHO the code must be refactored: the code to decompose a rational function into a sum must not live in combinat/.
comment:97 Changed 5 years ago by
 Status changed from needs_review to needs_work
comment:98 followup: ↓ 108 Changed 5 years ago by
Moreover, I could reproduce the results from the four doctests of univariate_decomposition
using the existing QuotientFields.element_class.partial_fraction_decomposition
and Expression.partial_fraction
functionality. So, why not use these?
comment:99 Changed 4 years ago by
 Commit changed from 974d997af25eb9239d016da2667e38d47b7baa8c to 1c995c5f965e6218f4e1f47082106d616be027ac
comment:100 Changed 4 years ago by
Merged in current stable SageMath 6.8
comment:101 Changed 4 years ago by
 Commit changed from 1c995c5f965e6218f4e1f47082106d616be027ac to a62ed348cc2fe2c9eafee35d7fcab42ee90f7000
comment:102 Changed 4 years ago by
Merged in current stable SageMath 7.0
comment:103 in reply to: ↑ 95 Changed 4 years ago by
Replying to mmezzarobba:
 Isn't at least some of the code generalpurpose enough that it could live in
rings/
orsymbolic/
rather thancombinat/
? If not, perhaps it would be worth at least linking to it from the documentation of related objects.
Moved to sage.rings.asymptotic
(which was created last summer for asymptotic expansions #17601) as this seems very suitable.
comment:104 Changed 4 years ago by
 Commit changed from a62ed348cc2fe2c9eafee35d7fcab42ee90f7000 to 6a44c8c436f7227a0bf1bb0dccc0ba94886d5801
Branch pushed to git repo; I updated commit sha1. New commits:
6a44c8c  Trac #10519: update index in doc tree

comment:105 Changed 4 years ago by
 Commit changed from 6a44c8c436f7227a0bf1bb0dccc0ba94886d5801 to 1f21184f37244dbdf0395c75f474e4ca9429557f
Branch pushed to git repo; I updated commit sha1. New commits:
b99c64a  Trac #10519: introduce numerator_ring and denominator_ring

328a75d  Trac #10519: fix doctests

34845ff  Trac #10519: speed up for univariate_decomposition

9699c67  Trac #10519: fix ReST documentation

340c34d  Trac #10519: mark class as experimental

874b4c3  Trac #10519: update authors and copyright

1f21184  Trac #10519: fix indention in ReST

comment:106 in reply to: ↑ 96 Changed 4 years ago by
Replying to dimpase:
Replying to mmezzarobba:
 Isn't at least some of the code generalpurpose enough that it could live in
rings/
orsymbolic/
rather thancombinat/
? If not, perhaps it would be worth at least linking to it from the documentation of related objects.I have mentioned that in an old comment; IMHO the code must be refactored: the code to decompose a rational function into a sum must not live in combinat/.
Changed; now sage.rings.asymptotic
, see comment:103.
comment:107 in reply to: ↑ 95 Changed 4 years ago by
Replying to mmezzarobba:
Just two minor comments:
 If
FractionWithFactoredDenominatorRing
is intended to actually be a ring, shouldn't the numerators also be restricted to some given parent? (i.e., shouldn't there be anumerator_ring
and adenominator_ring
, or something like that, instead of just aring
?)
I agree; now there is.
comment:108 in reply to: ↑ 98 Changed 4 years ago by
Replying to rws:
Moreover, I could reproduce the results from the four doctests of
univariate_decomposition
using the existingQuotientFields.element_class.partial_fraction_decomposition
andExpression.partial_fraction
functionality. So, why not use these?
In univariate_decomposition
the alreadyknown factorization of the denominator is used. This gives a speedup for not too small instances. Below the timings,
 No speedup for the first (small) example in the doctest:
sage: sage: from sage.rings.asymptotic.asymptotics_multivariate_generating_functions import FractionWithFactoredDenominatorRing sage: sage: R.<x> = PolynomialRing(QQ) sage: sage: FFPD = FractionWithFactoredDenominatorRing(R) /local/dakrenn/sage/7.0/local/lib/python2.7/sitepackages/sage/structure/unique_representation.py:1021: FutureWarning: This class/method/function is marked as experimental. It, its functionality or its interface might change without a formal deprecation. See http://trac.sagemath.org/10519 for details. instance = typecall(cls, *args, **options) sage: sage: f = 5*x^3 + 1/x + 1/(x1) + 1/(3*x^2 + 1) sage: sage: ff = FFPD(f) sage: sage: %timeit n 1 r 1 ff.univariate_decomposition() 1 loops, best of 1: 2.24 ms per loop sage: sage: %timeit n 1 r 1 f.partial_fraction_decomposition() 1 loops, best of 1: 1.02 ms per loop
 But adding some more terms, we have a speedup:
sage: sage: from sage.rings.asymptotic.asymptotics_multivariate_generating_functions import FractionWithFactoredDenominatorRing sage: sage: R.<x> = PolynomialRing(QQ) sage: sage: FFPD = FractionWithFactoredDenominatorRing(R) /local/dakrenn/sage/7.0/local/lib/python2.7/sitepackages/sage/structure/unique_representation.py:1021: FutureWarning: This class/method/function is marked as experimental. It, its functionality or its interface might change without a formal deprecation. See http://trac.sagemath.org/10519 for details. instance = typecall(cls, *args, **options) sage: sage: f = 5*x^3 + 1/x + 1/(x1) + 1/(3*x^2 + 1) + 1/(x2) + 1/(x3) + 1/(x4) + 1/(x5) + 1/(x6) + 1/(x7) # + 1/(x8) + 1/(x9) + 1/(x10) + 1/(x11) + 1/(x12) + 1/(x13) sage: sage: ff = FFPD(f) sage: sage: %timeit n 1 r 1 ff.univariate_decomposition() 1 loops, best of 1: 1.53 ms per loop sage: sage: %timeit n 1 r 1 f.partial_fraction_decomposition() 1 loops, best of 1: 3.3 ms per loop
 The second example of the doctest is already faster with
univariate_decomposition
as it is:sage: sage: from sage.rings.asymptotic.asymptotics_multivariate_generating_functions import FractionWithFactoredDenominatorRing sage: sage: R.<x> = PolynomialRing(QQ) sage: sage: FFPD = FractionWithFactoredDenominatorRing(R, SR) /local/dakrenn/sage/7.0/local/lib/python2.7/sitepackages/sage/structure/unique_representation.py:1021: FutureWarning: This class/method/function is marked as experimental. It, its functionality or its interface might change without a formal deprecation. See http://trac.sagemath.org/10519 for details. instance = typecall(cls, *args, **options) sage: sage: f = 5*x^3 + 1/x + 1/(x1) + exp(x)/(3*x^2 + 1) sage: sage: ff = FFPD(f) sage: sage: %timeit n 1 r 1 ff.univariate_decomposition() 1 loops, best of 1: 6.07 ms per loop sage: sage: %timeit n 1 r 1 f.partial_fraction() 1 loops, best of 1: 9.7 ms per loop
I've added a not in the docstring of the method, where this is pointed out.
comment:109 followup: ↓ 110 Changed 4 years ago by
 Commit changed from 1f21184f37244dbdf0395c75f474e4ca9429557f to ae42ad6539aaf99a7986a2bb1c2f018262296d5b
comment:110 in reply to: ↑ 109 Changed 4 years ago by
comment:111 Changed 4 years ago by
 Cc behackl added
 Status changed from needs_work to needs_review
Ticket is again at needs_review
. I've incorporated the comments above; please crossreview these changes.
A short summary (since the ticket is open for over 5 years now): The original code was posted by Alex Raichev. I've reviewed this code about two years ago. Mathematically it is fine, but it had to be included into SageMath better (see comments above). This is now done and from my part a positive review. However, since I made quite a lot of changes, these changes need a crossreview. Note that I've now marked the code as experimental.
comment:112 followup: ↓ 114 Changed 4 years ago by
A few very quick thoughts from a very quick glance:
 Remove input/output blocks that have nothing. IMO this adds clutter to the docstrings.
 How experimental/unstable do you think this code really is?
comment:113 Changed 4 years ago by
 Commit changed from ae42ad6539aaf99a7986a2bb1c2f018262296d5b to 2056884ccadd2eee615c612cb137b5dd7d7a94f2
Branch pushed to git repo; I updated commit sha1. New commits:
2056884  Trac #10519: remove "Nothing" input/output blocks

comment:114 in reply to: ↑ 112 ; followup: ↓ 115 Changed 4 years ago by
Replying to tscrim:
 Remove input/output blocks that have nothing. IMO this adds clutter to the docstrings.
Done.
 How experimental/unstable do you think this code really is?
I think the code is quite stable; AFAIK, Mark Wilson (one of the authors of the corresponding theory behind this) uses basically this code (not from the ticket, but a fork) for his research now for some years. I've marked it "experimental" since it is a new module and the interplay of the code with the whole SageMathinfrastructure was changed on this ticket. This is the part, where there is not that much experience, but this will change once it is in SageMath. If you feel that "experimental" should be remove...I'm fine with any choice.
comment:115 in reply to: ↑ 114 ; followups: ↓ 117 ↓ 118 Changed 4 years ago by
Replying to dkrenn:
Replying to tscrim:
 How experimental/unstable do you think this code really is?
I think the code is quite stable; AFAIK, Mark Wilson (one of the authors of the corresponding theory behind this) uses basically this code (not from the ticket, but a fork) for his research now for some years. I've marked it "experimental" since it is a new module and the interplay of the code with the whole SageMathinfrastructure was changed on this ticket. This is the part, where there is not that much experience, but this will change once it is in SageMath. If you feel that "experimental" should be remove...I'm fine with any choice.
I would be surprised if the (public) API changed much, the current version of the code fits in with the category framework, and it has been/will be (well) reviewed. So I feel that it should not be considered experimental.
We should also update the references (I can do this on my review changes).
comment:116 Changed 4 years ago by
 Commit changed from 2056884ccadd2eee615c612cb137b5dd7d7a94f2 to e3668f46714d262e20b7ab7adc514ac6f8e09cd8
Branch pushed to git repo; I updated commit sha1. New commits:
e3668f4  Trac #10519: Revert "mark class as experimental"

comment:117 in reply to: ↑ 115 Changed 4 years ago by
Replying to tscrim:
Replying to dkrenn:
Replying to tscrim:
 How experimental/unstable do you think this code really is?
[...]
I would be surprised if the (public) API changed much, the current version of the code fits in with the category framework, and it has been/will be (well) reviewed. So I feel that it should not be considered experimental.
Good; I did git revert
on the corresponding commit.
comment:118 in reply to: ↑ 115 Changed 4 years ago by
Replying to tscrim:
We should also update the references (I can do this on my review changes).
Yes, we should. Thanks for doing.
comment:119 Changed 4 years ago by
 Description modified (diff)
 Milestone changed from sage6.4 to sage7.1
comment:120 Changed 4 years ago by
 Commit changed from e3668f46714d262e20b7ab7adc514ac6f8e09cd8 to badafce7372353c16c1b6ca658c183957ac2021b
comment:121 followup: ↓ 123 Changed 4 years ago by
 Reviewers changed from Daniel Krenn, David Loeffler to Daniel Krenn, David Loeffler, Travis Scrimshaw
So I made my pass through the code (finally). I think it looks good with my changes:
 I added a
__classcall_private__
to parse the input forUniqueRepresentation
.  I moved the (other) static methods to separate functions within the module since (IMO) they were not strongly associated with the
FractionWithFactoredDenominatorRing
class. It also allows their doc to be included by default (since they do not have to be _hidden) and allows them to potentially be used outside of the class.  I moved around some of the documentation within methods as I feel the descriptive information should come before the
INPUT
/OUTPUT
blocks. The input signature of the method is the first set of information given by?
and the documentation.  I moved more common imports to the start. There is no danger of circular imports when the file in question is not imported into the global namespace (it is also faster, easier to maintain in the long term, and I'm not as paranoid about these thing).
 Replaced some Sage implementations with there standard python equivalents.
 Other misc changes.
If you're happy with my changes, then you can set a positive review.
Perhaps for a followup, we should figure out what the best way is to expose this functionality into the global namespace. Should we just do a lazy import of FractionWithFactoredDenominatorRing
?
comment:122 Changed 4 years ago by
 Commit changed from badafce7372353c16c1b6ca658c183957ac2021b to a30a18a230a1f77fac00e636b779df8f571eda62
Branch pushed to git repo; I updated commit sha1. New commits:
a30a18a  Trac #10519: two small crossreviewing changes

comment:123 in reply to: ↑ 121 ; followup: ↓ 124 Changed 4 years ago by
 Status changed from needs_review to positive_review
Replying to tscrim:
So I made my pass through the code (finally).
Thank you very much.
 I added a
__classcall_private__
to parse the input forUniqueRepresentation
.
Good; checked.
 I moved the (other) static methods to separate functions within the module since (IMO) they were not strongly associated with the
FractionWithFactoredDenominatorRing
class. It also allows their doc to be included by default (since they do not have to be _hidden) and allows them to potentially be used outside of the class.
I agree that this is a good idea.
 I moved around some of the documentation within methods as I feel the descriptive information should come before the
INPUT
/OUTPUT
blocks. The input signature of the method is the first set of information given by?
and the documentation.
Ok, looks good.
 I moved more common imports to the start. There is no danger of circular imports when the file in question is not imported into the global namespace (it is also faster, easier to maintain in the long term, and I'm not as paranoid about these thing).
I'm fine with it. Just out of curiosity, why is this faster?
 Replaced some Sage implementations with there standard python equivalents.
Ok.
 Other misc changes.
I've checked the diffs (all 200 hunks); LGTM
If you're happy with my changes, then you can set a positive review.
I've added one doctest to make sagecoverage happier and removed one fullstop.
Perhaps for a followup, we should figure out what the best way is to expose this functionality into the global namespace. Should we just do a lazy import of
FractionWithFactoredDenominatorRing
?
Maybe. (A lazy import is indeed suitable.)
I set this to positive; all tests pass, doc builds and looks good.
comment:124 in reply to: ↑ 123 ; followup: ↓ 125 Changed 4 years ago by
Replying to dkrenn:
Replying to tscrim:
 I moved more common imports to the start. There is no danger of circular imports when the file in question is not imported into the global namespace (it is also faster, easier to maintain in the long term, and I'm not as paranoid about these thing).
I'm fine with it. Just out of curiosity, why is this faster?
Every time the function gets called, Python needs to check to see if it has imported the object. While this is more on the level of microoptimization, it can matter in those methods used in a tight loop.
I've added one doctest to make sagecoverage happier and removed one fullstop.
Whoops. Good catch.
Perhaps for a followup, we should figure out what the best way is to expose this functionality into the global namespace. Should we just do a lazy import of
FractionWithFactoredDenominatorRing
?Maybe. (A lazy import is indeed suitable.)
I set this to positive; all tests pass, doc builds and looks good.
We also should remove the deprecation warnings in _element_constructor_
on said followup as I forgot to remove them here.
comment:125 in reply to: ↑ 124 ; followup: ↓ 126 Changed 4 years ago by
Replying to tscrim:
Replying to dkrenn:
Replying to tscrim:
 I moved more common imports to the start. There is no danger of circular imports when the file in question is not imported into the global namespace (it is also faster, easier to maintain in the long term, and I'm not as paranoid about these thing).
I'm fine with it. Just out of curiosity, why is this faster?
Every time the function gets called, Python needs to check to see if it has imported the object. While this is more on the level of microoptimization, it can matter in those methods used in a tight loop.
Ok, thank you for your explanation.
We also should remove the deprecation warnings in
_element_constructor_
on said followup as I forgot to remove them here.
Not a strong preference, but actually, I am for keeping the deprecation for some time. The code of this ticket has been around for about 5 years outside of SageMath (more or less as https://github.com/araichev/amgf), and there the deprecated parameters were used. People who are using this package will transition to the one soon to be included in SageMath, but I think some hints on what to change could be very helpful.
comment:126 in reply to: ↑ 125 Changed 4 years ago by
Replying to dkrenn:
Replying to tscrim:
We also should remove the deprecation warnings in
_element_constructor_
on said followup as I forgot to remove them here.Not a strong preference, but actually, I am for keeping the deprecation for some time. The code of this ticket has been around for about 5 years outside of SageMath (more or less as https://github.com/araichev/amgf), and there the deprecated parameters were used. People who are using this package will transition to the one soon to be included in SageMath, but I think some hints on what to change could be very helpful.
Fair enough. Although I think because it had not been reviewed and included in Sage, it is fair game to change the API. However, I don't have a stake in this, but it is something we will eventually want to remove.
comment:127 followup: ↓ 128 Changed 4 years ago by
 Status changed from positive_review to needs_work
There are some tests that depend on ordering of symbolic variables:
sage t long src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py ********************************************************************** File "src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py", line 98, in sage.rings.asymptotic.asymptotics_multivariate_generating_functions Failed example: s Expected: [{y: 1, x: 1}] Got: [{x: 1, y: 1}] ********************************************************************** File "src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py", line 2828, in sage.rings.asymptotic.asymptotics_multivariate_generating_functions.FractionWithFactoredDenominator.smooth_critical_ideal Failed example: F.smooth_critical_ideal(alpha) Expected: Ideal (y^2 + 2*a1/a2*y  1, x + ((a2)/a1)*y + (a1 + a2)/a1) of Multivariate Polynomial Ring in x, y over Fraction Field of Multivariate Polynomial Ring in a1, a2 over Rational Field Got: Ideal (y^2 + 2*a1/a2*y  1, x + ((a2)/a1)*y + (a2  a1)/a1) of Multivariate Polynomial Ring in x, y over Fraction Field of Multivariate Polynomial Ring in a2, a1 over Rational Field ********************************************************************** File "src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py", line 4373, in sage.rings.asymptotic.asymptotics_multivariate_generating_functions.coerce_point Failed example: p Expected: {y: 7/8, x: 1} Got: {x: 1, y: 7/8} ********************************************************************** File "src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py", line 4375, in sage.rings.asymptotic.asymptotics_multivariate_generating_functions.coerce_point Failed example: for k in sorted(p.keys()): print k, k.parent() Expected: y Symbolic Ring x Symbolic Ring Got: x Symbolic Ring y Symbolic Ring ********************************************************************** 3 items had failures: 1 of 77 in sage.rings.asymptotic.asymptotics_multivariate_generating_functions 1 of 16 in sage.rings.asymptotic.asymptotics_multivariate_generating_functions.FractionWithFactoredDenominator.smooth_critical_ideal 2 of 11 in sage.rings.asymptotic.asymptotics_multivariate_generating_functions.coerce_point [809 tests, 4 failures, 74.86 s]
comment:128 in reply to: ↑ 127 Changed 4 years ago by
Replying to vbraun:
sage t long src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py ********************************************************************** File "src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py", line 98, in sage.rings.asymptotic.asymptotics_multivariate_generating_functions Failed example: s Expected: [{y: 1, x: 1}] Got: [{x: 1, y: 1}]
Hmmm...I thought there is something like a displayhook, which catches such things (orderings in dicts and sets).
********************************************************************** File "src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py", line 4373, in sage.rings.asymptotic.asymptotics_multivariate_generating_functions.coerce_point Failed example: p Expected: {y: 7/8, x: 1} Got: {x: 1, y: 7/8}
The same here...
For the other issues: I am confident to fix.
comment:129 Changed 4 years ago by
 Commit changed from a30a18a230a1f77fac00e636b779df8f571eda62 to f58efc98ea4a1781e64250af5fe08339eaab47c8
Branch pushed to git repo; I updated commit sha1. New commits:
f58efc9  Trac #10519: fix sorting of variables (make it platform independent)

comment:130 Changed 4 years ago by
 Commit changed from f58efc98ea4a1781e64250af5fe08339eaab47c8 to 85c1f3793979b44878c9e729d2e97b29258f2a7c
comment:131 followup: ↓ 133 Changed 4 years ago by
comment:132 followup: ↓ 134 Changed 4 years ago by
I've now fixed all (at least I hope I got all) platformdependent. Can someone please check with other platform than Linux, x86_64 on Intel i54690?
comment:133 in reply to: ↑ 131 Changed 4 years ago by
Replying to vbraun:
The displayhook sorts but x, y have no particular order
Oh, I see (I thought, that display hooks sort by str
in such a case). Thanks.
comment:134 in reply to: ↑ 132 ; followup: ↓ 136 Changed 4 years ago by
Replying to dkrenn:
I've now fixed all (at least I hope I got all) platformdependent. Can someone please check with other platform than Linux, x86_64 on Intel i54690?
I didn't see a difference from the original doctests on my laptop, so I can't give an explicit check. However, from looking over the doctestvs and Volker's failures, this seems to do the trick. Although I don't like the changes on 85c1f37. Instead, I think you should just explicitly check that the dictionary of solutions is the correct one:
sage: s == [{SR(x): 1, SR(y): 1}] True
comment:135 Changed 4 years ago by
 Commit changed from 85c1f3793979b44878c9e729d2e97b29258f2a7c to 3182c5b134f527de94a3728e7394e7fc27014c3e
comment:136 in reply to: ↑ 134 Changed 4 years ago by
Replying to tscrim: Although I don't like the changes on 85c1f37. Instead, I think you should just explicitly check that the dictionary of solutions is the correct one:
sage: s == [{SR(x): 1, SR(y): 1}] True
Reverted and changed; indeed much nicer.
comment:137 Changed 4 years ago by
 Status changed from needs_work to needs_review
comment:139 Changed 4 years ago by
 Commit changed from 3182c5b134f527de94a3728e7394e7fc27014c3e to a951f08123d038f97b809095208bb04c22671a5e
 Status changed from positive_review to needs_review
Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:
a951f08  Trac #10519: trivial ReST error

comment:140 Changed 4 years ago by
 Status changed from needs_review to positive_review
comment:141 Changed 4 years ago by
 Branch changed from public/combinat/10519 to a951f08123d038f97b809095208bb04c22671a5e
 Resolution set to fixed
 Status changed from positive_review to closed
Hi Alex,
I can't address the mathematics on this one, but can give some hints about getting this reviewed.
Doublecolons start verbatim blocks and sometimes print as colons.
Sage code samples needs indentation.
All your functions won't be available in teh global namespace (where they could conflict with other). You should find an object (like maybe some kind of polynomial, especially if it is already int eh combinatorial library?) and make your functions be methods on that object.
Thanks for your contribution  I hope the above is helpful for you.
Rob