#17979 closed defect (fixed)
Reimplementation of IntegerListsLex
Reported by:  Anne Schilling  Owned by:  

Priority:  blocker  Milestone:  sage6.6 
Component:  combinatorics  Keywords:  days64 
Cc:  Nicolas M. Thiéry, Travis Scrimshaw, Nathann Cohen, Vincent Delecroix, Bryan Gillespie  Merged in:  
Authors:  Bryan Gillespie, Anne Schilling, Nicolas M. Thiéry  Reviewers:  Nathann Cohen, Jeroen Demeyer, Travis Scrimshaw 
Report Upstream:  N/A  Work issues:  
Branch:  ea2b006 (Commits, GitHub, GitLab)  Commit:  
Dependencies:  Stopgaps: 
Change History (489)
comment:1 Changed 8 years ago by
Priority:  major → blocker 

comment:2 Changed 8 years ago by
comment:3 followup: 6 Changed 8 years ago by
Some people at Sage Days 64 are planning to work on this. Give us some time!
comment:4 Changed 8 years ago by
Description:  modified (diff) 

Keywords:  days64 added 
comment:5 Changed 8 years ago by
Cc:  Nathann Cohen added 

comment:6 followups: 8 9 Changed 8 years ago by
comment:7 Changed 8 years ago by
Another note: it would be very good if you didn't have any strange conditions on which input is allowed. Mathematically, all combinations of input constraints make sense, so they should all be allowed.
comment:8 followups: 10 45 Changed 8 years ago by
Hi Jeroen,
Replying to jdemeyer:
Replying to aschilling:
Give us some time!
It was a question, not an attack...
Oops, sorry, I guess there just has been a bit too much turmoil on the topic lately :) We just got uncomfortable with the "blocker", for at this stage it's hard to predict how much time this will take (Sage days are great for sprints, but you get easily sidetracked). Any idea when the next release of Sage is likely to come out?
In any cases, here is the current plan. We are having a sprint here to work on reimplementing IntegerListLex? from scratch. We believe it's possible to have a correct iteration algorithm, with complexity roughly linear in the output in the common use cases, that will detect and report any invalid input. There will be situations where computing the next element may run forever. In those cases, we will report beforehand a warning, which the user will be able to silence by signing a waiver after having read the fine prints in the documentation.
If we can use the occasion to get generalizations for free, we will do so; but otherwise we will focus on getting the existing features right. Similarly, we will try to design the algorithm to potentially support cythonization / parallelism / implementation as a standalone C++ library, but postpone those for later.
And we will reuse everything we can from your work!
Cheers,
Nicolas
comment:9 Changed 8 years ago by
Replying to jdemeyer:
Replying to aschilling:
Give us some time!
It was a question, not an attack...
Yes, no problem :) We are discussing the algorithms, so once we are convinced it will all work, there is a group of people here that will try to implement it.
comment:10 Changed 8 years ago by
Replying to nthiery:
We just got uncomfortable with the "blocker", for at this stage it's hard to predict how much time this will take
I made it a blocker not because of this specific ticket, but because something needs to be done: either a proper stopgap needs to be put back (which is essentially reverting #17898), or we switch to my correctbutslow polyhedron implementation, or this ticket needs to be finished.
comment:12 followup: 13 Changed 8 years ago by
Cc:  Vincent Delecroix added 

comment:13 Changed 8 years ago by
Brief update from Sage Days 64: Bryan Gillespie implemented the algorithm we discussed! The code runs and all doc tests pass, including all the previous failures that Jeroen pointed out! The code is still about 10 times slower than the current implementation of IntegerListsLex?, but at least appears to have no bugs and no restrictions any longer on the parameters. We will try to work on making it more efficient.
comment:14 Changed 8 years ago by
Only twice slower now that it uses +inf instead of infinity. infinity really needs to be optimized!
comment:15 followup: 102 Changed 8 years ago by
I would be 1 to using float('inf')
just because it's faster. The Right Thing to do is to use Sage's Infinity
and optimize that.
comment:16 followup: 17 Changed 8 years ago by
Where is the code...?
Given that rc0 has been released, we need to decide on a strategy to fix IntegerListsLex
(either this ticket or a "plan B" if this ticket doesn't get finished).
comment:17 followup: 18 Changed 8 years ago by
Replying to jdemeyer:
Where is the code...?
Given that rc0 has been released, we need to decide on a strategy to fix
IntegerListsLex
(either this ticket or a "plan B" if this ticket doesn't get finished).
I can push the code, but currently the interface with partitions and compositions is still broken and a lot of functions (like next, first etc ) that are also used in integer_vector need to be deprecated. That has not been done yet.
Best,
Anne
comment:18 Changed 8 years ago by
Replying to aschilling:
I can push the code, but currently the interface with partitions and compositions is still broken
How come? I didn't have this issue with #17920.
comment:19 Changed 8 years ago by
Authors:  → Bryan Gillespie, Anne Schilling, Nicolas M. Thiery 

Branch:  → public/ticket/17979 
Commit:  → fb341ea0e6edf9f5958d9d911023c5be201ec9b2 
Last 10 new commits:
3793cc9  17989: added docs for min_part and max_part

b61fc8c  17979 added waiver

afffd99  Merge branch 'develop' into public/ticket/17979

0356dc1  Merge branch 'public/ticket/17979' of trac.sagemath.org:sage into public/ticket/17979

8b9f643  17979 Small changes to IntegerVector and Partition related to floor and ceiling functions in IntegerListsLex

79d0a65  17979 fixed input in integer_matrices

ee0269f  Merge branch 'public/ticket/17979' of trac.sagemath.org:sage into public/ticket/17979

dc26f9d  17979: update integer vectors w.r.t. the new IntegerListLex, using inheritance to reduce the amount of code + cleanup

7333951  17979 fixed doc tests in integer_list_old

fb341ea  Merge branch 'public/ticket/17979' of trac.sagemath.org:sage into ticket/17979

comment:20 Changed 8 years ago by
Commit:  fb341ea0e6edf9f5958d9d911023c5be201ec9b2 → a3244c09abcea9c9d25fe5043d340692096ccd90 

comment:21 Changed 8 years ago by
Commit:  a3244c09abcea9c9d25fe5043d340692096ccd90 → e91350397834e04c939029b6677a51da25231194 

comment:22 Changed 8 years ago by
Commit:  e91350397834e04c939029b6677a51da25231194 → 865a2af4abb9c5a677990c54e435c5d6861f3cf5 

comment:23 Changed 8 years ago by
Commit:  865a2af4abb9c5a677990c54e435c5d6861f3cf5 → 6153cf8d39dc23cb41a3d0c2ea66ba5dc3abd2c0 

comment:24 Changed 8 years ago by
Here are the failures I got upon make ptestlong:
sage t long src/sage/doctest/test.py # 1 doctest failed sage t long src/sage/tests/interrupt.pyx # 1 doctest failed sage t long src/sage/parallel/decorate.py # 1 doctest failed sage t long src/sage/schemes/elliptic_curves/lseries_ell.py # Timed out sage t long src/sage/modular/arithgroup/arithgroup_perm.py # Timed out sage t long src/sage/sets/set_from_iterator.py # 3 doctests failed sage t long src/sage/combinat/words/words.py # 5 doctests failed sage t long src/sage/algebras/weyl_algebra.py # 3 doctests failed
The last three are diagnosed (the new IntegerListLex? was missing the feature of accepting an iterable for n) and is being fixed. The rest look more like unrelated failures.
comment:25 Changed 8 years ago by
Status:  new → needs_review 

Work issues:  → support n in an iterable 
comment:26 Changed 8 years ago by
Status:  needs_review → needs_work 

comment:27 followups: 28 54 55 65 Changed 8 years ago by
Helloooooooooooo,
Here are some comments (mostly doc) about the current branch
 About
An integer list is a list l of nonnegative integers, its parts. The length of l is the number of its parts Note Two valid integer lists are considered equivalent if they only differ by trailing zeroes.
Unless the length of a list is the number of its nonzero entries, it does not seem to be properly defined.
The constraints on the lists are as follows:
 in what follows you use a variablel
often (probably one of the lists): could you say so explicitly?
 It seems that currently the method accepts input that does not satisfy the constraints that you list, i.e.:
sage: IntegerListsLex(min_n=4) Integer lists of sum between 4 and 0 satisfying certain constraints sage: list(IntegerListsLex(min_n=4)) []
Should they really be considered as 'constraints', if the code accepts them and returns sensible output (i.e. empty sets)? When I read those lines, I expected the code to raise a
ValueError
exception on them.
Lower and upper bounds
: the text about constant values for floor/ceiling belongs to the INPUT block.
waiver
 the description ofwaiver
in the INPUT block is very mysterious. If it is only meant for internal purposes, could you say so in its description?
Next we obtain all lists of sum 4 and length 4 such that l[i] <= i:
 missing backticks at the end.
 Comparative timings: should they really appear in the function's documentation? To me the trac ticket is the right place for that.
 There are two 'TESTS' sections
self.warning = False # warning for dangerous (but possibly valid) usage
 could say what this flag does?
 the INPUT blocks says that
n
can be a list. Could you add there an explanation of what it means?
 About the message
warn("""When the user specifies a method, then (s)he is responsible that the algorithm will not hang. Also note that the specified function should start at 0 rather than 1. Before trac#17979 the indexing was ambiguous and sometimes started at 1.""")
From time to time we receive bug reports on sagedevel or sagesupport in which the users beg us to forgive them in case what they think might be a bug could actually be their mistake. Could this message be changed to something more
technical
? Something like `you defined ceiling=[...] to be a function, and we cannot swear that this call will not hang`?
 About the copyright header: I never saw any patch remove the name of other persons in a copyright header. Don't know what the policy is.
# Copyright (C) 2007 Mike Hansen <mhansen@gmail.com>, # Copyright (C) 2012 Travis Scrimshaw <tscrim@ucdavis.edu> +# Copyright (C) 2015 Bryan Gillespie <Brg008@gmail.com>,
Thanks,
Nathann
comment:28 followup: 29 Changed 8 years ago by
Replying to ncohen:
 About the copyright header: I never saw any patch remove the name of other persons in a copyright header.
That's not really true, there are many tickets which just remove whole modules, including the copyright header. If the whole module is completely rewritten (but only then), it's valid to remove the copyright header.
comment:29 Changed 8 years ago by
That's not really true, there are many tickets which just remove whole modules, including the copyright header. If the whole module is completely rewritten (but only then), it's valid to remove the copyright header.
Okay, no prob then.
comment:30 Changed 8 years ago by
I would prefer min_sum
and max_sum
instead of min_n
and max_n
(n
is just a letter and doesn't mean anything). I also think the defaults should be 0
and Infinity
instead of 0
and 0
.
In this case, you probably do not need support for iteratable n
since (AFAIK) all cases of iterables are really intervals and can be specified with min_sum
and max_sum
instead.
comment:31 Changed 8 years ago by
Replace
list(IntegerListsLex(4, length = 4, ceiling = lambda i: i, waiver=True))
by
list(IntegerListsLex(4, length=4, ceiling=lambda i: i, waiver=True))
and the same for similar places.
comment:32 Changed 8 years ago by
There should be empty lines between the bullet points in the INPUT
block.
comment:33 followup: 163 Changed 8 years ago by
The heading should be formatted like http://www.sagemath.org/doc/developer/coding_basics.html#headingsofsagelibrarycodefiles (in particular, it's bad to mention the GPL without version number).
comment:34 followup: 68 Changed 8 years ago by
Why do you want to supporting floor
and ceiling
being a number? We already have min_part
and max_part
for that.
comment:35 Changed 8 years ago by
Is this still true?
This is a generic low level tool. The interface has been designed with efficiency in mind. It is subject to incompatible changes in the future. More user friendly interfaces are provided by high level tools like :class:`Partitions` or :class:`Compositions`.
comment:36 followup: 69 Changed 8 years ago by
Is this really true?
Before trac#17979 the indexing was ambiguous and sometimes started at 1.
comment:37 Changed 8 years ago by
Use newstyle doctest formatting: indent with ....:
instead of ...
comment:38 Changed 8 years ago by
I agree with Nathann that the stuff about timings should be removed.
comment:39 followups: 70 133 Changed 8 years ago by
There is still this bug:
sage: it = iter(IntegerListsLex(4)) sage: for _ in range(20): print next(it) [4] [3, 1] [3, 0, 1] [3, 0, 0, 1] [3, 0, 0, 0, 1] [3, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1]
It seems that [1,3]
will never appear in the output!
comment:40 followups: 43 88 Changed 8 years ago by
This takes forever, even though the list trivially contains just one element:
sage: IntegerListsLex(10^100, max_length=1).list()
comment:41 followup: 176 Changed 8 years ago by
Some implementations might not use keyword arguments for length
, so the min_n
and max_n
arguments (preferably renamed to min_sum
and max_sum
) should be moved towards the end of the argument list.
comment:42 Changed 8 years ago by
I would prefer negative values of min_part
, max_part
to raise a NotImplementedError
since the question makes sense mathematically, it's just not implemented.
comment:44 Changed 8 years ago by
Note that this example is instant with #17920:
sage: IntegerLists(10^100, max_length=1).list()
comment:45 followups: 97 154 Changed 8 years ago by
comment:46 followup: 89 Changed 8 years ago by
Remove
from sage.structure.list_clone import ClonableArray from sage.rings.integer import Integer
comment:47 Changed 8 years ago by
This comment is silly:
In the following example, the floor conditions do not satisfy the slope conditions since the floor for the third part is also 3. The algorithm will nonetheless give the correct result::
comment:48 followup: 71 Changed 8 years ago by
I dislike the fact that the warning shows even in cases where the output is obviously finite:
sage: IntegerListsLex(5, ceiling=lambda i:i, length=5) /usr/local/src/sageconfig/local/lib/python2.7/sitepackages/sage/combinat/integer_list.py:606: UserWarning: When the user specifies a method, then (s)he is responsible that the algorithm will not hang. Also note that the specified function should start at 0 rather than 1. Before trac#17979 the indexing was ambiguous and sometimes started at 1. Before trac#17979 the indexing was ambiguous and sometimes started at 1.""") Integer lists of sum 5 satisfying certain constraints
Also note that the formatting of the warning is not quite right.
comment:50 followup: 52 Changed 8 years ago by
It's a pity that this code is sometimes very fast and sometimes very slow depending on the input. My approach #17920 was slower, but in a more "uniform" way, never so slow that it was unusable.
comment:51 followup: 95 Changed 8 years ago by
What is IntegerVectors
and why is it not an alias of IntegerListsLex
?
comment:52 followup: 63 Changed 8 years ago by
It's a pity that this code is sometimes very fast and sometimes very slow depending on the input. My approach #17920 was slower, but in a more "uniform" way, never so slow that it was unusable.
This is probably because it is hard to check whether the list that you are trying to build can be "extended" into a list that satisfies all conditions.
I have not gone through the code yet, but it seems that the strategy is to try all possible choices for the first integer, then try all possible choices for the second (etc.) each time checking the constraints on what has already been decided (but not guessing anything about the future)
Thus, and still assuming that I did not misunderstand anything, the following set (which contains only one element) will only be returned after around 2^n
operations:
sage: n=20; IntegerLists(n, length=n,max_part=1).list()
Certainly some "cuts" can be added to detect when a partial sequence cannot be extended.
Nathann
comment:53 followup: 101 Changed 8 years ago by
Please use Infinity
instead of infinity
such that, if we ever use Infinity
from sage.rings.infinity
, we don't need to change infinity
to Infinity
everywhere.
comment:54 Changed 8 years ago by
Replying to ncohen:
 It seems that currently the method accepts input that does not satisfy the constraints that you list, i.e.:
sage: IntegerListsLex(min_n=4) Integer lists of sum between 4 and 0 satisfying certain constraints sage: list(IntegerListsLex(min_n=4)) []Should they really be considered as 'constraints', if the code accepts them and returns sensible output (i.e. empty sets)?
I think that returning the empty set is the right answer here. As long as the question makes sense mathematically, there should be an answer, not an exception.
The only thing which can be a ValueError
exception would be a negative length, since that doesn't even have a mathematical meaning. But I know from #17920 that some Partitions
code gives a negative minimum length, so a negative value for min_length
should just be treated as 0.
comment:55 Changed 8 years ago by
Replying to ncohen:
 the INPUT blocks says that
n
can be a list. Could you add there an explanation of what it means?
Alternatively, remove support for n
being a list. It's nowhere used in Sage. The old code "supported" it but it was never documented.
comment:56 followups: 73 106 Changed 8 years ago by
This limitation should be mentioned somewhere in the docs:
sage: IntegerListsLex(length=2, max_n=Infinity, ceiling=[Infinity, 0], floor=[0,1]).list() Traceback (most recent call last): ... ValueError: infinite upper bound for values of m
(this is another example which "just works" with #17920).
comment:57 Changed 8 years ago by
There are a lot of TODO
items in the code and #commented out code which should be cleaned up.
comment:58 Changed 8 years ago by
Errors like these should be TypeError
instead of ValueError
:
raise(ValueError("unable to parse value of min_part"))
comment:59 followup: 77 Changed 8 years ago by
What's the point of setting self.floor_type
if you don't use it?
comment:60 Changed 8 years ago by
This is not a tricky question but still takes forever:
sage: IntegerLists(1, min_part=0, max_part=0).list()
comment:62 followup: 64 Changed 8 years ago by
Cc:  Bryan Gillespie added 

Thanks for the thorough commentsNicholas, Anne and I have been working on this ticket persistently for just the last week at Sage Days 64, and we didn't have the time to polish every facet yet. I'll do my best to answer your questions about the algorithm and some of the design choices.
comment:63 Changed 8 years ago by
Replying to ncohen:
It's a pity that this code is sometimes very fast and sometimes very slow depending on the input. My approach #17920 was slower, but in a more "uniform" way, never so slow that it was unusable.
This is probably because it is hard to check whether the list that you are trying to build can be "extended" into a list that satisfies all conditions.
I have not gone through the code yet, but it seems that the strategy is to try all possible choices for the first integer, then try all possible choices for the second (etc.) each time checking the constraints on what has already been decided (but not guessing anything about the future)
In fact, the point of the algorithm is that there *is* guessing on the future; in most nottoodegenerate cases, one can detect that a branch will lead to nowhere and cut it.
Thus, and still assuming that I did not misunderstand anything, the following set (which contains only one element) will only be returned after around
2^n
operations:sage: n=20; IntegerLists(n, length=n,max_part=1).list()Certainly some "cuts" can be added to detect when a partial sequence cannot be extended.
At this point, the complexity of the following is not linear as it ought to be (one should be able to do the detection work faster by caching critical data), but it definitely is polynomial with a small degree (most likely quadratic), and very far from 2^{n: }
sage: n=20; IntegerLists(n, length=n,max_part=1).list() sage: n=1000 sage: %time IntegerListsLex(n, length=n,max_part=1).list() CPU times: user 852 ms, sys: 25.5 ms, total: 877 ms Wall time: 831 ms sage: n=2000 sage: %time x = IntegerListsLex(n, length=n,max_part=1).list() CPU times: user 3.15 s, sys: 24.2 ms, total: 3.17 s Wall time: 3.15 s
Cheers,
Nicolas
comment:64 Changed 8 years ago by
Replying to bgillespie:
Thanks for the thorough comments
Indeed! Thanks Nathann and Jeroen; I know how much time this takes.
Now, guys, if I may, Brian would deserve some words of appreciation from you for all the hard work he put into this.
Nicolas
comment:65 followup: 82 Changed 8 years ago by
Replying to ncohen:
Helloooooooooooo,
Here are some comments (mostly doc) about the current branch
 About
An integer list is a list l of nonnegative integers, its parts. The length of l is the number of its parts Note Two valid integer lists are considered equivalent if they only differ by trailing zeroes.Unless the length of a list is the number of its nonzero entries, it does not seem to be properly defined.
The length of a list is the number of its entries, including entries of size zero. i.e. [2, 0, 1, 0] is a list of length 4. It is equivalent to the list [2, 0, 1], but has a different length.
The constraints on the lists are as follows:
 in what follows you use a variablel
often (probably one of the lists): could you say so explicitly?
I've added a note to that effect.
 It seems that currently the method accepts input that does not satisfy the constraints that you list, i.e.:
sage: IntegerListsLex(min_n=4) Integer lists of sum between 4 and 0 satisfying certain constraints sage: list(IntegerListsLex(min_n=4)) []Should they really be considered as 'constraints', if the code accepts them and returns sensible output (i.e. empty sets)? When I read those lines, I expected the code to raise a
ValueError
exception on them.
The results from the algorithm should be mathematically correct if an error isn't raisedin this case, the set of such lists is empty, as advertised. While I was working through the initialization code yesterday, I did notice that it would be reasonable to include as few constraints on the initialization as possible and just give an empty output when conditions are contradictory, but I didn't have time to ensure that the algorithm was sound under arbitrary permutations of bad constraints. At the moment, everything that is returned should be correct.
Lower and upper bounds
: the text about constant values for floor/ceiling belongs to the INPUT block.
Updated.
waiver
 the description ofwaiver
in the INPUT block is very mysterious. If it is only meant for internal purposes, could you say so in its description?
Also updated. The waiver parameter is meant to be userfacing; it's purpose is to suppress a warning raised when the input parameters can't be checked computationally for cases that don't hang. This situation can occur when the user specifies an arbitrary function for the floor and ceiling parameters, so the purpose here is to verify that the user has thought carefully about what they are asking the algorithm to compute.
Next we obtain all lists of sum 4 and length 4 such that l[i] <= i:
 missing backticks at the end.
Fixed.
 Comparative timings: should they really appear in the function's documentation? To me the trac ticket is the right place for that.
Probably not, that was mainly for comparison during development. It's also old at this point, so I'll add current comparative timings to another comment.
 There are two 'TESTS' sections
That is true. Fixed.
self.warning = False # warning for dangerous (but possibly valid) usage
 could say what this flag does?
This is mostly an internal marker, and just keeps track of whether we are in a potentially
hanging use case (custom user function) that requires a warning to the user. I've
changed it to self._warning
to indicate that it's an internal marker, and made
the comment more verbose for the curious.
 the INPUT blocks says that
n
can be a list. Could you add there an explanation of what it means?
Added an explanation. (This just allows you to specify multiple allowable values for the list sum.)
 About the message
warn("""When the user specifies a method, then (s)he is responsible that the algorithm will not hang. Also note that the specified function should start at 0 rather than 1. Before trac#17979 the indexing was ambiguous and sometimes started at 1.""")From time to time we receive bug reports on sagedevel or sagesupport in which the users beg us to forgive them in case what they think might be a bug could actually be their mistake. Could this message be changed to something more
technical
? Something like `you defined ceiling=[...] to be a function, and we cannot swear that this call will not hang`?
Updated the message to be more specific about the issue.
 About the copyright header: I never saw any patch remove the name of other persons in a copyright header. Don't know what the policy is.
# Copyright (C) 2007 Mike Hansen <mhansen@gmail.com>, # Copyright (C) 2012 Travis Scrimshaw <tscrim@ucdavis.edu> +# Copyright (C) 2015 Bryan Gillespie <Brg008@gmail.com>,
The update is a complete rewrite, so probably a new author list makes sense.
 Bryan
comment:66 Changed 8 years ago by
Commit:  6153cf8d39dc23cb41a3d0c2ea66ba5dc3abd2c0 → cb18ced22db714063e744bb907a035b4fe3afa24 

Branch pushed to git repo; I updated commit sha1. New commits:
cb18ced  17979 Updates primarily to documentation of combinat/integer_list.py in response to comment 27 in trac ticket 17979

comment:67 Changed 8 years ago by
Here are some comparative timings Re: the ones stripped from the docs.
sage: from sage.combinat.integer_list_old import IntegerListsLex as IntegerListsLexOld sage: P = IntegerListsLex(n=20, max_slope=0, min_part=1) sage: %time x = list(P) CPU times: user 159 ms, sys: 25.8 ms, total: 185 ms Wall time: 164 ms sage: P = IntegerListsLexOld(n=20, max_slope=0, min_part=1) sage: %time x = list(P) CPU times: user 170 ms, sys: 12.9 ms, total: 183 ms Wall time: 162 ms sage: len(x) 627 sage: P = IntegerListsLex(n=30, max_slope=0, min_part=1) sage: %time x = list(P) CPU times: user 1.74 s, sys: 21.9 ms, total: 1.76 s Wall time: 1.66 s sage: P = IntegerListsLexOld(n=30, max_slope=0, min_part=1) sage: %time x = list(P) CPU times: user 1.44 s, sys: 18.1 ms, total: 1.46 s Wall time: 1.42 s sage: len(x) 5604 sage: P = IntegerListsLex(n=40, max_slope=0, min_part=1) sage: %time x = list(P) CPU times: user 12.8 s, sys: 0 ns, total: 12.8 s Wall time: 12.7 s sage: P = IntegerListsLexOld(n=40, max_slope=0, min_part=1) sage: %time x = list(P) CPU times: user 10.3 s, sys: 1.98 ms, total: 10.3 s Wall time: 10.3 s sage: len(x) 37338 sage: P = IntegerListsLex(n=50, max_slope=0, min_part=1) sage: %time x = list(P) CPU times: user 1min 20s, sys: 216 ms, total: 1min 20s Wall time: 1min 20s sage: P = IntegerListsLexOld(n=50, max_slope=0, min_part=1) sage: %time x = list(P) CPU times: user 1min 1s, sys: 153 ms, total: 1min 2s Wall time: 1min 2s sage: len(x) 204226 sage: P = IntegerListsLex(n=60, max_slope=0, min_part=1) sage: %time x = list(P) CPU times: user 7min 5s, sys: 823 ms, total: 7min 6s Wall time: 7min 5s sage: P = IntegerListsLexOld(n=60, max_slope=0, min_part=1) sage: %time x = list(P) CPU times: user 5min 12s, sys: 495 ms, total: 5min 12s Wall time: 5min 12s sage: len(x) 966467
comment:68 followup: 72 Changed 8 years ago by
Replying to jdemeyer:
Why do you want to supporting
floor
andceiling
being a number? We already havemin_part
andmax_part
for that.
The main reason is that min_part
and max_part
are redundant in purpose with floor
and ceiling
, so the hope would be to deprecate that usage at some point. In the current implementation, all of the cases that can be handled with min_part
and max_part
plus floor
and ceiling
can also be handled using floor
and ceiling
alone.
comment:69 followup: 94 Changed 8 years ago by
Replying to jdemeyer:
Is this really true?
Before trac#17979 the indexing was ambiguous and sometimes started at 1.
There were places in the code of the old integer_list.py that used either convention, and integer_vector.py consistently started indexing at 1.
comment:70 followup: 74 Changed 8 years ago by
Replying to jdemeyer:
There is still this bug:
sage: it = iter(IntegerListsLex(4)) sage: for _ in range(20): print next(it) [4] [3, 1] [3, 0, 1] [3, 0, 0, 1] [3, 0, 0, 0, 1] [3, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1]It seems that
[1,3]
will never appear in the output!
Not a bug, but an issue that's worth discussing. The premise of IntegerListsLex?, as I understand it, is that it should return integer lists satisfying certain constraints, in lexicographic ordering, starting with the largest. The lists returned in your example are exactly what they should be for this specificationnone of them is smaller than [1,3]
in lex ordering, since the 4
or 3
in the first position is larger than the corresponding 1
.
The issue is in specifying a priori a total ordering on the set that may not be isomorphic with that on NN (in fact, may not even be wellordered). Does it even make sense to call an object which iterates through a proper countable subset of a set an iterator? On the other hand, the iteration itself might still be useful in this case.
At the very least, this behavior is shared with that of the old implementation.
comment:71 Changed 8 years ago by
Replying to jdemeyer:
I dislike the fact that the warning shows even in cases where the output is obviously finite:
sage: IntegerListsLex(5, ceiling=lambda i:i, length=5) /usr/local/src/sageconfig/local/lib/python2.7/sitepackages/sage/combinat/integer_list.py:606: UserWarning: When the user specifies a method, then (s)he is responsible that the algorithm will not hang. Also note that the specified function should start at 0 rather than 1. Before trac#17979 the indexing was ambiguous and sometimes started at 1. Before trac#17979 the indexing was ambiguous and sometimes started at 1.""") Integer lists of sum 5 satisfying certain constraintsAlso note that the formatting of the warning is not quite right.
I updated the formatting of the warning (also the message to be more explicit/verbose), so check if it looks reasonable to you.
Here's what our thought process was concerning when to raise a warning message. We could easily do some additional computations to find certain cases where the specified parameters make giving a custom function safe. However, one of the complaints with the old version was that it was difficult to understand how the parameters affected the output. If we make it "sometimes" verifiably safe to use a custom function, depending on the circumstances, then that's another point of complexity for the user to followbut if we just raise a warning whenever a user uses a custom floor or ceiling function (but only if they haven't "signed a waiver" by specifying waiver=True
), that simplifies the interface for the user.
Also note that the example you gave could be handled by the following specification without raising a warning:
sage: IntegerListsLex(5, ceiling=[0,1,2,3,4], length=5)
comment:72 followup: 75 Changed 8 years ago by
Replying to bgillespie:
The main reason is that
min_part
andmax_part
are redundant in purpose withfloor
andceiling
, so the hope would be to deprecate that usage at some point.
I disagree. The advantage of min_part
and max_part
is they are known to be constant, which can lead to optimizations which cannot be done with floor
and ceiling
functions. Even if you don't do these optimizations at the moment, I would leave open the possibility of doing that in the future (I do so in #17920).
comment:73 Changed 8 years ago by
Replying to jdemeyer:
This limitation should be mentioned somewhere in the docs:
sage: IntegerListsLex(length=2, max_n=Infinity, ceiling=[Infinity, 0], floor=[0,1]).list() Traceback (most recent call last): ... ValueError: infinite upper bound for values of m(this is another example which "just works" with #17920).
I have plans to implement some parameter adjustments and cardinality checking for the cases when a user doesn't specify a custom floor or ceiling function which would catch this issue. Currently the code doesn't do any extra handling on cases where the floor and ceiling functions intersect, so currently it tries to find the largest possible value for the first position in the list, and determines that there is no largest one. The new checks would also make use of the slope conditions to catch something like:
sage: IntegerListsLex(length=3, max_n=Infinity, max_slope=1, ceiling=[Infinity, 1, 3], floor=[0, 1, 3])
For the moment, it does raise an error in this kind of situation, but it also doesn't hang or return an incorrect result. It also might be useful to give a more descriptive error message for when the possible values in a position are unbounded.
comment:74 followup: 76 Changed 8 years ago by
Replying to bgillespie:
Replying to jdemeyer:
It seems that
[1,3]
will never appear in the output!Not a bug, but an issue that's worth discussing.
It is a bug, see also the discussion starting at 29:ticket:17548.
comment:75 followup: 85 Changed 8 years ago by
Replying to jdemeyer:
Replying to bgillespie:
The main reason is that
min_part
andmax_part
are redundant in purpose withfloor
andceiling
, so the hope would be to deprecate that usage at some point.I disagree. The advantage of
min_part
andmax_part
is they are known to be constant, which can lead to optimizations which cannot be done withfloor
andceiling
functions. Even if you don't do these optimizations at the moment, I would leave open the possibility of doing that in the future (I do so in #17920).
Note that floor
and ceiling
take multiple different types of parameters, not just functions. This code checks for the type of the input parameter and optimizes when using a constant or a list of integers.
comment:76 followup: 83 Changed 8 years ago by
Replying to jdemeyer:
Replying to bgillespie:
Replying to jdemeyer:
It seems that
[1,3]
will never appear in the output!Not a bug, but an issue that's worth discussing.
It is a bug, see also the discussion starting at 29:ticket:17548.
Yes, I have glanced through that discussion.
The point is that if it is a bug, then it's a bug in the specification, not the code, since we are requiring the output to be in lexicographic order. However, if we don't want to call it an iterator because it doesn't satisfy the contract of eventually reaching every element in the set, then the class won't interact well with the many places that use iterators in Python and Sage. Can you propose a solution to this?
comment:77 followup: 84 Changed 8 years ago by
Replying to jdemeyer:
What's the point of setting
self.floor_type
if you don't use it?
I have plans to use it in an upcoming update which determines, in cases where a user doesn't specify custom functions, whether the set is finite/infinite, and if it can be enumerated in Lex ordering. (In particular this will be useful for properly setting the Category of the object, which currently defaults to FiniteEnumeratedSets
.
comment:78 Changed 8 years ago by
Hi Brian,
I should have some time tonight to work on this ticket. Let me know what your plans are to synchronize; in particular what areas I can hack in freely.
Thanks!
comment:79 Changed 8 years ago by
Hi Nicolas,
All my current changes are pushed to the ticketI made changes Re: comment 27, but haven't gotten to the other misc. changes suggested in various comments. I'll need to prepare a talk for a conference this weekend, so I'll only be able to put in parttime for the next few daysso feel free to hack wherever tonight. I'll check back in tomorrow during the day to look over some of the other recommendations from comments. Let me know if there's anything else you want me to look over then.
comment:80 Changed 8 years ago by
Commit:  cb18ced22db714063e744bb907a035b4fe3afa24 → 370068c5bab3821ce60ad216c732553de075f765 

Branch pushed to git repo; I updated commit sha1. New commits:
370068c  17979: readded support for a list or iterable for n, using DistjointUnionEnumeratedSets; simplified code

comment:81 Changed 8 years ago by
Commit:  370068c5bab3821ce60ad216c732553de075f765 → 3efcb0a067bb039d28d29b3fd8c9115c18c90d15 

Branch pushed to git repo; I updated commit sha1. New commits:
3efcb0a  17979: Reworked documentation, and updated sage.combinat.tutorial

comment:82 Changed 8 years ago by
Hellooooo,
The length of a list is the number of its entries, including entries of size zero. i.e. [2, 0, 1, 0] is a list of length 4. It is equivalent to the list [2, 0, 1], but has a different length.
May I ask where in the function it is used that two lists are equivalent when they only differ by the number of trailing zeroes ?
If it is only when min_length<max_length
, could you add this mention as a note in the documentation of those parameters (input block)?
sage: IntegerListsLex(min_n=4) Integer lists of sum between 4 and 0 satisfying certain constraints sage: list(IntegerListsLex(min_n=4)) []Should they really be considered as 'constraints', if the code accepts them and returns sensible output (i.e. empty sets)? When I read those lines, I expected the code to raise a
ValueError
exception on them.The results from the algorithm should be mathematically correct if an error isn't raisedin this case, the set of such lists is empty, as advertised. While I was working through the initialization code yesterday, I did notice that it would be reasonable to include as few constraints on the initialization as possible and just give an empty output when conditions are contradictory, but I didn't have time to ensure that the algorithm was sound under arbitrary permutations of bad constraints.
Oh, the current behaviour is fine for me! If unsatisfiable parameters lead to an empty set there is no reason to complain: I was merely saying that the documentation made it sound like it was 'bad' to create such objects. Thus, I expected an exception. But if they are handled correctly, why is it even mentionned in the doc? Empty sets will be returned and so everything is fine, isn't it?
Also updated. The waiver parameter is meant to be userfacing; it's purpose is to suppress a warning raised when the input parameters can't be checked computationally for cases that don't hang. This situation can occur when the user specifies an arbitrary function for the floor and ceiling parameters, so the purpose here is to verify that the user has thought carefully about what they are asking the algorithm to compute.
I wonder about that... Instead of letting the code hang, wouldn't it be better to first "explore a bit the floor/ceiling parameters" ? If you see that up to 10^{10} all the values of ceiling do not sum to n, then say that something is wrong straight away?
This is mostly an internal marker, and just keeps track of whether we are in a potentially hanging use case (custom user function) that requires a warning to the user. I've changed it to
self._warning
to indicate that it's an internal marker, and made the comment more verbose for the curious.
Thanks,
Nathann
comment:83 followup: 103 Changed 8 years ago by
Replying to bgillespie:
The point is that if it is a bug, then it's a bug in the specification, not the code, since we are requiring the output to be in lexicographic order. However, if we don't want to call it an iterator because it doesn't satisfy the contract of eventually reaching every element in the set, then the class won't interact well with the many places that use iterators in Python and Sage. Can you propose a solution to this?
The are two possible solutions:
 raise an exception if the iterator doesn't iterate over all elements.
 drop the "lexicographic order" requirement.
comment:84 Changed 8 years ago by
Replying to bgillespie:
Replying to jdemeyer:
What's the point of setting
self.floor_type
if you don't use it?I have plans to use it in an upcoming update
In that case, I would prefer to introduce these attributes in that upcoming update.
comment:85 followup: 105 Changed 8 years ago by
Replying to bgillespie:
Note that
floor
andceiling
take multiple different types of parameters, not just functions. This code checks for the type of the input parameter and optimizes when using a constant or a list of integers.
However, without min_part
, there is absolutely no way to specify "floor
is a function which is always at least 1". I should be able to specify such an input with floor=myfunc, min_part=1
and the code can optimize this case better than when just specifying the function. 60 is an excellent example of this.
comment:86 followup: 90 Changed 8 years ago by
By the say, sorry for my earlier comment about the 2^n
runtime of the function. I am pretty sure I ran that test several times (reloading the branch in between) and that it was hanging with n=20
(running fine with n=10
, and slow with n=15
), but I cannot reproduce it now and the answer is immediate. Soooo well, my mistake O_o
Nathann
P.S.: currently, this branch keeps a copy of integer_list.py
as integer_list_old.py
.
comment:87 Changed 8 years ago by
Commit:  3efcb0a067bb039d28d29b3fd8c9115c18c90d15 → 7b6838c3c12e1144949349bcef3697894d44f66d 

comment:88 followup: 113 Changed 8 years ago by
Replying to jdemeyer:
This takes forever, even though the list trivially contains just one element:
sage: IntegerListsLex(10^100, max_length=1).list()
Thanks! This should be fixed now. I put in a test as well.
comment:89 followup: 91 Changed 8 years ago by
Replying to jdemeyer:
Remove
from sage.structure.list_clone import ClonableArray from sage.rings.integer import Integer
Why? ClonableArray? is used!
comment:90 followup: 99 Changed 8 years ago by
Replying to ncohen:
P.S.: currently, this branch keeps a copy of
integer_list.py
asinteger_list_old.py
.
This is because some other classes refer to next, first etc in combinat.integer_list which we do not have any longer in the new implementation. It is also useful right now to compare against the timing of the old implementation!
comment:91 Changed 8 years ago by
Replying to aschilling:
Why? ClonableArray? is used!
It was imported twice, but that's already fixed.
comment:92 Changed 8 years ago by
Commit:  7b6838c3c12e1144949349bcef3697894d44f66d → ba68b9d7d80c4c50f124d803f21e3a07b92187d6 

comment:93 Changed 8 years ago by
Commit:  ba68b9d7d80c4c50f124d803f21e3a07b92187d6 → e03611509b03f79e1c55b2cc347a427fc51a9f51 

Branch pushed to git repo; I updated commit sha1. New commits:
e036115  17919: infinity > _infinity

comment:94 Changed 8 years ago by
Replying to bgillespie:
Replying to jdemeyer:
Is this really true?
Before trac#17979 the indexing was ambiguous and sometimes started at 1.There were places in the code of the old integer_list.py that used either convention, and integer_vector.py consistently started indexing at 1.
Sorry, my bad: actually the 1based indexing was only used internally in the old IntegerListLex?
. I removed that comment.
comment:95 followup: 110 Changed 8 years ago by
Replying to jdemeyer:
What is
IntegerVectors
and why is it not an alias ofIntegerListsLex
?
Essentially it's a short hand for IntegerListsLex
when the length is fixed. Kind of like Partitions is a short hand for IntegerListsLex
when min_part=1
and max_slope=0
. It also adds some more methods, and specialized counting. In any case, this ticket is not really touching this class except for its interface to IntegerListsLex
.
comment:96 Changed 8 years ago by
Commit:  e03611509b03f79e1c55b2cc347a427fc51a9f51 → 39d1993d70a837967109be12de261f4f504901cc 

Branch pushed to git repo; I updated commit sha1. New commits:
39d1993  17919: slightly better phrasing

comment:97 Changed 8 years ago by
Replying to jdemeyer:
Replying to nthiery:
And we will reuse everything we can from your work!
The following takes forever, which is a problem that I solved in #17920, so I'm slightly disappointed this doesn't really work:
sage: IntegerListsLex(499499, length=1000, min_slope=1).list()
Agreed. I am pretty sure that the lookahead could be improved to handle this properly (Bryan: probably by doing some dichotomy in m_interval). I am going to throw this in the examples as a reminder for further work on this in later tickets.
comment:98 Changed 8 years ago by
Description:  modified (diff) 

Work issues:  support n in an iterable 
comment:99 followup: 100 Changed 8 years ago by
This is because some other classes refer to next, first etc in combinat.integer_list which we do not have any longer in the new implementation. It is also useful right now to compare against the timing of the old implementation!
It is also code which returns wrong results. If you insist on keeping it around, could you add a stopgap in there?
Nathann
comment:100 Changed 8 years ago by
It is also code which returns wrong results. If you insist on keeping it around, could you add a stopgap in there?
My mistake, it is there.
Nathann
comment:101 followup: 111 Changed 8 years ago by
Replying to jdemeyer:
Please use
Infinity
instead ofinfinity
such that, if we ever useInfinity
fromsage.rings.infinity
, we don't need to changeinfinity
toInfinity
everywhere.
I just changed infinity
to _infinity
to mark that we are currently doing something special; it's a one line change at the begining of the file to switch to _infinity=Infinity
when the later will be optimized (looking forward to it). That being said, I don't mind changing _infinity
to Infinity
in the code if you think this won't bring confusion.
comment:102 Changed 8 years ago by
Replying to jdemeyer:
I would be 1 to using
float('inf')
just because it's faster. The Right Thing to do is to use Sage'sInfinity
and optimize that.
Agreed, that's the right thing to do in the mid term. But for now float('inf')
does the job, and it will be one line change anyway once Infinity
will be optimized. So let's not add a dependency on it.
comment:103 Changed 8 years ago by
Replying to jdemeyer:
Replying to bgillespie:
The point is that if it is a bug, then it's a bug in the specification, not the code, since we are requiring the output to be in lexicographic order. However, if we don't want to call it an iterator because it doesn't satisfy the contract of eventually reaching every element in the set, then the class won't interact well with the many places that use iterators in Python and Sage. Can you propose a solution to this?
The are two possible solutions:
 raise an exception if the iterator doesn't iterate over all elements.
 drop the "lexicographic order" requirement.
Having alternative implementations that take the second route to
handle those cases is indeed a worthwhile goal. But that's not
IntegerListsLex
's job :)
Here, we shall aim for 1., whenever possible: that is systematically when floor/ceiling are not functions, and when it's obvious and cheap otherwise.
Cheers,
Nicolas
comment:104 Changed 8 years ago by
Bryan: it would be useful if all the attributes self.floor
, ... were specified, typically in comments above or in the __init__
method.
Btw: shall we rename those attributes as self._floor
to mark them as private?
comment:105 followup: 112 Changed 8 years ago by
Replying to jdemeyer:
Replying to bgillespie:
Note that
floor
andceiling
take multiple different types of parameters, not just functions. This code checks for the type of the input parameter and optimizes when using a constant or a list of integers.However, without
min_part
, there is absolutely no way to specify "floor
is a function which is always at least 1". I should be able to specify such an input withfloor=myfunc, min_part=1
and the code can optimize this case better than when just specifying the function. 60 is an excellent example of this.
We were experimenting a bit with the API to try to minimize redundancy. At this point, I have settled for:
min_part
to specify a lower bound for all partsfloor
to specify lower bounds on the individual parts
What do you think?
Question: if the users passes floor=f, min_part=i
should IntegerListsLex
assume that f(k)
is always at most i
, or should it wrap f
to add this guarantee? At this point it does the latter, which of course adds a bit of overhead (which could be tamed with appropriate caching which we will anyway want to do during the Cythonization).
comment:106 followup: 114 Changed 8 years ago by
Replying to jdemeyer:
This limitation should be mentioned somewhere in the docs:
sage: IntegerListsLex(length=2, max_n=Infinity, ceiling=[Infinity, 0], floor=[0,1]).list() Traceback (most recent call last): ... ValueError: infinite upper bound for values of m(this is another example which "just works" with #17920).
I added this to the documentation, specifying that this example could be enumerated in lexicographically increasing order but not in lexicographically decreasing order as does IntegerListsLex
.
Two questions:
 Does anyone have a good suggestion for a better error message?
 Should the error message be created upon creating the parent, or when starting the iteration? The advantage of doing it only upon iteration is that we can still use the parent for checking containment, constructing the polytope, ...
comment:107 Changed 8 years ago by
Commit:  39d1993d70a837967109be12de261f4f504901cc → f8f9a0202625c2eaaccfd8fb35f7ce95e495dc1a 

Branch pushed to git repo; I updated commit sha1. New commits:
f8f9a02  17919: imported Jeroen's example from trac

comment:108 Changed 8 years ago by
I believe I have taken care of Jeroen's stylistic comments about raising execptions, type or not implemented errors instead of value errors, comment:47,
comment:109 followup: 130 Changed 8 years ago by
OSError: [combinat ] /usr/local/src/sageconfig/local/lib/python2.7/sitepackages/sage/combinat/integer_list.py:docstring of sage.combinat.integer_list.IntegerListsLex:370: WARNING: Literal block expected; none found.
comment:110 followup: 122 Changed 8 years ago by
Replying to nthiery:
In any case, this ticket is not really touching this class except for its interface to
IntegerListsLex
.
Looking at the diff, I see lots of changes to integer_vector.py
.
comment:111 Changed 8 years ago by
Replying to nthiery:
That being said, I don't mind changing
_infinity
toInfinity
in the code if you think this won't bring confusion.
I would prefer Infinity
.
comment:112 Changed 8 years ago by
Replying to nthiery:
At this point, I have settled for:
min_part
to specify a lower bound for all partsfloor
to specify lower bounds on the individual partsWhat do you think?
Question: if the users passes
floor=f, min_part=i
shouldIntegerListsLex
assume thatf(k)
is always at mosti
, or should it wrapf
to add this guarantee? At this point it does the latter.
The latter is the approach I took at #17920, so I agree completely :)
It fits well with the philosophy that all constraints have to be taken into account.
comment:113 Changed 8 years ago by
Replying to aschilling:
Replying to jdemeyer:
This takes forever, even though the list trivially contains just one element:
sage: IntegerListsLex(10^100, max_length=1).list()Thanks! This should be fixed now. I put in a test as well.
I see you "fixed" this by adding one small heuristic, but similar examples still don't work:
sage: IntegerListsLex(10^100, length=2, min_slope=2, max_slope=2).list() ...
comment:114 followup: 123 Changed 8 years ago by
Replying to nthiery:
 Should the error message be created upon creating the parent, or when starting the iteration? The advantage of doing it only upon iteration is that we can still use the parent for checking containment, constructing the polytope, ...
During iteration, mainly because I think that expensive checks should not be done during __init__
.
comment:115 Changed 8 years ago by
Commit:  f8f9a0202625c2eaaccfd8fb35f7ce95e495dc1a → 1a1fac1f7de8d5ae8d45138c594f7c8531024cbb 

comment:116 Changed 8 years ago by
The tree traversal code in the iterator class needed some cleanup to make it more clear what was supposed to be happening where, so I did that in the above commit. I checked the running time to make sure it wasn't affected, and it seems to run as quickly as it did before the modifications.
comment:117 followups: 118 128 Changed 8 years ago by
Hello !
I just finished reading the iterator part of that patch, and it looks solid.
Just a couple of details:
 Shouldn't
i in ZZ
appear before the others in the following line ?
return lambda i: l[i] if (i >= 0 and i < len(l) and i in ZZ) else default
 The documentation reads that
n
can be an iterable, but the code of__contains__
does not agree.
What features would be needed in this new version of integer_list
to get rid of the _old
one? We would be better without it.
Nathann
comment:118 followup: 121 Changed 8 years ago by
Replying to ncohen:
What features would be needed in this new version of
integer_list
to get rid of the_old
one? We would be better without it.
Let's first fix IntegerLists
(Lex
), we can remove integer_list_old.py
later.
comment:119 Changed 8 years ago by
Commit:  1a1fac1f7de8d5ae8d45138c594f7c8531024cbb → c2705b80d619c99317b1a4ad780f28ea513361d1 

Branch pushed to git repo; I updated commit sha1. New commits:
c2705b8  17979: ReST fix + updated doctest

comment:120 Changed 8 years ago by
Commit:  c2705b80d619c99317b1a4ad780f28ea513361d1 → 01ef7dbbc89b07b8dd583a0546e94497bf6aee18 

Branch pushed to git repo; I updated commit sha1. New commits:
01ef7db  17979: _infinity > Infinity

comment:121 followup: 126 Changed 8 years ago by
Let's first fix
IntegerLists
(Lex
), we can removeinteger_list_old.py
later.
Yes probably. There is a stogap in there, and nobody knows that this file exists, so it is not too dangerous. I was just wondering what the new code couldn't do that the old one handled.
Nathann
comment:122 followup: 124 Changed 8 years ago by
Replying to jdemeyer:
Replying to nthiery:
In any case, this ticket is not really touching this class except for its interface to
IntegerListsLex
.Looking at the diff, I see lots of changes to
integer_vector.py
.
Oh, right, I forgot that I had used the occasion to get rid of quite some code in IntegerVectors
by using inheritance. Nevertheless, the main point remains: the API of IntegerVectors
hasn't changed; only its relation to IntegerListsLex
.
comment:123 Changed 8 years ago by
Replying to jdemeyer:
Replying to nthiery:
 Should the error message be created upon creating the parent, or when starting the iteration? The advantage of doing it only upon iteration is that we can still use the parent for checking containment, constructing the polytope, ...
During iteration, mainly because I think that expensive checks should not be done during
__init__
.
Sounds good.
comment:124 followup: 129 Changed 8 years ago by
Replying to nthiery:
Oh, right, I forgot that I had used the occasion to get rid of quite some code in
IntegerVectors
by using inheritance. Nevertheless, the main point remains: the API ofIntegerVectors
hasn't changed; only its relation toIntegerListsLex
.
Perhaps such changes would better be done in a different ticket, it can only increase the changes of this ticket getting merged.
comment:125 Changed 8 years ago by
Commit:  01ef7dbbc89b07b8dd583a0546e94497bf6aee18 → 3530b5383cb02406034f6a1c8ffa2de50f777455 

comment:126 Changed 8 years ago by
I was just wondering what the new code couldn't do that the old one handled.
Basicaclly just the next
and prev
features. There is a single spot using next
in the Sage library (in Compositions
IIRC), and I doubt they are much used elsewhere.
next
should be rather straightforward to implement if someone needs it. I created #18058 for this.
comment:127 Changed 8 years ago by
Commit:  3530b5383cb02406034f6a1c8ffa2de50f777455 → 8e51e7ba310308d0ef8787519986d01ca24bc79e 

comment:128 Changed 8 years ago by
Replying to ncohen:
I just finished reading the iterator part of that patch, and it looks solid.
Cool :) Thanks for checking!
Just a couple of details:
 Shouldn't
i in ZZ
appear before the others in the following line ?
return lambda i: l[i] if (i >= 0 and i < len(l) and i in ZZ) else default
Given that this is a critical section and an internal function, I just changed this to assume that i is a non negative integer, and only check on i < len(l). Does this sound ok?
 The documentation reads that
n
can be an iterable, but the code of__contains__
does not agree.
This is because IntegerListsLex(n, ...)
returns a DisjointEnumeratedSets
of IntegerListsLex
's if n
is an iterable. This way all the rest of the code can just ignore the existence of this feature.
The downside is that __contains__
is slower (it will run through the different IntegerListsLex
, and check __contains__
there). Especially if the iterable is infinite. But that's not an important feature, so that's ok I believe.
comment:129 followup: 137 Changed 8 years ago by
Replying to jdemeyer:
Perhaps such changes would better be done in a different ticket, it can only increase the changes of this ticket getting merged.
Yeah, I see your point. If really needed, we could do that. But this means some non trivial work. It was quicker to first cleanup the interface between IntegerVectors
and IntegerListsLex
before adapting it to the new IntegerListsLex
.
Ah, I should mention that there probably will be a minor conflict with #17927. I can handle the merge in #17927 once this one is finalized.
comment:130 Changed 8 years ago by
Replying to jdemeyer:
OSError: [combinat ] /usr/local/src/sageconfig/local/lib/python2.7/sitepackages/sage/combinat/integer_list.py:docstring of sage.combinat.integer_list.IntegerListsLex:370: WARNING: Literal block expected; none found.
Fixed.
comment:131 Changed 8 years ago by
Description:  modified (diff) 

comment:132 Changed 8 years ago by
Commit:  8e51e7ba310308d0ef8787519986d01ca24bc79e → da793a3bf5508f3ef375aa6fded1c7b7a0a51acb 

comment:133 Changed 8 years ago by
Replying to jdemeyer:
There is still this bug:
sage: it = iter(IntegerListsLex(4)) sage: for _ in range(20): print next(it) [4] [3, 1] [3, 0, 1] [3, 0, 0, 1] [3, 0, 0, 0, 1] [3, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] [3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1]It seems that
[1,3]
will never appear in the output!
With the last commit this should be fixed!
comment:134 Changed 8 years ago by
Commit:  da793a3bf5508f3ef375aa6fded1c7b7a0a51acb → fcaa99cd2b40c3e85a7d15b4775983eb300ead24 

Branch pushed to git repo; I updated commit sha1. New commits:
fcaa99c  17979: added comment to _check_lexicographic_iterable, and inserted example by Jeroen

comment:135 Changed 8 years ago by
Hello !
I still get an error upon "make docclean && make dochtml"
OSError: [combinat ] /home/ncohen/.Sage/local/lib/python2.7/sitepackages/sage/combinat/integer_list.py:docstring of sage.combinat.integer_list.IntegerListsLex:338: WARNING: undefined label: _sectiongenericintegerlistlex (if the link has no caption the label must precede a section header)
Nathann
comment:136 followups: 145 161 Changed 8 years ago by
Replace
raise ValueError("The specified parameters do not allow for a lexicographic iterator!")
by
raise RuntimeError("the specified parameters do not allow for a lexicographic iterator")
comment:137 followups: 142 164 Changed 8 years ago by
Replying to nthiery:
Replying to jdemeyer:
Perhaps such changes would better be done in a different ticket, it can only increase the changes of this ticket getting merged.
Yeah, I see your point. If really needed, we could do that. But this means some non trivial work.
It think it is quite trivial to split it up, just make IntegerVectors
use integer_list_old.py
. You will also avoid the conflict with #17927 this way.
comment:138 Changed 8 years ago by
This hangs (please add this as doctest when you fix it):
sage: L = IntegerListsLex(ceiling=[0], min_slope=1, max_slope=1) sage: it = iter(L) sage: for _ in range(10): ....: print next(it)
comment:139 Changed 8 years ago by
This should be added as a different example which cannot be iterated in lexicographic order:
sage: L = IntegerListsLex(ceiling=[0], min_slope=1, max_slope=2)
comment:140 followup: 148 Changed 8 years ago by
Please add also this example:
sage: sage: L = IntegerListsLex(ceiling=[1], min_slope=1, max_slope=1) sage: it = iter(L) sage: for _ in range(10): ....: print next(it)
comment:141 followups: 152 175 Changed 8 years ago by
Concerning terminology: is "lexicographic order" really the standard way of refering to this ordering? I would call it "reverse lexicographic" because it starts with the largest element first (but I'm not in combinatorics, so if this is standard, then it's fine).
However, I do think this "lexicographic order" needs to be documented somewhere, especially with the behaviour of implicit trailing zeros. Add this example, because it might look counterintuitive that the [1]
appears in the middle here:
sage: list(IntegerListsLex(max_length=4, max_part=1)) [[1, 1, 1, 1], [1, 1, 1], [1, 1, 0, 1], [1, 1], [1, 0, 1, 1], [1, 0, 1], [1, 0, 0, 1], [1], [0, 1, 1, 1], [0, 1, 1], [0, 1, 0, 1], [0, 1], [0, 0, 1, 1], [0, 0, 1], [0, 0, 0, 1], []]
comment:142 followup: 143 Changed 8 years ago by
Replying to jdemeyer:
Replying to nthiery:
Replying to jdemeyer:
Perhaps such changes would better be done in a different ticket, it can only increase the changes of this ticket getting merged.
Yeah, I see your point. If really needed, we could do that. But this means some non trivial work.
It think it is quite trivial to split it up, just make
IntegerVectors
useinteger_list_old.py
. You will also avoid the conflict with #17927 this way.
Note that IntegerVectors
is used in other classes, such as Partitions
, so if we wanted to leave it referencing integer_list_old.py
, then we would probably also want to port the uses of IntegerVectors
to IntegerListsLex
wherever that occurs in the library. IntegerVectors
also uses some auxiliary input formats such as inner=[...]
and outer=[...]
, so we would need to support those in IntegerListsLex
if we wanted to use this approach. Feels a little like a separate ticket to me, but it certainly could be done.
comment:143 Changed 8 years ago by
Replying to bgillespie:
Note that
IntegerVectors
is used in other classes, such asPartitions
, so if we wanted to leave it referencinginteger_list_old.py
, then we would probably also want to port the uses ofIntegerVectors
toIntegerListsLex
wherever that occurs in the library.IntegerVectors
also uses some auxiliary input formats such asinner=[...]
andouter=[...]
, so we would need to support those inIntegerListsLex
if we wanted to use this approach. Feels a little like a separate ticket to me, but it certainly could be done.
I don't quite understand your comment, but my proposal is: on this ticket, fix only IntegerListsLex
and leave the rest for followup tickets.
comment:144 Changed 8 years ago by
Commit:  fcaa99cd2b40c3e85a7d15b4775983eb300ead24 → ba6db5768d13c38b5a3cf90de75aa847c6c51efe 

Branch pushed to git repo; I updated commit sha1. New commits:
ba6db57  17979 changed ValueError to RuntimeError and lex order to reverse lex order

comment:145 Changed 8 years ago by
Replying to jdemeyer:
Replace
raise ValueError("The specified parameters do not allow for a lexicographic iterator!")by
raise RuntimeError("the specified parameters do not allow for a lexicographic iterator")
Fixed. Also changed lex order to reverse lex order!
comment:146 Changed 8 years ago by
Commit:  ba6db5768d13c38b5a3cf90de75aa847c6c51efe → 0a80fd49fed43754d61af0a02633394877f7ba63 

Branch pushed to git repo; I updated commit sha1. New commits:
0a80fd4  17979: fixed crosslink

comment:147 Changed 8 years ago by
Commit:  0a80fd49fed43754d61af0a02633394877f7ba63 → 56e831a1e2bbde6ccac2b883e69987b743201a37 

comment:148 Changed 8 years ago by
Replying to jdemeyer:
Please add also this example:
sage: sage: L = IntegerListsLex(ceiling=[1], min_slope=1, max_slope=1) sage: it = iter(L) sage: for _ in range(10): ....: print next(it)
Fixed. The _check_lexicographic_iterable now also catches that this is not enumeratable under reverse lex order. I added the two tests that you mentioned.
comment:149 Changed 8 years ago by
Commit:  56e831a1e2bbde6ccac2b883e69987b743201a37 → 709f9ccfa7fe584febf107fe84e5e5303a5b292d 

Branch pushed to git repo; I updated commit sha1. New commits:
709f9cc  17979 added Jeroen's example about trailing zeroes

comment:150 followup: 153 Changed 8 years ago by
What do you think of that ?
sage: [2,2,0] in IntegerListsLex(4,min_length=3,max_length=4) # appears in .list() True sage: [2,2,0,0] in IntegerListsLex(4,min_length=3,max_length=4) # does not appear in .list() True sage: [2,2,0,0,0] in IntegerListsLex(4,min_length=3,max_length=4) # does not appear in .list() False
Nathann
comment:151 Changed 8 years ago by
Commit:  709f9ccfa7fe584febf107fe84e5e5303a5b292d → 652a6d552c10b95fd3c735094fe105e4081e47ce 

Branch pushed to git repo; I updated commit sha1. New commits:
652a6d5  17979 fixed doc compilation issue

comment:152 Changed 8 years ago by
Replying to jdemeyer:
Concerning terminology: is "lexicographic order" really the standard way of refering to this ordering? I would call it "reverse lexicographic" because it starts with the largest element first (but I'm not in combinatorics, so if this is standard, then it's fine).
However, I do think this "lexicographic order" needs to be documented somewhere, especially with the behaviour of implicit trailing zeros. Add this example, because it might look counterintuitive that the
[1]
appears in the middle here:sage: list(IntegerListsLex(max_length=4, max_part=1)) [[1, 1, 1, 1], [1, 1, 1], [1, 1, 0, 1], [1, 1], [1, 0, 1, 1], [1, 0, 1], [1, 0, 0, 1], [1], [0, 1, 1, 1], [0, 1, 1], [0, 1, 0, 1], [0, 1], [0, 0, 1, 1], [0, 0, 1], [0, 0, 0, 1], []]
Added. The doc compilation issues should also be fixed now!
comment:153 followups: 155 156 Changed 8 years ago by
Replying to ncohen:
What do you think of that ?
sage: [2,2,0] in IntegerListsLex(4,min_length=3,max_length=4) # appears in .list() True sage: [2,2,0,0] in IntegerListsLex(4,min_length=3,max_length=4) # does not appear in .list() True sage: [2,2,0,0,0] in IntegerListsLex(4,min_length=3,max_length=4) # does not appear in .list() False
The reason for this behavior is the following: we identify elements which differ by trailing zeroes up to max_length. That is why the first and second example gives True and the last one gives False (since in this case we are beyond the max_length).
comment:154 Changed 8 years ago by
Replying to jdemeyer:
Replying to nthiery:
And we will reuse everything we can from your work!
The following takes forever, which is a problem that I solved in #17920, so I'm slightly disappointed this doesn't really work:
sage: IntegerListsLex(499499, length=1000, min_slope=1).list()
This example and
sage: IntegerListsLex(10^100, max_length=1).list()
will be optimized in #18055.
comment:155 followups: 157 159 165 Changed 8 years ago by
The reason for this behavior is the following: we identify elements which differ by trailing zeroes up to max_length. That is why the first and second example gives True and the last one gives False (since in this case we are beyond the max_length).
Soooooooooo when you get the list [2,2,0]
in the output of .list()
, it represents "all lists beginning by 2,2,0
whose length is included between 3 and 4"? This information is not included in the object itself, it is to be understood by how it was first produced.
This identification of list worries me a bit. The exception in __iter__
was added because we consider it a bug that some element of the set may never be listed in __iter__
, and this is exactly the problem we have again here. For a different reason, i.e. because some lists are identified.
Nathann
comment:156 Changed 8 years ago by
Replying to aschilling:
The reason for this behavior is the following: we identify elements which differ by trailing zeroes up to max_length.
The "up to max_length
" part is a bit arbitrary. I would prefer that these should give the same answer (either both True
or both False
):
sage: [2,2,0,0] in IntegerListsLex(4,min_length=3,max_length=4) sage: [2,2,0,0,0] in IntegerListsLex(4,min_length=3,max_length=4)
comment:157 Changed 8 years ago by
Replying to ncohen:
This identification of list worries me a bit. The exception in
__iter__
was added because we consider it a bug that some element of the set may never be listed in__iter__
, and this is exactly the problem we have again here. For a different reason, i.e. because some lists are identified.
It's pretty natural to follow this equivalence (think for instance monomials x*y^2
and x*y^2*z^0
), but I definitely see your point. Would it be useful to specify a more featureful class IntegerList
(returned by this class) which takes into account these equivalences and provides comparison operations for lexicographic ordering? This would help to make more clear the assumptions being made on the lists during iteration, and would result in both IntegerList([2,2,0,0])
and IntegerList([2,2,0,0,0])
being contained in IntegerListsLex(4,min_length=3,max_length=4)
in the example above, since they are the same object, and at least one representative satisfies the desired criterion.
comment:158 Changed 8 years ago by
Commit:  652a6d552c10b95fd3c735094fe105e4081e47ce → ae225b3af4329dcbedbbfe83151a000b09ef44d3 

Branch pushed to git repo; I updated commit sha1. New commits:
ae225b3  17979: reverse lexicographic > inverse lexicographic

comment:159 Changed 8 years ago by
Replying to ncohen:
The reason for this behavior is the following: we identify elements which differ by trailing zeroes up to max_length. That is why the first and second example gives True and the last one gives False (since in this case we are beyond the max_length).
Soooooooooo when you get the list
[2,2,0]
in the output of.list()
, it represents "all lists beginning by2,2,0
whose length is included between 3 and 4"? This information is not included in the object itself, it is to be understood by how it was first produced.
The parent knows about the min_length and max_length, so it makes sense to identify objects with trailing zeroes in the correct parameter range. In any case, this is the same behavior as in the old version of the code and I do not think we should change this here.
This identification of list worries me a bit. The exception in
__iter__
was added because we consider it a bug that some element of the set may never be listed in__iter__
, and this is exactly the problem we have again here. For a different reason, i.e. because some lists are identified.
Nathann, this is a different issue! The above issue is just about identifying objects, not about not listing all of them. The issue about not listing all of them is due to the fact that inverse lexicographic order intrinsically (by definition) does not list them all.
Anne
New commits:
ae225b3  17979: reverse lexicographic > inverse lexicographic

comment:160 Changed 8 years ago by
Commit:  ae225b3af4329dcbedbbfe83151a000b09ef44d3 → 0c5305c958517701a68b4419f8a173f544cbefd4 

comment:161 followup: 169 Changed 8 years ago by
Replying to jdemeyer:
Replace
raise ValueError("The specified parameters do not allow for a lexicographic iterator!")by
raise RuntimeError("the specified parameters do not allow for a lexicographic iterator")
Really? RuntimeError
is "for an error that doesn’t fall in any of the
other categories", where as we do fit within the ValueError
category:
"when a builtin operation or function receives an argument that has
the right type but an inappropriate value". Here IntegerListsLex
did
receive inappropriate value which makes the lexicographic enumeration
improper.
Nicolas
comment:162 Changed 8 years ago by
Commit:  0c5305c958517701a68b4419f8a173f544cbefd4 → 611f5c73f0d5b8af4c150abc1785e5ea305b164d 

comment:163 followup: 170 Changed 8 years ago by
Replying to jdemeyer:
The heading should be formatted like http://www.sagemath.org/doc/developer/coding_basics.html#headingsofsagelibrarycodefiles (in particular, it's bad to mention the GPL without version number).
Yup: I made GPL into GPLv2+ and added a short history. However I kept the short version of the header without the four lines of verbiage. It's really inconvenient to have a bunch of useless information at the top of a file when this is the very first thing that pops up when opening a file. As far as I can remember, this was already discussed on sagedevel and considered ok.
In fact, I would vote for updating accordingly the dev manual, but that's another discussion.
New commits:
67450ee  17979: updated header

6819cf5  Merge branch 'public/ticket/17979' of trac.sagemath.org:sage into ticket/17979

611f5c7  17979: GPL > GPL v2+

comment:164 followup: 182 Changed 8 years ago by
Replying to jdemeyer:
It think it is quite trivial to split it up, just make
IntegerVectors
useinteger_list_old.py
.
Thanks for the suggestion, but no :) I haven't spent so much time on
this to still have some non trivial usage of integer_list_old.py
lying around. If I don't find someone to review this very soon, I'll
reconsider.
comment:165 followup: 166 Changed 8 years ago by
Replying to ncohen:
Soooooooooo when you get the list
[2,2,0]
in the output of.list()
, it represents "all lists beginning by2,2,0
whose length is included between 3 and 4"? This information is not included in the object itself, it is to be understood by how it was first produced.This identification of list worries me a bit.
I agree: 15 years ago, from the use cases I had under hand, I though that this was a neat feature to identify lists up to trailing zeroes. However this is non trivial to specify properly, and I am now convinced that this is just a can of worms. We should seriously consider dropping this feature.
However I believe that this is out of the scope of this ticket, especially since this would require a change in the specifications, and cause backward incompatibilities. Up to the fuzziness in this piece of the specification, it sounds like the code should by now be correct w.r.t. the current specifications; let's get it done.
Cheers,
Nicolas
comment:166 Changed 8 years ago by
Replying to nthiery:
However I believe that this is out of the scope of this ticket, especially since this would require a change in the specifications
Where was it specified that lists with trailing zeros are identified up to max_length? It makes absolutely no sense at all that these two questions give a different answer:
sage: [2,2,0,0] in IntegerListsLex(4,min_length=3,max_length=4) sage: [2,2,0,0,0] in IntegerListsLex(4,min_length=3,max_length=4)
comment:167 Changed 8 years ago by
Commit:  611f5c73f0d5b8af4c150abc1785e5ea305b164d → 46d01a95002b3b498c9af1ed6784fa0fd4960ae5 

Branch pushed to git repo; I updated commit sha1. New commits:
46d01a9  17979: added Nathann's example of dubious behavior with trailing zeroes

comment:168 Changed 8 years ago by
For the record: I added a warning and Nathann's example in the doc about this.
New commits:
46d01a9  17979: added Nathann's example of dubious behavior with trailing zeroes

comment:169 followup: 172 Changed 8 years ago by
Replying to nthiery:
Replying to jdemeyer:
Replace
raise ValueError("The specified parameters do not allow for a lexicographic iterator!")by
raise RuntimeError("the specified parameters do not allow for a lexicographic iterator")Really?
RuntimeError
is "for an error that doesn’t fall in any of the other categories", where as we do fit within theValueError
category: "when a builtin operation or function receives an argument that has the right type but an inappropriate value". HereIntegerListsLex
did receive inappropriate value which makes the lexicographic enumeration improper.
Fine, I don't care so much (but there is also the formatting issue of not using a capital letter and exclamation mark). I felt that RuntimeError
was more appropriate because it is not really a specific value which is bad, but some computation based on the input values from which it can be concluded that the input is bad.
comment:170 followup: 174 Changed 8 years ago by
Replying to nthiery:
However I kept the short version of the header without the four lines of verbiage. It's really inconvenient to have a bunch of useless information at the top of a file when this is the very first thing that pops up when opening a file.
If you feel like this, then first change http://www.sagemath.org/doc/developer/coding_basics.html#headingsofsagelibrarycodefiles. Don't just change conventions on your own because you find it more convenient.
As far as I can remember, this was already discussed on sagedevel and considered ok.
I'd like to see a link to that discussion.
comment:171 Changed 8 years ago by
Commit:  46d01a95002b3b498c9af1ed6784fa0fd4960ae5 → f634ab0b514edc2c62da1310420756163f616946 

Branch pushed to git repo; I updated commit sha1. New commits:
f634ab0  17979: RuntimeError > ValueError + fixed message

comment:172 Changed 8 years ago by
Replying to jdemeyer:
Fine, I don't care so much (but there is also the formatting issue of not using a capital letter and exclamation mark).
formatting fixed.
I felt that
RuntimeError
was more appropriate because it is not really a specific value which is bad, but some computation based on the input values from which it can be concluded that the input is bad.
I agree that it's borderline.
New commits:
f634ab0  17979: RuntimeError > ValueError + fixed message

comment:173 Changed 8 years ago by
Commit:  f634ab0b514edc2c62da1310420756163f616946 → ad238f9f80726ac8b872a6bb44f6bfeeb243270b 

Branch pushed to git repo; I updated commit sha1. New commits:
ad238f9  17979: formally compliant long copyright header

comment:174 Changed 8 years ago by
Replying to jdemeyer:
Replying to nthiery:
However I kept the short version of the header without the four lines of verbiage. It's really inconvenient to have a bunch of useless information at the top of a file when this is the very first thing that pops up when opening a file.
If you feel like this, then first change http://www.sagemath.org/doc/developer/coding_basics.html#headingsofsagelibrarycodefiles. Don't just change conventions on your own because you find it more convenient.
Will do.
For now I don't want to waste time on this stupid issue, so voilà, formal header there is.
New commits:
ad238f9  17979: formally compliant long copyright header

comment:175 Changed 8 years ago by
Replying to jdemeyer:
Concerning terminology: is "lexicographic order" really the standard way of refering to this ordering? I would call it "reverse lexicographic" because it starts with the largest element first (but I'm not in combinatorics, so if this is standard, then it's fine).
Yup, we indeed wanted to be more specific about this. This is done now. Note that we have used "inverse lexicographic" since "reverse lexicographic" usually means reading the words in reverse order.
http://en.wikipedia.org/wiki/Lexicographical_order#Reverse_lexicographic_order
comment:176 followup: 198 Changed 8 years ago by
Replying to jdemeyer:
Some implementations might not use keyword arguments for
length
, so themin_n
andmax_n
arguments (preferably renamed tomin_sum
andmax_sum
) should be moved towards the end of the argument list.
I'd be rather surprised if this was used anywhere (it was not in the Sage sources), especially since the documentation never mentionned this possibility. And it's neat to have all arguments be grouped by theme. But ok, better be safe than sorry. Done.
comment:177 Changed 8 years ago by
Commit:  ad238f9f80726ac8b872a6bb44f6bfeeb243270b → f73c43fd4423675f9ce279da9bb929a44db31483 

comment:178 followup: 181 Changed 8 years ago by
Description:  modified (diff) 

Status:  needs_work → needs_review 
Ok, I believe all the points that have been raised have been catered for (but some may have slipped through in this long thread). So this is up for formal review.
Thanks for all the comments and suggestions!
Note: please see the description where I left two points where feedback is specifically welcome.
New commits:
9bf94c4  17979: moved min_sum and max_sum later in the __init__ arguments

f73c43f  17979: trivial doctest fix

comment:179 Changed 8 years ago by
Reviewers:  → Nathann Cohen, Jeroen Demeyer 

comment:180 followup: 208 Changed 8 years ago by
I agree with this comment:
.. TODO:: Maybe this should be ``check=False`` instead?
The standard terminology for such an option is indeed check=False
and waiver
appears only in integer_list.py
.
comment:181 Changed 8 years ago by
Replying to nthiery:
Ok, I believe all the points that have been raised have been catered for (but some may have slipped through in this long thread). So this is up for formal review.
Let me remind everybody here that #17920 is also up for formal review.
Comparing both approaches (I am of course not completely unbiased, but I'll really try to be objective):
 Bugs: neither #17979 nor #17920 have obvious bugs (although I find 166 dubious at least), both fix #17548. I assume both pass doctests.
 Features: #17979 tries to replicate the old behaviour as closely as possible, #17920 generalizes certain conditions (e.g. allowing negative numbers; allowing iteration in noninvlex order) but also adds a few restrictions (e.g. not allowing an iterable for
n
).
 Interface with rest of Sage: #17920 only uses the new
IntegerLists
code forIntegerListsLex
,Partitions
andCompositions
(in the other places in Sage whereIntegerListsLex
was used, I didn't find any bugs so I left those). This ticket #17979 replaces the old code in almost all cases (except partially inIntegerVectors
).
comment:182 followup: 193 Changed 8 years ago by
Replying to nthiery:
Thanks for the suggestion, but no :) I haven't spent so much time on this to still have some non trivial usage of
integer_list_old.py
lying around. If I don't find someone to review this very soon, I'll reconsider.
For the record: I will not review the changes to integer_vector.py
on this ticket. If somebody else wants to do that, that's fine for me.
comment:183 Changed 8 years ago by
This is certainly false:
The complexity of the algorithm has not been formally proven, but the average runtime for producing each list `l` is suspected to be bounded by a lowdegree polynomial in ``lmax``, where ``lmax`` is the length of the longest list. Similarly, the space complexity of the algorithm is bounded by a lowdegree polynomial in ``lmax``.
(in fact, this statement is probably more true of #17920 than it is for #17979)
comment:184 followup: 188 Changed 8 years ago by
The code in _IntegerListsLexIter
needs to be documented much more, it is hard to understand the code without documentation. Since most of the internal state is contained in attributes like self.rho
, you should document what these mean (and # list of current search ranges
is not sufficient documentation).
Also: please use terminology consistently. I think the same thing is called "part", "entry" and "value" in different places.
comment:185 Changed 8 years ago by
Status:  needs_review → needs_work 

comment:186 Changed 8 years ago by
Description:  modified (diff) 

comment:187 followup: 199 Changed 8 years ago by
This should return the list containg 1 element []
:
sage: list(IntegerListsLex(ceiling=[0], max_slope=0))
comment:188 followup: 206 Changed 8 years ago by
Since most of the internal state is contained in attributes like
self.rho
, you should document what these mean (and# list of current search ranges
is not sufficient documentation).
+1 to that. This terminology made it much harder for me to understand what the code was doing. Instead of writing this in the code:
self.rho = [] # list of current search ranges self.mu = [] # list of integers self.j = 1 # index of last element of mu self.nu = 0 # sum of values in mu
It would probably be clearer to rename those variables (respectively) as
self._search_range self._current_list self._j self._current_sum
Nathann
P.S.: And indeed, as Jeroen says, it would be cool to be a bit more verbose about what these things do. Once you know how the code works I agree that 'current search range' is a rather good explanation, but until you do it is rather crytic. I have firsthand knowledge of that ^^;
comment:189 followups: 192 194 Changed 8 years ago by
I don't like this:
.. WARNING:: The specifications of this feature are fuzzy, leading to potentially surprising consequences (see the examples below). It is recommended not to rely on it, as it may eventually be discontinued.
The specifications are not fuzzy. They might be strange, unlogical, arbitrary, badly chosen but not fuzzy. To make it less fuzzy, you should document explicitly the fact that the equivalence only works up to max_length
in the NOTE
about this WARNING
.
(to compare: in #17920 I took the convention that x in L
is equivalent to x in L.list()
, so I don't really identify lists with trailing zeros, I just output the list with the least number of trailing zeros)
comment:190 followup: 209 Changed 8 years ago by
I would also prefer to remove the text concerning algorithmic complexity in src/sage/combinat/tutorial.py
. What I dislike most is that it seems to hide behind the "degenerate cases" exception without really specifying what that means.
comment:191 followups: 216 218 Changed 8 years ago by
This hangs:
sage: list(IntegerListsLex(1, min_length=2, min_slope=0, max_slope=0))
(it works fine without the min_length
though)
comment:192 Changed 8 years ago by
I don't like this:
.. WARNING:: The specifications of this feature are fuzzy, leading to potentially surprising consequences (see the examples below). It is recommended not to rely on it, as it may eventually be discontinued.
+1 to that. I also fear that this warning may be used later as an authorization to not document behaviors and to overlook inconsistencies because it is, after all, 'documented'.
Nathann
comment:193 Changed 8 years ago by
Replying to jdemeyer:
For the record: I will not review the changes to
integer_vector.py
on this ticket.
Sure thing! That's what I had in mind.
comment:194 followups: 195 197 Changed 8 years ago by
Replying to jdemeyer:
I don't like this:
.. WARNING:: The specifications of this feature are fuzzy, leading to potentially surprising consequences (see the examples below). It is recommended not to rely on it, as it may eventually be discontinued.The specifications are not fuzzy. They might be strange, unlogical, arbitrary, badly chosen but not fuzzy. To make it less fuzzy, you should document explicitly the fact that the equivalence only works up to
max_length
in theNOTE
about thisWARNING
.
Well, my point was: the specifications *as they are currently written* are fuzzy. I meant to propose an alternative specification, but somehow my comment did not make its way into trac. Here it is:
When several lists satisfying the constraint differ only by trailing zeroes, only the shortest one is enumerated (and therefore counted).
I believe this is not fuzzy anymore, and matches the current behavior of the code; and therefore does not require breaking backward compatibility at this stage.
What do you think?
As a separate question: do you believe like me that we should, in a later ticket, get rid of this "feature"?
Cheers,
Nicolas
comment:195 followup: 204 Changed 8 years ago by
Replying to nthiery:
When several lists satisfying the constraint differ only by trailing zeroes, only the shortest one is enumerated (and therefore counted).
constraint
> constraints
comment:196 followup: 203 Changed 8 years ago by
Please add this somewhere in __init__
:
if min_length < 0: min_length = 0
comment:197 followup: 207 Changed 8 years ago by
Replying to nthiery:
As a separate question: do you believe like me that we should, in a later ticket, get rid of this "feature"?
I do think that, by default, we shouldn't output lists with trailing zeros, since this will lead in many cases to infinitely many lists satisfying the constraints. However, I think it's best if the behaviour of __contains__
really matches the iterator.
If you ever allow negative parts, then the convention of having no trailing zeros becomes very strange, since "nonzero" is no longer a convex condition.
In #17920 I solved this by setting a minimum/maximum value for the last part of a list, if the list is longer than min_length
. By default, this minimum is 1 with no maximum which gives the same lists as the "identify trailing zeros" convention.
comment:198 followup: 202 Changed 8 years ago by
Replying to nthiery:
I'd be rather surprised if this was used anywhere (it was not in the Sage sources), especially since the documentation never mentionned this possibility.
Somebody had to change src/sage/combinat/integer_matrices.py
for this reason :)
comment:199 Changed 8 years ago by
Replying to jdemeyer:
This should return the list containg 1 element
[]
:sage: list(IntegerListsLex(ceiling=[0], max_slope=0))
This is fixed now!
comment:200 Changed 8 years ago by
Commit:  f73c43fd4423675f9ce279da9bb929a44db31483 → 31013b932d8f0c0e941713dc8e44c02cc323f5c5 

Branch pushed to git repo; I updated commit sha1. New commits:
31013b9  17979: more checks on length, min_length, max_length

comment:201 Changed 8 years ago by
Commit:  31013b932d8f0c0e941713dc8e44c02cc323f5c5 → 39ee52d817c0b10ad5795cc2b138a4a83475fc25 

Branch pushed to git repo; I updated commit sha1. New commits:
39ee52d  17979: proper specification of the trailing zeroes 'feature'

comment:202 Changed 8 years ago by
Replying to jdemeyer:
Somebody had to change
src/sage/combinat/integer_matrices.py
for this reason :)
Good point :) Well, it was good to make this change anyway for clarity :)
comment:203 followup: 211 Changed 8 years ago by
Replying to jdemeyer:
Please add this somewhere in
__init__
:if min_length < 0: min_length = 0
I am not sure whether I prefer this, or barking, but that's fine. Done, together with further typechecks.
comment:204 Changed 8 years ago by
comment:205 Changed 8 years ago by
Commit:  39ee52d817c0b10ad5795cc2b138a4a83475fc25 → 4bcf7dc9ee28539f166c14f973f26401ceb39de3 

comment:206 Changed 8 years ago by
Replying to ncohen:
Since most of the internal state is contained in attributes like
self.rho
, you should document what these mean (and# list of current search ranges
is not sufficient documentation).+1 to that. This terminology made it much harder for me to understand what the code was doing. Instead of writing this in the code:
self.rho = [] # list of current search ranges self.mu = [] # list of integers self.j = 1 # index of last element of mu self.nu = 0 # sum of values in muIt would probably be clearer to rename those variables (respectively) as
self._search_range self._current_list self._j self._current_sum
Fixed.
New commits:
fd645e4  17979 changed names of iterator attributes

39ee52d  17979: proper specification of the trailing zeroes 'feature'

4bcf7dc  Merge branch 'public/ticket/17979' of git://trac.sagemath.org/sage into public/ticket/17979

comment:207 Changed 8 years ago by
Replying to jdemeyer:
However, I think it's best if the behaviour of
__contains__
really matches the iterator.
If you take upon you the responsibility of this backward incompatible
change of __contains__
, I'll go for it. Otherwise, I'd rather not
change this now.
I do think that, by default, we shouldn't output lists with trailing zeros, since this will lead in many cases to infinitely many lists satisfying the constraints.
Yeah, that was my original motivation too.
If you ever allow negative parts, then the convention of having no trailing zeros becomes very strange, since "nonzero" is no longer a convex condition.
Yup, one more can of worms.
In #17920 I solved this by setting a minimum/maximum value for the last part of a list, if the list is longer than
min_length
. By default, this minimum is 1 with no maximum which gives the same lists as the "identify trailing zeros" convention.
I definitely prefer this approach. This is also why I hesitated having
min_part
take precedence over floor=[...]
, for otherwise you could
just do floor=[1,1,0,3], min_part=1
. Well, it's still possible to
achieve this through a floor function but if the limit of the function
is not specified, the code can't decide certain things.
Anyway, let's keep the "feature" for now, and take care of it in a later ticket in a consistent way with #17920.
Cheers,
Nicolas
New commits:
fd645e4  17979 changed names of iterator attributes

4bcf7dc  Merge branch 'public/ticket/17979' of git://trac.sagemath.org/sage into public/ticket/17979

comment:208 followup: 214 Changed 8 years ago by
Replying to jdemeyer:
I agree with this comment:
.. TODO:: Maybe this should be ``check=False`` instead?The standard terminology for such an option is indeed
check=False
andwaiver
appears only ininteger_list.py
.
The thing is that there really are two different use cases here:
(1) I know what I am doing, you do not need to check my input.
(2) I know what I am doing, don't show me again this warning when
accessing the more tricky features.
The first use case definitely fits within the usual check=False
terminology. I am not so sure about the second one. In fact, I could
imagine situations where I would want (2) without (1): "I'll be using
the tricky features, still double check everything you can".
But maybe it's not worth the additional API complexity, and everything
should just fall into check=False
. Or rename "waiver=..." to
warnings=False
. I don't have a strong opinion.
Cheers,
Nicolas
comment:209 followup: 213 Changed 8 years ago by
Replying to jdemeyer:
I would also prefer to remove the text concerning algorithmic complexity in
src/sage/combinat/tutorial.py
. What I dislike most is that it seems to hide behind the "degenerate cases" exception without really specifying what that means.
Well, defining precisely the "degenerate cases" is a little research project by itself :) But the point is that, in most practical use cases, the complexity is low (or will be low once an improved lookahead will be implemented #18055). I am happy to reformulate it this way if you prefer. But I'd rather keep some short sentence about this topic here, as it explains the rationale of the approach to the reader.
comment:210 Changed 8 years ago by
Commit:  4bcf7dc9ee28539f166c14f973f26401ceb39de3 → 49dd343182197e2707cf30d5fa118bafede16769 

Branch pushed to git repo; I updated commit sha1. New commits:
49dd343  17979 debugging Jeroen's example; added doc test that catches the hang

comment:211 followup: 284 Changed 8 years ago by
Replying to nthiery:
Replying to jdemeyer:
Please add this somewhere in
__init__
:if min_length < 0: min_length = 0I am not sure whether I prefer this, or barking, but that's fine. Done, together with further typechecks.
Well, I also prefer raise ValueError(...)
in this case, but some partitions code really sends a negative value for min_length
to IntegerListsLex
.
comment:212 followup: 223 Changed 8 years ago by
Concerning type checks: instead of x in ZZ
, it's better to simply convert to a known type: use x = ZZ(x)
instead (or see my function integer_or_infinity()
in #17920).
comment:213 followup: 237 Changed 8 years ago by
Replying to nthiery:
But I'd rather keep some short sentence about this topic here, as it explains the rationale of the approach to the reader.
Fine, I understand your point. However, I think it should perhaps be phrased in a more informal way. Since you talk about polynomialtime, it sounds like the statement of some mathematical theorem, but it isn't.
You can just say something like "it's fast in practice for simple examples".
comment:214 followups: 226 235 Changed 8 years ago by
Replying to nthiery:
(1) I know what I am doing, you do not need to check my input.
(2) I know what I am doing, don't show me again this warning when
accessing the more tricky features.
To be honest, I don't think there is much difference between these two. Suppose hypothetically that we would add two different flags for (1) and (2), which checks would be controlled by (1) and which by (2)?
I prefer the name check=False
mainly because it's very standard in Sage.
comment:215 Changed 8 years ago by
Commit:  49dd343182197e2707cf30d5fa118bafede16769 → 3630fb51346d426a75ea0991027663e003185157 

Branch pushed to git repo; I updated commit sha1. New commits:
3630fb5  17979: fixed hang in _possible_m

comment:216 Changed 8 years ago by
Replying to jdemeyer:
This hangs:
sage: list(IntegerListsLex(1, min_length=2, min_slope=0, max_slope=0))(it works fine without the
min_length
though)
Thank you for catching this! It should be fixed now! There was a wrong variable in _possible_m.
comment:217 Changed 8 years ago by
Commit:  3630fb51346d426a75ea0991027663e003185157 → 3356cc375a40ddbff4efc8d1e76512ba027a25de 

Branch pushed to git repo; I updated commit sha1. New commits:
3356cc3  17979: fixed hang in _possible_m: inserted original test from trac

comment:218 Changed 8 years ago by
Replying to jdemeyer:
This hangs:
sage: list(IntegerListsLex(1, min_length=2, min_slope=0, max_slope=0))(it works fine without the
min_length
though)
You really are shaking this guy out! That's good :)
We looked this up with Anne and the hang was in ._possible_m
; the issue was similar to one we had elsewhere: if the ceiling is 0 at some point and max_slope=0, then we know this should be treated as if there was a ceiling limit of 0. In fact, this was already tested, but not on a moving position; so this was a 1 character fix at the end.
I'll document this method in detail later today.
comment:219 Changed 8 years ago by
Commit:  3356cc375a40ddbff4efc8d1e76512ba027a25de → a962d5bcc024dd87caf98c8e2657137ef7582ed1 

Branch pushed to git repo; I updated commit sha1. New commits:
a962d5b  17979: work on the documentation of _possible_m

comment:220 Changed 8 years ago by
Commit:  a962d5bcc024dd87caf98c8e2657137ef7582ed1 → 13b7a803b96e3b73a8bf1cd986d46f1ad8e1e89c 

Branch pushed to git repo; I updated commit sha1. New commits:
13b7a80  17979: Improved documentation of internal function + some code cleaning there

comment:221 Changed 8 years ago by
Commit:  13b7a803b96e3b73a8bf1cd986d46f1ad8e1e89c → 49664f7bf16bb05f507398998ef5ac72ec9d071a 

Branch pushed to git repo; I updated commit sha1. New commits:
49664f7  17979 change x in ZZ to x = ZZ(x)

comment:222 Changed 8 years ago by
Commit:  49664f7bf16bb05f507398998ef5ac72ec9d071a → f102509c1c5d59632acfa7caf811104baf70fb6f 

Branch pushed to git repo; I updated commit sha1. New commits:
f102509  17979 more x=ZZ(x)

comment:223 Changed 8 years ago by
comment:224 Changed 8 years ago by
Commit:  f102509c1c5d59632acfa7caf811104baf70fb6f → 43100fa2cd1a03747089c9be9890fcaa0040f7de 

comment:225 Changed 8 years ago by
Commit:  43100fa2cd1a03747089c9be9890fcaa0040f7de → 422d972596908dfa24dd4ff90ba71ae891abb9d1 

Branch pushed to git repo; I updated commit sha1. New commits:
422d972  17979 switched waiver to check

comment:226 Changed 8 years ago by
Replying to jdemeyer:
Replying to nthiery:
(1) I know what I am doing, you do not need to check my input.
(2) I know what I am doing, don't show me again this warning when
accessing the more tricky features.
To be honest, I don't think there is much difference between these two. Suppose hypothetically that we would add two different flags for (1) and (2), which checks would be controlled by (1) and which by (2)?
I prefer the name
check=False
mainly because it's very standard in Sage.
Fixed!
comment:227 Changed 8 years ago by
Commit:  422d972596908dfa24dd4ff90ba71ae891abb9d1 → 4b0f3d983b1284bbab73c91f5aadbc52872f60fb 

Branch pushed to git repo; I updated commit sha1. New commits:
4b0f3d9  17979 made all attributes private

comment:228 Changed 8 years ago by
Commit:  4b0f3d983b1284bbab73c91f5aadbc52872f60fb → 0fe6dcd962a734b21e49cd58a7e56c3ec664bf8f 

Branch pushed to git repo; I updated commit sha1. New commits:
0fe6dcd  17979 small doc fixes

comment:229 Changed 8 years ago by
Commit:  0fe6dcd962a734b21e49cd58a7e56c3ec664bf8f → 93ad012c301ab9b565080d336378cc0edef6ff9a 

comment:230 Changed 8 years ago by
Description:  modified (diff) 

comment:231 Changed 8 years ago by
Commit:  93ad012c301ab9b565080d336378cc0edef6ff9a → b2b30103f152d8c4a3ea566b8a436153e2b07afb 

Branch pushed to git repo; I updated commit sha1. New commits:
b2b3010  17979: added test from the http://wiki.sagemath.org/combinat/Weirdness

comment:232 Changed 8 years ago by
Commit:  b2b30103f152d8c4a3ea566b8a436153e2b07afb → 37ae5e48a5448def4b76a5b4d38baa9c3cb7e9b4 

Branch pushed to git repo; I updated commit sha1. New commits:
37ae5e4  17979: added link to IntegerListsLex in the 'enumerated sets' index of the reference manual

comment:233 Changed 8 years ago by
Commit:  37ae5e48a5448def4b76a5b4d38baa9c3cb7e9b4 → 7e9c0b6c1b1e6e26422e6a0238880d4cdcc5ef34 

comment:234 Changed 8 years ago by
Commit:  7e9c0b6c1b1e6e26422e6a0238880d4cdcc5ef34 → dba4c6233d2af762986501528370c84c1d24736a 

comment:235 Changed 8 years ago by
Replying to jdemeyer:
To be honest, I don't think there is much difference between these two. Suppose hypothetically that we would add two different flags for (1) and (2), which checks would be controlled by (1) and which by (2)?
Well, I would know, but you are probably right: let's keep it simple for the user.
comment:236 Changed 8 years ago by
Description:  modified (diff) 

Status:  needs_work → needs_review 
comment:237 Changed 8 years ago by
Replying to jdemeyer:
Fine, I understand your point. However, I think it should perhaps be phrased in a more informal way. Since you talk about polynomialtime, it sounds like the statement of some mathematical theorem, but it isn't.
You can just say something like "it's fast in practice for simple examples".
Ok. Fast being very vague I tried to reformulate this, as well as the
comment on the complexity in IntegerListsLex
, to be less formal
while still giving some useful indication to the reader.
I very much hope that at some point we will be able to replace this by precise complexity information, at least within well defined cases.
comment:238 Changed 8 years ago by
Commit:  dba4c6233d2af762986501528370c84c1d24736a → ac1365cdf11ed413a3e534594176cd24fe75cabd 

Branch pushed to git repo; I updated commit sha1. New commits:
ac1365c  17979: improved _search_range > _search_ranges; IntegerListsLex._IntegerListLexIter > IntegerListsLex._Iter + micro doc improvement

comment:239 Changed 8 years ago by
Ok, we believe we took care of all the comments here, hence back to
needs review. Anne had a first look at the changes in
integer_vectors
, and Travis will double check probably on Monday.
I have been trough the internal documentation, and spent quite some time improving it. It could be further improved. Yet, it's probably best not to spend too much time on it either, since it's likely to get updated once better look ahead are implemented.
New commits:
ac1365c  17979: improved _search_range > _search_ranges; IntegerListsLex._IntegerListLexIter > IntegerListsLex._Iter + micro doc improvement

comment:240 followup: 251 Changed 8 years ago by
Status:  needs_review → needs_work 

sage: L = IntegerListsLex(length=2, max_part=0) sage: [0,0] in L True sage: L.list() []
comment:241 followup: 252 Changed 8 years ago by
I think this input should be allowed:
sage: IntegerListsLex(7, min_slope=Infinity).list()
comment:242 Changed 8 years ago by
This list is obviously finite:
sage: L = IntegerListsLex(max_part=1, min_slope=10) sage: L.list() ... ValueError: The specified parameters do not allow for an inverse lexicographic iterator
comment:243 Changed 8 years ago by
The following are also very clearly finite (but still ValueError
):
sage: L = IntegerListsLex(length=0) sage: L = IntegerListsLex(max_length=0, min_length=1)
comment:245 Changed 8 years ago by
Commit:  ac1365cdf11ed413a3e534594176cd24fe75cabd → 5cc08d541980a52c41eb22203659f779be291e36 

Branch pushed to git repo; I updated commit sha1. New commits:
5cc08d5  17979: added tests for _check_lexicographic_iterable from Jeroen

comment:246 Changed 8 years ago by
Commit:  5cc08d541980a52c41eb22203659f779be291e36 → a005d80a7b123ecee62da097a9c93a94da241e8c 

Branch pushed to git repo; I updated commit sha1. New commits:
a005d80  17979 fixed bounded region cases

comment:247 Changed 8 years ago by
Commit:  a005d80a7b123ecee62da097a9c93a94da241e8c → 6de41768a385f5742dd72eed35746cd5ca22afc9 

Branch pushed to git repo; I updated commit sha1. New commits:
6de4176  17919: take the enveloppe of the ceiling and floor when they are lists (yields better look ahead and value error detection)

comment:248 followup: 256 Changed 8 years ago by
Reviewers:  Nathann Cohen, Jeroen Demeyer → Nathann Cohen, Jeroen Demeyer, Travis Scrimshaw 

Here are my comments on the current state of things:
 In
integer_list.py
: I don't understand this sentence in the header: "It was then completely rewritten in 2015 by Gillespie, Schilling, and Thiery, with the help of many, to catter for limitations and lack of robustness w.r.t. input." I think by "catter" you mean "cater", but that isn't correct usage of the word.
 "dyck words" capitalization.
 I don't like the fact that when the answer is known to be infinite, that the category is
FiniteEnumeratedSets
.  You should test also when the input
n
is a tuple.  In
_check_lexicographic_iterable
, "Checks" should be "Check"
 In
tutorial.py
,predict when a sequence `\ell_0,\dot,\ell_k` is a prefix of some
, it should be "\dots".
 In
integer_vector.py
 Use absolute paths instead of relative paths:
from combinat import CombinatorialClass
 In
list2func
, could we codeafy the doc?  In the
__init__
, this is missing the doublecolon: "All the attributes below are private; don't use them!"  Could we split the long line in the
_repr_
?  Should we formally deprecate the
next
method?  In the error message "If k is a list, no optional argument is supported", let's make it lowercase.
 Use absolute paths instead of relative paths:
Otherwise I'm okay with how the code looks (but I did not run tests like Jeroen).
comment:249 Changed 8 years ago by
Commit:  6de41768a385f5742dd72eed35746cd5ca22afc9 → 4e96d307a311f37312aa5b161d12e48c8348d668 

Branch pushed to git repo; I updated commit sha1. New commits:
4e96d30  17979: reworked the logic of _possible_m to make it clearer

comment:250 Changed 8 years ago by
Commit:  4e96d307a311f37312aa5b161d12e48c8348d668 → 48cbd1f2ca8d6e1fd73f8e6dad0a94c4b987ba3b 

Branch pushed to git repo; I updated commit sha1. New commits:
48cbd1f  17979: fixed Iter._possible_m

comment:251 Changed 8 years ago by
comment:252 followup: 253 Changed 8 years ago by
Replying to jdemeyer:
I think this input should be allowed:
sage: IntegerListsLex(7, min_slope=Infinity).list()
Hmm, this would be generating lists of length at most 1.
Do you see any real use case?
It seems to me that the specification that min_slope
is either oo
or an integer (and symmetrically for max_slope
) is quite natural,
and allowing for +oo
would only mean adding more special cases and
complications to handle for no added value.
Cheers,
Nicolas
Btw: thanks for all the interesting corner cases you posted!
comment:253 followup: 259 Changed 8 years ago by
Replying to nthiery:
Do you see any real use case?
I certainly have no use case. It just seems a bit strange to allow every possible value for min_slope
except +Infinity
.
At least make it a ValueError
if min_slope=Infinity
or max_slope=Infinity
is given.
comment:254 Changed 8 years ago by
Commit:  48cbd1f2ca8d6e1fd73f8e6dad0a94c4b987ba3b → 126c9e7cb7dac2a9f2c66708125b2385ff9b4b3b 

Branch pushed to git repo; I updated commit sha1. New commits:
126c9e7  17979 addressed Travis' comments

comment:255 Changed 8 years ago by
Commit:  126c9e7cb7dac2a9f2c66708125b2385ff9b4b3b → 3a8f47a93266b82928539304ae21212e9885716f 

Branch pushed to git repo; I updated commit sha1. New commits:
6f3f524  Revert "17919: take the enveloppe of the ceiling and floor when they are lists (yields better look ahead and value error detection)"

f14c8cc  17919: added tests and documentation to _m_interval; fixed typo

3a8f47a  Merge branch 'public/ticket/17979' of trac.sagemath.org:sage into combinat/integer_lists_lex

comment:256 followup: 257 Changed 8 years ago by
Replying to tscrim:
Here are my comments on the current state of things:
Travis' comments are fixed now. Here are some further responses:
 I don't like the fact that when the answer is known to be infinite, that the category is
FiniteEnumeratedSets
.
When IntegerListsLex? is enumerable (i.e. the vectors can be iterated over in inverse lex order), then the list is finite. We will explain this in the code.
 Should we formally deprecate the
next
method?
No, since the plan is to implement this later, so there is no need to deprecate it now.
New commits:
6f3f524  Revert "17919: take the enveloppe of the ceiling and floor when they are lists (yields better look ahead and value error detection)"

f14c8cc  17919: added tests and documentation to _m_interval; fixed typo

3a8f47a  Merge branch 'public/ticket/17979' of trac.sagemath.org:sage into combinat/integer_lists_lex

comment:257 Changed 8 years ago by
Replying to aschilling:
When IntegerListsLex? is enumerable (i.e. the vectors can be iterated over in inverse lex order), then the list is finite. We will explain this in the code.
Oh, actually not quite. Sorry, my bad. I applied Koenig's lemma to quick. The equivalence finite <=> inverse lexicographically enumerable is almost true, except for extreme cases like:
sage: IntegerListsLex(n=1) > [1], [0,1], [0,0,1] ...
We will think about this a bit more and update the code accordingly.
comment:258 Changed 8 years ago by
Commit:  3a8f47a93266b82928539304ae21212e9885716f → 9278051dd34ba2c5967ef191d0c9ca9e124275cf 

Branch pushed to git repo; I updated commit sha1. New commits:
9278051  17979: type checking on min_slope and max_slope

comment:259 Changed 8 years ago by
Replying to jdemeyer:
Replying to nthiery:
Do you see any real use case?
I certainly have no use case. It just seems a bit strange to allow every possible value for
min_slope
except+Infinity
.At least make it a
ValueError
ifmin_slope=Infinity
ormax_slope=Infinity
is given.
Oh, I see your point now. I somehow thought this was already checked for. Done now: if min_slope
is not oo
, then it's converted to an integer. Thanks.
comment:260 Changed 8 years ago by
Commit:  9278051dd34ba2c5967ef191d0c9ca9e124275cf → f3b5a70855c6bc80c83f0967006ecfcc9a811140 

Branch pushed to git repo; I updated commit sha1. New commits:
f3b5a70  17979: further renamed local variables

comment:261 followup: 264 Changed 8 years ago by
I know this hasn't been set back to needs_review, but just as a reminder:
OSError: [combinat ] /usr/local/src/sageconfig/local/lib/python2.7/sitepackages/sage/combinat/integer_list.py:docstring of sage.combinat.integer_list.IntegerListsLex:9: WARNING: Inline literal startstring without endstring.
comment:262 Changed 8 years ago by
Commit:  f3b5a70855c6bc80c83f0967006ecfcc9a811140 → e06c09eba54005807aeff9e056ee4ff150596c20 

Branch pushed to git repo; I updated commit sha1. New commits:
e06c09e  17979: reworked the logic of next and push_search; this fixes the handling of length=0

comment:263 Changed 8 years ago by
Commit:  e06c09eba54005807aeff9e056ee4ff150596c20 → d36d0e7d5819e94e1e6ffb011f0f52460e5cb5a6 

Branch pushed to git repo; I updated commit sha1. New commits:
d36d0e7  17979: fixed ReST typo, and started reworking the discussion about finiteness

comment:264 Changed 8 years ago by
Replying to jdemeyer:
I know this hasn't been set back to needs_review, but just as a reminder:
OSError: [combinat ] /usr/local/src/sageconfig/local/lib/python2.7/sitepackages/sage/combinat/integer_list.py:docstring of sage.combinat.integer_list.IntegerListsLex:9: WARNING: Inline literal startstring without endstring.
Fixed, thanks!
New commits:
d36d0e7  17979: fixed ReST typo, and started reworking the discussion about finiteness

New commits:
d36d0e7  17979: fixed ReST typo, and started reworking the discussion about finiteness

comment:265 Changed 8 years ago by
Description:  modified (diff) 

comment:266 followup: 279 Changed 8 years ago by
Suggestion: use the function is_trivially_zero
from #17920 and don't raise ValueError
(for infinite ceiling or noninverselexicographicallyenumerable) if this returns True
.
comment:267 followups: 269 283 Changed 8 years ago by
After some more testing, I wasn't able to find any more cases of wrong output or hangs.
However, the are many cases where a ValueError
is raised despite the fact that only finitely many lists satisfy the constraints.
Perhaps the exception The specified parameters do not allow for an inverse lexicographic iterator
should be weakened to it looks like the specified parameters do not allow for an inverse lexicographic iterator
or something.
comment:268 Changed 8 years ago by
Commit:  d36d0e7d5819e94e1e6ffb011f0f52460e5cb5a6 → 715dc67379dadab0e77c1c5aaa354e3eab0c256b 

Branch pushed to git repo; I updated commit sha1. New commits:
715dc67  17979 weakened the noiterator message plus trivial doc changes

comment:269 Changed 8 years ago by
Replying to jdemeyer:
After some more testing, I wasn't able to find any more cases of wrong output or hangs.
However, the are many cases where a
ValueError
is raised despite the fact that only finitely many lists satisfy the constraints.Perhaps the exception
The specified parameters do not allow for an inverse lexicographic iterator
should be weakened toit looks like the specified parameters do not allow for an inverse lexicographic iterator
or something.
Yes, I agree with this and changed the message. Jeroen, you are doing a very detailed review of the code and its functioning. It is very helpful! Thank you!
comment:270 Changed 8 years ago by
Commit:  715dc67379dadab0e77c1c5aaa354e3eab0c256b → 04a620591cae0412dc0ed6c39666891e46876459 

Branch pushed to git repo; I updated commit sha1. New commits:
04a6205  17979 explained iterable versus finiteness issue; changed message accordingly

comment:271 Changed 8 years ago by
Description:  modified (diff) 

comment:272 Changed 8 years ago by
Commit:  04a620591cae0412dc0ed6c39666891e46876459 → fa3790140fc5fe801ef3c49a36afbeab98283a79 

Branch pushed to git repo; I updated commit sha1. New commits:
fa37901  17979 paramter>constraint and .parent > ._parent

comment:273 followup: 278 Changed 8 years ago by
Could you please document the new algorithm somewhere ? I downloaded the branch again today and had no idea what the values "decreasing, push, pop, me" actually meant O_o
Nathann
comment:274 Changed 8 years ago by
Commit:  fa3790140fc5fe801ef3c49a36afbeab98283a79 → 00b01087a6afdb118d68d87b9264f021432b8f59 

Branch pushed to git repo; I updated commit sha1. New commits:
00b0108  17979: extracted a separate class to handle envelopes

comment:275 Changed 8 years ago by
Commit:  00b01087a6afdb118d68d87b9264f021432b8f59 → 1d5ab6bfb820219c7929fad164079cf6f5b12ed3 

Branch pushed to git repo; I updated commit sha1. New commits:
1d5ab6b  17917: proofread discussion about finiteness

comment:276 Changed 8 years ago by
Commit:  1d5ab6bfb820219c7929fad164079cf6f5b12ed3 → 4b2f96bf0a032c069ec0240af8e8938926a9990c 

Branch pushed to git repo; I updated commit sha1. New commits:
4b2f96b  17979: added documentation about the different states for the iteration

comment:277 Changed 8 years ago by
Description:  modified (diff) 

comment:278 Changed 8 years ago by
Replying to ncohen:
Could you please document the new algorithm somewhere ? I downloaded the branch again today and had no idea what the values "decreasing, push, pop, me" actually meant
O_o
Done!
It's in fact the same algorithm as before; just trying to better highlight the structure, and reorganizing it to fix the logic for the corner case of length 0 (fixes comment:243).
Cheers,
comment:279 Changed 8 years ago by
Replying to jdemeyer:
Suggestion: use the function
is_trivially_zero
from #17920 and don't raiseValueError
(for infinite ceiling or noninverselexicographicallyenumerable) if this returnsTrue
.
I must admit that I have been focusing on getting this ticket done, at the price of looking at the details of your ticket right now ... So thanks much for your pointers; that's helpful!
In this specific case, it turns out that it's really the logic that
had to be fixed, and I won't need is_trivially_zero
.
Cheers,
Nicolas
comment:280 Changed 8 years ago by
Commit:  4b2f96bf0a032c069ec0240af8e8938926a9990c → a14ed209e342f8e942393ec554a27530dfc3ee34 

Branch pushed to git repo; I updated commit sha1. New commits:
a14ed20  17979 doc clean up

comment:281 Changed 8 years ago by
Commit:  a14ed209e342f8e942393ec554a27530dfc3ee34 → 4b923e15fddaac5751595717e91bb154b493c638 

comment:282 Changed 8 years ago by
Commit:  4b923e15fddaac5751595717e91bb154b493c638 → a939fd59bfcf043bce3c9a61ae072337961873da 

Branch pushed to git repo; I updated commit sha1. New commits:
a939fd5  17979: fixed typos in the documentation

comment:283 followup: 290 Changed 8 years ago by
Replying to jdemeyer:
However, the are many cases where a
ValueError
is raised despite the fact that only finitely many lists satisfy the constraints.
With the forward smoothing and partial backward smoothing of the
envelope w.r.t. min_slope
and max_slope
the situation should be
better now. At least all the examples your provided work smoothly,
and I am not sure I have an example under hand that would be finite
and not detected as such.
Perhaps the exception
The specified parameters do not allow for an inverse lexicographic iterator
should be weakened toit looks like the specified parameters do not allow for an inverse lexicographic iterator
or something.
Yes, until we have something guaranteed, that's the right thing to do.
Cheers,
Nicolas
comment:284 Changed 8 years ago by
Replying to jdemeyer:
Well, I also prefer
raise ValueError(...)
in this case, but some partitions code really sends a negative value formin_length
toIntegerListsLex
.
Gasp. Ok, fair enough :)
comment:285 Changed 8 years ago by
Description:  modified (diff) 

Status:  needs_work → needs_review 
New commits:
fa37901  17979 paramter>constraint and .parent > ._parent

00b0108  17979: extracted a separate class to handle envelopes

1d5ab6b  17917: proofread discussion about finiteness

4b2f96b  17979: added documentation about the different states for the iteration

919076a  17979: added missing docstring to Envelope.__init__

a14ed20  17979 doc clean up

4b923e1  Merge branch 'public/ticket/17979' of trac.sagemath.org:sage into combinat/integer_lists_lex

a939fd5  17979: fixed typos in the documentation

comment:286 Changed 8 years ago by
Description:  modified (diff) 

comment:287 Changed 8 years ago by
For the record:
sage: P = IntegerListsLex(n=40, max_slope=0, min_part=1) sage: sage: %time x = list(P) CPU times: user 14.9 s, sys: 23.7 ms, total: 15 s Wall time: 15 s
This used to be 12s before I introduced the Envelope
class. This is
due to the fact that we are not using anymore a ConstantFunction? for
the floor in this case. We could special case that, but this slow down
should disappear as soon as Envelope
will be Cythonized, so I'd say
that's good enough for now.
Cheers,
Nicolas
comment:288 Changed 8 years ago by
Commit:  a939fd59bfcf043bce3c9a61ae072337961873da → aec1e101e8078ed90c1c6c906f4b79dcfa93330f 

Branch pushed to git repo; I updated commit sha1. New commits:
aec1e10  17979: implement Iter.__iter__ to satisfy the iterator protocol

comment:289 Changed 8 years ago by
For the record: with the last commit all long tests pass on sage.math.upsud.fr (Debian 64 bits)
comment:290 followup: 295 Changed 8 years ago by
Replying to nthiery:
I am not sure I have an example under hand that would be finite and not detected as such.
Here are some:
IntegerListsLex(min_sum=1, floor=[1,2], max_part=1).list() IntegerListsLex(min_length=2, max_length=1).list()
(after more testing, it looks like these are essentially the only examples)
comment:291 followup: 293 Changed 8 years ago by
Hello,
There are several things that I do not quite understand. Could you explain or modify it:
 The iterator
IntegerListLex
aims to be fast and lowlevel. What is the point of using theParent
/Element
stuff? WhyClonableArray
are better than Python lists?
 Having a nested class seems overkill. The class
_Iter
is created only once in__iter__
. Moreover, all methods in it starts withp = self.parent
. Why do you need to create this extra_Iter
class? Why does it need to be a nested class?
 Do you have a use case for
sage: IntegerListsLex(NN, max_length=3) Disjoint union of Lazy family (<lambda>(i))_{i in Non negative integer semiring}
The feature only appears once in the doc in a place which does not appear in the reference manual.
 Why
_check_lexicographic_iterable
is a cached method? And I do not get why is it called from_Iter
and not at the initialization ofIntegerListsLex
.
Vincent
comment:292 Changed 8 years ago by
Commit:  aec1e101e8078ed90c1c6c906f4b79dcfa93330f → aa89bb267303a9c424d6e6883ee35b2d7e592d7c 

Branch pushed to git repo; I updated commit sha1. New commits:
aa89bb2  17979 extra case for finite region

comment:293 followup: 296 Changed 8 years ago by
Salut Vincent!
Thanks for the feedback.
On Tue, Mar 31, 2015 at 12:46:35PM 0000, sagetrac wrote:
There are several things that I do not quite understand. Could you explain or modify it:
 The iterator
IntegerListLex
aims to be fast and lowlevel. What is the point of using theParent
/Element
stuff? WhyClonableArray
are better than Python lists?
We haven't changed this aspect (in this ticket we focused on refactoring without changing the API): internally, Python lists are used; by default, they are converted to ClonableArray? upon being yielded. The element constructor can be customized to return plain lists if so desired.
In the current state of affairs, this does not really make a difference:
# ClonableArray sage: L = IntegerListsLex(50, min_part=1, max_slope=0) sage: it = iter(L) sage: %timeit x = it.next() 10000 loops, best of 3: 148 µs per loop # plain lists sage: L = IntegerListsLex(50, min_part=1, max_slope=0, element_constructor=list) sage: it = iter(L) sage: %timeit x = it.next() 10000 loops, best of 3: 134 µs per loop
The overhead comes from the containment test that we do in the check
method:
# ClonableArray, with check made trivial sage: sage: L = IntegerListsLex(50, min_part=1, max_slope=0) sage: sage: it = iter(L) sage: sage: %timeit x = it.next() 10000 loops, best of 3: 135 µs per loop
I am not sure this containment check is useful. We could just disable it. What do you think?
For the record: using the parent/element protocol does not necessarily cause a large overhead; ClonableArray? is almost as fast as list (timings to be of course taken with a grain of salt given how small values we are speaking about here):
sage: sage: L = IntegerListsLex(50, min_part=1, max_slope=0) sage: l = range(1000) sage: %timeit x =list(l) 100000 loops, best of 3: 2.4 µs per loop sage: c = L.element_class sage: %timeit x = c(L, l) 100000 loops, best of 3: 2.85 µs per loop sage: %timeit [x[i] for i in range(100)] 100000 loops, best of 3: 6.84 µs per loop sage: %timeit [l[i] for i in range(100)] 100000 loops, best of 3: 5.61 µs per loop
In the long run, when IntegerListsLex
will be cythonized, the
relative situation may change, since we can hope for speedups of
10100. Note in particular that we most likely will want to use arrays
of ints internally; ClonableIntArray
might be a good candidate for
this. Or just STL vectors.
 Having a nested class seems overkill. The class
_Iter
is created only once in__iter__
. Moreover, all methods in it starts with `p = self.parent. Why do you need to create this extra
_Iter` class? Why does it need to be a nested class?
The class is needed because the iterator has an internal state. So we need to create a separate object for each concurrently running iterator.
I find that using a nested class IntegerListsLex._Iter
, rather than
IntegerListsLexIter
makes the relation between the two classes
explicit (_Iter
is for internal use for IntegerListsLex?`). It's also
consistent with what we do elsewhere (Element
, ...). And there is no
overhead in doing so.
 Do you have a use case for
sage: IntegerListsLex(NN, max_length=3) Disjoint union of Lazy family (<lambda>(i))_{i in Non negative integer semiring}The feature only appears once in the doc in a place which does not appear in the reference manual.
It does appear in the reference manual: see section `Input list or
iterable for the sum of the main
IntegerListLex?` class.
The feature of iterating by increasing sum is certainly useful. Whether we want the above syntactic sugar  instead of just using DisjointUnionEnumeratedSets?  is indeed questionable. The feature was already there, so we kept it to not change the API in this ticket.
 Why
_check_lexicographic_iterable
is a cached method? And I do not get why is it called from_Iter
and not at the initialization ofIntegerListsLex
.
We discussed this with Jeroen in some earlier comment. Putting it in
the iterator let the user create the IntegerListsLex
object, even if
it's not finite/iterable. This could be useful for other things than
iteration, like membership testing or building the corresponding
polytopes (once #17920 will be available).
With that, it's natural to cache errorfree runs (error runs won't be cached) to not redo the work in later iterator constructions.
Cheers,
Nicolas
comment:294 Changed 8 years ago by
Commit:  aa89bb267303a9c424d6e6883ee35b2d7e592d7c → dcbad454879b348c727b87a46b0fef0e360f0471 

Branch pushed to git repo; I updated commit sha1. New commits:
dcbad45  17979: more documentation about the iterator algorithm + make sure an invariant is satisfied

comment:295 followup: 297 Changed 8 years ago by
Replying to jdemeyer:
Replying to nthiery:
I am not sure I have an example under hand that would be finite and not detected as such.
Here are some:
IntegerListsLex(min_sum=1, floor=[1,2], max_part=1).list() IntegerListsLex(min_length=2, max_length=1).list()(after more testing, it looks like these are essentially the only examples)
Cool, in the mean time we fixed both of them. We also looked at your is_trivialy_zero
function, and we indeed believe that all listed cases there are treated one way or the other.
comment:296 followup: 305 Changed 8 years ago by
Replying to nthiery:
Salut Vincent!
Thanks for the feedback.
On Tue, Mar 31, 2015 at 12:46:35PM 0000, sagetrac wrote:
There are several things that I do not quite understand. Could you explain or modify it:
 The iterator
IntegerListLex
aims to be fast and lowlevel. What is the point of using theParent
/Element
stuff? WhyClonableArray
are better than Python lists?We haven't changed this aspect (in this ticket we focused on refactoring without changing the API): internally, Python lists are used; by default, they are converted to ClonableArray? upon being yielded. The element constructor can be customized to return plain lists if so desired.
In the current state of affairs, this does not really make a difference:
...
For the record: using the parent/element protocol does not necessarily cause a large overhead; ClonableArray? is almost as fast as list (timings to be of course taken with a grain of salt given how small values we are speaking about here):
I know that it has not changed. If you modify the constructor to return list, the list is copied twice instead of once. I would not call that a solution.
Most importantly, that was not my point. It makes no sense that a plain Python iterator inherit from Parent. It is a question of design, not of timings. The thing is that tuples and lists are the standard Python objects. This is the way the Python module itertools
behaves. Ideally, the IntegerListLex
should be plainly Python compatible.
The overhead comes from the containment test that we do in the
check
method:
# ClonableArray, with check made trivial sage: sage: L = IntegerListsLex(50, min_part=1, max_slope=0) sage: sage: it = iter(L) sage: sage: %timeit x = it.next() 10000 loops, best of 3: 135 µs per loopI am not sure this containment check is useful. We could just disable it. What do you think?
Definitely!
In the long run, when
IntegerListsLex
will be cythonized, the relative situation may change, since we can hope for speedups of 10100. Note in particular that we most likely will want to use arrays of ints internally;ClonableIntArray
might be a good candidate for this. Or just STL vectors.
Note that in Python 3 there are arrays of int (as in numpy in Python 2):
But I do not think that itertools
will use that.
 Having a nested class seems overkill. The class
_Iter
is created only once in__iter__
. Moreover, all methods in it starts with `p = self.parent. Why do you need to create this extra
_Iter` class? Why does it need to be a nested class?The class is needed because the iterator has an internal state. So we need to create a separate object for each concurrently running iterator.
Right. But why is it nested? It will be a mess with Cythonization.
I find that using a nested class
IntegerListsLex._Iter
, rather thanIntegerListsLexIter
makes the relation between the two classes explicit (_Iter
is for internal use for IntegerListsLex?`). It's also consistent with what we do elsewhere (Element
, ...). And there is no overhead in doing so.
Having two classes in a file called IntegerListLex
and IntegerListLexIterator
is rather explicit. I am not sure that following the Parent/Element? direction is the best here. As I said before, it would be cool if this file would be Python compatible.
 Do you have a use case for
sage: IntegerListsLex(NN, max_length=3) Disjoint union of Lazy family (<lambda>(i))_{i in Non negative integer semiring}The feature only appears once in the doc in a place which does not appear in the reference manual.It does appear in the reference manual: see section `Input list or iterable for the sum
of the main
IntegerListLex?` class.The feature of iterating by increasing sum is certainly useful. Whether we want the above syntactic sugar  instead of just using DisjointUnionEnumeratedSets?  is indeed questionable. The feature was already there, so we kept it to not change the API in this ticket.
It is reasonable to keep it in the ticket. But what if I do remove it in another ticket?
 Why
_check_lexicographic_iterable
is a cached method? And I do not get why is it called from_Iter
and not at the initialization ofIntegerListsLex
.We discussed this with Jeroen in some earlier comment. Putting it in the iterator let the user create the
IntegerListsLex
object, even if it's not finite/iterable. This could be useful for other things than iteration, like membership testing or building the corresponding polytopes (once #17920 will be available).
Right. (And counting).
Vincent
comment:297 followup: 302 Changed 8 years ago by
Adding extra conditions breaks things:
sage: IntegerListsLex(ceiling=[2], floor=[4]).list() # good! [[]] sage: IntegerListsLex(7, ceiling=[2], floor=[4]).list() ... ValueError: Could not check that the specified constraints yield a finite set
comment:298 followup: 311 Changed 8 years ago by
Similarly:
sage: IntegerListsLex(max_part=0).list() [[]] sage: IntegerListsLex(7, max_part=0).list() ... ValueError: Could not check that the specified constraints yield a finite set
comment:299 followup: 312 Changed 8 years ago by
This is one more example which currently does not work:
sage: IntegerListsLex(length=1, max_slope=0, min_slope=1).list()
comment:300 Changed 8 years ago by
Status:  needs_review → needs_work 

comment:301 Changed 8 years ago by
Commit:  dcbad454879b348c727b87a46b0fef0e360f0471 → 3f534ca86284b0cebb461c2e0a45a7eb74de7543 

Branch pushed to git repo; I updated commit sha1. New commits:
3f534ca  17979 moved one of the finiteness tests

comment:302 Changed 8 years ago by
Replying to jdemeyer:
Adding extra conditions breaks things:
sage: IntegerListsLex(ceiling=[2], floor=[4]).list() # good! [[]] sage: IntegerListsLex(7, ceiling=[2], floor=[4]).list() ... ValueError: Could not check that the specified constraints yield a finite set
Oops, sorry, my mistake. I had put the test in the wrong spot. This part should be fixed now.
comment:303 followup: 307 Changed 8 years ago by
Please use ....:
for doctest continuation (see patchbot report)
comment:304 Changed 8 years ago by
Commit:  3f534ca86284b0cebb461c2e0a45a7eb74de7543 → a993265c284c12b96f777104ee6dba6d1eee4a9e 

Branch pushed to git repo; I updated commit sha1. New commits:
224cdcd  17979: avoid a copy if the element constructor is copy safe (list or tuple for now)

dd90722  17979: disable check for elements

0b64f4a  17979: avoid a copy if the element constructor is copy safe: added ClonableArray

00577b0  17979: disable check for elements: better implementation that does not prevent from manually checking elements

a993265  Merge branch 'public/ticket/17979' of trac.sagemath.org:sage into combinat/integer_lists_lex

comment:305 Changed 8 years ago by
On Wed, Apr 01, 2015 at 08:15:51AM 0000, sagetrac wrote:
I know that it has not changed.
Then please discuss this in another ticket to not delay this one.
If you modify the constructor to return list, the list is copied
twice instead of once. I would not call that a solution.
It's trivial to introduce a special case to avoid the copy if the element constructor is known to be safe. In fact it's done now.
Most importantly, that was not my point. It makes no sense that a plain Python iterator inherit from Parent. It is a question of design, not of timings. The thing is that tuples and lists are the standard Python objects. This is the way the Python module
itertools
behaves. Ideally, theIntegerListLex
should be plainly Python compatible.
(for the record, the iterator itself does not inherit from Parent).
I would go even further than you: IntegerListsLex? uses nothing specific of Python either. It would be best implemented as a standalone C++ library. It could then be reused by software outside of the Python world, be templated by whatever structure we want to use for the lists, possibly benefit from further low level optimizations (silk, special processor instructions), etc.
But this discussion belongs to later tickets. Here the goal is to get a correct algorithm. The next step is to get an algorithm with reasonably optimal complexity (while further clarifying its structure). And then should come the rewriting in a low level language.
The overhead comes from the containment test that we do in the
check
method:
# ClonableArray, with check made trivial sage: sage: L = IntegerListsLex(50, min_part=1, max_slope=0) sage: sage: it = iter(L) sage: sage: %timeit x = it.next() 10000 loops, best of 3: 135 µs per loopI am not sure this containment check is useful. We could just disable it. What do you think?
Definitely!
Done. Easy to revert if anyone is uncomfortable with this.
Right. But why is it nested? It will be a mess with Cythonization.
At the end, it's all about stylistic preference. It's instantaneous to change if/when desired. Whoever will work next on this can change to his own preferred style. I am not discussing this further.
Having two classes in a file called
IntegerListLex
andIntegerListLexIterator
is rather explicit. I am not sure that following the Parent/Element? direction is the best here. As I said before, it would be cool if this file would be Python compatible.
Nested classes are a feature of plain Python, and of many other programming languages. It turns out that Cython does not support them now, but I don't see any theoretical obstruction (and it can be easily emulated).
Altogether I see no compelling reason not to use this feature when it helps better structure the code.
It is reasonable to keep it in the ticket. But what if I do remove it in another ticket?
I don't have an objection if someone takes the responsibility for this backward incompatible change in a later ticket :)
Or maybe, if the use case emerges, one should actually go the other way round: make it syntactically trivial to have variants of IntegerListsLex?, graded by any or both of the length and size parameters: it's not as generic as DisjointUnionEnumeratedSets?, but this could save on time by sharing quite some stuff between the graded components (e.g. the parsing of the arguments, the upper and lower envelopes, ...).
Cheers,
Nicolas
comment:306 Changed 8 years ago by
Commit:  a993265c284c12b96f777104ee6dba6d1eee4a9e → 56192a9a186bd197616321045fb10c06b1c0c07c 

Branch pushed to git repo; I updated commit sha1. New commits:
56192a9  17979: fixed old continuation string in integer_list_old.py

comment:307 Changed 8 years ago by
Replying to chapoton:
Please use
....:
for doctest continuation (see patchbot report)
Fixed, I believe.
comment:308 Changed 8 years ago by
Status:  needs_work → needs_review 

comment:309 Changed 8 years ago by
Status:  needs_review → needs_work 

comment:310 Changed 8 years ago by
Commit:  56192a9a186bd197616321045fb10c06b1c0c07c → 4b4c54e075e768ba24186583d4ba033419982cba 

Branch pushed to git repo; I updated commit sha1. New commits:
4b4c54e  17979 fixed another case in _check_lexicographic_iterable

comment:311 Changed 8 years ago by
Replying to jdemeyer:
Similarly:
sage: IntegerListsLex(max_part=0).list() [[]] sage: IntegerListsLex(7, max_part=0).list() ... ValueError: Could not check that the specified constraints yield a finite set
Fixed.
comment:312 followup: 314 Changed 8 years ago by
Replying to jdemeyer:
This is one more example which currently does not work:
sage: IntegerListsLex(length=1, max_slope=0, min_slope=1).list()
The current output is correct, isn't it? [Infinity] would be the output in inverse lexicographic order, which results in the error message that m is unbounded.
comment:313 Changed 8 years ago by
Status:  needs_work → needs_review 

comment:314 followup: 333 Changed 8 years ago by
Replying to aschilling:
Replying to jdemeyer:
This is one more example which currently does not work:
sage: IntegerListsLex(length=1, max_slope=0, min_slope=1).list()The current output is correct, isn't it? [Infinity] would be the output in inverse lexicographic order, which results in the error message that m is unbounded.
Sorry, I obviously meant
sage: IntegerListsLex(length=2, max_slope=0, min_slope=1).list()
which should have an empty output.
comment:315 followup: 336 Changed 8 years ago by
Status:  needs_review → needs_work 

Another case of "adding a constraint break things":
sage: IntegerListsLex(max_sum=1, min_sum=4).list() [] sage: IntegerListsLex(max_sum=1, min_sum=4, min_slope=0).list() ... ValueError: Could not check that the specified constraints yield a finite set
comment:316 followup: 354 Changed 8 years ago by
Design comment: the code for Envelope
has a lot of duplication because it needs to deal with upper and lower bounds. Instead, I would propose to have Envelope
deal only with upper bounds. The Envelope
for the lower bound could then be implemented by adding minus signs in the input and output of Envelope
.
comment:317 followup: 351 Changed 8 years ago by
The code in IntegerListsLex.__init__
could be simplified.
Compare this from #17920:
if n is not None: n = integer_or_infinity(n) min_sum = n max_sum = n # Set self.n, which is not used by IntegerLists_polyhedron, # but by some derived classes self.n = n if length is not None: min_length = length max_length = length if min_length < 0: min_length = 0 self.min_sum = integer_or_infinity(min_sum) self.max_sum = integer_or_infinity(max_sum) self.min_length = integer_or_infinity(min_length) self.max_length = integer_or_infinity(max_length) self.min_part = integer_or_infinity(min_part) self.max_part = integer_or_infinity(max_part) self.min_slope = integer_or_infinity(min_slope) self.max_slope = integer_or_infinity(max_slope)
to this from #17979:
if n is not None: n = ZZ(n) self._min_sum = n self._max_sum = n else: self._min_sum = min_sum self._max_sum = max_sum if length is not None: length = ZZ(length) min_length = length max_length = length else: min_length = ZZ(min_length) if min_length < 0: min_length = 0 if max_length != Infinity: max_length = ZZ(max_length) self._max_length = max_length self._min_length = min_length if min_slope != Infinity: min_slope = ZZ(min_slope) self._min_slope = min_slope if max_slope != Infinity: max_slope = ZZ(max_slope) self._max_slope = max_slope min_part = ZZ(min_part) if min_part < 0: raise NotImplementedError("strictly negative min_part") if max_part != Infinity: max_part = ZZ(max_part)
comment:318 followup: 332 Changed 8 years ago by
The call to _check_lexicographic_iterable
should be moved to IntegerListsLex.__iter__
comment:319 followup: 322 Changed 8 years ago by
The global_options
is undocumented and is used only there:
if global_options is not None: self.global_options = global_options
Also (see Jeroen's message) the following line
if min_length < 0: min_length = 0
Can be rewritten as min_length=max(min_length,0)
.
Nathann
comment:320 Changed 8 years ago by
This should either return []
or raise a ValueError
saying that min_sum=Infinity
is not allowed:
sage: IntegerListsLex(min_sum=Infinity).list() ... ValueError: Could not check that the specified constraints yield a finite set
comment:321 followup: 342 Changed 8 years ago by
Commit:  4b4c54e075e768ba24186583d4ba033419982cba → c5f8c92e14e3a507f262799872902bf3d0b720df 

comment:322 Changed 8 years ago by
Replying to ncohen:
The
global_options
is undocumented and is used only there:if global_options is not None: self.global_options = global_options
It is actually used by Partitions
. Given that this is not a regression, I don't consider this a problem.
comment:323 Changed 8 years ago by
def _check_lexicographic_iterable(self): """ Check whether the constraints give a finite set.
If this function checks that the constraints give a finite set, could you pick a name for it which reflects it ?
Nathann
comment:324 Changed 8 years ago by
Commit:  c5f8c92e14e3a507f262799872902bf3d0b720df → e60c3321ea62eeec8e8a1a07d964198ed8205479 

Branch pushed to git repo; I updated commit sha1. New commits:
e60c332  trac #17979: Equivalent local rewrite for better readability

comment:325 followup: 328 Changed 8 years ago by
The first lines of _check_lexicographic_iterable
are if self._warning or not self._check: return
.
It sounds a bit wrong that the check function would do nothing when explicitly asked to. Instead of stopping early in this situation, could you remove those two lines and only call the function when you mean to?
This would give the function its original meaning: check the data.
Note that the function is only called once.
Nathann
comment:326 followup: 349 Changed 8 years ago by
The function _possible_m(self, m, j, min_sum, max_sum)
takes four parameters, all of which are attributes of self
.
if self._next_state == LOOKAHEAD: m = self._current_list[1] if self._possible_m(m, self._j, min_sum  (self._current_summ), max_sum  (self._current_summ)):
It would make more sense to me if this function had no arguments at all.
comment:327 Changed 8 years ago by
Commit:  e60c3321ea62eeec8e8a1a07d964198ed8205479 → 8e772296baa21463a7a8f1957fd4e4e918c5414e 

Branch pushed to git repo; I updated commit sha1. New commits:
8e77229  trac #17979: list[:] is faster than copy(l) and harmless comments

comment:328 Changed 8 years ago by
Replying to ncohen:
The first lines of
_check_lexicographic_iterable
areif self._warning or not self._check: return
.It sounds a bit wrong that the check function would do nothing when explicitly asked to. Instead of stopping early in this situation, could you remove those two lines and only call the function when you mean to?
This would give the function its original meaning: check the data.
+1
comment:329 Changed 8 years ago by
Commit:  8e772296baa21463a7a8f1957fd4e4e918c5414e → 24d6494a2b19e32d3858e67455a2857d078117c6 

Branch pushed to git repo; I updated commit sha1. New commits:
24d6494  trac #17979: No need for a STOP state

comment:330 Changed 8 years ago by
Commit:  24d6494a2b19e32d3858e67455a2857d078117c6 → 8e772296baa21463a7a8f1957fd4e4e918c5414e 

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
comment:332 followup: 338 Changed 8 years ago by
Replying to jdemeyer:
The call to
_check_lexicographic_iterable
should be moved toIntegerListsLex.__iter__
Why? That breaks a lot of tests.
comment:333 followup: 339 Changed 8 years ago by
Replying to jdemeyer:
Replying to aschilling:
Replying to jdemeyer:
This is one more example which currently does not work:
sage: IntegerListsLex(length=1, max_slope=0, min_slope=1).list()The current output is correct, isn't it? [Infinity] would be the output in inverse lexicographic order, which results in the error message that m is unbounded.
Sorry, I obviously meant
sage: IntegerListsLex(length=2, max_slope=0, min_slope=1).list()which should have an empty output.
Even in this case, I think Sage is currently correct, unless you can define what InfinityInfinity is (which would be used in the slope conditions).
comment:334 followup: 340 Changed 8 years ago by
Commit:  8e772296baa21463a7a8f1957fd4e4e918c5414e → 58dced5c7b2eab36e50ba5df66d5cc562b14b2a8 

Branch pushed to git repo; I updated commit sha1. New commits:
58dced5  17979 address some review comments

comment:335 Changed 8 years ago by
Commit:  58dced5c7b2eab36e50ba5df66d5cc562b14b2a8 → d66d70dd8325ccb638289870c626652ac81d0fc7 

Branch pushed to git repo; I updated commit sha1. New commits:
d66d70d  17979 fixed another corner case

comment:336 Changed 8 years ago by
Replying to jdemeyer:
Another case of "adding a constraint break things":
sage: IntegerListsLex(max_sum=1, min_sum=4).list() [] sage: IntegerListsLex(max_sum=1, min_sum=4, min_slope=0).list() ... ValueError: Could not check that the specified constraints yield a finite set
Fixed.
comment:337 Changed 8 years ago by
Status:  needs_work → needs_review 

comment:338 Changed 8 years ago by
Replying to aschilling:
Replying to jdemeyer:
The call to
_check_lexicographic_iterable
should be moved toIntegerListsLex.__iter__
Why?
Because it is really more logical that such a check would happen in the parent before creating the iterator. The iterator should just iterate. The check belongs to the code creating the iterator. Also, the check_finiteness
refers a lot to attributes of the parent, which means that it really belongs there.
comment:339 Changed 8 years ago by
Replying to aschilling:
Sorry, I obviously meant
sage: IntegerListsLex(length=2, max_slope=0, min_slope=1).list()which should have an empty output.
Even in this case, I think Sage is currently correct
Sage is indeed correct that there is an infinite upper bound for part[0]
. However, my point is that the resulting list is still finite, so this example could work.
unless you can define what InfinityInfinity is (which would be used in the slope conditions).
I don't see why I would need to define Infinity  Infinity for this. My point is that the set of lists satisfying those constraints is clearly empty.
comment:340 followup: 341 Changed 8 years ago by
Replying to git:
Branch pushed to git repo; I updated commit sha1. New commits:
58dced5 17979 address some review comments
You literally added just a check for min_sum == Infinity
? That's just completely inconsistent with the rest of the code. Please look at IntegerListsLex.__init__
. Really, do it. You will agree that it's an ugly mess, see also 317 (which just got worse).
comment:341 followup: 352 Changed 8 years ago by
comment:342 Changed 8 years ago by
Replying to git:
Branch pushed to git repo; I updated commit sha1. New commits:
c9a047c trac #17979: Move imports to the (only) place in which they are used
For the import of plain Python modules, I don't really see the
point. It's very unlikely that we will save on Sage startup time. On
the other hand, for e.g. import collections
, we will pay a (small)
penalty each time an IntegerListsLex
object is created.
c5f8c92 trac #17979: Replace l with sum(l) as it is only used twice
Agreed for using sum(l)
instead of l
as notation.
On the other hand, I found useful to mention all the relevant parameters on which we will put constraints in the introductory paragraph, even if they are indeed trivial. Please revert if you agree with that.
Cheers,
Nicolas
comment:343 Changed 8 years ago by
Commit:  d66d70dd8325ccb638289870c626652ac81d0fc7 → 64980f5081fbf83f2bfffe654ce18f53b407b3b5 

Branch pushed to git repo; I updated commit sha1. New commits:
64980f5  17979: avoid a copy if the element constructor is copy safe: Oops: added ClonableArray in the correct place now

comment:344 Changed 8 years ago by
Commit:  64980f5081fbf83f2bfffe654ce18f53b407b3b5 → b535b54ff8c571583d6f94da7a6be7ec7f369b3e 

Branch pushed to git repo; I updated commit sha1. New commits:
b535b54  17979: type checking on min_sum and max_sum

comment:345 Changed 8 years ago by
Commit:  b535b54ff8c571583d6f94da7a6be7ec7f369b3e → 7d5bad06bf5ce400409cb749af2bf244e4ced160 

Branch pushed to git repo; I updated commit sha1. New commits:
7d5bad0  17979: type checking on min_sum and max_sum: updated doctests + tiny formating change

comment:346 Changed 8 years ago by
Commit:  7d5bad06bf5ce400409cb749af2bf244e4ced160 → 277905127aa2f446a30bc831c5b810c439709c10 

Branch pushed to git repo; I updated commit sha1. New commits:
2779051  17979: ._warning > ._floor_or_ceiling_is_function + make _check_finiteness report an error instead of hanging when the latter is True

comment:347 Changed 8 years ago by
Commit:  277905127aa2f446a30bc831c5b810c439709c10 → 5b32ad4d265c923364dc0b61056c791a76afe9fb 

Branch pushed to git repo; I updated commit sha1. New commits:
5b32ad4  17979: reinserted deleted comment + minor formating

comment:348 Changed 8 years ago by
Commit:  5b32ad4d265c923364dc0b61056c791a76afe9fb → d976b2087e17107f748b1cbe05f3fab93ea81734 

Branch pushed to git repo; I updated commit sha1. New commits:
d976b20  17979: moved call to _check_finiteness to __iter__

comment:349 followup: 356 Changed 8 years ago by
Replying to ncohen:
The function
_possible_m(self, m, j, min_sum, max_sum)
takes four parameters, all of which are attributes ofself
.if self._next_state == LOOKAHEAD: m = self._current_list[1] if self._possible_m(m, self._j, min_sum  (self._current_summ), max_sum  (self._current_summ)):It would make more sense to me if this function had no arguments at all.
I agree that this should eventually become an argumentless
look_ahead
method that tests if the current list could possibly be a
prefix of some valid list.
I would like to postpone this change to #18055 however: anyway this
method will need to be rewritten there (in particular to handle an
empty current_list
), and changing the interface now would require
rewriting most of the current tests of _possible_m
to construct a
bunch of different IntegerListsLex? objects instead of just passing
various arguments. Note also that, as specified in the doc, min_sum
and max_sum
do not exactly match the corresponding attributes: they
are bounds on the tail of the list only (agreed, the difference above
could be done in _possible_m).
Cheers,
Nicolas
comment:350 Changed 8 years ago by
Commit:  d976b2087e17107f748b1cbe05f3fab93ea81734 → ffa4d20e61f5d8d71e5a2cd48ae39a345793f45b 

Branch pushed to git repo; I updated commit sha1. New commits:
ffa4d20  17979: simplification in __init__

comment:351 Changed 8 years ago by
Replying to jdemeyer:
The code in
IntegerListsLex.__init__
could be simplified.
Done. Thanks for the for #17920' model.
I ended up not using integer_or_infinity
: here I prefer to not
accept both oo
and +oo
when only one makes sense, and having two
functions (or one with parameters) seemed like overkill. This is
explicit and simple enough:
self._max_length = ZZ(max_length) if max_length != Infinity else max_length
Cheers,
Nicolas
comment:352 Changed 8 years ago by
comment:353 Changed 8 years ago by
Commit:  ffa4d20e61f5d8d71e5a2cd48ae39a345793f45b → 80ad5c8897ea2714a76a7a341b5652d622ae291a 

Branch pushed to git repo; I updated commit sha1. New commits:
80ad5c8  17979: Fixed corner case of comment:314

comment:354 followups: 357 360 369 Changed 8 years ago by
Replying to jdemeyer:
Design comment: the code for
Envelope
has a lot of duplication because it needs to deal with upper and lower bounds. Instead, I would propose to haveEnvelope
deal only with upper bounds. TheEnvelope
for the lower bound could then be implemented by adding minus signs in the input and output ofEnvelope
.
I am also not so happy about this. I had considered doing something along the lines you propose, and ended up dropping it for now. This is mainly because, in the next step, the main functionality to add will be the computation of the area below the envelope for which we won't have this symmetry anymore. Also, at this point, we are speaking about 56 lines of code that are duplicated very locally. Doing the magic would not take much less than this, and the code would be less straightforward. Sooo, well.
comment:355 Changed 8 years ago by
I believe all the comments have been taken care of. Back to needs review!
Nathann: in case you are around, I am roughly in my office until 2pm.
comment:356 followup: 361 Changed 8 years ago by
Hello,
In 322 Jeroen agreed above that 319 was in fact ok.
Many times in the past I had to fix code which accepts a **kwds
and did not check that what it contains is actually read. This
lead to silent errors or wrong output, and so I see
things like global_options
as the highway to bugs.
Jeroen noted that this variable is actually used somewhere else, so I guess it probably should not be removed in this ticket. My comment at 319 still need to be adressed, however, as there is no documentation for this parameter. Please make it explain the uses of this flag, possibly by pointing to some other part of the doc if it is already explained somewhere else.
The function
_possible_m(self, m, j, min_sum, max_sum)
takes four parameters, all of which are attributes ofself
.I agree that this should eventually become an argumentless
look_ahead
method that tests if the current list could possibly be a prefix of some valid list. I would like to postpone this change to #18055 however
As the method appears in this branch, I see no reason to let it be corrected in a future ticket.
Nathann
comment:357 followup: 379 Changed 8 years ago by
Why is there duplication of Envelope
and _upper_envelope
?
comment:358 Changed 8 years ago by
Commit:  80ad5c8897ea2714a76a7a341b5652d622ae291a → a0d2e639b0705327281759a89f6cda05a2288e25 

Branch pushed to git repo; I updated commit sha1. New commits:
a0d2e63  17979: documentation for global_options

comment:359 Changed 8 years ago by
Commit:  a0d2e639b0705327281759a89f6cda05a2288e25 → 3e3c7f6075e3b673911eb22faf427b0fb2a17b87 

Branch pushed to git repo; I updated commit sha1. New commits:
3e3c7f6  Simplify Envelope by using a sign

comment:360 followup: 482 Changed 8 years ago by
Replying to nthiery:
Also, at this point, we are speaking about 56 lines of code that are duplicated very locally.
It's more than that and it can only get worse if more features are added to Envelope
.
and the code would be less straightforward.
I disagree with this. I think code duplication is always a high risk for bugs.
Anyway, I implemented this in this last commit.
comment:361 followup: 362 Changed 8 years ago by
Replying to ncohen:
Many times in the past I had to fix code which accepts a
**kwds
and did not check that what it contains is actually read. This lead to silent errors or wrong output, and so I see things likeglobal_options
as the highway to bugs.
**kwds
arguments can be painful, I certainly agree.
But fear not, __init__
takes no kwds. It only accepts a preexisting
global_options object, and assigns it to the attribute
_global_options
, that's it.
Jeroen noted that this variable is actually used somewhere else, so I guess it probably should not be removed in this ticket. My comment at 319 still need to be adressed, however, as there is no documentation for this parameter. Please make it explain the uses of this flag, possibly by pointing to some other part of the doc if it is already explained somewhere else.
I had not documented it to not advertise it, since we may well get rid of it. Now there is a documentation that spells exactly what it does.
New commits:
a0d2e63  17979: documentation for global_options

3e3c7f6  Simplify Envelope by using a sign

comment:362 followups: 365 366 376 Changed 8 years ago by
Status:  needs_review → needs_work 

Hello,
**kwds
arguments can be painful, I certainly agree.But fear not,
__init__
takes no kwds. It only accepts a preexisting global_options object, and assigns it to the attribute_global_options
, that's it.
I think that my explanation above applies anyway. Unless there are checks that everything which is stored in global_options
makes sense (and that there are exceptions when I do MyObject(global_options={'whatever':'whatever'}
then **kwds
and global_options
are as dangerous as each other.
I set the ticket back to needs_work
because of the previous comments on _possible_m(self, m, j, min_sum, max_sum)
.
Nathann
comment:363 followup: 364 Changed 8 years ago by
Hi Jeroen,
I appreciate that you substantiate your point of view with action. I
am not going to waste time debating this for I want this ticket to
move forward. But I still think that the original Envelope was better,
for the reasons I mentionned above. Besides, I had voluntarily used
==Infinity
in my tests to not set in stone which infinity was
returned.
Nicolas
comment:364 followup: 368 Changed 8 years ago by
Replying to nthiery:
Besides, I had voluntarily used
==Infinity
in my tests to not set in stone which infinity was returned.
I understood that, but it's cleaner this way. And if Infinity
ever changes, it's a trivial change anyway.
comment:365 followup: 367 Changed 8 years ago by
Replying to ncohen:
I think that my explanation above applies anyway. Unless there are checks that everything which is stored in
global_options
makes sense (and that there are exceptions when I doMyObject(global_options={'whatever':'whatever'}
then**kwds
andglobal_options
are as dangerous as each other.
Whatever garbage is stored in global_options
has zero influence on
IntegerListsLex
. If you are not happy with other classes using this
feature, then change it out there. This has nothing to do with this
ticket.
comment:366 Changed 8 years ago by
Replying to ncohen:
I think that my explanation above applies anyway. Unless there are checks that everything which is stored in
global_options
makes sense (and that there are exceptions when I doMyObject(global_options={'whatever':'whatever'}
then**kwds
andglobal_options
are as dangerous as each other.
I think this is outside the scope of this ticket.
comment:367 Changed 8 years ago by
Whatever garbage is stored in
global_options
has zero influence onIntegerListsLex
. If you are not happy with other classes using this feature, then change it out there. This has nothing to do with this ticket.
It is true. I do not think that I asked for this to be changed. I merely pointed the lack of documentation (now fixed) and explained the reason why I believe that it is a very bad practice.
Nathann
comment:368 Changed 8 years ago by
Replying to jdemeyer:
Replying to nthiery:
Besides, I had voluntarily used
==Infinity
in my tests to not set in stone which infinity was returned.I understood that, but it's cleaner this way. And if
Infinity
ever changes, it's a trivial change anyway.
I don't see why it's cleaner; it's just a different specification. But let's move on.
comment:369 followups: 370 377 Changed 8 years ago by
Replying to nthiery:
the computation of the area below the envelope for which we won't have this symmetry anymore.
Why not? It's just the sum of the first n
values, right?
comment:370 followup: 371 Changed 8 years ago by
comment:371 followup: 373 Changed 8 years ago by
Replying to aschilling:
The point is that this function would take backward smoothing (using the slope conditions) into account.
Even then, I don't see why this is incompatible with the "sign" option.
comment:372 Changed 8 years ago by
Commit:  3e3c7f6075e3b673911eb22faf427b0fb2a17b87 → 855685a47831a829bd3f9e850da2a5dbcfeaab5a 

comment:373 Changed 8 years ago by
Replying to jdemeyer:
Replying to aschilling:
The point is that this function would take backward smoothing (using the slope conditions) into account.
Even then, I don't see why this is incompatible with the "sign" option.
You are probably right with the correct definition of the slopes.
I believe all comments have been taken into account now?
comment:374 Changed 8 years ago by
Status:  needs_work → needs_review 

comment:375 Changed 8 years ago by
Commit:  855685a47831a829bd3f9e850da2a5dbcfeaab5a → 4ff20b7d6fb8fb7379673318bbaa59203db8c2e4 

comment:376 Changed 8 years ago by
Replying to ncohen:
I set the ticket back to
needs_work
because of the previous comments on_possible_m(self, m, j, min_sum, max_sum)
.
Done.
comment:377 Changed 8 years ago by
Replying to jdemeyer:
Replying to nthiery:
the computation of the area below the envelope for which we won't have this symmetry anymore.
Why not? It's just the sum of the first
n
values, right?
Mathematically, and up to smoothing, yes. The algorithmic will be somewhat more involved than this for achieving good complexity, but fair enough, I guess it can be made to work.
comment:378 Changed 8 years ago by
Commit:  4ff20b7d6fb8fb7379673318bbaa59203db8c2e4 → 03f007c702d2baf546f00442f60ee941795789d8 

Branch pushed to git repo; I updated commit sha1. New commits:
03f007c  17979: improved doc of lower/upper_envelope

comment:379 Changed 8 years ago by
Replying to jdemeyer:
Why is there duplication of
Envelope
and_upper_envelope
?
The role of _upper_envelope
is to slightly tweak the global ceiling
(an existing already smoothed Envelope
object) to take into account
the additional local constraint that the current value at position j
is m
. Similarly for _lower_envelope
.
So the two features are similar in the nature of their goal, but differ in what they actually need to do to achieve it. So merging them is unlikely to save any duplication while likely to add complexity.
On the other hand, I agree it would be nice to better clarify this distinction between the two features in the method names. Suggestions welcome.
New commits:
03f007c  17979: improved doc of lower/upper_envelope

comment:380 followup: 382 Changed 8 years ago by
Status:  needs_review → needs_info 

Since _upper_envelope
deals with ceiling bounds and refers only to information which is already contained in _ceiling
, it looks like _upper_envelope
should really be a method of Envelope
(then better without the leading underscore). So please justify why you think this should not be the case.
comment:381 Changed 8 years ago by
Commit:  03f007c702d2baf546f00442f60ee941795789d8 → 2c7019c64047f5f84d89d72fec81a7af483cdc66 

Branch pushed to git repo; I updated commit sha1. New commits:
2c7019c  17979: _upper_bound / _lower_bound > adapt method of Envelope

comment:382 Changed 8 years ago by
Replying to jdemeyer:
Since
_upper_envelope
deals with ceiling bounds and refers only to information which is already contained in_ceiling
, it looks like_upper_envelope
should really be a method ofEnvelope
(then better without the leading underscore). So please justify why you think this should not be the case.
I agree that it's better; thanks for the suggestion! Done.
Cheers,
Nicolas
comment:383 followup: 385 Changed 8 years ago by
We have been working hard to make the deadline for the release. Like in any piece of code, there certainly are other internal microrefactoring that could possibly be done. If you note one, please be specific on whether you believe it really needs to be done now, or could be postponed to one of the follow up tickets; especially since some of those tickets may well induce complete rewrite of the ditto microrefactored code anyway.
comment:384 Changed 8 years ago by
Status:  needs_info → needs_review 

comment:385 followup: 391 Changed 8 years ago by
We have been working hard to make the deadline for the release. Like in any piece of code, there certainly are other internal microrefactoring that could possibly be done. If you note one, please be specific on whether you believe it really needs to be done now, or could be postponed to one of the follow up tickets; especially since some of those tickets may well induce complete rewrite of the ditto microrefactored code anyway.
Have you had the impression that some of our previous requests were abusive? We try to understand your code, make sure that it is correct maintenable and thus that it will be easy to understand and work on it in the future.
Many of the things that seem obvious to the author are not easily deduced when you only look at the code, and unexpected design choices often raise more questions.
I personally gave up raising some arguments (that still seem legitimate to me) only to lessen the load on this ticket. I still plan to read the code you implement totally (I haven't done that yet), and I will probably have more time to do so next week.
Nathann
comment:386 Changed 8 years ago by
Status:  needs_review → needs_work 

One more "adding constraints break" issue:
sage: IntegerListsLex(5, max_part=0).list() [] sage: IntegerListsLex(5, max_part=0, min_slope=0).list() ... ValueError: Could not check that the specified constraints yield a finite set
comment:387 Changed 8 years ago by
This is a more difficult example where the list is finite (because the sum of the lower envelope eventually becomes larger than the sum):
sage: IntegerListsLex(7, floor=[4], max_part=4, min_slope=1).list() ... ValueError: Could not check that the specified constraints yield a finite set
This should either be fixed or be documented as an example where the check isn't good enough.
comment:388 followup: 395 Changed 8 years ago by
I do find it surprisingly inconsistent that
sage: IntegerListsLex(7, floor=[4,3,2,1], max_part=4, min_slope=1).list()
works but
sage: IntegerListsLex(7, floor=[4], max_part=4, min_slope=1).list()
does not.
comment:389 Changed 8 years ago by
This hangs:
sage: IntegerListsLex(7, max_part=0, ceiling=lambda i:i).list()
comment:390 followup: 393 Changed 8 years ago by
In _check_finiteness()
, I think you should move from a blacklist model to a whitelist model: don't raise an exception if certain conditions are satisfied, but raise an error unless the input can be seen to be finite. This logic could not have the problem that adding conditions breaks things.
comment:391 followup: 403 Changed 8 years ago by
Replying to ncohen:
Have you had the impression that some of our previous requests were abusive? We try to understand your code, make sure that it is correct maintenable and thus that it will be easy to understand and work on it in the future.
Many of the things that seem obvious to the author are not easily deduced when you only look at the code, and unexpected design choices often raise more questions.
Abusive, no: they all had to be handled at some point or the other. Urgent: I did wonder for some of them; I agree that we absolutely want the code to be correct (at least to the best of our knowledge) for this rc. And this of course requires a complete understanding of it by the reviewers, and clarification of the design choices. But maybe for some of the issues it's sufficient, once things are clarified, to leave a note in upcoming tickets for the next step that need to be done.
The big thing is that I have the impression to be holding off the upcoming rc, and that's rather uncomfortable. Also having a stable base here would allow me to move on to the following tasks, in particular working of the merge and review of #17920, as well as your ticket about IntegerVectors?. And also would allow me or others to work on to the follow up tickets.
I personally gave up raising some arguments (that still seem legitimate to me) only to lessen the load on this ticket.
I appreciate this! Please add these comments to the followup tickets (or some new one if appropriate), for I want to hear about them.
I still plan to read the code you implement totally (I haven't done that yet), and I will probably have more time to do so next week.
Great, thanks!
From the many discussions with you, Jeroen, Bryan, and Anne and myself, it seems that the code has been scrutinized quite some. As Jeroen pointed out, there are still cases that could be handled in theory, and that the code rejects at this point. But outside of those situations, I pretty much trust that the code gives correct result. Which achieves the original goal of this ticket.
Cheers,
Nicolas
comment:392 Changed 8 years ago by
Commit:  2c7019c64047f5f84d89d72fec81a7af483cdc66 → 7a35dc6ccf60379d060237e544287fda755861ce 

Branch pushed to git repo; I updated commit sha1. New commits:
7a35dc6  17979: rewrite _check_finiteness using a whitelist of proven good cases

comment:393 Changed 8 years ago by
Replying to jdemeyer:
In
_check_finiteness()
, I think you should move from a blacklist model to a whitelist model: don't raise an exception if certain conditions are satisfied, but raise an error unless the input can be seen to be finite. This logic could not have the problem that adding conditions breaks things.
Agreed. It's also easier to check step by step the correctness of each good case. Done.
I am pretty sure I got the list of good cases right. But it's 1 am, so please double check that I did not inadvertently remove a good case. At least all tests in this file pass, and 386 is now fixed.
New commits:
7a35dc6  17979: rewrite _check_finiteness using a whitelist of proven good cases

comment:394 Changed 8 years ago by
Commit:  7a35dc6ccf60379d060237e544287fda755861ce → 3fab366c21e8f479deb8ffbbd6dcb1eb88b72b35 

Branch pushed to git repo; I updated commit sha1. New commits:
3fab366  17979: document the existence of false negatives for _check_finiteness, illustrated with Jeroen's example

comment:395 Changed 8 years ago by
Replying to jdemeyer:
I do find it surprisingly inconsistent that
sage: IntegerListsLex(7, floor=[4,3,2,1], max_part=4, min_slope=1).list()works but
sage: IntegerListsLex(7, floor=[4], max_part=4, min_slope=1).list()does not.
Annoying indeed. The fine point is in the heuristic to decide how deep we want to lookahead to find a lower bound on the total floor area. In a case like this we could potentially compute how deep to go until the floor would reach its limit of zero.
I would tend to postpone that: there is no risk of wrong answer, the
existence of false negatives is now documented in
_check_finiteness
(using the above examples), and the user can set
check=False
to workaround the limitation.
What do you think?
comment:396 Changed 8 years ago by
Commit:  3fab366c21e8f479deb8ffbbd6dcb1eb88b72b35 → 11afea36402955c127a9d6090ecaeaf9e5f7943d 

Branch pushed to git repo; I updated commit sha1. New commits:
11afea3  17979: we *want* to run the finiteness checks even if the input are functions + added related documentation

comment:397 Changed 8 years ago by
Commit:  11afea36402955c127a9d6090ecaeaf9e5f7943d → 3ae7f09acc2f7c2285164f8024fc242b8a668cc7 

Branch pushed to git repo; I updated commit sha1. New commits:
3ae7f09  17979: removed useless lines detected by pyflakes

comment:398 Changed 8 years ago by
Commit:  3ae7f09acc2f7c2285164f8024fc242b8a668cc7 → f5e9eef2776587e85867e42d1c63fbef117788ad 

Branch pushed to git repo; I updated commit sha1. New commits:
f5e9eef  17979: fixed hang reported in comment:389

comment:399 Changed 8 years ago by
Commit:  f5e9eef2776587e85867e42d1c63fbef117788ad → 43a55e3300d63c890f189ce642dd17f0650246ba 

Branch pushed to git repo; I updated commit sha1. New commits:
43a55e3  17979: non negative > nonnegative

comment:400 Changed 8 years ago by
Status:  needs_work → needs_review 

Time to call it a day.
Back to needs review (assuming for now that comment:395 is ok).
comment:401 followup: 402 Changed 8 years ago by
Commit:  43a55e3300d63c890f189ce642dd17f0650246ba → e151d78ea32b9cac2047e2faff3247bdcce1f5d5 

Branch pushed to git repo; I updated commit sha1. New commits:
e151d78  17979 trivial doc fixes

comment:402 followup: 405 Changed 8 years ago by
Regarding Jeroen's comment:395, I think this could possibly be fixed by adjusting ._floor.limit_start() after the smoothing procedure. Note that
sage: C=IntegerListsLex(7, floor=[4,0], max_part=4, min_slope=1) sage: C.list() [[4, 3]]
also works fine. The reason is that
sage: C._floor.limit_start() 2
so that
floor_sum_lower_bound = sum(self._floor(i) for i in range(self._floor.limit_start()))
in line 1076 computes a high enough bound that is caught in line 1082. However, in
sage: C=IntegerListsLex(7, floor=[4], max_part=4, min_slope=1) sage: C._floor.limit_start() 1
even though
sage: for i in range(5): ....: print C._floor(i) ....: 4 3 2 1 0
comment:403 followup: 404 Changed 8 years ago by
Replying to nthiery:
I pretty much trust that the code gives correct result.
To be clear: during all my testing I didn't find a single example where the code actually returned a wrong result. On the other hand, there were many hangs or cases where a superfluous ValueError
was raised.
comment:404 Changed 8 years ago by
Replying to jdemeyer:
Replying to nthiery:
I pretty much trust that the code gives correct result.
To be clear: during all my testing I didn't find a single example where the code actually returned a wrong result. On the other hand, there were many hangs or cases where a superfluous
ValueError
was raised.
This indeed was my overall impression of your comments. Thanks for confirming!
comment:405 Changed 8 years ago by
Replying to aschilling:
Regarding Jeroen's comment:395, I think this could possibly be fixed by adjusting ._floor.limit_start() after the smoothing procedure.
Agreed: we could imagine, in the constructor of Envelope and when a
list is given as input, to set limit_start
not to the end of the
list, but to the point where the limit is actually reached after
smoothing. It should be just a couple lines.
Potential downside: if the parts in the list are very high, this may induce a similarly high limit start, which will trigger more calculations elsewhere. Probably not a common use case, so we might not care.
The other thing is that I could well imagine that, once the new
lookahead is implemented in #18055, the finiteness checking  or at
least the partial lookahead we are doing in _check_finiteness

would become a side product; so might not be worth having something
temporary.
So, reviewers: let us know if this should be done right now.
Cheers,
Nicolas
comment:406 Changed 8 years ago by
In the interest of ever releasing sage6.6 I would prefer to finish a version that provides correct answers now and optimize it later...
comment:407 followups: 408 409 Changed 8 years ago by
I personally have no further comments regarding this ticket. I have tested it a lot in practice, trying hard to break it. I have read most of the structural code, but not the actual algorithm. I would agree with a positive_review for this ticket except for the changes to integer_vector.py
.
comment:408 Changed 8 years ago by
Replying to jdemeyer:
I personally have no further comments regarding this ticket. I have tested it a lot in practice, trying hard to break it. I have read most of the structural code, but not the actual algorithm.
I will do a full review today or tomorrow. Most probably all changes have already been made.
Nathann
comment:409 followup: 410 Changed 8 years ago by
Replying to jdemeyer:
I personally have no further comments regarding this ticket. I have tested it a lot in practice, trying hard to break it.
To say the least!
I have read most of the structural code, but not the actual algorithm. I would agree with a positive_review for this ticket
Thanks for the hard work :)
except for the changes to
integer_vector.py
.
Yup. Note for the release manager: those were checked and validated by Travis and Anne.
comment:410 followup: 411 Changed 8 years ago by
Replying to nthiery:
Yup. Note for the release manager: those were checked and validated by Travis and Anne.
I prefer to hear this from them instead of you speaking for them.
comment:411 Changed 8 years ago by
comment:412 followups: 413 418 419 423 428 434 437 Changed 8 years ago by
Status:  needs_review → needs_work 

Hello,
This is what I did during the last 3~4 hours. I stopped before the end and did
not review m_interval
, _lookahead
nor the code of Envelope
, as I really
should be working on mathematics instead of Sage T_T
Some are easy, some are harder. Also, let me write somewhere that I am against
keeping integer_list_old
in Sage, as I am afraid that it will still be here
several years from now. Here are my comments:
 Module documentation  in the 'itemize' section listing
IntegerListsLex
andEnvelope
, could you add a short description of what they are meant for?
 Why a 'history' section?
 Documentation of
IntegerListsLex
: instead of stating the *purpose* of the class (which is more something one would explain on a trac ticket), what about a SEEALSO section? I have the following paragraph in mind:The main purpose is to provide a generic iteration engine for all the enumerated sets like :class:`Partitions`, class:`Compositions`, :class:`IntegerVectors`. It can also be used to generate many other combinatorial objects like Dyck paths, Motzkin paths, etc.
I thought that it would make more sense as a SEEALSO section pointing toward the mentionned objects.
 About this paragraph:
The set of allowable constraints has been specifically designed to enable iteration with a good time and memory complexity in most practical use cases, and in inverse lexicographic order (see below)
I do not believe that it is true, i.e. that the set of allowable contraints has been specifically designed to enable iteration with a good time and memory complexity.
In particular, it is possible to get great speed improvements by writing a Constant Amortized Algorithm to list only partitions satisfying a smaller set of constraints like (sum,length,min/max part).
This statement sounds wrong to me, and so I believe that it should be removed.
 Documentation of the parameter
n
 you say that a list of integers can be provided but do not explain what the output will be.
 Are
min_sum
andmax_sum
also ignored whenn
is a list? From the doc it seems to be, though I am not sure that it is the best design choice in this case.
 I was surprised by the following output:
sage: IntegerListsLex(3,max_length=3,floor=[1,1,1]).list() [[3], [2, 1], [1, 2], [1, 1, 1]]
I woud have expected the length of the lists to be at least 3, as I requested the first three parts to be>=1
. The documentation is consistent, but I still find it surprising.
check
seems misnamed. It is not about checking the input or output, only about displaying warnings. What about
disable_warnings
instead?
 In the following text which says that one can force the enumeration when it is
formally impossible, can you explicitly say what will happen? "All possible
lists are enumerated, but the ordering is incorrect" or something?
If one wants to proceed anyway, one can sign a waiver by setting check=False:
 About the finiteness check: what about a specific
allow_infinite_iterator
independent from the current 'check'.
 Building the doc of
integer_list.py
withwarnlinks
fails.
sage: list(IntegerListsLex(3, max_length=2, ))
 Lexicographic ordering is broken when
n
is a list.sage: print IntegerListsLex([1,2],length=3).list() [[1, 0, 0], [0, 1, 0], [0, 0, 1], [2, 0, 0], [1, 1, 0], [1, 0, 1], [0, 2, 0], [0, 1, 1], [0, 0, 2]]
In particular, the output differs depending on how
n
is sorted.
 Cardinality is broken when
n
is a listsage: IntegerListsLex(3,length=3).cardinality() 10 sage: IntegerListsLex([3,3],length=3).cardinality() 20
return typecall(cls, n=n, **kwargs)
 for clarity I find the normal syntax better. This place is not a critical part for speed, especially when you createDisjointUnionEnumeratedSets
with lambda functions just above.
 I had not noticed that
IntegerListsLex
objects could have a 'name' argument.. As all arguments, it must be documented in the INPUT section.
 Same for
element_constructor
andelement_class
.
self._max_length = ZZ(max_length) if max_length != Infinity else max_length
Just my two cents: I would return 'Infinity' instead of max_length. You defined yourInfinity
in order to be fast, and you don't know whatmax_length
may be. This occurs several times.
 You can save space and turn the two following tests into one (using the same
'all'). Occurs twice.
if not all(i in ZZ for i in floor): raise TypeError("the parts of floor={} should be nonnegative integers".format(floor)) if not all(i >= 0 for i in floor): raise NotImplementedError("negative parts in floor={}".format(floor))
This would also solve the following, which testsceiling
but mentionsfloor
if not all(i >= 0 for i in ceiling): raise NotImplementedError("negative parts in floor={}".format(ceiling))
# constructor is known to be safe and don't claim ownership on
 "does not".
 Typing
IntegerListsLex.<tab>
in the console is very entertaining. I would be very glad if we some day decide to consider this as a bug.
 about
check_finiteness
> what aboutguess_finiteness
instead, to emphasize that the function makes mistakes?
 The error message when the set is infinite is misleading:
sage: L = IntegerListsLex(4) sage: L._check_finiteness() ... ValueError: Could not check that the specified constraints yield a finite set
The code was able to perform the check, though it was not "able to decide that the set is finite".
 I do not understand this comment:
If a part has no bound on its value, it will be detected at some point
Do you mean that "at some point in iter" it will be detected? Probably not, as this function is called only once.
 The function
_check_finiteness
assumes that the alphabet size is bounded. It is always true when this function is called, but the following raises no warning:sage: for x in IntegerListsLex(NonNegativeIntegers(),max_length=3): ....: pass
For the reason given earlier, the output is not sorted lexicographically. It is not detected as infinite either.
 The many
if A: return
from_check_finiteness
can be replaced by a `if A or B or C or ...: return`.
 in
_check_finiteness
: the documentation oflimit()
says that it is only an upper bound. Thus you cannot write the following:if self._ceiling.limit() < self._floor.limit(): return
 Same comment here
if self._floor.limit() > 0 or self._min_slope > 0: floor_sum_lower_bound = Infinity
 Also, it seems that
limit_start()
can beInfinity
, in which case one cannot deduce anything from the value oflimit
. Please add checks.
 I stop reviewing
_check_finiteness
, as it is complicated while the situation oflimit()
is not cleared.
Which specific bound is returned is not set in stone
. Be more accurate.
Nathann
comment:413 Changed 8 years ago by
Replying to ncohen:
 About this paragraph:
The set of allowable constraints has been specifically designed to enable iteration with a good time and memory complexity in most practical use cases, and in inverse lexicographic order (see below)...
This statement sounds wrong to me, and so I believe that it should be removed.
Agreed.
 I was surprised by the following output:
sage: IntegerListsLex(3,max_length=3,floor=[1,1,1]).list() [[3], [2, 1], [1, 2], [1, 1, 1]]I woud have expected the length of the lists to be at least 3, as I requested the first three parts to be>=1
. The documentation is consistent, but I still find it surprising.
What should be done to make it less surprising? It is completely consistent with min_part=1
.
check
seems misnamed. It is not about checking the input or output, only about displaying warnings. What about
disable_warnings
instead?
I asked for this argument to be called check
. Usually, it's exceptions which are controlled by a check
argument, but I don't see why this cannot be warnings instead.
self._max_length = ZZ(max_length) if max_length != Infinity else max_length
Just my two cents: I would return 'Infinity' instead of max_length. You defined yourInfinity
in order to be fast, and you don't know whatmax_length
may be. This occurs several times.
Agreed, see also integer_or_infinity
from #17920.
 I do not understand this comment:
If a part has no bound on its value, it will be detected at some point
Do you mean that "at some point in iter" it will be detected? Probably not, as this function is called only once.
Agreed that this is confusing. This comment should really be moved to and explained the docstring.
 The many
if A: return
from_check_finiteness
can be replaced by a `if A or B or C or ...: return`.
That's just a matter of style. The many if A: return
might be more clear to read...
comment:415 Changed 8 years ago by
Thanks Nathann for the comments. I'll work on them tomorrow in the plane, taking off at 1pm here. In case you'd have a chance to throw some more before then, I could investigate them at the same occasion.
Cheers,
Nicolas
comment:416 Changed 8 years ago by
Commit:  e151d78ea32b9cac2047e2faff3247bdcce1f5d5 → 887d2b824a55902e3c5d1c944af8f6810bd6a5c2 

Branch pushed to git repo; I updated commit sha1. New commits:
887d2b8  17979: more details in the module description + tiny doc improvement in Envelope

comment:417 Changed 8 years ago by
Commit:  887d2b824a55902e3c5d1c944af8f6810bd6a5c2 → 8c6d433b54d953f877f37accdb2292dbde05e01a 

Branch pushed to git repo; I updated commit sha1. New commits:
8c6d433  17979: convert all input to use our Infinity in __init__

comment:418 Changed 8 years ago by
Hi,
I'll answer in several chunks, since I am not sure if I can take care of all before taking off.
Replying to ncohen:
 Module documentation  in the 'itemize' section listing
IntegerListsLex
andEnvelope
, could you add a short description of what they are meant for?
Done. This is quite redundant, so I was not sure what to put. Feel free to edit to your taste.
 Why a 'history' section?
Quite often the history is unnecessary because all the information is in the git history. But here the history spans other software and is harder to follow since the previous file was moved. This also gives credit/blame record, and some sort of bibliography since there is no published description of the algorithm (at least not yet).
self._max_length = ZZ(max_length) if max_length != Infinity else max_length
Just my two cents: I would return 'Infinity' instead of max_length. You defined yourInfinity
in order to be fast, and you don't know whatmax_length
may be. This occurs several times.
Good point; I had hesitated but this is better. Fixed.
 You can save space and turn the two following tests into one (using the same 'all'). Occurs twice.
if not all(i in ZZ for i in floor): raise TypeError("the parts of floor={} should be nonnegative integers".format(floor)) if not all(i >= 0 for i in floor): raise NotImplementedError("negative parts in floor={}".format(floor))This would also solve the following, which testsceiling
but mentionsfloor
if not all(i >= 0 for i in ceiling): raise NotImplementedError("negative parts in floor={}".format(ceiling))
Jeroen asked for a different error message (TypeError
w.r.t. NotImplementedError
), and I agree with him; so I did not
change this. But I fixed the floor to ceiling in the error
message. Note btw that the TypeError
is now done through a
conversion to a tuple of ZZ.
New commits:
887d2b8  17979: more details in the module description + tiny doc improvement in Envelope

8c6d433  17979: convert all input to use our Infinity in __init__

comment:419 followup: 422 Changed 8 years ago by
Replying to ncohen: Also, let me write somewhere that I
am against keeping
integer_list_old
in Sage, as I am afraid that it will still be here several years from now.
We definitely should keep it around for benchmarking purposes at least
until #18055 is finished. I am fine adding the removal of
integer_list_old
to the todo list for this ticket.
 Documentation of
IntegerListsLex
: instead of stating the *purpose* of the class (which is more something one would explain on a trac ticket), what about a SEEALSO section? I have the following paragraph in mind:The main purpose is to provide a generic iteration engine for all the enumerated sets like :class:`Partitions`, class:`Compositions`, :class:`IntegerVectors`. It can also be used to generate many other combinatorial objects like Dyck paths, Motzkin paths, etc.I thought that it would make more sense as a SEEALSO section pointing toward the mentionned objects.
A user reading this documentation is likely to know about integer partitions, compositions or such. Mentioning them early on gives immediately an idea of the range of applications, and thus a better understanding of the upcoming description of the specific input. So I would want this text to come before the long description of the input. I am fine making it into a SEEALSO if that's ok to put one before INPUT.
Also it's also a useful piece of information for users, even more for developers, to better understand the architecture, and know when to use this class or another one. Such information really belongs to the documentation, not trac.
comment:420 Changed 8 years ago by
Commit:  8c6d433b54d953f877f37accdb2292dbde05e01a → ea044ade1cb9638b8232b11b9c297f734ec276bb 

Branch pushed to git repo; I updated commit sha1. New commits:
ea044ad  17979: fixed cross links + typo in error message

comment:421 Changed 8 years ago by
Commit:  ea044ade1cb9638b8232b11b9c297f734ec276bb → ac68bde6207f8afb059dbfcdce38d4a7c1f5c1a8 

Branch pushed to git repo; I updated commit sha1. New commits:
ac68bde  17979: documentation for

comment:422 followup: 446 Changed 8 years ago by
We definitely should keep it around for benchmarking purposes at least until #18055 is finished. I am fine adding the removal of
integer_list_old
to the todo list for this ticket.
I do not see the point. You can checkout Sage 6.5 whenever you like if you ever need to benchmark this old (and broken) code.
A user reading this documentation is likely to know about integer partitions, compositions or such.
You cannot make assumptions like that. A user might find this class because he was redirected there after reading the doc of IntegerVectors
(for instance).
I am fine making it into a SEEALSO if that's ok to put one before INPUT.
Works for me.
Nathann
comment:423 Changed 8 years ago by
Replying to ncohen:
 Documentation of the parameter
n
 you say that a list of integers can be provided but do not explain what the output will be. Building the doc of
integer_list.py
withwarnlinks
fails.
Fixed.
comment:424 followup: 426 Changed 8 years ago by
I would prefer not to have integer_list_old
in the reference manual. It's deprecated, you're not supposed to use it. So let's at least pretend that it doesn't exist.
comment:425 Changed 8 years ago by
Commit:  ac68bde6207f8afb059dbfcdce38d4a7c1f5c1a8 → 84489c6ea9a37862e68200625eb5c838012c75a4 

Branch pushed to git repo; I updated commit sha1. New commits:
84489c6  17979 removed integer_list_old from reference manual

comment:426 followup: 447 Changed 8 years ago by
Replying to jdemeyer:
I would prefer not to have
integer_list_old
in the reference manual. It's deprecated, you're not supposed to use it. So let's at least pretend that it doesn't exist.
I agree with this. Fixed!
comment:427 Changed 8 years ago by
Commit:  84489c6ea9a37862e68200625eb5c838012c75a4 → 88436500facd79bdb7fe80693459373354d4ea95 

Branch pushed to git repo; I updated commit sha1. New commits:
8843650  17979 explained list with repeated entries

comment:428 followup: 429 Changed 8 years ago by
 Are
min_sum
andmax_sum
also ignored whenn
is a list? From the doc it seems to be, though I am not sure that it is the best design choice in this case.
Yes. As far as I know this is how it was before.
 I was surprised by the following output:
sage: IntegerListsLex(3,max_length=3,floor=[1,1,1]).list() [[3], [2, 1], [1, 2], [1, 1, 1]]I woud have expected the length of the lists to be at least 3, as I requested the first three parts to be>=1
. The documentation is consistent, but I still find it surprising.
As Jeroen mentioned, floor just requires that if there is a part, then it satisfies the constraint. If no part is present, that is ok. If you want at least three parts, you need to specify min_length.
check
seems misnamed. It is not about checking the input or output, only about displaying warnings. What about
disable_warnings
instead?
Jeroen had asked us to change this. So please first agree among yourself before asking to change this again.
 In the following text which says that one can force the enumeration when it is formally impossible, can you explicitly say what will happen? "All possible lists are enumerated, but the ordering is incorrect" or something?
If one wants to proceed anyway, one can sign a waiver by setting check=False:
When a function for the floor or ceiling is given, it is impossible to check that the conditions give a finite set since the list of values is in principle infinite. In this case the algorithm can either hang (as it computes more and more parts of the integer list) or it can happen that a tail of 000100000.... will appear in which case nor all elements in the list will be iterated over.
sage: list(IntegerListsLex(3, max_length=2, ))
Fixed.
 Lexicographic ordering is broken when
n
is a list.sage: print IntegerListsLex([1,2],length=3).list() [[1, 0, 0], [0, 1, 0], [0, 0, 1], [2, 0, 0], [1, 1, 0], [1, 0, 1], [0, 2, 0], [0, 1, 1], [0, 0, 2]]In particular, the output differs depending on how
n
is sorted.
 Cardinality is broken when
n
is a listsage: IntegerListsLex(3,length=3).cardinality() 10 sage: IntegerListsLex([3,3],length=3).cardinality() 20
See the documentation!
comment:429 followup: 431 Changed 8 years ago by
 Are
min_sum
andmax_sum
also ignored whenn
is a list? From the doc it seems to be, though I am not sure that it is the best design choice in this case.Yes. As far as I know this is how it was before.
What do you think of it?
 In the following text which says that one can force the enumeration when it is formally impossible, can you explicitly say what will happen? "All possible lists are enumerated, but the ordering is incorrect" or something?
If one wants to proceed anyway, one can sign a waiver by setting check=False:
When a function for the floor or ceiling is given, it is impossible to check that the conditions give a finite set since the list of values is in principle infinite. In this case the algorithm can either hang (as it computes more and more parts of the integer list) or it can happen that a tail of 000100000.... will appear in which case nor all elements in the list will be iterated over.
Can you make this explicit in the doc?
See the documentation!
It does not address the problem that output is not sorted as it should.
Nathann
comment:430 Changed 8 years ago by
Commit:  88436500facd79bdb7fe80693459373354d4ea95 → d6ead16b70d759dcc084bac3481e9d4f88121146 

Branch pushed to git repo; I updated commit sha1. New commits:
0a31f21  17979: fixed typo

293e6fb  17979: more documentation and caveat about n=[...]

1b8ce07  17979: more documentation and caveat about n=[...] ...

7fdaf5d  17979: typo fix

66643f0  17979: documentation for name, element_class, element_constructor + use Parent's element_constructor option

570d61d  17979: improved documentation and error reporting in _check_finiteness

0774e3f  17979: documentation and tests for the limit bound for lower envelopes

de23fcf  17919: more precise specification of Envelope.limit

d6ead16  Merge branch 'public/ticket/17979' of trac.sagemath.org:sage into combinat/integer_lists_lex

comment:431 Changed 8 years ago by
Replying to ncohen:
 Are
min_sum
andmax_sum
also ignored whenn
is a list? From the doc itseems to be, though I am not sure that it is the best design choice in this case.
Yes. As far as I know this is how it was before.
What do you think of it?
As stated in the documentation, this feature is kept for backward compatibility, see
sage: from sage.combinat.integer_list_old import IntegerListsLex as IntegerListsLexOld sage: IntegerListsLexOld([2,2],length=2).list() /Applications/sage/src/bin/sageipython:1: ******************************************************************************** The old implementation of IntegerListsLex does not allow for arbitrary input; nonallowed input can return wrong results, please see the documentation for IntegerListsLex for details. This issue is being tracked at http://trac.sagemath.org/sage_trac/ticket/17548. ******************************************************************************** [[2, 0], [1, 1], [0, 2], [2, 0], [1, 1], [0, 2]]
 In the following text which says that one can force the enumeration when it is
formally impossible, can you explicitly say what will happen? "All possible lists are enumerated, but the ordering is incorrect" or something?
If one wants to proceed anyway, one can sign a waiver by setting check=False:
When a function for the floor or ceiling is given, it is impossible to check that the conditions give a finite set since the list of values is in principle infinite. In this case the algorithm can either hang (as it computes more and more parts of the integer list) or it can happen that a tail of 000100000.... will appear in which case nor all elements in the list will be iterated over.
Can you make this explicit in the doc?
It is. See line 403 onward.
See the documentation!
It does not address the problem that output is not sorted as it should.
It is documented what it does and that it does not sort it the way you suggest. See line 496 onward.
comment:432 Changed 8 years ago by
Commit:  d6ead16b70d759dcc084bac3481e9d4f88121146 → 92bc243feb2f3f8645dbe28970a77fd5e8edd578 

Branch pushed to git repo; I updated commit sha1. New commits:
92bc243  17979 fixed doubled up doc test

comment:433 followup: 436 Changed 8 years ago by
The following is weird behavior that needs to be fixed!!
sage: IntegerListsLex([2,2],length=2).list() [[2, 0], [1, 1], [0, 2], [2, 0], [1, 1], [0, 2]] sage: IntegerListsLex([2,2],length=3).list() [[2, 0], [1, 1], [0, 2], [2, 0], [1, 1], [0, 2]]
The answer should really be
sage: IntegerListsLex([2,2],length=3).list() [[2, 0, 0], [1, 1, 0], [1, 0, 1], [0, 2, 0], [0, 1, 1], [0, 0, 2], [2, 0, 0], [1, 1, 0], [1, 0, 1], [0, 2, 0], [0, 1, 1], [0, 0, 2]]
New commits:
92bc243  17979 fixed doubled up doc test

comment:434 Changed 8 years ago by
Replying to ncohen:
 I do not understand this comment:
If a part has no bound on its value, it will be detected at some point
Do you mean that "at some point in iter" it will be detected? Probably not, as this function is called only once.
It will be detected during the algorithm that builds up the integer vector successively. The algorithm tries to add each part and if at some point the bound on a part is infinite, then it will raise an error.
 The function
_check_finiteness
assumes that the alphabet size is bounded. It is always true when this function is called, but the following raises no warning:sage: for x in IntegerListsLex(NonNegativeIntegers(),max_length=3): ....: passFor the reason given earlier, the output is not sorted lexicographically. It is not detected as infinite either.
_check_finiteness
only tests this for each piece in the DisjointEnumeratedSet?
(when a list is given for n
) and checks that each piece is a finite set.
comment:435 Changed 8 years ago by
Commit:  92bc243feb2f3f8645dbe28970a77fd5e8edd578 → 2380fd4fcf61347f9b86ee09f7488dac7e1d9fe2 

Branch pushed to git repo; I updated commit sha1. New commits:
2380fd4  17979: safe if not perfect implementation of equality tests

comment:436 Changed 8 years ago by
Replying to aschilling:
The following is weird behavior that needs to be fixed!!
sage: IntegerListsLex([2,2],length=2).list() [[2, 0], [1, 1], [0, 2], [2, 0], [1, 1], [0, 2]] sage: IntegerListsLex([2,2],length=3).list() [[2, 0], [1, 1], [0, 2], [2, 0], [1, 1], [0, 2]]The answer should really be
sage: IntegerListsLex([2,2],length=3).list() [[2, 0, 0], [1, 1, 0], [1, 0, 1], [0, 2, 0], [0, 1, 1], [0, 0, 2], [2, 0, 0], [1, 1, 0], [1, 0, 1], [0, 2, 0], [0, 1, 1], [0, 0, 2]]
Fixed!
comment:437 Changed 8 years ago by
On Tue, Apr 07, 2015 at 03:06:42PM 0000, sagetrac wrote:
 Lexicographic ordering is broken when
n
is a list.sage: print IntegerListsLex([1,2],length=3).list() [[1, 0, 0], [0, 1, 0], [0, 0, 1], [2, 0, 0], [1, 1, 0], [1, 0, 1], [0, 2, 0], [0, 1, 1], [0, 0, 2]]In particular, the output differs depending on how
n
is sorted.
Indeed, and this is in fact a feature. I reworked the documentation to better highlight this.
 Cardinality is broken when
n
is a listsage: IntegerListsLex(3,length=3).cardinality() 10 sage: IntegerListsLex([3,3],length=3).cardinality() 20
I documented this behavior some more. That's part of the specifications that this returns a disjoint union. A different specification might look desirable, but there would be no efficient way to handle it.
return typecall(cls, n=n, **kwargs)
 for clarity I find the normal syntax better. This place is not a critical part for speed, especially when you createDisjointUnionEnumeratedSets
with lambda functions just above.
I am not sure what you mean by "normal syntax". That you prefer using DisjointUnionEnumeratedSets? directly rather than this syntactic sugar?
 Are
min_sum
andmax_sum
also ignored whenn
is a list? From the doc it seems to be, though I am not sure that it is the best design choice in this case.
Indeed they are ignored. I don't see a simple way to implement it otherwise.
Speaking of which: should there be a warning when a userspecified
value for min_sum
or max_sum
is overridden by n
? Same for
length
versus min_length
and max_length
.
 I was surprised by the following output:
sage: IntegerListsLex(3,max_length=3,floor=[1,1,1]).list() [[3], [2, 1], [1, 2], [1, 1, 1]]
I would have expected the length of the lists to be at least 3, as I requested the first three parts to be
>=1
. The documentation is consistent, but I still find it surprising.
I agree it can be surprising at first sight, but the other way round would have prevented interesting use cases. Not that some of the specialized classes, like partitions or integer vectors, take a separate argument inner and outer which does impose length restrictions, according to the usual math vocable in those contexts.
check
seems misnamed
 About the finiteness check: what about a specific
allow_infinite_iterator
independent from the current 'check'.
I also wondered, but see the discussion with Jeroen: let's keep things simple until we actually meet a serious use case.
 {{{# constructor is known to be safe and don't claim ownership
on}}}  "does not".
Done.
 Typing
IntegerListsLex.<tab>
in the console is very entertaining. I would be very glad if we some day decide to consider this as a bug.
Agreed: about one half of the items should not be there. But that's a different discussion.
 I had not noticed that
IntegerListsLex
objects could have a 'name' argument.. As all arguments, it must be documented in the INPUT section. Same for
element_constructor
andelement_class
.
Done.
 The error message when the set is infinite is misleading:
sage: L = IntegerListsLex(4) sage: L._check_finiteness() ... ValueError: Could not check that the specified constraints yield a finite setThe code was able to perform the check, though it was not "able to decide that the set is finite".
Good point. At the end of the day, I made it into "could not prove that the set is finite" which better highlights the lack of symmetry.
 I do not understand this comment: {{{If a part has no bound on its value, it will be detected at some point}}} Do you mean that "at some point in iter" it will be detected? Probably not, as this function is called only once.
I rewrote the documentation of _check_finiteness
to be more specific
and discuss this point.
 about
check_finiteness
> what aboutguess_finiteness
instead, to emphasize that the function makes mistakes?
I see your point; however guess
improperly suggests that it's going
to return a boolean, whereas check
conveys that it's about trying to
catch and report bad situations.
Another issue with this name, which is even more apparent with the rewrite of the documentation, is that this method is really about trying to prove the existence of a bound on the length.
Oh well, I believe it's good enough for now; it's a private method
with an extensive documentation giving a precise specification; if
someone comes up with a perfect name, it's a trivial change. Besides
check
conveys that the verification needs not be comprehensive.
 The function
_check_finiteness
assumes that the alphabet size is bounded. It is always true when this function is called, but the following raises no warning:sage: for x in IntegerListsLex(NonNegativeIntegers(),max_length=3): ....: passFor the reason given earlier, the output is not sorted lexicographically. It is not detected as infinite either.
Correct, which is fine: the above example is properly iterable, and it's nowhere claimed to be finite:
sage: C = IntegerListsLex(NonNegativeIntegers(),max_length=3) sage: C in EnumeratedSets().Finite() False
In general, it's documented that n=iterable
is nothing but a
convenience, and that it does not return an IntegerListsLex
object
but a disjoint union thereof. I would not want to pollute the
documentation everywhere with straightforward consequences.
 The many
if A: return
from_check_finiteness
can be replaced by a `if A or B or C or ...: return`.
As Jeroen says, that's a matter of style. Here I like that it highlights the fact that each test is independent. So the reader can think about just one at a time.
 in
_check_finiteness
: the documentation oflimit()
says that it is only an upper bound. Thus you cannot write the following:if self._ceiling.limit() < self._floor.limit(): return Same comment here
if self._floor.limit() > 0 or self._min_slope > 0: floor_sum_lower_bound = Infinity
Jeroen's fault! (Just kidding :) )
That's actually correct: for the floor, limit
in fact returns a
lower bound. I reinstated the documentation and tests for this as they
had gotten scrambled in the signrefactoring of Envelope.
 Also, it seems that
limit_start()
can beInfinity
, in which case one cannot deduce anything from the value oflimit
. Please add checks.
Ah yes, the specifications of limit
/ limit_start
were not
explicit in this case. Fixed. With those specs, the deduction is
actually correct.
 I stop reviewing
_check_finiteness
, as it is complicated while the situation oflimit()
is not cleared.
Hopefully it's cleared now!
Which specific bound is returned is not set in stone
. Be more accurate.
I tried to make the sentence clearer.
More tomorrow. Off to bed now!
Cheers from Montreal,
Nicolas
comment:438 Changed 8 years ago by
Commit:  2380fd4fcf61347f9b86ee09f7488dac7e1d9fe2 → 0bff4490123fc1366799be4a92d5d5ddfb82a5cc 

Branch pushed to git repo; I updated commit sha1. New commits:
0bff449  17979: minor improvement to the doc of limit_start

comment:439 followup: 440 Changed 8 years ago by
Hello Nicolas,
I reported the following problems:
 From the doumentation: infinite set, no warning:
sage: for x in IntegerListsLex(NonNegativeIntegers(),length=1): ....: pass
 Non ordered output:
sage: IntegerListsLex([1,2],length=3).list() [[1, 0, 0], [0, 1, 0], [0, 0, 1], [2, 0, 0], [1, 1, 0], [1, 0, 1], [0, 2, 0], [0, 1, 1], [0, 0, 2]]
Indeed, and this is in fact a feature. I reworked the documentation to better highlight this.
I consider this example to break what the class promises (by being called
IntegerListsLex
): its output is not sorted lexicograpically.
Now, I agree that this is hard to fix inside of the class. Thus instead of
claiming that it is not a bug by adding a line of documentation (which is why
you are rewriting the class today) please consider deprecating it. Updating the
code that calls it should not be a problem, as it can call
DisjointUnionEnumeratedSets
directly.
Nathann
comment:440 followup: 441 Changed 8 years ago by
Replying to ncohen:
Now, I agree that this is hard to fix inside of the class. Thus instead of claiming that it is not a bug by adding a line of documentation (which is why you are rewriting the class today) please consider deprecating it.
I completely agree with you in principle. However, I would be against adding even more changes to other parts of Sage.
As far as I can tell, within the Sage library, IntegerListsLex
is only called in the following ways:
 with
n
a single number > this is good  with
range(a,b)
> this can easily be changed to usemin_sum
andmax_sum
 with
NN
> keep this for now
For now, I agree with deprecating lists or iterables. I would keep support for NN
and deal with that on a followup ticket.
comment:441 Changed 8 years ago by
I completely agree with you in principle. However, I would be against adding even more changes to other parts of Sage.
Then a stopgap can be added (in this ticket) when IntegerListsLex
is created from something which is not an integer. It does not change any of the doctests.
Nathann
comment:442 Changed 8 years ago by
Nathann, I'll have a look. Perhaps the changes are not so dramatic as I thought.
comment:443 Changed 8 years ago by
Commit:  0bff4490123fc1366799be4a92d5d5ddfb82a5cc → 3363aeb30397b74178949e0d9fbba292e68b65c8 

Branch pushed to git repo; I updated commit sha1. New commits:
3363aeb  Deprecate IntegerListsLex(n) where n is an iterable

comment:445 followup: 449 Changed 8 years ago by
Nathann, is this OK for you?
I would have changed the calls to make them use DisjointUnionEnumeratedSet
directly, but if you think that this deserves a function then no proble.
I noticed something wrong in the words file, and created ticket #18148 to address it.
Nathann
comment:446 Changed 8 years ago by
Replying to ncohen:
We definitely should keep it around for benchmarking purposes at least until #18055 is finished. I am fine adding the removal of
integer_list_old
to the todo list for this ticket.I do not see the point. You can checkout Sage 6.5 whenever you like if you ever need to benchmark this old (and broken) code.
Yes, and wait for the recompilation. Or keep yet another copy of Sage around just for this. It also makes it more complicated to compare outputs. Really, there is no risks associated to keeping it around for a bit more time, and *not* keeping it is just another useless hurdle in the way of those who will be working on #18055.
A user reading this documentation is likely to know about integer partitions, compositions or such.
You cannot make assumptions like that. A user might find this class because he was redirected there after reading the doc of
IntegerVectors
(for instance).
I am making no assumption. The user does not *need* to know about integer partitions. But if he does, he gets an additional hint.
I am fine making it into a SEEALSO if that's ok to put one before INPUT.
Works for me.
Ok, will do.
comment:447 Changed 8 years ago by
Replying to aschilling:
Replying to jdemeyer:
I would prefer not to have
integer_list_old
in the reference manual. It's deprecated, you're not supposed to use it. So let's at least pretend that it doesn't exist.I agree with this. Fixed!
Then we need to remove the dandling crosslink from integer_list
as well (fixing this crosslink was the reason why I had inserted integer_list_old
in the ref man). Done.
comment:448 Changed 8 years ago by
Commit:  3363aeb30397b74178949e0d9fbba292e68b65c8 → 2e38ce42d71d3dfdf6ea8777cbf8c65b52c25612 

comment:449 followups: 450 451 452 Changed 8 years ago by
Replying to ncohen:
Nathann, is this OK for you?
I believe deciding on API changes like this is going beyond the scope of this ticket; we are taking decisions in a rush on things that are debatable (see the discussion with Vincent). But oh well, let's move on. Thanks Jeroen for taking action toward some state that is acceptable to everyone.
I would have changed the calls to make them use
DisjointUnionEnumeratedSet
directly, but if you think that this deserves a function then no proble.
I really would much prefer a direct use of DisjointUnionEnumeratedSet?, in particular to set an example for others that would need a similar feature.
Also, I spent a good deal of time working on documentation and tests that were just wiped out by this commit. The right thing to do is to recycle them whenever this can be useful, and at the very least adapt the tests. I'll work on this now.
Cheers,
Nicolas
PS: It's Pycon today; I'll see what I can do to handle the remaining comments by Nathann. In the mean time, it would be helpful if we could get comments on the rest (lookahead, Envelope, ...).
comment:450 Changed 8 years ago by
Replying to nthiery:
I believe deciding on API changes like this is going beyond the scope of this ticket; we are taking decisions in a rush on things that are debatable
Also, I spent a good deal of time working on documentation and tests that were just wiped out by this commit. The right thing to do is to recycle them whenever this can be useful
Everything is still in the git
history, you can always roll back my commit... (perhaps indeed after agreeing on a good API)
comment:451 Changed 8 years ago by
Replying to nthiery:
Also, I spent a good deal of time working on documentation and tests that were just wiped out by this commit. The right thing to do is to recycle them whenever this can be useful, and at the very least adapt the tests.
Let me remark that the tests involving Partitions()
didn't actually test what you claimed they tested (Partitions
itself handles NN
).
comment:452 followup: 454 Changed 8 years ago by
comment:453 Changed 8 years ago by
Commit:  2e38ce42d71d3dfdf6ea8777cbf8c65b52c25612 → 37b8dd0e14a98f85056d31f53d0fd16e30ed1ad9 

Branch pushed to git repo; I updated commit sha1. New commits:
37b8dd0  17979: recycled doc and tests deleted in 3363aeb30397b74178949e0d9fbba292e68b65c8

comment:454 Changed 8 years ago by
comment:455 followups: 456 458 Changed 8 years ago by
Jeroen: is it ok if I switch to using DisjointUnionEnumeratedSets
in Words / ... ?
For the API change: let's just move on; that will do.
comment:456 Changed 8 years ago by
Replying to nthiery:
Jeroen: is it ok if I switch to using
DisjointUnionEnumeratedSets
in Words / ... ?
I would do it only for NN
, not for the range.
comment:457 Changed 8 years ago by
Commit:  37b8dd0e14a98f85056d31f53d0fd16e30ed1ad9 → 820526e2bc74824b180601d6b0684dc9e2231650 

Branch pushed to git repo; I updated commit sha1. New commits:
820526e  17979: Added TODO's about replacement of the IntegerListsNN calls to IntegerVectors + warning about its potential deletion

comment:458 Changed 8 years ago by
Replying to nthiery:
Jeroen: is it ok if I switch to using
DisjointUnionEnumeratedSets
in Words / ... ?
I started doing this, and then realized that the two locations where
we are using IntegerListsNN
would be best written using
IntegerVectors(length=..., ...)
. However this feature is broken (see
#17927). So I switch gear: let's keep things are they are for now,
switch to IntegerVectors
in the upcoming #17927, and probably get rid of the
temporary IntegerListsNN
then.
I left TODO notes in the code.
comment:459 Changed 8 years ago by
Commit:  820526e2bc74824b180601d6b0684dc9e2231650 → 2f3752774e05cccbca4bdde305d2a80ca6b9d2e4 

Branch pushed to git repo; I updated commit sha1. New commits:
2f37527  17979: small wording improvement

comment:460 Changed 8 years ago by
 In the following text which says that one can force the enumeration when it is formally impossible, can you explicitly say what will happen? "All possible lists are enumerated, but the ordering is incorrect" or something?
If one wants to proceed anyway, one can sign a waiver by setting check=False:
It's mentioned just above:
the list ``[1, 1, 1]`` will never appear in the enumeration
Isn't this enough?
Btw: I just made minor improvements to the doc around there.
comment:461 Changed 8 years ago by
 About this paragraph:
The set of allowable constraints has been specifically designed to enable iteration with a good time and memory complexity in most practical use cases, and in inverse lexicographic order (see below)
I do not believe that it is true, i.e. that the set of allowable contraints has been specifically designed to enable iteration with a good time and memory complexity.
Well, this certainly was our design goal when we came up with it with Florent! I am not saying iteration with a good time and complexity is currently implemented, but I do believe this is possible in most practical use cases.
Anyway, just rephrase this to whatever you wish. I don't really care. Or more precisely I care more about this ticket being done.
In particular, it is possible to get great speed improvements by writing a Constant Amortized Time (CAT) Algorithm to list only partitions satisfying a smaller set of constraints like (sum,length,min/max part).
If you take the current algorithm, specialize the lookahead to be trivial (because, for plain partitions, the prediction is indeed trivial: any prefix can be extended to at least one integer partition), and avoid a copy of the result, you recover exactly the standard CAT algorithm for enumerating integer partitions in inverse lexicographic order.
In fact that's exactly how we came up with this design: by getting tired of reimplementing exactly the same CAT algorithm for integer partitions, compositions, and looking for some unifying context.
More precisely we are shooting for LAT (Linear Amortized Time): the iterator protocol is indeed not really favorable to pure CAT: if one yields a reference to the current list at each step, things are likely to break, unless the user makes an immediate read only use of it. So for now we assume that we make a copy of each list.
I am not claiming we can always achieve LAT. But I believe that we can get pretty close to it in the common use cases, which will qualify for "good time and memory complexity".
comment:462 followup: 464 Changed 8 years ago by
Status:  needs_work → needs_review 

Up to the aforementioned sentence that I let Nathann edit to his taste, I believe all the comments have been adressed one way or the other. Hence back to needs review.
comment:463 Changed 8 years ago by
Commit:  2f3752774e05cccbca4bdde305d2a80ca6b9d2e4 → eda24717a8e942ec25bde17fe0d8a710d0846d28 

Branch pushed to git repo; I updated commit sha1. New commits:
eda2471  trac #17979: Just some doc

comment:464 followup: 465 Changed 8 years ago by
Hello,
Up to the aforementioned sentence that I let Nathann edit to his taste
I just did that. I added ten words to the sentence which mentions the argument 'check', and removed the part of the doc about the design of that class.
My idea of what an efficient implementation of this feature should be is closer to chapter 16 of the fxtbook [1].
In a previous message you mentionned #17927. Would anybody be willing to review it? It has been lying there for 4 weeks, and is now in conflict with the commits that have been added here since.
Nathann
comment:465 followup: 466 Changed 8 years ago by
Replying to ncohen:
I just did that. I added ten words to the sentence which mentions the argument 'check', and removed the part of the doc about the design of that class.
I just check the changes and am ok with me (I am keeping a mental note to reinsert the statement about the design when we will have provable arguments)
Where do we stand now? Are there things left that remain to review?
My idea of what an efficient implementation of this feature should be is closer to chapter 16 of the fxtbook [1].
Juste a note: the code for next in 16.2 is precisely how next worked in the previous implementation of IntegerListsLex? (except that we had more checks to handle the extra arguments).
Altogether, I don't think we are far from ftxbook. The only thing is that there remains to make sure that our code does specialize well in the trivial cases like plain partitions. And of course to make it into compiled code. Once we will be there, we should certainly compare to the ftxbook benchmarks.
In a previous message you mentionned #17927. Would anybody be willing to review it? It has been lying there for 4 weeks, and is now in conflict with the commits that have been added here since.
As I mentioned earlier, I volunteered to handle the merge and review of #17927, when this one will be done.
comment:466 followup: 469 Changed 8 years ago by
Juste a note: the code for next in 16.2 is precisely how next worked in the previous implementation of IntegerListsLex? (except that we had more checks to handle the extra arguments).
Altogether, I don't think we are far from ftxbook.
The asymptotic complexity is not the only thing I had in mind when I pointed toward that book. For things as easy to enumerate as integer partitions (wiht min/max n, min/max part, min/max length) I believe that we should have Cython implementation (no Python needed). When called at C level, it would be infinitely faster to enumerate and filter permutations satisfying a given predicate. It also couldn't hurt if IntegerListsLex
relied on it in thos simple cases.
Nathann
comment:467 followup: 468 Changed 8 years ago by
As always: First it has to be correct, then you can make it fast.
comment:468 Changed 8 years ago by
As always: First it has to be correct, then you can make it fast.
Of course. I was not trying to defend the idea of reimplementing this code in Cython right now. I was only discussing with Nicolas a paragraph of its documentation.
Nathann
comment:469 followup: 470 Changed 8 years ago by
Replying to ncohen:
The asymptotic complexity is not the only thing I had in mind when I pointed toward that book.
Yes, I know! Same for me.
For things as easy to enumerate as integer partitions (wiht min/max n, min/max part, min/max length) I believe that we should have Cython implementation (no Python needed). When called at C level, it would be infinitely faster to enumerate and filter permutations satisfying a given predicate. It also couldn't hurt if
IntegerListsLex
relied on it in thos simple cases.
In summary, the plan is:
 Correct implementation of IntegerListsLex? (this ticket)
 Asymptotically good implementation (#18055)
 Cython/C/C++ implementation (#18056)
 Serious benchmarking to see whether it's worth having specialized implementations for the "trivial" cases, and use "filtering from trivial" for the small cases.
Cheers,
Nicolas
comment:470 Changed 8 years ago by
Replying to nthiery:
Replying to ncohen:
The asymptotic complexity is not the only thing I had in mind when I pointed toward that book.
Yes, I know! Same for me.
For things as easy to enumerate as integer partitions (wiht min/max n, min/max part, min/max length) I believe that we should have Cython implementation (no Python needed). When called at C level, it would be infinitely faster to enumerate and filter permutations satisfying a given predicate. It also couldn't hurt if
IntegerListsLex
relied on it in thos simple cases.In summary, the plan is:
 Correct implementation of IntegerListsLex? (this ticket)
 Asymptotically good implementation (#18055)
FYI, Bryan and I talked about the algorithm for #18055 yesterday at Berkeley!
comment:471 Changed 8 years ago by
Hi!
Is there anything we can do to help the final steps of the review?
comment:472 Changed 8 years ago by
Status:  needs_review → positive_review 

I'm going to set this to positive review since it seems like there are currently no objections to the current state of the code, it is a definite improvement over the previous code, and we can always do more work later on on followup tickets (thus we can get the next version of Sage released).
comment:473 Changed 8 years ago by
Branch:  public/ticket/17979 → eda24717a8e942ec25bde17fe0d8a710d0846d28 

Resolution:  → fixed 
Status:  positive_review → closed 
comment:474 Changed 8 years ago by
Commit:  eda24717a8e942ec25bde17fe0d8a710d0846d28 

Oops, I hope Nathann was ok with merging this ticket as is. It's probably alright since it was looked over quite extensively, and it was costly to hold up 6.6 even more. Worst case we can change things in later tickets.
In any cases: thanks everybody for all the hard work implementing and reviewing this ticket! One less big issue in Sage. Yeah!
Cheers,
Nicolas
comment:475 Changed 8 years ago by
Resolution:  fixed 

Status:  closed → new 
Documentation doesn't build
[combinat ] /mnt/SSD1/mod_buildslave/sage_git/build/local/lib/python2.7/sitepackages/sage/combinat/quickref.py:docstring of sage.combinat.quickref:72: WARNING: undefined label: sage.graphs (if the link has no caption the label must precede a section header) Error building the documentation. Traceback (most recent call last): File "/mnt/SSD1/mod_buildslave/sage_git/build/src/doc/common/builder.py", line 1626, in <module> getattr(get_builder(name), type)() File "/mnt/SSD1/mod_buildslave/sage_git/build/src/doc/common/builder.py", line 292, in _wrapper getattr(get_builder(document), 'inventory')(*args, **kwds) File "/mnt/SSD1/mod_buildslave/sage_git/build/src/doc/common/builder.py", line 503, in _wrapper x.get(99999) File "/mnt/SSD1/mod_buildslave/sage_git/build/local/lib/python/multiprocessing/pool.py", line 558, in get raise self._value OSError: [combinat ] /mnt/SSD1/mod_buildslave/sage_git/build/local/lib/python2.7/sitepackages/sage/combinat/integer_list.py:docstring of sage.combinat.integer_list.IntegerListsLex:151: ERROR: Unexpected indentation.
comment:476 Changed 8 years ago by
Branch:  eda24717a8e942ec25bde17fe0d8a710d0846d28 → public/ticket/17979 

Commit:  → 16f21fc1ffd6a8725a48a7752ecdecc714a62be1 
Status:  new → needs_review 
I think I caught the error. Rebuilding doc now... (someone with a potentially faster computer, also do so).
Last 10 new commits:
2380fd4  17979: safe if not perfect implementation of equality tests

0bff449  17979: minor improvement to the doc of limit_start

238b3aa  17979: removed crosslink to integer_lists_old

3363aeb  Deprecate IntegerListsLex(n) where n is an iterable

2e38ce4  Merge branch 'public/ticket/17979' of trac.sagemath.org:sage into combinat/integer_lists_lex

37b8dd0  17979: recycled doc and tests deleted in 3363aeb30397b74178949e0d9fbba292e68b65c8

820526e  17979: Added TODO's about replacement of the IntegerListsNN calls to IntegerVectors + warning about its potential deletion

2f37527  17979: small wording improvement

eda2471  trac #17979: Just some doc

16f21fc  Some tweaks, hopefully the doc builds.

comment:477 Changed 8 years ago by
Commit:  16f21fc1ffd6a8725a48a7752ecdecc714a62be1 → 75f32a01b6776a761c931b7f0d68acc1d22c75be 

comment:478 Changed 8 years ago by
Commit:  75f32a01b6776a761c931b7f0d68acc1d22c75be → ea2b00697833d38e42dc0c9bbfc7ac741ba5ae0b 

comment:479 Changed 8 years ago by
Status:  needs_review → positive_review 

Okay, Nicolas and I found the issue (simultaneously but independently with Anne). Nicolas did a full doc rebuild, which returned clean. So back to positive review.
comment:480 followup: 481 Changed 8 years ago by
Good that this is now merged. I think the next steps should be doing some of the cleanup mentioned here. In particular:
 Stop using
global_options
 Remove
integer_list_old.py
 Get rid of
element_constructor
comment:481 followup: 483 Changed 8 years ago by
Replying to jdemeyer:
Good that this is now merged. I think the next steps should be doing some of the cleanup mentioned here. In particular:
 Stop using
global_options
IntegerListsLex? is not really using it. Just passing it on for other classes that need it. But if there is a way to refactor those classes to not impose this burden on IntegerListsLex?, that would be better indeed.
 Remove
integer_list_old.py
Yes, at the end of #18055.
 Get rid of
element_constructor
We probably want to change the default value. But we certainly want to keep the feature.
Cheers,
Nicolas
comment:482 Changed 8 years ago by
Replying to jdemeyer:
I disagree with this. I think code duplication is always a high risk for bugs.
This gave me a good laugh: usually people complain at me for tending to overdesign to remove the very last duplicated bit :)
comment:483 Changed 8 years ago by
comment:485 followup: 487 Changed 8 years ago by
I see your point. What I really meant is: stop using integer_list_old.py
in the Sage library (it's still used by integer_vector.py
).
comment:486 Changed 8 years ago by
Branch:  public/ticket/17979 → ea2b00697833d38e42dc0c9bbfc7ac741ba5ae0b 

Resolution:  → fixed 
Status:  positive_review → closed 
comment:487 Changed 8 years ago by
Commit:  ea2b00697833d38e42dc0c9bbfc7ac741ba5ae0b 

Replying to jdemeyer:
I see your point. What I really meant is: stop using
integer_list_old.py
in the Sage library (it's still used byinteger_vector.py
).
Oh, I see. This requires a small additional feature (initializing the iterator from a specified prefix instead of []) which should be easy to add, typically as part of #18055 unless someone wants to jump in before.
comment:488 Changed 8 years ago by
Description:  modified (diff) 

comment:489 Changed 8 years ago by
Authors:  Bryan Gillespie, Anne Schilling, Nicolas M. Thiery → Bryan Gillespie, Anne Schilling, Nicolas M. Thiéry 

Is anybody planning to work on this ticket, or it is just a "somebody should do this" ticket?
You might want to recycle some code of #17920, for example the computation of
floor
andceiling
using the various inputs. Also see that ticket for lots of doctests.