Opened 3 years ago
Closed 3 years ago
#23565 closed enhancement (fixed)
update arb to version 2.11.1
Reported by:  dimpase  Owned by:  

Priority:  major  Milestone:  sage8.1 
Component:  packages: standard  Keywords:  
Cc:  fbissey, fredrik.johansson, rws  Merged in:  
Authors:  Dima Pasechnik, Ralf Stephan  Reviewers:  Dima Pasechnik 
Report Upstream:  N/A  Work issues:  
Branch:  c51f1a5 (Commits)  Commit:  c51f1a50ac40cc38efba2d57cdaf9ae1b5723558 
Dependencies:  #23179, #18386  Stopgaps: 
Description
we are few versions behind already. ALso, it fixes the building problem on FreeBSD.
The tarball is here: https://github.com/fredrikjohansson/arb/archive/2.11.1.tar.gz
Change History (29)
comment:1 Changed 3 years ago by
 Commit changed from 070176fe563b0df608092b77c6b9fd7d7e49acfb to ab828b9a92667b8104e5444f38b1ab0c4a74e7ae
comment:2 Changed 3 years ago by
 Status changed from new to needs_info
is arb used anywhere in files that don't have arb
in their names?
comment:3 Changed 3 years ago by
Indirectly, almost certainly. I'll do some runs to check.
comment:4 Changed 3 years ago by
sageongentoo after upgrading (I had an ebuild ready for some time)
!!! existing preserved libs: >>> package: scimathematics/arb2.11.1r1 *  /usr/lib64/libarb.so.1 *  /usr/lib64/libarb.so.1.1.1 * used by /usr/lib64/python2.7/sitepackages/sage/libs/arb/arith.so (scimathematics/sage9999) * used by /usr/lib64/python2.7/sitepackages/sage/matrix/matrix_complex_ball_dense.so (scimathematics/sage9999) * used by /usr/lib64/python2.7/sitepackages/sage/rings/complex_arb.so (scimathematics/sage9999) * used by 7 other files
So those are a bit different from your list already. I am guessing you checked stuff in libs/arb/
and I am not quite sure what the other 7 files are apart from probably from the one you already patch not on that list. A full doctest run is needed to make sure. Is there any optional packages depending on arb?
comment:5 Changed 3 years ago by
On OS X, arb passes its selftests and I got a few doctest failures:
sage t long warnlong 66.3 src/sage/functions/other.py ********************************************************************** File "src/sage/functions/other.py", line 1502, in sage.functions.other.Function_factorial.__init__ Failed example: factorial(RBF(4.2)) Expected: [32.5780960503313 +/ 6.71e14] Got: [32.5780960503313 +/ 6.72e14] **********************************************************************
sage t long warnlong 66.3 src/sage/functions/log.py ********************************************************************** File "src/sage/functions/log.py", line 444, in sage.functions.log.Function_polylog.__init__ Failed example: polylog(2, 1.0) Expected: NaN Got: 1.64493406684823 ********************************************************************** File "src/sage/functions/log.py", line 446, in sage.functions.log.Function_polylog.__init__ Failed example: polylog(2.0, 1.0) Expected: NaN Got: 1.64493406684823
sage t long warnlong 66.3 src/sage/libs/pynac/pynac.pyx ********************************************************************** File "src/sage/libs/pynac/pynac.pyx", line 1817, in sage.libs.pynac.pynac.py_atan2 Failed example: atan2(CBF(I), CBF(I+1)) Expected: [0.55357435889705 +/ 5.75e15] + [0.40235947810852 +/ 6.01e15]*I Got: [0.55357435889705 +/ 5.58e15] + [0.402359478108525 +/ 7.11e16]*I
I don't know anything about polylogs, but the others look like numerical noise.
comment:6 Changed 3 years ago by
See also #18386 for the polylog doctests.
comment:7 Changed 3 years ago by
I was just preparing exactly the same report from my linux box.
comment:8 followup: ↓ 9 Changed 3 years ago by
comment:9 in reply to: ↑ 8 Changed 3 years ago by
Replying to jhpalmieri:
Or maybe #21034? The file says "Check if :trac:
18386
is fixed::" followed by these doctests, but I don't know enough to say whether the new behavior fixes the doctests or not. #18386 has not yet been merged.
Yes. Not merged, but the doctests we are worrying about haven't been touched. You can just see them at the top of the commit. The ticket is relevant though. Maxima agrees with the new value (pi^2 / 6
). And actually other test in the same file give that answer:
class Function_polylog(GinacFunction): def __init__(self): r""" The polylog function `\text{Li}_s(z) = \sum_{k=1}^{\infty} z^k / k^s`. This definition is valid for arbitrary complex order `s` and for all complex arguments `z` with `z < 1`; it can be extended to `z \ge 1` by the process of analytic continuation. So the function may have a discontinuity at `z=1` which can cause a `NaN` value returned for floating point arguments. EXAMPLES:: sage: polylog(2.7, 0) 0 sage: polylog(2, 1) 1/6*pi^2
And where we are now is:
Check if :trac:`18386` is fixed:: sage: polylog(2.0, 1) 1.64493406684823 sage: polylog(2, 1.0) NaN sage: polylog(2.0, 1.0) NaN
I am tempted to say this upgrade is now fixing it. Although why upgrading arb fix a pynac behavior is a bit of mystery to me since pynac doesn't link to arb.
comment:10 Changed 3 years ago by
There is one more thing about this ticket and all package upgrade tickets (actually I am holding off a number of upgrades I want to go through this cycle) #23179 has now been merged and closed. It will be in the next beta but this ticket and any package upgrade ticket really should be done of top of it to save yourselves from some trouble later on.
comment:11 Changed 3 years ago by
 Commit changed from ab828b9a92667b8104e5444f38b1ab0c4a74e7ae to 4019be3548ec7bd02e8d946af68b854751f26853
Branch pushed to git repo; I updated commit sha1. Last 10 new commits:
8d19362  Pass write_script_wrapper the absolute path to the script it's writing

be6559d  Use a variable for the path to the temporary file for clarity's sake

954630f  Remove this check from sagespkg since spkginstalls will no longer be written in Python

1b96a66  Make it a mere warning on Cygwin if any of the scripts in build/pkgs are executable, but a hard error on other platforms

c447855  Use a heredoc instead of a quoted variable, for clarity's sake.

f53ee4d  Updated the developer docs to reflect the changes in #23179

6e322b8  Set some variables in the wrapper script itself.

caf64bf  Fix typos in this comment

9dfaeeb  Fix obvious typo

4019be3  Merge branch 'u/embray/build/scriptwrappers' of trac.sagemath.org:sage into arbupdate

comment:12 Changed 3 years ago by
 Dependencies set to #23179
 Status changed from needs_info to needs_work
comment:13 Changed 3 years ago by
 Commit changed from 4019be3548ec7bd02e8d946af68b854751f26853 to 20c5508517c97d7755905b75705328bec4468307
Branch pushed to git repo; I updated commit sha1. New commits:
20c5508  one more arbrelated doctest fix

comment:14 Changed 3 years ago by
 Commit changed from 20c5508517c97d7755905b75705328bec4468307 to 07aad1a5e740a693a02e607ac727fd9745fbba50
Branch pushed to git repo; I updated commit sha1. New commits:
51aeae3  18386: doctest dilog/polylog fixes

074034a  Merge branch 'develop' into t/18386/183862

f854f36  Merge branch 'u/rws/183862' of trac.sagemath.org:sage into pynacupd

58cc73b  merged more doctests from #18386, updated output

07aad1a  arbrelated numerical noise in pynac

comment:15 Changed 3 years ago by
 Cc rws added
 Status changed from needs_work to needs_review
OK, all done, also added tests from #18386, and added Ralf to the authors here.
comment:16 followup: ↓ 17 Changed 3 years ago by
Is this making #18386 a duplicate? Otherwise I think we have everything for a positive review.
comment:17 in reply to: ↑ 16 Changed 3 years ago by
Replying to fbissey:
Is this making #18386 a duplicate? Otherwise I think we have everything for a positive review.
Yes it does. Note that I have merged the branch of #18386 here (see f854f36) and adjusted wrong (for arb 2.11.1) test outputs in 51aeae3.
As arb update alleviates some of the issues on #18386 I thought it's more logical this way.
comment:18 followup: ↓ 20 Changed 3 years ago by
The usual process is to make #18386 a dependency (not vice versa). Then it can be merged independently EDIT: by the maintainer.
comment:19 Changed 3 years ago by
 Dependencies changed from #23179 to #23179, #18386
comment:20 in reply to: ↑ 18 Changed 3 years ago by
Replying to rws:
The usual process is to make #18386 a dependency (not vice versa). Then it can be merged independently EDIT: by the maintainer.
Except that in this case it would be more work for everyone (including my poor laptop that would have had to run more rounds of make ptestlong
:)) involved.
comment:21 Changed 3 years ago by
I am personally not fussy about making one of the ticket duplicate or metaticket. But someone marked the other ticket with positive review without making it a duplicate or anything like that. It implies then that this ticket should depend on it.
I think enough people did testing around here to put a reworked branch to positive review without putting your laptop through the stress again :)
comment:22 Changed 3 years ago by
 Branch changed from u/dimpase/arbupdate to u/fbissey/arb2.11.1
 Commit changed from 07aad1a5e740a693a02e607ac727fd9745fbba50 to 6861b5b016dee39e2ef55c701ee280d1b7db5b45
 Status changed from needs_review to positive_review
comment:23 Changed 3 years ago by
 Branch changed from u/fbissey/arb2.11.1 to u/dimpase/arbupdate
 Commit changed from 6861b5b016dee39e2ef55c701ee280d1b7db5b45 to 22a6096e2930d987c2302afd559b5308ca233239
 Reviewers set to Dima Pasechnik
comment:24 followup: ↓ 25 Changed 3 years ago by
Just FYI  #18386 is marked as a duplicate/invalid/wontfix.
comment:25 in reply to: ↑ 24 Changed 3 years ago by
Replying to tscrim:
Just FYI  #18386 is marked as a duplicate/invalid/wontfix.
Oops. We did have some slight disagreement on how to properly proceed, I don't recall details any more. It seems Ralf wanted it merged, but forgot to unmark it as duplicate. As everything merges fine, let's merge #18386.
comment:26 Changed 3 years ago by
 Status changed from positive_review to needs_work
sage t long warnlong 69.8 src/sage/libs/pynac/pynac.pyx ********************************************************************** File "src/sage/libs/pynac/pynac.pyx", line 1817, in sage.libs.pynac.pynac.py_atan2 Failed example: atan2(CBF(I), CBF(I+1)) Expected: [0.55357435889705 +/ 5.75e15] + [0.40235947810852 +/ 6.01e15]*I Got: [0.55357435889705 +/ 5.58e15] + [0.402359478108525 +/ 7.11e16]*I ********************************************************************** 1 item had failures: 1 of 14 in sage.libs.pynac.pynac.py_atan2 [334 tests, 1 failure, 2.85 s]
comment:27 Changed 3 years ago by
 Commit changed from 22a6096e2930d987c2302afd559b5308ca233239 to c51f1a50ac40cc38efba2d57cdaf9ae1b5723558
Branch pushed to git repo; I updated commit sha1. New commits:
c51f1a5  one more doctest fix

comment:28 Changed 3 years ago by
 Status changed from needs_work to positive_review
oops, sorry, fixed.
comment:29 Changed 3 years ago by
 Branch changed from u/dimpase/arbupdate to c51f1a50ac40cc38efba2d57cdaf9ae1b5723558
 Resolution set to fixed
 Status changed from positive_review to closed
Branch pushed to git repo; I updated commit sha1. New commits:
arb doctest fixes; few more, less obvious, might be needed