Opened 9 years ago
Closed 9 years ago
#9969 closed enhancement (fixed)
Update extension code for mpmath-0.17
Reported by: | fredrik.johansson | Owned by: | |
---|---|---|---|
Priority: | blocker | Milestone: | sage-4.7 |
Component: | packages: standard | Keywords: | |
Cc: | Merged in: | sage-4.7.alpha5 | |
Authors: | Fredrik Johansson | Reviewers: | François Bissey |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description (last modified by )
The patch adds fast Cython version of some more mpmath functions to sage.libs.mpmath.
This ticket contains a new spkg for mpmath-0.17 and two patches that need to be applied to sage itself. First mpmath_update_fixed_4.6.1.patch, then truediv_fix.patch.
It can be tested with:
sage: import mpmath sage: mpmath.runtests() sage: mpmath.doctests()
New SPKG: http://boxen.math.washington.edu/home/jdemeyer/spkg/mpmath-0.17.spkg
Apply:
Attachments (5)
Change History (46)
Changed 9 years ago by
comment:1 Changed 9 years ago by
- Status changed from new to needs_review
Here is an spkg: http://sage.math.washington.edu/home/fredrik/mpmath-0.16.spkg
It should work fine together with the patch. Sorry for the very long delay!
comment:2 Changed 9 years ago by
- Status changed from needs_review to needs_work
REPORT:
- All tests passon sage.math.
- Your code needs "::\n\n" before any sage sessions for sphinx to format it right.
See the template here and note rightafterwords: http://sagemath.blogspot.com/ right now if somebody introspects one of your functions in the notebook, sphinx will butcher it.
- You define "isqrt" but sage integers already have an isqrt method that is exactly the same. Clarify in the documentation the distinction.
Bug me again by email or chat when you've posted another patch (or patch on top of the above) that fixes the above two little things.
comment:3 Changed 9 years ago by
Oh, could you have at least a short comment explaining what every single function does. E.g.,
cdef cy_exp_basecase(mpz_t y, mpz_t x, int prec): # <what this function does>
Changed 9 years ago by
comment:4 Changed 9 years ago by
- Owner changed from tbd to (none)
Added second patch with docstring fixes.
comment:5 Changed 9 years ago by
- Status changed from needs_work to needs_review
comment:6 Changed 9 years ago by
If I understand correctly you need to apply 14600.patch first, then docstring-fixes.patch? This goes in sage-on-gentoo tonight for testing.
comment:7 Changed 9 years ago by
I forgot, for it to go in sage proper a new spkg will be needed. Are you working on that?
comment:8 Changed 9 years ago by
Yes, the patches should be applied in that order.
The spkg was linked in a post above: http://sage.math.washington.edu/home/fredrik/mpmath-0.16.spkg
comment:9 Changed 9 years ago by
- Description modified (diff)
- Milestone set to sage-4.7
I should get a reader since I am obviously blind :) I say we try to get it formally in 4.7, I rewrite the description a little bit.
comment:10 Changed 9 years ago by
I just saw your post about mpmath-0.17 release, are you planing to update this ticket for mpmath 0.17?
comment:11 follow-up: ↓ 14 Changed 9 years ago by
Yes, I'll create an spkg for 0.17 immediately to replace the 0.16 one.
Nothing should have changed in the way of Sage compatibility, so the patches should still be fine.
comment:12 Changed 9 years ago by
- Description modified (diff)
- Summary changed from Update extension code for mpmath-0.16 to Update extension code for mpmath-0.17
comment:13 Changed 9 years ago by
By the way, I noticed (too late) that there are two failing doctests if you run mpmath.doctests() as per the instructions. These failures a trivial (output formatting) and can be ignored.
comment:14 in reply to: ↑ 11 Changed 9 years ago by
Replying to fredrik.johansson:
Yes, I'll create an spkg for 0.17 immediately to replace the 0.16 one.
Nothing should have changed in the way of Sage compatibility, so the patches should still be fine.
Good to know, that means I won't have to change anything to support mpmath-0.17 in sage-on-gentoo when 4.6.2 is released.
Changed 9 years ago by
Patch that fixes some mpmath test failures due to use of the truediv operator
comment:15 Changed 9 years ago by
- Description modified (diff)
comment:16 Changed 9 years ago by
The two new patches together are smaller than the two previous patches. Is docstring-fixes.patch really not needed anymore?
comment:17 follow-up: ↓ 18 Changed 9 years ago by
Most of docstring-fixes.patch consisted of reformatting existing docstrings, and there's a lot of air in the diff format, so I think the numbers add up.
comment:18 in reply to: ↑ 17 Changed 9 years ago by
Replying to fredrik.johansson:
Most of docstring-fixes.patch consisted of reformatting existing docstrings, and there's a lot of air in the diff format, so I think the numbers add up.
I thought it could be the case. I will try to review this quickly so we can have it included in 4.7.alpha.
comment:19 Changed 9 years ago by
tests are not looking good to me.
Python 2.6.6 (r266:84292, Jan 28 2011, 01:59:55) [GCC 4.5.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import mpmath >>> mpmath.runtests() Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib64/python2.6/site-packages/mpmath/__init__.py", line 413, in runtests from .tests import runtests as tests ImportError: No module named tests
I get pretty much the same thing from sage.
By the way that looks more like a procedure to do a spkg-check than a doctest.
comment:20 Changed 9 years ago by
Hmm... it doesn't seem like mpmath installed correctly for you.
Is "/usr/lib64/python2.6/site-packages" actually the location of your Sage site-packages library, or is this a standalone installation of mpmath 0.17?
comment:21 Changed 9 years ago by
sorry for the noise I shouldn't post past 11pm. There is an issue in Gentoo and sage-on-gentoo but there shouldn't be any in a pure sage environment. It may take a little bit of time testing this on various hardware.
comment:22 Changed 9 years ago by
Something I have noticed in the gentoo ebuild. There is now an option to use matplotlib. Since matplotlib is shipped in sage mpmath may have to depend on it or configured not to use it.
Usually people choose the first option in this case, unless there is major trouble. If you want to do that, the deps file in spkg/standard will need to be updated.
comment:23 Changed 9 years ago by
I got a number of failing mpmath.doctests on my x86 box. A formatting issue really. Does any of the code interacts with ecl or maxima? The install I tested it on is based on 4.6.2.alpha4 with ecl-11.1.1 (#10766) and maxima-5.23.2 (#10773) and a couple of other patch that should be orthogonal (ppl #10039 and associated patches).
almosteq 0.004 findroot ********************************************************************** File "/home/francois/Work/sandbox/sage-4.6.2.alpha4/local/lib/python2.6/site-packages/mpmath/calculus/optimization.py", line 835, in NoName Failed example: findroot(f, -10, solver='anewton', verbose=True) Expected: x: -9.88888888888888888889 error: 0.111111111111111111111 converging slowly x: -9.77890011223344556678 error: 0.10998877665544332211 converging slowly x: -9.67002233332199662166 error: 0.108877778911448945119 converging slowly accelerating convergence x: -9.5622443299551077669 error: 0.107778003366888854764 converging slowly x: 0.99999999999999999214 error: 10.562244329955107759 x: 1.0 error: 7.8598304758094664213e-18 1.0 Got: ('x: ', -9.88888888888888888889) ('error:', 0.111111111111111111111) converging slowly ('x: ', -9.77890011223344556678) ('error:', 0.10998877665544332211) converging slowly ('x: ', -9.67002233332199662166) ('error:', 0.108877778911448945119) converging slowly accelerating convergence ('x: ', -9.5622443299551077669) ('error:', 0.107778003366888854764) converging slowly ('x: ', 0.99999999999999999214) ('error:', 10.562244329955107759) ('x: ', 1.0) ('error:', 7.8598304758094664213e-18) 1.0 0.132 __name__ 0.001
and
superfac 0.05 secondzeta ********************************************************************** File "/home/francois/Work/sandbox/sage-4.6.2.alpha4/local/lib/python2.6/site-packages/mpmath/functions/zeta.py", line 983, in NoName Failed example: secondzeta(0.5 + 40j, error=True, verbose=True) Expected: main term = (-30190318549.138656312556 - 13964804384.624622876523j) computed using 19 zeros of zeta prime term = (132717176.89212754625045 + 188980555.17563978290601j) computed using 9 values of the von Mangoldt function exponential term = (542447428666.07179812536 + 362434922978.80192435203j) singular term = (512124392939.98154322355 + 348281138038.65531023921j) ((0.059471043 + 0.3463514534j), 1.455191523e-11) Got: ('main term =', (-30190318549.138656312556 - 13964804384.624622876523j)) (' computed using', 19, 'zeros of zeta') ('prime term =', (132717176.89212754625045 + 188980555.17563978290601j)) (' computed using', 9, 'values of the von Mangoldt function') ('exponential term =', (542447428666.07179812536 + 362434922978.80192435203j)) ('singular term =', (512124392939.98154322355 + 348281138038.65531023921j)) ((0.059471043 + 0.3463514534j), 1.455191523e-11) ********************************************************************** File "/home/francois/Work/sandbox/sage-4.6.2.alpha4/local/lib/python2.6/site-packages/mpmath/functions/zeta.py", line 992, in NoName Failed example: secondzeta(0.5 + 40j, a=0.04, error=True, verbose=True) Expected: main term = (-151962888.19606243907725 - 217930683.90210294051982j) computed using 9 zeros of zeta prime term = (2476659342.3038722372461 + 28711581821.921627163136j) computed using 37 values of the von Mangoldt function exponential term = (178506047114.7838188264 + 819674143244.45677330576j) singular term = (175877424884.22441310708 + 790744630738.28669174871j) ((0.059471043 + 0.3463514534j), 1.455191523e-11) Got: ('main term =', (-151962888.19606243907725 - 217930683.90210294051982j)) (' computed using', 9, 'zeros of zeta') ('prime term =', (2476659342.3038722372461 + 28711581821.921627163136j)) (' computed using', 37, 'values of the von Mangoldt function') ('exponential term =', (178506047114.7838188264 + 819674143244.45677330576j)) ('singular term =', (175877424884.22441310708 + 790744630738.28669174871j)) ((0.059471043 + 0.3463514534j), 1.455191523e-11) 34.812 inf 0.002
I am preparing a run on amd64 with a fresh 4.6.2.rc0 without any patches.
comment:24 follow-up: ↓ 25 Changed 9 years ago by
These two failures were noted in a previous comment. They can safely be ignored.
comment:25 in reply to: ↑ 24 Changed 9 years ago by
Replying to fredrik.johansson:
These two failures were noted in a previous comment. They can safely be ignored.
I didn't realise they were the same one. I guess I expected they were fixed but that would require a new version of mpmath, not just sage patch I imagine. Once I have tested this at least on amd64 I can give a positive review.
comment:26 Changed 9 years ago by
OK so I tested this on linux-amd64 and OS X (10.5). and the tests perform ok. Although there is some noise on OS X because the wrong version of freetype is detected. I am not sure that the spkg fault or not.
test_visualization axes dyld: Library not loaded: /usr/X11/lib/libfreetype.6.dylib Referenced from: /usr/X11/bin/fc-list Reason: Incompatible library version: fc-list requires version 13.0.0 or later, but libfreetype.6.dylib provides version 10.0.0 dyld: Library not loaded: /usr/X11/lib/libfreetype.6.dylib Referenced from: /usr/X11/bin/fc-list Reason: Incompatible library version: fc-list requires version 13.0.0 or later, but libfreetype.6.dylib provides version 10.0.0 ok 6.5380421 s finished tests in 17.99 seconds
On further inspection this test is run because matplotlib is present and I assume that this message originates from matplotlib. So the problem is probably in matplotlib.
The last thing is whether we make matplotlib a dependency of mpmath or not. I will post a patch making this the default. Voice any opposition then.
comment:27 Changed 9 years ago by
Fredrik, a question about mpmath behavior with regards to matplotlib. Is mpmath detecting matplotlib at compilation time or its presence at runtime?
comment:28 Changed 9 years ago by
Runtime. In fact, it only attempts to import matplotlib from inside the plotting functions (which are pure Python).
comment:29 Changed 9 years ago by
- Status changed from needs_review to positive_review
Thanks, that means we don't need to depend on it. I am giving this a positive review. Hopefully it will be picked up for 4.7.
comment:30 Changed 9 years ago by
- Description modified (diff)
comment:31 Changed 9 years ago by
- Reviewers set to François Bissey
comment:32 Changed 9 years ago by
- Status changed from positive_review to needs_work
Please change the commit message (using hg qrefresh -e
) such that the ticket number appears on the first line.
comment:33 Changed 9 years ago by
- Status changed from needs_work to positive_review
comment:34 Changed 9 years ago by
- Merged in set to sage-4.7.alpha5
- Resolution set to fixed
- Status changed from positive_review to closed
comment:35 Changed 9 years ago by
Sorry I meant to do the refresh but I was unable to get it working.
comment:36 Changed 9 years ago by
- Resolution fixed deleted
- Status changed from closed to new
The files SPKG.txt
and spkg-install
should be put under hg control. Also, SPKG.txt should not be executable. Please fix these trivial issues.
comment:37 Changed 9 years ago by
- Priority changed from major to blocker
comment:38 follow-up: ↓ 39 Changed 9 years ago by
I can fix the permissions in the spkg. What is involved to put SPKG.txt and spkg-install under hg control?
comment:39 in reply to: ↑ 38 Changed 9 years ago by
- Status changed from new to needs_review
Replying to fredrik.johansson:
I can fix the permissions in the spkg. What is involved to put SPKG.txt and spkg-install under hg control?
Never mind. I did it myself: http://boxen.math.washington.edu/home/jdemeyer/spkg/mpmath-0.17.spkg
comment:40 Changed 9 years ago by
- Description modified (diff)
comment:41 Changed 9 years ago by
- Resolution set to fixed
- Status changed from needs_review to closed
updated mpmath Cython extension code