Opened 7 years ago
Closed 7 years ago
#17643 closed enhancement (fixed)
Update scipy to 0.16.1
Reported by: | jpflori | Owned by: | |
---|---|---|---|
Priority: | major | Milestone: | sage-6.10 |
Component: | packages: standard | Keywords: | |
Cc: | Merged in: | ||
Authors: | François Bissey | Reviewers: | Volker Braun |
Report Upstream: | N/A | Work issues: | |
Branch: | cc6accc (Commits, GitHub, GitLab) | Commit: | cc6accce6a2b0622296f6c2c9f3f21395dfcc046 |
Dependencies: | Stopgaps: |
Description (last modified by )
Upgrade to scipy 0.16.1 this is intended to be done at the same time as numpy 1.10.1 and matplotlib 1.5.0 as noted in the ticket dependencies.
Change History (36)
comment:1 Changed 7 years ago by
comment:2 Changed 7 years ago by
scipy 0.16.0 is out, one doctest broken:
sage -t --long usr/share/doc/sage/en/faq/faq-usage.rst Running doctests with ID 2015-08-05-11-07-08-20037f0b. Using --optional=optional,sage Doctesting 1 file. sage -t --long --warn-long 64.8 usr/share/doc/sage/en/faq/faq-usage.rst ********************************************************************** File "usr/share/doc/sage/en/faq/faq-usage.rst", line 351, in faq-usage Failed example: stats.ttest_ind(list([1,2,3,4,5]),list([2,3,4,5,.6])) Expected: (array(0.07675295564533369), 0.94070490247380478) Got: Ttest_indResult(statistic=array(0.07675295564533369), pvalue=0.94070490247380478) ********************************************************************** 1 item had failures: 1 of 36 in faq-usage [24 tests, 1 failure, 0.68 s] ---------------------------------------------------------------------- sage -t --long --warn-long 64.8 usr/share/doc/sage/en/faq/faq-usage.rst # 1 doctest failed ----------------------------------------------------------------------
this is on top of 6.9.beta0.
comment:3 Changed 7 years ago by
- Description modified (diff)
- Milestone changed from sage-6.5 to sage-6.10
- Summary changed from Update scipy to 0.15 to Update scipy to 0.16.1
comment:4 Changed 7 years ago by
- Branch set to u/fbissey/scipy_0.16.1
- Commit set to f3ff13922552d775a054cec05af925351370de44
New commits:
05c84c1 | upgrade to numpy 1.10.1, updating the package including a few cherrypicked patch from master
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de8f740 | Merge branch 'develop' into numpy-1.10
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ebdf899 | Fix to get rid of the problem with result_type. Pending upstream approval or suggestion of an alternative.
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d12591f | Upgarde matplotlib to 1.5.0
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f3ff139 | Fix the doctest warning by adding it to the expected out. I am expecting the warning to originate from matplotlib and to be
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comment:5 Changed 7 years ago by
- Dependencies set to #17642 #19556
comment:6 Changed 7 years ago by
- Description modified (diff)
comment:7 Changed 7 years ago by
- Commit changed from f3ff13922552d775a054cec05af925351370de44 to 31669f2db8ae1ae6484fb5654ab049caa418a15b
Branch pushed to git repo; I updated commit sha1. New commits:
31669f2 | Correct further warnings
|
comment:8 Changed 7 years ago by
- Commit changed from 31669f2db8ae1ae6484fb5654ab049caa418a15b to b21be98e75eb044998b061e5f8da47ddf6a810a3
Branch pushed to git repo; I updated commit sha1. New commits:
b21be98 | Removing line numbers from doctest
|
comment:9 Changed 7 years ago by
New branch compatible with the new push at #19556 coming soon.
comment:10 Changed 7 years ago by
- Branch changed from u/fbissey/scipy_0.16.1 to u/fbissey/scipy-0.16.1
- Commit changed from b21be98e75eb044998b061e5f8da47ddf6a810a3 to 6d59bad6f1aec57f7d0f4cb7b057a990d8ce3dcf
New commits:
7177516 | Upgrade matplotlib to 1.5.0
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7ce23d0 | Fix deprecation warnings in doctests.
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c7ac0a7 | Updated numpy patch according to feedback from upstream
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52a45f4 | Merge branch 'numpy-1.10' into mpl-1.5.0
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a733692 | remove test for a limitation that doesn't exist anymore.
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6d59bad | Upgrade to scipy 0.16.1 and fix affected doctest
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comment:11 Changed 7 years ago by
- Status changed from new to needs_review
comment:12 Changed 7 years ago by
Just a confirmation that with the three tickets applied all tests pass (debian 64bits).
Could you replace
if np.array_equal(vert1, tpath.vertices) and np.array_equal(code1, tpath.codes): return True else: return False
with
return np.array_equal(vert1, tpath.vertices) and np.array_equal(code1, tpath.codes)
Or there is a reason to let it as you did?
comment:13 follow-up: ↓ 15 Changed 7 years ago by
No reason I didn't do that. I was so focused in finding a replacement for that particular line (it took some effort for me) that I didn't realise the code could be streamlined. I will make the change your suggest in a few hours. Would you otherwise be happy to review positively the tickets?
comment:14 Changed 7 years ago by
- Commit changed from 6d59bad6f1aec57f7d0f4cb7b057a990d8ce3dcf to 8b383de997ace1bc57564e4297c82b4b0a85a040
comment:15 in reply to: ↑ 13 Changed 7 years ago by
Replying to fbissey:
I will make the change your suggest in a few hours. Would you otherwise be happy to review positively the tickets?
All done.
comment:16 Changed 7 years ago by
- Reviewers set to Volker Braun
- Status changed from needs_review to positive_review
comment:17 Changed 7 years ago by
- Status changed from positive_review to needs_work
Fails on arm
gfortran: error: unrecognized command line option '-msse2' error: Command "gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O2 -march=x86-64 -DMS_WIN64 -mtune=generic -msse2 -I/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/numpy/core/include -c -c scipy/fftpack/src/dfftpack/dfftf1.f -o build/temp.linux-armv7l-2.7/scipy/fftpack/src/dfftpack/dfftf1.o" failed with exit status 1
comment:18 Changed 7 years ago by
- Dependencies changed from #17642 #19556 to #19556
comment:19 Changed 7 years ago by
- Dependencies #19556 deleted
comment:20 Changed 7 years ago by
Serious fail from distutils
customize Gnu95FCompiler customize Gnu95FCompiler using build_clib building 'dfftpack' library compiling Fortran sources Fortran f77 compiler: gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O2 -march=x86-64 -DMS_WIN64 -mtune=generic -msse2 Fortran f90 compiler: gfortran -Wall -g -fno-second-underscore -fPIC -O2 -march=x86-64 -DMS_WIN64 -mtune=generic -msse2 Fortran fix compiler: gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O2 -march=x86-64 -DMS_WIN64 -mtune=generic -msse2
arm being mistaken for windows64?
comment:21 Changed 7 years ago by
Looking around distros that provide arm
support I am wondering how it was building on arm before. I think none of fedora, debian or gentoo have trouble with arm but they all pass config_fc --noarch
to setup.py
which was done at some point in sage but has been removed a while ago.
I note from https://pkgs.fedoraproject.org/cgit/numpy.git/tree/numpy.spec
* Wed Oct 14 2015 Thomas Spura <tomspur@fedoraproject.org> - 1:1.10.1-3 - Remove fortran flags or arm would build with -march=x86-64
I am guessing from this that the bug is recent but because everyone but sage
passes --noarch
it did go unnoticed in scipy
. I'll add it and put this back to need_review.
comment:22 Changed 7 years ago by
- Commit changed from 8b383de997ace1bc57564e4297c82b4b0a85a040 to d40c0e9a97ca9d2a0a05b7596ab84d368ea97bc0
Branch pushed to git repo; I updated commit sha1. New commits:
d40c0e9 | Adding "config_fc --noarch" to setup.py call so we don't get miscompilation on ARM.
|
comment:23 Changed 7 years ago by
- Status changed from needs_work to needs_review
comment:24 Changed 7 years ago by
- Status changed from needs_review to positive_review
Can you report it somewhere upstream?
comment:25 Changed 7 years ago by
I'll look into it. I am guessing it is technically a bug in numpy
's distutils rather than scipy
but I have no idea how to fix it or how it happens.
comment:26 Changed 7 years ago by
It looks like someone already acted in upstream numpy
, I guess an option is to try to backport the commit in the numpy
we ship.
https://github.com/numpy/numpy/commit/a08437e12d6b6796f4b0beda49bce9adc37db63d
comment:27 follow-up: ↓ 28 Changed 7 years ago by
I think I might have removed the no_arch
stuff when I began to clean up the spkg mess.
Backporting the fix looks a good idea for a further ticket.
Or we just wait for a numpy version bump.
comment:28 in reply to: ↑ 27 Changed 7 years ago by
Replying to jpflori:
Backporting the fix looks a good idea for a further ticket. Or we just wait for a numpy version bump.
The danger with those two scenario is that the removal will be forgotten. However considering that everyone else has it with some variations (Gentoo has noopt
and fedora has fcompiler=gunf95
[or something]) I guess it doesn't hurt to keep it.
comment:29 Changed 7 years ago by
- Branch changed from u/fbissey/scipy-0.16.1 to d40c0e9a97ca9d2a0a05b7596ab84d368ea97bc0
- Resolution set to fixed
- Status changed from positive_review to closed
comment:30 Changed 7 years ago by
- Commit d40c0e9a97ca9d2a0a05b7596ab84d368ea97bc0 deleted
I must say I spent a bit of my night worrying that it was the wrong fix. Good that it really works.
comment:31 Changed 7 years ago by
- Branch changed from d40c0e9a97ca9d2a0a05b7596ab84d368ea97bc0 to u/fbissey/scipy-0.16.1
- Commit set to d40c0e9a97ca9d2a0a05b7596ab84d368ea97bc0
- Resolution fixed deleted
- Status changed from closed to new
Argh still doesn't work... http://build.sagedev.org/release/builders/%20%20slow%20Oxford%20ARM%20%28Ubuntu%2012.10%29%20incremental/builds/330/steps/compile/logs/scipy
Last 10 new commits:
ebdf899 | Fix to get rid of the problem with result_type. Pending upstream approval or suggestion of an alternative.
|
7177516 | Upgrade matplotlib to 1.5.0
|
7ce23d0 | Fix deprecation warnings in doctests.
|
c7ac0a7 | Updated numpy patch according to feedback from upstream
|
52a45f4 | Merge branch 'numpy-1.10' into mpl-1.5.0
|
a733692 | remove test for a limitation that doesn't exist anymore.
|
6d59bad | Upgrade to scipy 0.16.1 and fix affected doctest
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04997f6 | Simplify flow in arrow.py
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8b383de | Merge branch 'mpl-1.5.0' into scipy0.16.1
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d40c0e9 | Adding "config_fc --noarch" to setup.py call so we don't get miscompilation on ARM.
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comment:32 Changed 7 years ago by
OK so I was right to worry it was the wrong fix. I'll remove the last commit on the scipy branch and add the upstream commit in numpy
. I guess if I had gone for noopt
instead of noarch
it would have worked.
comment:33 Changed 7 years ago by
- Commit changed from d40c0e9a97ca9d2a0a05b7596ab84d368ea97bc0 to 93a8c3d8da5af43e14d2cbb63b3df77da9aa0c06
Branch pushed to git repo; I updated commit sha1. New commits:
93a8c3d | Revert "Adding "config_fc --noarch" to setup.py call so we don't get miscompilation on ARM."
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comment:34 Changed 7 years ago by
- Commit changed from 93a8c3d8da5af43e14d2cbb63b3df77da9aa0c06 to cc6accce6a2b0622296f6c2c9f3f21395dfcc046
comment:35 Changed 7 years ago by
- Status changed from new to needs_review
comment:36 Changed 7 years ago by
- Branch changed from u/fbissey/scipy-0.16.1 to cc6accce6a2b0622296f6c2c9f3f21395dfcc046
- Resolution set to fixed
- Status changed from needs_review to closed
Didn't know it was out. Not in the Gentoo tree yet so I have no idea so far.