Opened 9 years ago
Closed 9 years ago
#10493 closed enhancement (fixed)
Upgrade Cython to 0.14.1
Reported by: | jason | Owned by: | tbd |
---|---|---|---|
Priority: | blocker | Milestone: | sage-4.7 |
Component: | packages: standard | Keywords: | cython spkg |
Cc: | robertwb, fbissey | Merged in: | sage-4.7.alpha1 |
Authors: | Robert Bradshaw | Reviewers: | François Bissey |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description (last modified by )
Version 0.14.1 was recently released, and has some bugfixes and nice features.
Use the following spkg and patch:
Attachments (2)
Change History (32)
comment:1 follow-up: ↓ 9 Changed 9 years ago by
comment:2 Changed 9 years ago by
- Keywords cython spkg added
Is the __getattr__
patch (in the 0.13 Cython spkg) still needed?
comment:3 Changed 9 years ago by
No, that is now handled via a flag. There are several bugfixes in 0.14.1 that I'd like to get in, which should be out shortly (before 4.6.2 is at release candidate for sure, and I knew we missed the window for 4.6.1) which is why I haven't done anything on this ticket yet.
comment:4 Changed 9 years ago by
Updated package with just the __getattr__
patches removed as they are now in the upstream source:
comment:5 Changed 9 years ago by
Thanks, but that is not sufficient, as we need to pass the appropriate flags.
The most recent spkg can be found at https://sage.math.washington.edu:8091/hudson/job/sage-build/lastSuccessfulBuild/artifact/cython-devel.spkg (though the Sage library requires a couple of patches as well).
comment:6 Changed 9 years ago by
- Description modified (diff)
- Summary changed from Upgrade Cython to 0.14 to Upgrade Cython to 0.14.1
Updating the description to upgrade to 0.14.1, which is now the most recent release. Has anyone worked on an 0.14.1 spkg?
Changed 9 years ago by
comment:7 Changed 9 years ago by
- Status changed from new to needs_review
comment:8 Changed 9 years ago by
- Cc fbissey added
comment:9 in reply to: ↑ 1 Changed 9 years ago by
Replying to robertwb:
There's a couple of minor patches to the library that need to go in
Is this still the case with the 0.14.1 spkg?
comment:10 Changed 9 years ago by
I think that's what the patch is all about. I applied it to 4.6.2.alpha4 and it happily built and sage -testall did not show any problems for me. But may be the following warnings should be addressed
warning: sage/combinat/combinat_cython.pyx:14:0: 'stdlib' is deprecated, use 'libc.stdlib' warning: sage/ext/interpreters/wrapper_rdf.pxd:3:0: 'python_object' is deprecated, use 'cpython' warning: sage/rings/polynomial/polynomial_real_mpfr_dense.pyx:7:0: 'python_int' is deprecated, use 'cpython' warning: sage/rings/polynomial/polynomial_real_mpfr_dense.pyx:8:0: 'python_float' is deprecated, use 'cpython' warning: sage/ext/interpreters/wrapper_cdf.pxd:3:0: 'python_object' is deprecated, use 'cpython' warning: sage/ext/interpreters/wrapper_rdf.pxd:3:0: 'python_object' is deprecated, use 'cpython' warning: sage/ext/interpreters/wrapper_py.pxd:3:0: 'python_object' is deprecated, use 'cpython' warning: sage/ext/interpreters/wrapper_rr.pxd:3:0: 'python_object' is deprecated, use 'cpython' warning: sage/ext/interpreters/wrapper_el.pxd:3:0: 'python_object' is deprecated, use 'cpython'
And possibly
warning: sage/modular/modsym/p1list.pyx:703:17: cdef variable 'i' declared after it is used
Finally I am wondering about these
warning: sage/matrix/matrix0.pyx:53:22: Function signature does not match previous declaration warning: sage/matrix/matrix_window.pyx:9:17: Function signature does not match previous declaration warning: sage/matrix/matrix_sparse.pyx:18:33: Function signature does not match previous declaration
But all these were present before upgrading to cython-0.14.1. We could use the opportunity to fix some of them before they bite us later, especially the deprecated ones.
comment:11 Changed 9 years ago by
Forgot these two:
warning: sage/structure/parent.pyx:124:4: dict already a builtin Cython type warning: sage/symbolic/pynac.pyx:589:5: Function 'py_get_parent_char' previously declared as 'extern'
comment:12 Changed 9 years ago by
Yes, the (attached) patch is still needed. There's some significant cleanup that I want to do, including fixing these warnings, but I think that should be a separate ticket.
comment:13 Changed 9 years ago by
- Description modified (diff)
- Status changed from needs_review to positive_review
Well if you open a separate ticket for these warnings I am quite happy to give this a positive review. I have built it on linux-86, linux-amd64 and OS X 10.5. It all looks good to me.
comment:14 Changed 9 years ago by
Ticket for warnings at #10764.
comment:15 Changed 9 years ago by
- Milestone changed from sage-4.6.2 to sage-4.7
- Reviewers set to François Bissey
comment:16 Changed 9 years ago by
- Status changed from positive_review to needs_work
After building sage-4.6.2.rc0 and applying the spkg and patch from this ticket:
$ ./sage -ba-force [...] gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/src/sage-4.6.2.rc0/local//include -I/usr/local/src/sage-4.6.2.rc0/local//include/csage -I/usr/local/src/sage-4.6.2.rc0/devel//sage/sage/ext -I/usr/local/src/sage-4.6.2.rc0/local/include/python2.6 -c sage/combinat/combinat_cython.c -o build/temp.linux-x86_64-2.6/sage/combinat/combinat_cython.o -w sage/combinat/combinat_cython.c: In function '__pyx_pf_4sage_8combinat_15combinat_cython__stirling_number2': sage/combinat/combinat_cython.c:2431:13: error: incompatible types when assigning to type 'mpz_t' from type 'struct __mpz_struct *' error: command 'gcc' failed with exit status 1 sage: There was an error installing modified sage library code.
This is using
$ gcc --version gcc-4.4.3 (Gentoo 4.4.3-r2 p1.2) 4.4.3 Copyright (C) 2010 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
comment:17 Changed 9 years ago by
Why is the deprecation warning in polynomial_compiled.pyx commented out in this patch? If it is not being used, shouldn't it just be removed?
comment:18 Changed 9 years ago by
I'm not sure why the gcc error--I'll take a look at that. (I'm guessing that's some new code?)
As for commenting out the deprecation warning, the issue is that decorators aren't implemented for Cython special functions. They used to be silently ignored, but now an error is raised. When they're supported, we should put this back in.
comment:19 follow-up: ↓ 21 Changed 9 years ago by
Somehow one of the fixes for http://trac.cython.org/cython_trac/ticket/654 was merged into the release at the last minute, which is incompatible with how we declare many of the *_t types. I'll post a new spkg disabling this "fix."
comment:20 Changed 9 years ago by
- Description modified (diff)
- Status changed from needs_work to needs_review
I've created a new spkg. All tests pass.
comment:21 in reply to: ↑ 19 Changed 9 years ago by
Replying to robertwb:
Somehow one of the fixes for http://trac.cython.org/cython_trac/ticket/654 was merged into the release at the last minute, which is incompatible with how we declare many of the *_t types. I'll post a new spkg disabling this "fix."
How come you and I never got affected by it?
comment:22 Changed 9 years ago by
I'm not sure, but maybe the last spkg was the rc, and the fix for this issue was not supposed to go in this release, but we messed up and it did.
comment:23 Changed 9 years ago by
- Status changed from needs_review to positive_review
It works for me now, so I'm putting back the positive review.
comment:24 Changed 9 years ago by
Thanks.
comment:25 Changed 9 years ago by
- Merged in set to sage-4.7.alpha1
- Resolution set to fixed
- Status changed from positive_review to closed
comment:26 Changed 9 years ago by
- Priority changed from major to blocker
- Resolution fixed deleted
- Status changed from closed to new
Please fix: the SPKG.txt must be updated, there is no mention of this ticket.
comment:27 Changed 9 years ago by
- Description modified (diff)
- Status changed from new to needs_review
The SPKG.txt has been updated, see http://sage.math.washington.edu/home/robertwb/cython/cython-0.14.1.p2.spkg
Changed 9 years ago by
comment:28 Changed 9 years ago by
- Description modified (diff)
I made some further changes to SPKG.txt: http://boxen.math.washington.edu/home/jdemeyer/spkg/cython-0.14.1.p3.spkg
comment:29 Changed 9 years ago by
- Status changed from needs_review to positive_review
I'm happy with your spkg.txt.
comment:30 Changed 9 years ago by
- Resolution set to fixed
- Status changed from positive_review to closed
We're in pretty good shape. There's a couple of minor patches to the library that need to go in, but other than that upgrading to 0.14 should be pretty straightforward. See, e.g. https://sage.math.washington.edu:8091/hudson/view/ExtLibs/job/sage-tests/