Upgrade Cython to 0.14.1 #10493

jasongrout · 2010-12-18T20:26:50Z

Version 0.14.1 was recently released, and has some bugfixes and nice features.

Use the following spkg and patch:

CC: @robertwb @kiwifb

Component: packages: standard

Keywords: cython spkg

Author: Robert Bradshaw

Reviewer: François Bissey

Merged: sage-4.7.alpha1

Issue created by migration from https://trac.sagemath.org/ticket/10493

robertwb · 2010-12-19T09:43:39Z

comment:1

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/

jdemeyer · 2011-01-12T01:46:59Z

Changed keywords from none to cython spkg

jdemeyer · 2011-01-12T01:46:59Z

comment:2

Is the __getattr__ patch (in the 0.13 Cython spkg) still needed?

robertwb · 2011-01-12T02:01:26Z

comment:3

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.

vbraun · 2011-01-12T04:38:08Z

comment:4

Updated package with just the __getattr__ patches removed as they are now in the upstream source:

http://www.stp.dias.ie/~vbraun/Sage/spkg/cython-0.14.spkg

robertwb · 2011-01-12T06:29:31Z

comment:5

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).

jasongrout · 2011-02-08T20:36:10Z

comment:6

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?

robertwb · 2011-02-09T07:41:28Z

comment:7

Attachment: 10493-cython-0.14.1.patch.gz

Spkg at http://sage.math.washington.edu/home/robertwb/cython/cython-0.14.1.spkg

jasongrout · 2011-02-09T22:25:39Z

comment:9

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?

kiwifb · 2011-02-09T23:13:49Z

comment:10

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.

kiwifb · 2011-02-09T23:16:54Z

comment:11

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'

robertwb · 2011-02-09T23:20:41Z

comment:12

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.

kiwifb · 2011-02-09T23:41:06Z

comment:13

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.

robertwb · 2011-02-10T03:17:05Z

comment:14

Ticket for warnings at #10764.

jdemeyer · 2011-02-10T08:11:21Z

Reviewer: François Bissey

jdemeyer · 2011-02-10T08:11:21Z

Author: Robert Bradshaw

jdemeyer · 2011-02-24T10:42:35Z

comment:16

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.

robertwb · 2011-02-25T05:52:56Z

comment:20

I've created a new spkg. All tests pass.

kiwifb · 2011-02-25T08:19:41Z

comment:21

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?

robertwb · 2011-02-25T08:27:50Z

comment:22

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.

jdemeyer · 2011-02-25T16:44:32Z

comment:23

It works for me now, so I'm putting back the positive review.

robertwb · 2011-02-25T17:20:41Z

comment:24

Thanks.

jdemeyer · 2011-03-08T21:46:01Z

Merged: sage-4.7.alpha1

jdemeyer · 2011-05-04T09:01:19Z

comment:26

Please fix: the SPKG.txt must be updated, there is no mention of this ticket.

robertwb · 2011-05-05T06:59:36Z

comment:27

The SPKG.txt has been updated, see http://sage.math.washington.edu/home/robertwb/cython/cython-0.14.1.p2.spkg

jdemeyer · 2011-05-05T09:58:00Z

comment:28

Attachment: cython-SPKG.txt.diff.gz

I made some further changes to SPKG.txt: http://boxen.math.washington.edu/home/jdemeyer/spkg/cython-0.14.1.p3.spkg

robertwb · 2011-05-06T06:17:36Z

comment:29

I'm happy with your spkg.txt.

jasongrout added this to the sage-4.6.2 milestone Dec 18, 2010

jasongrout added c: packages: standard labels Dec 18, 2010

jdemeyer added the c: cython label Jan 12, 2011

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robertwb mentioned this issue Jul 2, 2012

Cleanup a few Cython warnings #10764

Closed

jasongrout mentioned this issue Dec 3, 2021

Make cython support SAGE_SPKG_INSTALL_DOCS #10827

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jhpalmieri mentioned this issue Apr 11, 2011

update SAGE_ROOT/local/bin/.hgignore #11141

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Upgrade Cython to 0.14.1 #10493

Upgrade Cython to 0.14.1 #10493

jasongrout commented Dec 18, 2010

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Upgrade Cython to 0.14.1 #10493

Upgrade Cython to 0.14.1 #10493

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jasongrout commented Dec 18, 2010

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