Upgrade cython to version 0.20.1

[ohanar]

Upstream tarball: http://cython.org/release/Cython-0.20.1.tar.gz

CC: @robertwb @mezzarobba @jpflori

Component: packages: standard

Author: R. Andrew Ohana, Jeroen Demeyer

Branch/Commit: faf410f

Reviewer: R. Andrew Ohana

Issue created by migration from https://trac.sagemath.org/ticket/15755

[ohanar]

Branch: u/ohanar/upgrade_cython

[ohanar]

Commit: 8ab4be3

[ohanar]

comment:1

Still needs some work. There seems to be some new overflow issues popping up with the libgap and polybori interfaces (at least that appears to be the issue with the failing doctests in sage.groups.matrix_gps.finitely_generated and sage.rings.polynomial.pbori).

---

New commits:

019d4d0	cython: upgrade to 0.20
8ab4be3	cython-0.20: fix doctests

[kiwifb]

comment:3

well we have some fun with cython-0.20 in sage-on-gentoo since yesterday. We have a whole series of tests that fail in matroids.
cschwan/sage-on-gentoo#275 I also posted about it on the cython user list earlier today.

[ohanar]

comment:4

Replying to @kiwifb:

well we have some fun with cython-0.20 in sage-on-gentoo since yesterday. We have a whole series of tests that fail in matroids.

Yes, I already added a patch to revert the broken optimizations.

[kiwifb]

comment:5

I didn't see that one before posting. That's quite a lot of broken doctests without.

[ohanar]

comment:6

Replying to @kiwifb:

I didn't see that one before posting. That's quite a lot of broken doctests without.

Yes, it is really amazing that these are the first doctests that actually test list multiplication with more than two terms (i.e. [None] * 2 * 3 fails to produce the correct result in Cython-0.20) and that there are no tests in the Cython test suite that test such basic functionality.

[jdemeyer]

comment:7

Remember to document the patch in SPKG.txt.

[robertwb]

comment:9

Did you run into issues with PPL? E.g.

https://sage.math.washington.edu:8091/hudson/job/sage-git-build/40/consoleText

sage/libs/ppl.cpp: In function 'PyObject* __pyx_pf_4sage_4libs_3ppl_11MIP_Problem_30solve(__pyx_obj_4sage_4libs_3ppl_MIP_Problem*)':
sage/libs/ppl.cpp:5514:33: error: 'PPL_MIP_Problem_Status' in namespace 'Parma_Polyhedra_Library' does not name a type
sage/libs/ppl.cpp:5514:67: error: invalid type in declaration before ';' token
sage/libs/ppl.cpp: In function 'PyObject* __pyx_pf_4sage_4libs_3ppl_9Generator_16type(__pyx_obj_4sage_4libs_3ppl_Generator*)':
sage/libs/ppl.cpp:19487:3: error: 'PPL_GeneratorType' is not a member of 'Parma_Polyhedra_Library::Generator'
sage/libs/ppl.cpp:19487:57: error: expected ';' before '__pyx_v_t'
sage/libs/ppl.cpp:19502:3: error: '__pyx_v_t' was not declared in this scope
sage/libs/ppl.cpp: In function 'PyObject* __pyx_pf_4sage_4libs_3ppl_9Generator_40__reduce__(__pyx_obj_4sage_4libs_3ppl_Generator*)':
sage/libs/ppl.cpp:20508:3: error: 'PPL_GeneratorType' is not a member of 'Parma_Polyhedra_Library::Generator'
sage/libs/ppl.cpp:20508:57: error: expected ';' before '__pyx_v_t'
sage/libs/ppl.cpp:20527:3: error: '__pyx_v_t' was not declared in this scope
sage/libs/ppl.cpp: In function 'PyObject* __pyx_pf_4sage_4libs_3ppl_10Constraint_8type(__pyx_obj_4sage_4libs_3ppl_Constraint*)':
sage/libs/ppl.cpp:23983:3: error: 'PPL_ConstraintType' is not a member of 'Parma_Polyhedra_Library::Constraint'
sage/libs/ppl.cpp:23983:59: error: expected ';' before '__pyx_v_t'
sage/libs/ppl.cpp:23995:3: error: '__pyx_v_t' was not declared in this scope

[kiwifb]

comment:10

I didn't when I built sage against pristine cython-0.20 here. In fact it all built, it just failed so many doctests on matroids it wasn't funny.

[kiwifb]

comment:11

Would you actually be getting ppl headers from the distro rather than sage's one?

[jdemeyer]

Changed branch from u/ohanar/upgrade_cython to u/jdemeyer/ticket/15755

[jdemeyer]

Changed commit from 8ab4be3 to 38687c9

[jdemeyer]

comment:13

PPL problem confirmed.

---

New commits:

38687c9

Cython: upgrade to 0.20.1

[jdemeyer]

Author: R. Andrew Ohana

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

cf1bb52

Cython: upgrade to 0.20.1

[sagetrac-git]

Changed commit from 38687c9 to cf1bb52

[sagetrac-git]

Changed commit from cf1bb52 to 0bbdc9c

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

0bbdc9c

Fix PPL declarations

[sagetrac-git]

Changed commit from 0bbdc9c to 2b6f3da

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

2b6f3da

Fix PPL and libGAP declarations

[vbraun]

Changed branch from u/jdemeyer/ticket/15755 to 115c8fc

[vbraun]

comment:24

Full rebuild doesn't work:

Successfully installed eclib-20140128
Deleting temporary build directory
/home/release/Sage/local/var/tmp/sage/build/eclib-20140128
Finished installing eclib-20140128.spkg
if [ -z "$SAGE_INSTALL_FETCH_ONLY" ]; then \
	cd /home/release/Sage/src && source bin/sage-env && \
	/home/release/Sage/build/pipestatus 'time python setup.py install 2>&1' 'tee -a /home/release/Sage/logs/pkgs/sage-6.2.beta2.log' && \
	touch /home/release/Sage/local/var/lib/sage/installed/sage; \
fi
Updating Cython code....
Traceback (most recent call last):
  File "setup.py", line 501, in <module>
    from Cython.Build import cythonize
ImportError: No module named Cython.Build

[vbraun]

Changed commit from 115c8fc to none

[jdemeyer]

Commit: 115c8fc

[jdemeyer]

Changed branch from 115c8fc to u/jdemeyer/ticket/15755

[jdemeyer]

New commits:

cf1bb52	Cython: upgrade to 0.20.1
b17f7c8	Fix various declarations
115c8fc	Fix version and checksum for Cython 0.20.1

[jdemeyer]

comment:26

Replying to @vbraun:

Full rebuild doesn't work:

What does the "full rebuild" script do? Works for me after make distclean.

[jdemeyer]

comment:27

Do you have a link to the complete install.log from that build?

[vbraun]

comment:28

Thats what I meant... maybe the failure was from another ticket. Will try again...

[vbraun]

Changed branch from u/jdemeyer/ticket/15755 to 115c8fc

[jdemeyer]

comment:30

Fails on 32-bit: http://build.sagemath.org/sage/builders/%20%20slow%20Skynet%20cicero%20%28Fedora%2016%20i686%29%20full/builds/20/steps/shell_5/logs/stdio

[jdemeyer]

Changed commit from 115c8fc to none

[jdemeyer]

New commits:

cf1bb52	Cython: upgrade to 0.20.1
b17f7c8	Fix various declarations
115c8fc	Fix version and checksum for Cython 0.20.1

[jdemeyer]

Commit: 115c8fc

[jdemeyer]

Changed branch from 115c8fc to u/jdemeyer/ticket/15755

[jdemeyer]

Changed commit from 115c8fc to faf410f

[jdemeyer]

New commits:

413ab85	Make sure PolyBoRi hashes return Py_ssize_t
faf410f	Merge branch 'u/jdemeyer/ticket/15755' of git://trac.sagemath.org/sage into ticket/15755

[vbraun]

Changed branch from u/jdemeyer/ticket/15755 to faf410f