Opened 7 years ago
Closed 7 years ago
#15755 closed enhancement (fixed)
Upgrade cython to version 0.20.1
Reported by:  ohanar  Owned by:  

Priority:  major  Milestone:  sage6.2 
Component:  packages: standard  Keywords:  
Cc:  robertwb, mmezzarobba, jpflori  Merged in:  
Authors:  R. Andrew Ohana, Jeroen Demeyer  Reviewers:  R. Andrew Ohana 
Report Upstream:  N/A  Work issues:  
Branch:  faf410f (Commits)  Commit:  faf410f9f73d3e77c7f4062d9ea917cc87f27d3a 
Dependencies:  Stopgaps: 
Description (last modified by )
Upstream tarball: http://cython.org/release/Cython0.20.1.tar.gz
Change History (36)
comment:1 Changed 7 years ago by
 Branch set to u/ohanar/upgrade_cython
 Commit set to 8ab4be380e5df96263acb8a815d3ccad9438a382
comment:2 Changed 7 years ago by
 Description modified (diff)
comment:3 followup: ↓ 4 Changed 7 years ago by
well we have some fun with cython0.20 in sageongentoo since yesterday. We have a whole series of tests that fail in matroids. https://github.com/cschwan/sageongentoo/issues/275 I also posted about it on the cython user list earlier today.
comment:4 in reply to: ↑ 3 Changed 7 years ago by
Replying to fbissey:
well we have some fun with cython0.20 in sageongentoo since yesterday. We have a whole series of tests that fail in matroids.
Yes, I already added a patch to revert the broken optimizations.
comment:5 followup: ↓ 6 Changed 7 years ago by
I didn't see that one before posting. That's quite a lot of broken doctests without.
comment:6 in reply to: ↑ 5 Changed 7 years ago by
Replying to fbissey:
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 Cython0.20) and that there are no tests in the Cython test suite that test such basic functionality.
comment:7 Changed 7 years ago by
Remember to document the patch in SPKG.txt
.
comment:8 Changed 7 years ago by
 Milestone changed from sage6.1 to sage6.2
comment:9 Changed 7 years ago by
Did you run into issues with PPL? E.g.
https://sage.math.washington.edu:8091/hudson/job/sagegitbuild/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
comment:10 Changed 7 years ago by
I didn't when I built sage against pristine cython0.20 here. In fact it all built, it just failed so many doctests on matroids it wasn't funny.
comment:11 Changed 7 years ago by
Would you actually be getting ppl headers from the distro rather than sage's one?
comment:12 Changed 7 years ago by
 Branch changed from u/ohanar/upgrade_cython to u/jdemeyer/ticket/15755
 Created changed from 01/28/14 22:35:29 to 01/28/14 22:35:29
 Modified changed from 01/31/14 21:10:21 to 01/31/14 21:10:21
comment:13 Changed 7 years ago by
 Commit changed from 8ab4be380e5df96263acb8a815d3ccad9438a382 to 38687c94b71a467513f0f79000e9973142545d66
 Description modified (diff)
 Summary changed from upgrade cython to version 0.20 to Upgrade cython to version 0.20.1
comment:14 Changed 7 years ago by
 Commit changed from 38687c94b71a467513f0f79000e9973142545d66 to cf1bb527e67f43b87a5661b969e6d1dcf4f295da
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
cf1bb52  Cython: upgrade to 0.20.1

comment:15 Changed 7 years ago by
 Commit changed from cf1bb527e67f43b87a5661b969e6d1dcf4f295da to 0bbdc9ce50c8c5d3e50820639048e5fe6bc78470
Branch pushed to git repo; I updated commit sha1. New commits:
0bbdc9c  Fix PPL declarations

comment:16 Changed 7 years ago by
 Commit changed from 0bbdc9ce50c8c5d3e50820639048e5fe6bc78470 to 2b6f3da7781a9d41b4a0022f67cdfaf8d1a1a315
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
2b6f3da  Fix PPL and libGAP declarations

comment:17 Changed 7 years ago by
 Commit changed from 2b6f3da7781a9d41b4a0022f67cdfaf8d1a1a315 to b17f7c80784b19b7fe7f58ea01dc9c911d545825
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
b17f7c8  Fix various declarations

comment:18 Changed 7 years ago by
This last version passes doctests, but we should wait until Cython 0.20.1 is officially released.
comment:19 Changed 7 years ago by
 Description modified (diff)
comment:20 Changed 7 years ago by
 Commit changed from b17f7c80784b19b7fe7f58ea01dc9c911d545825 to 115c8fcc196567a2f18c8dd3508cbee0ec11f809
Branch pushed to git repo; I updated commit sha1. New commits:
115c8fc  Fix version and checksum for Cython 0.20.1

comment:21 Changed 7 years ago by
 Status changed from new to needs_review
comment:22 Changed 7 years ago by
 Reviewers set to R. Andrew Ohana
 Status changed from needs_review to positive_review
comment:23 Changed 7 years ago by
 Branch changed from u/jdemeyer/ticket/15755 to 115c8fcc196567a2f18c8dd3508cbee0ec11f809
 Resolution set to fixed
 Status changed from positive_review to closed
comment:24 followup: ↓ 26 Changed 7 years ago by
 Commit 115c8fcc196567a2f18c8dd3508cbee0ec11f809 deleted
 Resolution fixed deleted
 Status changed from closed to new
Full rebuild doesn't work:
Successfully installed eclib20140128 Deleting temporary build directory /home/release/Sage/local/var/tmp/sage/build/eclib20140128 Finished installing eclib20140128.spkg if [ z "$SAGE_INSTALL_FETCH_ONLY" ]; then \ cd /home/release/Sage/src && source bin/sageenv && \ /home/release/Sage/build/pipestatus 'time python setup.py install 2>&1' 'tee a /home/release/Sage/logs/pkgs/sage6.2.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
comment:25 Changed 7 years ago by
 Branch changed from 115c8fcc196567a2f18c8dd3508cbee0ec11f809 to u/jdemeyer/ticket/15755
 Commit set to 115c8fcc196567a2f18c8dd3508cbee0ec11f809
comment:26 in reply to: ↑ 24 Changed 7 years ago by
Replying to vbraun:
Full rebuild doesn't work:
What does the "full rebuild" script do? Works for me after make distclean
.
comment:27 Changed 7 years ago by
Do you have a link to the complete install.log
from that build?
comment:28 Changed 7 years ago by
Thats what I meant... maybe the failure was from another ticket. Will try again...
comment:29 Changed 7 years ago by
 Branch changed from u/jdemeyer/ticket/15755 to 115c8fcc196567a2f18c8dd3508cbee0ec11f809
 Resolution set to fixed
 Status changed from new to closed
comment:30 Changed 7 years ago by
 Commit 115c8fcc196567a2f18c8dd3508cbee0ec11f809 deleted
comment:31 Changed 7 years ago by
 Branch changed from 115c8fcc196567a2f18c8dd3508cbee0ec11f809 to u/jdemeyer/ticket/15755
 Commit set to 115c8fcc196567a2f18c8dd3508cbee0ec11f809
comment:32 Changed 7 years ago by
 Commit changed from 115c8fcc196567a2f18c8dd3508cbee0ec11f809 to faf410f9f73d3e77c7f4062d9ea917cc87f27d3a
 Resolution fixed deleted
 Status changed from closed to new
comment:33 Changed 7 years ago by
 Status changed from new to needs_review
comment:34 Changed 7 years ago by
 Cc mmezzarobba added
comment:35 Changed 7 years ago by
 Cc jpflori added
comment:36 Changed 7 years ago by
 Branch changed from u/jdemeyer/ticket/15755 to faf410f9f73d3e77c7f4062d9ea917cc87f27d3a
 Resolution set to fixed
 Status changed from needs_review to closed
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
andsage.rings.polynomial.pbori
).New commits:
cython: upgrade to 0.20
cython0.20: fix doctests