Opened 18 months ago
Closed 17 months ago
#15755 closed enhancement (fixed)
Upgrade cython to version 0.20.1
Reported by: | ohanar | Owned by: | |
---|---|---|---|
Priority: | major | Milestone: | sage-6.2 |
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 jdemeyer)
Upstream tarball: http://cython.org/release/Cython-0.20.1.tar.gz
Change History (36)
comment:1 Changed 18 months ago by ohanar
- Branch set to u/ohanar/upgrade_cython
- Commit set to 8ab4be380e5df96263acb8a815d3ccad9438a382
comment:2 Changed 18 months ago by ohanar
- Description modified (diff)
comment:3 follow-up: ↓ 4 Changed 18 months ago by fbissey
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.
https://github.com/cschwan/sage-on-gentoo/issues/275 I also posted about it on the cython user list earlier today.
comment:4 in reply to: ↑ 3 Changed 18 months ago by ohanar
Replying to fbissey:
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.
comment:5 follow-up: ↓ 6 Changed 18 months ago by fbissey
I didn't see that one before posting. That's quite a lot of broken doctests without.
comment:6 in reply to: ↑ 5 Changed 18 months ago by ohanar
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 Cython-0.20) and that there are no tests in the Cython test suite that test such basic functionality.
comment:7 Changed 18 months ago by jdemeyer
Remember to document the patch in SPKG.txt.
comment:8 Changed 18 months ago by vbraun_spam
- Milestone changed from sage-6.1 to sage-6.2
comment:9 Changed 18 months ago by robertwb
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
comment:10 Changed 18 months ago by fbissey
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.
comment:11 Changed 18 months ago by fbissey
Would you actually be getting ppl headers from the distro rather than sage's one?
comment:12 Changed 18 months ago by jdemeyer
- Branch changed from u/ohanar/upgrade_cython to u/jdemeyer/ticket/15755
- Created changed from 01/28/14 14:35:29 to 01/28/14 14:35:29
- Modified changed from 01/31/14 13:10:21 to 01/31/14 13:10:21
comment:13 Changed 18 months ago by jdemeyer
- 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 18 months ago by git
- 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 18 months ago by git
- Commit changed from cf1bb527e67f43b87a5661b969e6d1dcf4f295da to 0bbdc9ce50c8c5d3e50820639048e5fe6bc78470
Branch pushed to git repo; I updated commit sha1. New commits:
0bbdc9c | Fix PPL declarations |
comment:16 Changed 18 months ago by git
- 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 18 months ago by git
- 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 18 months ago by jdemeyer
This last version passes doctests, but we should wait until Cython 0.20.1 is officially released.
comment:19 Changed 18 months ago by jdemeyer
- Description modified (diff)
comment:20 Changed 18 months ago by git
- 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 18 months ago by jdemeyer
- Status changed from new to needs_review
comment:22 Changed 18 months ago by ohanar
- Reviewers set to R. Andrew Ohana
- Status changed from needs_review to positive_review
comment:23 Changed 18 months ago by vbraun
- Branch changed from u/jdemeyer/ticket/15755 to 115c8fcc196567a2f18c8dd3508cbee0ec11f809
- Resolution set to fixed
- Status changed from positive_review to closed
comment:24 follow-up: ↓ 26 Changed 18 months ago by vbraun
- Commit 115c8fcc196567a2f18c8dd3508cbee0ec11f809 deleted
- Resolution fixed deleted
- Status changed from closed to new
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
comment:25 Changed 18 months ago by jdemeyer
- Branch changed from 115c8fcc196567a2f18c8dd3508cbee0ec11f809 to u/jdemeyer/ticket/15755
- Commit set to 115c8fcc196567a2f18c8dd3508cbee0ec11f809
comment:26 in reply to: ↑ 24 Changed 18 months ago by jdemeyer
Replying to vbraun:
Full rebuild doesn't work:
What does the "full rebuild" script do? Works for me after make distclean.
comment:27 Changed 18 months ago by jdemeyer
Do you have a link to the complete install.log from that build?
comment:28 Changed 18 months ago by vbraun
Thats what I meant... maybe the failure was from another ticket. Will try again...
comment:29 Changed 18 months ago by vbraun
- Branch changed from u/jdemeyer/ticket/15755 to 115c8fcc196567a2f18c8dd3508cbee0ec11f809
- Resolution set to fixed
- Status changed from new to closed
comment:30 Changed 17 months ago by jdemeyer
- Commit 115c8fcc196567a2f18c8dd3508cbee0ec11f809 deleted
comment:31 Changed 17 months ago by jdemeyer
- Branch changed from 115c8fcc196567a2f18c8dd3508cbee0ec11f809 to u/jdemeyer/ticket/15755
- Commit set to 115c8fcc196567a2f18c8dd3508cbee0ec11f809
comment:32 Changed 17 months ago by jdemeyer
- Commit changed from 115c8fcc196567a2f18c8dd3508cbee0ec11f809 to faf410f9f73d3e77c7f4062d9ea917cc87f27d3a
- Resolution fixed deleted
- Status changed from closed to new
comment:33 Changed 17 months ago by jdemeyer
- Status changed from new to needs_review
comment:34 Changed 17 months ago by mmezzarobba
- Cc mmezzarobba added
comment:35 Changed 17 months ago by jpflori
- Cc jpflori added
comment:36 Changed 17 months ago by vbraun
- 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 and sage.rings.polynomial.pbori).
New commits: