Patch scipy to fix issue with python3.7

[vinklein]

Installing scipy 0.19.1 (source release) with python 3.7 generate multiple errors of this kind:

scipy/cluster/_vq.c: In function ‘__Pyx__ExceptionSave’:
    scipy/cluster/_vq.c:9728:19: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’
         *type = tstate->exc_type;
                       ^
    scipy/cluster/_vq.c:9729:20: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’
         *value = tstate->exc_value;
                        ^
    scipy/cluster/_vq.c:9730:17: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’
         *tb = tstate->exc_traceback;

This can be fixed by forcing *.pyx files to be recythonized.

Component: packages: standard

Author: Vincent Klein

Branch/Commit: u/vklein/patch_scipy_to_fix_issue_with_python3_7 @ 158885c

Issue created by migration from https://trac.sagemath.org/ticket/25759

[vinklein]

Branch: u/vklein/patch_scipy_to_fix_issue_with_python3_7

[jdemeyer]

comment:2

Do you have to remove cythonize.dat? If so, document why.

---

New commits:

6df21c3	Trac #25759: Force scipy to cythonize *.pyx files
bb3787d	Trac #25759: update package version

[jdemeyer]

Commit: bb3787d

[vinklein]

comment:3

from ​6df21c3 comment:

- Remove cythonize.dat file : That contains the hashcode
used to define if the *.pyx files has been modified

You mean in file fix-scipy-0.19.1-for-python37.patch ?

[sagetrac-git]

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

158885c

Trac #25759: add some doc in .patch file

[sagetrac-git]

Changed commit from bb3787d to 158885c

[jdemeyer]

comment:6

If you really must remove cythonize.dat, I would do it with a rm -f instead of a patch. The problem with a patch is that it must be updated every time we upgrade scipy.

[jdemeyer]

comment:7

Maybe we should try #24766 first, that might also fix the issue.

[vinklein]

comment:8

Replying to @jdemeyer:

Maybe we should try #24766 first, that might also fix the issue.

Yes ! #24766 works.

[jdemeyer]

comment:9

Sorry for the wasted effort Vincent.

[vinklein]

comment:10

No problem ! Upgrading is better than patching.