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Upgrade to Python 3.7.x #25680

Closed jdemeyer closed 5 years ago

jdemeyer commented 5 years ago

Tarball: https://www.python.org/ftp/python/3.7.3/Python-3.7.3.tar.xz

CC: @fchapoton @embray @kiwifb @mkoeppe @slel

Component: packages: standard

Keywords: upgrade

Author: Jeroen Demeyer

Branch: 5a09cf1

Reviewer: Vincent Klein, Erik Bray, Frédéric Chapoton

Issue created by migration from https://trac.sagemath.org/ticket/25680

jdemeyer commented 5 years ago

Branch: u/jdemeyer/upgrade_to_python_3_7_0

jdemeyer commented 5 years ago

New commits:

2c67605Upgrade to Python 3.7.0
jdemeyer commented 5 years ago

Commit: 2c67605

jdemeyer commented 5 years ago

Author: Jeroen Demeyer

embray commented 5 years ago
comment:3

I don't think we should be in any hurry on this. All the last ~year's work of Python 3 porting has been targeting Python 3.6, and I think I'd rather stick with that before risking throwing everything out of whack again.

Between Python 3.6 and 3.7 I suspect the differences, if any, will be minor. But I'd rather try to stabilize on 3.6 first (to which we're quite close), then deal with those differences, rather than change Python versions again. Also I don't know that Python 3.7 has been ported to Cygwin yet (although it does contain a number of useful fixes for Cygwin, I do know).

That said, if you know any specific changes in Python 3.7 (other than the aforementioned Cygwin fixes) that would actively make our porting effort easier I'd consider it...

fchapoton commented 5 years ago
comment:5

Jeroen has said elsewhere that islice will accept Sage integers instead of just ints.

I am again becoming tired and frustated by the slow pace of progress towards py3. And by the large amount of difficult work that remains..

embray commented 5 years ago
comment:6

Ah, I remember making an issue about that, but I don't think I followed what the resolution was.

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 5 years ago

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

1bfcdc8Upgrade to Python 3.7.0
7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 5 years ago

Changed commit from 2c67605 to 1bfcdc8

embray commented 5 years ago
comment:8

Well there's this https://github.com/python/cpython/pull/1918 But unless there are other fixes I'm not seeing it's annoying that this was only fixed for islice, where I believe there is other code affected by the same issue (e.g. range). Also we've already worked aroudn the majority of those cases (sigh...)

embray commented 5 years ago
comment:9

Replying to @fchapoton:

I am again becoming tired and frustated by the slow pace of progress towards py3. And by the large amount of difficult work that remains..

Unfortunately I'm not convinced that upgrading Python yet again is going to make that go any faster. In any case I don't actually have that much "difficult" work remaining. Just dozens of little issues. My Python 3 branch has < 600 modules failing, and most of it appears to minor issues (at one point I had it down to ~400 and I don't know why it ballooned up again, but one or two small changes in just the right places can do that with Sage...)

Also I'll add if you're not using a patched pynac you're going to have lots, lots more "serious" looking issues. We still need to get a pynac upgrade in (I've been manually installing pynac with my Python 3 fixes every time I re-build sage).

jdemeyer commented 5 years ago
comment:10

Replying to @embray:

That said, if you know any specific changes in Python 3.7 (other than the aforementioned Cygwin fixes) that would actively make our porting effort easier I'd consider it...

25391 is a pretty serious issue which is fixed by a Python upgrade (probably also by upgrading to 3.6.6 but I haven't tested that).

jdemeyer commented 5 years ago
comment:11

Replying to @embray:

I don't think we should be in any hurry on this. All the last ~year's work of Python 3 porting has been targeting Python 3.6, and I think I'd rather stick with that before risking throwing everything out of whack again.

First of all, I do not think that this 3.6 -> 3.7 will throw everything out of whack.

However, regardless of that, we'll have to upgrade sooner or later. I don't see the point of having a perfectly working Sage on an outdated Python version. And for the many issues that we still have to fix, it would be better to make sure that they work on Python 3.7 from the start.

fchapoton commented 5 years ago
comment:12

I still think we have very hard remaining problems, among which

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago

Attachment: python3-3.7.0.log

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:14

I get the following error

$ ./configure --with-python=3
...
$ make build
...
[python3-3.7.0] Testing importing of various modules...
[python3-3.7.0] Traceback (most recent call last):
[python3-3.7.0]   File "<string>", line 1, in <module>
[python3-3.7.0]   File "/home/vklein/odk/sage/local/var/tmp/sage/build/python3-3.7.0/src/Lib/ctypes/__init__.py", line 7, in <module>
[python3-3.7.0]     from _ctypes import Union, Structure, Array
[python3-3.7.0] ModuleNotFoundError: No module named '_ctypes'
[python3-3.7.0] ctypes module failed to import
[python3-3.7.0] math module imported OK
[python3-3.7.0] hashlib module imported OK
[python3-3.7.0] crypt module imported OK
[python3-3.7.0] readline module imported OK
[python3-3.7.0] socket module imported OK
[python3-3.7.0] Error: One or more modules failed to import.
...

full python3.7 install log in attachement

kiwifb commented 5 years ago
comment:15

Failure to build _ctypes usually means a problem with ffi (sometimes called libffi) may be there is minimum version requirement?

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:16

Indeed i don't get the error after installing libffi-dev. Thanks !

Note : sage make build works fine in python 3.6 without that.

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:17

next error during the build is :

Installing collected packages: ipykernel
  Running setup.py install for ipykernel: started
    Running command /home/vklein/odk/sage/local/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-qoxsao1r-build/setup.py';f=getattr(tokenize
, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-vc23lh
pc-record/install-record.txt --single-version-externally-managed --compile
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-qoxsao1r-build/setup.py", line 91, in <module>
        from ipykernel.kernelspec import write_kernel_spec, make_ipkernel_cmd, KERNEL_NAME
...
      File "/home/vklein/odk/sage/local/lib/python3.7/site-packages/pexpect/spawnbase.py", line 224
        def expect(self, pattern, timeout=-1, searchwindowsize=-1, async=False):
                                                                       ^
    SyntaxError: invalid syntax
    Running setup.py install for ipykernel: finished with status 'error'
Cleaning up...

Issue reference : https://github.com/pypa/pipenv/issues/956

kiwifb commented 5 years ago
comment:18

To be honest we haven't updated pexpect in vanilla sage for a while. It may be a good idea to do that - in a separate ticket.

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:19

Do we need to update pexpect or to patch pipenv ?

jdemeyer commented 5 years ago
comment:20

No, pexpect.

kiwifb commented 5 years ago
comment:21

I am at pexpect-4.2.1 in sage-on-gentoo (without any patches) and sage is at 4.1.0 + some patches.

jdemeyer commented 5 years ago
comment:22

Replying to @kiwifb:

I am at pexpect-4.2.1 in sage-on-gentoo (without any patches) and sage is at 4.1.0 + some patches.

The patches in Sage are for performance. Without those patches, pexpect is really a lot slower.

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:23

Let's do that #25700.

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago

Dependencies: #25700

embray commented 5 years ago
comment:24

Replying to @fchapoton:

I still think we have very hard remaining problems, among which

  • sorting issues in graphs
  • hashing and comparisons, especially for groups
  • coercion framework have broken parts

Most of which Python 3.7 won't help with. The one area where it might is sorting of dicts, since dict insertion order is now preserved (hooray!)

Well, I'm not completely opposed to upgrading, just skeptical, and don't want to rush into it. When I get a chance I'll compare how my python3 branch fares with and without it.

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:25

Replying to @embray:

Well, I'm not completely opposed to upgrading, just skeptical, and don't want to rush into it. When I get a chance I'll compare how my python3 branch fares with and without it.

One of my goal reviewing this ticket is to produce a kind of diff between the doctests failures in 3.6 and 3.7. It can be helpful to decide what to do.

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:26

And now it's numpy's turn :

$ ./configure --with-python=3
...
$ make build
...
/home/vklein/odk/sage/local/lib/python3.7/distutils/dist.py:274: UserWarning: Un
known distribution option: 'define_macros'
  warnings.warn(msg)
numpy/random/mtrand/mtrand.c: In function '__Pyx__ExceptionSave':
numpy/random/mtrand/mtrand.c:45208:19: error: 'PyThreadState {aka struct _ts}' h
as no member named 'exc_type'
     *type = tstate->exc_type;
                   ^
numpy/random/mtrand/mtrand.c:45209:20: error: 'PyThreadState {aka struct _ts}' h
as no member named 'exc_value'
     *value = tstate->exc_value;
...

numpy's issue #10500. I am not sure what is the right call here i will try with numpy 1.14.5

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:27

When updating to numpy 1.14.5 with this following patch :

diff --git a/numpy/distutils/system_info.py b/numpy/distutils/system_info.py
index 93a8e6f..6e31d30 100644
--- a/numpy/distutils/system_info.py
+++ b/numpy/distutils/system_info.py
@@ -1740,7 +1740,7 @@ class blas_info(system_info):
             lib = self.has_cblas(info)
             if lib is not None:
                 info['language'] = 'c'
-                info['libraries'] = [lib]
+                info['libraries'] = lib
                 info['define_macros'] = [('HAVE_CBLAS', None)]
         self.set_info(**info)

@@ -1772,16 +1772,16 @@ class blas_info(system_info):
                 # check for cblas lib, and if not present check for blas lib.
                 try:
                     c.link_executable(obj, os.path.join(tmpdir, "a.out"),
-                                      libraries=["cblas"],
+                                      libraries=["libraries"],
                                       library_dirs=info['library_dirs'],
                                       extra_postargs=info.get('extra_link_args', []))
-                    res = "cblas"
+                    res = info["libraries"]
                 except distutils.ccompiler.LinkError:
                     c.link_executable(obj, os.path.join(tmpdir, "a.out"),
                                       libraries=["blas"],
                                       library_dirs=info['library_dirs'],
                                       extra_postargs=info.get('extra_link_args', []))
-                    res = "blas"
+                    res = ["blas"]
             except distutils.ccompiler.CompileError:
                 res = None
         finally:

I get the following error :

Found local metadata for numpy-1.14.5.p0
Using cached file /home/vklein/odk/sage/upstream/numpy-1.14.5.zip
numpy-1.14.5.p0
====================================================
Setting up build directory for numpy-1.14.5.p0
Finished extraction
Applying patches from ../patches...
Applying ../patches/numpy-1.14.5-no-hardcode-blas.patch
patching file numpy/distutils/system_info.py
****************************************************
Host system:
Linux tuono 4.13.0-45-generic #50~16.04.1-Ubuntu SMP Wed May 30 11:18:27 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/5/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.10' --with-bugurl=file:///usr/s
hare/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suff
ix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=po
six --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcx
x-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --en
able-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/
usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 -
-with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share
/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --wit
h-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-g
nu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.10) 
****************************************************

Note: if you need reliable uninstall behavior, then install
with pip instead of using `setup.py install`:

  - `pip install .`       (from a git repo or downloaded source
                           release)
  - `pip install numpy`   (last NumPy release on PyPi)

blas_opt_info:
blas_mkl_info:
Disabled blas_mkl_info: (MKLROOT is None)
Disabled blas_mkl_info: (MKLROOT is None)
customize UnixCCompiler
  libraries mkl_rt not found in []
  NOT AVAILABLE

blis_info:
customize UnixCCompiler
  libraries blis not found in ['/home/vklein/odk/sage/local/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-li
nux-gnu']
  NOT AVAILABLE

openblas_info:
customize UnixCCompiler
Disabled openblas_info: (OPENBLAS is None)
customize UnixCCompiler
  libraries openblas not found in []
  NOT AVAILABLE

atlas_3_10_blas_threads_info:
Disabled atlas_3_10_blas_threads_info: (PTATLAS is None)
customize UnixCCompiler
  libraries tatlas not found in []
  NOT AVAILABLE

atlas_3_10_blas_info:
Disabled atlas_3_10_blas_info: (ATLAS is None)
customize UnixCCompiler
  libraries satlas not found in []
  NOT AVAILABLE

atlas_blas_threads_info:
Disabled atlas_blas_threads_info: (PTATLAS is None)
customize UnixCCompiler
  libraries ptf77blas,ptcblas,atlas not found in []
  NOT AVAILABLE

atlas_blas_info:
Disabled atlas_blas_info: (ATLAS is None)
customize UnixCCompiler
  libraries f77blas,cblas,atlas not found in []
  NOT AVAILABLE

blas_info:
customize UnixCCompiler
customize UnixCCompiler
C compiler: gcc -DNDEBUG -g -fwrapv -O3 -Wall -D__CEPHES_COMPLEX_H -fPIC

creating /tmp/tmpyq7p80or/tmp
creating /tmp/tmpyq7p80or/tmp/tmpyq7p80or
compile options: '-I/home/vklein/odk/sage/local/include -c'
gcc: /tmp/tmpyq7p80or/source.c
gcc /tmp/tmpyq7p80or/tmp/tmpyq7p80or/source.o -L/home/vklein/odk/sage/local/lib -llibraries -o /tmp/tmpyq7p80or/a.o
ut
/usr/bin/ld: cannot find -llibraries
collect2: error: ld returned 1 exit status
/usr/bin/ld: cannot find -llibraries
collect2: error: ld returned 1 exit status
gcc /tmp/tmpyq7p80or/tmp/tmpyq7p80or/source.o -L/home/vklein/odk/sage/local/lib -lblas -o /tmp/tmpyq7p80or/a.out
Running from numpy source directory.
/home/vklein/odk/sage/local/var/tmp/sage/build/numpy-1.14.5.p0/src/numpy/distutils/system_info.py:624: UserWarning:

    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  self.calc_info()
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
Traceback (most recent call last):
  File "/home/vklein/odk/sage/local/lib/python3.7/distutils/unixccompiler.py", line 197, in link
    self.spawn(linker + ld_args)
  File "/home/vklein/odk/sage/local/var/tmp/sage/build/numpy-1.14.5.p0/src/numpy/distutils/ccompiler.py", line 89, 
in <lambda>
    m = lambda self, *args, **kw: func(self, *args, **kw)
  File "/home/vklein/odk/sage/local/var/tmp/sage/build/numpy-1.14.5.p0/src/numpy/distutils/ccompiler.py", line 152,
 in CCompiler_spawn
    raise DistutilsExecError('Command "%s" failed with exit status %d%s' % (cmd, s, msg))
distutils.errors.DistutilsExecError: Command "gcc /tmp/tmpyq7p80or/tmp/tmpyq7p80or/source.o -L/home/vklein/odk/sage
/local/lib -llibraries -o /tmp/tmpyq7p80or/a.out" failed with exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/vklein/odk/sage/local/var/tmp/sage/build/numpy-1.14.5.p0/src/numpy/distutils/system_info.py", line 17
77, in has_cblas
    extra_postargs=info.get('extra_link_args', []))
  File "/home/vklein/odk/sage/local/lib/python3.7/distutils/ccompiler.py", line 734, in link_executable
    debug, extra_preargs, extra_postargs, None, target_lang)
  File "/home/vklein/odk/sage/local/lib/python3.7/distutils/unixccompiler.py", line 199, in link
    raise LinkError(msg)
distutils.errors.LinkError: Command "gcc /tmp/tmpyq7p80or/tmp/tmpyq7p80or/source.o -L/home/vklein/odk/sage/local/li
b -llibraries -o /tmp/tmpyq7p80or/a.out" failed with exit status 1

Advices or help are welcome. I get the same errors with a sage with python2.7.

jdemeyer commented 5 years ago
comment:28

Replying to @vinklein:

numpy's issue #10500.

The solution seems to be recythonizing. Maybe we should just do that when building numpy.

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:29

Ok i will try.

jdemeyer commented 5 years ago
comment:30

Replying to @vinklein:

Ok i will try.

If you look in the setup.py file of numpy, you'll see

    from setuptools import setup
    if run_build:
        from numpy.distutils.core import setup
        cwd = os.path.abspath(os.path.dirname(__file__))
        if not os.path.exists(os.path.join(cwd, 'PKG-INFO')):
            # Generate Cython sources, unless building from source release
            generate_cython()

So I guess that removing the PKG-INFO file in spkg-install will force recythonization.

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:31

Your trick almost work. The problem is that the numpy file tools/cythonize.py is not in numpy's source releases.

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:32

I confirm that numpy's install work if we remove PKG-INFO and add cythonize.py file.

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago

Changed branch from u/jdemeyer/upgrade_to_python_3_7_0 to u/vklein/upgrade_to_python_3_7_0

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago

Changed commit from 1bfcdc8 to 6e0c5b4

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:34

Adding a patch to fix numpy's ​issue #10500.

New commits:

6e0c5b4Trac #25680: Patch numpy to fix issue with python3.7
jdemeyer commented 5 years ago
comment:35

Can we please deal with numpy in a separate ticket.

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:36

I don't know. The patch doesn't make sense without python 3.7.

jdemeyer commented 5 years ago
comment:37

Replying to @vinklein:

I don't know. The patch doesn't make sense without python 3.7.

It's needed for Python 3.7, but the fix is unrelated to it.

jdemeyer commented 5 years ago
comment:38

If you're patching the sources anyway, I would prefer to patch setup.py instead of removing PKG-INFO.

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:39

Sure ! It will be cleaner to patch setup.py.

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 5 years ago

Changed commit from 6e0c5b4 to 1bfcdc8

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 5 years ago

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

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago

Changed dependencies from #25700 to #25700, #25755

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:42

scipy errors seems pretty similar to numpy's:

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;

With likely the same cause. In setup.py file of scipy :

        if not os.path.exists(os.path.join(cwd, 'PKG-INFO')):
            # Generate Cython sources, unless building from source release
            generate_cython()
4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago

Changed dependencies from #25700, #25755 to #25700, #25755, #25759

4a781b2b-eada-4ae4-9b46-f6cbb63459b9 commented 5 years ago
comment:44

Building sage with this ticket and it's dependencies works fine.

I have made two run of sage -t -a --long, one with a sage python3.6 and one with this ticket. Comparing the logs of the two runs (and weakly idenfying a failure by the tuple (, ) with a little script, i get the following results:

nb doctests failures with python3.6: 42990
nb doctests failures with python3.7: 43643
new python3.7 failures : 1366
python3.6 failures not appearing with python 3.7 : 713

Two exemple failures among 1366 :

File "src/sage/combinat/finite_state_machine.py", line 10190, in sage.combinat.finite_state_machine.FiniteStateMachine.asymptotic_moments
Failed example:
    moments = T.asymptotic_moments()
Exception raised:
    Traceback (most recent call last):
      File "/home/vklein/odk/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 573, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/vklein/odk/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 983, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.combinat.finite_state_machine.FiniteStateMachine.asymptotic_moments[2]>", line 1, in <module>
        moments = T.asymptotic_moments()
      File "/home/vklein/odk/sage/local/lib/python3.7/site-packages/sage/combinat/finite_state_machine.py", line 10540, in asymptotic_moments
        if not final_component.digraph().is_aperiodic():
      File "/home/vklein/odk/sage/local/lib/python3.7/site-packages/sage/graphs/digraph.py", line 3330, in is_aperiodic
        import networkx
      File "/home/vklein/odk/sage/local/lib/python3.7/site-packages/networkx/__init__.py", line 114, in <module>
        import networkx.generators
      File "/home/vklein/odk/sage/local/lib/python3.7/site-packages/networkx/generators/__init__.py", line 13, in <module>
        from networkx.generators.geometric import *
      File "/home/vklein/odk/sage/local/lib/python3.7/site-packages/networkx/generators/geometric.py", line 27, in <module>
        from scipy.spatial import cKDTree as KDTree
      File "/home/vklein/odk/sage/local/lib/python3.7/site-packages/scipy/spatial/__init__.py", line 95, in <module>
        from .qhull import *
      File "qhull.pyx", line 2224, in init scipy.spatial.qhull
    AttributeError: 'cython_function_or_method' object has no attribute '__func__'

sage -t --long src/sage/combinat/dyck_word.py
**********************************************************************
File "src/sage/combinat/dyck_word.py", line 873, in sage.combinat.dyck_word.DyckWord.plot
Failed example:
    w.plot()
Expected:
    Graphics object consisting of 1 graphics primitive
Got:
    doctest:warning
      File "/home/vklein/odk/sage/src/bin/sage-runtests", line 127, in <module>
        err = DC.run()
      File "/home/vklein/odk/sage/local/lib/python3.7/site-packages/sage/doctest/control.py", line 1172, in run
        self.run_doctests()
      ...
      File "/home/vklein/odk/sage/local/lib/python3.7/collections/__init__.py", line 52, in __getattr__
        DeprecationWarning, stacklevel=2)
            File "/home/vklein/odk/sage/local/lib/python3.7/warnings.py", line 99, in _showwarnmsg
        msg.file, msg.line)
    :
    DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
    Graphics object consisting of 1 graphics primitive

Note : To see the script and logs used https://github.com/vinklein/Trac25680

jdemeyer commented 5 years ago

Changed dependencies from #25700, #25755, #25759 to #25700, #25755, #24766