[sage-release] Re: Sage 9.5.rc1 released

[Marc Culler]

Hi Matthias,

I have posted binary releases for 9.5.rc1 on macOS with Intel or Arm CPUs 
at https://github.com/3-manifolds/Sage_macOS/releases/tag/v1.3-rc1.  There 
are two separate disk images.  You may recall that I do not use Homebrew or 
Conda, but I did have to use an experimental binary release of gfortran for 
M1 since I was not able to build the gfortran spkg.

- Marc

On Saturday, January 15, 2022 at 3:01:14 PM UTC-6 matthia...@gmail.com 
wrote:

> Based on the runs on GH Actions, I have updated the summary of platform 
> support in https://wiki.sagemath.org/ReleaseTours/sage-9.5#Sources
>
> TL;DR: It's all good now on all platforms tested on GH Actions, including 
> Cygwin.
> But I would urge that 9.5 still merge the positively reviews tickets 
> marked "critical"/"blocker", such as 
> https://trac.sagemath.org/ticket/29285 (which fixes the build in the 
> presence of pyenv).
> Also *note we have absolutely no automatic testing for the Apple Silicon 
> (M1) platform.* So it would be good if users/developers who have access 
> to this platform test the release candidate.
>
>
>
> On Friday, January 14, 2022 at 8:14:13 AM UTC-8 Matthias Köppe wrote:
>
>> On Thursday, January 13, 2022 at 3:22:03 PM UTC-8 Volker Braun wrote:
>>
>>> As always, you can get the latest beta version from the "develop" git 
>>> branch. Alternatively, the self-contained source tarball is at 
>>> http://www.sagemath.org/download-latest.html
>>>
>>> 3da1b22c25 (HEAD -> develop, tag: 9.5.rc1, trac/develop) Updated 
>>> SageMath version to 9.5.rc1
>>>
>>
>> Thanks for the new rc. Tests are running at 
>> https://github.com/sagemath/sage/actions/runs/1690315877 (Linux, macOS) 
>> and https://github.com/sagemath/sage/actions/runs/1690315874 (Cygwin).
>>
>>
>>
>>
>>
>>  
>>
>

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[sage-release] Re: Sage 9.5.rc2 release

[Marc Culler]

Adding $(PYTHON_TOOLCHAIN) to the cryptominisat dependencies fixed the 
build failure that I encountered.
On Sunday, January 16, 2022 at 4:09:02 PM UTC-6 matthia...@gmail.com wrote:

> The sqlite doctest failure is tracked at 
> https://trac.sagemath.org/ticket/29092
>
> On Sunday, January 16, 2022 at 1:42:06 PM UTC-8 jonatha...@googlemail.com 
> wrote:
>
>> Thanks Volker for preparing the release.
>>
>> All tests pass on debian buster, except
>>
>> sage -t --long --random-seed=146168601452887490256495561253701871534 
>> src/sage/tests/cmdline.py  # 3 doctests failed 
>>
>> as squlite executable is not available.
>>
>> Volker Braun schrieb am Sonntag, 16. Januar 2022 um 18:17:36 UTC+1:
>>
>>> As always, you can get the latest beta version from the "develop" git 
>>> branch. Alternatively, the self-contained source tarball is at 
>>> http://www.sagemath.org/download-latest.html
>>>
>>> f9b2db94f6 (tag: 9.5.rc2, trac/develop) Updated SageMath version to 
>>> 9.5.rc2
>>> 7a9347dbc0 Trac #33155: Broken install using system pythons < 3.10 from 
>>> python.org macOS packages
>>> fe634f8613 Trac #33162: Fix installation of cryptominisat and pycryptosat
>>> 9ceaaea7a7 Trac #33153: opensuse-tumbleweed: sagelib build fails
>>> 3da1b22c25 (tag: 9.5.rc1) Updated SageMath version to 9.5.rc1
>>>
>>

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[sage-release] Re: Sage 9.5.rc2 release

[Marc Culler]

My attempt to build rc2 on macOS with arm CPU failed with this error:

Installing cryptominisat-5.6.8
/private/var/tmp/sage-9.5-current/local/var/lib/sage/venv-python3.9.9/bin/python3:
 
No module named pip

Maybe a pip dependency is missing now for cryptominisat?

- Marc
On Sunday, January 16, 2022 at 4:09:02 PM UTC-6 matthia...@gmail.com wrote:

> The sqlite doctest failure is tracked at 
> https://trac.sagemath.org/ticket/29092
>
> On Sunday, January 16, 2022 at 1:42:06 PM UTC-8 jonatha...@googlemail.com 
> wrote:
>
>> Thanks Volker for preparing the release.
>>
>> All tests pass on debian buster, except
>>
>> sage -t --long --random-seed=146168601452887490256495561253701871534 
>> src/sage/tests/cmdline.py  # 3 doctests failed 
>>
>> as squlite executable is not available.
>>
>> Volker Braun schrieb am Sonntag, 16. Januar 2022 um 18:17:36 UTC+1:
>>
>>> As always, you can get the latest beta version from the "develop" git 
>>> branch. Alternatively, the self-contained source tarball is at 
>>> http://www.sagemath.org/download-latest.html
>>>
>>> f9b2db94f6 (tag: 9.5.rc2, trac/develop) Updated SageMath version to 
>>> 9.5.rc2
>>> 7a9347dbc0 Trac #33155: Broken install using system pythons < 3.10 from 
>>> python.org macOS packages
>>> fe634f8613 Trac #33162: Fix installation of cryptominisat and pycryptosat
>>> 9ceaaea7a7 Trac #33153: opensuse-tumbleweed: sagelib build fails
>>> 3da1b22c25 (tag: 9.5.rc1) Updated SageMath version to 9.5.rc1
>>>
>>

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[sage-release] Re: Sage 9.5.rc1 released

[Marc Culler]

While many things work in the binary macOS app for Arm CPU, I discovered by 
accident that the following produces a segfault:

sage: M = Manifold()

In fact, even trying to import manifold from sage.manifolds segfaults.  
This does not happen on the Intel version of the app built from the same 
branch of the repository.

I have not been able to run a debugger on sage at all.  Of course cysignals 
cannot produce a backtrace on macOS.  With lldb -p I get an error saying 
that lldb is not allowed to attach to the process and referring me to 
non-existent messages in system.log for explanations.  Running the 
debugserver directly produces:
error: failed to attach process 6619: unable to start the exception thread

This occurs even if I run sage directly in the repo after the build 
finishes - it does not have anything to do with the app.  (And the debugger 
similarly refuses to attach to the process.)  I tried to run the debugger 
as root and I also tried adding debugger entitlements and resigning the 
app.  Neither make it possible for me to use lldb on sage itself.

I am able to start the sage python3 in lldb.  If I knew how to import the 
Manifold class from python I might be able to get somewhere.  But if I run
>>> from sage.manifolds import manifold
I get a python exception whose traceback ends with:
File "sage/structure/category_object.pyx", line 60, in init 
sage.structure.category_object 
(build/cythonized/sage/structure/category_object.c:9914)
ImportError: cannot import name Category

- Marc

On Saturday, January 15, 2022 at 4:30:08 PM UTC-6 Marc Culler wrote:

> Hi Matthias,
>
> I have posted binary releases for 9.5.rc1 on macOS with Intel or Arm CPUs 
> at https://github.com/3-manifolds/Sage_macOS/releases/tag/v1.3-rc1.  
> There are two separate disk images.  You may recall that I do not use 
> Homebrew or Conda, but I did have to use an experimental binary release of 
> gfortran for M1 since I was not able to build the gfortran spkg.
>
> - Marc
>
> On Saturday, January 15, 2022 at 3:01:14 PM UTC-6 matthia...@gmail.com 
> wrote:
>
>> Based on the runs on GH Actions, I have updated the summary of platform 
>> support in https://wiki.sagemath.org/ReleaseTours/sage-9.5#Sources
>>
>> TL;DR: It's all good now on all platforms tested on GH Actions, including 
>> Cygwin.
>> But I would urge that 9.5 still merge the positively reviews tickets 
>> marked "critical"/"blocker", such as 
>> https://trac.sagemath.org/ticket/29285 (which fixes the build in the 
>> presence of pyenv).
>> Also *note we have absolutely no automatic testing for the Apple Silicon 
>> (M1) platform.* So it would be good if users/developers who have access 
>> to this platform test the release candidate.
>>
>>
>>
>> On Friday, January 14, 2022 at 8:14:13 AM UTC-8 Matthias Köppe wrote:
>>
>>> On Thursday, January 13, 2022 at 3:22:03 PM UTC-8 Volker Braun wrote:
>>>
>>>> As always, you can get the latest beta version from the "develop" git 
>>>> branch. Alternatively, the self-contained source tarball is at 
>>>> http://www.sagemath.org/download-latest.html
>>>>
>>>> 3da1b22c25 (HEAD -> develop, tag: 9.5.rc1, trac/develop) Updated 
>>>> SageMath version to 9.5.rc1
>>>>
>>>
>>> Thanks for the new rc. Tests are running at 
>>> https://github.com/sagemath/sage/actions/runs/1690315877 (Linux, macOS) 
>>> and https://github.com/sagemath/sage/actions/runs/1690315874 (Cygwin).
>>>
>>>
>>>
>>>
>>>
>>>  
>>>
>>

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[sage-release] Re: Sage 9.5.rc1 released

[Marc Culler]

I get the same exception on both Intel and Arm when I try to import 
sage.all from the sage python.  There is no exception if I do the same 
import in sage -python.  But that is no help in terms of running lldb.  
However, perhaps if I knew how to set up the correct environment first I 
would be able to start the sage python in lldb and then actually be able to 
do the import.

- Marc


On Monday, January 17, 2022 at 3:18:05 PM UTC-6 matthia...@gmail.com wrote:

> Try "import sage.all" first.
>
> On Monday, January 17, 2022 at 1:13:38 PM UTC-8 marc@gmail.com wrote:
>
>> While many things work in the binary macOS app for Arm CPU, I discovered 
>> by accident that the following produces a segfault:
>>
>> sage: M = Manifold()
>>
>> In fact, even trying to import manifold from sage.manifolds segfaults.  
>> This does not happen on the Intel version of the app built from the same 
>> branch of the repository.
>>
>> I have not been able to run a debugger on sage at all.  Of course 
>> cysignals cannot produce a backtrace on macOS.  With lldb -p I get an error 
>> saying that lldb is not allowed to attach to the process and referring me 
>> to non-existent messages in system.log for explanations.  Running the 
>> debugserver directly produces:
>> error: failed to attach process 6619: unable to start the exception thread
>>
>> This occurs even if I run sage directly in the repo after the build 
>> finishes - it does not have anything to do with the app.  (And the debugger 
>> similarly refuses to attach to the process.)  I tried to run the debugger 
>> as root and I also tried adding debugger entitlements and resigning the 
>> app.  Neither make it possible for me to use lldb on sage itself.
>>
>> I am able to start the sage python3 in lldb.  If I knew how to import the 
>> Manifold class from python I might be able to get somewhere.  But if I run
>> >>> from sage.manifolds import manifold
>> I get a python exception whose traceback ends with:
>> File "sage/structure/category_object.pyx", line 60, in init 
>> sage.structure.category_object 
>> (build/cythonized/sage/structure/category_object.c:9914)
>> ImportError: cannot import name Category
>>
>> - Marc
>>
>> On Saturday, January 15, 2022 at 4:30:08 PM UTC-6 Marc Culler wrote:
>>
>>> Hi Matthias,
>>>
>>> I have posted binary releases for 9.5.rc1 on macOS with Intel or Arm 
>>> CPUs at https://github.com/3-manifolds/Sage_macOS/releases/tag/v1.3-rc1.  
>>> There are two separate disk images.  You may recall that I do not use 
>>> Homebrew or Conda, but I did have to use an experimental binary release of 
>>> gfortran for M1 since I was not able to build the gfortran spkg.
>>>
>>> - Marc
>>>
>>> On Saturday, January 15, 2022 at 3:01:14 PM UTC-6 matthia...@gmail.com 
>>> wrote:
>>>
>> Based on the runs on GH Actions, I have updated the summary of platform 
>>>> support in https://wiki.sagemath.org/ReleaseTours/sage-9.5#Sources
>>>>
>>>> TL;DR: It's all good now on all platforms tested on GH Actions, 
>>>> including Cygwin.
>>>> But I would urge that 9.5 still merge the positively reviews tickets 
>>>> marked "critical"/"blocker", such as 
>>>> https://trac.sagemath.org/ticket/29285 (which fixes the build in the 
>>>> presence of pyenv).
>>>> Also *note we have absolutely no automatic testing for the Apple 
>>>> Silicon (M1) platform.* So it would be good if users/developers who 
>>>> have access to this platform test the release candidate.
>>>>
>>>>
>>>>
>>>> On Friday, January 14, 2022 at 8:14:13 AM UTC-8 Matthias Köppe wrote:
>>>>
>>>>> On Thursday, January 13, 2022 at 3:22:03 PM UTC-8 Volker Braun wrote:
>>>>>
>>>>>> As always, you can get the latest beta version from the "develop" git 
>>>>>> branch. Alternatively, the self-contained source tarball is at 
>>>>>> http://www.sagemath.org/download-latest.html
>>>>>>
>>>>>> 3da1b22c25 (HEAD -> develop, tag: 9.5.rc1, trac/develop) Updated 
>>>>>> SageMath version to 9.5.rc1
>>>>>>
>>>>>
>>>>> Thanks for the new rc. Tests are running at 
>>>>> https://github.com/sagemath/sage/actions/runs/1690315877 (Linux, 
>>>>> macOS) and https://github.com/sagemath/sage/actions/runs/1690315874 
>>>>> (Cygwin).
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>  
>>>>>
>>>>

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[sage-release] Re: Sage 9.5.rc1 released

[Marc Culler]

(lldb) r
Process 6983 launched: 
'/Users/culler/programs/Sage_macOS/Sage_framework/bigrepo/sage/venv/bin/python3.9'
 
(arm64)
Python 3.9.9 (main, Jan 16 2022, 17:10:52) 
[Clang 13.0.0 (clang-1300.0.29.30)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import sage.all
Traceback (most recent call last):
  File "", line 1, in 
  File 
"/Users/culler/programs/Sage_macOS/Sage_framework/bigrepo/sage/venv/lib/python3.9/site-packages/sage/all.py",
 
line 131, in 
from sage.rings.all  import *
  File 
"/Users/culler/programs/Sage_macOS/Sage_framework/bigrepo/sage/venv/lib/python3.9/site-packages/sage/rings/all.py",
 
line 87, in 
from .qqbar import (AlgebraicRealField, AA,
  File 
"/Users/culler/programs/Sage_macOS/Sage_framework/bigrepo/sage/venv/lib/python3.9/site-packages/sage/rings/qqbar.py",
 
line 2810, in 
QQxy = QQ['x', 'y']
  File "sage/structure/parent.pyx", line 1276, in 
sage.structure.parent.Parent.__getitem__ 
(build/cythonized/sage/structure/parent.c:11409)
  File 
"/Users/culler/programs/Sage_macOS/Sage_framework/bigrepo/sage/venv/lib/python3.9/site-packages/sage/categories/rings.py",
 
line 1177, in __getitem__
return PolynomialRing(self, elts)
  File 
"/Users/culler/programs/Sage_macOS/Sage_framework/bigrepo/sage/venv/lib/python3.9/site-packages/sage/rings/polynomial/polynomial_ring_constructor.py",
 
line 647, in PolynomialRing
return _multi_variate(base_ring, names, **kwds)
  File 
"/Users/culler/programs/Sage_macOS/Sage_framework/bigrepo/sage/venv/lib/python3.9/site-packages/sage/rings/polynomial/polynomial_ring_constructor.py",
 
line 775, in _multi_variate
from sage.rings.polynomial.multi_polynomial_libsingular import 
MPolynomialRing_libsingular
  File "sage/rings/polynomial/multi_polynomial_libsingular.pyx", line 1, in 
init sage.rings.polynomial.multi_polynomial_libsingular 
(build/cythonized/sage/rings/polynomial/multi_polynomial_libsingular.cpp:50026)
  File "sage/libs/singular/singular.pyx", line 1558, in init 
sage.libs.singular.singular 
(build/cythonized/sage/libs/singular/singular.cpp:15752)
  File "sage/libs/singular/singular.pyx", line 1525, in 
sage.libs.singular.singular.init_libsingular 
(build/cythonized/sage/libs/singular/singular.cpp:12870)
  File 
"/Users/culler/programs/Sage_macOS/Sage_framework/bigrepo/sage/venv/lib/python3.9/posixpath.py",
 
line 152, in dirname
p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not NoneType
>>> 


On Monday, January 17, 2022 at 3:18:05 PM UTC-6 matthia...@gmail.com wrote:

> Try "import sage.all" first.
>
> On Monday, January 17, 2022 at 1:13:38 PM UTC-8 marc@gmail.com wrote:
>
>> While many things work in the binary macOS app for Arm CPU, I discovered 
>> by accident that the following produces a segfault:
>>
>> sage: M = Manifold()
>>
>> In fact, even trying to import manifold from sage.manifolds segfaults.  
>> This does not happen on the Intel version of the app built from the same 
>> branch of the repository.
>>
>> I have not been able to run a debugger on sage at all.  Of course 
>> cysignals cannot produce a backtrace on macOS.  With lldb -p I get an error 
>> saying that lldb is not allowed to attach to the process and referring me 
>> to non-existent messages in system.log for explanations.  Running the 
>> debugserver directly produces:
>> error: failed to attach process 6619: unable to start the exception thread
>>
>> This occurs even if I run sage directly in the repo after the build 
>> finishes - it does not have anything to do with the app.  (And the debugger 
>> similarly refuses to attach to the process.)  I tried to run the debugger 
>> as root and I also tried adding debugger entitlements and resigning the 
>> app.  Neither make it possible for me to use lldb on sage itself.
>>
>> I am able to start the sage python3 in lldb.  If I knew how to import the 
>> Manifold class from python I might be able to get somewhere.  But if I run
>> >>> from sage.manifolds import manifold
>> I get a python exception whose traceback ends with:
>> File "sage/structure/category_object.pyx", line 60, in init 
>> sage.structure.category_object 
>> (build/cythonized/sage/structure/category_object.c:9914)
>> ImportError: cannot import name Category
>>
>> - Marc
>>
>> On Saturday, January 15, 2022 at 4:30:08 PM UTC-6 Marc Culler wrote:
>>
>>> Hi Matthias,
>>>
>>> I have posted binary releases for 9.5.rc1 on macOS with Intel or Arm 
>>> CPUs at htt

[sage-release] Re: Sage 9.5.rc1 released

[Marc Culler]

I was able to get a bit further in python by running:

>>> from sage.structure import *

Then when I tried

>>> from sage.manifolds import manifold

I get an exception whose traceback ends with

AttributeError: module 'sage.structure' has no attribute 'sage_object'

This seems strange, since there is no exception when I run

>>> from sage.structure import sage_object
>>> dir(sage_object)
['LazyImport', 'SageObject', '__all__', '__builtins__', '__doc__', 
'__file__', '__loader__', '__name__', '__package__', '__spec__', 
'_base_dumps', '_base_save', '_interface_init_with_interface', 'dumps', 
'load', 'loads', 'make_None', 'register_unpickle_override', 'save', 
'unpickle_all', 'unpickle_global', 'unpickle_override']

But it seems consistent with:

>>> dir(sage.structure)
['__builtins__', '__cached__', '__doc__', '__file__', '__loader__', 
'__name__', '__package__', '__path__', '__spec__', 'category_object', 
'coerce', 'coerce_actions', 'coerce_dict', 'coerce_exceptions', 
'coerce_maps', 'dynamic_class', 'element', 'parent', 'richcmp', 'sage', 
'unique_representation']

I suppose there is some opaque monkey-patching going on.  So, I am not sure 
where to go next ...

- Marc

On Saturday, January 15, 2022 at 4:49:42 PM UTC-6 matthia...@gmail.com 
wrote:

> Hi Marc,
> Awesome! I've added it to 
> https://wiki.sagemath.org/ReleaseTours/sage-9.5#Binaries
> Matthias
>
> On Saturday, January 15, 2022 at 2:30:08 PM UTC-8 marc@gmail.com 
> wrote:
>
>> Hi Matthias,
>>
>> I have posted binary releases for 9.5.rc1 on macOS with Intel or Arm CPUs 
>> at https://github.com/3-manifolds/Sage_macOS/releases/tag/v1.3-rc1.  
>> There are two separate disk images.  You may recall that I do not use 
>> Homebrew or Conda, but I did have to use an experimental binary release of 
>> gfortran for M1 since I was not able to build the gfortran spkg.
>>
>> - Marc
>>
>> On Saturday, January 15, 2022 at 3:01:14 PM UTC-6 matthia...@gmail.com 
>> wrote:
>>
>>> Based on the runs on GH Actions, I have updated the summary of platform 
>>> support in https://wiki.sagemath.org/ReleaseTours/sage-9.5#Sources
>>>
>>> TL;DR: It's all good now on all platforms tested on GH Actions, 
>>> including Cygwin.
>>> But I would urge that 9.5 still merge the positively reviews tickets 
>>> marked "critical"/"blocker", such as 
>>> https://trac.sagemath.org/ticket/29285 (which fixes the build in the 
>>> presence of pyenv).
>>> Also *note we have absolutely no automatic testing for the Apple 
>>> Silicon (M1) platform.* So it would be good if users/developers who 
>>> have access to this platform test the release candidate.
>>>
>>>
>>>
>>> On Friday, January 14, 2022 at 8:14:13 AM UTC-8 Matthias Köppe wrote:
>>>
 On Thursday, January 13, 2022 at 3:22:03 PM UTC-8 Volker Braun wrote:

> As always, you can get the latest beta version from the "develop" git 
> branch. Alternatively, the self-contained source tarball is at 
> http://www.sagemath.org/download-latest.html
>
> 3da1b22c25 (HEAD -> develop, tag: 9.5.rc1, trac/develop) Updated 
> SageMath version to 9.5.rc1
>

 Thanks for the new rc. Tests are running at 
 https://github.com/sagemath/sage/actions/runs/1690315877 (Linux, 
 macOS) and https://github.com/sagemath/sage/actions/runs/1690315874 
 (Cygwin).





  

>>>

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Re: [sage-release] Re: Sage 9.5.rc1 released

[Marc Culler]

That worked like a charm!

  * frame #0: 0x83c0f9024900
frame #1: 0x000153ff8b7c _dop.cpython-39-darwin.so`PyFortranObject_New
+ 40
frame #2: 0x000153ff66fc _dop.cpython-39-darwin.so`PyInit__dop +
1020

And it turns out that this problem was independently reported by William
Stein.  I used an external gfortran compiler installed in /usr/local to
build this sage.  So I need to also embed the fortran runtime library into
my Sage.framework and patch the load paths of all executable files that
load it.  This would be a lot easier if someone could get the gfortran spkg
to build on an M1 CPU.

Anyway, thanks!  I think I am on track to make this work now.

If anyone knows what dop stands for, I am all ears.

- Marc

On Mon, Jan 17, 2022 at 5:35 PM Matthias Köppe 
wrote:

> Use "./sage -sh" and run python / the debugger from there?
>
> On Monday, January 17, 2022 at 2:35:38 PM UTC-8 marc@gmail.com wrote:
>
>> I get the same exception on both Intel and Arm when I try to import
>> sage.all from the sage python.  There is no exception if I do the same
>> import in sage -python.  But that is no help in terms of running lldb.
>> However, perhaps if I knew how to set up the correct environment first I
>> would be able to start the sage python in lldb and then actually be able to
>> do the import.
>>
>> - Marc
>>
>>
>> On Monday, January 17, 2022 at 3:18:05 PM UTC-6 matthia...@gmail.com
>> wrote:
>>
>>> Try "import sage.all" first.
>>>
>>> On Monday, January 17, 2022 at 1:13:38 PM UTC-8 marc@gmail.com
>>> wrote:
>>>
>>>> While many things work in the binary macOS app for Arm CPU, I
>>>> discovered by accident that the following produces a segfault:
>>>>
>>>> sage: M = Manifold()
>>>>
>>>> In fact, even trying to import manifold from sage.manifolds segfaults.
>>>> This does not happen on the Intel version of the app built from the same
>>>> branch of the repository.
>>>>
>>>> I have not been able to run a debugger on sage at all.  Of course
>>>> cysignals cannot produce a backtrace on macOS.  With lldb -p I get an error
>>>> saying that lldb is not allowed to attach to the process and referring me
>>>> to non-existent messages in system.log for explanations.  Running the
>>>> debugserver directly produces:
>>>> error: failed to attach process 6619: unable to start the exception
>>>> thread
>>>>
>>>> This occurs even if I run sage directly in the repo after the build
>>>> finishes - it does not have anything to do with the app.  (And the debugger
>>>> similarly refuses to attach to the process.)  I tried to run the debugger
>>>> as root and I also tried adding debugger entitlements and resigning the
>>>> app.  Neither make it possible for me to use lldb on sage itself.
>>>>
>>>> I am able to start the sage python3 in lldb.  If I knew how to import
>>>> the Manifold class from python I might be able to get somewhere.  But if I
>>>> run
>>>> >>> from sage.manifolds import manifold
>>>> I get a python exception whose traceback ends with:
>>>> File "sage/structure/category_object.pyx", line 60, in init
>>>> sage.structure.category_object
>>>> (build/cythonized/sage/structure/category_object.c:9914)
>>>> ImportError: cannot import name Category
>>>>
>>>> - Marc
>>>>
>>>> On Saturday, January 15, 2022 at 4:30:08 PM UTC-6 Marc Culler wrote:
>>>>
>>>>> Hi Matthias,
>>>>>
>>>>> I have posted binary releases for 9.5.rc1 on macOS with Intel or Arm
>>>>> CPUs at
>>>>> https://github.com/3-manifolds/Sage_macOS/releases/tag/v1.3-rc1.
>>>>> There are two separate disk images.  You may recall that I do not use
>>>>> Homebrew or Conda, but I did have to use an experimental binary release of
>>>>> gfortran for M1 since I was not able to build the gfortran spkg.
>>>>>
>>>>> - Marc
>>>>>
>>>>> On Saturday, January 15, 2022 at 3:01:14 PM UTC-6 matthia...@gmail.com
>>>>> wrote:
>>>>>
>>>> Based on the runs on GH Actions, I have updated the summary of platform
>>>>>> support in https://wiki.sagemath.org/ReleaseTours/sage-9.5#Sources
>>>>>>
>>>>>> TL;DR: It's all good now on all platforms tested on GH Actions,
>>>>>&

[sage-release] Re: Sage 9.5.rc2 release

[Marc Culler]

I have resolved all of the issues I know of in the binary prelease of sage 
9.5 
https://github.com/3-manifolds/Sage_macOS/releases/download/v1.3-rc1/SageMath-9.5_arm64.dmg
 
.

I switched to using the homebrew version of gfortran-11.  That resolved the 
crash when importing sage.manifolds.manifold (which was actually happening 
when importing the scpy integration module.)  I believe that the problem 
was that the other gfortran compiler implements fortran 2018 and some of 
the scipy modules are not compliant with that.

I also added a copy of the gfortran runtime, suitably adjusted to work in 
the Sage framework in the app bundle.

Matthias, I think you should revise your recommendation so it specifies the 
homebrew gfortran-11.
On Monday, January 17, 2022 at 3:13:38 PM UTC-6 Marc Culler wrote:

> My attempt to build rc2 on macOS with arm CPU failed with this error:
>
> Installing cryptominisat-5.6.8
> /private/var/tmp/sage-9.5-current/local/var/lib/sage/venv-python3.9.9/bin/python3:
>  
> No module named pip
>
> Maybe a pip dependency is missing now for cryptominisat?
>
> - Marc
> On Sunday, January 16, 2022 at 4:09:02 PM UTC-6 matthia...@gmail.com 
> wrote:
>
>> The sqlite doctest failure is tracked at 
>> https://trac.sagemath.org/ticket/29092
>>
>> On Sunday, January 16, 2022 at 1:42:06 PM UTC-8 jonatha...@googlemail.com 
>> wrote:
>>
>>> Thanks Volker for preparing the release.
>>>
>>> All tests pass on debian buster, except
>>>
>>> sage -t --long --random-seed=146168601452887490256495561253701871534 
>>> src/sage/tests/cmdline.py  # 3 doctests failed 
>>>
>>> as squlite executable is not available.
>>>
>>> Volker Braun schrieb am Sonntag, 16. Januar 2022 um 18:17:36 UTC+1:
>>>
>>>> As always, you can get the latest beta version from the "develop" git 
>>>> branch. Alternatively, the self-contained source tarball is at 
>>>> http://www.sagemath.org/download-latest.html
>>>>
>>>> f9b2db94f6 (tag: 9.5.rc2, trac/develop) Updated SageMath version to 
>>>> 9.5.rc2
>>>> 7a9347dbc0 Trac #33155: Broken install using system pythons < 3.10 from 
>>>> python.org macOS packages
>>>> fe634f8613 Trac #33162: Fix installation of cryptominisat and 
>>>> pycryptosat
>>>> 9ceaaea7a7 Trac #33153: opensuse-tumbleweed: sagelib build fails
>>>> 3da1b22c25 (tag: 9.5.rc1) Updated SageMath version to 9.5.rc1
>>>>
>>>

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Re: [sage-release] Re: Sage 9.5.rc2 release

[Marc Culler]

Thanks, Matthias.  It is actually 9.5.rc2 now.

On Fri, Jan 21, 2022 at 11:58 AM Matthias Köppe 
wrote:

> Thanks Marc, I have updated
> https://wiki.sagemath.org/ReleaseTours/sage-9.5#Sources
>
> On Thursday, January 20, 2022 at 11:31:36 PM UTC-8 marc@gmail.com
> wrote:
>
>> I have resolved all of the issues I know of in the binary prelease of
>> sage 9.5
>> https://github.com/3-manifolds/Sage_macOS/releases/download/v1.3-rc1/SageMath-9.5_arm64.dmg
>> .
>>
>> I switched to using the homebrew version of gfortran-11.  That resolved
>> the crash when importing sage.manifolds.manifold (which was actually
>> happening when importing the scpy integration module.)  I believe that the
>> problem was that the other gfortran compiler implements fortran 2018 and
>> some of the scipy modules are not compliant with that.
>>
>> I also added a copy of the gfortran runtime, suitably adjusted to work in
>> the Sage framework in the app bundle.
>>
>> Matthias, I think you should revise your recommendation so it specifies
>> the homebrew gfortran-11.
>> On Monday, January 17, 2022 at 3:13:38 PM UTC-6 Marc Culler wrote:
>>
>>> My attempt to build rc2 on macOS with arm CPU failed with this error:
>>>
>>> Installing cryptominisat-5.6.8
>>> /private/var/tmp/sage-9.5-current/local/var/lib/sage/venv-python3.9.9/bin/python3:
>>> No module named pip
>>>
>>> Maybe a pip dependency is missing now for cryptominisat?
>>>
>>> - Marc
>>> On Sunday, January 16, 2022 at 4:09:02 PM UTC-6 matthia...@gmail.com
>>> wrote:
>>>
>>>> The sqlite doctest failure is tracked at
>>>> https://trac.sagemath.org/ticket/29092
>>>>
>>>> On Sunday, January 16, 2022 at 1:42:06 PM UTC-8
>>>> jonatha...@googlemail.com wrote:
>>>>
>>>>> Thanks Volker for preparing the release.
>>>>>
>>>>> All tests pass on debian buster, except
>>>>>
>>>>> sage -t --long --random-seed=146168601452887490256495561253701871534
>>>>> src/sage/tests/cmdline.py  # 3 doctests failed
>>>>>
>>>>> as squlite executable is not available.
>>>>>
>>>>> Volker Braun schrieb am Sonntag, 16. Januar 2022 um 18:17:36 UTC+1:
>>>>>
>>>>>> As always, you can get the latest beta version from the "develop" git
>>>>>> branch. Alternatively, the self-contained source tarball is at
>>>>>> http://www.sagemath.org/download-latest.html
>>>>>>
>>>>>> f9b2db94f6 (tag: 9.5.rc2, trac/develop) Updated SageMath version to
>>>>>> 9.5.rc2
>>>>>> 7a9347dbc0 Trac #33155: Broken install using system pythons < 3.10
>>>>>> from python.org macOS packages
>>>>>> fe634f8613 Trac #33162: Fix installation of cryptominisat and
>>>>>> pycryptosat
>>>>>> 9ceaaea7a7 Trac #33153: opensuse-tumbleweed: sagelib build fails
>>>>>> 3da1b22c25 (tag: 9.5.rc1) Updated SageMath version to 9.5.rc1
>>>>>>
>>>>> --
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[sage-release] Re: Sage 9.7.beta4 released

[Marc Culler]

When I tried to build 9.7.beta4 on an M1 mac mini with macOS 12.4 using no 
external libraries except the Homebrew gfortran I got this error:

 





* error: Multiple top-level packages discovered in a flat-layout: ['cmake', 
'symengine'].  To avoid accidental inclusion of unwanted files or 
directories,  setuptools will not proceed with this build.  If you are 
trying to create a single distribution with multiple packages  on purpose, 
you should not rely on automatic discovery.*

Indeed, the symengine setup.py does not specify any packages, so pip tries 
to automatically discover the packages and it decides that the cmake 
directory is a package.

I don't seem to have the option of attaching the log file, but it does not 
have much more information than what is above.

- Marc

On Friday, July 8, 2022 at 4:22:21 PM UTC-5 Volker Braun wrote:

> As always, you can get the latest beta version from the "develop" git 
> branch. Alternatively, the self-contained source tarball is at 
> http://www.sagemath.org/download-latest.html
>
> 843eb03e7e (tag: 9.7.beta4, trac/develop) Updated SageMath version to 
> 9.7.beta4
> 232d0434cf Trac #33866: Make jupyter_packaging standard; add hatchling, 
> editables, pathspec, poetry_core, tomlkit, deprecation; update tomli, 
> flit_core, setuptools, pip, wheel
> 9307820a88 Trac #33821: Remove use of SAGE_LIB in sage.misc
> b23b788586 Trac #33409: Size of docker images has increased in 9.5
> b5d2fcaeb0 Trac #33029: Feature and doctest tag for runtime cython
> be2bda4921 Trac #29779: pkgconf: Update to 1.8.0, remove runtime dep on 
> environment variable SAGE_LOCAL
> c02edcb15b Trac #25374: Upgrade cryptominisat to 5.8.0, fix build on Cygwin
> e22b33a0c1 Trac #34017: Fix tox-docker builds after #29941
> c4236d0844 Trac #34008: pycodestyle cleanup in 
> sage.graphs.generic_graph_pyx.pyx
> 6f961ffa38 Trac #34007: Allow start parameter in Python's sum
> c59c86cfbd Trac #33996: ascii_art fail in jupyter notebook
> c40983afcd Trac #33991: remove some unused imports
> b02c408763 Trac #33978: various details about typing in combinat
> 6fb1e3f13a Trac #34037: Make doctest from #25626 more robust
> 4169d7d6c0 Trac #34035: Add __reversed__ method to FrozenBitsets
> 45c963e0c7 Trac #34030: move supercommutator to superalgebras
> d4706f96f9 Trac #34019: minor code details in combinat
> 3d336f0435 Trac #34014: Clean src/sage/graphs/pq_trees.py
> c9aa34b34c Trac #33957: Manifold.options.omit_function_arguments 
> ineffective for arguments not in alphabetic order
> 0b2741d399 Trac #33619: clean up ell_curve_isogeny.py
> c0e59251e2 Trac #34036: fix the linter
> 2b36879ae1 Trac #34025: Fix doctest in 
> sage/modular/overconvergent/hecke_series.py
> c0abe3f5ee Trac #33213: Replace SAGE_TMP by the system location in the 
> sage library
> 7ab174a70d Trac #32340: document behavior of .is_prime() for number fields
> c69f4af336 Trac #28263: Degree for Affine Morphism or Affine Dynamical 
> System
> e516392523 Trac #34001: Add flag to avoid OrePolynomialRing cast to 
> PolynomialRing
> 01b8bcb85f Trac #33993: pep cleanup for words/morphism.py
> 716c5ce262 Trac #33992: remove class inheritance of object in remaining 
> places
> de375bce02 Trac #33990: Subset_s _an_element_
> 0593e83957 Trac #33987: modernize super() in structure, symbolic, doctest, 
> databases
> d9a45e29eb Trac #33985: modernize super() in monoids,modules,modular
> 7ed404657b Trac #33984: modernize super() in schemes,libs,sets,quivers
> 1df260e842 Trac #33979: .roots() does not always return elements of the 
> base ring
> c6c2b85405 Trac #33974: Documentation addition for symmetric functions - 
> Cauchy identity
> f92916e358 Trac #33840: bool(matrix) ignores exceptions raised while 
> comparing entries
> f8df80820d (tag: 9.7.beta3) Updated SageMath version to 9.7.beta3
>

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[sage-release] Re: Sage 9.7.beta5 released

[Marc Culler]

I am not able to build beta5 after running make distclean using my standard 
build script that includes no external libraries.  I am seeing errors about 
missing autoconf commands:

make: `configure' is up to date.
./configure: line 4932: AC_LIB_RPATH: command not found
./configure: line 24924: AC_LIB_PREPARE_PREFIX: command not found
./configure: line 24925: AC_LIB_RPATH: command not found
./configure: line 24930: syntax error near unexpected token `iconv'
./configure: line 24930: `  AC_LIB_LINKFLAGS_BODY(iconv)'

The make build run then fails with the same errors:

-
Checking whether SageMath should install SPKG gsl...
checking whether any of openblas is installed as or will be installed as 
SPKG... yes; install gsl as well
configure: no suitable system package found for SPKG gsl
./configure: line 24924: AC_LIB_PREPARE_PREFIX: command not found
./configure: line 24925: AC_LIB_RPATH: command not found
./configure: line 24930: syntax error near unexpected token `iconv'
./configure: line 24930: `  AC_LIB_LINKFLAGS_BODY(iconv)'

Since the recently discovered issues with primecount were very closely 
related to the way that the primecount spkg (an no other spkgs) uses 
@rpath, I am concerned that care may be required when defining 
AC_LIB_RPATH.  Currently all spkgs, except for primecount, set the rpath in 
a dylib to an absolute path to the directory containing the library.  Also 
most libraries have multiple copies of the LC_RPATH load command with sets 
that rpath.  (There are usually between 2 and 5 LS_RPATH load commands.)

- Marc
On Sunday, July 10, 2022 at 6:24:36 PM UTC-5 Volker Braun wrote:

> As always, you can get the latest beta version from the "develop" git 
> branch. Alternatively, the self-contained source tarball is at 
> http://www.sagemath.org/download-latest.html
>
> 625ac58151 (trac/develop, tag: 9.7.beta5) Updated SageMath version to 
> 9.7.beta5
> 413ff13c54 Trac #34056: cleaning two files in quadratic forms
> cb65d06dd2 Trac #34055: Remove "ssl" target from Makefile
> 0740d209ca Trac #34053: pycodestyle cleanup in 
> src/sage/graphs/base/static_sparse_graph.pyx
> 539a5c073c Trac #34046: pycodestyle cleanup in 
> src/sage/graphs/base/boost_graph.pyx
> 6790b30aeb Trac #34044: pycodestyle cleanup in 
> src/sage/graphs/generators/smallgraphs.py (part 3)
> 6e4de5191b Trac #34043: pycodestyle cleanup in 
> src/sage/graphs/generators/smallgraphs.py (part 2)
> 3d2f91c326 Trac #34042: pycodestyle cleanup in 
> src/sage/graphs/generators/smallgraphs.py (part 1)
> 45c1d36c3a Trac #34034: pycodestyle cleanup in 
> src/sage/graphs/generators/random.py
> 9f1388bac5 Trac #34032: pycodestyle cleanup in 
> src/sage/graphs/generators/world_map.py
> 248a6e15e6 Trac #34023: pycodestyle cleanup in distance_regular.pyx (part 
> 1)
> 0a77b4496f Trac #34022: pycodestyle cleanup in 
> src/sage/graphs/generators/classical_geometries.py
> 0cec8684d7 Trac #34135: modernize super() in groups
> 38b2bf7529 Trac #34058: sage 9.6 special function translation issue with 
> fricas. elliptic_ec
> 720adde3bb Trac #32716: pkgs/sagemath-*/tox.ini: Create environment that 
> uses Sage's python as the basepython, fix sagemath-standard deps
> 6294f36ee4 Trac #28925: Modify find_python_sources to support 
> modularization of sagelib by native namespace packages (PEP 420)
> 5063ca7441 Trac #34021: pycodestyle in 5 files of 
> src/sage/graphs/generators
> 648ea02cda Trac #34018: pycodestyle cleanup in 
> src/sage/graphs/graph_decompositions/
> 44562ec0cf Trac #34016: improve pycodestyle in 4 files in graphs
> aa79451a04 Trac #34015: pycodestyle cleanup in planarity.pyx and 
> path_enumeration.pyx
> 3268d19fa5 Trac #34013: pycodestyle cleanup in schnyder.py and 
> print_graphs.py
> a6f5a56109 Trac #34012: pycodestyle cleanup in 
> sage.graphs.spanning_tree.pyx, weakly_chordal.pyx
> b5041b18ad Trac #34011: pycodestyle cleanup in sage.graphs.views.pyx, 
> trees.pyx, traversals.pyx
> 81f843e76b Trac #34010: pycodestyle cleanup in 
> sage.graphs.tutte_polynomial.py
> c2550f7093 Trac #34009: pycodestyle cleanup in 
> sage.graphs.hyperbolicity.pyx
> 44a5f5b3d9 Trac #33952: Add methods to compute holomorphic differentials 
> of function field
> 6ea1dc5f9e Trac #33868: Add modules over integral domain
> b593b48ed7 Trac #33791: ci-cygwin: Refactor using reusable workflows
> 1fc79b83f6 Trac #33788: GH Actions: Split ci-macos.yml out from tox.yml
> 931d6ac039 Trac #33777: Deprecate Sage's CHomP interface
> c364788de0 Trac #33708: make elliptic-curve isogenies compute Montgomery 
> codomains
> 64e29cf9d9 Trac #33144: Remove some py2 tags in explain_pickle
> 1c0f22aabf Trac #34132: Update primesieve to 8.0, primecount to 7.4
> 9793520438 <(979)%20352-0438> Trac #34121: Heegner point method can 
> return a point defined over the wrong field
> 3208d2c51f Trac #34112: some details in L-functions
> 65722f53c1 Trac #34111: 'PosixPath' object has no attribute '_libga

Re: [sage-release] Re: Sage 9.7.beta5 released

[Marc Culler]

Yes, I tried that but there was no change.

However when I deleted the calls to the undefined autoconf commands from 
the configure script (which meant changing about 5 lines in the script) I 
was able to run configure and the make build appears to be running normally 
after that.  Incidentally, the bootstrap script generates warning about the 
same commands, as well as AC_LIB_APPENDTOVAR:

*m4/sage_spkg_configures.m4:605: warning: AC_LIB_PREPARE_PREFIX is 
m4_require'd but not m4_defun'd*
*m4/sage_spkg_configures.m4:605: warning: AC_LIB_RPATH is m4_require'd but 
not m4_defun'd*
*m4/sage_spkg_configures.m4:605: the top level*





*configure.ac:52: error: possibly undefined macro: AC_LIB_RPATH  If 
this token and others are legitimate, please use m4_pattern_allow.  See 
the Autoconf documentation.configure:24924: error: possibly undefined 
macro: AC_LIB_PREPARE_PREFIXconfigure:24930: error: possibly undefined 
macro: AC_LIB_LINKFLAGS_BODYconfigure:24938: error: possibly undefined 
macro: AC_LIB_APPENDTOVAR*


Here are the changes I had to make to get a working configure script:


















*4932c4932< AC_LIB_RPATH---> #AC_LIB_RPATH24924,24925c24924,24925< 
AC_LIB_PREPARE_PREFIX< AC_LIB_RPATH---> #AC_LIB_PREPARE_PREFIX> 
#AC_LIB_RPATH24930c24930<   AC_LIB_LINKFLAGS_BODY(iconv)---> # 
 AC_LIB_LINKFLAGS_BODY(iconv)24938c24938<   AC_LIB_APPENDTOVAR(CPPFLAGS, 
$INCICONV)---> #  AC_LIB_APPENDTOVAR(CPPFLAGS, $INCICONV)*


- Marc
On Monday, July 11, 2022 at 7:11:21 AM UTC-5 Dima Pasechnik wrote:

>
> did you run
> ./bootstrap
> ?
> On Mon, 11 Jul 2022, 13:08 Marc Culler,  wrote:
>
>> I am not able to build beta5 after running make distclean using my 
>> standard build script that includes no external libraries.  I am seeing 
>> errors about missing autoconf commands:
>>
>> make: `configure' is up to date.
>> ./configure: line 4932: AC_LIB_RPATH: command not found
>> ./configure: line 24924: AC_LIB_PREPARE_PREFIX: command not found
>> ./configure: line 24925: AC_LIB_RPATH: command not found
>> ./configure: line 24930: syntax error near unexpected token `iconv'
>> ./configure: line 24930: `  AC_LIB_LINKFLAGS_BODY(iconv)'
>>
>> The make build run then fails with the same errors:
>>
>>
>> -
>> Checking whether SageMath should install SPKG gsl...
>> checking whether any of openblas is installed as or will be installed as 
>> SPKG... yes; install gsl as well
>> configure: no suitable system package found for SPKG gsl
>> ./configure: line 24924: AC_LIB_PREPARE_PREFIX: command not found
>> ./configure: line 24925: AC_LIB_RPATH: command not found
>> ./configure: line 24930: syntax error near unexpected token `iconv'
>> ./configure: line 24930: `  AC_LIB_LINKFLAGS_BODY(iconv)'
>>
>> Since the recently discovered issues with primecount were very closely 
>> related to the way that the primecount spkg (an no other spkgs) uses 
>> @rpath, I am concerned that care may be required when defining 
>> AC_LIB_RPATH.  Currently all spkgs, except for primecount, set the rpath in 
>> a dylib to an absolute path to the directory containing the library.  Also 
>> most libraries have multiple copies of the LC_RPATH load command with sets 
>> that rpath.  (There are usually between 2 and 5 LS_RPATH load commands.)
>>
>> - Marc
>> On Sunday, July 10, 2022 at 6:24:36 PM UTC-5 Volker Braun wrote:
>>
>>> As always, you can get the latest beta version from the "develop" git 
>>> branch. Alternatively, the self-contained source tarball is at 
>>> http://www.sagemath.org/download-latest.html
>>>
>>> 625ac58151 (trac/develop, tag: 9.7.beta5) Updated SageMath version to 
>>> 9.7.beta5
>>> 413ff13c54 Trac #34056: cleaning two files in quadratic forms
>>> cb65d06dd2 Trac #34055: Remove "ssl" target from Makefile
>>> 0740d209ca Trac #34053: pycodestyle cleanup in 
>>> src/sage/graphs/base/static_sparse_graph.pyx
>>> 539a5c073c Trac #34046: pycodestyle cleanup in 
>>> src/sage/graphs/base/boost_graph.pyx
>>> 6790b30aeb Trac #34044: pycodestyle cleanup in 
>>> src/sage/graphs/generators/smallgraphs.py (part 3)
>>> 6e4de5191b Trac #34043: pycodestyle cleanup in 
>>> src/sage/graphs/generators/smallgraphs.py (part 2)
>>> 3d2f91c326 Trac #34042: pycodestyle cleanup in 
>>> src/sage/graphs/generators/smallgraphs.py (part 1)
>>> 45c1d36c3a Trac #34034: pycodestyle cleanup in 
>>> src/sage/graphs/generators/random.py
>>> 9f1388bac5 Trac #34032: 

Re: [sage-release] Re: Sage 9.7.beta5 released

[Marc Culler]

As I said, I am not using any homebrew packages or any other external 
libraries for this build.  Sage should be able to build without homebrew,.  
The binary macOS app needs to be self-contained and relocatable.

The configure file for previous betas did not use the AC_LIB_RPATH command, 
although it is mentioned in configure.ac.  The other undefined autoconf 
commands do not appear at all in earlier betas.

- Marc

On Monday, July 11, 2022 at 8:25:27 AM UTC-5 Kenji Iohara wrote:

> On my Mac OS 12.4 with Intel Core i5, with homebrew and Xcode 13.4.1, it 
> compiled from the first build. 
>
>
> 2022年7月11日(月) 15:21 Marc Culler :
>
>> Yes, I tried that but there was no change.
>>
>> However when I deleted the calls to the undefined autoconf commands from 
>> the configure script (which meant changing about 5 lines in the script) I 
>> was able to run configure and the make build appears to be running normally 
>> after that.  Incidentally, the bootstrap script generates warning about the 
>> same commands, as well as AC_LIB_APPENDTOVAR:
>>
>> *m4/sage_spkg_configures.m4:605: warning: AC_LIB_PREPARE_PREFIX is 
>> m4_require'd but not m4_defun'd*
>> *m4/sage_spkg_configures.m4:605: warning: AC_LIB_RPATH is m4_require'd 
>> but not m4_defun'd*
>> *m4/sage_spkg_configures.m4:605: the top level*
>>
>>
>>
>>
>>
>> *configure.ac:52 <http://configure.ac:52>: error: possibly undefined 
>> macro: AC_LIB_RPATH  If this token and others are legitimate, please 
>> use m4_pattern_allow.  See the Autoconf documentation.configure:24924: 
>> error: possibly undefined macro: AC_LIB_PREPARE_PREFIXconfigure:24930: 
>> error: possibly undefined macro: AC_LIB_LINKFLAGS_BODYconfigure:24938: 
>> error: possibly undefined macro: AC_LIB_APPENDTOVAR*
>>
>>
>> Here are the changes I had to make to get a working configure script:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *4932c4932< AC_LIB_RPATH---> #AC_LIB_RPATH24924,24925c24924,24925< 
>> AC_LIB_PREPARE_PREFIX< AC_LIB_RPATH---> #AC_LIB_PREPARE_PREFIX> 
>> #AC_LIB_RPATH24930c24930<   AC_LIB_LINKFLAGS_BODY(iconv)---> # 
>>  AC_LIB_LINKFLAGS_BODY(iconv)24938c24938<   AC_LIB_APPENDTOVAR(CPPFLAGS, 
>> $INCICONV)---> #  AC_LIB_APPENDTOVAR(CPPFLAGS, $INCICONV)*
>>
>>
>> - Marc
>> On Monday, July 11, 2022 at 7:11:21 AM UTC-5 Dima Pasechnik wrote:
>>
>>>
>>> did you run
>>> ./bootstrap
>>> ?
>>> On Mon, 11 Jul 2022, 13:08 Marc Culler,  wrote:
>>>
>>>> I am not able to build beta5 after running make distclean using my 
>>>> standard build script that includes no external libraries.  I am seeing 
>>>> errors about missing autoconf commands:
>>>>
>>>> make: `configure' is up to date.
>>>> ./configure: line 4932: AC_LIB_RPATH: command not found
>>>> ./configure: line 24924: AC_LIB_PREPARE_PREFIX: command not found
>>>> ./configure: line 24925: AC_LIB_RPATH: command not found
>>>> ./configure: line 24930: syntax error near unexpected token `iconv'
>>>> ./configure: line 24930: `  AC_LIB_LINKFLAGS_BODY(iconv)'
>>>>
>>>> The make build run then fails with the same errors:
>>>>
>>>>
>>>> -
>>>> Checking whether SageMath should install SPKG gsl...
>>>> checking whether any of openblas is installed as or will be installed 
>>>> as SPKG... yes; install gsl as well
>>>> configure: no suitable system package found for SPKG gsl
>>>> ./configure: line 24924: AC_LIB_PREPARE_PREFIX: command not found
>>>> ./configure: line 24925: AC_LIB_RPATH: command not found
>>>> ./configure: line 24930: syntax error near unexpected token `iconv'
>>>> ./configure: line 24930: `  AC_LIB_LINKFLAGS_BODY(iconv)'
>>>>
>>>> Since the recently discovered issues with primecount were very closely 
>>>> related to the way that the primecount spkg (an no other spkgs) uses 
>>>> @rpath, I am concerned that care may be required when defining 
>>>> AC_LIB_RPATH.  Currently all spkgs, except for primecount, set the rpath 
>>>> in 
>>>> a dylib to an absolute path to the directory containing the library.  Also 
>>>> most libraries have multiple copies of the LC_RPATH load command with s

Re: [sage-release] Re: Sage 9.7.beta5 released

[Marc Culler]

I do not install anything on my build system (except I am forced to install
the homebrew gfortran on the arm64 build system).  Everything needed to
build sage must be included in the sage repo, and until 9.7.beta5 that was
the case.

I do not think it would be wise to require people to install gettext and
autotools in order to build sage and it is clearly not necessary since it
was not necessary until this moment.  If you read configure.ac you will see
this in the comments:

dnl The AC_LIB_RPATH macro comes from gettext, which is one of our bootstrap
dnl packages. It defines, among other things, the $acl_shlibext variable
that
dnl contains the shared library extension for this system. We already use
the
dnl AM_ICONV macro from gettext (which ultimately calls AC_LIB_RPATH), and
we
dnl avoid involving libtool by using it to get the shared library extension.

It would appear that somehow gettext was silently removed from the list of
bootstrap packages for beta5, which is clearly not a good idea.

- Marc

- Marc

On Mon, Jul 11, 2022 at 9:08 AM Dima Pasechnik  wrote:

> On Mon, Jul 11, 2022 at 2:21 PM Marc Culler  wrote:
> >
> > Yes, I tried that but there was no change.
> Was it succesfully run?
>
> Do you have autotools and gettext installed?
>
> >
> > However when I deleted the calls to the undefined autoconf commands from
> the configure script (which meant changing about 5 lines in the script) I
> was able to run configure and the make build appears to be running normally
> after that.  Incidentally, the bootstrap script generates warning about the
> same commands, as well as AC_LIB_APPENDTOVAR:
> >
> > m4/sage_spkg_configures.m4:605: warning: AC_LIB_PREPARE_PREFIX is
> m4_require'd but not m4_defun'd
> > m4/sage_spkg_configures.m4:605: warning: AC_LIB_RPATH is m4_require'd
> but not m4_defun'd
> > m4/sage_spkg_configures.m4:605: the top level
> > configure.ac:52: error: possibly undefined macro: AC_LIB_RPATH
> >   If this token and others are legitimate, please use
> m4_pattern_allow.
> >   See the Autoconf documentation.
> > configure:24924: error: possibly undefined macro: AC_LIB_PREPARE_PREFIX
> > configure:24930: error: possibly undefined macro: AC_LIB_LINKFLAGS_BODY
> > configure:24938: error: possibly undefined macro: AC_LIB_APPENDTOVAR
> >
> >
> > Here are the changes I had to make to get a working configure script:
> >
> > 4932c4932
> > < AC_LIB_RPATH
> > ---
> > > #AC_LIB_RPATH
> > 24924,24925c24924,24925
> > < AC_LIB_PREPARE_PREFIX
> > < AC_LIB_RPATH
> > ---
> > > #AC_LIB_PREPARE_PREFIX
> > > #AC_LIB_RPATH
> > 24930c24930
> > <   AC_LIB_LINKFLAGS_BODY(iconv)
> > ---
> > > #  AC_LIB_LINKFLAGS_BODY(iconv)
> > 24938c24938
> > <   AC_LIB_APPENDTOVAR(CPPFLAGS, $INCICONV)
> > ---
> > > #  AC_LIB_APPENDTOVAR(CPPFLAGS, $INCICONV)
> >
> >
> > - Marc
> > On Monday, July 11, 2022 at 7:11:21 AM UTC-5 Dima Pasechnik wrote:
> >>
> >>
> >> did you run
> >> ./bootstrap
> >> ?
> >> On Mon, 11 Jul 2022, 13:08 Marc Culler,  wrote:
> >>>
> >>> I am not able to build beta5 after running make distclean using my
> standard build script that includes no external libraries.  I am seeing
> errors about missing autoconf commands:
> >>>
> >>> make: `configure' is up to date.
> >>> ./configure: line 4932: AC_LIB_RPATH: command not found
> >>> ./configure: line 24924: AC_LIB_PREPARE_PREFIX: command not found
> >>> ./configure: line 24925: AC_LIB_RPATH: command not found
> >>> ./configure: line 24930: syntax error near unexpected token `iconv'
> >>> ./configure: line 24930: `  AC_LIB_LINKFLAGS_BODY(iconv)'
> >>>
> >>> The make build run then fails with the same errors:
> >>>
> >>>
> -
> >>> Checking whether SageMath should install SPKG gsl...
> >>> checking whether any of openblas is installed as or will be installed
> as SPKG... yes; install gsl as well
> >>> configure: no suitable system package found for SPKG gsl
> >>> ./configure: line 24924: AC_LIB_PREPARE_PREFIX: command not found
> >>> ./configure: line 24925: AC_LIB_RPATH: command not found
> >>> ./configure: line 24930: syntax error near unexpected token `iconv'
> >>> ./configure: line 24930: `  AC_LIB_LINKFLAGS_BODY(iconv)'
> >>>
> >>> Since the recently discovered issues with primecount were

Re: [sage-release] Re: Sage 9.7.beta5 released

[Marc Culler]

On Mon, Jul 11, 2022 at 10:01 AM Dima Pasechnik  wrote:

>
> One way to fix it is to re-create ./configure from ./bootstrap
>

The problem with this is that the bootstrap script in beta5 generates
warnings about the exact same commands, but then it still goes ahead and
produces a configure script that requires those missing commands.

- Marc

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[sage-release] Re: Sage 9.7.beta5 released

[Marc Culler]

After working around the issues with the bootstrap script and symengine_py 
I have managed to build 9.7.beta5 on an arm mac mini.  This was an 
incremental build from beta4.  When the build finished I noticed that both 
sage/local/var/lib/sage/venv-python3.10.3 and 
sage/local/var/lib/sage/venv-python3.10.5 existed.  The 3.10.3 venv cannot 
be required, because it never gets created if make distclean is run first.  
So it seems to be doing nothing but wasting disk space.  Shouldn't it get 
removed once the build finishes?

- Marc

On Sunday, July 10, 2022 at 6:24:36 PM UTC-5 Volker Braun wrote:

> As always, you can get the latest beta version from the "develop" git 
> branch. Alternatively, the self-contained source tarball is at 
> http://www.sagemath.org/download-latest.html
>
> 625ac58151 (trac/develop, tag: 9.7.beta5) Updated SageMath version to 
> 9.7.beta5
> 413ff13c54 Trac #34056: cleaning two files in quadratic forms
> cb65d06dd2 Trac #34055: Remove "ssl" target from Makefile
> 0740d209ca Trac #34053: pycodestyle cleanup in 
> src/sage/graphs/base/static_sparse_graph.pyx
> 539a5c073c Trac #34046: pycodestyle cleanup in 
> src/sage/graphs/base/boost_graph.pyx
> 6790b30aeb Trac #34044: pycodestyle cleanup in 
> src/sage/graphs/generators/smallgraphs.py (part 3)
> 6e4de5191b Trac #34043: pycodestyle cleanup in 
> src/sage/graphs/generators/smallgraphs.py (part 2)
> 3d2f91c326 Trac #34042: pycodestyle cleanup in 
> src/sage/graphs/generators/smallgraphs.py (part 1)
> 45c1d36c3a Trac #34034: pycodestyle cleanup in 
> src/sage/graphs/generators/random.py
> 9f1388bac5 Trac #34032: pycodestyle cleanup in 
> src/sage/graphs/generators/world_map.py
> 248a6e15e6 Trac #34023: pycodestyle cleanup in distance_regular.pyx (part 
> 1)
> 0a77b4496f Trac #34022: pycodestyle cleanup in 
> src/sage/graphs/generators/classical_geometries.py
> 0cec8684d7 Trac #34135: modernize super() in groups
> 38b2bf7529 Trac #34058: sage 9.6 special function translation issue with 
> fricas. elliptic_ec
> 720adde3bb Trac #32716: pkgs/sagemath-*/tox.ini: Create environment that 
> uses Sage's python as the basepython, fix sagemath-standard deps
> 6294f36ee4 Trac #28925: Modify find_python_sources to support 
> modularization of sagelib by native namespace packages (PEP 420)
> 5063ca7441 Trac #34021: pycodestyle in 5 files of 
> src/sage/graphs/generators
> 648ea02cda Trac #34018: pycodestyle cleanup in 
> src/sage/graphs/graph_decompositions/
> 44562ec0cf Trac #34016: improve pycodestyle in 4 files in graphs
> aa79451a04 Trac #34015: pycodestyle cleanup in planarity.pyx and 
> path_enumeration.pyx
> 3268d19fa5 Trac #34013: pycodestyle cleanup in schnyder.py and 
> print_graphs.py
> a6f5a56109 Trac #34012: pycodestyle cleanup in 
> sage.graphs.spanning_tree.pyx, weakly_chordal.pyx
> b5041b18ad Trac #34011: pycodestyle cleanup in sage.graphs.views.pyx, 
> trees.pyx, traversals.pyx
> 81f843e76b Trac #34010: pycodestyle cleanup in 
> sage.graphs.tutte_polynomial.py
> c2550f7093 Trac #34009: pycodestyle cleanup in 
> sage.graphs.hyperbolicity.pyx
> 44a5f5b3d9 Trac #33952: Add methods to compute holomorphic differentials 
> of function field
> 6ea1dc5f9e Trac #33868: Add modules over integral domain
> b593b48ed7 Trac #33791: ci-cygwin: Refactor using reusable workflows
> 1fc79b83f6 Trac #33788: GH Actions: Split ci-macos.yml out from tox.yml
> 931d6ac039 Trac #33777: Deprecate Sage's CHomP interface
> c364788de0 Trac #33708: make elliptic-curve isogenies compute Montgomery 
> codomains
> 64e29cf9d9 Trac #33144: Remove some py2 tags in explain_pickle
> 1c0f22aabf Trac #34132: Update primesieve to 8.0, primecount to 7.4
> 9793520438 <(979)%20352-0438> Trac #34121: Heegner point method can 
> return a point defined over the wrong field
> 3208d2c51f Trac #34112: some details in L-functions
> 65722f53c1 Trac #34111: 'PosixPath' object has no attribute '_libgap_init_'
> d860f2e146 Trac #34098: Installation manual: Improvements for homebrew, 
> conda
> afb3761f26 Trac #34090: Update python3 to 3.10.5
> f56dc7b1f3 Trac #34085: fix some details in braid groups
> b1a00624dc Trac #34082: Add an option up_to_isomorphism for is_subgraph
> 8c5d4ca3a4 Trac #34080: pycodestyle cleanup in src/sage/graphs/digraph.py
> 7ad1358ac7 Trac #34062: enhance our conversion system
> 9c530f7a59 Trac #34061: fix pyflakes warnings in src/sage/misc/cython.py
> b221b0d7e1 Trac #34060: Height function for polynomials on number fields
> 57ec521c2a Trac #34052: tweaking the giac / libgiac interface
> 99fba2a5de Trac #34051: Update FriCAS to 1.3.8
> 0de1a2c955 Trac #34049: fix wrong use of Path inside libgap.Read
> 9d189b384a Trac #34045: OpenSSL 3.0.4 security update
> f0e2346cbf Trac #34041: improve and document GAP and libgap memory 
> customisation
> 59188e4443 Trac #34040: fix W605 in all pyx files inside matrix/
> ac0188973e Trac #34039: fix pycodestyle E306 in categories and part of 
> combinat
> 890daa517b Trac #34029: bug in elliptic curve saturation: update to ecli

[sage-release] Re: Sage 9.7.beta5 released

[Marc Culler]

I don't want to have to remember to do this by hand.  If I delete all of 
the venvs before starting an incremental build will the build still work, 
and will it create a new venv that is appropriate for its python, even if 
the python version has not changed?

- Marc

On Wednesday, July 13, 2022 at 4:55:02 PM UTC-5 matthia...@gmail.com wrote:

> Yes, you can delete the old venv. We do not uninstall other venvs that may 
> have been built previously. 
>
> On Wednesday, July 13, 2022 at 1:08:57 PM UTC-7 marc@gmail.com wrote:
>
>> After working around the issues with the bootstrap script and 
>> symengine_py I have managed to build 9.7.beta5 on an arm mac mini.  This 
>> was an incremental build from beta4.  When the build finished I noticed 
>> that both sage/local/var/lib/sage/venv-python3.10.3 and 
>> sage/local/var/lib/sage/venv-python3.10.5 existed.  The 3.10.3 venv cannot 
>> be required, because it never gets created if make distclean is run first.  
>> So it seems to be doing nothing but wasting disk space.  Shouldn't it get 
>> removed once the build finishes?
>>
>> - Marc
>>
>> On Sunday, July 10, 2022 at 6:24:36 PM UTC-5 Volker Braun wrote:
>>
>>> As always, you can get the latest beta version from the "develop" git 
>>> branch. Alternatively, the self-contained source tarball is at 
>>> http://www.sagemath.org/download-latest.html
>>>
>>> 625ac58151 (trac/develop, tag: 9.7.beta5) Updated SageMath version to 
>>> 9.7.beta5
>>> 413ff13c54 Trac #34056: cleaning two files in quadratic forms
>>> cb65d06dd2 Trac #34055: Remove "ssl" target from Makefile
>>> 0740d209ca Trac #34053: pycodestyle cleanup in 
>>> src/sage/graphs/base/static_sparse_graph.pyx
>>> 539a5c073c Trac #34046: pycodestyle cleanup in 
>>> src/sage/graphs/base/boost_graph.pyx
>>> 6790b30aeb Trac #34044: pycodestyle cleanup in 
>>> src/sage/graphs/generators/smallgraphs.py (part 3)
>>> 6e4de5191b Trac #34043: pycodestyle cleanup in 
>>> src/sage/graphs/generators/smallgraphs.py (part 2)
>>> 3d2f91c326 Trac #34042: pycodestyle cleanup in 
>>> src/sage/graphs/generators/smallgraphs.py (part 1)
>>> 45c1d36c3a Trac #34034: pycodestyle cleanup in 
>>> src/sage/graphs/generators/random.py
>>> 9f1388bac5 Trac #34032: pycodestyle cleanup in 
>>> src/sage/graphs/generators/world_map.py
>>> 248a6e15e6 Trac #34023: pycodestyle cleanup in distance_regular.pyx 
>>> (part 1)
>>> 0a77b4496f Trac #34022: pycodestyle cleanup in 
>>> src/sage/graphs/generators/classical_geometries.py
>>> 0cec8684d7 Trac #34135: modernize super() in groups
>>> 38b2bf7529 Trac #34058: sage 9.6 special function translation issue with 
>>> fricas. elliptic_ec
>>> 720adde3bb Trac #32716: pkgs/sagemath-*/tox.ini: Create environment that 
>>> uses Sage's python as the basepython, fix sagemath-standard deps
>>> 6294f36ee4 Trac #28925: Modify find_python_sources to support 
>>> modularization of sagelib by native namespace packages (PEP 420)
>>> 5063ca7441 Trac #34021: pycodestyle in 5 files of 
>>> src/sage/graphs/generators
>>> 648ea02cda Trac #34018: pycodestyle cleanup in 
>>> src/sage/graphs/graph_decompositions/
>>> 44562ec0cf Trac #34016: improve pycodestyle in 4 files in graphs
>>> aa79451a04 Trac #34015: pycodestyle cleanup in planarity.pyx and 
>>> path_enumeration.pyx
>>> 3268d19fa5 Trac #34013: pycodestyle cleanup in schnyder.py and 
>>> print_graphs.py
>>> a6f5a56109 Trac #34012: pycodestyle cleanup in 
>>> sage.graphs.spanning_tree.pyx, weakly_chordal.pyx
>>> b5041b18ad Trac #34011: pycodestyle cleanup in sage.graphs.views.pyx, 
>>> trees.pyx, traversals.pyx
>>> 81f843e76b Trac #34010: pycodestyle cleanup in 
>>> sage.graphs.tutte_polynomial.py
>>> c2550f7093 Trac #34009: pycodestyle cleanup in 
>>> sage.graphs.hyperbolicity.pyx
>>> 44a5f5b3d9 Trac #33952: Add methods to compute holomorphic differentials 
>>> of function field
>>> 6ea1dc5f9e Trac #33868: Add modules over integral domain
>>> b593b48ed7 Trac #33791: ci-cygwin: Refactor using reusable workflows
>>> 1fc79b83f6 Trac #33788: GH Actions: Split ci-macos.yml out from tox.yml
>>> 931d6ac039 Trac #33777: Deprecate Sage's CHomP interface
>>> c364788de0 Trac #33708: make elliptic-curve isogenies compute Montgomery 
>>> codomains
>>> 64e29cf9d9 Trac #33144: Remove some py2 tags in explain_pickle
>>> 1c0f22aabf Trac #34132: Update primesieve to 8.0, primecount to 7.4
>>> 9793520438 <(979)%20352-0438> Trac #34121: Heegner point method can 
>>> return a point defined over the wrong field
>>> 3208d2c51f Trac #34112: some details in L-functions
>>> 65722f53c1 Trac #34111: 'PosixPath' object has no attribute 
>>> '_libgap_init_'
>>> d860f2e146 Trac #34098: Installation manual: Improvements for homebrew, 
>>> conda
>>> afb3761f26 Trac #34090: Update python3 to 3.10.5
>>> f56dc7b1f3 Trac #34085: fix some details in braid groups
>>> b1a00624dc Trac #34082: Add an option up_to_isomorphism for is_subgraph
>>> 8c5d4ca3a4 Trac #34080: pycodestyle cleanup in src/sage/graphs/digraph.py
>>> 7ad1358ac7 Trac #34062: enhance ou

[sage-release] Re: Sage 9.7.beta5 released

[Marc Culler]

That statement is actually false.  I think this issue needs to be 
addressed.  I think the old venvs should be removed when doing an 
incremental build, since I cannot think of any use for them.

Here is the problem.  When I did an incremental build with the 
venv-python3.10.3 in place, a new venv named python3.10.5 was created.  But 
that new venv depends on the old 3.10.3 venv.  In fact, there are at least 
16 executable files in sage/venv-python3.10.5/bin for which the shebang 
points to
sage/venv-python3.10.3/bin/python3
This prevents sage from working after the 3.10.3 venv is removed.  There 
may be other dependencies between the two venvs as well.

It seems like bad practice to create a venv which depends on another venv.  
That defeats the purpose of a venv.  Also it does not make sense to me for 
incremental builds to cause the sage directory to contain an ever-expanding 
set of virtual envs each of which depends on the previous one.

I am guessing that these bad shebangs are created because the old venv is 
actually being used to build the new venv. 

Here is a list of the files with bad shebangs in sage/venv-python3.10.5/bin
math-readline
sage-cleaner
sage-coverage
sage-cython
sage-eval
sage-fixdoctests
sage-ipython
sage-list-packages
sage-notebook
sage-num-threads.py
sage-preparse
sage-run
sage-run-cython
sage-runtests
sage-startuptime.py
sage-venv-config

- Marc





On Wednesday, July 13, 2022 at 4:55:02 PM UTC-5 matthia...@gmail.com wrote:

> Yes, you can delete the old venv. We do not uninstall other venvs that may 
> have been built previously. 
>
> On Wednesday, July 13, 2022 at 1:08:57 PM UTC-7 marc@gmail.com wrote:
>
>> After working around the issues with the bootstrap script and 
>> symengine_py I have managed to build 9.7.beta5 on an arm mac mini.  This 
>> was an incremental build from beta4.  When the build finished I noticed 
>> that both sage/local/var/lib/sage/venv-python3.10.3 and 
>> sage/local/var/lib/sage/venv-python3.10.5 existed.  The 3.10.3 venv cannot 
>> be required, because it never gets created if make distclean is run first.  
>> So it seems to be doing nothing but wasting disk space.  Shouldn't it get 
>> removed once the build finishes?
>>
>> - Marc
>>
>> On Sunday, July 10, 2022 at 6:24:36 PM UTC-5 Volker Braun wrote:
>>
>>> As always, you can get the latest beta version from the "develop" git 
>>> branch. Alternatively, the self-contained source tarball is at 
>>> http://www.sagemath.org/download-latest.html
>>>
>>> 625ac58151 (trac/develop, tag: 9.7.beta5) Updated SageMath version to 
>>> 9.7.beta5
>>> 413ff13c54 Trac #34056: cleaning two files in quadratic forms
>>> cb65d06dd2 Trac #34055: Remove "ssl" target from Makefile
>>> 0740d209ca Trac #34053: pycodestyle cleanup in 
>>> src/sage/graphs/base/static_sparse_graph.pyx
>>> 539a5c073c Trac #34046: pycodestyle cleanup in 
>>> src/sage/graphs/base/boost_graph.pyx
>>> 6790b30aeb Trac #34044: pycodestyle cleanup in 
>>> src/sage/graphs/generators/smallgraphs.py (part 3)
>>> 6e4de5191b Trac #34043: pycodestyle cleanup in 
>>> src/sage/graphs/generators/smallgraphs.py (part 2)
>>> 3d2f91c326 Trac #34042: pycodestyle cleanup in 
>>> src/sage/graphs/generators/smallgraphs.py (part 1)
>>> 45c1d36c3a Trac #34034: pycodestyle cleanup in 
>>> src/sage/graphs/generators/random.py
>>> 9f1388bac5 Trac #34032: pycodestyle cleanup in 
>>> src/sage/graphs/generators/world_map.py
>>> 248a6e15e6 Trac #34023: pycodestyle cleanup in distance_regular.pyx 
>>> (part 1)
>>> 0a77b4496f Trac #34022: pycodestyle cleanup in 
>>> src/sage/graphs/generators/classical_geometries.py
>>> 0cec8684d7 Trac #34135: modernize super() in groups
>>> 38b2bf7529 Trac #34058: sage 9.6 special function translation issue with 
>>> fricas. elliptic_ec
>>> 720adde3bb Trac #32716: pkgs/sagemath-*/tox.ini: Create environment that 
>>> uses Sage's python as the basepython, fix sagemath-standard deps
>>> 6294f36ee4 Trac #28925: Modify find_python_sources to support 
>>> modularization of sagelib by native namespace packages (PEP 420)
>>> 5063ca7441 Trac #34021: pycodestyle in 5 files of 
>>> src/sage/graphs/generators
>>> 648ea02cda Trac #34018: pycodestyle cleanup in 
>>> src/sage/graphs/graph_decompositions/
>>> 44562ec0cf Trac #34016: improve pycodestyle in 4 files in graphs
>>> aa79451a04 Trac #34015: pycodestyle cleanup in planarity.pyx and 
>>> path_enumeration.pyx
>>> 3268d19fa5 Trac #34013: pycodestyle cleanup in schnyder.py and 
>>> print_graphs.py
>>> a6f5a56109 Trac #34012: pycodestyle cleanup in 
>>> sage.graphs.spanning_tree.pyx, weakly_chordal.pyx
>>> b5041b18ad Trac #34011: pycodestyle cleanup in sage.graphs.views.pyx, 
>>> trees.pyx, traversals.pyx
>>> 81f843e76b Trac #34010: pycodestyle cleanup in 
>>> sage.graphs.tutte_polynomial.py
>>> c2550f7093 Trac #34009: pycodestyle cleanup in 
>>> sage.graphs.hyperbolicity.pyx
>>> 44a5f5b3d9 Trac #33952: Add methods to compute holomorphic differentials 
>>> of function field
>>> 6ea1dc5f9e Trac 

[sage-release] Re: Sage 9.7.beta5 released

[Marc Culler]

I used sed to fix the 16 files with bad shebangs in 
sage/venv-python3.10.5/bin and that appeared to produce a working copy of 
sage.  So perhaps the bad shebangs are the only reason that 
venv-python3.10.5 depends on venv-python3.10.3.

- Marc

On Thursday, July 14, 2022 at 7:30:47 AM UTC-5 Marc Culler wrote:

> That statement is actually false.  I think this issue needs to be 
> addressed.  I think the old venvs should be removed when doing an 
> incremental build, since I cannot think of any use for them.
>
> Here is the problem.  When I did an incremental build with the 
> venv-python3.10.3 in place, a new venv named python3.10.5 was created.  But 
> that new venv depends on the old 3.10.3 venv.  In fact, there are at least 
> 16 executable files in sage/venv-python3.10.5/bin for which the shebang 
> points to
> sage/venv-python3.10.3/bin/python3
> This prevents sage from working after the 3.10.3 venv is removed.  There 
> may be other dependencies between the two venvs as well.
>
> It seems like bad practice to create a venv which depends on another 
> venv.  That defeats the purpose of a venv.  Also it does not make sense to 
> me for incremental builds to cause the sage directory to contain an 
> ever-expanding set of virtual envs each of which depends on the previous 
> one.
>
> I am guessing that these bad shebangs are created because the old venv is 
> actually being used to build the new venv. 
>
> Here is a list of the files with bad shebangs in sage/venv-python3.10.5/bin
> math-readline
> sage-cleaner
> sage-coverage
> sage-cython
> sage-eval
> sage-fixdoctests
> sage-ipython
> sage-list-packages
> sage-notebook
> sage-num-threads.py
> sage-preparse
> sage-run
> sage-run-cython
> sage-runtests
> sage-startuptime.py
> sage-venv-config
>
> - Marc
>
>
>
>
>
> On Wednesday, July 13, 2022 at 4:55:02 PM UTC-5 matthia...@gmail.com 
> wrote:
>
>> Yes, you can delete the old venv. We do not uninstall other venvs that 
>> may have been built previously. 
>>
>> On Wednesday, July 13, 2022 at 1:08:57 PM UTC-7 marc@gmail.com wrote:
>>
>>> After working around the issues with the bootstrap script and 
>>> symengine_py I have managed to build 9.7.beta5 on an arm mac mini.  This 
>>> was an incremental build from beta4.  When the build finished I noticed 
>>> that both sage/local/var/lib/sage/venv-python3.10.3 and 
>>> sage/local/var/lib/sage/venv-python3.10.5 existed.  The 3.10.3 venv cannot 
>>> be required, because it never gets created if make distclean is run first.  
>>> So it seems to be doing nothing but wasting disk space.  Shouldn't it get 
>>> removed once the build finishes?
>>>
>>> - Marc
>>>
>>> On Sunday, July 10, 2022 at 6:24:36 PM UTC-5 Volker Braun wrote:
>>>
>>>> As always, you can get the latest beta version from the "develop" git 
>>>> branch. Alternatively, the self-contained source tarball is at 
>>>> http://www.sagemath.org/download-latest.html
>>>>
>>>> 625ac58151 (trac/develop, tag: 9.7.beta5) Updated SageMath version to 
>>>> 9.7.beta5
>>>> 413ff13c54 Trac #34056: cleaning two files in quadratic forms
>>>> cb65d06dd2 Trac #34055: Remove "ssl" target from Makefile
>>>> 0740d209ca Trac #34053: pycodestyle cleanup in 
>>>> src/sage/graphs/base/static_sparse_graph.pyx
>>>> 539a5c073c Trac #34046: pycodestyle cleanup in 
>>>> src/sage/graphs/base/boost_graph.pyx
>>>> 6790b30aeb Trac #34044: pycodestyle cleanup in 
>>>> src/sage/graphs/generators/smallgraphs.py (part 3)
>>>> 6e4de5191b Trac #34043: pycodestyle cleanup in 
>>>> src/sage/graphs/generators/smallgraphs.py (part 2)
>>>> 3d2f91c326 Trac #34042: pycodestyle cleanup in 
>>>> src/sage/graphs/generators/smallgraphs.py (part 1)
>>>> 45c1d36c3a Trac #34034: pycodestyle cleanup in 
>>>> src/sage/graphs/generators/random.py
>>>> 9f1388bac5 Trac #34032: pycodestyle cleanup in 
>>>> src/sage/graphs/generators/world_map.py
>>>> 248a6e15e6 Trac #34023: pycodestyle cleanup in distance_regular.pyx 
>>>> (part 1)
>>>> 0a77b4496f Trac #34022: pycodestyle cleanup in 
>>>> src/sage/graphs/generators/classical_geometries.py
>>>> 0cec8684d7 Trac #34135: modernize super() in groups
>>>> 38b2bf7529 Trac #34058: sage 9.6 special function translation issue 
>>>> with fricas. elliptic_ec
>>>> 720adde3bb Trac #32716: pkgs/sagemath-*/tox.ini: Create environment 
>>>>

Re: [sage-release] Sage 9.7.beta8 released

[Marc Culler]

This is fixed in ticket #34221 .  
Cython 2.9 does not find  .pxd files in directories which do not contain an 
__init__.py file, and the __init__.py files were removed from several 
directories by ticket #33011 . The 
patch in #34221 backports a feature from Cython 3 which causes it to look 
in those directories.  Maybe #34221 will be included in the next release?

- Marc

On Monday, August 8, 2022 at 4:39:05 AM UTC-5 tdumont wrote:

>
>
> On my Debian testing, incremental upgrade ok.
>

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[sage-release] Re: Sage 9.8 released

[Marc Culler]

I am trying to build the binary release of Sage 9.8 for macOS and I have 
run into a mysterious problem.  I wonder if anyone on this list has any 
insight into it.

There are really two separate binary releases: one for Intel and one for 
Apple Silicon.  These are built using the same build script but on two 
separate machines whose native architecture matches the target.  That is, 
there is no cross-compilation involved.

This is what I see on Intel:
sage: %gap LoadPackage("semigroups");
true

This is what I see on Apple M1:
sage: %gap LoadPackage("semigroups");
** Gap crashed or quit executing 'LoadPackage("semigroups");' **
Restarting Gap and trying again
** Gap crashed or quit executing 'LoadPackage("semigroups");' **
Restarting Gap and trying again
** Gap crashed or quit executing 'LoadPackage("semigroups");' **
Restarting Gap and trying again
^C---

(You have to kill Sage or it will keep restarting Gap forever.)

Does anyone have any ideas? 

- Marc



On Saturday, February 11, 2023 at 7:47:09 AM UTC-6 Volker Braun wrote:

> The "master" git branch has been updated to Sage-9.8. As always, you can 
> get the latest beta version from the "develop" git branch. Alternatively, 
> the self-contained source tarball is at 
> http://www.sagemath.org/download-latest.html
>
> And as you are undoubtedly aware, the git repository is now hosted at 
> https://github.com/sagemath/sage, so update your git remote.
>
> To commemorate the move (and because we are getting really close to .10), 
> I'm proposing to target Sage version 10 as the next release. 
>
> The changes over 9.8.rc0 are mainly housekeeping for the new repository 
> location. 
>
> I'll try to finish up merging remaining positively reviewed trac issues, 
> and then move on to github pull requests.
>  
>
> c000c953eb6 (HEAD -> develop, github/master, github/develop, tag: 9.8) 
> Updated SageMath version to 9.8
> 104dde9eaa8 Merge pull request #35022 from tobiasdiez/pr-template-title
> 17d8a73296f Merge pull request #35018 from x4/public/35017
> 6a4667bb5c5 Merge pull request #34983 from tobiasdiez/add-issue-templates
> 66b319baffb Merge pull request #35011 from dimpase/develop
> 872b32b0c20 Merge pull request #34987 from mezzarobba/missing_long_time
> d57804e6dec Merge pull request #34964 from x4/public/linter-20230206
> 698001b0e6a remove prohibition, promise details
> 0c5f7baf6c2 remove trac references, promise details soon
> 200557e00c3 (tag: 9.8.rc1) Updated SageMath version to 9.8.rc1
>

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[sage-release] Re: Sage 9.8 released

[Marc Culler]

By running the load command in sage -gap I can see that GAP is crashing 
with an illegal instruction error while trying to load the semigroups 
package.

- Marc

On Sunday, February 19, 2023 at 10:04:51 AM UTC-6 Marc Culler wrote:

> I am trying to build the binary release of Sage 9.8 for macOS and I have 
> run into a mysterious problem.  I wonder if anyone on this list has any 
> insight into it.
>
> There are really two separate binary releases: one for Intel and one for 
> Apple Silicon.  These are built using the same build script but on two 
> separate machines whose native architecture matches the target.  That is, 
> there is no cross-compilation involved.
>
> This is what I see on Intel:
> sage: %gap LoadPackage("semigroups");
> true
>
> This is what I see on Apple M1:
> sage: %gap LoadPackage("semigroups");
> ** Gap crashed or quit executing 'LoadPackage("semigroups");' **
> Restarting Gap and trying again
> ** Gap crashed or quit executing 'LoadPackage("semigroups");' **
> Restarting Gap and trying again
> ** Gap crashed or quit executing 'LoadPackage("semigroups");' **
> Restarting Gap and trying again
>
> ^C---
>
> (You have to kill Sage or it will keep restarting Gap forever.)
>
> Does anyone have any ideas? 
>
> - Marc
>
>
>
> On Saturday, February 11, 2023 at 7:47:09 AM UTC-6 Volker Braun wrote:
>
>> The "master" git branch has been updated to Sage-9.8. As always, you can 
>> get the latest beta version from the "develop" git branch. Alternatively, 
>> the self-contained source tarball is at 
>> http://www.sagemath.org/download-latest.html
>>
>> And as you are undoubtedly aware, the git repository is now hosted at 
>> https://github.com/sagemath/sage, so update your git remote.
>>
>> To commemorate the move (and because we are getting really close to .10), 
>> I'm proposing to target Sage version 10 as the next release. 
>>
>> The changes over 9.8.rc0 are mainly housekeeping for the new repository 
>> location. 
>>
>> I'll try to finish up merging remaining positively reviewed trac issues, 
>> and then move on to github pull requests.
>>  
>>
>> c000c953eb6 (HEAD -> develop, github/master, github/develop, tag: 9.8) 
>> Updated SageMath version to 9.8
>> 104dde9eaa8 Merge pull request #35022 from tobiasdiez/pr-template-title
>> 17d8a73296f Merge pull request #35018 from x4/public/35017
>> 6a4667bb5c5 Merge pull request #34983 from tobiasdiez/add-issue-templates
>> 66b319baffb Merge pull request #35011 from dimpase/develop
>> 872b32b0c20 Merge pull request #34987 from mezzarobba/missing_long_time
>> d57804e6dec Merge pull request #34964 from x4/public/linter-20230206
>> 698001b0e6a remove prohibition, promise details
>> 0c5f7baf6c2 remove trac references, promise details soon
>> 200557e00c3 (tag: 9.8.rc1) Updated SageMath version to 9.8.rc1
>>
>

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Re: [sage-release] Re: Sage 9.8 released

[Marc Culler]

Thanks for the suggestions!

I have found the problem, although I cannot begin to explain it.  Many of 
the libraries in sage/local targeted x86_64 even though they were built on 
an M1 system.  Executables and libraries in the venv targeted the correct 
arm64 architecture.  I can only guess that there was some very weird 
environment in place when I did the build.  Anyway, rebuilding after make 
distclean seems to be working correctly.  So this thread can now be 
ignored.  Thanks.

- Marc

On Sunday, February 19, 2023 at 11:16:27 AM UTC-6 Dima Pasechnik wrote:

> One reason might be is that this version of the package is just too old.
> It was released long before all those macOS updates, and it is quite heavy 
> C++ stuff.
>
> You might get better luck with using positively reviewed update with GAP 
> 4.12.2
>
>
>
> On Sun, 19 Feb 2023, 17:13 Dima Pasechnik,  wrote:
>
>> does
>>
>>  sage: libgap.LoadPackage("semigroup")
>>
>> crash, as well?
>>
>> and how about the same at GAP prompt:
>>
>> ./sage --gap
>> ..
>>
>>gap> LoadPackage("semigroup");
>>
>>
>>
>>
>>
>> On Sun, 19 Feb 2023, 16:11 Marc Culler,  wrote:
>>
>>> By running the load command in sage -gap I can see that GAP is crashing 
>>> with an illegal instruction error while trying to load the semigroups 
>>> package.
>>>
>>> - Marc
>>>
>>> On Sunday, February 19, 2023 at 10:04:51 AM UTC-6 Marc Culler wrote:
>>>
>>>> I am trying to build the binary release of Sage 9.8 for macOS and I 
>>>> have run into a mysterious problem.  I wonder if anyone on this list has 
>>>> any insight into it.
>>>>
>>>> There are really two separate binary releases: one for Intel and one 
>>>> for Apple Silicon.  These are built using the same build script but on two 
>>>> separate machines whose native architecture matches the target.  That is, 
>>>> there is no cross-compilation involved.
>>>>
>>>> This is what I see on Intel:
>>>> sage: %gap LoadPackage("semigroups");
>>>> true
>>>>
>>>> This is what I see on Apple M1:
>>>> sage: %gap LoadPackage("semigroups");
>>>> ** Gap crashed or quit executing 'LoadPackage("semigroups");' **
>>>> Restarting Gap and trying again
>>>> ** Gap crashed or quit executing 'LoadPackage("semigroups");' **
>>>> Restarting Gap and trying again
>>>> ** Gap crashed or quit executing 'LoadPackage("semigroups");' **
>>>> Restarting Gap and trying again
>>>>
>>>> ^C---
>>>>
>>>> (You have to kill Sage or it will keep restarting Gap forever.)
>>>>
>>>> Does anyone have any ideas? 
>>>>
>>>> - Marc
>>>>
>>>>
>>>>
>>>> On Saturday, February 11, 2023 at 7:47:09 AM UTC-6 Volker Braun wrote:
>>>>
>>>>> The "master" git branch has been updated to Sage-9.8. As always, you 
>>>>> can get the latest beta version from the "develop" git branch. 
>>>>> Alternatively, the self-contained source tarball is at 
>>>>> http://www.sagemath.org/download-latest.html
>>>>>
>>>>> And as you are undoubtedly aware, the git repository is now hosted at 
>>>>> https://github.com/sagemath/sage, so update your git remote.
>>>>>
>>>>> To commemorate the move (and because we are getting really close to 
>>>>> .10), I'm proposing to target Sage version 10 as the next release. 
>>>>>
>>>>> The changes over 9.8.rc0 are mainly housekeeping for the new 
>>>>> repository location. 
>>>>>
>>>>> I'll try to finish up merging remaining positively reviewed trac 
>>>>> issues, and then move on to github pull requests.
>>>>>  
>>>>>
>>>>> c000c953eb6 (HEAD -> develop, github/master, github/develop, tag: 9.8) 
>>>>> Updated SageMath version to 9.8
>>>>> 104dde9eaa8 Merge pull request #35022 from tobiasdiez/pr-template-title
>>>>> 17d8a73296f Merge pull request #35018 from x4/public/35017
>>>>> 6a4667bb5c5 Merge pull request #34983 from 
>>>>> tobiasdiez/add-issue-templates
>>>>> 66b319baff

[sage-release] Re: Sage 10.0.rc1 released

[Marc Culler]

While  preparing a binary release for macOS I discovered that in 10.0.rc1 
the gap-packages spkg fails to install the script BuildPackages.sh in 
sage/local/lib/gap/bin.  This breaks installation of GAP packages with 
libgap.InstallPackage.  All that needs to be done to fix it is to copy that 
script into place.

- Marc

On Friday, April 28, 2023 at 6:15:04 PM UTC-5 Volker Braun wrote:

> As always, you can get the latest beta version from the "develop" git 
> branch. Alternatively, the self-contained source tarball is at 
> http://www.sagemath.org/download-latest.html
>
> 5bd81deae14 (HEAD -> develop, tag: 10.0.rc1, github/develop) Updated 
> SageMath version to 10.0.rc1
> 9185befce0c gh-35558: `sage.quadratic_forms`: Fix use of `staticmethod` 
> for Python < 3.10
> 2bedb53b5ea gh-35415: `givaro`, `zeromq`: Add patches for GCC 13 support
> f3acd42678a (tag: 10.0.rc0) Updated SageMath version to 10.0.rc0
>

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[sage-release] Re: Sage 10.1.beta4 released

[Marc Culler]

I am not able to build the documentation for 10.1beta4 on macOS.

First, there are inconsistent paths for the  file references/objects.inv.  
At different times it is expected to be in two different places:

local/share/doc/sage/inventory/en/reference/references/objects.inv
local/share/doc/sage/inventory/en/reference/objects.inv

Presumably the second one is an error.

If the objects.inv file is duplicated so that it appears both places then 
the doc build gets past [reference] and fails for [manifolds].  The error 
is:
OSError: XXX/sage/src/doc/en/reference/manifolds/index.rst:4: WARNING: 
undefined label: 'tensors-on-free-modules'

- Marc

On Wednesday, June 21, 2023 at 5:38:54 PM UTC-5 Volker Braun wrote:

> As always, you can get the latest beta version from the "develop" git 
> branch. Alternatively, the self-contained source tarball is at 
> http://www.sagemath.org/download-latest.html
>
>
> 3230f00aeb4 (tag: 10.1.beta4, github/develop) Updated SageMath version to 
> 10.1.beta4
> 4fa9c1c33b6 gh-35787: adjust random tests for generators of elliptic curves
> cf43e35862e gh-35780: Reduce dependency to rainbow in 
> sage.graphs.graph_coloring
> af6ec5a545c gh-35776: cylint: no more xrange in matroids
> 8f46a634443 gh-35773: Document that GLPK/exact can be inexact
> 527295907a9 gh-35772: getting rid of many uses of xrange in pyx files
> 361ba993142 gh-35770: cylint: remove some unused variables in rings/
> 02ab7005dc2 gh-35768: fix most E301 warnings
> ccf11a907f5 gh-35766: fixing most E222 warnings in py files
> 48559c692c6 gh-35765: more fixes for superfluous cython imports
> 3d25722f1f2 gh-35764: fix all remaining E251 warnings
> c32c4f0c9e2 gh-35760: gap: adapt get_global to use official libgap API
> 643bb2c582a gh-35759: gap: fix a comment
> 277d965b08b gh-35758: `sage.matrix.misc`: Split by library dependency
> c55e7168d15 gh-35757: Implementing the type B Ish arrangement.
> 17033c2cf3d gh-35754: remove deprecated in #32894 python module 
> interfaces/primecount
> bcd9128a17b gh-35752: Clarification on the MAX_MODULUS of float matrices 
> modulo `n`
> 7272357ae17 gh-35751: Add a note on a doctest that randomly behaves
> 6252db6a222 gh-35741: `sage.combinat`: Split some Cython modules 
> (modularization fixes)
> 81075d662d6 gh-35739: .github/workflows/docker.yml: Remove defunct steps 
> that refer to Trac
> 344128b2af7 gh-35735: gap: use CALL_WITH_STREAM to redirect output to 
> string
> 3e54effae56 gh-35734: Reference manual: Show modularized sagelib packages 
> separately
> e0e8473b232 gh-35730: little refreshment of code in Weyl groups
> dd8845d2d53 gh-35729: sage.coding: Modularization fixes, doctest 
> cosmetics, add `# optional`
> 882cd19fc6a gh-35728: New feature annotations `# optional - sage.schemes 
> sage.modular sage.libs.flint` etc.
> c4a70ab7271 gh-35724: fix some pep8 warnings in modform_hecketriangle
> bb0ea9851b0 gh-35719: `sage.matroids`: Modularization fixes
> ad35d8c77ba gh-35652: CI Build & Test: First build incrementally and test 
> changed files only
> b0af318c2fd gh-35629: Implement the exceptional Jordan algebra
> 1c782f25fdc gh-35620: doctester: Check for consistency of `# optional` 
> annotations
> 3aa3644a9e5 gh-35564: `sage.misc.misc`, `sage.combinat`: Modularization 
> fixes
> 443b7549ad3 (tag: 10.1.beta3) Updated SageMath version to 10.1.beta3
>

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[sage-release] Re: Sage 10.1.beta4 released

[Marc Culler]

I can get the documentation to build if I modify sphinxbuild.py to make it 
ignore the following warnings (instead of raising an OSErr):

WARNING: citation not found
WARNING: undefined label
WARNING: failed to reach any of the inventories

The missing citations and labels appear to all be in [manifolds].

When the inventory warning is ignored the object.inv files do in fact get 
built later, and they get installed in the correct place.

- Marc

On Sunday, June 25, 2023 at 2:21:05 PM UTC-5 Marc Culler wrote:

> I am not able to build the documentation for 10.1beta4 on macOS.
>
> First, there are inconsistent paths for the  file references/objects.inv.  
> At different times it is expected to be in two different places:
>
> local/share/doc/sage/inventory/en/reference/references/objects.inv
> local/share/doc/sage/inventory/en/reference/objects.inv
>
> Presumably the second one is an error.
>
> If the objects.inv file is duplicated so that it appears both places then 
> the doc build gets past [reference] and fails for [manifolds].  The error 
> is:
> OSError: XXX/sage/src/doc/en/reference/manifolds/index.rst:4: WARNING: 
> undefined label: 'tensors-on-free-modules'
>
> - Marc
>
> On Wednesday, June 21, 2023 at 5:38:54 PM UTC-5 Volker Braun wrote:
>
>> As always, you can get the latest beta version from the "develop" git 
>> branch. Alternatively, the self-contained source tarball is at 
>> http://www.sagemath.org/download-latest.html
>>
>>
>> 3230f00aeb4 (tag: 10.1.beta4, github/develop) Updated SageMath version to 
>> 10.1.beta4
>> 4fa9c1c33b6 gh-35787: adjust random tests for generators of elliptic 
>> curves
>> cf43e35862e gh-35780: Reduce dependency to rainbow in 
>> sage.graphs.graph_coloring
>> af6ec5a545c gh-35776: cylint: no more xrange in matroids
>> 8f46a634443 gh-35773: Document that GLPK/exact can be inexact
>> 527295907a9 gh-35772: getting rid of many uses of xrange in pyx files
>> 361ba993142 gh-35770: cylint: remove some unused variables in rings/
>> 02ab7005dc2 gh-35768: fix most E301 warnings
>> ccf11a907f5 gh-35766: fixing most E222 warnings in py files
>> 48559c692c6 gh-35765: more fixes for superfluous cython imports
>> 3d25722f1f2 gh-35764: fix all remaining E251 warnings
>> c32c4f0c9e2 gh-35760: gap: adapt get_global to use official libgap API
>> 643bb2c582a gh-35759: gap: fix a comment
>> 277d965b08b gh-35758: `sage.matrix.misc`: Split by library dependency
>> c55e7168d15 gh-35757: Implementing the type B Ish arrangement.
>> 17033c2cf3d gh-35754: remove deprecated in #32894 python module 
>> interfaces/primecount
>> bcd9128a17b gh-35752: Clarification on the MAX_MODULUS of float matrices 
>> modulo `n`
>> 7272357ae17 gh-35751: Add a note on a doctest that randomly behaves
>> 6252db6a222 gh-35741: `sage.combinat`: Split some Cython modules 
>> (modularization fixes)
>> 81075d662d6 gh-35739: .github/workflows/docker.yml: Remove defunct steps 
>> that refer to Trac
>> 344128b2af7 gh-35735: gap: use CALL_WITH_STREAM to redirect output to 
>> string
>> 3e54effae56 gh-35734: Reference manual: Show modularized sagelib packages 
>> separately
>> e0e8473b232 gh-35730: little refreshment of code in Weyl groups
>> dd8845d2d53 gh-35729: sage.coding: Modularization fixes, doctest 
>> cosmetics, add `# optional`
>> 882cd19fc6a gh-35728: New feature annotations `# optional - sage.schemes 
>> sage.modular sage.libs.flint` etc.
>> c4a70ab7271 gh-35724: fix some pep8 warnings in modform_hecketriangle
>> bb0ea9851b0 gh-35719: `sage.matroids`: Modularization fixes
>> ad35d8c77ba gh-35652: CI Build & Test: First build incrementally and test 
>> changed files only
>> b0af318c2fd gh-35629: Implement the exceptional Jordan algebra
>> 1c782f25fdc gh-35620: doctester: Check for consistency of `# optional` 
>> annotations
>> 3aa3644a9e5 gh-35564: `sage.misc.misc`, `sage.combinat`: Modularization 
>> fixes
>> 443b7549ad3 (tag: 10.1.beta3) Updated SageMath version to 10.1.beta3
>>
>

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[sage-release] Re: Sage 10.1.beta4 released

[Marc Culler]

I have resolved my problem with building the documentation, and I now 
understand why no one could help me with it.  Thanks.

- Marc

On Sunday, June 25, 2023 at 5:07:17 PM UTC-5 Marc Culler wrote:

> I can get the documentation to build if I modify sphinxbuild.py to make it 
> ignore the following warnings (instead of raising an OSErr):
>
> WARNING: citation not found
> WARNING: undefined label
> WARNING: failed to reach any of the inventories
>
> The missing citations and labels appear to all be in [manifolds].
>
> When the inventory warning is ignored the object.inv files do in fact get 
> built later, and they get installed in the correct place.
>
> - Marc
>
> On Sunday, June 25, 2023 at 2:21:05 PM UTC-5 Marc Culler wrote:
>
>> I am not able to build the documentation for 10.1beta4 on macOS.
>>
>> First, there are inconsistent paths for the  file 
>> references/objects.inv.  At different times it is expected to be in two 
>> different places:
>>
>> local/share/doc/sage/inventory/en/reference/references/objects.inv
>> local/share/doc/sage/inventory/en/reference/objects.inv
>>
>> Presumably the second one is an error.
>>
>> If the objects.inv file is duplicated so that it appears both places then 
>> the doc build gets past [reference] and fails for [manifolds].  The error 
>> is:
>> OSError: XXX/sage/src/doc/en/reference/manifolds/index.rst:4: WARNING: 
>> undefined label: 'tensors-on-free-modules'
>>
>> - Marc
>>
>> On Wednesday, June 21, 2023 at 5:38:54 PM UTC-5 Volker Braun wrote:
>>
>>> As always, you can get the latest beta version from the "develop" git 
>>> branch. Alternatively, the self-contained source tarball is at 
>>> http://www.sagemath.org/download-latest.html
>>>
>>>
>>> 3230f00aeb4 (tag: 10.1.beta4, github/develop) Updated SageMath version 
>>> to 10.1.beta4
>>> 4fa9c1c33b6 gh-35787: adjust random tests for generators of elliptic 
>>> curves
>>> cf43e35862e gh-35780: Reduce dependency to rainbow in 
>>> sage.graphs.graph_coloring
>>> af6ec5a545c gh-35776: cylint: no more xrange in matroids
>>> 8f46a634443 gh-35773: Document that GLPK/exact can be inexact
>>> 527295907a9 gh-35772: getting rid of many uses of xrange in pyx files
>>> 361ba993142 gh-35770: cylint: remove some unused variables in rings/
>>> 02ab7005dc2 gh-35768: fix most E301 warnings
>>> ccf11a907f5 gh-35766: fixing most E222 warnings in py files
>>> 48559c692c6 gh-35765: more fixes for superfluous cython imports
>>> 3d25722f1f2 gh-35764: fix all remaining E251 warnings
>>> c32c4f0c9e2 gh-35760: gap: adapt get_global to use official libgap API
>>> 643bb2c582a gh-35759: gap: fix a comment
>>> 277d965b08b gh-35758: `sage.matrix.misc`: Split by library dependency
>>> c55e7168d15 gh-35757: Implementing the type B Ish arrangement.
>>> 17033c2cf3d gh-35754: remove deprecated in #32894 python module 
>>> interfaces/primecount
>>> bcd9128a17b gh-35752: Clarification on the MAX_MODULUS of float matrices 
>>> modulo `n`
>>> 7272357ae17 gh-35751: Add a note on a doctest that randomly behaves
>>> 6252db6a222 gh-35741: `sage.combinat`: Split some Cython modules 
>>> (modularization fixes)
>>> 81075d662d6 gh-35739: .github/workflows/docker.yml: Remove defunct steps 
>>> that refer to Trac
>>> 344128b2af7 gh-35735: gap: use CALL_WITH_STREAM to redirect output to 
>>> string
>>> 3e54effae56 gh-35734: Reference manual: Show modularized sagelib 
>>> packages separately
>>> e0e8473b232 gh-35730: little refreshment of code in Weyl groups
>>> dd8845d2d53 gh-35729: sage.coding: Modularization fixes, doctest 
>>> cosmetics, add `# optional`
>>> 882cd19fc6a gh-35728: New feature annotations `# optional - sage.schemes 
>>> sage.modular sage.libs.flint` etc.
>>> c4a70ab7271 gh-35724: fix some pep8 warnings in modform_hecketriangle
>>> bb0ea9851b0 gh-35719: `sage.matroids`: Modularization fixes
>>> ad35d8c77ba gh-35652: CI Build & Test: First build incrementally and 
>>> test changed files only
>>> b0af318c2fd gh-35629: Implement the exceptional Jordan algebra
>>> 1c782f25fdc gh-35620: doctester: Check for consistency of `# optional` 
>>> annotations
>>> 3aa3644a9e5 gh-35564: `sage.misc.misc`, `sage.combinat`: Modularization 
>>> fixes
>>> 443b7549ad3 (tag: 10.1.beta3) Updated SageMath version to 10.1.beta3
>>>
>>

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[sage-release] A detail that matters - please help

[Marc Culler]

Details really do matter.  The devil is in them.  Here is one which makes a 
major difference to my efforts to distribute Sage.  I hope that I can 
convince people to pay attention to it.

DETAIL: An svg image can be compressed very efficiently and will look good 
at all resolutions.  A png image can not be compressed, being already 
compressed, and pixelates at high resolutions.

BACK STORY: I am working on adding documentation to the Sage_macOS 
distribution.  Size is important.  For 10.1beta3 the English documentation 
occupied 631MB, and compressed down to 104MB.  For 10.1beta4 the 
uncompressed size increased by over 100MB due to the addition of 100MB of 
png images.  Now it only compresses to 207MB, doubling the compressed size.

There is no need for this wastefulness.  Here is an example:

sage: D = graphs.DodecahedralGraph()
sage: p = D.plot()
sage: p.save_image('/tmp/dodec.svg')
sage: p.save_image('/tmp/dodec.png')

The result:
% ls -l /tmp/dodec*
-rw-r--r--@ 1 culler  wheel  42735 Jun 28 08:48 /tmp/dodec.png
-rw-r--r--  1 culler  wheel  18524 Jun 28 08:48 /tmp/dodec.svg
% gzip /tmp/dodec*
% ls -l /tmp/dodec*
-rw-r--r--@ 1 culler  wheel  39473 Jun 28 08:48 /tmp/dodec.png.gz
-rw-r--r--  1 culler  wheel   3815 Jun 28 08:48 /tmp/dodec.svg.gz

BOTTOM LINE: we get more than a 90% reduction in size simply by choosing to 
use the .svg extension when saving the plot instead of the .png extension.

I am not allowed to upload an svg file to google groups, so you will have 
to verify for yourself that the svg looks better than the png, but it does.

- Marc


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Re: [sage-release] A detail that matters - please help

[Marc Culler]

As far as I can tell it is a choice that is being made at various places in 
the sage_docbuild module to use png as the default image format.  But I 
haven't been able to find exactly where.  One place appears to be line 117 
in src/sage_docbuild/conf.py, but that is not the only place.

- Marc

On Wednesday, June 28, 2023 at 10:49:51 AM UTC-5 Vincent Delecroix wrote:

> I agree with Marc that svg is almost always preferable than png for
> graphics : it scales and compresses. Thanks for raising the issue.
>
> Do you have a concrete proposal for making the change png -> svg
> happen? I guess there is a lot of files that would be involved in the
> transition.
>
> Vincent
>
> On Wed, 28 Jun 2023 at 16:23, Marc Culler  wrote:
> >
> > Details really do matter. The devil is in them. Here is one which makes 
> a major difference to my efforts to distribute Sage. I hope that I can 
> convince people to pay attention to it.
> >
> > DETAIL: An svg image can be compressed very efficiently and will look 
> good at all resolutions. A png image can not be compressed, being already 
> compressed, and pixelates at high resolutions.
> >
> > BACK STORY: I am working on adding documentation to the Sage_macOS 
> distribution. Size is important. For 10.1beta3 the English documentation 
> occupied 631MB, and compressed down to 104MB. For 10.1beta4 the 
> uncompressed size increased by over 100MB due to the addition of 100MB of 
> png images. Now it only compresses to 207MB, doubling the compressed size.
> >
> > There is no need for this wastefulness. Here is an example:
> >
> > sage: D = graphs.DodecahedralGraph()
> > sage: p = D.plot()
> > sage: p.save_image('/tmp/dodec.svg')
> > sage: p.save_image('/tmp/dodec.png')
> >
> > The result:
> > % ls -l /tmp/dodec*
> > -rw-r--r--@ 1 culler wheel 42735 Jun 28 08:48 /tmp/dodec.png
> > -rw-r--r-- 1 culler wheel 18524 Jun 28 08:48 /tmp/dodec.svg
> > % gzip /tmp/dodec*
> > % ls -l /tmp/dodec*
> > -rw-r--r--@ 1 culler wheel 39473 Jun 28 08:48 /tmp/dodec.png.gz
> > -rw-r--r-- 1 culler wheel 3815 Jun 28 08:48 /tmp/dodec.svg.gz
> >
> > BOTTOM LINE: we get more than a 90% reduction in size simply by choosing 
> to use the .svg extension when saving the plot instead of the .png 
> extension.
> >
> > I am not allowed to upload an svg file to google groups, so you will 
> have to verify for yourself that the svg looks better than the png, but it 
> does.
> >
> > - Marc
> >
> >
> > --
> > You received this message because you are subscribed to the Google 
> Groups "sage-release" group.
> > To unsubscribe from this group and stop receiving emails from it, send 
> an email to sage-release...@googlegroups.com.
> > To view this discussion on the web visit 
> https://groups.google.com/d/msgid/sage-release/8ce7a804-3be1-4551-959e-cc770fe589ecn%40googlegroups.com
> .
>

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Re: [sage-release] A detail that matters - please help

[Marc Culler]

No, that is not correct.  The fundamental issue is the size of the 
compressed file.  And this is an issue with documentation, not with 
arbitrary graphics.  The matplotlib images in the Sage documentation do not 
involve millions of lines of svg code.  The svg files are small to start 
with and compress very efficiently.  Of course it would be possible to 
generate images which are naturally rasterized and would be very 
inefficiently represented by svg.  But that is not happening with the 
matplotlib images in the documentation.

- Marc

On Wednesday, June 28, 2023 at 11:31:01 AM UTC-5 Harald Schilly wrote:

> On Wed, Jun 28, 2023 at 6:17 PM Dima Pasechnik  wrote:
>
>> are there any setbacks in using svg nowadays?
>>
>>
> The only fundamental issue is file size. It's proportional to the number 
> of elements you want to plot. So, e.g. when there are a million points, you 
> end up with a million lines of text in the svg – while with a raster image 
> format like png, the points are "fused" to a large blob and file size stays 
> constant or even decreases. My guess is, all those plots in the 
> documentation have only a small number of elements, so, all fine :-)
>
> -- Harald
>
>
>
>  
>

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Re: [sage-release] Sage 10.4.beta6 released

[Marc Culler]

I see the same failure od fflas_ffpack on macOS 14.1.

- Marc

On Monday, May 13, 2024 at 5:53:22 AM UTC-5 david@gmail.com wrote:

> I’m unable to compile on macOS 12.7.4 on a fresh clone (and fresh shell).
>
> The compilation of fflas_ffpack-2.5.0 is failing. See attached log.
>
>

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[sage-release] Re: Sage 10.4.rc4 released

[Marc Culler]

I hope that #38360  can also 
be merged before the release of 10.4, because the current reversion to the 
naive bounds for the complex interval inverse operator breaks many of the 
verified computations in the SnapPy test suite, and makes it harder to do 
verified computations in general.

- Marc

On Tuesday, July 16, 2024 at 11:35:18 PM UTC-5 Kwankyu Lee wrote:

> Hopefully the last release candidate...
>
>
> Yes. But it would be nice to merge 
> https://github.com/sagemath/sage/pull/38378 to the final release.
>

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