subject:"\[sage\-release\] Sage 9.7.beta7 released"

Re: [sage-release] Sage 9.7.beta7 released

2022-08-03 Thread Matthias Köppe

I've opened https://trac.sagemath.org/ticket/34268 (Reduce R to a dummy 
package, upgrade rpy2 to 3.4.5)

On Tuesday, August 2, 2022 at 11:34:22 AM UTC-7 Matthias Köppe wrote:

> Yes, our R package is wildly outdated, which is problematic given that it 
> is a standard package.
>
>
>
> On Tuesday, August 2, 2022 at 11:23:08 AM UTC-7 isu...@gmail.com wrote:
>
>> Is there an issue for the R build failure? This seems like an upstream R 
>> issue and maybe updating to a newer R version will help. (R-3.6 is 3 years 
>> old)
>>
>> ```
>> In file included from gdi.c:26:
>> /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda/include/omp.h:492:39:
>>  
>> error: expected 'match' clause on 'omp declare variant' directive
>> #pragma omp begin declare variant match(device={kind(host)})
>>   ^
>> /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/local/var/tmp/sage/build/r-3.6.3/src/include/Rinternals.h:1492:17:
>>  
>> note: expanded from macro 'match'
>> #define match   Rf_match
>> ```
>>
>> On Tue, Aug 2, 2022 at 1:06 PM Matthias Köppe  
>> wrote:
>>
>>> On Tuesday, August 2, 2022 at 10:51:04 AM UTC-7 isu...@gmail.com wrote:
>>>
 We build conda packages regularly with non-Xcode clang on macOS.

>>>
>>> Yes, we do also test the Sage distribution build on conda-forge-macos, 
>>> which uses clang.
>>>
>>> conda-forge-macos-standard succeeds, using lots of conda packages (
>>> https://github.com/mkoeppe/sage/runs/7592834217?check_suite_focus=true)
>>>
>>> but conda-forge-macos-minimal fails (
>>> https://github.com/mkoeppe/sage/runs/7592834169?check_suite_focus=true)
>>> while building R.
>>>
>>> -- 
>>> You received this message because you are subscribed to the Google 
>>> Groups "sage-release" group.
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>>> an email to sage-release...@googlegroups.com.
>>>
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>>> https://groups.google.com/d/msgid/sage-release/eb4bb2c3-a10c-47cd-8168-c0b884fa12ecn%40googlegroups.com
>>>  
>>> 
>>> .
>>>
>>

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Re: [sage-release] Sage 9.7.beta7 released

2022-08-03 Thread David Coudert

And also https://trac.sagemath.org/ticket/22349 Deprecate sorting of Graph 
vertices and edges by default
This ticket touches many files and so can lead to conflicts.

Best,
David.

> Le 3 août 2022 à 13:33, Kwankyu Lee  a écrit :
> 
> It would make a sense to release sage beta8 quickly that just contains
> 
> https://trac.sagemath.org/ticket/34252
> 
> so that developers can make use of the revived Build Documentation badge in 
> trac.
> 
> 
> 
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>  
> .

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Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread Matthias Köppe

Yes, our R package is wildly outdated, which is problematic given that it 
is a standard package.



On Tuesday, August 2, 2022 at 11:23:08 AM UTC-7 isu...@gmail.com wrote:

> Is there an issue for the R build failure? This seems like an upstream R 
> issue and maybe updating to a newer R version will help. (R-3.6 is 3 years 
> old)
>
> ```
> In file included from gdi.c:26:
> /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda/include/omp.h:492:39:
>  
> error: expected 'match' clause on 'omp declare variant' directive
> #pragma omp begin declare variant match(device={kind(host)})
>   ^
> /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/local/var/tmp/sage/build/r-3.6.3/src/include/Rinternals.h:1492:17:
>  
> note: expanded from macro 'match'
> #define match   Rf_match
> ```
>
> On Tue, Aug 2, 2022 at 1:06 PM Matthias Köppe  
> wrote:
>
>> On Tuesday, August 2, 2022 at 10:51:04 AM UTC-7 isu...@gmail.com wrote:
>>
>>> We build conda packages regularly with non-Xcode clang on macOS.
>>>
>>
>> Yes, we do also test the Sage distribution build on conda-forge-macos, 
>> which uses clang.
>>
>> conda-forge-macos-standard succeeds, using lots of conda packages (
>> https://github.com/mkoeppe/sage/runs/7592834217?check_suite_focus=true)
>>
>> but conda-forge-macos-minimal fails (
>> https://github.com/mkoeppe/sage/runs/7592834169?check_suite_focus=true)
>> while building R.
>>
>> -- 
>> 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/eb4bb2c3-a10c-47cd-8168-c0b884fa12ecn%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread Isuru Fernando

Is there an issue for the R build failure? This seems like an upstream R
issue and maybe updating to a newer R version will help. (R-3.6 is 3 years
old)

```
In file included from gdi.c:26:
/Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/conda/include/omp.h:492:39:
error: expected 'match' clause on 'omp declare variant' directive
#pragma omp begin declare variant match(device={kind(host)})
  ^
/Users/runner/work/sage/sage/.tox/local-conda-forge-macos-minimal/local/var/tmp/sage/build/r-3.6.3/src/include/Rinternals.h:1492:17:
note: expanded from macro 'match'
#define match   Rf_match
```

On Tue, Aug 2, 2022 at 1:06 PM Matthias Köppe 
wrote:

> On Tuesday, August 2, 2022 at 10:51:04 AM UTC-7 isu...@gmail.com wrote:
>
>> We build conda packages regularly with non-Xcode clang on macOS.
>>
>
> Yes, we do also test the Sage distribution build on conda-forge-macos,
> which uses clang.
>
> conda-forge-macos-standard succeeds, using lots of conda packages (
> https://github.com/mkoeppe/sage/runs/7592834217?check_suite_focus=true)
>
> but conda-forge-macos-minimal fails (
> https://github.com/mkoeppe/sage/runs/7592834169?check_suite_focus=true)
> while building R.
>
> --
> You received this message because you are subscribed to the Google Groups
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> 
> .
>

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Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread Matthias Köppe

On Tuesday, August 2, 2022 at 10:51:04 AM UTC-7 isu...@gmail.com wrote:

> We build conda packages regularly with non-Xcode clang on macOS.
>

Yes, we do also test the Sage distribution build on conda-forge-macos, 
which uses clang.

conda-forge-macos-standard succeeds, using lots of conda packages 
(https://github.com/mkoeppe/sage/runs/7592834217?check_suite_focus=true)

but conda-forge-macos-minimal fails 
(https://github.com/mkoeppe/sage/runs/7592834169?check_suite_focus=true)
while building R.

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Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread Matthias Köppe

I've added the sentence "An alternative is to use a sufficiently recent 
version of clang (LLVM)."
But having more details would be better.

On Tuesday, August 2, 2022 at 10:46:32 AM UTC-7 Dima Pasechnik wrote:

>
>
> On Tue, 2 Aug 2022, 18:33 Matthias Köppe,  wrote:
>
>> On Tuesday, August 2, 2022 at 10:24:39 AM UTC-7 Dima Pasechnik wrote:
>>
>>>
>>> there is a bit of vagueness there:
>>> Support for system GCC older than 6.3 dropped ¶ 
>>> 
>>>
>>> Building Sage from source now requires a system installation of GCC >= 
>>> 6.3 (except on macOS, where the compilers from an up-to-date Xcode or Xcode 
>>> CLT installation should be used). #33316 
>>> 
>>>
>>> -
>>>
>>> One can build Sage with clang on Linux (and on freebsd). As well, I 
>>> think, one can build Sage with non-Xcode clang on macOS.
>>>
>> We do not test such configurations. When did you last test this, and on 
>> what platform?
>>
>
> My point is that we do not *require* gcc on Linux.
>
> I tested Homebrew clang on macOS in some 9.6 betas, it worked after minor 
> tweaks. There was ea ticket about it:
>
> https://trac.sagemath.org/ticket/32207
>
>
>>
>> -- 
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>>  
>> 
>> .
>>
>

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Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread Isuru Fernando

We build conda packages regularly with non-Xcode clang on macOS.

Isuru

On Tue, Aug 2, 2022 at 12:33 PM Matthias Köppe 
wrote:

> On Tuesday, August 2, 2022 at 10:24:39 AM UTC-7 Dima Pasechnik wrote:
>
>>
>> there is a bit of vagueness there:
>> Support for system GCC older than 6.3 dropped ¶
>> 
>>
>> Building Sage from source now requires a system installation of GCC >=
>> 6.3 (except on macOS, where the compilers from an up-to-date Xcode or Xcode
>> CLT installation should be used). #33316
>> 
>>
>> -
>>
>> One can build Sage with clang on Linux (and on freebsd). As well, I
>> think, one can build Sage with non-Xcode clang on macOS.
>>
> We do not test such configurations. When did you last test this, and on
> what platform?
>
>
> --
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> 
> .
>

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Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread Matthias Köppe

Do you know which versions of clang work if the user is using clang? 
Our compiler requirements are currently coming from 
https://docs.scipy.org/doc/scipy/dev/toolchain.html#c-language-standards, 
which unfortunately does not talk about clang.

On Tuesday, August 2, 2022 at 10:46:32 AM UTC-7 Dima Pasechnik wrote:

>
>
> On Tue, 2 Aug 2022, 18:33 Matthias Köppe,  wrote:
>
>> On Tuesday, August 2, 2022 at 10:24:39 AM UTC-7 Dima Pasechnik wrote:
>>
>>>
>>> there is a bit of vagueness there:
>>> Support for system GCC older than 6.3 dropped ¶ 
>>> 
>>>
>>> Building Sage from source now requires a system installation of GCC >= 
>>> 6.3 (except on macOS, where the compilers from an up-to-date Xcode or Xcode 
>>> CLT installation should be used). #33316 
>>> 
>>>
>>> -
>>>
>>> One can build Sage with clang on Linux (and on freebsd). As well, I 
>>> think, one can build Sage with non-Xcode clang on macOS.
>>>
>> We do not test such configurations. When did you last test this, and on 
>> what platform?
>>
>
> My point is that we do not *require* gcc on Linux.
>
> I tested Homebrew clang on macOS in some 9.6 betas, it worked after minor 
> tweaks. There was ea ticket about it:
>
> https://trac.sagemath.org/ticket/32207
>
>
>>
>> -- 
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>> "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/45ae1269-250b-4ea8-b547-54317798dde5n%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread Dima Pasechnik

On Tue, 2 Aug 2022, 18:33 Matthias Köppe,  wrote:

> On Tuesday, August 2, 2022 at 10:24:39 AM UTC-7 Dima Pasechnik wrote:
>
>>
>> there is a bit of vagueness there:
>> Support for system GCC older than 6.3 dropped ¶
>> 
>>
>> Building Sage from source now requires a system installation of GCC >=
>> 6.3 (except on macOS, where the compilers from an up-to-date Xcode or Xcode
>> CLT installation should be used). #33316
>> 
>>
>> -
>>
>> One can build Sage with clang on Linux (and on freebsd). As well, I
>> think, one can build Sage with non-Xcode clang on macOS.
>>
> We do not test such configurations. When did you last test this, and on
> what platform?
>

My point is that we do not *require* gcc on Linux.

I tested Homebrew clang on macOS in some 9.6 betas, it worked after minor
tweaks. There was ea ticket about it:

https://trac.sagemath.org/ticket/32207


>
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> 
> .
>

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Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread Matthias Köppe

On Tuesday, August 2, 2022 at 10:24:39 AM UTC-7 Dima Pasechnik wrote:

>
> there is a bit of vagueness there:
> Support for system GCC older than 6.3 dropped ¶ 
> 
>
> Building Sage from source now requires a system installation of GCC >= 6.3 
> (except on macOS, where the compilers from an up-to-date Xcode or Xcode CLT 
> installation should be used). #33316 
> 
>
> -
>
> One can build Sage with clang on Linux (and on freebsd). As well, I think, 
> one can build Sage with non-Xcode clang on macOS.
>
We do not test such configurations. When did you last test this, and on 
what platform?


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Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread Dima Pasechnik

On Tue, 2 Aug 2022, 18:17 Matthias Köppe,  wrote:

> On Tuesday, August 2, 2022 at 10:13:05 AM UTC-7 david@gmail.com wrote:
>
>> With this new beta, I see that the source code and the compiled code are
>> mixed.
>> For instance
>> sapristi:sage dcoudert$ ll src/sage/graphs/
>> total 76264
>> drwxr-xr-x  123 dcoudert  coati 3936  2 aoû 16:10 .
>> drwxr-xr-x   69 dcoudert  coati 2208  1 aoû 23:18 ..
>> drwxr-xr-x   19 dcoudert  coati  608  2 aoû 11:06 __pycache__
>> -rw-r--r--1 dcoudert  coati 1275 11 jan  2022 all.py
>> -rw-r--r--1 dcoudert  coati   63  1 aoû 23:58 asteroidal_triples.c
>> -rwxr-xr-x1 dcoudert  coati90616  2 aoû 00:13
>> asteroidal_triples.cpython-39-darwin.so
>> -rw-r--r--1 dcoudert  coati10385 25 jul 08:35
>> asteroidal_triples.pyx
>> ...
>>
>> Is this an expected behavior or is it an error ?
>> My source tree is now completely polluted. It makes it harder to find
>> source files :(
>>
>
> It's the new default
>
> https://trac.sagemath.org/wiki/ReleaseTours/sage-9.7#Editableinstallationisnowthedefault
>

there is a bit of vagueness there:

Support for system GCC older than 6.3 dropped ¶


Building Sage from source now requires a system installation of GCC >= 6.3
(except on macOS, where the compilers from an up-to-date Xcode or Xcode CLT
installation should be used). #33316


-

One can build Sage with clang on Linux (and on freebsd). As well, I think,
one can build Sage with non-Xcode clang on macOS.




>
>
>
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> 
> .
>

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Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread David Coudert

I see. Thank you for the answers.
So I will have to live with it.
Best.

> Le 2 août 2022 à 19:19, Dima Pasechnik  a écrit :
> 
> it's the -- enable-editable option which is now the default. 
> 
> One advantage is that after changing a .py file, one does not need ./sage -b
> 
> One can turn it off by running ./configure 
> 
> 
> 
> On Tue, 2 Aug 2022, 18:13 David Coudert,  > wrote:
> With this new beta, I see that the source code and the compiled code are 
> mixed.
> For instance
> sapristi:sage dcoudert$ ll src/sage/graphs/
> total 76264
> drwxr-xr-x  123 dcoudert  coati 3936  2 aoû 16:10 .
> drwxr-xr-x   69 dcoudert  coati 2208  1 aoû 23:18 ..
> drwxr-xr-x   19 dcoudert  coati  608  2 aoû 11:06 __pycache__
> -rw-r--r--1 dcoudert  coati 1275 11 jan  2022 all.py
> -rw-r--r--1 dcoudert  coati   63  1 aoû 23:58 asteroidal_triples.c
> -rwxr-xr-x1 dcoudert  coati90616  2 aoû 00:13 
> asteroidal_triples.cpython-39-darwin.so 
> 
> -rw-r--r--1 dcoudert  coati10385 25 jul 08:35 asteroidal_triples.pyx
> drwxr-xr-x   38 dcoudert  coati 1216  2 aoû 16:10 base
> -rw-r--r--1 dcoudert  coati91222 31 jul 08:47 bipartite_graph.py
> -rw-r--r--1 dcoudert  coati   568709  1 aoû 23:58 bliss.cpp
> -rwxr-xr-x1 dcoudert  coati   142952  2 aoû 00:14 
> bliss.cpython-39-darwin.so 
> -rw-r--r--1 dcoudert  coati34879 25 jul 08:35 bliss.pyx
> -rw-r--r--1 dcoudert  coati  1067208  1 aoû 23:58 centrality.c
> -rwxr-xr-x1 dcoudert  coati   184776  2 aoû 00:14 
> centrality.cpython-39-darwin.so 
> -rwxr-xr-x1 dcoudert  coati34829 25 jul 08:35 centrality.pyx
> -rw-r--r--1 dcoudert  coati   765584  1 aoû 23:58 chrompoly.c
> -rwxr-xr-x1 dcoudert  coati   234744  2 aoû 00:14 
> chrompoly.cpython-39-darwin.so 
> -rw-r--r--1 dcoudert  coati20227 25 jul 08:35 chrompoly.pyx
> ...
> 
> 
> Is this an expected behavior or is it an error ?
> My source tree is now completely polluted. It makes it harder to find source 
> files :(
> 
> 
> 
> 
>> Le 1 août 2022 à 23:09, Volker Braun > > a écrit :
>> 
>> 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 
>> 
>> 
>> cd1e2b13af (HEAD -> develop, tag: 9.7.beta7, trac/develop) Updated SageMath 
>> version to 9.7.beta7
>> c94df55711 Trac #34254: 32-bit failure in src/sage/symbolic/expression.pyx
>> 20dea3b0a1 Trac #34169: Fix docstring markup in sage/interacts and sage/rings
>> c29832b57c Trac #34165: Fix docstring markup in 
>> sage/tests/book_stein_modform.py
>> a129ff5fa2 Trac #34162: Fix docstring markup in sage/doctest
>> a1c99f1a13 Trac #34161: Fix docstring markup in sage/databases
>> 83ba832260 Trac #34159: Fix docstring markup in sage/modular
>> e3d426a9ea Trac #34158: Fix docstring markup in sage/manifolds
>> 5b15182517 Trac #34156: Fix docstring markup in sage/game_theory
>> 252d1327ec Trac #34153: pycodestyle cleanup in 
>> sage/geometry/hyperplane_arrangement/hyperplane.py
>> f75cc20505 Trac #34146: Modernize super in coding/
>> 59c889ef3d Trac #34143: three-argument pow() on integers returns IntegerMod
>> c7817820c0 Trac #34101: cutwidth_dyn use after free
>> 9bc7be1aaa Trac #34086: E231 in src/sage/graphs/strongly_regular_db.pyx - 
>> part 1
>> a89efd4a28 Trac #34079: pycodestyle cleanup in 6 files of src/sage/graphs/
>> 3cd360b4f5 Trac #34078: pycodestyle cleanup in src/sage/graphs/graph_plot.py
>> fac74d59ab Trac #34077: pycodestyle cleanup in src/sage/graphs/graph_input.py
>> 4c67a04450 Trac #34073: pycodestyle cleanup in 
>> src/sage/graphs/graph_coloring.pyx
>> ead25a50eb Trac #34068: pycodestyle cleanup in 
>> src/sage/graphs/connectivity.pyx
>> 288834efb2 Trac #33971: Height of a dynamical system is wrong
>> c3f96d4208 Trac #22857: Using symbolic variables in domain 'positive' makes 
>> Sage crash
>> c89955d2e5 Trac #34227: Compute the similarity class type of a given matrix; 
>> compute invariant subspace generating function from similarity class type
>> 8b0adc2da8 Trac #34218: Implement longest_increasing_subsequence_number
>> b0107b91e9 Trac #34216: configure: Use 
>> --with-system-{gfortran,openssl,python3}=force on Cygwin
>> d9568109f7 Trac #34214: Faster version of 
>> longest_increasing_subsequence_length
>> 1b0314ac79 Trac #34208: Remove package sip
>> 79199e67bb Trac #34200: Add importlib_metadata to Sphinx's dependencies
>> 7ec4ff6b19 Trac #34189: Remove imports from sage.all and sage.rings.all in 
>> sage.rings
>> aae8d2dd33 Trac #34187: Remove src/sage/__init__.py
>> 5bfd77d7d3 Trac #34177: Update setuptools to 63.2.0
>> 0e5ef88d17 Trac #34176: update curl to version

Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread Dima Pasechnik

it's the -- enable-editable option which is now the default.

One advantage is that after changing a .py file, one does not need ./sage -b

One can turn it off by running ./configure



On Tue, 2 Aug 2022, 18:13 David Coudert,  wrote:

> With this new beta, I see that the source code and the compiled code are
> mixed.
> For instance
> sapristi:sage dcoudert$ ll src/sage/graphs/
> total 76264
> drwxr-xr-x  123 dcoudert  coati 3936  2 aoû 16:10 .
> drwxr-xr-x   69 dcoudert  coati 2208  1 aoû 23:18 ..
> drwxr-xr-x   19 dcoudert  coati  608  2 aoû 11:06 __pycache__
> -rw-r--r--1 dcoudert  coati 1275 11 jan  2022 all.py
> -rw-r--r--1 dcoudert  coati   63  1 aoû 23:58 asteroidal_triples.c
> -rwxr-xr-x1 dcoudert  coati90616  2 aoû 00:13
> asteroidal_triples.cpython-39-darwin.so
> -rw-r--r--1 dcoudert  coati10385 25 jul 08:35
> asteroidal_triples.pyx
> drwxr-xr-x   38 dcoudert  coati 1216  2 aoû 16:10 base
> -rw-r--r--1 dcoudert  coati91222 31 jul 08:47 bipartite_graph.py
> -rw-r--r--1 dcoudert  coati   568709  1 aoû 23:58 bliss.cpp
> -rwxr-xr-x1 dcoudert  coati   142952  2 aoû 00:14
> bliss.cpython-39-darwin.so
> -rw-r--r--1 dcoudert  coati34879 25 jul 08:35 bliss.pyx
> -rw-r--r--1 dcoudert  coati  1067208  1 aoû 23:58 centrality.c
> -rwxr-xr-x1 dcoudert  coati   184776  2 aoû 00:14
> centrality.cpython-39-darwin.so
> -rwxr-xr-x1 dcoudert  coati34829 25 jul 08:35 centrality.pyx
> -rw-r--r--1 dcoudert  coati   765584  1 aoû 23:58 chrompoly.c
> -rwxr-xr-x1 dcoudert  coati   234744  2 aoû 00:14
> chrompoly.cpython-39-darwin.so
> -rw-r--r--1 dcoudert  coati20227 25 jul 08:35 chrompoly.pyx
> ...
>
>
> Is this an expected behavior or is it an error ?
> My source tree is now completely polluted. It makes it harder to find
> source files :(
>
>
>
>
> Le 1 août 2022 à 23:09, Volker Braun  a écrit :
>
> 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
>
> cd1e2b13af (HEAD -> develop, tag: 9.7.beta7, trac/develop) Updated
> SageMath version to 9.7.beta7
> c94df55711 Trac #34254: 32-bit failure in src/sage/symbolic/expression.pyx
> 20dea3b0a1 Trac #34169: Fix docstring markup in sage/interacts and
> sage/rings
> c29832b57c Trac #34165: Fix docstring markup in
> sage/tests/book_stein_modform.py
> a129ff5fa2 Trac #34162: Fix docstring markup in sage/doctest
> a1c99f1a13 Trac #34161: Fix docstring markup in sage/databases
> 83ba832260 Trac #34159: Fix docstring markup in sage/modular
> e3d426a9ea Trac #34158: Fix docstring markup in sage/manifolds
> 5b15182517 Trac #34156: Fix docstring markup in sage/game_theory
> 252d1327ec Trac #34153: pycodestyle cleanup in
> sage/geometry/hyperplane_arrangement/hyperplane.py
> f75cc20505 Trac #34146: Modernize super in coding/
> 59c889ef3d Trac #34143: three-argument pow() on integers returns IntegerMod
> c7817820c0 Trac #34101: cutwidth_dyn use after free
> 9bc7be1aaa Trac #34086: E231 in src/sage/graphs/strongly_regular_db.pyx -
> part 1
> a89efd4a28 Trac #34079: pycodestyle cleanup in 6 files of src/sage/graphs/
> 3cd360b4f5 Trac #34078: pycodestyle cleanup in
> src/sage/graphs/graph_plot.py
> fac74d59ab Trac #34077: pycodestyle cleanup in
> src/sage/graphs/graph_input.py
> 4c67a04450 Trac #34073: pycodestyle cleanup in
> src/sage/graphs/graph_coloring.pyx
> ead25a50eb Trac #34068: pycodestyle cleanup in
> src/sage/graphs/connectivity.pyx
> 288834efb2 Trac #33971: Height of a dynamical system is wrong
> c3f96d4208 Trac #22857: Using symbolic variables in domain 'positive'
> makes Sage crash
> c89955d2e5 Trac #34227: Compute the similarity class type of a given
> matrix; compute invariant subspace generating function from similarity
> class type
> 8b0adc2da8 Trac #34218: Implement longest_increasing_subsequence_number
> b0107b91e9 Trac #34216: configure: Use
> --with-system-{gfortran,openssl,python3}=force on Cygwin
> d9568109f7 Trac #34214: Faster version of
> longest_increasing_subsequence_length
> 1b0314ac79 Trac #34208: Remove package sip
> 79199e67bb Trac #34200: Add importlib_metadata to Sphinx's dependencies
> 7ec4ff6b19 Trac #34189: Remove imports from sage.all and sage.rings.all in
> sage.rings
> aae8d2dd33 Trac #34187: Remove src/sage/__init__.py
> 5bfd77d7d3 Trac #34177: Update setuptools to 63.2.0
> 0e5ef88d17 Trac #34176: update curl to version 7.84
> 9b6a99a720 Trac #33817: GH Actions: Add test of the modularized
> distributions
> fd93be8851 Trac #32406: Make "./configure --enable-editable" the default
> dcd778b1a9 Trac #31568: Add commands "sage --lldb", "sage -t --lldb"
> 7f0a555ccb Trac #31451: Faster version of longest_increasing_subsequences
> b5baa7d3f9 Trac #34115: tox.yml: Refactor using reusable workflows, update
> Linux platforms
> be272221fa Trac #33627: Remove sage-gdb-commands from src/bin
> c19c47fd63 Trac #34174: insufficient

Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread Matthias Köppe

On Tuesday, August 2, 2022 at 10:13:05 AM UTC-7 david@gmail.com wrote:

> With this new beta, I see that the source code and the compiled code are 
> mixed.
> For instance
> sapristi:sage dcoudert$ ll src/sage/graphs/
> total 76264
> drwxr-xr-x  123 dcoudert  coati 3936  2 aoû 16:10 .
> drwxr-xr-x   69 dcoudert  coati 2208  1 aoû 23:18 ..
> drwxr-xr-x   19 dcoudert  coati  608  2 aoû 11:06 __pycache__
> -rw-r--r--1 dcoudert  coati 1275 11 jan  2022 all.py
> -rw-r--r--1 dcoudert  coati   63  1 aoû 23:58 asteroidal_triples.c
> -rwxr-xr-x1 dcoudert  coati90616  2 aoû 00:13 
> asteroidal_triples.cpython-39-darwin.so
> -rw-r--r--1 dcoudert  coati10385 25 jul 08:35 
> asteroidal_triples.pyx
> ...
>
> Is this an expected behavior or is it an error ?
> My source tree is now completely polluted. It makes it harder to find 
> source files :(
>

It's the new default
https://trac.sagemath.org/wiki/ReleaseTours/sage-9.7#Editableinstallationisnowthedefault

 

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Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread David Coudert

With this new beta, I see that the source code and the compiled code are mixed.
For instance
sapristi:sage dcoudert$ ll src/sage/graphs/
total 76264
drwxr-xr-x  123 dcoudert  coati 3936  2 aoû 16:10 .
drwxr-xr-x   69 dcoudert  coati 2208  1 aoû 23:18 ..
drwxr-xr-x   19 dcoudert  coati  608  2 aoû 11:06 __pycache__
-rw-r--r--1 dcoudert  coati 1275 11 jan  2022 all.py
-rw-r--r--1 dcoudert  coati   63  1 aoû 23:58 asteroidal_triples.c
-rwxr-xr-x1 dcoudert  coati90616  2 aoû 00:13 
asteroidal_triples.cpython-39-darwin.so
-rw-r--r--1 dcoudert  coati10385 25 jul 08:35 asteroidal_triples.pyx
drwxr-xr-x   38 dcoudert  coati 1216  2 aoû 16:10 base
-rw-r--r--1 dcoudert  coati91222 31 jul 08:47 bipartite_graph.py
-rw-r--r--1 dcoudert  coati   568709  1 aoû 23:58 bliss.cpp
-rwxr-xr-x1 dcoudert  coati   142952  2 aoû 00:14 bliss.cpython-39-darwin.so
-rw-r--r--1 dcoudert  coati34879 25 jul 08:35 bliss.pyx
-rw-r--r--1 dcoudert  coati  1067208  1 aoû 23:58 centrality.c
-rwxr-xr-x1 dcoudert  coati   184776  2 aoû 00:14 
centrality.cpython-39-darwin.so
-rwxr-xr-x1 dcoudert  coati34829 25 jul 08:35 centrality.pyx
-rw-r--r--1 dcoudert  coati   765584  1 aoû 23:58 chrompoly.c
-rwxr-xr-x1 dcoudert  coati   234744  2 aoû 00:14 
chrompoly.cpython-39-darwin.so
-rw-r--r--1 dcoudert  coati20227 25 jul 08:35 chrompoly.pyx
...


Is this an expected behavior or is it an error ?
My source tree is now completely polluted. It makes it harder to find source 
files :(




> Le 1 août 2022 à 23:09, Volker Braun  a écrit :
> 
> 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
> 
> cd1e2b13af (HEAD -> develop, tag: 9.7.beta7, trac/develop) Updated SageMath 
> version to 9.7.beta7
> c94df55711 Trac #34254: 32-bit failure in src/sage/symbolic/expression.pyx
> 20dea3b0a1 Trac #34169: Fix docstring markup in sage/interacts and sage/rings
> c29832b57c Trac #34165: Fix docstring markup in 
> sage/tests/book_stein_modform.py
> a129ff5fa2 Trac #34162: Fix docstring markup in sage/doctest
> a1c99f1a13 Trac #34161: Fix docstring markup in sage/databases
> 83ba832260 Trac #34159: Fix docstring markup in sage/modular
> e3d426a9ea Trac #34158: Fix docstring markup in sage/manifolds
> 5b15182517 Trac #34156: Fix docstring markup in sage/game_theory
> 252d1327ec Trac #34153: pycodestyle cleanup in 
> sage/geometry/hyperplane_arrangement/hyperplane.py
> f75cc20505 Trac #34146: Modernize super in coding/
> 59c889ef3d Trac #34143: three-argument pow() on integers returns IntegerMod
> c7817820c0 Trac #34101: cutwidth_dyn use after free
> 9bc7be1aaa Trac #34086: E231 in src/sage/graphs/strongly_regular_db.pyx - 
> part 1
> a89efd4a28 Trac #34079: pycodestyle cleanup in 6 files of src/sage/graphs/
> 3cd360b4f5 Trac #34078: pycodestyle cleanup in src/sage/graphs/graph_plot.py
> fac74d59ab Trac #34077: pycodestyle cleanup in src/sage/graphs/graph_input.py
> 4c67a04450 Trac #34073: pycodestyle cleanup in 
> src/sage/graphs/graph_coloring.pyx
> ead25a50eb Trac #34068: pycodestyle cleanup in 
> src/sage/graphs/connectivity.pyx
> 288834efb2 Trac #33971: Height of a dynamical system is wrong
> c3f96d4208 Trac #22857: Using symbolic variables in domain 'positive' makes 
> Sage crash
> c89955d2e5 Trac #34227: Compute the similarity class type of a given matrix; 
> compute invariant subspace generating function from similarity class type
> 8b0adc2da8 Trac #34218: Implement longest_increasing_subsequence_number
> b0107b91e9 Trac #34216: configure: Use 
> --with-system-{gfortran,openssl,python3}=force on Cygwin
> d9568109f7 Trac #34214: Faster version of 
> longest_increasing_subsequence_length
> 1b0314ac79 Trac #34208: Remove package sip
> 79199e67bb Trac #34200: Add importlib_metadata to Sphinx's dependencies
> 7ec4ff6b19 Trac #34189: Remove imports from sage.all and sage.rings.all in 
> sage.rings
> aae8d2dd33 Trac #34187: Remove src/sage/__init__.py
> 5bfd77d7d3 Trac #34177: Update setuptools to 63.2.0
> 0e5ef88d17 Trac #34176: update curl to version 7.84
> 9b6a99a720 Trac #33817: GH Actions: Add test of the modularized distributions
> fd93be8851 Trac #32406: Make "./configure --enable-editable" the default
> dcd778b1a9 Trac #31568: Add commands "sage --lldb", "sage -t --lldb"
> 7f0a555ccb Trac #31451: Faster version of longest_increasing_subsequences
> b5baa7d3f9 Trac #34115: tox.yml: Refactor using reusable workflows, update 
> Linux platforms
> be272221fa Trac #33627: Remove sage-gdb-commands from src/bin
> c19c47fd63 Trac #34174: insufficient precision in scaling elliptic curves 
> over number fields by units
> aa8a4647f9 Trac #34172: Fix docstring markup in sage/groups and sage/misc
> 4142099591 Trac #34168: Fix docstring markup in sage/categories
> e9be1728bb Trac #34166: Fix docstring markup in sage/tests except 
>

Re: [sage-release] Sage 9.7.beta7 released

2022-08-02 Thread Thierry Dumont


On Debian TESTING (Amd 64):

-installation ok.

- make ptestlong:
2 tests failed:

67134 src/sage/combinat/nu_dyck_word.py
[179 tests, 1.17 s]
sage -t --long --warn-long 34.1 
--random-seed=3139455004425827870060396354068704

67134 src/sage/libs/gap/test_long.py
[6 tests, 34.43 s]
--
sage -t --long --warn-long 34.1 
--random-seed=313945500442582787006039635406870467134 
src/sage/tests/cmdline.py  # 1 doctest failed

--


and:

7134 src/sage/libs/gap/test_long.py
[6 tests, 34.43 s]
--
sage -t --long --warn-long 34.1 
--random-seed=313945500442582787006039635406870467134 
src/sage/tests/cmdline.py  # 1 doctest failed

--

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Re: [sage-release] Sage 9.7.beta7 released

2022-08-01 Thread G. M.-S.

This is on Apple Silicon Macs with Homebrew up to date (make and make pytest
 and  make ptestlong).

Nothing new:

On macOS 12.5 (Monterey) with Xcode 13.4.1:  no problems.

On macOS 11.6.8 (Big Sur) with Xcode 13.2.1:  make ptestlong gives the
usual matrix_gf2e_dense.pyx error (see
https://trac.sagemath.org/ticket/33212).

Remarks for interested people:

1) As usual, the following
--
sage -t --long --warn-long 52.1
--random-seed=324722062500301071147824685967887717794
src/sage/interfaces/expect.py  # 2 doctests failed
--
eventually succeeds when tried alone enough times.

2)
The following
% brew uninstall --ignore-dependencies jpeg-xl
% brew install jpeg-xl
seemed necessary on one machine because of a persistent error when
installing sagemath_doc_html-none (details on request).

Guillermo

On Mon, 1 Aug 2022 at 23:09, 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
>
> cd1e2b13af (HEAD -> develop, tag: 9.7.beta7, trac/develop) Updated
> SageMath version to 9.7.beta7
> c94df55711 Trac #34254: 32-bit failure in src/sage/symbolic/expression.pyx
> 20dea3b0a1 Trac #34169: Fix docstring markup in sage/interacts and
> sage/rings
> c29832b57c Trac #34165: Fix docstring markup in
> sage/tests/book_stein_modform.py
> a129ff5fa2 Trac #34162: Fix docstring markup in sage/doctest
> a1c99f1a13 Trac #34161: Fix docstring markup in sage/databases
> 83ba832260 Trac #34159: Fix docstring markup in sage/modular
> e3d426a9ea Trac #34158: Fix docstring markup in sage/manifolds
> 5b15182517 Trac #34156: Fix docstring markup in sage/game_theory
> 252d1327ec Trac #34153: pycodestyle cleanup in
> sage/geometry/hyperplane_arrangement/hyperplane.py
> f75cc20505 Trac #34146: Modernize super in coding/
> 59c889ef3d Trac #34143: three-argument pow() on integers returns IntegerMod
> c7817820c0 Trac #34101: cutwidth_dyn use after free
> 9bc7be1aaa Trac #34086: E231 in src/sage/graphs/strongly_regular_db.pyx -
> part 1
> a89efd4a28 Trac #34079: pycodestyle cleanup in 6 files of src/sage/graphs/
> 3cd360b4f5 Trac #34078: pycodestyle cleanup in
> src/sage/graphs/graph_plot.py
> fac74d59ab Trac #34077: pycodestyle cleanup in
> src/sage/graphs/graph_input.py
> 4c67a04450 Trac #34073: pycodestyle cleanup in
> src/sage/graphs/graph_coloring.pyx
> ead25a50eb Trac #34068: pycodestyle cleanup in
> src/sage/graphs/connectivity.pyx
> 288834efb2 Trac #33971: Height of a dynamical system is wrong
> c3f96d4208 Trac #22857: Using symbolic variables in domain 'positive'
> makes Sage crash
> c89955d2e5 Trac #34227: Compute the similarity class type of a given
> matrix; compute invariant subspace generating function from similarity
> class type
> 8b0adc2da8 Trac #34218: Implement longest_increasing_subsequence_number
> b0107b91e9 Trac #34216: configure: Use
> --with-system-{gfortran,openssl,python3}=force on Cygwin
> d9568109f7 Trac #34214: Faster version of
> longest_increasing_subsequence_length
> 1b0314ac79 Trac #34208: Remove package sip
> 79199e67bb Trac #34200: Add importlib_metadata to Sphinx's dependencies
> 7ec4ff6b19 Trac #34189: Remove imports from sage.all and sage.rings.all in
> sage.rings
> aae8d2dd33 Trac #34187: Remove src/sage/__init__.py
> 5bfd77d7d3 Trac #34177: Update setuptools to 63.2.0
> 0e5ef88d17 Trac #34176: update curl to version 7.84
> 9b6a99a720 Trac #33817: GH Actions: Add test of the modularized
> distributions
> fd93be8851 Trac #32406: Make "./configure --enable-editable" the default
> dcd778b1a9 Trac #31568: Add commands "sage --lldb", "sage -t --lldb"
> 7f0a555ccb Trac #31451: Faster version of longest_increasing_subsequences
> b5baa7d3f9 Trac #34115: tox.yml: Refactor using reusable workflows, update
> Linux platforms
> be272221fa Trac #33627: Remove sage-gdb-commands from src/bin
> c19c47fd63 Trac #34174: insufficient precision in scaling elliptic curves
> over number fields by units
> aa8a4647f9 Trac #34172: Fix docstring markup in sage/groups and sage/misc
> 4142099591 Trac #34168: Fix docstring markup in sage/categories
> e9be1728bb Trac #34166: Fix docstring markup in sage/tests except
> sage/tests/book_stein_modform.py
> 6e41b53b09 Trac #34164: Fix docstring markup in sage/plot and sage/graphs
> b03229e112 Trac #34163: Fix docstring markup in sage/interfaces
> 46849b8d41 Trac #34160: Fix docstring markup in sage/schemes
> 984137bbb8 Trac #34155: OpenSSL 3.0.5 security update
> ced8f29e11 Trac #34151: get rid of Oops messages in quadratic forms
> b0456638af Trac #34149: make documentation building compatible with sphinx
> 5
> 07d4b909f0 Trac #34105: ZeroDivisionError while reducing a polynomial
> w.r.t. the zero ideal
> db21903ace Trac #33798: Implement the Links-Gould polynomial invariant for
> links
> 04ad7f9577 Trac #33705:

[sage-release] Sage 9.7.beta7 released

2022-08-01 Thread Volker Braun

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

cd1e2b13af (HEAD -> develop, tag: 9.7.beta7, trac/develop) Updated SageMath 
version to 9.7.beta7
c94df55711 Trac #34254: 32-bit failure in src/sage/symbolic/expression.pyx
20dea3b0a1 Trac #34169: Fix docstring markup in sage/interacts and 
sage/rings
c29832b57c Trac #34165: Fix docstring markup in 
sage/tests/book_stein_modform.py
a129ff5fa2 Trac #34162: Fix docstring markup in sage/doctest
a1c99f1a13 Trac #34161: Fix docstring markup in sage/databases
83ba832260 Trac #34159: Fix docstring markup in sage/modular
e3d426a9ea Trac #34158: Fix docstring markup in sage/manifolds
5b15182517 Trac #34156: Fix docstring markup in sage/game_theory
252d1327ec Trac #34153: pycodestyle cleanup in 
sage/geometry/hyperplane_arrangement/hyperplane.py
f75cc20505 Trac #34146: Modernize super in coding/
59c889ef3d Trac #34143: three-argument pow() on integers returns IntegerMod
c7817820c0 Trac #34101: cutwidth_dyn use after free
9bc7be1aaa Trac #34086: E231 in src/sage/graphs/strongly_regular_db.pyx - 
part 1
a89efd4a28 Trac #34079: pycodestyle cleanup in 6 files of src/sage/graphs/
3cd360b4f5 Trac #34078: pycodestyle cleanup in src/sage/graphs/graph_plot.py
fac74d59ab Trac #34077: pycodestyle cleanup in 
src/sage/graphs/graph_input.py
4c67a04450 Trac #34073: pycodestyle cleanup in 
src/sage/graphs/graph_coloring.pyx
ead25a50eb Trac #34068: pycodestyle cleanup in 
src/sage/graphs/connectivity.pyx
288834efb2 Trac #33971: Height of a dynamical system is wrong
c3f96d4208 Trac #22857: Using symbolic variables in domain 'positive' makes 
Sage crash
c89955d2e5 Trac #34227: Compute the similarity class type of a given 
matrix; compute invariant subspace generating function from similarity 
class type
8b0adc2da8 Trac #34218: Implement longest_increasing_subsequence_number
b0107b91e9 Trac #34216: configure: Use 
--with-system-{gfortran,openssl,python3}=force on Cygwin
d9568109f7 Trac #34214: Faster version of 
longest_increasing_subsequence_length
1b0314ac79 Trac #34208: Remove package sip
79199e67bb Trac #34200: Add importlib_metadata to Sphinx's dependencies
7ec4ff6b19 Trac #34189: Remove imports from sage.all and sage.rings.all in 
sage.rings
aae8d2dd33 Trac #34187: Remove src/sage/__init__.py
5bfd77d7d3 Trac #34177: Update setuptools to 63.2.0
0e5ef88d17 Trac #34176: update curl to version 7.84
9b6a99a720 Trac #33817: GH Actions: Add test of the modularized 
distributions
fd93be8851 Trac #32406: Make "./configure --enable-editable" the default
dcd778b1a9 Trac #31568: Add commands "sage --lldb", "sage -t --lldb"
7f0a555ccb Trac #31451: Faster version of longest_increasing_subsequences
b5baa7d3f9 Trac #34115: tox.yml: Refactor using reusable workflows, update 
Linux platforms
be272221fa Trac #33627: Remove sage-gdb-commands from src/bin
c19c47fd63 Trac #34174: insufficient precision in scaling elliptic curves 
over number fields by units
aa8a4647f9 Trac #34172: Fix docstring markup in sage/groups and sage/misc
4142099591 Trac #34168: Fix docstring markup in sage/categories
e9be1728bb Trac #34166: Fix docstring markup in sage/tests except 
sage/tests/book_stein_modform.py
6e41b53b09 Trac #34164: Fix docstring markup in sage/plot and sage/graphs
b03229e112 Trac #34163: Fix docstring markup in sage/interfaces
46849b8d41 Trac #34160: Fix docstring markup in sage/schemes
984137bbb8 Trac #34155: OpenSSL 3.0.5 security update
ced8f29e11 Trac #34151: get rid of Oops messages in quadratic forms
b0456638af Trac #34149: make documentation building compatible with sphinx 5
07d4b909f0 Trac #34105: ZeroDivisionError while reducing a polynomial 
w.r.t. the zero ideal
db21903ace Trac #33798: Implement the Links-Gould polynomial invariant for 
links
04ad7f9577 Trac #33705: "make doc-clean" should remove inventory, doctrees
977e691dc1 Trac #33636: replace loadable_module_extension() by 
importlib.machinery.EXTENSION_SUFFIXES
c744d7c09c Trac #29097: build/make/Makefile.in: Rename make targets 
SPKG-clean to SPKG-uninstall
8312ee1e90 Trac #33530: Upgrade ipython to 8.x
067a66c7e9 Trac #33428: prompt_toolkit 3.0.25+ breaks Ctrl-C
79ed9e5ddb Trac #33160: update Singular to 4.3.1
4cc4817aeb Trac #32088: gfan testsuite hangs on 32bit
10247d5f2a Trac #31049: "setup.py develop" rewrites the installed 
sage-version.sh as if it is a Python script
7f7149489c (tag: 9.7.beta6) Updated SageMath version to 9.7.beta6

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