Sage 9.2.beta8 released

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Volker Braun

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Aug 10, 2020, 6:51:35 PM8/10/20
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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 


415221a9a8 (trac/develop, tag: 9.2.beta8) Updated SageMath version to 9.2.beta8
ab502c6901 Trac #30287: sage.tensor.modules.free_module_basis: Add testsuite
f148ee505b Trac #30237: Make .coxeter_matrix() return a CoxeterMatrix for coxeter3-implemented groups
075edbb1f6 Trac #30177: build/bin/sage-system-python: Improve check for a suitable python
2f73418deb Trac #30159: Adding new small graph structures
b78fa7bc86 Trac #30318: Dot and cross products along a differentiable map
8f4e3779f6 Trac #30291: Scalar Field Arithmetics: Trivial Cases
d423d08e7d Trac #30280: Immutability of Affine Connections
e336f00ef3 Trac #30194: Extend FreeModule factory to construction of FiniteRankFreeModule and CombinatorialFreeModule
2c85de4715 Trac #29701: Replace use of module_list and OptionalExtension by extending find_python_sources
d600162861 Trac #29205: character art fails for LieAlgebra elements
05d310c5cf Trac #30314: p-adic nth-root fails for some extensions
315bde2aec Trac #30289: Error in display of a continuous map between open intervals
7190161153 Trac #30288: Immutability for Sections
a9e4141b37 Trac #30285: Affine Connection with Copy
61d70b1f6d Trac #30282: Make symmetrica/spkg-configure.m4 respect quiet mode
81635f190c Trac #30279: Update FAQ
70d7d21bd3 Trac #30274: Immutability of Tensor Fields
35d9d52b25 Trac #30270: Random failure in number_field_ideal_rel.py
7b224d83c0 Trac #30266: Immutability for scalar fields
b679a2d444 Trac #30255: FiniteRankFreeModule: Move all module identifications to methods exterior_power, dual_exterior_power, tensor_module
dfdae6fa93 Trac #30176: Update matplotlib to 3.3
ed79ba3a3f Trac #30248: Normaliz backend is broken with double description input
f55701e735 Trac #28197: upgrade to ipython 7
663c71bb89 Trac #30299: Minimal fix for broken jupyter notebook
775cce3cf3 Trac #3360: Upgrade sympow to 2.023.6 (for GCC 10 support)
85dbda0b65 Trac #30167: Allow Coxeter groups implemented with coxeter3 to respect the relabelling of a CartanType
f7e1cca52e Trac #30160: Deprecate "sage --ba-force"
29cee91214 Trac #30136: Three.js: Examples for documentation need online=True
f48b893d25 Trac #30119: Implement functions to construct unicode sub/superscripts from integers
bb3fd3963c Trac #27895: Add custom bounding box for matrix_plot
a10868b3bd Trac #30267: Coercion via restriction of chart functions
8a544963b1 Trac #30254: TensorFreeModule._an_element_: Create a default basis in the base module if necessary
2c0efbdfa4 Trac #30253: Coset graph of linear codes
4f0836fc14 Trac #30250: FiniteRankFreeModule: Simplify unique representation code for dependent modules
9911c15488 Trac #30227: Use both SINGULAR_INCDIR and SINGULAR_CFLAGS
760b7d8daf Trac #30225: Fix deprecation warnings when unpickling pynac objects with Python 3.8
26f3a5e7b8 Trac #30224: Fix configure quiet mode as it lets a few things through
8a015f485a Trac #30208: List Assignment for Bundle Connections
71b530802d Trac #30181: Immutable elements of FreeModuleTensor
7579d4e363 Trac #30169: FiniteRankFreeModule needs __classcall__
4fbd27b488 Trac #29825: Clean-up for src/bin/sage-env, move src/bin/sage-clone-source, src/bin/sage-sdist to build/bin
e9c25be297 Trac #22760: Add support for __matmul__ in the coercion model
31bc43bf8c Trac #20970: Gabidulin Codes
b539712d44 Trac #30231: Fix gp2c spkg-configure
34e01d1ef4 Trac #29766: Upgrade NumPy to 1.19.1, scipy to 1.5.2, networkx to 2.4, add pybind11 package
3925b0f008 Trac #30230: Fix docstrings in sage/coding/linear_rank_metric.py
83caa4befa (tag: 9.2.beta7) Updated SageMath version to 9.2.beta7

Emmanuel Charpentier

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Aug 11, 2020, 7:39:38 AM8/11/20
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On Debian testing running on core i7 + 16 GB RAM, upgrading 9.2.beta7 configured for use of all possible system libraries an runningptestlong gets me the same transient an same three permanent failures already reported for 9.2.beta7 and 9.2.beta5 :

sage -t --long --warn-long 175.4 --random-seed=0 src/sage/tests/parigp.py  # Timed out
sage -t --long --warn-long 175.4 --random-seed=0 src/sage/rings/complex_arb.pyx  # 6 doctests failed
sage -t --long --warn-long 175.4 --random-seed=0 src/sage/tests/gap_packages.py  # 1 doctest failed
sage -t --long --warn-long 175.4 --random-seed=0 src/sage/rings/real_arb.pyx  # 2 doctests failed

HTH,

Emmanuel Charpentier

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Aug 11, 2020, 11:39:29 AM8/11/20
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Damn !

This release breaks sage-shell-mode support for a sage session into emacs. After starting an emacs session, I get the normal banner and a normal prompt. A little while after that (about 0.5 to 1 second), a warning WARNING: your terminal doesn't support cursor position requests (CPR). appears immediately below the banner and above the prompt, then the cursor goes right to the right margin (i. e. in the right scrollbar).

I still can type Sage code, which appears at the left margin on the line immediately below the prompt. Typing <Return> displays a continuation prompt (.....:) 7 spaces,, then my code,which gets executed and the answer printed on tjhe line below the continuation prompt. Example :

┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.2.beta8, Release Date: 2020-08-10               │
│ Using Python 3.7.3. Type "help()" for help.                        │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable.     ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
WARNING: your terminal doesn't support cursor position requests (CPR).
sage: sage:                                                                      
....:       1+1                                                                  
2
sage:

No error message appears in the terminal window from which I launched emacs ; nothing unusual in the *Messages* buffer either.

I’m stymied…

Dima Pasechnik

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Aug 11, 2020, 11:47:00 AM8/11/20
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maybe,
https://stackoverflow.com/questions/60534394/ipython-warning-in-emacs-your-terminal-doesnt-support-cursor-position-requests
?
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Emmanuel Charpentier

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Aug 11, 2020, 11:47:19 AM8/11/20
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I I filed [this issue](https://github.com/sagemath/sage-shell-mode/issues/53) against `sage-shell-mode` on Github.

HTH,

Dima Pasechnik

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Aug 11, 2020, 11:48:43 AM8/11/20
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it is probably a newer iPython that gives this, nothing Sage-specific it seems.
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Matthias Köppe

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Aug 11, 2020, 11:53:24 AM8/11/20
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The solution in that thread, using "--simple-prompt", is of course not support by sage. 
There's already a ticket for that: https://trac.sagemath.org/ticket/25363
which needs work
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Matthias Köppe

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Aug 11, 2020, 11:54:37 AM8/11/20
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Yes, 9.2.beta8 did the overdue update from ipython 5 to 7 in https://trac.sagemath.org/ticket/28197
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Emmanuel Charpentier

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Aug 11, 2020, 12:04:01 PM8/11/20
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FWIW, i left a comment there pointing to the present thread. I do not know how to re-open a closed ticket...

Emmanuel Charpentier

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Aug 11, 2020, 12:20:00 PM8/11/20
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Further bad news : this also somehow breaks the communication between emacs and sage :

  • quit in the sage session never returns ; you have to kill emacs to get your damn prompt back…

  • Any attempt to use sage from an org-mode document never returns : same issue…

HTH,

John H Palmieri

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Aug 11, 2020, 12:26:04 PM8/11/20
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I had no experience with sage-shell-mode until about 5 minutes ago, but it works for me, except for some weird artifacts when it reprints what I typed at the command line:

┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.2.beta8, Release Date: 2020-08-10               │
│ Using Python 3.7.3. Type "help()" for help.                        │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable.     ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
sage: Sq(3)
SSSqqq(((333)))))))))
Sq(3)
sage: Sq(3)*Sq(4)
SSSSqqqq((((3333))))****SSSSqqqq((((4444))))))))))))
Sq(7)
sage: quit()
qqqqquuuuuiiiiittttt((((()))))))))))))))
Exiting Sage (CPU time 0m0.31s, Wall time 0m47.95s).

Process Sage finished

Emmanuel Charpentier

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Aug 11, 2020, 12:32:20 PM8/11/20
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John, what is your current emacs version ?

John H Palmieri

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Aug 11, 2020, 12:38:00 PM8/11/20
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It's version 26.3. I also just quit emacs and restarted, and now I'm having the same problems you were having. Modifying 'src/bin/sage' to accept a '--simple-prompt' option and then using that seems to work.

Emmanuel Charpentier

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Aug 11, 2020, 12:44:15 PM8/11/20
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Le mardi 11 août 2020 18:38:00 UTC+2, John H Palmieri a écrit :
It's version 26.3. I also just quit emacs and restarted, and now I'm having the same problems you were having. Modifying 'src/bin/sage' to accept a '--simple-prompt'

How do you do that ? Care to post a diff (possibly in Trac#25363 ?



John H Palmieri

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Aug 11, 2020, 12:54:30 PM8/11/20
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Done. I haven't figured out the sage-shell customizations so that it automatically uses '--simple-prompt' whenever you ask it to start Sage, but that's a separate problem.

Matthias Köppe

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Aug 11, 2020, 12:54:49 PM8/11/20
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On Tuesday, August 11, 2020 at 9:04:01 AM UTC-7, Emmanuel Charpentier wrote:
I do not know how to re-open a closed ticket...

One doesn't. 

I'd suggest to use https://trac.sagemath.org/ticket/25363 (simple-prompt) for the things that need to be prepared on the sage side, 
and https://github.com/sagemath/sage-shell-mode/issues/53 for subsequent changes in sage-shell-mode.

Emmanuel Charpentier

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Aug 11, 2020, 4:44:18 PM8/11/20
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Ticket Trac25363 positively reviewed. Github issue against sage-shell-mode updated.

HTH,

Kenji Iohara

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Aug 11, 2020, 6:12:38 PM8/11/20
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I could compile Sage 9.2.beta 8 on Mac OS.10.15.6 and run sage. Quitting sage has evoked no problem…
But, for ptestlong, it has some errors. I don’t know whether this is completely local porblem…
ptestlong.log

Matthias Köppe

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Aug 11, 2020, 8:07:00 PM8/11/20
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On Tuesday, August 11, 2020 at 3:12:38 PM UTC-7, Kenji Iohara wrote:
I could compile Sage 9.2.beta 8 on Mac OS.10.15.6 and run sage. Quitting sage has evoked no problem…
But, for ptestlong, it has some errors. I don’t know whether this is completely local porblem…

These doctest failures seem to come from locale issues. We have a ticket for these already - https://trac.sagemath.org/ticket/30053 - which needs help


Matthias Köppe

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Aug 11, 2020, 9:20:55 PM8/11/20
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On Monday, August 10, 2020 at 3:51:35 PM UTC-7, 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 


415221a9a8 (trac/develop, tag: 9.2.beta8) Updated SageMath version to 9.2.beta8

Thanks for preparing the latest beta. 

Tests ran automatically at https://github.com/sagemath/sage/actions/runs/203191522 (with only sparse results because of current reliability issues of GitHub Actions).

ubuntu-trusty-standard - clean
linuxmint-17 - Lots of doctest failures due to "setlocale" warning messages reported previously
centos-7-minimal, -standard - clean
fedora-32-standard - clean
gentoo-minimal, -standard - clean
slackware-14.2-standard - clean
homebrew-macos-minimal (https://github.com/sagemath/sage/runs/968871522) - some doctest timeouts
homebrew-macos-python3_xcode-nokegonly-standard (https://github.com/sagemath/sage/runs/968871676) - r spkg fails in configure phase "linking to Fortran libraries from C fails"
conda-forge-macos-standard (https://github.com/sagemath/sage/runs/968871892), standard - sagelib build fails "linbox/algorithms/det-rational.h:95:39: error: no viable overloaded '='"

Could someone please fix the errors in "sagetex" due to Python 2 syntax?




Dima Pasechnik

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Aug 12, 2020, 8:00:17 AM8/12/20
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There is https://trac.sagemath.org/ticket/30342
to update sagetex with all the needed py3 fixes.

please test.
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John H Palmieri

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Aug 13, 2020, 1:35:50 AM8/13/20
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I'm having a problem with this on OS X: both with an incremental upgrade (after doing "make doc-clean") and a build from scratch, the build hangs during the docbuilding stage. If I manually build "constructions" and "thematic_tutorials" with "sage --docbuild constructions html" etc., the build completes, but not otherwise. This isn't happening with 9.2.beta7, but it is happening consistently with 9.2.beta8. Any ideas?


On Monday, August 10, 2020 at 3:51:35 PM UTC-7, Volker Braun wrote:

David Coudert

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Aug 13, 2020, 3:36:42 AM8/13/20
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on my side, incremental build from beta7 (including documentation) on OSX went well.

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Dima Pasechnik

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Aug 13, 2020, 4:55:44 AM8/13/20
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different versions of macOS?
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David Coudert

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Aug 13, 2020, 4:58:18 AM8/13/20
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macOS Mojave 10.14.6
macbook air early 2014 with core i7 1.7GHz
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Samuel Lelièvre

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Aug 13, 2020, 7:27:03 AM8/13/20
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2020-08-13 05:35 UTC, John H Palmieri:
>
> I'm having a problem with this on OS X: both with an incremental
> upgrade (after doing "make doc-clean") and a build from scratch,
> the build hangs during the docbuilding stage.

Same here with this configuration:
- MacBook Air, Early 2014
- macOS 10.14.6 Mojave
- Homebrew installed with many packages
Trying to build Sage 9.2.beta8 hangs on dochtml.
There was no such problem with Sage 9.2.beta7.

> If I manually build "constructions" and "thematic_tutorials" with
> "sage --docbuild constructions html" etc., the build completes,
> but not otherwise.

I have not tried that but indeed the build hangs on "constructions":

```
$ tail -n 7 /.../logs/dochtml.log
[faq ] The HTML pages are in local/share/doc/sage/html/en/faq.
Build finished. The built documents can be found in
/.../local/share/doc/sage/html/en/faq

Building en/constructions.

[construct] building [html]: targets for 16 source files that are out of date
[construct] updating environment: [new config] 16 added, 0 changed, 0 removed
```

Samuel Lelièvre

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Aug 13, 2020, 7:35:54 AM8/13/20
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Le mar. 11 août 2020 à 00:51, Volker Braun <vbrau...@gmail.com> 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

Thanks! On Debian 10, success with `make`, and a few transient
timeouts and failures for `make testalllong`.

```
----------------------------------------------------------------------
./sage -t --long --random-seed=0 src/sage/calculus/calculus.py # Timed out
./sage -t --long --random-seed=0 src/sage/databases/findstat.py # 17
doctests failed
./sage -t --long --random-seed=0 src/sage/databases/oeis.py # 1 doctest failed
./sage -t --long --random-seed=0 src/sage/doctest/external.py # Timed out
./sage -t --long --random-seed=0 src/sage/functions/gamma.py # Timed out
./sage -t --long --random-seed=0 src/sage/interfaces/maple.py # 15
doctests failed
./sage -t --long --random-seed=0 src/sage/interfaces/interface.py # Timed out
./sage -t --long --random-seed=0 src/sage/interfaces/mathematica.py # Timed out
./sage -t --long --random-seed=0 src/sage/interfaces/octave.py # 3
doctests failed
./sage -t --long --random-seed=0 src/sage/interfaces/scilab.py # Timed out
./sage -t --long --random-seed=0 src/sage/matrix/matrix1.pyx # Timed out
./sage -t --long --random-seed=0 src/sage/misc/remote_file.py # 1
doctest failed
./sage -t --long --random-seed=0 src/sage/misc/functional.py # Timed out
./sage -t --long --random-seed=0
src/sage/modules/free_module_element.pyx # Timed out
./sage -t --long --random-seed=0 src/sage/plot/plot.py # 88 doctests failed
./sage -t --long --random-seed=0 src/sage/plot/graphics.py # 63 doctests failed
./sage -t --long --random-seed=0 src/sage/symbolic/constants_c.pyx # Timed out
./sage -t --long --random-seed=0 src/sage/symbolic/constants.py # Timed out
./sage -t --long --random-seed=0 src/sage/symbolic/expression.pyx # Timed out
./sage -t --long --random-seed=0
src/sage/symbolic/integration/integral.py # Timed out
./sage -t --long --random-seed=0 src/sage/tests/benchmark.py # Timed out
./sage -t --long --random-seed=0
src/doc/en/constructions/interface_issues.rst # 1 doctest failed
./sage -t --long --random-seed=0
src/doc/en/constructions/linear_algebra.rst # 1 doctest failed
./sage -t --long --random-seed=0
src/doc/en/developer/coding_in_other.rst # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 36318.7 seconds
cpu time: 10268.6 seconds
cumulative wall time: 10657.8 seconds
External software detected for doctesting:
ffmpeg,graphviz,imagemagick,internet,latex,macaulay2,maple,octave,pandoc
make: *** [Makefile:181: testalllong] Error 5
```

Doctesting these files individually afterwards,
each of them gave "All tests passed!"

Dima Pasechnik

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Aug 13, 2020, 7:38:22 AM8/13/20
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could it be https://trac.sagemath.org/ticket/30345 ?
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Samuel Lelièvre

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Aug 13, 2020, 7:45:16 AM8/13/20
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2020-08-13 11:35 UTC, Samuel Lelièvre:
>
> Thanks! On Debian 10, success with `make`, and a few transient
> timeouts and failures for `make testalllong`.
>
> Doctesting these files individually afterwards,
> each of them gave "All tests passed!"

... but that's because when doctesting individually
I forgot to put the appropriate "--optional=...".

John H Palmieri

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Aug 13, 2020, 12:47:17 PM8/13/20
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I'm using 10.15.6, 2017 iMac. Same thing with the system Python vs. Sage's own. I have a bunch of homebrew packages installed, too.
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John H Palmieri

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Aug 13, 2020, 12:48:18 PM8/13/20
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What happens if you do "make doc-clean; make"?
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Samuel Lelievre

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Aug 13, 2020, 2:44:59 PM8/13/20
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I opened a ticket for the issue reported by John:

- Fix building html documentation on macOS

I tried applying #30345 but the problem persisted.
Then I realised Dima mentioned #30345 in relation to
timeouts when running make testalllong on Debian,
not in relation to the dochtml issue on macOS.  : /

John H Palmieri

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Aug 13, 2020, 3:03:50 PM8/13/20
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Thank you for opening the ticket. Independently I had tried #30345 to see if it would fix the problem, but I also see the problem with "make doc-clean" followed by "./sage --docbuild all html", which should not be affected by #30345.

Dima Pasechnik

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Aug 13, 2020, 3:24:05 PM8/13/20
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#30345 matters if you set MAKE to "make -jX" for X>1


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Justin C. Walker

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Aug 13, 2020, 3:29:51 PM8/13/20
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> On Aug 10, 2020, at 15:51 , Volker Braun <vbrau...@gmail.com> 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

Built from fresh clones of the 9.2.b8 branch, on three macOS systems: 10.13.6 (2019 iMac Pro, 18-core Xeon W); 10.14.6 (2017 MBP, Quad-core Core i7); and 10.15.6 (2019 MBP, 8-core Core i9).

No problems with any of the builds, and testing (‘ptestlong’) on each completed with no failures.

Justin

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John H Palmieri

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Aug 13, 2020, 4:31:25 PM8/13/20
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On Thursday, August 13, 2020 at 12:24:05 PM UTC-7, Dima Pasechnik wrote:


On Thu, 13 Aug 2020, 20:03 John H Palmieri, <jhpalm...@gmail.com> wrote:


On Thursday, August 13, 2020 at 11:44:59 AM UTC-7, Samuel Lelievre wrote:
I opened a ticket for the issue reported by John:

- Fix building html documentation on macOS

I tried applying #30345 but the problem persisted.
Then I realised Dima mentioned #30345 in relation to
timeouts when running make testalllong on Debian,
not in relation to the dochtml issue on macOS.  : /

Thank you for opening the ticket. Independently I had tried #30345 to see if it would fix the problem, but I also see the problem with "make doc-clean" followed by "./sage --docbuild all html", which should not be affected by #30345.

#30345 matters if you set MAKE to "make -jX" for X>1

Yes, but if you build the docs with "sage --docbuild ...", the changes in #30345 should have no effect: they should only matter if you use "make". The fact that the problem persists whether using "make doc-html" or "sage --docbuild ..." means that #30345 won't fix the problem.


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Dima Pasechnik

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Aug 13, 2020, 5:59:31 PM8/13/20
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OK, I tried to reproduce this on a Mac, and indeed the build hangs
waiting for some parallel process to finish:
On hitting ctrl-C, it always (the stage of the docbuild may differ though)
shows the following backtrace:
...
[dochtml] [a_tour_of] dumping search index in English (code: en)... done
[dochtml] [a_tour_of] The HTML pages are in
local/share/doc/sage/html/tr/a_tour_of_sage.
[dochtml] Build finished. The built documents can be found in
/Users/dima/software/sagetrac-mirror/local/share/doc/sage/html/tr/a_tour_of_sage

^C[dochtml] Error building the documentation.
[dochtml] Traceback (most recent call last):
[dochtml] File
"/usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",
line 193, in _run_module_as_main
[dochtml] "__main__", mod_spec)
[dochtml] File
"/usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py",
line 85, in _run_code
[dochtml] exec(code, run_globals)
[dochtml] File
"/Users/dima/software/sagetrac-mirror/local/lib/python3.7/site-packages/sage_setup/docbuild/__main__.py",
line 2, in <module>
[dochtml] main()
[dochtml] File
"/Users/dima/software/sagetrac-mirror/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
line 1721, in main
[dochtml] builder()
[dochtml] File
"/Users/dima/software/sagetrac-mirror/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
line 337, in _wrapper
[dochtml] build_many(build_other_doc, L)
[dochtml] File
"/Users/dima/software/sagetrac-mirror/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
line 281, in build_many
[dochtml] _build_many(target, args, processes=NUM_THREADS)
[dochtml] File
"/Users/dima/software/sagetrac-mirror/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py",
line 263, in build_many
[dochtml] waited_pid, waited_exitcode = wait_for_one()
[dochtml] File
"/Users/dima/software/sagetrac-mirror/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py",
line 179, in wait_for_one
[dochtml] pid, sts = os.wait()
[dochtml] File "src/cysignals/signals.pyx", line 320, in
cysignals.signals.python_check_interrupt
[dochtml] KeyboardInterrupt
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Samuel Lelievre

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Aug 13, 2020, 8:43:15 PM8/13/20
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2020-08-13 21:59:31 UTC, Dima Pasechnik:
OK, I tried to reproduce this on a Mac, and indeed the build hangs
waiting for some parallel process to finish:
On hitting ctrl-C, it always (the stage of the docbuild may differ though)
shows the following backtrace:
...
[dochtml] KeyboardInterrupt

The hang occurs even with `make -j1`.

David Coudert

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Aug 14, 2020, 7:44:38 AM8/14/20
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Same here on a fresh clone with macOS 10.15.16


[dochtml] Building en/constructions.
[dochtml] 
[dochtml] [construct] building [html]: targets for 16 source files that are out of date
[dochtml] [construct] updating environment: [new config] 16 added, 0 changed, 0 removed
^C[dochtml] Error building the documentation.
[dochtml] Traceback (most recent call last):
[dochtml]   File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/python3.7/runpy.py", line 193, in _run_module_as_main
[dochtml]     "__main__", mod_spec)
[dochtml]   File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/python3.7/runpy.py", line 85, in _run_code
[dochtml]     exec(code, run_globals)
[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__main__.py", line 2, in <module>
[dochtml]     main()
[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 1721, in main
[dochtml]     builder()
[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 337, in _wrapper
[dochtml]     build_many(build_other_doc, L)
[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 281, in build_many
[dochtml]     _build_many(target, args, processes=NUM_THREADS)
[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", line 263, in build_many
[dochtml]     waited_pid, waited_exitcode = wait_for_one()
[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", line 179, in wait_for_one
[dochtml]     pid, sts = os.wait()
[dochtml]   File "src/cysignals/signals.pyx", line 320, in cysignals.signals.python_check_interrupt
[dochtml] KeyboardInterrupt
[dochtml] 
[dochtml]     Note: incremental documentation builds sometimes cause spurious
[dochtml]     error messages. To be certain that these are real errors, run
[dochtml]     "make doc-clean" first and try again.
make[3]: *** [doc-html] Error 1
make[2]: *** [all-start] Interrupt: 2
make[1]: *** [all-start] Interrupt: 2
make: *** [all] Interrupt: 2



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Sébastien Labbé

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Aug 14, 2020, 11:34:49 AM8/14/20
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Running tests with few optional and external packages (but not internet due to some issue with my current installation), I get

Using --optional=4ti2,cbc,ccache,cryptominisat,dot2tex,e_antic,external,fricas,glucose,latte_int,lidia,lrslib,memlimit,normaliz,notedown,openssl,pandoc_attributes,pycosat,pynormaliz,python_openid,rst2ipynb,sage,sage_numerical_backends_coin,speaklater

----------------------------------------------------------------------
sage -t --long --random-seed=0 src/sage/sat/boolean_polynomials.py  # 1 doctest failed
sage -t --long --random-seed=0 src/sage_setup/optional_extension.py  # 1 doctest failed
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,graphviz,imagemagick,latex,octave,pandoc

Rerunning tests, I get:

----------------------------------------------------------------------
sage -t --long --random-seed=0 src/sage_setup/optional_extension.py  # 1 doctest failed
----------------------------------------------------------------------

That failure is copied below.

sage -t --long --random-seed=0 src/sage_setup/optional_extension.py
**********************************************************************
File "src/sage_setup/optional_extension.py", line 82, in sage_setup.optional_extension.OptionalExtension
Failed example:
    print(ext.__class__.__name__)
Expected:
    Extension
Got:
    CythonizeExtension
**********************************************************************
1 item had failures:
   1 of  10 in sage_setup.optional_extension.OptionalExtension
    0 tests not run because we ran out of time
    [12 tests, 1 failure, 0.43 s]
sage -t --long --random-seed=0 src/sage/sat/boolean_polynomials.py
    0 tests not run because we ran out of time
    [46 tests, 80.74 s]

E. Madison Bray

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Aug 19, 2020, 10:04:18 AM8/19/20
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As I noted at [1], this implies that one or more of the docbuilds are running some code that hangs forever, so it would help narrow it down by finding out what code it's running to cause a hang.  Normally in docbuilds the most likely code to run will be some plotting code, so you can try to take the plot code present in the relevant documentation pages, run it, and see if it hangs.  Chances are if you run it in a single process it might *not* hang--frequently this happens only in a forked subprocess.  So you can try something like:

from multiprocessing import Process
p = Process(target=<function implementing the plotting code>)
p.start()

and see if it hangs. I've often found this to be the case with calls to np.dot(), which matpotlib uses sometimes to perform various transformations, and which in turn often results in a call to a multi-threaded OpenBLAS function which are sometimes buggy.

As an aside, I would like to make the parallel doc build code more robust to this kind of hang, but it's hard to say exactly what the right solution is (I know more or less what the technical solution is, but I mean more the UX solution).  Because as far as the docbuild code is concerned, it doesn't know that the process is "hung".  It's just taking however long it needs to take, and the code will wait for it to finish.  Perhaps we could implement some kind of timeout to kill docbuild processes that are taking too long (but what should the timeout be)? Or report back to the user exactly which docbuilds are still running (like, a log message at some interval) so that the user can decide whether or not to take action.

Dima Pasechnik

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Aug 20, 2020, 4:43:07 PM8/20/20
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I found out that the problem is due to OpenMP, see https://trac.sagemath.org/ticket/30351#comment:50
The workaround (or perhaps the only way to proceed, I don't know) is to set env.var. OMP_NUM_THREADS=1

 

Markus Wageringel

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Aug 21, 2020, 4:37:21 PM8/21/20
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With Neovim as editor, the same warning appears in its builtin terminal, followed by some error messages that break the REPL. Luckily, upgrading Neovim from 0.2.2 to 0.4.3 fixed it on my end.

emanuel.c...@gmail.com schrieb am Dienstag, 11. August 2020 um 17:39:29 UTC+2:

Damn !

This release breaks sage-shell-mode support for a sage session into emacs. After starting an emacs session, I get the normal banner and a normal prompt. A little while after that (about 0.5 to 1 second), a warning WARNING: your terminal doesn't support cursor position requests (CPR). appears immediately below the banner and above the prompt, then the cursor goes right to the right margin (i. e. in the right scrollbar).

I still can type Sage code, which appears at the left margin on the line immediately below the prompt. Typing <Return> displays a continuation prompt (.....:) 7 spaces,, then my code,which gets executed and the answer printed on tjhe line below the continuation prompt. Example :

┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.2.beta8, Release Date: 2020-08-10               │
│ Using Python 3.7.3. Type "help()" for help.                        │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable.     ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
WARNING: your terminal doesn't support cursor position requests (CPR).
sage: sage:                                                                      
....:       1+1                                                                  
2
sage:

No error message appears in the terminal window from which I launched emacs ; nothing unusual in the *Messages* buffer either.

I’m stymied…


Le mardi 11 août 2020 13:39:38 UTC+2, Emmanuel Charpentier a écrit :

On Debian testing running on core i7 + 16 GB RAM, upgrading 9.2.beta7 configured for use of all possible system libraries an runningptestlong gets me the same transient an same three permanent failures already reported for 9.2.beta7 and 9.2.beta5 :

sage -t --long --warn-long 175.4 --random-seed=0 src/sage/tests/parigp.py  # Timed out
sage -t --long --warn-long 175.4 --random-seed=0 src/sage/rings/complex_arb.pyx  # 6 doctests failed
sage -t --long --warn-long 175.4 --random-seed=0 src/sage/tests/gap_packages.py  # 1 doctest failed
sage -t --long --warn-long 175.4 --random-seed=0 src/sage/rings/real_arb.pyx  # 2 doctests failed

HTH,



Le mardi 11 août 2020 00:51:35 UTC+2, 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 


John H Palmieri

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Aug 22, 2020, 12:12:13 AM8/22/20
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On Friday, August 21, 2020 at 1:37:21 PM UTC-7, Markus Wageringel wrote:
With Neovim as editor, the same warning appears in its builtin terminal, followed by some error messages that break the REPL. Luckily, upgrading Neovim from 0.2.2 to 0.4.3 fixed it on my end.

Does https://trac.sagemath.org/ticket/25363, together with running "sage --simple-prompt", fix the problem?

Markus Wageringel

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Aug 22, 2020, 3:31:47 AM8/22/20
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Yes, using "sage —simple-prompt“ did fix the problem as well. However, the simple prompt lacks a lot of functionality, like cursor movement, tab-completion or colors. I assume that Emacs is more advanced and implements these features by different means, but for Vim this is not really an option.

Emmanuel Charpentier

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Aug 25, 2020, 11:55:49 AM8/25/20
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FWIW, I just submitted a pull request against sage-shell-mode to fix this issue (by reverting to readline and using --simple-prompt).

A better solution (manage CPR requests in emacs) is out of my abilities...

Le mardi 11 août 2020 à 18:54:30 UTC+2, John H Palmieri a écrit :
Done. I haven't figured out the sage-shell customizations so that it automatically uses '--simple-prompt' whenever you ask it to start Sage, but that's a separate problem.


On Tuesday, August 11, 2020 at 9:44:15 AM UTC-7, Emmanuel Charpentier wrote:


Le mardi 11 août 2020 18:38:00 UTC+2, John H Palmieri a écrit :
It's version 26.3. I also just quit emacs and restarted, and now I'm having the same problems you were having. Modifying 'src/bin/sage' to accept a '--simple-prompt'

How do you do that ? Care to post a diff (possibly in Trac#25363 ?



 
option and then using that seems to work.

On Tuesday, August 11, 2020 at 9:32:20 AM UTC-7, Emmanuel Charpentier wrote:

John, what is your current emacs version ?



Le mardi 11 août 2020 18:26:04 UTC+2, John H Palmieri a écrit :
I had no experience with sage-shell-mode until about 5 minutes ago, but it works for me, except for some weird artifacts when it reprints what I typed at the command line:

┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.2.beta8, Release Date: 2020-08-10               │
│ Using Python 3.7.3. Type "help()" for help.                        │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable.     ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
sage: Sq(3)
SSSqqq(((333)))))))))
Sq(3)
sage: Sq(3)*Sq(4)
SSSSqqqq((((3333))))****SSSSqqqq((((4444))))))))))))
Sq(7)
sage: quit()
qqqqquuuuuiiiiittttt((((()))))))))))))))
Exiting Sage (CPU time 0m0.31s, Wall time 0m47.95s).

Process Sage finished



On Tuesday, August 11, 2020 at 9:20:00 AM UTC-7, Emmanuel Charpentier wrote:

Further bad news : this also somehow breaks the communication between emacs and sage :

  • quit in the sage session never returns ; you have to kill emacs to get your damn prompt back…

  • Any attempt to use sage from an org-mode document never returns : same issue…

HTH,

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