Sage 9.3.beta4 released

[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 

02b0be1ff8 Updated SageMath version to 9.2.beta4

3e65aa67cc Trac #29878: Remove `sage -twistd` from `src/bin/sage`

a3308ffb43 Trac #29862: Installation guide: change python version in conda instructions

a6215602a5 Trac #29828: Broken conversion from ZZ['x'] to Qp['y']

5d2577a0ce Trac #29746: Document integer overflow bug in vector_space_dimension()

d0e1751d76 Trac #30050: add even more missing empty lines in the doc

87d9811918 Trac #30048: get rid of python2 mentioned in .github/workflows and README.md

aaa2bdf045 Trac #30042: clarify docs of nauty_geng

381891c57c Trac #30028: remove some traces of __cmp__

917f8de0eb Trac #30021: FPLLL 5.3.3

837e9ad07a Trac #30005: Small documentation fixes in combinat

063c266cbf Trac #29997: a bunch of typos

ac7ee1abe6 Trac #29994: Add integral curves over QQ

55556612f2 Trac #29917: Move ChainComplexes from sage.categories.category_types to a separate module

736ceffc41 Trac #29910: sage.rings.finite_rings.element_givaro: Remove dependency on NTL

2bb470b2f2 Trac #29897: database_stein_watkins_mini installation is broken

ad109e3649 Trac #29851: tox.ini: debian-bullseye, -sid have Python3.8 instead of 3.7

8de8febcb6 Trac #29808: fix left and right actions of permutations on matrices

76f6767a09 Trac #29794: spring cleanup in modsym/space.py

f62fb5f99e Trac #29787: 1 optional internet oeis doctest failing (busy beaver ordering)

1f983640f6 Trac #29733: Create gitattributes file specifying proper line endings

bed0bc6493 Trac #29714: some micro optimisations in comparison to empty list

d000965b0a Trac #29668: map_coefficients for Laurent polynomials

5ef2540085 Trac #29605: plotting function for forests

98a1c9be6d Trac #29514: implement formatting of elements in RDF/CDF

6629f4c3a9 Trac #12074: real nth root function

8cb2f93213 Trac #8111: gcd of rationals is trouble

55663b6cc7 Trac #30057: remove some old "known bug" tags about log

48a6328304 Trac #30047: add missing empty lines in the doc

8aebea9275 Trac #30034: Description of ramification_index in local_generic is wrong

aa4e325083 Trac #30030: Prevent JSmol from phoning home

20ea231df1 Trac #30019: 1 internet doctest failing in combinat/quickref.py

030a4794fe Trac #30009: using coprime_integers in more places

1cecf97864 Trac #30007: Allow regular partition tuples to have different \ell values on different components

684446ab04 Trac #30006: implement multiplicative_order for elements of AA

1a9e4473b1 Trac #30004: Added new constructions for BIBDs

a01f419522 Trac #30003: some details in Kloosterman sums

d4caf56bd2 Trac #29987: build/make/install: Do not depend on src/bin/sage-version.sh

02e6a8d2bd Trac #29959: Extended the construction of BIBDs to allow for \lambda different from 1

7d65facffb Trac #29955: Reduction from dancing links instance to MILP instance

9b8c6b24d7 Trac #29953: Let diff() act on chart functions and differentiable forms

aba874e2bc Trac #29952: simplify Seifert matrix code

0feaa365b4 Trac #29940: sage.doctest: Remove handling of sagenb

1c1284c0f5 Trac #29937: remove deprecated things in plot3d and structure

08f24ca812 Trac #29933: refresh faq-contribute

cf4d9ff8ae Trac #29928: implement action of DifferentialWeylAlgebra on polynomials

568d80a378 Trac #29926: shifting issue in padic function: preprocess_list

0e4aa016a8 Trac #29925: shifting issue in padic function: _polynomial_list

2de06fc429 Trac #29920: Remove deprecated scripts sage-list-optional, sage-list-experimental, sage-list-standard

df41dca2b0 Trac #29916: sage.structure, sage.misc: Replace import of sage.categories.all by more specific imports

f9fdd736af Trac #29914: cython code for Moebius and Coxeter matrices of posets

bfacdd6bdf Trac #29909: Add tox as a type=optional, source=pip package

b0e01a3202 Trac #29906: Run tests for `an_affine_basis`

12eddec434 Trac #29903: Run many test suite examples for polyhedra

c6e56b30f2 Trac #29883: sage.structure: Remove some module-level imports

a70567b122 Trac #29894: add minimal interface for using ZZ[x]-matrices from flint

a061db04bc Trac #29893: Another speedup of hypergeometric trace formula

62b405c4f3 Trac #29892: Move sage.misc.misc.coeff_repr, repr_lincomb to new module sage.misc.repr

699bf78e8c Trac #29867: Remove __div__ methods from cython modules

5eaa10e139 Trac #29855: sagelib setup.py: Fix dependencies on header files of packages gmp, ntl

184cd6cc13 Trac #29723: inverses of ring homomorphisms

fc1f2cce4c Trac #29615: Fusion Ring Operations; Central Charge

128a94d513 Trac #27934: Implement efficient all eccentricity computation for undirected graphs

9ed0896af5 Trac #27036: FusionRing enhancements

1af2945a15 Trac #20104: sage --package: Add commands "list :standard:", "update-latest" (for packages from PyPI), "upload"

7e1f35fb32 Trac #15496: Incorrect result for divergent integral

b5858f5710 Trac #30014: freetype version comparison in spkg-configure.m4 is wrong

1e9f325d06 Trac #30002: force C locale in docbuild and remove some obsolete stuff

5deea3dc41 Trac #29192: MR41: Add option to persist camera state to three.js viewer.

a79b0fc01d Updated SageMath version to 9.2.beta3

[Thierry Dumont]

No installation problem migrating from 9.2 beta3 to beta4 on Ubuntu
20-04, 4 cores, with:

export MAKE="make -j4"
*and*
export LANG=C.UTF-8

yours
t.d.

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[Emmanuel Charpentier]

On Debian testing running on core i5 + 8 GB Ram, after upgrading from 9.2.beta2 to 9.2.beta4, ptestlong gives results identical to those already reported for 9.2.beta2 and 9.2.beta3 : permanent failures on gp_packages, real_arb and complex_arb.

HTH,

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> <mailto:sage-release+unsub...@googlegroups.com>.

[David Coudert]

upgrade and docbuid OK from beta3 on macOS.

Thank you.

David.

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[Dima Pasechnik]

just in case.

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[Emmanuel Charpentier]

Identical results (modulo a couple of timeouts) on Debian testing running on core i7 + 16 GB RAM, upgraded from 9.2.beta3.

HTH,

[Sébastien Labbé]

Running tests with various optional+external packages, 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,rst2ipynb,sage,sage_numerical_backends_coin,sage_numerical_backends_cplex,sage_numerical_backends_gurobi

----------------------------------------------------------------------

sage -t --long src/sage/combinat/designs/bibd.py  # 2 doctests failed
sage -t --long src/sage/combinat/species/library.py  # 1 doctest failed
sage -t --long src/sage/combinat/tutorial.py  # 1 doctest failed
sage -t --long src/sage/databases/findstat.py  # 17 doctests failed
sage -t --long src/sage/geometry/polyhedron/base.py  # Bad exit: 1
sage -t --long src/sage/graphs/generators/smallgraphs.py  # 2 doctests failed
sage -t --long src/sage/sat/boolean_polynomials.py  # 1 doctest failed
----------------------------------------------------------------------
External software detected for doctesting: cplex,ffmpeg,graphviz,imagemagick,internet,latex,pandoc

Only sat/boolean_polynomials.py does not reproduce while rerunning failed tests.

library.py and tutorial.py were dealt in https://trac.sagemath.org/ticket/30020

Failure with bibd.py is new and is copied below

Follow up at https://trac.sagemath.org/ticket/25536


sage -t --long src/sage/combinat/designs/bibd.py
**********************************************************************
File "src/sage/combinat/designs/bibd.py", line 109, in sage.combinat.designs.bibd.balanced_incomplete_block_design
Failed example:
    B                                                              # optional - internet
Expected:
    Incidence structure with 66 points and 143 blocks
Got:
    (66,6,1)-Balanced Incomplete Block Design
**********************************************************************
File "src/sage/combinat/designs/bibd.py", line 113, in sage.combinat.designs.bibd.balanced_incomplete_block_design
Failed example:
    designs.balanced_incomplete_block_design(66, 6, 1, use_LJCR=True)  # optional - internet
Expected:
    Incidence structure with 66 points and 143 blocks
Got:
    (66,6,1)-Balanced Incomplete Block Design
**********************************************************************
1 item had failures:
   2 of  26 in sage.combinat.designs.bibd.balanced_incomplete_block_design
    0 tests not run because we ran out of time
    [120 tests, 2 failures, 5.32 s]

[Jonathan Kliem]

https://trac.sagemath.org/ticket/30030 broke the jupyter notebook for me.

Please wait while the Sage Jupyter Notebook server starts...
[I 14:23:35.535 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js
[I 14:23:35.655 NotebookApp] Serving notebooks from local directory: /home/mi/kliem
[I 14:23:35.655 NotebookApp] The Jupyter Notebook is running at:
[I 14:23:35.655 NotebookApp] http://localhost:8888/?token=13410c6dbd032a2e31784207d69dcb1bbf54374b475a6449
[I 14:23:35.656 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 14:23:35.658 NotebookApp]
   
    To access the notebook, open this file in a browser:
        file:///run/user/284784/jupyter/nbserver-12512-open.html
    Or copy and paste one of these URLs:
        http://localhost:8888/?token=13410c6dbd032a2e31784207d69dcb1bbf54374b475a6449
[I 14:23:47.500 NotebookApp] 302 GET /?token=13410c6dbd032a2e31784207d69dcb1bbf54374b475a6449 (127.0.0.1) 0.33ms
[I 14:23:55.390 NotebookApp] Creating new notebook in
[W 14:23:55.908 NotebookApp] 404 GET /nbextensions/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML-full,Safe&delayStartupUntil=configured (127.0.0.1) 5.67ms referer=http://localhost:8888/notebooks/Untitled2.ipynb?kernel_name=sagemath
[W 14:24:54.535 NotebookApp] 404 GET /nbextensions/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML-full,Safe&delayStartupUntil=configured (127.0.0.1) 1.72ms referer=http://localhost:8888/notebooks/Dokumente/SageDays109/CombinatorialPolyhedron.ipynb

All I'm seeing is something like this. I can navigate the folders, but when I open a file I just see a blank page in the browser.

It worked just fine on debian buster and ubuntu bionic. Reverting the commit it works fine again. I'm using firefox, but I cannot get it to work on chromium either.

[Dima Pasechnik]

I can confirm that it does break things for me too (and reverting fixes)
on Linux/Firefox.

But if I re-revert back, everything works. So this is some kind of
caching issue, I gather.

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[Jonathan Kliem]

Ok, I think it has nothing to do with #30030.

Running

make build

leads to the blank screen for the notebook (also with "./configure" before).

Running

sage -b

fixes it (but only until you run `make build` again).

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[Dima Pasechnik]

perhaps we should update notebook to 5.7.10 ?

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[Kenji Iohara]

I couldn’t compile it; it stops at scipy-1.2.3.  I am using Mac OS X.15.5 with Intel Core i5,

and the log-file is attached to this email.

[Volker Braun]

Typo: Sage 9.2.beta4 

[Dima Pasechnik]

gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/icopy.f
error: Command "gfortran -Wall -g -ffixed-form
-fno-second-underscore -fPIC -O3 -funroll-loops
-Iscipy/sparse/linalg/eigen/arpack/ARPACK/SRC
-I/Users/iohara/Desktop/sage-9.2.beta4/local/lib/python3.7/site-packages/numpy/core/include
-c -c scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/dsaitr.f -o
build/temp.macosx-10.14-x86_64-3.7/scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/dsaitr.o"
failed with exit status 1

what is the version of gfortran you use?

It is by any chance gfortran-10 (from Homebrew) ?
(unfortunately scipy log does not say)
In this case please uninstall package gcc and install package gfortran
https://formulae.brew.sh/cask/gfortran#default

On Sun, Jul 12, 2020 at 8:22 AM Kenji Iohara <simplye...@gmail.com> wrote:
>
> I couldn’t compile it; it stops at scipy-1.2.3. I am using Mac OS X.15.5 with Intel Core i5,
> and the log-file is attached to this email.
>

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>
>
> 2020/07/11 16:31、Dima Pasechnik <dim...@gmail.com>のメール:

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAAWYfq2%3DvXBSiA8e5Fz0kc7gy3GArNmq933KnA%2BDQ%3DmMOAAwaA%40mail.gmail.com.

>
>
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[Kenji Iohara]

The version of gfortran I use is 10.1.0. Via Homebrew, it seems impossible to install only gfortran (i.e., without gcc).

2020/07/12 11:52、Dima Pasechnik <dim...@gmail.com>のメール:

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAAWYfq2OYF0%2BkXr4f9wUCfZ_iZqp4FKq%2BSBUFOUbiuG2KSrdzQ%40mail.gmail.com.

[Dima Pasechnik]

On Sun, 12 Jul 2020, 14:26 Kenji Iohara, <simplye...@gmail.com> wrote:

The version of gfortran I use is 10.1.0. Via Homebrew, it seems impossible to install only gfortran (i.e., without gcc).

2020/07/12 11:52、Dima Pasechnik <dim...@gmail.com>のメール:

   gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/icopy.f
   error: Command "gfortran -Wall -g -ffixed-form
-fno-second-underscore -fPIC -O3 -funroll-loops
-Iscipy/sparse/linalg/eigen/arpack/ARPACK/SRC
-I/Users/iohara/Desktop/sage-9.2.beta4/local/lib/python3.7/site-packages/numpy/core/include
-c -c scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/dsaitr.f -o
build/temp.macosx-10.14-x86_64-3.7/scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/dsaitr.o"
failed with exit status 1

what is the version of gfortran you use?

It is by any chance gfortran-10 (from Homebrew) ?
(unfortunately scipy log does not say)
In this case please uninstall package gcc and install package gfortran
https://formulae.brew.sh/cask/gfortran#default

this gfortran package is the right version.

(probably requires un-install of gcc package - which is not needed to build sage)

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[Matthias Köppe]

Sage does not support gcc/gfortran 10 yet. 

See https://trac.sagemath.org/ticket/30067 for a workaround

and https://trac.sagemath.org/ticket/29456 for the task of adding support for 10.

On Sunday, July 12, 2020 at 6:26:37 AM UTC-7, Kenji Iohara wrote:

The version of gfortran I use is 10.1.0. Via Homebrew, it seems impossible to install only gfortran (i.e., without gcc).

2020/07/12 11:52、Dima Pasechnik <dim...@gmail.com>のメール:

   gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/icopy.f
   error: Command "gfortran -Wall -g -ffixed-form
-fno-second-underscore -fPIC -O3 -funroll-loops
-Iscipy/sparse/linalg/eigen/arpack/ARPACK/SRC
-I/Users/iohara/Desktop/sage-9.2.beta4/local/lib/python3.7/site-packages/numpy/core/include
-c -c scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/dsaitr.f -o
build/temp.macosx-10.14-x86_64-3.7/scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/dsaitr.o"
failed with exit status 1

what is the version of gfortran you use?

It is by any chance gfortran-10 (from Homebrew) ?
(unfortunately scipy log does not say)
In this case please uninstall package gcc and install package gfortran
https://formulae.brew.sh/cask/gfortran#default

On Sun, Jul 12, 2020 at 8:22 AM Kenji Iohara <simplye...@gmail.com> wrote:

I couldn’t compile it; it stops at scipy-1.2.3.  I am using Mac OS X.15.5 with Intel Core i5,
and the log-file is attached to this email.

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[Justin C. Walker]

> On Jul 8, 2020, at 15:50 , 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

Filling in the record. Built from fresh clones of the 9.2.b4 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 the builds, and testing (‘ptestlong’) on each completed with no failures.

Justin

--
Justin C. Walker, Curmudgeon-At-Large
Institute for the Absorption of Federal Funds
--------
Men are from Earth.
Women are from Earth.
Deal with it.
--------