Sage 9.5.beta7 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 

cc60cfebc4 (tag: 9.5.beta7, trac/develop) Updated SageMath version to 9.5.beta7

cdb3614b34 Trac #32858: tiny doctest formatting fix in integer_mod_ring.py

b122005655 Trac #32791: Human Readable Error-Message for Elliptic curve constructor.

40b1190a59 Trac #32320: Ideal() with fraction-field elements is a small footgun

e19fc456be Trac #32875: fix Krull dimension of zero univariate quotient ring

7a358f2e9e Trac #32872: some details in plot

b3c05505e6 Trac #32863: fix E713 and E714 in coding

a95cfc54db Trac #32696: 1 internet doctest failing in src/sage/finance/stock.py

c87b264772 Trac #27744: Make pynormaliz a Feature

8b54c36d5e Trac #32859: Wrong display from type() with %display latex

76a8d311d5 Trac #32405: sage-bootstrap-python: Prefer pythons that support ssl with SNI

05aa11f3f7 Trac #32850: random doctest failure in tests/books/computational-mathematics-with-sagemath/sol/linsolve_doctest.py

ad620c4e4b Trac #32819: Determinant for multi-component links

b686ceb88c Trac #32816: random doctest failure in rings/polynomial/polynomial_element_generic.py

6dab8f4668 Trac #32715: flit_core: Use sdh_pip_install --no-deps

f46a88e77d Trac #32713: Apply "configure --enable-editable" also to other sage distribution packages

f69aa7bd6b Trac #32689: AG code construction: a place given as input gets converted to a prime divisor

28d573549c Trac #32380: make NumberFieldFractionalIdeal inherit from Ideal_fractional

402efc30a9 Trac #32871: CBF(f(i)) loops for a builtin function f with no corresponding method

311fd3481e Trac #32869: fix improper names of several special functions for CBF

ec03b51b74 Trac #32864: fix E713 and E714 in graphs

69a4cc6a68 Trac #32861: Add memory_allocator/distros/conda.txt

effa97500f Trac #32857: src/requirements.txt: Add memory_allocator

1114cde255 Trac #32851: Provide real ball erfi, Ei, Si, Ci, Shi, Chi, li, Li, beta, gamma_inc, gamma_inc_lower via arb

a95252313a Trac #32815: Update numpy to 1.21.4, networkx to 2.6.3

44a35355cc Trac #32778: sage.rings.infinity: Remove hard dependency on real_lazy and real_mpfi

f560fdc2df Trac #32733: Remove more .all imports

ac64d4f4f2 Trac #32208: Jupyter notebook receives invalid LaTeX output via MathJax

aa66d526cf Trac #16567: Use libsingular for polynomial rings over function fields

45515aface Trac #32848: various code details in combinat

a5c797bdd5 Trac #32844: fix some details in sloane_functions

befd4a21ba Trac #32842: use PARI's fflog() for binary finite fields

69d8b99468 Trac #32840: Fix unpickle_global when register_unpickle_override appears in a module not loaded at startup

033bbb02d6 Trac #32838: tox.ini: Add gentoo-python3.10

2de30a8587 Trac #32833: use libgap in coding

85b46be3de Trac #32831: Failure with specific random seed in sandpile.py

9d5d4efd54 Trac #32830: fix category of subgroups of finite matrix groups

d8affa1b28 Trac #32829: fix eps_monom function in RightQuantumWord

e47173be0a Trac #32824: Bug computing kernel of ring homomorphism GCA

2ad6448169 Trac #32823: fix E713 and E714 in interfaces

548c83d9ac Trac #32822: fix E713 and E714 in dynamics

7ddaf7ad7c Trac #32821: fix E713 and E714 in geometry

e5da507620 Trac #32813: improved error message 'unknown file extension' provided by sage -t

a6019fbe40 Trac #32812: remove the "bound method" py2/py3 adapter in doctest parsing

a99f383bb6 Trac #32807: cleanup various details in combinat

95fd5dfa38 Trac #32796: update GMP to version 6.2.1

d4ecc2a5e1 Trac #32795: docbuild fails in Sphinx conf.py when certain extensions aren't present

0d57d68903 Trac #32780: sage.geometry.polyhedron.library: Delay import of rings

23ff9d435f Trac #32764: SAGE_ROOT/tox.ini: Make tox -p auto and tox --listenvs useful again

f16835c8bb Trac #32763: Increase tolerance in doctests of `modular/modform/numerical.py`

d263f3cb8b Trac #32761: Pick up random seed for doctesting from environment variable

c962a2fa9a Trac #31356: Restructure docbuild as script packages sagemath_doc_html, sagemath_doc_pdf

8fe0743bea Trac #30566: random_spanning_tree ignores weights

f52d21a46c Trac #32852: Update traitlets to 5.1.1 (for python 3.9.8, 3.10)

6ec717a56d (tag: 9.5.beta6) Updated SageMath version to 9.5.beta6

[Samuel Lelièvre]

2021-11-20 10:25 UTC, Volker Braun:
>
> cc60cfebc4 (tag: 9.5.beta7) Updated SageMath version to 9.5.beta7

Thanks for this new release!

On Debian 10 buster, using many system packages,
Sage 9.5.beta7 pulled on an existing older develop
built but failed its tests. After `make distclean` though:
```
$ ./bootstrap -q && ./configure -q && make -s V=0 ptestlong
...
All tests passed!
```

See two reports on running tests for Sage 9.5.beta7:

- on Debian testing, by Emmanuel Charpentier
- on macOS 10.14.6 Mojave, by me

in this other sage-release thread:

https://groups.google.com/g/sage-release/c/M3D6URci2gk

The following tickets address most doctest failures reported there:

- #32886 (needs work): 1 fricas optional doctest failing in interfaces/fricas.py
- #32905 (needs review): Add abs tol to some CBF and RBF doctests
- #32880 (needs review): Replace Singular example with GAP in
_get_shared_lib_path()
- #32797 (positive review): Update pari to 2.13.3

Thanks everyone for your work on Sage! --Samuel

[Justin C. Walker]

I just built 9.5-b7 on my 2019 MBP (16” 8-Core Core i9) with macOS 10.15.7.

All went well, no build or “ptestlong” problems.

However, unlike the previous builds, this time there is no log file for the doc build.

Is this a change? I did not notice anything in the changeless below that seemed relevant.

Thanks!

Justin

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--
Justin C. Walker
Director, Institute for the Absorption of Federal Funds
--
Taxes, n.:
Of life's two certainties, the only one
for which you can get an extension.
--

[Matthias Köppe]

On Saturday, November 20, 2021 at 12:10:18 PM UTC-8 jus...@mac.com wrote:

 unlike the previous builds, this time there is no log file for the doc build.

Is this a change? I did not notice anything in the changeless below that seemed relevant.

Yes, it is coming from this change:

c962a2fa9a Trac #31356: Restructure docbuild as script packages sagemath_doc_html, sagemath_doc_pdf

These are now packages, and you find the build log in logs/pkgs/sagemath_doc...

 

[Justin C. Walker]

> These are now packages, and you find the build log in logs/pkgs/sagemath_doc…

I saw those dots, but did not connect them.

Thanks for the clarification.

Justin

[William Stein]

Trying to build on an M1 ARM Mac with MacOS 12.x finally gets past the
very first package (GMP), due to upgrading to 6.2.1. It fails with
gfortran, with an error about this version of macOS being "unreleased"
(which is not true, of course -- it is released):

[gfortran-10.3.0] checking if mkdir takes one argument... no
[gfortran-10.3.0] Error: configuring for an unreleased macOS version
arm-apple-darwin21.1.0
[gfortran-10.3.0] make[6]: *** [configure-gcc] Error 1
[gfortran-10.3.0] make[5]: *** [all] Error 2

So, I do "brew install gfortran", and start the build again with
"make". This fails in the same way, of course, since I need to do
./configure again, then make.

The build then fails with openblas:

[openblas-0.3.18] make[6]: *** No rule to make target
`../kernel/arm64/amin.S', needed by `samin_k.o'. Stop.

So I do "brew install openblas && ./configure && make" to continue onward:

This fundamentally fails, because the brew installed openblas doesn't
get detected by ./configure, and make results in immediately building
trying to build it, which fails again.

So Sage continues to be unsupported on the latest version of Apple's product.

At a minimum, it would be good to amend this sentence in the README:

"Sage fully supports all major Linux distributions, recent versions of
macOS, and Windows (using Cygwin, Windows Subsystem for Linux, or
using virtualization)."

to

"Sage fully supports all major Linux distributions, recent versions of
macOS on x86 hardware, and Windows (using Cygwin, Windows Subsystem
for Linux, or using virtualization). Sage does NOT support the latest
version of macOS on Apple Silicon (M1) hardware, except by running
Sage in a Linux virtual machine or by using a binary built via Mambaforge."

I'm not sure how to word the mamba part. The issue is that the Sage build
system can't build Sage on M1 macs, but the mamba forge people can, since
they have a completely different build system.

- William

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William (http://wstein.org)

[Matthias Köppe]

On Saturday, November 20, 2021 at 1:57:40 PM UTC-8 William Stein wrote:

So I do "brew install openblas && ./configure && make" to continue onward:

This fundamentally fails, because the brew installed openblas doesn't
get detected by ./configure, and make results in immediately building
trying to build it, which fails again.

A message at the end of the configure run tells you an extra step for homebrew.

[William Stein]

Detection of openblas does not work for me, even when doing that extra step.

/Users/wstein/build/sage$ ./config.status --recheck 2>&1 |grep
openblas && ./config.status 2>&1 | grep openblas
running CONFIG_SHELL=/bin/sh /bin/sh ./configure
PKG_CONFIG_PATH=/opt/homebrew/opt/sqlite/lib/pkgconfig:/opt/homebrew/opt/readline/lib/pkgconfig:/opt/homebrew/opt/openblas/lib/pkgconfig:/opt/homebrew/lib/pkgconfig:
--no-create --no-recursion
Checking whether SageMath should install SPKG openblas...
checking for library containing openblas_get_config... no
configure: no suitable system package found for SPKG openblas
checking whether any of openblas zlib bzip2 is installed as or will be
installed as SPKG... yes; install cbc as well
checking whether any of givaro gmp openblas is installed as or will be
installed as SPKG... yes; install fflas_ffpack as well
checking whether any of openblas is installed as or will be installed
as SPKG... yes; install gsl as well
checking whether any of glpk openblas gmp is installed as or will be
installed as SPKG... yes; install igraph as well
checking whether any of gmp openblas is installed as or will be
installed as SPKG... yes; install iml as well
checking whether any of openblas iconv readline bzip2 liblzma pcre
curl is installed as or will be installed as SPKG... yes; install r as
well
checking whether any of openblas is installed as or will be installed
as SPKG... yes; install suitesparse as well
openblas-0.3.18: no suitable system
package; standard, will be installed as an SPKG


The openblas brew package is definitely installed:

/Users/wstein/build/sage$ find /opt/homebrew |grep openblas
/opt/homebrew/Library/Taps/homebrew/homebrew-core/Formula/openblas.rb
/opt/homebrew/opt/openblas
/opt/homebrew/Cellar/openblas
/opt/homebrew/Cellar/openblas/0.3.18
/opt/homebrew/Cellar/openblas/0.3.18/INSTALL_RECEIPT.json
/opt/homebrew/Cellar/openblas/0.3.18/LICENSE
/opt/homebrew/Cellar/openblas/0.3.18/.brew
/opt/homebrew/Cellar/openblas/0.3.18/.brew/openblas.rb
/opt/homebrew/Cellar/openblas/0.3.18/include
/opt/homebrew/Cellar/openblas/0.3.18/include/lapacke_utils.h
/opt/homebrew/Cellar/openblas/0.3.18/include/lapacke.h
/opt/homebrew/Cellar/openblas/0.3.18/include/f77blas.h
/opt/homebrew/Cellar/openblas/0.3.18/include/openblas_config.h
/opt/homebrew/Cellar/openblas/0.3.18/include/lapacke_config.h
/opt/homebrew/Cellar/openblas/0.3.18/include/cblas.h
/opt/homebrew/Cellar/openblas/0.3.18/include/lapack.h
/opt/homebrew/Cellar/openblas/0.3.18/include/lapacke_mangling.h
/opt/homebrew/Cellar/openblas/0.3.18/README.md
/opt/homebrew/Cellar/openblas/0.3.18/lib
/opt/homebrew/Cellar/openblas/0.3.18/lib/libopenblas.a
/opt/homebrew/Cellar/openblas/0.3.18/lib/liblapack.dylib
/opt/homebrew/Cellar/openblas/0.3.18/lib/pkgconfig
/opt/homebrew/Cellar/openblas/0.3.18/lib/pkgconfig/openblas.pc
/opt/homebrew/Cellar/openblas/0.3.18/lib/cmake
/opt/homebrew/Cellar/openblas/0.3.18/lib/cmake/openblas
/opt/homebrew/Cellar/openblas/0.3.18/lib/cmake/openblas/OpenBLASConfigVersion.cmake
/opt/homebrew/Cellar/openblas/0.3.18/lib/cmake/openblas/OpenBLASConfig.cmake
/opt/homebrew/Cellar/openblas/0.3.18/lib/libopenblasp-r0.3.18.a
/opt/homebrew/Cellar/openblas/0.3.18/lib/libopenblasp-r0.3.18.dylib
/opt/homebrew/Cellar/openblas/0.3.18/lib/libopenblas.dylib
/opt/homebrew/Cellar/openblas/0.3.18/lib/libblas.dylib
/opt/homebrew/Cellar/openblas/0.3.18/lib/libopenblas.0.dylib
/opt/homebrew/Cellar/openblas/0.3.18/Changelog.txt

>
>
>
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--
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[Matthias Köppe]

> checking for library containing openblas_get_config... no

config.log please

[Matthias Köppe]

On Saturday, November 20, 2021 at 1:57:40 PM UTC-8 William Stein wrote:

it would be good to amend this sentence in the README:

"Sage fully supports all major Linux distributions, recent versions of
macOS, and Windows (using Cygwin, Windows Subsystem for Linux, or
using virtualization)."

I have updated README in https://trac.sagemath.org/ticket/32917, needs review.

 

[Steven Trogdon]

Perhaps not directly related to this release but I have numerous jobserver warnings when building the pdf documentation :

make[5]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.

that seems to mostly occur when changing folders to run the LaTeX Makefile

[reference] The LaTeX files are in local/share/doc/sage/latex/en/reference/references.

[reference] Run 'make' in that directory to run these through (pdf)latex

[reference] (use `make latexpdf' here to do that automatically).

LaTeX file written to /local/sage-git/sage/local/share/doc/sage/latex/en/reference/references

make[5]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.

latexmk -pdf -dvi- -ps-  'references.tex'

I believe the jobserver warning occurs when recursive 'makes' are not being handled properly. Should this be addressed?

[Kenji Iohara]

I use Mac OS 12.0.1 on my mac book pro (intel Core i5).
From the first built, I couldn’t compile Sage 9.5.beta6 and beta7, it has some problems to compile scipy-1.6.3.
Up to beta5, I had no problem on the compilation.

> 20/11/2021 22:12、'Justin C. Walker' via sage-release <sage-r...@googlegroups.com>のメール:

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[William Stein]

On Sat, Nov 20, 2021 at 3:53 PM Matthias Köppe <matthia...@gmail.com> wrote:
>
> > checking for library containing openblas_get_config... no
>
> config.log please

See attached. It's looks like a gfortran linking issue involving a
test program, but I don't really know...

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/9cc3e707-f4de-4bb7-97d1-e7260612374en%40googlegroups.com.



--
William (http://wstein.org)

[Dima Pasechnik]

Hi William,

please do

brew install pkg-config

and try again. From your log, it appears missing,for some reason,

configure:6572: checking for pkg-config
configure:6605: result: no


and this breaks everything in ./configure that relies on it.
Yes, for some packages there are workarounds for corner cases which
are meant to work without it, but I'd rather
not spend time debugging them too much...

Cheers
Dima

On Sun, Nov 21, 2021 at 5:06 PM William Stein <wst...@gmail.com> wrote:
>
> On Sat, Nov 20, 2021 at 3:53 PM Matthias Köppe <matthia...@gmail.com> wrote:
> >
> > > checking for library containing openblas_get_config... no
> >
> > config.log please
>
> See attached. It's looks like a gfortran linking issue involving a
> test program, but I don't really know...

Normally speaking,

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CACLE5GB-BLhN_Kn5Gwm6yP_KxXoJJAHAqr9i3r5B4rKn7Jm5xQ%40mail.gmail.com.

[Dima Pasechnik]

On Sun, Nov 21, 2021 at 6:10 PM Dima Pasechnik <dim...@gmail.com> wrote:
>
> Hi William,
>
> please do
>
> brew install pkg-config
>
> and try again. From your log, it appears missing,for some reason,
>
> configure:6572: checking for pkg-config
> configure:6605: result: no
>
>
> and this breaks everything in ./configure that relies on it.
> Yes, for some packages there are workarounds for corner cases which
> are meant to work without it, but I'd rather
> not spend time debugging them too much...

in this particular case it's probably just the following fix:

--- a/.homebrew-build-env
+++ b/.homebrew-build-env
@@ -23,7 +23,7 @@ export PKG_CONFIG_PATH
LIBRARY_PATH="$HOMEBREW/lib$LIBRARY_PATH"
[ -z "$CPATH" ] || CPATH=":${CPATH}"
CPATH="$HOMEBREW/include$CPATH"
-for l in readline bzip2 ntl polymake; do
+for l in readline bzip2 ntl polymake openblas; do
if [ -d "$HOMEBREW/opt/$l/lib" ]; then
LIBRARY_PATH="$HOMEBREW/opt/$l/lib:$LIBRARY_PATH"
fi

but on Homebrew openblas has pkg-config .pc file installed, so
strictly speaking it's not needed
(unless pkg-config is somehow gone AWOL)

Dima

[Dima Pasechnik]

PS. IM¬HO we just rise a hard error in ./configure if there is no pkg-config

[Eric Gourgoulhon]

On Ubuntu 20.04 running on Xeon E5-2623 + 16 GB RAM:
- incremental build (-j16) from 9.5.beta6, with system python (3.8.10): OK

- make ptestlong --> "All tests passed!"

Eric.

[Henri Girard]

For a few months i couldn't compile sage but today from a fresh ubuntu 20.04, it succeded, from a rizen 16 cors and 16 Go RAM

Henri

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[Steven Trogdon]

I have provided a solution to the jobserver warnings at https://trac.sagemath.org/ticket/32928

[Sébastien Labbé]

On Ubuntu 18.04, running tests with many optional and external packages, the tests stops at some point and among the files that are killed at this point are findstat.py and doctest/external.py. More precisely,

Using --optional=4ti2,build,ccache,cryptominisat,debian,dot2tex,e_antic,external,fricas,glucose,latte_int,lidia,normaliz,notedown,pandoc_attributes,pip,pycosat,pynormaliz,rst2ipynb,sage,sage.geometry.polyhedron,sage.rings.real_double,sage_numerical_backends_coin,sage_spkg

External software to be detected: 4ti2,cplex,dvipng,ffmpeg,graphviz,gurobi,imagemagick,internet,latex,lualatex,macaulay2,magma,maple,mathematica,matlab,octave,pandoc,pdf2svg,pdflatex,rubiks,scilab,xelatex

finishes with:

**********************************************************************
File "src/sage/databases/findstat.py", line 1231, in sage.databases.findstat.findmap
Failed example:
    q = findmap([(pi, pi.complement().increasing_tree_shape()) for pi in l], depth=2); q  # optional -- internet
Expected:
    0: Mp00061oMp00069 (quality [100])
Got:
    0: Mp00061oMp00069 (quality [97])
**********************************************************************
File "src/sage/databases/findstat.py", line 1236, in sage.databases.findstat.findmap
Failed example:
    p = findmap({pi: pi.complement().increasing_tree_shape() for pi in l}, depth=2); p    # optional -- internet
Expected:
    0: Mp00061oMp00069 (quality [100])
Got:
    0: Mp00061oMp00069 (quality [97])
Killing test src/sage/databases/findstat.py
Killing test src/sage/combinat/designs/ext_rep.py
Killing test src/sage/doctest/external.py
Killing test src/doc/en/constructions/number_theory.rst
Killing test src/sage/interfaces/jmoldata.py
Killing test src/doc/ja/tutorial/tour_polynomial.rst
Killing test src/sage/combinat/root_system/type_C.py
----------------------------------------------------------------------
----------------------------------------------------------------------
sage -t --long --random-seed=114684091447841116365620770388766582718 src/sage/combinat/designs/incidence_structures.py  # 1 doctest failed
sage -t --long --random-seed=114684091447841116365620770388766582718 src/sage/graphs/generic_graph.py  # 2 doctests failed
sage -t --long --random-seed=114684091447841116365620770388766582718 src/sage/graphs/graph.py  # 2 doctests failed
sage -t --long --random-seed=114684091447841116365620770388766582718 src/sage/interfaces/fricas.py  # 1 doctest failed
sage -t --long --random-seed=114684091447841116365620770388766582718 src/sage/sat/solvers/dimacs.py  # 2 doctests failed
sage -t --long --random-seed=114684091447841116365620770388766582718 src/sage/tests/cmdline.py  # 10 doctests failed
Doctests interrupted: 1676/4397 files tested
----------------------------------------------------------------------

The above failures are already listed at https://trac.sagemath.org/ticket/25536

I will re-run the tests hoping they will finish this time.

[Sébastien Labbé]

Again, running

./sage -t -p --all --long --optional=sage,optional,external,build --show-skipped

stops at findstat.py. Also src/sage/combinat/designs/ext_rep.py seems to again be among the tests that are killed:

    0: Mp00061oMp00069 (quality [100])

Got:
    0: Mp00061oMp00069 (quality [97])
**********************************************************************
File "src/sage/databases/findstat.py", line 1236, in sage.databases.findstat.findmap
Failed example:
    p = findmap({pi: pi.complement().increasing_tree_shape() for pi in l}, depth=2); p    # optional -- internet
Expected:
    0: Mp00061oMp00069 (quality [100])
Got:
    0: Mp00061oMp00069 (quality [97])
Killing test src/sage/databases/findstat.py
Killing test src/sage/combinat/designs/ext_rep.py

Killing test src/sage/numerical/backends/generic_backend.pyx
Killing test src/sage/combinat/words/word_infinite_datatypes.py
Killing test src/sage/combinat/baxter_permutations.py
Killing test src/sage/rings/polynomial/polynomial_complex_arb.pyx
Killing test src/sage/topology/simplicial_complex_catalog.py
----------------------------------------------------------------------
sage -t --long --random-seed=50431416943257225489127275634010530880 src/sage/tests/cmdline.py  # 10 doctests failed
sage -t --long --random-seed=50431416943257225489127275634010530880 src/sage/graphs/generic_graph.py  # 2 doctests failed
sage -t --long --random-seed=50431416943257225489127275634010530880 src/sage/interfaces/fricas.py  # 1 doctest failed
sage -t --long --random-seed=50431416943257225489127275634010530880 src/sage/graphs/graph.py  # 2 doctests failed
sage -t --long --random-seed=50431416943257225489127275634010530880 src/sage/sat/solvers/dimacs.py  # 2 doctests failed
sage -t --long --random-seed=50431416943257225489127275634010530880 src/sage/combinat/designs/incidence_structures.py  # 1 doctest failed
Doctests interrupted: 1658/4397 files tested
----------------------------------------------------------------------
Total time for all tests: 2605.3 seconds
    cpu time: 16433.5 seconds
    cumulative wall time: 20302.4 seconds

[Samuel Lelièvre]

On Cygwin, build failure on sagemath_doc_html-none,
apparently having something to do with Singular.

Details:

https://www.math.u-psud.fr/~lelievre/t/slel-2021-11-27-s95b7-cygwin-fail.zip

[Matthias Köppe]

I have added this report to https://trac.sagemath.org/ticket/32789