Sage 9.3.rc0 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 

2c25f07cfd (tag: 9.3.rc0, trac/develop) Updated SageMath version to 9.3.rc0

5e86bf2b7a Trac #31326: macos-11.0: scipy build fails

ba54691142 Trac #31253: Put equations in stable position for backend cdd

badd79c19c Trac #30284: Immutability of Bundle Connections

db46bf9d2f Trac #31340: memory leak when constructing a row of an integer matrix

b80a47c7e6 Trac #29537: build not portable despite using SAGE_FAT_BINARY=yes, NTL/openblas/numpy-related

3071aad95c Trac #24688: implement Faltings height of an elliptic curve

fd64106d4a Trac #31524: refresh one file about quadratic forms

f990b22594 Trac #31520: refresh similarity class

eb11d77df7 Trac #31518: refresh necklace.py

73239ab0bd Trac #31313: Memory leak in bipartite_graph (and so in generalised_quadrangle_with_spread)

2322da7448 Trac #23801: subfields of large finite fields raises a TypeError

a452b31351 Trac #23459: QuadraticField(D) fails for large D

5ed8983af9 Trac #31503: Updates: pillow 8.1.2, matplotlib 3.3.4, imagesize 1.2.0

4c24441cf3 Trac #31047: Conversion of symbolic functions with latex_name or nargs from maxima and sympy is broken

35b61abdf1 Trac #31242: adding some capital letters to names

91d4938f2a Trac #31109: Add degree method to function  field element

6a9769caff Trac #29330: checking for skew_hermitian

077f2779f7 Trac #31497: fix some annotations and flake8 E702

b570e32462 Trac #31493: tox.ini, build/bin/write-dockerfile.sh: Use configure --enable-download-from-upstream-url --enable-experimental-packages instead of setting SAGE_SPKG directly

ab9ca9cf1b Trac #31374: Fix an if statement that is never called in normal_form

f81c402442 Trac #31471: Matrix-wise functions for univariate polynomial matrices

d1b5a25c8e Trac #31460: add_condition method improved

324fff0a5f Trac #30504: System package information for MacPorts

61eb20b36f Trac #28530: Bug in polynomial rootfinding over QQbar related to QQbar → CC → pari conversions

96b4d505ad Trac #10147: conversions of constant polynomials

1eeda605ac Trac #9825: desolve_system unable to interpret ilt and Maxima's temporary variables

69cfd456c4 Trac #31482: Update latte_int

1a15085c66 Trac #30383: Add "configure --disable-notebook"; show descriptions of optional packages in "configure --help"

ca83d06475 Trac #25993: Upgrade Singular

941137bddc Trac #30826: Fix doubled word typos

30432b5769 Trac #23332: Calculating eigenvectors of symbolic matrices leads to a crash.

ea68cd5537 Trac #31504: details in relint config

e5683e76f0 Trac #31500: avoid empty list as default argument

06e0c36e96 Trac #31492: GH Actions: Reduce/reorder macOS tests

dc5a69bc14 Trac #31484: Allow keyboard interrupt of mcqd

86d50d6f57 Trac #31474: Upgrade cysignals to 1.10.3

e6fc887b24 Trac #31470: Allow matrices and vectors over Ore polynomial rings

309144acbb Trac #31467: Upgrade cvxopt to 1.2.6

30ed1a8ef1 Trac #31466: Upgrade numpy to 1.19.5

80b87cd65b Trac #31461: Fix tests formatting in `graphs/generators/families.py`

9ab135682a Trac #31454: Fix bug in WordMorphism.growing_letters() and periodic_points()

0ad9af13cb Trac #31394: add Gritsenko's SRG(65, 32, 15, 16)

b5d584dcbb Trac #31375: bootstrap: Give advice regarding bootstrap prerequisites on failure

1ee782e9ad Trac #31360: git: Reduce from a normal standard package to an optional script package

d1372cbb71 Trac #31330: less usage of deepcopy in quadratic forms

80303834d3 Trac #26912: Test failure in doctest framework

8d80eae366 Trac #31468: texttable: Add missing dependencies

b48adf62e5 Trac #31423: Do not use sage-pip-uninstall for PEP-517 packages, do not give up if sage-pip-uninstall fails

114dd26166 Trac #31335: homebrew: Unused packages (singular, pari, ...) in /usr/local leak into sagelib/cysignals builds via distutils.cfg

3a6e07dab4 Trac #31204: doctests: Filter out linker warning messages

5cb72aade9 (tag: 9.3.beta9) Updated SageMath version to 9.3.beta9

[Samuel Lelièvre]

Thanks for this new release.

On macOS 10.14.6 with Homebrew and many packages,
running `make` led to an error while building dochtml.

```
Traceback (most recent call last):
File "/usr/local/Cellar/python@3.9/3.9.2_2/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py",
line 188, in _run_module_as_main
mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
File "/usr/local/Cellar/python@3.9/3.9.2_2/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py",
line 147, in _get_module_details
return _get_module_details(pkg_main_name, error)
File "/usr/local/Cellar/python@3.9/3.9.2_2/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py",
line 111, in _get_module_details
__import__(pkg_name)
File "/opt/s/sage93f/local/lib/python3.9/site-packages/sage_docbuild/__init__.py",
line 57, in <module>
import sage.all
File "/opt/s/sage93f/local/lib/python3.9/site-packages/sage/all.py",
line 142, in <module>
from sage.rings.all import *
File "/opt/s/sage93f/local/lib/python3.9/site-packages/sage/rings/all.py",
line 83, in <module>
from .polynomial.all import *
File "/opt/s/sage93f/local/lib/python3.9/site-packages/sage/rings/polynomial/all.py",
line 42, in <module>
from sage.rings.polynomial.laurent_polynomial_ring import
LaurentPolynomialRing
File "/opt/s/sage93f/local/lib/python3.9/site-packages/sage/rings/polynomial/laurent_polynomial_ring.py",
line 50, in <module>
from sage.rings.polynomial.laurent_polynomial import
LaurentPolynomial_mpair, LaurentPolynomial_univariate
File "sage/rings/polynomial/laurent_polynomial.pyx", line 1, in init
sage.rings.polynomial.laurent_polynomial
(build/cythonized/sage/rings/polynomial/laurent_polynomial.c:40841)
File "sage/matrix/matrix0.pyx", line 28, in init sage.matrix.matrix0
(build/cythonized/sage/matrix/matrix0.c:44271)
File "/opt/s/sage93f/local/lib/python3.9/site-packages/sage/modules/free_module.py",
line 167, in <module>
import sage.matrix.matrix_space
File "/opt/s/sage93f/local/lib/python3.9/site-packages/sage/matrix/matrix_space.py",
line 55, in <module>
from . import matrix_mpolynomial_dense
ImportError: dlopen(/opt/s/sage93f/local/lib/python3.9/site-packages/sage/matrix/matrix_mpolynomial_dense.cpython-39-darwin.so,
2): Library not loaded:
/opt/s/sage93f/local/lib/libSingular-4.1.1.dylib
Referenced from:
/opt/s/sage93f/local/lib/python3.9/site-packages/sage/matrix/matrix_mpolynomial_dense.cpython-39-darwin.so
Reason: image not found
```

Logs:

https://www.math.u-psud.fr/~lelievre/t/slel-2021-03-24-s93rc0.zip

[Matthias Köppe]

We updated Singular. You may have to use "make sagelib-clean" to rebuild the Sage library from scratch.

(See https://trac.sagemath.org/ticket/29711 for the issue that sagelib does not have proper dependencies on the libraries that it uses.)

[Samuel Lelièvre]

Le mer. 24 mars 2021 à 03:14, Matthias Köppe:

>
> We updated Singular. You may have to use "make sagelib-clean"
> to rebuild the Sage library from scratch.
>
> (See https://trac.sagemath.org/ticket/29711 for the issue that
> sagelib does not have proper dependencies on the libraries
> that it uses.)

That allowed the build to complete and tests to pass. Thanks!
```
$ make -s V=0 sagelib-clean
...
$ make -s V=0
...
$ make -s V=0 testlong
...
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 16511.8 seconds
cpu time: 13343.4 seconds
cumulative wall time: 16077.7 seconds
```

[David Joyner]

This release built from scratch on my mini mac, OS 11.2.3.

--
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/5448d585-d490-42fe-9c5e-78588e554ecfn%40googlegroups.com.

[Sébastien Labbé]

On Ubuntu 18.04, with various optional/external packages, I get:

Using --optional=4ti2,build,cbc,ccache,cryptominisat,database_jones_numfield,debian,dot2tex,e_antic,external,fricas,glucose,latte_int,libnauty,lidia,lrslib,memlimit,normaliz,notedown,pandoc_attributes,pip,pycosat,pynormaliz,rst2ipynb,sage,sage_numerical_backends_coin,sage_spkg

----------------------------------------------------------------------
sage -t --long --warn-long 74.9 --random-seed=0 src/sage/symbolic/integration/integral.py  # 1 doctest failed
sage -t --long --warn-long 74.9 --random-seed=0 src/sage/symbolic/integration/external.py  # 1 doctest failed
sage -t --long --warn-long 74.9 --random-seed=0 src/sage/tests/cmdline.py  # 1 doctest failed
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,graphviz,imagemagick,internet,latex,octave,pandoc

Above failures reproduce and are copied below.

The integration issues are new : the behavior of sqrt seems to have changed in mathematica free.

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

sage -t --long --warn-long 79.7 --random-seed=0 src/sage/symbolic/integration/integral.py
**********************************************************************
File "src/sage/symbolic/integration/integral.py", line 579, in sage.symbolic.integration.integral.integrate
Failed example:
    f.integrate(x, algorithm="mathematica_free")   # optional - internet
Expected:
    x*y^z + sqrt(1/2)*sqrt(pi)*fresnel_sin(sqrt(2)*x/sqrt(pi))
Got:
    x*y^z + Sqrt(1/2*pi)*fresnel_sin(x*Sqrt(2/pi))
**********************************************************************


sage -t --long --warn-long 79.7 --random-seed=0 src/sage/symbolic/integration/external.py
**********************************************************************
File "src/sage/symbolic/integration/external.py", line 110, in sage.symbolic.integration.external.mma_free_integrator
Failed example:
    mma_free_integrator(exp(-x^2)*log(x), x) # optional - internet
Expected:
    1/2*sqrt(pi)*erf(x)*log(x) - x*hypergeometric((1/2, 1/2), (3/2, 3/2), -x^2)
Got:
    1/2*Sqrt(pi)*erf(x)*log(x) - x*hypergeometric((1/2, 1/2), (3/2, 3/2), -x^2)
**********************************************************************



sage -t --long --warn-long 79.7 --random-seed=0 src/sage/tests/cmdline.py
**********************************************************************
File "src/sage/tests/cmdline.py", line 607, in sage.tests.cmdline.test_executable
Failed example:
    err  # optional - internet
Expected:
    ''
Got:
    '/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/misc/package.py:114: UserWarning: failed to fetch the version of pkg=\'ore_algebra\' at https://pypi.org/pypi/ore_algebra/json\n  warnings.warn("failed to fetch the version of pkg={!r} at {}".format(pkg, url))\n'
**********************************************************************

[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM :

• upgrading 9.3.beta9 (configured to use all available system packages) to 9.3.rc0 fails, due to a bunch of expecting str, found bytes errors in various places (not easy to find, due to excessive verbosity of the error reports…) ;

• rebuilding from scratch (make distclean ; ./bootstrap ; ./configure --enable-download-from-upstream-url ; make) succeeds, with the exceptions that :

  • configure suggests the systemwide installation of texlive-latex-extra texlive-xetex latexmk dvipng default-jdk ffmpeg libavdevice-dev libcdd-dev libcdd-tools libec-dev eclib-tools libgiac-dev xcas pari-gp2c lcalc liblfunction-dev libhomfly-dev pari-gp2c libpari-dev pari-doc pari-elldata pari-galdata pari-galpol pari-seadata, all of which are already installed systemwide (alrady reported)
    ;

  • similarly, the reinstallation of some optional packages succeeds, but ~pari_jupyter~ fails to install ; due to dependencies, I ended up having the following optional packages installed :

    • cypari2 [D?]
    • dot2tex
    • fricas
    • gap_jupyter
    • gap_packages
    • json5 [D?]
    • jupyter_kernel_gap [D?]
    • jupyter_kernel_singular [D?]
    • jupyterlab
    • jupyterlab_server [D?]
    • kenzo
    • libsemigroups [D?]
    • pysingular
    • python_dateutil [D?]
    • sagemath_standard [D?]
    • singular_jupyter

    [D?] denotes probable dependencies (packages that ended up
    installed without request from me…).

• ptestlong results in one transient and two permanent failures
  (identical to those already reported for previous betas) :

File	Results	P/T
src/sage/tests/parigp.py	Timed out	T
src/sage/tests/gap_packages.py	1 doctest failed	P
src/sage/groups/abelian_gps/abelian_group_gap.py	1 doctest failed	P

HTH,

​

[Markus Wageringel]

This is caused by the changes to symbolic functions in ticket #31047 and also affects the Mathematica interface. I have opened https://trac.sagemath.org/ticket/31756 for it.

[Emmanuel Charpentier]

Thank you very much ! I was hunting this one, but somebody seems to have found it.

BTW, conversion to maxima also happens in the most unexpected places (e. g. `simplify`), and I got burned by this one in unrelated work...

Now that we have diagnosis, onward to therapeutics : I took the liberty to Cc Trac#31756 the participants to Trac#31047.