Sage 9.3.beta1 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 

222059565b (tag: 9.3.beta1, trac/develop) Updated SageMath version to 9.3.beta1

8e72e1b9c9 Trac #30821: some typos found using "sage --tox"

4c68ef35bc Trac #30707: Fix indent in Cython file

3e2a55a530 Trac #30684: make "a in NN" work in more cases

d5ab47b4b4 Trac #30555: Incorrect gt() and lt() functions in Berkovich space

2caf9642a5 Trac #30836: minor flake8 changes in typeset/ and games/

04442e4922 Trac #30792: Homebrew: add $HOMEBREWPREFIX/opt/texinfo/bin to PATH

54d7fde4c2 Trac #30790: a few details in misc/misc.py

f383048d1b Trac #30789: refresh cyclotomic coefficients

cc0a316d25 Trac #30788: flake8 for new_kschur

dfff7d47d8 Trac #30739: Remove a few more .all imports

ea79e615f4 Trac #30715: Remove a few .all imports

e244981b08 Trac #30712: Gracefully fail if pip is not correctly installed

da6cf243c4 Trac #30708: Remove Python 2 code in autogenerated interpreters

e6e1172703 Trac #30697: Derived subalgebra of semisimple Lie algebra

61fe2f0934 Trac #30673: Add compiled cython and virtual environments in gitignore

155d8377c7 Trac #30646: sage.knots, sage.game_theory: Change 'optional - cbc' to 'optional - sage_numerical_backends_coin`

01d7cc0514 Trac #30630: findstat error handling

8fc1dc613d Trac #30626: Fix build/pkgs/libhomfly/distros/debian.txt

00a2f89e5b Trac #30615: flake8 and other details in posets.py

5a0e4abce8 Trac #30591: some flake8 cleanup in plane conics

d925f48012 Trac #30565: build/bin/sage-guess-package-system: Fix up /bin/sh-ification

31dfd9fd11 Trac #30558: Implement the conjugate of a set partition

973606c531 Trac #30553: some cleanup (flake8) in poset files

8c33299b26 Trac #30552: display options for matrices

c19f59acc3 Trac #30545: A 1-dimensional polytope has no edge

38bab5ad77 Trac #30542: various flake8 fixes

c71679ac49 Trac #30530: some flake8 cleanup in elliptic curve

6d28b20968 Trac #30508: remove obsolete lazy imports

2cfbbbeac2 Trac #30471: Change "can not" to "cannot" in many places

5f84554640 Trac #30466: unicode_art for elements of AffineGroup

3f22cb3f8e Trac #30462: Dark theme for Three.js viewer

b74b62e57e Trac #30458: Outsource some functions in bit_vector_operations.cc

3fdfdd1047 Trac #30457: fix typos in occurrence, occurred, occurring

394252d1fb Trac #30418: Missing PDF icons in the Sage documentation website

3db1a2ffb7 Trac #30361: Add pyright config and linting documentation

538ee1c5e1 Trac #30305: Lifting doesn't work for an augmented valuation over a number field

189723087b Trac #30141: Potential good reduction for dynamical systems

0cdb6c22dd Trac #29246: Improve handling of easy cases in lift_to_sl2z()

b2e2dd8381 Trac #28467: wrong bound in "Cannot compute primes beyond ..."

0787a77169 Trac #28294: Ordered Set Partition Inversion Statistic

83063d63e4 Trac #26606: Bug in latex for power series with greek variable names

8cbd28fe67 Trac #23174: p and p^n-th roots in function fields

be8479b04d Trac #19120: efficient algorithm to compute continued fraction of a sum of continued fractions

a0b507b535 Trac #19112: Add a function "isometry" to the quadratic forms package.

84fe0c9e67 Trac #30839: Add more conda.txt

2c69b7dfe1 Trac #30838: Generators for homology of simplicial complexes

c186f8b88a Trac #30834: build/pkgs/sage_sws2rst: Fix metadata

eb04180ce7 Trac #30829: typos found with sage --tox in graphs (3)

2097d857ca Trac #30828: typos found with sage --tox in graphs (2)

b3f3c553b9 Trac #30827: typos found with sage --tox in graphs (1)

1d7508b311 Trac #30820: some CI details

7737bd2409 Trac #30815: better fricas and giac conversion for symbolic matrices

3033562322 Trac #30811: Speed up truncation of polynomials

37dac75a83 Trac #30808: refresh symmetric group algebra

8d52566195 Trac #30807: refresh partition_algebra.py

b1fa725151 Trac #30841: bootstrap: Do not depend on sage-env, sage-env-config

fec8cd23b1 Trac #30753: Further improvements in method subgraph

adec03d4b0 Trac #30625: upgrade GMP to version 6.2.0

2c87dc16f2 (tag: 9.3.beta0) Updated SageMath version to 9.3.beta0

[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM, upgrading 9.3.beta0 to 9.3.beta1 configured to use all available system packages leads to :

• ./configure insists on installing :

  • texlive-generic-extra
  • texlive-xetex (*)
  • latexmk (*)
  • pandoc (*)
  • dvipng (*)
  • default-jdk (*)
  • ffmpeg (*)
  • libavdevice-dev
  • libec-dev (*)
  • eclib-tools (*)
  • libgiac-dev (*)
  • xcas (*)
  • pari-gp2c (*)
  • lcalc (*)
  • liblfunction-dev
  • pari-gp2c (*)
  • libpari-dev (*)
  • pari-doc (*)
  • pari-elldata (*)
  • pari-galdata (*)
  • pari-galpol (*)
  • pari-seadata (*)

  notwithstanding the fact that most of them (marked (*) above) are already installed. Re-installing them hads no effect, and Sage upgrade reinstalls (at least) its own versions of pari and giac.

• ptestlong results in three permanent failures, all already
  reported for previous versions :

File	Results	P/T
src/sage/modules/fg_pid/fgp_module.py	3 doctests failed	P
src/doc/en/constructions/algebraic_geometry.rst	1 doctest failed	P
src/sage/modules/free_module_morphism.py	3 doctests failed	P

HTH,

​

[Sébastien Labbé]

On Ubuntu 18.04, running tests with various optional and external packages, I get

Using --optional=4ti2,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

[...]

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

All tests passed!
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,graphviz,imagemagick,internet,latex,octave,pandoc

First time in 2 years that such a thing happens. Congratulation!

This is with the version of sympow which is in Sage:

$ sage -standard | grep sympow
sympow..................................2.023.6 (2.023.6)

Follow up at (including the ticket fixing sympow issue which now have a positive review):

https://trac.sagemath.org/ticket/25536

[Sébastien Labbé]

• notwithstanding the fact that most of them (marked (*) above) are already installed. Re-installing them hads no effect,

I created a ticket related to this issue earlier this week here:

https://trac.sagemath.org/ticket/30863

 

[Kenji Iohara]

I could compile from the first built on Mac OS 10.15.7 with XCode 12, but make ptestlong failed: 

[Thierry Dumont]

Ubuntu 2-10, from beta0 to beta1.

-Compilation: no problem.
- make ptestlong:

----------------------------------------------------------------------
sage -t --long --warn-long 90.3 --random-seed=0
src/sage/tests/cmdline.py # 2 doctests failed
sage -t --long --warn-long 90.3 --random-seed=0
src/sage/modules/fg_pid/fgp_module.py # 3 doctests failed
sage -t --long --warn-long 90.3 --random-seed=0
src/doc/en/constructions/algebraic_geometry.rst # 1 doctest failed
sage -t --long --warn-long 90.3 --random-seed=0
src/doc/en/developer/coding_in_other.rst # 1 doctest failed
sage -t --long --warn-long 90.3 --random-seed=0
src/sage/modules/free_module_morphism.py # 3 doctests failed
----------------------------------------------------------------------

[Dima Pasechnik]

most if not all of these are fixed by https://trac.sagemath.org/ticket/29719
>
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[Andrew]

I am using macosx 10.15.7 with homebrew. After a few initial missteps I got 9.3.beta1 to compile with the doctest errors listed below.

I have been having trouble compiling sage for a while so I have been avoiding compiling it on my main computer since 9.1 was released. After reading https://groups.google.com/forum/#!topic/sage-devel/5lBTr4gZuic I felt courageous and decided to try again. Unfortunately, for me, with 9.3.beta1 on mac osx 10.15.7, the build fails almost straight away. After typing `make` I saw:

make -j3 build/make/Makefile --stop
./bootstrap -d
rm -rf config configure build/make/Makefile-auto.in
rm -f src/doc/en/installation/*.txt
rm -rf src/doc/en/reference/spkg/*.rst
rm -f src/doc/en/reference/repl/*.txt
src/doc/bootstrap:60: installing src/doc/en/installation/arch*.txt
src/doc/bootstrap:60: installing src/doc/en/installation/debian*.txt
src/doc/bootstrap:60: installing src/doc/en/installation/fedora*.txt
src/doc/bootstrap:60: installing src/doc/en/installation/cygwin*.txt
src/doc/bootstrap:60: installing src/doc/en/installation/homebrew*.txt
src/doc/bootstrap:70: installing src/doc/en/reference/spkg/*.rst
src/doc/bootstrap:102: installing src/doc/en/reference/repl/options.txt
must source sage-env-config before sage-env
Error setting environment variables by sourcing '/usr/local/src/sage/src/bin/sage-env';
possibly contact sage-devel (see http://groups.google.com/group/sage-devel).
make[1]: *** [configure] Error 1
make: *** [base-toolchain] Error 2

I don't know if this is a problem with the make scripts or an idiosyncrasy with my setup. After looking through the scripts I manually ran

source src/bin/sage-env-config.in

This fixed the sage-env-config problem as now `make` runs `configure` kicked after which sage started to build, however, the compilation eventually failed even after a `make distclean`. It then occurred to me that the problem might be due to the ccache, so I tried:

make distclean

local/bin/ccache --clear

source .homebrew-build-env # even though I didn't mention it before, I used this with the failed build attempts...

make

This time sage built correctly and `make ptestlong` resulted in the following failures:

----------------------------------------------------------------------
sage -t --long --warn-long 72.0 --random-seed=0 src/sage/tests/cmdline.py  # 1 doctest failed
sage -t --long --warn-long 72.0 --random-seed=0 src/sage/functions/other.py  # 1 doctest failed
sage -t --long --warn-long 72.0 --random-seed=0 src/sage/repl/preparse.py  # 12 doctests failed
sage -t --long --warn-long 72.0 --random-seed=0 src/sage/parallel/map_reduce.py  # Timed out
sage -t --long --warn-long 72.0 --random-seed=0 src/sage/data_structures/mutable_poset.py  # 1 doctest failed
sage -t --long --warn-long 72.0 --random-seed=0 src/sage/rings/polynomial/pbori/randompoly.py  # 1 doctest failed
----------------------------------------------------------------------

I can post more details if needed.

In my case, clearing the ccache seemed to fix he issues that I was having.

[Dima Pasechnik]

Well, that's 3rd or so report that could have been avoided, but
https://trac.sagemath.org/ticket/30795#comment:6
"Better development experience can't be a blocker" (c) Volker Braun

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[Samuel Lelievre]

> From: Volker
> Subject: Sage 9.3.beta1 released

>
> 222059565b (tag: 9.3.beta1, trac/develop)
> Updated SageMath version to 9.3.beta1

Thanks for this new release!

All tests passed here when running  `make testlong`
(more detail below), but I could not install JupyterLab.

Setup

- macOS 10.14.6 Mojave
- many homebrew packages
- existing Sage installation previously at some 9.2.rcN

Commands

```
$ git pull origin develop -q
$ source .homebrew-build-env
$ MAKE='make -j1'
$ V=0
$ ./bootstrap -q
$ ./configure --enable-openssl -q
$ make -s V=0 && make -s V=0 testlong
...
All tests passed!
```

```
$ V=0 ./sage -i jupyterlab_widgets
...
[nodeenv] Requirement already satisfied: nodeenv~=1.4.0 in /opt/s/sage93b/local/lib/python3.8/site-packages (from -r /opt/s/sage93b/build/pkgs/nodeenv/requirements.txt (line 1)) (1.4.0)
make --no-print-directory nodejs-no-deps
cd '/opt/s/sage93b/build/pkgs/nodejs' && . '/opt/s/sage93b/src/bin/sage-env-config' && . '/opt/s/sage93b/src/bin/sage-env' && . '/opt/s/sage93b/build/bin/sage-build-env-config' && sage-logger -p '/opt/s/sage93b/build/pkgs/nodejs/spkg-install' '/opt/s/sage93b/logs/pkgs/nodejs-12.18.3.log'
[nodejs-12.18.3] Will use/install nodejs in nodeenv located at /opt/s/sage93b/local/share/nodejs/12.18.3 ...
[nodejs-12.18.3]  * Environment already exists: /opt/s/sage93b/local/share/nodejs/12.18.3
[nodejs-12.18.3]  * Install prebuilt node (12.18.3) .
[nodejs-12.18.3] Traceback (most recent call last):
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/urllib/request.py", line 1350, in do_open
[nodejs-12.18.3]     h.request(req.get_method(), req.selector, req.data, headers,
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/http/client.py", line 1255, in request
[nodejs-12.18.3]     self._send_request(method, url, body, headers, encode_chunked)
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/http/client.py", line 1301, in _send_request
[nodejs-12.18.3]     self.endheaders(body, encode_chunked=encode_chunked)
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/http/client.py", line 1250, in endheaders
[nodejs-12.18.3]     self._send_output(message_body, encode_chunked=encode_chunked)
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/http/client.py", line 1010, in _send_output
[nodejs-12.18.3]     self.send(msg)
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/http/client.py", line 950, in send
[nodejs-12.18.3]     self.connect()
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/http/client.py", line 1424, in connect
[nodejs-12.18.3]     self.sock = self._context.wrap_socket(self.sock,
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/ssl.py", line 500, in wrap_socket
[nodejs-12.18.3]     return self.sslsocket_class._create(
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/ssl.py", line 1040, in _create
[nodejs-12.18.3]     self.do_handshake()
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/ssl.py", line 1309, in do_handshake
[nodejs-12.18.3]     self._sslobj.do_handshake()
[nodejs-12.18.3] ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1123)
[nodejs-12.18.3]
[nodejs-12.18.3] During handling of the above exception, another exception occurred:
[nodejs-12.18.3]
[nodejs-12.18.3] Traceback (most recent call last):
[nodejs-12.18.3]   File "/opt/s/sage93b/local/bin/nodeenv", line 8, in <module>
[nodejs-12.18.3]     sys.exit(main())
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/site-packages/nodeenv.py", line 1046, in main
[nodejs-12.18.3]     create_environment(env_dir, opt)
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/site-packages/nodeenv.py", line 935, in create_environment
[nodejs-12.18.3]     install_node(env_dir, src_dir, opt)
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/site-packages/nodeenv.py", line 700, in install_node
[nodejs-12.18.3]     install_node_wrapped(env_dir, src_dir, opt)
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/site-packages/nodeenv.py", line 722, in install_node_wrapped
[nodejs-12.18.3]     download_node_src(node_url, src_dir, opt)
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/site-packages/nodeenv.py", line 553, in download_node_src
[nodejs-12.18.3]     dl_contents = io.BytesIO(urlopen(node_url).read())
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/site-packages/nodeenv.py", line 585, in urlopen
[nodejs-12.18.3]     return urllib2.urlopen(req)
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/urllib/request.py", line 222, in urlopen
[nodejs-12.18.3]     return opener.open(url, data, timeout)
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/urllib/request.py", line 525, in open
[nodejs-12.18.3]     response = self._open(req, data)
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/urllib/request.py", line 542, in _open
[nodejs-12.18.3]     result = self._call_chain(self.handle_open, protocol, protocol +
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/urllib/request.py", line 502, in _call_chain
[nodejs-12.18.3]     result = func(*args)
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/urllib/request.py", line 1393, in https_open
[nodejs-12.18.3]     return self.do_open(http.client.HTTPSConnection, req,
[nodejs-12.18.3]   File "/opt/s/sage93b/local/lib/python3.8/urllib/request.py", line 1353, in do_open
[nodejs-12.18.3]     raise URLError(err)
[nodejs-12.18.3] urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1123)>
[nodejs-12.18.3] Error installing nodejs ... exiting
make[2]: *** [nodejs-no-deps] Error 1
make[1]: *** [/opt/s/sage93b/local/var/lib/sage/installed/nodejs-12.18.3] Error 2

real 0m5.159s
user 0m3.140s
sys 0m1.242s
***************************************************************
Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make jupyterlab_widgets'):

* package:         nodejs-12.18.3
  last build time: Nov 18 15:50
  log file:        /opt/s/sage93b/logs/pkgs/nodejs-12.18.3.log

It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

make: *** [jupyterlab_widgets] Error 1
```

[Dima Pasechnik]

On Fri, Nov 20, 2020 at 12:42 AM Samuel Lelievre
<samuel....@gmail.com> wrote:
>
>
> > From: Volker
> > Subject: Sage 9.3.beta1 released
> >
> > 222059565b (tag: 9.3.beta1, trac/develop)
> > Updated SageMath version to 9.3.beta1
>
> Thanks for this new release!
>
> All tests passed here when running `make testlong`
> (more detail below), but I could not install JupyterLab.

the usual ssl blues, no?
Can one use nodejs from Homebrew instead?
(this is something we need to enable properly, via spkg-configure)

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[Matthias Köppe]

On Friday, November 20, 2020 at 12:32:38 AM UTC-8 Dima Pasechnik wrote:

Can one use nodejs from Homebrew instead?
(this is something we need to enable properly, via spkg-configure)

Ticket https://trac.sagemath.org/ticket/30476, with the modest goal of just *documenting* how to get a fully functional Sage running in a system jupyter notebook or jupyterlab, needs help.

 

[Matthias Köppe]

Samuel, you didn't include config.log, but my guess is that it would reveal that you are not using python3 from system or homebrew. config.log contains the relevant information why the system python3 is rejected by Sage.

[Samuel Lelievre]

Sorry for the sloppy report without a config.log.

For the record, my workaround to the problem
was to use the brew-installed Jupyter + JupyterLab.
One can install the SageMath Jupyter kernel for it
quite easily. The following works on macOS
(to find out what to put for KERNELS, one can run
commands such as `jupyter kernelspec list`
or `jupyter --paths`):
```
$ SAGE_LOCAL=`sage -c 'print(SAGE_LOCAL)'`
$ SAGE_KERNEL=$SAGE_LOCAL/share/jupyter/kernels/sagemath
$ KERNELS=$HOME/Library/Jupyter/kernels
$ ln -s $SAGE_KERNEL $KERNELS
```
Then instead of `sage -n jupyter` or `sage -n jupyterlab`,
Jupyter Notebook and JupyterLab can be launched
the "normal" (non-Sage-specific) way:
```
$ jupyter notebook
$ jupyter lab
```


Fri 2020-11-20 18:08:00 UTC, Matthias Köppe:

>
> Samuel, you didn't include config.log, but my guess

> is that it would reveal that you are not using python3

>  from system or homebrew. config.log contains the

> relevant information why the system python3 is

> rejected by Sage.
>
> Fri 2020-11-20 00:42:07 UTC Samuel Lelievre: