Sage 9.0.beta9 released

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Volker Braun

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Dec 8, 2019, 4:41:25 PM12/8/19
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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 


87c3057957 (tag: 9.0.beta9, trac/develop) Updated SageMath version to 9.0.beta9
abea10f4ae (origin/develop) Trac #28843: typo ticket: explicitely -> explicitly
3988ae0c3b Trac #28841: fix some little details in doc
d370054b01 Trac #28839: adding a minimal lgtm.yml file
9466c95d7f Trac #28835: Remove python3-known-passing.txt and the corresponding parts of the Makefile
368a68abad Trac #28830: cleaning the file dlx.py
08421c59a1 Trac #28792: SageNB, message about removal
6a92dab9a4 Trac #28840: pari 2.11.2
1d1e3a3cac Trac #28833: ResourceWarning: unclosed file with SAGE_DEBUG=yes
d3e64db048 Trac #28818: from gap to libgap in strongly_regular_db
6147d1a5c6 Trac #28639: Polyhedron_normaliz: Initialize new cone from both Vrep and Hrep
f312974943 Trac #28834: Doctesting: don't test SageNB files unless SageNB has been installed
9e0670240c Trac #28822: Use assert on a condition that should always be true
3814db49b8 Trac #28826: a few typos
b2254ebec7 Trac #28476: norm returns a negative number
71ec07fb58 Trac #28289: Settings in ipython_config.py can cause tests to fail
f1b8ad8d50 Trac #28825: refresh the file combinat/tuple
4c75b8087d Trac #28821: get rid of filter
1c63696cfb Trac #28801: Fix ThreeJS script paths for Firefox on Windows
fb1c004e14 Trac #28541: bug in change_ring for polynomials
680649c354 Trac #24398: Document function initialization parameters
0a1ddb16a2 Trac #28710: update sagenb to 1.1.3
6d8849ca36 Trac #28258: Fork errors in sage.misc.cython doctests
cf9673bc59 (tag: 9.0.beta8) Updated SageMath version to 9.0.beta8

Travis Scrimshaw

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Dec 8, 2019, 10:24:24 PM12/8/19
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I am unable to build using my Python2 install as it fails at cysignals (it works on Python3). It might not have been this precise version as I tried from beta3. I am trying after a distclean, but I don't expect a different result. I known non-Python3 is a low priority, but I think we should still try to get this to work. Any thoughts?

Best,
Travis
cysignals-1.10.2.log

Travis Scrimshaw

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Dec 8, 2019, 11:27:36 PM12/8/19
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Surprisingly it did work after a distclean. Strange... Sorry for the noise.

Best,
Travis

Eric Gourgoulhon

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Dec 9, 2019, 8:12:26 AM12/9/19
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On Ubuntu 18.04 running on a bi-Xeon E5-2623 (8 cores) + 16 GB RAM computer:

  - incremental build (with -j16) from 9.0.beta8: OK
  - all tests from ptestlong passed

Eric

Emmanuel Charpentier

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Dec 9, 2019, 8:24:34 AM12/9/19
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On Debian testing running on core i5 + 8 GB RAM, upgrading a 9.0.beta8 Python3-based Sage and running ptestalllong gives nine transient failures and no permanent one:

| File                                          | Result            |
|-----------------------------------------------+-------------------+
| src/sage/plot/animate.py                      | 7 doctests failed |
| src/doc/en/constructions/linear_algebra.rst   | 1 doctest failed  |
| src/sage/misc/latex.py                        | 1 doctest failed  |
| src/doc/en/constructions/interface_issues.rst | 1 doctest failed  |
| src/sage/repl/load.py                         | 1 doctest failed  |
| src/doc/en/developer/coding_in_other.rst      | 1 doctest failed  |
| src/sage/interfaces/octave.py                 | 3 doctests failed |
| src/sage/databases/findstat.py                | 1 doctest failed  |
| src/sage/interfaces/magma_free.py             | 2 doctests failed |

One notes that three of these those transient failures (those occuring in .rst files) were not observed in previous 9.0betas.

HTH,

E. Madison Bray

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Dec 9, 2019, 11:10:24 AM12/9/19
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On Mon, Dec 9, 2019 at 5:27 AM Travis Scrimshaw <tsc...@ucdavis.edu> wrote:
>
> Surprisingly it did work after a distclean. Strange... Sorry for the noise.

Make sure that if `./configure` was re-run that it kept
`--with-python=2`. There is a bug that if configure gets re-run
needlessly sometimes it doesn't keep the previous flags. There was
discussion about this in the last release thread.
> --
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E. Madison Bray

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Dec 9, 2019, 11:11:32 AM12/9/19
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Can somebody please review the blocker ticket
https://trac.sagemath.org/ticket/28829 ?

It depends on https://trac.sagemath.org/ticket/28832 which now has
positive review.

Emmanuel Charpentier

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Dec 9, 2019, 6:17:59 PM12/9/19
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On a slightly larger machine (Debian testing running on core i7 + 16 GB RAM, with gap-packages installed),ptestalllong gets me seven temporary failures and three permanent ones:

File                                         | Result            | P/T
---------------------------------------------+-------------------+----
src/sage/plot/animate.py                     | 7 doctests failed | T  
src/sage/interfaces/psage.py                 | 1 doctest failed  | T  
src/sage/numerical/backends/glpk_backend.pyx | 1 doctest failed  | P  
src/sage/tests/gap_packages.py               | 1 doctest failed  | P  
src/sage/symbolic/integration/external.py    | 1 doctest failed  | T  
src/sage/misc/latex.py                       | 1 doctest failed  | T  
src/sage/libs/glpk/error.pyx                 | 1 doctest failed  | P  
src/sage/repl/load.py                        | 1 doctest failed  | T  
src/sage/combinat/designs/ext_rep.py         | 1 doctest failed  | T  
src/sage/databases/findstat.py               | 1 doctest failed  | Y  

All of these failures have already been reported.

HTH,

Justin C. Walker

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Dec 9, 2019, 7:37:37 PM12/9/19
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> On Dec 8, 2019, at 13:41 , 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 w/o problems from a fresh clone of the develop branch on two macOS systems: 10.13.6 (2017 iMac Pro, 18-core Xeon W) and 10.14.6 (2017 MBP, Quad-core Core i7). All tests passed on both (‘ptestlong;).

Justin

--
Justin C. Walker, Curmudgeon-At-Large
Institute for the Enhancement of the Director's Income
--------
Experience is what you get
when you don't get what you want.
--------



Sébastien Labbé

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Dec 10, 2019, 2:47:47 AM12/10/19
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Running tests for many optional/external packages, I get

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

----------------------------------------------------------------------
sage -t --long src/doc/en/thematic_tutorials/linear_programming.rst  # 1 doctest failed
sage -t --long src/sage/databases/findstat.py  # 1 doctest failed
sage -t --long src/sage/geometry/polyhedron/base.py  # Killed due to abort
sage -t --long src/sage/graphs/generators/families.py  # 7 doctests failed
sage -t --long src/sage/graphs/generators/smallgraphs.py  # 2 doctests failed
sage -t --long src/sage/misc/latex.py  # 1 doctest failed
sage -t --long src/sage/plot/animate.py  # 7 doctests failed
sage -t --long src/sage/repl/load.py  # 1 doctest failed
sage -t --long src/sage/tests/cmdline.py  # 2 doctests failed
----------------------------------------------------------------------
External software detected for doctesting: cplex,ffmpeg,graphviz,gurobi,imagemagick,internet,latex,pandoc

Reruning failed tests I get:

----------------------------------------------------------------------
sage -t --long src/doc/en/thematic_tutorials/linear_programming.rst  # 1 doctest failed
sage -t --long src/sage/databases/findstat.py  # 1 doctest failed
sage -t --long src/sage/geometry/polyhedron/base.py  # Killed due to abort
sage -t --long src/sage/graphs/generators/smallgraphs.py  # 2 doctests failed
sage -t --long src/sage/misc/latex.py  # 1 doctest failed
sage -t --long src/sage/plot/animate.py  # 7 doctests failed
sage -t --long src/sage/repl/load.py  # 1 doctest failed
sage -t --long src/sage/tests/cmdline.py  # 2 doctests failed
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,imagemagick,internet,latex,pandoc

which means that the following is not reproduced:

sage -t --long src/sage/graphs/generators/families.py  # 7 doctests failed

The following now has positive review (https://trac.sagemath.org/ticket/28762):

sage -t --long src/sage/tests/cmdline.py  # 2 doctests failed

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

Dima Pasechnik

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Dec 15, 2019, 6:49:51 AM12/15/19
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Volker,
can we please get #28883 and #27870 (highly anticipated, allows the use of openblas from the system, modifies ./configure) in 9.0?

Emmanuel Charpentier

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Dec 15, 2019, 7:23:47 AM12/15/19
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I'd add Trac#28884 (another Dima' ticket to which I just gave positive review) to this suggestion (a large headache off the shoulders of Sage's R users...).

This might even justify one more week before 9.0... 

Jaap Spies

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Dec 21, 2019, 6:30:02 AM12/21/19
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On Fedora 30 with lscpu:
Architecture:        x86_64
CPU op-mode(s):      32-bit, 64-bit
Byte Order:          Little Endian
Address sizes:       39 bits physical, 48 bits virtual
CPU(s):              8
On-line CPU(s) list: 0-7
Thread(s) per core:  2
Core(s) per socket:  4
Socket(s):           1
NUMA node(s):        1
Vendor ID:           GenuineIntel
CPU family:          6
Model:               60
Model name:          Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz
Stepping:            3
CPU MHz:             1440.883
CPU max MHz:         3900,0000
CPU min MHz:         800,0000
BogoMIPS:            6796.31
Virtualization:      VT-x
L1d cache:           32K
L1i cache:           32K
L2 cache:            256K
L3 cache:            8192K
NUMA node0 CPU(s):   0-7
Flags:               fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dt
s acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts r
ep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2
ssse3 sdbg fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx
f16c rdrand lahf_lm abm cpuid_fault epb invpcid_single pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpri
ority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid xsaveopt dtherm ida arat pln
pts md_clear flush_l1d

All test from make ptestlong passed.

Total time for all tests: 2384.4 seconds
   cpu time: 14491.9 seconds
   cumulative wall time: 18460.7 seconds



Jaap Spies

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Dec 21, 2019, 7:16:45 AM12/21/19
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Got it running on a Raspberry Pi 4B 2GB Raspbian with 'make -j4'
Architecture:        armv7l
Byte Order:          Little Endian
CPU(s):              4
On-line CPU(s) list: 0-3
Thread(s) per core:  1
Core(s) per socket:  4
Socket(s):           1
Vendor ID:           ARM
Model:               3
Model name:          Cortex-A72
Stepping:            r0p3
CPU max MHz:         1500.0000
CPU min MHz:         600.0000
BogoMIPS:            270.00
Flags:               half thumb fastmult vfp edsp neon vfpv3 tls vfpv4 idiva idivt vfpd32 lpae evtstrm crc32

The RPi 4 is not very stable. I've got some 'freeze' moments, but in the end the build finished.
Even the make doc finished! In sage-8.9 building doc stopped every time at the same point.

Running 'make ptest' a lot of errors: 30 ../sysdeps/unix/sysv/linux/waitpid.c No such file or directory
No module name 'Cython'

pi@rasp4:~/.sage/crash_logs $ ls -lt
total 43160
-rw------- 1 pi pi 234386 Dec 21 12:49 crash_4umks3yo.log
-rw------- 1 pi pi 268715 Dec 21 12:47 crash_q0lkok60.log
-rw------- 1 pi pi 331798 Dec 21 12:46 crash_d9zl8jcg.log
-rw------- 1 pi pi 351876 Dec 21 12:43 crash_y4j3wd5n.log
...
132 files in total

Is this a known issue? What can I do?

One more I catched:
sage -t src/sage/structure/coerce_dict.pyx
**********************************************************************
File "src/sage/structure/coerce_dict.pyx", line 49, in sage.structure.coerce_dict
Failed example:
    len(LE)
Expected:
    1
Got:
    50

[snipped]
sage -t src/sage/geometry/polyhedron/base_ZZ.py  # Timed out
sage -t src/sage/schemes/elliptic_curves/kraus.py  # Killed due to segmentation fault
sage -t src/sage/combinat/free_module.py  # Killed due to segmentation fault
sage -t src/sage/groups/abelian_gps/abelian_aut.py  # Timed out
sage -t src/sage/schemes/plane_conics/con_field.py  # Timed out
sage -t src/sage/quadratic_forms/genera/normal_form.py  # Timed out
sage -t src/sage/rings/number_field/bdd_height.py  # Timed out
sage -t src/sage/quadratic_forms/quadratic_form__split_local_covering.py  # Timed out
sage -t src/sage/schemes/generic/scheme.py  # Timed out
sage -t src/sage/schemes/elliptic_curves/formal_group.py  # Timed out
sage -t src/sage/rings/padics/padic_lattice_element.py  # 3 doctests failed
sage -t src/doc/en/thematic_tutorials/explicit_methods_in_number_theory/half_integral.rst  # Timed out
sage -t src/sage/rings/valuation/gauss_valuation.py  # Timed out
sage -t src/sage/categories/finite_dimensional_modules_with_basis.py  # Timed out
sage -t src/sage/coding/abstract_code.py  # Timed out
sage -t src/sage/modular/modform/submodule.py  # Timed out
sage -t src/sage/schemes/elliptic_curves/weierstrass_transform.py  # Timed out
sage -t src/sage/misc/weak_dict.pyx  # 11 doctests failed
sage -t src/sage/quadratic_forms/qfsolve.py  # Timed out
sage -t src/sage/structure/coerce_dict.pyx  # 1 doctest failed
sage -t src/sage/structure/parent.pyx  # Timed out
sage -t src/sage/rings/morphism.pyx  # Timed out
----------------------------------------------------------------------
Total time for all tests: 12425.0 seconds
    cpu time: 20073.8 seconds
    cumulative wall time: 26235.4 seconds
make: *** [Makefile:172: ptest] Error 21
pi@rasp4:~/sagemath/sage-9.0.beta9 $ 

Cheers
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