Sage 8.4.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

23a2b10da6 (tag: 8.4.beta1) Updated SageMath version to 8.4.beta1

3d7965cb6f Trac #25523: Raise Exception if DynamicalSystem initialized with coeffs not in given domain

703aa6e339 Trac #25446: compute all orbits of minimal models of dynamical systems

18ee14bee3 Trac #25441: Allow more substitutions for non-classical rational function field valuations

a4e70dddc9 Trac #25360: Honor global proof setting for "polynomial" in factorization code

a5c0546809 Trac #25241: fix issue with change_ring for polynomials with Maps

ef293c6e38 Trac #25229: Fix bug in BooleanMonomialMonoid._element_constructor_

4c940be147 Trac #25226: Do not sort inductive valuations

8f6c04568e Trac #23430: Cannot create a RealBall with rational radius

2cffe40b73 Trac #22345: Elliptic curve isogenies over number fields II: implement Billerey's algorithm for reducible primes

912e88cfbe Trac #22157: Add SPQR-tree decomposition for 2-vertex-connected graphs

db0b3a5a48 Trac #22156: Clarifying eps_abs and eps_rel in numerical_integral

a3e4977917 Trac #21946: solve(x==x, x) returns [x == r1]

705d59f725 Trac #26025: Sage should not use GP_DATA_DIR

cf8a36f533 Trac #26020: py3: src/sage/numerical/backends/glpk_graph_backend

2bd1923f8a Trac #26013: lots of warnings when uninstalling spkgs

cbe8c4550f Trac #25939: error in Well's algorithm for canonical height

6fb4f97eb3 Trac #25749: fixing invalid escape sequences in modular (final)

c96ee846de Trac #25315: Find libraries in DYLD_LIBRARY_PATH as fallback

df9d24fd40 Trac #25276: Bugs with GradedCommutativeAlgebra

2274331e6e Trac #26012: Fix bug concerning restrictions of tensorfields

e674750080 Trac #26008: Upgrade setuptools and pip

eeb4a217fb Trac #26002: Support pari compiled with threads

0e78774b03 Trac #25999: Compile errors due to struct

f32c9bd7dc Trac #25984: Minor cleanup related to Monsky-Washnitzer

ce3cf8444f Trac #25975: py3: small fix for Lfunction names

c087f48b43 Trac #25974: py3: fix unnecessary map() in sage.calculus.riemann

4273770ad2 Trac #25970: Improve "Inverse does not exist" error messages

42694c6526 Trac #25966: Upgrade Arb to 2.14.0

0f3a8439b3 Trac #25144: Add DESTDIR support for palp

ed1a6bd434 Trac #25103: Minimal polynomials of elements in p-adic fields

2e783bb5a8 Trac #24843: Issue with p-adic printing

dc76f7d1fd Trac #24669: Re-enable threads on OpenBLAS

5e6587ef2e Trac #23218: Ramified extensions of general p-adic rings and fields

f1ef83ac07 Trac #26021: tides does not build on 32-bit systems

1389c4f117 Trac #25722: Test jupyter kernel symlinks in tmpdir

c694dfe2ed Trac #26007: Missing sagelib dependencies

77cf54bfb2 Trac #23627: Update points() in projective_homset.py  and affine_homset.py to work over CC and CDF

8e656e77aa Trac #25697: Implement enumeration over QQ for product projective schemes

a12e31cdbc Trac #25781: add Comparison operator for morphism between product

32c9872c18 Trac #25792: add dehomogenize function for product projective point

7687c443b9 Trac #25821: implement height functions for product points

6451eb7c7f Trac #25958: py3: clean up use of map/filter in sage.graphs.generators.classical_geometries

d0ef067dd1 Trac #25947: py3: miscellaneous map -> list fixes

73c89a342d Trac #25940: Python 3: Chain complex fixes

4553736c25 Trac #25935: Make __eq__ and __hash__ of AbelianGroup_class consistent

b9bdea5ef1 Trac #25926: Cleanup generalized_Young_walls documentation

915800af78 Trac #25923: cleanup of any(...) outside of schemes folder

302de5422d Trac #25920: some changes about all() and any() in schemes

8992f88bb4 Trac #25918: Queer supercrystals

99023a94b7 Trac #25917: Add definition of crystal to catalog of crystals

574d72f1db Trac #25908: Printing of p-adic extensions

fc68b6b1ec Trac #25906: Upgrade to zeromq 4.2.5 and pyzmq 17.1.0

2a82aeb5e5 Trac #25835: Move gap packages to features

6081d6f06d Trac #25345: Make it possible to test sage without htmldoc

0d3e496088 Trac #25602: implement translation of fricas.rootOf

807bf5b461 Trac #25596: Add random tests for finite posets

6dd6958964 Trac #25083: Upgrade to IPython 5.8

4664730ffe Trac #24883: Endless symbolic computation

8fdfaa1607 Trac #22415: Add operator class membership tests for matrices

ada43b34b3 (tag: 8.4.beta0, trac/develop) Updated SageMath version to 8.4.beta0

[Steven Trogdon]

Incremental upgrade 8.4.beta0 -> 8.4.beta1 fails here with

Successfully installed pip-18.0

Cleaning up...

Removed build tracker '/tmp/pip-req-tracker-eqpf3wqk'

Usage:

  /64bitdev/storage/sage-git_develop/sage/local/bin/python2 -m pip install [options] <requirement specifier> [package-index-options] ...

  /64bitdev/storage/sage-git_develop/sage/local/bin/python2 -m pip install [options] -r <requirements file> [package-index-options] ...

  /64bitdev/storage/sage-git_develop/sage/local/bin/python2 -m pip install [options] [-e] <vcs project url> ...

  /64bitdev/storage/sage-git_develop/sage/local/bin/python2 -m pip install [options] [-e] <local project path> ...

  /64bitdev/storage/sage-git_develop/sage/local/bin/python2 -m pip install [options] <archive url/path> ...

no such option: --no-build-isolation

********************************************************************************

Error building / installing pip2

********************************************************************************

real    0m5.341s

user    0m4.944s

sys     0m0.472s

************************************************************************

Error installing package pip-18.0

************************************************************************

[fchap...@gmail.com]

going from 8.4.b0 to 8.4.b1 fails (on my three machines) with

[sagelib-8.4.beta1] && sage-python23 -u setup.py --no-user-cfg build install
[sagelib-8.4.beta1] ************************************************************************
[sagelib-8.4.beta1] Traceback (most recent call last):
[sagelib-8.4.beta1]   File "setup.py", line 67, in <module>
[sagelib-8.4.beta1]     from module_list import ext_modules, library_order
[sagelib-8.4.beta1]   File "/home/chapoton/sage/src/module_list.py", line 114, in <module>
[sagelib-8.4.beta1]     from sage_setup.optional_extension import OptionalExtension
[sagelib-8.4.beta1]   File "/home/chapoton/sage/src/sage_setup/optional_extension.py", line 24, in <module>
[sagelib-8.4.beta1]     all_packages = list_packages(local=True)
[sagelib-8.4.beta1]   File "/home/chapoton/sage/src/sage/misc/package.py", line 225, in list_packages
[sagelib-8.4.beta1]     installed = installed_packages(exclude_pip)
[sagelib-8.4.beta1]   File "/home/chapoton/sage/src/sage/misc/package.py", line 285, in installed_packages
[sagelib-8.4.beta1]     installed.update(pip_installed_packages())
[sagelib-8.4.beta1]   File "/home/chapoton/sage/src/sage/misc/package.py", line 147, in pip_installed_packages
[sagelib-8.4.beta1]     return {package['name'].lower():package['version'] for package in json.loads(stdout)}
[sagelib-8.4.beta1]   File "/home/chapoton/sage/local/lib/python2.7/json/__init__.py", line 339, in loads
[sagelib-8.4.beta1]     return _default_decoder.decode(s)
[sagelib-8.4.beta1]   File "/home/chapoton/sage/local/lib/python2.7/json/decoder.py", line 364, in decode
[sagelib-8.4.beta1]     obj, end = self.raw_decode(s, idx=_w(s, 0).end())
[sagelib-8.4.beta1]   File "/home/chapoton/sage/local/lib/python2.7/json/decoder.py", line 382, in raw_decode
[sagelib-8.4.beta1]     raise ValueError("No JSON object could be decoded")
[sagelib-8.4.beta1] ValueError: No JSON object could be decoded
[sagelib-8.4.beta1] ************************************************************************
[sagelib-8.4.beta1] Error building the Sage library
[sagelib-8.4.beta1] ************************************************************************

see https://patchbot.sagemath.org/log/0/Ubuntu/18.04/x86_64/4.15.0-30-generic/petitbonum/2018-08-15%2017:58:36?short

Frédéric

[fchap...@gmail.com]

This failure was probably caused by the presence of a personal file pip.conf. Trying again now after removing this file.

[Erik Bray]

On Cygwin: Incremental upgrade from 8.4.beta0 built fine.

With

$ make ptestlong

I got the following failures:

----------------------------------------------------------------------
sage -t --long src/sage/tests/py3_syntax.py # 3 doctests failed
sage -t --long src/sage/graphs/generators/families.py # 1 doctest failed
sage -t --long src/sage/tests/books/judson-abstract-algebra/sylow-sage.py
# 27 doctests failed
sage -t --long src/sage/groups/perm_gps/partn_ref/data_structures.pyx
# 12 doctests failed
sage -t --long src/sage/groups/perm_gps/cubegroup.py # 72 doctests failed
sage -t --long src/sage/modular/modform_hecketriangle/readme.py # 40
doctests failed
----------------------------------------------------------------------

But they appear to have been transient. Upon running

$ ./sage -t -a --long --failed -p 4

those tests passed.

I might look into what was going on there (there were a few fork()
failures in some of them), but as long as they pass on their own I'm
satisfied.

[Steven Trogdon]

I've attached the complete build log for this. I does seem that pip3 did install but I'm at a loss as to why when building/installing pip2 there is the 'no such option: --no-build-isolation'.

[Steven Trogdon]

I'm beginning to think that my 'local/lib/python2.7/site-packages/pip' folder is not being cleared before the instal

of pip-18.0. I have:

ls -al local/lib/python2.7/site-packages/pip/

total 256

drwxr-xr-x  10 strogdon math  4096 Aug 15 20:25 .

drwxr-xr-x 203 strogdon math 24576 Aug 15 20:25 ..

-rw-r--r--   1 strogdon math  9884 May 19 12:16 __init__.pyo

-rw-r--r--   1 strogdon math   525 May 19 12:16 __main__.pyo

drwxr-xr-x  16 strogdon math  4096 Aug 15 20:25 _vendor

-rw-r--r--   1 strogdon math  9345 May 19 12:16 basecommand.pyo

-rw-r--r--   1 strogdon math 11734 May 19 12:16 baseparser.pyo

-rw-r--r--   1 strogdon math 16446 May 19 12:16 cmdoptions.pyo

drwxr-xr-x   2 strogdon math  4096 Aug 15 20:25 commands

drwxr-xr-x   2 strogdon math  4096 Aug 15 20:25 compat

-rw-r--r--   1 strogdon math 27016 May 19 12:16 download.pyo

-rw-r--r--   1 strogdon math 14006 May 19 12:16 exceptions.pyo

-rw-r--r--   1 strogdon math 38425 May 19 12:16 index.pyo

-rw-r--r--   1 strogdon math  4881 May 19 12:16 locations.pyo

drwxr-xr-x   2 strogdon math  4096 Aug 15 20:25 models

drwxr-xr-x   2 strogdon math  4096 Aug 15 20:25 operations

-rw-r--r--   1 strogdon math 10176 May 19 12:16 pep425tags.pyo

drwxr-xr-x   2 strogdon math  4096 Aug 15 20:25 req

-rw-r--r--   1 strogdon math   434 May 19 12:16 status_codes.pyo

drwxr-xr-x   2 strogdon math  4096 Aug 15 20:25 utils

drwxr-xr-x   2 strogdon math  4096 Aug 15 20:25 vcs

-rw-r--r--   1 strogdon math 26526 May 19 12:16 wheel.pyo

And I think some of the files there should not be there. Note the timestamp. This was attempted on Aug 15th.

[Emmanuel Charpentier]

FWIW, on Debian testing running on core I7 + 16 GB RAM, (incrementally) builds (from 8.4.beta0) and passes ptestlong without any failure whatsoever.

HTH,

Le jeudi 16 août 2018 00:03:33 UTC+2, Volker Braun a écrit :

[Emmanuel Charpentier]

Ditto but for one transient failure (sage -t --long --warn-long 52.5 src/sage/misc/sagedoc.py  # Timed out) on a slightly smaller machine (cor i5, 8 GB RAM).

HTH,

[Steven Trogdon]

The real issue with this is that I did not have a functioning pip installed, i.e. local/bin/pip was missing, even though 'local/bin/python2 -m pip list | grep pip' indicated that pip-8.1.2 was installed. This is a mystery. To correct things I did 'local/bin/python2 -m pip install --upgrade pip' which re-installed pip-8.1.2 with a corresponding local/bin/pip. This allowed 8.4.beta1 to build including the upgrade to pip-18.0.

On Wednesday, August 15, 2018 at 8:59:21 PM UTC-5, Steven Trogdon wrote:

[Sébastien Labbé]

Running Ubuntu 16.06, I get

Using --optional=bliss,cbc,ccache,cmake,dot2tex,external,gmpy2,lrslib,mpir,notedown,pandoc_attributes,python2,rst2ipynb,sage

the command

./sage -t -p --all --long --optional=sage,optional,external --show-skipped --logfile=logs/ptestallshowskipped.log

gives:

----------------------------------------------------------------------
sage -t --long src/sage/databases/findstat.py  # 2 doctests failed
sage -t --long src/sage/databases/oeis.py  # 3 doctests failed
sage -t --long src/sage/symbolic/integration/integral.py  # 1 doctest failed
sage -t --long src/sage/finance/stock.py  # 20 doctests failed
sage -t --long src/sage/symbolic/integration/external.py  # 3 doctests failed
sage -t --long src/sage/repl/load.py  # 1 doctest failed
sage -t --long src/sage/misc/persist.pyx  # 2 doctests failed
----------------------------------------------------------------------

I am able to reproduce them with:

sage -t --long --optional=sage,optional,external src/sage/databases/findstat.py src/sage/databases/oeis.py src/sage/symbolic/integration/integral.py src/sage/finance/stock.py src/sage/symbolic/integration/external.py src/sage/repl/load.py src/sage/misc/persist.pyx

Some failures depending on internet with files findstat.py and oeis.py are "new" and are copied below:

sage -t --long src/sage/databases/findstat.py
**********************************************************************
File "src/sage/databases/findstat.py", line 1016, in sage.databases.findstat.FindStatStatistic._find_by_values
Failed example:
    FindStatStatistic(id=0,data=data, first_terms = first_terms, collection = collection, depth=0)._find_by_values() # optional -- internet
Expected:
    0: (St000012: The area of a Dyck path., [], 14)
Got:
    0: (St000012: The area of a Dyck path., [], 14)
    1: (St001228: The vector space dimension of the space of module homomorphisms between J and itself when J denotes the Jacobson radical of the corresponding Nakayama algebra., [], 14)
**********************************************************************
File "src/sage/databases/findstat.py", line 2211, in sage.databases.findstat.FindStatCollection.to_string
Failed example:
    c.to_string()(p)                                              # optional -- internet
Expected:
    '([(0, 2), (2, 1)], 3)'
Got:
    '([(1, 2), (2, 0)], 3)'
**********************************************************************
2 items had failures:
   1 of   5 in sage.databases.findstat.FindStatCollection.to_string
   1 of   9 in sage.databases.findstat.FindStatStatistic._find_by_values
    [247 tests, 2 failures, 61.87 s]

sage -t --long src/sage/databases/oeis.py
**********************************************************************
File "src/sage/databases/oeis.py", line 1423, in sage.databases.oeis.OEISSequence.links
Failed example:
    f.links(format='url')                             # optional -- internet
Expected:
    0: http://oeis.org/A000045/b000045.txt
    1: http://library.thinkquest.org/27890/theSeries.html
    ...
Got:
      0: http://oeis.org/A000045/b000045.txt
      1: http://dx.doi.org/10.1016/j.disc.2014.06.026
      2: http://library.thinkquest.org/27890/theSeries.html

...

    177: http://www.cs.uwaterloo.ca/journals/JIS/VOL8/Zhang/zhang56.html
    178: http://oeis.org/index/Cor#core
    179: http://oeis.org/index/Di#divseq
    180: http://oeis.org/index/Par#partN
    181: http://oeis.org/index/Rec#order_02
    182: http://oeis.org/index/Tu#2wis
    183: http://oeis.org/index/Be#Benford
**********************************************************************

**********************************************************************
File "src/sage/databases/oeis.py", line 1428, in sage.databases.oeis.OEISSequence.links
Failed example:
    f.links(format='raw')                 # optional -- internet
Expected:
    0: N. J. A. Sloane, <a href="/A000045/b000045.txt">The first 2000 Fibonacci numbers: Table of n, F(n) for n = 0..2000</a>
    1: Matt Anderson, Jeffrey Frazier and Kris Popendorf, <a href="http://library.thinkquest.org/27890/theSeries.html">The Fibonacci series: the section index</a> [broken link]
    ...
Got:
      0: N. J. A. Sloane, <a href="/A000045/b000045.txt">The first 2000 Fibonacci numbers: Table of n, F(n) for n = 0..2000</a>
      1: Marco Abrate, Stefano Barbero, Umberto Cerruti, Nadir Murru, <a href="http://dx.doi.org/10.1016/j.disc.2014.06.026">Colored compositions, Invert operator and elegant compositions with the "black tie"</a>, Discrete Math. 335 (2014), 1--7. MR3248794.
      2: Matt Anderson, Jeffrey Frazier and Kris Popendorf, <a href="http://library.thinkquest.org/27890/theSeries.html">The Fibonacci series: the section index</a> [broken link]

...

    171: <a href="/index/Di#divseq">Index to divisibility sequences</a>
    172: <a href="/index/Par#partN">Index entries for related partition-counting sequences</a>
    173: <a href="/index/Rec#order_02">Index entries for linear recurrences with constant coefficients</a>, signature (1,1).
    174: <a href="/index/Tu#2wis">Index entries for two-way infinite sequences</a>
    175: <a href="/index/Be#Benford">Index entries for sequences related to Benford's law</a>
**********************************************************************
File "src/sage/databases/oeis.py", line 1522, in sage.databases.oeis.OEISSequence.cross_references
Failed example:
    nbalanced.cross_references(fetch=True)    # optional -- internet
Expected:
    0: A049703: a(0) = 0; for n>0, a(n) = A005598(n)/2.
    1: A049695: Array T read by diagonals; T(i,j)=number of nonnegative slopes of lines determined by 2 lattice points in [ 0,i ] X [ 0,j ] if i>0; T(0,j)=1 if j>0; T(0,0)=0.
    2: A103116: a(n) = A005598(n) - 1.
    3: A000010: Euler totient function phi(n): count numbers <= n and prime to n.
Got:
    0: A049703: a(0) = 0; for n>0, a(n) = A005598(n)/2.
    1: A049695: Array T read by diagonals; T(i,j) is the number of nonnegative slopes of lines determined by 2 lattice points in [ 0,i ] X [ 0,j ] if i > 0; T(0,j)=1 if j > 0; T(0,0)=0.
    2: A103116: a(n) = A005598(n) - 1.
    3: A000010: Euler totient function phi(n): count numbers <= n and prime to n.
**********************************************************************
2 items had failures:
   1 of   7 in sage.databases.oeis.OEISSequence.cross_references
   2 of   9 in sage.databases.oeis.OEISSequence.links
    [259 tests, 3 failures, 43.23 s]

Follow-up in the meta-ticket on optional doctest failures at https://trac.sagemath.org/ticket/25536

[Andrew]

It turns out that my problem with compiling 8.4.beta3+ is the same issue that Steven flagged. In fact, Steven suggested this in sage-devel but when I tried his fix it didn't work for me so I thought that it was unrelated. When I found out that I could compile 8.4.beta0 and not sage-8.4.beta1 I tried again. The work around that I needed required more steps:

• I first fired up sage -sh
• Next I used local/bin/easy_install-2.7 and local/bin/easy_install-3.6 to install pip by hand. Perhaps I'm wrong but this seemed to be required for both python2 and python3
• Then I exited the sage shell and ran local/bin/python2 -m pip install --upgrade pip (this time only python2...?!)
• the compile of sage now finished when I ran make

Doing this allowed me to compile 8.4.beta1. I had to repeat these steps to compile 8.4.beta4. I am running:

ProductName:    Mac OS X
ProductVersion:    10.13.6
BuildVersion:    17G65
Xcode 9.4.1
Build version 9F2000

I didn't run the tests for 8.4.beta1 but I am doing that now for 8.4.beta4 and will post the results when it finishes.

Andrew