Re: [sage-release] Re: Sage 8.5.beta5 released

2018-12-20 Thread Sébastien Labbé 


On Wednesday, November 28, 2018 at 9:49:53 AM UTC+1, François Bissey wrote:
>
> That’s interesting. I thought the failures in sage/databases/sql_db.py in 
> sage-on-gentoo 
> were due to the use of a newer version of sqlite. But if you see it too 
> that must be something 
> more subtle. 
>
>
I just created
https://trac.sagemath.org/ticket/26920 
for the issue with sql_db.py since it is still a problem with 8.5.rc0.

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[sage-release] Re: Sage 8.5.beta5 released

2018-11-29 Thread Timo Kaufmann 
I've created https://trac.sagemath.org/ticket/26791 for the rpy2 issue, 
please post there.

Am Donnerstag, 29. November 2018 21:54:42 UTC+1 schrieb Timo Kaufmann:
>
> Probably due to https://trac.sagemath.org/ticket/26596, sorry. Was that a 
> build using sage's build system (`make -j4 ptestlong` or similar) or the 
> debian package?
>
> Am Donnerstag, 29. November 2018 18:39:05 UTC+1 schrieb Emmanuel 
> Charpentier:
>>
>> On Debian testing running onCore i5 + 8 GB RAM, I get three failures in 
>> one doctest :
>>
>> --
>> sage -t --long --warn-long 47.5 src/sage/interfaces/r.py  # 3 doctests 
>> failed
>> --
>>
>>  All three are dociuentation discordances in R (see attached file).
>>
>> Probably a booboo, but I don't understand the root of the problem.
>>
>> --
>> Emmanuel Charpentier
>>
>> Le lundi 26 novembre 2018 01:36:04 UTC+1, Volker Braun a écrit :
>>>
>>> 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
>>>
>>> b36eca1990 (tag: 8.5.beta5, trac/develop) Updated SageMath version to 
>>> 8.5.beta5
>>> 50d5520f60 Trac #26747: py3: final fixes for cluster_algebra.py
>>> acb2071e3c Trac #26738: py3: fix all doctests in game_theory
>>> c0fcb1222a Trac #26748: clean graph_generators_pyx.pyx
>>> b7d04438fb Trac #26746: provide translation of fresnel to fricas
>>> 99fe4d2534 Trac #26745: py3: fix doctest in Grossman-Larsson
>>> 285956f06c Trac #26744: remove a bunch of deprecated renamed keywords
>>> 959468f7a2 Trac #26743: cyclotomic_part should not include powers of x
>>> 9c0a66df99 Trac #26739: py3: some fixes in Monsky-Washnitzer
>>> 47998f15f4 Trac #26736: some work on cluster mutation again
>>> e7a1a04d8f Trac #26732: Docker image fails to start jupyter notebook
>>> 73b2d3962e Trac #26734: small cleanup for alternating sign matrices
>>> 9713da62ea Trac #25708: Rename SBox methods for 
>>> difference_distribution_matrix and similar to _table
>>> d45e4d9b7e Trac #26742: py3: fix threejs viewer interface
>>> 53b87f160d Trac #26737: py3: some work on finite state machines
>>> 3ce4503500 Trac #26728: Remove ellipsis in one findstat doctest
>>> 7853331f91 Trac #26726: Py3: Some python3 fixes in geometry module.
>>> 7d7d7eaca0 Trac #26704: Py3 : database.oeis  implement __getitem__ to 
>>> replace __getslice__
>>> 2599afd5c4 Trac #26596: Replace expect r interface with rpy2
>>> a38120a74e Trac #26168: Add parallelism for two tensor calculus functions
>>> b150b57dd2 Trac #25473: 20 internet doctests failed in 
>>> sage/finance/stock.py
>>> d11cabb0c9 Trac #23547: isl + polylib + barvinok packages
>>> 269bd3da76 Trac #23341: port lcalc to C++11
>>> 514e0f5e50 Trac #26729: update curl to 7.62
>>> b054b079e5 Trac #26405: Root finding for p-adic polynomials
>>> 7b564b0ed6 Trac #25443: bijections for set partitions
>>> 6eba589bce Trac #26720: py3: some fixes for misc/abstract_method
>>> fda5bdab57 Trac #26717: converting some http to https in install 
>>> instructions
>>> e235693068 Trac #26712: avoid .vertices() in independent_sets.pyx
>>> cbe26c565f Trac #26711: avoid .vertices() in graph_coloring.py
>>> b138c8a7a4 Trac #26702: Py3: Fix database/sql_db module for python3
>>> 9e6743fa4c Trac #26420: More flexible constructor of  GroupHomomorphisms
>>> 75bc4c6d91 Trac #25519: Upgrade gmpy2
>>> 10d1b6810c Trac #26715: build/pkgs/gfortran/spkg-configure.m4 works 
>>> incorrectly if CC and CXX are already there
>>> 51d1404842 Trac #26723: remove deprecated stuff in posets and Hasse
>>> 2615da94d8 Trac #26724: py3: one small fix for elliptic curves over 
>>> number fields
>>> 4332897d03 Trac #26721: py3: fix function fields
>>> 7928e4c3a0 Trac #26719: py3: fix doctests in symmetric group algebra
>>> 5d8ab92872 Trac #26630: clean generic_graph.py (part 3)
>>> 5c49a279ea Trac #26709: Upgrade to jupyter notebook 5.7.1
>>> cc373ffd76 Trac #26661: pep cleanup of old integer lists
>>> 208fd1182c Trac #26574: remove deprecated stuff in integer lists
>>> 1a6f4e9862 Trac #26560: remove deprecated stuff in element wrapper
>>> da82efd125 Trac #26708: clean connectivity.pyx (part 3)
>>> 3fa1ec45df Trac #26705: Fix is_formal for hyperplane arrangements with 
>>> no cycles
>>> bbe7f47574 Trac #26597: Update boost/boost_cropped to 1.66.0
>>> 0cbf26ce26 Trac #26026: Updates to Huffman codings
>>> 523b1f8cb6 Trac #26667: distutils no longer shows compiler commands
>>> f894105d0d (tag: 8.5.beta4) Updated SageMath version to 8.5.beta4
>>>
>>>

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[sage-release] Re: Sage 8.5.beta5 released

2018-11-29 Thread Timo Kaufmann 
Probably due to https://trac.sagemath.org/ticket/26596, sorry. Was that a 
build using sage's build system (`make -j4 ptestlong` or similar) or the 
debian package?

Am Donnerstag, 29. November 2018 18:39:05 UTC+1 schrieb Emmanuel 
Charpentier:
>
> On Debian testing running onCore i5 + 8 GB RAM, I get three failures in 
> one doctest :
>
> --
> sage -t --long --warn-long 47.5 src/sage/interfaces/r.py  # 3 doctests 
> failed
> --
>
>  All three are dociuentation discordances in R (see attached file).
>
> Probably a booboo, but I don't understand the root of the problem.
>
> --
> Emmanuel Charpentier
>
> Le lundi 26 novembre 2018 01:36:04 UTC+1, Volker Braun a écrit :
>>
>> 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
>>
>> b36eca1990 (tag: 8.5.beta5, trac/develop) Updated SageMath version to 
>> 8.5.beta5
>> 50d5520f60 Trac #26747: py3: final fixes for cluster_algebra.py
>> acb2071e3c Trac #26738: py3: fix all doctests in game_theory
>> c0fcb1222a Trac #26748: clean graph_generators_pyx.pyx
>> b7d04438fb Trac #26746: provide translation of fresnel to fricas
>> 99fe4d2534 Trac #26745: py3: fix doctest in Grossman-Larsson
>> 285956f06c Trac #26744: remove a bunch of deprecated renamed keywords
>> 959468f7a2 Trac #26743: cyclotomic_part should not include powers of x
>> 9c0a66df99 Trac #26739: py3: some fixes in Monsky-Washnitzer
>> 47998f15f4 Trac #26736: some work on cluster mutation again
>> e7a1a04d8f Trac #26732: Docker image fails to start jupyter notebook
>> 73b2d3962e Trac #26734: small cleanup for alternating sign matrices
>> 9713da62ea Trac #25708: Rename SBox methods for 
>> difference_distribution_matrix and similar to _table
>> d45e4d9b7e Trac #26742: py3: fix threejs viewer interface
>> 53b87f160d Trac #26737: py3: some work on finite state machines
>> 3ce4503500 Trac #26728: Remove ellipsis in one findstat doctest
>> 7853331f91 Trac #26726: Py3: Some python3 fixes in geometry module.
>> 7d7d7eaca0 Trac #26704: Py3 : database.oeis  implement __getitem__ to 
>> replace __getslice__
>> 2599afd5c4 Trac #26596: Replace expect r interface with rpy2
>> a38120a74e Trac #26168: Add parallelism for two tensor calculus functions
>> b150b57dd2 Trac #25473: 20 internet doctests failed in 
>> sage/finance/stock.py
>> d11cabb0c9 Trac #23547: isl + polylib + barvinok packages
>> 269bd3da76 Trac #23341: port lcalc to C++11
>> 514e0f5e50 Trac #26729: update curl to 7.62
>> b054b079e5 Trac #26405: Root finding for p-adic polynomials
>> 7b564b0ed6 Trac #25443: bijections for set partitions
>> 6eba589bce Trac #26720: py3: some fixes for misc/abstract_method
>> fda5bdab57 Trac #26717: converting some http to https in install 
>> instructions
>> e235693068 Trac #26712: avoid .vertices() in independent_sets.pyx
>> cbe26c565f Trac #26711: avoid .vertices() in graph_coloring.py
>> b138c8a7a4 Trac #26702: Py3: Fix database/sql_db module for python3
>> 9e6743fa4c Trac #26420: More flexible constructor of  GroupHomomorphisms
>> 75bc4c6d91 Trac #25519: Upgrade gmpy2
>> 10d1b6810c Trac #26715: build/pkgs/gfortran/spkg-configure.m4 works 
>> incorrectly if CC and CXX are already there
>> 51d1404842 Trac #26723: remove deprecated stuff in posets and Hasse
>> 2615da94d8 Trac #26724: py3: one small fix for elliptic curves over 
>> number fields
>> 4332897d03 Trac #26721: py3: fix function fields
>> 7928e4c3a0 Trac #26719: py3: fix doctests in symmetric group algebra
>> 5d8ab92872 Trac #26630: clean generic_graph.py (part 3)
>> 5c49a279ea Trac #26709: Upgrade to jupyter notebook 5.7.1
>> cc373ffd76 Trac #26661: pep cleanup of old integer lists
>> 208fd1182c Trac #26574: remove deprecated stuff in integer lists
>> 1a6f4e9862 Trac #26560: remove deprecated stuff in element wrapper
>> da82efd125 Trac #26708: clean connectivity.pyx (part 3)
>> 3fa1ec45df Trac #26705: Fix is_formal for hyperplane arrangements with no 
>> cycles
>> bbe7f47574 Trac #26597: Update boost/boost_cropped to 1.66.0
>> 0cbf26ce26 Trac #26026: Updates to Huffman codings
>> 523b1f8cb6 Trac #26667: distutils no longer shows compiler commands
>> f894105d0d (tag: 8.5.beta4) Updated SageMath version to 8.5.beta4
>>
>>

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[sage-release] Re: Sage 8.5.beta5 released

2018-11-29 Thread Emmanuel Charpentier 
On Debian testing running onCore i5 + 8 GB RAM, I get three failures in one 
doctest :

--
sage -t --long --warn-long 47.5 src/sage/interfaces/r.py  # 3 doctests 
failed
--

 All three are dociuentation discordances in R (see attached file).

Probably a booboo, but I don't understand the root of the problem.

--
Emmanuel Charpentier

Le lundi 26 novembre 2018 01:36:04 UTC+1, Volker Braun a écrit :
>
> 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
>
> b36eca1990 (tag: 8.5.beta5, trac/develop) Updated SageMath version to 
> 8.5.beta5
> 50d5520f60 Trac #26747: py3: final fixes for cluster_algebra.py
> acb2071e3c Trac #26738: py3: fix all doctests in game_theory
> c0fcb1222a Trac #26748: clean graph_generators_pyx.pyx
> b7d04438fb Trac #26746: provide translation of fresnel to fricas
> 99fe4d2534 Trac #26745: py3: fix doctest in Grossman-Larsson
> 285956f06c Trac #26744: remove a bunch of deprecated renamed keywords
> 959468f7a2 Trac #26743: cyclotomic_part should not include powers of x
> 9c0a66df99 Trac #26739: py3: some fixes in Monsky-Washnitzer
> 47998f15f4 Trac #26736: some work on cluster mutation again
> e7a1a04d8f Trac #26732: Docker image fails to start jupyter notebook
> 73b2d3962e Trac #26734: small cleanup for alternating sign matrices
> 9713da62ea Trac #25708: Rename SBox methods for 
> difference_distribution_matrix and similar to _table
> d45e4d9b7e Trac #26742: py3: fix threejs viewer interface
> 53b87f160d Trac #26737: py3: some work on finite state machines
> 3ce4503500 Trac #26728: Remove ellipsis in one findstat doctest
> 7853331f91 Trac #26726: Py3: Some python3 fixes in geometry module.
> 7d7d7eaca0 Trac #26704: Py3 : database.oeis  implement __getitem__ to 
> replace __getslice__
> 2599afd5c4 Trac #26596: Replace expect r interface with rpy2
> a38120a74e Trac #26168: Add parallelism for two tensor calculus functions
> b150b57dd2 Trac #25473: 20 internet doctests failed in 
> sage/finance/stock.py
> d11cabb0c9 Trac #23547: isl + polylib + barvinok packages
> 269bd3da76 Trac #23341: port lcalc to C++11
> 514e0f5e50 Trac #26729: update curl to 7.62
> b054b079e5 Trac #26405: Root finding for p-adic polynomials
> 7b564b0ed6 Trac #25443: bijections for set partitions
> 6eba589bce Trac #26720: py3: some fixes for misc/abstract_method
> fda5bdab57 Trac #26717: converting some http to https in install 
> instructions
> e235693068 Trac #26712: avoid .vertices() in independent_sets.pyx
> cbe26c565f Trac #26711: avoid .vertices() in graph_coloring.py
> b138c8a7a4 Trac #26702: Py3: Fix database/sql_db module for python3
> 9e6743fa4c Trac #26420: More flexible constructor of  GroupHomomorphisms
> 75bc4c6d91 Trac #25519: Upgrade gmpy2
> 10d1b6810c Trac #26715: build/pkgs/gfortran/spkg-configure.m4 works 
> incorrectly if CC and CXX are already there
> 51d1404842 Trac #26723: remove deprecated stuff in posets and Hasse
> 2615da94d8 Trac #26724: py3: one small fix for elliptic curves over number 
> fields
> 4332897d03 Trac #26721: py3: fix function fields
> 7928e4c3a0 Trac #26719: py3: fix doctests in symmetric group algebra
> 5d8ab92872 Trac #26630: clean generic_graph.py (part 3)
> 5c49a279ea Trac #26709: Upgrade to jupyter notebook 5.7.1
> cc373ffd76 Trac #26661: pep cleanup of old integer lists
> 208fd1182c Trac #26574: remove deprecated stuff in integer lists
> 1a6f4e9862 Trac #26560: remove deprecated stuff in element wrapper
> da82efd125 Trac #26708: clean connectivity.pyx (part 3)
> 3fa1ec45df Trac #26705: Fix is_formal for hyperplane arrangements with no 
> cycles
> bbe7f47574 Trac #26597: Update boost/boost_cropped to 1.66.0
> 0cbf26ce26 Trac #26026: Updates to Huffman codings
> 523b1f8cb6 Trac #26667: distutils no longer shows compiler commands
> f894105d0d (tag: 8.5.beta4) Updated SageMath version to 8.5.beta4
>
>

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Re: [sage-release] Re: Sage 8.5.beta5 released

2018-11-28 Thread François Bissey 
This is definitely it. It introduced the doctests in question. I guess
I should have provided that extra info.


> On 28/11/2018, at 22:11, fchapot...@gmail.com wrote:
> 
> Could be caused by https://trac.sagemath.org/ticket/26702
> 
> Le mercredi 28 novembre 2018 09:49:53 UTC+1, François Bissey a écrit :
> That’s interesting. I thought the failures in sage/databases/sql_db.py in 
> sage-on-gentoo 
> were due to the use of a newer version of sqlite. But if you see it too that 
> must be something 
> more subtle. 
> 
> François 
> 
> > On 28/11/2018, at 21:46, Sébastien Labbé  wrote: 
> > 
> > On Ubuntu 16.04, the command 
> > 
> > sage -t --all --optional=sage,optional,external 
> > 
> > tests the following optional and external doctests: 
> > 
> > Using 
> > --optional=bliss,cbc,ccache,cmake,dot2tex,external,gmpy2,lrslib,memlimit,mpir,normaliz,notedown,pandoc_attributes,pycosat,pynormaliz,python2,rst2ipynb,sage
> >  
> > External software detected for doctesting: 
> > ffmpeg,graphviz,gurobi,imagemagick,internet,latex,pandoc 
> > 
> > 
> > and gives All tests passed except the following ones: 
> > 
> > -- 
> > sage -t --long src/sage/databases/findstat.py  # 5 doctests failed 
> > sage -t --long src/sage/symbolic/integration/integral.py  # 1 doctest 
> > failed 
> > sage -t --long src/sage/combinat/tutorial.py  # 1 doctest failed 
> > sage -t --long src/sage/symbolic/integration/external.py  # 3 doctests 
> > failed 
> > sage -t --long src/sage/combinat/designs/ext_rep.py  # 1 doctest failed 
> > sage -t --long src/sage/repl/load.py  # 1 doctest failed 
> > sage -t --long src/sage/misc/persist.pyx  # 2 doctests failed 
> > sage -t --long src/sage/databases/sql_db.py  # 2 doctests failed 
> > -- 
> > 
> > 
> > Follow up at https://trac.sagemath.org/ticket/25536. New failures are 
> > copied below. 
> > 
> > 
> > 
> > sage -t --long src/sage/combinat/tutorial.py 
> > ** 
> > File "src/sage/combinat/tutorial.py", line 224, in sage.combinat.tutorial 
> > Failed example: 
> > oeis([1,1,2,5,14])# optional -- internet 
> > Expected: 
> > 0: A000108: Catalan numbers: C(n) = binomial(2n,n)/(n+1) = 
> > (2n)!/(n!(n+1)!). Also called Segner numbers. 
> > 1: A120588: G.f. satisfies: 3*A(x) = 2 + x + A(x)^2, with a(0) = 1. 
> > 2: ... 
> > Got: 
> > 0: A000108: Catalan numbers: C(n) = binomial(2n,n)/(n+1) = 
> > (2n)!/(n!(n+1)!). Also called Segner numbers. 
> > 1: A124302: Number of set partitions with at most 3 blocks; number of 
> > Dyck paths of height at most 4; dimension of space of symmetric polynomials 
> > in 3 noncommuting variables. 
> > 2: A120588: G.f. satisfies: 3*A(x) = 2 + x + A(x)^2, with a(0) = 1. 
> > ** 
> > 1 item had failures: 
> >1 of 249 in sage.combinat.tutorial 
> > 5 tests for not implemented functionality not run 
> > 6 not tested tests not run 
> > 0 tests not run because we ran out of time 
> > [248 tests, 1 failure, 24.70 s] 
> > 
> > 
> > sage -t --long src/sage/databases/sql_db.py 
> > ** 
> > File "src/sage/databases/sql_db.py", line 956, in 
> > sage.databases.sql_db.SQLDatabase.__init__ 
> > Failed example: 
> > D.show('simon') 
> > Expected: 
> > graph6   vertices edges 
> >  
> > ?00 
> > @10 
> > A?   20 
> > A_   21 
> > B?   30 
> > BG   31 
> > BW   32 
> > Bw   33 
> > C?   40 
> > C@   41 
> > CB   42 
> > CF   43 
> > CJ   43 
> > CK   42 
> > CL   43 
> > CN   44 
> > C]   44 
> > C^   45 
> > C~   46 
> > Got: 
> > graph6   vertices edges   
> >  
> > ?00   
> > @10   
> > A?

Re: [sage-release] Re: Sage 8.5.beta5 released

2018-11-28 Thread fchapoton2 
Could be caused by https://trac.sagemath.org/ticket/26702

Le mercredi 28 novembre 2018 09:49:53 UTC+1, François Bissey a écrit :
>
> That’s interesting. I thought the failures in sage/databases/sql_db.py in 
> sage-on-gentoo 
> were due to the use of a newer version of sqlite. But if you see it too 
> that must be something 
> more subtle. 
>
> François 
>
> > On 28/11/2018, at 21:46, Sébastien Labbé > 
> wrote: 
> > 
> > On Ubuntu 16.04, the command 
> > 
> > sage -t --all --optional=sage,optional,external 
> > 
> > tests the following optional and external doctests: 
> > 
> > Using 
> --optional=bliss,cbc,ccache,cmake,dot2tex,external,gmpy2,lrslib,memlimit,mpir,normaliz,notedown,pandoc_attributes,pycosat,pynormaliz,python2,rst2ipynb,sage
>  
>
> > External software detected for doctesting: 
> ffmpeg,graphviz,gurobi,imagemagick,internet,latex,pandoc 
> > 
> > 
> > and gives All tests passed except the following ones: 
> > 
> > -- 
> > sage -t --long src/sage/databases/findstat.py  # 5 doctests failed 
> > sage -t --long src/sage/symbolic/integration/integral.py  # 1 doctest 
> failed 
> > sage -t --long src/sage/combinat/tutorial.py  # 1 doctest failed 
> > sage -t --long src/sage/symbolic/integration/external.py  # 3 doctests 
> failed 
> > sage -t --long src/sage/combinat/designs/ext_rep.py  # 1 doctest failed 
> > sage -t --long src/sage/repl/load.py  # 1 doctest failed 
> > sage -t --long src/sage/misc/persist.pyx  # 2 doctests failed 
> > sage -t --long src/sage/databases/sql_db.py  # 2 doctests failed 
> > -- 
> > 
> > 
> > Follow up at https://trac.sagemath.org/ticket/25536. New failures are 
> copied below. 
> > 
> > 
> > 
> > sage -t --long src/sage/combinat/tutorial.py 
> > ** 
> > File "src/sage/combinat/tutorial.py", line 224, in 
> sage.combinat.tutorial 
> > Failed example: 
> > oeis([1,1,2,5,14])# optional -- internet 
> > Expected: 
> > 0: A000108: Catalan numbers: C(n) = binomial(2n,n)/(n+1) = 
> (2n)!/(n!(n+1)!). Also called Segner numbers. 
> > 1: A120588: G.f. satisfies: 3*A(x) = 2 + x + A(x)^2, with a(0) = 1. 
> > 2: ... 
> > Got: 
> > 0: A000108: Catalan numbers: C(n) = binomial(2n,n)/(n+1) = 
> (2n)!/(n!(n+1)!). Also called Segner numbers. 
> > 1: A124302: Number of set partitions with at most 3 blocks; number 
> of Dyck paths of height at most 4; dimension of space of symmetric 
> polynomials in 3 noncommuting variables. 
> > 2: A120588: G.f. satisfies: 3*A(x) = 2 + x + A(x)^2, with a(0) = 1. 
> > ** 
> > 1 item had failures: 
> >1 of 249 in sage.combinat.tutorial 
> > 5 tests for not implemented functionality not run 
> > 6 not tested tests not run 
> > 0 tests not run because we ran out of time 
> > [248 tests, 1 failure, 24.70 s] 
> > 
> > 
> > sage -t --long src/sage/databases/sql_db.py 
> > ** 
> > File "src/sage/databases/sql_db.py", line 956, in 
> sage.databases.sql_db.SQLDatabase.__init__ 
> > Failed example: 
> > D.show('simon') 
> > Expected: 
> > graph6   vertices edges 
> >  
> > ?00 
> > @10 
> > A?   20 
> > A_   21 
> > B?   30 
> > BG   31 
> > BW   32 
> > Bw   33 
> > C?   40 
> > C@   41 
> > CB   42 
> > CF   43 
> > CJ   43 
> > CK   42 
> > CL   43 
> > CN   44 
> > C]   44 
> > C^   45 
> > C~   46 
> > Got: 
> > graph6   vertices edges   
> >  
> > ?00   
> > @10   
> > A?   20   
> > A_   21   
> > B?   30   
> >

Re: [sage-release] Re: Sage 8.5.beta5 released

2018-11-28 Thread François Bissey 
That’s interesting. I thought the failures in sage/databases/sql_db.py in 
sage-on-gentoo
were due to the use of a newer version of sqlite. But if you see it too that 
must be something
more subtle.

François

> On 28/11/2018, at 21:46, Sébastien Labbé  wrote:
> 
> On Ubuntu 16.04, the command 
> 
> sage -t --all --optional=sage,optional,external
> 
> tests the following optional and external doctests:
> 
> Using 
> --optional=bliss,cbc,ccache,cmake,dot2tex,external,gmpy2,lrslib,memlimit,mpir,normaliz,notedown,pandoc_attributes,pycosat,pynormaliz,python2,rst2ipynb,sage
> External software detected for doctesting: 
> ffmpeg,graphviz,gurobi,imagemagick,internet,latex,pandoc
> 
> 
> and gives All tests passed except the following ones:
> 
> --
> sage -t --long src/sage/databases/findstat.py  # 5 doctests failed
> sage -t --long src/sage/symbolic/integration/integral.py  # 1 doctest failed
> sage -t --long src/sage/combinat/tutorial.py  # 1 doctest failed
> sage -t --long src/sage/symbolic/integration/external.py  # 3 doctests failed
> sage -t --long src/sage/combinat/designs/ext_rep.py  # 1 doctest failed
> sage -t --long src/sage/repl/load.py  # 1 doctest failed
> sage -t --long src/sage/misc/persist.pyx  # 2 doctests failed
> sage -t --long src/sage/databases/sql_db.py  # 2 doctests failed
> --
> 
> 
> Follow up at https://trac.sagemath.org/ticket/25536. New failures are copied 
> below.
> 
> 
> 
> sage -t --long src/sage/combinat/tutorial.py
> **
> File "src/sage/combinat/tutorial.py", line 224, in sage.combinat.tutorial
> Failed example:
> oeis([1,1,2,5,14])# optional -- internet
> Expected:
> 0: A000108: Catalan numbers: C(n) = binomial(2n,n)/(n+1) = 
> (2n)!/(n!(n+1)!). Also called Segner numbers.
> 1: A120588: G.f. satisfies: 3*A(x) = 2 + x + A(x)^2, with a(0) = 1.
> 2: ...
> Got:
> 0: A000108: Catalan numbers: C(n) = binomial(2n,n)/(n+1) = 
> (2n)!/(n!(n+1)!). Also called Segner numbers.
> 1: A124302: Number of set partitions with at most 3 blocks; number of 
> Dyck paths of height at most 4; dimension of space of symmetric polynomials 
> in 3 noncommuting variables.
> 2: A120588: G.f. satisfies: 3*A(x) = 2 + x + A(x)^2, with a(0) = 1.
> **
> 1 item had failures:
>1 of 249 in sage.combinat.tutorial
> 5 tests for not implemented functionality not run
> 6 not tested tests not run
> 0 tests not run because we ran out of time
> [248 tests, 1 failure, 24.70 s]
> 
> 
> sage -t --long src/sage/databases/sql_db.py
> **
> File "src/sage/databases/sql_db.py", line 956, in 
> sage.databases.sql_db.SQLDatabase.__init__
> Failed example:
> D.show('simon')
> Expected:
> graph6   vertices edges
> 
> ?00
> @10
> A?   20
> A_   21
> B?   30
> BG   31
> BW   32
> Bw   33
> C?   40
> C@   41
> CB   42
> CF   43
> CJ   43
> CK   42
> CL   43
> CN   44
> C]   44
> C^   45
> C~   46
> Got:
> graph6   vertices edges   
> 
> ?00   
> @10   
> A?   20   
> A_   21   
> B?   30   
> BG   31   
> BW   32   
> Bw   33   
> C?   40   
> C@   41   
> CB   42

[sage-release] Re: Sage 8.5.beta5 released

2018-11-28 Thread Sébastien Labbé 
On Ubuntu 16.04, the command 

sage -t --all --optional=sage,optional,external

tests the following optional and external doctests:

Using 
--optional=bliss,cbc,ccache,cmake,dot2tex,external,gmpy2,lrslib,memlimit,mpir,normaliz,notedown,pandoc_attributes,pycosat,pynormaliz,python2,rst2ipynb,sage
External software detected for doctesting: 
ffmpeg,graphviz,gurobi,imagemagick,internet,latex,pandoc


and gives All tests passed except the following ones:

--
sage -t --long src/sage/databases/findstat.py  # 5 doctests failed
sage -t --long src/sage/symbolic/integration/integral.py  # 1 doctest failed
sage -t --long src/sage/combinat/tutorial.py  # 1 doctest failed
sage -t --long src/sage/symbolic/integration/external.py  # 3 doctests 
failed
sage -t --long src/sage/combinat/designs/ext_rep.py  # 1 doctest failed
sage -t --long src/sage/repl/load.py  # 1 doctest failed
sage -t --long src/sage/misc/persist.pyx  # 2 doctests failed
sage -t --long src/sage/databases/sql_db.py  # 2 doctests failed
--


Follow up at https://trac.sagemath.org/ticket/25536. New failures are 
copied below.



sage -t --long src/sage/combinat/tutorial.py
**
File "src/sage/combinat/tutorial.py", line 224, in sage.combinat.tutorial
Failed example:
oeis([1,1,2,5,14])# optional -- internet
Expected:
0: A000108: Catalan numbers: C(n) = binomial(2n,n)/(n+1) = 
(2n)!/(n!(n+1)!). Also called Segner numbers.
1: A120588: G.f. satisfies: 3*A(x) = 2 + x + A(x)^2, with a(0) = 1.
2: ...
Got:
0: A000108: Catalan numbers: C(n) = binomial(2n,n)/(n+1) = 
(2n)!/(n!(n+1)!). Also called Segner numbers.
1: A124302: Number of set partitions with at most 3 blocks; number of 
Dyck paths of height at most 4; dimension of space of symmetric polynomials 
in 3 noncommuting variables.
2: A120588: G.f. satisfies: 3*A(x) = 2 + x + A(x)^2, with a(0) = 1.
**
1 item had failures:
   1 of 249 in sage.combinat.tutorial
5 tests for not implemented functionality not run
6 not tested tests not run
0 tests not run because we ran out of time
[248 tests, 1 failure, 24.70 s]


sage -t --long src/sage/databases/sql_db.py
**
File "src/sage/databases/sql_db.py", line 956, in 
sage.databases.sql_db.SQLDatabase.__init__
Failed example:
D.show('simon')
Expected:
graph6   vertices edges

?00
@10
A?   20
A_   21
B?   30
BG   31
BW   32
Bw   33
C?   40
C@   41
CB   42
CF   43
CJ   43
CK   42
CL   43
CN   44
C]   44
C^   45
C~   46
Got:
graph6   vertices edges   

?00   
@10   
A?   20   
A_   21   
B?   30   
BG   31   
BW   32   
Bw   33   
C?   40   
C@   41   
CB   42   
CF   43   
CJ   43   
C`   42   
CR   43   
CN   44   
Cr   44   
C^   45

[sage-release] Re: Sage 8.5.beta5 released

2018-11-27 Thread Eric Gourgoulhon 
On Ubuntu 18.04 running on Xeon E5-2623 + 16 GB RAM:

- python2: 
  - incremental build (-j16) from 8.5.beta4 OK
  - all tests from ptestlong passed
 
- python3: 
  - incremental build (-j16) from 8.5.beta4 OK
  - threejs viewer is now fully functional (at least as functional as with 
python2); 
for instance the S^2 notebook 

 
runs with python3 as well as with python2

Eric. 

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Re: [sage-release] Re: Sage 8.5.beta5 released

2018-11-26 Thread E. Madison Bray 
On Mon, Nov 26, 2018 at 5:37 AM Steven Trogdon  wrote:
>
> On my Gentoo changing the ownership was not sufficient. After changing the 
> ownership I had to
>
> git reset --hard HEAD
>
> which revealed that
>
> Updating f894105d0d..b36eca1990
> error: The following untracked working tree files would be overwritten by 
> merge:
>
> To correct this:
>
> git clean -f build/pkgs/barvinok/
> git clean -f build/pkgs/isl/
> git clean -f build/pkgs/lcalc/patches/
> git clean -f build/pkgs/polylib/
>
> and now 'git pull' is up to date. This is all very strange.

At some point you probably did *something* as root (and by "you" it
might not have even been an action you personally took, but maybe some
cron job you forgot about; who knows).  But otherwise I don't think
there's any way that would have happened.  This happens to me too
sometimes ¯\_(ツ)_/¯  Git repos don't store anything about uid/gid of
files (that would be disastrous); in fact IIRC the only information it
stores about file permissions is whether or not the executable bit
should be set.


> On Sunday, November 25, 2018 at 9:41:58 PM UTC-6, Samuel Lelievre wrote:
>>
>> > As far as I can recall 'git pull' was always done as a normal user.
>> > Note the timestamp on the folders, which predates 8.5.beta4.
>> > And this issue did not manifest itself then. But going forward,
>> > how to correct things?
>>
>> Change to your SAGE_ROOT directory and run this as a normal user
>>
>> $ sudo chown -v -R $(id -u):$(id -g) .
>>
>> to set the owner and group of SAGE_ROOT (and recursively all
>> the included files and directories) to your user and your group.
>
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Re: [sage-release] Re: Sage 8.5.beta5 released

2018-11-25 Thread Steven Trogdon 
On my Gentoo changing the ownership was not sufficient. After changing the 
ownership I had to

git reset --hard HEAD

which revealed that

Updating f894105d0d..b36eca1990
error: The following untracked working tree files would be overwritten by 
merge:

To correct this:

git clean -f build/pkgs/barvinok/
git clean -f build/pkgs/isl/
git clean -f build/pkgs/lcalc/patches/
git clean -f build/pkgs/polylib/

and now 'git pull' is up to date. This is all very strange.

On Sunday, November 25, 2018 at 9:41:58 PM UTC-6, Samuel Lelievre wrote:
>
> > As far as I can recall 'git pull' was always done as a normal user. 
> > Note the timestamp on the folders, which predates 8.5.beta4. 
> > And this issue did not manifest itself then. But going forward, 
> > how to correct things? 
>
> Change to your SAGE_ROOT directory and run this as a normal user 
>
> $ sudo chown -v -R $(id -u):$(id -g) . 
>
> to set the owner and group of SAGE_ROOT (and recursively all 
> the included files and directories) to your user and your group. 
>

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Re: [sage-release] Re: Sage 8.5.beta5 released

2018-11-25 Thread Samuel Lelièvre 
> As far as I can recall 'git pull' was always done as a normal user.
> Note the timestamp on the folders, which predates 8.5.beta4.
> And this issue did not manifest itself then. But going forward,
> how to correct things?

Change to your SAGE_ROOT directory and run this as a normal user

$ sudo chown -v -R $(id -u):$(id -g) .

to set the owner and group of SAGE_ROOT (and recursively all
the included files and directories) to your user and your group.

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[sage-release] Re: Sage 8.5.beta5 released

2018-11-25 Thread Steven Trogdon 
As far as I can recall 'git pull' was always done as a normal user. Note 
the timestamp on the folders, which predates 8.5.beta4. And this issue did 
not manifest itself then. But going forward, how to correct things?

On Sunday, November 25, 2018 at 8:53:10 PM UTC-6, Samuel Lelievre wrote:
>
>
>
> Mon 2018-11-26 03:21:58 UTC+1, Steven Trogdon:
>>
>> Something rather weird here. I'm unable to complete a pull of the latest 
>> 8.5.beta5 because of
>>
>> Updating f894105d0d..b36eca1990
>> error: unable to unlink old 'docker/entrypoint.sh': Permission denied
>>
>> Now entrypoint.sh is owned by root which I find strange
>>
>> ls -al docker/entrypoint.sh
>> -rwxr-xr-x 1 root root 315 Aug 26 12:46 docker/entrypoint.sh
>>
>> In fact in SAGE_ROOT there are numerous folders and a file owned by root
>>
>> ls -al | grep 'root '
>> drwxr-xr-x  2 root root   4096 Aug 26 12:46 .ci
>> drwxr-xr-x  2 root root   4096 Aug 26 12:46 .circleci
>> lrwxrwxrwx  1 root root 10 Aug 26 12:46 .dockerignore -> 
>> .gitignore
>> -rw-r--r--  1 root root   6753 Aug 26 12:46 .gitlab-ci.yml
>> drwxr-xr-x  3 root root   4096 Aug 26 12:46 docker
>>
>> Any idea as to what's with this? 8.5.beta4 was just fine.
>>
>
> I don't see anything like that here.
> Did you maybe perform a "git pull" as root at some point?
>

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[sage-release] Re: Sage 8.5.beta5 released

2018-11-25 Thread Samuel Lelievre 


Mon 2018-11-26 03:21:58 UTC+1, Steven Trogdon:
>
> Something rather weird here. I'm unable to complete a pull of the latest 
> 8.5.beta5 because of
>
> Updating f894105d0d..b36eca1990
> error: unable to unlink old 'docker/entrypoint.sh': Permission denied
>
> Now entrypoint.sh is owned by root which I find strange
>
> ls -al docker/entrypoint.sh
> -rwxr-xr-x 1 root root 315 Aug 26 12:46 docker/entrypoint.sh
>
> In fact in SAGE_ROOT there are numerous folders and a file owned by root
>
> ls -al | grep 'root '
> drwxr-xr-x  2 root root   4096 Aug 26 12:46 .ci
> drwxr-xr-x  2 root root   4096 Aug 26 12:46 .circleci
> lrwxrwxrwx  1 root root 10 Aug 26 12:46 .dockerignore -> .gitignore
> -rw-r--r--  1 root root   6753 Aug 26 12:46 .gitlab-ci.yml
> drwxr-xr-x  3 root root   4096 Aug 26 12:46 docker
>
> Any idea as to what's with this? 8.5.beta4 was just fine.
>

I don't see anything like that here.
Did you maybe perform a "git pull" as root at some point?

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[sage-release] Re: Sage 8.5.beta5 released

2018-11-25 Thread Steven Trogdon 
Something rather weird here. I'm unable to complete a pull of the latest 
8.5.beta5 because of

Updating f894105d0d..b36eca1990
error: unable to unlink old 'docker/entrypoint.sh': Permission denied

Now entrypoint.sh is owned by root which I find strange

ls -al docker/entrypoint.sh
-rwxr-xr-x 1 root root 315 Aug 26 12:46 docker/entrypoint.sh

In fact in SAGE_ROOT there are numerous folders and a file owned by root

ls -al | grep 'root '
drwxr-xr-x  2 root root   4096 Aug 26 12:46 .ci
drwxr-xr-x  2 root root   4096 Aug 26 12:46 .circleci
lrwxrwxrwx  1 root root 10 Aug 26 12:46 .dockerignore -> .gitignore
-rw-r--r--  1 root root   6753 Aug 26 12:46 .gitlab-ci.yml
drwxr-xr-x  3 root root   4096 Aug 26 12:46 docker

Any idea as to what's with this? 8.5.beta4 was just fine.

On Sunday, November 25, 2018 at 6:36:04 PM UTC-6, Volker Braun 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
>
> b36eca1990 (tag: 8.5.beta5, trac/develop) Updated SageMath version to 
> 8.5.beta5
> 50d5520f60 Trac #26747: py3: final fixes for cluster_algebra.py
> acb2071e3c Trac #26738: py3: fix all doctests in game_theory
> c0fcb1222a Trac #26748: clean graph_generators_pyx.pyx
> b7d04438fb Trac #26746: provide translation of fresnel to fricas
> 99fe4d2534 Trac #26745: py3: fix doctest in Grossman-Larsson
> 285956f06c Trac #26744: remove a bunch of deprecated renamed keywords
> 959468f7a2 Trac #26743: cyclotomic_part should not include powers of x
> 9c0a66df99 Trac #26739: py3: some fixes in Monsky-Washnitzer
> 47998f15f4 Trac #26736: some work on cluster mutation again
> e7a1a04d8f Trac #26732: Docker image fails to start jupyter notebook
> 73b2d3962e Trac #26734: small cleanup for alternating sign matrices
> 9713da62ea Trac #25708: Rename SBox methods for 
> difference_distribution_matrix and similar to _table
> d45e4d9b7e Trac #26742: py3: fix threejs viewer interface
> 53b87f160d Trac #26737: py3: some work on finite state machines
> 3ce4503500 Trac #26728: Remove ellipsis in one findstat doctest
> 7853331f91 Trac #26726: Py3: Some python3 fixes in geometry module.
> 7d7d7eaca0 Trac #26704: Py3 : database.oeis  implement __getitem__ to 
> replace __getslice__
> 2599afd5c4 Trac #26596: Replace expect r interface with rpy2
> a38120a74e Trac #26168: Add parallelism for two tensor calculus functions
> b150b57dd2 Trac #25473: 20 internet doctests failed in 
> sage/finance/stock.py
> d11cabb0c9 Trac #23547: isl + polylib + barvinok packages
> 269bd3da76 Trac #23341: port lcalc to C++11
> 514e0f5e50 Trac #26729: update curl to 7.62
> b054b079e5 Trac #26405: Root finding for p-adic polynomials
> 7b564b0ed6 Trac #25443: bijections for set partitions
> 6eba589bce Trac #26720: py3: some fixes for misc/abstract_method
> fda5bdab57 Trac #26717: converting some http to https in install 
> instructions
> e235693068 Trac #26712: avoid .vertices() in independent_sets.pyx
> cbe26c565f Trac #26711: avoid .vertices() in graph_coloring.py
> b138c8a7a4 Trac #26702: Py3: Fix database/sql_db module for python3
> 9e6743fa4c Trac #26420: More flexible constructor of  GroupHomomorphisms
> 75bc4c6d91 Trac #25519: Upgrade gmpy2
> 10d1b6810c Trac #26715: build/pkgs/gfortran/spkg-configure.m4 works 
> incorrectly if CC and CXX are already there
> 51d1404842 Trac #26723: remove deprecated stuff in posets and Hasse
> 2615da94d8 Trac #26724: py3: one small fix for elliptic curves over number 
> fields
> 4332897d03 Trac #26721: py3: fix function fields
> 7928e4c3a0 Trac #26719: py3: fix doctests in symmetric group algebra
> 5d8ab92872 Trac #26630: clean generic_graph.py (part 3)
> 5c49a279ea Trac #26709: Upgrade to jupyter notebook 5.7.1
> cc373ffd76 Trac #26661: pep cleanup of old integer lists
> 208fd1182c Trac #26574: remove deprecated stuff in integer lists
> 1a6f4e9862 Trac #26560: remove deprecated stuff in element wrapper
> da82efd125 Trac #26708: clean connectivity.pyx (part 3)
> 3fa1ec45df Trac #26705: Fix is_formal for hyperplane arrangements with no 
> cycles
> bbe7f47574 Trac #26597: Update boost/boost_cropped to 1.66.0
> 0cbf26ce26 Trac #26026: Updates to Huffman codings
> 523b1f8cb6 Trac #26667: distutils no longer shows compiler commands
> f894105d0d (tag: 8.5.beta4) Updated SageMath version to 8.5.beta4
>
>

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