[sage-devel] Re: Grepping Trac

2019-08-02 Thread John H Palmieri


On Friday, August 2, 2019 at 1:36:36 PM UTC-7, Nils Bruin wrote:
>
> On Friday, August 2, 2019 at 11:39:47 AM UTC-7, Timo Kaufmann wrote:
>>
>> Hi!
>>
>> As part of my packaging workflow, I find myself pasting error messages 
>> into the trac search pretty frequently to discover if something is a known 
>> issue or due to packaging complications. Trac search isn't very helpful 
>> here though, since it will try to split words and look for them 
>> individually. All I want is a literal search. A regex search would be even 
>> better.
>>
>>
> I find that google with "site:trac.sagemath.org" is fairly good at 
> finding relevant tickets. 
>

Searching the Google group sage-trac is also pretty good.

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[sage-devel] Re: Grepping Trac

2019-08-02 Thread Nils Bruin
On Friday, August 2, 2019 at 11:39:47 AM UTC-7, Timo Kaufmann wrote:
>
> Hi!
>
> As part of my packaging workflow, I find myself pasting error messages 
> into the trac search pretty frequently to discover if something is a known 
> issue or due to packaging complications. Trac search isn't very helpful 
> here though, since it will try to split words and look for them 
> individually. All I want is a literal search. A regex search would be even 
> better.
>
>
I find that google with "site:trac.sagemath.org" is fairly good at finding 
relevant tickets. 

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[sage-devel] Re: maxima 5.43.0

2019-08-02 Thread Antonio Rojas


El jueves, 1 de agosto de 2019, 2:00:02 (UTC+2), François Bissey escribió:
>
> Hi all, 
>
> I am giving a shot at getting maxima-5.43.0 working for sage-on-gentoo 
> and it looks good overall but there are couple of things that needs 
> attention. 
> ** 
> File 
> "/usr/lib64/python2.7/site-packages/sage/symbolic/integration/integral.py", 
>
> line 829, in sage.symbolic.integration.integral.integrate 
> Failed example: 
>  abs(N(a - pi*log(2)/8)) < 1e-15  # long time 
> Expected: 
>  True 
> Got: 
>  False 
> **


This one is caused 
by 
https://sourceforge.net/p/maxima/code/ci/47a6afd1d4691b83bedd197dea322dfd64f4f0f9/

Note that this same commit broke some of maxima's own tests, which they 
'fixed' by skipping them. So it might make sense to do the same here.
 

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Re: [sage-devel] sage 8.9beta4 ntl

2019-08-02 Thread Dima Pasechnik
On Fri, Aug 2, 2019 at 10:42 PM Dima Pasechnik  wrote:
>
> On Fri, Aug 2, 2019 at 10:10 PM Han Frederic  wrote:
> >
> > Hello,
> > I have something strange (fedora 29, amd64)
> > I have cloned sage 8.9beta4
> > and make it. All seems functionnal but I realised that ntl is not built. 
> > This looks strange because giac is built and ntl is listed in the file:
> >
> > build/pkgs/giac/dependencies
> >
> > Moreover I have ntl and other giac deps from fedora and now the system ntl 
> > is used.
> >
> > (sage-sh) fred@localhost:sage$ ldd local/lib/libgiac.so
> > linux-vdso.so.1 (0x7ffc4ffc2000)
> > libntl.so.38 => /lib64/libntl.so.38 (0x7f312e038000)
> > libpari-gmp.so.6 => 
> > /home/fred-dev/sage/develop/sage/local/lib/libpari-gmp.so.6 
> > (0x7f312d791000)
> > libgsl.so.23 => /home/fred-dev/sage/develop/sage/local/lib/libgsl.so.23 
> > (0x7f312d50e000)
> >
> > I don't think it happened on sage 8.8.

in fact, https://trac.sagemath.org/ticket/27822 was already in 8.8
and system NTL is already usable there. But you need to rebuild from scratch
or, at least, expicitly uninstall Sage's NTL (and rebuild) to use the
system NTL.

> >
> > Can you reproduce this?
>
> Well, this is how it is meant to be!
> See https://trac.sagemath.org/ticket/27330
>
> E.g. if you have a compatible NTL installed, it will be used instead
> of a vendored version.
>
>
>
>
> >
> > --
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Re: [sage-devel] sage 8.9beta4 ntl

2019-08-02 Thread Dima Pasechnik
On Fri, Aug 2, 2019 at 10:10 PM Han Frederic  wrote:
>
> Hello,
> I have something strange (fedora 29, amd64)
> I have cloned sage 8.9beta4
> and make it. All seems functionnal but I realised that ntl is not built. This 
> looks strange because giac is built and ntl is listed in the file:
>
> build/pkgs/giac/dependencies
>
> Moreover I have ntl and other giac deps from fedora and now the system ntl is 
> used.
>
> (sage-sh) fred@localhost:sage$ ldd local/lib/libgiac.so
> linux-vdso.so.1 (0x7ffc4ffc2000)
> libntl.so.38 => /lib64/libntl.so.38 (0x7f312e038000)
> libpari-gmp.so.6 => 
> /home/fred-dev/sage/develop/sage/local/lib/libpari-gmp.so.6 
> (0x7f312d791000)
> libgsl.so.23 => /home/fred-dev/sage/develop/sage/local/lib/libgsl.so.23 
> (0x7f312d50e000)
>
> I don't think it happened on sage 8.8.
>
> Can you reproduce this?

Well, this is how it is meant to be!
See https://trac.sagemath.org/ticket/27330

E.g. if you have a compatible NTL installed, it will be used instead
of a vendored version.




>
> --
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[sage-devel] sage 8.9beta4 ntl

2019-08-02 Thread Han Frederic
Hello,
I have something strange (fedora 29, amd64)
I have cloned sage 8.9beta4
and make it. All seems functionnal but I realised that ntl is not built. 
This looks strange because giac is built and ntl is listed in the file:

build/pkgs/giac/dependencies

Moreover I have ntl and other giac deps from fedora and now the system ntl 
is used. 

(sage-sh) fred@localhost:sage$ ldd local/lib/libgiac.so
linux-vdso.so.1 (0x7ffc4ffc2000)
libntl.so.38 => /lib64/libntl.so.38 (0x7f312e038000)
libpari-gmp.so.6 => /home/fred-dev/sage/develop/sage/local/lib/libpari-
gmp.so.6 (0x7f312d791000)
libgsl.so.23 => /home/fred-dev/sage/develop/sage/local/lib/libgsl.so.23 
(0x7f312d50e000)

I don't think it happened on sage 8.8.

Can you reproduce this?

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[sage-devel] Grepping Trac

2019-08-02 Thread Timo Kaufmann
Hi!

As part of my packaging workflow, I find myself pasting error messages into 
the trac search pretty frequently to discover if something is a known issue 
or due to packaging complications. Trac search isn't very helpful here 
though, since it will try to split words and look for them individually. 
All I want is a literal search. A regex search would be even better.

Is something like that possible? Can one maybe export all trac tickets in 
some plain text format?


Timo

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Re: [sage-devel] save/loads and the pickle jar

2019-08-02 Thread Nils Bruin
On Friday, August 2, 2019 at 2:47:04 AM UTC-7, E. Madison Bray wrote:
>
> As I have written before, pickle is not an appropriate format for 
> long-term stable serialization, and never has been, as it is 
> inherently tied to the code which produced it (and is highly 
> Python-specific, at that).  If this is an endemic problem for someone, 
> they should use a different serialization format. 
>
> If one reads the documentation of "pickle" in python then one does get the 
idea that it is designed to provide serialization that should also work 
over longer time stretches. It would take a lot of discipline to do the 
versioning correctly and one shouldn't start supporting pickling on new 
data structures too soon (it could lead to horribly expensive legacy 
support when one changes the way data is stored). It's certainly the kind 
of serialization format one comes up with for storing complicated data 
structures such as those in computer algebra.
In principle, the discipline can be helped a lot by having a pickle jar 
that provides good coverage of (legacy) pickles.
I agree that it's very ambitious to try and support pickling across sage, 
across time, and with the loose feature management and high diversity in 
developer interests it may well be unachievable/unmaintainable. But I think 
this is more a problem with the task, not with the pickle format.

I agree that for data storage that really needs to be able to stand the 
test of time, one needs to go with something human readable/copy-pastable. 
It's still open for misinterpretation, but at least one stands a chance of 
decoding it when the original tools have disappeared. In reality, the 
important thing is to properly document how the data was generated in the 
first place.

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Re: [sage-devel] docker images "latest" and "develop" are old

2019-08-02 Thread Julian Rüth
Hi Erik,

I think this is not a problem on GitLab anymore. I can restart protected 
jobs at least, so probably also entire pipelines.

On Friday, August 2, 2019 at 11:14:24 AM UTC+2, E. Madison Bray wrote:
>
> Wow--do I understand you correctly that, if a branch is marked 
> "unprotected" , GitLab won't receive the secrets credentials?  And yet 
> the only way to manually restart a pipeline is to "unprotect" the 
> branch (which I did, as you say, in order to restart)? 
>

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[sage-devel] Re: save/loads and the pickle jar

2019-08-02 Thread Simon King
Hi,

On 2019-08-02, E. Madison Bray  wrote:
> Sage's use of pickle for save()/load() is a mis-feature IMO.  One that
> made sense at a time, for lack of a better choice.  And that's still
> useful as a means of saving/restoring some objects between sessions.
> But I don't think you can always guarantee it to be stable.

What better format do you suggest?

I am surprised that you see a fundamental problem with Sage's pickling: If
code or even the data structures change, then it is still possible to
fit old data (pickles) into the new data format. Evidently, when you
decide to change the data structures in your algorithms, you *have* to
write a function that translates old data into the new format - but
on the positive side, you *can* write such a function.

Is there a different approach that allows to change your code over time
(evidently that's absolutely needed for a project that isn't dead!)
while still being able to read data that you have stored with your old
code?

Best regards,
Simon

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Re: [sage-devel] save/loads and the pickle jar

2019-08-02 Thread E. Madison Bray
On Wed, Jul 31, 2019 at 7:32 PM Vincent Delecroix
<20100.delecr...@gmail.com> wrote:
>
> Dear developers,
>
> It appears that a sage object saved with the "save" command can
> sometimes be not loaded again with "load". It is the second time
> in a month that people complains that it is not working (because
> of Sage version mismatch).
>
>   situation number 1: Attached to https://arxiv.org/abs/1802.06923
>   there are various sobj files (storing matrices over number fields).
>   These files do not load anymore on more recent sage versions!
>
>   (For some strange reason the pickle is half broken because the
>pickle contains "implementation='flint'" (which is not available
>over number fields).
>
>   situation number 2: a colleague has access to 2 Sage versions. On
>   his laptop and on some server. He hoped that doing "save" on the
>   server and "load" on his laptop he would be able to transfer
>   data... Again it does not work (with symbolic expressions).
>
> In the current situation I think we should disable the save/load (or at
> least warn) to make it clear that it is not safe across version.
>
> I opened the following for the issue
>
> https://trac.sagemath.org/ticket/28302
>
> On the other hand, I think this feature is almost essential to Sage
> (just because two people complained to me about this). The early
> developers of Sage had the wonderful idea of the pickle jar. But it
> only contains old objects. Let me recall the existence of the long
> standing
>
>  https://trac.sagemath.org/ticket/10768

As I have written before, pickle is not an appropriate format for
long-term stable serialization, and never has been, as it is
inherently tied to the code which produced it (and is highly
Python-specific, at that).  If this is an endemic problem for someone,
they should use a different serialization format.

Unfortunately, Sage does not currently have a standard, non-pickle way
of serializing most objects (and indeed the formats one might use to
serialize an object might depend heavily on what type of object it is,
and how it is to be used).

Sage's use of pickle for save()/load() is a mis-feature IMO.  One that
made sense at a time, for lack of a better choice.  And that's still
useful as a means of saving/restoring some objects between sessions.
But I don't think you can always guarantee it to be stable.

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Re: [sage-devel] Problem installing giacpy_sage

2019-08-02 Thread François Bissey
This is https://trac.sagemath.org/ticket/28082

> On 2/08/2019, at 8:41 PM, 'PJ' via sage-devel  
> wrote:
> 
> When trying to install giacpy_sage via
> 
> sage -i giacpy_sage
> 
> I'm encountering errors that seem to indicate that C++11 should be used but 
> isn't. I haven't managed to fix the install, and would appreciate any advice. 
> This is on macOS 10.13.6. Log output of the install with all occurring errors 
> attached as sage_install.log. 
> 
> Thank you!
> 
> 
> 
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> 

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[sage-devel] Problem installing giacpy_sage

2019-08-02 Thread 'PJ' via sage-devel
When trying to install giacpy_sage via

sage -i giacpy_sage

I'm encountering errors that seem to indicate that C++11 should be used but 
isn't. I haven't managed to fix the install, and would appreciate any 
advice. This is on macOS 10.13.6. Log output of the install with all 
occurring errors attached as sage_install.log. 

Thank you!


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Found local metadata for giacpy_sage-0.6.7
Attempting to download package giacpy_sage-0.6.7.tar.gz from mirrors
Downloading the Sage mirror list
Searching fastest mirror
  219ms: http://files.sagemath.org/
  803ms: http://ftp.kaist.ac.kr/sage/
  342ms: http://ftp.leg.uct.ac.za/pub/packages/sage/
  159ms: http://ftp.ntua.gr/pub/sagemath/
  143ms: http://ftp.rediris.es/mirror/sagemath/
  582ms: http://ftp.riken.jp/sagemath/
  350ms: http://ftp.sun.ac.za/ftp/pub/mirrors/www.sagemath.org/
  568ms: http://ftp.yz.yamagata-u.ac.jp/pub/math/sage/
  615ms: http://linorg.usp.br/sage/
 1228ms: http://mirror.aarnet.edu.au/pub/sage/
  368ms: http://mirror.ufs.ac.za/sagemath/
  119ms: http://mirror.yandex.ru/mirrors/sage.math.washington.edu/
  128ms: http://mirrors.mit.edu/sage/
 1532ms: http://mirrors.tuna.tsinghua.edu.cn/sagemath/
WARNING [mirror_list|_rank_mirrors:136]: timed out: 
http://mirrors.ustc.edu.cn/sagemath/
  305ms: http://mirrors.xmission.com/sage/
  336ms: http://sage.mirror.garr.it/mirrors/sage/
  295ms: http://sagemath.c3sl.ufpr.br/
  453ms: http://sagemath.mirror.ac.za/
  590ms: http://sagemath.nust.na/sage/
   81ms: http://www-ftp.lip6.fr/pub/math/sagemath/
  344ms: http://www.cecm.sfu.ca/sage/
   52ms: http://www.mirrorservice.org/sites/www.sagemath.org/
  260ms: https://mirror-hk.koddos.net/sagemath/
   66ms: https://mirror.koddos.net/sagemath/
   86ms: https://mirrors.up.pt/pub/sage/
Fastest mirror: http://www.mirrorservice.org/sites/www.sagemath.org/
http://www.mirrorservice.org/sites/www.sagemath.org/spkg/upstream/giacpy_sage/giacpy_sage-0.6.7.tar.gz
[..]
giacpy_sage-0.6.7

Setting up build directory for giacpy_sage-0.6.7
Finished extraction
No patch files found in ../patches

Host system:
Darwin Julias-MBP.lan 17.7.0 Darwin Kernel Version 17.7.0: Thu Dec 20 21:47:19 
PST 2018; root:xnu-4570.71.22~1/RELEASE_X86_64 x86_64

C compiler: gcc
C compiler version:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
--with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1
Apple LLVM version 10.0.0 (clang-1000.11.45.5)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Package 'giacpy_sage' is currently not installed
No legacy uninstaller found for 'giacpy_sage'; nothing to do
Deleting /Users/julia/sage_mac/SageMath/local/lib/python*/site-packages/giacpy-*
Deleting 
/Users/julia/sage_mac/SageMath/local/lib/python*/site-packages/giacpy.so
Deleting 
/Users/julia/sage_mac/SageMath/local/lib/python*/site-packages/giacpy_sage*
Installing giacpy_sage-0.6.7
/Users/julia/sage_mac/SageMath/local/lib/python2.7/site-packages/Cython/Compiler/Main.py:367:
 FutureWarning: Cython directive 'language_level' not set, using 2 for now 
(Py2). This will change in a later release! File: 
/Users/julia/sage_mac/SageMath/local/var/tmp/sage/build/giacpy_sage-0.6.7/src/giacpy_sage.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
Warning: This package has a badly-behaved setup.py which outputs
more than the package name for 'setup.py --name'; using the last
line as the package name: giacpy_sage
Installing package giacpy_sage using pip2
Ignoring indexes: https://pypi.org/simple
Created temporary directory: 
/private/var/folders/vb/pgn0bx7j4b55mr90x034wyl8gn/T/pip-ephem-wheel-cache-Rqwyuh
Created temporary directory: 
/private/var/folders/vb/pgn0bx7j4b55mr90x034wyl8gn/T/pip-req-tracker-5JHTxr
Created requirements tracker 
'/private/var/folders/vb/pgn0bx7j4b55mr90x034wyl8gn/T/pip-req-tracker-5JHTxr'
Created temporary directory: 
/private/var/folders/vb/pgn0bx7j4b55mr90x034wyl8gn/T/pip-install-kVZ9JL
Processing 
/Users/julia/sage_mac/SageMath/local/var/tmp/sage/build/giacpy_sage-0.6.7/src
  Created temporary directory: 
/private/var/folders/vb/pgn0bx7j4b55mr90x034wyl8gn/T/pip-req-build-35Ij1v
  Added 
file:///Users/julia/sage_mac/

Re: [sage-devel] SPAM on trac from github users

2019-08-02 Thread E. Madison Bray
On Thu, Aug 1, 2019 at 1:45 PM Frédéric Chapoton  wrote:
>
> Hello,
>
> The user gh-mohdazher has just open a spam-ticket on trac. I have nuked this 
> ticket.
>
> This is the second time in one month that we observe spamming behaviour from 
> github users.
>
> * How to avoid that ?

You don't.  If you want to run a service where people are given access
to post content you're going to have occasional spammers no matter
what, without completely locking things down as was the case
previously.

By allowing GitHub users to log in we are pushing spam prevention on
to GitHub which does a lot more in the first place than we can do
alone.

Even if the project were moved to GitHub, or GitLab, a large-enough
project will attract some spam.  CPython has been getting spam PRs
sometimes, for example.  Just have to accept it, up to a point where
it becomes unmanageable at least.

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Re: [sage-devel] docker images "latest" and "develop" are old

2019-08-02 Thread E. Madison Bray
On Thu, Aug 1, 2019 at 7:09 PM Julian Rüth  wrote:
>
> Hi Markus,
>
> Sorry, I had missed this discussion initially. The credentials for docker hub 
> are protected secrets in GitLab CI. They are only provided to protected 
> branches and tags. All tags are protected so they were correctly uploaded to 
> Docker Hub. However, as I wrote on another thread, the branch were 
> unprotected (probably because somebody wanted to restart the pipelines 
> manually?) so they did not receive the secrets and (as you found) were 
> missing the credentials to upload. It seems to work again now.

Wow--do I understand you correctly that, if a branch is marked
"unprotected" , GitLab won't receive the secrets credentials?  And yet
the only way to manually restart a pipeline is to "unprotect" the
branch (which I did, as you say, in order to restart)?

I understand the idea behind not passing secrets to builds of
unprotected branches.  These two cases seem to be at odds with each
other:  How are you supposed restart a pipeline for a protected branch
if it fails for external reasons?

I think we should probably open an issue with GitLab about this.  It
seems like an impossible bind otherwise...


> On Thursday, August 1, 2019 at 12:19:03 PM UTC+2, Markus Wageringel wrote:
>>
>> There also appears to be a problem with the credentials, causing the last 
>> step, pushing the image to DockerHub, to silently fail. For example, this is 
>> the log for the last run on the develop branch [1], which last ran for 
>> 8.8.rc1.
>>
>> $ sh .ci/push-dockerhub.sh sagemath
>> + sh .ci/push-dockerhub.sh sagemath
>> + '[' -z develop ]
>> + '[' -z  -o -z  ]
>> + echo 'DOCKER_USER/SECRET_DOCKER_PASS variables have not been configured in 
>> your Continuous Integration setup. Not pushing built images to Docker Hub.'
>> DOCKER_USER/SECRET_DOCKER_PASS variables have not been configured in your 
>> Continuous Integration setup. Not pushing built images to Docker Hub.
>> Job succeeded
>>
>> I am not sure why this has not run for any more recent updates to the 
>> develop branch, though. The sagemath:develop image at [2] is up to date at 
>> least. Perhaps, the develop branch in the gitlab mirror just does not get 
>> updated regularly.
>>
>>
>> [1] https://gitlab.com/sagemath/sage/-/jobs/231098209
>> [2] https://gitlab.com/sagemath/dev/trac/container_registry
>>
>>
>> Am Freitag, 26. Juli 2019 16:28:02 UTC+2 schrieb E. Madison Bray:
>>>
>>> On Thu, Jul 25, 2019 at 10:49 PM Vincent Delecroix
>>> <20100.d...@gmail.com> wrote:
>>> >
>>> > Dear all,
>>> >
>>> > According to the page [docker] the images with tag "latest" and
>>> > "develop" are supposed to be the latest stable and development
>>> > versions. However sagemath/sagemath-dev:latest is stuck at 8.7
>>> > while 8.8 is released since July 7th (and the corresponding
>>> > docker image is available on docker hub). Similarly,
>>> > sagemath/sagemath-dev:develop is 8.8.beta5 while we are now
>>> > at 8.9.beta3 (8.9.beta2 is available on docker but not
>>> > 8.9.beta3).
>>> >
>>> > Shouldn't "latest" and "develop" be automatically updated?
>>> >
>>> >   [docker] https://hub.docker.com/u/sagemath/sagemath
>>>
>>> According to one of the build scripts [1], if the "master" branch is
>>> built, it will be tagged as "latest".  I'm not sure about "develop".
>>> Apparently, although the build for the 8.8 *tag* completed
>>> successfully [2], the one for "master" (at 8.8) failed sort of
>>> randomly [3], due to a problem we've been seeing where `make` is
>>> taking longer and longer (and longer than it should) so the build
>>> times out.  Need to investigate why it's taking so much longer.
>>>
>>> In general, it would certainly be welcome to have more volunteers
>>> monitoring and debugging issues with the CI pipeline, since getting
>>> this working smoothly would be a huge benefit.  But we haven't had
>>> enough resources or people looking at it...
>>>
>>> [1] 
>>> https://gitlab.com/sagemath/sage/blob/b5c9cf037cbce672101725f269470135b9b2c5c4/.ci/update-env.sh#L37
>>> [2] https://gitlab.com/sagemath/sage/pipelines/68209174
>>> [3] https://gitlab.com/sagemath/sage/pipelines/68212724
>
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