[sage-devel] multi-user jupyter(hub)

[Volker Braun]

If you want to play around with jupyterhub but are scared by the 
dependencies, I wrote a script to bootstrap it locally (no silly global 
installations of npm packages):

https://github.com/vbraun/run-jupyter-hub


Run JupyterHub / Jupyter


Self-contained dependencies for JupyterHub and Jupyter; All you need
is Python 2.x and a C compiler. Builds Python 3.x and Nodejs for you
using hashdist. Nothing is installed globally, you don't need root for
anything.


Quickstart
--

Check out the repository and run

make

This builds and launches the multi-user jupyterhub at
http://localhost:8000. You'll have to log in with your system username
and password because it is multi-user.


Sage Kernel
---

To link the sage kernel into your jupyter[hub] run:

make link-sage

This picks up Sage from the PATH, that is, just running "sage" on the
commandline must work. 


Jupyter without Hub
---

Just the single-user Jupyter notebook:

make jupyter

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[sage-devel] Trac - internal error

[Clemens Heuberger]

Trac detected an internal error:

OSError: [Errno 2] No such file or directory: '/tmp/tmp7BmVNV'

The action that triggered the error was:

GET: /ticket/19306

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[sage-devel] Re: Trac - internal error

[david . lucas]

Hello,

Same thing with some of tickets: #19653, #19666, #19722, #19422 and #19623

David

Le vendredi 15 janvier 2016 15:37:58 UTC+1, Clemens Heuberger a écrit :
>
> Trac detected an internal error: 
>
> OSError: [Errno 2] No such file or directory: '/tmp/tmp7BmVNV' 
>
> The action that triggered the error was: 
>
> GET: /ticket/19306 
>
>

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Re: [sage-devel] incremental migration to github?

[William Stein]

Why Python moved to github:

http://www.snarky.ca/the-history-behind-the-decision-to-move-python-to-github


On Monday, January 11, 2016, William Stein  wrote:

> On Mon, Jan 11, 2016 at 11:39 AM, Volker Braun  > wrote:
> > On Monday, January 11, 2016 at 8:20:45 PM UTC+1, William wrote:
> >>
> >> Following up on this, that we don't fully support people doing
> >> development for Sage by creating independent pip-installable packages
> >
> >
> > Where is the problem, I did that before and it works just fine.
>
> Technically there is no problem.  The problem is mostly one of
> documentation and culture.  How many sage dependent packages are on
> pypi?
>
> >
> > Of course sage isn't on pypi so you can't auto-download it as a
> dependency,
> > but then its doubtful that this would work anyways. There are way too may
> > specialized shared-library dependencies, and if there is one thing that
> > really sucks then that's (pip,npm,rvm,...)-packages that start compiling
> > gobs of third-party C/C++ code when installing. Neither is pip/wheel/...
> > made for distributing binaries of third-party code. So realistically
> there
> > should always be a "sage runtime" to compile the dependencies before
> > installing Sage-the-python-library. But you can just use pip to install
> > packages depending on Sage on top of that, no problem.
>
> Yes, the latter.  We could have a simple dependency, e.g., "sagelib"
> or something, that pip pulls in, and it simply checks that sage is
> installed, and if not, explains the situation.  Then in a few years
> when I prove you wrong regarding "you can't auto-download it as a
> dependency, but then its doubtful that this would work anyways." then
> we can replace that with sage itself.
>
> William
>
> >
> > --
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> .
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>
>
>
> --
> William (http://wstein.org)
>


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[sage-devel] Re: plateform specific implantation

[Volker Braun]

THats fine (except that you should use new-style classes)


On Friday, January 15, 2016 at 5:34:35 PM UTC+1, fhivert wrote:
>
>  Dear all, 
>
> I'd like to have a class with a method with some implementation internal 
> that 
> differ if the os is MacOS of anything else. 
>
> Context 
> === 
>
> I'm Fixing #13580 "Parallel map reduce on SearchForest" where I'm writing 
> code 
> to parallelize some specific computation. In the internal, I need some 
> synchronizing primitive such as semaphore. However, on MacOS the semaphore 
> are 
> broken (or at least are not fully POSIX compliant). In particular, on 
> standard 
> unixes, when two processes are trying to acquire a semaphore whose value 
> is 
> more than two, they always both succeeded. On MacOS, one of them may fail. 
> As 
> a consequence, I'm writing a different code form MacOS relying on a Lock 
> and a 
> shared integer. It may be slower on system where semaphore are implemented 
> in 
> a lockless way. 
>
> Question 
>  
>
> I'd like to write a *Python* (not C/C++/Cython) code which is supposed to 
> work 
> fast on any Posix compliant plateform and an alternative implementation on 
> MacOS. Surprisingly, I can't find any other instance on the whole Sage 
> library. Do you think it's ok to do that ? Is a code like 
>
> class foo: 
> if sys.platform != 'darwin': 
> def meth(self): 
> print "I'm on a good Posix compliant OS" 
> else: 
> def meth(self): 
> print "I'm using the fallback implementation" 
>
> the right way to do it ? 
>
> Thanks for any suggestions. 
>
> Cheers, 
>
> Florent 
>

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[sage-devel] Re: Trac - internal error

[Johan S . R . Nielsen]

Same thing here, #19251.

Johan

david.lu...@inria.fr writes:

> Hello,
>
> Same thing with some of tickets: #19653, #19666, #19722, #19422 and #19623
>
> David
>
> Le vendredi 15 janvier 2016 15:37:58 UTC+1, Clemens Heuberger a écrit :
>>
>> Trac detected an internal error: 
>>
>> OSError: [Errno 2] No such file or directory: '/tmp/tmp7BmVNV' 
>>
>> The action that triggered the error was: 
>>
>> GET: /ticket/19306 
>>
>>

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Re: [sage-devel] Re: Trac - internal error

[VulK]

Same here:
http://trac.sagemath.org/ticket/19667
S.


* Johan S. R. Nielsen  [2016-01-15 16:40:37]:

> Same thing here, #19251.
> 
> Johan
> 
> david.lu...@inria.fr writes:
> 
> > Hello,
> >
> > Same thing with some of tickets: #19653, #19666, #19722, #19422 and #19623
> >
> > David
> >
> > Le vendredi 15 janvier 2016 15:37:58 UTC+1, Clemens Heuberger a écrit :
> >>
> >> Trac detected an internal error: 
> >>
> >> OSError: [Errno 2] No such file or directory: '/tmp/tmp7BmVNV' 
> >>
> >> The action that triggered the error was: 
> >>
> >> GET: /ticket/19306 
> >>
> >>
> 
> -- 
> 
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[sage-devel] Re: Trac - internal error

[Volker Braun]

The trac vm disk was full again. 

Some of the apache2 logs weren't named *.log so logrotate wouldn't actually 
rotate them. I changed them to all end in .log

Also, I reduced logrotate from 52 down to 10 (weeks worth) to prevent this 
in the future.



On Friday, January 15, 2016 at 3:37:58 PM UTC+1, Clemens Heuberger wrote:
>
> Trac detected an internal error: 
>
> OSError: [Errno 2] No such file or directory: '/tmp/tmp7BmVNV' 
>
> The action that triggered the error was: 
>
> GET: /ticket/19306 
>
>

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[sage-devel] plateform specific implantation

[Florent Hivert]

  Dear all,

I'd like to have a class with a method with some implementation internal that
differ if the os is MacOS of anything else.

Context
===

I'm Fixing #13580 "Parallel map reduce on SearchForest" where I'm writing code
to parallelize some specific computation. In the internal, I need some
synchronizing primitive such as semaphore. However, on MacOS the semaphore are
broken (or at least are not fully POSIX compliant). In particular, on standard
unixes, when two processes are trying to acquire a semaphore whose value is
more than two, they always both succeeded. On MacOS, one of them may fail. As
a consequence, I'm writing a different code form MacOS relying on a Lock and a
shared integer. It may be slower on system where semaphore are implemented in
a lockless way.

Question


I'd like to write a *Python* (not C/C++/Cython) code which is supposed to work
fast on any Posix compliant plateform and an alternative implementation on
MacOS. Surprisingly, I can't find any other instance on the whole Sage
library. Do you think it's ok to do that ? Is a code like

class foo:
if sys.platform != 'darwin':
def meth(self):
print "I'm on a good Posix compliant OS"
else:
def meth(self):
print "I'm using the fallback implementation"

the right way to do it ?

Thanks for any suggestions.

Cheers,

Florent

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Re: [sage-devel] incremental migration to github?

[Vincent Delecroix]

On 15/01/16 15:29, William Stein wrote:

On Friday, January 15, 2016, Jeroen Demeyer  wrote:


On 2016-01-15 16:00, William Stein wrote:


Why Python moved to github:


http://www.snarky.ca/the-history-behind-the-decision-to-move-python-to-github
<
http://www.snarky.ca/the-history-behind-the-decision-to-move-python-to-github#toc_3






It seems to boil down to "we use GitHub because everybody uses GitHub". I
see the point, but I would certainly miss Trac




That was the argument for github versus gitlab.  It was  not the argument
for switching away from hosting their own infrastructure.


Their infrastructure was terrible. This is not the case of Sage. It is 
not clear to me what would be better with github? Does anybody has a 
serious proposal for a github workflow? If you do so, then open a trac 
ticket with it! I only see a potential increase of the number of pull 
requests. Which would actually be bad since we have a lot of pending 
tickets.


Doing as "Guido says" or "as everybody does" is by far the worse 
arguments I can imagine. And I agreed with something in the post: just 
pay attention to people who are clearly willing to do the job.


Vincent

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Re: [sage-devel] incremental migration to github?

[Jeroen Demeyer]

On 2016-01-15 16:00, William Stein wrote:

Why Python moved to github:

http://www.snarky.ca/the-history-behind-the-decision-to-move-python-to-github


It seems to boil down to "we use GitHub because everybody uses GitHub". 
I see the point, but I would certainly miss Trac :-(


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Re: [sage-devel] incremental migration to github?

[William Stein]

On Friday, January 15, 2016, Jeroen Demeyer  wrote:

> On 2016-01-15 16:00, William Stein wrote:
>
>> Why Python moved to github:
>>
>>
>> http://www.snarky.ca/the-history-behind-the-decision-to-move-python-to-github
>> <
>> http://www.snarky.ca/the-history-behind-the-decision-to-move-python-to-github#toc_3
>> >
>>
>
> It seems to boil down to "we use GitHub because everybody uses GitHub". I
> see the point, but I would certainly miss Trac



That was the argument for github versus gitlab.  It was  not the argument
for switching away from hosting their own infrastructure.



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[sage-devel] default "contours" option for implicit_plot

[Francois Bissey]

Hi,

Does anyone knows why the default option for “contours” is
set to “(0,0)” in implicit_plot (sage/plot/contour_plot.py line 571-572)?
Instead of being left alone to “None”.
The value “(0,0)” causes a lot of doctest failures when moving from 
matplotlib 1.5 to 1.5.1 (not yet a ticket for that, spotted in sage-on-gentoo):
File "/usr/lib64/python2.7/site-packages/sage/plot/graphics.py", line 2563, in 
sage.plot.graphics.Graphics.?
Failed example:
gm = g.matplotlib() # long time # without the patch, this goes BOOM -- er, 
TypeError
Exception raised:
Traceback (most recent call last):
  File "/usr/lib64/python2.7/site-packages/sage/doctest/forker.py", line 
499, in _run
self.compile_and_execute(example, compiler, test.globs)
  File "/usr/lib64/python2.7/site-packages/sage/doctest/forker.py", line 
861, in compile_and_execute
exec(compiled, globs)
  File "", line 1, in 
gm = g.matplotlib() # long time # without the patch, this goes BOOM -- 
er, TypeError
  File "/usr/lib64/python2.7/site-packages/sage/plot/graphics.py", line 
2635, in matplotlib
g._render_on_subplot(subplot)
  File "/usr/lib64/python2.7/site-packages/sage/plot/contour_plot.py", line 
195, in _render_on_subplot
linewidths=linewidths, linestyles=linestyles, 
label=options['legend_label'])
  File "/usr/lib64/python2.7/site-packages/matplotlib/__init__.py", line 
1812, in inner
return func(ax, *args, **kwargs)
  File "/usr/lib64/python2.7/site-packages/matplotlib/axes/_axes.py", line 
5644, in contour
return mcontour.QuadContourSet(self, *args, **kwargs)
  File "/usr/lib64/python2.7/site-packages/matplotlib/contour.py", line 
1424, in __init__
ContourSet.__init__(self, ax, *args, **kwargs)
  File "/usr/lib64/python2.7/site-packages/matplotlib/contour.py", line 
863, in __init__
self._process_args(*args, **kwargs)
  File "/usr/lib64/python2.7/site-packages/matplotlib/contour.py", line 
1445, in _process_args
x, y, z = self._contour_args(args, kwargs)
  File "/usr/lib64/python2.7/site-packages/matplotlib/contour.py", line 
1540, in _contour_args
self._contour_level_args(z, args)
  File "/usr/lib64/python2.7/site-packages/matplotlib/contour.py", line 
1189, in _contour_level_args
raise ValueError("Contour levels must be increasing")
ValueError: Contour levels must be increasing

Any time “implicit_plot” is called we get a failure because of this.

François

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[sage-devel] Re: plateform specific implantation

[Travis Scrimshaw]

In the interest of speed, to avoid calls to `sys,platform`, I would make 
foo a (module level) @lazy_attribute or @cached_function. IMO a full class 
is a lot more than you need.

Best,
Travis


On Friday, January 15, 2016 at 8:49:40 AM UTC-8, Volker Braun wrote:
>
> THats fine (except that you should use new-style classes)
>
>
> On Friday, January 15, 2016 at 5:34:35 PM UTC+1, fhivert wrote:
>>
>>  Dear all, 
>>
>> I'd like to have a class with a method with some implementation internal 
>> that 
>> differ if the os is MacOS of anything else. 
>>
>> Context 
>> === 
>>
>> I'm Fixing #13580 "Parallel map reduce on SearchForest" where I'm writing 
>> code 
>> to parallelize some specific computation. In the internal, I need some 
>> synchronizing primitive such as semaphore. However, on MacOS the 
>> semaphore are 
>> broken (or at least are not fully POSIX compliant). In particular, on 
>> standard 
>> unixes, when two processes are trying to acquire a semaphore whose value 
>> is 
>> more than two, they always both succeeded. On MacOS, one of them may 
>> fail. As 
>> a consequence, I'm writing a different code form MacOS relying on a Lock 
>> and a 
>> shared integer. It may be slower on system where semaphore are 
>> implemented in 
>> a lockless way. 
>>
>> Question 
>>  
>>
>> I'd like to write a *Python* (not C/C++/Cython) code which is supposed to 
>> work 
>> fast on any Posix compliant plateform and an alternative implementation 
>> on 
>> MacOS. Surprisingly, I can't find any other instance on the whole Sage 
>> library. Do you think it's ok to do that ? Is a code like 
>>
>> class foo: 
>> if sys.platform != 'darwin': 
>> def meth(self): 
>> print "I'm on a good Posix compliant OS" 
>> else: 
>> def meth(self): 
>> print "I'm using the fallback implementation" 
>>
>> the right way to do it ? 
>>
>> Thanks for any suggestions. 
>>
>> Cheers, 
>>
>> Florent 
>>
>

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[sage-devel] Re: plateform specific implantation

[Nils Bruin]

On Friday, January 15, 2016 at 3:36:24 PM UTC-8, Travis Scrimshaw wrote:
>
> In the interest of speed, to avoid calls to `sys,platform`, I would make 
> foo a (module level) @lazy_attribute or @cached_function. IMO a full class 
> is a lot more than you need.
>
> According to https://docs.python.org/2/library/sys.html#sys.platform 
sys.platform is already a string. Are you worried about the overhead of the 
two dictionary lookups to find the value of the global "sys" and then of 
"platform" in its namespace? I'd be surprised if any kind of function call 
can compete with that.

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Re: [sage-devel] incremental migration to github?

[Ralf Stephan]

On Friday, January 15, 2016 at 7:45:23 PM UTC+1, vdelecroix wrote:
>
> And I agreed with something in the post: just 
> pay attention to people who are clearly willing to do the job. 
>
Right. No one in this thread has even looked at the original questions,
apparently. I was explicitly not proposing moving completely to github.

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Re: [sage-devel] incremental migration to github?

[Ralf Stephan]

On Monday, January 11, 2016 at 8:25:32 PM UTC+1, Jeroen Demeyer wrote:
>
> What I mostly dislike about github is that "issues" and "pull requests" 
> are different things. I very much prefer the trac model where you create 
> a ticket, discuss things, then have multiple people work together on a 
> branch all on the same page. With github, it sometimes happens that you 
> have one issue and several pull requests by different people which are 
> all about the same thing. I get lost more easily in the github forest. 
>
On the other hand you can unsubscribe from each of these branches of
conversation. Also, since a new code branch is a separate pull request
the old branch stays visible until it's explicitly closed. It's up to you 
to add
# links if you want. Moreover, backlinks from any of the conversation 
branches
are shown automatically ("user referenced this pull request 5 days ago 
").

Another useful thing is that everything on trac is in one git tree. I 
> can do "git fetch" and have all tickets ready to check out without any 
> hassle. I don't know if you can easily checkout a pull request from 
> github. 
>
Of course you can.
 

> Finally a stupid thing: I don't get why github discussions don't have a 
> "reply" button.
>
That is easily enhanced by custom scripts:
https://github.com/jerone/UserScripts
Can you do that with trac? Are there people interested, at all? 

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