Re: [sage-devel] Is CMake OK for a standard spkg?

[Francois Bissey]

Cmake is a reverse approach compared to autotools. You need cmake installed 
to configure the software. The system to build (make or something else) is
somewhat OS dependent. autotool generate a script and you don’t need 
auto tool installed on the target system.

The main issue that you need to bootstrap it. i.e. cmake is used to build cmake.

Francois

> On 6/02/2015, at 19:54, Jeroen Demeyer  wrote:
> 
> On 2015-02-05 23:06, William wrote:
>> I wonder what is the latest on Sage and cmake? Ondrej  Certik was
>> just telling me about csympy, which uses cmake, and wondered whether
>> that would be a deal break for inclusion of csympy as standard in Sage.
>>Definitely 4 years ago it would have been.
> 
> Isn't cmake more like automake, i.e. run at packaging-time, not build-time?
> 
> I don't know how reliable/portable cmake is, but generally I don't like "yet 
> another build system". IMHO, nothing beats autotools and SCons is a disaster 
> (but I'm sure other people have other opinions on this). I don't know where 
> on this scale CMake lies.
> 
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Re: [sage-devel] Is CMake OK for a standard spkg?

[Jeroen Demeyer]

On 2015-02-05 23:06, William wrote:

I wonder what is the latest on Sage and cmake? Ondrej  Certik was
just telling me about csympy, which uses cmake, and wondered whether
that would be a deal break for inclusion of csympy as standard in Sage.
Definitely 4 years ago it would have been.


Isn't cmake more like automake, i.e. run at packaging-time, not build-time?

I don't know how reliable/portable cmake is, but generally I don't like 
"yet another build system". IMHO, nothing beats autotools and SCons is a 
disaster (but I'm sure other people have other opinions on this). I 
don't know where on this scale CMake lies.


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[sage-devel] Re: flint-2.4.4 compile error for Sage-6.4 on MacOSX Mavericks

[Xander Faber]

attached!

On Thursday, February 5, 2015 at 4:17:26 PM UTC-5, Bill Hart wrote:
>
> Can you post sage/local/include/gmp.h here. I can't see how it is getting 
> the wrong symbol name, under any circumstances.
>
> On Thursday, 5 February 2015 22:04:55 UTC+1, Bill Hart wrote:
>>
>> Actually, we call mpn_com_n in flint. In flint.h this becomes mpn_com.
>>
>> In gmp.h in MPIR this becomes __MPN(com_n) which must be ___gmpn_com_n on 
>> your machine.
>>
>> If headers are included in the reverse order, mpn_com_n becomes directly 
>> ___gmpn_com_n in gmp.h.
>>
>> This is indeed the name of the symbol we export. I can't see why it 
>> should be looking for the symbol ___gmpn_com, which certainly doesn't exist.
>>
>> I don't see why this is happening.
>>
>> On Thursday, 5 February 2015 21:50:59 UTC+1, Bill Hart wrote:
>>>
>>> I can't shed much light on this.
>>>
>>> We do indeed call mpn_com_n from those flint functions. In flint.h 
>>> mpn_com_n is #defined to mpn_com for compatibility with various versions of 
>>> MPIR.
>>>
>>> The latter becomes xxxmpn_com where xxx can be g, _g, __g or ___g 
>>> depending on the global symbol prefix on your platform.
>>>
>>> On lines 23 and 24 of mpn/generic/com_n.c in MPIR we have
>>>
>>> #undef mpn_com_n
>>> #define mpn_com_n __MPN(com_n)
>>>
>>> Who knows what the effect of this is.
>>>
>>> But on a core i5, this should all be irrelevant, since for all core2 and 
>>> later Intel processors, mpn/x86_64/core2/com_n.as should be compiled 
>>> and should use the standard symbol prefix for your system regardless.
>>>
>>> I'd be inclined to look at the MPIR build log and see if it detected 
>>> your processor correctly, or whether it thought it was just a generic 
>>> x86_64.
>>>
>>> Unless your OS kernel is 32 bits somehow. But even in that case, 
>>> mpn/x86/core2/com_n.asm should take care of it for you.
>>>
>>> Bill.
>>>
>>> On Tuesday, 3 February 2015 13:33:18 UTC+1, Xander Faber wrote:

 I was building Sage 6.4 on a Mac Pro 2.6 GHz Intel Core i5. 

 Tail end of the flint log file:


  

  CC ../build/fq_zech_poly_factor/../fq_zech_poly_factor.lo 

  CXX build/interfaces/NTL-interface.lo 

 Undefined symbols for architecture x86_64: 

  "___gmpn_com", referenced from: 

  _fmpz_bit_pack in fmpz.lo 

  _fmpz_bit_unpack in fmpz.lo 

 ld: symbol(s) not found for architecture x86_64 

 collect2: error: ld returned 1 exit status 

 make[4]: *** [libflint.dylib] Error 1 

 make[3]: *** [library] Error 2 

 Error: Failed to build FLINT shared library. 


  

 real 3m30.826s 

 user 2m32.253s 

 sys 0m51.078s 

  

 Error installing package flint-2.4.4 

  

 Please email sage-devel (http://groups.google.com/group/sage-devel) 

 explaining the problem and including the relevant part of the log file 

  /Users/xander/sage/logs/pkgs/flint-2.4.4.log 

 Describe your computer, operating system, etc. 

 If you want to try to fix the problem yourself, *don't* just cd to 

 /Users/xander/sage/local/var/tmp/sage/build/flint-2.4.4 and type 'make' 
 or whatever is appropriate. 

 Instead, the following commands setup all environment variables 

 correctly and load a subshell for you to debug the error: 

  (cd '/Users/xander/sage/local/var/tmp/sage/build/flint-2.4.4' && '/
 Users/xander/sage/sage' --sh) 

 When you are done debugging, you can type "exit" to leave the subshell. 

 

 Any thoughts on what's going on?



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/* Definitions for GNU multiple precision functions.   -*- mode: c -*-

Copyright 1991, 1993, 1994, 1995, 1996, 1997, 1999, 2000, 2001, 2002, 2003,
2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, Inc.

Copyright 2008 William Hart, Gonzalo Tornaria

This file is part of the MPIR Library.

The MPIR Library is free software; you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation; either version 3 of the License, or (at your
option) any later version.

The MPIR Library is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of MERCH

Re: [sage-devel] Is CMake OK for a standard spkg?

[William]

On Monday, March 1, 2010 at 4:39:59 AM UTC-8, William wrote:
>
> On Sun, Feb 28, 2010 at 11:40 PM, Peter Jeremy  
> wrote:
>
> >>For what is worth, we use cmake in FEMhub (femhub.org) as a standard
> >>package and we never had any problems with that.
> >
> > If CMake was widely used (and hence can be listed as a prerequisite for
> > building Sage - like gmake, bash etc) then it would have no overhead
> > for Sage.
>
> CMake is definitely not as widely used as gmake and bash, so I'm
> against making it a prerequisite for Sage. In the history of the Sage
> project, the only prerequisite that was ever added was gfortran, and
> that is really part of GCC (Gnu Compiler Collection), so fairly
> standard.
>
> Anyway, as mentioned before, according to this thread:
>
>
> http://groups.google.com/group/sage-devel/browse_thread/thread/e91a204a2902afd/ccbdaa4792872282?lnk=gst&q=Heads+up#ccbdaa4792872282
>
> singular is migrating to CMake.  If that really happens, Sage will
> have to include CMake, whether we want to or not.
>

Hi,

I wonder what is the latest on Sage and cmake? Ondrej  Certik was just 
telling me about csympy, which uses cmake, and wondered whether that would 
be a deal break for inclusion of csympy as standard in Sage.Definitely 
4 years ago it would have been.

William

 

>  -- William
>
>

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Re: [sage-devel] coercion issue

[Jonas Jermann]

Hi

Set x=GF(5)['x'].gen()
I dunno if this helps but here is an explanation why one gets a
different behavior for x/7 than cm.bin_op(x,7,operator.div):

If you do "x/7" then I think it calls __div__ from polynomial_element 
(Polynomial class):


try:
  if not isinstance(right, Element) or right.parent() != self.parent():
R = self.parent().base_ring()
x = R._coerce_(right)
return self * ~x
except (TypeError, ValueError):
  pass
return RingElement.__div__(self, right)

Here right=ZZ(7), self=x, so right.parent() != self.parent()
so it does x = GF(5)._coerce_(7)
which is why you end up without the Fraction Field...

If on the other hand you do cm.bin_op(x,7,operator.div) or x._div_(7) 
you get a Fraction Field element at the moment.



Best
Jonas

On 05.02.2015 22:08, Vincent Delecroix wrote:

2015-02-05 21:38 UTC+01:00, John Cremona :

If you ask for operator.mul instead of operator.div then you get the
poly ring.  Is that it, perhaps?


Nope. I want to get rid of many hacks in rings/polynomial. In order to
do that I need the div operation to be correctly handled by the
coercion (or perhaps I missed something about the aim of coercion?).
Namely, if p is an element of GF(5)['x,y'] then (p/Integer(2)) should
be an element of GF(5)['x,y']. You can argue that this is what you get
in Sage

sage: R = GF(5)['x','y']
sage: (R.an_element() / 2).parent()
Multivariate Polynomial Ring in x, y over Finite Field of size 5

But the reason why is a bit of a hack that actually introduce many
bugs in other places:

sage: R = GF(5)['x,y']
sage: (R.one() / R.one()).parent()
Multivariate Polynomial Ring in x, y over Finite Field of size 5

the above should be an element of the fraction field! And you can
build more involved examples.

Vincent



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[sage-devel] Re: flint-2.4.4 compile error for Sage-6.4 on MacOSX Mavericks

[Bill Hart]

Can you post sage/local/include/gmp.h here. I can't see how it is getting 
the wrong symbol name, under any circumstances.

On Thursday, 5 February 2015 22:04:55 UTC+1, Bill Hart wrote:
>
> Actually, we call mpn_com_n in flint. In flint.h this becomes mpn_com.
>
> In gmp.h in MPIR this becomes __MPN(com_n) which must be ___gmpn_com_n on 
> your machine.
>
> If headers are included in the reverse order, mpn_com_n becomes directly 
> ___gmpn_com_n in gmp.h.
>
> This is indeed the name of the symbol we export. I can't see why it should 
> be looking for the symbol ___gmpn_com, which certainly doesn't exist.
>
> I don't see why this is happening.
>
> On Thursday, 5 February 2015 21:50:59 UTC+1, Bill Hart wrote:
>>
>> I can't shed much light on this.
>>
>> We do indeed call mpn_com_n from those flint functions. In flint.h 
>> mpn_com_n is #defined to mpn_com for compatibility with various versions of 
>> MPIR.
>>
>> The latter becomes xxxmpn_com where xxx can be g, _g, __g or ___g 
>> depending on the global symbol prefix on your platform.
>>
>> On lines 23 and 24 of mpn/generic/com_n.c in MPIR we have
>>
>> #undef mpn_com_n
>> #define mpn_com_n __MPN(com_n)
>>
>> Who knows what the effect of this is.
>>
>> But on a core i5, this should all be irrelevant, since for all core2 and 
>> later Intel processors, mpn/x86_64/core2/com_n.as should be compiled and 
>> should use the standard symbol prefix for your system regardless.
>>
>> I'd be inclined to look at the MPIR build log and see if it detected your 
>> processor correctly, or whether it thought it was just a generic x86_64.
>>
>> Unless your OS kernel is 32 bits somehow. But even in that case, 
>> mpn/x86/core2/com_n.asm should take care of it for you.
>>
>> Bill.
>>
>> On Tuesday, 3 February 2015 13:33:18 UTC+1, Xander Faber wrote:
>>>
>>> I was building Sage 6.4 on a Mac Pro 2.6 GHz Intel Core i5. 
>>>
>>> Tail end of the flint log file:
>>>
>>>
>>>  
>>>
>>>  CC ../build/fq_zech_poly_factor/../fq_zech_poly_factor.lo 
>>>
>>>  CXX build/interfaces/NTL-interface.lo 
>>>
>>> Undefined symbols for architecture x86_64: 
>>>
>>>  "___gmpn_com", referenced from: 
>>>
>>>  _fmpz_bit_pack in fmpz.lo 
>>>
>>>  _fmpz_bit_unpack in fmpz.lo 
>>>
>>> ld: symbol(s) not found for architecture x86_64 
>>>
>>> collect2: error: ld returned 1 exit status 
>>>
>>> make[4]: *** [libflint.dylib] Error 1 
>>>
>>> make[3]: *** [library] Error 2 
>>>
>>> Error: Failed to build FLINT shared library. 
>>>
>>>
>>>  
>>>
>>> real 3m30.826s 
>>>
>>> user 2m32.253s 
>>>
>>> sys 0m51.078s 
>>>
>>>  
>>>
>>> Error installing package flint-2.4.4 
>>>
>>>  
>>>
>>> Please email sage-devel (http://groups.google.com/group/sage-devel) 
>>>
>>> explaining the problem and including the relevant part of the log file 
>>>
>>>  /Users/xander/sage/logs/pkgs/flint-2.4.4.log 
>>>
>>> Describe your computer, operating system, etc. 
>>>
>>> If you want to try to fix the problem yourself, *don't* just cd to 
>>>
>>> /Users/xander/sage/local/var/tmp/sage/build/flint-2.4.4 and type 'make' 
>>> or whatever is appropriate. 
>>>
>>> Instead, the following commands setup all environment variables 
>>>
>>> correctly and load a subshell for you to debug the error: 
>>>
>>>  (cd '/Users/xander/sage/local/var/tmp/sage/build/flint-2.4.4' && '/
>>> Users/xander/sage/sage' --sh) 
>>>
>>> When you are done debugging, you can type "exit" to leave the subshell. 
>>>
>>> 
>>>
>>> Any thoughts on what's going on?
>>>
>>>

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Re: [sage-devel] Sagemath : wild experiments

[Julien Puydt]

Hi!

Le 05/02/2015 18:56, Julien Puydt a écrit :

Hi,

Le 05/02/2015 17:11, Vincent Delecroix a écrit :

Hello,

After all packages installed the compilation of the sage library
failed. There is a problem with pari headers. I do have the pari
headers in /usr/include/x86_64-linux-gnu/pari/ but there is no
pari/anal.h there!


I don't have that file anywhere on my system, I don't have build flags
which look like they're coming from dpkg-buildflags and I don't have
that problem. This is embarassing !

I'm also puzzled because I get my sage-exp/ directory using "cp -R
sage.git sage-exp", and :

jpuydt@cauchy:~$ diff -u sage.git/src/sage/libs/pari/decl.pxi
sage-exp/src/sage/libs/pari/decl.pxi
--- sage.git/src/sage/libs/pari/decl.pxi2015-02-05
18:41:48.016395568 +0100
+++ sage-exp/src/sage/libs/pari/decl.pxi2015-02-05
18:40:49.624035981 +0100
@@ -164,8 +164,7 @@
  extern int INIT_JMPm, INIT_SIGm, INIT_DFTm
  extern int new_galois_format, precdl
  # The "except 0" here is to ensure compatibility with
-# _pari_err_handle() in handle_error.pyx
-extern int (*cb_pari_err_handle)(GEN) except 0
+# _pari_handle_exception() in handle_error.pyx
  extern int (*cb_pari_handle_exception)(long) except 0
  extern void (*cb_pari_err_recover)(long)

@@ -3757,6 +3756,3 @@
  unsigned long flags

  extern gp_data* GP_DATA
-
-cdef extern from 'pari/anal.h':
-char* closure_func_err()


on a file which isn't modified by my patch!

Oh, and I still need sqlalchemy here (using the 6.5.rc0 tag). And graphs
is still the 20120404 version when I see 20130920 on the spkg page.

I think I'll need a short evening and a long night of sleep...



Good news ! I did some cleaning, and I now have all your symptoms !

Well, perhaps that's not that good a piece of news, but at least now I 
have something to play with.


Snark on #debian-science

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Re: [sage-devel] coercion issue

[Vincent Delecroix]

2015-02-05 21:38 UTC+01:00, John Cremona :
> If you ask for operator.mul instead of operator.div then you get the
> poly ring.  Is that it, perhaps?

Nope. I want to get rid of many hacks in rings/polynomial. In order to
do that I need the div operation to be correctly handled by the
coercion (or perhaps I missed something about the aim of coercion?).
Namely, if p is an element of GF(5)['x,y'] then (p/Integer(2)) should
be an element of GF(5)['x,y']. You can argue that this is what you get
in Sage

sage: R = GF(5)['x','y']
sage: (R.an_element() / 2).parent()
Multivariate Polynomial Ring in x, y over Finite Field of size 5

But the reason why is a bit of a hack that actually introduce many
bugs in other places:

sage: R = GF(5)['x,y']
sage: (R.one() / R.one()).parent()
Multivariate Polynomial Ring in x, y over Finite Field of size 5

the above should be an element of the fraction field! And you can
build more involved examples.

Vincent

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[sage-devel] Re: flint-2.4.4 compile error for Sage-6.4 on MacOSX Mavericks

[Bill Hart]

Actually, we call mpn_com_n in flint. In flint.h this becomes mpn_com.

In gmp.h in MPIR this becomes __MPN(com_n) which must be ___gmpn_com_n on 
your machine.

If headers are included in the reverse order, mpn_com_n becomes directly 
___gmpn_com_n in gmp.h.

This is indeed the name of the symbol we export. I can't see why it should 
be looking for the symbol ___gmpn_com, which certainly doesn't exist.

I don't see why this is happening.

On Thursday, 5 February 2015 21:50:59 UTC+1, Bill Hart wrote:
>
> I can't shed much light on this.
>
> We do indeed call mpn_com_n from those flint functions. In flint.h 
> mpn_com_n is #defined to mpn_com for compatibility with various versions of 
> MPIR.
>
> The latter becomes xxxmpn_com where xxx can be g, _g, __g or ___g 
> depending on the global symbol prefix on your platform.
>
> On lines 23 and 24 of mpn/generic/com_n.c in MPIR we have
>
> #undef mpn_com_n
> #define mpn_com_n __MPN(com_n)
>
> Who knows what the effect of this is.
>
> But on a core i5, this should all be irrelevant, since for all core2 and 
> later Intel processors, mpn/x86_64/core2/com_n.as should be compiled and 
> should use the standard symbol prefix for your system regardless.
>
> I'd be inclined to look at the MPIR build log and see if it detected your 
> processor correctly, or whether it thought it was just a generic x86_64.
>
> Unless your OS kernel is 32 bits somehow. But even in that case, 
> mpn/x86/core2/com_n.asm should take care of it for you.
>
> Bill.
>
> On Tuesday, 3 February 2015 13:33:18 UTC+1, Xander Faber wrote:
>>
>> I was building Sage 6.4 on a Mac Pro 2.6 GHz Intel Core i5. 
>>
>> Tail end of the flint log file:
>>
>>
>>  
>>
>>  CC ../build/fq_zech_poly_factor/../fq_zech_poly_factor.lo 
>>
>>  CXX build/interfaces/NTL-interface.lo 
>>
>> Undefined symbols for architecture x86_64: 
>>
>>  "___gmpn_com", referenced from: 
>>
>>  _fmpz_bit_pack in fmpz.lo 
>>
>>  _fmpz_bit_unpack in fmpz.lo 
>>
>> ld: symbol(s) not found for architecture x86_64 
>>
>> collect2: error: ld returned 1 exit status 
>>
>> make[4]: *** [libflint.dylib] Error 1 
>>
>> make[3]: *** [library] Error 2 
>>
>> Error: Failed to build FLINT shared library. 
>>
>>
>>  
>>
>> real 3m30.826s 
>>
>> user 2m32.253s 
>>
>> sys 0m51.078s 
>>
>>  
>>
>> Error installing package flint-2.4.4 
>>
>>  
>>
>> Please email sage-devel (http://groups.google.com/group/sage-devel) 
>>
>> explaining the problem and including the relevant part of the log file 
>>
>>  /Users/xander/sage/logs/pkgs/flint-2.4.4.log 
>>
>> Describe your computer, operating system, etc. 
>>
>> If you want to try to fix the problem yourself, *don't* just cd to 
>>
>> /Users/xander/sage/local/var/tmp/sage/build/flint-2.4.4 and type 'make' 
>> or whatever is appropriate. 
>>
>> Instead, the following commands setup all environment variables 
>>
>> correctly and load a subshell for you to debug the error: 
>>
>>  (cd '/Users/xander/sage/local/var/tmp/sage/build/flint-2.4.4' && '/Users
>> /xander/sage/sage' --sh) 
>>
>> When you are done debugging, you can type "exit" to leave the subshell. 
>>
>> 
>>
>> Any thoughts on what's going on?
>>
>>

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[sage-devel] Re: flint-2.4.4 compile error for Sage-6.4 on MacOSX Mavericks

[Bill Hart]

I can't shed much light on this.

We do indeed call mpn_com_n from those flint functions. In flint.h 
mpn_com_n is #defined to mpn_com for compatibility with various versions of 
MPIR.

The latter becomes xxxmpn_com where xxx can be g, _g, __g or ___g depending 
on the global symbol prefix on your platform.

On lines 23 and 24 of mpn/generic/com_n.c in MPIR we have

#undef mpn_com_n
#define mpn_com_n __MPN(com_n)

Who knows what the effect of this is.

But on a core i5, this should all be irrelevant, since for all core2 and 
later Intel processors, mpn/x86_64/core2/com_n.as should be compiled and 
should use the standard symbol prefix for your system regardless.

I'd be inclined to look at the MPIR build log and see if it detected your 
processor correctly, or whether it thought it was just a generic x86_64.

Unless your OS kernel is 32 bits somehow. But even in that case, 
mpn/x86/core2/com_n.asm should take care of it for you.

Bill.

On Tuesday, 3 February 2015 13:33:18 UTC+1, Xander Faber wrote:
>
> I was building Sage 6.4 on a Mac Pro 2.6 GHz Intel Core i5. 
>
> Tail end of the flint log file:
>
>
>  
>
>  CC ../build/fq_zech_poly_factor/../fq_zech_poly_factor.lo 
>
>  CXX build/interfaces/NTL-interface.lo 
>
> Undefined symbols for architecture x86_64: 
>
>  "___gmpn_com", referenced from: 
>
>  _fmpz_bit_pack in fmpz.lo 
>
>  _fmpz_bit_unpack in fmpz.lo 
>
> ld: symbol(s) not found for architecture x86_64 
>
> collect2: error: ld returned 1 exit status 
>
> make[4]: *** [libflint.dylib] Error 1 
>
> make[3]: *** [library] Error 2 
>
> Error: Failed to build FLINT shared library. 
>
>
>  
>
> real 3m30.826s 
>
> user 2m32.253s 
>
> sys 0m51.078s 
>
>  
>
> Error installing package flint-2.4.4 
>
>  
>
> Please email sage-devel (http://groups.google.com/group/sage-devel) 
>
> explaining the problem and including the relevant part of the log file 
>
>  /Users/xander/sage/logs/pkgs/flint-2.4.4.log 
>
> Describe your computer, operating system, etc. 
>
> If you want to try to fix the problem yourself, *don't* just cd to 
>
> /Users/xander/sage/local/var/tmp/sage/build/flint-2.4.4 and type 'make' 
> or whatever is appropriate. 
>
> Instead, the following commands setup all environment variables 
>
> correctly and load a subshell for you to debug the error: 
>
>  (cd '/Users/xander/sage/local/var/tmp/sage/build/flint-2.4.4' && '/Users/
> xander/sage/sage' --sh) 
>
> When you are done debugging, you can type "exit" to leave the subshell. 
>
> 
>
> Any thoughts on what's going on?
>
>

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Re: [sage-devel] coercion issue

[John Cremona]

If you ask for operator.mul instead of operator.div then you get the
poly ring.  Is that it, perhaps?

John

On 5 February 2015 at 18:48, Vincent Delecroix
<20100.delecr...@gmail.com> wrote:
> sage: cm = sage.structure.element.get_coercion_model()
> sage: cm.explain(GF(5)['x'], ZZ, operator.div)
> Coercion on right operand via
> Composite map:
>   From: Integer Ring
>   To:   Univariate Polynomial Ring in x over Finite Field of size 5
>   Defn:   Natural morphism:
>   From: Integer Ring
>   To:   Finite Field of size 5
> then
>   Polynomial base injection morphism:
>   From: Finite Field of size 5
>   To:   Univariate Polynomial Ring in x over Finite Field of size 
> 5
> Arithmetic performed after coercions.
> Result lives in Fraction Field of Univariate Polynomial Ring in x over
> Finite Field of size 5
> Fraction Field of Univariate Polynomial Ring in x over Finite Field of size 5
>
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[sage-devel] Re: coercion issue

[Vincent Delecroix]

Sorry, I press enter to fast. There is a coercion problem. The result
of division of GF(5)['x'] by ZZ should live in GF(5)['x']. But right
now the coercion model thinks that it should go to the fraction
field... (see the example in my first mail).

Is there a ticket related to that issue? Does anybody knows how to solve this?

It completely prevent me to continue #17692.

Vincent

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[sage-devel] coercion issue

[Vincent Delecroix]

sage: cm = sage.structure.element.get_coercion_model()
sage: cm.explain(GF(5)['x'], ZZ, operator.div)
Coercion on right operand via
Composite map:
  From: Integer Ring
  To:   Univariate Polynomial Ring in x over Finite Field of size 5
  Defn:   Natural morphism:
  From: Integer Ring
  To:   Finite Field of size 5
then
  Polynomial base injection morphism:
  From: Finite Field of size 5
  To:   Univariate Polynomial Ring in x over Finite Field of size 5
Arithmetic performed after coercions.
Result lives in Fraction Field of Univariate Polynomial Ring in x over
Finite Field of size 5
Fraction Field of Univariate Polynomial Ring in x over Finite Field of size 5

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Re: [sage-devel] Sagemath : wild experiments

[Julien Puydt]

Hi,

Le 05/02/2015 17:11, Vincent Delecroix a écrit :

Hello,

After all packages installed the compilation of the sage library
failed. There is a problem with pari headers. I do have the pari
headers in /usr/include/x86_64-linux-gnu/pari/ but there is no
pari/anal.h there!


I don't have that file anywhere on my system, I don't have build flags 
which look like they're coming from dpkg-buildflags and I don't have 
that problem. This is embarassing !


I'm also puzzled because I get my sage-exp/ directory using "cp -R 
sage.git sage-exp", and :


jpuydt@cauchy:~$ diff -u sage.git/src/sage/libs/pari/decl.pxi 
sage-exp/src/sage/libs/pari/decl.pxi
--- sage.git/src/sage/libs/pari/decl.pxi2015-02-05 
18:41:48.016395568 +0100
+++ sage-exp/src/sage/libs/pari/decl.pxi2015-02-05 
18:40:49.624035981 +0100

@@ -164,8 +164,7 @@
 extern int INIT_JMPm, INIT_SIGm, INIT_DFTm
 extern int new_galois_format, precdl
 # The "except 0" here is to ensure compatibility with
-# _pari_err_handle() in handle_error.pyx
-extern int (*cb_pari_err_handle)(GEN) except 0
+# _pari_handle_exception() in handle_error.pyx
 extern int (*cb_pari_handle_exception)(long) except 0
 extern void (*cb_pari_err_recover)(long)

@@ -3757,6 +3756,3 @@
 unsigned long flags

 extern gp_data* GP_DATA
-
-cdef extern from 'pari/anal.h':
-char* closure_func_err()


on a file which isn't modified by my patch!

Oh, and I still need sqlalchemy here (using the 6.5.rc0 tag). And graphs 
is still the 20120404 version when I see 20130920 on the spkg page.


I think I'll need a short evening and a long night of sleep...

Snark on #debian-science

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Re: [sage-devel] sage -t src/sage/repl/notebook_ipython.py # 9 doctests failed

[kcrisman]

>
>
> > sage -t src/sage/repl/notebook_ipython.py  # 9 doctests failed 
> And what exactly are the failed tests...? 
>

See also http://ask.sagemath.org/question/25741/openssl-installed/ though 
it doesn't say there either. 

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Re: [sage-devel] Re: Can a Parent have different Element classes?

[Eric Gourgoulhon]

Le jeudi 5 février 2015 17:01:20 UTC+1, Jeroen Demeyer a écrit :
>
> On 2015-02-05 16:13, Eric Gourgoulhon wrote: 
> > What about isomorphisms ? Shall one use a cached is_isomorphism and 
> > implement an __invert__() method for all elements, raising an error if 
> > is_isomorphism is False ? 
> If it's not an isomorphism, I expect the computation of the inverse to 
> fail somewhere.

Indeed ! 

> Just handle that exception... 
>
> OK, thanks. 

Eric. 

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[sage-devel] Re: Is it possible to support drawing ROI on image with interact widget

[kcrisman]

 

> Hi everyone,
> Sage notebook is cool, and I am creating some web app with sage cell 
> server. The problem is, I would like to let my user draw a Region Of 
> Interest (such as point, rectangle, oval etc.) on an image, but currently I 
> can't find such a widget allow me to do that. 
>
> Any suggestion on how to make it happen? 
>
>
I don't think this is currently possible in sagenb; we would need to use 
something with a lot more javascript or using canvas more intelligently.  I 
think William may be trying to implement something like this with graphics 
in SMC, and some proofs of concept have worked with flot (see 
e.g. http://www.flotcharts.org/flot/examples/selection/index.html) and 
other js libraries.

- kcrisman

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Re: [sage-devel] Sagemath : wild experiments

[Jeroen Demeyer]

On 2015-02-05 17:11, Vincent Delecroix wrote:

  #include "pari/anal.h"


That file has to be copied manually, see

build/pkgs/pari/spkg-install

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Re: [sage-devel] Sagemath : wild experiments

[Vincent Delecroix]

Hello,

After all packages installed the compilation of the sage library
failed. There is a problem with pari headers. I do have the pari
headers in /usr/include/x86_64-linux-gnu/pari/ but there is no
pari/anal.h there!

Vincent

PS: the end of the log

x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions
-Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong
-Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g
-fstack-protector-strong -Wformat -Werror=format-security
build/temp.linux-x86_64-2.7/build/cythonized/sage/ext/c_lib.o
-L/home/sage/sage/local/lib -lcsage -o
build/lib.linux-x86_64-2.7/sage/ext/c_lib.so
gcc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes
-fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong
-Wformat -Werror=format-security -fPIC -I/home/sage/sage/local/include
-I/home/sage/sage/local/include/csage -I/home/sage/sage/src
-I/home/sage/sage/src/sage/ext -I/usr/include/python2.7 -c
build/cythonized/sage/ext/fast_callable.c -o
build/temp.linux-x86_64-2.7/build/cythonized/sage/ext/fast_callable.o
-fno-strict-aliasing
build/cythonized/sage/ext/fast_callable.c:254:23: fatal error:
pari/anal.h: No such file or directory
 #include "pari/anal.h"
   ^
compilation terminated.

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Re: [sage-devel] Re: Can a Parent have different Element classes?

[Jeroen Demeyer]

On 2015-02-05 16:13, Eric Gourgoulhon wrote:

What about isomorphisms ? Shall one use a cached is_isomorphism and
implement an __invert__() method for all elements, raising an error if
is_isomorphism is False ?
If it's not an isomorphism, I expect the computation of the inverse to 
fail somewhere. Just handle that exception...


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Re: [sage-devel] Sagemath : wild experiments

[Vincent Delecroix]

2015-02-05 16:52 UTC+01:00, Julien Puydt :
> Hi,
>
> Le 05/02/2015 16:18, Vincent Delecroix a écrit :
>> Hello,
>>
>> 2015-02-05 15:37 UTC+01:00, Julien Puydt :
>>> Hmmm... if it hasn't propagated to testing yet, then use
>>> debian-science's git repository.
>>
>> $ git clone
>> https://anonscm.debian.org/git/debian-science/packages/flintqs.git
>> Cloning into 'flintqs'...
>> fatal: repository
>> 'https://anonscm.debian.org/git/debian-science/packages/flintqs.git/'
>> not found
>
> Sigh... the repository should be there... and in fact, I tried to get a
> few other packages, and failed. Perhaps the server has issues ?

I was able to pull from polybori few seconds before.

> In the mean time I'm pretty sure you can safely install directly the
> binary unstable package. Indeed it would already be in testing, if I
> hadn't blocked it!

Will do that.

Thanks again.
Vincent

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Re: [sage-devel] Sagemath : wild experiments

[Julien Puydt]

Hi,

Le 05/02/2015 16:18, Vincent Delecroix a écrit :

Hello,

2015-02-05 15:37 UTC+01:00, Julien Puydt :

Hmmm... if it hasn't propagated to testing yet, then use
debian-science's git repository.


$ git clone https://anonscm.debian.org/git/debian-science/packages/flintqs.git
Cloning into 'flintqs'...
fatal: repository
'https://anonscm.debian.org/git/debian-science/packages/flintqs.git/'
not found


Sigh... the repository should be there... and in fact, I tried to get a 
few other packages, and failed. Perhaps the server has issues ?


In the mean time I'm pretty sure you can safely install directly the 
binary unstable package. Indeed it would already be in testing, if I 
hadn't blocked it!


Snark on #debian-science

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[sage-devel] Is it possible to support drawing ROI on image with interact widget

[Will Ouyang]

Hi everyone,
Sage notebook is cool, and I am creating some web app with sage cell 
server. The problem is, I would like to let my user draw a Region Of 
Interest (such as point, rectangle, oval etc.) on an image, but currently I 
can't find such a widget allow me to do that. 

Any suggestion on how to make it happen? 

Best,
Wei

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Re: [sage-devel] Sagemath : wild experiments

[Vincent Delecroix]

Hello,

2015-02-05 15:37 UTC+01:00, Julien Puydt :
> Hi,
>
> Le 05/02/2015 10:56, Vincent Delecroix a écrit :
>> Hi,
>>
>> Still got two packages missing. See below.
>>
>> 2015-02-05 8:08 UTC+01:00, Julien Puydt :
 flintqs will not come from debian!
>>>
>>> The debian package is flintqs.
>>
>> I did not find this one (in testing).
>
> Hmmm... if it hasn't propagated to testing yet, then use
> debian-science's git repository.

$ git clone https://anonscm.debian.org/git/debian-science/packages/flintqs.git
Cloning into 'flintqs'...
fatal: repository
'https://anonscm.debian.org/git/debian-science/packages/flintqs.git/'
not found

 polybori will not come from debian!
>>>
>>> Should come from debian-science's git and will give you
>>> libpolybori-0.8-3, libpolybori-dev, libpolybori-groebner-0.8-3,
>>> libpolybori-groebner-dev and python-polybori.
>>
>> After successful cloning, the package builder failed.
>>
>> polybori$ git-buildpackage
>> gbp:warning: Pristine-tar branch "pristine-tar" not found
>> pristine-tar: successfully generated
>> /home/sage/polybori_0.8.3.orig.tar.gz
>>   dpkg-buildpackage -rfakeroot -D -us -uc -i -I
>> dpkg-buildpackage: source package polybori
>> dpkg-buildpackage: source version 0.8.3-4
>> dpkg-buildpackage: source distribution UNRELEASED
>> dpkg-buildpackage: source changed by Julien Puydt
>> 
>>   dpkg-source -i -I --before-build polybori
>> dpkg-buildpackage: host architecture amd64
>> dpkg-source: info: applying
>> 0001-Added-libraries-symlinks-to-testsuite-dependencies-t.patch
>> dpkg-source: info: applying
>> 0002-Generate-clean-.pc-files-from-upstream.patch
>> dpkg-source: info: applying
>> 0003-Protect-CErrorInfo-from-invalid-array-access.patch
>> dpkg-checkbuilddeps: Unmet build dependencies: python-all-dev tex4ht
>> dpkg-buildpackage: warning: build dependencies/conflicts unsatisfied;
>> aborting
>> dpkg-buildpackage: warning: (Use -d flag to override.)
>> debuild: fatal error at line 1376:
>> dpkg-buildpackage -rfakeroot -D -us -uc -i -I failed
>> gbp:error: 'debuild -i -I' failed: it exited with 29
>
> Well, the package builder tries to build the packages with what you have
> on the box, so if you don't have python-all-dev and tex4ht, it won't be
> able to build anything!
>
> Either install the necessary dependencies or use something like
> "pbuilder", which will do the build in a chroot, taking care of all
> build-deps.

Right, right. I did not saw that in the log. It works now for polybori. Thanks.

Vincent

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[sage-devel] Re: Can a Parent have different Element classes?

[Eric Gourgoulhon]

Hi,

Le jeudi 5 février 2015 15:15:54 UTC+1, Volker Braun a écrit :
>
> How often do you think people want to compute the image under the identity 
> map? If that is a common code path you could just have an cached 
> is_identity() and check it before doing the matrix multiplication. 
>
> Writing a specialization for a particular value precisely saves you that 
> one check of a boolean flag at the end of the day. Unless you have 
> benchmarked the need for this minor optimization it you are almost 
> certainly wasting your time.
>
>  
Thanks for your answer. I am convinced by your argument. Indeed, I prefer 
having a clean parent/element implementation than having specific optimized 
subclasses. Actually, I am already using the cached is_identity trick to 
avoid a matrix multiplication in the method _call_() of free module 
morphisms in #15916. 

What about isomorphisms ? Shall one use a cached is_isomorphism and 
implement an __invert__() method for all elements, raising an error if 
is_isomorphism is False ?

Eric.

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Re: [sage-devel] Re: .one() vs .one_element()

[Nicolas M. Thiery]

On Fri, Jan 30, 2015 at 12:15:25PM +0100, Nathann Cohen wrote:
> > +1 to using .zero() and .one() and to deprecating .zero_element() and
> > .one_element().

+1 as well. Thanks!
Nicolas
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Re: [sage-devel] Sagemath : wild experiments

[Julien Puydt]

Hi,

Le 05/02/2015 10:56, Vincent Delecroix a écrit :

Hi,

Still got two packages missing. See below.

2015-02-05 8:08 UTC+01:00, Julien Puydt :

flintqs will not come from debian!


The debian package is flintqs.


I did not find this one (in testing).


Hmmm... if it hasn't propagated to testing yet, then use 
debian-science's git repository.



polybori will not come from debian!


Should come from debian-science's git and will give you
libpolybori-0.8-3, libpolybori-dev, libpolybori-groebner-0.8-3,
libpolybori-groebner-dev and python-polybori.


After successful cloning, the package builder failed.

polybori$ git-buildpackage
gbp:warning: Pristine-tar branch "pristine-tar" not found
pristine-tar: successfully generated /home/sage/polybori_0.8.3.orig.tar.gz
  dpkg-buildpackage -rfakeroot -D -us -uc -i -I
dpkg-buildpackage: source package polybori
dpkg-buildpackage: source version 0.8.3-4
dpkg-buildpackage: source distribution UNRELEASED
dpkg-buildpackage: source changed by Julien Puydt 
  dpkg-source -i -I --before-build polybori
dpkg-buildpackage: host architecture amd64
dpkg-source: info: applying
0001-Added-libraries-symlinks-to-testsuite-dependencies-t.patch
dpkg-source: info: applying 0002-Generate-clean-.pc-files-from-upstream.patch
dpkg-source: info: applying
0003-Protect-CErrorInfo-from-invalid-array-access.patch
dpkg-checkbuilddeps: Unmet build dependencies: python-all-dev tex4ht
dpkg-buildpackage: warning: build dependencies/conflicts unsatisfied; aborting
dpkg-buildpackage: warning: (Use -d flag to override.)
debuild: fatal error at line 1376:
dpkg-buildpackage -rfakeroot -D -us -uc -i -I failed
gbp:error: 'debuild -i -I' failed: it exited with 29


Well, the package builder tries to build the packages with what you have 
on the box, so if you don't have python-all-dev and tex4ht, it won't be 
able to build anything!


Either install the necessary dependencies or use something like 
"pbuilder", which will do the build in a chroot, taking care of all 
build-deps.


Snark

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[sage-devel] Re: Can a Parent have different Element classes?

[Volker Braun]

How often do you think people want to compute the image under the identity 
map? If that is a common code path you could just have an cached 
is_identity() and check it before doing the matrix multiplication. 

Writing a specialization for a particular value precisely saves you that 
one check of a boolean flag at the end of the day. Unless you have 
benchmarked the need for this minor optimization it you are almost 
certainly wasting your time.



On Wednesday, February 4, 2015 at 11:47:07 AM UTC-5, Eric Gourgoulhon wrote:
>
> As for the "identity map" example, if that were a subclass then you would 
>> also have to check that a map is the identity whenever you compose maps and 
>> construct the subclass. From a performance point of view that is most 
>> likely sub-optimal.
>>
>
> Well, probably this depends on the use case, i.e. if you compose maps more 
> often than you use them to get images of elements of their domains. If the 
> latter operation is performed, let's say, via some matrix multiplication, 
> it is clear that having def __call__(x): return x is more efficient than 
> multiplying by the identity matrix. 
>
>

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Re: [sage-devel] Re: how to explicitly recompile the python part of sage (no pkgs)

[Jeroen Demeyer]

On 2015-02-05 14:13, Jakob Kroeker wrote:

rebuild a package worked as described (sage -f singular),
thanks!

However, I have problems with 'sage -b':

sometimes it does not rebuild all python and cython stuff
Use ./sage -ba to explicitly rebuild everything (although it's a bug if 
./sage -b doesn't work, Cython should have proper dependency checking)


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[sage-devel] Re: how to explicitly recompile the python part of sage (no pkgs)

[Jakob Kroeker]

rebuild a package worked as described (sage -f singular),
thanks!

However, I have problems with 'sage -b':

sometimes it does not rebuild all python and cython stuff,
even not after a 'ccache -C'  and  'make clean'.
Do I miss something? 


Jakob


Am Montag, 2. Februar 2015 16:15:36 UTC+1 schrieb Volker Braun:
>
> On Monday, February 2, 2015 at 10:13:39 AM UTC-5, Jakob Kroeker wrote:
>>
>> - how to recompile only the python and cython part (no pkgs) ?
>>
>
> sage -b
>  
>
>> - in case that sage is in a broken state, how to rebuild a single pkgs( 
>> e.g. Singular) in case a patch file was updated ?
>>
>
> sage -f singular
>  
>

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[sage-devel] Re: singular 4.0.1 upgrade: cython compile for 'plural' peeks wrong lib

[Jakob Kroeker]

Now I tracked the issue down and solved it:
libs for plural in 'src/module_list.py' were incorrect. Since I'm new to 
python/cython, i didn't knew that and grep for 'singular' was not an option 
(too many hits)

Sorry for the noise.


Jakob


Am Donnerstag, 5. Februar 2015 13:38:34 UTC+1 schrieb Jakob Kroeker:
>
> I'm getting a strange cython behaviour when compiling 
> u/jakobkroeker/ticket.17254.squashed , 
> 
>
> cython tries to pick -lsingular instead of -lSingular when compiling 
> plural:
>
> g++ -pthread -shared -L~/Projects/sage/local/lib 
> build/temp.linux-x86_64-2.7/build/cythonized/sage/rings/polynomial/plural.o 
> -L~/Projects/sage/local/lib -L~/Projects/sage/local/lib -lcsage -lm 
> -lreadline -lsingular -lgivaro -lgmpxx -lgmp -lstdc++ -lpython2.7 -o 
> build/lib.linux-x86_64-2.7/sage/rings/polynomial/plural.so
>
> this does not happen for other modules (for them  libSingular.so  is 
> picked correctly !!)
>
> Remark: Singular v 4.0 and later changed the libnames from 'libsingular.so'  
> to  'libSingular.so'
>
>
> Any idea what is going on or where ask for help?
>
>
>
>
>

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[sage-devel] singular 4.0.1 upgrade: cython compile for 'plural' peeks wrong lib

[Jakob Kroeker]

I'm getting a strange cython behaviour when compiling 
u/jakobkroeker/ticket.17254.squashed , 


cython tries to pick -lsingular instead of -lSingular when compiling plural:

g++ -pthread -shared -L~/Projects/sage/local/lib 
build/temp.linux-x86_64-2.7/build/cythonized/sage/rings/polynomial/plural.o 
-L~/Projects/sage/local/lib -L~/Projects/sage/local/lib -lcsage -lm 
-lreadline -lsingular -lgivaro -lgmpxx -lgmp -lstdc++ -lpython2.7 -o 
build/lib.linux-x86_64-2.7/sage/rings/polynomial/plural.so

this does not happen for other modules (for them  libSingular.so  is picked 
correctly !!)

Remark: Singular v 4.0 and later changed the libnames from 'libsingular.so'  
to  'libSingular.so'


Any idea what is going on or where ask for help?




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[sage-devel] Asymptotic Expressions in Sage

[Benjamin Hackl]

Hello everyone!

I just wanted to let you know -- as suggested 
in https://groups.google.com/forum/#!topic/sage-devel/uR_bv7PrZpk -- that 
Clemens Heuberger, Daniel Krenn, and myself are currently working on 
improving the situation of asymptotic expressions in Sage. In order to do 
so, we have created some tickets, all of which can be found at the 
respective meta-ticket (#17601, http://trac.sagemath.org/ticket/17601). 
This ticket also contains the basic structure for our implementation.

Several question (and answers) which came up during a discussion of the 
data structure we want to use can be found in the comments of the 
respective ticket (#17693, http://trac.sagemath.org/ticket/17693), and in 
the description of the ticket belonging to our "AsymptoticExpression"-class 
(#17716, http://trac.sagemath.org/ticket/17716).

Let us know if you have an opinion about this, we would be happy to 
exchange some thoughts or explain our plan in more detail! :-)

Kind regards,
Benjamin

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Re: [sage-devel] sage -t src/sage/repl/notebook_ipython.py # 9 doctests failed

[Jeroen Demeyer]

On 2015-02-05 01:37, Toan Trac wrote:

sage -t src/sage/repl/notebook_ipython.py  # 9 doctests failed

And what exactly are the failed tests...?

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Re: [sage-devel] Sagemath : wild experiments

[Vincent Delecroix]

Hi,

Still got two packages missing. See below.

2015-02-05 8:08 UTC+01:00, Julien Puydt :
>> flintqs will not come from debian!
>
> The debian package is flintqs.

I did not find this one (in testing).

>> polybori will not come from debian!
>
> Should come from debian-science's git and will give you
> libpolybori-0.8-3, libpolybori-dev, libpolybori-groebner-0.8-3,
> libpolybori-groebner-dev and python-polybori.

After successful cloning, the package builder failed.

polybori$ git-buildpackage
gbp:warning: Pristine-tar branch "pristine-tar" not found
pristine-tar: successfully generated /home/sage/polybori_0.8.3.orig.tar.gz
 dpkg-buildpackage -rfakeroot -D -us -uc -i -I
dpkg-buildpackage: source package polybori
dpkg-buildpackage: source version 0.8.3-4
dpkg-buildpackage: source distribution UNRELEASED
dpkg-buildpackage: source changed by Julien Puydt 
 dpkg-source -i -I --before-build polybori
dpkg-buildpackage: host architecture amd64
dpkg-source: info: applying
0001-Added-libraries-symlinks-to-testsuite-dependencies-t.patch
dpkg-source: info: applying 0002-Generate-clean-.pc-files-from-upstream.patch
dpkg-source: info: applying
0003-Protect-CErrorInfo-from-invalid-array-access.patch
dpkg-checkbuilddeps: Unmet build dependencies: python-all-dev tex4ht
dpkg-buildpackage: warning: build dependencies/conflicts unsatisfied; aborting
dpkg-buildpackage: warning: (Use -d flag to override.)
debuild: fatal error at line 1376:
dpkg-buildpackage -rfakeroot -D -us -uc -i -I failed
gbp:error: 'debuild -i -I' failed: it exited with 29

Vincent

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