Re: [sage-devel] cross-post from flint-devel: python bindings for Flint and Arb (work in progress)

[Clemens Heuberger]

On 2015-01-08 18:49, Fredrik Johansson wrote:
> On Thu, Jan 8, 2015 at 5:19 PM, William Stein  wrote:
>> On Thu, Jan 8, 2015 at 5:56 AM, John Cremona  wrote:
>>> http://fredrikj.net/blog/2015/01/arb-and-flint-in-python/
>>
>> Hi Fredrik,
>>
>> Any chance you could make this trivial to install into an existing
>> Sage install?   E.g. a sage package?  Since you know where FLINT is
>> there, what the version is, have the SAGE_LOCAL variable, etc...
> 
> I could create an spkg. Later this month, hopefully.
> 
> Note that Clemens Heuberger has started working on proper Sage
> bindings for Arb (http://trac.sagemath.org/ticket/17194 and sequel
> tickets). I think this is the right way to go.

This arb binding needs review (including the upgrade to flint 2.5 in
http://trac.sagemath.org/ticket/17688).

Thank you, CH

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

[Volker Braun]

Sage is compiled with GCC. Can you enter a sage shell "sage -sh" and then 
try again the compilation, then that'll use the same compiler.

Also, your header search path should be something like:

$ sage -sh

Starting subshell with Sage environment variables set.  Don't forget
to exit when you are done.  Beware:
 * Do not do anything with other copies of Sage on your system.
 * Do not use this for installing Sage packages using "sage -i" or for
   running "make" at Sage's root directory.  These should be done
   outside the Sage shell.

Bypassing shell configuration files...

Note: SAGE_ROOT=/Users/vbraun/Sage

$ cpp -v
Using built-in specs.
COLLECT_GCC=cpp
Target: x86_64-apple-darwin14.0.0
Configured with: ../src/configure --prefix=/Users/vbraun/Sage/local 
--with-local-prefix=/Users/vbraun/Sage/local 
--with-gmp=/Users/vbraun/Sage/local --with-mpfr=/Users/vbraun/Sage/local 
--with-mpc=/Users/vbraun/Sage/local --with-system-zlib --disable-multilib 
--disable-nls --enable-languages=c,c++,fortran --disable-libitm 
--without-isl --without-cloog  
Thread model: posix
gcc version 4.9.2 (GCC) 
COLLECT_GCC_OPTIONS='-E' '-mmacosx-version-min=10.9' '-v' '-mtune=core2'
 /Users/vbraun/Sage/local/libexec/gcc/x86_64-apple-darwin14.0.0/4.9.2/cc1 
-E -quiet -v -D__DYNAMIC__ - -fPIC -mmacosx-version-min=10.9 -mtune=core2
ignoring nonexistent directory 
"/Users/vbraun/Sage/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../../x86_64-apple-darwin14.0.0/include"
ignoring duplicate directory "/Users/vbraun/Sage/local/include"
  as it is a non-system directory that duplicates a system directory
#include "..." search starts here:
#include <...> search starts here:
 /Users/vbraun/Sage/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/include
 /Users/vbraun/Sage/local/include
 /Users/vbraun/Sage/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/include-fixed
 /usr/include
 /System/Library/Frameworks
 /Library/Frameworks
End of search list.
^C




On Saturday, February 7, 2015 at 4:42:49 AM UTC+1, Xander Faber wrote:
>
> Hi Bill,
>
> Thanks for the detailed instructions. mpir-2.7.0  and mpfr-3.1.2 build 
> fine on my system. When I run the makefile for flint, I get the following 
> messages after a while:
>
>  `   CC   ../build/fq_zech_poly_factor/fq_zech_poly_factor_print.o
> CC   ../build/fq_zech_poly_factor/fq_zech_poly_factor_print_pretty.o
> CC   ../build/fq_zech_poly_factor/fq_zech_poly_factor_realloc.o
> CC   ../build/fq_zech_poly_factor/fq_zech_poly_factor_set.o
> AR   libflint.a
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
>  
> file: libflint.a(fq_zech_clear.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
>  
> file: libflint.a(fq_zech_clear.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
>  
> file: libflint.a(fq_zech_clear.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
>  
> file: libflint.a(fq_zech_clear.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
>  
> file: libflint.a(fq_zech_clear.o) has no symbols`
>
> It does, however, proceed beyond the point where Sage's flint compile 
> crashes. 
>
> Afterward, I ran 
>  
> make check
>
> and everything passed. S ... Sage specific problem, you're thinking? 
> Since I've now compiled mpir-2.70, mpfr-3.1.2, and flint-2.4.4 separately, 
> is it feasible to just copy these libraries into the Sage directory and 
> proceed with the Sage build? Any idea where I would put them?
>
> -Xander
>

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

[Xander Faber]

Volker - 

I'm in over my head here. Can you be more specific about which commands you 
want me to run? 
Or do you just want to see the output of the commands you used below? If 
the latter, they're below.

-Xander


`
Xanders-MacBook-Pro:~ xander$ cd 
'/Users/xander/sage/local/var/tmp/sage/build/flint-2.4.4' && 
'/Users/xander/sage/sage' --sh 

Starting subshell with Sage environment variables set. Don't forget 
to exit when you are done. Beware: 
* Do not do anything with other copies of Sage on your system. 
* Do not use this for installing Sage packages using "sage -i" or for 
running "make" at Sage's root directory. These should be done 
outside the Sage shell. 

Bypassing shell configuration files... 

Note: SAGE_ROOT=/Users/xander/sage 
(sage-sh) xander@Xanders-MBP:flint-2.4.4$ cpp -v 
Using built-in specs. 
COLLECT_GCC=cpp 
Target: x86_64-apple-darwin14.1.0 
Configured with: ../src/configure --prefix=/Users/xander/sage/local 
--with-local-prefix=/Users/xander/sage/local 
--with-gmp=/Users/xander/sage/local --with-mpfr=/Users/xander/sage/local 
--with-mpc=/Users/xander/sage/local --with-system-zlib --disable-multilib 
--disable-nls --enable-languages=c,c++,fortran --disable-libitm 
--without-isl --without-cloog 
Thread model: posix 
gcc version 4.9.2 (GCC) 
COLLECT_GCC_OPTIONS='-E' '-mmacosx-version-min=10.9' '-v' '-mtune=core2' 
/Users/xander/sage/local/libexec/gcc/x86_64-apple-darwin14.1.0/4.9.2/cc1 -E 
-quiet -v -D__DYNAMIC__ - -fPIC -mmacosx-version-min=10.9 -mtune=core2 
ignoring nonexistent directory 
"/Users/xander/sage/local/lib/gcc/x86_64-apple-darwin14.1.0/4.9.2/../../../../x86_64-apple-darwin14.1.0/include"
 

ignoring duplicate directory "/Users/xander/sage/local/include" 
as it is a non-system directory that duplicates a system directory 
#include "..." search starts here: 
#include <...> search starts here: 
/usr/local/include 
/Users/xander/sage/local/lib/gcc/x86_64-apple-darwin14.1.0/4.9.2/include 
/Users/xander/sage/local/include 
/Users/xander/sage/local/lib/gcc/x86_64-apple-darwin14.1.0/4.9.2/include-fixed 

/usr/include 
/System/Library/Frameworks 
/Library/Frameworks 
End of search list. 
^C
`


On Sunday, February 8, 2015 at 4:24:53 AM UTC-5, Volker Braun wrote:
>
> Sage is compiled with GCC. Can you enter a sage shell "sage -sh" and then 
> try again the compilation, then that'll use the same compiler.
>
> Also, your header search path should be something like:
>
> $ sage -sh
>
> Starting subshell with Sage environment variables set.  Don't forget
> to exit when you are done.  Beware:
>  * Do not do anything with other copies of Sage on your system.
>  * Do not use this for installing Sage packages using "sage -i" or for
>running "make" at Sage's root directory.  These should be done
>outside the Sage shell.
>
> Bypassing shell configuration files...
>
> Note: SAGE_ROOT=/Users/vbraun/Sage
>
> $ cpp -v
> Using built-in specs.
> COLLECT_GCC=cpp
> Target: x86_64-apple-darwin14.0.0
> Configured with: ../src/configure --prefix=/Users/vbraun/Sage/local 
> --with-local-prefix=/Users/vbraun/Sage/local 
> --with-gmp=/Users/vbraun/Sage/local --with-mpfr=/Users/vbraun/Sage/local 
> --with-mpc=/Users/vbraun/Sage/local --with-system-zlib --disable-multilib 
> --disable-nls --enable-languages=c,c++,fortran --disable-libitm 
> --without-isl --without-cloog  
> Thread model: posix
> gcc version 4.9.2 (GCC) 
> COLLECT_GCC_OPTIONS='-E' '-mmacosx-version-min=10.9' '-v' '-mtune=core2'
>  /Users/vbraun/Sage/local/libexec/gcc/x86_64-apple-darwin14.0.0/4.9.2/cc1 
> -E -quiet -v -D__DYNAMIC__ - -fPIC -mmacosx-version-min=10.9 -mtune=core2
> ignoring nonexistent directory 
> "/Users/vbraun/Sage/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../../x86_64-apple-darwin14.0.0/include"
> ignoring duplicate directory "/Users/vbraun/Sage/local/include"
>   as it is a non-system directory that duplicates a system directory
> #include "..." search starts here:
> #include <...> search starts here:
>  /Users/vbraun/Sage/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/include
>  /Users/vbraun/Sage/local/include
>
>  
> /Users/vbraun/Sage/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/include-fixed
>  /usr/include
>  /System/Library/Frameworks
>  /Library/Frameworks
> End of search list.
> ^C
>
>
>
>
> On Saturday, February 7, 2015 at 4:42:49 AM UTC+1, Xander Faber wrote:
>>
>> Hi Bill,
>>
>> Thanks for the detailed instructions. mpir-2.7.0  and mpfr-3.1.2 build 
>> fine on my system. When I run the makefile for flint, I get the following 
>> messages after a while:
>>
>>  `   CC   ../build/fq_zech_poly_factor/fq_zech_poly_factor_print.o
>> CC   ../build/fq_zech_poly_factor/fq_zech_poly_factor_print_pretty.o
>> CC   ../build/fq_zech_poly_factor/fq_zech_poly_factor_realloc.o
>> CC   ../build/fq_zech_poly_factor/fq_zech_poly_factor_set.o
>> AR   libflint.a
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
>>  
>> file: libflint.a(fq_zech_clear

[sage-devel] Re: GSoC 2015

[Harald Schilly]

Update.

On Monday, January 26, 2015 at 2:06:23 PM UTC+1, Harald Schilly wrote:
>
> In two weeks...
>

Tomorrow, the application period starts. A major and important part of the 
application is a good list of prospective projects. This is a list of ideas 
on  what students can base their project proposal on. It should include a 
description, prerequisites, possible mentors, etc. Without that, 
organizations aren't accepted.

Our list is here: http://wiki.sagemath.org/GSoC/2015

For comparison, SymPy's looks like this:
https://github.com/sympy/sympy/wiki/GSoC-2015-Ideas

-- Harald

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

[Jakob Kroeker]

>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.

For good or bad, Singular did not migrate to CMake. There was too much 
opposition, I guess.


Jakob

Am Montag, 1. März 2010 13:39:59 UTC+1 schrieb William:
>
> 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.
>
>  -- William
>
>

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[sage-devel] Re: Integrate sage into spyder

[Harald Schilly]

On Saturday, February 7, 2015 at 4:14:08 PM UTC+1, mmarco wrote:
>
> I thinki it would be good to have some kind of IDE to work on sage 
> development.
>

I have a (limited, but for our purposes fine) group license for PyCharm 
under the name of the Sage OSS project.
Anyone who is interested, please email me. 

-- harald

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

[Volker Braun]

On Sunday, February 8, 2015 at 1:55:26 PM UTC+1, Xander Faber wrote:
>
> #include "..." search starts here: 
> #include <...> search starts here: 
> /usr/local/include 
> /Users/xander/sage/local/lib/gcc/x86_64-apple-darwin14.1.0/4.9.2/include 
> /Users/xander/sage/local/include 
>

I'm guessing you have a /usr/local/include/gmp.h that is not ours, this 
explains your problem. Do you have homebrew installed in /usr/local? This 
conflicts with Sage, the easiest workaround is to rename /usr/local while 
building Sage.

Also, can you post the log of the gcc build, maybe we can add a workaround 
there.

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[sage-devel] self in the INPUT section of the docstring

[martin . vgagern]

Hello.

This post is motivated by #17567 
. There I implemented a 
method which is only defined for vectors of length 3 and 7. I felt like 
documenting the fact “self has to be length 3 or 7” in the INPUT section of 
the docstring would be a good idea. The reviewer however felt otherwise, 
claiming that self should not be documented at all. I'd like to have some 
discussion about this question. My personal feeling is that in most cases 
you can indeed leave out the self argument, since it can be any instance of 
the class in question. If, however, there are additional restrictions like 
in this case, then I'd very much like to see them described as such. I feel 
that this might make the documentation a bit less uniform, but a bit more 
useful. What do you think?

Martin

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Re: [sage-devel] self in the INPUT section of the docstring

[John Cremona]

As long as the restriction is documented somewhere in the docstring,
and there is a reasonable error raised when the conditions are not
met, it does not seem to me to be essential to include self in the
INPUT block.

For a common example I looked at the factor() method for ZZ, which
certainly does raise an error if you try 0.factor().  But the
restriction to nonzero input is not mentioned in the docstring at all,
and there is no test to show in the documentation what happens when
you try 0.factor().  That is not good!

John

On 8 February 2015 at 21:19,   wrote:
> Hello.
>
> This post is motivated by #17567. There I implemented a method which is only
> defined for vectors of length 3 and 7. I felt like documenting the fact
> “self has to be length 3 or 7” in the INPUT section of the docstring would
> be a good idea. The reviewer however felt otherwise, claiming that self
> should not be documented at all. I'd like to have some discussion about this
> question. My personal feeling is that in most cases you can indeed leave out
> the self argument, since it can be any instance of the class in question.
> If, however, there are additional restrictions like in this case, then I'd
> very much like to see them described as such. I feel that this might make
> the documentation a bit less uniform, but a bit more useful. What do you
> think?
>
> Martin
>
> --
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[sage-devel] Re: self in the INPUT section of the docstring

[Volker Braun]

IMHO thats unnecessarily confusing for novices. You shouldn't have to 
understand Python OOP to be able to read the documentation. INPUT documents 
the parameters, and nothing else. Of course such restrictions need to be 
mentioned elsewhere in the docstring.



On Sunday, February 8, 2015 at 10:19:57 PM UTC+1, martin@gmx.net wrote:
>
> Hello.
>
> This post is motivated by #17567 
> . There I implemented a 
> method which is only defined for vectors of length 3 and 7. I felt like 
> documenting the fact “self has to be length 3 or 7” in the INPUT section of 
> the docstring would be a good idea. The reviewer however felt otherwise, 
> claiming that self should not be documented at all. I'd like to have some 
> discussion about this question. My personal feeling is that in most cases 
> you can indeed leave out the self argument, since it can be any instance of 
> the class in question. If, however, there are additional restrictions like 
> in this case, then I'd very much like to see them described as such. I feel 
> that this might make the documentation a bit less uniform, but a bit more 
> useful. What do you think?
>
> Martin
>
>

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

[Xander Faber]

Woot! Successful build!

Yes, I had my own install of gmp. I renamed /usr/local before the build and
everything went smoothly.

Many thanks, Volker and Bill, for diagnosing the problem.

Cheers,
Xander



On Sun, Feb 8, 2015 at 9:38 AM, Volker Braun  wrote:

> On Sunday, February 8, 2015 at 1:55:26 PM UTC+1, Xander Faber wrote:
>>
>> #include "..." search starts here:
>> #include <...> search starts here:
>> /usr/local/include
>> /Users/xander/sage/local/lib/gcc/x86_64-apple-darwin14.1.0/4.9.2/include
>> /Users/xander/sage/local/include
>>
>
> I'm guessing you have a /usr/local/include/gmp.h that is not ours, this
> explains your problem. Do you have homebrew installed in /usr/local? This
> conflicts with Sage, the easiest workaround is to rename /usr/local while
> building Sage.
>
> Also, can you post the log of the gcc build, maybe we can add a workaround
> there.
>
>  --
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