add experimental libFES package

[sagetrac-Bouillaguet]

libfes is a library (under development) that solves systems of boolean equations by exhaustive search. It is dramatically faster than Groebner bases in general.

Installation Guide

• Download the fes-0.1 spkg here
• Apply attachment: fes.2.patch to the sage library
• Test:

sage: from sage.libs.fes import exhaustive_search
sage: R.<x,y,z> = BooleanPolynomialRing()
sage: f = [x*y + z + y + 1, x+y+z, x*y + y*z]
sage: ideal(f).variety()
sage: exhaustive_search(f)

Note to release manage the SPKG should be added to the experimental repository, but the patch should be applied to Sage.

Depends on #13202

CC: @malb

Component: packages: experimental

Author: Charles Bouillaguet

Reviewer: Martin Albrecht

Merged: sage-5.7.beta1

Issue created by migration from https://trac.sagemath.org/ticket/13162

[malb]

Reviewer: Martin Albrecht

[malb]

comment:4

Hi, I found a few small issues (so far) :)

SPKG

• little error in SPKG.txt

  === mypackage-0.1 (Charles Bouillaguet, 25 June 2012) ===

• hg status in the SPKG reports files that are not checked in.
• please include the Trac ticket number in the SPKG.txt changelog (and the hg commit message of your SPKG)

Patch

• since FES is a library its interface should live in sage.libs.fes and not sage.rings.polynomial.fes
• exhaustive_search has neither documentation nor doctests

[sagetrac-Bouillaguet]

comment:6

patch and spkg updated

[malb]

comment:7

Hi, almost there IMHO:

• the docstring isn't properly formated:
  • INPUT shouldn't get a double ":" but a single one
  • AFAIK the argument list after input should look like

INPUT:

 - ``foo`` - description

• There shouldn't be leading "#" in your comments between code blocks, indentation does take care of it
• sage: blocks should be indented by four spaces wrt to the preceding block ending with :: this includes the comments in between these code blocks
• who frees dense_rep_eqs?

[sagetrac-Bouillaguet]

comment:8

Hi,

patch modified again (use the second one, not the first one). I updated the docstrings according to the standard. Also, NOW, dense_rep_eqs is freed :)

[malb]

comment:10

SPKG

• This looks bad:

wrapper.c: In function ‘exhaustive_search_wrapper’:
wrapper.c:17:5: warning: implicit declaration of function ‘exhaustive_ia32’ [-Wimplicit-function-declaration]
wrapper.c:23:5: warning: implicit declaration of function ‘exhaustive_simd’ [-Wimplicit-function-declaration]

• You should add "-fPIC" to CFLAGS in spkg-install, it won't compile without it (on my machine)

Patch

• Your patch was incorrectly indented, I fixed this in the updated patch attached to this ticket.

[sagetrac-Bouillaguet]

comment:13

spkg updated (-fPIC and no compilation warnings)

[malb]

comment:15

I still get:

main_simd.c: In function ‘main’:
main_simd.c:58:3: warning: implicit declaration of function ‘exhaustive_simd’ [-Wimplicit-function-declaration]

Btw. is there an upstream repository/website?

[sagetrac-Bouillaguet]

comment:16

Replying to @malb:

Btw. is there an upstream repository/website?

https://bitbucket.org/fes/fes

It's fresh :)

[malb]

comment:17

And it's private, i.e., I cannot access it :)

[sagetrac-Bouillaguet]

comment:18

Replying to @malb:

And it's private, i.e., I cannot access it :)

fixed

[malb]

comment:19

Hi, can you reproduce the error I am seeing (above)?

[jdemeyer]

comment:38

There are uncommitted changes in the spkg:

jdemeyer@sage:~/spkg/fes-0.1$ hg status
M spkg-install

[jdemeyer]

comment:39

The following can be removed from spkg-install:

unset RM

INCLUDES="-I$SAGE_LOCAL/include"
LIBDIRS="-L$SAGE_LOCAL/lib"

And if $MAKE check actually does something, it should be inside spkg-check and not in spkg-install.

[jdemeyer]

comment:41

All doctests in fes.pyx need to be marked

# optional - fes

such that doctests succeed when libFES is not installed.

[sagetrac-Bouillaguet]

comment:42

I updated the spkg (taking into account Jeroen's comments).

I don't think that marking the doctests as optional is necessary, as the .pyx file is NOT included in the source tree when the spkg is not installed (cf. magic in module_list.py).

However, the more I think about this, the more I am convinced that the right way to access this library from sage is through #13850. In that case, the doctest involving libFES in the documentation of .solve() would need to be marked optional, of course.

[jdemeyer]

comment:43

Replying to @sagetrac-Bouillaguet:

I updated the spkg (taking into account Jeroen's comments).

I don't think that marking the doctests as optional is necessary, as the .pyx file is NOT included in the source tree when the spkg is not installed (cf. magic in module_list.py).

That's not true. The module_list.py magic is only about compiling the Cython file, which is completely orthogonal to doctests. The fes.pyx file is always there (regardless of whether it is compiled), so the doctests are there.

[sagetrac-Bouillaguet]

Changed dependencies from #13202 to #13202,#13964

[sagetrac-Bouillaguet]

new patch, because the library interface has changed

[sagetrac-Bouillaguet]

Changed dependencies from #13202,#13964 to #13202

[sagetrac-Bouillaguet]

comment:45

Attachment: fes.2.patch.gz

Hi malb & Jeroen. OK, I get it now, sorry for the noise. I marked the doctests as optional and fixed the spkg.

Since I have installed the libFES package in my sage tree, I don't see how I could test without it? (how to uninstall a spkg ?).

[malb]

comment:46

I don't think you can (well, you can delete the files by hand of course).

[sagetrac-Bouillaguet]

comment:47

@malb : if you don't have the libFES spkg installed, can you check that this patch applies and passes the tests ?

[malb]

comment:48

Yep, all tests pass. Sorry for the delay!

[haraldschilly]

comment:49

spkg is on the servers ...

[jdemeyer]

Merged: sage-5.7.beta1