sagemath-7.6-2.parabola1: updating version

5 files changed, 125 insertions, 38 deletions

diff --git a/libre/sagemath/PKGBUILD b/libre/sagemath/PKGBUILD
index e5841661f..32e892716 100644
--- a/libre/sagemath/PKGBUILD
+++ b/libre/sagemath/PKGBUILD
@@ -1,4 +1,4 @@
-# $Id: PKGBUILD 213281 2017-02-21 09:01:02Z arojas $
+# $Id: PKGBUILD 219758 2017-03-28 19:08:08Z arojas $
 # Maintainer (Arch): Evgeniy Alekseev <arcanis.arch at gmail dot com>
 # Maintainer (Arch): Antonio Rojas <arojas@archlinux.org>
 # Contributor (Arch): Daniel Wallace <danielwallace at gtmanfred dot com>
@@ -10,8 +10,8 @@
 # Maintainer: André Silva <emulatorman@parabola.nu>
 
 pkgname=sagemath
-pkgver=7.5.1
-pkgrel=7.parabola1
+pkgver=7.6
+pkgrel=2.parabola1
 pkgdesc="Free Mathematics Software, free software replacement of Magma, Maple, Mathematica, and Matlab, without nonfree nauty support"
 arch=(i686 x86_64 armv7h)
 url="http://www.sagemath.org"
@@ -30,6 +30,7 @@ optdepends=('cython2: to compile cython code' 'python2-pkgconfig: to compile cyt
   'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes'
   'libhomfly: for computing the homfly polynomial of links' 'libbraiding: for computing in braid groups'
   'libfes: exhaustive search of solutions for boolean equations' 'python2-pynormaliz: Normaliz backend for polyhedral computations'
+  'latte-integrale: integral point count in polyhedra'
   'three.js: alternative 3D plots engine' 'tachyon: alternative 3D plots engine'
   'sagemath-jupyter: Jupyter kernel')
 makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding
@@ -38,22 +39,22 @@ conflicts=(sage-mathematics)
 replaces=(sage-mathematics)
 provides=(sage-mathematics)
 source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
-        env.patch skip-check.patch cython-sys-path.patch is-package-installed.patch package.patch
-        jupyter-path.patch test-optional.patch ecm-7.patch increase-rtol.patch sagemath-gslcblas.patch r-no-readline.patch
-        sagemath-no-anal.h.patch sagemath-planarity3.patch fes02.patch sagemath-singular-4.1.0.p2.patch)
-sha256sums=('3cd9af3e3bfd7f5cc966b7c36168d04b9a1213aa9a7af3286b5d53d40e7653e3'
+        env.patch skip-check.patch cython-sys-path.patch is-package-installed.patch package.patch latte-count.patch
+        jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch ecm-7.patch increase-rtol.patch r-no-readline.patch
+        sagemath-planarity3.patch fes02.patch sagemath-singular-4.1.0.p2.patch)
+sha256sums=('e6e0729ab25446e7c922058db0eee4b0b294b32c196e34842e843ea9fae41423'
             '9dba04ff13626a7b6c338a8b18a6c27d343f68a547a218533cf773af3dae6635'
             'b02b3d2d5620ca20f96adb62b6fef05e4676c0a60983310a1450fdf3d923cb04'
             'ff7e034d08ab084fdb193484f7fe3a659ebcd8ab33a2b7177237d65b26de7872'
             'd60fb0fbd27991ce9496ca035a54b03334b5b53f244227a8d6e13f3327ce75d2'
             '4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212'
+            'b816c71d345fb1188c3faa01c4e75cfa04ba6506080231d5d2c303a2288e9b50'
             '775051aa9076ebf631c8a291af38b6ec4a13c904740dc9da831641d592d8bcd8'
+            '27aa73d427d92aeb2c181a233aa3a574a4158cd7dee33832808f69edaec55ea2'
             '81d08c6a760f171f3381455b66a6c84789c9f0eefddbe6ca5794075514ad8c3a'
             '65ad84c83d5f956fde8eab961f2caad56d64044324c4abc0e56bcd9f44061cb6'
             'be925eefeac3f28e639794ddc20d64e6faafd7181804e29417a510224d19ccc7'
-            '973224f53e9a6fcfaa9c6cb842b02430a601d1c7ce0abb41b3591470d128930c'
             'ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf'
-            '8126c92a5fc15738c4f7982aadb5a4033230fc2d5da05af9133a96ad1181419e'
             'a1c562ebe4538d672404ca3ac2e954a3c955afeb7463f7b4fe6eaa6fa74fe5c7'
             'a39da083c038ada797ffc5bedc9ba47455a3f77057d42f86484ae877ef9172ea'
             'e1912afec58b834fac3b9161c2d5a1794bb618126c6bd7a4be85c834231360e7')
@@ -78,22 +79,22 @@ prepare(){
   patch -p1 -i ../ecm-7.patch
 # increase numerical tolerance, needed by scipy 0.18
   patch -p1 -i ../increase-rtol.patch
-# fix cblas linking in gsl modules
-  patch -p1 -i ../sagemath-gslcblas.patch
 # fix freezes in R interface with readline 7 (Debian)
   patch -p1 -i ../r-no-readline.patch
 # fix build with planarity 3 (Debian)
   patch -p2 -i ../sagemath-planarity3.patch
 # fix build with Singular 4.1.0-p2
   patch -p0 -i ../sagemath-singular-4.1.0.p2.patch
+# use correct latte-count binary name
+  patch -p1 -i ../latte-count.patch
+# make 'sage -notebook=jupyter' work with our python3 jupyter-notebook package
+  patch -p1 -i ../sagemath-python3-notebook.patch
 
 # Upstream patches  
 # fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
   patch -p1 -i ../fes02.patch
 # replace is_package_installed usage http://trac.sagemath.org/ticket/20377
   patch -p1 -i ../is-package-installed.patch
-# Allow compiling without pari's anal.h https://trac.sagemath.org/ticket/22195
-  patch -p1 -i ../sagemath-no-anal.h.patch
 
 # use python2
   sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/*
diff --git a/libre/sagemath/latte-count.patch b/libre/sagemath/latte-count.patch
new file mode 100644
index 000000000..623259294
--- /dev/null
+++ b/libre/sagemath/latte-count.patch
@@ -0,0 +1,84 @@
+diff --git a/src/sage/geometry/polyhedron/base.py b/src/sage/geometry/polyhedron/base.py
+index 50d99f99e4..3a3a8cb214 100644
+--- a/src/sage/geometry/polyhedron/base.py
++++ b/src/sage/geometry/polyhedron/base.py
+@@ -4629,7 +4629,7 @@ class Polyhedron_base(Element):
+             ...
+             RuntimeError: LattE integrale program failed (exit code 1):
+             ...
+-            Invocation: count '--redundancy-check=none' --cdd /dev/stdin
++            Invocation: latte-count '--redundancy-check=none' --cdd /dev/stdin
+             ...
+             Parse error in CDD-style input file /dev/stdin
+             sage: Q.integral_points_count(verbose=True) # optional - latte_int
+diff --git a/src/sage/geometry/polyhedron/base_ZZ.py b/src/sage/geometry/polyhedron/base_ZZ.py
+index 268af9db0d..70d41dfa30 100644
+--- a/src/sage/geometry/polyhedron/base_ZZ.py
++++ b/src/sage/geometry/polyhedron/base_ZZ.py
+@@ -228,7 +228,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             sage: p = P.ehrhart_polynomial(maxdet=5, verbose=True)  # optional - latte_int
+             This is LattE integrale ...
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin
+             ...
+             sage: p    # optional - latte_int
+             1/2*t^2 + 3/2*t + 1
+@@ -236,7 +236,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             sage: p = P.ehrhart_polynomial(dual=True, verbose=True)  # optional - latte_int
+             This is LattE integrale ...
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin
+             ...
+             sage: p   # optional - latte_int
+             1/2*t^2 + 3/2*t + 1
+@@ -244,7 +244,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             sage: p = P.ehrhart_polynomial(irrational_primal=True, verbose=True)   # optional - latte_int
+             This is LattE integrale ...
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin
+             ...
+             sage: p   # optional - latte_int
+             1/2*t^2 + 3/2*t + 1
+@@ -252,7 +252,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             sage: p = P.ehrhart_polynomial(irrational_all_primal=True, verbose=True)  # optional - latte_int
+             This is LattE integrale ...
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin
+             ...
+             sage: p   # optional - latte_int
+             1/2*t^2 + 3/2*t + 1
+@@ -264,7 +264,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             ...
+             RuntimeError: LattE integrale program failed (exit code 1):
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin
+             Unknown command/option --bim-bam-boum=19
+         """
+         if self.is_empty():
+diff --git a/src/sage/interfaces/latte.py b/src/sage/interfaces/latte.py
+index 066cedd401..302b39910d 100644
+--- a/src/sage/interfaces/latte.py
++++ b/src/sage/interfaces/latte.py
+@@ -86,7 +86,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False,
+         sage: n = count(cddin, cdd=True, verbose=True, raw_output=True)  # optional - latte_int
+         This is LattE integrale ...
+         ...
+-        Invocation: count '--redundancy-check=none' --cdd /dev/stdin
++        Invocation: latte-count '--redundancy-check=none' --cdd /dev/stdin
+         ...
+         Total Unimodular Cones: ...
+         Maximum number of simplicial cones in memory at once: ...
+@@ -106,7 +106,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False,
+     from sage.misc.misc import SAGE_TMP
+     from sage.rings.integer import Integer
+ 
+-    args = ['count']
++    args = ['latte-count']
+     if ehrhart_polynomial and multivariate_generating_function:
+         raise ValueError
+     if ehrhart_polynomial:
diff --git a/libre/sagemath/sagemath-gslcblas.patch b/libre/sagemath/sagemath-gslcblas.patch
deleted file mode 100644
index 9ef3094b0..000000000
--- a/libre/sagemath/sagemath-gslcblas.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/module_list.py b/src/module_list.py
-index 96e8081..4728e9a 100644
---- a/src/module_list.py
-+++ b/src/module_list.py
-@@ -45,6 +45,7 @@ givaro_library_dirs = givaro_pc['library_dirs']
- gsl_pc = pkgconfig.parse('gsl')
- gsl_libs = gsl_pc['libraries']
- gsl_libs.remove('gslcblas')
-+gsl_libs.extend(cblas_libs)
- gsl_library_dirs = gsl_pc['library_dirs']
- gsl_include_dirs = gsl_pc['include_dirs']
- 
-
diff --git a/libre/sagemath/sagemath-no-anal.h.patch b/libre/sagemath/sagemath-no-anal.h.patch
deleted file mode 100644
index f1b261321..000000000
--- a/libre/sagemath/sagemath-no-anal.h.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/src/sage/libs/cypari2/paripriv.pxd b/src/sage/libs/cypari2/paripriv.pxd
-index b6ea381..921599d 100644
---- a/src/sage/libs/cypari2/paripriv.pxd
-+++ b/src/sage/libs/cypari2/paripriv.pxd
-@@ -26,5 +26,5 @@ cdef extern from "pari/paripriv.h":
- 
-     extern gp_data* GP_DATA
- 
--cdef extern from "pari/anal.h":
--    char* closure_func_err()
-+cdef extern:  # Declared in private PARI header file "anal.h"
-+    const char* closure_func_err()
diff --git a/libre/sagemath/sagemath-python3-notebook.patch b/libre/sagemath/sagemath-python3-notebook.patch
new file mode 100644
index 000000000..cae225615
--- /dev/null
+++ b/libre/sagemath/sagemath-python3-notebook.patch
@@ -0,0 +1,27 @@
+diff --git a/src/bin/sage-notebook b/src/bin/sage-notebook
+index 74192da240..0ede281aad 100755
+--- a/src/bin/sage-notebook
++++ b/src/bin/sage-notebook
+@@ -96,8 +96,7 @@ class NotebookJupyter(object):
+         if not have_prerequisites():
+             print(self.PREREQUISITE_ERROR)
+             raise SystemExit(1)
+-        from notebook.notebookapp import main
+-        main(argv)
++        os.execvp('jupyter-notebook', ['jupyter-notebook'] + argv)
+ 
+ 
+ class SageNBExport(NotebookJupyter):
+diff --git a/src/sage/repl/ipython_kernel/install.py b/src/sage/repl/ipython_kernel/install.py
+index 3912b8cdf5..bd40cdadda 100644
+--- a/src/sage/repl/ipython_kernel/install.py
++++ b/src/sage/repl/ipython_kernel/install.py
+@@ -281,7 +281,6 @@ def have_prerequisites(debug=True):
+         True
+     """
+     try:
+-        from notebook.notebookapp import NotebookApp
+         return True
+     except ImportError:
+         if debug:
+