Sync with stable

5 files changed, 65 insertions, 33 deletions

diff --git a/.SRCINFO b/.SRCINFO
index c77dc8debe29..cd2a259b4c3f 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = sagemath-git
 	pkgdesc = Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab
-	pkgver = 8.1.beta4.r0.gf34394d84e
+	pkgver = 8.1.beta6.r0.g6cd99718a8
 	pkgrel = 1
 	url = http://www.sagemath.org
 	arch = i686
@@ -89,6 +89,7 @@ pkgbase = sagemath-git
 	optdepends = python2-pynormaliz: Normaliz backend for polyhedral computations
 	optdepends = latte-integrale: integral point count in polyhedra
 	optdepends = polymake: polymake backend for polyhedral computations
+	optdepends = meataxe: faster matrix arithmetic over finite fields
 	optdepends = sirocco: for computing the fundamental group of the complement of a plane curve
 	optdepends = three.js: alternative 3D plots engine
 	optdepends = tachyon: alternative 3D plots engine
@@ -102,7 +103,8 @@ pkgbase = sagemath-git
 	source = r-no-readline.patch
 	source = fes02.patch
 	source = sagemath-ecl-no-sigfpe.patch
-	source = sagemath-pynac-0.7.11.patch
+	source = sagemath-detect-igraph.patch
+	source = sagemath-networkx2.patch
 	sha256sums = SKIP
 	sha256sums = e0b5b8673300857fde823209a7e90faecf9e754ab812cc5e54297eddc0c79571
 	sha256sums = 4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212
@@ -113,7 +115,8 @@ pkgbase = sagemath-git
 	sha256sums = ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf
 	sha256sums = a39da083c038ada797ffc5bedc9ba47455a3f77057d42f86484ae877ef9172ea
 	sha256sums = c31809f887bf9acc45c5bd9dd30bb93e73601d3efbf3016594c3c1d241731c8a
-	sha256sums = 3e23ff449a5a3a032684287722455633762636b93ecfc35fb00e875c69eff240
+	sha256sums = 90be1d1a90120bd5bd3620769480106ba809dd23e896bc4a3f8931e5340f3cda
+	sha256sums = a1a0ab5b794136b518f5f66fe9f1689411fabb3b81560b159eae81f6f69000e3
 
 pkgname = sagemath-git
 	optdepends = cython2: to compile cython code
@@ -140,6 +143,7 @@ pkgname = sagemath-git
 	optdepends = python2-pynormaliz: Normaliz backend for polyhedral computations
 	optdepends = latte-integrale: integral point count in polyhedra
 	optdepends = polymake: polymake backend for polyhedral computations
+	optdepends = meataxe: faster matrix arithmetic over finite fields
 	optdepends = sirocco: for computing the fundamental group of the complement of a plane curve
 	optdepends = three.js: alternative 3D plots engine
 	optdepends = tachyon: alternative 3D plots engine
diff --git a/PKGBUILD b/PKGBUILD
index c94df29f2b5e..1eacbedc4a2a 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -8,7 +8,7 @@
 
 pkgbase=sagemath-git
 pkgname=(sagemath-git sagemath-jupyter-git)
-pkgver=8.1.beta4.r0.gf34394d84e
+pkgver=8.1.beta6.r0.g6cd99718a8
 pkgrel=1
 pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"
 arch=(i686 x86_64)
@@ -29,13 +29,15 @@ optdepends=('cython2: to compile cython code' 'python2-pkgconfig: to compile cyt
   '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' 'polymake: polymake backend for polyhedral computations'
+  'meataxe: faster matrix arithmetic over finite fields'
   'sirocco: for computing the fundamental group of the complement of a plane curve'
   'three.js: alternative 3D plots engine' 'tachyon: alternative 3D plots engine')
 makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding sirocco
   mcqd coxeter3 modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe libfes git)
 source=(git://git.sagemath.org/sage.git#branch=develop
         env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch
-        r-no-readline.patch fes02.patch sagemath-ecl-no-sigfpe.patch sagemath-pynac-0.7.11.patch)
+        r-no-readline.patch fes02.patch sagemath-ecl-no-sigfpe.patch
+        sagemath-detect-igraph.patch sagemath-networkx2.patch)
 sha256sums=('SKIP'
             'e0b5b8673300857fde823209a7e90faecf9e754ab812cc5e54297eddc0c79571'
             '4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212'
@@ -46,7 +48,8 @@ sha256sums=('SKIP'
             'ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf'
             'a39da083c038ada797ffc5bedc9ba47455a3f77057d42f86484ae877ef9172ea'
             'c31809f887bf9acc45c5bd9dd30bb93e73601d3efbf3016594c3c1d241731c8a'
-            '3e23ff449a5a3a032684287722455633762636b93ecfc35fb00e875c69eff240')
+            '90be1d1a90120bd5bd3620769480106ba809dd23e896bc4a3f8931e5340f3cda'
+            'a1a0ab5b794136b518f5f66fe9f1689411fabb3b81560b159eae81f6f69000e3')
 
 pkgver() {
   cd sage
@@ -74,14 +77,16 @@ prepare(){
 # fix Cremona database detection
   sed -e "s|is_package_installed('database_cremona_ellcurve')|os.path.exists('/usr/share/cremona/cremona.db')|" \
    -i src/sage/databases/cremona.py
+# fix python-igraph detection
+  patch -p1 -i ../sagemath-detect-igraph.patch
+# adapt to networkx 2 changes
+  patch -p1 -i ../sagemath-networkx2.patch
 
 # Upstream patches  
 # fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
   patch -p1 -i ../fes02.patch
 # disable SIGFPE for ecl https://trac.sagemath.org/ticket/22191
-  patch -p1 -i ../sagemath-ecl-no-sigfpe.patch
-# fix build with pynac 0.7.11 https://trac.sagemath.org/ticket/23820
-  patch -p1 -i ../sagemath-pynac-0.7.11.patch
+# patch -p1 -i ../sagemath-ecl-no-sigfpe.patch
 
 # use python2
   sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/*
@@ -141,9 +146,6 @@ package_sagemath-git() {
 
 # Split jupyter kernel
   rm -r "$pkgdir"/usr/share/jupyter
-
-# Drop meataxe extension, it segfaults
-#  rm "$pkgdir"/usr/lib/python2.7/site-packages/sage/matrix/matrix_gfpn_dense.*
 }
 
 package_sagemath-jupyter-git() {
diff --git a/sagemath-detect-igraph.patch b/sagemath-detect-igraph.patch
new file mode 100644
index 000000000000..89965d45e286
--- /dev/null
+++ b/sagemath-detect-igraph.patch
@@ -0,0 +1,21 @@
+diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
+index 252984f..ce19682 100644
+--- a/src/sage/graphs/generic_graph.py
++++ b/src/sage/graphs/generic_graph.py
+@@ -7876,10 +7875,12 @@ class GenericGraph(GenericGraph_pyx):
+         if algorithm is None:
+             if vertex_bound:
+                 algorithm = "LP"
+-            elif is_package_installed("python_igraph"):
+-                algorithm = "igraph"
+             else:
+-                algorithm = "FF"
++                algorithm = "igraph"
++                try:
++                    import igraph
++                except ImportError:
++                    algorithm = "FF"
+ 
+         if (algorithm == "FF"):
+             return self._ford_fulkerson(x,y, value_only=value_only, integer=integer, use_edge_labels=use_edge_labels)
+
diff --git a/sagemath-networkx2.patch b/sagemath-networkx2.patch
new file mode 100644
index 000000000000..b26160b6ffb1
--- /dev/null
+++ b/sagemath-networkx2.patch
@@ -0,0 +1,26 @@
+diff --git a/src/sage/graphs/digraph.py b/src/sage/graphs/digraph.py
+index 8c29602da6..e7a185d586 100644
+--- a/src/sage/graphs/digraph.py
++++ b/src/sage/graphs/digraph.py
+@@ -751,7 +751,7 @@ class DiGraph(GenericGraph):
+             self.allow_multiple_edges(multiedges,check=False)
+             self.allow_loops(loops,check=False)
+             self.add_vertices(data.nodes())
+-            self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True))
++            self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True))
+         elif format == 'igraph':
+             if not data.is_directed():
+                 raise ValueError("A *directed* igraph graph was expected. To "+
+diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py
+index b63135d8e6..5775042976 100644
+--- a/src/sage/graphs/graph.py
++++ b/src/sage/graphs/graph.py
+@@ -1199,7 +1199,7 @@ class Graph(GenericGraph):
+             self.allow_loops(loops, check=False)
+             self.allow_multiple_edges(multiedges, check=False)
+             self.add_vertices(data.nodes())
+-            self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True))
++            self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True))
+         elif format == 'igraph':
+             if data.is_directed():
+                 raise ValueError("An *undirected* igraph graph was expected. "+
diff --git a/sagemath-pynac-0.7.11.patch b/sagemath-pynac-0.7.11.patch
deleted file mode 100644
index b846d9883287..000000000000
--- a/sagemath-pynac-0.7.11.patch
+++ /dev/null
@@ -1,21 +0,0 @@
---- a/src/sage/libs/pynac/pynac.pxd
-+++ b/src/sage/libs/pynac/pynac.pxd
-@@ -302,7 +302,6 @@ cdef extern from "sage/libs/pynac/wrap.h":
-     bint is_a_fderivative "is_a<GiNaC::fderivative>" (GEx e)
-     bint is_a_function "is_a<GiNaC::function>" (GEx e)
-     bint is_exactly_a_function "is_exactly_a<GiNaC::function>" (GEx e)
--    bint is_a_ncmul "is_a<GiNaC::ncmul>" (GEx e)
- 
-     # Arithmetic
-     int ginac_error()
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -5536,7 +5536,7 @@ cdef class Expression(CommutativeRingElement):
-         cdef unsigned serial
-         if is_a_add(self._gobj):
-             return add_vararg
--        elif is_a_mul(self._gobj) or is_a_ncmul(self._gobj):
-+        elif is_a_mul(self._gobj):
-             return mul_vararg
-         elif is_a_power(self._gobj):
-             return operator.pow