[arch-commits] Commit in sagemath/trunk (13 files)
Antonio Rojas
arojas at archlinux.org
Sun Dec 23 13:32:01 UTC 2018
Date: Sunday, December 23, 2018 @ 13:32:00
Author: arojas
Revision: 417615
Update to 8.5
Added:
sagemath/trunk/sagemath-singular-4.1.1.p4.patch
Modified:
sagemath/trunk/PKGBUILD
sagemath/trunk/sagemath-cremona.patch
sagemath/trunk/sagemath-cypari2.patch
sagemath/trunk/sagemath-env.patch
sagemath/trunk/sagemath-networkx-2.2.patch
sagemath/trunk/sagemath-python3-notebook.patch
sagemath/trunk/sagemath-sphinx-1.8.patch
sagemath/trunk/test-optional.patch
Deleted:
sagemath/trunk/sagemath-cython-0.29.patch
sagemath/trunk/sagemath-gap-4.8.patch
sagemath/trunk/sagemath-lcalc-c++11.patch
sagemath/trunk/sagemath-numpy-1.15.patch
----------------------------------+
PKGBUILD | 50 --
sagemath-cremona.patch | 4
sagemath-cypari2.patch | 318 ------------
sagemath-cython-0.29.patch | 65 --
sagemath-env.patch | 12
sagemath-gap-4.8.patch | 26 -
sagemath-lcalc-c++11.patch | 10
sagemath-networkx-2.2.patch | 16
sagemath-numpy-1.15.patch | 912 -------------------------------------
sagemath-python3-notebook.patch | 2
sagemath-singular-4.1.1.p4.patch | 78 +++
sagemath-sphinx-1.8.patch | 6
test-optional.patch | 2
13 files changed, 115 insertions(+), 1386 deletions(-)
Modified: PKGBUILD
===================================================================
--- PKGBUILD 2018-12-23 13:10:47 UTC (rev 417614)
+++ PKGBUILD 2018-12-23 13:32:00 UTC (rev 417615)
@@ -7,14 +7,14 @@
pkgbase=sagemath
pkgname=(sagemath sagemath-jupyter)
-pkgver=8.4
-pkgrel=4
+pkgver=8.5
+pkgrel=1
pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"
arch=(x86_64)
url="http://www.sagemath.org"
license=(GPL)
depends=(ipython2 ppl palp brial cliquer maxima-ecl gfan sympow nauty python2-rpy2 python2-fpylll python2-psutil python2-cypari2
- python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow python2-future libgap flintqs lcalc lrcalc arb
+ python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow python2-future gap flintqs lcalc lrcalc arb
eclib gmp-ecm zn_poly gd python2-cvxopt pynac linbox m4rie rubiks pari-galdata pari-seadata-small planarity rankwidth tachyon
sage-data-combinatorial_designs sage-data-elliptic_curves sage-data-graphs sage-data-polytopes_db sage-data-conway_polynomials
libgiac libhomfly libbraiding three.js openblas)
@@ -24,7 +24,7 @@
'coin-or-cbc: COIN backend for numerical computations' 'coin-or-csdp: for computing Lovász theta-function of graphs'
'buckygen: for generating fullerene graphs' 'plantri: for generating some classes of graphs' 'benzene: for generating fusenes and benzenoids'
'ffmpeg: to export animations to video' 'imagemagick: to show animations'
- 'coxeter: Coxeter groups implementation' 'gap-4.8-data: for computing Galois groups'
+ 'coxeter: Coxeter groups implementation'
'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes'
'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'
@@ -43,29 +43,25 @@
fes02.patch
sagemath-threejs.patch
sagemath-cremona.patch
- sagemath-lcalc-c++11.patch
- sagemath-gap-4.8.patch
+ sagemath-gap-4.10.patch
sagemath-sphinx-1.8.patch
sagemath-networkx-2.2.patch
- sagemath-cython-0.29.patch
- sagemath-numpy-1.15.patch
- sagemath-cypari2.patch)
-sha256sums=('961a21f60d251531db4b9935cfb6f67f7a207e1029288b4dc5b807f021078ab0'
- '6032ec3d0c983e70d4daa1391bc5daa0c948d350f3697932fc2e8472f0778037'
+ sagemath-cypari2.patch
+ sagemath-singular-4.1.1.p4.patch)
+sha256sums=('369810fac9ad7fb6cb1eb2a82d3e3679edee015778de34c56670d4ee80bde690'
+ 'f26ab0f22d7d916a621f02b9d9fc806eb6825f8d34cdf45accb0e2601c82f049'
'960afe4fcbffe2762b66119b8f14355386ced0d8ee52b535d0dac1dba90d365b'
'ef265f88ceb6caf4aac2d86ea74850861d99a63d11c94fc52b2ce88053c26d1e'
- '769fd5a9c377be61de41e1e30004dadb23818da901cceb6e1bece7712ba7cb83'
- '3a0ebda1df708f263be830751cc5ddb430ca1f685b25b08d4b6592b65b123ebe'
+ 'bd2744c6564bbf71bd6ea3cd7b9031e2126cc1423bcdc1fcc258d90d750a129d'
+ 'f12bd2a53ad51549015093aacc89978f4d796d9ab5bcd3d737aa0d57a5815b54'
'7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94'
'f6b48abf34f64ea3fc092b0f0179e89633f7d3ecc0d62c2acacbfa1217751d63'
- '7efb38ba511037feb3abbd88576323320555ba50235ddc7e3d423ca294dd42ed'
- '5114c912f821900e5bfae1e2cfeb7984de946d0b23e1182b0bf15be1d803dfd0'
- '7304d6242bf0e8241d3d83b772d92f00f905c425b894d36a25c264edca279986'
- '7dd2ab94fddda8e7c2cdd5250642c4cdd00b7702815d88762fbcd68416bacaee'
- '0e3436a68cca4165d3d8519a7d4357b1a59515e9e4cc8bd816a852ca4097e274'
- 'd1af7916e21d0a4de7b3ab5d4054c6b3175b84551ea6639a2680e6102c0b990b'
- '9ef22633ae5d0dde9afe922d5616e49cea4ef6178a4991c96a258981cba674b7'
- 'ef9e2d5b7bd9c2b79121fe771a97963527d97ac9c1d6736d931f00e3eb7f540a')
+ '4c6df9e4e5a7b29ecf6189eda3e5a79f69b6e1b4d29c1b9559663149b8c0af96'
+ '224f8d1db783d7ae25408912c4891687d6a8a1dacc8c5b3a00b725a28d951b6c'
+ '22f5e44a42c8276025b8512f45cac1c36d576c29c7fd9d36fde8b19ff87867d8'
+ '27e2590d3ff8242dd76579defdcf3d17ce54937e1bc8c847089fd3b681e98008'
+ '1677bcaa3fe19bf978b6ffaae7b64b7ec32df63fa3d0e28b179cfa831fcfa896'
+ '482887fe43d89cef3270e89300ab9e2238fa74cd5b7c875688b68fb1b10c4fdf')
prepare(){
cd sage-$pkgver
@@ -83,10 +79,6 @@
patch -p1 -i ../sagemath-python3-notebook.patch
# fix three.js plotting backend
patch -p1 -i ../sagemath-threejs.patch
-# don't force c++98 for lcalc (fixes build with NTL 11)
- patch -p1 -i ../sagemath-lcalc-c++11.patch
-# Adjust paths for gap-4.8
- patch -p1 -i ../sagemath-gap-4.8.patch
# fix introspection with sphinx 1.8
patch -p1 -i ../sagemath-sphinx-1.8.patch
@@ -97,12 +89,12 @@
patch -p1 -i ../sagemath-cremona.patch
# Fix graph generators with networkx 2.2 https://trac.sagemath.org/ticket/26326
patch -p1 -i ../sagemath-networkx-2.2.patch
-# Fix build with cython 0.29 https://trac.sagemath.org/ticket/25292
- patch -p1 -i ../sagemath-cython-0.29.patch
-# Fixes for numpy 1.15 https://trac.sagemath.org/ticket/25260
- patch -p1 -i ../sagemath-numpy-1.15.patch
# Fix build with cypari 2.0 https://trac.sagemath.org/ticket/26442
patch -p1 -i ../sagemath-cypari2.patch
+# Build with GAP 4.10 https://trac.sagemath.org/ticket/22626
+ patch -p1 -i ../sagemath-gap-4.10.patch
+# Fixes for singular 4.1.1p4 https://trac.sagemath.org/ticket/25993
+ patch -p1 -i ../sagemath-singular-4.1.1.p4.patch
# use python2
sed -e 's|sage-python23|python2|' -e 's|#!/usr/bin/env python\b|#!/usr/bin/env python2|' -i src/bin/*
Modified: sagemath-cremona.patch
===================================================================
--- sagemath-cremona.patch 2018-12-23 13:10:47 UTC (rev 417614)
+++ sagemath-cremona.patch 2018-12-23 13:32:00 UTC (rev 417615)
@@ -11,7 +11,7 @@
from sage.env import CREMONA_MINI_DATA_DIR, CREMONA_LARGE_DATA_DIR
from sage.misc.all import walltime
-@@ -825,7 +825,7 @@ class MiniCremonaDatabase(SQLDatabase):
+@@ -835,7 +835,7 @@ class MiniCremonaDatabase(SQLDatabase):
if N < self.largest_conductor():
message = "There is no elliptic curve with label " + label \
+ " in the database"
@@ -20,7 +20,7 @@
message = "There is no elliptic curve with label " + label \
+ " in the currently available databases"
else:
-@@ -1673,7 +1673,7 @@ def CremonaDatabase(name=None,mini=None,set_global=None):
+@@ -1683,7 +1683,7 @@ def CremonaDatabase(name=None,mini=None,set_global=None):
if name is None and not set_global:
return _db
if set_global and name is None:
Modified: sagemath-cypari2.patch
===================================================================
--- sagemath-cypari2.patch 2018-12-23 13:10:47 UTC (rev 417614)
+++ sagemath-cypari2.patch 2018-12-23 13:32:00 UTC (rev 417615)
@@ -1,321 +1,3 @@
-diff --git a/src/sage/rings/finite_rings/element_pari_ffelt.pxd
-b/src/sage/rings/finite_rings/element_pari_ffelt.pxd
-index 10885d4..0b66436 100644
---- a/src/sage/rings/finite_rings/element_pari_ffelt.pxd
-+++ b/src/sage/rings/finite_rings/element_pari_ffelt.pxd
-@@ -1,9 +1,12 @@
- from cypari2.types cimport GEN
- from sage.rings.finite_rings.element_base cimport FinitePolyExtElement
-
-+
- cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
-- cdef GEN val # PARI t_FFELT describing the element
-- cdef void* chunk # memory block containing the data
-- cdef FiniteFieldElement_pari_ffelt _new(FiniteFieldElement_pari_ffelt self)
-- cdef void construct(FiniteFieldElement_pari_ffelt self, GEN g)
-- cdef void construct_from(FiniteFieldElement_pari_ffelt self, object x) except *
-+ # PARI t_FFELT describing the element.
-+ # This holds a reference to a PARI clone.
-+ cdef GEN val
-+
-+ cdef FiniteFieldElement_pari_ffelt _new(self)
-+ cdef void construct(self, GEN g)
-+ cdef int construct_from(self, x) except -1
-diff --git a/src/sage/rings/finite_rings/element_pari_ffelt.pyx
-b/src/sage/rings/finite_rings/element_pari_ffelt.pyx
-index 78a35fe..727a058 100644
---- a/src/sage/rings/finite_rings/element_pari_ffelt.pyx
-+++ b/src/sage/rings/finite_rings/element_pari_ffelt.pyx
-@@ -24,7 +24,7 @@ from cysignals.signals cimport sig_on, sig_off
- from cypari2.paridecl cimport *
- from cypari2.paripriv cimport *
- from sage.libs.pari.convert_gmp cimport _new_GEN_from_mpz_t
--from cypari2.stack cimport new_gen, clear_stack, deepcopy_to_python_heap
-+from cypari2.stack cimport new_gen, new_gen_noclear, clear_stack
- from cypari2.gen cimport Gen as pari_gen, objtogen
-
- from .element_base cimport FinitePolyExtElement
-@@ -316,7 +316,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- 0
- """
-
-- def __init__(FiniteFieldElement_pari_ffelt self, object parent, object x):
-+ def __init__(self, parent, x):
- """
- Initialise ``self`` with the given ``parent`` and value
- converted from ``x``.
-@@ -335,13 +335,14 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- self._parent = parent
- self.construct_from(x)
-
-- def __dealloc__(FiniteFieldElement_pari_ffelt self):
-+ def __dealloc__(self):
- """
-- Cython deconstructor.
-+ Cython destructor.
- """
-- sig_free(self.chunk)
-+ if self.val is not NULL:
-+ gunclone_deep(self.val)
-
-- cdef FiniteFieldElement_pari_ffelt _new(FiniteFieldElement_pari_ffelt self):
-+ cdef FiniteFieldElement_pari_ffelt _new(self):
- """
- Create an empty element with the same parent as ``self``.
- """
-@@ -350,17 +351,17 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- x._parent = self._parent
- return x
-
-- cdef void construct(FiniteFieldElement_pari_ffelt self, GEN g):
-+ cdef void construct(self, GEN g):
- """
- Initialise ``self`` to the FFELT ``g``, reset the PARI stack,
- and call sig_off().
-
- This should be called exactly once on every instance.
- """
-- self.val = deepcopy_to_python_heap(g, &self.chunk)
-+ self.val = gcloneref(g)
- clear_stack()
-
-- cdef void construct_from(FiniteFieldElement_pari_ffelt self, object x) except *:
-+ cdef int construct_from(self, x) except -1:
- """
- Initialise ``self`` to an FFELT constructed from the Sage
- object `x`.
-@@ -424,29 +425,29 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- sig_on()
- if gequal0(x_GEN):
- self.construct(FF_zero(g))
-- return
-+ return 0
- elif gequal1(x_GEN):
- self.construct(FF_1(g))
-- return
-+ return 0
-
- t = typ(x_GEN)
- if t == t_FFELT:
- if FF_samefield(x_GEN, g):
- self.construct(x_GEN)
-- return
-+ return 0
- elif t == t_INT:
- self.construct(_INT_to_FFELT(g, x_GEN))
-- return
-+ return 0
- elif t == t_INTMOD:
- if gequal0(modii(gel(x_GEN, 1), FF_p_i(g))):
- self.construct(_INT_to_FFELT(g, gel(x_GEN, 2)))
-- return
-+ return 0
- elif t == t_FRAC:
- if not gequal0(modii(gel(x_GEN, 2), FF_p_i(g))):
- elt = FF_div(_INT_to_FFELT(g, gel(x_GEN, 1)),
- _INT_to_FFELT(g, gel(x_GEN, 2)))
- self.construct(elt)
-- return
-+ return 0
- sig_off()
- raise TypeError(f"unable to convert PARI {x.type()} to finite field element")
-
-@@ -460,7 +461,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- sig_on()
- if n == 0:
- self.construct(FF_zero(g))
-- return
-+ return 0
- if t == t_FF_FpXQ:
- f = cgetg(n + 2, t_POL)
- set_gel(f, 1, gmael(g, 2, 1))
-@@ -515,7 +516,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- else:
- raise TypeError("no coercion defined")
-
-- def _repr_(FiniteFieldElement_pari_ffelt self):
-+ def _repr_(self):
- """
- Return the string representation of ``self``.
-
-@@ -525,10 +526,9 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- sage: c^20 # indirect doctest
- c^4 + 2*c^3
- """
-- sig_on()
-- return str(new_gen(self.val))
-+ return str(new_gen_noclear(self.val))
-
-- def __hash__(FiniteFieldElement_pari_ffelt self):
-+ def __hash__(self):
- """
- Return the hash of ``self``. This is by definition equal to
- the hash of ``self.polynomial()``.
-@@ -542,7 +542,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- """
- return hash(self.polynomial())
-
-- def __reduce__(FiniteFieldElement_pari_ffelt self):
-+ def __reduce__(self):
- """
- For pickling.
-
-@@ -554,7 +554,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- """
- return unpickle_FiniteFieldElement_pari_ffelt, (self._parent, str(self))
-
-- def __copy__(FiniteFieldElement_pari_ffelt self):
-+ def __copy__(self):
- """
- Return a copy of ``self``.
-
-@@ -701,7 +701,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- (<FiniteFieldElement_pari_ffelt>right).val))
- return x
-
-- def is_zero(FiniteFieldElement_pari_ffelt self):
-+ def is_zero(self):
- """
- Return ``True`` if ``self`` equals 0.
-
-@@ -715,7 +715,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- """
- return bool(FF_equal0(self.val))
-
-- def is_one(FiniteFieldElement_pari_ffelt self):
-+ def is_one(self):
- """
- Return ``True`` if ``self`` equals 1.
-
-@@ -729,7 +729,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- """
- return bool(FF_equal1(self.val))
-
-- def is_unit(FiniteFieldElement_pari_ffelt self):
-+ def is_unit(self):
- """
- Return ``True`` if ``self`` is non-zero.
-
-@@ -743,7 +743,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
-
- __nonzero__ = is_unit
-
-- def __pos__(FiniteFieldElement_pari_ffelt self):
-+ def __pos__(self):
- """
- Unitary positive operator...
-
-@@ -755,7 +755,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- """
- return self
-
-- def __neg__(FiniteFieldElement_pari_ffelt self):
-+ def __neg__(self):
- """
- Negation.
-
-@@ -770,7 +770,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- x.construct(FF_neg_i((<FiniteFieldElement_pari_ffelt>self).val))
- return x
-
-- def __invert__(FiniteFieldElement_pari_ffelt self):
-+ def __invert__(self):
- """
- Return the multiplicative inverse of ``self``.
-
-@@ -791,7 +791,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- x.construct(FF_inv((<FiniteFieldElement_pari_ffelt>self).val))
- return x
-
-- def __pow__(FiniteFieldElement_pari_ffelt self, object exp, object other):
-+ def __pow__(FiniteFieldElement_pari_ffelt self, exp, other):
- """
- Exponentiation.
-
-@@ -836,7 +836,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- x.construct(FF_pow(self.val, (<pari_gen>exp).g))
- return x
-
-- def polynomial(FiniteFieldElement_pari_ffelt self, name=None):
-+ def polynomial(self, name=None):
- """
- Return the unique representative of ``self`` as a polynomial
- over the prime field whose degree is less than the degree of
-@@ -889,7 +889,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- sig_on()
- return self._parent.polynomial_ring(var)(new_gen(FF_minpoly(self.val)))
-
-- def charpoly(FiniteFieldElement_pari_ffelt self, object var='x'):
-+ def charpoly(self, var='x'):
- """
- Return the characteristic polynomial of ``self``.
-
-@@ -907,7 +907,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- sig_on()
- return self._parent.polynomial_ring(var)(new_gen(FF_charpoly(self.val)))
-
-- def is_square(FiniteFieldElement_pari_ffelt self):
-+ def is_square(self):
- """
- Return ``True`` if and only if ``self`` is a square in the
- finite field.
-@@ -938,7 +938,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- sig_off()
- return bool(i)
-
-- def sqrt(FiniteFieldElement_pari_ffelt self, extend=False, all=False):
-+ def sqrt(self, extend=False, all=False):
- """
- Return a square root of ``self``, if it exists.
-
-@@ -1015,7 +1015,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- else:
- raise ValueError("element is not a square")
-
-- def log(FiniteFieldElement_pari_ffelt self, object base):
-+ def log(self, base):
- """
- Return a discrete logarithm of ``self`` with respect to the
- given base.
-@@ -1087,7 +1087,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- x = FF_log(self.val, (<FiniteFieldElement_pari_ffelt>base).val, base_order)
- return Integer(new_gen(x))
-
-- def multiplicative_order(FiniteFieldElement_pari_ffelt self):
-+ def multiplicative_order(self):
- """
- Returns the order of ``self`` in the multiplicative group.
-
-@@ -1106,7 +1106,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- order = FF_order(self.val, NULL)
- return Integer(new_gen(order))
-
-- def lift(FiniteFieldElement_pari_ffelt self):
-+ def lift(self):
- """
- If ``self`` is an element of the prime field, return a lift of
- this element to an integer.
-@@ -1192,10 +1192,6 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- """
- Return a PARI object representing ``self``.
-
-- INPUT:
--
-- - var -- ignored
--
- EXAMPLES::
-
- sage: k.<a> = FiniteField(3^3, impl='pari_ffelt')
-@@ -1203,8 +1199,7 @@ cdef class FiniteFieldElement_pari_ffelt(FinitePolyExtElement):
- sage: b.__pari__()
- a^2 + 2*a + 1
- """
-- sig_on()
-- return new_gen(self.val)
-+ return new_gen_noclear(self.val)
-
- def _pari_init_(self):
- """
diff --git a/src/sage/rings/finite_rings/element_pari_ffelt.pyx b/src/sage/rings/finite_rings/element_pari_ffelt.pyx
index ff73a1f..fba303a 100644
--- a/src/sage/rings/finite_rings/element_pari_ffelt.pyx
Deleted: sagemath-cython-0.29.patch
===================================================================
--- sagemath-cython-0.29.patch 2018-12-23 13:10:47 UTC (rev 417614)
+++ sagemath-cython-0.29.patch 2018-12-23 13:32:00 UTC (rev 417615)
@@ -1,65 +0,0 @@
-diff --git a/src/sage/arith/long.pxd b/src/sage/arith/long.pxd
-index b8cc019..c7a1d8e 100644
---- a/src/sage/arith/long.pxd
-+++ b/src/sage/arith/long.pxd
-@@ -19,7 +19,7 @@ from cpython.object cimport Py_SIZE
- from cpython.int cimport PyInt_AS_LONG
- from cpython.long cimport PyLong_AsLong
- from cpython.number cimport PyNumber_Index, PyIndex_Check
--from cpython.longintrepr cimport PyLongObject, PyLong_SHIFT, digit
-+from cpython.longintrepr cimport py_long, PyLong_SHIFT, digit
-
- from sage.libs.gmp.mpz cimport mpz_fits_slong_p, mpz_get_si
- from sage.rings.integer_fake cimport is_Integer, Integer_AS_MPZ
-@@ -208,7 +208,7 @@ cdef inline bint integer_check_long_py(x, long* value, int* err):
- return 0
-
- # x is a Python "long" (called "int" on Python 3)
-- cdef const digit* D = (<PyLongObject*>x).ob_digit
-+ cdef const digit* D = (<py_long>x).ob_digit
- cdef Py_ssize_t size = Py_SIZE(x)
-
- # We assume that PyLong_SHIFT is 15 on a 32-bit system and 30 on a
-diff --git a/src/sage/libs/gmp/pylong.pyx b/src/sage/libs/gmp/pylong.pyx
-index 168e485..9c214f6 100644
---- a/src/sage/libs/gmp/pylong.pyx
-+++ b/src/sage/libs/gmp/pylong.pyx
-@@ -28,7 +28,7 @@ AUTHORS:
- from cpython.object cimport Py_SIZE
- from cpython.int cimport PyInt_FromLong
- from cpython.long cimport PyLong_FromLong
--from cpython.longintrepr cimport _PyLong_New, PyLongObject, digit, PyLong_SHIFT
-+from cpython.longintrepr cimport _PyLong_New, py_long, digit, PyLong_SHIFT
- from .mpz cimport *
-
- cdef extern from *:
-@@ -54,7 +54,7 @@ cdef mpz_get_pylong_large(mpz_srcptr z):
- cdef size_t nbits = mpz_sizeinbase(z, 2)
- cdef size_t pylong_size = (nbits + PyLong_SHIFT - 1) // PyLong_SHIFT
- L = _PyLong_New(pylong_size)
-- mpz_export((<PyLongObject*>L).ob_digit, NULL,
-+ mpz_export(L.ob_digit, NULL,
- -1, sizeof(digit), 0, PyLong_nails, z)
- if mpz_sgn(z) < 0:
- # Set correct size (use a pointer to hack around Cython's
-@@ -91,7 +91,7 @@ cdef int mpz_set_pylong(mpz_ptr z, L) except -1:
- if pylong_size < 0:
- pylong_size = -pylong_size
- mpz_import(z, pylong_size, -1, sizeof(digit), 0, PyLong_nails,
-- (<PyLongObject*>L).ob_digit)
-+ (<py_long>L).ob_digit)
- if Py_SIZE(L) < 0:
- mpz_neg(z, z)
-
-diff --git a/src/setup.py b/src/setup.py
-index 6a89cf8..bc8fe12 100755
---- a/src/setup.py
-+++ b/src/setup.py
-@@ -284,6 +284,7 @@ class sage_build_cython(Command):
- cdivision=True,
- embedsignature=True,
- fast_getattr=True,
-+ language_level="2",
- preliminary_late_includes_cy28=True,
- profile=self.profile,
- )
Modified: sagemath-env.patch
===================================================================
--- sagemath-env.patch 2018-12-23 13:10:47 UTC (rev 417614)
+++ sagemath-env.patch 2018-12-23 13:32:00 UTC (rev 417615)
@@ -79,13 +79,12 @@
# The compilers are set in order of priority by
# 1) environment variables
-@@ -296,8 +296,9 @@
+@@ -296,8 +296,8 @@
export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
export SAGE_SPKG_SCRIPTS="$SAGE_LOCAL/var/lib/sage/scripts"
export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
-export SAGE_SRC="$SAGE_ROOT/src"
-export SAGE_DOC_SRC="$SAGE_SRC/doc"
-+export GAP_ROOT_DIR="/usr/lib/gap-4.8"
+export SAGE_SRC="$SAGE_LOCAL/lib/python2.7/site-packages"
+export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
export SAGE_DOC="$SAGE_SHARE/doc/sage"
@@ -161,12 +160,3 @@
try:
sitepackages_dirs = site.getsitepackages()
-@@ -164,7 +164,7 @@
- _add_variable_or_fallback('GRAPHS_DATA_DIR', opj('$SAGE_SHARE','graphs'))
- _add_variable_or_fallback('ELLCURVE_DATA_DIR',opj('$SAGE_SHARE','ellcurves'))
- _add_variable_or_fallback('POLYTOPE_DATA_DIR',opj('$SAGE_SHARE','reflexive_polytopes'))
--_add_variable_or_fallback('GAP_ROOT_DIR', opj('$SAGE_LOCAL','gap','latest'))
-+_add_variable_or_fallback('GAP_ROOT_DIR', opj('$SAGE_LOCAL','lib','gap-4.8'))
- _add_variable_or_fallback('THEBE_DIR', opj('$SAGE_SHARE','thebe'))
- _add_variable_or_fallback('COMBINATORIAL_DESIGN_DATA_DIR', opj('$SAGE_SHARE', 'combinatorial_designs'))
- _add_variable_or_fallback('CREMONA_MINI_DATA_DIR', opj('$SAGE_SHARE', 'cremona'))
Deleted: sagemath-gap-4.8.patch
===================================================================
--- sagemath-gap-4.8.patch 2018-12-23 13:10:47 UTC (rev 417614)
+++ sagemath-gap-4.8.patch 2018-12-23 13:32:00 UTC (rev 417615)
@@ -1,26 +0,0 @@
-diff --git a/src/sage/interfaces/gap.py b/src/sage/interfaces/gap.py
-index 177fc1b6eb..51c67bdd09 100644
---- a/src/sage/interfaces/gap.py
-+++ b/src/sage/interfaces/gap.py
-@@ -202,7 +202,7 @@ import string
-
- first_try = True
-
--gap_cmd = "gap -r"
-+gap_cmd = "gap-4.8 -r"
- if platform.processor() == 'ia64' and os.path.exists('/usr/bin/prctl'):
- # suppress unaligned access to 0x..., ip=0x... warnings
- gap_cmd = 'prctl --unaligned=silent ' + gap_cmd
-diff --git a/src/sage/libs/gap/util.pyx b/src/sage/libs/gap/util.pyx
-index 7bffcfc00d..51dad178d5 100644
---- a/src/sage/libs/gap/util.pyx
-+++ b/src/sage/libs/gap/util.pyx
-@@ -170,7 +170,7 @@ def gap_root():
- if os.path.exists(GAP_ROOT_DIR):
- return GAP_ROOT_DIR
- print('The gap-4.5.5.spkg (or later) seems to be not installed!')
-- gap_sh = open(os.path.join(SAGE_LOCAL, 'bin', 'gap')).read().splitlines()
-+ gap_sh = open(os.path.join(SAGE_LOCAL, 'bin', 'gap-4.8')).read().splitlines()
- gapdir = filter(lambda dir:dir.strip().startswith('GAP_DIR'), gap_sh)[0]
- gapdir = gapdir.split('"')[1]
- gapdir = gapdir.replace('$SAGE_LOCAL', SAGE_LOCAL)
Deleted: sagemath-lcalc-c++11.patch
===================================================================
--- sagemath-lcalc-c++11.patch 2018-12-23 13:10:47 UTC (rev 417614)
+++ sagemath-lcalc-c++11.patch 2018-12-23 13:32:00 UTC (rev 417615)
@@ -1,10 +0,0 @@
---- a/src/sage/libs/lcalc/lcalc_Lfunction.pxd
-+++ b/src/sage/libs/lcalc/lcalc_Lfunction.pxd
-@@ -1,6 +1,5 @@
- # Lcalc requires GNU extensions, it does not strictly conform to any
- # C++ standard: https://trac.sagemath.org/ticket/23341
--# distutils: extra_compile_args = -std=gnu++98
-
- cdef extern from "lcalc_sage.h":
- ctypedef struct doublevec "std::vector<double>":
-
Modified: sagemath-networkx-2.2.patch
===================================================================
--- sagemath-networkx-2.2.patch 2018-12-23 13:10:47 UTC (rev 417614)
+++ sagemath-networkx-2.2.patch 2018-12-23 13:32:00 UTC (rev 417615)
@@ -150,7 +150,7 @@
import networkx
return Graph(networkx.powerlaw_cluster_graph(n, m, p, seed=seed))
-@@ -838,7 +838,7 @@ def RandomLobster(n, p, q, seed=None):
+@@ -1239,7 +1239,7 @@ def RandomLobster(n, p, q, seed=None):
- ``q`` - probability of adding an edge (claw) to the
arms
@@ -159,7 +159,7 @@
EXAMPLES: We show the edge list of a random graph with 3 backbone
nodes and probabilities `p = 0.7` and `q = 0.3`::
-@@ -852,7 +852,7 @@ def RandomLobster(n, p, q, seed=None):
+@@ -1253,7 +1253,7 @@ def RandomLobster(n, p, q, seed=None):
sage: G.show() # long time
"""
if seed is None:
@@ -168,7 +168,7 @@
import networkx
return Graph(networkx.random_lobster(n, p, q, seed=seed))
-@@ -943,7 +943,7 @@ def RandomTreePowerlaw(n, gamma=3, tries=100, seed=None):
+@@ -1344,7 +1344,7 @@ def RandomTreePowerlaw(n, gamma=3, tries=100, seed=None):
- ``tries`` - number of attempts to adjust sequence to
make a tree
@@ -177,7 +177,7 @@
EXAMPLES: We show the edge list of a random graph with 10 nodes and
a power law exponent of 2.
-@@ -960,7 +960,7 @@ def RandomTreePowerlaw(n, gamma=3, tries=100, seed=None):
+@@ -1361,7 +1361,7 @@ def RandomTreePowerlaw(n, gamma=3, tries=100, seed=None):
....: G.show() # random output, long time
"""
if seed is None:
@@ -186,7 +186,7 @@
import networkx
try:
return Graph(networkx.random_powerlaw_tree(n, gamma, seed=seed, tries=tries))
-@@ -981,7 +981,7 @@ def RandomRegular(d, n, seed=None):
+@@ -1382,7 +1382,7 @@ def RandomRegular(d, n, seed=None):
- ``d`` - degree
@@ -195,7 +195,7 @@
EXAMPLES: We show the edge list of a random graph with 8 nodes each
-@@ -1009,7 +1009,7 @@ def RandomRegular(d, n, seed=None):
+@@ -1410,7 +1410,7 @@ def RandomRegular(d, n, seed=None):
regular graphs quickly. Prob. and Comp. 8 (1999), pp 377-396.
"""
if seed is None:
@@ -204,7 +204,7 @@
import networkx
try:
N = networkx.random_regular_graph(d, n, seed=seed)
-@@ -1034,7 +1034,7 @@ def RandomShell(constructor, seed=None):
+@@ -1435,7 +1435,7 @@ def RandomShell(constructor, seed=None):
- ``d`` - the ratio of inter (next) shell edges to
intra shell edges
@@ -213,7 +213,7 @@
EXAMPLES::
-@@ -1044,7 +1044,7 @@ def RandomShell(constructor, seed=None):
+@@ -1445,7 +1445,7 @@ def RandomShell(constructor, seed=None):
sage: G.show() # long time
"""
if seed is None:
Deleted: sagemath-numpy-1.15.patch
===================================================================
--- sagemath-numpy-1.15.patch 2018-12-23 13:10:47 UTC (rev 417614)
+++ sagemath-numpy-1.15.patch 2018-12-23 13:32:00 UTC (rev 417615)
@@ -1,912 +0,0 @@
-diff --git a/src/doc/en/faq/faq-usage.rst b/src/doc/en/faq/faq-usage.rst
-index d64a4ac..ee729b0 100644
---- a/src/doc/en/faq/faq-usage.rst
-+++ b/src/doc/en/faq/faq-usage.rst
-@@ -341,7 +341,7 @@ ints. For example::
- sage: RealNumber = float; Integer = int
- sage: from scipy import stats
- sage: stats.ttest_ind(list([1,2,3,4,5]),list([2,3,4,5,.6]))
-- Ttest_indResult(statistic=0.076752955645333687, pvalue=0.94070490247380478)
-+ Ttest_indResult(statistic=0.0767529..., pvalue=0.940704...)
- sage: stats.uniform(0,15).ppf([0.5,0.7])
- array([ 7.5, 10.5])
-
-diff --git a/src/doc/en/thematic_tutorials/numerical_sage/cvxopt.rst
-b/src/doc/en/thematic_tutorials/numerical_sage/cvxopt.rst
-index 314811c..e5f54ec 100644
---- a/src/doc/en/thematic_tutorials/numerical_sage/cvxopt.rst
-+++ b/src/doc/en/thematic_tutorials/numerical_sage/cvxopt.rst
-@@ -48,11 +48,13 @@ we could do the following.
- sage: B = numpy.array([1.0]*5)
- sage: B.shape=(5,1)
- sage: print(B)
-- [[ 1.]
-- [ 1.]
-- [ 1.]
-- [ 1.]
-- [ 1.]]
-+ [[1.]
-+ [1.]
-+ [1.]
-+ [1.]
-+ [1.]]
-+
-+
- sage: print(A)
- [ 2.00e+00 3.00e+00 0 0 0 ]
- [ 3.00e+00 0 4.00e+00 0 6.00e+00]
-diff --git a/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst
-b/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst
-index 5b89cd7..e50b2ea 100644
---- a/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst
-+++ b/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst
-@@ -84,7 +84,7 @@ well as take slices
- sage: l[3]
- 3.0
- sage: l[3:6]
-- array([ 3., 4., 5.])
-+ array([3., 4., 5.])
-
- You can do basic arithmetic operations
-
-@@ -147,11 +147,11 @@ also do matrix vector multiplication, and matrix addition
- sage: n = numpy.matrix([[1,2],[3,4]],dtype=float)
- sage: v = numpy.array([[1],[2]],dtype=float)
- sage: n*v
-- matrix([[ 5.],
-- [ 11.]])
-+ matrix([[ 5.],
-+ [11.]])
- sage: n+n
-- matrix([[ 2., 4.],
-- [ 6., 8.]])
-+ matrix([[2., 4.],
-+ [6., 8.]])
-
- If ``n`` was created with :meth:`numpy.array`, then to do matrix vector
- multiplication, you would use ``numpy.dot(n,v)``.
-@@ -170,11 +170,11 @@ to manipulate
- 22., 23., 24.])
- sage: n.shape=(5,5)
- sage: n
-- array([[ 0., 1., 2., 3., 4.],
-- [ 5., 6., 7., 8., 9.],
-- [ 10., 11., 12., 13., 14.],
-- [ 15., 16., 17., 18., 19.],
-- [ 20., 21., 22., 23., 24.]])
-+ array([[ 0., 1., 2., 3., 4.],
-+ [ 5., 6., 7., 8., 9.],
-+ [10., 11., 12., 13., 14.],
-+ [15., 16., 17., 18., 19.],
-+ [20., 21., 22., 23., 24.]])
-
- This changes the one-dimensional array into a `5\times 5` array.
-
-@@ -187,8 +187,8 @@ NumPy arrays can be sliced as well
- sage: n=numpy.array(range(25),dtype=float)
- sage: n.shape=(5,5)
- sage: n[2:4,1:3]
-- array([[ 11., 12.],
-- [ 16., 17.]])
-+ array([[11., 12.],
-+ [16., 17.]])
-
- It is important to note that the sliced matrices are references to
- the original
-@@ -224,8 +224,8 @@ Some particularly useful commands are
-
- sage: x=numpy.arange(0,2,.1,dtype=float)
- sage: x
-- array([ 0. , 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1. ,
-- 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9])
-+ array([0. , 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1. , 1.1, 1.2,
-+ 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9])
-
- You can see that :meth:`numpy.arange` creates an array of floats increasing by 0.1
- from 0 to 2. There is a useful command :meth:`numpy.r_` that is best explained by example
-@@ -240,10 +240,11 @@ from 0 to 2. There is a useful command :meth:`numpy.r_` that is best explained b
- sage: Integer=int
- sage: n=r_[0.0:5.0]
- sage: n
-- array([ 0., 1., 2., 3., 4.])
-+ array([0., 1., 2., 3., 4.])
- sage: n=r_[0.0:5.0, [0.0]*5]
- sage: n
-- array([ 0., 1., 2., 3., 4., 0., 0., 0., 0., 0.])
-+ array([0., 1., 2., 3., 4., 0., 0., 0., 0., 0.])
-+
-
- :meth:`numpy.r_` provides a shorthand for constructing NumPy arrays efficiently.
- Note in the above ``0.0:5.0`` was shorthand for ``0.0, 1.0, 2.0, 3.0, 4.0``.
-@@ -255,7 +256,7 @@ intervals. We can do this as follows
- ::
-
- sage: r_[0.0:5.0:11*j]
-- array([ 0. , 0.5, 1. , 1.5, 2. , 2.5, 3. , 3.5, 4. , 4.5, 5. ])
-+ array([0. , 0.5, 1. , 1.5, 2. , 2.5, 3. , 3.5, 4. , 4.5, 5. ])
-
- The notation ``0.0:5.0:11*j`` expands to a list of 11 equally space
- points between 0 and 5 including both endpoints. Note that ``j`` is the
-@@ -287,23 +288,23 @@ an equally spaced grid with `\Delta x = \Delta y = .25` for
- sage: y=numpy.r_[0.0:1.0:5*j]
- sage: xx,yy= meshgrid(x,y)
- sage: xx
-- array([[ 0. , 0.25, 0.5 , 0.75, 1. ],
-- [ 0. , 0.25, 0.5 , 0.75, 1. ],
-- [ 0. , 0.25, 0.5 , 0.75, 1. ],
-- [ 0. , 0.25, 0.5 , 0.75, 1. ],
-- [ 0. , 0.25, 0.5 , 0.75, 1. ]])
-+ array([[0. , 0.25, 0.5 , 0.75, 1. ],
-+ [0. , 0.25, 0.5 , 0.75, 1. ],
-+ [0. , 0.25, 0.5 , 0.75, 1. ],
-+ [0. , 0.25, 0.5 , 0.75, 1. ],
-+ [0. , 0.25, 0.5 , 0.75, 1. ]])
- sage: yy
-- array([[ 0. , 0. , 0. , 0. , 0. ],
-- [ 0.25, 0.25, 0.25, 0.25, 0.25],
-- [ 0.5 , 0.5 , 0.5 , 0.5 , 0.5 ],
-- [ 0.75, 0.75, 0.75, 0.75, 0.75],
-- [ 1. , 1. , 1. , 1. , 1. ]])
-+ array([[0. , 0. , 0. , 0. , 0. ],
-+ [0.25, 0.25, 0.25, 0.25, 0.25],
-+ [0.5 , 0.5 , 0.5 , 0.5 , 0.5 ],
-+ [0.75, 0.75, 0.75, 0.75, 0.75],
-+ [1. , 1. , 1. , 1. , 1. ]])
- sage: f(xx,yy)
-- array([[ 0. , 0.0625, 0.25 , 0.5625, 1. ],
-- [ 0.0625, 0.125 , 0.3125, 0.625 , 1.0625],
-- [ 0.25 , 0.3125, 0.5 , 0.8125, 1.25 ],
-- [ 0.5625, 0.625 , 0.8125, 1.125 , 1.5625],
-- [ 1. , 1.0625, 1.25 , 1.5625, 2. ]])
-+ array([[0. , 0.0625, 0.25 , 0.5625, 1. ],
-+ [0.0625, 0.125 , 0.3125, 0.625 , 1.0625],
-+ [0.25 , 0.3125, 0.5 , 0.8125, 1.25 ],
-+ [0.5625, 0.625 , 0.8125, 1.125 , 1.5625],
-+ [1. , 1.0625, 1.25 , 1.5625, 2. ]])
-
- You can see that :meth:`numpy.meshgrid` produces a pair of matrices, here denoted
- `xx` and `yy`, such that `(xx[i,j],yy[i,j])` has coordinates
-@@ -324,7 +325,7 @@ equation `Ax=b` do
- sage: b=numpy.array(range(1,6))
- sage: x=linalg.solve(A,b)
- sage: numpy.dot(A,x)
-- array([ 1., 2., 3., 4., 5.])
-+ array([1., 2., 3., 4., 5.])
-
- This creates a random 5x5 matrix ``A``, and solves `Ax=b` where
- ``b=[0.0,1.0,2.0,3.0,4.0]``. There are many other routines in the :mod:`numpy.linalg`
-diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx
-index 60f37f7..4ac3ded 100644
---- a/src/sage/calculus/riemann.pyx
-+++ b/src/sage/calculus/riemann.pyx
-@@ -1191,30 +1191,30 @@ cpdef complex_to_spiderweb(np.ndarray[COMPLEX_T, ndim = 2] z_values,
- sage: zval = numpy.array([[0, 1, 1000],[.2+.3j,1,-.3j],[0,0,0]],dtype = numpy.complex128)
- sage: deriv = numpy.array([[.1]],dtype = numpy.float64)
- sage: complex_to_spiderweb(zval, deriv,deriv, 4,4,[0,0,0],1,False,0.001)
-- array([[[ 1., 1., 1.],
-- [ 1., 1., 1.],
-- [ 1., 1., 1.]],
-+ array([[[1., 1., 1.],
-+ [1., 1., 1.],
-+ [1., 1., 1.]],
- <BLANKLINE>
-- [[ 1., 1., 1.],
-- [ 0., 0., 0.],
-- [ 1., 1., 1.]],
-+ [[1., 1., 1.],
-+ [0., 0., 0.],
-+ [1., 1., 1.]],
- <BLANKLINE>
-- [[ 1., 1., 1.],
-- [ 1., 1., 1.],
-- [ 1., 1., 1.]]])
-+ [[1., 1., 1.],
-+ [1., 1., 1.],
-+ [1., 1., 1.]]])
-
- sage: complex_to_spiderweb(zval, deriv,deriv, 4,4,[0,0,0],1,True,0.001)
-- array([[[ 1. , 1. , 1. ],
-- [ 1. , 0.05558355, 0.05558355],
-- [ 0.17301243, 0. , 0. ]],
-+ array([[[1. , 1. , 1. ],
-+ [1. , 0.05558355, 0.05558355],
-+ [0.17301243, 0. , 0. ]],
- <BLANKLINE>
-- [[ 1. , 0.96804683, 0.48044583],
-- [ 0. , 0. , 0. ],
-- [ 0.77351965, 0.5470393 , 1. ]],
-+ [[1. , 0.96804683, 0.48044583],
-+ [0. , 0. , 0. ],
-+ [0.77351965, 0.5470393 , 1. ]],
- <BLANKLINE>
-- [[ 1. , 1. , 1. ],
-- [ 1. , 1. , 1. ],
-- [ 1. , 1. , 1. ]]])
-+ [[1. , 1. , 1. ],
-+ [1. , 1. , 1. ],
-+ [1. , 1. , 1. ]]])
- """
- cdef Py_ssize_t i, j, imax, jmax
- cdef FLOAT_T x, y, mag, arg, width, target, precision, dmag, darg
-@@ -1279,14 +1279,14 @@ cpdef complex_to_rgb(np.ndarray[COMPLEX_T, ndim = 2] z_values):
- sage: from sage.calculus.riemann import complex_to_rgb
- sage: import numpy
- sage: complex_to_rgb(numpy.array([[0, 1, 1000]], dtype = numpy.complex128))
-- array([[[ 1. , 1. , 1. ],
-- [ 1. , 0.05558355, 0.05558355],
-- [ 0.17301243, 0. , 0. ]]])
-+ array([[[1. , 1. , 1. ],
-+ [1. , 0.05558355, 0.05558355],
-+ [0.17301243, 0. , 0. ]]])
-
- sage: complex_to_rgb(numpy.array([[0, 1j, 1000j]], dtype = numpy.complex128))
-- array([[[ 1. , 1. , 1. ],
-- [ 0.52779177, 1. , 0.05558355],
-- [ 0.08650622, 0.17301243, 0. ]]])
-+ array([[[1. , 1. , 1. ],
-+ [0.52779177, 1. , 0.05558355],
-+ [0.08650622, 0.17301243, 0. ]]])
-
-
- TESTS::
-diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index 37fb7aa..2569c0d 100644
---- a/src/sage/combinat/fully_packed_loop.py
-+++ b/src/sage/combinat/fully_packed_loop.py
-@@ -72,11 +72,11 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
- sage: _make_color_list(5, ['blue', 'red'])
- ['blue', 'red', 'blue', 'red', 'blue']
- sage: _make_color_list(5, color_map='summer')
-- [(0.0, 0.5, 0.40000000000000002),
-- (0.25098039215686274, 0.62549019607843137, 0.40000000000000002),
-- (0.50196078431372548, 0.75098039215686274, 0.40000000000000002),
-- (0.75294117647058822, 0.87647058823529411, 0.40000000000000002),
-- (1.0, 1.0, 0.40000000000000002)]
-+ [(0.0, 0.5, 0.4),
-+ (0.25098039215686274, 0.6254901960784314, 0.4),
-+ (0.5019607843137255, 0.7509803921568627, 0.4),
-+ (0.7529411764705882, 0.8764705882352941, 0.4),
-+ (1.0, 1.0, 0.4)]
- sage: _make_color_list(8, ['blue', 'red'], randomize=True)
- ['blue', 'blue', 'red', 'blue', 'red', 'red', 'red', 'blue']
- """
-diff --git a/src/sage/finance/time_series.pyx b/src/sage/finance/time_series.pyx
-index 2877936..3ab0282 100644
---- a/src/sage/finance/time_series.pyx
-+++ b/src/sage/finance/time_series.pyx
-@@ -111,8 +111,8 @@ cdef class TimeSeries:
-
- sage: import numpy
- sage: v = numpy.array([[1,2], [3,4]], dtype=float); v
-- array([[ 1., 2.],
-- [ 3., 4.]])
-+ array([[1., 2.],
-+ [3., 4.]])
- sage: finance.TimeSeries(v)
- [1.0000, 2.0000, 3.0000, 4.0000]
- sage: finance.TimeSeries(v[:,0])
-@@ -2100,14 +2100,14 @@ cdef class TimeSeries:
-
- sage: w[0] = 20
- sage: w
-- array([ 20. , -3. , 4.5, -2. ])
-+ array([20. , -3. , 4.5, -2. ])
- sage: v
- [20.0000, -3.0000, 4.5000, -2.0000]
-
- If you want a separate copy do not give the ``copy=False`` option. ::
-
- sage: z = v.numpy(); z
-- array([ 20. , -3. , 4.5, -2. ])
-+ array([20. , -3. , 4.5, -2. ])
- sage: z[0] = -10
- sage: v
- [20.0000, -3.0000, 4.5000, -2.0000]
-diff --git a/src/sage/functions/hyperbolic.py b/src/sage/functions/hyperbolic.py
-index aff552f..7a6df93 100644
---- a/src/sage/functions/hyperbolic.py
-+++ b/src/sage/functions/hyperbolic.py
-@@ -214,7 +214,7 @@ class Function_coth(GinacFunction):
- sage: import numpy
- sage: a = numpy.arange(2, 5)
- sage: coth(a)
-- array([ 1.03731472, 1.00496982, 1.00067115])
-+ array([1.03731472, 1.00496982, 1.00067115])
- """
- return 1.0 / tanh(x)
-
-@@ -267,7 +267,7 @@ class Function_sech(GinacFunction):
- sage: import numpy
- sage: a = numpy.arange(2, 5)
- sage: sech(a)
-- array([ 0.26580223, 0.09932793, 0.03661899])
-+ array([0.26580223, 0.09932793, 0.03661899])
- """
- return 1.0 / cosh(x)
-
-@@ -318,7 +318,7 @@ class Function_csch(GinacFunction):
- sage: import numpy
- sage: a = numpy.arange(2, 5)
- sage: csch(a)
-- array([ 0.27572056, 0.09982157, 0.03664357])
-+ array([0.27572056, 0.09982157, 0.03664357])
- """
- return 1.0 / sinh(x)
-
-@@ -586,7 +586,7 @@ class Function_arccoth(GinacFunction):
- sage: import numpy
- sage: a = numpy.arange(2,5)
- sage: acoth(a)
-- array([ 0.54930614, 0.34657359, 0.25541281])
-+ array([0.54930614, 0.34657359, 0.25541281])
- """
- return arctanh(1.0 / x)
-
-diff --git a/src/sage/functions/orthogonal_polys.py b/src/sage/functions/orthogonal_polys.py
-index bae363c..386ba4d 100644
---- a/src/sage/functions/orthogonal_polys.py
-+++ b/src/sage/functions/orthogonal_polys.py
-@@ -810,12 +810,12 @@ class Func_chebyshev_T(ChebyshevFunction):
- sage: z2 = numpy.array([[1,2],[1,2]])
- sage: z3 = numpy.array([1,2,3.])
- sage: chebyshev_T(1,z)
-- array([ 1., 2.])
-+ array([1., 2.])
- sage: chebyshev_T(1,z2)
-- array([[ 1., 2.],
-- [ 1., 2.]])
-+ array([[1., 2.],
-+ [1., 2.]])
- sage: chebyshev_T(1,z3)
-- array([ 1., 2., 3.])
-+ array([1., 2., 3.])
- sage: chebyshev_T(z,0.1)
- array([ 0.1 , -0.98])
- """
-@@ -1095,12 +1095,12 @@ class Func_chebyshev_U(ChebyshevFunction):
- sage: z2 = numpy.array([[1,2],[1,2]])
- sage: z3 = numpy.array([1,2,3.])
- sage: chebyshev_U(1,z)
-- array([ 2., 4.])
-+ array([2., 4.])
- sage: chebyshev_U(1,z2)
-- array([[ 2., 4.],
-- [ 2., 4.]])
-+ array([[2., 4.],
-+ [2., 4.]])
- sage: chebyshev_U(1,z3)
-- array([ 2., 4., 6.])
-+ array([2., 4., 6.])
- sage: chebyshev_U(z,0.1)
- array([ 0.2 , -0.96])
- """
-diff --git a/src/sage/functions/other.py b/src/sage/functions/other.py
-index 1883daa..9885222 100644
---- a/src/sage/functions/other.py
-+++ b/src/sage/functions/other.py
-@@ -389,7 +389,7 @@ class Function_ceil(BuiltinFunction):
- sage: import numpy
- sage: a = numpy.linspace(0,2,6)
- sage: ceil(a)
-- array([ 0., 1., 1., 2., 2., 2.])
-+ array([0., 1., 1., 2., 2., 2.])
-
- Test pickling::
-
-@@ -553,7 +553,7 @@ class Function_floor(BuiltinFunction):
- sage: import numpy
- sage: a = numpy.linspace(0,2,6)
- sage: floor(a)
-- array([ 0., 0., 0., 1., 1., 2.])
-+ array([0., 0., 0., 1., 1., 2.])
- sage: floor(x)._sympy_()
- floor(x)
-
-@@ -869,7 +869,7 @@ def sqrt(x, *args, **kwds):
- sage: import numpy
- sage: a = numpy.arange(2,5)
- sage: sqrt(a)
-- array([ 1.41421356, 1.73205081, 2. ])
-+ array([1.41421356, 1.73205081, 2. ])
- """
- if isinstance(x, float):
- return math.sqrt(x)
-diff --git a/src/sage/functions/spike_function.py b/src/sage/functions/spike_function.py
-index 1e021de..56635ca 100644
---- a/src/sage/functions/spike_function.py
-+++ b/src/sage/functions/spike_function.py
-@@ -157,7 +157,7 @@ class SpikeFunction:
- sage: S = spike_function([(-3,4),(-1,1),(2,3)]); S
- A spike function with spikes at [-3.0, -1.0, 2.0]
- sage: P = S.plot_fft_abs(8)
-- sage: p = P[0]; p.ydata
-+ sage: p = P[0]; p.ydata # abs tol 1e-8
- [5.0, 5.0, 3.367958691924177, 3.367958691924177, 4.123105625617661, 4.123105625617661, 4.759921664218055, 4.759921664218055]
- """
- w = self.vector(samples = samples, xmin=xmin, xmax=xmax)
-@@ -176,8 +176,8 @@ class SpikeFunction:
- sage: S = spike_function([(-3,4),(-1,1),(2,3)]); S
- A spike function with spikes at [-3.0, -1.0, 2.0]
- sage: P = S.plot_fft_arg(8)
-- sage: p = P[0]; p.ydata
-- [0.0, 0.0, -0.211524990023434..., -0.211524990023434..., 0.244978663126864..., 0.244978663126864..., -0.149106180027477..., -0.149106180027477...]
-+ sage: p = P[0]; p.ydata # abs tol 1e-8
-+ [0.0, 0.0, -0.211524990023434, -0.211524990023434, 0.244978663126864, 0.244978663126864, -0.149106180027477, -0.149106180027477]
- """
- w = self.vector(samples = samples, xmin=xmin, xmax=xmax)
- xmin, xmax = self._ranges(xmin, xmax)
-diff --git a/src/sage/functions/trig.py b/src/sage/functions/trig.py
-index 501e7ff..5f76091 100644
---- a/src/sage/functions/trig.py
-+++ b/src/sage/functions/trig.py
-@@ -724,7 +724,7 @@ class Function_arccot(GinacFunction):
- sage: import numpy
- sage: a = numpy.arange(2, 5)
- sage: arccot(a)
-- array([ 0.46364761, 0.32175055, 0.24497866])
-+ array([0.46364761, 0.32175055, 0.24497866])
- """
- return math.pi/2 - arctan(x)
-
-@@ -780,7 +780,7 @@ class Function_arccsc(GinacFunction):
- sage: import numpy
- sage: a = numpy.arange(2, 5)
- sage: arccsc(a)
-- array([ 0.52359878, 0.33983691, 0.25268026])
-+ array([0.52359878, 0.33983691, 0.25268026])
- """
- return arcsin(1.0/x)
-
-@@ -838,7 +838,7 @@ class Function_arcsec(GinacFunction):
- sage: import numpy
- sage: a = numpy.arange(2, 5)
- sage: arcsec(a)
-- array([ 1.04719755, 1.23095942, 1.31811607])
-+ array([1.04719755, 1.23095942, 1.31811607])
- """
- return arccos(1.0/x)
-
-@@ -913,13 +913,13 @@ class Function_arctan2(GinacFunction):
- sage: a = numpy.linspace(1, 3, 3)
- sage: b = numpy.linspace(3, 6, 3)
- sage: atan2(a, b)
-- array([ 0.32175055, 0.41822433, 0.46364761])
-+ array([0.32175055, 0.41822433, 0.46364761])
-
- sage: atan2(1,a)
-- array([ 0.78539816, 0.46364761, 0.32175055])
-+ array([0.78539816, 0.46364761, 0.32175055])
-
- sage: atan2(a, 1)
-- array([ 0.78539816, 1.10714872, 1.24904577])
-+ array([0.78539816, 1.10714872, 1.24904577])
-
- TESTS::
-
-diff --git a/src/sage/matrix/constructor.pyx b/src/sage/matrix/constructor.pyx
-index 12136f1..491bf22 100644
---- a/src/sage/matrix/constructor.pyx
-+++ b/src/sage/matrix/constructor.pyx
-@@ -503,8 +503,8 @@ def matrix(*args, **kwds):
- [7 8 9]
- Full MatrixSpace of 3 by 3 dense matrices over Integer Ring
- sage: n = matrix(QQ, 2, 2, [1, 1/2, 1/3, 1/4]).numpy(); n
-- array([[ 1. , 0.5 ],
-- [ 0.33333333, 0.25 ]])
-+ array([[1. , 0.5 ],
-+ [0.33333333, 0.25 ]])
- sage: matrix(QQ, n)
- [ 1 1/2]
- [1/3 1/4]
-diff --git a/src/sage/matrix/matrix_double_dense.pyx b/src/sage/matrix/matrix_double_dense.pyx
-index c4d7368..8d51651 100644
---- a/src/sage/matrix/matrix_double_dense.pyx
-+++ b/src/sage/matrix/matrix_double_dense.pyx
-@@ -606,6 +606,9 @@ cdef class Matrix_double_dense(Matrix_dense):
- [ 3.0 + 9.0*I 4.0 + 16.0*I 5.0 + 25.0*I]
- [6.0 + 36.0*I 7.0 + 49.0*I 8.0 + 64.0*I]
- sage: B.condition()
-+ doctest:warning
-+ ...
-+ ComplexWarning: Casting complex values to real discards the imaginary part
- 203.851798...
- sage: B.condition(p='frob')
- 203.851798...
-@@ -654,9 +657,7 @@ cdef class Matrix_double_dense(Matrix_dense):
- True
- sage: B = A.change_ring(CDF)
- sage: B.condition()
-- Traceback (most recent call last):
-- ...
-- LinAlgError: Singular matrix
-+ +Infinity
-
- Improper values of ``p`` are caught. ::
-
-@@ -2519,7 +2520,7 @@ cdef class Matrix_double_dense(Matrix_dense):
- sage: P.is_unitary(algorithm='orthonormal')
- Traceback (most recent call last):
- ...
-- ValueError: failed to create intent(cache|hide)|optional array-- must have defined dimensions but got (0,)
-+ error: ((lwork==-1)||(lwork >= MAX(1,2*n))) failed for 3rd keyword lwork: zgees:lwork=0
-
- TESTS::
-
-@@ -3635,8 +3636,8 @@ cdef class Matrix_double_dense(Matrix_dense):
- [0.0 1.0 2.0]
- [3.0 4.0 5.0]
- sage: m.numpy()
-- array([[ 0., 1., 2.],
-- [ 3., 4., 5.]])
-+ array([[0., 1., 2.],
-+ [3., 4., 5.]])
-
- Alternatively, numpy automatically calls this function (via
- the magic :meth:`__array__` method) to convert Sage matrices
-@@ -3647,16 +3648,16 @@ cdef class Matrix_double_dense(Matrix_dense):
- [0.0 1.0 2.0]
- [3.0 4.0 5.0]
- sage: numpy.array(m)
-- array([[ 0., 1., 2.],
-- [ 3., 4., 5.]])
-+ array([[0., 1., 2.],
-+ [3., 4., 5.]])
- sage: numpy.array(m).dtype
- dtype('float64')
- sage: m = matrix(CDF, 2, range(6)); m
- [0.0 1.0 2.0]
- [3.0 4.0 5.0]
- sage: numpy.array(m)
-- array([[ 0.+0.j, 1.+0.j, 2.+0.j],
-- [ 3.+0.j, 4.+0.j, 5.+0.j]])
-+ array([[0.+0.j, 1.+0.j, 2.+0.j],
-+ [3.+0.j, 4.+0.j, 5.+0.j]])
- sage: numpy.array(m).dtype
- dtype('complex128')
-
-diff --git a/src/sage/matrix/special.py b/src/sage/matrix/special.py
-index ccbd208..c3f9a65 100644
---- a/src/sage/matrix/special.py
-+++ b/src/sage/matrix/special.py
-@@ -706,7 +706,7 @@ def diagonal_matrix(arg0=None, arg1=None, arg2=None, sparse=True):
-
- sage: import numpy
- sage: entries = numpy.array([1.2, 5.6]); entries
-- array([ 1.2, 5.6])
-+ array([1.2, 5.6])
- sage: A = diagonal_matrix(3, entries); A
- [1.2 0.0 0.0]
- [0.0 5.6 0.0]
-@@ -716,7 +716,7 @@ def diagonal_matrix(arg0=None, arg1=None, arg2=None, sparse=True):
-
- sage: j = numpy.complex(0,1)
- sage: entries = numpy.array([2.0+j, 8.1, 3.4+2.6*j]); entries
-- array([ 2.0+1.j , 8.1+0.j , 3.4+2.6j])
-+ array([2. +1.j , 8.1+0.j , 3.4+2.6j])
- sage: A = diagonal_matrix(entries); A
- [2.0 + 1.0*I 0.0 0.0]
- [ 0.0 8.1 0.0]
-diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx
-index 37d92c1..955d083 100644
---- a/src/sage/modules/free_module_element.pyx
-+++ b/src/sage/modules/free_module_element.pyx
-@@ -988,7 +988,7 @@ cdef class FreeModuleElement(Vector): # abstract base class
- sage: v.numpy()
- array([1, 2, 5/6], dtype=object)
- sage: v.numpy(dtype=float)
-- array([ 1. , 2. , 0.83333333])
-+ array([1. , 2. , 0.83333333])
- sage: v.numpy(dtype=int)
- array([1, 2, 0])
- sage: import numpy
-@@ -999,7 +999,7 @@ cdef class FreeModuleElement(Vector): # abstract base class
- be more efficient but may have unintended consequences::
-
- sage: v.numpy(dtype=None)
-- array([ 1. , 2. , 0.83333333])
-+ array([1. , 2. , 0.83333333])
-
- sage: w = vector(ZZ, [0, 1, 2^63 -1]); w
- (0, 1, 9223372036854775807)
-diff --git a/src/sage/modules/vector_double_dense.pyx b/src/sage/modules/vector_double_dense.pyx
-index 39fc297..2badf98 100644
---- a/src/sage/modules/vector_double_dense.pyx
-+++ b/src/sage/modules/vector_double_dense.pyx
-@@ -807,13 +807,13 @@ cdef class Vector_double_dense(FreeModuleElement):
-
- sage: v = vector(CDF,4,range(4))
- sage: v.numpy()
-- array([ 0.+0.j, 1.+0.j, 2.+0.j, 3.+0.j])
-+ array([0.+0.j, 1.+0.j, 2.+0.j, 3.+0.j])
- sage: v = vector(CDF,0)
- sage: v.numpy()
- array([], dtype=complex128)
- sage: v = vector(RDF,4,range(4))
- sage: v.numpy()
-- array([ 0., 1., 2., 3.])
-+ array([0., 1., 2., 3.])
- sage: v = vector(RDF,0)
- sage: v.numpy()
- array([], dtype=float64)
-@@ -823,11 +823,11 @@ cdef class Vector_double_dense(FreeModuleElement):
- sage: import numpy
- sage: v = vector(CDF, 3, range(3))
- sage: v.numpy()
-- array([ 0.+0.j, 1.+0.j, 2.+0.j])
-+ array([0.+0.j, 1.+0.j, 2.+0.j])
- sage: v.numpy(dtype=numpy.float64)
-- array([ 0., 1., 2.])
-+ array([0., 1., 2.])
- sage: v.numpy(dtype=numpy.float32)
-- array([ 0., 1., 2.], dtype=float32)
-+ array([0., 1., 2.], dtype=float32)
- """
- if dtype is None or dtype is self._vector_numpy.dtype:
- from copy import copy
-diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
-index ad9693d..758fb70 100644
---- a/src/sage/plot/complex_plot.pyx
-+++ b/src/sage/plot/complex_plot.pyx
-@@ -61,9 +61,9 @@ cdef inline double mag_to_lightness(double r):
-
- sage: from sage.plot.complex_plot import complex_to_rgb
- sage: complex_to_rgb([[0, 1, 10]])
-- array([[[ 0. , 0. , 0. ],
-- [ 0.77172568, 0. , 0. ],
-- [ 1. , 0.22134776, 0.22134776]]])
-+ array([[[0. , 0. , 0. ],
-+ [0.77172568, 0. , 0. ],
-+ [1. , 0.22134776, 0.22134776]]])
- """
- return atan(log(sqrt(r)+1)) * (4/PI) - 1
-
-@@ -82,13 +82,13 @@ def complex_to_rgb(z_values):
-
- sage: from sage.plot.complex_plot import complex_to_rgb
- sage: complex_to_rgb([[0, 1, 1000]])
-- array([[[ 0. , 0. , 0. ],
-- [ 0.77172568, 0. , 0. ],
-- [ 1. , 0.64421177, 0.64421177]]])
-+ array([[[0. , 0. , 0. ],
-+ [0.77172568, 0. , 0. ],
-+ [1. , 0.64421177, 0.64421177]]])
- sage: complex_to_rgb([[0, 1j, 1000j]])
-- array([[[ 0. , 0. , 0. ],
-- [ 0.38586284, 0.77172568, 0. ],
-- [ 0.82210588, 1. , 0.64421177]]])
-+ array([[[0. , 0. , 0. ],
-+ [0.38586284, 0.77172568, 0. ],
-+ [0.82210588, 1. , 0.64421177]]])
- """
- import numpy
- cdef unsigned int i, j, imax, jmax
-diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
-index 5d28473..fc4b204 100644
---- a/src/sage/plot/histogram.py
-+++ b/src/sage/plot/histogram.py
-@@ -53,10 +53,17 @@ class Histogram(GraphicPrimitive):
- """
- import numpy as np
- self.datalist=np.asarray(datalist,dtype=float)
-+ if 'normed' in options:
-+ from sage.misc.superseded import deprecation
-+ deprecation(25260, "the 'normed' option is deprecated. Use 'density' instead.")
- if 'linestyle' in options:
- from sage.plot.misc import get_matplotlib_linestyle
- options['linestyle'] = get_matplotlib_linestyle(
- options['linestyle'], return_type='long')
-+ if options.get('range', None):
-+ # numpy.histogram performs type checks on "range" so this must be
-+ # actual floats
-+ options['range'] = [float(x) for x in options['range']]
- GraphicPrimitive.__init__(self, options)
-
- def get_minmax_data(self):
-@@ -80,10 +87,14 @@ class Histogram(GraphicPrimitive):
- {'xmax': 4.0, 'xmin': 0, 'ymax': 2, 'ymin': 0}
-
- TESTS::
--
- sage: h = histogram([10,3,5], normed=True)[0]
-- sage: h.get_minmax_data() # rel tol 1e-15
-- {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.4761904761904765, 'ymin': 0}
-+ doctest:warning...:
-+ DeprecationWarning: the 'normed' option is deprecated. Use 'density' instead.
-+ See https://trac.sagemath.org/25260 for details.
-+ sage: h.get_minmax_data()
-+ doctest:warning ...:
-+ VisibleDeprecationWarning: Passing `normed=True` on non-uniform bins has always been broken, and computes neither the probability density function nor the probability mass function. The result is only correct if the bins are uniform, when density=True will produce the same result anyway. The argument will be removed in a future version of numpy.
-+ {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
- """
- import numpy
-
-@@ -152,7 +163,7 @@ class Histogram(GraphicPrimitive):
- 'rwidth': 'The relative width of the bars as a fraction of the bin width',
- 'cumulative': '(True or False) If True, then a histogram is computed in which each bin gives the counts in that bin plus all bins for smaller values. Negative values give a reversed direction of accumulation.',
- 'range': 'A list [min, max] which define the range of the histogram. Values outside of this range are treated as outliers and omitted from counts.',
-- 'normed': 'Deprecated alias for density',
-+ 'normed': 'Deprecated. Use density instead.',
- 'density': '(True or False) If True, the counts are normalized to form a probability density. (n/(len(x)*dbin)',
- 'weights': 'A sequence of weights the same length as the data list. If supplied, then each value contributes its associated weight to the bin count.',
- 'stacked': '(True or False) If True, multiple data are stacked on top of each other.',
-@@ -199,7 +210,7 @@ class Histogram(GraphicPrimitive):
- subplot.hist(self.datalist.transpose(), **options)
-
-
-- at options(aspect_ratio='automatic',align='mid', weights=None, range=None, bins=10, edgecolor='black')
-+ at options(aspect_ratio='automatic', align='mid', weights=None, range=None, bins=10, edgecolor='black')
- def histogram(datalist, **options):
- """
- Computes and draws the histogram for list(s) of numerical data.
-@@ -231,8 +242,9 @@ def histogram(datalist, **options):
- - ``linewidth`` -- (float) width of the lines defining the bars
- - ``linestyle`` -- (default: 'solid') Style of the line. One of 'solid'
- or '-', 'dashed' or '--', 'dotted' or ':', 'dashdot' or '-.'
-- - ``density`` -- (boolean - default: False) If True, the counts are
-- normalized to form a probability density.
-+ - ``density`` -- (boolean - default: False) If True, the result is the
-+ value of the probability density function at the bin, normalized such
-+ that the integral over the range is 1.
- - ``range`` -- A list [min, max] which define the range of the
- histogram. Values outside of this range are treated as outliers and
- omitted from counts
-diff --git a/src/sage/plot/line.py b/src/sage/plot/line.py
-index 23f5e61..18695bb 100644
---- a/src/sage/plot/line.py
-+++ b/src/sage/plot/line.py
-@@ -502,14 +502,9 @@ def line2d(points, **options):
- from sage.plot.all import Graphics
- from sage.plot.plot import xydata_from_point_list
- from sage.rings.all import CC, CDF
-- if points in CC or points in CDF:
-- pass
-- else:
-- try:
-- if not points:
-- return Graphics()
-- except ValueError: # numpy raises a ValueError if not empty
-- pass
-+ points = list(points) # make sure points is a python list
-+ if len(points) == 0:
-+ return Graphics()
- xdata, ydata = xydata_from_point_list(points)
- g = Graphics()
- g._set_extra_kwds(Graphics._extract_kwds_for_show(options))
-diff --git a/src/sage/plot/plot_field.py b/src/sage/plot/plot_field.py
-index 0025098..23c8090 100644
---- a/src/sage/plot/plot_field.py
-+++ b/src/sage/plot/plot_field.py
-@@ -49,9 +49,10 @@ class PlotField(GraphicPrimitive):
- sage: r.xpos_array
- [0.0, 0.0, 1.0, 1.0]
- sage: r.yvec_array
-- masked_array(data = [0.0 0.70710678118... 0.70710678118... 0.89442719...],
-- mask = [False False False False],
-- fill_value = 1e+20)
-+ masked_array(data=[0.0, 0.70710678118..., 0.70710678118...,
-+ 0.89442719...],
-+ mask=[False, False, False, False],
-+ fill_value=1e+20)
-
- TESTS:
-
-diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
-index f3da57c..3806f4b 100644
---- a/src/sage/plot/streamline_plot.py
-+++ b/src/sage/plot/streamline_plot.py
-@@ -38,16 +38,14 @@ class StreamlinePlot(GraphicPrimitive):
- sage: r.options()['plot_points']
- 2
- sage: r.xpos_array
-- array([ 0., 1.])
-+ array([0., 1.])
- sage: r.yvec_array
-- masked_array(data =
-- [[1.0 1.0]
-- [0.5403023058681398 0.5403023058681398]],
-- mask =
-- [[False False]
-- [False False]],
-- fill_value = 1e+20)
-- <BLANKLINE>
-+ masked_array(
-+ data=[[1.0, 1.0],
-+ [0.5403023058681398, 0.5403023058681398]],
-+ mask=[[False, False],
-+ [False, False]],
-+ fill_value=1e+20)
-
- TESTS:
-
-diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index 1b119e3..3290b00 100644
---- a/src/sage/probability/probability_distribution.pyx
-+++ b/src/sage/probability/probability_distribution.pyx
-@@ -130,7 +130,17 @@ cdef class ProbabilityDistribution:
- 0.0,
- 1.4650000000000003]
- sage: b
-- [0.0, 0.20000000000000001, 0.40000000000000002, 0.60000000000000009, 0.80000000000000004, 1.0, 1.2000000000000002, 1.4000000000000001, 1.6000000000000001, 1.8, 2.0]
-+ [0.0,
-+ 0.2,
-+ 0.4,
-+ 0.6000000000000001,
-+ 0.8,
-+ 1.0,
-+ 1.2000000000000002,
-+ 1.4000000000000001,
-+ 1.6,
-+ 1.8,
-+ 2.0]
- """
- import pylab
- l = [float(self.get_random_element()) for _ in range(num_samples)]
-diff --git a/src/sage/rings/rational.pyx b/src/sage/rings/rational.pyx
-index 75e0861..8a7e7e9 100644
---- a/src/sage/rings/rational.pyx
-+++ b/src/sage/rings/rational.pyx
-@@ -1041,7 +1041,7 @@ cdef class Rational(sage.structure.element.FieldElement):
- dtype('O')
-
- sage: numpy.array([1, 1/2, 3/4])
-- array([ 1. , 0.5 , 0.75])
-+ array([1. , 0.5 , 0.75])
- """
- if mpz_cmp_ui(mpq_denref(self.value), 1) == 0:
- if mpz_fits_slong_p(mpq_numref(self.value)):
-diff --git a/src/sage/rings/real_mpfr.pyx b/src/sage/rings/real_mpfr.pyx
-index 9b90c88..1ce05b9 100644
---- a/src/sage/rings/real_mpfr.pyx
-+++ b/src/sage/rings/real_mpfr.pyx
-@@ -1439,7 +1439,7 @@ cdef class RealNumber(sage.structure.element.RingElement):
-
- sage: import numpy
- sage: numpy.arange(10.0)
-- array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.])
-+ array([0., 1., 2., 3., 4., 5., 6., 7., 8., 9.])
- sage: numpy.array([1.0, 1.1, 1.2]).dtype
- dtype('float64')
- sage: numpy.array([1.000000000000000000000000000000000000]).dtype
-diff --git a/src/sage/schemes/elliptic_curves/height.py b/src/sage/schemes/elliptic_curves/height.py
-index de31fe9..7a33ea6 100644
---- a/src/sage/schemes/elliptic_curves/height.py
-+++ b/src/sage/schemes/elliptic_curves/height.py
-@@ -1627,18 +1627,18 @@ class EllipticCurveCanonicalHeight:
- even::
-
- sage: H.wp_on_grid(v,4)
-- array([[ 25.43920182, 5.28760943, 5.28760943, 25.43920182],
-- [ 6.05099485, 1.83757786, 1.83757786, 6.05099485],
-- [ 6.05099485, 1.83757786, 1.83757786, 6.05099485],
-- [ 25.43920182, 5.28760943, 5.28760943, 25.43920182]])
-+ array([[25.43920182, 5.28760943, 5.28760943, 25.43920182],
-+ [ 6.05099485, 1.83757786, 1.83757786, 6.05099485],
-+ [ 6.05099485, 1.83757786, 1.83757786, 6.05099485],
-+ [25.43920182, 5.28760943, 5.28760943, 25.43920182]])
-
- The array of values on the half-grid::
-
- sage: H.wp_on_grid(v,4,True)
-- array([[ 25.43920182, 5.28760943],
-- [ 6.05099485, 1.83757786],
-- [ 6.05099485, 1.83757786],
-- [ 25.43920182, 5.28760943]])
-+ array([[25.43920182, 5.28760943],
-+ [ 6.05099485, 1.83757786],
-+ [ 6.05099485, 1.83757786],
-+ [25.43920182, 5.28760943]])
- """
- tau = self.tau(v)
- fk, err = self.fk_intervals(v, 15, CDF)
-diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 9da3800..d61e74b 100644
---- a/src/sage/symbolic/ring.pyx
-+++ b/src/sage/symbolic/ring.pyx
-@@ -1136,7 +1136,7 @@ cdef class NumpyToSRMorphism(Morphism):
- sage: cos(numpy.int('2'))
- cos(2)
- sage: numpy.cos(numpy.int('2'))
-- -0.41614683654714241
-+ -0.4161468365471424
- """
- cdef _intermediate_ring
Modified: sagemath-python3-notebook.patch
===================================================================
--- sagemath-python3-notebook.patch 2018-12-23 13:10:47 UTC (rev 417614)
+++ sagemath-python3-notebook.patch 2018-12-23 13:32:00 UTC (rev 417615)
@@ -16,7 +16,7 @@
index 3912b8cdf5..bd40cdadda 100644
--- a/src/sage/repl/ipython_kernel/install.py
+++ b/src/sage/repl/ipython_kernel/install.py
-@@ -292,7 +292,6 @@ def have_prerequisites(debug=True):
+@@ -303,7 +303,6 @@ def have_prerequisites(debug=True):
True
"""
try:
Added: sagemath-singular-4.1.1.p4.patch
===================================================================
--- sagemath-singular-4.1.1.p4.patch (rev 0)
+++ sagemath-singular-4.1.1.p4.patch 2018-12-23 13:32:00 UTC (rev 417615)
@@ -0,0 +1,78 @@
+diff --git a/src/sage/libs/singular/function.pyx b/src/sage/libs/singular/function.pyx
+index 87342e8..9a0d37d 100644
+--- a/src/sage/libs/singular/function.pyx
++++ b/src/sage/libs/singular/function.pyx
+@@ -1258,7 +1258,7 @@ cdef class SingularFunction(SageObject):
+ Traceback (most recent call last):
+ ...
+ RuntimeError: error in Singular function call 'size':
+- Wrong number of arguments (got 2 arguments, arity code is 300)
++ Wrong number of arguments (got 2 arguments, arity code is 302)
+ sage: size('foobar', ring=P)
+ 6
+
+@@ -1667,17 +1667,17 @@ def singular_function(name):
+ Traceback (most recent call last):
+ ...
+ RuntimeError: error in Singular function call 'factorize':
+- Wrong number of arguments (got 0 arguments, arity code is 303)
++ Wrong number of arguments (got 0 arguments, arity code is 305)
+ sage: factorize(f, 1, 2)
+ Traceback (most recent call last):
+ ...
+ RuntimeError: error in Singular function call 'factorize':
+- Wrong number of arguments (got 3 arguments, arity code is 303)
++ Wrong number of arguments (got 3 arguments, arity code is 305)
+ sage: factorize(f, 1, 2, 3)
+ Traceback (most recent call last):
+ ...
+ RuntimeError: error in Singular function call 'factorize':
+- Wrong number of arguments (got 4 arguments, arity code is 303)
++ Wrong number of arguments (got 4 arguments, arity code is 305)
+
+ The Singular function ``list`` can be called with any number of
+ arguments::
+diff --git a/src/sage/algebras/letterplace/free_algebra_element_letterplace.pyx b/src/sage/algebras/letterplace/free_algebra_element_letterplace.pyx
+index 8f6576b477..deaf0f5769 100644
+--- a/src/sage/algebras/letterplace/free_algebra_element_letterplace.pyx
++++ b/src/sage/algebras/letterplace/free_algebra_element_letterplace.pyx
+@@ -447,7 +447,7 @@ cdef class FreeAlgebraElement_letterplace(AlgebraElement):
+ return True
+ for i from 0 <= i < p_d-s_d:
+ s_poly = singular_system("stest",s_poly,1,
+- A._degbound,A.__ngens,ring=P)
++ ring=P)
+ if P.monomial_divides(s_poly,p_poly):
+ return True
+ return False
+@@ -601,7 +601,7 @@ cdef class FreeAlgebraElement_letterplace(AlgebraElement):
+ # we must put the polynomials into the same ring
+ left._poly = A._current_ring(left._poly)
+ right._poly = A._current_ring(right._poly)
+- rshift = singular_system("stest",right._poly,left._poly.degree(),A._degbound,A.__ngens, ring=A._current_ring)
++ rshift = singular_system("stest",right._poly,left._poly.degree(), ring=A._current_ring)
+ return FreeAlgebraElement_letterplace(A,left._poly*rshift, check=False)
+
+ def __pow__(FreeAlgebraElement_letterplace self, int n, k):
+@@ -629,7 +629,7 @@ cdef class FreeAlgebraElement_letterplace(AlgebraElement):
+ q = p = self._poly
+ cdef int i
+ for i from 0<i<n:
+- q = singular_system("stest",q,d,A._degbound,A.__ngens,
++ q = singular_system("stest",q,d,
+ ring=A._current_ring)
+ p *= q
+ return FreeAlgebraElement_letterplace(A, p, check=False)
+diff --git a/src/sage/algebras/letterplace/free_algebra_letterplace.pyx b/src/sage/algebras/letterplace/free_algebra_letterplace.pyx
+index 7a8400052e..b3474fa07c 100644
+--- a/src/sage/algebras/letterplace/free_algebra_letterplace.pyx
++++ b/src/sage/algebras/letterplace/free_algebra_letterplace.pyx
+@@ -683,7 +683,7 @@ cdef class FreeAlgebra_letterplace(Algebra):
+ degbound = self._degbound
+ cdef list G = [C(x._poly) for x in g]
+ for y in G:
+- out.extend([y]+[singular_system("stest",y,n+1,degbound,ngens,ring=C) for n in xrange(d-y.degree())])
++ out.extend([y]+[singular_system("stest",y,n+1,ring=C) for n in xrange(d-y.degree())])
+ return C.ideal(out)
+
+ ###########################
Modified: sagemath-sphinx-1.8.patch
===================================================================
--- sagemath-sphinx-1.8.patch 2018-12-23 13:10:47 UTC (rev 417614)
+++ sagemath-sphinx-1.8.patch 2018-12-23 13:32:00 UTC (rev 417615)
@@ -1,6 +1,6 @@
--- a/src/sage/misc/sphinxify.py 2018-09-14 20:13:32.788831484 +0200
+++ b/src/sage/misc/sphinxify.py 2018-09-14 20:14:07.142478667 +0200
-@@ -64,6 +64,7 @@
+@@ -68,6 +68,7 @@
sage: assert n == len(sys.path)
"""
srcdir = mkdtemp()
@@ -8,7 +8,7 @@
base_name = os.path.join(srcdir, 'docstring')
rst_name = base_name + '.rst'
-@@ -71,7 +72,7 @@
+@@ -75,7 +76,7 @@
suffix = '.html'
else:
suffix = '.txt'
@@ -17,7 +17,7 @@
with open(rst_name, 'w') as filed:
filed.write(docstring)
-@@ -89,7 +90,7 @@
+@@ -93,7 +94,7 @@
import sys
old_sys_path = list(sys.path) # Sphinx modifies sys.path
Modified: test-optional.patch
===================================================================
--- test-optional.patch 2018-12-23 13:10:47 UTC (rev 417614)
+++ test-optional.patch 2018-12-23 13:32:00 UTC (rev 417615)
@@ -1,6 +1,6 @@
--- src/sage/doctest/control.py.orig 2016-10-20 19:39:53.714618246 +0200
+++ src/sage/doctest/control.py 2016-10-20 19:40:15.158049920 +0200
-@@ -346,22 +346,6 @@
+@@ -347,22 +347,6 @@
# Special case to run all optional tests
options.optional = True
else:
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