sage: 8.3 -> 8.4.beta0

pkgs/applications/science/math/sage/patches/numpy-1.14.3.patch

@@ -1,5 +1,5 @@
 diff --git a/src/doc/en/faq/faq-usage.rst b/src/doc/en/faq/faq-usage.rst
-index 79b4205fd3..9a89bd2136 100644
+index 2347a1190d..f5b0fe71a4 100644
 --- a/src/doc/en/faq/faq-usage.rst
 +++ b/src/doc/en/faq/faq-usage.rst
 @@ -338,7 +338,7 @@ ints. For example::
@@ -248,7 +248,7 @@ index df85cce43d..34ea164be0 100644
  
      TESTS::
 diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index 61b1003002..4baee9cbbd 100644
+index 0a9bd61267..d2193cc2d6 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):
@@ -269,10 +269,10 @@ index 61b1003002..4baee9cbbd 100644
          ['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 c37700d14e..49b7298d0b 100644
+index 28779365df..3ab0282861 100644
 --- a/src/sage/finance/time_series.pyx
 +++ b/src/sage/finance/time_series.pyx
-@@ -109,8 +109,8 @@ cdef class TimeSeries:
+@@ -111,8 +111,8 @@ cdef class TimeSeries:
  
              sage: import numpy
              sage: v = numpy.array([[1,2], [3,4]], dtype=float); v
@@ -283,7 +283,7 @@ index c37700d14e..49b7298d0b 100644
              sage: finance.TimeSeries(v)
              [1.0000, 2.0000, 3.0000, 4.0000]
              sage: finance.TimeSeries(v[:,0])
-@@ -2098,14 +2098,14 @@ cdef class TimeSeries:
+@@ -2100,14 +2100,14 @@ cdef class TimeSeries:
  
              sage: w[0] = 20
              sage: w
@@ -379,10 +379,10 @@ index 017c85a96f..33fbb499c5 100644
              array([ 0.2 , -0.96])
          """
 diff --git a/src/sage/functions/other.py b/src/sage/functions/other.py
-index 679384c907..d63b295a4c 100644
+index 1883daa3e6..9885222817 100644
 --- a/src/sage/functions/other.py
 +++ b/src/sage/functions/other.py
-@@ -390,7 +390,7 @@ class Function_ceil(BuiltinFunction):
+@@ -389,7 +389,7 @@ class Function_ceil(BuiltinFunction):
              sage: import numpy
              sage: a = numpy.linspace(0,2,6)
              sage: ceil(a)
@@ -391,7 +391,7 @@ index 679384c907..d63b295a4c 100644
  
          Test pickling::
  
-@@ -539,7 +539,7 @@ class Function_floor(BuiltinFunction):
+@@ -553,7 +553,7 @@ class Function_floor(BuiltinFunction):
              sage: import numpy
              sage: a = numpy.linspace(0,2,6)
              sage: floor(a)
@@ -400,7 +400,7 @@ index 679384c907..d63b295a4c 100644
              sage: floor(x)._sympy_()
              floor(x)
  
-@@ -840,7 +840,7 @@ def sqrt(x, *args, **kwds):
+@@ -869,7 +869,7 @@ def sqrt(x, *args, **kwds):
              sage: import numpy
              sage: a = numpy.arange(2,5)
              sage: sqrt(a)
@@ -410,10 +410,10 @@ index 679384c907..d63b295a4c 100644
          if isinstance(x, float):
              return math.sqrt(x)
 diff --git a/src/sage/functions/trig.py b/src/sage/functions/trig.py
-index e7e7a311cd..e7ff78a9de 100644
+index 501e7ff6b6..5f760912f0 100644
 --- a/src/sage/functions/trig.py
 +++ b/src/sage/functions/trig.py
-@@ -731,7 +731,7 @@ class Function_arccot(GinacFunction):
+@@ -724,7 +724,7 @@ class Function_arccot(GinacFunction):
              sage: import numpy
              sage: a = numpy.arange(2, 5)
              sage: arccot(a)
@@ -422,7 +422,7 @@ index e7e7a311cd..e7ff78a9de 100644
          """
          return math.pi/2 - arctan(x)
  
-@@ -787,7 +787,7 @@ class Function_arccsc(GinacFunction):
+@@ -780,7 +780,7 @@ class Function_arccsc(GinacFunction):
              sage: import numpy
              sage: a = numpy.arange(2, 5)
              sage: arccsc(a)
@@ -431,7 +431,7 @@ index e7e7a311cd..e7ff78a9de 100644
          """
          return arcsin(1.0/x)
  
-@@ -845,7 +845,7 @@ class Function_arcsec(GinacFunction):
+@@ -838,7 +838,7 @@ class Function_arcsec(GinacFunction):
              sage: import numpy
              sage: a = numpy.arange(2, 5)
              sage: arcsec(a)
@@ -440,7 +440,7 @@ index e7e7a311cd..e7ff78a9de 100644
          """
          return arccos(1.0/x)
  
-@@ -920,13 +920,13 @@ class Function_arctan2(GinacFunction):
+@@ -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)
@@ -458,10 +458,10 @@ index e7e7a311cd..e7ff78a9de 100644
          TESTS::
  
 diff --git a/src/sage/matrix/constructor.pyx b/src/sage/matrix/constructor.pyx
-index 19a1d37df0..5780dfae1c 100644
+index 12136f1773..491bf22e62 100644
 --- a/src/sage/matrix/constructor.pyx
 +++ b/src/sage/matrix/constructor.pyx
-@@ -494,8 +494,8 @@ class MatrixFactory(object):
+@@ -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
@@ -473,10 +473,10 @@ index 19a1d37df0..5780dfae1c 100644
          [  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 48e0a8a97f..1be5d35b19 100644
+index 66e54a79a4..5e1d270b02 100644
 --- a/src/sage/matrix/matrix_double_dense.pyx
 +++ b/src/sage/matrix/matrix_double_dense.pyx
-@@ -2546,7 +2546,7 @@ cdef class Matrix_double_dense(Matrix_dense):
+@@ -2519,7 +2519,7 @@ cdef class Matrix_double_dense(Matrix_dense):
              sage: P.is_unitary(algorithm='orthonormal')
              Traceback (most recent call last):
              ...
@@ -485,7 +485,7 @@ index 48e0a8a97f..1be5d35b19 100644
  
          TESTS::
  
-@@ -3662,8 +3662,8 @@ cdef class Matrix_double_dense(Matrix_dense):
+@@ -3635,8 +3635,8 @@ cdef class Matrix_double_dense(Matrix_dense):
              [0.0 1.0 2.0]
              [3.0 4.0 5.0]
              sage: m.numpy()
@@ -496,7 +496,7 @@ index 48e0a8a97f..1be5d35b19 100644
  
          Alternatively, numpy automatically calls this function (via
          the magic :meth:`__array__` method) to convert Sage matrices
-@@ -3674,16 +3674,16 @@ cdef class Matrix_double_dense(Matrix_dense):
+@@ -3647,16 +3647,16 @@ cdef class Matrix_double_dense(Matrix_dense):
              [0.0 1.0 2.0]
              [3.0 4.0 5.0]
              sage: numpy.array(m)
@@ -518,10 +518,10 @@ index 48e0a8a97f..1be5d35b19 100644
              dtype('complex128')
  
 diff --git a/src/sage/matrix/special.py b/src/sage/matrix/special.py
-index c698ba5e97..b743bab354 100644
+index ccbd208810..c3f9a65093 100644
 --- a/src/sage/matrix/special.py
 +++ b/src/sage/matrix/special.py
-@@ -705,7 +705,7 @@ def diagonal_matrix(arg0=None, arg1=None, arg2=None, sparse=True):
+@@ -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
@@ -530,7 +530,7 @@ index c698ba5e97..b743bab354 100644
          sage: A = diagonal_matrix(3, entries); A
          [1.2 0.0 0.0]
          [0.0 5.6 0.0]
-@@ -715,7 +715,7 @@ def diagonal_matrix(arg0=None, arg1=None, arg2=None, sparse=True):
+@@ -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
@@ -540,10 +540,10 @@ index c698ba5e97..b743bab354 100644
          [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 230f142117..2ab1c0ae68 100644
+index 3b9a37e9ee..3f5ea14a9d 100644
 --- a/src/sage/modules/free_module_element.pyx
 +++ b/src/sage/modules/free_module_element.pyx
-@@ -982,7 +982,7 @@ cdef class FreeModuleElement(Vector):   # abstract base class
+@@ -987,7 +987,7 @@ cdef class FreeModuleElement(Vector):   # abstract base class
              sage: v.numpy()
              array([1, 2, 5/6], dtype=object)
              sage: v.numpy(dtype=float)
@@ -552,7 +552,7 @@ index 230f142117..2ab1c0ae68 100644
              sage: v.numpy(dtype=int)
              array([1, 2, 0])
              sage: import numpy
-@@ -993,7 +993,7 @@ cdef class FreeModuleElement(Vector):   # abstract base class
+@@ -998,7 +998,7 @@ cdef class FreeModuleElement(Vector):   # abstract base class
          be more efficient but may have unintended consequences::
  
              sage: v.numpy(dtype=None)
@@ -596,22 +596,6 @@ index 39fc2970de..2badf98284 100644
          """
          if dtype is None or dtype is self._vector_numpy.dtype:
              from copy import copy
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index 17b5ebb84b..92ce35c502 100644
---- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -486,9 +486,9 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
-                 else:
-                     min = optimize.fmin_tnc(f, x0, approx_grad=True, bounds=cons, messages=0, **args)[0]
-         elif isinstance(cons[0], function_type) or isinstance(cons[0], Expression):
--            min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args)
-+            min = optimize.fmin_cobyla(f, x0, cons, disp=0, **args)
-     elif isinstance(cons, function_type) or isinstance(cons, Expression):
--        min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args)
-+        min = optimize.fmin_cobyla(f, x0, cons, disp=0, **args)
-     return vector(RDF, min)
- 
- 
 diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
 index ad9693da62..758fb709b7 100644
 --- a/src/sage/plot/complex_plot.pyx
@@ -718,7 +702,7 @@ index f3da57c370..3806f4b32f 100644
          TESTS:
  
 diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index f66cd898b9..35995886d5 100644
+index 797ca571bc..38a707b7fb 100644
 --- a/src/sage/probability/probability_distribution.pyx
 +++ b/src/sage/probability/probability_distribution.pyx
 @@ -130,7 +130,17 @@ cdef class ProbabilityDistribution:
@@ -741,10 +725,10 @@ index f66cd898b9..35995886d5 100644
          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 a0bfe080f5..7d95e7a1a8 100644
+index 12ca1b222b..9bad7dae0c 100644
 --- a/src/sage/rings/rational.pyx
 +++ b/src/sage/rings/rational.pyx
-@@ -1056,7 +1056,7 @@ cdef class Rational(sage.structure.element.FieldElement):
+@@ -1041,7 +1041,7 @@ cdef class Rational(sage.structure.element.FieldElement):
              dtype('O')
  
              sage: numpy.array([1, 1/2, 3/4])
@@ -754,10 +738,10 @@ index a0bfe080f5..7d95e7a1a8 100644
          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 4c630867a4..64e2187f5b 100644
+index 9b90c8833e..1ce05b937d 100644
 --- a/src/sage/rings/real_mpfr.pyx
 +++ b/src/sage/rings/real_mpfr.pyx
-@@ -1438,7 +1438,7 @@ cdef class RealNumber(sage.structure.element.RingElement):
+@@ -1439,7 +1439,7 @@ cdef class RealNumber(sage.structure.element.RingElement):
  
              sage: import numpy
              sage: numpy.arange(10.0)
@@ -767,7 +751,7 @@ index 4c630867a4..64e2187f5b 100644
              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 3d270ebf9d..1144f168e3 100644
+index 443599a9c1..1ba5e36559 100644
 --- a/src/sage/schemes/elliptic_curves/height.py
 +++ b/src/sage/schemes/elliptic_curves/height.py
 @@ -1623,18 +1623,18 @@ class EllipticCurveCanonicalHeight:
@@ -798,7 +782,7 @@ index 3d270ebf9d..1144f168e3 100644
          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 2dcb0492b9..2b1a06385c 100644
+index 5b37859c93..3ca64124d4 100644
 --- a/src/sage/symbolic/ring.pyx
 +++ b/src/sage/symbolic/ring.pyx
 @@ -1135,7 +1135,7 @@ cdef class NumpyToSRMorphism(Morphism):

pkgs/applications/science/math/sage/patches/spkg-scripts.patch

@@ -1,46 +0,0 @@
-commit f02714d4aea80e17cb8df62bab75d7c1a1b61a8e
-Author: Timo Kaufmann <timokau@zoho.com>
-Date:   Mon Jul 9 18:26:18 2018 +0200
-
-    Don't attempt to create dirs when showing pkg info
-    
-    The script dir cannot be assumed to be writeable after installation.
-
-diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg
-index f3e02aeae5..190d558ad1 100755
---- a/build/bin/sage-spkg
-+++ b/build/bin/sage-spkg
-@@ -167,14 +167,6 @@ if [ -z "$SAGE_BUILD_DIR" ]; then
-     export SAGE_BUILD_DIR="$SAGE_LOCAL/var/tmp/sage/build"
- fi
- 
--for dir in "$SAGE_SPKG_INST" "$SAGE_SPKG_SCRIPTS"; do
--    mkdir -p "$dir"
--    if [ $? -ne 0 ]; then
--        error_msg "Error creating directory $dir"
--        exit 1
--    fi
--done
--
- 
- # Remove '.' from PYTHONPATH, which may also come from SAGE_PATH, to avoid
- # trouble with setuptools / easy_install (cf. #10192, #10176):
-@@ -563,11 +555,13 @@ fi
- # Setup directories
- ##################################################################
- 
--mkdir -p "$SAGE_BUILD_DIR"
--if [ $? -ne 0 ]; then
--    error_msg "Error creating directory $SAGE_BUILD_DIR"
--    exit 1
--fi
-+for dir in "$SAGE_SPKG_INST" "$SAGE_SPKG_SCRIPTS" "$SAGE_BUILD_DIR"; do
-+    mkdir -p "$dir"
-+    if [ $? -ne 0 ]; then
-+        error_msg "Error creating directory $dir"
-+        exit 1
-+    fi
-+done
- 
- # Trac #5852: check write permissions
- if [ ! -w "$SAGE_BUILD_DIR" ]; then

pkgs/applications/science/math/sage/sage-src.nix

@@ -3,32 +3,17 @@
 , fetchpatch
 }:
 stdenv.mkDerivation rec {
-  version = "8.3";
+  version = "8.4.beta0";
   name = "sage-src-${version}";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    sha256 = "0mbm99m5xry21xpi4q3q96gx392liwbifywf5awvl0j85a7rkfyx";
+    sha256 = "1jph4slscpni0smp2fxs3s12282c9r3mdfbgxpyx67gic0d9iya8";
   };
 
   nixPatches = [
-    # https://trac.sagemath.org/ticket/25809
-    ./patches/spkg-scripts.patch
-
-    # https://trac.sagemath.org/ticket/25309
-    (fetchpatch {
-      name = "spkg-paths.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=97f06fddee920399d4fcda65aa9b0925774aec69&id=a86151429ccce1ddd085e8090ada8ebdf02f3310";
-      sha256 = "1xb9108rzzkdhn71vw44525620d3ww9jv1fph5a77v9y7nf9wgr7";
-    })
-    (fetchpatch {
-      name = "maxima-fas.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=97f06fddee920399d4fcda65aa9b0925774aec69";
-      sha256 = "14s50yg3hpw9cp3v581dx7zfmpm2j972im7x30iwki8k45mjvk3i";
-    })
-
     # https://trac.sagemath.org/ticket/25722
     ./patches/test-in-tmpdir.patch
 
@@ -63,12 +48,6 @@ stdenv.mkDerivation rec {
   ];
 
   packageUpgradePatches = [
-    (fetchpatch {
-      name = "cypari2-1.2.1.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=62fe6eb15111327d930336d4252d5b23cbb22ab9";
-      sha256 = "1xax7vvs8h4xip16xcsp47xdb6lig6f2r3pl8cksvlz8lhgbyxh2";
-    })
-
     # matplotlib 2.2.2 deprecated `normed` (replaced by `density`).
     # This patch only ignores the warning. It would be equally easy to fix it
     # (by replacing all mentions of `normed` by `density`), but its better to
@@ -104,12 +83,7 @@ stdenv.mkDerivation rec {
     # https://trac.sagemath.org/ticket/24735
     ./patches/singular-4.1.1p2.patch
 
-    # https://trac.sagemath.org/ticket/25567 and dependency #25635
+    # https://trac.sagemath.org/ticket/25567
-    (fetchpatch {
-      name = "pari-upgrade-dependency.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?id=6995e7cae1b3476ad0145f8dfc897cf91f0c3c4d";
-      sha256 = "1dvhabl1c9pwd9xkjvbjjg15mvb14b24p1f3cby1mlqk34d4lrs6";
-    })
     (fetchpatch {
       name = "pari-2.11.0.patch";
       url = "https://git.sagemath.org/sage.git/patch/?id=7af4748cab37d651eaa88be501db88f4a5ffc584";
@@ -122,13 +96,6 @@ stdenv.mkDerivation rec {
       url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/sagemath-lcalc-c++11.patch?h=packages/sagemath&id=0e31ae526ab7c6b5c0bfacb3f8b1c4fd490035aa";
       sha256 = "0p5wnvbx65i7cp0bjyaqgp4rly8xgnk12pqwaq3dqby0j2bk6ijb";
     })
-
-    # cddlib 0.94i -> 0.94j
-    (fetchpatch {
-      name = "cddlib-0.94j.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?id=2ab1546b3e21d1d0ab3b4fcd58576848b3a2d888";
-      sha256 = "1c5gnasq7y9xxj762bn79bis0zi8d9bgg7jzlf64ifixsrc5cymb";
-    })
   ];
 
   patches = nixPatches ++ packageUpgradePatches ++ [

pkgs/applications/science/math/sage/sagelib.nix

@@ -47,6 +47,8 @@
 , singular
 , pip
 , jupyter_core
+, libhomfly
+, libbraiding
 }:
 
 buildPythonPackage rec {
@@ -109,6 +111,8 @@ buildPythonPackage rec {
     pip
     cython
     cysignals
+    libhomfly
+    libbraiding
   ];
 
   buildPhase = ''