Update to latest upstream release

2025-04-18 10:19:03 -04:00 · 2019-11-08 08:46:01 -03:00 · 2019-11-08 08:46:01 -03:00 · 7b54d2115b
commit 7b54d2115b
parent fa050d6863
20 changed files with 285 additions and 834 deletions
--- a/sagemath-arb.patch
+++ b/sagemath-arb.patch
@ -1,141 +1,32 @@
-diff -up src/sage/libs/arb/acb_hypgeom.pxd.orig src/sage/libs/arb/acb_hypgeom.pxd
+diff -up src/sage/libs/arb/arb_wrap.h.orig src/sage/libs/arb/arb_wrap.h
--- src/sage/libs/arb/acb_hypgeom.pxd.orig	2018-12-22 16:37:08.000000000 -0700
+--- src/sage/libs/arb/arb_wrap.h.orig	2019-10-25 14:39:21.831699616 -0300
-+++ src/sage/libs/arb/acb_hypgeom.pxd	2019-01-16 09:46:54.148469344 -0700
+++ src/sage/libs/arb/arb_wrap.h	2019-10-25 14:39:53.520890155 -0300
-@@ -2,7 +2,7 @@
+@@ -11,17 +11,17 @@
 #define ulong mp_limb_t
 #define slong mp_limb_signed_t
- from sage.libs.arb.types cimport *
+-#include <acb.h>
 -#include <acb_calc.h>
 -#include <acb_elliptic.h>
 -#include <acb_hypgeom.h>
 -#include <acb_mat.h>
 -#include <acb_modular.h>
 -#include <acb_poly.h>
 -#include <arb.h>
 -#include <arf.h>
 -#include <bernoulli.h>
 -#include <mag.h>
 +#include <arb/acb.h>
 +#include <arb/acb_calc.h>
 +#include <arb/acb_elliptic.h>
 +#include <arb/acb_hypgeom.h>
 +#include <arb/acb_mat.h>
 +#include <arb/acb_modular.h>
 +#include <arb/acb_poly.h>
 +#include <arb/arb.h>
 +#include <arb/arf.h>
 +#include <arb/bernoulli.h>
 +#include <arb/mag.h>
-cdef extern from "acb_hypgeom.h":
+ #undef ulong
-+cdef extern from "arb/acb_hypgeom.h":
+ #undef slong
     void acb_hypgeom_pfq_bound_factor(mag_t C, acb_srcptr a, long p, acb_srcptr b, long q, const acb_t z, unsigned long n)
     long acb_hypgeom_pfq_choose_n(acb_srcptr a, long p, acb_srcptr b, long q, const acb_t z, long prec)
     void acb_hypgeom_pfq_sum_forward(acb_t s, acb_t t, acb_srcptr a, long p, acb_srcptr b, long q, const acb_t z, long n, long prec)
 diff -up src/sage/libs/arb/acb_mat.pxd.orig src/sage/libs/arb/acb_mat.pxd
 --- src/sage/libs/arb/acb_mat.pxd.orig	2018-12-22 16:37:08.000000000 -0700
 +++ src/sage/libs/arb/acb_mat.pxd	2019-01-16 09:46:54.148469344 -0700
@@ -1,6 +1,6 @@
 from sage.libs.arb.types cimport acb_t, acb_mat_t, acb_poly_t
 -cdef extern from "acb_mat.h":
 +cdef extern from "arb/acb_mat.h":
     unsigned int acb_mat_nrows(acb_mat_t mat)
     unsigned int acb_mat_ncols(acb_mat_t mat)
     acb_t acb_mat_entry(acb_mat_t mat, unsigned long i, unsigned long j)
 diff -up src/sage/libs/arb/acb_modular.pxd.orig src/sage/libs/arb/acb_modular.pxd
 --- src/sage/libs/arb/acb_modular.pxd.orig	2018-12-22 16:37:08.000000000 -0700
 +++ src/sage/libs/arb/acb_modular.pxd	2019-01-16 09:46:54.149469326 -0700
@@ -3,7 +3,7 @@
 from sage.libs.arb.types cimport *
 from sage.libs.flint.types cimport fmpz_poly_t
 -cdef extern from "acb_modular.h":
 +cdef extern from "arb/acb_modular.h":
     void acb_modular_theta(acb_t theta1, acb_t theta2, acb_t theta3, acb_t theta4, const acb_t z, const acb_t tau, long prec)
     void acb_modular_j(acb_t z, const acb_t tau, long prec)
     void acb_modular_eta(acb_t z, const acb_t tau, long prec)
 diff -up src/sage/libs/arb/acb_poly.pxd.orig src/sage/libs/arb/acb_poly.pxd
 --- src/sage/libs/arb/acb_poly.pxd.orig	2018-12-22 16:37:08.000000000 -0700
 +++ src/sage/libs/arb/acb_poly.pxd	2019-01-16 09:46:54.149469326 -0700
@@ -3,7 +3,7 @@
 from sage.libs.arb.types cimport *
 from sage.libs.flint.types cimport fmpz_poly_t, fmpq_poly_t
 -cdef extern from "acb_poly.h":
 +cdef extern from "arb/acb_poly.h":
     void acb_poly_init(acb_poly_t poly)
     void acb_poly_clear(acb_poly_t poly)
     void acb_poly_fit_length(acb_poly_t poly, long len)
 diff -up src/sage/libs/arb/acb.pxd.orig src/sage/libs/arb/acb.pxd
 --- src/sage/libs/arb/acb.pxd.orig	2018-12-22 16:37:08.000000000 -0700
 +++ src/sage/libs/arb/acb.pxd	2019-01-16 09:46:54.149469326 -0700
@@ -3,7 +3,7 @@
 from sage.libs.arb.types cimport *
 from sage.libs.flint.types cimport fmpz_t, fmpq_t
 -cdef extern from "acb.h":
 +cdef extern from "arb/acb.h":
     arb_t acb_realref(acb_t x)
     arb_t acb_imagref(acb_t x)
 diff -up src/sage/libs/arb/arf.pxd.orig src/sage/libs/arb/arf.pxd
 --- src/sage/libs/arb/arf.pxd.orig	2018-12-22 16:37:08.000000000 -0700
 +++ src/sage/libs/arb/arf.pxd	2019-01-16 09:46:54.149469326 -0700
@@ -5,7 +5,7 @@ from sage.libs.gmp.types cimport mpz_t
 from sage.libs.flint.types cimport fmpz_t
 from sage.libs.mpfr.types cimport mpfr_t, mpfr_rnd_t
 -cdef extern from "arf.h":
 +cdef extern from "arb/arf.h":
     void arf_init(arf_t x)
     void arf_clear(arf_t x)
     void arf_zero(arf_t x)
 diff -up src/sage/libs/arb/bernoulli.pxd.orig src/sage/libs/arb/bernoulli.pxd
 --- src/sage/libs/arb/bernoulli.pxd.orig	2018-12-22 16:37:08.000000000 -0700
 +++ src/sage/libs/arb/bernoulli.pxd	2019-01-16 09:46:54.149469326 -0700
@@ -2,5 +2,5 @@
 from ..flint.types cimport fmpq_t, ulong
 -cdef extern from "bernoulli.h":
 +cdef extern from "arb/bernoulli.h":
     void bernoulli_fmpq_ui(fmpq_t b, ulong n)
 diff -up src/sage/libs/arb/mag.pxd.orig src/sage/libs/arb/mag.pxd
 --- src/sage/libs/arb/mag.pxd.orig	2018-12-22 16:37:08.000000000 -0700
 +++ src/sage/libs/arb/mag.pxd	2019-01-16 09:46:54.150469309 -0700
@@ -3,7 +3,7 @@
 from sage.libs.arb.types cimport *
 from sage.libs.flint.types cimport fmpz_t, fmpq_t
 -cdef extern from "mag.h":
 +cdef extern from "arb/mag.h":
     void mag_init(mag_t x)
     void mag_clear(mag_t x)
     void mag_init_set(mag_t x, const mag_t y)
 diff -up src/sage/libs/arb/types.pxd.orig src/sage/libs/arb/types.pxd
 --- src/sage/libs/arb/types.pxd.orig	2018-12-22 16:37:08.000000000 -0700
 +++ src/sage/libs/arb/types.pxd	2019-01-16 09:46:54.150469309 -0700
@@ -1,4 +1,4 @@
 -cdef extern from "mag.h":
 +cdef extern from "arb/mag.h":
     ctypedef struct mag_struct:
         pass
     ctypedef mag_struct mag_t[1]
@@ -6,7 +6,7 @@ cdef extern from "mag.h":
     ctypedef const mag_struct * mag_srcptr
     long MAG_BITS
 -cdef extern from "arf.h":
 +cdef extern from "arb/arf.h":
     ctypedef struct arf_struct:
         pass
     ctypedef arf_struct arf_t[1]
@@ -20,25 +20,25 @@ cdef extern from "arf.h":
         ARF_RND_NEAR
     long ARF_PREC_EXACT
 -cdef extern from "arb.h":
 +cdef extern from "arb/arb.h":
     ctypedef struct arb_struct:
         pass
     ctypedef arb_struct arb_t[1]
     ctypedef arb_struct * arb_ptr
 -cdef extern from "acb.h":
 +cdef extern from "arb/acb.h":
     ctypedef struct acb_struct:
         pass
     ctypedef acb_struct[1] acb_t
     ctypedef acb_struct * acb_ptr
     ctypedef const acb_struct * acb_srcptr
 -cdef extern from "acb_mat.h":
 +cdef extern from "arb/acb_mat.h":
     ctypedef struct acb_mat_struct:
         pass
     ctypedef acb_mat_struct[1] acb_mat_t
 -cdef extern from "acb_poly.h":
 +cdef extern from "arb/acb_poly.h":
     ctypedef struct acb_poly_struct:
         pass
     ctypedef acb_poly_struct[1] acb_poly_t
--- a/sagemath-buildroot.patch
+++ b/sagemath-buildroot.patch
@ -1,7 +1,7 @@
 diff -up src/setup.py.orig src/setup.py
--- src/setup.py.orig	2019-01-04 11:05:11.337077724 -0700
+--- src/setup.py.orig	2019-10-03 16:02:47.728642827 -0300
-+++ src/setup.py	2019-01-16 09:45:32.570933224 -0700
+++ src/setup.py	2019-10-03 16:03:22.041859763 -0300
-@@ -334,6 +334,9 @@ class sage_build_cython(Command):
+@@ -335,6 +335,9 @@ class sage_build_cython(Command):
         with open(self._version_file, 'w') as f:
             f.write(self._version_stamp)
--- a/sagemath-cremona.patch
+++ b/sagemath-cremona.patch
@ -1,7 +1,7 @@
 diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
--- src/sage/databases/cremona.py.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/sage/databases/cremona.py.orig	2019-10-03 14:57:32.516349793 -0300
-+++ src/sage/databases/cremona.py	2019-09-09 15:37:13.321511378 -0600
+++ src/sage/databases/cremona.py	2019-10-03 14:57:45.084423307 -0300
-@@ -842,7 +842,8 @@ class MiniCremonaDatabase(SQLDatabase):
+@@ -850,7 +850,8 @@ class MiniCremonaDatabase(SQLDatabase):
                 message = "There is no elliptic curve with label " \
                     + label + " in the default database; try installing " \
                     + "the optional package database_cremona_ellcurve which " \
@ -11,11 +11,11 @@ diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
             raise ValueError(message)
         ainvs = eval(c[0])
         data = {'cremona_label': label,
-@@ -1640,6 +1641,7 @@ class LargeCremonaDatabase(MiniCremonaDa
+@@ -1649,6 +1650,7 @@ class LargeCremonaDatabase(MiniCremonaDa
             con.executemany("UPDATE t_curve SET gens=? WHERE curve=?", \
                 curve_data)
             print("Committing...")
 +            self.commit()
             if largest_conductor and int(v[0]) > largest_conductor: break
- _db = None
+ 
--- a/sagemath-env.patch
+++ b/sagemath-env.patch
@ -1,6 +1,6 @@
 diff -up src/sage/env.py.orig src/sage/env.py
--- src/sage/env.py.orig	2019-06-27 11:45:30.915744723 -0600
+--- src/sage/env.py.orig	2019-10-03 16:59:18.202495553 -0300
-+++ src/sage/env.py	2019-06-28 11:31:09.965474086 -0600
+++ src/sage/env.py	2019-10-03 17:00:31.167931299 -0300
@@ -151,11 +151,11 @@ var('SAGE_DATE',           version.date)
 var('SAGE_VERSION_BANNER', version.banner)
@ -27,13 +27,15 @@ diff -up src/sage/env.py.orig src/sage/env.py
 var('CONWAY_POLYNOMIALS_DATA_DIR',   join(SAGE_SHARE, 'conway_polynomials'))
 var('GRAPHS_DATA_DIR',               join(SAGE_SHARE, 'graphs'))
 var('ELLCURVE_DATA_DIR',             join(SAGE_SHARE, 'ellcurves'))
-@@ -181,9 +181,9 @@ var('CREMONA_MINI_DATA_DIR',         joi
+@@ -181,11 +181,11 @@ var('CREMONA_MINI_DATA_DIR',         joi
 var('CREMONA_LARGE_DATA_DIR',        join(SAGE_SHARE, 'cremona'))
 var('JMOL_DIR',                      join(SAGE_SHARE, 'jmol'))
 var('JSMOL_DIR',                     join(SAGE_SHARE, 'jsmol'))
 -var('MATHJAX_DIR',                   join(SAGE_SHARE, 'mathjax'))
 +var('MATHJAX_DIR',                   join('/usr', 'share', 'javascript', 'mathjax'))
 var('MTXLIB',                        join(SAGE_SHARE, 'meataxe'))
 var('THREEJS_DIR',                   join(SAGE_SHARE, 'threejs'))
 var('SINGULARPATH',                  join(SAGE_SHARE, 'singular'))
 -var('PPLPY_DOCS',                    join(SAGE_SHARE, 'doc', 'pplpy'))
 +var('PPLPY_DOCS',                    join('/usr', 'share', 'doc', 'python3-pplpy'))
 var('MAXIMA_FAS')
--- a/sagemath-escape.patch
+++ b/sagemath-escape.patch
@ -1,36 +0,0 @@
 diff -up src/sage/algebras/clifford_algebra.py.orig src/sage/algebras/clifford_algebra.py
 --- src/sage/algebras/clifford_algebra.py.orig	2019-06-26 14:41:04.000000000 -0600
 +++ src/sage/algebras/clifford_algebra.py	2019-09-11 15:46:56.658681891 -0600
@@ -1520,7 +1520,7 @@ class ExteriorAlgebra(CliffordAlgebra):
         return term
     def _ascii_art_term(self, m):
 -        """
 +        r"""
         Return ascii art for the basis element indexed by ``m``.
         EXAMPLES::
 diff -up src/sage/combinat/crystals/alcove_path.py.orig src/sage/combinat/crystals/alcove_path.py
 --- src/sage/combinat/crystals/alcove_path.py.orig	2019-06-26 14:41:04.000000000 -0600
 +++ src/sage/combinat/crystals/alcove_path.py	2019-06-27 11:46:03.613253846 -0600
@@ -383,7 +383,7 @@ class CrystalOfAlcovePaths(UniqueReprese
         One can compute all vertices of the crystal by finding all the
         admissible subsets of the `\lambda`-chain  (see method
 -        is_admissible, for definition).  We use the breath first
 +        is_admissible, for definition).  We use the breadth first
         search algorithm.
         .. WARNING::
 diff -up src/sage/rings/lazy_laurent_series_ring.py.orig src/sage/rings/lazy_laurent_series_ring.py
 --- src/sage/rings/lazy_laurent_series_ring.py.orig	2019-06-26 14:41:05.000000000 -0600
 +++ src/sage/rings/lazy_laurent_series_ring.py	2019-09-11 15:41:19.871081870 -0600
@@ -260,7 +260,7 @@ class LazyLaurentSeriesRing(UniqueRepres
         return self._element_constructor_(0)
     def series(self, coefficient, valuation, constant=None):
 -        """
 +        r"""
         Return a lazy Laurent series.
         INPUT:
--- a/sagemath-extensions.patch
+++ b/sagemath-extensions.patch
@ -1,7 +1,7 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/module_list.py.orig	2019-10-03 14:49:13.122428790 -0300
-+++ src/module_list.py	2019-09-17 16:06:38.678583204 -0600
+++ src/module_list.py	2019-10-03 14:49:25.274499871 -0300
-@@ -357,16 +357,16 @@ ext_modules = [
+@@ -389,16 +389,16 @@ ext_modules = [
     Extension('sage.graphs.matchpoly',
               sources = ['sage/graphs/matchpoly.pyx']),
@ -23,7 +23,7 @@ diff -up src/module_list.py.orig src/module_list.py
     Extension('sage.graphs.planarity',
               sources = ['sage/graphs/planarity.pyx'],
-@@ -385,10 +385,10 @@ ext_modules = [
+@@ -417,10 +417,10 @@ ext_modules = [
     Extension('sage.graphs.graph_decompositions.cutwidth',
               sources = ['sage/graphs/graph_decompositions/cutwidth.pyx']),
@ -38,7 +38,7 @@ diff -up src/module_list.py.orig src/module_list.py
     Extension('sage.graphs.spanning_tree',
               sources = ['sage/graphs/spanning_tree.pyx']),
-@@ -440,9 +440,9 @@ ext_modules = [
+@@ -476,9 +476,9 @@ ext_modules = [
     ##
     ################################
@ -50,7 +50,7 @@ diff -up src/module_list.py.orig src/module_list.py
     Extension('*', ['sage/interfaces/*.pyx']),
-@@ -461,21 +461,19 @@ ext_modules = [
+@@ -497,21 +497,19 @@ ext_modules = [
     ##
     ################################
@ -77,7 +77,7 @@ diff -up src/module_list.py.orig src/module_list.py
     Extension('sage.libs.flint.flint',
               sources = ["sage/libs/flint/flint.pyx"],
-@@ -504,10 +502,9 @@ ext_modules = [
+@@ -540,10 +538,9 @@ ext_modules = [
                       sources = ["sage/libs/homfly.pyx"],
                       libraries = ["homfly", "gc"]),
@ -89,7 +89,7 @@ diff -up src/module_list.py.orig src/module_list.py
                       language = 'c++'),
     Extension('*', ['sage/libs/linbox/*.pyx']),
-@@ -527,10 +524,10 @@ ext_modules = [
+@@ -563,10 +560,10 @@ ext_modules = [
     Extension('sage.libs.lrcalc.lrcalc',
               sources = ["sage/libs/lrcalc/lrcalc.pyx"]),
@ -104,7 +104,7 @@ diff -up src/module_list.py.orig src/module_list.py
     Extension('*', ['sage/libs/pari/*.pyx']),
-@@ -841,10 +838,10 @@ ext_modules = [
+@@ -874,10 +871,10 @@ ext_modules = [
     Extension('sage.matrix.matrix_window',
               sources = ['sage/matrix/matrix_window.pyx']),
@ -119,7 +119,7 @@ diff -up src/module_list.py.orig src/module_list.py
     Extension('sage.matrix.misc',
               sources = ['sage/matrix/misc.pyx']),
-@@ -1021,26 +1018,25 @@ ext_modules = [
+@@ -1053,26 +1050,25 @@ ext_modules = [
     Extension("sage.numerical.backends.interactivelp_backend",
               ["sage/numerical/backends/interactivelp_backend.pyx"]),
@ -128,17 +128,18 @@ diff -up src/module_list.py.orig src/module_list.py
 -              libraries = ["gurobi"],
 -              condition = os.path.isfile(SAGE_INC + "/gurobi_c.h") and
 -                  os.path.isfile(SAGE_LOCAL + "/lib/libgurobi.so")),
-+#    OptionalExtension("sage.numerical.backends.gurobi_backend",
+-
 +#              ["sage/numerical/backends/gurobi_backend.pyx"],
 +#              libraries = ["gurobi"],
 +#              condition = os.path.isfile(SAGE_INC + "/gurobi_c.h") and
 +#                  os.path.isfile(SAGE_LOCAL + "/lib/libgurobi.so")),
 -    OptionalExtension("sage.numerical.backends.cplex_backend",
 -              ["sage/numerical/backends/cplex_backend.pyx"],
 -              libraries = ["cplex"],
 -              condition = os.path.isfile(SAGE_INC + "/cplex.h") and
 -                  os.path.isfile(SAGE_LOCAL + "/lib/libcplex.a")),
 +#    OptionalExtension("sage.numerical.backends.gurobi_backend",
 +#              ["sage/numerical/backends/gurobi_backend.pyx"],
 +#              libraries = ["gurobi"],
 +#              condition = os.path.isfile(SAGE_INC + "/gurobi_c.h") and
 +#                  os.path.isfile(SAGE_LOCAL + "/lib/libgurobi.so")),
 +
 +#    OptionalExtension("sage.numerical.backends.cplex_backend",
 +#              ["sage/numerical/backends/cplex_backend.pyx"],
 +#              libraries = ["cplex"],
--- a/sagemath-fes.patch
+++ b/sagemath-fes.patch
@ -1,7 +1,7 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2019-09-11 08:51:57.722696682 -0600
+--- src/module_list.py.orig	2019-10-03 16:04:08.373152682 -0300
-+++ src/module_list.py	2019-09-11 08:52:38.084040542 -0600
+++ src/module_list.py	2019-10-03 16:04:19.877225413 -0300
-@@ -470,10 +470,10 @@ ext_modules = [
+@@ -506,10 +506,10 @@ ext_modules = [
     Extension('sage.libs.ecl',
               sources = ["sage/libs/ecl.pyx"]),
--- a/sagemath-formatargspec.patch
+++ b/sagemath-formatargspec.patch
@ -1,173 +0,0 @@
 diff -up src/sage/misc/sageinspect.py.orig src/sage/misc/sageinspect.py
 --- src/sage/misc/sageinspect.py.orig	2019-06-26 14:41:05.000000000 -0600
 +++ src/sage/misc/sageinspect.py	2019-09-11 08:58:24.194413905 -0600
@@ -1658,6 +1658,121 @@ def sage_getargspec(obj):
         defaults = None
     return inspect.ArgSpec(args, varargs, varkw, defaults)
 +def formatannotation(annotation, base_module=None):
 +    """
 +    This is taken from Python 3.7's inspect.py; the only change is to
 +    add documentation.
 +
 +    INPUT:
 +
 +    - ``annotation`` -- annotation for a function
 +    - ``base_module`` (optional, default ``None``)
 +
 +    This is only relevant with Python 3, so the doctests are marked
 +    accordingly.
 +
 +    EXAMPLES::
 +
 +        sage: from sage.misc.sageinspect import formatannotation
 +        sage: import inspect
 +        sage: def foo(a, *, b:int, **kwargs): # py3
 +        ....:     pass
 +        ....:
 +        sage: s = inspect.signature(foo) # py3
 +
 +        sage: a = s.parameters['a'].annotation # py3
 +        sage: a # py3
 +        <class 'inspect._empty'>
 +        sage: formatannotation(a) # py3
 +        'inspect._empty'
 +
 +        sage: b = s.parameters['b'].annotation # py3
 +        sage: b # py3
 +        <class 'int'>
 +        sage: formatannotation(b) # py3
 +        'int'
 +    """
 +    if getattr(annotation, '__module__', None) == 'typing':
 +        return repr(annotation).replace('typing.', '')
 +    if isinstance(annotation, type):
 +        if annotation.__module__ in ('builtins', base_module):
 +            return annotation.__qualname__
 +        return annotation.__module__+'.'+annotation.__qualname__
 +    return repr(annotation)
 +
 +def sage_formatargspec(args, varargs=None, varkw=None, defaults=None,
 +                       kwonlyargs=(), kwonlydefaults={}, annotations={},
 +                       formatarg=str,
 +                       formatvarargs=lambda name: '*' + name,
 +                       formatvarkw=lambda name: '**' + name,
 +                       formatvalue=lambda value: '=' + repr(value),
 +                       formatreturns=lambda text: ' -> ' + text,
 +                       formatannotation=formatannotation):
 +    """
 +    Format an argument spec from the values returned by getfullargspec.
 +
 +    The first seven arguments are (args, varargs, varkw, defaults,
 +    kwonlyargs, kwonlydefaults, annotations).  The other five arguments
 +    are the corresponding optional formatting functions that are called to
 +    turn names and values into strings.  The last argument is an optional
 +    function to format the sequence of arguments.
 +
 +    This is taken from Python 3.7's inspect.py, where it is
 +    deprecated. The only change, aside from documentation (this
 +    paragraph and the next, plus doctests), is to remove the
 +    deprecation warning.
 +
 +    Sage uses this function to format arguments, as obtained by
 +    :func:`sage_getargspec`. Since :func:`sage_getargspec` works for
 +    Cython functions while Python's inspect module does not, it makes
 +    sense to keep this function for formatting instances of
 +    ``inspect.ArgSpec``.
 +
 +    EXAMPLES::
 +
 +        sage: from sage.misc.sageinspect import sage_formatargspec
 +        sage: from inspect import formatargspec # deprecated in Python 3
 +        sage: args = ['a', 'b', 'c']
 +        sage: defaults = [3]
 +        sage: sage_formatargspec(args, defaults=defaults)
 +        '(a, b, c=3)'
 +        sage: formatargspec(args, defaults=defaults) == sage_formatargspec(args, defaults=defaults) # py2
 +        True
 +        sage: formatargspec(args, defaults=defaults) == sage_formatargspec(args, defaults=defaults) # py3
 +        doctest:...: DeprecationWarning: `formatargspec` is deprecated since Python 3.5. Use `signature` and the `Signature` object directly
 +        True
 +    """
 +    def formatargandannotation(arg):
 +        result = formatarg(arg)
 +        if arg in annotations:
 +            result += ': ' + formatannotation(annotations[arg])
 +        return result
 +    specs = []
 +    if defaults:
 +        firstdefault = len(args) - len(defaults)
 +    for i, arg in enumerate(args):
 +        spec = formatargandannotation(arg)
 +        if defaults and i >= firstdefault:
 +            spec = spec + formatvalue(defaults[i - firstdefault])
 +        specs.append(spec)
 +    if varargs is not None:
 +        specs.append(formatvarargs(formatargandannotation(varargs)))
 +    else:
 +        if kwonlyargs:
 +            specs.append('*')
 +    if kwonlyargs:
 +        for kwonlyarg in kwonlyargs:
 +            spec = formatargandannotation(kwonlyarg)
 +            if kwonlydefaults and kwonlyarg in kwonlydefaults:
 +                spec += formatvalue(kwonlydefaults[kwonlyarg])
 +            specs.append(spec)
 +    if varkw is not None:
 +        specs.append(formatvarkw(formatargandannotation(varkw)))
 +    result = '(' + ', '.join(specs) + ')'
 +    if 'return' in annotations:
 +        result += formatreturns(formatannotation(annotations['return']))
 +    return result
 +
 def sage_getdef(obj, obj_name=''):
     r"""
@@ -1693,7 +1808,7 @@ def sage_getdef(obj, obj_name=''):
     """
     try:
         spec = sage_getargspec(obj)
 -        s = str(inspect.formatargspec(*spec))
 +        s = str(sage_formatargspec(*spec))
         s = s.strip('(').strip(')').strip()
         if s[:4] == 'self':
             s = s[4:]
 diff -up src/sage_setup/docbuild/ext/sage_autodoc.py.orig src/sage_setup/docbuild/ext/sage_autodoc.py
 --- src/sage_setup/docbuild/ext/sage_autodoc.py.orig	2019-06-26 14:41:05.000000000 -0600
 +++ src/sage_setup/docbuild/ext/sage_autodoc.py	2019-09-11 08:59:53.728932096 -0600
@@ -38,7 +38,7 @@ from six import PY2, iteritems, itervalu
 import sphinx
 from sphinx.errors import ExtensionError
 from sphinx.ext.autodoc.importer import mock, import_object, get_object_members
 -from sphinx.ext.autodoc.inspector import format_annotation, formatargspec
 +from sphinx.ext.autodoc.inspector import format_annotation
 from sphinx.locale import _, __
 from sphinx.pycode import ModuleAnalyzer
 from sphinx.errors import ExtensionError, PycodeError
@@ -51,7 +51,8 @@ from sphinx.util.inspect import Signatur
 from sphinx.util.inspect import getargspec
 from sage.misc.sageinspect import (sage_getdoc_original,
 -        sage_getargspec, isclassinstance)
 +                                   sage_getargspec, isclassinstance,
 +                                   sage_formatargspec)
 from sage.misc.lazy_import import LazyImport
 # This is used to filter objects of classes that inherit from
@@ -123,6 +124,16 @@ def bool_option(arg):
     return True
 +def formatargspec(function, args, varargs=None, varkw=None, defaults=None,
 +                  kwonlyargs=(), kwonlydefaults={}, annotations={}):
 +    """
 +    Sphinx's version of formatargspec is deprecated, so use Sage's instead.
 +    """
 +    return sage_formatargspec(args, varargs=varargs, varkw=varkw, defaults=defaults,
 +                              kwonlyargs=kwonlyargs, kwonlydefaults=kwonlydefaults,
 +                              annotations=annotations)
 +
 +
 class AutodocReporter(object):
     """
     A reporter replacement that assigns the correct source name
--- a/sagemath-includes.patch
+++ b/sagemath-includes.patch
@ -1,6 +1,6 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2019-09-11 08:52:38.084040542 -0600
+--- src/module_list.py.orig	2019-10-03 16:21:27.371721895 -0300
-+++ src/module_list.py	2019-09-11 09:03:51.394981074 -0600
+++ src/module_list.py	2019-10-03 16:28:36.076432442 -0300
@@ -44,6 +44,9 @@ zlib_libs = zlib_pc['libraries']
 zlib_library_dirs = zlib_pc['library_dirs']
 zlib_include_dirs = zlib_pc['include_dirs']
@ -26,7 +26,7 @@ diff -up src/module_list.py.orig src/module_list.py
 ### Library order
 #########################################################
-@@ -133,7 +144,8 @@ ext_modules = [
+@@ -134,7 +145,8 @@ ext_modules = [
                language='c++',
                libraries = ["gmp", "m", "ntl"]),
@ -36,7 +36,7 @@ diff -up src/module_list.py.orig src/module_list.py
     Extension('*', sources = ['sage/algebras/finite_dimensional_algebras/*.pyx']),
-@@ -522,7 +534,8 @@ ext_modules = [
+@@ -558,7 +570,8 @@ ext_modules = [
                                                         [])),
     Extension('sage.libs.lrcalc.lrcalc',
@ -46,7 +46,7 @@ diff -up src/module_list.py.orig src/module_list.py
 #    OptionalExtension("sage.libs.meataxe",
 #              sources = ['sage/libs/meataxe.pyx'],
-@@ -544,23 +557,28 @@ ext_modules = [
+@@ -580,23 +593,28 @@ ext_modules = [
               sources = ['sage/libs/readline.pyx'],
               libraries = ['readline']),
@ -80,7 +80,7 @@ diff -up src/module_list.py.orig src/module_list.py
     ###################################
     ##
-@@ -568,7 +586,8 @@ ext_modules = [
+@@ -604,7 +622,8 @@ ext_modules = [
     ##
     ###################################
@ -90,17 +90,17 @@ diff -up src/module_list.py.orig src/module_list.py
     ###################################
     ##
-@@ -740,7 +759,8 @@ ext_modules = [
+@@ -776,7 +795,8 @@ ext_modules = [
     Extension("sage.matrix.matrix_complex_ball_dense",
               ["sage/matrix/matrix_complex_ball_dense.pyx"],
-              libraries=['arb']),
+-              libraries=[arb_dylib_name]),
 +              include_dirs = arb_include_dirs,
 +              libraries=arb_libs),
     Extension('sage.matrix.matrix_complex_double_dense',
               sources = ['sage/matrix/matrix_complex_double_dense.pyx']),
-@@ -748,6 +768,7 @@ ext_modules = [
+@@ -784,6 +804,7 @@ ext_modules = [
     Extension('sage.matrix.matrix_cyclo_dense',
               sources = ['sage/matrix/matrix_cyclo_dense.pyx'],
               language = "c++",
@ -108,7 +108,7 @@ diff -up src/module_list.py.orig src/module_list.py
               libraries=['ntl']),
     Extension('sage.matrix.matrix_gap',
-@@ -810,6 +831,7 @@ ext_modules = [
+@@ -844,6 +865,7 @@ ext_modules = [
               sources = ['sage/matrix/matrix_modn_sparse.pyx']),
     Extension('sage.matrix.matrix_mpolynomial_dense',
@ -116,7 +116,7 @@ diff -up src/module_list.py.orig src/module_list.py
               sources = ['sage/matrix/matrix_mpolynomial_dense.pyx']),
     Extension('sage.matrix.matrix_polynomial_dense',
-@@ -1099,7 +1121,8 @@ ext_modules = [
+@@ -1131,7 +1153,8 @@ ext_modules = [
               language = 'c++'),
     Extension("sage.rings.complex_arb",
@ -126,7 +126,7 @@ diff -up src/module_list.py.orig src/module_list.py
     Extension('sage.rings.complex_double',
               sources = ['sage/rings/complex_double.pyx'],
-@@ -1175,7 +1198,8 @@ ext_modules = [
+@@ -1207,7 +1230,8 @@ ext_modules = [
               sources = ['sage/rings/real_interval_absolute.pyx']),
     Extension("sage.rings.real_arb",
@ -136,7 +136,7 @@ diff -up src/module_list.py.orig src/module_list.py
     Extension('sage.rings.real_lazy',
               sources = ['sage/rings/real_lazy.pyx']),
-@@ -1258,6 +1282,7 @@ ext_modules = [
+@@ -1290,6 +1314,7 @@ ext_modules = [
     Extension('sage.rings.number_field.number_field_element_quadratic',
               sources = ['sage/rings/number_field/number_field_element_quadratic.pyx'],
@ -144,7 +144,7 @@ diff -up src/module_list.py.orig src/module_list.py
               libraries=['ntl'],
               language = 'c++'),
-@@ -1397,12 +1422,15 @@ ext_modules = [
+@@ -1429,12 +1454,15 @@ ext_modules = [
               sources = ['sage/rings/polynomial/multi_polynomial.pyx']),
     Extension('sage.rings.polynomial.multi_polynomial_ideal_libsingular',
@ -160,7 +160,7 @@ diff -up src/module_list.py.orig src/module_list.py
               sources = ['sage/rings/polynomial/multi_polynomial_libsingular.pyx']),
     Extension('sage.rings.polynomial.multi_polynomial_ring_base',
-@@ -1415,7 +1443,8 @@ ext_modules = [
+@@ -1447,7 +1475,8 @@ ext_modules = [
               sources = ['sage/rings/polynomial/polydict.pyx']),
     Extension('sage.rings.polynomial.polynomial_complex_arb',
@ -171,8 +171,8 @@ diff -up src/module_list.py.orig src/module_list.py
     Extension('sage.rings.polynomial.polynomial_compiled',
                sources = ['sage/rings/polynomial/polynomial_compiled.pyx']),
 diff -up src/setup.py.orig src/setup.py
--- src/setup.py.orig	2019-09-11 08:51:46.080885941 -0600
+--- src/setup.py.orig	2019-10-03 16:28:47.206502813 -0300
-+++ src/setup.py	2019-09-11 09:03:51.394981074 -0600
+++ src/setup.py	2019-10-03 16:29:08.059634660 -0300
@@ -85,6 +85,7 @@ keep_going = False
 # search for dependencies and add to gcc -I<path>
--- a/sagemath-latte.patch
+++ b/sagemath-latte.patch
@ -1,16 +1,16 @@
 diff -up src/sage/interfaces/latte.py.orig src/sage/interfaces/latte.py
--- src/sage/interfaces/latte.py.orig	2019-04-08 12:05:07.092855841 -0600
+--- src/sage/interfaces/latte.py.orig	2019-10-03 16:52:46.496156266 -0300
-+++ src/sage/interfaces/latte.py	2019-04-08 13:37:31.377803169 -0600
+++ src/sage/interfaces/latte.py	2019-10-03 16:53:00.776241550 -0300
-@@ -113,7 +113,7 @@ def count(arg, ehrhart_polynomial=False,
+@@ -117,7 +117,7 @@ def count(arg, ehrhart_polynomial=False,
-     # Check that LattE is present
+ 
-     Latte().require()
+     arg = str_to_bytes(arg)
 -    args = ['count']
 +    args = ['latte-count']
     if ehrhart_polynomial and multivariate_generating_function:
         raise ValueError
     if ehrhart_polynomial:
-@@ -308,7 +308,7 @@ def integrate(arg, polynomial=None, algo
+@@ -317,7 +317,7 @@ def integrate(arg, polynomial=None, algo
     from sage.rings.rational import Rational
--- a/sagemath-lcalc.patch
+++ b/sagemath-lcalc.patch
@ -1,7 +1,7 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2019-06-27 11:30:20.794201914 -0600
+--- src/module_list.py.orig	2019-10-03 16:00:44.899866273 -0300
-+++ src/module_list.py	2019-06-27 11:38:23.103196674 -0600
+++ src/module_list.py	2019-10-03 16:00:56.451939308 -0300
-@@ -514,7 +514,7 @@ ext_modules = [
+@@ -548,7 +548,7 @@ ext_modules = [
     Extension('sage.libs.lcalc.lcalc_Lfunction',
               sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'],
               libraries = ['m', 'ntl', 'Lfunction'],
@ -10,3 +10,12 @@ diff -up src/module_list.py.orig src/module_list.py
               language = 'c++'),
     Extension('sage.libs.libecm',
 diff -up src/sage/libs/lcalc/lcalc_sage.h.orig src/sage/libs/lcalc/lcalc_sage.h
 --- src/sage/libs/lcalc/lcalc_sage.h.orig	2019-10-25 15:58:31.890166910 -0300
 +++ src/sage/libs/lcalc/lcalc_sage.h	2019-10-25 15:59:02.535343196 -0300
@@ -1,4 +1,4 @@
 -#include "Lfunction/L.h"
 +#include "libLfunction/L.h"
 int *new_ints(int l)
 {
     return new int[l];
--- a/sagemath-openblas.patch
+++ b/sagemath-openblas.patch
@ -1,6 +1,6 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2019-04-08 15:06:42.789735582 -0600
+--- src/module_list.py.orig	2019-10-03 16:51:55.350850836 -0300
-+++ src/module_list.py	2019-04-08 15:09:46.553467045 -0600
+++ src/module_list.py	2019-10-03 16:52:06.479917297 -0300
@@ -11,20 +11,17 @@ SAGE_INC = '/usr/include'
 import pkgconfig
@ -29,9 +29,9 @@ diff -up src/module_list.py.orig src/module_list.py
 # GD image library
 gd_pc = pkgconfig.parse('gdlib')
 diff -up src/sage/misc/cython.py.orig src/sage/misc/cython.py
--- src/sage/misc/cython.py.orig	2019-04-08 15:05:22.838157654 -0600
+--- src/sage/misc/cython.py.orig	2019-10-03 16:51:42.848776173 -0300
-+++ src/sage/misc/cython.py	2019-04-08 15:11:50.191262902 -0600
+++ src/sage/misc/cython.py	2019-10-03 16:52:06.480917303 -0300
-@@ -38,10 +38,9 @@ from sage.misc.sage_ostools import resto
+@@ -35,10 +35,9 @@ from sage.misc.sage_ostools import resto
 # CBLAS can be one of multiple implementations
--- a/sagemath-python3.patch
+++ b/sagemath-python3.patch
@ -1,6 +1,6 @@
 diff -up build/pkgs/sagenb/src/sagenb/misc/support.py.orig build/pkgs/sagenb/src/sagenb/misc/support.py
--- build/pkgs/sagenb/src/sagenb/misc/support.py.orig	2019-02-01 06:34:20.000000000 -0700
+--- build/pkgs/sagenb/src/sagenb/misc/support.py.orig	2019-10-09 15:29:08.866640263 -0300
-+++ build/pkgs/sagenb/src/sagenb/misc/support.py	2019-04-08 12:02:29.162692936 -0600
+++ build/pkgs/sagenb/src/sagenb/misc/support.py	2019-10-09 15:29:13.695667468 -0300
@@ -178,7 +178,7 @@ def completions(s, globs, format=False,
     try:
         if not '.' in s and not '(' in s:
@ -11,8 +11,8 @@ diff -up build/pkgs/sagenb/src/sagenb/misc/support.py.orig build/pkgs/sagenb/src
             if not ')' in s:
                 i = s.rfind('.')
 diff -up build/pkgs/sagenb/src/sagenb/notebook/docHTMLProcessor.py.orig build/pkgs/sagenb/src/sagenb/notebook/docHTMLProcessor.py
--- build/pkgs/sagenb/src/sagenb/notebook/docHTMLProcessor.py.orig	2019-02-01 05:37:36.000000000 -0700
+--- build/pkgs/sagenb/src/sagenb/notebook/docHTMLProcessor.py.orig	2019-10-09 15:29:08.867640268 -0300
-+++ build/pkgs/sagenb/src/sagenb/notebook/docHTMLProcessor.py	2019-04-08 11:59:49.259545960 -0600
+++ build/pkgs/sagenb/src/sagenb/notebook/docHTMLProcessor.py	2019-10-09 15:29:13.696667474 -0300
@@ -25,7 +25,7 @@ This module contains three classes:
 .. NOTE::
@ -32,8 +32,8 @@ diff -up build/pkgs/sagenb/src/sagenb/notebook/docHTMLProcessor.py.orig build/pk
         # HTMLParser, and may never actually be visibly called here.
 diff -up build/pkgs/sagenb/src/sagenb/notebook/wiki2html.py.orig build/pkgs/sagenb/src/sagenb/notebook/wiki2html.py
--- build/pkgs/sagenb/src/sagenb/notebook/wiki2html.py.orig	2019-02-01 05:37:36.000000000 -0700
+--- build/pkgs/sagenb/src/sagenb/notebook/wiki2html.py.orig	2019-10-09 15:29:08.870640285 -0300
-+++ build/pkgs/sagenb/src/sagenb/notebook/wiki2html.py	2019-04-08 11:59:49.260545943 -0600
+++ build/pkgs/sagenb/src/sagenb/notebook/wiki2html.py	2019-10-09 15:29:13.697667479 -0300
@@ -59,7 +59,7 @@ class Parser:
         'parent': r'(?:%s)?' % re.escape(PARENT_PREFIX),
     }
@ -44,8 +44,8 @@ diff -up build/pkgs/sagenb/src/sagenb/notebook/wiki2html.py.orig build/pkgs/sage
         'punct': punct_pattern,
     }
 diff -up build/pkgs/sagetex/src/extractsagecode.py.orig build/pkgs/sagetex/src/extractsagecode.py
--- build/pkgs/sagetex/src/extractsagecode.py.orig	2019-01-09 09:51:28.000000000 -0700
+--- build/pkgs/sagetex/src/extractsagecode.py.orig	2019-10-09 15:29:08.872640297 -0300
-+++ build/pkgs/sagetex/src/extractsagecode.py	2019-06-27 11:33:54.098080502 -0600
+++ build/pkgs/sagetex/src/extractsagecode.py	2019-10-09 15:29:13.697667479 -0300
@@ -45,7 +45,7 @@ See the SageTeX documentation for more d
 try:
@ -56,8 +56,8 @@ diff -up build/pkgs/sagetex/src/extractsagecode.py.orig build/pkgs/sagetex/src/e
   usage()
   sys.exit(2)
 diff -up build/pkgs/sagetex/src/makestatic.py.orig build/pkgs/sagetex/src/makestatic.py
--- build/pkgs/sagetex/src/makestatic.py.orig	2019-01-09 09:51:28.000000000 -0700
+--- build/pkgs/sagetex/src/makestatic.py.orig	2019-10-09 15:29:08.874640308 -0300
-+++ build/pkgs/sagetex/src/makestatic.py	2019-06-27 11:33:54.098080502 -0600
+++ build/pkgs/sagetex/src/makestatic.py	2019-10-09 15:29:13.698667485 -0300
@@ -45,7 +45,7 @@ See the SageTeX documentation for more d
 try:
@ -68,8 +68,8 @@ diff -up build/pkgs/sagetex/src/makestatic.py.orig build/pkgs/sagetex/src/makest
   usage()
   sys.exit(2)
 diff -up build/pkgs/sagetex/src/remote-sagetex.py.orig build/pkgs/sagetex/src/remote-sagetex.py
--- build/pkgs/sagetex/src/remote-sagetex.py.orig	2019-01-09 09:51:28.000000000 -0700
+--- build/pkgs/sagetex/src/remote-sagetex.py.orig	2019-10-09 15:29:08.876640319 -0300
-+++ build/pkgs/sagetex/src/remote-sagetex.py	2019-04-08 11:59:49.263545889 -0600
+++ build/pkgs/sagetex/src/remote-sagetex.py	2019-10-09 15:29:13.698667485 -0300
@@ -24,12 +24,11 @@
 ## You should have received a copy of the GNU General Public License along
 ## with this program.  If not, see <http://www.gnu.org/licenses/>.
@ -133,8 +133,8 @@ diff -up build/pkgs/sagetex/src/remote-sagetex.py.orig build/pkgs/sagetex/src/re
 if not password:
     from getpass import getpass
 diff -up build/pkgs/sagetex/src/sagetexparse.py.orig build/pkgs/sagetex/src/sagetexparse.py
--- build/pkgs/sagetex/src/sagetexparse.py.orig	2019-01-09 09:51:28.000000000 -0700
+--- build/pkgs/sagetex/src/sagetexparse.py.orig	2019-10-09 15:29:08.877640325 -0300
-+++ build/pkgs/sagetex/src/sagetexparse.py	2019-09-10 12:24:06.752516723 -0600
+++ build/pkgs/sagetex/src/sagetexparse.py	2019-10-09 15:29:13.699667491 -0300
@@ -132,7 +132,7 @@ class SageCodeExtractor():
   def plotout(self, s, l, t):
@ -144,42 +144,9 @@ diff -up build/pkgs/sagetex/src/sagetexparse.py.orig build/pkgs/sagetex/src/sage
       self.result += '# format: %s' % t.format[0][1:-1] + '\n'
     self.result += t.code[1:-1] + '\n\n'
 diff -up src/doc/common/conf.py.orig src/doc/common/conf.py
 --- src/doc/common/conf.py.orig	2019-06-26 14:41:04.000000000 -0600
 +++ src/doc/common/conf.py	2019-06-27 11:33:54.099080488 -0600
@@ -566,7 +566,7 @@ skip_picklability_check_modules = [
     #'sage.misc.nested_class_test', # for test only
     'sage.misc.latex',
     'sage.misc.explain_pickle',
 -    '__builtin__',
 +    'builtins',
 ]
 def check_nested_class_picklability(app, what, name, obj, skip, options):
@@ -615,7 +615,7 @@ def skip_member(app, what, name, obj, sk
     if 'SAGE_CHECK_NESTED' in os.environ:
         check_nested_class_picklability(app, what, name, obj, skip, options)
 -    if getattr(obj, '__module__', None) == '__builtin__':
 +    if getattr(obj, '__module__', None) == 'builtins':
         return True
     objname = getattr(obj, "__name__", None)
 diff -up src/sage/coding/linear_code.py.orig src/sage/coding/linear_code.py
 --- src/sage/coding/linear_code.py.orig	2019-06-26 14:41:04.000000000 -0600
 +++ src/sage/coding/linear_code.py	2019-09-10 12:21:10.421332817 -0600
@@ -3793,7 +3793,7 @@ class LinearCode(AbstractLinearCode):
             [1 2 1]
             [2 1 1]
         """
 -        if encoder_name is None or encoder_name is 'GeneratorMatrix':
 +        if encoder_name is None or encoder_name == 'GeneratorMatrix':
             g = self._generator_matrix
         else:
             g = super(LinearCode, self).generator_matrix(encoder_name, **kwargs)
 diff -up src/sage/combinat/finite_state_machine.py.orig src/sage/combinat/finite_state_machine.py
--- src/sage/combinat/finite_state_machine.py.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/sage/combinat/finite_state_machine.py.orig	2019-10-09 15:29:08.880640342 -0300
-+++ src/sage/combinat/finite_state_machine.py	2019-06-27 11:36:38.804783269 -0600
+++ src/sage/combinat/finite_state_machine.py	2019-10-09 15:29:13.703667513 -0300
@@ -936,7 +936,7 @@ from six.moves import range, zip_longest
 from six import itervalues
@ -189,7 +156,7 @@ diff -up src/sage/combinat/finite_state_machine.py.orig src/sage/combinat/finite
 import itertools
 from copy import copy, deepcopy
-@@ -14207,7 +14207,7 @@ def is_FSMProcessIterator(PI):
+@@ -14166,7 +14166,7 @@ def is_FSMProcessIterator(PI):
 class FSMProcessIterator(SageObject,
@ -199,8 +166,8 @@ diff -up src/sage/combinat/finite_state_machine.py.orig src/sage/combinat/finite
     This class takes an input, feeds it into a finite state machine
     (automaton or transducer, in particular), tests whether this was
 diff -up src/sage/combinat/multiset_partition_into_sets_ordered.py.orig src/sage/combinat/multiset_partition_into_sets_ordered.py
--- src/sage/combinat/multiset_partition_into_sets_ordered.py.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/sage/combinat/multiset_partition_into_sets_ordered.py.orig	2019-10-09 15:29:08.882640353 -0300
-+++ src/sage/combinat/multiset_partition_into_sets_ordered.py	2019-09-10 12:20:47.787694285 -0600
+++ src/sage/combinat/multiset_partition_into_sets_ordered.py	2019-10-09 15:29:13.704667519 -0300
@@ -1952,7 +1952,7 @@ class OrderedMultisetPartitionsIntoSets(
         # slice by 'order'
@ -211,8 +178,8 @@ diff -up src/sage/combinat/multiset_partition_into_sets_ordered.py.orig src/sage
         # slice by 'size'
 diff -up src/sage/combinat/root_system/branching_rules.py.orig src/sage/combinat/root_system/branching_rules.py
--- src/sage/combinat/root_system/branching_rules.py.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/sage/combinat/root_system/branching_rules.py.orig	2019-10-09 15:29:08.884640364 -0300
-+++ src/sage/combinat/root_system/branching_rules.py	2019-09-09 15:08:59.383139652 -0600
+++ src/sage/combinat/root_system/branching_rules.py	2019-10-09 15:29:13.707667536 -0300
@@ -1750,7 +1750,7 @@ def branching_rule(Rtype, Stype, rule="d
     elif rule == "tensor" or rule == "tensor-debug":
         if not Stype.is_compound():
@ -222,33 +189,10 @@ diff -up src/sage/combinat/root_system/branching_rules.py.orig src/sage/combinat
             raise ValueError("Not implemented")
         if Rtype[0] == 'A':
             nr = Rtype[1]+1
 diff -up src/sage/cpython/dict_del_by_value.pyx.orig src/sage/cpython/dict_del_by_value.pyx
 --- src/sage/cpython/dict_del_by_value.pyx.orig	2019-06-26 14:41:04.000000000 -0600
 +++ src/sage/cpython/dict_del_by_value.pyx	2019-09-09 15:32:24.921024261 -0600
@@ -291,7 +291,7 @@ ELIF PY_VERSION_HEX>=0x03060000:
             #general lookup function (which can deal with DKIX_DUMMY)
             PyDict_GetItemWithError(<dict>mp,None)
             #this can actually fail if mp is a dictionary with split table
 -            assert DK_LOOKUP(mp) == lookdict
 +            #assert DK_LOOKUP(mp) == lookdict
     cdef del_dictitem_by_exact_value(PyDictObject *mp, PyObject *value, Py_hash_t hash):
         """
@@ -347,8 +347,8 @@ ELIF PY_VERSION_HEX>=0x03060000:
         cdef MyPyDictKeysObject * keys = <MyPyDictKeysObject *>(mp.ma_keys)
         cdef size_t perturb
         cdef size_t mask = <size_t> keys.dk_size-1
 -        cdef PyDictKeyEntry *entries, *ep
 -        entries = DK_ENTRIES(keys)
 +        cdef PyDictKeyEntry *ep
 +        cdef PyDictKeyEntry *entries = DK_ENTRIES(keys)
         if mp.ma_values != NULL:
             print ("del_dictitem_by_exact_value cannot be applied to a shared key dict")
 diff -up src/sage/geometry/triangulation/point_configuration.py.orig src/sage/geometry/triangulation/point_configuration.py
--- src/sage/geometry/triangulation/point_configuration.py.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/sage/geometry/triangulation/point_configuration.py.orig	2019-10-09 15:29:08.886640376 -0300
-+++ src/sage/geometry/triangulation/point_configuration.py	2019-06-27 11:33:54.103080432 -0600
+++ src/sage/geometry/triangulation/point_configuration.py	2019-10-09 15:29:13.707667536 -0300
-@@ -623,7 +623,7 @@ class PointConfiguration(UniqueRepresent
+@@ -619,7 +619,7 @@ class PointConfiguration(UniqueRepresent
             ['{{0,1,2,4},{1,2,3,4}}']
         """
         timeout = 600
@ -257,82 +201,21 @@ diff -up src/sage/geometry/triangulation/point_configuration.py.orig src/sage/ge
         proc.expect(r'Evaluating Commandline Options \.\.\.')
         proc.expect(r'\.\.\. done\.')
         proc.setecho(0)
 diff -up src/sage/graphs/graph_latex.py.orig src/sage/graphs/graph_latex.py
 --- src/sage/graphs/graph_latex.py.orig	2019-06-26 14:41:04.000000000 -0600
 +++ src/sage/graphs/graph_latex.py	2019-09-10 12:23:28.891121378 -0600
@@ -1156,7 +1156,7 @@ class GraphLatex(SageObject):
             #
             elif name in color_dicts:
                 if not isinstance(value, dict):
 -                    raise TypeError('%s option must be a dictionary, not %s' (name, value))
 +                    raise TypeError('%s option must be a dictionary, not %s' % (name, value))
                 else:
                     for key, c in value.items():
                         try:
@@ -1165,42 +1165,42 @@ class GraphLatex(SageObject):
                             raise ValueError('%s option for %s needs to be a matplotlib color (always as a string), not %s' % (name, key, c))
             elif name in positive_scalar_dicts:
                 if not isinstance(value, dict):
 -                    raise TypeError('%s option must be a dictionary, not %s' (name, value))
 +                    raise TypeError('%s option must be a dictionary, not %s' % (name, value))
                 else:
                     for key, x in value.items():
                         if not type(x) in [int, Integer, float, RealLiteral] or not x >= 0.0:
                             raise ValueError('%s option for %s needs to be a positive number, not %s' % (name, key, x))
             elif name in boolean_dicts:
                 if not isinstance(value, dict):
 -                    raise TypeError('%s option must be a dictionary, not %s' (name, value))
 +                    raise TypeError('%s option must be a dictionary, not %s' % (name, value))
                 else:
                     for key, b in value.items():
                         if not isinstance(b, bool):
                             raise ValueError('%s option for %s needs to be True or False, not %s' % (name, key, b))
             elif name == 'vertex_shapes':
                 if not isinstance(value, dict):
 -                    raise TypeError('%s option must be a dictionary, not %s' (name, value))
 +                    raise TypeError('%s option must be a dictionary, not %s' % (name, value))
                 else:
                     for key, s in value.items():
                         if s not in shape_names:
                             raise ValueError('%s option for %s needs to be a vertex shape, not %s' % (name, key, s))
             elif name == 'vertex_label_placements':
                 if not isinstance(value, dict):
 -                    raise TypeError('%s option must be a dictionary, not %s' (name, value))
 +                    raise TypeError('%s option must be a dictionary, not %s' % (name, value))
                 else:
                     for key, p in value.items():
                         if not(p == 'center') and not(isinstance(p, tuple) and len(p) == 2 and type(p[0]) in number_types and p[0] >= 0 and type(p[1]) in number_types and p[1] >= 0):
                             raise ValueError('%s option for %s needs to be None or a pair of positive numbers, not %s' % (name, key, p))
             elif name == 'edge_label_placements':
                 if not isinstance(value, dict):
 -                    raise TypeError('%s option must be a dictionary, not %s' (name, value))
 +                    raise TypeError('%s option must be a dictionary, not %s' % (name, value))
                 else:
                     for key, p in value.items():
                         if not(type(p) in [float, RealLiteral] and (0 <= p) and (p <= 1)) and not(p in label_places):
                             raise ValueError('%s option for %s needs to be a number between 0.0 and 1.0 or a place (like "above"), not %s' % (name, key, p))
             elif name == 'loop_placements':
                 if not isinstance(value, dict):
 -                    raise TypeError('%s option must be a dictionary, not %s' (name, value))
 +                    raise TypeError('%s option must be a dictionary, not %s' % (name, value))
                 else:
                     for key, p in value.items():
                         if not((isinstance(p, tuple)) and (len(p) == 2) and (p[0] >= 0) and (p[1] in compass_points)):
 diff -up src/sage/interfaces/frobby.py.orig src/sage/interfaces/frobby.py
--- src/sage/interfaces/frobby.py.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/sage/interfaces/frobby.py.orig	2019-10-09 15:29:08.888640387 -0300
-+++ src/sage/interfaces/frobby.py	2019-06-27 11:33:54.103080432 -0600
+++ src/sage/interfaces/frobby.py	2019-10-09 15:29:13.707667536 -0300
@@ -77,7 +77,7 @@ class Frobby:
             print("Frobby command: ", repr(command))
             print("Frobby input:\n", input)
 -        process = Popen(command, stdin = PIPE, stdout = PIPE, stderr = PIPE)
-+        process = Popen(command, stdin = PIPE, stdout = PIPE, stderr = PIPE, encoding='utf-8')
+        process = Popen(command, stdin = PIPE, stdout = PIPE, stderr = PIPE, enconding='utf-8')
         output, err = process.communicate(input = input)
         if verbose:
 diff -up src/sage/interfaces/gfan.py.orig src/sage/interfaces/gfan.py
--- src/sage/interfaces/gfan.py.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/sage/interfaces/gfan.py.orig	2019-10-09 15:29:08.889640393 -0300
-+++ src/sage/interfaces/gfan.py	2019-06-27 11:33:54.104080419 -0600
+++ src/sage/interfaces/gfan.py	2019-10-09 15:29:13.708667541 -0300
@@ -66,7 +66,7 @@ class Gfan(object):
         if six.PY2:
             enc_kwargs = {}
@ -343,8 +226,8 @@ diff -up src/sage/interfaces/gfan.py.orig src/sage/interfaces/gfan.py
         gfan_processes = Popen(cmd, stdin=PIPE, stdout=PIPE, stderr=PIPE,
                                **enc_kwargs)
 diff -up src/sage/interfaces/gp.py.orig src/sage/interfaces/gp.py
--- src/sage/interfaces/gp.py.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/sage/interfaces/gp.py.orig	2019-10-09 15:29:08.891640404 -0300
-+++ src/sage/interfaces/gp.py	2019-06-27 11:33:54.104080419 -0600
+++ src/sage/interfaces/gp.py	2019-10-09 15:29:13.709667547 -0300
@@ -934,17 +934,6 @@ class GpElement(ExpectElement):
         """
         return repr(self.type()) == 't_STR'
@ -364,9 +247,9 @@ diff -up src/sage/interfaces/gp.py.orig src/sage/interfaces/gp.py
         """
         Return Python float.
 diff -up src/sage/interfaces/latte.py.orig src/sage/interfaces/latte.py
--- src/sage/interfaces/latte.py.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/sage/interfaces/latte.py.orig	2019-10-09 15:29:08.893640415 -0300
-+++ src/sage/interfaces/latte.py	2019-06-27 11:33:54.104080419 -0600
+++ src/sage/interfaces/latte.py	2019-10-09 15:29:13.709667547 -0300
-@@ -148,6 +148,7 @@ def count(arg, ehrhart_polynomial=False,
+@@ -152,6 +152,7 @@ def count(arg, ehrhart_polynomial=False,
     latte_proc = Popen(args,
                        stdin=PIPE, stdout=PIPE,
                        stderr=(None if verbose else PIPE),
@ -374,7 +257,7 @@ diff -up src/sage/interfaces/latte.py.orig src/sage/interfaces/latte.py
                        cwd=str(SAGE_TMP))
     ans, err = latte_proc.communicate(arg)
-@@ -355,6 +356,7 @@ def integrate(arg, polynomial=None, algo
+@@ -364,6 +365,7 @@ def integrate(arg, polynomial=None, algo
     latte_proc = Popen(args,
                        stdin=PIPE, stdout=PIPE,
                        stderr=(None if verbose else PIPE),
@ -383,8 +266,8 @@ diff -up src/sage/interfaces/latte.py.orig src/sage/interfaces/latte.py
     ans, err = latte_proc.communicate(arg)
 diff -up src/sage/interfaces/sagespawn.pyx.orig src/sage/interfaces/sagespawn.pyx
--- src/sage/interfaces/sagespawn.pyx.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/sage/interfaces/sagespawn.pyx.orig	2019-10-09 15:29:08.894640421 -0300
-+++ src/sage/interfaces/sagespawn.pyx	2019-06-27 11:33:54.104080419 -0600
+++ src/sage/interfaces/sagespawn.pyx	2019-10-09 15:29:13.709667547 -0300
@@ -1,6 +1,6 @@
 """
 Sage wrapper around pexpect's ``spawn`` class and
@ -433,9 +316,9 @@ diff -up src/sage/interfaces/sagespawn.pyx.orig src/sage/interfaces/sagespawn.py
                     pass
             self.fileobj.close()
 diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.pyx
--- src/sage/libs/coxeter3/coxeter.pyx.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/libs/coxeter3/coxeter.pyx.orig	2019-10-09 15:29:08.896640432 -0300
-+++ src/sage/libs/coxeter3/coxeter.pyx	2019-09-12 14:57:59.755712128 -0600
+++ src/sage/libs/coxeter3/coxeter.pyx	2019-10-09 15:29:13.709667547 -0300
-@@ -32,7 +32,7 @@ cdef class String:
+@@ -33,7 +33,7 @@ cdef class String:
         EXAMPLES::
             sage: from sage.libs.coxeter3.coxeter import String       # optional - coxeter3
@ -444,7 +327,7 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
             hello
             sage: del s                                               # optional - coxeter3
         """
-@@ -43,11 +43,11 @@ cdef class String:
+@@ -44,11 +44,11 @@ cdef class String:
         EXAMPLES::
             sage: from sage.libs.coxeter3.coxeter import String       # optional - coxeter3
@ -453,12 +336,12 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
             sage: s                                                   # optional - coxeter3
             Hi
         """
-        return self.x.ptr()
+-        return bytes_to_str(self.x.ptr())
 +        return self.x.ptr().decode('utf-8')
     def __hash__(self):
         """
-@@ -59,7 +59,7 @@ cdef class String:
+@@ -60,7 +60,7 @@ cdef class String:
         EXAMPLES::
             sage: from sage.libs.coxeter3.coxeter import String        # optional - coxeter3
@ -467,7 +350,7 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
             sage: hash(s) == hash('hello')                             # optional - coxeter3
             True
         """
-@@ -70,9 +70,9 @@ cdef class String:
+@@ -71,9 +71,9 @@ cdef class String:
         EXAMPLES::
             sage: from sage.libs.coxeter3.coxeter import String        # optional - coxeter3
@ -480,7 +363,7 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
             sage: ta1 == ta2                                           # optional - coxeter3
             True
             sage: tb != ta1                                            # optional - coxeter3
-@@ -108,7 +108,7 @@ cdef class String:
+@@ -109,7 +109,7 @@ cdef class String:
         EXAMPLES::
             sage: from sage.libs.coxeter3.coxeter import String       # optional - coxeter3
@ -489,7 +372,7 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
             sage: len(s)                                              # optional - coxeter3
             2
         """
-@@ -119,7 +119,7 @@ cdef class String:
+@@ -120,7 +120,7 @@ cdef class String:
         EXAMPLES::
             sage: from sage.libs.coxeter3.coxeter import String       # optional - coxeter3
@ -498,7 +381,7 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
             sage: TestSuite(s).run()                                  # optional - coxeter3
         """
         return (String, (repr(self),) )
-@@ -133,7 +133,7 @@ cdef class Type:
+@@ -134,7 +134,7 @@ cdef class Type:
         EXAMPLES::
             sage: from sage.libs.coxeter3.coxeter import Type         # optional - coxeter3
@ -507,7 +390,7 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
             A
             sage: del t                                               # optional - coxeter3
         """
-@@ -144,17 +144,17 @@ cdef class Type:
+@@ -145,7 +145,7 @@ cdef class Type:
         EXAMPLES::
             sage: from sage.libs.coxeter3.coxeter import Type         # optional - coxeter3
@ -515,11 +398,8 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
 +            sage: t = Type(b'A'); t                                   # optional - coxeter3
             A
         """
-        return self.x.name().ptr()
+         return bytes_to_str(self.x.name().ptr())
-+        return self.x.name().ptr().decode('utf-8')
+@@ -155,7 +155,7 @@ cdef class Type:
     def name(self):
         """
         EXAMPLES::
             sage: from sage.libs.coxeter3.coxeter import Type         # optional - coxeter3
@ -528,7 +408,7 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
             sage: t.name()                                            # optional - coxeter3
             A
         """
-@@ -170,8 +170,8 @@ cdef class Type:
+@@ -171,8 +171,8 @@ cdef class Type:
         EXAMPLES::
             sage: from sage.libs.coxeter3.coxeter import Type          # optional - coxeter3
@ -539,7 +419,7 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
             sage: hash(a) == hash(b)                                   # optional - coxeter3
             False
             sage: d = {a: 1, b: 2}                                     # optional - coxeter3
-@@ -183,9 +183,9 @@ cdef class Type:
+@@ -184,9 +184,9 @@ cdef class Type:
         EXAMPLES::
             sage: from sage.libs.coxeter3.coxeter import Type          # optional - coxeter3
@ -552,7 +432,7 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
             sage: ta1 == ta2                                           # optional - coxeter3
             True
             sage: tb != ta1                                            # optional - coxeter3
-@@ -219,7 +219,7 @@ cdef class Type:
+@@ -220,7 +220,7 @@ cdef class Type:
         EXAMPLES::
             sage: from sage.libs.coxeter3.coxeter import Type           # optional - coxeter3
@ -561,7 +441,7 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
             sage: TestSuite(t).run()                                    # optional - coxeter3
         """
         return (Type, (repr(self), ))
-@@ -256,7 +256,7 @@ cdef class CoxGroup(SageObject):
+@@ -257,7 +257,7 @@ cdef class CoxGroup(SageObject):
             type = type.lower()
             rank = rank + 1
@ -571,8 +451,8 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
         if rank == 0:
             raise NotImplementedError("Coxeter group of type ['A',0] using Coxeter 3 not yet implemented")
 diff -up src/sage/misc/parser.pyx.orig src/sage/misc/parser.pyx
--- src/sage/misc/parser.pyx.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/misc/parser.pyx.orig	2019-10-09 15:29:08.898640443 -0300
-+++ src/sage/misc/parser.pyx	2019-06-27 11:33:54.105080405 -0600
+++ src/sage/misc/parser.pyx	2019-10-09 15:30:11.051990579 -0300
@@ -96,7 +96,7 @@ def token_to_str(int token):
@ -810,7 +690,7 @@ diff -up src/sage/misc/parser.pyx.orig src/sage/misc/parser.pyx
             operand2 = self.p_factor(tokens)
             return operand1 ** operand2
 -        elif token == "!":
-+        elif token == c'!':
+        elif token == c"!":
             from sage.functions.all import factorial
             operand1 = factorial(operand1)
 -            if tokens.peek() == '^':
@ -867,25 +747,13 @@ diff -up src/sage/misc/parser.pyx.orig src/sage/misc/parser.pyx
             tokens.next()
             return name, self.p_expr(tokens)
 -        if token == "[" :
-+        if token == c'[' :
+        if token == c"[" :
             tokens.backtrack()
             return self.p_list(tokens)
         else:
 diff -up src/sage/modular/abvar/abvar.py.orig src/sage/modular/abvar/abvar.py
 --- src/sage/modular/abvar/abvar.py.orig	2019-06-26 14:41:05.000000000 -0600
 +++ src/sage/modular/abvar/abvar.py	2019-09-09 15:08:24.875810751 -0600
@@ -3703,7 +3703,7 @@ class ModularAbelianVariety_abstract(Par
             C = self.__complement
         except AttributeError:
             pass
 -        if self.dimension() is 0:
 +        if self.dimension() == 0:
             if A is None:
                 C = self.ambient_variety()
             else:
 diff -up src/sage/plot/plot3d/plot3d.py.orig src/sage/plot/plot3d/plot3d.py
--- src/sage/plot/plot3d/plot3d.py.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/plot/plot3d/plot3d.py.orig	2019-10-09 15:29:08.899640449 -0300
-+++ src/sage/plot/plot3d/plot3d.py	2019-06-27 11:33:54.105080405 -0600
+++ src/sage/plot/plot3d/plot3d.py	2019-10-09 15:29:13.710667553 -0300
@@ -188,7 +188,8 @@ class _Coordinates(object):
             sage: arb((x+z,y*z,z), z, (x,y))
             Arbitrary Coordinates coordinate transform (z in terms of x, y)
@ -897,8 +765,8 @@ diff -up src/sage/plot/plot3d/plot3d.py.orig src/sage/plot/plot3d/plot3d.py
             raise ValueError('variables were specified incorrectly for this coordinate system; incorrect variables were %s'%list(set(all_vars).symmetric_difference(set(indep_vars+[dep_var]))))
         self.dep_var = dep_var
 diff -up src/sage/plot/point.py.orig src/sage/plot/point.py
--- src/sage/plot/point.py.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/plot/point.py.orig	2019-10-09 15:29:08.901640460 -0300
-+++ src/sage/plot/point.py	2019-06-27 11:33:54.105080405 -0600
+++ src/sage/plot/point.py	2019-10-09 15:29:13.711667558 -0300
@@ -29,7 +29,7 @@ TESTS::
 from sage.misc.decorators import options, rename_keyword
 from sage.plot.colors import to_mpl_color
@ -918,8 +786,8 @@ diff -up src/sage/plot/point.py.orig src/sage/plot/point.py
     try:
 diff -up src/sage/repl/display/fancy_repr.py.orig src/sage/repl/display/fancy_repr.py
--- src/sage/repl/display/fancy_repr.py.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/repl/display/fancy_repr.py.orig	2019-10-09 15:29:08.903640471 -0300
-+++ src/sage/repl/display/fancy_repr.py	2019-06-27 11:33:54.106080391 -0600
+++ src/sage/repl/display/fancy_repr.py	2019-10-09 15:29:13.711667558 -0300
@@ -15,7 +15,7 @@ Representations of objects.
 import types
@ -939,8 +807,8 @@ diff -up src/sage/repl/display/fancy_repr.py.orig src/sage/repl/display/fancy_re
         else:
             # A user-provided repr. Find newlines and replace them with p.break_()
 diff -up src/sage/repl/ipython_kernel/interact.py.orig src/sage/repl/ipython_kernel/interact.py
--- src/sage/repl/ipython_kernel/interact.py.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/repl/ipython_kernel/interact.py.orig	2019-10-09 15:29:08.904640477 -0300
-+++ src/sage/repl/ipython_kernel/interact.py	2019-06-27 11:33:54.106080391 -0600
+++ src/sage/repl/ipython_kernel/interact.py	2019-10-09 15:29:13.711667558 -0300
@@ -35,7 +35,8 @@ EXAMPLES::
 from ipywidgets.widgets import SelectionSlider, ValueWidget, ToggleButtons
@ -952,9 +820,9 @@ diff -up src/sage/repl/ipython_kernel/interact.py.orig src/sage/repl/ipython_ker
 from .widgets_sagenb import input_grid
 from sage.structure.element import parent
 diff -up src/sage/rings/integer.pyx.orig src/sage/rings/integer.pyx
--- src/sage/rings/integer.pyx.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/rings/integer.pyx.orig	2019-10-09 15:29:08.906640488 -0300
-+++ src/sage/rings/integer.pyx	2019-06-27 11:33:54.107080377 -0600
+++ src/sage/rings/integer.pyx	2019-10-09 15:29:13.712667564 -0300
-@@ -6989,7 +6989,7 @@ cdef int mpz_set_str_python(mpz_ptr z, c
+@@ -7124,7 +7124,7 @@ cdef int mpz_set_str_python(mpz_ptr z, c
     while x[0] == c' ': x += 1  # Strip spaces
     # Disallow a sign here
@ -964,9 +832,9 @@ diff -up src/sage/rings/integer.pyx.orig src/sage/rings/integer.pyx
     assert base >= 2
 diff -up src/sage/rings/multi_power_series_ring_element.py.orig src/sage/rings/multi_power_series_ring_element.py
--- src/sage/rings/multi_power_series_ring_element.py.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/rings/multi_power_series_ring_element.py.orig	2019-10-09 15:29:08.908640499 -0300
-+++ src/sage/rings/multi_power_series_ring_element.py	2019-09-09 15:01:45.746217568 -0600
+++ src/sage/rings/multi_power_series_ring_element.py	2019-10-09 15:29:13.712667564 -0300
-@@ -1417,7 +1417,7 @@ class MPowerSeries(PowerSeries):
+@@ -1396,7 +1396,7 @@ class MPowerSeries(PowerSeries):
             # at this stage, self is probably a non-zero
             # element of the base ring
             for a in range(len(self._bg_value.list())):
@ -976,21 +844,21 @@ diff -up src/sage/rings/multi_power_series_ring_element.py.orig src/sage/rings/m
     def is_nilpotent(self):
 diff -up src/sage/rings/polynomial/pbori.pyx.orig src/sage/rings/polynomial/pbori.pyx
--- src/sage/rings/polynomial/pbori.pyx.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/rings/polynomial/pbori.pyx.orig	2019-10-09 15:29:08.910640511 -0300
-+++ src/sage/rings/polynomial/pbori.pyx	2019-06-27 11:33:54.123080154 -0600
+++ src/sage/rings/polynomial/pbori.pyx	2019-10-09 15:29:13.713667570 -0300
@@ -4765,8 +4765,7 @@ cdef class PolynomialConstruct:
             # So, it is just a conversion. [Simon King]
             return (<BooleanPolynomialRing>ring)._element_constructor_(x)
-        raise TypeError("Cannot generate Boolean polynomial from %s , %s%" %
+-        raise TypeError("Cannot generate Boolean polynomial from %s , %s" %
 -                        (type(x), type(ring)))
 +        raise TypeError(f"Cannot generate Boolean polynomial from {type(x)}, {type(ring)}")
 cdef class MonomialConstruct:
 diff -up src/sage/rings/real_mpfi.pyx.orig src/sage/rings/real_mpfi.pyx
--- src/sage/rings/real_mpfi.pyx.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/rings/real_mpfi.pyx.orig	2019-10-09 15:29:08.911640516 -0300
-+++ src/sage/rings/real_mpfi.pyx	2019-06-27 11:33:54.124080141 -0600
+++ src/sage/rings/real_mpfi.pyx	2019-10-09 15:29:13.715667581 -0300
@@ -1943,12 +1943,12 @@ cdef class RealIntervalFieldElement(Ring
         cdef long digits
@ -1016,8 +884,8 @@ diff -up src/sage/rings/real_mpfi.pyx.orig src/sage/rings/real_mpfi.pyx
             mant_string = bytes_to_str(tmp_cstr+1)
             sign_string = bytes_to_str(b'-')
 diff -up src/sage/rings/real_mpfr.pyx.orig src/sage/rings/real_mpfr.pyx
--- src/sage/rings/real_mpfr.pyx.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/rings/real_mpfr.pyx.orig	2019-10-09 15:29:08.913640528 -0300
-+++ src/sage/rings/real_mpfr.pyx	2019-06-27 11:33:54.125080127 -0600
+++ src/sage/rings/real_mpfr.pyx	2019-10-09 15:29:13.715667581 -0300
@@ -2039,7 +2039,7 @@ cdef class RealNumber(sage.structure.ele
         if s is NULL:
             raise RuntimeError("unable to convert an mpfr number to a string")
@ -1028,8 +896,8 @@ diff -up src/sage/rings/real_mpfr.pyx.orig src/sage/rings/real_mpfr.pyx
             t = char_to_str(s + 1)
         else:
 diff -up src/sage/structure/sage_object.pyx.orig src/sage/structure/sage_object.pyx
--- src/sage/structure/sage_object.pyx.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/structure/sage_object.pyx.orig	2019-10-09 15:29:08.915640539 -0300
-+++ src/sage/structure/sage_object.pyx	2019-06-27 11:33:54.126080113 -0600
+++ src/sage/structure/sage_object.pyx	2019-10-09 15:29:13.715667581 -0300
@@ -665,7 +665,7 @@ cdef class SageObject:
             try:
                 s = self._interface_init_(I)
@ -1040,9 +908,9 @@ diff -up src/sage/structure/sage_object.pyx.orig src/sage/structure/sage_object.
         if c:
             try:
 diff -up src/sage/symbolic/expression.pyx.orig src/sage/symbolic/expression.pyx
--- src/sage/symbolic/expression.pyx.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/symbolic/expression.pyx.orig	2019-10-09 15:29:08.917640550 -0300
-+++ src/sage/symbolic/expression.pyx	2019-06-27 11:33:54.128080085 -0600
+++ src/sage/symbolic/expression.pyx	2019-10-09 15:29:13.719667603 -0300
-@@ -12960,7 +12960,7 @@ cdef class hold_class:
+@@ -12916,7 +12916,7 @@ cdef class hold_class:
             sage: SR(2)^5
             32
         """
@ -1051,7 +919,7 @@ diff -up src/sage/symbolic/expression.pyx.orig src/sage/symbolic/expression.pyx
     def __exit__(self, *args):
         """
-@@ -12973,7 +12973,7 @@ cdef class hold_class:
+@@ -12929,7 +12929,7 @@ cdef class hold_class:
             sage: SR(2)^5
             32
         """
@ -1061,9 +929,9 @@ diff -up src/sage/symbolic/expression.pyx.orig src/sage/symbolic/expression.pyx
     def start(self):
         """
 diff -up src/setup.py.orig src/setup.py
--- src/setup.py.orig	2019-06-27 11:30:20.794201914 -0600
+--- src/setup.py.orig	2019-10-09 15:28:16.478345141 -0300
-+++ src/setup.py	2019-06-27 11:33:54.128080085 -0600
+++ src/setup.py	2019-10-09 15:29:13.720667609 -0300
-@@ -232,7 +232,7 @@ class sage_build_cython(Command):
+@@ -233,7 +233,7 @@ class sage_build_cython(Command):
             cdivision=True,
             embedsignature=True,
             fast_getattr=True,
--- a/sagemath-rpmbuild.patch
+++ b/sagemath-rpmbuild.patch
@ -1,6 +1,6 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2019-06-27 11:29:54.622601184 -0600
+--- src/module_list.py.orig	2019-10-03 14:49:57.072685858 -0300
-+++ src/module_list.py	2019-06-27 11:30:20.794201914 -0600
+++ src/module_list.py	2019-10-03 14:50:05.889737429 -0300
@@ -2,7 +2,7 @@ import os
 from distutils.extension import Extension
 from sage.env import SAGE_LOCAL
@ -11,9 +11,9 @@ diff -up src/module_list.py.orig src/module_list.py
 #########################################################
 ### pkg-config setup
 diff -up src/sage/misc/cython.py.orig src/sage/misc/cython.py
--- src/sage/misc/cython.py.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/misc/cython.py.orig	2019-10-03 14:49:48.553636029 -0300
-+++ src/sage/misc/cython.py	2019-06-27 11:30:20.794201914 -0600
+++ src/sage/misc/cython.py	2019-10-03 14:50:05.890737435 -0300
-@@ -49,7 +49,7 @@ standard_libs = [
+@@ -46,7 +46,7 @@ standard_libs = [
 ] + cblas_libs + [
     'ntl']
@ -22,69 +22,3 @@ diff -up src/sage/misc/cython.py.orig src/sage/misc/cython.py
 ################################################################
 diff -up src/setup.py.orig src/setup.py
 --- src/setup.py.orig	2019-06-26 14:41:05.000000000 -0600
 +++ src/setup.py	2019-06-27 11:30:20.794201914 -0600
@@ -318,9 +318,8 @@ class sage_build_cython(Command):
             # Debugging
             gdb_debug=self.debug,
             output_dir=os.path.join(self.build_lib, "sage"),
 -            # Disable Cython caching, which is currently too broken to
 -            # use reliably: http://trac.sagemath.org/ticket/17851
 -            cache=False,
 +            # Enable Cython caching (the cache is stored in ~/.cycache)
 +            cache=True,
             )
         # Filter out extensions with skip_build=True
@@ -795,9 +794,6 @@ class sage_install(install):
         install.run(self)
         self.install_kernel_spec()
         log.info('Cleaning up stale installed files....')
 -        t = time.time()
 -        self.clean_stale_files()
 -        log.info('Finished cleaning, time: %.2f seconds.' % (time.time() - t))
     def install_kernel_spec(self):
         """
@@ -814,40 +810,6 @@ class sage_install(install):
         # the install_data directory for installing our Jupyter files.
         SageKernelSpec.update(prefix=self.install_data)
 -    def clean_stale_files(self):
 -        """
 -        Remove stale installed files.
 -
 -        This removes files which are built/installed but which do not
 -        exist in the Sage sources (typically because some source file
 -        has been deleted). Files are removed from the build directory
 -        ``build/lib-*`` and from the install directory ``site-packages``.
 -        """
 -        dist = self.distribution
 -        cmd_build_py = self.get_finalized_command("build_py")
 -        cmd_build_cython = self.get_finalized_command("build_cython")
 -
 -        # Determine all Python modules inside all packages
 -        py_modules = []
 -        for package in dist.packages:
 -            package_dir = cmd_build_py.get_package_dir(package)
 -            py_modules += cmd_build_py.find_package_modules(package, package_dir)
 -        # modules is a list of triples (package, module, module_file).
 -        # Construct the complete module name from this.
 -        py_modules = ["{0}.{1}".format(*m) for m in py_modules]
 -
 -        # Clean install directory (usually, purelib and platlib are the same)
 -        # and build directory.
 -        output_dirs = [self.install_purelib, self.install_platlib, self.build_lib]
 -        from sage_setup.clean import clean_install_dir
 -        for output_dir in set(output_dirs):
 -            log.info('- cleaning {0}'.format(output_dir))
 -            clean_install_dir(output_dir,
 -                    dist.packages,
 -                    py_modules,
 -                    dist.ext_modules,
 -                    cmd_build_cython.get_cythonized_package_files())
 -
 #########################################################
 ### Distutils
--- a/sagemath-sagedoc.patch
+++ b/sagemath-sagedoc.patch
@ -1,6 +1,6 @@
 diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
--- src/sage/doctest/control.py.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/sage/doctest/control.py.orig	2019-10-03 14:51:45.323319025 -0300
-+++ src/sage/doctest/control.py	2019-06-27 11:30:37.222951288 -0600
+++ src/sage/doctest/control.py	2019-10-03 14:52:24.063545626 -0300
@@ -106,7 +106,6 @@ class DocTestDefaults(SageObject):
         self.valgrind = False
         self.massif = False
@ -46,18 +46,18 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
             return self.run_val_gdb()
         else:
 diff -up src/sage/interfaces/singular.py.orig src/sage/interfaces/singular.py
--- src/sage/interfaces/singular.py.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage/interfaces/singular.py.orig	2019-10-03 14:52:35.554612838 -0300
-+++ src/sage/interfaces/singular.py	2019-06-27 11:30:37.223951272 -0600
+++ src/sage/interfaces/singular.py	2019-10-03 14:53:22.502887441 -0300
-@@ -2261,7 +2261,7 @@ def generate_docstring_dictionary():
+@@ -2262,7 +2262,7 @@ def generate_docstring_dictionary():
     nodes.clear()
     node_names.clear()
-    singular_docdir = os.environ['SINGULARPATH']+"/../info/"
+-    singular_docdir = SINGULARPATH + "/../info/"
 +    singular_docdir = "/usr/share/info/"
     new_node = re.compile(r"File: singular\.hlp,  Node: ([^,]*),.*")
     new_lookup = re.compile(r"\* ([^:]*):*([^.]*)\..*")
-@@ -2269,8 +2269,9 @@ def generate_docstring_dictionary():
+@@ -2270,8 +2270,9 @@ def generate_docstring_dictionary():
     L, in_node, curr_node = [], False, None
     # singular.hlp contains a few iso-5559-1 encoded special characters
@ -70,8 +70,8 @@ diff -up src/sage/interfaces/singular.py.orig src/sage/interfaces/singular.py
             m = re.match(new_node,line)
             if m:
 diff -up src/sage_setup/docbuild/ext/multidocs.py.orig src/sage_setup/docbuild/ext/multidocs.py
--- src/sage_setup/docbuild/ext/multidocs.py.orig	2019-06-26 14:41:05.000000000 -0600
+--- src/sage_setup/docbuild/ext/multidocs.py.orig	2019-10-03 14:53:32.585946418 -0300
-+++ src/sage_setup/docbuild/ext/multidocs.py	2019-06-27 11:30:37.224951257 -0600
+++ src/sage_setup/docbuild/ext/multidocs.py	2019-10-03 14:54:02.207119676 -0300
@@ -85,8 +85,11 @@ def merge_environment(app, env):
             for ind in newalldoc:
                 # treat subdocument source as orphaned file and don't complain
@ -86,23 +86,3 @@ diff -up src/sage_setup/docbuild/ext/multidocs.py.orig src/sage_setup/docbuild/e
             # merge the citations
             newcite = {}
             citations = docenv.domaindata["std"]["citations"]
 diff -up src/sage_setup/docbuild/__init__.py.orig src/sage_setup/docbuild/__init__.py
 --- src/sage_setup/docbuild/__init__.py.orig	2019-06-26 14:41:05.000000000 -0600
 +++ src/sage_setup/docbuild/__init__.py	2019-06-27 11:30:37.225951242 -0600
@@ -284,13 +284,14 @@ if not (CYGWIN_VERSION and CYGWIN_VERSIO
         # map_async handles KeyboardInterrupt correctly. Plain map and
         # apply_async does not, so don't use it.
         x = pool.map_async(target, args, 1)
 +        ret = []
         try:
 -            ret = x.get(99999)
 +            ret = x.get(3600)
             pool.close()
             pool.join()
         except Exception:
 -            pool.terminate()
             if ABORT_ON_ERROR:
 +                pool.terminate()
                 raise
         return ret
 else:
--- a/sagemath-sagetex.patch
+++ b/sagemath-sagetex.patch
@ -1,11 +1,11 @@
 diff -up build/pkgs/sagetex/src/run-sagetex-if-necessary.py.orig build/pkgs/sagetex/src/run-sagetex-if-necessary.py
--- build/pkgs/sagetex/src/run-sagetex-if-necessary.py.orig	2019-01-09 09:51:28.000000000 -0700
+--- build/pkgs/sagetex/src/run-sagetex-if-necessary.py.orig	2019-10-03 16:56:05.217343030 -0300
-+++ build/pkgs/sagetex/src/run-sagetex-if-necessary.py	2019-04-09 11:39:25.457566883 -0600
+++ build/pkgs/sagetex/src/run-sagetex-if-necessary.py	2019-10-03 16:56:23.334451227 -0300
-@@ -63,7 +63,7 @@ if not uses_sagetex:
+@@ -64,7 +64,7 @@ if not uses_sagetex:
 # if something goes wrong, assume we need to run Sage
 run_sage = True
-        ignore = r"^( _st_.goboom|print('SageT| ?_st_.current_tex_line))"
+-ignore = r"^( _st_.goboom|print\('SageT| ?_st_.current_tex_line)"
 +ignore = r"^( _st_.goboom|print('SageT| ?_st_.current_tex_line))"
 try:
--- a/sagemath-scripts.patch
+++ b/sagemath-scripts.patch
@ -1,6 +1,6 @@
 diff -up src/bin/sage.orig src/bin/sage
--- src/bin/sage.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/bin/sage.orig	2019-10-03 14:38:40.429507574 -0300
-+++ src/bin/sage	2019-06-27 11:28:35.352810438 -0600
+++ src/bin/sage	2019-10-03 14:47:00.852631198 -0300
@@ -26,13 +26,10 @@ usage() {
     echo "  file.[sage|py|spyx] -- run given .sage, .py or .spyx file"
     echo "  -advanced           -- list all command line options"
@ -55,13 +55,13 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "  -inotebook [...]    -- start the *insecure* Sage notebook (deprecated)"
     echo "  -n, -notebook [...] -- start the default Sage notebook (options are the"
     echo "                         same as for the notebook command in Sage).  See the"
-@@ -119,18 +106,11 @@ usage_advanced() {
+@@ -119,18 +106,12 @@ usage_advanced() {
     echo "                         Sage), passing additional options to IPython"
     echo "  -ipython3 [...]     -- same as above, but using Python 3"
     echo "  -jupyter [...]      -- run Sage's Jupyter with given arguments"
 -    echo "  -kash [...]         -- run Sage's Kash with given arguments"
 -    command -v kash &>/dev/null || \
-    echo "                         (not installed currently, run sage -i kash)"
+     echo "                         (not installed currently, run sage -i kash)"
     echo "  -lisp [...]         -- run Lisp interpreter included with Sage"
     echo "  -M2 [...]           -- run Sage's Macaulay2 with given arguments"
 -    command -v M2 &>/dev/null || \
@ -74,7 +74,7 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "  -python [...]       -- run the Python interpreter"
     echo "  -python2 [...]      -- run the Python 2 interpreter"
     echo "  -python3 [...]      -- run the Python 3 interpreter"
-@@ -144,55 +124,7 @@ usage_advanced() {
+@@ -144,55 +125,7 @@ usage_advanced() {
     echo
     ####  1.......................26..................................................78
     ####  |.....................--.|...................................................|
@ -131,7 +131,7 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "  -startuptime [module] -- display how long each component of Sage takes to"
     echo "                         start up; optionally specify a module to get more"
     echo "                         details about that particular module"
-@@ -226,7 +158,6 @@ usage_advanced() {
+@@ -226,7 +159,6 @@ usage_advanced() {
     echo "  -coverage <files>   -- give info about doctest coverage of files"
     echo "  -coverageall        -- give summary info about doctest coverage of all"
     echo "                         files in the Sage library"
@ -139,7 +139,7 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "  -search_src <string> -- search through all the Sage library code for string"
     echo "  -search_doc <string> -- search through the Sage documentation for string"
     echo "  -grep <string>      -- same as -search_src"
-@@ -252,16 +183,6 @@ usage_advanced() {
+@@ -252,16 +184,6 @@ usage_advanced() {
     echo
     ####  1.......................26..................................................78
     ####  |.....................--.|...................................................|
@ -156,7 +156,7 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "Valgrind memory debugging:"
     echo "  -cachegrind         -- run Sage using Valgrind's cachegrind tool.  The log"
     echo "                         files are named sage-cachegrind.PID can be found in"
-@@ -275,9 +196,6 @@ usage_advanced() {
+@@ -275,9 +197,6 @@ usage_advanced() {
     echo "  -memcheck           -- run Sage using Valgrind's memcheck tool.  The log"
     echo "                         files are named sage-memcheck.PID can be found in"
     echo "                         $DOT_SAGE"
@ -166,7 +166,7 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "  -valgrind           -- this is an alias for -memcheck"
     echo
     echo "You can also use -- before a long option, e.g., 'sage --optional'."
-@@ -287,116 +205,6 @@ usage_advanced() {
+@@ -287,116 +206,6 @@ usage_advanced() {
 #####################################################################
@ -283,27 +283,12 @@ diff -up src/bin/sage.orig src/bin/sage
 # Report information about the Sage environment
 #####################################################################
-@@ -425,35 +233,8 @@ if [ $# -gt 0 ]; then
+@@ -445,20 +254,6 @@ fi
 fi
 -#####################################################################
 -# Source sage-env ($0 is the name of this "sage" script, so we can just
 -# append -env to that). We redirect stdout to stderr, which is safer
 -# for scripts.
 -#####################################################################
 -. "$0-env" >&2
 -if [ $? -ne 0 ]; then
 -    echo >&2 "Error setting environment variables by sourcing '$0-env';"
 -    echo >&2 "possibly contact sage-devel (see http://groups.google.com/group/sage-devel)."
 -    exit 1
 -fi
 -
 -
 # Prepare for running Sage, either interactively or non-interactively.
 sage_setup() {
 -    # Check that we're not in a source tarball which hasn't been built yet (#13561).
-    if [ ! -x "$SAGE_LOCAL/bin/sage" ]; then
+-    if [ ! -z "$SAGE_LOCAL" ] && [ ! -x "$SAGE_LOCAL/bin/sage" ]; then
 -        echo >&2 '************************************************************************'
 -        echo >&2 'It seems that you are attempting to run Sage from an unpacked source'
 -        echo >&2 'tarball, but you have not compiled it yet (or maybe the build has not'
@ -319,7 +304,7 @@ diff -up src/bin/sage.orig src/bin/sage
     if [ ! -d "$IPYTHONDIR" ]; then
         # make sure that $DOT_SAGE exists so that ipython will happily
         # create its config directories there.  If DOT_SAGE doesn't
-@@ -464,20 +245,6 @@ sage_setup() {
+@@ -469,20 +264,6 @@ sage_setup() {
 }
@ -340,7 +325,7 @@ diff -up src/bin/sage.orig src/bin/sage
 # Start an interactive Sage session, this function never returns.
 interactive_sage() {
     sage_setup
-@@ -561,16 +328,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
+@@ -566,16 +347,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
     exec ecl "$@"
 fi
@ -357,7 +342,7 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
     shift
     exec maxima "$@"
-@@ -601,11 +358,6 @@ if [ "$1" = '--pip3' ]; then
+@@ -606,11 +377,6 @@ if [ "$1" = '--pip3' ]; then
     exec python3 -m pip "$@"
 fi
@ -369,7 +354,7 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ "$1" = '-python' -o "$1" = '--python' ]; then
     shift
     if [ "$SAGE_PYTHON3" = 'yes' ]; then
-@@ -645,16 +397,6 @@ if [ "$1" = '-jupyter' -o "$1" = '--jupy
+@@ -650,16 +416,6 @@ if [ "$1" = '-jupyter' -o "$1" = '--jupy
     exec jupyter "$@"
 fi
@ -386,7 +371,7 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
     # AUTHORS:
     # - Carl Witty and William Stein: initial version
-@@ -774,20 +516,6 @@ EOF
+@@ -779,20 +535,6 @@ EOF
 fi
 #####################################################################
@ -407,7 +392,7 @@ diff -up src/bin/sage.orig src/bin/sage
 # File conversion
 #####################################################################
-@@ -818,11 +546,6 @@ fi
+@@ -823,11 +565,6 @@ fi
 # Run Sage's versions of the standard Algebra/Geometry etc. software
 #####################################################################
@ -419,7 +404,7 @@ diff -up src/bin/sage.orig src/bin/sage
 if [[ "$1" =~ ^--notebook=.* || "$1" =~ ^-n=.* || "$1" =~ ^-notebook=.* ]] ; then
     sage-cleaner &>/dev/null &
     exec sage-notebook "$@"
-@@ -833,13 +556,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
+@@ -838,13 +575,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
     exec sage-notebook "$@"
 fi
@ -433,7 +418,7 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
     shift
     sage-cleaner &>/dev/null &
-@@ -858,34 +574,15 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
+@@ -863,31 +593,12 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
     exit 0
 fi
@ -465,12 +450,8 @@ diff -up src/bin/sage.orig src/bin/sage
 +if [ "$1" = '-t' -o "$1" = '-tp' ]; then
     sage_setup
     export PYTHONIOENCODING="utf-8"  # Fix encoding for doctests
-    if [ "$1" = '-tp' -o "$1" = '-btp' ]; then
+     if [ "$1" = '-tp' -o "$1" = '-btp' ]; then
-+    if [ "$1" = '-tp' ]; then
+@@ -899,16 +610,6 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
         shift
         exec sage-runtests -p "$@"
     else
@@ -894,10 +591,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
     fi
 fi
@ -478,11 +459,16 @@ diff -up src/bin/sage.orig src/bin/sage
 -    if [ "$1" = '-btnew' ]; then
 -        build_sage
 -    fi
-+if [ "$1" = '-tnew' ]; then
+-    shift
 -    sage_setup
 -    export PYTHONIOENCODING="utf-8"  # Fix encoding for doctests
 -    exec sage-runtests --new "$@"
 -fi
 -
 if [ "$1" = '-testall' -o "$1" = "--testall" ]; then
     shift
     sage_setup
-     export PYTHONIOENCODING="utf-8"  # Fix encoding for doctests
+@@ -923,122 +624,6 @@ if [ "$1" = '-c' ]; then
@@ -918,122 +612,6 @@ if [ "$1" = '-c' ]; then
     exec sage-eval "$@"
 fi
@ -605,7 +591,7 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
     shift
     sage_setup
-@@ -1083,12 +661,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
+@@ -1088,12 +673,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
     exec sage-callgrind "$@"
 fi
@ -618,25 +604,12 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ "$1" = '-startuptime' -o "$1" = '--startuptime' ]; then
     exec sage-startuptime.py "$@"
 fi
 diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
 --- src/bin/sage-runtests.orig	2019-06-26 14:41:04.000000000 -0600
 +++ src/bin/sage-runtests	2019-06-27 11:22:47.435227309 -0600
@@ -95,10 +95,6 @@ if __name__ == "__main__":
                       help="run doctests using Valgrind's cachegrind tool.  The log "
                          "files are named sage-cachegrind.PID and can be found in " +
                          os.path.join(DOT_SAGE, "valgrind"))
 -    parser.add_option("--omega", action="store_true", default=False,
 -                      help="run doctests using Valgrind's omega tool.  The log "
 -                         "files are named sage-omega.PID and can be found in " +
 -                         os.path.join(DOT_SAGE, "valgrind"))
     parser.add_option("-f", "--failed", action="store_true", default=False,
         help="doctest only those files that failed in the previous run")
 diff -up src/bin/sage-valgrind.orig src/bin/sage-valgrind
--- src/bin/sage-valgrind.orig	2019-06-26 14:41:04.000000000 -0600
+--- src/bin/sage-valgrind.orig	2019-10-03 14:47:13.247708565 -0300
-+++ src/bin/sage-valgrind	2019-06-27 11:22:47.435227309 -0600
+++ src/bin/sage-valgrind	2019-10-03 14:47:46.404915531 -0300
-@@ -1,16 +1,6 @@
+@@ -4,17 +4,7 @@ if [ -z $SAGE_EXTCODE ]; then
- #!/usr/bin/env bash
+     SAGE_EXTCODE=`${0/-valgrind} -c "from sage.env import SAGE_EXTCODE; print(SAGE_EXTCODE)"`
 fi
 -SUPP=""
 -if [ -f "$SAGE_EXTCODE/valgrind/python.supp" ]; then
--- a/sagemath-sympy.patch
+++ b/sagemath-sympy.patch
@ -1,6 +1,6 @@
 diff -up src/sage/env.py.orig src/sage/env.py
--- src/sage/env.py.orig	2019-04-08 12:41:09.686920533 -0600
+--- src/sage/env.py.orig	2019-10-03 16:07:45.910528067 -0300
-+++ src/sage/env.py	2019-04-08 12:42:41.240282849 -0600
+++ src/sage/env.py	2019-10-03 16:08:40.659874228 -0300
@@ -159,9 +159,9 @@ var('SAGE_DOC',            join(SAGE_SHA
 var('SAGE_SPKG_INST',      join(SAGE_LOCAL, 'var', 'lib', 'sage', 'installed'))
 var('SAGE_LIB',            os.path.dirname(os.path.dirname(sage.__file__)))
@ -8,7 +8,7 @@ diff -up src/sage/env.py.orig src/sage/env.py
 -var('SAGE_ROOT')           # no fallback for SAGE_ROOT
 +var('SAGE_ROOT',           '@@SAGE_ROOT@@')
 var('SAGE_SRC',            join(SAGE_ROOT, 'src'), SAGE_LIB)
-var('SAGE_DOC_SRC',        join(SAGE_SRC, 'doc'))
+-var('SAGE_DOC_SRC',        join(SAGE_ROOT, 'src', 'doc'), SAGE_DOC)
 +var('SAGE_DOC_SRC',        '@@SAGE_DOC@@')
 var('SAGE_PKGS',           join(SAGE_ROOT, 'build', 'pkgs'))
 var('SAGE_ROOT_GIT',       join(SAGE_ROOT, '.git'))
--- a/sagemath.spec
+++ b/sagemath.spec
@ -60,15 +60,15 @@
 %global polytopes_db_pkg	polytopes_db-20170220
 %global rubiks_pkg		rubiks-20070912
 %global	sagenb_pkg		sagenb-1.1.2
-%global sagetex_pkg		sagetex-3.2
+%global sagetex_pkg		sagetex-3.3
 %global Sphinx_pkg		Sphinx-1.8.5
-%global singular_pkg		singular-4.1.1p3
+%global singular_pkg		singular-4.1.1p2
 %if %{with bundled_thebe}
 %global thebe_ver		9624e0a0
 %global thebe_pkg		thebe-%{thebe_ver}
 %endif
 %if %{with bundled_threejs}
-%global threejs_ver		r100
+%global threejs_ver		r105
 %global threejs_pkg		threejs-%{threejs_ver}
 %endif
 %if %{with bundled_widgetsnbextension}
@ -94,8 +94,8 @@
 Name:		sagemath
 Summary:	A free open-source mathematics software system
-Version:	8.8
+Version:	8.9
-Release:	7%{?dist}
+Release:	1%{?dist}
 # The file ${SAGE_ROOT}/COPYING.txt is the upstream license breakdown file
 # Additionally, every $files section has a comment with the license name
 # before files with that license
@ -180,45 +180,37 @@ Patch20:	%{name}-sympy.patch
 # Correct unable to start QEPCAD within sage
 # https://bugzilla.redhat.com/show_bug.cgi?id=1243590
-Patch22:	%{name}-qepcad.patch
+Patch21:	%{name}-qepcad.patch
 # Correct path to arb headers
-Patch23:	%{name}-arb.patch
+Patch22:	%{name}-arb.patch
 # Add missing escapes, or convert strings to raw strings
 Patch24:	%{name}-escape.patch
 # Add missing include paths
-Patch25:	%{name}-includes.patch
+Patch23:	%{name}-includes.patch
 # Use openblas
-Patch26:	%{name}-openblas.patch
+Patch24:	%{name}-openblas.patch
 # Fix paths to latte-integrale binaries
-Patch27:	%{name}-latte.patch
+Patch25:	%{name}-latte.patch
 # Upstream fixes for random SIGFPEs due to ecl messing with the fp state
-Patch28:	%{name}-sigfpe.patch
+Patch26:	%{name}-sigfpe.patch
 # Add some missing #includes and types in the rubiks code
-Patch29:	%{name}-rubiks.patch
+Patch27:	%{name}-rubiks.patch
 # Fix an indentation error in sagetex
-Patch30:	%{name}-sagetex.patch
+Patch28:	%{name}-sagetex.patch
 # Fix some path settings in the sage environment
-Patch31:	%{name}-env.patch
+Patch29:	%{name}-env.patch
 # Make notebook minimally function until upstream finally removes it
-Patch32:	%{name}-sagenb-python3.patch
+Patch30:	%{name}-sagenb-python3.patch
 # Replace python's deprecated formatargspec with a custom implementation
 # https://trac.sagemath.org/ticket/27971
 # https://git.sagemath.org/sage.git/commit/?id=bbd5b28fc8e451bea4f87c2f2b0c27586386262a
 Patch33:	%{name}-formatargspec.patch
 # Adapt to primecount 5.x
-Patch34:	%{name}-primecount.patch
+Patch31:	%{name}-primecount.patch
 BuildRequires:	4ti2
 BuildRequires:	arb-devel
@ -908,6 +900,7 @@ popd
 %endif
 %patch20
 %patch21
 %patch22
 %patch23
 %patch24
@ -918,9 +911,6 @@ popd
 %patch29
 %patch30
 %patch31
 %patch32
 %patch33
 %patch34
 sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
    -e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \
@ -1279,6 +1269,10 @@ pushd $SAGE_LOCAL/bin/
 	spkg-install
 popd
 #------------------------------------------------------------------------
 (
    source build/bin/sage-dist-helpers
 #------------------------------------------------------------------------
 pushd build/pkgs/combinatorial_designs
    chmod a+x spkg-install
@ -1318,7 +1312,7 @@ pushd build/pkgs/sagetex/src
    %py3_install "--install-purelib=%{python3_sitearch}"
    mv %{buildroot}%{_texmf}/tex/latex/sagetex/CONTRIBUTORS \
 	 %{buildroot}%{_docdir}/sagetex
-    for file in PKG-INFO README; do
+    for file in PKG-INFO; do
 	install -p -m 0644 $file %{buildroot}%{_docdir}/sagetex/$file
    done
 popd
@ -1358,6 +1352,9 @@ pushd build/pkgs/widgetsnbextension/src
 popd
 %endif
 #------------------------------------------------------------------------
 ) # source build/bin/sage-dist-helpers
 #------------------------------------------------------------------------
 cat > %{buildroot}%{SAGE_LOCAL}/bin/sage-env << EOF
 export CUR=\$PWD
@ -1485,11 +1482,6 @@ perl -pi -e 's|%{buildroot}||g;' \
 # with docs
 %endif
 # Script was used to build documentation
 perl -pi -e 's|%{buildroot}||g;s|^##||g;' \
 	%{buildroot}%{_bindir}/sage \
 	%{buildroot}%{SAGE_LOCAL}/bin/sage-env
 #------------------------------------------------------------------------
 # Fix links
 export SAGE_SRC=%{buildroot}%{SAGE_SRC}
@ -1635,8 +1627,8 @@ popd
 #------------------------------------------------------------------------
 # Build the large Cremona database
-PATH=%{buildroot}%{SAGE_LOCAL}/bin:$PATH
+export PATH=%{buildroot}%{SAGE_LOCAL}/bin:$PATH
-PYTHONPATH=%{buildroot}%{SAGE_PYTHONPATH}:%{buildroot}%{python3_sitearch}
+export PYTHONPATH=%{buildroot}%{SAGE_PYTHONPATH}:%{buildroot}%{python3_sitearch}
 cat > cremona.sage << EOF
 import sage.databases.cremona
 db_path = '%{buildroot}%{SAGE_SHARE}/cremona/cremona'
@ -1645,6 +1637,12 @@ c._init_from_ftpdata('ecdata-%{cremona_ver}')
 EOF
 %{buildroot}%{SAGE_LOCAL}/bin/sage cremona.sage
 #------------------------------------------------------------------------
 # Script was used to build documentation and possibly other operations
 perl -pi -e 's|%{buildroot}||g;s|^##||g;' \
 	%{buildroot}%{_bindir}/sage \
 	%{buildroot}%{SAGE_LOCAL}/bin/sage-env
 # last install command
 rm -fr $DOT_SAGE
@ -1929,6 +1927,10 @@ rm -fr %{SAGE_LOCAL}/var/lib/sage/installed/database_cremona_ellcurve-%{cremona_
 ########################################################################
 %changelog
 * Thu Nov  7 2019 pcpa <paulo.cesar.pereira.de.andrade@gmail.com> - 8.9-1
 - Update to latest upstream release
 - Drop no longer need patches and rediff current ones
 * Fri Oct 11 2019 Jerry James <loganjerry@gmail.com> - 8.8-7
 - Rebuild for mpfr 4
 - Drop -mpfr patch
--- a/2
+++ b/2
@ -1,2 +1,2 @@
 SHA512 (sage-8.8.tar.gz) = bac6cdd07e1c1bb36cf8617bc5b580818048702f9f73ba1d034e0ae100bbdb7f2ef3f2133d7cea739c98f103ca9e3b90a7c29d87314fb398b9d7984f194d0357
 SHA512 (cremona-2016-10-17.tar.gz) = 61f55ec5c15e32b5fdaf1fe8f2f3d50ba9afa542d8634918ec9493d739127f8c06a44b3cb1227a2979522baf61951ac37a67ae2b12c920958b04f8198d07ff57
 SHA512 (sage-8.9.tar.gz) = 056646488f0b3fc092057c7ff807762c2f98d13748e14540ae9a67ceb3a3d62f8c0263c80c61a36c423353d7051e2dfae466a3f452f3910d9ba95ef26b385e94