diff --git a/sagemath-env.patch b/sagemath-env.patch
new file mode 100644
index 0000000..7f69094
--- /dev/null
+++ b/sagemath-env.patch
@@ -0,0 +1,41 @@
+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	2019-06-28 11:31:09.965474086 -0600
+@@ -151,11 +151,11 @@ var('SAGE_DATE',           version.date)
+ var('SAGE_VERSION_BANNER', version.banner)
+ 
+ # bunch of sage directories and files
+-var('SAGE_LOCAL',          os.path.abspath(sys.prefix))
+-var('SAGE_ETC',            join(SAGE_LOCAL, 'etc'))
+-var('SAGE_INC',            join(SAGE_LOCAL, 'include'))
+-var('SAGE_SHARE',          join(SAGE_LOCAL, 'share'))
+-var('SAGE_DOC',            join(SAGE_SHARE, 'doc', 'sage'))
++var('SAGE_LOCAL',          '@@SAGE_LOCAL@@')
++var('SAGE_ETC',            join('/usr', 'share', 'sagemath', 'etc'))
++var('SAGE_INC',            join('/usr', 'include'))
++var('SAGE_SHARE',          join('/usr', 'share', 'sagemath'))
++var('SAGE_DOC',            join('/usr', 'share', 'doc', 'sagemath'))
+ var('SAGE_SPKG_INST',      join(SAGE_LOCAL, 'var', 'lib', 'sage', 'installed'))
+ var('SAGE_LIB',            os.path.dirname(os.path.dirname(sage.__file__)))
+ 
+@@ -169,7 +169,7 @@ var('DOT_SAGE',            join(os.envir
+ var('SAGE_STARTUP_FILE',   join(DOT_SAGE, 'init.sage'))
+ 
+ # installation directories for various packages
+-var('SAGE_EXTCODE',                  join(SAGE_SHARE, 'sage', 'ext'))
++var('SAGE_EXTCODE',                  join('/usr', 'share', 'sagemath', 'etc'))
+ 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
+ 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('THREEJS_DIR',                   join(SAGE_SHARE, 'threejs'))
+-var('PPLPY_DOCS',                    join(SAGE_SHARE, 'doc', 'pplpy'))
++var('PPLPY_DOCS',                    join('/usr', 'share', 'doc', 'python3-pplpy'))
+ var('MAXIMA_FAS')
+ 
+ # misc
diff --git a/sagemath-escape.patch b/sagemath-escape.patch
index 57e58ae..16ee016 100644
--- a/sagemath-escape.patch
+++ b/sagemath-escape.patch
@@ -1,6 +1,6 @@
 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	2019-03-23 16:20:34.000000000 -0600
-+++ src/sage/combinat/crystals/alcove_path.py	2019-04-08 13:33:18.101386015 -0600
+--- 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
@@ -11,8 +11,8 @@ diff -up src/sage/combinat/crystals/alcove_path.py.orig src/sage/combinat/crysta
  
          .. WARNING::
 diff -up src/sage/homology/homology_group.py.orig src/sage/homology/homology_group.py
---- src/sage/homology/homology_group.py.orig	2019-03-23 16:20:40.000000000 -0600
-+++ src/sage/homology/homology_group.py	2019-04-08 13:33:22.436307576 -0600
+--- src/sage/homology/homology_group.py.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/sage/homology/homology_group.py	2019-06-27 11:46:03.614253830 -0600
 @@ -109,7 +109,7 @@ class HomologyGroup_class(AdditiveAbelia
              sage: from sage.homology.homology_group import HomologyGroup
              sage: H = HomologyGroup(7, ZZ, [4,4,4,4,4,7,7])
@@ -22,36 +22,3 @@ diff -up src/sage/homology/homology_group.py.orig src/sage/homology/homology_gro
              sage: latex(HomologyGroup(6, ZZ))
              \ZZ^{6}
          """
-diff -up src/sage/rings/function_field/differential.py.orig src/sage/rings/function_field/differential.py
---- src/sage/rings/function_field/differential.py.orig	2019-03-23 16:20:42.000000000 -0600
-+++ src/sage/rings/function_field/differential.py	2019-04-09 10:42:43.202792022 -0600
-@@ -360,7 +360,7 @@ class FunctionFieldDifferential_global(F
-             return to_R(c)
- 
-     def cartier(self):
--        """
-+        r"""
-         Return the image of the differential by the Cartier operator.
- 
-         The Cartier operator operates on differentials. Let `x` be a separating
-diff -up src/sage/rings/function_field/divisor.py.orig src/sage/rings/function_field/divisor.py
---- src/sage/rings/function_field/divisor.py.orig	2019-03-23 16:20:42.000000000 -0600
-+++ src/sage/rings/function_field/divisor.py	2019-04-09 10:42:22.061135616 -0600
-@@ -531,7 +531,7 @@ class FunctionFieldDivisor(ModuleElement
-         return basis, coordinates_func
- 
-     def basis_differential_space(self):
--        """
-+        r"""
-         Return a basis of the space of differentials `\Omega(D)`
-         for the divisor `D`.
- 
-@@ -554,7 +554,7 @@ class FunctionFieldDivisor(ModuleElement
-         return [W.element_class(W, f) for f in fbasis]
- 
-     def differential_space(self):
--        """
-+        r"""
-         Return the vector space of the differential space `\Omega(D)` of the divisor `D`.
- 
-         OUTPUT:
diff --git a/sagemath-extensions.patch b/sagemath-extensions.patch
index ba0a447..01b43b2 100644
--- a/sagemath-extensions.patch
+++ b/sagemath-extensions.patch
@@ -1,6 +1,6 @@
-diff -up src/module_list.py.origsrc/module_list.py
---- src/module_list.py.orig	2018-12-22 16:37:06.000000000 -0700
-+++ src/module_list.py	2019-01-16 09:42:29.021226961 -0700
+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	2019-06-27 11:29:54.622601184 -0600
 @@ -357,16 +357,16 @@ ext_modules = [
      Extension('sage.graphs.matchpoly',
                sources = ['sage/graphs/matchpoly.pyx']),
@@ -42,7 +42,7 @@ diff -up src/module_list.py.origsrc/module_list.py
  
      Extension('sage.graphs.spanning_tree',
                sources = ['sage/graphs/spanning_tree.pyx']),
-@@ -460,21 +460,20 @@ ext_modules = [
+@@ -461,21 +461,20 @@ ext_modules = [
      ##
      ################################
  
@@ -72,7 +72,7 @@ diff -up src/module_list.py.origsrc/module_list.py
  
      Extension('sage.libs.flint.flint',
                sources = ["sage/libs/flint/flint.pyx"],
-@@ -840,10 +839,10 @@ ext_modules = [
+@@ -841,10 +840,10 @@ ext_modules = [
      Extension('sage.matrix.matrix_window',
                sources = ['sage/matrix/matrix_window.pyx']),
  
@@ -87,7 +87,7 @@ diff -up src/module_list.py.origsrc/module_list.py
  
      Extension('sage.matrix.misc',
                sources = ['sage/matrix/misc.pyx']),
-@@ -1020,26 +1019,25 @@ ext_modules = [
+@@ -1021,26 +1020,25 @@ ext_modules = [
      Extension("sage.numerical.backends.interactivelp_backend",
                ["sage/numerical/backends/interactivelp_backend.pyx"]),
  
diff --git a/sagemath-fes.patch b/sagemath-fes.patch
index 25c447b..4bb46d1 100644
--- 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	2019-01-16 09:45:43.332740109 -0700
-+++ src/module_list.py	2019-01-16 09:46:10.613250567 -0700
-@@ -470,10 +470,10 @@ ext_modules = [
+--- src/module_list.py.orig	2019-06-27 11:38:23.103196674 -0600
++++ src/module_list.py	2019-06-27 11:44:42.052478294 -0600
+@@ -471,10 +471,10 @@ ext_modules = [
      Extension('sage.libs.ecl',
                sources = ["sage/libs/ecl.pyx"]),
  
diff --git a/sagemath-includes.patch b/sagemath-includes.patch
index 11e9334..3ed9e79 100644
--- 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	2019-01-16 09:46:10.613250567 -0700
-+++ src/module_list.py	2019-01-16 09:47:07.804224297 -0700
+--- src/module_list.py.orig	2019-06-27 11:38:23.103196674 -0600
++++ src/module_list.py	2019-06-27 11:47:48.026686317 -0600
 @@ -44,6 +44,9 @@ zlib_libs = zlib_pc['libraries']
  zlib_library_dirs = zlib_pc['library_dirs']
  zlib_include_dirs = zlib_pc['include_dirs']
@@ -36,7 +36,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('*', sources = ['sage/algebras/finite_dimensional_algebras/*.pyx']),
  
-@@ -523,7 +535,8 @@ ext_modules = [
+@@ -524,7 +536,8 @@ 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'],
-@@ -545,23 +558,28 @@ ext_modules = [
+@@ -546,23 +559,28 @@ ext_modules = [
                sources = ['sage/libs/readline.pyx'],
                libraries = ['readline']),
  
@@ -80,7 +80,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      ###################################
      ##
-@@ -569,7 +587,8 @@ ext_modules = [
+@@ -570,7 +588,8 @@ ext_modules = [
      ##
      ###################################
  
@@ -90,7 +90,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      ###################################
      ##
-@@ -741,7 +760,8 @@ ext_modules = [
+@@ -742,7 +761,8 @@ ext_modules = [
  
      Extension("sage.matrix.matrix_complex_ball_dense",
                ["sage/matrix/matrix_complex_ball_dense.pyx"],
@@ -100,7 +100,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.matrix.matrix_complex_double_dense',
                sources = ['sage/matrix/matrix_complex_double_dense.pyx']),
-@@ -749,6 +769,7 @@ ext_modules = [
+@@ -750,6 +770,7 @@ 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',
-@@ -811,6 +832,7 @@ ext_modules = [
+@@ -812,6 +833,7 @@ 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',
-@@ -1108,7 +1130,8 @@ ext_modules = [
+@@ -1101,7 +1123,8 @@ 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'],
-@@ -1184,7 +1207,8 @@ ext_modules = [
+@@ -1177,7 +1200,8 @@ 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']),
-@@ -1267,6 +1291,7 @@ ext_modules = [
+@@ -1260,6 +1284,7 @@ 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++'),
  
-@@ -1406,12 +1431,15 @@ ext_modules = [
+@@ -1399,12 +1424,15 @@ 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',
-@@ -1424,7 +1452,8 @@ ext_modules = [
+@@ -1417,7 +1445,8 @@ ext_modules = [
                sources = ['sage/rings/polynomial/polydict.pyx']),
  
      Extension('sage.rings.polynomial.polynomial_complex_arb',
@@ -171,9 +171,9 @@ 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	2019-01-16 09:45:32.570933224 -0700
-+++ src/setup.py	2019-01-16 09:47:07.805224279 -0700
-@@ -85,6 +85,7 @@ except KeyError:
+--- src/setup.py.orig	2019-06-27 11:38:14.984320180 -0600
++++ src/setup.py	2019-06-27 11:47:48.027686302 -0600
+@@ -85,6 +85,7 @@ keep_going = False
  
  # search for dependencies and add to gcc -I<path>
  include_dirs = sage_include_directories(use_sources=True)
diff --git a/sagemath-lcalc.patch b/sagemath-lcalc.patch
index 122c93c..1279dda 100644
--- 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	2019-01-16 09:42:41.397004883 -0700
-+++ src/module_list.py	2019-01-16 09:45:43.332740109 -0700
-@@ -513,7 +513,7 @@ ext_modules = [
+--- src/module_list.py.orig	2019-06-27 11:30:20.794201914 -0600
++++ src/module_list.py	2019-06-27 11:38:23.103196674 -0600
+@@ -514,7 +514,7 @@ ext_modules = [
      Extension('sage.libs.lcalc.lcalc_Lfunction',
                sources = ['sage/libs/lcalc/lcalc_Lfunction.pyx'],
                libraries = ['m', 'ntl', 'Lfunction'],
diff --git a/sagemath-libgap.patch b/sagemath-libgap.patch
index d7c5733..ff9976c 100644
--- a/sagemath-libgap.patch
+++ b/sagemath-libgap.patch
@@ -1,6 +1,6 @@
 diff -up src/sage/env.py.orig src/sage/env.py
---- src/sage/env.py.orig	2019-04-08 12:21:12.403515647 -0600
-+++ src/sage/env.py	2019-04-08 12:22:37.165993394 -0600
+--- src/sage/env.py.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/sage/env.py	2019-06-27 11:39:02.780593101 -0600
 @@ -174,7 +174,7 @@ var('CONWAY_POLYNOMIALS_DATA_DIR',   joi
  var('GRAPHS_DATA_DIR',               join(SAGE_SHARE, 'graphs'))
  var('ELLCURVE_DATA_DIR',             join(SAGE_SHARE, 'ellcurves'))
@@ -10,274 +10,3 @@ diff -up src/sage/env.py.orig src/sage/env.py
  var('THEBE_DIR',                     join(SAGE_SHARE, 'thebe'))
  var('COMBINATORIAL_DESIGN_DATA_DIR', join(SAGE_SHARE, 'combinatorial_designs'))
  var('CREMONA_MINI_DATA_DIR',         join(SAGE_SHARE, 'cremona'))
-diff -up src/sage/interfaces/tests.py.orig src/sage/interfaces/tests.py
---- src/sage/interfaces/tests.py.orig	2019-03-23 16:20:41.000000000 -0600
-+++ src/sage/interfaces/tests.py	2019-04-08 12:32:57.223857758 -0600
-@@ -33,7 +33,7 @@ Test that write errors to stderr are han
-     sage: kwds = dict(shell=True, stdout=f, stderr=f)
-     sage: subprocess.call("echo syntax error | ecl", **kwds)
-     0
--    sage: subprocess.call("echo syntax error | gap", **kwds)
-+    sage: subprocess.call("echo syntax error | gap", **kwds) in (0, 1)
-     0
-     sage: subprocess.call("echo syntax error | gp", **kwds)
-     0
-diff -up src/sage/libs/gap/gap_includes.pxd.orig src/sage/libs/gap/gap_includes.pxd
---- src/sage/libs/gap/gap_includes.pxd.orig	2019-03-23 16:20:41.000000000 -0600
-+++ src/sage/libs/gap/gap_includes.pxd	2019-04-08 12:34:27.782231417 -0600
-@@ -76,18 +76,16 @@ cdef extern from "<gap/io.h>":
- 
- 
- cdef extern from "<gap/libgap-api.h>":
--    ctypedef void (*CallbackFunc)()
--    void GAP_Initialize(int argc, char ** argv, char ** env,
--        CallbackFunc, CallbackFunc)
-+    """
-+    #define sig_GAP_Enter() {int t = GAP_Enter(); if (!t) sig_error();}
-+    """
-+    ctypedef void (*GAP_CallbackFunc)()
-+    void GAP_Initialize(int argc, char ** argv,
-+            GAP_CallbackFunc markBagsCallback, GAP_CallbackFunc errorCallback,
-+            int handleSignals)
-     Obj GAP_EvalString(const char *) except *
-     Obj GAP_EvalStringNoExcept "GAP_EvalString"(const char *)
-     Obj GAP_ValueGlobalVariable(const char *)
--
--
--cdef extern from "<gap/libgap-api.h>" nogil:
--    """
--    #define sig_GAP_Enter()  {int t = GAP_Enter(); if (!t) sig_error();}
--    """
-     cdef void GAP_EnterStack()
-     cdef void GAP_LeaveStack()
-     cdef int GAP_Enter() except 0
-@@ -121,26 +119,31 @@ cdef extern from "<gap/objects.h>":
-     UInt TNUM_OBJ(Obj obj)
-     char* TNAM_OBJ(Obj obj)
- 
--    cdef int T_INTPOS
--    cdef int T_INTNEG
--    cdef int T_RAT
--    cdef int T_CYC
--    cdef int T_FFE
--    cdef int T_PERM2
--    cdef int T_PERM4
--    cdef int T_BOOL
--    cdef int T_CHAR
--    cdef int T_FUNCTION
--    cdef int T_MACFLOAT
--    cdef int T_PLIST
--    cdef int T_PLIST_CYC
--    cdef int T_BLIST
--    cdef int T_STRING
--    cdef int T_COMOBJ
--    cdef int T_POSOBJ
--    cdef int T_DATOBJ
--    cdef int T_WPOBJ
--
-+    cdef enum TNUM:
-+        T_INT
-+        T_INTPOS
-+        T_INTNEG
-+        T_RAT
-+        T_CYC
-+        T_FFE
-+        T_MACFLOAT
-+        T_PERM2
-+        T_PERM4
-+        T_TRANS2
-+        T_TRANS4
-+        T_PPERM2
-+        T_PPERM4
-+        T_BOOL
-+        T_CHAR
-+        T_FUNCTION
-+        T_PLIST
-+        T_PLIST_CYC
-+        T_BLIST
-+        T_STRING
-+        T_COMOBJ
-+        T_POSOBJ
-+        T_DATOBJ
-+        T_WPOBJ
- 
- cdef extern from "<gap/precord.h>":
-     Obj NEW_PREC(int len)
-diff -up src/sage/libs/gap/libgap.pyx.orig src/sage/libs/gap/libgap.pyx
---- src/sage/libs/gap/libgap.pyx.orig	2019-03-23 16:20:41.000000000 -0600
-+++ src/sage/libs/gap/libgap.pyx	2019-04-08 12:25:35.700787082 -0600
-@@ -233,14 +233,6 @@ from sage.misc.superseded import depreca
- ############################################################################
- 
- 
--cdef void report(Obj bag):
--    print(TNAM_OBJ(bag),  <int>SIZE_OBJ(bag))
--
--
--cdef void print_gasman_objects():
--    CallbackForAllBags(report)
--
--
- from sage.misc.lazy_import import is_during_startup
- if is_during_startup():
-     import sys, traceback
-diff -up src/sage/libs/gap/util.pyx.orig src/sage/libs/gap/util.pyx
---- src/sage/libs/gap/util.pyx.orig	2019-03-23 16:20:41.000000000 -0600
-+++ src/sage/libs/gap/util.pyx	2019-04-08 12:37:02.323035697 -0600
-@@ -14,19 +14,16 @@ Utility functions for GAP
- 
- from __future__ import print_function, absolute_import
- 
--import os
--import signal
--import warnings
-+from libc.signal cimport signal, SIGCHLD, SIG_DFL
- from posix.dlfcn cimport dlopen, dlclose, RTLD_NOW, RTLD_GLOBAL
--from libc.string cimport strcpy, strlen
- 
- from cpython.exc cimport PyErr_Fetch, PyErr_Restore
- from cpython.object cimport Py_LT, Py_LE, Py_EQ, Py_NE, Py_GT, Py_GE
- from cpython.ref cimport PyObject, Py_XINCREF, Py_XDECREF
--from cysignals.memory cimport sig_malloc
--from cysignals.pysignals import containsignals
--from cysignals.signals cimport sig_on, sig_off, sig_error
-+from cysignals.signals cimport sig_on, sig_off
- 
-+import os
-+import warnings
- import sage.env
- 
- from .gap_includes cimport *
-@@ -105,7 +102,7 @@ cdef class ObjWrapper(object):
-             sage: hash(x)
-             0
-         """
--        return <int>(self.value)
-+        return <Py_hash_t>(self.value)
- 
- 
- cdef ObjWrapper wrap_obj(Obj obj):
-@@ -178,7 +175,7 @@ def gap_root():
- 
-         sage: from sage.libs.gap.util import gap_root
-         sage: gap_root()   # random output
--        '/home/vbraun/opt/sage-5.3.rc0/local/gap/latest'
-+        '/usr/lib/gap'
-     """
-     if os.path.exists(sage.env.GAP_ROOT_DIR):
-         return sage.env.GAP_ROOT_DIR
-@@ -197,7 +194,6 @@ def gap_root():
- 
- # To ensure that we call initialize_libgap only once.
- cdef bint _gap_is_initialized = False
--cdef extern char **environ
- 
- 
- cdef char* _reset_error_output_cmd = """\
-@@ -216,33 +212,6 @@ MakeImmutable(libgap_errout);
- """
- 
- 
--cdef char** copy_environ(char** env):
--    """
--    Make a copy of the environment block given by ``env``.
--
--    Returns a pointer to the copy, which is the caller's responsibility to
--    free.
--    """
--
--    cdef char** env_copy
--    cdef int envc = 0;
--    cdef int idx
--    cdef size_t size
--
--    while env[envc]:
--        envc += 1
--
--    env_copy = <char**>sig_malloc((envc + 1) * sizeof(char*))
--
--    for idx in range(envc):
--        size = strlen(env[idx]) + 1
--        env_copy[idx] = <char*>sig_malloc(size)
--        strcpy(env_copy[idx], env[idx])
--
--    env_copy[envc] = NULL
--    return env_copy
--
--
- cdef initialize():
-     """
-     Initialize the GAP library, if it hasn't already been
-@@ -253,25 +222,23 @@ cdef initialize():
-         sage: libgap(123)   # indirect doctest
-         123
-     """
--    global _gap_is_initialized, environ
-+    global _gap_is_initialized
-     if _gap_is_initialized: return
-     # Hack to ensure that all symbols provided by libgap are loaded into the
-     # global symbol table
-     # Note: we could use RTLD_NOLOAD and avoid the subsequent dlclose() but
-     # this isn't portable
-     cdef void* handle
--    libgapname = str_to_bytes(sage.env.GAP_SO)
--    handle = dlopen(libgapname, RTLD_NOW | RTLD_GLOBAL)
-+    handle = dlopen("libgap.so", RTLD_NOW | RTLD_GLOBAL)
-     if handle is NULL:
-         raise RuntimeError(
-                 "Could not dlopen() libgap even though it should already "
-                 "be loaded!")
-     dlclose(handle)
- 
--    # Define argv and environ variables, which we will pass in to
-+    # Define argv variable, which we will pass in to
-     # initialize GAP. Note that we must pass define the memory pool
-     # size!
--    cdef char** env
-     cdef char* argv[18]
-     argv[0] = "sage"
-     argv[1] = "-l"
-@@ -318,21 +285,15 @@ cdef initialize():
- 
-     argv[argc] = NULL
- 
--    env = copy_environ(environ)
-+    sig_on()
-+    # Initialize GAP but disable their SIGINT handler
-+    GAP_Initialize(argc, argv, gasman_callback, error_handler,
-+                   handleSignals=False)
-+    sig_off()
- 
--    # Need to save/restore current SIGINT handling since GAP_Initialize
--    # currently clobbers it; it doesn't matter what we set SIGINT to
--    # temporarily.
--    with containsignals():
--        sig_on()
--        try:
--            # Initialize GAP and capture any error messages. The
--            # initialization just prints any errors and does not
--            # use the error handler.
--            GAP_Initialize(argc, argv, env, &gasman_callback,
--                           &error_handler)
--        finally:
--            sig_off()
-+    # Disable GAP's SIGCHLD handler ChildStatusChanged(), which calls
-+    # waitpid() on random child processes.
-+    signal(SIGCHLD, SIG_DFL)
- 
-     # Set the ERROR_OUTPUT global in GAP to an output stream in which to
-     # receive error output
-diff -up src/sage/tests/books/judson-abstract-algebra/sylow-sage.py.orig src/sage/tests/books/judson-abstract-algebra/sylow-sage.py
---- src/sage/tests/books/judson-abstract-algebra/sylow-sage.py.orig	2019-03-23 16:20:43.000000000 -0600
-+++ src/sage/tests/books/judson-abstract-algebra/sylow-sage.py	2019-04-08 12:37:39.859183332 -0600
-@@ -225,8 +225,8 @@ r"""
- 
- ~~~~~~~~~~~~~~~~~~~~~~ ::
- 
--    sage: gap.version()
--    '4.10.0'
-+    sage: gap.version()  # random
-+    '4.10.1'
- 
- ~~~~~~~~~~~~~~~~~~~~~~ ::
- 
diff --git a/sagemath-nauty.patch b/sagemath-nauty.patch
index 9f01c6b..bf4eaf1 100644
--- a/sagemath-nauty.patch
+++ b/sagemath-nauty.patch
@@ -1,7 +1,7 @@
 diff -up src/sage/graphs/graph_generators.py.orig src/sage/graphs/graph_generators.py
---- src/sage/graphs/graph_generators.py.orig	2018-12-22 16:37:08.000000000 -0700
-+++ src/sage/graphs/graph_generators.py	2019-01-16 09:45:21.999122930 -0700
-@@ -924,7 +924,7 @@ class GraphGenerators():
+--- src/sage/graphs/graph_generators.py.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/sage/graphs/graph_generators.py	2019-06-27 11:37:46.100759559 -0600
+@@ -907,7 +907,7 @@ class GraphGenerators():
          else:
              enc_kwargs = {'encoding': 'latin-1'}
  
diff --git a/sagemath-python3.patch b/sagemath-python3.patch
index 1dd9d82..28cc7bf 100644
--- a/sagemath-python3.patch
+++ b/sagemath-python3.patch
@@ -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	2019-04-08 11:59:49.261545925 -0600
-+++ build/pkgs/sagetex/src/extractsagecode.py	2019-04-08 12:04:16.915757233 -0600
+--- build/pkgs/sagetex/src/extractsagecode.py.orig	2019-01-09 09:51:28.000000000 -0700
++++ build/pkgs/sagetex/src/extractsagecode.py	2019-06-27 11:33:54.098080502 -0600
 @@ -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	2019-04-08 11:59:49.262545907 -0600
-+++ build/pkgs/sagetex/src/makestatic.py	2019-04-08 12:04:42.619295492 -0600
+--- build/pkgs/sagetex/src/makestatic.py.orig	2019-01-09 09:51:28.000000000 -0700
++++ build/pkgs/sagetex/src/makestatic.py	2019-06-27 11:33:54.098080502 -0600
 @@ -45,7 +45,7 @@ See the SageTeX documentation for more d
  
  try:
@@ -133,9 +133,9 @@ diff -up build/pkgs/sagetex/src/remote-sagetex.py.orig build/pkgs/sagetex/src/re
  if not password:
      from getpass import getpass
 diff -up src/doc/common/conf.py.orig src/doc/common/conf.py
---- src/doc/common/conf.py.orig	2019-03-23 16:20:31.000000000 -0600
-+++ src/doc/common/conf.py	2019-04-08 12:05:07.088855913 -0600
-@@ -547,7 +547,7 @@ skip_picklability_check_modules = [
+--- 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',
@@ -144,7 +144,7 @@ diff -up src/doc/common/conf.py.orig src/doc/common/conf.py
  ]
  
  def check_nested_class_picklability(app, what, name, obj, skip, options):
-@@ -596,7 +596,7 @@ def skip_member(app, what, name, obj, sk
+@@ -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)
  
@@ -154,18 +154,18 @@ diff -up src/doc/common/conf.py.orig src/doc/common/conf.py
  
      objname = getattr(obj, "__name__", None)
 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	2019-03-23 16:20:38.000000000 -0600
-+++ src/sage/combinat/finite_state_machine.py	2019-04-08 12:05:07.090855877 -0600
-@@ -932,7 +932,7 @@ import six
- from six.moves import range, zip_longest, zip
+--- src/sage/combinat/finite_state_machine.py.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/sage/combinat/finite_state_machine.py	2019-06-27 11:36:38.804783269 -0600
+@@ -936,7 +936,7 @@ from six.moves import range, zip_longest
  from six import itervalues
  
+ from IPython.lib.pretty import pretty
 -import collections
-+import collections.abc
++import collections, collections.abc
  import itertools
  from copy import copy, deepcopy
  
-@@ -14201,7 +14201,7 @@ def is_FSMProcessIterator(PI):
+@@ -14207,7 +14207,7 @@ def is_FSMProcessIterator(PI):
  
  
  class FSMProcessIterator(SageObject,
@@ -175,8 +175,8 @@ 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/cpython/dict_del_by_value.pyx.orig src/sage/cpython/dict_del_by_value.pyx
---- src/sage/cpython/dict_del_by_value.pyx.orig	2019-03-23 16:20:40.000000000 -0600
-+++ src/sage/cpython/dict_del_by_value.pyx	2019-04-08 12:05:07.091855859 -0600
+--- 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	2019-06-27 11:33:54.103080432 -0600
 @@ -347,8 +347,8 @@ ELIF PY_VERSION_HEX>=0x03060000:
          cdef MyPyDictKeysObject * keys = <MyPyDictKeysObject *>(mp.ma_keys)
          cdef size_t perturb
@@ -189,8 +189,8 @@ diff -up src/sage/cpython/dict_del_by_value.pyx.orig src/sage/cpython/dict_del_b
          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	2019-03-23 16:20:40.000000000 -0600
-+++ src/sage/geometry/triangulation/point_configuration.py	2019-04-08 12:05:07.091855859 -0600
+--- src/sage/geometry/triangulation/point_configuration.py.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/sage/geometry/triangulation/point_configuration.py	2019-06-27 11:33:54.103080432 -0600
 @@ -623,7 +623,7 @@ class PointConfiguration(UniqueRepresent
              ['{{0,1,2,4},{1,2,3,4}}']
          """
@@ -201,8 +201,8 @@ diff -up src/sage/geometry/triangulation/point_configuration.py.orig src/sage/ge
          proc.expect(r'\.\.\. done\.')
          proc.setecho(0)
 diff -up src/sage/interfaces/frobby.py.orig src/sage/interfaces/frobby.py
---- src/sage/interfaces/frobby.py.orig	2019-03-23 16:20:40.000000000 -0600
-+++ src/sage/interfaces/frobby.py	2019-04-08 12:05:07.091855859 -0600
+--- src/sage/interfaces/frobby.py.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/sage/interfaces/frobby.py	2019-06-27 11:33:54.103080432 -0600
 @@ -77,7 +77,7 @@ class Frobby:
              print("Frobby command: ", repr(command))
              print("Frobby input:\n", input)
@@ -213,8 +213,8 @@ diff -up src/sage/interfaces/frobby.py.orig src/sage/interfaces/frobby.py
  
          if verbose:
 diff -up src/sage/interfaces/gfan.py.orig src/sage/interfaces/gfan.py
---- src/sage/interfaces/gfan.py.orig	2019-03-23 16:20:41.000000000 -0600
-+++ src/sage/interfaces/gfan.py	2019-04-08 12:05:07.092855841 -0600
+--- src/sage/interfaces/gfan.py.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/sage/interfaces/gfan.py	2019-06-27 11:33:54.104080419 -0600
 @@ -66,7 +66,7 @@ class Gfan(object):
          if six.PY2:
              enc_kwargs = {}
@@ -225,8 +225,8 @@ 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	2019-03-23 16:20:41.000000000 -0600
-+++ src/sage/interfaces/gp.py	2019-04-08 12:05:07.092855841 -0600
+--- src/sage/interfaces/gp.py.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/sage/interfaces/gp.py	2019-06-27 11:33:54.104080419 -0600
 @@ -934,17 +934,6 @@ class GpElement(ExpectElement):
          """
          return repr(self.type()) == 't_STR'
@@ -246,8 +246,8 @@ 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	2019-03-23 16:20:41.000000000 -0600
-+++ src/sage/interfaces/latte.py	2019-04-08 12:05:07.092855841 -0600
+--- src/sage/interfaces/latte.py.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/sage/interfaces/latte.py	2019-06-27 11:33:54.104080419 -0600
 @@ -148,6 +148,7 @@ def count(arg, ehrhart_polynomial=False,
      latte_proc = Popen(args,
                         stdin=PIPE, stdout=PIPE,
@@ -265,8 +265,8 @@ 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	2019-03-23 16:20:41.000000000 -0600
-+++ src/sage/interfaces/sagespawn.pyx	2019-04-08 12:05:07.092855841 -0600
+--- src/sage/interfaces/sagespawn.pyx.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/sage/interfaces/sagespawn.pyx	2019-06-27 11:33:54.104080419 -0600
 @@ -1,6 +1,6 @@
  """
  Sage wrapper around pexpect's ``spawn`` class and
@@ -315,8 +315,8 @@ diff -up src/sage/interfaces/sagespawn.pyx.orig src/sage/interfaces/sagespawn.py
                      pass
              self.fileobj.close()
 diff -up src/sage/misc/parser.pyx.orig src/sage/misc/parser.pyx
---- src/sage/misc/parser.pyx.orig	2019-03-23 16:20:41.000000000 -0600
-+++ src/sage/misc/parser.pyx	2019-04-08 12:05:07.093855823 -0600
+--- src/sage/misc/parser.pyx.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/misc/parser.pyx	2019-06-27 11:33:54.105080405 -0600
 @@ -96,7 +96,7 @@ def token_to_str(int token):
  
  
@@ -616,8 +616,8 @@ diff -up src/sage/misc/parser.pyx.orig src/sage/misc/parser.pyx
              return self.p_list(tokens)
          else:
 diff -up src/sage/plot/plot3d/plot3d.py.orig src/sage/plot/plot3d/plot3d.py
---- src/sage/plot/plot3d/plot3d.py.orig	2019-03-23 16:20:42.000000000 -0600
-+++ src/sage/plot/plot3d/plot3d.py	2019-04-08 12:05:07.093855823 -0600
+--- src/sage/plot/plot3d/plot3d.py.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/plot/plot3d/plot3d.py	2019-06-27 11:33:54.105080405 -0600
 @@ -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)
@@ -629,8 +629,8 @@ 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	2019-03-23 16:20:42.000000000 -0600
-+++ src/sage/plot/point.py	2019-04-08 12:05:07.094855805 -0600
+--- src/sage/plot/point.py.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/plot/point.py	2019-06-27 11:33:54.105080405 -0600
 @@ -29,7 +29,7 @@ TESTS::
  from sage.misc.decorators import options, rename_keyword
  from sage.plot.colors import to_mpl_color
@@ -650,8 +650,8 @@ 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	2019-03-23 16:20:42.000000000 -0600
-+++ src/sage/repl/display/fancy_repr.py	2019-04-08 12:05:07.094855805 -0600
+--- src/sage/repl/display/fancy_repr.py.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/repl/display/fancy_repr.py	2019-06-27 11:33:54.106080391 -0600
 @@ -15,7 +15,7 @@ Representations of objects.
  import types
  
@@ -671,8 +671,8 @@ 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	2019-03-23 16:20:42.000000000 -0600
-+++ src/sage/repl/ipython_kernel/interact.py	2019-04-08 12:05:07.094855805 -0600
+--- src/sage/repl/ipython_kernel/interact.py.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/repl/ipython_kernel/interact.py	2019-06-27 11:33:54.106080391 -0600
 @@ -35,7 +35,8 @@ EXAMPLES::
  
  from ipywidgets.widgets import SelectionSlider, ValueWidget, ToggleButtons
@@ -681,11 +681,11 @@ diff -up src/sage/repl/ipython_kernel/interact.py.orig src/sage/repl/ipython_ker
 +from collections.abc import Iterable, Iterator
 +from collections import OrderedDict
  from .widgets import EvalText, SageColorPicker
+ from .widgets_sagenb import input_grid
  from sage.structure.element import parent
- from sage.symbolic.ring import SR
 diff -up src/sage/rings/integer.pyx.orig src/sage/rings/integer.pyx
---- src/sage/rings/integer.pyx.orig	2019-03-23 16:20:42.000000000 -0600
-+++ src/sage/rings/integer.pyx	2019-04-08 12:05:07.095855787 -0600
+--- src/sage/rings/integer.pyx.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/rings/integer.pyx	2019-06-27 11:33:54.107080377 -0600
 @@ -6989,7 +6989,7 @@ cdef int mpz_set_str_python(mpz_ptr z, c
      while x[0] == c' ': x += 1  # Strip spaces
  
@@ -696,9 +696,9 @@ diff -up src/sage/rings/integer.pyx.orig src/sage/rings/integer.pyx
  
      assert base >= 2
 diff -up src/sage/rings/polynomial/pbori.pyx.orig src/sage/rings/polynomial/pbori.pyx
---- src/sage/rings/polynomial/pbori.pyx.orig	2019-03-23 16:20:42.000000000 -0600
-+++ src/sage/rings/polynomial/pbori.pyx	2019-04-08 12:05:07.096855769 -0600
-@@ -4774,8 +4774,7 @@ cdef class PolynomialConstruct:
+--- src/sage/rings/polynomial/pbori.pyx.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/rings/polynomial/pbori.pyx	2019-06-27 11:33:54.123080154 -0600
+@@ -4765,8 +4765,7 @@ cdef class PolynomialConstruct:
              # So, it is just a conversion. [Simon King]
              return (<BooleanPolynomialRing>ring)._element_constructor_(x)
  
@@ -709,8 +709,8 @@ diff -up src/sage/rings/polynomial/pbori.pyx.orig src/sage/rings/polynomial/pbor
  
  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	2019-03-23 16:20:42.000000000 -0600
-+++ src/sage/rings/real_mpfi.pyx	2019-04-08 12:05:07.097855751 -0600
+--- src/sage/rings/real_mpfi.pyx.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/rings/real_mpfi.pyx	2019-06-27 11:33:54.124080141 -0600
 @@ -1943,12 +1943,12 @@ cdef class RealIntervalFieldElement(Ring
  
          cdef long digits
@@ -736,8 +736,8 @@ 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	2019-03-23 16:20:42.000000000 -0600
-+++ src/sage/rings/real_mpfr.pyx	2019-04-08 12:05:07.098855733 -0600
+--- src/sage/rings/real_mpfr.pyx.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/rings/real_mpfr.pyx	2019-06-27 11:33:54.125080127 -0600
 @@ -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")
@@ -748,8 +748,8 @@ 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	2019-03-23 16:20:43.000000000 -0600
-+++ src/sage/structure/sage_object.pyx	2019-04-08 12:05:07.098855733 -0600
+--- src/sage/structure/sage_object.pyx.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/structure/sage_object.pyx	2019-06-27 11:33:54.126080113 -0600
 @@ -665,7 +665,7 @@ cdef class SageObject:
              try:
                  s = self._interface_init_(I)
@@ -760,9 +760,9 @@ 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	2019-03-23 16:20:43.000000000 -0600
-+++ src/sage/symbolic/expression.pyx	2019-04-08 12:05:07.100855697 -0600
-@@ -12915,7 +12915,7 @@ cdef class hold_class:
+--- src/sage/symbolic/expression.pyx.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/symbolic/expression.pyx	2019-06-27 11:33:54.128080085 -0600
+@@ -12960,7 +12960,7 @@ cdef class hold_class:
              sage: SR(2)^5
              32
          """
@@ -771,7 +771,7 @@ diff -up src/sage/symbolic/expression.pyx.orig src/sage/symbolic/expression.pyx
  
      def __exit__(self, *args):
          """
-@@ -12928,7 +12928,7 @@ cdef class hold_class:
+@@ -12973,7 +12973,7 @@ cdef class hold_class:
              sage: SR(2)^5
              32
          """
@@ -781,8 +781,8 @@ 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	2019-04-08 11:45:58.283274716 -0600
-+++ src/setup.py	2019-04-08 12:05:07.101855679 -0600
+--- src/setup.py.orig	2019-06-27 11:30:20.794201914 -0600
++++ src/setup.py	2019-06-27 11:33:54.128080085 -0600
 @@ -232,7 +232,7 @@ class sage_build_cython(Command):
              cdivision=True,
              embedsignature=True,
diff --git a/sagemath-readonly.patch b/sagemath-readonly.patch
index 9b30f80..4031056 100644
--- a/sagemath-readonly.patch
+++ b/sagemath-readonly.patch
@@ -1,13 +1,13 @@
 diff -up src/sage/all.py.orig src/sage/all.py
---- src/sage/all.py.orig	2018-12-22 16:37:06.000000000 -0700
-+++ src/sage/all.py	2019-01-16 09:43:07.639533969 -0700
-@@ -284,11 +284,11 @@ def _write_started_file():
- 
-     Check that the file exists when Sage is running::
+--- src/sage/all.py.orig	2019-06-27 11:31:07.149494781 -0600
++++ src/sage/all.py	2019-06-27 11:32:11.332515672 -0600
+@@ -286,11 +286,11 @@ def _write_started_file():
+     Check that the file exists when Sage is running (note, this file is not
+     necessarily installed or used by downstream packages of Sage)::
  
 -        sage: started_file = os.path.join(SAGE_LOCAL, 'etc', 'sage-started.txt')
 +        sage: started_file = os.path.join(DOT_SAGE, 'sage-started.txt')
-         sage: os.path.isfile(started_file)
+         sage: os.path.isfile(started_file)  # optional - build
          True
      """
 -    started_file = os.path.join(SAGE_LOCAL, 'etc', 'sage-started.txt')
diff --git a/sagemath-rpmbuild.patch b/sagemath-rpmbuild.patch
index d826315..2af74dd 100644
--- 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	2019-04-08 11:45:44.437520141 -0600
-+++ src/module_list.py	2019-04-08 11:45:58.268274982 -0600
+--- src/module_list.py.orig	2019-06-27 11:29:54.622601184 -0600
++++ src/module_list.py	2019-06-27 11:30:20.794201914 -0600
 @@ -2,7 +2,7 @@ import os
  from distutils.extension import Extension
  from sage.env import SAGE_LOCAL
@@ -11,8 +11,8 @@ 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	2019-04-08 11:45:58.269274964 -0600
-+++ src/sage/misc/cython.py	2019-04-08 11:48:23.582699337 -0600
+--- src/sage/misc/cython.py.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/misc/cython.py	2019-06-27 11:30:20.794201914 -0600
 @@ -49,7 +49,7 @@ standard_libs = [
  ] + cblas_libs + [
      'ntl']
@@ -23,8 +23,8 @@ 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	2019-03-23 16:20:43.000000000 -0600
-+++ src/setup.py	2019-04-08 11:45:58.283274716 -0600
+--- 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,
@@ -37,7 +37,7 @@ diff -up src/setup.py.orig src/setup.py
              )
  
          # Filter out extensions with skip_build=True
-@@ -829,9 +828,6 @@ class sage_install(install):
+@@ -795,9 +794,6 @@ class sage_install(install):
          install.run(self)
          self.install_kernel_spec()
          log.info('Cleaning up stale installed files....')
@@ -47,7 +47,7 @@ diff -up src/setup.py.orig src/setup.py
  
      def install_kernel_spec(self):
          """
-@@ -848,40 +844,6 @@ class sage_install(install):
+@@ -814,40 +810,6 @@ class sage_install(install):
          # the install_data directory for installing our Jupyter files.
          SageKernelSpec.update(prefix=self.install_data)
  
diff --git a/sagemath-sagedoc.patch b/sagemath-sagedoc.patch
index e189517..223bfdb 100644
--- 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	2019-03-23 16:20:40.000000000 -0600
-+++ src/sage/doctest/control.py	2019-04-08 11:49:50.428160023 -0600
+--- src/sage/doctest/control.py.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/sage/doctest/control.py	2019-06-27 11:30:37.222951288 -0600
 @@ -106,7 +106,6 @@ class DocTestDefaults(SageObject):
          self.valgrind = False
          self.massif = False
@@ -46,8 +46,8 @@ 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	2019-03-23 16:20:41.000000000 -0600
-+++ src/sage/interfaces/singular.py	2019-04-08 11:54:23.579318505 -0600
+--- src/sage/interfaces/singular.py.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/interfaces/singular.py	2019-06-27 11:30:37.223951272 -0600
 @@ -2261,7 +2261,7 @@ def generate_docstring_dictionary():
      nodes.clear()
      node_names.clear()
@@ -70,9 +70,9 @@ 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	2019-03-23 16:20:43.000000000 -0600
-+++ src/sage_setup/docbuild/ext/multidocs.py	2019-04-08 11:49:50.430159987 -0600
-@@ -84,8 +84,11 @@ def merge_environment(app, env):
+--- src/sage_setup/docbuild/ext/multidocs.py.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage_setup/docbuild/ext/multidocs.py	2019-06-27 11:30:37.224951257 -0600
+@@ -85,8 +85,11 @@ def merge_environment(app, env):
              for ind in newalldoc:
                  # treat subdocument source as orphaned file and don't complain
                  md = env.metadata.get(ind, dict())
@@ -87,9 +87,9 @@ diff -up src/sage_setup/docbuild/ext/multidocs.py.orig src/sage_setup/docbuild/e
              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	2019-04-08 11:49:50.431159970 -0600
-+++ src/sage_setup/docbuild/__init__.py	2019-04-08 11:56:02.609563240 -0600
-@@ -287,13 +287,14 @@ if not (CYGWIN_VERSION and CYGWIN_VERSIO
+--- 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)
diff --git a/sagemath-scripts.patch b/sagemath-scripts.patch
index e2eea68..68cbfd5 100644
--- 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	2019-03-23 16:20:31.000000000 -0600
-+++ src/bin/sage	2019-04-08 11:42:38.305818631 -0600
+--- src/bin/sage.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/bin/sage	2019-06-27 11:28:35.352810438 -0600
 @@ -26,13 +26,10 @@ usage() {
      echo "  file.[sage|py|spyx] -- run given .sage, .py or .spyx file"
      echo "  -advanced           -- list all command line options"
@@ -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'."
-@@ -287,115 +205,6 @@ usage_advanced() {
+@@ -287,116 +205,6 @@ usage_advanced() {
  
  
  #####################################################################
@@ -193,7 +193,7 @@ diff -up src/bin/sage.orig src/bin/sage
 -    # We set PYTHONPATH to that directory such that the system Python
 -    # should also find the sage_patchbot package.
 -    cmd='import sage_patchbot as p; import os; print(os.path.dirname(p.__path__[0]))'
--    export PYTHONPATH=`"$SAGE_ROOT/sage" --python -c "$cmd"`
+-    export PYTHONPATH=`"$SAGE_ROOT/sage" --python3 -c "$cmd"`
 -    if [ -z "$PYTHONPATH" ]; then
 -        # Something went wrong, assume that the patchbot is not installed
 -        echo >&2 "Error: cannot find installation path for sage_patchbot"
@@ -201,13 +201,10 @@ diff -up src/bin/sage.orig src/bin/sage
 -        exit 1
 -    fi
 -
--    # Try "python2.7", then "python2", then "python"
 -    shopt -s execfail  # Do not exit if "exec" fails
--    exec python2.7 -m sage_patchbot.patchbot "$@"
--    exec python2 -m sage_patchbot.patchbot "$@"
--    exec python -m sage_patchbot.patchbot "$@"
--    echo >&2 "Error: cannot find a suitable Python program."
--    echo >&2 "The SageMath patchbot requires a system Python installation."
+-    exec python3 -m sage_patchbot.patchbot "$@"
+-    echo >&2 "Error: cannot find a suitable Python 3 program."
+-    echo >&2 "The SageMath patchbot requires a system Python 3 installation."
 -    exit 127
 -fi
 -
@@ -274,6 +271,10 @@ diff -up src/bin/sage.orig src/bin/sage
 -        fi
 -        $MAKE SAGE_SPKG="sage-spkg $INSTALL_OPTIONS" "$PKG"
 -    done
+-
+-    echo "New packages may have been installed."
+-    echo "Re-running configure and make in case any dependent packages need updating."
+-    touch "$SAGE_ROOT/configure" && $MAKE all-build
 -    exit 0
 -fi
 -
@@ -282,7 +283,7 @@ diff -up src/bin/sage.orig src/bin/sage
  # Report information about the Sage environment
  #####################################################################
  
-@@ -424,35 +233,8 @@ if [ $# -gt 0 ]; then
+@@ -425,35 +233,8 @@ if [ $# -gt 0 ]; then
  fi
  
  
@@ -318,7 +319,7 @@ 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
-@@ -463,20 +245,6 @@ sage_setup() {
+@@ -464,20 +245,6 @@ sage_setup() {
  }
  
  
@@ -339,7 +340,7 @@ diff -up src/bin/sage.orig src/bin/sage
  # Start an interactive Sage session, this function never returns.
  interactive_sage() {
      sage_setup
-@@ -560,16 +328,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
+@@ -561,16 +328,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
      exec ecl "$@"
  fi
  
@@ -356,8 +357,8 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
      shift
      exec maxima "$@"
-@@ -595,11 +353,6 @@ if [ "$1" = '-pip' -o "$1" = '--pip' ];
-     exec sage-python23 -m pip "$@"
+@@ -601,11 +358,6 @@ if [ "$1" = '--pip3' ]; then
+     exec python3 -m pip "$@"
  fi
  
 -if [ "$1" = '-fix-pkg-checksums' -o "$1" = '--fix-pkg-checksums' ]; then
@@ -368,7 +369,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-python' -o "$1" = '--python' ]; then
      shift
      if [ "$SAGE_PYTHON3" = 'yes' ]; then
-@@ -639,16 +392,6 @@ if [ "$1" = '-jupyter' -o "$1" = '--jupy
+@@ -645,16 +397,6 @@ if [ "$1" = '-jupyter' -o "$1" = '--jupy
      exec jupyter "$@"
  fi
  
@@ -385,7 +386,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
      # AUTHORS:
      # - Carl Witty and William Stein: initial version
-@@ -768,20 +511,6 @@ EOF
+@@ -774,20 +516,6 @@ EOF
  fi
  
  #####################################################################
@@ -406,7 +407,7 @@ diff -up src/bin/sage.orig src/bin/sage
  # File conversion
  #####################################################################
  
-@@ -812,11 +541,6 @@ fi
+@@ -818,11 +546,6 @@ fi
  # Run Sage's versions of the standard Algebra/Geometry etc. software
  #####################################################################
  
@@ -418,7 +419,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [[ "$1" =~ ^--notebook=.* || "$1" =~ ^-n=.* || "$1" =~ ^-notebook=.* ]] ; then
      sage-cleaner &>/dev/null &
      exec sage-notebook "$@"
-@@ -827,13 +551,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
+@@ -833,13 +556,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
      exec sage-notebook "$@"
  fi
  
@@ -432,7 +433,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
      shift
      sage-cleaner &>/dev/null &
-@@ -852,34 +569,15 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
+@@ -858,34 +574,15 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
      exit 0
  fi
  
@@ -469,7 +470,7 @@ diff -up src/bin/sage.orig src/bin/sage
          shift
          exec sage-runtests -p "$@"
      else
-@@ -888,10 +586,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
+@@ -894,10 +591,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
      fi
  fi
  
@@ -481,7 +482,7 @@ diff -up src/bin/sage.orig src/bin/sage
      shift
      sage_setup
      export PYTHONIOENCODING="utf-8"  # Fix encoding for doctests
-@@ -912,122 +607,6 @@ if [ "$1" = '-c' ]; then
+@@ -918,122 +612,6 @@ if [ "$1" = '-c' ]; then
      exec sage-eval "$@"
  fi
  
@@ -604,7 +605,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
      shift
      sage_setup
-@@ -1077,12 +656,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
+@@ -1083,12 +661,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
      exec sage-callgrind "$@"
  fi
  
@@ -618,9 +619,9 @@ diff -up src/bin/sage.orig src/bin/sage
      exec sage-startuptime.py "$@"
  fi
 diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
---- src/bin/sage-runtests.orig	2019-03-23 16:20:31.000000000 -0600
-+++ src/bin/sage-runtests	2019-04-08 11:40:35.881987545 -0600
-@@ -79,10 +79,6 @@ if __name__ == "__main__":
+--- 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"))
@@ -632,8 +633,8 @@ diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
      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	2019-03-23 16:20:31.000000000 -0600
-+++ src/bin/sage-valgrind	2019-04-08 11:40:35.881987545 -0600
+--- src/bin/sage-valgrind.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/bin/sage-valgrind	2019-06-27 11:22:47.435227309 -0600
 @@ -1,16 +1,6 @@
  #!/usr/bin/env bash
  
diff --git a/sagemath.spec b/sagemath.spec
index f779bbc..c458db1 100644
--- a/sagemath.spec
+++ b/sagemath.spec
@@ -40,15 +40,18 @@
 
 %global combinatorial_designs_pkg	combinatorial_designs-20140630
 %global conway_polynomials_pkg	conway_polynomials-0.5
-%global	elliptic_curves_pkg	elliptic_curves-0.8
+%global	elliptic_curves_pkg	elliptic_curves-0.8.1
 %global	flintqs_pkg		flintqs-1.0
 %global graphs_pkg		graphs-20161026
 %if %{with bundled_ipython}
-%global ipython_pkg		ipython-5.8.0
-%global prompt_tookit_pkg	prompt_toolkit-1.0.15
+%global ipython_ver		5.8.0
+%global ipython_pkg		ipython-%{ipython_ver}
+%global prompt_toolkit_ver	1.0.15
+%global prompt_tookit_pkg	prompt_toolkit-%{prompt_toolkit_ver}
 %endif
 %if %{with bundled_ipywidgets}
-%global ipywidgets_pkg		ipywidgets-7.4.2
+%global ipywidgets_ver		7.4.2
+%global ipywidgets_pkg		ipywidgets-%{ipywidgets_ver}
 %endif
 %if %{with bundled_pexpect}
 %global pexpect_pkg		pexpect-4.6.0
@@ -58,16 +61,19 @@
 %global	sagenb_pkg		sagenb-1.1.2
 %global sagenb_export_pkg	sagenb_export-3.2
 %global sagetex_pkg		sagetex-3.2
-%global Sphinx_pkg		Sphinx-1.7.6
+%global Sphinx_pkg		Sphinx-1.8.5
 %global singular_pkg		singular-4.1.1p3
 %if %{with bundled_thebe}
-%global thebe_pkg		thebe-9624e0a0
+%global thebe_ver		9624e0a0
+%global thebe_pkg		thebe-%{thebe_ver}
 %endif
 %if %{with bundled_threejs}
-%global threejs_pkg		threejs-r80
+%global threejs_ver		r100
+%global threejs_pkg		threejs-%{threejs_ver}
 %endif
 %if %{with bundled_widgetsnbextension}
-%global widgetsnbextension_pkg	widgetsnbextension-3.4.2
+%global widgetsnbextension_ver	3.4.2
+%global widgetsnbextension_pkg	widgetsnbextension-%{widgetsnbextension_ver}
 %endif
 
 # Spkg equivalents of required rpms; we pretend they are installed as spkgs.
@@ -86,7 +92,7 @@
 
 Name:		sagemath
 Summary:	A free open-source mathematics software system
-Version:	8.7
+Version:	8.8
 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
@@ -108,7 +114,6 @@ Patch1:		%{name}-random.patch
 Patch2:		%{name}-scripts.patch
 
 # remove call to not implemented sagemath "is_package_installed" interfaces
-# need to package coin-or solver in fedora
 # remove check for non free solvers
 Patch3:		%{name}-extensions.patch
 
@@ -148,8 +153,6 @@ Patch11:	%{name}-cremona.patch
 Patch12:	%{name}-python3.patch
 
 # correct path to the nauty geng program
-# http://cs.anu.edu.au/~bdm/nauty/
-# http://pallini.di.uniroma1.it/
 Patch13:	%{name}-nauty.patch
 
 # remove the buildroot path from Cython output
@@ -204,6 +207,9 @@ Patch29:	%{name}-rubiks.patch
 # Fix an indentation error in sagetex
 Patch30:	%{name}-sagetex.patch
 
+# Fix some path settings in the sage environment
+Patch31:	%{name}-env.patch
+
 BuildRequires:	4ti2
 BuildRequires:	arb-devel
 BuildRequires:	boost-devel
@@ -228,10 +234,14 @@ BuildRequires:	gap-pkg-crime
 BuildRequires:	gap-pkg-design
 BuildRequires:	gap-pkg-guava
 BuildRequires:	gap-pkg-hapcryst
+BuildRequires:	gap-pkg-happrime
 BuildRequires:	gap-pkg-sonata
 BuildRequires:	gap-pkg-toric
 BuildRequires:	gc-devel
 BuildRequires:	gcc-c++
+BuildRequires:	gcc-gfortran
+BuildRequires:	gcc-objc
+BuildRequires:	gcc-objc++
 BuildRequires:	gd-devel
 BuildRequires:	gdb
 BuildRequires:	gfan
@@ -272,6 +282,7 @@ BuildRequires:	pari-devel
 BuildRequires:	pari-galdata
 BuildRequires:	pari-gp
 BuildRequires:	pari-seadata
+BuildRequires:	perl-generators
 BuildRequires:	planarity-devel
 BuildRequires:	ppl-devel
 BuildRequires:	pynac-devel
@@ -281,9 +292,6 @@ BuildRequires:	python3-cysignals-devel
 BuildRequires:	python3-pillow-devel
 BuildRequires:	python3-pplpy-devel
 BuildRequires:	python3dist(brial)
-%if %{with sphinx_hack}
-BuildRequires:	python3dist(configparser)
-%endif
 BuildRequires:	python3dist(cvxopt)
 BuildRequires:	python3dist(cython)
 BuildRequires:	python3dist(docutils)
@@ -320,7 +328,7 @@ BuildRequires:	python3dist(psutil)
 BuildRequires:	python3dist(ptyprocess)
 BuildRequires:	python3dist(pycryptosat)
 %if %{with bundled_ipython}
-BuildRequires:  python3dist(pyzmq)
+BuildRequires:	python3dist(pyzmq)
 %endif
 BuildRequires:	python3dist(rpy2)
 BuildRequires:	python3dist(scipy)
@@ -368,6 +376,7 @@ Requires:	gap-pkg-crime
 Requires:	gap-pkg-design
 Requires:	gap-pkg-guava
 Requires:	gap-pkg-hapcryst
+Requires:	gap-pkg-happrime
 Requires:	gap-pkg-sonata
 Requires:	gap-pkg-toric
 Requires:	gfan
@@ -387,9 +396,6 @@ Requires:	pari-galdata
 Requires:	pari-gp
 Requires:	pari-seadata
 Requires:	python3dist(brial)
-%if %{with sphinx_hack}
-Requires:	python3dist(configparser)
-%endif
 Requires:	python3dist(cypari2)
 Requires:	python3dist(cysignals)
 Requires:	python3dist(cvxopt)
@@ -460,10 +466,10 @@ Requires:	texlive
 Requires:	vecmath
 
 %if %{with bundled_thebe}
-Provides:	bundled(thebe) = %(cut -d- -f2- <<< %{thebe_pkg})
+Provides:	bundled(thebe) = %{thebe_ver}
 %endif
 %if %{with bundled_threejs}
-Provides:	bundled(threejs) = %(cut -d- -f2- <<< %{threejs_pkg})
+Provides:	bundled(threejs) = %{threejs_ver}
 %endif
 
 %description
@@ -476,14 +482,14 @@ packages into a common Python-based interface.
 Summary:	Open Source Mathematics Software
 Requires:	%{name}%{?_isa} = %{version}-%{release}
 %if %{with bundled_ipython}
-Provides:	bundled(ipython) = %(cut -d- -f2- <<< %{ipython_pkg})
-Provides:	bundled(prompt_toolkit) = %(cut -d- -f2- <<< %{prompt_tookit_pkg})
+Provides:	bundled(ipython) = %{ipython_ver}
+Provides:	bundled(prompt_toolkit) = %{prompt_toolkit_ver}
 %endif
 %if %{with bundled_ipywidgets}
-Provides:	bundled(ipywidgets) = %(cut -d- -f2- <<< %{ipywidgets_pkg})
+Provides:	bundled(ipywidgets) = %{ipywidgets_ver}
 %endif
 %if %{with bundled_widgetsnbextension}
-Provides:	bundled(widgetsnbextension) = %(cut -d- -f2- <<< %{widgetsnbextension_pkg})
+Provides:	bundled(widgetsnbextension) = %{widgetsnbextension_ver}
 %endif
 
 %description	core
@@ -772,7 +778,7 @@ pushd build/pkgs/pexpect
     tar zxf ../../../upstream/%{pexpect_pkg}.tar.gz
     mv %{pexpect_pkg} src
     pushd src
-	for diff in `ls ../patches/*.patch`; do
+	for diff in ../patches/*.patch; do
 	    patch -p1 < $diff
 	done
     popd
@@ -788,7 +794,7 @@ pushd build/pkgs/rubiks
     tar jxf ../../../upstream/%{rubiks_pkg}.tar.bz2
     mv %{rubiks_pkg} src
     pushd src
-	for diff in `ls ../patches/*.patch`; do
+	for diff in ../patches/*.patch; do
 	    patch -p1 < $diff
 	done
     popd
@@ -808,7 +814,7 @@ pushd build/pkgs/sagetex
     tar zxf ../../../upstream/%{sagetex_pkg}.tar.gz
     mv %{sagetex_pkg} src
     # Fix the style file install path
-    texmfdir=$(cut -d/ -f3- <<< "%{_texmf_main}")
+    texmfdir=$(cut -d/ -f3- <<< "%{_texmf}")
     sed -i "s,share/texmf,$texmfdir," src/setup.py
 popd
 
@@ -818,7 +824,7 @@ pushd build/pkgs/sphinx
     tar zxf ../../../upstream/%{Sphinx_pkg}.tar.gz
     mv %{Sphinx_pkg} src
     pushd src
-	for diff in `ls ../patches/*.patch`; do
+	for diff in ../patches/*.patch; do
 	    patch -p1 < $diff
 	done
     popd
@@ -884,9 +890,11 @@ popd
 %patch28
 %patch29
 %patch30
+%patch31
 
 sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
     -e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \
+    -e 's|@@SAGE_LOCAL@@|%{SAGE_LOCAL}|' \
     -i src/sage/env.py
 
 sed -e 's|@@CYSIGNALS@@|%{python3_sitearch}/cysignals|' \
@@ -898,7 +906,7 @@ sed -e "/flask-oldsessions/d" \
 
 #------------------------------------------------------------------------
 # some .c files are not (re)generated
-find src/sage \( -name \*.pyx -o -name \*.pxd \) | xargs touch
+find src/sage \( -name \*.pyx -o -name \*.pxd \) -exec touch {} \+
 
 # remove bundled jar files before build
 rm build/pkgs/sagenb/src/sagenb/data/sage3d/lib/sage3d.jar
@@ -915,11 +923,15 @@ sed -e "s,\(SINGULAR_SO = \)SAGE.*,\1'%{_libdir}/libSingular-$singver.so'," \
     -i src/sage/env.py
 
 # fix shebangs; some paths contains spaces, so use the null byte facility
+grep -FrlZ '#!%{_bindir}/env python3' | \
+  xargs -0 sed -i 's,#!%{_bindir}/env python3,#!%{__python3},g'
 grep -FrlZ '#!%{_bindir}/env python' | \
-  xargs -0 sed -i 's,#!%{_bindir}/env python,#!%{__python3},'
+  xargs -0 sed -i 's,#!%{_bindir}/env python,#!%{__python3},g'
+grep -FrlZ '#!%{_bindir}/env sage-system-python' | \
+  xargs -0 sed -i 's,#!%{_bindir}/env sage-system-python,#!%{__python3},g'
 grep -FrlZ '#!%{_bindir}/env sage-python23' | \
-  xargs -0 sed -i 's,#!%{_bindir}/env sage-python23,#!%{__python3},'
-grep -FrlZ 'sage-python23' | xargs -0 sed -i 's,sage-python23,#!%{__python3},'
+  xargs -0 sed -i 's,#!%{_bindir}/env sage-python23,#!%{__python3},g'
+grep -FrlZ 'sage-python23' | xargs -0 sed -i 's,sage-python23,python3,g'
 grep -FrlZ '#!%{_bindir}/env' | \
   xargs -0 sed -i 's,#!%{_bindir}/env ,#!%{_bindir}/,'
 grep -rlZ '#!%{_bindir}/python$' | xargs -0 sed -i 's,#!%{_bindir}/python$,&3,'
@@ -938,7 +950,7 @@ sed -e "s|'%{_bindir}/env', 'which'|'%{_bindir}/which'|" \
 %endif
 
 # GAP does not have enough memory to load the entire workspace
-sed -i 's/64m/128m/' src/sage/libs/gap/util.pyx
+sed -i 's/64m/128m/' src/sage/interfaces/gap.py
 
 
 ########################################################################
@@ -947,6 +959,7 @@ export CC=%{__cc}
 export CFLAGS="%{optflags}"
 export CXXFLAGS="%{optflags}"
 export SAGE_PYTHON_VERSION=3
+export SAGE_PYTHON3=yes
 export SAGE_ROOT=%{buildroot}%{SAGE_ROOT}
 export SAGE_LOCAL=%{buildroot}%{SAGE_LOCAL}
 # Avoid buildroot in gcc command line (use _builddir instead)
@@ -974,6 +987,22 @@ export PYTHON=%{_bindir}/python3
 export PYTHONPATH=%{buildroot}%{python3_sitearch}:$PYTHONPATH
 
 #------------------------------------------------------------------------
+# Generate sage-env-config
+sed -e 's,@prefix@,%{SAGE_LOCAL},' \
+    -e 's,@CC@,gcc,' \
+    -e 's,@CXX@,g++,' \
+    -e 's,@FC@,gfortran,' \
+    -e 's,@OBJC@,gcc,' \
+    -e 's,@OBJCXX@,g++,' \
+    -e 's,@SAGE_PYTHON_VERSION@,3,' \
+    -e 's,@SAGE_GMP_PREFIX@,,' \
+    -e 's,@SAGE_GMP_INCLUDE@,%{_includedir},' \
+    -e 's,@SAGE_MPFR_PREFIX@,,' \
+    -e 's,@SAGE_MPC_PREFIX@,,' \
+    -e 's,@SAGE_NTL_PREFIX@,,' \
+    src/bin/sage-env-config.in > src/bin/sage-env-config
+
+#------------------------------------------------------------------------
 # Save and update environment to generate bundled interfaces
 save_PATH=$PATH
 save_LOCAL=$SAGE_LOCAL
@@ -1036,6 +1065,10 @@ pushd build/pkgs/sagenb_export/src
     %__python3 ./setup.py build
 popd
 
+pushd build/pkgs/sagetex/src
+    %__python3 ./setup.py build
+popd
+
 #------------------------------------------------------------------------
 pushd build/pkgs/flintqs/src
     %configure
@@ -1088,7 +1121,7 @@ ln -sf %{_datadir} $SAGE_LOCAL/share
 #------------------------------------------------------------------------
 pushd src/ext
     mkdir -p $SAGE_ETC
-    for dir in 			\
+    for dir in			\
 	gap			\
 	graphs			\
 	images			\
@@ -1159,6 +1192,7 @@ pushd src/bin
 	ln -sf %{_bindir}/gp sage_pari
 	ln -sf %{_bindir}/gap gap
 	ln -sf %{_bindir}/gmp-ecm ecm
+	rm -f sage-env-config.in
     popd
 popd
 install -p -m755 src/bin/sage $SAGE_LOCAL/bin
@@ -1260,7 +1294,7 @@ popd
 #------------------------------------------------------------------------
 pushd build/pkgs/sagetex/src
     %py3_install "--install-purelib=%{python3_sitearch}"
-    mv %{buildroot}%{_texmf_main}/tex/latex/sagetex/CONTRIBUTORS \
+    mv %{buildroot}%{_texmf}/tex/latex/sagetex/CONTRIBUTORS \
 	 %{buildroot}%{_docdir}/sagetex
     for file in PKG-INFO README; do
 	install -p -m 0644 $file %{buildroot}%{_docdir}/sagetex/$file
@@ -1316,6 +1350,7 @@ export SAGE_SHARE="$SAGE_SHARE"
 export SAGE_EXTCODE="$SAGE_ETC"
 export SAGE_ETC="$SAGE_ETC"
 export SAGE_SRC="%{buildroot}%{SAGE_SRC}"
+export SAGE_PYTHON3=yes
 ##export SAGE_DOC="$SAGE_DOC"
 ##export SAGE_DOC_SRC="\$SAGE_DOC"
 ##export SAGE_PKGS="\$SAGE_LOCAL/var/lib/sage/installed"
@@ -1330,11 +1365,10 @@ export SINGULAR_SO=%{_libdir}/libSingular-4.1.1.so
 export SAGE_FORTRAN=%{_bindir}/gfortran
 export SAGE_FORTRAN_LIB=\`gfortran --print-file-name=libgfortran.so\`
 export SYMPOW_DIR="\$DOT_SAGE/sympow"
-export LD_LIBRARY_PATH=\$SAGE_ROOT/lib:\$LD_LIBRARY_PATH
 # Required for sage -gdb
 : \${SAGE_DEBUG:=no}
 export SAGE_DEBUG
-$SAGE_LOCAL/bin/sage "\$@"
+exec $SAGE_LOCAL/bin/sage "\$@"
 EOF
 #------------------------------------------------------------------------
 chmod +x %{buildroot}%{_bindir}/sage
@@ -1379,9 +1413,9 @@ pushd src/doc
 
 %if %{with sphinx_hack}
     pushd ../../build/pkgs/sphinx/src
-        %py3_build
-        %py3_install "--install-purelib=%{python3_sitearch}"
-        rm -f %{buildroot}%{_bindir}/sphinx*
+	%py3_build
+	%py3_install "--install-purelib=%{python3_sitearch}"
+	rm -f %{buildroot}%{_bindir}/sphinx*
     popd
 %endif
 
@@ -1461,7 +1495,7 @@ EOF
 desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop
 
 # Fix permissions
-find %{buildroot} -name '*.so' | xargs chmod 755
+find %{buildroot} -name '*.so' -exec chmod 755 {} \+
 pushd %{buildroot}%{SAGE_LOCAL}/bin
     chmod 755 QuadraticSieve
     chmod 755 mcube dikcube cu2 size222 cubex optimal
@@ -1476,7 +1510,7 @@ done
 chmod -x %{buildroot}%{SAGE_DOC}/en/prep/media/Rplot001.png
 
 # Documentation is not rebuilt (also corrects rpmlint warning of hidden file)
-find %{buildroot}%{SAGE_DOC} -name .buildinfo -exec rm {} \+
+find %{buildroot}%{SAGE_DOC} -name .buildinfo -delete
 rm -fr %{buildroot}%{SAGE_DOC}/output/inventory
 find %{buildroot}%{SAGE_DOC} -type d -name _sources -exec rm -fr {} \+
 %endif
@@ -1507,7 +1541,7 @@ done
 popd
 pushd %{buildroot}%{SAGE_SPKG_INST}
     for pkg in %{SAGE_REQUIRED_PKGS}; do
-        mkdir $pkg
+	mkdir $pkg
     done
 popd
 #------------------------------------------------------------------------
@@ -1519,7 +1553,7 @@ while [ \$# -gt 0 ]; do
     if [ x\$1 = x--no-version ]; then
 	NOVERSION=true
     elif [ x\$1 = xinstalled ]; then
-        INSTALLED=yes
+	INSTALLED=yes
     fi
     shift
 done
@@ -1547,7 +1581,7 @@ chmod +x %{buildroot}%{SAGE_LOCAL}/bin/sage-list-packages
 
 #------------------------------------------------------------------------
 # Byte compile python files in nonstandard places
-%py_byte_compile %{__python3} %{buildroot}%{_texmf_main}/tex/latex/sagetex
+%py_byte_compile %{__python3} %{buildroot}%{_texmf}/tex/latex/sagetex
 
 #------------------------------------------------------------------------
 # Jupyter integration
@@ -1829,11 +1863,19 @@ rm -fr $DOT_SAGE
 %files		sagetex
 # GPLv2+
 %{python3_sitearch}/sagetex*
-%{_texmf_main}/tex/latex/sagetex
+%{python3_sitearch}/__pycache__/sagetex*
+%{_texmf}/tex/latex/sagetex
 %doc %{_docdir}/sagetex
 
 ########################################################################
 %changelog
+* Mon Jul  1 2019 Jerry James <loganjerry@gmail.com> - 8.8-1
+- Update to sagemath 8.8 (bz 1724394)
+- Remove configparser dependencies (bz 1706597)
+- Fix broken sed conversion (bz 1706234)
+- Fix python2 versus python3 snafu (bz 1706337, 1707166)
+- Build and install sagetex (bz 1706322)
+
 * Sat Apr 27 2019 Jerry James <loganjerry@gmail.com> - 8.7-1
 - Update to sagemath 8.7
 - Drop upstreamed -giac patch
diff --git a/sources b/sources
index 3e15ebc..c8f0d25 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-SHA512 (sage-8.7.tar.gz) = 6d89ad388d667c67970f4378fe1208115436d70e913d53e81241766996677b827cd5e97348325d1dc069e5de03b755a25c02c7487c6dc2a15103ffbf25c00a1d
+SHA512 (sage-8.8.tar.gz) = bac6cdd07e1c1bb36cf8617bc5b580818048702f9f73ba1d034e0ae100bbdb7f2ef3f2133d7cea739c98f103ca9e3b90a7c29d87314fb398b9d7984f194d0357