Update to sagemath 8.2.

Also: - Create the sagemath-data-combinatorial_designs subpackage. - Create the sagemath-notebook-export subpackage. - Unbundle the LaTeX makecmds style. - Install LaTeX style files in a more canonical place.
2025-04-04 04:28:51 -04:00 · 2018-06-03 07:13:30 -06:00 · 2018-06-03 07:13:30 -06:00 · 925e91dade
commit 925e91dade
parent b46cd4759a
28 changed files with 743 additions and 795 deletions
--- a/.gitignore
+++ b/.gitignore
@ -14,3 +14,4 @@
 /sage-7.5.1.tar.gz
 /sage-7.6.tar.gz
 /sage-8.0.tar.gz
+/sage-8.2.tar.gz
--- a/makecmds.sty
+++ b/makecmds.sty
@ -1,95 +0,0 @@
-%%
-%% This is file `makecmds.sty',
-%% generated with the docstrip utility.
-%%
-%% The original source files were:
-%%
-%% makecmds.dtx  (with options: `usc')
-%% 
-%%  Copyright 2000 Peter R. Wilson
-%% 
-%%  This program is provided under the terms of the
-%%  LaTeX Project Public License distributed from CTAN
-%%  archives in directory macros/latex/base/lppl.txt.
-%% 
-%% Author: Peter Wilson (CUA)
-%%         now at: peter.r.wilson@boeing.com
-%% 
-\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{makecmds}[2000/05/27 v1.0 extra command making commands]
-
-\newif\ifm@kwarn
-  \m@kwarnfalse
-\DeclareOption{warn}{\m@kwarntrue}
-\ProcessOptions\relax
-
-\def\makecommand{\@star@or@long\m@ke@command}
-\def\m@ke@command#1{%
-  \ifx #1\undefined\else
-    \ifm@kwarn
-      \PackageWarning{makecmds}{Redefining command `\protect#1'}
-    \fi
-  \fi
-  \let\@ifdefinable\@rc@ifdefinable
-  \new@command#1}
-
-\def\provideenvironment{%
-  \@star@or@long\m@kprovide@environment}
-\def\m@kprovide@environment#1{%
-  \@ifundefined{#1}{%
-    \expandafter\let\csname#1\endcsname\relax
-    \expandafter\let\csname end#1\endcsname\relax
-    \new@environment{#1}}{\m@kdiscardenvargs{#1}}
-}
-\def\m@kdiscardenvargs#1{%
-  \@testopt{\m@kenva#1}0}
-\def\m@kenva#1[#2]{%
-  \@ifnextchar [{\m@kenvb#1[#2]}{\m@kthrowenv{#1}{[#2]}}}
-\def\m@kenvb#1[#2][#3]{\m@kthrowenv{#1}{[#2][#3]}}
-\def\m@kthrowenv#1#2#3#4{}
-
-\def\makeenvironment{\@star@or@long\m@ke@environment}
-\def\m@ke@environment#1{%
-  \@ifundefined{#1}{\new@environment{#1}}{%
-    \ifm@kwarn
-      \PackageWarning{makecmds}{Redefining environment `#1'}
-    \fi
-    \renew@environment{#1}}
-}
-
-\def\providelength#1{%
-  \ifx #1\undefined
-    \newlength{#1}
-  \fi
-}
-\def\makelength#1{%
-  \ifx #1\undefined
-    \newlength{#1}
-  \else
-    \ifm@kwarn
-      \PackageWarning{makecmds}{Redefining length `\protect#1'}
-    \fi
-    \newskip#1
-  \fi
-}
-
-\def\providecounter#1{%
-  \@ifundefined{c@#1}{\newcounter{#1}}{%
-    \@ifnextchar[{\m@k@gobbleendoptarg}{}}%
-}
-\def\makecounter#1{%
-  \expandafter\ifx \csname c@#1\endcsname \undefined
-  \else
-    \ifm@kwarn
-      \PackageWarning{makecmds}{Redefining counter `#1'}
-    \fi
-  \fi
-  \@definecounter{#1}%
-  \@ifnextchar[{\@newctr{#1}}{}
-}
-
-\def\m@k@gobbleendoptarg[#1]{}
-
-\endinput
-%%
-%% End of file `makecmds.sty'.
--- a/sagemath-4ti2.patch
+++ b/sagemath-4ti2.patch
@ -1,7 +1,7 @@
 diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
--- src/sage/sandpiles/sandpile.py.orig	2017-04-11 09:56:54.907264014 -0400
-+++ src/sage/sandpiles/sandpile.py	2017-04-11 09:57:04.274264373 -0400
-@@ -347,9 +347,6 @@ from sage.arith.all import falling_facto
+--- src/sage/sandpiles/sandpile.py.orig	2018-05-05 16:21:26.000000000 -0600
+++ src/sage/sandpiles/sandpile.py	2018-05-16 13:28:24.939025388 -0600
+@@ -342,9 +342,6 @@ from sage.arith.all import falling_facto
 from sage.rings.all import Integer, PolynomialRing, QQ, ZZ
 from sage.symbolic.all import I, pi
 
@ -11,7 +11,7 @@ diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
 class Sandpile(DiGraph):
     """
     Class for Dhar's abelian sandpile model.
-@@ -5202,7 +5199,7 @@ class SandpileDivisor(dict):
+@@ -5199,7 +5196,7 @@ class SandpileDivisor(dict):
         sign_file.close()
         # compute
         try:
--- a/sagemath-arb.patch
+++ b/sagemath-arb.patch
@ -1,6 +1,6 @@
 diff -up src/sage/libs/arb/acb.pxd.orig src/sage/libs/arb/acb.pxd
--- src/sage/libs/arb/acb.pxd.orig	2016-08-08 14:02:11.176595456 -0400
-+++ src/sage/libs/arb/acb.pxd	2016-08-08 14:02:17.514595699 -0400
+--- src/sage/libs/arb/acb.pxd.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/libs/arb/acb.pxd	2018-05-16 13:59:18.715290712 -0600
@@ -3,7 +3,7 @@
 from sage.libs.arb.types cimport *
 from sage.libs.flint.types cimport fmpz_t, fmpq_t
@ -10,45 +10,9 @@ diff -up src/sage/libs/arb/acb.pxd.orig src/sage/libs/arb/acb.pxd
 
     arb_t acb_realref(acb_t x)
     arb_t acb_imagref(acb_t x)
-diff -up src/sage/libs/arb/arb.pxd.orig src/sage/libs/arb/arb.pxd
--- src/sage/libs/arb/arb.pxd.orig	2016-08-08 14:02:26.528596044 -0400
-+++ src/sage/libs/arb/arb.pxd	2016-08-08 14:02:33.554596313 -0400
-@@ -4,7 +4,7 @@ from sage.libs.arb.types cimport *
- from sage.libs.flint.types cimport fmpz_t, fmpq_t
- from sage.libs.mpfr cimport mpfr_t
- 
-cdef extern from "arb.h":
-+cdef extern from "arb/arb.h":
- 
-     arf_t arb_midref(arb_t x)
-     mag_t arb_radref(arb_t x)
-diff -up src/sage/libs/arb/arf.pxd.orig src/sage/libs/arb/arf.pxd
--- src/sage/libs/arb/arf.pxd.orig	2016-08-08 14:02:45.928596787 -0400
-+++ src/sage/libs/arb/arf.pxd	2016-08-08 14:02:53.194597065 -0400
-@@ -5,7 +5,7 @@ from sage.libs.gmp.types cimport mpz_t
- from sage.libs.flint.types cimport fmpz_t
- from sage.libs.mpfr 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/mag.pxd.orig src/sage/libs/arb/mag.pxd
--- src/sage/libs/arb/mag.pxd.orig	2016-08-08 14:03:03.208597449 -0400
-+++ src/sage/libs/arb/mag.pxd	2016-08-08 14:03:10.010597709 -0400
-@@ -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/acb_hypgeom.pxd.orig src/sage/libs/arb/acb_hypgeom.pxd
--- src/sage/libs/arb/acb_hypgeom.pxd.orig	2016-08-09 14:18:12.798626773 -0400
-+++ src/sage/libs/arb/acb_hypgeom.pxd	2016-08-09 14:18:18.591626994 -0400
+--- src/sage/libs/arb/acb_hypgeom.pxd.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/libs/arb/acb_hypgeom.pxd	2018-05-16 13:59:18.717290684 -0600
@@ -2,7 +2,7 @@
 
 from sage.libs.arb.types cimport *
@ -59,8 +23,8 @@ diff -up src/sage/libs/arb/acb_hypgeom.pxd.orig src/sage/libs/arb/acb_hypgeom.px
     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	2016-08-09 14:18:29.126627398 -0400
-+++ src/sage/libs/arb/acb_mat.pxd	2016-08-09 14:18:33.559627568 -0400
+--- src/sage/libs/arb/acb_mat.pxd.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/libs/arb/acb_mat.pxd	2018-05-16 13:59:18.717290684 -0600
@@ -1,6 +1,6 @@
 from sage.libs.arb.types cimport acb_t, acb_mat_t
 
@ -70,8 +34,8 @@ diff -up src/sage/libs/arb/acb_mat.pxd.orig src/sage/libs/arb/acb_mat.pxd
     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	2016-08-09 14:18:42.526627911 -0400
-+++ src/sage/libs/arb/acb_modular.pxd	2016-08-09 14:18:46.191628051 -0400
+--- src/sage/libs/arb/acb_modular.pxd.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/libs/arb/acb_modular.pxd	2018-05-16 13:59:18.718290670 -0600
@@ -3,7 +3,7 @@
 from sage.libs.arb.types cimport *
 from sage.libs.flint.types cimport fmpz_poly_t
@ -81,19 +45,9 @@ diff -up src/sage/libs/arb/acb_modular.pxd.orig src/sage/libs/arb/acb_modular.px
     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/bernoulli.pxd.orig src/sage/libs/arb/bernoulli.pxd
--- src/sage/libs/arb/bernoulli.pxd.orig	2016-08-09 14:19:29.102629695 -0400
-+++ src/sage/libs/arb/bernoulli.pxd	2016-08-09 14:19:33.495629863 -0400
-@@ -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/acb_poly.pxd.orig src/sage/libs/arb/acb_poly.pxd
--- src/sage/libs/arb/acb_poly.pxd.orig	2017-03-29 18:10:08.675927202 -0400
-+++ src/sage/libs/arb/acb_poly.pxd	2017-03-29 18:10:13.934927403 -0400
+--- src/sage/libs/arb/acb_poly.pxd.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/libs/arb/acb_poly.pxd	2018-05-16 13:59:18.719290655 -0600
@@ -3,7 +3,7 @@
 from sage.libs.arb.types cimport *
 from sage.libs.flint.types cimport fmpz_poly_t, fmpq_poly_t
@ -103,9 +57,43 @@ diff -up src/sage/libs/arb/acb_poly.pxd.orig src/sage/libs/arb/acb_poly.pxd
     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/arf.pxd.orig src/sage/libs/arb/arf.pxd
+--- src/sage/libs/arb/arf.pxd.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/libs/arb/arf.pxd	2018-05-16 13:59:18.716290698 -0600
+@@ -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	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/libs/arb/bernoulli.pxd	2018-05-16 13:59:18.718290670 -0600
+@@ -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	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/libs/arb/mag.pxd	2018-05-16 13:59:18.717290684 -0600
+@@ -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	2017-03-29 18:08:42.979923920 -0400
-+++ src/sage/libs/arb/types.pxd	2017-03-29 18:09:18.413925277 -0400
+--- src/sage/libs/arb/types.pxd.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/libs/arb/types.pxd	2018-05-16 13:59:18.719290655 -0600
@@ -1,4 +1,4 @@
 -cdef extern from "mag.h":
 +cdef extern from "arb/mag.h":
--- a/sagemath-atlas.patch
+++ b/sagemath-atlas.patch
@ -1,6 +1,6 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2017-11-08 08:34:54.635233833 -0500
-+++ src/module_list.py	2017-11-08 08:36:05.888236561 -0500
+--- src/module_list.py.orig	2018-05-16 14:13:22.021406801 -0600
+++ src/module_list.py	2018-05-16 14:15:57.654208949 -0600
@@ -12,7 +12,7 @@ SAGE_INC = '/usr/include'
 import pkgconfig
 
@ -23,23 +23,12 @@ diff -up src/module_list.py.orig src/module_list.py
 +lapack_library_dirs = []
 +lapack_include_dirs = [ SAGE_INC + '/lapack' ]
 
- # FFLAS-FFPACK
- fflas_ffpack_pc = pkgconfig.parse('fflas-ffpack')
-@@ -44,7 +42,9 @@ givaro_cflags = pkgconfig.cflags('givaro
- # The above cblas should already be in the list thanks to #20646
- gsl_pc = pkgconfig.parse('gsl')
- gsl_libs = gsl_pc['libraries']
-gsl_library_dirs = gsl_pc['library_dirs']
-+gsl_libs.remove('gslcblas')
-+gsl_libs.extend(cblas_libs)
-+gsl_library_dirs = list(cblas_pc['library_dirs'])
- gsl_include_dirs = gsl_pc['include_dirs']
- 
 # 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	2017-11-08 08:36:27.499237389 -0500
-+++ src/sage/misc/cython.py	2017-11-08 08:36:37.240237762 -0500
-@@ -30,7 +30,7 @@ import pkgconfig
+--- src/sage/misc/cython.py.orig	2018-05-16 13:16:29.207708998 -0600
+++ src/sage/misc/cython.py	2018-05-16 14:15:57.656208921 -0600
+@@ -40,7 +40,7 @@ from sage.misc.sage_ostools import resto
 
 
 # CBLAS can be one of multiple implementations
--- a/sagemath-cbc.patch
+++ b/sagemath-cbc.patch
@ -1,14 +1,14 @@
 diff -up src/sage/numerical/backends/coin_backend.pyx.orig src/sage/numerical/backends/coin_backend.pyx
--- src/sage/numerical/backends/coin_backend.pyx.orig	2017-11-08 08:23:51.731208448 -0500
-+++ src/sage/numerical/backends/coin_backend.pyx	2017-11-08 08:24:02.347208854 -0500
-@@ -759,8 +759,8 @@ cdef class CoinBackend(GenericBackend):
+--- src/sage/numerical/backends/coin_backend.pyx.orig	2018-05-16 13:40:23.571130540 -0600
+++ src/sage/numerical/backends/coin_backend.pyx	2018-05-16 13:41:06.750534427 -0600
+@@ -762,8 +762,8 @@ cdef class CoinBackend(GenericBackend):
         model.setLogLevel(old_logLevel)
 
         # multithreading
 -        import multiprocessing
-        model.setNumberThreads(multiprocessing.cpu_count())
+-        model.setNumberThreads(ncpus())
 +        #import multiprocessing
-+        #model.setNumberThreads(multiprocessing.cpu_count())
+        #model.setNumberThreads(ncpus())
 
         model.branchAndBound()
 
--- a/sagemath-extensions.patch
+++ b/sagemath-extensions.patch
@ -1,52 +1,33 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2017-11-08 06:12:26.727906504 -0500
-+++ src/module_list.py	2017-11-08 06:14:29.020911187 -0500
-@@ -163,7 +163,6 @@ library_order["stdc++"] = 1000
- ###
- #############################################################
- 
-from sage_setup.optional_extension import OptionalExtension
- UNAME = os.uname()
- 
- def uname_specific(name, value, alternative):
-@@ -391,21 +390,21 @@ ext_modules = [
-               sources = ['sage/graphs/matchpoly.pyx'],
-               extra_compile_args = ['-std=c99']),
+--- src/module_list.py.orig	2018-05-05 16:21:22.000000000 -0600
+++ src/module_list.py	2018-05-18 07:46:16.531947286 -0600
+@@ -358,16 +358,16 @@ ext_modules = [
+     Extension('sage.graphs.matchpoly',
+               sources = ['sage/graphs/matchpoly.pyx']),
 
 -    OptionalExtension("sage.graphs.mcqd",
 -              ["sage/graphs/mcqd.pyx"],
 -              language = "c++",
 -              package = 'mcqd'),
-
+#    OptionalExtension("sage.graphs.mcqd",
+#              ["sage/graphs/mcqd.pyx"],
+#              language = "c++",
+#              package = 'mcqd'),
+ 
 -    OptionalExtension("sage.graphs.bliss",
 -              ["sage/graphs/bliss.pyx"],
 -              language = "c++",
 -              libraries = ['bliss'],
 -              package = 'bliss'),
-
-    OptionalExtension('sage.graphs.modular_decomposition',
-              sources = ['sage/graphs/modular_decomposition.pyx'],
-              libraries = ['modulardecomposition'],
-              package = 'modular_decomposition'),
-+#    OptionalExtension("sage.graphs.mcqd",
-+#              ["sage/graphs/mcqd.pyx"],
-+#              language = "c++",
-+#              package = 'mcqd'),
-+
 +#    OptionalExtension("sage.graphs.bliss",
 +#              ["sage/graphs/bliss.pyx"],
 +#              language = "c++",
 +#              libraries = ['bliss'],
 +#              package = 'bliss'),
-+
-+#    OptionalExtension('sage.graphs.modular_decomposition',
-+#              sources = ['sage/graphs/modular_decomposition.pyx'],
-+#              libraries = ['modulardecomposition'],
-+#              package = 'modular_decomposition'),
 
     Extension('sage.graphs.planarity',
               sources = ['sage/graphs/planarity.pyx'],
-@@ -424,10 +423,10 @@ ext_modules = [
+@@ -386,10 +386,10 @@ ext_modules = [
     Extension('sage.graphs.graph_decompositions.cutwidth',
               sources = ['sage/graphs/graph_decompositions/cutwidth.pyx']),
 
@ -61,7 +42,7 @@ diff -up src/module_list.py.orig src/module_list.py
 
     Extension('sage.graphs.spanning_tree',
               sources = ['sage/graphs/spanning_tree.pyx']),
-@@ -514,17 +513,17 @@ ext_modules = [
+@@ -454,21 +454,20 @@ ext_modules = [
     ##
     ################################
 
@ -85,8 +66,13 @@ diff -up src/module_list.py.orig src/module_list.py
 +    Extension("sage.libs.fes",
              ["sage/libs/fes.pyx"],
              language = "c",
-              libraries = ['fes'],
-@@ -548,23 +547,23 @@ ext_modules = [
+-             libraries = ['fes'],
+-             package = 'fes'),
+             libraries = ['fes']),
+ 
+     Extension('sage.libs.flint.flint',
+               sources = ["sage/libs/flint/flint.pyx"],
+@@ -488,22 +487,22 @@ ext_modules = [
     Extension('sage.libs.gmp.pylong',
               sources = ['sage/libs/gmp/pylong.pyx']),
 
@ -95,39 +81,35 @@ diff -up src/module_list.py.orig src/module_list.py
 -                      libraries = ["braiding"],
 -                      package="libbraiding",
 -                      language = 'c++'),
-
-
-    OptionalExtension('sage.libs.homfly',
-                      sources = ["sage/libs/homfly.pyx"],
-                      libraries = ["homfly", "gc"],
-                      package="libhomfly"),
-
-    OptionalExtension('sage.libs.sirocco',
-                      sources = ["sage/libs/sirocco.pyx"],
-                      libraries = ["sirocco", "mpfr", "gmp"],
-                      package="sirocco",
-                      language = 'c++'),
 +#    OptionalExtension('sage.libs.braiding',
 +#                      sources = ["sage/libs/braiding.pyx"],
 +#                      libraries = ["braiding"],
 +#                      package="libbraiding",
 +#                      language = 'c++'),
-+
-+
+ 
+-    OptionalExtension('sage.libs.homfly',
+-                      sources = ["sage/libs/homfly.pyx"],
+-                      libraries = ["homfly", "gc"],
+-                      package="libhomfly"),
 +#    OptionalExtension('sage.libs.homfly',
 +#                      sources = ["sage/libs/homfly.pyx"],
 +#                      libraries = ["homfly", "gc"],
 +#                      package="libhomfly"),
-+
+ 
+-    OptionalExtension('sage.libs.sirocco',
+-                      sources = ["sage/libs/sirocco.pyx"],
+-                      libraries = ["sirocco"],
+-                      package="sirocco",
+-                      language = 'c++'),
 +#    OptionalExtension('sage.libs.sirocco',
 +#                      sources = ["sage/libs/sirocco.pyx"],
-+#                      libraries = ["sirocco", "mpfr", "gmp"],
+#                      libraries = ["sirocco"],
 +#                      package="sirocco",
 +#                      language = 'c++'),
 
     Extension('*', ['sage/libs/linbox/*.pyx']),
 
-@@ -901,10 +900,10 @@ ext_modules = [
+@@ -844,10 +843,10 @@ ext_modules = [
     Extension('sage.matrix.matrix_window',
               sources = ['sage/matrix/matrix_window.pyx']),
 
@ -141,31 +123,30 @@ diff -up src/module_list.py.orig src/module_list.py
 +#              package = 'meataxe'),
 
     Extension('sage.matrix.misc',
-               sources = ['sage/matrix/misc.pyx'],
-@@ -1089,19 +1088,19 @@ ext_modules = [
+               sources = ['sage/matrix/misc.pyx']),
+@@ -1024,26 +1023,25 @@ ext_modules = [
     Extension("sage.numerical.backends.interactivelp_backend",
               ["sage/numerical/backends/interactivelp_backend.pyx"]),
 
 -    OptionalExtension("sage.numerical.backends.gurobi_backend",
 -              ["sage/numerical/backends/gurobi_backend.pyx"],
-              libraries = ["stdc++", "gurobi"],
+-              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 = ["stdc++", "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 = ["stdc++", "gurobi"],
+#              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.cplex_backend",
 +#              ["sage/numerical/backends/cplex_backend.pyx"],
-+#              libraries = ["stdc++", "cplex"],
+#              libraries = ["cplex"],
 +#              condition = os.path.isfile(SAGE_INC + "/cplex.h") and
 +#                  os.path.isfile(SAGE_LOCAL + "/lib/libcplex.a")),
 
@ -174,3 +155,11 @@ diff -up src/module_list.py.orig src/module_list.py
               ["sage/numerical/backends/coin_backend.pyx"],
               language = 'c++',
               libraries = ["Cbc", "CbcSolver", "Cgl", "Clp", "CoinUtils",
+                            "OsiCbc", "OsiClp", "Osi"] + lapack_libs,
+               library_dirs = lapack_library_dirs,
+-              include_dirs = lapack_include_dirs,
+-              package = 'cbc'),
+              include_dirs = lapack_include_dirs),
+ 
+     ################################
+     ##
--- a/sagemath-fes.patch
+++ b/sagemath-fes.patch
@ -1,20 +1,18 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2017-11-08 08:27:07.539215946 -0500
-+++ src/module_list.py	2017-11-08 08:27:17.051216310 -0500
-@@ -523,11 +523,11 @@ ext_modules = [
+--- src/module_list.py.orig	2018-05-18 09:34:28.942183178 -0600
+++ src/module_list.py	2018-05-18 09:35:15.210542150 -0600
+@@ -464,10 +464,10 @@ ext_modules = [
     Extension('sage.libs.ecl',
               sources = ["sage/libs/ecl.pyx"]),
 
 -    Extension("sage.libs.fes",
 -             ["sage/libs/fes.pyx"],
 -             language = "c",
-             libraries = ['fes'],
-             package = 'fes'),
+-             libraries = ['fes']),
 +#    Extension("sage.libs.fes",
 +#             ["sage/libs/fes.pyx"],
 +#             language = "c",
-+#             libraries = ['fes'],
-+#             package = 'fes'),
+#             libraries = ['fes']),
 
     Extension('sage.libs.flint.flint',
               sources = ["sage/libs/flint/flint.pyx"],
--- a/sagemath-gap-hap.patch
+++ b/sagemath-gap-hap.patch
@ -1,6 +1,6 @@
 diff -up src/sage/groups/perm_gps/permgroup.py.orig src/sage/groups/perm_gps/permgroup.py
--- src/sage/groups/perm_gps/permgroup.py.orig	2017-11-08 08:23:18.884207190 -0500
-+++ src/sage/groups/perm_gps/permgroup.py	2017-11-08 08:23:27.988207539 -0500
+--- src/sage/groups/perm_gps/permgroup.py.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/groups/perm_gps/permgroup.py	2018-05-16 13:38:07.049015293 -0600
@@ -166,6 +166,10 @@ def load_hap():
         gap.load_package("hap")
     except Exception:
@ -17,7 +17,7 @@ diff -up src/sage/groups/perm_gps/permgroup.py.orig src/sage/groups/perm_gps/per
     @wraps(f)
     def wrapped(self, n, p=0):
 -        if not is_package_installed('gap_packages'):
-            raise RuntimeError("You must install the optional gap_packages package.")
+-            raise PackageNotFoundError("gap_packages")
         load_hap()
         from sage.arith.all import is_prime
         if not (p == 0 or is_prime(p)):
--- a/sagemath-gcc6.patch
+++ b/sagemath-gcc6.patch
@ -1,12 +0,0 @@
-diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2017-11-08 08:30:43.611224220 -0500
-+++ src/module_list.py	2017-11-08 08:30:51.131224508 -0500
-@@ -861,7 +861,7 @@ ext_modules = [
-               library_dirs = m4ri_library_dirs,
-               include_dirs = m4ri_include_dirs,
-               depends = [SAGE_INC + "/m4rie/m4rie.h"],
-              extra_compile_args = ['-std=c99'] + m4ri_extra_compile_args),
-+              extra_compile_args = ['-std=c++11'] + m4ri_extra_compile_args),
- 
-     Extension('sage.matrix.matrix_modn_dense_float',
-               sources = ['sage/matrix/matrix_modn_dense_float.pyx'],
--- a/sagemath-includes.patch
+++ b/sagemath-includes.patch
@ -1,15 +1,32 @@
 diff -up src/module_list.py.orig src/module_list.py
--- src/module_list.py.orig	2017-11-08 08:30:03.588222687 -0500
-+++ src/module_list.py	2017-11-08 08:30:21.532223375 -0500
-@@ -62,6 +62,7 @@ linbox_cflags = pkgconfig.cflags('linbox
- # Singular
- singular_pc = pkgconfig.parse('Singular')
- singular_libs = singular_pc['libraries']
-+singular_incs = [SAGE_INC + '/singular', SAGE_INC + '/factory']
- singular_library_dirs = singular_pc['library_dirs']
- singular_cflags = pkgconfig.cflags('Singular').split()
+--- src/module_list.py.orig	2018-05-22 15:41:19.892745329 -0600
+++ src/module_list.py	2018-05-22 15:42:40.289863491 -0600
+@@ -45,6 +45,9 @@ zlib_libs = zlib_pc['libraries']
+ zlib_library_dirs = zlib_pc['library_dirs']
+ zlib_include_dirs = zlib_pc['include_dirs']
 
-@@ -185,7 +186,8 @@ ext_modules = [
+# Singular
+singular_incs = [SAGE_INC + '/singular', SAGE_INC + '/factory']
+
+ #########################################################
+ ### M4RI flags
+ #########################################################
+@@ -61,6 +64,14 @@ except ValueError:
+     pass
+ 
+ #########################################################
+### ARB flags
+#########################################################
+
+arb_include_dirs = [os.path.join(SAGE_INC, 'flint'),
+                    os.path.join(SAGE_INC, 'arb')]
+arb_libs = ['arb']
+
+#########################################################
+ ### Library order
+ #########################################################
+ 
+@@ -134,7 +145,8 @@ ext_modules = [
                language='c++',
                libraries = ["gmp", "m", "ntl"]),
 
@ -17,9 +34,9 @@ diff -up src/module_list.py.orig src/module_list.py
 +    Extension('*', sources = ['sage/algebras/letterplace/*.pyx'],
 +              include_dirs = singular_incs),
 
-     Extension('sage.algebras.quatalg.quaternion_algebra_cython',
-                sources = ['sage/algebras/quatalg/quaternion_algebra_cython.pyx'],
-@@ -581,7 +583,8 @@ ext_modules = [
+     Extension('*', sources = ['sage/algebras/finite_dimensional_algebras/*.pyx']),
+ 
+@@ -519,7 +531,8 @@ ext_modules = [
                                                         [])),
 
     Extension('sage.libs.lrcalc.lrcalc',
@ -27,9 +44,9 @@ diff -up src/module_list.py.orig src/module_list.py
 +              sources = ["sage/libs/lrcalc/lrcalc.pyx"],
 +              include_dirs = [os.path.join(SAGE_INC, 'lrcalc')]),
 
-     Extension('*', ['sage/libs/pari/*.pyx']),
- 
-@@ -598,7 +601,8 @@ ext_modules = [
+     OptionalExtension("sage.libs.meataxe",
+               sources = ['sage/libs/meataxe.pyx'],
+@@ -541,23 +554,28 @@ ext_modules = [
               sources = ['sage/libs/readline.pyx'],
               libraries = ['readline']),
 
@ -39,18 +56,16 @@ diff -up src/module_list.py.orig src/module_list.py
 
     Extension('sage.libs.symmetrica.symmetrica',
               sources = ["sage/libs/symmetrica/symmetrica.pyx"],
-@@ -606,17 +610,21 @@ ext_modules = [
+               libraries = ["symmetrica"]),
 
     Extension('sage.libs.mpmath.utils',
-               sources = ["sage/libs/mpmath/utils.pyx"],
-              libraries = ['mpfr']),
-+              libraries = ['mpfr'],
+-              sources = ["sage/libs/mpmath/utils.pyx"]),
+              sources = ["sage/libs/mpmath/utils.pyx"],
 +              include_dirs = [os.path.join(SAGE_INC, "flint")]),
 
     Extension('sage.libs.mpmath.ext_impl',
-               sources = ["sage/libs/mpmath/ext_impl.pyx"],
-              libraries = ['mpfr']),
-+              libraries = ['mpfr'],
+-              sources = ["sage/libs/mpmath/ext_impl.pyx"]),
+              sources = ["sage/libs/mpmath/ext_impl.pyx"],
 +              include_dirs = [os.path.join(SAGE_INC, "flint")]),
 
     Extension('sage.libs.mpmath.ext_main',
@ -65,25 +80,35 @@ diff -up src/module_list.py.orig src/module_list.py
 
     ###################################
     ##
-@@ -624,7 +632,8 @@ ext_modules = [
+@@ -565,7 +583,8 @@ ext_modules = [
     ##
     ###################################
 
 -    Extension('*', ["sage/libs/arb/*.pyx"]),
 +    Extension('*', ["sage/libs/arb/*.pyx"],
-+              include_dirs = [SAGE_INC + '/flint', SAGE_INC + '/arb']),
+              include_dirs = arb_include_dirs),
 
     ###################################
     ##
-@@ -805,6 +814,7 @@ ext_modules = [
+@@ -745,7 +764,8 @@ ext_modules = [
+ 
     Extension("sage.matrix.matrix_complex_ball_dense",
               ["sage/matrix/matrix_complex_ball_dense.pyx"],
-               libraries=['arb', 'mpfi', 'mpfr'],
-+              include_dirs=[SAGE_INC + '/flint', SAGE_INC + '/arb'],
-               language = "c++"),
+-              libraries=['arb']),
+              include_dirs = arb_include_dirs,
+              libraries=arb_libs),
 
     Extension('sage.matrix.matrix_complex_double_dense',
-@@ -872,6 +882,7 @@ ext_modules = [
+               sources = ['sage/matrix/matrix_complex_double_dense.pyx']),
+@@ -753,6 +773,7 @@ ext_modules = [
+     Extension('sage.matrix.matrix_cyclo_dense',
+               sources = ['sage/matrix/matrix_cyclo_dense.pyx'],
+               language = "c++",
+              include_dirs = arb_include_dirs,
+               libraries=['ntl']),
+ 
+     Extension('sage.matrix.matrix_gap',
+@@ -815,6 +836,7 @@ ext_modules = [
               sources = ['sage/matrix/matrix_modn_sparse.pyx']),
 
     Extension('sage.matrix.matrix_mpolynomial_dense',
@ -91,23 +116,35 @@ diff -up src/module_list.py.orig src/module_list.py
               sources = ['sage/matrix/matrix_mpolynomial_dense.pyx']),
 
     Extension('sage.matrix.matrix_polynomial_dense',
-@@ -1201,6 +1212,7 @@ ext_modules = [
-     Extension("sage.rings.complex_arb",
-               ["sage/rings/complex_arb.pyx"],
-               libraries=['mpfi', 'mpfr', 'gmp'],
-+              include_dirs=[SAGE_INC + '/flint', SAGE_INC + '/arb'],
+@@ -1112,7 +1134,8 @@ ext_modules = [
               language = 'c++'),
 
+     Extension("sage.rings.complex_arb",
+-              ["sage/rings/complex_arb.pyx"]),
+              ["sage/rings/complex_arb.pyx"],
+              include_dirs = arb_include_dirs),
+ 
     Extension('sage.rings.complex_double',
-@@ -1276,6 +1288,7 @@ ext_modules = [
+               sources = ['sage/rings/complex_double.pyx'],
+@@ -1182,7 +1205,8 @@ ext_modules = [
+               sources = ['sage/rings/real_interval_absolute.pyx']),
+ 
     Extension("sage.rings.real_arb",
-               ["sage/rings/real_arb.pyx"],
-               libraries = ['mpfi', 'mpfr'],
-+              include_dirs=[SAGE_INC + '/flint', SAGE_INC + '/arb'],
-               language = 'c++'),
+-              ["sage/rings/real_arb.pyx"]),
+              ["sage/rings/real_arb.pyx"],
+              include_dirs = arb_include_dirs),
 
     Extension('sage.rings.real_lazy',
-@@ -1481,12 +1494,15 @@ ext_modules = [
+               sources = ['sage/rings/real_lazy.pyx']),
+@@ -1265,6 +1289,7 @@ ext_modules = [
+ 
+     Extension('sage.rings.number_field.number_field_element_quadratic',
+               sources = ['sage/rings/number_field/number_field_element_quadratic.pyx'],
+              include_dirs = arb_include_dirs,
+               libraries=['ntl'],
+               language = 'c++'),
+ 
+@@ -1387,12 +1412,15 @@ ext_modules = [
               sources = ['sage/rings/polynomial/multi_polynomial.pyx']),
 
     Extension('sage.rings.polynomial.multi_polynomial_ideal_libsingular',
@ -123,20 +160,22 @@ 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_generic',
-@@ -1500,6 +1516,7 @@ ext_modules = [
+@@ -1405,7 +1433,8 @@ ext_modules = [
+               sources = ['sage/rings/polynomial/polydict.pyx']),
 
     Extension('sage.rings.polynomial.polynomial_complex_arb',
-                sources = ['sage/rings/polynomial/polynomial_complex_arb.pyx'],
-+               include_dirs=[SAGE_INC + '/flint', SAGE_INC + '/arb'],
-                language="c++"),
+-               sources = ['sage/rings/polynomial/polynomial_complex_arb.pyx']),
+               sources = ['sage/rings/polynomial/polynomial_complex_arb.pyx'],
+               include_dirs = arb_include_dirs),
 
     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	2017-11-08 08:30:03.589222688 -0500
-+++ src/setup.py	2017-11-08 08:30:21.533223375 -0500
-@@ -89,6 +89,7 @@ except KeyError:
+--- src/setup.py.orig	2018-05-22 15:41:19.893745318 -0600
+++ src/setup.py	2018-05-22 15:41:27.805658536 -0600
+@@ -85,6 +85,7 @@ except KeyError:
+ 
 # search for dependencies and add to gcc -I<path>
- # this depends on SAGE_CYTHONIZED
 include_dirs = sage_include_directories(use_sources=True)
 +include_dirs.extend(['@@CYSIGNALS@@'])
 
--- a/sagemath-jmol.patch
+++ b/sagemath-jmol.patch
@ -1,7 +1,7 @@
 diff -up src/sage/interfaces/jmoldata.py.orig src/sage/interfaces/jmoldata.py
--- src/sage/interfaces/jmoldata.py.orig	2016-08-08 13:34:51.199532656 -0400
-+++ src/sage/interfaces/jmoldata.py	2016-08-08 13:36:16.474535921 -0400
-@@ -147,8 +147,6 @@ class JmolData(SageObject):
+--- src/sage/interfaces/jmoldata.py.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/interfaces/jmoldata.py	2018-05-16 13:30:58.803927423 -0600
+@@ -148,8 +148,6 @@ class JmolData(SageObject):
             sage: print(os.path.exists(testfile)) # optional -- java
             True
         """
@ -10,16 +10,16 @@ diff -up src/sage/interfaces/jmoldata.py.orig src/sage/interfaces/jmoldata.py
         target_native = targetfile
         import sys
         if sys.platform == 'cygwin':
-@@ -173,10 +171,8 @@ class JmolData(SageObject):
+@@ -174,10 +172,8 @@ class JmolData(SageObject):
             env = dict(os.environ)
             env['LC_ALL'] = 'C'
             env['LANG'] = 'C'
 -            subprocess.call(["java", "-Xmx512m", "-Djava.awt.headless=true",
-                "-jar", jmolpath, "-iox", "-g", sizeStr,
+-                "-jar", jmolpath, "-iox", "-g", size_arg,
 -                "-J", launchscript, "-j", imagescript],
 -                stdout=jout, stderr=jout, env=env)
-+            subprocess.call(["jmol", "-n", "-g", sizeStr,
-+                "-J",launchscript, "-j", imagescript], stdout=jout)
+            subprocess.call(["jmol", "-n", "-g", size_arg,
+                "-J", launchscript, "-j", imagescript], stdout=jout)
         if not os.path.isfile(targetfile):
             raise RuntimeError("Jmol failed to create file %s, see %s for details"%(repr(targetfile), repr(scratchout)))
         os.unlink(scratchout)
--- a/sagemath-lcalc.patch
+++ b/sagemath-lcalc.patch
@ -1,6 +1,17 @@
+diff -up src/sage/libs/lcalc/lcalc_Lfunction.pxd.orig src/sage/libs/lcalc/lcalc_Lfunction.pxd
+--- src/sage/libs/lcalc/lcalc_Lfunction.pxd.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/libs/lcalc/lcalc_Lfunction.pxd	2018-05-22 13:31:10.717337490 -0600
+@@ -1,6 +1,6 @@
+ # Lcalc requires GNU extensions, it does not strictly conform to any
+ # C++ standard: https://trac.sagemath.org/ticket/23341
+-# distutils: extra_compile_args = -std=gnu++98
+# distutils: extra_compile_args = -std=gnu++11
+ 
+ cdef extern from "lcalc_sage.h":
+     ctypedef struct doublevec "std::vector<double>":
 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	2016-08-08 13:40:43.480546146 -0400
-+++ src/sage/libs/lcalc/lcalc_sage.h	2016-08-08 13:40:49.561546379 -0400
+--- src/sage/libs/lcalc/lcalc_sage.h.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/libs/lcalc/lcalc_sage.h	2018-05-22 13:30:32.012839737 -0600
@@ -1,4 +1,4 @@
 -#include "libLfunction/L.h"
 +#include "Lfunction/L.h"
--- a/sagemath-lrslib.patch
+++ b/sagemath-lrslib.patch
@ -1,21 +1,12 @@
 diff -up src/sage/geometry/polyhedron/base.py.orig src/sage/geometry/polyhedron/base.py
--- src/sage/geometry/polyhedron/base.py.orig	2017-11-08 08:21:45.693203621 -0500
-+++ src/sage/geometry/polyhedron/base.py	2017-11-08 08:21:56.893204050 -0500
-@@ -22,7 +22,6 @@ from sage.structure.element import Eleme
- from sage.structure.richcmp import rich_to_bool, op_NE
- 
- from sage.misc.all import cached_method, prod
-from sage.misc.package import is_package_installed
- 
- from sage.rings.all import QQ, ZZ, AA
- from sage.rings.real_double import RDF
-@@ -4188,10 +4187,6 @@ class Polyhedron_base(Element):
+--- src/sage/geometry/polyhedron/base.py.orig	2018-05-16 13:31:55.930138769 -0600
+++ src/sage/geometry/polyhedron/base.py	2018-05-16 13:35:12.219428900 -0600
+@@ -4281,9 +4281,6 @@ class Polyhedron_base(Element):
 
              David Avis's lrs program.
         """
 -        if not is_package_installed('lrslib'):
-            raise NotImplementedError('You must install the optional lrslib package '
-                                       'for this function to work')
+-            raise PackageNotFoundError('lrslib')
 -
         from sage.misc.temporary_file import tmp_filename
         from subprocess import Popen, PIPE
--- a/sagemath-maxima.patch
+++ b/sagemath-maxima.patch
@ -1,6 +1,6 @@
 diff -up src/bin/sage-maxima.lisp.orig src/bin/sage-maxima.lisp
--- src/bin/sage-maxima.lisp.orig	2017-11-08 08:16:44.346192082 -0500
-+++ src/bin/sage-maxima.lisp	2017-11-08 08:16:54.098192455 -0500
+--- src/bin/sage-maxima.lisp.orig	2018-05-05 16:21:22.000000000 -0600
+++ src/bin/sage-maxima.lisp	2018-05-16 13:25:51.499101380 -0600
@@ -4,3 +4,8 @@
 
 (setf *prompt-prefix* "<sage-display>")
@ -11,18 +11,18 @@ diff -up src/bin/sage-maxima.lisp.orig src/bin/sage-maxima.lisp
 +  *standard-input* (open "/dev/stdin" :direction :input)
 +  *standard-output* (open "/dev/stdout" :direction :output))
 diff -up src/sage/interfaces/maxima.py.orig src/sage/interfaces/maxima.py
--- src/sage/interfaces/maxima.py.orig	2017-11-08 08:16:38.516191858 -0500
-+++ src/sage/interfaces/maxima.py	2017-11-08 08:16:54.099192455 -0500
-@@ -555,7 +555,7 @@ class Maxima(MaximaAbstract, Expect):
+--- src/sage/interfaces/maxima.py.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/interfaces/maxima.py	2018-05-16 13:27:01.240157806 -0600
+@@ -556,7 +556,7 @@ class Maxima(MaximaAbstract, Expect):
         Expect.__init__(self,
                         name = 'maxima',
                         prompt = '\(\%i[0-9]+\) ',
 -                        command = 'maxima --userdir="%s" -p "%s"'%(SAGE_MAXIMA_DIR,STARTUP),
-+                        command = 'maxima --disable-readline --userdir="%s" -p "%s"'%(SAGE_MAXIMA_DIR,STARTUP), 
+                        command = 'maxima --disable-readline --userdir="%s" -p "%s"'%(SAGE_MAXIMA_DIR,STARTUP),
+                         env = {'TMPDIR': str(ECL_TMP)},
                         script_subdirectory = script_subdirectory,
                         restart_on_ctrlc = False,
-                         verbose_start = False,
-@@ -622,7 +622,8 @@ class Maxima(MaximaAbstract, Expect):
+@@ -624,7 +624,8 @@ class Maxima(MaximaAbstract, Expect):
 
         # Remove limit on the max heapsize (since otherwise it defaults
         # to 256MB with ECL).
--- a/sagemath-mpfr.patch
+++ b/sagemath-mpfr.patch
@ -0,0 +1,47 @@
+diff -up src/sage/libs/mpfr/__init__.pxd.orig src/sage/libs/mpfr/__init__.pxd
+--- src/sage/libs/mpfr/__init__.pxd.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/libs/mpfr/__init__.pxd	2018-05-25 15:01:25.576043678 -0600
+@@ -96,7 +96,6 @@ cdef extern from "mpfr.h":
+     int mpfr_sqrt(mpfr_t rop, mpfr_t op, mpfr_rnd_t rnd)
+     int mpfr_sqrt_ui(mpfr_t rop, unsigned long int op, mpfr_rnd_t rnd)
+     int mpfr_cbrt(mpfr_t rop, mpfr_t op, mpfr_rnd_t rnd)
+-    int mpfr_rootn_ui(mpfr_t rop, mpfr_t op, unsigned long int k, mpfr_rnd_t rnd)
+     int mpfr_root(mpfr_t rop, mpfr_t op, unsigned long int k, mpfr_rnd_t rnd)
+     int mpfr_pow(mpfr_t rop, mpfr_t op1, mpfr_t op2, mpfr_rnd_t rnd)
+     int mpfr_pow_ui(mpfr_t rop, mpfr_t op1, unsigned long int op2, mpfr_rnd_t rnd)
+diff -up src/sage/rings/complex_mpc.pyx.orig src/sage/rings/complex_mpc.pyx
+--- src/sage/rings/complex_mpc.pyx.orig	2018-05-05 16:21:25.000000000 -0600
+++ src/sage/rings/complex_mpc.pyx	2018-05-25 15:02:11.567712409 -0600
+@@ -2221,7 +2221,7 @@ cdef class MPComplexNumber(sage.structur
+         cdef RealNumber a,r
+         a = self.argument()/n
+         r = self.abs()
+-        mpfr_rootn_ui(r.value, r.value, n, rrnd)
+        mpfr_root(r.value, r.value, n, rrnd)
+ 
+         cdef MPComplexNumber z
+         z = self._new()
+diff -up src/sage/rings/complex_number.pyx.orig src/sage/rings/complex_number.pyx
+--- src/sage/rings/complex_number.pyx.orig	2018-05-05 16:21:25.000000000 -0600
+++ src/sage/rings/complex_number.pyx	2018-05-25 15:01:52.328850983 -0600
+@@ -2276,7 +2276,7 @@ cdef class ComplexNumber(sage.structure.
+         rho = abs(self)
+         arg = self.argument() / n
+         mpfr_init2(r, self._prec)
+-        mpfr_rootn_ui(r, rho.value, n, rnd)
+        mpfr_root(r, rho.value, n, rnd)
+ 
+         mpfr_sin_cos(z.__im, z.__re, arg.value, rnd)
+         mpfr_mul(z.__re, z.__re, r, rnd)
+diff -up src/sage/rings/real_mpfr.pyx.orig src/sage/rings/real_mpfr.pyx
+--- src/sage/rings/real_mpfr.pyx.orig	2018-05-05 16:21:26.000000000 -0600
+++ src/sage/rings/real_mpfr.pyx	2018-05-25 11:33:48.009144647 -0600
+@@ -5369,7 +5369,7 @@ cdef class RealNumber(sage.structure.ele
+         if algorithm == 1:
+             x = self._new()
+             sig_on()
+-            mpfr_rootn_ui(x.value, self.value, n, (<RealField_class>self._parent).rnd)
+            mpfr_root(x.value, self.value, n, (<RealField_class>self._parent).rnd)
+             sig_off()
+             return x
+ 
--- 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	2017-11-08 08:22:46.174205937 -0500
-+++ src/sage/graphs/graph_generators.py	2017-11-08 08:22:54.470206255 -0500
-@@ -882,7 +882,7 @@ class GraphGenerators():
+--- src/sage/graphs/graph_generators.py.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/graphs/graph_generators.py	2018-05-16 13:35:59.299778933 -0600
+@@ -886,7 +886,7 @@ class GraphGenerators():
             >A geng -d0D3 n=4 e=0-6
         """
         import subprocess
--- a/sagemath-nofstring.patch
+++ b/sagemath-nofstring.patch
@ -1,60 +1,60 @@
 diff -up src/sage/arith/multi_modular.pyx.orig src/sage/arith/multi_modular.pyx
--- src/sage/arith/multi_modular.pyx.orig	2017-11-08 08:29:36.259221641 -0500
-+++ src/sage/arith/multi_modular.pyx	2017-11-08 08:29:38.843221740 -0500
-@@ -172,9 +172,9 @@ cdef class MultiModularBasis_base(object
+--- src/sage/arith/multi_modular.pyx.orig	2018-05-05 16:21:22.000000000 -0600
+++ src/sage/arith/multi_modular.pyx	2018-05-18 09:39:53.247690061 -0600
+@@ -173,9 +173,9 @@ cdef class MultiModularBasis_base(object
             ArithmeticError: The inverse of 6 modulo 10 is not defined.
         """
         if l_bound < 2:
 -            raise ValueError(f"minimum value for lower bound is 2, given: {l_bound}")
-+            raise ValueError("minimum value for lower bound is 2, given: {l_bound}")
+            raise ValueError("minimum value for lower bound is 2, given: {l_bound}".format(l_bound=l_bound))
         if u_bound > MAX_MODULUS:
 -            raise ValueError(f"upper bound cannot be greater than {MAX_MODULUS}, given: {u_bound}")
-+            raise ValueError("upper bound cannot be greater than {MAX_MODULUS}, given: {u_bound}")
+            raise ValueError("upper bound cannot be greater than {MAX_MODULUS}, given: {u_bound}".format(MAX_MODULUS=MAX_MODULUS, u_bound=u_bound))
 
         self._l_bound = l_bound
         self._u_bound = u_bound
-@@ -233,7 +233,7 @@ cdef class MultiModularBasis_base(object
+@@ -234,7 +234,7 @@ cdef class MultiModularBasis_base(object
         if check:
             for p in plist:
                 if p > MAX_MODULUS:
 -                    raise OverflowError(f"given modulus {p} is larger than {MAX_MODULUS}")
-+                    raise OverflowError("given modulus {p} is larger than {MAX_MODULUS}")
+                    raise OverflowError("given modulus {p} is larger than {MAX_MODULUS}".format(p=p, MAX_MODULUS=MAX_MODULUS))
         self._realloc_to_new_count(self.n + len_plist)
 
         cdef Py_ssize_t i
 diff -up src/sage/rings/finite_rings/integer_mod.pyx.orig src/sage/rings/finite_rings/integer_mod.pyx
--- src/sage/rings/finite_rings/integer_mod.pyx.orig	2017-11-08 08:29:14.256220798 -0500
-+++ src/sage/rings/finite_rings/integer_mod.pyx	2017-11-08 08:29:38.845221740 -0500
-@@ -391,7 +391,7 @@ cdef class IntegerMod_abstract(FiniteRin
-         from integer_mod_ring import IntegerModRing
+--- src/sage/rings/finite_rings/integer_mod.pyx.orig	2018-05-05 16:21:25.000000000 -0600
+++ src/sage/rings/finite_rings/integer_mod.pyx	2018-05-18 09:41:48.412094505 -0600
+@@ -457,7 +457,7 @@ cdef class IntegerMod_abstract(FiniteRin
+         from .integer_mod_ring import IntegerModRing
         R = IntegerModRing(modulus)
         if (<Element>self)._parent._IntegerModRing_generic__order % R.order():
 -            raise ArithmeticError(f"reduction modulo {modulus!r} not defined")
-+            raise ArithmeticError("reduction modulo {modulus!r} not defined")
+            raise ArithmeticError("reduction modulo {modulus} not defined".format(modulus=repr(modulus)))
         return R(self)
 
     def is_nilpotent(self):
 diff -up src/sage/structure/parent.pyx.orig src/sage/structure/parent.pyx
--- src/sage/structure/parent.pyx.orig	2017-11-08 08:29:14.260220799 -0500
-+++ src/sage/structure/parent.pyx	2017-11-08 08:29:38.846221740 -0500
-@@ -714,7 +714,7 @@ cdef class Parent(sage.structure.categor
+--- src/sage/structure/parent.pyx.orig	2018-05-05 16:21:26.000000000 -0600
+++ src/sage/structure/parent.pyx	2018-05-18 09:42:38.685397989 -0600
+@@ -726,7 +726,7 @@ cdef class Parent(sage.structure.categor
     cdef int init_coerce(self, bint warn=True) except -1:
         if self._coerce_from_hash is None:
             if warn:
 -                raise AssertionError(f"unexpected call of init_coerce() for {type(self)}")
-+                raise AssertionError("unexpected call of init_coerce() for {type(self)}")
+                raise AssertionError("unexpected call of init_coerce() for {typ}".format(typ=type(self)))
             self._initial_coerce_list = []
             self._initial_action_list = []
             self._initial_convert_list = []
 diff -up src/sage/symbolic/ring.pyx.orig src/sage/symbolic/ring.pyx
--- src/sage/symbolic/ring.pyx.orig	2017-11-08 08:29:14.264220799 -0500
-+++ src/sage/symbolic/ring.pyx	2017-11-08 08:29:38.847221740 -0500
-@@ -376,7 +376,7 @@ cdef class SymbolicRing(CommutativeRing)
+--- src/sage/symbolic/ring.pyx.orig	2018-05-05 16:21:26.000000000 -0600
+++ src/sage/symbolic/ring.pyx	2018-05-18 09:43:07.395000229 -0600
+@@ -378,7 +378,7 @@ cdef class SymbolicRing(CommutativeRing)
             from sage.misc.all import prod
             return prod([SR(p)**e for p,e in x], SR(x.unit()))
         else:
 -            raise TypeError(f"unable to convert {x!r} to a symbolic expression")
-+            raise TypeError("unable to convert {x!r} to a symbolic expression")
+            raise TypeError("unable to convert {x} to a symbolic expression".format(x=repr(x)))
 
         return new_Expression_from_GEx(self, exp)
 
--- a/sagemath-ntl.patch
+++ b/sagemath-ntl.patch
@ -1,50 +0,0 @@
-diff -up src/sage/libs/polybori/decl.pxd.orig src/sage/libs/polybori/decl.pxd
--- src/sage/libs/polybori/decl.pxd.orig	2017-03-04 13:33:54.155492361 -0500
-+++ src/sage/libs/polybori/decl.pxd	2017-03-04 13:34:09.926492965 -0500
-@@ -291,10 +291,10 @@ cdef extern from "sage/libs/polybori/pb_
-         int (* size)()
-         PBPolyEntry (* get "operator[]")(int)
- 
-    ctypedef struct PBFglmStrategy "PBWrappedPtr<FGLMStrategy>":
-+    ctypedef struct PBFglmStrategy "WrappedPointer<FGLMStrategy>":
-         PBPolyVector (* main "operator->()->main")()
- 
-    PBFglmStrategy PBFglmStrategy_Constructor "PBWrappedPtr<FGLMStrategy>" \
-+    PBFglmStrategy PBFglmStrategy_Constructor "WrappedPointer<FGLMStrategy>" \
-         (PBRing from_ring, PBRing to_ring, PBPolyVector vec)
- 
-     cdef cppclass PBGBStrategy "GroebnerStrategy":
-diff -up src/sage/libs/polybori/pb_wrap.h.orig src/sage/libs/polybori/pb_wrap.h
--- src/sage/libs/polybori/pb_wrap.h.orig	2017-03-04 13:34:07.773492882 -0500
-+++ src/sage/libs/polybori/pb_wrap.h	2017-03-04 13:34:09.928492965 -0500
-@@ -177,23 +177,23 @@ PyObject* preallocated_to_PyString(const
- 
- 
- template <class Type>
-class PBWrappedPtr:
-+class WrappedPointer:
-   public boost::shared_ptr<Type> {
-    typedef PBWrappedPtr self;
-+    typedef WrappedPointer self;
-     typedef boost::shared_ptr<Type> base;
- 
-  public:
-    PBWrappedPtr(): base() {}
-    PBWrappedPtr(const self& rhs): base(rhs) {}
-+    WrappedPointer(): base() {}
-+    WrappedPointer(const self& rhs): base(rhs) {}
- 
-     template <class T1>
-    PBWrappedPtr(const T1& arg): base(new Type(arg)) {}
-+    WrappedPointer(const T1& arg): base(new Type(arg)) {}
- 
-     template <class T1, class T2>
-    PBWrappedPtr(const T1& arg1, const T2& arg2): base(new Type(arg1, arg2)) {}
-+    WrappedPointer(const T1& arg1, const T2& arg2): base(new Type(arg1, arg2)) {}
- 
-       template <class T1, class T2, class T3>
-        PBWrappedPtr(const T1& arg1, const T2& arg2, const T3& arg3):
-+        WrappedPointer(const T1& arg1, const T2& arg2, const T3& arg3):
-         base(new Type(arg1, arg2, arg3)) {}
- 
-     operator Type&() { return base::operator*();}
--- a/sagemath-qepcad.patch
+++ b/sagemath-qepcad.patch
@ -1,18 +1,16 @@
 diff -up src/sage/interfaces/qepcad.py.orig src/sage/interfaces/qepcad.py
--- src/sage/interfaces/qepcad.py.orig	2017-11-08 08:28:33.908219253 -0500
-+++ src/sage/interfaces/qepcad.py	2017-11-08 08:28:43.336219614 -0500
-@@ -530,8 +530,8 @@ TESTS:
+--- src/sage/interfaces/qepcad.py.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/interfaces/qepcad.py	2018-05-16 13:58:34.360913275 -0600
+@@ -530,7 +530,7 @@ TESTS:
 
 Check the qepcad configuration file::
 
-    sage: open('%s/default.qepcadrc'%SAGE_LOCAL).readlines()[-1]
-    'SINGULAR .../bin\n'
-+    sage: open('/usr/share/qepcad/default.qepcadrc').readlines()[-1]
-+    'SINGULAR /usr/bin\n'
+-    sage: with open(os.path.join(SAGE_LOCAL, 'default.qepcadrc')) as f:
+    sage: with open('/usr/share/qepcad/default.qepcadrc')) as f:
+     ....:     f.readlines()[-1]
+     'SINGULAR .../bin\n'
 
- Tests related to the not tested examples (nondeterministic order of atoms)::
- 
-@@ -607,7 +607,6 @@ from __future__ import print_function
+@@ -608,7 +608,6 @@ from __future__ import print_function
 from __future__ import absolute_import
 from six import string_types
 
@ -20,7 +18,7 @@ diff -up src/sage/interfaces/qepcad.py.orig src/sage/interfaces/qepcad.py
 import pexpect
 import re
 import sys
-@@ -620,6 +619,8 @@ from sage.docs.instancedoc import instan
+@@ -621,6 +620,8 @@ from sage.docs.instancedoc import instan
 from .expect import Expect, ExpectFunction, AsciiArtString
 
 
@ -29,7 +27,7 @@ diff -up src/sage/interfaces/qepcad.py.orig src/sage/interfaces/qepcad.py
 def _qepcad_atoms(formula):
     r"""
     Return the atoms of a qepcad quantifier-free formula, as a set of strings.
-@@ -649,17 +650,17 @@ def _qepcad_cmd(memcells=None):
+@@ -650,17 +651,17 @@ def _qepcad_cmd(memcells=None):
 
         sage: from sage.interfaces.qepcad import _qepcad_cmd
         sage: s = _qepcad_cmd()
@ -50,7 +48,7 @@ diff -up src/sage/interfaces/qepcad.py.orig src/sage/interfaces/qepcad.py
 
 _command_info_cache = None
 
-@@ -684,7 +685,7 @@ def _update_command_info():
+@@ -685,7 +686,7 @@ def _update_command_info():
 
     cache = {}
 
--- a/sagemath-readonly.patch
+++ b/sagemath-readonly.patch
@ -1,7 +1,6 @@
-diff -up src/sage/all.py.orig src/sage/all.py
--- src/sage/all.py.orig	2017-11-08 08:16:05.331190588 -0500
-+++ src/sage/all.py	2017-11-08 08:16:14.195190927 -0500
-@@ -295,11 +295,11 @@ def _write_started_file():
+--- src/sage/all.py.orig	2018-05-05 16:21:22.000000000 -0600
+++ src/sage/all.py	2018-05-16 13:25:28.300415250 -0600
+@@ -290,11 +290,11 @@ def _write_started_file():
 
     Check that the file exists when Sage is running::
 
--- 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	2017-11-08 06:16:18.175915367 -0500
-+++ src/module_list.py	2017-11-08 06:16:29.412915797 -0500
+--- src/module_list.py.orig	2018-05-16 12:35:55.223524926 -0600
+++ src/module_list.py	2018-05-16 13:13:20.467262594 -0600
@@ -3,7 +3,7 @@ from glob import glob
 from distutils.extension import Extension
 from sage.env import SAGE_LOCAL
@ -11,33 +11,33 @@ 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	2017-11-08 06:16:39.095916168 -0500
-+++ src/sage/misc/cython.py	2017-11-08 06:17:35.580918331 -0500
-@@ -497,7 +497,7 @@ extra_compile_args = %s
- 
- ext_modules = [Extension('%s', sources=['%s.%s', %s],
-                      libraries=%s,
-                     library_dirs=[SAGE_LOCAL + '/lib/'] + %s,
-+                     library_dirs=[os.path.realpath(SAGE_LOCAL + '/lib/')] + %s,
-                      extra_compile_args = extra_compile_args,
-                      language = '%s' )]
+--- src/sage/misc/cython.py.orig	2018-05-16 13:13:20.468262581 -0600
+++ src/sage/misc/cython.py	2018-05-16 13:16:29.207708998 -0600
+@@ -601,7 +601,7 @@ def cython(filename, verbose=0, compile_
+     ext = Extension(name,
+                     sources=[pyxfile] + extra_sources,
+                     libraries=libs,
+-                    library_dirs=[os.path.join(SAGE_LOCAL, "lib")] + libdirs,
+                    library_dirs=[os.path.realpath(os.path.join(SAGE_LOCAL, "lib"))] + libdirs,
+                     extra_compile_args=extra_args,
+                     language=language)
 
 diff -up src/setup.py.orig src/setup.py
--- src/setup.py.orig	2017-11-08 06:17:50.231918892 -0500
-+++ src/setup.py	2017-11-08 06:18:48.924921139 -0500
-@@ -422,9 +422,8 @@ class sage_build_cython(Command):
+--- src/setup.py.orig	2018-05-05 16:21:27.000000000 -0600
+++ src/setup.py	2018-05-16 13:17:40.774740719 -0600
+@@ -370,9 +370,8 @@ class sage_build_cython(Command):
             # Debugging
             gdb_debug=self.debug,
-             output_dir=self.build_dir,
+             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 which is
+            # Enable Cython caching (the cache is stored in ~/.cycache)
 +            cache=True,
             )
 
-         log.info("Finished Cythonizing, time: %.2f seconds." % (time.time() - t))
-@@ -850,9 +849,6 @@ class sage_install(install):
+         # Filter out extensions with skip_build=True
+@@ -881,9 +880,6 @@ 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):
         """
-@@ -866,40 +862,6 @@ class sage_install(install):
+@@ -897,40 +893,6 @@ class sage_install(install):
         from sage.repl.ipython_kernel.install import SageKernelSpec
         SageKernelSpec.update()
 
--- a/sagemath-sagedoc.patch
+++ b/sagemath-sagedoc.patch
@ -1,19 +1,7 @@
-diff -up src/doc/common/conf.py.orig src/doc/common/conf.py
--- src/doc/common/conf.py.orig	2017-11-08 08:08:07.554172292 -0500
-+++ src/doc/common/conf.py	2017-11-08 08:08:33.656173291 -0500
-@@ -220,7 +220,7 @@ if (os.environ.get('SAGE_DOC_MATHJAX', '
-     html_theme_options['mathjax_macros'] = sage_mathjax_macros()
- 
-     from pkg_resources import Requirement, working_set
-    sagenb_path = working_set.find(Requirement.parse('sagenb')).location
-+    sagenb_path = SAGE_SRC
-     mathjax_relative = os.path.join('sagenb','data','mathjax')
- 
-     # It would be really nice if sphinx would copy the entire mathjax directory,
 diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
--- src/sage/doctest/control.py.orig	2017-11-08 08:08:44.186173695 -0500
-+++ src/sage/doctest/control.py	2017-11-08 08:09:24.904175254 -0500
-@@ -96,7 +96,6 @@ class DocTestDefaults(SageObject):
+--- src/sage/doctest/control.py.orig	2018-05-05 16:21:23.000000000 -0600
+++ src/sage/doctest/control.py	2018-05-16 13:20:01.420837824 -0600
+@@ -102,7 +102,6 @@ class DocTestDefaults(SageObject):
         self.valgrind = False
         self.massif = False
         self.cachegrind = False
@ -21,7 +9,7 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
         self.failed = False
         self.new = False
         self.show_skipped = False
-@@ -285,7 +284,7 @@ class DocTestController(SageObject):
+@@ -292,7 +291,7 @@ class DocTestController(SageObject):
             if options.gdb or options.debug:
                 # Interactive debuggers: "infinite" timeout
                 options.timeout = 0
@ -30,7 +18,7 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
                 # Non-interactive debuggers: 48 hours
                 options.timeout = int(os.getenv('SAGE_TIMEOUT_VALGRIND', 48 * 60 * 60))
             elif options.long:
-@@ -1049,13 +1048,8 @@ class DocTestController(SageObject):
+@@ -1071,13 +1070,8 @@ class DocTestController(SageObject):
             elif opt.cachegrind:
                 toolname = "cachegrind"
                 flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "")
@ -44,7 +32,7 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
             if "%s" in flags:
                 flags %= toolname + ".%p" # replace %s with toolname
         cmd += flags + sage_cmd
-@@ -1115,10 +1109,10 @@ class DocTestController(SageObject):
+@@ -1137,10 +1131,10 @@ class DocTestController(SageObject):
             0
         """
         opt = self.options
@ -58,9 +46,9 @@ 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	2017-11-08 08:09:36.306175691 -0500
-+++ src/sage/interfaces/singular.py	2017-11-08 08:09:57.144176489 -0500
-@@ -2287,7 +2287,7 @@ def generate_docstring_dictionary():
+--- src/sage/interfaces/singular.py.orig	2018-05-05 16:21:24.000000000 -0600
+++ src/sage/interfaces/singular.py	2018-05-16 13:20:01.421837810 -0600
+@@ -2258,7 +2258,7 @@ def generate_docstring_dictionary():
     nodes.clear()
     node_names.clear()
 
@ -70,8 +58,8 @@ diff -up src/sage/interfaces/singular.py.orig src/sage/interfaces/singular.py
     new_node = re.compile("File: singular\.hlp,  Node: ([^,]*),.*")
     new_lookup = re.compile("\* ([^:]*):*([^.]*)\..*")
 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	2017-11-08 08:10:07.010176866 -0500
-+++ src/sage_setup/docbuild/ext/multidocs.py	2017-11-08 08:10:30.319177759 -0500
+--- src/sage_setup/docbuild/ext/multidocs.py.orig	2018-05-05 16:21:26.000000000 -0600
+++ src/sage_setup/docbuild/ext/multidocs.py	2018-05-16 13:20:01.421837810 -0600
@@ -82,8 +82,11 @@ def merge_environment(app, env):
             for ind in newalldoc:
                 # treat subdocument source as orphaned file and don't complain
@ -85,11 +73,11 @@ diff -up src/sage_setup/docbuild/ext/multidocs.py.orig src/sage_setup/docbuild/e
 +                    env.metadata[ind] = {'orphan'}
             # merge the citations
             newcite = {}
-             for ind, (path, tag) in six.iteritems(docenv.domaindata["std"]["citations"]):
+             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	2017-11-08 08:10:41.962178205 -0500
-+++ src/sage_setup/docbuild/__init__.py	2017-11-08 08:11:16.448179525 -0500
-@@ -248,13 +248,14 @@ if NUM_THREADS > 1:
+--- src/sage_setup/docbuild/__init__.py.orig	2018-05-05 16:21:26.000000000 -0600
+++ src/sage_setup/docbuild/__init__.py	2018-05-16 13:20:01.422837797 -0600
+@@ -242,13 +242,14 @@ if NUM_THREADS > 1:
         # map_async handles KeyboardInterrupt correctly. Plain map and
         # apply_async does not, so don't use it.
         x = pool.map_async(target, args, 1)
--- a/sagemath-scripts.patch
+++ b/sagemath-scripts.patch
@ -1,24 +1,7 @@
 diff -up src/bin/sage.orig src/bin/sage
--- src/bin/sage.orig	2017-11-08 06:04:08.687887432 -0500
-+++ src/bin/sage	2017-11-08 06:10:52.452902893 -0500
-@@ -1,5 +1,16 @@
- #!/usr/bin/env bash
- 
-+# Display the Sage startup banner, used in src/bin/sage
-+sage_banner() {
-+    if [ "$SAGE_BANNER" = "bare" ]; then
-+        cat "$SAGE_ROOT/VERSION.txt"
-+    elif [ "$SAGE_BANNER" != "no" ]; then
-+        # This file sage-banner is not yet available during the build
-+        # of Sage, so we ignore errors from cat.
-+        cat "$SAGE_LOCAL/bin/sage-banner" 2>/dev/null
-+    fi
-+}
-+
- help_banner() {
-     sage_banner | grep -v 'Type'
-     echo
-@@ -13,13 +24,10 @@ usage() {
+--- src/bin/sage.orig	2018-05-05 16:21:22.000000000 -0600
+++ src/bin/sage	2018-05-16 12:29:16.699989835 -0600
+@@ -13,13 +13,10 @@ usage() {
     echo "  file.[sage|py|spyx] -- run given .sage, .py or .spyx file"
     echo "  -advanced           -- list all command line options"
     echo "  -c <cmd>            -- Evaluates cmd as sage code"
@ -32,7 +15,7 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "  -inotebook [...]    -- start the *insecure* Sage notebook (deprecated)"
     echo "  -maxima [...]       -- run Sage's Maxima with given arguments"
     echo "  -mwrank [...]       -- run Sage's mwrank with given arguments"
-@@ -27,7 +35,6 @@ usage() {
+@@ -27,7 +24,6 @@ usage() {
     echo "                         'default', 'sagenb', 'jupyter', and 'export')"
     echo "                         Current default is 'export' from sagenb to jupyter"
     echo "  -n, --notebook      -- shortcut for --notebook=default"
@ -40,7 +23,7 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "  -python [...]       -- run the Python 2 interpreter"
     echo "  -python3 [...]      -- run the Python 3 interpreter"
     echo "  -R [...]            -- run Sage's R with given arguments"
-@@ -44,10 +51,6 @@ usage() {
+@@ -44,10 +40,6 @@ usage() {
     echo "                           --optional - controls which optional tests are run"
     echo "                           --sagenb - test all sagenb files"
     echo "                           --help - show all testing options"
@ -51,7 +34,7 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "  -v, -version        -- display Sage version information"
     exit 0
 }
-@@ -66,11 +69,8 @@ usage_advanced() {
+@@ -66,11 +58,8 @@ usage_advanced() {
     echo "  -preparse <file.sage> -- preparse file.sage and produce corresponding file.sage.py"
     echo "  -q                  -- quiet; start with no banner"
     echo "  -root               -- print the Sage root directory"
@ -63,7 +46,7 @@ diff -up src/bin/sage.orig src/bin/sage
 
     echo
     ####  1.......................26..................................................78
-@@ -82,8 +82,6 @@ usage_advanced() {
+@@ -82,8 +71,6 @@ usage_advanced() {
     echo "                         See the output of sage --notebook --help"
     echo "                         for more details and examples of how to pass"
     echo "                         optional arguments"
@ -72,10 +55,10 @@ 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"
-@@ -102,18 +100,11 @@ usage_advanced() {
-     echo "  -gp [...]           -- run Sage's PARI/GP calculator with given arguments"
+@@ -103,18 +90,11 @@ usage_advanced() {
     echo "  -ipython [...]      -- run Sage's IPython using the default environment (not"
     echo "                         Sage), passing additional options to IPython"
+     echo "  -ipython3 [...]     -- same as above, but using Python 3"
 -    echo "  -kash [...]         -- run Sage's Kash with given arguments"
 -    command -v kash &>/dev/null || \
 -    echo "                         (not installed currently, run sage -i kash)"
@ -91,7 +74,7 @@ diff -up src/bin/sage.orig src/bin/sage
     echo "  -python [...]       -- run the Python interpreter"
     echo "  -R [...]            -- run Sage's R with given arguments"
     echo "  -scons [...]        -- run Sage's scons"
-@@ -125,55 +116,7 @@ usage_advanced() {
+@@ -126,55 +106,7 @@ usage_advanced() {
     echo
     ####  1.......................26..................................................78
     ####  |.....................--.|...................................................|
@ -148,7 +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"
-@@ -203,7 +146,6 @@ usage_advanced() {
+@@ -205,7 +137,6 @@ 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"
@ -156,7 +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"
-@@ -225,16 +167,6 @@ usage_advanced() {
+@@ -227,16 +158,6 @@ usage_advanced() {
     echo
     ####  1.......................26..................................................78
     ####  |.....................--.|...................................................|
@ -173,7 +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"
-@@ -248,9 +180,6 @@ usage_advanced() {
+@@ -250,9 +171,6 @@ 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"
@ -183,7 +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'."
-@@ -259,121 +188,6 @@ usage_advanced() {
+@@ -261,128 +179,6 @@ usage_advanced() {
 }
 
 
@ -251,40 +234,47 @@ diff -up src/bin/sage.orig src/bin/sage
 -    fi
 -
 -    set -e
-
 -    cd "$SAGE_ROOT"
 -
-    # First of all, make sure that the toolchain is up-to-date
-    # (which is a dependency of every package)
-    ./sage --location
-    $MAKE all-toolchain
-    echo
-
+-    # Parse options
+-    PACKAGES=""         # Packages to install
 -    INSTALL_OPTIONS=""  # Options to sage-spkg
-    for PKG in "$@"
-    do
-        case "$PKG" in
+-    for OPT in "$@"; do
+-        case "$OPT" in
 -            -info|--info)
-                echo >&2 "Error: 'sage -i $PKG <package>' is no longer supported, use 'sage --info <package>' instead."
+-                echo >&2 "Error: 'sage -i $OPT <package>' is no longer supported, use 'sage --info <package>' instead."
 -                exit 2;;
 -            -f) FORCE_INSTALL=yes;;
-            -*) INSTALL_OPTIONS="$INSTALL_OPTIONS $PKG";;
-            *)
-                # First check that $PKG is actually a Makefile target
-                if ! grep "^$PKG: " build/make/Makefile >/dev/null; then
-                    echo >&2 "Error: package '$PKG' not found"
-                    echo >&2 "Assuming it is an old-style package... (this is deprecated: use -p instead of -i to install old-style packages)"
-                    echo >&2
-                    sleep 5
-                    ./sage -p $INSTALL_OPTIONS "$PKG"
-                else
-                    if [ x$FORCE_INSTALL = xyes ]; then
-                        $MAKE "$PKG-clean"
-                    fi
-                    $MAKE SAGE_SPKG="sage-spkg $INSTALL_OPTIONS" "$PKG"
-                fi;;
+-            -*) INSTALL_OPTIONS="$INSTALL_OPTIONS $OPT";;
+-            *) PACKAGES="$PACKAGES $OPT";;
 -        esac
 -    done
+-
+-    # First, uninstall the packages if -f was given
+-    if [ "$FORCE_INSTALL" = yes ]; then
+-        for PKG in $PACKAGES; do
+-            $MAKE "$PKG-clean" || true  # Ignore errors
+-        done
+-    fi
+-
+-    # Make sure that the toolchain is up-to-date
+-    # (which is a dependency of every package)
+-    $MAKE all-toolchain
+-
+-    ALL_TARGETS="$($MAKE list 2>/dev/null)"
+-
+-    # Now install the packages
+-    for PKG in $PACKAGES; do
+-        echo
+-        # First check that $PKG is actually a Makefile target
+-        # See https://trac.sagemath.org/ticket/25078
+-        if ! echo "$ALL_TARGETS" | grep "^${PKG}$" >/dev/null; then
+-            echo >&2 "Error: package '$PKG' not found"
+-            echo >&2 "Note: if it is an old-style package, use -p instead of -i to install it"
+-            exit 1
+-        fi
+-        $MAKE SAGE_SPKG="sage-spkg $INSTALL_OPTIONS" "$PKG"
+-    done
 -    exit 0
 -fi
 -
@ -305,11 +295,8 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ $# -gt 0 ]; then
   if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then
      usage
-@@ -383,25 +197,12 @@ if [ $# -gt 0 ]; then
-   fi
- fi
+@@ -394,20 +190,6 @@ 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).
@ -324,15 +311,12 @@ diff -up src/bin/sage.orig src/bin/sage
 -        exit 1
 -    fi
 -
-     # Display the startup banner (unless SAGE_BANNER is explicitly "no")
-     sage_banner
- 
 -    maybe_sage_location
 -
     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
-@@ -412,20 +213,6 @@ sage_setup() {
+@@ -418,20 +200,6 @@ sage_setup() {
 }
 
 
@ -353,7 +337,7 @@ diff -up src/bin/sage.orig src/bin/sage
 # Start an interactive Sage session, this function never returns.
 interactive_sage() {
     sage_setup
-@@ -530,16 +317,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
+@@ -536,16 +304,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
     exec ecl "$@"
 fi
 
@ -370,7 +354,7 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
     shift
     exec maxima "$@"
-@@ -565,11 +342,6 @@ if [ "$1" = '-pip' -o "$1" = '--pip' ];
+@@ -571,11 +329,6 @@ if [ "$1" = '-pip' -o "$1" = '--pip' ];
     exec pip "$@"
 fi
 
@ -382,8 +366,8 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ "$1" = '-python' -o "$1" = '--python' ]; then
     shift
     exec python "$@"
-@@ -595,16 +367,6 @@ if [ "$1" = '-ipython' -o "$1" = '--ipyt
-     exec ipython "$@"
+@@ -606,16 +359,6 @@ if [ "$1" = '-ipython3' -o "$1" = '--ipy
+     exec ipython3 "$@"
 fi
 
 -if [ "$1" = '-git' -o "$1" = '--git' ]; then
@ -399,7 +383,7 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
     # AUTHORS:
     # - Carl Witty and William Stein: initial version
-@@ -724,20 +486,6 @@ EOF
+@@ -735,20 +478,6 @@ EOF
 fi
 
 #####################################################################
@ -420,7 +404,7 @@ diff -up src/bin/sage.orig src/bin/sage
 # File conversion
 #####################################################################
 
-@@ -760,11 +508,6 @@ fi
+@@ -771,11 +500,6 @@ fi
 # Run Sage's versions of the standard Algebra/Geometry etc. software
 #####################################################################
 
@ -432,7 +416,7 @@ diff -up src/bin/sage.orig src/bin/sage
 if [[ "$1" =~ ^--notebook=.* || "$1" =~ ^-n=.* || "$1" =~ ^-notebook=.* ]] ; then
     sage-cleaner &>/dev/null &
     exec sage-notebook "$@"
-@@ -775,13 +518,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
+@@ -786,13 +510,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
     exec sage-notebook "$@"
 fi
 
@ -446,8 +430,8 @@ diff -up src/bin/sage.orig src/bin/sage
 if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
     shift
     sage-cleaner &>/dev/null &
-@@ -800,34 +536,15 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
-    exit 0
+@@ -811,34 +528,15 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
+     exit 0
 fi
 
 -if [ "$1" = '-b' ]; then
@ -461,8 +445,8 @@ diff -up src/bin/sage.orig src/bin/sage
 -fi
 -
 if [ "$1" = '-r' ]; then
-    shift
-    interactive_sage
+     shift
+     interactive_sage
 fi
 
 -if [ "$1" = '-ba' -o "$1" = '-ba-force' -o "$1" = '--ba-force' ]; then
@ -476,14 +460,14 @@ diff -up src/bin/sage.orig src/bin/sage
 -        build_sage
 -    fi
 +if [ "$1" = '-t' -o "$1" = '-tp' ]; then
-     SAGE_BANNER=no sage_setup
+     sage_setup
     export PYTHONIOENCODING="utf-8"  # Fix encoding for doctests
 -    if [ "$1" = '-tp' -o "$1" = '-btp' ]; then
 +    if [ "$1" = '-tp' ]; then
         shift
         exec sage-runtests -p "$@"
     else
-@@ -836,10 +553,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
+@@ -847,10 +545,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
     fi
 fi
 
@ -493,9 +477,9 @@ diff -up src/bin/sage.orig src/bin/sage
 -    fi
 +if [ "$1" = '-tnew' ]; then
     shift
-     SAGE_BANNER=no sage_setup
+     sage_setup
     export PYTHONIOENCODING="utf-8"  # Fix encoding for doctests
-@@ -860,119 +574,6 @@ if [ "$1" = '-c' ]; then
+@@ -871,119 +566,6 @@ if [ "$1" = '-c' ]; then
     exec sage-eval "$@"
 fi
 
@ -609,13 +593,13 @@ diff -up src/bin/sage.orig src/bin/sage
 -
 -if [ "$1" = "-docbuild" -o "$1" = "--docbuild" ]; then
 -    shift
-    exec python -m "sage_setup.docbuild" "$@"
+-    exec sage-python23 -m "sage_setup.docbuild" "$@"
 -fi
 -
 if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
     shift
     sage_setup
-@@ -1023,12 +624,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
+@@ -1033,12 +615,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
     exec sage-callgrind "$@"
 fi
 
@ -628,10 +612,9 @@ 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	2017-11-08 06:11:02.679903285 -0500
-+++ src/bin/sage-runtests	2017-11-08 06:11:18.876903905 -0500
-@@ -64,10 +64,6 @@ if __name__ == "__main__":
+--- src/bin/sage-runtests.orig	2018-05-05 16:21:22.000000000 -0600
+++ src/bin/sage-runtests	2018-05-16 12:16:10.707645467 -0600
+@@ -67,10 +67,6 @@ 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"))
@ -642,9 +625,8 @@ 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	2017-11-08 06:11:27.655904241 -0500
-+++ src/bin/sage-valgrind	2017-11-08 06:11:40.964904751 -0500
+--- src/bin/sage-valgrind.orig	2018-05-05 16:21:22.000000000 -0600
+++ src/bin/sage-valgrind	2018-05-16 12:16:10.708645454 -0600
@@ -1,16 +1,6 @@
 #!/usr/bin/env bash
 
--- a/sagemath-sympy.patch
+++ b/sagemath-sympy.patch
@ -1,7 +1,7 @@
 diff -up src/sage/env.py.orig src/sage/env.py
--- src/sage/env.py.orig	2017-11-08 08:27:50.523217592 -0500
-+++ src/sage/env.py	2017-11-08 08:27:58.147217884 -0500
-@@ -90,7 +90,7 @@ _add_variable_or_fallback('HOSTNAME',
+--- src/sage/env.py.orig	2018-05-05 16:21:23.000000000 -0600
+++ src/sage/env.py	2018-05-16 13:42:40.591238911 -0600
+@@ -117,7 +117,7 @@ _add_variable_or_fallback('HOSTNAME',
 _add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid())
 
 # bunch of sage directories and files
@ -10,7 +10,7 @@ diff -up src/sage/env.py.orig src/sage/env.py
 _add_variable_or_fallback('SAGE_LOCAL',      None)
 _add_variable_or_fallback('SAGE_ETC',        opj('$SAGE_LOCAL', 'etc'))
 _add_variable_or_fallback('SAGE_INC',        opj('$SAGE_LOCAL', 'include'))
-@@ -116,7 +116,7 @@ _add_variable_or_fallback('SAGE_PKGS', o
+@@ -141,7 +141,7 @@ _add_variable_or_fallback('SAGE_PKGS', o
 _add_variable_or_fallback('SAGE_EXTCODE',    opj('$SAGE_SHARE', 'sage', 'ext'))
 _add_variable_or_fallback('SAGE_LOGS',       opj('$SAGE_ROOT', 'logs', 'pkgs'))
 _add_variable_or_fallback('SAGE_SPKG_INST',  opj('$SAGE_LOCAL', 'var', 'lib', 'sage', 'installed'))
--- a/sagemath.spec
+++ b/sagemath.spec
--- a/2
+++ b/2
@ -1 +1 @@
-SHA512 (sage-8.0.tar.gz) = f0a7aaf9fc157b031ceba2d298d74a56bb38f6be5ae4350f91058a24360273f2599c1d50dfe8941e7c462d0a1bf436090da859256fc8e687097e6c419345c493
+SHA512 (sage-8.2.tar.gz) = 32afa401d0c0a825e9507a445de9a5abb19b3f2444c70ae0e5d7fea0fe319f6a43a94e5eee032fd85c21b87487a42d0c70177766dfa6ea1ea42d3a22e1395663
--- a/testjava.sh
+++ b/testjava.sh