From 925e91dadef3485c25b240eccef23afd421459ef Mon Sep 17 00:00:00 2001
From: Jerry James <loganjerry@gmail.com>
Date: Sun, 3 Jun 2018 07:13:30 -0600
Subject: [PATCH] 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.
---
.gitignore | 1 +
makecmds.sty | 95 -------
sagemath-4ti2.patch | 8 +-
sagemath-arb.patch | 104 ++++----
sagemath-atlas.patch | 23 +-
sagemath-cbc.patch | 10 +-
sagemath-extensions.patch | 113 ++++----
sagemath-fes.patch | 12 +-
sagemath-gap-hap.patch | 6 +-
sagemath-gcc6.patch | 12 -
sagemath-includes.patch | 137 ++++++----
sagemath-jmol.patch | 14 +-
sagemath-lcalc.patch | 15 +-
sagemath-lrslib.patch | 17 +-
sagemath-maxima.patch | 16 +-
sagemath-mpfr.patch | 47 ++++
sagemath-nauty.patch | 6 +-
sagemath-nofstring.patch | 40 +--
sagemath-ntl.patch | 50 ----
sagemath-qepcad.patch | 24 +-
sagemath-readonly.patch | 7 +-
sagemath-rpmbuild.patch | 40 +--
sagemath-sagedoc.patch | 42 ++-
sagemath-scripts.patch | 160 +++++-------
sagemath-sympy.patch | 8 +-
sagemath.spec | 529 ++++++++++++++++++++++----------------
sources | 2 +-
testjava.sh | 0
28 files changed, 743 insertions(+), 795 deletions(-)
delete mode 100644 makecmds.sty
delete mode 100644 sagemath-gcc6.patch
create mode 100644 sagemath-mpfr.patch
delete mode 100644 sagemath-ntl.patch
mode change 100755 => 100644 testjava.sh
diff --git a/.gitignore b/.gitignore
index 2b6e120..139bf42 100644
--- 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
diff --git a/makecmds.sty b/makecmds.sty
deleted file mode 100644
index 7805257..0000000
--- a/makecmds.sty
+++ /dev/null
@@ -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'.
diff --git a/sagemath-4ti2.patch b/sagemath-4ti2.patch
index 1c256e6..7caaeff 100644
--- 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:
diff --git a/sagemath-arb.patch b/sagemath-arb.patch
index 7649f4a..7ad3797 100644
--- 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":
diff --git a/sagemath-atlas.patch b/sagemath-atlas.patch
index 0813db7..211dba2 100644
--- 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
diff --git a/sagemath-cbc.patch b/sagemath-cbc.patch
index 27d5dd7..709f238 100644
--- 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()
diff --git a/sagemath-extensions.patch b/sagemath-extensions.patch
index 1610fd8..6758840 100644
--- 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),
+
+ ################################
+ ##
diff --git a/sagemath-fes.patch b/sagemath-fes.patch
index 2e02f9f..7fbb79d 100644
--- 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"],
diff --git a/sagemath-gap-hap.patch b/sagemath-gap-hap.patch
index 9eeed4f..08816e6 100644
--- 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)):
diff --git a/sagemath-gcc6.patch b/sagemath-gcc6.patch
deleted file mode 100644
index 3258b5b..0000000
--- a/sagemath-gcc6.patch
+++ /dev/null
@@ -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'],
diff --git a/sagemath-includes.patch b/sagemath-includes.patch
index 45ee224..ea0cc17 100644
--- 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@@'])
diff --git a/sagemath-jmol.patch b/sagemath-jmol.patch
index a15281a..41efb18 100644
--- 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)
diff --git a/sagemath-lcalc.patch b/sagemath-lcalc.patch
index 337c952..fb52eec 100644
--- 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"
diff --git a/sagemath-lrslib.patch b/sagemath-lrslib.patch
index b33f938..8212b43 100644
--- 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
diff --git a/sagemath-maxima.patch b/sagemath-maxima.patch
index 105e540..94e9d9c 100644
--- 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).
diff --git a/sagemath-mpfr.patch b/sagemath-mpfr.patch
new file mode 100644
index 0000000..0e54f02
--- /dev/null
+++ 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
+
diff --git a/sagemath-nauty.patch b/sagemath-nauty.patch
index bdb77d6..5173c5b 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 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
diff --git a/sagemath-nofstring.patch b/sagemath-nofstring.patch
index 8e24b59..9008492 100644
--- 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)
diff --git a/sagemath-ntl.patch b/sagemath-ntl.patch
deleted file mode 100644
index cc8e36f..0000000
--- a/sagemath-ntl.patch
+++ /dev/null
@@ -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*();}
diff --git a/sagemath-qepcad.patch b/sagemath-qepcad.patch
index 0c71de0..527415b 100644
--- 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 = {}
diff --git a/sagemath-readonly.patch b/sagemath-readonly.patch
index a0a2473..0c959b9 100644
--- 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::
diff --git a/sagemath-rpmbuild.patch b/sagemath-rpmbuild.patch
index c8faa8a..b8bd336 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 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()
diff --git a/sagemath-sagedoc.patch b/sagemath-sagedoc.patch
index 13ec5d7..21da4ff 100644
--- 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)
diff --git a/sagemath-scripts.patch b/sagemath-scripts.patch
index 051e8fc..d91d51f 100644
--- 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
diff --git a/sagemath-sympy.patch b/sagemath-sympy.patch
index 70d562a..8f561cc 100644
--- 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'))
diff --git a/sagemath.spec b/sagemath.spec
index ad448b7..c2af9ca 100644
--- a/sagemath.spec
+++ b/sagemath.spec
@@ -32,24 +32,26 @@
%global SAGE_TIMEOUT 60
%global SAGE_TIMEOUT_LONG 180
+%global combinatorial_designs_pkg combinatorial_designs-20140630
%global conway_polynomials_pkg conway_polynomials-0.5
%global elliptic_curves_pkg elliptic_curves-0.8
%global flintqs_pkg flintqs-1.0
%global graphs_pkg graphs-20161026
%if %{with bundled_ipython}
-%global ipython_pkg ipython-5.1.0
+%global ipython_pkg ipython-5.5.0
%endif
%if %{with bundled_ipywidgets}
-%global ipywidgets_pkg ipywidgets-6.0.0
+%global ipywidgets_pkg ipywidgets-7.1.1
%endif
%if %{with bundled_pexpect}
%global pexpect_pkg pexpect-4.1.0
%endif
-%global polytopes_db_pkg polytopes_db-20120220
+%global polytopes_db_pkg polytopes_db-20170220
%global rubiks_pkg rubiks-20070912
%global sagenb_pkg sagenb-1.0.1
+%global sagenb_export_pkg sagenb_export-3.2
%global sagetex_pkg sagetex-3.0
-%global Sphinx_pkg Sphinx-1.5.3
+%global Sphinx_pkg Sphinx-1.6.3
%global SAGE_ROOT %{_libdir}/sagemath
%global SAGE_LOCAL %{SAGE_ROOT}/local
@@ -61,18 +63,16 @@
%global SAGE_SPKG_INST %{SAGE_LOCAL}/var/lib/sage/installed
Name: sagemath
-Group: Applications/Engineering
Summary: A free open-source mathematics software system
-Version: 8.0
-Release: 3%{?dist}
+Version: 8.2
+Release: 1%{?dist}
# The file ${SAGE_ROOT}/COPYING.txt is the upstream license breakdown file
# Additionally, every $files section has a comment with the license name
# before files with that license
License: ASL 2.0 and BSD and GPL+ and GPLv2+ and LGPLv2+ and MIT and Public Domain
URL: http://www.sagemath.org
-Source0: http://boxen.math.washington.edu/home/%{name}/sage-mirror/src/sage-%{version}.tar.gz
+Source0: http://files.sagemath.org/src/sage-%{version}.tar.gz
Source1: gprc.expect
-Source2: makecmds.sty
# Follow maxima's ExclusiveArch
ExclusiveArch: aarch64 %{arm} %{ix86} x86_64 ppc sparcv9
@@ -127,11 +127,11 @@ Patch12: %{name}-lrslib.patch
# http://pallini.di.uniroma1.it/
Patch13: %{name}-nauty.patch
-# gap hap package not (yet) available
-# http://www-gap.mcs.st-and.ac.uk/Packages/hap.html
+# gap hap package is a requires
Patch14: %{name}-gap-hap.patch
# correct path to Lfunction include
+# update c++ standard to fix FTBFS
Patch15: %{name}-lcalc.patch
# avoid assertion in coin backend
@@ -149,8 +149,8 @@ Patch19: %{name}-fes.patch
# https://bugzilla.redhat.com/show_bug.cgi?id=974769
Patch20: %{name}-sympy.patch
-# Fix a name clash with NTL
-Patch21: %{name}-ntl.patch
+# Adapt to MPFR 3.x. Remove this once Fedora updates to MPFR 4.x.
+Patch21: %{name}-mpfr.patch
# Correct unable to start QEPCAD within sage
# https://bugzilla.redhat.com/show_bug.cgi?id=1243590
@@ -160,32 +160,23 @@ Patch22: %{name}-qepcad.patch
Patch23: %{name}-arb.patch
# No support for f" notation
-Patch25: %{name}-nofstring.patch
+Patch24: %{name}-nofstring.patch
# Add missing include paths
-Patch26: %{name}-includes.patch
-
-# https://trac.sagemath.org/ticket/20926
-# #error This file requires compiler and library support for the ISO C++ \
-# 2011 standard. This support must be enabled with the -std=c++11 \
-# or -std=gnu++11 compiler options.
-Patch27: %{name}-gcc6.patch
+Patch25: %{name}-includes.patch
# Use atlas blas
-Patch28: %{name}-atlas.patch
+Patch26: %{name}-atlas.patch
BuildRequires: 4ti2
-BuildRequires: apache-commons-cli
BuildRequires: arb-devel
BuildRequires: atlas-devel
+BuildRequires: boost-devel
BuildRequires: brial-devel
BuildRequires: cddlib-tools
BuildRequires: cliquer-devel
BuildRequires: coin-or-Cbc-devel
-BuildRequires: cryptominisat-devel
-BuildRequires: Cython >= 0.24.1
BuildRequires: desktop-file-utils
-BuildRequires: dos2unix
BuildRequires: dvipng
BuildRequires: ecl
BuildRequires: eclib-devel
@@ -194,25 +185,25 @@ BuildRequires: factory-devel
BuildRequires: fes-devel
%endif
BuildRequires: flint-devel
-BuildRequires: gmp-ecm-devel
BuildRequires: gap
BuildRequires: GAPDoc
BuildRequires: gap-libs
BuildRequires: gap-pkg-atlasrep
-BuildRequires: gap-pkg-ctbllib
+BuildRequires: gap-pkg-crime
BuildRequires: gap-pkg-design
BuildRequires: gap-pkg-guava
-BuildRequires: gap-pkg-hap
+BuildRequires: gap-pkg-hapcryst
BuildRequires: gap-pkg-sonata
-BuildRequires: gap-pkg-tomlib
+BuildRequires: gap-pkg-toric
BuildRequires: gc-devel
BuildRequires: gcc-c++
BuildRequires: gd-devel
BuildRequires: genus2reduction
BuildRequires: gfan
+BuildRequires: giac-devel
BuildRequires: glpk-devel
BuildRequires: gmp-ecm
-BuildRequires: gnutls-devel
+BuildRequires: gmp-ecm-devel
BuildRequires: gsl-devel
BuildRequires: ImageMagick
BuildRequires: iml-devel
@@ -222,7 +213,7 @@ BuildRequires: jsmath-fonts
BuildRequires: jsmol
BuildRequires: L-function-devel
BuildRequires: lapack-devel
-BuildRequires: libfac-devel
+BuildRequires: latte-integrale
BuildRequires: libfplll-devel
BuildRequires: libgap-devel
BuildRequires: libmpc-devel
@@ -236,49 +227,72 @@ BuildRequires: maxima-runtime-ecl
BuildRequires: mpfi-devel
BuildRequires: nauty
BuildRequires: ntl-devel
-BuildRequires: numpy
+BuildRequires: openssl
BuildRequires: palp
BuildRequires: pari-devel
+BuildRequires: pari-galdata
BuildRequires: pari-gp
+BuildRequires: pari-seadata
BuildRequires: planarity-devel
BuildRequires: ppl-devel
BuildRequires: pynac-devel
BuildRequires: python2-devel
-BuildRequires: python-backports-shutil_get_terminal_size
-BuildRequires: python-brial
-BuildRequires: python-cypari2-devel
-BuildRequires: python-cysignals-devel
-BuildRequires: python-crypto
-BuildRequires: python-cvxopt
-BuildRequires: python-docutils
-BuildRequires: python-flask-autoindex
-BuildRequires: python-flask-babel
-BuildRequires: python-flask-openid
-BuildRequires: python-flask-silk
+%if %{with bundled_ipython}
+BuildRequires: python2-backports-shutil_get_terminal_size
+%endif
+BuildRequires: python2-brial
+%if %{with sphinx_hack}
+BuildRequires: python2-configparser
+%endif
+BuildRequires: python2-cypari2-devel
+BuildRequires: python2-cysignals-devel
+BuildRequires: python2-Cython
+BuildRequires: python2-crypto
+BuildRequires: python2-cryptominisat
+BuildRequires: python2-cvxopt
+BuildRequires: python2-docutils
+BuildRequires: python2-flask-autoindex
+BuildRequires: python2-flask-babel
+BuildRequires: python2-flask-openid
+BuildRequires: python2-flask-silk
+BuildRequires: python2-fpylll
+BuildRequires: python2-future
+BuildRequires: python2-gmpy2
+%if %{with sphinx_hack}
+BuildRequires: python2-html5lib
+BuildRequires: python2-imagesize
+%endif
+BuildRequires: python2-ipykernel
%if %{without bundled_ipython}
-BuildRequires: python-ipython
+BuildRequires: python2-ipython
%endif
-BuildRequires: python-future
-BuildRequires: python-ipykernel
-BuildRequires: python-jupyter-core
-BuildRequires: python-matplotlib
-BuildRequires: python-networkx
-BuildRequires: python-pathlib2
+BuildRequires: python2-matplotlib
+BuildRequires: python2-networkx
+BuildRequires: python2-notebook
+%if %{with bundled_ipython}
+BuildRequires: python2-path
+%endif
+BuildRequires: python2-pathlib2
%if %{without bundled_pexpect}
-BuildRequires: python-pexpect
+BuildRequires: python2-pexpect
%endif
-BuildRequires: python-pickleshare
-BuildRequires: python-prompt_toolkit
-BuildRequires: python-pkgconfig
-BuildRequires: python-psutil
-BuildRequires: python-six
-BuildRequires: python-speaklater
-BuildRequires: python-sphinx
-BuildRequires: python-traitlets
-BuildRequires: python-twisted
-BuildRequires: python-twisted-mail
-BuildRequires: python-twisted-web
-BuildRequires: python-ZODB3
+BuildRequires: python2-pickleshare
+BuildRequires: python2-pillow-devel
+BuildRequires: python2-prompt_toolkit
+BuildRequires: python2-pkgconfig
+BuildRequires: python2-psutil
+BuildRequires: python2-ptyprocess
+BuildRequires: python2-scipy
+BuildRequires: python2-setuptools
+%if %{with bundled_ipython}
+BuildRequires: python2-simplegeneric
+%endif
+BuildRequires: python2-six
+BuildRequires: python2-speaklater
+BuildRequires: python2-sphinx
+BuildRequires: python2-sympy
+BuildRequires: python2-twisted
+BuildRequires: python2-ZODB3
BuildRequires: qepcad-B
BuildRequires: R
BuildRequires: ratpoints-devel
@@ -290,10 +304,10 @@ BuildRequires: Singular-devel
BuildRequires: stix-math-fonts
BuildRequires: symmetrica-devel
BuildRequires: sympow
-BuildRequires: sympy
BuildRequires: tachyon
BuildRequires: texlive
BuildRequires: tex(anyfontsize.sty)
+BuildRequires: tex(makecmds.sty)
BuildRequires: vecmath
# For _jsdir macro
BuildRequires: web-assets-devel
@@ -302,66 +316,88 @@ BuildRequires: xorg-x11-server-Xvfb
BuildRequires: zn_poly-devel
Requires: 4ti2
-Requires: apache-commons-cli
Requires: cddlib-tools
-Requires: Cython
Requires: ecl
Requires: gap
Requires: GAPDoc
Requires: gap-libs
Requires: gap-pkg-atlasrep
-Requires: gap-pkg-ctbllib
+Requires: gap-pkg-crime
Requires: gap-pkg-design
Requires: gap-pkg-guava
-Requires: gap-pkg-hap
+Requires: gap-pkg-hapcryst
Requires: gap-pkg-sonata
-Requires: gap-pkg-tomlib
+Requires: gap-pkg-toric
Requires: genus2reduction
Requires: gfan
Requires: gmp-ecm
Requires: jmol
Requires: jsmol
Requires: jsmath-fonts
+Requires: latte-integrale
Requires: lrslib-utils
Requires: mathjax
Requires: maxima-gui
Requires: maxima-runtime-ecl
Requires: nauty
Requires: palp
+Requires: pari-galdata
Requires: pari-gp
-Requires: python-backports-shutil_get_terminal_size
-Requires: python-brial
-Requires: python-cysignals
-Requires: python-crypto
-Requires: python-cvxopt
-Requires: python-docutils
-Requires: python-flask-autoindex
-Requires: python-flask-babel
-Requires: python-flask-openid
-Requires: python-flask-silk
-Requires: python-future
+Requires: pari-seadata
+%if %{with bundled_ipython}
+Requires: python2-backports-shutil_get_terminal_size
+%endif
+Requires: python2-brial
+%if %{with sphinx_hack}
+Requires: python2-configparser
+%endif
+Requires: python2-cypari2
+Requires: python2-cysignals
+Requires: python2-crypto
+Requires: python2-cryptominisat
+Requires: python2-cvxopt
+Requires: python2-Cython
+Requires: python2-docutils
+Requires: python2-flask-autoindex
+Requires: python2-flask-babel
+Requires: python2-flask-openid
+Requires: python2-flask-silk
+Requires: python2-fpylll
+Requires: python2-future
+Requires: python2-gmpy2
+%if %{with sphinx_hack}
+Requires: python2-html5lib
+Requires: python2-imagesize
+%endif
+Requires: python2-ipykernel
%if %{without bundled_ipython}
-Requires: python-ipython
+Requires: python2-ipython
%endif
-Requires: python-ipykernel
-Requires: python-jupyter-core
-Requires: python-matplotlib
-Requires: python-networkx
-Requires: python-pathlib2
+Requires: python2-matplotlib
+Requires: python2-networkx
+Requires: python2-notebook
+%if %{with bundled_ipython}
+Requires: python2-path
+%endif
+Requires: python2-pathlib2
%if %{without bundled_pexpect}
-Requires: python-pexpect
+Requires: python2-pexpect
%endif
-Requires: python-pickleshare
-Requires: python-prompt_toolkit
-Requires: python-psutil
-Requires: python-six
-Requires: python-speaklater
-Requires: python-sphinx
-Requires: python-traitlets
-Requires: python-twisted
-Requires: python-twisted-mail
-Requires: python-twisted-web
-Requires: python-ZODB3
+Requires: python2-pickleshare
+Requires: python2-pillow
+Requires: python2-prompt_toolkit
+Requires: python2-psutil
+Requires: python2-ptyprocess
+Requires: python2-scipy
+%if %{with bundled_ipython}
+BuildRequires: python2-simplegeneric
+%endif
+Requires: python2-six
+Requires: python2-speaklater
+Requires: python2-sphinx
+Requires: python2-sympy
+Requires: python2-twisted
+Requires: python2-ZODB3
Requires: qepcad-B
Requires: R
Requires: rpy
@@ -376,7 +412,6 @@ Requires: %{name}-sagetex
Requires: Singular
Requires: stix-math-fonts
Requires: sympow
-Requires: sympy
Requires: tachyon
Requires: texlive
Requires: vecmath
@@ -389,7 +424,6 @@ packages into a common Python-based interface.
#------------------------------------------------------------------------
%package core
Summary: Open Source Mathematics Software
-Group: Applications/Engineering
Requires: %{name}%{?_isa} = %{version}-%{release}
Obsoletes: %{name}-devel < 6.8-1
@@ -399,8 +433,8 @@ This package contains the core sagemath python modules.
#------------------------------------------------------------------------
%package data
Summary: Databases and scripts for %{name}
-Group: Applications/Engineering
Requires: %{name} = %{version}-%{release}
+Requires: %{name}-data-combinatorial_designs = %{version}-%{release}
Requires: %{name}-data-conway_polynomials = %{version}-%{release}
Requires: %{name}-data-elliptic_curves = %{version}-%{release}
Requires: %{name}-data-etc = %{version}-%{release}
@@ -411,10 +445,19 @@ BuildArch: noarch
%description data
Collection of databases and interface customization scripts for sagemath.
+#------------------------------------------------------------------------
+%package data-combinatorial_designs
+Summary: Table of MOLS from the Handbook of Combinatorial Designs
+Requires: %{name}-data = %{version}-%{release}
+BuildArch: noarch
+
+%description data-combinatorial_designs
+The table of MOLS (10000 integers) from the Handbook of Combinatorial
+Designs, 2nd edition.
+
#------------------------------------------------------------------------
%package data-conway_polynomials
Summary: Conway Polynomials Database
-Group: Applications/Engineering
Requires: %{name}-data = %{version}-%{release}
BuildArch: noarch
@@ -424,7 +467,6 @@ Small database of Conway polynomials for sagemath.
#------------------------------------------------------------------------
%package data-elliptic_curves
Summary: Databases of elliptic curves
-Group: Applications/Engineering
Requires: %{name}-data = %{version}-%{release}
BuildArch: noarch
@@ -440,7 +482,6 @@ Includes two databases:
#------------------------------------------------------------------------
%package data-etc
Summary: Extcode for Sagemath
-Group: Applications/Engineering
Requires: %{name}-data = %{version}-%{release}
Obsoletes: %{name}-data-extcode < %{version}
BuildArch: noarch
@@ -451,7 +492,6 @@ Collection of scripts and interfaces to sagemath.
#------------------------------------------------------------------------
%package data-graphs
Summary: Sagemath database of graphs
-Group: Applications/Engineering
Requires: %{name}-data = %{version}-%{release}
BuildArch: noarch
@@ -462,7 +502,6 @@ Grout. Since April 2012 it also contains the ISGCI graph database.
#------------------------------------------------------------------------
%package data-polytopes_db
Summary: Lists of 2- and 3-dimensional reflexive polytopes
-Group: Applications/Engineering
Requires: %{name}-data = %{version}-%{release}
BuildArch: noarch
@@ -479,7 +518,6 @@ ReflexivePolytope and ReflexivePolytopes commands.
#------------------------------------------------------------------------
%package doc
Summary: Documentation infrastructure files for %{name}
-Group: Documentation
%description doc
This package contains the documentation infrastructure for %{name}.
@@ -487,7 +525,6 @@ This package contains the documentation infrastructure for %{name}.
#------------------------------------------------------------------------
%package doc-ca
Summary: Catalan documentation files for %{name}
-Group: Documentation
Requires: %{name}-doc = %{version}-%{release}
%description doc-ca
@@ -496,7 +533,6 @@ This package contains the Catalan %{name} documentation.
#------------------------------------------------------------------------
%package doc-de
Summary: German documentation files for %{name}
-Group: Documentation
Requires: %{name}-doc = %{version}-%{release}
%description doc-de
@@ -505,7 +541,6 @@ This package contains the German %{name} documentation.
#------------------------------------------------------------------------
%package doc-en
Summary: English documentation files for %{name}
-Group: Documentation
Requires: %{name}-doc = %{version}-%{release}
%description doc-en
@@ -514,7 +549,6 @@ This package contains the English %{name} documentation.
#------------------------------------------------------------------------
%package doc-fr
Summary: French documentation files for %{name}
-Group: Documentation
Requires: %{name}-doc = %{version}-%{release}
%description doc-fr
@@ -523,7 +557,6 @@ This package contains the French %{name} documentation.
#------------------------------------------------------------------------
%package doc-hu
Summary: Hungarian documentation files for %{name}
-Group: Documentation
Requires: %{name}-doc = %{version}-%{release}
%description doc-hu
@@ -532,7 +565,6 @@ This package contains the Hungarian %{name} documentation.
#------------------------------------------------------------------------
%package doc-it
Summary: Italian documentation files for %{name}
-Group: Documentation
Requires: %{name}-doc = %{version}-%{release}
%description doc-it
@@ -541,7 +573,6 @@ This package contains the Italian %{name} documentation.
#------------------------------------------------------------------------
%package doc-pt
Summary: Portuguese documentation files for %{name}
-Group: Documentation
Requires: %{name}-doc = %{version}-%{release}
%description doc-pt
@@ -550,7 +581,6 @@ This package contains the Portuguese %{name} documentation.
#------------------------------------------------------------------------
%package doc-ru
Summary: Russian documentation files for %{name}
-Group: Documentation
Requires: %{name}-doc = %{version}-%{release}
%description doc-ru
@@ -559,7 +589,6 @@ This package contains the Russian %{name} documentation.
#------------------------------------------------------------------------
%package doc-tr
Summary: Turkish documentation files for %{name}
-Group: Documentation
Requires: %{name}-doc = %{version}-%{release}
%description doc-tr
@@ -570,17 +599,26 @@ This package contains the Turkish %{name} documentation.
#------------------------------------------------------------------------
%package notebook
Summary: The Sage Notebook
-Group: Applications/Engineering
Requires: %{name}%{?_isa} = %{version}-%{release}
%description notebook
The Sage Notebook is a web-based graphical user interface for
mathematical software.
+#------------------------------------------------------------------------
+%package notebook-export
+Summary: The Sage Notebook Exporter
+Requires: %{name}%{?_isa} = %{version}-%{release}
+Requires: %{name}-notebook = %{version}-%{release}
+BuildArch: noarch
+
+%description notebook-export
+The Sage Notebook Exporter converts SageNB notebooks to other formats,
+in particular IPython/Jupyter notebooks.
+
#------------------------------------------------------------------------
%package rubiks
Summary: Several programs for working with Rubik's cubes
-Group: Applications/Engineering
Requires: %{name}%{?_isa} = %{version}-%{release}
%description rubiks
@@ -604,8 +642,16 @@ Eric Dietz (GPL) http://www.wrongway.org/?rubiksource
#------------------------------------------------------------------------
%package sagetex
Summary: Sagemath into LaTeX documents
-Group: Applications/Engineering
Requires: %{name}%{?_isa} = %{version}-%{release}
+Requires: tex(color.sty)
+Requires: tex(fancyvrb.sty)
+Requires: tex(graphicx.sty)
+Requires: tex(ifpdf.sty)
+Requires: tex(ifthen.sty)
+Requires: tex(ifxetex.sty)
+Requires: tex(listings.sty)
+Requires: tex(makecmds.sty)
+Requires: tex(verbatim.sty)
%description sagetex
This is the SageTeX package. It allows you to embed code, results of
@@ -616,6 +662,11 @@ computations, and plots from the Sage mathematics software suite
%prep
%setup -q -n sage-%{version}
+pushd build/pkgs/combinatorial_designs
+ tar jxf ../../../upstream/%{combinatorial_designs_pkg}.tar.bz2
+ mv %{combinatorial_designs_pkg} src
+popd
+
pushd build/pkgs/conway_polynomials
tar jxf ../../../upstream/%{conway_polynomials_pkg}.tar.bz2
mv %{conway_polynomials_pkg} src
@@ -682,9 +733,17 @@ pushd build/pkgs/sagenb
mv %{sagenb_pkg} src
popd
+pushd build/pkgs/sagenb_export
+ tar zxf ../../../upstream/%{sagenb_export_pkg}.tar.gz
+ mv %{sagenb_export_pkg} src
+popd
+
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}")
+ sed -i "s,share/texmf,$texmfdir," src/setup.py
popd
%if %{with docs}
@@ -729,16 +788,15 @@ popd
%patch21
%patch22
%patch23
+%patch24
%patch25
%patch26
-%patch27
-%patch28
sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
-e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \
-i src/sage/env.py
-sed -e 's|@@CYSIGNALS@@|%{python_sitearch}/cysignals|' \
+sed -e 's|@@CYSIGNALS@@|%{python2_sitearch}/cysignals|' \
-i src/setup.py
sed -e "s|, 'flask-oldsessions>=0.10'||" \
@@ -760,6 +818,14 @@ sed -e "s,SINGULARPATH=\",&%{_datadir}/singular/LIB:," \
-e "s,\(SINGULAR_EXECUTABLE=\"\).*\",\1%{_libdir}/Singular/Singular\"," \
-i src/bin/sage-env
+# fix shebangs
+sed -i 's,#!%{_bindir}/env python,#!%{_bindir}/python2,' \
+ $(grep -Frl '#!%{_bindir}/env python')
+sed -i 's,#!%{_bindir}/env sage-python23,#!%{_bindir}/python2,' \
+ $(grep -Frl '#!%{_bindir}/env sage-python23')
+sed -i 's,#!%{_bindir}/env ,#!%{_bindir}/,' $(grep -Frl '#!%{_bindir}/env')
+sed -i 's,#!%{_bindir}/python$,&2,' $(grep -Frl '#!%{_bindir}/python')
+
########################################################################
%build
export CC=%{__cc}
@@ -788,7 +854,8 @@ ln -sf %{_includedir} $SAGE_LOCAL/include
ln -sf %{_datadir} $SAGE_LOCAL/share
export PATH=%{buildroot}%{_bindir}:$PATH
-export PYTHONPATH=%{buildroot}%{python_sitearch}:$PYTHONPATH
+export PYTHON=%{_bindir}/python2
+export PYTHONPATH=%{buildroot}%{python2_sitearch}:$PYTHONPATH
#------------------------------------------------------------------------
# Save and update environment to generate bundled interfaces
@@ -812,9 +879,9 @@ popd
%endif
%if %{with cython_hack}
- cp -far %{python_sitearch}/Cython %{_builddir}%{python_sitearch}
+ cp -far %{python2_sitearch}/Cython %{_builddir}%{python2_sitearch}
BASE=$PWD/build/pkgs/cython/patches/
- pushd %{_builddir}%{python_sitearch}
+ pushd %{_builddir}%{python2_sitearch}
for PATCH in pxi_sys_path.patch
do
patch -p1 < $BASE/$PATCH
@@ -827,6 +894,8 @@ popd
# Restore environment used to generate bundled interfaces
export PATH=$save_PATH
export SAGE_LOCAL=$save_LOCAL
+mkdir -p %{buildroot}%{SAGE_SPKG_INST}
+mkdir -p %{buildroot}%{_libdir}/sagemath/build/pkgs
pushd src
%__python2 -u ./setup.py build
@@ -837,6 +906,10 @@ pushd build/pkgs/sagenb/src
%__python2 ./setup.py build
popd
+pushd build/pkgs/sagenb_export/src
+ %__python2 ./setup.py build
+popd
+
#------------------------------------------------------------------------
pushd build/pkgs/flintqs/src
%configure
@@ -881,8 +954,9 @@ export DOT_SAGE=/tmp/sage$$
mkdir -p $DOT_SAGE/tmp
export PATH=%{buildroot}%{_bindir}:$PATH
-export PYTHONPATH=%{buildroot}%{python_sitearch}:$PYTHONPATH
-export PYTHONPATH=%{_builddir}%{python_sitearch}:$PYTHONPATH
+export PYTHON=%{_bindir}/python2
+export PYTHONPATH=%{buildroot}%{python2_sitearch}:$PYTHONPATH
+export PYTHONPATH=%{_builddir}%{python2_sitearch}:$PYTHONPATH
#------------------------------------------------------------------------
mkdir -p %{buildroot}%{_bindir}
@@ -917,11 +991,10 @@ popd
#------------------------------------------------------------------------
pushd src
%if %{without install_hack}
- # FIXME tries to rebuild everything
- %__python2 -u setup.py install --root=%{buildroot}
+ %py2_install
%else
- mkdir -p %{buildroot}%{python_sitearch}
- cp -far build/lib.linux-*/sage %{buildroot}%{python_sitearch}
+ mkdir -p %{buildroot}%{python2_sitearch}
+ cp -far build/lib.linux-*/sage %{buildroot}%{python2_sitearch}
%endif
%if %{with docs}
# install documentation sources
@@ -932,18 +1005,23 @@ popd
#------------------------------------------------------------------------
pushd build/pkgs/sagenb/src
- rm -f %{buildroot}%{python_sitearch}/sagenb/data/sage3d/sage3d
- %__python2 setup.py install --root=%{buildroot} --install-purelib=%{python_sitearch}
+ rm -f %{buildroot}%{python2_sitearch}/sagenb/data/sage3d/sage3d
+ %py2_install "--install-purelib=%{python2_sitearch}"
# jsmol
ln -sf %{_jsdir}/jsmol $SAGE_SHARE/jsmol
# sage3d
rm -f %{buildroot}%{_bindir}/sage3d
%if %{with sage3d}
- ln -sf %{SAGE_LOCAL}/bin/sage3d %{buildroot}%{python_sitearch}/sagenb/data/sage3d/sage3d
+ ln -sf %{SAGE_LOCAL}/bin/sage3d %{buildroot}%{python2_sitearch}/sagenb/data/sage3d/sage3d
%endif
- ln -sf %{python_sitearch}/sagenb %{buildroot}%{SAGE_SRC}/sagenb
+ ln -sf %{python2_sitearch}/sagenb %{buildroot}%{SAGE_SRC}/sagenb
# use system mathjax
- ln -sf %{_jsdir}/mathjax %{buildroot}%{python_sitearch}/sagenb/data/mathjax
+ ln -sf %{_jsdir}/mathjax %{buildroot}%{python2_sitearch}/sagenb/data/mathjax
+popd
+
+#------------------------------------------------------------------------
+pushd build/pkgs/sagenb_export/src
+ %py2_install
popd
#------------------------------------------------------------------------
@@ -1031,9 +1109,14 @@ pushd $SAGE_LOCAL/bin/
done
popd
+#------------------------------------------------------------------------
+pushd build/pkgs/combinatorial_designs
+ bash ./spkg-install
+popd
+
#------------------------------------------------------------------------
pushd build/pkgs/conway_polynomials
- %__python2 ./spkg-install
+ %__python2 ./spkg-install.py
popd
#------------------------------------------------------------------------
@@ -1044,7 +1127,7 @@ pushd build/pkgs/elliptic_curves
tar jxf ../../../upstream/%{elliptic_curves_pkg}.tar.bz2
mv %{elliptic_curves_pkg} src
fi
- %__python2 ./spkg-install
+ %__python2 ./spkg-install.py
popd
#------------------------------------------------------------------------
@@ -1061,10 +1144,8 @@ popd
#------------------------------------------------------------------------
pushd build/pkgs/sagetex/src
- %__python2 setup.py install --root=%{buildroot} --install-purelib=%{python_sitearch}
- install -p -m 0644 -D %{SOURCE2} \
- %{buildroot}%{_datadir}/texmf/tex/latex/sagetex/makecmds.sty
- mv %{buildroot}%{_datadir}/texmf/tex/latex/sagetex/CONTRIBUTORS \
+ %py2_install "--install-purelib=%{python2_sitearch}"
+ mv %{buildroot}%{_texmf_main}/tex/latex/sagetex/CONTRIBUTORS \
%{buildroot}%{_docdir}/sagetex
for file in PKG-INFO README; do
install -p -m 0644 $file %{buildroot}%{_docdir}/sagetex/$file
@@ -1073,13 +1154,13 @@ popd
#------------------------------------------------------------------------
%if %{with bundled_ipython}
-mv %{_builddir}%{python_sitelib}/IPython %{buildroot}%{SAGE_PYTHONPATH}
+mv %{_builddir}%{python2_sitelib}/IPython %{buildroot}%{SAGE_PYTHONPATH}
mv %{_builddir}%{_bindir}/ip* %{buildroot}%{SAGE_LOCAL}/bin
%endif
#------------------------------------------------------------------------
%if %{with bundled_ipywidgets}
-mv %{_builddir}%{python_sitelib}/ipywidgets %{buildroot}%{SAGE_PYTHONPATH}
+mv %{_builddir}%{python2_sitelib}/ipywidgets %{buildroot}%{SAGE_PYTHONPATH}
%endif
#------------------------------------------------------------------------
@@ -1105,14 +1186,13 @@ module load surf-geometry-%{_arch}
export PATH=$SAGE_LOCAL/bin:\$PATH
export SINGULAR_DATA_DIR=%{_datadir}
export SINGULAR_BIN_DIR=%{_libdir}/Singular
-export SINGULAR_SO=%{_libdir}/libSingular-4.1.0.so
+export SINGULAR_SO=%{_libdir}/libSingular-4.1.1.so
##export PYTHONPATH="$SAGE_PYTHONPATH:\$SAGE_LOCAL/bin"
export SAGE_CBLAS=blas
export SAGE_FORTRAN=%{_bindir}/gfortran
export SAGE_FORTRAN_LIB=\`gfortran --print-file-name=libgfortran.so\`
export SYMPOW_DIR="\$DOT_SAGE/sympow"
-export LC_MESSAGES=C
-export LC_NUMERIC=C
+export LC_ALL=C.UTF-8
export LD_LIBRARY_PATH=\$SAGE_ROOT/lib:\$LD_LIBRARY_PATH
# Required for sage -gdb
export SAGE_DEBUG=no
@@ -1137,17 +1217,17 @@ chmod +x %{buildroot}%{SAGE_LOCAL}/bin/sage3d
# o install .pxi and .pxd files
pushd src
for f in `find sage \( -name \*.pxi -o -name \*.pxd -o -name \*.pyx \)`; do
- install -p -D -m 0644 $f %{buildroot}%{python_sitearch}/$f
+ install -p -D -m 0644 $f %{buildroot}%{python2_sitearch}/$f
done
# need this or will not "find" the files in the directory, and
# fail to link with gmp
- touch %{buildroot}%{python_sitearch}/sage/libs/gmp/__init__.py
+ touch %{buildroot}%{python2_sitearch}/sage/libs/gmp/__init__.py
popd
%if %{with docs}
#------------------------------------------------------------------------
%if %{with bundled_pexpect}
-cp -fa $SAGE_PYTHONPATH/pexpect %{buildroot}%{python_sitearch}
+cp -fa $SAGE_PYTHONPATH/pexpect %{buildroot}%{python2_sitearch}
%endif
# Build documentation, using %#{buildroot} environment
@@ -1158,12 +1238,12 @@ pushd src/doc
export SINGULARPATH=%{_datadir}/singular/LIB
export SINGULAR_BIN_DIR=%{_libdir}/Singular
export LD_LIBRARY_PATH=%{_libdir}/atlas:$LD_LIBRARY_PATH
- export PYTHONPATH=$SAGE_SETUP:%{buildroot}%{python_sitearch}:$SAGE_PYTHONPATH:$SAGE_DOC
+ export PYTHONPATH=$SAGE_SETUP:%{buildroot}%{python2_sitearch}:$SAGE_PYTHONPATH:$SAGE_DOC
%if %{with sphinx_hack}
pushd ../../build/pkgs/sphinx/src
- %__python2 setup.py build
- %__python2 setup.py install --root %{buildroot} --install-purelib=%{python_sitearch}
+ %py2_build
+ %py2_install "--install-purelib=%{python2_sitearch}"
rm -f %{buildroot}%{_bindir}/sphinx*
popd
%endif
@@ -1193,12 +1273,12 @@ sed -i 's|%{buildroot}||g' $SAGE_DOC/test.log
%endif
%if %{with bundled_pexpect}
- rm -f %{buildroot}%{python_sitearch}/pexpect
+ rm -f %{buildroot}%{python2_sitearch}/pexpect
%endif
%if %{with sphinx_hack}
- rm -fr %{buildroot}%{python_sitearch}/sphinx \
- %{buildroot}%{python_sitearch}/Sphinx*
+ rm -fr %{buildroot}%{python2_sitearch}/sphinx \
+ %{buildroot}%{python2_sitearch}/Sphinx*
%endif
# More wrong buildroot references
@@ -1216,8 +1296,8 @@ perl -pi -e 's|%{buildroot}||g;s|^##||g;' %{buildroot}%{_bindir}/sage
export SAGE_SRC=%{buildroot}%{SAGE_SRC}
rm -fr $SAGE_SRC/sage $SAGE_ETC/sage $SAGE_ROOT/doc $SAGE_SRC/doc
rm -fr $SAGE_ROOT/share $SAGE_ROOT/devel
-ln -sf %{python_sitearch}/sage $SAGE_SRC/sage
-ln -sf %{python_sitearch} $SAGE_ETC/sage
+ln -sf %{python2_sitearch}/sage $SAGE_SRC/sage
+ln -sf %{python2_sitearch} $SAGE_ETC/sage
ln -sf %{SAGE_DOC} $SAGE_ROOT/doc
%if %{with docs}
ln -sf %{SAGE_DOC} $SAGE_SRC/doc
@@ -1259,17 +1339,16 @@ 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 -exec rm {} \+
rm -fr %{buildroot}%{SAGE_DOC}/output/inventory
-find %{buildroot}%{SAGE_DOC} -type d -name _sources | xargs rm -fr
-find %{buildroot}%{SAGE_DOC} -name 'core.*' -exec rm {} \;
+find %{buildroot}%{SAGE_DOC} -type d -name _sources -exec rm -fr {} \+
%endif
# remove .po files
-rm %{buildroot}%{python_sitearch}/sagenb/translations/*/LC_MESSAGES/*.po
+rm %{buildroot}%{python2_sitearch}/sagenb/translations/*/LC_MESSAGES/*.po
%if %{without sage3d}
-rm -r %{buildroot}%{python_sitearch}/sagenb/data/sage3d
+rm -r %{buildroot}%{python2_sitearch}/sagenb/data/sage3d
%endif
# remove build directory in buildroot
@@ -1278,7 +1357,7 @@ rm -r %{buildroot}%{python_sitearch}/sagenb/data/sage3d
%if %{without install_hack}
# remove sage_setup
-rm -r %{buildroot}%{python_sitearch}/sage_setup
+rm -r %{buildroot}%{python2_sitearch}/sage_setup
%endif
# pretend sagemath spkgs are installed to reduce number of errors
@@ -1330,7 +1409,7 @@ rm -fr $DOT_SAGE
########################################################################
%pretrans -p /usr/bin/lua
posix = require('posix')
-path = "%{python_sitearch}/sagenb/data/mathjax"
+path = "%{python2_sitearch}/sagenb/data/mathjax"
st = posix.stat(path)
if st and st.type == "directory" then
status = os.rename(path, path .. ".rpmmoved")
@@ -1344,13 +1423,7 @@ if st and st.type == "directory" then
end
end
-%post core
-/sbin/ldconfig
-exit 0
-
-%postun core
-/sbin/ldconfig
-exit 0
+%ldconfig_scriptlets core
%if %{with docs}
# Upgrade correction for change from directory to symlink
@@ -1369,15 +1442,9 @@ fi
exit 0
%endif
-%post sagetex
-%{_bindir}/mktexlsr
-exit 0
+%post sagetex -p %{_bindir}/mktexlsr
-%postun sagetex
-if [ $1 -eq 0 ] ; then
- %{_bindir}/mktexlsr
-fi
-exit 0
+%postun sagetex -p %{_bindir}/mktexlsr
########################################################################
%files
@@ -1416,9 +1483,9 @@ exit 0
#------------------------------------------------------------------------
%files core
# GPLv2+
-%{python_sitearch}/sage
+%{python2_sitearch}/sage
%if %{without install_hack}
-%{python_sitearch}/sage-*.egg-info
+%{python2_sitearch}/sage-*.egg-info
%endif
%if %{with bundled_ipython}
%{SAGE_PYTHONPATH}/IPython
@@ -1434,6 +1501,11 @@ exit 0
%{SAGE_ETC}/sage
%{SAGE_ETC}/gprc.expect
+#------------------------------------------------------------------------
+%files data-combinatorial_designs
+# Public Domain
+%{SAGE_SHARE}/combinatorial_designs
+
#------------------------------------------------------------------------
%files data-conway_polynomials
# GPLv2+
@@ -1534,69 +1606,75 @@ exit 0
%{SAGE_ETC}/notebook-ipython
# GPLv2+
%{SAGE_SRC}/sagenb
-%dir %{python_sitearch}/sagenb
-%{python_sitearch}/sagenb/*.py*
-%{python_sitearch}/sagenb-*.egg-info
-%dir %{python_sitearch}/sagenb/data
+%dir %{python2_sitearch}/sagenb
+%{python2_sitearch}/sagenb/*.py*
+%{python2_sitearch}/sagenb-*.egg-info
+%dir %{python2_sitearch}/sagenb/data
# BSD
-%{python_sitearch}/sagenb/data/codemirror
+%{python2_sitearch}/sagenb/data/codemirror
# MIT
-%{python_sitearch}/sagenb/data/graph_editor
+%{python2_sitearch}/sagenb/data/graph_editor
# ASL 2.0
-%{python_sitearch}/sagenb/data/highlight
+%{python2_sitearch}/sagenb/data/highlight
# LGPLv2+
%{SAGE_SHARE}/jsmol
# (MIT or GPLv2) and (MIT and BSD and GPL)
-%{python_sitearch}/sagenb/data/jquery
+%{python2_sitearch}/sagenb/data/jquery
# (MIT or GPLv2) and (MIT and BSD and GPL)
-%{python_sitearch}/sagenb/data/jqueryui
+%{python2_sitearch}/sagenb/data/jqueryui
# Public Domain
-%{python_sitearch}/sagenb/data/json
+%{python2_sitearch}/sagenb/data/json
# Symbolic link to $_jsdir/mathjax
-%{python_sitearch}/sagenb/data/mathjax
-%ghost %{python_sitearch}/sagenb/data/mathjax.rpmmoved
+%{python2_sitearch}/sagenb/data/mathjax
+%ghost %{python2_sitearch}/sagenb/data/mathjax.rpmmoved
# Empty (do not run doctests flag file)
-%{python_sitearch}/sagenb/data/nodoctest.py*
+%{python2_sitearch}/sagenb/data/nodoctest.py*
# BSD
-%{python_sitearch}/sagenb/data/openid-realselector
+%{python2_sitearch}/sagenb/data/openid-realselector
# GPLv2+
-%{python_sitearch}/sagenb/data/sage
+%{python2_sitearch}/sagenb/data/sage
%if %{with sage3d}
# GPLv2+
-%{python_sitearch}/sagenb/data/sage3d
+%{python2_sitearch}/sagenb/data/sage3d
%endif
# LGPLv2+
-%{python_sitearch}/sagenb/data/tiny_mce
+%{python2_sitearch}/sagenb/data/tiny_mce
# LGPLv2+
-%{python_sitearch}/sagenb/data/zorn
+%{python2_sitearch}/sagenb/data/zorn
# GPLv2+
-%{python_sitearch}/sagenb/flask_version
+%{python2_sitearch}/sagenb/flask_version
# GPLv2+
-%{python_sitearch}/sagenb/interfaces
+%{python2_sitearch}/sagenb/interfaces
# GPLv2+
-%{python_sitearch}/sagenb/misc
+%{python2_sitearch}/sagenb/misc
# GPLv2+
-%{python_sitearch}/sagenb/notebook
+%{python2_sitearch}/sagenb/notebook
# GPLv2+
-%{python_sitearch}/sagenb/simple
+%{python2_sitearch}/sagenb/simple
# GPLv2+
-%{python_sitearch}/sagenb/storage
+%{python2_sitearch}/sagenb/storage
# GPLv2+
-%dir %{python_sitearch}/sagenb/testing
-%{python_sitearch}/sagenb/testing/*.py*
-%{python_sitearch}/sagenb/testing/tests
+%dir %{python2_sitearch}/sagenb/testing
+%{python2_sitearch}/sagenb/testing/*.py*
+%{python2_sitearch}/sagenb/testing/tests
# ASL 2.0
-%{python_sitearch}/sagenb/testing/selenium
+%{python2_sitearch}/sagenb/testing/selenium
# GPLv2+
-%dir %{python_sitearch}/sagenb/translations
-%lang(cs_CZ) %{python_sitearch}/sagenb/translations/cs_CZ
-%lang(de_AT) %{python_sitearch}/sagenb/translations/de_AT
-%lang(de_AT) %{python_sitearch}/sagenb/translations/en_US
-%lang(de_AT) %{python_sitearch}/sagenb/translations/es_ES
-%lang(de_AT) %{python_sitearch}/sagenb/translations/fr_FR
-%lang(pt_BR) %{python_sitearch}/sagenb/translations/pt_BR
-%lang(ru_RU) %{python_sitearch}/sagenb/translations/ru_RU
-%lang(uk_UA) %{python_sitearch}/sagenb/translations/uk_UA
+%dir %{python2_sitearch}/sagenb/translations
+%lang(cs_CZ) %{python2_sitearch}/sagenb/translations/cs_CZ
+%lang(de_AT) %{python2_sitearch}/sagenb/translations/de_AT
+%lang(de_AT) %{python2_sitearch}/sagenb/translations/en_US
+%lang(de_AT) %{python2_sitearch}/sagenb/translations/es_ES
+%lang(de_AT) %{python2_sitearch}/sagenb/translations/fr_FR
+%lang(pt_BR) %{python2_sitearch}/sagenb/translations/pt_BR
+%lang(ru_RU) %{python2_sitearch}/sagenb/translations/ru_RU
+%lang(uk_UA) %{python2_sitearch}/sagenb/translations/uk_UA
+
+#------------------------------------------------------------------------
+%files notebook-export
+# GPL+
+%{python2_sitelib}/sagenb_export
+%{python2_sitelib}/sagenb_export-*.egg-info
#------------------------------------------------------------------------
%files rubiks
@@ -1613,12 +1691,19 @@ exit 0
#------------------------------------------------------------------------
%files sagetex
# GPLv2+
-%{python_sitearch}/sagetex*
-%{_datadir}/texmf/tex/latex/sagetex
+%{python2_sitearch}/sagetex*
+%{_texmf_main}/tex/latex/sagetex
%doc %{_docdir}/sagetex
########################################################################
%changelog
+* Fri May 18 2018 Jerry James <loganjerry@gmailc.om> - 8.2-1
+- Update to sagemath 8.2
+- 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
+
* Fri Feb 09 2018 Fedora Release Engineering <releng@fedoraproject.org> - 8.0-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
diff --git a/sources b/sources
index 0bf7da2..0ed0dd8 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-SHA512 (sage-8.0.tar.gz) = f0a7aaf9fc157b031ceba2d298d74a56bb38f6be5ae4350f91058a24360273f2599c1d50dfe8941e7c462d0a1bf436090da859256fc8e687097e6c419345c493
+SHA512 (sage-8.2.tar.gz) = 32afa401d0c0a825e9507a445de9a5abb19b3f2444c70ae0e5d7fea0fe319f6a43a94e5eee032fd85c21b87487a42d0c70177766dfa6ea1ea42d3a22e1395663
diff --git a/testjava.sh b/testjava.sh
old mode 100755
new mode 100644