Update to sagemath 8.3 (bz 1612867).

Also:
- Drop -lrslib, -gap-hap, and -flask patches.
- Drop obsolete scriplets to fix F24 to F25 upgrade (bz 1594429 and 1618934).
- Drop obsolete mktexlsr invocations.
- Fix more Singular paths.
- Fix still more uses of /usr/bin/env.
- Drop disallow/dissallow fixup for cython; now fixed in cython itself.

.gitignore

@@ -1,17 +1 @@
-/sage-5.8.tar
+/sage-*.tar.gz
-/sage-5.9.tar
-/sage-5.10.tar
-/sage-5.12.tar
-/sage-5.13.tar
-/sage-6.1.1.tar.gz
-/sage-6.2.tar.gz
-/sage-6.3.tar.gz
-/sage-6.4.1.tar.gz
-/sage-6.5.tar.gz
-/sage-6.8.tar.gz
-/sage-7.3.tar.gz
-/sage-7.4.tar.gz
-/sage-7.5.1.tar.gz
-/sage-7.6.tar.gz
-/sage-8.0.tar.gz
-/sage-8.2.tar.gz

sagemath-4ti2.patch

@@ -1,6 +1,6 @@
 diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
---- src/sage/sandpiles/sandpile.py.orig	2018-05-05 16:21:26.000000000 -0600
+--- src/sage/sandpiles/sandpile.py.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/sage/sandpiles/sandpile.py	2018-05-16 13:28:24.939025388 -0600
++++ src/sage/sandpiles/sandpile.py	2018-08-29 08:47:29.728055776 -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.
-@@ -5199,7 +5196,7 @@ class SandpileDivisor(dict):
+@@ -5197,7 +5194,7 @@ class SandpileDivisor(dict):
          sign_file.close()
          # compute
          try:

sagemath-arb.patch

@@ -1,18 +1,6 @@
-diff -up src/sage/libs/arb/acb.pxd.orig src/sage/libs/arb/acb.pxd
---- 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
- 
--cdef extern from "acb.h":
-+cdef extern from "arb/acb.h":
- 
-     arb_t acb_realref(acb_t x)
-     arb_t acb_imagref(acb_t x)
 diff -up src/sage/libs/arb/acb_hypgeom.pxd.orig src/sage/libs/arb/acb_hypgeom.pxd
---- src/sage/libs/arb/acb_hypgeom.pxd.orig	2018-05-05 16:21:24.000000000 -0600
+--- src/sage/libs/arb/acb_hypgeom.pxd.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/libs/arb/acb_hypgeom.pxd	2018-05-16 13:59:18.717290684 -0600
++++ src/sage/libs/arb/acb_hypgeom.pxd	2018-08-29 10:43:48.572622995 -0600
 @@ -2,7 +2,7 @@
  
  from sage.libs.arb.types cimport *
@@ -23,10 +11,10 @@ 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	2018-05-05 16:21:24.000000000 -0600
+--- src/sage/libs/arb/acb_mat.pxd.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/libs/arb/acb_mat.pxd	2018-05-16 13:59:18.717290684 -0600
++++ src/sage/libs/arb/acb_mat.pxd	2018-08-29 10:43:48.572622995 -0600
 @@ -1,6 +1,6 @@
- from sage.libs.arb.types cimport acb_t, acb_mat_t
+ from sage.libs.arb.types cimport acb_t, acb_mat_t, acb_poly_t
  
 -cdef extern from "acb_mat.h":
 +cdef extern from "arb/acb_mat.h":
@@ -34,8 +22,8 @@ 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	2018-05-05 16:21:24.000000000 -0600
+--- src/sage/libs/arb/acb_modular.pxd.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/libs/arb/acb_modular.pxd	2018-05-16 13:59:18.718290670 -0600
++++ src/sage/libs/arb/acb_modular.pxd	2018-08-29 10:43:48.572622995 -0600
 @@ -3,7 +3,7 @@
  from sage.libs.arb.types cimport *
  from sage.libs.flint.types cimport fmpz_poly_t
@@ -46,8 +34,8 @@ diff -up src/sage/libs/arb/acb_modular.pxd.orig src/sage/libs/arb/acb_modular.px
      void acb_modular_j(acb_t z, const acb_t tau, long prec)
      void acb_modular_eta(acb_t z, const acb_t tau, long prec)
 diff -up src/sage/libs/arb/acb_poly.pxd.orig src/sage/libs/arb/acb_poly.pxd
---- src/sage/libs/arb/acb_poly.pxd.orig	2018-05-05 16:21:24.000000000 -0600
+--- src/sage/libs/arb/acb_poly.pxd.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/libs/arb/acb_poly.pxd	2018-05-16 13:59:18.719290655 -0600
++++ src/sage/libs/arb/acb_poly.pxd	2018-08-29 10:43:48.572622995 -0600
 @@ -3,7 +3,7 @@
  from sage.libs.arb.types cimport *
  from sage.libs.flint.types cimport fmpz_poly_t, fmpq_poly_t
@@ -57,9 +45,21 @@ 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/acb.pxd.orig src/sage/libs/arb/acb.pxd
+--- src/sage/libs/arb/acb.pxd.orig	2018-08-03 05:10:08.000000000 -0600
++++ src/sage/libs/arb/acb.pxd	2018-08-29 10:43:48.571623007 -0600
+@@ -3,7 +3,7 @@
+ from sage.libs.arb.types cimport *
+ from sage.libs.flint.types cimport fmpz_t, fmpq_t
+ 
+-cdef extern from "acb.h":
++cdef extern from "arb/acb.h":
+ 
+     arb_t acb_realref(acb_t x)
+     arb_t acb_imagref(acb_t x)
 diff -up src/sage/libs/arb/arf.pxd.orig src/sage/libs/arb/arf.pxd
---- src/sage/libs/arb/arf.pxd.orig	2018-05-05 16:21:24.000000000 -0600
+--- src/sage/libs/arb/arf.pxd.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/libs/arb/arf.pxd	2018-05-16 13:59:18.716290698 -0600
++++ src/sage/libs/arb/arf.pxd	2018-08-29 10:43:48.572622995 -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
@@ -70,8 +70,8 @@ diff -up src/sage/libs/arb/arf.pxd.orig src/sage/libs/arb/arf.pxd
      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.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/libs/arb/bernoulli.pxd	2018-05-16 13:59:18.718290670 -0600
++++ src/sage/libs/arb/bernoulli.pxd	2018-08-29 10:43:48.572622995 -0600
 @@ -2,5 +2,5 @@
  
  from ..flint.types cimport fmpq_t, ulong
@@ -80,8 +80,8 @@ diff -up src/sage/libs/arb/bernoulli.pxd.orig src/sage/libs/arb/bernoulli.pxd
 +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.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/libs/arb/mag.pxd	2018-05-16 13:59:18.717290684 -0600
++++ src/sage/libs/arb/mag.pxd	2018-08-29 10:43:48.573622983 -0600
 @@ -3,7 +3,7 @@
  from sage.libs.arb.types cimport *
  from sage.libs.flint.types cimport fmpz_t, fmpq_t
@@ -92,8 +92,8 @@ diff -up src/sage/libs/arb/mag.pxd.orig src/sage/libs/arb/mag.pxd
      void mag_clear(mag_t x)
      void mag_init_set(mag_t x, const mag_t y)
 diff -up src/sage/libs/arb/types.pxd.orig src/sage/libs/arb/types.pxd
---- src/sage/libs/arb/types.pxd.orig	2018-05-05 16:21:24.000000000 -0600
+--- src/sage/libs/arb/types.pxd.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/libs/arb/types.pxd	2018-05-16 13:59:18.719290655 -0600
++++ src/sage/libs/arb/types.pxd	2018-08-29 10:43:48.573622983 -0600
 @@ -1,4 +1,4 @@
 -cdef extern from "mag.h":
 +cdef extern from "arb/mag.h":

sagemath-cremona.patch

@@ -1,6 +1,6 @@
 diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
---- src/sage/databases/cremona.py.orig	2016-10-20 08:11:03.521544935 -0400
+--- src/sage/databases/cremona.py.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/databases/cremona.py	2016-10-20 08:11:13.681545324 -0400
++++ src/sage/databases/cremona.py	2018-08-29 08:48:43.090148635 -0600
 @@ -53,7 +53,6 @@ from sage.misc.prandom import randint
  
  import sage.schemes.elliptic_curves.constructor as elliptic
@@ -9,7 +9,7 @@ diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
  from sage.env import SAGE_SHARE
  from sage.misc.all import walltime
  
-@@ -824,14 +823,6 @@ class MiniCremonaDatabase(SQLDatabase):
+@@ -825,14 +824,6 @@ class MiniCremonaDatabase(SQLDatabase):
              if N < self.largest_conductor():
                  message = "There is no elliptic curve with label " + label \
                      + " in the database"

sagemath-extensions.patch

@@ -1,6 +1,6 @@
 diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig	2018-05-05 16:21:22.000000000 -0600
+--- src/module_list.py.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/module_list.py	2018-05-18 07:46:16.531947286 -0600
++++ src/module_list.py	2018-08-29 08:34:50.846439644 -0600
 @@ -358,16 +358,16 @@ ext_modules = [
      Extension('sage.graphs.matchpoly',
                sources = ['sage/graphs/matchpoly.pyx']),
@@ -42,7 +42,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.graphs.spanning_tree',
                sources = ['sage/graphs/spanning_tree.pyx']),
-@@ -454,21 +454,20 @@ ext_modules = [
+@@ -461,21 +461,20 @@ ext_modules = [
      ##
      ################################
  
@@ -72,7 +72,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.libs.flint.flint',
                sources = ["sage/libs/flint/flint.pyx"],
-@@ -488,22 +487,22 @@ ext_modules = [
+@@ -495,22 +494,22 @@ ext_modules = [
      Extension('sage.libs.gmp.pylong',
                sources = ['sage/libs/gmp/pylong.pyx']),
  
@@ -109,7 +109,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('*', ['sage/libs/linbox/*.pyx']),
  
-@@ -844,10 +843,10 @@ ext_modules = [
+@@ -843,10 +842,10 @@ ext_modules = [
      Extension('sage.matrix.matrix_window',
                sources = ['sage/matrix/matrix_window.pyx']),
  
@@ -124,7 +124,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.matrix.misc',
                sources = ['sage/matrix/misc.pyx']),
-@@ -1024,26 +1023,25 @@ ext_modules = [
+@@ -1023,26 +1022,25 @@ ext_modules = [
      Extension("sage.numerical.backends.interactivelp_backend",
                ["sage/numerical/backends/interactivelp_backend.pyx"]),
  

sagemath-fes.patch

@@ -1,7 +1,7 @@
 diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig	2018-05-18 09:34:28.942183178 -0600
+--- src/module_list.py.orig	2018-08-29 08:35:19.927079956 -0600
-+++ src/module_list.py	2018-05-18 09:35:15.210542150 -0600
++++ src/module_list.py	2018-08-29 10:41:05.127643255 -0600
-@@ -464,10 +464,10 @@ ext_modules = [
+@@ -471,10 +471,10 @@ ext_modules = [
      Extension('sage.libs.ecl',
                sources = ["sage/libs/ecl.pyx"]),
  

sagemath-flask.patch

@@ -1,201 +0,0 @@
---- build/pkgs/sagenb/src/sagenb/flask_version/admin.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/flask_version/admin.py	2018-06-15 16:07:44.250325912 -0600
-@@ -1,7 +1,7 @@
- import os
- from flask import Blueprint, url_for, render_template, request, session, redirect, g, current_app
- from .decorators import login_required, admin_required, with_lock
--from flask.ext.babel import Babel, gettext, ngettext, lazy_gettext
-+from flask_babel import Babel, gettext, ngettext, lazy_gettext
- _ = gettext
- 
- admin = Blueprint('admin', 'sagenb.flask_version.admin')
---- build/pkgs/sagenb/src/sagenb/flask_version/authentication.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/flask_version/authentication.py	2018-06-15 16:06:44.083100080 -0600
-@@ -2,7 +2,7 @@ import os
- import random
- from flask import Blueprint, url_for, render_template, request, session, redirect, g, current_app
- from .decorators import with_lock
--from flask.ext.babel import gettext, ngettext, lazy_gettext
-+from flask_babel import gettext, ngettext, lazy_gettext
- _ = gettext
- 
- authentication = Blueprint('authentication',
---- build/pkgs/sagenb/src/sagenb/flask_version/base.py.orig	2018-06-15 13:17:46.940191938 -0600
-+++ build/pkgs/sagenb/src/sagenb/flask_version/base.py	2018-06-15 16:09:19.512516887 -0600
-@@ -8,11 +8,11 @@ from flask import Flask, Blueprint, url_
- from .decorators import login_required, guest_or_login_required, with_lock
- from .decorators import global_lock
- 
--from flask.ext.autoindex import AutoIndex
-+from flask_autoindex import AutoIndex
- from sage.env import SAGE_SRC, SAGE_DOC
- SRC = os.path.join(SAGE_SRC, 'sage')
--from flask.ext.openid import OpenID
--from flask.ext.babel import Babel, gettext, ngettext, lazy_gettext, get_locale
-+from flask_openid import OpenID
-+from flask_babel import Babel, gettext, ngettext, lazy_gettext, get_locale
- from sagenb.misc.misc import SAGENB_ROOT, DATA, translations_path, N_, nN_, unicode_str
- from json import dumps
- from sagenb.notebook.cell import number_of_rows
---- build/pkgs/sagenb/src/sagenb/flask_version/decorators.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/flask_version/decorators.py	2018-06-15 16:09:33.447105994 -0600
-@@ -1,6 +1,6 @@
- from functools import wraps
- from flask import Flask, url_for, render_template, request, session, redirect, g, current_app
--from flask.ext.babel import Babel, gettext, ngettext, lazy_gettext
-+from flask_babel import Babel, gettext, ngettext, lazy_gettext
- _ = gettext
- 
- from threading import Lock
---- build/pkgs/sagenb/src/sagenb/flask_version/doc.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/flask_version/doc.py	2018-06-15 16:09:43.966795797 -0600
-@@ -18,7 +18,7 @@ import os
- from flask import Blueprint, url_for, render_template, request, session, redirect, g, current_app
- from .decorators import login_required, guest_or_login_required
- 
--from flask.ext.babel import gettext, ngettext, lazy_gettext
-+from flask_babel import gettext, ngettext, lazy_gettext
- _ = gettext
- 
- doc = Blueprint('doc', 'sagenb.flask_version.doc')
---- build/pkgs/sagenb/src/sagenb/flask_version/settings.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/flask_version/settings.py	2018-06-15 16:09:55.078468143 -0600
-@@ -2,7 +2,7 @@ import os
- import random
- from flask import Blueprint, url_for, render_template, request, session, redirect, g, current_app
- from .decorators import login_required, with_lock
--from flask.ext.babel import gettext, ngettext, lazy_gettext
-+from flask_babel import gettext, ngettext, lazy_gettext
- _ = gettext
- 
- 
---- build/pkgs/sagenb/src/sagenb/flask_version/worksheet_listing.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/flask_version/worksheet_listing.py	2018-06-15 16:07:22.393970396 -0600
-@@ -5,7 +5,7 @@ import os
- import urllib, urlparse
- from flask import Blueprint, url_for, render_template, request, session, redirect, g, current_app
- from .decorators import login_required, guest_or_login_required, with_lock
--from flask.ext.babel import Babel, gettext, ngettext, lazy_gettext
-+from flask_babel import Babel, gettext, ngettext, lazy_gettext
- _ = gettext
- 
- worksheet_listing = Blueprint('worksheet_listing',
---- build/pkgs/sagenb/src/sagenb/flask_version/worksheet.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/flask_version/worksheet.py	2018-06-15 16:07:04.820488591 -0600
-@@ -8,7 +8,7 @@ from flask import Blueprint, make_respon
- from .decorators import login_required, with_lock
- from collections import defaultdict
- from werkzeug.utils import secure_filename
--from flask.ext.babel import Babel, gettext, ngettext, lazy_gettext
-+from flask_babel import Babel, gettext, ngettext, lazy_gettext
- _ = gettext
- 
- from sagenb.notebook.interact import INTERACT_UPDATE_PREFIX
---- build/pkgs/sagenb/src/sagenb/notebook/challenge.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/notebook/challenge.py	2018-06-15 16:10:52.222783112 -0600
-@@ -32,7 +32,7 @@ from six.moves.urllib.parse import urlen
- from six.moves.urllib.request import urlopen, Request
- 
- from sagenb.notebook.template import template
--from flask.ext.babel import gettext, lazy_gettext
-+from flask_babel import gettext, lazy_gettext
- _ = lazy_gettext
- 
- class ChallengeResponse(object):
---- build/pkgs/sagenb/src/sagenb/notebook/conf.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/notebook/conf.py	2018-06-15 16:10:52.223783083 -0600
-@@ -10,7 +10,7 @@ from __future__ import absolute_import
- #  The full text of the GPL is available at:
- #                  http://www.gnu.org/licenses/
- #############################################################################
--from flask.ext.babel import gettext, lazy_gettext
-+from flask_babel import gettext, lazy_gettext
- 
- POS = 'pos'
- DESC = 'desc'
---- build/pkgs/sagenb/src/sagenb/notebook/notebook.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/notebook/notebook.py	2018-06-15 16:10:52.236782699 -0600
-@@ -51,7 +51,7 @@ from . import server_conf  # server conf
- from . import user_conf    # user configuration
- from . import user         # users
- from   .template import template, prettify_time_ago
--from flask.ext.babel import gettext, lazy_gettext
-+from flask_babel import gettext, lazy_gettext
- 
- try:
-     # sage is installed
---- build/pkgs/sagenb/src/sagenb/notebook/register.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/notebook/register.py	2018-06-15 16:10:52.236782699 -0600
-@@ -12,7 +12,7 @@
- """
- Helper functions dealing with the verification of user  
- """
--from flask.ext.babel import gettext as _
-+from flask_babel import gettext as _
- 
- def build_msg(key, username, addr, port, secure):
-     url_prefix = "https" if secure else "http"
---- build/pkgs/sagenb/src/sagenb/notebook/server_conf.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/notebook/server_conf.py	2018-06-15 16:10:52.238782641 -0600
-@@ -8,7 +8,7 @@ from . import conf
- from .conf import (POS, DESC, GROUP, TYPE, CHOICES, T_BOOL, T_INTEGER,
-                    T_CHOICE, T_REAL, T_COLOR, T_STRING, T_LIST, T_INFO)
- from sagenb.misc.misc import get_languages, N_
--from flask.ext.babel import gettext, lazy_gettext
-+from flask_babel import gettext, lazy_gettext
- _ = lazy_gettext
- 
- defaults = {'word_wrap_cols':72,
---- build/pkgs/sagenb/src/sagenb/notebook/template.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/notebook/template.py	2018-06-15 16:10:52.238782641 -0600
-@@ -21,7 +21,7 @@ import jinja2
- import os, re, sys
- 
- from sagenb.misc.misc import SAGE_VERSION, DATA
--from flask.ext.babel import gettext, ngettext, lazy_gettext
-+from flask_babel import gettext, ngettext, lazy_gettext
- from flask import current_app as app
- 
- if 'SAGENB_TEMPLATE_PATH' in os.environ:
---- build/pkgs/sagenb/src/sagenb/notebook/tutorial.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/notebook/tutorial.py	2018-06-15 16:10:52.239782611 -0600
-@@ -348,7 +348,7 @@ the "save" command), and get back to whe
- 
- #####################################
- 
--from flask.ext.babel import lazy_gettext as _
-+from flask_babel import lazy_gettext as _
- 
- notebook_help = [
-     (_('Find Help and Documentation'),
---- build/pkgs/sagenb/src/sagenb/notebook/user_conf.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/notebook/user_conf.py	2018-06-15 16:10:52.239782611 -0600
-@@ -8,7 +8,7 @@ from . import server_conf
- from .conf import (Configuration, POS, DESC, GROUP, TYPE, CHOICES, T_BOOL,
-                    T_INTEGER, T_CHOICE, T_REAL, T_COLOR, T_STRING, T_LIST)
- from sagenb.misc.misc import SAGENB_ROOT, get_languages
--from flask.ext.babel import lazy_gettext
-+from flask_babel import lazy_gettext
- 
- defaults = {'max_history_length':1000,
-             'default_system':'sage',
---- build/pkgs/sagenb/src/sagenb/notebook/worksheet.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/notebook/worksheet.py	2018-06-15 16:10:52.248782346 -0600
-@@ -57,7 +57,7 @@ from sagenb.misc.format import relocate_
- # Imports specifically relevant to the sage notebook
- from .cell import Cell, TextCell
- from .template import template, clean_name, prettify_time_ago
--from flask.ext.babel import gettext, lazy_gettext
-+from flask_babel import gettext, lazy_gettext
- _ = gettext
- 
- # Set some constants that will be used for regular expressions below.
-@@ -4527,7 +4527,7 @@ def convert_time_to_string(t):
-     Converts ``t`` (in Unix time) to a locale-specific string
-     describing the time and date.
-     """
--    from flask.ext.babel import format_datetime
-+    from flask_babel import format_datetime
-     import datetime, time
-     try:
-         return format_datetime(datetime.datetime.fromtimestamp(float(t)))

sagemath-gap-hap.patch

@@ -1,23 +0,0 @@
-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	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:
-         gap.load_package("hap")
-+        try:
-+            gap.load_package("hap")
-+        except Exception:
-+            raise RuntimeError("gap-hap package failed to load.")
- 
- def hap_decorator(f):
-     """
-@@ -191,8 +195,6 @@ def hap_decorator(f):
-     """
-     @wraps(f)
-     def wrapped(self, n, p=0):
--        if not is_package_installed('gap_packages'):
--            raise PackageNotFoundError("gap_packages")
-         load_hap()
-         from sage.arith.all import is_prime
-         if not (p == 0 or is_prime(p)):

sagemath-includes.patch

@@ -1,6 +1,6 @@
 diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig	2018-05-22 15:41:19.892745329 -0600
+--- src/module_list.py.orig	2018-08-29 10:41:05.127643255 -0600
-+++ src/module_list.py	2018-05-22 15:42:40.289863491 -0600
++++ src/module_list.py	2018-08-29 10:44:16.376279329 -0600
 @@ -45,6 +45,9 @@ zlib_libs = zlib_pc['libraries']
  zlib_library_dirs = zlib_pc['library_dirs']
  zlib_include_dirs = zlib_pc['include_dirs']
@@ -36,7 +36,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('*', sources = ['sage/algebras/finite_dimensional_algebras/*.pyx']),
  
-@@ -519,7 +531,8 @@ ext_modules = [
+@@ -526,7 +538,8 @@ ext_modules = [
                                                          [])),
  
      Extension('sage.libs.lrcalc.lrcalc',
@@ -46,7 +46,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      OptionalExtension("sage.libs.meataxe",
                sources = ['sage/libs/meataxe.pyx'],
-@@ -541,23 +554,28 @@ ext_modules = [
+@@ -548,23 +561,28 @@ ext_modules = [
                sources = ['sage/libs/readline.pyx'],
                libraries = ['readline']),
  
@@ -80,7 +80,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      ###################################
      ##
-@@ -565,7 +583,8 @@ ext_modules = [
+@@ -572,7 +590,8 @@ ext_modules = [
      ##
      ###################################
  
@@ -90,7 +90,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      ###################################
      ##
-@@ -745,7 +764,8 @@ ext_modules = [
+@@ -744,7 +763,8 @@ ext_modules = [
  
      Extension("sage.matrix.matrix_complex_ball_dense",
                ["sage/matrix/matrix_complex_ball_dense.pyx"],
@@ -100,7 +100,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.matrix.matrix_complex_double_dense',
                sources = ['sage/matrix/matrix_complex_double_dense.pyx']),
-@@ -753,6 +773,7 @@ ext_modules = [
+@@ -752,6 +772,7 @@ ext_modules = [
      Extension('sage.matrix.matrix_cyclo_dense',
                sources = ['sage/matrix/matrix_cyclo_dense.pyx'],
                language = "c++",
@@ -108,7 +108,7 @@ diff -up src/module_list.py.orig src/module_list.py
                libraries=['ntl']),
  
      Extension('sage.matrix.matrix_gap',
-@@ -815,6 +836,7 @@ ext_modules = [
+@@ -814,6 +835,7 @@ ext_modules = [
                sources = ['sage/matrix/matrix_modn_sparse.pyx']),
  
      Extension('sage.matrix.matrix_mpolynomial_dense',
@@ -116,7 +116,7 @@ diff -up src/module_list.py.orig src/module_list.py
                sources = ['sage/matrix/matrix_mpolynomial_dense.pyx']),
  
      Extension('sage.matrix.matrix_polynomial_dense',
-@@ -1112,7 +1134,8 @@ ext_modules = [
+@@ -1111,7 +1133,8 @@ ext_modules = [
                language = 'c++'),
  
      Extension("sage.rings.complex_arb",
@@ -126,7 +126,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.rings.complex_double',
                sources = ['sage/rings/complex_double.pyx'],
-@@ -1182,7 +1205,8 @@ ext_modules = [
+@@ -1181,7 +1204,8 @@ ext_modules = [
                sources = ['sage/rings/real_interval_absolute.pyx']),
  
      Extension("sage.rings.real_arb",
@@ -136,7 +136,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.rings.real_lazy',
                sources = ['sage/rings/real_lazy.pyx']),
-@@ -1265,6 +1289,7 @@ ext_modules = [
+@@ -1264,6 +1288,7 @@ ext_modules = [
  
      Extension('sage.rings.number_field.number_field_element_quadratic',
                sources = ['sage/rings/number_field/number_field_element_quadratic.pyx'],
@@ -144,7 +144,7 @@ diff -up src/module_list.py.orig src/module_list.py
                libraries=['ntl'],
                language = 'c++'),
  
-@@ -1387,12 +1412,15 @@ ext_modules = [
+@@ -1386,12 +1411,15 @@ ext_modules = [
                sources = ['sage/rings/polynomial/multi_polynomial.pyx']),
  
      Extension('sage.rings.polynomial.multi_polynomial_ideal_libsingular',
@@ -159,8 +159,8 @@ diff -up src/module_list.py.orig src/module_list.py
 +              include_dirs = singular_incs,
                sources = ['sage/rings/polynomial/multi_polynomial_libsingular.pyx']),
  
-     Extension('sage.rings.polynomial.multi_polynomial_ring_generic',
+     Extension('sage.rings.polynomial.multi_polynomial_ring_base',
-@@ -1405,7 +1433,8 @@ ext_modules = [
+@@ -1404,7 +1432,8 @@ ext_modules = [
                sources = ['sage/rings/polynomial/polydict.pyx']),
  
      Extension('sage.rings.polynomial.polynomial_complex_arb',
@@ -171,8 +171,8 @@ diff -up src/module_list.py.orig src/module_list.py
      Extension('sage.rings.polynomial.polynomial_compiled',
                 sources = ['sage/rings/polynomial/polynomial_compiled.pyx']),
 diff -up src/setup.py.orig src/setup.py
---- src/setup.py.orig	2018-05-22 15:41:19.893745318 -0600
+--- src/setup.py.orig	2018-08-29 08:35:19.955079610 -0600
-+++ src/setup.py	2018-05-22 15:41:27.805658536 -0600
++++ src/setup.py	2018-08-29 10:44:16.376279329 -0600
 @@ -85,6 +85,7 @@ except KeyError:
  
  # search for dependencies and add to gcc -I<path>

sagemath-jmol.patch

@@ -1,6 +1,6 @@
 diff -up src/sage/interfaces/jmoldata.py.orig src/sage/interfaces/jmoldata.py
---- src/sage/interfaces/jmoldata.py.orig	2018-05-05 16:21:24.000000000 -0600
+--- src/sage/interfaces/jmoldata.py.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/interfaces/jmoldata.py	2018-05-16 13:30:58.803927423 -0600
++++ src/sage/interfaces/jmoldata.py	2018-08-29 08:47:39.203938604 -0600
 @@ -148,8 +148,6 @@ class JmolData(SageObject):
              sage: print(os.path.exists(testfile)) # optional -- java
              True
@@ -8,9 +8,9 @@ diff -up src/sage/interfaces/jmoldata.py.orig src/sage/interfaces/jmoldata.py
 -        # Set up paths, file names and scripts
 -        jmolpath = os.path.join(SAGE_LOCAL, "share", "jmol", "JmolData.jar")
          target_native = targetfile
-         import sys
+ 
          if sys.platform == 'cygwin':
-@@ -174,10 +172,8 @@ class JmolData(SageObject):
+@@ -173,10 +171,8 @@ class JmolData(SageObject):
              env = dict(os.environ)
              env['LC_ALL'] = 'C'
              env['LANG'] = 'C'

sagemath-libgap.patch

@@ -1,6 +1,30 @@
+diff -up src/sage/env.py.orig src/sage/env.py
+--- src/sage/env.py.orig	2018-08-03 05:10:08.000000000 -0600
++++ src/sage/env.py	2018-08-29 11:25:26.833962117 -0600
+@@ -164,7 +164,7 @@ _add_variable_or_fallback('CONWAY_POLYNO
+ _add_variable_or_fallback('GRAPHS_DATA_DIR',  opj('$SAGE_SHARE','graphs'))
+ _add_variable_or_fallback('ELLCURVE_DATA_DIR',opj('$SAGE_SHARE','ellcurves'))
+ _add_variable_or_fallback('POLYTOPE_DATA_DIR',opj('$SAGE_SHARE','reflexive_polytopes'))
+-_add_variable_or_fallback('GAP_ROOT_DIR',     opj('$SAGE_LOCAL','gap','latest'))
++_add_variable_or_fallback('GAP_ROOT_DIR',     opj('usr','lib','gap'))
+ _add_variable_or_fallback('THEBE_DIR',        opj('$SAGE_SHARE','thebe'))
+ 
+ # locate singular shared object
+diff -up src/sage/interfaces/gap.py.orig src/sage/interfaces/gap.py
+--- src/sage/interfaces/gap.py.orig	2018-08-03 05:10:08.000000000 -0600
++++ src/sage/interfaces/gap.py	2018-08-29 11:21:43.180584324 -0600
+@@ -197,7 +197,7 @@ import string
+ 
+ WORKSPACE = gap_workspace_file()
+ 
+-GAP_BINARY = os.path.join(SAGE_LOCAL, 'bin', 'gap')
++GAP_BINARY = os.path.join('usr', 'bin', 'gap')
+ 
+ first_try = True
+ 
 diff -up src/sage/libs/gap/test/main.c.orig src/sage/libs/gap/test/main.c
---- src/sage/libs/gap/test/main.c.orig	2017-07-21 13:10:16.000000000 -0600
+--- src/sage/libs/gap/test/main.c.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/libs/gap/test/main.c	2017-11-24 10:40:06.024865775 -0700
++++ src/sage/libs/gap/test/main.c	2018-08-29 10:38:22.512653256 -0600
 @@ -22,7 +22,7 @@ void eval(char* cmd) {
    libgap_start_interaction(cmd);
  
@@ -11,40 +35,29 @@ diff -up src/sage/libs/gap/test/main.c.orig src/sage/libs/gap/test/main.c
    char* out = libgap_get_output();
    libgap_exit();
 diff -up src/sage/libs/gap/util.pyx.orig src/sage/libs/gap/util.pyx
---- src/sage/libs/gap/util.pyx.orig	2017-07-21 13:10:16.000000000 -0600
+--- src/sage/libs/gap/util.pyx.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/libs/gap/util.pyx	2017-11-24 10:41:12.757621519 -0700
++++ src/sage/libs/gap/util.pyx	2018-08-29 11:32:06.654205922 -0600
-@@ -22,6 +22,8 @@ from sage.interfaces.gap_workspace impor
+@@ -25,6 +25,8 @@ from sage.cpython.string cimport str_to_
+ from sage.interfaces.gap_workspace import prepare_workspace_dir
  from sage.env import SAGE_LOCAL, GAP_ROOT_DIR
- from .element cimport *
  
 +import re
 +
  
  ############################################################################
  ### Hooking into the GAP memory management #################################
-@@ -160,17 +162,9 @@ def gap_root():
+@@ -164,7 +166,7 @@ def gap_root():
  
          sage: from sage.libs.gap.util import gap_root
          sage: gap_root()   # random output
 -        '/home/vbraun/opt/sage-5.3.rc0/local/gap/latest'
 +        '/usr/lib/gap'
      """
--    import os.path
+     import os.path
--    if os.path.exists(GAP_ROOT_DIR):
+     if os.path.exists(GAP_ROOT_DIR):
--        return GAP_ROOT_DIR
+@@ -232,6 +234,7 @@ cdef initialize():
--    print('The gap-4.5.5.spkg (or later) seems to be not installed!')
--    gap_sh = open(os.path.join(SAGE_LOCAL, 'bin', 'gap')).read().splitlines()
--    gapdir = filter(lambda dir:dir.strip().startswith('GAP_DIR'), gap_sh)[0]
--    gapdir = gapdir.split('"')[1]
--    gapdir = gapdir.replace('$SAGE_LOCAL', SAGE_LOCAL)
--    return gapdir
-+    return '/usr/lib/gap'
- 
- 
- cdef initialize():
-@@ -224,6 +218,7 @@ cdef initialize():
      libgap_initialize(argc, argv)
-     gap_error_msg = str(libgap_get_output())
+     gap_error_msg = char_to_str(libgap_get_output())
      libgap_finish_interaction()
 +    gap_error_msg = re.sub(r'#I.*\n?', '', gap_error_msg, flags=re.MULTILINE)
      if gap_error_msg:

sagemath-lrslib.patch

@@ -1,13 +0,0 @@
-diff -up src/sage/geometry/polyhedron/base.py.orig src/sage/geometry/polyhedron/base.py
---- 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 PackageNotFoundError('lrslib')
--
-         from sage.misc.temporary_file import tmp_filename
-         from subprocess import Popen, PIPE
-         in_str = self.cdd_Vrepresentation()

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	2018-05-05 16:21:22.000000000 -0600
+--- src/bin/sage-maxima.lisp.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/bin/sage-maxima.lisp	2018-05-16 13:25:51.499101380 -0600
++++ src/bin/sage-maxima.lisp	2018-08-29 08:45:21.302643791 -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	2018-05-05 16:21:24.000000000 -0600
+--- src/sage/interfaces/maxima.py.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/interfaces/maxima.py	2018-05-16 13:27:01.240157806 -0600
++++ src/sage/interfaces/maxima.py	2018-08-29 08:47:09.779302448 -0600
-@@ -556,7 +556,7 @@ class Maxima(MaximaAbstract, Expect):
+@@ -546,7 +546,7 @@ 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 -p "{0}"'.format(STARTUP),
-+                        command = 'maxima --disable-readline --userdir="%s" -p "%s"'%(SAGE_MAXIMA_DIR,STARTUP),
++                        command = 'maxima --disable-readline -p "{0}"'.format(STARTUP),
                          env = {'TMPDIR': str(ECL_TMP)},
                          script_subdirectory = script_subdirectory,
                          restart_on_ctrlc = False,
-@@ -624,7 +624,8 @@ class Maxima(MaximaAbstract, Expect):
+@@ -615,7 +615,8 @@ class Maxima(MaximaAbstract, Expect):
  
          # Remove limit on the max heapsize (since otherwise it defaults
          # to 256MB with ECL).

sagemath-mpfr.patch

@@ -1,6 +1,6 @@
 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.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/libs/mpfr/__init__.pxd	2018-05-25 15:01:25.576043678 -0600
++++ src/sage/libs/mpfr/__init__.pxd	2018-08-29 10:41:34.027286042 -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)
@@ -10,8 +10,8 @@ diff -up src/sage/libs/mpfr/__init__.pxd.orig src/sage/libs/mpfr/__init__.pxd
      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.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/sage/rings/complex_mpc.pyx	2018-05-25 15:02:11.567712409 -0600
++++ src/sage/rings/complex_mpc.pyx	2018-08-29 10:41:34.027286042 -0600
 @@ -2221,7 +2221,7 @@ cdef class MPComplexNumber(sage.structur
          cdef RealNumber a,r
          a = self.argument()/n
@@ -22,8 +22,8 @@ diff -up src/sage/rings/complex_mpc.pyx.orig src/sage/rings/complex_mpc.pyx
          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.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/sage/rings/complex_number.pyx	2018-05-25 15:01:52.328850983 -0600
++++ src/sage/rings/complex_number.pyx	2018-08-29 10:41:34.027286042 -0600
 @@ -2276,7 +2276,7 @@ cdef class ComplexNumber(sage.structure.
          rho = abs(self)
          arg = self.argument() / n
@@ -34,9 +34,9 @@ diff -up src/sage/rings/complex_number.pyx.orig src/sage/rings/complex_number.py
          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.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/sage/rings/real_mpfr.pyx	2018-05-25 11:33:48.009144647 -0600
++++ src/sage/rings/real_mpfr.pyx	2018-08-29 10:41:34.028286030 -0600
-@@ -5369,7 +5369,7 @@ cdef class RealNumber(sage.structure.ele
+@@ -5370,7 +5370,7 @@ cdef class RealNumber(sage.structure.ele
          if algorithm == 1:
              x = self._new()
              sig_on()

sagemath-nauty.patch

@@ -1,12 +1,12 @@
 diff -up src/sage/graphs/graph_generators.py.orig src/sage/graphs/graph_generators.py
---- src/sage/graphs/graph_generators.py.orig	2018-05-05 16:21:24.000000000 -0600
+--- src/sage/graphs/graph_generators.py.orig	2018-08-29 08:52:26.099392035 -0600
-+++ src/sage/graphs/graph_generators.py	2018-05-16 13:35:59.299778933 -0600
++++ src/sage/graphs/graph_generators.py	2018-08-29 08:56:44.782205619 -0600
-@@ -886,7 +886,7 @@ class GraphGenerators():
+@@ -906,7 +906,7 @@ class GraphGenerators():
-             >A geng -d0D3 n=4 e=0-6
+         else:
-         """
+             enc_kwargs = {'encoding': 'latin-1'}
-         import subprocess
+ 
 -        sp = subprocess.Popen("geng {0}".format(options), shell=True,
 +        sp = subprocess.Popen("nauty-geng {0}".format(options), shell=True,
                                stdin=subprocess.PIPE, stdout=subprocess.PIPE,
-                               stderr=subprocess.PIPE, close_fds=True)
+                               stderr=subprocess.PIPE, close_fds=True,
-         if debug:
+                               **enc_kwargs)

sagemath-nofstring.patch

@@ -1,6 +1,6 @@
 diff -up src/sage/arith/multi_modular.pyx.orig src/sage/arith/multi_modular.pyx
---- src/sage/arith/multi_modular.pyx.orig	2018-05-05 16:21:22.000000000 -0600
+--- src/sage/arith/multi_modular.pyx.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/arith/multi_modular.pyx	2018-05-18 09:39:53.247690061 -0600
++++ src/sage/arith/multi_modular.pyx	2018-08-29 10:44:04.624424587 -0600
 @@ -173,9 +173,9 @@ cdef class MultiModularBasis_base(object
              ArithmeticError: The inverse of 6 modulo 10 is not defined.
          """
@@ -23,9 +23,9 @@ diff -up src/sage/arith/multi_modular.pyx.orig src/sage/arith/multi_modular.pyx
  
          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	2018-05-05 16:21:25.000000000 -0600
+--- src/sage/rings/finite_rings/integer_mod.pyx.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/sage/rings/finite_rings/integer_mod.pyx	2018-05-18 09:41:48.412094505 -0600
++++ src/sage/rings/finite_rings/integer_mod.pyx	2018-08-29 10:44:04.624424587 -0600
-@@ -457,7 +457,7 @@ cdef class IntegerMod_abstract(FiniteRin
+@@ -468,7 +468,7 @@ cdef class IntegerMod_abstract(FiniteRin
          from .integer_mod_ring import IntegerModRing
          R = IntegerModRing(modulus)
          if (<Element>self)._parent._IntegerModRing_generic__order % R.order():
@@ -35,8 +35,8 @@ diff -up src/sage/rings/finite_rings/integer_mod.pyx.orig src/sage/rings/finite_
  
      def is_nilpotent(self):
 diff -up src/sage/structure/parent.pyx.orig src/sage/structure/parent.pyx
---- src/sage/structure/parent.pyx.orig	2018-05-05 16:21:26.000000000 -0600
+--- src/sage/structure/parent.pyx.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/sage/structure/parent.pyx	2018-05-18 09:42:38.685397989 -0600
++++ src/sage/structure/parent.pyx	2018-08-29 10:44:04.625424574 -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:
@@ -47,8 +47,8 @@ diff -up src/sage/structure/parent.pyx.orig src/sage/structure/parent.pyx
              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	2018-05-05 16:21:26.000000000 -0600
+--- src/sage/symbolic/ring.pyx.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/sage/symbolic/ring.pyx	2018-05-18 09:43:07.395000229 -0600
++++ src/sage/symbolic/ring.pyx	2018-08-29 10:44:04.625424574 -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()))

sagemath-qepcad.patch

@@ -1,12 +1,12 @@
 diff -up src/sage/interfaces/qepcad.py.orig src/sage/interfaces/qepcad.py
---- src/sage/interfaces/qepcad.py.orig	2018-05-05 16:21:24.000000000 -0600
+--- src/sage/interfaces/qepcad.py.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/interfaces/qepcad.py	2018-05-16 13:58:34.360913275 -0600
++++ src/sage/interfaces/qepcad.py	2018-08-29 10:43:25.856903772 -0600
 @@ -530,7 +530,7 @@ TESTS:
  
  Check the qepcad configuration file::
  
--    sage: with open(os.path.join(SAGE_LOCAL, 'default.qepcadrc')) as f:
+-    sage: with open(os.path.join(SAGE_LOCAL, 'default.qepcadrc')) as f:  # optional - qepcad
-+    sage: with open('/usr/share/qepcad/default.qepcadrc')) as f:
++    sage: with open('/usr/share/qepcad/default.qepcadrc')) as f:  # optional - qepcad
      ....:     f.readlines()[-1]
      'SINGULAR .../bin\n'
  
@@ -52,8 +52,8 @@ diff -up src/sage/interfaces/qepcad.py.orig src/sage/interfaces/qepcad.py
  
      cache = {}
  
--    with open('%s/bin/qepcad.help'%SAGE_LOCAL) as help:
+-    with open(os.path.join(SAGE_LOCAL, 'bin', 'qepcad.help')) as help:
-+    with open('%s/bin/qepcad.help'%QEPCAD_LOCAL) as help:
++    with open(os.path.join(QEPCAD_LOCAL, 'bin', 'qepcad.help')) as help:
          assert(help.readline().strip() == '@')
  
          while True:

sagemath-readonly.patch

@@ -1,6 +1,7 @@
---- src/sage/all.py.orig	2018-05-05 16:21:22.000000000 -0600
+diff -up src/sage/all.py.orig src/sage/all.py
-+++ src/sage/all.py	2018-05-16 13:25:28.300415250 -0600
+--- src/sage/all.py.orig	2018-08-03 05:10:08.000000000 -0600
-@@ -290,11 +290,11 @@ def _write_started_file():
++++ src/sage/all.py	2018-08-29 08:45:06.117831555 -0600
+@@ -284,11 +284,11 @@ def _write_started_file():
  
      Check that the file exists when Sage is running::
  

sagemath-rpmbuild.patch

@@ -1,6 +1,6 @@
 diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig	2018-05-16 12:35:55.223524926 -0600
+--- src/module_list.py.orig	2018-08-29 08:34:50.846439644 -0600
-+++ src/module_list.py	2018-05-16 13:13:20.467262594 -0600
++++ src/module_list.py	2018-08-29 08:35:19.927079956 -0600
 @@ -3,7 +3,7 @@ from glob import glob
  from distutils.extension import Extension
  from sage.env import SAGE_LOCAL
@@ -11,8 +11,8 @@ diff -up src/module_list.py.orig src/module_list.py
  #########################################################
  ### pkg-config setup
 diff -up src/sage/misc/cython.py.orig src/sage/misc/cython.py
---- src/sage/misc/cython.py.orig	2018-05-16 13:13:20.468262581 -0600
+--- src/sage/misc/cython.py.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/sage/misc/cython.py	2018-05-16 13:16:29.207708998 -0600
++++ src/sage/misc/cython.py	2018-08-29 08:35:19.954079622 -0600
 @@ -601,7 +601,7 @@ def cython(filename, verbose=0, compile_
      ext = Extension(name,
                      sources=[pyxfile] + extra_sources,
@@ -23,8 +23,8 @@ diff -up src/sage/misc/cython.py.orig src/sage/misc/cython.py
                      language=language)
  
 diff -up src/setup.py.orig src/setup.py
---- src/setup.py.orig	2018-05-05 16:21:27.000000000 -0600
+--- src/setup.py.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/setup.py	2018-05-16 13:17:40.774740719 -0600
++++ src/setup.py	2018-08-29 08:35:19.955079610 -0600
 @@ -370,9 +370,8 @@ class sage_build_cython(Command):
              # Debugging
              gdb_debug=self.debug,
@@ -47,9 +47,9 @@ diff -up src/setup.py.orig src/setup.py
  
      def install_kernel_spec(self):
          """
-@@ -897,40 +893,6 @@ class sage_install(install):
+@@ -900,40 +896,6 @@ class sage_install(install):
-         from sage.repl.ipython_kernel.install import SageKernelSpec
+         # the install_data directory for installing our Jupyter files.
-         SageKernelSpec.update()
+         SageKernelSpec.update(prefix=self.install_data)
  
 -    def clean_stale_files(self):
 -        """

sagemath-sagedoc.patch

@@ -1,6 +1,6 @@
 diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
---- src/sage/doctest/control.py.orig	2018-05-05 16:21:23.000000000 -0600
+--- src/sage/doctest/control.py.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/doctest/control.py	2018-05-16 13:20:01.420837824 -0600
++++ src/sage/doctest/control.py	2018-08-29 08:36:07.805487927 -0600
 @@ -102,7 +102,6 @@ class DocTestDefaults(SageObject):
          self.valgrind = False
          self.massif = False
@@ -46,9 +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	2018-05-05 16:21:24.000000000 -0600
+--- src/sage/interfaces/singular.py.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/interfaces/singular.py	2018-05-16 13:20:01.421837810 -0600
++++ src/sage/interfaces/singular.py	2018-08-29 08:36:07.818487766 -0600
-@@ -2258,7 +2258,7 @@ def generate_docstring_dictionary():
+@@ -2262,7 +2262,7 @@ def generate_docstring_dictionary():
      nodes.clear()
      node_names.clear()
  
@@ -58,9 +58,9 @@ 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	2018-05-05 16:21:26.000000000 -0600
+--- src/sage_setup/docbuild/ext/multidocs.py.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/sage_setup/docbuild/ext/multidocs.py	2018-05-16 13:20:01.421837810 -0600
++++ src/sage_setup/docbuild/ext/multidocs.py	2018-08-29 08:36:07.829487630 -0600
-@@ -82,8 +82,11 @@ def merge_environment(app, env):
+@@ -84,8 +84,11 @@ def merge_environment(app, env):
              for ind in newalldoc:
                  # treat subdocument source as orphaned file and don't complain
                  md = env.metadata.get(ind, dict())
@@ -75,9 +75,9 @@ diff -up src/sage_setup/docbuild/ext/multidocs.py.orig src/sage_setup/docbuild/e
              newcite = {}
              citations = docenv.domaindata["std"]["citations"]
 diff -up src/sage_setup/docbuild/__init__.py.orig src/sage_setup/docbuild/__init__.py
---- src/sage_setup/docbuild/__init__.py.orig	2018-05-05 16:21:26.000000000 -0600
+--- src/sage_setup/docbuild/__init__.py.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/sage_setup/docbuild/__init__.py	2018-05-16 13:20:01.422837797 -0600
++++ src/sage_setup/docbuild/__init__.py	2018-08-29 08:36:07.837487531 -0600
-@@ -242,13 +242,14 @@ if NUM_THREADS > 1:
+@@ -272,13 +272,14 @@ 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)

sagemath-sagenb.patch

@@ -1,6 +1,6 @@
 diff -up build/pkgs/sagenb/src/sagenb/flask_version/base.py.orig build/pkgs/sagenb/src/sagenb/flask_version/base.py
---- build/pkgs/sagenb/src/sagenb/flask_version/base.py.orig	2017-11-08 08:11:53.546180946 -0500
+--- build/pkgs/sagenb/src/sagenb/flask_version/base.py.orig	2018-01-24 04:17:47.000000000 -0700
-+++ build/pkgs/sagenb/src/sagenb/flask_version/base.py	2017-11-08 08:13:13.400184004 -0500
++++ build/pkgs/sagenb/src/sagenb/flask_version/base.py	2018-08-29 08:44:38.823169061 -0600
 @@ -7,8 +7,6 @@ from functools import partial
  from flask import Flask, Blueprint, url_for, request, session, redirect, g, make_response, current_app, render_template
  from .decorators import login_required, guest_or_login_required, with_lock
@@ -40,8 +40,8 @@ diff -up build/pkgs/sagenb/src/sagenb/flask_version/base.py.orig build/pkgs/sage
          mimetypes.add_type('text/plain','.jmol')
  
 diff -up build/pkgs/sagenb/src/sagenb/misc/misc.py.orig build/pkgs/sagenb/src/sagenb/misc/misc.py
---- build/pkgs/sagenb/src/sagenb/misc/misc.py.orig	2017-11-08 08:13:24.162184416 -0500
+--- build/pkgs/sagenb/src/sagenb/misc/misc.py.orig	2017-06-02 16:24:20.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/misc/misc.py	2017-11-08 08:13:41.928185096 -0500
++++ build/pkgs/sagenb/src/sagenb/misc/misc.py	2018-08-29 08:44:38.823169061 -0600
 @@ -184,7 +184,8 @@ def pad_zeros(s, size=3):
  
  SAGENB_ROOT = os.path.split(resource_filename(__name__, ''))[0]
@@ -53,8 +53,8 @@ diff -up build/pkgs/sagenb/src/sagenb/misc/misc.py.orig build/pkgs/sagenb/src/sa
  if 'DOT_SAGENB' in os.environ:
      DOT_SAGENB = os.environ['DOT_SAGENB']
 diff -up build/pkgs/sagenb/src/sagenb/notebook/cell.py.orig build/pkgs/sagenb/src/sagenb/notebook/cell.py
---- build/pkgs/sagenb/src/sagenb/notebook/cell.py.orig	2017-11-08 08:13:51.658185469 -0500
+--- build/pkgs/sagenb/src/sagenb/notebook/cell.py.orig	2018-01-24 04:17:38.000000000 -0700
-+++ build/pkgs/sagenb/src/sagenb/notebook/cell.py	2017-11-08 08:14:22.016186631 -0500
++++ build/pkgs/sagenb/src/sagenb/notebook/cell.py	2018-08-29 08:44:38.823169061 -0600
 @@ -2384,8 +2384,8 @@ class Cell(Cell_generic):
              with open(jmol_name, 'r') as f:
                  jmol_script = f.read()
@@ -67,9 +67,9 @@ diff -up build/pkgs/sagenb/src/sagenb/notebook/cell.py.orig build/pkgs/sagenb/sr
                  f.write(jmol_script)
   
 diff -up build/pkgs/sagenb/src/sagenb/notebook/run_notebook.py.orig build/pkgs/sagenb/src/sagenb/notebook/run_notebook.py
---- build/pkgs/sagenb/src/sagenb/notebook/run_notebook.py.orig	2017-11-08 08:14:30.274186948 -0500
+--- build/pkgs/sagenb/src/sagenb/notebook/run_notebook.py.orig	2018-05-22 10:16:28.000000000 -0600
-+++ build/pkgs/sagenb/src/sagenb/notebook/run_notebook.py	2017-11-08 08:15:04.624188263 -0500
++++ build/pkgs/sagenb/src/sagenb/notebook/run_notebook.py	2018-08-29 08:44:38.824169048 -0600
-@@ -49,12 +49,11 @@ sagenb.notebook.misc.DIR = %(cwd)r #We s
+@@ -53,12 +53,11 @@ sagenb.notebook.misc.DIR = %(cwd)r #We s
  # Flask #
  #########
  import os, sys, random

sagemath-scripts.patch

@@ -1,7 +1,7 @@
 diff -up src/bin/sage.orig src/bin/sage
---- src/bin/sage.orig	2018-05-05 16:21:22.000000000 -0600
+--- src/bin/sage.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/bin/sage	2018-05-16 12:29:16.699989835 -0600
++++ src/bin/sage	2018-08-29 08:32:06.325478480 -0600
-@@ -13,13 +13,10 @@ usage() {
+@@ -26,13 +26,10 @@ 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"
@@ -15,15 +15,15 @@ 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 +24,6 @@ usage() {
+@@ -40,7 +37,6 @@ usage() {
      echo "                         'default', 'sagenb', 'jupyter', and 'export')"
      echo "                         Current default is 'export' from sagenb to jupyter"
      echo "  -n, --notebook      -- shortcut for --notebook=default"
 -    echo "  -optional           -- list all optional packages that can be installed"
-     echo "  -python [...]       -- run the Python 2 interpreter"
+     echo "  -python [...]       -- run the Python interpreter"
+     echo "  -python2 [...]      -- run the Python 2 interpreter"
      echo "  -python3 [...]      -- run the Python 3 interpreter"
-     echo "  -R [...]            -- run Sage's R with given arguments"
+@@ -58,10 +54,6 @@ 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"
@@ -34,7 +34,7 @@ diff -up src/bin/sage.orig src/bin/sage
      echo "  -v, -version        -- display Sage version information"
      exit 0
  }
-@@ -66,11 +58,8 @@ usage_advanced() {
+@@ -81,11 +73,8 @@ 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"
@@ -46,7 +46,7 @@ diff -up src/bin/sage.orig src/bin/sage
  
      echo
      ####  1.......................26..................................................78
-@@ -82,8 +71,6 @@ usage_advanced() {
+@@ -97,8 +86,6 @@ usage_advanced() {
      echo "                         See the output of sage --notebook --help"
      echo "                         for more details and examples of how to pass"
      echo "                         optional arguments"
@@ -55,7 +55,7 @@ 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"
-@@ -103,18 +90,11 @@ usage_advanced() {
+@@ -118,18 +105,11 @@ 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"
@@ -74,7 +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"
-@@ -126,55 +106,7 @@ usage_advanced() {
+@@ -141,55 +121,7 @@ usage_advanced() {
      echo
      ####  1.......................26..................................................78
      ####  |.....................--.|...................................................|
@@ -131,7 +131,7 @@ diff -up src/bin/sage.orig src/bin/sage
      echo "  -startuptime [module] -- display how long each component of Sage takes to"
      echo "                         start up; optionally specify a module to get more"
      echo "                         details about that particular module"
-@@ -205,7 +137,6 @@ usage_advanced() {
+@@ -220,7 +152,6 @@ usage_advanced() {
      echo "  -coverage <files>   -- give info about doctest coverage of files"
      echo "  -coverageall        -- give summary info about doctest coverage of all"
      echo "                         files in the Sage library"
@@ -139,7 +139,7 @@ diff -up src/bin/sage.orig src/bin/sage
      echo "  -search_src <string> -- search through all the Sage library code for string"
      echo "  -search_doc <string> -- search through the Sage documentation for string"
      echo "  -grep <string>      -- same as -search_src"
-@@ -227,16 +158,6 @@ usage_advanced() {
+@@ -244,16 +175,6 @@ usage_advanced() {
      echo
      ####  1.......................26..................................................78
      ####  |.....................--.|...................................................|
@@ -156,7 +156,7 @@ diff -up src/bin/sage.orig src/bin/sage
      echo "Valgrind memory debugging:"
      echo "  -cachegrind         -- run Sage using Valgrind's cachegrind tool.  The log"
      echo "                         files are named sage-cachegrind.PID can be found in"
-@@ -250,9 +171,6 @@ usage_advanced() {
+@@ -267,9 +188,6 @@ usage_advanced() {
      echo "  -memcheck           -- run Sage using Valgrind's memcheck tool.  The log"
      echo "                         files are named sage-memcheck.PID can be found in"
      echo "                         $DOT_SAGE"
@@ -166,11 +166,10 @@ 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'."
-@@ -261,128 +179,6 @@ usage_advanced() {
+@@ -279,115 +197,6 @@ usage_advanced() {
- }
  
  
--#####################################################################
+ #####################################################################
 -# Special options to be processed without sage-env
 -#####################################################################
 -
@@ -279,6 +278,14 @@ diff -up src/bin/sage.orig src/bin/sage
 -fi
 -
 -
+-#####################################################################
+ # Report information about the Sage environment
+ #####################################################################
+ 
+@@ -416,35 +225,8 @@ if [ $# -gt 0 ]; then
+ fi
+ 
+ 
 -#####################################################################
 -# Source sage-env ($0 is the name of this "sage" script, so we can just
 -# append -env to that). We redirect stdout to stderr, which is safer
@@ -292,11 +299,6 @@ diff -up src/bin/sage.orig src/bin/sage
 -fi
 -
 -
- if [ $# -gt 0 ]; then
-   if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then
-      usage
-@@ -394,20 +190,6 @@ fi
- 
  # Prepare for running Sage, either interactively or non-interactively.
  sage_setup() {
 -    # Check that we're not in a source tarball which hasn't been built yet (#13561).
@@ -316,7 +318,7 @@ diff -up src/bin/sage.orig src/bin/sage
      if [ ! -d "$IPYTHONDIR" ]; then
          # make sure that $DOT_SAGE exists so that ipython will happily
          # create its config directories there.  If DOT_SAGE doesn't
-@@ -418,20 +200,6 @@ sage_setup() {
+@@ -455,20 +237,6 @@ sage_setup() {
  }
  
  
@@ -337,7 +339,7 @@ diff -up src/bin/sage.orig src/bin/sage
  # Start an interactive Sage session, this function never returns.
  interactive_sage() {
      sage_setup
-@@ -536,16 +304,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
+@@ -552,16 +320,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
      exec ecl "$@"
  fi
  
@@ -354,7 +356,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
      shift
      exec maxima "$@"
-@@ -571,11 +329,6 @@ if [ "$1" = '-pip' -o "$1" = '--pip' ];
+@@ -587,11 +345,6 @@ if [ "$1" = '-pip' -o "$1" = '--pip' ];
      exec pip "$@"
  fi
  
@@ -365,8 +367,8 @@ diff -up src/bin/sage.orig src/bin/sage
 -
  if [ "$1" = '-python' -o "$1" = '--python' ]; then
      shift
-     exec python "$@"
+     if [ "$SAGE_PYTHON3" = 'yes' ]; then
-@@ -606,16 +359,6 @@ if [ "$1" = '-ipython3' -o "$1" = '--ipy
+@@ -626,16 +379,6 @@ if [ "$1" = '-ipython3' -o "$1" = '--ipy
      exec ipython3 "$@"
  fi
  
@@ -383,7 +385,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
      # AUTHORS:
      # - Carl Witty and William Stein: initial version
-@@ -735,20 +478,6 @@ EOF
+@@ -755,20 +498,6 @@ EOF
  fi
  
  #####################################################################
@@ -404,7 +406,7 @@ diff -up src/bin/sage.orig src/bin/sage
  # File conversion
  #####################################################################
  
-@@ -771,11 +500,6 @@ fi
+@@ -796,11 +525,6 @@ fi
  # Run Sage's versions of the standard Algebra/Geometry etc. software
  #####################################################################
  
@@ -416,7 +418,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [[ "$1" =~ ^--notebook=.* || "$1" =~ ^-n=.* || "$1" =~ ^-notebook=.* ]] ; then
      sage-cleaner &>/dev/null &
      exec sage-notebook "$@"
-@@ -786,13 +510,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
+@@ -811,13 +535,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
      exec sage-notebook "$@"
  fi
  
@@ -430,7 +432,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
      shift
      sage-cleaner &>/dev/null &
-@@ -811,34 +528,15 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
+@@ -836,34 +553,15 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
      exit 0
  fi
  
@@ -467,7 +469,7 @@ diff -up src/bin/sage.orig src/bin/sage
          shift
          exec sage-runtests -p "$@"
      else
-@@ -847,10 +545,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
+@@ -872,10 +570,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
      fi
  fi
  
@@ -479,7 +481,7 @@ diff -up src/bin/sage.orig src/bin/sage
      shift
      sage_setup
      export PYTHONIOENCODING="utf-8"  # Fix encoding for doctests
-@@ -871,119 +566,6 @@ if [ "$1" = '-c' ]; then
+@@ -896,122 +591,6 @@ if [ "$1" = '-c' ]; then
      exec sage-eval "$@"
  fi
  
@@ -545,7 +547,7 @@ diff -up src/bin/sage.orig src/bin/sage
 -
 -if [ "$1" = '-installed' -o "$1" = "--installed" ]; then
 -    shift
--    exec sage-list-packages installed $@
+-    exec sage-list-packages all --installed-only $@
 -fi
 -
 -if [ "$1" = '-p' ]; then
@@ -592,14 +594,17 @@ diff -up src/bin/sage.orig src/bin/sage
 -fi
 -
 -if [ "$1" = "-docbuild" -o "$1" = "--docbuild" ]; then
+-    # Redirect stdin from /dev/null. This helps with running TeX which
+-    # tends to ask interactive questions if something goes wrong. These
+-    # cause the build to hang. If stdin is /dev/null, TeX just aborts.
 -    shift
--    exec sage-python23 -m "sage_setup.docbuild" "$@"
+-    exec sage-python23 -m sage_setup.docbuild "$@" </dev/null
 -fi
 -
  if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
      shift
      sage_setup
-@@ -1033,12 +615,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
+@@ -1061,12 +640,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
      exec sage-callgrind "$@"
  fi
  
@@ -612,8 +617,9 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-startuptime' -o "$1" = '--startuptime' ]; then
      exec sage-startuptime.py "$@"
  fi
---- src/bin/sage-runtests.orig	2018-05-05 16:21:22.000000000 -0600
+diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
-+++ src/bin/sage-runtests	2018-05-16 12:16:10.707645467 -0600
+--- src/bin/sage-runtests.orig	2018-08-03 05:10:08.000000000 -0600
++++ src/bin/sage-runtests	2018-08-29 08:27:37.703807389 -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 " +
@@ -625,8 +631,9 @@ diff -up src/bin/sage.orig src/bin/sage
  
      parser.add_option("-f", "--failed", action="store_true", default=False,
          help="doctest only those files that failed in the previous run")
---- src/bin/sage-valgrind.orig	2018-05-05 16:21:22.000000000 -0600
+diff -up src/bin/sage-valgrind.orig src/bin/sage-valgrind
-+++ src/bin/sage-valgrind	2018-05-16 12:16:10.708645454 -0600
+--- src/bin/sage-valgrind.orig	2018-08-03 05:10:08.000000000 -0600
++++ src/bin/sage-valgrind	2018-08-29 08:27:37.703807389 -0600
 @@ -1,16 +1,6 @@
  #!/usr/bin/env bash
  

sagemath.spec

@@ -47,17 +47,18 @@
 %global ipython_pkg		ipython-5.5.0
 %endif
 %if %{with bundled_ipywidgets}
-%global ipywidgets_pkg		ipywidgets-7.1.1
+%global ipywidgets_pkg		ipywidgets-7.2.0
 %endif
 %if %{with bundled_pexpect}
 %global pexpect_pkg		pexpect-4.1.0
 %endif
 %global polytopes_db_pkg	polytopes_db-20170220
 %global rubiks_pkg		rubiks-20070912
-%global	sagenb_pkg		sagenb-1.0.1
+%global	sagenb_pkg		sagenb-1.0.3
 %global sagenb_export_pkg	sagenb_export-3.2
 %global sagetex_pkg		sagetex-3.0
-%global Sphinx_pkg		Sphinx-1.6.3
+%global Sphinx_pkg		Sphinx-1.7.5
+%global singular_pkg		singular-4.1.0p3
 %if %{with bundled_thebe}
 %global thebe_pkg		thebe-9624e0a0
 %endif
@@ -65,9 +66,14 @@
 %global threejs_pkg		threejs-r80
 %endif
 %if %{with bundled_widgetsnbextension}
-%global widgetsnbextension_pkg	widgetsnbextension-3.1.1
+%global widgetsnbextension_pkg	widgetsnbextension-3.2.0
 %endif
 
+# Spkg equivalents of required rpms; we pretend they are installed as spkgs.
+# The version numbers shown are those of the latest released spkg, if the Fedora
+# version is not behind.
+%global SAGE_REQUIRED_PKGS 4ti2-1.6.7 cbc-2.9.4 CoCoALib-0.99564 cryptominisat-5.0.1 gap_packages-4.8.6new2 gmp-6.1.2 gmpy2-2.1.0a1 lrslib-062+autotools-2017-03-03 qepcad-B.1.69 saclib-2.2.6 surf-1.0.6-gcc6
+
 %global SAGE_ROOT		%{_libdir}/sagemath
 %global SAGE_LOCAL		%{SAGE_ROOT}/local
 %global SAGE_SRC		%{SAGE_ROOT}/src
@@ -79,8 +85,8 @@
 
 Name:		sagemath
 Summary:	A free open-source mathematics software system
-Version:	8.2
+Version:	8.3
-Release:	4%{?dist}
+Release:	1%{?dist}
 # The file ${SAGE_ROOT}/COPYING.txt is the upstream license breakdown file
 # Additionally, every $files section has a comment with the license name
 # before files with that license
@@ -134,17 +140,11 @@ Patch10:	%{name}-jmol.patch
 # FIXME actually it should be already available in pari-elldata
 Patch11:	%{name}-cremona.patch
 
-# lrslib is a requires
-Patch12:	%{name}-lrslib.patch
-
 # correct path to the nauty geng program
 # http://cs.anu.edu.au/~bdm/nauty/
 # http://pallini.di.uniroma1.it/
 Patch13:	%{name}-nauty.patch
 
-# 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
@@ -183,11 +183,8 @@ Patch25:	%{name}-includes.patch
 # Use atlas blas
 Patch26:	%{name}-atlas.patch
 
-# Adapt to recent versions of the flask packages
-Patch27:	%{name}-flask.patch
-
 # Adapt to recent versions of eclib
-Patch28:	%{name}-eclib.patch
+Patch27:	%{name}-eclib.patch
 
 BuildRequires:	4ti2
 BuildRequires:	arb-devel
@@ -237,6 +234,7 @@ BuildRequires:	latte-integrale
 BuildRequires:	libfplll-devel
 BuildRequires:	libgap-devel
 BuildRequires:	libmpc-devel
+BuildRequires:	libpng-devel
 BuildRequires:	linbox-devel
 BuildRequires:	lrcalc-devel
 BuildRequires:	lrslib-utils
@@ -298,11 +296,13 @@ BuildRequires:	python2-pexpect
 %endif
 BuildRequires:	python2-pickleshare
 BuildRequires:	python2-pillow-devel
+BuildRequires:	python2-pip
 BuildRequires:	python2-prompt_toolkit
 BuildRequires:	python2-pkgconfig
 BuildRequires:	python2-psutil
 BuildRequires:	python2-ptyprocess
 BuildRequires:	python2-scipy
+BuildRequires:	python2-send2trash
 BuildRequires:	python2-setuptools
 %if %{with bundled_ipython}
 BuildRequires:	python2-simplegeneric
@@ -312,7 +312,11 @@ BuildRequires:	python2-speaklater
 BuildRequires:	python2-sphinx
 BuildRequires:	python2-sympy
 BuildRequires:	python2-twisted
+%if %{with bundled_ipython}
+BuildRequires:	python2-zmq
+%endif
 BuildRequires:	python2-ZODB3
+BuildRequires:	python3-Cython
 BuildRequires:	qepcad-B
 BuildRequires:	R
 BuildRequires:	ratpoints-devel
@@ -333,6 +337,7 @@ BuildRequires:	vecmath
 BuildRequires:	web-assets-devel
 BuildRequires:	xorg-x11-fonts-Type1
 BuildRequires:	xorg-x11-server-Xvfb
+BuildRequires:	zlib-devel
 BuildRequires:	zn_poly-devel
 
 Requires:	4ti2
@@ -408,6 +413,7 @@ Requires:	python2-prompt_toolkit
 Requires:	python2-psutil
 Requires:	python2-ptyprocess
 Requires:	python2-scipy
+Requires:	python2-send2trash
 %if %{with bundled_ipython}
 BuildRequires:	python2-simplegeneric
 %endif
@@ -416,6 +422,9 @@ Requires:	python2-speaklater
 Requires:	python2-sphinx
 Requires:	python2-sympy
 Requires:	python2-twisted
+%if %{with bundled_ipython}
+Requires:	python2-zmq
+%endif
 Requires:	python2-ZODB3
 Requires:	qepcad-B
 Requires:	R
@@ -827,9 +836,7 @@ popd
 %patch9
 %patch10
 %patch11
-%patch12
 %patch13
-%patch14
 %patch15
 %patch16
 %patch17
@@ -848,7 +855,6 @@ popd
 %patch25
 %patch26
 %patch27
-%patch28
 
 sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
     -e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \
@@ -857,8 +863,7 @@ sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
 sed -e 's|@@CYSIGNALS@@|%{python2_sitearch}/cysignals|' \
     -i src/setup.py
 
-sed -e "s|, 'flask-oldsessions>=0.10'||" \
+sed -e "/flask-oldsessions/d" \
-    -e "s|'http://github.com/mitsuhiko/flask-oldsessions/tarball/master#egg=flask-oldsessions-0.10'||" \
     -i build/pkgs/sagenb/src/setup.py
 
 #------------------------------------------------------------------------
@@ -872,21 +877,34 @@ rm build/pkgs/sagenb/src/sagenb/data/sage3d/lib/sage3d.jar
 rm -r build/pkgs/sagenb/src/sagenb.egg-info
 
 # fix Singular paths
+singver=$(sed 's/.*-\([.[:digit:]]*\).*/\1/' <<< %{singular_pkg})
 sed -e "s,SINGULARPATH=\",&%{_datadir}/singular/LIB:," \
     -e "s,\(SINGULAR_EXECUTABLE=\"\).*\",\1%{_libdir}/Singular/Singular\"," \
     -i src/bin/sage-env
+sed -e "s,\(SINGULAR_SO = \)SAGE.*,\1'%{_libdir}/libSingular-$singver.so'," \
+    -i src/sage/env.py
 
-# fix shebangs
+# fix shebangs; some paths contains spaces, so use the null byte facility
-sed -i 's,#!%{_bindir}/env python,#!%{_bindir}/python2,' \
+grep -FrlZ '#!%{_bindir}/env python' | \
-  $(grep -Frl '#!%{_bindir}/env python')
+  xargs -0 sed -i 's,#!%{_bindir}/env python,#!%{__python2},'
-sed -i 's,#!%{_bindir}/env sage-python23,#!%{_bindir}/python2,' \
+grep -FrlZ '#!%{_bindir}/env sage-python23' | \
-  $(grep -Frl '#!%{_bindir}/env sage-python23')
+  xargs -0 sed -i 's,#!%{_bindir}/env sage-python23,#!%{__python2},'
-sed -i 's,#!%{_bindir}/env ,#!%{_bindir}/,' $(grep -Frl '#!%{_bindir}/env')
+grep -FrlZ '#!%{_bindir}/env' | \
-sed -i 's,#!%{_bindir}/python$,&2,' $(grep -Frl '#!%{_bindir}/python')
+  xargs -0 sed -i 's,#!%{_bindir}/env ,#!%{_bindir}/,'
+grep -rlZ '#!%{_bindir}/python$' | xargs -0 sed -i 's,#!%{_bindir}/python$,&2,'
+sed -i 's,%{_bindir}/env python,%{__python2},' \
+%if %{with bundled_pexpect}
+    build/pkgs/pexpect/src/examples/python.py \
+%endif
+    build/pkgs/sagetex/src/sagetex.ins
 sed -i 's,%{_bindir}/python,&2,' src/sage/misc/dev_tools.py
 sed -e 's,local/bin/python,bin/python,' \
     -e 's,#!%{_bindir}/python,&2,' \
     -i src/sage/repl/preparse.py
+%if %{with bundled_ipython}
+sed -e "s|'%{_bindir}/env', 'which'|'%{_bindir}/which'|" \
+    -i build/pkgs/ipython/src/IPython/utils/_process_posix.py
+%endif
 
 ########################################################################
 %build
@@ -955,8 +973,6 @@ popd
 	do
 	    patch -p1 < $BASE/$PATCH
 	done
-	# https://bugzilla.redhat.com/show_bug.cgi?id=1406533
-	sed -i 's/disallow/dissallow/' Cython/Compiler/Options.py
     popd
 %endif
 
@@ -1134,7 +1150,7 @@ popd
 
 #------------------------------------------------------------------------
 pushd $SAGE_LOCAL/bin/
-    for file in \
+    rm -f \
 	sage-arch-env \
 	sage-bdist \
 	sage-build \
@@ -1173,14 +1189,13 @@ pushd $SAGE_LOCAL/bin/
 	sage-update-src \
 	sage-update-version \
 	sage-upgrade \
-	spkg-install; do
+	spkg-install
-	rm -f $file
-    done
 popd
 
 #------------------------------------------------------------------------
 pushd build/pkgs/combinatorial_designs
-    bash ./spkg-install
+    chmod a+x spkg-install
+    bash -c '. ../../../src/bin/sage-dist-helpers; ./spkg-install'
 popd
 
 #------------------------------------------------------------------------
@@ -1460,6 +1475,11 @@ for file in *.tar.*; do
     mkdir %{buildroot}%{SAGE_SPKG_INST}/$(echo $file | sed -e 's|\.tar.*||')
 done
 popd
+pushd %{buildroot}%{SAGE_SPKG_INST}
+    for pkg in %{SAGE_REQUIRED_PKGS}; do
+        mkdir $pkg
+    done
+popd
 #------------------------------------------------------------------------
 cat > %{buildroot}%{SAGE_LOCAL}/bin/sage-list-packages << EOF
 #!/bin/sh
@@ -1503,45 +1523,8 @@ chmod +x %{buildroot}%{SAGE_LOCAL}/bin/sage-list-packages
 rm -fr $DOT_SAGE
 
 ########################################################################
-%pretrans	-p /usr/bin/lua
-posix = require('posix')
-path = "%{python2_sitearch}/sagenb/data/mathjax"
-st = posix.stat(path)
-if st and st.type == "directory" then
-  status = os.rename(path, path .. ".rpmmoved")
-  if not status then
-    suffix = 0
-    while not status do
-      suffix = suffix + 1
-      status = os.rename(path .. ".rpmmoved", path .. ".rpmmoved." .. suffix)
-    end
-    os.rename(path, path .. ".rpmmoved")
-  end
-end
-
 %ldconfig_scriptlets core
 
-%if %{with docs}
-# Upgrade correction for change from directory to symlink
-%post		doc
-if [ ! -e %{SAGE_DOC}/common ]; then
-    ln -sf . %{SAGE_DOC}/common
-fi
-exit 0
-
-%preun		doc
-if [ $1 -eq 0 ] ; then
-    if [ -h %{SAGE_DOC}/common ]; then
-	rm %{SAGE_DOC}/common
-    fi
-fi
-exit 0
-%endif
-
-%post		sagetex -p %{_bindir}/mktexlsr
-
-%postun		sagetex -p %{_bindir}/mktexlsr
-
 ########################################################################
 %files
 # GPLv2+
@@ -1811,6 +1794,15 @@ exit 0
 
 ########################################################################
 %changelog
+* Sat Sep 22 2018 Jerry James <loganjerry@gmail.com> - 8.3-1
+- Update to sagemath 8.3 (bz 1612867)
+- Drop -lrslib, -gap-hap, and -flask patches
+- Drop obsolete scriplets to fix F24 to F25 upgrade (bz 1594429 and 1618934)
+- Drop obsolete mktexlsr invocations
+- Fix more Singular paths
+- Fix still more uses of /usr/bin/env
+- Drop disallow/dissallow fixup for cython; now fixed in cython itself
+
 * Fri Aug 10 2018 Jerry James <loganjerry@gmail.com> - 8.2-4
 - Rebuild for arb 2.14.0, eclib 20180710, ntl 11.2.1, and pari 2.11.0
 - Drop unneeded genus2reduction dependency; pari is used instead now

sources

@@ -1 +1 @@
-SHA512 (sage-8.2.tar.gz) = 32afa401d0c0a825e9507a445de9a5abb19b3f2444c70ae0e5d7fea0fe319f6a43a94e5eee032fd85c21b87487a42d0c70177766dfa6ea1ea42d3a22e1395663
+SHA512 (sage-8.3.tar.gz) = d0b971896738adc6604e51a00ff38f41b5c2e7595e8d257346fd975106519a1b3a1734a07229e7bf6e9373073d0cc0ca45c259dece1e7c97a3debd12914485d6