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Update to sagemath 8.3 (bz 1612867).

Browse source 
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.
This commit is contained in:
Jerry James 2018-09-23 08:28:54 -06:00
parent 3dc6dbb3c1
commit 1a0bd1afc6
24 changed files with 285 additions and 525 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

18
.gitignore vendored
View file

@ -1,17 +1 @@
/sage-5.8.tar
/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
/sage-*.tar.gz

6
sagemath-4ti2.patch
View file

@ -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 2018-05-16 13:28:24.939025388 -0600
--- src/sage/sandpiles/sandpile.py.orig 2018-08-03 05:10:09.000000000 -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:

58
sagemath-arb.patch
View file

@ -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 2018-05-16 13:59:18.717290684 -0600
--- src/sage/libs/arb/acb_hypgeom.pxd.orig 2018-08-03 05:10:08.000000000 -0600
+++ src/sage/libs/arb/acb_hypgeom.pxd 2018-08-29 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 2018-05-16 13:59:18.717290684 -0600
--- src/sage/libs/arb/acb_mat.pxd.orig 2018-08-03 05:10:08.000000000 -0600
+++ src/sage/libs/arb/acb_mat.pxd 2018-08-29 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 2018-05-16 13:59:18.718290670 -0600
--- src/sage/libs/arb/acb_modular.pxd.orig 2018-08-03 05:10:08.000000000 -0600
+++ src/sage/libs/arb/acb_modular.pxd 2018-08-29 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 2018-05-16 13:59:18.719290655 -0600
--- src/sage/libs/arb/acb_poly.pxd.orig 2018-08-03 05:10:08.000000000 -0600
+++ src/sage/libs/arb/acb_poly.pxd 2018-08-29 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 2018-05-16 13:59:18.716290698 -0600
--- src/sage/libs/arb/arf.pxd.orig 2018-08-03 05:10:08.000000000 -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 2018-05-16 13:59:18.718290670 -0600
--- src/sage/libs/arb/bernoulli.pxd.orig 2018-08-03 05:10:08.000000000 -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 2018-05-16 13:59:18.717290684 -0600
--- src/sage/libs/arb/mag.pxd.orig 2018-08-03 05:10:08.000000000 -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 2018-05-16 13:59:18.719290655 -0600
--- src/sage/libs/arb/types.pxd.orig 2018-08-03 05:10:08.000000000 -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":

6
sagemath-cremona.patch
View file

@ -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 2016-10-20 08:11:13.681545324 -0400
--- src/sage/databases/cremona.py.orig 2018-08-03 05:10:08.000000000 -0600
+++ 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"

12
sagemath-extensions.patch
View file

@ -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 2018-05-18 07:46:16.531947286 -0600
--- src/module_list.py.orig 2018-08-03 05:10:08.000000000 -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"]),

6
sagemath-fes.patch
View file

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

201
sagemath-flask.patch
View file

@ -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)))

23
sagemath-gap-hap.patch
View file

@ -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)):

32
sagemath-includes.patch
View file

@ -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 2018-05-22 15:42:40.289863491 -0600
--- src/module_list.py.orig 2018-08-29 10:41:05.127643255 -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',
@@ -1405,7 +1433,8 @@ ext_modules = [
Extension('sage.rings.polynomial.multi_polynomial_ring_base',
@@ -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 2018-05-22 15:41:27.805658536 -0600
--- src/setup.py.orig 2018-08-29 08:35:19.955079610 -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>

8
sagemath-jmol.patch
View file

@ -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 2018-05-16 13:30:58.803927423 -0600
--- src/sage/interfaces/jmoldata.py.orig 2018-08-03 05:10:08.000000000 -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'

57
sagemath-libgap.patch
View file

@ -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 2017-11-24 10:40:06.024865775 -0700
--- src/sage/libs/gap/test/main.c.orig 2018-08-03 05:10:08.000000000 -0600
+++ 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 2017-11-24 10:41:12.757621519 -0700
@@ -22,6 +22,8 @@ from sage.interfaces.gap_workspace impor
--- src/sage/libs/gap/util.pyx.orig 2018-08-03 05:10:08.000000000 -0600
+++ src/sage/libs/gap/util.pyx 2018-08-29 11:32:06.654205922 -0600
@@ -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
- if os.path.exists(GAP_ROOT_DIR):
- return GAP_ROOT_DIR
- 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():
import os.path
if os.path.exists(GAP_ROOT_DIR):
@@ -232,6 +234,7 @@ 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:

13
sagemath-lrslib.patch
View file

@ -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()

16
sagemath-maxima.patch
View file

@ -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 2018-05-16 13:25:51.499101380 -0600
--- src/bin/sage-maxima.lisp.orig 2018-08-03 05:10:08.000000000 -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 2018-05-16 13:27:01.240157806 -0600
@@ -556,7 +556,7 @@ class Maxima(MaximaAbstract, Expect):
--- src/sage/interfaces/maxima.py.orig 2018-08-03 05:10:08.000000000 -0600
+++ src/sage/interfaces/maxima.py 2018-08-29 08:47:09.779302448 -0600
@@ -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 --disable-readline --userdir="%s" -p "%s"'%(SAGE_MAXIMA_DIR,STARTUP),
- command = 'maxima -p "{0}"'.format(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).

18
sagemath-mpfr.patch
View file

@ -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 2018-05-25 15:01:25.576043678 -0600
--- src/sage/libs/mpfr/__init__.pxd.orig 2018-08-03 05:10:08.000000000 -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 2018-05-25 15:02:11.567712409 -0600
--- src/sage/rings/complex_mpc.pyx.orig 2018-08-03 05:10:09.000000000 -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 2018-05-25 15:01:52.328850983 -0600
--- src/sage/rings/complex_number.pyx.orig 2018-08-03 05:10:09.000000000 -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 2018-05-25 11:33:48.009144647 -0600
@@ -5369,7 +5369,7 @@ cdef class RealNumber(sage.structure.ele
--- src/sage/rings/real_mpfr.pyx.orig 2018-08-03 05:10:09.000000000 -0600
+++ src/sage/rings/real_mpfr.pyx 2018-08-29 10:41:34.028286030 -0600
@@ -5370,7 +5370,7 @@ cdef class RealNumber(sage.structure.ele
if algorithm == 1:
x = self._new()
sig_on()

16
sagemath-nauty.patch
View file

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

18
sagemath-nofstring.patch
View file

@ -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 2018-05-18 09:39:53.247690061 -0600
--- src/sage/arith/multi_modular.pyx.orig 2018-08-03 05:10:08.000000000 -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 2018-05-18 09:41:48.412094505 -0600
@@ -457,7 +457,7 @@ cdef class IntegerMod_abstract(FiniteRin
--- 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 2018-08-29 10:44:04.624424587 -0600
@@ -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 2018-05-18 09:42:38.685397989 -0600
--- src/sage/structure/parent.pyx.orig 2018-08-03 05:10:09.000000000 -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 2018-05-18 09:43:07.395000229 -0600
--- src/sage/symbolic/ring.pyx.orig 2018-08-03 05:10:09.000000000 -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()))

12
sagemath-qepcad.patch
View file

@ -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 2018-05-16 13:58:34.360913275 -0600
--- src/sage/interfaces/qepcad.py.orig 2018-08-03 05:10:08.000000000 -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('/usr/share/qepcad/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: # 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('%s/bin/qepcad.help'%QEPCAD_LOCAL) as help:
- with open(os.path.join(SAGE_LOCAL, 'bin', 'qepcad.help')) as help:
+ with open(os.path.join(QEPCAD_LOCAL, 'bin', 'qepcad.help')) as help:
assert(help.readline().strip() == '@')
while True:

7
sagemath-readonly.patch
View file

@ -1,6 +1,7 @@
--- 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():
diff -up src/sage/all.py.orig src/sage/all.py
--- src/sage/all.py.orig 2018-08-03 05:10:08.000000000 -0600
+++ 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::

18
sagemath-rpmbuild.patch
View file

@ -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 2018-05-16 13:13:20.467262594 -0600
--- src/module_list.py.orig 2018-08-29 08:34:50.846439644 -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 2018-05-16 13:16:29.207708998 -0600
--- src/sage/misc/cython.py.orig 2018-08-03 05:10:09.000000000 -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 2018-05-16 13:17:40.774740719 -0600
--- src/setup.py.orig 2018-08-03 05:10:09.000000000 -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):
from sage.repl.ipython_kernel.install import SageKernelSpec
SageKernelSpec.update()
@@ -900,40 +896,6 @@ class sage_install(install):
# the install_data directory for installing our Jupyter files.
SageKernelSpec.update(prefix=self.install_data)
- def clean_stale_files(self):
- """

22
sagemath-sagedoc.patch
View file

@ -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 2018-05-16 13:20:01.420837824 -0600
--- src/sage/doctest/control.py.orig 2018-08-03 05:10:08.000000000 -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 2018-05-16 13:20:01.421837810 -0600
@@ -2258,7 +2258,7 @@ def generate_docstring_dictionary():
--- src/sage/interfaces/singular.py.orig 2018-08-03 05:10:08.000000000 -0600
+++ src/sage/interfaces/singular.py 2018-08-29 08:36:07.818487766 -0600
@@ -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 2018-05-16 13:20:01.421837810 -0600
@@ -82,8 +82,11 @@ def merge_environment(app, env):
--- src/sage_setup/docbuild/ext/multidocs.py.orig 2018-08-03 05:10:09.000000000 -0600
+++ src/sage_setup/docbuild/ext/multidocs.py 2018-08-29 08:36:07.829487630 -0600
@@ -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 2018-05-16 13:20:01.422837797 -0600
@@ -242,13 +242,14 @@ if NUM_THREADS > 1:
--- src/sage_setup/docbuild/__init__.py.orig 2018-08-03 05:10:09.000000000 -0600
+++ src/sage_setup/docbuild/__init__.py 2018-08-29 08:36:07.837487531 -0600
@@ -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)

18
sagemath-sagenb.patch
View file

@ -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 2017-11-08 08:13:13.400184004 -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 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 2017-11-08 08:13:41.928185096 -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 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 2017-11-08 08:14:22.016186631 -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 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 2017-11-08 08:15:04.624188263 -0500
@@ -49,12 +49,11 @@ sagenb.notebook.misc.DIR = %(cwd)r #We s
--- 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 2018-08-29 08:44:38.824169048 -0600
@@ -53,12 +53,11 @@ sagenb.notebook.misc.DIR = %(cwd)r #We s
# Flask #
#########
import os, sys, random

87
sagemath-scripts.patch
View file

@ -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 2018-05-16 12:29:16.699989835 -0600
@@ -13,13 +13,10 @@ usage() {
--- src/bin/sage.orig 2018-08-03 05:10:08.000000000 -0600
+++ src/bin/sage 2018-08-29 08:32:06.325478480 -0600
@@ -26,13 +26,10 @@ usage() {
echo " file.[sage|py|spyx] -- run given .sage, .py or .spyx file"
echo " -advanced -- list all command line options"
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"
@@ -44,10 +40,6 @@ usage() {
@@ -58,10 +54,6 @@ 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 "$1" = '--python' ]; then
shift
exec python "$@"
@@ -606,16 +359,6 @@ if [ "$1" = '-ipython3' -o "$1" = '--ipy
if [ "$SAGE_PYTHON3" = 'yes' ]; then
@@ -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
+++ src/bin/sage-runtests 2018-05-16 12:16:10.707645467 -0600
diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
--- 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
+++ src/bin/sage-valgrind 2018-05-16 12:16:10.708645454 -0600
diff -up src/bin/sage-valgrind.orig src/bin/sage-valgrind
--- 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

136
sagemath.spec
View file

@ -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
Release: 4%{?dist}
Version: 8.3
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'||" \
-e "s|'http://github.com/mitsuhiko/flask-oldsessions/tarball/master#egg=flask-oldsessions-0.10'||" \
sed -e "/flask-oldsessions/d" \
-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
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,' $(grep -Frl '#!%{_bindir}/python')
# fix shebangs; some paths contains spaces, so use the null byte facility
grep -FrlZ '#!%{_bindir}/env python' | \
xargs -0 sed -i 's,#!%{_bindir}/env python,#!%{__python2},'
grep -FrlZ '#!%{_bindir}/env sage-python23' | \
xargs -0 sed -i 's,#!%{_bindir}/env sage-python23,#!%{__python2},'
grep -FrlZ '#!%{_bindir}/env' | \
xargs -0 sed -i 's,#!%{_bindir}/env ,#!%{_bindir}/,'
grep -rlZ '#!%{_bindir}/python$' | 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
rm -f $file
done
spkg-install
popd
#------------------------------------------------------------------------
pushd build/pkgs/combinatorial_designs
bash ./spkg-install
chmod a+x spkg-install
bash -c '. ../../../src/bin/sage-dist-helpers; ./spkg-install'
popd
#------------------------------------------------------------------------
@ -1460,6 +1475,11 @@ for file in *.tar.*; do
mkdir %{buildroot}%{SAGE_SPKG_INST}/$(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

2
sources
View file

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