zyppe/sagemath
1
0
Fork 0
mirror of https://src.fedoraproject.org/rpms/sagemath.git synced 2025-04-04 04:28:51 -04:00
Code Issues Projects Releases Packages Wiki Activity

Version 9.3.

Browse source 
- Drop -arb and -openblas patches.
- Add -cvxopt patch.
- Add metainfo file.
This commit is contained in:
Jerry James 2021-06-18 11:37:21 -06:00
parent 26b688d416
commit 0a1b42ef2b
21 changed files with 1096 additions and 1037 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

108
org.sagemath.sage.metainfo.xml Normal file
View file

@ -0,0 +1,108 @@
<?xml version="1.0" encoding="UTF-8"?>
<component type="desktop-application">
<id>org.sagemath.sage</id>
<metadata_license>CC0-1.0</metadata_license>
<project_license>GPL-2.0-or-later</project_license>
<name>sagemath</name>
<summary>Mathematics Software System</summary>
<description>
<p>
Sage is a free open-source mathematics software system licensed
under the GPL. It combines the power of many existing open-source
packages into a common Python-based interface.
</p>
</description>
<launchable type="desktop-id">org.sagemath.sage.desktop</launchable>
<screenshots>
<screenshot type="default">
<image>https://www.flickr.com/photos/sagescreenshots/2131280369/in/album-72157603532209437/</image>
<caption>Notebook</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2131280403/in/album-72157603532209437/</image>
<caption>Symbolic computation</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2131280441/in/album-72157603532209437/</image>
<caption>More symbolic computation</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2132057124/in/album-72157603532209437/</image>
<caption>Basic plotting</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2131280543/in/album-72157603532209437/</image>
<caption>Plotting multiple functions</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2131280585/in/album-72157603532209437/</image>
<caption>Plotting options</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2131280629/in/album-72157603532209437/</image>
<caption>Polygons</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2131280689/in/album-72157603532209437/</image>
<caption>Text annotations</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2131280719/in/album-72157603532209437/</image>
<caption>Parametric plotting</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2132057406/in/album-72157603532209437/</image>
<caption>List comprehensions</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2132057442/in/album-72157603532209437/</image>
<caption>Rubik's cube</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2132057494/in/album-72157603532209437/</image>
<caption>Scrambled cube</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2132057548/in/album-72157603532209437/</image>
<caption>3D cube</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2131280959/in/album-72157603532209437/</image>
<caption>Interactive 3D cube</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2132057724/in/album-72157603532209437/</image>
<caption>3D plotting with Tachyon</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2132057802/in/album-72157603532209437/</image>
<caption>Parametric 3D plotting</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2132057836/in/album-72157603532209437/</image>
<caption>JSMath and LaTeX</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2132057874/in/album-72157603532209437/</image>
<caption>Matrix operations</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2131281199/in/album-72157603532209437/</image>
<caption>Plotting of graphs</caption>
</screenshot>
<screenshot>
<image>https://www.flickr.com/photos/sagescreenshots/2131281877/in/album-72157603532209437/</image>
<caption>Contour plot</caption>
</screenshot>
</screenshots>
<update_contact>loganjerry@gmail.com</update_contact>
<url type="homepage">https://www.sagemath.org/</url>
<url type="bugtracker">https://trac.sagemath.org/</url>
<url type="faq">https://doc.sagemath.org/html/en/faq/</url>
<url type="help">https://doc.sagemath.org/</url>
<url type="donation">https://github.com/sponsors/sagemath</url>
<content_rating type="oars-1.0"></content_rating>
<provides>
<binary>sage</binary>
</provides>
</component>

14
sagemath-4ti2.patch
View file

@ -1,9 +1,9 @@
diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
--- src/sage/sandpiles/sandpile.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/sandpiles/sandpile.py 2020-10-30 14:00:00.744208307 -0600
@@ -347,9 +347,6 @@ from sage.arith.all import falling_facto
from sage.rings.all import Integer, PolynomialRing, QQ, ZZ
from sage.symbolic.all import I, pi, SR
--- src/sage/sandpiles/sandpile.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/sandpiles/sandpile.py 2021-05-28 11:34:47.438557513 -0600
@@ -347,9 +347,6 @@ from sage.rings.all import Integer, Poly
from sage.symbolic.constants import I, pi
from sage.symbolic.ring import SR
-# TODO: remove the following line once 4ti2 functions are removed
-path_to_zsolve = os.path.join(SAGE_LOCAL, 'bin', 'zsolve')
@ -11,8 +11,8 @@ diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
def _sandpile_help(cls, usage, verbose=True):
@@ -5174,7 +5171,7 @@ class SandpileDivisor(dict):
sign_file.close()
@@ -5172,7 +5169,7 @@ class SandpileDivisor(dict):
sign_file.write('\n')
# compute
try:
- os.system(path_to_zsolve+' -q ' + lin_sys + ' > ' + lin_sys_log)

34
sagemath-arb.patch
View file

@ -1,34 +0,0 @@
diff -up src/sage/libs/arb/arb_wrap.h.orig src/sage/libs/arb/arb_wrap.h
--- src/sage/libs/arb/arb_wrap.h.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/libs/arb/arb_wrap.h 2020-10-30 16:10:40.145976088 -0600
@@ -11,18 +11,18 @@
#define ulong mp_limb_t
#define slong mp_limb_signed_t
-#include <acb.h>
-#include <acb_calc.h>
-#include <acb_elliptic.h>
-#include <acb_hypgeom.h>
-#include <acb_mat.h>
-#include <acb_modular.h>
-#include <acb_poly.h>
-#include <arb.h>
-#include <arb_hypgeom.h>
-#include <arf.h>
-#include <bernoulli.h>
-#include <mag.h>
+#include <arb/acb.h>
+#include <arb/acb_calc.h>
+#include <arb/acb_elliptic.h>
+#include <arb/acb_hypgeom.h>
+#include <arb/acb_mat.h>
+#include <arb/acb_modular.h>
+#include <arb/acb_poly.h>
+#include <arb/arb.h>
+#include <arb/arb_hypgeom.h>
+#include <arb/arf.h>
+#include <arb/bernoulli.h>
+#include <arb/mag.h>
#undef ulong
#undef slong

10
sagemath-cremona.patch
View file

@ -1,7 +1,7 @@
diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
--- src/sage/databases/cremona.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/databases/cremona.py 2020-10-30 14:02:27.778960819 -0600
@@ -854,7 +854,8 @@ class MiniCremonaDatabase(SQLDatabase):
--- src/sage/databases/cremona.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/databases/cremona.py 2021-05-28 11:39:00.005575551 -0600
@@ -885,7 +885,8 @@ class MiniCremonaDatabase(SQLDatabase):
message = "There is no elliptic curve with label " \
+ label + " in the default database; try installing " \
+ "the optional package database_cremona_ellcurve which " \
@ -11,8 +11,8 @@ diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
raise ValueError(message)
ainvs = eval(c[0])
data = {'cremona_label': label,
@@ -1659,6 +1660,7 @@ class LargeCremonaDatabase(MiniCremonaDa
con.executemany("UPDATE t_curve SET gens=? WHERE curve=?", \
@@ -1663,6 +1664,7 @@ class LargeCremonaDatabase(MiniCremonaDa
con.executemany("UPDATE t_curve SET gens=? WHERE curve=?",
curve_data)
print("Committing...")
+ self.commit()

24
sagemath-cvxopt.patch Normal file
View file

@ -0,0 +1,24 @@
diff -up src/sage/numerical/backends/cvxopt_backend.pyx.orig src/sage/numerical/backends/cvxopt_backend.pyx
--- src/sage/numerical/backends/cvxopt_backend.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/numerical/backends/cvxopt_backend.pyx 2021-05-28 12:05:47.551650940 -0600
@@ -550,7 +550,7 @@ cdef class CVXOPTBackend(GenericBackend)
self.answer = solvers.lp(c,G,h)
#possible outcomes
- if self.answer['status'] == 'optimized':
+ if self.answer['status'] in ['optimized', 'optimal']:
pass
elif self.answer['status'] == 'primal infeasible':
raise MIPSolverException("CVXOPT: primal infeasible")
diff -up src/sage/numerical/backends/cvxopt_sdp_backend.pyx.orig src/sage/numerical/backends/cvxopt_sdp_backend.pyx
--- src/sage/numerical/backends/cvxopt_sdp_backend.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/numerical/backends/cvxopt_sdp_backend.pyx 2021-05-28 12:05:47.552650940 -0600
@@ -150,7 +150,7 @@ cdef class CVXOPTSDPBackend(MatrixSDPBac
self.answer = solvers.sdp(c,Gs=G_matrix,hs=h_matrix)
#possible outcomes
- if self.answer['status'] == 'optimized':
+ if self.answer['status'] in ['optimized', 'optimal']:
pass
elif self.answer['status'] == 'primal infeasible':
raise SDPSolverException("CVXOPT: primal infeasible")

93
sagemath-env.patch
View file

@ -1,43 +1,56 @@
diff -up src/sage/env.py.orig src/sage/env.py
--- src/sage/env.py.orig 2020-10-30 16:09:54.834029866 -0600
+++ src/sage/env.py 2020-10-30 16:10:20.089999891 -0600
@@ -159,14 +159,14 @@ var('SAGE_DATE', version.date)
var('SAGE_VERSION_BANNER', version.banner)
--- src/sage/env.py.orig 2021-05-29 21:01:26.503474025 -0600
+++ src/sage/env.py 2021-05-29 21:03:06.389635554 -0600
@@ -166,16 +166,16 @@ SAGE_DATE = var("SAGE_DATE", version.dat
SAGE_VERSION_BANNER = var("SAGE_VERSION_BANNER", version.banner)
# bunch of sage directories and files
-var('SAGE_LOCAL', os.path.abspath(sys.prefix))
-var('SAGE_ETC', join(SAGE_LOCAL, 'etc'))
-var('SAGE_INC', join(SAGE_LOCAL, 'include'))
-var('SAGE_SHARE', join(SAGE_LOCAL, 'share'))
-var('SAGE_DOC', join(SAGE_SHARE, 'doc', 'sage'))
+var('SAGE_LOCAL', '@@SAGE_LOCAL@@')
+var('SAGE_ETC', join('/usr', 'share', 'sagemath', 'etc'))
+var('SAGE_INC', join('/usr', 'include'))
+var('SAGE_SHARE', join('/usr', 'share', 'sagemath'))
+var('SAGE_DOC', join('/usr', 'share', 'doc', 'sagemath'))
var('SAGE_SPKG_INST', join(SAGE_LOCAL, 'var', 'lib', 'sage', 'installed'))
var('SAGE_LIB', os.path.dirname(os.path.dirname(sage.__file__)))
-var('SAGE_EXTCODE', join(SAGE_LIB, 'sage', 'ext_data'))
+var('SAGE_EXTCODE', join('/usr', 'share', 'sagemath', 'etc'))
# virtual environment where sagelib is installed
-SAGE_VENV = var("SAGE_VENV", os.path.abspath(sys.prefix))
+SAGE_VENV = var("SAGE_VENV", "@@SAGE_LOCAL@@")
SAGE_LIB = var("SAGE_LIB", os.path.dirname(os.path.dirname(sage.__file__)))
-SAGE_EXTCODE = var("SAGE_EXTCODE", join(SAGE_LIB, "sage", "ext_data"))
+SAGE_EXTCODE = var("SAGE_EXTCODE", join("/usr", "share", "sagemath", "etc"))
var('SAGE_ROOT') # no fallback for SAGE_ROOT
var('SAGE_SRC', join(SAGE_ROOT, 'src'), SAGE_LIB)
@@ -187,13 +187,13 @@ var('THEBE_DIR', joi
var('COMBINATORIAL_DESIGN_DATA_DIR', join(SAGE_SHARE, 'combinatorial_designs'))
var('CREMONA_MINI_DATA_DIR', join(SAGE_SHARE, 'cremona'))
var('CREMONA_LARGE_DATA_DIR', join(SAGE_SHARE, 'cremona'))
-var('JMOL_DIR', join(SAGE_SHARE, 'jmol'))
-var('JSMOL_DIR', join(SAGE_SHARE, 'jsmol'))
-var('MATHJAX_DIR', join(SAGE_SHARE, 'mathjax'))
-var('MTXLIB', join(SAGE_SHARE, 'meataxe'))
+var('JMOL_DIR', join('/usr', 'share', 'java', 'jmol'))
+var('JSMOL_DIR', join('/usr', 'share', 'javascript', 'jsmol'))
+var('MATHJAX_DIR', join('/usr', 'share', 'javascript', 'mathjax'))
+var('MTXLIB', join(DOT_SAGE, 'meataxe'))
var('THREEJS_DIR', join(SAGE_SHARE, 'threejs'))
var('SINGULARPATH', join(SAGE_SHARE, 'singular'))
-var('PPLPY_DOCS', join(SAGE_SHARE, 'doc', 'pplpy'))
+var('PPLPY_DOCS', join('/usr', 'share', 'doc', 'python3-pplpy'))
var('MAXIMA', 'maxima')
var('MAXIMA_FAS')
var('SAGE_NAUTY_BINS_PREFIX', '')
# prefix hierarchy where non-Python packages are installed
SAGE_LOCAL = var("SAGE_LOCAL", SAGE_VENV)
-SAGE_ETC = var("SAGE_ETC", join(SAGE_LOCAL, "etc"))
-SAGE_INC = var("SAGE_INC", join(SAGE_LOCAL, "include"))
-SAGE_SHARE = var("SAGE_SHARE", join(SAGE_LOCAL, "share"))
-SAGE_DOC = var("SAGE_DOC", join(SAGE_SHARE, "doc", "sage"))
+SAGE_ETC = var("SAGE_ETC", join("/usr", "share", "sagemath", "etc"))
+SAGE_INC = var("SAGE_INC", join("/usr", "include"))
+SAGE_SHARE = var("SAGE_SHARE", join("/usr", "share", "sagemath"))
+SAGE_DOC = var("SAGE_DOC", join("/usr", "share", "doc", "sagemath"))
SAGE_SPKG_INST = var("SAGE_SPKG_INST", join(SAGE_LOCAL, "var", "lib", "sage", "installed"))
# source tree of the Sage distribution
@@ -199,12 +199,12 @@ THEBE_DIR = var("THEBE_DIR", join(SAGE_S
COMBINATORIAL_DESIGN_DATA_DIR = var("COMBINATORIAL_DESIGN_DATA_DIR", join(SAGE_SHARE, "combinatorial_designs"))
CREMONA_MINI_DATA_DIR = var("CREMONA_MINI_DATA_DIR", join(SAGE_SHARE, "cremona"))
CREMONA_LARGE_DATA_DIR = var("CREMONA_LARGE_DATA_DIR", join(SAGE_SHARE, "cremona"))
-JMOL_DIR = var("JMOL_DIR", join(SAGE_SHARE, "jmol"))
-MATHJAX_DIR = var("MATHJAX_DIR", join(SAGE_SHARE, "mathjax"))
-MTXLIB = var("MTXLIB", join(SAGE_SHARE, "meataxe"))
+JMOL_DIR = var("JMOL_DIR", join("/usr", "share", "java", "jmol"))
+MATHJAX_DIR = var("MATHJAX_DIR", join("/usr", "share", "javascript", "mathjax"))
+MTXLIB = var("MTXLIB", join(DOT_SAGE, "meataxe"))
THREEJS_DIR = var("THREEJS_DIR", join(SAGE_SHARE, "threejs"))
SINGULARPATH = var("SINGULARPATH", join(SAGE_SHARE, "singular"))
-PPLPY_DOCS = var("PPLPY_DOCS", join(SAGE_SHARE, "doc", "pplpy"))
+PPLPY_DOCS = var("PPLPY_DOCS", join("/usr", "share", "doc", "python3-pplpy"))
MAXIMA = var("MAXIMA", "maxima")
MAXIMA_FAS = var("MAXIMA_FAS")
SAGE_NAUTY_BINS_PREFIX = var("SAGE_NAUTY_BINS_PREFIX", "")
@@ -301,10 +301,10 @@ def _get_shared_lib_path(*libnames: str)
# locate singular shared object
# On Debian it's libsingular-Singular so try that as well
-SINGULAR_SO = var("SINGULAR_SO", _get_shared_lib_path("Singular", "singular-Singular"))
+SINGULAR_SO = var("SINGULAR_SO", "@@LIBDIR@@/libSingular.so")
# locate libgap shared object
-GAP_SO = var("GAP_SO", _get_shared_lib_path("gap", ""))
+GAP_SO = var("GAP_SO", "@@LIBDIR@@/libgap.so")
# post process
if ' ' in DOT_SAGE:

450
sagemath-escape.patch
View file

File diff suppressed because it is too large Load diff

119
sagemath-extensions.patch
View file

@ -1,7 +1,7 @@
diff -up src/sage/env.py.orig src/sage/env.py
--- src/sage/env.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/env.py 2020-10-30 15:44:29.575821493 -0600
@@ -413,7 +413,8 @@ def cython_aliases():
--- src/sage/env.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/env.py 2021-05-28 11:18:15.134457599 -0600
@@ -430,7 +430,8 @@ def cython_aliases():
aliases[var + "INCDIR"] = pc['include_dirs']
aliases[var + "LIBDIR"] = pc['library_dirs']
aliases[var + "LIBEXTRA"] = list(filter(lambda s: not s.startswith(('-l','-L')), libs.split()))
@ -12,25 +12,25 @@ diff -up src/sage/env.py.orig src/sage/env.py
# uname-specific flags
UNAME = os.uname()
diff -up src/sage/graphs/mcqd.pyx.orig src/sage/graphs/mcqd.pyx
--- src/sage/graphs/mcqd.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/graphs/mcqd.pyx 2020-10-30 15:47:32.294609185 -0600
--- src/sage/graphs/mcqd.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/graphs/mcqd.pyx 2021-05-28 11:18:15.134457599 -0600
@@ -1,4 +1,5 @@
# distutils: language = c++
+# distutils: libraries = mcqd
# sage_setup: distribution = sage-mcqd
from sage.ext.memory_allocator cimport MemoryAllocator
from cysignals.signals cimport sig_on, sig_off
diff -up src/sage/interfaces/primecount.pyx.orig src/sage/interfaces/primecount.pyx
--- src/sage/interfaces/primecount.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/interfaces/primecount.pyx 2020-10-30 15:47:42.766597012 -0600
--- src/sage/interfaces/primecount.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/interfaces/primecount.pyx 2021-05-28 11:18:15.134457599 -0600
@@ -1,3 +1,4 @@
+# distutils: libraries = primecount
# sage_setup: distribution = sage-primecount
r"""
diff -up src/sage/libs/arb/arb.pxd.orig src/sage/libs/arb/arb.pxd
--- src/sage/libs/arb/arb.pxd.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/libs/arb/arb.pxd 2020-10-30 15:47:18.918624733 -0600
--- src/sage/libs/arb/arb.pxd.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/libs/arb/arb.pxd 2021-05-28 11:18:15.135457599 -0600
@@ -1,4 +1,5 @@
# distutils: libraries = gmp flint ARB_LIBRARY
+# distutils: include_dirs = /usr/include/arb /usr/include/flint
@ -38,8 +38,8 @@ diff -up src/sage/libs/arb/arb.pxd.orig src/sage/libs/arb/arb.pxd
from sage.libs.arb.types cimport *
diff -up src/sage/libs/arb/arb_version.pyx.orig src/sage/libs/arb/arb_version.pyx
--- src/sage/libs/arb/arb_version.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/libs/arb/arb_version.pyx 2020-10-30 15:54:30.743122593 -0600
--- src/sage/libs/arb/arb_version.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/libs/arb/arb_version.pyx 2021-05-28 11:18:15.135457599 -0600
@@ -1,4 +1,5 @@
# -*- coding: utf-8
+# distutils: include_dirs = /usr/include/arb /usr/include/flint
@ -47,48 +47,48 @@ diff -up src/sage/libs/arb/arb_version.pyx.orig src/sage/libs/arb/arb_version.py
from sage.cpython.string cimport char_to_str
diff -up src/sage/libs/arb/arith.pyx.orig src/sage/libs/arb/arith.pyx
--- src/sage/libs/arb/arith.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/libs/arb/arith.pyx 2020-10-30 15:54:53.191096510 -0600
--- src/sage/libs/arb/arith.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/libs/arb/arith.pyx 2021-05-28 11:18:15.135457599 -0600
@@ -1,3 +1,4 @@
+# distutils: include_dirs = /usr/include/arb /usr/include/flint
"""
Arithmetic functions using the arb library
"""
diff -up src/sage/libs/mpmath/ext_impl.pyx.orig src/sage/libs/mpmath/ext_impl.pyx
--- src/sage/libs/mpmath/ext_impl.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/libs/mpmath/ext_impl.pyx 2020-10-30 15:52:15.823279433 -0600
--- src/sage/libs/mpmath/ext_impl.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/libs/mpmath/ext_impl.pyx 2021-05-28 11:18:15.135457599 -0600
@@ -1,3 +1,4 @@
+# distutils: include_dirs = /usr/include/flint
"""
This module provides the core implementation of multiprecision
floating-point arithmetic. Operations are done in-place.
diff -up src/sage/libs/mpmath/ext_libmp.pyx.orig src/sage/libs/mpmath/ext_libmp.pyx
--- src/sage/libs/mpmath/ext_libmp.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/libs/mpmath/ext_libmp.pyx 2020-10-30 15:53:01.023226835 -0600
--- src/sage/libs/mpmath/ext_libmp.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/libs/mpmath/ext_libmp.pyx 2021-05-28 11:18:15.135457599 -0600
@@ -1,3 +1,4 @@
+# distutils: include_dirs = /usr/include/flint
"""
Faster versions of some key functions in mpmath.libmp
"""
diff -up src/sage/libs/mpmath/ext_main.pyx.orig src/sage/libs/mpmath/ext_main.pyx
--- src/sage/libs/mpmath/ext_main.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/libs/mpmath/ext_main.pyx 2020-10-30 15:52:35.663256336 -0600
--- src/sage/libs/mpmath/ext_main.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/libs/mpmath/ext_main.pyx 2021-05-28 11:18:15.135457599 -0600
@@ -1,3 +1,4 @@
+# distutils: include_dirs = /usr/include/flint
"""
mpmath floating-point numbers
diff -up src/sage/libs/mpmath/utils.pyx.orig src/sage/libs/mpmath/utils.pyx
--- src/sage/libs/mpmath/utils.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/libs/mpmath/utils.pyx 2020-10-30 15:51:33.798328356 -0600
--- src/sage/libs/mpmath/utils.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/libs/mpmath/utils.pyx 2021-05-28 11:18:15.136457599 -0600
@@ -1,3 +1,4 @@
+# distutils: include_dirs = /usr/include/flint
"""
Utilities for Sage-mpmath interaction
diff -up src/sage/matrix/matrix_complex_ball_dense.pyx.orig src/sage/matrix/matrix_complex_ball_dense.pyx
--- src/sage/matrix/matrix_complex_ball_dense.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/matrix/matrix_complex_ball_dense.pyx 2020-10-30 15:55:44.799036557 -0600
--- src/sage/matrix/matrix_complex_ball_dense.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/matrix/matrix_complex_ball_dense.pyx 2021-05-28 11:18:15.136457599 -0600
@@ -1,4 +1,5 @@
# distutils: libraries = ARB_LIBRARY
+# distutils: include_dirs = /usr/include/arb /usr/include/flint
@ -96,26 +96,28 @@ diff -up src/sage/matrix/matrix_complex_ball_dense.pyx.orig src/sage/matrix/matr
Arbitrary precision complex ball matrices using Arb
diff -up src/sage/matrix/matrix_cyclo_dense.pyx.orig src/sage/matrix/matrix_cyclo_dense.pyx
--- src/sage/matrix/matrix_cyclo_dense.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/matrix/matrix_cyclo_dense.pyx 2020-10-30 15:56:45.647965864 -0600
@@ -1,5 +1,6 @@
--- src/sage/matrix/matrix_cyclo_dense.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/matrix/matrix_cyclo_dense.pyx 2021-05-28 12:09:14.100657210 -0600
@@ -1,7 +1,7 @@
# distutils: language = c++
# distutils: libraries = ntl
+# distutils: include_dirs = /usr/include/arb /usr/include/flint
# distutils: libraries = NTL_LIBRARIES
# distutils: extra_compile_args = NTL_CFLAGS
-# distutils: include_dirs = NTL_INCDIR
+# distutils: include_dirs = NTL_INCDIR /usr/include/arb /usr/include/flint
# distutils: library_dirs = NTL_LIBDIR
# distutils: extra_link_args = NTL_LIBEXTRA
"""
Matrices over Cyclotomic Fields
diff -up src/sage/matrix/matrix_mpolynomial_dense.pyx.orig src/sage/matrix/matrix_mpolynomial_dense.pyx
--- src/sage/matrix/matrix_mpolynomial_dense.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/matrix/matrix_mpolynomial_dense.pyx 2020-10-30 15:57:50.862889413 -0600
--- src/sage/matrix/matrix_mpolynomial_dense.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/matrix/matrix_mpolynomial_dense.pyx 2021-05-28 11:18:15.136457599 -0600
@@ -1,3 +1,4 @@
+# distutils: include_dirs = /usr/include/singular /usr/include/factory
"""
Dense matrices over multivariate polynomials over fields
diff -up src/sage/rings/complex_arb.pyx.orig src/sage/rings/complex_arb.pyx
--- src/sage/rings/complex_arb.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/rings/complex_arb.pyx 2020-11-05 15:42:05.494453973 -0700
--- src/sage/rings/complex_arb.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/rings/complex_arb.pyx 2021-05-28 11:18:15.137457600 -0600
@@ -1,4 +1,5 @@
# -*- coding: utf-8
+# distutils: include_dirs = /usr/include/arb /usr/include/flint
@ -123,42 +125,43 @@ diff -up src/sage/rings/complex_arb.pyx.orig src/sage/rings/complex_arb.pyx
Arbitrary precision complex balls using Arb
diff -up src/sage/rings/number_field/number_field_element_quadratic.pyx.orig src/sage/rings/number_field/number_field_element_quadratic.pyx
--- src/sage/rings/number_field/number_field_element_quadratic.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/rings/number_field/number_field_element_quadratic.pyx 2020-11-05 15:48:03.436448764 -0700
@@ -1,5 +1,6 @@
# distutils: libraries = ntl
--- src/sage/rings/number_field/number_field_element_quadratic.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/rings/number_field/number_field_element_quadratic.pyx 2021-05-28 11:18:15.138457600 -0600
@@ -4,6 +4,7 @@
# distutils: library_dirs = NTL_LIBDIR
# distutils: extra_link_args = NTL_LIBEXTRA
# distutils: language = c++
+# distutils: include_dirs = /usr/include/arb /usr/include/flint
"""
Optimized Quadratic Number Field Elements
diff -up src/sage/rings/polynomial/multi_polynomial_libsingular.pyx.orig src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
--- src/sage/rings/polynomial/multi_polynomial_libsingular.pyx.orig 2020-10-30 11:34:26.064980206 -0600
+++ src/sage/rings/polynomial/multi_polynomial_libsingular.pyx 2020-10-30 16:02:19.239570828 -0600
--- src/sage/rings/polynomial/multi_polynomial_libsingular.pyx.orig 2021-05-28 11:01:44.993275358 -0600
+++ src/sage/rings/polynomial/multi_polynomial_libsingular.pyx 2021-05-28 11:18:15.138457600 -0600
@@ -1,3 +1,4 @@
+# distutils: include_dirs = /usr/include/singular /usr/include/factory
r"""
Multivariate Polynomials via libSINGULAR
diff -up src/sage/rings/polynomial/multi_polynomial.pyx.orig src/sage/rings/polynomial/multi_polynomial.pyx
--- src/sage/rings/polynomial/multi_polynomial.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/rings/polynomial/multi_polynomial.pyx 2020-11-05 15:42:05.505453973 -0700
--- src/sage/rings/polynomial/multi_polynomial.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/rings/polynomial/multi_polynomial.pyx 2021-05-28 11:18:15.139457600 -0600
@@ -1,3 +1,4 @@
+# distutils: include_dirs = /usr/include/singular /usr/include/factory
r"""
Base class for elements of multivariate polynomial rings
"""
diff -up src/sage/rings/polynomial/plural.pyx.orig src/sage/rings/polynomial/plural.pyx
--- src/sage/rings/polynomial/plural.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/rings/polynomial/plural.pyx 2020-11-05 15:42:05.507453973 -0700
--- src/sage/rings/polynomial/plural.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/rings/polynomial/plural.pyx 2021-05-28 11:18:15.139457600 -0600
@@ -1,3 +1,4 @@
+# distutils: include_dirs = /usr/include/singular /usr/include/factory
r"""
Noncommutative Polynomials via libSINGULAR/Plural
diff -up src/sage/rings/polynomial/polynomial_complex_arb.pyx.orig src/sage/rings/polynomial/polynomial_complex_arb.pyx
--- src/sage/rings/polynomial/polynomial_complex_arb.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/rings/polynomial/polynomial_complex_arb.pyx 2020-10-30 16:03:19.870498851 -0600
--- src/sage/rings/polynomial/polynomial_complex_arb.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/rings/polynomial/polynomial_complex_arb.pyx 2021-05-28 11:18:15.139457600 -0600
@@ -1,4 +1,5 @@
# -*- coding: utf-8
+# distutils: include_dirs = /usr/include/arb /usr/include/flint
@ -166,8 +169,8 @@ diff -up src/sage/rings/polynomial/polynomial_complex_arb.pyx.orig src/sage/ring
Univariate polynomials over `\CC` with interval coefficients using Arb.
diff -up src/sage/rings/real_arb.pyx.orig src/sage/rings/real_arb.pyx
--- src/sage/rings/real_arb.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/rings/real_arb.pyx 2020-11-05 15:42:05.510453973 -0700
--- src/sage/rings/real_arb.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/rings/real_arb.pyx 2021-05-28 11:18:15.140457600 -0600
@@ -1,4 +1,5 @@
# -*- coding: utf-8
+# distutils: include_dirs = /usr/include/arb /usr/include/flint
@ -175,13 +178,13 @@ diff -up src/sage/rings/real_arb.pyx.orig src/sage/rings/real_arb.pyx
Arbitrary precision real balls using Arb
diff -up src/sage_setup/command/sage_build_cython.py.orig src/sage_setup/command/sage_build_cython.py
--- src/sage_setup/command/sage_build_cython.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage_setup/command/sage_build_cython.py 2020-10-30 16:04:33.325411659 -0600
@@ -59,6 +59,7 @@ if subprocess.call("""$CC --version | gr
--- src/sage_setup/command/sage_build_cython.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage_setup/command/sage_build_cython.py 2021-05-28 12:09:14.113657210 -0600
@@ -209,6 +209,7 @@ class sage_build_cython(Command):
self.library_order = library_order
# Search for dependencies in the source tree and add to the list of include directories
self.sage_include_dirs = sage_include_directories(use_sources=True)
+ self.sage_include_dirs.extend(['@@CYSIGNALS@@'])
# Search for dependencies in the source tree and add to the list of include directories
include_dirs = sage_include_directories(use_sources=True)
+include_dirs.extend(['@@CYSIGNALS@@'])
# Look for libraries only in what is configured already through distutils
# and environment variables
from Cython.Build import cythonize
import Cython.Compiler.Options

389
sagemath-flexiblas.patch
View file

@ -1,116 +1,283 @@
diff -up src/sage/env.py.orig src/sage/env.py
--- src/sage/env.py.orig 2020-10-30 16:10:20.089999891 -0600
+++ src/sage/env.py 2020-10-31 12:11:19.256615196 -0600
@@ -391,7 +391,7 @@ def cython_aliases():
aliases = {}
diff -up configure.orig configure
--- configure.orig 2021-05-09 16:01:38.000000000 -0600
+++ configure 2021-06-03 06:44:51.137915577 -0600
@@ -12184,12 +12184,12 @@ if test -n "$OPENBLAS_CFLAGS"; then
pkg_cv_OPENBLAS_CFLAGS="$OPENBLAS_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
- { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"openblas >= 0.2.20\""; } >&5
- ($PKG_CONFIG --exists --print-errors "openblas >= 0.2.20") 2>&5
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"flexiblas >= 3.0.0\""; } >&5
+ ($PKG_CONFIG --exists --print-errors "flexiblas >= 3.0.0") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
- pkg_cv_OPENBLAS_CFLAGS=`$PKG_CONFIG --cflags "openblas >= 0.2.20" 2>/dev/null`
+ pkg_cv_OPENBLAS_CFLAGS=`$PKG_CONFIG --cflags "flexiblas >= 3.0.0" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
@@ -12201,12 +12201,12 @@ if test -n "$OPENBLAS_LIBS"; then
pkg_cv_OPENBLAS_LIBS="$OPENBLAS_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
- { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"openblas >= 0.2.20\""; } >&5
- ($PKG_CONFIG --exists --print-errors "openblas >= 0.2.20") 2>&5
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"flexiblas >= 3.0.0\""; } >&5
+ ($PKG_CONFIG --exists --print-errors "flexiblas >= 3.0.0") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
- pkg_cv_OPENBLAS_LIBS=`$PKG_CONFIG --libs "openblas >= 0.2.20" 2>/dev/null`
+ pkg_cv_OPENBLAS_LIBS=`$PKG_CONFIG --libs "flexiblas >= 3.0.0" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
@@ -12227,9 +12227,9 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
- OPENBLAS_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "openblas >= 0.2.20" 2>&1`
+ OPENBLAS_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "flexiblas >= 3.0.0" 2>&1`
else
- OPENBLAS_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "openblas >= 0.2.20" 2>&1`
+ OPENBLAS_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "flexiblas >= 3.0.0" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$OPENBLAS_PKG_ERRORS" >&5
@@ -12257,16 +12257,16 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_
#ifdef __cplusplus
extern "C"
#endif
-char openblas_get_config ();
+char flexiblas_get_version ();
int
main ()
{
-return openblas_get_config ();
+return flexiblas_get_version ();
;
return 0;
}
_ACEOF
-for ac_lib in '' openblas cblas blas; do
+for ac_lib in '' flexiblas cblas blas; do
if test -z "$ac_lib"; then
ac_res="none required"
else
@@ -12319,22 +12319,22 @@ else
/* end confdefs.h. */
#include <stdio.h>
- char *openblas_get_config(void);
+ void flexiblas_get_version(void);
int version[3];
int
main ()
{
version[0] = version[1] = version[2] = 0;
/*printf("%s", openblas_get_config());*/
- if (sscanf(openblas_get_config(), "OpenBLAS %d.%d.%d",
- version, version+1, version+2) < 1)
- return 1;
+ flexiblas_get_version(&version[0], &version[1], &version[2]);
+
+
if ( 10000 * version[0]
+ 100 * version[1]
+ version[2]
- < 10000 * 0
- + 100 * 2
- + 20)
+ < 10000 * 3
+ + 100 * 0
+ + 0)
return 1;
;
return 0;
@@ -12387,7 +12387,7 @@ return cblas_dgemm ();
return 0;
}
_ACEOF
-for ac_lib in '' openblas cblas blas; do
+for ac_lib in '' flexiblas cblas blas; do
if test -z "$ac_lib"; then
ac_res="none required"
else
@@ -12451,7 +12451,7 @@ return dgeqrf ();
return 0;
}
_ACEOF
-for ac_lib in '' openblas lapack; do
+for ac_lib in '' flexiblas lapack; do
if test -z "$ac_lib"; then
ac_res="none required"
else
@@ -12515,7 +12515,7 @@ return dgeqrf_ ();
return 0;
}
_ACEOF
-for ac_lib in '' openblas lapack; do
+for ac_lib in '' flexiblas lapack; do
if test -z "$ac_lib"; then
ac_res="none required"
else
@@ -12579,7 +12579,7 @@ return DGEQRF ();
return 0;
}
_ACEOF
-for ac_lib in '' openblas lapack; do
+for ac_lib in '' flexiblas lapack; do
if test -z "$ac_lib"; then
ac_res="none required"
else
@@ -12643,7 +12643,7 @@ return DGEQRF_ ();
return 0;
}
_ACEOF
-for ac_lib in '' openblas lapack; do
+for ac_lib in '' flexiblas lapack; do
if test -z "$ac_lib"; then
ac_res="none required"
else
@@ -12731,16 +12731,16 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_
#ifdef __cplusplus
extern "C"
#endif
-char openblas_get_config ();
+char flexiblas_get_version ();
int
main ()
{
-return openblas_get_config ();
+return flexiblas_get_version ();
;
return 0;
}
_ACEOF
-for ac_lib in '' openblas cblas blas; do
+for ac_lib in '' flexiblas cblas blas; do
if test -z "$ac_lib"; then
ac_res="none required"
else
@@ -12793,22 +12793,22 @@ else
/* end confdefs.h. */
#include <stdio.h>
- char *openblas_get_config(void);
+ void flexiblas_get_version(void);
int version[3];
int
main ()
{
version[0] = version[1] = version[2] = 0;
/*printf("%s", openblas_get_config());*/
- if (sscanf(openblas_get_config(), "OpenBLAS %d.%d.%d",
- version, version+1, version+2) < 1)
- return 1;
+ flexiblas_get_version(&version[0], &version[1], &version[2]);
+
+
if ( 10000 * version[0]
+ 100 * version[1]
+ version[2]
- < 10000 * 0
- + 100 * 2
- + 20)
+ < 10000 * 3
+ + 100 * 0
+ + 0)
return 1;
;
return 0;
@@ -12861,7 +12861,7 @@ return cblas_dgemm ();
return 0;
}
_ACEOF
-for ac_lib in '' openblas cblas blas; do
+for ac_lib in '' flexiblas cblas blas; do
if test -z "$ac_lib"; then
ac_res="none required"
else
@@ -12925,7 +12925,7 @@ return dgeqrf ();
return 0;
}
_ACEOF
-for ac_lib in '' openblas lapack; do
+for ac_lib in '' flexiblas lapack; do
if test -z "$ac_lib"; then
ac_res="none required"
else
@@ -12989,7 +12989,7 @@ return dgeqrf_ ();
return 0;
}
_ACEOF
-for ac_lib in '' openblas lapack; do
+for ac_lib in '' flexiblas lapack; do
if test -z "$ac_lib"; then
ac_res="none required"
else
@@ -13053,7 +13053,7 @@ return DGEQRF ();
return 0;
}
_ACEOF
-for ac_lib in '' openblas lapack; do
+for ac_lib in '' flexiblas lapack; do
if test -z "$ac_lib"; then
ac_res="none required"
else
@@ -13117,7 +13117,7 @@ return DGEQRF_ ();
return 0;
}
_ACEOF
-for ac_lib in '' openblas lapack; do
+for ac_lib in '' flexiblas lapack; do
if test -z "$ac_lib"; then
ac_res="none required"
else
@@ -13192,12 +13192,12 @@ if test -n "$OPENBLASPCDIR"; then
pkg_cv_OPENBLASPCDIR="$OPENBLASPCDIR"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
- { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"openblas\""; } >&5
- ($PKG_CONFIG --exists --print-errors "openblas") 2>&5
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"flexiblas\""; } >&5
+ ($PKG_CONFIG --exists --print-errors "flexiblas") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
- pkg_cv_OPENBLASPCDIR=`$PKG_CONFIG --variable="pcfiledir" "openblas" 2>/dev/null`
+ pkg_cv_OPENBLASPCDIR=`$PKG_CONFIG --variable="pcfiledir" "flexiblas" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
@@ -13412,7 +13412,7 @@ fi
if test x$sage_spkg_install_openblas != xyes; then :
- SAGE_OPENBLAS_PC_COMMAND="\$(LN) -sf \"$OPENBLASPCDIR/openblas.pc\" \"\$(@)\""
+ SAGE_OPENBLAS_PC_COMMAND="\$(LN) -sf \"$OPENBLASPCDIR/flexiblas.pc\" \"\$(@)\""
if test x$sage_install_blas_pc = xyes; then :
diff -up src/sage/env.py.orig src/sage/env.py
--- src/sage/env.py.orig 2021-06-16 13:13:15.378722205 -0600
+++ src/sage/env.py 2021-06-16 13:42:26.443996772 -0600
@@ -209,7 +209,7 @@ MAXIMA = var("MAXIMA", "maxima")
MAXIMA_FAS = var("MAXIMA_FAS")
SAGE_NAUTY_BINS_PREFIX = var("SAGE_NAUTY_BINS_PREFIX", "")
ARB_LIBRARY = var("ARB_LIBRARY", "arb")
-CBLAS_PC_MODULES = var("CBLAS_PC_MODULES", "cblas:openblas:blas")
+CBLAS_PC_MODULES = var("CBLAS_PC_MODULES", "flexiblas:cblas:openblas:blas")
ECL_CONFIG = var("ECL_CONFIG", "ecl-config")
NTL_INCDIR = var("NTL_INCDIR")
NTL_LIBDIR = var("NTL_LIBDIR")
@@ -408,7 +408,7 @@ def cython_aliases():
for lib in ['fflas-ffpack', 'givaro', 'gsl', 'linbox', 'Singular',
- 'libpng', 'gdlib', 'm4ri', 'zlib', 'cblas', 'lapack']:
+ 'libpng', 'gdlib', 'm4ri', 'zlib', 'flexiblas']:
'libpng', 'gdlib', 'm4ri', 'zlib', 'cblas', 'lapack']:
var = lib.upper().replace("-", "") + "_"
- if lib == 'cblas':
+ if lib == 'cblas' or lib == 'lapack':
lib = get_cblas_pc_module_name()
if lib == 'zlib':
aliases[var + "CFLAGS"] = ""
diff -up src/sage/matrix/matrix_integer_dense.pyx.orig src/sage/matrix/matrix_integer_dense.pyx
--- src/sage/matrix/matrix_integer_dense.pyx.orig 2020-10-30 11:52:49.737274785 -0600
+++ src/sage/matrix/matrix_integer_dense.pyx 2020-10-31 17:58:56.243063508 -0600
@@ -1,8 +1,8 @@
# -*- coding: utf-8 -*-
# distutils: extra_compile_args = M4RI_CFLAGS
-# distutils: libraries = iml ntl gmp m CBLAS_LIBRARIES
-# distutils: library_dirs = CBLAS_LIBDIR
-# distutils: include_dirs = M4RI_INCDIR CBLAS_INCDIR
+# distutils: libraries = iml ntl gmp m FLEXIBLAS_LIBRARIES
+# distutils: library_dirs = FLEXIBLAS_LIBDIR
+# distutils: include_dirs = M4RI_INCDIR FLEXIBLAS_INCDIR
"""
Dense matrices over the integer ring
diff -up src/sage/matrix/matrix_modn_dense_double.pyx.orig src/sage/matrix/matrix_modn_dense_double.pyx
--- src/sage/matrix/matrix_modn_dense_double.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/matrix/matrix_modn_dense_double.pyx 2020-11-05 15:44:59.390454421 -0700
@@ -1,7 +1,7 @@
# distutils: language = c++
-# distutils: libraries = CBLAS_LIBRARIES
-# distutils: library_dirs = CBLAS_LIBDIR
-# distutils: include_dirs = CBLAS_INCDIR
+# distutils: libraries = FLEXIBLAS_LIBRARIES
+# distutils: library_dirs = FLEXIBLAS_LIBDIR
+# distutils: include_dirs = FLEXIBLAS_INCDIR
# distutils: extra_compile_args = -D_XPG6
"""
Dense matrices over `\ZZ/n\ZZ` for `n < 2^{23}` using LinBox's ``Modular<double>``
diff -up src/sage/matrix/matrix_modn_dense_float.pyx.orig src/sage/matrix/matrix_modn_dense_float.pyx
--- src/sage/matrix/matrix_modn_dense_float.pyx.orig 2020-11-05 15:44:59.391454421 -0700
+++ src/sage/matrix/matrix_modn_dense_float.pyx 2020-11-05 15:45:54.965454564 -0700
@@ -1,7 +1,7 @@
# distutils: language = c++
-# distutils: libraries = CBLAS_LIBRARIES
-# distutils: library_dirs = CBLAS_LIBDIR
-# distutils: include_dirs = CBLAS_INCDIR
+# distutils: libraries = FLEXIBLAS_LIBRARIES
+# distutils: library_dirs = FLEXIBLAS_LIBDIR
+# distutils: include_dirs = FLEXIBLAS_INCDIR
"""
Dense matrices over `\ZZ/n\ZZ` for `n < 2^{11}` using LinBox's ``Modular<float>``
diff -up src/sage/matrix/matrix_rational_dense.pyx.orig src/sage/matrix/matrix_rational_dense.pyx
--- src/sage/matrix/matrix_rational_dense.pyx.orig 2020-10-30 11:34:26.031980257 -0600
+++ src/sage/matrix/matrix_rational_dense.pyx 2020-10-31 17:58:10.490106273 -0600
@@ -1,7 +1,7 @@
# distutils: extra_compile_args = -D_XPG6 M4RI_CFLAGS
-# distutils: libraries = iml ntl m CBLAS_LIBRARIES
-# distutils: library_dirs = CBLAS_LIBDIR
-# distutils: include_dirs = M4RI_INCDIR CBLAS_INCDIR
+# distutils: libraries = iml ntl m FLEXIBLAS_LIBRARIES
+# distutils: library_dirs = FLEXIBLAS_LIBDIR
+# distutils: include_dirs = M4RI_INCDIR FLEXIBLAS_INCDIR
"""
Dense matrices over the rational field
diff -up src/sage/misc/cython.py.orig src/sage/misc/cython.py
--- src/sage/misc/cython.py.orig 2020-10-30 16:08:06.039158996 -0600
+++ src/sage/misc/cython.py 2020-10-30 16:24:09.037024792 -0600
@@ -35,10 +35,9 @@ from sage.cpython.string import str_to_b
# CBLAS can be one of multiple implementations
-cblas_pc = pkgconfig.parse('cblas')
-cblas_libs = list(cblas_pc['libraries'])
-cblas_library_dirs = list(cblas_pc['library_dirs'])
-cblas_include_dirs = list(cblas_pc['include_dirs'])
+cblas_libs = ['flexiblas']
+cblas_library_dirs = ['/usr/lib']
+cblas_include_dirs = ['/usr/include/flexiblas']
standard_libs = [
'mpfr', 'gmp', 'gmpxx', 'pari', 'm',
diff -up src/sage_setup/library_order.py.orig src/sage_setup/library_order.py
--- src/sage_setup/library_order.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage_setup/library_order.py 2020-10-31 12:11:54.313540360 -0600
@@ -10,20 +10,18 @@ import os
import pkgconfig
# CBLAS can be one of multiple implementations
-cblas_pc = pkgconfig.parse('cblas')
-cblas_libs = cblas_pc['libraries']
-cblas_library_dirs = cblas_pc['library_dirs']
-cblas_include_dirs = cblas_pc['include_dirs']
+cblas_libs = ['flexiblas']
+cblas_library_dirs = ['/usr/lib']
+cblas_include_dirs = ['/usr/include/flexiblas']
# TODO: Remove Cygwin hack by installing a suitable cblas.pc
if os.path.exists('/usr/lib/libblas.dll.a'):
cblas_libs = ['gslcblas']
# LAPACK can be one of multiple implementations
-lapack_pc = pkgconfig.parse('lapack')
-lapack_libs = lapack_pc['libraries']
-lapack_library_dirs = lapack_pc['library_dirs']
-lapack_include_dirs = lapack_pc['include_dirs']
+lapack_libs = ['flexiblas']
+lapack_library_dirs = ['/usr/lib']
+lapack_include_dirs = ['/usr/include/flexiblas']
# GD image library
gd_pc = pkgconfig.parse('gdlib')

6
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 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/interfaces/jmoldata.py 2020-10-30 14:01:33.291052531 -0600
--- src/sage/interfaces/jmoldata.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/interfaces/jmoldata.py 2021-05-28 11:36:18.844565672 -0600
@@ -148,8 +148,6 @@ class JmolData(SageObject):
sage: print(os.path.exists(testfile)) # optional -- java
True
@ -21,5 +21,5 @@ diff -up src/sage/interfaces/jmoldata.py.orig src/sage/interfaces/jmoldata.py
+ subprocess.call(["jmol", "-n", "-g", size_arg,
+ "-J", launchscript, "-j", imagescript], stdout=jout)
if not os.path.isfile(targetfile):
raise RuntimeError("Jmol failed to create file %s, see %s for details"%(repr(targetfile), repr(scratchout)))
raise RuntimeError(f"Jmol failed to create file {targetfile}: {Path(scratchout).read_text()}")
os.unlink(scratchout)

16
sagemath-lcalc.patch
View file

@ -1,10 +1,10 @@
diff -up src/sage/libs/lcalc/lcalc_Lfunction.pyx.orig src/sage/libs/lcalc/lcalc_Lfunction.pyx
--- src/sage/libs/lcalc/lcalc_Lfunction.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/libs/lcalc/lcalc_Lfunction.pyx 2020-10-30 14:40:53.875121354 -0600
--- src/sage/libs/lcalc/lcalc_Lfunction.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/libs/lcalc/lcalc_Lfunction.pyx 2021-06-02 17:12:56.077802570 -0600
@@ -1,5 +1,5 @@
# distutils: libraries = m ntl Lfunction
-# distutils: extra_compile_args = -O3 -ffast-math
+# distutils: extra_compile_args = -std=gnu++11 -ffast-math
# distutils: language = c++
r"""
Rubinstein's lcalc library
# distutils: libraries = m NTL_LIBRARIES Lfunction
-# distutils: extra_compile_args = NTL_CFLAGS -O3 -ffast-math
+# distutils: extra_compile_args = NTL_CFLAGS -std=gnu++11 -ffast-math
# distutils: include_dirs = NTL_INCDIR
# distutils: library_dirs = NTL_LIBDIR
# distutils: extra_link_args = NTL_LIBEXTRA

36
sagemath-libgap.patch
View file

@ -1,18 +1,18 @@
diff -up src/sage/env.py.orig src/sage/env.py
--- src/sage/env.py.orig 2020-10-30 15:44:29.575821493 -0600
+++ src/sage/env.py 2020-10-30 16:09:54.834029866 -0600
@@ -182,7 +182,7 @@ var('CONWAY_POLYNOMIALS_DATA_DIR', joi
var('GRAPHS_DATA_DIR', join(SAGE_SHARE, 'graphs'))
var('ELLCURVE_DATA_DIR', join(SAGE_SHARE, 'ellcurves'))
var('POLYTOPE_DATA_DIR', join(SAGE_SHARE, 'reflexive_polytopes'))
-var('GAP_ROOT_DIR', join(SAGE_SHARE, 'gap'))
+var('GAP_ROOT_DIR', join('/usr','lib','gap'))
var('THEBE_DIR', join(SAGE_SHARE, 'thebe'))
var('COMBINATORIAL_DESIGN_DATA_DIR', join(SAGE_SHARE, 'combinatorial_designs'))
var('CREMONA_MINI_DATA_DIR', join(SAGE_SHARE, 'cremona'))
--- src/sage/env.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/env.py 2021-06-02 17:13:07.387813291 -0600
@@ -194,7 +194,7 @@ CONWAY_POLYNOMIALS_DATA_DIR = var("CONWA
GRAPHS_DATA_DIR = var("GRAPHS_DATA_DIR", join(SAGE_SHARE, "graphs"))
ELLCURVE_DATA_DIR = var("ELLCURVE_DATA_DIR", join(SAGE_SHARE, "ellcurves"))
POLYTOPE_DATA_DIR = var("POLYTOPE_DATA_DIR", join(SAGE_SHARE, "reflexive_polytopes"))
-GAP_ROOT_DIR = var("GAP_ROOT_DIR", join(SAGE_SHARE, "gap"))
+GAP_ROOT_DIR = var("GAP_ROOT_DIR", join('/usr', 'lib', "gap"))
THEBE_DIR = var("THEBE_DIR", join(SAGE_SHARE, "thebe"))
COMBINATORIAL_DESIGN_DATA_DIR = var("COMBINATORIAL_DESIGN_DATA_DIR", join(SAGE_SHARE, "combinatorial_designs"))
CREMONA_MINI_DATA_DIR = var("CREMONA_MINI_DATA_DIR", join(SAGE_SHARE, "cremona"))
diff -up src/sage/libs/gap/element.pyx.orig src/sage/libs/gap/element.pyx
--- src/sage/libs/gap/element.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/libs/gap/element.pyx 2020-10-30 14:42:23.392975217 -0600
--- src/sage/libs/gap/element.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/libs/gap/element.pyx 2021-05-28 11:43:51.678593573 -0600
@@ -264,7 +264,7 @@ cdef Obj make_gap_string(sage_string) ex
try:
GAP_Enter()
@ -104,8 +104,8 @@ diff -up src/sage/libs/gap/element.pyx.orig src/sage/libs/gap/element.pyx
if isinstance(i, tuple):
diff -up src/sage/libs/gap/gap_includes.pxd.orig src/sage/libs/gap/gap_includes.pxd
--- src/sage/libs/gap/gap_includes.pxd.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/libs/gap/gap_includes.pxd 2020-10-30 14:42:23.392975217 -0600
--- src/sage/libs/gap/gap_includes.pxd.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/libs/gap/gap_includes.pxd 2021-05-28 11:43:51.679593573 -0600
@@ -13,8 +13,8 @@ from libc.stdint cimport uintptr_t, uint
cdef extern from "gap/system.h" nogil:
@ -225,9 +225,9 @@ diff -up src/sage/libs/gap/gap_includes.pxd.orig src/sage/libs/gap/gap_includes.
+ Obj NEW_STRING(Int len)
+ Obj MakeStringWithLen(const char *buf, size_t len)
diff -up src/sage/libs/gap/util.pyx.orig src/sage/libs/gap/util.pyx
--- src/sage/libs/gap/util.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/libs/gap/util.pyx 2020-10-30 14:42:23.393975216 -0600
@@ -386,7 +386,7 @@ cdef Obj gap_eval(str gap_string) except
--- src/sage/libs/gap/util.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/libs/gap/util.pyx 2021-05-28 11:43:51.679593573 -0600
@@ -387,7 +387,7 @@ cdef Obj gap_eval(str gap_string) except
"""
initialize()
cdef Obj result

116
sagemath-openblas.patch
View file

@ -1,116 +0,0 @@
diff -up src/sage/env.py.orig src/sage/env.py
--- src/sage/env.py.orig 2020-10-30 16:10:20.089999891 -0600
+++ src/sage/env.py 2020-10-31 12:11:19.256615196 -0600
@@ -391,7 +391,7 @@ def cython_aliases():
aliases = {}
for lib in ['fflas-ffpack', 'givaro', 'gsl', 'linbox', 'Singular',
- 'libpng', 'gdlib', 'm4ri', 'zlib', 'cblas', 'lapack']:
+ 'libpng', 'gdlib', 'm4ri', 'zlib', 'openblas']:
var = lib.upper().replace("-", "") + "_"
if lib == 'zlib':
aliases[var + "CFLAGS"] = ""
diff -up src/sage/matrix/matrix_integer_dense.pyx.orig src/sage/matrix/matrix_integer_dense.pyx
--- src/sage/matrix/matrix_integer_dense.pyx.orig 2020-10-30 11:52:49.737274785 -0600
+++ src/sage/matrix/matrix_integer_dense.pyx 2020-10-31 17:58:56.243063508 -0600
@@ -1,8 +1,8 @@
# -*- coding: utf-8 -*-
# distutils: extra_compile_args = M4RI_CFLAGS
-# distutils: libraries = iml ntl gmp m CBLAS_LIBRARIES
-# distutils: library_dirs = CBLAS_LIBDIR
-# distutils: include_dirs = M4RI_INCDIR CBLAS_INCDIR
+# distutils: libraries = iml ntl gmp m OPENBLAS_LIBRARIES
+# distutils: library_dirs = OPENBLAS_LIBDIR
+# distutils: include_dirs = M4RI_INCDIR OPENBLAS_INCDIR
"""
Dense matrices over the integer ring
diff -up src/sage/matrix/matrix_modn_dense_double.pyx.orig src/sage/matrix/matrix_modn_dense_double.pyx
--- src/sage/matrix/matrix_modn_dense_double.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/matrix/matrix_modn_dense_double.pyx 2020-11-05 15:54:31.940411433 -0700
@@ -1,7 +1,7 @@
# distutils: language = c++
-# distutils: libraries = CBLAS_LIBRARIES
-# distutils: library_dirs = CBLAS_LIBDIR
-# distutils: include_dirs = CBLAS_INCDIR
+# distutils: libraries = OPENBLAS_LIBRARIES
+# distutils: library_dirs = OPENBLAS_LIBDIR
+# distutils: include_dirs = OPENBLAS_INCDIR
# distutils: extra_compile_args = -D_XPG6
"""
Dense matrices over `\ZZ/n\ZZ` for `n < 2^{23}` using LinBox's ``Modular<double>``
diff -up src/sage/matrix/matrix_modn_dense_float.pyx.orig src/sage/matrix/matrix_modn_dense_float.pyx
--- src/sage/matrix/matrix_modn_dense_float.pyx.orig 2020-11-05 15:54:31.940411433 -0700
+++ src/sage/matrix/matrix_modn_dense_float.pyx 2020-11-05 15:55:38.853405001 -0700
@@ -1,7 +1,7 @@
# distutils: language = c++
-# distutils: libraries = CBLAS_LIBRARIES
-# distutils: library_dirs = CBLAS_LIBDIR
-# distutils: include_dirs = CBLAS_INCDIR
+# distutils: libraries = OPENBLAS_LIBRARIES
+# distutils: library_dirs = OPENBLAS_LIBDIR
+# distutils: include_dirs = OPENBLAS_INCDIR
"""
Dense matrices over `\ZZ/n\ZZ` for `n < 2^{11}` using LinBox's ``Modular<float>``
diff -up src/sage/matrix/matrix_rational_dense.pyx.orig src/sage/matrix/matrix_rational_dense.pyx
--- src/sage/matrix/matrix_rational_dense.pyx.orig 2020-10-30 11:34:26.031980257 -0600
+++ src/sage/matrix/matrix_rational_dense.pyx 2020-10-31 17:58:10.490106273 -0600
@@ -1,7 +1,7 @@
# distutils: extra_compile_args = -D_XPG6 M4RI_CFLAGS
-# distutils: libraries = iml ntl m CBLAS_LIBRARIES
-# distutils: library_dirs = CBLAS_LIBDIR
-# distutils: include_dirs = M4RI_INCDIR CBLAS_INCDIR
+# distutils: libraries = iml ntl m OPENBLAS_LIBRARIES
+# distutils: library_dirs = OPENBLAS_LIBDIR
+# distutils: include_dirs = M4RI_INCDIR OPENBLAS_INCDIR
"""
Dense matrices over the rational field
diff -up src/sage/misc/cython.py.orig src/sage/misc/cython.py
--- src/sage/misc/cython.py.orig 2020-10-30 16:08:06.039158996 -0600
+++ src/sage/misc/cython.py 2020-10-30 16:24:09.037024792 -0600
@@ -35,10 +35,9 @@ from sage.cpython.string import str_to_b
# CBLAS can be one of multiple implementations
-cblas_pc = pkgconfig.parse('cblas')
-cblas_libs = list(cblas_pc['libraries'])
-cblas_library_dirs = list(cblas_pc['library_dirs'])
-cblas_include_dirs = list(cblas_pc['include_dirs'])
+cblas_libs = ['openblas']
+cblas_library_dirs = ['/usr/lib']
+cblas_include_dirs = ['/usr/include/openblas']
standard_libs = [
'mpfr', 'gmp', 'gmpxx', 'pari', 'm',
diff -up src/sage_setup/library_order.py.orig src/sage_setup/library_order.py
--- src/sage_setup/library_order.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage_setup/library_order.py 2020-10-31 12:11:54.313540360 -0600
@@ -10,20 +10,18 @@ import os
import pkgconfig
# CBLAS can be one of multiple implementations
-cblas_pc = pkgconfig.parse('cblas')
-cblas_libs = cblas_pc['libraries']
-cblas_library_dirs = cblas_pc['library_dirs']
-cblas_include_dirs = cblas_pc['include_dirs']
+cblas_libs = ['openblas']
+cblas_library_dirs = ['/usr/lib']
+cblas_include_dirs = ['/usr/include/openblas']
# TODO: Remove Cygwin hack by installing a suitable cblas.pc
if os.path.exists('/usr/lib/libblas.dll.a'):
cblas_libs = ['gslcblas']
# LAPACK can be one of multiple implementations
-lapack_pc = pkgconfig.parse('lapack')
-lapack_libs = lapack_pc['libraries']
-lapack_library_dirs = lapack_pc['library_dirs']
-lapack_include_dirs = lapack_pc['include_dirs']
+lapack_libs = ['openblas']
+lapack_library_dirs = ['/usr/lib']
+lapack_include_dirs = ['/usr/include/openblas']
# GD image library
gd_pc = pkgconfig.parse('gdlib')

177
sagemath-python3.patch
View file

@ -1,83 +1,6 @@
diff -up build/pkgs/sagetex/src/remote-sagetex.py.orig build/pkgs/sagetex/src/remote-sagetex.py
--- build/pkgs/sagetex/src/remote-sagetex.py.orig 2020-08-12 02:35:31.000000000 -0600
+++ build/pkgs/sagetex/src/remote-sagetex.py 2020-10-30 14:03:01.286904419 -0600
@@ -24,12 +24,11 @@
## You should have received a copy of the GNU General Public License along
## with this program. If not, see <http://www.gnu.org/licenses/>.
##
-from __future__ import print_function
import json
import sys
import time
import re
-import urllib
+import urllib.request, urllib.parse, urllib.error
import hashlib
import os
import os.path
@@ -156,7 +155,7 @@ class RemoteSage:
'\n*(?P<output>.*)', re.DOTALL)
self._404 = re.compile('404 Not Found')
self._session = self._get_url('login',
- urllib.urlencode({'username': user,
+ urllib.parse.urlencode({'username': user,
'password':
password}))['session']
self._codewrap = """try:
@@ -176,18 +175,18 @@ except:
_p_.save(filename=plotfilename, **kwargs)""")
def _encode(self, d):
- return 'session={0}&'.format(self._session) + urllib.urlencode(d)
+ return 'session={0}&'.format(self._session) + urllib.parse.urlencode(d)
def _get_url(self, action, u):
- with closing(urllib.urlopen(self._srv + '/simple/' + action +
- '?' + u)) as h:
+ with closing(urllib.request.urlopen(self._srv + '/simple/' + action +
+ '?' + u)) as h:
data = self._response.match(h.read())
result = json.loads(data.group('header'))
result['output'] = data.group('output').rstrip()
return result
def _get_file(self, fn, cell, ofn=None):
- with closing(urllib.urlopen(self._srv + '/simple/' + 'file' + '?' +
+ with closing(urllib.request.urlopen(self._srv + '/simple/' + 'file' + '?' +
self._encode({'cell': cell, 'file': fn}))) as h:
myfn = ofn if ofn else fn
data = h.read()
@@ -277,13 +276,13 @@ if login_info_file:
password = get_val(line)
if not server:
- server = raw_input('Enter server: ')
+ server = input('Enter server: ')
if not server.startswith('http'):
server = 'https://' + server
if not username:
- username = raw_input('Enter username: ')
+ username = input('Enter username: ')
if not password:
from getpass import getpass
diff -up build/pkgs/sagetex/src/sagetexparse.py.orig build/pkgs/sagetex/src/sagetexparse.py
--- build/pkgs/sagetex/src/sagetexparse.py.orig 2020-08-12 02:35:31.000000000 -0600
+++ build/pkgs/sagetex/src/sagetexparse.py 2020-10-30 14:03:01.286904419 -0600
@@ -132,7 +132,7 @@ class SageCodeExtractor():
def plotout(self, s, l, t):
self.result += '# \\sageplot{} from line %s:\n' % lineno(l, s)
- if t.format is not '':
+ if t.format != '':
self.result += '# format: %s' % t.format[0][1:-1] + '\n'
self.result += t.code[1:-1] + '\n\n'
diff -up src/sage/cpython/debugimpl.c.orig src/sage/cpython/debugimpl.c
--- src/sage/cpython/debugimpl.c.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/cpython/debugimpl.c 2020-10-30 14:03:01.299904398 -0600
--- src/sage/cpython/debugimpl.c.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/cpython/debugimpl.c 2021-05-28 11:39:54.261578894 -0600
@@ -148,6 +148,7 @@ static void _type_debug(PyTypeObject* tp
printf(" tp_basicsize: %ld\n", (long)tp->tp_basicsize);
printf(" tp_itemsize: %ld\n", (long)tp->tp_itemsize);
@ -95,9 +18,9 @@ diff -up src/sage/cpython/debugimpl.c.orig src/sage/cpython/debugimpl.c
attr_pointer_meth(tp_call, "__call__");
attr_pointer_meth(tp_str, "__str__");
diff -up src/sage/cpython/debug.pyx.orig src/sage/cpython/debug.pyx
--- src/sage/cpython/debug.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/cpython/debug.pyx 2020-10-30 14:03:01.300904396 -0600
@@ -232,6 +232,7 @@ def type_debug(cls):
--- src/sage/cpython/debug.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/cpython/debug.pyx 2021-05-28 11:39:54.261578894 -0600
@@ -231,6 +231,7 @@ def type_debug(cls):
tp_basicsize: 16
tp_itemsize: 0
tp_dictoffset: 0
@ -105,7 +28,7 @@ diff -up src/sage/cpython/debug.pyx.orig src/sage/cpython/debug.pyx
tp_weaklistoffset: 0
tp_base (__base__): NULL
tp_bases (__bases__): tuple:
@@ -259,7 +260,6 @@ def type_debug(cls):
@@ -258,7 +259,6 @@ def type_debug(cls):
tp_dealloc (__dealloc__): 0x7fc57d757010
tp_free: PyObject_Del
tp_repr (__repr__): 0x7fc57d75b990
@ -114,9 +37,9 @@ diff -up src/sage/cpython/debug.pyx.orig src/sage/cpython/debug.pyx
tp_call (__call__): NULL
tp_str (__str__): 0x7fc57d757020
diff -up src/sage/geometry/triangulation/point_configuration.py.orig src/sage/geometry/triangulation/point_configuration.py
--- src/sage/geometry/triangulation/point_configuration.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/geometry/triangulation/point_configuration.py 2020-10-30 14:03:01.301904394 -0600
@@ -619,11 +619,11 @@ class PointConfiguration(UniqueRepresent
--- src/sage/geometry/triangulation/point_configuration.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/geometry/triangulation/point_configuration.py 2021-05-28 11:39:54.263578895 -0600
@@ -618,11 +618,11 @@ class PointConfiguration(UniqueRepresent
['{{0,1,2,4},{1,2,3,4}}']
"""
timeout = 600
@ -131,9 +54,9 @@ diff -up src/sage/geometry/triangulation/point_configuration.py.orig src/sage/ge
if verbose:
print("#### TOPCOM input ####")
diff -up src/sage/interfaces/frobby.py.orig src/sage/interfaces/frobby.py
--- src/sage/interfaces/frobby.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/interfaces/frobby.py 2020-10-30 14:03:02.534902319 -0600
@@ -79,7 +79,7 @@ class Frobby:
--- src/sage/interfaces/frobby.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/interfaces/frobby.py 2021-05-28 11:39:54.264578894 -0600
@@ -78,7 +78,7 @@ class Frobby:
print("Frobby command: ", repr(command))
print("Frobby input:\n", input)
@ -143,9 +66,9 @@ diff -up src/sage/interfaces/frobby.py.orig src/sage/interfaces/frobby.py
frinput = str_to_bytes(input)
else:
diff -up src/sage/interfaces/gfan.py.orig src/sage/interfaces/gfan.py
--- src/sage/interfaces/gfan.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/interfaces/gfan.py 2020-10-30 14:11:30.550047499 -0600
@@ -62,7 +62,7 @@ class Gfan(object):
--- src/sage/interfaces/gfan.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/interfaces/gfan.py 2021-05-28 11:39:54.264578894 -0600
@@ -61,7 +61,7 @@ class Gfan(object):
print("gfan input:\n%s" % I)
gfan_processes = Popen(cmd, stdin=PIPE, stdout=PIPE, stderr=PIPE,
@ -155,9 +78,9 @@ diff -up src/sage/interfaces/gfan.py.orig src/sage/interfaces/gfan.py
# sometimes, gfan outputs stuff to stderr even though everything is fine
diff -up src/sage/interfaces/latte.py.orig src/sage/interfaces/latte.py
--- src/sage/interfaces/latte.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/interfaces/latte.py 2020-10-30 14:03:03.974899895 -0600
@@ -152,6 +152,7 @@ def count(arg, ehrhart_polynomial=False,
--- src/sage/interfaces/latte.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/interfaces/latte.py 2021-05-28 11:39:54.265578894 -0600
@@ -162,6 +162,7 @@ def count(arg, ehrhart_polynomial=False,
latte_proc = Popen(args,
stdin=PIPE, stdout=PIPE,
stderr=(None if verbose else PIPE),
@ -165,7 +88,7 @@ diff -up src/sage/interfaces/latte.py.orig src/sage/interfaces/latte.py
cwd=str(SAGE_TMP))
ans, err = latte_proc.communicate(arg)
@@ -364,6 +365,7 @@ def integrate(arg, polynomial=None, algo
@@ -385,6 +386,7 @@ def integrate(arg, polynomial=None, algo
latte_proc = Popen(args,
stdin=PIPE, stdout=PIPE,
stderr=(None if verbose else PIPE),
@ -174,8 +97,8 @@ diff -up src/sage/interfaces/latte.py.orig src/sage/interfaces/latte.py
ans, err = latte_proc.communicate(arg)
diff -up src/sage/interfaces/sagespawn.pyx.orig src/sage/interfaces/sagespawn.pyx
--- src/sage/interfaces/sagespawn.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/interfaces/sagespawn.pyx 2020-10-30 14:03:03.975899894 -0600
--- src/sage/interfaces/sagespawn.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/interfaces/sagespawn.pyx 2021-05-28 11:39:54.266578895 -0600
@@ -1,6 +1,6 @@
"""
Sage wrapper around pexpect's ``spawn`` class and
@ -224,8 +147,8 @@ diff -up src/sage/interfaces/sagespawn.pyx.orig src/sage/interfaces/sagespawn.py
pass
self.fileobj.close()
diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.pyx
--- src/sage/libs/coxeter3/coxeter.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/libs/coxeter3/coxeter.pyx 2020-10-30 14:03:03.976899892 -0600
--- src/sage/libs/coxeter3/coxeter.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/libs/coxeter3/coxeter.pyx 2021-05-28 11:39:54.267578895 -0600
@@ -37,7 +37,7 @@ cdef class String:
EXAMPLES::
@ -359,9 +282,9 @@ diff -up src/sage/libs/coxeter3/coxeter.pyx.orig src/sage/libs/coxeter3/coxeter.
if rank == 0:
raise NotImplementedError("Coxeter group of type ['A',0] using Coxeter 3 not yet implemented")
diff -up src/sage/misc/sageinspect.py.orig src/sage/misc/sageinspect.py
--- src/sage/misc/sageinspect.py.orig 2020-11-01 10:38:08.203022437 -0700
+++ src/sage/misc/sageinspect.py 2020-11-01 10:43:43.355143620 -0700
@@ -463,12 +463,9 @@ class SageArgSpecVisitor(ast.NodeVisitor
--- src/sage/misc/sageinspect.py.orig 2021-05-28 11:01:40.384274506 -0600
+++ src/sage/misc/sageinspect.py 2021-05-28 11:39:54.269578895 -0600
@@ -462,12 +462,9 @@ class SageArgSpecVisitor(ast.NodeVisitor
"""
return node.id
@ -377,7 +300,7 @@ diff -up src/sage/misc/sageinspect.py.orig src/sage/misc/sageinspect.py
INPUT:
@@ -476,17 +473,21 @@ class SageArgSpecVisitor(ast.NodeVisitor
@@ -475,17 +472,21 @@ class SageArgSpecVisitor(ast.NodeVisitor
OUTPUT:
@ -405,7 +328,7 @@ diff -up src/sage/misc/sageinspect.py.orig src/sage/misc/sageinspect.py
"""
return node.value
@@ -520,57 +521,6 @@ class SageArgSpecVisitor(ast.NodeVisitor
@@ -519,57 +520,6 @@ class SageArgSpecVisitor(ast.NodeVisitor
"""
return node.arg
@ -464,9 +387,9 @@ diff -up src/sage/misc/sageinspect.py.orig src/sage/misc/sageinspect.py
"""
Visit a Python AST :class:`ast.List` node.
diff -up src/sage/plot/plot3d/plot3d.py.orig src/sage/plot/plot3d/plot3d.py
--- src/sage/plot/plot3d/plot3d.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/plot/plot3d/plot3d.py 2020-10-30 14:24:36.813732073 -0600
@@ -186,7 +186,7 @@ class _Coordinates(object):
--- src/sage/plot/plot3d/plot3d.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/plot/plot3d/plot3d.py 2021-05-28 11:39:54.270578895 -0600
@@ -185,7 +185,7 @@ class _Coordinates(object):
sage: arb((x+z,y*z,z), z, (x,y))
Arbitrary Coordinates coordinate transform (z in terms of x, y)
"""
@ -476,9 +399,9 @@ diff -up src/sage/plot/plot3d/plot3d.py.orig src/sage/plot/plot3d/plot3d.py
raise ValueError('variables were specified incorrectly for this coordinate system; incorrect variables were %s'%list(set(all_vars).symmetric_difference(set(indep_vars+[dep_var]))))
self.dep_var = dep_var
diff -up src/sage/rings/integer.pyx.orig src/sage/rings/integer.pyx
--- src/sage/rings/integer.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/rings/integer.pyx 2020-10-30 14:03:05.737896928 -0600
@@ -7093,7 +7093,7 @@ cdef int mpz_set_str_python(mpz_ptr z, c
--- src/sage/rings/integer.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/rings/integer.pyx 2021-05-28 11:39:54.274578895 -0600
@@ -7089,7 +7089,7 @@ cdef int mpz_set_str_python(mpz_ptr z, c
x += 1 # Strip spaces
# Disallow a sign here
@ -488,9 +411,9 @@ diff -up src/sage/rings/integer.pyx.orig src/sage/rings/integer.pyx
assert base >= 2
diff -up src/sage/rings/polynomial/pbori/pbori.pyx.orig src/sage/rings/polynomial/pbori/pbori.pyx
--- src/sage/rings/polynomial/pbori/pbori.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/rings/polynomial/pbori/pbori.pyx 2020-11-05 15:44:02.756454276 -0700
@@ -4800,8 +4800,7 @@ cdef class PolynomialConstruct:
--- src/sage/rings/polynomial/pbori/pbori.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/rings/polynomial/pbori/pbori.pyx 2021-05-28 11:39:54.278578895 -0600
@@ -4704,8 +4704,7 @@ cdef class PolynomialConstruct:
# So, it is just a conversion. [Simon King]
return (<BooleanPolynomialRing>ring)._element_constructor_(x)
@ -501,9 +424,9 @@ diff -up src/sage/rings/polynomial/pbori/pbori.pyx.orig src/sage/rings/polynomia
cdef class MonomialConstruct:
diff -up src/sage/rings/real_mpfi.pyx.orig src/sage/rings/real_mpfi.pyx
--- src/sage/rings/real_mpfi.pyx.orig 2020-10-30 11:34:28.078977132 -0600
+++ src/sage/rings/real_mpfi.pyx 2020-10-30 14:03:09.088891288 -0600
@@ -1955,12 +1955,12 @@ cdef class RealIntervalFieldElement(Ring
--- src/sage/rings/real_mpfi.pyx.orig 2021-05-28 11:01:45.006275360 -0600
+++ src/sage/rings/real_mpfi.pyx 2021-05-28 11:39:54.280578896 -0600
@@ -1944,12 +1944,12 @@ cdef class RealIntervalFieldElement(Ring
cdef long digits
digits = strlen(lower_s)
@ -518,7 +441,7 @@ diff -up src/sage/rings/real_mpfi.pyx.orig src/sage/rings/real_mpfi.pyx
digits -= 1
upper_expo -= digits
@@ -2129,7 +2129,7 @@ cdef class RealIntervalFieldElement(Ring
@@ -2118,7 +2118,7 @@ cdef class RealIntervalFieldElement(Ring
raise MemoryError("Unable to allocate memory for the mantissa of an interval")
mpz_get_str(tmp_cstr, base, lower_mpz)
digits = strlen(tmp_cstr)
@ -528,9 +451,9 @@ diff -up src/sage/rings/real_mpfi.pyx.orig src/sage/rings/real_mpfi.pyx
mant_string = bytes_to_str(tmp_cstr+1)
sign_string = bytes_to_str(b'-')
diff -up src/sage/rings/real_mpfr.pyx.orig src/sage/rings/real_mpfr.pyx
--- src/sage/rings/real_mpfr.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/rings/real_mpfr.pyx 2020-11-05 15:44:02.769454276 -0700
@@ -2091,7 +2091,7 @@ cdef class RealNumber(sage.structure.ele
--- src/sage/rings/real_mpfr.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/rings/real_mpfr.pyx 2021-05-28 11:39:54.283578896 -0600
@@ -2095,7 +2095,7 @@ cdef class RealNumber(sage.structure.ele
if s is NULL:
raise RuntimeError("unable to convert an mpfr number to a string")
# t contains just digits (no sign, decimal point or exponent)
@ -540,8 +463,8 @@ diff -up src/sage/rings/real_mpfr.pyx.orig src/sage/rings/real_mpfr.pyx
t = char_to_str(s + 1)
else:
diff -up src/sage/structure/sage_object.pyx.orig src/sage/structure/sage_object.pyx
--- src/sage/structure/sage_object.pyx.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/structure/sage_object.pyx 2020-10-30 14:03:09.091891283 -0600
--- src/sage/structure/sage_object.pyx.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/structure/sage_object.pyx 2021-05-28 11:39:54.284578896 -0600
@@ -688,7 +688,7 @@ cdef class SageObject:
try:
s = self._interface_init_(I)
@ -552,9 +475,9 @@ diff -up src/sage/structure/sage_object.pyx.orig src/sage/structure/sage_object.
if c:
try:
diff -up src/sage/symbolic/expression.pyx.orig src/sage/symbolic/expression.pyx
--- src/sage/symbolic/expression.pyx.orig 2020-10-30 12:10:19.747169301 -0600
+++ src/sage/symbolic/expression.pyx 2020-10-30 14:03:09.095891276 -0600
@@ -13071,7 +13071,7 @@ cdef class hold_class:
--- src/sage/symbolic/expression.pyx.orig 2021-05-28 11:01:45.016275362 -0600
+++ src/sage/symbolic/expression.pyx 2021-05-28 11:39:54.289578896 -0600
@@ -13201,7 +13201,7 @@ cdef class hold_class:
sage: SR(2)^5
32
"""
@ -563,7 +486,7 @@ diff -up src/sage/symbolic/expression.pyx.orig src/sage/symbolic/expression.pyx
def __exit__(self, *args):
"""
@@ -13084,7 +13084,7 @@ cdef class hold_class:
@@ -13214,7 +13214,7 @@ cdef class hold_class:
sage: SR(2)^5
32
"""

14
sagemath-qepcad.patch
View file

@ -1,6 +1,6 @@
diff -up src/sage/interfaces/qepcad.py.orig src/sage/interfaces/qepcad.py
--- src/sage/interfaces/qepcad.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/interfaces/qepcad.py 2020-10-30 14:49:41.431265953 -0600
--- src/sage/interfaces/qepcad.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/interfaces/qepcad.py 2021-05-28 11:52:46.749626841 -0600
@@ -530,7 +530,7 @@ TESTS:
Check the qepcad configuration file::
@ -10,15 +10,15 @@ diff -up src/sage/interfaces/qepcad.py.orig src/sage/interfaces/qepcad.py
....: f.readlines()[-1]
'SINGULAR .../bin\n'
@@ -606,7 +606,6 @@ AUTHORS:
@@ -605,7 +605,6 @@ AUTHORS:
# http://www.gnu.org/licenses/
#*****************************************************************************
from __future__ import print_function, absolute_import
-from sage.env import SAGE_LOCAL
import pexpect
import re
import sys
@@ -621,6 +620,8 @@ from .expect import Expect, ExpectFuncti
@@ -620,6 +619,8 @@ from .expect import Expect, ExpectFuncti
from sage.interfaces.interface import AsciiArtString
@ -27,7 +27,7 @@ diff -up src/sage/interfaces/qepcad.py.orig src/sage/interfaces/qepcad.py
def _qepcad_atoms(formula):
r"""
Return the atoms of a qepcad quantifier-free formula, as a set of strings.
@@ -650,17 +651,17 @@ def _qepcad_cmd(memcells=None):
@@ -649,17 +650,17 @@ def _qepcad_cmd(memcells=None):
sage: from sage.interfaces.qepcad import _qepcad_cmd
sage: s = _qepcad_cmd()
@ -48,7 +48,7 @@ diff -up src/sage/interfaces/qepcad.py.orig src/sage/interfaces/qepcad.py
_command_info_cache = None
@@ -685,7 +686,7 @@ def _update_command_info():
@@ -684,7 +685,7 @@ def _update_command_info():
cache = {}

20
sagemath-rpmbuild.patch
View file

@ -1,12 +1,12 @@
diff -up src/sage/misc/cython.py.orig src/sage/misc/cython.py
--- src/sage/misc/cython.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/misc/cython.py 2020-10-30 16:08:06.039158996 -0600
@@ -46,7 +46,7 @@ standard_libs = [
] + cblas_libs + [
'ntl']
--- src/sage/misc/cython.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/misc/cython.py 2021-05-28 11:28:14.608518654 -0600
@@ -53,7 +53,7 @@ def _standard_libs_libdirs_incdirs_alias
'ec', 'gsl',
] + aliases["CBLAS_LIBRARIES"] + [
'ntl']
- standard_libdirs = [os.path.join(SAGE_LOCAL, "lib")] + aliases["CBLAS_LIBDIR"] + aliases["NTL_LIBDIR"]
+ standard_libdirs = [os.path.realpath(os.path.join(SAGE_LOCAL, "lib"))] + aliases["CBLAS_LIBDIR"] + aliases["NTL_LIBDIR"]
standard_incdirs = sage_include_directories() + aliases["CBLAS_INCDIR"] + aliases["NTL_INCDIR"]
return standard_libs, standard_libdirs, standard_incdirs, aliases
-standard_libdirs = [os.path.join(SAGE_LOCAL, "lib")] + cblas_library_dirs
+standard_libdirs = [os.path.realpath(os.path.join(SAGE_LOCAL, "lib"))] + cblas_library_dirs
################################################################

103
sagemath-sagedoc.patch
View file

@ -1,78 +1,7 @@
diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
--- src/sage/doctest/control.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/doctest/control.py 2020-10-30 13:55:37.330649309 -0600
@@ -115,7 +115,6 @@ class DocTestDefaults(SageObject):
self.valgrind = False
self.massif = False
self.cachegrind = False
- self.omega = False
self.failed = False
self.new = False
self.show_skipped = False
@@ -318,7 +317,7 @@ class DocTestController(SageObject):
if options.gdb or options.debug:
# Interactive debuggers: "infinite" timeout
options.timeout = 0
- elif options.valgrind or options.massif or options.cachegrind or options.omega:
+ elif options.valgrind or options.massif or options.cachegrind:
# Non-interactive debuggers: 48 hours
options.timeout = int(os.getenv('SAGE_TIMEOUT_VALGRIND', 48 * 60 * 60))
elif options.long:
@@ -1109,13 +1108,8 @@ class DocTestController(SageObject):
elif opt.cachegrind:
toolname = "cachegrind"
flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "")
- elif opt.omega:
- toolname = "exp-omega"
- flags = os.getenv("SAGE_OMEGA_FLAGS", "")
cmd = "exec valgrind --tool=%s "%(toolname)
flags += ''' --log-file="%s" ''' % logfile
- if opt.omega:
- toolname = "omega"
if "%s" in flags:
flags %= toolname + ".%p" # replace %s with toolname
cmd += flags + sage_cmd
@@ -1201,10 +1195,10 @@ class DocTestController(SageObject):
"""
opt = self.options
- L = (opt.gdb, opt.valgrind, opt.massif, opt.cachegrind, opt.omega)
+ L = (opt.gdb, opt.valgrind, opt.massif, opt.cachegrind)
if any(L):
if L.count(True) > 1:
- self.log("You may only specify one of gdb, valgrind/memcheck, massif, cachegrind, omega")
+ self.log("You may only specify one of gdb, valgrind/memcheck, massif, cachegrind")
return 2
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 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/interfaces/singular.py 2020-10-30 13:55:37.332649306 -0600
@@ -2349,7 +2349,7 @@ def generate_docstring_dictionary():
nodes.clear()
node_names.clear()
- singular_docdir = SINGULARPATH + "/../info/"
+ singular_docdir = "/usr/share/info/"
new_node = re.compile(r"File: singular\.hlp, Node: ([^,]*),.*")
new_lookup = re.compile(r"\* ([^:]*):*([^.]*)\..*")
@@ -2357,8 +2357,9 @@ def generate_docstring_dictionary():
L, in_node, curr_node = [], False, None
# singular.hlp contains a few iso-5559-1 encoded special characters
- with io.open(os.path.join(singular_docdir, 'singular.hlp'),
- encoding='latin-1') as f:
+ import gzip
+ with gzip.open(os.path.join(singular_docdir, 'singular.hlp.gz'),
+ encoding='utf-8') as f:
for line in f:
m = re.match(new_node,line)
if m:
diff -up src/sage_setup/docbuild/ext/multidocs.py.orig src/sage_setup/docbuild/ext/multidocs.py
--- src/sage_setup/docbuild/ext/multidocs.py.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage_setup/docbuild/ext/multidocs.py 2020-10-30 13:55:37.332649306 -0600
@@ -82,8 +82,11 @@ def merge_environment(app, env):
diff -up src/sage_docbuild/ext/multidocs.py.orig src/sage_docbuild/ext/multidocs.py
--- src/sage_docbuild/ext/multidocs.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage_docbuild/ext/multidocs.py 2021-05-28 11:32:20.056542939 -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())
@ -86,3 +15,27 @@ diff -up src/sage_setup/docbuild/ext/multidocs.py.orig src/sage_setup/docbuild/e
# merge the citations
newcite = {}
for ind, (path, tag, lineno) in citations.items():
diff -up src/sage/interfaces/singular.py.orig src/sage/interfaces/singular.py
--- src/sage/interfaces/singular.py.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/interfaces/singular.py 2021-05-28 11:29:00.597523201 -0600
@@ -2365,7 +2365,7 @@ def generate_docstring_dictionary():
nodes.clear()
node_names.clear()
- singular_docdir = SINGULARPATH + "/../info/"
+ singular_docdir = "/usr/share/info/"
new_node = re.compile(r"File: singular\.hlp, Node: ([^,]*),.*")
new_lookup = re.compile(r"\* ([^:]*):*([^.]*)\..*")
@@ -2373,8 +2373,9 @@ def generate_docstring_dictionary():
L, in_node, curr_node = [], False, None
# singular.hlp contains a few iso-5559-1 encoded special characters
- with io.open(os.path.join(singular_docdir, 'singular.hlp'),
- encoding='latin-1') as f:
+ import gzip
+ with gzip.open(os.path.join(singular_docdir, 'singular.hlp.gz'),
+ encoding='utf-8') as f:
for line in f:
m = re.match(new_node,line)
if m:

98
sagemath-scripts.patch
View file

@ -1,7 +1,7 @@
diff -up src/bin/sage.orig src/bin/sage
--- src/bin/sage.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/bin/sage 2020-10-30 13:43:06.816896461 -0600
@@ -29,7 +29,6 @@ usage() {
--- src/bin/sage.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/bin/sage 2021-05-28 11:16:43.936440802 -0600
@@ -109,7 +109,6 @@ usage() {
echo " --gap [...] -- run Sage's Gap with given arguments"
echo " --gp [...] -- run Sage's PARI/GP calculator with given arguments"
echo " -h -- print this help message"
@ -9,8 +9,8 @@ diff -up src/bin/sage.orig src/bin/sage
echo " --maxima [...] -- run Sage's Maxima with given arguments"
echo " --mwrank [...] -- run Sage's mwrank with given arguments"
echo " --notebook=[...] -- start the Sage notebook (valid options are"
@@ -59,119 +58,6 @@ usage() {
# below, after sourcing sage-env.
@@ -159,111 +158,6 @@ if [ -f "${SELF}-env-config" ]; then
fi
#####################################################################
-# Special options to be processed without sage-env
@ -22,7 +22,7 @@ diff -up src/bin/sage.orig src/bin/sage
-if [ "$1" = '--nodotsage' ]; then
- export DOT_SAGE=`mktemp -d ${TMPDIR:-/tmp}/dotsageXXXXXX`
- shift
- command "$0" "$@"
- command "${SELF}" "$@"
- status=$?
- rm -rf "$DOT_SAGE"
- exit $status
@ -51,14 +51,6 @@ diff -up src/bin/sage.orig src/bin/sage
- exit 127
-fi
-
-# Check for '--upgrade' before sourcing sage-env: the top-level "make"
-# should be run outside of the Sage shell, see #15517.
-if [ "$1" = '-upgrade' -o "$1" = "--upgrade" ]; then
- shift
- cd "$SAGE_ROOT"
- exec local/bin/sage-upgrade "$@"
-fi
-
-# Check for '-i' before sourcing sage-env: running "make"
-# should be run outside of the Sage shell.
-if [ "$1" = '-f' ]; then
@ -129,7 +121,7 @@ diff -up src/bin/sage.orig src/bin/sage
# Report information about the Sage environment
#####################################################################
@@ -217,20 +103,6 @@ fi
@@ -308,20 +202,6 @@ fi
# Prepare for running Sage, either interactively or non-interactively.
sage_setup() {
@ -150,7 +142,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ ! -d "$IPYTHONDIR" ]; then
# make sure that $DOT_SAGE exists so that ipython will happily
# create its config directories there. If DOT_SAGE doesn't
@@ -241,20 +113,6 @@ sage_setup() {
@@ -332,20 +212,6 @@ sage_setup() {
}
@ -160,7 +152,7 @@ diff -up src/bin/sage.orig src/bin/sage
-# if Python and sage-location haven't been installed yet.
-maybe_sage_location()
-{
- if [ -w "$SAGE_LOCAL" ]; then
- if [ -n "$SAGE_LOCAL" -a -w "$SAGE_LOCAL" ]; then
- if [ -x "$SAGE_LOCAL/bin/python" ] && [ -x "$SAGE_LOCAL/bin/sage-location" ]; then
- sage-location || exit $?
- fi
@ -171,7 +163,7 @@ diff -up src/bin/sage.orig src/bin/sage
# Start an interactive Sage session, this function never returns.
interactive_sage() {
sage_setup
@@ -292,8 +150,6 @@ usage_advanced() {
@@ -383,8 +249,6 @@ usage_advanced() {
echo " --nodotsage -- run Sage without using the user's"
echo " .sage directory: create and use a temporary"
echo " .sage directory instead."
@ -180,7 +172,7 @@ diff -up src/bin/sage.orig src/bin/sage
echo " --simple-prompt -- pass the option through to IPython: use"
echo " this option with sage-shell mode in emacs"
if [ -n "$SAGE_SRC" -a -d "$SAGE_SRC" ]; then
@@ -327,18 +183,9 @@ usage_advanced() {
@@ -418,18 +282,9 @@ usage_advanced() {
echo " environment (not Sage), passing additional"
echo " additional options to IPython"
echo " --jupyter [...] -- run Sage's Jupyter with given arguments"
@ -199,7 +191,7 @@ diff -up src/bin/sage.orig src/bin/sage
echo " --python [...], --python3 [...]"
echo " -- run the Python 3 interpreter"
echo " -R [...] -- run Sage's R with the given arguments"
@@ -601,11 +448,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
@@ -678,11 +533,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
exec ecl "$@"
fi
@ -211,7 +203,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
shift
maxima_cmd=$(sage-config MAXIMA 2>/dev/null)
@@ -630,11 +472,6 @@ if [ "$1" = '-R' -o "$1" = '--R' ]; then
@@ -707,11 +557,6 @@ if [ "$1" = '-R' -o "$1" = '--R' ]; then
exec R "$@"
fi
@ -223,19 +215,19 @@ diff -up src/bin/sage.orig src/bin/sage
#####################################################################
# sage --sh and sage --buildsh
#####################################################################
@@ -804,11 +641,6 @@ fi
@@ -883,11 +728,6 @@ fi
# build_sage, sage -b, sage -br, etc. could be moved to
# build/bin/sage-site. See #29111.
-build_sage() {
- maybe_sage_location
- ( cd "$SAGE_ROOT/build/make" && $MAKE sagelib-no-deps ) || exit $?
- ( cd "$SAGE_ROOT/build/make" && ./install sagelib-no-deps ) || exit $?
-}
-
if [[ "$1" =~ ^--notebook=.* || "$1" =~ ^-n=.* || "$1" =~ ^-notebook=.* ]] ; then
sage-cleaner &>/dev/null &
exec sage-notebook "$@"
@@ -819,13 +651,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
@@ -898,13 +738,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
exec sage-notebook "$@"
fi
@ -249,12 +241,12 @@ diff -up src/bin/sage.orig src/bin/sage
if [ -n "$SAGE_SRC" -a -d "$SAGE_SRC" ]; then
# Source inspection facilities, supported on sage-the-distribution and on distributions
# that package the Sage sources.
@@ -842,40 +667,12 @@ if [ -n "$SAGE_SRC" -a -d "$SAGE_SRC" ];
@@ -921,36 +754,11 @@ if [ -n "$SAGE_SRC" -a -d "$SAGE_SRC" ];
fi
fi
-if [ "$1" = '-b' ]; then
- time build_sage
- build_sage
- exit $?
-fi
-
@ -283,15 +275,22 @@ diff -up src/bin/sage.orig src/bin/sage
- exit $?
-fi
-
exec-runtests() {
sage_setup
export PYTHONIOENCODING="utf-8" # Fix encoding for doctests
@@ -967,10 +775,7 @@ exec-runtests() {
exec sage-runtests "$@"
}
-if [ "$1" = '-t' -o "$1" = '-bt' -o "$1" = '-tp' -o "$1" = '-btp' ]; then
- if [ "$1" = '-bt' -o "$1" = '-btp' ]; then
- build_sage
- fi
+if [ "$1" = '-t' -o "$1" = '-tp' ]; then
sage_setup
export PYTHONIOENCODING="utf-8" # Fix encoding for doctests
if [ "$1" = '-tp' -o "$1" = '-btp' ]; then
@@ -887,16 +684,6 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
shift
exec-runtests -p "$@"
@@ -980,34 +785,11 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
fi
fi
@ -300,16 +299,12 @@ diff -up src/bin/sage.orig src/bin/sage
- build_sage
- fi
- shift
- sage_setup
- export PYTHONIOENCODING="utf-8" # Fix encoding for doctests
- exec sage-runtests --new "$@"
- exec-runtests --new "$@"
-fi
-
if [ "$1" = '-testall' -o "$1" = "--testall" ]; then
shift
sage_setup
@@ -904,21 +691,6 @@ if [ "$1" = '-testall' -o "$1" = "--test
exec sage-runtests -a "$@"
exec-runtests -a "$@"
fi
-if [ "$1" = '-fixdoctests' -o "$1" = '--fixdoctests' ]; then
@ -324,13 +319,13 @@ diff -up src/bin/sage.orig src/bin/sage
-
-if [ "$1" = "-coverageall" -o "$1" = "--coverageall" ]; then
- shift
- exec sage-coverageall "$@"
- exec sage-coverage --all "$@"
-fi
-
if [ "$1" = '-startuptime' -o "$1" = '--startuptime' ]; then
exec sage-startuptime.py "$@"
fi
@@ -941,53 +713,6 @@ fi
@@ -1030,59 +812,11 @@ fi
# Creating and handling Sage distributions
#####################################################################
@ -364,27 +359,11 @@ diff -up src/bin/sage.orig src/bin/sage
- exit 1
- fi
- done
- # Display a message if we actually installed something (using this
- # file, generated by sage-spkg, is a bit of a hack though)
- if [ -f "$SAGE_LOCAL/lib/sage-force-relocate.txt" ]; then
- echo
- echo "Warning: it might be needed to update the Sage library before"
- echo "installed packages work: you should run 'make' from \$SAGE_ROOT"
- echo "before running Sage."
- fi
- exit 0
-}
-
-
-if [ "$1" = '-package' -o "$1" = "--package" ]; then
- shift
- exec sage-package $@
-fi
-
if [ "$1" = '-optional' -o "$1" = "--optional" ]; then
if [ "$1" = '-installed' -o "$1" = "--installed" ]; then
shift
exec sage-list-packages optional $@
@@ -1008,30 +733,6 @@ if [ "$1" = '-installed' -o "$1" = "--in
exec sage-list-packages all --installed-only $@
fi
@ -397,15 +376,6 @@ diff -up src/bin/sage.orig src/bin/sage
- install "$@"
-fi
-
-if [ "$1" = '-info' -o "$1" = '--info' ]; then
- shift
- for PKG in "$@"
- do
- sage-spkg --info "$PKG" || exit $?
- done
- exit 0
-fi
-
-if [ "$1" = '-sdist' -o "$1" = "--sdist" ]; then
- maybe_sage_location
- shift
@ -415,7 +385,7 @@ diff -up src/bin/sage.orig src/bin/sage
#####################################################################
# Debugging tools
#####################################################################
@@ -1075,12 +776,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
@@ -1126,12 +860,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
exec sage-callgrind "$@"
fi

6
sagemath-tdlib.patch
View file

@ -1,6 +1,6 @@
diff -up src/sage/graphs/graph_decompositions/tdlib/sage_tdlib.cpp.orig src/sage/graphs/graph_decompositions/tdlib/sage_tdlib.cpp
--- src/sage/graphs/graph_decompositions/tdlib/sage_tdlib.cpp.orig 2020-10-24 11:37:59.000000000 -0600
+++ src/sage/graphs/graph_decompositions/tdlib/sage_tdlib.cpp 2020-10-30 16:40:43.904036700 -0600
diff -up src/sage/graphs/graph_decompositions/sage_tdlib.cpp.orig src/sage/graphs/graph_decompositions/sage_tdlib.cpp
--- src/sage/graphs/graph_decompositions/sage_tdlib.cpp.orig 2021-05-09 16:00:11.000000000 -0600
+++ src/sage/graphs/graph_decompositions/sage_tdlib.cpp 2021-06-16 08:33:47.325415307 -0600
@@ -2,8 +2,8 @@
#include <map>

298
sagemath.spec
View file

@ -6,19 +6,11 @@
%bcond_with bundled_pexpect
%bcond_with bundled_ipython
%bcond_without bundled_ipywidgets
%bcond_without bundled_jupyter_jsmol
%bcond_without bundled_thebe
%bcond_without bundled_threejs
%bcond_without install_hack
%if 0%{?fedora} >= 33
%bcond_without flexiblas
%endif
%if %{with flexiblas}
%global blaslib flexiblas
%else
%global blaslib openblas
%endif
# for faster full rpm test builds
%ifarch %{ix86} x86_64
%bcond_without docs
@ -48,7 +40,7 @@
%global cremona_ver 2019-10-29
%global elliptic_curves_pkg elliptic_curves-0.8.1
%global flintqs_pkg flintqs-1.0
%global graphs_pkg graphs-20161026
%global graphs_pkg graphs-20210214
%if %{with bundled_ipython}
%global ipython_ver 7.13.0
%global ipython_pkg ipython-%{ipython_ver}
@ -56,27 +48,31 @@
%global prompt_tookit_pkg prompt_toolkit-%{prompt_toolkit_ver}
%endif
%if %{with bundled_ipywidgets}
%global ipywidgets_ver 7.5.1
%global ipywidgets_ver 7.6.3
%global ipywidgets_pkg ipywidgets-%{ipywidgets_ver}
%endif
%if %{with bundled_jupyter_jsmol}
%global jupyter_jsmol_ver 0.2.4
%global jupyter_jsmol_pkg jupyter_jsmol-%{jupyter_jsmol_ver}
%endif
%if %{with bundled_pexpect}
%global pexpect_pkg pexpect-4.8.0
%endif
%global polytopes_db_pkg polytopes_db-20170220
%global sagetex_pkg sagetex-3.5
%global Sphinx_pkg Sphinx-3.1.2
%global singular_pkg singular-4.1.1p2
%global singular_pkg singular-4.2.0p2
%if %{with bundled_thebe}
%global thebe_ver 9624e0a0
%global thebe_pkg thebe-%{thebe_ver}
%endif
%if %{with bundled_threejs}
%global threejs_ver r117
%global threejs_pkg threejs-%{threejs_ver}
%global threejs_ver r122
%global threejs_pkg threejs-sage-%{threejs_ver}
%endif
# Spkg equivalents of required rpms; we pretend they are installed as spkgs.
%global SAGE_REQUIRED_PKGS 4ti2-1.6.9 bliss-0.73 CoCoALib-0.99710 coxeter3-3.1 cryptominisat-5.7.1 database_cremona_ellcurve-%{cremona_ver} gap_packages-4.11.0 libsirocco-2.0.2 lrslib-071 mcqd-1.0 meataxe-1.0 primecount-6.1 qepcad-B.1.72 saclib-2.2.7 surf-1.0.6-gcc6 tdlib-0.9.0
%global SAGE_REQUIRED_PKGS 4ti2-1.6.9 bliss-0.73 CoCoALib-0.99712 coxeter3-3.1 cryptominisat-5.8.0 database_cremona_ellcurve-%{cremona_ver} gap_packages-4.11.0 libsirocco-2.0.2 lrslib-071a mcqd-1.0 meataxe-1.0 primecount-7.0 qepcad-B.1.74 saclib-2.2.8 surf-1.0.6-gcc6 tdlib-0.9.0
%ifarch %{ix86} x86_64
%global SAGE_REQUIRED_PKGS %{SAGE_REQUIRED_PKGS} fes-0.2
@ -93,8 +89,8 @@
Name: sagemath
Summary: A free open-source mathematics software system
Version: 9.2
Release: 5%{?dist}
Version: 9.3
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
@ -103,6 +99,7 @@ URL: http://www.sagemath.org
Source0: http://files.sagemath.org/src/sage-%{version}.tar.gz
Source1: https://github.com/JohnCremona/ecdata/archive/%{cremona_ver}/cremona-%{cremona_ver}.tar.gz
Source2: gprc.expect
Source3: org.sagemath.sage.metainfo.xml
# Follow maxima's ExclusiveArch, except exclude 32-bit ARM. The source RPM is
# now about 2GB in size. The 32-bit ARM builders run out of memory trying to
# create the SRPM and also trying to unpack the SRPM before starting a build.
@ -171,46 +168,49 @@ Patch16: %{name}-env.patch
# https://bugzilla.redhat.com/show_bug.cgi?id=1243590
Patch17: %{name}-qepcad.patch
# Correct path to arb headers
Patch18: %{name}-arb.patch
# Make the cvxopt backend check for 'optimal' as well as 'optimized'
Patch18: %{name}-cvxopt.patch
# Use flexiblas
Patch19: %{name}-flexiblas.patch
# Use openblas
Patch20: %{name}-openblas.patch
# Fix paths to latte-integrale binaries
Patch21: %{name}-latte.patch
Patch20: %{name}-latte.patch
# Change rubiks binary names to match Fedora
Patch22: %{name}-rubiks.patch
Patch21: %{name}-rubiks.patch
# Adapt to recent tdlib 0.9
Patch23: %{name}-tdlib.patch
Patch22: %{name}-tdlib.patch
# Use local objects.inv for intersphinx since no network on koji builders
Patch24: %{name}-intersphinx.patch
Patch23: %{name}-intersphinx.patch
# Remove an unused call to a primecount function that no longer exists
Patch25: %{name}-primecount.patch
Patch24: %{name}-primecount.patch
BuildRequires: make
BuildRequires: 4ti2
BuildRequires: appstream
BuildRequires: arb-devel
BuildRequires: bc
BuildRequires: bliss-devel
BuildRequires: boost-devel
BuildRequires: brial-devel
BuildRequires: cmake
BuildRequires: cddlib-devel
BuildRequires: cddlib-tools
BuildRequires: cliquer-devel
BuildRequires: cocoalib-devel
BuildRequires: coxeter-devel
BuildRequires: cryptominisat-devel
BuildRequires: csdp-devel
BuildRequires: desktop-file-utils
BuildRequires: dvipng
BuildRequires: ecl
%if %{with fes}
BuildRequires: fes-devel
%endif
BuildRequires: flexiblas-devel
BuildRequires: flint-devel
BuildRequires: gap-devel
BuildRequires: gap-pkg-aclib
@ -264,7 +264,9 @@ BuildRequires: gdb
BuildRequires: gfan
BuildRequires: giac-devel
BuildRequires: giac-doc
BuildRequires: git-core
BuildRequires: glpk-devel
BuildRequires: glpk-utils
BuildRequires: gmp-ecm
BuildRequires: gmp-ecm-devel
BuildRequires: ImageMagick
@ -274,42 +276,58 @@ BuildRequires: jmol
BuildRequires: jsmol
BuildRequires: jsmath-fonts
BuildRequires: L-function-devel
BuildRequires: latexmk
BuildRequires: latte-integrale
BuildRequires: libbraiding-devel
BuildRequires: libfrobby-devel
BuildRequires: libgap
BuildRequires: libhomfly-devel
BuildRequires: libmpc-devel
BuildRequires: lrcalc-devel
BuildRequires: lrslib-utils
BuildRequires: make
BuildRequires: mathjax
BuildRequires: maxima-runtime-ecl
BuildRequires: mcqd-devel
BuildRequires: mpfi-devel
BuildRequires: nauty
BuildRequires: ninja-build
BuildRequires: ntl-devel
BuildRequires: %{blaslib}-devel
BuildRequires: openssl
BuildRequires: palp
BuildRequires: pandoc
BuildRequires: pari-devel
BuildRequires: pari-elldata
BuildRequires: pari-galdata
BuildRequires: pari-galpol
BuildRequires: pari-gp
BuildRequires: pari-seadata
BuildRequires: perl-generators
BuildRequires: perl(ExtUtils::MakeMaker)
BuildRequires: perl(File::Slurp)
BuildRequires: pkgconfig(bdw-gc)
BuildRequires: pkgconfig(cbc)
BuildRequires: pkgconfig(eclib)
BuildRequires: pkgconfig(factory)
BuildRequires: pkgconfig(fplll)
BuildRequires: pkgconfig(gdlib)
BuildRequires: pkgconfig(gf2x)
BuildRequires: pkgconfig(gsl)
BuildRequires: pkgconfig(igraph)
BuildRequires: pkgconfig(libcurl)
BuildRequires: pkgconfig(libpng)
BuildRequires: pkgconfig(libsemigroups)
BuildRequires: pkgconfig(libzmq)
BuildRequires: pkgconfig(linbox)
BuildRequires: pkgconfig(m4ri)
BuildRequires: pkgconfig(m4rie)
BuildRequires: pkgconfig(nauty)
BuildRequires: pkgconfig(openssl)
BuildRequires: pkgconfig(pynac)
BuildRequires: pkgconfig(readline)
BuildRequires: pkgconfig(Singular)
BuildRequires: pkgconfig(sqlite3)
BuildRequires: pkgconfig(tk)
BuildRequires: pkgconfig(zlib)
BuildRequires: planarity-devel
BuildRequires: ppl-devel
@ -324,6 +342,8 @@ BuildRequires: python3-ipython-sphinx
BuildRequires: python3-pillow-devel
BuildRequires: python3-pplpy-devel
BuildRequires: python3-tdlib-devel
BuildRequires: python3-tkinter
BuildRequires: %{py3_dist argon2-cffi}
%if %{with bundled_ipython}
BuildRequires: %{py3_dist backcall}
%endif
@ -362,6 +382,7 @@ BuildRequires: %{py3_dist pkgconfig}
BuildRequires: %{py3_dist psutil}
BuildRequires: %{py3_dist ptyprocess}
BuildRequires: %{py3_dist pycryptosat}
BuildRequires: %{py3_dist pyopenssl}
%if %{with bundled_ipython}
BuildRequires: %{py3_dist pyzmq}
%endif
@ -369,12 +390,14 @@ BuildRequires: %{py3_dist rpy2}
BuildRequires: %{py3_dist scipy}
BuildRequires: %{py3_dist scons}
BuildRequires: %{py3_dist setuptools}
BuildRequires: %{py3_dist setuptools_scm}
%if %{with bundled_ipython}
BuildRequires: %{py3_dist simplegeneric}
%endif
BuildRequires: %{py3_dist six}
BuildRequires: %{py3_dist sphinx}
BuildRequires: %{py3_dist sympy}
BuildRequires: %{py3_dist tox}
BuildRequires: %{py3_dist wheel}
BuildRequires: %{py3_dist widgetsnbextension}
BuildRequires: %{py3_dist zodb3}
@ -383,9 +406,11 @@ BuildRequires: R
BuildRequires: ratpoints-devel
BuildRequires: rubiks
BuildRequires: rw-devel
BuildRequires: saclib-devel
BuildRequires: sharedmeataxe-devel
BuildRequires: sirocco-devel
BuildRequires: suitesparse-devel
BuildRequires: surf-geometry
BuildRequires: symmetrica-devel
BuildRequires: sympow
BuildRequires: tachyon
@ -396,6 +421,7 @@ BuildRequires: tex(makecmds.sty)
BuildRequires: web-assets-devel
BuildRequires: xorg-x11-fonts-Type1
BuildRequires: xorg-x11-server-Xvfb
BuildRequires: yasm-devel
BuildRequires: zn_poly-devel
Requires: hicolor-icon-theme
@ -415,10 +441,6 @@ Provides: bundled(thebe) = %{thebe_ver}
Provides: bundled(threejs) = %{threejs_ver}
%endif
# This can be removed when Fedora 30 reaches EOL
Obsoletes: %{name}-notebook-export < 8.8-5
Provides: %{name}-notebook-export = %{version}-%{release}
%description
Sage is a free open-source mathematics software system licensed
under the GPL. It combines the power of many existing open-source
@ -486,7 +508,9 @@ Requires: mathjax
Requires: maxima-runtime-ecl
Requires: nauty
Requires: palp
Requires: pari-elldata
Requires: pari-galdata
Requires: pari-galpol
Requires: pari-gp
Requires: pari-seadata
Requires: python3-tdlib
@ -551,6 +575,9 @@ Provides: bundled(prompt_toolkit) = %{prompt_toolkit_ver}
%if %{with bundled_ipywidgets}
Provides: bundled(ipywidgets) = %{ipywidgets_ver}
%endif
%if %{with bundled_jupyter_jsmol}
Provides: bundled(jupyter-jsmol) = %{jupyter_jsmol_ver}
%endif
%description core
This package contains the core sagemath python modules.
@ -737,12 +764,9 @@ This package contains the Turkish %{name} documentation.
Summary: Jupyter integration for sagemath
Requires: %{name}%{?_isa} = %{version}-%{release}
Requires: python-jupyter-filesystem
Requires: %{py3_dist argon2-cffi}
Requires: %{py3_dist widgetsnbextension}
# This can be removed when Fedora 31 reaches EOL
Obsoletes: sagemath-notebook < 9.0-1
Provides: sagemath-notebook = %{version}-%{release}
%description jupyter
This package contains a Jupyter integration for sagemath, replacing the
defunct notebook functionality.
@ -819,6 +843,13 @@ pushd build/pkgs/ipywidgets
popd
%endif
%if %{with bundled_jupyter_jsmol}
pushd build/pkgs/jupyter_jsmol
tar zxf ../../../upstream/%{jupyter_jsmol_pkg}.tar.gz
mv %{jupyter_jsmol_pkg} src
popd
%endif
%if %{with bundled_pexpect}
pushd build/pkgs/pexpect
tar zxf ../../../upstream/%{pexpect_pkg}.tar.gz
@ -891,20 +922,16 @@ popd
%patch16
%patch17
%patch18
%if "%{blaslib}" == "flexiblas"
%patch19
%else
%patch20
%endif
%patch21
%patch22
%patch23
%patch24
%patch25
sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
-e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \
-e 's|@@SAGE_LOCAL@@|%{SAGE_LOCAL}|' \
-e 's|@@LIBDIR@@|%{_libdir}|g' \
-i src/sage/env.py
sed -e 's|@@CYSIGNALS@@|%{python3_sitearch}/cysignals|' \
@ -916,23 +943,20 @@ sed -e 's|@@CYSIGNALS@@|%{python3_sitearch}/cysignals|' \
find src/sage \( -name \*.pyx -o -name \*.pxd \) -exec touch {} \+
# fix Singular paths
singver=$(sed 's/.*-\([.[:digit:]]*\).*/\1/' <<< %{singular_pkg})
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-$singver.so'," \
-i src/sage/env.py
# fix shebangs; some paths contains spaces, so use the null byte facility
grep -FrlZ '#!%{_bindir}/env python3' | \
xargs -0 sed -i 's,#!%{_bindir}/env python3,#!%{python3},g'
grep -FrlZ '#!%{_bindir}/env python' | \
xargs -0 sed -i 's,#!%{_bindir}/env python,#!%{python3},g'
grep -FrlZ '#!%{_bindir}/env sage-system-python' | \
xargs -0 sed -i 's,#!%{_bindir}/env sage-system-python,#!%{python3},g'
grep -FrlZ '#!%{_bindir}/env sage-bootstrap-python' | \
xargs -0 sed -i 's,#!%{_bindir}/env sage-bootstrap-python,#!%{python3},g'
grep -FrlZ '#!%{_bindir}/env sage-python' | \
xargs -0 sed -i 's,#!%{_bindir}/env sage-python,#!%{python3},g'
grep -FrlZ 'sage-python23' | xargs -0 sed -i 's,sage-python23,python3,g'
grep -FrlZ '#!%{_bindir}/env' | \
xargs -0 sed -i 's,#!%{_bindir}/env ,#!%{_bindir}/,'
grep -rlZ '#!%{_bindir}/python$' | xargs -0 sed -i 's,#!%{_bindir}/python$,&3,'
@ -945,7 +969,7 @@ sed -i 's,%{_bindir}/python,&3,' src/sage/misc/dev_tools.py
sed -e 's,local/bin/python,bin/python,' \
-e 's,#!%{_bindir}/python,&3,' \
-i src/sage/repl/preparse.py
sed -i 's,"$SAGE_LOCAL"/bin/python,%{_bindir}/python,g' src/bin/sage
sed -i 's,$SAGE_LOCAL/bin/python,%{_bindir}/python,g' src/bin/sage
%if %{with bundled_ipython}
sed -e "s|'%{_bindir}/env', 'which'|'%{_bindir}/which'|" \
-i build/pkgs/ipython/src/IPython/utils/_process_posix.py
@ -955,15 +979,38 @@ sed -e "s|'%{_bindir}/env', 'which'|'%{_bindir}/which'|" \
sed -i 's/64m/256m/' src/sage/interfaces/gap.py
# GAP does not have enough memory to build docs
sed -i 's/80/128/' src/sage_setup/docbuild/build_options.py
sed -i 's/80/128/' src/sage_docbuild/build_options.py
# Fix detection of Fedora
sed -i 's/yum/rpm/' build/bin/sage-guess-package-system
# Allow use of python 3.10
sed -i 's/3\.10\.0/3.11.0/g' configure
# Allow use of GCC 11
sed -i 's/1\[1-9\]/1[2-9]/' configure
# Allow use of pari 2.13.1
sed -i 's/Mod(0, 2)/0/' configure
# Allow use of fplll 5.4.1
sed -i 's/5\.4\.0/5.4.1/g' configure
# Allow use of giac 1.7
sed -i 's/1\.6\.999/1.7.999/g' configure
# Do not build with -march=native
sed -i 's/CFLAGS_MARCH="-march=native"/CFLAGS_MARCH=""/' configure
########################################################################
%build
export LC_ALL=C.UTF-8
export CC=%{__cc}
export CFLAGS="%{optflags}"
export CXXFLAGS="%{optflags}"
export CPPFLAGS="-I%{_includedir}/arb -I%{_includedir}/cddlib"
export CFLAGS="%{build_cflags}"
export CXXFLAGS="%{build_cxxflags}"
export ECMBIN=%{_bindir}/gmp-ecm
export SAGE_PYTHON_VERSION=3
export SAGE_ROOT=%{buildroot}%{SAGE_ROOT}
export SAGE_LOCAL=%{buildroot}%{SAGE_LOCAL}
@ -992,20 +1039,30 @@ export PYTHON=%{_bindir}/python3
export PYTHONPATH=%{buildroot}%{python3_sitearch}:$PYTHONPATH
#------------------------------------------------------------------------
# Generate sage-env-config
sed -e 's,@prefix@,%{SAGE_LOCAL},' \
-e 's,@CC@,gcc,' \
-e 's,@CXX@,g++,' \
-e 's,@FC@,gfortran,' \
-e 's,@OBJC@,gcc,' \
-e 's,@OBJCXX@,g++,' \
-e 's,@SAGE_PYTHON_VERSION@,3,' \
-e 's,@SAGE_GMP_PREFIX@,,' \
-e 's,@SAGE_GMP_INCLUDE@,%{_includedir},' \
-e 's,@SAGE_MPFR_PREFIX@,,' \
-e 's,@SAGE_MPC_PREFIX@,,' \
-e 's,@SAGE_NTL_PREFIX@,,' \
src/bin/sage-env-config.in > src/bin/sage-env-config
# Run the configure script to generate files
export GSL_LIBS="-lgsl -lflexiblas -lm"
%configure \
--prefix=$SAGE_LOCAL \
--disable-silent-rules \
--enable-4ti2 \
--enable-bliss \
--enable-cocoalib \
--enable-cryptominisat \
--enable-csdp \
--enable-database_cremona_ellcurve \
--enable-frobby \
--enable-mcqd \
--enable-meataxe \
--enable-primecount \
--enable-qepcad \
--enable-saclib \
--enable-sirocco \
--enable-surf \
--enable-tdlib
#------------------------------------------------------------------------
# Link with flexiblas instead of gslcblas
grep -FrlZ gslcblas | xargs -0 sed -i 's/gslcblas/flexiblas/g'
#------------------------------------------------------------------------
# Save and update environment to generate bundled interfaces
@ -1016,20 +1073,27 @@ export SAGE_LOCAL=%{_builddir}
%if %{with bundled_ipython}
pushd build/pkgs/ipython/src
%__python3 setup.py build
%__python3 setup.py install --root %{_builddir}
%{python3} setup.py build
%{python3} setup.py install --root %{_builddir}
popd
pushd build/pkgs/prompt_toolkit/src
%__python3 setup.py build
%__python3 setup.py install --root %{_builddir}
%{python3} setup.py build
%{python3} setup.py install --root %{_builddir}
popd
%endif
%if %{with bundled_ipywidgets}
pushd build/pkgs/ipywidgets/src
%__python3 setup.py build
%__python3 setup.py install --root %{_builddir}
%{python3} setup.py build
%{python3} setup.py install --root %{_builddir}
popd
%endif
%if %{with bundled_jupyter_jsmol}
pushd build/pkgs/jupyter_jsmol/src
%{python3} setup.py build
%{python3} setup.py install --root %{_builddir}
popd
%endif
@ -1051,12 +1115,14 @@ mkdir -p %{buildroot}%{SAGE_SPKG_INST}
mkdir -p %{buildroot}%{_libdir}/sagemath/build/pkgs
pushd src
%__python3 -u ./setup.py build
%{python3} -u ./setup.py build
tar cf - $(find sage -type f \! \( -name \*.c -o -name \*.cc -o -name \*.cpp -o -name .gitignore -o -name \*.hpp \) ) | (cd build/lib.*; tar xf -)
tar cf - $(find sage_setup -name \*.py) | (cd build/lib.*; tar xf -)
popd
#------------------------------------------------------------------------
pushd build/pkgs/sagetex/src
%__python3 ./setup.py build
%{python3} ./setup.py build
popd
#------------------------------------------------------------------------
@ -1208,7 +1274,7 @@ popd
#------------------------------------------------------------------------
pushd build/pkgs/conway_polynomials
%__python3 ./spkg-install.py
%{python3} ./spkg-install.py
popd
#------------------------------------------------------------------------
@ -1219,7 +1285,7 @@ pushd build/pkgs/elliptic_curves
tar jxf ../../../upstream/%{elliptic_curves_pkg}.tar.bz2
mv %{elliptic_curves_pkg} src
fi
%__python3 ./spkg-install.py
%{python3} ./spkg-install.py
popd
#------------------------------------------------------------------------
@ -1256,6 +1322,11 @@ mv %{_builddir}%{_bindir}/ip* %{buildroot}%{SAGE_LOCAL}/bin
mv %{_builddir}%{python3_sitelib}/ipywidgets* %{buildroot}%{SAGE_PYTHONPATH}
%endif
#------------------------------------------------------------------------
%if %{with bundled_jupyter_jsmol}
mv %{_builddir}%{python3_sitelib}/jupyter_jsmol* %{buildroot}%{SAGE_PYTHONPATH}
%endif
#------------------------------------------------------------------------
%if %{with bundled_thebe}
pushd build/pkgs/thebe
@ -1275,6 +1346,7 @@ popd
) # source build/bin/sage-dist-helpers
#------------------------------------------------------------------------
singver=$(sed 's/^.*-\([.[:digit:]]*\).*$/\1/' <<< %{singular_pkg})
cat > %{buildroot}%{SAGE_LOCAL}/bin/sage-env << EOF
export CUR=\$PWD
##export DOT_SAGE="\$HOME/.sage"
@ -1295,7 +1367,7 @@ module load surf-geometry-%{_arch}
export PATH=$SAGE_LOCAL/bin:\$PATH
export SINGULAR_DATA_DIR=%{_datadir}
export SINGULAR_BIN_DIR=%{_libdir}/Singular
export SINGULAR_SO=%{_libdir}/libSingular-4.1.1.so
export SINGULAR_SO=%{_libdir}/libSingular-$singver.so
##export PYTHONPATH="$SAGE_PYTHONPATH:\$SAGE_LOCAL/bin"
export SAGE_FORTRAN=%{_bindir}/gfortran
export SAGE_FORTRAN_LIB=\`gfortran --print-file-name=libgfortran.so\`
@ -1339,7 +1411,7 @@ pushd src/doc
export PATH=%{buildroot}%{_bindir}:$SAGE_LOCAL/bin:$PATH
export SINGULARPATH=%{_datadir}/singular/LIB
export SINGULAR_BIN_DIR=%{_libdir}/Singular
export PYTHONPATH=$SAGE_SETUP:%{buildroot}%{python3_sitearch}:$SAGE_PYTHONPATH:$SAGE_DOC
export PYTHONPATH=$SAGE_SETUP:%{buildroot}%{python3_sitearch}:$SAGE_PYTHONPATH:$SAGE_SRC
%if %{with sphinx_hack}
pushd ../../build/pkgs/sphinx/src
@ -1353,10 +1425,9 @@ pushd src/doc
ln -sf %{buildroot}%{SAGE_DOC} %{buildroot}%{SAGE_SRC}/doc
export SAGE_DOC=%{buildroot}%{SAGE_DOC}
export SAGE_DOC_SRC=$SAGE_DOC
# python -m sage_setup.docbuild
# Build with an X server running, required by some doc builders
SAGE_NUM_THREADS=2 \
xvfb-run -d %__python3 -m docbuild --no-pdf-links -k all html -j
xvfb-run -d %{python3} -m sage_docbuild --no-pdf-links -k all html -j
rm -f %{buildroot}%{SAGE_SRC}/doc
ln -sf %{SAGE_DOC} %{buildroot}%{SAGE_SRC}/doc
@ -1409,7 +1480,7 @@ ln -sf src $SAGE_ROOT/devel
install -p -m644 -D src/sage/ext_data/notebook-ipython/logo.svg \
%{buildroot}%{_datadir}/icons/hicolor/scalable/apps/sagemath.svg
mkdir -p %{buildroot}%{_datadir}/applications
cat > %{buildroot}%{_datadir}/applications/%{name}.desktop << EOF
cat > %{buildroot}%{_datadir}/applications/org.%{name}.sage.desktop << EOF
[Desktop Entry]
Name=Sagemath
Comment=A free open-source mathematics software system
@ -1419,7 +1490,13 @@ Terminal=true
Type=Application
Categories=Education;Science;Math;
EOF
desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop
desktop-file-validate %{buildroot}%{_datadir}/applications/org.%{name}.sage.desktop
# Install the AppData file
mkdir -p %{buildroot}%{_metainfodir}
cp -p %{SOURCE3} %{buildroot}%{_metainfodir}
appstreamcli validate --no-net \
%{buildroot}%{_metainfodir}/org.%{name}.sage.metainfo.xml
# Fix permissions
find %{buildroot} -name '*.so' -exec chmod 755 {} \+
@ -1449,6 +1526,9 @@ find %{buildroot}%{SAGE_DOC} -type d -name _sources -exec rm -fr {} \+
rm -r %{buildroot}%{python3_sitearch}/sage_setup
%endif
# remove files we do not want to install
rm %{buildroot}%{SAGE_LOCAL}/bin/sage-src-env-config.in
# pretend sagemath spkgs are installed to reduce number of errors
# in doctests
mkdir -p %{buildroot}%{SAGE_SPKG_INST}
@ -1465,6 +1545,7 @@ pushd %{buildroot}%{SAGE_SPKG_INST}
mkdir $pkg
done
popd
#------------------------------------------------------------------------
cat > %{buildroot}%{SAGE_LOCAL}/bin/sage-list-packages << EOF
#!/bin/sh
@ -1541,19 +1622,26 @@ popd
# Build the large Cremona database
export PATH=%{buildroot}%{SAGE_LOCAL}/bin:$PATH
export PYTHONPATH=%{buildroot}%{SAGE_PYTHONPATH}:%{buildroot}%{python3_sitearch}
touch %{buildroot}%{SAGE_SHARE}/cremona/cremona.db
cat > cremona.sage << EOF
import sage.env
import sage.databases.cremona
db_path = '%{buildroot}%{SAGE_SHARE}/cremona/cremona'
c = sage.databases.cremona.LargeCremonaDatabase(db_path, False, True)
sage.env.SAGE_SHARE = '%{buildroot}%{SAGE_SHARE}'
c = sage.databases.cremona.LargeCremonaDatabase('cremona', False, True)
c._init_from_ftpdata('ecdata-%{cremona_ver}')
EOF
%{buildroot}%{SAGE_LOCAL}/bin/sage cremona.sage
#------------------------------------------------------------------------
# Script was used to build documentation and possibly other operations
perl -pi -e 's|%{buildroot}||g;s|^##||g;' \
# Scripts were used to build documentation and possibly other operations
sed -i 's|%{buildroot}||g;s|^##||g;' \
%{buildroot}%{_bindir}/sage \
%{buildroot}%{SAGE_LOCAL}/bin/sage-env
%{buildroot}%{SAGE_LOCAL}/bin/sage-env \
%{buildroot}%{SAGE_LOCAL}/bin/sage-env-config \
%{buildroot}%{SAGE_LOCAL}/bin/sage-src-env-config
sed -i "s|$PWD|%{SAGE_ROOT}|g" \
%{buildroot}%{SAGE_LOCAL}/bin/sage-env-config \
%{buildroot}%{SAGE_LOCAL}/bin/sage-src-env-config
# last install command
rm -fr $DOT_SAGE
@ -1659,20 +1747,12 @@ end
%files
# GPLv2+
%dir %{SAGE_ROOT}
%license COPYING.txt
%doc %{SAGE_ROOT}/COPYING.txt
%dir %{SAGE_ROOT}
%dir %{SAGE_LOCAL}/
%dir %{SAGE_LOCAL}/bin/
%dir %{SAGE_SHARE}/
%{SAGE_LOCAL}/bin/QuadraticSieve
%{SAGE_LOCAL}/bin/ecm
%{SAGE_LOCAL}/bin/gap
%{SAGE_LOCAL}/bin/jmol
%if %{with bundled_ipython}
%{SAGE_LOCAL}/bin/ip*
%endif
%{SAGE_LOCAL}/bin/python
%{SAGE_LOCAL}/bin/sage*
%{SAGE_LOCAL}/bin/
%{SAGE_LOCAL}/include
%{SAGE_LOCAL}/lib
%{SAGE_LOCAL}/share
@ -1681,16 +1761,13 @@ end
%{SAGE_ROOT}/devel
%{SAGE_ROOT}/doc
%{SAGE_ROOT}/share
%dir %{SAGE_SRC}/
%if %{with docs}
%{SAGE_SRC}/doc
%endif
%{SAGE_SRC}/sage
%{SAGE_SRC}/
%dir %{SAGE_PYTHONPATH}
# GPLv2+
%{_bindir}/sage
%{_datadir}/icons/hicolor/scalable/apps/%{name}.svg
%{_datadir}/applications/%{name}.desktop
%{_datadir}/applications/org.%{name}.sage.desktop
%{_metainfodir}/org.%{name}.sage.metainfo.xml
%if %{with bundled_thebe}
# MIT
%{SAGE_SHARE}/thebe/
@ -1714,10 +1791,12 @@ end
%if %{with bundled_ipywidgets}
%{SAGE_PYTHONPATH}/ipywidgets*
%endif
%if %{with bundled_jupyter_jsmol}
%{SAGE_PYTHONPATH}/jupyter_jsmol*
%endif
#------------------------------------------------------------------------
%files data
%dir %{SAGE_SHARE}/
%dir %{SAGE_ETC}/
%{SAGE_ETC}/sage
%{SAGE_ETC}/gprc.expect
@ -1775,6 +1854,7 @@ end
#------------------------------------------------------------------------
%files doc
# GPLv2+
%license COPYING.txt
%dir %{SAGE_DOC}/
%{SAGE_DOC}/common/
%dir %{SAGE_DOC}/html/
@ -1909,8 +1989,6 @@ end
%{SAGE_ETC}/notebook-ipython/
# LGPLv2+
%{_datadir}/jupyter/kernels/sagemath/
%{_datadir}/jupyter/nbextensions/jsmol
%{_datadir}/jupyter/nbextensions/mathjax
%{_datadir}/jupyter/nbextensions/threejs
#------------------------------------------------------------------------
@ -1923,6 +2001,12 @@ end
########################################################################
%changelog
* Thu Jun 17 2021 Jerry James <loganjerry@gmail.com> - 9.3-1
- Version 9.3
- Drop -arb and -openblas patches
- Add -cvxopt patch
- Add metainfo file
* Fri Jun 04 2021 Python Maint <python-maint@redhat.com> - 9.2-5
- Rebuilt for Python 3.10

2
sources
View file

@ -1,2 +1,2 @@
SHA512 (cremona-2019-10-29.tar.gz) = 32fbb828f26f87191e39123762cfbd796aac9abf346f0dc981e8e3f390435b22d281be3031ea92ae7e18f4ce41af8054784ca0d550a08f17b05c54ca08b4c9c8
SHA512 (sage-9.2.tar.gz) = d7e833919740dd9249b14fb0fc7fdc93ad6265dae9363fa2495c88274f0683c7aae2f7625f842584a95bd4f6a439d575a6532a945d6e50054355853d68e0275d
SHA512 (sage-9.3.tar.gz) = e5775aeff52fde3176f73340050e373e010a96f965c4b939b2ab105a941260d163185be2495ad38de6fbcaed81e897b6ad4180874ccfc778542beb79287bc912