Version 9.5.

Drop unnecessary -4ti2 and -primecount patches.

README.md

@@ -0,0 +1,5 @@
+# sagemath
+
+[Sage](https://www.sagemath.org/) 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.

sagemath-4ti2.patch

@@ -1,22 +0,0 @@
-diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
---- 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')
--
- 
- 
- def _sandpile_help(cls, usage, verbose=True):
-@@ -5172,7 +5169,7 @@ class SandpileDivisor(dict):
-             sign_file.write('\n')
-         # compute
-         try:
--            os.system(path_to_zsolve+' -q ' + lin_sys + ' > ' + lin_sys_log)
-+            os.system('zsolve -q ' + lin_sys + ' > ' + lin_sys_log)
-             # process the results
-             zhom_file = open(lin_sys_zhom,'r')
-         except IOError:

sagemath-env.patch

@@ -1,22 +1,6 @@
-diff -up src/bin/sage-env.orig src/bin/sage-env
---- src/bin/sage-env.orig	2021-08-22 02:44:33.000000000 -0600
-+++ src/bin/sage-env	2021-08-27 08:49:17.252812930 -0600
-@@ -333,10 +333,8 @@ if [ -n "$SAGE_LOCAL" ]; then
-     export CPATH="$SAGE_LOCAL/include${CPATH}"
- fi
- 
--if [ -n "$SAGE_LOCAL" ]; then
--    SINGULARPATH="$SAGE_LOCAL/share/singular" && export SINGULARPATH
--    SINGULAR_EXECUTABLE="$SAGE_LOCAL/bin/Singular" && export SINGULAR_EXECUTABLE
--fi
-+SINGULARPATH="/usr/share/singular" && export SINGULARPATH
-+SINGULAR_EXECUTABLE="/usr/bin/Singular" && export SINGULAR_EXECUTABLE
- 
- if [ -z "$SAGE_REPO_ANONYMOUS" ]; then
-     SAGE_REPO_ANONYMOUS="https://gitlab.com/sagemath/dev/tracmirror.git"
 diff -up src/sage/env.py.orig src/sage/env.py
---- src/sage/env.py.orig	2021-08-27 08:46:35.399958049 -0600
+--- src/sage/env.py.orig	2022-03-04 16:22:20.700225896 -0700
-+++ src/sage/env.py	2021-08-27 08:46:48.584192481 -0600
++++ src/sage/env.py	2022-03-04 16:23:09.566306142 -0700
 @@ -166,15 +166,15 @@ SAGE_DATE = var("SAGE_DATE", version.dat
  SAGE_VERSION_BANNER = var("SAGE_VERSION_BANNER", version.banner)
  
@@ -53,16 +37,3 @@ diff -up src/sage/env.py.orig src/sage/env.py
  MAXIMA = var("MAXIMA", "maxima")
  MAXIMA_FAS = var("MAXIMA_FAS")
  KENZO_FAS = var("KENZO_FAS")
-@@ -309,10 +309,10 @@ 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 DOT_SAGE is not None and ' ' in DOT_SAGE:

sagemath-extensions.patch

@@ -1,7 +1,7 @@
 diff -up src/sage/env.py.orig src/sage/env.py
---- src/sage/env.py.orig	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/env.py.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/env.py	2021-05-28 11:18:15.134457599 -0600
++++ src/sage/env.py	2022-03-04 16:04:55.067452303 -0700
-@@ -430,7 +430,8 @@ def cython_aliases():
+@@ -496,7 +496,8 @@ def cython_aliases(required_modules=None
          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 +12,17 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/graphs/mcqd.pyx.orig	2022-03-04 16:04:55.068452305 -0700
-+++ src/sage/graphs/mcqd.pyx	2021-05-28 11:18:15.134457599 -0600
++++ src/sage/graphs/mcqd.pyx	2022-03-04 16:05:55.226537259 -0700
 @@ -1,4 +1,5 @@
  # distutils: language = c++
 +# distutils: libraries = mcqd
- # sage_setup: distribution = sage-mcqd
+ # sage_setup: distribution = sagemath-mcqd
  
  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	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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/libs/arb/arb.pxd.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/libs/arb/arb.pxd	2021-05-28 11:18:15.135457599 -0600
++++ src/sage/libs/arb/arb.pxd	2022-03-04 16:05:03.939464830 -0700
 @@ -1,4 +1,5 @@
  # distutils: libraries = gmp flint ARB_LIBRARY
 +# distutils: include_dirs = /usr/include/arb /usr/include/flint
@@ -38,8 +30,8 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/libs/arb/arb_version.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/libs/arb/arb_version.pyx	2021-05-28 11:18:15.135457599 -0600
++++ src/sage/libs/arb/arb_version.pyx	2022-03-04 16:05:03.939464830 -0700
 @@ -1,4 +1,5 @@
  # -*- coding: utf-8
 +# distutils: include_dirs = /usr/include/arb /usr/include/flint
@@ -47,48 +39,48 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/libs/arb/arith.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/libs/arb/arith.pyx	2021-05-28 11:18:15.135457599 -0600
++++ src/sage/libs/arb/arith.pyx	2022-03-04 16:05:03.939464830 -0700
 @@ -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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/libs/mpmath/ext_impl.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/libs/mpmath/ext_impl.pyx	2021-05-28 11:18:15.135457599 -0600
++++ src/sage/libs/mpmath/ext_impl.pyx	2022-03-04 16:05:03.939464830 -0700
 @@ -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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/libs/mpmath/ext_libmp.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/libs/mpmath/ext_libmp.pyx	2021-05-28 11:18:15.135457599 -0600
++++ src/sage/libs/mpmath/ext_libmp.pyx	2022-03-04 16:05:03.940464832 -0700
 @@ -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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/libs/mpmath/ext_main.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/libs/mpmath/ext_main.pyx	2021-05-28 11:18:15.135457599 -0600
++++ src/sage/libs/mpmath/ext_main.pyx	2022-03-04 16:05:03.940464832 -0700
 @@ -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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/libs/mpmath/utils.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/libs/mpmath/utils.pyx	2021-05-28 11:18:15.136457599 -0600
++++ src/sage/libs/mpmath/utils.pyx	2022-03-04 16:05:03.940464832 -0700
 @@ -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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/matrix/matrix_complex_ball_dense.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/matrix/matrix_complex_ball_dense.pyx	2021-05-28 11:18:15.136457599 -0600
++++ src/sage/matrix/matrix_complex_ball_dense.pyx	2022-03-04 16:05:03.941464833 -0700
 @@ -1,4 +1,5 @@
  # distutils: libraries = ARB_LIBRARY
 +# distutils: include_dirs = /usr/include/arb /usr/include/flint
@@ -96,8 +88,8 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/matrix/matrix_cyclo_dense.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/matrix/matrix_cyclo_dense.pyx	2021-05-28 12:09:14.100657210 -0600
++++ src/sage/matrix/matrix_cyclo_dense.pyx	2022-03-04 16:05:03.941464833 -0700
 @@ -1,7 +1,7 @@
  # distutils: language = c++
  # distutils: libraries = NTL_LIBRARIES
@@ -108,16 +100,16 @@ diff -up src/sage/matrix/matrix_cyclo_dense.pyx.orig src/sage/matrix/matrix_cycl
  # distutils: extra_link_args = NTL_LIBEXTRA
  """
 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/matrix/matrix_mpolynomial_dense.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/matrix/matrix_mpolynomial_dense.pyx	2021-05-28 11:18:15.136457599 -0600
++++ src/sage/matrix/matrix_mpolynomial_dense.pyx	2022-03-04 16:05:03.941464833 -0700
 @@ -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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/rings/complex_arb.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/rings/complex_arb.pyx	2021-05-28 11:18:15.137457600 -0600
++++ src/sage/rings/complex_arb.pyx	2022-03-04 16:05:03.942464834 -0700
 @@ -1,4 +1,5 @@
  # -*- coding: utf-8
 +# distutils: include_dirs = /usr/include/arb /usr/include/flint
@@ -125,8 +117,8 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/rings/number_field/number_field_element_quadratic.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/rings/number_field/number_field_element_quadratic.pyx	2021-05-28 11:18:15.138457600 -0600
++++ src/sage/rings/number_field/number_field_element_quadratic.pyx	2022-03-04 16:05:03.942464834 -0700
 @@ -4,6 +4,7 @@
  # distutils: library_dirs = NTL_LIBDIR
  # distutils: extra_link_args = NTL_LIBEXTRA
@@ -136,32 +128,32 @@ diff -up src/sage/rings/number_field/number_field_element_quadratic.pyx.orig src
  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	2021-05-28 11:01:44.993275358 -0600
+--- src/sage/rings/polynomial/multi_polynomial_libsingular.pyx.orig	2022-03-04 15:50:57.344269364 -0700
-+++ src/sage/rings/polynomial/multi_polynomial_libsingular.pyx	2021-05-28 11:18:15.138457600 -0600
++++ src/sage/rings/polynomial/multi_polynomial_libsingular.pyx	2022-03-04 16:05:03.943464836 -0700
 @@ -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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/rings/polynomial/multi_polynomial.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/rings/polynomial/multi_polynomial.pyx	2021-05-28 11:18:15.139457600 -0600
++++ src/sage/rings/polynomial/multi_polynomial.pyx	2022-03-04 16:05:03.944464837 -0700
 @@ -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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/rings/polynomial/plural.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/rings/polynomial/plural.pyx	2021-05-28 11:18:15.139457600 -0600
++++ src/sage/rings/polynomial/plural.pyx	2022-03-04 16:05:03.944464837 -0700
 @@ -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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/rings/polynomial/polynomial_complex_arb.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/rings/polynomial/polynomial_complex_arb.pyx	2021-05-28 11:18:15.139457600 -0600
++++ src/sage/rings/polynomial/polynomial_complex_arb.pyx	2022-03-04 16:05:03.944464837 -0700
 @@ -1,4 +1,5 @@
  # -*- coding: utf-8
 +# distutils: include_dirs = /usr/include/arb /usr/include/flint
@@ -169,8 +161,8 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/rings/real_arb.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/rings/real_arb.pyx	2021-05-28 11:18:15.140457600 -0600
++++ src/sage/rings/real_arb.pyx	2022-03-04 16:05:03.945464839 -0700
 @@ -1,4 +1,5 @@
  # -*- coding: utf-8
 +# distutils: include_dirs = /usr/include/arb /usr/include/flint
@@ -178,8 +170,8 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage_setup/command/sage_build_cython.py.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage_setup/command/sage_build_cython.py	2021-05-28 12:09:14.113657210 -0600
++++ src/sage_setup/command/sage_build_cython.py	2022-03-04 16:05:03.945464839 -0700
 @@ -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

sagemath-flexiblas.patch

@@ -1,7 +1,7 @@
 diff -up configure.orig configure
---- configure.orig	2021-08-22 02:45:52.000000000 -0600
+--- configure.orig	2022-01-30 06:43:09.000000000 -0700
-+++ configure	2021-08-26 13:40:30.029000877 -0600
++++ configure	2022-03-04 16:30:36.953830625 -0700
-@@ -12703,12 +12703,12 @@ if test -n "$OPENBLAS_CFLAGS"; then
+@@ -16226,12 +16226,12 @@ if test -n "$OPENBLAS_CFLAGS"; then
      pkg_cv_OPENBLAS_CFLAGS="$OPENBLAS_CFLAGS"
   elif test -n "$PKG_CONFIG"; then
      if test -n "$PKG_CONFIG" && \
@@ -17,7 +17,7 @@ diff -up configure.orig configure
  		      test "x$?" != "x0" && pkg_failed=yes
  else
    pkg_failed=yes
-@@ -12720,12 +12720,12 @@ if test -n "$OPENBLAS_LIBS"; then
+@@ -16243,12 +16243,12 @@ if test -n "$OPENBLAS_LIBS"; then
      pkg_cv_OPENBLAS_LIBS="$OPENBLAS_LIBS"
   elif test -n "$PKG_CONFIG"; then
      if test -n "$PKG_CONFIG" && \
@@ -33,7 +33,7 @@ diff -up configure.orig configure
  		      test "x$?" != "x0" && pkg_failed=yes
  else
    pkg_failed=yes
-@@ -12746,9 +12746,9 @@ else
+@@ -16269,9 +16269,9 @@ else
          _pkg_short_errors_supported=no
  fi
          if test $_pkg_short_errors_supported = yes; then
@@ -45,7 +45,7 @@ diff -up configure.orig configure
          fi
  	# Put the nasty error message in config.log where it belongs
  	echo "$OPENBLAS_PKG_ERRORS" >&5
-@@ -12776,16 +12776,16 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_
+@@ -16299,16 +16299,16 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_
  #ifdef __cplusplus
  extern "C"
  #endif
@@ -65,7 +65,7 @@ diff -up configure.orig configure
    if test -z "$ac_lib"; then
      ac_res="none required"
    else
-@@ -12835,22 +12835,22 @@ else
+@@ -16358,22 +16358,22 @@ else
  /* end confdefs.h.  */
  
                             #include <stdio.h>
@@ -95,7 +95,7 @@ diff -up configure.orig configure
                                                 return 1;
    ;
    return 0;
-@@ -12903,7 +12903,7 @@ return cblas_dgemm ();
+@@ -16426,7 +16426,7 @@ return cblas_dgemm ();
    return 0;
  }
  _ACEOF
@@ -104,7 +104,7 @@ diff -up configure.orig configure
    if test -z "$ac_lib"; then
      ac_res="none required"
    else
-@@ -12967,7 +12967,7 @@ return dgeqrf ();
+@@ -16490,7 +16490,7 @@ return dgeqrf ();
    return 0;
  }
  _ACEOF
@@ -113,7 +113,7 @@ diff -up configure.orig configure
    if test -z "$ac_lib"; then
      ac_res="none required"
    else
-@@ -13031,7 +13031,7 @@ return dgeqrf_ ();
+@@ -16554,7 +16554,7 @@ return dgeqrf_ ();
    return 0;
  }
  _ACEOF
@@ -122,7 +122,7 @@ diff -up configure.orig configure
    if test -z "$ac_lib"; then
      ac_res="none required"
    else
-@@ -13095,7 +13095,7 @@ return DGEQRF ();
+@@ -16618,7 +16618,7 @@ return DGEQRF ();
    return 0;
  }
  _ACEOF
@@ -131,7 +131,7 @@ diff -up configure.orig configure
    if test -z "$ac_lib"; then
      ac_res="none required"
    else
-@@ -13159,7 +13159,7 @@ return DGEQRF_ ();
+@@ -16682,7 +16682,7 @@ return DGEQRF_ ();
    return 0;
  }
  _ACEOF
@@ -140,7 +140,7 @@ diff -up configure.orig configure
    if test -z "$ac_lib"; then
      ac_res="none required"
    else
-@@ -13247,16 +13247,16 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_
+@@ -16770,16 +16770,16 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_
  #ifdef __cplusplus
  extern "C"
  #endif
@@ -160,7 +160,7 @@ diff -up configure.orig configure
    if test -z "$ac_lib"; then
      ac_res="none required"
    else
-@@ -13306,22 +13306,22 @@ else
+@@ -16829,22 +16829,22 @@ else
  /* end confdefs.h.  */
  
                             #include <stdio.h>
@@ -190,7 +190,7 @@ diff -up configure.orig configure
                                                 return 1;
    ;
    return 0;
-@@ -13374,7 +13374,7 @@ return cblas_dgemm ();
+@@ -16897,7 +16897,7 @@ return cblas_dgemm ();
    return 0;
  }
  _ACEOF
@@ -199,7 +199,7 @@ diff -up configure.orig configure
    if test -z "$ac_lib"; then
      ac_res="none required"
    else
-@@ -13438,7 +13438,7 @@ return dgeqrf ();
+@@ -16961,7 +16961,7 @@ return dgeqrf ();
    return 0;
  }
  _ACEOF
@@ -208,7 +208,7 @@ diff -up configure.orig configure
    if test -z "$ac_lib"; then
      ac_res="none required"
    else
-@@ -13502,7 +13502,7 @@ return dgeqrf_ ();
+@@ -17025,7 +17025,7 @@ return dgeqrf_ ();
    return 0;
  }
  _ACEOF
@@ -217,7 +217,7 @@ diff -up configure.orig configure
    if test -z "$ac_lib"; then
      ac_res="none required"
    else
-@@ -13566,7 +13566,7 @@ return DGEQRF ();
+@@ -17089,7 +17089,7 @@ return DGEQRF ();
    return 0;
  }
  _ACEOF
@@ -226,7 +226,7 @@ diff -up configure.orig configure
    if test -z "$ac_lib"; then
      ac_res="none required"
    else
-@@ -13630,7 +13630,7 @@ return DGEQRF_ ();
+@@ -17153,7 +17153,7 @@ return DGEQRF_ ();
    return 0;
  }
  _ACEOF
@@ -235,7 +235,7 @@ diff -up configure.orig configure
    if test -z "$ac_lib"; then
      ac_res="none required"
    else
-@@ -13705,12 +13705,12 @@ if test -n "$OPENBLASPCDIR"; then
+@@ -17228,12 +17228,12 @@ if test -n "$OPENBLASPCDIR"; then
      pkg_cv_OPENBLASPCDIR="$OPENBLASPCDIR"
   elif test -n "$PKG_CONFIG"; then
      if test -n "$PKG_CONFIG" && \
@@ -251,7 +251,7 @@ diff -up configure.orig configure
  		      test "x$?" != "x0" && pkg_failed=yes
  else
    pkg_failed=yes
-@@ -13925,7 +13925,7 @@ fi
+@@ -17448,7 +17448,7 @@ fi
       if test x$sage_spkg_install_openblas != xyes; then :
  
  
@@ -261,18 +261,18 @@ diff -up configure.orig configure
  
           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	2021-08-26 13:39:46.040938448 -0600
+--- src/sage/env.py.orig	2022-03-04 16:23:09.566306142 -0700
-+++ src/sage/env.py	2021-08-26 13:40:30.029000877 -0600
++++ src/sage/env.py	2022-03-04 16:30:36.953830625 -0700
-@@ -212,7 +212,7 @@ MAXIMA_FAS = var("MAXIMA_FAS")
+@@ -221,7 +221,7 @@ FOURTITWO_PPI = var("FOURTITWO_PPI")
- KENZO_FAS = var("KENZO_FAS")
+ FOURTITWO_CIRCUITS = var("FOURTITWO_CIRCUITS")
- SAGE_NAUTY_BINS_PREFIX = var("SAGE_NAUTY_BINS_PREFIX", "")
+ FOURTITWO_GROEBNER = var("FOURTITWO_GROEBNER")
  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")
-@@ -456,7 +456,7 @@ def cython_aliases(required_modules=('ff
+@@ -467,7 +467,7 @@ def cython_aliases(required_modules=None
      for lib, required in itertools.chain(((lib, True) for lib in required_modules),
                                           ((lib, False) for lib in optional_modules)):
          var = lib.upper().replace("-", "") + "_"

sagemath-infinite-recursion.patch

@@ -0,0 +1,22 @@
+Fix this warning:
+
+sage/matrix/matrix_rational_dense.cpp: In function ‘__pyx_f_4sage_4libs_3gmp_9randomize_mpq_randomize_entry_recip_uniform_nonzero(__mpq_struct*)’:
+sage/matrix/matrix_rational_dense.cpp:28763:27: warning: infinite recursion detected [-Winfinite-recursion]
+28763 | static CYTHON_INLINE void __pyx_f_4sage_4libs_3gmp_9randomize_mpq_randomize_entry_recip_uniform_nonzero(__mpq_struct *__pyx_v_x) {
+      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+sage/matrix/matrix_rational_dense.cpp:28775:80: note: recursive call
+28775 |   __pyx_f_4sage_4libs_3gmp_9randomize_mpq_randomize_entry_recip_uniform_nonzero(__pyx_v_x);
+      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
+
+diff -up src/sage/libs/gmp/randomize.pxd.orig src/sage/libs/gmp/randomize.pxd
+--- src/sage/libs/gmp/randomize.pxd.orig	2022-01-30 06:41:50.000000000 -0700
++++ src/sage/libs/gmp/randomize.pxd	2022-03-06 12:36:38.591777518 -0700
+@@ -51,6 +51,6 @@ cdef inline void mpq_randomize_entry_rec
+     mpq_canonicalize(x)
+ 
+ cdef inline void mpq_randomize_entry_recip_uniform_nonzero(mpq_t x):
+-    mpq_randomize_entry_recip_uniform_nonzero(x)
++    mpq_randomize_entry_recip_uniform(x)
+     while mpq_sgn(x) == 0:
+-        mpq_randomize_entry_recip_uniform_nonzero(x)
++        mpq_randomize_entry_recip_uniform(x)

sagemath-intersphinx-disabled-reftypes.patch

@@ -0,0 +1,17 @@
+Fix this error:
+
+[polynomia] updating environment: [new config] 62 added, 0 changed, 0 removed
+[polynomia] Extension error (sage.docs.conf):
+[polynomia] Handler <function find_sage_dangling_links at 0x7f92ac43f520> for event 'missing-reference' threw an exception (exception: No such config value: intersphinx_disabled_reftypes)
+
+diff -up src/sage/docs/conf.py.orig src/sage/docs/conf.py
+--- src/sage/docs/conf.py.orig	2022-03-04 16:33:15.479009340 -0700
++++ src/sage/docs/conf.py	2022-03-06 18:49:34.742628130 -0700
+@@ -910,6 +910,7 @@ def setup(app):
+     if app.srcdir.startswith(SAGE_DOC_SRC):
+         app.add_config_value('intersphinx_mapping', {}, False)
+         app.add_config_value('intersphinx_cache_limit', 5, False)
++        app.add_config_value('intersphinx_disabled_reftypes', [], False)
+         app.connect('config-inited', set_intersphinx_mappings)
+         app.connect('builder-inited', intersphinx.load_mappings)
+         # We do *not* fully initialize intersphinx since we call it by hand

sagemath-primecount.patch

@@ -1,10 +0,0 @@
-diff -up src/sage/libs/primecount.pxd.orig src/sage/libs/primecount.pxd
---- src/sage/libs/primecount.pxd.orig	2020-10-24 11:37:59.000000000 -0600
-+++ src/sage/libs/primecount.pxd	2020-10-30 16:41:47.431983226 -0600
-@@ -17,6 +17,5 @@ cdef extern from "primecount.hpp" namesp
-     int get_num_threads()
- 
-     cppstring get_max_x()
--    cppstring get_max_x(double alpha)
- 
-     cppstring primecount_version()

sagemath-python3.patch

@@ -1,6 +1,6 @@
 diff -up src/sage/cpython/debugimpl.c.orig src/sage/cpython/debugimpl.c
---- src/sage/cpython/debugimpl.c.orig	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/cpython/debugimpl.c.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/cpython/debugimpl.c	2021-05-28 11:39:54.261578894 -0600
++++ src/sage/cpython/debugimpl.c	2022-03-04 16:16:45.900676037 -0700
 @@ -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);
@@ -18,8 +18,8 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/cpython/debug.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/cpython/debug.pyx	2021-05-28 11:39:54.261578894 -0600
++++ src/sage/cpython/debug.pyx	2022-03-04 16:16:45.900676037 -0700
 @@ -231,6 +231,7 @@ def type_debug(cls):
            tp_basicsize: 16
            tp_itemsize: 0
@@ -37,9 +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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/geometry/triangulation/point_configuration.py.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/geometry/triangulation/point_configuration.py	2021-05-28 11:39:54.263578895 -0600
++++ src/sage/geometry/triangulation/point_configuration.py	2022-03-04 16:16:45.901676039 -0700
-@@ -618,11 +618,11 @@ class PointConfiguration(UniqueRepresent
+@@ -619,11 +619,11 @@ class PointConfiguration(UniqueRepresent
              ['{{0,1,2,4},{1,2,3,4}}']
          """
          timeout = 600
@@ -54,8 +54,8 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/interfaces/frobby.py.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/interfaces/frobby.py	2021-05-28 11:39:54.264578894 -0600
++++ src/sage/interfaces/frobby.py	2022-03-04 16:16:45.901676039 -0700
 @@ -78,7 +78,7 @@ class Frobby:
              print("Frobby command: ", repr(command))
              print("Frobby input:\n", input)
@@ -66,8 +66,8 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/interfaces/gfan.py.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/interfaces/gfan.py	2021-05-28 11:39:54.264578894 -0600
++++ src/sage/interfaces/gfan.py	2022-03-04 16:16:45.901676039 -0700
 @@ -61,7 +61,7 @@ class Gfan(object):
              print("gfan input:\n%s" % I)
  
@@ -78,8 +78,8 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/interfaces/latte.py.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/interfaces/latte.py	2021-05-28 11:39:54.265578894 -0600
++++ src/sage/interfaces/latte.py	2022-03-04 16:16:45.901676039 -0700
 @@ -162,6 +162,7 @@ def count(arg, ehrhart_polynomial=False,
      latte_proc = Popen(args,
                         stdin=PIPE, stdout=PIPE,
@@ -97,8 +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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/interfaces/sagespawn.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/interfaces/sagespawn.pyx	2021-05-28 11:39:54.266578895 -0600
++++ src/sage/interfaces/sagespawn.pyx	2022-03-04 16:16:45.902676041 -0700
 @@ -1,6 +1,6 @@
  """
  Sage wrapper around pexpect's ``spawn`` class and
@@ -147,8 +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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/libs/coxeter3/coxeter.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/libs/coxeter3/coxeter.pyx	2021-05-28 11:39:54.267578895 -0600
++++ src/sage/libs/coxeter3/coxeter.pyx	2022-03-04 16:16:45.902676041 -0700
 @@ -37,7 +37,7 @@ cdef class String:
          EXAMPLES::
  
@@ -282,9 +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	2021-05-28 11:01:40.384274506 -0600
+--- src/sage/misc/sageinspect.py.orig	2022-03-04 15:50:57.336269352 -0700
-+++ src/sage/misc/sageinspect.py	2021-05-28 11:39:54.269578895 -0600
++++ src/sage/misc/sageinspect.py	2022-03-04 16:19:08.779910689 -0700
-@@ -462,12 +462,9 @@ class SageArgSpecVisitor(ast.NodeVisitor
+@@ -504,12 +504,9 @@ class SageArgSpecVisitor(ast.NodeVisitor
          """
          return node.id
  
@@ -300,96 +300,27 @@ diff -up src/sage/misc/sageinspect.py.orig src/sage/misc/sageinspect.py
  
          INPUT:
  
-@@ -475,17 +472,21 @@ class SageArgSpecVisitor(ast.NodeVisitor
+@@ -523,7 +520,7 @@ class SageArgSpecVisitor(ast.NodeVisitor
  
-         OUTPUT:
+             sage: import ast, sage.misc.sageinspect as sms
- 
+             sage: visitor = sms.SageArgSpecVisitor()
--        - None, True, False.
+-            sage: vis = lambda x: visitor.visit_NameConstant(ast.parse(x).body[0].value)
-+        - the boolean, number, or string the ``node`` represents
- 
-         EXAMPLES::
- 
--            sage: import ast, sage.misc.sageinspect as sms  # py3
--            sage: visitor = sms.SageArgSpecVisitor()  # py3
--            sage: vis = lambda x: visitor.visit_NameConstant(ast.parse(x).body[0].value)  # py3
--            sage: [vis(n) for n in ['True', 'False', 'None']]  # py3
-+            sage: import ast, sage.misc.sageinspect as sms
-+            sage: visitor = sms.SageArgSpecVisitor()
 +            sage: vis = lambda x: visitor.visit_Constant(ast.parse(x).body[0].value)
-+            sage: [vis(n) for n in ['True', 'False', 'None']]
+             sage: [vis(n) for n in ['True', 'False', 'None']]
              [True, False, None]
--            sage: [type(vis(n)) for n in ['True', 'False', 'None']]  # py3
+             sage: [type(vis(n)) for n in ['True', 'False', 'None']]
-+            sage: [type(vis(n)) for n in ['True', 'False', 'None']]
-             [<type 'bool'>, <type 'bool'>, <type 'NoneType'>]
-+            sage: [vis(s) for s in ['"abstract"', "u'syntax'", r'''r"tr\ee"''']]
-+            ['abstract', u'syntax', 'tr\\ee']
-+            sage: [vis(n) for n in ['123', '0.0']]
-+            [123, 0.0]
-         """
- 
-         return node.value
-@@ -519,57 +520,6 @@ class SageArgSpecVisitor(ast.NodeVisitor
-         """
-         return node.arg
- 
--    def visit_Num(self, node):
--        """
--        Visit a Python AST :class:`ast.Num` node.
--
--        INPUT:
--
--        - ``node`` - the node instance to visit
--
--        OUTPUT:
--
--        - the number the ``node`` represents
--
--        EXAMPLES::
--
--            sage: import ast, sage.misc.sageinspect as sms
--            sage: visitor = sms.SageArgSpecVisitor()
--            sage: vis = lambda x: visitor.visit_Num(ast.parse(x).body[0].value)
--            sage: [vis(n) for n in ['123', '0.0', str(-pi.n())]]  # py2
--            [123, 0.0, -3.14159265358979]
--            sage: [vis(n) for n in ['123', '0.0']]  # py3
--            [123, 0.0]
--
--        .. NOTE::
--
--            On Python 3 negative numbers are parsed first, for some reason, as
--            a UnaryOp node.
--        """
--        return node.n
--
--    def visit_Str(self, node):
--        r"""
--        Visit a Python AST :class:`ast.Str` node.
--
--        INPUT:
--
--        - ``node`` - the node instance to visit
--
--        OUTPUT:
--
--        - the string the ``node`` represents
--
--        EXAMPLES::
--
--            sage: import ast, sage.misc.sageinspect as sms
--            sage: visitor = sms.SageArgSpecVisitor()
--            sage: vis = lambda x: visitor.visit_Str(ast.parse(x).body[0].value)
--            sage: [vis(s) for s in ['"abstract"', "u'syntax'", r'''r"tr\ee"''']]
--            ['abstract', u'syntax', 'tr\\ee']
--        """
--        return node.s
--
-     def visit_List(self, node):
-         """
-         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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/plot/plot3d/plot3d.py.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/plot/plot3d/plot3d.py	2021-05-28 11:39:54.270578895 -0600
++++ src/sage/plot/plot3d/plot3d.py	2022-03-06 19:41:13.399013881 -0700
-@@ -185,7 +185,7 @@ class _Coordinates(object):
+@@ -148,6 +148,7 @@ from .shapes import arrow3d
+ from .base import Graphics3dGroup
+ from sage.plot.colors import rainbow
+ from .texture import Texture
++import inspect
+ 
+ from sage.functions.trig import cos, sin
+ from sage.misc.sageinspect import sage_getargspec, is_function_or_cython_function
+@@ -182,7 +183,7 @@ class _Coordinates(object):
              sage: arb((x+z,y*z,z), z, (x,y))
              Arbitrary Coordinates coordinate transform (z in terms of x, y)
          """
@@ -399,9 +330,9 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/rings/integer.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/rings/integer.pyx	2021-05-28 11:39:54.274578895 -0600
++++ src/sage/rings/integer.pyx	2022-03-04 16:16:45.904676044 -0700
-@@ -7089,7 +7089,7 @@ cdef int mpz_set_str_python(mpz_ptr z, c
+@@ -7023,7 +7023,7 @@ cdef int mpz_set_str_python(mpz_ptr z, c
          x += 1  # Strip spaces
  
      # Disallow a sign here
@@ -411,9 +342,9 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/rings/polynomial/pbori/pbori.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/rings/polynomial/pbori/pbori.pyx	2021-05-28 11:39:54.278578895 -0600
++++ src/sage/rings/polynomial/pbori/pbori.pyx	2022-03-04 16:16:45.905676046 -0700
-@@ -4704,8 +4704,7 @@ cdef class PolynomialConstruct:
+@@ -4730,8 +4730,7 @@ cdef class PolynomialConstruct:
              # So, it is just a conversion. [Simon King]
              return (<BooleanPolynomialRing>ring)._element_constructor_(x)
  
@@ -424,9 +355,9 @@ 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	2021-05-28 11:01:45.006275360 -0600
+--- src/sage/rings/real_mpfi.pyx.orig	2022-03-04 15:50:57.348269369 -0700
-+++ src/sage/rings/real_mpfi.pyx	2021-05-28 11:39:54.280578896 -0600
++++ src/sage/rings/real_mpfi.pyx	2022-03-04 16:16:45.905676046 -0700
-@@ -1944,12 +1944,12 @@ cdef class RealIntervalFieldElement(Ring
+@@ -1943,12 +1943,12 @@ cdef class RealIntervalFieldElement(Ring
  
          cdef long digits
          digits = strlen(lower_s)
@@ -441,7 +372,7 @@ diff -up src/sage/rings/real_mpfi.pyx.orig src/sage/rings/real_mpfi.pyx
              digits -= 1
          upper_expo -= digits
  
-@@ -2118,7 +2118,7 @@ cdef class RealIntervalFieldElement(Ring
+@@ -2117,7 +2117,7 @@ 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)
@@ -451,9 +382,9 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/rings/real_mpfr.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/rings/real_mpfr.pyx	2021-05-28 11:39:54.283578896 -0600
++++ src/sage/rings/real_mpfr.pyx	2022-03-04 16:16:45.906676047 -0700
-@@ -2095,7 +2095,7 @@ cdef class RealNumber(sage.structure.ele
+@@ -2092,7 +2092,7 @@ 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)
@@ -463,9 +394,9 @@ 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	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/structure/sage_object.pyx.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/structure/sage_object.pyx	2021-05-28 11:39:54.284578896 -0600
++++ src/sage/structure/sage_object.pyx	2022-03-04 16:16:45.906676047 -0700
-@@ -688,7 +688,7 @@ cdef class SageObject:
+@@ -690,7 +690,7 @@ cdef class SageObject:
              try:
                  s = self._interface_init_(I)
              except Exception:
@@ -475,9 +406,9 @@ 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	2021-05-28 11:01:45.016275362 -0600
+--- src/sage/symbolic/expression.pyx.orig	2022-03-04 16:01:04.179126250 -0700
-+++ src/sage/symbolic/expression.pyx	2021-05-28 11:39:54.289578896 -0600
++++ src/sage/symbolic/expression.pyx	2022-03-04 16:16:45.908676050 -0700
-@@ -13201,7 +13201,7 @@ cdef class hold_class:
+@@ -14016,7 +14016,7 @@ cdef class hold_class:
              sage: SR(2)^5
              32
          """
@@ -486,7 +417,7 @@ diff -up src/sage/symbolic/expression.pyx.orig src/sage/symbolic/expression.pyx
  
      def __exit__(self, *args):
          """
-@@ -13214,7 +13214,7 @@ cdef class hold_class:
+@@ -14029,7 +14029,7 @@ cdef class hold_class:
              sage: SR(2)^5
              32
          """

sagemath-qepcad.patch

@@ -1,14 +1,14 @@
 diff -up src/sage/interfaces/qepcad.py.orig src/sage/interfaces/qepcad.py
---- src/sage/interfaces/qepcad.py.orig	2021-05-09 16:00:11.000000000 -0600
+--- src/sage/interfaces/qepcad.py.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/interfaces/qepcad.py	2021-05-28 11:52:46.749626841 -0600
++++ src/sage/interfaces/qepcad.py	2022-03-04 16:29:29.109754141 -0700
 @@ -530,7 +530,7 @@ TESTS:
  
  Check the qepcad configuration file::
  
--    sage: with open(os.path.join(SAGE_LOCAL, 'default.qepcadrc')) as f:  # optional - qepcad
+-    sage: with open(os.path.join(SAGE_LOCAL, 'etc', 'default.qepcadrc')) as f:  # optional - qepcad
-+    sage: with open('/usr/share/qepcad/default.qepcadrc')) as f:  # optional - qepcad
++    sage: with open(os.path.join('/usr/share/qepcad/default.qepcadrc')) as f:  # optional - qepcad
      ....:     f.readlines()[-1]
-     'SINGULAR .../bin\n'
+     'SINGULAR yes\n'
  
 @@ -605,7 +605,6 @@ AUTHORS:
  #                  http://www.gnu.org/licenses/
@@ -52,7 +52,7 @@ diff -up src/sage/interfaces/qepcad.py.orig src/sage/interfaces/qepcad.py
  
      cache = {}
  
--    with open(os.path.join(SAGE_LOCAL, 'bin', 'qepcad.help')) as help:
+-    with open(os.path.join(SAGE_LOCAL, 'share/qepcad', 'qepcad.help')) as help:
 +    with open(os.path.join(QEPCAD_LOCAL, 'bin', 'qepcad.help')) as help:
          assert(help.readline().strip() == '@')
  

sagemath-sagedoc.patch

@@ -1,6 +1,6 @@
 diff -up src/sage_docbuild/ext/multidocs.py.orig src/sage_docbuild/ext/multidocs.py
---- src/sage_docbuild/ext/multidocs.py.orig	2021-08-22 02:44:34.000000000 -0600
+--- src/sage_docbuild/ext/multidocs.py.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage_docbuild/ext/multidocs.py	2021-08-26 13:11:24.937824557 -0600
++++ src/sage_docbuild/ext/multidocs.py	2022-03-04 16:08:42.795455456 -0700
 @@ -84,8 +84,11 @@ def merge_environment(app, env):
              for ind in newalldoc:
                  # treat subdocument source as orphaned file and don't complain
@@ -16,15 +16,15 @@ diff -up src/sage_docbuild/ext/multidocs.py.orig src/sage_docbuild/ext/multidocs
              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	2021-08-26 13:11:24.940824561 -0600
+--- src/sage/interfaces/singular.py.orig	2022-01-30 06:41:50.000000000 -0700
-+++ src/sage/interfaces/singular.py	2021-08-26 13:17:49.831262334 -0600
++++ src/sage/interfaces/singular.py	2022-03-04 16:09:20.555418442 -0700
-@@ -2370,11 +2370,11 @@ def generate_docstring_dictionary():
+@@ -2330,11 +2330,11 @@ def generate_docstring_dictionary():
  
      L, in_node, curr_node = [], False, None
  
 -    from sage.libs.singular.singular import get_resource
 -    singular_info_file = get_resource('i')
-+    singular_info_file = '/usr/share/info/singular.hlp.gz'
++    singular_info_file = '/usr/share/info/singular.info.gz'
  
      # singular.hlp contains a few iso-8859-1 encoded special characters
 -    with io.open(singular_info_file,

sagemath-use-after-free.patch

@@ -0,0 +1,19 @@
+diff -up src/sage/graphs/graph_decompositions/cutwidth.pyx.orig src/sage/graphs/graph_decompositions/cutwidth.pyx
+--- src/sage/graphs/graph_decompositions/cutwidth.pyx.orig	2022-01-30 06:41:50.000000000 -0700
++++ src/sage/graphs/graph_decompositions/cutwidth.pyx	2022-03-06 17:04:36.234711622 -0700
+@@ -522,12 +522,12 @@ def cutwidth_dyn(G, lower_bound=0):
+                 if exists(g, neighborhoods, 0, 0, i, k) <= k:
+                     order = find_order(g, neighborhoods, k)
+                     return k, [g.int_to_vertices[i] for i in order]
++
++        order = find_order(g, neighborhoods, k)
++        return k, [g.int_to_vertices[i] for i in order]
+     finally:
+         sig_free(neighborhoods)
+ 
+-    order = find_order(g, neighborhoods, k)
+-    return k, [g.int_to_vertices[i] for i in order]
+-
+ cdef inline int exists(FastDigraph g, uint8_t* neighborhoods, int S, int cost_S, int v, int k):
+     r"""
+     Check whether an ordering with the given cost `k` exists, and updates data

sagemath.rpmlintrc

@@ -1,21 +0,0 @@
-# THIS FILE IS FOR WHITELISTING RPMLINT ERRORS AND WARNINGS IN TASKOTRON
-# https://fedoraproject.org/wiki/Taskotron/Tasks/dist.rpmlint#Whitelisting_errors
-
-# The dictionary is missing some technical terms
-addFilter(r'W: spelling-error .* (Extcode|iteratively|polytopes?|pre)')
-
-# The Requires ensure the symlinks will not dangle
-addFilter(r'W: dangling-symlink')
-
-# This file is incorrectly detected as a devel file
-addFilter(r'W: devel-file-in-non-devel-package .*sage-env-config')
-
-# objects.inv files are not text
-addFilter(r'W: file-not-utf8 .*objects\.inv')
-addFilter(r'W: wrong-file-end-of-line-encoding .*objects\.inv')
-
-# This file uses no symbols from glibc
-addFilter(r'E: library-not-linked-against-libc .*/bit_vector_operations/cc\.cpython-38-x86_64-linux-gnu\.so')
-
-# Documentation is in the -doc subpackages
-addFilter(r'W: no-documentation')

sagemath.spec

@@ -41,9 +41,9 @@
 %global	elliptic_curves_pkg	elliptic_curves-0.8.1
 %global graphs_pkg		graphs-20210214
 %if %{with bundled_ipython}
-%global ipython_ver		7.16.1
+%global ipython_ver		7.29.0
 %global ipython_pkg		ipython-%{ipython_ver}
-%global prompt_toolkit_ver	3.0.5
+%global prompt_toolkit_ver	3.0.22
 %global prompt_tookit_pkg	prompt_toolkit-%{prompt_toolkit_ver}
 %endif
 %if %{with bundled_jupyter_jsmol}
@@ -51,7 +51,7 @@
 %global jupyter_jsmol_pkg	jupyter_jsmol-%{jupyter_jsmol_ver}
 %endif
 %if %{with bundled_memory_allocator}
-%global memory_allocator_ver	0.1.0
+%global memory_allocator_ver	0.1.1
 %global memory_allocator_pkg	memory_allocator-%{memory_allocator_ver}
 %endif
 %if %{with bundled_pexpect}
@@ -59,8 +59,8 @@
 %endif
 %global polytopes_db_pkg	polytopes_db-20170220
 %global sagetex_pkg		sagetex-3.5
-%global Sphinx_pkg		Sphinx-4.0.1
+%global Sphinx_pkg		Sphinx-4.2.0
-%global singular_pkg		singular-4.2.0p3
+%global singular_pkg		singular-4.2.1p3
 %if %{with bundled_thebe}
 %global thebe_ver		9624e0a0
 %global thebe_pkg		thebe-%{thebe_ver}
@@ -71,7 +71,7 @@
 %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-0.99713 coxeter3-3.1 cryptominisat-5.8.0 database_cremona_ellcurve-%{cremona_ver} gap_packages-4.11.1 libsirocco-2.1.0 lrslib-071b mcqd-1.0 meataxe-1.0 primecount-7.1 qepcad-B.1.74 saclib-2.2.8 surf-1.0.6-gcc6 tdlib-0.9.1
+%global SAGE_REQUIRED_PKGS 4ti2-1.6.9 bliss-0.77 CoCoALib-0.99718 coxeter3-3.1 cryptominisat-5.8.0 database_cremona_ellcurve-%{cremona_ver} gap_packages-4.11.1 libsirocco-2.1.0 lrslib-071b mcqd-1.0.0 meataxe-1.0 primecount-7.2 qepcad-B.1.74 saclib-2.2.8 surf-1.0.6-gcc6 tdlib-0.9.2
 
 %ifarch %{ix86} x86_64
 %global SAGE_REQUIRED_PKGS %{SAGE_REQUIRED_PKGS} fes-0.2
@@ -88,8 +88,8 @@
 
 Name:		sagemath
 Summary:	A free open-source mathematics software system
-Version:	9.4
+Version:	9.5
-Release:	3%{?dist}
+Release:	1%{?dist}
 # The file ${SAGE_ROOT}/COPYING.txt is the upstream license breakdown file
 # Additionally, every $files section has a comment with the license name
 # before files with that license
@@ -128,64 +128,68 @@ Patch4:		%{name}-rpmbuild.patch
 Patch5:		%{name}-sagedoc.patch
 
 # work with all maxima-runtime lisp backend packages
-Patch7:		%{name}-maxima.patch
+Patch6:		%{name}-maxima.patch
-
-# execute 4ti2 programs in $PATH not in $SAGE_ROOT/local/bin
-Patch8:		%{name}-4ti2.patch
 
 # use jmol itself to export preview images
 # FIXME besides not using X and told so, fails if DISPLAY is not set
-Patch9:		%{name}-jmol.patch
+Patch7:		%{name}-jmol.patch
 
 # tell the user how to install the large Cremona database
 # add a missing commit() that causes large database construction to fail
-Patch10:	%{name}-cremona.patch
+Patch8:		%{name}-cremona.patch
 
 # adapt to python 3 and cython running in python 3 mode
-Patch11:	%{name}-python3.patch
+Patch9:		%{name}-python3.patch
 
 # remove the buildroot path from Cython output
-Patch12:	%{name}-buildroot.patch
+Patch10:	%{name}-buildroot.patch
 
 # update c++ standard to fix FTBFS
-Patch13:	%{name}-lcalc.patch
+Patch11:	%{name}-lcalc.patch
 
 # Use system gap directories and modernize libgap interface
-Patch14:	%{name}-libgap.patch
+Patch12:	%{name}-libgap.patch
 
 # Build fes
-Patch15:	%{name}-fes-build.patch
+Patch13:	%{name}-fes-build.patch
 
 # Side effect of using distro packages
 # https://bugzilla.redhat.com/show_bug.cgi?id=974769
-Patch16:	%{name}-env.patch
+Patch14:	%{name}-env.patch
 
 # Correct unable to start QEPCAD within sage
 # https://bugzilla.redhat.com/show_bug.cgi?id=1243590
-Patch17:	%{name}-qepcad.patch
+Patch15:	%{name}-qepcad.patch
 
 # Make the cvxopt backend check for 'optimal' as well as 'optimized'
-Patch18:	%{name}-cvxopt.patch
+Patch16:	%{name}-cvxopt.patch
 
 # Use flexiblas
-Patch19:	%{name}-flexiblas.patch
+Patch17:	%{name}-flexiblas.patch
 
 # Fix paths to latte-integrale binaries
-Patch20:	%{name}-latte.patch
+Patch18:	%{name}-latte.patch
 
 # Change rubiks binary names to match Fedora
-Patch21:	%{name}-rubiks.patch
+Patch19:	%{name}-rubiks.patch
 
 # Adapt to recent tdlib 0.9
-Patch22:	%{name}-tdlib.patch
+Patch20:	%{name}-tdlib.patch
 
 # Use local objects.inv for intersphinx since no network on koji builders
-Patch23:	%{name}-intersphinx.patch
+Patch21:	%{name}-intersphinx.patch
 
-# Remove an unused call to a primecount function that no longer exists
+# Fix a typo that leads to infinite recursion
-Patch24:	%{name}-primecount.patch
+Patch22:	%{name}-infinite-recursion.patch
+
+# Fix a use-after-free bug
+Patch23:	%{name}-use-after-free.patch
+
+# Add a missing Sphinx config value
+Patch24:	%{name}-intersphinx-disabled-reftypes.patch
 
 BuildRequires:	4ti2
+BuildRequires:	4ti2-devel
 BuildRequires:	appstream
 BuildRequires:	arb-devel
 BuildRequires:	bc
@@ -207,18 +211,22 @@ BuildRequires:	ecl
 %if %{with fes}
 BuildRequires:	fes-devel
 %endif
+BuildRequires:	ffmpeg-free
 BuildRequires:	flexiblas-devel
 BuildRequires:	flint-devel
 BuildRequires:	flintqs
+BuildRequires:	fonttools
 BuildRequires:	gap-devel
 BuildRequires:	gap-pkg-aclib
 BuildRequires:	gap-pkg-alnuth
 BuildRequires:	gap-pkg-atlasrep
+BuildRequires:	gap-pkg-autodoc
 BuildRequires:	gap-pkg-autpgrp
 BuildRequires:	gap-pkg-cohomolo
 BuildRequires:	gap-pkg-corelg
 BuildRequires:	gap-pkg-crime
 BuildRequires:	gap-pkg-crisp
+BuildRequires:	gap-pkg-cryst
 BuildRequires:	gap-pkg-crystcat
 BuildRequires:	gap-pkg-ctbllib
 BuildRequires:	gap-pkg-design
@@ -227,15 +235,17 @@ BuildRequires:	gap-pkg-factint
 BuildRequires:	gap-pkg-fga
 BuildRequires:	gap-pkg-gbnp
 BuildRequires:	gap-pkg-genss
-BuildRequires:	gap-pkg-grape
 BuildRequires:	gap-pkg-guava
+BuildRequires:	gap-pkg-hap
 BuildRequires:	gap-pkg-hapcryst
 BuildRequires:	gap-pkg-hecke
+BuildRequires:	gap-pkg-images
 BuildRequires:	gap-pkg-irredsol
 BuildRequires:	gap-pkg-jupyterkernel
 BuildRequires:	gap-pkg-laguna
 BuildRequires:	gap-pkg-liealgdb
 BuildRequires:	gap-pkg-liepring
+BuildRequires:	gap-pkg-liering
 BuildRequires:	gap-pkg-loops
 BuildRequires:	gap-pkg-lpres
 BuildRequires:	gap-pkg-mapclass
@@ -259,6 +269,7 @@ BuildRequires:	gcc-gfortran
 BuildRequires:	gcc-objc
 BuildRequires:	gcc-objc++
 BuildRequires:	gdb
+BuildRequires:	gengetopt
 BuildRequires:	gfan
 BuildRequires:	giac-devel
 BuildRequires:	giac-doc
@@ -302,6 +313,7 @@ BuildRequires:	pari-galpol
 BuildRequires:	pari-gp
 BuildRequires:	pari-nftables
 BuildRequires:	pari-seadata
+BuildRequires:	pdf2svg
 BuildRequires:	perl-generators
 BuildRequires:	perl(ExtUtils::MakeMaker)
 BuildRequires:	perl(File::Slurp)
@@ -310,11 +322,15 @@ BuildRequires:	pkgconfig(cbc)
 BuildRequires:	pkgconfig(eclib)
 BuildRequires:	pkgconfig(factory)
 BuildRequires:	pkgconfig(fplll)
+BuildRequires:	pkgconfig(freetype2)
 BuildRequires:	pkgconfig(gdlib)
 BuildRequires:	pkgconfig(gf2x)
 BuildRequires:	pkgconfig(gsl)
 BuildRequires:	pkgconfig(igraph)
+BuildRequires:	pkgconfig(isl)
+BuildRequires:	pkgconfig(libavdevice)
 BuildRequires:	pkgconfig(libcurl)
+BuildRequires:	pkgconfig(libgvc)
 BuildRequires:	pkgconfig(libpng)
 BuildRequires:	pkgconfig(libsemigroups)
 BuildRequires:	pkgconfig(libzmq)
@@ -323,14 +339,15 @@ BuildRequires:	pkgconfig(m4ri)
 BuildRequires:	pkgconfig(m4rie)
 BuildRequires:	pkgconfig(nauty)
 BuildRequires:	pkgconfig(openssl)
-BuildRequires:	pkgconfig(pynac)
+BuildRequires:	pkgconfig(primecount)
+BuildRequires:	pkgconfig(primesieve)
 BuildRequires:	pkgconfig(readline)
 BuildRequires:	pkgconfig(Singular)
 BuildRequires:	pkgconfig(tk)
 BuildRequires:	pkgconfig(zlib)
 BuildRequires:	planarity-devel
+BuildRequires:	polymake
 BuildRequires:	ppl-devel
-BuildRequires:	primecount-devel
 BuildRequires:	python3-devel
 BuildRequires:	python3-docs
 BuildRequires:	python3-cypari2-devel
@@ -342,20 +359,29 @@ BuildRequires:	python3-pillow-devel
 BuildRequires:	python3-pplpy-devel
 BuildRequires:	python3-tdlib-devel
 BuildRequires:	python3-tkinter
+BuildRequires:	pythran
+BuildRequires:	%{py3_dist argcomplete}
 BuildRequires:	%{py3_dist argon2-cffi}
 %if %{with bundled_ipython}
 BuildRequires:	%{py3_dist backcall}
 %endif
+BuildRequires:	%{py3_dist beniget}
 BuildRequires:	%{py3_dist brial}
+BuildRequires:	%{py3_dist charset-normalizer}
+BuildRequires:	%{py3_dist cppy}
 BuildRequires:	%{py3_dist cvxopt}
 BuildRequires:	%{py3_dist cython}
 BuildRequires:	%{py3_dist docutils}
+BuildRequires:	%{py3_dist flit-core}
 BuildRequires:	%{py3_dist fpylll}
+BuildRequires:	%{py3_dist gast}
 BuildRequires:	%{py3_dist gmpy2}
 %if %{with sphinx_hack}
 BuildRequires:	%{py3_dist html5lib}
 BuildRequires:	%{py3_dist imagesize}
 %endif
+BuildRequires:	%{py3_dist idna}
+BuildRequires:	%{py3_dist importlib-metadata}
 BuildRequires:	%{py3_dist ipykernel}
 %if %{without bundled_ipython}
 BuildRequires:	%{py3_dist ipython}
@@ -364,8 +390,14 @@ BuildRequires:	%{py3_dist ipywidgets}
 %if %{with bundled_ipython}
 BuildRequires:	%{py3_dist jedi}
 %endif
+BuildRequires:	%{py3_dist jupyterlab-pygments}
 BuildRequires:	%{py3_dist kiwisolver}
 BuildRequires:	%{py3_dist matplotlib}
+BuildRequires:	%{py3_dist matplotlib-inline}
+BuildRequires:	%{py3_dist nbclient}
+BuildRequires:	%{py3_dist nbconvert}
+BuildRequires:	%{py3_dist nbformat}
+BuildRequires:	%{py3_dist nest-asyncio}
 BuildRequires:	%{py3_dist networkx}
 BuildRequires:	%{py3_dist notebook}
 BuildRequires:	%{py3_dist pari-jupyter}
@@ -381,7 +413,8 @@ BuildRequires:	%{py3_dist pickleshare}
 BuildRequires:	%{py3_dist pip}
 BuildRequires:	%{py3_dist pkgconfig}
 BuildRequires:	%{py3_dist pluggy}
-BuildRequires:	%{py3_dist psutil}
+BuildRequires:	%{py3_dist ply}
+BuildRequires:	%{py3_dist primecountpy}
 BuildRequires:	%{py3_dist ptyprocess}
 BuildRequires:	%{py3_dist py}
 BuildRequires:	%{py3_dist pycryptosat}
@@ -394,6 +427,7 @@ BuildRequires:	%{py3_dist scipy}
 BuildRequires:	%{py3_dist scons}
 BuildRequires:	%{py3_dist setuptools}
 BuildRequires:	%{py3_dist setuptools_scm}
+BuildRequires:	%{py3_dist setuptools_scm_git_archive}
 %if %{with bundled_ipython}
 BuildRequires:	%{py3_dist simplegeneric}
 %endif
@@ -401,12 +435,15 @@ BuildRequires:	%{py3_dist six}
 BuildRequires:	%{py3_dist sphinx}
 BuildRequires:	%{py3_dist sympy}
 BuildRequires:	%{py3_dist toml}
+BuildRequires:	%{py3_dist tomli}
 BuildRequires:	%{py3_dist tox}
 BuildRequires:	%{py3_dist typing-extensions}
+BuildRequires:	%{py3_dist urllib3}
 BuildRequires:	%{py3_dist wheel}
 BuildRequires:	%{py3_dist widgetsnbextension}
 BuildRequires:	%{py3_dist zodb3}
 BuildRequires:	qepcad-B
+BuildRequires:	qhull
 BuildRequires:	R
 BuildRequires:	ratpoints-devel
 BuildRequires:	rubiks
@@ -426,7 +463,6 @@ 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
@@ -462,11 +498,13 @@ Requires:	gap
 Requires:	gap-pkg-aclib
 Requires:	gap-pkg-alnuth
 Requires:	gap-pkg-atlasrep
+Requires:	gap-pkg-autodoc
 Requires:	gap-pkg-autpgrp
 Requires:	gap-pkg-cohomolo
 Requires:	gap-pkg-corelg
 Requires:	gap-pkg-crime
 Requires:	gap-pkg-crisp
+Requires:	gap-pkg-cryst
 Requires:	gap-pkg-crystcat
 Requires:	gap-pkg-ctbllib
 Requires:	gap-pkg-design
@@ -475,15 +513,17 @@ Requires:	gap-pkg-factint
 Requires:	gap-pkg-fga
 Requires:	gap-pkg-gbnp
 Requires:	gap-pkg-genss
-Requires:	gap-pkg-grape
 Requires:	gap-pkg-guava
+Requires:	gap-pkg-hap
 Requires:	gap-pkg-hapcryst
 Requires:	gap-pkg-hecke
+Requires:	gap-pkg-images
 Requires:	gap-pkg-irredsol
 Requires:	gap-pkg-jupyterkernel
 Requires:	gap-pkg-laguna
 Requires:	gap-pkg-liealgdb
 Requires:	gap-pkg-liepring
+Requires:	gap-pkg-liering
 Requires:	gap-pkg-loops
 Requires:	gap-pkg-lpres
 Requires:	gap-pkg-mapclass
@@ -522,21 +562,29 @@ Requires:	pari-gp
 Requires:	pari-nftables
 Requires:	pari-seadata
 Requires:	python3-tdlib
+Requires:	%{py3_dist argcomplete}
 %if %{with bundled_ipython}
 Requires:	%{py3_dist backcall}
 %endif
+Requires:	%{py3_dist beniget}
 Requires:	%{py3_dist brial}
+Requires:	%{py3_dist charset-normalizer}
+Requires:	%{py3_dist cppy}
 Requires:	%{py3_dist cypari2}
 Requires:	%{py3_dist cysignals}
 Requires:	%{py3_dist cvxopt}
 Requires:	%{py3_dist cython}
 Requires:	%{py3_dist docutils}
+Requires:	%{py3_dist flit-core}
 Requires:	%{py3_dist fpylll}
+Requires:	%{py3_dist gast}
 Requires:	%{py3_dist gmpy2}
 %if %{with sphinx_hack}
 Requires:	%{py3_dist html5lib}
 Requires:	%{py3_dist imagesize}
 %endif
+Requires:	%{py3_dist idna}
+Requires:	%{py3_dist importlib-metadata}
 Requires:	%{py3_dist ipykernel}
 %if %{without bundled_ipython}
 Requires:	%{py3_dist ipython}
@@ -546,6 +594,10 @@ Requires:	%{py3_dist ipywidgets}
 Requires:	%{py3_dist jedi}
 %endif
 Requires:	%{py3_dist matplotlib}
+Requires:	%{py3_dist nbclient}
+Requires:	%{py3_dist nbconvert}
+Requires:	%{py3_dist nbformat}
+Requires:	%{py3_dist nest-asyncio}
 Requires:	%{py3_dist networkx}
 %if %{with bundled_ipython}
 Requires:	%{py3_dist path.py}
@@ -557,7 +609,7 @@ Requires:	%{py3_dist pexpect}
 Requires:	%{py3_dist pickleshare}
 %endif
 Requires:	%{py3_dist pplpy}
-Requires:	%{py3_dist psutil}
+Requires:	%{py3_dist primecountpy}
 Requires:	%{py3_dist ptyprocess}
 Requires:	%{py3_dist pycryptosat}
 %if %{with bundled_ipython}
@@ -571,6 +623,7 @@ Requires:	%{py3_dist simplegeneric}
 Requires:	%{py3_dist six}
 Requires:	%{py3_dist sphinx}
 Requires:	%{py3_dist sympy}
+Requires:	%{py3_dist urllib3}
 Requires:	%{py3_dist zodb3}
 Requires:	qepcad-B
 Requires:	Singular
@@ -588,6 +641,10 @@ Provides:	bundled(jupyter-jsmol) = %{jupyter_jsmol_ver}
 Provides:	bundled(memory-allocator) = %{memory_allocator_ver}
 %endif
 
+# This can be removed when Fedora 40 reaches EOL
+Obsoletes:      pynac < 0.7.29-3
+Obsoletes:      pynac-devel < 0.7.29-3
+
 %description	core
 This package contains the core sagemath python modules.
 
@@ -774,6 +831,8 @@ Summary:	Jupyter integration for sagemath
 Requires:	%{name}%{?_isa} = %{version}-%{release}
 Requires:	python-jupyter-filesystem
 Requires:	%{py3_dist argon2-cffi}
+Requires:	%{py3_dist jupyterlab-pygments}
+Requires:	%{py3_dist matplotlib-inline}
 Requires:	%{py3_dist pari-jupyter}
 Requires:	%{py3_dist widgetsnbextension}
 
@@ -909,31 +968,31 @@ popd
 %patch3
 %patch4
 %patch5
+%patch6
 %patch7
 %patch8
 %patch9
 %patch10
 %patch11
 %patch12
-%patch13
-%patch14
 
 %if %{with fes}
-%patch15
+%patch13
 %endif
 
+%patch14
+%patch15
 %patch16
 %patch17
 %patch18
 %patch19
+%patch20
 %patch21
 %patch22
 %patch23
 %patch24
 
-sed -e 's|@@SAGE_LOCAL@@|%{SAGE_LOCAL}|' \
+sed -i 's|@@SAGE_LOCAL@@|%{SAGE_LOCAL}|' src/sage/env.py
-    -e 's|@@LIBDIR@@|%{_libdir}|g' \
-    -i src/sage/env.py
 
 sed -e 's|@@CYSIGNALS@@|%{python3_sitearch}/cysignals|' \
     -e 's|@@BUILDROOT@@|%{buildroot}|' \
@@ -943,12 +1002,6 @@ sed -e 's|@@CYSIGNALS@@|%{python3_sitearch}/cysignals|' \
 # some .c files are not (re)generated
 find src/sage \( -name \*.pyx -o -name \*.pxd \) -exec touch {} \+
 
-# fix Singular paths
-singver=$(sed 's/^.*-\([.[:digit:]]*\).*$/\1/' <<< %{singular_pkg})
-sed -e "s,SINGULARPATH=\",&%{_datadir}/singular/LIB:," \
-    -e "s,\(SINGULAR_EXECUTABLE=\"\).*\",\1%{_libdir}/Singular/Singular\"," \
-    -i src/bin/sage-env
-
 # 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'
@@ -978,14 +1031,14 @@ sed -e "s|'%{_bindir}/env', 'which'|'%{_bindir}/which'|" \
 # GAP does not have enough memory to load the entire workspace
 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_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
+# Allow use of gcc 12
-sed -i 's/3\.10\.0/3.11.0/g' configure
+sed -i 's/1\[2-9\]\.\*)/1[3-9].*)/' configure
+
+# Allow use of python 3.11
+sed -i 's/3\.11\.0/3.12.0/g' configure
 
 # Do not build with -march=native
 sed -i 's/CFLAGS_MARCH="-march=native"/CFLAGS_MARCH=""/' configure
@@ -995,18 +1048,13 @@ sed -i 's/CFLAGS_MARCH="-march=native"/CFLAGS_MARCH=""/' configure
 %build
 export LC_ALL=C.UTF-8
 export CC=%{__cc}
-export CPPFLAGS="-I%{_includedir}/arb -I%{_includedir}/cddlib"
+export CPPFLAGS="-I%{_includedir}/4ti2 -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}
 # Avoid buildroot in gcc command line (use _builddir instead)
 export SAGE_SRC="$PWD/src"
 export SAGE_INC=%{_includedir}
-export SAGE_FORTRAN=%{_bindir}/gfortran
-export SAGE_FORTRAN_LIB=`gfortran --print-file-name=libgfortran.so`
 export DESTDIR=%{buildroot}
 export SAGE_DEBUG=no
 # Use file in /tmp because there are issues with long pathnames
@@ -1026,6 +1074,14 @@ export PATH=%{buildroot}%{_bindir}:$PATH
 export PYTHON=%{_bindir}/python3
 export PYTHONPATH=%{buildroot}%{python3_sitearch}:%{buildroot}%{python3_sitelib}:$PYTHONPATH
 
+# Make various programs visible to configure
+module load 4ti2-%{_arch}
+module load lrcalc-%{_arch}
+module load surf-geometry-%{_arch}
+
+# Initialize polymake
+polymake --reconfigure - <<< exit;
+
 #------------------------------------------------------------------------
 # Run the configure script to generate files
 export GSL_LIBS="-lgsl -lflexiblas -lm"
@@ -1042,7 +1098,6 @@ export GSL_LIBS="-lgsl -lflexiblas -lm"
   --enable-frobby \
   --enable-mcqd \
   --enable-meataxe \
-  --enable-primecount \
   --enable-qepcad \
   --enable-saclib \
   --enable-sirocco \
@@ -1348,8 +1403,6 @@ export SINGULAR_DATA_DIR=%{_datadir}
 export SINGULAR_BIN_DIR=%{_libdir}/Singular
 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\`
 export SYMPOW_DIR="\$DOT_SAGE/sympow"
 # Required for sage -gdb
 : \${SAGE_DEBUG:=no}
@@ -1986,6 +2039,10 @@ end
 
 ########################################################################
 %changelog
+* Mon Mar 21 2022 Jerry James <loganjerry@gmail.com> - 9.5-1
+- Version 9.5
+- Drop unnecessary -4ti2 and -primecount patches
+
 * Sat Jan 22 2022 Fedora Release Engineering <releng@fedoraproject.org> - 9.4-3
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
 

sources

@@ -1,2 +1,2 @@
 SHA512 (cremona-2019-10-29.tar.gz) = 32fbb828f26f87191e39123762cfbd796aac9abf346f0dc981e8e3f390435b22d281be3031ea92ae7e18f4ce41af8054784ca0d550a08f17b05c54ca08b4c9c8
-SHA512 (sage-9.4.tar.gz) = cb634a14c5c594e1f76b1d1aa0fdd38560ffc5190df440e9e7d580eee7ddd7f7935d11fb993521eb26c6f68b7c76d1e4c146c53d3bc14435b9c8fb7dc9e56517
+SHA512 (sage-9.5.tar.gz) = 0c3649592b2ddf31f301e48c0727e16870fe9062c92ec8cd24f13728cf6ff1e45cbc263a967ca060a91f976eaee73fc6aa5a0dfd0b95b393e22cfaac1ef6767e