Update to sagemath 8.4.

Also:
- Build for python 3 instead of python 2 due to upcoming python 2 removal.
- Add -python3 and -escape patches to fix problems with python 3.
- Drop -nofstring patch, only needed for python 2.
- Drop upstreamed -eclib patch.
- Switch from atlas to openblas and rename -atlas patch to -openblas.
- Add -buildroot patch and only build cython interfaces once.

sagemath-4ti2.patch

@@ -1,17 +1,17 @@
 diff -up src/sage/sandpiles/sandpile.py.orig src/sage/sandpiles/sandpile.py
---- src/sage/sandpiles/sandpile.py.orig	2018-08-03 05:10:09.000000000 -0600
+--- src/sage/sandpiles/sandpile.py.orig	2018-10-17 17:14:17.000000000 -0600
-+++ src/sage/sandpiles/sandpile.py	2018-08-29 08:47:29.728055776 -0600
++++ src/sage/sandpiles/sandpile.py	2018-10-25 13:18:34.198894883 -0600
-@@ -342,9 +342,6 @@ from sage.arith.all import falling_facto
+@@ -344,9 +344,6 @@ from sage.arith.all import falling_facto
  from sage.rings.all import Integer, PolynomialRing, QQ, ZZ
- from sage.symbolic.all import I, pi
+ from sage.symbolic.all import I, pi, SR
  
 -# TODO: remove the following line once 4ti2 functions are removed
--path_to_zsolve = os.path.join(SAGE_LOCAL,'bin','zsolve')
+-path_to_zsolve = os.path.join(SAGE_LOCAL, 'bin', 'zsolve')
 -
- class Sandpile(DiGraph):
+ 
-     """
+ 
-     Class for Dhar's abelian sandpile model.
+ def _sandpile_help(cls, usage, verbose=True):
-@@ -5197,7 +5194,7 @@ class SandpileDivisor(dict):
+@@ -5150,7 +5147,7 @@ class SandpileDivisor(dict):
          sign_file.close()
          # compute
          try:

sagemath-buildroot.patch

@@ -0,0 +1,12 @@
+--- src/setup.py.orig	2018-10-16 09:07:30.086993782 -0600
++++ src/setup.py	2018-10-16 09:10:20.586710425 -0600
+@@ -387,6 +387,9 @@ class sage_build_cython(Command):
+         with open(self._version_file, 'w') as f:
+             f.write(self._version_stamp)
+ 
++        # Remove buildroot paths from the generated files
++        subprocess.run(["find", "build/cythonized/sage", "-type", "f", "-exec", "sed", "-i", "s|@@BUILDROOT@@||g", "{}", "+"], check=True)
++
+         # Finally, copy relevant cythonized files from build/cythonized
+         # tree into the build-lib tree
+         for (dst_dir, src_files) in self.get_cythonized_package_files():

sagemath-cremona.patch

@@ -1,12 +1,12 @@
 diff -up src/sage/databases/cremona.py.orig src/sage/databases/cremona.py
---- src/sage/databases/cremona.py.orig	2018-08-03 05:10:08.000000000 -0600
+--- src/sage/databases/cremona.py.orig	2018-10-17 17:13:36.000000000 -0600
-+++ src/sage/databases/cremona.py	2018-08-29 08:48:43.090148635 -0600
++++ src/sage/databases/cremona.py	2018-10-25 13:24:02.644939224 -0600
 @@ -53,7 +53,6 @@ from sage.misc.prandom import randint
  
  import sage.schemes.elliptic_curves.constructor as elliptic
  from .sql_db import SQLDatabase, verify_column
 -from sage.misc.package import is_package_installed
- from sage.env import SAGE_SHARE
+ from sage.env import CREMONA_MINI_DATA_DIR, CREMONA_LARGE_DATA_DIR
  from sage.misc.all import walltime
  
 @@ -825,14 +824,6 @@ class MiniCremonaDatabase(SQLDatabase):

sagemath-eclib.patch

@@ -1,22 +0,0 @@
---- src/sage/libs/eclib/wrap.cpp.orig	2018-05-05 16:21:24.000000000 -0600
-+++ src/sage/libs/eclib/wrap.cpp	2018-08-09 21:57:02.055392569 -0600
-@@ -133,8 +133,8 @@ char* Curvedata_isogeny_class(struct Cur
- 
- 
- int mw_process(struct Curvedata* curve, struct mw* m,
--                      const struct bigint* x, const struct bigint* y,
--                      const struct bigint* z, int sat)
-+                      const bigint* x, const bigint* y,
-+                      const bigint* z, int sat)
- {
-   Point P(*curve, *x, *y, *z);
-   if (!P.isvalid())
-@@ -188,7 +188,7 @@ int mw_rank(struct mw* m)
- }
- 
- /* Returns index and unsat long array, which user must deallocate */
--int mw_saturate(struct mw* m, struct bigint* index, char** unsat,
-+int mw_saturate(struct mw* m, bigint* index, char** unsat,
-                        long sat_bd, int odd_primes_only)
- {
-   vector<long> v;

sagemath-escape.patch

@@ -0,0 +1,108 @@
+--- build/pkgs/sagenb/src/sagenb/misc/sphinxify.py.orig	2018-10-25 14:14:33.031253545 -0600
++++ build/pkgs/sagenb/src/sagenb/misc/sphinxify.py	2018-10-25 15:33:56.358876835 -0600
+@@ -133,7 +133,7 @@ def sphinxify(docstring, format='html'):
+         #    "/media/...path.../blah.png"
+         # to
+         #    "/doc/static/reference/media/...path.../blah.png"
+-        output = re.sub("""src=['"](/?\.\.)*/?media/([^"']*)['"]""",
++        output = re.sub("""src=['"](/?\\.\\.)*/?media/([^"']*)['"]""",
+                           'src="/doc/static/reference/media/\\2"',
+                           output)
+         # Remove spurious \(, \), \[, \].
+--- build/pkgs/sagenb/src/sagenb/misc/support.py.orig	2018-10-25 13:30:02.499892169 -0600
++++ build/pkgs/sagenb/src/sagenb/misc/support.py	2018-10-25 14:14:33.032253542 -0600
+@@ -550,7 +550,7 @@ try:
+             return args[0].__getattribute__(str(self))(*args[1:], **kwds)
+ 
+     def automatic_name_eval(s, globals, max_names=10000):
+-        """
++        r"""
+         Exec the string ``s`` in the scope of the ``globals``
+         dictionary, and if any :exc:`NameError`\ s are raised, try to
+         fix them by defining the variable that caused the error to be
+--- build/pkgs/sagenb/src/sagenb/notebook/cell.py.orig	2018-10-25 13:30:55.707737342 -0600
++++ build/pkgs/sagenb/src/sagenb/notebook/cell.py	2018-10-25 14:14:33.032253542 -0600
+@@ -441,7 +441,7 @@ class Cell_generic(object):
+         return isinstance(self, Cell)
+ 
+     def is_auto_cell(self):
+-        """
++        r"""
+         Returns whether this is an automatically evaluated generic
+         cell.  This is always false for :class:`Cell_generic`\ s and
+         :class:`TextCell`\ s.
+@@ -647,7 +647,7 @@ class TextCell(Cell_generic):
+         return self._text
+ 
+     def set_cell_output_type(self, typ='wrap'):
+-        """
++        r"""
+         Sets this text cell's output type.  This does nothing for
+         :class:`TextCell`\ s.
+ 
+@@ -1320,8 +1320,8 @@ class Cell(Cell_generic):
+         if len(s) == 0:
+             return False
+         s = s[0]
+-        return bool(re.search('(?<!\w)interact\s*\(.*\).*', s) or
+-                    re.search('\s*@\s*interact', s))
++        return bool(re.search(r'(?<!\w)interact\s*\(.*\).*', s) or
++                    re.search(r'\s*@\s*interact', s))
+ 
+     def is_interacting(self):
+         r"""
+@@ -1344,7 +1344,7 @@ class Cell(Cell_generic):
+         return hasattr(self, 'interact')
+ 
+     def stop_interacting(self):
+-        """
++        r"""
+         Stops :func:`sagenb.notebook.interact.interact`\ ion for this
+         compute cell.
+ 
+--- build/pkgs/sagenb/src/sagenb/notebook/worksheet.py.orig	2018-05-22 10:01:48.000000000 -0600
++++ build/pkgs/sagenb/src/sagenb/notebook/worksheet.py	2018-10-17 14:41:08.634154908 -0600
+@@ -61,8 +61,8 @@ from flask_babel import gettext, lazy_ge
+ _ = gettext
+ 
+ # Set some constants that will be used for regular expressions below.
+-whitespace = re.compile('\s')  # Match any whitespace character
+-non_whitespace = re.compile('\S')
++whitespace = re.compile(r'\s')  # Match any whitespace character
++non_whitespace = re.compile(r'\S')
+ 
+ # The file to which the Sage code that will be evaluated is written.
+ CODE_PY = "___code___.py"
+--- src/sage/combinat/cluster_algebra_quiver/quiver_mutation_type.py.orig	2018-10-17 17:13:35.000000000 -0600
++++ src/sage/combinat/cluster_algebra_quiver/quiver_mutation_type.py	2018-10-25 14:14:33.033253539 -0600
+@@ -2023,7 +2023,7 @@ class QuiverMutationType_Reducible(Quive
+ 
+     @cached_method
+     def class_size(self):
+-        """
++        r"""
+         If it is known, the size of the mutation class of all quivers
+         which are mutation equivalent to the standard quiver of
+         ``self`` (up to isomorphism) is returned.
+--- src/sage/combinat/crystals/alcove_path.py.orig	2018-10-17 17:13:35.000000000 -0600
++++ src/sage/combinat/crystals/alcove_path.py	2018-10-25 15:37:04.294360718 -0600
+@@ -389,7 +389,7 @@ class CrystalOfAlcovePaths(UniqueReprese
+ 
+         One can compute all vertices of the crystal by finding all the
+         admissible subsets of the `\lambda`-chain  (see method
+-        is_admissible, for definition).  We use the breath first
++        is_admissible, for definition).  We use the breadth first
+         search algorithm.
+ 
+         .. WARNING::
+--- src/sage/homology/homology_group.py.orig	2018-10-17 17:13:47.000000000 -0600
++++ src/sage/homology/homology_group.py	2018-10-25 15:54:54.683421705 -0600
+@@ -109,7 +109,7 @@ class HomologyGroup_class(AdditiveAbelia
+             sage: from sage.homology.homology_group import HomologyGroup
+             sage: H = HomologyGroup(7, ZZ, [4,4,4,4,4,7,7])
+             sage: H._latex_()
+-            'C_{4}^{5} \\times C_{7} \\times C_{7}'
++            'C_{4}^{5} \times C_{7} \times C_{7}'
+             sage: latex(HomologyGroup(6, ZZ))
+             \ZZ^{6}
+         """

sagemath-extensions.patch

@@ -1,6 +1,6 @@
 diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig	2018-08-03 05:10:08.000000000 -0600
+--- src/module_list.py.orig	2018-10-17 17:13:35.000000000 -0600
-+++ src/module_list.py	2018-08-29 08:34:50.846439644 -0600
++++ src/module_list.py	2018-10-25 11:33:55.361930982 -0600
 @@ -358,16 +358,16 @@ ext_modules = [
      Extension('sage.graphs.matchpoly',
                sources = ['sage/graphs/matchpoly.pyx']),
@@ -72,44 +72,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.libs.flint.flint',
                sources = ["sage/libs/flint/flint.pyx"],
-@@ -495,22 +494,22 @@ ext_modules = [
+@@ -841,10 +840,10 @@ ext_modules = [
-     Extension('sage.libs.gmp.pylong',
-               sources = ['sage/libs/gmp/pylong.pyx']),
- 
--    OptionalExtension('sage.libs.braiding',
--                      sources = ["sage/libs/braiding.pyx"],
--                      libraries = ["braiding"],
--                      package="libbraiding",
--                      language = 'c++'),
-+#    OptionalExtension('sage.libs.braiding',
-+#                      sources = ["sage/libs/braiding.pyx"],
-+#                      libraries = ["braiding"],
-+#                      package="libbraiding",
-+#                      language = 'c++'),
- 
--    OptionalExtension('sage.libs.homfly',
--                      sources = ["sage/libs/homfly.pyx"],
--                      libraries = ["homfly", "gc"],
--                      package="libhomfly"),
-+#    OptionalExtension('sage.libs.homfly',
-+#                      sources = ["sage/libs/homfly.pyx"],
-+#                      libraries = ["homfly", "gc"],
-+#                      package="libhomfly"),
- 
--    OptionalExtension('sage.libs.sirocco',
--                      sources = ["sage/libs/sirocco.pyx"],
--                      libraries = ["sirocco"],
--                      package="sirocco",
--                      language = 'c++'),
-+#    OptionalExtension('sage.libs.sirocco',
-+#                      sources = ["sage/libs/sirocco.pyx"],
-+#                      libraries = ["sirocco"],
-+#                      package="sirocco",
-+#                      language = 'c++'),
- 
-     Extension('*', ['sage/libs/linbox/*.pyx']),
- 
-@@ -843,10 +842,10 @@ ext_modules = [
      Extension('sage.matrix.matrix_window',
                sources = ['sage/matrix/matrix_window.pyx']),
  
@@ -124,7 +87,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.matrix.misc',
                sources = ['sage/matrix/misc.pyx']),
-@@ -1023,26 +1022,25 @@ ext_modules = [
+@@ -1021,26 +1020,25 @@ ext_modules = [
      Extension("sage.numerical.backends.interactivelp_backend",
                ["sage/numerical/backends/interactivelp_backend.pyx"]),
  

sagemath-includes.patch

@@ -1,6 +1,6 @@
 diff -up src/module_list.py.orig src/module_list.py
---- src/module_list.py.orig	2018-08-29 10:41:05.127643255 -0600
+--- src/module_list.py.orig	2018-10-25 11:40:44.400943439 -0600
-+++ src/module_list.py	2018-08-29 10:44:16.376279329 -0600
++++ src/module_list.py	2018-10-25 16:16:46.618825285 -0600
 @@ -45,6 +45,9 @@ zlib_libs = zlib_pc['libraries']
  zlib_library_dirs = zlib_pc['library_dirs']
  zlib_include_dirs = zlib_pc['include_dirs']
@@ -36,7 +36,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('*', sources = ['sage/algebras/finite_dimensional_algebras/*.pyx']),
  
-@@ -526,7 +538,8 @@ ext_modules = [
+@@ -524,7 +536,8 @@ ext_modules = [
                                                          [])),
  
      Extension('sage.libs.lrcalc.lrcalc',
@@ -46,7 +46,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      OptionalExtension("sage.libs.meataxe",
                sources = ['sage/libs/meataxe.pyx'],
-@@ -548,23 +561,28 @@ ext_modules = [
+@@ -546,23 +559,28 @@ ext_modules = [
                sources = ['sage/libs/readline.pyx'],
                libraries = ['readline']),
  
@@ -80,7 +80,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      ###################################
      ##
-@@ -572,7 +590,8 @@ ext_modules = [
+@@ -570,7 +588,8 @@ ext_modules = [
      ##
      ###################################
  
@@ -90,7 +90,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      ###################################
      ##
-@@ -744,7 +763,8 @@ ext_modules = [
+@@ -742,7 +761,8 @@ ext_modules = [
  
      Extension("sage.matrix.matrix_complex_ball_dense",
                ["sage/matrix/matrix_complex_ball_dense.pyx"],
@@ -100,7 +100,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.matrix.matrix_complex_double_dense',
                sources = ['sage/matrix/matrix_complex_double_dense.pyx']),
-@@ -752,6 +772,7 @@ ext_modules = [
+@@ -750,6 +770,7 @@ ext_modules = [
      Extension('sage.matrix.matrix_cyclo_dense',
                sources = ['sage/matrix/matrix_cyclo_dense.pyx'],
                language = "c++",
@@ -108,7 +108,7 @@ diff -up src/module_list.py.orig src/module_list.py
                libraries=['ntl']),
  
      Extension('sage.matrix.matrix_gap',
-@@ -814,6 +835,7 @@ ext_modules = [
+@@ -812,6 +833,7 @@ ext_modules = [
                sources = ['sage/matrix/matrix_modn_sparse.pyx']),
  
      Extension('sage.matrix.matrix_mpolynomial_dense',
@@ -116,7 +116,7 @@ diff -up src/module_list.py.orig src/module_list.py
                sources = ['sage/matrix/matrix_mpolynomial_dense.pyx']),
  
      Extension('sage.matrix.matrix_polynomial_dense',
-@@ -1111,7 +1133,8 @@ ext_modules = [
+@@ -1109,7 +1131,8 @@ ext_modules = [
                language = 'c++'),
  
      Extension("sage.rings.complex_arb",
@@ -126,7 +126,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.rings.complex_double',
                sources = ['sage/rings/complex_double.pyx'],
-@@ -1181,7 +1204,8 @@ ext_modules = [
+@@ -1179,7 +1202,8 @@ ext_modules = [
                sources = ['sage/rings/real_interval_absolute.pyx']),
  
      Extension("sage.rings.real_arb",
@@ -136,7 +136,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.rings.real_lazy',
                sources = ['sage/rings/real_lazy.pyx']),
-@@ -1264,6 +1288,7 @@ ext_modules = [
+@@ -1262,6 +1286,7 @@ ext_modules = [
  
      Extension('sage.rings.number_field.number_field_element_quadratic',
                sources = ['sage/rings/number_field/number_field_element_quadratic.pyx'],
@@ -144,7 +144,7 @@ diff -up src/module_list.py.orig src/module_list.py
                libraries=['ntl'],
                language = 'c++'),
  
-@@ -1386,12 +1411,15 @@ ext_modules = [
+@@ -1401,12 +1426,15 @@ ext_modules = [
                sources = ['sage/rings/polynomial/multi_polynomial.pyx']),
  
      Extension('sage.rings.polynomial.multi_polynomial_ideal_libsingular',
@@ -160,7 +160,7 @@ diff -up src/module_list.py.orig src/module_list.py
                sources = ['sage/rings/polynomial/multi_polynomial_libsingular.pyx']),
  
      Extension('sage.rings.polynomial.multi_polynomial_ring_base',
-@@ -1404,7 +1432,8 @@ ext_modules = [
+@@ -1419,7 +1447,8 @@ ext_modules = [
                sources = ['sage/rings/polynomial/polydict.pyx']),
  
      Extension('sage.rings.polynomial.polynomial_complex_arb',
@@ -170,9 +170,9 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.rings.polynomial.polynomial_compiled',
                 sources = ['sage/rings/polynomial/polynomial_compiled.pyx']),
-diff -up src/setup.py.orig src/setup.py
+diff -du src/setup.py.orig src/setup.py
---- src/setup.py.orig	2018-08-29 08:35:19.955079610 -0600
+--- src/setup.py.orig	2018-10-25 14:05:20.779815082 -0600
-+++ src/setup.py	2018-08-29 10:44:16.376279329 -0600
++++ src/setup.py	2018-10-25 16:16:46.619825283 -0600
 @@ -85,6 +85,7 @@ except KeyError:
  
  # search for dependencies and add to gcc -I<path>

sagemath-jmol.patch

@@ -1,12 +1,12 @@
 diff -up src/sage/interfaces/jmoldata.py.orig src/sage/interfaces/jmoldata.py
---- src/sage/interfaces/jmoldata.py.orig	2018-08-03 05:10:08.000000000 -0600
+--- src/sage/interfaces/jmoldata.py.orig	2018-10-17 17:13:47.000000000 -0600
-+++ src/sage/interfaces/jmoldata.py	2018-08-29 08:47:39.203938604 -0600
++++ src/sage/interfaces/jmoldata.py	2018-10-25 13:22:07.965272901 -0600
 @@ -148,8 +148,6 @@ class JmolData(SageObject):
              sage: print(os.path.exists(testfile)) # optional -- java
              True
          """
 -        # Set up paths, file names and scripts
--        jmolpath = os.path.join(SAGE_LOCAL, "share", "jmol", "JmolData.jar")
+-        jmolpath = os.path.join(JMOL_DIR, "JmolData.jar")
          target_native = targetfile
  
          if sys.platform == 'cygwin':

sagemath-libgap.patch

@@ -1,30 +1,18 @@
 diff -up src/sage/env.py.orig src/sage/env.py
---- src/sage/env.py.orig	2018-08-03 05:10:08.000000000 -0600
+--- src/sage/env.py.orig	2018-10-17 17:13:36.000000000 -0600
-+++ src/sage/env.py	2018-08-29 11:25:26.833962117 -0600
++++ src/sage/env.py	2018-10-25 14:10:21.564960823 -0600
 @@ -164,7 +164,7 @@ _add_variable_or_fallback('CONWAY_POLYNO
  _add_variable_or_fallback('GRAPHS_DATA_DIR',  opj('$SAGE_SHARE','graphs'))
  _add_variable_or_fallback('ELLCURVE_DATA_DIR',opj('$SAGE_SHARE','ellcurves'))
  _add_variable_or_fallback('POLYTOPE_DATA_DIR',opj('$SAGE_SHARE','reflexive_polytopes'))
 -_add_variable_or_fallback('GAP_ROOT_DIR',     opj('$SAGE_LOCAL','gap','latest'))
-+_add_variable_or_fallback('GAP_ROOT_DIR',     opj('usr','lib','gap'))
++_add_variable_or_fallback('GAP_ROOT_DIR',     opj('/usr','lib','gap'))
  _add_variable_or_fallback('THEBE_DIR',        opj('$SAGE_SHARE','thebe'))
- 
+ _add_variable_or_fallback('COMBINATORIAL_DESIGN_DATA_DIR', opj('$SAGE_SHARE', 'combinatorial_designs'))
- # locate singular shared object
+ _add_variable_or_fallback('CREMONA_MINI_DATA_DIR', opj('$SAGE_SHARE', 'cremona'))
-diff -up src/sage/interfaces/gap.py.orig src/sage/interfaces/gap.py
---- src/sage/interfaces/gap.py.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/interfaces/gap.py	2018-08-29 11:21:43.180584324 -0600
-@@ -197,7 +197,7 @@ import string
- 
- WORKSPACE = gap_workspace_file()
- 
--GAP_BINARY = os.path.join(SAGE_LOCAL, 'bin', 'gap')
-+GAP_BINARY = os.path.join('usr', 'bin', 'gap')
- 
- first_try = True
- 
 diff -up src/sage/libs/gap/test/main.c.orig src/sage/libs/gap/test/main.c
---- src/sage/libs/gap/test/main.c.orig	2018-08-03 05:10:08.000000000 -0600
+--- src/sage/libs/gap/test/main.c.orig	2018-10-17 17:13:52.000000000 -0600
-+++ src/sage/libs/gap/test/main.c	2018-08-29 10:38:22.512653256 -0600
++++ src/sage/libs/gap/test/main.c	2018-10-25 14:05:51.458727612 -0600
 @@ -22,7 +22,7 @@ void eval(char* cmd) {
    libgap_start_interaction(cmd);
  
@@ -35,8 +23,8 @@ diff -up src/sage/libs/gap/test/main.c.orig src/sage/libs/gap/test/main.c
    char* out = libgap_get_output();
    libgap_exit();
 diff -up src/sage/libs/gap/util.pyx.orig src/sage/libs/gap/util.pyx
---- src/sage/libs/gap/util.pyx.orig	2018-08-03 05:10:08.000000000 -0600
+--- src/sage/libs/gap/util.pyx.orig	2018-10-25 13:50:51.168295628 -0600
-+++ src/sage/libs/gap/util.pyx	2018-08-29 11:32:06.654205922 -0600
++++ src/sage/libs/gap/util.pyx	2018-10-25 14:05:51.458727612 -0600
 @@ -25,6 +25,8 @@ from sage.cpython.string cimport str_to_
  from sage.interfaces.gap_workspace import prepare_workspace_dir
  from sage.env import SAGE_LOCAL, GAP_ROOT_DIR

sagemath-maxima.patch

@@ -1,6 +1,6 @@
 diff -up src/bin/sage-maxima.lisp.orig src/bin/sage-maxima.lisp
---- src/bin/sage-maxima.lisp.orig	2018-08-03 05:10:08.000000000 -0600
+--- src/bin/sage-maxima.lisp.orig	2018-10-17 17:13:34.000000000 -0600
-+++ src/bin/sage-maxima.lisp	2018-08-29 08:45:21.302643791 -0600
++++ src/bin/sage-maxima.lisp	2018-10-25 13:14:53.465538639 -0600
 @@ -4,3 +4,8 @@
  
  (setf *prompt-prefix* "<sage-display>")
@@ -11,12 +11,12 @@ diff -up src/bin/sage-maxima.lisp.orig src/bin/sage-maxima.lisp
 +  *standard-input* (open "/dev/stdin" :direction :input)
 +  *standard-output* (open "/dev/stdout" :direction :output))
 diff -up src/sage/interfaces/maxima.py.orig src/sage/interfaces/maxima.py
---- src/sage/interfaces/maxima.py.orig	2018-08-03 05:10:08.000000000 -0600
+--- src/sage/interfaces/maxima.py.orig	2018-10-17 17:13:51.000000000 -0600
-+++ src/sage/interfaces/maxima.py	2018-08-29 08:47:09.779302448 -0600
++++ src/sage/interfaces/maxima.py	2018-10-25 13:16:00.326343444 -0600
 @@ -546,7 +546,7 @@ class Maxima(MaximaAbstract, Expect):
          Expect.__init__(self,
                          name = 'maxima',
-                         prompt = '\(\%i[0-9]+\) ',
+                         prompt = r'\(\%i[0-9]+\) ',
 -                        command = 'maxima -p "{0}"'.format(STARTUP),
 +                        command = 'maxima --disable-readline -p "{0}"'.format(STARTUP),
                          env = {'TMPDIR': str(ECL_TMP)},

sagemath-mpfr.patch

@@ -12,7 +12,7 @@ diff -up src/sage/libs/mpfr/__init__.pxd.orig src/sage/libs/mpfr/__init__.pxd
 diff -up src/sage/rings/complex_mpc.pyx.orig src/sage/rings/complex_mpc.pyx
 --- src/sage/rings/complex_mpc.pyx.orig	2018-08-03 05:10:09.000000000 -0600
 +++ src/sage/rings/complex_mpc.pyx	2018-08-29 10:41:34.027286042 -0600
-@@ -2221,7 +2221,7 @@ cdef class MPComplexNumber(sage.structur
+@@ -2225,7 +2225,7 @@ cdef class MPComplexNumber(sage.structur
          cdef RealNumber a,r
          a = self.argument()/n
          r = self.abs()

sagemath-nauty.patch

@@ -1,7 +1,7 @@
 diff -up src/sage/graphs/graph_generators.py.orig src/sage/graphs/graph_generators.py
---- src/sage/graphs/graph_generators.py.orig	2018-08-29 08:52:26.099392035 -0600
+--- src/sage/graphs/graph_generators.py.orig	2018-10-17 17:13:47.000000000 -0600
-+++ src/sage/graphs/graph_generators.py	2018-08-29 08:56:44.782205619 -0600
++++ src/sage/graphs/graph_generators.py	2018-10-25 14:04:50.496901422 -0600
-@@ -906,7 +906,7 @@ class GraphGenerators():
+@@ -911,7 +911,7 @@ class GraphGenerators():
          else:
              enc_kwargs = {'encoding': 'latin-1'}
  

sagemath-nofstring.patch

@@ -1,60 +0,0 @@
-diff -up src/sage/arith/multi_modular.pyx.orig src/sage/arith/multi_modular.pyx
---- src/sage/arith/multi_modular.pyx.orig	2018-08-03 05:10:08.000000000 -0600
-+++ src/sage/arith/multi_modular.pyx	2018-08-29 10:44:04.624424587 -0600
-@@ -173,9 +173,9 @@ cdef class MultiModularBasis_base(object
-             ArithmeticError: The inverse of 6 modulo 10 is not defined.
-         """
-         if l_bound < 2:
--            raise ValueError(f"minimum value for lower bound is 2, given: {l_bound}")
-+            raise ValueError("minimum value for lower bound is 2, given: {l_bound}".format(l_bound=l_bound))
-         if u_bound > MAX_MODULUS:
--            raise ValueError(f"upper bound cannot be greater than {MAX_MODULUS}, given: {u_bound}")
-+            raise ValueError("upper bound cannot be greater than {MAX_MODULUS}, given: {u_bound}".format(MAX_MODULUS=MAX_MODULUS, u_bound=u_bound))
- 
-         self._l_bound = l_bound
-         self._u_bound = u_bound
-@@ -234,7 +234,7 @@ cdef class MultiModularBasis_base(object
-         if check:
-             for p in plist:
-                 if p > MAX_MODULUS:
--                    raise OverflowError(f"given modulus {p} is larger than {MAX_MODULUS}")
-+                    raise OverflowError("given modulus {p} is larger than {MAX_MODULUS}".format(p=p, MAX_MODULUS=MAX_MODULUS))
-         self._realloc_to_new_count(self.n + len_plist)
- 
-         cdef Py_ssize_t i
-diff -up src/sage/rings/finite_rings/integer_mod.pyx.orig src/sage/rings/finite_rings/integer_mod.pyx
---- src/sage/rings/finite_rings/integer_mod.pyx.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/sage/rings/finite_rings/integer_mod.pyx	2018-08-29 10:44:04.624424587 -0600
-@@ -468,7 +468,7 @@ cdef class IntegerMod_abstract(FiniteRin
-         from .integer_mod_ring import IntegerModRing
-         R = IntegerModRing(modulus)
-         if (<Element>self)._parent._IntegerModRing_generic__order % R.order():
--            raise ArithmeticError(f"reduction modulo {modulus!r} not defined")
-+            raise ArithmeticError("reduction modulo {modulus} not defined".format(modulus=repr(modulus)))
-         return R(self)
- 
-     def is_nilpotent(self):
-diff -up src/sage/structure/parent.pyx.orig src/sage/structure/parent.pyx
---- src/sage/structure/parent.pyx.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/sage/structure/parent.pyx	2018-08-29 10:44:04.625424574 -0600
-@@ -726,7 +726,7 @@ cdef class Parent(sage.structure.categor
-     cdef int init_coerce(self, bint warn=True) except -1:
-         if self._coerce_from_hash is None:
-             if warn:
--                raise AssertionError(f"unexpected call of init_coerce() for {type(self)}")
-+                raise AssertionError("unexpected call of init_coerce() for {typ}".format(typ=type(self)))
-             self._initial_coerce_list = []
-             self._initial_action_list = []
-             self._initial_convert_list = []
-diff -up src/sage/symbolic/ring.pyx.orig src/sage/symbolic/ring.pyx
---- src/sage/symbolic/ring.pyx.orig	2018-08-03 05:10:09.000000000 -0600
-+++ src/sage/symbolic/ring.pyx	2018-08-29 10:44:04.625424574 -0600
-@@ -378,7 +378,7 @@ cdef class SymbolicRing(CommutativeRing)
-             from sage.misc.all import prod
-             return prod([SR(p)**e for p,e in x], SR(x.unit()))
-         else:
--            raise TypeError(f"unable to convert {x!r} to a symbolic expression")
-+            raise TypeError("unable to convert {x} to a symbolic expression".format(x=repr(x)))
- 
-         return new_Expression_from_GEx(self, exp)
- 

sagemath-openblas.patch

@@ -6,7 +6,7 @@ diff -up src/module_list.py.orig src/module_list.py
  
  # CBLAS can be one of multiple implementations
 -cblas_pc = pkgconfig.parse('cblas')
-+cblas_pc = pkgconfig.parse('atlas')
++cblas_pc = pkgconfig.parse('openblas')
  cblas_libs = cblas_pc['libraries']
  cblas_library_dirs = cblas_pc['library_dirs']
  cblas_include_dirs = cblas_pc['include_dirs']
@@ -33,7 +33,7 @@ diff -up src/sage/misc/cython.py.orig src/sage/misc/cython.py
  
  # CBLAS can be one of multiple implementations
 -cblas_pc = pkgconfig.parse('cblas')
-+cblas_pc = pkgconfig.parse('atlas')
++cblas_pc = pkgconfig.parse('openblas')
  cblas_libs = list(cblas_pc['libraries'])
  cblas_library_dirs = list(cblas_pc['library_dirs'])
  cblas_include_dirs = list(cblas_pc['include_dirs'])

sagemath-sagedoc.patch

@@ -1,7 +1,7 @@
 diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
---- src/sage/doctest/control.py.orig	2018-08-03 05:10:08.000000000 -0600
+--- src/sage/doctest/control.py.orig	2018-10-17 17:13:36.000000000 -0600
-+++ src/sage/doctest/control.py	2018-08-29 08:36:07.805487927 -0600
++++ src/sage/doctest/control.py	2018-10-25 11:40:58.936908341 -0600
-@@ -102,7 +102,6 @@ class DocTestDefaults(SageObject):
+@@ -106,7 +106,6 @@ class DocTestDefaults(SageObject):
          self.valgrind = False
          self.massif = False
          self.cachegrind = False
@@ -9,7 +9,7 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
          self.failed = False
          self.new = False
          self.show_skipped = False
-@@ -292,7 +291,7 @@ class DocTestController(SageObject):
+@@ -308,7 +307,7 @@ class DocTestController(SageObject):
              if options.gdb or options.debug:
                  # Interactive debuggers: "infinite" timeout
                  options.timeout = 0
@@ -18,7 +18,7 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
                  # Non-interactive debuggers: 48 hours
                  options.timeout = int(os.getenv('SAGE_TIMEOUT_VALGRIND', 48 * 60 * 60))
              elif options.long:
-@@ -1071,13 +1070,8 @@ class DocTestController(SageObject):
+@@ -1094,13 +1093,8 @@ class DocTestController(SageObject):
              elif opt.cachegrind:
                  toolname = "cachegrind"
                  flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "")
@@ -32,8 +32,8 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
              if "%s" in flags:
                  flags %= toolname + ".%p" # replace %s with toolname
          cmd += flags + sage_cmd
-@@ -1137,10 +1131,10 @@ class DocTestController(SageObject):
+@@ -1185,10 +1179,10 @@ class DocTestController(SageObject):
-             0
+ 
          """
          opt = self.options
 -        L = (opt.gdb, opt.valgrind, opt.massif, opt.cachegrind, opt.omega)
@@ -46,20 +46,32 @@ diff -up src/sage/doctest/control.py.orig src/sage/doctest/control.py
              return self.run_val_gdb()
          else:
 diff -up src/sage/interfaces/singular.py.orig src/sage/interfaces/singular.py
---- src/sage/interfaces/singular.py.orig	2018-08-03 05:10:08.000000000 -0600
+--- src/sage/interfaces/singular.py.orig	2018-10-25 11:40:58.937908339 -0600
-+++ src/sage/interfaces/singular.py	2018-08-29 08:36:07.818487766 -0600
++++ src/sage/interfaces/singular.py	2018-10-25 13:11:10.256190334 -0600
-@@ -2262,7 +2262,7 @@ def generate_docstring_dictionary():
+@@ -2264,7 +2264,7 @@ def generate_docstring_dictionary():
-     nodes.clear()
      node_names.clear()
  
--    singular_docdir = SAGE_LOCAL+"/share/info/"
+     import os
-+    singular_docdir = os.environ["SINGULAR_BIN_DIR"]+"/info/"
+-    singular_docdir = os.environ['SINGULARPATH']+"/../info/"
++    singular_docdir = "/usr/share/info/"
  
-     new_node = re.compile("File: singular\.hlp,  Node: ([^,]*),.*")
+     new_node = re.compile(r"File: singular\.hlp,  Node: ([^,]*),.*")
-     new_lookup = re.compile("\* ([^:]*):*([^.]*)\..*")
+     new_lookup = re.compile(r"\* ([^:]*):*([^.]*)\..*")
+@@ -2272,8 +2272,9 @@ 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_doctir, 'singular.hlp.gz'),
++                   encoding='latin-1') 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	2018-08-03 05:10:09.000000000 -0600
+--- src/sage_setup/docbuild/ext/multidocs.py.orig	2018-10-17 17:14:18.000000000 -0600
-+++ src/sage_setup/docbuild/ext/multidocs.py	2018-08-29 08:36:07.829487630 -0600
++++ src/sage_setup/docbuild/ext/multidocs.py	2018-10-25 11:40:58.937908339 -0600
 @@ -84,8 +84,11 @@ def merge_environment(app, env):
              for ind in newalldoc:
                  # treat subdocument source as orphaned file and don't complain
@@ -75,22 +87,22 @@ diff -up src/sage_setup/docbuild/ext/multidocs.py.orig src/sage_setup/docbuild/e
              newcite = {}
              citations = docenv.domaindata["std"]["citations"]
 diff -up src/sage_setup/docbuild/__init__.py.orig src/sage_setup/docbuild/__init__.py
---- src/sage_setup/docbuild/__init__.py.orig	2018-08-03 05:10:09.000000000 -0600
+--- src/sage_setup/docbuild/__init__.py.orig	2018-10-25 11:40:58.938908336 -0600
-+++ src/sage_setup/docbuild/__init__.py	2018-08-29 08:36:07.837487531 -0600
++++ src/sage_setup/docbuild/__init__.py	2018-10-25 13:12:56.110881282 -0600
-@@ -272,13 +272,14 @@ if NUM_THREADS > 1:
+@@ -279,13 +279,14 @@ def build_many(target, args):
-         # map_async handles KeyboardInterrupt correctly. Plain map and
+     # map_async handles KeyboardInterrupt correctly. Plain map and
-         # apply_async does not, so don't use it.
+     # apply_async does not, so don't use it.
-         x = pool.map_async(target, args, 1)
+     x = pool.map_async(target, args, 1)
-+        ret = []
++    ret = []
-         try:
+     try:
--            ret = x.get(99999)
+-        ret = x.get(99999)
-+            ret = x.get(3600)
++        ret = x.get(3600)
-             pool.close()
+         pool.close()
-             pool.join()
+         pool.join()
-         except Exception:
+     except Exception:
--            pool.terminate()
+-        pool.terminate()
-             if ABORT_ON_ERROR:
+         if ABORT_ON_ERROR:
-+                pool.terminate()
++            pool.terminate()
-                 raise
+             raise
-         return ret
+     return ret
- else:
+ 

sagemath-scripts.patch

@@ -1,6 +1,6 @@
 diff -up src/bin/sage.orig src/bin/sage
---- src/bin/sage.orig	2018-08-03 05:10:08.000000000 -0600
+--- src/bin/sage.orig	2018-10-17 17:13:34.000000000 -0600
-+++ src/bin/sage	2018-08-29 08:32:06.325478480 -0600
++++ src/bin/sage	2018-10-24 15:19:11.805131334 -0600
 @@ -26,13 +26,10 @@ usage() {
      echo "  file.[sage|py|spyx] -- run given .sage, .py or .spyx file"
      echo "  -advanced           -- list all command line options"
@@ -131,7 +131,7 @@ diff -up src/bin/sage.orig src/bin/sage
      echo "  -startuptime [module] -- display how long each component of Sage takes to"
      echo "                         start up; optionally specify a module to get more"
      echo "                         details about that particular module"
-@@ -220,7 +152,6 @@ usage_advanced() {
+@@ -223,7 +155,6 @@ usage_advanced() {
      echo "  -coverage <files>   -- give info about doctest coverage of files"
      echo "  -coverageall        -- give summary info about doctest coverage of all"
      echo "                         files in the Sage library"
@@ -139,7 +139,7 @@ diff -up src/bin/sage.orig src/bin/sage
      echo "  -search_src <string> -- search through all the Sage library code for string"
      echo "  -search_doc <string> -- search through the Sage documentation for string"
      echo "  -grep <string>      -- same as -search_src"
-@@ -244,16 +175,6 @@ usage_advanced() {
+@@ -249,16 +180,6 @@ usage_advanced() {
      echo
      ####  1.......................26..................................................78
      ####  |.....................--.|...................................................|
@@ -156,7 +156,7 @@ diff -up src/bin/sage.orig src/bin/sage
      echo "Valgrind memory debugging:"
      echo "  -cachegrind         -- run Sage using Valgrind's cachegrind tool.  The log"
      echo "                         files are named sage-cachegrind.PID can be found in"
-@@ -267,9 +188,6 @@ usage_advanced() {
+@@ -272,9 +193,6 @@ usage_advanced() {
      echo "  -memcheck           -- run Sage using Valgrind's memcheck tool.  The log"
      echo "                         files are named sage-memcheck.PID can be found in"
      echo "                         $DOT_SAGE"
@@ -166,7 +166,7 @@ diff -up src/bin/sage.orig src/bin/sage
      echo "  -valgrind           -- this is an alias for -memcheck"
      echo
      echo "You can also use -- before a long option, e.g., 'sage --optional'."
-@@ -279,115 +197,6 @@ usage_advanced() {
+@@ -284,115 +202,6 @@ usage_advanced() {
  
  
  #####################################################################
@@ -282,7 +282,7 @@ diff -up src/bin/sage.orig src/bin/sage
  # Report information about the Sage environment
  #####################################################################
  
-@@ -416,35 +225,8 @@ if [ $# -gt 0 ]; then
+@@ -421,35 +230,8 @@ if [ $# -gt 0 ]; then
  fi
  
  
@@ -318,7 +318,7 @@ diff -up src/bin/sage.orig src/bin/sage
      if [ ! -d "$IPYTHONDIR" ]; then
          # make sure that $DOT_SAGE exists so that ipython will happily
          # create its config directories there.  If DOT_SAGE doesn't
-@@ -455,20 +237,6 @@ sage_setup() {
+@@ -460,20 +242,6 @@ sage_setup() {
  }
  
  
@@ -339,7 +339,7 @@ diff -up src/bin/sage.orig src/bin/sage
  # Start an interactive Sage session, this function never returns.
  interactive_sage() {
      sage_setup
-@@ -552,16 +320,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
+@@ -557,16 +325,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
      exec ecl "$@"
  fi
  
@@ -356,8 +356,8 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
      shift
      exec maxima "$@"
-@@ -587,11 +345,6 @@ if [ "$1" = '-pip' -o "$1" = '--pip' ];
+@@ -592,11 +350,6 @@ if [ "$1" = '-pip' -o "$1" = '--pip' ];
-     exec pip "$@"
+     exec sage-python23 -m pip "$@"
  fi
  
 -if [ "$1" = '-fix-pkg-checksums' -o "$1" = '--fix-pkg-checksums' ]; then
@@ -368,7 +368,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-python' -o "$1" = '--python' ]; then
      shift
      if [ "$SAGE_PYTHON3" = 'yes' ]; then
-@@ -626,16 +379,6 @@ if [ "$1" = '-ipython3' -o "$1" = '--ipy
+@@ -631,16 +384,6 @@ if [ "$1" = '-ipython3' -o "$1" = '--ipy
      exec ipython3 "$@"
  fi
  
@@ -385,7 +385,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
      # AUTHORS:
      # - Carl Witty and William Stein: initial version
-@@ -755,20 +498,6 @@ EOF
+@@ -760,20 +503,6 @@ EOF
  fi
  
  #####################################################################
@@ -406,7 +406,7 @@ diff -up src/bin/sage.orig src/bin/sage
  # File conversion
  #####################################################################
  
-@@ -796,11 +525,6 @@ fi
+@@ -804,11 +533,6 @@ fi
  # Run Sage's versions of the standard Algebra/Geometry etc. software
  #####################################################################
  
@@ -418,7 +418,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [[ "$1" =~ ^--notebook=.* || "$1" =~ ^-n=.* || "$1" =~ ^-notebook=.* ]] ; then
      sage-cleaner &>/dev/null &
      exec sage-notebook "$@"
-@@ -811,13 +535,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
+@@ -819,13 +543,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
      exec sage-notebook "$@"
  fi
  
@@ -432,7 +432,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
      shift
      sage-cleaner &>/dev/null &
-@@ -836,34 +553,15 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
+@@ -844,34 +561,15 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
      exit 0
  fi
  
@@ -469,7 +469,7 @@ diff -up src/bin/sage.orig src/bin/sage
          shift
          exec sage-runtests -p "$@"
      else
-@@ -872,10 +570,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
+@@ -880,10 +578,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
      fi
  fi
  
@@ -481,7 +481,7 @@ diff -up src/bin/sage.orig src/bin/sage
      shift
      sage_setup
      export PYTHONIOENCODING="utf-8"  # Fix encoding for doctests
-@@ -896,122 +591,6 @@ if [ "$1" = '-c' ]; then
+@@ -904,122 +599,6 @@ if [ "$1" = '-c' ]; then
      exec sage-eval "$@"
  fi
  
@@ -604,7 +604,7 @@ diff -up src/bin/sage.orig src/bin/sage
  if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
      shift
      sage_setup
-@@ -1061,12 +640,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
+@@ -1069,12 +648,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
      exec sage-callgrind "$@"
  fi
  
@@ -618,9 +618,9 @@ diff -up src/bin/sage.orig src/bin/sage
      exec sage-startuptime.py "$@"
  fi
 diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
---- src/bin/sage-runtests.orig	2018-08-03 05:10:08.000000000 -0600
+--- src/bin/sage-runtests.orig	2018-10-17 17:13:34.000000000 -0600
-+++ src/bin/sage-runtests	2018-08-29 08:27:37.703807389 -0600
++++ src/bin/sage-runtests	2018-10-24 15:19:11.805131334 -0600
-@@ -67,10 +67,6 @@ if __name__ == "__main__":
+@@ -76,10 +76,6 @@ if __name__ == "__main__":
                        help="run doctests using Valgrind's cachegrind tool.  The log "
                           "files are named sage-cachegrind.PID and can be found in " +
                           os.path.join(DOT_SAGE, "valgrind"))
@@ -632,8 +632,8 @@ diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
      parser.add_option("-f", "--failed", action="store_true", default=False,
          help="doctest only those files that failed in the previous run")
 diff -up src/bin/sage-valgrind.orig src/bin/sage-valgrind
---- src/bin/sage-valgrind.orig	2018-08-03 05:10:08.000000000 -0600
+--- src/bin/sage-valgrind.orig	2018-10-17 17:13:34.000000000 -0600
-+++ src/bin/sage-valgrind	2018-08-29 08:27:37.703807389 -0600
++++ src/bin/sage-valgrind	2018-10-24 15:19:11.805131334 -0600
 @@ -1,16 +1,6 @@
  #!/usr/bin/env bash
  

sagemath.spec

@@ -1,6 +1,6 @@
 %global __provides_exclude_from	.*/site-packages/.*\\.so
 
-# This package install python files in nonstandard places
+# This package installs python files in nonstandard places
 %global _python_bytecompile_extra 0
 
 %bcond_with bundled_pexpect
@@ -44,21 +44,21 @@
 %global	flintqs_pkg		flintqs-1.0
 %global graphs_pkg		graphs-20161026
 %if %{with bundled_ipython}
-%global ipython_pkg		ipython-5.5.0
+%global ipython_pkg		ipython-5.8.0
 %endif
 %if %{with bundled_ipywidgets}
 %global ipywidgets_pkg		ipywidgets-7.2.0
 %endif
 %if %{with bundled_pexpect}
-%global pexpect_pkg		pexpect-4.1.0
+%global pexpect_pkg		pexpect-4.6.0
 %endif
 %global polytopes_db_pkg	polytopes_db-20170220
 %global rubiks_pkg		rubiks-20070912
 %global	sagenb_pkg		sagenb-1.0.3
 %global sagenb_export_pkg	sagenb_export-3.2
 %global sagetex_pkg		sagetex-3.0
-%global Sphinx_pkg		Sphinx-1.7.5
+%global Sphinx_pkg		Sphinx-1.7.6
-%global singular_pkg		singular-4.1.0p3
+%global singular_pkg		singular-4.1.1p3
 %if %{with bundled_thebe}
 %global thebe_pkg		thebe-9624e0a0
 %endif
@@ -72,7 +72,7 @@
 # Spkg equivalents of required rpms; we pretend they are installed as spkgs.
 # The version numbers shown are those of the latest released spkg, if the Fedora
 # version is not behind.
-%global SAGE_REQUIRED_PKGS 4ti2-1.6.7 cbc-2.9.4 CoCoALib-0.99564 cryptominisat-5.0.1 gap_packages-4.8.6new2 gmp-6.1.2 gmpy2-2.1.0a1 lrslib-062+autotools-2017-03-03 qepcad-B.1.69 saclib-2.2.6 surf-1.0.6-gcc6
+%global SAGE_REQUIRED_PKGS 4ti2-1.6.7 cbc-2.9.4 CoCoALib-0.99564 cryptominisat-5.0.1 gap_packages-4.8.6new2 gmp-6.1.2 gmpy2-2.1.0a1 lrslib-062+autotools-2017-03-03 qepcad-B.1.71 saclib-2.2.7 sirocco-2.0 surf-1.0.6-gcc6
 
 %global SAGE_ROOT		%{_libdir}/sagemath
 %global SAGE_LOCAL		%{SAGE_ROOT}/local
@@ -85,7 +85,7 @@
 
 Name:		sagemath
 Summary:	A free open-source mathematics software system
-Version:	8.3
+Version:	8.4
 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
@@ -97,9 +97,6 @@ Source1:	gprc.expect
 # Follow maxima's ExclusiveArch
 ExclusiveArch: aarch64 %{arm} %{ix86} x86_64 ppc sparcv9
 
-# Upstream uses mpir not gmp, but the rpm package is tailored to use gmp
-Patch1:		%{name}-gmp.patch
-
 # Set of patches to work with system wide packages
 Patch2:		%{name}-scripts.patch
 
@@ -140,11 +137,17 @@ Patch10:	%{name}-jmol.patch
 # FIXME actually it should be already available in pari-elldata
 Patch11:	%{name}-cremona.patch
 
+# adapt to python 3 and cython running in python 3 mode
+Patch12:	%{name}-python3.patch
+
 # correct path to the nauty geng program
 # http://cs.anu.edu.au/~bdm/nauty/
 # http://pallini.di.uniroma1.it/
 Patch13:	%{name}-nauty.patch
 
+# remove the buildroot path from Cython output
+Patch14:	%{name}-buildroot.patch
+
 # correct path to Lfunction include
 # update c++ standard to fix FTBFS
 Patch15:	%{name}-lcalc.patch
@@ -174,21 +177,19 @@ Patch22:	%{name}-qepcad.patch
 # Correct path to arb headers
 Patch23:	%{name}-arb.patch
 
-# No support for f" notation
+# Add missing escapes, or convert strings to raw strings
-Patch24:       %{name}-nofstring.patch
+Patch24:	%{name}-escape.patch
 
 # Add missing include paths
 Patch25:	%{name}-includes.patch
 
-# Use atlas blas
+# Use openblas
-Patch26:	%{name}-atlas.patch
+Patch26:	%{name}-openblas.patch
 
-# Adapt to recent versions of eclib
+BuildRequires:	gdb
-Patch27:	%{name}-eclib.patch
 
 BuildRequires:	4ti2
 BuildRequires:	arb-devel
-BuildRequires:	atlas-devel
 BuildRequires:	boost-devel
 BuildRequires:	brial-devel
 BuildRequires:	cddlib-tools
@@ -231,8 +232,10 @@ BuildRequires:	jsmol
 BuildRequires:	L-function-devel
 BuildRequires:	lapack-devel
 BuildRequires:	latte-integrale
+BuildRequires:	libbraiding-devel
 BuildRequires:	libfplll-devel
 BuildRequires:	libgap-devel
+BuildRequires:	libhomfly-devel
 BuildRequires:	libmpc-devel
 BuildRequires:	libpng-devel
 BuildRequires:	linbox-devel
@@ -245,6 +248,7 @@ BuildRequires:	maxima-runtime-ecl
 BuildRequires:	mpfi-devel
 BuildRequires:	nauty
 BuildRequires:	ntl-devel
+BuildRequires:	openblas-devel
 BuildRequires:	openssl
 BuildRequires:	palp
 BuildRequires:	pari-devel
@@ -254,77 +258,74 @@ BuildRequires:	pari-seadata
 BuildRequires:	planarity-devel
 BuildRequires:	ppl-devel
 BuildRequires:	pynac-devel
-BuildRequires:	python2-devel
+BuildRequires:	python3-devel
-%if %{with bundled_ipython}
+BuildRequires:	python3-cypari2-devel
-BuildRequires:	python2-backports-shutil_get_terminal_size
+BuildRequires:	python3-cysignals-devel
-%endif
+BuildRequires:	python3-pillow-devel
-BuildRequires:	python2-brial
+BuildRequires:	python3dist(brial)
 %if %{with sphinx_hack}
-BuildRequires:	python2-configparser
+BuildRequires:	python3dist(configparser)
 %endif
-BuildRequires:	python2-cypari2-devel
+BuildRequires:	python3dist(cvxopt)
-BuildRequires:	python2-cysignals-devel
+BuildRequires:	python3dist(cython)
-BuildRequires:	python2-Cython
+BuildRequires:	python3dist(docutils)
-BuildRequires:	python2-crypto
+BuildRequires:	python3dist(flask-autoindex)
-BuildRequires:	python2-cryptominisat
+BuildRequires:	python3dist(flask-babel)
-BuildRequires:	python2-cvxopt
+BuildRequires:	python3dist(flask-openid)
-BuildRequires:	python2-docutils
+BuildRequires:	python3dist(flask-silk)
-BuildRequires:	python2-flask-autoindex
+BuildRequires:	python3dist(fpylll)
-BuildRequires:	python2-flask-babel
+BuildRequires:	python3dist(future)
-BuildRequires:	python2-flask-openid
+BuildRequires:	python3dist(gmpy2)
-BuildRequires:	python2-flask-silk
-BuildRequires:	python2-fpylll
-BuildRequires:	python2-future
-BuildRequires:	python2-gmpy2
 %if %{with sphinx_hack}
-BuildRequires:	python2-html5lib
+BuildRequires:	python3dist(html5lib)
-BuildRequires:	python2-imagesize
+BuildRequires:	python3dist(imagesize)
 %endif
-BuildRequires:	python2-ipykernel
+BuildRequires:	python3dist(ipykernel)
 %if %{without bundled_ipython}
-BuildRequires:	python2-ipython
+BuildRequires:	python3dist(ipython)
 %endif
-BuildRequires:	python2-matplotlib
+BuildRequires:	python3dist(kiwisolver)
-BuildRequires:	python2-networkx
+BuildRequires:	python3dist(matplotlib)
-BuildRequires:	python2-notebook
+BuildRequires:	python3dist(networkx)
+BuildRequires:	python3dist(notebook)
 %if %{with bundled_ipython}
-BuildRequires:	python2-path
+BuildRequires:	python3dist(path.py)
 %endif
-BuildRequires:	python2-pathlib2
+BuildRequires:	python3dist(pathlib2)
 %if %{without bundled_pexpect}
-BuildRequires:	python2-pexpect
+BuildRequires:	python3dist(pexpect)
 %endif
-BuildRequires:	python2-pickleshare
+BuildRequires:	python3dist(pickleshare)
-BuildRequires:	python2-pillow-devel
+BuildRequires:	python3dist(pip)
-BuildRequires:	python2-pip
+BuildRequires:	python3dist(prompt-toolkit)
-BuildRequires:	python2-prompt_toolkit
+BuildRequires:	python3dist(pkgconfig)
-BuildRequires:	python2-pkgconfig
+BuildRequires:	python3dist(psutil)
-BuildRequires:	python2-psutil
+BuildRequires:	python3dist(ptyprocess)
-BuildRequires:	python2-ptyprocess
+BuildRequires:	python3dist(pycryptosat)
-BuildRequires:	python2-scipy
-BuildRequires:	python2-send2trash
-BuildRequires:	python2-setuptools
 %if %{with bundled_ipython}
-BuildRequires:	python2-simplegeneric
+BuildRequires:  python3dist(pyzmq)
 %endif
-BuildRequires:	python2-six
+BuildRequires:	python3dist(rpy2)
-BuildRequires:	python2-speaklater
+BuildRequires:	python3dist(scipy)
-BuildRequires:	python2-sphinx
+BuildRequires:	python3dist(scons)
-BuildRequires:	python2-sympy
+BuildRequires:	python3dist(send2trash)
-BuildRequires:	python2-twisted
+BuildRequires:	python3dist(setuptools)
 %if %{with bundled_ipython}
-BuildRequires:	python2-zmq
+BuildRequires:	python3dist(simplegeneric)
 %endif
-BuildRequires:	python2-ZODB3
+BuildRequires:	python3dist(six)
-BuildRequires:	python3-Cython
+BuildRequires:	python3dist(speaklater)
+BuildRequires:	python3dist(sphinx)
+BuildRequires:	python3dist(sympy)
+BuildRequires:	python3dist(twisted)
+BuildRequires:	python3dist(zodb3)
 BuildRequires:	qepcad-B
 BuildRequires:	R
 BuildRequires:	ratpoints-devel
 BuildRequires:	readline-devel
-BuildRequires:	rpy
 BuildRequires:	rw-devel
-BuildRequires:	scons
 BuildRequires:	Singular-devel
+BuildRequires:	sirocco-devel
 BuildRequires:	stix-math-fonts
 BuildRequires:	symmetrica-devel
 BuildRequires:	sympow
@@ -368,67 +369,64 @@ Requires:	palp
 Requires:	pari-galdata
 Requires:	pari-gp
 Requires:	pari-seadata
-%if %{with bundled_ipython}
+Requires:	python3dist(brial)
-Requires:	python2-backports-shutil_get_terminal_size
-%endif
-Requires:	python2-brial
 %if %{with sphinx_hack}
-Requires:	python2-configparser
+Requires:	python3dist(configparser)
 %endif
-Requires:	python2-cypari2
+Requires:	python3dist(cypari2)
-Requires:	python2-cysignals
+Requires:	python3dist(cysignals)
-Requires:	python2-crypto
+Requires:	python3dist(cvxopt)
-Requires:	python2-cryptominisat
+Requires:	python3dist(cython)
-Requires:	python2-cvxopt
+Requires:	python3dist(docutils)
-Requires:	python2-Cython
+Requires:	python3dist(flask-autoindex)
-Requires:	python2-docutils
+Requires:	python3dist(flask-babel)
-Requires:	python2-flask-autoindex
+Requires:	python3dist(flask-openid)
-Requires:	python2-flask-babel
+Requires:	python3dist(flask-silk)
-Requires:	python2-flask-openid
+Requires:	python3dist(fpylll)
-Requires:	python2-flask-silk
+Requires:	python3dist(future)
-Requires:	python2-fpylll
+Requires:	python3dist(gmpy2)
-Requires:	python2-future
-Requires:	python2-gmpy2
 %if %{with sphinx_hack}
-Requires:	python2-html5lib
+Requires:	python3dist(html5lib)
-Requires:	python2-imagesize
+Requires:	python3dist(imagesize)
 %endif
-Requires:	python2-ipykernel
+Requires:	python3dist(ipykernel)
 %if %{without bundled_ipython}
-Requires:	python2-ipython
+Requires:	python3dist(ipython)
 %endif
-Requires:	python2-matplotlib
+Requires:	python3dist(kiwisolver)
-Requires:	python2-networkx
+Requires:	python3dist(matplotlib)
-Requires:	python2-notebook
+Requires:	python3dist(networkx)
+Requires:	python3dist(notebook)
 %if %{with bundled_ipython}
-Requires:	python2-path
+Requires:	python3dist(path)
 %endif
-Requires:	python2-pathlib2
+Requires:	python3dist(pathlib2)
 %if %{without bundled_pexpect}
-Requires:	python2-pexpect
+Requires:	python3dist(pexpect)
 %endif
-Requires:	python2-pickleshare
+Requires:	python3dist(pickleshare)
-Requires:	python2-pillow
+Requires:	python3dist(pillow)
-Requires:	python2-prompt_toolkit
+Requires:	python3dist(prompt-toolkit)
-Requires:	python2-psutil
+Requires:	python3dist(psutil)
-Requires:	python2-ptyprocess
+Requires:	python3dist(ptyprocess)
-Requires:	python2-scipy
+Requires:	python3dist(pycryptosat)
-Requires:	python2-send2trash
+Requires:	python3dist(rpy2)
+Requires:	python3dist(scipy)
+Requires:	python3dist(send2trash)
 %if %{with bundled_ipython}
-BuildRequires:	python2-simplegeneric
+BuildRequires:	python3dist(simplegeneric)
 %endif
-Requires:	python2-six
+Requires:	python3dist(six)
-Requires:	python2-speaklater
+Requires:	python3dist(speaklater)
-Requires:	python2-sphinx
+Requires:	python3dist(sphinx)
-Requires:	python2-sympy
+Requires:	python3dist(sympy)
-Requires:	python2-twisted
+Requires:	python3dist(twisted)
 %if %{with bundled_ipython}
-Requires:	python2-zmq
+Requires:	python3dist(zmq)
 %endif
-Requires:	python2-ZODB3
+Requires:	python3dist(zodb3)
 Requires:	qepcad-B
 Requires:	R
-Requires:	rpy
 Requires:	%{name}-core
 Requires:	%{name}-data
 %if %{with docs}
@@ -825,7 +823,6 @@ pushd build/pkgs/widgetsnbextension
 popd
 %endif
 
-%patch1
 %patch2
 %patch3
 %patch4
@@ -836,7 +833,9 @@ popd
 %patch9
 %patch10
 %patch11
+%patch12
 %patch13
+%patch14
 %patch15
 %patch16
 %patch17
@@ -854,13 +853,13 @@ popd
 %patch24
 %patch25
 %patch26
-%patch27
 
 sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
     -e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \
     -i src/sage/env.py
 
-sed -e 's|@@CYSIGNALS@@|%{python2_sitearch}/cysignals|' \
+sed -e 's|@@CYSIGNALS@@|%{python3_sitearch}/cysignals|' \
+    -e 's|@@BUILDROOT@@|%{buildroot}|' \
     -i src/setup.py
 
 sed -e "/flask-oldsessions/d" \
@@ -886,31 +885,39 @@ sed -e "s,\(SINGULAR_SO = \)SAGE.*,\1'%{_libdir}/libSingular-$singver.so'," \
 
 # fix shebangs; some paths contains spaces, so use the null byte facility
 grep -FrlZ '#!%{_bindir}/env python' | \
-  xargs -0 sed -i 's,#!%{_bindir}/env python,#!%{__python2},'
+  xargs -0 sed -i 's,#!%{_bindir}/env python,#!%{__python3},'
 grep -FrlZ '#!%{_bindir}/env sage-python23' | \
-  xargs -0 sed -i 's,#!%{_bindir}/env sage-python23,#!%{__python2},'
+  xargs -0 sed -i 's,#!%{_bindir}/env sage-python23,#!%{__python3},'
 grep -FrlZ '#!%{_bindir}/env' | \
   xargs -0 sed -i 's,#!%{_bindir}/env ,#!%{_bindir}/,'
-grep -rlZ '#!%{_bindir}/python$' | xargs -0 sed -i 's,#!%{_bindir}/python$,&2,'
+grep -rlZ '#!%{_bindir}/python$' | xargs -0 sed -i 's,#!%{_bindir}/python$,&3,'
-sed -i 's,%{_bindir}/env python,%{__python2},' \
+sed -i 's,%{_bindir}/env python,%{__python3},' \
 %if %{with bundled_pexpect}
     build/pkgs/pexpect/src/examples/python.py \
 %endif
     build/pkgs/sagetex/src/sagetex.ins
-sed -i 's,%{_bindir}/python,&2,' src/sage/misc/dev_tools.py
+sed -i 's,%{_bindir}/python,&3,' src/sage/misc/dev_tools.py
 sed -e 's,local/bin/python,bin/python,' \
-    -e 's,#!%{_bindir}/python,&2,' \
+    -e 's,#!%{_bindir}/python,&3,' \
     -i src/sage/repl/preparse.py
 %if %{with bundled_ipython}
 sed -e "s|'%{_bindir}/env', 'which'|'%{_bindir}/which'|" \
     -i build/pkgs/ipython/src/IPython/utils/_process_posix.py
 %endif
 
+# fix path to pip for python 3
+sed -i 's/"pip",/"pip3",/' src/sage/misc/package.py
+
+# GAP does not have enough memory to load the entire workspace
+sed -i 's/64m/128m/' src/sage/libs/gap/util.pyx
+
+
 ########################################################################
 %build
 export CC=%{__cc}
 export CFLAGS="%{optflags}"
 export CXXFLAGS="%{optflags}"
+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)
@@ -934,8 +941,8 @@ ln -sf %{_includedir} $SAGE_LOCAL/include
 ln -sf %{_datadir} $SAGE_LOCAL/share
 
 export PATH=%{buildroot}%{_bindir}:$PATH
-export PYTHON=%{_bindir}/python2
+export PYTHON=%{_bindir}/python3
-export PYTHONPATH=%{buildroot}%{python2_sitearch}:$PYTHONPATH
+export PYTHONPATH=%{buildroot}%{python3_sitearch}:$PYTHONPATH
 
 #------------------------------------------------------------------------
 # Save and update environment to generate bundled interfaces
@@ -946,29 +953,29 @@ export SAGE_LOCAL=%{_builddir}
 
 %if %{with bundled_ipython}
 pushd build/pkgs/ipython/src
-    %__python2 setup.py build
+    %__python3 setup.py build
-    %__python2 setup.py install --root %{_builddir}
+    %__python3 setup.py install --root %{_builddir}
 popd
 %endif
 
 %if %{with bundled_ipywidgets}
 pushd build/pkgs/ipywidgets/src
-    %__python2 setup.py build
+    %__python3 setup.py build
-    %__python2 setup.py install --root %{_builddir}
+    %__python3 setup.py install --root %{_builddir}
 popd
 %endif
 
 %if %{with bundled_widgetsnbextension}
 pushd build/pkgs/widgetsnbextension/src
-    %__python2 setup.py build
+    %__python3 setup.py build
-    %__python2 setup.py install --root %{_builddir}
+    %__python3 setup.py install --root %{_builddir}
 popd
 %endif
 
 %if %{with cython_hack}
-    cp -far %{python2_sitearch}/Cython %{_builddir}%{python2_sitearch}
+    cp -far %{python3_sitearch}/Cython %{_builddir}%{python3_sitearch}
     BASE=$PWD/build/pkgs/cython/patches/
-    pushd %{_builddir}%{python2_sitearch}
+    pushd %{_builddir}%{python3_sitearch}
 	for PATCH in pxi_sys_path.patch
 	do
 	    patch -p1 < $BASE/$PATCH
@@ -983,16 +990,16 @@ mkdir -p %{buildroot}%{SAGE_SPKG_INST}
 mkdir -p %{buildroot}%{_libdir}/sagemath/build/pkgs
 
 pushd src
-    %__python2 -u ./setup.py build
+    %__python3 -u ./setup.py build
 popd
 
 #------------------------------------------------------------------------
 pushd build/pkgs/sagenb/src
-    %__python2 ./setup.py build
+    %__python3 ./setup.py build
 popd
 
 pushd build/pkgs/sagenb_export/src
-    %__python2 ./setup.py build
+    %__python3 ./setup.py build
 popd
 
 #------------------------------------------------------------------------
@@ -1005,16 +1012,6 @@ pushd build/pkgs/rubiks/src
     make %{?_smp_mflags} CC="gcc -fPIC" CXX="g++ -fPIC" CFLAGS="%{optflags}" CXXFLAGS="%{optflags}"
 popd
 
-# Remove buildroot reference from cython comments
-perl -pi -e 's|%{buildroot}||g;' `find src/build/cythonized -type f`
-
-# Try hard to remove buildroot from binaries
-rm -f `grep -lr "%{buildroot}" src/build/lib.linux-*/`
-rm -f `grep -lr "%{buildroot}" src/build/temp.linux-*/`
-pushd src
-    %__python2 ./setup.py build
-popd
-
 # last build command
 rm -fr $DOT_SAGE
 
@@ -1039,9 +1036,9 @@ export DOT_SAGE=/tmp/sage$$
 mkdir -p $DOT_SAGE/tmp
 
 export PATH=%{buildroot}%{_bindir}:$PATH
-export PYTHON=%{_bindir}/python2
+export PYTHON=%{_bindir}/python3
-export PYTHONPATH=%{buildroot}%{python2_sitearch}:$PYTHONPATH
+export PYTHONPATH=%{buildroot}%{python3_sitearch}:$PYTHONPATH
-export PYTHONPATH=%{_builddir}%{python2_sitearch}:$PYTHONPATH
+export PYTHONPATH=%{_builddir}%{python3_sitearch}:$PYTHONPATH
 
 #------------------------------------------------------------------------
 mkdir -p %{buildroot}%{_bindir}
@@ -1076,10 +1073,10 @@ popd
 #------------------------------------------------------------------------
 pushd src
 %if %{without install_hack}
-    %py2_install
+    %py3_install
 %else
-    mkdir -p %{buildroot}%{python2_sitearch}
+    mkdir -p %{buildroot}%{python3_sitearch}
-    cp -far build/lib.linux-*/sage %{buildroot}%{python2_sitearch}
+    cp -far build/lib.linux-*/sage %{buildroot}%{python3_sitearch}
 %endif
 %if %{with docs}
     # install documentation sources
@@ -1090,23 +1087,23 @@ popd
 
 #------------------------------------------------------------------------
 pushd build/pkgs/sagenb/src
-    rm -f %{buildroot}%{python2_sitearch}/sagenb/data/sage3d/sage3d
+    rm -f %{buildroot}%{python3_sitearch}/sagenb/data/sage3d/sage3d
-    %py2_install "--install-purelib=%{python2_sitearch}"
+    %py3_install "--install-purelib=%{python3_sitearch}"
     # jsmol
     ln -sf %{_jsdir}/jsmol $SAGE_SHARE/jsmol
     # sage3d
     rm -f %{buildroot}%{_bindir}/sage3d
 %if %{with sage3d}
-    ln -sf %{SAGE_LOCAL}/bin/sage3d %{buildroot}%{python2_sitearch}/sagenb/data/sage3d/sage3d
+    ln -sf %{SAGE_LOCAL}/bin/sage3d %{buildroot}%{python3_sitearch}/sagenb/data/sage3d/sage3d
 %endif
-    ln -sf %{python2_sitearch}/sagenb %{buildroot}%{SAGE_SRC}/sagenb
+    ln -sf %{python3_sitearch}/sagenb %{buildroot}%{SAGE_SRC}/sagenb
     # use system mathjax
-    ln -sf %{_jsdir}/mathjax %{buildroot}%{python2_sitearch}/sagenb/data/mathjax
+    ln -sf %{_jsdir}/mathjax %{buildroot}%{python3_sitearch}/sagenb/data/mathjax
 popd
 
 #------------------------------------------------------------------------
 pushd build/pkgs/sagenb_export/src
-    %py2_install
+    %py3_install
 popd
 
 #------------------------------------------------------------------------
@@ -1123,8 +1120,8 @@ pushd src/bin
     cp -fa sage-* $SAGE_LOCAL/bin
     pushd $SAGE_LOCAL/bin
 	ln -sf %{_bindir}/jmol jmol
-	ln -sf %{_bindir}/python sage.bin
+	ln -sf %{_bindir}/python3 sage.bin
-	ln -sf %{_bindir}/python python
+	ln -sf %{_bindir}/python3 python
 	ln -sf %{_bindir}/gp sage_pari
 	ln -sf %{_bindir}/gap gap
 	ln -sf %{_bindir}/gmp-ecm ecm
@@ -1200,7 +1197,7 @@ popd
 
 #------------------------------------------------------------------------
 pushd build/pkgs/conway_polynomials
-    %__python2 ./spkg-install.py
+    %__python3 ./spkg-install.py
 popd
 
 #------------------------------------------------------------------------
@@ -1211,7 +1208,7 @@ pushd build/pkgs/elliptic_curves
 	tar jxf ../../../upstream/%{elliptic_curves_pkg}.tar.bz2
 	mv %{elliptic_curves_pkg} src
     fi
-    %__python2 ./spkg-install.py
+    %__python3 ./spkg-install.py
 popd
 
 #------------------------------------------------------------------------
@@ -1228,7 +1225,7 @@ popd
 
 #------------------------------------------------------------------------
 pushd build/pkgs/sagetex/src
-    %py2_install "--install-purelib=%{python2_sitearch}"
+    %py3_install "--install-purelib=%{python3_sitearch}"
     mv %{buildroot}%{_texmf_main}/tex/latex/sagetex/CONTRIBUTORS \
 	 %{buildroot}%{_docdir}/sagetex
     for file in PKG-INFO README; do
@@ -1238,13 +1235,13 @@ popd
 
 #------------------------------------------------------------------------
 %if %{with bundled_ipython}
-mv %{_builddir}%{python2_sitelib}/IPython %{buildroot}%{SAGE_PYTHONPATH}
+mv %{_builddir}%{python3_sitelib}/IPython %{buildroot}%{SAGE_PYTHONPATH}
 mv %{_builddir}%{_bindir}/ip* %{buildroot}%{SAGE_LOCAL}/bin
 %endif
 
 #------------------------------------------------------------------------
 %if %{with bundled_ipywidgets}
-mv %{_builddir}%{python2_sitelib}/ipywidgets %{buildroot}%{SAGE_PYTHONPATH}
+mv %{_builddir}%{python3_sitelib}/ipywidgets %{buildroot}%{SAGE_PYTHONPATH}
 %endif
 
 #------------------------------------------------------------------------
@@ -1265,7 +1262,7 @@ popd
 #------------------------------------------------------------------------
 %if %{with bundled_widgetsnbextension}
 pushd build/pkgs/widgetsnbextension/src
-    %py2_install "--install-purelib=%{python2_sitelib}"
+    %py3_install "--install-purelib=%{python3_sitelib}"
     mv %{buildroot}%{_prefix}%{_sysconfdir} %{buildroot}%{_sysconfdir}
 popd
 %endif
@@ -1324,17 +1321,17 @@ chmod +x %{buildroot}%{SAGE_LOCAL}/bin/sage3d
 # o install .pxi and .pxd files
 pushd src
     for f in `find sage \( -name \*.pxi -o -name \*.pxd -o -name \*.pyx \)`; do
-	install -p -D -m 0644 $f %{buildroot}%{python2_sitearch}/$f
+	install -p -D -m 0644 $f %{buildroot}%{python3_sitearch}/$f
     done
     # need this or will not "find" the files in the directory, and
     # fail to link with gmp
-    touch %{buildroot}%{python2_sitearch}/sage/libs/gmp/__init__.py
+    touch %{buildroot}%{python3_sitearch}/sage/libs/gmp/__init__.py
 popd
 
 %if %{with docs}
 #------------------------------------------------------------------------
 %if %{with bundled_pexpect}
-cp -fa $SAGE_PYTHONPATH/pexpect %{buildroot}%{python2_sitearch}
+cp -fa $SAGE_PYTHONPATH/pexpect %{buildroot}%{python3_sitearch}
 %endif
 
 # Build documentation, using %#{buildroot} environment
@@ -1344,13 +1341,12 @@ pushd src/doc
     export PATH=%{buildroot}%{_bindir}:$SAGE_LOCAL/bin:$PATH
     export SINGULARPATH=%{_datadir}/singular/LIB
     export SINGULAR_BIN_DIR=%{_libdir}/Singular
-    export LD_LIBRARY_PATH=%{_libdir}/atlas:$LD_LIBRARY_PATH
+    export PYTHONPATH=$SAGE_SETUP:%{buildroot}%{python3_sitearch}:$SAGE_PYTHONPATH:$SAGE_DOC
-    export PYTHONPATH=$SAGE_SETUP:%{buildroot}%{python2_sitearch}:$SAGE_PYTHONPATH:$SAGE_DOC
 
 %if %{with sphinx_hack}
     pushd ../../build/pkgs/sphinx/src
-        %py2_build
+        %py3_build
-        %py2_install "--install-purelib=%{python2_sitearch}"
+        %py3_install "--install-purelib=%{python3_sitearch}"
         rm -f %{buildroot}%{_bindir}/sphinx*
     popd
 %endif
@@ -1362,7 +1358,7 @@ pushd src/doc
     # python -m sage_setup.docbuild
     # Build with an X server running, required by some doc builders
     SAGE_NUM_THREADS=2 LANGUAGES="ca de en fr hu it ja pt ru tr" \
-	xvfb-run -a -n 1 %__python2 -m docbuild --no-pdf-links -k all html -j
+	xvfb-run -a -n 1 %__python3 -m docbuild --no-pdf-links -k all html -j
     rm -f %{buildroot}%{SAGE_SRC}/doc
     ln -sf %{SAGE_DOC} %{buildroot}%{SAGE_SRC}/doc
 
@@ -1380,12 +1376,12 @@ sed -i 's|%{buildroot}||g' $SAGE_DOC/test.log
 %endif
 
 %if %{with bundled_pexpect}
-    rm -f %{buildroot}%{python2_sitearch}/pexpect
+    rm -f %{buildroot}%{python3_sitearch}/pexpect
 %endif
 
 %if %{with sphinx_hack}
-    rm -fr %{buildroot}%{python2_sitearch}/sphinx \
+    rm -fr %{buildroot}%{python3_sitearch}/sphinx \
-	%{buildroot}%{python2_sitearch}/Sphinx*
+	%{buildroot}%{python3_sitearch}/Sphinx*
 %endif
 
 # More wrong buildroot references
@@ -1403,8 +1399,8 @@ perl -pi -e 's|%{buildroot}||g;s|^##||g;' %{buildroot}%{_bindir}/sage
 export SAGE_SRC=%{buildroot}%{SAGE_SRC}
 rm -fr $SAGE_SRC/sage $SAGE_ETC/sage $SAGE_ROOT/doc $SAGE_SRC/doc
 rm -fr $SAGE_ROOT/share $SAGE_ROOT/devel
-ln -sf %{python2_sitearch}/sage $SAGE_SRC/sage
+ln -sf %{python3_sitearch}/sage $SAGE_SRC/sage
-ln -sf %{python2_sitearch} $SAGE_ETC/sage
+ln -sf %{python3_sitearch} $SAGE_ETC/sage
 ln -sf %{SAGE_DOC} $SAGE_ROOT/doc
 %if %{with docs}
 ln -sf %{SAGE_DOC} $SAGE_SRC/doc
@@ -1452,10 +1448,10 @@ find %{buildroot}%{SAGE_DOC} -type d -name _sources -exec rm -fr {} \+
 %endif
 
 # remove .po files
-rm %{buildroot}%{python2_sitearch}/sagenb/translations/*/LC_MESSAGES/*.po
+rm %{buildroot}%{python3_sitearch}/sagenb/translations/*/LC_MESSAGES/*.po
 
 %if %{without sage3d}
-rm -r %{buildroot}%{python2_sitearch}/sagenb/data/sage3d
+rm -r %{buildroot}%{python3_sitearch}/sagenb/data/sage3d
 %endif
 
 # remove build directory in buildroot
@@ -1464,7 +1460,7 @@ rm -r %{buildroot}%{python2_sitearch}/sagenb/data/sage3d
 
 %if %{without install_hack}
 # remove sage_setup
-rm -r %{buildroot}%{python2_sitearch}/sage_setup
+rm -r %{buildroot}%{python3_sitearch}/sage_setup
 %endif
 
 # pretend sagemath spkgs are installed to reduce number of errors
@@ -1517,7 +1513,7 @@ chmod +x %{buildroot}%{SAGE_LOCAL}/bin/sage-list-packages
 
 #------------------------------------------------------------------------
 # Byte compile python files in nonstandard places
-%py_byte_compile %{__python2} %{buildroot}%{_texmf_main}/tex/latex/sagetex
+%py_byte_compile %{__python3} %{buildroot}%{_texmf_main}/tex/latex/sagetex
 
 # last install command
 rm -fr $DOT_SAGE
@@ -1545,6 +1541,7 @@ rm -fr $DOT_SAGE
 %{SAGE_LOCAL}/include
 %{SAGE_LOCAL}/lib
 %{SAGE_LOCAL}/share
+%{SAGE_LOCAL}/var
 %{SAGE_ROOT}/doc
 %{SAGE_ROOT}/devel
 %{SAGE_ROOT}/share
@@ -1558,7 +1555,6 @@ rm -fr $DOT_SAGE
 %{_bindir}/sage
 %{_datadir}/pixmaps/%{name}.png
 %{_datadir}/applications/%{name}.desktop
-%{SAGE_SPKG_INST}
 %if %{with bundled_thebe}
 # MIT
 %{SAGE_SHARE}/thebe
@@ -1571,9 +1567,9 @@ rm -fr $DOT_SAGE
 #------------------------------------------------------------------------
 %files		core
 # GPLv2+
-%{python2_sitearch}/sage
+%{python3_sitearch}/sage
 %if %{without install_hack}
-%{python2_sitearch}/sage-*.egg-info
+%{python3_sitearch}/sage-*.egg-info
 %endif
 %if %{with bundled_ipython}
 %{SAGE_PYTHONPATH}/IPython
@@ -1587,7 +1583,7 @@ rm -fr $DOT_SAGE
 %dir %{_sysconfdir}/jupyter/nbconfig/notebook.d
 %config(noreplace) %{_sysconfdir}/jupyter/nbconfig/notebook.d/*.json
 %{_datadir}/jupyter/
-%{python2_sitelib}/widgetsnbextension*
+%{python3_sitelib}/widgetsnbextension*
 %endif
 
 #------------------------------------------------------------------------
@@ -1702,76 +1698,79 @@ rm -fr $DOT_SAGE
 %{SAGE_ETC}/notebook-ipython
 # GPLv2+
 %{SAGE_SRC}/sagenb
-%dir %{python2_sitearch}/sagenb
+%dir %{python3_sitearch}/sagenb
-%{python2_sitearch}/sagenb/*.py*
+%{python3_sitearch}/sagenb/*.py*
-%{python2_sitearch}/sagenb-*.egg-info
+%{python3_sitearch}/sagenb/__pycache__/
-%dir %{python2_sitearch}/sagenb/data
+%{python3_sitearch}/sagenb/data/__pycache__/
+%{python3_sitearch}/sagenb/testing/__pycache__/
+%{python3_sitearch}/sagenb-*.egg-info
+%dir %{python3_sitearch}/sagenb/data
 # BSD
-%{python2_sitearch}/sagenb/data/codemirror
+%{python3_sitearch}/sagenb/data/codemirror
 # MIT
-%{python2_sitearch}/sagenb/data/graph_editor
+%{python3_sitearch}/sagenb/data/graph_editor
 # ASL 2.0
-%{python2_sitearch}/sagenb/data/highlight
+%{python3_sitearch}/sagenb/data/highlight
 # LGPLv2+
 %{SAGE_SHARE}/jsmol
 # (MIT or GPLv2) and (MIT and BSD and GPL)
-%{python2_sitearch}/sagenb/data/jquery
+%{python3_sitearch}/sagenb/data/jquery
 # (MIT or GPLv2) and (MIT and BSD and GPL)
-%{python2_sitearch}/sagenb/data/jqueryui
+%{python3_sitearch}/sagenb/data/jqueryui
 # Public Domain
-%{python2_sitearch}/sagenb/data/json
+%{python3_sitearch}/sagenb/data/json
 # Symbolic link to $_jsdir/mathjax
-%{python2_sitearch}/sagenb/data/mathjax
+%{python3_sitearch}/sagenb/data/mathjax
-%ghost %{python2_sitearch}/sagenb/data/mathjax.rpmmoved
+%ghost %{python3_sitearch}/sagenb/data/mathjax.rpmmoved
 # Empty (do not run doctests flag file)
-%{python2_sitearch}/sagenb/data/nodoctest.py*
+%{python3_sitearch}/sagenb/data/nodoctest.py*
 # BSD
-%{python2_sitearch}/sagenb/data/openid-realselector
+%{python3_sitearch}/sagenb/data/openid-realselector
 # GPLv2+
-%{python2_sitearch}/sagenb/data/sage
+%{python3_sitearch}/sagenb/data/sage
 %if %{with sage3d}
 # GPLv2+
-%{python2_sitearch}/sagenb/data/sage3d
+%{python3_sitearch}/sagenb/data/sage3d
 %endif
 # LGPLv2+
-%{python2_sitearch}/sagenb/data/tiny_mce
+%{python3_sitearch}/sagenb/data/tiny_mce
 # LGPLv2+
-%{python2_sitearch}/sagenb/data/zorn
+%{python3_sitearch}/sagenb/data/zorn
 # GPLv2+
-%{python2_sitearch}/sagenb/flask_version
+%{python3_sitearch}/sagenb/flask_version
 # GPLv2+
-%{python2_sitearch}/sagenb/interfaces
+%{python3_sitearch}/sagenb/interfaces
 # GPLv2+
-%{python2_sitearch}/sagenb/misc
+%{python3_sitearch}/sagenb/misc
 # GPLv2+
-%{python2_sitearch}/sagenb/notebook
+%{python3_sitearch}/sagenb/notebook
 # GPLv2+
-%{python2_sitearch}/sagenb/simple
+%{python3_sitearch}/sagenb/simple
 # GPLv2+
-%{python2_sitearch}/sagenb/storage
+%{python3_sitearch}/sagenb/storage
 # GPLv2+
-%dir %{python2_sitearch}/sagenb/testing
+%dir %{python3_sitearch}/sagenb/testing
-%{python2_sitearch}/sagenb/testing/*.py*
+%{python3_sitearch}/sagenb/testing/*.py*
-%{python2_sitearch}/sagenb/testing/tests
+%{python3_sitearch}/sagenb/testing/tests
 # ASL 2.0
-%{python2_sitearch}/sagenb/testing/selenium
+%{python3_sitearch}/sagenb/testing/selenium
 # GPLv2+
-%dir %{python2_sitearch}/sagenb/translations
+%dir %{python3_sitearch}/sagenb/translations
-%lang(cs_CZ) %{python2_sitearch}/sagenb/translations/cs_CZ
+%lang(cs_CZ) %{python3_sitearch}/sagenb/translations/cs_CZ
-%lang(de_AT) %{python2_sitearch}/sagenb/translations/de_AT
+%lang(de_AT) %{python3_sitearch}/sagenb/translations/de_AT
-%lang(de_AT) %{python2_sitearch}/sagenb/translations/en_US
+%lang(de_AT) %{python3_sitearch}/sagenb/translations/en_US
-%lang(de_AT) %{python2_sitearch}/sagenb/translations/es_ES
+%lang(de_AT) %{python3_sitearch}/sagenb/translations/es_ES
-%lang(de_AT) %{python2_sitearch}/sagenb/translations/fr_FR
+%lang(de_AT) %{python3_sitearch}/sagenb/translations/fr_FR
-%lang(pt_BR) %{python2_sitearch}/sagenb/translations/pt_BR
+%lang(pt_BR) %{python3_sitearch}/sagenb/translations/pt_BR
-%lang(ru_RU) %{python2_sitearch}/sagenb/translations/ru_RU
+%lang(ru_RU) %{python3_sitearch}/sagenb/translations/ru_RU
-%lang(uk_UA) %{python2_sitearch}/sagenb/translations/uk_UA
+%lang(uk_UA) %{python3_sitearch}/sagenb/translations/uk_UA
 
 #------------------------------------------------------------------------
 %files		notebook-export
 # GPL+
 %{_bindir}/sagenb-export
-%{python2_sitelib}/sagenb_export
+%{python3_sitelib}/sagenb_export
-%{python2_sitelib}/sagenb_export-*.egg-info
+%{python3_sitelib}/sagenb_export-*.egg-info
 
 #------------------------------------------------------------------------
 %files		rubiks
@@ -1788,12 +1787,21 @@ rm -fr $DOT_SAGE
 #------------------------------------------------------------------------
 %files		sagetex
 # GPLv2+
-%{python2_sitearch}/sagetex*
+%{python3_sitearch}/sagetex*
 %{_texmf_main}/tex/latex/sagetex
 %doc %{_docdir}/sagetex
 
 ########################################################################
 %changelog
+* Thu Oct 25 2018 Jerry James <loganjerry@gmail.com> - 8.4-1
+- Update to sagemath 8.4
+- Build for python 3 instead of python 2 due to upcoming python 2 removal
+- Add -python3 and -escape patches to fix problems with python 3
+- Drop -nofstring patch, only needed for python 2
+- Drop upstreamed -eclib patch
+- Switch from atlas to openblas and rename -atlas patch to -openblas
+- Add -buildroot patch and only build cython interfaces once
+
 * Sat Sep 22 2018 Jerry James <loganjerry@gmail.com> - 8.3-1
 - Update to sagemath 8.3 (bz 1612867)
 - Drop -lrslib, -gap-hap, and -flask patches

sources

@@ -1 +1 @@
-SHA512 (sage-8.3.tar.gz) = d0b971896738adc6604e51a00ff38f41b5c2e7595e8d257346fd975106519a1b3a1734a07229e7bf6e9373073d0cc0ca45c259dece1e7c97a3debd12914485d6
+SHA512 (sage-8.4.tar.gz) = 500c5005420c226993b79e89b761a3c9fe57d5ff6d6d71abedaf347ab2fd16b2f5e3b2caa660c4a0d984ba07038f9b4ffce8eb7b6cb28d2448c62d5e18acd871