sagemath: update to 9.8.

Also:
 - fix edge case of python 3.11 integer conversion on 32 bit
 - support tachyon 0.99.5
 - support singular 4.3.1p3
 - fix tests for giac 1.9.0.35
 - fix tests for numpy 1.24
 - skip unstable tests in klyachko.py
 - remove zn_poly dependency
 - fix very slow test in stream.py

srcpkgs/sagemath/files/sage_conf.py

@@ -1,3 +1,4 @@
 # configuration for sage on void linux
 SAGE_SHARE = "/usr/share/sagemath"
-GAP_ROOT_DIR = "/usr/share/gap"
+GAP_SHARE_DIR = "/usr/share/gap"
+GAP_LIB_DIR = "/usr/lib/gap"

srcpkgs/sagemath/patches/34980-avoid_factoring_in_is_prime.patch

@@ -0,0 +1,47 @@
+diff --git a/src/sage/rings/number_field/number_field_ideal.py b/src/sage/rings/number_field/number_field_ideal.py
+index d5f7157217f..1a9d11aec68 100644
+--- a/src/sage/rings/number_field/number_field_ideal.py
++++ b/src/sage/rings/number_field/number_field_ideal.py
+@@ -996,16 +996,36 @@ def is_prime(self):
+             False
+             sage: K.ideal(17).is_prime()  # ramified
+             False
++
++        TESTS:
++
++        Check that we do not factor the norm of the ideal, this used
++        to take half an hour, see :trac:`33360`::
++
++            sage: K.<a,b,c> = NumberField([x^2-2,x^2-3,x^2-5])
++            sage: t = (((-2611940*c + 1925290/7653)*b - 1537130/7653*c
++            ....:       + 10130950)*a + (1343014/7653*c - 8349770)*b
++            ....:       + 6477058*c - 2801449990/4002519)
++            sage: t.is_prime()
++            False
+         """
+         try:
+             return self._pari_prime is not None
+         except AttributeError:
+-            F = self.factor()  # factorization with caching
+-            if len(F) != 1 or F[0][1] != 1:
+-                self._pari_prime = None
+-            else:
+-                self._pari_prime = F[0][0]._pari_prime
+-            return self._pari_prime is not None
++            pass
++
++        K = self.number_field().pari_nf()
++        I = self.pari_hnf()
++
++        self._pari_prime = K.idealismaximal(I) or None
++
++        # PARI uses probabilistic primality testing inside idealismaximal().
++        if self._pari_prime \
++                and get_flag(None, 'arithmetic') \
++                and not self._pari_prime[0].isprime():
++            self._pari_prime = None
++
++        return self._pari_prime is not None
+
+     def pari_prime(self):
+         r"""

srcpkgs/sagemath/patches/34994-fix_tests_numpy_1.24.patch

@@ -0,0 +1,58 @@
+diff --git a/src/sage/misc/persist.pyx b/src/sage/misc/persist.pyx
+index 3ac5f1cc2b0..cb1f327c199 100644
+--- a/src/sage/misc/persist.pyx
++++ b/src/sage/misc/persist.pyx
+@@ -157,7 +157,7 @@ def load(*filename, compress=True, verbose=True, **kwargs):
+         ....:     _ = f.write(code)
+         sage: load(t)
+         sage: hello
+-        <fortran object>
++        <fortran ...>
+     """
+     import sage.repl.load
+     if len(filename) != 1:
+diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
+index 6f0aeab87ae..b77c69b2f77 100644
+--- a/src/sage/plot/complex_plot.pyx
++++ b/src/sage/plot/complex_plot.pyx
+@@ -461,6 +461,8 @@ def complex_to_rgb(z_values, contoured=False, tiled=False,
+             rgb[i, j, 2] = b
+
+     sig_off()
++    nan_indices = np.isnan(rgb).any(-1)     # Mask for undefined points
++    rgb[nan_indices] = 1                    # Make nan_indices white
+     return rgb
+
+
+diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
+index 3bc2b76b58e..388c2d1391d 100644
+--- a/src/sage/plot/histogram.py
++++ b/src/sage/plot/histogram.py
+@@ -87,13 +87,8 @@ def get_minmax_data(self):
+
+         TESTS::
+
+-            sage: h = histogram([10,3,5], normed=True)[0]
+-            doctest:warning...:
+-            DeprecationWarning: the 'normed' option is deprecated. Use 'density' instead.
+-            See https://trac.sagemath.org/25260 for details.
++            sage: h = histogram([10,3,5], density=True)[0]
+             sage: h.get_minmax_data()
+-            doctest:warning ...
+-            ...VisibleDeprecationWarning: Passing `normed=True` on non-uniform bins has always been broken, and computes neither the probability density function nor the probability mass function. The result is only correct if the bins are uniform, when density=True will produce the same result anyway. The argument will be removed in a future version of numpy.
+             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
+         """
+         import numpy
+diff --git a/src/sage/repl/ipython_extension.py b/src/sage/repl/ipython_extension.py
+index 798671aab42..cad6a47ca8b 100644
+--- a/src/sage/repl/ipython_extension.py
++++ b/src/sage/repl/ipython_extension.py
+@@ -405,7 +405,7 @@ def fortran(self, line, cell):
+             ....: C END FILE FIB1.F
+             ....: ''')
+             sage: fib
+-            <fortran object>
++            <fortran ...>
+             sage: from numpy import array
+             sage: a = array(range(10), dtype=float)
+             sage: fib(a, 10)

srcpkgs/sagemath/patches/34995-support_tachyon_0.99.2.patch

@@ -0,0 +1,57 @@
+diff --git a/src/sage/interfaces/tachyon.py b/src/sage/interfaces/tachyon.py
+index 23671e50892..ce1d50f71bc 100644
+--- a/src/sage/interfaces/tachyon.py
++++ b/src/sage/interfaces/tachyon.py
+@@ -683,12 +683,14 @@
+ #*****************************************************************************
+
+ import os
++import re
+
+ from sage.cpython.string import bytes_to_str
+ from sage.misc.pager import pager
+ from sage.misc.superseded import deprecation
+ from sage.misc.temporary_file import tmp_filename
+ from sage.structure.sage_object import SageObject
++from sage.misc.cachefunc import cached_method
+
+
+ class TachyonRT(SageObject):
+@@ -799,6 +801,11 @@ def __call__(self, model, outfile='sage.png', verbose=1, extra_opts=''):
+             Parser failed due to an input file syntax error.
+             Aborting render.
+         """
++        if self.version() >= '0.99.2':
++            # this keyword was changed in 0.99.2
++            model = model.replace(
++                    "              focallength ",
++                    "              focaldist ")
+         modelfile = tmp_filename(ext='.dat')
+         with open(modelfile, 'w') as file:
+             file.write(model)
+@@ -851,6 +858,25 @@ def usage(self, use_pager=True):
+         else:
+             print(r)
+
++    @cached_method
++    def version(self):
++        """
++        Returns the version of the Tachyon raytracer being used.
++
++        TESTS::
++
++            sage: tachyon_rt.version()  # random
++            0.98.9
++            sage: tachyon_rt.version() >= '0.98.9'
++            True
++        """
++        with os.popen('tachyon') as f:
++            r = f.readline()
++        res = re.search(r"Version ([\d.]*)", r)
++        # debian patches tachyon so it won't report the version
++        # we hardcode '0.99' since that's indeed the version they ship
++        return res[1] if res else '0.99'
++
+     def help(self, use_pager=True):
+         """
+         Deprecated: type 'sage.interfaces.tachyon?' for help

srcpkgs/sagemath/patches/34997-fix_edge_case_of_integer_check.patch

@@ -0,0 +1,36 @@
+diff --git a/src/sage/arith/long.pxd b/src/sage/arith/long.pxd
+index 1c9a53387a0..d96b98f247c 100644
+--- a/src/sage/arith/long.pxd
++++ b/src/sage/arith/long.pxd
+@@ -270,6 +270,17 @@ cdef inline bint integer_check_long_py(x, long* value, int* err):
+         sage: L += [-x for x in L] + [0, long_min()]
+         sage: for v in L:
+         ....:     assert check_long_py(int(v)) == v
++        sage: check_long_py(int(2^60))
++        1152921504606846976                 # 64-bit
++        'Overflow (...)'                    # 32-bit
++        sage: check_long_py(int(2^61))
++        2305843009213693952                 # 64-bit
++        'Overflow (...)'                    # 32-bit
++        sage: check_long_py(int(2^62))
++        4611686018427387904                 # 64-bit
++        'Overflow (...)'                    # 32-bit
++        sage: check_long_py(int(2^63))
++        'Overflow (...)'
+         sage: check_long_py(int(2^100))
+         'Overflow (...)'
+         sage: check_long_py(int(long_max() + 1))
+@@ -309,7 +320,12 @@ cdef inline bint integer_check_long_py(x, long* value, int* err):
+
+     cdef long lead
+     cdef long lead_2_overflow = (<long>1) << (BITS_IN_LONG - PyLong_SHIFT)
+-    cdef long lead_3_overflow = (<long>1) << (BITS_IN_LONG - 2 * PyLong_SHIFT)
++    cdef long lead_3_overflow
++    if BITS_IN_LONG < 2 * PyLong_SHIFT:
++        # in this case 3 digit is always overflow
++        lead_3_overflow = 0
++    else:
++        lead_3_overflow = (<long>1) << (BITS_IN_LONG - 2 * PyLong_SHIFT)
+     if size == 0:
+         value[0] = 0
+         err[0] = 0

srcpkgs/sagemath/patches/35058-skip_unstable_tests_klyachko.patch

@@ -0,0 +1,22 @@
+diff --git a/src/sage/schemes/toric/sheaf/klyachko.py b/src/sage/schemes/toric/sheaf/klyachko.py
+index b1304a16913..77fae4b7545 100644
+--- a/src/sage/schemes/toric/sheaf/klyachko.py
++++ b/src/sage/schemes/toric/sheaf/klyachko.py
+@@ -26,7 +26,7 @@
+     (0, 0, 18, 16, 1)
+     sage: Gtilde = G_sum.random_deformation()
+     sage: V = Gtilde.wedge(2) * K                     # long time
+-    sage: V.cohomology(dim=True, weight=(0,0,0,0))    # long time
++    sage: V.cohomology(dim=True, weight=(0,0,0,0))    # long time  # random failure (see #32773)
+     (0, 0, 3, 0, 0)
+
+ REFERENCES:
+@@ -948,7 +948,7 @@ def random_deformation(self, epsilon=None):
+            sage: V.cohomology(dim=True, weight=(0,))
+            (1, 0)
+            sage: Vtilde = V.random_deformation()
+-           sage: Vtilde.cohomology(dim=True, weight=(0,))
++           sage: Vtilde.cohomology(dim=True, weight=(0,))  # random failure (see #32773)
+            (1, 0)
+         """
+         filt = self._filt.random_deformation(epsilon)

srcpkgs/sagemath/patches/35068-fix_tests_giac_1.9.0.35.patch

@@ -0,0 +1,62 @@
+From 9ac7840134054155545e24fa3e66402d42b91c0f Mon Sep 17 00:00:00 2001
+From: Antonio Rojas <arojas@archlinux.org>
+Date: Fri, 20 Jan 2023 21:36:27 +0100
+Subject: [PATCH] Fix tests with giac 1.9.0.35
+
+---
+ src/sage/libs/giac/giac.pyx   |  3 +--
+ src/sage/symbolic/relation.py | 15 +++++----------
+ 2 files changed, 6 insertions(+), 12 deletions(-)
+
+diff --git a/src/sage/libs/giac/giac.pyx b/src/sage/libs/giac/giac.pyx
+index 4e451dba5e7..ccad5169836 100644
+--- a/src/sage/libs/giac/giac.pyx
++++ b/src/sage/libs/giac/giac.pyx
+@@ -374,8 +374,7 @@ def _giac(s):
+
+         sage: x = libgiac('x')
+         sage: (1+2*sin(3*x)).solve(x).simplify()
+-        Warning, argument is not an equation, solving 1+2*sin(3*x)=0
+-        list[-pi/18,7*pi/18]
++        ...list[-pi/18,7*pi/18]
+
+         sage: libgiac.solve('sin(3*x)>2*sin(x)',x)
+         Traceback (most recent call last):
+diff --git a/src/sage/symbolic/relation.py b/src/sage/symbolic/relation.py
+index e9dbc0fea30..b8896a94be9 100644
+--- a/src/sage/symbolic/relation.py
++++ b/src/sage/symbolic/relation.py
+@@ -935,8 +935,7 @@ def solve(f, *args, **kwds):
+
+         sage: f = (sin(x) - 8*cos(x)*sin(x))*(sin(x)^2 + cos(x)) - (2*cos(x)*sin(x) - sin(x))*(-2*sin(x)^2 + 2*cos(x)^2 - cos(x))
+         sage: solve(f, x, algorithm='giac')
+-        ...
+-        [-2*arctan(sqrt(2)), 0, 2*arctan(sqrt(2)), pi]
++        ...[-2*arctan(sqrt(2)), 0, 2*arctan(sqrt(2)), pi]
+
+         sage: x, y = SR.var('x,y')
+         sage: solve([x+y-4,x*y-3],[x,y],algorithm='giac')
+@@ -1440,19 +1439,15 @@ def _giac_solver(f, x, solution_dict=False):
+     EXAMPLES::
+
+         sage: solve([(2/3)^x-2], [x], algorithm='giac')
+-        ...
+-        [[-log(2)/(log(3) - log(2))]]
++        ...[[-log(2)/(log(3) - log(2))]]
+         sage: solve([(2/3)^x-2], [x], algorithm='giac', solution_dict=True)
+-        ...
+-        [{x: -log(2)/(log(3) - log(2))}]
++        ...[{x: -log(2)/(log(3) - log(2))}]
+
+         sage: f = (sin(x) - 8*cos(x)*sin(x))*(sin(x)^2 + cos(x)) - (2*cos(x)*sin(x) - sin(x))*(-2*sin(x)^2 + 2*cos(x)^2 - cos(x))
+         sage: solve(f, x, algorithm='giac')
+-        ...
+-        [-2*arctan(sqrt(2)), 0, 2*arctan(sqrt(2)), pi]
++        ...[-2*arctan(sqrt(2)), 0, 2*arctan(sqrt(2)), pi]
+         sage: solve(f, x, algorithm='giac', solution_dict=True)
+-        ...
+-        [{x: -2*arctan(sqrt(2))}, {x: 0}, {x: 2*arctan(sqrt(2))}, {x: pi}]
++        ...[{x: -2*arctan(sqrt(2))}, {x: 0}, {x: 2*arctan(sqrt(2))}, {x: pi}]
+
+         sage: x, y = SR.var('x,y')
+         sage: solve([x+y-7,x*y-10],[x,y],algorithm='giac')