Drop merged patch, add numpy 2.0 support

4 files changed, 714 insertions, 37 deletions

diff --git a/.SRCINFO b/.SRCINFO
index d29f5b6ea8db..42c1ebde27da 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = sagemath-git
 	pkgdesc = Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab
-	pkgver = 10.4.beta8.r0.ge5f42fac703
+	pkgver = 10.4.rc1.r0.gb7dd28d2456
 	pkgrel = 1
 	url = http://www.sagemath.org
 	arch = x86_64
@@ -16,7 +16,7 @@ pkgbase = sagemath-git
 	makedepends = python-setuptools
 	makedepends = shared_meataxe
 	makedepends = sirocco
-	makedepends = tdlib
+	makedepends = treedec
 	depends = brial
 	depends = cblas
 	depends = cliquer
@@ -129,9 +129,9 @@ pkgbase = sagemath-git
 	conflicts = sagemath
 	source = git+https://github.com/sagemath/sage#branch=develop
 	source = latte-count.patch
-	source = sagemath-tdlib-0.9.patch
+	source = sagemath-numpy-2.0.patch
 	sha256sums = SKIP
 	sha256sums = 5cd2f88965d7ebab9dfab6f5c2040d363a4a5ae41230219cc7070b907381da5a
-	sha256sums = 56a83abecf2ff5a500442adc7a50abbb70006037dd39c39dcdb04b3ca9fb51e2
+	sha256sums = bed395c2150fa7d812b565021b0b10ce0f8b2b027a594d8f19bb3639bccf9018
 
 pkgname = sagemath-git
diff --git a/PKGBUILD b/PKGBUILD
index 6e8deb762cb5..1ddc411f254d 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -6,7 +6,7 @@
 # Contributor: Stefan Husmann <stefan-husmann at t-online dot de>
 
 pkgname=sagemath-git
-pkgver=10.4.beta8.r0.ge5f42fac703
+pkgver=10.4.rc1.r0.gb7dd28d2456
 pkgrel=1
 pkgdesc='Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab'
 arch=(x86_64)
@@ -136,10 +136,10 @@ conflicts=(sagemath)
 provides=(sagemath)
 source=(git+https://github.com/sagemath/sage#branch=develop
         latte-count.patch
-        sagemath-tdlib-0.9.patch)
+        sagemath-numpy-2.0.patch)
 sha256sums=('SKIP'
             '5cd2f88965d7ebab9dfab6f5c2040d363a4a5ae41230219cc7070b907381da5a'
-            '56a83abecf2ff5a500442adc7a50abbb70006037dd39c39dcdb04b3ca9fb51e2')
+            'bed395c2150fa7d812b565021b0b10ce0f8b2b027a594d8f19bb3639bccf9018')
 _pkgs=(standard
        bliss
        coxeter3
@@ -158,8 +158,8 @@ prepare(){
 
 # use correct latte-count binary name
   patch -p1 -i ../latte-count.patch
-# update to tdlib 0.9 (Fedora)
-  patch -p1 -i ../sagemath-tdlib-0.9.patch
+# fix tests with numpy 2.0
+  patch -p1 -i ../sagemath-numpy-2.0.patch
 
   ./bootstrap
 }
diff --git a/sagemath-numpy-2.0.patch b/sagemath-numpy-2.0.patch
new file mode 100644
index 000000000000..23cd3c9b228d
--- /dev/null
+++ b/sagemath-numpy-2.0.patch
@@ -0,0 +1,705 @@
+From 9ff008b020c714428d3a9d79b0eeae3976bf76f7 Mon Sep 17 00:00:00 2001
+From: Dima Pasechnik <dimpase@gmail.com>
+Date: Thu, 20 Jun 2024 19:14:01 +0100
+Subject: [PATCH 1/2] provide compatibility with numpy 2.0
+
+---
+ src/doc/en/faq/faq-usage.rst                    |  2 +-
+ .../Statistics-and-Distributions.rst            |  2 ++
+ .../thematic_tutorials/numerical_sage/numpy.rst |  2 ++
+ src/doc/it/faq/faq-usage.rst                    |  2 +-
+ src/sage/arith/misc.py                          |  2 +-
+ src/sage/calculus/interpolators.pyx             |  3 +++
+ src/sage/calculus/riemann.pyx                   |  3 +++
+ src/sage/combinat/fully_packed_loop.py          |  3 +++
+ src/sage/env.py                                 |  2 +-
+ src/sage/functions/special.py                   |  3 +++
+ .../graphs/generators/classical_geometries.py   |  2 +-
+ src/sage/graphs/generic_graph.py                |  3 +++
+ src/sage/graphs/graph_generators_pyx.pyx        |  2 +-
+ src/sage/modules/free_module_element.pyx        |  8 ++++++++
+ src/sage/numerical/optimize.py                  | 17 +++++++++++++++++
+ src/sage/plot/arrow.py                          |  3 +++
+ src/sage/plot/complex_plot.pyx                  |  6 ++----
+ src/sage/plot/graphics.py                       |  2 +-
+ src/sage/plot/histogram.py                      |  2 ++
+ src/sage/plot/multigraphics.py                  |  6 ++++++
+ src/sage/plot/plot3d/implicit_surface.pyx       |  2 ++
+ src/sage/plot/scatter_plot.py                   |  4 ++--
+ src/sage/plot/streamline_plot.py                |  3 +++
+ .../probability/probability_distribution.pyx    |  3 +++
+ src/sage/rings/complex_double.pyx               | 10 +++++-----
+ src/sage/rings/integer.pyx                      |  2 ++
+ .../rings/polynomial/polynomial_element.pyx     |  2 +-
+ src/sage/rings/real_mpfi.pyx                    |  2 ++
+ .../elliptic_curves/period_lattice_region.pyx   | 10 ++++++++++
+ src/sage/stats/basic_stats.py                   |  4 ++++
+ src/sage/stats/time_series.pyx                  |  2 ++
+ src/sage/structure/coerce.pyx                   |  2 ++
+ src/sage/symbolic/expression.pyx                |  2 +-
+ src/sage/symbolic/function.pyx                  |  3 +++
+ src/sage/symbolic/ring.pyx                      |  2 ++
+ 35 files changed, 108 insertions(+), 20 deletions(-)
+
+diff --git a/src/doc/en/faq/faq-usage.rst b/src/doc/en/faq/faq-usage.rst
+index 53f225fd729..d03881c36a2 100644
+--- a/src/doc/en/faq/faq-usage.rst
++++ b/src/doc/en/faq/faq-usage.rst
+@@ -324,7 +324,7 @@ ints. For example::
+     sage: RealNumber = float; Integer = int
+     sage: from scipy import stats
+     sage: stats.ttest_ind([1,2,3,4,5], [2,3,4,5,.6])
+-    Ttest...Result(statistic=0.0767529..., pvalue=0.940704...)
++    Ttest...Result(statistic=...0.0767529..., pvalue=...0.940704...)
+     sage: stats.uniform(0,15).ppf([0.5,0.7])
+     array([  7.5,  10.5])
+ 
+diff --git a/src/doc/en/prep/Quickstarts/Statistics-and-Distributions.rst b/src/doc/en/prep/Quickstarts/Statistics-and-Distributions.rst
+index b5eb3d842a2..958a378f945 100644
+--- a/src/doc/en/prep/Quickstarts/Statistics-and-Distributions.rst
++++ b/src/doc/en/prep/Quickstarts/Statistics-and-Distributions.rst
+@@ -24,6 +24,8 @@ NumPy provides, for example, functions to compute the arithmetic mean and
+ the standard deviation::
+ 
+     sage: import numpy as np
++    sage: if int(np.version.short_version[0]) > 1:
++    ....:     np.set_printoptions(legacy="1.25")
+     sage: np.mean([1, 2, 3, 5])
+     2.75
+ 
+diff --git a/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst b/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst
+index dbc2de71d42..925e5312882 100644
+--- a/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst
++++ b/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst
+@@ -7,6 +7,8 @@ import it.
+ ::
+ 
+     sage: import numpy
++    sage: if int(numpy.version.short_version[0]) > 1:
++    ....:     numpy.set_printoptions(legacy="1.25")  # to ensure numpy 2.0 compatibility
+ 
+ The basic object of computation in NumPy is an array. It is simple to
+ create an array.
+diff --git a/src/doc/it/faq/faq-usage.rst b/src/doc/it/faq/faq-usage.rst
+index 37bef7b13c1..5d3183769f7 100644
+--- a/src/doc/it/faq/faq-usage.rst
++++ b/src/doc/it/faq/faq-usage.rst
+@@ -305,7 +305,7 @@ anziché Integer di Sage. Ad esempio::
+     sage: RealNumber = float; Integer = int
+     sage: from scipy import stats
+     sage: stats.ttest_ind([1,2,3,4,5], [2,3,4,5,.6])
+-    Ttest...Result(statistic=0.0767529..., pvalue=0.940704...)
++    Ttest...Result(statistic=...0.0767529..., pvalue=...0.940704...)
+     sage: stats.uniform(0,15).ppf([0.5,0.7])
+     array([  7.5,  10.5])
+ 
+diff --git a/src/sage/arith/misc.py b/src/sage/arith/misc.py
+index 310f2b0b189..6ffcc95ff8a 100644
+--- a/src/sage/arith/misc.py
++++ b/src/sage/arith/misc.py
+@@ -2277,7 +2277,7 @@ def power_mod(a, n, m):
+ 
+         sage: from numpy import int32                                                   # needs numpy
+         sage: power_mod(int32(2), int32(390), int32(391))                               # needs numpy
+-        285
++        ...285...
+         sage: from gmpy2 import mpz
+         sage: power_mod(mpz(2), mpz(390), mpz(391))
+         mpz(285)
+diff --git a/src/sage/calculus/interpolators.pyx b/src/sage/calculus/interpolators.pyx
+index 221b52369e2..bb0be7bab0c 100644
+--- a/src/sage/calculus/interpolators.pyx
++++ b/src/sage/calculus/interpolators.pyx
+@@ -27,6 +27,9 @@ Development supported by NSF award No. 0702939.
+ import numpy as np
+ cimport numpy as np
+ 
++if int(np.version.short_version[0]) > 1:
++    np.set_printoptions(legacy="1.25")
++
+ from math import pi
+ cdef double TWOPI = 2*pi
+ 
+diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx
+index 6ec80d89aa7..c09d93c4260 100644
+--- a/src/sage/calculus/riemann.pyx
++++ b/src/sage/calculus/riemann.pyx
+@@ -44,6 +44,9 @@ from sage.calculus.integration import numerical_integral
+ import numpy as np
+ cimport numpy as np
+ 
++if int(np.version.short_version[0]) > 1:
++    np.set_printoptions(legacy="1.25")
++
+ from math import pi
+ from math import sin
+ from math import cos
+diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
+index b198fed0c0d..b3ebd206cd2 100644
+--- a/src/sage/combinat/fully_packed_loop.py
++++ b/src/sage/combinat/fully_packed_loop.py
+@@ -66,6 +66,9 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False):
+     r"""
+     TESTS::
+ 
++        sage: import numpy as np
++        sage: if int(np.version.short_version[0]) > 1:
++        ....:     np.set_printoptions(legacy="1.25")
+         sage: from sage.combinat.fully_packed_loop import _make_color_list
+         sage: _make_color_list(5)
+         sage: _make_color_list(5, ['blue', 'red'])
+diff --git a/src/sage/env.py b/src/sage/env.py
+index 722649ab3da..abb9b19f9e3 100644
+--- a/src/sage/env.py
++++ b/src/sage/env.py
+@@ -296,7 +296,7 @@ def sage_include_directories(use_sources=False):
+         sage: import sage.env
+         sage: sage.env.sage_include_directories()
+         ['...',
+-         '.../numpy/core/include',
++         '.../numpy/...core/include',
+          '.../include/python...']
+ 
+     To check that C/C++ files are correctly found, we verify that we can
+diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
+index e100ba3ee23..2a03bb68f67 100644
+--- a/src/sage/functions/special.py
++++ b/src/sage/functions/special.py
+@@ -217,6 +217,9 @@ class SphericalHarmonic(BuiltinFunction):
+         sage: spherical_harmonic(1, 1, pi/2, pi).n()  # abs tol 1e-14                   # needs sage.symbolic
+         0.345494149471335
+         sage: from scipy.special import sph_harm  # NB: arguments x and y are swapped   # needs scipy
++        sage: import numpy as np                                                        # needs scipy
++        sage: if int(np.version.short_version[0]) > 1:                                  # needs scipy
++        ....:     np.set_printoptions(legacy="1.25")                                    # needs scipy
+         sage: sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                       # needs scipy sage.symbolic
+         (0.3454941494713355-4.231083042742082e-17j)
+ 
+diff --git a/src/sage/graphs/generators/classical_geometries.py b/src/sage/graphs/generators/classical_geometries.py
+index da04362eef3..957f88d2061 100644
+--- a/src/sage/graphs/generators/classical_geometries.py
++++ b/src/sage/graphs/generators/classical_geometries.py
+@@ -1315,7 +1315,7 @@ def CossidentePenttilaGraph(q):
+ 
+     from sage.libs.gap.libgap import libgap
+     adj_list = libgap.function_factory("""function(q)
+-        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x;
++        local z, e, so, G, nu, G1, G0, B, T, s, O1, O2, x, sqo;
+         LoadPackage("grape");
+         G0:=SO(3,q^2);
+         so:=GeneratorsOfGroup(G0);
+diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
+index d3d6a4e8b0c..402cc91107d 100644
+--- a/src/sage/graphs/generic_graph.py
++++ b/src/sage/graphs/generic_graph.py
+@@ -18418,6 +18418,9 @@ def shortest_path_all_pairs(self, by_weight=False, algorithm=None,
+                 M = self.adjacency_matrix(vertices=int_to_vertex)
+ 
+             # We call the Floyd-Warshall method from SciPy
++            import numpy  # to ensure numpy 2.0 compatibility
++            if int(numpy.version.short_version[0]) > 1:
++                numpy.set_printoptions(legacy="1.25")
+             from numpy import array as np_array
+             from scipy.sparse.csgraph import floyd_warshall
+             dd, pp = floyd_warshall(np_array(M), directed=self.is_directed(),
+diff --git a/src/sage/graphs/graph_generators_pyx.pyx b/src/sage/graphs/graph_generators_pyx.pyx
+index 033e8b22adc..04b20d3229b 100644
+--- a/src/sage/graphs/graph_generators_pyx.pyx
++++ b/src/sage/graphs/graph_generators_pyx.pyx
+@@ -57,7 +57,7 @@ def RandomGNP(n, p, bint directed=False, bint loops=False, seed=None):
+ 
+         sage: from numpy import mean                                                    # needs numpy
+         sage: abs(mean([RandomGNP(200, .2).density() for i in range(30)]) - .2) < .001  # needs numpy
+-        True
++        ...True...
+         sage: RandomGNP(150, .2, loops=True)
+         Traceback (most recent call last):
+         ...
+diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx
+index 4500695e297..649b532b99c 100644
+--- a/src/sage/modules/free_module_element.pyx
++++ b/src/sage/modules/free_module_element.pyx
+@@ -547,7 +547,11 @@ def vector(arg0, arg1=None, arg2=None, sparse=None, immutable=False):
+         R = None
+ 
+     try:
++        import numpy
+         from numpy import ndarray
++        if int(numpy.version.short_version[0]) > 1:
++            numpy.set_printoptions(legacy="1.25")
++
+     except ImportError:
+         pass
+     else:
+@@ -1180,7 +1184,11 @@ cdef class FreeModuleElement(Vector):   # abstract base class
+             over Rational Field to numpy array of type <... 'float'>:
+             setting an array element with a sequence.
+         """
++        import numpy
+         from numpy import array
++        if int(numpy.version.short_version[0]) > 1:
++            numpy.set_printoptions(legacy="1.25")
++
+         try:
+             return array(self, dtype=dtype)
+         except ValueError as e:
+diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
+index e3d94d1746e..7ae8ca4966f 100644
+--- a/src/sage/numerical/optimize.py
++++ b/src/sage/numerical/optimize.py
+@@ -155,6 +155,10 @@ def find_root(f, a, b, xtol=10e-13, rtol=2.0**-50, maxiter=100, full_output=Fals
+         b = max(s_1, s_2)
+ 
+     import scipy.optimize
++    import numpy
++    if int(numpy.version.short_version[0]) > 1:
++        numpy.set_printoptions(legacy="1.25")
++
+     g = lambda x: float(f(x))
+     brentqRes = scipy.optimize.brentq(g, a, b,
+                                  full_output=full_output, xtol=xtol, rtol=rtol, maxiter=maxiter)
+@@ -288,6 +292,10 @@ def find_local_minimum(f, a, b, tol=1.48e-08, maxfun=500):
+     a = float(a)
+     b = float(b)
+     import scipy.optimize
++    import numpy
++    if int(numpy.version.short_version[0]) > 1:
++        numpy.set_printoptions(legacy="1.25")
++
+     xmin, fval, iter, funcalls = scipy.optimize.fminbound(f, a, b, full_output=1, xtol=tol, maxfun=maxfun)
+     return fval, xmin
+ 
+@@ -376,6 +384,8 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
+         sage: def rosen(x):  # The Rosenbrock function
+         ....:    return sum(100.0r*(x[1r:]-x[:-1r]**2.0r)**2.0r + (1r-x[:-1r])**2.0r)
+         sage: import numpy
++        sage: if int(numpy.version.short_version[0]) > 1:
++        ....:     numpy.set_printoptions(legacy="1.25")
+         sage: from numpy import zeros
+         sage: def rosen_der(x):
+         ....:    xm = x[1r:-1r]
+@@ -393,6 +403,9 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
+     from sage.structure.element import Expression
+     from sage.ext.fast_callable import fast_callable
+     import numpy
++    if int(numpy.version.short_version[0]) > 1:
++        numpy.set_printoptions(legacy="1.25")
++
+     from scipy import optimize
+     if isinstance(func, Expression):
+         var_list = func.variables()
+@@ -530,6 +543,8 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
+     from sage.structure.element import Expression
+     from sage.ext.fast_callable import fast_callable
+     import numpy
++    if int(numpy.version.short_version[0]) > 1:
++        numpy.set_printoptions(legacy="1.25")
+     from scipy import optimize
+     function_type = type(lambda x,y: x+y)
+ 
+@@ -652,6 +667,8 @@ def find_fit(data, model, initial_guess=None, parameters=None, variables=None, s
+     ``lmdif`` and ``lmder`` algorithms.
+     """
+     import numpy
++    if int(numpy.version.short_version[0]) > 1:
++        numpy.set_printoptions(legacy="1.25")
+ 
+     if not isinstance(data, numpy.ndarray):
+         try:
+diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
+index ac1dc79d802..23e2517ca56 100644
+--- a/src/sage/plot/arrow.py
++++ b/src/sage/plot/arrow.py
+@@ -53,6 +53,9 @@ def get_minmax_data(self):
+ 
+         EXAMPLES::
+ 
++            sage: import numpy  # to ensure numpy 2.0 compatibility
++            sage: if int(numpy.version.short_version[0]) > 1:
++            ....:     numpy.set_printoptions(legacy="1.25")
+             sage: from sage.plot.arrow import CurveArrow
+             sage: b = CurveArrow(path=[[(0,0),(.5,.5),(1,0)],[(.5,1),(0,0)]],
+             ....:                options={})
+diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
+index f1f2671a803..4d71414e1c2 100644
+--- a/src/sage/plot/complex_plot.pyx
++++ b/src/sage/plot/complex_plot.pyx
+@@ -1282,15 +1282,13 @@ def rgb_to_hls(rgb):
+         raise ValueError("Last dimension of input array must be 3; "
+                          "shape {} was found.".format(rgb.shape))
+     in_shape = rgb.shape
+-    rgb = np.array(
+-        rgb, copy=False, dtype=np.dtype(float), ndmin=2
+-    )
++    rgb = np.asarray(rgb, dtype=np.dtype(float))
+     rgb_max = rgb.max(-1)
+     rgb_min = rgb.min(-1)
+     l = (rgb_max + rgb_min)/2.0  # lightness
+ 
+     hls = np.zeros_like(rgb)
+-    delta = rgb.ptp(-1)
++    delta = np.ptp(rgb, -1)
+     s = np.zeros_like(delta)
+ 
+     ipos = delta > 0
+diff --git a/src/sage/plot/graphics.py b/src/sage/plot/graphics.py
+index a5e46d07c2d..83595edab0c 100644
+--- a/src/sage/plot/graphics.py
++++ b/src/sage/plot/graphics.py
+@@ -2746,7 +2746,7 @@ def matplotlib(self, filename=None,
+             sage: xmin, xmax = sub.get_xlim()
+             sage: ymin, ymax = sub.get_ylim()
+             sage: xmin > xmax, ymin > ymax
+-            (True, True)
++            (...True..., ...True...)
+         """
+         if not isinstance(ticks, (list, tuple)):
+             ticks = (ticks, None)
+diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
+index fa86a44bd0a..a585cacf9cd 100644
+--- a/src/sage/plot/histogram.py
++++ b/src/sage/plot/histogram.py
+@@ -92,6 +92,8 @@ def get_minmax_data(self):
+             {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
+         """
+         import numpy
++        if int(numpy.version.short_version[0]) > 1:
++            numpy.set_printoptions(legacy="1.25")
+ 
+         # Extract these options (if they are not None) and pass them to
+         # histogram()
+diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
+index f657e1d369e..c6c71a72d7e 100644
+--- a/src/sage/plot/multigraphics.py
++++ b/src/sage/plot/multigraphics.py
+@@ -785,6 +785,9 @@ def _add_subplot(self, figure, index, **options):
+             True
+             sage: G.position(1)
+             (0.2, 0.3, 0.4, 0.1)
++            sage: import numpy  # to ensure numpy 2.0 compatibility
++            sage: if int(numpy.version.short_version[0]) > 1:
++            ....:     numpy.set_printoptions(legacy="1.25")
+             sage: ax1.get_position().bounds  # tol 1.0e-13
+             (0.2, 0.3, 0.4000000000000001, 0.10000000000000003)
+ 
+@@ -1296,6 +1299,9 @@ def position(self, index):
+             sage: g1 = plot(sin(x), (x, -pi, pi))
+             sage: g2 = circle((0,1), 1.)
+             sage: G = graphics_array([g1, g2])
++            sage: import numpy  # to ensure numpy 2.0 compatibility
++            sage: if int(numpy.version.short_version[0]) > 1:
++            ....:     numpy.set_printoptions(legacy="1.25")
+             sage: G.position(0)  # tol 5.0e-3
+             (0.025045451349937315,
+              0.03415488992713045,
+diff --git a/src/sage/plot/plot3d/implicit_surface.pyx b/src/sage/plot/plot3d/implicit_surface.pyx
+index ce0da48a4e0..f4d5059b620 100644
+--- a/src/sage/plot/plot3d/implicit_surface.pyx
++++ b/src/sage/plot/plot3d/implicit_surface.pyx
+@@ -468,6 +468,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
+             sage: cube_marcher.y_vertices.tolist()
+             [[[<1.0, 0.5, 0.0>, None]], [[None, None]]]
+             sage: cube_marcher.x_vertices.any() # This shouldn't affect the X vertices.
++            ...
+         """
+         (self.y_vertices, self.y_vertices_swapped) = \
+             (self.y_vertices_swapped, self.y_vertices)
+@@ -574,6 +575,7 @@ cdef class MarchingCubesTriangles(MarchingCubes):
+             sage: cube_marcher.x_vertices.tolist()
+             [[None, None], [None, <1.5, 1.0, 1.0>]]
+             sage: cube_marcher.y_vertices.any() or cube_marcher.z_vertices.any() # This shouldn't affect the Y or Z vertices.
++            ...
+         """
+         cdef bint has_prev = (_prev is not None)
+         cdef bint has_next = (_next is not None)
+diff --git a/src/sage/plot/scatter_plot.py b/src/sage/plot/scatter_plot.py
+index 4ad418f040b..781854d372c 100644
+--- a/src/sage/plot/scatter_plot.py
++++ b/src/sage/plot/scatter_plot.py
+@@ -63,9 +63,9 @@ def get_minmax_data(self):
+             sage: s = scatter_plot([[0,1],[2,4],[3.2,6]])
+             sage: d = s.get_minmax_data()
+             sage: d['xmin']
+-            0.0
++            ...0.0...
+             sage: d['ymin']
+-            1.0
++            ...1.0...
+         """
+         return {'xmin': self.xdata.min(),
+                 'xmax': self.xdata.max(),
+diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py
+index 663d3aee70b..d2cb11088c7 100644
+--- a/src/sage/plot/streamline_plot.py
++++ b/src/sage/plot/streamline_plot.py
+@@ -71,6 +71,9 @@ def get_minmax_data(self):
+         EXAMPLES::
+ 
+             sage: x, y = var('x y')
++            sage: import numpy  # to ensure numpy 2.0 compatibility
++            sage: if int(numpy.version.short_version[0]) > 1:
++            ....:     numpy.set_printoptions(legacy="1.25")
+             sage: d = streamline_plot((.01*x, x+y), (x,10,20), (y,10,20))[0].get_minmax_data()
+             sage: d['xmin']
+             10.0
+diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
+index e2c71af9c25..59ba4a95ab6 100644
+--- a/src/sage/probability/probability_distribution.pyx
++++ b/src/sage/probability/probability_distribution.pyx
+@@ -140,6 +140,9 @@ cdef class ProbabilityDistribution:
+              1.8,
+              2.0]
+         """
++        import numpy as np
++        if int(np.version.short_version[0]) > 1:
++            np.set_printoptions(legacy="1.25")
+         import pylab
+         ell = [float(self.get_random_element()) for _ in range(num_samples)]
+         S = pylab.hist(ell, bins, density=True)
+diff --git a/src/sage/rings/complex_double.pyx b/src/sage/rings/complex_double.pyx
+index 2f85cbd101a..f8c5a474229 100644
+--- a/src/sage/rings/complex_double.pyx
++++ b/src/sage/rings/complex_double.pyx
+@@ -2550,10 +2550,10 @@ cdef class ComplexToCDF(Morphism):
+ 
+         sage: # needs numpy
+         sage: import numpy
+-        sage: f = CDF.coerce_map_from(numpy.complex_)
+-        sage: f(numpy.complex_(I))
++        sage: f = CDF.coerce_map_from(numpy.complex128)
++        sage: f(numpy.complex128(I))
+         1.0*I
+-        sage: f(numpy.complex_(I)).parent()
++        sage: f(numpy.complex128(I)).parent()
+         Complex Double Field
+     """
+     def __init__(self, R):
+@@ -2570,7 +2570,7 @@ cdef class ComplexToCDF(Morphism):
+         EXAMPLES::
+ 
+             sage: import numpy                                                          # needs numpy
+-            sage: CDF(numpy.complex_(I))    # indirect doctest                          # needs numpy
++            sage: CDF(numpy.complex128(I))    # indirect doctest                          # needs numpy
+             1.0*I
+         """
+         cdef ComplexDoubleElement z = <ComplexDoubleElement>ComplexDoubleElement.__new__(ComplexDoubleElement)
+@@ -2584,7 +2584,7 @@ cdef class ComplexToCDF(Morphism):
+         EXAMPLES::
+ 
+             sage: import numpy                                                          # needs numpy
+-            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex_)            # needs numpy
++            sage: f = sage.rings.complex_double.ComplexToCDF(numpy.complex128)          # needs numpy
+             sage: f._repr_type()                                                        # needs numpy
+             'Native'
+         """
+diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx
+index 6d9155b643f..6dc0150ad96 100644
+--- a/src/sage/rings/integer.pyx
++++ b/src/sage/rings/integer.pyx
+@@ -585,6 +585,8 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement):
+         Test comparisons with numpy types (see :issue:`13386` and :issue:`18076`)::
+ 
+             sage: import numpy                                                          # needs numpy
++            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
++            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
+             sage: numpy.int8('12') == 12                                                # needs numpy
+             True
+             sage: 12 == numpy.int8('12')                                                # needs numpy
+diff --git a/src/sage/rings/polynomial/polynomial_element.pyx b/src/sage/rings/polynomial/polynomial_element.pyx
+index 1270c42ce2a..78a32005d04 100644
+--- a/src/sage/rings/polynomial/polynomial_element.pyx
++++ b/src/sage/rings/polynomial/polynomial_element.pyx
+@@ -8851,7 +8851,7 @@ cdef class Polynomial(CommutativePolynomial):
+                          'you expect.')
+ 
+                 import numpy
+-                from numpy.linalg.linalg import LinAlgError
++                from numpy.linalg import LinAlgError
+                 from sage.rings.complex_double import CDF
+ 
+                 numpy_dtype = ('complex' if input_complex else 'double')
+diff --git a/src/sage/rings/real_mpfi.pyx b/src/sage/rings/real_mpfi.pyx
+index 7007f1da8d7..66c6733ee49 100644
+--- a/src/sage/rings/real_mpfi.pyx
++++ b/src/sage/rings/real_mpfi.pyx
+@@ -231,6 +231,8 @@ specified if given a non-interval and an interval::
+ TESTS::
+ 
+     sage: import numpy                                                                  # needs numpy
++    sage: if int(numpy.version.short_version[0]) > 1:                                   # needs numpy
++    ....:     numpy.set_printoptions(legacy="1.25")                                     # needs numpy
+     sage: RIF(2) == numpy.int8('2')                                                     # needs numpy
+     True
+     sage: numpy.int8('2') == RIF(2)                                                     # needs numpy
+diff --git a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
+index 8f240627e77..70ce616f92f 100644
+--- a/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
++++ b/src/sage/schemes/elliptic_curves/period_lattice_region.pyx
+@@ -77,6 +77,8 @@ cdef class PeriodicRegion:
+         EXAMPLES::
+ 
+             sage: import numpy as np
++            sage: if int(np.version.short_version[0]) > 1:
++            ....:     np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((4, 4))
+             sage: PeriodicRegion(CDF(2), CDF(2*I), data).is_empty()
+@@ -295,6 +297,8 @@ cdef class PeriodicRegion:
+         EXAMPLES::
+ 
+             sage: import numpy as np
++            sage: if int(np.version.short_version[0]) > 1:
++            ....:     np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((10, 10))
+             sage: data[1:4,1:4] = True
+@@ -317,6 +321,8 @@ cdef class PeriodicRegion:
+         EXAMPLES::
+ 
+             sage: import numpy as np
++            sage: if int(np.version.short_version[0]) > 1:
++            ....:     np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((4, 4))
+             sage: data[1,1] = True
+@@ -370,6 +376,8 @@ cdef class PeriodicRegion:
+         EXAMPLES::
+ 
+             sage: import numpy as np
++            sage: if int(np.version.short_version[0]) > 1:
++            ....:     np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+ 
+             sage: data = np.zeros((20, 20))
+@@ -520,6 +528,8 @@ cdef class PeriodicRegion:
+         TESTS::
+ 
+             sage: import numpy as np
++            sage: if int(np.version.short_version[0]) > 1:
++            ....:     np.set_printoptions(legacy="1.25")
+             sage: from sage.schemes.elliptic_curves.period_lattice_region import PeriodicRegion
+             sage: data = np.zeros((4, 4))
+             sage: data[1, 1] = True
+diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
+index b2e6b301bf7..6937f6cb410 100644
+--- a/src/sage/stats/basic_stats.py
++++ b/src/sage/stats/basic_stats.py
+@@ -227,6 +227,8 @@ def std(v, bias=False):
+ 
+         sage: # needs numpy
+         sage: import numpy
++        sage: if int(numpy.version.short_version[0]) > 1:
++        ....:     numpy.set_printoptions(legacy="1.25")
+         sage: x = numpy.array([1,2,3,4,5])
+         sage: std(x, bias=False)
+         1.5811388300841898
+@@ -304,6 +306,8 @@ def variance(v, bias=False):
+         sage: variance([RIF(1.0103, 1.0103), RIF(2)])
+         0.4897530450000000?
+         sage: import numpy                                                              # needs numpy
++        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
++        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
+         sage: x = numpy.array([1,2,3,4,5])                                              # needs numpy
+         sage: variance(x, bias=False)                                                   # needs numpy
+         2.5
+diff --git a/src/sage/stats/time_series.pyx b/src/sage/stats/time_series.pyx
+index d6823f85add..3b17f232d0e 100644
+--- a/src/sage/stats/time_series.pyx
++++ b/src/sage/stats/time_series.pyx
+@@ -1720,6 +1720,8 @@ cdef class TimeSeries:
+         if len(v0) == 1:
+             return v1[0]/v0[0]
+         import numpy
++        if int(numpy.version.short_version[0]) > 1:
++            numpy.set_printoptions(legacy="1.25")
+         coeffs = numpy.polyfit(v0,v1,1)
+         return coeffs[0]
+ 
+diff --git a/src/sage/structure/coerce.pyx b/src/sage/structure/coerce.pyx
+index dfbd5ff82fa..955a256e9b4 100644
+--- a/src/sage/structure/coerce.pyx
++++ b/src/sage/structure/coerce.pyx
+@@ -520,6 +520,8 @@ cdef class CoercionModel:
+     Check that :issue:`8426` is fixed (see also :issue:`18076`)::
+ 
+         sage: import numpy                                                              # needs numpy
++        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
++        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
+ 
+         sage: # needs sage.rings.real_mpfr
+         sage: x = polygen(RR)
+diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
+index a92fe241355..7671338feaa 100644
+--- a/src/sage/symbolic/expression.pyx
++++ b/src/sage/symbolic/expression.pyx
+@@ -1167,7 +1167,7 @@ cdef class Expression(Expression_abc):
+             sage: unicode_art(SR(13 - I))
+             13 - ⅈ
+             sage: unicode_art(SR(1.3 - I))
+-            1.3 - ⅈ
++            1.3 - ...ⅈ
+             sage: unicode_art(cos(I))
+             cosh(1)
+ 
+diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
+index 2cb2f09c715..cd89ad2a256 100644
+--- a/src/sage/symbolic/function.pyx
++++ b/src/sage/symbolic/function.pyx
+@@ -964,6 +964,9 @@ cdef class BuiltinFunction(Function):
+             mpc(real='0.83373002513114902', imag='-0.98889770576286506')
+ 
+             sage: import numpy                                                          # needs numpy
++            sage: if int(numpy.version.short_version[0]) > 1:                           # needs numpy
++            ....:     numpy.set_printoptions(legacy="1.25")                             # needs numpy
++
+             sage: sin(numpy.int32(0))                                                   # needs numpy
+             0.0
+             sage: type(_)                                                               # needs numpy
+diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
+index e7a28be127a..18ad0d8f636 100644
+--- a/src/sage/symbolic/ring.pyx
++++ b/src/sage/symbolic/ring.pyx
+@@ -1162,6 +1162,8 @@ cdef class NumpyToSRMorphism(Morphism):
+     We check that :issue:`8949` and :issue:`9769` are fixed (see also :issue:`18076`)::
+ 
+         sage: import numpy                                                              # needs numpy
++        sage: if int(numpy.version.short_version[0]) > 1:                               # needs numpy
++        ....:     numpy.set_printoptions(legacy="1.25")                                 # needs numpy
+         sage: f(x) = x^2
+         sage: f(numpy.int8('2'))                                                        # needs numpy
+         4
+
+From 2092f81092c81c36b7596b701355c279b07fa175 Mon Sep 17 00:00:00 2001
+From: Dima Pasechnik <dimpase@gmail.com>
+Date: Mon, 24 Jun 2024 13:02:30 +0100
+Subject: [PATCH 2/2] rectify the test for numpy.typecodes
+
+---
+ src/sage/matrix/matrix1.pyx | 13 ++++++++-----
+ 1 file changed, 8 insertions(+), 5 deletions(-)
+
+diff --git a/src/sage/matrix/matrix1.pyx b/src/sage/matrix/matrix1.pyx
+index e03d45a212d..9e5844f2416 100644
+--- a/src/sage/matrix/matrix1.pyx
++++ b/src/sage/matrix/matrix1.pyx
+@@ -705,12 +705,15 @@ cdef class Matrix(Matrix0):
+         Type ``numpy.typecodes`` for a list of the possible
+         typecodes::
+ 
+-            sage: import numpy                                                          # needs numpy
+-            sage: sorted(numpy.typecodes.items())                                       # needs numpy
++            sage: import numpy                            # needs numpy
++            sage: numpy.typecodes.items()                 # needs numpy # random
+             [('All', '?bhilqpBHILQPefdgFDGSUVOMm'), ('AllFloat', 'efdgFDG'),
+-             ('AllInteger', 'bBhHiIlLqQpP'), ('Character', 'c'), ('Complex', 'FDG'),
+-             ('Datetime', 'Mm'), ('Float', 'efdg'), ('Integer', 'bhilqp'),
+-             ('UnsignedInteger', 'BHILQP')]
++            ...
++
++        For instance, you can see possibilities for real floating point numbers::
++
++            sage: numpy.typecodes['Float']                # needs numpy
++            'efdg'
+ 
+         Alternatively, numpy automatically calls this function (via
+         the magic :meth:`__array__` method) to convert Sage matrices
diff --git a/sagemath-tdlib-0.9.patch b/sagemath-tdlib-0.9.patch
deleted file mode 100644
index 50e4ed3690a6..000000000000
--- a/sagemath-tdlib-0.9.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-diff -up src/sage/graphs/graph_decompositions/sage_tdlib.cpp.orig src/sage/graphs/graph_decompositions/sage_tdlib.cpp
---- a/src/sage/graphs/graph_decompositions/sage_tdlib.cpp	2021-05-09 16:00:11.000000000 -0600
-+++ b/src/sage/graphs/graph_decompositions/sage_tdlib.cpp	2021-06-16 08:33:47.325415307 -0600
-@@ -2,8 +2,8 @@
- #include <map>
- 
- #include <boost/graph/adjacency_list.hpp>
--#include "tdlib/TD_combinations.hpp"
--#include "tdlib/TD_misc.hpp"
-+#include <treedec/combinations.hpp>
-+#include <treedec/misc.hpp>
- 
- #ifndef TD_STRUCT_VERTEX
- #define TD_STRUCT_VERTEX
-@@ -16,13 +16,6 @@ struct Vertex{
- 
- typedef boost::adjacency_list<boost::setS, boost::vecS, boost::undirectedS, Vertex> TD_graph_t;
- 
--struct bag{
--    std::set<unsigned int> bag;
--};
--
--typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, bag> TD_tree_dec_t;
--
--
- void make_tdlib_graph(TD_graph_t &G, std::vector<unsigned int> &V, std::vector<unsigned int> &E){
-     unsigned int max = 0;
-     for(unsigned int i = 0; i < V.size(); i++)