sagemath: rebuild for singular update

Also fix doctests for pkg updates:
 - matplotlib 3.7
 - ipython 8.12
 - nauty 2.8.6
 - pythran 0.12.1

We add patches from upstream sagemath to fix these.

Also add pythran and sphinx to checkdepends to make sure doctests pass
when they are installed.

srcpkgs/sagemath/patches/34980-avoid_factoring_in_is_prime.patch

@@ -1,8 +1,8 @@
 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
+index d5f7157217f..8ca1f958039 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):
+@@ -996,16 +996,38 @@ def is_prime(self):
              False
              sage: K.ideal(17).is_prime()  # ramified
              False
@@ -33,13 +33,15 @@ index d5f7157217f..1a9d11aec68 100644
 +        K = self.number_field().pari_nf()
 +        I = self.pari_hnf()
 +
-+        self._pari_prime = K.idealismaximal(I) or None
++        candidate = 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
++        if get_flag(None, 'arithmetic'):
++            # proof required, check using isprime()
++            if candidate and not candidate[0].isprime():
++                candidate = None
++
++        self._pari_prime = candidate
 +
 +        return self._pari_prime is not None
 

srcpkgs/sagemath/patches/35177-matplotlib_3.7.patch

@@ -0,0 +1,95 @@
+diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
+index b77c69b2f77..0586a96ae55 100644
+--- a/src/sage/plot/complex_plot.pyx
++++ b/src/sage/plot/complex_plot.pyx
+@@ -563,7 +563,7 @@ def complex_to_cmap_rgb(z_values, cmap='turbo', contoured=False, tiled=False,
+     import matplotlib as mpl
+
+     if isinstance(cmap, str):
+-        cmap = mpl.cm.get_cmap(cmap)
++        cmap = mpl.colormaps[cmap]
+
+     if contour_base is None:
+         if contour_type == "linear":
+@@ -1206,11 +1206,11 @@ def complex_plot(f, x_range, y_range, contoured=False, tiled=False, cmap=None,
+                 domain = np.linspace(0, 1, 256)
+                 shifted_domain = np.roll(domain, 128)
+                 default_cmap = mpl.colors.LinearSegmentedColormap.from_list(
+-                    "sage_default", mpl.cm.get_cmap('hsv')(shifted_domain)
++                    "sage_default", mpl.colormaps['hsv'](shifted_domain)
+                 )
+                 cmap = default_cmap
+             else:
+-                cmap = mpl.cm.get_cmap(cmap)
++                cmap = mpl.colormaps[cmap]
+         rgbs = complex_to_cmap_rgb(
+             z_values, cmap=cmap, contoured=contoured, tiled=tiled,
+             contour_type=contour_type, contour_base=contour_base,
+diff --git a/src/sage/plot/contour_plot.py b/src/sage/plot/contour_plot.py
+index c0cab456686..4accb309580 100644
+--- a/src/sage/plot/contour_plot.py
++++ b/src/sage/plot/contour_plot.py
+@@ -848,9 +848,7 @@ def f(x,y): return cos(x) + sin(y)
+
+         sage: contour_plot(lambda x,y: 0, (-1,1), (-1,1),
+         ....:              contours=[0], fill=False, cmap=['blue'])
+-        ...
+-        UserWarning: No contour levels were found within the data range.
+-        Graphics object consisting of 1 graphics primitive
++        ...Graphics object consisting of 1 graphics primitive
+
+     .. PLOT::
+
+@@ -874,8 +872,7 @@ def f(x,y): return cos(x) + sin(y)
+     Check that :trac:`18074` is fixed::
+
+         sage: contour_plot(0, (0,1), (0,1))
+-        ... UserWarning: No contour levels were found within the data range.
+-        Graphics object consisting of 1 graphics primitive
++        ...Graphics object consisting of 1 graphics primitive
+
+     Domain points in :trac:`11648` with complex output are now skipped::
+
+diff --git a/src/sage/plot/graphics.py b/src/sage/plot/graphics.py
+index 64ea1a7e10f..cdc99ced263 100644
+--- a/src/sage/plot/graphics.py
++++ b/src/sage/plot/graphics.py
+@@ -2341,7 +2341,7 @@ def _matplotlib_tick_formatter(self, subplot, base=(10, 10),
+             sage: subplot = Figure().add_subplot(111)
+             sage: p._objects[0]._render_on_subplot(subplot)
+             sage: p._matplotlib_tick_formatter(subplot, **d)
+-            (<AxesSubplot:...>,
++            (<Axes...>,
+             <matplotlib.ticker.MaxNLocator object at ...>,
+             <matplotlib.ticker.MaxNLocator object at ...>,
+             <matplotlib.ticker.ScalarFormatter object at ...>,
+diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py
+index 99c817f03a6..ae85183dc93 100644
+--- a/src/sage/plot/multigraphics.py
++++ b/src/sage/plot/multigraphics.py
+@@ -1207,7 +1207,7 @@ def _add_subplot(self, figure, index, **options):
+             sage: fig = Figure()
+             sage: ax1 = G._add_subplot(fig, 0)
+             sage: type(ax1)
+-            <class 'matplotlib.axes._subplots.AxesSubplot'>
++            <class 'matplotlib.axes...'>
+             sage: ax2 = G._add_subplot(fig, 1)
+             sage: fig.get_axes() == [ax1, ax2]
+             True
+diff --git a/src/sage/plot/plot3d/plot_field3d.py b/src/sage/plot/plot3d/plot_field3d.py
+index bdf39391d3e..fe10e27f58f 100644
+--- a/src/sage/plot/plot3d/plot_field3d.py
++++ b/src/sage/plot/plot3d/plot_field3d.py
+@@ -126,9 +126,9 @@ def plot_vector_field3d(functions, xrange, yrange, zrange,
+     vectors = [vector((ff(*point), gg(*point), hh(*point))) for point in points]
+
+     try:
+-        from matplotlib.cm import get_cmap
+-        cm = get_cmap(colors)
+-    except (TypeError, ValueError):
++        import matplotlib as mpl
++        cm = mpl.colormaps[colors]
++    except (TypeError, KeyError):
+         cm = None
+     if cm is None:
+         if isinstance(colors, (list, tuple)):

srcpkgs/sagemath/patches/35195-workaround_ecl_race.patch

@@ -0,0 +1,56 @@
+diff --git a/src/sage/interfaces/maxima_lib.py b/src/sage/interfaces/maxima_lib.py
+index c9ca5e30939..9459cb70334 100644
+--- a/src/sage/interfaces/maxima_lib.py
++++ b/src/sage/interfaces/maxima_lib.py
+@@ -77,6 +77,26 @@
+     sage: bar == foo
+     True
+
++TESTS:
++
++Check our workaround for a race in ecl works, see :trac:`26968`.
++We use a temporary `MAXIMA_USERDIR` so it's empty; we place it
++in `DOT_SAGE` since we expect it to have more latency than `/tmp`.
++
++    sage: import tempfile, subprocess
++    sage: tmpdir = tempfile.TemporaryDirectory(dir=DOT_SAGE)
++    sage: _ = subprocess.run(['sage', '-c',  # long time
++    ....: f'''
++    ....: import os
++    ....: os.environ["MAXIMA_USERDIR"] = "{tmpdir.name}"
++    ....: if not os.fork():
++    ....:     import sage.interfaces.maxima_lib
++    ....: else:
++    ....:     import sage.interfaces.maxima_lib
++    ....:     os.wait()
++    ....: '''])
++    sage: tmpdir.cleanup()
++
+ """
+
+ # ****************************************************************************
+@@ -116,7 +136,23 @@
+ ecl_eval("(setq $nolabels t))")
+ ecl_eval("(defvar *MAXIMA-LANG-SUBDIR* NIL)")
+ ecl_eval("(set-locale-subdir)")
+-ecl_eval("(set-pathnames)")
++
++try:
++    ecl_eval("(set-pathnames)")
++except RuntimeError:
++    # Recover from :trac:`26968` by creating `*maxima-objdir*` here.
++    # This cannot be done before calling `(set-pathnames)` since
++    # `*maxima-objdir*` is computed there.
++    # We use python `os.makedirs()` which is immune to the race.
++    # Using `(ensure-directories-exist ...)` in lisp would be
++    # subject to the same race condition and since `*maxima-objdir*`
++    # has multiple components this is quite plausible to happen.
++    maxima_objdir = ecl_eval("*maxima-objdir*").python()[1:-1]
++    import os
++    os.makedirs(maxima_objdir, exist_ok=True)
++    # Call `(set-pathnames)` again to complete its job.
++    ecl_eval("(set-pathnames)")
++
+ ecl_eval("(defun add-lineinfo (x) x)")
+ ecl_eval('(defun principal nil (cond ($noprincipal (diverg)) ((not pcprntd) (merror "Divergent Integral"))))')
+ ecl_eval("(remprop 'mfactorial 'grind)")  # don't use ! for factorials (#11539)

srcpkgs/sagemath/patches/35204-fix_sage-cleaner.patch

@@ -0,0 +1,28 @@
+diff --git a/src/bin/sage-cleaner b/src/bin/sage-cleaner
+index e2e578eec60..dc7d8f0482e 100755
+--- a/src/bin/sage-cleaner
++++ b/src/bin/sage-cleaner
+@@ -99,6 +99,15 @@ def cleanup():
+
+     return len(pid_list)
+
++def cleanup_cruft():
++    """ remove directories leftover from improper shutdown """
++    tmp_dirs = os.listdir(SAGE_TMP_ROOT)
++    for dir_entry in tmp_dirs:
++        baddir = os.path.join(SAGE_TMP_ROOT, dir_entry)
++        if os.path.isdir(baddir):
++            logger.warning('Removing old directory %s from SAGE_TMP_ROOT', baddir)
++            rm_rf(baddir)
++
+ def kill_spawned_jobs(jobfile, parent_pid):
+     logger.info("Killing %s's spawned jobs", parent_pid)
+     killed_them_all = True
+@@ -193,6 +202,7 @@ if __name__ == '__main__':
+     setup_daemon()
+     fix_old_mistakes()
+     logger.info("Starting sage-cleaner with PID %s", os.getpid())
++    cleanup_cruft()
+
+     if len(sys.argv) > 1:
+         wait = int(sys.argv[1])

srcpkgs/sagemath/patches/35250-nauty_2.8.6.patch

@@ -0,0 +1,35 @@
+diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
+index ec6a5c19e60..9dd7bc1cb1e 100644
+--- a/src/sage/graphs/generators/families.py
++++ b/src/sage/graphs/generators/families.py
+@@ -3660,7 +3660,7 @@ def nauty_gentreeg(options="", debug=False):
+
+         sage: gen = graphs.nauty_gentreeg("4", debug=True)
+         sage: print(next(gen))
+-        >A ...gentreeg Z=2:3 D=3 n=4
++        >A ...gentreeg ...
+         sage: gen = graphs.nauty_gentreeg("4 -q", debug=True)
+         sage: next(gen)
+         ''
+@@ -3687,7 +3687,7 @@ def nauty_gentreeg(options="", debug=False):
+         sage: list(graphs.nauty_gentreeg("3 -x", debug=True))
+         ['>E Usage: ...gentreeg [-D#] [-Z#:#] [-ulps] [-q] n [res/mod] ...
+         sage: list(graphs.nauty_gentreeg("3", debug=True))
+-        ['>A ...gentreeg Z=2:2 D=2 n=3\n', Graph on 3 vertices]
++        ['>A ...gentreeg ...\n', Graph on 3 vertices]
+     """
+     import shlex
+     from sage.features.nauty import NautyExecutable
+diff --git a/src/sage/graphs/graph_generators.py b/src/sage/graphs/graph_generators.py
+index df88bbe2713..1a8016976c2 100644
+--- a/src/sage/graphs/graph_generators.py
++++ b/src/sage/graphs/graph_generators.py
+@@ -966,7 +966,7 @@ def nauty_geng(self, options="", debug=False):
+             ...
+             ValueError: wrong format of parameter option
+             sage: list(graphs.nauty_geng("-c3", debug=True))
+-            ['>E Usage: ...geng [-cCmtfbd#D#] [-uygsnh] [-lvq] ...
++            ['>E Usage: ...geng ...\n']
+             sage: list(graphs.nauty_geng("-c 3", debug=True))
+             ['>A ...geng -cd1D2 n=3 e=2-3\n', Graph on 3 vertices, Graph on 3 vertices]
+         """

srcpkgs/sagemath/patches/35423-ipython_8.12.patch

@@ -0,0 +1,51 @@
+diff --git a/src/sage/repl/inputhook.py b/src/sage/repl/inputhook.py
+index da5df0268c0..7f7894f6dcf 100644
+--- a/src/sage/repl/inputhook.py
++++ b/src/sage/repl/inputhook.py
+@@ -17,6 +17,8 @@
+
+ import select
+ import errno
++import contextlib
++import io
+
+ from IPython import get_ipython
+ from IPython.terminal.pt_inputhooks import register
+@@ -47,15 +49,27 @@ def install():
+     """
+     Install the Sage input hook
+
+-    EXAMPLES::
++    EXAMPLES:
++
++    Make sure ipython is running so we really test this function::
++
++        sage: from sage.repl.interpreter import get_test_shell
++        sage: get_test_shell()
++        <sage.repl.interpreter.SageTestShell object at ...>
++
++    Run the function twice, to check it is idempotent (see :trac:`35235`)::
+
+         sage: from sage.repl.inputhook import install
+         sage: install()
++        sage: install()
+     """
+     ip = get_ipython()
+     if not ip:
+         return   # Not running in ipython, e.g. doctests
+-    ip.enable_gui('sage')
++    if ip._inputhook != sage_inputhook:
++        # silence `ip.enable_gui()` useless output
++        with contextlib.redirect_stdout(io.StringIO()):
++            ip.enable_gui('sage')
+
+
+ def uninstall():
+@@ -71,4 +85,6 @@ def uninstall():
+     if not ip:
+         return
+     if ip._inputhook == sage_inputhook:
+-        ip.enable_gui(None)
++        # silence `ip.enable_gui()` useless output
++        with contextlib.redirect_stdout(io.StringIO()):
++            ip.enable_gui(None)

srcpkgs/sagemath/patches/35438-pythran_0.12.1.patch

@@ -0,0 +1,41 @@
+From 532fbbaf71bb41c73920b584108eb2a09d6deeb1 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <[email protected]>
+Date: Tue, 4 Apr 2023 12:56:57 -0300
+Subject: [PATCH] Ignore deprecation warnings triggered by pythran 0.12.1
+
+These happen with python 3.11, setuptools 67.6.1, numpy 1.24.2.
+When pythran 0.12.1 is installed, I get 24 doctest failures due to
+deprecation warnings; they are all gone with this commit.
+
+[backported from 839a6e928c264a9863bd42860c78ae95a6d9f3e0]
+---
+ src/sage/all.py | 12 ++++++++++--
+ 1 file changed, 10 insertions(+), 2 deletions(-)
+
+diff --git a/src/sage/all.py b/src/sage/all.py
+index 93588df1b93..ee775aad0e9 100644
+--- a/src/sage/all.py
++++ b/src/sage/all.py
+@@ -96,9 +96,17 @@ warnings.filterwarnings('ignore', category=DeprecationWarning,
+ warnings.filterwarnings('ignore', category=DeprecationWarning,
+     module='(.*[.]_vendor[.])?packaging')
+
+-# Ignore numpy warnings triggered by pythran
++# Ignore a few warnings triggered by pythran 0.12.1
+ warnings.filterwarnings('ignore', category=DeprecationWarning,
+-                        module='pythran')
++    message='\n\n  `numpy.distutils` is deprecated since NumPy 1.23.0',
++    module='pythran.dist')
++warnings.filterwarnings('ignore', category=DeprecationWarning,
++    message='pkg_resources is deprecated as an API|'
++            'Deprecated call to `pkg_resources.declare_namespace(.*)`',
++    module='pkg_resources')
++warnings.filterwarnings('ignore', category=DeprecationWarning,
++    message='msvccompiler is deprecated and slated to be removed',
++    module='distutils.msvccompiler')
+
+ warnings.filterwarnings('ignore', category=DeprecationWarning,
+                         message='The distutils(.sysconfig module| package) is deprecated',
+-- 
+2.40.0
+

srcpkgs/sagemath/patches/get_patches

@@ -19,7 +19,7 @@ get_trac() {
 	ticket=$1
 	desc=$(echo "$2" | sed -e 's/ /_/g')
 	commit=$3
-	$DO wget "$URL_BASE_COMPARE$commit.diff" -O "trac-$ticket-$desc-$commit.patch"
+	$DO wget "$URL_BASE_COMPARE$commit.diff" -O "$ticket-$desc-$commit.patch"
 }
 
 # run from patches dir
@@ -29,13 +29,32 @@ cd $(dirname "$0")
 get_trac 34851 "support singular 4.3.1.p3" 5e5737a0c
 get_pr 35068 "fix tests giac 1.9.0.35" patch
 
-# positive review
+# merged in 10.0.beta1
+get_pr 35058 "skip unstable tests klyachko"
+
+# merged in 10.0.beta2
 get_pr 34994 "fix tests numpy 1.24"
 get_pr 34997 "fix edge case of integer_check"
-get_pr 35058 "skip unstable tests klyachko"
-get_pr 35094 "support gap 4.12"					# includes PR 35093
 
-# needs review 
+# merged in 10.0.beta3
 get_pr 34995 "support tachyon 0.99.2"
+
+# merged in 10.0.beta4
 get_pr 34980 "avoid factoring in is_prime"
+
+# merged in 10.0.beta5
+get_pr 35094 "support gap 4.12"					# includes PR 35093
+
+# merged in 10.0.beta6
 get_pr 35127 "fix very slow test stream.py"
+get_pr 35177 "matplotlib 3.7"
+get_pr 35195 "workaround ecl race"
+get_pr 35204 "fix sage-cleaner"
+
+# merged in 10.0.beta7
+get_pr 35250 "nauty 2.8.6"
+
+# merged in 10.0.beta8
+#get_pr 35337 "ipython 8.11"
+get_pr 35423 "ipython 8.12"						# includes PR 35337
+get_pr 35438 "pythran 0.12.1"