Re: [PR PATCH] [Updated] singular: update to 4.3.2, rebuild sagemath

[tornaria <tornaria@users.noreply.github.com>]

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There is an updated pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages sagemath
https://github.com/void-linux/void-packages/pull/43225

singular: update to 4.3.2, rebuild sagemath
<!-- Uncomment relevant sections and delete options which are not applicable -->

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

After this PR, sagemath testsuite should pass 100% with current versions of dependencies in void. All patches are taken from upstream.

#### Testing the changes
- I tested the changes in this PR: **briefly**

I'm running tests locally as well. Note that I'm doing this on top of #43153 to test the openblas update as well.

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#### New package
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-->

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- I built this PR locally for these architectures (if supported. mark crossbuilds):
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A patch file from https://github.com/void-linux/void-packages/pull/43225.patch is attached

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[-- Attachment #2: github-pr-sagemath-43225.patch --]
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From bcd09894152c6db0b95460127cedd256cb88de36 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 27 Mar 2023 00:31:35 -0300
Subject: [PATCH 1/3] singular: update to 4.3.2.

---
 common/shlibs             | 10 +++++-----
 srcpkgs/singular/template |  4 ++--
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/common/shlibs b/common/shlibs
index e282bbd1f588..08dac21a5b3e 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -4099,11 +4099,11 @@ libumfpack.so.6 SuiteSparse-6.0.1_1
 libecl.so.21.2 ecl-21.2.1_1
 libecm.so.1 ecm-7.0.4_3
 libcliquer.so.1 cliquer-1.22_1
-libSingular-4.3.1.so singular-4.3.1p2_1
-libfactory-4.3.1.so singular-4.3.1p2_1
-libpolys-4.3.1.so singular-4.3.1p2_1
-libomalloc-0.9.6.so singular-4.3.1p2_1
-libsingular_resources-4.3.1.so singular-4.3.1p2_1
+libomalloc-0.9.6.so singular-4.2.1_1
+libSingular-4.3.2.so singular-4.3.2_1
+libfactory-4.3.2.so singular-4.3.2_1
+libpolys-4.3.2.so singular-4.3.2_1
+libsingular_resources-4.3.2.so singular-4.3.2_1
 libbrial.so.3 brial-1.2.10_1
 libbrial_groebner.so.3 brial-1.2.10_1
 libm4ri-0.0.20200125.so m4ri-20200125_1
diff --git a/srcpkgs/singular/template b/srcpkgs/singular/template
index c73a020dcf15..0481f6cb1e11 100644
--- a/srcpkgs/singular/template
+++ b/srcpkgs/singular/template
@@ -1,6 +1,6 @@
 # Template file for 'singular'
 pkgname=singular
-version=4.3.1p3
+version=4.3.2
 revision=1
 _majver=${version%p*}
 build_style=gnu-configure
@@ -20,7 +20,7 @@ maintainer="dkwo <npiazza@disroot.org>"
 license="GPL-2.0-or-later"
 homepage="https://www.singular.uni-kl.de"
 distfiles="https://www.singular.uni-kl.de/ftp/pub/Math/Singular/SOURCES/${_majver//./-}/singular-${version}.tar.gz"
-checksum=66cfaeee7ab909272fd81050a09cae3ec115652a01adde014a5128a54b97397a
+checksum=3fd565d1bd4265fa8ba7cc189137a36d9daf9939b5bb411466c2028d9191f6db
 
 if [ -z "$CROSS_BUILD" ]; then
 	makedepends+=" ntl-devel"

From 3171129c048430254672b4b0828bd37bab9c1e7f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 15 Mar 2023 09:27:58 -0300
Subject: [PATCH 2/3] 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

And add support for:
 - networkx 3.1

We use patches from upstream sagemath to fix all of these.

We also add pythran and sphinx to checkdepends to make sure doctests
pass when they are installed.
---
 ...support_singular_4.3.1.p3-5e5737a0c.patch} |  0
 .../34980-avoid_factoring_in_is_prime.patch   | 16 ++--
 .../patches/35177-matplotlib_3.7.patch        | 95 +++++++++++++++++++
 .../patches/35195-workaround_ecl_race.patch   | 56 +++++++++++
 .../patches/35204-fix_sage-cleaner.patch      | 28 ++++++
 .../sagemath/patches/35250-nauty_2.8.6.patch  | 35 +++++++
 .../sagemath/patches/35423-ipython_8.12.patch | 51 ++++++++++
 .../patches/35438-pythran_0.12.1.patch        | 41 ++++++++
 .../sagemath/patches/35584-networkx_3.1.patch | 81 ++++++++++++++++
 srcpkgs/sagemath/patches/get_patches          | 32 ++++++-
 srcpkgs/sagemath/template                     |  4 +-
 11 files changed, 425 insertions(+), 14 deletions(-)
 rename srcpkgs/sagemath/patches/{trac-34851-support_singular_4.3.1.p3-5e5737a0c.patch => 34851-support_singular_4.3.1.p3-5e5737a0c.patch} (100%)
 create mode 100644 srcpkgs/sagemath/patches/35177-matplotlib_3.7.patch
 create mode 100644 srcpkgs/sagemath/patches/35195-workaround_ecl_race.patch
 create mode 100644 srcpkgs/sagemath/patches/35204-fix_sage-cleaner.patch
 create mode 100644 srcpkgs/sagemath/patches/35250-nauty_2.8.6.patch
 create mode 100644 srcpkgs/sagemath/patches/35423-ipython_8.12.patch
 create mode 100644 srcpkgs/sagemath/patches/35438-pythran_0.12.1.patch
 create mode 100644 srcpkgs/sagemath/patches/35584-networkx_3.1.patch

diff --git a/srcpkgs/sagemath/patches/trac-34851-support_singular_4.3.1.p3-5e5737a0c.patch b/srcpkgs/sagemath/patches/34851-support_singular_4.3.1.p3-5e5737a0c.patch
similarity index 100%
rename from srcpkgs/sagemath/patches/trac-34851-support_singular_4.3.1.p3-5e5737a0c.patch
rename to srcpkgs/sagemath/patches/34851-support_singular_4.3.1.p3-5e5737a0c.patch
diff --git a/srcpkgs/sagemath/patches/34980-avoid_factoring_in_is_prime.patch b/srcpkgs/sagemath/patches/34980-avoid_factoring_in_is_prime.patch
index ca61a2ada4eb..ee0f0e656b28 100644
--- a/srcpkgs/sagemath/patches/34980-avoid_factoring_in_is_prime.patch
+++ b/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
  
diff --git a/srcpkgs/sagemath/patches/35177-matplotlib_3.7.patch b/srcpkgs/sagemath/patches/35177-matplotlib_3.7.patch
new file mode 100644
index 000000000000..007f3324cfe4
--- /dev/null
+++ b/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)):
diff --git a/srcpkgs/sagemath/patches/35195-workaround_ecl_race.patch b/srcpkgs/sagemath/patches/35195-workaround_ecl_race.patch
new file mode 100644
index 000000000000..1e0a708e8068
--- /dev/null
+++ b/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)
diff --git a/srcpkgs/sagemath/patches/35204-fix_sage-cleaner.patch b/srcpkgs/sagemath/patches/35204-fix_sage-cleaner.patch
new file mode 100644
index 000000000000..fc3e40da2a88
--- /dev/null
+++ b/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])
diff --git a/srcpkgs/sagemath/patches/35250-nauty_2.8.6.patch b/srcpkgs/sagemath/patches/35250-nauty_2.8.6.patch
new file mode 100644
index 000000000000..ea210e20ae52
--- /dev/null
+++ b/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]
+         """
diff --git a/srcpkgs/sagemath/patches/35423-ipython_8.12.patch b/srcpkgs/sagemath/patches/35423-ipython_8.12.patch
new file mode 100644
index 000000000000..46bda084e48e
--- /dev/null
+++ b/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)
diff --git a/srcpkgs/sagemath/patches/35438-pythran_0.12.1.patch b/srcpkgs/sagemath/patches/35438-pythran_0.12.1.patch
new file mode 100644
index 000000000000..2cdc674d4f9e
--- /dev/null
+++ b/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?= <tornaria@cmat.edu.uy>
+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
+
diff --git a/srcpkgs/sagemath/patches/35584-networkx_3.1.patch b/srcpkgs/sagemath/patches/35584-networkx_3.1.patch
new file mode 100644
index 000000000000..66eedecff7c6
--- /dev/null
+++ b/srcpkgs/sagemath/patches/35584-networkx_3.1.patch
@@ -0,0 +1,81 @@
+diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py
+index c2e42bcbd3..b6a10efbf4 100644
+--- a/src/sage/graphs/graph.py
++++ b/src/sage/graphs/graph.py
+@@ -6786,13 +6786,21 @@ def cliques_number_of(self, vertices=None, cliques=None):
+             {(0, 0): 2, (0, 1): 3, (0, 2): 2, (1, 0): 2, (1, 1): 3, (1, 2): 2}
+             sage: F.cliques_number_of(vertices=[(0, 1), (1, 2)])
+             {(0, 1): 3, (1, 2): 2}
++            sage: F.cliques_number_of(vertices=(0, 1))
++            3
+             sage: G = Graph({0:[1,2,3], 1:[2], 3:[0,1]})
+             sage: G.show(figsize=[2,2])
+             sage: G.cliques_number_of()
+             {0: 2, 1: 2, 2: 1, 3: 1}
+         """
+-        import networkx
+-        return networkx.number_of_cliques(self.networkx_graph(), vertices, cliques)
++        if cliques is None:
++            cliques = self.cliques_maximal()
++
++        if vertices in self: # single vertex
++            return sum(1 for c in cliques if vertices in c)
++        else:
++            return { v : sum(1 for c in cliques if v in c)
++                     for v in vertices or self }
+ 
+     @doc_index("Clique-related methods")
+     def cliques_get_max_clique_graph(self):
+@@ -7493,17 +7501,32 @@ def cliques_containing_vertex(self, vertices=None, cliques=None):
+ 
+             sage: C = Graph('DJ{')
+             sage: C.cliques_containing_vertex()
+-            {0: [[4, 0]], 1: [[4, 1, 2, 3]], 2: [[4, 1, 2, 3]], 3: [[4, 1, 2, 3]], 4: [[4, 0], [4, 1, 2, 3]]}
++            {0: [[0, 4]],
++             1: [[1, 2, 3, 4]],
++             2: [[1, 2, 3, 4]],
++             3: [[1, 2, 3, 4]],
++             4: [[0, 4], [1, 2, 3, 4]]}
++            sage: C.cliques_containing_vertex(4)
++            [[0, 4], [1, 2, 3, 4]]
++            sage: C.cliques_containing_vertex([0, 1])
++            {0: [[0, 4]], 1: [[1, 2, 3, 4]]}
+             sage: E = C.cliques_maximal()
+             sage: E
+             [[0, 4], [1, 2, 3, 4]]
+             sage: C.cliques_containing_vertex(cliques=E)
+-            {0: [[0, 4]], 1: [[1, 2, 3, 4]], 2: [[1, 2, 3, 4]], 3: [[1, 2, 3, 4]], 4: [[0, 4], [1, 2, 3, 4]]}
++            {0: [[0, 4]],
++             1: [[1, 2, 3, 4]],
++             2: [[1, 2, 3, 4]],
++             3: [[1, 2, 3, 4]],
++             4: [[0, 4], [1, 2, 3, 4]]}
+ 
+             sage: G = Graph({0:[1,2,3], 1:[2], 3:[0,1]})
+             sage: G.show(figsize=[2,2])
+             sage: G.cliques_containing_vertex()
+-            {0: [[0, 1, 2], [0, 1, 3]], 1: [[0, 1, 2], [0, 1, 3]], 2: [[0, 1, 2]], 3: [[0, 1, 3]]}
++            {0: [[0, 1, 2], [0, 1, 3]],
++             1: [[0, 1, 2], [0, 1, 3]],
++             2: [[0, 1, 2]],
++             3: [[0, 1, 3]]}
+ 
+         Since each clique of a 2 dimensional grid corresponds to an edge, the
+         number of cliques in which a vertex is involved equals its degree::
+@@ -7518,8 +7541,14 @@ def cliques_containing_vertex(self, vertices=None, cliques=None):
+             sage: sorted(sorted(x for x in L) for L in d[(0, 1)])
+             [[(0, 0), (0, 1)], [(0, 1), (0, 2)], [(0, 1), (1, 1)]]
+         """
+-        import networkx
+-        return networkx.cliques_containing_node(self.networkx_graph(), vertices, cliques)
++        if cliques is None:
++            cliques = self.cliques_maximal()
++
++        if vertices in self: # single vertex
++            return [c for c in cliques if vertices in c]
++        else:
++            return { v : [c for c in cliques if v in c]
++                     for v in vertices or self }
+ 
+     @doc_index("Clique-related methods")
+     def clique_complex(self):
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index c98da68683cc..871ae38577fd 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/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 +29,35 @@ 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"
+
+# needs review
+get_pr 35584 "networkx 3.1"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 75695f0e5f87..66a543efd21d 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
 version=9.8
-revision=1
+revision=2
 build_wrksrc=pkgs/sagemath-standard
 build_style=python3-module
 _bindir=/usr/lib/sagemath/$version/bin
@@ -26,7 +26,7 @@ depends="FlintQS eclib-devel fflas-ffpack flintlib-devel gcc-fortran gd-devel
  python3-sympy python3-traitlets sage-data-combinatorial_designs
  sage-data-conway_polynomials sage-data-elliptic_curves sage-data-graphs
  sage-data-polytopes_db sympow tachyon threejs-sage"
-checkdepends="$depends"
+checkdepends="$depends pythran python3-Sphinx"
 short_desc="Open source mathematics software"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-2.0-or-later"

From 09713264ff96b25e7f8e00b02770e7f0bf9891ca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Fri, 28 Apr 2023 19:38:50 -0300
Subject: [PATCH 3/3] python3-networkx: update to 3.1.

---
 srcpkgs/python3-networkx/template | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/srcpkgs/python3-networkx/template b/srcpkgs/python3-networkx/template
index 83e21291feb8..526f4c5e259a 100644
--- a/srcpkgs/python3-networkx/template
+++ b/srcpkgs/python3-networkx/template
@@ -1,6 +1,6 @@
 # Template file for 'python3-networkx'
 pkgname=python3-networkx
-version=2.8.8
+version=3.1
 revision=1
 build_style=python3-module
 # failing in i686
@@ -10,12 +10,12 @@ depends="python3"
 checkdepends="python3-numpy python3-scipy python3-matplotlib python3-pandas
  python3-lxml python3-sympy python3-pytest-xdist"
 short_desc="Python3 package for creating and manipulating graphs and networks"
-maintainer="Orphaned <orphan@voidlinux.org>"
+maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="BSD-3-Clause"
 homepage="https://networkx.org"
-changelog="https://networkx.org/documentation/stable/release/"
+changelog="https://github.com/networkx/networkx/raw/main/doc/release/release_${version}.rst"
 distfiles="${PYPI_SITE}/n/networkx/networkx-${version}.tar.gz"
-checksum=230d388117af870fce5647a3c52401fcf753e94720e6ea6b4197a5355648885e
+checksum=de346335408f84de0eada6ff9fafafff9bcda11f0a0dfaa931133debb146ab61
 
 post_install() {
 	vlicense LICENSE.txt