Re: [PR PATCH] [Updated] sagemath: rebuild for dep updates and fixes

[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/42048

sagemath: rebuild for dep updates and fixes
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#### Testing the changes
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A patch file from https://github.com/void-linux/void-packages/pull/42048.patch is attached

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From 5d152512a8d7045fc17abbd99c272c42fe20cf33 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 30 Jan 2023 11:04:46 -0300
Subject: [PATCH 1/2] brial: update to 1.2.12.

---
 srcpkgs/brial/template | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/srcpkgs/brial/template b/srcpkgs/brial/template
index 8f988c1296c6..2f8e195a8804 100644
--- a/srcpkgs/brial/template
+++ b/srcpkgs/brial/template
@@ -1,6 +1,6 @@
 # Template file for 'brial'
 pkgname=brial
-version=1.2.11
+version=1.2.12
 revision=1
 build_style=gnu-configure
 hostmakedepends="pkg-config"
@@ -9,8 +9,9 @@ short_desc="BRiAl (Boolean Ring Algebra) is the successor to PolyBoRi"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-2.0-or-later"
 homepage="https://github.com/BRiAl/BRiAl"
+changelog="https://github.com/BRiAl/BRiAl/releases"
 distfiles="https://github.com/BRiAl/BRiAl/releases/download/$version/brial-$version.tar.bz2"
-checksum=6c0f622009dcd9928295d748226baa9cdc1a87c32552e13772fddf95bbb6f02c
+checksum=ca009e3722dd3f0a60d15501caed1413146c80abced57423e32ae0116f407494
 
 if [ -n "$CROSS_BUILD" ]; then
 	configure_args+=" --with-boost-unit-test-framework=no"

From d1ea2ee3ae5ae9e7a255c13d021540e8410a3ed4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 2 Feb 2023 19:03:34 -0300
Subject: [PATCH 2/2] sagemath: rebuild for updates

Also:
 - rebuild for boost update in sync with brial (same PR)
 - fixes for numpy 1.24 (already updated)
 - fixes to support updating giac to 1.9.0.37
 - fixes to support updating tachyon 0.99.5
 - fixes to doctest failures in 32 bit after upgrade of pari to 2.15.2
 - fix an edge case of python 3.11 integer conversion on 32 bit
 - fix singular interface bug that triggers under very heavy load (e.g. on CI)
 - tarball was moved; sha256 changed only b/c of main dirname change
---
 ...4623a4b7404f5e4f9d152366d53e9c21cfa6.patch |  75 ++++
 ...1c2fc8bcfb5e6555716d05ce70511795ffa1.patch | 106 +++++
 .../trac-34537-sagemath-pari-2.15c.patch      | 403 ++++++++++++++++++
 .../patches/trac-34816-numpy_1.24.patch       |  76 ++++
 ...c3c9be2ca04e799fa6baf4ad09f21ed6eb91.patch |  65 +++
 .../zz-fix_edge_case_of_integer_check.patch   |  38 ++
 srcpkgs/sagemath/template                     |   6 +-
 srcpkgs/sagemath/update                       |   2 +
 8 files changed, 768 insertions(+), 3 deletions(-)
 create mode 100644 srcpkgs/sagemath/patches/trac-23712-support_tachyon_0.99.2-55c04623a4b7404f5e4f9d152366d53e9c21cfa6.patch
 create mode 100644 srcpkgs/sagemath/patches/trac-33907-fix_singular_interface-6f5c1c2fc8bcfb5e6555716d05ce70511795ffa1.patch
 create mode 100644 srcpkgs/sagemath/patches/trac-34537-sagemath-pari-2.15c.patch
 create mode 100644 srcpkgs/sagemath/patches/trac-34816-numpy_1.24.patch
 create mode 100644 srcpkgs/sagemath/patches/trac-34926-fix_tests_with_giac_1.9.0.35-3c98c3c9be2ca04e799fa6baf4ad09f21ed6eb91.patch
 create mode 100644 srcpkgs/sagemath/patches/zz-fix_edge_case_of_integer_check.patch
 create mode 100644 srcpkgs/sagemath/update

diff --git a/srcpkgs/sagemath/patches/trac-23712-support_tachyon_0.99.2-55c04623a4b7404f5e4f9d152366d53e9c21cfa6.patch b/srcpkgs/sagemath/patches/trac-23712-support_tachyon_0.99.2-55c04623a4b7404f5e4f9d152366d53e9c21cfa6.patch
new file mode 100644
index 000000000000..77c0dcb9a95b
--- /dev/null
+++ b/srcpkgs/sagemath/patches/trac-23712-support_tachyon_0.99.2-55c04623a4b7404f5e4f9d152366d53e9c21cfa6.patch
@@ -0,0 +1,75 @@
+From 55c04623a4b7404f5e4f9d152366d53e9c21cfa6 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
+Date: Wed, 21 Dec 2022 19:43:02 -0300
+Subject: Trac #23712: support tachyon >= 0.99.2
+
+In tachyon 0.99.2 the keyword `focallength` was changed to `focaldist`.
+To support it, when running on version >= 0.99.2 we "patch" the model as
+constructed by class `sage.plot.plot3d.tachyon.Tachyon`.
+
+In the future (possibly when tachyon in sage gets upgraded), all the
+focallength occurences in sage.plot.plot3d.tachyon can be replaced by
+focaldist for consistency with new tachyon, and the logic here can be
+reversed (i.e. patch the model when self.version() < '0.99.2') or just
+drop support for old versions.
+---
+ src/sage/interfaces/tachyon.py | 23 +++++++++++++++++++++++
+ 1 file changed, 23 insertions(+)
+
+diff --git a/src/sage/interfaces/tachyon.py b/src/sage/interfaces/tachyon.py
+index 23671e5..21cc1db 100644
+--- a/src/sage/interfaces/tachyon.py
++++ b/src/sage/interfaces/tachyon.py
+@@ -683,12 +683,14 @@ properly.
+ #*****************************************************************************
+ 
+ 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 @@ class TachyonRT(SageObject):
+             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 +858,22 @@ class TachyonRT(SageObject):
+         else:
+             print(r)
+ 
++    @cached_method
++    def version(self):
++        """
++        Returns the version of the Tachyon raytracer being used.
++
++        TESTS::
++
++            sage: tachyon_rt.version()  # not tested
++            0.98.9
++            sage: tachyon_rt.version() >= '0.98.9'
++            True
++        """
++        with os.popen('tachyon') as f:
++            r = f.read()
++        return re.search(r"Version ([\d.]*)", r)[1]
++
+     def help(self, use_pager=True):
+         """
+         Deprecated: type 'sage.interfaces.tachyon?' for help
+-- 
+cgit v1.0-1-gd88e
+
diff --git a/srcpkgs/sagemath/patches/trac-33907-fix_singular_interface-6f5c1c2fc8bcfb5e6555716d05ce70511795ffa1.patch b/srcpkgs/sagemath/patches/trac-33907-fix_singular_interface-6f5c1c2fc8bcfb5e6555716d05ce70511795ffa1.patch
new file mode 100644
index 000000000000..3db3bb94cdcf
--- /dev/null
+++ b/srcpkgs/sagemath/patches/trac-33907-fix_singular_interface-6f5c1c2fc8bcfb5e6555716d05ce70511795ffa1.patch
@@ -0,0 +1,106 @@
+From 6f5c1c2fc8bcfb5e6555716d05ce70511795ffa1 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
+Date: Fri, 16 Dec 2022 15:25:38 -0300
+Subject: Trac 33907: fix singular interface
+
+This essentially reverts 85f65bf and a10d19d from trac #31846.
+It turns out this was originaly written for #30945, but that issue was
+fixed by upgrading cysignals.
+
+Singular really needs a custom `_send_interrupt()` method, because the
+default one will quit singular. Moreover, this handles two quirks of
+singular:
+
+ - a small delay before sending `chr(3)` works around a bug in singular.
+ - sometimes one needs to send `;` a few times after interrupt to get
+   back a prompt.
+
+The original author of the custom `_send_interrupt()` is Jeroen Demeyer
+in commit 17d23e9 (trac #10476). I changed the timeout for a smaller
+one, and rewrote the doctest to call `interrupt()` explicitly instead of
+using `alarm()` which introduces more noise.
+---
+ src/sage/interfaces/expect.py   |  1 -
+ src/sage/interfaces/singular.py | 47 +++++++++++++++++++++++++++++++++++++++++
+ 2 files changed, 47 insertions(+), 1 deletion(-)
+
+diff --git a/src/sage/interfaces/expect.py b/src/sage/interfaces/expect.py
+index c4dc2d4..eb25daf 100644
+--- a/src/sage/interfaces/expect.py
++++ b/src/sage/interfaces/expect.py
+@@ -941,7 +941,6 @@ If this all works, you can then make calls like:
+         The interface still works after this interrupt::
+ 
+             sage: singular('2+3')
+-            Singular crashed -- automatically restarting.
+             5
+ 
+         Last, we demonstrate that by default the execution of a command
+diff --git a/src/sage/interfaces/singular.py b/src/sage/interfaces/singular.py
+index 9c9586d..2c377f0 100644
+--- a/src/sage/interfaces/singular.py
++++ b/src/sage/interfaces/singular.py
+@@ -341,6 +341,7 @@ import re
+ import sys
+ import pexpect
+ import shlex
++import time
+ 
+ from .expect import Expect, ExpectElement, FunctionElement, ExpectFunction
+ 
+@@ -508,6 +509,52 @@ class Singular(ExtraTabCompletion, Expect):
+         """
+         return 'quit;'
+ 
++    def _send_interrupt(self):
++        """
++        Send an interrupt to Singular. If needed, additional
++        semi-colons are sent until we get back at the prompt.
++
++        TESTS:
++
++        The following works without restarting Singular::
++
++            sage: a = singular(1)
++            sage: _ = singular._expect.sendline('while(1){};')
++            sage: singular.interrupt()
++            True
++
++        We can still access a::
++
++            sage: 2*a
++            2
++
++        Interrupting nothing or unfinished input also works::
++
++            sage: singular.interrupt()
++            True
++            sage: _ = singular._expect.sendline('1+')
++            sage: singular.interrupt()
++            True
++            sage: 3*a
++            3
++
++        """
++        # Work around for Singular bug
++        # http://www.singular.uni-kl.de:8002/trac/ticket/727
++        time.sleep(0.1)
++
++        E = self._expect
++        E.sendline(chr(3))
++        # The following is needed so interrupt() works even when
++        # there is no computation going on.
++        for i in range(5):
++            try:
++                E.expect_upto(self._prompt, timeout=0.1)
++                return
++            except pexpect.TIMEOUT:
++                pass
++            E.sendline(";")
++
+     def _read_in_file_command(self, filename):
+         r"""
+         EXAMPLES::
+-- 
+cgit v1.0-1-gd88e
+
diff --git a/srcpkgs/sagemath/patches/trac-34537-sagemath-pari-2.15c.patch b/srcpkgs/sagemath/patches/trac-34537-sagemath-pari-2.15c.patch
new file mode 100644
index 000000000000..e199fff237e7
--- /dev/null
+++ b/srcpkgs/sagemath/patches/trac-34537-sagemath-pari-2.15c.patch
@@ -0,0 +1,403 @@
+From 77b7786c653d5dd3c9b3040e895643798f3f6fb2 Mon Sep 17 00:00:00 2001
+From: John Cremona <john.cremona@gmail.com>
+Date: Thu, 5 Jan 2023 10:31:52 +0000
+Subject: [PATCH 1/5] #34537: make number_field_element tests more robust
+
+---
+ .../number_field/number_field_element.pyx     | 51 ++++++++++---------
+ 1 file changed, 27 insertions(+), 24 deletions(-)
+
+diff --git a/src/sage/rings/number_field/number_field_element.pyx b/src/sage/rings/number_field/number_field_element.pyx
+index 8330dea3b35..bbe5b90fb34 100644
+--- a/src/sage/rings/number_field/number_field_element.pyx
++++ b/src/sage/rings/number_field/number_field_element.pyx
+@@ -1637,10 +1637,10 @@ cdef class NumberFieldElement(FieldElement):
+             sage: K.<a> = NumberField(x^3 + x + 1)
+             sage: Q.<X> = K[]
+             sage: L.<b> = NumberField(X^4 + a)
+-            sage: t = (-a).is_norm(L, element=True); t
+-            (True, -b^3 - 1)
+-            sage: t[1].norm(K)
+-            -a
++            sage: t, u = (-a).is_norm(L, element=True); u # random (not unique)
++            b^3 + 1
++            sage: t and u.norm(K) == -a
++            True
+ 
+         Verify that :trac:`27469` has been fixed::
+ 
+@@ -1648,8 +1648,7 @@ cdef class NumberFieldElement(FieldElement):
+             Cyclotomic Field of order 24 and degree 8
+             sage: K = L.subfield(z24^3, 'z8')[0]; K
+             Number Field in z8 with defining polynomial x^4 + 1 with z8 = 0.7071067811865475? + 0.7071067811865475?*I
+-            sage: flag, c = K(-7).is_norm(K, element=True)
+-            sage: flag
++            sage: flag, c = K(-7).is_norm(K, element=True); flag
+             True
+             sage: c.norm(K)
+             -7
+@@ -1746,30 +1745,34 @@ cdef class NumberFieldElement(FieldElement):
+             sage: K.<a> = NumberField(x^3 + x^2 - 2*x - 1, 'a')
+             sage: P.<X> = K[]
+             sage: L = NumberField(X^2 + a^2 + 2*a + 1, 'b')
+-            sage: K(17)._rnfisnorm(L)  # representation depends, not tested
+-            ((a^2 - 2)*b - 4, 1)
++            sage: y, q = K(17)._rnfisnorm(L)
++            sage: q==1
++            True
++            sage: y # random (not unique)
++            (a^2 - 2)*b - 4
+ 
+             sage: K.<a> = NumberField(x^3 + x + 1)
+             sage: Q.<X> = K[]
+             sage: L.<b> = NumberField(X^4 + a)
+-            sage: t = (-a)._rnfisnorm(L); t
+-            (-b^3 - 1, 1)
+-            sage: t[0].norm(K)
+-            -a
+-            sage: t = K(3)._rnfisnorm(L); t
++            sage: y, q = (-a)._rnfisnorm(L)
++            sage: y # random (not unique)
++            b^3 + 1
++            sage: q == 1 and y.norm(K) == -a
++            True
++            sage: y, q = K(3)._rnfisnorm(L); y, q # random (not unique)
+             (b^3 + a*b^2 + a^2*b - 1, 3*a^2 - 3*a + 6)
+-            sage: t[0].norm(K)*t[1]
+-            3
++            sage: y.norm(K)*q == 3
++            True
+ 
+         An example where the base field is a relative field::
+ 
+             sage: K.<a, b> = NumberField([x^2 - 2, x^2 - 3])
+             sage: L.<c> = K.extension(x^3 + 2)
+             sage: s = 2*a + b
+-            sage: t = s._rnfisnorm(L)
+-            sage: t[1] == 1 # True iff s is a norm
++            sage: y, q = s._rnfisnorm(L)
++            sage: q == 1 # True iff s is a norm
+             False
+-            sage: s == t[0].norm(K)*t[1]
++            sage: s == y.norm(K)*q
+             True
+ 
+         TESTS:
+@@ -1779,7 +1782,9 @@ cdef class NumberFieldElement(FieldElement):
+ 
+             sage: K.<a> = NumberField(x^2 + 1/2)
+             sage: L.<b> = K.extension(x^2 - 1/2)
+-            sage: a._rnfisnorm(L)
++            sage: y, q = a._rnfisnorm(L)
++            sage: y # random (not unique)
++            q == 1 and y.norm(K) == a
+             (a*b + a + 1/2, 1)
+ 
+         We test the above doctest, which was not tested.
+@@ -1788,12 +1793,10 @@ cdef class NumberFieldElement(FieldElement):
+             sage: K.<a> = NumberField(x^3 + x^2 - 2*x - 1, 'a')
+             sage: P.<X> = K[]
+             sage: L.<b> = NumberField(X^2 + a^2 + 2*a + 1, 'b')
+-            sage: (xbar, q) = K(17)._rnfisnorm(L)
+-            sage: q == 1
+-            1
+-            sage: xbar.norm()
++            sage: y, q = K(17)._rnfisnorm(L)
++            sage: y.norm()
+             4913
+-            sage: xbar in ((a^2 - 2)*b - 4, (a^2 - 2)*b + 4)
++            sage: q == 1 and y in ((a^2 - 2)*b - 4, (a^2 - 2)*b + 4)
+             True
+ 
+         AUTHORS:
+-- 
+2.39.1
+
+
+From 37dcd374ce2f63b38b3f3be27cc10fb5eb5256c2 Mon Sep 17 00:00:00 2001
+From: John Cremona <john.cremona@gmail.com>
+Date: Thu, 5 Jan 2023 10:51:05 +0000
+Subject: [PATCH 2/5] #34537: make number_field_ideal_rel tests more robust
+
+---
+ .../number_field/number_field_ideal_rel.py    | 20 +++++++++----------
+ 1 file changed, 9 insertions(+), 11 deletions(-)
+
+diff --git a/src/sage/rings/number_field/number_field_ideal_rel.py b/src/sage/rings/number_field/number_field_ideal_rel.py
+index f64bd5b761c..192c8f15034 100644
+--- a/src/sage/rings/number_field/number_field_ideal_rel.py
++++ b/src/sage/rings/number_field/number_field_ideal_rel.py
+@@ -204,8 +204,6 @@ class NumberFieldFractionalIdeal_rel(NumberFieldFractionalIdeal):
+         r"""
+         Convert the absolute ideal id to a relative number field ideal.
+ 
+-        Assumes id.number_field() == self.absolute_field('a').
+-
+         WARNING:  This is an internal helper function.
+ 
+         TESTS::
+@@ -218,18 +216,18 @@ class NumberFieldFractionalIdeal_rel(NumberFieldFractionalIdeal):
+             True
+             sage: J.absolute_norm()
+             22584817
+-            sage: J.absolute_ideal()
+-            Fractional ideal (22584817, -1473/812911*a^5 + 8695/4877466*a^4 - 1308209/4877466*a^3 + 117415/443406*a^2 - 22963264/2438733*a - 13721081784272/2438733)
+-            sage: J.absolute_ideal().norm()
++            sage: Labs.<c> = L.absolute_field(); Labs # random (polynomial not unique)
++            Number Field in c with defining polynomial x^6 + 217*x^4 - 2*x^3 + 15127*x^2 + 422*x + 338032
++            sage: Jabs = J.absolute_ideal(names='c')
++            sage: Jabs == Labs.ideal(22584817, -1473/812911*c^5 + 8695/4877466*c^4 - 1308209/4877466*c^3 + 117415/443406*c^2 - 22963264/2438733*c - 13721081784272/2438733)
++            True
++            sage: Jabs.norm()
+             22584817
+-
+-            sage: J._from_absolute_ideal(J.absolute_ideal()) == J
++            sage: J._from_absolute_ideal(Jabs) == J
+             True
+         """
+-        L = self.number_field()
+-        K = L.absolute_field('a')
+-        to_L = K.structure()[0]
+-        return L.ideal([to_L(_) for _ in id.gens()])
++        f, _ = id.number_field().structure()
++        return self.number_field().ideal([f(_) for _ in id.gens()])
+ 
+     def free_module(self):
+         r"""
+-- 
+2.39.1
+
+
+From 52e18fba1a4d77ddae9b27a94e736a940ab25ac3 Mon Sep 17 00:00:00 2001
+From: John Cremona <john.cremona@gmail.com>
+Date: Thu, 5 Jan 2023 11:30:39 +0000
+Subject: [PATCH 3/5] #34537: make qqbar tests more robust
+
+---
+ src/sage/rings/qqbar.py | 50 ++++++++++++++++++++++++++++++-----------
+ 1 file changed, 37 insertions(+), 13 deletions(-)
+
+diff --git a/src/sage/rings/qqbar.py b/src/sage/rings/qqbar.py
+index 31e0a721a52..18228844684 100644
+--- a/src/sage/rings/qqbar.py
++++ b/src/sage/rings/qqbar.py
+@@ -2656,9 +2656,11 @@ def number_field_elements_from_algebraics(numbers, minimal=False, same_field=Fal
+ 
+         sage: elems = [sqrt(5), 2^(1/3)+sqrt(3)*I, 3/4]
+         sage: nf, nums, hom = number_field_elements_from_algebraics(elems, embedded=True)
+-        sage: nf
++        sage: nf # random (polynomial and root not unique)
+         Number Field in a with defining polynomial y^24 - 6*y^23 ...- 9*y^2 + 1
+           with a = 0.2598679? + 0.0572892?*I
++        sage: nf.is_isomorphic(NumberField(x^24 - 9*x^22 + 135*x^20 - 720*x^18 + 1821*x^16 - 3015*x^14 + 3974*x^12 - 3015*x^10 + 1821*x^8 - 720*x^6 + 135*x^4 - 9*x^2 + 1, 'a'))
++        True
+         sage: list(map(QQbar, nums)) == elems == list(map(hom, nums))
+         True
+ 
+@@ -7857,16 +7859,21 @@ class ANExtensionElement(ANDescr):
+             sage: b = a._descr
+             sage: type(b)
+             <class 'sage.rings.qqbar.ANExtensionElement'>
+-            sage: b.neg(a)
+-            -1/3*a^3 + 1/3*a^2 - a - 1 where a^4 - 2*a^3 + a^2 + 6*a + 3 = 0 and a in 1.724744871391589? + 1.573132184970987?*I
+-            sage: b.neg("ham spam and eggs")
++            sage: c = b.neg(None); c # random (not uniquely represented)
+             -1/3*a^3 + 1/3*a^2 - a - 1 where a^4 - 2*a^3 + a^2 + 6*a + 3 = 0 and a in 1.724744871391589? + 1.573132184970987?*I
++            sage: c.generator() == b.generator() and c.field_element_value() + b.field_element_value() == 0
++            True
++
++        The parameter is ignored::
++
++            sage: b.neg("random").generator() == c.generator() and b.neg("random").field_element_value() == c.field_element_value()
++            True
+         """
+         return ANExtensionElement(self._generator, -self._value)
+ 
+     def invert(self, n):
+         r"""
+-        1/self.
++        Reciprocal of self.
+ 
+         EXAMPLES::
+ 
+@@ -7875,16 +7882,20 @@ class ANExtensionElement(ANDescr):
+             sage: b = a._descr
+             sage: type(b)
+             <class 'sage.rings.qqbar.ANExtensionElement'>
+-            sage: b.invert(a)
+-            -7/3*a^3 + 19/3*a^2 - 7*a - 9 where a^4 - 2*a^3 + a^2 + 6*a + 3 = 0 and a in 1.724744871391589? + 1.573132184970987?*I
+-            sage: b.invert("ham spam and eggs")
++            sage: c = b.invert(None); c # random (not uniquely represented)
+             -7/3*a^3 + 19/3*a^2 - 7*a - 9 where a^4 - 2*a^3 + a^2 + 6*a + 3 = 0 and a in 1.724744871391589? + 1.573132184970987?*I
++            sage: c.generator() == b.generator() and c.field_element_value() * b.field_element_value() == 1
++            True
++
++        The parameter is ignored::
++
++            sage: b.invert("random").generator() == c.generator() and b.invert("random").field_element_value() == c.field_element_value()
++            True
+         """
+         return ANExtensionElement(self._generator, ~self._value)
+ 
+     def conjugate(self, n):
+-        r"""
+-        Negation of self.
++        r"""Complex conjugate of self.
+ 
+         EXAMPLES::
+ 
+@@ -7893,10 +7904,23 @@ class ANExtensionElement(ANDescr):
+             sage: b = a._descr
+             sage: type(b)
+             <class 'sage.rings.qqbar.ANExtensionElement'>
+-            sage: b.conjugate(a)
+-            1/3*a^3 - 1/3*a^2 + a + 1 where a^4 - 2*a^3 + a^2 + 6*a + 3 = 0 and a in 1.724744871391589? - 1.573132184970987?*I
+-            sage: b.conjugate("ham spam and eggs")
++            sage: c = b.conjugate(None); c # random (not uniquely represented)
+             1/3*a^3 - 1/3*a^2 + a + 1 where a^4 - 2*a^3 + a^2 + 6*a + 3 = 0 and a in 1.724744871391589? - 1.573132184970987?*I
++
++        Internally, complex conjugation is implemented by taking the
++        same abstract field element but conjugating the complex embedding of
++        the field::
++
++            sage: c.generator() == b.generator().conjugate()
++            True
++            sage: c.field_element_value() == b.field_element_value()
++            True
++
++        The parameter is ignored::
++
++            sage: b.conjugate("random").generator() == c.generator() and b.conjugate("random").field_element_value() == c.field_element_value()
++            True
++
+         """
+         if self._exactly_real:
+             return self
+-- 
+2.39.1
+
+
+From 238f4de34714989b866757523f2a46088dbfb720 Mon Sep 17 00:00:00 2001
+From: Dima Pasechnik <dima@pasechnik.info>
+Date: Fri, 20 Jan 2023 01:25:39 +0000
+Subject: [PATCH 4/5] fixed doctests for elliptic curves on 32-bit
+
+---
+ .../schemes/elliptic_curves/ell_number_field.py     | 13 ++++++++-----
+ .../schemes/elliptic_curves/isogeny_small_degree.py | 13 ++-----------
+ 2 files changed, 10 insertions(+), 16 deletions(-)
+
+diff --git a/src/sage/schemes/elliptic_curves/ell_number_field.py b/src/sage/schemes/elliptic_curves/ell_number_field.py
+index c44c803aa82..656ccbf86bc 100644
+--- a/src/sage/schemes/elliptic_curves/ell_number_field.py
++++ b/src/sage/schemes/elliptic_curves/ell_number_field.py
+@@ -2294,9 +2294,10 @@ class EllipticCurve_number_field(EllipticCurve_field):
+             sage: E = EllipticCurve(K, [1, 0, 5*y^2 + 16, 0, 0])
+             sage: E.gens(lim1=1, lim3=1)
+             []
+-            sage: E.rank(), E.gens(lim3=12)  # long time (about 4s)
+-            (1,
+-             [(369/25*y^3 + 539/25*y^2 + 1178/25*y + 1718/25 : -29038/125*y^3 - 43003/125*y^2 - 92706/125*y - 137286/125 : 1)])
++            sage: E.rank()
++            1
++            sage: E.gens(lim3=13)  # long time (about 4s)
++            [(... : 1)]
+ 
+         Here is a curve of rank 2::
+ 
+@@ -2644,7 +2645,7 @@ class EllipticCurve_number_field(EllipticCurve_field):
+             sage: [phi.codomain().cm_discriminant() for phi in E.isogenies_prime_degree()]  # long time
+             [-92, -23, -23]
+ 
+-            sage: C.matrix()  # long time
++            sage: C.matrix()  # long time # random
+             [1 2 2 4 4 2]
+             [2 1 2 4 2 4]
+             [2 2 1 2 4 4]
+@@ -2676,13 +2677,15 @@ class EllipticCurve_number_field(EllipticCurve_field):
+         determined::
+ 
+             sage: G = C.graph()  # long time
+-            sage: G.adjacency_matrix()  # long time
++            sage: G.adjacency_matrix()  # long time # random
+             [0 1 1 0 0 1]
+             [1 0 1 0 1 0]
+             [1 1 0 1 0 0]
+             [0 0 1 0 1 1]
+             [0 1 0 1 0 1]
+             [1 0 0 1 1 0]
++            sage: Graph(polytopes.simplex(2).prism().adjacency_matrix()).is_isomorphic(G) # long time
++            True
+ 
+         To display the graph without any edge labels::
+ 
+diff --git a/src/sage/schemes/elliptic_curves/isogeny_small_degree.py b/src/sage/schemes/elliptic_curves/isogeny_small_degree.py
+index 11bb61c9f21..f5657f2cf19 100644
+--- a/src/sage/schemes/elliptic_curves/isogeny_small_degree.py
++++ b/src/sage/schemes/elliptic_curves/isogeny_small_degree.py
+@@ -1205,17 +1205,8 @@ def isogenies_13_0(E, minimal_models=True):
+         sage: K.<a> = NumberField(f)
+         sage: E = EllipticCurve(j=K(0)); E.ainvs()
+         (0, 0, 0, 0, 1)
+-        sage: [phi.codomain().ainvs() for phi in isogenies_13_0(E)]  # long time (4s)
+-        [(0,
+-          0,
+-          20360599/165164973653422080*a^11 - 3643073/41291243413355520*a^10 + 1887439/1146978983704320*a^9 + 5557619461/573489491852160*a^8 - 82824971/11947697746920*a^7 + 1030632647/7965131831280*a^6 - 475752603733/29409717530880*a^5 + 87205112531/7352429382720*a^4 - 43618899433/204234149520*a^3 + 5858744881/12764634345*a^2 - 1858703809/2836585410*a + 2535050171/1418292705,
+-          -139861295/2650795873449984*a^11 - 3455957/5664093746688*a^10 - 345310571/50976843720192*a^9 - 500530795/118001953056*a^8 - 12860048113/265504394376*a^7 - 25007420461/44250732396*a^6 + 458134176455/1416023436672*a^5 + 16701880631/9077073312*a^4 + 155941666417/9077073312*a^3 + 3499310115/378211388*a^2 - 736774863/94552847*a - 21954102381/94552847,
+-          8342795944891/198197968384106496*a^11 + 8908625263589/20645621706677760*a^10 + 53130542636623/6881873902225920*a^9 + 376780111042213/114697898370432*a^8 + 614884052146333/15930263662560*a^7 + 3566768133324359/7965131831280*a^6 - 1885593809102545/35291661037056*a^5 - 2443732172026523/3676214691360*a^4 - 9525729503937541/1225404897120*a^3 + 51990274442321/40846829904*a^2 + 67834019370596/4254878115*a + 267603083706812/1418292705),
+-         (0,
+-          0,
+-          20360599/165164973653422080*a^11 - 3643073/41291243413355520*a^10 + 1887439/1146978983704320*a^9 + 5557619461/573489491852160*a^8 - 82824971/11947697746920*a^7 + 1030632647/7965131831280*a^6 - 475752603733/29409717530880*a^5 + 87205112531/7352429382720*a^4 - 43618899433/204234149520*a^3 + 5858744881/12764634345*a^2 - 1858703809/2836585410*a + 2535050171/1418292705,
+-          -6465569317/1325397936724992*a^11 - 112132307/1960647835392*a^10 - 17075412917/25488421860096*a^9 - 207832519229/531008788752*a^8 - 1218275067617/265504394376*a^7 - 9513766502551/177002929584*a^6 + 4297077855437/708011718336*a^5 + 354485975837/4538536656*a^4 + 4199379308059/4538536656*a^3 - 30841577919/189105694*a^2 - 181916484042/94552847*a - 2135779171614/94552847,
+-          -1316873026840277/34172063514501120*a^11 - 18637401045099413/41291243413355520*a^10 - 36382234917217247/6881873902225920*a^9 - 61142238484016213/19775499719040*a^8 - 576888119306045123/15930263662560*a^7 - 3378443313906256321/7965131831280*a^6 + 326466167429333279/6084769144320*a^5 + 4620083325391594991/7352429382720*a^4 + 9018783894167184149/1225404897120*a^3 - 9206015742300283/7042556880*a^2 - 65141531411426446/4254878115*a - 254321286054666133/1418292705)]
++        sage: len([phi.codomain().ainvs() for phi in isogenies_13_0(E)])  # long time (4s)
++        2
+     """
+     if E.j_invariant()!=0:
+         raise ValueError("j-invariant must be 0.")
+-- 
+2.39.1
+
+
+From c7654e85a763eb42e4c547c4a4627112b850f8c2 Mon Sep 17 00:00:00 2001
+From: Dima Pasechnik <dima@pasechnik.info>
+Date: Fri, 20 Jan 2023 14:12:05 +0000
+Subject: [PATCH 5/5] rename the gen, and do basic tests on the found generator
+
+---
+ .../schemes/elliptic_curves/ell_number_field.py     | 13 ++++++++++---
+ 1 file changed, 10 insertions(+), 3 deletions(-)
+
+diff --git a/src/sage/schemes/elliptic_curves/ell_number_field.py b/src/sage/schemes/elliptic_curves/ell_number_field.py
+index 656ccbf86bc..b9787c1fd6b 100644
+--- a/src/sage/schemes/elliptic_curves/ell_number_field.py
++++ b/src/sage/schemes/elliptic_curves/ell_number_field.py
+@@ -2290,15 +2290,22 @@ class EllipticCurve_number_field(EllipticCurve_field):
+         It can happen that no points are found if the height bounds
+         used in the search are too small (see :trac:`10745`)::
+ 
+-            sage: K.<y> = NumberField(x^4 + x^2 - 7)
+-            sage: E = EllipticCurve(K, [1, 0, 5*y^2 + 16, 0, 0])
++            sage: K.<t> = NumberField(x^4 + x^2 - 7)
++            sage: E = EllipticCurve(K, [1, 0, 5*t^2 + 16, 0, 0])
+             sage: E.gens(lim1=1, lim3=1)
+             []
+             sage: E.rank()
+             1
+-            sage: E.gens(lim3=13)  # long time (about 4s)
++            sage: gg=E.gens(lim3=13); gg  # long time (about 4s)
+             [(... : 1)]
+ 
++        Check that the the point found has infinite order, and that it is on the curve::
++
++            sage: P=gg[0]; P.order()  # long time
++            +Infinity
++            sage: E.defining_polynomial()(*P)  # long time
++            0
++
+         Here is a curve of rank 2::
+ 
+             sage: K.<t> = NumberField(x^2-17)
+-- 
+2.39.1
+
diff --git a/srcpkgs/sagemath/patches/trac-34816-numpy_1.24.patch b/srcpkgs/sagemath/patches/trac-34816-numpy_1.24.patch
new file mode 100644
index 000000000000..5fbab81ebcde
--- /dev/null
+++ b/srcpkgs/sagemath/patches/trac-34816-numpy_1.24.patch
@@ -0,0 +1,76 @@
+commit 1f22dea27235eeb7dd74cab2cee60cffa55fff2a
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Wed Jan 4 22:16:32 2023 -0300
+
+    complex_plot: fix plot of undefined values
+    
+    Undefined values would get some random color.
+    Rreplace all undefined values by white.
+    
+    In numpy 1.24 this avoids a runtime warning (cast of nan to uint8).
+
+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
+ 
+ 
+
+commit c57458d245f9e24c0283d72d5b97ace0ff011fd6
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Wed Jan 4 20:25:15 2023 -0300
+
+    doctest: fixes for numpy 1.24
+
+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/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 @@ class Histogram(GraphicPrimitive):
+ 
+         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 @@ class SageMagics(Magics):
+             ....: 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)
diff --git a/srcpkgs/sagemath/patches/trac-34926-fix_tests_with_giac_1.9.0.35-3c98c3c9be2ca04e799fa6baf4ad09f21ed6eb91.patch b/srcpkgs/sagemath/patches/trac-34926-fix_tests_with_giac_1.9.0.35-3c98c3c9be2ca04e799fa6baf4ad09f21ed6eb91.patch
new file mode 100644
index 000000000000..7b072e2ba18e
--- /dev/null
+++ b/srcpkgs/sagemath/patches/trac-34926-fix_tests_with_giac_1.9.0.35-3c98c3c9be2ca04e799fa6baf4ad09f21ed6eb91.patch
@@ -0,0 +1,65 @@
+From f28961e88271c6685f9d7e4697f36affe3bbe65c Mon Sep 17 00:00:00 2001
+From: Antonio Rojas <arojas@archlinux.org>
+Date: Fri, 20 Jan 2023 21:36:27 +0100
+Subject: 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 4e451db..ccad516 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 e9dbc0f..b8896a9 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')
+-- 
+cgit v1.0-1-gd88e
+
diff --git a/srcpkgs/sagemath/patches/zz-fix_edge_case_of_integer_check.patch b/srcpkgs/sagemath/patches/zz-fix_edge_case_of_integer_check.patch
new file mode 100644
index 000000000000..384d73283a2e
--- /dev/null
+++ b/srcpkgs/sagemath/patches/zz-fix_edge_case_of_integer_check.patch
@@ -0,0 +1,38 @@
+commit d95ccbdc02a63124bd5dd2743a2356c6f873c5b4
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Wed Jan 4 20:21:51 2023 -0300
+
+    sage.arith.long: fix edge case of integer_check_py
+
+diff --git a/src/sage/arith/long.pxd b/src/sage/arith/long.pxd
+index 1c9a53387a0..16d13512f68 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))
+@@ -310,6 +321,9 @@ 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)
++    if BITS_IN_LONG < 2 * PyLong_SHIFT:
++        # in this case 3 digit is always overflow
++        lead_3_overflow = 0
+     if size == 0:
+         value[0] = 0
+         err[0] = 0
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 74445c3aa8c1..c5af07ee73a9 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
 version=9.7
-revision=4
+revision=5
 build_wrksrc=pkgs/sagemath-standard
 build_style=python3-module
 _bindir=/usr/lib/sagemath/$version/bin
@@ -31,8 +31,8 @@ short_desc="Open source mathematics software"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-2.0-or-later"
 homepage="http://sagemath.org/"
-distfiles="https://github.com/sagemath/sage/archive/refs/tags/$version.tar.gz"
-checksum=9f26f14aa322e3cf38a71835b12ac34b23026b467f74d54b064c5d025e76fbfd
+distfiles="https://github.com/sagemath/sage-archive-2023-02-01/archive/refs/tags/$version.tar.gz"
+checksum=7c09f0ab84fa44380146cf1305b9c0e8ec7aea86d975259ca264be6798202bde
 
 do_configure() {
 	# git tree needs bootstrapping
diff --git a/srcpkgs/sagemath/update b/srcpkgs/sagemath/update
new file mode 100644
index 000000000000..68be3c5752d0
--- /dev/null
+++ b/srcpkgs/sagemath/update
@@ -0,0 +1,2 @@
+pkgname="sage"
+site="https://mirrors.mit.edu/sage/src/index.html"