[PR PATCH] python3-scipy: update to 1.15.0.

[PR PATCH] python3-scipy: update to 1.15.0.

[tornaria]

[-- Attachment #1: Type: text/plain, Size: 1334 bytes --]

There is a new pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages scipy
https://github.com/void-linux/void-packages/pull/53863

python3-scipy: update to 1.15.0.
- **python3-scipy: update to 1.15.0.**
- **sagemath: patch doctests for scipy-1.15**

<!-- Uncomment relevant sections and delete options which are not applicable -->

#### Testing the changes
- I tested the changes in this PR: **briefly** (tested with sagemath)

<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->

<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
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and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
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<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
  - aarch64-musl
  - armv7l
  - armv6l-musl
-->


A patch file from https://github.com/void-linux/void-packages/pull/53863.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-scipy-53863.patch --]
[-- Type: text/x-diff, Size: 7274 bytes --]

From c9e1c341577c46d92ac82b38401dfe835480c9f0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Fri, 3 Jan 2025 19:25:26 -0300
Subject: [PATCH 1/2] python3-scipy: update to 1.15.0.

---
 .../python3-scipy/patches/test-32bit.patch    | 24 +++++++++++++++++++
 srcpkgs/python3-scipy/template                |  6 ++---
 2 files changed, 27 insertions(+), 3 deletions(-)
 create mode 100644 srcpkgs/python3-scipy/patches/test-32bit.patch

diff --git a/srcpkgs/python3-scipy/patches/test-32bit.patch b/srcpkgs/python3-scipy/patches/test-32bit.patch
new file mode 100644
index 00000000000000..99b145962fe4be
--- /dev/null
+++ b/srcpkgs/python3-scipy/patches/test-32bit.patch
@@ -0,0 +1,24 @@
+diff -ru a/scipy/special/tests/test_data.py b/scipy/special/tests/test_data.py
+--- a/scipy/special/tests/test_data.py  2025-01-02 19:53:29.000000000 -0300
++++ b/scipy/special/tests/test_data.py  2025-01-05 16:03:47.063791703 -0300
+@@ -591,7 +591,7 @@
+         data(elliprg, 'ellint_rg_xyy_ipp-ellint_rg_xyy', (0, 1, 2), 3,
+              rtol=7.5e-16),
+         data(elliprg, 'ellint_rg_xy0_ipp-ellint_rg_xy0', (0, 1, 2), 3,
+-             rtol=5e-16),
++             rtol=6e-15),
+         data(elliprg, 'ellint_rg_00x_ipp-ellint_rg_00x', (0, 1, 2), 3,
+              rtol=5e-16),
+         data(elliprj, 'ellint_rj_data_ipp-ellint_rj_data', (0, 1, 2, 3), 4,
+diff -ru a/scipy/special/tests/test_hyp2f1.py b/scipy/special/tests/test_hyp2f1.py
+--- a/scipy/special/tests/test_hyp2f1.py        2025-01-02 19:53:29.000000000 -0300
++++ b/scipy/special/tests/test_hyp2f1.py        2025-01-05 15:59:52.380864607 -0300
+@@ -1135,7 +1135,7 @@
+                     c=8.5,
+                     z=(0.7368421052631575+0.5263157894736841j),
+                     expected=(6.468457061368628+24.190040684917374j),
+-                    rtol=5e-16,
++                    rtol=5e-14,
+                 ),
+             ),
+             pytest.param(
diff --git a/srcpkgs/python3-scipy/template b/srcpkgs/python3-scipy/template
index 61ec0f8fa66d1f..107f0470558217 100644
--- a/srcpkgs/python3-scipy/template
+++ b/srcpkgs/python3-scipy/template
@@ -1,7 +1,7 @@
 # Template file for 'python3-scipy'
 pkgname=python3-scipy
-version=1.14.1
-revision=2
+version=1.15.0
+revision=1
 build_style=python3-pep517
 build_helper="meson numpy"
 # SciPy imposes strict and unnecessary restrictions on build dependencies
@@ -21,7 +21,7 @@ license="BSD-3-Clause"
 homepage="https://scipy.org/"
 changelog="https://github.com/scipy/scipy/releases"
 distfiles="${PYPI_SITE}/s/scipy/scipy-${version}.tar.gz"
-checksum=5a275584e726026a5699459aa72f828a610821006228e841b94275c4a7c08417
+checksum=300742e2cc94e36a2880ebe464a1c8b4352a7b0f3e36ec3d2ac006cdbe0219ac
 # must be tested from site dir of installed version (see dev.py:739)
 make_check_pre='eval env -C "${testdir}/${py3_sitelib}"'
 

From ea5ea6cd97040938bd4ca56316d077db86b211e9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Fri, 3 Jan 2025 19:26:17 -0300
Subject: [PATCH 2/2] sagemath: patch doctests for scipy-1.15

---
 .../sagemath/patches/39261-scipy_1.15.patch   | 36 +++++++++++++++++++
 srcpkgs/sagemath/patches/get_patches          |  1 +
 2 files changed, 37 insertions(+)
 create mode 100644 srcpkgs/sagemath/patches/39261-scipy_1.15.patch

diff --git a/srcpkgs/sagemath/patches/39261-scipy_1.15.patch b/srcpkgs/sagemath/patches/39261-scipy_1.15.patch
new file mode 100644
index 00000000000000..02ad169c0703c9
--- /dev/null
+++ b/srcpkgs/sagemath/patches/39261-scipy_1.15.patch
@@ -0,0 +1,36 @@
+diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
+index 308171af3cd..f511190aeff 100644
+--- a/src/sage/functions/special.py
++++ b/src/sage/functions/special.py
+@@ -216,11 +216,16 @@ 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
++        sage: import scipy.version
++        sage: if scipy.version.version < '1.15.0':
++        ....:     from scipy.special import sph_harm # NB: arguments x and y are swapped   # needs scipy
++        ....:     sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                   # needs scipy sage.symbolic
++        ....: else:
++        ....:     from scipy.special import sph_harm_y                                  # needs scipy
++        ....:     sph_harm_y(1, 1, (pi/2).n(), pi.n()).item()  # abs tol 1e-9           # needs scipy sage.symbolic
+         (0.3454941494713355-4.231083042742082e-17j)
+ 
+     Note that this convention differs from the one in Maxima, as revealed by
+diff --git a/src/sage/matrix/matrix2.pyx b/src/sage/matrix/matrix2.pyx
+index dec25a76e54..31aaf8b8234 100644
+--- a/src/sage/matrix/matrix2.pyx
++++ b/src/sage/matrix/matrix2.pyx
+@@ -15901,7 +15901,7 @@ cdef class Matrix(Matrix1):
+             sage: a.exp()                                                               # needs sage.symbolic
+             [ 1/11882424341266*((11*sqrt(227345670387496707609) + 5941212170633)*e^(3/1275529100*sqrt(227345670387496707609)) - 11*sqrt(227345670387496707609) + 5941212170633)*e^(-3/2551058200*sqrt(227345670387496707609) + 101/200)                            445243650/75781890129165569203*(sqrt(227345670387496707609)*e^(3/1275529100*sqrt(227345670387496707609)) - sqrt(227345670387496707609))*e^(-3/2551058200*sqrt(227345670387496707609) + 101/200)]
+             [                                     10000/53470909535697*(sqrt(227345670387496707609)*e^(3/1275529100*sqrt(227345670387496707609)) - sqrt(227345670387496707609))*e^(-3/2551058200*sqrt(227345670387496707609) + 101/200) -1/11882424341266*((11*sqrt(227345670387496707609) - 5941212170633)*e^(3/1275529100*sqrt(227345670387496707609)) - 11*sqrt(227345670387496707609) - 5941212170633)*e^(-3/2551058200*sqrt(227345670387496707609) + 101/200)]
+-            sage: a.change_ring(RDF).exp()  # rel tol 6e-14                             # needs sage.symbolic
++            sage: a.change_ring(RDF).exp()  # rel tol 1e-13                             # needs sage.symbolic
+             [42748127.31532951 7368259.244159399]
+             [234538976.1381042 40426191.45156228]
+ 
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 97bf36df52e4df..571d8939163695 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -41,6 +41,7 @@ get_pr 39201 "python 3.13 fix spyx_tmp"
 get_pr 38749 "pari 2.17"
 get_pr 38962 "eclib 20241112"
 get_pr 39178 "giac 1.9.0.998"
+get_pr 39261 "scipy 1.15"
 
 get_pr 38940 "fix flaky simplicial set test"
 

Re: [PR PATCH] [Updated] python3-scipy: update to 1.15.0.

[tornaria]

[-- Attachment #1: Type: text/plain, Size: 1339 bytes --]

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

https://github.com/tornaria/void-packages scipy
https://github.com/void-linux/void-packages/pull/53863

python3-scipy: update to 1.15.0.
- **python3-scipy: update to 1.15.0.**
- **sagemath: patch doctests for scipy-1.15**

<!-- Uncomment relevant sections and delete options which are not applicable -->

#### Testing the changes
- I tested the changes in this PR: **briefly** (tested with sagemath)

<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->

<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
  - aarch64-musl
  - armv7l
  - armv6l-musl
-->


A patch file from https://github.com/void-linux/void-packages/pull/53863.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-scipy-53863.patch --]
[-- Type: text/x-diff, Size: 9639 bytes --]

From be2a637f242cf4a4b50db5678ce63fda9c5af7bc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Fri, 3 Jan 2025 19:25:26 -0300
Subject: [PATCH 1/2] python3-scipy: update to 1.15.0.

---
 .../python3-scipy/patches/test-32bit.patch    | 73 +++++++++++++++++++
 srcpkgs/python3-scipy/template                |  6 +-
 2 files changed, 76 insertions(+), 3 deletions(-)
 create mode 100644 srcpkgs/python3-scipy/patches/test-32bit.patch

diff --git a/srcpkgs/python3-scipy/patches/test-32bit.patch b/srcpkgs/python3-scipy/patches/test-32bit.patch
new file mode 100644
index 00000000000000..26db514a083a94
--- /dev/null
+++ b/srcpkgs/python3-scipy/patches/test-32bit.patch
@@ -0,0 +1,73 @@
+diff -ru a/scipy/linalg/tests/test_decomp.py b/scipy/linalg/tests/test_decomp.py
+--- a/scipy/linalg/tests/test_decomp.py	2025-01-02 19:53:29.000000000 -0300
++++ b/scipy/linalg/tests/test_decomp.py	2025-01-05 22:08:01.177300618 -0300
+@@ -1185,6 +1185,7 @@
+ # Allocating an array of such a size leads to _ArrayMemoryError(s)
+ # since the maximum memory that can be in 32-bit (WASM) is 4GB
+ @pytest.mark.skipif(IS_WASM, reason="out of memory in WASM")
++@pytest.mark.xfail_on_32bit("out of memory in 32 bit")
+ @pytest.mark.fail_slow(10)
+ def test_svd_gesdd_nofegfault():
+     # svd(a) with {U,VT}.size > INT_MAX does not segfault
+diff -ru a/scipy/special/tests/test_data.py b/scipy/special/tests/test_data.py
+--- a/scipy/special/tests/test_data.py	2025-01-02 19:53:29.000000000 -0300
++++ b/scipy/special/tests/test_data.py	2025-01-05 18:43:38.713539218 -0300
+@@ -591,7 +591,7 @@
+         data(elliprg, 'ellint_rg_xyy_ipp-ellint_rg_xyy', (0, 1, 2), 3,
+              rtol=7.5e-16),
+         data(elliprg, 'ellint_rg_xy0_ipp-ellint_rg_xy0', (0, 1, 2), 3,
+-             rtol=5e-16),
++             rtol=6e-15),
+         data(elliprg, 'ellint_rg_00x_ipp-ellint_rg_00x', (0, 1, 2), 3,
+              rtol=5e-16),
+         data(elliprj, 'ellint_rj_data_ipp-ellint_rj_data', (0, 1, 2, 3), 4,
+diff -ru a/scipy/special/tests/test_hyp2f1.py b/scipy/special/tests/test_hyp2f1.py
+--- a/scipy/special/tests/test_hyp2f1.py	2025-01-02 19:53:29.000000000 -0300
++++ b/scipy/special/tests/test_hyp2f1.py	2025-01-05 18:43:38.714539233 -0300
+@@ -1135,7 +1135,7 @@
+                     c=8.5,
+                     z=(0.7368421052631575+0.5263157894736841j),
+                     expected=(6.468457061368628+24.190040684917374j),
+-                    rtol=5e-16,
++                    rtol=5e-14,
+                 ),
+             ),
+             pytest.param(
+diff -ru a/scipy/stats/tests/test_distributions.py b/scipy/stats/tests/test_distributions.py
+--- a/scipy/stats/tests/test_distributions.py	2025-01-02 19:53:29.000000000 -0300
++++ b/scipy/stats/tests/test_distributions.py	2025-01-06 21:23:10.351597184 -0300
+@@ -5750,7 +5750,7 @@
+ 
+         # some tests break on linux 32 bit
+         uname = platform.uname()
+-        is_linux_32 = uname.system == 'Linux' and uname.machine == 'i686'
++        is_linux_32 = uname.system == 'Linux' and "32bit" in platform.architecture()[0]
+         platform_desc = "/".join(
+             [uname.system, uname.machine, uname.processor])
+ 
+@@ -5843,6 +5843,7 @@
+                     np.isin(r['pct'], pct_range) &
+                     np.isin(r['alpha'], alpha_range) &
+                     np.isin(r['beta'], beta_range) &
++                    (not is_linux_32 or r['alpha'] != 1.5) &
+                     (r['alpha'] > 0.2) &
+                     (r['alpha'] != 1.)
+                 )
+@@ -5860,7 +5861,7 @@
+             ],
+             # for small alpha very slightly reduced accuracy
+             [
+-                'piecewise', 2.5e-10, lambda r: (
++                'piecewise', 1e-8, lambda r: (
+                     np.isin(r['pct'], pct_range) &
+                     np.isin(r['alpha'], alpha_range) &
+                     np.isin(r['beta'], beta_range) &
+@@ -5965,7 +5966,7 @@
+         tests = [
+             # piecewise generally good accuracy
+             [
+-                'piecewise', 2e-12, lambda r: (
++                'piecewise', 2e-10, lambda r: (
+                     np.isin(r['pct'], pct_range) &
+                     np.isin(r['alpha'], alpha_range) &
+                     np.isin(r['beta'], beta_range) &
diff --git a/srcpkgs/python3-scipy/template b/srcpkgs/python3-scipy/template
index 61ec0f8fa66d1f..107f0470558217 100644
--- a/srcpkgs/python3-scipy/template
+++ b/srcpkgs/python3-scipy/template
@@ -1,7 +1,7 @@
 # Template file for 'python3-scipy'
 pkgname=python3-scipy
-version=1.14.1
-revision=2
+version=1.15.0
+revision=1
 build_style=python3-pep517
 build_helper="meson numpy"
 # SciPy imposes strict and unnecessary restrictions on build dependencies
@@ -21,7 +21,7 @@ license="BSD-3-Clause"
 homepage="https://scipy.org/"
 changelog="https://github.com/scipy/scipy/releases"
 distfiles="${PYPI_SITE}/s/scipy/scipy-${version}.tar.gz"
-checksum=5a275584e726026a5699459aa72f828a610821006228e841b94275c4a7c08417
+checksum=300742e2cc94e36a2880ebe464a1c8b4352a7b0f3e36ec3d2ac006cdbe0219ac
 # must be tested from site dir of installed version (see dev.py:739)
 make_check_pre='eval env -C "${testdir}/${py3_sitelib}"'
 

From 2bada5d47912fc84f2f92a0ae0ccc7e57d189447 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Fri, 3 Jan 2025 19:26:17 -0300
Subject: [PATCH 2/2] sagemath: patch doctests for scipy-1.15

---
 .../sagemath/patches/39261-scipy_1.15.patch   | 36 +++++++++++++++++++
 srcpkgs/sagemath/patches/get_patches          |  1 +
 2 files changed, 37 insertions(+)
 create mode 100644 srcpkgs/sagemath/patches/39261-scipy_1.15.patch

diff --git a/srcpkgs/sagemath/patches/39261-scipy_1.15.patch b/srcpkgs/sagemath/patches/39261-scipy_1.15.patch
new file mode 100644
index 00000000000000..02ad169c0703c9
--- /dev/null
+++ b/srcpkgs/sagemath/patches/39261-scipy_1.15.patch
@@ -0,0 +1,36 @@
+diff --git a/src/sage/functions/special.py b/src/sage/functions/special.py
+index 308171af3cd..f511190aeff 100644
+--- a/src/sage/functions/special.py
++++ b/src/sage/functions/special.py
+@@ -216,11 +216,16 @@ 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
++        sage: import scipy.version
++        sage: if scipy.version.version < '1.15.0':
++        ....:     from scipy.special import sph_harm # NB: arguments x and y are swapped   # needs scipy
++        ....:     sph_harm(1, 1, pi.n(), (pi/2).n())  # abs tol 1e-14                   # needs scipy sage.symbolic
++        ....: else:
++        ....:     from scipy.special import sph_harm_y                                  # needs scipy
++        ....:     sph_harm_y(1, 1, (pi/2).n(), pi.n()).item()  # abs tol 1e-9           # needs scipy sage.symbolic
+         (0.3454941494713355-4.231083042742082e-17j)
+ 
+     Note that this convention differs from the one in Maxima, as revealed by
+diff --git a/src/sage/matrix/matrix2.pyx b/src/sage/matrix/matrix2.pyx
+index dec25a76e54..31aaf8b8234 100644
+--- a/src/sage/matrix/matrix2.pyx
++++ b/src/sage/matrix/matrix2.pyx
+@@ -15901,7 +15901,7 @@ cdef class Matrix(Matrix1):
+             sage: a.exp()                                                               # needs sage.symbolic
+             [ 1/11882424341266*((11*sqrt(227345670387496707609) + 5941212170633)*e^(3/1275529100*sqrt(227345670387496707609)) - 11*sqrt(227345670387496707609) + 5941212170633)*e^(-3/2551058200*sqrt(227345670387496707609) + 101/200)                            445243650/75781890129165569203*(sqrt(227345670387496707609)*e^(3/1275529100*sqrt(227345670387496707609)) - sqrt(227345670387496707609))*e^(-3/2551058200*sqrt(227345670387496707609) + 101/200)]
+             [                                     10000/53470909535697*(sqrt(227345670387496707609)*e^(3/1275529100*sqrt(227345670387496707609)) - sqrt(227345670387496707609))*e^(-3/2551058200*sqrt(227345670387496707609) + 101/200) -1/11882424341266*((11*sqrt(227345670387496707609) - 5941212170633)*e^(3/1275529100*sqrt(227345670387496707609)) - 11*sqrt(227345670387496707609) - 5941212170633)*e^(-3/2551058200*sqrt(227345670387496707609) + 101/200)]
+-            sage: a.change_ring(RDF).exp()  # rel tol 6e-14                             # needs sage.symbolic
++            sage: a.change_ring(RDF).exp()  # rel tol 1e-13                             # needs sage.symbolic
+             [42748127.31532951 7368259.244159399]
+             [234538976.1381042 40426191.45156228]
+ 
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index 97bf36df52e4df..571d8939163695 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -41,6 +41,7 @@ get_pr 39201 "python 3.13 fix spyx_tmp"
 get_pr 38749 "pari 2.17"
 get_pr 38962 "eclib 20241112"
 get_pr 39178 "giac 1.9.0.998"
+get_pr 39261 "scipy 1.15"
 
 get_pr 38940 "fix flaky simplicial set test"
 

Re: python3-scipy: update to 1.15.0.

[tornaria]

[-- Attachment #1: Type: text/plain, Size: 260 bytes --]

New comment by tornaria on void-packages repository

https://github.com/void-linux/void-packages/pull/53863#issuecomment-2574217817

Comment:
@ahesford: now i686 seems to be all fixed, and the x86_64 failure is just some random (unrelated to my fixes afaict).

Re: [PR PATCH] [Merged]: python3-scipy: update to 1.15.0.

[ahesford]

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There's a merged pull request on the void-packages repository

python3-scipy: update to 1.15.0.
https://github.com/void-linux/void-packages/pull/53863

Description:
- **python3-scipy: update to 1.15.0.**
- **sagemath: patch doctests for scipy-1.15**

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- I tested the changes in this PR: **briefly** (tested with sagemath)

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Re: python3-scipy: update to 1.15.0.

[ahesford]

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New comment by ahesford on void-packages repository

https://github.com/void-linux/void-packages/pull/53863#issuecomment-2574272699

Comment:
Thanks!