[PR PATCH] https://github.com/tornaria/void-packages/pull/new/scipy

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

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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/48317

https://github.com/tornaria/void-packages/pull/new/scipy
<!-- Uncomment relevant sections and delete options which are not applicable -->

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

I enabled tests for scipy let's see if CI can manage or we have to disable in CI (we only run "not slow" tests for -Q).

Updated sagemath since it needs a patch for scipy 1.12 (https://github.com/sagemath/sage/pull/37123). Took the chance to apply a few minor fixes that didn't justify an update on their own.

@ahesford I'll be done with testing in a couple days at most, in principle everything looks good.

BTW: I run scipy tests with `export SCIPY_XSLOW=1` and `-m xslow` which gave me one failure:
```
FAILED scipy/sparse/linalg/tests/test_onenormest.py::TestOnenormest::test_onenormest_table_6_t_1
====== 1 failed, 321 passed, 40 skipped, 15 xfailed in 9042.78s (2:30:42) ======
```

Running check normally gave me:
```
== 45224 passed, 2467 skipped, 149 xfailed, 12 xpassed in 3836.63s (1:03:56) ===
```
(with `-m "not slow"`) and
```
== 59100 passed, 2501 skipped, 259 xfailed, 14 xpassed in 5444.99s (1:30:44) ===
```

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A patch file from https://github.com/void-linux/void-packages/pull/48317.patch is attached

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[-- Attachment #2: github-pr-scipy-48317.patch --]
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From 33657b9465a62615ae6b389c7d39d8270f41cbd7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 22 Jan 2024 00:30:44 -0300
Subject: [PATCH 1/2] python3-scipy: update to 1.12.0.

---
 srcpkgs/python3-scipy/patches/19909.patch     | 40 +++++++++++++++++++
 .../python3-scipy/patches/dep-versions.patch  | 23 -----------
 srcpkgs/python3-scipy/template                | 13 ++++--
 3 files changed, 50 insertions(+), 26 deletions(-)
 create mode 100644 srcpkgs/python3-scipy/patches/19909.patch
 delete mode 100644 srcpkgs/python3-scipy/patches/dep-versions.patch

diff --git a/srcpkgs/python3-scipy/patches/19909.patch b/srcpkgs/python3-scipy/patches/19909.patch
new file mode 100644
index 0000000000000..b861d2b96c33c
--- /dev/null
+++ b/srcpkgs/python3-scipy/patches/19909.patch
@@ -0,0 +1,40 @@
+See: https://github.com/scipy/scipy/pull/19909
+
+From 8c96a1f742335bca283aae418763aaba62c03378 Mon Sep 17 00:00:00 2001
+From: Ilhan Polat <ilhanpolat@gmail.com>
+Date: Thu, 18 Jan 2024 14:47:42 +0100
+Subject: [PATCH] MAINT:linalg:Adjust lwork/liwork changes OpenBLAS 0.3.26
+
+See https://github.com/Reference-LAPACK/lapack/pull/942
+---
+ scipy/linalg/flapack_sym_herm.pyf.src | 10 +++++-----
+ 1 file changed, 5 insertions(+), 5 deletions(-)
+
+diff --git a/scipy/linalg/flapack_sym_herm.pyf.src b/scipy/linalg/flapack_sym_herm.pyf.src
+index f07dbaecbc72..af04e0d8d8d8 100644
+--- a/scipy/linalg/flapack_sym_herm.pyf.src
++++ b/scipy/linalg/flapack_sym_herm.pyf.src
+@@ -762,8 +762,8 @@ subroutine <prefix2>syevr(compute_v,range,lower,n,a,lda,vl,vu,il,iu,abstol,w,z,m
+     <ftype2> optional,intent(in) :: vl=0.0
+     <ftype2> optional,intent(in),check(vu>=vl),depend(vl) :: vu=1.0
+     <ftype2> intent(in) :: abstol=0.0
+-    integer optional,intent(in),depend(n),check(lwork>=max(1,26*n)||lwork==-1) :: lwork=max(26*n,1)
+-    integer optional,intent(in),depend(n),check(liwork>=max(1,10*n)||liwork==-1):: liwork= max(1,10*n)
++    integer optional,intent(in),depend(n),check(lwork>=(n <= 1 ? 1 : max(1,26*n))||lwork==-1) :: lwork=max(26*n,1)
++    integer optional,intent(in),depend(n),check(liwork>=(n <= 1 ? 1 : max(1,10*n))||liwork==-1):: liwork= max(1,10*n)
+ 
+     integer intent(hide),depend(a) :: n=shape(a,0)
+     integer intent(hide),depend(n) :: lda=max(1,n)
+@@ -832,9 +832,9 @@ subroutine <prefix2c>heevr(compute_v,range,lower,n,a,lda,vl,vu,il,iu,abstol,w,z,
+     <ftype2> optional,intent(in) :: vl=0.0
+     <ftype2> optional,intent(in),check(vu>vl),depend(vl) :: vu=1.0
+     <ftype2> intent(in) :: abstol=0.0
+-    integer optional,intent(in),depend(n),check(lwork>=max(2*n,1)||lwork==-1) :: lwork=max(2*n,1)
+-    integer optional,intent(in),depend(n),check(lrwork>=max(24*n,1)||lrwork==-1) :: lrwork=max(24*n,1)
+-    integer optional,intent(in),depend(n),check(liwork>=max(1,10*n)||liwork==-1):: liwork= max(1,10*n)
++    integer optional,intent(in),depend(n),check(lwork>=(n <= 1 ? 1 : max(1,2*n))||lwork==-1) :: lwork=max(2*n,1)
++    integer optional,intent(in),depend(n),check(lrwork>=(n <= 1 ? 1 : max(1,24*n))||lrwork==-1) :: lrwork=max(24*n,1)
++    integer optional,intent(in),depend(n),check(liwork>=(n <= 1 ? 1 : max(1,10*n))||liwork==-1):: liwork= max(1,10*n)
+ 
+     integer intent(hide),depend(a) :: n=shape(a,0)
+     integer intent(hide),depend(n) :: lda=max(1,n)
diff --git a/srcpkgs/python3-scipy/patches/dep-versions.patch b/srcpkgs/python3-scipy/patches/dep-versions.patch
deleted file mode 100644
index ac62f0b7fb069..0000000000000
--- a/srcpkgs/python3-scipy/patches/dep-versions.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-Several dependencies have needlessly restrictive version requirements, which
-causes build failures against more up-to-date Void packages.
-
---- a/pyproject.toml
-+++ b/pyproject.toml
-@@ -11,13 +11,13 @@
- build-backend = 'mesonpy'
- requires = [
-     # Reason for `<`: future-proofing (0.14.0 released and known to work)
--    "meson-python>=0.12.1,<0.15.0",
-+    "meson-python>=0.12.1",
-     # Reason for `<`: we want to build the 1.11.x releases with 0.29.x (too many changes in 3.0)
--    "Cython>=0.29.35,<3.0",   # when updating version, also update check in meson.build
-+    "Cython>=0.29.35",
-     # Reason for `<`: future-proofing (2.11.1 is the most recent version)
--    "pybind11>=2.10.4,<2.11.1",
-+    "pybind11>=2.10.4",
-     # Reason for `<`: future-proofing (0.14.0 released and known to work)
--    "pythran>=0.12.0,<0.15.0",
-+    "pythran>=0.12.0",
- 
-     # NumPy dependencies - to update these, sync from
-     # https://github.com/scipy/oldest-supported-numpy/, and then
diff --git a/srcpkgs/python3-scipy/template b/srcpkgs/python3-scipy/template
index 88128aaa3a3bb..3915ca79f5f0e 100644
--- a/srcpkgs/python3-scipy/template
+++ b/srcpkgs/python3-scipy/template
@@ -1,6 +1,6 @@
 # Template file for 'python3-scipy'
 pkgname=python3-scipy
-version=1.11.4
+version=1.12.0
 revision=1
 build_style=python3-pep517
 build_helper="meson numpy"
@@ -12,13 +12,16 @@ hostmakedepends="python3-meson-python python3-Cython python3-pybind11
 makedepends="python3-devel python3-pybind11 python3-numpy pythran
  $(vopt_if openblas openblas-devel "lapack-devel cblas-devel")"
 depends="python3-numpy"
+checkdepends="python3-pytest python3-pytest-xdist python3-hypothesis python3-pooch
+ python3-matplotlib python3-mpmath python3-psutil python3-sympy"
 short_desc="Scientific library for Python3"
 maintainer="Andrew J. Hesford <ajh@sideband.org>"
 license="BSD-3-Clause"
 homepage="https://scipy.org/"
 distfiles="${PYPI_SITE}/s/scipy/scipy-${version}.tar.gz"
-checksum=90a2b78e7f5733b9de748f589f09225013685f9b218275257f8a8168ededaeaa
-make_check="no" # Tests need an installed copy to run and meson makes this tough
+checksum=4bf5abab8a36d20193c698b0f1fc282c1d083c94723902c447e5d2f1780936a3
+# must be tested from site dir of installed version (see dev.py:739)
+make_check_pre='eval env -C "${testdir}/${py3_sitelib}"'
 
 build_options="openblas"
 
@@ -37,6 +40,10 @@ if [ "$build_option_openblas" ]; then
 	esac
 fi
 
+if [ "$XBPS_CHECK_PKGS" != full ]; then
+	make_check_args="-m 'not slow'"
+fi
+
 post_install() {
 	vlicense LICENSE.txt
 }

From cd2f090ba8b51d57a80bd5287ce535d93c1d7ef1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 22 Jan 2024 00:34:32 -0300
Subject: [PATCH 2/2] sagemath: patch for scipy 1.12.

See: https://github.com/sagemath/sage/pull/37123

Also apply a few minor fixes.
---
 srcpkgs/sagemath/files/sage_conf.py           |  1 +
 .../patches/36862-giac_1.9.0-73.patch         | 15 +++++++++++
 .../sagemath/patches/37123-scipy_1.12.patch   | 26 +++++++++++++++++++
 srcpkgs/sagemath/patches/get_patches          |  7 ++++-
 srcpkgs/sagemath/template                     |  8 +++---
 5 files changed, 52 insertions(+), 5 deletions(-)
 create mode 100644 srcpkgs/sagemath/patches/36862-giac_1.9.0-73.patch
 create mode 100644 srcpkgs/sagemath/patches/37123-scipy_1.12.patch

diff --git a/srcpkgs/sagemath/files/sage_conf.py b/srcpkgs/sagemath/files/sage_conf.py
index bc5388de8956d..b5b2360311844 100644
--- a/srcpkgs/sagemath/files/sage_conf.py
+++ b/srcpkgs/sagemath/files/sage_conf.py
@@ -1,3 +1,4 @@
 # configuration for sage on void linux
 SAGE_SHARE = "/usr/share/sagemath"
 GAP_SHARE_DIR = "/usr/share/gap"
+JMOL_DIR = "/usr/share/jmol"
diff --git a/srcpkgs/sagemath/patches/36862-giac_1.9.0-73.patch b/srcpkgs/sagemath/patches/36862-giac_1.9.0-73.patch
new file mode 100644
index 0000000000000..8eb2c20a34c52
--- /dev/null
+++ b/srcpkgs/sagemath/patches/36862-giac_1.9.0-73.patch
@@ -0,0 +1,15 @@
+diff --git a/src/sage/calculus/calculus.py b/src/sage/calculus/calculus.py
+index dfaafb4353f..8d62ade24c8 100644
+--- a/src/sage/calculus/calculus.py
++++ b/src/sage/calculus/calculus.py
+@@ -568,8 +568,8 @@ def symbolic_sum(expression, v, a, b, algorithm='maxima', hold=False):
+ 
+     An example of this summation with Giac::
+ 
+-        sage: symbolic_sum(1/(1+k^2), k, -oo, oo, algorithm='giac')
+-        (pi*e^(2*pi) - pi*e^(-2*pi))/(e^(2*pi) + e^(-2*pi) - 2)
++        sage: symbolic_sum(1/(1+k^2), k, -oo, oo, algorithm='giac').factor()
++        pi*(e^(2*pi) + 1)/((e^pi + 1)*(e^pi - 1))
+ 
+     The same summation is solved by SymPy::
+ 
diff --git a/srcpkgs/sagemath/patches/37123-scipy_1.12.patch b/srcpkgs/sagemath/patches/37123-scipy_1.12.patch
new file mode 100644
index 0000000000000..3973b55cdbd51
--- /dev/null
+++ b/srcpkgs/sagemath/patches/37123-scipy_1.12.patch
@@ -0,0 +1,26 @@
+diff --git a/src/sage/matrix/matrix_double_dense.pyx b/src/sage/matrix/matrix_double_dense.pyx
+index 5d19067f2ed..97e50fb2616 100644
+--- a/src/sage/matrix/matrix_double_dense.pyx
++++ b/src/sage/matrix/matrix_double_dense.pyx
+@@ -867,7 +867,7 @@ cdef class Matrix_double_dense(Matrix_numpy_dense):
+         # set cutoff as RDF element
+         if eps == 'auto':
+             if scipy is None: import scipy
+-            eps = 2*max(self._nrows, self._ncols)*scipy.finfo(float).eps*sv[0]
++            eps = 2*max(self._nrows, self._ncols)*numpy.finfo(float).eps*sv[0]
+         eps = RDF(eps)
+         # locate non-zero entries
+         rank = 0
+diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
+index 708d440a205..9f973c6bd69 100644
+--- a/src/sage/numerical/optimize.py
++++ b/src/sage/numerical/optimize.py
+@@ -426,7 +426,7 @@ def minimize(func, x0, gradient=None, hessian=None, algorithm="default",
+                 hess = func.hessian()
+                 hess_fast = [ [fast_callable(a, vars=var_names, domain=float) for a in row] for row in hess]
+                 hessian = lambda p: [[a(*p) for a in row] for row in hess_fast]
+-                from scipy import dot
++                from numpy import dot
+                 hessian_p = lambda p,v: dot(numpy.array(hessian(p)),v)
+                 min = optimize.fmin_ncg(f, [float(_) for _ in x0], fprime=gradient,
+                       fhess=hessian, fhess_p=hessian_p, disp=verbose, **args)
diff --git a/srcpkgs/sagemath/patches/get_patches b/srcpkgs/sagemath/patches/get_patches
index a552b402727d3..b7836e27910d5 100755
--- a/srcpkgs/sagemath/patches/get_patches
+++ b/srcpkgs/sagemath/patches/get_patches
@@ -20,6 +20,11 @@ get_pr() {
 # run from patches dir
 cd $(dirname "$0")
 
-# needs review
+# all merged in 10.3.beta6 or before
 get_pr  35848   "flintlib 3.0"
 get_pr  36769   "fix jmol detect"
+get_pr  36862   "giac 1.9.0-73"
+get_pr  37004   "fix save_session when cython changes"
+
+# positive review
+get_pr  37123   "scipy 1.12"
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 5d5bdccd70a25..7bc92e7c10735 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
 version=10.2
-revision=1
+revision=2
 build_wrksrc=pkgs/sagemath-standard
 build_style=python3-module
 _bindir=/usr/lib/sagemath/$version/bin
@@ -15,7 +15,7 @@ makedepends="boost-devel brial-devel cliquer-devel ecl eclib-devel
  mpfr-devel ntl-devel openblas-devel pari-devel planarity-devel python3-cypari2
  python3-cysignals python3-devel python3-gmpy2 python3-memory_allocator
  python3-numpy rankwidth-devel singular symmetrica-devel"
-depends="eclib-devel fflas-ffpack flintlib-devel gcc-fortran gd-devel
+depends="eclib-devel fflas-ffpack flintlib-devel gcc-fortran meson gd-devel
  gfan giac gsl-devel gzip libpng-devel linbox-devel m4ri-devel maxima-ecl
  mpfr-devel nauty ntl-devel palp pari-devel pari-elldata-small pari-galdata
  pari-galpol-small pari-seadata-small pkg-config python3-Cython python3-cypari2
@@ -26,7 +26,7 @@ depends="eclib-devel fflas-ffpack flintlib-devel gcc-fortran gd-devel
  python3-sympy python3-traitlets sage-data-combinatorial_designs
  sage-data-conway_polynomials sage-data-elliptic_curves sage-data-graphs
  sage-data-polytopes_db sympow tachyon threejs-sage"
-checkdepends="$depends pythran python3-Sphinx meson"
+checkdepends="$depends pythran python3-Sphinx"
 short_desc="Open source mathematics software"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-2.0-or-later"
@@ -34,7 +34,7 @@ homepage="https://www.sagemath.org/"
 changelog="https://github.com/sagemath/sage/releases"
 distfiles="https://github.com/sagemath/sage/archive/refs/tags/$version.tar.gz"
 checksum=e7125f13495e1068edab73735aca7f9b2c655688096e9d109e628c023e76411f
-nocross="due to ntl (eclib), fflas-ffpack, givaro, linbox, sympow, maxima"
+nocross="due to ntl (eclib, singular), fflas-ffpack, givaro, linbox, sympow, maxima"
 
 post_patch() {
 	# git tree needs bootstrapping