Merge branch 'vbraun' for 10.2.beta6

dev-python/cysignals/Manifest

@@ -1 +1,2 @@
 DIST cysignals-1.11.2.tar.gz 99014 BLAKE2B ad292a2873a3c88191c731a9370c8cc58f95a261a76882b9af19cfb2b41500c66d5ef79f0d91e647a0c751be22bb9cace8a472563d58721e641b2a44f07bd3be SHA512 8f02ed2cb9c454e3b4e5cf186ccacb8eeb1dc9e30b1643085c603e0ef41d4ebb91d303188251acb76e0566d924ac00ef134646c92e96f36abfeeaa7a8dd33797
+DIST cysignals-1.11.4.tar.gz 105100 BLAKE2B c21c5cae69332885dd4b9f13d0fbe9ab836466dd699f0d51908d129107ce4922f4076fafa8dce3650983fd69d25182464f9831545a8da3535699d36d198ec6a7 SHA512 b083a62bcca71634cdd21ca6c8d1363e7754ed97d6f2ad0280b0ae97fdf1264be3dc202acf67added4c12a0815420d9641269da1212b83472ea304883d3b85ab

dev-python/cysignals/cysignals-1.11.4.ebuild

@@ -0,0 +1,26 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+DISTUTILS_EXT=1
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="interrupt and signal handling for Cython"
+HOMEPAGE="https://github.com/sagemath/cysignals"
+
+LICENSE="LGPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=sci-mathematics/pari-2.13.0:="
+RDEPEND="${DEPEND}"
+BDEPEND=">=dev-python/cython-0.29.24[${PYTHON_USEDEP}]"
+
+python_test(){
+	PATH="${BUILD_DIR}/scripts:${PATH}" "${EPYTHON}" -B "${S}"/rundoctests.py "${S}"/src/cysignals/*.pyx
+}

dev-python/jupyter-threejs-sage/jupyter-threejs-sage-122.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
 DISTUTILS_USE_PEP517=setuptools
 
 inherit distutils-r1 pypi

dev-python/memory_allocator/memory_allocator-0.1.3.ebuild

@@ -3,8 +3,9 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
 DISTUTILS_USE_PEP517=setuptools
+DISTUTILS_EXT=1
 inherit distutils-r1 pypi
 
 DESCRIPTION="An extension class for memory aalocation in cython"

dev-python/primecountpy/primecountpy-0.1.0.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
 DISTUTILS_USE_PEP517=setuptools
 DISTUTILS_EXT=1
 inherit distutils-r1 pypi

sci-mathematics/knot_floer_homology/knot_floer_homology-1.1.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
 DISTUTILS_USE_PEP517=setuptools
 DISTUTILS_EXT=1
 
@@ -22,3 +22,7 @@ KEYWORDS="~amd64 ~x86"
 BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
 
 S="${WORKDIR}/${P}_as_released"
+
+python_test() {
+	"${EPYTHON}" -m knot_floer_homology.test
+}

sci-mathematics/plink/plink-2.4.1.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
 DISTUTILS_USE_PEP517=setuptools
 
 inherit distutils-r1 pypi

sci-mathematics/sage-conf/files/sage-conf-10.2.patch

@@ -0,0 +1,34 @@
+diff --git a/setup.cfg b/setup.cfg
+index 8946cbf..60f5245 100644
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -13,8 +13,6 @@ packages =
+ 	_sage_conf
+ py_modules = 
+ 	sage_conf
+-scripts = 
+-	bin/sage-env-config
+
+ [options.entry_points]
+ console_scripts = 
+diff --git a/setup.py b/setup.py
+index 16686a8..bfb1cbd 100644
+--- a/setup.py
++++ b/setup.py
+@@ -108,7 +108,6 @@ class build_py(setuptools_build_py):
+ class build_scripts(distutils_build_scripts):
+
+     def run(self):
+-        self.distribution.scripts.append(os.path.join('bin', 'sage-env-config'))
+         if not self.distribution.entry_points:
+             self.entry_points = self.distribution.entry_points = dict()
+         distutils_build_scripts.run(self)
+@@ -123,7 +122,6 @@ class editable_wheel(setuptools_editable_wheel):
+
+
+ setup(
+-    cmdclass=dict(build_py=build_py,
+-                  build_scripts=build_scripts,
++    cmdclass=dict(build_scripts=build_scripts,
+                   editable_wheel=editable_wheel)
+ )

sci-mathematics/sage-conf/files/sage-conf.py-10.2

@@ -0,0 +1,33 @@
+r"""
+Sage variables definitions for Gentoo
+"""
+VERSION      = "@SAGE_VERSION@"
+
+SAGE_SHARE   = "@GENTOO_PORTAGE_EPREFIX@/usr/share/sage"
+SAGE_DOC     = "@GENTOO_PORTAGE_EPREFIX@/usr/share/doc/@GENTOO_PORTAGE_PF@"
+
+GAP_LIB_DIR  = "@GENTOO_PORTAGE_EPREFIX@/usr/@libdir@/gap"
+GAP_SHARE_DIR= "@GENTOO_PORTAGE_EPREFIX@/usr/share/gap"
+THEBE_DIR    = "@GENTOO_PORTAGE_EPREFIX@/usr/share/thebe"
+JMOL_DIR     = "@GENTOO_PORTAGE_EPREFIX@/usr/share/sage-jmol-bin/lib"
+MATHJAX_DIR  = "@GENTOO_PORTAGE_EPREFIX@/usr/share/mathjax"
+MTXLIB       = "@GENTOO_PORTAGE_EPREFIX@/usr/share/meataxe"
+SINGULARPATH = "@GENTOO_PORTAGE_EPREFIX@/usr/share/singular"
+PPLPY_DOCS   = "@GENTOO_PORTAGE_EPREFIX@/usr/share/doc/@PPLY_DOC_VERS@/html"
+THREEJS_DIR  = "@GENTOO_PORTAGE_EPREFIX@/usr/share/sage/threejs"
+
+LIE_INFO_DIR = "@GENTOO_PORTAGE_EPREFIX@/usr/share/lie"
+
+MAXIMA       = "maxima -l ecl"
+
+# Names or paths of the 4ti2 executables
+FOURTITWO_HILBERT = "hilbert"
+FOURTITWO_MARKOV = "markov"
+FOURTITWO_GRAVER = "graver"
+FOURTITWO_ZSOLVE = "zsolve"
+FOURTITWO_QSOLVE = "qsolve"
+FOURTITWO_RAYS = "rays"
+FOURTITWO_PPI = "ppi"
+FOURTITWO_CIRCUITS = "circuits"
+FOURTITWO_GROEBNER = "groebner"
+

sci-mathematics/sage-conf/sage-conf-9999.ebuild

@@ -28,11 +28,12 @@ SLOT="0"
 RESTRICT="test mirror"
 
 # pplpy needs to be installed to get documentation folder right :(
-DEPEND="~dev-python/pplpy-0.8.7:=[doc,${PYTHON_USEDEP}]"
+DEPEND=""
 RDEPEND=""
+BDEPEND="dev-python/pplpy[doc,${PYTHON_USEDEP}]"
 
 PATCHES=(
-	"${FILESDIR}/${PN}-9.7.patch"
+	"${FILESDIR}/${PN}-10.2.patch"
 )
 
 python_prepare_all() {
@@ -43,7 +44,7 @@ python_prepare_all() {
 	distutils-r1_python_prepare_all
 
 	# sage on gentoo environment variables
-	cp -f "${FILESDIR}"/${PN}.py-9.8 _sage_conf/_conf.py
+	cp -f "${FILESDIR}"/${PN}.py-10.2 _sage_conf/_conf.py
 	eprefixify _sage_conf/_conf.py
 	# set the documentation location to the externally provided sage-doc package
 	sed -i "s:@GENTOO_PORTAGE_PF@:sage-doc-${PV}:" _sage_conf/_conf.py
@@ -53,4 +54,7 @@ python_prepare_all() {
 	local pplpyver=$(best_version dev-python/pplpy)
 	# using pplpyver from character 11 to remove "dev-python/"
 	sed -i "s:@PPLY_DOC_VERS@:${pplpyver:11}:" _sage_conf/_conf.py
+	# Set sage version as stated in VERSION.txt
+	local sage_version=$(cat VERSION.txt)
+	sed -i "s:@SAGE_VERSION@:${sage_version}:" _sage_conf/_conf.py
 }

sci-mathematics/sage-data-combinatorial_designs/sage-data-combinatorial_designs-20140630.ebuild

@@ -1,7 +1,7 @@
 # Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 MY_PN="combinatorial_designs"
 MY_P="${MY_PN}-$(ver_rs 1 '.')"

sci-mathematics/sage-data-conway_polynomials/sage-data-conway_polynomials-0.5.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
 
 inherit python-any-r1
 

sci-mathematics/sage-data-elliptic_curves/sage-data-elliptic_curves-0.8.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
 PYTHON_REQ_USE="sqlite"
 
 inherit python-any-r1

sci-mathematics/sage_setup/sage_setup-9999.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
 PYTHON_REQ_USE="readline,sqlite"
 DISTUTILS_USE_PEP517=setuptools