Merge branch 'vbraun' for 10.5

sci-mathematics/sage-conf/Manifest

@@ -1 +1,2 @@
 DIST sage_conf-10.4.tar.gz 3011621 BLAKE2B 20d5c4e787af278fd9815120035bdcccbb47088a334e35ae875f1fce2faca507eae90e6c38d4d718596d99a2b18226c9aac2817c421b2251a20649b3708f0149 SHA512 eeec9ed9040a406643880c7029a65c6107accc58bd20c5f043f1e0f5ab164a736c4a73bb10af318c8c8f62fb2dab80fe4af9ed461fd8c4c06962ff7ad3276e94
+DIST sage_conf-10.5.tar.gz 2914331 BLAKE2B 9a432da28007420538d60621a179699847859f166fdba7015fcf82aad9b7beb17ddf50128a91df049ed7d632cf66cbc2ccf59dc41c28e1e4ef62ccb535301813 SHA512 0788f13b6200bff6f6c0458a2e7221b83182edb96e81552e510b7088d50f472f1a843951b2f86b3436166eb587f7fd853f90f3493c822d6fa427b9b5de1615c1

sci-mathematics/sage-conf/sage-conf-10.5.ebuild

@@ -0,0 +1,53 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_REQ_USE="readline,sqlite"
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 prefix
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3 sage-git
+	SAGE_PKG="${PN}_pypi"
+else
+	inherit pypi
+	KEYWORDS="~amd64 ~amd64-linux ~ppc-macos ~x64-macos"
+fi
+
+DESCRIPTION="Math software for abstract and numerical computations"
+HOMEPAGE="https://www.sagemath.org"
+
+LICENSE="GPL-2"
+SLOT="0"
+
+# No real tests here in spite of QA warnings.
+RESTRICT="test mirror"
+
+# pplpy needs to be installed to get documentation folder right :(
+BDEPEND="dev-python/pplpy[doc,${PYTHON_USEDEP}]"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-10.2.patch"
+)
+
+python_prepare_all() {
+	distutils-r1_python_prepare_all
+
+	# sage on gentoo environment variables
+	cp -f "${FILESDIR}"/${PN}.py-10.3 _sage_conf/_conf.py
+	eprefixify _sage_conf/_conf.py
+	# set the documentation location to the externally provided sage-doc package
+	sed -i "s:@GENTOO_PORTAGE_PF@:sage-doc-${PV}:" _sage_conf/_conf.py
+	# set lib/lib64 - only useful for GAP_LIB_DIR for now
+	sed -i "s:@libdir@:$(get_libdir):g" _sage_conf/_conf.py
+	# Fix finding pplpy documentation with intersphinx
+	local pplpyver=$(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-doc/Manifest

@@ -1,2 +1,3 @@
 DIST sage-doc-10.4.tar.gz 30684315 BLAKE2B 590e9f3be831547b8a846b281fab6577cfa6b62364c66a7c1c27e23adf8e126860c25851c560f65c5273d4830648964e36178fea49eb79b650c85ca60996419b SHA512 5cc6e7d38f0c901cc5a716ad4e225710e35807a564963832df420b0d80db0864809ce79c2b1b6b0c6dfe1422de51e8caf709c6fe7bdf7512ce525b2fbe85836a
+DIST sage-doc-10.5.tar.gz 30803195 BLAKE2B 630e774104a87423896f130e42c53a8ed764e01c327a3af91b3603c01d3299e6249a86bccce7b95abd00eeffc89e05dd3c61faa3eb4367db94406b518f68a58f SHA512 18959835f001a4c7f201bf544204583459ab26d95b0ef49675c8a91a19b86edf5ffd3df6a2aa244c04a33fdbd36a58726550aceccc8b50e21fbaeabdc7ced655
 DIST sagemath_PR38250.patch 32944 BLAKE2B d7f61864066c168f18075a05e2bea9ab650d571c3ee64bf0751c31582610afcf47ecc534719d5cd3be8677163e55ad3fdcd4cd586ec33abf35467551db57c4d2 SHA512 bce008341646de8a8913a2cb49dad44b31f3ddd72edb6f6f6fd9a3e2e676f955afb1c4f5cd9b4605ee720c150afae24d27837590050c63c2a47c64612fdbef69

sci-mathematics/sage-doc/sage-doc-10.5.ebuild

@@ -0,0 +1,173 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_REQ_USE="readline,sqlite"
+
+inherit multiprocessing python-any-r1
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/sagemath/sage.git"
+	EGIT_BRANCH=develop
+	EGIT_CHECKOUT_DIR="${WORKDIR}/${P}"
+else
+	SRC_URI="https://github.com/sagemath/sage/archive/${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos"
+	S="${WORKDIR}/sage-${PV}"
+fi
+
+DESCRIPTION="Build the sage documentation"
+HOMEPAGE="https://www.sagemath.org"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="doc-pdf"
+L10N_USEDEP="l10n_en,"
+LANGS="ca de es fr hu it ja pt ru tr"
+for X in ${LANGS} ; do
+	IUSE="${IUSE} l10n_${X}"
+	L10N_USEDEP="${L10N_USEDEP}l10n_${X}?,"
+done
+L10N_USEDEP="${L10N_USEDEP%?}"
+
+RESTRICT="mirror test"
+
+# There is a trick to use $PV in python_gen_any_deps
+# But it breaks checking with pkgcheck, reports of "missing check for ... "
+# may be safely ignored most of the time.
+BDEPEND="$(python_gen_any_dep "
+	dev-python/sphinx[\${PYTHON_USEDEP}]
+	dev-python/furo[\${PYTHON_USEDEP}]
+	dev-python/jupyter-sphinx[\${PYTHON_USEDEP}]
+	dev-python/sphinx-copybutton[\${PYTHON_USEDEP}]
+	dev-python/sphinx-inline-tabs[\${PYTHON_USEDEP}]
+	~sci-mathematics/sagemath-standard-${PV}[\${PYTHON_USEDEP},jmol]
+	~sci-mathematics/sage_docbuild-${PV}[\${PYTHON_USEDEP}]
+	")
+	doc-pdf? (
+		>=app-text/texlive-2023[extra,luatex,${L10N_USEDEP}]
+		>=app-text/texlive-core-2023[xindy]
+		media-fonts/freefont
+	)
+"
+RDEPEND="dev-libs/mathjax"
+DEPEND="dev-libs/mathjax"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-10.4-makefile.patch
+)
+
+HTML_DOCS="${WORKDIR}/build_doc/html/*"
+DOCS=(
+	"${WORKDIR}/build_doc/index.html"
+	"${S}/src/doc/common"
+)
+
+# python_check_deps happilly processes $PV.
+python_check_deps() {
+	python_has_version -b "dev-python/sphinx[${PYTHON_USEDEP}]" &&
+	python_has_version -b "~sci-mathematics/sagemath-standard-${PV}[${PYTHON_USEDEP},jmol]" &&
+	python_has_version -b "~sci-mathematics/sage_docbuild-${PV}[${PYTHON_USEDEP}]" &&
+	python_has_version -b "dev-python/furo[${PYTHON_USEDEP}]" &&
+	python_has_version -b "dev-python/jupyter-sphinx[${PYTHON_USEDEP}]" &&
+	python_has_version -b "dev-python/sphinx-copybutton[${PYTHON_USEDEP}]" &&
+	python_has_version -b "dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]"
+}
+
+src_unpack(){
+	if [[ ${PV} == 9999 ]]; then
+		git-r3_src_unpack
+	fi
+
+	default
+}
+
+src_prepare(){
+	default
+
+	einfo "bootstrapping the documentation - be patient"
+	SAGE_ROOT="${S}" PATH="${S}/build/bin:${PATH}" src/doc/bootstrap || die "cannot bootstrap the documentation"
+
+	# remove all the sources outside of src/doc to avoid interferences
+	for object in src/* ; do
+		if [ $object != "src/doc" ] ; then
+			rm -rf $object || die "failed to remove $object"
+		fi
+	done
+}
+
+src_configure(){
+	export SAGE_DOC="${WORKDIR}"/build_doc
+	export SAGE_DOC_SRC="${S}"/src/doc
+	export SAGE_DOC_MATHJAX=yes
+	export VARTEXFONTS="${T}"/fonts
+	export SAGE_NUM_THREADS=$(makeopts_jobs)
+	export SAGE_NUM_THREADS_PARALLEL=$(makeopts_jobs)
+	# try to fix random sphinx crash during the building of the documentation
+	export MPLCONFIGDIR="${T}"/matplotlib
+	# Avoid spurious message from the gtk backend by making sure it is never tried
+	export MPLBACKEND=Agg
+	local mylang="en "
+	for lang in ${LANGS} ; do
+		use l10n_$lang && mylang+="$lang "
+	done
+	export LANGUAGES="${mylang}"
+}
+
+src_compile(){
+	cd src/doc
+
+	# Needs to be created beforehand or it gets created as a file with the content of _static/plot_directive.css
+	mkdir -p "${SAGE_DOC}"/html/en/reference/_static
+
+	# for some reason luatex check whether it can write there.
+	# Of course it should fail, but it triggers the sandbox.
+	addpredict /var/lib/texmf/m_t_x_t_e_s_t.tmp
+	# for some reason opened for write during inventory of reference/plotting(?) - no write happens.
+	# This manifest as root
+	addpredict "${ESYSROOT}/usr/share/sage/cremona/cremona_mini.db"
+	# For some reason java/jmol ignores HOME and uses portage's home as home directory
+	# Nothing seem to happen though
+	addpredict "${ESYSROOT}/var/lib/portage/home/.java"
+
+	emake doc-html
+	if use doc-pdf ; then
+		DOCS+=( "${SAGE_DOC}/pdf" )
+		emake doc-pdf
+	fi
+}
+
+src_install(){
+	####################################
+	# Prepare the documentation for installation
+	####################################
+
+	pushd "${WORKDIR}"
+	# Prune _static folders
+	cp -r build_doc/html/en/_static build_doc/html/ || die "failed to copy _static folder"
+	for sdir in `find build_doc -name _static` ; do
+		if [ $sdir != "build_doc/html/_static" ] ; then
+			rm -rf $sdir || die "failed to remove $sdir"
+			ln -rst ${sdir%_static} build_doc/html/_static
+		fi
+	done
+	# Linking to local copy of mathjax folders rather than copying them
+	for sobject in $(ls "${ESYSROOT}"/usr/share/mathjax/) ; do
+		rm -rf build_doc/html/_static/${sobject} \
+			|| die "failed to remove mathjax object $sobject"
+		ln -st build_doc/html/_static/ ../../../../mathjax/$sobject
+	done
+	# prune .buildinfo files, those are internal to sphinx and are not used after building.
+	find build_doc -name .buildinfo -delete || die "failed to prune buildinfo files"
+	# prune the jupyter_execute folder created by jupyter-sphinx
+	rm -rf build_doc/html/en/reference/jupyter_execute
+	popd
+
+	docompress -x /usr/share/doc/"${PF}"/common
+	einstalldocs
+
+	dosym -r /usr/share/doc/"${PF}" /usr/share/jupyter/kernels/sagemath/doc
+}

sci-mathematics/sage-sws2rst/Manifest

@@ -1 +1,2 @@
 DIST sage_sws2rst-10.4.tar.gz 327256 BLAKE2B b5e74fa50fbee8e0f66177c0cab3657576605f8844ebc4b2fdb68c5e349a140dd9982318ca94e2433f2593f8fa88c08a9e381d16f93467b28c26e1fe4c0c3847 SHA512 d418c20e2dc84828e0b6d5499399bbf98c723583fab61878ba9cbcd663b40c5319a4e61246040bcd2ba76b092871340f826768fd8df77e0651eee6acf923b308
+DIST sage_sws2rst-10.5.tar.gz 327246 BLAKE2B 4198b764030b2722c6ee8d3dd96ece3c09a50ac74a3a61ae920df77919d2c4e05f35477af30a66b0b0fd41dcfafb0595ffb54cd646568b229b0da7b8707c0856 SHA512 8816a771e6a74f9667b055e16bbdceb695de91beb93101b0a941e005993f57c3de7f3fd10b810049e4f33302ace38da5e154fb55f7e4acc43ea304825c080e66

sci-mathematics/sage-sws2rst/sage-sws2rst-10.5.ebuild

@@ -0,0 +1,28 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_REQ_USE="readline,sqlite"
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3 sage-git
+else
+	inherit pypi
+	KEYWORDS="~amd64 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos"
+fi
+
+DESCRIPTION="SageNB worksheet converter"
+HOMEPAGE="https://www.sagemath.org"
+
+LICENSE="GPL-2"
+SLOT="0"
+
+RESTRICT="mirror test"
+
+DEPEND="dev-python/beautifulsoup4[${PYTHON_USEDEP}]"
+RDEPEND="${DEPEND}"

sci-mathematics/sage_docbuild/Manifest

@@ -1,4 +1,5 @@
 DIST sage_docbuild-10.4.tar.gz 73094 BLAKE2B ee7813a17670aa278ee5d03942c0a01a58d73fb03c10f76176b0845f6d6297dde56d87876f0d0858f50ad838264fd9de94579c7cf071af9786fb6b7f576b2326 SHA512 634cbbd014333b80fa850227474884b1e7d4226c07d108e0081300fab4f523d483e8449a031fa55f363622beb2fe9413336ddbaddda19fad8b368f2bc6505188
+DIST sage_docbuild-10.5.tar.gz 73781 BLAKE2B ecc071e9186f69c9a347b3e26ac3d372d1aaccdd9945c22189e63c12188ec4f9252ecb15f72b3626bf906f229860a991c4ceda1e886d49bbdad78ce794a9d891 SHA512 683c4f74bc02e51c55d576b890c5ad86d977fc6794e0f7680f7cdcdd8025887e5f0a4fd4e47319914724a903885ff444717b32a76267230c987ce4c7b2edfb96
 DIST sagemath_PR38549.patch 27158 BLAKE2B 3425125a30f265f8ed1c8c3edfab7278348116c743880d79d11d294d1d5c846e32ddafdada4b32f3c329c91716a7785fa07d68e2412e9ef3dd1f452ea4153278 SHA512 31f96449cd0547f6d97a1069c612fb321d8fd557a6638777f1c450dd5e6faf74bcbae322785961593883733d5b2fe829738f5f3a4c2ce35b64697ec862411915
 DIST sagemath_PR38619.patch 12559 BLAKE2B 74fbdf0ee5ab6e484aaff0583ba061ac67081902424185a72e20944dbac1b65ab52b6661e2caa06e876b127292d4cd0bfccac30c1cc9a00e3b3aa1fbaf891a3d SHA512 5048fe34da72c78ecd1d651728e6a6feff9a13c8dbe77661e81c2cdd8304e6bdaf8b05e4c1fa13693f37a0c8f6a9900c31b429800f77b4b5c482aea102761ba5
 DIST sagemath_PR38957.patch 11708 BLAKE2B 82f76ce208aee093278862049bbce15c7380257be4d28040e61cd396facb4952ae49711fe4be5f725ea85b6cc1d91d0728a9414f4d5908ae9bd083c4fc7f40d8 SHA512 c1873a8502a455ca2ce9437611ef6aab3fd9a18c2acd67cef3181b8b0db4e2f11d281b48848db8b252134cdf1e256d4df14c664ea95c54044a2203a7a828430a

sci-mathematics/sage_docbuild/sage_docbuild-10.5.ebuild

@@ -0,0 +1,35 @@
+# 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
+
+inherit distutils-r1
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3 sage-git
+	SAGE_PKG="sage-docbuild"
+else
+	inherit pypi
+	KEYWORDS="~amd64 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos"
+fi
+
+DESCRIPTION="Tool to build doc for sage and sage related packages"
+HOMEPAGE="https://www.sagemath.org"
+
+LICENSE="GPL-2"
+SLOT="0"
+
+RESTRICT="mirror test"
+
+RDEPEND="
+	>=dev-python/sphinx-7.4.7[${PYTHON_USEDEP}]
+	dev-python/jupyter-sphinx[${PYTHON_USEDEP}]
+"
+PDEPEND="~sci-mathematics/sagemath-standard-${PV}[${PYTHON_USEDEP}]"
+
+PATCHES=(
+	"${FILESDIR}"/sage-9.3-linguas.patch
+)

sci-mathematics/sage_setup/Manifest

@@ -1 +1,2 @@
 DIST sage_setup-10.4.tar.gz 80656 BLAKE2B 7b4ebf5a26b03daa884e772b5ba89cf53a0e01530327c07fe004765f50dcb121ae08a51666fff83a3431595c673b70610fa07978b390654314e6376edfd67958 SHA512 f12ea54f07beb0471896197f233c5acca5bc73931c14d59df39b44bc4fab134baa976ea05296987c6f4c2dd2ec78e87007b04cd1bdc66e306f1bfcdc94b33777
+DIST sage_setup-10.5.tar.gz 81500 BLAKE2B dc57c75906f8b174a40129a0981d12c819d5844425548e326dd59ea4fd572da1c984d0dafb2cd41beab185bec53e36990f995540ac834630dd49fc0961bdaae1 SHA512 8597e641777a2ea0ba7ec64087ba2ad00bd650a317619baf28e737d77de6bbc0fd4151cf7d713c1ce2f6f7cca4751727dc87bbd39bfd8a37604e2ee32309c16c

sci-mathematics/sage_setup/sage_setup-10.5.ebuild

@@ -0,0 +1,39 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_REQ_USE="readline,sqlite"
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3 sage-git
+	SAGE_PKG="sage-setup"
+else
+	inherit pypi
+	KEYWORDS="~amd64 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos"
+fi
+
+DESCRIPTION="Tool to help install sage and sage related packages"
+HOMEPAGE="https://www.sagemath.org"
+
+LICENSE="GPL-2"
+SLOT="0"
+
+RESTRICT="mirror test"
+
+DEPEND="
+	>=dev-python/pkgconfig-1.2.2[${PYTHON_USEDEP}]
+"
+RDEPEND="
+	${DEPEND}
+	>=dev-python/cython-3.0.0[${PYTHON_USEDEP}]
+	dev-python/jinja2[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-9.6-verbosity.patch
+)

sci-mathematics/sagemath-bliss/Manifest

@@ -1 +1,2 @@
 DIST sagemath_bliss-10.4.tar.gz 11740 BLAKE2B dc76a4e61467a534c6ab63effbea4f3b68897e0ad5e16c5aa366ecd9f8c0051df962fc677e5b07fcf3dbb3ac5b0dd8d11e55cc4d7f4e99c785968cd9b3c6f70b SHA512 95bf22896eb8bda79c1b2f23e3144e523df40495a256524ea62ce7a06c988c6755f59cb03725225f6cd03180f5b97976e4e824c1de8290771a5f4da9ef261db3
+DIST sagemath_bliss-10.5.tar.gz 11890 BLAKE2B 7ac4a6ceaa25cb6ffdec7c2b83f3742e7f55d9449d48e562efe4e302973813f8af41a30358cd58919889f16e20cd19d6e16fbabf392e28ef3fbac945950b5c13 SHA512 2e9d499ba1f3b5ff0167a157e77117075a12e2ddb83d49b29dad9ccce6e987c35113bf9c9610beb5a6ebeb867ae75f487b17755cdb0ca6f07632373f627c9647

sci-mathematics/sagemath-bliss/sagemath-bliss-10.5.ebuild

@@ -0,0 +1,37 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_REQ_USE="readline,sqlite"
+DISTUTILS_EXT=1
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3 sage-git
+else
+	inherit pypi
+	KEYWORDS="~amd64 ~amd64-linux ~ppc-macos ~x64-macos"
+fi
+
+DESCRIPTION="Graph (iso/auto)morphisms with bliss in sage"
+HOMEPAGE="https://www.sagemath.org"
+
+LICENSE="GPL-2+"
+SLOT="0"
+
+RESTRICT="test"
+
+DEPEND="~sci-mathematics/sagemath-standard-${PV}[${PYTHON_USEDEP}]
+	~sci-libs/bliss-0.77"
+RDEPEND="${DEPEND}"
+BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+
+python_install() {
+	distutils-r1_python_install
+
+	find "${D}$(python_get_sitedir)/sage" -name interpreter -delete
+}

sci-mathematics/sagemath-meataxe/Manifest

@@ -1 +1,2 @@
 DIST sagemath_meataxe-10.4.tar.gz 22498 BLAKE2B f48fe6f9e2dda5ff538c15df0c098f7c679cb1494ec193fb727a1d05be86122c57c9754772a16113fd6606946530d10a01aeefbbef5338241b304df89bb2f61a SHA512 2b92410fcb9b48c111684004966a8589845908ea6e531f9f190d6a6d754e0a777a0382e994f1c3eb033c8168dcf87676088812e22ef9b64b6508882a455bc629
+DIST sagemath_meataxe-10.5.tar.gz 22658 BLAKE2B 2cc53f49a88dd29335129174940a4cebae892201eadc642bcd4de49a2adb24e66cc81424ad876f9360f183542d46c746ccfc3a09d43289352bdc9552253d4c4b SHA512 e5dcc17ebc78cfef3b296e1955be21b663ebe4a04d4a02a2fb48827619fef0fac3d2b741d3bae43710ac7e2d4b24141f63f4d01deeaaa734d43e2340eb97eac3