Merge branch 'vbraun' for sage 10.3

profiles/updates/1Q-2024

@@ -4,3 +4,4 @@ move dev-gap/Alnuth dev-gap/alnuth
 move dev-gap/AutoDoc dev-gap/autodoc
 move dev-gap/HAPcryst dev-gap/hapcryst
 move dev-gap/MapClass dev-gap/mapclass
+move sci-mathematics/sage sci-mathematics/sagemath-standard

sci-mathematics/database_knotinfo/Manifest

@@ -1,2 +1 @@
-DIST database_knotinfo-2023.6.1.tar.gz 5833881 BLAKE2B e1e9d1fb104a7791276918fda17febf4b6fa72bbd5eb716c034e673e96ea6d588e3e6a2bedf0ab1029b950a7dc696e45c13e1c6a779c12af7dd85fdeaaf03063 SHA512 8fdd4c87184b0643b6bf5194c5e00ac16dde848fd14886f9144622234689d8aa2eb8bdd94e39e3341366cf8c9360bf0872d554d2fcb6b375ff2d97b21993d338
 DIST database_knotinfo-2024.2.1.tar.gz 14057457 BLAKE2B b9bdf6b3280177491fb2291aa22f9a1885d87af8b913d59b206d210d96c1f477bf5e0d307c09a6aa3e47d92409e0de2838cbfe8e120589f75073302e0abbd06a SHA512 9258527bcd66298e83b597cecbf616cc0548829e3d3da9c1d2d54d6f57fa7296f92a1e7e85cc3a4f8da763c14c25238e212b8bcad50a91d91c1a8a7acfdede97

sci-mathematics/database_knotinfo/database_knotinfo-2024.2.1.ebuild

@@ -16,6 +16,6 @@ IUSE="test"
 LICENSE="GPL-3"
 SLOT="0"
 
-DEPEND="test? ( >=sci-mathematics/sage-10.3 )"
+DEPEND="test? ( >=sci-mathematics/sagemath-standard-10.3 )"
 
 RESTRICT="!test? ( test )"

sci-mathematics/pGroupCohomology/pGroupCohomology-3.3.2.ebuild

@@ -18,7 +18,7 @@ LICENSE="GPL-2+"
 SLOT="0"
 KEYWORDS="~amd64"
 
-DEPEND=">=sci-mathematics/sage-9.3[meataxe,${PYTHON_USEDEP}]
+DEPEND=">=sci-mathematics/sagemath-standard-9.3[meataxe,${PYTHON_USEDEP}]
 	sci-mathematics/shared_meataxe
 	sci-mathematics/modular_resolution"
 RDEPEND="${DEPEND}

sci-mathematics/sage-conf/Manifest

@@ -1 +1 @@
-DIST sage-conf-10.2.tar.gz 2998959 BLAKE2B ca16168f905c9b42f4f5de3b13e102166db9d4969e67da3dbe26bcfdf100afb8a3e01414947e0eb1e47a2a3ec03b9579e398f2f6d8aa934648adc901e19ba9b4 SHA512 c73c01b24e9a1ed31dd72e0fbb35887d4aa63a86ee9279350762062d353e5e721857daa862ae4a8d67d2efd5af1ed0f2fbe17c83ce3800d20596016aa45308e4
+DIST sage-conf-10.3.tar.gz 3007359 BLAKE2B f24bebc326f400f5ca2c2af2b4391ac4203b34f34255ce53d2fd241d3c6c6c27dc788c16bfeb57ab51e5a43c390e9196cefb6690bde9d5e713c9490d7d7dca3d SHA512 231f7a308cfea6b15a275d8499a2b65b335a13aa7f7cd33cd2c00c3676a7abc158d24d06b045cf5738253487cb212b316545eedf6edbe86d6231d14d695370f5

sci-mathematics/sage-conf/sage-conf-10.2.ebuild → sci-mathematics/sage-conf/sage-conf-10.3.ebuild

@@ -11,7 +11,7 @@ inherit distutils-r1 prefix
 
 if [[ ${PV} == 9999 ]]; then
 	inherit git-r3 sage-git
-	EGIT_REPO_URI="https://github.com/sagemath/sage.git"
+	SAGE_PKG="${PN}_pypi"
 else
 	PYPI_NO_NORMALIZE=1
 	inherit pypi
@@ -35,14 +35,10 @@ PATCHES=(
 )
 
 python_prepare_all() {
-	if [[ ${PV} == 9999 ]]; then
-		sage-git_src_prepare "${PN}_pypi"
-	fi
-
 	distutils-r1_python_prepare_all
 
 	# sage on gentoo environment variables
-	cp -f "${FILESDIR}"/${PN}.py-10.2 _sage_conf/_conf.py
+	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

sci-mathematics/sage-doc/Manifest

@@ -1 +1 @@
-DIST sage-doc-10.2.tar.gz 29368872 BLAKE2B 2e8dbde8438b6e801c3b78bc680e95bfdef9cdf63a4468117fe6b71e05e33e1044c60daf11d66559ad7d77f02a7589a66c5513b7bd5d268399b5060ae33a9ff9 SHA512 b9eec42aaab22dc28585472ecec16306d10219654930867baf1a15ca490037f9bc87c640bdfbb7a269c48d361e57f80d25d3ed132588612ade02786f527ca06d
+DIST sage-doc-10.3.tar.gz 29748722 BLAKE2B bf41813b795738c2fea16176364f70445e9b6327a8647a459dfc5c9b54116cf0b6805bf1664b21f785af4e5698a3e418ae62d946f591b9e6674da857a41c5501 SHA512 b43a052aa7fe2d9b18dafd4ec452f0e6deb3aceafa5d29562282d985dfc89385f1ab29a553975b254456c2744b5c46a9b31deb0707fc92bd1b19daf3b82f8580

sci-mathematics/sage-doc/sage-doc-10.2.ebuild → sci-mathematics/sage-doc/sage-doc-10.3.ebuild

@@ -6,11 +6,11 @@ EAPI=8
 PYTHON_COMPAT=( python3_{10..12} )
 PYTHON_REQ_USE="readline,sqlite"
 
-inherit python-any-r1
+inherit multiprocessing python-any-r1
 
 if [[ ${PV} == 9999 ]]; then
 	inherit git-r3
-	EGIT_REPO_URI="https://github.com/vbraun/sage.git"
+	EGIT_REPO_URI="https://github.com/sagemath/sage.git"
 	EGIT_BRANCH=develop
 	EGIT_CHECKOUT_DIR="${WORKDIR}/${P}"
 else
@@ -35,17 +35,24 @@ L10N_USEDEP="${L10N_USEDEP%?}"
 
 RESTRICT="mirror test"
 
-# cannot use $PV in python_gen_any_deps :(
-# This section to checked on release for sage/sage_docbuild versions
-BDEPEND="$(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}]
-	~sci-mathematics/sage-10.2[${PYTHON_USEDEP},jmol]
-	~sci-mathematics/sage_docbuild-10.2[${PYTHON_USEDEP}]
-	')
-	doc-pdf? ( app-text/texlive[extra,${L10N_USEDEP}] )"
+# 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[extra,luatex,${L10N_USEDEP}]
+		app-text/texlive-core[xindy]
+		media-fonts/freefont
+	)
+"
 RDEPEND="dev-libs/mathjax"
 DEPEND="dev-libs/mathjax"
 
@@ -60,18 +67,15 @@ DOCS=(
 	"${S}/src/doc/common"
 )
 
-# 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"
-
 # python_check_deps happilly processes $PV.
 python_check_deps() {
 	python_has_version -b "dev-python/sphinx[${PYTHON_USEDEP}]" &&
-	python_has_version -b "~sci-mathematics/sage-${PV}[${PYTHON_USEDEP},jmol]" &&
+	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[${PYTHON_USEDEP}]"
+	python_has_version -b "dev-python/sphinx-copybutton[${PYTHON_USEDEP}]" &&
+	python_has_version -b "dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]"
 }
 
 src_unpack(){
@@ -101,6 +105,8 @@ src_configure(){
 	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="${T}"/matplotlib
 	# Avoid spurious message from the gtk backend by making sure it is never tried
@@ -118,6 +124,16 @@ src_compile(){
 	# Needs to be created beforehand or it gets created as a file with the content of _static/plot_directive.css
 	mkdir -p "${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" )

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

@@ -44,7 +44,7 @@ BDEPEND="$(python_gen_any_dep "
 	dev-python/jupyter-sphinx[\${PYTHON_USEDEP}]
 	dev-python/sphinx-copybutton[\${PYTHON_USEDEP}]
 	dev-python/sphinx-inline-tabs[\${PYTHON_USEDEP}]
-	~sci-mathematics/sage-${PV}[\${PYTHON_USEDEP},jmol]
+	~sci-mathematics/sagemath-standard-${PV}[\${PYTHON_USEDEP},jmol]
 	~sci-mathematics/sage_docbuild-${PV}[\${PYTHON_USEDEP}]
 	")
 	doc-pdf? (
@@ -70,7 +70,7 @@ DOCS=(
 # python_check_deps happilly processes $PV.
 python_check_deps() {
 	python_has_version -b "dev-python/sphinx[${PYTHON_USEDEP}]" &&
-	python_has_version -b "~sci-mathematics/sage-${PV}[${PYTHON_USEDEP},jmol]" &&
+	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}]" &&

sci-mathematics/sage-flatsurf/sage-flatsurf-0.4.6.ebuild

@@ -15,7 +15,7 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64"
 
-DEPEND=">=sci-mathematics/sage-9.7[${PYTHON_USEDEP}]
+DEPEND=">=sci-mathematics/sagemath-standard-9.7[${PYTHON_USEDEP}]
 	sci-mathematics/surface-dynamics[${PYTHON_USEDEP}]"
 RDEPEND="${DEPEND}"
 

sci-mathematics/sage-sws2rst/Manifest

@@ -0,0 +1 @@
+DIST sage-sws2rst-10.3.tar.gz 327244 BLAKE2B 16261c6a6393aeda64a4588031ef5719b58664fc81a5a199d3a407ce359760e3cee43a10a159dff7ee25842257503428d9676809747a31beed0127904ced9b5b SHA512 88ccc41ad3bef2c9a4aed0b4afd26e717c741cb92f3be0d0caec00f6826db3096b01e485923fc00015d1ca484a702df04da41361cc4d40c9eb26fa28c28e03ed

sci-mathematics/sage-sws2rst/sage-sws2rst-10.3.ebuild

@@ -0,0 +1,33 @@
+# 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
+
+SAGE_PKG="sage-sws2rst"
+MY_P="${SAGE_PKG}-${PV}"
+
+if [[ ${PV} == 9999 ]]; then
+	inherit git-r3 sage-git
+else
+	inherit pypi
+	SRC_URI="$(pypi_sdist_url --no-normalize "${SAGE_PKG}")"
+	KEYWORDS="~amd64 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos"
+	S="${WORKDIR}/${MY_P}"
+fi
+
+DESCRIPTION="SageNB worksheet converter"
+HOMEPAGE="https://www.sagemath.org"
+
+LICENSE="GPL-2"
+SLOT="0"
+
+RESTRICT="mirror test"
+
+DEPEND="dev-python/beautifulsoup4[${PYTHON_USEDEP}]"
+RDEPEND="${DEPEND}"