Cleanup and python 3.13

sci-libs/libsigrok/Manifest

@@ -0,0 +1,6 @@
+AUX libsigrok-0.5.2-py313.patch 1897 BLAKE2B b4221654e1a056e9e2bcf04b79685f231204984eb40e31eecd09d04774956fc6e9fd474c0070255a130dbd67e9b191b013da8fc6568b3673bae759ca7e6d253d SHA512 081674a2d92b4562efadf812b70fece9d9a2373ff31c34e42189ea3ba5a9f49ce10f4bed70a24efdee77834f0a105fa3f54231669ff7ba8216e8761472150fe7
+AUX libsigrok-0.5.2-sipeed-slogic.patch 42177 BLAKE2B e2451273f22091c4c6c550f5ee729e5ae298684de680599bb403e44474d9471c408718403a11a679403a404c45f12fe2aea1be0897ac24fb6433f6610135a954 SHA512 c0fdcb6b39d1e76a928116e8b31cced8b63421f551fd89729f03188da1988b94b6349b35c5d9516faadec4d7ba4071380e0b58608e049e1878250ab294bf0568
+AUX libsigrok-0.5.2-swig-4.1.patch 377 BLAKE2B f795f46bce213e9444ea3d8b362a4d82d3e34676a9aae49f45764679effa388afcc15bc04e14fdc89cb25fbd700ca3bf80234b291c3607b0454ecf997d20997d SHA512 0334cbb95fbba961d9f16b18978dd15dbf68b80b897af54d25660dd0bcb049d21ea681f39bae3884c4869ecce4efd2601bce7825fbd41160ddddbe92ad678740
+DIST libsigrok-f6d0f7a.zip 1761945 BLAKE2B 719965bb29636232ca9cdf8ea61b8365e23a875ba300e75ff1662cb43217df2cb0eb9bac796ae1debc9236e17a7bff575442e0d42f70b22e94bd928e05d3f013 SHA512 b3d59cc60845bfc46c72c7a67145e5e0b9641793d590a0a814f60f22fdb02bf6e9373219c0dca4d1805fd47321b12c6dea4c40a31fc412571b70a37cec267642
+EBUILD libsigrok-0.6.0.ebuild 3506 BLAKE2B 21f395a147c87a9f3c924fc137c773700d211d55dd8500dab3101d1d79fe9469f6d7d7f0b83477da096f28eb6f9394d1d0f141fce1f6a953f7925c73f608b33d SHA512 55a8a11ad36e8d8b04f95e53ad1afc51f2e3d7cf5d71c947d662defca8233f5e740363ea64ae505578344a8bd9252264a2eeef60000d808b21ae96e8d7e01a1d
+MISC metadata.xml 886 BLAKE2B cb7cece1f79a4affb612e55f147eb93895a805e43aed6bbabfed2e3b925b0714d64651c00294da2742f8c09ce9984a58888b89025d73712400c8bd026296b2cb SHA512 79c9697b3fe6954108cb60ae79c06cee280ef6d73bcd9e35ab148750a4fa55c8e5118c21cdb4e3ae009d4c160a26c98132448476ef90ac6d7a19a79138c3b2f6

sci-libs/libsigrok/files/libsigrok-0.5.2-py313.patch

@@ -0,0 +1,46 @@
+http://sigrok.org/gitweb/?p=libsigrok.git;a=commit;h=5bc8174531df86991ba8aa6d12942923925d9e72
+
+From: Gerhard Sittig <redacted>
+Date: Mon, 2 Oct 2023 16:33:08 +0000 (+0200)
+Subject: bindings/python: rephrase for Python 3.9 deprecation (call API)
+X-Git-Url: http://sigrok.org/gitweb/?p=libsigrok.git;a=commitdiff_plain;h=5bc8174531df86991ba8aa6d12942923925d9e72;hp=1711287ee9e5e4d37cab1cf9fcda5c98f732a137
+
+bindings/python: rephrase for Python 3.9 deprecation (call API)
+
+The PyEval_CallObject() routine was deprecated in Python 3.9, use
+PyObject_CallObject() instead which has existed since at least 3.0.
+
+There are also PyEval_InitThreads() deprecation warnings, but these
+originate from SWIG generated code and are outside of our control.
+Requires SWIG version 4.1 to silence these.
+
+Tested-By: Sascha Silbe <redacted>
+--- a/bindings/python/sigrok/core/classes.i
++++ b/bindings/python/sigrok/core/classes.i
+@@ -134,7 +134,7 @@ typedef guint pyg_flags_type;
+ 
+         auto arglist = Py_BuildValue("(OO)", log_obj, string_obj);
+ 
+-        auto result = PyEval_CallObject($input, arglist);
++        auto result = PyObject_CallObject($input, arglist);
+ 
+         Py_XDECREF(arglist);
+         Py_XDECREF(log_obj);
+@@ -177,7 +177,7 @@ typedef guint pyg_flags_type;
+     $1 = [=] () {
+         const auto gstate = PyGILState_Ensure();
+ 
+-        const auto result = PyEval_CallObject($input, nullptr);
++        const auto result = PyObject_CallObject($input, nullptr);
+         const bool completed = !PyErr_Occurred();
+         const bool valid_result = (completed && result == Py_None);
+ 
+@@ -221,7 +221,7 @@ typedef guint pyg_flags_type;
+ 
+         auto arglist = Py_BuildValue("(OO)", device_obj, packet_obj);
+ 
+-        auto result = PyEval_CallObject($input, arglist);
++        auto result = PyObject_CallObject($input, arglist);
+ 
+         Py_XDECREF(arglist);
+         Py_XDECREF(device_obj);

sci-libs/libsigrok/files/libsigrok-0.5.2-swig-4.1.patch

@@ -0,0 +1,11 @@
+https://bugs.gentoo.org/878395
+--- a/bindings/cxx/enums.py
++++ b/bindings/cxx/enums.py
+@@ -73,6 +73,8 @@
+ code = open(os.path.join(outdirname, 'cxx/enums.cpp'), 'w')
+ swig = open(os.path.join(outdirname, 'swig/enums.i'), 'w')
+ 
++print('%include "attribute.i" \n', file=swig)
++
+ for file in (header, code):
+     print("/* Generated file - edit enums.py instead! */", file=file)

sci-libs/libsigrok/libsigrok-0.6.0.ebuild

@@ -0,0 +1,156 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI="8"
+
+PYTHON_COMPAT=( python3_{10..13} )
+GIT_COMMIT="f6d0f7a"
+
+inherit autotools python-r1 java-pkg-opt-2 udev xdg
+
+if [[ ${PV} == *9999* ]]; then
+	EGIT_REPO_URI="git://sigrok.org/${PN}"
+	inherit git-r3
+else
+	SRC_URI="http://sigrok.org/gitweb/?p=${PN}.git;a=snapshot;h=${GIT_COMMIT};sf=zip -> ${PN}-${GIT_COMMIT}.zip"
+	KEYWORDS="~amd64 ~arm ~arm64 ~x86"
+	S="${WORKDIR}/${PN}-${GIT_COMMIT}"
+fi
+
+DESCRIPTION="Basic hardware drivers for logic analyzers and input/output file format support"
+HOMEPAGE="https://sigrok.org/wiki/Libsigrok"
+
+LICENSE="GPL-3"
+SLOT="0/4"
+IUSE="bluetooth +cxx ftdi hidapi java nettle parport python serial static-libs test +udev usb"
+REQUIRED_USE="java? ( cxx )
+	python? ( cxx ${PYTHON_REQUIRED_USE} )"
+
+RESTRICT="!test? ( test )"
+
+# We also support librevisa, but that isn't in the tree ...
+LIB_DEPEND="
+	>=dev-libs/glib-2.32.0[static-libs(+)]
+	>=dev-libs/libzip-0.8:=[static-libs(+)]
+	bluetooth? ( >=net-wireless/bluez-4.0:= )
+	cxx? ( dev-cpp/glibmm:2[static-libs(+)] )
+	ftdi? ( dev-embedded/libftdi:1[static-libs(+)] )
+	hidapi? ( >=dev-libs/hidapi-0.8.0 )
+	nettle? ( dev-libs/nettle:=[static-libs(+)] )
+	parport? ( sys-libs/libieee1284[static-libs(+)] )
+	python? (
+		${PYTHON_DEPS}
+		>=dev-python/pygobject-3.0.0[${PYTHON_USEDEP}]
+	)
+	serial? ( >=dev-libs/libserialport-0.1.1[static-libs(+)] )
+	usb? ( virtual/libusb:1[static-libs(+)] )
+"
+RDEPEND="
+	java? ( >=virtual/jre-1.8:* )
+	!static-libs? ( ${LIB_DEPEND//\[static-libs(+)]} )
+	static-libs? ( ${LIB_DEPEND} )
+"
+DEPEND="${LIB_DEPEND//\[static-libs(+)]}
+	cxx? ( app-text/doxygen )
+	java? (
+		>=dev-lang/swig-3.0.6
+		>=virtual/jdk-1.8:*
+	)
+	python? (
+		>=dev-lang/swig-3.0.6
+		dev-python/numpy[${PYTHON_USEDEP}]
+		dev-python/setuptools[${PYTHON_USEDEP}]
+	)
+	test? ( >=dev-libs/check-0.9.4 )
+	virtual/pkgconfig
+"
+
+BDEPEND="app-arch/unzip"
+
+PATCHES=(
+	# https://bugs.gentoo.org/878395
+	"${FILESDIR}/${PN}-0.5.2-swig-4.1.patch"
+	"${FILESDIR}/${PN}-0.5.2-sipeed-slogic.patch"
+	"${FILESDIR}/${PN}-0.5.2-py313.patch"
+)
+
+pkg_setup() {
+	use python && python_setup
+	java-pkg-opt-2_pkg_setup
+}
+
+src_unpack() {
+	[[ ${PV} == *9999* ]] && git-r3_src_unpack || default
+}
+
+sigrok_src_prepare() {
+	eautoreconf
+}
+
+src_prepare() {
+	default
+	sigrok_src_prepare
+	use python && python_copy_sources
+}
+
+sigrok_src_configure() {
+	econf \
+		$(use_with bluetooth libbluez) \
+		$(use_with ftdi libftdi) \
+		$(use_with hidapi libhidapi) \
+		$(use_with nettle libnettle) \
+		$(use_with parport libieee1284) \
+		$(use_with serial libserialport) \
+		$(use_with usb libusb) \
+		$(use_enable cxx) \
+		$(use_enable java) \
+		$(use_enable static-libs static) \
+		"${@}"
+}
+
+each_python_configure() {
+	cd "${BUILD_DIR}"
+	sigrok_src_configure --disable-ruby --enable-python
+}
+
+src_configure() {
+	sigrok_src_configure --disable-ruby --disable-python
+	use python && python_foreach_impl each_python_configure
+}
+
+each_python_compile() {
+	cd "${BUILD_DIR}"
+	emake python-build
+}
+
+src_compile() {
+	default
+	use python && python_foreach_impl each_python_compile
+}
+
+src_test() {
+	emake check
+}
+
+each_python_install() {
+	cd "${BUILD_DIR}"
+	emake python-install DESTDIR="${D}"
+	python_optimize
+}
+
+src_install() {
+	default
+	use python && python_foreach_impl each_python_install
+	use udev && udev_dorules contrib/*.rules
+	find "${D}" -name '*.la' -type f -delete || die
+}
+
+pkg_postinst() {
+	udev_reload
+	xdg_pkg_postinst
+}
+
+pkg_postrm() {
+	udev_reload
+	xdg_pkg_postrm
+}

sci-libs/libsigrok/metadata.xml

@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<maintainer type="project">
+ <email>embedded@gentoo.org</email>
+ <name>Embedded Gentoo</name>
+</maintainer>
+<longdescription>
+  libsigrok is a shared library written in C, which provides the basic
+  hardware access drivers for logic analyzers and other supported devices,
+  as well as input/output file format support.
+</longdescription>
+<use>
+ <flag name="ftdi">Enable drivers that need <pkg>dev-embedded/libftdi</pkg></flag>
+ <flag name="hidapi">Enable drivers that need <pkg>dev-libs/hidapi</pkg></flag>
+ <flag name="nettle">Enable drivers that need <pkg>dev-libs/nettle</pkg></flag>
+ <flag name="parport">Enable drivers that are parallel (IEEE1284) based</flag>
+ <flag name="serial">Enable drivers that are serial (RS232) based</flag>
+</use>
+</pkgmetadata>

sci-libs/libsigrokdecode/Manifest

@@ -0,0 +1,3 @@
+DIST libsigrokdecode-782c35b.zip 837923 BLAKE2B 9c1fcbd3eb19a55f840aab53e79a7409e4508a6c47dfe384b94a8ca76be193a98b67d6b488bf7c9efa79899d9d96acb87a2a4b103ba13a26a5b8bc46727fc54e SHA512 beb954d793647e0756abfa3a54641b5db7dc566cb31d205796e4fdb38f3dcf97320046d88fb2d9ee55e0ec91864c021ded362ba7bc5a3ac1e4dfccc98bd2dd6b
+EBUILD libsigrokdecode-0.6.0.ebuild 1229 BLAKE2B fc32c61a3720624c6d536400832f76ac2ecb28a497621c666c34654ae4e187e3073a0cb188ce4386501aa46698d4f6d82b5beba94716cf9fde1f908031d012f7 SHA512 18b0b338b1c07c7fd8932a60a9ff52a81ee3cd42c6ed5618dc7d74859cacc92259ef31b69cbb28cab8f245366b2fd5206b43f750e0c249f8aeda262b1bd94773
+MISC metadata.xml 248 BLAKE2B 9858a97a2186d5b06e272fe28021e0e668897630d8b99023000e8e58e852e80e16b399d8f864b9dff6c9fda25e1519ac8b4331792a4b441be23922707c4ad6a9 SHA512 a1e8f757e473af3ab0ccf695f849dc91e1be877dd505d339bdd26e35a2cf7fb5ffd8f5bf34e933873a462023aecb0edbddefbbda455289279182059cd6c1b0e5

sci-libs/libsigrokdecode/libsigrokdecode-0.6.0.ebuild

@@ -0,0 +1,58 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI="8"
+
+GIT_COMMIT="782c35b"
+
+PYTHON_COMPAT=( python3_{10..13} )
+inherit autotools python-single-r1
+
+if [[ ${PV} == *9999* ]]; then
+	EGIT_REPO_URI="git://sigrok.org/${PN}"
+	inherit git-r3
+else
+	SRC_URI="http://sigrok.org/gitweb/?p=${PN}.git;a=snapshot;h=${GIT_COMMIT};sf=zip -> ${PN}-${GIT_COMMIT}.zip"
+	KEYWORDS="~amd64 ~arm ~arm64 ~x86"
+	S="${WORKDIR}/${PN}-${GIT_COMMIT}"
+fi
+
+DESCRIPTION="Provide (streaming) protocol decoding functionality"
+HOMEPAGE="https://sigrok.org/wiki/Libsigrokdecode"
+
+LICENSE="GPL-3"
+SLOT="0/4"
+IUSE="static-libs"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+	>=dev-libs/glib-2.34.0
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	app-arch/unzip
+	virtual/pkgconfig
+"
+
+src_prepare() {
+	default
+
+	# bug #794592
+	sed -i -e "s/\[SRD_PKGLIBS\],\$/& [python-${EPYTHON#python}-embed], [python-${EPYTHON#python}],/" configure.ac || die
+
+	eautoreconf
+}
+
+src_configure() {
+	econf $(use_enable static-libs static) PYTHON3="${PYTHON}"
+}
+
+src_test() {
+	emake check
+}
+
+src_install() {
+	default
+	python_optimize "${D}"/usr/share/libsigrokdecode/decoders
+	find "${D}" -name '*.la' -type f -delete || die
+}

sci-libs/libsigrokdecode/metadata.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<maintainer type="project">
+	<email>embedded@gentoo.org</email>
+	<name>Embedded Gentoo</name>
+</maintainer>
+</pkgmetadata>

sci-libs/vtk/Manifest

@@ -0,0 +1,17 @@
+AUX vtk-9.2.5-pegtl-3.x.patch 4679 BLAKE2B 0c0be426ac07c2dcab275fb84ef68f6fe3e914d83a9434ef07b2d184bd313ed2ce62d471531c330a32cc734f7b3fcb8859a0c49c8bc5ac461191c86ea9755778 SHA512 75e8a740a784ba811eff27f0ba60d8889b24f97b1fcdf7feda4a73f0324d36060d7b35dba74bf6de2a16136201dc772ee5825e93ec0e5337e74299baea3444a0
+AUX vtk-9.3.0-ThirdParty-gcc15.patch 2444 BLAKE2B cc3e209a1c9df09a03dd365cd6999b9666bdcbfc9e7b922394e420e0d8089b120040c1b44260918908e133e2e283fd2ddd1d9e35506737831bab1d08ccd22beb SHA512 e45b8b1f08d9a9a1a7b0c220cc5ee96647394a1bbd079f5900e76e51438ac9795dcbeee7fcf8201bf13e17cc1e8908d35146320331e6e02ccfa76b8e6f1ae731
+AUX vtk-9.3.0-ThrustPatches.patch 2026 BLAKE2B e51c72b9d2bfb0e7e968f1c9f0896a70d6215f60d21dd234c26feb7a47653c46c8d75b24b1ab0286e51d228b6c4ff7fefd34c01f5b8e885dc1cab6190fc9c6f7 SHA512 b326839c82682e7c1fc1e19d836fb55837417bbf0c23ccb28edc84dd519f085cce0a07221bf6c9e794d1b8a73ecd77c154f82cb602feef9e8d8962b2e8fabd92
+AUX vtk-9.3.0-core-octree_node.txx.patch 670 BLAKE2B 6f53735716d6c75bfcf41dbc27331a4ac495f474c540b06c7a1b62e71b84af88304c2364e88060aae9cd015866138240f40ba28e0db8470e7a841cfb06ef827e SHA512 36d9b12f29e60bb773745263996eaf9fed2f6dee4e3be7f593f5a72e25909d30cde90828c54e1981290640b9f4cae85b20292ae054b6b5f2ee4420f27d23c07f
+AUX vtk-9.3.0-java.patch 372 BLAKE2B ec11a69bf2e7b467b00648b0bc725f838f9931bce2f2cd1cbabe6d4c8fdcd4ef807dd14eedf06d524eecc3c9bc77850cc8de5e55ceaf8a238efa501c8bb36cf9 SHA512 6d326f95b05fd86d87a0566e45efb484d92d482a916895d3aaca1e019ceac65ecbcdab2957a8686545898551a3382aa718a57ad0d9e9cd16937166bf3f0729d8
+AUX vtk-9.3.0-opencascade-7.8.0.patch 819 BLAKE2B 51f4af785af5f44b21b641a631fe63c5e308558d573c03d02646691fd3762dce89670be80da2284769fe30129861982a062aea8574c90ea7472d7875ba8b2fbb SHA512 6d3bec28921d7e3b61fa10cbe68a529190248519f67d52365b0d73f2ce265aae028b7db4601b60c13fdd309db8b4164f2134961acf27e8f0778ec649674442a0
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+DIST VTK-9.3.1.tar.gz 99964158 BLAKE2B b85aae0aef1a22bd0496e0f5d2c7d3a5c20bbd7db8951ab1f9fe29a48c01ce960e90dc85f36cb6858c2b7dfd7f12cd1cf2e7d0fbb115fc9fd709dd7b481c598e SHA512 5dcd6764b2d9fe476bcc7bd195fab8230b7628579d94656ab037dcaecd07c7d40d0fc4afba446942ca15cd881df17f4c84581047e75a6e11d2e2d339d97c7fa3
+DIST VTKData-9.3.1.tar.gz 612744946 BLAKE2B 6b3a09f6cc98630e817aaeca8094c6a6625372269abfa9003212cd1cdbc101b198f5eeb3474ca675be7f03046c58a5d11b4092ab19ed230422c4100011abfee4 SHA512 befc6b68e33d2c2fb6928006d4fe6feda7e0bbaf31df4488911ab8e3865e3fc1cf3834301301aa2b6de94c4489eebf5e2e8521e8830315d2a1f0e65cb73a6fd3
+DIST VTKDataFiles-9.3.1.tar.gz 628903288 BLAKE2B cf5919a627ee49809f79d29577d65a48c3332255551c3c229875b25fce911c75c3edeca8d0dfdf9926f93543963ab0e2c992c7469e2c9eed041c39cfd995647d SHA512 360fadd31ab304a27b208745c674eb31759552e98f587569f481c1bda62c7f8ae72598cd40b2c628bb211aace8f62df2ea7ca66f192f8d2e71bca7a4deaa9e89
+DIST VTKLargeData-9.3.1.tar.gz 247523669 BLAKE2B 88ec5046f502db14dd6a26ef81e386babaf560619e16d769834e96046eab46cf762d8c80f9b51c434b77e4e145d8f60e32efbdb4f57d8305494177abec0806ef SHA512 edf5610edfae90f8465d68e0e06e82018978ba27f5b2ae9701939aeb72019acaabeda435c15787f1c4828b44e34c79e2837565a81d6a3accd368a92c6eacebd1
+DIST VTKLargeDataFiles-9.3.1.tar.gz 247505524 BLAKE2B 5de069309c59a8a73365fb9faba9904189d723fb72976f372e40db3eb100342a19fecd582bd0aa42fc1012675b442a8e42611632004d6b6d6708468c27a4265e SHA512 bbbf0c193432cb5d8a5618c41e66609c7e6f3e4f24f588124c46b537ecec28b5670420b7f77185da534e4098f8b95d8ec4e392fc017df934a84bfc9dc833f634
+DIST vtkDocHtml-9.3.1.tar.gz 165542400 BLAKE2B da8084137b2848f82bf091535950738bd718e65cac8f461fdfb8e9c63ef6db68acfa02655531c8fe22e35f89395d2d066aa5b051abac0e774883552c898de6d9 SHA512 de0d2153c97864b49a8b99e6fbfc8bab78c1522d25bf40ed1f271a8bb4f1f205b008d6bd39f835816972c8439d01f78b68f34d1f88f87755174f0d559841ba29
+EBUILD vtk-9.3.1.ebuild 34551 BLAKE2B de8ccdc6c7fe67148bf1df104bf6549669fba842ed3b483fb6bcd98b5f3c6d53c236ab363b68fc1240611230eecc6cd7faeb5e91dacf1f98831e1f36ac65aab5 SHA512 dc0896391c8c716dc6e6588aed121842cca755912d856c7251ba5dfe7e9443723c7ef23d43974ffd55c81f94401bf199927179fdc2c6aa6f4116512dbd392c42
+MISC metadata.xml 1699 BLAKE2B befce4e1f61b6cb0d772a2826ed9349cf36832ebc0507edc2dff658441b44be351c1fe97c74ac9b21eed8310a254dd2a3b408bc93a15c4b2db8cd55a5e3f703a SHA512 d9921a30c66ef3a3d2a27da1add22a29352cd3fd71c49e834523931b8edf21ca0d785290cddabbe29b068ce00fa05a898c331a1ad80ffaa190e9f92b1a1ab64d

sci-libs/vtk/files/vtk-9.2.5-pegtl-3.x.patch

@@ -0,0 +1,128 @@
+From: 31058da34eeb26165011b07fe41baf825f7df1a3 Mon Sep 17 00:00:00 2001
+From: Alexander Neumann <30894796+Neumann-A@users.noreply.github.com>
+From: https://github.com/microsoft/vcpkg/pull/29730
+Date: Sat, 18 Feb 2023 10:12:04 +0100
+Subject: [PATCH 1/3] [vtk] update pegtl to version 3
+
+--- a/IO/MotionFX/vtkMotionFXCFGGrammar.h
++++ b/IO/MotionFX/vtkMotionFXCFGGrammar.h
+@@ -23,7 +23,7 @@
+ 
+ // for debugging
+ // clang-format off
+-#include VTK_PEGTL(pegtl/contrib/tracer.hpp)
++#include VTK_PEGTL(pegtl/contrib/trace.hpp)
+ // clang-format on
+ 
+ namespace MotionFX
+--- a/IO/MotionFX/vtkMotionFXCFGReader.cxx
++++ b/IO/MotionFX/vtkMotionFXCFGReader.cxx
+@@ -1213,7 +1213,7 @@ bool PositionFileMotion::read_position_file(const std::string& rootDir) const
+     }
+     return true;
+   }
+-  catch (const tao::pegtl::input_error& e)
++  catch (const tao::pegtl::parse_error& e)
+   {
+     vtkGenericWarningMacro("PositionFileMotion::read_position_file failed: " << e.what());
+   }
+@@ -1232,7 +1232,7 @@ bool UniversalTransformMotion::read_universaltransform_file(const std::string& r
+       in, numbers, this->transforms);
+     return true;
+   }
+-  catch (const tao::pegtl::input_error& e)
++  catch (const tao::pegtl::parse_error& e)
+   {
+     vtkGenericWarningMacro(
+       "UniversalTransformMotion::read_universaltransform_file failed: " << e.what());
+@@ -1267,7 +1267,7 @@ public:
+       if (getenv("MOTIONFX_DEBUG_GRAMMAR") != nullptr)
+       {
+         tao::pegtl::read_input<> in2(filename);
+-        tao::pegtl::parse<MotionFX::CFG::Grammar, tao::pegtl::nothing, tao::pegtl::tracer>(in2);
++        tao::pegtl::complete_trace<MotionFX::CFG::Grammar>(in2);
+       }
+       return false;
+     }
+--- a/ThirdParty/pegtl/CMakeLists.txt
++++ b/ThirdParty/pegtl/CMakeLists.txt
+@@ -5,7 +5,6 @@ vtk_module_third_party(
+     VERSION       "2.8.3"
+   EXTERNAL
+     PACKAGE PEGTL
+-    VERSION 2.0.0
+     TARGETS PEGTL::PEGTL
+     STANDARD_INCLUDE_DIRS)
+ 
+--- a/CMake/FindPEGTL.cmake
++++ b/CMake/FindPEGTL.cmake
+@@ -19,31 +19,43 @@
+ # Copyright (c) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
+ # Redistribution and use is allowed according to the terms of the 2-clause BSD license.
+ 
+-find_path(PEGTL_INCLUDE_DIR
+-  NAMES pegtl/version.hpp
+-  PATH_SUFFIXES tao
+-  DOC "Path to PEGTL headers")
+-mark_as_advanced(PEGTL_INCLUDE_DIR)
++message(STATUS "Searching for PEGTL")
++find_package(PEGTL CONFIG REQUIRED)
++if(TARGET taocpp::pegtl)
++    message(STATUS "Searching for PEGTL - found target taocpp::pegtl")
++    set_target_properties(taocpp::pegtl PROPERTIES IMPORTED_GLOBAL TRUE)
++    if(NOT TARGET PEGTL::PEGTL)
++       add_library(PEGTL::PEGTL IMPORTED INTERFACE)
++       target_link_libraries(PEGTL::PEGTL INTERFACE taocpp::pegtl)
++    endif()
++else()
++    find_path(PEGTL_INCLUDE_DIR
++      NAMES pegtl/version.hpp
++      PATH_SUFFIXES tao
++      DOC "Path to PEGTL headers")
++    mark_as_advanced(PEGTL_INCLUDE_DIR)
+ 
+-if (PEGTL_INCLUDE_DIR)
+-  file(STRINGS "${PEGTL_INCLUDE_DIR}/pegtl/version.hpp" _pegtl_version_header
+-    REGEX "TAO_PEGTL_VERSION")
+-  string(REGEX MATCH "define[ \t]+TAO_PEGTL_VERSION[ \t]+\"([0-9.]+)\"" _pegtl_version_match "${_pegtl_version_header}")
+-  set(PEGTL_VERSION "${CMAKE_MATCH_1}")
+-  unset(_pegtl_version_header)
+-  unset(_pegtl_version_match)
+-endif ()
++    if (PEGTL_INCLUDE_DIR)
++      file(STRINGS "${PEGTL_INCLUDE_DIR}/pegtl/version.hpp" _pegtl_version_header
++        REGEX "TAO_PEGTL_VERSION")
++      string(REGEX MATCH "define[ \t]+TAO_PEGTL_VERSION[ \t]+\"([0-9.]+)\"" _pegtl_version_match "${_pegtl_version_header}")
++      set(PEGTL_VERSION "${CMAKE_MATCH_1}")
++      unset(_pegtl_version_header)
++      unset(_pegtl_version_match)
++    endif ()
+ 
+-include(FindPackageHandleStandardArgs)
+-find_package_handle_standard_args(PEGTL
+-  REQUIRED_VARS PEGTL_INCLUDE_DIR
+-  VERSION_VAR PEGTL_VERSION)
++    include(FindPackageHandleStandardArgs)
++    find_package_handle_standard_args(PEGTL
++      REQUIRED_VARS PEGTL_INCLUDE_DIR
++      VERSION_VAR PEGTL_VERSION)
+ 
+-if (PEGTL_FOUND)
+-  set(PEGTL_INCLUDE_DIRS "${PEGTL_INCLUDE_DIR}")
+-  if (NOT TARGET PEGTL::PEGTL)
+-    add_library(PEGTL::PEGTL INTERFACE IMPORTED)
+-    set_target_properties(PEGTL::PEGTL PROPERTIES
+-      INTERFACE_INCLUDE_DIRECTORIES "${PEGTL_INCLUDE_DIR}")
+-  endif ()
+-endif ()
++    if (PEGTL_FOUND)
++      set(PEGTL_INCLUDE_DIRS "${PEGTL_INCLUDE_DIR}")
++      if (NOT TARGET PEGTL::PEGTL)
++        add_library(PEGTL::PEGTL INTERFACE IMPORTED)
++        set_target_properties(PEGTL::PEGTL PROPERTIES
++          INTERFACE_INCLUDE_DIRECTORIES "${PEGTL_INCLUDE_DIR}")
++      endif ()
++      message(STATUS "Searching for PEGTL - found")
++    endif ()
++endif ()
+\ No newline at end of file

sci-libs/vtk/files/vtk-9.3.0-ThirdParty-gcc15.patch

@@ -0,0 +1,47 @@
+From d00b98bd8ef02f854f1068e8ab8fd2fb28244c3b Mon Sep 17 00:00:00 2001
+From: Ted Rodgers <ted.d.rodgers@gmail.com>
+Date: Sat, 10 Aug 2024 16:13:09 -0400
+Subject: [PATCH] include cstdint + correct case/words
+
+--- a/ThirdParty/vtkm/vtkvtkm/vtk-m/vtkm/filter/contour/worklet/mir/MIRTables.h
++++ b/ThirdParty/vtkm/vtkvtkm/vtk-m/vtkm/filter/contour/worklet/mir/MIRTables.h
+@@ -11402,7 +11402,7 @@ public:
+ 
+     VTKM_EXEC vtkm::UInt8 GetPoint(vtkm::Id pointIndex) const
+     {
+-      return this->CellFacePortal.Get(pointIndex);
++      return this->CellEdgesPortal.Get(pointIndex);
+     }
+ 
+   private:
+--- a/ThirdParty/vtkm/vtkvtkm/vtk-m/vtkm/filter/scalar_topology/worklet/contourtree_distributed/HierarchicalContourTree.h
++++ b/ThirdParty/vtkm/vtkvtkm/vtk-m/vtkm/filter/scalar_topology/worklet/contourtree_distributed/HierarchicalContourTree.h
+@@ -663,7 +663,7 @@ std::string HierarchicalContourTree<FieldType>::PrintDotSuperStructure(const cha
+   auto hyperarcsPortal = this->Hyperarcs.ReadPortal();
+   auto regularNodeGlobalIdsPortal = this->RegularNodeGlobalIds.ReadPortal();
+   auto whichIterationPortal = this->WhichIteration.ReadPortal();
+-  auto whichRoundPortal = this->whichRound.ReadPortal();
++  auto whichRoundPortal = this->WhichRound.ReadPortal();
+   auto superarcsPortal = this->Superarcs.ReadPortal();
+   auto superparentsPortal = this->Superparents.ReadPortal();
+   for (vtkm::Id supernode = 0; supernode < this->Supernodes.GetNumberOfValues(); supernode++)
+@@ -708,7 +708,7 @@ std::string HierarchicalContourTree<FieldType>::PrintDotSuperStructure(const cha
+     if (contourtree_augmented::NoSuchElement(superarcTo))
+     { // no superarc
+       // if it occurred on the final round, it's the global root and is shown as the NULL node
+-      if (whichRoundPortal.Get(superarcFrom) == this->NRounds)
++      if (whichRoundPortal.Get(superarcFrom) == this->NumRounds)
+       { // root node
+         outstream << "\tSN" << std::setw(1) << superarcFrom << " -> SA" << std::setw(1) << superarc
+                   << " [label=\"S" << std::setw(1) << superarc << "\",style=dotted]\n";
+--- a/ThirdParty/vtkm/vtkvtkm/vtk-m/vtkm/thirdparty/diy/vtkmdiy/include/vtkmdiy/thirdparty/chobo/small_vector.hpp
++++ b/ThirdParty/vtkm/vtkvtkm/vtk-m/vtkm/thirdparty/diy/vtkmdiy/include/vtkmdiy/thirdparty/chobo/small_vector.hpp
+@@ -136,6 +136,7 @@
+ //
+ #pragma once
+ 
++#include <cstdint>
+ #include <type_traits>
+ #include <cstddef>
+ #include <memory>
+

sci-libs/vtk/files/vtk-9.3.0-ThrustPatches.patch

@@ -0,0 +1,51 @@
+From 4a4466e7c8cd44d2be2bd3fe6f359faa8e9547aa Mon Sep 17 00:00:00 2001
+From: Kenneth Moreland <morelandkd@ornl.gov>
+Date: Tue, 4 Jun 2024 10:04:42 -0400
+Subject: [PATCH] Disable Thrust patch that is no longer needed in modern
+ Thrust
+
+There is a Thrust patch that works around an issue in Thrust 1.9.4
+(https://github.com/NVIDIa/ThirdParty/vtkm/vtkvtkm/vtk-m/thrust/issues/972). The underlying issue
+should be fixed in recent versions. In recent versions of CUDA, the patch
+breaks (https://gitlab.kitware.com/vtk/vtk-m/-/issues/818).
+
+This change fixes the problem by disabling the patch where it is not
+needed.
+--- /dev/null
++++ b/ThirdParty/vtkm/vtkvtkm/vtk-m/docs/changelog/obsolete-thrust-patch.md
+@@ -0,0 +1,9 @@
++# Disable Thrust patch that is no longer needed in modern Thrust
++
++There is a Thrust patch that works around an issue in Thrust 1.9.4
++(https://github.com/NVIDIa/ThirdParty/vtkm/vtkvtkm/vtk-m/thrust/issues/972). The underlying issue
++should be fixed in recent versions. In recent versions of CUDA, the patch
++breaks (https://gitlab.kitware.com/vtk/vtk-m/-/issues/818).
++
++This change fixes the problem by disabling the patch where it is not
++needed.
+--- a/ThirdParty/vtkm/vtkvtkm/vtk-m/vtkm/exec/cuda/internal/ThrustPatches.h
++++ b/ThirdParty/vtkm/vtkvtkm/vtk-m/vtkm/exec/cuda/internal/ThrustPatches.h
+@@ -170,9 +170,9 @@ ALIGN_RE_PAIR(vtkm::Int64, vtkm::Float64);
+ #undef ALIGN_RE_PAIR
+ }
+ }
+-#endif //THRUST_VERSION >= 100900
++#endif //THRUST_VERSION >= 100900 && THRUST_VERSION < 100906
+ 
+-#if THRUST_VERSION >= 100904
++#if (THRUST_VERSION >= 100904) && (THRUST_VERSION < 100909)
+ //So for thrust 1.9.4+ (CUDA 10.1+) the stateless_resource_allocator has a bug
+ //where it is not marked as __host__ __device__ && __thrust_exec_check_disable__.
+ //To fix this we add a new partial specialization on cuda::memory_resource
+@@ -236,7 +236,7 @@ public:
+ };
+ }
+ }
+-#endif //THRUST_VERSION >= 100903
++#endif //(THRUST_VERSION >= 100904) && (THRUST_VERSION < 100909)
+ 
+ 
+ #if THRUST_VERSION < 100900
+-- 
+GitLab
+

sci-libs/vtk/files/vtk-9.3.0-core-octree_node.txx.patch

@@ -0,0 +1,18 @@
+From b5f466a66771621a3aaa15434910f413ab7168f7 Mon Sep 17 00:00:00 2001
+From: Ted Rodgers <ted.d.rodgers@gmail.com>
+Date: Sat, 10 Aug 2024 16:10:13 -0400
+Subject: [PATCH] octree_node.txx fix chilren typo
+
+Signed-off-by: Paul Zander <negril.nx+gentoo@gmail.com>
+
+--- a/Utilities/octree/octree/octree_node.txx
++++ b/Utilities/octree/octree/octree_node.txx
+@@ -210,7 +210,7 @@ const octree_node<T_, d_, A_>& octree_node<T_, d_, A_>::operator[](int child) co
+   {
+     throw std::domain_error("Attempt to access children of an octree leaf node.");
+   }
+-  return this->_M_chilren[child];
++  return this->m_children[child];
+ }
+ 
+ /**\brief Return a reference to a child node.

sci-libs/vtk/files/vtk-9.3.0-java.patch

@@ -0,0 +1,11 @@
+--- a/Wrapping/Java/Testing/Java/CMakeLists.txt
++++ b/Wrapping/Java/Testing/Java/CMakeLists.txt
+@@ -22,6 +22,8 @@ if (WIN32)
+ endif ()
+ set(vtk_test_classpath
+   "$<TARGET_FILE:VTK::vtkjava>")
++list(APPEND vtk_test_classpath
++  ${java_classpath})
+ string(REPLACE ";" "${classpath_separator}" vtk_test_classpath "${vtk_test_classpath}")
+ 
+ add_library(vtkjava_tests STATIC

sci-libs/vtk/files/vtk-9.3.0-opencascade-7.8.0.patch

@@ -0,0 +1,29 @@
+--- a/IO/OCCT/CMakeLists.txt
++++ b/IO/OCCT/CMakeLists.txt
+@@ -5,11 +5,11 @@ vtk_module_find_package(
+ )
+ 
+ set(opencascade_req_targets
+-  TKSTEP
+-  TKIGES
++  TKDESTEP
++  TKDEIGES
+   TKMesh
+-  TKXDESTEP
+-  TKXDEIGES)
++  TKXSDRAWSTEP
++  TKXSDRAWIGES)
+ set(opencascade_missing_targets)
+ foreach (opencascade_req_target IN LISTS opencascade_req_targets)
+   if (NOT TARGET "${opencascade_req_target}")
+--- a/IO/OCCT/vtkOCCTReader.cxx
++++ b/IO/OCCT/vtkOCCTReader.cxx
+@@ -348,7 +348,7 @@ public:
+   int GetHash(const TDF_Label& label)
+   {
+     TopoDS_Shape aShape;
+-    return this->ShapeTool->GetShape(label, aShape) ? aShape.HashCode(INT_MAX) : 0;
++    return this->ShapeTool->GetShape(label, aShape) ? opencascade::hash(aShape) : 0;
+   }
+ 
+   //----------------------------------------------------------------------------

sci-libs/vtk/files/vtk-9.3.0-opencascade.patch

@@ -0,0 +1,15 @@
+From: https://gitlab.archlinux.org/archlinux/packaging/packages/vtk/-/blob/main/vtk-occt.patch
+From: Sven-Hendrik Haase <svenstaro@archlinux.org>
+--- a/IO/OCCT/vtkOCCTReader.h
++++ b/IO/OCCT/vtkOCCTReader.h
+@@ -48,8 +48,8 @@ public:
+    * It can be either STEP or IGES.
+    * Default is FILE_FORMAT::STEP
+    */
+-  VTK_DEPRECATED_IN_9_3_0("Use SetFormat with unsigned int instead.")
+-  vtkSetEnumMacro(FileFormat, Format);
++  // VTK_DEPRECATED_IN_9_3_0("Use SetFormat with unsigned int instead.")
++  // vtkSetEnumMacro(FileFormat, Format);
+   vtkSetClampMacro(FileFormat, unsigned int, Format::STEP, Format::IGES);
+   ///@}
+

sci-libs/vtk/files/vtk-9.3.0-update-for-cuda-12.6.patch

@@ -0,0 +1,22 @@
+From f568d669465f5825006be2fba8a117060e832618 Mon Sep 17 00:00:00 2001
+From: Paul Zander <negril.nx+gentoo@gmail.com>
+Date: Sun, 8 Sep 2024 22:27:09 +0200
+Subject: [PATCH] update for cuda 12.6
+
+https://github.com/NVIDIA/cccl/commit/733eb94a2b98b8d5b5ab1e39cbd8ac1aed9173ec
+
+Bug: https://bugs.gentoo.org/938673
+Signed-off-by: Paul Zander <negril.nx+gentoo@gmail.com>
+
+--- a/ThirdParty/vtkm/vtkvtkm/vtk-m/vtkm/exec/cuda/internal/WrappedOperators.h
++++ b/ThirdParty/vtkm/vtkvtkm/vtk-m/vtkm/exec/cuda/internal/WrappedOperators.h
+@@ -195,7 +195,7 @@ namespace detail
+ //
+ template <typename T, typename F>
+ struct is_commutative<vtkm::exec::cuda::internal::WrappedBinaryOperator<T, F>>
+-  : public thrust::detail::is_arithmetic<T>
++  : public ::cuda::std::is_arithmetic<T>
+ {
+ };
+ }
+

sci-libs/vtk/files/vtk-9.3.1-fix-fmt-11.patch

@@ -0,0 +1,70 @@
+From a811c0c4aca246a89f85a1eecc805e388a645178 Mon Sep 17 00:00:00 2001
+From: Paul Zander <negril.nx+gentoo@gmail.com>
+Date: Tue, 17 Sep 2024 18:45:03 +0200
+Subject: [PATCH] fix fmt-11
+
+Signed-off-by: Paul Zander <negril.nx+gentoo@gmail.com>
+
+diff --git a/ThirdParty/ioss/vtkioss/Ioss_Decomposition.C b/ThirdParty/ioss/vtkioss/Ioss_Decomposition.C
+index 388d524..a94afc6 100644
+--- a/ThirdParty/ioss/vtkioss/Ioss_Decomposition.C
++++ b/ThirdParty/ioss/vtkioss/Ioss_Decomposition.C
+@@ -15,6 +15,7 @@
+ #include <cassert>
+ #include "vtk_fmt.h"
+ #include VTK_FMT(fmt/ostream.h)
++#include VTK_FMT(fmt/ranges.h)
+ #include <numeric>
+ 
+ #if !defined(NO_ZOLTAN_SUPPORT)
+diff --git a/ThirdParty/ioss/vtkioss/Ioss_IOFactory.C b/ThirdParty/ioss/vtkioss/Ioss_IOFactory.C
+index 440f352..ca71a90 100644
+--- a/ThirdParty/ioss/vtkioss/Ioss_IOFactory.C
++++ b/ThirdParty/ioss/vtkioss/Ioss_IOFactory.C
+@@ -12,6 +12,7 @@
+ #include <cstddef> // for nullptr
+ #include "vtk_fmt.h"
+ #include VTK_FMT(fmt/ostream.h)
++#include VTK_FMT(fmt/ranges.h)
+ #include <map>     // for _Rb_tree_iterator, etc
+ #include <ostream> // for basic_ostream, etc
+ #include <set>
+diff --git a/ThirdParty/ioss/vtkioss/Ioss_StructuredBlock.C b/ThirdParty/ioss/vtkioss/Ioss_StructuredBlock.C
+index 1609c31..85b67e2 100644
+--- a/ThirdParty/ioss/vtkioss/Ioss_StructuredBlock.C
++++ b/ThirdParty/ioss/vtkioss/Ioss_StructuredBlock.C
+@@ -15,6 +15,7 @@
+ #include <Ioss_StructuredBlock.h>
+ #include "vtk_fmt.h"
+ #include VTK_FMT(fmt/ostream.h)
++#include VTK_FMT(fmt/ranges.h)
+ 
+ #include <cstddef> // for size_t
+ #include <numeric>
+diff --git a/ThirdParty/ioss/vtkioss/Ioss_Utils.C b/ThirdParty/ioss/vtkioss/Ioss_Utils.C
+index 57021ab..cc5b8a4 100644
+--- a/ThirdParty/ioss/vtkioss/Ioss_Utils.C
++++ b/ThirdParty/ioss/vtkioss/Ioss_Utils.C
+@@ -21,6 +21,7 @@
+ #include VTK_FMT(fmt/chrono.h)
+ #include VTK_FMT(fmt/format.h)
+ #include VTK_FMT(fmt/ostream.h)
++#include VTK_FMT(fmt/ranges.h)
+ #include <fstream>
+ #include <sstream>
+ #include <string>
+diff --git a/ThirdParty/ioss/vtkioss/Ioss_ZoneConnectivity.C b/ThirdParty/ioss/vtkioss/Ioss_ZoneConnectivity.C
+index 5d32481..5cb3c02 100644
+--- a/ThirdParty/ioss/vtkioss/Ioss_ZoneConnectivity.C
++++ b/ThirdParty/ioss/vtkioss/Ioss_ZoneConnectivity.C
+@@ -9,6 +9,7 @@
+ #include <cstddef> // for size_t
+ #include "vtk_fmt.h"
+ #include VTK_FMT(fmt/ostream.h)
++#include VTK_FMT(fmt/ranges.h)
+ #include <string> // for string
+ #include <vector> // for vector
+ 
+-- 
+2.46.0
+

sci-libs/vtk/metadata.xml

@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person" proxied="yes">
+    <email>negril.nx+gentoo@gmail.com</email>
+    <name>Paul Zander</name>
+  </maintainer>
+  <maintainer type="project" proxied="proxy">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <maintainer type="project" proxied="proxy">
+    <email>proxy-maint@gentoo.org</email>
+    <name>Proxy Maintainers</name>
+  </maintainer>
+  <use>
+    <flag name="all-modules">Build all modules</flag>
+    <flag name="boost">Add support for boost</flag>
+    <flag name="cgns">Build support to handle CGNS data files</flag>
+    <flag name="gdal">Support for gdal formated data</flag>
+    <flag name="imaging">Building Imaging modules</flag>
+    <flag name="las">Build support for LiDAR files</flag>
+    <flag name="logging">Build the logging module</flag>
+    <flag name="opencascade">Enable OpenCASCADE support</flag>
+    <flag name="openvdb">Build support to handle VDB data files</flag>
+    <flag name="pdal">Build support to handle point cloud data files</flag>
+    <flag name="qt6">Use Qt6 packages instead of Qt5</flag>
+    <flag name="rendering">Building Redering modules</flag>
+    <flag name="sdl">Enable SDL2 support for rendering modules</flag>
+    <flag name="tbb">Use <pkg>dev-cpp/tbb</pkg> to handle smp support</flag>
+    <flag name="views">Building Views modules</flag>
+    <flag name="vtkm">Build the vtkm accelerations modules</flag>
+    <flag name="web">Install web component</flag>
+  </use>
+  <upstream>
+    <remote-id type="github">Kitware/VTK</remote-id>
+  </upstream>
+</pkgmetadata>