gentoo auto-resync : 11:03:2025 - 01:49:36HEADmaster

28 files changed, 635 insertions, 25 deletions

diff --git a/sci-libs/HighFive/HighFive-2.10.1.ebuild b/sci-libs/HighFive/HighFive-2.10.1.ebuild
new file mode 100644
index 000000000000..8995434dd26f
--- /dev/null
+++ b/sci-libs/HighFive/HighFive-2.10.1.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DOCS_BUILDER="doxygen"
+DOCS_DEPEND="app-text/doxygen[dot]"
+DOCS_DIR="doc"
+
+inherit cmake docs
+
+DESCRIPTION="Header-only C++ interface for libhdf5"
+HOMEPAGE="https://github.com/BlueBrain/HighFive"
+SRC_URI="https://github.com/BlueBrain/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Boost-1.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="mpi test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	sci-libs/hdf5[mpi?]
+"
+DEPEND="
+	${RDEPEND}
+	test? (
+		>=dev-cpp/catch-3.4.0:0
+		dev-libs/boost
+		dev-cpp/eigen
+		media-libs/opencv
+	)
+"
+
+DOCS=( {README,CHANGELOG}.md )
+
+src_configure() {
+	default
+	local mycmakeargs=(
+		-DHIGHFIVE_PARALLEL_HDF5=$(usex mpi)
+
+		-DHIGHFIVE_USE_BOOST=$(usex test)
+		-DHIGHFIVE_USE_EIGEN=$(usex test)
+		-DHIGHFIVE_USE_OPENCV=$(usex test)
+		-DHIGHFIVE_USE_XTENSOR=OFF
+
+		-DHIGHFIVE_EXAMPLES=$(usex test)
+		-DHIGHFIVE_UNIT_TESTS=$(usex test)
+	)
+	cmake_src_configure
+}
+
+src_compile() {
+	default
+	use test && cmake_src_compile
+	use doc && doxygen_compile
+}
+
+src_test() {
+	# Set -j1 to prevent race
+	cmake_src_test -j1
+}
diff --git a/sci-libs/HighFive/HighFive-2.8.0.ebuild b/sci-libs/HighFive/HighFive-2.8.0.ebuild
index 066cfc924888..74fdeecedc86 100644
--- a/sci-libs/HighFive/HighFive-2.8.0.ebuild
+++ b/sci-libs/HighFive/HighFive-2.8.0.ebuild
@@ -13,9 +13,9 @@ DESCRIPTION="Header-only C++ interface for libhdf5"
 HOMEPAGE="https://github.com/BlueBrain/HighFive"
 SRC_URI="https://github.com/BlueBrain/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
 
-KEYWORDS="amd64 ~x86"
 LICENSE="Boost-1.0"
 SLOT="0"
+KEYWORDS="amd64 ~x86"
 IUSE="mpi test"
 RESTRICT="!test? ( test )"
 
diff --git a/sci-libs/HighFive/Manifest b/sci-libs/HighFive/Manifest
index f97e8caae161..75d36c8c1f66 100644
--- a/sci-libs/HighFive/Manifest
+++ b/sci-libs/HighFive/Manifest
@@ -1,3 +1,5 @@
+DIST HighFive-2.10.1.tar.gz 559344 BLAKE2B e605eb336c740ad2665130af35b05c92c9aa54c50e2b811ae97e56446b6f67047bc65278a1260850971b0ff5ec19daf48fb266f699636da63a5268987c839e43 SHA512 3daf16c2ced165ddc7a8f1e9a0d3bf3388836e3878c86f8bf3faf2c42996d5bfd449e71e75a871447c1e7ea9a3e87d4f4a80a2382f1b24095d6051b89f27d6d3
 DIST HighFive-2.8.0.tar.gz 538050 BLAKE2B ad856be95365c6d94add457d76366e0a3143fd09bbb6354048f896e16f5445d1037367eaaeaa233a3b5f9c45d2a2611173e051d2bd9e7aff4a3472665d96ec7f SHA512 cabcf8f1507b4466b7438249a813ea36de5e5d220c5caf7656312e24dbe09042bf9573388ca7c3caa22f71bd3b8106923710f9459127f87c341e2b0ab953eede
-EBUILD HighFive-2.8.0.ebuild 1152 BLAKE2B 23aaa5e9d688077c8991dd4e947414d4817e150947b53793c475966110b6c1e9a804e9633d479383d56aee17ce2e0c6e621db536bed1e93c015ae26894bb7bff SHA512 2ffb7449fc6e8d09b108f7d2437caaca305ea5dde8932fce8563f0b40f8612cb024f7b306b1542440bbe10b586f6e3f83e4ef9cebf9034fbf7e39677be452170
+EBUILD HighFive-2.10.1.ebuild 1153 BLAKE2B c937de448fe71acaa6e803273fca36b38d93bf458a2047190582de9139c20a9b085373941c26a5cc91ec4eec7cdf6e4089e4f025f9ea788e8dccfbc5f97f358d SHA512 16fa5f956b190833a146845d7734fa70023150a3578e4b29e794d7d4121cf47d80b4a8a50e8437e3d3ff8850f117c48adea88a2923508fcd5572f0f2830fb0fa
+EBUILD HighFive-2.8.0.ebuild 1152 BLAKE2B b16fea5958269705b39c64e96072d47e223c744390d64584e98deb69234e542e19db8278ac95b94f2f936d47aa70f36ee964e49e2dd970956342fea3b9eac963 SHA512 61fb4baf68c01766ab15ca10af3cb246f4266bff2f3a82e5620a05760f1580622c98297df61fc761ce1f937b1120b979fef230b2a2c3cfbe0e2fb2c15b69ffcb
 MISC metadata.xml 470 BLAKE2B 22d0ea29f74f9d6924646cda2d547c25f88c6716fb84ab590e2d5adb7eabe434bcbcc79c1b0842d7ea49bb2c7a189a5adead6e7d873df4fd07107cbe838af2a0 SHA512 4d625697c4edd55658d6353842e299ab0ed6a3552824bf871e5c9f75986842be50b54fafa3ec0b3b87ac799901951ec07987ed1bddf30678f7f00171a73f3fed
diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index 5395f9afa3ba..2fd01b981c4d 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/cantera/Manifest b/sci-libs/cantera/Manifest
index 6e7b2e8f262f..fdd3b5140aef 100644
--- a/sci-libs/cantera/Manifest
+++ b/sci-libs/cantera/Manifest
@@ -1,7 +1,11 @@
 AUX cantera-3.0.0_env.patch 1439 BLAKE2B 8f4cd901f24f0b526887501ba16a0552acf8572f154f8494d66d3dd8096434621d6f2baaa57f905233919fc1b7872993bada9f373950330663c8315075d507b9 SHA512 065cdbcf620a3036c1bb0bb8b79503f76dbe7e6b2522e9f53fc582c15e5e10f1790f1b40cf0315d64cab4f858764446f4094370124bb9b5c4ee6dbcfd5e61b87
 AUX cantera-3.0.1_add_fmt11_support.patch 1465 BLAKE2B 42130ee99361fab47f3fd41e3bec8f4994f503daffee1a6ecbb0dfd75cce2429c6020061ec27eda5078ff67e4613d95b635c4bfc1a39fc76a2c8abed096f0251 SHA512 dd929eaf899564f8d06263b45eec1ec33245090c2c5a5128098ab2b9ec35eaa36f5025cce1726ceede0e35a8f9cca3fe279199ac083473d0ee2c72e8e63a864c
 AUX cantera-3.0.1_fix_fmt_with_c++20.patch 13515 BLAKE2B e32655074dc2780ad765d96f297957c54ced57279b6f1b90e968b408b628cb46f688a21720f0738fbaef815ab72e0f04ecc359a5dfe1c236b7569026f8b7ada4 SHA512 7ca318959f86be4436d9923bc7611fb0b0f17ebeaea1c919df2282858ba2a51946cbb7dfcfc3a9ab5098d15fac0a9bc0169b20f9072cbc0177d81898a8037941
+AUX cantera-3.1.0_env.patch 1460 BLAKE2B 55eebc16f0ecd8874ef22d320881af307217c17fc5c76a755db1c0daec111c857a583a109a70d644c2fb6b4a499609fa07f4b48ccf5cc4b5419c7962d84aa3be SHA512 8d7a6c332ef0bc6ed2491235cb5d53362c3f278695200e9218fc4060e166d1d9d4c7f15f4378c745c5b84ca731142a90f8963cd870a85802a3da35a96c390610
 DIST cantera-3.0.1.tar.gz 2451841 BLAKE2B b05771021a81d5266dfed382e2a6357e5b70653c6d9cfb5f03a6755095f4f8f4e7c0f78b79e0bf131c01fefce46bbc647c790ee412b6457c515cda39d4fc3054 SHA512 fa993b33867c6c0a0ca539f52116c4cdea739dfcd30deb5d2f66042f290f7f2f60112d7a37c38fbd8a38a119e5af00a7a85fd80b6e36388202b666be0ddd7715
+DIST cantera-3.1.0.tar.gz 2605640 BLAKE2B 6912b4e6b96ff71f02484a8fa051f8d34d0fc24c933e08e129531c6fe10e80fea74fcf6a6f7b00736de7b6ed5d4ab483f37a51b532d9bf154646546a8856e2a2 SHA512 0400a01ed0e244e6a34c9c04ffd5174ce6632c713c9bf003ab96e22b6f5a62713ee6a7eb07d7ae614e9f4e303e17df7fd234d66a48e43e46ede0246bb2bac52b
+DIST cantera-3.1.0_example_data.tar.gz 244545 BLAKE2B c341a7d530ad2486660b1dfe870f6ddd49280101bc7e98d3a88dea3aaaab0ae6c25383746f688164a04385a462a513f706d0ee248a675806de22df467d4f074f SHA512 a6171a106460f8b7a84bf825db38826444c30f921ba27896a50e1b52177550deaa5f66e11f6f91a2b91c4023e3dfb55b46233d2b6176afa771154dd81f8b34ab
 EBUILD cantera-3.0.1-r1.ebuild 3416 BLAKE2B 67c638a33afe183ed672426bb38b8a91128ea8e6910fa39c0df986bfcb0842ac9f2f209f4bfb350f7cd40de6d88314b51d22e980a9fd38003783fefebca8b0a0 SHA512 53cec4ecb207e97faa92e204dea3a180c65b23aec570b5b261c0bc753900954165c4c5cb98ee973629e1332a407d9a3d3b616ddacd34c4aa7f29e498df7671d2
 EBUILD cantera-3.0.1-r2.ebuild 3502 BLAKE2B d05ab5655059653d2f6db34b82dcac637adb29ca57426c96b810ffa2269f4a861a6270a8c29545ea5def545fc8f794e31a10e450b8a93d36a08ff6f4a8c02613 SHA512 daa644d36c411ae0ed67e9de1f5373bb7432d2b3aac10da51051f61fc60be3ce36c96689fc55077b47404cf09b2b47cbc5143607a61405a465807aef27769ab7
+EBUILD cantera-3.1.0.ebuild 3629 BLAKE2B 26e11bd8bf710df1a586b85739be43d59431f739a9ab437e5fcac7a211941a6685aece319901dd824f0c6c4ea2b611ff35dbf17872e3fb51ca1aea3c47d88330 SHA512 56c00d5d55538464fce7c39a278ce5d31457aaa5912f022cf7d3e9cc2a83dd6c56f7995bb7659af1c9e854e8a24eaae6cd6663dafc750d2c03a6c1d8f7de52e2
 MISC metadata.xml 884 BLAKE2B 0f67510f6c09c58b0af3b820c9b38b88b0c60b0adb28c64148550f07df085cd8ea3d46f5afb59105c56bb7ccf2ca3fee4f2000bee2592ebafb835b9cf415b660 SHA512 0cdbc4cbd0dfdc90bb74c79f06d5f5d28a4edd0dcfacbddcc83ed804c592694eba27f337ce20a2a57248dd0456517bab2298faa22b78154f03e9369973fc174b
diff --git a/sci-libs/cantera/cantera-3.1.0.ebuild b/sci-libs/cantera/cantera-3.1.0.ebuild
new file mode 100644
index 000000000000..2f918ec6b1b6
--- /dev/null
+++ b/sci-libs/cantera/cantera-3.1.0.ebuild
@@ -0,0 +1,155 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+
+FORTRAN_NEEDED=fortran
+FORTRAN_STANDARD="77 90"
+
+inherit flag-o-matic fortran-2 python-single-r1 scons-utils toolchain-funcs
+
+DESCRIPTION="Object-oriented tool suite for chemical kinetics, thermodynamics, and transport"
+HOMEPAGE="https://www.cantera.org"
+SRC_URI="
+	https://github.com/Cantera/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz
+	https://github.com/Cantera/cantera-example-data/archive/refs/tags/v${PV}.tar.gz -> ${P}_example_data.tar.gz
+"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="fortran hdf5 lapack +python test"
+RESTRICT="!test? ( test )"
+
+REQUIRED_USE="
+	${PYTHON_REQUIRED_USE}
+"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	dev-cpp/yaml-cpp
+	hdf5? ( sci-libs/HighFive )
+	!lapack? ( sci-libs/sundials:0= )
+	lapack? (
+		>=sci-libs/sundials-6.5.0:0=[lapack?]
+		virtual/lapack
+	)
+	python? (
+		$(python_gen_cond_dep '
+			dev-python/numpy[${PYTHON_USEDEP}]
+			dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+		')
+	)
+"
+
+DEPEND="
+	${RDEPEND}
+	dev-cpp/eigen:3
+	dev-libs/boost:=
+	dev-libs/libfmt
+	python? (
+		$(python_gen_cond_dep '
+			dev-python/cython[${PYTHON_USEDEP}]
+			dev-python/pip[${PYTHON_USEDEP}]
+		')
+	)
+	test? (
+		>=dev-cpp/gtest-1.11.0
+		python? (
+			$(python_gen_cond_dep '
+				dev-python/h5py[${PYTHON_USEDEP}]
+				dev-python/pandas[${PYTHON_USEDEP}]
+				dev-python/pytest[${PYTHON_USEDEP}]
+				dev-python/scipy[${PYTHON_USEDEP}]
+			')
+		)
+	)
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-3.1.0_env.patch"
+)
+
+src_unpack() {
+	default
+	mv -T "${WORKDIR}/${PN}-example-data-${PV}" "${S}"/data/example_data || die
+}
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	python-single-r1_pkg_setup
+}
+
+## Full list of configuration options of Cantera is presented here:
+## https://cantera.org/3.1/develop/compiling/config-options.html
+src_configure() {
+	# -Werror=odr, -Werror=lto-type-mismatch
+	# https://github.com/Cantera/cantera/issues/1783
+	filter-lto
+
+	scons_vars=(
+		AR="$(tc-getAR)"
+		CC="$(tc-getCC)"
+		CXX="$(tc-getCXX)"
+		cc_flags="${CXXFLAGS}"
+		cxx_flags="-std=c++20"
+		debug="no"
+		FORTRAN="$(tc-getFC)"
+		FORTRANFLAGS="${FCFLAGS}"
+		optimize_flags="-Wno-inline"
+		renamed_shared_libraries="no"
+		use_pch="no"
+		## In some cases other order can break the detection of right location of Boost: ##
+		system_fmt="y"
+		system_sundials="y"
+		system_eigen="y"
+		system_yamlcpp="y"
+		hdf_support=$(usex hdf5 y n)
+		system_blas_lapack=$(usex lapack y n)
+		env_vars="all"
+		extra_inc_dirs="/usr/include/eigen3"
+		use_rpath_linkage="yes"
+		extra_lib_dirs="/usr/$(get_libdir)/${PN}"
+	)
+	use hdf5 && scons_vars+=( system_highfive="y" )
+	use lapack && scons_vars+=( blas_lapack_libs="lapack,blas" )
+	use test || scons_vars+=( googletest="none" )
+
+	scons_targets=(
+		f90_interface=$(usex fortran y n)
+	)
+
+	if use python ; then
+		scons_targets+=( python_package="y" python_cmd="${EPYTHON}" )
+	else
+		scons_targets+=( python_package="n" )
+	fi
+}
+
+src_compile() {
+	escons build "${scons_vars[@]}" "${scons_targets[@]}" prefix="/usr"
+}
+
+src_test() {
+	escons test
+}
+
+src_install() {
+	escons install stage_dir="${D}" libdirname="$(get_libdir)"
+	if ! use python ; then
+		rm -r "${D}/usr/share/man" || die "Can't remove man files."
+	else
+		# Run the byte-compile of modules
+		python_optimize "${D}$(python_get_sitedir)/${PN}"
+	fi
+
+	# User could remove this line if require static libs for development purpose
+	find "${ED}" -name '*.a' -delete || die
+}
+
+pkg_postinst() {
+	local post_msg=$(usex fortran "and Fortran " "")
+	elog "C++ ${post_msg}samples are installed to '/usr/share/${PN}/samples/' directory."
+}
diff --git a/sci-libs/cantera/files/cantera-3.1.0_env.patch b/sci-libs/cantera/files/cantera-3.1.0_env.patch
new file mode 100644
index 000000000000..31766f1afb13
--- /dev/null
+++ b/sci-libs/cantera/files/cantera-3.1.0_env.patch
@@ -0,0 +1,37 @@
+diff '--color=auto' -Naur a/SConstruct b/SConstruct
+--- a/SConstruct
++++ b/SConstruct
+@@ -170,11 +170,7 @@
+ 
+ cantera_git_commit = os.environ.get("CT_GIT_COMMIT")
+ if not cantera_git_commit:
+-    try:
+-        cantera_git_commit = get_command_output("git", "rev-parse", "--short", "HEAD")
+-        logger.info(f"Building Cantera from git commit {cantera_git_commit!r}")
+-    except (subprocess.CalledProcessError, FileNotFoundError):
+-        cantera_git_commit = "unknown"
++    cantera_git_commit = "unknown"
+ else:
+     logger.info(f"Building Cantera from git commit {cantera_git_commit!r}")
+ 
+@@ -866,7 +862,7 @@
+     toolchain = ["default"]
+ 
+ env = Environment(tools=toolchain+["textfile", "subst", "recursiveInstall", "UnitsInterfaceBuilder", "wix", "gch"],
+-                  ENV={"PATH": os.environ["PATH"]},
++                  ENV={'PATH': os.environ['PATH'], 'CCACHE_DIR': os.environ.get('CCACHE_DIR','')},
+                   toolchain=toolchain,
+                   **extraEnvArgs)
+ 
+diff '--color=auto' -Naur a/src/SConscript b/src/SConscript
+--- a/src/SConscript
++++ b/src/SConscript
+@@ -90,7 +90,7 @@
+     shim = pyenv.SharedObject("extensions/pythonShim.cpp")
+     pylibname = f"../lib/cantera_python{pyenv['py_version_short'].replace('.', '_')}"
+     lib = build(pyenv.SharedLibrary(pylibname, shim, SPAWN=get_spawn(pyenv)))
+-    install("$inst_shlibdir", lib)
++    install("$inst_shlibdir/cantera", lib)
+ 
+ 
+ # build the Cantera static library
diff --git a/sci-libs/cfitsio/Manifest b/sci-libs/cfitsio/Manifest
index c00ec013eba6..0d4ad980a2a3 100644
--- a/sci-libs/cfitsio/Manifest
+++ b/sci-libs/cfitsio/Manifest
@@ -1,3 +1,5 @@
+AUX cfitsio-4.5.0-rename-nullptr.patch 1818 BLAKE2B c4accd8ebd77efa7cba49d531822b2c91e4b083556410f6ac924bfa266a45274a7b92266a412e65c02868c5123a86aa6ebf297fe3bb16011b195702c17e0135d SHA512 95558623d93a8733d5407136ef11413d05ed3707ef71a755fa92754876b930935abb0e85e97dcf8ee81e95ed19afaf3147b2d255e4600d56869b4cfa446095c7
 DIST cfitsio-4.5.0.tar.gz 4648097 BLAKE2B 5e0e09a3e6f43ce00bb5e5dd90e88c1aa2a873b407f3156147b064904ab341da219e69dc2a763e6b02eea0392a78e0ce74c15f921054bf72cac9b6e425765f99 SHA512 03746bf49cfcd97991be54f3e4dd51fb45c7b3a75f581dc6ab9ee5726a342dc11b651667807fd67e5318576d9b15e3580dd62ceab02fd684feff7ee6bb2edc7c
+EBUILD cfitsio-4.5.0-r1.ebuild 1564 BLAKE2B dc25c9254e63fcca390b4b06e35704903521d774dc0edd9f3ef6696ba79a511537ff857d02421b65bc69d432e9f571ae49db32cee212a446fb6c501f2957fe59 SHA512 593758480da7280a11ec4cf091784727f69e61c0009f6e6d5a14cd19c45697b665024f716f3bb200a9787c50aa7b13ae3d6f1e0ee6b42561e340cb7f1011b526
 EBUILD cfitsio-4.5.0.ebuild 1508 BLAKE2B 550442eed75e8fe7e01493b21a298481aea1d4e134a38dc2f91043cb5603bea515ca9ba29857e3ff4ba7362aa64a144852737c361ac2f8d89665011e9b7df780 SHA512 4c983f1098a573e09ccebca7351d3226e3cad83d16823320168ca4ce600e56761dc6c4a55f72b55541e6f49fbcec0c7b048752502e30f8841b383d4b0ac54390
 MISC metadata.xml 1032 BLAKE2B 4479a1c6a42796e7effcc1b53ecc30d11e7302140cee2a34f7deaa1270497d0b0add85ddf1ce38223b357a9cac5f11af9039246f41228aca7d73653fd58a0fcf SHA512 ad32ecfbeceae8d768e9fa63386bdf89887d36ca18a68a72965b4f9206d779a26ece545d618540538246be5307c066e823ce55117208533cd9e668a6010222df
diff --git a/sci-libs/cfitsio/cfitsio-4.5.0-r1.ebuild b/sci-libs/cfitsio/cfitsio-4.5.0-r1.ebuild
new file mode 100644
index 000000000000..c50383b46670
--- /dev/null
+++ b/sci-libs/cfitsio/cfitsio-4.5.0-r1.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake-multilib fortran-2
+
+DESCRIPTION="C and Fortran library for manipulating FITS files"
+HOMEPAGE="https://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html"
+SRC_URI="https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/${P}.tar.gz"
+
+LICENSE="ISC"
+SLOT="0/10-r1"
+KEYWORDS="~alpha ~amd64 ~hppa ~loong ~ppc ~ppc64 ~riscv ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos"
+IUSE="bzip2 curl test tools"
+RESTRICT="!test? ( test )"
+
+BDEPEND="
+	app-alternatives/yacc
+	app-alternatives/lex
+"
+RDEPEND="
+	sys-libs/zlib[${MULTILIB_USEDEP}]
+	bzip2? ( app-arch/bzip2[${MULTILIB_USEDEP}] )
+	curl? ( net-misc/curl[${MULTILIB_USEDEP}] )
+"
+# Bug #803350
+DEPEND="
+	${RDEPEND}
+	<dev-lang/cfortran-20110621
+"
+
+PATCHES=( "${FILESDIR}/${P}-rename-nullptr.patch" )
+
+pkg_setup() {
+	fortran-2_pkg_setup
+}
+
+src_prepare() {
+	cmake_src_prepare
+
+	# fix libdir
+	sed -e 's:lib/::' -i CMakeLists.txt || die
+
+	# Avoid internal cfortran
+	rm cfortran.h || die
+}
+
+multilib_src_configure() {
+	local libdir=$(get_libdir)
+	local mycmakeargs=(
+		# used for .pc file
+		-DLIB_SUFFIX=${libdir#lib}
+
+		-DUSE_BZIP2=$(usex bzip2)
+		-DUSE_CURL=$(usex curl)
+		-DUSE_PTHREADS=ON
+		# just appending CFLAGS
+		-DUSE_SSE2=OFF
+		-DUSE_SSSE3=OFF
+
+		-DTESTS=$(usex test)
+		-DUTILS=$(multilib_native_usex tools)
+	)
+	cmake_src_configure
+}
+
+multilib_src_install_all() {
+	dodoc README.md docs/*.pdf
+
+	docinto examples
+	dodoc utilities/{cookbook.{c,f},testprog.c,testf77.f,speed.c,smem.c}
+}
diff --git a/sci-libs/cfitsio/files/cfitsio-4.5.0-rename-nullptr.patch b/sci-libs/cfitsio/files/cfitsio-4.5.0-rename-nullptr.patch
new file mode 100644
index 000000000000..6281d7f7e324
--- /dev/null
+++ b/sci-libs/cfitsio/files/cfitsio-4.5.0-rename-nullptr.patch
@@ -0,0 +1,51 @@
+Nullptr is reserved keyword in C23. Rename to something that describes usage better
+https://bugs.gentoo.org/944747
+--- a/putcol.c
++++ b/putcol.c
+@@ -1226,7 +1226,7 @@
+     long rept, rowrept, width, tnull, naxes[9] = {1,1,1,1,1,1,1,1,1}, groups;
+     double zeros = 0.;
+     char message[FLEN_ERRMSG], keyname[FLEN_KEYWORD], nullstr[FLEN_VALUE];
+-    char **stringptr, *nullptr, *cptr;
++    char **stringptr, *ptr_to_null, *cptr;
+ 
+     if (*status > 0)
+         return(*status);
+@@ -2081,24 +2081,24 @@
+           {
+             stringptr = cols[jj].array;
+             dataptr = stringptr + 1;
+-            nullptr = *stringptr;
++            ptr_to_null = *stringptr;
+             nbytes = 2;
+           }
+           else
+           {
+             dataptr = (char *) cols[jj].array + col[jj].nullsize;
+-            nullptr = (char *) cols[jj].array;
++            ptr_to_null = (char *) cols[jj].array;
+             nbytes = col[jj].nullsize;
+           }
+ 
+-          if (memcmp(nullptr, &zeros, nbytes) ) 
++          if (memcmp(ptr_to_null, &zeros, nbytes) ) 
+           {
+             /* null value flag not zero; must check for and write nulls */
+             if (hdutype == IMAGE_HDU)   
+             {
+                 if (ffppn(cols[jj].fptr, cols[jj].datatype, 
+                       felement, cols[jj].repeat * ntodo, dataptr,
+-                      nullptr, &tstatus) > 0)
++                      ptr_to_null, &tstatus) > 0)
+                 break;
+             }
+             else
+@@ -2113,7 +2113,7 @@
+ 
+                 if (ffpcn(cols[jj].fptr, cols[jj].datatype, cols[jj].colnum, frow,
+                       felement, cols[jj].repeat * ntodo, dataptr,
+-                      nullptr, &tstatus) > 0)
++                      ptr_to_null, &tstatus) > 0)
+                 break;
+             }
+           }
diff --git a/sci-libs/dcmtk/Manifest b/sci-libs/dcmtk/Manifest
index dd30d596f2a7..6d0e22dc9a08 100644
--- a/sci-libs/dcmtk/Manifest
+++ b/sci-libs/dcmtk/Manifest
@@ -5,5 +5,5 @@ DIST dcmtk-3.6.8.tar.gz 9628364 BLAKE2B 367885c3fda65b7b2e42555ba648800f9585cbd4
 DIST dcmtk-3.6.9.tar.gz 9628334 BLAKE2B c60a9620a522b2a2fb976549ec1a3addce9ccd2fee90dad85376b56c105b28450d8ac2c8e8afe397e1bce532f8dd08f3fdb1135513bce3b314bdd7bbae7c06c9 SHA512 1ea4140940f33b34e21895cd7aa6b05be109fcecfbed45f61f8a4a248ea98deae59f2b362e518051d6054f588189d5ef9bba0ab81afa73b219c9ebcf415a0ca0
 EBUILD dcmtk-3.6.7-r1.ebuild 1989 BLAKE2B 47958171848d55e4e648abec64258fe3c6547f6c18daf6dc3f46e6e5e0c88afb3787d86dab6bda6c53ae13909cf1f7fd8fe956e1b4f1653a068fc6b3f06d5898 SHA512 902b2bd3dabfce90711f811eb0eafb14f3d61f9ff545046c3b223eda15aeb2985c6c7dfcd765014b179e4b177e5ca61a37561bbf5b19201fe19614ec8e7c4780
 EBUILD dcmtk-3.6.8.ebuild 1963 BLAKE2B cedac0e5bbbd5ef840347d3af28ef8951cca68b4c00170ab2109286dd8d33e5ef25980e51f761da8404cc96c7bed494aa3d4c975388f4257a43722387aac86fd SHA512 a558ad80d191b25e120c92fe66aca9b1689a2a5de9b3c4df89fb8279addc35bc6e012e24c4b52308ab83786934c682d0da01bb3e5f54ebc0efc2964db17408cc
-EBUILD dcmtk-3.6.9.ebuild 1751 BLAKE2B 22e2943d04bb9449ab7d03a016eb2a6c83d1521c4c29186bc92559c2a71a8dc140e633207ed8bf541a00b73281ff1cbf0eb0271954f74f944a1895d4a343688a SHA512 a29f07be93e3f9264624ef5934f4a716945efc8eff100f6e221472cdfc2fd7b074d7d5de558b9e6dbd067e8e9520248dc99b032fb9ed6ebca5a9db962b3e599e
+EBUILD dcmtk-3.6.9.ebuild 1750 BLAKE2B e1cedd166cdfc485d055d43cda3076104f66d14df6aefd0f1b9cbaa29a6886d6c9bfe9864aaf920d2de780e740b04046de84ac55ec160c00d705d8683ad72928 SHA512 832c794a92f0b28813f2a103eeae46ce69986b8af879dd9bb76a91da89d74659ea0576f11a4412d5698f0480d9d14ffe650a70bf13cfb3c1fd5846f833f312f0
 MISC metadata.xml 308 BLAKE2B 394345b977e2dd7598cd2acdf2af966f2efecef502a4f460e4fe323c095e3de8523c4217873d18f68198996e4ee08580f46543bf7e357a227f66dcd558191615 SHA512 b8117feeab19b0128c2378d36370e907338873a177c5d8f1cfaef79bf16e877fc455cc5096bccadb99a7238c02fd01c02ae9018a81aab013e0d1a1ccc4cd650c
diff --git a/sci-libs/dcmtk/dcmtk-3.6.9.ebuild b/sci-libs/dcmtk/dcmtk-3.6.9.ebuild
index 605e334411ec..cfcea801a361 100644
--- a/sci-libs/dcmtk/dcmtk-3.6.9.ebuild
+++ b/sci-libs/dcmtk/dcmtk-3.6.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -11,7 +11,7 @@ SRC_URI="https://dicom.offis.de/download/dcmtk/release/${P}.tar.gz"
 
 LICENSE="OFFIS"
 SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~ppc64 ~riscv ~x86"
+KEYWORDS="amd64 ~arm ~arm64 ~ppc64 ~riscv ~x86"
 IUSE="doc png ssl tcpd tiff +threads xml zlib"
 
 RDEPEND="
diff --git a/sci-libs/flann/Manifest b/sci-libs/flann/Manifest
index 607844580ad6..16d0b8df74f6 100644
--- a/sci-libs/flann/Manifest
+++ b/sci-libs/flann/Manifest
@@ -13,5 +13,5 @@ DIST flann-1.9.2_p20221027-patches.tar.xz 10232 BLAKE2B 197dd8b81f4a7a43472e440d
 DIST flann-1.9.2_p20221027.tar.gz 34644592 BLAKE2B 822afa518a1efcfd552cee7c9bd9e14587a450d5ddae50c4d225453ab56d7297ca73f5b5bda153aea9ff37e736942057ae071ac41e3d26ac1aeb03a408171162 SHA512 14cd7d3249109ce66c43258f8b9d158efa3b57f654708e76751290eba25e2cb7fc8044a1d882c6b24d0cda1a8b206709acdb5338086ca1f2d60fef35f0fa85be
 EBUILD flann-1.9.1-r6.ebuild 2281 BLAKE2B 60ae0b559e56a67e9283aa2330f3c244ec9bfe86a77f0dcc93fa44359f5badcf4df4107d2166a3ff504d3d0e17429836b4d0886b6aea05fe53159d9ec77c5ad4 SHA512 3b2e76a51c792ae720e9aadb134c1ddc40690065016bd0733692c43fd6ba16cea739e3481a64beabb2aff157cc73642a90af61e12e0ba6614386045657b25234
 EBUILD flann-1.9.1-r7.ebuild 2331 BLAKE2B 3719c9a7e6c1eae072e94fca69ed06a036cc09f30a05a08943165ca484583ee60bc40a73b9ae00d376ed3ff75854811f08ce8dbe411e306997b7208d4c2ae05a SHA512 0e4b3d8c30d2a4de19fa16c5e45ed3ef8425d11c8c45242755aaefef4e0c0cf67c741344f6e5a58198418d5d711418622ecffc48f24ccb25c83c6106f781fcd6
-EBUILD flann-1.9.2_p20221027.ebuild 2794 BLAKE2B 2209493b04f3839be8b7a52418fa36dd3fc9d837451f67691b1007bcf0f50c9c4e1b48aabebf5c1caf7d54300d1637473750fbac4e8061610c6da66d633c8f4b SHA512 a5fe3acfaed3cde42a12dc160b3058f6f68a45e89b9a3f2c6305f54ca06bc3d4a441252eddde3a41275cee5b889dceb33408c94dd35280c5c3e53b16fbfc7223
+EBUILD flann-1.9.2_p20221027.ebuild 2792 BLAKE2B 13def83051132ba0d8a398d3ec6cea6fbcb1b8cc72af58d184f7985c471d2c8e088f6febd397c8854c99417dab6041807e3b2cd7b5346a6ad742d1982ae6cdc8 SHA512 f4733f08b70d49c13ce7ed30c0bfd4477d6c8c840b7c738bfd2b3dce2251dd2831576ab91f68e93681930bf9be1d7b047081e0c4488f5f4df7f48ef178f26448
 MISC metadata.xml 911 BLAKE2B 91ff495b936d1f5314be65367c332cab0ca78f618e6ed8197f2aa4762670feb61e6bb8155b11f5127224e4ee0c716b3e71e290030be5331db4f0722b63d151b4 SHA512 996d48a77a00584b4fe2f0c170ddbfbb92282a0a3fdde5bf0619ffc2f1f1168d50fae282e5e7758da8b94a8cb284d7744d52e8b0ac12eaaff67339942f3f667b
diff --git a/sci-libs/flann/flann-1.9.2_p20221027.ebuild b/sci-libs/flann/flann-1.9.2_p20221027.ebuild
index d628a4efa00f..a683eaeb0953 100644
--- a/sci-libs/flann/flann-1.9.2_p20221027.ebuild
+++ b/sci-libs/flann/flann-1.9.2_p20221027.ebuild
@@ -17,7 +17,7 @@ S="${WORKDIR}/${PN}-${COMMIT}"
 
 LICENSE="BSD"
 SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ~arm arm64 ~ppc ~x86 ~amd64-linux ~x86-linux"
 IUSE="cuda doc examples mpi octave openmp test"
 RESTRICT="!test? ( test )"
 
diff --git a/sci-libs/geos/Manifest b/sci-libs/geos/Manifest
index 257aaab58cc7..821859958169 100644
--- a/sci-libs/geos/Manifest
+++ b/sci-libs/geos/Manifest
@@ -1,5 +1,5 @@
 DIST geos-3.12.1.tar.bz2 6727199 BLAKE2B 4ffc9cb63f3ac15b3dcb0ba9fec6a1ccaeaf35962a057234f4da38d6bba19df39e800805badfd56fe927da09c9392f0feaf2b7d02085e8f293c4d9503ab28ff9 SHA512 192eba83c651e935b3c9a5cc19321285e4d28b9da9d7a1fa15d9471803027e630db7a7ecea96343d9c5f9846d279062ca3694fe47916a4ebf5698ae66dd5210d
 DIST geos-3.13.0.tar.bz2 6801211 BLAKE2B 8de35093e2819268df2cd15f1661dcbaba6b9c3bd978904fb992fd91905b0056cfa6580cae602511bd8c4b19686597abb81e0af71a8a73a684cafd8013755bad SHA512 8ffaa3f49a8365db693ac948e9d66cf55321eb12151734c7da2775070b7804ffa607de2474b7019d6ea2a99d5e037fb1e8561bf9025e65ddd4bd1ba049382b28
 EBUILD geos-3.12.1.ebuild 990 BLAKE2B 9f113c7063dd91d7e09992c2a9d38fcd53b43ce281306ea7110d7128b7544b9249e977ef66a196887d0205a041495fcd7c9b9192f2e2c46c9c0928e0e63efbd2 SHA512 20f351d8ce25e4a923fb9b62c4c18f966c434752b3df7e7be5457e4e5a6bc75a98c9fa58c4ff70d9d800072d68f9fa2e66ddba90ecb6563dff32dc1a440cace8
-EBUILD geos-3.13.0.ebuild 995 BLAKE2B 5fc1f384b0c9d2b6cbeafd1d3f460aad12a635d026e7babeb0ad1286e1d88c87724d0133da4d85c3c4463dd4b99e808d6ff23e6af608e0e86fe694916f8a0697 SHA512 52563044f760f6894ec000c3ee8ba3860907c07783ffdbde8af931e65c81e20bdcebbf8262b5777aa30edd20bfd510167394db2a48739945b6ddde9de8462f3d
+EBUILD geos-3.13.0.ebuild 990 BLAKE2B 57c38f024285712c0812fba8735e3a14764c763badac9bb14eb2fa9a7138d48a84541d452c870b8e15d1e7f9ab7e69fc5e88839de4f1fc78575ad07d79a67854 SHA512 38b15fcc581b3c19cd7bf8bdc29f55e00ca37177248d9c626e79f93c6bef56958febea26b618f2647ec0f3207e169f5e41d23f2d59a89763df6f88abd480a224
 MISC metadata.xml 1101 BLAKE2B 10f27c3a69ee1ebe859c4862d0e9f0b2bc46f544e64e7fa5124b0e2fadd4d64a372cd59ccb96f92cfabb98c93ff6222d5ba5e1772def9a1174f49dba195d13d8 SHA512 4d100b031aa128cb98ea46963319e13a4c71c3de51e85b6cc7efafcafcf69bd32a11b0d4ff3dbbb55d145146df0fb9f709cdb5a70c6b47c9d69542259a71205b
diff --git a/sci-libs/geos/geos-3.13.0.ebuild b/sci-libs/geos/geos-3.13.0.ebuild
index bd059b420ac0..6131ff8c9f0b 100644
--- a/sci-libs/geos/geos-3.13.0.ebuild
+++ b/sci-libs/geos/geos-3.13.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -11,7 +11,7 @@ SRC_URI="https://download.osgeo.org/geos/${P}.tar.bz2"
 
 LICENSE="LGPL-2.1"
 SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~ppc ~ppc64 ~riscv ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x64-solaris"
+KEYWORDS="amd64 arm arm64 ~ppc ppc64 ~riscv x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x64-solaris"
 IUSE="doc test"
 RESTRICT="!test? ( test )"
 
diff --git a/sci-libs/gmsh/Manifest b/sci-libs/gmsh/Manifest
index 9c2539daebc9..109061ff497a 100644
--- a/sci-libs/gmsh/Manifest
+++ b/sci-libs/gmsh/Manifest
@@ -7,4 +7,5 @@ DIST gmsh-4.13.1-source.tgz 18383962 BLAKE2B bf0d002b7d0fa187b47440f167fc02ad41a
 EBUILD gmsh-4.11.1-r3.ebuild 3113 BLAKE2B dce0182a83b100cd3028c338dab8c6d925420f2e46faf5a0ce88cb15e9ff40937078f536b977b6b2537084c2b639d81aa0829543201279b1a5b86da92dbda1b6 SHA512 9e4f4141fbb7de0ddfce6bdc5f08c914111591611f65749a1bbd2e4fc85cf17240247c6ffc098168d1b51d15c205f91d125cf2c107f9d7d171e0d9fd44b1e126
 EBUILD gmsh-4.12.2-r2.ebuild 3069 BLAKE2B 6e1068a7ab1e48a416c6fba8653dafa08d1318cbb73c90d8e8947d4c5a38b645e4116b47ced263f17287f0020e5e1fae8923365899616ad639e6a0d7cfa1c06c SHA512 f9aa6007672bd78c14222c414232461f88b73847c93cf7bf3e57706f73a6d4bfd6402ad3f601206e34f0eaae65ab206eaca4ae99255b34cb12aef9a4756c5524
 EBUILD gmsh-4.13.1-r1.ebuild 3069 BLAKE2B 9ae3283caf14c2c39cc3396a577df6b0073e25045a2d72e5ddab5575d22afbe81d22f2824607284fd1c673f7f360c30c84b5103578180f7cac793a30fd988cab SHA512 118faccfc47e9560a144749ecb26d8b479333b2f8ab3a50fb6a7f7e99d8039b7c9c09fe6f913125ffe677bb7ec8cc27b7f32e23f1c0800815f989eec11294573
+EBUILD gmsh-4.13.1-r2.ebuild 3212 BLAKE2B a36fa5a1c420cdb808b137795961e116f79ce3d6f524ac46fe1091c2843082374080aa0fec5b671a6c430b44547ab2cf210206825387e8dfb0eccdeede117578 SHA512 fd85b33a5cebfacfd6f78e752308dbde9f4ba86656c73177ffff2b4aecb75ddec8e88f950265f34efd7b71ac6b560a0dee5dfc7cdaa3e9f69751df2b5ef8b065
 MISC metadata.xml 1271 BLAKE2B 7ea0644b5ffb89478ba859f0bbd33fa5fcc8ebb57e64f2ca6ccba8123e23b4a7a44626d5fb1bd416d99071557652b247e90cc05b11d50bdded732f41f2acc524 SHA512 013798cf979fcb7fb954490970abdfc6ebbe23e8263a22cf8791af21f593aa46b7348e7673fa7fa318ce3cb8436c2d58435911984b40be3dafda40253ebcc71c
diff --git a/sci-libs/gmsh/gmsh-4.13.1-r2.ebuild b/sci-libs/gmsh/gmsh-4.13.1-r2.ebuild
new file mode 100644
index 000000000000..c12bdced483b
--- /dev/null
+++ b/sci-libs/gmsh/gmsh-4.13.1-r2.ebuild
@@ -0,0 +1,143 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit cmake desktop fortran-2 python-r1 toolchain-funcs xdg-utils
+
+DESCRIPTION="Three-dimensional finite element mesh generator"
+HOMEPAGE="https://gmsh.info https://gitlab.onelab.info/gmsh/gmsh"
+SRC_URI="https://gmsh.info/src/${P}-source.tgz"
+S="${WORKDIR}/${P}-source"
+
+LICENSE="
+	GPL-2+ free-noncomm
+	alglib? ( MIT )
+	gmm? ( LGPL-2.1+ )
+	metis? ( Apache-2.0 )
+	netgen? ( LGPL-2.1+ )
+	voro? ( BSD )
+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+## cgns is not compiling ATM, maybe fix cgns lib first
+IUSE="+alglib +blas cgns eigen examples +gmm jpeg med metis mpi mumps netgen opencascade petsc pdf png python shared slepc X voro zlib"
+
+REQUIRED_USE="
+	^^ ( blas eigen )
+	mumps? ( blas )
+	slepc? ( petsc )
+	python? ( shared ${PYTHON_REQUIRED_USE} )
+	"
+
+RDEPEND="
+	virtual/fortran
+	X? ( x11-libs/fltk:1=[xft(+)] )
+	alglib? ( sci-libs/alglib )
+	blas? (
+		virtual/blas
+		virtual/lapack
+		sci-libs/fftw:3.0
+	)
+	cgns? (
+		sci-libs/cgnslib
+		sci-libs/hdf5:=[mpi=]
+	)
+	eigen? ( dev-cpp/eigen )
+	gmm? ( sci-mathematics/gmm )
+	jpeg? ( media-libs/libjpeg-turbo )
+	med? (
+		sci-libs/med[mpi=]
+		sci-libs/hdf5:=[mpi=]
+	)
+	metis? ( >=sci-libs/metis-5.2.0 )
+	mpi? ( virtual/mpi[cxx] )
+	mumps? ( sci-libs/mumps[mpi=] )
+	opencascade? ( sci-libs/opencascade:* )
+	pdf? ( app-text/poppler:= )
+	png? ( media-libs/libpng:0 )
+	petsc? ( sci-mathematics/petsc[mpi=] )
+	python? ( ${PYTHON_DEPS} )
+	slepc? ( sci-mathematics/slepc[mpi=] )
+	voro? ( sci-libs/voro++ )
+	zlib? ( sys-libs/zlib )
+	"
+
+DEPEND="${RDEPEND}
+	${PYTHON_DEPS}
+	virtual/pkgconfig
+	python? ( dev-lang/swig:0 )
+	"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.9.5-opencascade.patch
+	"${FILESDIR}"/${PN}-4.11.1-metis-5-2.patch
+)
+
+pkg_setup() {
+	fortran-2_pkg_setup
+}
+
+src_configure() {
+	local mycmakeargs=( )
+
+	use blas && \
+		mycmakeargs+=(-DCMAKE_Fortran_COMPILER=$(tc-getF77))
+
+	mycmakeargs+=(
+		-DENABLE_ALGLIB="$(usex alglib)"
+		-DENABLE_BLAS_LAPACK="$(usex blas)"
+		-DENABLE_BUILD_DYNAMIC="$(usex shared)"
+		-DENABLE_CGNS="$(usex cgns)"
+		-DENABLE_EIGEN="$(usex eigen)"
+		-DENABLE_FLTK="$(usex X)"
+		-DENABLE_GMM="$(usex gmm)"
+		-DENABLE_GRAPHICS="$(usex X)"
+		-DENABLE_MED="$(usex med)"
+		-DENABLE_MPI="$(usex mpi)"
+		-DENABLE_METIS="$(usex metis)"
+		-DENABLE_MUMPS="$(usex mumps)"
+		-DENABLE_NETGEN="$(usex netgen)"
+		-DENABLE_OCC="$(usex opencascade)"
+		-DENABLE_PETSC="$(usex petsc)"
+		-DENABLE_POPPLER="$(usex pdf)"
+		-DENABLE_SLEPC="$(usex slepc)"
+		-DENABLE_PRIVATE_API="$(usex shared)"
+		-DENABLE_SYSTEM_CONTRIB="YES"
+		-DENABLE_VOROPP="$(usex voro)"
+		-DENABLE_WRAP_PYTHON="$(usex python)")
+
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+
+	if use examples ; then
+		dodoc -r examples tutorials
+		docompress -x /usr/share/doc/${PF}/{examples,tutorials}
+	fi
+
+	if use python; then
+		python_foreach_impl python_domodule api/gmsh.py
+	fi
+
+	if use X ; then
+		newicon -s 64 "/${S}/utils/icons/gmsh-no-text.png" gmsh.png
+		make_desktop_entry "/usr/bin/gmsh" "Gmsh ${PV}" "gmsh" "Science;Math"
+	fi
+}
+
+pkg_postinst() {
+	if use X ; then
+		xdg_icon_cache_update
+	fi
+}
+
+pkg_postrm() {
+	if use X ; then
+		xdg_icon_cache_update
+	fi
+}
diff --git a/sci-libs/med/Manifest b/sci-libs/med/Manifest
index 585e3f4d296f..c3c17a16d79d 100644
--- a/sci-libs/med/Manifest
+++ b/sci-libs/med/Manifest
@@ -5,5 +5,5 @@ AUX med-4.1.0-0003-build-against-hdf5-1.14.patch 4749 BLAKE2B 2968edac958b96a66c
 DIST med-4.1.1.tar.gz 50506725 BLAKE2B fb9bc3239c18c53fa42c5dd1101559746e8d38db2a3cb5fb47d1bf0cb578facc4ab95409af8524f5c20251848842cc1a331f6a816ce0754e9a6c95f507174ed1 SHA512 8917e7ecfe30e1259b0927c8e1c3d6efd86ed2386813f6d90217bd95589199478e587f0815031ab65cacf7901a30b77a6307414f9073caffe6e7f013e710d768
 EBUILD med-4.1.1-r1.ebuild 3420 BLAKE2B 57dd4c3ffd7c3d9cd7413252ae04a58f0cbe86223e7bca74eafc4caf808c7c194232ada980d652528f727e19a9a12a8e9d098d805d00d7b63169d30b05113de1 SHA512 30c185c5e7b88b8756af77c207138900745e7906721ab9fe675f663c01670754774ce34f366dc154bc128803f614453d1c448ea828f06d03320c39c8f2a31a2d
 EBUILD med-4.1.1-r3.ebuild 3187 BLAKE2B a0507b98b5f91eca0fad6a99f85e1ca886248deeacc00f6174774fc3d8fe3b5345fb7a7e3e43c05c56604e7aa6e5b20feed3dcf4cf91ca5c02785da2e26f4c07 SHA512 ead43d7ba64af6ee56ea6060294f194939d5311790e5b326b2c4f4d1ae54980e848c3812c8b341523a807afd6e2f7615ac2b2b456d15461004a927f420a2870d
-EBUILD med-4.1.1-r4.ebuild 3294 BLAKE2B e83528ccf87e99a460b4901ad48bd52a55ef5b281e8323bfb713e52c5a63c95615673d3875e73e13343b306e6d39c05d634f5aaf89a26ec7b303ee14f12cc6b3 SHA512 343f4ab9c74a6b2193135a6d5db9f72e08d52584187abe566dafac119fd07b00794bd5abff81569aa22ca0badba157f8e4e3ff42058312938468f99e4d3e5b58
+EBUILD med-4.1.1-r4.ebuild 3293 BLAKE2B b40f0eb28cfe476173dbcf6e802c482f5792dcb3389c56e434506a6520920bf743a1d7c57c981fc22080afb13a6fe7b3919cf67b470b2144b9ce98c648852a3d SHA512 aa0c3a15d22cc96587a1f49d86ba16168724ba619a30b51e012d43fa17efd50a687c37d2f4af9eff1b7424516b60e8d790129afa868a95678691cfe76c5c0bdd
 MISC metadata.xml 636 BLAKE2B de5e1c1d3f715459d5ca0945d0d795c1c549e6e20c27283140190bdc24289f4ccc0c12940e00aa689b90fd9af53749f0eabab44cecaf6815ef37adc1795f43e9 SHA512 60a3c3afd0db34569993b73d795830d86eb51778f9a7f0375d0b196c6f0862ca10a77c4c33ad2c906c56c6715be6f4452b61ffab5a25c254e480e50b64c021e4
diff --git a/sci-libs/med/med-4.1.1-r4.ebuild b/sci-libs/med/med-4.1.1-r4.ebuild
index 2b8c3a7cf96c..3d13e18e8117 100644
--- a/sci-libs/med/med-4.1.1-r4.ebuild
+++ b/sci-libs/med/med-4.1.1-r4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -16,7 +16,7 @@ S="${WORKDIR}/${P}_SRC"
 LICENSE="LGPL-3"
 
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="amd64 ~x86"
 IUSE="doc fortran mpi python test"
 REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
 RESTRICT="!test? ( test ) python? ( test )"
diff --git a/sci-libs/openblas/Manifest b/sci-libs/openblas/Manifest
index 1001a30767c9..97252ce8eeb1 100644
--- a/sci-libs/openblas/Manifest
+++ b/sci-libs/openblas/Manifest
@@ -6,5 +6,5 @@ DIST OpenBLAS-0.3.29.tar.gz 24671913 BLAKE2B 54075d623c2241c0153d84111b94945dbb2
 EBUILD openblas-0.3.25-r1.ebuild 5998 BLAKE2B b34389f4c292ab5ac1506616c31d0be394e256206c2db8ded4574626a0298a5ee0d0d745c96fd9c68d063543b7be51e9a980f6a2f4a73c6c9c23f83f01770de5 SHA512 d0fb3979242ba04ccbf437a97e77ef4780d57b102c92c1596e6455e13581fc03c5bdc2b03a25a01385ef0cdbb9ef01cd3e4cd30215a8237fa440f6be8fd483e9
 EBUILD openblas-0.3.26-r1.ebuild 6058 BLAKE2B 2091a64c7555c0db8f6dfd825e91a8a872e5c4d387bc7a65d97871b8bec26b9e8442e625fef2aac717d213f1235c0b446233ae4eb146b3d35507c652e923be5b SHA512 f2f4c50250ae2d33dc70483ed6c8971b11c39a2f3e41141f3ba6c9aef30f822bc63b13f24ca49e04b07b5fb2446505da9537735e6108edadb45ee717e67c175c
 EBUILD openblas-0.3.26.ebuild 5999 BLAKE2B cc659bbc1ba9856927e05dd331848a0c58214d513ad49cf168a52498c0ec81fe305e8e3e681d70e2a4da577f16ccee1cdbd2e1eba0cb7757d4c1018190373f69 SHA512 efa071a6469fa258c200c2548bd6c3b0cd6842898c7ac40d1b0dff36ee8d6165b83a4abbafa4b887ae30d3aa7a002516c2f647f38bbd98c26ee6f0b1ae58db6a
-EBUILD openblas-0.3.29.ebuild 6059 BLAKE2B 1166996b0aff57998d916846172443656e2418b3b6d6aedda40224ba28041ed36be8ea26eb6b892cd45a02934b80e38c798548498d1105e507c9e3e0a8325e1f SHA512 4d0226ab6a674683cc494891746dc9d1dddb15c7491bc92e56da78c79cb3a39b4822a5c5fbc50361d652cd9158447396047692456656880dd871dc39f3c66c57
+EBUILD openblas-0.3.29.ebuild 6058 BLAKE2B 3f5bd539837838d96e008c2270f5cd6e218e8562839d65bae889602342bcf608de7530d67d642d240fb36335a63cdec25f53e4992f79088f337f035dc7779613 SHA512 99dce0e7bc1788836bd80ef41312fb2e845758b662537451497d00ce955b79836b3b39c4ffec1cf1b26286a682ccc02ca7d9d2424d6e37a2b82177f61dda84d8
 MISC metadata.xml 1561 BLAKE2B 5ba7ec66dd8ba7ca8bc29bc0193b48b6a82b4949bb79bab461400040667aa66aac3cfd2ad9c7323798048fd43d18ac96a562d53b68f3f7ae8bf8505ac7a04691 SHA512 05272eb56480ff82b240d0f430df3df03981e24b971dbd37c13d464f4f4b334bac19b54915446a09326a334aa76249bb79a4fa389d26150365f21389992f9a48
diff --git a/sci-libs/openblas/openblas-0.3.29.ebuild b/sci-libs/openblas/openblas-0.3.29.ebuild
index 61819fb85337..e52f67a83318 100644
--- a/sci-libs/openblas/openblas-0.3.29.ebuild
+++ b/sci-libs/openblas/openblas-0.3.29.ebuild
@@ -13,7 +13,7 @@ S="${WORKDIR}"/${MY_P}
 
 LICENSE="BSD"
 SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~loong ~riscv ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+KEYWORDS="amd64 ~arm ~arm64 ~loong ~riscv ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="dynamic eselect-ldso index-64bit openmp pthread relapack test"
 REQUIRED_USE="?? ( openmp pthread )"
 RESTRICT="!test? ( test )"
diff --git a/sci-libs/pdal/Manifest b/sci-libs/pdal/Manifest
index d856df48af33..21781d51e005 100644
--- a/sci-libs/pdal/Manifest
+++ b/sci-libs/pdal/Manifest
@@ -3,5 +3,5 @@ DIST PDAL-2.8.1-src.tar.bz2 87507277 BLAKE2B 634ba5f2c5548bfa1fbdcc257185dcd99d2
 DIST PDAL-2.8.2-src.tar.bz2 87504277 BLAKE2B b2037a4fe5ac369380d2b2d83a2210a3c17757f9e6f749e819854d7356ba07d85b83fe3221ab9024f40f8a9f0ec6ee86573092914ac633af56b361a2f128cb00 SHA512 82dc84192e0cda809f4b12233e009c0c92328bf78001fc6394f56b28514a4b20de17dd354904d44cebc40c28a78828c47a1324b749143cc5b41b6c322902a442
 EBUILD pdal-2.8.0.ebuild 1499 BLAKE2B 70d7f4061f630eace363b334efa95fa7e56dcf602d7b5036ff3300108175385563072907dc9dde305d302e07ad851485032ae1ea72c0ac74e8f184a9927b60f4 SHA512 9fa63a1b410e51a5b8ceaa13c44ad5a741c0dcd263dd0d024c27eb1a4a5ef0efcafb103a705fe837ffd4630d7062d76094fc75d4a76fbd2f8301a0b279ddf73f
 EBUILD pdal-2.8.1.ebuild 1499 BLAKE2B 70d7f4061f630eace363b334efa95fa7e56dcf602d7b5036ff3300108175385563072907dc9dde305d302e07ad851485032ae1ea72c0ac74e8f184a9927b60f4 SHA512 9fa63a1b410e51a5b8ceaa13c44ad5a741c0dcd263dd0d024c27eb1a4a5ef0efcafb103a705fe837ffd4630d7062d76094fc75d4a76fbd2f8301a0b279ddf73f
-EBUILD pdal-2.8.2.ebuild 1500 BLAKE2B 45c7dc32cfaf105bbb3848dd46360c02b41f7cb927b182e469ad6ec47a7e2048f0c66fc898421800a5be50bec9f0c6bb4b7a9afac43cff5fe3a656f9255b3e52 SHA512 d0564d156c9d19fb02bb73ef2ef4ed5d7ab8397998d83531e52d9d619e6e8d83a5b49b6196a366b2f88d0f3afe12678fa157c02f20b19c305ba9d3b3517cd9af
+EBUILD pdal-2.8.2.ebuild 1499 BLAKE2B efc6c643627cc7dfd8b9f35752a1256ad9cf044f13c76245d578d3104612e0a1d1691ea2257c11ef562e88967390139a1a7a8304f5131c68b0f1e4c6895894b1 SHA512 53ea602871426911ab071fa6387f1abc701d7a40e6f00df47ca070849184be0baec3e23b94c9d24cf424ec8b4bc57b559882daeb8ea42fd73f76d261dfdb86db
 MISC metadata.xml 799 BLAKE2B 44fff88edc36553687a49ecf5113b1f7f3c8d092e82ef4e45f0d96cf53cc619647f45b3d3439a5b98bf43a8965e1b80582e7b074489dcd69f6f3aad9e5c7f59a SHA512 da405bacd840b714fe274fa5ca658f7a51b0078054058dcce46f690b33e641579981739de9511f4a876ff0f88aec5c2dbaa59e4db035eb9a85bdd8e9725bc7c2
diff --git a/sci-libs/pdal/pdal-2.8.2.ebuild b/sci-libs/pdal/pdal-2.8.2.ebuild
index d1a156dda0ca..12a63f0852e2 100644
--- a/sci-libs/pdal/pdal-2.8.2.ebuild
+++ b/sci-libs/pdal/pdal-2.8.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 2021-2024 Gentoo Authors
+# Copyright 2021-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -12,7 +12,7 @@ S="${WORKDIR}/PDAL-${PV}-src"
 
 LICENSE="BSD"
 SLOT="0/18"
-KEYWORDS="~amd64 ~arm ~arm64 ~x86"
+KEYWORDS="amd64 ~arm ~arm64 ~x86"
 IUSE="debug postgres test"
 
 BDEPEND="
diff --git a/sci-libs/qfits/Manifest b/sci-libs/qfits/Manifest
index 6d4cb9e2fa5d..b55c46946e41 100644
--- a/sci-libs/qfits/Manifest
+++ b/sci-libs/qfits/Manifest
@@ -1,5 +1,7 @@
+AUX qfits-6.2.0-includes.patch 834 BLAKE2B a72dbd038c9f753b98d7bde23b8eceffd80e2bc639bb618fb0200a0c4559ee2afb2e9bb219d37cecf93b3cce5d4562c4ea77bfed76ca85bbbf7e7bb2d70f2d6b SHA512 260b1b68e02142dc490e11d1c66e3c0876df3c331f5a5ad799fd984456c6eda56b4265be899f20cfff404d84ad770843c7c1947aeb8cb59cafc787015bca8151
+AUX qfits-6.2.0-m4.patch 725 BLAKE2B 66950bbfda444e58bab84197443c9746f71e75251f73b24d76c8ba023f4c5b1a4abc997c3416e2a6016a70bd6e403d5bee4a37f7dfb1f523517fc91e180d44f6 SHA512 77f001a3e45d8d85abed5c7933cfba9157fbb3f7530e905c1f581a58b90bf8492ccc4d1f2be42f836d67dba2697a7c8ff41a3292deffc2ce87e622bb61b97047
 AUX qfits-6.2.0-open.patch 512 BLAKE2B a3701d2a9f8d6cbee3d5d9e95b281068b29b2d2f327140086830462a89cb657b00fd1a6e57fd5b593ada0788ba398cfda1fbdd15c9bf302fe84d6b7e09d32e14 SHA512 83bb2d96725e62fd1f593cd38f86d7c4dba2248b34d9eeecb6af11d41b20fde2a5b0bf22e3b64001d9d473b0344120f3df604982ab7d998c37c08771f17309b5
 AUX qfits-6.2.0-ttest.patch 304 BLAKE2B a5cebbd782f1d8fd9090a20f51a52fd756509b479ec199c1efea734e557eae5994515ab003ac920dde1781ee98afff0cb25ed0eb91a92e8821d269e1e9188c8d SHA512 dde0bfbe7aef8ec381ec57b4fdae5419c9ad23ec20d90ee795bf5cc124abf3e6e936f7069d3cc56ff86b766425c2a94304048263310fcf3f7c84415638e073f8
 DIST qfits-6.2.0.tar.gz 475191 BLAKE2B fea94bf77b07e5fbc9493f4bafbf37387b4f9ae83212ffc5a6c0607cad972a592e3937ba042ee94f053f30fd05cbafb8fcbcf2df1c4cd6ee4d2422bf108d9395 SHA512 a0f6863a9e5b26d08de487cfdf468b3d04218a36a01cd9df8b786b1cdf2ffa61acf12b087f4fbd751ba023f02b5a32410949a4ee08432108a7129a283ab3d824
-EBUILD qfits-6.2.0.ebuild 596 BLAKE2B 90ec42dfc65cdc7352b05d357ac0974ebbc0283b35bc07dbd883ffd0f0c92b1bed80a3b017a54341e5d6710a16eee8ac8a25c7a653e9c196a21c820004c8a0ed SHA512 4ca8e8669e922ebf91bd1a4fa1295bf33abec479e050211531af77c969574ec4dacd7f51b0743d5d7e651acbe72c521db6f160168a13956d6a9c5b2f772da41e
+EBUILD qfits-6.2.0-r1.ebuild 744 BLAKE2B 06a83bb880abbe28a4eb72e3f48dda87a503c46eb0155be7d49a162e06810bac1823c1ae14fd3c00f8c8724f9cc86fb28b0977dd6b8c548cc118b2d54f1bc6eb SHA512 25fcb91cb89427d0e48f5e4d028d612e5e6423e82ee85ab68fcfd4e3f163146d2361c3a2b40c14fff5c4333aa9597a33ff19d433d8c8d5ae5120c58ab413ac37
 MISC metadata.xml 852 BLAKE2B 8845945452ba7410e80bc386662acfdf3dc2fa5ff512f22964efdccb3b10207f0276c781a4ee81fccedd60fcc995049a7ff3010fd53e8b5f3c14508b1b57ae46 SHA512 8dff179d349cb4f91e2b1292b8830071a22d3611fa8800be6ff015a4750277587153a19213fe458e2b7b6632ef60b06c9e00ff782d955ae7ab04b279cd0a9e7c
diff --git a/sci-libs/qfits/files/qfits-6.2.0-includes.patch b/sci-libs/qfits/files/qfits-6.2.0-includes.patch
new file mode 100644
index 000000000000..7589b49301a1
--- /dev/null
+++ b/sci-libs/qfits/files/qfits-6.2.0-includes.patch
@@ -0,0 +1,32 @@
+Missing includes in main library and in tests
+https://bugs.gentoo.org/886463
+--- a/main/dtfits.c
++++ b/main/dtfits.c
+@@ -33,6 +33,7 @@
+ #include <string.h>
+ 
+ #include "qfits_table.h"
++#include "qfits_tools.h"
+ 
+ /*-----------------------------------------------------------------------------
+                                    Define
+--- a/main/qextract.c
++++ b/main/qextract.c
+@@ -32,6 +32,7 @@
+ #include "qfits_table.h" 
+ #include "qfits_image.h" 
+ #include "qfits_rw.h" 
++#include "qfits_tools.h"
+ 
+ /*-----------------------------------------------------------------------------
+                                Function prototypes
+--- a/test/test_pixio.c
++++ b/test/test_pixio.c
+@@ -41,6 +41,7 @@
+ 
+ #include "qfits_header.h"
+ #include "qfits_image.h"
++#include "qfits_rw.h"
+ #include "qfits_md5.h"
+ #include "qfits_memory.h"
+ 
diff --git a/sci-libs/qfits/files/qfits-6.2.0-m4.patch b/sci-libs/qfits/files/qfits-6.2.0-m4.patch
new file mode 100644
index 000000000000..99b39bdad451
--- /dev/null
+++ b/sci-libs/qfits/files/qfits-6.2.0-m4.patch
@@ -0,0 +1,36 @@
+Missing system inlude in self-defined autoconf tests
+https://bugs.gentoo.org/908483
+--- a/m4macros/eso.m4
++++ b/m4macros/eso.m4
+@@ -252,6 +252,7 @@
+                        AC_RUN_IFELSE([
+ #include <stdio.h>
+ #include <stdarg.h>
++#include <stdlib.h>
+ 
+ int
+ doit(char * s, ...)
+@@ -701,6 +702,7 @@
+                    [
+                        AC_RUN_IFELSE([
+ #include <stdarg.h>
++#include <stdlib.h>
+ 
+ void f(int i, ...)
+ {
+@@ -733,6 +735,7 @@
+                    [
+                        AC_RUN_IFELSE([
+ #include <stdarg.h>
++#include <stdlib.h>
+ 
+ void f(int i, ...)
+ {
+@@ -784,6 +787,7 @@
+                    [
+                        AC_RUN_IFELSE([
+ #include <stdarg.h>
++#include <stdlib.h>
+ 
+ void f(int i, ...)
+ {
diff --git a/sci-libs/qfits/qfits-6.2.0.ebuild b/sci-libs/qfits/qfits-6.2.0-r1.ebuild
index 181c4777ba8a..99af0c8cacb7 100644
--- a/sci-libs/qfits/qfits-6.2.0.ebuild
+++ b/sci-libs/qfits/qfits-6.2.0-r1.ebuild
@@ -1,10 +1,12 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
+
+inherit autotools
 
 DESCRIPTION="ESO stand-alone C library offering easy access to FITS files"
-HOMEPAGE="http://www.eso.org/projects/aot/qfits/"
+HOMEPAGE="https://www.eso.org/sci/software/eclipse/qfits/"
 SRC_URI="ftp://ftp.hq.eso.org/pub/${PN}/${P}.tar.gz"
 
 LICENSE="GPL-2"
@@ -12,10 +14,18 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="doc"
 
-PATCHES=( "${FILESDIR}"/${P}-{ttest,open}.patch )
+PATCHES=(
+	"${FILESDIR}/${P}-ttest.patch"
+	"${FILESDIR}/${P}-open.patch"
+	"${FILESDIR}/${P}-includes.patch"
+	"${FILESDIR}/${P}-m4.patch"
+)
+
+src_prepare() {
+	default
 
-src_configure() {
-	econf --disable-static
+	# https://bugs.gentoo.org/908483
+	eautoreconf
 }
 
 src_install() {