gentoo auto-resync : 05:12:2024 - 02:07:17

9 files changed, 119 insertions, 6 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index 014f4e577638..84542deb67c3 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/dcmtk/Manifest b/sci-libs/dcmtk/Manifest
index 18dd4c33670d..c2d8a38311e6 100644
--- a/sci-libs/dcmtk/Manifest
+++ b/sci-libs/dcmtk/Manifest
@@ -2,5 +2,5 @@ AUX dcmtk-3.6.8-docdir.patch 754 BLAKE2B 3e2ee8a6a213015b14489f63ef002c8d2568e2c
 DIST dcmtk-3.6.7.tar.gz 6877857 BLAKE2B 242ba19ed3876b27c8eeb6917f9264911c951e91ab27d2ebd3e95ab5dcf55a0e18986cede87c8ab7e6280eafeb19fda120ccb2114d24a16f222b411b44cc28d8 SHA512 b9c227f496de65424256636fa7ad266affc6593f72c6849271da94837b68c93a5b8e056ecd09d46550b6ac0530c406ab9f71751d317a5fd4171a222f9fc9ca45
 DIST dcmtk-3.6.8.tar.gz 9628364 BLAKE2B 367885c3fda65b7b2e42555ba648800f9585cbd4c4d94e01f737110fc726ce3396df50ccd6f2c9bacc59284fc1381683b72506a3c566f795c8157da39a95fb2a SHA512 1bb2aad1aa63e0a1b79d92d7c932a969deccde03fdb484dbd44198effb58d50de44a2b0cda150ce7df63e4e986af5bc1f694c8a7988b4c049c578d83ba81184a
 EBUILD dcmtk-3.6.7-r1.ebuild 1989 BLAKE2B 47958171848d55e4e648abec64258fe3c6547f6c18daf6dc3f46e6e5e0c88afb3787d86dab6bda6c53ae13909cf1f7fd8fe956e1b4f1653a068fc6b3f06d5898 SHA512 902b2bd3dabfce90711f811eb0eafb14f3d61f9ff545046c3b223eda15aeb2985c6c7dfcd765014b179e4b177e5ca61a37561bbf5b19201fe19614ec8e7c4780
-EBUILD dcmtk-3.6.8.ebuild 1964 BLAKE2B 3ab45e0ddc8a9d1310ea6a0e447e8f5fc87b200dca2967a07df56418fa86404e616565680125a16fe45a814a555587956c117630edf8b5aca40581d5aededcf8 SHA512 7d74b24785c7c2987efc75e1550529d8fe59b7d3bcf8ba084e47f554e5a04081dbc45a642ef58e89249d552852139398e1867b32ac7c25c81f0b2d1f82fad33d
+EBUILD dcmtk-3.6.8.ebuild 1963 BLAKE2B cedac0e5bbbd5ef840347d3af28ef8951cca68b4c00170ab2109286dd8d33e5ef25980e51f761da8404cc96c7bed494aa3d4c975388f4257a43722387aac86fd SHA512 a558ad80d191b25e120c92fe66aca9b1689a2a5de9b3c4df89fb8279addc35bc6e012e24c4b52308ab83786934c682d0da01bb3e5f54ebc0efc2964db17408cc
 MISC metadata.xml 308 BLAKE2B 394345b977e2dd7598cd2acdf2af966f2efecef502a4f460e4fe323c095e3de8523c4217873d18f68198996e4ee08580f46543bf7e357a227f66dcd558191615 SHA512 b8117feeab19b0128c2378d36370e907338873a177c5d8f1cfaef79bf16e877fc455cc5096bccadb99a7238c02fd01c02ae9018a81aab013e0d1a1ccc4cd650c
diff --git a/sci-libs/dcmtk/dcmtk-3.6.8.ebuild b/sci-libs/dcmtk/dcmtk-3.6.8.ebuild
index ed291a83e208..ed8e58cef155 100644
--- a/sci-libs/dcmtk/dcmtk-3.6.8.ebuild
+++ b/sci-libs/dcmtk/dcmtk-3.6.8.ebuild
@@ -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/gsl/Manifest b/sci-libs/gsl/Manifest
index 37b9541551fd..0d2bbcd80191 100644
--- a/sci-libs/gsl/Manifest
+++ b/sci-libs/gsl/Manifest
@@ -3,5 +3,5 @@ AUX gsl-2.7.1-test-tolerance.patch 1700 BLAKE2B 5964fe42d8238dbb4d508f5bdce62463
 DIST gsl-2.7-cblas.patch.bz2 12073 BLAKE2B 71f2bdafdb1f42ca5c3515f8e39266242185218495705018d88e523be9bc776b39749156500cdc5746a16e481e9cfe2b79660e250eb1a70f3b18819d16fe11c5 SHA512 5b9b2a798079610d7d4981b83672cc978ed44b66aaf6e671794685f10bd4069764bb358870019dc0eec1e251639cde12aaa3598cae0e2fc050ea39c79435fe2f
 DIST gsl-2.7.1.tar.gz 7509209 BLAKE2B dd216c2fdb536e57b6e29613e46e1a05183fd18c47434039caac68fefffc0390cfe2f21eb117347d4bbdf9004de837ef2db02c17c01eaea4b615e3e45a4fd90f SHA512 3300a748b63b583374701d5ae2a9db7349d0de51061a9f98e7c145b2f7de9710b3ad58b3318d0be2a9a287ace4cc5735bb9348cdf48075b98c1f6cc1029df131
 EBUILD gsl-2.7.1-r2.ebuild 1461 BLAKE2B 7ac8ff18a2d22854219e11dc46fb238f7fbe1a6f585cd3f2e973d4d1e8ae2a0af80a2578af3d06b72d014d2388668fbfd520175aaf762f6484a34bd4e87dee9c SHA512 c6479af5b7f42f26f9511c0921056983b7176285f82d71ad0059dd82a392d71f41026f1a500b6171a0ba699a88ce7805397245159afa96d5424a1ad3fcfce56e
-EBUILD gsl-2.7.1-r3.ebuild 1512 BLAKE2B ee8037963ca2d8d728b34b68ac5827ab13c4bada71f7a5924d9829173e441985b86f0c62841d6c7b9c4986686d8f6de4e9bdb3d7454faf3131cc7f15ea0724eb SHA512 79f6fedb469813c50d0942a8cf586ddcbb6a4e4b0a4bba2acd7c217f93a4fd314fa784427d12d29d2daf97c31a1c445a79a02c6bf862d7355a160e54ef01cd83
+EBUILD gsl-2.7.1-r3.ebuild 1511 BLAKE2B 2984be15dc49b892386b345fcb8fd43dc64bdf684a3a74a4f07d27ab5981f576802d313f562aa5a6f91ebb83a5ea5cb4bb18e85898847da735c35668d2e034ac SHA512 20bcd3290a6c572d105a35a49c9164a5f619ab405f6514d20fbaad1698a17c2e9421e4ceec03a2e37e4261db3eb2eb9b7629be76fe9fbfa13ae2d118d88f5057
 MISC metadata.xml 1339 BLAKE2B 65c2b4eb597ccc4fe4ffb92d37e5800af6f9136fb3186bef0167d52584565faca0778ef775c0e736508cdf8eb480d26bc9a74dc799f37ff6fcd2131410f1660c SHA512 f8201bb6adb83ba875315a2201a97e1653d08665f5889d3fde83cb7ff196ae9f904372552d980b5e3c210e5aa855915827c1af32255539cab236e2b938d39888
diff --git a/sci-libs/gsl/gsl-2.7.1-r3.ebuild b/sci-libs/gsl/gsl-2.7.1-r3.ebuild
index 92ba86d4f2ba..1141ba3c0fd4 100644
--- a/sci-libs/gsl/gsl-2.7.1-r3.ebuild
+++ b/sci-libs/gsl/gsl-2.7.1-r3.ebuild
@@ -13,7 +13,7 @@ SRC_URI="mirror://gnu/${PN}/${P}.tar.gz
 LICENSE="GPL-3+"
 # Usually 0/${PV} but check
 SLOT="0/27"
-KEYWORDS="~alpha ~amd64 arm arm64 ~hppa ~loong ~mips ~ppc ppc64 ~riscv ~s390 ~sparc x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~alpha amd64 arm arm64 ~hppa ~loong ~mips ~ppc ppc64 ~riscv ~s390 ~sparc x86 ~amd64-linux ~x86-linux"
 IUSE="cblas-external +deprecated static-libs"
 
 RDEPEND="cblas-external? ( virtual/cblas:= )"
diff --git a/sci-libs/iml/Manifest b/sci-libs/iml/Manifest
index 7914f41eaf15..5a2eca706b83 100644
--- a/sci-libs/iml/Manifest
+++ b/sci-libs/iml/Manifest
@@ -1,5 +1,5 @@
 AUX iml-1.0.4-use-any-cblas-implementation.patch 865 BLAKE2B 5167ab1a5f82e5fce596dd3f7cdb3a711f0fd5c86fefc6a36574bcbc63e464115895e43d81eba3d4d04bd016266817440098eed18fab04b30bc45dee37497ffd SHA512 36181f90032b6f4d786d50b327cb342d5c8f4431dd556e4267e99b02e92161adbb9c23d7815e1764d8f237b1f008b2abebc27bdc422ba7296144999f0cde3c19
 DIST iml-1.0.5.tar.bz2 391757 BLAKE2B 5895b353269ce19e17e2522f78eb705c89a47ed3c6cce54d1b7ab3003f59d0a13050b30ce9cedbf38392c737c169740b6c2433f1a74856b0f9d4e6e007ebf804 SHA512 b5a85982636035cc50acba7dcff5478c6271be3669313f01915b2761302d4c77617c0dd7932daf74433098670d3ffdb2ef19eb24450b40709750a0b7c8f797f1
-EBUILD iml-1.0.5-r1.ebuild 817 BLAKE2B 83ce2f1e1c5a5a8aca8754fb198f2164636a38257a1441b2bb22685781a72aba68434b8c16168201a672705f9c10c023322f86b921abb8010a52f591953d5763 SHA512 f4c14882a71f9b59addacc315109c66b1ac29e9e869197231444b87d9e85674f83093648422c9776461a2504a6ecd96ffc8b5ea01e440578be183e1668aa32df
+EBUILD iml-1.0.5-r1.ebuild 816 BLAKE2B 35ebaaa0b53f0abc05978c3fffa358f5f9d88c01a2566f8288409eb226f6fba2d5e1cc0bf42dcc92ee722dd0fed7ff5068b885212173c08c35f7bc9c0a4df9b1 SHA512 38db336a064e344ea9085a8ae7f3ce6885e345995db439fb9665fef5455cf1b4ced91d86b54c5c2df9e83fa6f84b7547fc54e9597c1c590d3ddb77f2391e1abf
 EBUILD iml-1.0.5.ebuild 766 BLAKE2B 4c9b448852590c3cb49c8c0c8f4c9d8ffc8f37022f7a3f16d18ef2c2f4defc5cc4aeefdadf62798c5f7c335d21db3c456bc8350feacc5a5814ffa1a9ee5d7d86 SHA512 033e3935ef2d5dec173cd1ebe54d366fd118b4989a411f97875e2d23adb21d0558181670d39f5ce274f600f2e00f177dbd82ac7fb0f86a26edc737cefb4bbd55
 MISC metadata.xml 435 BLAKE2B 2dcbbbbeab2b53ad1407e3e52e4a0067853099061866f8a1f20eabd82ef7eeafc34fc806701a0b496ea874d5c47ed46c3963d5f0996e623eaf5172bd99141ce0 SHA512 f3ed1aacb63866ab9e5df4d62d8c5dd50a264d32fa1c52f1b960822904c185cbdc0ae708b391e321378b1bdf1de29bb4073752c43bb82609877ff607d65d2c16
diff --git a/sci-libs/iml/iml-1.0.5-r1.ebuild b/sci-libs/iml/iml-1.0.5-r1.ebuild
index f967cdfd1ab6..94dfc5229ec5 100644
--- a/sci-libs/iml/iml-1.0.5-r1.ebuild
+++ b/sci-libs/iml/iml-1.0.5-r1.ebuild
@@ -12,7 +12,7 @@ SRC_URI="https://www.cs.uwaterloo.ca/~astorjoh/${P}.tar.bz2"
 # COPYING is GPL-2, but the files under src/ all have a BSD header
 LICENSE="GPL-2 BSD"
 SLOT="0"
-KEYWORDS="~amd64 ~riscv ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ~riscv ~x86 ~amd64-linux ~x86-linux"
 
 DEPEND="virtual/cblas"
 RDEPEND="${DEPEND}"
diff --git a/sci-libs/med/Manifest b/sci-libs/med/Manifest
index 0cc83975addd..8ae14bfd34e8 100644
--- a/sci-libs/med/Manifest
+++ b/sci-libs/med/Manifest
@@ -5,4 +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 3252 BLAKE2B eff71ed92899dfdc8434e0dd9c0bab6cc1c8f41b54dfb7c735a53e3e6ce837a7c5029f74c187bd9b3bd007628b24e28482db451115eaf6fecf061b742ebe8b13 SHA512 a825b4327303a4132a21a2689b6c8ed69f67426a2b797a8134460114a8360d45018c2f7d383c0922b031970eb424efa72a4417c1a72c8258cfeb8a86d3807814
 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
new file mode 100644
index 000000000000..ce0d521ecfd1
--- /dev/null
+++ b/sci-libs/med/med-4.1.1-r4.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+FORTRAN_NEEDED=fortran
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit cmake flag-o-matic fortran-2 optfeature python-single-r1
+
+DESCRIPTION="A library to store and exchange meshed data or computation results"
+HOMEPAGE="https://www.salome-platform.org/user-section/about/med"
+SRC_URI="https://files.salome-platform.org/Salome/other/${P}.tar.gz"
+S="${WORKDIR}/${P}_SRC"
+LICENSE="LGPL-3"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc fortran mpi python test"
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+RESTRICT="!test? ( test ) python? ( test )"
+
+RDEPEND="
+	!sci-libs/libmed
+	>=sci-libs/hdf5-1.10.2:=[fortran?,mpi(+)?]
+	mpi? ( virtual/mpi[fortran?] )
+	python? ( ${PYTHON_DEPS} )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="python? ( >=dev-lang/swig-3.0.8 )"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-4.1.0-0001-Gentoo-specific-Adjust-install-path-for-build-dir.patch"
+	"${FILESDIR}/${PN}-4.1.0-0002-Re-add-option-for-building-Fortran-library.patch"
+	"${FILESDIR}/${PN}-4.1.0-0003-build-against-hdf5-1.14.patch"
+)
+
+DOCS=( AUTHORS ChangeLog NEWS README README.CMAKE TODO )
+
+pkg_setup() {
+	use python && python-single-r1_pkg_setup
+	use fortran && fortran-2_pkg_setup
+}
+
+src_prepare() {
+	if use python; then
+		# fixes for correct libdir name
+		local pysite=$(python_get_sitedir)
+		pysite="${pysite##/usr/}"
+		sed \
+			-e 's@SET(_install_dir lib/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages/med)@SET(_install_dir '${pysite}'/med)@' \
+			-i ./python/CMakeLists.txt || die "sed on ./python/CMakeLists.txt failed"
+	fi
+	sed -e 's/med-fichier/med/' -i CMakeLists.txt || die "fix paths failed"
+	sed -e 's|doc/med-${MED_STR_VERSION}|doc/'${PF}'/html|' \
+		-i CMakeLists.txt || die "fix doc path failed"
+
+	# bug #862900, already reported upstream. CHECK on updates!
+	filter-lto
+
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		# as indicated in the CMakeLists.txt, the shipped documentation is generated by a custom doxygen,
+		# so let's avoid rebuilding it because it will be different
+		-DMEDFILE_BUILD_DOC=OFF
+		-DMEDFILE_BUILD_FORTRAN=$(usex fortran)
+		-DMEDFILE_BUILD_PYTHON=$(usex python)
+		-DMEDFILE_BUILD_SHARED_LIBS=ON
+		-DMEDFILE_BUILD_STATIC_LIBS=OFF
+		-DMEDFILE_BUILD_TESTS=$(usex test)
+		-DMEDFILE_INSTALL_DOC=$(usex doc)
+		-DMEDFILE_USE_MPI=$(usex mpi)
+		-DMEDFILE_USE_UNICODE=ON
+	)
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+
+	# we don't need old 2.3.6 include files
+	rm -r "${ED}"/usr/include/2.3.6 || die "failed to delete obsolete include dir"
+
+	# the optimization done in CMakeLists.txt has been disabled so
+	# we need to do it manually
+	use python && python_optimize
+
+	# Prevent test executables being installed
+	if use test; then
+		rm -r "${ED}"/usr/bin/testc || die "failed to delete C test executables"
+		if use fortran; then
+			rm -r "${ED}"/usr/bin/testf || die "failed to delete fortran test executables"
+		fi
+		if use python; then
+			rm -r "${ED}"/usr/bin/testpy || die "failed to delete python test executables"
+		fi
+	fi
+}
+
+src_test() {
+	# override parallel mode only for tests
+	local myctestargs=( "-j 1" )
+	cmake_src_test
+}
+
+pkg_postinst() {
+	optfeature "xmdump scripts support" dev-lang/tk
+}