gentoo auto-resync : 02:01:2023 - 20:24:39

9 files changed, 131 insertions, 9 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index ee678489e30b..f00a5d0cbba8 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/dealii/Manifest b/sci-libs/dealii/Manifest
index 2288d92ad23b..bcd0abf27c4b 100644
--- a/sci-libs/dealii/Manifest
+++ b/sci-libs/dealii/Manifest
@@ -9,5 +9,5 @@ DIST dealii-9.4.1.tar.gz 30298204 BLAKE2B 499f542c7a7f071d04048127199c7bebf5668b
 DIST dealii-9.4.1.tar.gz.asc 246 BLAKE2B dbb1dc7b3e8a97f29287f154d11cd3db2566fdc4c7667fa57e686e2feba33f2115546408365f0e8f490ba593cb582b12489de373da3e33e8702b6e16804c7ebf SHA512 eb987d34f19b59d523d79f3c2c99f5f3125b1d0c71af0eb32b77ad5959d6197b79f1971a8a79dbc52bab698335dcb6091aac88c51d845a1e07d3681c089754c7
 EBUILD dealii-9.4.0-r1.ebuild 5816 BLAKE2B 137b29949c766c705c7a52b664e068d8bfb5cbaaa18f0f1529100e72b86c15822385c705d0466863f2bb79056e7bdddfc0b62037ee985dc584d10c3d80562086 SHA512 19653f1d97a14ee787d29c56cc5b8dac6f6d54641da4789cb6764001ce4990fb3a951f8e27b6760cc32719846adc18c32870e42fd33ab937d5b1d1194ca8da86
 EBUILD dealii-9.4.1-r1.ebuild 5816 BLAKE2B 137b29949c766c705c7a52b664e068d8bfb5cbaaa18f0f1529100e72b86c15822385c705d0466863f2bb79056e7bdddfc0b62037ee985dc584d10c3d80562086 SHA512 19653f1d97a14ee787d29c56cc5b8dac6f6d54641da4789cb6764001ce4990fb3a951f8e27b6760cc32719846adc18c32870e42fd33ab937d5b1d1194ca8da86
-EBUILD dealii-9999.ebuild 5425 BLAKE2B 67f73b1cbc01c9884d8ab921f8e1eb8238ea31cb735ece3edb5706cb594cac7decc57e62df3819be85f4bf0ad8ae650ac5c2a43da38320a3131aa3eccd8d9280 SHA512 fd560c46dbb2fc9c440f00c3c48f9168d38c3d38f461c87c72ba168858a47d43258a72564c3c03dfbc09c47bff77e1cfe7541dc6acc85a14664594ba079c3378
+EBUILD dealii-9999.ebuild 5457 BLAKE2B 563555bc48094b503054f1b4ffe08a82f36c455c1aaa9fb4fe75e501bac9d6112418c5b438069cca49002436e453a11afdf9db03bc1e5c9b430ff674ed0f2e0b SHA512 5e774ba521cb02c2b20cb7b9c62dee2642831eddc20322244f287f28019ecaa32e1bd1cbfea1339ba1c2f9466b54723b3e5cae7968ed3ffd6e17f300fc16a7aa
 MISC metadata.xml 2391 BLAKE2B 904b31425264a2da185a49a388bfb9415ca95c818e3c97774ccdf8e26baa706f0d2f4e6478dec4854a0164e5cdac512e4476f09ba6e3ec84d8a4b45b0e4d5131 SHA512 1bda00424bf63b1520818b3b350f08fc995200214a659435ce16b979de95077b82ed581320c15c9799d1934c0b58fcb56552329ebd4c5e9d93f01110027091d0
diff --git a/sci-libs/dealii/dealii-9999.ebuild b/sci-libs/dealii/dealii-9999.ebuild
index 3204e3f77632..3d175695c483 100644
--- a/sci-libs/dealii/dealii-9999.ebuild
+++ b/sci-libs/dealii/dealii-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -49,6 +49,7 @@ RDEPEND="dev-libs/boost:=
 	adolc? ( sci-libs/adolc )
 	arpack? ( sci-libs/arpack[mpi=] )
 	assimp? ( media-libs/assimp:= )
+	cgal? ( sci-mathematics/cgal )
 	cuda? ( dev-util/nvidia-cuda-toolkit )
 	ginkgo? ( sci-libs/ginkgo )
 	gmsh? ( sci-libs/gmsh )
diff --git a/sci-libs/mumps/Manifest b/sci-libs/mumps/Manifest
index 05e869900f81..ae40e3b48fa2 100644
--- a/sci-libs/mumps/Manifest
+++ b/sci-libs/mumps/Manifest
@@ -1,3 +1,3 @@
 DIST MUMPS_5.3.5.tar.gz 3940501 BLAKE2B f1767483bb23744a2c5ed11b0823c5b023377d5212abbe29a177cce5b5e51e6f2f391d7caa17022646e36c9e4b4fb4af80b03ac6cf8e89f37502ed960138bbbe SHA512 6e3bb081f38af8540ada7b4fb54c6e766739c854e2a3dd253e3e012eee05dae30064b1b4a8d7493f10691725aba4cc9e80544b0fe5b71670cb0b2726ccfc4439
-EBUILD mumps-5.3.5-r1.ebuild 5889 BLAKE2B ab6947b760ad7de40d66e463f4eb9427c190909adb1e8f097f441f65f91252e1080bfb1d3a005a1f07f336bef98603095b470f2a8a314ac3e431f5f56f856136 SHA512 e8d307e47b57ce914759b9abe6f78a43c1f69aeb071b75220f3bce5ff19bc177405eeb9bcdfa1890df514722cc1e8067f9fb1851f99abaa40fd4ddeae8ff9e82
+EBUILD mumps-5.3.5-r1.ebuild 5941 BLAKE2B b51ab50f65c1772c8e55d247619673e24a7974d2a35c3e678ac2d94e8864e0fe9729ee2ee7484f51f97c5af2cac73259727525b6ab803501893985a2daa65ac1 SHA512 decb09d642d058d82adc8fb323a037cefd147b739cfe306651ef2258b8963772b1dfd57372301d75ac21659b505a52a02f5119db02b6dc30236c58a502c5fb77
 MISC metadata.xml 865 BLAKE2B c00217ca50d3cecaef1efd26df1e449ea0a4d37a228b760f7f99e5d7e98d2355d3a1f535e13f44a9b829793d2a66c54e7546e9d630d28336d15bd46476532398 SHA512 836d7249823f0afee607588dcda0e1af2002857b90292a9b28f22649b784ca2040fc363c6d3da5360d21514c28aac88313a19337d5b9614e8d586f85506d76a5
diff --git a/sci-libs/mumps/mumps-5.3.5-r1.ebuild b/sci-libs/mumps/mumps-5.3.5-r1.ebuild
index 76020a68524a..7afc88c08537 100644
--- a/sci-libs/mumps/mumps-5.3.5-r1.ebuild
+++ b/sci-libs/mumps/mumps-5.3.5-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -145,7 +145,8 @@ src_compile() {
 	# Workaround #462602
 	export FAKEROOTKEY=1
 
-	emake alllib PIC="-fPIC"
+	# Use "-j1" to avoid a spurious race condition
+	emake -j1 alllib PIC="-fPIC"
 	if ! use mpi; then
 		#$(tc-getAR) crs lib/libmumps_common.a libseq/*.o || die
 		LIBADD+=" -Llibseq -lmpiseq"
diff --git a/sci-libs/pyshp/Manifest b/sci-libs/pyshp/Manifest
index 518a8f3248ed..0da2a5a4dece 100644
--- a/sci-libs/pyshp/Manifest
+++ b/sci-libs/pyshp/Manifest
@@ -1,5 +1,5 @@
 DIST pyshp-2.1.3.tar.gz 219626 BLAKE2B 2da94cb4b1514a504b9f961b58add973a73dea641ad5867b670860000decd29af72092079b5d16f516b99a59be83028f4698faa2cb013200e533bbe772746d48 SHA512 249302e784bb38860037242b70899faaf504ef626c37decca44dc0d7c4f9482737e3234c0002393d1ef9800778715fc2b9946f3e3f3ecf507921e9db218d0d33
 DIST pyshp-2.3.1..gh.tar.gz 2213685 BLAKE2B ca5b87dec442508bc4a0612982984ba0fb91aa8acffddb6a448c43ccf42285305600a5e28e1fb781a3d94e8ce0624d027642fddcc5f2176dca3df095e59df170 SHA512 08844492b8d1d824c639844f7f314909d946bd4d3703a4f8d4cb64d400729671b42ff5b0f80aa68d9469f3939a3c7619ba13c9efdcba3b244ec01d7be3a371c5
 EBUILD pyshp-2.1.3.ebuild 549 BLAKE2B a48d9defa84bed8d33e05da68c64daa98d2f4af0265e35d7ddecb7458d8104536b9c7f16070fb009d0aa72d244440ca13e1effec239efbcd9efce276df07abc5 SHA512 ff101b2859f9d70b3f4b06356820709f55d6451d3b7116a3ed17f3e0331d364a2c76f9e405ec078a39b09a829e50848b8ca4b602b5c1d54ef8a9ddc8a3f439b3
-EBUILD pyshp-2.3.1.ebuild 697 BLAKE2B 8ac219194cbb868665340e4f087e9d88a4939ce3ff10fb22b38679bc6014704f2ed47a369a8e8090fb287dde821927863cb00498b39e6ff2c508719272ce89a9 SHA512 716e6f063da3d13bff5e75ac5017d3e2ff34ae39f437abe17955472e84eb1ccf07cf2eebe794cf796e1506c40b40213facc025be02ff0888f3d99151c05e474a
+EBUILD pyshp-2.3.1.ebuild 744 BLAKE2B 1d455bfd51f242582fb23d65ed7a14d5b4c57ebd083e5e1432c7e87c635f21f9f6a1d776fdce13d1db0af09e699b48325de1bb06185ef9fff23af6fb7ce257c1 SHA512 b9102ce180168dea3b9790e57af68fbe424ea0847bdd7d43cb7924ed35e9d6787658a89f7125346955435d01c6c4d839199fa6b4ef3f98f879c5d55e14424d88
 MISC metadata.xml 392 BLAKE2B d0502636f7a083b4eca21dd9c9cb2604d96ec91616c88566f42687e53be965090683984d3289ae332c94309e89b25f39a12b601467abec718365d53f423fe21d SHA512 b3914985e7b8857a7f0841d4e987746f64a571a83ed3a237621c048e073c1f5a77512c40011ee1808c3ffadff08c03adc53ffe767e8a5f35c628882df779b771
diff --git a/sci-libs/pyshp/pyshp-2.3.1.ebuild b/sci-libs/pyshp/pyshp-2.3.1.ebuild
index af715dcb9263..dc041f721f8e 100644
--- a/sci-libs/pyshp/pyshp-2.3.1.ebuild
+++ b/sci-libs/pyshp/pyshp-2.3.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI="8"
 
-PYTHON_COMPAT=( python3_{7..11} )
+PYTHON_COMPAT=( python3_{8..11} )
 inherit distutils-r1
 
 DESCRIPTION="Pure Python read/write support for ESRI Shapefile format"
@@ -20,7 +20,8 @@ RESTRICT="!test? ( test )"
 
 RDEPEND=""
 DEPEND="${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]"
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
 
 python_test() {
 	epytest test_shapefile.py -m "not network" || die
diff --git a/sci-libs/sundials/Manifest b/sci-libs/sundials/Manifest
index f2337ea859ea..e37b90164d5c 100644
--- a/sci-libs/sundials/Manifest
+++ b/sci-libs/sundials/Manifest
@@ -3,7 +3,9 @@ AUX sundials-5.8.0-fix-license-install-path.patch 874 BLAKE2B 134158ced2c1850aed
 DIST sundials-5.2.0.tar.gz 18639221 BLAKE2B c10e6deb5839993b8601347be94412d0b0c058084b4dc0d380681f7b4debd535f9736c2ef734e9fd84c6ddc190ab05f46abcb711225ec1f156a18d8edb6317fb SHA512 99163a104e436dab4779c77519502b5614b65d726324b29b14236315f6916beb5863fcd56b5acf19f62985c033b227fba1ebd3d3c4607ce991d94ee7739bb55f
 DIST sundials-5.8.0.tar.gz 24012815 BLAKE2B f707ad7465218532f3dc4df7627b87933b2bc52be6f1ad290b91ab83a3414ae83bc64503126af8772daa000f58a89855d7ca35fe74fa21bd91180695582442c7 SHA512 d22e699aaddaeef026e91e18dd070d06278c75b6980b36c6fb2e50203ba6445420e4a8e0612a6317dcaa521aeffbdf62ab88737be235ef70cef3a8be02a13dbb
 DIST sundials-6.2.0.tar.gz 82410068 BLAKE2B c6aa9735198465bb458590ef1a90101e246202632afd6bd7f48970b9a2752810ce8c5be7983097cd816189cb994efbddf8d34706665846c67d6442bd7c12db38 SHA512 0dd0a2bf6390a13a5846caf440aa6d459f3890f6d13c0eff8c8180a92a636d6eae7f64679d45acd2048de742d4c644e2ae112cb09028b3fdef10a247bee44c0b
+DIST sundials-6.5.0.tar.gz 89142911 BLAKE2B 3605686f813928fe55e5aafd409c478cf782411b5d2e510121fe15cc15eae84a5d0fe7470c7c0c976fbe11e7f0fd0e9fb449ae45b4c34aa077ac1acb25255cf5 SHA512 30ad3d3f998df6a6381a14b0c8fe247a5507e386ed1b9b55afae87b976f15026d7b4e8609c3cf8423ad79e1b55bade40dc66b274dc3422e040cb12fec981d502
 EBUILD sundials-5.2.0.ebuild 2173 BLAKE2B c7765f5fbb12395c2474f352a3200225cb2ec75360fa2089bf34ee0ddb313d136b0e66ad1955936bac2bf6f6e63bca055e7077d46fb92a69771417c51b86fb9a SHA512 00d5b62fabe026e5637cd655dc53ba12e4ff8db286b451e79a993b18ef09dcbce58805424c903bfb35ebbfcd2881873f91cfb63faa353f1789bd95fba7f17a17
 EBUILD sundials-5.8.0.ebuild 2759 BLAKE2B 2f2872218e337cda6e067925f4f67ce4021a284d0d4badb31737efd6fc0917808769c24b74df4086aaef08384bd36dd744358b9d797da08c40d34f5b1aa34bdc SHA512 7cdaed08db6eab4713df5477d3051d009881cb1ef38714496618f56f831ab9e3973a0b37092cc716512c5d8dc6ed73cbb7da2fb46d0373b066290c48993cd805
 EBUILD sundials-6.2.0.ebuild 2723 BLAKE2B 3d0bdf7847bb61ff87b78a3fdc806d3edcf9d72422d5c27dc05c69ffbf69a609777e25d9b2931bd11b70c911de76e84dcb06843f39aed05f5c76d56474abf78f SHA512 a3e17643240fbcb9383cccf5b90122f53f19d27213d978aa0315db52e1afa20d8c0afa57a52f6315a7050f8112e0f03d558d3b60448bc661cc4054a328ed6ff8
+EBUILD sundials-6.5.0.ebuild 2666 BLAKE2B d92105ee36fff4071b4be0f3a3c6d2d90fbd552e80d4c269cd8dfd89d3f01dde8e5603b2ae4f5a0232d34e0e044c4a74cc95fe5466b7993ff9ce37c9e07d9489 SHA512 6c556101069f9d55724372aa71e208c5db8f322a168365322a132f8b9e06cd94e1cf6a9d193aebe7b04b13ab4900434209ec03e96cdf9c46e18d69201e0cf13c
 MISC metadata.xml 1170 BLAKE2B b2ddcc6f5a958ed045bea77fef0c8842f76fd9f3756bd82870bd605b7dcf5ae5be64c0b5a00a248d17518d0411c90f6b9da539aa5b35bf00d532f84867ed46cf SHA512 539f5e1c372b48f0f6d81a444b52c0ab2a80ecf3e7d278ed870d7189c330e8bfa3c296ddc4ea10e09029b7e44860cde62af6a4bda58d4bcd841704f5920ca23d
diff --git a/sci-libs/sundials/sundials-6.5.0.ebuild b/sci-libs/sundials/sundials-6.5.0.ebuild
new file mode 100644
index 000000000000..ac6b57bf182b
--- /dev/null
+++ b/sci-libs/sundials/sundials-6.5.0.ebuild
@@ -0,0 +1,117 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+FORTRAN_NEEDED=fortran
+FORTRAN_STANDARD="77 90 2003"
+# if FFLAGS and FCFLAGS are set then should be equal
+
+inherit cmake flag-o-matic fortran-2 toolchain-funcs
+
+DESCRIPTION="Suite of nonlinear solvers"
+HOMEPAGE="https://computing.llnl.gov/projects/sundials"
+SRC_URI="https://github.com/LLNL/${PN}/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0/$(ver_cut 1)"
+KEYWORDS="~amd64 ~arm ~arm64 ~ppc ~ppc64 ~riscv ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc examples fortran hypre +int64 lapack mpi openmp sparse +static-libs superlumt threads"
+REQUIRED_USE="
+	fortran? ( static-libs )
+	hypre? ( mpi )
+"
+
+BDEPEND="virtual/pkgconfig"
+RDEPEND="
+	lapack? ( virtual/lapack )
+	mpi? (
+		sci-libs/hypre:=[fortran?,mpi?]
+		virtual/mpi[fortran?]
+	)
+	sparse? ( sci-libs/klu )
+	superlumt? ( sci-libs/superlu_mt:=[int64=] )
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-5.8.0-fix-license-install-path.patch
+)
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+
+	use fortran && fortran-2_pkg_setup
+}
+
+src_prepare() {
+	# bug #707240
+	append-cflags -fcommon
+	use threads && append-ldflags -pthread
+
+	cmake_src_prepare
+}
+
+src_configure() {
+	mycmakeargs+=(
+		-DBUILD_FORTRAN_MODULE_INTERFACE=$(usex fortran)
+		-DBUILD_SHARED_LIBS=ON
+		-DBUILD_STATIC_LIBS=$(usex static-libs)
+		-DENABLE_HYPRE=$(usex hypre)
+		-DENABLE_KLU=$(usex sparse)
+		-DENABLE_LAPACK=$(usex lapack)
+		-DENABLE_MPI=$(usex mpi)
+		-DENABLE_OPENMP=$(usex openmp)
+		-DENABLE_PTHREAD=$(usex threads)
+		-DENABLE_SUPERLUMT=$(usex superlumt)
+		-DEXAMPLES_INSTALL=ON
+		-DEXAMPLES_INSTALL_PATH="/usr/share/doc/${PF}/examples"
+		-DSUNDIALS_INDEX_SIZE="$(usex int64 64 32)"
+		-DSUPERLUMT_INCLUDE_DIR="${EPREFIX}/usr/include/superlu_mt"
+		-DSUPERLUMT_LIBRARY="-lsuperlu_mt"
+		-DUSE_GENERIC_MATH=ON
+	)
+
+	if use examples; then
+		mycmakeargs+=(
+			-DEXAMPLES_ENABLE_C=ON
+			-DEXAMPLES_ENABLE_CXX=ON
+		)
+		if use fortran; then
+			mycmakeargs+=(
+				-DEXAMPLES_ENABLE_F2003=ON
+			)
+		fi
+	fi
+
+	if use fortran; then
+		mycmakeargs+=(
+			-DFortran_INSTALL_MODDIR="${EPREFIX}/usr/$(get_libdir)/fortran"
+		)
+	fi
+
+	if use hypre; then
+		mycmakeargs+=(
+			-DHYPRE_INCLUDE_DIR="${EPREFIX}/usr/include/hypre"
+			-DHYPRE_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libHYPRE.so"
+		)
+	fi
+
+	if use sparse; then
+		mycmakeargs+=(
+			-DKLU_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libklu.so"
+		)
+	fi
+
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+	use doc && dodoc doc/*/*.pdf
+}