gentoo resync : 25.01.2020

11 files changed, 114 insertions, 4 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index 1d717e84d3f4..9c64c497efda 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/getdata/Manifest b/sci-libs/getdata/Manifest
index da01af919db2..9c848458cfea 100644
--- a/sci-libs/getdata/Manifest
+++ b/sci-libs/getdata/Manifest
@@ -1,4 +1,4 @@
 AUX getdata-0.9.0-remove-python-test.patch 257 BLAKE2B bc60176d361d2cb891742c0ee8b443d0cb5c1350478bec1047e56d6a38b50021096ad8bab6ed4b1205744785f002227b22a80a4ab888c4bd52d517de8503e12b SHA512 7a8b5e8e1f2164fca9caba81c7b24f705c6caac036f8f2a3c6dd436961311e4dc34aa6a669eb0bd9e50fb50c09a8b22d32fe04961085c983a29da00e438cbc7c
 DIST getdata-0.9.0.tar.xz 920652 BLAKE2B d5f0659474dfab9f4e589a28a7788b5a51de3c0064b58de37bdb11dad27b56daa05d8e705da743c5da271bd8c4e1343ac6ac41adfdfabfcaef0006e46c45d2bf SHA512 28d720141e34cc56a5166594d0a6ac293144d123706988ed170e40dd9d7aaf13b920305e8bd8343ecd7cbe43eee5d83720e3e5f5d2da0cdccdc1444725cc6844
-EBUILD getdata-0.9.0-r1.ebuild 1566 BLAKE2B ef80ee67141b2fd5be341ac23426d4568bb2bece6b1f66b962bad6655afa0d82644b28a89be6a40c8823938fd0364d62df11e486846ec823b51fb94dae32d156 SHA512 06a261916043012214ff5fb3abb9a3eac9e320505bc46f66310269c5915992853f77655ab8764c1bfff9050e0467038c4b9f4078bda9eb5562e60dd2141bd610
+EBUILD getdata-0.9.0-r2.ebuild 1566 BLAKE2B ef80ee67141b2fd5be341ac23426d4568bb2bece6b1f66b962bad6655afa0d82644b28a89be6a40c8823938fd0364d62df11e486846ec823b51fb94dae32d156 SHA512 06a261916043012214ff5fb3abb9a3eac9e320505bc46f66310269c5915992853f77655ab8764c1bfff9050e0467038c4b9f4078bda9eb5562e60dd2141bd610
 MISC metadata.xml 660 BLAKE2B 74c050abc2e0978cc5c7d16625a6858f9a0a22d9c4ce4fbf0c303cb3361ef460d5d50d09845e5c8b9be82a73b22e9d159a554fec12f5dd7058602c99b7b5073d SHA512 d821e374438aad1beb22199383ebbc8a48247867b08370f08c370e02d7abaf7273a62e750a9ed3befc5e9674489a2a8e56453a6dad09a363a514986a79eb7460
diff --git a/sci-libs/getdata/getdata-0.9.0-r1.ebuild b/sci-libs/getdata/getdata-0.9.0-r2.ebuild
index 65085d535e5b..65085d535e5b 100644
--- a/sci-libs/getdata/getdata-0.9.0-r1.ebuild
+++ b/sci-libs/getdata/getdata-0.9.0-r2.ebuild
diff --git a/sci-libs/libgeodecomp/files/libgeodecomp-0.4.0-lfa.patch b/sci-libs/libgeodecomp/files/libgeodecomp-0.4.0-lfa.patch
new file mode 100644
index 000000000000..463d416b3bf6
--- /dev/null
+++ b/sci-libs/libgeodecomp/files/libgeodecomp-0.4.0-lfa.patch
@@ -0,0 +1,37 @@
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 673017f0..28704461 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -528,18 +528,20 @@ foreach(dir ${LIBDIRS})
+ endforeach(dir)
+ 
+ # install libflatarray, too
+-file(GLOB HEADERS "${CMAKE_CURRENT_SOURCE_DIR}/../lib/libflatarray/src/*.hpp")
+-foreach(i ${HEADERS})
+-  install(FILES ${i} DESTINATION include/libflatarray)
+-endforeach()
+-file(GLOB HEADERS "${CMAKE_CURRENT_SOURCE_DIR}/../lib/libflatarray/src/detail/*.hpp")
+-foreach(i ${HEADERS})
+-  install(FILES ${i} DESTINATION include/libflatarray/detail)
+-endforeach()
+-file(GLOB HEADERS "${CMAKE_CURRENT_SOURCE_DIR}/../lib/libflatarray/src/testbed/*.hpp")
+-foreach(i ${HEADERS})
+-  install(FILES ${i} DESTINATION include/libflatarray/testbed)
+-endforeach()
++if(NOT libflatarray_FOUND)
++  file(GLOB HEADERS "${CMAKE_CURRENT_SOURCE_DIR}/../lib/libflatarray/src/*.hpp")
++  foreach(i ${HEADERS})
++    install(FILES ${i} DESTINATION include/libflatarray)
++  endforeach()
++  file(GLOB HEADERS "${CMAKE_CURRENT_SOURCE_DIR}/../lib/libflatarray/src/detail/*.hpp")
++  foreach(i ${HEADERS})
++    install(FILES ${i} DESTINATION include/libflatarray/detail)
++  endforeach()
++  file(GLOB HEADERS "${CMAKE_CURRENT_SOURCE_DIR}/../lib/libflatarray/src/testbed/*.hpp")
++  foreach(i ${HEADERS})
++    install(FILES ${i} DESTINATION include/libflatarray/testbed)
++  endforeach()
++endif()
+ 
+ # link against the libs we need
+ set(INSTALLER_LINK_FLAGS "-L${CMAKE_INSTALL_PREFIX}/${LIB_DIR} -Wl,-rpath,${CMAKE_INSTALL_PREFIX}/${LIB_DIR} -lgeodecomp ")
diff --git a/sci-libs/libgeodecomp/libgeodecomp-0.4.0-r1.ebuild b/sci-libs/libgeodecomp/libgeodecomp-0.4.0-r1.ebuild
new file mode 100644
index 000000000000..5237072823ec
--- /dev/null
+++ b/sci-libs/libgeodecomp/libgeodecomp-0.4.0-r1.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake cuda
+
+DESCRIPTION="An auto-parallelizing library to speed up computer simulations"
+HOMEPAGE="http://www.libgeodecomp.org"
+SRC_URI="http://www.libgeodecomp.org/archive/${P}.tar.bz2"
+
+SLOT="0"
+LICENSE="Boost-1.0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE="doc mpi cuda opencl opencv silo hpx visit"
+
+BDEPEND="
+	doc? (
+		app-doc/doxygen
+		app-text/texlive
+		media-gfx/graphviz
+		)"
+RDEPEND=">=dev-libs/boost-1.48"
+DEPEND="${RDEPEND}
+	hpx? ( sys-cluster/hpx )
+	<=dev-libs/libflatarray-0.2.0
+	mpi? ( virtual/mpi )
+	cuda? ( dev-util/nvidia-cuda-toolkit )
+	opencl? ( virtual/opencl )
+	opencv? ( media-libs/opencv )
+	silo? ( sci-libs/silo )"
+
+S="${WORKDIR}/${P}"
+PATCHES=(
+	"${FILESDIR}/${P}-scotch.patch"
+	"${FILESDIR}/${P}-libdir.patch"
+	"${FILESDIR}/${P}-lfa.patch"
+)
+
+src_prepare() {
+	cmake_src_prepare
+	use cuda && cuda_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DWITH_MPI=$(usex mpi)
+		-DWITH_CUDA=$(usex cuda)
+		-DWITH_OPENCL=$(usex opencl)
+		-DWITH_OPENCV=$(usex opencv)
+		-DWITH_SILO=$(usex silo)
+		-DWITH_SCOTCH=false
+		-DWITH_HPX=$(usex hpx)
+		-DWITH_VISIT=false
+		-DWITH_TYPEMAPS=false
+	)
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+	use doc && cmake_build doc
+}
+
+src_install() {
+	DOCS=( README )
+	use doc && HTML_DOCS=( doc/html/* )
+	cmake_src_install
+}
+
+src_test() {
+	cmake_build check
+}
diff --git a/sci-libs/mathgl/Manifest b/sci-libs/mathgl/Manifest
index 74a4c40f26b6..9dc6483cded7 100644
--- a/sci-libs/mathgl/Manifest
+++ b/sci-libs/mathgl/Manifest
@@ -1,5 +1,5 @@
 AUX mathgl-2.4.1-mutex.patch 424 BLAKE2B 2077654d0b17d2a1ba63bfcc17bcc82dac7dcc274253357a70cd0b2d49f9c99b73b380c1d09ad70e302fd04449b9adb6392c12cbd03fcefae4a36a50491cf012 SHA512 d0a0101041c91ba4d295484b8b06825d66787600b98acc2ee6e3cb8ec54e86939deadc40924bce42b6eb782bf5c03c6a7687ac853d7bc393e75bcf9a809d7849
 DIST STIX_font.tgz 2450541 BLAKE2B f725eb0264d9c3cb7c32a935e8857c4a21cb905a1dc6c9cc8a16408afdc7dd9b6fcd312a8c2f77aff5484605a39a9ee36e86ad0234adb5d6bcc5c8839101194c SHA512 c9124ec552074c98f15d6d3572a063598ca6bc598e3e78dcb5a5d57ae3928b5327a1374635f428ea1cefc9e51ee1d1aa9bd6ba9a306429fc6965140251d368b5
 DIST mathgl-2.4.1.tar.gz 22665490 BLAKE2B a9c9e0ec7d145262994a754dfbcf1f789d2777f9334c8b4e73696265adba4d2fd7283621857318264c2162841e81427df21f7bc7b951d83876fbc066d3b9068f SHA512 10fd016662ca60b9507942691f85b4d9151104319627732f4add0175475f7e8dff16e3645bb858c283b747f34e58f410d0532e94dc64cf8cf472938d3966402d
-EBUILD mathgl-2.4.1.ebuild 4429 BLAKE2B 805b251b076fea7884f091a76b3dd5c4e7f45849b2ab09754ec11e789e4df4905299bbf7f9c2d0f3501e7a102c2b9851db206b416e8db7cf61f07e5c70b4ec72 SHA512 ae68b5ad9b5c8d247d74ed83b125c72a060ff3db1a34aaa3b0015e1394de1a9c9a6c17138d9c1c5ecce92bc6d45822dcddc0aeee8f27c923812de2d3f6a70bfa
+EBUILD mathgl-2.4.1-r1.ebuild 4429 BLAKE2B 805b251b076fea7884f091a76b3dd5c4e7f45849b2ab09754ec11e789e4df4905299bbf7f9c2d0f3501e7a102c2b9851db206b416e8db7cf61f07e5c70b4ec72 SHA512 ae68b5ad9b5c8d247d74ed83b125c72a060ff3db1a34aaa3b0015e1394de1a9c9a6c17138d9c1c5ecce92bc6d45822dcddc0aeee8f27c923812de2d3f6a70bfa
 MISC metadata.xml 800 BLAKE2B baa75251910016e5d059cebeebd85632d290ab0c3c50089de0485ffbcd08ee8ac59cbfe33824347a5a5c339c74ea7a56c516d4d38661e56f7498d628d748f64a SHA512 8b75db0a01ce59f22543701447630c56a82f9091b5901f85ae102de7deca281e09dbcb443b8ff2930cf18145d63504646a289fd5e77defccc4d38480596d1968
diff --git a/sci-libs/mathgl/mathgl-2.4.1.ebuild b/sci-libs/mathgl/mathgl-2.4.1-r1.ebuild
index 81c1241a2fa6..81c1241a2fa6 100644
--- a/sci-libs/mathgl/mathgl-2.4.1.ebuild
+++ b/sci-libs/mathgl/mathgl-2.4.1-r1.ebuild
diff --git a/sci-libs/nlopt/Manifest b/sci-libs/nlopt/Manifest
index af9896a7af36..c503ace00d75 100644
--- a/sci-libs/nlopt/Manifest
+++ b/sci-libs/nlopt/Manifest
@@ -3,5 +3,5 @@ AUX nlopt-2.3-pkgconfig.patch 318 BLAKE2B 3569931fb9e2fceebf46c542e10fcd2562c8ac
 AUX nlopt-2.4.2-fix-dynamic-underlinking.patch 2522 BLAKE2B 5cdb8ea93cb44c25b1814431962259727c5c4dc97b4cf78d239189187f953a4b9458849a9afe77979841768b78226c6218ecc531328cb5752d26b9df63468ee5 SHA512 bdb07b216ffb68b68cb3f03076336234c558db3953c48b02511883bf9fb12f5915c04950a2e3222577c7af4fb1e288a165af2e8adf211fc853e747c98a65cd19
 AUX nlopt-2.4.2-octave-4-map.patch 1858 BLAKE2B 34b1696762a9690a5ef5f3abc265b37d5de2f92b29e514952aa062faf1553a77ed3dba6f2abf7c8f1f7cbcc1cc63c9546967f3a317a773aa5e7c5c1e9c13f7e3 SHA512 00c45fe04fdc1acf4ccbb77aaf39feab0cb2b811b45edf791db7e87aa9e965c23b6131400eebd68335be8dcb86f346c01892e718f739f07dc0853b3dd9ea5ad4
 DIST nlopt-2.4.2.tar.gz 2361992 BLAKE2B c1c9f533c7e7b3bb61e81343ebd26b87e05434fdbea1f347fc5f6a6c10160289ce105a51c6540296f3f1d122d31b415452da49b84516cd13fabc73372e4cfd0e SHA512 136aacc00a69f77e8a7ce5dc26a5f3f027bc8c01b97aa1f43919462e0a412154eabfb01be258e082dffe61f9b554bb2bfbb550a7b82c7c77c7b22874a64a9703
-EBUILD nlopt-2.4.2-r1.ebuild 2714 BLAKE2B 3939763ab3da6e8708c10b3ca39f1c001f2d9913e883648cade9d58b83c3242804991373fdd36599474715840562533881c8ab0ffd98cda54ad71d3d4c12cbe4 SHA512 c2a7e3336ccb1887c2c6074aed5fffb254dd11e607d871bd3ed864794d04cdfb7a3aff711b8cb5f7f0a98629f34a196f4f5fa7221f5c07324b2439b48cc9e5c9
+EBUILD nlopt-2.4.2-r2.ebuild 2714 BLAKE2B 3939763ab3da6e8708c10b3ca39f1c001f2d9913e883648cade9d58b83c3242804991373fdd36599474715840562533881c8ab0ffd98cda54ad71d3d4c12cbe4 SHA512 c2a7e3336ccb1887c2c6074aed5fffb254dd11e607d871bd3ed864794d04cdfb7a3aff711b8cb5f7f0a98629f34a196f4f5fa7221f5c07324b2439b48cc9e5c9
 MISC metadata.xml 1095 BLAKE2B e5032d65fbb49b125b6cb5abe332c52a1e058271c71aec2d2522cc78874a079f8987e2e8356290295bcb886c32e1cf794df9b157ebc712a862605105b80abe31 SHA512 74a37bc3e6fa74d0f96c3390fadf16e76caf904f43cf9ac0496f70e3e3bc458727e58d9fc65c39a81302b081575e530c27be3812488df20fab42aff5494437f7
diff --git a/sci-libs/nlopt/nlopt-2.4.2-r1.ebuild b/sci-libs/nlopt/nlopt-2.4.2-r2.ebuild
index 5a937cd80edd..5a937cd80edd 100644
--- a/sci-libs/nlopt/nlopt-2.4.2-r1.ebuild
+++ b/sci-libs/nlopt/nlopt-2.4.2-r2.ebuild
diff --git a/sci-libs/pymmlib/Manifest b/sci-libs/pymmlib/Manifest
index 445557d14a2f..a02cc28daa49 100644
--- a/sci-libs/pymmlib/Manifest
+++ b/sci-libs/pymmlib/Manifest
@@ -1,3 +1,3 @@
 DIST pymmlib-1.2.1.tar.gz 37480403 BLAKE2B 9dc57144f5ac1a8055f1759b21c9b7c580bf33705e168ad92eec5bb9542650a006ba1dff4d45a05cce9fcb81e3633ee29eecc7a3aec46343467ec1940166353b SHA512 96328fcb8af70a271c0960be753c677f716d3b15c41519c320a1240fd9ad584fee173ab3a8e528c9ae198efea95d20863f64627e44d1a6726513f2916d93b464
-EBUILD pymmlib-1.2.1.ebuild 1090 BLAKE2B 514f67f0561c203c18e303f660e94d82071ff35cdd345478d653a6bab3a36b879f509d6b1b10a06083498dd64fa90d7e253c72fc0d346b2a9b531bb2ada5c02a SHA512 5b3878abef4db8be7e3b86eae12e79e4d0e545420520a4399684e90681d506f04259da933b7f5769446e37883e85e52ec80ea7704257ed4e1101a89769b05a83
+EBUILD pymmlib-1.2.1-r1.ebuild 1090 BLAKE2B 514f67f0561c203c18e303f660e94d82071ff35cdd345478d653a6bab3a36b879f509d6b1b10a06083498dd64fa90d7e253c72fc0d346b2a9b531bb2ada5c02a SHA512 5b3878abef4db8be7e3b86eae12e79e4d0e545420520a4399684e90681d506f04259da933b7f5769446e37883e85e52ec80ea7704257ed4e1101a89769b05a83
 MISC metadata.xml 352 BLAKE2B 34a1fc3435528c5b6d9ebcdcc8c2fccb94c73905c18470cc1637ddd83030997173f8799f50c6f80e900949bbf7f1d1eed94d026e37a91fb0d708977fc607cbbc SHA512 0b30b2c2b407b9955227536ad72a0ad7583cd4ef5b2b691d44b0adc98e854b8051204666f6c5364a242cb81cefb17669e28744c1c062bbeb7bc207849f77384b
diff --git a/sci-libs/pymmlib/pymmlib-1.2.1.ebuild b/sci-libs/pymmlib/pymmlib-1.2.1-r1.ebuild
index e05c2a381dd1..e05c2a381dd1 100644
--- a/sci-libs/pymmlib/pymmlib-1.2.1.ebuild
+++ b/sci-libs/pymmlib/pymmlib-1.2.1-r1.ebuild