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-rw-r--r--sci-chemistry/Manifest.gzbin8369 -> 8360 bytes
-rw-r--r--sci-chemistry/avogadro2/Manifest3
-rw-r--r--sci-chemistry/avogadro2/avogadro2-1.95.1.ebuild82
-rw-r--r--sci-chemistry/gromacs/Manifest4
-rw-r--r--sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild5
-rw-r--r--sci-chemistry/gromacs/gromacs-2025.9999.ebuild5
6 files changed, 6 insertions, 93 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 9c2f83a60c9c..dfb62c2bb500 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
Binary files differ
diff --git a/sci-chemistry/avogadro2/Manifest b/sci-chemistry/avogadro2/Manifest
index 67fa487939a8..58a80f9492da 100644
--- a/sci-chemistry/avogadro2/Manifest
+++ b/sci-chemistry/avogadro2/Manifest
@@ -1,8 +1,5 @@
AUX avogadro2-1.95.1-qttest.patch 522 BLAKE2B f7a61dfc89e2066340a2e73deab81439d88b3d2e28853ec4df538a699e90189075d3c647e4d09b791771f3d24d108e6ebe8ebe25cf66b1104c78c2f110cd57a2 SHA512 c3507fcb4d9e57800a405683a05b84009c65b0bf488294b9fdf94ebc872c4019d296e59a9b3479da0696ac6e495754b517ed08274a5640737f96c79bd5f53c47
-DIST avogadro2-1.95.1-i18n.tar.gz 800520 BLAKE2B f68edce572335621deb9698d1cc97d4d8e900ea91bb7a428a4da63d9060c38b31181b91b868378ab5da29c7a61ccb0f6efd9b422bba2d9dc9bb86578c23152c4 SHA512 1182578a9b91f49d114fa3a201e5fe5c37d3abdd10dff82be04f6d5fd193dd3b1140e7abdf2cf721523f523d762fbdc97780887184b83edbc9d3fa87fd8f7428
-DIST avogadro2-1.95.1.tar.gz 2888376 BLAKE2B 00ad2b9daccec77207d42bd0db0cf404bd5b92941385f19ac35400cf497884d198785da60f87fd68e92f6d864abea31f07526c2053b34cbf75d1202fd9232694 SHA512 15300da0ecc85be0e369758aafa50ca5c236132988da68611f198637ea49f4a88da93d58ecd177aeb3c2ac363c0da79b91064156e61c828a059277aa09245604
DIST avogadro2-1.97.0-i18n.tar.gz 990218 BLAKE2B e76b2d69b74f2a2964383564018e61ff0248e53c62a4a2abb1033100bd7fadaefbc261e64bf9e809d6e12ef851bd1ca3661d78b70d07728476586f6564e44e63 SHA512 6a01a05d4a62f83a75ae13100229f2ac6f9e697412868a75f5a9fde6025fc4e886c7ac80704fe5b8390a2af437c7848b0dce19897a6f9da1c5cf4c83418523db
DIST avogadro2-1.97.0.tar.gz 2931223 BLAKE2B b2f2146ebe94ef25f4f684b13f9b9c5fbba933978208524ee197c8971f96c733f687ec68e566d032381a5f45cf22defb2bf909bd738becdd70da0abccebc0755 SHA512 19a0bcf01a840da29c4bab6eed55c879c10d773ee5dcfab613e6666708916bfd8398e44237c18de4e5bb3247d3c4bed3844cac47cf7f3a94dc96d7df8eb13579
-EBUILD avogadro2-1.95.1.ebuild 1924 BLAKE2B ce0ce22884425351e6f1e6eefab52f16ff3d9b74c373985edbe929325927b1709aa7ec3bd0db89d46d340058e584e97be5c313b5051cb9a519ec7a36f3b12d3e SHA512 3fb570d830111e918bcb5b4d16a11717b115a0e5231db44960028ca09208ba4a27e7428d7bfb8ae40fd1518cdde664139134865a3bd2f6822869de9b20ab59b8
EBUILD avogadro2-1.97.0.ebuild 1932 BLAKE2B 3b90d66a4c66c69d8f18d35ad37bce703c4c13026a05ceb0b3ab846b2d722ad834a51fa70e165e286f17295d08f133a0750b5af2d24f3c6eda0a91ac87f7e7a6 SHA512 0877b2a81a53e131add80a06742dbfa792b1b2a1fc4f92cbe6493bda63a8bc1e3bf4069d8d49eb3e60288dec666bae6e9f3e91e2ecd3c9e14b70f1d6dee5124a
MISC metadata.xml 514 BLAKE2B 0a88a4b92fef923690f6e9767c572875d86c8522936aff89354f4b08ee74fe7c2f49e1eba143c850753d8f2cb5a7e7dc063e9864e433b70068ef7edcd0163683 SHA512 e7729ed111cfade53f238b9b49067c55c1a229489dbc1665d428ba8643c0f9ad0af402e8bf4c81399df1d1a786c7831a7a769bf9a5608157642546a1d0f45ee9
diff --git a/sci-chemistry/avogadro2/avogadro2-1.95.1.ebuild b/sci-chemistry/avogadro2/avogadro2-1.95.1.ebuild
deleted file mode 100644
index e4a5c22f11fc..000000000000
--- a/sci-chemistry/avogadro2/avogadro2-1.95.1.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-MY_PN=avogadroapp
-
-DOCS_BUILDER="doxygen"
-DOCS_DEPEND="media-gfx/graphviz"
-DOCS_DIR="${WORKDIR}/${MY_PN}-${PV}_build/docs"
-# docs/CMakeLists.txt overwrites docs.eclass outdir if we do not set this
-DOCS_OUTDIR="${DOCS_DIR}/html"
-DOCS_CONFIG_NAME="doxyfile"
-inherit desktop docs cmake xdg
-
-I18N_COMMIT="3b8a86cc37e988b043d1503d2f11068389b0aca3"
-
-DESCRIPTION="Advanced molecule editor and visualizer 2"
-HOMEPAGE="https://www.openchemistry.org/"
-SRC_URI="
- https://github.com/OpenChemistry/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/OpenChemistry/avogadro-i18n/archive/${I18N_COMMIT}.tar.gz -> ${P}-i18n.tar.gz
-"
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-SLOT="0"
-LICENSE="BSD GPL-2+"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="rpc test vtk"
-
-RDEPEND="
- dev-qt/qtcore:5
- dev-qt/qtgui:5
- dev-qt/qtwidgets:5
- >=sci-libs/avogadrolibs-${PV}[qt5,vtk?]
- sci-libs/hdf5:=
- rpc? ( sci-chemistry/molequeue )
-"
-DEPEND="${RDEPEND}
- dev-cpp/eigen:3
- test? ( dev-qt/qttest:5 )
-"
-
-RESTRICT="test"
-
-PATCHES=(
- "${FILESDIR}/${P}-qttest.patch"
-)
-
-src_unpack() {
- default
- mv "${WORKDIR}/avogadro-i18n-${I18N_COMMIT}" "${WORKDIR}/avogadro-i18n" || die
-}
-
-src_prepare() {
- cmake_src_prepare
- sed -e "/LICENSE/d" -i CMakeLists.txt || die
-}
-
-src_configure() {
- local mycmakeargs=(
- -DINSTALL_DOC_DIR="${EPREFIX}/usr/share/doc/${PF}"
- -DBUILD_DOCUMENTATION=$(usex doc)
- -DAvogadro_ENABLE_RPC=$(usex rpc)
- -DENABLE_TESTING=$(usex test)
- -DUSE_VTK=$(usex vtk)
- )
- # Need this to prevent overwriting the documentation OUTDIR
- use doc && mycmakeargs+=( -DChemData_BINARY_DIR="${DOCS_OUTDIR}" )
- cmake_src_configure
-}
-
-src_compile() {
- cmake_src_compile
- docs_compile
-}
-
-src_install() {
- cmake_src_install
- for size in 64 128 256 512; do
- newicon -s "${size}" avogadro/icons/"${PN}"_"${size}".png "${PN}".png
- done
-}
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index e2905644bf92..9a2618b30ac5 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -16,7 +16,7 @@ EBUILD gromacs-2023.9999.ebuild 9810 BLAKE2B 29946a30ec5fc7c19233790c48a8e665700
EBUILD gromacs-2024.3.ebuild 9861 BLAKE2B f7fa0c2bf44ebf280967ef0e259d99f5381555965b5fc96707ef0873ebcbaad2f1c5b77bb7307fefb40ef56bae2819b3677a501e478fb5c84f051c285fd90faa SHA512 0975c94642c19ec6d2a2c7a0ea6f55dd758b2b3775b106a09e8839c6f2e124d25610003e24c6a8c82e48575a894be7e5eb0a0309da9fdb8cead2e93121bf34fe
EBUILD gromacs-2024.4.ebuild 9863 BLAKE2B 77657c52384762485cc3aa7615b65058dbcd23bd353b8184f99c1a4665c6a17bdf4ddbb62af650f99622e449768cb05d1e8cecefe1a307139ad5e63495c263f2 SHA512 aa550e1f89af67496b00b4a3469f74aff3477e12dd583d9b8ed15f38790b286a7eb90a3a30a8799b4c6258928c91b32e4307d3da9ef236bd6b12cf7da55867d5
EBUILD gromacs-2024.9999.ebuild 9817 BLAKE2B 5ef6b37d8c37ca3109be40e004f959cbad36e7b0334808acdf5711c5f06d22a8e199c0e6cd41aa010401134221ca4539810d7d67865f2d8145bb1669afae4471 SHA512 b288eaf90645a5dcc0904332f0c924fd62adbefd723a8f771d7990f3fdb243eaed13d466e91b4ffae2ec10cbebbbe8edb181136a19b2214fe33d01e2be1a0a94
-EBUILD gromacs-2025.0_beta.ebuild 10180 BLAKE2B f9910bdcb8f506487a29431429a7440be72777c8b0d13c74c17998b51a6e05dd87bbd90e70f73cbb6a85362e33b0664680c32efd3e95b307b287bc1c6f8f5eb8 SHA512 8b9d8d8992d599003cd6cf6264b423fe5175bf90e95a883de74ba2b16a8d902f355e1e3e79a564d958f482f6d2a255ad1d8074ec5a442967a8c6be8fa98d2457
-EBUILD gromacs-2025.9999.ebuild 10131 BLAKE2B 9e39c3615616ee18584c5778b1faf306c5763af1162b36e28940c65d9c12634cc089f95a1f5098a60a9f087bc35c81375534ff8e6781e31681b187bc728338c4 SHA512 7b3fbf70ce73eacf8c6ed20910be83f4d3083886eda8af3a3546bf2b4ae5b964d31bb93710c0dc2856d00dd1de4cee1ea04f7de2a90a4fbf99e1e09eb99bb380
+EBUILD gromacs-2025.0_beta.ebuild 10141 BLAKE2B f950507f63acc6443e10602d17de77d980585abd611391edec41a84e1d51d4cb9243a4dd3c50ef1078c83961f70d5c520dc199f486e17dc902c3dca0f0b8b502 SHA512 d2f7a2844574f301050f8d83c1e1d73ff04dd66fda56f0b9e916683415f846a3c1ca6b1555630d977e6cb6b3d5b7fa03d0a1e17856cc232a821209e2f7483540
+EBUILD gromacs-2025.9999.ebuild 10092 BLAKE2B 15d351a5aa48ac092fc6c969156701f2fd9bec93ffb8c2f26a63e64ec4543dd1af01666cb6cd3b579097c10e23411ac60610db65e3d6106a356989bd4e5537cf SHA512 90d7f60f25b43f349fb0da8dbc62028468bc49e8187d6019a3421877e1c08817dd7186d63883a51c0742510f7f7b27a19fa544dc6bc7c498ba62152652f2e347
EBUILD gromacs-9999.ebuild 10131 BLAKE2B 9e39c3615616ee18584c5778b1faf306c5763af1162b36e28940c65d9c12634cc089f95a1f5098a60a9f087bc35c81375534ff8e6781e31681b187bc728338c4 SHA512 7b3fbf70ce73eacf8c6ed20910be83f4d3083886eda8af3a3546bf2b4ae5b964d31bb93710c0dc2856d00dd1de4cee1ea04f7de2a90a4fbf99e1e09eb99bb380
MISC metadata.xml 1394 BLAKE2B d387fba17fee85119e42ff18968f18d26bcbf5997361b4b1e93eeea1a8df54a9173b614f7d315000ecd0e4fa247becfb1236697825c0579fa7dcaff51a8185e5 SHA512 f8d9ebc33ad1f391dde1b7e056ad9b7860a902b805363c988962743cd4f37af69a0b1acd3323a95b9740ded0abf20904895605d78fecebdf94a4562ccd3ab9e8
diff --git a/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild b/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild
index 83abd5053722..972995fab90d 100644
--- a/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild
@@ -40,7 +40,7 @@ HOMEPAGE="https://www.gromacs.org/"
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${PV}"
-IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
blas? ( virtual/blas )
@@ -51,7 +51,6 @@ CDEPEND="
sys-devel/clang-runtime[openmp]
)
fftw? ( sci-libs/fftw:3.0= )
- hdf5? ( sci-libs/hdf5 )
hwloc? ( sys-apps/hwloc:= )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
@@ -239,7 +238,7 @@ src_configure() {
-DGMX_COOL_QUOTES=$(usex offensive)
-DGMX_USE_TNG=$(usex tng)
-DGMX_BUILD_MANUAL=$(usex build-manual)
- -DGMX_USE_HDF5=$(usex hdf5)
+ -DGMX_USE_HDF5=off
-DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
#-DGMX_BUILD_HELP=on
diff --git a/sci-chemistry/gromacs/gromacs-2025.9999.ebuild b/sci-chemistry/gromacs/gromacs-2025.9999.ebuild
index 71ac8186ede9..8cd0e7684046 100644
--- a/sci-chemistry/gromacs/gromacs-2025.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2025.9999.ebuild
@@ -40,7 +40,7 @@ HOMEPAGE="https://www.gromacs.org/"
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${PV}"
-IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
blas? ( virtual/blas )
@@ -51,7 +51,6 @@ CDEPEND="
sys-devel/clang-runtime[openmp]
)
fftw? ( sci-libs/fftw:3.0= )
- hdf5? ( sci-libs/hdf5 )
hwloc? ( sys-apps/hwloc:= )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
@@ -237,7 +236,7 @@ src_configure() {
-DGMX_COOL_QUOTES=$(usex offensive)
-DGMX_USE_TNG=$(usex tng)
-DGMX_BUILD_MANUAL=$(usex build-manual)
- -DGMX_USE_HDF5=$(usex hdf5)
+ -DGMX_USE_HDF5=off
-DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_BUILD_HELP=on
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-31 15:10:03 +0000