From 4cbcc855382a06088e2f016f62cafdbcb7e40665 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 20 Mar 2022 00:40:44 +0000 Subject: gentoo resync : 20.03.2022 --- sci-chemistry/Manifest.gz | Bin 11034 -> 10870 bytes sci-chemistry/ParmEd/Manifest | 3 + sci-chemistry/ParmEd/ParmEd-3.4.3.ebuild | 22 ++ sci-chemistry/ParmEd/metadata.xml | 12 + sci-chemistry/avogadro2/Manifest | 6 +- sci-chemistry/avogadro2/avogadro2-1.93.0.ebuild | 56 ---- sci-chemistry/avogadro2/avogadro2-1.95.1.ebuild | 82 +++++ .../avogadro2/files/avogadro2-1.95.1-qttest.patch | 15 + sci-chemistry/dssp/Manifest | 2 + sci-chemistry/dssp/dssp-4.0.4.ebuild | 31 ++ sci-chemistry/gromacs/Manifest | 46 ++- .../gromacs/files/gromacs-2021-musl-stdint.patch | 25 ++ .../gromacs/files/gromacs-2021-nblib.patch | 53 --- sci-chemistry/gromacs/gromacs-2018.8-r1.ebuild | 9 +- sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild | 9 +- sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild | 9 +- sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild | 10 +- sci-chemistry/gromacs/gromacs-2020.6-r1.ebuild | 353 -------------------- sci-chemistry/gromacs/gromacs-2020.7.ebuild | 351 ++++++++++++++++++++ sci-chemistry/gromacs/gromacs-2021.2-r1.ebuild | 360 --------------------- sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild | 14 +- sci-chemistry/gromacs/gromacs-2021.4.ebuild | 356 -------------------- sci-chemistry/gromacs/gromacs-2021.5.ebuild | 8 +- sci-chemistry/gromacs/gromacs-2021.9999.ebuild | 14 +- sci-chemistry/gromacs/gromacs-2022.9999.ebuild | 41 +-- sci-chemistry/gromacs/gromacs-2022.ebuild | 336 +++++++++++++++++++ sci-chemistry/gromacs/gromacs-2022_rc1.ebuild | 349 -------------------- sci-chemistry/gromacs/gromacs-9999.ebuild | 41 +-- sci-chemistry/gromacs/metadata.xml | 2 + sci-chemistry/molden/Manifest | 3 + .../molden/files/molden-6.9-ldflags.patch | 87 +++++ sci-chemistry/molden/molden-6.9.ebuild | 81 +++++ sci-chemistry/molscript/Manifest | 8 - sci-chemistry/molscript/files/2.1.2-ldflags.patch | 22 -- sci-chemistry/molscript/files/2.1.2-libpng15.patch | 19 -- sci-chemistry/molscript/files/2.1.2-prll.patch | 10 - .../molscript/files/fix-makefile-shared.patch | 62 ---- sci-chemistry/molscript/files/glutbitmap.h | 32 -- sci-chemistry/molscript/metadata.xml | 8 - sci-chemistry/molscript/molscript-2.1.2-r2.ebuild | 67 ---- sci-chemistry/molsketch/Manifest | 2 + sci-chemistry/molsketch/molsketch-0.7.2.ebuild | 39 +++ sci-chemistry/openbabel/Manifest | 8 +- .../openbabel/files/openbabel-2.4.1-gcc10.patch | 62 ---- .../openbabel/files/openbabel-python.cmake | 104 ------ sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild | 101 ------ .../openbabel/openbabel-3.1.1_p20210225.ebuild | 6 +- sci-chemistry/openbabel/openbabel-9999.ebuild | 4 +- sci-chemistry/pdbcat/Manifest | 2 +- sci-chemistry/pdbcat/pdbcat-1.3-r1.ebuild | 26 ++ sci-chemistry/pdbcat/pdbcat-1.3.ebuild | 23 -- sci-chemistry/pdbmat/Manifest | 4 +- sci-chemistry/pdbmat/files/CMakeLists.txt | 6 +- sci-chemistry/pdbmat/pdbmat-3.89-r1.ebuild | 30 ++ sci-chemistry/pdbmat/pdbmat-3.89.ebuild | 31 -- sci-chemistry/povscript+/Manifest | 4 - .../files/povscript+-2.1.2.2.19-libpng15.patch | 19 -- sci-chemistry/povscript+/metadata.xml | 8 - .../povscript+/povscript+-2.1.2.2.20.ebuild | 55 ---- sci-chemistry/tm-align/Manifest | 2 +- sci-chemistry/tm-align/tm-align-20150914-r1.ebuild | 24 ++ sci-chemistry/tm-align/tm-align-20150914.ebuild | 26 -- sci-chemistry/votca-csg/Manifest | 15 +- sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild | 99 ------ sci-chemistry/votca-csg/votca-csg-1.6.4.ebuild | 4 +- sci-chemistry/votca-csg/votca-csg-2021.1.ebuild | 87 ----- sci-chemistry/votca-csg/votca-csg-2021.2.ebuild | 4 +- sci-chemistry/votca-csg/votca-csg-2021.ebuild | 85 ----- sci-chemistry/votca-csg/votca-csg-9999.ebuild | 86 ----- sci-chemistry/votca-csgapps/Manifest | 2 - .../votca-csgapps/votca-csgapps-1.5.1.ebuild | 32 -- sci-chemistry/votca-xtp/Manifest | 5 - sci-chemistry/votca-xtp/votca-xtp-2021.1.ebuild | 51 --- sci-chemistry/votca-xtp/votca-xtp-2021.ebuild | 43 --- sci-chemistry/votca-xtp/votca-xtp-9999.ebuild | 52 --- sci-chemistry/votca/Manifest | 6 +- sci-chemistry/votca/votca-2022.ebuild | 14 +- sci-chemistry/votca/votca-2022_rc2.ebuild | 70 ---- sci-chemistry/votca/votca-9999.ebuild | 16 +- 79 files changed, 1289 insertions(+), 2982 deletions(-) create mode 100644 sci-chemistry/ParmEd/Manifest create mode 100644 sci-chemistry/ParmEd/ParmEd-3.4.3.ebuild create mode 100644 sci-chemistry/ParmEd/metadata.xml delete mode 100644 sci-chemistry/avogadro2/avogadro2-1.93.0.ebuild create mode 100644 sci-chemistry/avogadro2/avogadro2-1.95.1.ebuild create mode 100644 sci-chemistry/avogadro2/files/avogadro2-1.95.1-qttest.patch create mode 100644 sci-chemistry/dssp/dssp-4.0.4.ebuild create mode 100644 sci-chemistry/gromacs/files/gromacs-2021-musl-stdint.patch delete mode 100644 sci-chemistry/gromacs/files/gromacs-2021-nblib.patch delete mode 100644 sci-chemistry/gromacs/gromacs-2020.6-r1.ebuild create mode 100644 sci-chemistry/gromacs/gromacs-2020.7.ebuild delete mode 100644 sci-chemistry/gromacs/gromacs-2021.2-r1.ebuild delete mode 100644 sci-chemistry/gromacs/gromacs-2021.4.ebuild create mode 100644 sci-chemistry/gromacs/gromacs-2022.ebuild delete mode 100644 sci-chemistry/gromacs/gromacs-2022_rc1.ebuild create mode 100644 sci-chemistry/molden/files/molden-6.9-ldflags.patch create mode 100644 sci-chemistry/molden/molden-6.9.ebuild delete mode 100644 sci-chemistry/molscript/Manifest delete mode 100644 sci-chemistry/molscript/files/2.1.2-ldflags.patch delete mode 100644 sci-chemistry/molscript/files/2.1.2-libpng15.patch delete mode 100644 sci-chemistry/molscript/files/2.1.2-prll.patch delete mode 100644 sci-chemistry/molscript/files/fix-makefile-shared.patch delete mode 100644 sci-chemistry/molscript/files/glutbitmap.h delete mode 100644 sci-chemistry/molscript/metadata.xml delete mode 100644 sci-chemistry/molscript/molscript-2.1.2-r2.ebuild create mode 100644 sci-chemistry/molsketch/molsketch-0.7.2.ebuild delete mode 100644 sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch delete mode 100644 sci-chemistry/openbabel/files/openbabel-python.cmake delete mode 100644 sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild create mode 100644 sci-chemistry/pdbcat/pdbcat-1.3-r1.ebuild delete mode 100644 sci-chemistry/pdbcat/pdbcat-1.3.ebuild create mode 100644 sci-chemistry/pdbmat/pdbmat-3.89-r1.ebuild delete mode 100644 sci-chemistry/pdbmat/pdbmat-3.89.ebuild delete mode 100644 sci-chemistry/povscript+/Manifest delete mode 100644 sci-chemistry/povscript+/files/povscript+-2.1.2.2.19-libpng15.patch delete mode 100644 sci-chemistry/povscript+/metadata.xml delete mode 100644 sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild create mode 100644 sci-chemistry/tm-align/tm-align-20150914-r1.ebuild delete mode 100644 sci-chemistry/tm-align/tm-align-20150914.ebuild delete mode 100644 sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild delete mode 100644 sci-chemistry/votca-csg/votca-csg-2021.1.ebuild delete mode 100644 sci-chemistry/votca-csg/votca-csg-2021.ebuild delete mode 100644 sci-chemistry/votca-csg/votca-csg-9999.ebuild delete mode 100644 sci-chemistry/votca-csgapps/votca-csgapps-1.5.1.ebuild delete mode 100644 sci-chemistry/votca-xtp/votca-xtp-2021.1.ebuild delete mode 100644 sci-chemistry/votca-xtp/votca-xtp-2021.ebuild delete mode 100644 sci-chemistry/votca-xtp/votca-xtp-9999.ebuild delete mode 100644 sci-chemistry/votca/votca-2022_rc2.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz index 6069fe7ad961..8889ac5c94c3 100644 Binary files a/sci-chemistry/Manifest.gz and b/sci-chemistry/Manifest.gz differ diff --git a/sci-chemistry/ParmEd/Manifest b/sci-chemistry/ParmEd/Manifest new file mode 100644 index 000000000000..86601bc06f47 --- /dev/null +++ b/sci-chemistry/ParmEd/Manifest @@ -0,0 +1,3 @@ +DIST ParmEd-3.4.3.tar.gz 42174964 BLAKE2B 4f425156318595217c9fde3f65f7c147bea3c73404269bf31567cbfb17020dba6f06d66dc5b514483df1eeedb56f87243df0274782363ca427a740837fcc1c32 SHA512 489996555d05f88dce2304e65455424b1acd746ad7b55d5a42e36705bce812c8aa51c293afad8307f9ab1ecdeade3072d00c194eb2c567528e1fe596defbd1da +EBUILD ParmEd-3.4.3.ebuild 520 BLAKE2B 12b8036cc5b9122a5c120631cbd25157bb344d5b5407f3f00818191fb6afc9fb41411beb5c14da3455941d2eba5f4a433318be8c5031b5355ec1f24b136df82f SHA512 a55d1ab85f3c00f86dad78418b165b9b8bcd502d66aa85514225ae82c9394eacc180b0ef7decc96023052c4369e399b5390f93abd267fa4a2bce9d489f7e21f1 +MISC metadata.xml 375 BLAKE2B 949d039d3cd24da52efe20f58e7da07b4371e90ef72f314d076110b4604af1c0b7a77c1241172cf5e0a1c40363a00728d14d6faf30af73d27317f24d5a6c2289 SHA512 52791b3cb6a3998676f23e16346b9c4f447f42de8a58e612eebdf8ebfd34bc724c4994c3accebf00d552187bc80d1c097f73bd02b6fd6874a84441627eb785ca diff --git a/sci-chemistry/ParmEd/ParmEd-3.4.3.ebuild b/sci-chemistry/ParmEd/ParmEd-3.4.3.ebuild new file mode 100644 index 000000000000..e344e71ef07e --- /dev/null +++ b/sci-chemistry/ParmEd/ParmEd-3.4.3.ebuild @@ -0,0 +1,22 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{8..10} ) + +inherit distutils-r1 + +DESCRIPTION="Parameter and topology file editor and molecular mechanical simulator engine" +HOMEPAGE="https://parmed.github.io/ParmEd/html/index.html" +SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="LGPL-2" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND="" +RDEPEND="${DEPEND}" +BDEPEND="" + +distutils_enable_tests pytest diff --git a/sci-chemistry/ParmEd/metadata.xml b/sci-chemistry/ParmEd/metadata.xml new file mode 100644 index 000000000000..22631b58bc2b --- /dev/null +++ b/sci-chemistry/ParmEd/metadata.xml @@ -0,0 +1,12 @@ + + + + + alexxy@gentoo.org + Alexey Shvetsov + + + sci-chemistry@gentoo.org + Gentoo Chemistry Project + + diff --git a/sci-chemistry/avogadro2/Manifest b/sci-chemistry/avogadro2/Manifest index 86f6632f51a3..a6a5dc3e81ad 100644 --- a/sci-chemistry/avogadro2/Manifest +++ b/sci-chemistry/avogadro2/Manifest @@ -1,3 +1,5 @@ -DIST avogadro2-1.93.0.tar.gz 2905461 BLAKE2B db51e4574fdf2a31657b8bef7b06eb0d563484deaae1a6d75649187d6f5fd7b02a99506cfb850e09792555d7c27d9937d0df0f7172fafc3ddcbccaa7502c5bb6 SHA512 8e4e15b6c2d1935f8c585c83761b28a6397bc1dc22cd5f66464d59dd25327b1cffec809af492586be4b56793448f94f9375c16e8a4c4969f7b8f2591049cc5fc -EBUILD avogadro2-1.93.0.ebuild 1225 BLAKE2B 7dd01683f6f875b7e66457c6debd02f40ba7860f44e1ac1744088496524074944356518ffcac04603b7b86b09f9172268d1f0b67d4afdcf78f0fc9faeaedca0a SHA512 726f46a48c7087a34eed8fe7ad6ce7a9f4b0bb001850a2915ad6a2b47c0e17d4a082cc10bc4317fa4fe64ba44bc8e132e55ae1a389745d2751fa7bd43602bce7 +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 +EBUILD avogadro2-1.95.1.ebuild 1924 BLAKE2B ce0ce22884425351e6f1e6eefab52f16ff3d9b74c373985edbe929325927b1709aa7ec3bd0db89d46d340058e584e97be5c313b5051cb9a519ec7a36f3b12d3e SHA512 3fb570d830111e918bcb5b4d16a11717b115a0e5231db44960028ca09208ba4a27e7428d7bfb8ae40fd1518cdde664139134865a3bd2f6822869de9b20ab59b8 MISC metadata.xml 514 BLAKE2B 0a88a4b92fef923690f6e9767c572875d86c8522936aff89354f4b08ee74fe7c2f49e1eba143c850753d8f2cb5a7e7dc063e9864e433b70068ef7edcd0163683 SHA512 e7729ed111cfade53f238b9b49067c55c1a229489dbc1665d428ba8643c0f9ad0af402e8bf4c81399df1d1a786c7831a7a769bf9a5608157642546a1d0f45ee9 diff --git a/sci-chemistry/avogadro2/avogadro2-1.93.0.ebuild b/sci-chemistry/avogadro2/avogadro2-1.93.0.ebuild deleted file mode 100644 index 82feebc5aff7..000000000000 --- a/sci-chemistry/avogadro2/avogadro2-1.93.0.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -MY_PN=avogadroapp - -inherit desktop cmake-utils xdg - -DESCRIPTION="Advanced molecule editor and visualizer 2" -HOMEPAGE="https://www.openchemistry.org/" -SRC_URI="https://github.com/OpenChemistry/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="BSD GPL-2+" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc rpc test vtk" - -RDEPEND=" - dev-qt/qtcore:5 - dev-qt/qtgui:5 - dev-qt/qtwidgets:5 - >=sci-libs/avogadrolibs-${PV}[qt5,vtk?] - sci-libs/hdf5:= - rpc? ( sci-chemistry/molequeue ) -" -DEPEND="${RDEPEND} - dev-cpp/eigen:3 - test? ( dev-qt/qttest:5 ) -" - -RESTRICT="test" - -S="${WORKDIR}/${MY_PN}-${PV}" - -src_prepare() { - cmake-utils_src_prepare - sed -e "/LICENSE/d" -i CMakeLists.txt || die -} - -src_configure() { - local mycmakeargs=( - -DCMAKE_INSTALL_DOCDIR="${EPREFIX}/usr/share/doc/${PF}" - -DBUILD_DOCUMENTATION=$(usex doc) - -DAvogadro_ENABLE_RPC=$(usex rpc) - -DENABLE_TESTING=$(usex test) - -DUSE_VTK=$(usex vtk) - ) - cmake-utils_src_configure -} - -src_install() { - cmake-utils_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/avogadro2/avogadro2-1.95.1.ebuild b/sci-chemistry/avogadro2/avogadro2-1.95.1.ebuild new file mode 100644 index 000000000000..e4a5c22f11fc --- /dev/null +++ b/sci-chemistry/avogadro2/avogadro2-1.95.1.ebuild @@ -0,0 +1,82 @@ +# 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/avogadro2/files/avogadro2-1.95.1-qttest.patch b/sci-chemistry/avogadro2/files/avogadro2-1.95.1-qttest.patch new file mode 100644 index 000000000000..ed12da21e3f6 --- /dev/null +++ b/sci-chemistry/avogadro2/files/avogadro2-1.95.1-qttest.patch @@ -0,0 +1,15 @@ +diff --git a/avogadro/CMakeLists.txt b/avogadro/CMakeLists.txt +index d2245ff..fe1857c 100644 +--- a/avogadro/CMakeLists.txt ++++ b/avogadro/CMakeLists.txt +@@ -80,8 +80,8 @@ endif() + + if(ENABLE_TESTING) + find_package(Qt5 COMPONENTS Test REQUIRED) +- find_package(QtTesting REQUIRED NO_MODULE) +- include_directories(${QtTesting_INCLUDE_DIRS}) ++ find_package(Qt5Test REQUIRED NO_MODULE) ++ include_directories(${Qt5Test_INCLUDE_DIRS}) + link_directories(${QtTesting_LIBRARY_DIR}) + add_definitions(-DQTTESTING) + endif() diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest index 4f8f627f4089..a36c6d3c1089 100644 --- a/sci-chemistry/dssp/Manifest +++ b/sci-chemistry/dssp/Manifest @@ -4,7 +4,9 @@ AUX dssp-2.2.1-boost-1.65-tr1-removal.patch 2126 BLAKE2B dc59d21a6be26ee96b636c1 DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811 DIST dssp-3.0.11.tar.gz 168085 BLAKE2B e1c42fd22cfb2287f10b5deae48b56a4583d4a67737a3485dcbd160d1597a15c2d5105c3794c875d8001abede1c014efb4f7f5b7c250f867bdf9ed95a0860217 SHA512 a0cfe44e517ff1f909ef2928b62ae2c639c6bddfd8a0fb538883f647fd2771e00da68e0fd2521aa02ba3c6d1b0c9b784b7fe142392af3a3abf6ea89f1546bd9d DIST dssp-4.0.3.tar.gz 122872 BLAKE2B f88c330370645b4bd4e89656ad676e443a33c38d7882145bc60e329f823eb761777713df6c7ae44550d10bcd22256ac16db358587cadd39efd6268dd869655d4 SHA512 31ca481b097c9c59f407e35eb8175638b5e4102991007090b5b4ea30db0b076f97cff45d0aa9ae01a826f7673258464b572d68714f00e210db26020cea4be094 +DIST dssp-4.0.4.tar.gz 122183 BLAKE2B b12702c482ad58f09d96e9c85759ebe9455961978277e25d1ee554d07a643b342acf2dbcd3c18d539f058b970c24888a43827b6bac47899ca61bf96dd0c2723b SHA512 e0646bb20f10617174b0970c549fd44990750f46f7a550e4c3bc89487a8d3b7a175d53b2abb0684f9d96203a23d64ae67c6c10688fd4f5f59ff19995f9149ef8 EBUILD dssp-2.2.1-r3.ebuild 880 BLAKE2B 057a862fbc9ff19fbf487f9df0faf661a7db5406c28e6cb91d5e38dfaa2e9d24eead9ba78d4e92b5b5022e2be5c69b30ff6c386aeac8160062b5f7f35b449889 SHA512 747ac74fd95400759569e657db85c3dc5c5a7ee0753761bc4b4927f4d119d168f0d5dcbd9ca16f37486358e7117e773d812034fb07953aae88c63ac1e706f8f7 EBUILD dssp-3.0.11.ebuild 873 BLAKE2B aa7a2dcf710a344bbd18c28f05c1b8f32c4fc3469a054382b4232c567bd3f53622558bfd42824415cd0b486342b766eb42bf3349901f4fcd59cc3cf08e5292f1 SHA512 190ecb2e8103f2b3d6bd5d201342e7763b8c43a64f4a831d4fb0a794e54721dd6679774b6a76539b79b3ba6bbd9ac6c0bdbc73a4e14b65897c2086452fac8c60 EBUILD dssp-4.0.3.ebuild 778 BLAKE2B f550bf8d7063b30f4fe15641b92e2973288c6da16317e74a041ada8e043133e4d6d6e125882d05f0e063b60ab421f039442951f9c92b9778e5435d82a512ed8a SHA512 7d853da1d0f4a1a623acd3e801fb8fcc3c50a4006cf75a8c999d8f6aec985c3fe92d8aae50bde624d67ddb559ae7bb49d701de36800ae5d2f8abaed523f0888d +EBUILD dssp-4.0.4.ebuild 782 BLAKE2B dacbb5b4b6e1e3fa5ff602a54fa9ba42b75bd9df587847b776e67483ac4e2b0baf4b143e832bdd268080eddb6343868ce80a78a119f84709cbad1a525808c847 SHA512 9d2c3268ca704d2b71c268b5179e9055d03acacb7a1f0b8bc20e956a1c4945f9489958ae7e0db2568f49f35954d93ee5a2c8fc389038d60b214879f5c691dd87 MISC metadata.xml 217 BLAKE2B f8189b02494f180dac078dcd5c275d3c795f20f360f8b172c66065a2d937e396b24b8631bba4cd8567d60285ce89fc77b9539f2233bf33899c820613c48c33ba SHA512 f0c9e5b3d281fecd21b1e23a6f44c94c1c0b3220de46a177d35932111b7f1ab4399061c42833ac1ee9bd0324b139fc8db66e0d2890224d607bd3be38ae469be9 diff --git a/sci-chemistry/dssp/dssp-4.0.4.ebuild b/sci-chemistry/dssp/dssp-4.0.4.ebuild new file mode 100644 index 000000000000..5fe497f48e02 --- /dev/null +++ b/sci-chemistry/dssp/dssp-4.0.4.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit cmake + +DESCRIPTION="The protein secondary structure standard" +HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp" + +SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +BDEPEND=" + >=dev-libs/boost-1.70.0:=[zlib,threads(+)] + >=sci-libs/libcifpp-2.0.0 +" +DEPEND="" +RDEPEND="${BDEPEND}" + +pkg_postinst() { + if has_version "<=sci-chemistry/gromacs-2022"; then + ewarn "DSSP > 3.0.x is not compatible with gmx do_dssp:" + ewarn "https://gitlab.com/gromacs/gromacs/-/issues/4129" + ewarn + ewarn "Feel free to mask newer versions if needed." + fi +} diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 4b19626b924a..1e530a201c6a 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,44 +1,36 @@ AUX gromacs-2019.6-missing-include.patch 1052 BLAKE2B 01d7e592caa1e975a1fcea99bc37dd61ea7c039ed32243852f532c87d08911f9e83d0752d3a09e46643ca433339fe7c8d510c09e4af1070060735f9ee8a151d0 SHA512 8ed2e1de98cd35d87c0a0ea6867a99d4c1b33940040506feac09da929389afd1e19f34691c9032b1f59b156986b56c49aed1d0c8f8e7e64ad7a78e6dfd521912 AUX gromacs-2020-pytest.patch 1346 BLAKE2B 4b0b34bf4f46ec1acc3d0088ac11323938ee44b700beecc32b083885727d31904649798e38b824a6cf04ea7f9129dbd40e66bdde6e5a88fa4734db51bdf4cc46 SHA512 2c05e243b0e7bb8f9d25051d7bc86463dffa722502586799f0a8ce53bebd24fd0e367b6840365ac4ebc30595ffb8bbccb10a88d0c81148ae198941966cebddb0 -AUX gromacs-2021-nblib.patch 1860 BLAKE2B 3f9d8e5683fee23434ca7bd0d9264eaed5834c3e4164176006fefea27b74ea50e67b743c4d0fa329486545ac1237d9fb288a0fbe7b6a4c06a37c8e85a22cb255 SHA512 1630eacd632519d5440fcae8aba511615ac031ce9828a059308c8ec2f33588c43dc055ab3d435efd622f23a46afa5caa14a6acad5aacb15bed33b9a9be5009f9 +AUX gromacs-2021-musl-stdint.patch 601 BLAKE2B 2e871d22655950ee9b9951229e78bc022f74ce7a8aa8063bafa30e0fd97cd0451e0621ab48f985d813fd5d890c0f2d0c9ced6d4b26d86e9d1f6774c084f169af SHA512 d36497423beb86a26ad011432dd6da7169ae42dc00d15bc90ba14de6ecf5eb3217ac987260dce479e5f92d5f3a40fa28c5eb1b51816a92b6a37745f674581280 DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122 DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8 DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9e65234b9459b71471827032654acacb58ed6ae87ec6e0e593a0acd799683cc4461b06cc883b089d740708619345e SHA512 0c56f058741af70660baf0177724ec940dd984c05ea141ede91ee51ce3744f76d00e31bdb5db907e46fa1639de5dca637b3ace26e89f908c2e74c69f0c21ed3a -DIST gromacs-2020.6.tar.gz 29196621 BLAKE2B b350fc62fd8eeb3f2b042fa74a4ed42e43a7b74efd8fddb60ec086a814048a52b8625da65fa5c4cf2cb1e22f8347562bc84d38bf34441fc5ebc6abaa38b0eea0 SHA512 4ce4d6b9ae33e9cd2a1ad3313e80acf63ded21dac897b01dbf87df2e318181796ef64c8a1d3e0a6058b972d8d88d00f710cd0277db12f38fc2c9b29772c98bea -DIST gromacs-2021.2.tar.gz 37976386 BLAKE2B 8818321bbcbdee25356bbf909d9c667f9d7cf180e696a323a61017683234d1269decc8f8d72b8012a8cc207f69e5cd97e2ab48dbbff06d82bbb407bc0578854b SHA512 51b1728f41932274436ab807d569109e2b0e145abcb5cf9c9b7daf6a7396f2f8716dc28fb93cf178c97a7eaeab2a88878d0bc71dd6c6abe7e829d579e7968615 +DIST gromacs-2020.7.tar.gz 29175554 BLAKE2B 98f1aa415946f8eb113febc81105f0c1b0919b96fc3c55a0ab83bf3950ff509b81eade92e645adb0bc2b407df239e20cf3f19828b6e08616437c8693c1fddcc8 SHA512 1d375c44cec38445e56cea252623b5b6c565680268999d4b6c14d6dc38759a27227655b2d29efaab9f9115d3677b446cb555e11cddafa0dc10c4827caaa2477b DIST gromacs-2021.3.tar.gz 37987972 BLAKE2B d71995c7d5a34978246e33dc637ac3d273e547afcf72d1a107026650f03286ecdf27e4b9a70113b3c3a01af59ad49ac5c813aa6e5d2e8eb29fd05582a7a28d34 SHA512 da420917d06de2e192dfbb4e1b9f46989ed05b5c7e641c657104ed8f2bd8b22509bffd1ecfd7c965c80544eafa6af12d6d0aba7e1e7d9d14a4a88fb3fbf394a5 -DIST gromacs-2021.4.tar.gz 38023262 BLAKE2B 4e1c9ca23f8bd89a990bac2730f846ce9fd6423aa6934866734272ac8f5ca29cdb51daec440b7ef2af56c68bdbab504c0c1b1a4d5f4af0b16666850bf286c5b2 SHA512 35b26b3df02d151373fab49022281b89e987c867257a998acc926b2b7151f5d4e46f11c398a24f4a174f668dd24a828b07d36594ac5d5506e10e40d4578427a2 DIST gromacs-2021.5.tar.gz 38023772 BLAKE2B 45e1f080b86626423e471f06b48b615db1913048f9f6998da8ce45408339b32f829d33dd2af57297a7d307fcffd556c333a58c309ee0f2adb021ca3755619b05 SHA512 56c1b312fc8e52ec6f86e445d2fa2d07107c461b35d4dc8cdf95580f05fd8e6c5fd671d0e72b2b9e74e3232bc8c41db496fe4bcaf2b9a3ae3c2cfa93489a31c5 -DIST gromacs-2022-rc1.tar.gz 39674628 BLAKE2B 8943a1e8445aa286305bb786e1303973e58325c01ce86883e5a72075b8ddd57453c61c8a0087a9ec73ea2903b04596109322151d8fadda350a4eace713cd962f SHA512 d6f45e46b653237154fefce95e3799ed2fc96d6a0365d027ef0aabd03cd3c3507108985caca8907c02479f05a10ab833efd3217e7def100897fa845e0ebf029f +DIST gromacs-2022.tar.gz 40353044 BLAKE2B e9ba72092467c143be7de0739e71181f384a6bb463338c58c60a5d56f30b960651bda60c1df4fa424e237f1ae90d5d7bab19670ec22cd21bba3cb638f8e5b1ba SHA512 f256b032b226c14407ba21c7b825b6bf3f7b3595318b8638594d81ed6346b0b8563098f6ff7005c2ba125447c5d2dff750829b24781c8f1ea266e6465f627db1 DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5 DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb DIST manual-2020.4.pdf 11851608 BLAKE2B 7b7bdf08e8946fcc448543b08391b94a67fee60a8c810597c1f09f70443f9d7db817c99622dd0c21c6317f5fdcd6c4a88589ecac57055cb0cd8597d6021026e7 SHA512 928555663c77de36393e625c29d388d4e1c8c1298e7a993d871839e0d4d8d18d190221ad8f1d975bd072bdd6a061e9ea5b9295f2ecf45f24b6523ea5ea290fed -DIST manual-2020.6.pdf 11850850 BLAKE2B 155e4eb9c200dcd0a38e3669b26077fcf310d437b82d9a593d333dada3989c2c8a936d62c642e195f98bb474b1673b8142405c467348fc96a74d57fb12106d76 SHA512 be508ebec597b82a2c4056029f8bb731b22cb8902628a45462ed21af54c554d28e07d5381efaaa96565202b7b47d33aea67950206cd9e8936211ae721b21b3e1 -DIST manual-2021.2.pdf 12252501 BLAKE2B 0dbf9024e1516076b0eeb46e41523b966d1d81f57504fe0501c7bc8575e74fb19e3452ac584757e425bcccbc737367fe83be87fd21a4287f4675cf87184b960b SHA512 14156d3b1017990e0be3ceb7ec055777a1aec4c347ac2e821a042d51c931f84ebca862f60644a90ed7ba4070cb14ff8babcde3e4351e4dbec84df8563e350984 +DIST manual-2020.7.pdf 11850780 BLAKE2B 38594e87993badfbbcf47d6010a7f67d3c3426dab85e1462916b4d62be27b5764953f912cf2b71ee24877e0bfa27b3f74431da2da81b4977d58cb66b2cc795a3 SHA512 4f184f2c90e0bac01a48069cc546cd5b04fa5f543f90dd2d68c6d17be278152fd09456b6a6c5c8236f8fb85a174d6ec7a1c7b44d437b4e6fea5d0ada73cec0f6 DIST manual-2021.3.pdf 12255076 BLAKE2B 6ca516b6832507c9d4100679d1f9bc9e3ab17d226849b050764b0d0626247dc57ce49985f9a7fc0061f3df278923a83faa367ca8ab91c37e5624dc584a51a822 SHA512 5d53798f30ea00fcb4e1b35f7eaa4bebfc05dafa4f2d0c197dcf2b57a624ad3a98b74fd90722e40d0ac13a6fff4ca231f9d6340f52ba94659c827c53c2f1cb16 -DIST manual-2021.4.pdf 12253232 BLAKE2B 0b859c08a07d5a615ac7a822b61d5a4f4296ca9773d383a07960dc629d6b1df23e1dec51561a4ac26789b84e49cc98b6d7cc10d943c61d7784052664ac1bacf9 SHA512 024f17a670518fc19a2a462186ed2a74f331c5c83b8ba4bbe148a53767515ba19e6af887a1baae3a7770af2095fad5c513784cc54f9d0f881395ad8a89760cba DIST manual-2021.5.pdf 12253641 BLAKE2B 8850715a2bb21345e1c9735aca1a5dd2ad916e5a18881e7c9f3dda6f055ca12d9d379b74218138999ce50769efd8b9dd6447afbf70bbbefa2564dfb9fb276b91 SHA512 7635108c935e4953d722df6a16ee43edf97eef7e49f047218728f68f61f8f185192ff1d8b13a573b643b040955af211355a7b560c8a894c858d7f71249d41296 -DIST manual-2022_rc1.pdf 13051892 BLAKE2B 99b0a2110a0a7601d4e2d00f4bb3210fed8e0e4dcc2c3a17fa8e902cc713c8aee90eebbcd9b0cb3fd20fb539be6bcf32414fcd3c35a3f9b4677240877623ca93 SHA512 5ff91b2486792a525fc5fc08bfd31225e3c64018b519592ce899ce0a6f92fb366ea4d1b5df3473d264bc93a651c11583757b6603a855cdcd9ad18ec86e160fdc +DIST manual-2022.pdf 13060966 BLAKE2B e1684d22e16d2bad878cd0adbac0df74a268f89034756a34374908afc7f2562a05dbdf91b3dcbdb98a45b3d21140b02a2df26e0f997c1f501347e102069f22c2 SHA512 0d9bd1fbe2db122f434df1565ba7c9ea5ad168f73855724a6cb488244eda13d8d47b2d534a6873dc7204012156fbf669bdaf7ca7d03a914745f60950392e6d28 DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036 DIST regressiontests-2020.4.tar.gz 48542144 BLAKE2B 1dcde67525d40ababa74d9e8ba2dd3fdef1de7d1018491e102edd71d3a622925f213b5a0812e5448882b4cb5fb578317e8e5029bdc4bd53008aa8441a3d9dea1 SHA512 7c71f36a1cef22562f14dcd233e90ad2fe370ae1a7d3b5268727259b374e12d4754253735ac8745d3738bdbc1cc2067780fda5e393be2ff264f632fe4e0c1978 -DIST regressiontests-2020.6.tar.gz 48541232 BLAKE2B dbb405bd9168775984de8c9fb9e3fa2398d2790e2e4de23711c51a01dc3ea570d172a35d4924742ad5eda463eb0a885e6924512801e82b241600ceaefd5db70d SHA512 497a9e7d438b0b7b0734a97cf3683baf480ecc056e96b09f1e143c362ff047a4e51e323216750501c954559579716dc024d3c51319bd2c85fa719466ce4330b2 -DIST regressiontests-2021.2.tar.gz 48514312 BLAKE2B 81b007d5e5e1d054349c73dc8bc3589db328752e48a66687c0ad36be87ebe580df9cbd93b193a724669bd5765af06ec306f2e12af00a228af616de03943d6f05 SHA512 b687ddfd3dc6ec1051af2a3253633703ef1c82335d1df23379819ea47e44dfcd417e81e29610cc584d4c5fb1ee1cbc76731a3fd31b529d8cdd0b9c22f432c7ec +DIST regressiontests-2020.7.tar.gz 48541487 BLAKE2B 255608b52158c6c01e7c7c4dcf075128ecf22b2f26d32e8c203de8a4bc69c60ec95f49cf8ccd64abc3073c5e8dca9d6b01daed9dfb8f67bce2dd068ed01acd05 SHA512 2458582f94f3c9f4e1454824ce3940b4f5b6cb2151d06846c42e7a9448296fd2a6df4f53be9624e0d3317d2b59f89bb5348eb8b2970d7b46ac22ca989ef3458a DIST regressiontests-2021.3.tar.gz 48515038 BLAKE2B ee79d8adddc9c68f7d59d9e568b12bf4d1fe0e44c2810fee846ad6f689bbcacf60f5c266433946329e64e3127bc2d37a3f81f69c070c636b411b38067650c2cf SHA512 e14baa22ef2902a23125bbd9143ae7a9a4810498b321794ff1989f8d044d47db5db41d5225798fda08016c05e5f7f315178b5a6e35cdf01e3b6604670a8ce7a2 -DIST regressiontests-2021.4.tar.gz 48541736 BLAKE2B 37b8e65e333dcfcfc795da631475807ffa4ecc3a85426b4de6dd2ccb50f40a78159149789da13f988340a62d21e7d6b1d4f0c6e7fe69120d4c94ab2252b4c440 SHA512 18663693cf9ce2ca3bd8df0f668e7a0c8236a7f5ae4ee02f621cbe52c139c506b61ac4cab200cc59caab41e9983ea93dfa062d7b52f6558a619096a8d439fb56 DIST regressiontests-2021.5.tar.gz 48537298 BLAKE2B 860ac34aa8706ecdafab4472162775ce12726d93839079ebf9b7df8c2c6a1b47baa8a635c24cf4cb4551a32237c3de7da3197ec136b5bbf48663edc3943720ad SHA512 3605d04b2602339fb7d33e2776da2ada337ca58a3802472d47f490d4e8dd04249a950bf34608a498eedebf69f344c0311bac8f7fcb58ce0ebbb6d608ee39aa2e -DIST regressiontests-2022-rc1.tar.gz 48609151 BLAKE2B b5ec84b9f3f506636136bf9112ea71f7ce5bad8b3dbec6d8c6b21ab13ddab8252a3038f1dd06e1f97cde47f918aff2c62325d09d51bc5632e1db7b84311dbd91 SHA512 a378f724a728fbadbad3b9013f85bf6fb1945e500151d9dacdaea9371f432ce3449dc812f672b77896800c3c46a3893b239101404a1fab63364e62afd7f18097 -EBUILD gromacs-2018.8-r1.ebuild 6946 BLAKE2B 299b68d1a3d07e2691930de85bcee504885ae160ffc44fa4c65aeffd621fb54f15db86625a4c6339214fdfdd2e0f690c147d32abacd392fdb10c4ffc6d834b0b SHA512 0a511e8367cee468c5321df6bb5fada42950df2bda4355087b4b499e869f4167e22196a7a9d4dcdc286320cc8bd465daaf8c3da9ad9d22145bdc9024b4aeed17 -EBUILD gromacs-2019.6-r1.ebuild 7269 BLAKE2B c3c66eb2fed62426d80a83fece8e5c03bb5f143f786cda937f7c54fbd279a3892148d68d7147f5e8e6610b91b1521d83fd14f241819193bc6cb6be63b7e5ef80 SHA512 4c93feca7343482e6c86ad83fcabfca16c647bf85955b8d41ef9c4a684ed87f98f153e1b7bba0da47de44127ac7abf4eb955454ba03eb29ce0a9fa11eb3a76ca -EBUILD gromacs-2019.6-r2.ebuild 7326 BLAKE2B 4850899d3e4b8affe9724870215cb6a08e57ce07c7587d01e58788c509c8a8577b41e6ff8685f2f540df33d0e47bd08fad9482bf35d1c71c7f11626208897189 SHA512 c138b4a3fef43d310469cb74583aa7b12b0c565dfe07c4f9b0805bc0c1e724ccdfedbeb9fb6fdaa836e8c3eaad3f40358070054f67b6ac8655f5e715bd32824c -EBUILD gromacs-2020.4-r1.ebuild 10139 BLAKE2B 3e9851ed038cdeab3896f24c3538ebea5dd46aae402c86b900c3720db15e6cd674dd38f432efb78ce4a34324241f5d9dc1881e6ab30edc1396cf2685ff0a3ebb SHA512 a422c0fd42f721cfbfaa83aa4d300ccf3c8de089ad8f7c392528c6df86898b3b25c05c9b7131a68a0aaf75995872820b61e48f54c1b878ea162f53f917c02364 -EBUILD gromacs-2020.6-r1.ebuild 10142 BLAKE2B d212ebd8e184b68d0f77173467252de2587fef6babc48a602f0fd289b15a9923d7ea47fce1459451c56df5ab31e6e975e3e0c381993322a08b424b21a5c8d31d SHA512 0a14ad921a3fd48d1a980b08ce3470f9d27f6056d9bb8addb26c14adb6dc30c8933a96bdb6ecde9e491798cceb9ffb41a3c244fa67f127c3eba5095277c6baa9 -EBUILD gromacs-2021.2-r1.ebuild 10364 BLAKE2B 6d9e48d7d4c75927a1f87aae70a3458d519850be2e09f5fa358f3b16a03ad3b8916ca97805257b03558a12c173d08167c4fee056de44742d85ac83859fc63c17 SHA512 68ab6dd6fdbc3fa8f628be0fd7ab05e528492a6f626ae8edcd15785ef816c47515390667d8f36c10cd1d4eeb1e73655611572d55234e9c957517f4c85df1e971 -EBUILD gromacs-2021.3-r1.ebuild 10291 BLAKE2B 7a53f7c5f5365d3efb6d8a35552aa751c4e83a3ee259d315c85d0faa7117c0bc3510f9752dd76d54bd55024ad80de7ad31d2e54cccf2c651a4414e7a0d452e7a SHA512 611076dc6d41ccab6f86ed8cbc96a6ec36ad405652a2c0c4da68fa78cd3346545efd38bdedd115d4a60d657dbbafd0019e84ed9554af211005352e6d26fad5ae -EBUILD gromacs-2021.4.ebuild 10293 BLAKE2B cb2304e0355f30d2b3549aed33db6db7229458e504c4ccd3c0cf1d2d2a66751c71c33c6b3c5f46a01129b7891dfa22d7f6b2d731275dc9396f20400a7585593d SHA512 b07b8ba64de11de4ecee1c6e3ad2638ac582e93f6122ee8cd90f5430f4ea16435f7cb4778e88a5c62a7d83989c4eb13932f7ff6e61f8f4fafd691a0a30f057cc -EBUILD gromacs-2021.5.ebuild 10286 BLAKE2B 6a8911759a385f3ee4eeee68b3c4121736699821ba1fd246e46f31b6cd7f16ba95728ea9c0ea97562a486718a090b116cbfcbcaad6b2ab4bba3b4e59b3d71542 SHA512 7e66263511cf43de48e7561c4ae88640782fa21238b92978cdc9e67c12cd4775365ee666aa32cdfc1aa365ba8eed5287295cb64535459a921006f2b27e630354 -EBUILD gromacs-2021.9999.ebuild 10293 BLAKE2B eafc12c1354eaa5c641b4c41735a8abce7d385b06c4ed6b9bdf2c60b54c96396030b5a0b8bc953ee41d4426b8ba69cb776bdc0dde0dda2c9caa7d0f025247ce6 SHA512 639fa70a146044ce2be2fd18302f99589edcd0028df24c884dd536cc5a54bd24b01008346bd1f62fa6c1c854113f25370da289bd1500b1903cf4d3371db781f2 -EBUILD gromacs-2022.9999.ebuild 10233 BLAKE2B f3dae6a5105eb9cd31c88fe9cae8c469020010cd34c11b2934b294ec32d37500a16cca5b711ab2dd02a574228f7dcda678230a8709ca8c4e5152f918085437dc SHA512 4176081090b9f3c1a95a40c88e4c6bf92a304833083ed7f350bdf9f8a6442cba3f559f80c48ebeeb197cb16fdf670fa593518a548ee35cb4fd87881203f7f74a -EBUILD gromacs-2022_rc1.ebuild 10232 BLAKE2B 34558e1bbe90beabc67d12dc98214299924b3ce71500544cd523344f1160981beba772af9a274474a98cbc583723346b6ac48ce6c78bcca3ee6b097d27ddeece SHA512 dc65c6d4e7c500e340705ca989f0ab5c42960fed2b1c4f39bcea6a79b52f2d931984f615643fd352a7634f075e220e382d49e99ccbfec31c8358ec1ef0dc94eb -EBUILD gromacs-9999.ebuild 10233 BLAKE2B f3dae6a5105eb9cd31c88fe9cae8c469020010cd34c11b2934b294ec32d37500a16cca5b711ab2dd02a574228f7dcda678230a8709ca8c4e5152f918085437dc SHA512 4176081090b9f3c1a95a40c88e4c6bf92a304833083ed7f350bdf9f8a6442cba3f559f80c48ebeeb197cb16fdf670fa593518a548ee35cb4fd87881203f7f74a -MISC metadata.xml 1224 BLAKE2B dc6de7f135e5cbd7bdb94bc630d3c7344f5f5387305ada4f3f0fd3f027f9fa4e2c5e44120c8eab8e983fcda314680ac3d140ab61873ab21b839f912a52b21dde SHA512 d036cffac5fd3c4b8d26efdee0f4b4db8d3520f771754a0859f8e99f64d558795b6cab1efba1d4f1700027707a05a724ae96a7e257434d3894ef5fa6eed7ccba +DIST regressiontests-2022.tar.gz 48616817 BLAKE2B 5d303f365a8b3c4554232ca3e583f0eacc1973dd62faaed769d297efb5d7dde3ca04b8071786ecee992a83d7980aa244965212856f48c8832ca55805af61b1c1 SHA512 4566b76b5eb3bbdcdfed8330d4fcd7ada02eb6802434aa9f2ed4f775da780e4bde7daa35d79a72b3f25c540cb1c2b347aa2e6d504a77c095830da024a933fab5 +EBUILD gromacs-2018.8-r1.ebuild 6911 BLAKE2B 7c58e3fd507f54c17e3268bb3dc634f1b708c8c2662d33ae1e125cc2a11591cfefa4a38e6922dee789f63829abe3917a245a12ef06ca43686221c37c65ad9dbe SHA512 f9512b277a696aeb2d287cf1c37f982153889027ef69c3b766519c80049f363a491bd22d0d018f93ca63f41e448fc6b2f93121ac5a66f37c2ef4951bb473b8e8 +EBUILD gromacs-2019.6-r1.ebuild 7250 BLAKE2B 906b6a7c5757f2035600752b8dbbb40c99c68fd441fcaa4e6228cbc04fe93fea40fe42aef37f86804833db25625a16b6b6a52a947ec23fc571915a129dad5658 SHA512 9b32eb868e2b5caffb0d041764350fd45307565246dd0937443ab09d818b51ae4af898d4aaceb2c4fe1673c8c3992d067a89164cb3cf862a21825a0e432ec0dc +EBUILD gromacs-2019.6-r2.ebuild 7307 BLAKE2B 0105b1602f8fc59d398e24ee5b820916be92962b1e37bb40da03c13641fa02f6fabb484cb6ca481e051c5ec82d446e337e297a8e08004c46634edd586c1399c3 SHA512 058fe35d2b2bfb135f7675d27fa676364c0f6506ca74c8f8a760596d74cc60dac5ac8b95b8886df0c375bc4839c465106e3f7e6af24cfd8a504c2189a4f6e16c +EBUILD gromacs-2020.4-r1.ebuild 10081 BLAKE2B 87104c721cab6ac70218d6d7cea6280ecf0c8dfd11118ffc086ad2264ab4c52f9904ae55f4dd67d8a21a9e1b4309c50ecc65fe969fdfd4dc214663c1c56e4b2b SHA512 d2fceb44f67f1f08609d6cfc3f6e4ecdc607c12b7cf3676f7180a3558e91ca2cdddcc449b5ebc7e09dd20f1bfae2fc6d01ecfd7861a196cf36976b23c72ff4f2 +EBUILD gromacs-2020.7.ebuild 10086 BLAKE2B a8dbbf44bafe6d8c3c3b8c2faf7976ca8dc34e3e73209c2f34a16e301d62404689a40de03ba78c602d4d99d687bc555428dd7eb13d8badab4ba997de09fc1812 SHA512 ef212496eb06fc88d53ba190a3ea9d4835b0686ce49278ced3eda0eb39ccfda27c72739962d25ba5a504f7125db18389475335a016df945fe296830429609b15 +EBUILD gromacs-2021.3-r1.ebuild 10288 BLAKE2B 0a2a11221d22689fbc514c9748b58e9289a2a5ab1628504aab9515b660be38a2f830da6d40c265898e323646275479b49fd08e9101911996dc9c56be9f345f4e SHA512 ac9cecdf06429435077ddba2932e07c6b580aa41a59a738314383a583bdbf49303bf09f8aef37f494abbd4193efddffac7049cded59590ecc6b470dd9a8ed185 +EBUILD gromacs-2021.5.ebuild 10293 BLAKE2B c1c9e5b72fdcba071e5bf045e76b0cc0c2bc4297d09287d305611dd922307509f384b9dd32c64de1c78c6acbb0bc824c1b246688d0ea891b45a2f052eb7a4398 SHA512 56e25ae7a1081dfc11c7b88ea62d3f8df145385b9172409c045d1a74de71dfd11010cb18622ec9a0868677044b7c3dd03852f0a4d883ac48bdfd7d0aef309a71 +EBUILD gromacs-2021.9999.ebuild 10237 BLAKE2B 68e2da935cbd8985cbfc00aa114c40c906e82ab87e683d837cc79abef9e480bb3edad1675f996a871d3970b7895315bd946195e19e6d2f9393f6e884664143b3 SHA512 2e452a67c43e08fb8fac5b7c0ce0c54f7e6de67936b0812d257f703f0ab9ba4dd66df307da51fe1173301fd53b569d89b34022e0d3b39d1a768edb77c61a6859 +EBUILD gromacs-2022.9999.ebuild 9374 BLAKE2B f8ebda163073d2cdd6a11fe096d1d0aa47637ab94a2d64e14929041066cfb84f63a1c17ee7432454c405b92629cfe12824dc29defb18291bca97cc384fafedec SHA512 1aec18c9918aeed944a2bf36660acead13df7b455b9361f70c97f972b3abef44b3ef6c8df707e7f886c6785abe16cd3a4e9b63508e8a8994e3033bd8e98fbc53 +EBUILD gromacs-2022.ebuild 9772 BLAKE2B 7003fa53b924757e9a2215116163b67db174bf1bc358be41caf2067d794331f4deead2a83d6429c9e02bd90348b22f20e5a7bf8d57a481eeda4ecaa131e8dc6b SHA512 642e23a6ee26a9acec9ad4bffa4ac101ac932db2c77dde04a72aebb8890cb5705af21b289acfc340ddcb4822a495181839418011b1571bc716d0ded093e60754 +EBUILD gromacs-9999.ebuild 9374 BLAKE2B f8ebda163073d2cdd6a11fe096d1d0aa47637ab94a2d64e14929041066cfb84f63a1c17ee7432454c405b92629cfe12824dc29defb18291bca97cc384fafedec SHA512 1aec18c9918aeed944a2bf36660acead13df7b455b9361f70c97f972b3abef44b3ef6c8df707e7f886c6785abe16cd3a4e9b63508e8a8994e3033bd8e98fbc53 +MISC metadata.xml 1375 BLAKE2B 321b7db8536061655a6efaa40110f4858633921292eba465b85fe0cb50280842e511f2f11385fe5d62bbdfb40e9c0c76e8e986a1efce8eac25d52c438d7ed5f4 SHA512 cc61e0b477f6576079a0f7910475b9091c1c521fbb48efab365d355e3c0a80cd19e1ea9028cb269d37c2572546b1be66a210512e40ff0f2d6314d1b0138cdba6 diff --git a/sci-chemistry/gromacs/files/gromacs-2021-musl-stdint.patch b/sci-chemistry/gromacs/files/gromacs-2021-musl-stdint.patch new file mode 100644 index 000000000000..c94fc5598f91 --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-2021-musl-stdint.patch @@ -0,0 +1,25 @@ +From 8a38303c52fbca07c850e0c4cd03a783aabf9e49 Mon Sep 17 00:00:00 2001 +From: Paul Bauer +Date: Mon, 21 Feb 2022 09:53:46 +0100 +Subject: [PATCH] Fix missing includes for musl libc + +Fixes #4404 +--- + src/gromacs/math/vectypes.h | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/src/gromacs/math/vectypes.h b/src/gromacs/math/vectypes.h +index d4d5211d11..bd9d31de20 100644 +--- a/src/gromacs/math/vectypes.h ++++ b/src/gromacs/math/vectypes.h +@@ -40,6 +40,7 @@ + + #include + #include ++#include + + #include + #include +-- +2.35.1 + diff --git a/sci-chemistry/gromacs/files/gromacs-2021-nblib.patch b/sci-chemistry/gromacs/files/gromacs-2021-nblib.patch deleted file mode 100644 index 67ea6f6f63c8..000000000000 --- a/sci-chemistry/gromacs/files/gromacs-2021-nblib.patch +++ /dev/null @@ -1,53 +0,0 @@ -From 5771842a06f483ad52781f4f2cdf5311ddb5cfa1 Mon Sep 17 00:00:00 2001 -From: Alexey Shvetsov -Date: Fri, 23 Apr 2021 13:15:10 +0300 -Subject: [PATCH 1/2] Allow to build and install nblib without GMX TESTS - enabled - -Without it you'll get error like this: - - CMake Error at api/nblib/CMakeLists.txt:79 (add_dependencies): - Cannot add target-level dependencies to non-existent target "tests". - - The add_dependencies works for top-level logical targets created by the - add_executable, add_library, or add_custom_target commands. If you want to - add file-level dependencies see the DEPENDS option of the add_custom_target - and add_custom_command commands. - -Signed-off-by: Alexey Shvetsov ---- - api/nblib/CMakeLists.txt | 18 ++++++++++-------- - 1 file changed, 10 insertions(+), 8 deletions(-) - -diff --git a/api/nblib/CMakeLists.txt b/api/nblib/CMakeLists.txt -index a2ce06596e..51211c3d70 100644 ---- a/api/nblib/CMakeLists.txt -+++ b/api/nblib/CMakeLists.txt -@@ -76,14 +76,16 @@ add_custom_target(nblib-tests - ) - # Ensure that "make tests" builds all nblib tests so the top-level - # "make check" will work. --add_dependencies(tests nblib-tests) -- --# this allows all nblib tests to be run with "make check-nblib" --add_custom_target(check-nblib -- COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -R NbLib -- COMMENT "Running nblib tests" -- USES_TERMINAL VERBATIM) --add_dependencies(check-nblib nblib-tests) -+if (BUILD_TESTING) -+ add_dependencies(tests nblib-tests) -+ -+ # this allows all nblib tests to be run with "make check-nblib" -+ add_custom_target(check-nblib -+ COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -R NbLib -+ COMMENT "Running nblib tests" -+ USES_TERMINAL VERBATIM) -+ add_dependencies(check-nblib nblib-tests) -+endif() - - set(NBLIB_MAJOR 0) - set(NBLIB_MINOR 1) --- -2.31.1 - diff --git a/sci-chemistry/gromacs/gromacs-2018.8-r1.ebuild b/sci-chemistry/gromacs/gromacs-2018.8-r1.ebuild index 5266a60f632d..4423a8eed2ad 100644 --- a/sci-chemistry/gromacs/gromacs-2018.8-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2018.8-r1.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake cuda multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda readme.gentoo-r1 toolchain-funcs xdg-utils SRC_URI=" http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz @@ -232,9 +232,8 @@ src_install() { pkg_postinst() { einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" + einfo "Please read and cite gromacs related papers from list:" + einfo "https://www.gromacs.org/Gromacs_papers" einfo readme.gentoo_print_elog } diff --git a/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild b/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild index 0c9aa1c428a4..7a2a36b88257 100644 --- a/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake cuda multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda python-utils-r1 readme.gentoo-r1 toolchain-funcs xdg-utils SRC_URI=" http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz @@ -245,9 +245,8 @@ src_install() { pkg_postinst() { einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" + einfo "Please read and cite gromacs related papers from list:" + einfo "https://www.gromacs.org/Gromacs_papers" einfo readme.gentoo_print_elog } diff --git a/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild b/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild index 35bbc972de69..15ec95dcc47e 100644 --- a/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake cuda multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda python-utils-r1 readme.gentoo-r1 toolchain-funcs xdg-utils SRC_URI=" http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz @@ -247,9 +247,8 @@ src_install() { pkg_postinst() { einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" + einfo "Please read and cite gromacs related papers from list:" + einfo "https://www.gromacs.org/Gromacs_papers" einfo readme.gentoo_print_elog } diff --git a/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild index b12df9964c0c..cd8f59f82ed7 100644 --- a/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -10,7 +10,7 @@ PYTHON_COMPAT=( python3_{8,9} ) DISTUTILS_USE_SETUPTOOLS=no DISTUTILS_SINGLE_IMPL=1 -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils if [[ ${PV} = *9999* ]]; then EGIT_REPO_URI=" @@ -55,7 +55,6 @@ CDEPEND=" mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) ${PYTHON_DEPS} - !sci-chemistry/gmxapi " BDEPEND="${CDEPEND} virtual/pkgconfig @@ -345,9 +344,8 @@ src_install() { pkg_postinst() { einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" + einfo "Please read and cite gromacs related papers from list:" + einfo "https://www.gromacs.org/Gromacs_papers" einfo readme.gentoo_print_elog } diff --git a/sci-chemistry/gromacs/gromacs-2020.6-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.6-r1.ebuild deleted file mode 100644 index 125ab0332663..000000000000 --- a/sci-chemistry/gromacs/gromacs-2020.6-r1.ebuild +++ /dev/null @@ -1,353 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python3_{8,9} ) - -DISTUTILS_USE_SETUPTOOLS=no -DISTUTILS_SINGLE_IMPL=1 - -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ ${PV} = *9999* ]]; then - EGIT_REPO_URI=" - https://gitlab.com/gromacs/gromacs.git - https://github.com/gromacs/gromacs.git - git://git.gromacs.org/gromacs.git" - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" -fi - -ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# 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="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) - opencl? ( virtual/opencl ) - fftw? ( sci-libs/fftw:3.0= ) - hwloc? ( sys-apps/hwloc:= ) - lapack? ( virtual/lapack ) - lmfit? ( sci-libs/lmfit:= ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - ${PYTHON_DEPS} - !sci-chemistry/gmxapi - " -BDEPEND="${CDEPEND} - virtual/pkgconfig - build-manual? ( - app-doc/doxygen - $(python_gen_cond_dep ' - dev-python/sphinx[${PYTHON_USEDEP}] - ') - media-gfx/mscgen - media-gfx/graphviz - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - )" -RDEPEND="${CDEPEND}" - -REQUIRED_USE=" - || ( single-precision double-precision ) - doc? ( !build-manual ) - cuda? ( single-precision ) - cuda? ( !opencl ) - mkl? ( !blas !fftw !lapack ) - ${PYTHON_REQUIRED_USE}" - -DOCS=( AUTHORS README ) - -RESTRICT="!test? ( test )" - -if [[ ${PV} != *9999 ]]; then - S="${WORKDIR}/${PN}-${PV/_/-}" -fi - -PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) - -pkg_pretend() { - [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" - use openmp && ! tc-has-openmp && \ - die "Please switch to an openmp compatible compiler" -} - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_unpack() { - if [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="${EGIT_BRANCH}" \ - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ - git-r3_src_unpack - fi - fi -} - -src_prepare() { - #notes/todos - # -on apple: there is framework support - - xdg_environment_reset #591952 - - cmake_src_prepare - - use cuda && cuda_src_prepare - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - - if use test; then - for x in ${GMX_DIRS}; do - mkdir -p "${WORKDIR}/${P}_${x}" || die - cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die - done - fi - - DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" - if use build-manual; then - # try to create policy for imagemagik - mkdir -p ${HOME}/.config/ImageMagick - cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF - - - !ATTLIST policymap xmlns CDATA #FIXED ''> - - - ]> - - - - - - - - - EOF - fi -} - -src_configure() { - local mycmakeargs_pre=( ) extra fft_opts=( ) - - if use custom-cflags; then - #go from slowest to fastest acceleration - local acce="None" - use cpu_flags_x86_sse2 && acce="SSE2" - use cpu_flags_x86_sse4_1 && acce="SSE4.1" - use cpu_flags_x86_fma4 && acce="AVX_128_FMA" - use cpu_flags_x86_avx && acce="AVX_256" - use cpu_flags_x86_avx2 && acce="AVX2_256" - else - strip-flags - fi - - #to create man pages, build tree binaries are executed (bug #398437) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${MKLROOT}/include" - -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" - ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) - else - fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) - fi - - if use lmfit; then - local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) - else - local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) - fi - - mycmakeargs_pre+=( - "${fft_opts[@]}" - "${lmfit_opts[@]}" - -DGMX_X11=$(usex X) - -DGMX_EXTERNAL_BLAS=$(usex blas) - -DGMX_EXTERNAL_LAPACK=$(usex lapack) - -DGMX_OPENMP=$(usex openmp) - -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex build-manual) - -DGMX_HWLOC=$(usex hwloc) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$acce" - -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" - -DBUILD_TESTING=$(usex test) - -DGMX_BUILD_UNITTESTS=$(usex test) - -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" - ${extra} - ) - - for x in ${GMX_DIRS}; do - einfo "Configuring for ${x} precision" - local suffix="" - #if we build single and double - double is suffixed - use double-precision && use single-precision && \ - [[ ${x} = "double" ]] && suffix="_d" - local p - [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" - local cuda=( "-DGMX_GPU=OFF" ) - [[ ${x} = "float" ]] && use cuda && \ - cuda=( "-DGMX_GPU=ON" ) - local opencl=( "-DGMX_USE_OPENCL=OFF" ) - use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF - -DGMX_THREAD_MPI=$(usex threads) - -DGMXAPI=$(usex gmxapi) - -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) - "${opencl[@]}" - "${cuda[@]}" - "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" - -DGMX_BINARY_SUFFIX="${suffix}" - -DGMX_LIBS_SUFFIX="${suffix}" - -DGMX_PYTHON_PACKAGE=$(usex python) - ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - use mpi || continue - einfo "Configuring for ${x} precision with mpi" - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON - -DGMX_OPENMM=OFF - -DGMXAPI=OFF - "${opencl[@]}" - "${cuda[@]}" - -DGMX_BUILD_MDRUN_ONLY=ON - -DBUILD_SHARED_LIBS=OFF - -DGMX_BUILD_MANUAL=OFF - -DGMX_BINARY_SUFFIX="_mpi${suffix}" - -DGMX_LIBS_SUFFIX="_mpi${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile python_packaging/all - BUILD_DIR="${WORKDIR}/${P}" \ - distutils-r1_src_compile - fi - # not 100% necessary for rel ebuilds as available from website - if use build-manual; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile manual - fi - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake_src_compile - done -} - -src_test() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile check - done -} - -src_install() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install python_packaging/install - fi - if use build-manual; then - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi - - if use doc; then - if [[ ${PV} != *9999* ]]; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" - fi - fi - - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake_src_install - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${ED}"/usr/bin/GMXRC* || die - for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do - local n=${x##*/gmx-completion-} - n="${n%.bash}" - cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"/usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2020.7.ebuild b/sci-chemistry/gromacs/gromacs-2020.7.ebuild new file mode 100644 index 000000000000..b5211f6374ac --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2020.7.ebuild @@ -0,0 +1,351 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python3_{8..10} ) + +DISTUTILS_USE_SETUPTOOLS=no +DISTUTILS_SINGLE_IMPL=1 + +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ ${PV} = *9999* ]]; then + EGIT_REPO_URI=" + https://gitlab.com/gromacs/gromacs.git + https://github.com/gromacs/gromacs.git + git://git.gromacs.org/gromacs.git" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 +else + SRC_URI=" + http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) + test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# 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="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) + opencl? ( virtual/opencl ) + fftw? ( sci-libs/fftw:3.0= ) + hwloc? ( sys-apps/hwloc:= ) + lapack? ( virtual/lapack ) + lmfit? ( sci-libs/lmfit:= ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + ${PYTHON_DEPS} + " +BDEPEND="${CDEPEND} + virtual/pkgconfig + build-manual? ( + app-doc/doxygen + $(python_gen_cond_dep ' + dev-python/sphinx[${PYTHON_USEDEP}] + ') + media-gfx/mscgen + media-gfx/graphviz + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + doc? ( !build-manual ) + cuda? ( single-precision ) + cuda? ( !opencl ) + mkl? ( !blas !fftw !lapack ) + ${PYTHON_REQUIRED_USE}" + +DOCS=( AUTHORS README ) + +RESTRICT="!test? ( test )" + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + cmake_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" + if use build-manual; then + # try to create policy for imagemagik + mkdir -p ${HOME}/.config/ImageMagick + cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + + + !ATTLIST policymap xmlns CDATA #FIXED ''> + + + ]> + + + + + + + + + EOF + fi +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + if use custom-cflags; then + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + else + strip-flags + fi + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + if use lmfit; then + local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) + else + local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + "${lmfit_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex build-manual) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=$(usex test) + -DGMX_BUILD_UNITTESTS=$(usex test) + -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( "-DGMX_GPU=ON" ) + local opencl=( "-DGMX_USE_OPENCL=OFF" ) + use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + -DGMXAPI=$(usex gmxapi) + -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) + "${opencl[@]}" + "${cuda[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + -DGMX_PYTHON_PACKAGE=$(usex python) + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON + -DGMX_OPENMM=OFF + -DGMXAPI=OFF + "${opencl[@]}" + "${cuda[@]}" + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile python_packaging/all + BUILD_DIR="${WORKDIR}/${P}" \ + distutils-r1_src_compile + fi + # not 100% necessary for rel ebuilds as available from website + if use build-manual; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install python_packaging/install + fi + if use build-manual; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + + if use doc; then + if [[ ${PV} != *9999* ]]; then + newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" + fi + fi + + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"/usr/bin/GMXRC* || die + for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"/usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite gromacs related papers from list:" + einfo "https://www.gromacs.org/Gromacs_papers" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-2021.2-r1.ebuild b/sci-chemistry/gromacs/gromacs-2021.2-r1.ebuild deleted file mode 100644 index 5067010bc65f..000000000000 --- a/sci-chemistry/gromacs/gromacs-2021.2-r1.ebuild +++ /dev/null @@ -1,360 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python3_{8,9} ) - -DISTUTILS_USE_SETUPTOOLS=no -DISTUTILS_SINGLE_IMPL=1 - -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ ${PV} = *9999* ]]; then - EGIT_REPO_URI=" - https://gitlab.com/gromacs/gromacs.git - https://github.com/gromacs/gromacs.git - git://git.gromacs.org/gromacs.git" - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" -fi - -ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# 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="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] ) - opencl? ( virtual/opencl ) - fftw? ( sci-libs/fftw:3.0= ) - hwloc? ( sys-apps/hwloc:= ) - lapack? ( virtual/lapack ) - lmfit? ( sci-libs/lmfit:= ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - ${PYTHON_DEPS} - !sci-chemistry/gmxapi - " -BDEPEND="${CDEPEND} - virtual/pkgconfig - build-manual? ( - app-doc/doxygen - $(python_gen_cond_dep ' - dev-python/sphinx[${PYTHON_USEDEP}] - ') - media-gfx/mscgen - media-gfx/graphviz - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - )" -RDEPEND="${CDEPEND}" - -REQUIRED_USE=" - || ( single-precision double-precision ) - doc? ( !build-manual ) - cuda? ( single-precision ) - cuda? ( !opencl ) - mkl? ( !blas !fftw !lapack ) - ${PYTHON_REQUIRED_USE}" - -DOCS=( AUTHORS README ) - -RESTRICT="!test? ( test )" - -if [[ ${PV} != *9999 ]]; then - S="${WORKDIR}/${PN}-${PV/_/-}" -fi - -PATCHES=( - "${FILESDIR}/${PN}-2020-pytest.patch" - "${FILESDIR}/${PN}-2021-nblib.patch" -) - -pkg_pretend() { - [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" - use openmp && ! tc-has-openmp && \ - die "Please switch to an openmp compatible compiler" -} - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_unpack() { - if [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="${EGIT_BRANCH}" \ - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ - git-r3_src_unpack - fi - fi -} - -src_prepare() { - #notes/todos - # -on apple: there is framework support - - xdg_environment_reset #591952 - - cmake_src_prepare - - use cuda && cuda_src_prepare - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - - if use test; then - for x in ${GMX_DIRS}; do - mkdir -p "${WORKDIR}/${P}_${x}" || die - cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die - done - fi - - DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" - if use build-manual; then - # try to create policy for imagemagik - mkdir -p ${HOME}/.config/ImageMagick - cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF - - - !ATTLIST policymap xmlns CDATA #FIXED ''> - - - ]> - - - - - - - - - EOF - fi -} - -src_configure() { - local mycmakeargs_pre=( ) extra fft_opts=( ) - - if use custom-cflags; then - #go from slowest to fastest acceleration - local acce="None" - if (use amd64 || use x86); then - use cpu_flags_x86_sse2 && acce="SSE2" - use cpu_flags_x86_sse4_1 && acce="SSE4.1" - use cpu_flags_x86_fma4 && acce="AVX_128_FMA" - use cpu_flags_x86_avx && acce="AVX_256" - use cpu_flags_x86_avx2 && acce="AVX2_256" - use cpu_flags_x86_avx512f && acce="AVX_512" - elif (use arm); then - use cpu_flags_arm_neon && acce="ARM_NEON" - elif (use arm64); then - use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" - fi - else - strip-flags - fi - - #to create man pages, build tree binaries are executed (bug #398437) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${MKLROOT}/include" - -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" - ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) - else - fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) - fi - - if use lmfit; then - local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) - else - local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) - fi - - mycmakeargs_pre+=( - "${fft_opts[@]}" - "${lmfit_opts[@]}" - -DGMX_X11=$(usex X) - -DGMX_EXTERNAL_BLAS=$(usex blas) - -DGMX_EXTERNAL_LAPACK=$(usex lapack) - -DGMX_OPENMP=$(usex openmp) - -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex build-manual) - -DGMX_HWLOC=$(usex hwloc) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$acce" - -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" - -DBUILD_TESTING=$(usex test) - -DGMX_BUILD_UNITTESTS=$(usex test) - -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" - ${extra} - ) - - for x in ${GMX_DIRS}; do - einfo "Configuring for ${x} precision" - local suffix="" - #if we build single and double - double is suffixed - use double-precision && use single-precision && \ - [[ ${x} = "double" ]] && suffix="_d" - local p - [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" - local gpu=( "-DGMX_GPU=OFF" ) - [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) - use opencl && gpu=( "-DGMX_GPU=OPENCL" ) - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF - -DGMX_THREAD_MPI=$(usex threads) - -DGMXAPI=$(usex gmxapi) - -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) - "${gpu[@]}" - "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" - -DGMX_BINARY_SUFFIX="${suffix}" - -DGMX_LIBS_SUFFIX="${suffix}" - -DGMX_PYTHON_PACKAGE=$(usex python) - ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - use mpi || continue - einfo "Configuring for ${x} precision with mpi" - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON - -DGMX_OPENMM=OFF - -DGMXAPI=OFF - "${opencl[@]}" - "${cuda[@]}" - -DGMX_BUILD_MDRUN_ONLY=ON - -DBUILD_SHARED_LIBS=OFF - -DGMX_BUILD_MANUAL=OFF - -DGMX_BINARY_SUFFIX="_mpi${suffix}" - -DGMX_LIBS_SUFFIX="_mpi${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile python_packaging/all - BUILD_DIR="${WORKDIR}/${P}" \ - distutils-r1_src_compile - fi - # not 100% necessary for rel ebuilds as available from website - if use build-manual; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile manual - fi - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake_src_compile - done -} - -src_test() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile check - done -} - -src_install() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install python_packaging/install - fi - if use build-manual; then - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi - - if use doc; then - if [[ ${PV} != *9999* ]]; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" - fi - fi - - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake_src_install - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${ED}"/usr/bin/GMXRC* || die - for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do - local n=${x##*/gmx-completion-} - n="${n%.bash}" - cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"/usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild b/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild index ade6f56115a9..9ebdeb01146c 100644 --- a/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -10,7 +10,7 @@ PYTHON_COMPAT=( python3_{8,9} ) DISTUTILS_USE_SETUPTOOLS=no DISTUTILS_SINGLE_IMPL=1 -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils if [[ ${PV} = *9999* ]]; then EGIT_REPO_URI=" @@ -24,7 +24,7 @@ else http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="amd64 arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" + KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" @@ -55,7 +55,6 @@ CDEPEND=" mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) ${PYTHON_DEPS} - !sci-chemistry/gmxapi " BDEPEND="${CDEPEND} virtual/pkgconfig @@ -84,6 +83,8 @@ DOCS=( AUTHORS README ) RESTRICT="!test? ( test )" +PATCHES=( "${FILESDIR}/${PN}-2021-musl-stdint.patch" ) + if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi @@ -348,9 +349,8 @@ src_install() { pkg_postinst() { einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" + einfo "Please read and cite gromacs related papers from list:" + einfo "https://www.gromacs.org/Gromacs_papers" einfo readme.gentoo_print_elog } diff --git a/sci-chemistry/gromacs/gromacs-2021.4.ebuild b/sci-chemistry/gromacs/gromacs-2021.4.ebuild deleted file mode 100644 index ab6c1d40dd0b..000000000000 --- a/sci-chemistry/gromacs/gromacs-2021.4.ebuild +++ /dev/null @@ -1,356 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python3_{8,9} ) - -DISTUTILS_USE_SETUPTOOLS=no -DISTUTILS_SINGLE_IMPL=1 - -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ ${PV} = *9999* ]]; then - EGIT_REPO_URI=" - https://gitlab.com/gromacs/gromacs.git - https://github.com/gromacs/gromacs.git - git://git.gromacs.org/gromacs.git" - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" -fi - -ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# 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="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] ) - opencl? ( virtual/opencl ) - fftw? ( sci-libs/fftw:3.0= ) - hwloc? ( sys-apps/hwloc:= ) - lapack? ( virtual/lapack ) - lmfit? ( sci-libs/lmfit:= ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - ${PYTHON_DEPS} - !sci-chemistry/gmxapi - " -BDEPEND="${CDEPEND} - virtual/pkgconfig - build-manual? ( - app-doc/doxygen - $(python_gen_cond_dep ' - dev-python/sphinx[${PYTHON_USEDEP}] - ') - media-gfx/mscgen - media-gfx/graphviz - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - )" -RDEPEND="${CDEPEND}" - -REQUIRED_USE=" - || ( single-precision double-precision ) - doc? ( !build-manual ) - cuda? ( single-precision ) - cuda? ( !opencl ) - mkl? ( !blas !fftw !lapack ) - ${PYTHON_REQUIRED_USE}" - -DOCS=( AUTHORS README ) - -RESTRICT="!test? ( test )" - -if [[ ${PV} != *9999 ]]; then - S="${WORKDIR}/${PN}-${PV/_/-}" -fi - -pkg_pretend() { - [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" - use openmp && ! tc-has-openmp && \ - die "Please switch to an openmp compatible compiler" -} - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_unpack() { - if [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="${EGIT_BRANCH}" \ - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ - git-r3_src_unpack - fi - fi -} - -src_prepare() { - #notes/todos - # -on apple: there is framework support - - xdg_environment_reset #591952 - - cmake_src_prepare - - use cuda && cuda_src_prepare - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - - if use test; then - for x in ${GMX_DIRS}; do - mkdir -p "${WORKDIR}/${P}_${x}" || die - cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die - done - fi - - DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" - if use build-manual; then - # try to create policy for imagemagik - mkdir -p ${HOME}/.config/ImageMagick - cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF - - - !ATTLIST policymap xmlns CDATA #FIXED ''> - - - ]> - - - - - - - - - EOF - fi -} - -src_configure() { - local mycmakeargs_pre=( ) extra fft_opts=( ) - local acce="AUTO" - - if use custom-cflags; then - #go from slowest to fastest acceleration - acce="None" - if (use amd64 || use x86); then - use cpu_flags_x86_sse2 && acce="SSE2" - use cpu_flags_x86_sse4_1 && acce="SSE4.1" - use cpu_flags_x86_fma4 && acce="AVX_128_FMA" - use cpu_flags_x86_avx && acce="AVX_256" - use cpu_flags_x86_avx2 && acce="AVX2_256" - use cpu_flags_x86_avx512f && acce="AVX_512" - elif (use arm); then - use cpu_flags_arm_neon && acce="ARM_NEON" - elif (use arm64); then - use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" - fi - else - strip-flags - fi - - #to create man pages, build tree binaries are executed (bug #398437) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${MKLROOT}/include" - -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" - ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) - else - fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) - fi - - if use lmfit; then - local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) - else - local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) - fi - - mycmakeargs_pre+=( - "${fft_opts[@]}" - "${lmfit_opts[@]}" - -DGMX_X11=$(usex X) - -DGMX_EXTERNAL_BLAS=$(usex blas) - -DGMX_EXTERNAL_LAPACK=$(usex lapack) - -DGMX_OPENMP=$(usex openmp) - -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex build-manual) - -DGMX_HWLOC=$(usex hwloc) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$acce" - -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" - -DBUILD_TESTING=$(usex test) - -DGMX_BUILD_UNITTESTS=$(usex test) - -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" - ${extra} - ) - - for x in ${GMX_DIRS}; do - einfo "Configuring for ${x} precision" - local suffix="" - #if we build single and double - double is suffixed - use double-precision && use single-precision && \ - [[ ${x} = "double" ]] && suffix="_d" - local p - [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" - local gpu=( "-DGMX_GPU=OFF" ) - [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) - use opencl && gpu=( "-DGMX_GPU=OPENCL" ) - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF - -DGMX_THREAD_MPI=$(usex threads) - -DGMXAPI=$(usex gmxapi) - -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) - "${gpu[@]}" - "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" - -DGMX_BINARY_SUFFIX="${suffix}" - -DGMX_LIBS_SUFFIX="${suffix}" - -DGMX_PYTHON_PACKAGE=$(usex python) - ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - use mpi || continue - einfo "Configuring for ${x} precision with mpi" - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON - -DGMX_OPENMM=OFF - -DGMXAPI=OFF - "${opencl[@]}" - "${cuda[@]}" - -DGMX_BUILD_MDRUN_ONLY=ON - -DBUILD_SHARED_LIBS=OFF - -DGMX_BUILD_MANUAL=OFF - -DGMX_BINARY_SUFFIX="_mpi${suffix}" - -DGMX_LIBS_SUFFIX="_mpi${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile python_packaging/all - BUILD_DIR="${WORKDIR}/${P}" \ - distutils-r1_src_compile - fi - # not 100% necessary for rel ebuilds as available from website - if use build-manual; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile manual - fi - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake_src_compile - done -} - -src_test() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile check - done -} - -src_install() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install python_packaging/install - fi - if use build-manual; then - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi - - if use doc; then - if [[ ${PV} != *9999* ]]; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" - fi - fi - - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake_src_install - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${ED}"/usr/bin/GMXRC* || die - for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do - local n=${x##*/gmx-completion-} - n="${n%.bash}" - cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"/usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2021.5.ebuild b/sci-chemistry/gromacs/gromacs-2021.5.ebuild index c40fa7838c07..abf5ed8ec5ef 100644 --- a/sci-chemistry/gromacs/gromacs-2021.5.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.5.ebuild @@ -55,7 +55,6 @@ CDEPEND=" mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) ${PYTHON_DEPS} - !sci-chemistry/gmxapi " BDEPEND="${CDEPEND} virtual/pkgconfig @@ -84,6 +83,8 @@ DOCS=( AUTHORS README ) RESTRICT="!test? ( test )" +PATCHES=( "${FILESDIR}/${PN}-2021-musl-stdint.patch" ) + if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi @@ -348,9 +349,8 @@ src_install() { pkg_postinst() { einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" + einfo "Please read and cite gromacs related papers from list:" + einfo "https://www.gromacs.org/Gromacs_papers" einfo readme.gentoo_print_elog } diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild index c135dc43d747..d9c7e8a5269e 100644 --- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild @@ -1,16 +1,16 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 CMAKE_MAKEFILE_GENERATOR="ninja" -PYTHON_COMPAT=( python3_{8,9} ) +PYTHON_COMPAT=( python3_{8..10} ) DISTUTILS_USE_SETUPTOOLS=no DISTUTILS_SINGLE_IMPL=1 -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils if [[ ${PV} = *9999* ]]; then EGIT_REPO_URI=" @@ -55,7 +55,6 @@ CDEPEND=" mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) ${PYTHON_DEPS} - !sci-chemistry/gmxapi " BDEPEND="${CDEPEND} virtual/pkgconfig @@ -348,9 +347,8 @@ src_install() { pkg_postinst() { einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" + einfo "Please read and cite gromacs related papers from list:" + einfo "https://www.gromacs.org/Gromacs_papers" einfo readme.gentoo_print_elog } diff --git a/sci-chemistry/gromacs/gromacs-2022.9999.ebuild b/sci-chemistry/gromacs/gromacs-2022.9999.ebuild index 8b7107ecad96..655c647a73dd 100644 --- a/sci-chemistry/gromacs/gromacs-2022.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2022.9999.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 CMAKE_MAKEFILE_GENERATOR="ninja" -PYTHON_COMPAT=( python3_{8,9,10} ) +PYTHON_COMPAT=( python3_{8..10} ) DISTUTILS_USE_SETUPTOOLS=no DISTUTILS_SINGLE_IMPL=1 @@ -41,7 +41,7 @@ IUSE="blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi CDEPEND=" blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-11[profiler] ) opencl? ( virtual/opencl ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) @@ -51,7 +51,6 @@ CDEPEND=" sci-libs/lmfit:= >=dev-cpp/muParser-2.3:= ${PYTHON_DEPS} - !sci-chemistry/gmxapi " BDEPEND="${CDEPEND} virtual/pkgconfig @@ -235,7 +234,7 @@ src_configure() { use opencl && gpu=( "-DGMX_GPU=OPENCL" ) mycmakeargs=( ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF + -DGMX_MPI=$(usex mpi) -DGMX_THREAD_MPI=$(usex threads) -DGMXAPI=$(usex gmxapi) -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) @@ -248,25 +247,6 @@ src_configure() { BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure [[ ${CHOST} != *-darwin* ]] || \ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - use mpi || continue - einfo "Configuring for ${x} precision with mpi" - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON - -DGMX_OPENMM=OFF - -DGMXAPI=OFF - "${opencl[@]}" - "${cuda[@]}" - -DGMX_BUILD_MDRUN_ONLY=ON - -DBUILD_SHARED_LIBS=OFF - -DGMX_BUILD_MANUAL=OFF - -DGMX_BINARY_SUFFIX="_mpi${suffix}" - -DGMX_LIBS_SUFFIX="_mpi${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die done } @@ -286,10 +266,6 @@ src_compile() { BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake_src_compile manual fi - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake_src_compile done } @@ -317,10 +293,6 @@ src_install() { newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" fi fi - - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake_src_install done if use tng; then @@ -341,9 +313,8 @@ src_install() { pkg_postinst() { einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" + einfo "Please read and cite gromacs related papers from list:" + einfo "https://www.gromacs.org/Gromacs_papers" einfo readme.gentoo_print_elog } diff --git a/sci-chemistry/gromacs/gromacs-2022.ebuild b/sci-chemistry/gromacs/gromacs-2022.ebuild new file mode 100644 index 000000000000..338c03cc2a11 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2022.ebuild @@ -0,0 +1,336 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python3_{8..10} ) + +DISTUTILS_USE_SETUPTOOLS=no +DISTUTILS_SINGLE_IMPL=1 + +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ ${PV} = *9999* ]]; then + EGIT_REPO_URI=" + https://gitlab.com/gromacs/gromacs.git + https://github.com/gromacs/gromacs.git + git://git.gromacs.org/gromacs.git" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 +else + SRC_URI=" + http://ftp.gromacs.org/gromacs/${P}.tar.gz + doc? ( https://ftp.gromacs.org/manual/manual-${PV}.pdf ) + test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV}.tar.gz )" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-11[profiler] ) + opencl? ( virtual/opencl ) + fftw? ( sci-libs/fftw:3.0= ) + hwloc? ( sys-apps/hwloc:= ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi[cxx] ) + sci-libs/lmfit:= + >=dev-cpp/muParser-2.3:= + ${PYTHON_DEPS} + " +BDEPEND="${CDEPEND} + virtual/pkgconfig + clang? ( >=sys-devel/clang-6:* ) + build-manual? ( + app-doc/doxygen + $(python_gen_cond_dep ' + dev-python/sphinx[${PYTHON_USEDEP}] + ') + media-gfx/mscgen + media-gfx/graphviz + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND} + > ${HOME}/.config/ImageMagick/policy.xml <<- EOF + + + !ATTLIST policymap xmlns CDATA #FIXED ''> + + + ]> + + + + + + + + + EOF + fi +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + local acce="AUTO" + + if use custom-cflags; then + #go from slowest to fastest acceleration + acce="None" + if (use amd64 || use x86); then + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + use cpu_flags_x86_avx512f && acce="AVX_512" + elif (use arm); then + use cpu_flags_arm_neon && acce="ARM_NEON" + elif (use arm64); then + use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" + fi + else + strip-flags + fi + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + "${lmfit_opts[@]}" + -DGMX_USE_LMFIT=EXTERNAL + -DGMX_USE_MUPARSER=EXTERNAL + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex build-manual) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DGMX_DSSP_PROGRAM_PATH="${EPREFIX}/usr/bin/dssp" + -DBUILD_TESTING=$(usex test) + -DGMX_BUILD_UNITTESTS=$(usex test) + -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local gpu=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) + [[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" ) + use opencl && gpu=( "-DGMX_GPU=OPENCL" ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=$(usex mpi) + -DGMX_THREAD_MPI=$(usex threads) + -DGMXAPI=$(usex gmxapi) + -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) + "${gpu[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + -DGMX_PYTHON_PACKAGE=$(usex python) + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile python_packaging/all + BUILD_DIR="${WORKDIR}/${P}" \ + distutils-r1_src_compile + fi + # not 100% necessary for rel ebuilds as available from website + if use build-manual; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile manual + fi + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install python_packaging/install + fi + if use build-manual; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + + if use doc; then + if [[ ${PV} != *9999* ]]; then + newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" + fi + fi + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"/usr/bin/GMXRC* || die + for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"/usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite gromacs related papers from list:" + einfo "https://www.gromacs.org/Gromacs_papers" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-2022_rc1.ebuild b/sci-chemistry/gromacs/gromacs-2022_rc1.ebuild deleted file mode 100644 index 4077cbb9e4d1..000000000000 --- a/sci-chemistry/gromacs/gromacs-2022_rc1.ebuild +++ /dev/null @@ -1,349 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python3_{8..10} ) - -DISTUTILS_USE_SETUPTOOLS=no -DISTUTILS_SINGLE_IMPL=1 - -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ ${PV} = *9999* ]]; then - EGIT_REPO_URI=" - https://gitlab.com/gromacs/gromacs.git - https://github.com/gromacs/gromacs.git - git://git.gromacs.org/gromacs.git" - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf -> manual-${PV}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -fi - -ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib -LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" -SLOT="0/${PV}" -IUSE="blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] ) - opencl? ( virtual/opencl ) - fftw? ( sci-libs/fftw:3.0= ) - hwloc? ( sys-apps/hwloc:= ) - lapack? ( virtual/lapack ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi[cxx] ) - sci-libs/lmfit:= - >=dev-cpp/muParser-2.3:= - ${PYTHON_DEPS} - !sci-chemistry/gmxapi - " -BDEPEND="${CDEPEND} - virtual/pkgconfig - build-manual? ( - app-doc/doxygen - $(python_gen_cond_dep ' - dev-python/sphinx[${PYTHON_USEDEP}] - ') - media-gfx/mscgen - media-gfx/graphviz - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - )" -RDEPEND="${CDEPEND} - > ${HOME}/.config/ImageMagick/policy.xml <<- EOF - - - !ATTLIST policymap xmlns CDATA #FIXED ''> - - - ]> - - - - - - - - - EOF - fi -} - -src_configure() { - local mycmakeargs_pre=( ) extra fft_opts=( ) - local acce="AUTO" - - if use custom-cflags; then - #go from slowest to fastest acceleration - acce="None" - if (use amd64 || use x86); then - use cpu_flags_x86_sse2 && acce="SSE2" - use cpu_flags_x86_sse4_1 && acce="SSE4.1" - use cpu_flags_x86_fma4 && acce="AVX_128_FMA" - use cpu_flags_x86_avx && acce="AVX_256" - use cpu_flags_x86_avx2 && acce="AVX2_256" - use cpu_flags_x86_avx512f && acce="AVX_512" - elif (use arm); then - use cpu_flags_arm_neon && acce="ARM_NEON" - elif (use arm64); then - use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" - fi - else - strip-flags - fi - - #to create man pages, build tree binaries are executed (bug #398437) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${MKLROOT}/include" - -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" - ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) - else - fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) - fi - - mycmakeargs_pre+=( - "${fft_opts[@]}" - "${lmfit_opts[@]}" - -DGMX_USE_LMFIT=EXTERNAL - -DGMX_USE_MUPARSER=EXTERNAL - -DGMX_EXTERNAL_BLAS=$(usex blas) - -DGMX_EXTERNAL_LAPACK=$(usex lapack) - -DGMX_OPENMP=$(usex openmp) - -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex build-manual) - -DGMX_HWLOC=$(usex hwloc) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$acce" - -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" - -DGMX_DSSP_PROGRAM_PATH="${EPREFIX}/usr/bin/dssp" - -DBUILD_TESTING=$(usex test) - -DGMX_BUILD_UNITTESTS=$(usex test) - -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" - ${extra} - ) - - for x in ${GMX_DIRS}; do - einfo "Configuring for ${x} precision" - local suffix="" - #if we build single and double - double is suffixed - use double-precision && use single-precision && \ - [[ ${x} = "double" ]] && suffix="_d" - local p - [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" - local gpu=( "-DGMX_GPU=OFF" ) - [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) - use opencl && gpu=( "-DGMX_GPU=OPENCL" ) - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF - -DGMX_THREAD_MPI=$(usex threads) - -DGMXAPI=$(usex gmxapi) - -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) - "${gpu[@]}" - "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" - -DGMX_BINARY_SUFFIX="${suffix}" - -DGMX_LIBS_SUFFIX="${suffix}" - -DGMX_PYTHON_PACKAGE=$(usex python) - ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - use mpi || continue - einfo "Configuring for ${x} precision with mpi" - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON - -DGMX_OPENMM=OFF - -DGMXAPI=OFF - "${opencl[@]}" - "${cuda[@]}" - -DGMX_BUILD_MDRUN_ONLY=ON - -DBUILD_SHARED_LIBS=OFF - -DGMX_BUILD_MANUAL=OFF - -DGMX_BINARY_SUFFIX="_mpi${suffix}" - -DGMX_LIBS_SUFFIX="_mpi${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile python_packaging/all - BUILD_DIR="${WORKDIR}/${P}" \ - distutils-r1_src_compile - fi - # not 100% necessary for rel ebuilds as available from website - if use build-manual; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile manual - fi - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake_src_compile - done -} - -src_test() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile check - done -} - -src_install() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install python_packaging/install - fi - if use build-manual; then - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi - - if use doc; then - if [[ ${PV} != *9999* ]]; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" - fi - fi - - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake_src_install - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${ED}"/usr/bin/GMXRC* || die - for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do - local n=${x##*/gmx-completion-} - n="${n%.bash}" - cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"/usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 8b7107ecad96..655c647a73dd 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 CMAKE_MAKEFILE_GENERATOR="ninja" -PYTHON_COMPAT=( python3_{8,9,10} ) +PYTHON_COMPAT=( python3_{8..10} ) DISTUTILS_USE_SETUPTOOLS=no DISTUTILS_SINGLE_IMPL=1 @@ -41,7 +41,7 @@ IUSE="blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi CDEPEND=" blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-11[profiler] ) opencl? ( virtual/opencl ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) @@ -51,7 +51,6 @@ CDEPEND=" sci-libs/lmfit:= >=dev-cpp/muParser-2.3:= ${PYTHON_DEPS} - !sci-chemistry/gmxapi " BDEPEND="${CDEPEND} virtual/pkgconfig @@ -235,7 +234,7 @@ src_configure() { use opencl && gpu=( "-DGMX_GPU=OPENCL" ) mycmakeargs=( ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF + -DGMX_MPI=$(usex mpi) -DGMX_THREAD_MPI=$(usex threads) -DGMXAPI=$(usex gmxapi) -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) @@ -248,25 +247,6 @@ src_configure() { BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure [[ ${CHOST} != *-darwin* ]] || \ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - use mpi || continue - einfo "Configuring for ${x} precision with mpi" - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON - -DGMX_OPENMM=OFF - -DGMXAPI=OFF - "${opencl[@]}" - "${cuda[@]}" - -DGMX_BUILD_MDRUN_ONLY=ON - -DBUILD_SHARED_LIBS=OFF - -DGMX_BUILD_MANUAL=OFF - -DGMX_BINARY_SUFFIX="_mpi${suffix}" - -DGMX_LIBS_SUFFIX="_mpi${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die done } @@ -286,10 +266,6 @@ src_compile() { BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake_src_compile manual fi - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake_src_compile done } @@ -317,10 +293,6 @@ src_install() { newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" fi fi - - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake_src_install done if use tng; then @@ -341,9 +313,8 @@ src_install() { pkg_postinst() { einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" + einfo "Please read and cite gromacs related papers from list:" + einfo "https://www.gromacs.org/Gromacs_papers" einfo readme.gentoo_print_elog } diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index 0b64bbe8abdd..44ddb19d1d9d 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -11,6 +11,8 @@ Build manual instead of downloading it + Build gromacs with Clang instead of default compiler + Use clang for cuda units compilation Enable cuda non-bonded kernels More precise calculations at the expense of speed Add support for gmxapi library diff --git a/sci-chemistry/molden/Manifest b/sci-chemistry/molden/Manifest index 7ca2db01b867..68c6ed0731c0 100644 --- a/sci-chemistry/molden/Manifest +++ b/sci-chemistry/molden/Manifest @@ -3,6 +3,9 @@ AUX molden-4.8-ldflags.patch 866 BLAKE2B ba4e859d0706e17e926b3f55ed03bac5d50dcb0 AUX molden-5.0-ambfor.patch 523 BLAKE2B 1443a26ff5fbaab3092a6df6a5ab0d514547d59788030ea1c761b8867cf042ff53f6382b85c7aa5383a85504c99e625e9e9c13cd96e1c52a2e05347286be474a SHA512 f531d3bd50374bf658e710f2e4b649559503b378ab663f03cd9259b9105b6c25eab61318bb3d02814425ecb596802569aa3281741d611d4e1c8fc4da771fd481 AUX molden-5.0-overflow.patch 341 BLAKE2B c7285c87c0741ecf6bce3bad89883ed6e7720cb72a479c9bea7ad8a1dabcc1ae8894f6811e2d537555a00cb9138a7b579dee631221efb3a721b77b446abcb82d SHA512 342b7531179b8a3c3aedff085022d972bd795d2c56ebf4b49fce5ff60e6cc9ea48ed18258af53042ad72aae400f694aec9692bc0b1abfa960bc100ee02f57981 AUX molden-5.5-gcc8.patch 328 BLAKE2B e098e680a5b75ff09fbaecf44609055584b0f1c49edc0ea16b81dbff68b06883dc6317340b3dc6b26836958d1f561b3aed383964f7c65126079f74b3023f96dd SHA512 cc1a8c08b9081ff138aedda11887295f0eb31b97174ce45bffae8e563318388035948775f03d39823280103ea522a20939b6294e3d3721e599e6790e4a5695e2 +AUX molden-6.9-ldflags.patch 3244 BLAKE2B d5ddd71bade94310d9aaebb71c49dd138af46abbf65069920cfdc3b204cdb7fe21ce049bed90faeaf23da3ec5b9a1121bcab97d012e9ff8af9abdf5619953299 SHA512 2a8235c1bd07aff5ce9fb79d5a6b09353c63bb9fc157d7fe1ada397e567018f3052286a93a04df13573f2e561a6c1e302ee91822338c024e70654ce7dec488bd DIST molden5.5.tar.gz 4934764 BLAKE2B 6ce71f928ed9aacf8fe9830c4c36a675f81d63e97d08e96519ff74d172540ae0a9af25ca966d6c02cdcbbc43633a0ef80be9d31ef98a80d59a8e1a13374c2f51 SHA512 45269d2c7a52b3b2bf4fdb5f4ca3912637b3414ff9dfcd0d4f23815b3dcf7a53ffee717420d4fbf286b71c972539e756a440f5e37b7b7325ab312c25fc6c47b0 +DIST molden6.9.tar.gz 8536291 BLAKE2B f50fd9c6303d215f3b1ea73136a8ecada07102a33cfc5831c412341731d00bd166f59bc260615d4a96c59d50a6a308087f02b637f8a8d36bf19f256ac407ba72 SHA512 dbb4a602f2957d0b1d5afb8748fb8ad012a41fb0dfa816b78e4d2748ea78ee39251846a549fce4b276641d4838a336ecd9cf02b92fcf9739adeb25bb550656ec EBUILD molden-5.5.ebuild 1735 BLAKE2B bc176723397f3d0f6f6fe35247c065f333e718be7eaa3ed04487bc9138dca53d6c01653fb99dee79f3098a2aeff5b41427171aa75bc4dc534175fb8e59a3934a SHA512 d4c537301b603b410fbb9637bf97a2f912765545e497bb850335a8d1013d71b394ff12a25bfce5a4293b830f46beaa75597df51ad06bcadb8ea63bf6b57ba6f1 +EBUILD molden-6.9.ebuild 1675 BLAKE2B 49fa0a45fc3c33b7e10d5cfec661186f2e556e8849036710b4d85be0f32e4dbebac405ae6c4cb6ac21b23d7fbcb88a02f130ba6c9820ff9739afc0d8b183d20b SHA512 cfdfb33cae8c1deb203b13f0d9ab2b2e639e46004faf0a1725073913b158e77cdc846eb6c2317e4cb42a57d3375a8d64b962d3b25de6ecd4649083843ebbae31 MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c diff --git a/sci-chemistry/molden/files/molden-6.9-ldflags.patch b/sci-chemistry/molden/files/molden-6.9-ldflags.patch new file mode 100644 index 000000000000..9e8258aeacd7 --- /dev/null +++ b/sci-chemistry/molden/files/molden-6.9-ldflags.patch @@ -0,0 +1,87 @@ +diff --git a/makefile b/makefile +index f71a20df..564f9f4e 100644 +--- a/makefile ++++ b/makefile +@@ -299,11 +299,11 @@ src/xwin.o: src/xwin.c src/rots.h + src/xwingl.o: src/xwin.c src/rots.h + + molden: $(OBJS) src/mpdum.o src/xwin.o +- $(LDR) -o molden $(OBJS) src/mpdum.o src/xwin.o $(LIBS) ++ $(LDR) $(LDFLAGS) -o molden $(OBJS) src/mpdum.o src/xwin.o $(LIBS) + mv molden bin/molden + + gmolden: $(OBJS) src/mpdum.o src/xwingl.o +- $(LDR) -fno-builtin -o gmolden $(OBJS) src/mpdum.o src/xwingl.o $(LIBSG) ++ $(LDR) $(LDFLAGS) -fno-builtin -o gmolden $(OBJS) src/mpdum.o src/xwingl.o $(LIBSG) + mv gmolden bin/gmolden + + ambfor/ambfor: src/ambfor/*.f src/ambfor/*.c +@@ -322,14 +322,14 @@ surf/surf: src/surf/*.h src/surf/*.c + # noxwin will not work as long as the old ocglbck calls arent in dummys + + noxwin: $(OBJS) $(DOBJ) src/mpdum.o +- $(LDR) -o molden $(OBJS) $(DOBJ) src/mpdum.o -lm ++ $(LDR) $(LDFLAGS) -o molden $(OBJS) $(DOBJ) src/mpdum.o -lm + mv molden bin/molden.noxwin + + # This version allows the fitting of multipole moments to the electrostatic + # pontential + + molden.mpfit: $(OBJS) src/mpolefit.o src/xwinmp.o +- $(LDR) -o molden $(OBJS) src/mpolefit.o src/xwinmp.o $(LIBS) ++ $(LDR) $(LDFLAGS) -o molden $(OBJS) src/mpolefit.o src/xwinmp.o $(LIBS) + mv molden bin/molden.mpfit + + src/xwinmp.o: src/xwin.c +@@ -340,18 +340,18 @@ src/xwingl.o: src/xwin.c + $(CC) $(CFLAGS) -DDOGL -c src/xwin.c -o src/xwingl.o + + unmullik: src/unmullik.o +- $(LDR) -o bin/unmullik src/unmullik.o ++ $(LDR) $(LDFLAGS) -o bin/unmullik src/unmullik.o + + # short_wrl removes redundant vertices from molden's VRML2 files + # with the courtesy of Andreas Klamt of COSMOSlogic + # + short_wrl: src/short_wrl.o +- $(LDR) -o bin/short_wrl src/short_wrl.o ++ $(LDR) $(LDFLAGS) -o bin/short_wrl src/short_wrl.o + + # conversion of CADPAC output to molden format + + cad2mol: src/cad2mol.o +- $(LDR) -o bin/cad2mol src/cad2mol.o ++ $(LDR) $(LDFLAGS) -o bin/cad2mol src/cad2mol.o + + clean: + rm -f src/$(OBJS) src/mpdum.o src/xwin.o src/xwingl.o bin/molden bin/gmolden bin/ambfor bin/ambmd bin/surf src/ambfor/*.o src/surf/*.o +diff --git a/src/ambfor/makefile b/src/ambfor/makefile +index 9938527e..5de7c65e 100644 +--- a/src/ambfor/makefile ++++ b/src/ambfor/makefile +@@ -50,10 +50,10 @@ mpi: FFLAGS = -c -g -ffast-math -funroll-loops -O3 + mpi: ambfor.mpi ambmd.mpi + + ambfor: ambfor.o qvdw.o alloc.o optimise.o lbfgs.o $(OBJS) +- $(LDR) -o ambfor ambfor.o qvdw.o alloc.o optimise.o lbfgs.o $(OBJS) $(LIBS) ++ $(LDR) $(LDFLAGS) -o ambfor ambfor.o qvdw.o alloc.o optimise.o lbfgs.o $(OBJS) $(LIBS) + + ambmd: md.o verlet.o qvdw.o allocmd.o $(OBJS) +- $(LDR) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS) ++ $(LDR) $(LDFLAGS) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS) + + ambfor.o: ambfor.f + ${FC} -c -g -ffast-math -funroll-loops -o ambfor.o ambfor.f +diff --git a/src/surf/Makefile b/src/surf/Makefile +index 54b7af8e..f216c9eb 100644 +--- a/src/surf/Makefile ++++ b/src/surf/Makefile +@@ -25,7 +25,7 @@ OBJS = surf.o io.o compute.o dual.o utils.o lp.o chull.o tessel_cases.o \ + + # make objects + surf: $(OBJS) Makefile +- $(CC) $(CFLAGS) $(OBJS) -o surf $(LINCLUDE) ++ $(CC) $(CFLAGS) $(OBJS) -o surf $(LINCLUDE) $(LDFLAGS) + + lint: + lint $(INCLUDE) $(SRCS) diff --git a/sci-chemistry/molden/molden-6.9.ebuild b/sci-chemistry/molden/molden-6.9.ebuild new file mode 100644 index 000000000000..df6e76dbfe75 --- /dev/null +++ b/sci-chemistry/molden/molden-6.9.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit desktop fortran-2 flag-o-matic toolchain-funcs + +MY_P="${PN}${PV}" + +DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac" +HOMEPAGE="https://www.theochem.ru.nl/molden/" +SRC_URI="ftp://ftp.science.ru.nl/pub/Molden/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="MOLDEN" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="opengl" + +RDEPEND=" + x11-libs/libXmu + opengl? ( + media-libs/freeglut + virtual/opengl + virtual/glu + ) +" +DEPEND="${RDEPEND} + x11-misc/gccmakedep + app-editors/vim" + # vim provides ex, which the build system uses (surf/Makefile, at least) + +PATCHES=( + "${FILESDIR}/${P}-ldflags.patch" +) + +src_prepare() { + default + sed \ + -e 's:makedepend:gccmakedep:g' \ + -i src/surf/Makefile || die + sed 's:shell g77:shell $(FC):g' -i makefile || die +} + +src_compile() { + local args=() + + # Use -mieee on alpha, according to the Makefile + use alpha && append-flags -mieee + + # GCC 10 workaround + # bug #724556 + append-fflags $(test-flags-FC -fallow-argument-mismatch) + + args=( + CC="$(tc-getCC) ${CFLAGS}" + FC="$(tc-getFC)" + LDR="$(tc-getFC)" + FFLAGS="${FFLAGS}" + ) + + einfo "Building Molden..." + emake -j1 molden ambfor/ambfor ambfor/ambmd surf/surf "${args[@]}" + if use opengl ; then + einfo "Building Molden OpenGL helper..." + emake -j1 "${args[@]}" gmolden + fi +} + +src_install() { + dobin bin/molden bin/ambfor bin/ambmd bin/surf + if use opengl; then + dobin bin/gmolden + doicon -s 64 haux/gmolden.png + make_desktop_entry gmolden MOLDEN gmolden + fi + + dodoc HISTORY README REGISTER + cd doc || die + uncompress * && dodoc * +} diff --git a/sci-chemistry/molscript/Manifest b/sci-chemistry/molscript/Manifest deleted file mode 100644 index 38fb983d7b3e..000000000000 --- a/sci-chemistry/molscript/Manifest +++ /dev/null @@ -1,8 +0,0 @@ -AUX 2.1.2-ldflags.patch 818 BLAKE2B f36003fd8ac6a9c921dba8cac94612f1a7226361d4e3acb9903fd940d2e92729f4b9ed6d82890135185362f0ce2d417f1b836a11fed764d3db12709081e1bf77 SHA512 0e14bbf2869357e19360a977941995f8610cf2c5c4fe272a30480725350705f4d8dfa83541b1eca441c78079ca926a6449d488854d3b6b7ee1c84e644d6c023a -AUX 2.1.2-libpng15.patch 536 BLAKE2B 80cc7e5b6a82c6460d666e2f9dd3e7682ac00377fac15281888890aa1d79d98429a9a77b5bd57c033186fd368593cd3fca88dbfe32b6e9fb01e97bdff8c00287 SHA512 29f929401478beb652e04ca2b043b8dd10497251c7fd7d6668479269f06791f1419db37f0535c173ec6e29cbeb44da26d68b3413593517641d6fe9ae63090f72 -AUX 2.1.2-prll.patch 409 BLAKE2B 83eefcd062c9904a06a69ccafa9da14578f102af96ad1b3b61340223c78a2d744ebc5325db43a9181a9d81a3f3271fd97d45f1b2f48d716e69f5055dda1a2e1c SHA512 16b8566212cf06454a466678db61c2377c6080e8c72cd6e841b104f70f105fefa5d128ef96cb679f583a413d1d285a8f369dd2e757be347883d7e3e99bf88606 -AUX fix-makefile-shared.patch 2051 BLAKE2B 145edf9dc11ee0f59325fcc3e2f981de03aeaa582bea06ca80406cc88ce38971590b687aa9dd40b37fb8edd07c9b30a0f81aa20ab38dcdb02378a407ba068878 SHA512 0c12bd5aea0a6175b7647ed61ae139113329058c42cfb56105ee35af35bdab9f61adfe635a1c3322dbff00ddfcee06383bbd6bd048cc7ded1961f3997a527358 -AUX glutbitmap.h 845 BLAKE2B e5c5a6fed84021a35e132301c06efa9b877fc475a1230a58c93e9e24fb0b220cea1bcb68d411ed17897877dd3b9c4e3d6a1646906b0f09819449e6321e8f108a SHA512 a11e8c23472ed8950c8b56fdfd57ddd9c6539f427437ab26a2d3561ad388ca24a36029dee9ff6b8af759eeadf89fbd45dd10279d8089e6978eec07858624c7da -DIST molscript-2.1.2.tar.gz 412497 BLAKE2B ca28cf90cfbd1314351abd0c32e4a4012f2f6f178537e12918942f3c5e21e6875d045d46d76e645b4e9982d6d0784029b3d26eb17bb65aa486ecbea70842d9b4 SHA512 0f82936da3123770c0fdb703094dbb5289cc39e9f9ffd034d8dba563f8d615788f67040d38158ac2f203b480c5838a7d8e71ca07bc5098181c1e3cfea26703a4 -EBUILD molscript-2.1.2-r2.ebuild 1402 BLAKE2B 01e6bf7bf6b448ebb98c1ff3aa6d7efd58394c21d8091ec8f9696d618d8922d339b48df9f3969bf7b5d8026add28971d66a1442d958962957d67e16dd9f4012f SHA512 665a24745db7cfba2ed95bcc272430105a50ead3c4711cf3595f7b1f66bdcc08db51c7fb7ebdd54c6fb73ed223a75a613475d930a23b8bd5c3dc5dc95a657358 -MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c diff --git a/sci-chemistry/molscript/files/2.1.2-ldflags.patch b/sci-chemistry/molscript/files/2.1.2-ldflags.patch deleted file mode 100644 index 8867bc10a6b5..000000000000 --- a/sci-chemistry/molscript/files/2.1.2-ldflags.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff --git a/Makefile.complete b/Makefile.complete -index 4ad535a..b565266 100644 ---- a/Makefile.complete -+++ b/Makefile.complete -@@ -91,7 +91,7 @@ clean: - - #------------------------------------------------------------ - molscript: $(OBJ) clib/clib.a -- $(CC) -o molscript $(COPT) $(OBJ) $(YLIB) clib/clib.a \ -+ $(CC) $(LDFLAGS) -o molscript $(COPT) $(OBJ) $(YLIB) clib/clib.a \ - $(GLUTLINK) $(JPEGLINK) $(PNGLINK) $(GIFLINK) $(ZLIBLINK) -lm - - molscript.tab.o: molscript.tab.c molscript.tab.h -@@ -147,7 +147,7 @@ gif_img.o: gif_img.c gif_img.h global.h graphics.h image.h opengl.h - - #------------------------------------------------------------ - molauto: molauto.o clib/clib.a -- $(CC) -o molauto molauto.o clib/clib.a -lm -+ $(CC) $(LDFLAGS) -o molauto molauto.o clib/clib.a -lm - - molauto.o: molauto.c - diff --git a/sci-chemistry/molscript/files/2.1.2-libpng15.patch b/sci-chemistry/molscript/files/2.1.2-libpng15.patch deleted file mode 100644 index 9ed1b85909e8..000000000000 --- a/sci-chemistry/molscript/files/2.1.2-libpng15.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- png_img.c -+++ png_img.c -@@ -18,6 +18,7 @@ - - #include - -+#include - #include - - #include "clib/str_utils.h" -@@ -69,7 +70,7 @@ - info_ptr = png_create_info_struct (png_ptr); - if (info_ptr == NULL) - yyerror ("png_img: could not create PNG info structure"); -- if (setjmp (png_ptr->jmpbuf)) yyerror ("png_img: could not setjmp"); -+ if (setjmp (png_jmpbuf(png_ptr))) yyerror ("png_img: could not setjmp"); - - png_init_io (png_ptr, outfile); - png_set_compression_level (png_ptr, compression_level); diff --git a/sci-chemistry/molscript/files/2.1.2-prll.patch b/sci-chemistry/molscript/files/2.1.2-prll.patch deleted file mode 100644 index e4c972a10533..000000000000 --- a/sci-chemistry/molscript/files/2.1.2-prll.patch +++ /dev/null @@ -1,10 +0,0 @@ -diff --git a/Makefile.complete b/Makefile.complete -index 92ef20a..e3f68e3 100644 ---- a/Makefile.complete -+++ b/Makefile.complete -@@ -153,4 +153,4 @@ molauto.o: molauto.c - - #------------------------------------------------------------ - clib/clib.a: -- cd clib; make clib.a CFLAGS="-I. $(CFLAGS)" OPENGLCLIBOBJ="$(OPENGLCLIBOBJ)" -+ $(MAKE) -C clib clib.a CFLAGS="-I. $(CFLAGS)" OPENGLCLIBOBJ="$(OPENGLCLIBOBJ)" diff --git a/sci-chemistry/molscript/files/fix-makefile-shared.patch b/sci-chemistry/molscript/files/fix-makefile-shared.patch deleted file mode 100644 index a9947a61a665..000000000000 --- a/sci-chemistry/molscript/files/fix-makefile-shared.patch +++ /dev/null @@ -1,62 +0,0 @@ -diff -urN molscript-2.1.2.orig/Makefile.complete molscript-2.1.2/Makefile.complete ---- molscript-2.1.2.orig/Makefile.complete 1998-11-25 01:04:39.000000000 -0800 -+++ molscript-2.1.2/Makefile.complete 2005-11-21 12:28:06.000000000 -0800 -@@ -23,9 +23,9 @@ - - # OpenGL and GLUT for X (UNIX). - # Must be modified for Windows 95/NT. <--- --GLUTDIR = $(FREEWAREDIR)/glut --GLUTLINK = $(GLUTDIR)/lib/glut/libglut.a -lGLU -lGL -lXmu -lXext -lX11 --OPENGLFLAG = -DOPENGL_SUPPORT -I$(GLUTDIR)/include -+GLUTDIR = $(FREEWAREDIR) -+GLUTLINK = -lglut -lGLU -lGL -lXmu -lXext -lX11 -+OPENGLFLAG = -DOPENGL_SUPPORT -I$(GLUTDIR)/include/GL - OPENGLOBJ = opengl.o - OPENGLCLIBOBJ = ogl_utils.o ogl_body.o ogl_bitmap_character.o - -@@ -35,25 +35,25 @@ - - # JPEG image file format; requires the JPEG library. - # Comment out these lines if the JPEG library is not available. <--- --JPEGDIR = $(FREEWAREDIR)/jpeg --JPEGLINK = $(JPEGDIR)/libjpeg.a --JPEGFLAG = -DJPEG_SUPPORT -I$(JPEGDIR) -+JPEGDIR = $(FREEWAREDIR) -+JPEGLINK = -ljpeg -+JPEGFLAG = -DJPEG_SUPPORT - JPEGOBJ = jpeg_img.o - - # PNG image file format; requires the PNG library and the zlib library. - # Comment out these lines if the PNG and zlib libraries are not available. <--- --ZLIBDIR = $(FREEWAREDIR)/zlib --ZLIBLINK = $(ZLIBDIR)/libz.a --PNGDIR = $(FREEWAREDIR)/libpng --PNGLINK = $(PNGDIR)/libpng.a --PNGFLAG = -DPNG_SUPPORT -I$(PNGDIR) -I$(ZLIBDIR) -+ZLIBDIR = $(FREEWAREDIR) -+ZLIBLINK = -lz -+PNGDIR = $(FREEWAREDIR) -+PNGLINK = -lpng -+PNGFLAG = -DPNG_SUPPORT - PNGOBJ = png_img.o - - # GIF image file format; requires the gd 1.3 library. - # Comment out these lines if the gd 1.3 library is not available. <--- --GIFDIR = $(FREEWAREDIR)/gd --GIFLINK = $(GIFDIR)/libgd.a --GIFFLAG = -DGIF_SUPPORT -I$(GIFDIR) -+GIFDIR = $(FREEWAREDIR) -+GIFLINK = -lgd -+GIFFLAG = -DGIF_SUPPORT - GIFOBJ = gif_img.o - - # SGI IRIX's C compiler. -@@ -62,7 +62,7 @@ - COPT = -O1 - # Correctness flags: - #CCHECK = -ansi -fullwarn -g -DSELECT_DEBUG --CCHECK = -ansi -fullwarn -+CCHECK = -ansi - #CCHECK = -ansi -fullwarn -DNDEBUG - - # General cc compile flags. diff --git a/sci-chemistry/molscript/files/glutbitmap.h b/sci-chemistry/molscript/files/glutbitmap.h deleted file mode 100644 index 9584bb129daa..000000000000 --- a/sci-chemistry/molscript/files/glutbitmap.h +++ /dev/null @@ -1,32 +0,0 @@ -#ifndef __glutbitmap_h__ -#define __glutbitmap_h__ - -/* Copyright (c) Mark J. Kilgard, 1994, 1998. */ - -/* This program is freely distributable without licensing fees - and is provided without guarantee or warrantee expressed or - implied. This program is -not- in the public domain. */ - -#define GLUT_NO_LIB_PRAGMA /* Avoid auto library linking when building - the GLUT library itself. */ -#include - -typedef struct { - const GLsizei width; - const GLsizei height; - const GLfloat xorig; - const GLfloat yorig; - const GLfloat advance; - const GLubyte *bitmap; -} BitmapCharRec, *BitmapCharPtr; - -typedef struct { - const char *name; - const int num_chars; - const int first; - const BitmapCharRec * const *ch; -} BitmapFontRec, *BitmapFontPtr; - -typedef void *GLUTbitmapFont; - -#endif /* __glutbitmap_h__ */ diff --git a/sci-chemistry/molscript/metadata.xml b/sci-chemistry/molscript/metadata.xml deleted file mode 100644 index e490bcb8aa87..000000000000 --- a/sci-chemistry/molscript/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - - diff --git a/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild b/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild deleted file mode 100644 index eb7145817875..000000000000 --- a/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild +++ /dev/null @@ -1,67 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit epatch toolchain-funcs - -DESCRIPTION="Display 3D molecules (e.g., proteins) in schematic and detailed representations" -HOMEPAGE="http://www.avatar.se/molscript/" -SRC_URI="${P}.tar.gz" - -LICENSE="glut molscript" -SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -IUSE="" - -DEPEND=" - media-libs/freeglut - media-libs/gd:2= - media-libs/libpng:0= - virtual/jpeg:0= - || ( - x11-libs/libXmu - x11-libs/libXext - x11-libs/libX11 - )" -RDEPEND="${DEPEND}" - -RESTRICT="fetch" - -pkg_nofetch() { - elog "Please visit ${HOMEPAGE}" - elog "and get ${A}." - elog "Place it into your DISTDIR directory." -} - -src_prepare() { - epatch \ - "${FILESDIR}"/fix-makefile-shared.patch \ - "${FILESDIR}"/${PV}-ldflags.patch \ - "${FILESDIR}"/${PV}-prll.patch \ - "${FILESDIR}"/${PV}-libpng15.patch - - # Provide glutbitmap.h, because freeglut doesn't have it - cp "${FILESDIR}"/glutbitmap.h "${S}"/clib/ || die - - # Stop an incredibly hacky include - sed \ - -e 's:<../lib/glut/glutbitmap.h>:"glutbitmap.h":g' \ - -i "${S}"/clib/ogl_bitmap_character.c || die -} - -src_compile() { - # Prefix of programs it links with - export FREEWAREDIR="${EPREFIX}/usr" - - ln -s Makefile.complete Makefile || die - - emake \ - CC="$(tc-getCC)" \ - COPT="${CFLAGS}" -} - -src_install() { - dobin molscript molauto - dohtml "${S}"/doc/*.html -} diff --git a/sci-chemistry/molsketch/Manifest b/sci-chemistry/molsketch/Manifest index e3e572d45fda..4bb9f63aef0d 100644 --- a/sci-chemistry/molsketch/Manifest +++ b/sci-chemistry/molsketch/Manifest @@ -1,5 +1,7 @@ AUX molsketch-0.3.0-_DEFAULT_SOURCE.patch 661 BLAKE2B 48e877f41de2b27d1c6bbdac34d68893b58bf22e3d2ca8fa3e777f950f6906b100471b0a1287205e65bb5e97e9b3bd40b64377f513750ec039ebffdddbd0ea22 SHA512 9fd409ca55d5df0c61e84d3d9941f4855b7dcd32fd7521f24204570858dc6205c70ca4c645c5eee31bdc446a315e02081fa947677a4f22addce16ec4dad64c10 AUX molsketch-0.4.1-more-quotes.patch 478 BLAKE2B 857f6a6f2514a4322f2a178aed0232f6f18d06831fea72ac8bbfa2cb806cdb2f73f2daeb4e9b8326be9dbd96518047c24f2721c3509d1551d90cfa80ca0105a8 SHA512 015344abb4aaa7f214e4e8a7eebe1a7a8f4d43b8a76a9c5f984fc4c5cf8da450430330543fe69d481ceec25c5a59ee332439654fd4ce82ce080aa4883cc1d113 DIST Molsketch-0.4.1-src.tar.gz 1499842 BLAKE2B 22584f012e838037f9e23c16da6c63984604002884d279b2b6012d80eb08af9ee18b4d364fa29327572854fccad34840f97413b29b487cfbeb6496a2a8003d17 SHA512 263b088c2b8d01c1f13802b18aea6f6784580fe1a806de45b0e1ecd9f29024350e01a611bdeed1891938acc733a42746203d345d3be13ebaf4c309413e86bf26 +DIST Molsketch-0.7.2-src.tar.gz 1907992 BLAKE2B 6bd099d963f352e66f73741273e9dee17f2fb299aec32b053ca39aa731a27f6a73093f98a4dbde2b6a97b85015016d1136fa4ead5f564006991b83072009ee6a SHA512 5e06f177ed4e7e8457215e07b623b1d92fa111f696fd7a106b0a6e8c56cc9c7d953fc33e0c0955c19766599d41a82519db95e12c0c49d3e4d3392311af3cc034 EBUILD molsketch-0.4.1-r1.ebuild 1244 BLAKE2B afd73d8fcbdaa7bad2a61d4df7d7ec8e064eb204d549339328ee077e2dc75bc03d800fa16c2674e50af96f59054d21718f9422020564f7a991df16990cd4b622 SHA512 5aed6b4c27ce78c50e7dd0d12cfd18179d58500ce6c166f86c44d0edaba15e155c27e72acb77be07b7a562059b75e7c1cb03390275075cf03b7d6395b31de9b5 +EBUILD molsketch-0.7.2.ebuild 838 BLAKE2B 628cb8b51841fcf7d35f15a920a1eb07120e84a08b1de02538e97218ea1d497a0bbc3065e4a5097e3c66bfe391ff9411872ed54a4e93c5100207a8f441edce91 SHA512 b747ae529960160d5d8706e44032151533f529d58093277c12e93792270d62e7e4b4c42fbec1c9261605957e812f3a528da78517a9177e425cafbd7f084b3c79 MISC metadata.xml 610 BLAKE2B f7e80a8160010e450b7808ab92056dc1f514a5cd985c335e853f0a92d1d86a0d5818a8d95c4ac5b26eb68fe67309bf1231f2455b2498209b840eea04a0006c20 SHA512 fc7180beb4202b3fd4cecb9e384fc8617e89e173e92d62bdcb8e2cb68c32ef57802e34a906ea5a7cc216a1f5b52579309a9a944a4307b31de4b2d1f3fcadf846 diff --git a/sci-chemistry/molsketch/molsketch-0.7.2.ebuild b/sci-chemistry/molsketch/molsketch-0.7.2.ebuild new file mode 100644 index 000000000000..7dee9f3ea943 --- /dev/null +++ b/sci-chemistry/molsketch/molsketch-0.7.2.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake xdg + +DESCRIPTION="A drawing tool for 2D molecular structures" +HOMEPAGE="http://molsketch.sourceforge.net/" +SRC_URI="mirror://sourceforge/project/${PN}/Molsketch/${P^}-src.tar.gz" +S="${WORKDIR}/${P^}" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +DEPEND=" + >=sci-chemistry/openbabel-3 + dev-qt/linguist-tools:5 + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qtnetwork:5 + dev-qt/qtprintsupport:5 + dev-qt/qtsvg:5 + dev-qt/qtwidgets:5 +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-0.3.0-_DEFAULT_SOURCE.patch +) + +src_configure() { + local mycmakeargs=( + # fix the doc dir, this is relative to the install dir (i.e. /usr/) + -DMSK_INSTALL_DOCS="/share/doc/${PF}" + ) + cmake_src_configure +} diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest index 9b3acc76b6cf..c26e4e5832f4 100644 --- a/sci-chemistry/openbabel/Manifest +++ b/sci-chemistry/openbabel/Manifest @@ -1,10 +1,6 @@ -AUX openbabel-2.4.1-gcc10.patch 2317 BLAKE2B a76a4ef8b7502f8a80ebb807d2874d77f2ef5f532fa7b71a398245b737d1d55387121f4c24fc7dda7df47ddac4ad16e9cd12076787bedf0f63872708e9516d99 SHA512 ea37e5c53360728455be3d819c29fc27aa10556451a437e05c71c6a5e2bd5e1cfb4c229ff0e67e6c8ae7554f08b7bb16ad4be9ace36991c9c9f2417574b373f2 -AUX openbabel-python.cmake 4402 BLAKE2B 36c325a26f9b23c3957db22110628a0a922ad02b6a7415fc197713d3df8f1703475bf2f2c53b546b7915466ce30b6b3c72c505ea72443dd23a17a7f9131f4f6e SHA512 a7bcdf90588930b05d11312429e735d3cc6a94053e67117bef6c1614932651abee7c4e082916482a9012622c0f29c3ba62dd7788b72aca6c88293660c7f2a3db -DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6 DIST openbabel-3.1.1_p20210225.tar.gz 36674527 BLAKE2B bb82fc96f704249d211bd86c73de0cf4e7cfe5e2ba5c745aa8b4f6f19583837e2181d85101377810095f6b71fc3b91bf2f6f5636726fc8271c6905f1f8c59e7b SHA512 9ff7cb4acbfad7a9c5c8d0dd8930ac0390d0d0f2758d1a6120009071f47ffe718f92ad620d37f26f196babb14649c52b5eb7bb161c342ef36aec655e0a172de4 DIST openbabel.jpg 12159 BLAKE2B b701df2b8c29df607dc2bd3997a282aa9a726d56c789ff2db900d33234dc691f76b6af12a4c9ccda4f09984504b863c40c39e8bf91058939996714ede2dd37c7 SHA512 998ea526c8c92f87dd203527fdd9f4e001357e951409209f41ab68e0b730fe12d97f9079c12ca289be413854ea2abcf8bb691ae5af823a6f29d6a590e1a3e2b0 DIST openbabel.png 29060 BLAKE2B 8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3 SHA512 bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70 -EBUILD openbabel-2.4.1-r2.ebuild 2178 BLAKE2B fd0d324a28dac54a6b67359b9250ab4331195eeb32c10de46d9d5d4e5c4bce44298eb0953eb06006823b7c6bdc5ab0b7f22b0b3334800e2f06d080a3e24fe311 SHA512 494acf7a358eb01a8bc77713da9135195013833c8bc993adad25221715238e53309719c0e42bdcd8ee076d35b26228946cfad5e08aab3259119db741c27ae5bd -EBUILD openbabel-3.1.1_p20210225.ebuild 7237 BLAKE2B f0825a4ce1a6f2c504d8ea7b308cd5aa65e53be15055f92383e563cb38a5fb504d9bd2bcfd4c4b00e67673b2ca1e6ba85804f9fbd5d33a62ffa0f40369046282 SHA512 dec2f95380a9250941b743bffffca3fd83507137cd21daa87211327cc42ce8e7b77474c6d17b0b67a148832b81b44e1f245277226461c362e6a9809cbc6d5c3c -EBUILD openbabel-9999.ebuild 7197 BLAKE2B 77bfe052690916bda80ba7d38993f38fb1bff632f27d7d7d352bff6eddabe38cda89fe0f5574a37744091c80e59f1b575fea5a00da9c5a60f594a6c94ea4f9f2 SHA512 79781c3bff2a795c85dc4ca99640ee52c59130ddfd49c8452473fd2cb544991759f3c76f3cb9afa5a9671ee91508706707e9e02d8a95668f544274f315e4be03 +EBUILD openbabel-3.1.1_p20210225.ebuild 7234 BLAKE2B 5ea580096819ba3df0b18fe713d04f7811d6c65016ca18492ee4a1deada357261580e87bae9fca8cf9a9eea8214ca0fd7f7ac22f1272cd8f2577dd88c207a44d SHA512 0323ef9d33b9efe318b59c2de88073c3c30c5d90f470f0e8426f9a7563595e1e5e7446130a72c1a747ea080df7ee9189e473e3fc3a5464b07efd2066ed1dac91 +EBUILD openbabel-9999.ebuild 7196 BLAKE2B 07a467606b08dfa7c4b81cb58b25afc37cb06330e8d0c5012896905a672c206c0690898950d1b9bca35ea5ddc5dc415516341fe5f3c2095db7b91f169b9300b9 SHA512 1c1214ad4eb0ec7128feedb5708f814d3910ab0c6adbdaa19b8e34c11968daa8d92efafa2685b69558f5b884f9c09f27f19d75db26a5e522c357081496f4f378 MISC metadata.xml 862 BLAKE2B 56a35c050142f5a8939441d6a669986ad58321154f1a46fb78dcf6b861311bbb28d6f49507fff673519396533fbbfb8bf0214aa9dbdf1041ae7497c3287a3eb3 SHA512 7d289c49a91b4ae9a3910c6feb1014fa307ccc01b1e041e1aece7c8f135ac2eb1f5aae562dfd25d17e38d88c5747786a7406d6c09d10f74e80c08691599dec80 diff --git a/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch b/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch deleted file mode 100644 index 88d8c2add64a..000000000000 --- a/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch +++ /dev/null @@ -1,62 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 2e66dd1..ef4f16b 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -1,16 +1,11 @@ - # Please ensure that any changes remain compliant with 2.4.8. - if(NOT EMBED_OPENBABEL) -- cmake_minimum_required(VERSION 2.4.8) -+ cmake_minimum_required(VERSION 2.4.10) - endif() - - project(openbabel) - set(CMAKE_MODULE_PATH ${openbabel_SOURCE_DIR}/cmake/modules) - --# Allow loose loop constructs, i.e. no matching in if/else/endif or loops. --# Note that this is true by default in CMake 2.6.0, but we currently only --# require CMake 2.4.8 - remove this when the CMake requirement is bumped. --set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS 1) -- - if(COMMAND cmake_policy) - cmake_policy(SET CMP0003 NEW) - cmake_policy(SET CMP0005 OLD) # add_definitions need updating to set to NEW -@@ -20,7 +15,6 @@ if(COMMAND cmake_policy) - endif() - - include (CheckCXXCompilerFlag) --include (MacroEnsureVersion) - - # Version numbering - should be bumped for each release - # Note that for "beta" releases, we should start at x.90.0 -- we've -@@ -238,16 +232,21 @@ check_type_size(clock_t CLOCK_T) - - # Get the GCC version - from KDE4 cmake files - if(CMAKE_COMPILER_IS_GNUCXX) -- exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info) -- string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}") -- # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the -- # patch level, handle this here: -- if (NOT _gcc_version) -- string (REGEX REPLACE ".*\\(GCC\\).* ([34]\\.[0-9]) .*" "\\1.0" _gcc_version "${_gcc_version_info}") -- endif () -- macro_ensure_version("4.0.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_0) -- macro_ensure_version("4.1.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_1) -- macro_ensure_version("4.2.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_2) -+ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.0.0)) -+ set(GCC_IS_NEWER_THAN_4_0 TRUE) -+ else() -+ set(GCC_IS_NEWER_THAN_4_0 FALSE) -+ endif() -+ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.1.0)) -+ set(GCC_IS_NEWER_THAN_4_1 TRUE) -+ else() -+ set(GCC_IS_NEWER_THAN_4_1 FALSE) -+ endif() -+ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.2.0)) -+ set(GCC_IS_NEWER_THAN_4_2 TRUE) -+ else() -+ set(GCC_IS_NEWER_THAN_4_2 FALSE) -+ endif() - endif() - - if(UNIX) diff --git a/sci-chemistry/openbabel/files/openbabel-python.cmake b/sci-chemistry/openbabel/files/openbabel-python.cmake deleted file mode 100644 index 425b4656a9d2..000000000000 --- a/sci-chemistry/openbabel/files/openbabel-python.cmake +++ /dev/null @@ -1,104 +0,0 @@ -# The following is a cmake fragment taken from scripts/CMakeLists.txt and -# edited for Gentoo python multibuild compatibility. - -if (PYTHON_BINDINGS) - # Tags should be edited to reflect the active python implementation - set(EPYTHON @@EPYTHON@@) - set(PYTHON_INCUDE_DIR @@PYTHON_INCUDE_DIR@@) - set(PYTHON_LIBS @@PYTHON_LIBS@@) - set(PYTHON_SITEDIR @@PYTHON_SITEDIR@@) - - include_directories(${PYTHON_INCUDE_DIR}) - - add_custom_command( - OUTPUT ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py - COMMAND ${SWIG_EXECUTABLE} -python -c++ -small -O -templatereduce -naturalvar -I${CMAKE_SOURCE_DIR}/include -I${CMAKE_BINARY_DIR}/include -o ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${eigen_define} -outdir ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON} ${CMAKE_SOURCE_DIR}/scripts/openbabel-python.i - MAIN_DEPENDENCY openbabel-python.i - VERBATIM - ) - - configure_file(${CMAKE_SOURCE_DIR}/scripts/python/openbabel/__init__.py.in - ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py) - - add_library(bindings_python_${EPYTHON} MODULE ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp) - target_link_libraries(bindings_python_${EPYTHON} ${PYTHON_LIBS} ${BABEL_LIBRARY}) - - set_target_properties(bindings_python_${EPYTHON} - PROPERTIES - OUTPUT_NAME _openbabel - LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel - PREFIX "" - SUFFIX .so ) - - add_dependencies(bindings_python_${EPYTHON} openbabel) - - install(TARGETS bindings_python_${EPYTHON} - LIBRARY DESTINATION ${PYTHON_SITEDIR}/openbabel - COMPONENT bindings_python) - install(FILES ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py - DESTINATION ${PYTHON_SITEDIR}/openbabel - COMPONENT bindings_python) - install(FILES ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py - DESTINATION ${PYTHON_SITEDIR}/openbabel - COMPONENT bindings_python) - install(FILES ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py - DESTINATION ${PYTHON_SITEDIR}/openbabel - COMPONENT bindings_python) - - if (ENABLE_TESTS) - # Make sure all module files are together in the same directory for testing - add_custom_command(TARGET bindings_python_${EPYTHON} POST_BUILD - COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/ - COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/) - set(TEST_SOURCE_DIR ${CMAKE_SOURCE_DIR}/test) - # define TESTDATADIR for tests that need input files - add_definitions(-DTESTDATADIR="${TEST_SOURCE_DIR}/files/") - # define FORMATDIR for location of format plugin binaries - set(FORMATDIR "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/") - add_definitions(-DFORMATDIR="${FORMATDIR}/") - include_directories(${TEST_SOURCE_DIR}) - - # The macro is modified from cmake/modules/UsePythonTest.cmake - MACRO(ADD_PYTHON_TEST TESTNAME FILENAME) - GET_SOURCE_FILE_PROPERTY(loc ${FILENAME} LOCATION) - STRING(REGEX REPLACE ";" " " wo_semicolumn "${ARGN}") - FILE(WRITE ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake -" - MESSAGE(\"${PYTHONPATH}\") - EXECUTE_PROCESS( - COMMAND ${EPYTHON} ${loc} ${wo_semicolumn} - RESULT_VARIABLE import_res - OUTPUT_VARIABLE import_output - ERROR_VARIABLE import_output - ) - - # Pass the output back to ctest - IF(import_output) - MESSAGE(\${import_output}) - ENDIF(import_output) - IF(import_res) - MESSAGE(SEND_ERROR \${import_res}) - ENDIF(import_res) -" - ) - ADD_TEST(${TESTNAME} ${CMAKE_COMMAND} -P ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake) - ENDMACRO(ADD_PYTHON_TEST) - - set(pybindtests - bindings - _pybel - example - obconv_writers - cdjsonformat - pcjsonformat - roundtrip - ) - foreach(pybindtest ${pybindtests}) - ADD_PYTHON_TEST(pybindtest_${pybindtest}_${EPYTHON} ${TEST_SOURCE_DIR}/test${pybindtest}.py) - set_tests_properties(pybindtest_${pybindtest}_${EPYTHON} PROPERTIES - ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX};LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}:\$ENV{LD_LIBRARY_PATH};BABEL_LIBDIR=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/;BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data" - FAIL_REGULAR_EXPRESSION "ERROR;FAIL;Test failed" - ) - endforeach(pybindtest ${pybindtests}) - endif (ENABLE_TESTS) -endif(PYTHON_BINDINGS) diff --git a/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild deleted file mode 100644 index 95161d26d6d6..000000000000 --- a/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild +++ /dev/null @@ -1,101 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -WX_GTK_VER="3.0-gtk3" - -inherit cmake-utils desktop optfeature toolchain-funcs wxwidgets - -DESCRIPTION="Interconverts file formats used in molecular modeling" -HOMEPAGE="http://openbabel.org/wiki/Main_Page" -SRC_URI=" - mirror://sourceforge/openbabel/${P}.tar.gz - https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png -" - -# See src/CMakeLists.txt for LIBRARY_VERSION -SLOT="0/5.0.0" -LICENSE="GPL-2" -KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~ppc-macos" -IUSE="doc openmp test wxwidgets" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-cpp/eigen:3 - dev-libs/libxml2:2 - sci-libs/inchi - sys-libs/zlib - wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] ) -" -DEPEND="${RDEPEND}" -BDEPEND=" - >=dev-util/cmake-2.4.10 - doc? ( app-doc/doxygen ) -" - -DOCS=( AUTHORS NEWS.md README.md THANKS doc/dioxin.{inc,mol2} doc/README.{dioxin.pov,povray} ) - -PATCHES=( - "${FILESDIR}"/${P}-gcc10.patch -) - -pkg_setup() { - if use openmp; then - if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then - ewarn "OpenMP is not available in your current selected gcc" - die "need openmp capable gcc" - fi - FORTRAN_NEED_OPENMP=1 - fi -} - -src_prepare() { - sed \ - -e '/__GNUC__/s:== 4:>= 4:g' \ - -i include/openbabel/shared_ptr.h || die - cmake-utils_src_prepare -} - -src_configure() { - use wxwidgets && setup-wxwidgets - local mycmakeargs=( - -DOPENBABEL_USE_SYSTEM_INCHI=ON - -DENABLE_OPENMP=$(usex openmp) - -DBUILD_GUI=$(usex wxwidgets) - ) - - cmake-utils_src_configure -} - -src_install() { - docinto html - dodoc doc/{*.html,*.png} - if use doc ; then - docinto html/API - dodoc -r doc/API/html/* - fi - - make_desktop_entry obgui "Open Babel" "${PN}" - doicon "${DISTDIR}/${PN}.png" - - cmake-utils_src_install -} - -src_test() { - local mycmakeargs=( - -DOPENBABEL_USE_SYSTEM_INCHI=ON - -DPYTHON_EXECUTABLE=false - -DOPENMP=$(usex openmp) - -DBUILD_GUI=$(usex wxwidgets) - -DTESTS=$(usex test) - ) - - cmake-utils_src_configure - cmake-utils_src_compile - cmake-utils_src_test -E py -} - -pkg_postinst() { - optfeature "perl support" sci-chemistry/openbabel-perl - optfeature "python support" sci-chemistry/openbabel-python -} diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild index 67ac61c1741b..97dfa6e9a236 100644 --- a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild +++ b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -25,7 +25,7 @@ else SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz" S="${WORKDIR}/${PN}-${MY_P}" fi - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~ppc-macos" fi SRC_URI="${SRC_URI} @@ -181,7 +181,7 @@ src_configure() { ) if use test; then - # Help cmake find the python interpreter when dev-lang/python-exec is built + # Help cmake find the python interpreter when dev-lang/python-exec is built # without native-symlinks support. python_setup mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" ) diff --git a/sci-chemistry/openbabel/openbabel-9999.ebuild b/sci-chemistry/openbabel/openbabel-9999.ebuild index baf793cb651c..2c73801d2362 100644 --- a/sci-chemistry/openbabel/openbabel-9999.ebuild +++ b/sci-chemistry/openbabel/openbabel-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -181,7 +181,7 @@ src_configure() { ) if use test; then - # Help cmake find the python interpreter when dev-lang/python-exec is built + # Help cmake find the python interpreter when dev-lang/python-exec is built # without native-symlinks support. python_setup mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" ) diff --git a/sci-chemistry/pdbcat/Manifest b/sci-chemistry/pdbcat/Manifest index 59a153f5d9a6..d236b76b694a 100644 --- a/sci-chemistry/pdbcat/Manifest +++ b/sci-chemistry/pdbcat/Manifest @@ -1,5 +1,5 @@ AUX CMakeLists.txt 172 BLAKE2B 465647d1cff64bf52a75f35e9783bf7f9b80f214e0e950edb95598f8cd49dd3c4d4b06e78b73cd3e9b4a6c14ba612e323fedd0fb3decfeb9bfb7f3493f3ab8d9 SHA512 c8aa60098be10a25dcebf4c764e30f886f39a7d95da228d9d7fdcdedf3124ace32307197bbb2901b89ee3a8ce78411e61a4147eb395add65df6583683d3d5277 AUX pdbcat-1.3-gcc.patch 423 BLAKE2B 513fc1d200eb1abc4103e813f5b8a666c7cbb20d97c7da5381edbe33a75353b6b17659593196ee7be0197ac08546705901f02be77d733bfe68eaae5cdbc0d2fd SHA512 0a4b85ad2a4ec8014829e0c1449aecc90d65b57c4d0062ecd537991219c58c75dce138d901718a790c014d240afa9a063d46db5625d1e1c50727f1b1e468b032 DIST pdbcat-1.3.tar.gz 12750 BLAKE2B 45a229af85665bcdc82d8407eab69e2a3827988202401a2d1c5201647ececc76d4c5c908e001305fcb12b5dc0f5788989aa3fb87840711c9970db571c3bd263d SHA512 369ac0c4c1d8396eaa0450feb9852d2d75ebd9862a2e403ccd42a2801e924f99c28c5d71c0b66feb4588076a8948b503823d2c75420128dd04d020253f821f4c -EBUILD pdbcat-1.3.ebuild 590 BLAKE2B 940de99c7bc5eca8d12866afe3eea8300b2635a9b835135583c09ba59c1b2036505f5c48482d1714507a9032957e10498cf81997b989132505f9f94894415be8 SHA512 d9a9734e6df0dd3773fab52b617a1dd6dff2aeaf3110903ba3af5d11644db1b14013371ba020bdae412c311648f72f955c358bd995c2ef2df659984ab6090077 +EBUILD pdbcat-1.3-r1.ebuild 570 BLAKE2B 2718288c6ea56aaea1cbea794235bdcfa7d9a48e649fddf528aa7ed0e3ea5888302bc08d34e7f1d91f9e65ad13a440ec251f1d144bd0d5f8e81a03c7e68f2085 SHA512 c10fc1c109b77f365ce48bcdf1afff0b527d819909648a3b7344177b51d5556efe2af342dd80a9e5ec16c952d0e3121acede649bafa20dbc45fb00743e32baa5 MISC metadata.xml 1146 BLAKE2B 5111c6f43451b97682372f3cab46e82d8d07411c5ad8da3295aaf4fe36d1303672e4902d0854e9911188a3b44ecb989da39f6650be04633868b7e97783ffea65 SHA512 4c757ff166a83fe0dc2785800de45fea3cb6eb631facff0f87c4ca1c13085eb3984e2f38b2319471169461b01e6260d6f5c87af18e4c407fea35b38899905e99 diff --git a/sci-chemistry/pdbcat/pdbcat-1.3-r1.ebuild b/sci-chemistry/pdbcat/pdbcat-1.3-r1.ebuild new file mode 100644 index 000000000000..270e7b98fb36 --- /dev/null +++ b/sci-chemistry/pdbcat/pdbcat-1.3-r1.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="Manipulate and process PDB files using tools such as Perl, awk, etc" +HOMEPAGE="http://www.ks.uiuc.edu/Development/MDTools/pdbcat/" +SRC_URI="http://www.ks.uiuc.edu/Development/MDTools/${PN}/files/${P}.tar.gz" + +LICENSE="free-noncomm" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +PATCHES=( + "${FILESDIR}"/${P}-gcc.patch +) + +DOCS=( README ) + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + + cmake_src_prepare +} diff --git a/sci-chemistry/pdbcat/pdbcat-1.3.ebuild b/sci-chemistry/pdbcat/pdbcat-1.3.ebuild deleted file mode 100644 index ccdbd9928160..000000000000 --- a/sci-chemistry/pdbcat/pdbcat-1.3.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit cmake-utils - -DESCRIPTION="Manipulate and process PDB files using tools such as Perl, awk, etc" -HOMEPAGE="http://www.ks.uiuc.edu/Development/MDTools/pdbcat/" -SRC_URI="http://www.ks.uiuc.edu/Development/MDTools/${PN}/files/${P}.tar.gz" - -LICENSE="free-noncomm" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -PATCHES=( "${FILESDIR}"/${P}-gcc.patch ) -DOCS=( README ) - -src_prepare() { - cp "${FILESDIR}"/CMakeLists.txt . || die - cmake-utils_src_prepare -} diff --git a/sci-chemistry/pdbmat/Manifest b/sci-chemistry/pdbmat/Manifest index d57f17b0d3ea..de4213c342e2 100644 --- a/sci-chemistry/pdbmat/Manifest +++ b/sci-chemistry/pdbmat/Manifest @@ -1,4 +1,4 @@ -AUX CMakeLists.txt 414 BLAKE2B bdc6bbe4b5fc80e208dece51e29f3d7b429655d57e0406c5d08fd41b069577574f0cb1b75b406a21aed14479bc7679a386e92a6af66dbdac325291ef6414dbbe SHA512 d539a6cc947cf6f16d634ccc5e2c0f1783f000564cc78c2103c1bcbc8619cb7f0d97a461ffa91ab3fb7d4dbe11102614983456c9bd8597a2f4d9f9a6538185ff +AUX CMakeLists.txt 457 BLAKE2B 777b9e218731ffe6dc50f32996420703ddbc9778580c4040aafed7ca36192b3b689b6cd9311a9d12ccd8349ac41f974c8d518dcd87d6ff615e8e2d8403c8bd03 SHA512 1df9f68ccb2a5ad481695daf2845b62affe5bffad23b596f68e2589e199e009ce79b9c873a00c0e44afaf23a1e0f5dd7526ff828b45350d562505af1de795268 DIST pdbmat-3.89.tar.gz 124727 BLAKE2B ed74b4278d85d21f97a6268f2554478e5da0c871be6d071d54edf964b10f92518f1869a77a6718e2c2b6b8c61b8e4659ccb84f9ee829d4351f23abd727c113cf SHA512 2c7f8f32344fe1abc662878c2556c10bd6671e683787231827399866f485389c3a63253b00d5a5bdbe8d0b8b779891e846962c9372d927b94c45f0fac59a4fb6 -EBUILD pdbmat-3.89.ebuild 649 BLAKE2B 4ca393b9d4ac572b263f7f16a8d3bafe4710cad3630bd4617c7f184e01c56c1e2dfded7d14f2e5a95e0432178c3acebd9fa0a4cf2a48ab4abfb47c00f12296db SHA512 22e5765e35daab42e8c013ee1a2ddc8b08318d215c1eea6def16ff0559be4f5d521ed85f73fc82fbac3d0a0ae06fc07935bb666fdccf47f1268316a668b1f3e7 +EBUILD pdbmat-3.89-r1.ebuild 627 BLAKE2B 84059446492f20698941c11580733ec5f911aa23f325d2add1a29c3adb15fc91d652fc5fa8df8080e16dc94e87642c54814e1f9e7dd2a76e2f2769caf17ee8a3 SHA512 29a76ba319604baa5826d1bc4e3f285e73be18c9a2daf8eac560c35eb2beff6518ccabcacd0067b3d24308afc0164c745bd0cd6b6e8ba061b3b73ee6ee666ea8 MISC metadata.xml 1092 BLAKE2B 4dd0c655057ada7c10630baaab4c9e83c3617b57ccb05367db0b90362c3473b18b8cc7fb3daf3ce0bbcd513c364db7f8f3102a73bf111632b3f79567bc755788 SHA512 7d07b337f08658ef9fbdda6392a8b49ca77139e1d52136d74f4ce627a5fe1062fa52b33ae94eb6273ac7a4511c6c74da21549f9e6d46b3e49c6f4fbfe83aebe4 diff --git a/sci-chemistry/pdbmat/files/CMakeLists.txt b/sci-chemistry/pdbmat/files/CMakeLists.txt index 2f1937d84b3f..a20199bbca91 100644 --- a/sci-chemistry/pdbmat/files/CMakeLists.txt +++ b/sci-chemistry/pdbmat/files/CMakeLists.txt @@ -1,14 +1,16 @@ cmake_minimum_required (VERSION 2.6) project (PDBMAT Fortran) +include(GNUInstallDirs) + option (EXAMPLES "Instal additional example files" OFF) add_executable(diagstd diagstd.f) add_executable(pdbmat pdbmat.f) install (TARGETS diagstd pdbmat DESTINATION bin) -install (FILES diagstd.README pdbmat.README DESTINATION share/doc/pdbmat) +install (FILES diagstd.README pdbmat.README DESTINATION ${CMAKE_INSTALL_DOCDIR}) if ( EXAMPLES ) - install (DIRECTORY ../Try_ENM2011 DESTINATION share/pdbmat/examples) + install (DIRECTORY ../Try_ENM2011 DESTINATION ${CMAKE_INSTALL_DOCDIR}/examples) endif (EXAMPLES) diff --git a/sci-chemistry/pdbmat/pdbmat-3.89-r1.ebuild b/sci-chemistry/pdbmat/pdbmat-3.89-r1.ebuild new file mode 100644 index 000000000000..40ef7c9df2d3 --- /dev/null +++ b/sci-chemistry/pdbmat/pdbmat-3.89-r1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake fortran-2 + +DESCRIPTION="Calculate Tirion's model from pdb structures" +HOMEPAGE="http://ecole.modelisation.free.fr/modes.html" +SRC_URI="http://ecole.modelisation.free.fr/enm2011.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}"/Source_ENM2011 + +LICENSE="CeCILL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DEXAMPLES=$(usex examples) + ) + + cmake_src_configure +} diff --git a/sci-chemistry/pdbmat/pdbmat-3.89.ebuild b/sci-chemistry/pdbmat/pdbmat-3.89.ebuild deleted file mode 100644 index 6c14461b5019..000000000000 --- a/sci-chemistry/pdbmat/pdbmat-3.89.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit cmake-utils fortran-2 - -DESCRIPTION="Calculate Tirion's model from pdb structures" -HOMEPAGE="http://ecole.modelisation.free.fr/modes.html" -SRC_URI="http://ecole.modelisation.free.fr/enm2011.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="CeCILL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="examples" - -S="${WORKDIR}"/Source_ENM2011 - -src_prepare() { - cp "${FILESDIR}"/CMakeLists.txt . || die - - cmake-utils_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DEXAMPLES=$(usex examples) - ) - - cmake-utils_src_configure -} diff --git a/sci-chemistry/povscript+/Manifest b/sci-chemistry/povscript+/Manifest deleted file mode 100644 index c32b1a378566..000000000000 --- a/sci-chemistry/povscript+/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -AUX povscript+-2.1.2.2.19-libpng15.patch 542 BLAKE2B 1fcc229fd3e90a1c567ea42bd87b4b9de281b4976016a0c990f3a66ba2d9d3d8b7eacb80c1caf31326a4c35ff33863d9495b857163ee86bf7060e44debbe19f6 SHA512 5f795238f95adfa0712c92afda669d461cc292b358aa51907ceea1c2d5e5e470d1817d75f461a46efb962ffefafa2606400d32c1f681192f8e161d6e23ee5224 -DIST molscript-2.1.2pov2.20.tar.gz 822930 BLAKE2B da050db5124d04e7c0e2c06b0e666d631f214b4519b41ac4b4775dbdbf5be2608f5417f13fad45c36f796d486a8d9211d2fd3d9403afa1b6d27e52b4f0a7f248 SHA512 f7cae4d9b583a05962742ee36ec717f0ecac6bb88086bcfa484b51b0d2e16a15920bc7c09d9d777453d7ef7b81be444924d15a889e4725bfca7bf517d4e52db2 -EBUILD povscript+-2.1.2.2.20.ebuild 1260 BLAKE2B e87e2245fe685e882b8c4d794933a89fbcfb7a2d276f6153f89344e7cc79a240df6a76a27d27e02bea9408f1c88afc2ae79bf980a36f63d6e74a25641dd13e26 SHA512 e47e4402bcf2debf0b539db25971b068a7ca9253adebfdf84788d2aa0e0a12b44afa94e3dcff5559c906c480f98216c0ec211f59dcd0873382ac49ac0c2737b7 -MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c diff --git a/sci-chemistry/povscript+/files/povscript+-2.1.2.2.19-libpng15.patch b/sci-chemistry/povscript+/files/povscript+-2.1.2.2.19-libpng15.patch deleted file mode 100644 index 054967d6555c..000000000000 --- a/sci-chemistry/povscript+/files/povscript+-2.1.2.2.19-libpng15.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- src/png_img.c -+++ src/png_img.c -@@ -18,6 +18,7 @@ - - #include MS_GL_H - -+#include - #include - - #include "clib/str_utils.h" -@@ -69,7 +70,7 @@ - info_ptr = png_create_info_struct (png_ptr); - if (info_ptr == NULL) - yyerror ("png_img: could not create PNG info structure"); -- if (setjmp (png_ptr->jmpbuf)) yyerror ("png_img: could not setjmp"); -+ if (setjmp (png_jmpbuf(png_ptr))) yyerror ("png_img: could not setjmp"); - - png_init_io (png_ptr, outfile); - png_set_compression_level (png_ptr, compression_level); diff --git a/sci-chemistry/povscript+/metadata.xml b/sci-chemistry/povscript+/metadata.xml deleted file mode 100644 index e490bcb8aa87..000000000000 --- a/sci-chemistry/povscript+/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - - diff --git a/sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild b/sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild deleted file mode 100644 index a2caada48ed1..000000000000 --- a/sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit epatch versionator - -V1=$(get_version_component_range 1 ${PV}) -V2=$(get_version_component_range 2 ${PV}) -V3=$(get_version_component_range 3 ${PV}) -V4=$(get_version_component_range 4 ${PV}) -V5=$(get_version_component_range 5 ${PV}) - -MY_P=molscript-${V1}.${V2}.${V3}pov${V4}.${V5} - -DESCRIPTION="Modified molscript that uses POV-Ray, does thermal ellipsoids, and more" -HOMEPAGE="https://sites.google.com/site/timfenn/povscript" -SRC_URI="https://sites.google.com/site/timfenn/povscript/${MY_P}.tar.gz" - -SLOT="0" -LICENSE="glut molscript" -KEYWORDS="~amd64 ~ppc ~x86" -IUSE="" - -RDEPEND=" - dev-libs/glib:2 - media-libs/freeglut - media-libs/giflib - >=media-libs/libpng-1.4:0= - sci-libs/gts - sys-libs/zlib - virtual/glu - virtual/jpeg:0 - virtual/opengl - x11-libs/libX11" -DEPEND="${RDEPEND}" - -S=${WORKDIR}/${MY_P} - -src_prepare() { - epatch "${FILESDIR}"/${PN}-2.1.2.2.19-libpng15.patch -} - -src_install() { - default - - cd "${ED}"/usr/bin || die - mv molscript povscript+ || die - mv molauto povauto+ || die -} - -pkg_postinst() { - elog "You must install media-gfx/povray to use the POV backend," - elog "which is one of the main features of this over molscript." -} diff --git a/sci-chemistry/tm-align/Manifest b/sci-chemistry/tm-align/Manifest index 852bcefd468c..fff49a5c474a 100644 --- a/sci-chemistry/tm-align/Manifest +++ b/sci-chemistry/tm-align/Manifest @@ -1,4 +1,4 @@ AUX CMakeLists.txt 182 BLAKE2B a6bd5aedcbeb2b8019d59123da91cf668c3717a3e41c2259b2e023a4661aefeb2e4334d10ba7b236bfb6fb1cf52c87aae393c9af8b5e3d2f12663799aeccab32 SHA512 1e77edbfb2184e11c09fc2133eb40bd9d4b2fb04a30139134939482f4e817ebfa5c316e8d75a6fd5aa866ef1f6f56d65df924dc41cfb698330943e0bc433948d DIST TMtools20150914.tar.gz 982948 BLAKE2B 788f43040c1262c7e9eae2b47b0035d320a30fe7194e340d682b78e5961b82e46eef2b0a43d1ae458b9d5da6570f9c0ec0aca51b6ec3e25f0447fd43d629f592 SHA512 5fda29f6437ac9b0216a037496a01502de07e5a36736815833cb09217158a959370e750b75c55a54a49c733e4bd28be53b2dcbb25d71e2897273a4280ed3b530 -EBUILD tm-align-20150914.ebuild 718 BLAKE2B 3d75bb132c557625de6e05f26fcff119e0928e83839a0327dcf20c38c71454c4a8404668b55864c3d150da2b2ff9893b081cf2d0ab17ea0b28e6b8ede6087832 SHA512 7db6b71c5bd74fb88201999b0810f7ae6c7f366dd630f5abcde240bdac70b73758f2c71b5af0a97ea3548990a010efc728be1e768ed86e08a7d28a3821f0cec8 +EBUILD tm-align-20150914-r1.ebuild 623 BLAKE2B a29aad98e25a9538b9a0db2310c685ffd308648aa1309c7a393099aa514096bb648459cf01f690224e1ee0ae85ff6082fd0dc16bfb1bc6020353f0cadff53240 SHA512 5d48cc2e4736953b113323f732058199fa9ec71fecabfe9c6888fdfc74579af9dd99c4a9d28f8012d103a1bc977e7ddd7f8478f56c20deb6226f3881e8629fab MISC metadata.xml 1295 BLAKE2B 4dc3b05b67d6e27d90cd378d53ff5309e898ce56af4ffd6a02b3eb5f0827b1f05ec843325de35dd4efe82163797ffa0d430621af89a4669c2ee75cb8560e3e30 SHA512 fbffe7e094f35d8291d6bdee5f2900f170cadeb7811cfa17dcb0be5ab9b4e41527f1ce6a93f760103078285c254b84340c19ceefc33fde53814416d735c4f0d1 diff --git a/sci-chemistry/tm-align/tm-align-20150914-r1.ebuild b/sci-chemistry/tm-align/tm-align-20150914-r1.ebuild new file mode 100644 index 000000000000..0aa8d1461db7 --- /dev/null +++ b/sci-chemistry/tm-align/tm-align-20150914-r1.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake flag-o-matic fortran-2 + +DESCRIPTION="Quick & Accurate Structural Alignment" +HOMEPAGE="https://zhanggroup.org/TM-align/" +SRC_URI="http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools${PV}.tar.gz" +S="${WORKDIR}" + +LICENSE="tm-align" +SLOT="0" +KEYWORDS="amd64 ~ppc ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="custom-cflags" + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + cmake_src_prepare + + # Recommended by upstream + use custom-cflags || replace-flags -O* -O3 && append-fflags -ffast-math +} diff --git a/sci-chemistry/tm-align/tm-align-20150914.ebuild b/sci-chemistry/tm-align/tm-align-20150914.ebuild deleted file mode 100644 index 54a8bacf58f8..000000000000 --- a/sci-chemistry/tm-align/tm-align-20150914.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit cmake-utils flag-o-matic fortran-2 - -DESCRIPTION="Quick & Accurate Structural Alignment" -HOMEPAGE="http://zhanglab.ccmb.med.umich.edu/TM-align/" -SRC_URI="http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools${PV}.tar.gz" - -LICENSE="tm-align" -SLOT="0" -KEYWORDS="amd64 ~ppc ppc64 x86 ~amd64-linux ~x86-linux" -IUSE="custom-cflags static" - -S="${WORKDIR}" - -src_prepare() { - cp "${FILESDIR}"/CMakeLists.txt . || die - cmake-utils_src_prepare - - use static && append-fflags -static && append-ldflags -static - # recommended by upstream - use custom-cflags || replace-flags -O* -O3 && append-fflags -ffast-math -} diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest index 9f887c957af1..fd686915e851 100644 --- a/sci-chemistry/votca-csg/Manifest +++ b/sci-chemistry/votca-csg/Manifest @@ -1,19 +1,8 @@ -DIST votca-csg-1.5.1.tar.gz 708319 BLAKE2B 2ea75cf08dc3005bd08ebe85113d95743fe85bae4b7ac3c2e2d9b64be64a7103ecf30b9edf45cffa86b7588d5c57a0256aef02f4590fa6031cb63881480bd0fd SHA512 3559452182c325d5df72918ec6e12122c8214df9733d779c123ff199597fe47fc493fd75adf1f5dbc6b55016373863378ba3cc69fb6b61bc1531c6e591d8131c DIST votca-csg-1.6.4.tar.gz 537966 BLAKE2B c9ccc3aa28bdc4a2a2c080104b70602d8cf4be19a71e7d0b4a1c03d11f54b645984103d1662823a9308a4e4c4baedef731de06ff314b168f89e7326c0d3c8ee9 SHA512 4cdbf6c0a593720675f48f574ff9a93d038a48037543c1e09a4559d3eb262a2d8bf83d5f5dab85b4820a541e0c57f7cca78315d5b3382763e8acd8cc0fcb65ac -DIST votca-csg-2021.1.tar.gz 4300862 BLAKE2B 4ef287a8b0e14e97bcbc293bebdc3a0c45a08bd0033044ef8aa1ac18bac04928010ab3f5edfb656f1d062926f4572a1f3b0e55b3b3b635fdc388e5b850ec3bba SHA512 e1abdd34a3d88aea253cc10e7832a18d2cffc44286e4591c5a1239bf34e68d6c40054d3eb907a902e5ab6af5a9dea4ec266ff5ce59073b500413f4e122885e94 DIST votca-csg-2021.2.tar.gz 4300675 BLAKE2B 8db666e77bc7d6d8da34fed97b0466e5296019aa703f324d46531992c0af544c31b2e3e4595883791cef7acd6d2d52eff8edc7eeedecaae0eb9e0cbf334748ab SHA512 5808edd96199cad6e5fc803a0e489f3d2f376da3d64f565536cc37561a0fcd22960563af7d3f86522bcc7336c8d6f7c7f6501b36feb960aae5168904156bfbf6 -DIST votca-csg-2021.tar.gz 4300573 BLAKE2B ba589c97f22888b8a1a12c71314133c08c89e44c201bafa6e5f1d74dfe90c87dd84a5d1c2883b26402858b6aa990d37add57bdfb9db6836a7c287f0685a40a59 SHA512 8eacf4045ddc13d33e853cd35a67d03dfb63da60c3e879ea4f16e63f27a92aa13cbf4e367d9258778c9c09462443e4bb2b937c247c6246377ceeecf56bc6fc12 -DIST votca-csg-manual-1.5.1.pdf 1263719 BLAKE2B 29e2ce27215787a1121e45ec1e88ce7c61ba81709a2519aa0959eede505498b9aaf4f38666bb1a4f97837c98b862e7ed02405da07294a7ec76cc80390fe72e0d SHA512 7d9fb4c635383e1b9c9547691f8729e19f273fcafc4dab2a6b438b3ce98ea05bd31887d09bc4edc86ceb0b04d71a4371aed7aadc3ba6864f7be2ef3328ede642 DIST votca-csg-manual-1.6.4.pdf 1242124 BLAKE2B 003a255d2869c8185f9e03038f646a80b682be3daceb18757c791f5d52101379402aee20c5dcb65ef8ce651bd6f6590ad5249e835e53ce92e04eb33214017a9e SHA512 36956acd24a21cb0a1dd26d6640b41b7473132948327c05856191b4f9531b4d1d5f98be68a9d1a847935d47633d483e87c2300634233a6e617a010c1fb563690 -DIST votca-csg-tutorials-1.5.1.tar.gz 5949467 BLAKE2B c6de6084fbb1d2c4ac2ce75d01a1153eabc63386063de800ff2dc6b483b0568191e7f06ddcb8be46123224ccfd3a97f5fb4e7cd603c0ee99a8636d7143f6c701 SHA512 f2e709ae31d914fe12a4ce37b5019deb878b15ade14972f2a8204bec8970ba2c8946b71b94a5bfd6f7569e41173bfbc75275ea09cbee4358ad1de0e84751049c DIST votca-csg-tutorials-1.6.4.tar.gz 5944389 BLAKE2B 66f1d4947bb28ec602250226ad2c08cc02278a90776acbcadca2df3078361435fb2353ee0fa299d0d19697d36682f20aab709d45539d5ac7e7070942601ebc3f SHA512 7e40037f2e70c861fd7f5c63806c17ad56672a340a8795fa745414940c55f593bef32b9f6b9050400131ed9e66aa927149e9d324a1c264364d8504baf1921e28 -DIST votca-csg-tutorials-2021.1.tar.gz 5941978 BLAKE2B 5e6c5cfc3860e287d93cf8d59862a75e3afe7ac1610e696427e99302a99c86d12ce12f7a23281f36c8859e48a25be138466b9316f4c0667d5bf784f33c27e6df SHA512 8370ac9e2e859153f9a54b2e02cd18692fd06810dafb50a6bf3d81eca5211847e1b75d9832df80b1436ae0f9dcab455aa0bfb4c8122165c584cabd14203408ba DIST votca-csg-tutorials-2021.2.tar.gz 5942042 BLAKE2B a03627406a3b56ebf978dc82629e1f0950bfbb121a0f6c7fd60341986efe4892ba8bf1e6b526e6df2df5fb81351177ad97816568521b9dc6a91e72d6853c1e62 SHA512 3ddeb3e57353e6d4e59163ee1303b39d4e3b623309875f280bf8c02dde76d0615b32a27ea960a301b61b81034a538df87dfe97a53dfdd0c81f52629eadd64f1f -DIST votca-csg-tutorials-2021.tar.gz 5942031 BLAKE2B 60ef492c98bf07b5169c6f1be2298b6dac76003ef9981064463de9fdae649c215d469424e253d06b63637bb3eee9383c587a98322ab987995f8b4861bb0002e1 SHA512 844706407cb91d507c6b0433e23f4b27756dd4c882f6cef79d51f2b2acae6cd0114ccd91d626d090d0f61c58a57cc3c1eda0a0d10d6f4bfa522eda7ee8de21b3 -EBUILD votca-csg-1.5.1.ebuild 2522 BLAKE2B 0fe2b373307c76ebab320169b5ae837c463a734b029af1a328a87c2428b19484f138c75e7bb1e4ad91d0c099aa24c97c411c2f00308ebad051a81d0275e797be SHA512 2c6018212ae244e7387a2f63e186e970dd18825d77994f862c283131796ac93c6bb25a5233a41e306d8090ee75c82759025b74c3d1e0a0211adf67e0b3964449 -EBUILD votca-csg-1.6.4.ebuild 2290 BLAKE2B 1fa3398fce620103e69529a1b36f1b21fac4ff633ed602f218a61f8c41471376842c7e51e428bf6da165f225be8c54a6c76107fee7fd691c3cbf2a7fdcfcb6c8 SHA512 b794120a45fc6616873b31989e3d7df64c545673305ef714c189dce6f2725ab2f93e2e5625f38bf34fe6711583088e947ef3407e902ec0be5b5babac72316458 -EBUILD votca-csg-2021.1.ebuild 2097 BLAKE2B 3ff69560e5ed700f6c0cf3f15442d7ce277af2acab62e552fd921ca51f35348cd77ed25e89afa2208fdb6e0c8c4ac4771ada07fdb1fd85ba1bcb5d2d1dc647fd SHA512 5b52a2a2bb86cf0024fc64b60b3bd51fedb7f5d8dc4e2cfcb3e1e20dbd661469be79ec486c516c8c40b98d13e232ef5f3f7701e2c062ca3171beeebe047647ea -EBUILD votca-csg-2021.2.ebuild 2097 BLAKE2B 3ff69560e5ed700f6c0cf3f15442d7ce277af2acab62e552fd921ca51f35348cd77ed25e89afa2208fdb6e0c8c4ac4771ada07fdb1fd85ba1bcb5d2d1dc647fd SHA512 5b52a2a2bb86cf0024fc64b60b3bd51fedb7f5d8dc4e2cfcb3e1e20dbd661469be79ec486c516c8c40b98d13e232ef5f3f7701e2c062ca3171beeebe047647ea -EBUILD votca-csg-2021.ebuild 2033 BLAKE2B 77fc10474aff5882c3d99133175f67ee51704dd1a32e101a42afb5e4417f3c478b4311f9ed619d62c1eab13328b130cfb1e500ff1e890c518adc0b1fcf167c6c SHA512 de1e8c1d9cb22e75ebc8dc7c043aafb04dce6eaf3d7173f1e745a6578b7236e9f71ce3b75fa5698333eca7c5c74a41337eba3fb4cd5c037e8bf3172bf78296eb -EBUILD votca-csg-9999.ebuild 2072 BLAKE2B 1b13ee8b2bd47a7bd17fbddf1cc46f3ac38a21ba4c2d6d5a453ef3c55e2894b31c20c0f32d2b335b76d76ca56df6838b2ed6a616ee96e9dcb6fb7981f2f10346 SHA512 561f20660a4db6bca57c3bcf10c69aab2834b0a054c2ce95245a52536a1064c1481840001594cf2bcc4c060e3c407078d9d0b67497bd861d3f0a1df6b0ba3678 +EBUILD votca-csg-1.6.4.ebuild 2308 BLAKE2B 65ae92b9302300cbb0d18a0ca3cc3937040e5827dd9719907a6e8d8c93380205c538eae815718e4453ebf80a76c38aa250901a5b7a37617e7b5481d127788586 SHA512 5b50632329d68e1dd196e842c8118173391b266e086b3949bbc5afd93bd22bb25895c6d95728b82b5c908b8c759eddd7f8eb1e31a5392b6898a92522337a5d5f +EBUILD votca-csg-2021.2.ebuild 2115 BLAKE2B 7dbbec43db92a5b8c6420f468e6eb0d9488262dd70dd5ec23ee4482e4807e398bbca5cce619ea58f654521a8a7b5b50d20cd40630ef1a414ca5a0fec783e825b SHA512 54f8441f84c22134785b8297c5a7e96a0e7305b342631b82c9f4a3b06a0c97d5ee665848d4206100e1287c7a00ae8428fe7e1632584356b29544f3b89d6ba435 MISC metadata.xml 677 BLAKE2B 4d577f0229184293e80dca331cba9f8d234a73eb73b6eac92d7e87e2aefe90de69be1323d3e401cfedb0aa6f18ab77b7ae6f3f4c8c1aca836d7ac8a57184eb32 SHA512 f7999c1c10630ae72535609f9be857e7efbe89f0cc99f55268c66271625777e64c0a552317c49cde3ef5652be68c7e91630b8cd038b255b71a1566fac75b91e7 diff --git a/sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild b/sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild deleted file mode 100644 index 523b73df43ac..000000000000 --- a/sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild +++ /dev/null @@ -1,99 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -inherit bash-completion-r1 cmake-utils multilib - -IUSE="doc examples extras +gromacs hdf5" -PDEPEND="extras? ( ~sci-chemistry/${PN}apps-${PV} )" -if [ "${PV}" != "9999" ]; then - SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz - doc? ( https://github.com/${PN/-//}-manual/releases/download/v${PV}/${PN}-manual-${PV}.pdf ) - examples? ( https://github.com/${PN/-//}-tutorials/archive/v${PV}.tar.gz -> ${PN}-tutorials-${PV}.tar.gz )" - KEYWORDS="~amd64 ~x86 ~amd64-linux" - S="${WORKDIR}/${P#votca-}" -else - inherit git-r3 - EGIT_REPO_URI="https://github.com/${PN/-//}.git" - PDEPEND="${PDEPEND} doc? ( ~app-doc/${PN}-manual-${PV} )" -fi - -DESCRIPTION="Votca coarse-graining engine" -HOMEPAGE="http://www.votca.org" - -LICENSE="Apache-2.0" -SLOT="0" - -RDEPEND=" - ~sci-libs/votca-tools-${PV} - >=dev-cpp/eigen-3.3 - gromacs? (