diff options
Diffstat (limited to 'sci-chemistry')
99 files changed, 614 insertions, 3724 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex 08f6a519da1d..a1bf0e481100 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest deleted file mode 100644 index f00e4eaa7c6d..000000000000 --- a/sci-chemistry/apbs/Manifest +++ /dev/null @@ -1,6 +0,0 @@ -AUX apbs-1.4.1-manip.patch 1462 BLAKE2B f4559008a1fc4dc367bc770ed29b7fa9ae9489ab57cfc8dd6e5cff358e27e2ac71b1e786bf9a4e3d96dfb4eea3596305beb5078746324769b582abf8a702a1c5 SHA512 70679623621fb56eeffc79166aa6fd35b5fa2fec828f6800a27b795a4e94c9eee673a7ba5f872c3266c9e78af8935d684fb5c4679b57da6a969189ce45e31468 -AUX apbs-1.4.1-multilib.patch 3301 BLAKE2B 4268a21ec878d780c7a1efe433bf2c82ef2e72f49a6071b6df695bf672ee999be9c29fed06e949b80cc230333d8deca1094c946662ec657d31e3b6f86e873969 SHA512 cdd72fd23a57ee8413f72bf674ae246543b1c9f326727ff07c3b8848d59f98ab7d2daf28677460cb4726f919832079c1d280bcdc86a8bef5c0875583c789b7c0 -AUX apbs-1.4.1-python.patch 3979 BLAKE2B b21633655df329f5d445c4e53140367b0a8a6cfbfafccba8943206ed9bae46839bae532e3efd19d75e89bc70a1fa59d05f3ed977b1a59f949649d3e89b887a96 SHA512 a38ca3bbf692f42268d192aff61949ece95d9b043ac10b4eec33e383773beec1c60425a12e84843a602e828528f6cf0ed6b8c90e99aeea679c5abc8c093c68ae -DIST apbs-1.4.1.zip 37999283 BLAKE2B 2301deb7ab4eb2f20098cf63df180bb53189e42a89cd5559357cdcf08e84d27a44eafe8557bb460574802d24d29741ad4606dc3bd7f32911d0d0f2c7453d6470 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a -EBUILD apbs-1.4.1-r2.ebuild 3033 BLAKE2B c5373211c86c086bd7fd1898ba2437496c4a9fb8971a7847625b5a5a438ae21b10a2c733d323c692b5a6f1a8c94c78b4630a326c7af84bb90b3200f8970a197c SHA512 7fba09a563be088193ab58b57c5f45288497f222058ab2189decc755f6a761ec15ceacf5fe5a8619224c75603e80db86d427c77f37ec4edb163f6d75d63747ef -MISC metadata.xml 1048 BLAKE2B 53a61bd7e05e53b294f0cbd1a21b86f391429ad5f23a545e7cbb27625b152589247a08db06c5d7f6658425de032be970fae0230ad1ac14ac4f6de42663d6c97c SHA512 7d68049cb9b044676430fe879890cc4cd869b99f85696f579d9cbf3b156081301792fd7f03205a9b9d429d71c9a35b4815f4236573f68d3ef6b4718e6e1f0bb3 diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild deleted file mode 100644 index 4ea1cfcd1fad..000000000000 --- a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild +++ /dev/null @@ -1,129 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) -DISTUTILS_SINGLE_IMPL=true -COMMIT="74fcb8676de69ed04ddab8976a8b05a6caaf4d65" -inherit cmake-utils distutils-r1 flag-o-matic toolchain-funcs - -DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems" -HOMEPAGE="https://www.poissonboltzmann.org/apbs/" -#SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz" -SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${COMMIT}.zip -> ${P}.zip" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="debug doc examples fast +fetk iapbs mpi openmp python tools" - -REQUIRED_USE=" - iapbs? ( fetk ) - mpi? ( !python ) - python? ( tools fetk iapbs ${PYTHON_REQUIRED_USE} )" - -RDEPEND=" - dev-cpp/eigen:3 - dev-libs/maloc[mpi=] - sys-libs/readline - virtual/blas - fetk? ( - sci-libs/amd - sci-libs/fetk - sci-libs/superlu - sci-libs/umfpack - ) - mpi? ( virtual/mpi ) - python? ( ${PYTHON_DEPS} ) -" -DEPEND="${RDEPEND} - virtual/pkgconfig - doc? ( app-doc/doxygen ) -" - -S="${WORKDIR}"/${PN}-pdb2pqr-${COMMIT}/${PN} - -PATCHES=( - "${FILESDIR}"/${P}-multilib.patch - "${FILESDIR}"/${P}-manip.patch - "${FILESDIR}"/${P}-python.patch -) - -src_prepare() { - cmake-utils_src_prepare - append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) - - sed \ - -e "s:-lblas:$($(tc-getPKG_CONFIG) --libs blas):g" \ - -e "/TOOLS_PATH/d" \ - -i CMakeLists.txt || die - use doc && MAKEOPTS+=" -j1" - if use python; then - unset PATCHES || die - cd tools/python || die - distutils-r1_src_prepare - fi -} - -src_configure() { - local mycmakeargs=( - -DCMAKE_SKIP_RPATH=ON - -DTOOLS_PATH="${ED%/}"/usr - -DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir) - -DLIBRARY_INSTALL_PATH=$(get_libdir) - -DFETK_PATH="${EPREFIX}"/usr/ - -DBUILD_SHARED_LIBS=ON - -DENABLE_QUIT=OFF - -DBUILD_DOC=$(usex doc) - -DBUILD_TOOLS=$(usex tools) - -DENABLE_BEM=OFF -# ENABLE_BEM: Boundary element method using TABIPB - -DENABLE_DEBUG=$(usex debug) - -DENABLE_VERBOSE_DEBUG=$(usex debug) - -DENABLE_FAST=$(usex fast) - -DENABLE_FETK=$(usex fetk) - -DENABLE_MPI=$(usex mpi) - -DENABLE_PYTHON=$(usex python) -# ENABLE_TINKER: Enable TINKER support - -DENABLE_iAPBS=$(usex iapbs) -# MAX_MEMORY: Set the maximum memory (in MB) to be used for a job - ) - cmake-utils_src_configure - if use python; then - cd tools/python || die - distutils-r1_src_configure - fi -} - -src_compile() { - cmake-utils_src_compile - if use python; then - append-ldflags -L"${S}"/lib - cd tools/python || die - distutils-r1_src_compile - fi -} - -src_test() { - python_setup - cd tests || die - LD_LIBRARY_PATH="${S}"/lib "${PYTHON}" apbs_tester.py -l log || die - grep -q 'FAILED' log && die "Tests failed" -} - -src_install() { - dodir /usr/bin - cmake-utils_src_install - local i - for i in "${ED}"/usr/bin/*; do - if [[ ! "${i}" =~ .*apbs$ ]]; then - mv "${i}" "${i}-apbs" || die - fi - done - if use python; then - cd tools/python || die - distutils-r1_src_install - rm -rf "${ED}"/usr/share/apbs/tools/python || die - fi -} diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch deleted file mode 100644 index 090a27d8a5a6..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch +++ /dev/null @@ -1,50 +0,0 @@ - apbs/CMakeLists.txt | 2 +- - apbs/tools/CMakeLists.txt | 4 ---- - apbs/tools/mesh/CMakeLists.txt | 4 ++-- - 4 files changed, 5 insertions(+), 9 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 8917fc4..5152008 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -293,7 +293,7 @@ option(ENABLE_FETK "Enable the finite element solver" OFF) - - if(ENABLE_FETK) - message(STATUS "Checking for fetk components") -- set(FETK_ENALBED 1) -+ set(FETK_ENABLED 1) - - list(APPEND APBS_LIBS "-lstdc++") - list(APPEND APBS_LIBS "-L${FETK_PATH}/lib") -diff --git a/tools/manip/CMakeLists.txt b/tools/manip/CMakeLists.txt -index 937dac7..5768cc5 100644 ---- a/tools/manip/CMakeLists.txt -+++ b/tools/manip/CMakeLists.txt -@@ -4,9 +4,9 @@ set(LIBS "") - list(APPEND LIBS "apbs_generic") - list(APPEND LIBS "apbs_mg") - list(APPEND LIBS "apbs_pmgc") --if(FETK_ENALBED) -+if(FETK_ENABLED) - list(APPEND LIBS "apbs_fem") --endif(FETK_ENALBED) -+endif(FETK_ENABLED) - - message(STATUS "libraries: ${LIBS}") - -diff --git a/tools/mesh/CMakeLists.txt b/tools/mesh/CMakeLists.txt -index 1406377..6e6dfb9 100644 ---- a/tools/mesh/CMakeLists.txt -+++ b/tools/mesh/CMakeLists.txt -@@ -4,9 +4,9 @@ set(LIBS "") - list(APPEND LIBS "apbs_generic") - list(APPEND LIBS "apbs_mg") - list(APPEND LIBS "apbs_pmgc") --if(FETK_ENALBED) -+if(FETK_ENABLED) - list(APPEND LIBS "apbs_fem") --endif(FETK_ENALBED) -+endif(FETK_ENABLED) - - message(STATUS "libraries: ${LIBS}") - diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch b/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch deleted file mode 100644 index a4e2d1761cf4..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch +++ /dev/null @@ -1,92 +0,0 @@ - CMakeLists.txt | 18 +++++++++--------- - src/CMakeLists.txt | 1 - - src/fem/CMakeLists.txt | 2 +- - src/pmgc/CMakeLists.txt | 2 +- - 4 files changed, 11 insertions(+), 12 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 75ddbdd..c46f5e7 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -61,7 +61,7 @@ set(LIBRARY_OUTPUT_PATH ${APBS_ROOT}/lib) - set(TOOLS_PATH ${APBS_ROOT}/tools) - set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs) - --set(LIBRARY_INSTALL_PATH lib) -+set(LIBRARY_INSTALL_PATH ${CMAKE_INSTALL_LIBDIR}) - set(HEADER_INSTALL_PATH include/apbs) - set(EXECUTABLE_INSTALL_PATH bin) - set(SHARE_INSTALL_PATH share/apbs) -@@ -93,8 +93,6 @@ set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}") - list(APPEND CMAKE_INCLUDE_PATH /usr/include) - list(APPEND CMAKE_INCLUDE_PATH /usr/local/include) - --set(APBS_LIBS "-L${APBS_ROOT}/lib -lapbs_geoflow") -- - ################################################################################ - # Enable ansi pedantic compiling # - ################################################################################ -@@ -193,9 +191,11 @@ if(ENABLE_BEM) - else() - set(TABI_LIBRARY_BASENAME ${CMAKE_STATIC_LIBRARY_PREFIX}${TABI}${CMAKE_STATIC_LIBRARY_SUFFIX}) - endif() -- -+ -+ file(GLOB MODS ${LIBRARY_OUTPUT_PATH}/*.mod) -+ - install( -- FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${LIBRARY_OUTPUT_PATH}/*.mod -+ FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${MODS} - DESTINATION ${LIBRARY_INSTALL_PATH} - ) - set(TABI_LIBRARY ${APBS_ROOT}/${LIBRARY_INSTALL_PATH}/${TABI_LIBRARY_BASENAME}) -@@ -210,7 +210,7 @@ if(ENABLE_BEM) - endif() - get_filename_component(LIBGFORTRANPATH ${LIBGFORTRANPATH} PATH) - find_path(LIBGFORTRAN_PATH ${LIBGFORTRAN_NAME} PATH ${LIBGFORTRANPATH}) -- list(APPEND APBS_LIBS "-L${APBS_ROOT}/${LIBRARY_INSTALL_PATH} -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" ) -+ list(APPEND APBS_LIBS "-L${APBS_ROOT}/lib -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" ) - endif() # ENABLE_BEM - - find_file( # this should be find path... -@@ -228,7 +228,7 @@ endif() - - - find_library(MALOC_LIBRARY "maloc" -- PATHS ${FETK_PATH}/lib ${CONTRIB_PATH} -+ PATHS ${FETK_PATH}/${CMAKE_INSTALL_LIBDIR} ${CONTRIB_PATH} - DOC "The fetk/maloc library" - ) - if(MALOC_LIBRARY) -@@ -296,9 +296,9 @@ if(ENABLE_FETK) - set(FETK_ENALBED 1) - - list(APPEND APBS_LIBS "-lstdc++") -- list(APPEND APBS_LIBS "-L${FETK_PATH}/lib") -+ list(APPEND APBS_LIBS "-L${FETK_PATH}/${CMAKE_INSTALL_LIBDIR}") - list(APPEND APBS_LIBS -lamd -lpunc -lmc -lgamer -lsuperlu -lumfpack ---lblas -lvf2c -ltetgen -ltriangle -lg2c -lreadline ) -+-lblas -lvf2c -ltetgen -ltriangle -lreadline ) - - SET(HAVE_MC_H YES) - endif() -diff --git a/src/fem/CMakeLists.txt b/src/fem/CMakeLists.txt -index 5a950c2..dc37f48 100644 ---- a/src/fem/CMakeLists.txt -+++ b/src/fem/CMakeLists.txt -@@ -12,4 +12,4 @@ add_items( - vpee.h - ) - --add_sublibrary(fem) -+add_sublibrary(fem apbs_geoflow) -diff --git a/src/pmgc/CMakeLists.txt b/src/pmgc/CMakeLists.txt -index 85b0c1e..97c95f0 100644 ---- a/src/pmgc/CMakeLists.txt -+++ b/src/pmgc/CMakeLists.txt -@@ -42,4 +42,4 @@ add_items( - mgfasd.h - ) - --add_sublibrary(pmgc) -+add_sublibrary(pmgc apbs_geoflow) diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch deleted file mode 100644 index 5ad6613615f2..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch +++ /dev/null @@ -1,122 +0,0 @@ - apbs/contrib/iapbs/src/apbs_driver.c | 6 +++--- - apbs/src/CMakeLists.txt | 1 + - apbs/tools/CMakeLists.txt | 2 +- - apbs/tools/python/CMakeLists.txt | 1 + - apbs/tools/python/apbslib.c | 4 ++-- - apbs/tools/python/apbslib.i | 4 ++-- - apbs/tools/python/setup.py | 16 ++++++++++++++++ - 7 files changed, 26 insertions(+), 8 deletions(-) - -diff --git a/contrib/iapbs/src/apbs_driver.c b/contrib/iapbs/src/apbs_driver.c -index c9e443b..e1ad67f 100644 ---- a/contrib/iapbs/src/apbs_driver.c -+++ b/contrib/iapbs/src/apbs_driver.c -@@ -595,7 +595,7 @@ int apbsdrv_( - printPBEPARM(pbeparm); - - /* Refine mesh */ -- if (!preRefineFE(i, nosh, feparm, fetk)) { -+ if (!preRefineFE(i, feparm, fetk)) { - Vnm_tprint( 2, "Error pre-refining mesh!\n"); - VJMPERR1(0); - } -@@ -609,7 +609,7 @@ int apbsdrv_( - Vnm_tprint(1, " Beginning solve-estimate-refine cycle:\n"); - for (isolve=0; isolve<feparm->maxsolve; isolve++) { - Vnm_tprint(1, " Solve #%d...\n", isolve); -- if (!solveFE(i, nosh, pbeparm, feparm, fetk)) { -+ if (!solveFE(i, pbeparm, feparm, fetk)) { - Vnm_tprint(2, "ERROR SOLVING EQUATION!\n"); - VJMPERR1(0); - } -@@ -622,7 +622,7 @@ int apbsdrv_( - /* We're not going to refine if we've hit the max number - * of solves */ - if (isolve < (feparm->maxsolve)-1) { -- if (!postRefineFE(i, nosh, feparm, fetk)) break; -+ if (!postRefineFE(i, feparm, fetk)) break; - } - bytesTotal = Vmem_bytesTotal(); - highWater = Vmem_highWaterTotal(); -diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt -index 44d20fa..2577343 100644 ---- a/src/CMakeLists.txt -+++ b/src/CMakeLists.txt -@@ -68,6 +68,7 @@ configure_file( - - if(ENABLE_iAPBS) - ADD_LIBRARY(apbs_routines routines.c routines.h) -+ target_link_libraries(apbs_routines apbs_mg apbs_fem) - INSTALL(TARGETS apbs_routines DESTINATION ${LIBRARY_INSTALL_PATH}) - INSTALL(FILES apbscfg.h DESTINATION ${HEADER_INSTALL_PATH}) - endif() -diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt -index 1982a3c..4acbe68 100644 ---- a/tools/CMakeLists.txt -+++ b/tools/CMakeLists.txt -@@ -4,5 +4,5 @@ add_subdirectory(mesh) - add_subdirectory(manip) - - if(ENABLE_PYTHON) -- add_subdirectory(manip) -+ add_subdirectory(python) - endif(ENABLE_PYTHON) -diff --git a/tools/python/CMakeLists.txt b/tools/python/CMakeLists.txt -new file mode 100644 -index 0000000..8b13789 ---- /dev/null -+++ b/tools/python/CMakeLists.txt -@@ -0,0 +1 @@ -+ -diff --git a/tools/python/apbslib.c b/tools/python/apbslib.c -index fef5cc8..feaaa2c 100644 ---- a/tools/python/apbslib.c -+++ b/tools/python/apbslib.c -@@ -2504,8 +2504,8 @@ static swig_module_info swig_module = {swig_types, 24, 0, 0, 0, 0}; - #include "maloc/maloc.h" - #include "apbscfg.h" - #include "routines.h" --#include "apbs/valist.h" --#include "apbs/vatom.h" -+#include "generic/valist.h" -+#include "generic/vatom.h" - - - #include <limits.h> -diff --git a/tools/python/apbslib.i b/tools/python/apbslib.i -index 17fe521..44d05ea 100644 ---- a/tools/python/apbslib.i -+++ b/tools/python/apbslib.i -@@ -15,8 +15,8 @@ Header files: - #include "maloc/maloc.h" - #include "apbscfg.h" - #include "routines.h" --#include "apbs/valist.h" --#include "apbs/vatom.h" -+#include "generic/valist.h" -+#include "generic/vatom.h" - %} - - /* -diff --git a/tools/python/setup.py b/tools/python/setup.py -new file mode 100644 -index 0000000..4a20198 ---- /dev/null -+++ b/tools/python/setup.py -@@ -0,0 +1,16 @@ -+from distutils.core import setup, Extension -+setup(name='apbs', -+ version='1.4.1', -+ package_dir={'apbs': '', 'vgrid': 'vgrid'}, -+ packages=['apbs', 'vgrid'], -+ py_modules=['apbslib', 'main', 'noinput'], -+ ext_modules=[ -+ Extension( -+ '_apbslib', -+ ['apbslib.i'], -+ swig_opts=['-module', 'apbslib', '-I../include'], -+ include_dirs=["../../src"], -+ libraries=["apbs_generic", "apbs_routines"] -+ ) -+ ], -+ ) diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml deleted file mode 100644 index a33a5468d19c..000000000000 --- a/sci-chemistry/apbs/metadata.xml +++ /dev/null @@ -1,25 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <use> - <flag name="fetk">Include support for FeTK</flag> - <flag name="fast">APBS fast mode (experimental)</flag> - <flag name="iapbs">C/C++/Fortran interface</flag> - <flag name="tools">Install optional tools</flag> - </use> - <longdescription> -APBS is a software package for modeling biomolecular solvation through solution -of the Poisson-Boltzmann equation (PBE), one of the most popular continuum -models for describing electrostatic interactions between molecular solutes in -salty, aqueous media. Continuum electrostatics plays an important role in -several areas of biomolecular simulation - </longdescription> - <upstream> - <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id> - <remote-id type="sourceforge">apbs</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/bkchem/Manifest b/sci-chemistry/bkchem/Manifest deleted file mode 100644 index db9b3239f21c..000000000000 --- a/sci-chemistry/bkchem/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -AUX bkchem-0.14.0_pre2-nolauncher.patch 2967 BLAKE2B 0953c3c969bb2955f13de81db84eef2f24d6a3999b1f9e8d3ed837cf04718386eb44a2141f55f1775339856698d1c5242564177e998203110776128b7bfde87b SHA512 dbd7b8eef583c3b64dfc1755a3b5eae5eb8ab222454936636147de64e021166e29f915655f1acf2d7252983bf4873dc8f2fb69ca58b56955ab1ce07e8ec82789 -DIST bkchem-0.14.0-pre2.tar.gz 998916 BLAKE2B 07c01abb31325c3721cc478438c1b34f156bc589a186eeedd62b6ac058f8ec64b1ea86a3c25bb6ab8045e0aaa838f10c5d16b68516fdea5607795b64fb4c39bb SHA512 7fc3bbd7bfe27bc91cf69a98c347a3fb92f4ea25b45a13debd0646a6b02d7a40c5729ae1b2a9ac33c1049d6b90e38355c3cd80e06660a0a2fcc5dafb3514ef20 -EBUILD bkchem-0.14.0_pre2-r2.ebuild 888 BLAKE2B 68092928e3c841dcb59ffa485c0ab356116f69d24ffdb58d0e11140e3eaff2034dcf79981f386f08e73dd6e074c2789c75ce08899dad3caa81f4005dc726ddb3 SHA512 f6505dde2dee31398bfc5be9999e8f47313ac7fa2f477ec0dc8f425d25ee2fb0f8998f350f42d511cb6dcc16545c3e8030e164b9c1046d25c31080dba2413bf2 -MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r2.ebuild b/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r2.ebuild deleted file mode 100644 index d6162080214b..000000000000 --- a/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r2.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -PYTHON_REQ_USE="tk" - -inherit distutils-r1 eutils versionator - -MY_P="${PN}-$(replace_version_separator 3 -)" - -DESCRIPTION="Chemical drawing program" -HOMEPAGE="http://bkchem.zirael.org/" -SRC_URI="http://bkchem.zirael.org/download/${MY_P}.tar.gz" - -SLOT="0" -KEYWORDS="~amd64 ~x86" -LICENSE="GPL-2" -IUSE="cairo" - -DEPEND="cairo? ( dev-python/pycairo[${PYTHON_USEDEP}] )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/${MY_P} - -PATCHES=( - "${FILESDIR}"/${P}-nolauncher.patch -) - -python_install() { - distutils-r1_python_install "--strip=${ED}/_${EPYTHON}" -} - -python_install_all() { - distutils-r1_python_install_all - python_foreach_impl python_newscript ${PN}/${PN}.py ${PN} - make_desktop_entry bkchem BKChem "${EPREFIX}"/usr/share/${PN}/images/${PN}.png Science -} diff --git a/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch b/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch deleted file mode 100644 index 202c47a9c74f..000000000000 --- a/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch +++ /dev/null @@ -1,106 +0,0 @@ - bkchem/bkchem.py | 24 +++++++++++++----------- - setup.py | 23 ----------------------- - 2 files changed, 13 insertions(+), 34 deletions(-) - -diff --git a/bkchem/bkchem.py b/bkchem/bkchem.py -index b336b9c..bcb68b0 100644 ---- a/bkchem/bkchem.py -+++ b/bkchem/bkchem.py -@@ -1,3 +1,4 @@ -+#!/usr/bin/env python2 - #-------------------------------------------------------------------------- - # This file is part of BKChem - a chemical drawing program - # Copyright (C) 2002-2009 Beda Kosata <beda@zirael.org> -@@ -18,18 +19,19 @@ - #-------------------------------------------------------------------------- - - --"""this is just a starter of the application""" -+#"""this is just a starter of the application""" - - ## support for loading from outside of bkchem dir - --import os_support, sys -+from bkchem import os_support -+import sys - sys.path.insert( 1, os_support.get_module_path()) - - - ### now starting for real - --from singleton_store import Store --import pref_manager -+from bkchem.singleton_store import Store -+from bkchem import pref_manager - - # at first preference manager - Store.pm = pref_manager.pref_manager( -@@ -78,13 +80,13 @@ else: - - - --import config -+from bkchem import config - - if not config.debug: - # checking of important modules availability - # import modules -- import import_checker -- import messages -+ from bkchem import import_checker -+ from bkchem import messages - - # we need sets from the 2.3 version - if not import_checker.python_version_ok: -@@ -103,16 +105,16 @@ if not config.debug: - - - #import Tkinter --from main import BKChem --from splash import Splash --from singleton_store import Store -+from bkchem.main import BKChem -+from bkchem.splash import Splash -+from bkchem.singleton_store import Store - - myapp = BKChem() - myapp.withdraw() - - if __name__ == '__main__': - -- import messages -+ from bkchem import messages - enc = sys.getfilesystemencoding() - if not enc: - enc = sys.getdefaultencoding() -diff --git a/setup.py b/setup.py -index d4b2a21..2319216 100755 ---- a/setup.py -+++ b/setup.py -@@ -91,26 +91,3 @@ if len( sys.argv) > 1 and sys.argv[1] == 'install' and '--help' not in sys.argv: - print "file %s created" % config_name - - -- # the executable -- if not os.path.isdir( bin_dir): -- try: -- os.mkdir( bin_dir) -- except: -- print "ERROR: could not create directory %s" % bin_dir -- sys.exit( 201) -- exec_name = os.path.join( bin_dir, 'bkchem') -- try: -- file = open( exec_name, 'w') -- except: -- print "ERROR: couldn't open the file %s for write" % exec_name -- sys.exit( 201) -- file.write( "#!/bin/sh\n") -- file.write( 'python %s "$@"\n' % strip_path( os.path.join( py_dir, "bkchem", "bkchem.py"))) -- file.close() -- print "file %s created" % exec_name -- try: -- os.chmod( os.path.join( bin_dir, 'bkchem'), 5+5*8+7*8*8) -- except: -- print "ERROR: failed to make %s executable" % exec_name -- sys.exit( 201) -- print "file %s made executable" % exec_name diff --git a/sci-chemistry/bkchem/metadata.xml b/sci-chemistry/bkchem/metadata.xml deleted file mode 100644 index 8937bad0b175..000000000000 --- a/sci-chemistry/bkchem/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest index e0cd183bc7e8..446ce0b434b9 100644 --- a/sci-chemistry/chemex/Manifest +++ b/sci-chemistry/chemex/Manifest @@ -1,8 +1,6 @@ AUX chemex-2018.10.2-tests-package.patch 418 BLAKE2B 7547e44f73bba8f48dda46e1867cff75a4343b26732b59b011470a7a8143bc0b17c7a7f87d97672239b679406fc54662d68f04e2b1548adddd723ecced954205 SHA512 5e3c58ab4ba271672381308177c462e0813a2e43ced602090b527d99be3e3f38f53f822cfe62ed8f841a16f4c04a933f4ed08d2e71c04777745298e3354bfb4a -DIST chemex-0.6.1.tar.gz 1449216 BLAKE2B 6b7f7597b09cd43b9bec89b6359d1f650fdd7d4f3a373e706da80dafaf438417458f34af6bc378442b5b4a84cb8222103ebc8026c85583e8dece3fad0dc77204 SHA512 40f538ef9c162759c7a6863886da8d46746ac362fc19154f0a5f3dd8703f7fea7397c3f34092c86dbce486c452e0d3b09a76e4c11ae119834d7ca4912e7f3fdf DIST chemex-2018.10.2.tar.gz 546575 BLAKE2B c36ae3bc152459844633276ab286b6f750ed5b2538c4289ceb75de9a081ad74fe346a79357fd6fc2f8972722b3520473262c4d623e46d6a4b30395962164a51f SHA512 f8ed017c0881ea9188e150456827e2c6302bdfe546c8058bd0261e43d941fbd1ac9e6abf1621d82107a4f6bd4e9aa4bc70c46e42dc98eabf2dba45a4fa78f77e DIST chemex-2018.10.3.tar.gz 546696 BLAKE2B d283cfb94118686f1974780249641e0ea6f86cdb854c4a256897e361a300a94506813a5035ee2f300fca13263e8452b77e7a0817436cbd620ba16d801a541af7 SHA512 784bd03b354724d6aa52d663c6f661f865d4ef7ca345573bc8aae9ef63e5dbb3e65abba364de3ff441b78adfa588344c718809c5880b3fc70d8ed24be06a0826 -EBUILD chemex-0.6.1-r3.ebuild 1037 BLAKE2B 8d1d5ed8e4aea24247816a7db54644e421e720cc86e469abc62b3f0c61ad1b3178ecd6ab6318d0419f1e6d27796526f42c68f95574d65594c681142f64f71cd9 SHA512 5d0b85517336e7c47de49a0f5cc061c4eb46e6b6f02eff6d964e467cef78d19077635140d0150ad3cec698d5e98d1fae4abebcce834e1b31b485fe3b52efa75e EBUILD chemex-2018.10.2.ebuild 1155 BLAKE2B caf445596bf98c1b0fccaf1c894c23937fb2087d149254ff07bf1cd4d4c47acd4526f733f6c86739cb6206a73bf98b9b8f34fc074ed9d7d3f5ddb0551c34d8bc SHA512 c330644a70739efd68293d0cb9295bd3bae0635747fd402ab1b9ebd1d18e239f88eeadd95209e2cd660c0d1151e31c7d4bbfea9ed3493888360fcec57f287724 EBUILD chemex-2018.10.3.ebuild 1051 BLAKE2B b021e1ccff297a6cee7aa940e45c64b8067c109ac2f9c2d03825ee9ce86a7f4d215111ad0c8a66877d13f224cd6bba7bb781caf86903d7dab27e6df3f8dce048 SHA512 7eb418b6d8443cada7146755fe011862d90e0c5d2085ed6b565dea1fba530bcff6464261e8e73eeeb5e09d354b84e41e717c40a81d84a18c7fa84fcd01a1a0e3 MISC metadata.xml 216 BLAKE2B 0fbfa16661345362ff89f87adc0bb42fc5f5c9145cdedb36f3f537b39af4023b91c4dfb0d8e83a4f9ac963141f594ba8ae678371c338d992a96e02c11fd84195 SHA512 628a69805356b7458edaa2297901224178b016477a937f77e692a78ce3e7a0b6d2d7b4c4b7e70d0185d7112e6a59a5131e07d8c950e90b9c8722471d7511afc6 diff --git a/sci-chemistry/chemex/chemex-0.6.1-r3.ebuild b/sci-chemistry/chemex/chemex-0.6.1-r3.ebuild deleted file mode 100644 index c6facbd71020..000000000000 --- a/sci-chemistry/chemex/chemex-0.6.1-r3.ebuild +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 -DISTUTILS_SINGLE_IMPL="yes" -PYTHON_COMPAT=( python2_7 ) - -inherit distutils-r1 - -DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data" -HOMEPAGE="https://github.com/gbouvignies/chemex" -SRC_URI="https://github.com/gbouvignies/chemex/archive/${PV}.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64" -IUSE="" - -RDEPEND=" - $(python_gen_cond_dep ' - || ( - >=dev-python/matplotlib-python2-1.1[${PYTHON_MULTI_USEDEP}] - >=dev-python/matplotlib-1.1[${PYTHON_MULTI_USEDEP}] - ) - || ( - dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}] - dev-python/numpy[${PYTHON_MULTI_USEDEP}] - ) - || ( - >=sci-libs/scipy-python2-0.11[${PYTHON_MULTI_USEDEP}] - >=sci-libs/scipy-0.11[${PYTHON_MULTI_USEDEP}] - ) - ') -" -DEPEND="${RDEPEND}" - -src_prepare() { - # Fix quotes to detect the version properly - sed -i -e 's/matplotlib>=1.3.1/matplotlib>="1.3.1"/' setup.py || die - distutils-r1_python_prepare_all -} diff --git a/sci-chemistry/eden/Manifest b/sci-chemistry/eden/Manifest deleted file mode 100644 index 18b6162cbafa..000000000000 --- a/sci-chemistry/eden/Manifest +++ /dev/null @@ -1,7 +0,0 @@ -AUX 5.3-makefile-fixes.patch 1647 BLAKE2B ead9023a9ae4c2a94a22de4ff5ef97f89b7602e914ebcc0a3295eb53a3cdf25639d9c8d74b14b9f75f2c5009812b8a23afd51432accfa2daec80484e4b5c4a49 SHA512 3ec4f8ba8d3b600b729bfb32cef3fb1f82a1f51a485ebab143e01052ea1487a78c3395c902079fe0e5d5c3df8a2a83b2ce4d37d823e1d89426087874ec47391d -AUX eden-5.3-format-security.patch 3202 BLAKE2B a548dbb384d497a07806bcf9e25141d07a75a0381802b080eec02f14b6018e66c7d5b2a4c0caefc679d43736e15c4b00e460a82e3d40e65188a364d28469bde3 SHA512 01e100fe5481a73de2efa6652fe38c19337eae0dc13557ef0ad3e3a4f186becbfb8831aece0a619c08541e1a667e999c47b28438ec431f056c44f12849662c12 -AUX eden-5.3-impl-dec.patch 899 BLAKE2B 667a43677ff28192277ad3e259aa093ca03a05aa55bde0a175885823d2e48ddc64989c72e2c47884ff22c840addd87df9ea5925eeb6f20397be403f0e92cf44e SHA512 e89f1e0c028099e305a79befa558a86bc47d050c1e30394178999c7a1568bae9c3e525953bf152888690e0e1607dd72c522d2995f45b1eccfb9f7bf75e7866c2 -AUX makefile-fixes.patch 837 BLAKE2B fc20ba8c98e333b90bc3e028d572810fabe6305ec929a52aab5c4491b80fd370a604729ae29b22d078e872693fcab3e7d84f82524f29c09be74c8b41c128ec2f SHA512 818fe1d23fa940cb533afcb9e84bdc5c719651005136304ca66d368fc21cf4d7a1facb0a383c9689ab1658632cec30969322fdffccadae941a754900542237e7 -DIST eden_V5.3.tar.gz 1139981 BLAKE2B 237f054accbba72fcde3a43716915a8037412a26aee861839c4a6e404276126a3955e6e0a3c76078b2253658f3ab9bcf8ad628bba059421c5171d0394c41052b SHA512 c59d08004bdb72ef39fe205aef546fbcff9c57ee42942c0391052de9c501c7793ed3bd280569020c2b9ec6133a87362d184a2012b61c6be18b5f6ba9b59716c5 -EBUILD eden-5.3-r2.ebuild 1845 BLAKE2B c6b996398a511372ca4f8cec15d923056997747fc8c0bb37c1b88c57dc794d4aa304eca0bbfafc1d3d740d9f7534202da9113871c32f8d9a2adfe1f444971819 SHA512 5de7c7da62d7819ee74c8983ba5f222853995d9fae865a7a0802c7ee583f3406d6dbbdc335b3ad60c138d5642d6eb3df683c7a6f26ab91afd39707b63b1579a0 -MISC metadata.xml 383 BLAKE2B daa13ce13128bd1cd96fd95b063788d796bab9a455b7e552abfb76f2ce62369a3eaced99a7b53f248d99289774cfb8ff45b0848e759f3a2e6f89122f1e214141 SHA512 e23cc36f53622230ac9c70cb886cd9812e4bfefba8c0912059b3f072e063c235ba52cce893ea3b49ba05dda047097ba505c4ce5c53248d5acf720f16e123be84 diff --git a/sci-chemistry/eden/eden-5.3-r2.ebuild b/sci-chemistry/eden/eden-5.3-r2.ebuild deleted file mode 100644 index 8bf667224ba8..000000000000 --- a/sci-chemistry/eden/eden-5.3-r2.ebuild +++ /dev/null @@ -1,88 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils multilib python-r1 toolchain-funcs - -MY_P="${PN}_V${PV}" - -DESCRIPTION="A crystallographic real-space electron-density refinement & optimization program" -HOMEPAGE="http://www.gromacs.org/pipermail/eden-users/" -SRC_URI="mirror://gentoo/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="double-precision" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - sci-libs/fftw:2.1 - sci-libs/gsl - ${PYTHON_DEPS}" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -S="${WORKDIR}/${PN}" - -SRC="${S}/source" - -pkg_setup() { - export EDENHOME="${EPREFIX}/usr/$(get_libdir)/${PN}" -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${PV}-makefile-fixes.patch \ - "${FILESDIR}"/${P}-impl-dec.patch \ - "${FILESDIR}"/${P}-format-security.patch - - sed -i \ - -e "s:^\(FFTW.*=\).*:\1 ${EPREFIX}/usr:g" \ - -e "s:^\(LIB.*=.*\$(FFTW)/\).*:\1$(get_libdir):g" \ - -e "s:^\(BIN.*=\).*:\1 ${D}usr/bin:g" \ - -e "s:^\(CFLAGS.*=\).*:\1 ${CFLAGS}:g" \ - -e "s:-lgsl -lgslcblas:$($(tc-getPKG_CONFIG) --libs gsl):g" \ - ${SRC}/Makefile || die - - if ! use double-precision; then - sed -i -e "s:^\(DOUBLESWITCH.*=\).*:\1 OFF:g" ${SRC}/Makefile || die - EDEN_EXE="s${PN}" - else - EDEN_EXE="d${PN}" - fi -} - -src_compile() { - emake CC=$(tc-getCC) -C ${SRC} -} - -src_install() { - emake -C ${SRC} install - - python_foreach_impl python_newscript python/${PN}.py i${PN} - python_foreach_impl python_domodule python/FileListDialog.py - - rm python/*py || die - insinto ${EDENHOME}/python - doins python/* - - insinto ${EDENHOME}/help - doins help/* - - insinto ${EDENHOME}/tools - doins tools/* - - dodoc manual/UserManual.pdf - - cat >> "${T}"/60${PN} <<- EOF - EDENHOME="${EDENHOME}" - EOF - - doenvd "${T}"/60${PN} - - dosym ${EDEN_EXE} /usr/bin/${PN} -} diff --git a/sci-chemistry/eden/files/5.3-makefile-fixes.patch b/sci-chemistry/eden/files/5.3-makefile-fixes.patch deleted file mode 100644 index 632358341784..000000000000 --- a/sci-chemistry/eden/files/5.3-makefile-fixes.patch +++ /dev/null @@ -1,60 +0,0 @@ - source/Makefile | 17 ++++++++++------- - 1 files changed, 10 insertions(+), 7 deletions(-) - -diff --git a/source/Makefile b/source/Makefile -index 46d89cc..aa751c7 100644 ---- a/source/Makefile -+++ b/source/Makefile -@@ -78,8 +78,10 @@ CFLAGS = -Wall -pipe -g3 - #CFLAGS = -Wall -pipe -marchi686 -pedantic -gdwarf-2 -g3 - #CFLAGS = -Wall -O3 -march=i686 - ifneq ($(FFTW),/usr/local) -+ifneq ($(FFTW),/usr) - CFLAGS += -I$(INC) - endif -+endif - - # NOTE: - # DOUBLESWITCH = ON for double precision; -@@ -91,15 +93,15 @@ endif - DOUBLESWITCH = ON - - ifeq ($(DOUBLESWITCH),ON) --LDFLAGS = -L$(LIB) -ldfftw -lm -+LIBS = -L$(LIB) -ldfftw -lm - CFLAGS += -DDOUBLE - TARGET = deden - else --LDFLAGS = -L$(LIB) -lsfftw -lm -+LIBS = -L$(LIB) -lsfftw -lm - TARGET = seden - endif - --LDFLAGS += -g -lgsl -lgslcblas -+LIBS += -lgsl -lgslcblas - - # GSL_PREFIX:= /sw/lib - # LDFLAGS += -l$(GSL_PREFIX)/libgsl.a -l$(GSL_PREFIX)/libgslcblas.a -@@ -120,17 +122,18 @@ OBJ = addmaps.o apodfc.o apodfo.o back.o cadhkl.o \ - all: eden fbyteswap - - eden: eden.o $(OBJ) -- $(CC) $^ $(LDFLAGS) -o $@ -+ $(CC) $(LDFLAGS) -o $@ $^ $(LIBS) - - fbyteswap: fbyteswap.c -- $(CC) -o $@ $^ -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) - - install: all -+ mkdir -p $(BIN) - mv fbyteswap $(BIN) - mv eden $(BIN)/$(TARGET) - chmod 751 $(BIN)/$(TARGET) -- chmod +x mkeden.csh -- ./mkeden.csh $(BIN) $(BIN)/$(TARGET) -+# chmod +x mkeden.csh -+# ./mkeden.csh $(BIN) $(BIN)/$(TARGET) - - dist: clean - cd ../..; tar -cvf eden_$(VERSION).tar --exclude CVS --exclude \#\*\# --exclude \*~ --exclude Misc --exclude .\* eden; gzip -f eden_$(VERSION).tar diff --git a/sci-chemistry/eden/files/eden-5.3-format-security.patch b/sci-chemistry/eden/files/eden-5.3-format-security.patch deleted file mode 100644 index 04b5ecfddebb..000000000000 --- a/sci-chemistry/eden/files/eden-5.3-format-security.patch +++ /dev/null @@ -1,96 +0,0 @@ - source/back.c | 2 +- - source/concosts.c | 4 ++-- - source/count.c | 4 ++-- - source/eden.c | 2 +- - source/util.c | 4 ++-- - 5 files changed, 8 insertions(+), 8 deletions(-) - -diff --git a/source/back.c b/source/back.c -index fd517b9..185a02b 100644 ---- a/source/back.c -+++ b/source/back.c -@@ -112,7 +112,7 @@ void back_main(int argc, char *argv[]) - ballpark(caller) ; - - if (argc > optind+2) -- sprintf(sf_filename, argv[optind+2]) ; -+ sprintf(sf_filename, "%s", argv[optind+2]) ; - - /********************************************* - Pull off prefix defining whereabouts of input -diff --git a/source/concosts.c b/source/concosts.c -index d62d2e3..590f073 100644 ---- a/source/concosts.c -+++ b/source/concosts.c -@@ -452,7 +452,7 @@ void prepare_singlets(char *filename) - sprintf(message, - "s=%d, p=%d, n=%d, phase=%g, old phase=%g, delta=%g\n", - s, p, n, phase, *(checks+n), phase-*(checks+n)) ; -- fprintf(fp_log, message) ; -+ fprintf(fp_log, "%s", message) ; - } - } - /*********************************************** -@@ -556,7 +556,7 @@ void prepare_triplets(char *filename) - sprintf(message, - "Triplet (%d %d %d) from input (%d %d %d) corresponds to point w/o fobs info!\n", - newh, newk, newl, t_h[q], t_k[q], t_l[q]) ; -- fprintf(fp_log, message) ; -+ fprintf(fp_log, "%s", message) ; - legal_triplet = FALSE ; - } - } -diff --git a/source/count.c b/source/count.c -index c3bc390..ca13008 100644 ---- a/source/count.c -+++ b/source/count.c -@@ -460,12 +460,12 @@ void print_el_count(char *filename, - } - - sprintf(message, "\nTotal no. of electrons is %g\n", totnump*volvox) ; -- fprintf(fp, message) ; -+ fprintf(fp, "%s", message) ; - printTwice(message) ; - - sprintf(message, "Count of all remaining electrons: %g %g %g\n", - remainder0*volvox, remainder1*volvox, remainder2*volvox) ; -- fprintf(fp, message) ; -+ fprintf(fp, "%s", message) ; - printTwice(message) ; - - fclose(fp) ; -diff --git a/source/eden.c b/source/eden.c -index dea3246..5a9b389 100644 ---- a/source/eden.c -+++ b/source/eden.c -@@ -319,7 +319,7 @@ int main(int argc, char *argv[]) - - get_unique_logname() ; - -- sprintf(command_line, argv[0]) ; -+ sprintf(command_line, "%s", argv[0]) ; - - for (k = 1; k < argc; k++) { - strcat(command_line, " ") ; -diff --git a/source/util.c b/source/util.c -index 6fff179..41c624c 100644 ---- a/source/util.c -+++ b/source/util.c -@@ -266,7 +266,7 @@ void printTwice(char *mess) /* send info to terminal (stdout) and to log */ - - void prompt(char *mess) /* Send message to user, await reply */ - { -- fprintf(stdout, mess) ; -+ fprintf(stdout, "%s", mess) ; - - while (fgets(terminp, MAXSTRING, stdin) != NULL) { - if ((int)strlen(terminp) > 0) -@@ -722,7 +722,7 @@ void start_record() - int k ; - - rec_length = k = sprintf(record, "\n") ; -- rec_length += sprintf(record+k, timestamp()) ; -+ rec_length += sprintf(record+k, "%s", timestamp()) ; - k = rec_length ; - - if ((cwd = getcwd(NULL, 120)) == NULL) diff --git a/sci-chemistry/eden/files/eden-5.3-impl-dec.patch b/sci-chemistry/eden/files/eden-5.3-impl-dec.patch deleted file mode 100644 index af67508d090e..000000000000 --- a/sci-chemistry/eden/files/eden-5.3-impl-dec.patch +++ /dev/null @@ -1,28 +0,0 @@ - source/fbyteswap.c | 1 + - source/util.c | 1 + - 2 files changed, 2 insertions(+), 0 deletions(-) - -diff --git a/source/fbyteswap.c b/source/fbyteswap.c -index 83015b9..c9033c3 100644 ---- a/source/fbyteswap.c -+++ b/source/fbyteswap.c -@@ -39,6 +39,7 @@ and shall not be used for advertising or product endorsement purposes. - - #include <stdio.h> - #include <fcntl.h> -+#include <unistd.h> - #include <sys/stat.h> - #include <sys/types.h> - void byteswap(); -diff --git a/source/util.c b/source/util.c -index 6fff179..ca7a957 100644 ---- a/source/util.c -+++ b/source/util.c -@@ -89,6 +89,7 @@ and shall not be used for advertising or product endorsement purposes. - - *******************************************************************************/ - #include <sys/time.h> /* ... for picking up date & time */ -+#include <time.h> - #include <signal.h> /* ... for capturing kill */ - #include "util.h" - diff --git a/sci-chemistry/eden/files/makefile-fixes.patch b/sci-chemistry/eden/files/makefile-fixes.patch deleted file mode 100644 index 4cfff3f515df..000000000000 --- a/sci-chemistry/eden/files/makefile-fixes.patch +++ /dev/null @@ -1,25 +0,0 @@ -diff -ur eden.orig/source/Makefile eden/source/Makefile ---- eden.orig/source/Makefile 2004-10-18 10:40:03.000000000 -0700 -+++ eden/source/Makefile 2005-12-15 22:32:45.000000000 -0800 -@@ -78,8 +78,10 @@ - #CFLAGS = -Wall -pipe -marchi686 -pedantic -gdwarf-2 -g3 - #CFLAGS = -Wall -O3 -march=i686 - ifneq ($(FFTW),/usr/local) -+ifneq ($(FFTW),/usr) - CFLAGS += -I$(INC) - endif -+endif - - # NOTE: - # DOUBLESWITCH = ON for double precision; -@@ -129,8 +131,8 @@ - mv fbyteswap $(BIN) - mv eden $(BIN)/$(TARGET) - chmod 751 $(BIN)/$(TARGET) -- chmod +x mkeden.csh -- ./mkeden.csh $(BIN) $(BIN)/$(TARGET) -+# chmod +x mkeden.csh -+# ./mkeden.csh $(BIN) $(BIN)/$(TARGET) - - dist: clean - cd ../..; tar -cvf eden_$(VERSION).tar --exclude CVS --exclude \#\*\# --exclude \*~ --exclude Misc --exclude .\* eden; gzip -f eden_$(VERSION).tar diff --git a/sci-chemistry/eden/metadata.xml b/sci-chemistry/eden/metadata.xml deleted file mode 100644 index 6113635247f3..000000000000 --- a/sci-chemistry/eden/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <use> - <flag name="double-precision">More precise calculations at the expense of - speed</flag> - </use> -</pkgmetadata> diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 54979d004776..015a4eab9de9 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -4,6 +4,7 @@ DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8 DIST gromacs-2020.1.tar.gz 29153989 BLAKE2B b1c0313da945c57c74040c2bcd50495b238b0e131cc4ebecd74ae0d01465b47d732ea456a52a2f9d998cd37e2bfdb93d52bd15177328c4b7a14e6b1d8bc00117 SHA512 130394ec70e5d75ea451e9fa77c4ea2dd4adb0c51cc7663ac8579972bab7a0b75d9143d0eebb21802fc93305deca8831393a8cb3f51b6d01f9477f3dadece037 DIST gromacs-2020.2.tar.gz 29144614 BLAKE2B cd20b031dcec32d9a797d66f2679779077910c184702f12f12093d92e8417d42e07bfb17a8fe63e9d29a889d5f57461b5f86e11adfc26635f8d2b5a5df19473a SHA512 348c80fad93b34e6703906fec97c6c2294c0803c326d6145776b732e1c33cd58e0967ddb2ec4799e3583542c09e7a6a015e4d084d60cf97b81b3a92253cca76c +DIST gromacs-2020.3.tar.gz 29143950 BLAKE2B ea88fcacc3958f1123c1fe4852f7160a04e4daff15dd2eb87c23197bff2e6379f396df0747b078dc86e7bb909ecbb4b6d98530a34234c989a636dbdb2327562d SHA512 8dbd13f8c6dd9ac337e0bea683aeff38010ee9b4ef438de230beb76e5a54884a5c1eda72f20294b7920758978e247900ac3db32b95c7452350fc1f5ef0a4bcc8 DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5 DIST manual-2019.5.pdf 12702361 BLAKE2B cb80429a59019b190115bf2af689c0df23b0fec6e41a9ebc9eba20977d1b06eed79044c906c41228883767f673140e15d3a5ef947a0c1ec4fe84012089f4fa91 SHA512 baf27961b87e6120c49abc9dc58e25d12a15588b4ac787e1a086748d488692d4a1262229ac66e550d3cca3a6042545fb6ec472a2c98d6a8698b7a18b4397f605 DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb @@ -12,11 +13,13 @@ DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036 DIST regressiontests-2020.1.tar.gz 48541809 BLAKE2B 0fec2f0fb7fad0ad48bb790d7df6487e2c1931a0a2134795bf7da4a9087f0f2a3743288fc4ec057fa6b22412c2d8f312cfa3af38be8c5bea51d7a06afb5ac9f0 SHA512 664d29ce39629ed218de65179ce4a73e479d73d30bc96f5ae57624d7e4447298c6122dc09e7873b8cad458eaee0530866411fab20e009e46bf39b133e0de47e8 DIST regressiontests-2020.2.tar.gz 48539492 BLAKE2B 08222ec18e70f551194fc0a060facda394c0d9999e162dace06029aa5f36e7237aeb2468a80d1198257a45fb076f8f633a7279a85976484900bf4154176aa070 SHA512 3066d92a59dafade78807612681d82a7b8a0bd9b74fa7e8784063a908418c55b4427482dc7feb261ff6981fabb2d64a800d3e90ed647ab45e201f4847347bac7 -EBUILD gromacs-2018.8.ebuild 7012 BLAKE2B c54d0bce4d4ffca3365f6f574313ebdf9b0a7e71a8bd7e10c3ffe10f7bddce9854cc4707d1c9f0611e3a0d353fe4ec215d3ee385459748d5266d98f1b5e861a6 SHA512 1de3a0dbba1c03730f7709013515d2282951e0e87e962dce8c46f227bf0e9ddc2034b28ac797c3c2feb81a1c27f1fa10136ea60c861d266ca708e3aac687b8df -EBUILD gromacs-2019.5-r1.ebuild 7334 BLAKE2B 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9568558d0558311ed7a8b8d523ec287dea6682ff5eccb6b780e90739f876d262d20b9f938999bb3283a7c05677aa3a33e7c35071822be05fdd4cf4c74d9ec1d9 SHA512 86e3d58bedb8a87210a81bad1450c11dbfbc99623beac78a498c39dcef2628b2a9a6a7b85c036a79ead38e56ce40d3d15beba6072c4fa8cd62011181eacef97f +EBUILD gromacs-2020.9999.ebuild 9759 BLAKE2B bf1d5b859c466f05b4909113c90faaed916512809ec9563c474461906d49261baeca9b8f7e5bdf85a3fffd32b1b84b4ec47d4523105bba3ed32ce73491d6e7d1 SHA512 cac942e6effce1c0c7ff99ac56c88d9422a89b1b275d3555c5a15a00640c253bd3a98301b9509daf14b3e4d3f1577a8fe6647aab10bf645645ccf35b57470208 +EBUILD gromacs-9999.ebuild 9755 BLAKE2B ee04718fea528c500f797f0ee1ebfb2307772ff5ab4cfc3293f3bf6f93a25ee6155c0b888a4d25371c6a9c4fb022d9e79da9a9df85d7fc82a97442755314ff28 SHA512 5338d8d45908e0b618c21908162e16fff4fba74d671a756229f1f05bce9fd578e923d6289609344cd4a28a78995e2609908de0598cc5d60d45a029ac97b7bba4 MISC metadata.xml 1192 BLAKE2B 560c1c792102747fc16c22d475114480b9897263405da05946721dae5b781c599a02e1401adfa4d929bfb41b4d52791376438aa37d33de18beabc9edbeb779fa SHA512 136c49bfaca76e714e811077c7f7d214a5984c7b6c891c79ad4a754c304752e17450c9aee100dafce04d7bf3893a53224ef9b54504a278654d59fae9acdd0f77 diff --git a/sci-chemistry/gromacs/gromacs-2018.8.ebuild b/sci-chemistry/gromacs/gromacs-2018.8.ebuild index feaa75c10bff..f124a0eac166 100644 --- a/sci-chemistry/gromacs/gromacs-2018.8.ebuild +++ b/sci-chemistry/gromacs/gromacs-2018.8.ebuild @@ -5,7 +5,7 @@ EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf ) @@ -68,7 +68,7 @@ src_prepare() { xdg_environment_reset #591952 - cmake-utils_src_prepare + cmake_src_prepare use cuda && cuda_src_prepare @@ -158,7 +158,7 @@ src_configure() { -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + BUILD_DIR="${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 @@ -176,7 +176,7 @@ src_configure() { -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + BUILD_DIR="${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 @@ -186,31 +186,31 @@ src_compile() { for x in ${GMX_DIRS}; do einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile + cmake_src_compile use mpi || continue einfo "Compiling for ${x} precision with mpi" BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake-utils_src_compile + cmake_src_compile done } src_test() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_make check + cmake_src_make check done } src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install + cmake_src_install if use doc; then newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf" fi use mpi || continue BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install + cmake_src_install done if use tng; then diff --git a/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild b/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild index d5258ab6f232..7ea93b91af9f 100644 --- a/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild @@ -5,7 +5,7 @@ EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf ) @@ -71,7 +71,7 @@ src_prepare() { xdg_environment_reset #591952 - cmake-utils_src_prepare + cmake_src_prepare use cuda && cuda_src_prepare @@ -170,7 +170,7 @@ src_configure() { -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_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 @@ -189,7 +189,7 @@ src_configure() { -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + BUILD_DIR="${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 @@ -199,31 +199,31 @@ src_compile() { for x in ${GMX_DIRS}; do einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile + cmake_src_compile use mpi || continue einfo "Compiling for ${x} precision with mpi" BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake-utils_src_compile + cmake_src_compile done } src_test() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_make check + cmake_src_make check done } src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install + cmake_src_install if use doc; then newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf" fi use mpi || continue BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install + cmake_src_install done if use tng; then diff --git a/sci-chemistry/gromacs/gromacs-2019.6.ebuild b/sci-chemistry/gromacs/gromacs-2019.6.ebuild index e8541e9964ed..85004d2644a2 100644 --- a/sci-chemistry/gromacs/gromacs-2019.6.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.6.ebuild @@ -5,7 +5,7 @@ EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf ) @@ -71,7 +71,7 @@ src_prepare() { xdg_environment_reset #591952 - cmake-utils_src_prepare + cmake_src_prepare use cuda && cuda_src_prepare @@ -170,7 +170,7 @@ src_configure() { -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_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 @@ -189,7 +189,7 @@ src_configure() { -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + BUILD_DIR="${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 @@ -199,31 +199,31 @@ src_compile() { for x in ${GMX_DIRS}; do einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile + cmake_src_compile use mpi || continue einfo "Compiling for ${x} precision with mpi" BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake-utils_src_compile + cmake_src_compile done } src_test() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_make check + cmake_src_make check done } src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install + cmake_src_install if use doc; then newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf" fi use mpi || continue BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install + cmake_src_install done if use tng; then diff --git a/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild index 9d71d0f73354..ba456196edd8 100644 --- a/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild @@ -9,7 +9,7 @@ PYTHON_COMPAT=( python3_{6,7,8} ) DISTUTILS_SINGLE_IMPL=1 -inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils if [[ $PV = *9999* ]]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs.git @@ -116,7 +116,7 @@ src_prepare() { xdg_environment_reset #591952 - cmake-utils_src_prepare + cmake_src_prepare use cuda && cuda_src_prepare @@ -244,7 +244,7 @@ src_configure() { -DGMX_LIBS_SUFFIX="${suffix}" -DGMX_PYTHON_PACKAGE=$(usex python) ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_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 @@ -263,7 +263,7 @@ src_configure() { -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + BUILD_DIR="${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 @@ -273,46 +273,46 @@ src_compile() { for x in ${GMX_DIRS}; do einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile + cmake_src_compile if use python; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile python_packaging/all + cmake_src_compile python_packaging/all BUILD_DIR="${WORKDIR}/${P}" \ distutils-r1_src_compile fi # not 100% necessary for rel ebuilds as available from website if use doc; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile manual + cmake_src_compile manual fi use mpi || continue einfo "Compiling for ${x} precision with mpi" BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake-utils_src_compile + cmake_src_compile done } src_test() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_make check + cmake_src_make check done } src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install + cmake_src_install if use python; then BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install python_packaging/install + cmake_src_install python_packaging/install fi if use doc; then newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" fi use mpi || continue BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install + cmake_src_install done if use tng; then diff --git a/sci-chemistry/gromacs/gromacs-2020.2.ebuild b/sci-chemistry/gromacs/gromacs-2020.2.ebuild index 9d71d0f73354..ba456196edd8 100644 --- a/sci-chemistry/gromacs/gromacs-2020.2.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.2.ebuild @@ -9,7 +9,7 @@ PYTHON_COMPAT=( python3_{6,7,8} ) DISTUTILS_SINGLE_IMPL=1 -inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils if [[ $PV = *9999* ]]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs.git @@ -116,7 +116,7 @@ src_prepare() { xdg_environment_reset #591952 - cmake-utils_src_prepare + cmake_src_prepare use cuda && cuda_src_prepare @@ -244,7 +244,7 @@ src_configure() { -DGMX_LIBS_SUFFIX="${suffix}" -DGMX_PYTHON_PACKAGE=$(usex python) ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_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 @@ -263,7 +263,7 @@ src_configure() { -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + BUILD_DIR="${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 @@ -273,46 +273,46 @@ src_compile() { for x in ${GMX_DIRS}; do einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile + cmake_src_compile if use python; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile python_packaging/all + cmake_src_compile python_packaging/all BUILD_DIR="${WORKDIR}/${P}" \ distutils-r1_src_compile fi # not 100% necessary for rel ebuilds as available from website if use doc; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile manual + cmake_src_compile manual fi use mpi || continue einfo "Compiling for ${x} precision with mpi" BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake-utils_src_compile + cmake_src_compile done } src_test() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_make check + cmake_src_make check done } src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install + cmake_src_install if use python; then BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install python_packaging/install + cmake_src_install python_packaging/install fi if use doc; then newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" fi use mpi || continue BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install + cmake_src_install done if use tng; then diff --git a/sci-chemistry/gromacs/gromacs-2020.3.ebuild b/sci-chemistry/gromacs/gromacs-2020.3.ebuild new file mode 100644 index 000000000000..ba456196edd8 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2020.3.ebuild @@ -0,0 +1,341 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python3_{6,7,8} ) + +DISTUTILS_SINGLE_IMPL=1 + +inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + https://repo.or.cz/r/gromacs.git" + [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-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 -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 + doc? ( + app-doc/doxygen + $(python_gen_cond_dep ' + dev-python/sphinx[${PYTHON_MULTI_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 ) + 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_beta1-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" + + # try to create policy for imagemagik + mkdir -p ${HOME}/.config/ImageMagick + cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + <?xml version="1.0" encoding="UTF-8"?> + <!DOCTYPE policymap [ + <!ELEMENT policymap (policy)+> + !ATTLIST policymap xmlns CDATA #FIXED ''> + <!ELEMENT policy EMPTY> + <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED + name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED + stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> + ]> + <policymap> + <policy domain="coder" rights="read | write" pattern="PS" /> + <policy domain="coder" rights="read | write" pattern="PS2" /> + <policy domain="coder" rights="read | write" pattern="PS3" /> + <policy domain="coder" rights="read | write" pattern="EPS" /> + <policy domain="coder" rights="read | write" pattern="PDF" /> + <policy domain="coder" rights="read | write" pattern="XPS" /> + </policymap> + EOF +} + +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=$(usex doc) + -DGMX_HWLOC=$(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}/${P}" \ + distutils-r1_src_compile + fi + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${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_make 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}_${x}" \ + cmake_src_install python_packaging/install + fi + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + 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-2020.9999.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild index a2dcda755c8b..92600477ee91 100644 --- a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild @@ -9,7 +9,7 @@ PYTHON_COMPAT=( python3_{6,7} ) DISTUTILS_SINGLE_IMPL=1 -inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils if [[ $PV = *9999* ]]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs.git @@ -116,7 +116,7 @@ src_prepare() { xdg_environment_reset #591952 - cmake-utils_src_prepare + cmake_src_prepare use cuda && cuda_src_prepare @@ -240,7 +240,7 @@ src_configure() { -DGMX_LIBS_SUFFIX="${suffix}" -DGMX_PYTHON_PACKAGE=$(usex python) ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_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 @@ -259,7 +259,7 @@ src_configure() { -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + BUILD_DIR="${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 @@ -269,46 +269,46 @@ src_compile() { for x in ${GMX_DIRS}; do einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile + cmake_src_compile if use python; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile python_packaging/all + cmake_src_compile python_packaging/all BUILD_DIR="${WORKDIR}/${P}" \ distutils-r1_src_compile fi # not 100% necessary for rel ebuilds as available from website if use doc; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile manual + cmake_src_compile manual fi use mpi || continue einfo "Compiling for ${x} precision with mpi" BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake-utils_src_compile + cmake_src_compile done } src_test() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_make check + cmake_src_make check done } src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install + cmake_src_install if use python; then BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install python_packaging/install + cmake_src_install python_packaging/install fi if use doc; then newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" fi use mpi || continue BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install + cmake_src_install done if use tng; then diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 11c545362c66..203a0f716f57 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -9,7 +9,7 @@ PYTHON_COMPAT=( python3_{6,7} ) DISTUTILS_SINGLE_IMPL=1 -inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils if [[ $PV = *9999* ]]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs.git @@ -116,7 +116,7 @@ src_prepare() { xdg_environment_reset #591952 - cmake-utils_src_prepare + cmake_src_prepare use cuda && cuda_src_prepare @@ -240,7 +240,7 @@ src_configure() { -DGMX_LIBS_SUFFIX="${suffix}" -DGMX_PYTHON_PACKAGE=$(usex python) ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_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 @@ -259,7 +259,7 @@ src_configure() { -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + BUILD_DIR="${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 @@ -269,46 +269,46 @@ src_compile() { for x in ${GMX_DIRS}; do einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile + cmake_src_compile if use python; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile python_packaging/all + cmake_src_compile python_packaging/all BUILD_DIR="${WORKDIR}/${P}" \ distutils-r1_src_compile fi # not 100% necessary for rel ebuilds as available from website if use doc; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile manual + cmake_src_compile manual fi use mpi || continue einfo "Compiling for ${x} precision with mpi" BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake-utils_src_compile + cmake_src_compile done } src_test() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_make check + cmake_src_make check done } src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install + cmake_src_install if use python; then BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install python_packaging/install + cmake_src_install python_packaging/install fi if use doc; then newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" fi use mpi || continue BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install + cmake_src_install done if use tng; then diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest index 5ded7d1cda4a..cc936a87477e 100644 --- a/sci-chemistry/openbabel-python/Manifest +++ b/sci-chemistry/openbabel-python/Manifest @@ -1,4 +1,4 @@ AUX openbabel-python-2.3.2-gcc-6_and_7-backport.patch 637 BLAKE2B e913c1d1bc93fd8443faa20fc9d7b28b89b276f7561d4208a42abd379111d19ff26179b2fbdca946a9df38e42d31f32b68423be073611e79615dcd6ae20d8f0d SHA512 0108f7bc83e046e29b2ae0b822787f58c6930de775dc94df89ba741f41cb3873a3bd2b677c11ccad4c32172e486b8331c25492127c83e4ab8d066bd129aa5538 DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6 -EBUILD openbabel-python-2.4.1-r1.ebuild 2166 BLAKE2B 45ed425ebe47014c04d8f71661d0e29259d7b3d598695de0c7f0c7027b1488e70855ab4acb74b3d901f706bd58a8cb43ef7f4b1d5f927f8a16220f0cf7ffba41 SHA512 03bfaad27c45362252ebd719d7b526e977b1330e02251e8c82e0568c9f8a8759a5796dd2a22f22419d0f3465fe325d45c4f41a40b9a85edb14cd0a8ad4bed1b7 +EBUILD openbabel-python-2.4.1-r1.ebuild 2156 BLAKE2B 5d6def900a348c7d090e2caa177ca7b4a5c2dc08ed6e77bec76801b36d3bdc092a0fa31bc4ae18d4152c6391feaf35e8856cda50e4889d5c0643e25528fd53ed SHA512 df4c7d34a91ab093a39d99b342b36c9c9984e8bc9e7e18f31641873da86baef4f1141bef20cb2493287bd38e1099b48b6b212fae2e0d21eaf5b04a30943cf281 MISC metadata.xml 737 BLAKE2B 9a5fe97df44ce22c6ee27133bbc6144132ee3775db77440adcd6c3e9c44b87cefbace4ebe17906af87f841e07deef5183e451a8c193232d2a6ca7da05c7a0ed7 SHA512 7ff97ef3f6752a8fed578676aa2cb9706b7d68e31ee22d26e90d4bbb01c10ff410b66da20a91b078293add3bcb3a3711ad180d5174368e0d588ea718ad297d7e diff --git a/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild index 270018c23410..fe6933bd9868 100644 --- a/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild +++ b/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild @@ -3,7 +3,7 @@ EAPI=6 -PYTHON_COMPAT=( python2_7 python3_6 ) +PYTHON_COMPAT=( python3_6 ) inherit cmake-utils python-r1 diff --git a/sci-chemistry/p3d/Manifest b/sci-chemistry/p3d/Manifest deleted file mode 100644 index 8edb957e6d33..000000000000 --- a/sci-chemistry/p3d/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST p3d-0.4.3.tar.gz 7213577 BLAKE2B b614957be16ede7567bd6412d183b3cb79638a5033672afd725cafaf393e306d5d227e1bca444ea17d60a3cd3bb5d3b2c910f2bfc68a118d3bffcd29944b4c29 SHA512 b4cf472b849ece96fe0b2b7f633c496fe3d12bf8cb82a2af10180ce5c27c5465dd0c16cb912d22c56c933b68c06e7de28c0c640da29eaa6bc6f95009bf10277f -EBUILD p3d-0.4.3-r1.ebuild 649 BLAKE2B 9d2730c029ad4a75ed58af5cec21bc050e482064e915c2da565cc5c0035d562ba38b121f43731a28a42d49dfc81fd43b0996698d2e457d16da2872d9cd01b6cd SHA512 e979d59ce970454ef0f8de72bb616b658b489c657bcc3077c2002b6389d00ff4515128da8f549eee5c2ed345d3e229f36de8ff5002e3a21ee5c744d63042295a -EBUILD p3d-9999.ebuild 521 BLAKE2B 4d493463768caa477059286c3d14584d5ba779e7b88dd98125db6e96c0ef658cc3ca4aeae67103f9366a80e055dcfdfed1764d1281777b3e2922916c30a21002 SHA512 0484f573edd3b3df049d884f387e9d062bc6590a228ec70c88c99c70e72f24d94d29d53c5f5cfd0a71e1669590c3c1810eda4a5e9a62c218e1df808c863d2d9a -MISC metadata.xml 1151 BLAKE2B db264a2a0e24aedec15301bb5a6bfe6b83d815e5dc146ccdbcc427d97c0b78ba98050bbc06d230988e1643be858a56469271b92b118bea373a7e284a54f18fb0 SHA512 322b35766a1e71129165a8559fe3caac109dfa85be2b0fa630fa249b28cf603e86f152c47835020ff1f5f0d12b7cbbff8758c08248522a7d2b1188812ec99722 diff --git a/sci-chemistry/p3d/metadata.xml b/sci-chemistry/p3d/metadata.xml deleted file mode 100644 index bd505aa96a4e..000000000000 --- a/sci-chemistry/p3d/metadata.xml +++ /dev/null @@ -1,21 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <longdescription> -p3d was developed in order to offer a Python module that is powerful and fast, -yet intuitive to use. The simplicity of p3d is due to the usage of object -oriented programming (i.e. atoms are treated as vectors), the implementation -of a query parser that translates queries readable by humans into a combination -of algebra set operations the fact that no additional Python packages are -necessary. The speed is due to the usage of a binary space partitioning (BSP) -tree which allows very fast queries in 3D (Henry et al. 1980). The additional -synergy is obtained by the flexible combination of both speed and complexity in -the queries to the structural data. The combination of these factors makes p3d -the optimal module to rapidly develop new and powerful bioinformatic tools that -follow the Python philosophy of making the source code readable. -</longdescription> -</pkgmetadata> diff --git a/sci-chemistry/p3d/p3d-0.4.3-r1.ebuild b/sci-chemistry/p3d/p3d-0.4.3-r1.ebuild deleted file mode 100644 index 04d5f49cf7b2..000000000000 --- a/sci-chemistry/p3d/p3d-0.4.3-r1.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit distutils-r1 vcs-snapshot versionator - -MY_P="${PN}-$(replace_version_separator 3 -)" -GITHUB_ID="gb8b9a75" - -DESCRIPTION="Python module for structural bioinformatics" -HOMEPAGE="http://p3d.fufezan.net/" -SRC_URI="https://nodeload.github.com/fu/${PN}/tarball/${PV} -> ${P}.tar.gz" - -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -LICENSE="GPL-3" -IUSE="examples" - -src_install() { - distutils-r1_src_install - - if use examples; then - insinto /usr/share/${PN} - doins -r pdbs exampleScripts - fi -} diff --git a/sci-chemistry/p3d/p3d-9999.ebuild b/sci-chemistry/p3d/p3d-9999.ebuild deleted file mode 100644 index 5dd3fdc9a942..000000000000 --- a/sci-chemistry/p3d/p3d-9999.ebuild +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit distutils-r1 git-r3 versionator - -DESCRIPTION="Python module for structural bioinformatics" -HOMEPAGE="http://p3d.fufezan.net/" -SRC_URI="" -EGIT_REPO_URI="https://github.com/fu/p3d.git" - -SLOT="0" -KEYWORDS="" -LICENSE="GPL-3" -IUSE="examples" - -src_install() { - distutils-r1_src_install - - if use examples; then - insinto /usr/share/${PN} - doins -r pdbs exampleScripts - fi -} diff --git a/sci-chemistry/pdb-tools/Manifest b/sci-chemistry/pdb-tools/Manifest deleted file mode 100644 index 351e29ce5d76..000000000000 --- a/sci-chemistry/pdb-tools/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST pdbTools_0.2.1.tar.gz 103835 BLAKE2B ad4b5c8d6eb000c79a6d2797519b99027350fa34f6d543f6302f1a9edbe3497afe1a7b5c5c0e7243081cc709d9f1c37da5fc31605a0a225413851ce7288f64c9 SHA512 9c43c10e8739f8a34dbb1a3bba710cc727f7d8392ff979681371bd4460c67203253fb01852438eb93b214c4a009789608d200ca551f30399652fb76d702cf724 -EBUILD pdb-tools-0.2.1-r1.ebuild 1661 BLAKE2B c4e0dde9acb97813824bb8992c747fd850c47e6cd346d921e37cd39a4e1c0e18ee883ecdd90edec1eb8aa5e81afa90ad3d5719b4038a652244ed678e20a267fc SHA512 744eaff99bf693c803b20546a6a9d4b8a1083d7278fa363ba50ae709d6ab1c6e9bd3100ad992b3bce419ef5dd16036e6397465fb6b2a413764e73f10d2818721 -EBUILD pdb-tools-0.2.1-r2.ebuild 1734 BLAKE2B f1b28c6b9c60c5573c9bf6ab092c32f3e4aa6df7bc484dca74aeda8c12f78dafcd94db9f1976932264be4be24c01f29a38750cfe1081058fe0e964345bfe9565 SHA512 dd9a534af4c275a3fba95ce88e4a9e22e5f182c63210717fb66ab62afd67e179541e58d6d1a3af03a550f5718166f9d0974f7d2f47b401adf670b27376f73cf8 -MISC metadata.xml 413 BLAKE2B f3fc199d95acf174f2d5cf9e0ea9c645e3b49e7241122bde730db90a095a0ef0f763dd3dcbcd5f14c1da520630c58bf9e7fe40828d267cb5a2ad5c796b72993e SHA512 74abf290517514aa17fadf8271d2af124fef766b473199502959a662d3bf7a8fed59746b43b3084b83bc14f8d5b9048b419f59d901dec100cbdd81975864cce2 diff --git a/sci-chemistry/pdb-tools/metadata.xml b/sci-chemistry/pdb-tools/metadata.xml deleted file mode 100644 index 25095bc4b42e..000000000000 --- a/sci-chemistry/pdb-tools/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <upstream> - <remote-id type="google-code">pdb-tools</remote-id> - <remote-id type="github">harmslab/pdbtools</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild deleted file mode 100644 index 090b7c041dfe..000000000000 --- a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild +++ /dev/null @@ -1,79 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit fortran-2 python-single-r1 toolchain-funcs - -MY_PN="pdbTools" - -DESCRIPTION="Tools for manipulating and calculations on wwPDB macromolecule structure files" -HOMEPAGE="https://github.com/harmslab/pdbtools" -SRC_URI="https://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz" - -SLOT="0" -LICENSE="GPL-3" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS}" -DEPEND="${RDEPEND}" - -S="${WORKDIR}"/${MY_PN}_${PV} - -pkg_setup() { - python-single-r1_pkg_setup - fortran-2_pkg_setup -} - -src_prepare() { - sed \ - -e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \ - -i pdb_sasa.py || die - sed \ - -e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \ - -i pdb_satk.py || die - sed \ - -e 's:> %:>%:g' \ - -i pdb_seq.py || die -} - -src_compile() { - mkdir bin - cd satk - for i in *.f; do - einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}" - $(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die - $(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die - sed \ - -e "s:${i/.f}.out:${i/.f}:g" \ - -i ../pdb_satk.py || die - done -} - -src_install() { - local script - insinto /usr/share/${PN} - doins -r pdb_data/peptides - rm -rf pdb_data/peptides || die - - python_domodule helper pdb_data - - python_moduleinto ${PN/-/_} - python_domodule *.py - - for i in pdb_*.py; do - cat > ${i/.py} <<- EOF - #!${EPREFIX}/bin/bash - ${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@ - EOF - dobin ${i/.py} - done - - dobin bin/* - dodoc README -} diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild deleted file mode 100644 index a476a801611a..000000000000 --- a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild +++ /dev/null @@ -1,83 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit fortran-2 python-single-r1 toolchain-funcs - -MY_PN="pdbTools" - -DESCRIPTION="Tools for manipulating and calculations on wwPDB macromolecule structure files" -HOMEPAGE="https://github.com/harmslab/pdbtools" -SRC_URI="https://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz" - -SLOT="0" -LICENSE="GPL-3" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS}" -DEPEND="${RDEPEND}" - -S="${WORKDIR}"/${MY_PN}_${PV} - -pkg_setup() { - python-single-r1_pkg_setup - fortran-2_pkg_setup -} - -src_prepare() { - sed \ - -e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \ - -i pdb_sasa.py || die - sed \ - -e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \ - -i pdb_satk.py || die - sed \ - -e 's:> %:>%:g' \ - -i pdb_seq.py || die - - sed \ - -e "/import/s:helper:${PN/-/_}.helper:g" \ - -i *.py || die -} - -src_compile() { - mkdir bin - cd satk - for i in *.f; do - einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}" - $(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die - $(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die - sed \ - -e "s:${i/.f}.out:${i/.f}:g" \ - -i ../pdb_satk.py || die - done -} - -src_install() { - local script - insinto /usr/share/${PN} - doins -r pdb_data/peptides - rm -rf pdb_data/peptides || die - - python_domodule pdb_data - - python_moduleinto ${PN/-/_} - python_domodule helper *.py - - for i in pdb_*.py; do - cat > ${i/.py} <<- EOF - #!${EPREFIX}/bin/bash - ${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@ - EOF - dobin ${i/.py} - done - - dobin bin/* - dodoc README -} diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest deleted file mode 100644 index d057f25d651e..000000000000 --- a/sci-chemistry/pdb2pqr/Manifest +++ /dev/null @@ -1,7 +0,0 @@ -AUX pdb2pka 270 BLAKE2B c4b063cc22f416e5847ceec3377b43f2a7ddda7d204dd07c2870f499483d2ff9edada0632629336b268df904e960d4cb1dad92075ddf42b73d052e7214b20c45 SHA512 c6e66fa73a3119ea84a9bf304c9c8701a6eaf32870ba8c1755bfd8f2055e20af2f2ebc01fd2bf6a663e5873f3d6da7387a439efac3dcb7d4a415c176cb2f761b -AUX pdb2pqr 263 BLAKE2B 3cbd33cf9fb9fd6469c71d8d167ed0fb85ad7b87b6caf27dabb2490b28950961eeffac1c9e4c67102924ecaad002fc5c3d9f2a6955f66eb0699139486caa5372 SHA512 5f8c963fc5addf782579b9312f601ec4547573c7ab88df5a6e38c71c9e31e7b7eea3cde99bdac8f8270f3646d933a0b510a94046e3a30736f75953af5d160b8d -AUX pdb2pqr-1.9.0-flags.patch 1392 BLAKE2B b6b6ac64f98944d85fc93c076d7258c8f980a0391d2cf086edc46bca3f4ef15a5cb720ef8ae2dc38007962a462fb88e92eb4f439c4f3267a5d1d83de5a848dd6 SHA512 deed0aef88dc43515745204f2b4209bd6b42702d9004d48797d642b8f497229424bd0bb92017982cec54c448ea35de563bd42017cd5dc042840acae8495d135b -AUX pdb2pqr-1.9.0-install-py.patch 578 BLAKE2B 91ad4b40ce3d13b574ad6d9ea84e55b08803fa018490a7327dae5621a371adfeda509188c049144301cbc023f4407f6c0daf7b57e7d3c10d95d78ab570a6f540 SHA512 902ad717e32790e9c691851dc4b92412f07ac79caf74b2b5794a10fa75cca7fa19e8814df4d8ba71bd2ecc98a3d777d0b79e6e43009171a32e8c99756d81d4d2 -DIST pdb2pqr-src-1.9.0.tar.gz 9051969 BLAKE2B bacb2c65d319fb918a7a15b772c250398ffa991a93ee731ec15c8ae907304daf57282bf83c24f84d11945349a7f93f6f934575c117d4ce24d6530f14e60f3730 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f -EBUILD pdb2pqr-1.9.0-r3.ebuild 2679 BLAKE2B 882e244c9764c317df96195e4c9049a8a23872c458487ed4e897263cc99b5e1fa8bb7a3a70bf34fda447d71767ee4eb59fa49c4beecbd04fd2577438bb8aaf8e SHA512 f5037488f9ecdc9be44fb1dcc15ec55db932fc4268b61db7d95375e0e22d9f54f0315a5c0eb4398919f8620c167adbdd5e632bcdb241724ebc77efb7e7442802 -MISC metadata.xml 511 BLAKE2B 70a1bf9ff6db44bdbae39b1f58ac5b80769738b2ce8fbb19b3bcb9fbf7cec2a9eab215a7a922025b9110673cb834255240adf10613fd78a8fea47fa7be4fbba9 SHA512 11a010eea3bbbaaf4150a23dadcd10c45737745d51a3341cd7e69cc8537215f313d1ab57059eff265e73e34aeaef435585bb652f5497508dd12b99f67b8580c0 diff --git a/sci-chemistry/pdb2pqr/files/pdb2pka b/sci-chemistry/pdb2pqr/files/pdb2pka deleted file mode 100644 index 2406b0c4773f..000000000000 --- a/sci-chemistry/pdb2pqr/files/pdb2pka +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env python - -import subprocess -import site -import sys -import os - -sitepackages = site.getsitepackages()[0] - -_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pka", "pka.py")] -_cmd.extend(sys.argv[1:]) - -subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr) diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr b/sci-chemistry/pdb2pqr/files/pdb2pqr deleted file mode 100644 index 8c0635aea94e..000000000000 --- a/sci-chemistry/pdb2pqr/files/pdb2pqr +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env python - -import subprocess -import site -import sys -import os - -sitepackages = site.getsitepackages()[0] - -_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pqr.py")] -_cmd.extend(sys.argv[1:]) - -subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr) diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch deleted file mode 100644 index fac32b233e6b..000000000000 --- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch +++ /dev/null @@ -1,45 +0,0 @@ - pdb2pka/SConscript | 9 ++++++++- - pdb2pka/substruct/SConscript | 6 ++++++ - 2 files changed, 14 insertions(+), 1 deletion(-) - -diff --git a/pdb2pka/SConscript b/pdb2pka/SConscript -index 583cdc5..6c30011 100644 ---- a/pdb2pka/SConscript -+++ b/pdb2pka/SConscript -@@ -1,4 +1,11 @@ - Import('env')
-+import os
-+
-+env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())
-+env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())
-+env['CXX'] = os.environ['CXX']
-+env['LINK'] = os.environ['CXX']
-+
-
- if env['REBUILD_SWIG']:
- pyc = env.LoadableModule('_pMC_mult', ['pMC_mult.cpp', 'pMC_mult.i'])
-@@ -9,4 +16,4 @@ Default(pyc) -
- algorithms_module = SConscript('substruct/SConscript')
-
--Return('pyc algorithms_module') -\ No newline at end of file -+Return('pyc algorithms_module')
-diff --git a/pdb2pka/substruct/SConscript b/pdb2pka/substruct/SConscript -index 7dbcdb0..56fb577 100644 ---- a/pdb2pka/substruct/SConscript -+++ b/pdb2pka/substruct/SConscript -@@ -1,7 +1,13 @@ - import distutils
- import numpy
-+import os
- Import('env')
-
-+env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())
-+env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())
-+env['CXX'] = os.environ['CXX']
-+env['LINK'] = os.environ['CXX']
-+
- env.Append(CPPPATH=[distutils.sysconfig.get_python_inc(), numpy.get_include()])
-
- algorithms_pyc = env.LoadableModule('Algorithms', ['Algorithms.cpp'])
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch deleted file mode 100644 index 2695b013c66a..000000000000 --- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch +++ /dev/null @@ -1,15 +0,0 @@ - SConscript-install.py | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/SConscript-install.py b/SConscript-install.py -index e2f9f09..1fdf1a8 100644 ---- a/SConscript-install.py -+++ b/SConscript-install.py -@@ -41,6 +41,7 @@ def installFile(file_name, build_target='install'): - if GetOption("clean"):
- env.Default(result)
- Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), result))
-+ Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))
- else:
- Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))
-
diff --git a/sci-chemistry/pdb2pqr/metadata.xml b/sci-chemistry/pdb2pqr/metadata.xml deleted file mode 100644 index 36fd8c04ac52..000000000000 --- a/sci-chemistry/pdb2pqr/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <use> - <flag name="opal">Add web interface via opal</flag> - <flag name="pdb2pka">Install experimental pdb2pka interface</flag> - </use> - <upstream> - <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild deleted file mode 100644 index 179e6448d605..000000000000 --- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit scons-utils fortran-2 flag-o-matic python-single-r1 toolchain-funcs - -DESCRIPTION="Automated pipeline for performing Poisson-Boltzmann electrostatics calculations" -HOMEPAGE="https://www.poissonboltzmann.org/" -SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${PN}-src-${PV}.tar.gz" - -SLOT="0" -LICENSE="BSD" -IUSE="doc examples opal +pdb2pka" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - $(python_gen_cond_dep ' - || ( - dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}] - dev-python/numpy[${PYTHON_MULTI_USEDEP}] - ) - sci-chemistry/openbabel-python[${PYTHON_MULTI_USEDEP}] - opal? ( dev-python/zsi[${PYTHON_MULTI_USEDEP}] ) - ') - pdb2pka? ( sci-chemistry/apbs[${PYTHON_SINGLE_USEDEP},-mpi] )" -DEPEND="${RDEPEND} - dev-lang/swig:0" - -PATCHES=( - "${FILESDIR}"/${P}-flags.patch - "${FILESDIR}"/${P}-install-py.patch -) - -pkg_setup() { - if [[ -z ${MAXATOMS} ]]; then - einfo "If you like to have support for more then 10000 atoms," - einfo "export MAXATOMS=\"your value\"" - export MAXATOMS=10000 - else - einfo "Allow usage of ${MAXATOMS} during calculations" - fi - fortran-2_pkg_setup - python-single-r1_pkg_setup -} - -src_prepare() { - find -type f \( -name "*\.pyc" -o -name "*\.pyo" \) -delete || die - - export CXXFLAGS="${CXXFLAGS}" - export LDFLAGS="${LDFLAGS}" - - epatch "${PATCHES[@]}" - tc-export CXX - rm -rf scons || die -} - -src_configure() { - cat > build_config.py <<- EOF - PREFIX="${D}/$(python_get_sitedir)/${PN}" - #URL="http://<COMPUTER NAME>/pdb2pqr/" - APBS="${EPREFIX}/usr/bin/apbs" - #OPAL="http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_1.8" - #APBS_OPAL="http://nbcr-222.ucsd.edu/opal2/services/apbs_1.3" - MAX_ATOMS=${MAXATOMS} - BUILD_PDB2PKA=$(usex pdb2pka True False) - REBUILD_SWIG=True - EOF -} - -src_compile() { - escons -} - -src_test() { - local myesconsargs=( -j1 ) - escons test - escons advtest - escons complete-test -} - -src_install() { - dodir /usr/share/doc/${PF}/html - local lib - - escons install - - find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die - - python_doscript "${FILESDIR}"/{${PN},pdb2pka} - - for lib in apbslib.py{,c,o}; do - dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib} - done - dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so - python_optimize - - if use doc; then - pushd doc > /dev/null - docinto html - dodoc -r *.html images pydoc - popd > /dev/null - fi - - use examples && \ - insinto /usr/share/${PN}/ && \ - doins -r examples - - dodoc *md NEWS -} diff --git a/sci-chemistry/prodecomp/Manifest b/sci-chemistry/prodecomp/Manifest deleted file mode 100644 index 6a19b100ad23..000000000000 --- a/sci-chemistry/prodecomp/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST prodecomp-3.0.tar.bz2 18377446 BLAKE2B c6b4acf20a76029fc34eaea7a0adf1a04fb727b2e246fbcad27e2fa2bea606b2e712fb986fdd3e534534b32a22acae58a00bc2a3c6bde893d5befe91696523d3 SHA512 8d23f174e125d4c7776432a37b063d2f39af8497050bd7f7ff358c67d509b1eef2c2865596efae632855fd583fb52c233b67d0e667c6c2a03ba6f5a2f2ac9b0d -EBUILD prodecomp-3.0-r3.ebuild 1191 BLAKE2B 25903c84628554ea37a9d20ee8fc0b0315d30526ed2c7e41bc6697235c04e3f9682ebb64aed7358009fd45502fcfe1fb66355c3f7209e39aeee6a1064cb34a5d SHA512 692a231b2e180d4a4114ce2441eb178adafb9ab725fcc2b1a0bdbeb675134ee823fb694546d033832393d4562c948073f47715ee29daaad9a938ce5112dd5f1e -MISC metadata.xml 825 BLAKE2B 6874942c301b7d68f9184de8eb7482b790d2bd51c3a853132da3ed7bb0eacf54f608f816965bbfb27b81b90fecc3eee77596d73a78f5ec67703c53ad2bc2556d SHA512 94e41d5648ac93257f11f305bf2aaf926cc103240beec884142cda42c3d4e4fae5629e26b43cd945c945af706d5b5172fcd2c30ec6cb9067b152a22cd09bddcf diff --git a/sci-chemistry/prodecomp/metadata.xml b/sci-chemistry/prodecomp/metadata.xml deleted file mode 100644 index 168ce755cbc8..000000000000 --- a/sci-chemistry/prodecomp/metadata.xml +++ /dev/null @@ -1,18 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <longdescription> - PRODECOMP (PROjection DECOMPosition) is a software tool for - decomposition of 2D projections of high-dimensional NMR spectra to a set - of components (defined in turn by one-dimensional "shapes"). - Simultaneous analysis of projections from one or several - high-dimensional experiments provide unambigous chemical shifts for - large spin systems. The latter can be used for backbone and side-chain - assignments as well as structural studies of proteins - (Malmodin and Billeter 2005; 2006; Staykova et al. 2008a,b). - </longdescription> -</pkgmetadata> diff --git a/sci-chemistry/prodecomp/prodecomp-3.0-r3.ebuild b/sci-chemistry/prodecomp/prodecomp-3.0-r3.ebuild deleted file mode 100644 index 65683c21b0fa..000000000000 --- a/sci-chemistry/prodecomp/prodecomp-3.0-r3.ebuild +++ /dev/null @@ -1,53 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="tk" - -inherit python-single-r1 - -DESCRIPTION="Decomposition-based analysis of NMR projections" -HOMEPAGE="http://www.lundberg.gu.se/nmr/software.php?program=PRODECOMP" -SRC_URI="mirror://gentoo/${P}.tar.bz2" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="examples" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="${PYTHON_DEPS}" -RDEPEND="${DEPEND} - $(python_gen_cond_dep ' - || ( - sci-libs/scipy-python2[${PYTHON_MULTI_USEDEP}] - sci-libs/scipy[${PYTHON_MULTI_USEDEP}] - ) - ')" - -S="${WORKDIR}"/NMRProjAnalys - -src_install() { - python_export - if use examples; then - insinto /usr/share/${PN} - doins -r ExampleData Results - fi - - dodoc ProjTools/Manual.pdf - rm -rf ProjTools/Manual.pdf ProdecompOutput || die - - python_moduleinto ${PN} - python_domodule ProjTools/. - python_optimize - - cat >> "${T}"/${PN} <<- EOF - #!/bin/bash - ${PYTHON} -O $(python_get_sitedir)/${PN}/ProjAnalys.py \$@ - EOF - dobin "${T}"/${PN} - - dosym ../../../../share/doc/${PF}/Manual.pdf "${PYTHON_SITEDIR##${EPREFIX}}"/${PN}/Manual.pdf -} diff --git a/sci-chemistry/pymol-plugins-bni-tools/Manifest b/sci-chemistry/pymol-plugins-bni-tools/Manifest deleted file mode 100644 index 5cd55b7d9206..000000000000 --- a/sci-chemistry/pymol-plugins-bni-tools/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST bni-tools-027.zip 33753 BLAKE2B 3cf52b42709c0e08879b7f3174ab6e7fd6c052a2827a0ee6d102fa16f30a985d7ff766abc6dc27595973a1f6151f684e97b34da981196c411fdac178499f9a51 SHA512 9c0ef1ca5bbb3040192ab2668f354f947e93d42c91a0cfdde5d05be273e6ba9f29ec3c6ee86367f18d87316282b4e0141183b8d6259bd36d44010b7bbb7666e5 -EBUILD pymol-plugins-bni-tools-0.27.ebuild 912 BLAKE2B 8c99230d03b369b03a29496aecb82ea37b1968e87537a634c85c0373c2ea11ce3a9a42482127bdce82c902906ff6bb13dc0a3862b62ffe6298ae7a9ce58c983c SHA512 4e685c3c1c96849cf7f5144fa3ac6114c943e4feb2d66f2797f2b611150d06d1849a140ffc8a8ba50d20dd9ee032392c38c144ebc52576666229854ff21544dc -MISC metadata.xml 354 BLAKE2B 569e0dfba864883bafd31bf469136f0f710f1f035b4056babf6de5046b7a2cb7146d3f3d95970e75c5025230056249392cc664323cf2d4bf445b3d674ee36675 SHA512 b5f667e6315a0841a28c45fcd7c218d0b5c5e0ad3cdd63870001f1fcd2e4adf598d2b1270a77aa71c1d5d2fe985ca1d98d4c3f88cd540740e67f3469709a94a8 diff --git a/sci-chemistry/pymol-plugins-bni-tools/metadata.xml b/sci-chemistry/pymol-plugins-bni-tools/metadata.xml deleted file mode 100644 index 0f732a212193..000000000000 --- a/sci-chemistry/pymol-plugins-bni-tools/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">bni-tools</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.27.ebuild b/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.27.ebuild deleted file mode 100644 index 1de68c64d64f..000000000000 --- a/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.27.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit python-r1 versionator - -MY_PN="${PN#pymol-plugins-}" -MY_P="${MY_PN}-$(delete_version_separator 1)" -MY_P_DOT="${MY_PN}-${PV}" - -DESCRIPTION="Gives Pymol additional functionalities and presets to the PyMOL GUI" -HOMEPAGE="http://bni-tools.sourceforge.net/" -SRC_URI="mirror://sourceforge/${MY_PN}/${MY_PN}/${MY_P_DOT}/${MY_P}.zip" - -LICENSE="CNRI" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - sci-chemistry/pymol[${PYTHON_USEDEP}]" -DEPEND="${PYTHON_DEPS} - app-arch/unzip" - -S="${WORKDIR}" - -src_install() { - python_moduleinto pmg_tk/startup - python_foreach_impl python_domodule bni-tools.py - python_foreach_impl python_optimize - dodoc readme.txt - dohtml ShortCommandDescription.html -} diff --git a/sci-chemistry/pymol-plugins-caver/Manifest b/sci-chemistry/pymol-plugins-caver/Manifest deleted file mode 100644 index 9b6a67eb2228..000000000000 --- a/sci-chemistry/pymol-plugins-caver/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST Caver2_1_2_pymol_plugin.zip 5698331 BLAKE2B e1accfaea6faf1e8c545b88c965228ccb62710d4015ff681506971feba6bd18a4a8b0b6e6caf621c99830ba529a6ec17873cdd3d5e52ad6dc6f67d9457e4eb87 SHA512 9d28e059bb20f30cf6a0d25ed2eb080dcf9dbb753e9d4578d95e293b31c5cf5fe23d5177dccdb79c192ab3e65bb484b6eb22b26c267637b125404f871e01a52c -EBUILD pymol-plugins-caver-2.1.2.ebuild 1307 BLAKE2B 72eb31fe4fecbbe94d79c7aac5494e46f998746ebaa6d39f90f3355aab61587c893dd468f5a51a5f397f4991dd9814cbe7d6b3f4e1ae8690466aef1947c59c2c SHA512 0bdee2ba446432beed93bdd7625061edc50560b5b9947cf1a65c88531c42ddcba501d5580c1edc86ed62a3ec503510a59ca58b7b12a72e1e9b69026738b7c927 -MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/pymol-plugins-caver/metadata.xml b/sci-chemistry/pymol-plugins-caver/metadata.xml deleted file mode 100644 index 8937bad0b175..000000000000 --- a/sci-chemistry/pymol-plugins-caver/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild b/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild deleted file mode 100644 index e189f885dcc5..000000000000 --- a/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit multilib python-r1 eutils versionator java-utils-2 - -MY_PV="$(replace_all_version_separators _)" -MY_P="Caver${MY_PV}_pymol_plugin" - -DESCRIPTION="Calculation of pathways of proteins from buried cavities to outside solvent" -HOMEPAGE="http://loschmidt.chemi.muni.cz/caver/" -SRC_URI="${MY_P}.zip" - -LICENSE="CAVER" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - >=virtual/jre-1.6 - sci-chemistry/pymol[${PYTHON_USEDEP}] - ${PYTHON_DEPS}" -DEPEND="app-arch/unzip - ${PYTHON_DEPS}" - -RESTRICT="bindist fetch" - -S="${WORKDIR}/${MY_P}"/linux_mac - -pkg_nofetch() { - elog "Download ${A}" - elog "from ${HOMEPAGE}. This requires registration." - elog "Place tarballs into your DISTDIR directory." -} - -src_install() { - java-pkg_dojar Caver${MY_PV}/*.jar - - java-pkg_jarinto /usr/share/${PN}/lib/lib/ - java-pkg_dojar Caver${MY_PV}/lib/*.jar - - installation() { - sed \ - -e "s:directory/where/jar/with/plugin/is/located:${EPREFIX}/usr/share/${PN}/lib/:g" \ - -i Caver${MY_PV}.py || die - - python_moduleinto pmg_tk/startup/ - python_domodule Caver${MY_PV}.py - python_optimize - } - python_foreach_impl installation -} diff --git a/sci-chemistry/pymol-plugins-dssp/Manifest b/sci-chemistry/pymol-plugins-dssp/Manifest deleted file mode 100644 index 3c9bf42c8721..000000000000 --- a/sci-chemistry/pymol-plugins-dssp/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST pymol-plugins-dssp-110430.py.xz 6836 BLAKE2B d8a58d1ad85aaa45acdcac40d022bac8035baf9c95c05e2cd6abb1dd82f1cd390515e04b4c65ff96902655a366ca2e4eab8e86060dffb27ea146298f827fbd7c SHA512 521e0a32ca6d2c8c21c690815b0654bb44303bd7fb9a1eb76227030b2ad7311fadb0d748e49b8bbc16cd5e69acba375b5353de7bffef1ff69686e62021fe64f4 -EBUILD pymol-plugins-dssp-110430-r1.ebuild 885 BLAKE2B db52dd99fc40b04a8a832a4c565e450f35d098120546dabbf53a5e307233664e619ad988eba51c4f7b9b8a06714be96742446b63e28014fdb3098db1f87133bb SHA512 617949f73a08f3b53ceecbce15669202e935c18e4b052092a810b644c9d11e9b5cbf0663c4c830895d0f19c55d34a55c2e1bcf405d3ec0d1e4ec29c8a56c642c -MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/pymol-plugins-dssp/metadata.xml b/sci-chemistry/pymol-plugins-dssp/metadata.xml deleted file mode 100644 index 8937bad0b175..000000000000 --- a/sci-chemistry/pymol-plugins-dssp/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430-r1.ebuild b/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430-r1.ebuild deleted file mode 100644 index 11269a75591f..000000000000 --- a/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430-r1.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit python-r1 - -DESCRIPTION="DSSP Plugin for PyMOL" -HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/dssp_pymol/dssp_pymol.html" -SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.py.xz" - -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -LICENSE="BSD pymol" -IUSE="" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="${PYTHON_DEPS}" -RDEPEND="${DEPEND} - sci-chemistry/dssp - sci-biology/stride - sci-chemistry/pymol[${PYTHON_USEDEP}]" - -S="${WORKDIR}" - -src_prepare() { - sed \ - -e "s:GENTOO_DSSP:${EPREFIX}/usr/bin/dssp:g" \ - -e "s:GENTOO_STRIDE:${EPREFIX}/usr/bin/stride:g" \ - -i ${P}.py || die -} - -src_install() { - python_moduleinto pmg_tk/startup - python_foreach_impl python_domodule ${P}.py - python_foreach_impl python_optimize -} diff --git a/sci-chemistry/pymol-plugins-emovie/Manifest b/sci-chemistry/pymol-plugins-emovie/Manifest deleted file mode 100644 index bc3bedfdd4e6..000000000000 --- a/sci-chemistry/pymol-plugins-emovie/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -AUX 1.0.4-indent.patch 706 BLAKE2B f99a3554f0a00c5c075ba23179238d32ce7acddcace31e4c7cb0f995cf2c5a7a0ee4c5a0db4b2dc079a70d6e0ca34e52ac5276ffddcca441e49eb1746ba2962d SHA512 6788795d177db8c7597376a364eed79cc40a2423c6d86b837f4378308515d6f41a6c352df775de309d363ec284997a688285f2f851d5d84e891e78a771580b0e -DIST eMovie_package.zip 22840 BLAKE2B 593548d5f940432cbf71580410fba01bcf54f884d6ac1a726a0ce65a7efa4d90c283985f81b5348eadaf54f497a32e1d478ca803cb0fbdacd7bfde30b939d864 SHA512 5d4af5f8bd6e7e0f24f33d769925bd0444389b1c0fbdd14776f4073fd3e1e818c4623791bcb0cff5496729dc55e0429c48c3c16cb5fdbb91c51f9c5445c7afe4 -EBUILD pymol-plugins-emovie-1.0.4.ebuild 767 BLAKE2B de65bfdc624e16c23026729e7853a8f44e861583684c92c1574c7a8cab6442a86b2d9874e3456065d780bebd55e5046472326bb2d1914b16d784c008892ab94b SHA512 d915784d50895f04230189d39b8d819cbdca7fcf620ce6cd688139fd5a687ee8fef1415fb63f54758b588774c06672b9712943fed126a7de6db436034588de5f -MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a diff --git a/sci-chemistry/pymol-plugins-emovie/files/1.0.4-indent.patch b/sci-chemistry/pymol-plugins-emovie/files/1.0.4-indent.patch deleted file mode 100644 index a9a77e5055dd..000000000000 --- a/sci-chemistry/pymol-plugins-emovie/files/1.0.4-indent.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff --git a/eMovie.py b/eMovie.py -index a865732..8b5b068 100644 ---- a/eMovie.py -+++ b/eMovie.py -@@ -931,7 +931,7 @@ class Story(tkSimpleDialog.Dialog): - - if self.parent is not None: - self.geometry("+%d+%d" % (parent.winfo_rootx()+50,parent.winfo_rooty()+50)) -- self.initial_focus.focus_set() -+ self.initial_focus.focus_set() - - self.wait_window(self) - -@@ -2041,7 +2041,7 @@ class AddMorph(tkSimpleDialog.Dialog): - - if self.parent is not None: - self.geometry("+%d+%d" % (parent.winfo_rootx()+50,parent.winfo_rooty()+50)) -- self.initial_focus.focus_set() -+ self.initial_focus.focus_set() - - self.wait_window(self) - diff --git a/sci-chemistry/pymol-plugins-emovie/metadata.xml b/sci-chemistry/pymol-plugins-emovie/metadata.xml deleted file mode 100644 index da36ecbfcd6a..000000000000 --- a/sci-chemistry/pymol-plugins-emovie/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild b/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild deleted file mode 100644 index e7b2eb7d4771..000000000000 --- a/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils python-r1 - -DESCRIPTION="PyMOL plugin for convinient movie creation" -SRC_URI="http://www.weizmann.ac.il/ISPC/eMovie_package.zip" -HOMEPAGE="http://www.weizmann.ac.il/ISPC/eMovie.html" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - >sci-chemistry/pymol-0.99[${PYTHON_USEDEP}]" -DEPEND="app-arch/unzip" - -S="${WORKDIR}" - -src_prepare() { - epatch "${FILESDIR}"/${PV}-indent.patch -} - -src_install() { - python_moduleinto pmg_tk/startup - python_foreach_impl python_domodule eMovie.py - python_foreach_impl python_optimize -} diff --git a/sci-chemistry/pymol-plugins-promol/Manifest b/sci-chemistry/pymol-plugins-promol/Manifest deleted file mode 100644 index 7a00b495997e..000000000000 --- a/sci-chemistry/pymol-plugins-promol/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST pymol-plugins-promol-3.0.2.zip 2219295 BLAKE2B 7e81de98ee20f6b22fabeca35b0825250c3b839b9ea51f6c0b51f15062c73810474bd377d0e39d3c2ac0d61f1b5cfb4174c53f1dfc67a11dfcd707eee417a7ed SHA512 e40e9c08e2cb1b223390d751bb1f32069924f1c23aa2b4bdafb6689254e6aa673d4412aca587792f660869f97a389db8a9183033d8b2394c998d0f911104d8d7 -EBUILD pymol-plugins-promol-3.0.2-r1.ebuild 1560 BLAKE2B c4f52140e4baa9f5a6beddfbace78ff111a3f78f8bdfd0fb220b0e17555175d48533079a798f98eda32b7880f23a37fdbacd0904a988871a1b8eb91f6e9a23fb SHA512 1b3962ba9471e9c2d6af5ebac500a317b44fe261ceeeb8ee8f156211d9aad39ce720e29be5d859a5867df5b87904b2084eb95d21d63806ba0452222ef96ac6cb -MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/pymol-plugins-promol/metadata.xml b/sci-chemistry/pymol-plugins-promol/metadata.xml deleted file mode 100644 index 8937bad0b175..000000000000 --- a/sci-chemistry/pymol-plugins-promol/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild deleted file mode 100644 index 6cd842f3703d..000000000000 --- a/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit python-r1 - -DESCRIPTION="Fast and accurate regognition of active sites" -HOMEPAGE="https://www.rit.edu/cos/ezviz/ProMOL_dl.html" -SRC_URI="https://www.rit.edu/cos/ezviz/ProMOL.zip -> ${P}.zip" - -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux" -LICENSE="all-rights-reserved" -IUSE="" - -RESTRICT="mirror bindist" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-python/pmw:py2[${PYTHON_USEDEP}] - sci-chemistry/pymol[${PYTHON_USEDEP}]" -DEPEND="" - -S="${WORKDIR}/ProMOL Folder" - -src_prepare() { - python_copy_sources - preparation() { - cd "${BUILD_DIR}" || die - sed \ - -e "s:./modules/pmg_tk/startup:$(python_get_sitedir)/pmg_tk/startup/ProMol:g" \ - -i ProMOL_302.py || die - } - python_foreach_impl preparation -} - -src_install() { - dodoc *doc - dohtml -r Thanks.html EDMHelp.htm Help - - installation() { - cd "${BUILD_DIR}" || die - python_moduleinto pmg_tk/startup/ProMol - python_domodule PDB_List AminoPics Motifs *GIF pdb_entry_type.txt Master.txt Scripts - python_moduleinto pmg_tk/startup - python_domodule *.py - dosym ../../../../../../share/doc/${PF}/html/Help \ - $(python_get_sitedir)/pmg_tk/startup/ProMol/Help - dosym ../../../../../../share/doc/${PF}/html/Thanks.html \ - $(python_get_sitedir)/pmg_tk/startup/ProMol/Thanks.html - dosym ../../../../../../share/doc/${PF}/html/EDMHelp.htm \ - $(python_get_sitedir)/pmg_tk/startup/ProMol/EDMHelp.htm - } - python_foreach_impl installation -} diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index fcffc5ef7882..69bc84fa32a7 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1,5 +1,4 @@ DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05 SHA512 e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133 -EBUILD pymol-2.3.0-r2.ebuild 3189 BLAKE2B b696daab150edc9c5b69e330f68d0a79bb825d39d69e6b149a90be7f12a3956525b91373f330e528178b2732b84b86f6e9ae1624c8cad48eb1580e81b4bde38a SHA512 4c4c4e94c768325728584e6c424e7c7d87e4daab291c0f6bad2c6f527645056d0b9b4fefc822543542f27431f51a1f1a6cda1ab7fb9136d0f44a11c6129060be EBUILD pymol-2.3.0-r3.ebuild 3005 BLAKE2B 697c52ef412f18a8088c82c6f71ef7b10ffb28201aaaf5b651cfad512ce1f3340f74292dc54e9005e5c153d50bf8d3c9de1df1a71516c5258b4a6256fc9b9429 SHA512 9f248137b6cd1c4a0233c83738597e42b43b65f1331c6a19a841a36719328996fc9902f599848d791963f41e65dc9f7c76f967dae26286488a49b5cfd13572d1 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4 diff --git a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild deleted file mode 100644 index 5eadc9a8512d..000000000000 --- a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild +++ /dev/null @@ -1,118 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python2_7 ) - -inherit distutils-r1 desktop eutils flag-o-matic xdg-utils - -DESCRIPTION="A Python-extensible molecular graphics system" -HOMEPAGE="https://www.pymol.org/" -SRC_URI=" - https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz - https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz - " -RESTRICT="mirror" -LICENSE="PSF-2.2" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="web" - -DEPEND=" - dev-libs/msgpack[cxx] - dev-libs/mmtf-cpp - || ( - dev-python/numpy-python2[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - ) - dev-python/pmw:py2[${PYTHON_USEDEP}] - dev-python/pyopengl[${PYTHON_USEDEP}] - dev-python/PyQt5[opengl,${PYTHON_USEDEP}] - media-libs/freetype:2 - media-libs/glew:0= - media-libs/glm - media-libs/libpng:0= - media-video/mpeg-tools - sys-libs/zlib - !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}] - web? ( !dev-python/webpy[${PYTHON_USEDEP}] )" -RDEPEND="${DEPEND} - sci-chemistry/chemical-mime-data -" - -S="${WORKDIR}"/${PN}-open-source-${PV} - -python_prepare_all() { - sed \ - -e "s:\"/usr:\"${EPREFIX}/usr:g" \ - -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ - -e "/import/s:argparse:argparseX:g" \ - -i setup.py || die - - sed \ - -e "s:/opt/local:${EPREFIX}/usr:g" \ - -e '/ext_comp_args/s:\[.*\]:[]:g' \ - -i setup.py || die - sed \ - -e "s:\['msgpackc'\]:\['msgpack'\]:g" \ - -i setup.py || die - - append-cxxflags -std=c++0x - - distutils-r1_python_prepare_all -} - -python_install() { - distutils-r1_python_install \ - --pymol-path="${EPREFIX}/usr/share/pymol" - - sed \ - -e '1d' \ - -e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \ - -e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \ - -e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \ - -i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die -} - -python_install_all() { - distutils-r1_python_install_all - - sed \ - -e '1i#!/usr/bin/env python' \ - "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die - - python_foreach_impl python_doscript "${T}"/${PN} - - # These environment variables should not go in the wrapper script, or else - # it will be impossible to use the PyMOL libraries from Python. - cat >> "${T}"/20pymol <<- EOF - PYMOL_PATH="${EPREFIX}/usr/share/pymol" - PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" - PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" - EOF - - doenvd "${T}"/20pymol - - newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png - make_desktop_entry ${PN} PyMol ${PN} \ - "Graphics;Education;Science;Chemistry;" \ - "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" - - if ! use web; then - rm -rf "${D}/$(python_get_sitedir)/web" || die - fi - - rm -f "${ED}"/usr/share/${PN}/LICENSE || die -} - -pkg_postinst() { - xdg_desktop_database_update - xdg_mimeinfo_database_update - optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr -} - -pkg_postrm() { - xdg_desktop_database_update - xdg_mimeinfo_database_update -} diff --git a/sci-chemistry/relax/Manifest b/sci-chemistry/relax/Manifest deleted file mode 100644 index 56c32abe4254..000000000000 --- a/sci-chemistry/relax/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST relax-4.0.0.src.tar.bz2 105659752 BLAKE2B ce5fc9b7f31787f2189e75a543f8ba6fe3cd59ce7382c6c0f79c419b9f71b2d09bd16685e7fed3c9e3205be531efa2a8dc1cce707e77e2386d2a9f7a71b4b0c1 SHA512 28b5ddab2c83f95d7e1a502d05b5d3c93337fece68a1fef95ec8978f61fccf24cb37528cfef27cb20d132033535f4120b23cc76a75f34f52b27df17116351f8e -EBUILD relax-4.0.0-r4.ebuild 1883 BLAKE2B 83dbe09ddc6feb3b7ec4af472eeac4e49c2cda90c84d2f19f19bdcf9414b97f0e7221a9e048c68535e6d5239511013738f4d969b01233034212efcefd7dca3c8 SHA512 5f657c2798e1a83626056ff7849339d3bb05f014ea579a1697e022a7b9628256c7c14a37fa71869be9d66fb1a935bc4907329c45d9cb9af7c6270ba1690046ef -MISC metadata.xml 1373 BLAKE2B d5a9e36f0412ef757a23aa4991986bdc394edc035f59b0206b246affc884417eb8446a598b23054972c97dc5d883cd0242e306f9e8d61620c144939845c0bcf1 SHA512 575ccfdae744fc5d97e795a22989b377954edeacb8ec4887d987a59af813f126551743c4b29b9c2b4a26a1840f05d42fb26fd39b7ae9b38e24373fab18c0270e diff --git a/sci-chemistry/relax/metadata.xml b/sci-chemistry/relax/metadata.xml deleted file mode 100644 index 00870a633858..000000000000 --- a/sci-chemistry/relax/metadata.xml +++ /dev/null @@ -1,30 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <longdescription> - The program relax is a software package designed for the study of molecular - dynamics through the analysis of experimental NMR data. Organic molecules, - proteins, RNA, DNA, sugars, and other biomolecules are all supported. It - was originally written for the model-free analysis of protein dynamics, - though its scope has been significantly expanded. - - relax is a community driven project created by NMR spectroscopists for - NMR spectroscopists. It supports a diverse range of analyses: - - Model-free analysis - the Lipari and Szabo model-free analysis of NMR - relaxation data. - R1 and R2 - the exponential curve fitting for the calculation of the - Rx NMR relaxation rates. - NOE - the calculation of the steady-state NOE NMR relaxation data. - Consistency testing of multiple field NMR relaxation data. - RSDM - Reduced Spectral Density Mapping. - Frame order and N-state model - study of domain motions via the N-state - model and frame order dynamics theories using anisotropic - NMR parameters such as RDCs and PCSs. - Stereochemistry investigations. - </longdescription> -</pkgmetadata> diff --git a/sci-chemistry/relax/relax-4.0.0-r4.ebuild b/sci-chemistry/relax/relax-4.0.0-r4.ebuild deleted file mode 100644 index ba03dbad8454..000000000000 --- a/sci-chemistry/relax/relax-4.0.0-r4.ebuild +++ /dev/null @@ -1,83 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -WX_GTK_VER="3.0" - -inherit eutils multiprocessing python-single-r1 scons-utils toolchain-funcs wxwidgets virtualx - -DESCRIPTION="Molecular dynamics by NMR data analysis" -HOMEPAGE="https://www.nmr-relax.com/" -SRC_URI="http://download.gna.org/relax/${P}.src.tar.bz2" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - $(python_gen_cond_dep " - dev-python/Numdifftools[\${PYTHON_MULTI_USEDEP}] - || ( - dev-python/matplotlib-python2[\${PYTHON_MULTI_USEDEP}] - dev-python/matplotlib[\${PYTHON_MULTI_USEDEP}] - ) - || ( - dev-python/numpy-python2[\${PYTHON_MULTI_USEDEP}] - dev-python/numpy[\${PYTHON_MULTI_USEDEP}] - ) - dev-python/wxpython:${WX_GTK_VER}[\${PYTHON_MULTI_USEDEP}] - sci-chemistry/pymol[\${PYTHON_MULTI_USEDEP}] - >=sci-libs/bmrblib-1.0.3[\${PYTHON_MULTI_USEDEP}] - >=sci-libs/minfx-1.0.11[\${PYTHON_MULTI_USEDEP}] - || ( - sci-libs/scipy-python2[\${PYTHON_MULTI_USEDEP}] - sci-libs/scipy[\${PYTHON_MULTI_USEDEP}] - ) - ") - sci-chemistry/molmol - sci-chemistry/vmd - sci-visualization/grace - sci-visualization/opendx - x11-libs/wxGTK:${WX_GTK_VER}[X]" -DEPEND="${RDEPEND} - media-gfx/pngcrush - test? ( ${RDEPEND} ) - " - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_prepare() { - rm -rf minfx bmrblib extern/numdifftools || die - tc-export CC - need-wxwidgets unicode -} - -src_compile() { - escons -} - -src_test() { - VIRTUALX_COMMAND="${EPYTHON} ./${PN}.py -x --traceback" - virtualmake -} - -src_install() { - dodoc README docs/{CHANGES,COMMITTERS,JOBS,relax.pdf} - - python_moduleinto ${PN} - python_domodule * - - rm ${PN} README || die - - make_wrapper ${PN}-nmr "${EPYTHON} $(python_get_sitedir)/${PN}/${PN}.py $@" -} diff --git a/sci-chemistry/sparky/Manifest b/sci-chemistry/sparky/Manifest deleted file mode 100644 index 483d19fd9cfe..000000000000 --- a/sci-chemistry/sparky/Manifest +++ /dev/null @@ -1,8 +0,0 @@ -AUX 3.115-fix-c++14.patch 849 BLAKE2B fde4158bf18e4cba23e0bb93972b10236e88e8cd3db055b81e328ff2fbddd38c8f6a051525e949b237adebd7a534aaa7639863aa17c3536fe35387e930ca5806 SHA512 80bbfe8a2e853f8be84ed48da99605805a42bb05b091c851ddbefb5513745cdf51c5396e97ad4e3be7dd199270fb069e239e0c24f6642d956fd6571d8b14a7e1 -AUX 3.115-ldflags.patch 2713 BLAKE2B 26873b508c9b0ecd5122712b8e599393bdf1787e9608b4e7e451d1db95ba2831af42e8f9d2637181f21e3206689bd115601fdcb7b48c0011cc30a83037bec087 SHA512 1c439cc04af3e8e403257ccd45eecb16f0e36d4b51a28ab5ddda269bde271d23a20bb453cda48e03f58c31a9a614d4b19ca2b6aa7f75bdfec1f79b70e8c361de -AUX 3.115-makefile.patch 580 BLAKE2B 4beeca38c910e583235d2aef66137165fe4ae58f48591e4567f50a1d702ea0391e467dd6f4baab4019a05a8b5051329b0485fc1cc56a38c6bfcbd53a06034a09 SHA512 9ddd99de93656301f307aabb3284e86fe68f4c7957f0b5ff81da4615f850fc36b686908de84816f0ff8a3d75169ccd0d4d7cb5bb8afd88d96c913f766e7ee19a -AUX 3.115-paths.patch 415 BLAKE2B 9e959f54626f3eb34e963a571cb9a92e92f87af4fd593972490dc3bf299ba8b9e42a47768f78ea8463f0fb1c76274ec334be8f4d5b1e52d339aa90eec7b7dd19 SHA512 44c44c99cf2c5c51c8e506267efc4efc50eb2277ccdab362943da0c45c63f9e797ae699e99eda3ce6ca0b4e0a886393d1917ce8614eea3086e97446fc3c0c674 -AUX 3.115-wrapper-r1.patch 1518 BLAKE2B a5dd56c76a36f1a1e67599b1dcb25ba9f8edd639220d9f3c248d64b7bee88a108482137ec70acb5ee466048abf5939122842ae827ffba23dcef7c895dbf20f56 SHA512 be2c18a40ceabdb1c25a7849e1ee00438092f264c486e93b3bfb412fc417902a3b22b672d28a6cc104fedc5477ea2c0de66bc40dd5d4d607ed0201eee4d368a7 -DIST sparky-source-3.115.tar.gz 4103686 BLAKE2B c7811aa135b10f21b8807447e2ab173f407ccc1446ff1307006f7f885e6e69983647991600720e02e4e738bb68338de01bc5d57577eacf20298db6d53a54b183 SHA512 33b0fd368f15bf4d091d7152a189f57279aea54fb89a12f15314f2a1414b073f7bd282afedeb72e79192195b0b6ac212ca74da3def513592af5400c118ac8e89 -EBUILD sparky-3.115-r2.ebuild 3192 BLAKE2B 172ded57706c8aac3a4f9d268fd75f410d35dffc9c26352695c3961c2508dc08773e3a9c857d530ab47341ac3977daac78939661d14c8334da4eadba7852e610 SHA512 f2f5fe11666e85feca9d90c5fb6c9d93f42b9bde269f311a943c37b334d617d7dcdbc5ee45cb555fb6af278a648c0c0ab4ec28027143675ee0cc2c77dc41c10a -MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/sparky/files/3.115-fix-c++14.patch b/sci-chemistry/sparky/files/3.115-fix-c++14.patch deleted file mode 100644 index 3a05ea7d85ce..000000000000 --- a/sci-chemistry/sparky/files/3.115-fix-c++14.patch +++ /dev/null @@ -1,32 +0,0 @@ -Fix the custom new/new[] operators in order to account for changed -noexcept semantics in C++11. -See also: https://bugs.gentoo.org/show_bug.cgi?id=596012 - -Patch by Peter Levine - ---- a/c++/memalloc.cc -+++ b/c++/memalloc.cc -@@ -39,7 +39,10 @@ - - // ---------------------------------------------------------------------------- - // --void *operator new(size_t size) throw(std::bad_alloc) -+void *operator new(size_t size) -+#if __cplusplus < 201103L -+throw(std::bad_alloc) -+#endif - { - void *value = allocate(size); - if (tracking_memory) -@@ -72,7 +75,10 @@ - - // ---------------------------------------------------------------------------- - // --void *operator new[](size_t size) throw(std::bad_alloc) -+void *operator new[](size_t size) -+#if __cplusplus < 201103L -+throw(std::bad_alloc) -+#endif - { - void *value = allocate(size); - if (tracking_memory) diff --git a/sci-chemistry/sparky/files/3.115-ldflags.patch b/sci-chemistry/sparky/files/3.115-ldflags.patch deleted file mode 100644 index bd4020387682..000000000000 --- a/sci-chemistry/sparky/files/3.115-ldflags.patch +++ /dev/null @@ -1,61 +0,0 @@ -diff --git a/c++/Makefile b/c++/Makefile -index aeb4daa..5cab356 100644 ---- a/c++/Makefile -+++ b/c++/Makefile -@@ -131,28 +131,28 @@ $(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk: - chmod 755 $@ - - sparky-no-python$(EXE_SUFFIX): main.o $(SPARKY_OBJS) -- $(CXX) -o $@ main.o $(SPARKY_OBJS) $(LDFLAGS) $(LDLIBS) -+ $(CXX) $(LDFLAGS) -o $@ main.o $(SPARKY_OBJS) $(LDLIBS) - - ucsfdata$(EXE_SUFFIX): ucsfdata.o $(NMR_OBJS) -- $(CXX) -o $@ ucsfdata.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) -+ $(CXX) $(LDFLAGS) -o $@ ucsfdata.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) - - pipe2ucsf$(EXE_SUFFIX): pipe2ucsf.o $(NMR_OBJS) -- $(CXX) -o $@ pipe2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) -+ $(CXX) $(LDFLAGS) -o $@ pipe2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) - - vnmr2ucsf$(EXE_SUFFIX): vnmr2ucsf.o $(NMR_OBJS) -- $(CXX) -o $@ vnmr2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) -+ $(CXX) $(LDFLAGS) -o $@ vnmr2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) - - bruk2ucsf$(EXE_SUFFIX): bruk2ucsf.o $(NMR_OBJS) -- $(CXX) -o $@ bruk2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) -+ $(CXX) $(LDFLAGS) -o $@ bruk2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) - - peaks2ucsf$(EXE_SUFFIX): peaks2ucsf.o $(NMR_OBJS) -- $(CXX) -o $@ peaks2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) -+ $(CXX) $(LDFLAGS) -o $@ peaks2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) - - matrix2ucsf$(EXE_SUFFIX): matrix2ucsf.o $(NMR_OBJS) -- $(CXX) -o $@ matrix2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) -+ $(CXX) $(LDFLAGS) -o $@ matrix2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) - - spy.so: python.o $(SPARKY_OBJS) -- $(CXX) $(LDSHARED) -o $@ python.o $(SPARKY_OBJS) $(LDFLAGS) $(LDLIBS) -+ $(CXX) $(LDSHARED) $(LDFLAGS) -o $@ python.o $(SPARKY_OBJS) $(LDLIBS) - - winsystem-$(PLATFORM).o: winsystem-$(PLATFORM).cc - $(CXX) $(CXXFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/winsystem-$(PLATFORM).cc -@@ -161,7 +161,7 @@ python.o: python.cc - $(CXX) $(CXXFLAGS) $(PYFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/python.cc - - _tkinter.so: _tkinter.o -- $(CXX) $(LDSHARED) -o $@ _tkinter.o $(LDFLAGS) $(TKLIBS) -+ $(CXX) $(LDSHARED) $(LDFLAGS) -o $@ _tkinter.o $(TKLIBS) - - _tkinter.o: _tkinter.c - $(CC) $(CFLAGS) $(TKFLAGS) $(PYFLAGS) -c $(SPARKY_SRC)/_tkinter.c -@@ -188,8 +188,8 @@ PYLDFLAGS = -L$(PYTHON_LIB)/config -lpython$(PYTHON_VERSION) - PYIFLAGS = -I$(PYTHON_INC) - - debug-sparky: main-debug.o python.o _tkinter.o $(SPARKY_OBJS) -- $(CXX) -o $@ main-debug.o python.o _tkinter.o $(SPARKY_OBJS) \ -- $(LDFLAGS) $(PYLDFLAGS) $(LDLIBS) -+ $(CXX) $(LDFLAGS) -o $@ main-debug.o python.o _tkinter.o $(SPARKY_OBJS) \ -+ $(PYLDFLAGS) $(LDLIBS) - - main-debug.o: main-debug.cc - $(CXX) $(CXXFLAGS) $(PYIFLAGS) -c $(SPARKY_SRC)/main-debug.cc diff --git a/sci-chemistry/sparky/files/3.115-makefile.patch b/sci-chemistry/sparky/files/3.115-makefile.patch deleted file mode 100644 index 7c810dcbd8ae..000000000000 --- a/sci-chemistry/sparky/files/3.115-makefile.patch +++ /dev/null @@ -1,17 +0,0 @@ -diff --git a/Makefile b/Makefile -index bb27034..30979bd 100644 ---- a/Makefile -+++ b/Makefile -@@ -48,6 +48,12 @@ TKINTER_PYMOD = _tkinter$(PYMOD_SUFFIX) - all nopython $(SPY_PYMOD) $(TKINTER_PYMOD) $(EXECUTABLES) debug-sparky clean: force - cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $@ - -+libraries: -+ cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $(SPY_PYMOD) $(TKINTER_PYMOD) -+ -+binaries: -+ cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $(EXECUTABLES) debug-sparky -+ - Makefile.dep TAGS: force - cd $(SPARKY_SRC) && $(MAKE) -f Makefile -e $@ - diff --git a/sci-chemistry/sparky/files/3.115-paths.patch b/sci-chemistry/sparky/files/3.115-paths.patch deleted file mode 100644 index 20d9a801ecd6..000000000000 --- a/sci-chemistry/sparky/files/3.115-paths.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/c++/paths.h b/c++/paths.h -index 2a21366..38aff52 100644 ---- a/c++/paths.h -+++ b/c++/paths.h -@@ -19,7 +19,7 @@ - // Installation subdirectories and files - // - #define SPARKY_MANUAL "manual" --#define SPARKY_LIB "lib" -+#define SPARKY_LIB "." - #define SPARKY_PRINT "print-prolog.ps" // under lib directory - #define SPARKY_RESOURCE "Sparky" // under lib directory - #define SPARKY_SAMPLE_DATA "example" diff --git a/sci-chemistry/sparky/files/3.115-wrapper-r1.patch b/sci-chemistry/sparky/files/3.115-wrapper-r1.patch deleted file mode 100644 index d83b5b8510cc..000000000000 --- a/sci-chemistry/sparky/files/3.115-wrapper-r1.patch +++ /dev/null @@ -1,41 +0,0 @@ -diff --git a/bin/sparky b/bin/sparky -index 8b51212..270723a 100644 ---- a/bin/sparky -+++ b/bin/sparky -@@ -4,18 +4,6 @@ - # - - # ----------------------------------------------------------------------------- --# Figure out Sparky installation directory from $0. --# --set sparky_exe = "$0" --while (-l "$sparky_exe") -- set ls_sparky_exe = `ls -l "$sparky_exe"` -- set sparky_exe = `echo "$ls_sparky_exe" | sed 's/.* -> //'` --end --set sparky_bin = `dirname "$sparky_exe"` --set sparky_bin = `cd "$sparky_bin"; pwd` --set sparky_inst = `dirname "$sparky_bin"` -- --# ----------------------------------------------------------------------------- - # Sparky uses the SPARKY_INSTALL environment variable to find its - # application resource file and print prolog file. - # -@@ -25,7 +13,7 @@ setenv SPARKY_INSTALL "$sparky_inst" - # If Python is available start Sparky as a Python extension. - # Otherwise the standalone version of Sparky is started. - # --set PYTHON = "$SPARKY_INSTALL/python2.5/bin/python2.5" -+set PYTHON = GENTOO_PYTHON - if (! -e "$PYTHON") then - set PYTHON = python2.5 - endif -@@ -79,7 +67,7 @@ if ($status == 0) then - # --------------------------------------------------------------------------- - # Add the Sparky package and Tkinter to the Python path - # -- set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/lib-tk" -+ set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/sparky" - if ($?PYTHONPATH) then - setenv PYTHONPATH "${SPARKY_PYTHONPATH}:$PYTHONPATH" - else diff --git a/sci-chemistry/sparky/metadata.xml b/sci-chemistry/sparky/metadata.xml deleted file mode 100644 index 8937bad0b175..000000000000 --- a/sci-chemistry/sparky/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/sparky/sparky-3.115-r2.ebuild b/sci-chemistry/sparky/sparky-3.115-r2.ebuild deleted file mode 100644 index e664747fea13..000000000000 --- a/sci-chemistry/sparky/sparky-3.115-r2.ebuild +++ /dev/null @@ -1,117 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="tk" - -inherit flag-o-matic prefix python-single-r1 toolchain-funcs - -DESCRIPTION="Graphical NMR assignment and integration program for large polymers" -HOMEPAGE="http://www.cgl.ucsf.edu/home/sparky/" -SRC_URI="http://www.cgl.ucsf.edu/home/sparky/distrib-${PV}/${PN}-source-${PV}.tar.gz" - -LICENSE="sparky" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="examples" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - app-shells/tcsh - dev-lang/tcl:0= - dev-lang/tk:0=" -DEPEND="${RDEPEND}" - -RESTRICT="mirror" - -S="${WORKDIR}/${PN}" - -PATCHES=( - "${FILESDIR}"/${PV}-ldflags.patch - "${FILESDIR}"/${PV}-wrapper-r1.patch - "${FILESDIR}"/${PV}-paths.patch - "${FILESDIR}"/${PV}-makefile.patch - "${FILESDIR}"/${PV}-fix-c++14.patch -) - -pkg_setup() { - python-single-r1_pkg_setup - TKVER=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - PYVER=${EPYTHON#python} -} - -src_prepare() { - default - - sed -i \ - -e "s:^\(set PYTHON =\).*:\1 ${PYTHON}:g" \ - -e "s:^\(setenv SPARKY_INSTALL[[:space:]]*\).*:\1 ${EPREFIX}/usr/$(get_libdir)/${PN}:g" \ - -e "s:tcl8.4:tcl${TKVER}:g" \ - -e "s:tk8.4:tk${TKVER}:g" \ - -e "s:^\(setenv TCLTK_LIB[[:space:]]*\).*:\1 ${EPREFIX}/usr/$(get_libdir):g" \ - "${S}"/bin/sparky || die - eprefixify "${S}"/bin/sparky -} - -src_compile() { - emake \ - SPARKY="${S}" \ - PYTHON_VERSION="${PYVER}" \ - PYTHON_PREFIX="${EPREFIX}/usr" \ - PYTHON_LIB="${EPREFIX}/usr/$(get_libdir)" \ - PYTHON_INC="$(python_get_includedir)" \ - TK_PREFIX="${EPREFIX}/usr" \ - TCLTK_VERSION="${TKVER}" \ - TKLIBS="-L${EPREFIX}/usr/$(get_libdir)/ -ltk -ltcl -lX11" \ - CXX="$(tc-getCXX)" \ - CC="$(tc-getCC)" \ - LDSHARED="-shared" \ - binaries - - rm c++/*.o || die - - emake \ - SPARKY="${S}" \ - PYTHON_VERSION="${PYVER}" \ - PYTHON_PREFIX="${EPREFIX}/usr" \ - PYTHON_LIB="${EPREFIX}/usr/$(get_libdir)" \ - PYTHON_INC="$(python_get_includedir)" \ - TK_PREFIX="${EPREFIX}/usr" \ - TCLTK_VERSION="${TKVER}" \ - TKLIBS="-L${EPREFIX}/usr/$(get_libdir)/ -ltk -ltcl -lX11" \ - CXX="$(tc-getCXX)" \ - CC="$(tc-getCC)" \ - CXXFLAGS="${CXXFLAGS} -fPIC" \ - CFLAGS="${CFLAGS} -fPIC" \ - LDSHARED="-shared -fPIC" \ - libraries -} - -src_install() { - # The symlinks are needed to avoid hacking the complete code to fix the locations - dobin c++/{{bruk,matrix,peaks,pipe,vnmr}2ucsf,ucsfdata,sparky-no-python} bin/${PN} - - insinto /usr/share/${PN}/ - doins lib/{print-prolog.ps,Sparky} - dosym ../../share/${PN}/print-prolog.ps /usr/$(get_libdir)/${PN}/print-prolog.ps - dosym ../../share/${PN}/Sparky /usr/$(get_libdir)/${PN}/Sparky - - python_moduleinto ${PN} - python_domodule python/*.py c++/{spy.so,_tkinter.so} - dosym ../${EPYTHON}/site-packages /usr/$(get_libdir)/${PN}/python - - rm manual/{pkzip.cfg,Makefile} || die - mv {manual/,}manual.ps || die - local DOCS=( README manual.ps ) - local HTML_DOCS=( manual/. ) - einstalldocs - newdoc python/README README.python - dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/${PN}/manual - - if use examples; then - dodoc -r example - dosym ../../share/doc/${PF}/example /usr/$(get_libdir)/${PN}/example - fi -} diff --git a/sci-chemistry/viewmol/Manifest b/sci-chemistry/viewmol/Manifest deleted file mode 100644 index 7de430c5ed44..000000000000 --- a/sci-chemistry/viewmol/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -AUX 2.4.1-change-default-paths.patch 2745 BLAKE2B c604ab1ffbe992b49671f0f1c713ce95fa2cec18b39d625856bdf8cbc226f8965f3fc13b22003a8ec812954daf2533cac4a001255e07a5cd3bf0eeaeed6524dd SHA512 9dda6e39f43706f9868eb02402137573d58e90b14940ad5d10ede6088e49d2ebd8a114ffda3cf4a69bee5874cc0a16b83bb4ea86281203765c5d861cb8dac6dd -AUX 2.4.1-remove-icc-check.patch 1020 BLAKE2B 63c0b2c68be4bc745f8dbc184f1ca90bc0b5e2964508e686c811cb1a3f46d5ed8f401f789fce8e8f15b89e1ccaf7a657a2de830c2e829d6782f285031a89ee3c SHA512 ea2a1a58730561fcf2bc05a0f23dc2108cf2fd97d228a7a6305d3323abda5ce3510793dbebf2253cef9e6d60326889079bc6a9639228b1b2bfd9d9a3b8c03ebb -DIST viewmol-2.4.1.src.tgz 2229379 BLAKE2B c7d3d9f0a0a728f13be718e2b85a645d1824d2c9efd920a05a0693dfb5904e18da20fcef8080e99f497280effdb71cb21c58d9aeadf49d2477e1c931caa49389 SHA512 42701d570d97e77b84597950a9068dfdf48faf4e551957383c8eea38f082c1ad136c17b7cbd3903673478506116d6fc08d1288842e74d6a9776526c685083584 -EBUILD viewmol-2.4.1-r3.ebuild 2225 BLAKE2B 74563226fe1bcbe418bde909f202eead15aedf7610a592f8d6d7ae1b2e0d47cf2bdec2a91e21772f978512ddbe0cc0739028694f85a2fa13adcaa9fe9e79a6c6 SHA512 b290d08a50662422876d093b973ba7b4e44fe759258325d1f796beb8f929575861a0b8367d52b1ab8a5976dea8e5b805894454867f32751fbd768bd6c9a3476c -MISC metadata.xml 342 BLAKE2B 3d43fda7cef989246f20968757c7c9710832915b5aa7623026185e69f79901fdeed5503c04a87d7395bcc0f9fd47313a017673903df74cc7a55999fb5c24467a SHA512 f77c63597bc5df26ba6dd136ee943f78562c5d99fefc1b435633c602a6eb3433600976884085ea8aa8f87f2f79fd495e9b51f918290bc1751e66d7515fe4e039 diff --git a/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch b/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch deleted file mode 100644 index 4b1edef7ef8b..000000000000 --- a/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch +++ /dev/null @@ -1,68 +0,0 @@ -diff --git a/source/getrc.c b/source/getrc.c -index a39b436..c130096 100644 ---- a/getrc.c -+++ b/getrc.c -@@ -87,7 +87,7 @@ extern XtAppContext app; - - static char viewmolpath[MAXLENLINE]; - --#define DEFAULTPATH "/usr/local/lib/viewmol" -+#define DEFAULTPATH "@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR/viewmol" - - int getrc(void) - { -diff --git a/source/install b/source/install -index 580865b..f136af3 100755 ---- a/install -+++ b/install -@@ -54,24 +54,27 @@ fi - cp $dirorig/viewmol $ROOT/bin - chmod 711 $ROOT/bin/viewmol - --# install other files needed in $ROOT/lib/viewmol --if [ ! -d $ROOT/lib/viewmol/$dir ] -+# install other files needed in $ROOT/GENTOOLIBDIR/viewmol -+if [ ! -d $ROOT/GENTOOLIBDIR/viewmol/$dir ] - then -- mkdir -p $ROOT/lib/viewmol/$dir -- chmod 755 $ROOT/lib/viewmol/$dir -+ mkdir -p $ROOT/GENTOOLIBDIR/viewmol/$dir -+ chmod 755 $ROOT/GENTOOLIBDIR/viewmol/$dir - fi - cd $dirorig --cp tm bio readgamess readgauss readmopac readpdb $ROOT/lib/viewmol/$dir --chmod 711 $ROOT/lib/viewmol/$dir/* -+cp tm bio readgamess readgauss readmopac readpdb $ROOT/GENTOOLIBDIR/viewmol/$dir -+chmod 711 $ROOT/GENTOOLIBDIR/viewmol/$dir/* - cd ../.. --cp readdmol readdmol.awk readgulp readpqs writecar writegauss.py writemol writetm $ROOT/lib/viewmol --chmod 755 $ROOT/lib/viewmol/* --cp -r doc examples locale scripts tests $ROOT/lib/viewmol --find $ROOT/lib/viewmol -type f -exec chmod a+r {} \; --find $ROOT/lib/viewmol -type d -exec chmod a+rx {} \; --sed 's/\/source//g' viewmolrc > $ROOT/lib/viewmol/viewmolrc --chmod -R 644 $ROOT/lib/viewmol/viewmolrc --if [ -d /usr/X11R6/lib/X11/app-defaults ] -+cp readdmol readdmol.awk readgulp readpqs writecar writegauss.py writemol writetm $ROOT/GENTOOLIBDIR/viewmol -+chmod 755 $ROOT/GENTOOLIBDIR/viewmol/* -+mkdir -p $ROOT/usr/share/viewmol $ROOT/usr/share/doc/GENTOODOCDIR/ $ROOT/GENTOOLIBDIR/viewmol/ -+cp -r examples scripts tests $ROOT/usr/share/viewmol -+cp -r locale $ROOT/GENTOOLIBDIR/viewmol/ -+cp -r doc/* examples scripts tests $ROOT/usr/share/doc/GENTOODOCDIR/ -+find $ROOT/GENTOOLIBDIR/viewmol -type f -exec chmod a+r {} \; -+find $ROOT/GENTOOLIBDIR/viewmol -type d -exec chmod a+rx {} \; -+sed 's/\/source//g' viewmolrc > $ROOT/GENTOOLIBDIR/viewmol/viewmolrc -+chmod -R 644 $ROOT/GENTOOLIBDIR/viewmol/viewmolrc -+if [ -d $ROOT/X11R6/GENTOOLIBDIR/X11/app-defaults ] - then - locale=`echo $LANG | cut -c1-2` - if [ "$locale" = "en" ] -@@ -82,6 +85,6 @@ then - # The C locale is defined by default for rpm builds, overwrite it - locale="en_US" - fi -- cp locale/${locale}/Viewmol /usr/X11R6/lib/X11/app-defaults -- chmod a+r /usr/X11R6/lib/X11/app-defaults/Viewmol -+ cp locale/${locale}/Viewmol ${ROOT}/X11R6/GENTOOLIBDIR/X11/app-defaults -+ chmod a+r ${ROOT}/X11R6/GENTOOLIBDIR/X11/app-defaults/Viewmol - fi diff --git a/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch b/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch deleted file mode 100644 index fd91e0a5a434..000000000000 --- a/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- a/getmachine -+++ b/getmachine -@@ -269,19 +269,11 @@ - makedir - cat ../.config.$os > makefile - use_icc=`type icc 2> /dev/null` -- if [ "$use_icc" = "" ] -- then - findProcessor - echo 'COMPILER=gcc' >> makefile - echo "OPT=-O6 -mcpu=$processor -fomit-frame-pointer -ffast-math -malign-double" >> makefile - echo 'CFLAGS=-Wall -I/usr/X11R6/include -DLINUX -Wno-strict-aliasing' >> makefile - echo "LDFLAGS=$LINKFORSHARED" >> makefile -- else -- echo 'COMPILER=icc' >> makefile -- echo 'OPT=-O2 -ipo' >> makefile -- echo 'CFLAGS=-I/opt/intel/compiler50/ia32/include -I/usr/X11R6/include -DLINUX' >> makefile -- echo "LDFLAGS=$LINKFORSHARED -ipo" >> makefile -- fi - echo 'SCANDIR=' >> makefile - echo 'INCLUDE=$(TIFFINCLUDE) -I$(PNGINCLUDE) -I$(PYTHONINCLUDE)' >> makefile - echo 'LIBRARY=$(LIBTIFF) $(LIBPNG) -L$(LIBPYTHON)' >> makefile diff --git a/sci-chemistry/viewmol/metadata.xml b/sci-chemistry/viewmol/metadata.xml deleted file mode 100644 index 335c7edd503b..000000000000 --- a/sci-chemistry/viewmol/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">viewmol</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/viewmol/viewmol-2.4.1-r3.ebuild b/sci-chemistry/viewmol/viewmol-2.4.1-r3.ebuild deleted file mode 100644 index a82367bac3b7..000000000000 --- a/sci-chemistry/viewmol/viewmol-2.4.1-r3.ebuild +++ /dev/null @@ -1,89 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="tk(-)" - -inherit prefix python-single-r1 toolchain-funcs - -DESCRIPTION="Open-source graphical front end for computational chemistry programs" -HOMEPAGE="http://viewmol.sourceforge.net/" -SRC_URI="mirror://sourceforge/viewmol/${P}.src.tgz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - media-libs/libpng:0= - media-libs/tiff:0 - virtual/glu - virtual/opengl - x11-libs/libX11 - x11-libs/libXi - x11-libs/libXmu - x11-libs/libXt - x11-libs/motif:0 - ${PYTHON_DEPS}" -DEPEND="${RDEPEND} - x11-base/xorg-proto" - -S="${WORKDIR}/${P}/source" - -PATCHES=( - "${FILESDIR}"/${PV}-remove-icc-check.patch - "${FILESDIR}"/${PV}-change-default-paths.patch -) - -src_prepare() { - default - - eprefixify getrc.c - sed "s:GENTOOLIBDIR:$(get_libdir):g" -i install getrc.c || die - sed "s:GENTOODOCDIR:${PF}:g" -i install || die - - mkdir "$(uname -s)" || die - cd "$(uname -s)" || die - - cat >> ".config.$(uname -s)" <<- EOF || die - LIBTIFF = -L"${EPREFIX}/usr/$(get_libdir)" - TIFFINCLUDE = "${EPREFIX}/usr/include" - - LIBPNG = -L"${EPREFIX}/usr/$(get_libdir)" - PNGINCLUDE = "${EPREFIX}/usr/include" - - PYTHONVERSION = ${EPYTHON} - PYTHONINCLUDE = $(python_get_CFLAGS) - PYTHONLIB = $(python_get_LIBS) - - COMPILER = $(tc-getCC) - CFLAGS = ${CFLAGS} -DLINUX - LDFLAGS = ${LDFLAGS} - SCANDIR= - INCLUDE=\$(TIFFINCLUDE) -I\$(PNGINCLUDE) \$(PYTHONINCLUDE) - LIBRARY=\$(LIBTIFF) \$(LIBPNG) \$(PYTHONLIB) - LIBS=-L"${EPREFIX}/usr/$(get_libdir)" -ltiff -lpng -lz -lGLU -lGL -L"${EPREFIX}/usr/X11R6/lib" -lXm -lXmu -lXp -lXi -lXext -lXt -lX11 -lpthread -lutil -ldl -lm - EOF - - cp .config.$(uname -s) makefile || die - cat ../Makefile >> makefile || die -} - -src_compile() { - emake -C "$(uname -s)" viewmol_ tm_ bio_ readgamess_ readgauss_ readmopac_ readpdb_ - "${EPREFIX}"/bin/bash makeTranslations || die -} - -src_install() { - ./install "${ED%/}"/usr || die - - # fix broken layout - mv "${ED%/}"/usr/{usr/share,} || die - rm -rf "${ED%/}"/usr/usr || die - mv "${ED%/}"/usr/{$(get_libdir)/${PN}/locale,share} || die - mv "${ED%/}"/usr/{$(get_libdir),libexec} || die -} diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest index 1cd5411f26dc..7185dba46aa6 100644 --- a/sci-chemistry/vmd/Manifest +++ b/sci-chemistry/vmd/Manifest @@ -1,15 +1,7 @@ -AUX vmd-1.9.1-cuda-device_ptr.patch 894 BLAKE2B 96aeab7c2b9d29e5cd3558e69d1365d6b7dc2d78284bb1185d63a57300a83a4c7c0b8f1c1718027ff33333d34bba116d6898fbee74ab23dfd1a77c560160d659 SHA512 9a561773562873dad077f0f2903299952cb935c69ae4bd1463a5f79d6f27ae3845ac5a24ee295ff3569d9c65ae00a9fe3974f4ead003109246f97d130c2c48bf -AUX vmd-1.9.2-format-security.patch 550 BLAKE2B d50d05d8697c345f5888b1344c827be1282c5b2e06cfddac022d562688550a728a91a943f9b31c4247f683dcd062ab8fe8ed360aa97a202f20af0467a3148cd3 SHA512 81a71ee4c4c438d18f3a393ebad5c9a08f1a7bb95fa58b78a8798955a34ae2494f80fa074b973a1b595862080e9103d21e509443742cfe2bc3cf77f10c0e3c9d AUX vmd-1.9.3-configure-libtachyon.patch 613 BLAKE2B 5717e941102c4d759d6985087f74724df21312a61313d397da1bbac1969b76590117c70bc3b7fac6c7a84483df433d03613b245a05db8bb10bf7b8807369f415 SHA512 1eafa38022588e9b9bba3a15394a432f66693e64ba62c27e7aebf759d279cb04326f76bcc6545ef34cbcbd7446aead1a05a18072e99aa7df0940f11173ab3c00 AUX vmd-1.9.3-cuda.patch 15569 BLAKE2B a26ce893fd2808b7ce1ad36f6d2d690be482d24805f44030434fd3aadaa9f9a834ae8b73d7f1c759161e20041c2372181b90ae17f71eab50c94e6b38e3b133a3 SHA512 ba6f435601a53d5ed26ceab9ab86a9734e6a3b60f9cb61be5c9f59676a5145a4c64a538ddadf446e82608ade5a3d86ec6b8cb7257d9c402e245f845371feb571 AUX vmd-1.9.3-tmpdir.patch 673 BLAKE2B 074456a8a68a36f16a804aeb8caee9abf14505cb76a2661b03ad97119bf4afb13a994c9cf22eeb952a79a980fcf03bd3dee5c93cf63bf82a19831f71bcbd83c2 SHA512 f7f570c729259f9133fb6411047266312c3d5f802d4cffe316cfdc4094f0fd0830c3eaae6408f56ea17dadba283e1a1fdf86fec858a5211b1c00ed927f160ea4 -DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 BLAKE2B eb7c7fb982602f37bd8374bf8458a0a2ea2202161248caffd0d4e0f8124d627755304bb778976e1cf5598b6bfbbe5d8c8e6016c9ec562204d6782aaaf179b185 SHA512 0516b9e57b256ce822a64df420ebf3ab7391722757caeaa7e615526242043e9375fee8f4ee86fb4eb8de7a50d5cfc8f8d973ace5fa082e6f9010eb692cd6ee51 -DIST vmd-1.9.2.src.tar.gz 34903084 BLAKE2B f7f7048ef7bb72a8b0dcae955c7f90691085158c38a59229d5b929a4b52d3148bdb2f40084cf8c4544f01cb8bcb57de1d98a90bd17568a07c4ebb8f6985cec9b SHA512 b232b743d4ea97dcf76e3005e1c8716d7138602edc078c4846026ab67759c8559af956182cb1acf3c85890db10b6f658ac9c269d432f2595612cf376d6d505ef DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1 DIST vmd-1.9.3.src.tar 129566720 BLAKE2B 848f3280d51765dcd18722dd233e0cdee3b7c0ac3dd48324260ebe1604ba781ca0a1fe4cae6652501d23d5d41712020e17dbb6bc21a1856eb3289a4aab6b774b SHA512 0502df1e8b60c570ca88b779b4153acfaa599a78df53fa96fca36301bab902864118332b5524ae7d170d3a9e429cf1e13d69e1197268b5e841afc0bb56a737ba -EBUILD vmd-1.9.2.ebuild 7255 BLAKE2B d59ea537a43555104edd2effc973274abae483d739bf5051efce7c1ad15e131ff0156ce2129cf882c88194f359c69eb163571e23f47025ae26cc6f85ab4999a2 SHA512 bafeb7c0448920feaa77855d29cffd2e3d9df1994c528bb738ac01551d6eb5fea4d3e681f5d4c189366e8dff973c9f8c5633f18648c31026ce749041eb5358ee -EBUILD vmd-1.9.3-r1.ebuild 7612 BLAKE2B 62e0208cbe8fac390d942885f1e12713a88dc29eac68aa708dacfa9a2c0c0eff94982795ddc3bce47c459e8153692978744efdf520518705db0892208761dd9d SHA512 4529071928c4b63ebc35d92ff9ef7713a38d49d5579cf4351a979806ae81eb9ce3e02c438a9ce127eba217039341ae2c53e74710aa0151d4e9b0db865458facb -EBUILD vmd-1.9.3-r4.ebuild 7793 BLAKE2B 9f023e8efb5a095d2d6b46198a4137298d7e61c697e7f1eeb57ecfa5f1df7102840b9c42f4ceeb8c5052c59031d572a50eda0a2799a11432487b15a21e97eb5c SHA512 22326601bd6908b3495ebef7e9b45f3482dbd73c8b6bd54582d02e4721bcc483ef02ea67d8e582b59777cbfc923e4464a707281a06b6459de64a7f1e301d9268 EBUILD vmd-1.9.3-r5.ebuild 7822 BLAKE2B 2a3933c1008dcde65b37846ae5cfc993036d387a9a62a4cb207865187a22e8cf41401000171d083e059abc17c43adf773490aafcfbc576480b241fd359f6fb88 SHA512 9abc8facc673387ee0fcc77b27e4f421f2c7cb590b451b5d8ce4165a66be27ad1b69a45d9c939718a4359f1c76591855219bdb5956947aa2408d61f338eb78ca -EBUILD vmd-1.9.3.ebuild 7210 BLAKE2B a4c7a26b5c137c67adb5ea4b49acf0b8866a5b5a30840816a7c5a62c12355dfbb3bf17b2dfff39501c9d63e5bf3b479624c9186f7eaef65db455a9f29fe543a3 SHA512 fea1bf7019ae20f796be0c9fb9a5f912a491de16ecabeb6327b366120621c65401f8b4d32a575cf8d231b2c40d54f7c38537f3ce6a217856e1ec44fe49420e38 MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9 diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch deleted file mode 100644 index 67eb11bbd36b..000000000000 --- a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch +++ /dev/null @@ -1,28 +0,0 @@ - vmd-1.9.1/src/CUDAMarchingCubes.cu | 1 + - vmd-1.9.1/src/CUDAQuickSurf.cu | 1 + - 2 files changed, 2 insertions(+) - -diff --git a/vmd-1.9.1/src/CUDAMarchingCubes.cu b/vmd-1.9.1/src/CUDAMarchingCubes.cu -index 5bfe7bf..36faaf0 100755 ---- a/src/CUDAMarchingCubes.cu -+++ b/src/CUDAMarchingCubes.cu -@@ -45,6 +45,7 @@ - #include "CUDAMarchingCubes.h" - #include <thrust/scan.h> - #include <thrust/functional.h> -+#include <thrust/device_ptr.h> - - // The number of threads to use for triangle generation - // (limited by shared memory size) -diff --git a/vmd-1.9.1/src/CUDAQuickSurf.cu b/vmd-1.9.1/src/CUDAQuickSurf.cu -index a21ebde..56a42c8 100755 ---- a/src/CUDAQuickSurf.cu -+++ b/src/CUDAQuickSurf.cu -@@ -22,6 +22,7 @@ - #include <stdlib.h> - #include <string.h> - #include <cuda.h> -+#include <thrust/device_ptr.h> - - #if CUDART_VERSION < 4000 - #error The VMD QuickSurf feature requires CUDA 4.0 or later diff --git a/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch b/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch deleted file mode 100644 index 3f9ea5c8c2ef..000000000000 --- a/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch +++ /dev/null @@ -1,16 +0,0 @@ - plugins/molfile_plugin/src/maeffplugin.cxx | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/plugins/molfile_plugin/src/maeffplugin.cxx b/plugins/molfile_plugin/src/maeffplugin.cxx -index cfe1223..41d92bb 100644 ---- a/plugins/molfile_plugin/src/maeffplugin.cxx -+++ b/plugins/molfile_plugin/src/maeffplugin.cxx -@@ -1979,7 +1979,7 @@ namespace { - } - } - catch (std::exception &e) { -- fprintf(stderr, e.what()); -+ fprintf(stderr, "%s", e.what()); - return MOLFILE_ERROR; - } - return MOLFILE_SUCCESS; diff --git a/sci-chemistry/vmd/vmd-1.9.2.ebuild b/sci-chemistry/vmd/vmd-1.9.2.ebuild deleted file mode 100644 index 92daf0304775..000000000000 --- a/sci-chemistry/vmd/vmd-1.9.2.ebuild +++ /dev/null @@ -1,256 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs - -DESCRIPTION="Visual Molecular Dynamics" -HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" -SRC_URI=" - https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz - ${P}.src.tar.gz" - -SLOT="0" -LICENSE="vmd" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="cuda gromacs msms povray sqlite tachyon xinerama" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RESTRICT="fetch" - -# currently, tk-8.5* with USE=truetype breaks some -# tk apps such as Sequence Viewer or Timeline. -CDEPEND=" - >=dev-lang/tk-8.6.1 - dev-lang/perl - dev-libs/expat - $(python_gen_cond_dep ' - || ( - dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}] - dev-python/numpy[${PYTHON_MULTI_USEDEP}] - ) - ') - sci-libs/netcdf:0= - virtual/opengl - >=x11-libs/fltk-1.1.10-r2:1 - x11-libs/libXft - x11-libs/libXi - ${PYTHON_DEPS} - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) - gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1[tng] ) - sqlite? ( dev-db/sqlite:3= ) - tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) - xinerama? ( x11-libs/libXinerama )" -DEPEND="${CDEPEND} - virtual/pkgconfig - dev-lang/swig" -RDEPEND="${CDEPEND} - sci-biology/stride - sci-chemistry/surf - x11-terms/xterm - msms? ( sci-chemistry/msms-bin ) - povray? ( media-gfx/povray ) - " - -VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" -# Binary only plugin!! -QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" -QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" -QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" - -pkg_nofetch() { - elog "Please download ${P}.src.tar.gz from" - elog "${VMD_DOWNLOAD}" - elog "after agreeing to the license and get" - elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" - elog "Place both into your DISTDIR directory" -} - -src_prepare() { - use cuda && cuda_sanitize - - epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch - - cd "${WORKDIR}"/plugins || die - - epatch \ - "${WORKDIR}"/${P}-gentoo-plugins.patch \ - "${FILESDIR}"/${P}-format-security.patch - - [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) - - sed \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CXX = g++:CXX = $(tc-getCXX):" \ - -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ - -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ - -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ - -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ - -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ - -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ - -e "s:-ltcl8.5:-ltcl:" \ - -i Make-arch || die "Failed to set up plugins Makefile" - - sed \ - -e '/^AR /s:=:?=:g' \ - -e '/^RANLIB /s:=:?=:g' \ - -i ../plugins/*/Makefile || die - - tc-export AR RANLIB - - sed \ - -e "s:\$(CXXFLAGS)::g" \ - -i hesstrans/Makefile || die - - # prepare vmd itself - cd "${S}" || die - - epatch "${WORKDIR}"/${P}-gentoo-base.patch - - # PREFIX - sed \ - -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ - -i configure || die - - sed \ - -e "s:gentoo-bindir:${ED}/usr/bin:g" \ - -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ - -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ - -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-gcc:$(tc-getCC):g" \ - -e "s:gentoo-g++:$(tc-getCXX):g" \ - -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ - -e "s:gentoo-cflags:${CFLAGS}:g" \ - -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ - -e "s:gentoo-nvflags::g" \ - -e "s:gentoo-ldflags:${LDFLAGS}:g" \ - -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ - -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ - -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ - -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ - -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -i configure || die - - if use cuda; then - sed \ - -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ - -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ - -i configure src/Makefile || die - sed \ - -e '/compute_/d' \ - -i configure || die - sed \ - -e 's:-gencode .*code=sm_..::' \ - -i src/Makefile || die - fi - - sed \ - -e "s:LINUXPPC:LINUX:g" \ - -e "s:LINUXALPHA:LINUX:g" \ - -e "s:LINUXAMD64:LINUX:g" \ - -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ - -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ - -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ - -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" - - EMAKEOPTS=( - TCLINC="-I${EPREFIX}/usr/include" - TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" - TCLLDFLAGS="-shared" - NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" - NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf) ${EPREFIX}/usr/include" - NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" - NETCDFDYNAMIC=1 - EXPATINC="-I${EPREFIX}/usr/include" - EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" - EXPATLDFLAGS="-shared" - EXPATDYNAMIC=1 - ) - if use gromacs; then - EMAKEOPTS+=( - TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" - TNGINC="-I${EPREFIX}/usr/include" - TNGLDFLAGS="-shared" - TNGDYNAMIC=1 - ) - fi - if use sqlite; then - EMAKEOPTS+=( - SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" - SQLITEINC="-I${EPREFIX}/usr/include" - SQLITELDFLAGS="-shared" - SQLITEDYNAMIC=1 - ) - fi -} - -src_configure() { - local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" - rm -f configure.options && echo $myconf >> configure.options - - use cuda && myconf+=" CUDA" -# use mpi && myconf+=" MPI" - use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon" - use xinerama && myconf+=" XINERAMA" - - export \ - PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ - PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ - PYTHON_LIBRARY="$(python_get_LIBS)" \ - NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ - NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" - - perl ./configure LINUX \ - ${myconf} || die -} - -src_compile() { - # build plugins - cd "${WORKDIR}"/plugins || die - - emake \ - ${EMAKEOPTS[@]} \ - LINUX - - # build vmd - cd "${S}"/src || die - emake -} - -src_install() { - # install plugins - cd "${WORKDIR}"/plugins || die - emake \ - PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ - distrib - - # install vmd - cd "${S}"/src || die - emake install - - # install docs - cd "${S}" || die - dodoc Announcement README doc/ig.pdf doc/ug.pdf - - # remove some of the things we don't want and need in - # /usr/lib - cd "${ED}"/usr/$(get_libdir)/vmd || die - rm -fr doc README Announcement LICENSE || \ - die "failed to clean up /usr/lib/vmd directory" - - # adjust path in vmd wrapper - sed \ - -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ - -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ - || die "failed to set up vmd wrapper script" - - # install icon and generate desktop entry - insinto /usr/share/pixmaps - doins "${WORKDIR}"/vmd.png - eprefixify "${WORKDIR}"/vmd.desktop - sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die - domenu "${WORKDIR}"/vmd.desktop -} diff --git a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild deleted file mode 100644 index f42cb4d104fe..000000000000 --- a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild +++ /dev/null @@ -1,267 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -PYTHON_COMPAT=( python2_7 ) - -inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs - -DESCRIPTION="Visual Molecular Dynamics" -HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" -SRC_URI=" - https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz - ${P}.src.tar -" - -SLOT="0" -LICENSE="vmd" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="cuda gromacs msms povray sqlite tachyon xinerama" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RESTRICT="fetch" - -# currently, tk-8.5* with USE=truetype breaks some -# tk apps such as Sequence Viewer or Timeline. -CDEPEND=" - >=dev-lang/tk-8.6.1:0= - dev-lang/perl - dev-libs/expat - $(python_gen_cond_dep ' - || ( - dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}] - dev-python/numpy[${PYTHON_MULTI_USEDEP}] - ) - ') - sci-libs/netcdf:0= - virtual/opengl - >=x11-libs/fltk-1.1.10-r2:1 - x11-libs/libXft - x11-libs/libXi - ${PYTHON_DEPS} - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) - gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) - sqlite? ( dev-db/sqlite:3= ) - tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) - xinerama? ( x11-libs/libXinerama ) -" -DEPEND="${CDEPEND}" -BDEPEND=" - virtual/pkgconfig - dev-lang/swig -" -RDEPEND="${CDEPEND} - sci-biology/stride - sci-chemistry/surf - x11-terms/xterm - msms? ( sci-chemistry/msms-bin ) - povray? ( media-gfx/povray ) -" - -VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" -# Binary only plugin!! -QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" -QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" -QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" - -pkg_nofetch() { - elog "Please download ${P}.src.tar from" - elog "${VMD_DOWNLOAD}" - elog "after agreeing to the license and get" - elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" - elog "Place both into your DISTDIR directory" - elog - elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources" - elog "file may get downloaded as a compressed tarball or not. In that case" - elog "you will need to ensure you uncompress the file and rename it" - elog "as ${P}.src.tar" -} - -src_prepare() { - default - - use cuda && cuda_sanitize - - eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch - - cd "${WORKDIR}"/plugins || die - - eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch - - [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) - - sed \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CXX = g++:CXX = $(tc-getCXX):" \ - -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ - -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ - -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ - -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ - -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ - -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ - -e "s:-ltcl8.5:-ltcl:" \ - -i Make-arch || die "Failed to set up plugins Makefile" - - sed \ - -e '/^AR /s:=:?=:g' \ - -e '/^RANLIB /s:=:?=:g' \ - -i ../plugins/*/Makefile || die - - tc-export AR RANLIB - - sed \ - -e "s:\$(CXXFLAGS)::g" \ - -i hesstrans/Makefile || die - - # prepare vmd itself - cd "${S}" || die - - eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch - eapply "${FILESDIR}"/${P}-configure-libtachyon.patch - - # PREFIX - sed \ - -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ - -i configure || die - - sed \ - -e "s:gentoo-bindir:${ED}/usr/bin:g" \ - -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ - -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ - -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-gcc:$(tc-getCC):g" \ - -e "s:gentoo-g++:$(tc-getCXX):g" \ - -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ - -e "s:gentoo-cflags:${CFLAGS}:g" \ - -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ - -e "s:gentoo-nvflags::g" \ - -e "s:gentoo-ldflags:${LDFLAGS}:g" \ - -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ - -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ - -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ - -e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \ - -e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ - -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -i configure || die - - if use cuda; then - sed \ - -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ - -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ - -i configure src/Makefile || die - sed \ - -e '/compute_/d' \ - -i configure || die - sed \ - -e 's:-gencode .*code=sm_..::' \ - -i src/Makefile || die - fi - - sed \ - -e "s:LINUXPPC:LINUX:g" \ - -e "s:LINUXALPHA:LINUX:g" \ - -e "s:LINUXAMD64:LINUX:g" \ - -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ - -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ - -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ - -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" - - EMAKEOPTS=( - TCLINC="-I${EPREFIX}/usr/include" - TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" - TCLLDFLAGS="-shared" - NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" - NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include" - NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" - NETCDFDYNAMIC=1 - EXPATINC="-I${EPREFIX}/usr/include" - EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" - EXPATLDFLAGS="-shared" - EXPATDYNAMIC=1 - ) - if use gromacs; then - EMAKEOPTS+=( - TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" - TNGINC="-I${EPREFIX}/usr/include" - TNGLDFLAGS="-shared" - TNGDYNAMIC=1 - ) - fi - if use sqlite; then - EMAKEOPTS+=( - SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" - SQLITEINC="-I${EPREFIX}/usr/include" - SQLITELDFLAGS="-shared" - SQLITEDYNAMIC=1 - ) - fi -} - -src_configure() { - local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" - rm -f configure.options && echo $myconf >> configure.options - - use cuda && myconf+=" CUDA" -# use mpi && myconf+=" MPI" - use tachyon && myconf+=" LIBTACHYON" - use xinerama && myconf+=" XINERAMA" - - export \ - PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ - PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ - PYTHON_LIBRARY="$(python_get_LIBS)" \ - NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ - NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" - - perl ./configure LINUX \ - ${myconf} || die -} - -src_compile() { - # build plugins - cd "${WORKDIR}"/plugins || die - - emake \ - ${EMAKEOPTS[@]} \ - LINUX - - # build vmd - cd "${S}"/src || die - emake -} - -src_install() { - # install plugins - cd "${WORKDIR}"/plugins || die - emake \ - PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ - distrib - - # install vmd - cd "${S}"/src || die - emake install - - # install docs - cd "${S}" || die - dodoc Announcement README doc/ig.pdf doc/ug.pdf - - # remove some of the things we don't want and need in - # /usr/lib - cd "${ED}"/usr/$(get_libdir)/vmd || die - rm -fr doc README Announcement LICENSE || \ - die "failed to clean up /usr/lib/vmd directory" - - # adjust path in vmd wrapper - sed \ - -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ - -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ - || die "failed to set up vmd wrapper script" - - # install icon and generate desktop entry - insinto /usr/share/pixmaps - doins "${WORKDIR}"/vmd.png - eprefixify "${WORKDIR}"/vmd.desktop - sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die - domenu "${WORKDIR}"/vmd.desktop -} diff --git a/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild deleted file mode 100644 index 39e7a9751cee..000000000000 --- a/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild +++ /dev/null @@ -1,271 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -PYTHON_COMPAT=( python2_7 ) - -inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg - -DESCRIPTION="Visual Molecular Dynamics" -HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" -SRC_URI=" - https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz - ${P}.src.tar -" - -SLOT="0" -LICENSE="vmd" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="cuda gromacs msms povray sqlite tachyon xinerama" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RESTRICT="fetch" - -# currently, tk-8.5* with USE=truetype breaks some -# tk apps such as Sequence Viewer or Timeline. -CDEPEND=" - >=dev-lang/tk-8.6.1:0= - dev-lang/perl - dev-libs/expat - $(python_gen_cond_dep ' - || ( - dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}] - dev-python/numpy[${PYTHON_MULTI_USEDEP}] - ) - ') - sci-libs/netcdf:0= - virtual/opengl - >=x11-libs/fltk-1.1.10-r2:1 - x11-libs/libXft - x11-libs/libXi - ${PYTHON_DEPS} - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) - gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) - sqlite? ( dev-db/sqlite:3= ) - tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) - xinerama? ( x11-libs/libXinerama ) -" -DEPEND="${CDEPEND}" -BDEPEND=" - virtual/pkgconfig - dev-lang/swig -" -RDEPEND="${CDEPEND} - sci-biology/stride - sci-chemistry/chemical-mime-data - sci-chemistry/surf - x11-terms/xterm - msms? ( sci-chemistry/msms-bin ) - povray? ( media-gfx/povray ) -" - -VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" -# Binary only plugin!! -QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" -QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" -QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" - -pkg_nofetch() { - elog "Please download ${P}.src.tar from" - elog "${VMD_DOWNLOAD}" - elog "after agreeing to the license and get" - elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" - elog "Place both into your DISTDIR directory" - elog - elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources" - elog "file may get downloaded as a compressed tarball or not. In that case" - elog "you will need to ensure you uncompress the file and rename it" - elog "as ${P}.src.tar" -} - -src_prepare() { - xdg_src_prepare - - use cuda && cuda_sanitize - - eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch - - cd "${WORKDIR}"/plugins || die - - eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch - - [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) - - sed \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CXX = g++:CXX = $(tc-getCXX):" \ - -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ - -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ - -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ - -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ - -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ - -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ - -e "s:-ltcl8.5:-ltcl:" \ - -i Make-arch || die "Failed to set up plugins Makefile" - - sed \ - -e '/^AR /s:=:?=:g' \ - -e '/^RANLIB /s:=:?=:g' \ - -i ../plugins/*/Makefile || die - - tc-export AR RANLIB - - sed \ - -e "s:\$(CXXFLAGS)::g" \ - -i hesstrans/Makefile || die - - # prepare vmd itself - cd "${S}" || die - - eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch - eapply "${FILESDIR}"/${P}-configure-libtachyon.patch - eapply "${FILESDIR}"/${P}-tmpdir.patch - - # PREFIX - sed \ - -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ - -i configure || die - - sed \ - -e "s:gentoo-bindir:${ED}/usr/bin:g" \ - -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ - -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ - -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-gcc:$(tc-getCC):g" \ - -e "s:gentoo-g++:$(tc-getCXX):g" \ - -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ - -e "s:gentoo-cflags:${CFLAGS}:g" \ - -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ - -e "s:gentoo-nvflags::g" \ - -e "s:gentoo-ldflags:${LDFLAGS}:g" \ - -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ - -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ - -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ - -e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \ - -e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ - -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -i configure || die - - if use cuda; then - sed \ - -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ - -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ - -i configure src/Makefile || die - sed \ - -e '/compute_/d' \ - -i configure || die - sed \ - -e 's:-gencode .*code=sm_..::' \ - -i src/Makefile || die - fi - - sed \ - -e "s:LINUXPPC:LINUX:g" \ - -e "s:LINUXALPHA:LINUX:g" \ - -e "s:LINUXAMD64:LINUX:g" \ - -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ - -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ - -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ - -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" - - EMAKEOPTS=( - TCLINC="-I${EPREFIX}/usr/include" - TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" - TCLLDFLAGS="-shared" - NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" - NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include" - NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" - NETCDFDYNAMIC=1 - EXPATINC="-I${EPREFIX}/usr/include" - EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" - EXPATLDFLAGS="-shared" - EXPATDYNAMIC=1 - ) - if use gromacs; then - EMAKEOPTS+=( - TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" - TNGINC="-I${EPREFIX}/usr/include" - TNGLDFLAGS="-shared" - TNGDYNAMIC=1 - ) - fi - if use sqlite; then - EMAKEOPTS+=( - SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" - SQLITEINC="-I${EPREFIX}/usr/include" - SQLITELDFLAGS="-shared" - SQLITEDYNAMIC=1 - ) - fi -} - -src_configure() { - local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" - rm -f configure.options && echo $myconf >> configure.options - - use cuda && myconf+=" CUDA" -# use mpi && myconf+=" MPI" - use tachyon && myconf+=" LIBTACHYON" - use xinerama && myconf+=" XINERAMA" - - export \ - PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ - PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ - PYTHON_LIBRARY="$(python_get_LIBS)" \ - NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ - NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" - - perl ./configure LINUX \ - ${myconf} || die -} - -src_compile() { - # build plugins - cd "${WORKDIR}"/plugins || die - - emake \ - ${EMAKEOPTS[@]} \ - LINUX - - # build vmd - cd "${S}"/src || die - emake -} - -src_install() { - # install plugins - cd "${WORKDIR}"/plugins || die - emake \ - PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ - distrib - - # install vmd - cd "${S}"/src || die - emake install - - # install docs - cd "${S}" || die - dodoc Announcement README doc/ig.pdf doc/ug.pdf - - # remove some of the things we don't want and need in - # /usr/lib - cd "${ED}"/usr/$(get_libdir)/vmd || die - rm -fr doc README Announcement LICENSE || \ - die "failed to clean up /usr/lib/vmd directory" - - # adjust path in vmd wrapper - sed \ - -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ - -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ - || die "failed to set up vmd wrapper script" - - # install icon and generate desktop entry - insinto /usr/share/pixmaps - doins "${WORKDIR}"/vmd.png - eprefixify "${WORKDIR}"/vmd.desktop - sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die - # Open PDB files with VMD - echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die - domenu "${WORKDIR}"/vmd.desktop -} diff --git a/sci-chemistry/vmd/vmd-1.9.3.ebuild b/sci-chemistry/vmd/vmd-1.9.3.ebuild deleted file mode 100644 index 88394af1970d..000000000000 --- a/sci-chemistry/vmd/vmd-1.9.3.ebuild +++ /dev/null @@ -1,255 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs - -DESCRIPTION="Visual Molecular Dynamics" -HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" -SRC_URI=" - https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz - ${P}.src.tar" - -SLOT="0" -LICENSE="vmd" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="cuda gromacs msms povray sqlite tachyon xinerama" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RESTRICT="fetch" - -# currently, tk-8.5* with USE=truetype breaks some -# tk apps such as Sequence Viewer or Timeline. -CDEPEND=" - >=dev-lang/tk-8.6.1 - dev-lang/perl - dev-libs/expat - $(python_gen_cond_dep ' - || ( - dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}] - dev-python/numpy[${PYTHON_MULTI_USEDEP}] - ) - ') - sci-libs/netcdf:0= - virtual/opengl - >=x11-libs/fltk-1.1.10-r2:1 - x11-libs/libXft - x11-libs/libXi - ${PYTHON_DEPS} - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) - gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) - sqlite? ( dev-db/sqlite:3= ) - tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) - xinerama? ( x11-libs/libXinerama )" -DEPEND="${CDEPEND} - virtual/pkgconfig - dev-lang/swig" -RDEPEND="${CDEPEND} - sci-biology/stride - sci-chemistry/surf - x11-terms/xterm - msms? ( sci-chemistry/msms-bin ) - povray? ( media-gfx/povray ) - " - -VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" -# Binary only plugin!! -QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" -QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" -QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" - -pkg_nofetch() { - elog "Please download ${P}.src.tar.gz from" - elog "${VMD_DOWNLOAD}" - elog "after agreeing to the license and get" - elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" - elog "Place both into your DISTDIR directory" -} - -src_prepare() { - use cuda && cuda_sanitize - - epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch - - cd "${WORKDIR}"/plugins || die - - epatch \ - "${WORKDIR}"/${P}-gentoo-plugins.patch - - [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) - - sed \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CXX = g++:CXX = $(tc-getCXX):" \ - -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ - -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ - -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ - -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ - -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ - -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ - -e "s:-ltcl8.5:-ltcl:" \ - -i Make-arch || die "Failed to set up plugins Makefile" - - sed \ - -e '/^AR /s:=:?=:g' \ - -e '/^RANLIB /s:=:?=:g' \ - -i ../plugins/*/Makefile || die - - tc-export AR RANLIB - - sed \ - -e "s:\$(CXXFLAGS)::g" \ - -i hesstrans/Makefile || die - - # prepare vmd itself - cd "${S}" || die - - epatch "${WORKDIR}"/${P}-gentoo-base.patch - - # PREFIX - sed \ - -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ - -i configure || die - - sed \ - -e "s:gentoo-bindir:${ED}/usr/bin:g" \ - -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ - -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ - -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-gcc:$(tc-getCC):g" \ - -e "s:gentoo-g++:$(tc-getCXX):g" \ - -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ - -e "s:gentoo-cflags:${CFLAGS}:g" \ - -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ - -e "s:gentoo-nvflags::g" \ - -e "s:gentoo-ldflags:${LDFLAGS}:g" \ - -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ - -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ - -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ - -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ - -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -i configure || die - - if use cuda; then - sed \ - -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ - -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ - -i configure src/Makefile || die - sed \ - -e '/compute_/d' \ - -i configure || die - sed \ - -e 's:-gencode .*code=sm_..::' \ - -i src/Makefile || die - fi - - sed \ - -e "s:LINUXPPC:LINUX:g" \ - -e "s:LINUXALPHA:LINUX:g" \ - -e "s:LINUXAMD64:LINUX:g" \ - -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ - -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ - -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ - -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" - - EMAKEOPTS=( - TCLINC="-I${EPREFIX}/usr/include" - TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" - TCLLDFLAGS="-shared" - NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" - NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf) ${EPREFIX}/usr/include" - NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" - NETCDFDYNAMIC=1 - EXPATINC="-I${EPREFIX}/usr/include" - EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" - EXPATLDFLAGS="-shared" - EXPATDYNAMIC=1 - ) - if use gromacs; then - EMAKEOPTS+=( - TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" - TNGINC="-I${EPREFIX}/usr/include" - TNGLDFLAGS="-shared" - TNGDYNAMIC=1 - ) - fi - if use sqlite; then - EMAKEOPTS+=( - SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" - SQLITEINC="-I${EPREFIX}/usr/include" - SQLITELDFLAGS="-shared" - SQLITEDYNAMIC=1 - ) - fi -} - -src_configure() { - local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" - rm -f configure.options && echo $myconf >> configure.options - - use cuda && myconf+=" CUDA" -# use mpi && myconf+=" MPI" - use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon" - use xinerama && myconf+=" XINERAMA" - - export \ - PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ - PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ - PYTHON_LIBRARY="$(python_get_LIBS)" \ - NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ - NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" - - perl ./configure LINUX \ - ${myconf} || die -} - -src_compile() { - # build plugins - cd "${WORKDIR}"/plugins || die - - emake \ - ${EMAKEOPTS[@]} \ - LINUX - - # build vmd - cd "${S}"/src || die - emake -} - -src_install() { - # install plugins - cd "${WORKDIR}"/plugins || die - emake \ - PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ - distrib - - # install vmd - cd "${S}"/src || die - emake install - - # install docs - cd "${S}" || die - dodoc Announcement README doc/ig.pdf doc/ug.pdf - - # remove some of the things we don't want and need in - # /usr/lib - cd "${ED}"/usr/$(get_libdir)/vmd || die - rm -fr doc README Announcement LICENSE || \ - die "failed to clean up /usr/lib/vmd directory" - - # adjust path in vmd wrapper - sed \ - -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ - -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ - || die "failed to set up vmd wrapper script" - - # install icon and generate desktop entry - insinto /usr/share/pixmaps - doins "${WORKDIR}"/vmd.png - eprefixify "${WORKDIR}"/vmd.desktop - sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die - domenu "${WORKDIR}"/vmd.desktop -} diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest index abcd5ed980d5..df8a29f5511f 100644 --- a/sci-chemistry/votca-csg/Manifest +++ b/sci-chemistry/votca-csg/Manifest @@ -3,6 +3,7 @@ DIST votca-csg-1.4.tar.gz 346527 BLAKE2B 8f0a41f9aa9fd865e2e544d5fd587d93d631edc DIST votca-csg-1.5.1.tar.gz 708319 BLAKE2B 2ea75cf08dc3005bd08ebe85113d95743fe85bae4b7ac3c2e2d9b64be64a7103ecf30b9edf45cffa86b7588d5c57a0256aef02f4590fa6031cb63881480bd0fd SHA512 3559452182c325d5df72918ec6e12122c8214df9733d779c123ff199597fe47fc493fd75adf1f5dbc6b55016373863378ba3cc69fb6b61bc1531c6e591d8131c DIST votca-csg-1.5.tar.gz 429164 BLAKE2B da04bd9ce8e879e9a961006256e03d160fa49fe77aa2f1eff0986b338296b04137bb087ecfabb7f2fc855b0ccd83dc4ddddfd65c43303bf5f2eef0519d27b0ec SHA512 c5a77ded3c9b2582494bea55b464689d566d4155713af823dccc6999f98438444d51fae3948144f82c2aaf3914eee740fe21e8828af689d37ab0b5ffea0605fa DIST votca-csg-1.6.1.tar.gz 474044 BLAKE2B 36ededfffe7af5b87b2a031f69afbb9cc727af9454466163312e48c23719f6fe3cb727de96c419ae6e7d4901576013bd76f84d8e7e394cc65df4d83bd1ce30bb SHA512 b8f0f1bf2ca57ee9e2050b4a76e1d725ccb0908314886415f36d4e4554953b4e1c93f7c05502afb77f9b7b5ef3059ebbf7f223b965ba72ae45736798fa2e6ad9 +DIST votca-csg-1.6.2.tar.gz 522982 BLAKE2B e0376e04e7baabaa45cab2cc87ff3d7574a35a4a50d87763bb42232eb6f110904b9fb5cdee0a8f2b4057a441a8ca5e276a8d44e14ec3609301832c2ed18cfd94 SHA512 e1d88cc9d18718f323355736afaf309940234001abb39414dd4990f1ff231ef3e8f71d51c78929c422c296b96f304fa17f6c9671071148ff1446bdc1eb442708 DIST votca-csg-1.6.tar.gz 464175 BLAKE2B 1871c7edc4b4e848a06049a7c687e906f166312777bdbf5c65be8efe8d5032582fdca9dc7eca453b7013901f409326b0583c79731c68fa2b4e6366f021958b0b SHA512 76cda93023d46a66ae31edcec0ece709ddc70a9be9d098721b945006c197ed3b6cbd1e643158797be518c4fe66f7b23d3e8d8735cbd9e155db3db0d79929cfbe DIST votca-csg-1.6_rc1.tar.gz 479265 BLAKE2B c4ba3c81eefd375eea6f8c0b1cd60f9cc80898fb7e8e811ecc286f06d94bd4316edfca277649ec3f7f8b751b2f2928ca2dfe61cc3b1c3060a324ea783c62003f SHA512 6622648ddc3308ca2f8e98d6dbcd28e33a4e0fb44d96ef94ebcaa2e87e5ba3ca2ab83dcc1de4fd0803dbc20ba7192f5fdd2c935b364ed4e2122b5948c10d4936 DIST votca-csg-manual-1.4.1.pdf 1282641 BLAKE2B 370b7c8997649555fd2360b999cf381c340a74c3747afda23d0e9d346367cc6d14d4e9a0e9ac82184945427d30050dd623dd1b6d8218c6ff3d2f17331987aaae SHA512 e89f41af05eaeb9ea499e8625cc98e2632ec647ec2d8c9c9052dcd4d2935d082b29b51495514e3e06e73ce42b8cda7017fc523a013569378e2bc86bf88ad32d4 @@ -10,6 +11,7 @@ DIST votca-csg-manual-1.4.pdf 1281983 BLAKE2B 5659c2e327ba7bb00fac15adfb578288d5 DIST votca-csg-manual-1.5.1.pdf 1263719 BLAKE2B 29e2ce27215787a1121e45ec1e88ce7c61ba81709a2519aa0959eede505498b9aaf4f38666bb1a4f97837c98b862e7ed02405da07294a7ec76cc80390fe72e0d SHA512 7d9fb4c635383e1b9c9547691f8729e19f273fcafc4dab2a6b438b3ce98ea05bd31887d09bc4edc86ceb0b04d71a4371aed7aadc3ba6864f7be2ef3328ede642 DIST votca-csg-manual-1.5.pdf 1273566 BLAKE2B edfa2adb942d968cf79499e89342b7aaab64edfbfb6e02f76a66201df0920a58acc17bf4e2e4846d104519df163223c27f283cc5798ec7b64d9317a7728ff8c4 SHA512 da298ab0c27000ccf7fb5793c4252c4e17a969709db2649a5acb56af6208b954312c46a2ea8399cdb879b699e72a0ded0b2fe1bcd26431c6625f36b09c0267a5 DIST votca-csg-manual-1.6.1.pdf 1248350 BLAKE2B d4433974e38785fb968bd357ed2914515b2a22a78d6417597265bb1420b5af8b7b9849533a5faba571bcf635eff8385b244b2252bf7a20d3adb9318cd7115b03 SHA512 d627a9c7a71b8ac5e8d6ca109f0ea56978706b0dd1408aaf10b75b4b52f40b6150063248477ca2b5922f603e8d582ddd4dec3de73b3991db5fbb7bf204d347a3 +DIST votca-csg-manual-1.6.2.pdf 1241907 BLAKE2B 9d51682099081cb8301eed10e7bb4f3afea89561626da5f3b361939d8d9b4ed15bb49392074bc19c530d413f4913afbf4ce612ee62e0e4d22c30f856a2019cbb SHA512 a85094bfa9ae2fcef52f42af162eb1a94ed30de9d7785aac03d7591177f6982dd315874566ce2671df508a3139ce8816c6becf0e0c1d0bfb9b675063810eb3e7 DIST votca-csg-manual-1.6.pdf 1248178 BLAKE2B 5213d55787041db81fe8563febbf130db6aed9233e569039b66d69cfb173131353d45bef824640ee7b0a3fed7821ede4d5a6ce6ffc14d1548499317afdc0248a SHA512 e91d4b8397b67808c9671b9adbaad41fd9a0ede90066e220839d86f21a9bbcd4e433534faf1dfbca106d55af5a6cce0425a5bdfa3eb30ebe14469594da0129ca DIST votca-csg-manual-1.6_rc1.pdf 1248403 BLAKE2B b702eff4a36d27d592147f115f4e9080cbf580b6401141a14865395f0cb927c35f60035f92724e71e5edadbbe3e317f93989eb6f2e0a0e7b9f685e56851546d2 SHA512 2514bd2fee4bae787a3f8c07d1f1d90061a2b503255efe0730ed164bb002c7e7ad7309ccd3b5b931994f70b7ed99afde28955d9ea1b34c86df21bfcb8bfb39bb DIST votca-csg-tutorials-1.4.1.tar.gz 6339417 BLAKE2B e9acf8e421f6fce4d97be2d51fb559979c6fd3e6b042525cedf32cadeab1dddc5b1aaf80bbbfd387da3bce71672759c2e84d317c789f616dc71834c72a581fff SHA512 896ec9d6b2537a06301046a74c1957708eb96d9854b3ec855fe3457208c142f6fb26a03e323a2644862a1efd0030fcceb1189f73655b984462f0f7127a02de90 @@ -17,6 +19,7 @@ DIST votca-csg-tutorials-1.4.tar.gz 6348417 BLAKE2B 612fcbc4457a57be74e5306bf86d DIST votca-csg-tutorials-1.5.1.tar.gz 5949467 BLAKE2B c6de6084fbb1d2c4ac2ce75d01a1153eabc63386063de800ff2dc6b483b0568191e7f06ddcb8be46123224ccfd3a97f5fb4e7cd603c0ee99a8636d7143f6c701 SHA512 f2e709ae31d914fe12a4ce37b5019deb878b15ade14972f2a8204bec8970ba2c8946b71b94a5bfd6f7569e41173bfbc75275ea09cbee4358ad1de0e84751049c DIST votca-csg-tutorials-1.5.tar.gz 5947774 BLAKE2B d497f1e9282c4cacc070d09d901ad8f5d3042ab3a279aa4d1c3bcd3184dc22231d1f2a75ba0ffe245e6f6300fb740e562b24c8039594ec01307491a6068b55f6 SHA512 00447380fa887178ad02cc4e1425a04fc2fd2babdd4790d387fcd4aa2734dc14dacf4b4444d420937aa0a5b53e90741b44f9a4bca31bdcdae10fbfb8323e9848 DIST votca-csg-tutorials-1.6.1.tar.gz 5945945 BLAKE2B 18ea7e406acf70e37049b1f8676551d96b20825fba25bb9c1e674b0f94f5ee41bd74ce77619880dfb2e2f1f8fb0b40de9ce8a5e9e9d8470639af057376a19632 SHA512 82d60fcea4859e1caa6138147848427dbdb1ddcf4e0713b6f2d50cd624ceacdbce1ceb8e98fb85d079d8d9de02f501ec8c9236243fe75761e44486f27207249b +DIST votca-csg-tutorials-1.6.2.tar.gz 5945110 BLAKE2B 2871c89c763c8624deb877f90da10cd2021ec5b10a0d8473c4523b70a179247ad2e809aa5b0aab7c36a324d929b55f3b2070822914043382424b87fbf34ef05b SHA512 40f377a824f6c10be759adf3e1b87dbc5392b00e4a377ba04d998f96aa9b7ceb986c2e5cfac16ea3047f08d2d76deb7e9f3aadfba794f58b8f131861f7a7ff04 DIST votca-csg-tutorials-1.6.tar.gz 5946764 BLAKE2B 018bd00c86c0a85baf35afd2ea4206c96dee8f948dcbf331b53e6f685b69bf2c909731b15ba3261c86cee9e1960ec5cfa7b2ee0c6dcfabbbbc110789840184ad SHA512 36d3a66c19d230f2002170851345da7063aeef1f29841945b8a182f73922617823815dde5d7289fb0f80e771ac03780adacdf95af4814235edbf69a4772b3696 DIST votca-csg-tutorials-1.6_rc1.tar.gz 5946622 BLAKE2B 7bf0c7083ca7b148d16f7b77b9f785c11b16a8124a5435522e8c065859f4c2ae560c622f04021918b2683c9955d5a1b674c84fad179319f5fedb86616bbe24e7 SHA512 1c89f95944f8277a995d9d6d7dacfae2ae1be54a9a7b19c53d3464a4bdf5da0556e862033ba0a5f442b1ee5bd79bafd478655856fe266f4285c98e14512ce259 EBUILD votca-csg-1.4.1.ebuild 3204 BLAKE2B e447a6859d7ee4d722701f96634667529bd183f10dd4affeb2713023edfe52ab73988df7ef912963bd154b893bd2d401d2fd110a729040a2a2c52ec5fd44985c SHA512 df94c127269df2a2eaa9643005eeeae6925b458fbb0cb4d1661757a49e5ab4926a613c532e4df4475b34768e904d2388270c868c9ad675cd110e2b1737153e3d @@ -24,7 +27,8 @@ EBUILD votca-csg-1.4.ebuild 3200 BLAKE2B 041deefd8fc208525c636d00665f7ea70d0efaf EBUILD votca-csg-1.5.1.ebuild 2552 BLAKE2B a64b31b3b6a9297b6ead93e9f5605ace929fecf98ee377eff17a0b529b9176fe5d251e9efb5dada1c7d29b144b7e89dcd95ff3c6921b7584f225f842bc93f94b SHA512 3d96fac05c344f0986597ec6ce50f07a19327113d3b02238df60ce28ab2788f91a224f9c70ecdaaf6cfe6206f00f8e86e4ad2dde1c68c5c0a32f5d20eee658cd EBUILD votca-csg-1.5.ebuild 2550 BLAKE2B 7fb2a4280fca23370169fbf04c3b9251065f06d56d7df29a26f3bbaf642e3296e400a23cc3c7524a830cee0dd881e598569c82bbcfacbec35198dd564d379828 SHA512 9516699dbfab66505053d701a31440ce0ca16484b6b0f60b072f6d5a54740449c90ea96461e08d598933dd7f7803278dbc4e19df381f5b57c541b9d3de90c9d5 EBUILD votca-csg-1.6.1.ebuild 2369 BLAKE2B a6d8e7e9049f55f2e916614586bb6ec68e1223ea25cff260ee884f94f137afb798c51983ab7df7b54e918fc1b9eb4c315e380b1a4649e361b999753d11e5c210 SHA512 f72714b948a8c0ca93061aeeb9ff3bc358d8b0c0b5e369dbb732569ad302edf9198753e8e0921fae9cab5deb6ef3e5111d921c3fd4c0a4a8ec3deb41afb43825 +EBUILD votca-csg-1.6.2.ebuild 2340 BLAKE2B 97934fdd4b56cfbc58d5c2f47179ed3f747600ae870fe86fc7829fcdecb8e72e67ec129b49cc25e0a04b1dccb878ae79f7e693f59184da4e447eacbceb794b12 SHA512 30e0ef70ef8cf7c791a8579b01440fb7013ed4344a2132e955e17d1b8a5edac7982dae46d796122f8066584583f4b9356a478b512334ec4f0dae647ed4fa8f6e EBUILD votca-csg-1.6.ebuild 2365 BLAKE2B 585240513e8b06c9c35aab0dfb75962c59e2d42853837eaa67d86c728c5cd3d8485061a4974c71898caba41d6d44a1cf93ba27c16824427b767f965e8f9a07ab SHA512 38b6ff068367ac79717f9a364b2b6a83824cec0c804af934f15d3f19ca1cf50eddd8b94cc64c0b035724a6abca2f32a40ec598396c646f5a31c0ea0748bff976 EBUILD votca-csg-1.6_rc1.ebuild 2358 BLAKE2B 5124239dade6f735c1f1da0071e30bf245728431a46f4361271d1eea9962249ff1bcc621db193f69ae04b61343aaafa01c64cfb4a131c6ce83b9135c5a7f39c5 SHA512 a8f2298c212299689a96d4a15e73b851725f45c6ad9fc20610a155625c5d58d1d462ba7c01fdd206fba8b43fe032b65f992ee58107e1245565cb482f8507d6ac -EBUILD votca-csg-9999.ebuild 2358 BLAKE2B 5124239dade6f735c1f1da0071e30bf245728431a46f4361271d1eea9962249ff1bcc621db193f69ae04b61343aaafa01c64cfb4a131c6ce83b9135c5a7f39c5 SHA512 a8f2298c212299689a96d4a15e73b851725f45c6ad9fc20610a155625c5d58d1d462ba7c01fdd206fba8b43fe032b65f992ee58107e1245565cb482f8507d6ac +EBUILD votca-csg-9999.ebuild 2340 BLAKE2B 97934fdd4b56cfbc58d5c2f47179ed3f747600ae870fe86fc7829fcdecb8e72e67ec129b49cc25e0a04b1dccb878ae79f7e693f59184da4e447eacbceb794b12 SHA512 30e0ef70ef8cf7c791a8579b01440fb7013ed4344a2132e955e17d1b8a5edac7982dae46d796122f8066584583f4b9356a478b512334ec4f0dae647ed4fa8f6e MISC metadata.xml 676 BLAKE2B b3f2e43f5cb505876216b0a329410c9cef1b44a9bbd7e1c61faa4acd00dbe87ea0cebb00ed78dc00b9e1d2b08b95e3c40d25fecc0738c992a3f933e430f94e2b SHA512 14ecd498eeeed1576923d8da9bc5dc98e47c1d162173b7f2419ad367fa84e227555bd0365709be8a456dc5388ea6fa6734fa7df3c82fd4efcd1cf3460c7e12a1 diff --git a/sci-chemistry/votca-csg/votca-csg-1.6.2.ebuild b/sci-chemistry/votca-csg/votca-csg-1.6.2.ebuild new file mode 100644 index 000000000000..c77bb3e40fa8 --- /dev/null +++ b/sci-chemistry/votca-csg/votca-csg-1.6.2.ebuild @@ -0,0 +1,92 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake 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 ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="" + PDEPEND="${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-${PV} + >=dev-cpp/eigen-3.3 + gromacs? ( sci-chemistry/gromacs:= ) + hdf5? ( sci-libs/hdf5 ) + dev-lang/perl + app-shells/bash:*" + +DEPEND="${RDEPEND} + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +DOCS=( README.md NOTICE CHANGELOG.md ) + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use examples; then + EGIT_REPO_URI="https://github.com/${PN/-//}-tutorials.git" + EGIT_BRANCH="master" + EGIT_CHECKOUT_DIR="${WORKDIR}/${PN#votca-}-tutorials"\ + git-r3_src_unpack + fi + fi +} + +src_configure() { + mycmakeargs=( + -DWITH_GMX=$(usex gromacs) + -DCMAKE_DISABLE_FIND_PACKAGE_HDF5=$(usex '!hdf5') + -DWITH_RC_FILES=OFF + ) + cmake_src_configure +} + +src_install() { + cmake_src_install + newbashcomp "${ED}"/usr/share/votca/rc/csg-completion.bash csg_call + for i in "${ED}"/usr/bin/csg_*; do + [[ ${i} = *csg_call ]] && continue + bashcomp_alias csg_call "${i##*/}" + done + if use doc; then + [[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" + fi + if use examples; then + insinto "/usr/share/doc/${PF}/tutorials" + docompress -x "/usr/share/doc/${PF}/tutorials" + rm -rf "${WORKDIR}/${PN#votca-}"-tutorials*/CMake* + doins -r "${WORKDIR}/${PN#votca-}"-tutorials*/* + fi +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). " + einfo "https://dx.doi.org/10.1021/ct900369w" + einfo +} diff --git a/sci-chemistry/votca-csg/votca-csg-9999.ebuild b/sci-chemistry/votca-csg/votca-csg-9999.ebuild index 0e02baa215a8..c77bb3e40fa8 100644 --- a/sci-chemistry/votca-csg/votca-csg-9999.ebuild +++ b/sci-chemistry/votca-csg/votca-csg-9999.ebuild @@ -5,7 +5,7 @@ EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake-utils multilib +inherit bash-completion-r1 cmake multilib IUSE="doc examples extras +gromacs hdf5" PDEPEND="extras? ( ~sci-chemistry/${PN}apps-${PV} )" @@ -62,11 +62,11 @@ src_configure() { -DCMAKE_DISABLE_FIND_PACKAGE_HDF5=$(usex '!hdf5') -DWITH_RC_FILES=OFF ) - cmake-utils_src_configure + cmake_src_configure } src_install() { - cmake-utils_src_install + cmake_src_install newbashcomp "${ED}"/usr/share/votca/rc/csg-completion.bash csg_call for i in "${ED}"/usr/bin/csg_*; do [[ ${i} = *csg_call ]] && continue diff --git a/sci-chemistry/votca-csgapps/Manifest b/sci-chemistry/votca-csgapps/Manifest index 26ba926b94b7..da02e1913994 100644 --- a/sci-chemistry/votca-csgapps/Manifest +++ b/sci-chemistry/votca-csgapps/Manifest @@ -3,6 +3,7 @@ DIST votca-csgapps-1.4.tar.gz 21072 BLAKE2B 30c2f6692544741bfbec09efea2f68ae48cd DIST votca-csgapps-1.5.1.tar.gz 26006 BLAKE2B 8651978c15087fc7332fe229cfc33d8c4257faf46d72f7ac5fbaaf5f31133c4df3d97cae2b18730b5700e742c27e3db39696fdfe910ed884952ba0f832220c3d SHA512 4f83a46f16eb0a4cb9acc6c0d9523fa746dcf670107355c95fc02daa6ca91fb4f8d5e48bc920d8c13a9445390a25415f7217979903ea86f890df1d4704944c28 DIST votca-csgapps-1.5.tar.gz 25975 BLAKE2B 185e759d658c6f763da2d26770766ec8ee05017b4c6a67e13915de04fbf2ecf268f2f800c5e18ef0f38c615340b0db163e886dc98a9395a69359f94dc8773f60 SHA512 20dda9d07ef2f33c9decff2766ece8f24cf2562993b4dfb7dd637d84325b835a6ecd30d34c5cfb9c428dbf72c2b5dfe9fd49d266182704b981db151c3c4ea2e4 DIST votca-csgapps-1.6.1.tar.gz 20128 BLAKE2B 509f684b84e7ebb718fbcf5b48adc732dc8c6b9f6478269e243dda3c980a5d91a46208863ac6227a07d90f6e2ea4e5cf2b50a7b34b6dbe2567d9a95ede4ee1de SHA512 06e396c20990f7bb22ae8c888a36585b40a61280aa53a521c01128bbaadc1f449f85d4f41380ee3ce290defb64eca285be7dde1cd888f4cb69805695511a5b90 +DIST votca-csgapps-1.6.2.tar.gz 19549 BLAKE2B 8aad4ff143a2073b4d17a4af0766898882ed011be4de814b6dca3cb4c1776fbee925fb4fef4ba1fd20d3aa3097440caeaab7fddb68b35322b5123868e7e2fbea SHA512 f88f8ea41773b846ed7b3b910ad81c58a6dc1aabea5ae8ead030709c095e229b29443213854d358b4fa6518d8373b9a2acab741be2bbc33fec22d8f267f6cfe3 DIST votca-csgapps-1.6.tar.gz 20130 BLAKE2B 0c34fba42a70f756043aae89f51b94cc0a9c9a85680ed78c56b4c05f834d94c74aff59e4adf6155e5fab81d057da58ec420d843532af57beeaa6e81f82432d92 SHA512 5a85abaf6b09a225604f33f2e0cfb774525159e9bce89efd7ebfc0c9c37342e472503ff51c3065be2a4b87e95671f55164c630477f404f94b0510a83e262352f DIST votca-csgapps-1.6_rc1.tar.gz 20138 BLAKE2B 9374911f761fd78f01721e8e10f3b9c14f2ba894735735e4d09f5e29eb1d1b69f4fa081699d7a93abfad2ebe55d6439edbb6db547618e6d2cfbaf7bbc8a79ca8 SHA512 153bd6e537175c9908739c60ce80830ebf57c0686f11b21fc541995cb5355d4a3f7f7ee7d1707bb85f5fc859bf260a3a167450175ffe8feb92044e8018be996b EBUILD votca-csgapps-1.4.1.ebuild 653 BLAKE2B 208ae3538fcf42296a4a1077d222a9d6f752648834dc8f74941546fa2bdffb6fd9ea60ad31d124b8de52c3f59c089f48d4395b5166989fec19191076570e1bf0 SHA512 13ab1d118aea4f16664566f4e13965cc46a9e67e37157e23ad8c76a68d5db89b8db5b95104c23cf9cc16f78315dc9f632708cbd3920a545d964e2226dc6f9ff2 @@ -10,7 +11,8 @@ EBUILD votca-csgapps-1.4.ebuild 649 BLAKE2B 4b219583f5d5a1f7f4ed7635b4fedce2619d EBUILD votca-csgapps-1.5.1.ebuild 668 BLAKE2B c1a715dcf42281b13819c20b51fc0c16f0435059e4f1dcfe83babd15eda4dc179d50ffe4a6252cd3155aec9545f2e5fc3bba728e2a6f739097422f5c6d94f247 SHA512 23d3ed6be1ea715a367f6203c9431598068ec7b1494865e594a67bfc55bc0f65e86914ad04cff7eff5a9e83fb79cae46fb4abd7997752a1a72dd90a68e173f97 EBUILD votca-csgapps-1.5.ebuild 666 BLAKE2B de904c4c69f9b223466bc97f646a861a5e1ff64d061389a1a1ac845e7351f9626226354c7c080d7a52ef5db2eddf397b2bf48ce042e168a881cb12da14338333 SHA512 e768e56d45d9e8b4ce2c01358b9de4b876a7a4149947445d388a4a1cffb6ac6882b17cdd794b17eee7abdb75d34c4e108f399c28fbca5ae0b11bbe5d57e07202 EBUILD votca-csgapps-1.6.1.ebuild 676 BLAKE2B 7e91e674c0e4602b174877aac82562e75f9bcc5a8a5291910f5f801bb8335acc43417594c9a616ebe6fadd72ca165860a2bc3e2b4508e6d8546e1c59542c4cc1 SHA512 4b23fda3ec2857c773ffe2947ede48903f88a664c4e41f07637cbd2859b05c91108295791b53a02a33eab4777c53f89e30fb378721eec402e4abead2c2e8def4 +EBUILD votca-csgapps-1.6.2.ebuild 659 BLAKE2B e0c0b1b95d98f743f356923fae13cd7747dcb3846f2bf066e34624db9080ea16fb171319dc97ed4357d816622ade101375f0e41d9e549496701211916622aeae SHA512 24c0567317c698a1105a6999c8e696c7763fdfb8cb811d3749cbf717028cc6770d03cd56e46aa6b009ae8c40f03fe27fb9db988f007ef4be433191903984711b EBUILD votca-csgapps-1.6.ebuild 672 BLAKE2B 2737abc16e6a06485fb9e542bd620f3ee1c9b63f4fde290558e0674a4cd2488162d917f8654c108080c9370c49fe027e60fe417d33bf6a6be5d14ebd667dfd4f SHA512 af87122c3f45b6003b314373e2a87035a37f6540221c01f31b40573a9ed9973bb9124f35342e601c9c0667db9ee60042b7aca5dbf495079518d5cf62961da852 EBUILD votca-csgapps-1.6_rc1.ebuild 665 BLAKE2B 893814bcc1e8413a5c6454c32092aa51e3633f2917aedf47bc928c603554acf064a299208e9a1c8cf58437cebdee00f6d07fd30424540081ef3d0c7f2636d8d0 SHA512 a32d204985dd20ef8389cbfd44f6e45d44542480d0593ddaa17d5976e193db687f26d1e818251325c939552c7e9a1c1f95ec20ca952834cc4a4ca6c4836ea2b7 -EBUILD votca-csgapps-9999.ebuild 665 BLAKE2B 893814bcc1e8413a5c6454c32092aa51e3633f2917aedf47bc928c603554acf064a299208e9a1c8cf58437cebdee00f6d07fd30424540081ef3d0c7f2636d8d0 SHA512 a32d204985dd20ef8389cbfd44f6e45d44542480d0593ddaa17d5976e193db687f26d1e818251325c939552c7e9a1c1f95ec20ca952834cc4a4ca6c4836ea2b7 +EBUILD votca-csgapps-9999.ebuild 659 BLAKE2B e0c0b1b95d98f743f356923fae13cd7747dcb3846f2bf066e34624db9080ea16fb171319dc97ed4357d816622ade101375f0e41d9e549496701211916622aeae SHA512 24c0567317c698a1105a6999c8e696c7763fdfb8cb811d3749cbf717028cc6770d03cd56e46aa6b009ae8c40f03fe27fb9db988f007ef4be433191903984711b MISC metadata.xml 457 BLAKE2B 9d392be6c061ebd3d975308065fcdec4ee061268f4b8b79e122b183d2e4f7259fdb9e165b8b3f030f1edbbc4f112757b1de7a50929ac112d5633143f9585699a SHA512 42a8ccad09d35dd4677b70005606582207747ae39d62a7ea75e2f5de28f887fee4265c8ae3b38e5cdb3017cc84c8902e2a525ae31fa5dd0aa00369e9b428f563 diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-1.6.2.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-1.6.2.ebuild new file mode 100644 index 000000000000..4f5d6d7d4aa7 --- /dev/null +++ b/sci-chemistry/votca-csgapps/votca-csgapps-1.6.2.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake + +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="" +fi + +DESCRIPTION="Extra applications for votca-csg" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="" + +RDEPEND=" + >=dev-cpp/eigen-3.3 + ~sci-chemistry/${PN%apps}-${PV}" + +DEPEND="${RDEPEND}" + +DOCS=( README.md ) diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild index 463cba8e0e38..4f5d6d7d4aa7 100644 --- a/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild +++ b/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild @@ -5,7 +5,7 @@ EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit cmake-utils +inherit cmake if [ "${PV}" != "9999" ]; then SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" diff --git a/sci-chemistry/votca-xtp/Manifest b/sci-chemistry/votca-xtp/Manifest index 6a89b861c3c8..acae167993cd 100644 --- a/sci-chemistry/votca-xtp/Manifest +++ b/sci-chemistry/votca-xtp/Manifest @@ -3,6 +3,7 @@ DIST votca-xtp-1.4.tar.gz 15214266 BLAKE2B 435ba1603495d904ccce20b4fa665d3a1c62f DIST votca-xtp-1.5.1.tar.gz 14634849 BLAKE2B 84ee9fc531a530ba276a6fd3eccc78dd25c27346db76871f33fe307dde451956bf091b636dd5594bf3b8b24a727fe7e5a730fb85cd2cbb0e5605705996e69bd2 SHA512 8fb6891e84d4d685e26287344554b705c607e7cb9f497c00ac9cd8328e50210c56706abdb7004b83d4addbfbc7b35c3526b4feabf75f681362b3b7a39c54b668 DIST votca-xtp-1.5.tar.gz 14637712 BLAKE2B af04de706f0d100968928459a03b6a94a94a211b3f5bd056d123756d40760fb0ada70add429ed5b86e211dbdd3b91aa4cf12e51a260638766d04158e7b5a1201 SHA512 693f34004749edfbabcd0a19dc23b3de3c09858c7c0dfe1e420b92632397971e3687489c1074a489d4d2fd337ddc5749c419869db104c65736e7c01bf12cd140 DIST votca-xtp-1.6.1.tar.gz 1405246 BLAKE2B b32db1e50ebfd79683ea2bf990293d9dfcf7703f3d95467a3fac5f98ec98e9bf1d29bab079e8f328fab8998144af186e7f47e99d9312763f7d73a1ae364ce58a SHA512 8b1bb235e70c239d0c57ceac65cd384841ea136d61f28bc72cbe2cfb47f9d776d42e06180acd1d8da93d0a0586e0bc3884ed82830d0f31c498ce225ca79a45aa +DIST votca-xtp-1.6.2.tar.gz 1405868 BLAKE2B 4e5700cec41ede632b97904259040aef2b79f9698547bf508584e49ff5cb16ab627c31732136de67bed3f70af9bf890a25bf511e8d9278821107760fc29441b7 SHA512 64610239ef5b902daa4ff475b4fea194912ef2a50e24214fcecf7d63336208a642c5ae5f02b0f21d04a78acaef224ba9a29b06b9380dbd6a43553e704efc54fe DIST votca-xtp-1.6.tar.gz 1404955 BLAKE2B 1599281ea1cd6b5a93b1d91f69a793af7bb9cd2fbf70157e5d40a5bfc72f973f3d97338f92157c2c482ad041f8afda298282b1f83dda66d0bb189bdc07bb5a23 SHA512 cb99c31fe7f1af53b8ccf50cc9cc304ed5c5b5d1a165e1a72a456c0bbf5ac8bb9263c9eff829acc74be348192afbf80fd4d80a2c20d1dd5d7f909b1b50368670 DIST votca-xtp-1.6_rc1.tar.gz 13586771 BLAKE2B d5b72a7389b77df0570eac0021870bba3fa66a89b3a2df1e08632b1c1827884d101ef8d972762dae35e44e53e7a9fe9278d3204eec09c35d091ab3427b055be4 SHA512 0b54eddcf944967b1d41f75f4887eba9edc3be18b94d319e93e795a24f58a2877d7f60afd806290eacb41d329d1b1206ebaab83874d6be2d5b026f06dbc19dfd DIST votca-xtp-manual-1.4.1.pdf 1066873 BLAKE2B 8cbd4b55b013794a19a8b5867b929b8e2d9084e6780d777b2a2bbaea23006f4f4ec5b26bd4a07c59e1c6726f23471eb1756b668636e0c4e656a0807e64197586 SHA512 fdf1147f24785524f5e96020fcd29c32bbeef520eebf6afba32b59d7e777d586c452919478d2734c3f021e558b1147b945cdbc0833402be2b16e5af3a8e37f5f @@ -14,7 +15,8 @@ EBUILD votca-xtp-1.4.ebuild 1618 BLAKE2B bab1c2d4cd442bc2208f87ff16ed1218aaf6c34 EBUILD votca-xtp-1.5.1.ebuild 1628 BLAKE2B a89ea389a31edce013d2e41eca4a0a818fd3f0b359aa9e770ecf3e04089b99063106d8b20562b36ad83fdc318c6cc6ffc119a589d995db08175e704ff7ce53f1 SHA512 a90fd6523ef6d42af25b99509718511cf0303bef2e0b083b6e4e8cbb5160bf1cc802b0e60a682c7bd1301f5b17cbaf78c2d2e593d2528f9c24b5f6c3c1aa984f EBUILD votca-xtp-1.5.ebuild 1626 BLAKE2B 15b3e63d11348ac376e15769b6106c98144a0ce88bbc7149fcf98bede2f7a29ee4ea066cea67fadf14e60e6dbc6745de4bffa4cf11d6ce6f08d5631fad0af347 SHA512 ac39f8f262a40683ff267dd13ea17cdfb9bd3ba62d698e8e20c98ee1adce53bd002a10dd7805a4ba419ca80a4a3ffd0b3b5c8f9e4b040182eaa6ffd069df114e EBUILD votca-xtp-1.6.1.ebuild 992 BLAKE2B ec7860af210b86c57cecb6adb3ef42130f208a60f23f65dadde98ac751cf8dc0981861b5126c2f97b6e7e20e4d6ab78a847c4e644d21fdf741b91784ce85bdfe SHA512 7174ba2da6f0bc38e2532c525a98c2d4e5641bd6879b9a1d5ed133fbfcd0523420398793edb6a86d033b759e8e6fb5550312608639517c50c4d17876ef9a9cfc +EBUILD votca-xtp-1.6.2.ebuild 975 BLAKE2B 95533f87c2afefb78002e83099299e40b00fc5bd16e8e054810fa60f6d039ae1c35452f1fd14e586e9d8adbadf1293d85e93b0906b324854b0bc71e85231ba97 SHA512 497c6b1c081e56b64ca33bc0089946c32b1b0ec977f38a7bafba976087ea192d70b1535d49394a87b347b68872dd3b91970b647dd8bccc72713556daa955cd61 EBUILD votca-xtp-1.6.ebuild 988 BLAKE2B a0829b922e31fe3e14c60422ebaff3e26da19320b78d22fcdf22de032d9983a98f019a2469ffe9807cc34585fc8655c5a5cc7f80e81c8547e95aa9e569e240c5 SHA512 7643ea1c4b2c123169f8c3a06c4d04e5bccb9070afe70bcbe8c935f956b78ce29c83223e9c54df8915164f0107ffec50b50a639ba0c4407f9cb3e70ee5f93023 EBUILD votca-xtp-1.6_rc1.ebuild 981 BLAKE2B 029f87e4554e2d353b5ce31f3901b5d18ae56ae4165878066e93d2de5f4ff4c65b9532be077127ec4e605b22ff0c765b841a6f9978cc7e503e50554b0e7ff7b7 SHA512 e2d58abe5b8f8d6b3e2a696a0b0a0f7b27f0af4a88d00d2fc59053dbccd9b7fa840579a5bc3b854bcdf3ce9266d10bacd962d4bada0b5ed325e0074c2d873d3d -EBUILD votca-xtp-9999.ebuild 981 BLAKE2B 029f87e4554e2d353b5ce31f3901b5d18ae56ae4165878066e93d2de5f4ff4c65b9532be077127ec4e605b22ff0c765b841a6f9978cc7e503e50554b0e7ff7b7 SHA512 e2d58abe5b8f8d6b3e2a696a0b0a0f7b27f0af4a88d00d2fc59053dbccd9b7fa840579a5bc3b854bcdf3ce9266d10bacd962d4bada0b5ed325e0074c2d873d3d +EBUILD votca-xtp-9999.ebuild 975 BLAKE2B 95533f87c2afefb78002e83099299e40b00fc5bd16e8e054810fa60f6d039ae1c35452f1fd14e586e9d8adbadf1293d85e93b0906b324854b0bc71e85231ba97 SHA512 497c6b1c081e56b64ca33bc0089946c32b1b0ec977f38a7bafba976087ea192d70b1535d49394a87b347b68872dd3b91970b647dd8bccc72713556daa955cd61 MISC metadata.xml 453 BLAKE2B 51ee11d9c55f15fd0382a7c422d1c12364901a5ac257f57d04b91b8ca77acf9c1eb709879bfc6042b577961352cbc4e31b01ece3a8c650eaffa9b4ebc6d385fb SHA512 892c8f84df6bd19e969b372def9a485be9121d8f7ab410b532529980298e57d0705f73fac409d8f251449cf2119dd3f28133e08d21d0e73b27d5ec0e9a3f205e diff --git a/sci-chemistry/votca-xtp/votca-xtp-1.6.2.ebuild b/sci-chemistry/votca-xtp/votca-xtp-1.6.2.ebuild new file mode 100644 index 000000000000..116b226b03f4 --- /dev/null +++ b/sci-chemistry/votca-xtp/votca-xtp-1.6.2.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake multilib + +IUSE="" +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="" +fi + +DESCRIPTION="Votca excitation and charge properties module" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" + +RDEPEND=" + ~sci-libs/votca-tools-${PV} + >=dev-cpp/eigen-3.3 + sci-libs/hdf5[cxx] + ~sci-chemistry/votca-csg-${PV} + sci-libs/libxc" + +DEPEND="${RDEPEND} + virtual/pkgconfig" + +DOCS=( README.md NOTICE CHANGELOG.md ) + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA-XTP, J. Chem. Theo. Comp. 14, 6353 (2018)" + einfo "https://doi.org/10.1021/acs.jctc.8b00617" + einfo +} diff --git a/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild b/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild index 9e3b8ca0fa6d..116b226b03f4 100644 --- a/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild +++ b/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild @@ -5,7 +5,7 @@ EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake-utils multilib +inherit bash-completion-r1 cmake multilib IUSE="" if [ "${PV}" != "9999" ]; then |