diff options
author | Aaron Bauman <bman@gentoo.org> | 2020-07-28 14:45:29 -0400 |
---|---|---|
committer | Aaron Bauman <bman@gentoo.org> | 2020-07-28 14:45:29 -0400 |
commit | 3831172264494f42d621e760593f4d066900d922 (patch) | |
tree | 3a31692fd34affb4b8b80d14ac9029f7162213eb /sci-chemistry | |
parent | updates/2Q2018: drop slotmove for netmail/getmail (diff) | |
download | gentoo-3831172264494f42d621e760593f4d066900d922.tar.gz gentoo-3831172264494f42d621e760593f4d066900d922.tar.bz2 gentoo-3831172264494f42d621e760593f4d066900d922.zip |
*/*: Drop more Py2 last-rited pkgs
Bug: https://bugs.gentoo.org/715966
Closes: https://bugs.gentoo.org/714628
Closes: https://bugs.gentoo.org/606680
Closes: https://bugs.gentoo.org/686238
Closes: https://bugs.gentoo.org/710214
Closes: https://bugs.gentoo.org/710028
Closes: https://bugs.gentoo.org/710032
Closes: https://bugs.gentoo.org/656934
Closes: https://bugs.gentoo.org/592718
Closes: https://bugs.gentoo.org/446122
Closes: https://bugs.gentoo.org/547210
Closes: https://bugs.gentoo.org/359785
Closes: https://bugs.gentoo.org/571396
Closes: https://bugs.gentoo.org/600754
Closes: https://bugs.gentoo.org/677830
Closes: https://bugs.gentoo.org/710716
Closes: https://bugs.gentoo.org/651940
Closes: https://bugs.gentoo.org/695132
Closes: https://bugs.gentoo.org/708978
Closes: https://bugs.gentoo.org/710058
Signed-off-by: Aaron Bauman <bman@gentoo.org>
Diffstat (limited to 'sci-chemistry')
48 files changed, 0 insertions, 1742 deletions
diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest deleted file mode 100644 index 1a146495e053..000000000000 --- a/sci-chemistry/apbs/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST apbs-1.4.1.zip 37999283 BLAKE2B 2301deb7ab4eb2f20098cf63df180bb53189e42a89cd5559357cdcf08e84d27a44eafe8557bb460574802d24d29741ad4606dc3bd7f32911d0d0f2c7453d6470 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a 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/eden/Manifest b/sci-chemistry/eden/Manifest deleted file mode 100644 index ef7017e4ec14..000000000000 --- a/sci-chemistry/eden/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST eden_V5.3.tar.gz 1139981 BLAKE2B 237f054accbba72fcde3a43716915a8037412a26aee861839c4a6e404276126a3955e6e0a3c76078b2253658f3ab9bcf8ad628bba059421c5171d0394c41052b SHA512 c59d08004bdb72ef39fe205aef546fbcff9c57ee42942c0391052de9c501c7793ed3bd280569020c2b9ec6133a87362d184a2012b61c6be18b5f6ba9b59716c5 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/p3d/Manifest b/sci-chemistry/p3d/Manifest deleted file mode 100644 index 93d8b80b2f94..000000000000 --- a/sci-chemistry/p3d/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST p3d-0.4.3.tar.gz 7213577 BLAKE2B b614957be16ede7567bd6412d183b3cb79638a5033672afd725cafaf393e306d5d227e1bca444ea17d60a3cd3bb5d3b2c910f2bfc68a118d3bffcd29944b4c29 SHA512 b4cf472b849ece96fe0b2b7f633c496fe3d12bf8cb82a2af10180ce5c27c5465dd0c16cb912d22c56c933b68c06e7de28c0c640da29eaa6bc6f95009bf10277f 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/${PN} - doins -r pdbs exampleScripts - fi -} diff --git a/sci-chemistry/pdb-tools/Manifest b/sci-chemistry/pdb-tools/Manifest deleted file mode 100644 index f507aec00c53..000000000000 --- a/sci-chemistry/pdb-tools/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pdbTools_0.2.1.tar.gz 103835 BLAKE2B ad4b5c8d6eb000c79a6d2797519b99027350fa34f6d543f6302f1a9edbe3497afe1a7b5c5c0e7243081cc709d9f1c37da5fc31605a0a225413851ce7288f64c9 SHA512 9c43c10e8739f8a34dbb1a3bba710cc727f7d8392ff979681371bd4460c67203253fb01852438eb93b214c4a009789608d200ca551f30399652fb76d702cf724 diff --git a/sci-chemistry/pdb-tools/metadata.xml b/sci-chemistry/pdb-tools/metadata.xml deleted file mode 100644 index 25095bc4b42e..000000000000 --- a/sci-chemistry/pdb-tools/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <upstream> - <remote-id type="google-code">pdb-tools</remote-id> - <remote-id type="github">harmslab/pdbtools</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild deleted file mode 100644 index 090b7c041dfe..000000000000 --- a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild +++ /dev/null @@ -1,79 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit fortran-2 python-single-r1 toolchain-funcs - -MY_PN="pdbTools" - -DESCRIPTION="Tools for manipulating and calculations on wwPDB macromolecule structure files" -HOMEPAGE="https://github.com/harmslab/pdbtools" -SRC_URI="https://${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 0663d5136267..000000000000 --- a/sci-chemistry/pdb2pqr/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pdb2pqr-src-1.9.0.tar.gz 9051969 BLAKE2B bacb2c65d319fb918a7a15b772c250398ffa991a93ee731ec15c8ae907304daf57282bf83c24f84d11945349a7f93f6f934575c117d4ce24d6530f14e60f3730 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f 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 57d019e2f920..000000000000 --- a/sci-chemistry/prodecomp/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST prodecomp-3.0.tar.bz2 18377446 BLAKE2B c6b4acf20a76029fc34eaea7a0adf1a04fb727b2e246fbcad27e2fa2bea606b2e712fb986fdd3e534534b32a22acae58a00bc2a3c6bde893d5befe91696523d3 SHA512 8d23f174e125d4c7776432a37b063d2f39af8497050bd7f7ff358c67d509b1eef2c2865596efae632855fd583fb52c233b67d0e667c6c2a03ba6f5a2f2ac9b0d 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-caver/Manifest b/sci-chemistry/pymol-plugins-caver/Manifest deleted file mode 100644 index 4d7abe5d823c..000000000000 --- a/sci-chemistry/pymol-plugins-caver/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST Caver2_1_2_pymol_plugin.zip 5698331 BLAKE2B e1accfaea6faf1e8c545b88c965228ccb62710d4015ff681506971feba6bd18a4a8b0b6e6caf621c99830ba529a6ec17873cdd3d5e52ad6dc6f67d9457e4eb87 SHA512 9d28e059bb20f30cf6a0d25ed2eb080dcf9dbb753e9d4578d95e293b31c5cf5fe23d5177dccdb79c192ab3e65bb484b6eb22b26c267637b125404f871e01a52c 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 672421ffa008..000000000000 --- a/sci-chemistry/pymol-plugins-dssp/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pymol-plugins-dssp-110430.py.xz 6836 BLAKE2B d8a58d1ad85aaa45acdcac40d022bac8035baf9c95c05e2cd6abb1dd82f1cd390515e04b4c65ff96902655a366ca2e4eab8e86060dffb27ea146298f827fbd7c SHA512 521e0a32ca6d2c8c21c690815b0654bb44303bd7fb9a1eb76227030b2ad7311fadb0d748e49b8bbc16cd5e69acba375b5353de7bffef1ff69686e62021fe64f4 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-promol/Manifest b/sci-chemistry/pymol-plugins-promol/Manifest deleted file mode 100644 index 521213fb730c..000000000000 --- a/sci-chemistry/pymol-plugins-promol/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pymol-plugins-promol-3.0.2.zip 2219295 BLAKE2B 7e81de98ee20f6b22fabeca35b0825250c3b839b9ea51f6c0b51f15062c73810474bd377d0e39d3c2ac0d61f1b5cfb4174c53f1dfc67a11dfcd707eee417a7ed SHA512 e40e9c08e2cb1b223390d751bb1f32069924f1c23aa2b4bdafb6689254e6aa673d4412aca587792f660869f97a389db8a9183033d8b2394c998d0f911104d8d7 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/sparky/Manifest b/sci-chemistry/sparky/Manifest deleted file mode 100644 index abb7a3bc2696..000000000000 --- a/sci-chemistry/sparky/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST sparky-source-3.115.tar.gz 4103686 BLAKE2B c7811aa135b10f21b8807447e2ab173f407ccc1446ff1307006f7f885e6e69983647991600720e02e4e738bb68338de01bc5d57577eacf20298db6d53a54b183 SHA512 33b0fd368f15bf4d091d7152a189f57279aea54fb89a12f15314f2a1414b073f7bd282afedeb72e79192195b0b6ac212ca74da3def513592af5400c118ac8e89 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 -} |