summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/aqua/Manifest2
-rw-r--r--sci-chemistry/aqua/aqua-3.2-r3.ebuild97
-rw-r--r--sci-chemistry/aqua/files/aqua-3.2-flags.patch84
-rw-r--r--sci-chemistry/aqua/metadata.xml8
-rw-r--r--sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild3
-rw-r--r--sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-boost-1.85.patch21
-rw-r--r--sci-chemistry/chemex/chemex-2024.05.2-r1.ebuild (renamed from sci-chemistry/chemex/chemex-2024.05.2.ebuild)1
-rw-r--r--sci-chemistry/chemex/chemex-2024.05.3-r1.ebuild (renamed from sci-chemistry/chemex/chemex-2024.05.3.ebuild)1
-rw-r--r--sci-chemistry/gperiodic/metadata.xml3
-rw-r--r--sci-chemistry/gromacs/gromacs-2024.1.ebuild2
-rw-r--r--sci-chemistry/gromacs/gromacs-2024.2.ebuild2
-rw-r--r--sci-chemistry/gromacs/gromacs-2024.9999.ebuild2
-rw-r--r--sci-chemistry/gromacs/gromacs-9999.ebuild2
-rw-r--r--sci-chemistry/molmol/molmol-2k_p2-r9.ebuild2
-rw-r--r--sci-chemistry/namd/Manifest1
-rw-r--r--sci-chemistry/namd/files/namd-2.10-gentoo.patch124
-rw-r--r--sci-chemistry/namd/files/namd-2.7-iml-dec.patch24
-rw-r--r--sci-chemistry/namd/metadata.xml12
-rw-r--r--sci-chemistry/namd/namd-2.10.ebuild110
-rw-r--r--sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild280
-rw-r--r--sci-chemistry/procheck/Manifest3
-rw-r--r--sci-chemistry/procheck/files/procheck-3.5.4-close.patch35
-rw-r--r--sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch49
-rw-r--r--sci-chemistry/procheck/metadata.xml8
-rw-r--r--sci-chemistry/procheck/procheck-3.5.4-r3.ebuild87
-rw-r--r--sci-chemistry/threeV/threeV-1.2-r2.ebuild (renamed from sci-chemistry/threeV/threeV-1.2-r1.ebuild)17
-rw-r--r--sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild263
-rw-r--r--sci-chemistry/wxmacmolplt/Manifest1
-rw-r--r--sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch11
-rw-r--r--sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild48
-rw-r--r--sci-chemistry/xds-bin/Manifest4
-rw-r--r--sci-chemistry/xds-bin/xds-bin-20240831.ebuild (renamed from sci-chemistry/xds-bin/xds-bin-20170930.ebuild)24
-rw-r--r--sci-chemistry/xyza2pipe/Manifest1
-rw-r--r--sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch168
-rw-r--r--sci-chemistry/xyza2pipe/metadata.xml8
-rw-r--r--sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild34
36 files changed, 315 insertions, 1227 deletions
diff --git a/sci-chemistry/aqua/Manifest b/sci-chemistry/aqua/Manifest
deleted file mode 100644
index a6e19c27dff6..000000000000
--- a/sci-chemistry/aqua/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST aqua-3.2-nmr_manual.tar.gz 632031 BLAKE2B 1f595a111af4b5e91fc059b5af590a6c37a44654fcae42e6003b40cf7fdf542cb772d3ef25bf2475455ce8638cd0aebcbbc8c66bb57688ce919af2eac9b535cb SHA512 9b125b03507afebf15301c893efffae9be4e9695b9c577e5c2a80e83b620d04b4c27e867adf06336afa1556eddc96aa97de936028e503b1e85e156542664da0f
-DIST aqua3.2.tar.gz 688408 BLAKE2B 898e0e3bbc4ff7b6ce8a8128ce6ffef45db607c74e2d78a70cefc26818d39049e4d18159b65250a3651112f64318ccce838037e563d3a985be7ef369d89b594e SHA512 1939f662a68122da613368aa106d7a31525903014420035eba9d10c3bd99b04d654d156328d308673003854233a02c1da48c036f3187fa1f0f303cc5928edd6a
diff --git a/sci-chemistry/aqua/aqua-3.2-r3.ebuild b/sci-chemistry/aqua/aqua-3.2-r3.ebuild
deleted file mode 100644
index 78d987ec1460..000000000000
--- a/sci-chemistry/aqua/aqua-3.2-r3.ebuild
+++ /dev/null
@@ -1,97 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit fortran-2 toolchain-funcs
-
-DESCRIPTION="Program suite in this distribution calculates restraint violations"
-HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html"
-SRC_URI="
- ${PN}${PV}.tar.gz
- doc? ( ${P}-nmr_manual.tar.gz )"
-
-SLOT="0"
-LICENSE="procheck"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples"
-
-RDEPEND="sci-chemistry/procheck"
-DEPEND="app-shells/tcsh"
-
-RESTRICT="fetch"
-
-S="${WORKDIR}"/${PN}${PV}
-
-PATCHES=(
- "${FILESDIR}"/${P}-flags.patch
-)
-
-pkg_nofetch() {
- elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
- elog "And follow the instructions for downloading the following into your DISTDIR"
- elog "directory:"
- elog " ${PN}${PV}.tar.gz"
- if use doc; then
- elog " nmr_manual.tar.gz -> ${P}-nmr_manual.tar.gz"
- fi
-}
-
-src_prepare() {
- sed \
- -e 's:nawk:gawk:g' \
- -e "s:/bin/gawk:${EPREFIX}/usr/bin/gawk:g" \
- -e "s:/usr/local/bin/perl:${EPREFIX}/usr/bin/perl:g" \
- -i $(find . -type f) || die
- default
-}
-
-src_compile() {
- cd src || die
- emake \
- MYROOT="${WORKDIR}" \
- CC="$(tc-getCC)" \
- FC="$(tc-getFC)" \
- CFLAGS="${CFLAGS} -I../sub/lib" \
- FFLAGS="${FFLAGS}" \
- LDFLAGS="${LDFLAGS}" \
- exth
- emake \
- MYROOT="${WORKDIR}" \
- CC="$(tc-getCC)" \
- FC="$(tc-getFC)" \
- CFLAGS="${CFLAGS} -I../sub/lib" \
- FFLAGS="${FFLAGS}" \
- LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
- rm -f scripts/conv* || die
- dobin bin/* scripts/*
- dosym AquaWhat /usr/bin/qwhat
- dosym AquaHow /usr/bin/qhow
- dosym AquaPseudo /usr/bin/qpseudo
- dosym AquaDist /usr/bin/qdist
- dosym AquaCalc /usr/bin/qcalc
- dosym AquaAssign /usr/bin/qassign
- dosym AquaRedun /usr/bin/qredun
- dosym AquaCompl /usr/bin/qcompl
-
- dodoc HISTORY HOW_TO_USE NEW README doc/*
- dohtml html/*
-
- insinto /usr/share/${PN}
- doins data/*
- if use examples; then
- doins -r exmpls
- fi
-
- if use doc; then
- dohtml -r manual
- fi
-
- cat >> "${T}"/34aqua <<- EOF
- AQUADATADIR="${EPREFIX}/usr/share/${PN}"
- EOF
- doenvd "${T}"/34aqua
-}
diff --git a/sci-chemistry/aqua/files/aqua-3.2-flags.patch b/sci-chemistry/aqua/files/aqua-3.2-flags.patch
deleted file mode 100644
index a60841b8ce08..000000000000
--- a/sci-chemistry/aqua/files/aqua-3.2-flags.patch
+++ /dev/null
@@ -1,84 +0,0 @@
-diff --git a/src/makefile b/src/makefile
-index 3113471..dd7a320 100644
---- a/src/makefile
-+++ b/src/makefile
-@@ -176,47 +176,46 @@ nrutil.h:
- # Executable files
-
- $(BIN)/AquaWhat: AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS)
-- $(CC) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) $(LDFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS)
-
- $(BIN)/AquaHow: AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS)
-- $(CC) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS)
-
- $(BIN)/AquaPseudo: AquaPseudo.o $(OBJECTS) $(R_OBJECTS)
-- $(CC) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS) $(LDFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS)
-
- $(BIN)/AquaDist: AquaDist.o $(OBJECTS)
-- $(CC) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) $(LDFLAGS) -lm
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) -lm
-
- $(BIN)/AquaCalc: AquaCalc.o $(OBJECTS) $(RNG_OBJECTS)
-- $(CC) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) $(LDFLAGS) -lm
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) -lm
-
- $(BIN)/AquaAssign: AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
-- $(CC) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
-
- $(BIN)/AquaCompl: AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
-- $(CC) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) -lm
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) -lm
-
- $(BIN)/AquaRedun: AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
-- $(CC) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
-
- $(BIN)/testnew: testnew.o $(OBJECTS)
-- $(CC) -o $(BIN)/testnew testnew.o $(OBJECTS) $(LDFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/testnew testnew.o $(OBJECTS)
-
- $(BIN)/getproj: getproj.c
-- $(CC) -o $(BIN)/getproj -O getproj.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(BIN)/getproj getproj.c
-
- $(BIN)/AquaPlot: AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
-- $(CC) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
-
- $(BIN)/Qext: Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
-- $(CC) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
-
- $(BIN)/StarTest: StarTest.o
-- $(CC) -o $(BIN)/StarTest StarTest.o $(LDFLAGS) $(STARFLAGS) $(STARLIBS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/StarTest StarTest.o $(STARFLAGS) $(STARLIBS)
-
- exth: exth.f
-- f77 -o exth -O2 exth.f
-- strip exth
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o exth -O2 exth.f
-
-
- # Object files
-@@ -269,7 +268,7 @@ AquaCommon.o: AquaCommon.c AquaCommon.h nrutil.h \
- $(CC) -c AquaCommon.c $(CFLAGS)
-
- nrutil.o: nrutil.c nrutil.h
-- $(CC) -c nrutil.c -DANSI
-+ $(CC) $(CFLAGS) -c nrutil.c -DANSI
-
- AquaFuncts.o: AquaFuncts.c AquaFuncts.h AquaFuncts_cv.h AquaFuncts_io.h\
- AquaStrucset.h AquaFiles.h\
-@@ -319,7 +318,7 @@ $(LIB)/MenuFuncts.o: $(LIB)/MenuFuncts.c $(LIB)/MenuTypes.h $(LIB)/MenuFuncts.h\
- cd $(LIB); $(CC) -c MenuFuncts.c $(CFLAGS)
-
- cv_subs.o: cv_subs.f
-- f77 -c cv_subs.f $(FFLAGS)
-+ $(FC) -c cv_subs.f $(FFLAGS)
-
- Qext.o: Qext.c Qext.h\
- $(LIB)/MenuFuncts.h $(LIB)/Functs.h $(G_HEADERS)
diff --git a/sci-chemistry/aqua/metadata.xml b/sci-chemistry/aqua/metadata.xml
deleted file mode 100644
index d4ff1000a775..000000000000
--- a/sci-chemistry/aqua/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
index e9edf1f9c991..dd396732c357 100644
--- a/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
@@ -15,7 +15,7 @@ S="${WORKDIR}/${MY_PN}-${PV}/build/linux/release"
LICENSE="Apache-2.0"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="amd64 ~x86"
IUSE="debug"
RDEPEND="dev-libs/boost:="
@@ -23,6 +23,7 @@ DEPEND="${RDEPEND}"
PATCHES=(
"${FILESDIR}"/${P}-gentoo.patch
+ "${FILESDIR}"/${P}-boost-1.85.patch
)
src_prepare() {
diff --git a/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-boost-1.85.patch b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-boost-1.85.patch
new file mode 100644
index 000000000000..55906b093a49
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-boost-1.85.patch
@@ -0,0 +1,21 @@
+https://bugs.gentoo.org/932237
+--- a/src/lib/vina.h
++++ b/src/lib/vina.h
+@@ -35,7 +35,6 @@
+ #include <boost/program_options.hpp>
+ #include <boost/filesystem/fstream.hpp>
+ #include <boost/filesystem/exception.hpp>
+-#include <boost/filesystem/convenience.hpp> // filesystem::basename
+ #include <boost/thread/thread.hpp> // hardware_concurrency // FIXME rm ?
+ #include <boost/algorithm/string.hpp>
+ //#include <openbabel/mol.h>
+--- a/src/split/split.cpp
++++ b/src/split/split.cpp
+@@ -30,7 +30,6 @@
+ #include <boost/program_options.hpp>
+ #include <boost/filesystem/fstream.hpp>
+ #include <boost/filesystem/exception.hpp>
+-#include <boost/filesystem/convenience.hpp> // filesystem::basename
+
+ #include "file.h"
+ #include "parse_error.h"
diff --git a/sci-chemistry/chemex/chemex-2024.05.2.ebuild b/sci-chemistry/chemex/chemex-2024.05.2-r1.ebuild
index 449970b2c4ce..87646d2c3045 100644
--- a/sci-chemistry/chemex/chemex-2024.05.2.ebuild
+++ b/sci-chemistry/chemex/chemex-2024.05.2-r1.ebuild
@@ -35,7 +35,6 @@ RDEPEND="
>=dev-python/rapidfuzz-3.7.0[${PYTHON_USEDEP}]
>=dev-python/rich-13.7.1[${PYTHON_USEDEP}]
>=dev-python/scipy-1.13.0[${PYTHON_USEDEP}]
- >=dev-python/tomli-2.0.1[${PYTHON_USEDEP}]
')
"
DEPEND="${RDEPEND}"
diff --git a/sci-chemistry/chemex/chemex-2024.05.3.ebuild b/sci-chemistry/chemex/chemex-2024.05.3-r1.ebuild
index 449970b2c4ce..87646d2c3045 100644
--- a/sci-chemistry/chemex/chemex-2024.05.3.ebuild
+++ b/sci-chemistry/chemex/chemex-2024.05.3-r1.ebuild
@@ -35,7 +35,6 @@ RDEPEND="
>=dev-python/rapidfuzz-3.7.0[${PYTHON_USEDEP}]
>=dev-python/rich-13.7.1[${PYTHON_USEDEP}]
>=dev-python/scipy-1.13.0[${PYTHON_USEDEP}]
- >=dev-python/tomli-2.0.1[${PYTHON_USEDEP}]
')
"
DEPEND="${RDEPEND}"
diff --git a/sci-chemistry/gperiodic/metadata.xml b/sci-chemistry/gperiodic/metadata.xml
index 3050b77faba5..ca9404a805af 100644
--- a/sci-chemistry/gperiodic/metadata.xml
+++ b/sci-chemistry/gperiodic/metadata.xml
@@ -10,7 +10,4 @@
periodic table, based on the GTK2 toolkit. It also features a command line
interface.
</longdescription>
- <upstream>
- <remote-id type="sourceforge">downloads</remote-id>
- </upstream>
</pkgmetadata>
diff --git a/sci-chemistry/gromacs/gromacs-2024.1.ebuild b/sci-chemistry/gromacs/gromacs-2024.1.ebuild
index a3319899d419..33e343e23e7c 100644
--- a/sci-chemistry/gromacs/gromacs-2024.1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2024.1.ebuild
@@ -26,7 +26,7 @@ else
doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
# since 2022 arm support was dropped (but not arm64)
- KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+ KEYWORDS="~amd64 -arm ~arm64 ~riscv ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
diff --git a/sci-chemistry/gromacs/gromacs-2024.2.ebuild b/sci-chemistry/gromacs/gromacs-2024.2.ebuild
index a3319899d419..33e343e23e7c 100644
--- a/sci-chemistry/gromacs/gromacs-2024.2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2024.2.ebuild
@@ -26,7 +26,7 @@ else
doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
# since 2022 arm support was dropped (but not arm64)
- KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+ KEYWORDS="~amd64 -arm ~arm64 ~riscv ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
diff --git a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild b/sci-chemistry/gromacs/gromacs-2024.9999.ebuild
index a3319899d419..33e343e23e7c 100644
--- a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2024.9999.ebuild
@@ -26,7 +26,7 @@ else
doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
# since 2022 arm support was dropped (but not arm64)
- KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+ KEYWORDS="~amd64 -arm ~arm64 ~riscv ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index a3319899d419..33e343e23e7c 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -26,7 +26,7 @@ else
doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
# since 2022 arm support was dropped (but not arm64)
- KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+ KEYWORDS="~amd64 -arm ~arm64 ~riscv ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild
index 29769cede153..14378809c07a 100644
--- a/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild
+++ b/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild
@@ -25,7 +25,7 @@ S="${WORKDIR}"
LICENSE="molmol"
SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
RDEPEND="
|| (
diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest
deleted file mode 100644
index ffe7e0c005e5..000000000000
--- a/sci-chemistry/namd/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST NAMD_2.10_Source.tar.gz 9200234 BLAKE2B fe348a21309b279640da81ed4dd5447c1e6e467866270dc1730b26d02d5518b45bd662211c3cbe228bd8d9885edb062cf5d245d634bcd38773c36873febd2ee6 SHA512 3712a03841fad76c502ac4e41469162ff78e6152560d0f6855d61d2b5583241a661e2a3e7446029b56a6f6f1100f25cb51b2c3df6571542397961d3bb625bc92
diff --git a/sci-chemistry/namd/files/namd-2.10-gentoo.patch b/sci-chemistry/namd/files/namd-2.10-gentoo.patch
deleted file mode 100644
index ffef6dc3ad68..000000000000
--- a/sci-chemistry/namd/files/namd-2.10-gentoo.patch
+++ /dev/null
@@ -1,124 +0,0 @@
-diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw NAMD_2.10_Source/arch/Linux-x86_64.fftw
---- NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw 2015-03-06 17:53:44.170416075 -0700
-+++ NAMD_2.10_Source/arch/Linux-x86_64.fftw 2015-03-06 17:54:46.641162629 -0700
-@@ -1,7 +1,7 @@
-
--FFTDIR=/Projects/namd2/fftw/linux-x86_64
-+FFTDIR=/usr
- FFTINCL=-I$(FFTDIR)/include
--FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw
-+FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw
- FFTFLAGS=-DNAMD_FFTW
- FFT=$(FFTINCL) $(FFTFLAGS)
-
-diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl NAMD_2.10_Source/arch/Linux-x86_64.tcl
---- NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl 2015-03-06 17:53:44.170416075 -0700
-+++ NAMD_2.10_Source/arch/Linux-x86_64.tcl 2015-03-06 17:54:46.641162629 -0700
-@@ -1,9 +1,9 @@
-
- #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64
--TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded
-+TCLDIR=/usr
- TCLINCL=-I$(TCLDIR)/include
- #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl
--TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread
-+#TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread
- TCLFLAGS=-DNAMD_TCL
- TCL=$(TCLINCL) $(TCLFLAGS)
-
-diff -Naur NAMD_2.10_Source.orig/Makefile NAMD_2.10_Source/Makefile
---- NAMD_2.10_Source.orig/Makefile 2015-03-06 17:53:44.170416075 -0700
-+++ NAMD_2.10_Source/Makefile 2015-03-06 18:01:32.645966590 -0700
-@@ -389,10 +389,10 @@
- $(DSTDIR)/stringhash.o
-
- # definitions for Charm routines
--CHARMC = $(CHARM)/bin/charmc
--CHARMXI = $(CHARM)/bin/charmc
--CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
--CHARMLIB = $(CHARM)/lib
-+CHARMC = /usr/bin/charmc
-+CHARMXI = /usr/bin/charmc
-+CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1
-+CHARMLIB = /usr/gentoo-libdir
- CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -module CkMulticast
- #CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
- #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
-@@ -418,7 +418,7 @@
-
- # Add new executables here.
-
--BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb charmrun
-+BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb
-
- # This should be rebuilt at every compile, but not on Win32.
- BUILDINFO = $(DSTDIR)/buildinfo
-@@ -434,7 +434,7 @@
-
- namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS)
- $(MAKEBUILDINFO)
-- $(CHARMC) -verbose -ld++-option \
-+ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \
- '$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \
- "$(CHARM_MODULES)" -language charm++ \
- $(BUILDINFO).o \
-@@ -484,11 +484,8 @@
- charmd_faceless.exe:
- $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
-
--charmrun.exe:
-- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
--
- psfgen: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS)
-- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
-+ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
-
- psfgen.exe: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL)
- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
-@@ -506,7 +503,7 @@
- $(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm
-
- flipdcd: $(SRCDIR)/flipdcd.c
-- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
- echo "#!/bin/sh\necho unavailable on this platform" > $@; \
- chmod +x $@
-
-@@ -516,7 +513,7 @@
- chmod +x $@
-
- fixdcd: $(SRCDIR)/fixdcd.c
-- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
-
- dumpdcd: $(SRCDIR)/dumpdcd.c
- $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c
-@@ -711,9 +708,7 @@
-
- DOC_FILES = README.txt announce.txt license.txt notes.txt
-
--RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2
--
--WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL)
-+RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2
-
- release: all
- $(ECHO) Creating release $(RELEASE_DIR_NAME)
-@@ -724,17 +719,9 @@
- for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \
- /bin/rm -rf $$f; \
- done
-- if [ -r $(CHARM)/bin/charmd ]; then \
-- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
-- fi
-- if [ -r $(CHARM)/bin/charmd_faceless ]; then \
-- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
-- fi
- chmod -R a+rX $(RELEASE_DIR_NAME)
- tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
- gzip $(RELEASE_DIR_NAME).tar
-- echo $(CHARM)
-- ls -l $(CHARM)/lib
- -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done
-
- winrelease: winall
diff --git a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
deleted file mode 100644
index e5ee3bd6c818..000000000000
--- a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/src/flipbinpdb.c b/src/flipbinpdb.c
-index 94b71ba..01a2529 100644
---- a/src/flipbinpdb.c
-+++ b/src/flipbinpdb.c
-@@ -9,6 +9,7 @@
- #include <sys/mman.h>
- #include <fcntl.h>
- #include <stdio.h>
-+#include <stdlib.h>
-
- #ifndef MAP_FILE
- #define MAP_FILE 0
-diff --git a/src/flipdcd.c b/src/flipdcd.c
-index 8ec85b7..1c23433 100644
---- a/src/flipdcd.c
-+++ b/src/flipdcd.c
-@@ -13,6 +13,7 @@
- #include <sys/mman.h>
- #include <fcntl.h>
- #include <stdio.h>
-+#include <stdlib.h>
-
- #ifndef MAP_FILE
- #define MAP_FILE 0
diff --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml
deleted file mode 100644
index 11bbcb9bf2c8..000000000000
--- a/sci-chemistry/namd/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>nicolasbock@gentoo.org</email>
- <name>Nicolas Bock</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/namd/namd-2.10.ebuild b/sci-chemistry/namd/namd-2.10.ebuild
deleted file mode 100644
index 76a34c5a0a19..000000000000
--- a/sci-chemistry/namd/namd-2.10.ebuild
+++ /dev/null
@@ -1,110 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-MY_PN="NAMD"
-
-inherit multilib toolchain-funcs flag-o-matic
-
-DESCRIPTION="A powerful and highly parallelized molecular dynamics code"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/"
-SRC_URI="${MY_PN}_${PV}_Source.tar.gz"
-
-LICENSE="namd"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-RESTRICT="fetch"
-
-RDEPEND="
- >=sys-cluster/charm-6.5.1-r2
- sci-libs/fftw:3.0
- dev-lang/tcl:0="
-
-DEPEND="${RDEPEND}
- virtual/pkgconfig
- app-shells/tcsh"
-
-NAMD_ARCH="Linux-x86_64-g++"
-
-NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD"
-
-S="${WORKDIR}/${MY_PN}_${PV}_Source"
-
-PATCHES=(
- # apply a few small fixes to make NAMD compile and
- # link to the proper libraries
- "${FILESDIR}"/namd-2.10-gentoo.patch
- "${FILESDIR}"/namd-2.7-iml-dec.patch
-)
-
-pkg_nofetch() {
- echo
- einfo "Please download ${MY_PN}_${PV}_Source.tar.gz from"
- einfo "${NAMD_DOWNLOAD}"
- einfo "after agreeing to the license and then move it to"
- einfo "your DISTDIR directory."
- einfo "Be sure to select the ${PV} version!"
- echo
-}
-
-src_prepare() {
- CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3)
-
- default
-
- sed \
- -e "/CHARMBASE =/s:= .*:= /usr/bin/charm-${CHARM_VERSION}:" \
- -i Make.charm || die
-
- # Remove charm distribution. We don't need it.
- rm -f charm-*.tar || die
-
- # proper compiler and cflags
- sed \
- -e "s/g++.*/$(tc-getCXX)/" \
- -e "s/gcc.*/$(tc-getCC)/" \
- -e "s/CXXOPTS = .*/CXXOPTS = ${CXXFLAGS} ${LDFLAGS}/" \
- -e "s/COPTS = .*/COPTS = ${CFLAGS} ${LDFLAGS}/" \
- -i arch/${NAMD_ARCH}.arch || die
-
- sed \
- -e "s/gentoo-libdir/$(get_libdir)/g" \
- -e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \
- -i Makefile || die "Failed gentooizing Makefile."
- sed -e "s@/lib@/$(get_libdir)@g" -e '/FFTDIR=/s@=.*@=/usr@' -i arch/Linux-x86_64.fftw3 || die
- sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die
-}
-
-src_configure() {
- # configure
- ./config ${NAMD_ARCH} --with-fftw3 --charm-arch . || die
-}
-
-src_compile() {
- # build namd
- cd "${S}/${NAMD_ARCH}" || die
- TCLLIB="$($(tc-getPKG_CONFIG) --libs tcl) -ldl -pthread" \
- emake
-}
-
-src_install() {
- dodoc announce.txt license.txt notes.txt
- cd "${S}/${NAMD_ARCH}" || die
-
- # the binaries
- dobin ${PN}2 psfgen flipbinpdb flipdcd
-}
-
-pkg_postinst() {
- echo
- einfo "For detailed instructions on how to run and configure"
- einfo "NAMD please consults the extensive documentation at"
- einfo "http://www.ks.uiuc.edu/Research/namd/"
- einfo "and the NAMD tutorials available at"
- einfo "http://www.ks.uiuc.edu/Training/Tutorials/"
- einfo "Have fun :)"
- echo
-}
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild
deleted file mode 100644
index d6a0165b20c5..000000000000
--- a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild
+++ /dev/null
@@ -1,280 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{9..11} )
-WX_GTK_VER=3.0-gtk3
-
-inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="https://openbabel.org/"
-
-if [[ "${PV}" == *9999* ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/openbabel/${PN}.git"
-else
- if [[ "${PV}" == *_p* ]]; then # eg., openbabel-3.1.1_p20210325
- # Set to commit hash
- OPENBABEL_COMMIT=08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b
- SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
- S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
- else
- MY_P="${PN}-$(ver_rs 1- -)"
- SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz"
- S="${WORKDIR}/${PN}-${MY_P}"
- fi
- KEYWORDS="amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
-fi
-
-SRC_URI="${SRC_URI}
- https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png
- https://openbabel.org/OBTitle.jpg -> ${PN}.jpg"
-
-# See src/CMakeLists.txt for LIBRARY_VERSION
-SLOT="0/7.0.0"
-LICENSE="GPL-2"
-IUSE="cpu_flags_arm_neon cpu_flags_x86_sse2 cpu_flags_x86_sse4_2 doc examples +inchi json minimal openmp perl png python test wxwidgets"
-
-RESTRICT="!test? ( test )"
-
-# Inaccurate dependency logic upstream
-REQUIRED_USE="
- python? ( ${PYTHON_REQUIRED_USE} )
- test? ( inchi json !minimal wxwidgets )
-"
-
-BDEPEND="
- dev-lang/perl
- doc? (
- app-text/doxygen
- dev-texlive/texlive-latex
- )
- perl? ( >=dev-lang/swig-2 )
- python? ( >=dev-lang/swig-2 )
- test? ( dev-lang/python )
-"
-
-COMMON_DEPEND="
- dev-cpp/eigen:3
- dev-libs/libxml2:2
- sys-libs/zlib:=
- inchi? ( sci-libs/inchi )
- json? ( >=dev-libs/rapidjson-1.1.0 )
- png? ( x11-libs/cairo )
- python? ( ${PYTHON_DEPS} )
- wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )
-"
-
-DEPEND="
- ${COMMON_DEPEND}
- perl? ( dev-lang/perl )
-"
-
-RDEPEND="
- ${COMMON_DEPEND}
- perl? (
- dev-lang/perl:=
- !sci-chemistry/openbabel-perl
- )
-"
-
-PATCHES=(
- "${FILESDIR}"/openbabel-3.1.1-fix-time-check-cmake.patch
-)
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-prepare_python_bindings() {
- mkdir -p scripts/${EPYTHON} || die
- # Appends to scripts/CMakeLists.txt, substituting the correct tags, for
- # each valid python implementation,
- cat "${FILESDIR}"/${PN}-python.cmake | \
- sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
- -e "s|@@PYTHON_INCUDE_DIR@@|$(python_get_includedir)|" \
- -e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \
- -e "s|@@PYTHON_SITEDIR@@|$(python_get_sitedir)|" >> \
- scripts/CMakeLists.txt || die
-}
-
-src_prepare() {
- cmake_src_prepare
-
- if use perl; then
- perl_set_version
-
- sed -e "/\${LIB_INSTALL_DIR}\/auto/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \
- -e "/\${LIB_INSTALL_DIR}\/Chemistry/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \
- -i scripts/CMakeLists.txt || die
- fi
-
- if use python; then
- # Skip the python bindings sections as we'll append our own
- sed -e '/^if (PYTHON_BINDINGS)$/s|PYTHON_BINDINGS|false|' \
- -i {scripts,test}/CMakeLists.txt || die
- if use test; then
- # Problems with testbindings built with -O2
- local test_skip="@unittest.skip('Similar to Issue #2138')"
- sed -e "/def testTemplates/s|^| ${test_skip}\\n|" \
- -i test/testbindings.py || die
- test_skip="@unittest.skip('Similar to Issue #2246')"
- sed -e "/^def test_write_string/s|^|${test_skip}\\n|" \
- -i test/testobconv_writers.py || die
- fi
- python_foreach_impl prepare_python_bindings
- fi
-
- # Remove dependency automagic
- if ! use png; then
- sed -e '/^find_package(Cairo/d' -i CMakeLists.txt || die
- fi
- if ! use wxwidgets; then
- sed -e '/^find_package(wxWidgets/d' -i CMakeLists.txt || die
- fi
- if ! use inchi; then
- sed -e '/^else()$/s|else\(\)|elseif\(false\)|' \
- -i cmake/modules/FindInchi.cmake || die
- fi
-
- # Don't install example bins to /usr/bin
- if use examples; then
- sed -e "/RUNTIME DESTINATION/s|bin|share/doc/${PF}/examples|" \
- -i doc/examples/CMakeLists.txt || die
- fi
-
- # boost is only used if building with gcc-3.x, which isn't supported in
- # Gentoo. Still, it shouldn't look for, and include, its headers
- sed -e '/find_package(Boost/d' -i {{tools,src}/,}CMakeLists.txt || die
-}
-
-src_configure() {
- if use json; then
- # -DOPTIMIZE_NATIVE=ON also forces -march=native so use
- # cpu_flags to set defines instead
- use cpu_flags_x86_sse2 && append-cppflags -DRAPIDJSON_SSE2
- use cpu_flags_x86_sse4_2 && append-cppflags -DRAPIDJSON_SSE42
- use cpu_flags_arm_neon && append-cppflags -DRAPIDJSON_NEON
- fi
-
- use wxwidgets && setup-wxwidgets
-
- use_bindings() {
- (use perl || use python) && (echo 'yes' || die) || (echo 'no' || die)
- }
-
- local mycmakeargs=(
- -DBUILD_DOCS=$(usex doc)
- -DBUILD_EXAMPLES=$(usex examples)
- -DBUILD_GUI=$(usex wxwidgets)
- -DENABLE_OPENMP=$(usex openmp)
- -DENABLE_TESTS=$(usex test)
- -DMINIMAL_BUILD=$(usex minimal)
- # Set this, otherwise it defaults to true and forces WITH_INCHI=true
- -DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
- -DOPTIMIZE_NATIVE=OFF
- -DPERL_BINDINGS=$(usex perl)
- -DPYTHON_BINDINGS=$(usex python)
- -DRUN_SWIG=$(use_bindings)
- -DWITH_COORDGEN=false
- -DWITH_INCHI=$(usex inchi)
- -DWITH_JSON=$(usex json)
- -DWITH_MAEPARSER=false
- )
-
- if use test; then
- # Help cmake find the python interpreter when dev-lang/python-exec is built
- # without native-symlinks support.
- python_setup
- mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" )
- fi
-
- cmake_src_configure
-}
-
-src_test() {
- # Wierd deadlock causes system_load to keep rising
- cmake_src_test -j1
-}
-
-openbabel-optimize() {
- python_optimize "${D}/$(python_get_sitedir)"/openbabel || die
-}
-
-src_install() {
- cmake_src_install
-
- docinto html
- for x in doc/*.html; do
- [[ ${x} != doc/api*.html ]] && dodoc ${x}
- done
- # Rendered in some html pages
- newdoc "${DISTDIR}"/${PN}.png babel130.png
- newdoc "${DISTDIR}"/${PN}.jpg OBTitle.jpg
-
- if use doc; then
- cmake_src_install docs
- docinto html/API
- dodoc -r doc/API/html/.
- fi
-
- if use examples; then
- # no compression since we want ready-to-run scripts
- docompress -x /usr/share/doc/${PF}/examples
-
- # ${PV} doesn't correspond to the internal BABEL_VERSION for
- # live or patch release builds so we grep it
- local babel_ver=$(
- grep '^#define BABEL_VERSION' < \
- "${BUILD_DIR}"/include/openbabel/babelconfig.h | \
- cut -d \" -f 2 || die
- )
- docinto examples/povray
- dodoc doc/dioxin.* doc/README*.pov*
- # Needed by the povray example
- dosym ../../../../${PN}/${babel_ver}/babel_povray3.inc \
- /usr/share/doc/${PF}/examples/povray/babel31.inc
-
- fi
-
- if use perl; then
- docinto /
- newdoc scripts/perl/Changes Changes.perl
- newdoc scripts/perl/README README.perl
- if use examples; then
- docinto examples/perl
- dodoc -r scripts/perl/examples/.
- fi
- fi
-
- if use python; then
- python_foreach_impl openbabel-optimize
- docinto /
- newdoc scripts/python/README.rst README.python.rst
- docinto html
- dodoc scripts/python/*.html
- if use examples; then
- docinto examples/python
- dodoc -r scripts/python/examples/.
- fi
- fi
-
- if use wxwidgets; then
- make_desktop_entry obgui "Open Babel" ${PN}
- doicon "${DISTDIR}"/${PN}.png
- fi
-}
-
-pkg_postinst() {
- use wxwidgets && xdg_desktop_database_update
-}
-
-pkg_postrm() {
- use wxwidgets && xdg_desktop_database_update
-}
diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest
deleted file mode 100644
index 48f2a0e21fda..000000000000
--- a/sci-chemistry/procheck/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST procheck-3.5.4-README 6585 BLAKE2B c61606848f30728b67d2ab51e0beadec1c30aaa0ca65a68834bff3ed3e3f466e34a0e4b64323e80cce9cee83854650ebe0805abf0509c0a9154bf08e3e0a2d6b SHA512 c6eff94cef9b67fd61884e88fa77ec381553d4dba53f477023738e1e44a6191c4241b14543ee7ecb93b049f16f262db2a09cf5d1a63248057633aab290f1f82a
-DIST procheck-3.5.4-manual.tar.gz 517840 BLAKE2B 33c5da5888bcd263e900cf2839f9287373e032fdde234e0375af061ec1c588d1ea5d2718da2a050da8060ba4003748a8fef3ff35b22f424c1cf6a1892aec0fe6 SHA512 0fa9c7d50b7ca43c626d5261c524166938d3a92be1d02221721bc7ce7e91ac4919e7200b946ce563f9bb696d7dab9588c1d1b31a4d551cafa2f2bce4931a212c
-DIST procheck-3.5.4.tar.gz 522013 BLAKE2B be6764bc741ec3f868aee349fc7e23608c612758029d0b745c421f40b47c896dd48de84ee7df6d09a64a20695bd5a1ed0a96464e6dcaf44de03da1ae231787f8 SHA512 1dd78b53070484fbcdca51001fd147ab13fd5e51b3d1da54fd529531917c31012393751ee514f0c79d579b17a1701dde04f81b1c9ac27b2b835a43fa96785ecc
diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-close.patch b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch
deleted file mode 100644
index 16a0658e654d..000000000000
--- a/sci-chemistry/procheck/files/procheck-3.5.4-close.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-diff --git a/pplot.f b/pplot.f
-index 7e06e68..c86b2b2 100644
---- a/pplot.f
-+++ b/pplot.f
-@@ -4720,6 +4720,7 @@ C---- Initialise variables
- SCORE(IDIST) = 0.0
- 50 CONTINUE
-
-+ REWIND(3)
- C---- If the required residue is of a greater number than that required,
- C read through the file until come to it
- IF (IRESID.GT.INRES) THEN
-diff --git a/ps.f b/ps.f
-index b652a7d..858b8e5 100644
---- a/ps.f
-+++ b/ps.f
-@@ -1705,12 +1705,14 @@ CVAX - CARRIAGECONTROL='LIST',
- C---- If this is an existing file, then read through all its records until
- C get to the end of file
- IF (.NOT.NEWFIL) THEN
-+ CLOSE(14)
-+ OPEN(14, file=fname, status='old', position='append', err=900)
-
- C---- Loop through the file until reach the end
-- 100 CONTINUE
-- READ(14,110,END=500) IREC
-- 110 FORMAT(A)
-- GO TO 100
-+C 100 CONTINUE
-+C READ(14,110,END=500) IREC
-+C 110 FORMAT(A)
-+C GO TO 100
-
- C---- If this is a new file, then write the header records to it
- ELSE \ No newline at end of file
diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch b/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch
deleted file mode 100644
index 453aebe3211f..000000000000
--- a/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch
+++ /dev/null
@@ -1,49 +0,0 @@
-diff --git a/Makefile b/Makefile
-index c5bb58f..0394b0a 100644
---- a/Makefile
-+++ b/Makefile
-@@ -35,31 +35,31 @@ distrib :
- # Individual executables
- # ----------------------
- anglen : anglen.o
-- $(F77) $(FOPTS) -o $@ anglen.o
-+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ anglen.o
- clean : clean.o
-- $(F77) $(FOPTS) -o $@ clean.o
-+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ clean.o
- rmsdev : rmsdev.o
-- $(F77) $(FOPTS) -o $@ rmsdev.o
-+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ rmsdev.o
- secstr : secstr.o
-- $(F77) $(FOPTS) -o $@ secstr.o
-+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ secstr.o
- gfac2pdb : gfac2pdb.o ps.o
-- $(F77) $(FOPTS) -o $@ gfac2pdb.o ps.o
-+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ gfac2pdb.o ps.o
- pplot : pplot.o ps.o
-- $(F77) $(FOPTS) -o $@ pplot.o ps.o
-+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ pplot.o ps.o
- bplot : bplot.o ps.o
-- $(F77) $(FOPTS) -o $@ bplot.o ps.o
-+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ bplot.o ps.o
- tplot : tplot.o ps.o
-- $(F77) $(FOPTS) -o $@ tplot.o ps.o
-+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ tplot.o ps.o
- mplot : mplot.o ps.o
-- $(F77) $(FOPTS) -o $@ mplot.o ps.o
-+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ mplot.o ps.o
- vplot : vplot.o ps.o
-- $(F77) $(FOPTS) -o $@ vplot.o ps.o
-+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ vplot.o ps.o
- viol2pdb : viol2pdb.o ps.o
-- $(F77) $(FOPTS) -o $@ viol2pdb.o ps.o
-+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ viol2pdb.o ps.o
- wirplot : wirplot.o ps.o
-- $(F77) $(FOPTS) -o $@ wirplot.o ps.o
-+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ wirplot.o ps.o
- nb : nb.c
-- $(CC) $(COPTS) -o nb nb.c $(CLIBS)
-+ $(CC) $(COPTS) $(LDFLAGS) -o nb nb.c $(CLIBS)
-
- # Individual rules for FORTRAN files with .inc files
- # --------------------------------------------------
diff --git a/sci-chemistry/procheck/metadata.xml b/sci-chemistry/procheck/metadata.xml
deleted file mode 100644
index e490bcb8aa87..000000000000
--- a/sci-chemistry/procheck/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://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/procheck/procheck-3.5.4-r3.ebuild b/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild
deleted file mode 100644
index 3db0e3f24244..000000000000
--- a/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild
+++ /dev/null
@@ -1,87 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit fortran-2 multilib toolchain-funcs versionator
-
-DESCRIPTION="Checks the stereochemical quality of a protein structure"
-HOMEPAGE="https://www.ebi.ac.uk/thornton-srv/software/PROCHECK"
-SRC_URI="
- ${P}.tar.gz ${P}-README
- doc? ( ${P}-manual.tar.gz )"
-
-LICENSE="procheck"
-SLOT="0"
-KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc"
-
-RDEPEND="app-shells/tcsh"
-DEPEND="${RDEPEND}"
-
-RESTRICT="fetch"
-
-S="${WORKDIR}/${PN}"
-
-pkg_nofetch() {
- elog "Please visit https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
- elog "and follow the instruction for downloading."
- elog "Files should be renamed in the following way before being copied to your"
- elog "DISTDIR directory:"
- elog " ${PN}.tar.gz -> ${P}.tar.gz"
- elog " README -> ${P}-README"
- use doc && elog " manual.tar.gz -> ${P}-manual.tar.gz"
-}
-
-PATCHES=(
- "${FILESDIR}"/${P}-ldflags.patch
- "${FILESDIR}"/${P}-close.patch
-)
-
-src_compile() {
- emake \
- F77="$(tc-getFC)" \
- CC="$(tc-getCC)" \
- COPTS="${CFLAGS}" \
- FOPTS="${FFLAGS} -std=legacy"
-}
-
-src_install() {
- for i in *.scr; do
- newbin ${i} ${i%.scr}
- done
-
- exeinto /usr/libexec/${PN}/
- doexe \
- anglen \
- clean \
- rmsdev \
- secstr \
- gfac2pdb \
- pplot \
- bplot \
- tplot \
- mplot \
- vplot \
- viol2pdb \
- wirplot \
- nb
- dodoc "${DISTDIR}"/${P}-README
-
- insinto /usr/libexec/${PN}/
- doins *.dat *.prm
- newins resdefs.dat resdefs.data
-
- cat >> "${T}"/30${PN} <<- EOF
- prodir="${EPREFIX}/usr/libexec/${PN}/"
- EOF
-
- doenvd "${T}"/30${PN}
-
- if use doc; then
- pushd "${WORKDIR}" > /dev/null
- docinto html
- dodoc -r manual
- popd > /dev/null
- fi
-}
diff --git a/sci-chemistry/threeV/threeV-1.2-r1.ebuild b/sci-chemistry/threeV/threeV-1.2-r2.ebuild
index 1d4a1e1f3466..961b882887f2 100644
--- a/sci-chemistry/threeV/threeV-1.2-r1.ebuild
+++ b/sci-chemistry/threeV/threeV-1.2-r2.ebuild
@@ -1,29 +1,29 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=8
inherit toolchain-funcs
DESCRIPTION="3V: Voss Volume Voxelator"
HOMEPAGE="http://geometry.molmovdb.org/3v/"
SRC_URI="http://geometry.molmovdb.org/3v/3v-${PV}.tgz"
+S=${WORKDIR}/3v-${PV}/src
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
PDEPEND="sci-chemistry/msms-bin"
# sci-chemistry/usf-rave"
-S="${WORKDIR}/3v-${PV}/src"
-
PATCHES=(
"${FILESDIR}"/${P}-gentoo.patch
"${FILESDIR}"/${P}-format-security.patch
)
+DOCS=( ../AUTHORS ../ChangeLog ../QUICKSTART ../README ../TODO ../VERSION )
+
src_prepare() {
default
tc-export CXX
@@ -31,10 +31,3 @@ src_prepare() {
export MAKEOPTS+=" V=1"
}
-
-src_install() {
- emake DESTDIR="${ED}" install
-
- cd .. || die
- dodoc AUTHORS ChangeLog QUICKSTART README TODO VERSION
-}
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild
new file mode 100644
index 000000000000..18bdb88a4c0c
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild
@@ -0,0 +1,263 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit cuda desktop prefix python-single-r1 toolchain-funcs xdg
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+
+MY_PV="${PV/_alpha/a}"
+MY_P="${PN}-${MY_PV}"
+SRC_URI="
+ ${MY_P}.src.tar.gz
+ fetch+https://dev.gentoo.org/~pacho/${PN}/${PN}-1.9.4_alpha57-gentoo-patches.tar.xz
+"
+S="${WORKDIR}/${MY_P}"
+LICENSE="vmd"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RESTRICT="fetch"
+
+CDEPEND="${PYTHON_DEPS}
+ $(python_gen_cond_dep '
+ >=dev-python/numpy-2[${PYTHON_USEDEP}]
+ ')
+ >=dev-lang/tk-8.6.1:0=
+ dev-lang/perl
+ dev-libs/expat
+ sci-libs/netcdf:0=
+ virtual/opengl
+ >=x11-libs/fltk-1.1.10-r2:1
+ x11-libs/libXft
+ x11-libs/libXi
+ 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-misc/xdg-utils
+ 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/intersurf/bin/intersurf.so"
+QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil/volutil"
+QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil/volutil"
+
+pkg_nofetch() {
+ elog "Please download ${MY_P}.src.tar.gz from"
+ elog "${VMD_DOWNLOAD}"
+ elog "after agreeing to the license."
+ elog "Place it into your DISTDIR directory."
+}
+
+src_prepare() {
+ # Apply user patches from ${WORKDIR} to allow patching on patches
+ # subdir too
+ cd "${WORKDIR}"
+ default
+
+ # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html
+ # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html
+ eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4a51-gentoo-plugins.patch
+
+ use cuda && cuda_sanitize
+
+ # Prepare plugins
+ cd plugins || die
+
+ 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):" \
+ -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX):" \
+ -e "s:-ltcl8.5:-ltcl:" \
+ -i Make-arch || die "Failed to set up plugins Makefile"
+
+ sed \
+ -e '/^AR /s:=:?=:g' \
+ -e '/^RANLIB /s:=:?=:g' \
+ -i ../plugins/*/Makefile || die
+
+ tc-export AR RANLIB
+
+ sed \
+ -e "s:\$(CXXFLAGS)::g" \
+ -i hesstrans/Makefile || die
+
+ # prepare vmd itself
+ cd "${S}" || die
+
+ eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4a51-gentoo-paths.patch
+
+ # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html
+ eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4-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)"
+ 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)"
+ EXPATDYNAMIC=1
+ )
+ if use gromacs; then
+ EMAKEOPTS+=(
+ TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
+ TNGINC="-I${EPREFIX}/usr/include"
+ TNGDYNAMIC=1
+ )
+ fi
+ if use sqlite; then
+ EMAKEOPTS+=(
+ SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
+ SQLITEINC="-I${EPREFIX}/usr/include"
+ 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-patches/vmd.png
+ eprefixify "${WORKDIR}"/vmd-patches/vmd.desktop
+ domenu "${WORKDIR}"/vmd-patches/vmd.desktop
+}
diff --git a/sci-chemistry/wxmacmolplt/Manifest b/sci-chemistry/wxmacmolplt/Manifest
index 57b6c29fc905..2bd05b04b206 100644
--- a/sci-chemistry/wxmacmolplt/Manifest
+++ b/sci-chemistry/wxmacmolplt/Manifest
@@ -1,2 +1 @@
-DIST wxmacmolplt-7.5.tar.gz 1965376 BLAKE2B 01033266ae66a215582a62690e792ca4ae82c8a8885fe277e2e77ee67ff70f02f6a9c10467ea6f3cee15933c6c89ba3c6137c9d29e47322ac4f395a3efd41383 SHA512 a1064d5068136b2a91328c7f912ff57d4741081d6d61437e7b4567fbf732917485b391493d637b8892bdad50b539363cfa9c778bb35407a9c0a2bfed20e42bc0
DIST wxmacmolplt-7.7.2.tar.gz 2012054 BLAKE2B 0e419d9700dd6461a4520722f43cc36cdaa2f51920868a868bdd58db169ed92f88c71d4ce0d79446c4c564eb794f7327b0eef5f87d9ab5a639829287b29482d6 SHA512 bf4b3126bbc8657a604f8dee8b022a17dbf4633a877318ceb45d803456acb0da007c2edae23f581fb6eeafd6ea411d147fbc076acb07aba3dcb8ee55b9c486fa
diff --git a/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch b/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch
deleted file mode 100644
index 809d7723cbb0..000000000000
--- a/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/configure.ac
-+++ b/configure.ac
-@@ -20,7 +20,7 @@
- ;;
- *)
- HOST=LINUX
-- LIBGL="-lGL -lGLU"
-+ LIBGL=`${PKG_CONFIG} --libs glu glew`
- ;;
- esac
- AM_CONDITIONAL(HOST_IS_MSW, [test "x$HOST" == xMSW])
diff --git a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild
deleted file mode 100644
index d100dad51cbc..000000000000
--- a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-WX_GTK_VER=3.0
-inherit autotools desktop toolchain-funcs wxwidgets
-
-DESCRIPTION="Chemical 3D graphics program with GAMESS input builder"
-HOMEPAGE="http://www.scl.ameslab.gov/MacMolPlt/"
-SRC_URI="https://wxmacmolplt.googlecode.com/files/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- media-libs/glew:0=
- media-libs/mesa[X(+)]
- x11-libs/wxGTK:${WX_GTK_VER}[X,opengl]"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-PATCHES=( "${FILESDIR}"/${P}-glew.patch )
-
-src_prepare() {
- default
- sed \
- -e "/^dist_doc_DATA/d" \
- -i Makefile.am || die "Failed to disable installation of LICENSE file"
- eautoreconf
-}
-
-src_configure() {
- tc-export PKG_CONFIG
-
- setup-wxwidgets unicode
- econf \
- --with-glew \
- --without-ming
-}
-
-src_install() {
- default
-
- doicon resources/${PN}.png
- make_desktop_entry ${PN} wxMacMolPlt ${PN} "Science;DataVisualization;"
-}
diff --git a/sci-chemistry/xds-bin/Manifest b/sci-chemistry/xds-bin/Manifest
index ac4cfebc4b6f..880c0c05bfa0 100644
--- a/sci-chemistry/xds-bin/Manifest
+++ b/sci-chemistry/xds-bin/Manifest
@@ -1,2 +1,2 @@
-DIST XDS-INTEL64_Linux_x86_64-20170930.tar.gz 9501598 BLAKE2B 33eea09210e9196859f62e66770aef3b34ace7d0cbe50607ef03ba37943fdb13ddf570b53cb2a7e668e650284ff245767a9cca9f6595de9fdb1815bb9625b56e SHA512 8da1d75633e8bf8495c30926a622f57aa0a51ea3b724101c96da6fae0a303860a4a4a8eaf3ecdf66948f18e702211aab3800760ca498c4562e947e3f94c25a4d
-DIST XDS_html_doc-20170930.tar.gz 117249 BLAKE2B 81e0c216eee38f21acc4dba299a20c4790f4aa1dc58e2d0dab5474784bf01842db41ab869b6d36cdfc9a31771e0bcad41b062bbf000771552c7de36f36a2291e SHA512 bbc24eeb0f8a63e6186906b0c0ee67efa83d1cdd169b091878c323455e2448ee6cb1667467bc9701b4e1839af2d10d4cb3e8f8d080b7dd5e449fda03c2aa8f89
+DIST XDS-INTEL64_Linux_x86_64-20240831.tar.gz 11067644 BLAKE2B d8687af54aad5694937cc633f511766147bb52616a388f03d0d052239a0f81b6e3692be0f234ea012905c89e13f2ef45e0254babe1e23598d954b2e65ed93d20 SHA512 773f074237311c8ea2d6dda974250cf906f84db02589bb40b646ff77afac2ee7d978d272993ab5f9b9f55c9dde7965b8e4fba7222349bf3665679f90ec6ef658
+DIST XDS_html_doc-20240831.tar.gz 151503 BLAKE2B c559d1a7b4ca75b00d5d37d2c9248fea177cca6a2dac5a9b42443430477337f8bc99add4f89f9eac2d57592b6b5843e167d4e86c6c3ce0ccbb5ba91234d534d8 SHA512 5d3a20dd0b6458c5bfd8ed46f4963fd53f59208fff72278acac19237c988537bae9d7b3c993342c8a9abc03e2ab5aed98a002caeb853fb87c19ae19a32f05faa
diff --git a/sci-chemistry/xds-bin/xds-bin-20170930.ebuild b/sci-chemistry/xds-bin/xds-bin-20240831.ebuild
index 4e609092fa03..4fcd833d3071 100644
--- a/sci-chemistry/xds-bin/xds-bin-20170930.ebuild
+++ b/sci-chemistry/xds-bin/xds-bin-20240831.ebuild
@@ -1,21 +1,31 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=8
DESCRIPTION="Software for processing single-crystal X-ray monochromatic diffraction data"
-HOMEPAGE="http://xds.mpimf-heidelberg.mpg.de/"
+HOMEPAGE="https://xds.mr.mpg.de"
SRC_URI="
- ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz -> XDS-INTEL64_Linux_x86_64-${PV}.tar.gz
- ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS_html_doc.tar.gz -> XDS_html_doc-${PV}.tar.gz"
+ https://xds.mr.mpg.de/XDS-INTEL64_Linux_x86_64.tar.gz -> XDS-INTEL64_Linux_x86_64-${PVR}.tar.gz
+ https://xds.mr.mpg.de/XDS_html_doc.tar.gz -> XDS_html_doc-${PVR}.tar.gz"
LICENSE="free-noncomm"
SLOT="0"
KEYWORDS="-* ~amd64"
IUSE="smp"
+RESTRICT="fetch"
QA_PREBUILT="opt/xds-bin/*"
+# The web site uses a certificate that is not in the system certificate store.
+# Use a web browser to download, instead.
+pkg_nofetch() {
+ elog "Please visit"
+ elog "https://xds.mr.mpg.de/html_doc/downloading.html"
+ elog "and download XDS-INTEL64_Linux_x86_64.tar.gz and XDS_html_doc.tar.gz."
+ elog "Please save them as: ${A}. in your \${DISTDIR}"
+}
+
src_unpack() {
default
mv XDS-* "${S}" || die
@@ -33,7 +43,7 @@ src_install() {
dosym ../${PN}/${i}${suffix} /opt/bin/${i}
done
- for i in 2cbf cellparm forkcolspot forkintegrate merge2cbf pix2lab xdsconv; do
+ for i in 2cbf cellparm forkxds merge2cbf pix2lab xdsconv; do
dosym ../${PN}/${i} /opt/bin/${i}
done
@@ -42,5 +52,5 @@ src_install() {
}
pkg_postinst() {
- elog "This package will expire on September 30, 2017"
+ elog "This package will expire on August 31, 2024"
}
diff --git a/sci-chemistry/xyza2pipe/Manifest b/sci-chemistry/xyza2pipe/Manifest
deleted file mode 100644
index 673bfd1224c1..000000000000
--- a/sci-chemistry/xyza2pipe/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST xyza2pipe-20121001.tgz 61002 BLAKE2B 648e65b63cc0b363dd0087b7ef64a1e287654a165baaf7d967821f11cffb70dd7f0da864dfa3b915553546c8cbbc83fda411d9b979551d3d72334db6580e5d64 SHA512 b64abf46a8d7f3530eecaeec3bc8b143600c6823174a22727868087c2f7f17af0b538a0521e3a29806dc608b003948a1e31296ab395bc3c0089c5dc7a391d855
diff --git a/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch b/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch
deleted file mode 100644
index ec4220dd0695..000000000000
--- a/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch
+++ /dev/null
@@ -1,168 +0,0 @@
- Makefile | 106 +++++++++++++++++++++++++++++++++++++--------------------------
- 1 file changed, 63 insertions(+), 43 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 15d4bd3..e738ec2 100644
---- a/Makefile
-+++ b/Makefile
-@@ -4,7 +4,7 @@
- # Last modified: Feb/22/2012
- #
-
--CFLAGS = -O3
-+CFLAGS ?= -O3
- MFLAGS = -lm
-
- TARGETS = xyza2pipe ucsf2pipe nv2pipe xeasy2pipe azara2pipe vnmr2pipe xwnmr2pipe\
-@@ -62,89 +62,109 @@ clean:
- rm -f $(TARGETS) addxyza2pipe
-
- $(OBJECTS_MATH):
-- $(CC) $*.c -c -o $@ $(CFLAGS) -D__XYZA2PIPE__
-+ $(CC) $(CPPFLAGS) -D__XYZA2PIPE__ $(CFLAGS) $*.c -c -o $@
-
- .o:
-- $(CC) $< -c -o $@ $(CFLAGS)
-+ $(CC) $(CPPFLAGS) $(CFLAGS) $< -c -o $@
-
- xyza2pipe: $(OBJECTS_C) $(OBJECTS_XP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- pipe2xyza: $(OBJECTS_C) $(OBJECTS_PX)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- ucsf2pipe: $(OBJECTS_C) $(OBJECTS_UP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- pipe2ucsf: $(OBJECTS_C) $(OBJECTS_PU)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- nv2pipe: $(OBJECTS_C) $(OBJECTS_NP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- pipe2nv: $(OBJECTS_C) $(OBJECTS_PN)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- xeasy2pipe: $(OBJECTS_C) $(OBJECTS_EP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- pipe2xeasy: $(OBJECTS_C) $(OBJECTS_PE)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- azara2pipe: $(OBJECTS_C) $(OBJECTS_AP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- pipe2azara: $(OBJECTS_C) $(OBJECTS_PA)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- vnmr2pipe: $(OBJECTS_C) $(OBJECTS_VP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- xwnmr2pipe: $(OBJECTS_C) $(OBJECTS_BP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- pipe2proj: $(OBJECTS_C) $(OBJECTS_PJ)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- add2pipe: $(OBJECTS_C) $(OBJECTS_DXP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
- rm -f addxyza2pipe
- ln -s add2pipe addxyza2pipe
-
- adducsf2pipe: $(OBJECTS_C) $(OBJECTS_DUP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- addnv2pipe: $(OBJECTS_C) $(OBJECTS_DNP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- addxeasy2pipe: $(OBJECTS_C) $(OBJECTS_DEP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- addazara2pipe: $(OBJECTS_C) $(OBJECTS_DAP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- addvnmr2pipe: $(OBJECTS_C) $(OBJECTS_DVP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
-
- addxwnmr2pipe: $(OBJECTS_C) $(OBJECTS_DBP)
-- $(CC) $@.c $^ -o $@ \
-- $(CFLAGS) $(MFLAGS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \
-+ $(MFLAGS)
-+ mv -v $@ bin/
diff --git a/sci-chemistry/xyza2pipe/metadata.xml b/sci-chemistry/xyza2pipe/metadata.xml
deleted file mode 100644
index e490bcb8aa87..000000000000
--- a/sci-chemistry/xyza2pipe/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://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/xyza2pipe/xyza2pipe-20121001.ebuild b/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild
deleted file mode 100644
index e6ba5c19332f..000000000000
--- a/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Cross conversion environment of NMR spectra"
-HOMEPAGE="http://fermi.pharm.hokudai.ac.jp/olivia/api/index.php/Xyza2pipe_src"
-SRC_URI="http://fermi.pharm.hokudai.ac.jp/olivia/documents/xyza2pipe.tgz -> ${P}.tgz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="olivia"
-IUSE=""
-
-S="${WORKDIR}"/${PN}
-
-PATCHES=( "${FILESDIR}"/${P}-gentoo.patch )
-
-src_prepare() {
- default
- tc-export CC
- mkdir bin || die
-}
-
-src_install() {
- local i
- dodoc README FEEDBACK
- cd bin || die
- for i in *; do
- newbin ${i}{,-olivia}
- done
-}