diff options
Diffstat (limited to 'sci-chemistry')
85 files changed, 942 insertions, 1574 deletions
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.4.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.4.ebuild deleted file mode 100644 index e5c508fd6ca1..000000000000 --- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.4.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{9..11} ) -DISTUTILS_USE_PEP517=setuptools - -if [[ ${PV} = *9999* ]]; then - scm_eclass=git-r3 - EGIT_REPO_URI="https://github.com/Becksteinlab/${PN}.git" - EGIT_BRANCH="develop" - SRC_URI="" -else - scm_eclass=vcs-snapshot - SRC_URI="https://github.com/Becksteinlab/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -inherit distutils-r1 ${scm_eclass} - -DESCRIPTION="Python framework for Gromacs" -HOMEPAGE="https://gromacswrapper.readthedocs.io" - -LICENSE="GPL-3 LGPL-3" -SLOT="0" -IUSE="" - -RDEPEND=" - dev-python/six[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - sci-libs/numkit[${PYTHON_USEDEP}] -" -BDEPEND=" - ${RDEPEND} - test? ( >=dev-python/pandas-0.17[${PYTHON_USEDEP}] ) -" - -distutils_enable_tests pytest diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.5.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.5.ebuild index e5c508fd6ca1..92f160defd29 100644 --- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.5.ebuild +++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.5.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -10,7 +10,6 @@ if [[ ${PV} = *9999* ]]; then scm_eclass=git-r3 EGIT_REPO_URI="https://github.com/Becksteinlab/${PN}.git" EGIT_BRANCH="develop" - SRC_URI="" else scm_eclass=vcs-snapshot SRC_URI="https://github.com/Becksteinlab/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz" @@ -24,7 +23,6 @@ HOMEPAGE="https://gromacswrapper.readthedocs.io" LICENSE="GPL-3 LGPL-3" SLOT="0" -IUSE="" RDEPEND=" dev-python/six[${PYTHON_USEDEP}] diff --git a/sci-chemistry/GromacsWrapper/Manifest b/sci-chemistry/GromacsWrapper/Manifest index 59c53091950e..f9dc12e907fd 100644 --- a/sci-chemistry/GromacsWrapper/Manifest +++ b/sci-chemistry/GromacsWrapper/Manifest @@ -1,5 +1,3 @@ -DIST GromacsWrapper-0.8.4.tar.gz 1955167 BLAKE2B 59f0301263eefaa4d7c139b34a48172c218a76f0f9488477d6203d9cd732098468dae5a73ff46aa74eb2b4433268c77bc265e506129e4c14a357042453d5f97f SHA512 822edc33c77ca4dbfbc1e4172686744345ed3c0d2305f4b19abab15576a1433bbb3b23b96f637398ad4f72cd5414d96ee531ab4a329d3acb462d90b95437a6a5 DIST GromacsWrapper-0.8.5.tar.gz 1958570 BLAKE2B b8f79721a7566117206818144fc7087c4634d7fb71c77abef63dd9565a0655ce6b4a259ea5bf9cb3b5bc13df8f428f58e514f7871192d27a6d463e758e27f4b3 SHA512 8800afdbe92edad35df58e825546797ede1738b9029df0fb57a96e377d7be94f3d21fe1df9d5cb4490d12b984972d63d87e673d3d33af60a7dc8d0453574a5c6 -EBUILD GromacsWrapper-0.8.4.ebuild 911 BLAKE2B 827ac820482bd41895e02a218041fb1668899d7c80e95ee51021a92d6f7fe36452d1012330118266958f8313694b9c655cc32ddf995d62f3b08aad508c912301 SHA512 6d0f23fcc82cfd0097768a98a1d5755fb003437734f2c6ac90ccff21aa8a8c69bac8f7c0dd4803711e249ff66e513b906394394b71313b2a48f9f0bc37b2ce7e -EBUILD GromacsWrapper-0.8.5.ebuild 911 BLAKE2B 827ac820482bd41895e02a218041fb1668899d7c80e95ee51021a92d6f7fe36452d1012330118266958f8313694b9c655cc32ddf995d62f3b08aad508c912301 SHA512 6d0f23fcc82cfd0097768a98a1d5755fb003437734f2c6ac90ccff21aa8a8c69bac8f7c0dd4803711e249ff66e513b906394394b71313b2a48f9f0bc37b2ce7e +EBUILD GromacsWrapper-0.8.5.ebuild 891 BLAKE2B f337e51328aa8d4f3ae1c63080a2dfe016b5eb7ddfceea41ac6f8b4429dcb25d62f0c6b16614333240f7386eef99377c20a71293eecb5227909fd7d3008ffaee SHA512 5d19ef9c50dc98316d4891f36b9a4bed7bd31fc20e44c2ec4833ab39d33f7200ff9a336825050ed50b67679f1c6e49aaf1a60ef5997ac7e5ee8d8be5a5c031d2 MISC metadata.xml 483 BLAKE2B 1d8a7e888d8b95bd229ef72894ba02f583e3e3958f9cd5733ab6b466312bac0b0f5a9004135caa37a3ef137e8782fa93ff4bb90f35f31c058d8c528025b193d0 SHA512 70e5dc653ff21a0395b946e5f3548320d2abb8c63ae9f3ce04be6768e20b02ce55a612a2ad12b6c2262529ab753ca9fda02d9bdae7f6ac859bca49bbbad6f75f diff --git a/sci-chemistry/MDAnalysis/MDAnalysis-2.6.1.ebuild b/sci-chemistry/MDAnalysis/MDAnalysis-2.6.1.ebuild index d407b705b2c5..f83ee1eabaf1 100644 --- a/sci-chemistry/MDAnalysis/MDAnalysis-2.6.1.ebuild +++ b/sci-chemistry/MDAnalysis/MDAnalysis-2.6.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..12} ) DISTUTILS_USE_PEP517=setuptools PYPI_NO_NORMALIZE=1 @@ -12,9 +12,9 @@ inherit distutils-r1 pypi DESCRIPTION="A python library to analyze and manipulate molecular dynamics trajectories" HOMEPAGE="https://www.mdanalysis.org" +LICENSE="GPL-2" SLOT="0" -LICENSE="GPL-2" KEYWORDS="~amd64 ~amd64-linux" # TODO: fix this diff --git a/sci-chemistry/MDAnalysis/Manifest b/sci-chemistry/MDAnalysis/Manifest index cff859e1815b..73101a1d93f2 100644 --- a/sci-chemistry/MDAnalysis/Manifest +++ b/sci-chemistry/MDAnalysis/Manifest @@ -1,3 +1,3 @@ DIST MDAnalysis-2.6.1.tar.gz 4173280 BLAKE2B 14aae62733ace3eff686f6ba6be8326f86ba24c55e3870aa2e5dd88a858ca0de8d89589a622687bec3aafd332d9ccb5d6e6166eb370f56eaf79af5081f3a003e SHA512 421a27e508bcf7845b0c91f40c01bba4a48bf8ba9a3d3ed50fe555336c96fb1f64bccc5cf3ee048130d2eef9b18b8550ed5f73d3459f8962343ba694d00655bb -EBUILD MDAnalysis-2.6.1.ebuild 1128 BLAKE2B 7677f00e7aedca6495a1116715189a756485ed66bb556df6279c2ed12f1b1bc2dfe6f185dd952205d8f73a4083f04318226f5184f3443e0664ddc4d7f8943766 SHA512 66943087679841828505ed99ac5c0329a713f7d13689482b8daa867281cf28ea0c723a9685909a0f82dd0edd2feb40af3b898be41797c2b1a1c48117118fc4e4 +EBUILD MDAnalysis-2.6.1.ebuild 1129 BLAKE2B eefcde9e4552661923ad0e4ea73c42376aa8ddce7730a79b94a3d6dbaee560b23399fb7a857a77f93ca33ea8dc922905ce554ff9e6284b5f348216318f5bb769 SHA512 82add5c75078bb8c3b6a55cb322a2b88a5351e47d607194ab5834343f172cd5ce6daab8abf26957a83fa2d6b0d83a68fe5866d4e319d5946bdbde179cbd636ba MISC metadata.xml 497 BLAKE2B ddd8c6379dfe6b6fe33160d31bda254774e0c8eb5f862cc51560097efc5c273fa972388c6fe8fb1bbedc11ab125a5487bb1d19002489be967fa3e8e209d7cc81 SHA512 03c1eb9bef1bc10d600169b221c65c87794f8b9bf8d0efb1dc6ddaa61a09d665722ed7d32087e3137b36aa7256b76371b9ce2cc92b34b1ed7d1c78ede6550287 diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex 2eeeb6158656..a46ec2c846c6 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/aqua/Manifest b/sci-chemistry/aqua/Manifest deleted file mode 100644 index de2fa35a0b3d..000000000000 --- a/sci-chemistry/aqua/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -AUX aqua-3.2-flags.patch 4211 BLAKE2B 032048ea0f08aa798758489beda88aa0f07635e7ee965d25791b73a2995224920392c7eaf52b0da97d4e0df70df9901d5dd915c2a0adc499e6e17160e2fac467 SHA512 059cea5403fb4cb01b0fcd4d2a2fe4b4aea725e9362a6188ccd3756ced35e324cda5efb21d3ad2a95a842e9d83f8e728a16b36e4b6a479ae32da8816d7eafdfc -DIST aqua-3.2-nmr_manual.tar.gz 632031 BLAKE2B 1f595a111af4b5e91fc059b5af590a6c37a44654fcae42e6003b40cf7fdf542cb772d3ef25bf2475455ce8638cd0aebcbbc8c66bb57688ce919af2eac9b535cb SHA512 9b125b03507afebf15301c893efffae9be4e9695b9c577e5c2a80e83b620d04b4c27e867adf06336afa1556eddc96aa97de936028e503b1e85e156542664da0f -DIST aqua3.2.tar.gz 688408 BLAKE2B 898e0e3bbc4ff7b6ce8a8128ce6ffef45db607c74e2d78a70cefc26818d39049e4d18159b65250a3651112f64318ccce838037e563d3a985be7ef369d89b594e SHA512 1939f662a68122da613368aa106d7a31525903014420035eba9d10c3bd99b04d654d156328d308673003854233a02c1da48c036f3187fa1f0f303cc5928edd6a -EBUILD aqua-3.2-r3.ebuild 2087 BLAKE2B 053412cfb8802a1fd07e2ab53e19d8cca8f422063bd0d64723e2152b4d2fce4fc4597db2fd906b08b899937fac27c390abf73e1638f0a77f356e3bf86dea7d7f SHA512 1d5e6cdefb415613ade4170837b0092772a2c76bbb29b4c10e6ef75044f380c724371509fc5ec50144828bc6dcbd04b282135a0147561b424267331ad79b802a -MISC metadata.xml 266 BLAKE2B a03b1fcf7148cf43fb829f619c218219bcd4e66c45d12f563113401e3ae0b06cb0df9a8c0af01ea97e21453638d627d420e7df5b9b0d330ef1752253faa8aa32 SHA512 1dc293fa0d0296eba18ac2cbcd57f47ffc6cc822bf0d76e1cc86cb046700201f703d705375b5555b88cbe8780ef3750be05b8f9f8de092693e6d165c1734e049 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/Manifest b/sci-chemistry/autodock_vina/Manifest index 8cd80f22576c..6f84dbd72847 100644 --- a/sci-chemistry/autodock_vina/Manifest +++ b/sci-chemistry/autodock_vina/Manifest @@ -1,9 +1,10 @@ AUX 1.1.2-gentoo.patch 2448 BLAKE2B f63add1d0fec8716672672af78fe8f34053bf060044e78fcf30ca6054e4075a5f12ac3a903812c9cd619dc34fa854603c8369c8acfcf17130d1b24b50b3d5373 SHA512 d8165d88f3e91064c74f1506a7f58473a74f6ebf993165827694d78170b29227dc378c61a7f096a3c49708b713583aca3d5714827d1fe43a5bb37f3d648d2613 AUX autodock_vina-1.1.2-boost-filesystem.patch 2936 BLAKE2B 70c55e95e9728221ba80177989fde0cc6c93b479779aa0dda45dcad79b97018fe934ea56b4ede4af20ce867b6ed39c3958a5529b8f286aec33ec7ea53d339ada SHA512 4226fb0d7196362a02afa4e0b0616146ef816a439dd63e1bffbfef183975fe7e6260318f919e9d9835d2d47973542b5340e93ad35b070467e42c0990f9a635f7 AUX autodock_vina-1.1.2-missing-debug-decl.patch 365 BLAKE2B 959b46facdce27850a1f9fd6c66ecc297e4ad089e79896b9fe2127e425bd1bfcfce5d676cf2e4336c47d3a72b0e8319c791fdf1a5807f244cf5b4528de8cbb25 SHA512 ddbdca76fca16b46fd042b57eb941b7ba67f59f46c35dc18428ea6873c8ed5f03051247b8c667a08af8de40fccb0caf851848bb9082536225cacf8eb3e313c98 +AUX autodock_vina-1.2.5-boost-1.85.patch 733 BLAKE2B 4163ff875f28ba883a0a0b98f23ba8341f1eb7fd29831e3654c7bb739605dfb1edf2c40867289fb7eaf3c59cd9220d856d914f55dbaa211acdf016789c8e10e8 SHA512 2bcabc02d3456b461a118e1d14932c8c2a091e8176cd927c1b423bf24aefecfb82e0a446f66d97830bebdee7b56fc7c1bc4d45512ddfd81bb827b43b897a1696 AUX autodock_vina-1.2.5-gentoo.patch 2803 BLAKE2B a365f3c83e5cfa366e458ce87e0d1e0a305b137040fbf3e0c0b2549e3cfde617c6934aaa4da6a992440400fbaa3f73b42faa665b1a5d1464f2a8d103b5469af3 SHA512 46b5c10123cf721eb80c6fa8d87f2d8405d269915d6bfec3eff5f1d5ee870e301608748ae245f7997f5c8a4b7c27e50fa222eff192c84ec4c82946c1783fa44b DIST autodock_vina-1.2.5.tar.gz 24158966 BLAKE2B c11493fcb35d409b97f639c4da48967d5df450781d412d80a951b95162555f4b1dfba809a01062136a7f0664c0b9a01a42b5403ee1d278a57afd669cf1f96321 SHA512 d36908e5833d22bcbc4dae353ef32b905d6eb46511302f7583a291398bfadff5e75fc99ce7b380860578b2257e5c32434cc75b1ca51fafb4b5f12d9477a878e9 DIST autodock_vina_1_1_2.tgz 67366 BLAKE2B dc754bf522795ebfbfcf89a2df4e3761d941c1f0ce05cf56898720c1e855f5dd00fd2a583f5a8d218fa2e738d37e014a9b3239b9aa989b9018a6a33f8f0bd02c SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9 EBUILD autodock_vina-1.1.2-r1.ebuild 972 BLAKE2B aaad2df1b51bdd684ca5fd9aaa54353b161e4e5d72b59210919349993fb6ad2c796f8b6bff4d420ad64e52273a26bf9f7d9b90f95387db5f7814352ebdb5be1c SHA512 123083cc13a05fd10627f9750274de9f7070e4068b718b4407230f9af22ead0a4f6ef33cda4b86a2d1e08856c31a58f8cc0d0ef8d861f196275332095885e44b -EBUILD autodock_vina-1.2.5.ebuild 1034 BLAKE2B a123bd340d3c5763d39cad3e2d9d7afbd6e4e0d96d1041736978af88295c58645e3ea53e634f1bb41e905d54afa94e8baa784fd27d6a6f577915e8c3635acdcc SHA512 383fa58b584f9f3ec6e1eb403b1845d3e7cfd66e88b89e857ffedc4847444caede2953f581f20b7414d5a9ec20e3f8bc4c864ded5206b182eb5c9ea38055401e +EBUILD autodock_vina-1.2.5.ebuild 1070 BLAKE2B 69e0e7fce39fa45ed6cf5dc01fef51a575353bfdd2cb5c333c2d2269cc38dccf20bac1c1b3caa273929e4848e9c66add90336dba767a9adc269d3d455a4428da SHA512 1bd3e7de0795caf8379a03becb1db12f7a24a83efa26336ac07355c09bda4633e36604dd52afe906064dcd479c93d30a1e664699be820ba9e92cf706bea75e6e MISC metadata.xml 1002 BLAKE2B 775eb10f8c916ff2b5655243224d1608a865228b1e300b636c793c1c86a4634a33fdda3bf4a8f56f43ad8bb734413963e490b738d2baf69168bb8dea6e3e6106 SHA512 0ea67a95d4bb8f90323ceeeced2d47f4732ee5fb3daa45d8690c13b71daf67729b33cdf3024a4706d2ee9e296b67474141125e95801b9f799228391571395532 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/Manifest b/sci-chemistry/chemex/Manifest index fd0cf00cefa4..e79b0c6d82fe 100644 --- a/sci-chemistry/chemex/Manifest +++ b/sci-chemistry/chemex/Manifest @@ -1,5 +1,5 @@ -DIST chemex-2022.3.6.tar.gz 2843118 BLAKE2B e51b385dbf9e3c42f54f95f9929125e3263e12afa62beab8e5b8eb13e78a4fe9a0fb445f4f6c3cd4aa8e71748732ec58124682daa86be079eed036b78492ca71 SHA512 5c734e1b3ea39e9729bada93dfe5bc55f877b69ba6edd9612f95aab0d31949489582957a14f175646c7e6652644a5a55c26bcd74affc7fecc1e7b9cfdd4ceb63 -DIST chemex-2024.02.16.tar.gz 2756466 BLAKE2B 715499fc3c68079dd66b26a0c4c495029c506be6f009529196fd30a1ec8ff4c0ecbcc4580c9beafd4f3c7df82d6fee525d85c09b031a6dc31d511c1183d30f8d SHA512 7975157b86493c580ce00ef23549597743ff4aa03cebed7d0e0af1d644eed359b5dfa57c51e11f223acebe335d12cb43bd7694a46eeb2ccba70ac6147ba40eda -EBUILD chemex-2022.3.6.ebuild 1240 BLAKE2B 46d4f9fd57f5dbc8ad5b527e8568337cd57d3c03f25581d275e15204e5e2ee2c2224c6e8ada71c8d91aed01128be697987cc808bdfd7d7e3abc5f655eb2abb44 SHA512 814348dc6b404698634ecb33ee3956479dd1c05f91f7ca82e4f8a15776a582dd911e30a2070bff727f2aeae678a609fe2d8b676f107741904886c83315dbeb78 -EBUILD chemex-2024.02.16.ebuild 1343 BLAKE2B 1cd03445f8cf230a728b0a0b40ed39ccc11e5ff90b53d6358620a19f9aca2f5d630445bd0a2c9ee1f1dc74e11e5a79740584ace23556bd7ede76959295860868 SHA512 b5a330a8ba2db2f057c7d1cd12de4021e2eb0375474aa8eb0692f8248f448e86354a47e61313b6e37d965447073ed1cb84f300d7ba4e026f8e51f8dd823281a7 +DIST chemex-2024.05.2.tar.gz 2757082 BLAKE2B e231f2b4da566b633cdd10c54f413b319847e86ab909b81ca78e0cf5c368f4cd039fc26d4214f464de1ca618ea5bbd8579e9bfeaa4a97e01ef3ddecb1d8c8227 SHA512 29e137a1d275f5c6b078081350b8d9a6f9172858adb744afdbbdbbe94dc9953f1fb37ad49e10f2d39db89e90c2c8d5b17a53ec9be337772bb531052ae4ab86f1 +DIST chemex-2024.05.3.tar.gz 2757407 BLAKE2B 8f98cda5158224bf06b4e81271157b7d6dd6c28526a6fd0362090d51d2fb2402a5dffc422862f129ffe7db22ec87ee49a12a1bd1a812e88014d4b1956e626ff7 SHA512 f2a29c03d9375b440206e1cd08d0f656ec6f9c627b15645663ee0d249731adb9619fa2ad5792e55e7219e11165d20a7d25b00ee9766daf580490cb4c8ea77ebf +EBUILD chemex-2024.05.2-r1.ebuild 1298 BLAKE2B f5a3146ad927d9e00edf573abc5e93c028c9e0eeb806e9196e1dea31f431dccbdf2595a7781e52f1426d3d6a31baccb8a853e4b610ac06f6969e62748ba42d84 SHA512 471992fc58cad9cb9ec3d0420289e27aa0c54492b0a9e422f096b22212d4423aae0eaa25219b4139c834b1c8a0522dd49a9542e7e8fe87bc9b4e10211afc9785 +EBUILD chemex-2024.05.3-r1.ebuild 1298 BLAKE2B f5a3146ad927d9e00edf573abc5e93c028c9e0eeb806e9196e1dea31f431dccbdf2595a7781e52f1426d3d6a31baccb8a853e4b610ac06f6969e62748ba42d84 SHA512 471992fc58cad9cb9ec3d0420289e27aa0c54492b0a9e422f096b22212d4423aae0eaa25219b4139c834b1c8a0522dd49a9542e7e8fe87bc9b4e10211afc9785 MISC metadata.xml 300 BLAKE2B a1ad769918094ddbda13ac92462ec69fa469dfcacde1202c653a4aa7443db661ffa5739cd039b6e38b13f0345a2680f276b4e071362106b162c95cd92007b5a8 SHA512 755c273f6bf67f79c388d06d970702a1d4a9f84338f8d889dd9146905c6994621917952225406ffba5bfe1e1b69f0bfd0f471374178b15343f4927af9de49aef diff --git a/sci-chemistry/chemex/chemex-2024.02.16.ebuild b/sci-chemistry/chemex/chemex-2024.05.2-r1.ebuild index 403e48aa069d..87646d2c3045 100644 --- a/sci-chemistry/chemex/chemex-2024.02.16.ebuild +++ b/sci-chemistry/chemex/chemex-2024.05.2-r1.ebuild @@ -26,16 +26,15 @@ RESTRICT="test" RDEPEND=" $(python_gen_cond_dep ' >=dev-python/annotated-types-0.6.0[${PYTHON_USEDEP}] - >=dev-python/cachetools-5.3.2[${PYTHON_USEDEP}] + >=dev-python/cachetools-5.3.3[${PYTHON_USEDEP}] >=dev-python/emcee-3.1.4[${PYTHON_USEDEP}] >=dev-python/lmfit-1.2.2[${PYTHON_USEDEP}] - >=dev-python/matplotlib-3.8.0[${PYTHON_USEDEP}] - >=dev-python/numpy-1.26.1[${PYTHON_USEDEP}] - >=dev-python/pydantic-2.4.2[${PYTHON_USEDEP}] - >=dev-python/rapidfuzz-3.4.0[${PYTHON_USEDEP}] - >=dev-python/rich-13.6.0[${PYTHON_USEDEP}] - >=dev-python/scipy-1.11.3[${PYTHON_USEDEP}] - >=dev-python/tomli-2.0.1[${PYTHON_USEDEP}] + >=dev-python/matplotlib-3.8.4[${PYTHON_USEDEP}] + >=dev-python/numpy-1.26.4[${PYTHON_USEDEP}] + >=dev-python/pydantic-2.6.4[${PYTHON_USEDEP}] + >=dev-python/rapidfuzz-3.7.0[${PYTHON_USEDEP}] + >=dev-python/rich-13.7.1[${PYTHON_USEDEP}] + >=dev-python/scipy-1.13.0[${PYTHON_USEDEP}] ') " DEPEND="${RDEPEND}" diff --git a/sci-chemistry/chemex/chemex-2022.3.6.ebuild b/sci-chemistry/chemex/chemex-2024.05.3-r1.ebuild index 81b3e45f7856..87646d2c3045 100644 --- a/sci-chemistry/chemex/chemex-2022.3.6.ebuild +++ b/sci-chemistry/chemex/chemex-2024.05.3-r1.ebuild @@ -1,21 +1,21 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_SINGLE_IMPL="yes" DISTUTILS_USE_PEP517=pdm-backend -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{11..12} ) inherit distutils-r1 DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data" HOMEPAGE="https://github.com/gbouvignies/chemex" -SRC_URI="https://github.com/gbouvignies/ChemEx/archive/refs/tags/${PV/_p/-dev}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/gbouvignies/ChemEx/archive/refs/tags/v${PV/_p/-dev}.tar.gz -> ${P}.tar.gz" S="${WORKDIR}/ChemEx-${PV/_p/-dev}" -SLOT="0" LICENSE="BSD" +SLOT="0" KEYWORDS="~amd64" IUSE="test" @@ -25,15 +25,16 @@ RESTRICT="test" RDEPEND=" $(python_gen_cond_dep ' - >=dev-python/cachetools-5.3.1[${PYTHON_USEDEP}] - >=dev-python/lmfit-1.2.1[${PYTHON_USEDEP}] - >=dev-python/matplotlib-3.7.1[${PYTHON_USEDEP}] - >=dev-python/numpy-1.25.0[${PYTHON_USEDEP}] - >=dev-python/pydantic-2.0.1[${PYTHON_USEDEP}] - >=dev-python/rapidfuzz-3.1.1[${PYTHON_USEDEP}] - >=dev-python/rich-13.4.2[${PYTHON_USEDEP}] - >=dev-python/scipy-1.9.3[${PYTHON_USEDEP}] - >=dev-python/tomli-2.0.1[${PYTHON_USEDEP}] + >=dev-python/annotated-types-0.6.0[${PYTHON_USEDEP}] + >=dev-python/cachetools-5.3.3[${PYTHON_USEDEP}] + >=dev-python/emcee-3.1.4[${PYTHON_USEDEP}] + >=dev-python/lmfit-1.2.2[${PYTHON_USEDEP}] + >=dev-python/matplotlib-3.8.4[${PYTHON_USEDEP}] + >=dev-python/numpy-1.26.4[${PYTHON_USEDEP}] + >=dev-python/pydantic-2.6.4[${PYTHON_USEDEP}] + >=dev-python/rapidfuzz-3.7.0[${PYTHON_USEDEP}] + >=dev-python/rich-13.7.1[${PYTHON_USEDEP}] + >=dev-python/scipy-1.13.0[${PYTHON_USEDEP}] ') " DEPEND="${RDEPEND}" diff --git a/sci-chemistry/chemical-mime-data/Manifest b/sci-chemistry/chemical-mime-data/Manifest index 84729e6ca668..997736f7550a 100644 --- a/sci-chemistry/chemical-mime-data/Manifest +++ b/sci-chemistry/chemical-mime-data/Manifest @@ -1,11 +1,4 @@ -AUX chemical-mime-data-0.1.94-drop-turbomole-vibrational.patch 934 BLAKE2B 8c35adddc5dbed044a68c1f0f485faf01ae4d6fb4724e82956e9e73292e2b7e37f527a8225fce3fa4b3c6629038086f30912b8bce21d704244dc18ba52673f8a SHA512 f1ca2c08b33f77ccc1355edbbba53971e4c09ed004ec35554617d57cb6dd90c9a8a712ebfe1c7e0b01d9a97790004a048029a9e96323e7a105e9b15408a0d4cd -AUX chemical-mime-data-0.1.94-namespace-svg.patch 798 BLAKE2B 4ab826dd3c76234c903a740b2e59dd4403d01aff856327d31c6707ab4563931d9fe4d9d57bdc19d6102d63d860eb2d88220844b934aa63cc3be984621ac52d28 SHA512 64addfac817a7f056f381515561b4311936410dc46385a3ded8c65f8fbc3d5dda731c4ec02e9369299c8122e7c43a6dc53005a4957e4165bbf958f683708513d -AUX chemical-mime-data-0.1.94-pigz.patch 481 BLAKE2B dee47e41645b5d196326fb7439e1a96b3d46983fa9c9ec4295b17676d51f966f48ff51668203e59f18580939337d83d5ae904ef33fe2044dcc62fedd90fcb82e SHA512 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c689663c874f6b8d63153fd84326dc5b00b733e98f04d763506f4fff4cbee3e642c5b4633ec3b6a6b5d2950928ba318e226eef85ee25cc8ff00c1dc25a87c3b5 diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r4.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r4.ebuild deleted file mode 100644 index e11f018ac371..000000000000 --- a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r4.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -inherit autotools xdg - -DESCRIPTION="A collection of data files to add support for chemical MIME types" -HOMEPAGE="https://github.com/dleidert/chemical-mime" -SRC_URI="https://downloads.sourceforge.net/${PN/-data/}/${P}.tar.bz2" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="amd64 arm arm64 x86" -IUSE="" - -RDEPEND=" - x11-misc/shared-mime-info -" -DEPEND="${RDEPEND}" -BDEPEND=" - dev-util/intltool - dev-util/desktop-file-utils - dev-libs/libxslt - || ( - gnome-base/librsvg - media-gfx/imagemagick[xml,png,svg] - ) - media-gfx/imagemagick[png] - virtual/pkgconfig -" - -PATCHES=( - "${FILESDIR}"/${P}-turbomole.patch - "${FILESDIR}"/${P}-pigz.patch - "${FILESDIR}"/${P}-namespace-svg.patch - "${FILESDIR}"/${P}-rsvg-convert-r2.patch - # https://github.com/dleidert/chemical-mime/issues/1 - "${FILESDIR}"/${P}-drop-turbomole-vibrational.patch -) - -src_prepare() { - xdg_src_prepare - eautoreconf -} - -src_configure() { - econf \ - --disable-update-database \ - --without-gnome-mime \ - --without-pixmaps \ - --without-kde-mime -} diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.95_pre20171122.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.95_pre20171122.ebuild index 64827ef8db67..b6291c211fa1 100644 --- a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.95_pre20171122.ebuild +++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.95_pre20171122.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -8,11 +8,11 @@ DESCRIPTION="A collection of data files to add support for chemical MIME types" HOMEPAGE="https://github.com/dleidert/chemical-mime" COMMIT="4fd66e3b3b7d922555d1e25587908b036805c45b" SRC_URI="https://github.com/dleidert/chemical-mime/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN/-data/}-${COMMIT}" LICENSE="LGPL-2.1" SLOT="0" KEYWORDS="amd64 arm arm64 x86" -IUSE="" RDEPEND="x11-misc/shared-mime-info" DEPEND="${RDEPEND}" @@ -28,8 +28,6 @@ PATCHES=( "${FILESDIR}"/${PN}-0.1.95-turbomole.patch ) -S="${WORKDIR}/${PN/-data/}-${COMMIT}" - src_prepare() { default # https://github.com/dleidert/chemical-mime/issues/4 diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-drop-turbomole-vibrational.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-drop-turbomole-vibrational.patch deleted file mode 100644 index 4c25b1a18343..000000000000 --- a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-drop-turbomole-vibrational.patch +++ /dev/null @@ -1,20 +0,0 @@ -diff -up chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole_vibration chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in ---- chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole_vibration 2020-01-29 17:32:45.000000000 +0100 -+++ chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in 2020-01-29 17:32:45.000000000 +0100 -@@ -1401,16 +1401,6 @@ - <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-vibrational" support="yes"> -- <_comment>Turbomole Vibrational Data File</_comment> -- <glob pattern="???"/> -- <sub-class-of type="text/plain"/> -- <icon kde="qc"/> -- <supported-by> -- <application name="viewmol"/> -- </supported-by> -- <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> -- </mime-type> - - <mime-type type="chemical/x-vamas-iso14976" cm:support="no"> - <_comment>VAMAS document</_comment> diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch deleted file mode 100644 index 9860261af403..000000000000 --- a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch +++ /dev/null @@ -1,16 +0,0 @@ - icons/hicolor/gnome-mime-chemical.svg | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/icons/hicolor/gnome-mime-chemical.svg b/icons/hicolor/gnome-mime-chemical.svg -index 1a8d428..804514c 100644 ---- a/icons/hicolor/gnome-mime-chemical.svg -+++ b/icons/hicolor/gnome-mime-chemical.svg -@@ -5,7 +5,7 @@ - <!ENTITY ns_svg "http://www.w3.org/2000/svg"> - <!ENTITY ns_xlink "http://www.w3.org/1999/xlink"> - ]> --<svg xmlns="&ns_svg;" xmlns:xlink="&ns_xlink;" xmlns:a="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/" -+<svg xmlns:svg="&ns_svg;" xmlns:xlink="&ns_xlink;" xmlns:a="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/" - width="128" height="128" viewBox="0 0 128 128" overflow="visible" enable-background="new 0 0 128 128" xml:space="preserve"> - <g id="Layer_1"> - <g> diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch deleted file mode 100644 index 8b5ccfbc3fd9..000000000000 --- a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch +++ /dev/null @@ -1,16 +0,0 @@ - Makefile.am | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/Makefile.am b/Makefile.am -index 96e03ab..ba0847a 100644 ---- a/icons/hicolor/Makefile.am -+++ b/icons/hicolor/Makefile.am -@@ -21,7 +21,7 @@ icon_sizes = 16 22 24 32 36 48 64 72 96 128 192 - if BOOL_HICOLOR_THEME - - .svg.svgz: -- gzip $< -c > $@ -+ gzip -c $< > $@ - for size in $(icon_sizes) ; do \ - if test "x$(RSVG)" != "x" ; then \ - $(RSVG) -w $${size} -h $${size} -f png $< $*_$${size}.png ; \ diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-rsvg-convert-r2.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-rsvg-convert-r2.patch deleted file mode 100644 index 55039f8be07e..000000000000 --- a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-rsvg-convert-r2.patch +++ /dev/null @@ -1,36 +0,0 @@ ---- a/configure.ac.old 2020-03-20 23:32:05.866604992 +0100 -+++ b/configure.ac 2020-03-20 23:32:30.866022834 +0100 -@@ -97,14 +97,12 @@ - AC_PATH_PROG([CONVERT], [convert], [no]) - AC_SUBST([CONVERT]) - --if test "x$enable_convert" != "xyes" -a "x$CONVERT" = "xno" ; then -- AC_ARG_VAR( -- [RSVG], -- [The 'rsvg' binary with path. Use it to define or override the location of 'rsvg'.] -- ) -- AC_PATH_PROG([RSVG], [rsvg], [no]) -- AC_SUBST([RSVG]) --fi -+AC_ARG_VAR( -+ [RSVG], -+ [The 'rsvg' binary with path. Use it to define or override the location of 'rsvg'.] -+) -+AC_PATH_PROG([RSVG], [rsvg-convert], [no]) -+AC_SUBST([RSVG]) - - if test "x$RSVG" = "xno" -a "x$CONVERT" = "xno" ; then - AC_MSG_ERROR([Cannot find rsvg (librsvg binary) or convert (imagemagick). Please install one of them.]) ---- a/icons/hicolor/Makefile.am.old 2020-03-20 23:32:54.292414381 +0100 -+++ b/icons/hicolor/Makefile.am 2020-03-20 23:33:40.052179227 +0100 -@@ -23,8 +23,8 @@ - .svg.svgz: - gzip $< -c > $@ - for size in $(icon_sizes) ; do \ -- if test "x$(RSVG)" != "x" ; then \ -- $(RSVG) -w $${size} -h $${size} -f png $< $*_$${size}.png ; \ -+ if test "x$(RSVG)" != "xno" ; then \ -+ $(RSVG) -w $${size} -h $${size} -f png $< --output $*_$${size}.png ; \ - else \ - $(CONVERT) $< -resize $${size}x$${size} $*_$${size}.png ; \ - fi \ diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch deleted file mode 100644 index 852d6b0605be..000000000000 --- a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch +++ /dev/null @@ -1,57 +0,0 @@ -diff -up chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in ---- chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole 2009-08-10 09:37:06.000000000 +0200 -+++ chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in 2009-08-10 09:40:57.000000000 +0200 -@@ -1290,7 +1290,7 @@ - <specification url="http://ca.expasy.org/sprot/userman.html"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-basis" support="no"> -+ <mime-type type="chemical/x-turbomole-basis" support="yes"> - <_comment>Turbomole Basis Set File</_comment> - <glob pattern="basis"/> - <sub-class-of type="text/plain"/> -@@ -1304,7 +1304,7 @@ - <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-control" support="no"> -+ <mime-type type="chemical/x-turbomole-control" support="yes"> - <_comment>Turbomole Control File</_comment> - <glob pattern="control"/> - <sub-class-of type="text/plain"/> -@@ -1320,7 +1320,7 @@ - <specification url="http://www.cosmologic.de/data/DOK_HTML/node230.html"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-coord" support="no"> -+ <mime-type type="chemical/x-turbomole-coord" support="yes"> - <_comment>Turbomole Coordinate File</_comment> - <glob pattern="coord"/> - <glob pattern="*.tmol"/> -@@ -1335,7 +1335,7 @@ - <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-grad" support="no"> -+ <mime-type type="chemical/x-turbomole-grad" support="yes"> - <_comment>Turbomole Gradient File</_comment> - <glob pattern="gradient"/> - <sub-class-of type="text/plain"/> -@@ -1383,7 +1383,7 @@ - <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-scfmo" support="no"> -+ <mime-type type="chemical/x-turbomole-scfmo" support="yes"> - <_comment>Turbomole SCF Molecular Orbital File</_comment> - <acronym>MO</acronym> - <expanded-acronym>Molecular Orbital</expanded-acronym> -@@ -1401,7 +1401,7 @@ - <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-vibrational" support="no"> -+ <mime-type type="chemical/x-turbomole-vibrational" support="yes"> - <_comment>Turbomole Vibrational Data File</_comment> - <glob pattern="???"/> - <sub-class-of type="text/plain"/> diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest index fd6cdbe6dd2c..d34b4dbb6e5b 100644 --- a/sci-chemistry/dssp/Manifest +++ b/sci-chemistry/dssp/Manifest @@ -8,5 +8,5 @@ DIST dssp-4.4.7.tar.gz 163831 BLAKE2B 195c8fb183df00105098967850b01c0d6acf776f7c EBUILD dssp-2.2.1-r3.ebuild 870 BLAKE2B 9b7542d9ec45b60f5671830e5068e1d1cbcca4b82cf22cc0e2d9804c221f9977cfade439cc6e41a67375b438faca3ffa64fdec23db2b417b58615513fd60ad44 SHA512 964bfd70d98a80e6afd7f28fc6bf7359bbde105e77903211cec04c5adcdce273f1d7142a6d206d644300a1185cba1352bf584499d864809dadad69b2023e50d0 EBUILD dssp-3.0.11.ebuild 875 BLAKE2B 6344416239b93804755b1829dcfcb9e8e461606c217938945bb2fc75e9680f2849b39bdbf0ed361592e703fea493a2dacabca498b26e696c969735a585e5d183 SHA512 353f4f5d7b1b195753c738ecc9fb17b429cdeada757806f5cf9a3da65c6318e3885d2c92fa904d5b3a546756eb87ec90787d158e8a9450b4730dd97b45af970d EBUILD dssp-4.4.4.1.ebuild 1321 BLAKE2B ba06063adc7c9ac9a20c078eeb98c95f0003c5ae58c0db0b5bbb888b194de86e22de9c1549d1911e25e4d5b7a3f99089c0083c281441eeed3dde3ea5e3b8cd14 SHA512 77683bc3bc0aebeb867ffaf94d5f7ce1090f78a73fc739da01c73d3bdab142fc409bce66f85349b627e54376e1279b45a9096a71cac080be10ab0ba4f84d33cb -EBUILD dssp-4.4.7.ebuild 1311 BLAKE2B 6744df1780355e0ac3931c7d87426fc33132db57dbfe6dd237f7df94bb57c3de128f0fa5009391f0b166ce92f0b4e47e8a7f8c1bb2ea492459aeb8f22fdd015a SHA512 dc5ea7e546cb50b2737f0d185cd2f562865319b6bf5d9d1d6ffbdffaa72a4ba2ff9a5d59a37b68798a09b992640b0f57840c896e90641b0f6c02a4bb301cf6a9 +EBUILD dssp-4.4.7.ebuild 1329 BLAKE2B 61d8909411ff687ba6b11449b0c3acd307c28ac5901fe360886b980d49b88e301cbd539d794503e789e73973ce1ae6aa965e1846cf7453d41df96285a1710cdf SHA512 d3beb704dc3a3783c79ac73fdfdebf74e82fa15d8d7d792124a529c7a208e6349b8035585d0ee96eecaf13ef81ecaa407c2ee22edd8bfdbe5befc945ca5453a6 MISC metadata.xml 295 BLAKE2B 4355bbe00822cc702acdf70031ab9cd1f2a8f6e076d71016c1783f2a6c052c2da0a1a4a1860062562bb837161787f2481fa6f49c4319c546482a263ebe149bb0 SHA512 ace35ca21c614a7c0cbdea2496be3190a907295053566707c1875836a306cc9e9c96816cca6ce2b514935f6fcd494d2e813f4d94ba88552cd7b86831f30501f4 diff --git a/sci-chemistry/dssp/dssp-4.4.7.ebuild b/sci-chemistry/dssp/dssp-4.4.7.ebuild index cebac1ce3a1a..d5e51fe40fec 100644 --- a/sci-chemistry/dssp/dssp-4.4.7.ebuild +++ b/sci-chemistry/dssp/dssp-4.4.7.ebuild @@ -20,7 +20,9 @@ CDEPEND=" >=dev-libs/libmcfp-1.2.2 >=sci-libs/libcifpp-7.0.3 " -BDEPEND="${CDEPEND}" +BDEPEND="${CDEPEND} + dev-cpp/catch:0 +" # doc? ( # || ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc ) # dev-python/weasyprint diff --git a/sci-chemistry/elem/Manifest b/sci-chemistry/elem/Manifest index 32d180b6b25b..2e497e17d9ee 100644 --- a/sci-chemistry/elem/Manifest +++ b/sci-chemistry/elem/Manifest @@ -2,5 +2,5 @@ AUX elem-1.0.3-fix-build-system.patch 2544 BLAKE2B 174bfc3e2036a17d918534d02b51d AUX elem-1.0.3-fno-common.patch 496 BLAKE2B 90d5f78f7e1efcc9f195e432ab1f942f30002be476f0bf4a2a6ea92cc9f3c651c856aa5e1cceee66239e47cd84038417e640542c5299c55d968c7b3b62224efc SHA512 9c6a61667c23987fd047a649a178fbae75abf78fa6c974d1f6c1552790db50f5b4152d66af88afeaf242b77eb0d2ccb8862d2d69227fbf48f7c3dac183081e98 AUX elem-1.0.3-missing-stdlib.patch 133 BLAKE2B 2ab00632e93401db578910b4e44e8f0ad4e899fb3afce5b9d1b6612ba181fd0fc3922c8cc229404164bdef562850337f006cce4047e52b2e459954419bc05529 SHA512 769c5e19928ed64b5595cd37f16d4df893889c3c0ea7e6673e182646bcaca89a6e46e7c6611c586c9213a417c439de043c0beb84a9543e478f78e4d9843a1c3e DIST elem-src-1.0.3-Linux.tgz 58364 BLAKE2B bdedb844ca62f928fdae5b01b13b88e5f43f5e37f40b47f7b8b9b1a2cb11053b9aefa7b1b4bb78a8632f3329f37afeadfc34eddee1b9f7cd109bee89aa9cdf32 SHA512 24b163c5cc3019c1beb677ce7b432b21289352f7cdbad686ab9161c628d3aadbb90d8abf9bef49f1c7d077b706bbd4ea6b381f356cc85adf907f3c15a4f4893c -EBUILD elem-1.0.3-r2.ebuild 703 BLAKE2B 0cd3d221cd8ac0438b48e9ecc5d7f5112332cbd9e0da18da0a4d5d2a8d9e1db2456ff72cc6ae06195d50c9dc967ad07d279cef37fd654e6d0302d8938096a63f SHA512 bbf9832c1101e1b7426950b4c5b3a6a3a93e1f0ab947602854580ea10a78bb26a8c0b54e6de84fdda2fde5a2805f73c1e0a4525e1ee6b3a9221b99fc0287debd +EBUILD elem-1.0.3-r3.ebuild 697 BLAKE2B af73ad81632fc56129375b880770c6d71b5b6df5f355f96f76414b7199e9eb5510eadb8cbc6fa4e00c526cdc7d4307d8b1147590d91b02cb41b117d2d175b81a SHA512 01ae1d41a4625020232724c9d6c0159d9f088f96ed156487ab142e2501530720011d764e119efeaa70a7ac84f441d0818a29aa489f49665f4bdd4caed5ff4a6b MISC metadata.xml 340 BLAKE2B 1a764f9dff176031a6f20610e9fa4aa6cc706f1c2cd76c52c529f50254cc70b94c76dac3254a21f15a3af3965f4ac6bb2266f5dcb11161a00914ba1247d6c36e SHA512 a50dba6ad1704bb2c9cc4f7d8eddd2e23e5b315327bd70087830d7ce3d7d26758799be3f26421d5a60193d97ee81987827f8d5b97207d485dac5878c3aea4217 diff --git a/sci-chemistry/elem/elem-1.0.3-r2.ebuild b/sci-chemistry/elem/elem-1.0.3-r3.ebuild index 9c2ed9b8543b..7d06be84243b 100644 --- a/sci-chemistry/elem/elem-1.0.3-r2.ebuild +++ b/sci-chemistry/elem/elem-1.0.3-r3.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs @@ -10,8 +10,8 @@ HOMEPAGE="http://elem.sourceforge.net/" SRC_URI="https://downloads.sourceforge.net/elem/${PN}-src-${PV}-Linux.tgz" LICENSE="GPL-2" -KEYWORDS="amd64 sparc ~x86" SLOT="0" +KEYWORDS="amd64 ~x86" DEPEND="x11-libs/xforms" RDEPEND="${DEPEND}" diff --git a/sci-chemistry/gperiodic/Manifest b/sci-chemistry/gperiodic/Manifest index 569d688227fe..35a2c89303ef 100644 --- a/sci-chemistry/gperiodic/Manifest +++ b/sci-chemistry/gperiodic/Manifest @@ -1,3 +1,3 @@ DIST gperiodic-3.0.3.tar.gz 451559 BLAKE2B b91995046b9905a534e3b6f530aee0ad2b4e6ac42cd11755ea182fdaaf8970f34b1aea8a33870abb8767837606a42a0cf0d76c9a689236aa39fba686e1521ee8 SHA512 7226063cf7977f4283a199d4a3d1842d6c9be60c53f5a005541eb26f35cd6538b29f086dc13c28225779e1849a12d1c39150897055c03902cb00adc011bc1ce8 EBUILD gperiodic-3.0.3.ebuild 884 BLAKE2B 3d3389b62f81d204d39f846421fe87267e8cc877464cb7f93bb0355d2ac4e89973e0fff1364f60db9c4ecd38919a774223c0e967ca661835c87e05c1bc83a1b3 SHA512 7e0b3e5b80cb0566489ddeba299d5efceecfcc83ffc7faac61f4d0bfb0aa6bb68dd80cb8452e6e09f1f742a95ab0041e313047741b8be6e6a4ff45c475fc0c4f -MISC metadata.xml 551 BLAKE2B 820a6c68db9ca1c8e1138fcd82aa998c5e9a06a93ec19e2c7135d522b18b5410597ca1074b594ccaac896fdf69efa1a962328022b78c7c3d12f04a9b32a2d977 SHA512 8e3c92beae849c975057babf305a21df19f42d07bc122db73023ec3cb7a52937906cd2dcde9e9bd29f9b4f54b80ad23c907840e38bfdaf608e9b12373c47a7cb +MISC metadata.xml 472 BLAKE2B e0811caf393b542123014a9d910fde9c840e2ace704c63073287537a3176ebc8821c1c6603cf6c9fd39bf03f68f77a0778d51632da04e2c5b5daa216188af313 SHA512 6bd33a21ad9298bf9896f0da7b72d0857581255fa4c6e34aa2a133a32e2c91eee43b342138675e60885e65acc3482ea29158138d2695a1acddf6418d6fddc352 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/Manifest b/sci-chemistry/gromacs/Manifest index 05fca2bd57ec..cdfc78bc1836 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -28,9 +28,9 @@ EBUILD gromacs-2021.7-r1.ebuild 10139 BLAKE2B 9611b5c6e0d22255f1faf0f5223cf013ff EBUILD gromacs-2022.6.ebuild 9583 BLAKE2B 4700542f3a32bc3055617792d56fa63370438e949efaf073ae3e983f25184ed0f7fbf8a13c777c0da0a0965cfae8ad96625e76ec4d69e5ade60b71d6466fe4af SHA512 9c7c0a0692cd31102c4edce4b33d4e61afb12cf034ad804ba131d40f60cb2b3cf05a424b3f40e4001ea09ee5a5c354b4d98e9a709ee75d5c8d134ee0a579bd09 EBUILD gromacs-2023.4.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 EBUILD gromacs-2023.9999.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 -EBUILD gromacs-2024.1.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 -EBUILD gromacs-2024.2.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 -EBUILD gromacs-2024.9999.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 +EBUILD gromacs-2024.1.ebuild 9745 BLAKE2B 254a8fd8fd9b12cdb0afbbd98539add499934781db7a2a249b1fd5dd077227d6a50a23cadb87e409aaf51a7188491dc4662f305142ebc8388b9ef823bbe7b45d SHA512 e9d3a2346f38a64f125bb20031f37e3ffde9c17b50f7812b682818417dc2c68aef0afec206a58f91e5c9af091ce198b97e998ecf6fc5b6c64d861cfda31be755 +EBUILD gromacs-2024.2.ebuild 9745 BLAKE2B 254a8fd8fd9b12cdb0afbbd98539add499934781db7a2a249b1fd5dd077227d6a50a23cadb87e409aaf51a7188491dc4662f305142ebc8388b9ef823bbe7b45d SHA512 e9d3a2346f38a64f125bb20031f37e3ffde9c17b50f7812b682818417dc2c68aef0afec206a58f91e5c9af091ce198b97e998ecf6fc5b6c64d861cfda31be755 +EBUILD gromacs-2024.9999.ebuild 9745 BLAKE2B 254a8fd8fd9b12cdb0afbbd98539add499934781db7a2a249b1fd5dd077227d6a50a23cadb87e409aaf51a7188491dc4662f305142ebc8388b9ef823bbe7b45d SHA512 e9d3a2346f38a64f125bb20031f37e3ffde9c17b50f7812b682818417dc2c68aef0afec206a58f91e5c9af091ce198b97e998ecf6fc5b6c64d861cfda31be755 EBUILD gromacs-2024.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 -EBUILD gromacs-9999.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 +EBUILD gromacs-9999.ebuild 9745 BLAKE2B 254a8fd8fd9b12cdb0afbbd98539add499934781db7a2a249b1fd5dd077227d6a50a23cadb87e409aaf51a7188491dc4662f305142ebc8388b9ef823bbe7b45d SHA512 e9d3a2346f38a64f125bb20031f37e3ffde9c17b50f7812b682818417dc2c68aef0afec206a58f91e5c9af091ce198b97e998ecf6fc5b6c64d861cfda31be755 MISC metadata.xml 1375 BLAKE2B 321b7db8536061655a6efaa40110f4858633921292eba465b85fe0cb50280842e511f2f11385fe5d62bbdfb40e9c0c76e8e986a1efce8eac25d52c438d7ed5f4 SHA512 cc61e0b477f6576079a0f7910475b9091c1c521fbb48efab365d355e3c0a80cd19e1ea9028cb269d37c2572546b1be66a210512e40ff0f2d6314d1b0138cdba6 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/molequeue/Manifest b/sci-chemistry/molequeue/Manifest index 063a3a31863b..e5eadec596ab 100644 --- a/sci-chemistry/molequeue/Manifest +++ b/sci-chemistry/molequeue/Manifest @@ -1,3 +1,3 @@ DIST molequeue-0.9.0.tar.gz 604015 BLAKE2B 37e7f404a0fefb40defb198295659372121fbe770269c2f9fb92e856aceb8222bec5e83939ecea061b76f925c0cbde1be0a854db41f992a92a2b2b9e0651f2e1 SHA512 87ddd8ca59227cab60c0ce2643e5bd435d9ac7e23b929659b95f190478734a5b71d4935f37d03eeadbc39939cbffb3604e0a283d50b0a23a1a000b57c1fce335 -EBUILD molequeue-0.9.0-r1.ebuild 2058 BLAKE2B 8b42f68ca7223258bca37e2dbd84d402b5c93a681c315be7d7231bf39210452a132e49041d6f495d3ef7aeaf6c6ba635ef9f02d8fe767c8ed320861196a8fe04 SHA512 3290ea4c0c2c6ee7528a7076d89afd097c15dc89ef01b00f9e9ec465c471355b71f226bdaa483012166ef589547e035152bee2304703c6c98fda0c3338a3cb4a +EBUILD molequeue-0.9.0-r1.ebuild 2058 BLAKE2B 4ef1bb5f33632d398c47e9a9a7b6b5f91a3b1192a01f819525b419834243788b640664f8726b92b34213a1301878649910460bd32f0d29a3b90f0849031e8d1d SHA512 428875c6884c1682e0d6ec0999ed714a91b140bef6469ba33841a702dee1c5d42e1d0c7d90f53d16e4d28146175184295dd9bc53bae130667e00f2d7434e5936 MISC metadata.xml 1258 BLAKE2B db62408b81fa39c138916de98df72a14b7d66bfaa7ac50e6afe5e138ce4d3627cbb7f0544e075ecdaff70b04ee6023d5f2381bd0f130d5075b060c5ed8bfabb5 SHA512 b4b028602d96c58d8744d016176361d41a1ac4c3dbb0e14edb3526d683cfdd8607ba3c627529edcdd5fe97ba484cb8e1fcaf797e4c4d0253f0bb2321a2140512 diff --git a/sci-chemistry/molequeue/molequeue-0.9.0-r1.ebuild b/sci-chemistry/molequeue/molequeue-0.9.0-r1.ebuild index 9695faa7d9f5..ac726cf02fff 100644 --- a/sci-chemistry/molequeue/molequeue-0.9.0-r1.ebuild +++ b/sci-chemistry/molequeue/molequeue-0.9.0-r1.ebuild @@ -3,7 +3,7 @@ EAPI=7 -PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_COMPAT=( python3_{10..12} ) inherit cmake python-r1 virtualx diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest index 5fdb76ae39ea..76e5c78f437b 100644 --- a/sci-chemistry/molmol/Manifest +++ b/sci-chemistry/molmol/Manifest @@ -4,5 +4,5 @@ DIST molmol-2k.2.0-src.tar.gz 1088805 BLAKE2B cd649604f6ee491d3a4485391ecdaa48dc DIST molmol-patches.tbz2 17528 BLAKE2B b91270a980f290edc169be00639e86b3272281c9fe237750f5778eab1605ed482c09bdaf90660a5edf74bd04b3e31adc755e77e39aea6c75d88b6db9bf47a6d6 SHA512 bd94baf0a378f40f854f396963edd9b9e4afc5c56462ee6f8b68889290afdb4c5d9b10878aa5619d0a70153453fe6ee8e7540064522c6db0291ae9162bba9287 DIST molmol_256.png 22668 BLAKE2B c7d75b8e0d738b48790bea25e21ec60d57a8181253518c70d6f18d93c64eef3c9acf90213fdbdf2dde272e85a04a6442e4e4a9c375829f369380d88c9c0ca57c SHA512 5e7975f54a7462161dc630ee973e9a8126b9c120e0d8d6b62007384c970ce39792e52300edc25dc7a85209845801d749d9ecba02899f3e18b18f5a5fdbc28a97 EBUILD molmol-2k_p2-r8.ebuild 2284 BLAKE2B fa9954fca3dd8b52450beb1c0901abc71743672d7a76e2daa2bb05f52280ecf7dec5c401da24ce3e72f429cb69b27738117e33d41b49a96836b1b407efef67f0 SHA512 d813743572479b5eb0ed4181d42743402c4bd0a5a8e012f32bad03c4be68f38329722b749abc91845ba9c25642b19f5e2c4b5578ed9d3f7d03beaabbaa3345f5 -EBUILD molmol-2k_p2-r9.ebuild 2314 BLAKE2B f54b8793c88c3e5d14a128e922d9d22dcc5ad861c76a205b84a0a4d8f36ccdf8e6259955e71257689424ac48819fcd3350105e4472202681e8a9bc80c43d9d21 SHA512 56e0839d1f3d971d549c2bcde64115b17e3b7adccaf63b75e7221247684c7b7ee40df89d30c2b0d0acd28aa4e147523644f34ce496cf6a9e51ff540616123bda +EBUILD molmol-2k_p2-r9.ebuild 2313 BLAKE2B fecc271cadf3eb73478b1adc674a6d369ee7bbb05c38e10ae78ebbc886782962f7c33ea07ef4d065e643ee7f5a71e99801f72c290cb7ab437833141dcfe80a99 SHA512 d173ed8f60c833485bf639fa8fc0ace5ff1ae46316be319d2cd1feb5f5201484ed9e8bba46054dfc91303d71051b52d4fa943638ecf6b843514fa9585bc421a5 MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c 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/mopac7/Manifest b/sci-chemistry/mopac7/Manifest index 6b275a888424..25d061c91462 100644 --- a/sci-chemistry/mopac7/Manifest +++ b/sci-chemistry/mopac7/Manifest @@ -2,5 +2,5 @@ AUX Makefile 387 BLAKE2B b0c4b3a009c8bf8c779953edf3e233434656033a661cb307079eebc DIST dcart.f 11044 BLAKE2B 7414804ecfab9a7cbddee664b85e6e2e8c1d8fe1e1f73d480dd1a387c5e349d26ec4ae1a37f27e38b7c051fcce2c1bdf77de12ec628298fd3edf79040a8a0c5a SHA512 788a184fd8419ff742e49c1a652d5ea093f9114dbe4f272665b8fb9eeac2afb7f7042628c288f2b81d0f54d8a7ef2f400490cd3aff39dda59a6d70a0deab5b80 DIST gmxmop.f 38956 BLAKE2B e411feca5104e91ae8fd2008de61d18cc214beb3b2a7aa09a80269fb935e27ba1b1cb89fa30eedbfc4f6c4734c22d932e57d5905c175ae9f56c4affee7b0ca04 SHA512 38bb2e5749c4d3c8c24f15682f72e40cb4edb6517c7916cecee1d21675b1870c0fe331ba2ec40312408dec473141e7742d1e155d4b64f1c2a25bfa4e11885194 DIST mopac7-1.15.tar.gz 764547 BLAKE2B 6e037862007221955d0ad65f3c002a3d2e461950a2bc0efac9d195cf1d9d856842d02bc380ce236c3d48f863a144875950f5c86f8f3ac936b8b098472f7f7a0d SHA512 e0ccd643caa6dbd7e156867530d79e50e10243f5e3b5f8bc57781e68e1daf26f2a0e6987fff00afe07eb0fcb98cbd9f01e4cfa5d20acc0d8ab3cca632968636e -EBUILD mopac7-1.15-r1.ebuild 1855 BLAKE2B e3ecda4d53b2d1f8161cf5fbac788149302e1fbaf972fdba2e372c2ad6535e2c55055f1486788c5e2e8b0027fff6d9532ebd5566c032390a507f0b5b072b2d75 SHA512 3dc54baa3559c0bc297ba4b50337255774a4a74ba3d4a2a38fe213325e13aa13f288b2d783ec082ce042979fe3f57d914d570a17e5d6858833ba2f7a66af145f +EBUILD mopac7-1.15-r1.ebuild 1979 BLAKE2B 9ed2f685e1b787f1eece439ca75efe489601651712aa6dbab8fff05d78e0ce3d97a5116266568d985e2ca67749e4bd39dd606f8f419141ce39ccadf39de9fe22 SHA512 add91d8a0b7da52ecebed3f611fb259110ab4872554ea2db94bb476625ef2c09ea83220f6e16f69303c6bba368bbd1681ec293f013cfce05a05b6a3271438d0a MISC metadata.xml 435 BLAKE2B 12efd7ecfe6c9b07411d62992a225848f3787b58a59765e373fdc98ce22c3b50763243ac70efa1d7a7ec3309bc519dd433d41b778fe8f18cdfbdae971e0ee82c SHA512 d624b1181bdd0d66062507e7793eb25d24c447fa9ffbe8ee1645c88b843e6822e80af087bf6073ac191947074491159331f2021b884f8b7cd2237cf3e013ebb4 diff --git a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild index f785669fe7f4..c536575112e8 100644 --- a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild +++ b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -39,6 +39,12 @@ src_prepare() { } src_configure() { + # -Werror=lto-type-mismatch + # https://bugs.gentoo.org/927389 + # + # Unmaintained fortran code, no bug report. + filter-lto + econf --disable-static } diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest deleted file mode 100644 index 4d348875c0d2..000000000000 --- a/sci-chemistry/namd/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -AUX namd-2.10-gentoo.patch 4637 BLAKE2B 0439e424f3d2a73378c68052f9d9dd69dc9590b9f83fa4062d4abc156b3b682f0e8a2cffd8a1e1f751f8dfd71d067c0234ba56946773ca9139e73c57e775c631 SHA512 35afda71ad7567d1b2c4c1f4073792d5977edc997ba7a43cf71c8ed32308062edc5cb4923202d599d59ade2f98602a0fac21138ba205a3bf6b681c86a61411f8 -AUX namd-2.7-iml-dec.patch 520 BLAKE2B c16430d1161b9d7e3faf22257d84ff1090eccf906a296f91d4ec0731fa89d23334d5c39c7988f8ac6d5f5020d403d4491dadbe34b1e9800ada81ad18b2448b7d SHA512 50ddf91bcb0e370a98d6fe5329f00ec9a8016f0178e342b086f4b9d4130a41e525ed9d960e92dc83b4372f135ce9d454bef836d3e215fb6ac7933999278efa37 -DIST NAMD_2.10_Source.tar.gz 9200234 BLAKE2B fe348a21309b279640da81ed4dd5447c1e6e467866270dc1730b26d02d5518b45bd662211c3cbe228bd8d9885edb062cf5d245d634bcd38773c36873febd2ee6 SHA512 3712a03841fad76c502ac4e41469162ff78e6152560d0f6855d61d2b5583241a661e2a3e7446029b56a6f6f1100f25cb51b2c3df6571542397961d3bb625bc92 -EBUILD namd-2.10.ebuild 2644 BLAKE2B 6d91c9f7f90f2b304c18bb176e7fdfcfff98a077bf8d6ed720b24ee186b5dece164fde49cee6db3f3dff217a53bba76d6d1c00b45ca7633ab1d9fb2a0b53ef46 SHA512 816bc445d23cc15fcf7d17bacb11b7ae4566a7bf135a88f80b7587d9630db0650e0f8b54b828bbbe8454008b6967fc276fbfc347cda351ec4b9e370d08671e08 -MISC metadata.xml 377 BLAKE2B 727b1c499d11b56228aab0bb2c47c45f63c48a1406f52b5b3d3fe8d02b69d0113dbad00eca99bcff194fc164605b2b698bdd8581c20fb6401c54169265d73f6b SHA512 4dbe460b1b9a0a8112d7866a11a389a1e2847afa3404c57479bdf39e6b3600d403c5c1f70d76196cd1508770dcd8befcc73687969b6853ff1e5f25cf5d22fea7 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/Manifest b/sci-chemistry/openbabel/Manifest index d8db74c07b20..12ada1118c65 100644 --- a/sci-chemistry/openbabel/Manifest +++ b/sci-chemistry/openbabel/Manifest @@ -3,7 +3,6 @@ AUX openbabel-python.cmake 4402 BLAKE2B 36c325a26f9b23c3957db22110628a0a922ad02b DIST openbabel-3.1.1_p20210225.tar.gz 36674527 BLAKE2B bb82fc96f704249d211bd86c73de0cf4e7cfe5e2ba5c745aa8b4f6f19583837e2181d85101377810095f6b71fc3b91bf2f6f5636726fc8271c6905f1f8c59e7b SHA512 9ff7cb4acbfad7a9c5c8d0dd8930ac0390d0d0f2758d1a6120009071f47ffe718f92ad620d37f26f196babb14649c52b5eb7bb161c342ef36aec655e0a172de4 DIST openbabel.jpg 12159 BLAKE2B b701df2b8c29df607dc2bd3997a282aa9a726d56c789ff2db900d33234dc691f76b6af12a4c9ccda4f09984504b863c40c39e8bf91058939996714ede2dd37c7 SHA512 998ea526c8c92f87dd203527fdd9f4e001357e951409209f41ab68e0b730fe12d97f9079c12ca289be413854ea2abcf8bb691ae5af823a6f29d6a590e1a3e2b0 DIST openbabel.png 29060 BLAKE2B 8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3 SHA512 bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70 -EBUILD openbabel-3.1.1_p20210225-r1.ebuild 7464 BLAKE2B 3c3b12086a4b69c1ccfd92b5da672ff2ec4a1dc161832094d62b049977e0cb8d8717e5999f3138f857efb642a123a64fca804c5a109f69de939686fae9a08bd8 SHA512 0b516f2a8cb7194d2146397c3fc1ef375446d8dd6a29d862ed73e78455e41c0d9a86cdaee7de64cd2d4403dac34b0ec8fee4e68156df7562331d4577c82f411c -EBUILD openbabel-3.1.1_p20210225.ebuild 7424 BLAKE2B 6cb8b62d7aca60079f7dddf5917b5645dedb0a93ff4292d3f8e2f5a6d464e69becf2391ddda75f915e8d73c5133529e8553147219a375950a8707b48081a96e6 SHA512 f7eb0086a3a66327a5b126acf1886bf7cad7fcdb59b4f36a3ea29886280bc0684123edc17c8ad3c98bea6c16200d3a35d7562e15871cada9c4a67b5982405299 -EBUILD openbabel-9999.ebuild 7314 BLAKE2B 4bb03f325ec2876317c4f13d481b2f7738989358bd7707f27f6f650e3e41a9afe758721b4c4929a664eb09f82fbb8da0ba9dba8331f687c36758547345ce2ef0 SHA512 37b58ea4747b79b6dcfc5e5cd69af8f1d37b2a6a1c8bf414116396549094db9e89133b70a944ab3b7668eb9d815c7e4ae9fcff9a877cea85a00911e44682eb0a +EBUILD openbabel-3.1.1_p20210225-r1.ebuild 7465 BLAKE2B fedf37c6772c62b7d9d6a5c5cc2e89b396cfebe803d34abdd5a1a77248c9f4ce27fdcce42aa2aa625a79d29361d2fd9c31a104a8d4b886fbf63fe84af4e0066d SHA512 0089ac6f89ca13e1999fe440922f0bd864568d61f8cb8dac1519c2b1d2a9b73f278c325ffe177474f678991a4ebe1264baafdd4b419d5eacfebbaccebfd31195 +EBUILD openbabel-9999.ebuild 7465 BLAKE2B fedf37c6772c62b7d9d6a5c5cc2e89b396cfebe803d34abdd5a1a77248c9f4ce27fdcce42aa2aa625a79d29361d2fd9c31a104a8d4b886fbf63fe84af4e0066d SHA512 0089ac6f89ca13e1999fe440922f0bd864568d61f8cb8dac1519c2b1d2a9b73f278c325ffe177474f678991a4ebe1264baafdd4b419d5eacfebbaccebfd31195 MISC metadata.xml 921 BLAKE2B c0797440e50f813777c4858cc1ce893546d7785e57243318ec7d2c601c6ec2ecb7ec5ab3dbacce960c8b71196eef51ddce07802257fff0d4cba0293f940a773f SHA512 8ee8a50230f374904a9ddaaf7337caf018788ab25a1839dbf5a48b0e5c49ac4e285a1fa759900fa6d993bc220d3586a923ae21158687be971fc51a6c302f12ad diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild index bdfef2a675e8..fc4d6cab575e 100644 --- a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild +++ b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..12} ) WX_GTK_VER=3.2-gtk3 inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils 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}"/${PN}.png - fi -} - -pkg_postinst() { - use wxwidgets && xdg_desktop_database_update -} - -pkg_postrm() { - use wxwidgets && xdg_desktop_database_update -} diff --git a/sci-chemistry/openbabel/openbabel-9999.ebuild b/sci-chemistry/openbabel/openbabel-9999.ebuild index d533ec698acf..fc4d6cab575e 100644 --- a/sci-chemistry/openbabel/openbabel-9999.ebuild +++ b/sci-chemistry/openbabel/openbabel-9999.ebuild @@ -3,13 +3,13 @@ EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..12} ) WX_GTK_VER=3.2-gtk3 inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils DESCRIPTION="Interconverts file formats used in molecular modeling" -HOMEPAGE="https://openbabel.org/" +HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/" if [[ "${PV}" == *9999* ]]; then inherit git-r3 @@ -17,7 +17,7 @@ if [[ "${PV}" == *9999* ]]; then else if [[ "${PV}" == *_p* ]]; then # eg., openbabel-3.1.1_p20210325 # Set to commit hash - OPENBABEL_COMMIT= + OPENBABEL_COMMIT=08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz" S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}" else @@ -25,7 +25,7 @@ else SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz" S="${WORKDIR}/${PN}-${MY_P}" fi - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + KEYWORDS="amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos" fi SRC_URI="${SRC_URI} @@ -80,6 +80,10 @@ RDEPEND=" ) " +PATCHES=( + "${FILESDIR}"/openbabel-3.1.1-fix-time-check-cmake.patch +) + pkg_pretend() { [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp } diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest deleted file mode 100644 index 176af33f9d5a..000000000000 --- a/sci-chemistry/procheck/Manifest +++ /dev/null @@ -1,7 +0,0 @@ -AUX procheck-3.5.4-close.patch 1073 BLAKE2B 54e9857e3d3ee920becebfc50da34145384046be019a2fcd01d47afc4f9242a5311aac166dcde7dc79de584c2ea08bd8e766ae58310700bff45f6bb1a2829abf SHA512 3d18df23858acc46a12f884d4904ca3f60e05e663746e768f5f08d0370b2e335cfde09c08566c4869adfa0f9c0d75ae527fe0ed2666f603818b11f91a3349307 -AUX procheck-3.5.4-ldflags.patch 1649 BLAKE2B 64506db2dbe1eba43dfc07bca233d573646ac553862e8d6eecce7970362047cfd8fdcd18f7c83bb74a0476fde78222ea92e0c2a56b24fba2d71d9c97c563fbb1 SHA512 f7f2e06a77058f7e743a1c1367d40c2683a2aefbf2910a807d1b0a77d19024446f978ec34a8e5187338a7e98b6651592a37c024e8a2ea955d9bd736d47bfeb4f -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 -EBUILD procheck-3.5.4-r3.ebuild 1717 BLAKE2B 1919325faefdc9cad032d503166cdedc966f44c949bf1c2c34d3aa7b0132fdbb35a3a7e0f446a967166cbce66596143e114cea7b0c23aa9ca0c99acd9c29ec4a SHA512 04c58e977937275fd413ff217d97f7fa0dfacca2492c57b60d8f2d671565e640852c391e8c408618ed3e9da53f602f96c2863a009d8798011365a9b9f1fa93ec -MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c 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/propka/Manifest b/sci-chemistry/propka/Manifest index dc5a1eddff6a..2c45708435b7 100644 --- a/sci-chemistry/propka/Manifest +++ b/sci-chemistry/propka/Manifest @@ -1,3 +1,5 @@ DIST propka-3.4.0.gh.tar.gz 363641 BLAKE2B 87f495ba69028593cf3ebf98ed33da0944f7a3833f2d08cae4f0a0b5cbe2f3a67e9812685b896a7d89c88ba25653861f135dbac53dc6df7af426a290bacb3d22 SHA512 2ce431c66374d0692acb7504661caa870ab6460ace3a6478f88c1d46a7bfcd82c748bf153a1ce2ea6d1611bc4bbf2351c4f5149f4578e5f8a9f9ec8385298fe9 +DIST propka-3.5.1.gh.tar.gz 376176 BLAKE2B ef4f5f51a6d08da566aa8dc4d2ec73ca028137031dbe49ca329589fe9ceb7cdda672cac755735a11bed79db1f31be5401b083239214177c2d459207ae998ae29 SHA512 3a9a7fd773700850f14c3ef1cc4ef7614242ea1191001fdca6afd44953486f208cbc067b84752c89e97e82ef6bac5561907b2aeafbee80c4d83cbf3ab443aaa2 EBUILD propka-3.4.0.ebuild 750 BLAKE2B 811914f17aaa8c9ba8779d4267ecc372c7397394ccf87bb6ea25159759248861da362c13d1e70a991ddd08783c9d4c8c9edb59b99aaac0e253f99935ed2666ee SHA512 e5d23bb7cff54dfc009435da11de8f7e73e2da41e908d4efde1f722a15e2af2d3e5c126fdeb59c5177349a64e6fdeb18cd407a7bd9a6aad3cbeaa3ab6ec04312 +EBUILD propka-3.5.1.ebuild 751 BLAKE2B b3db6aebf5bcf519ae9f248b854d92defe476233d311601ac158763e07ed757ad74542ead5507f7d81de2f356c59efce29f8c501922de544189b51431595b5c8 SHA512 15ff70d3711166276c7b548ebddccf6684942d095fd941e093bd027d55d9bf632c70e50ed045e9a00f8a3ec577927018444c2b38f686c7e772894b01b3d6117d MISC metadata.xml 417 BLAKE2B 89fda735965e8ae53eb86dfd438137e7770718b5601d5cd753cce9a03001419e53404dde70fed53d37ccf407265ee387accb26640bb4fce479e01ff141702b70 SHA512 5a9f942fa28e679ee5e1795fddf91661c35c55df79e0d9b742353ad265057ceb030ef15d3bb218ad5e8217c61d462aa09206e261c14dc363e6d6bfc3d20c6500 diff --git a/sci-chemistry/propka/propka-3.5.1.ebuild b/sci-chemistry/propka/propka-3.5.1.ebuild new file mode 100644 index 000000000000..2c9eb2ee4f27 --- /dev/null +++ b/sci-chemistry/propka/propka-3.5.1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="pKa-value prediction of ionizable groups in protein and protein-ligand complexes" +HOMEPAGE="https://github.com/jensengroup/propka" +SRC_URI="https://github.com/jensengroup/propka/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +SLOT="0" +LICENSE="LGPL-2.1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" + +distutils_enable_tests pytest + +python_prepare_all() { + # Do not install the tests + sed -e "/exclude/s:scripts:\', \'tests:g" \ + -i setup.py || die + distutils-r1_python_prepare_all +} diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index dbc27f448a0d..1352ddf62ff9 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1,5 +1,12 @@ AUX pymol-2.5.0-format-security.patch 562 BLAKE2B 566f653ca3abd4498f9ee5d7255e1b06d8df320bd25a569620b1ee33da0cfb6a969fd3e0a65fbce7116cd6567d9a544c57f4d6d399bec00b9effa8273a52153c SHA512 4e93a0449470abdbd2d943ef0a5fac7f302485ca42c6d9ccdf1ab9a879029d5185c3f1a3a2e237fd8b3b3bf0a306bce07db3226257360127c97546480c233c4f +AUX pymol-3.0.0-SceneGetDrawFlag-indexing.patch 821 BLAKE2B c854aa49441b308ab7f12265442961ddeb3633b71234bd554d45c3950c3ddcf457ac98e0aa1d226ec7ee3abbd2d0207cce97e40144cb81992f241c3a964b1bcc SHA512 326e04f988ff585a062a342b9553ab6b074102c0599b210a5dfa769cb8841e1619e74b670a2d673a80b81c5a9218e052829e0cc574049a1363741e762cac59e7 +AUX pymol-3.0.0-distutils-py3.12.patch 2620 BLAKE2B 802ef75cf22b408ff8e280c561f4954f7f4d816887107f8db36b85988c345948e7d2cfe97b099cb79794d61d3594666e12f90a64c1f0af2206458ade776a1a2b SHA512 3911207f1a03b19675105cd707d644e76258aa9ab58be3891833873d41b460f6161ac83d495a6bc58bf281831376d17186083d447269d755d2e69ee78e6fc5c2 +AUX pymol-3.0.0-eof-maeffplugin.patch 1071 BLAKE2B b28941bd3fddb534fe150b3d98ef6a17058b25b59717a15ca9a807812f05d98f3f7b2cedee9230eab0465c493bbf375325259260bb1cd0d03beafbb4a8f306d0 SHA512 b39846fa9b3b90d5952f22fdde323039bd09a5c43abdd7975bc72880854f22ae39a0d3d30a6640e98c6d7e8734306e00af3fdae555a4292e48ad7b46a83753f8 +AUX pymol-3.0.0-lto-molfile-plugin.patch 5585 BLAKE2B d9cedbb270184d562373fc9e8a2e1a75b08c5d1a956c28eac55662b424996a6770ea46d45b0645a7b96ab465af0f6aafac3120ed13a29f12daea5ab7c947da5d SHA512 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40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c DIST pymol-3.0.0.tar.gz 29510174 BLAKE2B b67818e408045e386e44a203f29cd94a0ce34ec706776d29f78f1720bdc5c79d88f3b3e178882295b5a636d97fe70ff49eb1b021a9a6b96f0f4216bc392219d1 SHA512 eab05a46220339a05d8d4facdce6bfa08c6fc8a858a7b228236ef6c4054207059ef0f53a26bedebe4084a74b510015937fb4477f99612b21412cd75bf0c376a2 -EBUILD pymol-3.0.0.ebuild 2831 BLAKE2B b277127a25bc4b292238b374bd6945e372bbdfc6a7855a3e03c7855dd49fb2c75f3b064fbeb783f6dfc838f3069aeb65139a23caecc858c6557eed34a40cd79e SHA512 890933535af6f7bb0f49b554e6f9ab5fc2134a04c163ef28c61e2fb351faa5fd3c5aa166dd8bc444d649dd5688f1c5a2579acfdaeca41b8ca3f1247f24027351 +EBUILD pymol-3.0.0-r1.ebuild 3372 BLAKE2B 378b1587c25a4592b6e2e503e7280f38d44696a899d5931c6f3e5a2ef11ed5f28d2bd9ba2e8024e6ed223d6bf504a2b76f7b730926eac7bbdbfbb29f986b3287 SHA512 597918ca799ceb6b2a29704ddc96e2b67464d66dd27ce6d32b00294854d34a4abbeb340848f2d3101464b6f263fb4dd07314c54d14fb87be57b07a27ae06522a +EBUILD pymol-3.0.0.ebuild 2958 BLAKE2B 2eac68b0cf15c3369e243b7456e00b1c1119f0d8399bea7321794981f41911bd56bc10713c9102475a054e6a52353cef63c0f9416974bb1db5d91ddd9f6d2dfa SHA512 ca7a597cd909d5a04e77c0afb7e2c07413b13dd42d5788db97defabee23370695299e17193b431eb6190c87a0e06d8e741d2067de973652d1749b244cfeb0254 MISC metadata.xml 495 BLAKE2B 32d321e92c7e7c226747660c314f5cff9aabf9ee41c8a864064432ac9554879db7bf60640993dadae6e00a9b7d1367cb8ab228b63b8797ca84e5618eeeb192cc SHA512 36ef956d111c76182c70c81a830885f540fb2710f696b2711837d4bf1055a8792226f38b827f389a3a3861f259bae1394d6da50c2b33a0ddb4e6940262e1b25d diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-SceneGetDrawFlag-indexing.patch b/sci-chemistry/pymol/files/pymol-3.0.0-SceneGetDrawFlag-indexing.patch new file mode 100644 index 000000000000..c23bf79d6166 --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-3.0.0-SceneGetDrawFlag-indexing.patch @@ -0,0 +1,22 @@ +From 50be59fb4bd6706c7939a659f4477041e2f0619e Mon Sep 17 00:00:00 2001 +From: Jarrett Johnson <36459667+JarrettSJohnson@users.noreply.github.com> +Date: Sat, 6 Apr 2024 22:49:41 -0400 +Subject: [PATCH] PYMOL-4849: Fix SceneGetDrawFlag slot indexing + +--- + layer1/Scene.cpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/layer1/Scene.cpp b/layer1/Scene.cpp +index e4888db6d..ed211bdd6 100644 +--- a/layer1/Scene.cpp ++++ b/layer1/Scene.cpp +@@ -4448,7 +4448,7 @@ int SceneGetDrawFlag(GridInfo * grid, int *slot_vla, int slot) + { + if(((slot < 0) && grid->slot) || + ((slot == 0) && (grid->slot == 0)) || +- (slot_vla && (slot_vla[slot] == grid->slot))) { ++ (slot_vla && (slot >= 0 && slot_vla[slot] == grid->slot))) { + draw_flag = true; + } + } diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-distutils-py3.12.patch b/sci-chemistry/pymol/files/pymol-3.0.0-distutils-py3.12.patch new file mode 100644 index 000000000000..3ab0384bd5f6 --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-3.0.0-distutils-py3.12.patch @@ -0,0 +1,70 @@ +From 3d3c8963798d426e70675c3c40df146e12869b0a Mon Sep 17 00:00:00 2001 +From: Branch Vincent <branchevincent@gmail.com> +Date: Fri, 10 May 2024 22:12:58 -0700 +Subject: [PATCH] replace distutils for python 3.12 (#362) + +Co-authored-by: Jarrett Johnson <jarrett.johnson@schrodinger.com> +--- + create_shadertext.py | 3 +-- + modules/pymol/plugins/installation.py | 7 +++---- + testing/tests/system/pymolwin.py | 1 - + 3 files changed, 4 insertions(+), 7 deletions(-) + +diff --git a/create_shadertext.py b/create_shadertext.py +index 7bae72180..f6857087e 100644 +--- a/create_shadertext.py ++++ b/create_shadertext.py +@@ -7,7 +7,6 @@ + from collections import defaultdict + from os.path import dirname + from subprocess import Popen, PIPE +-from distutils import dir_util + + def create_all(generated_dir, pymoldir="."): + ''' +@@ -30,7 +29,7 @@ def __init__(self, filename): + self.out = cStringIO.StringIO() + self.filename = filename + else: +- dir_util.mkpath(os.path.dirname(filename)) ++ os.makedirs(os.path.dirname(filename), exist_ok=True) + self.out = open(filename, "w") + self.filename = None + def close(self): +diff --git a/modules/pymol/plugins/installation.py b/modules/pymol/plugins/installation.py +index 3a980545b..2fb8f6f03 100644 +--- a/modules/pymol/plugins/installation.py ++++ b/modules/pymol/plugins/installation.py +@@ -45,8 +45,6 @@ def cmp_version(v1, v2): + ''' + Compares two version strings. An empty version string is always considered + smaller than a non-empty version string. +- +- Uses distutils.version.StrictVersion to evaluate non-empty version strings. + ''' + if v1 == v2: + return 0 +@@ -55,8 +53,9 @@ def cmp_version(v1, v2): + if v2 == '': + return 1 + try: +- from distutils.version import StrictVersion as Version +- return cmp(Version(v1), Version(v2)) ++ v1_parts = list(map(int, v1.split('.'))) ++ v2_parts = list(map(int, v2.split('.'))) ++ return (v1_parts > v2_parts) - (v1_parts < v2_parts) + except: + print(' Warning: Version parsing failed for', v1, 'and/or', v2) + return 0 +diff --git a/testing/tests/system/pymolwin.py b/testing/tests/system/pymolwin.py +index 429fd28aa..e7885bd38 100644 +--- a/testing/tests/system/pymolwin.py ++++ b/testing/tests/system/pymolwin.py +@@ -7,7 +7,6 @@ + import subprocess
+ import sys
+ import unittest
+-from distutils.spawn import find_executable
+ from pymol import cmd, CmdException, testing, stored
+
+ @unittest.skipIf(not sys.platform.startswith('win'), 'windows only')
diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-eof-maeffplugin.patch b/sci-chemistry/pymol/files/pymol-3.0.0-eof-maeffplugin.patch new file mode 100644 index 000000000000..8eb8fbde318b --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-3.0.0-eof-maeffplugin.patch @@ -0,0 +1,22 @@ +From f005dde377e3e50b6e3f405939435c5061fa8b63 Mon Sep 17 00:00:00 2001 +From: Jarrett Johnson <36459667+JarrettSJohnson@users.noreply.github.com> +Date: Mon, 22 Apr 2024 11:12:21 -0400 +Subject: [PATCH] PYMOL-4869: Only compare eof token in maeffplugin parser + +--- + contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp +index efaede65b..0547ff91b 100644 +--- a/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp ++++ b/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp +@@ -248,7 +248,7 @@ const char * Tokenizer::token(bool ignore_single) { + char c = peek(); + bool good = false; + ssize_t diff; +- while(state != DONE && c >= 0) { ++ while(state != DONE && c != std::char_traits<char>::eof()) { + // make sure we have space in m_token for 2 more characters + if ((diff = ptr-m_token) >= max_token_size-1) { + m_token = (char *)realloc( m_token, 2*max_token_size ); diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-lto-molfile-plugin.patch b/sci-chemistry/pymol/files/pymol-3.0.0-lto-molfile-plugin.patch new file mode 100644 index 000000000000..445fc6bc3a10 --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-3.0.0-lto-molfile-plugin.patch @@ -0,0 +1,187 @@ +From 9d3061ca58d8b69d7dad74a68fc13fe81af0ff8e Mon Sep 17 00:00:00 2001 +From: Jarrett Johnson <jarrett.johnson@schrodinger.com> +Date: Thu, 5 Sep 2024 11:20:02 -0400 +Subject: [PATCH] Symbol renaming in molfile_plugin and internal linkage + +Fixes #395 +--- + contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h | 10 +++++----- + .../uiuc/plugins/molfile_plugin/src/parm7plugin.cpp | 8 +++++--- + contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp | 2 ++ + layer0/Isosurf.cpp | 6 ++++-- + layer0/Tetsurf.cpp | 6 ++++-- + ov/src/OVOneToAny.cpp | 2 ++ + ov/src/OVOneToOne.cpp | 2 ++ + 7 files changed, 24 insertions(+), 12 deletions(-) + +diff --git a/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h b/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h +index 21d967d79..6bd6ddb08 100644 +--- a/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h ++++ b/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h +@@ -59,7 +59,7 @@ + #endif + + +-typedef struct parm { ++typedef struct parm7 { + char title[85]; + char version[85]; + int IfBox, Nmxrs, IfCap, +@@ -70,7 +70,7 @@ typedef struct parm { + Ipatm, Natcap,Ifpert,Nbper,Ngper,Ndper,Mbper,Mgper,Mdper, + Numextra; + _REAL Box[3], Cutcap, Xcap, Ycap, Zcap; +-} parmstruct; ++} parm7struct; + + static int read_parm7_flag(FILE *file, const char *flag, const char *format) { + char buf[1024]; +@@ -359,10 +359,10 @@ static void close_parm7_file(FILE *fileptr, int popn) { + + static const char *parm7 = "%8d%8d%8d%8d%8d%8d%8d%8d%8d%8d\n"; + +-static parmstruct *read_parm7_header(FILE *file) { ++static parm7struct *read_parm7_header(FILE *file) { + char sdum[512]; +- parmstruct *prm; +- prm = new parmstruct; ++ parm7struct *prm; ++ prm = new parm7struct; + + /* READ VERSION */ + fgets(sdum, 512, file); +diff --git a/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp +index faf2717c6..2d46553b4 100644 +--- a/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp ++++ b/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp +@@ -24,13 +24,15 @@ + #include "molfile_plugin.h" + #include "ReadPARM7.h" + ++namespace { + typedef struct { +- parmstruct *prm; ++ parm7struct *prm; + int popn; + FILE *fd; + int nbonds; + int *from, *to; + } parmdata; ++} + + static void *open_parm7_read(const char *filename, const char *,int *natoms) { + FILE *fd; +@@ -39,7 +41,7 @@ static void *open_parm7_read(const char *filename, const char *,int *natoms) { + fprintf(stderr, "parm7plugin) Cannot open parm file '%s'\n", filename); + return NULL; + } +- parmstruct *prm = read_parm7_header(fd); ++ parm7struct *prm = read_parm7_header(fd); + if (!prm) { + close_parm7_file(fd, popn); + return NULL; +@@ -58,7 +60,7 @@ static void *open_parm7_read(const char *filename, const char *,int *natoms) { + + static int read_parm7_structure(void *mydata, int *optflags, molfile_atom_t *atoms) { + parmdata *p = (parmdata *)mydata; +- const parmstruct *prm = p->prm; ++ const parm7struct *prm = p->prm; + FILE *file = p->fd; + char buf[85]; + char field[85]; +diff --git a/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp +index acabcb1b5..4996383e1 100644 +--- a/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp ++++ b/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp +@@ -24,12 +24,14 @@ + #include "ReadPARM.h" + #include "molfile_plugin.h" + ++namespace { + typedef struct { + ReadPARM *rp; + FILE *parm; + int natoms; + int *from, *to; + } parmdata; ++} + + static void *open_parm_read(const char *filename, const char *, + int *natoms) { +diff --git a/layer0/Isosurf.cpp b/layer0/Isosurf.cpp +index 77cf42eeb..b2dfaedd7 100644 +--- a/layer0/Isosurf.cpp ++++ b/layer0/Isosurf.cpp +@@ -44,11 +44,13 @@ Z* ------------------------------------------------------------------- + + #define I4(field,P1,P2,P3,P4) ((field)->get<int>(P1,P2,P3,P4)) + +-typedef struct PointType { ++namespace { ++struct PointType { + float Point[3]; + int NLink; + struct PointType* Link[4]; +-} PointType; ++}; ++} + + #define EdgePtPtr(field,P2,P3,P4,P5) ((field)->ptr(P2,P3,P4,P5)) + +diff --git a/layer0/Tetsurf.cpp b/layer0/Tetsurf.cpp +index 0d78b535e..cb2f5b37b 100644 +--- a/layer0/Tetsurf.cpp ++++ b/layer0/Tetsurf.cpp +@@ -38,12 +38,14 @@ Z* ------------------------------------------------------------------- + + #define I3(field,P1,P2,P3) ((field)->get<int>(P1,P2,P3)) + +-typedef struct { ++namespace { ++struct PointType { + float Point[3]; + float Normal[3]; + int NormalFlag; + int Link; +-} PointType; ++}; ++} + + typedef struct { + PointType *p[3]; +diff --git a/ov/src/OVOneToAny.cpp b/ov/src/OVOneToAny.cpp +index 1a675a51b..5dbbc498c 100644 +--- a/ov/src/OVOneToAny.cpp ++++ b/ov/src/OVOneToAny.cpp +@@ -8,11 +8,13 @@ + + /* FYI: "up" stands for UniquePair -- a precursor to OneToAny */ + ++namespace { + typedef struct { + int active; + ov_word forward_value, reverse_value; + ov_size forward_next; + } up_element; ++} + + struct _OVOneToAny { + OVHeap *heap; +diff --git a/ov/src/OVOneToOne.cpp b/ov/src/OVOneToOne.cpp +index 6dfa8f457..4e9baf9c6 100644 +--- a/ov/src/OVOneToOne.cpp ++++ b/ov/src/OVOneToOne.cpp +@@ -8,11 +8,13 @@ + + /* FYI: "up" stands for UniquePair -- a precursor to OneToOne */ + ++namespace { + typedef struct { + int active; + ov_word forward_value, reverse_value; + ov_size forward_next, reverse_next; + } up_element; ++} + + struct _OVOneToOne { + OVHeap *heap; diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-numpy2.patch b/sci-chemistry/pymol/files/pymol-3.0.0-numpy2.patch new file mode 100644 index 000000000000..7cf2884ee201 --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-3.0.0-numpy2.patch @@ -0,0 +1,35 @@ +From 758cec338057b23007ffd14c960634ff0ee24af1 Mon Sep 17 00:00:00 2001 +From: Jarrett Johnson <jarrett.johnson@schrodinger.com> +Date: Tue, 27 Aug 2024 20:06:57 -0400 +Subject: [PATCH] Make numpy2 compatible + +--- + layer2/ObjectMap.cpp | 1 + + modules/chempy/brick.py | 2 +- + 2 files changed, 2 insertions(+), 1 deletion(-) + +diff --git a/layer2/ObjectMap.cpp b/layer2/ObjectMap.cpp +index ada826f8a..62e3457a4 100644 +--- a/layer2/ObjectMap.cpp ++++ b/layer2/ObjectMap.cpp +@@ -5596,6 +5596,7 @@ static int ObjectMapNumPyArrayToMapState(PyMOLGlobals * G, ObjectMapState * ms, + void * ptr; + + #ifdef _PYMOL_NUMPY ++ import_array1(0); + PyArrayObject * pao = (PyArrayObject *) ary; + const int itemsize = PyArray_ITEMSIZE(pao); + #endif +diff --git a/modules/chempy/brick.py b/modules/chempy/brick.py +index fc514eb3a..e4c0f1bbb 100644 +--- a/modules/chempy/brick.py ++++ b/modules/chempy/brick.py +@@ -31,7 +31,7 @@ def from_numpy(cls, data, grid, origin=(0.0, 0.0, 0.0)): + @param range: 3f sequence + @param origin: 3f sequence + ''' +- data = numpy.asfarray(data) ++ data = numpy.asarray(data, dtype=numpy.float64) + assert len(data.shape) == 3 + + self = cls() diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-py3.12-progress.patch b/sci-chemistry/pymol/files/pymol-3.0.0-py3.12-progress.patch new file mode 100644 index 000000000000..b09f36048b20 --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-3.0.0-py3.12-progress.patch @@ -0,0 +1,26 @@ +From 11325a6014565700be9673236c9b7b6c856ea6d9 Mon Sep 17 00:00:00 2001 +From: Jarrett Johnson <jarrett.johnson@schrodinger.com> +Date: Wed, 28 Aug 2024 22:07:15 -0400 +Subject: [PATCH] Python 3.12 TypeError: convert progress to int for progress + bar + +--- + modules/pmg_qt/pymol_qt_gui.py | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/modules/pmg_qt/pymol_qt_gui.py b/modules/pmg_qt/pymol_qt_gui.py +index f2d663204..6e935b0d6 100644 +--- a/modules/pmg_qt/pymol_qt_gui.py ++++ b/modules/pmg_qt/pymol_qt_gui.py +@@ -929,9 +929,9 @@ def command_set_cursor(self, i): + return self.lineedit.setCursorPosition(i) + + def update_progress(self): +- progress = self.cmd.get_progress() ++ progress = int(self.cmd.get_progress() * 100) + if progress >= 0: +- self.progressbar.setValue(progress * 100) ++ self.progressbar.setValue(progress) + self.progressbar.show() + self.abortbutton.show() + else: diff --git a/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild b/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild new file mode 100644 index 000000000000..aeb6bc85c7e1 --- /dev/null +++ b/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild @@ -0,0 +1,123 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..12} ) +DISTUTILS_USE_PEP517="setuptools" +DISTUTILS_EXT=1 + +inherit desktop flag-o-matic xdg distutils-r1 + +DESCRIPTION="A Python-extensible molecular graphics system" +HOMEPAGE="https://www.pymol.org/" +SRC_URI="https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +S="${WORKDIR}"/${PN}-open-source-${PV} + +LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" #844991 +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="+netcdf web" + +DEPEND=" + dev-cpp/msgpack-cxx + dev-libs/mmtf-cpp + dev-python/numpy[${PYTHON_USEDEP}] + sys-libs/zlib + media-libs/freetype:2 + media-libs/glew:0= + media-libs/glm + media-libs/libpng:0= + netcdf? ( sci-libs/netcdf:0= ) +" +BDEPEND="test? ( >=dev-cpp/catch-2:0 )" +RDEPEND=" + ${DEPEND} + media-video/mpeg-tools + dev-python/pyopengl[${PYTHON_USEDEP}] + dev-python/PyQt5[opengl,${PYTHON_USEDEP}] + dev-python/pmw[${PYTHON_USEDEP}] + sci-chemistry/chemical-mime-data +" + +distutils_enable_tests pytest + +# FIXME: We need to still figure out about how to make all the tests pass +# https://bugs.gentoo.org/932127 +RESTRICT="test" + +PATCHES=( + "${FILESDIR}/${P}-distutils-py3.12.patch" + "${FILESDIR}/${P}-SceneGetDrawFlag-indexing.patch" + "${FILESDIR}/${P}-eof-maeffplugin.patch" + "${FILESDIR}/${P}-numpy2.patch" + "${FILESDIR}/${P}-py3.12-progress.patch" + "${FILESDIR}/${P}-lto-molfile-plugin.patch" +) + +python_prepare_all() { + sed \ + -e "s:\"/usr:\"${EPREFIX}/usr:g" \ + -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ + -i setup.py || die + + sed \ + -e "s:/opt/local:${EPREFIX}/usr:g" \ + -e '/ext_comp_args/s:\[.*\]:[]:g' \ + -i setup.py || die + sed \ + -e "s:\['msgpackc'\]:\['msgpack'\]:g" \ + -i setup.py || die + + append-cxxflags -std=c++17 + + distutils-r1_python_prepare_all +} + +python_configure_all() { + use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins ) +} + +python_install() { + distutils-r1_python_install \ + --pymol-path="${EPREFIX}/usr/share/pymol" + + sed \ + -e '1i#!/usr/bin/env python' \ + "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die + python_doscript "${T}"/${PN} +} + +python_test() { + "${EPYTHON}" -m pymol -ckqy testing/testing.py --offline --no-mmlibs --no-undo --run all || die +} + +python_install_all() { + distutils-r1_python_install_all + + # Move data to correct location + dodir /usr/share/pymol + mv "${D}/$(python_get_sitedir)"/pymol/pymol_path/* "${ED}/usr/share/pymol" || die + + # These environment variables should not go in the wrapper script, or else + # it will be impossible to use the PyMOL libraries from Python. + cat >> "${T}"/20pymol <<- EOF || die + PYMOL_PATH="${EPREFIX}/usr/share/pymol" + PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" + PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" + EOF + + doenvd "${T}"/20pymol + + newicon "${S}"/data/pymol/icons/icon2.svg ${PN}.svg + make_desktop_entry "${PN} %u" PyMol ${PN} \ + "Graphics;Education;Science;Chemistry;" \ + "MimeType=chemical/x-pdb;chemical/pdby;chemical/x-mdl-sdfile;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;chemical/x-macromodel-input;chemical/x-vmd;" + + if ! use web; then + rm -rf "${D}/$(python_get_sitedir)/web" || die + fi + + rm -f "${ED}"/usr/share/${PN}/LICENSE || die +} diff --git a/sci-chemistry/pymol/pymol-3.0.0.ebuild b/sci-chemistry/pymol/pymol-3.0.0.ebuild index 150f7732d930..b6ec9fbef1e3 100644 --- a/sci-chemistry/pymol/pymol-3.0.0.ebuild +++ b/sci-chemistry/pymol/pymol-3.0.0.ebuild @@ -26,19 +26,20 @@ IUSE="+netcdf web" DEPEND=" dev-cpp/msgpack-cxx dev-libs/mmtf-cpp - dev-python/pyopengl[${PYTHON_USEDEP}] - dev-python/PyQt5[opengl,${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pmw[${PYTHON_USEDEP}] + sys-libs/zlib media-libs/freetype:2 media-libs/glew:0= media-libs/glm media-libs/libpng:0= - media-video/mpeg-tools - sys-libs/zlib netcdf? ( sci-libs/netcdf:0= ) " -RDEPEND="${DEPEND} +RDEPEND=" + ${DEPEND} + media-video/mpeg-tools + dev-python/pyopengl[${PYTHON_USEDEP}] + dev-python/PyQt5[opengl,${PYTHON_USEDEP}] + dev-python/pmw[${PYTHON_USEDEP}] sci-chemistry/chemical-mime-data " @@ -66,6 +67,11 @@ python_prepare_all() { } python_configure_all() { + # -Werror=odr + # https://bugs.gentoo.org/933235 + # https://github.com/schrodinger/pymol-open-source/issues/395 + filter-lto + use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins ) } diff --git a/sci-chemistry/threeV/Manifest b/sci-chemistry/threeV/Manifest index a211d0d34124..57bddec7fa8a 100644 --- a/sci-chemistry/threeV/Manifest +++ b/sci-chemistry/threeV/Manifest @@ -1,5 +1,5 @@ AUX threeV-1.2-format-security.patch 7116 BLAKE2B 6530128ba9ebe224bea5022af1b888181af3a37371dceb23f1900d2dfb94255bfae9362ad980eb48f170795f30bbb9dfbaf72a2ec3ce023756b0a06c60de7eee SHA512 9ed991640b297090a4b35a8d04f67da4eba21c0cf828a06120fd31a55ca809a3485da8e85db759311c1b136b37ae3214c5c1000cc8fb54491f59f454b22f87d3 AUX threeV-1.2-gentoo.patch 3085 BLAKE2B b6bf352a7de785ee5312b52d15f56d85fd1bd86c8d7d87e321237058722dc6ea1b416f259fbcf17498e5ad38345d5b1b69a9e67df57beeaa2874b046b3917691 SHA512 493fc39b2d3cf1325ea00ad572e8c4c62ae48f55a82fd5eb6a1f7e91900ecfdf6cb174ec43b2fb748d6708099ddb395af34045a4439f1dbc0c574169539344a0 DIST 3v-1.2.tgz 599194 BLAKE2B cc5f14cfe4d9adca54925ee9edea2616019c9780878e2a300dcdd9492b331fa9f186473548b4a38b2f006380440b6d53c52cf567f02dc1fb6342706fb21ecbb8 SHA512 063747e46be1ab8af585909185b735edbbb760945f9d4d345d478a264e3d90c551d72f578239e7eff7768482d18b34d2b00831f87e109ec87cb36b0fd4e6a757 -EBUILD threeV-1.2-r1.ebuild 745 BLAKE2B acd34138ac15191833df2f67d9cda08272e6e993da7b7b9941b0f36edfbfae48cb87562ace2b60346f6a6c803d65f9399f2e7703c8ab157d9baf3bdd616882f0 SHA512 eec0425c83705264670ccba3d8b839717bf1135114fe7baa637d638fe3214c6bc2ec9e7331b9bfc11e6e1bf530ed6ea73164c400c4344d9ca65b0b244338ee02 +EBUILD threeV-1.2-r2.ebuild 687 BLAKE2B 07fc0844f79adc8c4fff4d9a72de58f0849afb9b549099cac3d6d793cb904c042e4ebea0bdb6b5bd50469b23b79cd3f9c4bf7134842f61c652c03d0195b8bc8e SHA512 3e71a0da40e6a1ada6ec1f25937241c489fb9abe5d52c6a3575acb057b43072944473292091cc1b0b773e0b238f6b92a58c73b27b34738701d1fd0ed13a85f77 MISC metadata.xml 266 BLAKE2B a03b1fcf7148cf43fb829f619c218219bcd4e66c45d12f563113401e3ae0b06cb0df9a8c0af01ea97e21453638d627d420e7df5b9b0d330ef1752253faa8aa32 SHA512 1dc293fa0d0296eba18ac2cbcd57f47ffc6cc822bf0d76e1cc86cb046700201f703d705375b5555b88cbe8780ef3750be05b8f9f8de092693e6d165c1734e049 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/tinker/Manifest b/sci-chemistry/tinker/Manifest index 0d3471385728..46bf0037f904 100644 --- a/sci-chemistry/tinker/Manifest +++ b/sci-chemistry/tinker/Manifest @@ -1,4 +1,4 @@ AUX 8.2.1-openmp.patch 559 BLAKE2B 254a7b5d5d40bec938420527ad77e4ec96b9cee50392137eab3370df35a00a00b9488b5cd95c4e3c52d4904a6093216a782f52c82c2141cd913c6cf10f2fbcc7 SHA512 799b488ddba95ec75c2f5f97bdba10e297cad12d23239354b7d66af47b4e9ef1496e8f6b8a7446f85827a8303105af7552616bc865a4e8114b89d3e6e3302ed6 DIST tinker-8.2.1.tar.gz 33015410 BLAKE2B 0b7c94662248761459cf9d681056f5cf9c4d669a790a522f23f800bf355235f6a9f392e008b13d14cf1e17d9725abb6512077c24ff7772108d69c9cf35b43e6e SHA512 5039078781d1ce226456882dd95ad15715f1e91829d26efcdb29ceedc213973883699eb6710b0a162a74208809305b7fee734b175139e6df63d0460fe5751ae7 -EBUILD tinker-8.2.1-r1.ebuild 2387 BLAKE2B 2eec46ab90656d4336f4c130bac95f76aae850ce7bea72ce7ba5fde37897f4345c7ff8e714190dad5279592ad51fae37b5c96190614a67725d6f23c534ca94c3 SHA512 f89dcf18394067c9485fb8a85c8a6bd841bf485f3deb6671ed457e995bf008e6db64206b0903cda9e0e86dd4ffc9253ee2f1f8b469688d044e629c506a5c3abb +EBUILD tinker-8.2.1-r1.ebuild 2529 BLAKE2B 3ed97f45a8850f58cc79216127c51acca2d85f78f32e7d753e4e98e7a7bda004373664fe60cdd38f66b12d9f6c79fe70f1f78dd33d9ff27a9cca9373716e66a0 SHA512 cf263a10c4ff53074b4ecaa1c7f4fd936291043b0aafa47af25c371efd5a8b761e349e1d55bd65c03567b9970579996599657bda34bfb431a4918dcd7582defa MISC metadata.xml 349 BLAKE2B e2a70d46ddb77f5ea51a0d6d378cdcbe2c897464127bd86c34ec43615588a509ff038e035c24855c305248789eb0708d51d21208d2cc65e8507e4f767172582f SHA512 0cb63aaf7aadd62ea12289936ea25c8f5233c8784af96b71f103794d6bd7e0711b53728a2840f5768df2652c0b19e220b1f35223dbf27fc65f7871b6e3b4c756 diff --git a/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild b/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild index 9964b16b549f..8689a962c2fd 100644 --- a/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild +++ b/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -50,6 +50,11 @@ src_prepare() { } src_compile() { + # tests fail with weird results under LTO + # https://bugs.gentoo.org/878059 + # https://github.com/TinkerTools/tinker/issues/159 + filter-lto + local javalib= _omplib _fftwlib for i in $(java-config -g LDPATH | sed 's|:| |g'); do [[ -f ${i}/libjvm.so ]] && javalib=${i} diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest index b0ec15c4b961..1135f253ff10 100644 --- a/sci-chemistry/vmd/Manifest +++ b/sci-chemistry/vmd/Manifest @@ -1,4 +1,5 @@ DIST vmd-1.9.4_alpha57-gentoo-patches.tar.xz 14612 BLAKE2B e50a2fc734038207174dd5cc525f01824ce324a65b8ce604f83862ce50be6b1950d199188a717e2368b2b050256a4705662009e3530d621b19c52bb109b6a844 SHA512 6283076e47dfcd780bbc94f9ca2b044a028a472c09d78616d373813d81ec764bf1697e56a8f487f9f0999cf409c0f141bf248156f60851073347d1b640a6953c DIST vmd-1.9.4a57.src.tar.gz 43155120 BLAKE2B de0da96f6681c24e7b1d38890f109088187198cbdddb3d86d783322e837b7a71224085699f3addf2833cf293ab2689f06ab47df284b8fbe080162740094ae844 SHA512 0a3726d8fa279ac62c368cd18724cd09535618454ff6e299d147291ef5d4198ad9d58a94f0b05699ec8a23128753c55e7397c95a5ce194e36d3fabef1bcf454c -EBUILD vmd-1.9.4_alpha57.ebuild 7517 BLAKE2B a848eae8ebe51dfb121881094fa961a6efc21a996805b740c054c23eda23acf9597f027f60cec94f6afab38e68873197f2887c839a8c5b61086b8116208c9648 SHA512 30ecd04d695fee5321b00ea0b69c07588af65523909f8b74dd333f4694d0c2167e288d61993272f543699a0c08cfa4cc201068a1f1e50d2b8dabfcc02a5b818a +EBUILD vmd-1.9.4_alpha57-r1.ebuild 7407 BLAKE2B a2dd25449e23acbb09181e939b27c0bd5fd81344ffb1d64f49dc26a1bc89a8e550418c27bf436d291bb91cda4f1ce3d0b520ac43e5eba065ddc3ae54154f77db SHA512 480b04d19e75c51f6ecc77e2decca4b9e645985f5d4f2f7ee5f441a6c8530658e5c8d588fd3f77457c9cce8e4b43203281eb295cb985a926907a62459cb25557 +EBUILD vmd-1.9.4_alpha57.ebuild 7516 BLAKE2B 3694b45e09af9f1ca33854543a902230bef3b72f1c2b0cf0f0e446b0e1276720e84da17eee0c0bb70eb4321c7602bdb7e2490e619a260f616d9d664c53ac4127 SHA512 80d1c81faca51066b5a4c3e6f3bf437b3ac3e5c01c0b4d156d6bac219f4dc90e1652ef77032539cfff73e62b9e19a381ec30a8a77a0de32d724c32faf39730bf MISC metadata.xml 697 BLAKE2B fe7fd00b1802dba4e503212cf8e0a91723dd6d255e346bca099bb2eb8cdb6291b27d1cbe9229e652c6f113e93cc3285bbf346977647d186f5403bd153a2c6d17 SHA512 f1bacf679ce42835e525265af48429d58d65a9aedc268e699cba731a1ea0bbe481777c726c2e1fd6a0ad7465c0e666f8f58145619d985cd0675eb1aff6b15472 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/vmd/vmd-1.9.4_alpha57.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild index af9f38835c45..e0628f111574 100644 --- a/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild +++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..12} ) inherit cuda desktop prefix python-single-r1 toolchain-funcs xdg @@ -15,9 +15,10 @@ 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}/${MY_P}" +LICENSE="vmd" SLOT="0" -LICENSE="vmd" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="cuda gromacs msms povray sqlite tachyon xinerama" @@ -57,9 +58,6 @@ RDEPEND="${CDEPEND} msms? ( sci-chemistry/msms-bin ) povray? ( media-gfx/povray ) " - -S="${WORKDIR}/${MY_P}" - VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" # Binary only plugin diff --git a/sci-chemistry/votca/Manifest b/sci-chemistry/votca/Manifest index f8eb4f2293fe..adcbcc0ddad3 100644 --- a/sci-chemistry/votca/Manifest +++ b/sci-chemistry/votca/Manifest @@ -1,4 +1,4 @@ DIST votca-2022.1.tar.gz 61692029 BLAKE2B c58023098f596d7c6f301e94883df3e442761b8c1009823ef5a07e788fabb2a0fa572326e0d614f8102104ef5dcec89505da1c911bb703126c123d2a25a2031e SHA512 dda5cbf1835440abd1b0b511275e10e5facfa9f133062ae082cca4f5654e4af0be0b574b87c70004c0d07920519927bac5620b89ce073de9985bdf792f0dd21a -EBUILD votca-2022.1-r1.ebuild 1871 BLAKE2B 52840f4654fba69077c0950ba5ffee7abb9c4cd0c937bfe3331aa70ec1e0dc44af2309ddba033a660f31d77ade08bd74da90551586d16ceb4d71aa2894a1d7b0 SHA512 ea82eb9c580ff6e5337bf1d96d3c8c716d207d5515df03c466e3a775a89aeba59bc533ee3f047cae23bcefc3653c3a4f98cf752ca4585e7cbe61bab1a6059239 -EBUILD votca-9999.ebuild 1872 BLAKE2B cf72b8d2731e2dd7a11609a760bcdd918579eca872c8ffdc96931220df192d14e535b7a2c4e23861a44a0fa3acd56c5a0e65a324adf9322ecf7d79ebb0916f02 SHA512 7f068a887eb57eba03b83589cb474a5269179233b300f5f3c861a21f9aa40397ed8407cb89046c19f6ea42b89ae51b3b83e43fd73dd9c78952fbbf2aac0127a9 +EBUILD votca-2022.1-r1.ebuild 1872 BLAKE2B 3171180eafc258d421d6f9fdac5220b5421aae74724d8aae06e208c6be05f502e379dfb40800fe8364e445212df600291ef1db9e65c094bd9d704ee88d189b45 SHA512 c8134faa9fa5bd29526470260c0a30d148231d4ef8e460af037f7c2775c969525f9da19633007bc02c4aa68d2ed48cf9570ff134f73f437f004288118d6b7c2c +EBUILD votca-9999.ebuild 1872 BLAKE2B 3171180eafc258d421d6f9fdac5220b5421aae74724d8aae06e208c6be05f502e379dfb40800fe8364e445212df600291ef1db9e65c094bd9d704ee88d189b45 SHA512 c8134faa9fa5bd29526470260c0a30d148231d4ef8e460af037f7c2775c969525f9da19633007bc02c4aa68d2ed48cf9570ff134f73f437f004288118d6b7c2c MISC metadata.xml 465 BLAKE2B 3fe0aa7dbb87cfe5ec1b5d1500dccb087f2f582982ab7d41687675f7ad38ce3eae1c12141ab8a020d467114cc7017da64ceaa65a10bb37f55ff3aed3e113378b SHA512 b204a6c45aea2fc428a0e421cfc22a218e59ef4f9cb8e352bdf8983272c9f28baf2beec4650ca65e8fb640d713dbdb39d2f43b1ccfce8329b0c3669e6b4562c8 diff --git a/sci-chemistry/votca/votca-2022.1-r1.ebuild b/sci-chemistry/votca/votca-2022.1-r1.ebuild index ad5aa680498e..88d3c6a469fb 100644 --- a/sci-chemistry/votca/votca-2022.1-r1.ebuild +++ b/sci-chemistry/votca/votca-2022.1-r1.ebuild @@ -1,8 +1,8 @@ # Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 -PYTHON_COMPAT=( python3_{9..11} ) +EAPI=8 +PYTHON_COMPAT=( python3_{10..12} ) inherit bash-completion-r1 cmake python-single-r1 diff --git a/sci-chemistry/votca/votca-9999.ebuild b/sci-chemistry/votca/votca-9999.ebuild index 04064219f641..88d3c6a469fb 100644 --- a/sci-chemistry/votca/votca-9999.ebuild +++ b/sci-chemistry/votca/votca-9999.ebuild @@ -1,8 +1,8 @@ # Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 -PYTHON_COMPAT=( python3_{9..10} ) +EAPI=8 +PYTHON_COMPAT=( python3_{10..12} ) inherit bash-completion-r1 cmake python-single-r1 @@ -16,7 +16,7 @@ else MY_PV="${PV}" fi SRC_URI="https://github.com/votca/votca/archive/v${MY_PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux" + KEYWORDS="amd64 ~x86 ~amd64-linux" S="${WORKDIR}/votca-${MY_PV}" fi diff --git a/sci-chemistry/wxmacmolplt/Manifest b/sci-chemistry/wxmacmolplt/Manifest index 15e8ec679986..eed90ecfb010 100644 --- a/sci-chemistry/wxmacmolplt/Manifest +++ b/sci-chemistry/wxmacmolplt/Manifest @@ -1,6 +1,3 @@ -AUX wxmacmolplt-7.5-glew.patch 232 BLAKE2B 9e0bd2849cc20664ca4a6b6678d2d78a723ae3e730225355dd70db0cac56d501c14aaa34d86d2ff87932feb950178a7245a943b763bde728f64a07a49ed4ba29 SHA512 cf1f77f9a86224b866f55154316a044314fda47a82de9b5be4ee58ed4ea8f4a07f9540e7060f477249b773e147739f15f43df293110045bdbca9567c60fbd5dc -DIST wxmacmolplt-7.5.tar.gz 1965376 BLAKE2B 01033266ae66a215582a62690e792ca4ae82c8a8885fe277e2e77ee67ff70f02f6a9c10467ea6f3cee15933c6c89ba3c6137c9d29e47322ac4f395a3efd41383 SHA512 a1064d5068136b2a91328c7f912ff57d4741081d6d61437e7b4567fbf732917485b391493d637b8892bdad50b539363cfa9c778bb35407a9c0a2bfed20e42bc0 DIST wxmacmolplt-7.7.2.tar.gz 2012054 BLAKE2B 0e419d9700dd6461a4520722f43cc36cdaa2f51920868a868bdd58db169ed92f88c71d4ce0d79446c4c564eb794f7327b0eef5f87d9ab5a639829287b29482d6 SHA512 bf4b3126bbc8657a604f8dee8b022a17dbf4633a877318ceb45d803456acb0da007c2edae23f581fb6eeafd6ea411d147fbc076acb07aba3dcb8ee55b9c486fa -EBUILD wxmacmolplt-7.5-r1.ebuild 986 BLAKE2B 67cccea1d2e7886ee67f78ac54548047c2fe889dedfef45956a4614149d5597fd0376f0f01fd59085c9f925faa2284c2c22d4bae2d8ee98f2eca3be6b06e96ed SHA512 6e1d9051621a36deb7aeb997aa93a0b5becea1b3f7512fc56d2ee97788b5a9bedace25fb40a7a7b4e77a76830e7f8aa61ad0c32ea3e1afdb66b744197d50daf0 EBUILD wxmacmolplt-7.7.2.ebuild 982 BLAKE2B edc3b4383a20ec6039472319273947988aa77de31622a40bd604857560684612d79dd6743c2048fc423e928c5a9c8b45e38899568a68de32069591b7593ef2b7 SHA512 99e5cf215f4ef74d6c7480b9aa1732cc1eda079634e2e09e61b83f080b9093febea8d48c77d4e5dbf20bc32c3eecfef9e26b233ec7e549818b3714b13e8ac82f MISC metadata.xml 717 BLAKE2B e2344ebd6332d01a309edb0951483adff1342584fd1a9a6b6890c4cae7bba86f8e9f874b4200726845c1aed7712a4459fddda27ae544ee98da63098e897b499e SHA512 169c1aa0ff6cdfe7ed5e155bd1bdb2ea817c59501dde6c7caa1d25bc4826341516731e3082bf7960cc6f87fdf2a26983c04e26baea21b7bdff815eef45e4521b 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 f4e1a6e0072a..09c641ceac9d 100644 --- a/sci-chemistry/xds-bin/Manifest +++ b/sci-chemistry/xds-bin/Manifest @@ -1,4 +1,4 @@ -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 -EBUILD xds-bin-20170930.ebuild 1174 BLAKE2B 9a5a18719f52eab2f114ce58ba6ade158ae138b70c092967d5ed0adeae6867963c4cf6391f6bdedd0296a56fad46ab1214cde0faa02c4dab701d572268f3b8f6 SHA512 47963c7d31eaa1d6f2eaf172ef67a7d448e3bec36a9e6da35f85532bb878996ef6791977efd06874e0d3d790820306214e190af1ea07bca30f3320ed64605470 +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 +EBUILD xds-bin-20240831.ebuild 1459 BLAKE2B a03054c1af3d8ad3b972a08ca0bf6e07d252b047ad3fea490e8e71d751d33e9969d7853f1b00b6ee2080d5e10bfefd8a0e085a9eb4f25cbbf9f39ad3a55ff445 SHA512 4af84bc488142b629636b3a9516d3b56944b4078c865ab10c5acc0a8898b105c5677ad9bb588cc58823a6d34275dd8c6eb9610116ff748e3c55fc31ce75a2c79 MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c 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 d49a26f26741..000000000000 --- a/sci-chemistry/xyza2pipe/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -AUX xyza2pipe-20121001-gentoo.patch 3974 BLAKE2B cf3f4b58c6348a6295b7874ca20d7d88f6477e1174b54bac7089898ff7509fbf07d8d34aab2d333059c67f7ccc9d1b99e4e40c9bfd8a327f600fc4578a2f1a06 SHA512 7b8be1fd799d65e9a600766afb21e95a4722eff8a657f88d0adaf5aaf11ed369f6d8a27f3e003337570837abc45cfa9e758d1219af275773f79b81d1c1c322c4 -DIST xyza2pipe-20121001.tgz 61002 BLAKE2B 648e65b63cc0b363dd0087b7ef64a1e287654a165baaf7d967821f11cffb70dd7f0da864dfa3b915553546c8cbbc83fda411d9b979551d3d72334db6580e5d64 SHA512 b64abf46a8d7f3530eecaeec3bc8b143600c6823174a22727868087c2f7f17af0b538a0521e3a29806dc608b003948a1e31296ab395bc3c0089c5dc7a391d855 -EBUILD xyza2pipe-20121001.ebuild 682 BLAKE2B a1cbd50a946dc37ab1e55f998b2ad6631e53fd6138f886009ef28e4a121721c5a8e6ffcdd0d79c4b387e2016b456c14d9b3db039f95bd6d6c85f774d8fff71b2 SHA512 4253c166e0a2101b3a5b91aed25193107d588cfbc3db07b66f64ab98bb2888a5e3342d093db15c9686be6519d3ad3372cd6b53f52a4091ee35a458d210c428e6 -MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c 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 -} |