From 89553b6b47f66268074b385593005eacd7b65ccf Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 17 Sep 2023 23:04:25 +0100 Subject: gentoo auto-resync : 17:09:2023 - 23:04:24 --- .../GromacsWrapper/GromacsWrapper-0.8.2.ebuild | 40 ------- .../GromacsWrapper/GromacsWrapper-0.8.5.ebuild | 40 +++++++ sci-chemistry/GromacsWrapper/Manifest | 4 +- sci-chemistry/Manifest.gz | Bin 9523 -> 9529 bytes sci-chemistry/chemex/Manifest | 4 +- sci-chemistry/chemex/chemex-2022.3.4.ebuild | 42 -------- sci-chemistry/chemex/chemex-2022.3.6.ebuild | 43 ++++++++ sci-chemistry/tinker/Manifest | 4 +- sci-chemistry/tinker/metadata.xml | 3 + sci-chemistry/tinker/tinker-8.2.1-r1.ebuild | 115 +++++++++++++++++++++ sci-chemistry/tinker/tinker-8.2.1.ebuild | 113 -------------------- 11 files changed, 207 insertions(+), 201 deletions(-) delete mode 100644 sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.2.ebuild create mode 100644 sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.5.ebuild delete mode 100644 sci-chemistry/chemex/chemex-2022.3.4.ebuild create mode 100644 sci-chemistry/chemex/chemex-2022.3.6.ebuild create mode 100644 sci-chemistry/tinker/tinker-8.2.1-r1.ebuild delete mode 100644 sci-chemistry/tinker/tinker-8.2.1.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.2.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.2.ebuild deleted file mode 100644 index cf12f39f51df..000000000000 --- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.2.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -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 new file mode 100644 index 000000000000..e5c508fd6ca1 --- /dev/null +++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.5.ebuild @@ -0,0 +1,40 @@ +# 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/Manifest b/sci-chemistry/GromacsWrapper/Manifest index 20f6d340c98d..59c53091950e 100644 --- a/sci-chemistry/GromacsWrapper/Manifest +++ b/sci-chemistry/GromacsWrapper/Manifest @@ -1,5 +1,5 @@ -DIST GromacsWrapper-0.8.2.tar.gz 1954926 BLAKE2B c05995667f925a7519e07e59519e985693effa2fd511d228d236bff978d05430d422003e1360f9fda26564e40bb69183ae8e9b7334e0427c2b177f019df38a6a SHA512 b8a3e7da43eaabaf0fe12f4c06ff80f018847f9386c16eb66c96b3840c66b79d02ee47e675c08ed81df0ef495261c3b557d64c62caac0e484f661ef6b3a5be73 DIST GromacsWrapper-0.8.4.tar.gz 1955167 BLAKE2B 59f0301263eefaa4d7c139b34a48172c218a76f0f9488477d6203d9cd732098468dae5a73ff46aa74eb2b4433268c77bc265e506129e4c14a357042453d5f97f SHA512 822edc33c77ca4dbfbc1e4172686744345ed3c0d2305f4b19abab15576a1433bbb3b23b96f637398ad4f72cd5414d96ee531ab4a329d3acb462d90b95437a6a5 -EBUILD GromacsWrapper-0.8.2.ebuild 911 BLAKE2B bb0f003e877d03904ac5bcce4c73c103eb008670491070e593bbda3d5c5471c2cb766b020626c0dbf3f43694321f71b7d16a1a70b92abe6bb5b014f494ae1506 SHA512 c53c908443c871a87386c48195df4f052d0a211a3d16b298e2f82ac2f73e3078a6d2784c17e22f93598d2e0c80cffe31713b13b390600c4d7e036ddea0c0d390 +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 MISC metadata.xml 483 BLAKE2B 1d8a7e888d8b95bd229ef72894ba02f583e3e3958f9cd5733ab6b466312bac0b0f5a9004135caa37a3ef137e8782fa93ff4bb90f35f31c058d8c528025b193d0 SHA512 70e5dc653ff21a0395b946e5f3548320d2abb8c63ae9f3ce04be6768e20b02ce55a612a2ad12b6c2262529ab753ca9fda02d9bdae7f6ac859bca49bbbad6f75f diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz index 5156f0811930..b92065d97f52 100644 Binary files a/sci-chemistry/Manifest.gz and b/sci-chemistry/Manifest.gz differ diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest index 1986c9845998..910723bedde2 100644 --- a/sci-chemistry/chemex/Manifest +++ b/sci-chemistry/chemex/Manifest @@ -1,5 +1,5 @@ -DIST chemex-2022.3.4.tar.gz 2845201 BLAKE2B 91a76bdb54857710d482b14e36d24adec8706c385da7300d8cf7189426af28651877d487eb061e26656432575eb711de0e3a92724d1488d99efcdc8a682b59bd SHA512 304af730149a2f6723bbe36c0deafb826392cd571a2b4245bb42e28612ceef3ee2ca989f1909ddc7709081f742a997469565ef7d02994fda8087372f29e1dfe1 DIST chemex-2022.3.5.tar.gz 2845347 BLAKE2B 29b53ba8afcfd91e4f50119f212557de85d8576474b74d2ad925c8c2adb89397640e7b352b6785dc99a8c4e5007294609640219b2374cbb3144f94c5f9113d96 SHA512 3a92702d105e95e0a7b15e01b839d5982df55477afb98e58f7458a0e87230e94597c01d33c219ae469ed62e4ddaecdb787ae435453d428843d5a612159715d2b -EBUILD chemex-2022.3.4.ebuild 1250 BLAKE2B e6af845a61c59bc318e985d4e0b335aa526d426ff5186d07455768d2cf03e2ae6cdfd128fad40da16d33c13aba6dee6bf52f18e9eaeca9d2ddf8288312f3366a SHA512 b19b3336e0ac78b877463bc2431fb1daa57d5070444785ca47691cf21174b27277b3c41b49b136c18893a89015caab111edbb65b6a3dd1c90310f96388a85fdd +DIST chemex-2022.3.6.tar.gz 2843118 BLAKE2B e51b385dbf9e3c42f54f95f9929125e3263e12afa62beab8e5b8eb13e78a4fe9a0fb445f4f6c3cd4aa8e71748732ec58124682daa86be079eed036b78492ca71 SHA512 5c734e1b3ea39e9729bada93dfe5bc55f877b69ba6edd9612f95aab0d31949489582957a14f175646c7e6652644a5a55c26bcd74affc7fecc1e7b9cfdd4ceb63 EBUILD chemex-2022.3.5.ebuild 1250 BLAKE2B d1f61563a971c3c6795b2d398d71073e1db4cc5cca62a6ffc7d9bd2b22b6517417faddc037369fa545fb7f6493d95f658d850c1319eea4adb8bb51c9109e9df7 SHA512 2b1a3a0ca2eeadc7256efadd15a70bdb6b866da1a26a6c209b42fe6e010e871b675f1f2448a2dfdb8fefcbd9c0e97f54ac757a13fb0d29c03bb93ede9c8be97a +EBUILD chemex-2022.3.6.ebuild 1240 BLAKE2B 46d4f9fd57f5dbc8ad5b527e8568337cd57d3c03f25581d275e15204e5e2ee2c2224c6e8ada71c8d91aed01128be697987cc808bdfd7d7e3abc5f655eb2abb44 SHA512 814348dc6b404698634ecb33ee3956479dd1c05f91f7ca82e4f8a15776a582dd911e30a2070bff727f2aeae678a609fe2d8b676f107741904886c83315dbeb78 MISC metadata.xml 300 BLAKE2B a1ad769918094ddbda13ac92462ec69fa469dfcacde1202c653a4aa7443db661ffa5739cd039b6e38b13f0345a2680f276b4e071362106b162c95cd92007b5a8 SHA512 755c273f6bf67f79c388d06d970702a1d4a9f84338f8d889dd9146905c6994621917952225406ffba5bfe1e1b69f0bfd0f471374178b15343f4927af9de49aef diff --git a/sci-chemistry/chemex/chemex-2022.3.4.ebuild b/sci-chemistry/chemex/chemex-2022.3.4.ebuild deleted file mode 100644 index 3df32b1ac247..000000000000 --- a/sci-chemistry/chemex/chemex-2022.3.4.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_SINGLE_IMPL="yes" -DISTUTILS_USE_PEP517=poetry -PYTHON_COMPAT=( python3_{9..11} ) - -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/v${PV/_p/-dev}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/ChemEx-${PV/_p/-dev}" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64" -IUSE="test" - -#RESTRICT="!test? ( test )" -# FIXME: Restrict until tests are readded https://github.com/gbouvignies/ChemEx/issues/51 -RESTRICT="test" - -RDEPEND=" - $(python_gen_cond_dep ' - >=dev-python/asteval-0.9.25[${PYTHON_USEDEP}] - >=dev-python/cachetools-5.3.0[${PYTHON_USEDEP}] - >=dev-python/lmfit-1.2.0[${PYTHON_USEDEP}] - >=dev-python/matplotlib-3.7.1[${PYTHON_USEDEP}] - >=dev-python/numpy-1.24.2[${PYTHON_USEDEP}] - >=dev-python/pydantic-1.10.7[${PYTHON_USEDEP}] - >=dev-python/rapidfuzz-3.0.0[${PYTHON_USEDEP}] - >=dev-python/rich-13.3.4[${PYTHON_USEDEP}] - >=dev-python/scipy-1.10.1[${PYTHON_USEDEP}] - >=dev-python/tomli-2.0.1[${PYTHON_USEDEP}] - ') -" -DEPEND="${RDEPEND}" - -distutils_enable_tests pytest diff --git a/sci-chemistry/chemex/chemex-2022.3.6.ebuild b/sci-chemistry/chemex/chemex-2022.3.6.ebuild new file mode 100644 index 000000000000..81b3e45f7856 --- /dev/null +++ b/sci-chemistry/chemex/chemex-2022.3.6.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2023 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} ) + +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 -> ${P}.tar.gz" +S="${WORKDIR}/ChemEx-${PV/_p/-dev}" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64" +IUSE="test" + +#RESTRICT="!test? ( test )" +# FIXME: Restrict until tests are readded https://github.com/gbouvignies/ChemEx/issues/51 +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}] + ') +" +DEPEND="${RDEPEND}" + +distutils_enable_tests pytest + +export PDM_BUILD_SCM_VERSION=${PV} diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest index c426121ecf3e..0d3471385728 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.ebuild 2310 BLAKE2B bec87fef793e09143154b3d22b60dd7532469e87c10a67378b8fd87273b61b577478a7f21622ce6432339f8ca864cb3271aa23a20bb62f46269504d510869cf3 SHA512 9226fc0afc7e7d545376f09cda475f5ed7eda11cddcf099e4ecf4cd62ae478a4def5498a7ff5ebc8d80c32c54783fbb017e482aa322ca9e91f33204c79bd96c4 -MISC metadata.xml 266 BLAKE2B a03b1fcf7148cf43fb829f619c218219bcd4e66c45d12f563113401e3ae0b06cb0df9a8c0af01ea97e21453638d627d420e7df5b9b0d330ef1752253faa8aa32 SHA512 1dc293fa0d0296eba18ac2cbcd57f47ffc6cc822bf0d76e1cc86cb046700201f703d705375b5555b88cbe8780ef3750be05b8f9f8de092693e6d165c1734e049 +EBUILD tinker-8.2.1-r1.ebuild 2387 BLAKE2B 2eec46ab90656d4336f4c130bac95f76aae850ce7bea72ce7ba5fde37897f4345c7ff8e714190dad5279592ad51fae37b5c96190614a67725d6f23c534ca94c3 SHA512 f89dcf18394067c9485fb8a85c8a6bd841bf485f3deb6671ed457e995bf008e6db64206b0903cda9e0e86dd4ffc9253ee2f1f8b469688d044e629c506a5c3abb +MISC metadata.xml 349 BLAKE2B e2a70d46ddb77f5ea51a0d6d378cdcbe2c897464127bd86c34ec43615588a509ff038e035c24855c305248789eb0708d51d21208d2cc65e8507e4f767172582f SHA512 0cb63aaf7aadd62ea12289936ea25c8f5233c8784af96b71f103794d6bd7e0711b53728a2840f5768df2652c0b19e220b1f35223dbf27fc65f7871b6e3b4c756 diff --git a/sci-chemistry/tinker/metadata.xml b/sci-chemistry/tinker/metadata.xml index d4ff1000a775..9bfb6f28bafc 100644 --- a/sci-chemistry/tinker/metadata.xml +++ b/sci-chemistry/tinker/metadata.xml @@ -5,4 +5,7 @@ sci-chemistry@gentoo.org Gentoo Chemistry Project + + TinkerTools/tinker + diff --git a/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild b/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild new file mode 100644 index 000000000000..9964b16b549f --- /dev/null +++ b/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild @@ -0,0 +1,115 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic fortran-2 java-pkg-2 toolchain-funcs + +DESCRIPTION="Molecular modeling package that includes force fields, such as AMBER and CHARMM" +HOMEPAGE="https://dasher.wustl.edu/tinker/" +SRC_URI="https://dasher.wustl.edu/${PN}/downloads/${P}.tar.gz" + +SLOT="0" +LICENSE="Tinker" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" +RESTRICT="mirror" + +COMMON_DEPEND=" + >=sci-libs/fftw-3.2.2-r1[fortran,threads] + dev-libs/maloc + !sys-apps/bar + !dev-util/diffuse +" +RDEPEND="${COMMON_DEPEND} + >=virtual/jre-1.8:* +" +DEPEND=" + ${COMMON_DEPEND} + >=virtual/jdk-1.8:* +" +BDEPEND="virtual/pkgconfig" + +S="${WORKDIR}"/${PN}/source + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp +} + +pkg_setup() { + [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp + + fortran-2_pkg_setup +} + +src_prepare() { + sed 's:strip:true:g' -i ../make/Makefile || die + [[ $(tc-getFC) =~ "ifort" ]] && eapply "${FILESDIR}"/${PV}-openmp.patch + default + java-pkg-2_src_prepare +} + +src_compile() { + local javalib= _omplib _fftwlib + for i in $(java-config -g LDPATH | sed 's|:| |g'); do + [[ -f ${i}/libjvm.so ]] && javalib=${i} + done + + # use dummy routines in pmpb.f instead of apbs calls + rm pmpb.c || die + + if [[ $(tc-getFC) =~ "gfortran" ]]; then + append-flags -fopenmp + _omplib="-lgomp" + else + append-flags -openmp + _omplib="-liomp5" + fi + + _fftwlib="$($(tc-getPKG_CONFIG) --libs fftw3 fftw3_threads)" + + emake \ + -f ../make/Makefile \ + F77="$(tc-getFC)" \ + CC="$(tc-getCC) -c" \ + F77FLAGS=-c \ + OPTFLAGS="${FFLAGS}" \ + LINKFLAGS="${LDFLAGS} -Wl,-rpath ${javalib}" \ + INCLUDEDIR="$(java-pkg_get-jni-cflags) -I${EPREFIX}/usr/include" \ + LIBS="-lmaloc -L${javalib} -ljvm ${_omplib} ${_fftwlib}" \ + all + + mkdir "${S}"/../bin || die + + emake \ + -f ../make/Makefile \ + BINDIR="${S}"/../bin \ + rename_bin +} + +src_test() { + local test + cd "${WORKDIR}"/${PN}/test/ + for test in *.run; do + einfo "Testing ${test} ..." + bash ${test} || die + done +} + +src_install() { + dobin "${WORKDIR}"/${PN}/perl/mdavg "${WORKDIR}"/${PN}/bin/* + + insinto /usr/share/${PN}/ + doins -r "${WORKDIR}"/${PN}/params + + dodoc \ + "${WORKDIR}"/${PN}/doc/{*.txt,*.pdf,0README} + + if use examples; then + insinto /usr/share/${P} + doins -r "${WORKDIR}"/${PN}/example + + doins -r "${WORKDIR}"/${PN}/test + fi + +} diff --git a/sci-chemistry/tinker/tinker-8.2.1.ebuild b/sci-chemistry/tinker/tinker-8.2.1.ebuild deleted file mode 100644 index a54f1ecb210d..000000000000 --- a/sci-chemistry/tinker/tinker-8.2.1.ebuild +++ /dev/null @@ -1,113 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs - -DESCRIPTION="Molecular modeling package that includes force fields, such as AMBER and CHARMM" -HOMEPAGE="http://dasher.wustl.edu/tinker/" -SRC_URI="http://dasher.wustl.edu/${PN}/downloads/${P}.tar.gz" - -SLOT="0" -LICENSE="Tinker" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="examples" - -RDEPEND=" - >=sci-libs/fftw-3.2.2-r1[fortran,threads] - dev-libs/maloc - !sys-apps/bar - !dev-util/diffuse - >=virtual/jre-1.6 -" -DEPEND=" - ${RDEPEND} - >=virtual/jdk-1.6 - virtual/pkgconfig -" - -RESTRICT="mirror" - -S="${WORKDIR}"/${PN}/source - -pkg_pretend() { - [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp -} - -pkg_setup() { - [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp - - fortran-2_pkg_setup - java-pkg-opt-2_pkg_setup -} - -src_prepare() { - sed 's:strip:true:g' -i ../make/Makefile || die - [[ $(tc-getFC) =~ "ifort" ]] && eapply "${FILESDIR}"/${PV}-openmp.patch - default -} - -src_compile() { - local javalib= - for i in $(java-config -g LDPATH | sed 's|:| |g'); do - [[ -f ${i}/libjvm.so ]] && javalib=${i} - done - - # use dummy routines in pmpb.f instead of apbs calls - rm pmpb.c || die - - if [[ $(tc-getFC) =~ "gfortran" ]]; then - append-flags -fopenmp - _omplib="-lgomp" - else - append-flags -openmp - _omplib="-liomp5" - fi - - _fftwlib="$($(tc-getPKG_CONFIG) --libs fftw3 fftw3_threads)" - - emake \ - -f ../make/Makefile \ - F77="$(tc-getFC)" \ - CC="$(tc-getCC) -c" \ - F77FLAGS=-c \ - OPTFLAGS="${FFLAGS}" \ - LINKFLAGS="${LDFLAGS} -Wl,-rpath ${javalib}" \ - INCLUDEDIR="$(java-pkg_get-jni-cflags) -I${EPREFIX}/usr/include" \ - LIBS="-lmaloc -L${javalib} -ljvm ${_omplib} ${_fftwlib}" \ - all - - mkdir "${S}"/../bin || die - - emake \ - -f ../make/Makefile \ - BINDIR="${S}"/../bin \ - rename_bin -} - -src_test() { - cd "${WORKDIR}"/${PN}/test/ - for test in *.run; do - einfo "Testing ${test} ..." - bash ${test} || die - done -} - -src_install() { - dobin "${WORKDIR}"/${PN}/perl/mdavg "${WORKDIR}"/${PN}/bin/* - - insinto /usr/share/${PN}/ - doins -r "${WORKDIR}"/${PN}/params - - dodoc \ - "${WORKDIR}"/${PN}/doc/{*.txt,*.pdf,0README} - - if use examples; then - insinto /usr/share/${P} - doins -r "${WORKDIR}"/${PN}/example - - doins -r "${WORKDIR}"/${PN}/test - fi - -} -- cgit v1.2.3