From 34dea8e38f88007799629d0a56b12dec480b1d21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 20 Jun 2021 14:45:01 +0100 Subject: gentoo resync : 20.06.2021 --- sci-chemistry/Manifest.gz | Bin 11021 -> 11029 bytes sci-chemistry/autodock_vina/Manifest | 2 +- .../autodock_vina/autodock_vina-1.1.2-r1.ebuild | 48 +++ .../autodock_vina/autodock_vina-1.1.2.ebuild | 48 --- sci-chemistry/dssp/Manifest | 2 +- sci-chemistry/dssp/dssp-2.2.1-r1.ebuild | 45 --- sci-chemistry/dssp/dssp-2.2.1-r2.ebuild | 45 +++ sci-chemistry/gromacs/Manifest | 23 +- sci-chemistry/gromacs/gromacs-2020.4.ebuild | 6 +- sci-chemistry/gromacs/gromacs-2020.5.ebuild | 351 -------------------- sci-chemistry/gromacs/gromacs-2020.6.ebuild | 6 +- sci-chemistry/gromacs/gromacs-2020.9999.ebuild | 351 -------------------- sci-chemistry/gromacs/gromacs-2021.1.ebuild | 358 --------------------- sci-chemistry/gromacs/gromacs-2021.2.ebuild | 6 +- sci-chemistry/gromacs/gromacs-2021.9999.ebuild | 6 +- sci-chemistry/gromacs/gromacs-2021.ebuild | 355 -------------------- sci-chemistry/gromacs/gromacs-9999.ebuild | 61 ++-- sci-chemistry/tinker/Manifest | 2 +- sci-chemistry/tinker/tinker-8.2.1.ebuild | 9 +- 19 files changed, 158 insertions(+), 1566 deletions(-) create mode 100644 sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild delete mode 100644 sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild delete mode 100644 sci-chemistry/dssp/dssp-2.2.1-r1.ebuild create mode 100644 sci-chemistry/dssp/dssp-2.2.1-r2.ebuild delete mode 100644 sci-chemistry/gromacs/gromacs-2020.5.ebuild delete mode 100644 sci-chemistry/gromacs/gromacs-2020.9999.ebuild delete mode 100644 sci-chemistry/gromacs/gromacs-2021.1.ebuild delete mode 100644 sci-chemistry/gromacs/gromacs-2021.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz index 7b186967c586..5970caa3d8c2 100644 Binary files a/sci-chemistry/Manifest.gz and b/sci-chemistry/Manifest.gz differ diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest index d97143eb4ea6..4aa7ee3a38fc 100644 --- a/sci-chemistry/autodock_vina/Manifest +++ b/sci-chemistry/autodock_vina/Manifest @@ -2,5 +2,5 @@ AUX 1.1.2-gentoo.patch 2448 BLAKE2B f63add1d0fec8716672672af78fe8f34053bf060044e 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 DIST autodock_vina_1_1_2.tgz 67366 BLAKE2B dc754bf522795ebfbfcf89a2df4e3761d941c1f0ce05cf56898720c1e855f5dd00fd2a583f5a8d218fa2e738d37e014a9b3239b9aa989b9018a6a33f8f0bd02c SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9 -EBUILD autodock_vina-1.1.2.ebuild 948 BLAKE2B 4f5bd4de05bd0ad3839df02a8eceb845ac6d87128ebb841f9281a189deb648fc5e542fb0a4f9d6175150c55217eb9fe5aaa42b0f477edb17848f4da099afe565 SHA512 72c931a124bb5532baa934b55e146c859aec7fb5ae8803a2f52b3103adc126a3f4a1d0ee0552974c6aec5a7e13a25976f0a28e2d09711fa840b89c76d3666de8 +EBUILD autodock_vina-1.1.2-r1.ebuild 951 BLAKE2B 5b7805c212b019aca0be53fe329a1a8dcb423d8e6c2516256aa37417a991b57349c0567c9cc4a4da8e31651fee0e2cc370e6ee481ae9e160c901dd44c4158b1e SHA512 2d332538c9cf9d8b6ad2f742edfb83c27f97d18bf4da23afa4d99648b4839aafc836e9b624f7508de097d3bd682b5057159e5cde3bf4234f3d326d1a5326b211 MISC metadata.xml 1244 BLAKE2B 7df9f6f260c038c4f6b02a9fe35b54dbdc165975373ece6fb27856893536b3af7218ca1ff487ba908caa8c9beea43dc3f503fc83b6cf685754b8f17e53d771a9 SHA512 121a82bab7f4126fe5afe4ad39bbc9e397483c485e8a5771129d8eff883e87248acb1d689d47a57bf792ea8e1e23e82dec9bde811dae44e9b86a6736944c3484 diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild new file mode 100644 index 000000000000..a1782463270a --- /dev/null +++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit flag-o-matic toolchain-funcs + +MY_P="${PN}_$(ver_rs 1- _)" + +DESCRIPTION="Program for drug discovery, molecular docking and virtual screening" +HOMEPAGE="http://vina.scripps.edu/" +SRC_URI="http://vina.scripps.edu/download/${MY_P}.tgz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="debug" + +RDEPEND="dev-libs/boost:=[threads(+)]" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_P}/build/linux/release + +PATCHES=( + "${FILESDIR}"/${PV}-gentoo.patch + "${FILESDIR}"/${P}-boost-filesystem.patch + "${FILESDIR}"/${P}-missing-debug-decl.patch +) + +src_prepare() { + cd "${WORKDIR}"/${MY_P} || die + default +} + +src_configure() { + append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 -std=c++11 +} + +src_compile() { + emake \ + BASE="${EPREFIX}"/usr/ \ + GPP="$(tc-getCXX)" \ + C_OPTIONS=$(usex debug '' -DNDEBUG) +} + +src_install() { + dobin vina{,_split} +} diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild deleted file mode 100644 index 19a6a106be73..000000000000 --- a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit flag-o-matic toolchain-funcs - -MY_P="${PN}_$(ver_rs 1- _)" - -DESCRIPTION="Program for drug discovery, molecular docking and virtual screening" -HOMEPAGE="http://vina.scripps.edu/" -SRC_URI="http://vina.scripps.edu/download/${MY_P}.tgz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="debug" - -RDEPEND="dev-libs/boost:=[threads]" -DEPEND="${RDEPEND}" - -S="${WORKDIR}"/${MY_P}/build/linux/release - -PATCHES=( - "${FILESDIR}"/${PV}-gentoo.patch - "${FILESDIR}"/${P}-boost-filesystem.patch - "${FILESDIR}"/${P}-missing-debug-decl.patch -) - -src_prepare() { - cd "${WORKDIR}"/${MY_P} || die - default -} - -src_configure() { - append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 -std=c++11 -} - -src_compile() { - emake \ - BASE="${EPREFIX}"/usr/ \ - GPP="$(tc-getCXX)" \ - C_OPTIONS=$(usex debug '' -DNDEBUG) -} - -src_install() { - dobin vina{,_split} -} diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest index c312d16a2714..e64b097b41a1 100644 --- a/sci-chemistry/dssp/Manifest +++ b/sci-chemistry/dssp/Manifest @@ -1,5 +1,5 @@ AUX dssp-2.1.0-gentoo.patch 1513 BLAKE2B aabdcfff1083d7552392c35897eb8a84b07323c89dfdce014f4401b2e82e727e9fbc77dd3f7e6d5efda61a6e64fad905873516e5336f21627bda1f2f39caf5c2 SHA512 7d192019811a6892031c74e14ef9fc7461e77c050a164698f8c72cff08f81a0e6da202e0915b631a5cd6d910a6114a736c706d47b1fd6474ff77c3700efcd9f9 AUX dssp-2.2.1-boost-1.65-tr1-removal.patch 2126 BLAKE2B dc59d21a6be26ee96b636c13645163478999d5122f09d3a72963843be773210ea225e374941bd057ef6f083a13fb77980bd4390174df2a0c715f0386da7232e0 SHA512 8f84c6e163888d6a8192683a6555f7d6003634854f5cde0f6f962744e531165c7e0b2b08c55cbfb9c396d167c44317dd2e7a8290e4defd2c8def0a6511fbbd6c DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811 -EBUILD dssp-2.2.1-r1.ebuild 962 BLAKE2B 9db1a6eef5401ec278be424e3712765426ad1680bde4fe36d8afbcabe3a02e1020d31ad06c36e28e30e311651fdcba7359c977562dc18397ad51c338b3231794 SHA512 9488695b51ddfea2127b3b7e02e36095f494ba20f14eeb81b5ab9b6dd4a47bdaae6b517a6f27ad49af75202080f6fa511ea8efdd3aca8a7eee6fe8b7b31ec501 +EBUILD dssp-2.2.1-r2.ebuild 962 BLAKE2B 4badf2ae8647aab9c5e359d9e0763d051388afe3bf5763c8eeb99cb21b30283d72ace619f1b65c5ee248c42f8264cb31c2c1c079f75eacda1568cc4352cec5e3 SHA512 4a599b6e7cd068175bd89f4ea948ad1267df783c240ab46d3c6109bf3f2853de714ecf1e5776722309688599f28af545287fe5cb98d8b7a5f46d319df953b926 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild deleted file mode 100644 index b660e9ef3c96..000000000000 --- a/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="The protein secondary structure standard" -HOMEPAGE="http://swift.cmbi.ru.nl/gv/dssp/" -SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/${P}.tgz" - -LICENSE="Boost-1.0" -SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND="dev-libs/boost:=[threads]" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${PN}-2.1.0-gentoo.patch - "${FILESDIR}"/${PN}-2.2.1-boost-1.65-tr1-removal.patch -) - -src_configure() { - tc-export CXX - - cat >> make.config <<- EOF || die - BOOST_LIB_SUFFIX = -mt - BOOST_LIB_DIR = "${EPREFIX}/usr/$(get_libdir)" - BOOST_INC_DIR = "${EPREFIX}/usr/include" - EOF -} - -src_install() { - dobin mkdssp - dosym mkdssp /usr/bin/dssp - doman doc/mkdssp.1 - dodoc README.txt changelog - - cat >> "${T}"/30-${PN} <<- EOF || die - DSSP="${EPREFIX}"/usr/bin/${PN} - EOF - doenvd "${T}"/30-${PN} -} diff --git a/sci-chemistry/dssp/dssp-2.2.1-r2.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r2.ebuild new file mode 100644 index 000000000000..63075d4d4290 --- /dev/null +++ b/sci-chemistry/dssp/dssp-2.2.1-r2.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="The protein secondary structure standard" +HOMEPAGE="http://swift.cmbi.ru.nl/gv/dssp/" +SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/${P}.tgz" + +LICENSE="Boost-1.0" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="dev-libs/boost:=[threads(+)]" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-2.1.0-gentoo.patch + "${FILESDIR}"/${PN}-2.2.1-boost-1.65-tr1-removal.patch +) + +src_configure() { + tc-export CXX + + cat >> make.config <<- EOF || die + BOOST_LIB_SUFFIX = -mt + BOOST_LIB_DIR = "${EPREFIX}/usr/$(get_libdir)" + BOOST_INC_DIR = "${EPREFIX}/usr/include" + EOF +} + +src_install() { + dobin mkdssp + dosym mkdssp /usr/bin/dssp + doman doc/mkdssp.1 + dodoc README.txt changelog + + cat >> "${T}"/30-${PN} <<- EOF || die + DSSP="${EPREFIX}"/usr/bin/${PN} + EOF + doenvd "${T}"/30-${PN} +} diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 70b33b6727dc..1a2e29194577 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -3,36 +3,23 @@ AUX gromacs-2021-nblib.patch 1860 BLAKE2B 3f9d8e5683fee23434ca7bd0d9264eaed5834c DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122 DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8 DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9e65234b9459b71471827032654acacb58ed6ae87ec6e0e593a0acd799683cc4461b06cc883b089d740708619345e SHA512 0c56f058741af70660baf0177724ec940dd984c05ea141ede91ee51ce3744f76d00e31bdb5db907e46fa1639de5dca637b3ace26e89f908c2e74c69f0c21ed3a -DIST gromacs-2020.5.tar.gz 29148909 BLAKE2B ea439ae95d4af67a77d53182f7ddab702799edab8527c1b6ad20625d21a81f3e3c0cc699fa0b656625bffcca0bdd5a1e104aea4f592ee2db92b4f1a460ad0e80 SHA512 fe38fda36d31aef5ce01a3dbc29c9f50d3cc05b20bb34a9a8f10fda5aecde4f93ca8a3f85433139e1bb88fc23d77916a4aff5a292abaa528bd0e6138e84cba18 DIST gromacs-2020.6.tar.gz 29196621 BLAKE2B 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935f1635adb43e43f8f9d159826b43028a3c70bf70e26af5c5754a77401a177f2ed39834ce9cf6425d82a01ccf7193f4fe612ddfb3b728f079cd1a9cd882fd5f SHA512 47f930b93eb292d9194f8dedca487b3fda6ebbab2e5c3f320f9569d244deec8bff4fef27934cd21ec162f021571e48f6e9abded8719479a1220e18488a457360 -EBUILD gromacs-2021.9999.ebuild 10237 BLAKE2B 346372007800569bdf4517f9b710c71d7b5717e6dba1e7ea992027fb743c42ff94638eac40ae28fe4b51ff1fae27f89d320f7c44186d3ef01f8798d3533e8091 SHA512 d123afdfcc7a13a56babf650e2476e003790b705a9e59aa67cf98fd4a690a1969bb0b60e9b1ee5615edacbe49a880be722c4870c89b43f9ba814e716455dc8ba -EBUILD gromacs-2021.ebuild 10278 BLAKE2B c17da5a50ddd0b6e4b93779d59185fbe57d4b3bfec80a52a857eb53f86d2fcb6a1b7f63782d558e4a3eb8f3c7a54d75f73c4bd0036472272109fe1d6d6781c30 SHA512 80745295416d0e8e8c739da20aaff54bf2dca88d7b5dc8a800c1d334b7579ef7b85421388c0121acf2e0b3a43bed16545e65b8fc30f4618b5cfc18d8c81e4c7d -EBUILD gromacs-9999.ebuild 9932 BLAKE2B 45040b96ec2454338a1085048ef3b9c22a18b20167993de547b0f0226124bdb4be9b8b6acc19a998373d8438ea10a4e1e364c46f10def7e84b2d0542807b7e30 SHA512 a926a895411c07f18262f8f4a785028551ad5d1b1644429b112be5c1d9f14a830f07de7a0acff11582093fb0ee33c4122b67ce96e568736f76d11f20f7b6665a +EBUILD gromacs-2020.4.ebuild 10142 BLAKE2B 67561d5feb49c8133f2103c15759cb8824e98926fd83b64a7ae3ce4e15d9a35ff9a3b7f3e5fc38260006d42509235a65a39dee63f112b682e21336e561d0ea94 SHA512 4a2dd2fd2daec029e83b4ba9f7de4540a0b963842a0ccb3e4dbea66e4b6b30a28a7db1be4a17ffc0d0b5fdc241af32a80cfa7836b7d88f3d81c26ccb9ec04044 +EBUILD gromacs-2020.6.ebuild 10145 BLAKE2B 46db22597e4887bac67371d8ae340e5b707b0f6803ea9ad50148d254236266138f2ac53eef66301471933358e97bce72195dbe3772736d87676d90ff2d10e7be SHA512 fe0f1ebf7f5e96c3177858a36ac73e8e887536e570554885b47116be82703680940c5a4f0b3d571b665c776804a93351482c00bc6c13e6f691d5a9b5664db555 +EBUILD gromacs-2021.2.ebuild 10367 BLAKE2B 12d73f2b0e4412fba3bca6c55fef02f098d376094d045090b67201d776893d2709908113936bae8211f27c2d5231f86265c2e16018363b17e1d1aef5879e3253 SHA512 45255fe4eacec5caeb29696cb513b6c5c9a820e6d52bd543bdf89483e6a0d3710189403b7842e4af6ebaec14cb6a47b23130cc6dafa563740462382cff8d954e +EBUILD gromacs-2021.9999.ebuild 10277 BLAKE2B cb9936b80f4c3beb1cb2572318a878a120d2038a31d258868aa0d1318c1acf6e8cd3a01fe9e00e6129f69d79773464755ca3301a0ae87bd3429c97c8f36e46b9 SHA512 7bbb314d7c4bb6469f1ea7245dc3a925adce3ebd582908f3f62a60b294558726374fa3bfd46620d4d5c6032d124b9af00d5faa84d546f77791db572cf599d634 +EBUILD gromacs-9999.ebuild 10277 BLAKE2B cb9936b80f4c3beb1cb2572318a878a120d2038a31d258868aa0d1318c1acf6e8cd3a01fe9e00e6129f69d79773464755ca3301a0ae87bd3429c97c8f36e46b9 SHA512 7bbb314d7c4bb6469f1ea7245dc3a925adce3ebd582908f3f62a60b294558726374fa3bfd46620d4d5c6032d124b9af00d5faa84d546f77791db572cf599d634 MISC metadata.xml 1223 BLAKE2B 9e48794b267cdb031dcc680ecce38c0d9727c2706d95a0a52d3502d4aa73d245db419a77823d10c5022d65628390b2fd476e489ec764cdd1721c9dd8295a8232 SHA512 d9320e5896bd32e892a9be573da92943236d0cf912f3417b823a415c5470ad9e37a934eafcede6ab7487197854c515ef81270e44c8503540b14dc13356beb3de diff --git a/sci-chemistry/gromacs/gromacs-2020.4.ebuild b/sci-chemistry/gromacs/gromacs-2020.4.ebuild index 266941a81e30..4a9027a2d180 100644 --- a/sci-chemistry/gromacs/gromacs-2020.4.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.4.ebuild @@ -74,7 +74,7 @@ RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) - || ( doc build-manual ) + doc? ( !build-manual ) cuda? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) @@ -317,7 +317,9 @@ src_install() { fi if use doc; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" + if [[ ${PV} != *9999* ]]; then + newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" + fi fi use mpi || continue diff --git a/sci-chemistry/gromacs/gromacs-2020.5.ebuild b/sci-chemistry/gromacs/gromacs-2020.5.ebuild deleted file mode 100644 index 41ac7771497c..000000000000 --- a/sci-chemistry/gromacs/gromacs-2020.5.ebuild +++ /dev/null @@ -1,351 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python3_{7,8,9} ) - -DISTUTILS_USE_SETUPTOOLS=no -DISTUTILS_SINGLE_IMPL=1 - -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ ${PV} = *9999* ]]; then - EGIT_REPO_URI=" - https://gitlab.com/gromacs/gromacs.git - https://github.com/gromacs/gromacs.git - git://git.gromacs.org/gromacs.git" - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~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" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib -LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" -SLOT="0/${PV}" -IUSE="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) - opencl? ( virtual/opencl ) - fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( sys-apps/hwloc ) - lapack? ( virtual/lapack ) - lmfit? ( sci-libs/lmfit ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - ${PYTHON_DEPS} - !sci-chemistry/gmxapi - " -BDEPEND="${CDEPEND} - virtual/pkgconfig - build-manual? ( - app-doc/doxygen - $(python_gen_cond_dep ' - dev-python/sphinx[${PYTHON_MULTI_USEDEP}] - ') - media-gfx/mscgen - media-gfx/graphviz - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - )" -RDEPEND="${CDEPEND}" - -REQUIRED_USE=" - || ( single-precision double-precision ) - || ( doc build-manual ) - cuda? ( single-precision ) - cuda? ( !opencl ) - mkl? ( !blas !fftw !lapack ) - ${PYTHON_REQUIRED_USE}" - -DOCS=( AUTHORS README ) - -RESTRICT="!test? ( test )" - -if [[ ${PV} != *9999 ]]; then - S="${WORKDIR}/${PN}-${PV/_/-}" -fi - -PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) - -pkg_pretend() { - [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" - use openmp && ! tc-has-openmp && \ - die "Please switch to an openmp compatible compiler" -} - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_unpack() { - if [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="${EGIT_BRANCH}" \ - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ - git-r3_src_unpack - fi - fi -} - -src_prepare() { - #notes/todos - # -on apple: there is framework support - - xdg_environment_reset #591952 - - cmake_src_prepare - - use cuda && cuda_src_prepare - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - - if use test; then - for x in ${GMX_DIRS}; do - mkdir -p "${WORKDIR}/${P}_${x}" || die - cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die - done - fi - - DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" - if use build-manual; then - # try to create policy for imagemagik - mkdir -p ${HOME}/.config/ImageMagick - cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF - - - !ATTLIST policymap xmlns CDATA #FIXED ''> - - - ]> - - - - - - - - - EOF - fi -} - -src_configure() { - local mycmakeargs_pre=( ) extra fft_opts=( ) - - if use custom-cflags; then - #go from slowest to fastest acceleration - local acce="None" - use cpu_flags_x86_sse2 && acce="SSE2" - use cpu_flags_x86_sse4_1 && acce="SSE4.1" - use cpu_flags_x86_fma4 && acce="AVX_128_FMA" - use cpu_flags_x86_avx && acce="AVX_256" - use cpu_flags_x86_avx2 && acce="AVX2_256" - else - strip-flags - fi - - #to create man pages, build tree binaries are executed (bug #398437) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${MKLROOT}/include" - -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" - ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) - else - fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) - fi - - if use lmfit; then - local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) - else - local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) - fi - - mycmakeargs_pre+=( - "${fft_opts[@]}" - "${lmfit_opts[@]}" - -DGMX_X11=$(usex X) - -DGMX_EXTERNAL_BLAS=$(usex blas) - -DGMX_EXTERNAL_LAPACK=$(usex lapack) - -DGMX_OPENMP=$(usex openmp) - -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex build-manual) - -DGMX_HWLOC=$(usex hwloc) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$acce" - -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" - -DBUILD_TESTING=$(usex test) - -DGMX_BUILD_UNITTESTS=$(usex test) - -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" - ${extra} - ) - - for x in ${GMX_DIRS}; do - einfo "Configuring for ${x} precision" - local suffix="" - #if we build single and double - double is suffixed - use double-precision && use single-precision && \ - [[ ${x} = "double" ]] && suffix="_d" - local p - [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" - local cuda=( "-DGMX_GPU=OFF" ) - [[ ${x} = "float" ]] && use cuda && \ - cuda=( "-DGMX_GPU=ON" ) - local opencl=( "-DGMX_USE_OPENCL=OFF" ) - use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF - -DGMX_THREAD_MPI=$(usex threads) - -DGMXAPI=$(usex gmxapi) - -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) - "${opencl[@]}" - "${cuda[@]}" - "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" - -DGMX_BINARY_SUFFIX="${suffix}" - -DGMX_LIBS_SUFFIX="${suffix}" - -DGMX_PYTHON_PACKAGE=$(usex python) - ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - use mpi || continue - einfo "Configuring for ${x} precision with mpi" - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON - -DGMX_OPENMM=OFF - -DGMXAPI=OFF - "${opencl[@]}" - "${cuda[@]}" - -DGMX_BUILD_MDRUN_ONLY=ON - -DBUILD_SHARED_LIBS=OFF - -DGMX_BUILD_MANUAL=OFF - -DGMX_BINARY_SUFFIX="_mpi${suffix}" - -DGMX_LIBS_SUFFIX="_mpi${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile python_packaging/all - BUILD_DIR="${WORKDIR}/${P}" \ - distutils-r1_src_compile - fi - # not 100% necessary for rel ebuilds as available from website - if use build-manual; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile manual - fi - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake_src_compile - done -} - -src_test() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile check - done -} - -src_install() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install python_packaging/install - fi - if use build-manual; then - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi - - if use doc; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" - fi - - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake_src_install - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${ED}"/usr/bin/GMXRC* || die - for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do - local n=${x##*/gmx-completion-} - n="${n%.bash}" - cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"/usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2020.6.ebuild b/sci-chemistry/gromacs/gromacs-2020.6.ebuild index 41ac7771497c..0e2baeb3b302 100644 --- a/sci-chemistry/gromacs/gromacs-2020.6.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.6.ebuild @@ -74,7 +74,7 @@ RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) - || ( doc build-manual ) + doc? ( !build-manual ) cuda? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) @@ -317,7 +317,9 @@ src_install() { fi if use doc; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" + if [[ ${PV} != *9999* ]]; then + newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" + fi fi use mpi || continue diff --git a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild deleted file mode 100644 index 41ac7771497c..000000000000 --- a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild +++ /dev/null @@ -1,351 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python3_{7,8,9} ) - -DISTUTILS_USE_SETUPTOOLS=no -DISTUTILS_SINGLE_IMPL=1 - -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ ${PV} = *9999* ]]; then - EGIT_REPO_URI=" - https://gitlab.com/gromacs/gromacs.git - https://github.com/gromacs/gromacs.git - git://git.gromacs.org/gromacs.git" - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~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" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib -LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" -SLOT="0/${PV}" -IUSE="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) - opencl? ( virtual/opencl ) - fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( sys-apps/hwloc ) - lapack? ( virtual/lapack ) - lmfit? ( sci-libs/lmfit ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - ${PYTHON_DEPS} - !sci-chemistry/gmxapi - " -BDEPEND="${CDEPEND} - virtual/pkgconfig - build-manual? ( - app-doc/doxygen - $(python_gen_cond_dep ' - dev-python/sphinx[${PYTHON_MULTI_USEDEP}] - ') - media-gfx/mscgen - media-gfx/graphviz - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - )" -RDEPEND="${CDEPEND}" - -REQUIRED_USE=" - || ( single-precision double-precision ) - || ( doc build-manual ) - cuda? ( single-precision ) - cuda? ( !opencl ) - mkl? ( !blas !fftw !lapack ) - ${PYTHON_REQUIRED_USE}" - -DOCS=( AUTHORS README ) - -RESTRICT="!test? ( test )" - -if [[ ${PV} != *9999 ]]; then - S="${WORKDIR}/${PN}-${PV/_/-}" -fi - -PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) - -pkg_pretend() { - [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" - use openmp && ! tc-has-openmp && \ - die "Please switch to an openmp compatible compiler" -} - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_unpack() { - if [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="${EGIT_BRANCH}" \ - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ - git-r3_src_unpack - fi - fi -} - -src_prepare() { - #notes/todos - # -on apple: there is framework support - - xdg_environment_reset #591952 - - cmake_src_prepare - - use cuda && cuda_src_prepare - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - - if use test; then - for x in ${GMX_DIRS}; do - mkdir -p "${WORKDIR}/${P}_${x}" || die - cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die - done - fi - - DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" - if use build-manual; then - # try to create policy for imagemagik - mkdir -p ${HOME}/.config/ImageMagick - cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF - - - !ATTLIST policymap xmlns CDATA #FIXED ''> - - - ]> - - - - - - - - - EOF - fi -} - -src_configure() { - local mycmakeargs_pre=( ) extra fft_opts=( ) - - if use custom-cflags; then - #go from slowest to fastest acceleration - local acce="None" - use cpu_flags_x86_sse2 && acce="SSE2" - use cpu_flags_x86_sse4_1 && acce="SSE4.1" - use cpu_flags_x86_fma4 && acce="AVX_128_FMA" - use cpu_flags_x86_avx && acce="AVX_256" - use cpu_flags_x86_avx2 && acce="AVX2_256" - else - strip-flags - fi - - #to create man pages, build tree binaries are executed (bug #398437) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${MKLROOT}/include" - -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" - ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) - else - fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) - fi - - if use lmfit; then - local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) - else - local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) - fi - - mycmakeargs_pre+=( - "${fft_opts[@]}" - "${lmfit_opts[@]}" - -DGMX_X11=$(usex X) - -DGMX_EXTERNAL_BLAS=$(usex blas) - -DGMX_EXTERNAL_LAPACK=$(usex lapack) - -DGMX_OPENMP=$(usex openmp) - -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex build-manual) - -DGMX_HWLOC=$(usex hwloc) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$acce" - -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" - -DBUILD_TESTING=$(usex test) - -DGMX_BUILD_UNITTESTS=$(usex test) - -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" - ${extra} - ) - - for x in ${GMX_DIRS}; do - einfo "Configuring for ${x} precision" - local suffix="" - #if we build single and double - double is suffixed - use double-precision && use single-precision && \ - [[ ${x} = "double" ]] && suffix="_d" - local p - [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" - local cuda=( "-DGMX_GPU=OFF" ) - [[ ${x} = "float" ]] && use cuda && \ - cuda=( "-DGMX_GPU=ON" ) - local opencl=( "-DGMX_USE_OPENCL=OFF" ) - use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF - -DGMX_THREAD_MPI=$(usex threads) - -DGMXAPI=$(usex gmxapi) - -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) - "${opencl[@]}" - "${cuda[@]}" - "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" - -DGMX_BINARY_SUFFIX="${suffix}" - -DGMX_LIBS_SUFFIX="${suffix}" - -DGMX_PYTHON_PACKAGE=$(usex python) - ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - use mpi || continue - einfo "Configuring for ${x} precision with mpi" - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON - -DGMX_OPENMM=OFF - -DGMXAPI=OFF - "${opencl[@]}" - "${cuda[@]}" - -DGMX_BUILD_MDRUN_ONLY=ON - -DBUILD_SHARED_LIBS=OFF - -DGMX_BUILD_MANUAL=OFF - -DGMX_BINARY_SUFFIX="_mpi${suffix}" - -DGMX_LIBS_SUFFIX="_mpi${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile python_packaging/all - BUILD_DIR="${WORKDIR}/${P}" \ - distutils-r1_src_compile - fi - # not 100% necessary for rel ebuilds as available from website - if use build-manual; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile manual - fi - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake_src_compile - done -} - -src_test() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile check - done -} - -src_install() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install python_packaging/install - fi - if use build-manual; then - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi - - if use doc; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" - fi - - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake_src_install - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${ED}"/usr/bin/GMXRC* || die - for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do - local n=${x##*/gmx-completion-} - n="${n%.bash}" - cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"/usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2021.1.ebuild b/sci-chemistry/gromacs/gromacs-2021.1.ebuild deleted file mode 100644 index e8ea613693f0..000000000000 --- a/sci-chemistry/gromacs/gromacs-2021.1.ebuild +++ /dev/null @@ -1,358 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python3_{7,8,9} ) - -DISTUTILS_USE_SETUPTOOLS=no -DISTUTILS_SINGLE_IMPL=1 - -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ ${PV} = *9999* ]]; then - EGIT_REPO_URI=" - https://gitlab.com/gromacs/gromacs.git - https://github.com/gromacs/gromacs.git - git://git.gromacs.org/gromacs.git" - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~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" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib -LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" -SLOT="0/${PV}" -IUSE="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) - opencl? ( virtual/opencl ) - fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( sys-apps/hwloc ) - lapack? ( virtual/lapack ) - lmfit? ( sci-libs/lmfit ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - ${PYTHON_DEPS} - !sci-chemistry/gmxapi - " -BDEPEND="${CDEPEND} - virtual/pkgconfig - build-manual? ( - app-doc/doxygen - $(python_gen_cond_dep ' - dev-python/sphinx[${PYTHON_MULTI_USEDEP}] - ') - media-gfx/mscgen - media-gfx/graphviz - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - )" -RDEPEND="${CDEPEND}" - -REQUIRED_USE=" - || ( single-precision double-precision ) - || ( doc build-manual ) - cuda? ( single-precision ) - cuda? ( !opencl ) - mkl? ( !blas !fftw !lapack ) - ${PYTHON_REQUIRED_USE}" - -DOCS=( AUTHORS README ) - -RESTRICT="!test? ( test )" - -if [[ ${PV} != *9999 ]]; then - S="${WORKDIR}/${PN}-${PV/_/-}" -fi - -PATCHES=( - "${FILESDIR}/${PN}-2020-pytest.patch" - "${FILESDIR}/${PN}-2021-nblib.patch" -) - -pkg_pretend() { - [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" - use openmp && ! tc-has-openmp && \ - die "Please switch to an openmp compatible compiler" -} - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_unpack() { - if [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="${EGIT_BRANCH}" \ - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ - git-r3_src_unpack - fi - fi -} - -src_prepare() { - #notes/todos - # -on apple: there is framework support - - xdg_environment_reset #591952 - - cmake_src_prepare - - use cuda && cuda_src_prepare - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - - if use test; then - for x in ${GMX_DIRS}; do - mkdir -p "${WORKDIR}/${P}_${x}" || die - cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die - done - fi - - DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" - if use build-manual; then - # try to create policy for imagemagik - mkdir -p ${HOME}/.config/ImageMagick - cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF - - - !ATTLIST policymap xmlns CDATA #FIXED ''> - - - ]> - - - - - - - - - EOF - fi -} - -src_configure() { - local mycmakeargs_pre=( ) extra fft_opts=( ) - - if use custom-cflags; then - #go from slowest to fastest acceleration - local acce="None" - if (use amd64 || use x86); then - use cpu_flags_x86_sse2 && acce="SSE2" - use cpu_flags_x86_sse4_1 && acce="SSE4.1" - use cpu_flags_x86_fma4 && acce="AVX_128_FMA" - use cpu_flags_x86_avx && acce="AVX_256" - use cpu_flags_x86_avx2 && acce="AVX2_256" - use cpu_flags_x86_avx512f && acce="AVX_512" - elif (use arm); then - use cpu_flags_arm_neon && acce="ARM_NEON" - elif (use arm64); then - use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" - fi - else - strip-flags - fi - - #to create man pages, build tree binaries are executed (bug #398437) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${MKLROOT}/include" - -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" - ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) - else - fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) - fi - - if use lmfit; then - local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) - else - local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) - fi - - mycmakeargs_pre+=( - "${fft_opts[@]}" - "${lmfit_opts[@]}" - -DGMX_X11=$(usex X) - -DGMX_EXTERNAL_BLAS=$(usex blas) - -DGMX_EXTERNAL_LAPACK=$(usex lapack) - -DGMX_OPENMP=$(usex openmp) - -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex build-manual) - -DGMX_HWLOC=$(usex hwloc) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$acce" - -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" - -DBUILD_TESTING=$(usex test) - -DGMX_BUILD_UNITTESTS=$(usex test) - -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" - ${extra} - ) - - for x in ${GMX_DIRS}; do - einfo "Configuring for ${x} precision" - local suffix="" - #if we build single and double - double is suffixed - use double-precision && use single-precision && \ - [[ ${x} = "double" ]] && suffix="_d" - local p - [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" - local gpu=( "-DGMX_GPU=OFF" ) - [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) - use opencl && gpu=( "-DGMX_GPU=OPENCL" ) - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF - -DGMX_THREAD_MPI=$(usex threads) - -DGMXAPI=$(usex gmxapi) - -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) - "${gpu[@]}" - "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" - -DGMX_BINARY_SUFFIX="${suffix}" - -DGMX_LIBS_SUFFIX="${suffix}" - -DGMX_PYTHON_PACKAGE=$(usex python) - ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - use mpi || continue - einfo "Configuring for ${x} precision with mpi" - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON - -DGMX_OPENMM=OFF - -DGMXAPI=OFF - "${opencl[@]}" - "${cuda[@]}" - -DGMX_BUILD_MDRUN_ONLY=ON - -DBUILD_SHARED_LIBS=OFF - -DGMX_BUILD_MANUAL=OFF - -DGMX_BINARY_SUFFIX="_mpi${suffix}" - -DGMX_LIBS_SUFFIX="_mpi${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile python_packaging/all - BUILD_DIR="${WORKDIR}/${P}" \ - distutils-r1_src_compile - fi - # not 100% necessary for rel ebuilds as available from website - if use build-manual; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile manual - fi - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake_src_compile - done -} - -src_test() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile check - done -} - -src_install() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install python_packaging/install - fi - if use build-manual; then - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi - - if use doc; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" - fi - - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake_src_install - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${ED}"/usr/bin/GMXRC* || die - for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do - local n=${x##*/gmx-completion-} - n="${n%.bash}" - cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"/usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2021.2.ebuild b/sci-chemistry/gromacs/gromacs-2021.2.ebuild index 7b257ee4f40f..d3299c25bab8 100644 --- a/sci-chemistry/gromacs/gromacs-2021.2.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.2.ebuild @@ -74,7 +74,7 @@ RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) - || ( doc build-manual ) + doc? ( !build-manual ) cuda? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) @@ -324,7 +324,9 @@ src_install() { fi if use doc; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" + if [[ ${PV} != *9999* ]]; then + newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" + fi fi use mpi || continue diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild index 16825937690a..40f115d6a10e 100644 --- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild @@ -74,7 +74,7 @@ RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) - || ( doc build-manual ) + doc? ( !build-manual ) cuda? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) @@ -319,7 +319,9 @@ src_install() { fi if use doc; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" + if [[ ${PV} != *9999* ]]; then + newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" + fi fi use mpi || continue diff --git a/sci-chemistry/gromacs/gromacs-2021.ebuild b/sci-chemistry/gromacs/gromacs-2021.ebuild deleted file mode 100644 index a4fdab0dfaf7..000000000000 --- a/sci-chemistry/gromacs/gromacs-2021.ebuild +++ /dev/null @@ -1,355 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python3_{7,8,9} ) - -DISTUTILS_USE_SETUPTOOLS=no -DISTUTILS_SINGLE_IMPL=1 - -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ ${PV} = *9999* ]]; then - EGIT_REPO_URI=" - https://gitlab.com/gromacs/gromacs.git - https://github.com/gromacs/gromacs.git - git://git.gromacs.org/gromacs.git" - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~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" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib -LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" -SLOT="0/${PV}" -IUSE="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) - opencl? ( virtual/opencl ) - fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( sys-apps/hwloc ) - lapack? ( virtual/lapack ) - lmfit? ( sci-libs/lmfit ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - ${PYTHON_DEPS} - !sci-chemistry/gmxapi - " -BDEPEND="${CDEPEND} - virtual/pkgconfig - build-manual? ( - app-doc/doxygen - $(python_gen_cond_dep ' - dev-python/sphinx[${PYTHON_MULTI_USEDEP}] - ') - media-gfx/mscgen - media-gfx/graphviz - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - )" -RDEPEND="${CDEPEND}" - -REQUIRED_USE=" - || ( single-precision double-precision ) - || ( doc build-manual ) - cuda? ( single-precision ) - cuda? ( !opencl ) - mkl? ( !blas !fftw !lapack ) - ${PYTHON_REQUIRED_USE}" - -DOCS=( AUTHORS README ) - -RESTRICT="!test? ( test )" - -if [[ ${PV} != *9999 ]]; then - S="${WORKDIR}/${PN}-${PV/_/-}" -fi - -PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) - -pkg_pretend() { - [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" - use openmp && ! tc-has-openmp && \ - die "Please switch to an openmp compatible compiler" -} - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_unpack() { - if [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="${EGIT_BRANCH}" \ - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ - git-r3_src_unpack - fi - fi -} - -src_prepare() { - #notes/todos - # -on apple: there is framework support - - xdg_environment_reset #591952 - - cmake_src_prepare - - use cuda && cuda_src_prepare - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - - if use test; then - for x in ${GMX_DIRS}; do - mkdir -p "${WORKDIR}/${P}_${x}" || die - cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die - done - fi - - DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" - if use build-manual; then - # try to create policy for imagemagik - mkdir -p ${HOME}/.config/ImageMagick - cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF - - - !ATTLIST policymap xmlns CDATA #FIXED ''> - - - ]> - - - - - - - - - EOF - fi -} - -src_configure() { - local mycmakeargs_pre=( ) extra fft_opts=( ) - - if use custom-cflags; then - #go from slowest to fastest acceleration - local acce="None" - if (use amd64 || use x86); then - use cpu_flags_x86_sse2 && acce="SSE2" - use cpu_flags_x86_sse4_1 && acce="SSE4.1" - use cpu_flags_x86_fma4 && acce="AVX_128_FMA" - use cpu_flags_x86_avx && acce="AVX_256" - use cpu_flags_x86_avx2 && acce="AVX2_256" - use cpu_flags_x86_avx512f && acce="AVX_512" - elif (use arm); then - use cpu_flags_arm_neon && acce="ARM_NEON" - elif (use arm64); then - use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" - fi - else - strip-flags - fi - - #to create man pages, build tree binaries are executed (bug #398437) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${MKLROOT}/include" - -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" - ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) - else - fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) - fi - - if use lmfit; then - local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) - else - local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) - fi - - mycmakeargs_pre+=( - "${fft_opts[@]}" - "${lmfit_opts[@]}" - -DGMX_X11=$(usex X) - -DGMX_EXTERNAL_BLAS=$(usex blas) - -DGMX_EXTERNAL_LAPACK=$(usex lapack) - -DGMX_OPENMP=$(usex openmp) - -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex build-manual) - -DGMX_HWLOC=$(usex hwloc) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$acce" - -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" - -DBUILD_TESTING=$(usex test) - -DGMX_BUILD_UNITTESTS=$(usex test) - -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" - ${extra} - ) - - for x in ${GMX_DIRS}; do - einfo "Configuring for ${x} precision" - local suffix="" - #if we build single and double - double is suffixed - use double-precision && use single-precision && \ - [[ ${x} = "double" ]] && suffix="_d" - local p - [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" - local gpu=( "-DGMX_GPU=OFF" ) - [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) - use opencl && gpu=( "-DGMX_GPU=OPENCL" ) - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF - -DGMX_THREAD_MPI=$(usex threads) - -DGMXAPI=$(usex gmxapi) - -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) - "${gpu[@]}" - "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" - -DGMX_BINARY_SUFFIX="${suffix}" - -DGMX_LIBS_SUFFIX="${suffix}" - -DGMX_PYTHON_PACKAGE=$(usex python) - ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - use mpi || continue - einfo "Configuring for ${x} precision with mpi" - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON - -DGMX_OPENMM=OFF - -DGMXAPI=OFF - "${opencl[@]}" - "${cuda[@]}" - -DGMX_BUILD_MDRUN_ONLY=ON - -DBUILD_SHARED_LIBS=OFF - -DGMX_BUILD_MANUAL=OFF - -DGMX_BINARY_SUFFIX="_mpi${suffix}" - -DGMX_LIBS_SUFFIX="_mpi${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile python_packaging/all - BUILD_DIR="${WORKDIR}/${P}" \ - distutils-r1_src_compile - fi - # not 100% necessary for rel ebuilds as available from website - if use build-manual; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile manual - fi - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake_src_compile - done -} - -src_test() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile check - done -} - -src_install() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install python_packaging/install - fi - if use build-manual; then - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi - - if use doc; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" - fi - - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake_src_install - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${ED}"/usr/bin/GMXRC* || die - for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do - local n=${x##*/gmx-completion-} - n="${n%.bash}" - cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"/usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 19c3097b599b..40f115d6a10e 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -7,6 +7,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja" PYTHON_COMPAT=( python3_{7,8,9} ) +DISTUTILS_USE_SETUPTOOLS=no DISTUTILS_SINGLE_IMPL=1 inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils @@ -21,6 +22,7 @@ if [[ ${PV} = *9999* ]]; then else SRC_URI=" http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" fi @@ -35,7 +37,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +custom-cflags +doc double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( @@ -57,7 +59,7 @@ CDEPEND=" " BDEPEND="${CDEPEND} virtual/pkgconfig - doc? ( + build-manual? ( app-doc/doxygen $(python_gen_cond_dep ' dev-python/sphinx[${PYTHON_MULTI_USEDEP}] @@ -72,6 +74,7 @@ RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) + doc? ( !build-manual ) cuda? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) @@ -131,28 +134,29 @@ src_prepare() { fi DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" - - # try to create policy for imagemagik - mkdir -p ${HOME}/.config/ImageMagick - cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF - - - !ATTLIST policymap xmlns CDATA #FIXED ''> - - > ${HOME}/.config/ImageMagick/policy.xml <<- EOF + + + !ATTLIST policymap xmlns CDATA #FIXED ''> + + - ]> - - - - - - - - - EOF + ]> + + + + + + + + + EOF + fi } src_configure() { @@ -213,7 +217,7 @@ src_configure() { -DGMX_OPENMP=$(usex openmp) -DGMX_COOL_QUOTES=$(usex offensive) -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_BUILD_MANUAL=$(usex build-manual) -DGMX_HWLOC=$(usex hwloc) -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD="$acce" @@ -284,7 +288,7 @@ src_compile() { distutils-r1_src_compile fi # not 100% necessary for rel ebuilds as available from website - if use doc; then + if use build-manual; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake_src_compile manual fi @@ -310,9 +314,16 @@ src_install() { BUILD_DIR="${WORKDIR}/${P}_${x}" \ cmake_src_install python_packaging/install fi - if use doc; then + if use build-manual; then newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" fi + + if use doc; then + if [[ ${PV} != *9999* ]]; then + newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" + fi + fi + use mpi || continue BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ cmake_src_install diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest index 58eab1647163..eca4b084cf5a 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 2257 BLAKE2B 3464309efba4ec65effc9fa9c8fbab167116844f51f0101a22b9b964c610458f5daa5324d21affd93880bdd9c00a2b805bc09b1de80cff5dc2f17f45181ebd51 SHA512 51d5cd018b4146e6b68540dc7ec50a5f84c3f4ee2fa71c23417fc0a5005a847cd347d3d2223cdd6366e0a058a03a43ea5d2d1d12dacd7156c3f9f5ea93b01d37 +EBUILD tinker-8.2.1.ebuild 2269 BLAKE2B 81d02427bcbf41fe29eca4f9384b59a4be911acfed3ac7881cf1b96f1dac86aaaaa7412820d82807db2a5bc28c1b775b3097f7f5dfe9d1cdc175e39fc4f0a323 SHA512 cdbf3912bc1b45da9e2c84b1edda74b6dc1e80b922bf7dc5201e51c0bc3a42c142720c9c23128b4622c853cde38f396295dea96e24a40b797dae430b8a1191c9 MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a diff --git a/sci-chemistry/tinker/tinker-8.2.1.ebuild b/sci-chemistry/tinker/tinker-8.2.1.ebuild index d181dee95c44..bef87a09bfaa 100644 --- a/sci-chemistry/tinker/tinker-8.2.1.ebuild +++ b/sci-chemistry/tinker/tinker-8.2.1.ebuild @@ -14,10 +14,6 @@ LICENSE="Tinker" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="examples" -DEPEND=" - >=virtual/jdk-1.6 - virtual/pkgconfig -" RDEPEND=" >=sci-libs/fftw-3.2.2-r1[fortran,threads] dev-libs/maloc @@ -25,6 +21,11 @@ RDEPEND=" !dev-util/diffuse >=virtual/jre-1.6 " +DEPEND=" + ${RDEPEND} + >=virtual/jdk-1.6 + virtual/pkgconfig +" RESTRICT="mirror" -- cgit v1.2.3