diff options
Diffstat (limited to 'sci-chemistry')
36 files changed, 254 insertions, 1256 deletions
diff --git a/sci-chemistry/MDAnalysis/MDAnalysis-2.6.1.ebuild b/sci-chemistry/MDAnalysis/MDAnalysis-2.6.1.ebuild index f83ee1eabaf1..ca9d5382ae3b 100644 --- a/sci-chemistry/MDAnalysis/MDAnalysis-2.6.1.ebuild +++ b/sci-chemistry/MDAnalysis/MDAnalysis-2.6.1.ebuild @@ -26,7 +26,7 @@ RDEPEND=" >=dev-python/scipy-1.0.0[${PYTHON_USEDEP}] >=sci-biology/biopython-1.71[${PYTHON_USEDEP}] >=dev-python/networkx-1.0[${PYTHON_USEDEP}] - >=dev-python/GridDataFormats-0.4.0[${PYTHON_USEDEP}] + >=dev-python/griddataformats-0.4.0[${PYTHON_USEDEP}] >=dev-python/joblib-0.12[${PYTHON_USEDEP}] >=dev-python/matplotlib-1.5.1[${PYTHON_USEDEP}] >=dev-python/mmtf-python-1.0.0[${PYTHON_USEDEP}] diff --git a/sci-chemistry/autodock/autodock-4.2.6-r1.ebuild b/sci-chemistry/autodock/autodock-4.2.6-r1.ebuild index 463c23ee2e01..cd79276f14cd 100644 --- a/sci-chemistry/autodock/autodock-4.2.6-r1.ebuild +++ b/sci-chemistry/autodock/autodock-4.2.6-r1.ebuild @@ -12,7 +12,7 @@ DESCRIPTION="A suite of automated docking tools" HOMEPAGE="https://autodock.scripps.edu/" SRC_URI=" https://autodock.scripps.edu/downloads/autodock-registration/tars/dist$(ver_rs 1- '')/${MY_P}-src.tar.gz - https://dev.gentoo.org/~andrewammerlaan/${PN}-4.2.6-drop-register-keyword.patch + https://dev.gentoo.org/~nowa/${PN}-4.2.6-drop-register-keyword.patch " S="${WORKDIR}/src" diff --git a/sci-chemistry/avogadro2/Manifest b/sci-chemistry/avogadro2/Manifest index b65e97db421a..8bb2eb33f67b 100644 --- a/sci-chemistry/avogadro2/Manifest +++ b/sci-chemistry/avogadro2/Manifest @@ -1,4 +1,2 @@ -DIST avogadro2-1.95.1-i18n.tar.gz 800520 BLAKE2B f68edce572335621deb9698d1cc97d4d8e900ea91bb7a428a4da63d9060c38b31181b91b868378ab5da29c7a61ccb0f6efd9b422bba2d9dc9bb86578c23152c4 SHA512 1182578a9b91f49d114fa3a201e5fe5c37d3abdd10dff82be04f6d5fd193dd3b1140e7abdf2cf721523f523d762fbdc97780887184b83edbc9d3fa87fd8f7428 -DIST avogadro2-1.95.1.tar.gz 2888376 BLAKE2B 00ad2b9daccec77207d42bd0db0cf404bd5b92941385f19ac35400cf497884d198785da60f87fd68e92f6d864abea31f07526c2053b34cbf75d1202fd9232694 SHA512 15300da0ecc85be0e369758aafa50ca5c236132988da68611f198637ea49f4a88da93d58ecd177aeb3c2ac363c0da79b91064156e61c828a059277aa09245604 DIST avogadro2-1.97.0-i18n.tar.gz 990218 BLAKE2B e76b2d69b74f2a2964383564018e61ff0248e53c62a4a2abb1033100bd7fadaefbc261e64bf9e809d6e12ef851bd1ca3661d78b70d07728476586f6564e44e63 SHA512 6a01a05d4a62f83a75ae13100229f2ac6f9e697412868a75f5a9fde6025fc4e886c7ac80704fe5b8390a2af437c7848b0dce19897a6f9da1c5cf4c83418523db DIST avogadro2-1.97.0.tar.gz 2931223 BLAKE2B b2f2146ebe94ef25f4f684b13f9b9c5fbba933978208524ee197c8971f96c733f687ec68e566d032381a5f45cf22defb2bf909bd738becdd70da0abccebc0755 SHA512 19a0bcf01a840da29c4bab6eed55c879c10d773ee5dcfab613e6666708916bfd8398e44237c18de4e5bb3247d3c4bed3844cac47cf7f3a94dc96d7df8eb13579 diff --git a/sci-chemistry/avogadro2/avogadro2-1.95.1.ebuild b/sci-chemistry/avogadro2/avogadro2-1.95.1.ebuild deleted file mode 100644 index e4a5c22f11fc..000000000000 --- a/sci-chemistry/avogadro2/avogadro2-1.95.1.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 -MY_PN=avogadroapp - -DOCS_BUILDER="doxygen" -DOCS_DEPEND="media-gfx/graphviz" -DOCS_DIR="${WORKDIR}/${MY_PN}-${PV}_build/docs" -# docs/CMakeLists.txt overwrites docs.eclass outdir if we do not set this -DOCS_OUTDIR="${DOCS_DIR}/html" -DOCS_CONFIG_NAME="doxyfile" -inherit desktop docs cmake xdg - -I18N_COMMIT="3b8a86cc37e988b043d1503d2f11068389b0aca3" - -DESCRIPTION="Advanced molecule editor and visualizer 2" -HOMEPAGE="https://www.openchemistry.org/" -SRC_URI=" - https://github.com/OpenChemistry/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz - https://github.com/OpenChemistry/avogadro-i18n/archive/${I18N_COMMIT}.tar.gz -> ${P}-i18n.tar.gz -" -S="${WORKDIR}/${MY_PN}-${PV}" - -SLOT="0" -LICENSE="BSD GPL-2+" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="rpc test vtk" - -RDEPEND=" - dev-qt/qtcore:5 - dev-qt/qtgui:5 - dev-qt/qtwidgets:5 - >=sci-libs/avogadrolibs-${PV}[qt5,vtk?] - sci-libs/hdf5:= - rpc? ( sci-chemistry/molequeue ) -" -DEPEND="${RDEPEND} - dev-cpp/eigen:3 - test? ( dev-qt/qttest:5 ) -" - -RESTRICT="test" - -PATCHES=( - "${FILESDIR}/${P}-qttest.patch" -) - -src_unpack() { - default - mv "${WORKDIR}/avogadro-i18n-${I18N_COMMIT}" "${WORKDIR}/avogadro-i18n" || die -} - -src_prepare() { - cmake_src_prepare - sed -e "/LICENSE/d" -i CMakeLists.txt || die -} - -src_configure() { - local mycmakeargs=( - -DINSTALL_DOC_DIR="${EPREFIX}/usr/share/doc/${PF}" - -DBUILD_DOCUMENTATION=$(usex doc) - -DAvogadro_ENABLE_RPC=$(usex rpc) - -DENABLE_TESTING=$(usex test) - -DUSE_VTK=$(usex vtk) - ) - # Need this to prevent overwriting the documentation OUTDIR - use doc && mycmakeargs+=( -DChemData_BINARY_DIR="${DOCS_OUTDIR}" ) - cmake_src_configure -} - -src_compile() { - cmake_src_compile - docs_compile -} - -src_install() { - cmake_src_install - for size in 64 128 256 512; do - newicon -s "${size}" avogadro/icons/"${PN}"_"${size}".png "${PN}".png - done -} diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest index a78be349b4e6..a68267b02742 100644 --- a/sci-chemistry/chemex/Manifest +++ b/sci-chemistry/chemex/Manifest @@ -1,2 +1,2 @@ -DIST chemex-2024.05.2.tar.gz 2757082 BLAKE2B e231f2b4da566b633cdd10c54f413b319847e86ab909b81ca78e0cf5c368f4cd039fc26d4214f464de1ca618ea5bbd8579e9bfeaa4a97e01ef3ddecb1d8c8227 SHA512 29e137a1d275f5c6b078081350b8d9a6f9172858adb744afdbbdbbe94dc9953f1fb37ad49e10f2d39db89e90c2c8d5b17a53ec9be337772bb531052ae4ab86f1 DIST chemex-2024.05.3.tar.gz 2757407 BLAKE2B 8f98cda5158224bf06b4e81271157b7d6dd6c28526a6fd0362090d51d2fb2402a5dffc422862f129ffe7db22ec87ee49a12a1bd1a812e88014d4b1956e626ff7 SHA512 f2a29c03d9375b440206e1cd08d0f656ec6f9c627b15645663ee0d249731adb9619fa2ad5792e55e7219e11165d20a7d25b00ee9766daf580490cb4c8ea77ebf +DIST chemex-2024.09.25.tar.gz 2759061 BLAKE2B 28f39595db36476d30122ff4b7a163e6e09205a98c7bcb777503963a5790831eb40ffcc8363c5ff94cf6fc12cb88cf289fa295ffcf6c7bca6564e2b9e1654b4a SHA512 bbfce1903ebbd797001a1c526ffb20da08c33f8d142c3912711cdc87aa04a3044b0b176841223fbb341e1e90c9a28fa2c13716b4ac502753839fa310028be625 diff --git a/sci-chemistry/chemex/chemex-2024.05.2-r1.ebuild b/sci-chemistry/chemex/chemex-2024.09.25.ebuild index 87646d2c3045..87646d2c3045 100644 --- a/sci-chemistry/chemex/chemex-2024.05.2-r1.ebuild +++ b/sci-chemistry/chemex/chemex-2024.09.25.ebuild diff --git a/sci-chemistry/dssp/dssp-4.4.10.ebuild b/sci-chemistry/dssp/dssp-4.4.10.ebuild index d5e51fe40fec..52cf9b1a6a0f 100644 --- a/sci-chemistry/dssp/dssp-4.4.10.ebuild +++ b/sci-chemistry/dssp/dssp-4.4.10.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2024 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -10,7 +10,7 @@ SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${ LICENSE="BSD-2" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="amd64 ~x86" # doc disabled as it only generates a PDF from the manpage for now # https://github.com/PDB-REDO/dssp/issues/64 #IUSE="doc" diff --git a/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-fix_pointer_types.patch b/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-fix_pointer_types.patch new file mode 100644 index 000000000000..256a008b9f7d --- /dev/null +++ b/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-fix_pointer_types.patch @@ -0,0 +1,30 @@ +diff -Naur gnome-chemistry-utils-0.14.17_orig/libs/gccv/text.cc gnome-chemistry-utils-0.14.17_mod/libs/gccv/text.cc +--- gnome-chemistry-utils-0.14.17_orig/libs/gccv/text.cc 2017-02-12 10:10:09.000000000 +0100 ++++ gnome-chemistry-utils-0.14.17_mod/libs/gccv/text.cc 2024-09-02 22:58:57.724923903 +0200 +@@ -1126,7 +1126,7 @@ + if (event->state & GDK_CONTROL_MASK) { + /* move to end of word */ + char const* s = m_Text.c_str (); +- char *p = g_utf8_next_char (s + m_CurPos); ++ char const* p = g_utf8_next_char (s + m_CurPos); + while (*p && (!g_unichar_isgraph (g_utf8_get_char(p)) || g_unichar_ispunct (g_utf8_get_char(p)))) + p = g_utf8_next_char (p); + while (g_unichar_isgraph (g_utf8_get_char(p)) && !g_unichar_ispunct (g_utf8_get_char(p))) +@@ -1137,7 +1137,7 @@ + Invalidate (); + } else { + char const* s = m_Text.c_str (); +- char *p = g_utf8_next_char (s + m_CurPos); ++ char const* p = g_utf8_next_char (s + m_CurPos); + if (!p) + break; + m_CurPos = p - s; +@@ -1224,7 +1224,7 @@ + if (m_CurPos == m_Text.length ()) + break; + char const* s = m_Text.c_str (); +- char *p = g_utf8_next_char (s + m_CurPos); ++ char const* p = g_utf8_next_char (s + m_CurPos); + int new_pos = p - s; + ReplaceText (empty_st, m_CurPos, new_pos - m_CurPos); + if (client) diff --git a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17_p6-r2.ebuild b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17_p6-r2.ebuild index 33d0e163eb2a..591709b1fa59 100644 --- a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17_p6-r2.ebuild +++ b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17_p6-r2.ebuild @@ -10,10 +10,11 @@ SRC_URI=" http://download.savannah.gnu.org/releases/gchemutils/$(ver_cut 1-2)/${P/_p*}.tar.xz mirror://debian/pool/main/${PN:0:1}/${PN}/${PN}_${PV/_p*}-${PV/*_p}.debian.tar.xz " +S="${WORKDIR}/${P/_p*}" +LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" -LICENSE="GPL-3" IUSE="gnumeric" RDEPEND=" @@ -38,8 +39,6 @@ BDEPEND=" virtual/pkgconfig " -S="${WORKDIR}/${P/_p*}" - src_prepare() { default @@ -52,6 +51,9 @@ src_prepare() { eapply -p1 "${WORKDIR}/debian/patches/${p}" done + # From Fedora + eapply "${FILESDIR}"/${PN}-fix_pointer_types.patch + eautoreconf } diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 6409f7133958..24d9338ef70f 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,18 +1,12 @@ -DIST gromacs-2020.7.tar.gz 29175554 BLAKE2B 98f1aa415946f8eb113febc81105f0c1b0919b96fc3c55a0ab83bf3950ff509b81eade92e645adb0bc2b407df239e20cf3f19828b6e08616437c8693c1fddcc8 SHA512 1d375c44cec38445e56cea252623b5b6c565680268999d4b6c14d6dc38759a27227655b2d29efaab9f9115d3677b446cb555e11cddafa0dc10c4827caaa2477b -DIST gromacs-2021.7.tar.gz 38028032 BLAKE2B 2dc1b15ca8692ca5cf4ad1c7a266b9e2ced064d34a63cef61fea69e48231dd0310cfd8484d29c56cdb599f795d7655959f40038ac933b46ad2841d57bf2b3646 SHA512 ca478533da3bcb377fda30682660db8eb13beef6456fac6013a1a97ec3be60b5594567412e1e2a31392e484f9a40a22da1f12336f4738cf0422ff4f3e8814609 -DIST gromacs-2022.6.tar.gz 40330705 BLAKE2B fdafbd5b2a92d6022dec3e79e961fef220f1eba42850916e7cb70ef459a8d9c6ebc8c1bbe3c105f5b23161dd5c552ec00505d7c0036649b782cf52c311498743 SHA512 91217394f534ca8f78f73189059712e1c2cd354b658722f23768b12748f7bfaf1a5e95227c5ed1b69c1a9b72c3174e9600a712c157ea2f27156387efb823dd67 DIST gromacs-2023.5.tar.gz 42079310 BLAKE2B e50dbe76396230f4a886280bdebcf7b131506679240e77d2a2263c3b5dbfe7ef754c4265fc04e9acad7932c7691de7f694cc23140a25d0d5be649a4120f45b0c SHA512 f3a34cf0d379d6d4964d7494af6c6617c0c092293ea38a3a248af2dd2a90cae04696d52e68126176065efc480977942b00efa441028e526e1555c7e84551fc0c DIST gromacs-2024.3.tar.gz 42373103 BLAKE2B f45af72ecdf119b423d98b84818eaca1aa2e3f43eaf1aff7435de2a5891079a880f19a654627ee2f43e3a38c9dcfa0638bc6eb6da201b3c9ce89b2dc32fc683b SHA512 13f23e581c2b63f6262e8359e7bed6a1a5f3164047ea38d2b6a44bcd2b20b61332705167435fe2ad30fe6f24f8ab49b982388550cdecb49167e4156e36286d3d -DIST gromacs-2024.tar.gz 42455653 BLAKE2B 86446c5e95f9ddaf718126c409389730ee1642f36c3e0d844eb4b3a640c275e7979581365dacb57ac66daec296bbd94be6d5c0376f7255d3d3950f6759f8d69a SHA512 d64bf3cbe579003ce37dfd3d27c68746a04360d9d5491c638f3f2bd9af2c938504b0c9710c62e85225370ddf5418e6ebc2422033e46af5eee6e4aaa53699fed7 -DIST manual-2020.7.pdf 11850780 BLAKE2B 38594e87993badfbbcf47d6010a7f67d3c3426dab85e1462916b4d62be27b5764953f912cf2b71ee24877e0bfa27b3f74431da2da81b4977d58cb66b2cc795a3 SHA512 4f184f2c90e0bac01a48069cc546cd5b04fa5f543f90dd2d68c6d17be278152fd09456b6a6c5c8236f8fb85a174d6ec7a1c7b44d437b4e6fea5d0ada73cec0f6 -DIST manual-2021.7.pdf 12256526 BLAKE2B 6f298d7dac142f66914bbc2ea7d6ca70c4aeafaf33ccf12336d5cec64b1f1097b5332c767bb411ccef706ec6184479a84bcf59bda21c4249d45d8ce3dea08e79 SHA512 197765accb8ab6c5f1cc94b2697ff1817e157d85fa231dfe36a85036076e04da2a8035de66aba4f46c6dd7f553176357b94c92e1da5d1dabc574c627deee5279 -DIST manual-2022.6.pdf 13081140 BLAKE2B e7ae3f23ddc076c295be2c464fe2177d6d6848d070ee5eba2b572e996ae08adead898ec6432b123802907f64983aa4d2e17426be8d540c48d12398a479519f9e SHA512 4724888b3c33c4fa4a035d5fb2f8c51496f67e1ee312676510d5ba74bc3cc1571e71e84464585b87ad0133e8e736343ae382bf8f7b556633f86a99560213d271 +DIST gromacs-2024.4.tar.gz 42356162 BLAKE2B 3a1019128a2cfd47fb3ab23962a6fcd5bac3b5519d4bfa1239956740226468986ba93e645eb3bc20117968c024823e948fd819a603315399d573275c91c6e51b SHA512 32a08e9417d4d36a29bdfde4e0448bc136bd3db79b5d5c84fa99d9f022ffca6a94b7bd1c7e7a335430fb6bdcf0181e3cbabeb46d13978c0f87b5d88787ea8d63 +DIST gromacs-2025.0-beta.tar.gz 45067499 BLAKE2B 661607007af6d1f697f5aec72a88cefec5546dee2c0facaf2776354665f56fd71b1a7a2ea92185b4d64e764cd0ac10e865b740dda6d7438318acbbadd1bd7fd0 SHA512 831b4ba2631f5dd65c1b48d4ba0455af0b101af22d8cc78c246e7b36f4ce3c8f33f1cb8d94e42559741dbe1585c75a6e05a2538708d7e57c86ac2174aca302b9 DIST manual-2023.5.pdf 13579081 BLAKE2B 42f687ebcdb79bfc77aabac4fd382940c23ba27da380b8eff342c2e9255a58fc11a0458220d1f71f3c13ab1cf6fdabad00ac1bad741781d0b787899165bea2cc SHA512 0661f166f7a8dc24b4244c0139f366832ddfc1298129df2a6e29800b5d1567318781ab547bc7e9ee54de7a62abba4996f8e3010c91d6917c248117e5711d7dbb DIST manual-2024.3.pdf 13676383 BLAKE2B fa5b310ee8977c525781492c70a18d40f8842f5fa43831ad0283c033f39968ba98e74ea618a4a9c25d88c3ed694071327220617b17f316ba2f29777c3edc95ca SHA512 8dd09913b89213a6673a5f5e3462fb963d1f30d68e0d58b846b7e2cf2f73baacb14fabab6591b680849607f4ca617cf288899729939b2c32021b4ee5ba06835f -DIST manual-2024.pdf 13644437 BLAKE2B 19d547686d5c5be5e1236aba648e8afb174b281802ab76e020466953ab5d2dd98701f21eb4736cb449b61960b5b7aadce6711b2b0309a41dd1997d7383bce09e SHA512 b00048651f1f81f9024ba5c4c02ad66d2b07eb7b816f0489568fb64859cac515b885a5cb4640c8b5bd7c3620655a7ebc5fc2e4e4cbb8e952ffb0c9b5815ae661 -DIST regressiontests-2020.7.tar.gz 48541487 BLAKE2B 255608b52158c6c01e7c7c4dcf075128ecf22b2f26d32e8c203de8a4bc69c60ec95f49cf8ccd64abc3073c5e8dca9d6b01daed9dfb8f67bce2dd068ed01acd05 SHA512 2458582f94f3c9f4e1454824ce3940b4f5b6cb2151d06846c42e7a9448296fd2a6df4f53be9624e0d3317d2b59f89bb5348eb8b2970d7b46ac22ca989ef3458a -DIST regressiontests-2021.7.tar.gz 48537500 BLAKE2B b0c97fa652cb9b972c50f29822f530fcaa2ec9acb6d6442114fc6446c54aade5eb1bfa153c69a7e8bf64b66e8b041d7f8e0d51e7f7b0516f9e03f3d9ad626193 SHA512 7cbead90aa6d62346dcf7c2249c3cfa179884b987a749624444d2f59d93e0322f7721143bf6eb44d26102635dc70a73546ef82d4647558b6320bfdd459074017 -DIST regressiontests-2022.6.tar.gz 48615697 BLAKE2B 566adafbc36d3c1faae322fca9cf451f57245c4ceed63f90f26208025937dae0c1bbb8c372bce618f63305d0368113fecd96c7275a75d8b9c19c22a6e5aa9b96 SHA512 68aa9bedffbea37fb7703c18c3f66f607a91f16ece4bec58ced6e42a481156b2fe83760d0e40cecbdcaf87b168441b8ebde27cec30d98c89f516360ea45ddd43 +DIST manual-2024.4.pdf 13690684 BLAKE2B 7fac46df0da9d4cf7584599c7a71c4e1d11f75fc20a7a19ecc8069fdc2e9e35f0292e389f9c40d69dc96bdfea8d4ee370a54279b5531c0fb37c4cbd76caf7800 SHA512 5c4662527554171774adde5a3de220d775723154914838fd7fc3e40c981e1fccac0fd0def1acc500635cd39269d3bcc2edab5ec7aa85a7ea78350969d72ee13c +DIST manual-2025.0-beta.pdf 13788093 BLAKE2B 40652f32f35d73964dfb8146b916c0249d8b7044595114986108f209e98e3a0a402ead18842822ce12c9cdd24a224bb95f80fbe5eec908f013b1eddc14d2a2fd SHA512 eafc1fd060f4a5dd5e7317f0f0fa45cfd5ccc20518a9d67b9055a87c324893d92573dfd416fcbf0fc9b7a932a47e3a592fbc38837bccdd237466bb62cd3ad9ed DIST regressiontests-2023.5.tar.gz 48619605 BLAKE2B f2549a34750c6866f054614a00a3360a09b82306e6bd5e5b848e18cdd3a3fabaac6203c5ca734901019403225dd47e0d662838abe9a1db7d07662f1c745b8e4f SHA512 3ccaf9db7dfba641a5e98ebff3d735cae3f679926aba443ffedec20dd6c85e67f0e9711ebad5dfa8105122d5411f5de6ded1802a7da4ddf0599657832c8c597a DIST regressiontests-2024.3.tar.gz 32776961 BLAKE2B 6a74977a396f8e82f7aba7a384cc840275b86d470597a4bbb93e97f1c13cd8fcf6d86ab26bdd4a89464b863954c9ed7dbd49af095e821573845f7bda43c2b90b SHA512 1c4afbbca82c9b9ad371713ef5e7e093ca766f25f6fbda55c79ea1aecb2f0a06bdb042d3c8a86e3d9bf9e8b8091244827dbff544f66037ffa56b0bcb341a9d2c -DIST regressiontests-2024.tar.gz 48142685 BLAKE2B e24c29c2b534f2fe42e4abc122578ba618279f3182f83be604516e6ee2a34ff037b2604b4cda7a9b7e2ea9fce0a386b3efb7c8aa0cac378d6d8c1595be884c76 SHA512 6c4a847c379603590f618a4da7c691b51bbe180ca9dc59abf885ef8599e1b66758171eb05b7d7709d968f559b209c2fa4cfec8f15cc5d072fafe952567002c2e +DIST regressiontests-2024.4.tar.gz 32777006 BLAKE2B 41623de750b89410fa0a52037ea28d99a688b602b286cff732a6e8100b2b72072f579fc4f72bfe7c246ca086b6c6c1c10adb89874db6e1c9276494572e408a9f SHA512 dfbe8ee1b7c5b534842203f2295ea08875df6af3fb94798138b92ab8bc816719e3357db2935d2de4fd798d104ad7cb44860cd65887da7bb2438db422f35e6848 +DIST regressiontests-2025.0-beta.tar.gz 32653220 BLAKE2B 9f7388d7dfc59d89e719d693733f7ff2b3085e9c6b526238f62dc89ba9c30f9c778d99952ca170bf0ffc1d09fff6e4cd1bf1f0dc77c5b45e8613229043ebe409 SHA512 f3786ef08a54cc4a525a8af4ca7276dc6dfb624f13a82b9a9f168253729dd2e7161cecc5540b805bdfdaface8e272cea430bb561d0694970f5a394a718cdd8c3 diff --git a/sci-chemistry/gromacs/files/gromacs-2020-pytest.patch b/sci-chemistry/gromacs/files/gromacs-2020-pytest.patch deleted file mode 100644 index cc7730afecb9..000000000000 --- a/sci-chemistry/gromacs/files/gromacs-2020-pytest.patch +++ /dev/null @@ -1,35 +0,0 @@ -From e4e1263776844d660c471e3d1203acf54cdc855f Mon Sep 17 00:00:00 2001 -From: Alexey Shvetsov <alexxyum@gmail.com> -Date: Fri, 23 Apr 2021 13:21:24 +0300 -Subject: [PATCH 2/2] Allow to build python part without build testing enabled - -Signed-off-by: Alexey Shvetsov <alexxyum@gmail.com> ---- - python_packaging/src/CMakeLists.txt | 6 ++++-- - 1 file changed, 4 insertions(+), 2 deletions(-) - -diff --git a/python_packaging/src/CMakeLists.txt b/python_packaging/src/CMakeLists.txt -index c75549fc82..4f983fdd5f 100644 ---- a/python_packaging/src/CMakeLists.txt -+++ b/python_packaging/src/CMakeLists.txt -@@ -1,7 +1,7 @@ - # - # This file is part of the GROMACS molecular simulation package. - # --# Copyright (c) 2019,2020, by the GROMACS development team, led by -+# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by - # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, - # and including many others, as listed in the AUTHORS file in the - # top-level source directory and at http://www.gromacs.org. -@@ -252,5 +252,7 @@ endif() - # to the `check` target. Normal usage is to first install the Python package, - # then run `pytest` on the `tests` directory. Refer to gmxapi package documentation. - if(NOT GMXAPI_MASTER_PROJECT) -- add_subdirectory(test) -+ if (BUILD_TESTING) -+ add_subdirectory(test) -+ endif() - endif() --- -2.31.1 - diff --git a/sci-chemistry/gromacs/files/gromacs-2021-cstdint-include.patch b/sci-chemistry/gromacs/files/gromacs-2021-cstdint-include.patch deleted file mode 100644 index 5952aa3dd8e8..000000000000 --- a/sci-chemistry/gromacs/files/gromacs-2021-cstdint-include.patch +++ /dev/null @@ -1,12 +0,0 @@ -# https://bugs.gentoo.org/915694 -# Not needed for newer branches, that greatly refactored the code ---- a/src/gromacs/utility/flags.h~ 2023-01-31 12:45:46.000000000 +0100 -+++ b/src/gromacs/utility/flags.h 2023-10-16 10:15:24.087340444 +0200 -@@ -42,7 +42,7 @@ - */ - #ifndef GMX_UTILITY_FLAGS_H - #define GMX_UTILITY_FLAGS_H -- -+#include <cstdint> - namespace gmx - { diff --git a/sci-chemistry/gromacs/files/gromacs-2021-cuda-detection.patch b/sci-chemistry/gromacs/files/gromacs-2021-cuda-detection.patch deleted file mode 100644 index 8b458e96cb53..000000000000 --- a/sci-chemistry/gromacs/files/gromacs-2021-cuda-detection.patch +++ /dev/null @@ -1,339 +0,0 @@ ---- gromacs-2021.7/cmake/gmxManageNvccConfig.cmake 2023-01-31 12:45:45.000000000 +0100 -+++ gromacs-2022.5/cmake/gmxManageNvccConfig.cmake 2023-02-03 12:53:34.000000000 +0100 -@@ -1,11 +1,9 @@ - # - # This file is part of the GROMACS molecular simulation package. - # --# Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team. --# Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by --# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, --# and including many others, as listed in the AUTHORS file in the --# top-level source directory and at http://www.gromacs.org. -+# Copyright 2012- The GROMACS Authors -+# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel. -+# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details. - # - # GROMACS is free software; you can redistribute it and/or - # modify it under the terms of the GNU Lesser General Public License -@@ -19,7 +17,7 @@ - # - # You should have received a copy of the GNU Lesser General Public - # License along with GROMACS; if not, see --# http://www.gnu.org/licenses, or write to the Free Software Foundation, -+# https://www.gnu.org/licenses, or write to the Free Software Foundation, - # Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. - # - # If you want to redistribute modifications to GROMACS, please -@@ -28,10 +26,10 @@ - # consider code for inclusion in the official distribution, but - # derived work must not be called official GROMACS. Details are found - # in the README & COPYING files - if they are missing, get the --# official version at http://www.gromacs.org. -+# official version at https://www.gromacs.org. - # - # To help us fund GROMACS development, we humbly ask that you cite --# the research papers on the package. Check out http://www.gromacs.org. -+# the research papers on the package. Check out https://www.gromacs.org. - - # Manage CUDA nvcc compilation configuration, try to be smart to ease the users' - # pain as much as possible: -@@ -51,7 +49,7 @@ - # glibc source shows that _FORCE_INLINES is only used in this string.h - # feature and performance of memcpy variants is unimportant for CUDA - # code in GROMACS. So this workaround is good enough to keep problems --# away from users installing GROMACS. See Issue #1942. -+# away from users installing GROMACS. See Issue #1982. - function(work_around_glibc_2_23) - try_compile(IS_GLIBC_2_23_OR_HIGHER ${CMAKE_BINARY_DIR} ${CMAKE_SOURCE_DIR}/cmake/TestGlibcVersion.cpp) - if(IS_GLIBC_2_23_OR_HIGHER) -@@ -83,67 +81,158 @@ - mark_as_advanced(CUDA_HOST_COMPILER CUDA_HOST_COMPILER_OPTIONS) - endif() - -+# We would like to be helpful and reject the host compiler with a -+# clear error message at configure time, rather than let nvcc -+# later reject the host compiler as not supported when the first -+# CUDA source file is built. We've implemented that for current -+# nvcc running on Unix-like systems, but e.g. changes to nvcc -+# will further affect the limited portability of this checking -+# code. Set the CMake variable GMX_NVCC_WORKS on if you want to -+# bypass this check. -+if((_cuda_nvcc_executable_or_flags_changed OR CUDA_HOST_COMPILER_CHANGED OR NOT GMX_NVCC_WORKS) AND NOT WIN32) -+ message(STATUS "Check for working NVCC/C++ compiler combination with nvcc '${CUDA_NVCC_EXECUTABLE}'") -+ execute_process(COMMAND ${CUDA_NVCC_EXECUTABLE} --compiler-bindir=${CUDA_HOST_COMPILER} -c ${CUDA_NVCC_FLAGS} ${CUDA_NVCC_FLAGS_${_build_type}} ${CMAKE_SOURCE_DIR}/cmake/TestCUDA.cu -+ RESULT_VARIABLE _cuda_test_res -+ OUTPUT_VARIABLE _cuda_test_out -+ ERROR_VARIABLE _cuda_test_err -+ OUTPUT_STRIP_TRAILING_WHITESPACE) -+ -+ if(${_cuda_test_res}) -+ message(STATUS "Check for working NVCC/C compiler combination - broken") -+ message(STATUS "${CUDA_NVCC_EXECUTABLE} standard output: '${_cuda_test_out}'") -+ message(STATUS "${CUDA_NVCC_EXECUTABLE} standard error: '${_cuda_test_err}'") -+ if(${_cuda_test_err} MATCHES "nsupported") -+ message(FATAL_ERROR "NVCC/C++ compiler combination does not seem to be supported. CUDA frequently does not support the latest versions of the host compiler, so you might want to try an earlier C++ compiler version and make sure your CUDA compiler and driver are as recent as possible. Set the GMX_NVCC_WORKS CMake cache variable to bypass this check if you know what you are doing.") -+ elseif(CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 11.2 AND CUDA_VERSION VERSION_GREATER 11.4 AND CUDA_VERSION VERSION_LESS 11.7) # Issue #4574, #4641 -+ # Above, we should be checking for VERSION_LESS 11.6.2, but CUDA_VERSION is only "major.minor" -+ message(FATAL_ERROR "CUDA versions 11.5-11.6.1 are known to be incompatible with some GCC 11.x. Use a different GCC or update your CUDA installation to at least CUDA 11.6.2") -+ else() -+ message(FATAL_ERROR "CUDA compiler does not seem to be functional or is not compatible with the host compiler. Set the GMX_NVCC_WORKS CMake cache variable to bypass this check if you know what you are doing.") -+ endif() -+ elseif(NOT GMX_CUDA_TEST_COMPILER_QUIETLY) -+ message(STATUS "Check for working NVCC/C++ compiler combination - works") -+ set(GMX_NVCC_WORKS TRUE CACHE INTERNAL "Nvcc can compile a trivial test program") -+ endif() -+endif() # GMX_CHECK_NVCC -+ -+# Tests a single flag to use with nvcc. -+# -+# If the flags are accepted, they are appended to the variable named -+# in the first argument. The cache variable named in the second -+# argument is used to avoid rerunning the check in future invocations -+# of cmake. The list of flags to check follows these two required -+# arguments. -+# -+# Note that a space-separated string of flags, or a flag-value pair -+# separated by spaces will not work. Use the single-argument forms -+# accepted by nvcc, like "--arg=value". -+# -+# As this code is not yet tested on Windows, it always accepts the -+# flags in that case. -+function(gmx_add_nvcc_flag_if_supported _output_variable_name_to_append_to _flags_cache_variable_name) -+ # If the check has already been run, do not re-run it -+ if (NOT ${_flags_cache_variable_name} AND NOT WIN32) -+ message(STATUS "Checking if nvcc accepts flags ${ARGN}") -+ # See detailed comment about gcc 7 below -+ if (CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 8) -+ set(_cache_variable_value TRUE) -+ message(STATUS "Checking if nvcc accepts flags ${ARGN} - Assuming success when using gcc 7") -+ else() -+ if(NOT(CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 11)) -+ set(CCBIN "--compiler-bindir=${CUDA_HOST_COMPILER}") -+ endif() -+ execute_process( -+ COMMAND ${CUDA_NVCC_EXECUTABLE} ${ARGN} ${CCBIN} "${CMAKE_SOURCE_DIR}/cmake/TestCUDA.cu" -+ RESULT_VARIABLE _cuda_success -+ OUTPUT_QUIET -+ ERROR_QUIET -+ ) -+ # Convert the success value to a boolean and report status -+ if (_cuda_success EQUAL 0) -+ set(_cache_variable_value TRUE) -+ message(STATUS "Checking if nvcc accepts flags ${ARGN} - Success") -+ else() -+ set(_cache_variable_value FALSE) -+ message(STATUS "Checking if nvcc accepts flags ${ARGN} - Failed") -+ endif() -+ endif() -+ set(${_flags_cache_variable_name} ${_cache_variable_value} CACHE BOOL "Whether NVCC supports flag(s) ${ARGN}") -+ endif() -+ # Append the flags to the output variable if they have been tested to work -+ if (${_flags_cache_variable_name} OR WIN32) -+ list(APPEND ${_output_variable_name_to_append_to} ${ARGN}) -+ set(${_output_variable_name_to_append_to} ${${_output_variable_name_to_append_to}} PARENT_SCOPE) -+ endif() -+endfunction() -+ -+# Versions of gcc 7 have differing behavior when executing -+# -+# nvcc $args --compiler-bindir=gcc TestCUDA.cu -+# -+# and would need e.g. adding -lstdc++ to the command line so that -+# linking of a C++/CUDA object by the C-compiler flavor of gcc works. -+# This means we can't reliably test compiler flags in this case -+# without risking creating other problems. Instead we assume (above) -+# that all compiler flags will work, and issue this warning. -+# We also want to skip this warning during GROMACS CI testing. -+if (CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 8 -+ AND NOT DEFINED ENV{GITLAB_CI}) -+ message(WARNING "You are using gcc version 7 with the CUDA compiler nvcc. GROMACS cannot reliably test compiler arguments for this combination, so if you later experience errors in building GROMACS, please use a more recent version of gcc.") -+endif() -+ - # If any of these manual override variables for target CUDA GPU architectures - # or virtual architecture is set, parse the values and assemble the nvcc - # command line for these. Otherwise use our defaults. - # Note that the manual override variables require a semicolon separating - # architecture codes. -+set(GMX_CUDA_NVCC_GENCODE_FLAGS) - if (GMX_CUDA_TARGET_SM OR GMX_CUDA_TARGET_COMPUTE) -- set(GMX_CUDA_NVCC_GENCODE_FLAGS) - set(_target_sm_list ${GMX_CUDA_TARGET_SM}) - foreach(_target ${_target_sm_list}) -- list(APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_${_target},code=sm_${_target}") -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_${_target} "--generate-code=arch=compute_${_target},code=sm_${_target}") -+ if (NOT NVCC_HAS_GENCODE_COMPUTE_AND_SM_${_target} AND NOT WIN32) -+ message(FATAL_ERROR "Your choice of ${_target} in GMX_CUDA_TARGET_SM was not accepted by nvcc, please choose a target that it accepts") -+ endif() - endforeach() - set(_target_compute_list ${GMX_CUDA_TARGET_COMPUTE}) - foreach(_target ${_target_compute_list}) -- list(APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_${_target},code=compute_${_target}") -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_${_target} --generate-code=arch=compute_${_target},code=compute_${_target}) -+ if (NOT NVCC_HAS_GENCODE_COMPUTE_${_target} AND NOT WIN32) -+ message(FATAL_ERROR "Your choice of ${_target} in GMX_CUDA_TARGET_COMPUTE was not accepted by nvcc, please choose a target that it accepts") -+ endif() - endforeach() - else() - # Set the CUDA GPU architectures to compile for: -- # - with CUDA >=9.0 CC 7.0 is supported and CC 2.0 is no longer supported -- # => compile sm_30, sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70 SASS, and compute_35, compute_70 PTX -- # - with CUDA >=10.0 CC 7.5 is supported -- # => compile sm_30, sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70, sm_75 SASS, and compute_35, compute_75 PTX - # - with CUDA >=11.0 CC 8.0 is supported - # => compile sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70, sm_75, sm_80 SASS, and compute_35, compute_80 PTX - - # First add flags that trigger SASS (binary) code generation for physical arch -- if(CUDA_VERSION VERSION_LESS "11.0") -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_30,code=sm_30") -- endif() -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_35,code=sm_35") -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_37,code=sm_37") -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_50,code=sm_50") -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_52,code=sm_52") -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_60,code=sm_60") -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_61,code=sm_61") -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_70,code=sm_70") -- if(NOT CUDA_VERSION VERSION_LESS "10.0") -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_75,code=sm_75") -- endif() -- if(NOT CUDA_VERSION VERSION_LESS "11.0") -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_80,code=sm_80") -- # Requesting sm or compute 35, 37, or 50 triggers deprecation messages with -- # nvcc 11.0, which we need to suppress for use in CI -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-Wno-deprecated-gpu-targets") -- endif() -- if(NOT CUDA_VERSION VERSION_LESS "11.1") -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_86,code=sm_86") -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_35 --generate-code=arch=compute_35,code=sm_35) -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_37 --generate-code=arch=compute_37,code=sm_37) -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_50 --generate-code=arch=compute_50,code=sm_50) -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_52 --generate-code=arch=compute_52,code=sm_52) -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_60 --generate-code=arch=compute_60,code=sm_60) -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_61 --generate-code=arch=compute_61,code=sm_61) -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_70 --generate-code=arch=compute_70,code=sm_70) -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_75 --generate-code=arch=compute_75,code=sm_75) -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_80 --generate-code=arch=compute_80,code=sm_80) -+ # Don't attempt to add newest architectures with old GNU compiler, to avoid issues in CI -+ # related to being unable to test which flags are supported -+ if (NOT (CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 8)) -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_86 --generate-code=arch=compute_86,code=sm_86) -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_89 --generate-code=arch=compute_89,code=sm_89) -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_90 --generate-code=arch=compute_90,code=sm_90) - endif() -+ # Requesting sm or compute 35, 37, or 50 triggers deprecation messages with -+ # nvcc 11.0, which we need to suppress for use in CI -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_WARNING_NO_DEPRECATED_GPU_TARGETS -Wno-deprecated-gpu-targets) - - # Next add flags that trigger PTX code generation for the - # newest supported virtual arch that's useful to JIT to future architectures - # as well as an older one suitable for JIT-ing to any rare intermediate arch - # (like that of Jetson / Drive PX devices) -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_35,code=compute_35") -- if(CUDA_VERSION VERSION_LESS "11.0") -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_32,code=compute_32") -- else() -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_53,code=compute_53") -- endif() -- if(NOT CUDA_VERSION VERSION_LESS "11.0") -- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_80,code=compute_80") -- endif() -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_53 --generate-code=arch=compute_53,code=sm_53) -+ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_80 --generate-code=arch=compute_80,code=sm_80) - endif() - - if (GMX_CUDA_TARGET_SM) -@@ -158,27 +247,20 @@ - # FindCUDA.cmake is unaware of the mechanism used by cmake to embed - # the compiler flag for the required C++ standard in the generated - # build files, so we have to pass it ourselves --if (CUDA_VERSION VERSION_LESS 11.0) -- # CUDA doesn't formally support C++17 until version 11.0, so for -- # now host-side code that compiles with CUDA is restricted to -- # C++14. This needs to be expressed formally for older CUDA -- # version. -+ -+# gcc-7 pre-dated C++17, so uses the -std=c++1z compiler flag for it, -+# which modern nvcc does not recognize. So we work around that by -+# compiling in C++14 mode. Clang doesn't have this problem because nvcc -+# only supports version of clang that already understood -std=c++17 -+if (CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 8) - list(APPEND GMX_CUDA_NVCC_FLAGS "${CMAKE_CXX14_STANDARD_COMPILE_OPTION}") - else() -- # gcc-7 pre-dated C++17, so uses the -std=c++1z compiler flag for it, -- # which modern nvcc does not recognize. So we work around that by -- # compiling in C++14 mode. Clang doesn't have this problem because nvcc -- # only supports version of clang that already understood -std=c++17 -- if (CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 8) -- list(APPEND GMX_CUDA_NVCC_FLAGS "${CMAKE_CXX14_STANDARD_COMPILE_OPTION}") -- else() -- list(APPEND GMX_CUDA_NVCC_FLAGS "${CMAKE_CXX17_STANDARD_COMPILE_OPTION}") -- endif() -+ list(APPEND GMX_CUDA_NVCC_FLAGS "${CMAKE_CXX17_STANDARD_COMPILE_OPTION}") - endif() - - # assemble the CUDA flags - list(APPEND GMX_CUDA_NVCC_FLAGS "${GMX_CUDA_NVCC_GENCODE_FLAGS}") --list(APPEND GMX_CUDA_NVCC_FLAGS "-use_fast_math") -+gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_FLAGS NVCC_HAS_USE_FAST_MATH -use_fast_math) - - # assemble the CUDA host compiler flags - list(APPEND GMX_CUDA_NVCC_FLAGS "${CUDA_HOST_COMPILER_OPTIONS}") -@@ -187,12 +269,18 @@ - # CUDA header cuda_runtime_api.h in at least CUDA 10.1 uses 0 - # where nullptr would be preferable. GROMACS can't fix these, so - # must suppress them. -- GMX_TEST_CXXFLAG(CXXFLAGS_NO_ZERO_AS_NULL_POINTER_CONSTANT "-Wno-zero-as-null-pointer-constant" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS) -+ GMX_TEST_CXXFLAG(HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT "-Wno-zero-as-null-pointer-constant" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS) - - # CUDA header crt/math_functions.h in at least CUDA 10.x and 11.1 - # used throw() specifications that are deprecated in more recent - # C++ versions. GROMACS can't fix these, so must suppress them. -- GMX_TEST_CXXFLAG(CXXFLAGS_NO_DEPRECATED_DYNAMIC_EXCEPTION_SPEC "-Wno-deprecated-dynamic-exception-spec" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS) -+ GMX_TEST_CXXFLAG(HAS_WARNING_NO_DEPRECATED_DYNAMIC_EXCEPTION_SPEC "-Wno-deprecated-dynamic-exception-spec" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS) -+ -+ # CUDA headers cuda_runtime.h and channel_descriptor.h in at least -+ # CUDA 11.0 uses many C-style casts, which are ncessary for this -+ # header to work for C. GROMACS can't fix these, so must suppress -+ # the warnings they generate -+ GMX_TEST_CXXFLAG(HAS_WARNING_NO_OLD_STYLE_CAST "-Wno-old-style-cast" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS) - - # Add these flags to those used for the host compiler. The - # "-Xcompiler" prefix directs nvcc to only use them for host -@@ -205,37 +293,6 @@ - string(TOUPPER "${CMAKE_BUILD_TYPE}" _build_type) - gmx_check_if_changed(_cuda_nvcc_executable_or_flags_changed CUDA_NVCC_EXECUTABLE CUDA_NVCC_FLAGS CUDA_NVCC_FLAGS_${_build_type}) - --# We would like to be helpful and reject the host compiler with a --# clear error message at configure time, rather than let nvcc --# later reject the host compiler as not supported when the first --# CUDA source file is built. We've implemented that for current --# nvcc running on Unix-like systems, but e.g. changes to nvcc --# will further affect the limited portability of this checking --# code. Set the CMake variable GMX_NVCC_WORKS on if you want to --# bypass this check. --if((_cuda_nvcc_executable_or_flags_changed OR CUDA_HOST_COMPILER_CHANGED OR NOT GMX_NVCC_WORKS) AND NOT WIN32) -- message(STATUS "Check for working NVCC/C++ compiler combination with nvcc '${CUDA_NVCC_EXECUTABLE}'") -- execute_process(COMMAND ${CUDA_NVCC_EXECUTABLE} -ccbin ${CUDA_HOST_COMPILER} -c ${CUDA_NVCC_FLAGS} ${CUDA_NVCC_FLAGS_${_build_type}} ${CMAKE_SOURCE_DIR}/cmake/TestCUDA.cu -- RESULT_VARIABLE _cuda_test_res -- OUTPUT_VARIABLE _cuda_test_out -- ERROR_VARIABLE _cuda_test_err -- OUTPUT_STRIP_TRAILING_WHITESPACE) -- -- if(${_cuda_test_res}) -- message(STATUS "Check for working NVCC/C compiler combination - broken") -- message(STATUS "${CUDA_NVCC_EXECUTABLE} standard output: '${_cuda_test_out}'") -- message(STATUS "${CUDA_NVCC_EXECUTABLE} standard error: '${_cuda_test_err}'") -- if(${_cuda_test_err} MATCHES "nsupported") -- message(FATAL_ERROR "NVCC/C++ compiler combination does not seem to be supported. CUDA frequently does not support the latest versions of the host compiler, so you might want to try an earlier C++ compiler version and make sure your CUDA compiler and driver are as recent as possible.") -- else() -- message(FATAL_ERROR "CUDA compiler does not seem to be functional.") -- endif() -- elseif(NOT GMX_CUDA_TEST_COMPILER_QUIETLY) -- message(STATUS "Check for working NVCC/C++ compiler combination - works") -- set(GMX_NVCC_WORKS TRUE CACHE INTERNAL "Nvcc can compile a trivial test program") -- endif() --endif() # GMX_CHECK_NVCC -- - - # The flags are set as local variables which shadow the cache variables. The cache variables - # (can be set by the user) are appended. This is done in a macro to set the flags when all diff --git a/sci-chemistry/gromacs/files/gromacs-2021-musl-stdint.patch b/sci-chemistry/gromacs/files/gromacs-2021-musl-stdint.patch deleted file mode 100644 index c94fc5598f91..000000000000 --- a/sci-chemistry/gromacs/files/gromacs-2021-musl-stdint.patch +++ /dev/null @@ -1,25 +0,0 @@ -From 8a38303c52fbca07c850e0c4cd03a783aabf9e49 Mon Sep 17 00:00:00 2001 -From: Paul Bauer <paul.bauer.q@gmail.com> -Date: Mon, 21 Feb 2022 09:53:46 +0100 -Subject: [PATCH] Fix missing includes for musl libc - -Fixes #4404 ---- - src/gromacs/math/vectypes.h | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/src/gromacs/math/vectypes.h b/src/gromacs/math/vectypes.h -index d4d5211d11..bd9d31de20 100644 ---- a/src/gromacs/math/vectypes.h -+++ b/src/gromacs/math/vectypes.h -@@ -40,6 +40,7 @@ - - #include <cassert> - #include <cmath> -+#include <cstdint> - - #include <algorithm> - #include <type_traits> --- -2.35.1 - diff --git a/sci-chemistry/gromacs/files/gromacs-2025.0-beta-fix-man-build.patch b/sci-chemistry/gromacs/files/gromacs-2025.0-beta-fix-man-build.patch new file mode 100644 index 000000000000..2eb2d45035a2 --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-2025.0-beta-fix-man-build.patch @@ -0,0 +1,41 @@ +From 5c9a86c6c6ae3e9202e2feb0e1d33df40818c251 Mon Sep 17 00:00:00 2001 +From: Andrey Alekseenko <al42and@gmail.com> +Date: Tue, 10 Dec 2024 16:21:55 +0100 +Subject: [PATCH] Don't require GMXAPI for building man pages + +Refs #4767 +Fixes #5241 +--- + docs/conf.cmakein.py | 9 +++++++-- + 1 file changed, 7 insertions(+), 2 deletions(-) + +diff --git a/docs/conf.cmakein.py b/docs/conf.cmakein.py +index 577bcba9bd8..46986adbc07 100644 +--- a/docs/conf.cmakein.py ++++ b/docs/conf.cmakein.py +@@ -55,7 +55,12 @@ gmxapi_staging_path = "@GMXAPI_PYTHON_STAGING_DIR@" + if gmxapi_staging_path and os.path.isdir(gmxapi_staging_path): + sys.path.append(gmxapi_staging_path) + +-import gmxapi ++try: ++ import gmxapi ++except ImportError: ++ gmxapi_version_string = "N/A" ++else: ++ gmxapi_version_string = gmxapi.__version__ + + gmx_admin_scripts_path = "@GMX_ADMIN_DIR@" + gmx_containers_path = "@GMX_ADMIN_DIR@/containers" +@@ -277,7 +282,7 @@ rst_epilog += """ + .. |thisyear| replace:: {thisyear_string} + """.format( + gmx_version_string=gmx_version_string, +- gmxapi_version_string=gmxapi.__version__, ++ gmxapi_version_string=gmxapi_version_string, + regressiontest_version=regressiontest_version, + thisyear_string=thisyear_string, + ) +-- +GitLab + diff --git a/sci-chemistry/gromacs/files/gromacs-gcc-15.patch b/sci-chemistry/gromacs/files/gromacs-gcc-15.patch new file mode 100644 index 000000000000..45ac82493bec --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-gcc-15.patch @@ -0,0 +1,36 @@ +From 9dfaba553cb5aa0c0d689de1555a3bb45ae7dd3a Mon Sep 17 00:00:00 2001 +From: Alexey Shvetsov <alexxyum@gmail.com> +Date: Thu, 21 Nov 2024 10:56:17 +0300 +Subject: [PATCH] Fix build with gcc-15 +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + +Error is +energyhistory.h:89:5: error: ‘int64_t’ does not name a type + 89 | int64_t nsteps; //! The number of steps in the history + | ^~~~~~~ + +Ref: https://bugs.gentoo.org/939006 + +Signed-off-by: Alexey Shvetsov <alexxyum@gmail.com> +--- + src/gromacs/mdtypes/energyhistory.h | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/src/gromacs/mdtypes/energyhistory.h b/src/gromacs/mdtypes/energyhistory.h +index 0c8fecfae7..f80d4c56b9 100644 +--- a/src/gromacs/mdtypes/energyhistory.h ++++ b/src/gromacs/mdtypes/energyhistory.h +@@ -47,6 +47,8 @@ + #ifndef GMX_MDLIB_ENERGYHISTORY_H + #define GMX_MDLIB_ENERGYHISTORY_H + ++#include <cstdint> ++ + #include <memory> + #include <vector> + +-- +2.45.2 + diff --git a/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild deleted file mode 100644 index c93e5baf72ef..000000000000 --- a/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild +++ /dev/null @@ -1,351 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python3_{10..12} ) - -DISTUTILS_OPTIONAL=1 -DISTUTILS_USE_PEP517=no -DISTUTILS_SINGLE_IMPL=1 - -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic 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 - " - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI=" - https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${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="https://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 ) - openmp? ( - sys-devel/gcc[openmp] - sys-devel/clang-runtime[openmp] - ) - fftw? ( sci-libs/fftw:3.0= ) - hwloc? ( sys-apps/hwloc:= ) - lapack? ( virtual/lapack ) - lmfit? ( sci-libs/lmfit:= ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - ${PYTHON_DEPS} - " -BDEPEND="${CDEPEND} - virtual/pkgconfig - build-manual? ( - app-text/doxygen - $(python_gen_cond_dep ' - dev-python/sphinx[${PYTHON_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 ) - opencl? ( 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() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp -} - -pkg_setup() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp - python-single-r1_pkg_setup -} - -src_unpack() { - if [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \ - EGIT_BRANCH="${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 - <?xml version="1.0" encoding="UTF-8"?> - <!DOCTYPE policymap [ - <!ELEMENT policymap (policy)+> - !ATTLIST policymap xmlns CDATA #FIXED ''> - <!ELEMENT policy EMPTY> - <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED - name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED - stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> - ]> - <policymap> - <policy domain="coder" rights="read | write" pattern="PS" /> - <policy domain="coder" rights="read | write" pattern="PS2" /> - <policy domain="coder" rights="read | write" pattern="PS3" /> - <policy domain="coder" rights="read | write" pattern="EPS" /> - <policy domain="coder" rights="read | write" pattern="PDF" /> - <policy domain="coder" rights="read | write" pattern="XPS" /> - </policymap> - 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) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl; then - local bits=$(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" ) - local 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" - local 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 - 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 - 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 gromacs related papers from list:" - einfo "https://www.gromacs.org/articles.html" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2023.5.ebuild b/sci-chemistry/gromacs/gromacs-2023.5.ebuild index 4ee08b22a7f0..83ceb0fceb65 100644 --- a/sci-chemistry/gromacs/gromacs-2023.5.ebuild +++ b/sci-chemistry/gromacs/gromacs-2023.5.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 ~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" @@ -47,7 +47,7 @@ CDEPEND=" opencl? ( virtual/opencl ) openmp? ( sys-devel/gcc[openmp] - sys-devel/clang-runtime[openmp] + llvm-core/clang-runtime[openmp] ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) @@ -60,7 +60,7 @@ CDEPEND=" " BDEPEND="${CDEPEND} virtual/pkgconfig - clang? ( >=sys-devel/clang-6:* ) + clang? ( >=llvm-core/clang-6:* ) build-manual? ( app-text/doxygen $(python_gen_cond_dep ' diff --git a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild b/sci-chemistry/gromacs/gromacs-2023.9999.ebuild index 4ee08b22a7f0..5c6ffc9fc1a8 100644 --- a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2023.9999.ebuild @@ -47,7 +47,7 @@ CDEPEND=" opencl? ( virtual/opencl ) openmp? ( sys-devel/gcc[openmp] - sys-devel/clang-runtime[openmp] + llvm-core/clang-runtime[openmp] ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) @@ -60,7 +60,7 @@ CDEPEND=" " BDEPEND="${CDEPEND} virtual/pkgconfig - clang? ( >=sys-devel/clang-6:* ) + clang? ( >=llvm-core/clang-6:* ) build-manual? ( app-text/doxygen $(python_gen_cond_dep ' diff --git a/sci-chemistry/gromacs/gromacs-2024.3.ebuild b/sci-chemistry/gromacs/gromacs-2024.3.ebuild index 2101629ebc36..cc4c9393b140 100644 --- a/sci-chemistry/gromacs/gromacs-2024.3.ebuild +++ b/sci-chemistry/gromacs/gromacs-2024.3.ebuild @@ -26,7 +26,7 @@ else doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" # since 2022 arm support was dropped (but not arm64) - KEYWORDS="~amd64 -arm ~arm64 ~riscv ~x86 ~amd64-linux ~x86-linux ~x64-macos" + KEYWORDS="amd64 -arm arm64 ~riscv -x86 ~amd64-linux -x86-linux ~x64-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" @@ -47,7 +47,7 @@ CDEPEND=" opencl? ( virtual/opencl ) openmp? ( sys-devel/gcc[openmp] - sys-devel/clang-runtime[openmp] + llvm-core/clang-runtime[openmp] ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) @@ -60,7 +60,7 @@ CDEPEND=" " BDEPEND="${CDEPEND} virtual/pkgconfig - clang? ( >=sys-devel/clang-6:* ) + clang? ( >=llvm-core/clang-6:* ) build-manual? ( app-text/doxygen $(python_gen_cond_dep ' @@ -92,6 +92,8 @@ DOCS=( AUTHORS README ) RESTRICT="!test? ( test )" +PATCHES=( "${FILESDIR}/${PN}-gcc-15.patch" ) + if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi diff --git a/sci-chemistry/gromacs/gromacs-2024.ebuild b/sci-chemistry/gromacs/gromacs-2024.4.ebuild index a3319899d419..7f2e7152df0f 100644 --- a/sci-chemistry/gromacs/gromacs-2024.ebuild +++ b/sci-chemistry/gromacs/gromacs-2024.4.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" @@ -45,6 +45,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) opencl? ( virtual/opencl ) + openmp? ( + sys-devel/gcc[openmp] + llvm-core/clang-runtime[openmp] + ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) @@ -56,7 +60,7 @@ CDEPEND=" " BDEPEND="${CDEPEND} virtual/pkgconfig - clang? ( >=sys-devel/clang-6:* ) + clang? ( >=llvm-core/clang-6:* ) build-manual? ( app-text/doxygen $(python_gen_cond_dep ' @@ -88,6 +92,8 @@ DOCS=( AUTHORS README ) RESTRICT="!test? ( test )" +PATCHES=( "${FILESDIR}/${PN}-gcc-15.patch" ) + if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi diff --git a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild b/sci-chemistry/gromacs/gromacs-2024.9999.ebuild index 2101629ebc36..b681516f603a 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 ~riscv ~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" @@ -47,7 +47,7 @@ CDEPEND=" opencl? ( virtual/opencl ) openmp? ( sys-devel/gcc[openmp] - sys-devel/clang-runtime[openmp] + llvm-core/clang-runtime[openmp] ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) @@ -60,7 +60,7 @@ CDEPEND=" " BDEPEND="${CDEPEND} virtual/pkgconfig - clang? ( >=sys-devel/clang-6:* ) + clang? ( >=llvm-core/clang-6:* ) build-manual? ( app-text/doxygen $(python_gen_cond_dep ' diff --git a/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild b/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild index 8b99117678ed..b3605cdfa525 100644 --- a/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild @@ -18,14 +18,16 @@ if [[ ${PV} = *9999* ]]; then https://gitlab.com/gromacs/gromacs.git https://github.com/gromacs/gromacs.git " - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}" inherit git-r3 else SRC_URI=" https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" + # since 2022 arm support was dropped (but not arm64) + # since 2025 x86-32 support was dropped + 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" @@ -38,35 +40,46 @@ HOMEPAGE="https://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 build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi nnpot +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:=[profiler] ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) opencl? ( virtual/opencl ) openmp? ( sys-devel/gcc[openmp] - sys-devel/clang-runtime[openmp] + llvm-core/clang-runtime[openmp] ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) - lmfit? ( sci-libs/lmfit:= ) mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) + mpi? ( virtual/mpi[cxx] ) + nnpot? ( sci-libs/caffe2[cuda=,opencl=] ) + sci-libs/lmfit:= + >=dev-cpp/muParser-2.3:= ${PYTHON_DEPS} " BDEPEND="${CDEPEND} virtual/pkgconfig + clang? ( >=llvm-core/clang-6:* ) + doc? ( + $(python_gen_cond_dep ' + dev-python/sphinx[${PYTHON_USEDEP}] + dev-python/sphinx-copybutton[${PYTHON_USEDEP}] + dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}] + dev-python/sphinx-argparse[${PYTHON_USEDEP}] + dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}] + ') + ) build-manual? ( app-text/doxygen $(python_gen_cond_dep ' dev-python/sphinx[${PYTHON_USEDEP}] + dev-python/sphinx-copybutton[${PYTHON_USEDEP}] + dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}] + dev-python/sphinx-argparse[${PYTHON_USEDEP}] + dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}] ') media-gfx/mscgen media-gfx/graphviz @@ -82,6 +95,7 @@ REQUIRED_USE=" cuda? ( single-precision ) opencl? ( single-precision ) cuda? ( !opencl ) + clang-cuda? ( clang cuda ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" @@ -90,9 +104,8 @@ DOCS=( AUTHORS README ) RESTRICT="!test? ( test )" PATCHES=( - "${FILESDIR}/${PN}-2021-musl-stdint.patch" - "${FILESDIR}/${PN}-2021-cuda-detection.patch" - "${FILESDIR}/${PN}-2021-cstdint-include.patch" + "${FILESDIR}/${PN}-gcc-15.patch" + "${FILESDIR}/${PN}-2025.0-beta-fix-man-build.patch" ) if [[ ${PV} != *9999 ]]; then @@ -128,6 +141,19 @@ src_prepare() { xdg_environment_reset #591952 + # we can use clang as default + if use clang && ! tc-is-clang ; then + export CC=${CHOST}-clang + export CXX=${CHOST}-clang++ + else + tc-export CXX CC + fi + # clang-cuda need to filter mfpmath + if use clang-cuda ; then + filter-mfpmath sse + filter-mfpmath i386 + fi + cmake_src_prepare use cuda && cuda_src_prepare @@ -172,6 +198,11 @@ src_prepare() { src_configure() { local mycmakeargs_pre=( ) extra fft_opts=( ) local acce="AUTO" + local nnpot="OFF" + + if use nnpot; then + nnpot="TORCH" + fi if use custom-cflags; then #go from slowest to fastest acceleration @@ -208,25 +239,23 @@ src_configure() { fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) fi - if use lmfit; then - local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) - else - local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) - fi - mycmakeargs_pre+=( "${fft_opts[@]}" "${lmfit_opts[@]}" - -DGMX_X11=$(usex X) + -DGMX_USE_LMFIT=EXTERNAL + -DGMX_USE_MUPARSER=EXTERNAL -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_USE_HDF5=off -DGMX_HWLOC=$(usex hwloc) -DGMX_DEFAULT_SUFFIX=off + -DGMX_BUILD_HELP=$(usex doc) -DGMX_SIMD="$acce" + -DGMX_NNPOT="$nnpot" -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" -DBUILD_TESTING=$(usex test) -DGMX_BUILD_UNITTESTS=$(usex test) @@ -244,10 +273,11 @@ src_configure() { [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" local gpu=( "-DGMX_GPU=OFF" ) [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) + [[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" ) use opencl && gpu=( "-DGMX_GPU=OPENCL" ) local mycmakeargs=( ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF + -DGMX_MPI=$(usex mpi) -DGMX_THREAD_MPI=$(usex threads) -DGMXAPI=$(usex gmxapi) -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) @@ -260,25 +290,6 @@ src_configure() { BUILD_DIR="${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" - local 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 } @@ -287,6 +298,8 @@ src_compile() { einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake_src_compile + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile man if use python; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake_src_compile python_packaging/all @@ -298,10 +311,6 @@ src_compile() { 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 } @@ -326,13 +335,9 @@ src_install() { if use doc; then if [[ ${PV} != *9999* ]]; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" + newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf" fi fi - - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake_src_install done if use tng; then diff --git a/sci-chemistry/gromacs/gromacs-2022.6.ebuild b/sci-chemistry/gromacs/gromacs-2025.9999.ebuild index 92b1f497c860..bec110e3340c 100644 --- a/sci-chemistry/gromacs/gromacs-2022.6.ebuild +++ b/sci-chemistry/gromacs/gromacs-2025.9999.ebuild @@ -18,15 +18,16 @@ if [[ ${PV} = *9999* ]]; then https://gitlab.com/gromacs/gromacs.git https://github.com/gromacs/gromacs.git " - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}" inherit git-r3 else SRC_URI=" - https://ftp.gromacs.org/gromacs/${P}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV}.pdf ) - test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV}.tar.gz )" + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" # since 2022 arm support was dropped (but not arm64) - KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" + # since 2025 x86-32 support was dropped + KEYWORDS="~amd64 -arm ~arm64 ~riscv -x86 ~amd64-linux -x86-linux ~x64-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" @@ -39,7 +40,7 @@ HOMEPAGE="https://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" blas? ( virtual/blas ) @@ -47,24 +48,38 @@ CDEPEND=" opencl? ( virtual/opencl ) openmp? ( sys-devel/gcc[openmp] - sys-devel/clang-runtime[openmp] + llvm-core/clang-runtime[openmp] ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi[cxx] ) + nnpot? ( sci-libs/caffe2[cuda=,opencl=] ) sci-libs/lmfit:= >=dev-cpp/muParser-2.3:= ${PYTHON_DEPS} " BDEPEND="${CDEPEND} virtual/pkgconfig - clang? ( >=sys-devel/clang-6:* ) + clang? ( >=llvm-core/clang-6:* ) + doc? ( + $(python_gen_cond_dep ' + dev-python/sphinx[${PYTHON_USEDEP}] + dev-python/sphinx-copybutton[${PYTHON_USEDEP}] + dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}] + dev-python/sphinx-argparse[${PYTHON_USEDEP}] + dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}] + ') + ) build-manual? ( app-text/doxygen $(python_gen_cond_dep ' dev-python/sphinx[${PYTHON_USEDEP}] + dev-python/sphinx-copybutton[${PYTHON_USEDEP}] + dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}] + dev-python/sphinx-argparse[${PYTHON_USEDEP}] + dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}] ') media-gfx/mscgen media-gfx/graphviz @@ -72,8 +87,7 @@ BDEPEND="${CDEPEND} dev-texlive/texlive-latexextra media-gfx/imagemagick )" -RDEPEND="${CDEPEND} - <sci-chemistry/dssp-4" +RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) @@ -179,6 +193,11 @@ src_prepare() { src_configure() { local mycmakeargs_pre=( ) extra fft_opts=( ) local acce="AUTO" + local nnpot="OFF" + + if use nnpot; then + nnpot="TORCH" + fi if use custom-cflags; then #go from slowest to fastest acceleration @@ -226,11 +245,13 @@ src_configure() { -DGMX_COOL_QUOTES=$(usex offensive) -DGMX_USE_TNG=$(usex tng) -DGMX_BUILD_MANUAL=$(usex build-manual) + -DGMX_USE_HDF5=off -DGMX_HWLOC=$(usex hwloc) -DGMX_DEFAULT_SUFFIX=off + -DGMX_BUILD_HELP=$(usex doc) -DGMX_SIMD="$acce" + -DGMX_NNPOT="$nnpot" -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" - -DGMX_DSSP_PROGRAM_PATH="${EPREFIX}/usr/bin/dssp" -DBUILD_TESTING=$(usex test) -DGMX_BUILD_UNITTESTS=$(usex test) -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" @@ -272,6 +293,8 @@ src_compile() { einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake_src_compile + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile man if use python; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake_src_compile python_packaging/all @@ -307,7 +330,7 @@ src_install() { if use doc; then if [[ ${PV} != *9999* ]]; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" + newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf" fi fi done diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 01ebc8ab87b7..1cc913c0aeed 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -26,7 +26,8 @@ else doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" # since 2022 arm support was dropped (but not arm64) - KEYWORDS="~amd64 -arm ~arm64 ~riscv ~x86 ~amd64-linux ~x86-linux ~x64-macos" + # since 2025 x86-32 support was dropped + KEYWORDS="~amd64 -arm ~arm64 ~riscv -x86 ~amd64-linux -x86-linux ~x64-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" @@ -39,7 +40,7 @@ HOMEPAGE="https://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" blas? ( virtual/blas ) @@ -47,7 +48,7 @@ CDEPEND=" opencl? ( virtual/opencl ) openmp? ( sys-devel/gcc[openmp] - sys-devel/clang-runtime[openmp] + llvm-core/clang-runtime[openmp] ) fftw? ( sci-libs/fftw:3.0= ) hdf5? ( sci-libs/hdf5 ) @@ -62,7 +63,16 @@ CDEPEND=" " BDEPEND="${CDEPEND} virtual/pkgconfig - clang? ( >=sys-devel/clang-6:* ) + clang? ( >=llvm-core/clang-6:* ) + doc? ( + $(python_gen_cond_dep ' + dev-python/sphinx[${PYTHON_USEDEP}] + dev-python/sphinx-copybutton[${PYTHON_USEDEP}] + dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}] + dev-python/sphinx-argparse[${PYTHON_USEDEP}] + dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}] + ') + ) build-manual? ( app-text/doxygen $(python_gen_cond_dep ' @@ -239,7 +249,7 @@ src_configure() { -DGMX_USE_HDF5=$(usex hdf5) -DGMX_HWLOC=$(usex hwloc) -DGMX_DEFAULT_SUFFIX=off - -DGMX_BUILD_HELP=on + -DGMX_BUILD_HELP=$(usex doc) -DGMX_SIMD="$acce" -DGMX_NNPOT="$nnpot" -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index 518711308a02..43c6b2799b5c 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -18,7 +18,6 @@ <flag name="gmxapi">Add support for gmxapi library</flag> <flag name="gmxapi-legacy">Enable installing lagacy headers</flag> <flag name="hwloc">Enable HWLoc lib support</flag> - <flag name="lmfit">Use external <pkg>sci-libs/lmfit</pkg></flag> <flag name="nnpot">Allow to use <pkg>sci-libs/caffe2</pkg> for NN Potentials</flag> <flag name="opencl">Enable opencl non-bonded kernels</flag> <flag name="single-precision">Single precision version of gromacs (default)</flag> diff --git a/sci-chemistry/molden/Manifest b/sci-chemistry/molden/Manifest deleted file mode 100644 index cc2d629165b6..000000000000 --- a/sci-chemistry/molden/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST molden6.9.tar.gz 8536291 BLAKE2B f50fd9c6303d215f3b1ea73136a8ecada07102a33cfc5831c412341731d00bd166f59bc260615d4a96c59d50a6a308087f02b637f8a8d36bf19f256ac407ba72 SHA512 dbb4a602f2957d0b1d5afb8748fb8ad012a41fb0dfa816b78e4d2748ea78ee39251846a549fce4b276641d4838a336ecd9cf02b92fcf9739adeb25bb550656ec diff --git a/sci-chemistry/molden/files/molden-6.9-ldflags.patch b/sci-chemistry/molden/files/molden-6.9-ldflags.patch deleted file mode 100644 index 9e8258aeacd7..000000000000 --- a/sci-chemistry/molden/files/molden-6.9-ldflags.patch +++ /dev/null @@ -1,87 +0,0 @@ -diff --git a/makefile b/makefile -index f71a20df..564f9f4e 100644 ---- a/makefile -+++ b/makefile -@@ -299,11 +299,11 @@ src/xwin.o: src/xwin.c src/rots.h - src/xwingl.o: src/xwin.c src/rots.h - - molden: $(OBJS) src/mpdum.o src/xwin.o -- $(LDR) -o molden $(OBJS) src/mpdum.o src/xwin.o $(LIBS) -+ $(LDR) $(LDFLAGS) -o molden $(OBJS) src/mpdum.o src/xwin.o $(LIBS) - mv molden bin/molden - - gmolden: $(OBJS) src/mpdum.o src/xwingl.o -- $(LDR) -fno-builtin -o gmolden $(OBJS) src/mpdum.o src/xwingl.o $(LIBSG) -+ $(LDR) $(LDFLAGS) -fno-builtin -o gmolden $(OBJS) src/mpdum.o src/xwingl.o $(LIBSG) - mv gmolden bin/gmolden - - ambfor/ambfor: src/ambfor/*.f src/ambfor/*.c -@@ -322,14 +322,14 @@ surf/surf: src/surf/*.h src/surf/*.c - # noxwin will not work as long as the old ocglbck calls arent in dummys - - noxwin: $(OBJS) $(DOBJ) src/mpdum.o -- $(LDR) -o molden $(OBJS) $(DOBJ) src/mpdum.o -lm -+ $(LDR) $(LDFLAGS) -o molden $(OBJS) $(DOBJ) src/mpdum.o -lm - mv molden bin/molden.noxwin - - # This version allows the fitting of multipole moments to the electrostatic - # pontential - - molden.mpfit: $(OBJS) src/mpolefit.o src/xwinmp.o -- $(LDR) -o molden $(OBJS) src/mpolefit.o src/xwinmp.o $(LIBS) -+ $(LDR) $(LDFLAGS) -o molden $(OBJS) src/mpolefit.o src/xwinmp.o $(LIBS) - mv molden bin/molden.mpfit - - src/xwinmp.o: src/xwin.c -@@ -340,18 +340,18 @@ src/xwingl.o: src/xwin.c - $(CC) $(CFLAGS) -DDOGL -c src/xwin.c -o src/xwingl.o - - unmullik: src/unmullik.o -- $(LDR) -o bin/unmullik src/unmullik.o -+ $(LDR) $(LDFLAGS) -o bin/unmullik src/unmullik.o - - # short_wrl removes redundant vertices from molden's VRML2 files - # with the courtesy of Andreas Klamt of COSMOSlogic - # - short_wrl: src/short_wrl.o -- $(LDR) -o bin/short_wrl src/short_wrl.o -+ $(LDR) $(LDFLAGS) -o bin/short_wrl src/short_wrl.o - - # conversion of CADPAC output to molden format - - cad2mol: src/cad2mol.o -- $(LDR) -o bin/cad2mol src/cad2mol.o -+ $(LDR) $(LDFLAGS) -o bin/cad2mol src/cad2mol.o - - clean: - rm -f src/$(OBJS) src/mpdum.o src/xwin.o src/xwingl.o bin/molden bin/gmolden bin/ambfor bin/ambmd bin/surf src/ambfor/*.o src/surf/*.o -diff --git a/src/ambfor/makefile b/src/ambfor/makefile -index 9938527e..5de7c65e 100644 ---- a/src/ambfor/makefile -+++ b/src/ambfor/makefile -@@ -50,10 +50,10 @@ mpi: FFLAGS = -c -g -ffast-math -funroll-loops -O3 - mpi: ambfor.mpi ambmd.mpi - - ambfor: ambfor.o qvdw.o alloc.o optimise.o lbfgs.o $(OBJS) -- $(LDR) -o ambfor ambfor.o qvdw.o alloc.o optimise.o lbfgs.o $(OBJS) $(LIBS) -+ $(LDR) $(LDFLAGS) -o ambfor ambfor.o qvdw.o alloc.o optimise.o lbfgs.o $(OBJS) $(LIBS) - - ambmd: md.o verlet.o qvdw.o allocmd.o $(OBJS) -- $(LDR) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS) -+ $(LDR) $(LDFLAGS) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS) - - ambfor.o: ambfor.f - ${FC} -c -g -ffast-math -funroll-loops -o ambfor.o ambfor.f -diff --git a/src/surf/Makefile b/src/surf/Makefile -index 54b7af8e..f216c9eb 100644 ---- a/src/surf/Makefile -+++ b/src/surf/Makefile -@@ -25,7 +25,7 @@ OBJS = surf.o io.o compute.o dual.o utils.o lp.o chull.o tessel_cases.o \ - - # make objects - surf: $(OBJS) Makefile -- $(CC) $(CFLAGS) $(OBJS) -o surf $(LINCLUDE) -+ $(CC) $(CFLAGS) $(OBJS) -o surf $(LINCLUDE) $(LDFLAGS) - - lint: - lint $(INCLUDE) $(SRCS) diff --git a/sci-chemistry/molden/metadata.xml b/sci-chemistry/molden/metadata.xml deleted file mode 100644 index e490bcb8aa87..000000000000 --- a/sci-chemistry/molden/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/molden/molden-6.9-r1.ebuild b/sci-chemistry/molden/molden-6.9-r1.ebuild deleted file mode 100644 index 39ad93accf73..000000000000 --- a/sci-chemistry/molden/molden-6.9-r1.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit desktop fortran-2 flag-o-matic toolchain-funcs - -MY_P="${PN}${PV}" - -DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac" -HOMEPAGE="https://www.theochem.ru.nl/molden/" -SRC_URI="ftp://ftp.science.ru.nl/pub/Molden/${MY_P}.tar.gz" -S="${WORKDIR}/${MY_P}" - -LICENSE="MOLDEN" -SLOT="0" -KEYWORDS="amd64 ~x86" -IUSE="opengl" - -DEPEND=" - x11-libs/libXmu - opengl? ( - media-libs/freeglut - virtual/opengl - virtual/glu - ) -" -RDEPEND="${DEPEND} - sci-chemistry/surf -" - -PATCHES=( - "${FILESDIR}/${P}-ldflags.patch" -) - -src_prepare() { - default - sed 's:shell g77:shell $(FC):g' -i makefile || die -} - -src_compile() { - local args=() - - # Use -mieee on alpha, according to the Makefile - use alpha && append-flags -mieee - - # GCC 10 workaround - # bug #724556 - append-fflags $(test-flags-FC -fallow-argument-mismatch) - - args=( - CC="$(tc-getCC) ${CFLAGS}" - FC="$(tc-getFC)" - LDR="$(tc-getFC)" - FFLAGS="${FFLAGS}" - ) - - einfo "Building Molden..." - emake -j1 molden ambfor/ambfor ambfor/ambmd "${args[@]}" - if use opengl ; then - einfo "Building Molden OpenGL helper..." - emake -j1 "${args[@]}" gmolden - fi -} - -src_install() { - dobin bin/molden bin/ambfor bin/ambmd - if use opengl; then - dobin bin/gmolden - doicon -s 64 haux/gmolden.png - make_desktop_entry gmolden MOLDEN gmolden - fi - - dodoc HISTORY README REGISTER - cd doc || die - uncompress * && dodoc * -} diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index 2ef25b2b27fa..7b6fd1d91c5d 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1,2 +1 @@ -DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c DIST pymol-3.0.0.tar.gz 29510174 BLAKE2B b67818e408045e386e44a203f29cd94a0ce34ec706776d29f78f1720bdc5c79d88f3b3e178882295b5a636d97fe70ff49eb1b021a9a6b96f0f4216bc392219d1 SHA512 eab05a46220339a05d8d4facdce6bfa08c6fc8a858a7b228236ef6c4054207059ef0f53a26bedebe4084a74b510015937fb4477f99612b21412cd75bf0c376a2 diff --git a/sci-chemistry/pymol/files/pymol-2.5.0-format-security.patch b/sci-chemistry/pymol/files/pymol-2.5.0-format-security.patch deleted file mode 100644 index 080e5e8960e4..000000000000 --- a/sci-chemistry/pymol/files/pymol-2.5.0-format-security.patch +++ /dev/null @@ -1,15 +0,0 @@ -Author: Michael Banck <mbanck@debian.org> -Description: Fix "error: format not a string literal and no format arguments [-Werror=format-security]" (#759860) -Forwarded: yes - ---- a/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp -+++ b/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp -@@ -2004,7 +2004,7 @@ namespace { - } - } - catch (std::exception &e) { -- fprintf(stderr, "%s", e.what()); -+ fprintf(stderr, "Cannot write timestamp to mae file: %s\n", e.what()); - return MOLFILE_ERROR; - } - return MOLFILE_SUCCESS; diff --git a/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild b/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild index aeb6bc85c7e1..ff2b8174eeb4 100644 --- a/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild +++ b/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{9..12} ) +PYTHON_COMPAT=( python3_{10..12} ) DISTUTILS_USE_PEP517="setuptools" DISTUTILS_EXT=1 @@ -36,7 +36,7 @@ RDEPEND=" ${DEPEND} media-video/mpeg-tools dev-python/pyopengl[${PYTHON_USEDEP}] - dev-python/PyQt5[opengl,${PYTHON_USEDEP}] + dev-python/pyqt5[opengl,${PYTHON_USEDEP}] dev-python/pmw[${PYTHON_USEDEP}] sci-chemistry/chemical-mime-data " diff --git a/sci-chemistry/pymol/pymol-3.0.0.ebuild b/sci-chemistry/pymol/pymol-3.0.0.ebuild deleted file mode 100644 index b6ec9fbef1e3..000000000000 --- a/sci-chemistry/pymol/pymol-3.0.0.ebuild +++ /dev/null @@ -1,115 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{9..12} ) -DISTUTILS_USE_PEP517="setuptools" -DISTUTILS_EXT=1 - -inherit desktop flag-o-matic xdg distutils-r1 - -DESCRIPTION="A Python-extensible molecular graphics system" -HOMEPAGE="https://www.pymol.org/" -SRC_URI=" - https://dev.gentoo.org/~pacho/${PN}/${PN}-1.8.4.0.png.xz - https://github.com/schrodinger/pymol-open-source/archive/v${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= ) -" -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 -" - -PATCHES=( - "${FILESDIR}/${PN}-2.5.0-format-security.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() { - # -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 ) -} - -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}"/${PN} -} - -python_install_all() { - distutils-r1_python_install_all - - # Move data to correct location - dodir /usr/share/pymol - mv "${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 "${T}"/20pymol - - newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png - make_desktop_entry "${PN} %u" PyMol ${PN} \ - "Graphics;Education;Science;Chemistry;" \ - "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" - - if ! use web; then - rm -rf "${D}/$(python_get_sitedir)/web" || die - fi - - rm -f "${ED}"/usr/share/${PN}/LICENSE || die -} diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r2.ebuild index e0628f111574..9addf38da980 100644 --- a/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild +++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r2.ebuild @@ -35,7 +35,7 @@ CDEPEND="${PYTHON_DEPS} dev-libs/expat sci-libs/netcdf:0= virtual/opengl - >=x11-libs/fltk-1.1.10-r2:1 + x11-libs/fltk:1= x11-libs/libXft x11-libs/libXi cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r3.ebuild index 18bdb88a4c0c..cc5a157bf69a 100644 --- a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild +++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r3.ebuild @@ -35,7 +35,7 @@ CDEPEND="${PYTHON_DEPS} dev-libs/expat sci-libs/netcdf:0= virtual/opengl - >=x11-libs/fltk-1.1.10-r2:1 + x11-libs/fltk:1= x11-libs/libXft x11-libs/libXi cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) |