diff options
Diffstat (limited to 'sci-chemistry')
21 files changed, 240 insertions, 563 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex d843e08ae2e9..310ca9863ef8 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest index f2ac48471677..5924339ee9b5 100644 --- a/sci-chemistry/dssp/Manifest +++ b/sci-chemistry/dssp/Manifest @@ -4,11 +4,7 @@ AUX dssp-2.2.1-boost-1.65-tr1-removal.patch 2126 BLAKE2B dc59d21a6be26ee96b636c1 DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811 DIST dssp-3.0.11.tar.gz 168085 BLAKE2B e1c42fd22cfb2287f10b5deae48b56a4583d4a67737a3485dcbd160d1597a15c2d5105c3794c875d8001abede1c014efb4f7f5b7c250f867bdf9ed95a0860217 SHA512 a0cfe44e517ff1f909ef2928b62ae2c639c6bddfd8a0fb538883f647fd2771e00da68e0fd2521aa02ba3c6d1b0c9b784b7fe142392af3a3abf6ea89f1546bd9d DIST dssp-4.4.10.tar.gz 164259 BLAKE2B 5d82ce25779060f89b50742683102aea53984fca10e54aa3cd0b21c7be3684336f6561928282e40300bb164c5b881797fababa5175c139f5b304a952f21db661 SHA512 1bdbdd4b058801d78cc28dcb23478656dfb322ce81f4fe8ede2cd72640778084ce8c99aff367aff53c26ad221ffa6ebafcf9730005b1a873957d26eb42f724c8 -DIST dssp-4.4.7.tar.gz 163831 BLAKE2B 195c8fb183df00105098967850b01c0d6acf776f7cfa409fc536c8291e7a467da2adfb5f34d8191e33dbb29bfd254cd414c1b7b76ed3f3b854928c4dc8a5fcdd SHA512 2fe2d8a494b570934c0d28804fe69b6569089ded58ec92bf3d83b25ce60a3b9486490909e187b511328f13498ca9027869e922d95a355cf0e21c2564c2db1b5a -DIST dssp-4.4.8.tar.gz 164050 BLAKE2B 0f048b5425f3ecb0e9278da81e2274e817b5ba5ed33a372d0e4c0b0d0600f9ebee2b125f7411dcc4af5d56e2f86cf0d7f10608467b24dd886ca559f7c4b60e6a SHA512 a21c79e56662d926e8476ffc7ccd84dec182a7bbd98c08b3df61ed88c99ee82e1522b69156cdea0abf96d93bc69a0a491b04662a9312d2681785116074151a61 EBUILD dssp-2.2.1-r3.ebuild 870 BLAKE2B 9b7542d9ec45b60f5671830e5068e1d1cbcca4b82cf22cc0e2d9804c221f9977cfade439cc6e41a67375b438faca3ffa64fdec23db2b417b58615513fd60ad44 SHA512 964bfd70d98a80e6afd7f28fc6bf7359bbde105e77903211cec04c5adcdce273f1d7142a6d206d644300a1185cba1352bf584499d864809dadad69b2023e50d0 EBUILD dssp-3.0.11.ebuild 875 BLAKE2B 6344416239b93804755b1829dcfcb9e8e461606c217938945bb2fc75e9680f2849b39bdbf0ed361592e703fea493a2dacabca498b26e696c969735a585e5d183 SHA512 353f4f5d7b1b195753c738ecc9fb17b429cdeada757806f5cf9a3da65c6318e3885d2c92fa904d5b3a546756eb87ec90787d158e8a9450b4730dd97b45af970d EBUILD dssp-4.4.10.ebuild 1328 BLAKE2B 4e01021b9817c33434a3316aae5f44311735b243a0bea273b5b983629a3668f6a23ff7dfb5cf38b6128b925cac8236ba9d1df68fb5ad0692906b2e9ea2e2015d SHA512 c90c5543a7bea86cb8bc8534608518b8dc262767505d77e0de57c79c8d7d973152cba9985c85ac23c0deda1b1e5b92535274d94d98e79a73c4d2cbfb70edabab -EBUILD dssp-4.4.7.ebuild 1329 BLAKE2B 61d8909411ff687ba6b11449b0c3acd307c28ac5901fe360886b980d49b88e301cbd539d794503e789e73973ce1ae6aa965e1846cf7453d41df96285a1710cdf SHA512 d3beb704dc3a3783c79ac73fdfdebf74e82fa15d8d7d792124a529c7a208e6349b8035585d0ee96eecaf13ef81ecaa407c2ee22edd8bfdbe5befc945ca5453a6 -EBUILD dssp-4.4.8.ebuild 1329 BLAKE2B 61d8909411ff687ba6b11449b0c3acd307c28ac5901fe360886b980d49b88e301cbd539d794503e789e73973ce1ae6aa965e1846cf7453d41df96285a1710cdf SHA512 d3beb704dc3a3783c79ac73fdfdebf74e82fa15d8d7d792124a529c7a208e6349b8035585d0ee96eecaf13ef81ecaa407c2ee22edd8bfdbe5befc945ca5453a6 MISC metadata.xml 295 BLAKE2B 4355bbe00822cc702acdf70031ab9cd1f2a8f6e076d71016c1783f2a6c052c2da0a1a4a1860062562bb837161787f2481fa6f49c4319c546482a263ebe149bb0 SHA512 ace35ca21c614a7c0cbdea2496be3190a907295053566707c1875836a306cc9e9c96816cca6ce2b514935f6fcd494d2e813f4d94ba88552cd7b86831f30501f4 diff --git a/sci-chemistry/dssp/dssp-4.4.7.ebuild b/sci-chemistry/dssp/dssp-4.4.7.ebuild deleted file mode 100644 index d5e51fe40fec..000000000000 --- a/sci-chemistry/dssp/dssp-4.4.7.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 -inherit cmake - -DESCRIPTION="The protein secondary structure standard" -HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp" -SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -# doc disabled as it only generates a PDF from the manpage for now -# https://github.com/PDB-REDO/dssp/issues/64 -#IUSE="doc" - -CDEPEND=" - dev-libs/boost:=[zlib] - >=dev-libs/libmcfp-1.2.2 - >=sci-libs/libcifpp-7.0.3 -" -BDEPEND="${CDEPEND} - dev-cpp/catch:0 -" -# doc? ( -# || ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc ) -# dev-python/weasyprint -# ) -RDEPEND="${CDEPEND}" - -#src_prepare() { -# # wkhtmltopdf is not available on Gentoo -# sed -i -e \ -# 's/-t html/-t html --pdf-engine=weasyprint/' \ -# CMakeLists.txt -# cmake_src_prepare -#} - -src_configure() { - local mycmakeargs=( - #-DBUILD_DOCUMENTATION=$(usex doc) - -DBUILD_DOCUMENTATION=NO - ) - cmake_src_configure -} - -pkg_postinst() { - if has_version "<=sci-chemistry/gromacs-2022"; then - ewarn "DSSP > 3.0.x is not compatible with gmx do_dssp:" - ewarn "https://gitlab.com/gromacs/gromacs/-/issues/4129" - ewarn - ewarn "Feel free to mask newer versions if needed." - fi -} diff --git a/sci-chemistry/dssp/dssp-4.4.8.ebuild b/sci-chemistry/dssp/dssp-4.4.8.ebuild deleted file mode 100644 index d5e51fe40fec..000000000000 --- a/sci-chemistry/dssp/dssp-4.4.8.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 -inherit cmake - -DESCRIPTION="The protein secondary structure standard" -HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp" -SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -# doc disabled as it only generates a PDF from the manpage for now -# https://github.com/PDB-REDO/dssp/issues/64 -#IUSE="doc" - -CDEPEND=" - dev-libs/boost:=[zlib] - >=dev-libs/libmcfp-1.2.2 - >=sci-libs/libcifpp-7.0.3 -" -BDEPEND="${CDEPEND} - dev-cpp/catch:0 -" -# doc? ( -# || ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc ) -# dev-python/weasyprint -# ) -RDEPEND="${CDEPEND}" - -#src_prepare() { -# # wkhtmltopdf is not available on Gentoo -# sed -i -e \ -# 's/-t html/-t html --pdf-engine=weasyprint/' \ -# CMakeLists.txt -# cmake_src_prepare -#} - -src_configure() { - local mycmakeargs=( - #-DBUILD_DOCUMENTATION=$(usex doc) - -DBUILD_DOCUMENTATION=NO - ) - cmake_src_configure -} - -pkg_postinst() { - if has_version "<=sci-chemistry/gromacs-2022"; then - ewarn "DSSP > 3.0.x is not compatible with gmx do_dssp:" - ewarn "https://gitlab.com/gromacs/gromacs/-/issues/4129" - ewarn - ewarn "Feel free to mask newer versions if needed." - fi -} diff --git a/sci-chemistry/gperiodic/Manifest b/sci-chemistry/gperiodic/Manifest index 35a2c89303ef..9b40e7b1c8bb 100644 --- a/sci-chemistry/gperiodic/Manifest +++ b/sci-chemistry/gperiodic/Manifest @@ -1,3 +1,5 @@ +AUX gperiodic-3.0.3-incompatible-pointers.patch 480 BLAKE2B 18f520b24e789e6167a8dbfda01a1940c38c4bbe47fd245fbb64f44e33572880deb9747a4a80fed85a438cf32e1efc598da3c547aa372f574b02fb287db8fc2a SHA512 8abbdda2882d04c412bef1de387f1c86bfc2ac7edf720239c58e143580f7a8829ea114dc40c981fb749e63e0577e86d0a882f332c0ad4bade5ec36cca6ad6af0 DIST gperiodic-3.0.3.tar.gz 451559 BLAKE2B b91995046b9905a534e3b6f530aee0ad2b4e6ac42cd11755ea182fdaaf8970f34b1aea8a33870abb8767837606a42a0cf0d76c9a689236aa39fba686e1521ee8 SHA512 7226063cf7977f4283a199d4a3d1842d6c9be60c53f5a005541eb26f35cd6538b29f086dc13c28225779e1849a12d1c39150897055c03902cb00adc011bc1ce8 +EBUILD gperiodic-3.0.3-r1.ebuild 945 BLAKE2B 8d1fd608cd13e1749eae7c2c426188bb34652c4428964cd54bed9fc7ef6c9ee2bae592d531b15dccc6cdf6048dd33823b66d44ae6df3d5017820e664f6a3faf7 SHA512 ebcd27c5e79d94ab841d5e270a4c2efbaa686b88201d44b39e44a6d79bab4e2a7e8b0e17bb7117967a61a9628f4ed9f9c89bb5f9eeff0c6c30def5ef67866193 EBUILD gperiodic-3.0.3.ebuild 884 BLAKE2B 3d3389b62f81d204d39f846421fe87267e8cc877464cb7f93bb0355d2ac4e89973e0fff1364f60db9c4ecd38919a774223c0e967ca661835c87e05c1bc83a1b3 SHA512 7e0b3e5b80cb0566489ddeba299d5efceecfcc83ffc7faac61f4d0bfb0aa6bb68dd80cb8452e6e09f1f742a95ab0041e313047741b8be6e6a4ff45c475fc0c4f MISC metadata.xml 472 BLAKE2B e0811caf393b542123014a9d910fde9c840e2ace704c63073287537a3176ebc8821c1c6603cf6c9fd39bf03f68f77a0778d51632da04e2c5b5daa216188af313 SHA512 6bd33a21ad9298bf9896f0da7b72d0857581255fa4c6e34aa2a133a32e2c91eee43b342138675e60885e65acc3482ea29158138d2695a1acddf6418d6fddc352 diff --git a/sci-chemistry/gperiodic/files/gperiodic-3.0.3-incompatible-pointers.patch b/sci-chemistry/gperiodic/files/gperiodic-3.0.3-incompatible-pointers.patch new file mode 100644 index 000000000000..b156532e9b54 --- /dev/null +++ b/sci-chemistry/gperiodic/files/gperiodic-3.0.3-incompatible-pointers.patch @@ -0,0 +1,13 @@ +https://bugs.gentoo.org/919213 +Cast pointer as it is cast everywhere around it +--- a/gperiodic.c ++++ b/gperiodic.c +@@ -137,7 +137,7 @@ + if (col == 0) gtk_label_set_markup (GTK_LABEL (label), _(header.info[row])); + else { + gtk_label_set_markup (GTK_LABEL (label), _(entry->info[row])); +- gtk_label_set_selectable (label, TRUE); ++ gtk_label_set_selectable (GTK_LABEL (label), TRUE); + } + + gtk_misc_set_alignment(GTK_MISC(label), 0, 0); diff --git a/sci-chemistry/gperiodic/gperiodic-3.0.3-r1.ebuild b/sci-chemistry/gperiodic/gperiodic-3.0.3-r1.ebuild new file mode 100644 index 000000000000..6856fce733d8 --- /dev/null +++ b/sci-chemistry/gperiodic/gperiodic-3.0.3-r1.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs xdg-utils + +DESCRIPTION="Periodic table application for Linux" +HOMEPAGE="https://sourceforge.net/projects/gperiodic/" +SRC_URI="https://downloads.sourceforge.net/project/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="nls" + +BDEPEND=" + virtual/pkgconfig + nls? ( sys-devel/gettext )" +RDEPEND=" + sys-libs/ncurses:0 + x11-libs/gtk+:2 + x11-libs/cairo[X]" +DEPEND="${RDEPEND}" + +PATCHES=( "${FILESDIR}/${P}-incompatible-pointers.patch" ) + +src_compile() { + emake \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + CC="$(tc-getCC)" "enable_nls=$(usex nls 1 0)" +} + +src_install() { + emake DESTDIR="${D}" "enable_nls=$(usex nls 1 0)" install + dodoc AUTHORS ChangeLog README + newdoc po/README README.translation +} + +pkg_postinst() { + xdg_icon_cache_update +} + +pkg_postrm() { + xdg_icon_cache_update +} diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 3bcf83c4082d..983d1f784157 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,23 +1,21 @@ -AUX gromacs-2025.0-beta-fix-man-build.patch 1245 BLAKE2B cfb869d4ef7a0b8417e49721b58f6888e86ddf2000079069466743d71c0e8184117538f5f15d1c5e5a29c7533efa42b660d52002bbd8d5b65b9d91461ced6027 SHA512 9ff00cf6ef23332ee63f36d1ca3116f660d0d69cebc375cc1c1212bf0f2a723b09cefeea5f01e9712af2c98eac2a6277dd2aaa7e05d762369883a86f5e02af64 -AUX gromacs-gcc-15.patch 1003 BLAKE2B 557d2ca23180c0e7eb8d19518ba1b22a4fde9f1ccf225e05d00f21e3e6afaecc7f34c3614f783ac812fd03f0fe108099985f72dd6f6fa01d01a2daf6c17c0cc7 SHA512 b3c5430c21025b11a4fbb47785de1fe898183b9e5876e47648f3ddb47be69a808fd53bc96aee0f73bdfafefc4784e42a0a16870e57c92541d59063c2d822fa42 +AUX gromacs-gcc-15.patch 419 BLAKE2B 170134fea82c477672c915d2aa66a1a2df436bd69d7ef8993ec2d2f68ccb0b965f406c738da4af84a8fb62eb268b8f31ebabe2f9fa1a352961539c4f96bec582 SHA512 a3124dd9eb335886e73dc21b255b5ae9de18a9c1c637a2114350528e503f515d445126a34ad978eb6df12c705077ea706d5ae72f3b5a95fa3d60cccf06e87bed DIST gromacs-2023.5.tar.gz 42079310 BLAKE2B e50dbe76396230f4a886280bdebcf7b131506679240e77d2a2263c3b5dbfe7ef754c4265fc04e9acad7932c7691de7f694cc23140a25d0d5be649a4120f45b0c SHA512 f3a34cf0d379d6d4964d7494af6c6617c0c092293ea38a3a248af2dd2a90cae04696d52e68126176065efc480977942b00efa441028e526e1555c7e84551fc0c DIST gromacs-2024.3.tar.gz 42373103 BLAKE2B f45af72ecdf119b423d98b84818eaca1aa2e3f43eaf1aff7435de2a5891079a880f19a654627ee2f43e3a38c9dcfa0638bc6eb6da201b3c9ce89b2dc32fc683b SHA512 13f23e581c2b63f6262e8359e7bed6a1a5f3164047ea38d2b6a44bcd2b20b61332705167435fe2ad30fe6f24f8ab49b982388550cdecb49167e4156e36286d3d -DIST gromacs-2024.4.tar.gz 42356162 BLAKE2B 3a1019128a2cfd47fb3ab23962a6fcd5bac3b5519d4bfa1239956740226468986ba93e645eb3bc20117968c024823e948fd819a603315399d573275c91c6e51b SHA512 32a08e9417d4d36a29bdfde4e0448bc136bd3db79b5d5c84fa99d9f022ffca6a94b7bd1c7e7a335430fb6bdcf0181e3cbabeb46d13978c0f87b5d88787ea8d63 -DIST gromacs-2025.0-beta.tar.gz 45067499 BLAKE2B 661607007af6d1f697f5aec72a88cefec5546dee2c0facaf2776354665f56fd71b1a7a2ea92185b4d64e764cd0ac10e865b740dda6d7438318acbbadd1bd7fd0 SHA512 831b4ba2631f5dd65c1b48d4ba0455af0b101af22d8cc78c246e7b36f4ce3c8f33f1cb8d94e42559741dbe1585c75a6e05a2538708d7e57c86ac2174aca302b9 +DIST gromacs-2024.5.tar.gz 42353127 BLAKE2B c1fa6bd90390c9e13f11995ea9992902e136e15f6191ed47c9eac95384f97221533509ddd2bc4908f1d36fb790aab8a068fd1c00dd6f82e440f4719092b8ea37 SHA512 cb4f6bf4a6a53fb7ee4d8ed832d514d77d21eea3e1b86eec1bf51a4b6197a30aa8d68ca61919d7921c701af365077a9c84c12ef33d5584a1bc796b25709aa7af +DIST gromacs-2025.0.tar.gz 44417653 BLAKE2B 9fb55c6c5c842faefe1811e8e2da558cae2564d81767da13fab9f23f674d6451700885269cd25d70caae6a7553d8b6fd885922bb74976e6bc9a7251e01ce696b SHA512 0d3b2684827f6f9223a954fa5df408c2e7fbe2e61f6aef2d9a8b6bdd614045ed08a08d3229f3203064dc0c6b747de1b36449afc2de0b7da7300199bbcc2be77f DIST manual-2023.5.pdf 13579081 BLAKE2B 42f687ebcdb79bfc77aabac4fd382940c23ba27da380b8eff342c2e9255a58fc11a0458220d1f71f3c13ab1cf6fdabad00ac1bad741781d0b787899165bea2cc SHA512 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f8d9ebc33ad1f391dde1b7e056ad9b7860a902b805363c988962743cd4f37af69a0b1acd3323a95b9740ded0abf20904895605d78fecebdf94a4562ccd3ab9e8 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 deleted file mode 100644 index 2eb2d45035a2..000000000000 --- a/sci-chemistry/gromacs/files/gromacs-2025.0-beta-fix-man-build.patch +++ /dev/null @@ -1,41 +0,0 @@ -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 index 45ac82493bec..c0168ba9f21e 100644 --- a/sci-chemistry/gromacs/files/gromacs-gcc-15.patch +++ b/sci-chemistry/gromacs/files/gromacs-gcc-15.patch @@ -1,25 +1,5 @@ -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 +index 0c8fecfae70605d64613a2408755e715e5f9b6c5..f80d4c56b95caf6942b35222d8983c8ed8f10e1e 100644 --- a/src/gromacs/mdtypes/energyhistory.h +++ b/src/gromacs/mdtypes/energyhistory.h @@ -47,6 +47,8 @@ @@ -31,6 +11,3 @@ index 0c8fecfae7..f80d4c56b9 100644 #include <memory> #include <vector> --- -2.45.2 - diff --git a/sci-chemistry/gromacs/gromacs-2023.5.ebuild b/sci-chemistry/gromacs/gromacs-2023.5.ebuild index 83ceb0fceb65..4501472b953b 100644 --- a/sci-chemistry/gromacs/gromacs-2023.5.ebuild +++ b/sci-chemistry/gromacs/gromacs-2023.5.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2024 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 CMAKE_MAKEFILE_GENERATOR="ninja" -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{11..12} ) DISTUTILS_OPTIONAL=1 DISTUTILS_USE_PEP517=no diff --git a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild b/sci-chemistry/gromacs/gromacs-2023.9999.ebuild deleted file mode 100644 index 5c6ffc9fc1a8..000000000000 --- a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild +++ /dev/null @@ -1,339 +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 )" - # since 2022 arm support was dropped (but not arm64) - 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" - -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="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}" - -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 ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi[cxx] ) - sci-libs/lmfit:= - >=dev-cpp/muParser-2.3:= - ${PYTHON_DEPS} - " -BDEPEND="${CDEPEND} - virtual/pkgconfig - clang? ( >=llvm-core/clang-6:* ) - 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 - 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 ) - clang-cuda? ( clang cuda ) - mkl? ( !blas !fftw !lapack ) - ${PYTHON_REQUIRED_USE}" - -DOCS=( AUTHORS README ) - -RESTRICT="!test? ( test )" - -if [[ ${PV} != *9999 ]]; then - S="${WORKDIR}/${PN}-${PV/_/-}" -fi - -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="${WORKDIR}/regressiontests"\ - git-r3_src_unpack - fi - fi -} - -src_prepare() { - #notes/todos - # -on apple: there is framework support - - xdg_environment_reset #591952 - - # we can use clang as default - if use clang && ! tc-is-clang ; then - export CC=${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 - - 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=( ) - local acce="AUTO" - - if use custom-cflags; then - #go from slowest to fastest acceleration - 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) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) - else - fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) - fi - - mycmakeargs_pre+=( - "${fft_opts[@]}" - "${lmfit_opts[@]}" - -DGMX_USE_LMFIT=EXTERNAL - -DGMX_USE_MUPARSER=EXTERNAL - -DGMX_EXTERNAL_BLAS=$(usex blas) - -DGMX_EXTERNAL_LAPACK=$(usex lapack) - -DGMX_OPENMP=$(usex openmp) - -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex build-manual) - -DGMX_HWLOC=$(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" ) - [[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" ) - use opencl && gpu=( "-DGMX_GPU=OPENCL" ) - local mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=$(usex mpi) - -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 - 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 - 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-${PV}.pdf" - fi - fi - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${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 "${ED}"/usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite gromacs related papers from list:" - einfo "https://www.gromacs.org/articles.html" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2024.3.ebuild b/sci-chemistry/gromacs/gromacs-2024.3.ebuild index cc4c9393b140..d57a37462c1d 100644 --- a/sci-chemistry/gromacs/gromacs-2024.3.ebuild +++ b/sci-chemistry/gromacs/gromacs-2024.3.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2024 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 CMAKE_MAKEFILE_GENERATOR="ninja" -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{11..12} ) DISTUTILS_OPTIONAL=1 DISTUTILS_USE_PEP517=no diff --git a/sci-chemistry/gromacs/gromacs-2024.4.ebuild b/sci-chemistry/gromacs/gromacs-2024.5.ebuild index 7f2e7152df0f..d57a37462c1d 100644 --- a/sci-chemistry/gromacs/gromacs-2024.4.ebuild +++ b/sci-chemistry/gromacs/gromacs-2024.5.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2024 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 CMAKE_MAKEFILE_GENERATOR="ninja" -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{11..12} ) DISTUTILS_OPTIONAL=1 DISTUTILS_USE_PEP517=no @@ -26,7 +26,7 @@ else doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" # since 2022 arm support was dropped (but not arm64) - KEYWORDS="~amd64 -arm ~arm64 ~riscv -x86 ~amd64-linux -x86-linux ~x64-macos" + KEYWORDS="amd64 -arm arm64 ~riscv -x86 ~amd64-linux -x86-linux ~x64-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" diff --git a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild b/sci-chemistry/gromacs/gromacs-2024.9999.ebuild index b681516f603a..e30a7a974d56 100644 --- a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2024.9999.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2024 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 CMAKE_MAKEFILE_GENERATOR="ninja" -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{11..12} ) DISTUTILS_OPTIONAL=1 DISTUTILS_USE_PEP517=no diff --git a/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild b/sci-chemistry/gromacs/gromacs-2025.0.ebuild index b3605cdfa525..ea299e483a56 100644 --- a/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild +++ b/sci-chemistry/gromacs/gromacs-2025.0.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2024 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 CMAKE_MAKEFILE_GENERATOR="ninja" -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{11..12} ) DISTUTILS_OPTIONAL=1 DISTUTILS_USE_PEP517=no @@ -63,15 +63,13 @@ CDEPEND=" BDEPEND="${CDEPEND} virtual/pkgconfig clang? ( >=llvm-core/clang-6:* ) - doc? ( - $(python_gen_cond_dep ' + $(python_gen_cond_dep ' dev-python/sphinx[${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 $(python_gen_cond_dep ' @@ -103,11 +101,6 @@ DOCS=( AUTHORS README ) RESTRICT="!test? ( test )" -PATCHES=( - "${FILESDIR}/${PN}-gcc-15.patch" - "${FILESDIR}/${PN}-2025.0-beta-fix-man-build.patch" -) - if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi diff --git a/sci-chemistry/gromacs/gromacs-2025.9999.ebuild b/sci-chemistry/gromacs/gromacs-2025.9999.ebuild index bec110e3340c..ea299e483a56 100644 --- a/sci-chemistry/gromacs/gromacs-2025.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2025.9999.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2024 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 CMAKE_MAKEFILE_GENERATOR="ninja" -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{11..12} ) DISTUTILS_OPTIONAL=1 DISTUTILS_USE_PEP517=no @@ -63,15 +63,13 @@ CDEPEND=" BDEPEND="${CDEPEND} virtual/pkgconfig clang? ( >=llvm-core/clang-6:* ) - doc? ( - $(python_gen_cond_dep ' + $(python_gen_cond_dep ' dev-python/sphinx[${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 $(python_gen_cond_dep ' diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 1cc913c0aeed..834cbde74d22 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2024 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 CMAKE_MAKEFILE_GENERATOR="ninja" -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{11..12} ) DISTUTILS_OPTIONAL=1 DISTUTILS_USE_PEP517=no @@ -64,15 +64,13 @@ CDEPEND=" BDEPEND="${CDEPEND} virtual/pkgconfig clang? ( >=llvm-core/clang-6:* ) - doc? ( - $(python_gen_cond_dep ' + $(python_gen_cond_dep ' dev-python/sphinx[${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 ' diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest index e540122ad8fe..dcfce0f7a0c7 100644 --- a/sci-chemistry/molmol/Manifest +++ b/sci-chemistry/molmol/Manifest @@ -1,7 +1,9 @@ AUX molmol-2k_p2-gcc14-fix.patch 357 BLAKE2B e7c1692e7a45ed2b83c38fa8b7ffe1a563f752660f3e2dc2098eb1de4491cd8919190d04cdc9d31f036b42a8fda6d6200fa347dfc7aed0fa46d75e1e3103e6cb SHA512 6138806de3222b073ce0f77c2c6d7060cbc9e3ba729553f61b93e44c671008da0e1ce64bc6fc0d9293dba203d71ae76cff1bea698e03a42d3e5a5901e6e8ccc0 +AUX molmol-2k_p2-transform-makefiles.patch 966 BLAKE2B 0bb3b8a5801b29f21d961e48a3bbe1221c2ddb0961c685466ba802e22ff52632d81cd4f88c083923b1fd3ed51f8c3947ec4e55eefd11e06b10e67d38d9995d3b SHA512 b255e8f858d4960aebef88452297dce1ebf993fc7343f54e713bf219d41ec7d5661b16d63a1f363bba9d6e1c0282ba894864e489210ce6294e49f72c3d56209f DIST molmol-2k.2.0-doc.tar.gz 1062297 BLAKE2B 082d4eea5544bab52ffc1ff6364c50304348f76759dd3125cd74d02e629383d4a566f28ac77ab89ecf5e17a82617b8f61525e6f454689840b27899827399d866 SHA512 131f747a5762859398ebe9b676a07df56c82c8864ecc035ec914f1dea74dafcd67f87993421dfe5899c640470c7e1e1ef03ae262b04a9b360ae329eb19a331fe DIST molmol-2k.2.0-src.tar.gz 1088805 BLAKE2B cd649604f6ee491d3a4485391ecdaa48dc1bc4bcd82865cd4a01ca460a6653f8cbba636050bfab9027b9b95dbefa28a8deeff7065b9b461f518001242af4a849 SHA512 6ab01a6fd3d19752634a2cf22919a20e43d195768bd4bdacd5f0bbe016c3058c94915bad4c7fa64dcd86576be39cad0ae112cb62f5e69ffb10041518101e7a9b DIST molmol-patches.tbz2 17528 BLAKE2B b91270a980f290edc169be00639e86b3272281c9fe237750f5778eab1605ed482c09bdaf90660a5edf74bd04b3e31adc755e77e39aea6c75d88b6db9bf47a6d6 SHA512 bd94baf0a378f40f854f396963edd9b9e4afc5c56462ee6f8b68889290afdb4c5d9b10878aa5619d0a70153453fe6ee8e7540064522c6db0291ae9162bba9287 DIST molmol_256.png 22668 BLAKE2B c7d75b8e0d738b48790bea25e21ec60d57a8181253518c70d6f18d93c64eef3c9acf90213fdbdf2dde272e85a04a6442e4e4a9c375829f369380d88c9c0ca57c SHA512 5e7975f54a7462161dc630ee973e9a8126b9c120e0d8d6b62007384c970ce39792e52300edc25dc7a85209845801d749d9ecba02899f3e18b18f5a5fdbc28a97 +EBUILD molmol-2k_p2-r10.ebuild 2442 BLAKE2B 35313fce20508bcd7c09e7e748d8f00675acb6ece1139b8b3ea68f988bc749a6c47b8a00725514c81198de44f17e94295420ed05142247f8a44c9cfcebb475c3 SHA512 3fb8451bad09df6e6c895884b614e1e2773a39942b734eeefcc74531ae513d4a90e276f88adf0d71409539104e3164a7bda67e3652ac1ae9e0fccbf3cecabd45 EBUILD molmol-2k_p2-r9.ebuild 2562 BLAKE2B b197c856d551f1b634efe0d978a297362c9d1260029cc7ecc2644fc3a3ce6bde20a7000f3aa2f4056b34454b17f357103f74535315d2f530483ae72a051ae96e SHA512 7668a27c2962fdaa40e96f55e48bcd3307cf6d146bfeba6f27bc0ae8e924e0dcc7853bee3a6a57b861de2868fa220a7ba071e1944e44364519b2f60b4ff46b4a MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c diff --git a/sci-chemistry/molmol/files/molmol-2k_p2-transform-makefiles.patch b/sci-chemistry/molmol/files/molmol-2k_p2-transform-makefiles.patch new file mode 100644 index 000000000000..6129ed03b3ab --- /dev/null +++ b/sci-chemistry/molmol/files/molmol-2k_p2-transform-makefiles.patch @@ -0,0 +1,40 @@ +Transformed multiple seds to this patch. `MOLMOLHOME` is the runtime variable +that depends on knowledge of paths that I didn't think of how to correctly +pass beyond editing it with sed. For everything else, it is here and changed +to work correctly with build system. +Rolled up sed transformations were to made build system non-parallel, +fix environmental variables, remove sleep and add use right shell and +build dependencies in startup script. +--- a/makedef.lnx ++++ b/makedef.lnx +@@ -11,12 +11,12 @@ + + XINCL = -I/usr/X11R6/include + +-CC=gcc ++CC ?= gcc + MCPPFLAGS = +-MCFLAGS =-pipe -O3 -ffast-math -march=i686 -mcpu=i686 ++MCFLAGS := $(CFLAGS) + + RANLIB = /bin/true +-WAIT = sleep 2 ++WAIT = sleep 0 + SHELL = /bin/sh + CPP = /lib/cpp + +--- a/molmol ++++ b/molmol +@@ -1,9 +1,10 @@ +-#!/bin/ksh ++#!/bin/sh + # + # startup script for MOLMOL + # + +-MOLMOLHOME=/opt/group/MOLMOL ++MOLMOLHOME=/; ++MOLMOLDEV="Motif/OpenGL" + export MOLMOLHOME + export MOLMOLDEV + diff --git a/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild new file mode 100644 index 000000000000..f9425f749a99 --- /dev/null +++ b/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild @@ -0,0 +1,103 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit desktop toolchain-funcs flag-o-matic + +MY_PV="${PV/_p/.}.0" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="Publication-quality molecular visualization package" + +# Original page dead +#HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" +HOMEPAGE=" + http://www.csb.yale.edu/userguides/graphics/molmol/molmol_descrip.html + http://pjf.net/science/molmol.html +" +SRC_URI=" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz + https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2 + https://dev.gentoo.org/~pacho/${PN}/${PN}_256.png +" +S="${WORKDIR}" + +LICENSE="molmol" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=" + || ( + ( + media-libs/mesa[X(+)] + x11-libs/libGLw + ) + media-libs/mesa[motif(-),X(+)] + ) + media-libs/libjpeg-turbo:= + media-libs/libpng:= + media-libs/tiff:= + sys-libs/zlib + virtual/glu + x11-libs/libXpm + x11-libs/motif:0 + x11-apps/xdpyinfo + media-fonts/font-adobe-100dpi +" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-gcc14-fix.patch + # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided + "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff + "${WORKDIR}"/patches/ldflags.patch + "${WORKDIR}"/patches/opengl.patch + "${WORKDIR}"/patches/cast.patch + # patch from fink + # fixes numerous bad bracings and hopefully the OGL bug 429974 + "${WORKDIR}"/patches/${P}-fink.patch + "${WORKDIR}"/patches/wild.patch + + "${FILESDIR}"/${P}-transform-makefiles.patch +) + +pkg_setup() { + MMDIR="/usr/$(get_libdir)/molmol" +} + +src_prepare() { + default + eapply -p0 "${WORKDIR}"/patches/libpng15.patch + rm -rf tiff* + + sed \ + -e "s|^MOLMOLHOME.*|MOLMOLHOME=${EPREFIX}/${MMDIR}|" \ + -i "${S}"/molmol || die + + ln -s makedef.lnx "${S}"/makedef || die + + # Parallel build fails (#880621) and cannot be disabled by MAKEOPTS + # (#880621, #941488). + find . -name Makefile -exec sed -i -e "1i .NOTPARALLEL:" {} + || die + + # https://bugs.gentoo.org/944200 + # uses C polymorphism. Can't be trivially patched + append-cflags -std=gnu17 + tc-export AR CC +} + +src_install() { + dobin molmol + + exeinto ${MMDIR} + doexe src/main/molmol + insinto ${MMDIR} + doins -r auxil help macros man setup tips + + make_desktop_entry "${PN}" MOLMOL + newicon "${DISTDIR}/${PN}_256.png" "${PN}.png" + + einstalldocs + dodoc HISTORY +} |