diff options
Diffstat (limited to 'sci-chemistry')
44 files changed, 658 insertions, 842 deletions
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.4.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.4.ebuild deleted file mode 100644 index e5c508fd6ca1..000000000000 --- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.4.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{9..11} ) -DISTUTILS_USE_PEP517=setuptools - -if [[ ${PV} = *9999* ]]; then - scm_eclass=git-r3 - EGIT_REPO_URI="https://github.com/Becksteinlab/${PN}.git" - EGIT_BRANCH="develop" - SRC_URI="" -else - scm_eclass=vcs-snapshot - SRC_URI="https://github.com/Becksteinlab/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -inherit distutils-r1 ${scm_eclass} - -DESCRIPTION="Python framework for Gromacs" -HOMEPAGE="https://gromacswrapper.readthedocs.io" - -LICENSE="GPL-3 LGPL-3" -SLOT="0" -IUSE="" - -RDEPEND=" - dev-python/six[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - sci-libs/numkit[${PYTHON_USEDEP}] -" -BDEPEND=" - ${RDEPEND} - test? ( >=dev-python/pandas-0.17[${PYTHON_USEDEP}] ) -" - -distutils_enable_tests pytest diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.5.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.5.ebuild index e5c508fd6ca1..92f160defd29 100644 --- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.5.ebuild +++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.5.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -10,7 +10,6 @@ if [[ ${PV} = *9999* ]]; then scm_eclass=git-r3 EGIT_REPO_URI="https://github.com/Becksteinlab/${PN}.git" EGIT_BRANCH="develop" - SRC_URI="" else scm_eclass=vcs-snapshot SRC_URI="https://github.com/Becksteinlab/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz" @@ -24,7 +23,6 @@ HOMEPAGE="https://gromacswrapper.readthedocs.io" LICENSE="GPL-3 LGPL-3" SLOT="0" -IUSE="" RDEPEND=" dev-python/six[${PYTHON_USEDEP}] diff --git a/sci-chemistry/GromacsWrapper/Manifest b/sci-chemistry/GromacsWrapper/Manifest index 59c53091950e..f9dc12e907fd 100644 --- a/sci-chemistry/GromacsWrapper/Manifest +++ b/sci-chemistry/GromacsWrapper/Manifest @@ -1,5 +1,3 @@ -DIST GromacsWrapper-0.8.4.tar.gz 1955167 BLAKE2B 59f0301263eefaa4d7c139b34a48172c218a76f0f9488477d6203d9cd732098468dae5a73ff46aa74eb2b4433268c77bc265e506129e4c14a357042453d5f97f SHA512 822edc33c77ca4dbfbc1e4172686744345ed3c0d2305f4b19abab15576a1433bbb3b23b96f637398ad4f72cd5414d96ee531ab4a329d3acb462d90b95437a6a5 DIST GromacsWrapper-0.8.5.tar.gz 1958570 BLAKE2B b8f79721a7566117206818144fc7087c4634d7fb71c77abef63dd9565a0655ce6b4a259ea5bf9cb3b5bc13df8f428f58e514f7871192d27a6d463e758e27f4b3 SHA512 8800afdbe92edad35df58e825546797ede1738b9029df0fb57a96e377d7be94f3d21fe1df9d5cb4490d12b984972d63d87e673d3d33af60a7dc8d0453574a5c6 -EBUILD GromacsWrapper-0.8.4.ebuild 911 BLAKE2B 827ac820482bd41895e02a218041fb1668899d7c80e95ee51021a92d6f7fe36452d1012330118266958f8313694b9c655cc32ddf995d62f3b08aad508c912301 SHA512 6d0f23fcc82cfd0097768a98a1d5755fb003437734f2c6ac90ccff21aa8a8c69bac8f7c0dd4803711e249ff66e513b906394394b71313b2a48f9f0bc37b2ce7e -EBUILD GromacsWrapper-0.8.5.ebuild 911 BLAKE2B 827ac820482bd41895e02a218041fb1668899d7c80e95ee51021a92d6f7fe36452d1012330118266958f8313694b9c655cc32ddf995d62f3b08aad508c912301 SHA512 6d0f23fcc82cfd0097768a98a1d5755fb003437734f2c6ac90ccff21aa8a8c69bac8f7c0dd4803711e249ff66e513b906394394b71313b2a48f9f0bc37b2ce7e +EBUILD GromacsWrapper-0.8.5.ebuild 891 BLAKE2B f337e51328aa8d4f3ae1c63080a2dfe016b5eb7ddfceea41ac6f8b4429dcb25d62f0c6b16614333240f7386eef99377c20a71293eecb5227909fd7d3008ffaee SHA512 5d19ef9c50dc98316d4891f36b9a4bed7bd31fc20e44c2ec4833ab39d33f7200ff9a336825050ed50b67679f1c6e49aaf1a60ef5997ac7e5ee8d8be5a5c031d2 MISC metadata.xml 483 BLAKE2B 1d8a7e888d8b95bd229ef72894ba02f583e3e3958f9cd5733ab6b466312bac0b0f5a9004135caa37a3ef137e8782fa93ff4bb90f35f31c058d8c528025b193d0 SHA512 70e5dc653ff21a0395b946e5f3548320d2abb8c63ae9f3ce04be6768e20b02ce55a612a2ad12b6c2262529ab753ca9fda02d9bdae7f6ac859bca49bbbad6f75f diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex c4dade297655..ba253adfd993 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/chemical-mime-data/Manifest b/sci-chemistry/chemical-mime-data/Manifest index 84729e6ca668..997736f7550a 100644 --- a/sci-chemistry/chemical-mime-data/Manifest +++ b/sci-chemistry/chemical-mime-data/Manifest @@ -1,11 +1,4 @@ -AUX chemical-mime-data-0.1.94-drop-turbomole-vibrational.patch 934 BLAKE2B 8c35adddc5dbed044a68c1f0f485faf01ae4d6fb4724e82956e9e73292e2b7e37f527a8225fce3fa4b3c6629038086f30912b8bce21d704244dc18ba52673f8a SHA512 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4bea8dae65e28657ff75b5b613137c0f89f6de185db79297642616f208e841ba56181044eee194c619bad2c3bfb62454b7839b720d2f32fca0e768b75c842683 -AUX chemical-mime-data-0.1.94-turbomole.patch 2451 BLAKE2B 86b4b08b2af4503e0f8a525ebaa4231a3d0d3727c951b9e957c9fdac790bc41b7f01092350099a64cce66dbb61bc4cbd3654ef91834310c6c7cd1dc156ca87e8 SHA512 1bfa8818d159f0f917a24a06b0bfe926f0854f4242d8c2dbbedcd4210ffd38a459298862dc1d1aedbbe648a933db99c5d647c5409af74f88b03dd3033946df54 AUX chemical-mime-data-0.1.95-turbomole.patch 1924 BLAKE2B 6536df960d2fc87f9d9f5ebb0dcf0a1935d8efa0e811174585e0123c09cb5de55adfb2777b2a130a82b72c4ca66befab8a3790801d0e4d6674cb04c417b91226 SHA512 2eda91dc48a2924c1dce635c4490685f2ec65f7b10c04f85fb7af406d12eed11197be215221c019267fab6e8ba48249ba6a50bdf2ebf30e6b9d021d54df234df -DIST chemical-mime-data-0.1.94.tar.bz2 146077 BLAKE2B 9996c240446dc9571b6b4afbcdc6cf16a08e11314da9f785490b1b20933b6d18a333132492e30315c08f4441c048ec593a111815253050cfb5ab562aadb784f1 SHA512 7f3d967149f27ab1de53c948dc055959e661e1be9d778e3d56d06bea95769da7770ab5fb66afab6607747ef91ffb1dbbcf921e5f06e3303351781968594b5f00 DIST chemical-mime-data-0.1.95_pre20171122.tar.gz 84515 BLAKE2B 42f76b44408c04e5a254c17502ea2c297727bb58fa3e86b8bca7f0c4c056ae7400b31f06b7d0c64b0712e97ab8a1f82549f44a3677720cd37a301ba99adb3d7a SHA512 a031e7a5bc31a74adcd8e5d827de71b6e0eafdceba16cf6f7407aa0266a9a082b0011963b315d2369f39abf45c4b41cedafccddbc2171673bf96ccbea51a4790 -EBUILD chemical-mime-data-0.1.94-r4.ebuild 1104 BLAKE2B ba7db79e81270fee4f4a2f31b0930f4af5b1601a9481c494ffa812322ef4e44a3803ec2e5bb89b1707ee7723aa112a9b1a8509e93885ea969343f5dc2ecd4fb0 SHA512 a6fd009228745e68bf4ccb589fde3e935b6955be4641e0d02863d683e8a790d0a7abd49df2084adf4dfd47a9b28aabd02c36e7262ceba1c326dcf185dbd77454 -EBUILD chemical-mime-data-0.1.95_pre20171122.ebuild 1243 BLAKE2B 3138a766695780978467e8cbecb1ee5c378a60d68e9b6916a1fa551d9f35780e39058d15a0f3532d40d779b5ad450dec431488bbf9aae3f67568620f0ab7a08c SHA512 363c8bb18212f84718e3a74b5d02fba3060fab69e18f4e0e9b5ad95676ec702a6c7fde1d706f8d94f3f73e9fb0f093fffde708a4434dbe98c9a02ab65c01355f +EBUILD chemical-mime-data-0.1.95_pre20171122.ebuild 1234 BLAKE2B c8a398a7e66aaec2c977f93f98bb7ac57a9fde8fbf557547217a09120592b9a58c3460d388db2e355fa6515f51291769dadf54d85c7b0fb29a284eeeb166596e SHA512 672a7781cbfd3ea3c0396498ae74f1b615e5d7c945c61f3e69ab0e241db68b4096eb18b7c6faed37456b095a4680ea9490f0eea02cc5c8913734940248f0672a MISC metadata.xml 403 BLAKE2B 57e1752722094936b1d76d3198ee397d233b3069df3ef15a60b2f25989418736a9d8672b53d78259a2d4f50fa6e5a635331cf1003dd2cbf87f66a60c85e0ba07 SHA512 c689663c874f6b8d63153fd84326dc5b00b733e98f04d763506f4fff4cbee3e642c5b4633ec3b6a6b5d2950928ba318e226eef85ee25cc8ff00c1dc25a87c3b5 diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r4.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r4.ebuild deleted file mode 100644 index e11f018ac371..000000000000 --- a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r4.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -inherit autotools xdg - -DESCRIPTION="A collection of data files to add support for chemical MIME types" -HOMEPAGE="https://github.com/dleidert/chemical-mime" -SRC_URI="https://downloads.sourceforge.net/${PN/-data/}/${P}.tar.bz2" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="amd64 arm arm64 x86" -IUSE="" - -RDEPEND=" - x11-misc/shared-mime-info -" -DEPEND="${RDEPEND}" -BDEPEND=" - dev-util/intltool - dev-util/desktop-file-utils - dev-libs/libxslt - || ( - gnome-base/librsvg - media-gfx/imagemagick[xml,png,svg] - ) - media-gfx/imagemagick[png] - virtual/pkgconfig -" - -PATCHES=( - "${FILESDIR}"/${P}-turbomole.patch - "${FILESDIR}"/${P}-pigz.patch - "${FILESDIR}"/${P}-namespace-svg.patch - "${FILESDIR}"/${P}-rsvg-convert-r2.patch - # https://github.com/dleidert/chemical-mime/issues/1 - "${FILESDIR}"/${P}-drop-turbomole-vibrational.patch -) - -src_prepare() { - xdg_src_prepare - eautoreconf -} - -src_configure() { - econf \ - --disable-update-database \ - --without-gnome-mime \ - --without-pixmaps \ - --without-kde-mime -} diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.95_pre20171122.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.95_pre20171122.ebuild index 64827ef8db67..b6291c211fa1 100644 --- a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.95_pre20171122.ebuild +++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.95_pre20171122.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -8,11 +8,11 @@ DESCRIPTION="A collection of data files to add support for chemical MIME types" HOMEPAGE="https://github.com/dleidert/chemical-mime" COMMIT="4fd66e3b3b7d922555d1e25587908b036805c45b" SRC_URI="https://github.com/dleidert/chemical-mime/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN/-data/}-${COMMIT}" LICENSE="LGPL-2.1" SLOT="0" KEYWORDS="amd64 arm arm64 x86" -IUSE="" RDEPEND="x11-misc/shared-mime-info" DEPEND="${RDEPEND}" @@ -28,8 +28,6 @@ PATCHES=( "${FILESDIR}"/${PN}-0.1.95-turbomole.patch ) -S="${WORKDIR}/${PN/-data/}-${COMMIT}" - src_prepare() { default # https://github.com/dleidert/chemical-mime/issues/4 diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-drop-turbomole-vibrational.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-drop-turbomole-vibrational.patch deleted file mode 100644 index 4c25b1a18343..000000000000 --- a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-drop-turbomole-vibrational.patch +++ /dev/null @@ -1,20 +0,0 @@ -diff -up chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole_vibration chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in ---- chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole_vibration 2020-01-29 17:32:45.000000000 +0100 -+++ chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in 2020-01-29 17:32:45.000000000 +0100 -@@ -1401,16 +1401,6 @@ - <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-vibrational" support="yes"> -- <_comment>Turbomole Vibrational Data File</_comment> -- <glob pattern="???"/> -- <sub-class-of type="text/plain"/> -- <icon kde="qc"/> -- <supported-by> -- <application name="viewmol"/> -- </supported-by> -- <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> -- </mime-type> - - <mime-type type="chemical/x-vamas-iso14976" cm:support="no"> - <_comment>VAMAS document</_comment> diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch deleted file mode 100644 index 9860261af403..000000000000 --- a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch +++ /dev/null @@ -1,16 +0,0 @@ - icons/hicolor/gnome-mime-chemical.svg | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/icons/hicolor/gnome-mime-chemical.svg b/icons/hicolor/gnome-mime-chemical.svg -index 1a8d428..804514c 100644 ---- a/icons/hicolor/gnome-mime-chemical.svg -+++ b/icons/hicolor/gnome-mime-chemical.svg -@@ -5,7 +5,7 @@ - <!ENTITY ns_svg "http://www.w3.org/2000/svg"> - <!ENTITY ns_xlink "http://www.w3.org/1999/xlink"> - ]> --<svg xmlns="&ns_svg;" xmlns:xlink="&ns_xlink;" xmlns:a="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/" -+<svg xmlns:svg="&ns_svg;" xmlns:xlink="&ns_xlink;" xmlns:a="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/" - width="128" height="128" viewBox="0 0 128 128" overflow="visible" enable-background="new 0 0 128 128" xml:space="preserve"> - <g id="Layer_1"> - <g> diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch deleted file mode 100644 index 8b5ccfbc3fd9..000000000000 --- a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch +++ /dev/null @@ -1,16 +0,0 @@ - Makefile.am | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/Makefile.am b/Makefile.am -index 96e03ab..ba0847a 100644 ---- a/icons/hicolor/Makefile.am -+++ b/icons/hicolor/Makefile.am -@@ -21,7 +21,7 @@ icon_sizes = 16 22 24 32 36 48 64 72 96 128 192 - if BOOL_HICOLOR_THEME - - .svg.svgz: -- gzip $< -c > $@ -+ gzip -c $< > $@ - for size in $(icon_sizes) ; do \ - if test "x$(RSVG)" != "x" ; then \ - $(RSVG) -w $${size} -h $${size} -f png $< $*_$${size}.png ; \ diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-rsvg-convert-r2.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-rsvg-convert-r2.patch deleted file mode 100644 index 55039f8be07e..000000000000 --- a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-rsvg-convert-r2.patch +++ /dev/null @@ -1,36 +0,0 @@ ---- a/configure.ac.old 2020-03-20 23:32:05.866604992 +0100 -+++ b/configure.ac 2020-03-20 23:32:30.866022834 +0100 -@@ -97,14 +97,12 @@ - AC_PATH_PROG([CONVERT], [convert], [no]) - AC_SUBST([CONVERT]) - --if test "x$enable_convert" != "xyes" -a "x$CONVERT" = "xno" ; then -- AC_ARG_VAR( -- [RSVG], -- [The 'rsvg' binary with path. Use it to define or override the location of 'rsvg'.] -- ) -- AC_PATH_PROG([RSVG], [rsvg], [no]) -- AC_SUBST([RSVG]) --fi -+AC_ARG_VAR( -+ [RSVG], -+ [The 'rsvg' binary with path. Use it to define or override the location of 'rsvg'.] -+) -+AC_PATH_PROG([RSVG], [rsvg-convert], [no]) -+AC_SUBST([RSVG]) - - if test "x$RSVG" = "xno" -a "x$CONVERT" = "xno" ; then - AC_MSG_ERROR([Cannot find rsvg (librsvg binary) or convert (imagemagick). Please install one of them.]) ---- a/icons/hicolor/Makefile.am.old 2020-03-20 23:32:54.292414381 +0100 -+++ b/icons/hicolor/Makefile.am 2020-03-20 23:33:40.052179227 +0100 -@@ -23,8 +23,8 @@ - .svg.svgz: - gzip $< -c > $@ - for size in $(icon_sizes) ; do \ -- if test "x$(RSVG)" != "x" ; then \ -- $(RSVG) -w $${size} -h $${size} -f png $< $*_$${size}.png ; \ -+ if test "x$(RSVG)" != "xno" ; then \ -+ $(RSVG) -w $${size} -h $${size} -f png $< --output $*_$${size}.png ; \ - else \ - $(CONVERT) $< -resize $${size}x$${size} $*_$${size}.png ; \ - fi \ diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch deleted file mode 100644 index 852d6b0605be..000000000000 --- a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch +++ /dev/null @@ -1,57 +0,0 @@ -diff -up chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in ---- chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole 2009-08-10 09:37:06.000000000 +0200 -+++ chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in 2009-08-10 09:40:57.000000000 +0200 -@@ -1290,7 +1290,7 @@ - <specification url="http://ca.expasy.org/sprot/userman.html"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-basis" support="no"> -+ <mime-type type="chemical/x-turbomole-basis" support="yes"> - <_comment>Turbomole Basis Set File</_comment> - <glob pattern="basis"/> - <sub-class-of type="text/plain"/> -@@ -1304,7 +1304,7 @@ - <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-control" support="no"> -+ <mime-type type="chemical/x-turbomole-control" support="yes"> - <_comment>Turbomole Control File</_comment> - <glob pattern="control"/> - <sub-class-of type="text/plain"/> -@@ -1320,7 +1320,7 @@ - <specification url="http://www.cosmologic.de/data/DOK_HTML/node230.html"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-coord" support="no"> -+ <mime-type type="chemical/x-turbomole-coord" support="yes"> - <_comment>Turbomole Coordinate File</_comment> - <glob pattern="coord"/> - <glob pattern="*.tmol"/> -@@ -1335,7 +1335,7 @@ - <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-grad" support="no"> -+ <mime-type type="chemical/x-turbomole-grad" support="yes"> - <_comment>Turbomole Gradient File</_comment> - <glob pattern="gradient"/> - <sub-class-of type="text/plain"/> -@@ -1383,7 +1383,7 @@ - <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-scfmo" support="no"> -+ <mime-type type="chemical/x-turbomole-scfmo" support="yes"> - <_comment>Turbomole SCF Molecular Orbital File</_comment> - <acronym>MO</acronym> - <expanded-acronym>Molecular Orbital</expanded-acronym> -@@ -1401,7 +1401,7 @@ - <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> - </mime-type> - -- <mime-type type="chemical/x-turbomole-vibrational" support="no"> -+ <mime-type type="chemical/x-turbomole-vibrational" support="yes"> - <_comment>Turbomole Vibrational Data File</_comment> - <glob pattern="???"/> - <sub-class-of type="text/plain"/> diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest index d34b4dbb6e5b..aebec65cb5f0 100644 --- a/sci-chemistry/dssp/Manifest +++ b/sci-chemistry/dssp/Manifest @@ -3,10 +3,12 @@ AUX dssp-2.1.0-gentoo.patch 1513 BLAKE2B aabdcfff1083d7552392c35897eb8a84b07323c AUX dssp-2.2.1-boost-1.65-tr1-removal.patch 2126 BLAKE2B dc59d21a6be26ee96b636c13645163478999d5122f09d3a72963843be773210ea225e374941bd057ef6f083a13fb77980bd4390174df2a0c715f0386da7232e0 SHA512 8f84c6e163888d6a8192683a6555f7d6003634854f5cde0f6f962744e531165c7e0b2b08c55cbfb9c396d167c44317dd2e7a8290e4defd2c8def0a6511fbbd6c DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811 DIST dssp-3.0.11.tar.gz 168085 BLAKE2B e1c42fd22cfb2287f10b5deae48b56a4583d4a67737a3485dcbd160d1597a15c2d5105c3794c875d8001abede1c014efb4f7f5b7c250f867bdf9ed95a0860217 SHA512 a0cfe44e517ff1f909ef2928b62ae2c639c6bddfd8a0fb538883f647fd2771e00da68e0fd2521aa02ba3c6d1b0c9b784b7fe142392af3a3abf6ea89f1546bd9d -DIST dssp-4.4.4.1.tar.gz 162809 BLAKE2B 6c3f588a48778cf5f20b40b93736e150a4d366bf44d214b4064362c2a3bce69db415f5d12568a8523d99e2e5a47749d450ff0251dc3035628dbef9343d37e99a SHA512 291810391d74da7ab65bcf4aab61fa4ae1a5518a361fa02d5c15ed0e5c94139fde65e7612a978f5326bd7d93f2ac6ea01b2b65514d6b64f4d062adf112c48deb +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-4.4.4.1.ebuild 1321 BLAKE2B ba06063adc7c9ac9a20c078eeb98c95f0003c5ae58c0db0b5bbb888b194de86e22de9c1549d1911e25e4d5b7a3f99089c0083c281441eeed3dde3ea5e3b8cd14 SHA512 77683bc3bc0aebeb867ffaf94d5f7ce1090f78a73fc739da01c73d3bdab142fc409bce66f85349b627e54376e1279b45a9096a71cac080be10ab0ba4f84d33cb +EBUILD dssp-4.4.10.ebuild 1329 BLAKE2B 61d8909411ff687ba6b11449b0c3acd307c28ac5901fe360886b980d49b88e301cbd539d794503e789e73973ce1ae6aa965e1846cf7453d41df96285a1710cdf SHA512 d3beb704dc3a3783c79ac73fdfdebf74e82fa15d8d7d792124a529c7a208e6349b8035585d0ee96eecaf13ef81ecaa407c2ee22edd8bfdbe5befc945ca5453a6 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-4.4.4.1.ebuild b/sci-chemistry/dssp/dssp-4.4.10.ebuild index a274099244cf..d5e51fe40fec 100644 --- a/sci-chemistry/dssp/dssp-4.4.4.1.ebuild +++ b/sci-chemistry/dssp/dssp-4.4.10.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -18,14 +18,15 @@ KEYWORDS="~amd64 ~x86" CDEPEND=" dev-libs/boost:=[zlib] >=dev-libs/libmcfp-1.2.2 - >=sci-libs/libcifpp-5.2.0 + >=sci-libs/libcifpp-7.0.3 +" +BDEPEND="${CDEPEND} + dev-cpp/catch:0 " -BDEPEND="${CDEPEND}" # doc? ( # || ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc ) # dev-python/weasyprint # ) -DEPEND="" RDEPEND="${CDEPEND}" #src_prepare() { diff --git a/sci-chemistry/dssp/dssp-4.4.8.ebuild b/sci-chemistry/dssp/dssp-4.4.8.ebuild new file mode 100644 index 000000000000..d5e51fe40fec --- /dev/null +++ b/sci-chemistry/dssp/dssp-4.4.8.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit cmake + +DESCRIPTION="The protein secondary structure standard" +HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp" +SRC_URI="https://github.com/PDB-REDO/${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/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index cdfc78bc1836..d2d1863db84d 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -5,32 +5,28 @@ AUX gromacs-2021-musl-stdint.patch 601 BLAKE2B 2e871d22655950ee9b9951229e78bc022 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-2023.4.tar.gz 42044149 BLAKE2B 2c13a04ddbfc167a7887d44bb6fdacde4ece4e8cf2ba920f453fc6150423c3cae39cd1afe0eebb52b9fbc72fe37fee527c83227a0f3fe21b289655b5c1cd29c5 SHA512 7913348d0da25e095b795123894f4e2007f66cf2455664edeb7bc1edc09f2e0da9911bc9501e3001278ab59917ccef838c485e6b6533c1c816c54c6dbd56350c -DIST gromacs-2024.1.tar.gz 42324773 BLAKE2B 6600c802c39bf7c36d8e388ced202504dcceb3ec018d5f48af4f55e43dd170157a9b6335ce1b20a73623d05a391787936c2ab6ee48ab031d17078256eb7153c5 SHA512 fea88fac28ec142201eec1cea984eabd9db43346254ac555954a13fdbae5a5b00281a17efc8dba8ab0ac42794e3cce41b314c5cb36fb4292a1c6d2668b2ba192 -DIST gromacs-2024.2.tar.gz 42367929 BLAKE2B 3ffdbc075c3b92d1200376b45b0599eafc15454830f0a5b1c1e250a50d8fcd16a6a904c5f04979328b1afc89e6c77b15df44d9c240425507bafe0689107bf9a0 SHA512 aa6c0ae3849d6e58ae43ffef6ef90d06f62e53ab70047c643c90e9f3ac7305c2d52bb5c9da02b174a6244e8a6adfb6d205d1c9d22312709a1b358923f5d10741 +DIST gromacs-2023.5.tar.gz 42079310 BLAKE2B 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fddaab6e06c3a1da28f0e85f5edf03dea4ba38212e933f71f4d7f9e9efe7c042c140ef38492514b65adc4f38d341aa8ea74db5937ef22b84e0f28b1747560f98 SHA512 c3b521a32c3d0690580dfee163a9c21b016c7b7b696d617d7d5991e36de2610b32fd8f0debb05478e15e3d29c99114eeb7704c95dc13f9ff675d2e81cb1d06fb -EBUILD gromacs-2021.7-r1.ebuild 10139 BLAKE2B 9611b5c6e0d22255f1faf0f5223cf013ffff2407c3f272f7e0eb932414efc63324cca3fe515fbbbaaa318b14709458d338b18b5c38b87081c1f7fb15ff33b31b SHA512 e0c00ba782790361a354d203327e80820e2c5ef9d4fc1130ece1dc6866303059e505146b8dc18e34d1690e0cd153ac9e6c6015b55e92a047ba96e9a74387301b -EBUILD gromacs-2022.6.ebuild 9583 BLAKE2B 4700542f3a32bc3055617792d56fa63370438e949efaf073ae3e983f25184ed0f7fbf8a13c777c0da0a0965cfae8ad96625e76ec4d69e5ade60b71d6466fe4af SHA512 9c7c0a0692cd31102c4edce4b33d4e61afb12cf034ad804ba131d40f60cb2b3cf05a424b3f40e4001ea09ee5a5c354b4d98e9a709ee75d5c8d134ee0a579bd09 -EBUILD gromacs-2023.4.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 -EBUILD gromacs-2023.9999.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 -EBUILD gromacs-2024.1.ebuild 9745 BLAKE2B 254a8fd8fd9b12cdb0afbbd98539add499934781db7a2a249b1fd5dd077227d6a50a23cadb87e409aaf51a7188491dc4662f305142ebc8388b9ef823bbe7b45d SHA512 e9d3a2346f38a64f125bb20031f37e3ffde9c17b50f7812b682818417dc2c68aef0afec206a58f91e5c9af091ce198b97e998ecf6fc5b6c64d861cfda31be755 -EBUILD gromacs-2024.2.ebuild 9745 BLAKE2B 254a8fd8fd9b12cdb0afbbd98539add499934781db7a2a249b1fd5dd077227d6a50a23cadb87e409aaf51a7188491dc4662f305142ebc8388b9ef823bbe7b45d SHA512 e9d3a2346f38a64f125bb20031f37e3ffde9c17b50f7812b682818417dc2c68aef0afec206a58f91e5c9af091ce198b97e998ecf6fc5b6c64d861cfda31be755 -EBUILD gromacs-2024.9999.ebuild 9745 BLAKE2B 254a8fd8fd9b12cdb0afbbd98539add499934781db7a2a249b1fd5dd077227d6a50a23cadb87e409aaf51a7188491dc4662f305142ebc8388b9ef823bbe7b45d SHA512 e9d3a2346f38a64f125bb20031f37e3ffde9c17b50f7812b682818417dc2c68aef0afec206a58f91e5c9af091ce198b97e998ecf6fc5b6c64d861cfda31be755 +EBUILD gromacs-2020.7-r1.ebuild 9908 BLAKE2B 71b4d9bfd7def50f1ee99efd1f0355860aa3fb2ac160c4e3e79603d5b20f7f3aedc8cac0ee19b7b94cef310ee27656cd72d207531815735791856550a61a5c8c SHA512 f96a9bdc517356a89b1603e27a209149a3b5944d7b59c87e4318ea67f3c201475a7d263b81f25553935bbcc912d14b4ea276b1ab0962c6743010759bccaeca68 +EBUILD gromacs-2021.7-r1.ebuild 10211 BLAKE2B 93cdfb55a929a999fb261f1f00366bc77b8a6e2bad1233baf85d6dd23291d1574c62f898b8c8ec057aaf911164bbe3c08cdd00a92843040fc02c6521c9849d9b SHA512 022be04a04c5aa8198803941ddb20543961f01b8bd2c9e2901a2c879e15c8b3bba538f429ed50c6b88cf923262398fab304ceb8ee15176aeed5efff5d87f020e +EBUILD gromacs-2022.6.ebuild 9655 BLAKE2B 3d0e21ae4e04602b390ff7f810c355f5a79a4602e582e4d06103119d21ce3771ebd8ad230f33fd37f786b3e14ce614c949658241a700f75531b8d08077cd97d5 SHA512 9df7661a40d23a3bcec74dd962e021aca7a0a1f5d30ce42bacd4737860e71fb7ef665576079e75d72e7758d3aa3cf5b04a186dba6b02ab9ace90a24ef031bfbd +EBUILD gromacs-2023.5.ebuild 9810 BLAKE2B 29946a30ec5fc7c19233790c48a8e6657006b5a50fae49c188444a6d03f44e8f80ecbaff12b97041a22dd42e33485a8072859b9b3cca86f198cf0fee691e2b95 SHA512 6ac853da2413ebad69a010b66ff53941fe65fe2bdae5d9aec63de376036388c7dff3017243c528d3175126f118420e2187a48d804eb096440eea3d0d755ffacd +EBUILD gromacs-2023.9999.ebuild 9810 BLAKE2B 29946a30ec5fc7c19233790c48a8e6657006b5a50fae49c188444a6d03f44e8f80ecbaff12b97041a22dd42e33485a8072859b9b3cca86f198cf0fee691e2b95 SHA512 6ac853da2413ebad69a010b66ff53941fe65fe2bdae5d9aec63de376036388c7dff3017243c528d3175126f118420e2187a48d804eb096440eea3d0d755ffacd +EBUILD gromacs-2024.3.ebuild 9817 BLAKE2B 65f5ae4402abc5b2b2fac677fb2ca0a62c97ab9c9d7738ca3491d669772a233d65b8e61afa1f441b9b08f1ed31866cb3fed3aa0bd6b76ef894b5f066c7385f7d SHA512 fcc3c48c835590eb96a773981428435e4b048f1a5fbbdc71f8303a89f46257974ed12bfc1649516cb688d8a959f730d4d59dc5555b6982cf7b9fb5595f545a26 +EBUILD gromacs-2024.9999.ebuild 9817 BLAKE2B 65f5ae4402abc5b2b2fac677fb2ca0a62c97ab9c9d7738ca3491d669772a233d65b8e61afa1f441b9b08f1ed31866cb3fed3aa0bd6b76ef894b5f066c7385f7d SHA512 fcc3c48c835590eb96a773981428435e4b048f1a5fbbdc71f8303a89f46257974ed12bfc1649516cb688d8a959f730d4d59dc5555b6982cf7b9fb5595f545a26 EBUILD gromacs-2024.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 -EBUILD gromacs-9999.ebuild 9745 BLAKE2B 254a8fd8fd9b12cdb0afbbd98539add499934781db7a2a249b1fd5dd077227d6a50a23cadb87e409aaf51a7188491dc4662f305142ebc8388b9ef823bbe7b45d SHA512 e9d3a2346f38a64f125bb20031f37e3ffde9c17b50f7812b682818417dc2c68aef0afec206a58f91e5c9af091ce198b97e998ecf6fc5b6c64d861cfda31be755 -MISC metadata.xml 1375 BLAKE2B 321b7db8536061655a6efaa40110f4858633921292eba465b85fe0cb50280842e511f2f11385fe5d62bbdfb40e9c0c76e8e986a1efce8eac25d52c438d7ed5f4 SHA512 cc61e0b477f6576079a0f7910475b9091c1c521fbb48efab365d355e3c0a80cd19e1ea9028cb269d37c2572546b1be66a210512e40ff0f2d6314d1b0138cdba6 +EBUILD gromacs-9999.ebuild 10091 BLAKE2B 46b1f7c84e7cab89bfbe933b581fceea1d9a28fc5d733b0b5760297ee820325b5a340ada7f4b6129cf72cd49b378398572701014be9e6d29fcc0df4b9b8a158a SHA512 a62ec593636c8ac1b3ab18aecfa9ce7365dac9bc5c6fbca5b6413e10cf3751fd6b5cf924d8dfffe06e5d5fcea57500fd14b00ddb1b684a4b68c6d2d4c4aa2b14 +MISC metadata.xml 1461 BLAKE2B fa82d5e83fa403fe8c31d076b2cf577d4299b2c97e993b02634c32e8c74088825f8ef61417bc1294947408fddc5b831b983574dafaac5c6975c06af74d890f00 SHA512 ce2b73c332585d9cfb7d1c7cbc49e5fb94f828191c8805463c03e3f215a7137253796ab49718148ea0c5a6ab85b45794b2fe5d213e0d35b2013ea41f6079d484 diff --git a/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild index fa123d04defb..c93e5baf72ef 100644 --- a/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild @@ -49,6 +49,10 @@ CDEPEND=" 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 ) diff --git a/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild b/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild index 1b82d86998ee..8b99117678ed 100644 --- a/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild @@ -49,6 +49,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14:=[profiler] ) 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 ) diff --git a/sci-chemistry/gromacs/gromacs-2022.6.ebuild b/sci-chemistry/gromacs/gromacs-2022.6.ebuild index 8ebb3ae9a8dd..92b1f497c860 100644 --- a/sci-chemistry/gromacs/gromacs-2022.6.ebuild +++ b/sci-chemistry/gromacs/gromacs-2022.6.ebuild @@ -45,6 +45,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) 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 ) diff --git a/sci-chemistry/gromacs/gromacs-2023.4.ebuild b/sci-chemistry/gromacs/gromacs-2023.5.ebuild index a3319899d419..4ee08b22a7f0 100644 --- a/sci-chemistry/gromacs/gromacs-2023.4.ebuild +++ b/sci-chemistry/gromacs/gromacs-2023.5.ebuild @@ -45,6 +45,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) 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 ) diff --git a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild b/sci-chemistry/gromacs/gromacs-2023.9999.ebuild index a3319899d419..4ee08b22a7f0 100644 --- a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2023.9999.ebuild @@ -45,6 +45,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) 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 ) diff --git a/sci-chemistry/gromacs/gromacs-2024.2.ebuild b/sci-chemistry/gromacs/gromacs-2024.2.ebuild deleted file mode 100644 index 33e343e23e7c..000000000000 --- a/sci-chemistry/gromacs/gromacs-2024.2.ebuild +++ /dev/null @@ -1,335 +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 ~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" - -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 ) - 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? ( >=sys-devel/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-2024.1.ebuild b/sci-chemistry/gromacs/gromacs-2024.3.ebuild index 33e343e23e7c..2101629ebc36 100644 --- a/sci-chemistry/gromacs/gromacs-2024.1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2024.3.ebuild @@ -45,6 +45,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) 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 ) diff --git a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild b/sci-chemistry/gromacs/gromacs-2024.9999.ebuild index 33e343e23e7c..2101629ebc36 100644 --- a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2024.9999.ebuild @@ -45,6 +45,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) 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 ) diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 33e343e23e7c..01ebc8ab87b7 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -18,7 +18,7 @@ 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=" @@ -39,17 +39,23 @@ 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 +hdf5 +hwloc lapack mkl mpi nnpot +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] + sys-devel/clang-runtime[openmp] + ) fftw? ( sci-libs/fftw:3.0= ) + hdf5? ( sci-libs/hdf5 ) 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:= ${PYTHON_DEPS} @@ -178,6 +184,11 @@ src_prepare() { src_configure() { local mycmakeargs_pre=( ) extra fft_opts=( ) local acce="AUTO" + local nnpot="OFF" + + if use nnpot; then + nnpot="TORCH" + fi if use custom-cflags; then #go from slowest to fastest acceleration @@ -225,9 +236,12 @@ src_configure() { -DGMX_COOL_QUOTES=$(usex offensive) -DGMX_USE_TNG=$(usex tng) -DGMX_BUILD_MANUAL=$(usex build-manual) + -DGMX_USE_HDF5=$(usex hdf5) -DGMX_HWLOC=$(usex hwloc) -DGMX_DEFAULT_SUFFIX=off + -DGMX_BUILD_HELP=on -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) @@ -270,6 +284,8 @@ 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 diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index 44ddb19d1d9d..518711308a02 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -19,6 +19,7 @@ <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> <flag name="tng">Enable new trajectory format - tng</flag> diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest index 76e5c78f437b..e540122ad8fe 100644 --- a/sci-chemistry/molmol/Manifest +++ b/sci-chemistry/molmol/Manifest @@ -3,6 +3,5 @@ DIST molmol-2k.2.0-doc.tar.gz 1062297 BLAKE2B 082d4eea5544bab52ffc1ff6364c503043 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-r8.ebuild 2284 BLAKE2B fa9954fca3dd8b52450beb1c0901abc71743672d7a76e2daa2bb05f52280ecf7dec5c401da24ce3e72f429cb69b27738117e33d41b49a96836b1b407efef67f0 SHA512 d813743572479b5eb0ed4181d42743402c4bd0a5a8e012f32bad03c4be68f38329722b749abc91845ba9c25642b19f5e2c4b5578ed9d3f7d03beaabbaa3345f5 -EBUILD molmol-2k_p2-r9.ebuild 2313 BLAKE2B fecc271cadf3eb73478b1adc674a6d369ee7bbb05c38e10ae78ebbc886782962f7c33ea07ef4d065e643ee7f5a71e99801f72c290cb7ab437833141dcfe80a99 SHA512 d173ed8f60c833485bf639fa8fc0ace5ff1ae46316be319d2cd1feb5f5201484ed9e8bba46054dfc91303d71051b52d4fa943638ecf6b843514fa9585bc421a5 +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/molmol-2k_p2-r8.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r8.ebuild deleted file mode 100644 index 59bedaf2593d..000000000000 --- a/sci-chemistry/molmol/molmol-2k_p2-r8.ebuild +++ /dev/null @@ -1,102 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 -inherit desktop toolchain-funcs - -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 -" - -LICENSE="molmol" -SLOT="0" -KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -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 -" -DEPEND="${RDEPEND}" -BDEPEND="" - -S="${WORKDIR}" - -pkg_setup() { - MMDIR="/usr/$(get_libdir)/molmol" - MAKEOPTS="${MAKEOPTS} -j1" #880621 -} - -src_prepare() { - default - - rm -rf tiff* - # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided - eapply "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff - - eapply "${WORKDIR}"/patches/ldflags.patch - eapply "${WORKDIR}"/patches/opengl.patch - - ln -s makedef.lnx "${S}"/makedef || die - - sed \ - -e "s|ksh|sh|" \ - -e "s|^MOLMOLHOME.*|MOLMOLHOME=${EPREFIX}/${MMDIR};MOLMOLDEV=\"Motif/OpenGL\"|" \ - -i "${S}"/molmol || die - sed \ - -e "s|^MCFLAGS.*|MCFLAGS = ${CFLAGS}|" \ - -e "s|^CC.*|CC = $(tc-getCC)|" \ - -i "${S}"/makedef || die - - eapply "${WORKDIR}"/patches/cast.patch - eapply -p0 "${WORKDIR}"/patches/libpng15.patch - - # patch from fink - # fixes numerous bad bracings and hopefully the OGL bug 429974 - eapply "${WORKDIR}"/patches/${P}-fink.patch - - eapply "${WORKDIR}"/patches/wild.patch - tc-export AR -} - -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" "${PN}.png" - - einstalldocs - dodoc HISTORY -} diff --git a/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild index 14378809c07a..9a63d1dbb20d 100644 --- a/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild +++ b/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild @@ -52,7 +52,6 @@ PATCHES=( pkg_setup() { MMDIR="/usr/$(get_libdir)/molmol" - MAKEOPTS="${MAKEOPTS} -j1" #880621 } src_prepare() { @@ -85,6 +84,13 @@ src_prepare() { eapply "${WORKDIR}"/patches/wild.patch tc-export AR + + # Parallel build fails (#880621) and cannot be disabled by MAKEOPTS + # (#880621, #941488). + find . -name Makefile -exec sed -i -e "1i .NOTPARALLEL:" {} + || die + # Try to drop the ugly hardcoded sleep now that make is really + # serial + sed -i -e 's/sleep 2/sleep 0/g' makedef || die } src_install() { diff --git a/sci-chemistry/mopac7/Manifest b/sci-chemistry/mopac7/Manifest deleted file mode 100644 index 25d061c91462..000000000000 --- a/sci-chemistry/mopac7/Manifest +++ /dev/null @@ -1,6 +0,0 @@ -AUX Makefile 387 BLAKE2B b0c4b3a009c8bf8c779953edf3e233434656033a661cb307079eebc980a827215fcd0dc04cf1df245ec20a6f95c151e4f9a9816c56cf8d6c1da6f77214fb41a5 SHA512 5bde85940d1d850ae65d23802aefb57660fda512d452660fdc37a19ae1f50c7f1240bfeffdd81a52cbd0a3140dad76272ca60333b60d40d1d79fdfe7297857dd -DIST dcart.f 11044 BLAKE2B 7414804ecfab9a7cbddee664b85e6e2e8c1d8fe1e1f73d480dd1a387c5e349d26ec4ae1a37f27e38b7c051fcce2c1bdf77de12ec628298fd3edf79040a8a0c5a SHA512 788a184fd8419ff742e49c1a652d5ea093f9114dbe4f272665b8fb9eeac2afb7f7042628c288f2b81d0f54d8a7ef2f400490cd3aff39dda59a6d70a0deab5b80 -DIST gmxmop.f 38956 BLAKE2B e411feca5104e91ae8fd2008de61d18cc214beb3b2a7aa09a80269fb935e27ba1b1cb89fa30eedbfc4f6c4734c22d932e57d5905c175ae9f56c4affee7b0ca04 SHA512 38bb2e5749c4d3c8c24f15682f72e40cb4edb6517c7916cecee1d21675b1870c0fe331ba2ec40312408dec473141e7742d1e155d4b64f1c2a25bfa4e11885194 -DIST mopac7-1.15.tar.gz 764547 BLAKE2B 6e037862007221955d0ad65f3c002a3d2e461950a2bc0efac9d195cf1d9d856842d02bc380ce236c3d48f863a144875950f5c86f8f3ac936b8b098472f7f7a0d SHA512 e0ccd643caa6dbd7e156867530d79e50e10243f5e3b5f8bc57781e68e1daf26f2a0e6987fff00afe07eb0fcb98cbd9f01e4cfa5d20acc0d8ab3cca632968636e -EBUILD mopac7-1.15-r1.ebuild 1979 BLAKE2B 9ed2f685e1b787f1eece439ca75efe489601651712aa6dbab8fff05d78e0ce3d97a5116266568d985e2ca67749e4bd39dd606f8f419141ce39ccadf39de9fe22 SHA512 add91d8a0b7da52ecebed3f611fb259110ab4872554ea2db94bb476625ef2c09ea83220f6e16f69303c6bba368bbd1681ec293f013cfce05a05b6a3271438d0a -MISC metadata.xml 435 BLAKE2B 12efd7ecfe6c9b07411d62992a225848f3787b58a59765e373fdc98ce22c3b50763243ac70efa1d7a7ec3309bc519dd433d41b778fe8f18cdfbdae971e0ee82c SHA512 d624b1181bdd0d66062507e7793eb25d24c447fa9ffbe8ee1645c88b843e6822e80af087bf6073ac191947074491159331f2021b884f8b7cd2237cf3e013ebb4 diff --git a/sci-chemistry/mopac7/files/Makefile b/sci-chemistry/mopac7/files/Makefile deleted file mode 100644 index bcada8b0a889..000000000000 --- a/sci-chemistry/mopac7/files/Makefile +++ /dev/null @@ -1,18 +0,0 @@ -VERSION = GENTOOVERSION -MAJOR = 1 - -LIBS = -lgfortran -lf2c - -objects := $(patsubst %.f,%.o,$(wildcard *.f)) - -all: libgmxmopac7 - -clean: - rm -f moldat.*f deriv.* mopac7*.* compfg.* dcart.* - -%.o: %.f - $(FC) $(FFLAGS) -fPIC -c $< - -libgmxmopac7: $(objects) - $(FC) -shared $(LDFLAGS) -Wl,-soname,libgmxmopac7.so.$(MAJOR) -o $@.so.$(VERSION) $^ $(LIBS) - ln -sf $@.so.$(VERSION) libgmxmopac7.so diff --git a/sci-chemistry/mopac7/metadata.xml b/sci-chemistry/mopac7/metadata.xml deleted file mode 100644 index cd1cacd0abf9..000000000000 --- a/sci-chemistry/mopac7/metadata.xml +++ /dev/null @@ -1,14 +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> - <use> - <flag name="gmxmopac7">Add support library for gromacs</flag> - </use> - <upstream> - <remote-id type="sourceforge">mopac7</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild deleted file mode 100644 index c536575112e8..000000000000 --- a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild +++ /dev/null @@ -1,78 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit autotools fortran-2 flag-o-matic toolchain-funcs - -DESCRIPTION="Autotooled, updated version of a powerful, fast semi-empirical package" -HOMEPAGE="https://sourceforge.net/projects/mopac7/" -SRC_URI=" - http://www.bioinformatics.org/ghemical/download/current/${P}.tar.gz - http://wwwuser.gwdg.de/~ggroenh/qmmm/mopac/dcart.f - http://wwwuser.gwdg.de/~ggroenh/qmmm/mopac/gmxmop.f" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux" -IUSE="gmxmopac7" - -DEPEND="dev-libs/libf2c" -RDEPEND="${DEPEND}" - -src_prepare() { - default - - # Install the executable - sed -i \ - -e "s:noinst_PROGRAMS = mopac7:bin_PROGRAMS = mopac7:g" \ - fortran/Makefile.am \ - || die "sed failed: install mopac7" - # Install the script to run the executable - sed -i \ - -e "s:EXTRA_DIST = autogen.sh run_mopac7:bin_SCRIPTS = run_mopac7:g" \ - Makefile.am \ - || die "sed failed: install run_mopac7" - - eautoreconf - append-fflags -std=legacy -fno-automatic -} - -src_configure() { - # -Werror=lto-type-mismatch - # https://bugs.gentoo.org/927389 - # - # Unmaintained fortran code, no bug report. - filter-lto - - econf --disable-static -} - -src_compile() { - emake - if use gmxmopac7; then - einfo "Making mopac7 lib for gromacs" - mkdir "${S}"/fortran/libgmxmopac7 || die - cd "${S}"/fortran/libgmxmopac7 || die - cp -n ../SIZES ../*.f "${FILESDIR}"/Makefile . || die - emake clean - cp -n "${DISTDIR}"/gmxmop.f "${DISTDIR}"/dcart.f . || die - sed "s:GENTOOVERSION:${PV}:g" -i Makefile || die - emake FC="$(tc-getFC)" - fi -} - -src_install() { - # A correct fix would have a run_mopac7.in with @bindir@ that gets - # replaced by configure, and run_mopac7 added to AC_OUTPUT in configure.ac - sed -i "s:./fortran/mopac7:mopac7:g" run_mopac7 || die - - default - - if use gmxmopac7; then - cd "${S}"/fortran/libgmxmopac7 || die - dolib.so libgmxmopac7.so* - fi - - find "${ED}" -name '*.la' -delete || die -} diff --git a/sci-chemistry/psi/Manifest b/sci-chemistry/psi/Manifest index abf16d28e732..fe4d4b98e63d 100644 --- a/sci-chemistry/psi/Manifest +++ b/sci-chemistry/psi/Manifest @@ -5,10 +5,11 @@ AUX 3.4.0-gcc-4.3.patch 8000 BLAKE2B fe6762d9bd30f73357099f675dc31687dd4b81988b8 AUX 3.4.0-ldflags.patch 407 BLAKE2B 86184259773301499137c36c4a8ac938ad5b4743fb3e72a355e97a213a4a1d6f1ef22cecab64571ac7ca19949ef7e6b961825c8347892a0a28f11d0bee22578a SHA512 3442fbbd93e149fb585399b290cdb202b9b1d15602e4c923f351d182b3e579324123071dfb28e590b81c7b5d0de6158b774ed65e7a048342824befcb250056e6 AUX 3.4.0-man_paths.patch 611 BLAKE2B b0463f3ec16d89e91298de55b680475de819443cafcc228fe02a2efa63a07929fd98b11ed60b2343e9d35d517f2021dca25586e01ab3d6433d988524d7207d18 SHA512 561eb482cb505e3bed38ceefe7677ae8ea6e62d1465ba504276ccef3e4f8296855b271cf5fbbc263aaae34ca59e0261351b0a8b52b446846199882b14fc27632 AUX 3.4.0-parallel_fix.patch 10714 BLAKE2B 4e35122cb2f47432ecf4271dad43bf28c425395f0f0fc579b0d4564ef1363d2dcbe9c77f1175d332c15334d41a64fc6413e328ae5718df25b57c741f7493dd28 SHA512 931f6eedc58527447f2604af323db08c27b47e3cdf4c80c0937f5f1218c9f2cb126d8fd85b88f36a50f41d8b15d4bb23cb0d035bbc38cbd6bac74c944780c102 +AUX psi-3.4.0-C99.patch 438 BLAKE2B 961ff6091c51cc8d6fc67977545fa31b68a78989014d72e375e2f240df9ace552418a8d339bd9a0af65801cac7c62a402229b0b0a3c43a04d3e152d69f588f74 SHA512 ef931f52eb40122f4d81dc7cc1a61466fb6cbe831b1da7ce4b0e500cbfad13e0f34c7413e8d2c10730f91a6957eaf676ecdf59bd26be1f522954839bd1960017 AUX psi-3.4.0-format-security.patch 1021 BLAKE2B 58aebbd7d8d8fd8c78c8cce7ad28574210b6fecebbfe982426d14c355ee524e0ab07364e10a80c28db066208a7fbb1f7ec794fcfcc934bb339a8005d05dad8c8 SHA512 f828866ae90711f244104c6443c750a148e9c848eedfe38d9a74fc2e5b56543ced7ae0beadbafa3fe338eddd391969e197104838afb5820b50f227ecbfa472de AUX psi-3.4.0-parallel-make.patch 445 BLAKE2B e98ee4f5d0feb639058c3b589c6eb6747b35386276f48a6775ab40833364d0feadc55fb4f91abb58009b83f8122fbb119f0588acc13eabb5fb9857af202ac3d5 SHA512 bf574c6c9c1e1ffc8747fb51896b8f9d8b29c4796b0a06529a58a2ab1ed5ee0a4270fe071eb86ca745bad2c760701c4d9eb7f269cd390f6d9cadf4065962e52e AUX psi-3.4.0-perl-File-Temp.patch 488 BLAKE2B 03c5ab1f1b801321063f389e3ae9989061013cb645cbfecbb94043b809d14df9dbac9b650c9ee5afde5eed88f2f8707d8d8b57713b0134311c62bc36b5247e07 SHA512 683418b28dbdaf4161b679a4fb6aa875ac7834fd4a1b3829c89230be6cdc4b92dc2e23ee3a59a1d5fd3008fdbc7967101a6249a6d42715cedddc2ea756a7e54b AUX use-external-libint.patch 1359 BLAKE2B 24fe9d7eb369f6c6846915cd87471d4f2bcf66da09105d73c4b75cebfa7138d318d5dfca653368d80eb5b39a31eabde60da5b439786ed00d95b31b90e56a44ed SHA512 8b4749b0c449dbc89067eec466d3d557da86e7f2d950cc0a94409e158a31a3fb8ceafefd090168acd97975ff3ccc7859e6f2df3c2cd57a3571b79f71aca6fff7 DIST psi-3.4.0.tar.gz 7413072 BLAKE2B de8b5e0fb1692780446385bf13f6b9984f5be8d441730babacf6f59dd18be6e13b1cff17170cec87def1f743d7e634354b57afbc046e6f34c79c9fc52c31b146 SHA512 b13d2464502545cceec3a3b6048b505b918da26730c1614617b04ee6c1d637c9f799ef7fd92ad9554fa2db87617004aa810a6a81400a04df3c06787d51654ca6 -EBUILD psi-3.4.0-r2.ebuild 1970 BLAKE2B 4fc20b0e1ffa15732b3969c5eca0bb574d6a5ac9f7ba375344a6a365d52d58b9f9fc553e66d603d9f04d20716f95813a3bbfb57f67ee71a0d126b9b5c2c9b847 SHA512 f6f5bcc4720c4a570cadd0349dec4b06643e12e29ef50135c2b3c1f44a6d3e085bd21f47e151757145de74bfacefc9b09e866291d848f8226efa5e64bdbd1c0b +EBUILD psi-3.4.0-r3.ebuild 1999 BLAKE2B 286e40c5cbdec0f266d4e1e21d8b1d21a0913504da421383d0824865ca34783b80565f06629813f0f8662f56a67c32ee070252982dc9c80398408e6950725edb SHA512 6e84ced2af53722701923e4ed80600094ef38c5ebc4f2036c547b318f0a80cc2b62def849e6e444a61531e219a7e02cac965716ef3394f37116267054534b0f3 MISC metadata.xml 353 BLAKE2B 4205c6e944b90033531f13b347ceb80f0f4410993e400fafddce2501f73048f005ae73614bfdc10c41ff7655c4ce36bee084167ed984a5818ca050ab3be73fbf SHA512 9ccb40364500c7eb60dd1edb4551ed0e58cde5c4b52b184b0b0bfcf76957daeed1d098c7a04066011bf255ec869ba39316a875806329f2d4ec375955d69de5a5 diff --git a/sci-chemistry/psi/files/psi-3.4.0-C99.patch b/sci-chemistry/psi/files/psi-3.4.0-C99.patch new file mode 100644 index 000000000000..798e29fadd96 --- /dev/null +++ b/sci-chemistry/psi/files/psi-3.4.0-C99.patch @@ -0,0 +1,22 @@ +https://bugs.gentoo.org/886127 + +--- a/src/lib/libipv1/parse.y ++++ b/src/lib/libipv1/parse.y +@@ -1,6 +1,7 @@ + %{ + #include <stdio.h> + #include <tmpl.h> ++#include "ip_error.gbl" + #include "ip_types.h" + #include "ip_read.gbl" + %} +--- a/src/lib/libipv1/scan.l ++++ b/src/lib/libipv1/scan.l +@@ -1,6 +1,7 @@ + %{ + #include <string.h> + #include <tmpl.h> ++#include "ip_error.gbl" + #include "ip_types.h" + #include "ip_global.h" + #include "scan.gbl" diff --git a/sci-chemistry/psi/psi-3.4.0-r2.ebuild b/sci-chemistry/psi/psi-3.4.0-r3.ebuild index d719fe265a17..aaeed8c8d19c 100644 --- a/sci-chemistry/psi/psi-3.4.0-r2.ebuild +++ b/sci-chemistry/psi/psi-3.4.0-r3.ebuild @@ -1,13 +1,14 @@ # Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit autotools fortran-2 toolchain-funcs DESCRIPTION="Suite for ab initio quantum chemistry computing various molecular properties" HOMEPAGE="http://www.psicode.org/" SRC_URI="https://downloads.sourceforge.net/psicode/${P}.tar.gz" +S="${WORKDIR}/${PN}${PV:0:1}" LICENSE="GPL-2" SLOT="0" @@ -27,8 +28,6 @@ BDEPEND=" virtual/pkgconfig test? ( dev-lang/perl )" -S="${WORKDIR}/${PN}${PV:0:1}" - PATCHES=( "${FILESDIR}"/${PV}-dont-build-libint.patch "${FILESDIR}"/use-external-libint.patch @@ -41,6 +40,7 @@ PATCHES=( "${FILESDIR}"/${PV}-fortify.patch "${FILESDIR}"/${P}-format-security.patch "${FILESDIR}"/${P}-perl-File-Temp.patch + "${FILESDIR}"/${P}-C99.patch ) src_prepare() { diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index c2aeb2fb9df4..1352ddf62ff9 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1,5 +1,12 @@ AUX pymol-2.5.0-format-security.patch 562 BLAKE2B 566f653ca3abd4498f9ee5d7255e1b06d8df320bd25a569620b1ee33da0cfb6a969fd3e0a65fbce7116cd6567d9a544c57f4d6d399bec00b9effa8273a52153c SHA512 4e93a0449470abdbd2d943ef0a5fac7f302485ca42c6d9ccdf1ab9a879029d5185c3f1a3a2e237fd8b3b3bf0a306bce07db3226257360127c97546480c233c4f +AUX pymol-3.0.0-SceneGetDrawFlag-indexing.patch 821 BLAKE2B c854aa49441b308ab7f12265442961ddeb3633b71234bd554d45c3950c3ddcf457ac98e0aa1d226ec7ee3abbd2d0207cce97e40144cb81992f241c3a964b1bcc SHA512 326e04f988ff585a062a342b9553ab6b074102c0599b210a5dfa769cb8841e1619e74b670a2d673a80b81c5a9218e052829e0cc574049a1363741e762cac59e7 +AUX pymol-3.0.0-distutils-py3.12.patch 2620 BLAKE2B 802ef75cf22b408ff8e280c561f4954f7f4d816887107f8db36b85988c345948e7d2cfe97b099cb79794d61d3594666e12f90a64c1f0af2206458ade776a1a2b SHA512 3911207f1a03b19675105cd707d644e76258aa9ab58be3891833873d41b460f6161ac83d495a6bc58bf281831376d17186083d447269d755d2e69ee78e6fc5c2 +AUX pymol-3.0.0-eof-maeffplugin.patch 1071 BLAKE2B b28941bd3fddb534fe150b3d98ef6a17058b25b59717a15ca9a807812f05d98f3f7b2cedee9230eab0465c493bbf375325259260bb1cd0d03beafbb4a8f306d0 SHA512 b39846fa9b3b90d5952f22fdde323039bd09a5c43abdd7975bc72880854f22ae39a0d3d30a6640e98c6d7e8734306e00af3fdae555a4292e48ad7b46a83753f8 +AUX pymol-3.0.0-lto-molfile-plugin.patch 5585 BLAKE2B d9cedbb270184d562373fc9e8a2e1a75b08c5d1a956c28eac55662b424996a6770ea46d45b0645a7b96ab465af0f6aafac3120ed13a29f12daea5ab7c947da5d SHA512 babe47d4cbea390031d1880cf442c780f442d41bdeb181509df307550aa8d9c829af51a676665e8d55ed4cd6ab3f2cde363a087606cb064238bbc74be7e2fe51 +AUX pymol-3.0.0-numpy2.patch 1203 BLAKE2B bd06e70fea5a9a4940ecea226f2bd8d1f4753826ee246d6d418cd473c0ee738b9373c8f6e2f5e56e3708ab2934486286d43c33441e1e97f819c6ac0af731d060 SHA512 2c9445f013383fb534dca4306fa5f8ab8f55b33ed4bc53617e7765cb708a4ebc5380f8578ea1236f61e9e77a6d5a8e21588f7f081f6d6408195b9fa5b67c60b2 +AUX pymol-3.0.0-py3.12-progress.patch 985 BLAKE2B 77103dc94b2e9e304f65e429f5abb1cd2158d95a0b8b53e90d7e915b213a934ea8a598240355437b00cf95e0203c382d003034fa30a37dc00758351d13163e38 SHA512 ff7b75402a92d491145e1487fa018182a2a5a91f1736c63d07a194e6710d425f1bba59a7b4f0f49321e27db8c05e26feda7df12f42a66b1e1cdbf1e52f869a5b 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 +EBUILD pymol-3.0.0-r1.ebuild 3372 BLAKE2B 378b1587c25a4592b6e2e503e7280f38d44696a899d5931c6f3e5a2ef11ed5f28d2bd9ba2e8024e6ed223d6bf504a2b76f7b730926eac7bbdbfbb29f986b3287 SHA512 597918ca799ceb6b2a29704ddc96e2b67464d66dd27ce6d32b00294854d34a4abbeb340848f2d3101464b6f263fb4dd07314c54d14fb87be57b07a27ae06522a EBUILD pymol-3.0.0.ebuild 2958 BLAKE2B 2eac68b0cf15c3369e243b7456e00b1c1119f0d8399bea7321794981f41911bd56bc10713c9102475a054e6a52353cef63c0f9416974bb1db5d91ddd9f6d2dfa SHA512 ca7a597cd909d5a04e77c0afb7e2c07413b13dd42d5788db97defabee23370695299e17193b431eb6190c87a0e06d8e741d2067de973652d1749b244cfeb0254 MISC metadata.xml 495 BLAKE2B 32d321e92c7e7c226747660c314f5cff9aabf9ee41c8a864064432ac9554879db7bf60640993dadae6e00a9b7d1367cb8ab228b63b8797ca84e5618eeeb192cc SHA512 36ef956d111c76182c70c81a830885f540fb2710f696b2711837d4bf1055a8792226f38b827f389a3a3861f259bae1394d6da50c2b33a0ddb4e6940262e1b25d diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-SceneGetDrawFlag-indexing.patch b/sci-chemistry/pymol/files/pymol-3.0.0-SceneGetDrawFlag-indexing.patch new file mode 100644 index 000000000000..c23bf79d6166 --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-3.0.0-SceneGetDrawFlag-indexing.patch @@ -0,0 +1,22 @@ +From 50be59fb4bd6706c7939a659f4477041e2f0619e Mon Sep 17 00:00:00 2001 +From: Jarrett Johnson <36459667+JarrettSJohnson@users.noreply.github.com> +Date: Sat, 6 Apr 2024 22:49:41 -0400 +Subject: [PATCH] PYMOL-4849: Fix SceneGetDrawFlag slot indexing + +--- + layer1/Scene.cpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/layer1/Scene.cpp b/layer1/Scene.cpp +index e4888db6d..ed211bdd6 100644 +--- a/layer1/Scene.cpp ++++ b/layer1/Scene.cpp +@@ -4448,7 +4448,7 @@ int SceneGetDrawFlag(GridInfo * grid, int *slot_vla, int slot) + { + if(((slot < 0) && grid->slot) || + ((slot == 0) && (grid->slot == 0)) || +- (slot_vla && (slot_vla[slot] == grid->slot))) { ++ (slot_vla && (slot >= 0 && slot_vla[slot] == grid->slot))) { + draw_flag = true; + } + } diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-distutils-py3.12.patch b/sci-chemistry/pymol/files/pymol-3.0.0-distutils-py3.12.patch new file mode 100644 index 000000000000..3ab0384bd5f6 --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-3.0.0-distutils-py3.12.patch @@ -0,0 +1,70 @@ +From 3d3c8963798d426e70675c3c40df146e12869b0a Mon Sep 17 00:00:00 2001 +From: Branch Vincent <branchevincent@gmail.com> +Date: Fri, 10 May 2024 22:12:58 -0700 +Subject: [PATCH] replace distutils for python 3.12 (#362) + +Co-authored-by: Jarrett Johnson <jarrett.johnson@schrodinger.com> +--- + create_shadertext.py | 3 +-- + modules/pymol/plugins/installation.py | 7 +++---- + testing/tests/system/pymolwin.py | 1 - + 3 files changed, 4 insertions(+), 7 deletions(-) + +diff --git a/create_shadertext.py b/create_shadertext.py +index 7bae72180..f6857087e 100644 +--- a/create_shadertext.py ++++ b/create_shadertext.py +@@ -7,7 +7,6 @@ + from collections import defaultdict + from os.path import dirname + from subprocess import Popen, PIPE +-from distutils import dir_util + + def create_all(generated_dir, pymoldir="."): + ''' +@@ -30,7 +29,7 @@ def __init__(self, filename): + self.out = cStringIO.StringIO() + self.filename = filename + else: +- dir_util.mkpath(os.path.dirname(filename)) ++ os.makedirs(os.path.dirname(filename), exist_ok=True) + self.out = open(filename, "w") + self.filename = None + def close(self): +diff --git a/modules/pymol/plugins/installation.py b/modules/pymol/plugins/installation.py +index 3a980545b..2fb8f6f03 100644 +--- a/modules/pymol/plugins/installation.py ++++ b/modules/pymol/plugins/installation.py +@@ -45,8 +45,6 @@ def cmp_version(v1, v2): + ''' + Compares two version strings. An empty version string is always considered + smaller than a non-empty version string. +- +- Uses distutils.version.StrictVersion to evaluate non-empty version strings. + ''' + if v1 == v2: + return 0 +@@ -55,8 +53,9 @@ def cmp_version(v1, v2): + if v2 == '': + return 1 + try: +- from distutils.version import StrictVersion as Version +- return cmp(Version(v1), Version(v2)) ++ v1_parts = list(map(int, v1.split('.'))) ++ v2_parts = list(map(int, v2.split('.'))) ++ return (v1_parts > v2_parts) - (v1_parts < v2_parts) + except: + print(' Warning: Version parsing failed for', v1, 'and/or', v2) + return 0 +diff --git a/testing/tests/system/pymolwin.py b/testing/tests/system/pymolwin.py +index 429fd28aa..e7885bd38 100644 +--- a/testing/tests/system/pymolwin.py ++++ b/testing/tests/system/pymolwin.py +@@ -7,7 +7,6 @@ + import subprocess
+ import sys
+ import unittest
+-from distutils.spawn import find_executable
+ from pymol import cmd, CmdException, testing, stored
+
+ @unittest.skipIf(not sys.platform.startswith('win'), 'windows only')
diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-eof-maeffplugin.patch b/sci-chemistry/pymol/files/pymol-3.0.0-eof-maeffplugin.patch new file mode 100644 index 000000000000..8eb8fbde318b --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-3.0.0-eof-maeffplugin.patch @@ -0,0 +1,22 @@ +From f005dde377e3e50b6e3f405939435c5061fa8b63 Mon Sep 17 00:00:00 2001 +From: Jarrett Johnson <36459667+JarrettSJohnson@users.noreply.github.com> +Date: Mon, 22 Apr 2024 11:12:21 -0400 +Subject: [PATCH] PYMOL-4869: Only compare eof token in maeffplugin parser + +--- + contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp +index efaede65b..0547ff91b 100644 +--- a/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp ++++ b/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp +@@ -248,7 +248,7 @@ const char * Tokenizer::token(bool ignore_single) { + char c = peek(); + bool good = false; + ssize_t diff; +- while(state != DONE && c >= 0) { ++ while(state != DONE && c != std::char_traits<char>::eof()) { + // make sure we have space in m_token for 2 more characters + if ((diff = ptr-m_token) >= max_token_size-1) { + m_token = (char *)realloc( m_token, 2*max_token_size ); diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-lto-molfile-plugin.patch b/sci-chemistry/pymol/files/pymol-3.0.0-lto-molfile-plugin.patch new file mode 100644 index 000000000000..445fc6bc3a10 --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-3.0.0-lto-molfile-plugin.patch @@ -0,0 +1,187 @@ +From 9d3061ca58d8b69d7dad74a68fc13fe81af0ff8e Mon Sep 17 00:00:00 2001 +From: Jarrett Johnson <jarrett.johnson@schrodinger.com> +Date: Thu, 5 Sep 2024 11:20:02 -0400 +Subject: [PATCH] Symbol renaming in molfile_plugin and internal linkage + +Fixes #395 +--- + contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h | 10 +++++----- + .../uiuc/plugins/molfile_plugin/src/parm7plugin.cpp | 8 +++++--- + contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp | 2 ++ + layer0/Isosurf.cpp | 6 ++++-- + layer0/Tetsurf.cpp | 6 ++++-- + ov/src/OVOneToAny.cpp | 2 ++ + ov/src/OVOneToOne.cpp | 2 ++ + 7 files changed, 24 insertions(+), 12 deletions(-) + +diff --git a/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h b/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h +index 21d967d79..6bd6ddb08 100644 +--- a/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h ++++ b/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h +@@ -59,7 +59,7 @@ + #endif + + +-typedef struct parm { ++typedef struct parm7 { + char title[85]; + char version[85]; + int IfBox, Nmxrs, IfCap, +@@ -70,7 +70,7 @@ typedef struct parm { + Ipatm, Natcap,Ifpert,Nbper,Ngper,Ndper,Mbper,Mgper,Mdper, + Numextra; + _REAL Box[3], Cutcap, Xcap, Ycap, Zcap; +-} parmstruct; ++} parm7struct; + + static int read_parm7_flag(FILE *file, const char *flag, const char *format) { + char buf[1024]; +@@ -359,10 +359,10 @@ static void close_parm7_file(FILE *fileptr, int popn) { + + static const char *parm7 = "%8d%8d%8d%8d%8d%8d%8d%8d%8d%8d\n"; + +-static parmstruct *read_parm7_header(FILE *file) { ++static parm7struct *read_parm7_header(FILE *file) { + char sdum[512]; +- parmstruct *prm; +- prm = new parmstruct; ++ parm7struct *prm; ++ prm = new parm7struct; + + /* READ VERSION */ + fgets(sdum, 512, file); +diff --git a/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp +index faf2717c6..2d46553b4 100644 +--- a/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp ++++ b/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp +@@ -24,13 +24,15 @@ + #include "molfile_plugin.h" + #include "ReadPARM7.h" + ++namespace { + typedef struct { +- parmstruct *prm; ++ parm7struct *prm; + int popn; + FILE *fd; + int nbonds; + int *from, *to; + } parmdata; ++} + + static void *open_parm7_read(const char *filename, const char *,int *natoms) { + FILE *fd; +@@ -39,7 +41,7 @@ static void *open_parm7_read(const char *filename, const char *,int *natoms) { + fprintf(stderr, "parm7plugin) Cannot open parm file '%s'\n", filename); + return NULL; + } +- parmstruct *prm = read_parm7_header(fd); ++ parm7struct *prm = read_parm7_header(fd); + if (!prm) { + close_parm7_file(fd, popn); + return NULL; +@@ -58,7 +60,7 @@ static void *open_parm7_read(const char *filename, const char *,int *natoms) { + + static int read_parm7_structure(void *mydata, int *optflags, molfile_atom_t *atoms) { + parmdata *p = (parmdata *)mydata; +- const parmstruct *prm = p->prm; ++ const parm7struct *prm = p->prm; + FILE *file = p->fd; + char buf[85]; + char field[85]; +diff --git a/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp +index acabcb1b5..4996383e1 100644 +--- a/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp ++++ b/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp +@@ -24,12 +24,14 @@ + #include "ReadPARM.h" + #include "molfile_plugin.h" + ++namespace { + typedef struct { + ReadPARM *rp; + FILE *parm; + int natoms; + int *from, *to; + } parmdata; ++} + + static void *open_parm_read(const char *filename, const char *, + int *natoms) { +diff --git a/layer0/Isosurf.cpp b/layer0/Isosurf.cpp +index 77cf42eeb..b2dfaedd7 100644 +--- a/layer0/Isosurf.cpp ++++ b/layer0/Isosurf.cpp +@@ -44,11 +44,13 @@ Z* ------------------------------------------------------------------- + + #define I4(field,P1,P2,P3,P4) ((field)->get<int>(P1,P2,P3,P4)) + +-typedef struct PointType { ++namespace { ++struct PointType { + float Point[3]; + int NLink; + struct PointType* Link[4]; +-} PointType; ++}; ++} + + #define EdgePtPtr(field,P2,P3,P4,P5) ((field)->ptr(P2,P3,P4,P5)) + +diff --git a/layer0/Tetsurf.cpp b/layer0/Tetsurf.cpp +index 0d78b535e..cb2f5b37b 100644 +--- a/layer0/Tetsurf.cpp ++++ b/layer0/Tetsurf.cpp +@@ -38,12 +38,14 @@ Z* ------------------------------------------------------------------- + + #define I3(field,P1,P2,P3) ((field)->get<int>(P1,P2,P3)) + +-typedef struct { ++namespace { ++struct PointType { + float Point[3]; + float Normal[3]; + int NormalFlag; + int Link; +-} PointType; ++}; ++} + + typedef struct { + PointType *p[3]; +diff --git a/ov/src/OVOneToAny.cpp b/ov/src/OVOneToAny.cpp +index 1a675a51b..5dbbc498c 100644 +--- a/ov/src/OVOneToAny.cpp ++++ b/ov/src/OVOneToAny.cpp +@@ -8,11 +8,13 @@ + + /* FYI: "up" stands for UniquePair -- a precursor to OneToAny */ + ++namespace { + typedef struct { + int active; + ov_word forward_value, reverse_value; + ov_size forward_next; + } up_element; ++} + + struct _OVOneToAny { + OVHeap *heap; +diff --git a/ov/src/OVOneToOne.cpp b/ov/src/OVOneToOne.cpp +index 6dfa8f457..4e9baf9c6 100644 +--- a/ov/src/OVOneToOne.cpp ++++ b/ov/src/OVOneToOne.cpp +@@ -8,11 +8,13 @@ + + /* FYI: "up" stands for UniquePair -- a precursor to OneToOne */ + ++namespace { + typedef struct { + int active; + ov_word forward_value, reverse_value; + ov_size forward_next, reverse_next; + } up_element; ++} + + struct _OVOneToOne { + OVHeap *heap; diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-numpy2.patch b/sci-chemistry/pymol/files/pymol-3.0.0-numpy2.patch new file mode 100644 index 000000000000..7cf2884ee201 --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-3.0.0-numpy2.patch @@ -0,0 +1,35 @@ +From 758cec338057b23007ffd14c960634ff0ee24af1 Mon Sep 17 00:00:00 2001 +From: Jarrett Johnson <jarrett.johnson@schrodinger.com> +Date: Tue, 27 Aug 2024 20:06:57 -0400 +Subject: [PATCH] Make numpy2 compatible + +--- + layer2/ObjectMap.cpp | 1 + + modules/chempy/brick.py | 2 +- + 2 files changed, 2 insertions(+), 1 deletion(-) + +diff --git a/layer2/ObjectMap.cpp b/layer2/ObjectMap.cpp +index ada826f8a..62e3457a4 100644 +--- a/layer2/ObjectMap.cpp ++++ b/layer2/ObjectMap.cpp +@@ -5596,6 +5596,7 @@ static int ObjectMapNumPyArrayToMapState(PyMOLGlobals * G, ObjectMapState * ms, + void * ptr; + + #ifdef _PYMOL_NUMPY ++ import_array1(0); + PyArrayObject * pao = (PyArrayObject *) ary; + const int itemsize = PyArray_ITEMSIZE(pao); + #endif +diff --git a/modules/chempy/brick.py b/modules/chempy/brick.py +index fc514eb3a..e4c0f1bbb 100644 +--- a/modules/chempy/brick.py ++++ b/modules/chempy/brick.py +@@ -31,7 +31,7 @@ def from_numpy(cls, data, grid, origin=(0.0, 0.0, 0.0)): + @param range: 3f sequence + @param origin: 3f sequence + ''' +- data = numpy.asfarray(data) ++ data = numpy.asarray(data, dtype=numpy.float64) + assert len(data.shape) == 3 + + self = cls() diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-py3.12-progress.patch b/sci-chemistry/pymol/files/pymol-3.0.0-py3.12-progress.patch new file mode 100644 index 000000000000..b09f36048b20 --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-3.0.0-py3.12-progress.patch @@ -0,0 +1,26 @@ +From 11325a6014565700be9673236c9b7b6c856ea6d9 Mon Sep 17 00:00:00 2001 +From: Jarrett Johnson <jarrett.johnson@schrodinger.com> +Date: Wed, 28 Aug 2024 22:07:15 -0400 +Subject: [PATCH] Python 3.12 TypeError: convert progress to int for progress + bar + +--- + modules/pmg_qt/pymol_qt_gui.py | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/modules/pmg_qt/pymol_qt_gui.py b/modules/pmg_qt/pymol_qt_gui.py +index f2d663204..6e935b0d6 100644 +--- a/modules/pmg_qt/pymol_qt_gui.py ++++ b/modules/pmg_qt/pymol_qt_gui.py +@@ -929,9 +929,9 @@ def command_set_cursor(self, i): + return self.lineedit.setCursorPosition(i) + + def update_progress(self): +- progress = self.cmd.get_progress() ++ progress = int(self.cmd.get_progress() * 100) + if progress >= 0: +- self.progressbar.setValue(progress * 100) ++ self.progressbar.setValue(progress) + self.progressbar.show() + self.abortbutton.show() + else: diff --git a/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild b/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild new file mode 100644 index 000000000000..aeb6bc85c7e1 --- /dev/null +++ b/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild @@ -0,0 +1,123 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..12} ) +DISTUTILS_USE_PEP517="setuptools" +DISTUTILS_EXT=1 + +inherit desktop flag-o-matic xdg distutils-r1 + +DESCRIPTION="A Python-extensible molecular graphics system" +HOMEPAGE="https://www.pymol.org/" +SRC_URI="https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +S="${WORKDIR}"/${PN}-open-source-${PV} + +LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" #844991 +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="+netcdf web" + +DEPEND=" + dev-cpp/msgpack-cxx + dev-libs/mmtf-cpp + dev-python/numpy[${PYTHON_USEDEP}] + sys-libs/zlib + media-libs/freetype:2 + media-libs/glew:0= + media-libs/glm + media-libs/libpng:0= + netcdf? ( sci-libs/netcdf:0= ) +" +BDEPEND="test? ( >=dev-cpp/catch-2:0 )" +RDEPEND=" + ${DEPEND} + media-video/mpeg-tools + dev-python/pyopengl[${PYTHON_USEDEP}] + dev-python/PyQt5[opengl,${PYTHON_USEDEP}] + dev-python/pmw[${PYTHON_USEDEP}] + sci-chemistry/chemical-mime-data +" + +distutils_enable_tests pytest + +# FIXME: We need to still figure out about how to make all the tests pass +# https://bugs.gentoo.org/932127 +RESTRICT="test" + +PATCHES=( + "${FILESDIR}/${P}-distutils-py3.12.patch" + "${FILESDIR}/${P}-SceneGetDrawFlag-indexing.patch" + "${FILESDIR}/${P}-eof-maeffplugin.patch" + "${FILESDIR}/${P}-numpy2.patch" + "${FILESDIR}/${P}-py3.12-progress.patch" + "${FILESDIR}/${P}-lto-molfile-plugin.patch" +) + +python_prepare_all() { + sed \ + -e "s:\"/usr:\"${EPREFIX}/usr:g" \ + -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ + -i setup.py || die + + sed \ + -e "s:/opt/local:${EPREFIX}/usr:g" \ + -e '/ext_comp_args/s:\[.*\]:[]:g' \ + -i setup.py || die + sed \ + -e "s:\['msgpackc'\]:\['msgpack'\]:g" \ + -i setup.py || die + + append-cxxflags -std=c++17 + + distutils-r1_python_prepare_all +} + +python_configure_all() { + use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins ) +} + +python_install() { + distutils-r1_python_install \ + --pymol-path="${EPREFIX}/usr/share/pymol" + + sed \ + -e '1i#!/usr/bin/env python' \ + "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die + python_doscript "${T}"/${PN} +} + +python_test() { + "${EPYTHON}" -m pymol -ckqy testing/testing.py --offline --no-mmlibs --no-undo --run all || die +} + +python_install_all() { + distutils-r1_python_install_all + + # Move data to correct location + dodir /usr/share/pymol + mv "${D}/$(python_get_sitedir)"/pymol/pymol_path/* "${ED}/usr/share/pymol" || die + + # These environment variables should not go in the wrapper script, or else + # it will be impossible to use the PyMOL libraries from Python. + cat >> "${T}"/20pymol <<- EOF || die + PYMOL_PATH="${EPREFIX}/usr/share/pymol" + PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" + PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" + EOF + + doenvd "${T}"/20pymol + + newicon "${S}"/data/pymol/icons/icon2.svg ${PN}.svg + make_desktop_entry "${PN} %u" PyMol ${PN} \ + "Graphics;Education;Science;Chemistry;" \ + "MimeType=chemical/x-pdb;chemical/pdby;chemical/x-mdl-sdfile;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;chemical/x-macromodel-input;chemical/x-vmd;" + + if ! use web; then + rm -rf "${D}/$(python_get_sitedir)/web" || die + fi + + rm -f "${ED}"/usr/share/${PN}/LICENSE || die +} |