From 9c417bacd51da6d8b57fa9f37425161d30d4b95b Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 28 Nov 2020 20:40:51 +0000 Subject: gentoo resync : 28.11.2020 --- sci-chemistry/Manifest.gz | Bin 11222 -> 11216 bytes sci-chemistry/elem/Manifest | 3 +- sci-chemistry/elem/elem-1.0.3-r2.ebuild | 2 +- .../elem/files/elem-1.0.3-fno-common.patch | 24 +++++ sci-chemistry/pymol/Manifest | 4 +- sci-chemistry/pymol/pymol-2.3.0-r3.ebuild | 113 -------------------- sci-chemistry/pymol/pymol-2.4.0.ebuild | 115 +++++++++++++++++++++ 7 files changed, 144 insertions(+), 117 deletions(-) create mode 100644 sci-chemistry/elem/files/elem-1.0.3-fno-common.patch delete mode 100644 sci-chemistry/pymol/pymol-2.3.0-r3.ebuild create mode 100644 sci-chemistry/pymol/pymol-2.4.0.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz index 164880108d31..6e681ccbfc03 100644 Binary files a/sci-chemistry/Manifest.gz and b/sci-chemistry/Manifest.gz differ diff --git a/sci-chemistry/elem/Manifest b/sci-chemistry/elem/Manifest index eb14680d00f4..82c69422b596 100644 --- a/sci-chemistry/elem/Manifest +++ b/sci-chemistry/elem/Manifest @@ -1,5 +1,6 @@ AUX elem-1.0.3-fix-build-system.patch 2544 BLAKE2B 174bfc3e2036a17d918534d02b51def6d933e8799c15cc3e6b75a8580155be614b5691b3241e1fcf88ea7e8124c3e65d73101d862c21f7603a9a8b794d640e6a SHA512 2d691f1d0fdc0a786a45706b68243fab17706328e0417cf805f657576c462315551719a7168ad8e58e651c695a0d53da3f776f479dc540b6b01af899e1b97208 +AUX elem-1.0.3-fno-common.patch 496 BLAKE2B 90d5f78f7e1efcc9f195e432ab1f942f30002be476f0bf4a2a6ea92cc9f3c651c856aa5e1cceee66239e47cd84038417e640542c5299c55d968c7b3b62224efc SHA512 9c6a61667c23987fd047a649a178fbae75abf78fa6c974d1f6c1552790db50f5b4152d66af88afeaf242b77eb0d2ccb8862d2d69227fbf48f7c3dac183081e98 AUX elem-1.0.3-missing-stdlib.patch 133 BLAKE2B 2ab00632e93401db578910b4e44e8f0ad4e899fb3afce5b9d1b6612ba181fd0fc3922c8cc229404164bdef562850337f006cce4047e52b2e459954419bc05529 SHA512 769c5e19928ed64b5595cd37f16d4df893889c3c0ea7e6673e182646bcaca89a6e46e7c6611c586c9213a417c439de043c0beb84a9543e478f78e4d9843a1c3e DIST elem-src-1.0.3-Linux.tgz 58364 BLAKE2B bdedb844ca62f928fdae5b01b13b88e5f43f5e37f40b47f7b8b9b1a2cb11053b9aefa7b1b4bb78a8632f3329f37afeadfc34eddee1b9f7cd109bee89aa9cdf32 SHA512 24b163c5cc3019c1beb677ce7b432b21289352f7cdbad686ab9161c628d3aadbb90d8abf9bef49f1c7d077b706bbd4ea6b381f356cc85adf907f3c15a4f4893c -EBUILD elem-1.0.3-r2.ebuild 660 BLAKE2B add5eb74f17cd4a45283ef9f7012509d7b4e9ad3052249dd7035f6c7089b30baf55d558fa3e07066ddbb9cfba16fb262888ddfeca3e48ad94ae8a09c25b474ff SHA512 4694f0365e306d5ad9353f7b5436cb28ca2065c87734cb2ef5055af8fa153a4db2c085a7132f33fac8cf0addb877669fa2ad47b23f0c84ac42bb0e0d9e506484 +EBUILD elem-1.0.3-r2.ebuild 689 BLAKE2B 464dcb25ef4869d8def5c3b1444e586d56f30f9e9d84c8f8828a59f38a4f83e69983503be514724210d72c19ea88ba33d4f16f1517dccd724ee4e4e431da7f2b SHA512 0cc0d5b86907beb5de0317a58424d0ec2e230f59335bd80bf9b4329cef2fa742c44aec0e2524aeaacfc89d29643dd2be42e3250e8ad7bfefccb432dfef1d3386 MISC metadata.xml 339 BLAKE2B 73c4ef3e56cdf6f1061537c5c3a3932b7c38af40ec483cb4f12c21722a65dbeb0ce2dc162911a96a8f4147150a232eb398e2a4fecf7bde60ba2738994dc7a534 SHA512 daecddff7728e2a0b00d5e16bb4fc1c88bd316783f8921705dc76b41f427a8918ead92e663fa202ff57508242daa454cae2c04057c8bf9cf767b95d59e43c177 diff --git a/sci-chemistry/elem/elem-1.0.3-r2.ebuild b/sci-chemistry/elem/elem-1.0.3-r2.ebuild index 67290b4c6d85..d74c51bd8f06 100644 --- a/sci-chemistry/elem/elem-1.0.3-r2.ebuild +++ b/sci-chemistry/elem/elem-1.0.3-r2.ebuild @@ -12,7 +12,6 @@ SRC_URI="mirror://sourceforge/elem/${PN}-src-${PV}-Linux.tgz" LICENSE="GPL-2" KEYWORDS="amd64 sparc x86" SLOT="0" -IUSE="" DEPEND="x11-libs/xforms" RDEPEND="${DEPEND}" @@ -20,6 +19,7 @@ RDEPEND="${DEPEND}" PATCHES=( "${FILESDIR}"/${P}-fix-build-system.patch "${FILESDIR}"/${P}-missing-stdlib.patch + "${FILESDIR}"/${P}-fno-common.patch ) src_configure() { diff --git a/sci-chemistry/elem/files/elem-1.0.3-fno-common.patch b/sci-chemistry/elem/files/elem-1.0.3-fno-common.patch new file mode 100644 index 000000000000..402ae0790587 --- /dev/null +++ b/sci-chemistry/elem/files/elem-1.0.3-fno-common.patch @@ -0,0 +1,24 @@ +--- a/elem.c ++++ b/elem.c +@@ -11,6 +11,9 @@ + #include "deutsch.h" + #endif + ++double amsumme; ++FL_OBJECT *massensumme; ++ + + + FD_Periodensystem *create_form_Periodensystem(void) +--- a/elem.h ++++ b/elem.h +@@ -154,7 +154,7 @@ typedef struct { + void *vdata; + long ldata; + } FD_Periodensystem; +-double amsumme; ++extern double amsumme; + extern FD_Periodensystem * create_form_Periodensystem(void); +- FL_OBJECT *massensumme; ++extern FL_OBJECT *massensumme; + #endif /* FD_Periodensystem_h_ */ diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index 54467b7a712d..0c799502cd11 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1,4 +1,4 @@ DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c -DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05 SHA512 e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133 -EBUILD pymol-2.3.0-r3.ebuild 3018 BLAKE2B 86e626d7a8c0f1dbfd92d73f07895c61cbabcaf2a468a0f58635139fe0fd772f9a5418b5b16267831341f3c36e109be46d018518dca56ba10b6b224da4dd64b2 SHA512 f6f8feca5c943800b8df207b4c71ca1dbc92fc4e4a1df5a8a29205c349d915fe367d145bb29ec4044c1824b4a2a820377f8da37f4c430e2e2805f24508b6e8ed +DIST pymol-2.4.0.tar.gz 10552539 BLAKE2B 34e31dce99c1e838b00389c3d7c29657534dd037349769bd6c8cb17028cfaaa856d5729760d3768fd43f61086cac30749a864fb4156c14eda07f9027430f0523 SHA512 2b19294197d58a808bf7bb7fa9f829c2ec582ba47a4380783a2b1eedda2ce4118cd398e01885db8c449e7fd5e4c08a1c40508e679ef42d8e183a6a52b031c02a +EBUILD pymol-2.4.0.ebuild 3080 BLAKE2B cf0b1e7d50edf615fdf82e1a5f7920f6095e402feed21b860dc1e21a11e833bee430f7b0b11fe85c0f74e2aaf3852f09ab5f7e35beb6af7d775c7307523f0aad SHA512 bb0113cdcbe8a10bc59a0aee51d305a72bdbe5a0d5b17baa586d8a98b66e8ce7db8086e9c8671d77131a0d3d5541cdc8a3210ad0d2feef30d337f0cb3afd0411 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4 diff --git a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild deleted file mode 100644 index 0a2e041f0dad..000000000000 --- a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild +++ /dev/null @@ -1,113 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{6,7,8,9} ) - -inherit distutils-r1 desktop optfeature flag-o-matic xdg-utils - -DESCRIPTION="A Python-extensible molecular graphics system" -HOMEPAGE="https://www.pymol.org/" -SRC_URI=" - https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz - https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz - " -RESTRICT="mirror" -LICENSE="PSF-2.2" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="web" - -DEPEND=" - dev-libs/msgpack[cxx] - dev-libs/mmtf-cpp - dev-python/pyopengl[${PYTHON_USEDEP}] - dev-python/PyQt5[opengl,${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - media-libs/freetype:2 - media-libs/glew:0= - media-libs/glm - media-libs/libpng:0= - media-video/mpeg-tools - sys-libs/zlib -" -RDEPEND="${DEPEND} - sci-chemistry/chemical-mime-data -" - -S="${WORKDIR}"/${PN}-open-source-${PV} - -python_prepare_all() { - sed \ - -e "s:\"/usr:\"${EPREFIX}/usr:g" \ - -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ - -e "/import/s:argparse:argparseX: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++0x - - distutils-r1_python_prepare_all -} - -python_install() { - distutils-r1_python_install \ - --pymol-path="${EPREFIX}/usr/share/pymol" - - sed \ - -e '1d' \ - -e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \ - -e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \ - -e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \ - -i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die -} - -python_install_all() { - distutils-r1_python_install_all - - sed \ - -e '1i#!/usr/bin/env python' \ - "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die - - python_foreach_impl python_doscript "${T}"/${PN} - - # These environment variables should not go in the wrapper script, or else - # it will be impossible to use the PyMOL libraries from Python. - cat >> "${T}"/20pymol <<- EOF || die - PYMOL_PATH="${EPREFIX}/usr/share/pymol" - PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" - PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" - EOF - - doenvd "${T}"/20pymol - - newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png - make_desktop_entry ${PN} PyMol ${PN} \ - "Graphics;Education;Science;Chemistry;" \ - "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" - - if ! use web; then - rm -rf "${D}/$(python_get_sitedir)/web" || die - fi - - rm -f "${ED}"/usr/share/${PN}/LICENSE || die -} - -pkg_postinst() { - xdg_desktop_database_update - xdg_mimeinfo_database_update - optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr -} - -pkg_postrm() { - xdg_desktop_database_update - xdg_mimeinfo_database_update -} diff --git a/sci-chemistry/pymol/pymol-2.4.0.ebuild b/sci-chemistry/pymol/pymol-2.4.0.ebuild new file mode 100644 index 000000000000..6ff6e2326d92 --- /dev/null +++ b/sci-chemistry/pymol/pymol-2.4.0.ebuild @@ -0,0 +1,115 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{6,7,8,9} ) +DISTUTILS_USE_SETUPTOOLS=no + +inherit distutils-r1 desktop optfeature flag-o-matic xdg-utils + +DESCRIPTION="A Python-extensible molecular graphics system" +HOMEPAGE="https://www.pymol.org/" +SRC_URI=" + https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz + https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz + " +RESTRICT="mirror" +LICENSE="PSF-2.2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="web" + +DEPEND=" + dev-libs/msgpack[cxx] + dev-libs/mmtf-cpp + dev-python/pyopengl[${PYTHON_USEDEP}] + dev-python/PyQt5[opengl,${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pmw[${PYTHON_USEDEP}] + media-libs/freetype:2 + media-libs/glew:0= + media-libs/glm + media-libs/libpng:0= + media-video/mpeg-tools + sys-libs/zlib +" +RDEPEND="${DEPEND} + sci-chemistry/chemical-mime-data +" + +S="${WORKDIR}"/${PN}-open-source-${PV} + +python_prepare_all() { + sed \ + -e "s:\"/usr:\"${EPREFIX}/usr:g" \ + -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ + -e "/import/s:argparse:argparseX: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++0x + + distutils-r1_python_prepare_all +} + +python_install() { + distutils-r1_python_install \ + --pymol-path="${EPREFIX}/usr/share/pymol" + + sed \ + -e '1d' \ + -e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \ + -e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \ + -e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \ + -i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die +} + +python_install_all() { + distutils-r1_python_install_all + + sed \ + -e '1i#!/usr/bin/env python' \ + "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die + + python_foreach_impl python_doscript "${T}"/${PN} + + # These environment variables should not go in the wrapper script, or else + # it will be impossible to use the PyMOL libraries from Python. + cat >> "${T}"/20pymol <<- EOF || die + PYMOL_PATH="${EPREFIX}/usr/share/pymol" + PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" + PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" + EOF + + doenvd "${T}"/20pymol + + newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png + make_desktop_entry ${PN} PyMol ${PN} \ + "Graphics;Education;Science;Chemistry;" \ + "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" + + if ! use web; then + rm -rf "${D}/$(python_get_sitedir)/web" || die + fi + + rm -f "${ED}"/usr/share/${PN}/LICENSE || die +} + +pkg_postinst() { + xdg_desktop_database_update + xdg_mimeinfo_database_update + optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr +} + +pkg_postrm() { + xdg_desktop_database_update + xdg_mimeinfo_database_update +} -- cgit v1.2.3