diff options
Diffstat (limited to 'sci-chemistry')
90 files changed, 615 insertions, 2916 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex 893a1088c3e2..6b2ad67562c0 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest index 1b33c2abb01e..a89d41a10537 100644 --- a/sci-chemistry/apbs/Manifest +++ b/sci-chemistry/apbs/Manifest @@ -2,5 +2,5 @@ AUX apbs-1.4.1-manip.patch 1462 BLAKE2B f4559008a1fc4dc367bc770ed29b7fa9ae9489ab AUX apbs-1.4.1-multilib.patch 3301 BLAKE2B 4268a21ec878d780c7a1efe433bf2c82ef2e72f49a6071b6df695bf672ee999be9c29fed06e949b80cc230333d8deca1094c946662ec657d31e3b6f86e873969 SHA512 cdd72fd23a57ee8413f72bf674ae246543b1c9f326727ff07c3b8848d59f98ab7d2daf28677460cb4726f919832079c1d280bcdc86a8bef5c0875583c789b7c0 AUX apbs-1.4.1-python.patch 3979 BLAKE2B b21633655df329f5d445c4e53140367b0a8a6cfbfafccba8943206ed9bae46839bae532e3efd19d75e89bc70a1fa59d05f3ed977b1a59f949649d3e89b887a96 SHA512 a38ca3bbf692f42268d192aff61949ece95d9b043ac10b4eec33e383773beec1c60425a12e84843a602e828528f6cf0ed6b8c90e99aeea679c5abc8c093c68ae DIST apbs-1.4.1.zip 37999283 BLAKE2B 2301deb7ab4eb2f20098cf63df180bb53189e42a89cd5559357cdcf08e84d27a44eafe8557bb460574802d24d29741ad4606dc3bd7f32911d0d0f2c7453d6470 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a -EBUILD apbs-1.4.1-r2.ebuild 3038 BLAKE2B 52199b0b53f146f7ed915b0cf65e48de40b39e5df10fde56ab89fb43324e3d98e66ba9d09a85d4cc209427d0cd0fc24f7472bc55393703b4c8aa2a13c3d23cdd SHA512 d5b3e8008db4f59618dc08d7e5289929a4852856aea51e2b08e6151d8530f6dab882a0b7229b079afd4ef336023b0f0a0ff19accce91f980fe2a6aea71a6399c +EBUILD apbs-1.4.1-r2.ebuild 3032 BLAKE2B 7e8c4f17445e54a201d1d9279f80feee228f20d4d33a4596dfeee15f0ce066904c34c978db13a453e7e5589c356b26cfab2aa0bc80f38fa56dda8a8f7f025295 SHA512 ab8592cdf95689aecbadfee6f3ebd0b121f04e9e95dd5307f2d353c6e80609328a633417fe47d4a2f9e2572a965268354d99cf0aba5641aa6d42443d1d27f765 MISC metadata.xml 1048 BLAKE2B 53a61bd7e05e53b294f0cbd1a21b86f391429ad5f23a545e7cbb27625b152589247a08db06c5d7f6658425de032be970fae0230ad1ac14ac4f6de42663d6c97c SHA512 7d68049cb9b044676430fe879890cc4cd869b99f85696f579d9cbf3b156081301792fd7f03205a9b9d429d71c9a35b4815f4236573f68d3ef6b4718e6e1f0bb3 diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild index b3c4f192894b..88910ddde996 100644 --- a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild +++ b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild @@ -106,7 +106,7 @@ src_compile(){ } src_test() { - python_export_best + python_setup cd tests || die LD_LIBRARY_PATH="${S}"/lib "${PYTHON}" apbs_tester.py -l log || die grep -q 'FAILED' log && die "Tests failed" diff --git a/sci-chemistry/aria/Manifest b/sci-chemistry/aria/Manifest deleted file mode 100644 index 2b830596d521..000000000000 --- a/sci-chemistry/aria/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST aria2.3.2_08.26.2013.tar.gz 1878602 BLAKE2B 3044192853c0ed0653d20fea959d3b01321f559845c555289658f93b65e9148f8cd0f59619e8690887b2811d613e6cc2f67b67af7d84ade4b8fc18403367086c SHA512 a6d8c45218f5d494174587a5f8f1feec940ac8cc4cd7b707dac65b2378219ecf27967e70807e6cb7ae22a7d4aec7239af763f077ad7183c078b1991cac71bc3e -EBUILD aria-2.3.2_p20130826.ebuild 1930 BLAKE2B 129dfba9d6e9209e2d88a6c1357dd247d5089e18b9393f75fb23b2c1dcd98ea80768f20ba9f09e9b6b97213ab5140075c7d484aeb9cb4fa5ef116d248ad29644 SHA512 7a752e8c87b300b55ce0b50c0a3c45df26fc34f3205b55231f685ab76548077b7f70392c260cf23f5d09b91d2f7f172432771315227a4cecb069199596e33cea -MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild b/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild deleted file mode 100644 index c06c8d979bb6..000000000000 --- a/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild +++ /dev/null @@ -1,88 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="tk" - -inherit eutils python-single-r1 versionator - -MY_P="${PN}$(get_version_component_range 1-2 ${PV})" -DATE="08.26.2013" - -DESCRIPTION="Automated NOE assignment and NMR structure calculation" -HOMEPAGE="http://aria.pasteur.fr/" -SRC_URI="http://aria.pasteur.fr/archives/${MY_P}.2_${DATE}.tar.gz" - -SLOT="0" -LICENSE="cns" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="examples" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-tcltk/tix - dev-lang/tk:0= - >=dev-python/numpy-1.1[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP},tk] - >=sci-chemistry/cns-1.2.1-r7[aria,openmp] - >=sci-chemistry/ccpn-2.2[${PYTHON_USEDEP}] - sci-chemistry/clashlist - sci-chemistry/procheck - sci-libs/clashscore-db" -DEPEND="${RDEPEND}" - -RESTRICT="fetch" - -S="${WORKDIR}/${MY_P}" - -pkg_nofetch(){ - einfo "Go to http://aria.pasteur.fr/archives/aria2.3.2.tar.gz/view, download ${A}" - einfo "and place it into your DISTDIR directory." -} - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_test(){ - export CCPNMR_TOP_DIR=$(python_get_sitedir) - export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python - ${PYTHON} check.py || die -} - -src_install(){ - python_moduleinto ${PN} - python_domodule src aria2.py - python_moduleinto ${PN}/cns - python_domodule cns/{protocols,toppar,src/helplib} - - if use examples; then - insinto /usr/share/${P}/ - doins -r examples - fi - - # ENV - cat >> "${T}"/20aria <<- EOF - ARIA2="$(python_get_sitedir)/${PN}" - EOF - - doenvd "${T}"/20aria - - # Launch Wrapper - cat >> "${T}"/aria <<- EOF - #!/bin/sh - export CCPNMR_TOP_DIR="$(python_get_sitedir)" - export PYTHONPATH="$(python_get_sitedir)/ccpn/python" - exec "${PYTHON}" -O "\${ARIA2}"/aria2.py \$@ - EOF - - dobin "${T}"/aria - dosym aria /usr/bin/aria2 - - dodoc README - python_optimize "${D}/$(python_get_sitedir)" -} diff --git a/sci-chemistry/aria/metadata.xml b/sci-chemistry/aria/metadata.xml deleted file mode 100644 index 8937bad0b175..000000000000 --- a/sci-chemistry/aria/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/autodock/Manifest b/sci-chemistry/autodock/Manifest index 05fd5ff8103b..065022beda3e 100644 --- a/sci-chemistry/autodock/Manifest +++ b/sci-chemistry/autodock/Manifest @@ -1,4 +1,4 @@ AUX autodock-4.2.6-buildsystem.patch 1500 BLAKE2B d295cdc7e46ecad118b7747aa26c97c5d08d54f28fecbb09e1c356fcf1e977164acb57dfa3ecc57fef28e4a37b6d16f9741c1fdb6c8f1c3b3a3b3d9085fd75f6 SHA512 08a7643e2973f2ebdd01c54acb1e3e0802ea3d7a33cbed4c03f58d29c7e13a246418feb4a61088dae18c3ab78db6fd5b3c11f9974dec59fe46dbf7cfbbe98c3a DIST autodocksuite-4.2.6-src.tar.gz 35438010 BLAKE2B 88e036ecc0492fb83f31b90fd0983ec57d889a61d17249f672a3e30e942f6c329dc2494088a8fc7c5bc39a5bdbb38fb1514f1750c7145374f202a928d477faa9 SHA512 75b8878f948c4f6bc28adb442997192dad0c36bbede2fd698623903cb27b06b4df3ba038bfc70fc13b4bdee864fd2344f0f7208be2020da4e01a00b842b46bbb -EBUILD autodock-4.2.6.ebuild 2178 BLAKE2B ba9efd6481e64f6a91836f72ba95fe532fb0adbf9a6bf37eecde2b83cc1d3738b076c1d41c28633b28499eca4a30c6994e6e417caba6d391bbc8561ab355456a SHA512 f8b186454cec3e7deb6078cfa659d15eeebdc7e4bcb36d03327603ecda063b8a383a032001b8db9ad849dddb2c5992ec57c4f0bb6d8031a89cdad44fb3d82acb +EBUILD autodock-4.2.6.ebuild 2202 BLAKE2B f425ab34d6941523d6c8b1c8740b4b8a2aa89b49c965466af77c8dda0cc4ef3d24a9c5a40ad82156497f24f6d3afb341e697838446d96195fd6a990b909160b4 SHA512 516d12bbf27984ecd844bae777c408790f7288b08d025fc618920458181dc57abbe3442b69270c1209afa6ebb45b11e774f60e1721452d790119270157336252 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/autodock/autodock-4.2.6.ebuild b/sci-chemistry/autodock/autodock-4.2.6.ebuild index 862cda1437b9..6cfe76fbbfd0 100644 --- a/sci-chemistry/autodock/autodock-4.2.6.ebuild +++ b/sci-chemistry/autodock/autodock-4.2.6.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -18,6 +18,7 @@ LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="examples openmp test" +RESTRICT="!test? ( test )" RDEPEND="" DEPEND="test? ( ${PYTHON_DEPS} )" diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest deleted file mode 100644 index 92f35baaafb1..000000000000 --- a/sci-chemistry/ccpn/Manifest +++ /dev/null @@ -1,22 +0,0 @@ -AUX 2.3.1-parallel.patch 850 BLAKE2B 7a6368cde3e6352db8d61da151b5c4246e446453ad5ba4b164d2544c4aa044b224eec38dcdb5958360987ff03a01f99b293e257b210b0226406f9de05067b07f SHA512 0597e21c03baa27e2342249814fc0700b73cf2800173468574ef704d48f7e6e042ac6ae552bbb9e27fd4baca36cfaf60a1eac9813354916b3e8295a35b64dcdf -AUX analysis 283 BLAKE2B c487800b5a09f3cc6d0e86ffadf22fae6d33c9dea95e0485ac51b0e49313bc4318fae1fd12c892ea1103c5089d65f967cdac43b0712c15d6eab90ecc3c2a07d1 SHA512 f2dd8216021201b0f9307f8bb82033c3ebb1c9f21450ae206e59ad6442b0cf0f8fc6e4817d4347eb78a9528ba1ef60bd5395708067352d11330215e5ce2568ff -AUX dangle 279 BLAKE2B da9f1f48ea829315405b1fca6631ad0ae9aec70ad22b13ab2a344888a7a9e81d07feeb6a7dfc60e9b867b02c7a87c161d9c34cd9ad55e90f973e5aa9ea905529 SHA512 21fca09578aa13819a20f08ff414ca2b8d08d177a1ab09f8d85c53ae20fc6f38ab46e2933d72c239029b37ec5eebc3162f0c8e99f1ca1dd20aaa49277fac4e7d -AUX dataShifter 282 BLAKE2B 6a16d423b13d96ee939289daa1d456f8861721d29893065d2abb2915559af08d7cfde890a152388ee1f184a2e3fde2ad9159d7d6b5256aba4b29589079d7101a SHA512 f1c4a87d0d4d1a613ce8c9eacd9e3ba5047f1205404140c0c68a354bb790397b7ec49426660a48601a305906b60a8957d218dbc5ad1d6d48beb7030772a199b7 -AUX depositionFileImporter 286 BLAKE2B 9c2cfb9424defd3043d6164b33a435675fa90307cf67f6eea0c5dfa88db702a6f0736cccb26314dca5ba672820a20a044ac00514bbbdf3f58c86611cf1f87ff2 SHA512 f7d7caa4b2b2d91eb5dc27ec0ccd6251dab94f6d8e318190b2f2b1b997f825d6cee1e3a38ee77f9358102dcdaf7d93c4d18c7250855446580abd459db31eec6d -AUX eci 267 BLAKE2B 79cced29dcc1b50a1482641a64df5340ed0cce5791f7de245def0c8aeb57d12380bb082efa147de80dc14a7751e458df89a077d64a2f9ef24e8913540fb4c4ab SHA512 800b2624fe21c706a1bc30bc8fd4fefb9f4c18cb795266cb8afcb3db09776600785a453eed656b4b25b34fc5e39a0e7a599bff2417bedbd0ac6945d2ad900080 -AUX extendNmr 266 BLAKE2B fb5406150f66718cb2e90018e6403df446010c4fbeffd168bc662e7c9ddc5c6a5f75548a0f8f5e296e4ab10ee56f6997784ad0e7701e855bba107ea1ab74939c SHA512 b94d480c776bc2da31ed12419df1c3364036299553697b7d50eb0ebf073126041e8acd3f1c30051dc1dbc44fef9662001e718a29b8c7fcfc2ca19c0da90125ce -AUX formatConverter 286 BLAKE2B 37fa628a08c1b5293171f41b8322c8003c72e6a26f9e58446e4090881ac05c186c2cde66bbd328a03a53237bd5169d48c69846ef3ea8331b16a0a08c2a0dc1c2 SHA512 a987b73b10614a2616b62589004ae1e321903af08efea62f6c74f2cf5b1e7053454a382107056250824373bce9f281ad0af2e8f6928cdf2e556e9638646cfcda -AUX pipe2azara 290 BLAKE2B 6a366e968961119dee2d3e451d8c467b724bac5c011ef646b86807c7e71f8471e5b72c1a0b7059a6f88578e6f615c79dc370b48c0e7f06caa7e7dfb2013a7c3a SHA512 6f90a1720dc786d84576029cf77271e8eeb0b5c38506e93227064aafba1152a86762125d3bb9f26a741dcc215da87cf96ba9b8926568db79b56159f8839e8a80 -AUX xeasy2azara 288 BLAKE2B f79ab9f4add3f1c6574b64d3bdc52991ce798f273cf3989d1bd7b5ddcf219d99235b1be00453e29cad39f31fb7f46d5880d6709d40bd19a0947972a4cf0b5e6b SHA512 e9a3dedc155f9f7b163eead73099532653454a7f5f12042348abf87a4e8930cb8b0b66fd87ef9fcc3b395c92d7e4942829ec8f5e7a1c28c7b3ce51022b8fce6b -DIST analysis2.4.1.tar.gz 36088236 BLAKE2B 8aaf4ffe5a8dc7a6b805a7a66e163cb03b0fc8a45617ebf892268a2f3658e49c48e3c2de4ea654a840eef2c01cf3a3f28f45e053697e68bbc83ce22d19a29cf3 SHA512 db44468c360d51815614fe0055505001c0a7a722f980c2c049c00524672bdfd4a507134ce1d68b29ebf622ffe94e0c9bb9685fea5b3441790b997a64f78c0dc1 -DIST analysis2.4.2.tar.gz 36390919 BLAKE2B 5e7fa44b2029d834ef634b2cd9f2c34d7e6dbfd3e257b9344cff92d13750a21325a2a2f82eb072ae385c528a7406796959c8201edbc1422bc54a17e176d7db33 SHA512 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99893ca009ff76b015017b29cfd97e0ae935ed2d62aa5a99d52dd9a5f22cf0d369e5019273fe3c3811c28b32568721fb64f71c5927eb57d0cc91dcea44b0288d -DIST ccpn-update-2.4.2-150421.patch.xz 3788 BLAKE2B 125eed69e2593e0ab64e6d3cdcee026c4af067c3aa2e9742b033741cc65cc0391fb86c825b372c02dcd549ca260196fd4e8938516d218653d3db80f60ce9caf2 SHA512 0e8a10b6d9721b52574cd2fe0413dca0fac32a948eb31d3db6e2c4d4f7d85c341e8d53d70954341792ea598a37ec87e4392a615e1c2f6f8bbfc0e42a750be648 -EBUILD ccpn-2.4.1_p150226.ebuild 4568 BLAKE2B ed7b8ce6ab7a0309bfb92aadf6039b68b1e5b889cebfd4aa23ea95584885fb8f1560a2b13e280adf0ccd10ec728309ccd2b35aa35af6df80bb4bf8e501553294 SHA512 d69103a9da8022f9b37e9f995728fc7eeb2d7692e6c7de11816bae521dcfcd74aabbf0758646575f9cad67149204e3a79b4c8ec45afae9e28a7fcb6c659632d0 -EBUILD ccpn-2.4.2.ebuild 4569 BLAKE2B 9ad48cd3693d89a501645b59d3734f84fd9bc536f3140ca8b88d79defb9b9b70aa1a60b5a78a2b3da7ba5fdca3344d7a4f9772891c11df50cea77e16c6b2869a SHA512 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d69103a9da8022f9b37e9f995728fc7eeb2d7692e6c7de11816bae521dcfcd74aabbf0758646575f9cad67149204e3a79b4c8ec45afae9e28a7fcb6c659632d0 -MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild b/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild deleted file mode 100644 index a1755eca7d7d..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild +++ /dev/null @@ -1,165 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="ssl,tk" - -inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator - -PATCHSET="${PV##*_p}" -MY_PN="${PN}mr" -MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" -MY_MAJOR="$(get_version_component_range 1-3)" - -DESCRIPTION="The Collaborative Computing Project for NMR" -HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" -SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" -[[ -n ${PATCHSET} ]] \ - && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+opengl" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-lang/tk:0=[threads] - dev-python/numpy[${PYTHON_USEDEP}] - dev-tcltk/tix - =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet[${PYTHON_USEDEP}] - )" -DEPEND="${RDEPEND}" - -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch - - epatch "${FILESDIR}"/2.3.1-parallel.patch - - append-lfs-flags - - sed \ - -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ - -e "s:weights_s:weights:g" \ - -i python/ccpnmr/analysis/wrappers/Psipred.py || die - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_TRUE" - GL_DIR="${EPREFIX}/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="" - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - rm -rf data model doc license || die - - sed \ - -e "s|/usr|${EPREFIX}/usr|g" \ - -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ - -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ - -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ - -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ - -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ - -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ - -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ - -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ - -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ - -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ - -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ - -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ - -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ - -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ - c/environment_default.txt > c/environment.txt || die - - sed \ - -e 's:ln -s:cp -f:g' \ - -i $(find python -name linkSharedObjs) || die -} - -src_compile() { - emake -C c all - emake -C c links -} - -src_install() { - local libdir - local tkver - local _wrapper - - find . -name "*.pyc" -type f -delete || die - - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" - for wrapper in ${_wrapper}; do - sed \ - -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ - -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ - -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ - -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ - -e "s|gentoopython|${EPYTHON}|g" \ - -e "s|gentoousr|${EPREFIX}/usr|g" \ - -e "s|//|/|g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} - done - - local in_path=$(python_get_sitedir)/${PN} - local files - local pydocs - - pydocs="$(find python -name doc -type d)" - rm -rf ${pydocs} || die - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's|#from __future__|from __future__|g' \ - -i ${i} || die - done - - dodir ${in_path#${EPREFIX}}/c - - ebegin "Installing main files" - python_moduleinto ${PN} - python_domodule python - eend - - ebegin "Adjusting permissions" - for _file in $(find "${ED}" -type f -name "*so"); do - chmod 755 ${_file} - done - eend - python_optimize -} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2.ebuild deleted file mode 100644 index 6303b8d42837..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.4.2.ebuild +++ /dev/null @@ -1,165 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="ssl,tk" - -inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator - -#PATCHSET="${PV##*_p}" -MY_PN="${PN}mr" -MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" -MY_MAJOR="$(get_version_component_range 1-3)" - -DESCRIPTION="The Collaborative Computing Project for NMR" -HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" -SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" -[[ -n ${PATCHSET} ]] \ - && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+opengl" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-lang/tk:0=[threads] - dev-python/numpy[${PYTHON_USEDEP}] - dev-tcltk/tix - =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet[${PYTHON_USEDEP}] - )" -DEPEND="${RDEPEND}" - -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch - - epatch "${FILESDIR}"/2.3.1-parallel.patch - - append-lfs-flags - - sed \ - -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ - -e "s:weights_s:weights:g" \ - -i python/ccpnmr/analysis/wrappers/Psipred.py || die - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_TRUE" - GL_DIR="${EPREFIX}/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="" - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - rm -rf data model doc license || die - - sed \ - -e "s|/usr|${EPREFIX}/usr|g" \ - -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ - -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ - -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ - -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ - -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ - -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ - -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ - -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ - -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ - -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ - -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ - -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ - -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ - -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ - c/environment_default.txt > c/environment.txt || die - - sed \ - -e 's:ln -s:cp -f:g' \ - -i $(find python -name linkSharedObjs) || die -} - -src_compile() { - emake -C c all - emake -C c links -} - -src_install() { - local libdir - local tkver - local _wrapper - - find . -name "*.pyc" -type f -delete || die - - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" - for wrapper in ${_wrapper}; do - sed \ - -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ - -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ - -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ - -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ - -e "s|gentoopython|${EPYTHON}|g" \ - -e "s|gentoousr|${EPREFIX}/usr|g" \ - -e "s|//|/|g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} - done - - local in_path=$(python_get_sitedir)/${PN} - local files - local pydocs - - pydocs="$(find python -name doc -type d)" - rm -rf ${pydocs} || die - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's|#from __future__|from __future__|g' \ - -i ${i} || die - done - - dodir ${in_path#${EPREFIX}}/c - - ebegin "Installing main files" - python_moduleinto ${PN} - python_domodule python - eend - - ebegin "Adjusting permissions" - for _file in $(find "${ED}" -type f -name "*so"); do - chmod 755 ${_file} - done - eend - python_optimize -} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild deleted file mode 100644 index a1755eca7d7d..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild +++ /dev/null @@ -1,165 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="ssl,tk" - -inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator - -PATCHSET="${PV##*_p}" -MY_PN="${PN}mr" -MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" -MY_MAJOR="$(get_version_component_range 1-3)" - -DESCRIPTION="The Collaborative Computing Project for NMR" -HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" -SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" -[[ -n ${PATCHSET} ]] \ - && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+opengl" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-lang/tk:0=[threads] - dev-python/numpy[${PYTHON_USEDEP}] - dev-tcltk/tix - =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet[${PYTHON_USEDEP}] - )" -DEPEND="${RDEPEND}" - -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch - - epatch "${FILESDIR}"/2.3.1-parallel.patch - - append-lfs-flags - - sed \ - -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ - -e "s:weights_s:weights:g" \ - -i python/ccpnmr/analysis/wrappers/Psipred.py || die - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_TRUE" - GL_DIR="${EPREFIX}/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="" - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - rm -rf data model doc license || die - - sed \ - -e "s|/usr|${EPREFIX}/usr|g" \ - -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ - -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ - -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ - -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ - -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ - -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ - -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ - -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ - -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ - -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ - -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ - -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ - -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ - -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ - c/environment_default.txt > c/environment.txt || die - - sed \ - -e 's:ln -s:cp -f:g' \ - -i $(find python -name linkSharedObjs) || die -} - -src_compile() { - emake -C c all - emake -C c links -} - -src_install() { - local libdir - local tkver - local _wrapper - - find . -name "*.pyc" -type f -delete || die - - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" - for wrapper in ${_wrapper}; do - sed \ - -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ - -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ - -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ - -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ - -e "s|gentoopython|${EPYTHON}|g" \ - -e "s|gentoousr|${EPREFIX}/usr|g" \ - -e "s|//|/|g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} - done - - local in_path=$(python_get_sitedir)/${PN} - local files - local pydocs - - pydocs="$(find python -name doc -type d)" - rm -rf ${pydocs} || die - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's|#from __future__|from __future__|g' \ - -i ${i} || die - done - - dodir ${in_path#${EPREFIX}}/c - - ebegin "Installing main files" - python_moduleinto ${PN} - python_domodule python - eend - - ebegin "Adjusting permissions" - for _file in $(find "${ED}" -type f -name "*so"); do - chmod 755 ${_file} - done - eend - python_optimize -} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild deleted file mode 100644 index a1755eca7d7d..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild +++ /dev/null @@ -1,165 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="ssl,tk" - -inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator - -PATCHSET="${PV##*_p}" -MY_PN="${PN}mr" -MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" -MY_MAJOR="$(get_version_component_range 1-3)" - -DESCRIPTION="The Collaborative Computing Project for NMR" -HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" -SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" -[[ -n ${PATCHSET} ]] \ - && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+opengl" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-lang/tk:0=[threads] - dev-python/numpy[${PYTHON_USEDEP}] - dev-tcltk/tix - =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet[${PYTHON_USEDEP}] - )" -DEPEND="${RDEPEND}" - -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch - - epatch "${FILESDIR}"/2.3.1-parallel.patch - - append-lfs-flags - - sed \ - -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ - -e "s:weights_s:weights:g" \ - -i python/ccpnmr/analysis/wrappers/Psipred.py || die - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_TRUE" - GL_DIR="${EPREFIX}/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="" - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - rm -rf data model doc license || die - - sed \ - -e "s|/usr|${EPREFIX}/usr|g" \ - -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ - -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ - -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ - -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ - -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ - -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ - -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ - -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ - -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ - -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ - -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ - -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ - -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ - -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ - c/environment_default.txt > c/environment.txt || die - - sed \ - -e 's:ln -s:cp -f:g' \ - -i $(find python -name linkSharedObjs) || die -} - -src_compile() { - emake -C c all - emake -C c links -} - -src_install() { - local libdir - local tkver - local _wrapper - - find . -name "*.pyc" -type f -delete || die - - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" - for wrapper in ${_wrapper}; do - sed \ - -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ - -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ - -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ - -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ - -e "s|gentoopython|${EPYTHON}|g" \ - -e "s|gentoousr|${EPREFIX}/usr|g" \ - -e "s|//|/|g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} - done - - local in_path=$(python_get_sitedir)/${PN} - local files - local pydocs - - pydocs="$(find python -name doc -type d)" - rm -rf ${pydocs} || die - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's|#from __future__|from __future__|g' \ - -i ${i} || die - done - - dodir ${in_path#${EPREFIX}}/c - - ebegin "Installing main files" - python_moduleinto ${PN} - python_domodule python - eend - - ebegin "Adjusting permissions" - for _file in $(find "${ED}" -type f -name "*so"); do - chmod 755 ${_file} - done - eend - python_optimize -} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild deleted file mode 100644 index a1755eca7d7d..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild +++ /dev/null @@ -1,165 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="ssl,tk" - -inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator - -PATCHSET="${PV##*_p}" -MY_PN="${PN}mr" -MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" -MY_MAJOR="$(get_version_component_range 1-3)" - -DESCRIPTION="The Collaborative Computing Project for NMR" -HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" -SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" -[[ -n ${PATCHSET} ]] \ - && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+opengl" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-lang/tk:0=[threads] - dev-python/numpy[${PYTHON_USEDEP}] - dev-tcltk/tix - =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet[${PYTHON_USEDEP}] - )" -DEPEND="${RDEPEND}" - -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch - - epatch "${FILESDIR}"/2.3.1-parallel.patch - - append-lfs-flags - - sed \ - -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ - -e "s:weights_s:weights:g" \ - -i python/ccpnmr/analysis/wrappers/Psipred.py || die - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_TRUE" - GL_DIR="${EPREFIX}/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="" - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - rm -rf data model doc license || die - - sed \ - -e "s|/usr|${EPREFIX}/usr|g" \ - -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ - -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ - -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ - -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ - -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ - -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ - -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ - -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ - -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ - -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ - -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ - -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ - -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ - -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ - c/environment_default.txt > c/environment.txt || die - - sed \ - -e 's:ln -s:cp -f:g' \ - -i $(find python -name linkSharedObjs) || die -} - -src_compile() { - emake -C c all - emake -C c links -} - -src_install() { - local libdir - local tkver - local _wrapper - - find . -name "*.pyc" -type f -delete || die - - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" - for wrapper in ${_wrapper}; do - sed \ - -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ - -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ - -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ - -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ - -e "s|gentoopython|${EPYTHON}|g" \ - -e "s|gentoousr|${EPREFIX}/usr|g" \ - -e "s|//|/|g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} - done - - local in_path=$(python_get_sitedir)/${PN} - local files - local pydocs - - pydocs="$(find python -name doc -type d)" - rm -rf ${pydocs} || die - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's|#from __future__|from __future__|g' \ - -i ${i} || die - done - - dodir ${in_path#${EPREFIX}}/c - - ebegin "Installing main files" - python_moduleinto ${PN} - python_domodule python - eend - - ebegin "Adjusting permissions" - for _file in $(find "${ED}" -type f -name "*so"); do - chmod 755 ${_file} - done - eend - python_optimize -} diff --git a/sci-chemistry/ccpn/files/2.3.1-parallel.patch b/sci-chemistry/ccpn/files/2.3.1-parallel.patch deleted file mode 100644 index fcf44707e082..000000000000 --- a/sci-chemistry/ccpn/files/2.3.1-parallel.patch +++ /dev/null @@ -1,38 +0,0 @@ -diff --git a/ccpnmr2.3/c/Makefile b/ccpnmr2.3/c/Makefile -index 01fb25a..8e8e1fe 100644 ---- a/ccpnmr2.3/c/Makefile -+++ b/ccpnmr2.3/c/Makefile -@@ -5,22 +5,22 @@ all: compile - compile: global structure analysis clouds dynamics bayes - - global: -- cd memops/global && $(MAKE) -+ $(MAKE) -C memops/global - --structure: -- cd ccp/structure && $(MAKE) -+structure: global -+ $(MAKE) -C ccp/structure - --analysis: -- cd ccpnmr/analysis && $(MAKE) -+analysis: global -+ $(MAKE) -C ccpnmr/analysis - --clouds: -- cd ccpnmr/clouds && $(MAKE) -+clouds: global -+ $(MAKE) -C ccpnmr/clouds - --dynamics: -- cd ccpnmr/dynamics && $(MAKE) -+dynamics: global -+ $(MAKE) -C ccpnmr/dynamics - --bayes: -- cd other/cambridge/bayes && $(MAKE) -+bayes: global -+ $(MAKE) -C other/cambridge/bayes - - clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean bayes_clean - diff --git a/sci-chemistry/ccpn/files/analysis b/sci-chemistry/ccpn/files/analysis deleted file mode 100644 index 828ed4e64ae9..000000000000 --- a/sci-chemistry/ccpn/files/analysis +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -i -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/analysis/AnalysisGui.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/dangle b/sci-chemistry/ccpn/files/dangle deleted file mode 100644 index 6d8a42e615de..000000000000 --- a/sci-chemistry/ccpn/files/dangle +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/cambridge/dangle/DangleGui.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/dataShifter b/sci-chemistry/ccpn/files/dataShifter deleted file mode 100644 index c083960f2f60..000000000000 --- a/sci-chemistry/ccpn/files/dataShifter +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/DataShifter.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/depositionFileImporter b/sci-chemistry/ccpn/files/depositionFileImporter deleted file mode 100644 index 09505ccc4925..000000000000 --- a/sci-chemistry/ccpn/files/depositionFileImporter +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/pdbe/deposition/dataFileImport/dataFileImportGui.py $@ diff --git a/sci-chemistry/ccpn/files/eci b/sci-chemistry/ccpn/files/eci deleted file mode 100644 index 54d913348718..000000000000 --- a/sci-chemistry/ccpn/files/eci +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/eci/EntryCompletionGui.py $* diff --git a/sci-chemistry/ccpn/files/extendNmr b/sci-chemistry/ccpn/files/extendNmr deleted file mode 100644 index a2fe4c997c7c..000000000000 --- a/sci-chemistry/ccpn/files/extendNmr +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O -i -O ${CCPNMR_TOP_DIR}/ccpn/python/extendNmr/ExtendNmrGui.py $@ diff --git a/sci-chemistry/ccpn/files/formatConverter b/sci-chemistry/ccpn/files/formatConverter deleted file mode 100644 index 6cb273612352..000000000000 --- a/sci-chemistry/ccpn/files/formatConverter +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/FormatConverter.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/pipe2azara b/sci-chemistry/ccpn/files/pipe2azara deleted file mode 100644 index 5a3710a134a7..000000000000 --- a/sci-chemistry/ccpn/files/pipe2azara +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/NmrPipeData.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/xeasy2azara b/sci-chemistry/ccpn/files/xeasy2azara deleted file mode 100644 index 7b73714c2fa5..000000000000 --- a/sci-chemistry/ccpn/files/xeasy2azara +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/XeasyData.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/metadata.xml b/sci-chemistry/ccpn/metadata.xml deleted file mode 100644 index 8937bad0b175..000000000000 --- a/sci-chemistry/ccpn/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/chemical-mime-data/Manifest b/sci-chemistry/chemical-mime-data/Manifest index 737afa52d7ae..f0d861fd3d5a 100644 --- a/sci-chemistry/chemical-mime-data/Manifest +++ b/sci-chemistry/chemical-mime-data/Manifest @@ -3,6 +3,5 @@ AUX chemical-mime-data-0.1.94-pigz.patch 481 BLAKE2B dee47e41645b5d196326fb7439e AUX chemical-mime-data-0.1.94-rsvg-convert.patch 1039 BLAKE2B 2eff2aa39206181f56bc802c30b4b043a0aeccef55c5d4e34755dcca69cc3afadd6cac364307729d8d83c88b7ba1d91d7200a80c7bd577e22c6ec5aec3b1921d SHA512 9c12f96f16e7982a5ba11fc546293a2e74f8918ef6eb274e3b1a618fc28aff244402c9b28ffebc2e01c8f6eb0e9e2516da82852bd0f9142c10e97f027670e60d AUX chemical-mime-data-0.1.94-turbomole.patch 2451 BLAKE2B 86b4b08b2af4503e0f8a525ebaa4231a3d0d3727c951b9e957c9fdac790bc41b7f01092350099a64cce66dbb61bc4cbd3654ef91834310c6c7cd1dc156ca87e8 SHA512 1bfa8818d159f0f917a24a06b0bfe926f0854f4242d8c2dbbedcd4210ffd38a459298862dc1d1aedbbe648a933db99c5d647c5409af74f88b03dd3033946df54 DIST chemical-mime-data-0.1.94.tar.bz2 146077 BLAKE2B 9996c240446dc9571b6b4afbcdc6cf16a08e11314da9f785490b1b20933b6d18a333132492e30315c08f4441c048ec593a111815253050cfb5ab562aadb784f1 SHA512 7f3d967149f27ab1de53c948dc055959e661e1be9d778e3d56d06bea95769da7770ab5fb66afab6607747ef91ffb1dbbcf921e5f06e3303351781968594b5f00 -EBUILD chemical-mime-data-0.1.94-r2.ebuild 1340 BLAKE2B 34fb2296fd370aa2dc5ac9043db17c6c862d9c443f2e43c3043c25fd5a52170ef45e5237d6cc86cd96a7b2828c4e87035ef141403f4902e8bf971e9f454c8eab SHA512 bbbdb5aea48fef9f226fb2b7c94a9bc126e72647a94054ec58c307c159609855c655a070ddb8bb5fe110a77ec82b2cfeed965ff9ad8fd9c8d7a66aba9de9a8cc -EBUILD chemical-mime-data-0.1.94-r3.ebuild 1003 BLAKE2B f9d2752e808ef67bfb8f48182133ff94c1365042954e6c51fdf5368d6374f94f4e8db99ff2c58df2c5c4125f14a1644300c913067060b325762cad6f1ab99c2e SHA512 127d2bf314e3852c7e1330f74c70ea6ddfc4f4ca379ec95bb46a21b1708c210292f8c1192757e6495029ab910a340d31304e805febae160675080863941e8294 +EBUILD chemical-mime-data-0.1.94-r3.ebuild 1007 BLAKE2B 20203fada235e55c4614a8f5f80271adb91ecb8e21e553aeaf3ef2d0bb9f94b78ae7f4905db9698f2d4a0971cc309eb863277261dae0cb4fc19d60cc6a8037c4 SHA512 421ee83448926cc336065c22f270d2c8d4f7fdd0517b684ecd4faa002b16bad0113d9de3fb88a548a7e35e028d3572932a7fc8907d516d3878cc4cafb1474131 MISC metadata.xml 474 BLAKE2B c4d6ffbdf66f856fc9e404202d9a9956d8bbfaeb31eb1eb056300ca5049c02d0499ead32a2013080e397eba272bd3a290b81f343baab1fb40204364bfa5208ec SHA512 59cfe759a75bf49fb020652168434fb610c2d5ba56507945253f556b5542a119bc9c9dc4f2b71ceed93f6672b31e5713cc9d76c433e95b0a08c51e9e577bac00 diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild deleted file mode 100644 index d9d29973585b..000000000000 --- a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -AUTOTOOLS_AUTORECONF=true - -inherit autotools-utils fdo-mime - -DESCRIPTION="A collection of data files to add support for chemical MIME types" -HOMEPAGE="http://chemical-mime.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="" - -RDEPEND=" - gnome-base/gnome-mime-data - x11-misc/shared-mime-info" -DEPEND="${RDEPEND} - dev-util/intltool - dev-util/desktop-file-utils - dev-libs/libxslt - media-gfx/imagemagick[xml,png,svg] - media-gfx/inkscape - virtual/pkgconfig" - -PATCHES=( - "${FILESDIR}"/${P}-turbomole.patch - "${FILESDIR}"/${P}-pigz.patch - "${FILESDIR}"/${P}-namespace-svg.patch - ) - -src_prepare() { - # needed for convert/inkscape #464782 - export XDG_CONFIG_HOME=$HOME/.config - autotools-utils_src_prepare -} - -src_configure() { - local myeconfargs=( - --disable-update-database - --htmldir=/usr/share/doc/${PF}/html - ) - autotools-utils_src_configure -} - -pkg_postinst() { - fdo-mime_desktop_database_update - fdo-mime_mime_database_update - ewarn "You can ignore any 'Unknown media type in type' warnings." -} - -pkg_postrm() { - fdo-mime_desktop_database_update - fdo-mime_mime_database_update - ewarn "You can ignore any 'Unknown media type in type' warnings." -} diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild index ae7e62e898fc..a25326ccb709 100644 --- a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild +++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild @@ -6,7 +6,7 @@ EAPI=6 inherit autotools xdg DESCRIPTION="A collection of data files to add support for chemical MIME types" -HOMEPAGE="http://chemical-mime.sourceforge.net/" +HOMEPAGE="https://github.com/dleidert/chemical-mime" SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2" LICENSE="LGPL-2.1" diff --git a/sci-chemistry/cluster/Manifest b/sci-chemistry/cluster/Manifest index ce072c27449c..aff262f69648 100644 --- a/sci-chemistry/cluster/Manifest +++ b/sci-chemistry/cluster/Manifest @@ -2,5 +2,4 @@ AUX 1.3.081231-includes.patch 245 BLAKE2B 6bbe0621d49bc7af8091a5594ebcd52d29d99c AUX 1.3.081231-ldflags.patch 842 BLAKE2B 67085c3dd9ca5e97b28481fbf06a0f9b6294bd519eb3639c54b10cd9b11a4c44a48dbfa907cdf9ff8ec68761164e82d415c44ad0c3a551842416759c76d4b7a9 SHA512 9937f88e65ae94595ba2889e7f57d3b295e025d2ebd83817300a7f74a674fab84358e3b7fc9619ba473c586c51bd106e303b096cdb267d8fda05670f7815e9e4 DIST cluster.1.3.081231.src.tgz 8860 BLAKE2B 4bfc6fe9efa3dbde106ad12df7b23990a748fee5446f16fe4e3cf9232697313bd513366a2283ac732cf0c7306ac65af578155328d0b04e4b5b99536553c9b903 SHA512 af5851ef467458d45ee5f2309c6344ae16145ac371a1b9d0a3d8b5769a18b98877cf7cb65b85f71108d927b0e6c363e06b85a67e7cb2e5e0b41af375cb2db7ac EBUILD cluster-1.3.081231-r1.ebuild 664 BLAKE2B 1bb02947160c9306e9fbeb3fbc8197327b4e19d0ee585170ec2769f578e781ca092015f05f368923f9aae5887a491d9e8029db0e36731aa033d18c5691e15582 SHA512 2179d4beb99e86945b2afa8b0951da4f2c59ad13a0070429d7c0a24e0d363ee0a7f12a3710655305be332cec4744e3b22167e1c99986fcb1e22dec2fc46e6d59 -EBUILD cluster-1.3.081231.ebuild 646 BLAKE2B f15642c24f170c1f042a7b695aff41005b4b22c66e14ffa6002c3609864221934933f2e939516b20ccde2ddf53c5a219f11bbf8357094d8d2fbfaa66e9bf0750 SHA512 2bafc4cec0e46ad3749a5b005f629340bc2b0ec8e3fd062da5f20edcccb67597c6a3b1cb5c7045a2d3796de3b488f78ca7b53678c911d63f9dfaf0ff290f9a73 MISC metadata.xml 661 BLAKE2B 602330745970373b72472999d013a804a343da0ea3c2a1ef948d3fea97dfbb1f1533a0322d1b8295a19ea377725d503c36f37316f5168ea815053afde8388b50 SHA512 449c8965bd2f3039effcf1d6fc15fea1708cf5987aee36a4b8c470f85b59f7b04884a796a353f17fd890aa9d2e4ee7b1c25ed969febabaa54e577f8be31ed889 diff --git a/sci-chemistry/cluster/cluster-1.3.081231.ebuild b/sci-chemistry/cluster/cluster-1.3.081231.ebuild deleted file mode 100644 index e9d3b8999e1e..000000000000 --- a/sci-chemistry/cluster/cluster-1.3.081231.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=4 - -inherit eutils toolchain-funcs - -DESCRIPTION="Build lists of collections of interacting items" -HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php" -SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz" - -SLOT="0" -LICENSE="richardson" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="" - -S="${WORKDIR}"/${PN}1.3src - -src_prepare() { - epatch \ - "${FILESDIR}"/${PV}-ldflags.patch \ - "${FILESDIR}"/${PV}-includes.patch - tc-export CXX -} - -src_install() { - dobin ${PN} - dodoc README.cluster -} diff --git a/sci-chemistry/cns/Manifest b/sci-chemistry/cns/Manifest deleted file mode 100644 index fb9785137012..000000000000 --- a/sci-chemistry/cns/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -AUX 1.2.1-allow-gcc-openmp.patch 926 BLAKE2B 05278c040466c8d0c6f6ef2684457fa3b96309eec75d21cdc4f49f33c491d966d8a1ae77d128c54eaabacbf305071871c85eb82ac99748c2a3cae0a68092d7db SHA512 cdaae39096625ff1b84ec76b36d2ec3f2e4e4e532d347fa3f0d3e0aa239e2477301de6c768f14788a9b599694568422009bc1c0298ad677cab28d463e0ea8524 -AUX 1.2.1-aria2.3.patch 658 BLAKE2B 22bf941d31729220a8a1e7cae3dbd164502a6815ddb26452c1409aa65ab9f8145f98f280cf7ee2fb91466d4452f82b20297ebe6a3504569c6cc65dc8be8bb6bd SHA512 54758723bc4900673dff73e3aa4d9ead803c44ee3af514259b21c73f7495aaa077e29efe381e674d2a6c5c8d888d7c9cf4d4a998b6c4b6d91de488dc4526f7e4 -AUX 1.2.1-gentoo.patch 2071 BLAKE2B bc9e5bf684d8a82550a386a0e56aeb58105c224d2d7c9e7ade19fe7002222483052ff4730e5d03828a832314b2f6d24cf121a27471405aad2d8de637c4d97f32 SHA512 ecc545e66859d3a88c38cfd40abc278fdd8fca520d63b8d8ab3f2301352962cc70ba436078edec793fda90212fe44c0d333163d64c37afd65e19240f1044feb7 -AUX 1.2.1-ifort.patch 5346 BLAKE2B 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7a65fdf4c787b5adbf1730ecbbf74950ca29cdefa62f7a6dab085f0e85e773e117746559e6ec9f97cca36a8e0464b71ed92b33d18ab0babf2dd2566fc0a1b35e SHA512 235b5890c9c0aa9bfac0034e35c3641968b5b1f600bbbfa81240fe405f28910a00184b6fa2ec7a993883ba6db95f1fa9e44cb4b7b9e61ab3d9dcfa26869e1a4c -AUX cns_solve_env_sh 7070 BLAKE2B 733dc170c5bb009e4774486b95aeb18811cbf339ffda3ff1ee3e8b6b703c782996b291ed0a1aaee6fd314a86b429183fc5a632136bbe3e13524176325828801e SHA512 b012e46706f39d934ff27e4b381907ddd25ca1fbc0112c320b117d68cca3e81f571bfd1821b49477dc16bfd8a0a943c43469fe847cf99e6ab2d08ef238bada31 -AUX cns_solve_env_sh-1.3_p7 7332 BLAKE2B cc4a96591f5bb7716d981525a923413f5f723774cc6253e7483b0ef849a6c57e0fd31e27d4848fd2656e50d83935416a6de62016f9a054bc48313454df9c5548 SHA512 afe2f24c85eff265659e5b2ba2edab519c3193d30b2dcd815bc91a929fd4f4a9167148f8248237569f809d627a8fa623a46fe82d3e0a2cb1827bed910ce565cb -DIST aria2.3.1.tar.gz 1833973 BLAKE2B 4bf51626a4283452e75a834d0160a4204efd5a35ee8b07329f2a4f933ceea23e53177e6ed19bc9cc158b2a00491d20c75d443bdc04e7feb2d7eda3dc006818e1 SHA512 79a2cd89e2120acecb04f286a153dbf52c16500e8956c9dad49b1e1ed94a7b2449c7b044bae6f87e0d2b452a1467a2c02de74f0fa85b0eae66042386e2f5e2d5 -DIST aria2.3.2.tar.gz 1836270 BLAKE2B 725b0db2b5de36d1b132c5073b8a91f26fa19b48549f4c899041a2b140127524f660c4faeb8c35e94d3d19c24b0252f379de0e85c8fb08b86fc7834252239fb9 SHA512 009a1d0079f5cc162dc732749ddd2b33297268f0d988b2f37bda4ed50c7764ceef7ae5b56b322c7ac79427a4a2a92d1239199891445cb5e2b3d0908ed670e2aa -DIST cns_solve_1.21_all-mp.tar.gz 32748040 BLAKE2B 7c82fd9cddc56a00d791d6d5525491b91525962f000c2fdfb02a3ab81305c0c026c115c2328dac99ac7b30146ca591620f4f42019938fb49e7ce52235b281121 SHA512 383324d771570b501e388fba9bf20789f483a3a4044eb3334c7a7e7835e0c345b784e0d344b22d20a10fe1c33ed21c9013adb1af5912808af480b96abe275857 -DIST cns_solve_1.3_all.tar.gz 64167735 BLAKE2B 3901a597eb0deac7f2fad173e15d78bfcd753c4019739e22c8851194c9446305cd92bcff73f7f06dc21b6d055852863993412296e1e555ef0b3b730052934cbd SHA512 4fe73820e96999bb33a59ff6da979794628552f49bc03cdebcb9439b57e6042b92190e04bb7e4079157adf06a6facc5c16b8ae91621bd24a4b35ee382e53ae37 -EBUILD cns-1.2.1-r8.ebuild 6595 BLAKE2B 4a1b1f74950f5795a1fb78631808d3b9cff8cb5beb4a2c3bc939e2813fd3805e4a79a94d7903add989231185e23fef4dfffdc1efa531a1694ef1f82e82b91fe7 SHA512 7984a1aa41357c54363ab69480ce0324c89998adfa6085fa4c03c47d101bd82c6fe5e71154360d2583af0c63921222bbf70bcb2a6939771ed44e9fa8c16c6b07 -EBUILD cns-1.3_p7-r1.ebuild 5821 BLAKE2B d8e730c053d96c3321e60f7724fb61de96b4b6b1f720a4c97c8f6c03b6b44b3a5a9fce22f252606c097ffcfebbca2745225f0cbaf75ef1a4e4a21af055790366 SHA512 01befafeacfa8fe2450e0e5090c67d041813c362f50c4deb1ca3e0e5801b793b86b5acc7f9bb4f0e72baeb259fd40f3a6eb620890182774b82db40bc04695997 -MISC metadata.xml 954 BLAKE2B 69065a98205d1c37abcc868279491caf3fa82fc209f25b8570385302a7efb14f1e13e23eedaae5db86fecdd56c9cf3d5bfeb0e425dd824c3f1fa5150a9641aad SHA512 af24c501f427f9473a9ef8ec90dfd14b2abb0856e8bde8bb1c664fe49a23032895c4d28d06112791b78880be1ef9b781efe60c26bee5d8e9a40a40b41713159b diff --git a/sci-chemistry/cns/cns-1.2.1-r8.ebuild b/sci-chemistry/cns/cns-1.2.1-r8.ebuild deleted file mode 100644 index c9d9a80f36af..000000000000 --- a/sci-chemistry/cns/cns-1.2.1-r8.ebuild +++ /dev/null @@ -1,232 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic - -MY_PN="${PN}_solve" -MY_PV="$(delete_version_separator 2)" -MY_P="${MY_PN}_${MY_PV}" - -DESCRIPTION="Crystallography and NMR System" -HOMEPAGE="http://cns.csb.yale.edu/" -SRC_URI=" - ${MY_P}_all-mp.tar.gz - aria? ( aria2.3.2.tar.gz )" - -SLOT="0" -LICENSE="cns" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="aria openmp" - -RDEPEND="app-shells/tcsh" -DEPEND="${RDEPEND}" - -FORTRAN_NEED_OPENMP=1 - -S="${WORKDIR}/${MY_P}" - -RESTRICT="fetch test" - -pkg_nofetch() { - elog "Fill out the form at http://cns.csb.yale.edu/cns_request/" - use aria && elog "and http://aria.pasteur.fr/" - elog "and place these files:" - elog ${A} - elog "into your DISTDIR directory." -} - -get_fcomp() { - case $(tc-getFC) in - *gfortran* ) - FCOMP="gfortran" ;; - ifort ) - FCOMP="ifc" ;; - * ) - FCOMP=$(tc-getFC) ;; - esac -} - -pkg_setup() { - fortran-2_pkg_setup - get_fcomp -} - -get_bitness() { - echo > "${T}"/test.c - $(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o - case $(file "${T}"/test.o) in - *64-bit*|*ppc64*|*x86_64*) export _bitness="64";; - *32-bit*|*ppc*|*i386*) export _bitness="32";; - *) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";; - esac -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${PV}-gentoo.patch \ - "${FILESDIR}"/${PV}-parallel.patch - - get_bitness - - if use aria; then - pushd "${WORKDIR}"/aria* >& /dev/null - # Update the cns sources in aria for version 1.2.1 - epatch "${FILESDIR}"/1.2.1-aria2.3.patch - - # Update the code with aria specific things - cp -rf cns/src/* "${S}"/source/ || die - popd >& /dev/null - fi - - # the code uses Intel-compiler-specific directives - if [[ $(tc-getFC) =~ gfortran ]]; then - epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch - use openmp && \ - append-flags -fopenmp && append-ldflags -fopenmp - COMP="gfortran" - [[ ${_bitness} == 64 ]] && \ - append-fflags -fdefault-integer-8 - elif [[ $(tc-getFC) == if* ]]; then - epatch "${FILESDIR}"/${PV}-ifort.patch - use openmp && \ - append-flags -openmp && append-ldflags -openmp - COMP="ifort" - [[ ${_bitness} == 64 ]] && append-fflags -i8 - fi - - [[ ${_bitness} == 64 ]] && \ - append-cflags "-DINTEGER='long long int'" - - # Set up location for the build directory - # Uses obsolete `sort` syntax, so we set _POSIX2_VERSION - cp "${FILESDIR}"/cns_solve_env_sh "${T}"/ || die - sed \ - -e "s:_CNSsolve_location_:${S}:g" \ - -e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \ - -i "${S}"/cns_solve_env || die - sed \ - -e "s:_CNSsolve_location_:${S}:g" \ - -e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \ - -i "${T}"/cns_solve_env_sh || die - - einfo "Fixing shebangs..." - find "${S}" -type f \ - -exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die -} - -src_compile() { - local GLOBALS - local MALIGN - if [[ $(tc-getFC) =~ g77 ]]; then - GLOBALS="-fno-globals" - MALIGN='\$(CNS_MALIGN_I86)' - fi - - # Set up the compiler to use - ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die - - # make install really means build, since it's expected to be used in-place - # -j1 doesn't mean we do no respect MAKEOPTS! - emake -j1 \ - CC="$(tc-getCC)" \ - F77=$(tc-getFC) \ - LD=$(tc-getFC) \ - CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ - LDFLAGS="${LDFLAGS}" \ - F77OPT="${FCFLAGS} ${MALIGN}" \ - F77STD="${GLOBALS}" \ - OMPLIB="${OMPLIB}" \ - compiler="${COMP}" \ - install -} - -src_test() { - # We need to force on g77 manually, because we can't get aliases working - # when we source in a -c - einfo "Running tests ..." - csh -c \ - "export CNS_G77=ON; source ${S}/cns_solve_env; make run_tests" \ - || die "tests failed" - einfo "Displaying test results ..." - cat "${S}"/*_g77/test/*.diff-test -} - -src_install() { - # Install to locations resembling FHS - sed \ - -e "s:${S}:usr:g" \ - -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${EPREFIX}/usr:g" \ - -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns:g" \ - -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \ - -e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \ - -e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \ - -e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \ - -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ - -e "/^g77on/d" \ - -i "${S}"/cns_solve_env || die - # I don't entirely understand why the sh version requires a leading / - # for CNS_SOLVE and CNS_ROOT, but it does - sed \ - -e "s:${S}:/usr:g" \ - -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=${EPREFIX}/usr:g" \ - -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \ - -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \ - -e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \ - -e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \ - -e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \ - -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ - -e "/^g77on/d" \ - -e "/^g77off/d" \ - -i "${T}"/cns_solve_env_sh || die - - # Get rid of setup stuff we don't need in the installed script - sed \ - -e "83,$ d" \ - -e "37,46 d" \ - -i "${S}"/cns_solve_env || die - sed \ - -e "84,$ d" \ - -e "39,50 d" \ - -i "${T}"/cns_solve_env_sh || die - - newbin "${S}"/*linux*/bin/cns_solve* cns_solve - - # Can be run by either cns_solve or cns - dosym cns_solve /usr/bin/cns - - # Don't want to install this - rm -f "${S}"/*linux*/utils/Makefile || die - - dobin "${S}"/*linux*/utils/* - - sed \ - -e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \ - -i "${S}"/bin/cns_web || die - - dobin "${S}"/bin/cns_{edit,header,transfer,web} - - insinto /usr/share/cns - doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib - doins "${S}"/bin/cns_info - - insinto /etc/profile.d - newins "${S}"/cns_solve_env cns_solve_env.csh - newins "${T}"/cns_solve_env_sh cns_solve_env.sh - - dohtml \ - -A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \ - -f all_cns_info_template,omac,def \ - -r doc/html/* - # Conflits with app-text/dos2unix - rm -f "${D}"/usr/bin/dos2unix || die -} - -pkg_postinst() { - if use openmp; then - elog "Set OMP_NUM_THREADS to the number of threads you want." - elog "If you get segfaults on large structures, set the GOMP_STACKSIZE" - elog "variable if using gcc (16384 should be good)." - fi -} diff --git a/sci-chemistry/cns/cns-1.3_p7-r1.ebuild b/sci-chemistry/cns/cns-1.3_p7-r1.ebuild deleted file mode 100644 index 327d14b2488e..000000000000 --- a/sci-chemistry/cns/cns-1.3_p7-r1.ebuild +++ /dev/null @@ -1,215 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic - -MY_PN="${PN}_solve" -MY_PV="$(delete_version_separator 2)" -MY_P="${MY_PN}_${MY_PV}" - -DESCRIPTION="Crystallography and NMR System" -HOMEPAGE="http://cns.csb.yale.edu/" -SRC_URI=" - ${MY_P/p7}_all.tar.gz - aria? ( aria2.3.1.tar.gz )" - -SLOT="0" -LICENSE="cns" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="aria openmp" - -RDEPEND="app-shells/tcsh" -DEPEND="${RDEPEND}" - -FORTRAN_NEED_OPENMP=1 - -S="${WORKDIR}/${MY_P/p7}" - -RESTRICT="fetch" - -pkg_nofetch() { - elog "Fill out the form at http://cns.csb.yale.edu/cns_request/" - use aria && elog "and http://aria.pasteur.fr/" - elog "and place these files:" - elog ${A} - elog "into your DISTDIR directory." -} - -get_fcomp() { - case $(tc-getFC) in - *gfortran* ) - FCOMP="gfortran" ;; - ifort ) - FCOMP="ifc" ;; - * ) - FCOMP=$(tc-getFC) ;; - esac -} - -pkg_setup() { - fortran-2_pkg_setup - get_fcomp -} - -get_bitness() { - echo > "${T}"/test.c - $(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o - case $(file "${T}"/test.o) in - *64-bit*|*ppc64*|*x86_64*) export _bitness="64";; - *32-bit*|*ppc*|*i386*) export _bitness="32";; - *) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";; - esac -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${PV}-gentoo.patch \ - "${FILESDIR}"/${PV}-delete.patch - - get_bitness - - if use aria; then - pushd "${WORKDIR}"/aria* >& /dev/null - # Update the cns sources in aria for version 1.2.1 - epatch "${FILESDIR}"/1.2.1-aria2.3.patch - - # Update the code with aria specific things - cp -rf cns/src/* "${S}"/source/ || die - popd >& /dev/null - fi - - # the code uses Intel-compiler-specific directives - if [[ $(tc-getFC) =~ gfortran ]]; then - use openmp && \ - append-flags -fopenmp && append-ldflags -fopenmp - COMP="gfortran" - [[ ${_bitness} == 64 ]] && \ - append-fflags -fdefault-integer-8 - elif [[ $(tc-getFC) == if* ]]; then - use openmp && \ - append-flags -openmp && append-ldflags -openmp - COMP="ifort" - [[ ${_bitness} == 64 ]] && append-fflags -i8 - fi - - [[ ${_bitness} == 64 ]] && \ - append-cflags "-DINTEGER='long long int'" - - # Set up location for the build directory - # Uses obsolete `sort` syntax, so we set _POSIX2_VERSION - cp "${FILESDIR}"/cns_solve_env_sh-${PV} "${T}"/cns_solve_env_sh || die - sed \ - -e "s:_CNSsolve_location_:${S}:g" \ - -e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \ - -i "${S}"/cns_solve_env || die - sed \ - -e "s:_CNSsolve_location_:${S}:g" \ - -e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \ - -e "s:setenv OMP_STACKSIZE 256m:export OMP_STACKSIZE=256m:g" \ - -e "s:^limit:^ulimit:g" \ - -i "${T}"/cns_solve_env_sh || die - - ebegin "Fixing shebangs..." - find "${S}" -type f \ - -exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die - find . -name "Makefile*" \ - -exec \ - sed \ - -e "s:^SHELL=/bin/sh:SHELL=${EPREFIX}/bin/sh:g" \ - -e "s:/bin/ls:ls:g" \ - -e "s:/bin/rm:rm:g" \ - -i '{}' + || die - eend -} - -src_compile() { - local GLOBALS - local MALIGN - - # Set up the compiler to use - ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die - - # make install really means build, since it's expected to be used in-place - # -j1 doesn't mean we do no respect MAKEOPTS! - emake -j1 \ - CC="$(tc-getCC)" \ - CXX="$(tc-getCXX)" \ - F77=$(tc-getFC) \ - LD=$(tc-getFC) \ - CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ - CXXFLAGS="${CXXFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ - LDFLAGS="${LDFLAGS}" \ - F77OPT="${FCFLAGS} ${MALIGN}" \ - F77STD="${GLOBALS}" \ - OMPLIB="${OMPLIB}" \ - compiler="${COMP}" \ - install -} - -src_test() { - # We need to force on g77 manually, because we can't get aliases working - # when we source in a -c - einfo "Running tests ..." - sh -c \ - "export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \ - || die "tests failed" - einfo "Displaying test results ..." - cat "${S}"/*_g77/test/*.diff-test -} - -src_install() { - cat >> "${T}"/66cns <<- EOF - CNS_SOLVE="${EPREFIX}/usr" - CNS_ROOT="${EPREFIX}/usr" - CNS_DATA="${EPREFIX}/usr/share/cns" - CNS_DOC="${EPREFIX}/usr/share/doc/cns-1.3" - CNS_LIB="${EPREFIX}/usr/share/cns/libraries" - CNS_MODULE="${EPREFIX}/usr/share/cns/modules" - CNS_TOPPAR="${EPREFIX}/usr/share/cns/libraries/toppar" - CNS_CONFDB="${EPREFIX}/usr/share/cns/libraries/confdb" - CNS_XTALLIB="${EPREFIX}/usr/share/cns/libraries/xtal" - CNS_NMRLIB="${EPREFIX}/usr/share/cns/libraries/nmr" - CNS_XRAYLIB="${EPREFIX}/usr/share/cns/libraries/xray" - CNS_XTALMODULE="${EPREFIX}/usr/share/cns/modules/xtal" - CNS_NMRMODULE="${EPREFIX}/usr/share/cns/modules/nmr" - CNS_HELPLIB="${EPREFIX}/usr/share/cns/helplib" - EOF - - doenvd "${T}"/66cns || die - - # Don't want to install this - rm -f "${S}"/*linux*/utils/Makefile || die - - sed \ - -e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \ - -i "${S}"/bin/cns_web || die - - newbin "${S}"/*linux*/bin/cns_solve* cns_solve - - # Can be run by either cns_solve or cns - dosym cns_solve /usr/bin/cns - - dobin \ - "${S}"/*linux*/utils/* \ - "${S}"/bin/cns_{edit,header,import_cif,transfer,web} - - insinto /usr/share/cns - doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib "${S}"/bin/cns_info - - dohtml \ - -A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \ - -f all_cns_info_template,omac,def \ - -r doc/html/* - # Conflits with app-text/dos2unix - rm -f "${D}"/usr/bin/dos2unix || die -} - -pkg_postinst() { - if use openmp; then - elog "Set OMP_NUM_THREADS to the number of threads you want." - elog "If you get segfaults on large structures, set the GOMP_STACKSIZE" - elog "variable if using gcc (16384 should be good)." - fi -} diff --git a/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch b/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch deleted file mode 100644 index 42b9b0572231..000000000000 --- a/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- source/xfft.f.orig 2008-08-03 00:36:52.000000000 -0700 -+++ source/xfft.f 2008-08-03 00:37:06.000000000 -0700 -@@ -514,7 +514,7 @@ - LOGICAL QHERM - DOUBLE PRECISION XRCELL(9), MAPR - C local --!$ integer omp_get_max_threads, kmp_get_stacksize -+!$ integer omp_get_max_threads - LOGICAL DONE - DOUBLE PRECISION ZERO - PARAMETER (ZERO=0.0D0) -@@ -537,7 +537,7 @@ - NBPP=1 - ! The following command is only relevant for the ifort compiler (if -openmp option is used). - ! If your compiler is not ifort, and gives an error, just comment the next line out: --!$ if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23) -+! if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23) - ! Explanation: the default KMP_STACKSIZE of ifort is 2**21 bytes (2Mb) for 32bit, - ! and 2**22 bytes (4Mb) for 64bit. - ! This may be low for big structures, which leads to segmentation faults! diff --git a/sci-chemistry/cns/files/1.2.1-aria2.3.patch b/sci-chemistry/cns/files/1.2.1-aria2.3.patch deleted file mode 100644 index 8c6939d8eb92..000000000000 --- a/sci-chemistry/cns/files/1.2.1-aria2.3.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff --git a/cns/src/cns.f b/cns/src/cns.f -index a3c2cbe..51a34f8 100644 ---- a/cns/src/cns.f -+++ b/cns/src/cns.f -@@ -470,6 +470,7 @@ C local - INTEGER HNLEN, TMP, PTRSZ, STLEN - CHARACTER*(1) CNSPTMP - CHARACTER*(4) ST -+!$ integer omp_get_max_threads - C - C write header - WRITE(6,'(10X,A)') -@@ -526,6 +527,9 @@ C - WRITE(6,'(10X,7A)') - & ' Running on machine: ',HOSTNM(1:HNLEN), - & ' (',SYSNM(1:TMP),',',ST(1:STLEN),'-bit)' -+!$ write(6,'(31x,a,i3,a)') 'with',omp_get_max_threads(), -+!$ & ' threads' -+!$C (to change use setenv OMP_NUM_THREADS x) - C - CALL GETNAM(USERNM,12,TMP) - WRITE(6,'(10X,2A)') diff --git a/sci-chemistry/cns/files/1.2.1-gentoo.patch b/sci-chemistry/cns/files/1.2.1-gentoo.patch deleted file mode 100644 index 2b47bfcc7d86..000000000000 --- a/sci-chemistry/cns/files/1.2.1-gentoo.patch +++ /dev/null @@ -1,63 +0,0 @@ ---- cns_solve_1.21/instlib/source/Makefile.proto 2000-09-07 20:35:33.000000000 +0200 -+++ cns_solve_1.21/instlib/source/Makefile.proto.new 2009-07-14 09:18:37.000000000 +0200 -@@ -11,6 +11,8 @@ - - SHELL=/bin/sh - -+cns_string=`date "+%y%m%d%H%M"` -+ - # commands - RM = /bin/rm - -@@ -25,26 +27,20 @@ - - # rule for the fortran routines - $(OBJS): -- @ echo "compiling: $(@:.o=.f)"; \ -- $(F77) -c $(F77FLAGS) $(@:.o=.f) -+ $(F77) -c $(F77FLAGS) $(@:.o=.f) - - # rule for the dynamic memory allocation C routines - dmemory.o: dmemory.c -- @ echo ; echo "compiling: $?" -- @ $(CC) -c $(CCFLAGS) $? -+ $(CC) -c $(CCFLAGS) $? - - # rule for the machine specific C routines - machine_c.o: machine_c.c -- @ echo ; echo "compiling: $?" -- @ $(CC) -c $(CCFLAGS) $? -+ $(CC) -c $(CCFLAGS) $? - - # rule for the executable itself - ../bin/cns_solve: $(DEPENDS) -- @ echo ; echo "linking: cns_solve"; echo -- @ cns_string=`date "+%y%m%d%H%M"`; \ -- $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ -- $(LDFLAGS) \ -- $(CNS_FFTDIR) $(CNS_FFTLIB); \ -+ $(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ -+ $(CNS_FFTDIR) $(CNS_FFTLIB); \ - if [ -x cns_solve-$$cns_string.exe ]; \ - then echo "created executable file cns_solve-$$cns_string.exe"; \ - echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \ ---- cns_solve_1.21/instlib/utils/Makefile 2004-08-30 00:40:35.000000000 +0200 -+++ cns_solve_1.21/instlib/utils/Makefile.new 2009-07-14 09:50:27.000000000 +0200 -@@ -22,14 +22,14 @@ - make clean - - .f: -- $(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK) -+ $(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK) - - .c: -- $(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK) -+ $(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK) - - .l: - lex $(@).l -- $(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) -+ $(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) - - relink: - @ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile` diff --git a/sci-chemistry/cns/files/1.2.1-ifort.patch b/sci-chemistry/cns/files/1.2.1-ifort.patch deleted file mode 100644 index ba44bebd1b68..000000000000 --- a/sci-chemistry/cns/files/1.2.1-ifort.patch +++ /dev/null @@ -1,126 +0,0 @@ -diff --git a/source/angledb.f b/source/angledb.f -index 28ad657..eaa847d 100644 ---- a/source/angledb.f -+++ b/source/angledb.f -@@ -1416,10 +1416,10 @@ C include files - C local variables - INTEGER COUNT, SPTR, OLDCLASS, OLDMAXANGLEDBS - INTEGER THETYPE, CURPSIS, CURPHIS -- INTEGER CLASSINDEX -+ INTEGER CLASINDEX - DOUBLE PRECISION K1, CUTOFF - CHARACTER*4 THENAME -- CHARACTER*20 CLASSNAME -+ CHARACTER*20 CLASNAME - C begin - C - IF (ANGLEDBFLAG) THEN -@@ -1450,10 +1450,10 @@ C - ELSE IF (WD(1:4).EQ.'CLAS') THEN - OLDCLASS = CURANGLEDBCLASS - CALL NEXTWD('class name =') -- CLASSNAME = WD(1:20) -+ CLASNAME = WD(1:20) - ANGLEDBMODE = NEW - DO COUNT = 1, NANGLEDBCLASSES -- IF (ANGDBCLASSNAMES(COUNT).EQ.CLASSNAME) THEN -+ IF (ANGDBCLASSNAMES(COUNT).EQ.CLASNAME) THEN - ANGLEDBMODE = UPDATE - CURANGLEDBCLASS = COUNT - END IF -@@ -1472,7 +1472,7 @@ C - END IF - NANGLEDBCLASSES = NANGLEDBCLASSES + 1 - CURANGLEDBCLASS = NANGLEDBCLASSES -- ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASSNAME -+ ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASNAME - ANGLEDBASSNDX(CURANGLEDBCLASS) = NANGLEDBS - END IF - C -@@ -1733,16 +1733,16 @@ C - & HEAP(ANGLEDBTPTR)) - ELSE IF (WD(1:4).EQ.'CLAS') THEN - CALL NEXTWD('Class name>') -- CLASSNAME = WD(1:20) -- CLASSINDEX = 0 -+ CLASNAME = WD(1:20) -+ CLASINDEX = 0 - DO COUNT = 1, NANGLEDBCLASSES - IF (ANGDBCLASSNAMES(COUNT).EQ. -- & CLASSNAME) THEN -+ & CLASNAME) THEN - PRINTTHISCLASS(COUNT) = .TRUE. -- CLASSINDEX = COUNT -+ CLASINDEX = COUNT - END IF - END DO -- IF (CLASSINDEX.EQ.0) THEN -+ IF (CLASINDEX.EQ.0) THEN - CALL DSPERR('ANGLEDB', - & 'unknown class. Using first.') - PRINTTHISCLASS(1) = .TRUE. -diff --git a/source/rama.f b/source/rama.f -index c5d14f2..3063e7b 100644 ---- a/source/rama.f -+++ b/source/rama.f -@@ -1468,11 +1468,11 @@ C include files - C local variables - INTEGER COUNT, SPTR, OLDCLASS, OLDMAXRAMAS, - & THETYPE, CURPSIS, CURPHIS, -- & CURCHIS, CURTHTS, CLASSINDEX -+ & CURCHIS, CURTHTS, CLASINDEX - INTEGER CLEN - DOUBLE PRECISION K1, CUTOFF - CHARACTER*4 THENAME -- CHARACTER*50 CLASSNAME -+ CHARACTER*50 CLASNAME - C begin - C - C this is used by READRAMA2 to hold the selection -@@ -1503,10 +1503,10 @@ C - ELSE IF (WD(1:4).EQ.'CLAS') THEN - OLDCLASS = CURRAMACLASS - CALL NEXTWD('class name =') -- CLASSNAME = WD(1:50) -+ CLASNAME = WD(1:50) - RAMAMODE = NEW - DO COUNT = 1, NRAMACLASSES -- IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME) THEN -+ IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME) THEN - RAMAMODE = UPDATE - CURRAMACLASS = COUNT - END IF -@@ -1525,7 +1525,7 @@ C - END IF - NRAMACLASSES = NRAMACLASSES + 1 - CURRAMACLASS = NRAMACLASSES -- RAMACLASSNAMES(CURRAMACLASS) = CLASSNAME -+ RAMACLASSNAMES(CURRAMACLASS) = CLASNAME - END IF - C - C set force constant for current class, -@@ -1954,18 +1954,18 @@ C - & HEAP(RAMAATOMPTR), 0) - ELSE IF (WD(1:4).EQ.'CLAS') THEN - CALL NEXTWD('Class name>') -- CLASSINDEX = 0 -+ CLASINDEX = 0 - DO COUNT = 1, NRAMACLASSES -- IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME) -- & CLASSINDEX = COUNT -+ IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME) -+ & CLASINDEX = COUNT - END DO -- IF (CLASSINDEX.EQ.0) THEN -+ IF (CLASINDEX.EQ.0) THEN - CALL DSPERR('RAMA', - & 'unknown class. Using first.') -- CLASSINDEX = 1 -+ CLASINDEX = 1 - END IF - CALL PRINTRAMAS(CUTOFF, HEAP(CALCRAMAPTR), -- & HEAP(RAMAATOMPTR), CLASSINDEX) -+ & HEAP(RAMAATOMPTR), CLASINDEX) - ELSE - CALL DSPERR('RAMA', - & 'Expected ALL or CLASs.') diff --git a/sci-chemistry/cns/files/1.2.1-parallel.patch b/sci-chemistry/cns/files/1.2.1-parallel.patch deleted file mode 100644 index dfaa40021d66..000000000000 --- a/sci-chemistry/cns/files/1.2.1-parallel.patch +++ /dev/null @@ -1,17 +0,0 @@ -diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto -index 0d0dd3e..ae9e422 100644 ---- a/instlib/source/Makefile.proto -+++ b/instlib/source/Makefile.proto -@@ -19,9 +19,9 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o - - # the default is to make the cns executable - cns_solve: -- @ make -k printflags F77BUG="$(debug)" DEBUG="$(debug)" -- @ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" -- @ make -k exepurge -+ @ make printflags F77BUG="$(debug)" DEBUG="$(debug)" -+ @ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" -+ @ make exepurge - - # rule for the fortran routines - $(OBJS): diff --git a/sci-chemistry/cns/files/1.3_p7-delete.patch b/sci-chemistry/cns/files/1.3_p7-delete.patch deleted file mode 100644 index cbddf4289158..000000000000 --- a/sci-chemistry/cns/files/1.3_p7-delete.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/utils/cluster_struc.cpp b/utils/cluster_struc.cpp -index b64467a..5f727db 100644 ---- a/utils/cluster_struc.cpp -+++ b/utils/cluster_struc.cpp -@@ -173,7 +173,7 @@ int main(int argc, char *argv[]) { - for (int i = 0; i < nrstruc; i++) { - delete[] neighbor[i]; - } -- delete[] neighbor, neighborcount; -+ delete[] neighbor, delete[] neighborcount; - return 5; - } - if (rmsd < cutoff) { diff --git a/sci-chemistry/cns/files/1.3_p7-gentoo.patch b/sci-chemistry/cns/files/1.3_p7-gentoo.patch deleted file mode 100644 index 7942c55abfb9..000000000000 --- a/sci-chemistry/cns/files/1.3_p7-gentoo.patch +++ /dev/null @@ -1,80 +0,0 @@ -diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto -index 0d0dd3e..dd4b680 100644 ---- a/instlib/source/Makefile.proto -+++ b/instlib/source/Makefile.proto -@@ -11,6 +11,8 @@ - - SHELL=/bin/sh - -+cns_string=`date "+%y%m%d%H%M"` -+ - # commands - RM = /bin/rm - -@@ -19,32 +21,26 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o - - # the default is to make the cns executable - cns_solve: -- @ make -k printflags F77BUG="$(debug)" DEBUG="$(debug)" -- @ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" -- @ make -k exepurge -+ @ make printflags F77BUG="$(debug)" DEBUG="$(debug)" -+ @ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" -+ @ make exepurge - - # rule for the fortran routines - $(OBJS): -- @ echo "compiling: $(@:.o=.f)"; \ -- $(F77) -c $(F77FLAGS) $(@:.o=.f) -+ $(F77) -c $(F77FLAGS) $(@:.o=.f) - - # rule for the dynamic memory allocation C routines - dmemory.o: dmemory.c -- @ echo ; echo "compiling: $?" -- @ $(CC) -c $(CCFLAGS) $? -+ $(CC) -c $(CCFLAGS) $? - - # rule for the machine specific C routines - machine_c.o: machine_c.c -- @ echo ; echo "compiling: $?" -- @ $(CC) -c $(CCFLAGS) $? -+ $(CC) -c $(CCFLAGS) $? - - # rule for the executable itself - ../bin/cns_solve: $(DEPENDS) -- @ echo ; echo "linking: cns_solve"; echo -- @ cns_string=`date "+%y%m%d%H%M"`; \ -- $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ -- $(LDFLAGS) \ -- $(CNS_FFTDIR) $(CNS_FFTLIB); \ -+ $(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ -+ $(CNS_FFTDIR) $(CNS_FFTLIB); \ - if [ -x cns_solve-$$cns_string.exe ]; \ - then echo "created executable file cns_solve-$$cns_string.exe"; \ - echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \ -diff --git a/instlib/utils/Makefile b/instlib/utils/Makefile -index 98de84f..4f32b34 100644 ---- a/instlib/utils/Makefile -+++ b/instlib/utils/Makefile -@@ -22,17 +22,17 @@ utils: - make clean - - .f: -- $(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK) -+ $(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK) - - .c: -- $(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK) -+ $(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK) - - .cpp: -- $(CPP) -o $@ $(CCFLAGS) $(@).cpp $(CCLINK) -+ $(CXX) $(LDFLAGS) -o $@ $(CXXFLAGS) $(@).cpp $(CCLINK) - - .l: - lex $(@).l -- $(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) -+ $(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) - - relink: - @ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile` diff --git a/sci-chemistry/cns/files/cns_solve_env_sh b/sci-chemistry/cns/files/cns_solve_env_sh deleted file mode 100644 index 34e1a2b635cf..000000000000 --- a/sci-chemistry/cns/files/cns_solve_env_sh +++ /dev/null @@ -1,221 +0,0 @@ -#!/bin/sh -# -# This file sets up the appropriate environmental variables and paths -# for CNSsolve. In the case of the same machines with different versions -# of the OS, backward compatibility is assumed - ie. a later version will -# be setup for a previous version of the OS if nothing else is available. -# -# written by: Paul Adams -# -# copyright Yale University -# -# ========================================================================== -# -# >>>>>> Important: define the location of the CNSsolve directory <<<<<< -# -# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY - - CNS_SOLVE=_CNSsolve_location_ - -# -# ========================================================================== -# -# full expansion of the CNS_SOLVE variable prior to use. -# -export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE -# -# ========================================================================== -# -# set the number of threads for SGI multiprocessors -# if this causes a problem on other systems it can be commented out -# -export MP_SET_NUMTHREADS; MP_SET_NUMTHREADS=1 -# -# ========================================================================== -# -# get the machine architecture -# -if [ -d $CNS_SOLVE ]; then - if [ ! "$CNS_ARCH" ]; then - export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch` - fi -else - export CNS_ARCH; CNS_ARCH='unknown' -fi -# -# system variables (this is needed for openmp) -# -ulimit -s unlimited -# ========================================================================== -# -# general environmental variables -# -export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries -export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules -export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar -export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb -export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal -export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr -export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray -export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal -export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr -export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib -# -# general user aliases -# -cns_web () { $CNS_SOLVE/bin/cns_web; } -cns_header () { $CNS_SOLVE/bin/cns_header; } -cns_info () { cat $CNS_SOLVE/bin/cns_info; } -cns_transfer () { $CNS_SOLVE/bin/cns_transfer; } -if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then - cns_edit () { $CNS_SOLVE/bin/cns_edit_local; } -else - cns_edit () { $CNS_SOLVE/bin/cns_edit; } -fi -run_tutorial () { "csh -f tutorial.csh"; } -# -# g77 compilation and use -# -g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; } -g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; } -# -# developer aliases -# -run_tests () { $CNS_SOLVE/bin/run_tests; } -run_diffs () { $CNS_SOLVE/bin/run_diffs; } -maketar () { $CNS_SOLVE/bin/maketar; } -create_patch () { $CNS_SOLVE/bin/create_patch; } -# -# -# ========================================================================== -# -# to do expansions - unset noglob just in case user has it otherwise -# -set +f -# -# try to set up appropriate path -# -# first strip off any trailing information (eg. _g77) -# -CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'` -# -cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'` -cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'` -cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'` -cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'` -cns_minor=`echo $cns_major | sed -e 's/\./ /g'` -# -# if we are looking for a specific type of setup then limit search -# -cns_dirs="" -if [ ! "$CNS_G77" ]; then - if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then - cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" - fi -else - CNS_ARCH="${CNS_ARCH}_g77" - if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then - cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" - fi -fi -# -# first look for an exact match (with os version) -# -# -cns_found=0 -if [ -n "$cns_dirs" ]; then - for cns_dir in $cns_dirs ; do - cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'` - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \ - $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - done -# -# -# now look for an exact match (without os version) -# - if [ $cns_found -eq 0 ]; then - for cns_dir in $cns_dirs ; do - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \ - $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - done - fi -# -# now look for a backwards compatible match (with os version major/minor) -# - if [ $cns_found -eq 0 ]; then - for cns_dir in $cns_dirs ; do - if [ $cns_found -eq 0 ]; then - cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'` - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then - osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'` - if [ $osv_test -eq 1 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - fi - fi - done - fi -# -# now look for a wildcard match on cpu -# - if [ $cns_found -eq 0 ]; then - cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'` - cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'` - for cns_dir in $cns_dirs ; do - if [ $cns_found -eq 0 ]; then - cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'` - cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'` - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \ - $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then - cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'` - if [ $cpu_test -eq 1 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - fi - fi - done - fi -fi -# -# if found set environment -# -if [ $cns_found -eq 1 ]; then - # - # set installation and source directory - # - export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv - export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source - # - # path for CNSsolve utility programs - # - if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then - export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils` - fi - # - # path for CNSsolve executable if installed - # - if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then - export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin` - fi -fi -# -unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor -unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same -unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test -# diff --git a/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 b/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 deleted file mode 100644 index 12368f87b596..000000000000 --- a/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 +++ /dev/null @@ -1,229 +0,0 @@ -#!/bin/sh -# -# This file sets up the appropriate environmental variables and paths -# for CNSsolve. In the case of the same machines with different versions -# of the OS, backward compatibility is assumed - ie. a later version will -# be setup for a previous version of the OS if nothing else is available. -# -# written by: Paul Adams -# -# copyright Yale University -# -# ========================================================================== -# -# >>>>>> Important: define the location of the CNSsolve directory <<<<<< -# -# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY - - CNS_SOLVE=_CNSsolve_location_ - -# -# ========================================================================== -# -# full expansion of the CNS_SOLVE variable prior to use. -# -export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE -# -# ========================================================================== -# -# get the machine architecture -# -if [ -d $CNS_SOLVE ]; then - if [ ! "$CNS_ARCH" ]; then - export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch` - fi -else - export CNS_ARCH; CNS_ARCH='unknown' -fi -# -# ========================================================================== -# -# system variables for OpenMP -# -# The default stack sizes are usually insufficient, especially when -# CNS is compiled using OpenMP. If the stack sizes are too -# small segfaults may occur. Recommended setting for "stacksize": -limit stacksize unlimited -# -# KMP_STACKSIZE is specific for Intel ifort, icc: -##setenv KMP_STACKSIZE 256m -# -# OMP_STACKSIZE is used by all compilers: -setenv OMP_STACKSIZE 256m -# -# Uncomment the following line and change as appropriate to set the number -# of processors (threads) to use. -###setenv OMP_NUM_THREADS 4 -# -# ========================================================================== -# -# general environmental variables -# -export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries -export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules -export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar -export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb -export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal -export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr -export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray -export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal -export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr -export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib -# -# general user aliases -# -cns_web () { $CNS_SOLVE/bin/cns_web; } -cns_header () { $CNS_SOLVE/bin/cns_header; } -cns_info () { cat $CNS_SOLVE/bin/cns_info; } -cns_transfer () { $CNS_SOLVE/bin/cns_transfer; } -if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then - cns_edit () { $CNS_SOLVE/bin/cns_edit_local; } -else - cns_edit () { $CNS_SOLVE/bin/cns_edit; } -fi -# -# g77 compilation and use -# -g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; } -g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; } -# -# developer aliases -# -run_tests () { $CNS_SOLVE/bin/run_tests; } -run_diffs () { $CNS_SOLVE/bin/run_diffs; } -maketar () { $CNS_SOLVE/bin/maketar; } -create_patch () { $CNS_SOLVE/bin/create_patch; } -# -# -# ========================================================================== -# -# to do expansions - unset noglob just in case user has it otherwise -# -set +f -# -# try to set up appropriate path -# -# first strip off any trailing information (eg. _g77) -# -CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'` -# -cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'` -cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'` -cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'` -cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'` -cns_minor=`echo $cns_major | sed -e 's/\./ /g'` -# -# if we are looking for a specific type of setup then limit search -# -cns_dirs="" -if [ ! "$CNS_G77" ]; then - if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then - cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" - fi -else - CNS_ARCH="${CNS_ARCH}_g77" - if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then - cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" - fi -fi -# -# first look for an exact match (with os version) -# -# -cns_found=0 -if [ -n "$cns_dirs" ]; then - for cns_dir in $cns_dirs ; do - cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'` - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \ - $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - done -# -# -# now look for an exact match (without os version) -# - if [ $cns_found -eq 0 ]; then - for cns_dir in $cns_dirs ; do - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \ - $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - done - fi -# -# now look for a backwards compatible match (with os version major/minor) -# - if [ $cns_found -eq 0 ]; then - for cns_dir in $cns_dirs ; do - if [ $cns_found -eq 0 ]; then - cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'` - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then - osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'` - if [ $osv_test -eq 1 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - fi - fi - done - fi -# -# now look for a wildcard match on cpu -# - if [ $cns_found -eq 0 ]; then - cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'` - cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'` - for cns_dir in $cns_dirs ; do - if [ $cns_found -eq 0 ]; then - cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'` - cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'` - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \ - $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then - cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'` - if [ $cpu_test -eq 1 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - fi - fi - done - fi -fi -# -# if found set environment -# -if [ $cns_found -eq 1 ]; then - # - # set installation and source directory - # - export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv - export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source - # - # path for CNSsolve utility programs - # - if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then - export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils` - fi - # - # path for CNSsolve executable if installed - # - if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then - export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin` - fi -fi -# -unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor -unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same -unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test -# diff --git a/sci-chemistry/cns/metadata.xml b/sci-chemistry/cns/metadata.xml deleted file mode 100644 index 67326b6bd798..000000000000 --- a/sci-chemistry/cns/metadata.xml +++ /dev/null @@ -1,21 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://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="aria"> Support patch for sci-chemistry/aria</flag> - </use> - <longdescription> -Crystallography and NMR System (CNS) is the result of an international -collaborative effort among several research groups. The program has -been designed to provide a flexible multi-level hierachical approach for the -most commonly used algorithms in macromolecular structure determination. -Highlights include heavy atom searching, experimental phasing (including -MAD and MIR), density modification, crystallographic refinement with maximum -likelihood targets, and NMR structure calculation using NOEs, J-coupling, -chemical shift, and dipolar coupling data. -</longdescription> -</pkgmetadata> diff --git a/sci-chemistry/ksdssp/Manifest b/sci-chemistry/ksdssp/Manifest index 8691e1e8a7c1..29e85fc38b85 100644 --- a/sci-chemistry/ksdssp/Manifest +++ b/sci-chemistry/ksdssp/Manifest @@ -1,4 +1,3 @@ DIST ksdssp-040728.shar 104347 BLAKE2B f77ba1fd83e9dd959dabf49818c541605eb8fba895880dbd8324cd02a0528d7961ced200de4b64c18c897a18e9f78474293a9f95fee9beace36f5faba61fcaa2 SHA512 17c32bea1f32acfd31353d0378fe2a664a8922db8b929da4b9b10ac279013946911acd2a26ab3ab227ae160352c8313dcf742fae8c139a90ac11f772f17a1689 EBUILD ksdssp-040728-r1.ebuild 916 BLAKE2B 7d2461015ee5646fc30b2ce61f52c63b01340b32a8b79e70eff1c3762cf7e82967063abee0b12195e4ff2db6afd4f13b501faec4116a464de10fb63e376e0318 SHA512 90eeb66be6665ca20bbe2dfdf1515d4ff44480dba23c47511501750749f903c2a1f80394e7c026b0ed99f4e545dcf3d70c64bcf8f21b49d945ed6e99878b5d30 -EBUILD ksdssp-040728.ebuild 859 BLAKE2B ee6ce02895ff0dc3d6880d6dce5d92002f413fa1ac9d42096d27fd2339b50c80f18d34133aa52308e165c786af6a4ad024da1c9ad8d89c8a3168847eed626faf SHA512 9c75d28ec520923f51d9b985d4de7f99a65496797bd897d837e9d6a2abc92fa73e90832451f0c5ee198c6d0bccb2ad79b9189e93dab8efdd40070c2555c325a2 MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a diff --git a/sci-chemistry/ksdssp/ksdssp-040728.ebuild b/sci-chemistry/ksdssp/ksdssp-040728.ebuild deleted file mode 100644 index 9dcb38c517d6..000000000000 --- a/sci-chemistry/ksdssp/ksdssp-040728.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=4 - -inherit toolchain-funcs - -DESCRIPTION="ksdssp is an open source implementation of dssp" -HOMEPAGE="http://www.cgl.ucsf.edu/Overview/software.html" -SRC_URI="mirror://gentoo/${P}.shar" - -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -LICENSE="BSD" -IUSE="" - -RDEPEND="sci-libs/libpdb++" -DEPEND=" - ${RDEPEND} - app-arch/sharutils" - -S="${WORKDIR}"/${PN} - -src_unpack() { - "${EPREFIX}"/usr/bin/unshar "${DISTDIR}"/${A} -} - -src_compile() { - emake \ - CXX="$(tc-getCXX)" \ - PDBINCDIR="${EPREFIX}/usr/include/libpdb++" \ - BINDIR="${EPREFIX}/usr/bin" \ - .TARGET="${PN}.csh" \ - .CURDIR="${S}" \ - CC="$(tc-getCXX)" \ - LINKER="$(tc-getCXX)" \ - OPT="${CXXFLAGS}" \ - LFLAGS="${LDFLAGS}" \ - ${PN} ${PN}.csh -} - -src_install() { - dobin ${PN}{,.csh} -} diff --git a/sci-chemistry/mdtraj/Manifest b/sci-chemistry/mdtraj/Manifest index d4b7e143cac0..ed5b2ebbe93c 100644 --- a/sci-chemistry/mdtraj/Manifest +++ b/sci-chemistry/mdtraj/Manifest @@ -1,3 +1,3 @@ DIST mdtraj-1.9.1.tar.gz 1985711 BLAKE2B 625b7c1da998bd46732604dcc93c76f970f3c79f10e81aa9f4b3051ee45101efea8afd803d539ba1831dac3e7ed208d7c3773f74189a3887063cbff2b4d79df6 SHA512 015d9d1e258a7a207ac3b7e7a81b87c308e8684ee0a173ae9b722a90910e95e7f2ee18158c163212fae39d093b0cf397293d6e713538acb1fd20a7b70f2adc76 -EBUILD mdtraj-1.9.1.ebuild 889 BLAKE2B fd2423ca08f4666101c409c52be19c717d222c19da08424c2923e91bb9ad6961c64b3fb97a6b71e1d5a9a9cd568f0325510943c388c35c59049f4597ce0cca02 SHA512 61c0a2351c18155aec9bf5fcd6a3f7b2e319c096f493866f94789b11bfbef4a6bbfe849a111acad74503bb30d327c10e15b34338f752763f77e3033b2e287680 +EBUILD mdtraj-1.9.1.ebuild 913 BLAKE2B 219e598b0f693590a70c7221fb247587d17eb0214838e45517a099fcbcd936d342735a02da84ca81c74c6ab11ece7fe31cfc74d5610e728d79437867a2d12f9a SHA512 e169ea7efef0a9531657ee793a1bba5e020f3d5d013b8ffed5e6198d2057d98e0961fc734edfefe0b9592d60d22fd6d67c631c071073ce75d1359ea5dbfd774e MISC metadata.xml 259 BLAKE2B dfc879984b6adce945d0e0a50f6ede2bca87147b9db99491359cdeccc2e74a20d56e14ae8903dbb80c94854f89bee539f14a4e3ce864204e277accf3f124a748 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706 diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild index 2ac95db2c57d..889d5e8e0b26 100644 --- a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild +++ b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -15,6 +15,7 @@ SLOT="0" LICENSE="GPL-2" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="test" +RESTRICT="!test? 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857f3276e45d05f92f291b0189cdcb7aeacd9ede0eeaf1ebe6b6942d397bbdd83812b4a5c8163be75a5a3c7bd0b29c9304d29ae596e04ba9bfbb30960e899326 SHA512 bf45849bf4efb67bc552767c28a6df6e5106a7d8ac2d73db2c7218412fb6cd2f2785c2be83a8589a5664ba9c0ca052cef5eb155c665ee1f3d6c7fe208f806a6b DIST molden5.5.tar.gz 4934764 BLAKE2B 6ce71f928ed9aacf8fe9830c4c36a675f81d63e97d08e96519ff74d172540ae0a9af25ca966d6c02cdcbbc43633a0ef80be9d31ef98a80d59a8e1a13374c2f51 SHA512 45269d2c7a52b3b2bf4fdb5f4ca3912637b3414ff9dfcd0d4f23815b3dcf7a53ffee717420d4fbf286b71c972539e756a440f5e37b7b7325ab312c25fc6c47b0 -EBUILD molden-4.8-r2.ebuild 1726 BLAKE2B ed9494e53f93b3de114e1032c88658628efe0e30af1b8670a32b090f7b6bd720c9a0795a4a4e5ba1fc7d6f50439b8f6b85e671854e1ae79e18d952356dce0483 SHA512 ca0772ada2086f91150f8a0ab2a86c9a9a6169a89e2c8c0f6b4ab4d368906f5d5d2807cd228e1f42292c6562d980a0e206f568433b396d23c7846beb65dd6f5a -EBUILD molden-5.0.ebuild 1733 BLAKE2B 2d5e3657c53ae6f7ca67996d63ec98776d1de5330ae050b8d8191289d6800298bdccc1361b57df4573f2e99d2688edc09234a72b2c29431e482406c37bcf213e SHA512 0584ad6f157bab063a79b8e095dedec04e6a2f1d05d5483027dc8c7b0b8455956140ae69f9d6749b47ce69db30d62d391e9f7a7e00dba696d73687861d6bd604 EBUILD molden-5.5.ebuild 1639 BLAKE2B 7f3b42046e10a433442cc664c6552c9f74ca5bc142da2bc5fe813cc7deb78d4cb1e9231c0554b0ec3d500f72c6104595c053555f66c28e982394fc973bda8455 SHA512 185d8c4004d0023b3663f13b793fb99a6f17573c1dfdc87602b97f0735cb4a52f4c9f7f833f01ccbf837f311ded87f61418c16d918955a67c9c962d149f3d054 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/molden/files/molden-4.8-ambfor.patch b/sci-chemistry/molden/files/molden-4.8-ambfor.patch deleted file mode 100644 index 1ececa7f57e9..000000000000 --- a/sci-chemistry/molden/files/molden-4.8-ambfor.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naur molden4.8/ambfor/makefile molden4.8.new/ambfor/makefile ---- molden4.8/ambfor/makefile 2009-12-19 06:14:32.000000000 -0500 -+++ molden4.8.new/ambfor/makefile 2010-02-25 22:33:41.000000000 -0500 -@@ -32,7 +32,7 @@ - $(LDR) -o ambmd md.o verlet.o allocmd.o $(OBJS) $(LIBS) - - ambfor.o: ambfor.f -- ${FC} -c -g -ffast-math -funroll-loops -m32 -o ambfor.o ambfor.f -+ ${FC} $(FFLAGS) -c ambfor.f -o ambfor.o - - allocmd.o: alloc.c - $(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o diff --git a/sci-chemistry/molden/files/molden-4.8-overflow.patch b/sci-chemistry/molden/files/molden-4.8-overflow.patch deleted file mode 100644 index 7cbd7f436f57..000000000000 --- a/sci-chemistry/molden/files/molden-4.8-overflow.patch +++ /dev/null @@ -1,38 +0,0 @@ - xwin.c | 10 ++++++---- - 1 files changed, 6 insertions(+), 4 deletions(-) - -diff --git a/xwin.c b/xwin.c -index f395909..092edff 100644 ---- a/xwin.c -+++ b/xwin.c -@@ -13552,7 +13552,7 @@ void NewActiveStruct() - #ifdef CRAY - _fcd ztr; - #else -- char ztr; -+ char ztr[4]; - #endif - #endif - -@@ -13650,8 +13650,10 @@ void NewActiveStruct() - */ - clfpstr->ihashz = 0; - #else -- strncpy(&ztr,HetAtm[j],3); -- parhet_(&j1,&ztr); -+ if (HetAtm[j] != NULL) { -+ strncpy(ztr,HetAtm[j],3); -+ parhet_(&j1,ztr); -+ } - #endif - #endif - } -@@ -27353,7 +27355,7 @@ char *errstr; - UpdateZME(); - RedrawScroll(&zscroll); - } -- strcpy(ZMEerr,errstr); -+ strncpy(ZMEerr,errstr,MAXZMEERR); - RedrawStatus(); - } - diff --git a/sci-chemistry/molden/molden-4.8-r2.ebuild b/sci-chemistry/molden/molden-4.8-r2.ebuild deleted file mode 100644 index f00761130395..000000000000 --- a/sci-chemistry/molden/molden-4.8-r2.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=4 - -inherit eutils fortran-2 flag-o-matic toolchain-funcs - -MY_P="${PN}${PV}" - -DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac" -HOMEPAGE="http://www.cmbi.ru.nl/molden/" -SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molgraph/${PN}/${MY_P}.tar.gz" - -LICENSE="MOLDEN" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="opengl" - -RDEPEND=" - x11-libs/libXmu - virtual/glu - opengl? ( - media-libs/freeglut - virtual/opengl )" -DEPEND="${RDEPEND} - x11-misc/gccmakedep - app-editors/vim" - # vim provides ex, which the build system uses (surf/Makefile, at least) - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-ambfor.patch \ - "${FILESDIR}"/${P}-overflow.patch \ - "${FILESDIR}"/${P}-ldflags.patch \ - "${FILESDIR}"/${PN}-4.7-implicit-dec.patch - sed \ - -e 's:makedepend:gccmakedep:g' \ - -e "s:/usr/include/sgidefs.h::g" \ - -i surf/Makefile || die - sed 's:shell g77:shell $(FC):g' -i makefile || die -} - -src_compile() { - # Use -mieee on alpha, according to the Makefile - use alpha && append-flags -mieee - - # Honor CC, CFLAGS, FC, and FFLAGS from environment; - # unfortunately a bash bug prevents us from doing typeset and - # assignment on the same line. - typeset -a args - args=( - CC="$(tc-getCC) ${CFLAGS}" \ - FC="$(tc-getFC)" \ - LDR="$(tc-getFC)" \ - FFLAGS="${FFLAGS}" ) - - einfo "Building Molden..." - emake -j1 "${args[@]}" - if use opengl ; then - einfo "Building Molden OpenGL helper..." - emake -j1 "${args[@]}" moldenogl - fi -} - -src_install() { - dobin ${PN} g${PN} - if use opengl ; then - dobin ${PN}ogl - fi - - dodoc HISTORY README REGISTER - cd doc - uncompress * && dodoc * -} diff --git a/sci-chemistry/molden/molden-5.0.ebuild b/sci-chemistry/molden/molden-5.0.ebuild deleted file mode 100644 index 52f4ccdcfed0..000000000000 --- a/sci-chemistry/molden/molden-5.0.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=4 - -inherit eutils fortran-2 flag-o-matic toolchain-funcs - -MY_P="${PN}${PV}" - -DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac" -HOMEPAGE="http://www.cmbi.ru.nl/molden/" -SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molgraph/${PN}/${MY_P}.tar.gz" - -LICENSE="MOLDEN" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="opengl" - -RDEPEND=" - x11-libs/libXmu - virtual/glu - opengl? ( - media-libs/freeglut - virtual/opengl )" -DEPEND="${RDEPEND} - x11-misc/gccmakedep - app-editors/vim" - # vim provides ex, which the build system uses (surf/Makefile, at least) - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-ambfor.patch \ - "${FILESDIR}"/${P}-overflow.patch \ - "${FILESDIR}"/${PN}-4.8-ldflags.patch \ - "${FILESDIR}"/${PN}-4.7-implicit-dec.patch - sed \ - -e 's:makedepend:gccmakedep:g' \ - -e "s:/usr/include/sgidefs.h::g" \ - -i surf/Makefile || die - sed 's:shell g77:shell $(FC):g' -i makefile || die -} - -src_compile() { - # Use -mieee on alpha, according to the Makefile - use alpha && append-flags -mieee - - # Honor CC, CFLAGS, FC, and FFLAGS from environment; - # unfortunately a bash bug prevents us from doing typeset and - # assignment on the same line. - typeset -a args - args=( - CC="$(tc-getCC) ${CFLAGS}" \ - FC="$(tc-getFC)" \ - LDR="$(tc-getFC)" \ - FFLAGS="${FFLAGS}" ) - - einfo "Building Molden..." - emake -j1 "${args[@]}" - if use opengl ; then - einfo "Building Molden OpenGL helper..." - emake -j1 "${args[@]}" moldenogl - fi -} - -src_install() { - dobin ${PN} g${PN} - if use opengl ; then - dobin ${PN}ogl - fi - - dodoc HISTORY README REGISTER - cd doc - uncompress * && dodoc * -} diff --git a/sci-chemistry/moldy/Manifest b/sci-chemistry/moldy/Manifest index 473739395db5..6ab473c01cc1 100644 --- a/sci-chemistry/moldy/Manifest +++ b/sci-chemistry/moldy/Manifest @@ -1,4 +1,4 @@ AUX 2.16e-as-needed.patch 3226 BLAKE2B 777b34d43da82b036e401c398d0f59a5f268905a399f38277be73ba6bdaefd6f1de2ec748302edfc68c6389acb22fa50d72b465522b1f2d5bbd14eca289d7595 SHA512 b32461bb052c908106f0f8d74be4eba52daa41ba592a7ba6083edc2a54c4a14003cf33560572e57f2b370ad5ea1f703e388855e8e7fa67ccec40e3015a8f5803 DIST moldy-2.16e.tar.gz 488410 BLAKE2B 44ff1dacc66922ba11297ca54c645f209b782b8cde50e427d54d1d249a93b718eeb865357ea47b820801fdbca325d5f0d6027fe11ce6e0a842e77d1970a0467c SHA512 b672f4e5c8843277d1b66eedf5f7ad87be0b4c014e0d6bfda4ef941cd9bfeec68d94a361e28531cc3794ee2e4a6937f15c462c69f9adcfcfe5254c3c677fe877 -EBUILD moldy-2.16e-r2.ebuild 1811 BLAKE2B 1e03c508b0a5376efd64559517798bff39339e3815cb65bea7cbe7d72e622d40f49760a6872846e369fe0ef07a7e4040b5fcfceab26278c1b52f13bd8fad15aa SHA512 6f6280a30cef11539d27b6efa5326f3ca5b365e179dbc3f3e2b5b237b92e66786f4969ebd7ff1d67b3e3f53f2c52a3bc46ccb5ba45078db17e7d325c4640fff0 +EBUILD moldy-2.16e-r2.ebuild 1804 BLAKE2B 3c4865ada8baec131c5bb92e6856e3526a4aea05cb754423bf7cb896992c6e2732ad42b31808059c602549de7fd5054de780cfbe85218056c975f7c4c5fbda90 SHA512 5b8b76efa8f2132b50abd4ce3f0a137a8ed433c4e88b5b60df7043df00d5c78696c08dcfaade590842625429fa67656fa2d4537b158bedfb54da1eb79224bdcf MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a diff --git a/sci-chemistry/moldy/moldy-2.16e-r2.ebuild b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild index 8ba71f621898..0d3399860306 100644 --- a/sci-chemistry/moldy/moldy-2.16e-r2.ebuild +++ b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild @@ -61,7 +61,7 @@ src_install() { if use examples; then rm Makefile.in configure.in config.h.in insinto /usr/share/${PN}/examples/ - doins *.in *.out control.* || die + doins *.in *.out control.* fi if use doc; then insinto /usr/share/doc/${PF}/pdf diff --git a/sci-chemistry/molequeue/Manifest b/sci-chemistry/molequeue/Manifest index d70775668870..9b7a014b2025 100644 --- a/sci-chemistry/molequeue/Manifest +++ b/sci-chemistry/molequeue/Manifest @@ -1,4 +1,4 @@ AUX molequeue-0.9.0-qt-5.11b3.patch 6380 BLAKE2B 8d4a66dab1b233880269559cff9b566593ec271fc2b0982a92eec1d60a7c2c42e7186c0007be2afc956200d28c250822b36d3146d1a9ff1fb33b574f97969c60 SHA512 09429566422a1490c2621fd895238d4aeba3c324563cab411290a60942c749e9fa967dd6399f4f4efdc635fa77c339d08824def3e6a175aadc1061893df7df9c DIST molequeue-0.9.0.tar.gz 604015 BLAKE2B 37e7f404a0fefb40defb198295659372121fbe770269c2f9fb92e856aceb8222bec5e83939ecea061b76f925c0cbde1be0a854db41f992a92a2b2b9e0651f2e1 SHA512 87ddd8ca59227cab60c0ce2643e5bd435d9ac7e23b929659b95f190478734a5b71d4935f37d03eeadbc39939cbffb3604e0a283d50b0a23a1a000b57c1fce335 -EBUILD molequeue-0.9.0.ebuild 1479 BLAKE2B f00bb04fa08a720367daa464399daa71f47c4fe34263dc699811cc9ea0683a065d06a30e8be9d0ccd46071329829cae739a8c3fa5773998c1c3b8fb6d53653a1 SHA512 a6a5643849c85231652e9d1ff1c93e599a539eca0cc5572bab8ae9b837cc2f6ad8f5c04d96774493187f3f3cb216f163e7990a9d62abb60caefcde9ad610aedb +EBUILD molequeue-0.9.0.ebuild 1506 BLAKE2B e1e8a1a55cbe1da01199049ff97ca9e1950c5eb258a07e65e3d8e9eb3f5260e809c96a0abc96d1986f1fd822abc94a8a561538d8560195b8237284556e888edd SHA512 9fc628c00e53d86a4a0c9fc94bc4fc9f30375adb1ab9b89b64369770fb464544b2d49c2a8b62029f1319794d1dffcde0fdff4b6b99a3788ac5bb6d5f7792be12 MISC metadata.xml 1257 BLAKE2B 181f9234f11d0cb14fd6b93b42ef153c089d4df8dcb7cf72bc710dbee11bf4bb573f37ea703d02dbe17fa1f39c0aaf591c6d28ad1429abced5108b9ce39f2030 SHA512 10e3dd48ec1e54bc0d47d4c2f0aca427875cc0ceb59a93ab41ab2734607aa6474e80f3ae622e45fa319753591f16439118dd0b301068cb3e16fd79ff11a4f058 diff --git a/sci-chemistry/molequeue/molequeue-0.9.0.ebuild b/sci-chemistry/molequeue/molequeue-0.9.0.ebuild index 71e253b4283a..0a2c4acc3e53 100644 --- a/sci-chemistry/molequeue/molequeue-0.9.0.ebuild +++ b/sci-chemistry/molequeue/molequeue-0.9.0.ebuild @@ -15,6 +15,7 @@ SLOT="0" LICENSE="BSD" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="+client doc server test +zeromq" +RESTRICT="!test? ( test )" REQUIRED_USE="${PYTHON_REQUIRED_USE} server? ( client ) diff --git a/sci-chemistry/molsketch/Manifest b/sci-chemistry/molsketch/Manifest index be99a3ca0878..c7a1874bb71c 100644 --- a/sci-chemistry/molsketch/Manifest +++ b/sci-chemistry/molsketch/Manifest @@ -1,5 +1,5 @@ AUX molsketch-0.3.0-_DEFAULT_SOURCE.patch 661 BLAKE2B 48e877f41de2b27d1c6bbdac34d68893b58bf22e3d2ca8fa3e777f950f6906b100471b0a1287205e65bb5e97e9b3bd40b64377f513750ec039ebffdddbd0ea22 SHA512 9fd409ca55d5df0c61e84d3d9941f4855b7dcd32fd7521f24204570858dc6205c70ca4c645c5eee31bdc446a315e02081fa947677a4f22addce16ec4dad64c10 AUX molsketch-0.4.1-more-quotes.patch 478 BLAKE2B 857f6a6f2514a4322f2a178aed0232f6f18d06831fea72ac8bbfa2cb806cdb2f73f2daeb4e9b8326be9dbd96518047c24f2721c3509d1551d90cfa80ca0105a8 SHA512 015344abb4aaa7f214e4e8a7eebe1a7a8f4d43b8a76a9c5f984fc4c5cf8da450430330543fe69d481ceec25c5a59ee332439654fd4ce82ce080aa4883cc1d113 DIST Molsketch-0.4.1-src.tar.gz 1499842 BLAKE2B 22584f012e838037f9e23c16da6c63984604002884d279b2b6012d80eb08af9ee18b4d364fa29327572854fccad34840f97413b29b487cfbeb6496a2a8003d17 SHA512 263b088c2b8d01c1f13802b18aea6f6784580fe1a806de45b0e1ecd9f29024350e01a611bdeed1891938acc733a42746203d345d3be13ebaf4c309413e86bf26 -EBUILD molsketch-0.4.1-r1.ebuild 1359 BLAKE2B 2c455402f624b9fadf848b8e4f9ecbcf0d89f453f284bd907a55ef2118f6099af46d907216bf40319f5fece28b3d00c294286cdf82137f0a807299b707e05e50 SHA512 e1ecf0c0a0412cee651839204cd80039216a81bbd28cd37c23197a8270ce97e26b2df644b4b9144f139d7b8243b3437a2f13301c184152ad89fcf9778d6eaf82 +EBUILD molsketch-0.4.1-r1.ebuild 1383 BLAKE2B 58fa01d7f55eaf1394e2f44738b20395c9ca979076bf6ff32ae8db524f8d1d0b30e2da2a019e92d29de61e95d4077bc2aff47d8aa21b022fc20deeaab8ef3f86 SHA512 f41c9caa896b44939521a5badcf584de071bfd64c05524b8b1d7a9333a1579c83847a3f0151cd7c16cd213bf1739ac40a760638b92faac18e22d6d7d27e76256 MISC metadata.xml 609 BLAKE2B 07b5bc6ee3fbbbd071bac3959e4f42a6d38cb6dff2ca6e86f9d6e0108c9f3370dc1a99ea5b4a26b58769d45d064e85e9c0c5c6cacf980b68def32e7c63b1cf54 SHA512 34417299d583ff8a830dbe5e4898e999c3a4d72f11cc032f1274e12ad9dfb424d7d8eaaa2e5dac8efb748d7da68691e4ea1b4b1a426407b8dadc740ba109d61c diff --git a/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild b/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild index c34e60a0106c..87dc43370de6 100644 --- a/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild +++ b/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -17,6 +17,7 @@ LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="test" +RESTRICT="!test? ( test )" DEPEND=" >=sci-chemistry/openbabel-2.2 diff --git a/sci-chemistry/nmrglue/Manifest b/sci-chemistry/nmrglue/Manifest index c9c16933c73c..6b1e2c080a55 100644 --- a/sci-chemistry/nmrglue/Manifest +++ b/sci-chemistry/nmrglue/Manifest @@ -1,4 +1,4 @@ AUX nmrglue-0.5-nohyper.patch 1408 BLAKE2B 8e91e270183ce8f4c361fd3577dc4942b2afab81ee8f59df5c8dd9056dbf639653d2e84f9dc04026636dda98e28a244586ba5bc2cd4ed5c43c8a31d0c0cab4d1 SHA512 f68ea345f2692123e24fc41335001a0a8418b84003d864e9d673935d4a517aa82353e08f4f554b33ddc18cea96c9442827715cdabad6303dc60f5dd18cd103dd DIST nmrglue-0.5.tar.gz 142604 BLAKE2B 9a018a73bea46176fc06042013cb23b3eeb962df8a595388da536d17f1d2d4d550065c5492df28de860ea1290314d2fa1110af349be0c2a8b1b31677b3e4afbc SHA512 2a4b94eb6bae966000bfdee4dd16f4e312568915fb5f19f59f84c6deff690703f54f76366d3f9299f7ec187192ff64f2bf62836617a424d4c5c895c67d819af2 -EBUILD nmrglue-0.5-r1.ebuild 726 BLAKE2B f67232037b0cc6e96837387790d96a530aac385decb8f53317f4ea28221e798c6f1e61cce20e4665df92826291f3e730d8aac1c819fba562c77c6b6b13e6d7b4 SHA512 a896e0d38e5772ec35ec9da9ef198cde44b1b88adfb58d3df1229b3e04bff8e066a330549d852e0abbcd05163dd8f61c42953550ccd6368d72cc30b59b98f976 +EBUILD nmrglue-0.5-r1.ebuild 753 BLAKE2B 37b2d1f011c7cf4f44fbf4468154384173d40310c519b9a10c49cd684291c912add9abc9ea1b19254302a520a1dc3b204b80ad23056f78bc59d0f993c99fe3a4 SHA512 6242503f01772bf425bd6665b51f2a00288f1c352ac7b9f1ecc154a9c5ed99e19c58ddf09dd4e0a9cf9f5991fcdbe208b06300290c968ebd2d16f2894487562d MISC metadata.xml 1338 BLAKE2B 480651ef6112e93e3c70e734f4ca7d7b24653109f503fab6a340c9dc246b881b5ab103b90f8ffbc92a6d5352b399c15a33072292e549b4ffcc2689f049996cfd SHA512 7defa016b2c5f51327f282ef8dbb5f99767e554112baf10d72a6c86462d86bf7bd3129226340bbdb00f9e95b2349fc3594b6d0d8cd0175457bbb5f034e31aa7c diff --git a/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild index 939e9307cc50..97ddc5611088 100644 --- a/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild +++ b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild @@ -15,6 +15,7 @@ SLOT="0" LICENSE="BSD" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="test" +RESTRICT="!test? ( test )" RDEPEND=" dev-python/matplotlib[${PYTHON_USEDEP}] diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest index f7fb369c0129..2681ad9f8d71 100644 --- a/sci-chemistry/openbabel/Manifest +++ b/sci-chemistry/openbabel/Manifest @@ -2,6 +2,6 @@ AUX openbabel-2.3.2-gcc-6_and_7-backport.patch 635 BLAKE2B 4e98dedd149b14d5bb02f AUX openbabel-2.4.1-gcc-8.patch 706 BLAKE2B 085b2f5a1678c02a6a8efc5f760dc43ef311774a47d80c87efb75111ac750ec6bf520286fa74325eca71138eecff4b2772ab087d4de1b9b9a5f1c81806d6be87 SHA512 04884d47a9549d2c107bbeb9c36edbe18ee68a7edd447fce405f39a4297bdacf3f81ddf4c5c19e9728355f07960b836e684087573b3a2b7892225de8b7beaea1 DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6 DIST openbabel.png 29060 BLAKE2B 8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3 SHA512 bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70 -EBUILD openbabel-2.4.1-r1.ebuild 2181 BLAKE2B dab9ccf7576cc1b24eb6d7566f487b4f6d6711797cb6b15800d120f2226d3fa19977908bcae3535177fb7f938365673518266bae2f3eb4eb0cbc48c6850af7d0 SHA512 4d0783e28d81d0c8f61dcf9f4d8f8acc835de48d3d7299d555ef939bd447d120c722aab97efd1981e0148485e80956632119eeb07ca6d67328a9435ce81b86ac -EBUILD openbabel-2.4.1.ebuild 2013 BLAKE2B b7fe713786600ac7efc9b4541663b8049c0145863cd6efc397dbed8a858cb006746e8ae6ddb4b9148023d5bf3a7f1cca76a4327577a5f9809c8e17d5a4f78945 SHA512 2eddc590968cb39a8c87563eb724669742b795bbf1861d85d9892e87fa9137b989f36ba435f98fe1b8151a142aa73a73df49ab5ef5ad1617e2d3875ad655ee1e +EBUILD openbabel-2.4.1-r1.ebuild 2208 BLAKE2B 388a26c0e190f24a10081eaa0fb901fab153b05fe67cd82734a75265cdb9f18877f58ae5db0f9d0cf8b8ee0158ef967ee5eb2079245ea3b9becf41d5118439dd SHA512 e6dbdbaea505c769e6e639b8135c6da460a2918f02f72c817263425ff9618583642324a9aef3226713e20a3c500a6963b56602a289620581519c41f023822dac +EBUILD openbabel-2.4.1.ebuild 2037 BLAKE2B 8004d9f684cb960e9dfc933a97b9f2c5d7219323d6e2368086cc02d878d7b26dc444e335a532a02e8a3c7dd2b68f4ffaa3b15e2cfc74482fae06d5af594c3ec7 SHA512 126480882f9af4a12981609c7897da380cb89479b4df7e69ef4e1d6456f1eda1e4842243f23f0829fa17ed6103b9dbf7012f95e290dffb332d62f378bc4af0ca MISC metadata.xml 665 BLAKE2B 4657b85c826c006b6d69e06240dd908a72397a32cb0c0512810e22d1b02478eaa3ab460535b300eba653a334a79c81a102007da1a901d6d1dbd04fc5e795df73 SHA512 0555e7c7401dfd5fbeee339302f8eb7a104ad6538db2839d8e89c20ac5ad2184070335677671a58eb91be2780ae485467d33302f3a14d0caab4ae8c0148f03bb diff --git a/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild index 0834c411ef29..2d53613d1d29 100644 --- a/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild +++ b/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild @@ -18,6 +18,7 @@ SLOT="0/5.0.0" LICENSE="GPL-2" KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos" IUSE="doc openmp test wxwidgets" +RESTRICT="!test? ( test )" RDEPEND=" dev-cpp/eigen:3 diff --git a/sci-chemistry/openbabel/openbabel-2.4.1.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild index 4606746af57d..b76a75d78d9b 100644 --- a/sci-chemistry/openbabel/openbabel-2.4.1.ebuild +++ b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -16,6 +16,7 @@ SLOT="0/5.0.0" LICENSE="GPL-2" KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~ppc-macos" IUSE="doc openmp test wxwidgets" +RESTRICT="!test? ( test )" RDEPEND=" dev-cpp/eigen:3 diff --git a/sci-chemistry/p3d/Manifest b/sci-chemistry/p3d/Manifest index a9db6f559b15..8edb957e6d33 100644 --- a/sci-chemistry/p3d/Manifest +++ b/sci-chemistry/p3d/Manifest @@ -1,4 +1,4 @@ DIST p3d-0.4.3.tar.gz 7213577 BLAKE2B b614957be16ede7567bd6412d183b3cb79638a5033672afd725cafaf393e306d5d227e1bca444ea17d60a3cd3bb5d3b2c910f2bfc68a118d3bffcd29944b4c29 SHA512 b4cf472b849ece96fe0b2b7f633c496fe3d12bf8cb82a2af10180ce5c27c5465dd0c16cb912d22c56c933b68c06e7de28c0c640da29eaa6bc6f95009bf10277f EBUILD p3d-0.4.3-r1.ebuild 649 BLAKE2B 9d2730c029ad4a75ed58af5cec21bc050e482064e915c2da565cc5c0035d562ba38b121f43731a28a42d49dfc81fd43b0996698d2e457d16da2872d9cd01b6cd SHA512 e979d59ce970454ef0f8de72bb616b658b489c657bcc3077c2002b6389d00ff4515128da8f549eee5c2ed345d3e229f36de8ff5002e3a21ee5c744d63042295a -EBUILD p3d-9999.ebuild 528 BLAKE2B 529e0bd09acbb397f643eb1a9b091ebabf8121d5404f530a93c001dc5ea233727780fa626867fc857c3524802ce403e469ed3a9e8ec4bb9f862672c5dc140e43 SHA512 e8cdafe07f73c5b2b1f5573270214abf574d349f922f4514b3f00e00e09ecca731d35d1fe10ec7ee05ea95cc8154e26b876b031b68dcff2470acb810ae46ce07 +EBUILD p3d-9999.ebuild 521 BLAKE2B 4d493463768caa477059286c3d14584d5ba779e7b88dd98125db6e96c0ef658cc3ca4aeae67103f9366a80e055dcfdfed1764d1281777b3e2922916c30a21002 SHA512 0484f573edd3b3df049d884f387e9d062bc6590a228ec70c88c99c70e72f24d94d29d53c5f5cfd0a71e1669590c3c1810eda4a5e9a62c218e1df808c863d2d9a MISC metadata.xml 1151 BLAKE2B db264a2a0e24aedec15301bb5a6bfe6b83d815e5dc146ccdbcc427d97c0b78ba98050bbc06d230988e1643be858a56469271b92b118bea373a7e284a54f18fb0 SHA512 322b35766a1e71129165a8559fe3caac109dfa85be2b0fa630fa249b28cf603e86f152c47835020ff1f5f0d12b7cbbff8758c08248522a7d2b1188812ec99722 diff --git a/sci-chemistry/p3d/p3d-9999.ebuild b/sci-chemistry/p3d/p3d-9999.ebuild index f5eb1e8c1b42..5dd3fdc9a942 100644 --- a/sci-chemistry/p3d/p3d-9999.ebuild +++ b/sci-chemistry/p3d/p3d-9999.ebuild @@ -22,6 +22,6 @@ src_install() { if use examples; then insinto /usr/share/${PN} - doins -r pdbs exampleScripts || die + doins -r pdbs exampleScripts fi } diff --git a/sci-chemistry/parassign/Manifest b/sci-chemistry/parassign/Manifest deleted file mode 100644 index 7f53bcc9a2a9..000000000000 --- a/sci-chemistry/parassign/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST PARAssign_Linux_x64_86.tgz 76693208 BLAKE2B 9141b7f3e6b50efd84cfc2af13c170946220b3f02f90422c4759a6aab8073a0d28cf44e045f305f392055816e50052826dd403f1d71ff7edb04950bf5dfc5f2b SHA512 63018b0f1e3ce7821cebb90cd59ef5fdfa44b7ce6776956184b55a6247009f5e9df435332772dfa0db7294308c4d930ff0104daf45a46df709fb132dac10bd79 -EBUILD parassign-20130522.ebuild 1375 BLAKE2B cc8f36979dab81d6f1d19112631e37365ed4408943fc5173aabd3c9e4db53e5c155123d1874438d5caabbd9dae6328b6f2e494ed6285d6b66b516cb6f95d93cb SHA512 7634d41463024be7606e63cd6fda1a9645c5fea48922232e1b404fe486416e89a454ea63220772ba75a327cf4c03140beef332f857c3a283063cd4687abadd46 -MISC metadata.xml 1646 BLAKE2B 91f42dd65912632e8f19f6a2dfd6a5e4ea7e2be8c270516db4c5477841a78263352ec9f52c971e6a70e3ee32e86d952505068167cce62ec80e40b3b5d6566173 SHA512 73b07789bffc4fb45c5c3ca5c6b3e7fc75e358fc8a73b2cc2d76e8faf5bc1f2765fb1dcbdb2dcc34a21123d3f99bd8fc61ec3ca4a10e6887f26863b93fc1db1f diff --git a/sci-chemistry/parassign/metadata.xml b/sci-chemistry/parassign/metadata.xml deleted file mode 100644 index f230593f73e9..000000000000 --- a/sci-chemistry/parassign/metadata.xml +++ /dev/null @@ -1,27 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <longdescription> -The use of paramagnetic NMR data for the refinement of structures of proteins -and protein complexes is widespread. However, the power of paramagnetism for -protein assignment has not yet been fully exploited. PARAssign is software that -uses pseudocontact shift data derived from several paramagnetic centers attached -to the protein to obtain amide and methyl assignments. The ability of PARAssign -to perform assignment when the positions of the paramagnetic centers are known -and unknown is demonstrated. PARAssign has been tested using synthetic data for -methyl assignment of a 47 kDa protein, and using both synthetic and experimental -data for amide assignment of a 14 kDa protein. The complex fitting space -involved in such an assignment procedure necessitates that good starting -conditions are found, both regarding placement and strength of paramagnetic -centers. These starting conditions are obtained through automated tensor -placement and user-defined tensor parameters. The results presented herein -demonstrate that PARAssign is able to successfully perform resonance assignment -in large systems with a high degree of reliability. This software provides a -method for obtaining the assignments of large systems, which may previously have -been unassignable, by using 2D NMR spectral data and a known protein structure. -</longdescription> -</pkgmetadata> diff --git a/sci-chemistry/parassign/parassign-20130522.ebuild b/sci-chemistry/parassign/parassign-20130522.ebuild deleted file mode 100644 index c49d09b2ab0a..000000000000 --- a/sci-chemistry/parassign/parassign-20130522.ebuild +++ /dev/null @@ -1,64 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit distutils-r1 python-r1 - -DESCRIPTION="Assign protein nuclei solely on the basis of pseudocontact shifts (PCS)" -HOMEPAGE="http://protchem.lic.leidenuniv.nl/software/parassign/registration" -SRC_URI="PARAssign_Linux_x64_86.tgz" -RESTRICT="fetch" - -SLOT="0" -LICENSE="Apache-2.0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS}" -DEPEND="${RDEPEND} - dev-python/cython[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scientificpython[${PYTHON_USEDEP}] - sci-biology/biopython[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}]" - -S="${WORKDIR}"/PARAssign_Linux_x64_86/ - -src_prepare() { - sed \ - -e '1i#!/usr/bin/python2' \ - -i code/*py || die - - if use x86; then - sed \ - -e "s:munkres64:munkres:g" \ - -i modules/setup.py || die - elif use amd64; then - sed \ - -e "s:munkres:munkres64:g" \ - -i code/*py || die - fi - cd modules || die - rm *o *c || die - distutils-r1_src_prepare -} - -src_compile() { - cd modules || die - distutils-r1_src_compile -} - -src_install() { - python_foreach_impl python_doscript code/* || die - - dodoc PARAssign_Tutorial.pdf README - - cd modules || die - distutils-r1_src_install -} diff --git a/sci-chemistry/povscript+/Manifest b/sci-chemistry/povscript+/Manifest index 17c8df756f7c..02b58a98d2f0 100644 --- a/sci-chemistry/povscript+/Manifest +++ b/sci-chemistry/povscript+/Manifest @@ -1,6 +1,4 @@ AUX povscript+-2.1.2.2.19-libpng15.patch 542 BLAKE2B 1fcc229fd3e90a1c567ea42bd87b4b9de281b4976016a0c990f3a66ba2d9d3d8b7eacb80c1caf31326a4c35ff33863d9495b857163ee86bf7060e44debbe19f6 SHA512 5f795238f95adfa0712c92afda669d461cc292b358aa51907ceea1c2d5e5e470d1817d75f461a46efb962ffefafa2606400d32c1f681192f8e161d6e23ee5224 -DIST molscript-2.1.2pov2.19.tar.gz 845101 BLAKE2B c6b6219ad88df0a481fc4cfb96fe6340fe068cb16b2602a9328672bffccb6534d0dde56553f0d3cca42279ac1f2e02190adbea39d83af30667a74c4c6073d0eb SHA512 11796552a889ae309ebac31047440732921cd300d89ad284beb3655e2797fe1a68adf9a5a7e54e6668ea240c5b0897c22f65d839870ee43591854976000ab05f DIST molscript-2.1.2pov2.20.tar.gz 822930 BLAKE2B da050db5124d04e7c0e2c06b0e666d631f214b4519b41ac4b4775dbdbf5be2608f5417f13fad45c36f796d486a8d9211d2fd3d9403afa1b6d27e52b4f0a7f248 SHA512 f7cae4d9b583a05962742ee36ec717f0ecac6bb88086bcfa484b51b0d2e16a15920bc7c09d9d777453d7ef7b81be444924d15a889e4725bfca7bf517d4e52db2 -EBUILD povscript+-2.1.2.2.19.ebuild 1244 BLAKE2B d5881ff5b01720fc963724313dadb41c12b3d3a5f15a66792edf92abc2cdef31c6f402456faad65270e74bcbfa0aecc00602ab4d883585dd55f53e99d4d82329 SHA512 b3e58b153ee8a5e1145f87c24742de76518a6e0792185256b2d8463782a93e37357801bda4a586054576cde9040d39ac140a68af796c1661cbe1f06e4d448694 EBUILD povscript+-2.1.2.2.20.ebuild 1263 BLAKE2B 11784b37663618506624aa8f3f9b034ee01c387dbb286c226b01c35fcbf6075bb355ed96d7663f8c46feb9da08d2c92ef06521f1b64d0e9a50ffb3453957d2bb SHA512 54cebb95ef03430d1071a894b2a47f118ae0e952bcacc0f80f3d727aa18912d4701a116c97469bf2a37b28e01fa5fe51cf7aa02fe2fb69134bf98465210d4770 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/povscript+/povscript+-2.1.2.2.19.ebuild b/sci-chemistry/povscript+/povscript+-2.1.2.2.19.ebuild deleted file mode 100644 index ed9dc48f4d5c..000000000000 --- a/sci-chemistry/povscript+/povscript+-2.1.2.2.19.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=4 - -inherit eutils versionator - -V1=$(get_version_component_range 1 ${PV}) -V2=$(get_version_component_range 2 ${PV}) -V3=$(get_version_component_range 3 ${PV}) -V4=$(get_version_component_range 4 ${PV}) -V5=$(get_version_component_range 5 ${PV}) - -MY_P=molscript-${V1}.${V2}.${V3}pov${V4}.${V5} - -DESCRIPTION="Modified molscript that uses POV-Ray, does thermal ellipsoids, and more" -HOMEPAGE="https://sites.google.com/site/timfenn/povscript" -SRC_URI="https://sites.google.com/site/timfenn/povscript/${MY_P}.tar.gz" - -LICENSE="glut molscript" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86" -IUSE="" - -RDEPEND=" - dev-libs/glib:2 - media-libs/freeglut - media-libs/giflib - >=media-libs/libpng-1.4 - sci-libs/gts - sys-libs/zlib - virtual/glu - virtual/jpeg - virtual/opengl - x11-libs/libX11" -DEPEND="${RDEPEND}" - -S=${WORKDIR}/${MY_P} - -src_prepare() { - epatch "${FILESDIR}"/${P}-libpng15.patch -} - -src_install() { - emake DESTDIR="${D}" install - cd "${D}"/usr/bin - mv molscript povscript+ - mv molauto povauto+ -} - -pkg_postinst() { - elog "You must install media-gfx/povray to use the POV backend," - elog "which is one of the main features of this over molscript." -} diff --git a/sci-chemistry/psi/Manifest b/sci-chemistry/psi/Manifest index 2ec37e80f5d1..316132cafba5 100644 --- a/sci-chemistry/psi/Manifest +++ b/sci-chemistry/psi/Manifest @@ -9,5 +9,5 @@ AUX psi-3.4.0-format-security.patch 1021 BLAKE2B 58aebbd7d8d8fd8c78c8cce7ad28574 AUX psi-3.4.0-parallel-make.patch 445 BLAKE2B e98ee4f5d0feb639058c3b589c6eb6747b35386276f48a6775ab40833364d0feadc55fb4f91abb58009b83f8122fbb119f0588acc13eabb5fb9857af202ac3d5 SHA512 bf574c6c9c1e1ffc8747fb51896b8f9d8b29c4796b0a06529a58a2ab1ed5ee0a4270fe071eb86ca745bad2c760701c4d9eb7f269cd390f6d9cadf4065962e52e 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 1935 BLAKE2B 419b171d833160c8abcc7920f9f2d594eaa885e564a5ed9bfaedeeb17719ad94c55e1946e507020c8af578428b49b34d0f4458628f04b1675141bfad0aab5771 SHA512 75c1615bb6510bfa0ef2a771a78a4d262dfac80ce5c597d69cba1c030e0a3db90902d3a9330ce9d2440918e2ee649fc44bca9c7453ff5099d592188d8142bfda +EBUILD psi-3.4.0-r2.ebuild 1959 BLAKE2B b40aa3f7ea09f433373dafca0b535e4de2b302af81864212f8b989989ef7970657531e62f4c35e7501728da011a3266738a9af8fc0e145329e6994566513d3ca SHA512 414ba2b293b6b1edd8d82096706db88cc105602688c6b85a119c3b1ecd0ef2209f83d19efc1b982a85fb04533406d9faf9483f83b90b568f49304a732755e552 MISC metadata.xml 352 BLAKE2B a7c80467e6e67207a2a03e98071d1bbcec5024a528848f615ab38233c888a78032a9fe7a04dbf278964f9f9cb52d010ad592b1fe40436cb7839a1f2bfd4a375a SHA512 0ef2b193bcadef21bcad1e3fd3745b37f75bd65fe44645c667c99634d9047b28c82504002ed6967cf1cc2d5c8c43f5757ad08264613088ca36c7e94ac683b7e2 diff --git a/sci-chemistry/psi/psi-3.4.0-r2.ebuild b/sci-chemistry/psi/psi-3.4.0-r2.ebuild index 34dd75b6c1df..f40a13060173 100644 --- a/sci-chemistry/psi/psi-3.4.0-r2.ebuild +++ b/sci-chemistry/psi/psi-3.4.0-r2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=4 @@ -13,6 +13,7 @@ LICENSE="GPL-2" SLOT="0" KEYWORDS="amd64 x86" IUSE="static-libs test" +RESTRICT="!test? ( test )" RDEPEND=" !sci-visualization/extrema diff --git a/sci-chemistry/pymol-plugins-psico/Manifest b/sci-chemistry/pymol-plugins-psico/Manifest deleted file mode 100644 index 80c9aafbaa8f..000000000000 --- a/sci-chemistry/pymol-plugins-psico/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST pymol-plugins-psico-3.1.tar.gz 76136 BLAKE2B d1218b0d9da9326a47fb5e0d6268c43ee2d6266066260b83686aa664c500609fb87d61886a83d46a59a2270c3671cfdb7e2f3f761f7898b52932d5f92b2b4b31 SHA512 b0f57049ea6fc290a5abd48e0c98d4fda3c3f947898597b80e11cb3ab9ac14038aade0a016b21a525bf0ab4cf68e3be35c64b8ec34422268058414c20a755b0e -EBUILD pymol-plugins-psico-3.1-r1.ebuild 982 BLAKE2B 9a95ce4fc98f64a72f8ada9630597aa37931dbcbd33b163bd1e2a40964e2c8de753378a5650d5a2e04f54ddafbc808709269608d924a923cd2185ad30c4ba529 SHA512 33c405c0e95a1f040c58c8ed68d314dd6fee488fd92a5acf45014c692a0fe5d2168f46799a918683543e2e285e6c0decd9b94daf26aee1d98bc3f15a6841bb5a -MISC metadata.xml 359 BLAKE2B 209861a26fe54237d677fedc834fa833880ec97916f743df270b4e3a9e851f1233dd51756133a083cbd455bb4f682c63fb3c245ee5e934ef9f6278e74cb9de46 SHA512 1c94755813187e50e66f575868d2deabf6448e39bc6829ecdb60a29a4de5a37c58d28bdc7b21551f906101469614b2672949658220e5edea0fc4f10bad8d4116 diff --git a/sci-chemistry/pymol-plugins-psico/metadata.xml b/sci-chemistry/pymol-plugins-psico/metadata.xml deleted file mode 100644 index 29f0c024a2f1..000000000000 --- a/sci-chemistry/pymol-plugins-psico/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <upstream> - <remote-id type="github">speleo3/pymol-psico</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild deleted file mode 100644 index 0fca945ebee8..000000000000 --- a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit distutils-r1 vcs-snapshot - -DESCRIPTION="Pymol ScrIpt COllection" -HOMEPAGE="https://github.com/speleo3/pymol-psico/" -SRC_URI="https://github.com/speleo3/pymol-psico/tarball/${PV} -> ${P}.tar.gz" - -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -LICENSE="BSD-2" -IUSE="minimal" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - sci-biology/biopython[${PYTHON_USEDEP}] - sci-libs/mmtk[${PYTHON_USEDEP}] - sci-chemistry/pymol[${PYTHON_USEDEP}] - !minimal? ( - media-libs/qhull - media-video/mplayer - sci-biology/stride - sci-chemistry/dssp - sci-chemistry/mm-align - sci-chemistry/pdbmat - sci-chemistry/theseus - sci-chemistry/tm-align - sci-mathematics/diagrtb - )" - -pkg_postinst() { - if ! use minimal; then - elog "For full functionality you need to get DynDom from" - elog "http://fizz.cmp.uea.ac.uk/dyndom/dyndomMain.do" - fi -} diff --git a/sci-chemistry/relax/Manifest b/sci-chemistry/relax/Manifest index 1c2c7b89f8cb..7d477d91d72f 100644 --- a/sci-chemistry/relax/Manifest +++ b/sci-chemistry/relax/Manifest @@ -1,3 +1,3 @@ DIST relax-4.0.0.src.tar.bz2 105659752 BLAKE2B ce5fc9b7f31787f2189e75a543f8ba6fe3cd59ce7382c6c0f79c419b9f71b2d09bd16685e7fed3c9e3205be531efa2a8dc1cce707e77e2386d2a9f7a71b4b0c1 SHA512 28b5ddab2c83f95d7e1a502d05b5d3c93337fece68a1fef95ec8978f61fccf24cb37528cfef27cb20d132033535f4120b23cc76a75f34f52b27df17116351f8e -EBUILD relax-4.0.0-r1.ebuild 1567 BLAKE2B 09376d6d533a61e61fc3e118e2a6f52d18e72cf1efc79d0fa06515aa2e62b36a6be73d5b7c986c4b4431ba97518b0ebced17931aabe55fc4c7265bfba0022213 SHA512 4b334b6c1c64a8495d716e4d9032f79c24201e07b87a8a555412677c70e5794456c662364c9b3d839b65248cf8f31f091540575f6ba5a72518964e9078a3ab32 +EBUILD relax-4.0.0-r1.ebuild 1591 BLAKE2B 58569336b45732cafd601b30e8ef2db0666eceb49c4d5ee5b45aeec1cfec7cf4505f1b77c532bbfc550c2111e439bc8cf5b3fc686bd6216c0627cbad6dd5c0ba SHA512 fbb5be5c93e7dafe75f9c3a13a0d849fbf494a7018a35389b9284251f8231c1174c3cf1469ba24781ca030bc729ecb225edffed9db6305c83b37299fe373bc4c MISC metadata.xml 1373 BLAKE2B d5a9e36f0412ef757a23aa4991986bdc394edc035f59b0206b246affc884417eb8446a598b23054972c97dc5d883cd0242e306f9e8d61620c144939845c0bcf1 SHA512 575ccfdae744fc5d97e795a22989b377954edeacb8ec4887d987a59af813f126551743c4b29b9c2b4a26a1840f05d42fb26fd39b7ae9b38e24373fab18c0270e diff --git a/sci-chemistry/relax/relax-4.0.0-r1.ebuild b/sci-chemistry/relax/relax-4.0.0-r1.ebuild index c08c298b59f4..5a99d4554ba7 100644 --- a/sci-chemistry/relax/relax-4.0.0-r1.ebuild +++ b/sci-chemistry/relax/relax-4.0.0-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -17,6 +17,7 @@ SLOT="0" LICENSE="GPL-2" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="test" +RESTRICT="!test? ( test )" REQUIRED_USE="${PYTHON_REQUIRED_USE}" diff --git a/sci-chemistry/surf/Manifest b/sci-chemistry/surf/Manifest index 4eb052684bb0..5a66f3575403 100644 --- a/sci-chemistry/surf/Manifest +++ b/sci-chemistry/surf/Manifest @@ -1,3 +1,3 @@ DIST surf-1.0.tar.Z 74347 BLAKE2B 543696838470f8b263d3841e177bb9054eb24a1ff0978fa09d9617e32a3a3e6b0662b37c1faa83fa449321276c8b3dd4aed80e978ea3c8315ed5b11f37196a73 SHA512 55b0e771f880931e43d677498ef4cdd92e5f57980d90b686b13c7ae612c8d695353a6f3b5ad0dab184d44e67d8cc5244e7b3f45b4f067c4174ed4399c184d435 -EBUILD surf-1.0.ebuild 822 BLAKE2B 36d7470b934c3be20aa12016336f04e96a1a2a9bbb8917dc546ca2e60b57e50d9daf1936082fd7df38f6fd702c1a108d9f53240f2885d88705cafd4fd22f086b SHA512 94b7de7a59085f10b60c3aa8ab5280a441239cb63ea3723d15dac949295a07d401c820c5b24e7ff1d03571086c6a1ead3a43d2688a17d6ab4928c9728270f706 +EBUILD surf-1.0.ebuild 796 BLAKE2B 3e66904e8e7fd63a6577a64c011ced32e73031807a7470c9895c172743759133e7423404a4107c5f99d127124d2bb14457ff882627ace6e524257200b67bcef2 SHA512 774ac12030accc1959b6eb22bd52ddd32b3a4b53ade020a5e36d58d160c0b5c3beed3c49eb8ae13b02d68dc95a21675063eb4b9c4262f804bf60a700c0d0b31b MISC metadata.xml 261 BLAKE2B 509ce9958149f9cd522a2c68dd0d23ed851d19d02494611456592897093378d180a6006cddf1575fd60106119e72726255c49db2e10fde1b370bdf2f3cf8c94a SHA512 72682d17ec2b918131b551bd1ff41004965d3cf0c00d24222b34741d2eabf601cf36d4266be70ba7fb7bd0ab55d9dcb5b8e4ca41125bc31f176516797459c8c7 diff --git a/sci-chemistry/surf/surf-1.0.ebuild b/sci-chemistry/surf/surf-1.0.ebuild index 138830fe777c..5b6ff83975fd 100644 --- a/sci-chemistry/surf/surf-1.0.ebuild +++ b/sci-chemistry/surf/surf-1.0.ebuild @@ -33,11 +33,10 @@ src_compile() { && emake \ CC="$(tc-getCC)" \ OPT_CFLAGS="${CFLAGS} \$(INCLUDE)" \ - CFLAGS="${CFLAGS} \$(INCLUDE)" \ - || die + CFLAGS="${CFLAGS} \$(INCLUDE)" } src_install() { - dobin ${PN} || die - dodoc README || die + dobin ${PN} + dodoc README } diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest index e170171ba4f4..582201b861ab 100644 --- a/sci-chemistry/vmd/Manifest +++ b/sci-chemistry/vmd/Manifest @@ -1,11 +1,13 @@ AUX vmd-1.9.1-cuda-device_ptr.patch 894 BLAKE2B 96aeab7c2b9d29e5cd3558e69d1365d6b7dc2d78284bb1185d63a57300a83a4c7c0b8f1c1718027ff33333d34bba116d6898fbee74ab23dfd1a77c560160d659 SHA512 9a561773562873dad077f0f2903299952cb935c69ae4bd1463a5f79d6f27ae3845ac5a24ee295ff3569d9c65ae00a9fe3974f4ead003109246f97d130c2c48bf AUX vmd-1.9.2-format-security.patch 550 BLAKE2B d50d05d8697c345f5888b1344c827be1282c5b2e06cfddac022d562688550a728a91a943f9b31c4247f683dcd062ab8fe8ed360aa97a202f20af0467a3148cd3 SHA512 81a71ee4c4c438d18f3a393ebad5c9a08f1a7bb95fa58b78a8798955a34ae2494f80fa074b973a1b595862080e9103d21e509443742cfe2bc3cf77f10c0e3c9d AUX vmd-1.9.3-configure-libtachyon.patch 613 BLAKE2B 5717e941102c4d759d6985087f74724df21312a61313d397da1bbac1969b76590117c70bc3b7fac6c7a84483df433d03613b245a05db8bb10bf7b8807369f415 SHA512 1eafa38022588e9b9bba3a15394a432f66693e64ba62c27e7aebf759d279cb04326f76bcc6545ef34cbcbd7446aead1a05a18072e99aa7df0940f11173ab3c00 +AUX vmd-1.9.3-tmpdir.patch 673 BLAKE2B 074456a8a68a36f16a804aeb8caee9abf14505cb76a2661b03ad97119bf4afb13a994c9cf22eeb952a79a980fcf03bd3dee5c93cf63bf82a19831f71bcbd83c2 SHA512 f7f570c729259f9133fb6411047266312c3d5f802d4cffe316cfdc4094f0fd0830c3eaae6408f56ea17dadba283e1a1fdf86fec858a5211b1c00ed927f160ea4 DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 BLAKE2B eb7c7fb982602f37bd8374bf8458a0a2ea2202161248caffd0d4e0f8124d627755304bb778976e1cf5598b6bfbbe5d8c8e6016c9ec562204d6782aaaf179b185 SHA512 0516b9e57b256ce822a64df420ebf3ab7391722757caeaa7e615526242043e9375fee8f4ee86fb4eb8de7a50d5cfc8f8d973ace5fa082e6f9010eb692cd6ee51 DIST vmd-1.9.2.src.tar.gz 34903084 BLAKE2B f7f7048ef7bb72a8b0dcae955c7f90691085158c38a59229d5b929a4b52d3148bdb2f40084cf8c4544f01cb8bcb57de1d98a90bd17568a07c4ebb8f6985cec9b SHA512 b232b743d4ea97dcf76e3005e1c8716d7138602edc078c4846026ab67759c8559af956182cb1acf3c85890db10b6f658ac9c269d432f2595612cf376d6d505ef DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1 DIST vmd-1.9.3.src.tar 129566720 BLAKE2B 848f3280d51765dcd18722dd233e0cdee3b7c0ac3dd48324260ebe1604ba781ca0a1fe4cae6652501d23d5d41712020e17dbb6bc21a1856eb3289a4aab6b774b SHA512 0502df1e8b60c570ca88b779b4153acfaa599a78df53fa96fca36301bab902864118332b5524ae7d170d3a9e429cf1e13d69e1197268b5e841afc0bb56a737ba EBUILD vmd-1.9.2.ebuild 7155 BLAKE2B 734137c1a02d76da109d35faf11f29138a8e48dda6d84b7151f93f2095481127f136a5f8954a80912c85ae7031a01c3374783a042bf5461fd9d1049b577a082b SHA512 3f9fc1f4cc8f6f5031de74a8211db2a9e11d07de110689832d408c343a307ba25efa354f5862d4e6d8d06d3d18b567820401fc9fcdc8818f65a33ea24a3c657b EBUILD vmd-1.9.3-r1.ebuild 7512 BLAKE2B cfd3259efcf3457e520f8f9ebf809373a99b6d6d5d3ab36192bf7ddd694835d7dd5c113957591d9041b583e58ac419f6cb8649f24ded0e62c89cabf056d45020 SHA512 cb0fc6cbc37c39351d51a3535569adaa69f4aee81942c0eeb83fbd7f1ca5aa3005bc8c87a74002869cc4fd81fb917601ae1bfd0a3dfd474fcf345f696cfd7d21 +EBUILD vmd-1.9.3-r2.ebuild 7693 BLAKE2B e6a96e06546f562448d4c77ca4f5626c878b69a1385edf1ed5f1b01d388aae2f19a710cadd3c3da66974bbc6d3c5c075e220b83faee8b5d626d15c73d372737a SHA512 8ab709222532622b87720fefc80e0c057c23bad5a26bb812cf7539705493c04202980545639bd8e62ef855fca9c850c0e7d825b3ec323aca6fc9a5cdf837d84d EBUILD vmd-1.9.3.ebuild 7110 BLAKE2B d8ad6f495aaacdc4727e2c0e5d950a9670478aba7b55e62ed7074f06ad26151468f0f55a0786ce9dba80a181e7c36e912eaeaaa9ad7ae660739c65f482337c97 SHA512 c0eba398b6a815a59c9d8708dc796273ad3211ddc8e02aee8333f00f42f095c4d8999aaa246665ceb9282d2053c0631dc3c8ed7b60981d88ff9f8a2badf6b89a MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9 diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch b/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch new file mode 100644 index 000000000000..22712abf30b8 --- /dev/null +++ b/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch @@ -0,0 +1,22 @@ +--- a/scripts/vmd/vmdinit.tcl~ 2016-10-27 05:46:34.000000000 +0200 ++++ b/scripts/vmd/vmdinit.tcl 2019-12-03 16:29:01.894002827 +0100 +@@ -197,7 +197,7 @@ + set env(TMPDIR) /tmp + } + default { +- set env(TMPDIR) /usr/tmp ++ set env(TMPDIR) /tmp + } + } + } +--- a/scripts/vmd/chemical2vmd~ 2000-07-03 19:30:23.000000000 +0200 ++++ b/scripts/vmd/chemical2vmd 2019-12-03 16:28:49.316861178 +0100 +@@ -61,7 +61,7 @@ + + + # Make a temp. file to store the load command +-$ENV{'TMPDIR'} = '/usr/tmp' if !$ENV{'TMPDIR'}; ++$ENV{'TMPDIR'} = '/tmp' if !$ENV{'TMPDIR'}; + sub tmpfile { + local ($tempfile) = $ENV{'TMPDIR'} . '/chemical2vmd.' . $$; + local ($i); diff --git a/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild new file mode 100644 index 000000000000..02ad806afbeb --- /dev/null +++ b/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild @@ -0,0 +1,266 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 +PYTHON_COMPAT=( python2_7 ) + +inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg + +DESCRIPTION="Visual Molecular Dynamics" +HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" +SRC_URI=" + https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz + ${P}.src.tar +" + +SLOT="0" +LICENSE="vmd" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda gromacs msms povray sqlite tachyon xinerama" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RESTRICT="fetch" + +# currently, tk-8.5* with USE=truetype breaks some +# tk apps such as Sequence Viewer or Timeline. +CDEPEND=" + >=dev-lang/tk-8.6.1:0= + dev-lang/perl + dev-libs/expat + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/netcdf:0= + virtual/opengl + >=x11-libs/fltk-1.1.10-r2:1 + x11-libs/libXft + x11-libs/libXi + ${PYTHON_DEPS} + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) + gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) + sqlite? ( dev-db/sqlite:3= ) + tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) + xinerama? ( x11-libs/libXinerama ) +" +DEPEND="${CDEPEND}" +BDEPEND=" + virtual/pkgconfig + dev-lang/swig +" +RDEPEND="${CDEPEND} + sci-biology/stride + sci-chemistry/chemical-mime-data + sci-chemistry/surf + x11-terms/xterm + msms? ( sci-chemistry/msms-bin ) + povray? ( media-gfx/povray ) +" + +VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" +# Binary only plugin!! +QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" +QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" +QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" + +pkg_nofetch() { + elog "Please download ${P}.src.tar from" + elog "${VMD_DOWNLOAD}" + elog "after agreeing to the license and get" + elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" + elog "Place both into your DISTDIR directory" + elog + elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources" + elog "file may get downloaded as a compressed tarball or not. In that case" + elog "you will need to ensure you uncompress the file and rename it" + elog "as ${P}.src.tar" +} + +src_prepare() { + xdg_src_prepare + + use cuda && cuda_sanitize + + eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch + + cd "${WORKDIR}"/plugins || die + + eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch + + [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) + + sed \ + -e "s:CC = gcc:CC = $(tc-getCC):" \ + -e "s:CXX = g++:CXX = $(tc-getCXX):" \ + -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ + -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ + -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ + -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ + -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ + -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ + -e "s:-ltcl8.5:-ltcl:" \ + -i Make-arch || die "Failed to set up plugins Makefile" + + sed \ + -e '/^AR /s:=:?=:g' \ + -e '/^RANLIB /s:=:?=:g' \ + -i ../plugins/*/Makefile || die + + tc-export AR RANLIB + + sed \ + -e "s:\$(CXXFLAGS)::g" \ + -i hesstrans/Makefile || die + + # prepare vmd itself + cd "${S}" || die + + eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch + eapply "${FILESDIR}"/${P}-configure-libtachyon.patch + eapply "${FILESDIR}"/${P}-tmpdir.patch + + # PREFIX + sed \ + -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ + -i configure || die + + sed \ + -e "s:gentoo-bindir:${ED}/usr/bin:g" \ + -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ + -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ + -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -e "s:gentoo-gcc:$(tc-getCC):g" \ + -e "s:gentoo-g++:$(tc-getCXX):g" \ + -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ + -e "s:gentoo-cflags:${CFLAGS}:g" \ + -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ + -e "s:gentoo-nvflags::g" \ + -e "s:gentoo-ldflags:${LDFLAGS}:g" \ + -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ + -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ + -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ + -e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \ + -e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ + -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -i configure || die + + if use cuda; then + sed \ + -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ + -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ + -i configure src/Makefile || die + sed \ + -e '/compute_/d' \ + -i configure || die + sed \ + -e 's:-gencode .*code=sm_..::' \ + -i src/Makefile || die + fi + + sed \ + -e "s:LINUXPPC:LINUX:g" \ + -e "s:LINUXALPHA:LINUX:g" \ + -e "s:LINUXAMD64:LINUX:g" \ + -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ + -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ + -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ + -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" + + EMAKEOPTS=( + TCLINC="-I${EPREFIX}/usr/include" + TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" + TCLLDFLAGS="-shared" + NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" + NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include" + NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" + NETCDFDYNAMIC=1 + EXPATINC="-I${EPREFIX}/usr/include" + EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" + EXPATLDFLAGS="-shared" + EXPATDYNAMIC=1 + ) + if use gromacs; then + EMAKEOPTS+=( + TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" + TNGINC="-I${EPREFIX}/usr/include" + TNGLDFLAGS="-shared" + TNGDYNAMIC=1 + ) + fi + if use sqlite; then + EMAKEOPTS+=( + SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" + SQLITEINC="-I${EPREFIX}/usr/include" + SQLITELDFLAGS="-shared" + SQLITEDYNAMIC=1 + ) + fi +} + +src_configure() { + local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" + rm -f configure.options && echo $myconf >> configure.options + + use cuda && myconf+=" CUDA" +# use mpi && myconf+=" MPI" + use tachyon && myconf+=" LIBTACHYON" + use xinerama && myconf+=" XINERAMA" + + export \ + PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ + PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ + PYTHON_LIBRARY="$(python_get_LIBS)" \ + NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ + NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" + + perl ./configure LINUX \ + ${myconf} || die +} + +src_compile() { + # build plugins + cd "${WORKDIR}"/plugins || die + + emake \ + ${EMAKEOPTS[@]} \ + LINUX + + # build vmd + cd "${S}"/src || die + emake +} + +src_install() { + # install plugins + cd "${WORKDIR}"/plugins || die + emake \ + PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ + distrib + + # install vmd + cd "${S}"/src || die + emake install + + # install docs + cd "${S}" || die + dodoc Announcement README doc/ig.pdf doc/ug.pdf + + # remove some of the things we don't want and need in + # /usr/lib + cd "${ED}"/usr/$(get_libdir)/vmd || die + rm -fr doc README Announcement LICENSE || \ + die "failed to clean up /usr/lib/vmd directory" + + # adjust path in vmd wrapper + sed \ + -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ + -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ + || die "failed to set up vmd wrapper script" + + # install icon and generate desktop entry + insinto /usr/share/pixmaps + doins "${WORKDIR}"/vmd.png + eprefixify "${WORKDIR}"/vmd.desktop + sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die + # Open PDB files with VMD + echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die + domenu "${WORKDIR}"/vmd.desktop +} diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest index 0858402306b0..53ff74f8d77e 100644 --- a/sci-chemistry/votca-csg/Manifest +++ b/sci-chemistry/votca-csg/Manifest @@ -1,14 +1,18 @@ DIST votca-csg-1.4.1.tar.gz 347702 BLAKE2B 8c98804bafd75148fa72a9e119d4448ab9b04fb6f305e1e162a18013871d03778873a50670ce06bb218fc063f51ad67efc4a182c2d7bb46f91b59e30181b71d6 SHA512 87f2798c9b5f2d82ae1c158238f7a3b7007c7ceb7ce82503f0b002f605f2cc0b5ca4c8ef24fab571efae63a81e7a60bc476b5433962c239de4f5d42bae3c10ea DIST votca-csg-1.4.tar.gz 346527 BLAKE2B 8f0a41f9aa9fd865e2e544d5fd587d93d631edc2dabab8edfc3461582da2e0401a266a42be1c0f1e6647502cdcccee55b5bba891aa156394012b8b5e1b06f7e8 SHA512 26318644c7af2dfa1b81242b27ffac98f2180c3a1f05581bc50a00f644cec4b19ffbaf41c9d941a4714171b56ae93fe41f1a663cd0593ae2b0be2da379119d9b +DIST votca-csg-1.5.1.tar.gz 708319 BLAKE2B 2ea75cf08dc3005bd08ebe85113d95743fe85bae4b7ac3c2e2d9b64be64a7103ecf30b9edf45cffa86b7588d5c57a0256aef02f4590fa6031cb63881480bd0fd SHA512 3559452182c325d5df72918ec6e12122c8214df9733d779c123ff199597fe47fc493fd75adf1f5dbc6b55016373863378ba3cc69fb6b61bc1531c6e591d8131c DIST votca-csg-1.5.tar.gz 429164 BLAKE2B da04bd9ce8e879e9a961006256e03d160fa49fe77aa2f1eff0986b338296b04137bb087ecfabb7f2fc855b0ccd83dc4ddddfd65c43303bf5f2eef0519d27b0ec SHA512 c5a77ded3c9b2582494bea55b464689d566d4155713af823dccc6999f98438444d51fae3948144f82c2aaf3914eee740fe21e8828af689d37ab0b5ffea0605fa DIST votca-csg-manual-1.4.1.pdf 1282641 BLAKE2B 370b7c8997649555fd2360b999cf381c340a74c3747afda23d0e9d346367cc6d14d4e9a0e9ac82184945427d30050dd623dd1b6d8218c6ff3d2f17331987aaae SHA512 e89f41af05eaeb9ea499e8625cc98e2632ec647ec2d8c9c9052dcd4d2935d082b29b51495514e3e06e73ce42b8cda7017fc523a013569378e2bc86bf88ad32d4 DIST votca-csg-manual-1.4.pdf 1281983 BLAKE2B 5659c2e327ba7bb00fac15adfb578288d546b509366863f593776a62dd3064662535d4fd525f1063f5ccaf47446822f13fefd7f66aa9d68cd1a4a7c99d66a790 SHA512 2e1f4a4375d83df9bd357d4d17e79d26a3a31c9177f008de86721427ffc6f43a5000ec840691108b52a8aecf962321ba6363cd975c7445d7230ee5b0b151b3fa +DIST votca-csg-manual-1.5.1.pdf 1263719 BLAKE2B 29e2ce27215787a1121e45ec1e88ce7c61ba81709a2519aa0959eede505498b9aaf4f38666bb1a4f97837c98b862e7ed02405da07294a7ec76cc80390fe72e0d SHA512 7d9fb4c635383e1b9c9547691f8729e19f273fcafc4dab2a6b438b3ce98ea05bd31887d09bc4edc86ceb0b04d71a4371aed7aadc3ba6864f7be2ef3328ede642 DIST votca-csg-manual-1.5.pdf 1273566 BLAKE2B edfa2adb942d968cf79499e89342b7aaab64edfbfb6e02f76a66201df0920a58acc17bf4e2e4846d104519df163223c27f283cc5798ec7b64d9317a7728ff8c4 SHA512 da298ab0c27000ccf7fb5793c4252c4e17a969709db2649a5acb56af6208b954312c46a2ea8399cdb879b699e72a0ded0b2fe1bcd26431c6625f36b09c0267a5 DIST votca-csg-tutorials-1.4.1.tar.gz 6339417 BLAKE2B e9acf8e421f6fce4d97be2d51fb559979c6fd3e6b042525cedf32cadeab1dddc5b1aaf80bbbfd387da3bce71672759c2e84d317c789f616dc71834c72a581fff SHA512 896ec9d6b2537a06301046a74c1957708eb96d9854b3ec855fe3457208c142f6fb26a03e323a2644862a1efd0030fcceb1189f73655b984462f0f7127a02de90 DIST votca-csg-tutorials-1.4.tar.gz 6348417 BLAKE2B 612fcbc4457a57be74e5306bf86d6e031ea8cd55ebe3f4d246c0876e272e6e6dd535c8dd2f24f7593cb1ef31fbc18111269d29cb69120368ddef7b1b7d25825c SHA512 f3eb28a133ebc04eed07f84d5962943cb9c547c1099638127f15e0015dfdf3f0b25aab4c97d009d6040bf1d69d408cc178edd6e803d33bf1d831e12dca0671c7 +DIST votca-csg-tutorials-1.5.1.tar.gz 5949467 BLAKE2B c6de6084fbb1d2c4ac2ce75d01a1153eabc63386063de800ff2dc6b483b0568191e7f06ddcb8be46123224ccfd3a97f5fb4e7cd603c0ee99a8636d7143f6c701 SHA512 f2e709ae31d914fe12a4ce37b5019deb878b15ade14972f2a8204bec8970ba2c8946b71b94a5bfd6f7569e41173bfbc75275ea09cbee4358ad1de0e84751049c DIST votca-csg-tutorials-1.5.tar.gz 5947774 BLAKE2B d497f1e9282c4cacc070d09d901ad8f5d3042ab3a279aa4d1c3bcd3184dc22231d1f2a75ba0ffe245e6f6300fb740e562b24c8039594ec01307491a6068b55f6 SHA512 00447380fa887178ad02cc4e1425a04fc2fd2babdd4790d387fcd4aa2734dc14dacf4b4444d420937aa0a5b53e90741b44f9a4bca31bdcdae10fbfb8323e9848 EBUILD votca-csg-1.4.1.ebuild 3204 BLAKE2B e447a6859d7ee4d722701f96634667529bd183f10dd4affeb2713023edfe52ab73988df7ef912963bd154b893bd2d401d2fd110a729040a2a2c52ec5fd44985c SHA512 df94c127269df2a2eaa9643005eeeae6925b458fbb0cb4d1661757a49e5ab4926a613c532e4df4475b34768e904d2388270c868c9ad675cd110e2b1737153e3d EBUILD votca-csg-1.4.ebuild 3200 BLAKE2B 041deefd8fc208525c636d00665f7ea70d0efafb78fa98a3437823fb550e6c39a29d33e94860c3d8f01dbbdb050dd568c63dc1099d4da620f9044545850f40d1 SHA512 939608311d071b6abf8cc26dd73c9713c41476772bb37b41fc77fb3a02672989664b8a06e5465b2825285c3365ad3d70879e5c24a1c698cbb3c8ab6d2341fe31 +EBUILD votca-csg-1.5.1.ebuild 2546 BLAKE2B ef9552a84560fa785dab1752939be518dd310967077263f45334dfa942b5d2e8c0ad6d184e8721ba7e9ea1bf4465dbf6fe4a5745e4c90475dc71926a5ea960aa SHA512 be9245c6359e241944619366574bafe5216ee2ca096ee69fcf190caff4b8ff9ff7433f2961b166a25bc1c05ef7c76c59ebe32447ab10d75a10398498c507d964 EBUILD votca-csg-1.5.ebuild 2544 BLAKE2B e76bd6372f66745230d307d6214e031367f83ddf673e3f3a3e8e5263053de49e102c415baed7c6e709f164d6b994363540d4152f5202660c4b87894b8837cf37 SHA512 66a240156d31a389a91cd8a8e9f5e65236005683fef5d01657386297fb812706bcd43933cbf0d7d6fa9fa8456fe216e45ae651ebb52309ed845cd9dde076f02c EBUILD votca-csg-9999.ebuild 2540 BLAKE2B 7391ae1af857c92b688fab507417c875189725d8f121296aaefccecc903501cc6c50561b0a7a4f834d5713f2bdd75b2325594fbbc32e6d0a0d814cf5c7ca7b14 SHA512 fc36ac2de479e2766722b3eb64d8f4eb43233c9625c67124d2ec583e21e22f1c77d6bee2a71d9c3b35451eeb0c6ddc729f4726e8b56f7e45b2c64a9f45fd94ae MISC metadata.xml 676 BLAKE2B b3f2e43f5cb505876216b0a329410c9cef1b44a9bbd7e1c61faa4acd00dbe87ea0cebb00ed78dc00b9e1d2b08b95e3c40d25fecc0738c992a3f933e430f94e2b SHA512 14ecd498eeeed1576923d8da9bc5dc98e47c1d162173b7f2419ad367fa84e227555bd0365709be8a456dc5388ea6fa6734fa7df3c82fd4efcd1cf3460c7e12a1 diff --git a/sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild b/sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild new file mode 100644 index 000000000000..8ae77aec9f51 --- /dev/null +++ b/sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild @@ -0,0 +1,100 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils multilib + +IUSE="doc examples extras +gromacs hdf5" +PDEPEND="extras? ( ~sci-chemistry/${PN}apps-${PV} )" +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz + doc? ( https://github.com/${PN/-//}-manual/releases/download/v${PV}/${PN}-manual-${PV}.pdf ) + examples? ( https://github.com/${PN/-//}-tutorials/archive/v${PV}.tar.gz -> ${PN}-tutorials-${PV}.tar.gz )" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="~amd64" + PDEPEND="${PDEPEND} doc? ( ~app-doc/${PN}-manual-${PV} )" +fi + +DESCRIPTION="Votca coarse-graining engine" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" + +RDEPEND=" + ~sci-libs/votca-tools-${PV} + >=dev-cpp/eigen-3.3 + gromacs? ( sci-chemistry/gromacs:= ) + hdf5? ( sci-libs/hdf5 ) + dev-lang/perl + app-shells/bash:*" + +DEPEND="${RDEPEND} + doc? ( + app-doc/doxygen[dot] + dev-texlive/texlive-latexextra + virtual/latex-base + dev-tex/pgf + ) + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +DOCS=( README.md NOTICE CHANGELOG.md ) + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use examples; then + EGIT_REPO_URI="https://github.com/${PN/-//}-tutorials.git" + EGIT_BRANCH="master" + EGIT_CHECKOUT_DIR="${WORKDIR}/${PN#votca-}-tutorials"\ + git-r3_src_unpack + fi + fi +} + +src_configure() { + mycmakeargs=( + -DWITH_GMX=$(usex gromacs) + -DCMAKE_DISABLE_FIND_PACKAGE_HDF5=$(usex '!hdf5') + -DWITH_RC_FILES=OFF + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + newbashcomp scripts/csg-completion.bash csg_call + for i in "${ED}"/usr/bin/csg_*; do + [[ ${i} = *csg_call ]] && continue + bashcomp_alias csg_call "${i##*/}" + done + if use doc; then + [[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" + cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html + dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html + fi + if use examples; then + insinto "/usr/share/doc/${PF}/tutorials" + docompress -x "/usr/share/doc/${PF}/tutorials" + rm -rf "${WORKDIR}/${PN#votca-}"-tutorials*/CMake* + doins -r "${WORKDIR}/${PN#votca-}"-tutorials*/* + fi +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). " + einfo "https://dx.doi.org/10.1021/ct900369w" + einfo +} diff --git a/sci-chemistry/votca-csgapps/Manifest b/sci-chemistry/votca-csgapps/Manifest index aa724622e435..13065a99df56 100644 --- a/sci-chemistry/votca-csgapps/Manifest +++ b/sci-chemistry/votca-csgapps/Manifest @@ -1,8 +1,10 @@ DIST votca-csgapps-1.4.1.tar.gz 21066 BLAKE2B 8e1d25957b7c62d2182872de4d0c50c90fefdf699ec5e9e785916791e9cc06db2dbcbbdbaf7afe6921e34179e12dfa2326eb9464261801e48177ec69126ae2bb SHA512 80881ac173b56b07825c484f98c598de8d74bb8a54b888f06cc3a20d15670b49059e50adc210308e21ee4ea9038cf564c08d7ab33c4a43864acb1de97bc3fcef DIST votca-csgapps-1.4.tar.gz 21072 BLAKE2B 30c2f6692544741bfbec09efea2f68ae48cd4716e61e40d3da12a17ad941f2947cc6a8477229b80e420e217a95adff4152a07215e2e913e71736b61ba1ac226a SHA512 325c99606f17d7bb00e2cc3b1545f31dd4cf1fbc0d216f2da2c48e06b2011c9f99096643a6c6efd794a169de056f803f791c156afec4a73e41c58bc4ca1055f9 +DIST votca-csgapps-1.5.1.tar.gz 26006 BLAKE2B 8651978c15087fc7332fe229cfc33d8c4257faf46d72f7ac5fbaaf5f31133c4df3d97cae2b18730b5700e742c27e3db39696fdfe910ed884952ba0f832220c3d SHA512 4f83a46f16eb0a4cb9acc6c0d9523fa746dcf670107355c95fc02daa6ca91fb4f8d5e48bc920d8c13a9445390a25415f7217979903ea86f890df1d4704944c28 DIST votca-csgapps-1.5.tar.gz 25975 BLAKE2B 185e759d658c6f763da2d26770766ec8ee05017b4c6a67e13915de04fbf2ecf268f2f800c5e18ef0f38c615340b0db163e886dc98a9395a69359f94dc8773f60 SHA512 20dda9d07ef2f33c9decff2766ece8f24cf2562993b4dfb7dd637d84325b835a6ecd30d34c5cfb9c428dbf72c2b5dfe9fd49d266182704b981db151c3c4ea2e4 EBUILD votca-csgapps-1.4.1.ebuild 653 BLAKE2B 208ae3538fcf42296a4a1077d222a9d6f752648834dc8f74941546fa2bdffb6fd9ea60ad31d124b8de52c3f59c089f48d4395b5166989fec19191076570e1bf0 SHA512 13ab1d118aea4f16664566f4e13965cc46a9e67e37157e23ad8c76a68d5db89b8db5b95104c23cf9cc16f78315dc9f632708cbd3920a545d964e2226dc6f9ff2 EBUILD votca-csgapps-1.4.ebuild 649 BLAKE2B 4b219583f5d5a1f7f4ed7635b4fedce2619d6a0b13bcab7bde2f88cf177a9478fefcb71974deacc09eded4f278ae27c95bd2aa387c79ad4ae2268c2ff0f40a94 SHA512 b6400f2a28ce0c2953495c00aeaab0bfd15c52df28a5e6575b0f568c9a777678495b591cbce58fa61e1d54149fa3f684c6f9f99aaa82127e2eedcc67f6259ed8 +EBUILD votca-csgapps-1.5.1.ebuild 668 BLAKE2B c1a715dcf42281b13819c20b51fc0c16f0435059e4f1dcfe83babd15eda4dc179d50ffe4a6252cd3155aec9545f2e5fc3bba728e2a6f739097422f5c6d94f247 SHA512 23d3ed6be1ea715a367f6203c9431598068ec7b1494865e594a67bfc55bc0f65e86914ad04cff7eff5a9e83fb79cae46fb4abd7997752a1a72dd90a68e173f97 EBUILD votca-csgapps-1.5.ebuild 666 BLAKE2B de904c4c69f9b223466bc97f646a861a5e1ff64d061389a1a1ac845e7351f9626226354c7c080d7a52ef5db2eddf397b2bf48ce042e168a881cb12da14338333 SHA512 e768e56d45d9e8b4ce2c01358b9de4b876a7a4149947445d388a4a1cffb6ac6882b17cdd794b17eee7abdb75d34c4e108f399c28fbca5ae0b11bbe5d57e07202 EBUILD votca-csgapps-9999.ebuild 665 BLAKE2B 23030fd2ba47629a9285fc8c9b436bb45614ba3ca8198592aea4189e5d2ae005d88b96a745e6de4db8f913e37e73e07f33a15ec0ef5dda9932a99159286711d4 SHA512 a72ac9569a69e4d94180fd45daf1d06496ea8e253f97a4ec877eb66db62bb7b600ab122909994504b5f677d3424a79e9e663dfa8f5c8d5a5b1388bee325aa524 MISC metadata.xml 457 BLAKE2B 9d392be6c061ebd3d975308065fcdec4ee061268f4b8b79e122b183d2e4f7259fdb9e165b8b3f030f1edbbc4f112757b1de7a50929ac112d5633143f9585699a SHA512 42a8ccad09d35dd4677b70005606582207747ae39d62a7ea75e2f5de28f887fee4265c8ae3b38e5cdb3017cc84c8902e2a525ae31fa5dd0aa00369e9b428f563 diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-1.5.1.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-1.5.1.ebuild new file mode 100644 index 000000000000..a4a0669224d6 --- /dev/null +++ b/sci-chemistry/votca-csgapps/votca-csgapps-1.5.1.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils + +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="~amd64" +fi + +DESCRIPTION="Extra applications for votca-csg" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="" + +RDEPEND=" + >=dev-cpp/eigen-3.3 + ~sci-chemistry/${PN%apps}-${PV}" + +DEPEND="${RDEPEND}" + +DOCS=( README ) diff --git a/sci-chemistry/votca-ctp/Manifest b/sci-chemistry/votca-ctp/Manifest index dae27c257d5e..4aa7aa917476 100644 --- a/sci-chemistry/votca-ctp/Manifest +++ b/sci-chemistry/votca-ctp/Manifest @@ -1,5 +1,8 @@ +DIST votca-ctp-1.5.1.tar.gz 1345994 BLAKE2B 6e927c5d57abfff335412bdac085c9dd81696503310e58a89bf2207b07f9d9900d11d20176a11fbde6d6cdfa97f50faa5e877889e35201ad9ed5dd93dbc158cb SHA512 686d7193cdd6a763197dd4f332554c9c6c2022c539191d0a243e70450aa2a4c7048fff3c06636aee09525516fb3717fe49934d5daf2dfcdcbc08be416cc4b6c0 DIST votca-ctp-1.5.tar.gz 1345419 BLAKE2B 148846b9118cabfa541eb4fe0129e366d0c447e2daf969833beb5df91ca7b43f0262c5845303ccf05ed8d3f9e2c2a5e0f876ec97c2601419ed04a28d56640494 SHA512 bc4dbddcefb473015a6513f44f4fddd5995a8598f82505e81b3c50ae771e64e8c979f39a347ab2deb55054e7efffad28b5ff3f73d2c1b8905bcaf6f007ff2959 +DIST votca-ctp-manual-1.5.1.pdf 948647 BLAKE2B 4afec48d0e6bb29dc86d4d22fce74a8d2197d6b7a1ed35a5b09af84c5bbc0fc49b91e045c85e5b5ab79beb5a7de1db78a15e395a1a5faf4c11cc1b58c1ffca97 SHA512 b4ae79b2da0037cc325fdff3b0fd8d142d6bfdad5bc11991cee314f40f105bcdcb1189d17679a84eb37da7a9bb686d0c5ee57c7796a0c6b787b70d53222dbc17 DIST votca-ctp-manual-1.5.pdf 970539 BLAKE2B 8646215a4c2cd7be6d4c03820f00b8067e15c27f51fb6678540026cff1af0e28dffa528423ad47a4047a8f84fc1078d503a56a4a235e004735f0276ec1a6a33e SHA512 a315c1b4b37461f4f0d30ead1fec2ca33ff23d81c9d5e4d888ef7d7dd722f68f9596826f828f8a76841d6dde6889f623b73d9fe0f8a6c5a7cec1c16a83cf9030 +EBUILD votca-ctp-1.5.1.ebuild 1537 BLAKE2B 352a11fec91618444983028294c92cdb878396135f00ddecf0d316772f39d1c33e7be370b12efc59ae720b834eb47b8463eefdbb06c60f18d5ec732bcf789938 SHA512 c6685c4aa7e2fd14e15233cdd3671a4c39230901ef061d2af291bf74c39208457c17724588befd115cb491771409514597d06e5ec48915a3fcb3a840a185df84 EBUILD votca-ctp-1.5.ebuild 1537 BLAKE2B 352a11fec91618444983028294c92cdb878396135f00ddecf0d316772f39d1c33e7be370b12efc59ae720b834eb47b8463eefdbb06c60f18d5ec732bcf789938 SHA512 c6685c4aa7e2fd14e15233cdd3671a4c39230901ef061d2af291bf74c39208457c17724588befd115cb491771409514597d06e5ec48915a3fcb3a840a185df84 EBUILD votca-ctp-9999.ebuild 1537 BLAKE2B 352a11fec91618444983028294c92cdb878396135f00ddecf0d316772f39d1c33e7be370b12efc59ae720b834eb47b8463eefdbb06c60f18d5ec732bcf789938 SHA512 c6685c4aa7e2fd14e15233cdd3671a4c39230901ef061d2af291bf74c39208457c17724588befd115cb491771409514597d06e5ec48915a3fcb3a840a185df84 MISC metadata.xml 453 BLAKE2B a61c365529a1c877e5bad44f6e2f0a24a8797956e9e3a5b3d4649c58c27df9301b50c84bb5767ca52a151e2b509f46a92cd3f17c1020fb7bedf7fb2fe708b48d SHA512 53ace87a281559ae8881b8b010c76801696521de930dcfaf12a5e320456cb4a21a55a7873d173bdb5cc740f3cdbccf1daf62bc83579342f4f23329df7dbd2dba diff --git a/sci-chemistry/votca-ctp/votca-ctp-1.5.1.ebuild b/sci-chemistry/votca-ctp/votca-ctp-1.5.1.ebuild new file mode 100644 index 000000000000..892997f7af3e --- /dev/null +++ b/sci-chemistry/votca-ctp/votca-ctp-1.5.1.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils multilib + +IUSE="doc" +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz + doc? ( https://github.com/${PN/-//}/releases/download/v${PV}/${PN}-manual-${PV}.pdf )" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="" +fi + +DESCRIPTION="Votca charge transport module" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" + +RDEPEND=" + ~sci-libs/votca-tools-${PV}[sqlite] + >=dev-cpp/eigen-3.3 + sci-libs/gsl + ~sci-chemistry/votca-csg-${PV}" + +DEPEND="${RDEPEND} + virtual/pkgconfig" + +if [ "${PV}" != "9999" ]; then + DEPEND="${DEPEND} + doc? ( + app-doc/doxygen[dot] + dev-texlive/texlive-latexextra + virtual/latex-base + dev-tex/pgf + )" +fi + +DOCS=( README.md NOTICE CHANGELOG.md ) + +src_configure() { + [[ ${PV} = *9999* ]] && mycmakeargs=( + -DBUILD_XTP_MANUAL=$(usex doc) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + if use doc; then + [[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" + cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html + dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html + fi +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA-CTP, J. Chem. Theo. Comp. 7, 3335-3345 (2011)" + einfo "https://dx.doi.org/10.1021/ct200388s" + einfo +} diff --git a/sci-chemistry/votca-xtp/Manifest b/sci-chemistry/votca-xtp/Manifest index 6d10a9af7b2b..8f2cf4195de6 100644 --- a/sci-chemistry/votca-xtp/Manifest +++ b/sci-chemistry/votca-xtp/Manifest @@ -1,11 +1,14 @@ DIST votca-xtp-1.4.1.tar.gz 15214413 BLAKE2B 0f6e67179e2ee1fa8ab79ca0c2d810f9867dab474b50d49316aaed33a01b5cf93a129558792fff2851b8f1b7794ab423c25e4b6f6bce6809520ff40234b14e93 SHA512 1a3f5df3dc9a7f532464ef84ff4f4f8e60b9495529f349ab5e496595e73fff8f4678b8276b2c5733dd3f692ca03220e7d0bc4a82163017572428c0d1dd5f91fd DIST votca-xtp-1.4.tar.gz 15214266 BLAKE2B 435ba1603495d904ccce20b4fa665d3a1c62fc04005ea89cf83b431240fb78f8a44f09ad619af331802e43ca3d05b20a4c6bbbb0c75360940d4f786c0030fd7a SHA512 ffc32260331862393e199f7ab643b1008ee4f800cd017f175550a079afaa20e5c929cb8599bc0c2a2328253051895de7b979f5fec044243abc680a0dc87a69b9 +DIST votca-xtp-1.5.1.tar.gz 14634849 BLAKE2B 84ee9fc531a530ba276a6fd3eccc78dd25c27346db76871f33fe307dde451956bf091b636dd5594bf3b8b24a727fe7e5a730fb85cd2cbb0e5605705996e69bd2 SHA512 8fb6891e84d4d685e26287344554b705c607e7cb9f497c00ac9cd8328e50210c56706abdb7004b83d4addbfbc7b35c3526b4feabf75f681362b3b7a39c54b668 DIST votca-xtp-1.5.tar.gz 14637712 BLAKE2B af04de706f0d100968928459a03b6a94a94a211b3f5bd056d123756d40760fb0ada70add429ed5b86e211dbdd3b91aa4cf12e51a260638766d04158e7b5a1201 SHA512 693f34004749edfbabcd0a19dc23b3de3c09858c7c0dfe1e420b92632397971e3687489c1074a489d4d2fd337ddc5749c419869db104c65736e7c01bf12cd140 DIST votca-xtp-manual-1.4.1.pdf 1066873 BLAKE2B 8cbd4b55b013794a19a8b5867b929b8e2d9084e6780d777b2a2bbaea23006f4f4ec5b26bd4a07c59e1c6726f23471eb1756b668636e0c4e656a0807e64197586 SHA512 fdf1147f24785524f5e96020fcd29c32bbeef520eebf6afba32b59d7e777d586c452919478d2734c3f021e558b1147b945cdbc0833402be2b16e5af3a8e37f5f DIST votca-xtp-manual-1.4.pdf 1064006 BLAKE2B e4f0c20c6d40a5f58b863258cc122e5a7cf376b7138927c0a6bdd400841c330fc013287513258f6f68609e39f0bf39b965fd099171594c5e2730fba82a2488d4 SHA512 96d7f59dbcc3a6efdc297237025217d5a56d2c81e491d90680786ea4769a5ebbea379df3b06c4847307ee30accd7415e316dee4730361262f5aff73d2f5d387e +DIST votca-xtp-manual-1.5.1.pdf 912290 BLAKE2B 4511885f5506f542d639b5c7d2bb2e6f4f24df8d7929959ff707ae9c28c357346ebc7cde072f742309f3ef8a6b00a51d0873071cdc4cbcd291670fca788f46a7 SHA512 b410ddad0566933a2c9ad386fb6f4df0e71b316a84bce8c841e94df8f438959f0967ade63d1146549d453c2ecdb48e3d8b1fd147e53888e1717c6db3d07ba061 DIST votca-xtp-manual-1.5.pdf 923211 BLAKE2B 5d2c78260365c6339753e1663d707d642dea870183386f799e8fb34517fdb69680293b77356ae00c3ee6b66053c614b7174503e2e752790a56e7dd2976b3cb0a SHA512 86079339de1cb6e3d0487ad816e86deebe6a1bddcac1f06801e3f94eca2e19b30ec61b286f13429e257aa152129f5dbb4bbbc88ac9d58bf1a9aeb1c3f430d3e0 EBUILD votca-xtp-1.4.1.ebuild 1622 BLAKE2B 1358e16a21b653584fefdf8eb673744f18ba75ef59ae5410c609857ca0b6d73676b5f7ca101dd24d2d58ca1547ca062941c71296ca57e45cdfed29052dfc7cb2 SHA512 bee48dc7a8c0caba3a9a7ed546ad690fb9fc22310f512bc613aa76b35f72b39f4a2b620ab2789237465ce07a0be7b8fbb444eccd45e795b0c1cc3667b046f978 EBUILD votca-xtp-1.4.ebuild 1618 BLAKE2B bab1c2d4cd442bc2208f87ff16ed1218aaf6c34ccb229c63d9de14086055684ee9440102b0c9a5bf807ddad69d22ee1b680120f493f18891e8719211509a418f SHA512 affe412a6c4cb8139530d559ae4c12d519eb6b9190075743ed7806c2975a4647f48282893d71b4bef3477b0d35ee07815e416c33095be819967d235c9623a48a +EBUILD votca-xtp-1.5.1.ebuild 1628 BLAKE2B a89ea389a31edce013d2e41eca4a0a818fd3f0b359aa9e770ecf3e04089b99063106d8b20562b36ad83fdc318c6cc6ffc119a589d995db08175e704ff7ce53f1 SHA512 a90fd6523ef6d42af25b99509718511cf0303bef2e0b083b6e4e8cbb5160bf1cc802b0e60a682c7bd1301f5b17cbaf78c2d2e593d2528f9c24b5f6c3c1aa984f EBUILD votca-xtp-1.5.ebuild 1626 BLAKE2B 15b3e63d11348ac376e15769b6106c98144a0ce88bbc7149fcf98bede2f7a29ee4ea066cea67fadf14e60e6dbc6745de4bffa4cf11d6ce6f08d5631fad0af347 SHA512 ac39f8f262a40683ff267dd13ea17cdfb9bd3ba62d698e8e20c98ee1adce53bd002a10dd7805a4ba419ca80a4a3ffd0b3b5c8f9e4b040182eaa6ffd069df114e EBUILD votca-xtp-9999.ebuild 1622 BLAKE2B 0c99db3dbba224f0485838e5fddb8b857fd13d5e5d798bbaa4b64f89ffcbb1bbbb55a626ff601efd583bf32270c4a8be21a4f8357e6a67e1d8f3feac7c2eccdc SHA512 31a8520c2438ecd0407748b65d363c5ebf2027b71b19fd90810f75b25cf5ea90ed7eedde354fb17dbd0f087963b0b23923f29a9d028d899668fd90eda0806231 MISC metadata.xml 453 BLAKE2B 51ee11d9c55f15fd0382a7c422d1c12364901a5ac257f57d04b91b8ca77acf9c1eb709879bfc6042b577961352cbc4e31b01ece3a8c650eaffa9b4ebc6d385fb SHA512 892c8f84df6bd19e969b372def9a485be9121d8f7ab410b532529980298e57d0705f73fac409d8f251449cf2119dd3f28133e08d21d0e73b27d5ec0e9a3f205e diff --git a/sci-chemistry/votca-xtp/votca-xtp-1.5.1.ebuild b/sci-chemistry/votca-xtp/votca-xtp-1.5.1.ebuild new file mode 100644 index 000000000000..3d34efdc74c2 --- /dev/null +++ b/sci-chemistry/votca-xtp/votca-xtp-1.5.1.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils multilib + +IUSE="doc" +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz + doc? ( https://github.com/${PN/-//}/releases/download/v${PV}/${PN}-manual-${PV}.pdf )" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="~amd64" +fi + +DESCRIPTION="Votca excitation and charge properties module" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" + +RDEPEND=" + ~sci-libs/votca-tools-${PV}[sqlite] + >=dev-cpp/eigen-3.3 + ~sci-chemistry/votca-csg-${PV} + sci-libs/ceres-solver + sci-libs/libxc" + +DEPEND="${RDEPEND} + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +if [ "${PV}" != "9999" ]; then + DEPEND="${DEPEND} + doc? ( + app-doc/doxygen[dot] + dev-texlive/texlive-latexextra + virtual/latex-base + dev-tex/pgf + )" +fi + +DOCS=( README.md NOTICE CHANGELOG.md ) + +src_configure() { + [[ ${PV} = *9999* ]] && mycmakeargs=( + -DBUILD_XTP_MANUAL=$(usex doc) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + if use doc; then + [[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" + cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html + dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html + fi +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA-XTP, J. Chem. Theo. Comp. 14, 6353 (2018)" + einfo "https://doi.org/10.1021/acs.jctc.8b00617" + einfo +} |