diff options
| author |   Justin Lecher <jlec@gentoo.org> | 2013-06-16 13:31:24 +0200 |
|---|---|---|
| committer | Justin Lecher <jlec@gentoo.org> | 2013-06-16 13:31:24 +0200 |
| commit | 2e9cea16376950c1a30a2bb3a7096327d1070f1b (patch) | |
| tree | 03a02152e1ba190af905a34f7b49209f9e1d09b4 | |
| parent | x11-misc/envytools: Fix license (diff) | |
| parent | Update license (diff) | |
| download | sci-2e9cea16376950c1a30a2bb3a7096327d1070f1b.tar.gz sci-2e9cea16376950c1a30a2bb3a7096327d1070f1b.tar.bz2 sci-2e9cea16376950c1a30a2bb3a7096327d1070f1b.zip | |
Merge branch 'fixing'
* fixing:
Update license Signed-off-by: Justin Lecher <jlec@gentoo.org>
sci-biology/caftools: Drop old; Bump to EAPI=5 and fix license
New license Signed-off-by: Justin Lecher <jlec@gentoo.org>
sci-biology/YASRA: Version BUmp; add KEYWORDS
sci-biology/tablet-bin: Version BUmp; BUmp to EAPI5 and python-r1.eclass; drop addpredict
sci-chemistry/modeller: Version BUmp; BUmp to EAPI5 and distutils-r1.eclass
sci-chemistry/cnsface: Bump to EAPI5 and distutils-r1.eclass
sci-chemistry/chemBuild: Bump EAPI and python eclass
sci-biology/tablet-bin: Version BUmp; BUmp to EAPI5 and python-r1.eclass
Drop the license again Signed-off-by: Justin Lecher <jlec@gentoo.org>
tablet's modified for of BSD license Signed-off-by: Justin Lecher <jlec@gentoo.org>
sci-biology/cutadapt: Version BUmp; BUmp to EAPI5 and distutils-r1.eclass
dev-python/opal-client: Version BUmp; BUmp to EAPI5 and python-r1.eclass
36 files changed, 278 insertions, 350 deletions
diff --git a/dev-python/opal-client/ChangeLog b/dev-python/opal-client/ChangeLog index ac3fec3a2..d9bb7eb3e 100644 --- a/dev-python/opal-client/ChangeLog +++ b/dev-python/opal-client/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for dev-python/opal-client -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*opal-client-2.4.1 (15 Jun 2013) + + 15 Jun 2013; Justin Lecher <jlec@gentoo.org> -opal-client-2.2-r1.ebuild, + +opal-client-2.4.1.ebuild, metadata.xml: + Version BUmp; BUmp to EAPI5 and python-r1.eclass + *opal-client-2.2-r1 (02 Dec 2010) 02 Dec 2010; Justin Lecher <jlec@gentoo.org> -opal-client-2.2.ebuild, diff --git a/dev-python/opal-client/Manifest b/dev-python/opal-client/Manifest index 45e1445b1..adef77f5c 100644 --- a/dev-python/opal-client/Manifest +++ b/dev-python/opal-client/Manifest @@ -1 +1 @@ -DIST opal-py-2.2.tar.gz 1012870 SHA256 d11588ed29dac2812b4293204e0f0d75ba3b765f31af095e0e6333365afe0b47 +DIST opal-py-2.4.1.tar.gz 1089581 SHA256 78d82dbdab607a3acb40e0462a0418b856f3ef8c83cb302f55c4549d672e7085 SHA512 8b8563507d5905a2bc2d36552b52a9ce4da555910496242cfed207ea573da973ac78678fff158066db91154a6f38b5dc8701b8484781143ebd4134b440d01292 WHIRLPOOL 3ebd0992c2ff85974fc369820d42f44a866a1a5fcbbdca80839b14e66b27cb4f1cf2a70a9375078700b117316493934ef8e82965045f4d5602a6d669b6d38587 diff --git a/dev-python/opal-client/metadata.xml b/dev-python/opal-client/metadata.xml index efb490d78..4bf6dbc6b 100644 --- a/dev-python/opal-client/metadata.xml +++ b/dev-python/opal-client/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> + <herd>sci</herd> + <maintainer> + <email>sci@gentoo.org</email> + </maintainer> </pkgmetadata> diff --git a/dev-python/opal-client/opal-client-2.2-r1.ebuild b/dev-python/opal-client/opal-client-2.2-r1.ebuild deleted file mode 100644 index 69f0ed7e4..000000000 --- a/dev-python/opal-client/opal-client-2.2-r1.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="3" - -PYTHON_DEPEND="2" -SUPPORT_PYTHON_ABIS="1" -RESTRICT_PYTHON_ABIS="3.*" - -inherit python - -MY_PN="${PN/client/py}" -MY_P="${MY_PN}-${PV}" - -DESCRIPTION="Python Opal Web Service Client" -HOMEPAGE="http://nbcr.net/software/opal/" -SRC_URI="mirror://sourceforge/opaltoolkit/${MY_P}.tar.gz" - -LICENSE="opal" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=" - >=dev-python/zsi-2.1_alpha1 - !=sci-chemistry/apbs-1.1.0" -DEPEND="${RDEPEND}" - -S="${WORKDIR}"/${MY_P} - -src_prepare() { - python_copy_sources -} - -src_install() { - "${EPREFIX}"/usr/bin/wsdl2py wsdl/opal.wsdl || die - - installation() { - insinto $(python_get_sitedir)/AppService - doins AppService_*.py || die - } - python_execute_function -s installation - - dodoc README CHANGELOG etc/* *Client.py || die - dohtml docs/* || die -} - -pkg_postinst() { - python_mod_optimize AppService -} - -pkg_postrm() { - python_mod_cleanup AppService -} diff --git a/dev-python/opal-client/opal-client-2.4.1.ebuild b/dev-python/opal-client/opal-client-2.4.1.ebuild new file mode 100644 index 000000000..0eefd41b6 --- /dev/null +++ b/dev-python/opal-client/opal-client-2.4.1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit python-r1 versionator + +MY_PN="${PN/client/py}" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Python Opal Web Service Client" +HOMEPAGE="http://www.nbcr.net/data/docs/opal/documentation.html" +SRC_URI="mirror://sourceforge/opaltoolkit/opal-python/$(get_version_component_range 1-2)/${MY_P}.tar.gz" + +LICENSE="opal" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + >=dev-python/zsi-2.1_alpha1[${PYTHON_USEDEP}] + !=sci-chemistry/apbs-1.1.0" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_P} + +src_install() { + "${EPREFIX}"/usr/bin/wsdl2py wsdl/opal.wsdl || die + + installation() { + python_moduleinto AppService + python_domodule AppService_*.py + python_optimize "${ED}"/$(python_get_sitedir) + } + python_parallel_foreach_impl installation + + dodoc README CHANGELOG etc/* *Client.py + dohtml docs/* +} diff --git a/licenses/GRL b/licenses/GRL new file mode 100644 index 000000000..8a897b7c9 --- /dev/null +++ b/licenses/GRL @@ -0,0 +1,15 @@ +This software has been created by Genome Research Limited (GRL). +GRL hereby grants permission to use, copy, modify and distribute +this software and its documentation for non-commercial purposes +without fee at the user's own risk on the basis set out below. +GRL neither undertakes nor accepts any duty whether contractual or +otherwise in connection with the software, its use or the use of +any derivative, and makes no representations or warranties, express +or implied, concerning the software, its suitability, fitness for +a particular purpose or non-infringement. +In no event shall the authors of the software or GRL be +responsible or liable for any loss or damage whatsoever arising in +any way directly or indirectly out of the use of this software or + its derivatives, even if advised of the possibility of such damage. +Our software can be freely distributed under the conditions set +out above, and must contain this copyright notice.
\ No newline at end of file diff --git a/licenses/Tablet b/licenses/Tablet index 984a28b72..d81931aad 100644 --- a/licenses/Tablet +++ b/licenses/Tablet @@ -6,7 +6,7 @@ The licence and copyright for Tablet is as follows: - Copyright © 2009-2010, Plant Bioinformatics Group, SCRI + Copyright © 2009-2013, Information & Computational Sciences, JHI. All rights reserved. Redistribution and use in binary form, without modification, is @@ -15,9 +15,9 @@ - Redistributions must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. - - Neither the name of SCRI nor the names of its contributors may be - used to endorse or promote products derived from this software without - specific prior written permission. + - Neither the name of The James Hutton Institute nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED diff --git a/sci-biology/YASRA/ChangeLog b/sci-biology/YASRA/ChangeLog index 77b3b5e07..342684d59 100644 --- a/sci-biology/YASRA/ChangeLog +++ b/sci-biology/YASRA/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -YASRA-2.1.ebuild, + +YASRA-2.32.ebuild: + Version BUmp; add KEYWORDS + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> YASRA-2.1.ebuild, metadata.xml: Drop keywords as deps are unkeyworded diff --git a/sci-biology/YASRA/Manifest b/sci-biology/YASRA/Manifest index 4c218feef..f7399f074 100644 --- a/sci-biology/YASRA/Manifest +++ b/sci-biology/YASRA/Manifest @@ -1 +1 @@ -DIST YASRA-2.1.tar.gz 11949120 SHA256 d196cea91a69db3d2feb98d3a8dddbfe1c4c9b4689cdc706a58df44daba3d2d5 SHA512 1e5c648042b8c522c708eb80b90f5a7e965b4f0214a732ba19a46d826ea85bd7074946a2355e509df1ce1dfcec1700c7c6f3ad08c7052f754fed6241c078ec5b WHIRLPOOL 4419ce639b2afb95013b8896b059c037100dc58dc1664b2416ed05c68fd3fcce4eca01219dfa59874a26d566e1df393e975c8d6132811591a251f1acc3db00a4 +DIST YASRA-2.32.tar.gz 12404230 SHA256 03ce7d89949fdd44c97af51b65f57bb5f49f1ac1d5c2be225419513887ea1c61 SHA512 2bdf3f62567c5f2a12b58de9961c3fa55cf38b1000feb73170af6c0f0c035c79e8052009419d2d49423a4b9d52cb44196171bd7235108fdf3ada97c5e03c30c1 WHIRLPOOL 6fdda6a1abe64b5bb91fcb298fd867cff593c3bb0540cce5134cebd63a8254ef4ba24edc788830be963c001c8e915bb4f2546f37aadbbcf16d26aaf8a8fb6f40 diff --git a/sci-biology/YASRA/YASRA-2.1.ebuild b/sci-biology/YASRA/YASRA-2.32.ebuild index c8288fc52..246d65d40 100644 --- a/sci-biology/YASRA/YASRA-2.1.ebuild +++ b/sci-biology/YASRA/YASRA-2.32.ebuild @@ -2,23 +2,16 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 DESCRIPTION="Yet Another Short Read Assembler aligning to a reference using LASTZ" HOMEPAGE="http://www.bx.psu.edu/miller_lab/" -SRC_URI="http://www.bx.psu.edu/miller_lab/dist/YASRA-"${PV}".tar.gz" +SRC_URI="http://www.bx.psu.edu/miller_lab/dist/YASRA-${PV}.tar.gz" LICENSE="GPL-2" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" DEPEND="" -RDEPEND="${DEPEND} - sci-biology/lastz" - -S="${WORKDIR}"/YASRA - -src_install(){ - emake install DESTDIR="$D" -} +RDEPEND="sci-biology/lastz" diff --git a/sci-biology/caftools/ChangeLog b/sci-biology/caftools/ChangeLog new file mode 100644 index 000000000..af2ad47b4 --- /dev/null +++ b/sci-biology/caftools/ChangeLog @@ -0,0 +1,8 @@ +# ChangeLog for sci-biology/caftools +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -caftools-2.0.ebuild, + caftools-2.0.2.ebuild, metadata.xml: + Drop old; Bump to EAPI=5 and fix license + diff --git a/sci-biology/caftools/Manifest b/sci-biology/caftools/Manifest index 61d49e197..dbbbb7f44 100644 --- a/sci-biology/caftools/Manifest +++ b/sci-biology/caftools/Manifest @@ -1,2 +1,2 @@ -DIST caftools-2.0.2.tar.gz 2645554 SHA256 7be5eafbd6817a7869f73c7540b5fdfe184b0be28624cc6ca9a01c52a140d4a2 -DIST caftools-2.0.tar.gz 2644892 SHA256 b41f323ceb3fd260d6c2ecff1f285548f40301065cea54687eb96717534eaad9 +DIST caftools-2.0.2.tar.gz 2645554 SHA256 7be5eafbd6817a7869f73c7540b5fdfe184b0be28624cc6ca9a01c52a140d4a2 SHA512 0c1a7f2127538ef932139cfee6bc6acb2411765d1006d508e65647ec74d1677a6ecd25b98cc37075bd8e5b0b1a245c11c1029cbbc51eefb46023bd121fdb2f1d WHIRLPOOL 84313e00f6f4c018bc65b6e173827a6e1ef8fd2dc5e5e63e186fb56bc9e5b66b2f25037a1536a8cb57af71603b31ed74ff505dbc43d4deb7d2eeae57ea729bfe +DIST caftools-2.0.tar.gz 2644892 SHA256 b41f323ceb3fd260d6c2ecff1f285548f40301065cea54687eb96717534eaad9 SHA512 0b2b5d09d503b900b275efd61dfa1c5b01259e53c392d68626d9c5081add27ca87b324b5702ec18293415b788208c547eb31e461861f1244b759e28221244417 WHIRLPOOL 13c2e24ce803c09f1d596a4c05f146b869e5ebdeff9f648a0468853feb7d142927d3d78339ac2414482335e5f7ca8352ea9b196f8542f4b3ff5e36fef762398e diff --git a/sci-biology/caftools/caftools-2.0.2.ebuild b/sci-biology/caftools/caftools-2.0.2.ebuild index c1932e1f4..3f8ece67d 100644 --- a/sci-biology/caftools/caftools-2.0.2.ebuild +++ b/sci-biology/caftools/caftools-2.0.2.ebuild @@ -1,45 +1,45 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 inherit eutils DESCRIPTION="CAF is a text format for describing sequence assemblies" HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/" -SRC_URI="ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/caftools-2.0.2.tar.gz - ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/caftools-2.0.tar.gz" -# another source with only the old version is at -# ftp://ftp.sanger.ac.uk/pub4/resources/software/caf/caftools-2.0.tar.gz -# newer version will probably appear at ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/ +SRC_URI=" + ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${P}.tar.gz + ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${PN}-2.0.tar.gz" -LICENSE="as-is" +LICENSE="GRL" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="sci-libs/io_lib - >=dev-lang/perl-5.002" +DEPEND=" + sci-libs/io_lib + dev-lang/perl" RDEPEND="${DEPEND}" src_prepare(){ - epatch "${FILESDIR}"/Makefile.in-"${PV}".patch || die - mv "${WORKDIR}"/caftools-2.0/man/*.1 "${WORKDIR}"/caftools-2.0/man/*.5 "${S}"/man || die + epatch "${FILESDIR}"/Makefile.in-"${PV}".patch + mv "${WORKDIR}"/caftools-2.0/man/*.{1,5} "${S}"/man/ || die } src_configure(){ - econf || die - sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' Makefile || die - sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' src/Makefile || die + default + sed \ + -e 's:prefix = /usr:prefix = $(DESTDIR)/usr:' \ + -i Makefile src/Makefile || die } # TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME # The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files, # not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help. src_install(){ - emake install DESTDIR="${D}" || die + default doman man/*.[1-5] || die - einfo "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/" - einfo "for some reason caf_find_misassemblies is gone from 2.0.2 version" + elog "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/" + elog "for some reason caf_find_misassemblies is gone from 2.0.2 version" } diff --git a/sci-biology/caftools/caftools-2.0.ebuild b/sci-biology/caftools/caftools-2.0.ebuild deleted file mode 100644 index 482bddf92..000000000 --- a/sci-biology/caftools/caftools-2.0.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit eutils - -DESCRIPTION="CAF is a text format for describing sequence assemblies" -HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/" -SRC_URI="ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/caftools-2.0.tar.gz" -# another source with only the old version is at -# ftp://ftp.sanger.ac.uk/pub4/resources/software/caf/caftools-2.0.tar.gz -# newer version will probably appear at ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/ - -LICENSE="as-is" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="sci-libs/io_lib - >=dev-lang/perl-5.002" -RDEPEND="${DEPEND}" - -src_prepare(){ - epatch "${FILESDIR}"/Makefile.in.patch || die -} - -src_configure(){ - econf || die - sed -i 's#prefix = /usr#prefix = $(DESTDIR)/usr#' Makefile || die - sed -i 's#prefix = /usr#\#prefix = $(DESTDIR)/usr#' src/Makefile || die -} - -src_install(){ - emake install DESTDIR="${D}" || die - einfo "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/" -} diff --git a/sci-biology/caftools/metadata.xml b/sci-biology/caftools/metadata.xml index 4f255d9b2..e57f444c5 100644 --- a/sci-biology/caftools/metadata.xml +++ b/sci-biology/caftools/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <longdescription>CAF is a text format for describing sequence assemblies. It is acedb-compliant and is an extension of the ace-file format used earlier, but with support for base quality measures and a more extensive description of the Sequence data.</longdescription> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <longdescription> + CAF is a text format for describing sequence assemblies. It is acedb-compliant + and is an extension of the ace-file format used earlier, but with support for + base quality measures and a more extensive description of the Sequence data. + </longdescription> </pkgmetadata> diff --git a/sci-biology/cutadapt/ChangeLog b/sci-biology/cutadapt/ChangeLog index 7a23b4e2a..ad14cdd33 100644 --- a/sci-biology/cutadapt/ChangeLog +++ b/sci-biology/cutadapt/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/cutadapt -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -cutadapt-1.0.ebuild, + +cutadapt-1.2.1.ebuild, metadata.xml: + Version BUmp; BUmp to EAPI5 and distutils-r1.eclass + *cutadapt-1.0 (02 Mar 2012) 02 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/cutadapt/Manifest b/sci-biology/cutadapt/Manifest index 4bbdb1cc0..d1f5dc4ae 100644 --- a/sci-biology/cutadapt/Manifest +++ b/sci-biology/cutadapt/Manifest @@ -1 +1 @@ -DIST cutadapt-1.0.tar.gz 66166 SHA256 8b2a608eb6f73d9cbc3ee04eb4726d4067d6b128d23eba585ceed1aa532e4416 SHA512 dea81ab4ffd640ce43fd2184bb01223d6f23428bbb26ddaf8659046dbf1e635b8ec3e4d66fd0d5ffd26c4b43df3a1e981ea08345d0639c98e5ea887faa3f4adb WHIRLPOOL 7926863a727176ab13c381cd732207a55dc5f0220edabf83353ec16d4fbbb0dcf08558085bc7aec9b438a265010a85d020c9c92d81395cac8f0d63d370776eba +DIST cutadapt-1.2.1.tar.gz 104440 SHA256 1baf91c7351ee3464cd01a7f767fe474675ab1b1f7bb110ffe3722e8126ed5cf SHA512 5cd48f342ed75d18780ec63c73f2c42d239253d8dded3161c39f7a26e915f195055c8c4097305246a1418f8b4d3c8853adc1074cbe2a9c1a1b0af644e36771b6 WHIRLPOOL b5c6ceb65be0fcfe418b31cb4c2f8b427d017f71eed182585dc4353079df21ba2ae16354bb6cfcc17bfb39d155ae87fc97fed55b3d0f6ebc68197d98c395c31e diff --git a/sci-biology/cutadapt/cutadapt-1.0.ebuild b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild index add090cc6..40ece0c59 100644 --- a/sci-biology/cutadapt/cutadapt-1.0.ebuild +++ b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=2 -PYTHON_DEPEND="2:2.6" -SUPPORT_PYTHON_ABIS="1" +EAPI=5 -inherit distutils +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit distutils-r1 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data" HOMEPAGE="https://code.google.com/p/cutadapt/" @@ -16,6 +16,3 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" diff --git a/sci-biology/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml index 07b525505..2bc893037 100644 --- a/sci-biology/cutadapt/metadata.xml +++ b/sci-biology/cutadapt/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/sci-biology/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog index 3205cfc85..87308e6e1 100644 --- a/sci-biology/tablet-bin/ChangeLog +++ b/sci-biology/tablet-bin/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-biology/tablet-bin -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> tablet-bin-1.13.05.17.ebuild: + Version BUmp; BUmp to EAPI5 and python-r1.eclass; drop addpredict + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -tablet-bin-1.11.05.03.ebuild, + -tablet-bin-1.11.11.01.ebuild, +tablet-bin-1.13.05.17.ebuild, metadata.xml: + Version BUmp; BUmp to EAPI5 and python-r1.eclass + 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> tablet-bin-1.11.11.01.ebuild: adjust PATH to point to the installation place diff --git a/sci-biology/tablet-bin/Manifest b/sci-biology/tablet-bin/Manifest index ae6afbe26..18833160e 100644 --- a/sci-biology/tablet-bin/Manifest +++ b/sci-biology/tablet-bin/Manifest @@ -1,3 +1,2 @@ DIST coveragestats.py 4800 SHA256 358b686d00fd75d2cc9af490b0e7d635f74cbb1c0b153df22d8ff879884d47bc SHA512 d5688832c13dc9c2e2e015df0b5c50113f72e2eeae076d479c43b65a4b028f8dcfa5f0fb833b4341d76d3956ea27707c55a51389b73a2efed6abd2b96ccdc3cd WHIRLPOOL 0b1eb20189b343d6014097748c053f35f8ad162400312cfbde16bac7fee52f24ac8b0055e991c823dcb64d7a20df3fbb88d8cd6119f838d4e9a5f26e82604664 -DIST tablet_linux_x86_1_11_05_03.sh 24035425 SHA256 3c7de5f0e5d37019485612723dfd3b17fd34e24df8986eb535fcb0335f8b2e99 -DIST tablet_linux_x86_1_11_11_01.sh 23481558 SHA256 9dbbd9ecf1c20e39b978a4be88707593c37073407af951cbf7a9b3d16e6daf23 SHA512 95da451959304aafe36c70895cd9f0a89c1749a403e47a4f32b7605e6cbdb5b2f69b03b4177fd6db45cbdba76e2f054742179000d29b0574a1f4541f335aeaa2 WHIRLPOOL cae67ca8338aa23781f91cd235ecc1bd082b04ada80a158d827acf33c04d8bd63e89883790dd3945938e1405c2b6a0903d4e10ffe40c3fe7e0e042390ba1cabe +DIST tablet-bin-1.13.05.17.sh 35467547 SHA256 6da2cbb8d15433cdf022c93f466d355515a9c1c8f89dcdab4c2e9543bee415e4 SHA512 532900242ef3b3a46a6e6379c29b627c9f337198cf230273eb1da4c269b6f09a49bc7c5ea28a1ee4caa4f7d7a76ba0e0f18330a538428e49b8f1d36c3bfecb78 WHIRLPOOL 299f23da5f6192a7802f86e61e2c5655711d0d672e28cdd257fdd179d76e15e1b951fa42ec2b28e4568063197b14e1884d61992b7ff2e864fa86c3dad2141c14 diff --git a/sci-biology/tablet-bin/metadata.xml b/sci-biology/tablet-bin/metadata.xml index 07b525505..2bc893037 100644 --- a/sci-biology/tablet-bin/metadata.xml +++ b/sci-biology/tablet-bin/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/sci-biology/tablet-bin/tablet-bin-1.11.11.01.ebuild b/sci-biology/tablet-bin/tablet-bin-1.11.11.01.ebuild deleted file mode 100644 index 3e6d6e64f..000000000 --- a/sci-biology/tablet-bin/tablet-bin-1.11.11.01.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit java-pkg-2 python - -DESCRIPTION="Viewer of next generation sequence assemblies and alignments." -HOMEPAGE="http://bioinf.scri.ac.uk/tablet/" -SRC_URI="http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_1_11_11_01.sh - http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py" - -# Upstream says regarding source code unavailability: -# Tablet uses a modified version of the BSD License which has been edited to -# remove references to distribution and use in source forms. This means that -# we are happy for you to distribute and use Tablet however you please, but we -# do not (yet) want to make the source code publicly available. - -# The licence file itself is in the installer, and ends up on disk after -# installation at /opt/Tablet/docs/tablet.html -# The original BSD licence was modified to remove references to distribution -# and use in source forms, because we cannot make the source code available -# for Tablet. - -LICENSE="Tablet" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND} - virtual/jre - dev-lang/python" - -MYPV="$(replace_all_version_separators '_')" - -pkg_setup() { - einfo "Fixing java access violations ..." - # bug 387227 - addpredict /proc/self/coredump_filter -} - -src_install() { - # In theory it seems this binary package could be installed through ant - # instead of the install4j package which is not easy to be forced - # non-interactive. The below approach via install4j is not ideal but works. - sed "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile > "${DISTDIR}"/response.varfile || die "sed failed" - - # the intallation script somehow does not pickup - # -varfile="${DISTDIR}"/response.varfile from the commandline and therefore - # we place the file rather directly into the place where it should reside. - # In the file you can read details how the variables were mangled. For - # example, the trick with sys.symlinkDir in the response.varfile is to - # disable the installation process to symlink from /usr/local/bin/table to - # /opt/Tablet/tablet. That was logged in that file with the following line: - # - # /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String] - # - # The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile - mkdir -p "${D}"/opt/Tablet/.install4j || die "Cannot pre-create "${D}"/opt/Tablet/.install4j/" - cat "${DISTDIR}"/response.varfile > "${D}"/opt/Tablet/.install4j/response.varfile || die "Cannot write "${D}"/opt/Tablet/.install4j/response.varfile" - - # make sure we force java to point a to $HOME which is inside our sanbox - # directory area. We force -Duser.home . It seems also -Dinstall4j.userHome - # could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/ - sed "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" -i "${DISTDIR}"/tablet_linux_x86_"${MYPV}".sh || die "failed to set userHome value" - sh "${DISTDIR}"/tablet_linux_x86_"${MYPV}".sh -q -overwrite -varfile="${DISTDIR}"/response.varfile --destination="${D}"/opt/Tablet -dir "${D}"/opt/Tablet || die "Failed to run the self-extracting exe file" - dobin "${DISTDIR}"/coveragestats.py - - echo "PATH=/opt/Tablet" > 99Tablet - doenvd 99Tablet || die -} diff --git a/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild b/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild index 32cc463ee..762e888aa 100644 --- a/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild +++ b/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild @@ -1,15 +1,18 @@ -# Copyright 1999-2011 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 -inherit java-pkg-2 python +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit java-pkg-2 python-r1 DESCRIPTION="Viewer of next generation sequence assemblies and alignments." HOMEPAGE="http://bioinf.scri.ac.uk/tablet/" -SRC_URI="http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_1_11_05_03.sh - http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py" +SRC_URI=" + http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh + http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py" # Upstream says regarding source code unavailability: # Tablet uses a modified version of the BSD License which has been edited to @@ -28,16 +31,26 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="${PYTHON_DEPS}" RDEPEND="${DEPEND} - virtual/jre - dev-lang/python" + virtual/jre" + +S="${WORKDIR}" + +src_unpack() { + local file + for file in ${A}; do + cp "${DISTDIR}"/${file} "${WORKDIR}" || die + done +} src_install() { # In theory it seems this binary package could be installed through ant # instead of the install4j package which is not easy to be forced # non-interactive. The below approach via install4j is not ideal but works. - sed "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile > "${DISTDIR}"/response.varfile || die "sed failed" + sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed" # the intallation script somehow does not pickup # -varfile="${DISTDIR}"/response.varfile from the commandline and therefore @@ -47,16 +60,30 @@ src_install() { # disable the installation process to symlink from /usr/local/bin/table to # /opt/Tablet/tablet. That was logged in that file with the following line: # - # /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String] + # /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: + # Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String] # # The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile - mkdir -p "${D}"/opt/Tablet/.install4j || die "Cannot pre-create "${D}"/opt/Tablet/.install4j/" - cat "${DISTDIR}"/response.varfile > "${D}"/opt/Tablet/.install4j/response.varfile || die "Cannot write "${D}"/opt/Tablet/.install4j/response.varfile" + dodir /opt/Tablet/.install4j + cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die # make sure we force java to point a to $HOME which is inside our sanbox # directory area. We force -Duser.home . It seems also -Dinstall4j.userHome # could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/ - sed "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${D}"/../temp -Dinstall4j.jvmDir#" -i "${DISTDIR}"/tablet_linux_x86_1_11_05_03.sh || die "failed to set userHome value" - sh "${DISTDIR}"/tablet_linux_x86_1_11_05_03.sh -q -overwrite -varfile="${DISTDIR}"/response.varfile --destination="${D}"/opt/Tablet -dir "${D}"/opt/Tablet || die "Failed to run the self-extracting exe file" - dobin "${DISTDIR}"/coveragestats.py + sed \ + -e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \ + -i "${WORKDIR}"/${P}.sh || die + sh \ + "${WORKDIR}"/${P}.sh \ + -q -overwrite \ + -varfile="${DISTDIR}"/response.varfile \ + --destination="${ED}"/opt/Tablet \ + -dir "${ED}"/opt/Tablet || die + + rm -rf "${ED}"/opt/Tablet/jre || die + + python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py + + echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet + doenvd 99Tablet || die } diff --git a/sci-chemistry/chemBuild/ChangeLog b/sci-chemistry/chemBuild/ChangeLog index a592f6b45..7aa6b2ef5 100644 --- a/sci-chemistry/chemBuild/ChangeLog +++ b/sci-chemistry/chemBuild/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-chemistry/chemBuild -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> chemBuild-1.0.2.ebuild, + files/chemBuild, metadata.xml: + Bump EAPI and python eclass + 21 Sep 2012; Justin Lecher <jlec@gentoo.org> chemBuild-1.0.2.ebuild: Needs webkit support in pyside diff --git a/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild b/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild index dece95eb2..3f4733f8b 100644 --- a/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild +++ b/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 -PYTHON_DEPEND="2" +PYTHON_COMPAT=( python{2_6,2_7} ) -inherit python toolchain-funcs +inherit python-single-r1 toolchain-funcs DESCRIPTION="Graphical tool to construct chemical compound definitions for NMR" HOMEPAGE="http://www.ccpn.ac.uk/software/chembuild" @@ -17,7 +17,9 @@ LICENSE="|| ( CCPN LGPL-2.1 )" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" -RDEPEND="dev-python/pyside[webkit]" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="dev-python/pyside[webkit,${PYTHON_USEDEP}]" DEPEND="" S="${WORKDIR}"/ccpnmr/ccpnmr3.0/ @@ -28,11 +30,6 @@ S="${WORKDIR}"/ccpnmr/ccpnmr3.0/ #unbundle inchi #parallel build -pkg_setup() { - python_set_active_version 2 - python_pkg_setup -} - src_install() { local in_path=$(python_get_sitedir)/${PN} local _file @@ -44,25 +41,17 @@ src_install() { -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|$(PYTHON -a)|g" \ + -e "s|gentoopython|${PYTHON}|g" \ -e "s|gentoousr|${EPREFIX}/usr|g" \ -e "s|//|/|g" \ "${FILESDIR}"/${PN} > "${ED}"/usr/bin/${PN} || die fperms 755 /usr/bin/${PN} - insinto ${in_path} - rm -rf cNg license || die ebegin "Installing main files" - doins -r * + python_moduleinto ${PN} + python_domodule * + python_optimize eend } - -pkg_postinst() { - python_mod_optimize ${PN} -} - -pkg_postrm() { - python_mod_cleanup ${PN} -} diff --git a/sci-chemistry/chemBuild/files/chemBuild b/sci-chemistry/chemBuild/files/chemBuild index c6d3d31ac..308804158 100644 --- a/sci-chemistry/chemBuild/files/chemBuild +++ b/sci-chemistry/chemBuild/files/chemBuild @@ -1,7 +1,7 @@ #!/bin/bash export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/chemBuild/python +export PYTHONPATH=${CCPNMR_TOP_DIR}/chemBuild/python export LD_LIBRARY_PATH=gentoolibdir export TCL_LIBRARY=gentootcl export TK_LIBRARY=gentootk diff --git a/sci-chemistry/chemBuild/metadata.xml b/sci-chemistry/chemBuild/metadata.xml index d369d068f..897aa2e6b 100644 --- a/sci-chemistry/chemBuild/metadata.xml +++ b/sci-chemistry/chemBuild/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> + <herd>sci</herd> </pkgmetadata> diff --git a/sci-chemistry/cnsface/ChangeLog b/sci-chemistry/cnsface/ChangeLog index 8b8ef62da..91fb75e01 100644 --- a/sci-chemistry/cnsface/ChangeLog +++ b/sci-chemistry/cnsface/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-chemistry/cnsface -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> cnsface-0.0.12.ebuild, + metadata.xml: + Bump to EAPI5 and distutils-r1.eclass + *cnsface-0.0.12 (01 Dec 2010) 01 Dec 2010; Justin Lecher <jlec@gentoo.org> +files/0.0.12-binary.patch, diff --git a/sci-chemistry/cnsface/Manifest b/sci-chemistry/cnsface/Manifest index b1bdb72df..a9914275b 100644 --- a/sci-chemistry/cnsface/Manifest +++ b/sci-chemistry/cnsface/Manifest @@ -1 +1 @@ -DIST cnsface-0.0.12-altoona.tar.gz 1442309 SHA256 add1a1f17fc103a5bb3a75003d8c0e64626b35c6ebbb8e2aa87fed1a0c05b655 +DIST cnsface-0.0.12-altoona.tar.gz 1442309 SHA256 add1a1f17fc103a5bb3a75003d8c0e64626b35c6ebbb8e2aa87fed1a0c05b655 SHA512 73bfaf75e89da0066d3ddab1e005b487b837719d5fe4235f8ebad31e84ab715fe829b094769982784c65641cb8c4febc827b2abe7737cf2c251bf4ae293e37c7 WHIRLPOOL f91dfaa22e619f3ab88c0f42d0cbed7df0dfc3d50707097808dc676ec47c067104bb1fcc8ef365a72b7c8d0853ede8b4b52d047ee5dc95ccd48779c1afc9f4a3 diff --git a/sci-chemistry/cnsface/cnsface-0.0.12.ebuild b/sci-chemistry/cnsface/cnsface-0.0.12.ebuild index 6c2903879..55e42f653 100644 --- a/sci-chemistry/cnsface/cnsface-0.0.12.ebuild +++ b/sci-chemistry/cnsface/cnsface-0.0.12.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=5 -PYTHON_DEPEND="2" -SUPPORT_PYTHON_ABIS="1" -RESTRICT_PYTHON_ABIS="3.*" +PYTHON_COMPAT=( python{2_6,2_7} ) -inherit distutils eutils +inherit distutils-r1 DESCRIPTION="GUI for the Crystallography and NMR System" HOMEPAGE="http://cnsface.sourceforge.net" -SRC_URI="mirror://sourceforge/${P}-altoona.tar.gz" +SRC_URI="mirror://sourceforge/project/cnsface/cnsface/Altoona/${P}-altoona.tar.gz" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" @@ -20,13 +18,10 @@ LICENSE="GPL-2" IUSE="" RDEPEND=" - dev-python/wxpython:2.8 + dev-python/wxpython:2.8[${PYTHON_USEDEP}] sci-chemistry/cns" DEPEND="${RDEPEND}" S="${WORKDIR}"/${P}-altoona -src_prepare() { - epatch "${FILESDIR}"/${PV}-binary.patch - distutils_src_prepare -} +PATCHES=( "${FILESDIR}"/${PV}-binary.patch ) diff --git a/sci-chemistry/cnsface/metadata.xml b/sci-chemistry/cnsface/metadata.xml index 0fbe927f0..d410f1573 100644 --- a/sci-chemistry/cnsface/metadata.xml +++ b/sci-chemistry/cnsface/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-chemistry</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> + <herd>sci-chemistry</herd> + <maintainer> + <email>sci@gentoo.org</email> + </maintainer> </pkgmetadata> diff --git a/sci-chemistry/modeller/ChangeLog b/sci-chemistry/modeller/ChangeLog index 17fea516e..198256b1f 100644 --- a/sci-chemistry/modeller/ChangeLog +++ b/sci-chemistry/modeller/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-chemistry/modeller -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -modeller-9.8.ebuild, + +modeller-9.12.ebuild, metadata.xml: + Version BUmp; BUmp to EAPI5 and distutils-r1.eclass + *modeller-9.8 (16 Jun 2010) 16 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/9v5-setup.patch, diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest index f3078a1c8..a5b04d5c2 100644 --- a/sci-chemistry/modeller/Manifest +++ b/sci-chemistry/modeller/Manifest @@ -1 +1 @@ -DIST modeller-9v8.tar.gz 51539572 SHA256 3d5c629f97a2b89722fe5b7414ad97b0361799714db0323536df45f55b2777c7 +DIST modeller-9.12.tar.gz 29273842 SHA256 65051f7f1682cf7dcf77f0bc4d68f1ee5b64789f750e9aa6900e1cc92dc4e1f9 SHA512 5c0acaf453771347a9de3a0c7240f7ce376244803748edb28923dbaefda779041211ef4b26af5a2774bdf6bc63d7c7d7e62e1354e1550a6742c9575076864352 WHIRLPOOL a363efdd2bba8db8268774745f32b1e8e6a9d88e6a6154ce00c7be65861fc834ef1a804fa9f0575d2af2ff1211728aacf8408d28319df68b14f3a3598d55c307 diff --git a/sci-chemistry/modeller/metadata.xml b/sci-chemistry/modeller/metadata.xml index 9ac9ffdb3..51fdedab1 100644 --- a/sci-chemistry/modeller/metadata.xml +++ b/sci-chemistry/modeller/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-chemistry</herd> + <herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/modeller/modeller-9.8.ebuild b/sci-chemistry/modeller/modeller-9.12.ebuild index b0c24c18c..0cabf476a 100644 --- a/sci-chemistry/modeller/modeller-9.8.ebuild +++ b/sci-chemistry/modeller/modeller-9.12.ebuild @@ -1,19 +1,17 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=5 -PYTHON_DEPEND="2:2.6" +PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) +PYTHON_COMPAT=( python{2_6,2_7} ) -inherit distutils eutils versionator - -MY_PV="$(replace_all_version_separators v)" -MY_P="${PN}-${MY_PV}" +inherit distutils-r1 eutils versionator DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures" -SRC_URI="http://salilab.org/${PN}/${MY_PV}/${PN}-${MY_PV}.tar.gz" HOMEPAGE="http://salilab.org/modeller/" +SRC_URI="http://salilab.org/${PN}/${PV}/${P}.tar.gz" LICENSE="modeller" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" @@ -25,82 +23,77 @@ RESTRICT="mirror" DEPEND=">=dev-lang/swig-1.3" RDEPEND="" -S="${WORKDIR}/${MY_P}" - INPATH="${EPREFIX}"/opt/modeller${ver} -QA_TEXTRELS="${INPATH#/}/*" -QA_EXECSTACK="${INPATH#/}/*" -QA_PRESTRIPPED="${INPATH#/}/bin/.* ${INPATH#/}/lib/*/.*" -QA_DT_HASH=" - ${INPATH#/}/bin/.* - ${INPATH#/}/lib/*/.*" +QA_PREBUILT="/opt/*" -pkg_setup() { - python_set_active_version 2 +DISTUTILS_NO_PARALLEL_BUILD=true +pkg_setup() { case ${ARCH} in - x86) EXECTYPE="i386-intel8";; - amd64) EXECTYPE="x86_64-intel8";; - *) ewarn "Your arch "${ARCH}" does not appear supported at this time."||\ - die "Unsupported Arch";; + x86) + EXECTYPE="i386-intel8";; + amd64) + EXECTYPE="x86_64-intel8";; + *) + die "Your arch "${ARCH}" does not appear supported at this time.";; esac } -src_prepare(){ +python_prepare_all(){ sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die } -src_compile(){ +python_compile(){ + cd src/swig + swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die + distutils-r1_python_compile +} + +python_install() { cd src/swig - swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i - distutils_src_compile + distutils-r1_python_install } -src_install(){ +python_install_all(){ + cd "${S}" sed \ - -e "s:EXECUTABLE_TYPE${MY_PV}=xxx:EXECUTABLE_TYPE${MY_PV}=${EXECTYPE}:g" \ - -e "s:MODINSTALL${MY_PV}=xxx:MODINSTALL${MY_PV}=\"${INPATH}\":g" \ - bin/modscript > "${T}/mod${MY_PV}" + -e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \ + -e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \ + -i bin/modscript || die sed -e "s;@TOPDIR\@;\"${INPATH}\";" \ -e "s;@EXETYPE\@;${EXECTYPE};" \ bin/modpy.sh.in > "${T}/modpy.sh" insinto ${INPATH} - doins -r modlib || die + doins -r modlib + python_foreach_impl python_domodule modlib/modeller insinto ${INPATH}/bin - doins -r bin/{lib,*top} || die + doins -r bin/{lib,*top} + exeinto ${INPATH}/bin - doexe bin/{modslave.py,mod${MY_PV}_${EXECTYPE}} || die - doexe "${T}/mod${MY_PV}" || die - doexe "${T}/modpy.sh" || die - dosym ${INPATH}/bin/mod${MY_PV} /opt/bin/mod${MY_PV} || die - dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh || die + doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh + + python_foreach_impl python_doscript bin/modslave.py + dosym ${INPATH}/bin/modscript /opt/bin/mod${PV} + dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh exeinto ${INPATH}/lib/${EXECTYPE}/ - doexe lib/${EXECTYPE}/lib* || die - dosym libmodeller.so.5 ${INPATH}/lib/${EXECTYPE}/libmodeller.so || die - doexe src/swig/build/lib.linux-$(uname -m)-$(python_get_version)/_modeller.so || die + doexe lib/${EXECTYPE}/lib* + dosym libmodeller.so.5 ${INPATH}/lib/${EXECTYPE}/libmodeller.so + + use doc && HTML_DOCS=( doc/. ) + distutils-r1_python_install_all - dodoc README INSTALLATION || die - if use doc; then - dohtml doc/* || die - fi if use examples; then insinto /usr/share/${PN}/ - doins -r examples || die + doins -r examples fi - - dosym ${INPATH}/lib/${EXECTYPE}/_modeller.so \ - $(python_get_sitedir)/_modeller.so || die - dosym _modeller.so $(python_get_sitedir)/modeller.so || die } pkg_postinst() { - python_mod_optimize "${INPATH}/" - if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py fi @@ -117,7 +110,6 @@ pkg_postinst() { } pkg_postrm() { - python_mod_cleanup "${INPATH}/" ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py" ewarn "that you need to remove to completely get rid of modeller." } |