commit: 8f906e56d735e0cb1b85041448dbfadcf6d5e8c8 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Wed May 7 10:29:21 2014 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Wed May 7 10:29:21 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8f906e56
Imported to tree Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> --- sci-biology/biopython/ChangeLog | 40 ---------------- sci-biology/biopython/biopython-1.62-r3.ebuild | 53 ---------------------- sci-biology/biopython/biopython-1.62-r4.ebuild | 53 ---------------------- sci-biology/biopython/biopython-1.63-r1.ebuild | 53 ---------------------- .../biopython/files/SffIO_broken_padding.patch | 27 ----------- .../biopython/files/SffIO_error_in_check_eof.patch | 14 ------ .../biopython/files/biopython-1.51-flex.patch | 21 --------- .../biopython/files/biopython-1.62-SffIO.patch | 36 --------------- sci-biology/biopython/metadata.xml | 5 -- 9 files changed, 302 deletions(-) diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog deleted file mode 100644 index 796f6a9..0000000 --- a/sci-biology/biopython/ChangeLog +++ /dev/null @@ -1,40 +0,0 @@ -# ChangeLog for sci-biology/biopython -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 18 Apr 2014; Martin Mokrejs <[email protected]> - -files/SeqRecord.py.patch, -files/adjust-trimpoints.patch: - sci-biology/biopython: ops, taking back my own testing patches - -*biopython-1.62-r3 (18 Apr 2014) -*biopython-1.62-r4 (18 Apr 2014) - - 18 Apr 2014; Martin Mokrejs <[email protected]> - +biopython-1.62-r3.ebuild, +biopython-1.62-r4.ebuild, - +files/SeqRecord.py.patch, +files/SffIO_broken_padding.patch, - +files/adjust-trimpoints.patch, biopython-1.63-r1.ebuild, - files/SffIO_error_in_check_eof.patch, files/biopython-1.51-flex.patch, - files/biopython-1.62-SffIO.patch: - sci-biology/biopython: upstream patch to downgrade an assert to a warning - - 23 Mar 2014; Martin Mokrejs <[email protected]> - -biopython-1.62-r3.ebuild, -biopython-1.62-r4.ebuild, -biopython-1.63.ebuild, - -files/SeqRecord.py.patch, -files/adjust-trimpoints.patch, - biopython-1.63-r1.ebuild: - sci-biology/biopython-1.63-r1: added missing deps on dev-python/rdflib to sync - with official sci-biology/biopython-1.63; dropping sci-biology/biopython-1.63 - from overlay - -*biopython-1.62-r3 (23 Mar 2014) -*biopython-1.62-r4 (23 Mar 2014) -*biopython-1.63-r1 (23 Mar 2014) -*biopython-1.63 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <[email protected]> - +biopython-1.62-r3.ebuild, +biopython-1.62-r4.ebuild, - +biopython-1.63-r1.ebuild, +biopython-1.63.ebuild, +files/SeqRecord.py.patch, - +files/SffIO_error_in_check_eof.patch, +files/adjust-trimpoints.patch, - +files/biopython-1.51-flex.patch, +files/biopython-1.62-SffIO.patch, - +metadata.xml: - sci-biology/biopython-1.63-r1: version bump and an upstream patch to improve - error message diff --git a/sci-biology/biopython/biopython-1.62-r3.ebuild b/sci-biology/biopython/biopython-1.62-r3.ebuild deleted file mode 100644 index 09e6ed7..0000000 --- a/sci-biology/biopython/biopython-1.62-r3.ebuild +++ /dev/null @@ -1,53 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 2013/09/17 16:07:56 jlec Exp $ - -EAPI=5 - -PYTHON_COMPAT=( python{2_6,2_7} ) - -inherit distutils-r1 eutils - -DESCRIPTION="Python modules for computational molecular biology" -HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/"; -SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"; - -LICENSE="HPND" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="mysql postgres" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pygraphviz[${PYTHON_USEDEP}] - dev-python/reportlab[${PYTHON_USEDEP}] - media-gfx/pydot[${PYTHON_USEDEP}] - mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] ) - postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )" -DEPEND="${RDEPEND} - sys-devel/flex" - -DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) - -src_prepare() { - distutils-r1_src_prepare - epatch "${FILESDIR}/${PN}-1.62-SffIO.patch" - epatch "${FILESDIR}/SffIO_error_in_check_eof.patch" - epatch "${FILESDIR}/SffIO_broken_padding.patch" -} - -python_test() { - cd Tests || die - ${PYTHON} run_tests.py || die -} - -python_install_all() { - distutils-r1_python_install_all - - dodir /usr/share/${PN} - cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die -} diff --git a/sci-biology/biopython/biopython-1.62-r4.ebuild b/sci-biology/biopython/biopython-1.62-r4.ebuild deleted file mode 100644 index 09e6ed7..0000000 --- a/sci-biology/biopython/biopython-1.62-r4.ebuild +++ /dev/null @@ -1,53 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 2013/09/17 16:07:56 jlec Exp $ - -EAPI=5 - -PYTHON_COMPAT=( python{2_6,2_7} ) - -inherit distutils-r1 eutils - -DESCRIPTION="Python modules for computational molecular biology" -HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/"; -SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"; - -LICENSE="HPND" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="mysql postgres" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pygraphviz[${PYTHON_USEDEP}] - dev-python/reportlab[${PYTHON_USEDEP}] - media-gfx/pydot[${PYTHON_USEDEP}] - mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] ) - postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )" -DEPEND="${RDEPEND} - sys-devel/flex" - -DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) - -src_prepare() { - distutils-r1_src_prepare - epatch "${FILESDIR}/${PN}-1.62-SffIO.patch" - epatch "${FILESDIR}/SffIO_error_in_check_eof.patch" - epatch "${FILESDIR}/SffIO_broken_padding.patch" -} - -python_test() { - cd Tests || die - ${PYTHON} run_tests.py || die -} - -python_install_all() { - distutils-r1_python_install_all - - dodir /usr/share/${PN} - cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die -} diff --git a/sci-biology/biopython/biopython-1.63-r1.ebuild b/sci-biology/biopython/biopython-1.63-r1.ebuild deleted file mode 100644 index b600748..0000000 --- a/sci-biology/biopython/biopython-1.63-r1.ebuild +++ /dev/null @@ -1,53 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 2013/09/17 16:07:56 jlec Exp $ - -EAPI=5 - -PYTHON_COMPAT=( python{2_6,2_7} ) - -inherit distutils-r1 eutils - -DESCRIPTION="Python modules for computational molecular biology" -HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/"; -SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"; - -LICENSE="HPND" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="mysql postgres" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/rdflib[${PYTHON_USEDEP}] - dev-python/pygraphviz[${PYTHON_USEDEP}] - dev-python/reportlab[${PYTHON_USEDEP}] - media-gfx/pydot[${PYTHON_USEDEP}] - mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] ) - postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )" -DEPEND="${RDEPEND} - sys-devel/flex" - -DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) - -src_prepare() { - epatch "${FILESDIR}/SffIO_error_in_check_eof.patch" - epatch "${FILESDIR}/SffIO_broken_padding.patch" - distutils-r1_src_prepare -} - -python_test() { - cd Tests || die - ${PYTHON} run_tests.py || die -} - -python_install_all() { - distutils-r1_python_install_all - - dodir /usr/share/${PN} - cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die -} diff --git a/sci-biology/biopython/files/SffIO_broken_padding.patch b/sci-biology/biopython/files/SffIO_broken_padding.patch deleted file mode 100644 index a009c58..0000000 --- a/sci-biology/biopython/files/SffIO_broken_padding.patch +++ /dev/null @@ -1,27 +0,0 @@ -diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py -index 735d55b..b89cf41 100644 ---- a/Bio/SeqIO/SffIO.py -+++ b/Bio/SeqIO/SffIO.py -@@ -933,12 +933,20 @@ def _check_eof(handle, index_offset, index_length): - "null padding region ended '.sff' which could " - "be the start of a concatenated SFF file? " - "See offset %i" % (padding, offset)) -+ if padding and not extra: -+ #TODO - Is this error harmless enough to just ignore? -+ import warnings -+ from Bio import BiopythonParserWarning -+ warnings.warn("Your SFF file is technically invalid as it is missing " -+ "a terminal %i byte null padding region." % padding, -+ BiopythonParserWarning) -+ return - if extra.count(_null) != padding: - import warnings - from Bio import BiopythonParserWarning - warnings.warn("Your SFF file is invalid, post index %i byte " -- "null padding region contained data." % padding, -- BiopythonParserWarning) -+ "null padding region contained data: %r" -+ % (padding, extra), BiopythonParserWarning) - - offset = handle.tell() - assert offset % 8 == 0, \ diff --git a/sci-biology/biopython/files/SffIO_error_in_check_eof.patch b/sci-biology/biopython/files/SffIO_error_in_check_eof.patch deleted file mode 100644 index 9059604..0000000 --- a/sci-biology/biopython/files/SffIO_error_in_check_eof.patch +++ /dev/null @@ -1,14 +0,0 @@ -diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py -index 2bb0dac..735d55b 100644 ---- a/Bio/SeqIO/SffIO.py -+++ b/Bio/SeqIO/SffIO.py -@@ -941,7 +941,8 @@ def _check_eof(handle, index_offset, index_length): - BiopythonParserWarning) - - offset = handle.tell() -- assert offset % 8 == 0 -+ assert offset % 8 == 0, \ -+ "Wanted offset %i %% 8 = %i to be zero" % (offset, offset % 8) - # Should now be at the end of the file... - extra = handle.read(4) - if extra == _sff: diff --git a/sci-biology/biopython/files/biopython-1.51-flex.patch b/sci-biology/biopython/files/biopython-1.51-flex.patch deleted file mode 100644 index afd5094..0000000 --- a/sci-biology/biopython/files/biopython-1.51-flex.patch +++ /dev/null @@ -1,21 +0,0 @@ ---- setup.py.old 2008-11-25 18:03:16.000000000 +0100 -+++ setup.py 2008-11-25 18:04:14.000000000 +0100 -@@ -341,12 +341,12 @@ - include_dirs=["Bio"] - ), - #Commented out due to the build dependency on flex, see Bug 2619 --# Extension('Bio.PDB.mmCIF.MMCIFlex', --# ['Bio/PDB/mmCIF/lex.yy.c', --# 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], --# include_dirs=["Bio"], --# libraries=["fl"] --# ), -+ Extension('Bio.PDB.mmCIF.MMCIFlex', -+ ['Bio/PDB/mmCIF/lex.yy.c', -+ 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], -+ include_dirs=["Bio"], -+ libraries=["fl"] -+ ), - Extension('Bio.Nexus.cnexus', - ['Bio/Nexus/cnexus.c'] - ), diff --git a/sci-biology/biopython/files/biopython-1.62-SffIO.patch b/sci-biology/biopython/files/biopython-1.62-SffIO.patch deleted file mode 100644 index 7f2208e..0000000 --- a/sci-biology/biopython/files/biopython-1.62-SffIO.patch +++ /dev/null @@ -1,36 +0,0 @@ ---- Bio/SeqIO/SffIO.py.ori 2013-09-25 13:28:51.000000000 +0200 -+++ Bio/SeqIO/SffIO.py 2013-09-25 13:37:44.000000000 +0200 -@@ -383,7 +383,14 @@ - if padding: - padding = 8 - padding - if handle.read(padding).count(_null) != padding: -- raise ValueError("Post quality %i byte padding region contained data" -+ import warnings -+ from Bio import BiopythonParserWarning -+ warnings.warn("Your SFF file is valid but post quality %i byte " -+ "padding region contains UNUSED data. Was the " -+ "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? " -+ "It did not clear some internal buffer while writing " -+ "out new data so that previous values remained in the" -+ "output unless overwritten by new real values." - % padding) - #print read, name, record_offset - yield name, record_offset ---- Bio/SeqIO/SffIO.py.ori 2013-09-25 14:07:14.000000000 +0200 -+++ Bio/SeqIO/SffIO.py 2013-09-25 14:08:59.000000000 +0200 -@@ -596,7 +596,14 @@ - if padding: - padding = 8 - padding - if handle.read(padding).count(_null) != padding: -- raise ValueError("Post quality %i byte padding region contained data" -+ import warnings -+ from Bio import BiopythonParserWarning -+ warnings.warn("Your SFF file is valid but post quality %i byte " -+ "padding region contains UNUSED data. Was the " -+ "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? " -+ "It did not clear some internal buffer while writing " -+ "out new data so that previous values remained in the" -+ "output unless overwritten by new real values." - % padding) - #Follow Roche and apply most aggressive of qual and adapter clipping. - #Note Roche seems to ignore adapter clip fields when writing SFF, diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml deleted file mode 100644 index f17a827..0000000 --- a/sci-biology/biopython/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <herd>sci-biology</herd> -</pkgmetadata>
