diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/biopython/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-biology/biopython/biopython-1.57.ebuild | 55 | ||||
| -rw-r--r-- | sci-biology/biopython/biopython-1.64.ebuild | 47 | ||||
| -rw-r--r-- | sci-biology/biopython/files/SffIO_broken_padding.patch | 27 | ||||
| -rw-r--r-- | sci-biology/biopython/files/SffIO_error_in_check_eof.patch | 14 | ||||
| -rw-r--r-- | sci-biology/biopython/files/biopython-1.51-flex.patch | 21 | ||||
| -rw-r--r-- | sci-biology/biopython/files/biopython-1.62-SffIO.patch | 36 |
7 files changed, 7 insertions, 201 deletions
diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog index 569dca4c6a60..4d9275a04df8 100644 --- a/sci-biology/biopython/ChangeLog +++ b/sci-biology/biopython/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-biology/biopython # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.83 2015/03/28 21:39:49 ago Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.84 2015/03/29 09:35:53 jlec Exp $ + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> -biopython-1.57.ebuild, + -biopython-1.64.ebuild, -files/SffIO_broken_padding.patch, + -files/SffIO_error_in_check_eof.patch, -files/biopython-1.51-flex.patch, + -files/biopython-1.62-SffIO.patch: + Drop old 28 Mar 2015; Agostino Sarubbo <ago@gentoo.org> biopython-1.65.ebuild: Stable for ppc, wrt bug #544544 diff --git a/sci-biology/biopython/biopython-1.57.ebuild b/sci-biology/biopython/biopython-1.57.ebuild deleted file mode 100644 index 630ae3b9d3de..000000000000 --- a/sci-biology/biopython/biopython-1.57.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.57.ebuild,v 1.6 2012/12/14 10:00:10 ulm Exp $ - -EAPI=3 -PYTHON_DEPEND="2" -SUPPORT_PYTHON_ABIS="1" -RESTRICT_PYTHON_ABIS="3.* *-jython" - -inherit distutils 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/${P}.tar.gz" - -LICENSE="HPND" -SLOT="0" -KEYWORDS="amd64 ppc x86" -IUSE="mysql postgres" - -RDEPEND=" - dev-python/numpy - dev-python/reportlab - mysql? ( dev-python/mysql-python ) - postgres? ( dev-python/psycopg )" -DEPEND="${RDEPEND} - sys-devel/flex" - -PYTHON_CFLAGS=("2.* + -fno-strict-aliasing") - -DISTUTILS_USE_SEPARATE_SOURCE_DIRECTORIES="1" -DOCS="CONTRIB DEPRECATED NEWS README" -PYTHON_MODNAME="Bio BioSQL" - -src_prepare() { - distutils_src_prepare - epatch "${FILESDIR}/${PN}-1.51-flex.patch" -} - -src_test() { - testing() { - cd Tests - PYTHONPATH="$(ls -d ../build/lib.*)" "$(PYTHON)" run_tests.py - } - python_execute_function --nonfatal -s testing -} - -src_install() { - distutils_src_install - - insinto /usr/share/doc/${PF} - doins -r Doc/* || die "Installation of documentation failed" - insinto /usr/share/${PN} - cp -r --preserve=mode Scripts Tests "${ED}usr/share/${PN}" || die "Installation of shared files failed" -} diff --git a/sci-biology/biopython/biopython-1.64.ebuild b/sci-biology/biopython/biopython-1.64.ebuild deleted file mode 100644 index 09e531bc734d..000000000000 --- a/sci-biology/biopython/biopython-1.64.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.64.ebuild,v 1.2 2015/03/03 16:03:42 jlec Exp $ - -EAPI=5 - -PYTHON_COMPAT=( python2_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[${PYTHON_USEDEP}] ) - postgres? ( dev-python/psycopg:2[${PYTHON_USEDEP}] )" -DEPEND="${RDEPEND} - sys-devel/flex" - -DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) - -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 a009c58cbd04..000000000000 --- 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 9059604f6faa..000000000000 --- 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 afd509444c68..000000000000 --- 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 7f2208ef63c4..000000000000 --- 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, |