sci-biology/biopython: Import changes from sci overlay

(Portage version: 2.2.10/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

4 files changed, 100 insertions, 1 deletions

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
index 119ccab60910..b15feab77d1a 100644
--- a/sci-biology/biopython/ChangeLog
+++ b/sci-biology/biopython/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/biopython
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.74 2014/01/30 15:15:24 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.75 2014/05/07 11:00:43 jlec Exp $
+
+*biopython-1.63-r1 (07 May 2014)
+
+  07 May 2014; Justin Lecher <jlec@gentoo.org> +biopython-1.63-r1.ebuild,
+  +files/SffIO_broken_padding.patch, +files/SffIO_error_in_check_eof.patch:
+  Import changes from sci overlay
 
 *biopython-1.63 (30 Jan 2014)
 
diff --git a/sci-biology/biopython/biopython-1.63-r1.ebuild b/sci-biology/biopython/biopython-1.63-r1.ebuild
new file mode 100644
index 000000000000..eeeb100d40fc
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.63-r1.ebuild
@@ -0,0 +1,52 @@
+# 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-1.63-r1.ebuild,v 1.1 2014/05/07 11:00:43 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="${RDEPEND}
+	sys-devel/flex"
+
+DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
+
+PATCHES=(
+	"${FILESDIR}/SffIO_error_in_check_eof.patch"
+	"${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/files/SffIO_broken_padding.patch b/sci-biology/biopython/files/SffIO_broken_padding.patch
new file mode 100644
index 000000000000..a009c58cbd04
--- /dev/null
+++ b/sci-biology/biopython/files/SffIO_broken_padding.patch
@@ -0,0 +1,27 @@
+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
new file mode 100644
index 000000000000..9059604f6faa
--- /dev/null
+++ b/sci-biology/biopython/files/SffIO_error_in_check_eof.patch
@@ -0,0 +1,14 @@
+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: