[gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/

["Justin Lecher" <jlec@gentoo.org>]

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 <mmokrejs@fold.natur.cuni.cz>
-  -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 <mmokrejs@fold.natur.cuni.cz>
-  +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 <mmokrejs@fold.natur.cuni.cz>
-  -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 <mmokrejs@fold.natur.cuni.cz>
-  +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>