Drop old

(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

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,