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

[Marius Brehler]

commit:     df096482743b6bfa2598cc52bbb95117952f3b24
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 24 23:02:02 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sat Sep 24 23:02:50 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=df096482

sci-biology/biopython: remove, in main tree

 sci-biology/biopython/biopython-1.67-r1.ebuild     | 60 ---------------
 .../biopython/files/biopython-1.67-pull-884.patch  | 87 ----------------------
 sci-biology/biopython/metadata.xml                 |  8 --
 3 files changed, 155 deletions(-)

diff --git a/sci-biology/biopython/biopython-1.67-r1.ebuild b/sci-biology/biopython/biopython-1.67-r1.ebuild
deleted file mode 100644
index 197e265..0000000
--- a/sci-biology/biopython/biopython-1.67-r1.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_{3,4,5} pypy )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Python modules for computational molecular biology"
-HOMEPAGE="http://www.biopython.org/ https://pypi.python.org/pypi/biopython/"
-SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
-
-LICENSE="HPND"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	dev-python/matplotlib[$(python_gen_usedep 'python*')]
-	dev-python/networkx[$(python_gen_usedep 'python*')]
-	dev-python/numpy[$(python_gen_usedep 'python*')]
-	dev-python/rdflib[$(python_gen_usedep 'python*')]
-	dev-python/pygraphviz[$(python_gen_usedep 'python2*')]
-	dev-python/reportlab[$(python_gen_usedep 'python*')]
-	media-gfx/pydot[$(python_gen_usedep 'python2*')]
-	"
-DEPEND="${RDEPEND}
-	sys-devel/flex"
-
-DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
-
-src_prepare(){
-	epatch "${FILESDIR}"/biopython-1.67-pull-884.patch
-}
-
-python_test() {
-	distutils_install_for_testing
-	cp -r "${S}"/{Doc,Tests} "${TEST_DIR}"/lib/ || die
-	cd "${TEST_DIR}"/lib/Tests || die
-	rm ./test_BioSQL_psycopg2.py ./test_BioSQL_MySQLdb.py ./test_BioSQL_mysql_connector.py || die
-	${PYTHON} run_tests.py --offline --verbose || die
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	dodir /usr/share/${PN}
-	cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
-}
-
-pkg_postinst() {
-	elog "For database support you need to install:"
-	optfeature "MySQL" dev-python/mysql-python
-	optfeature "PostGreSQL" dev-python/psycopg
-	echo
-	elog "Some applications need extra packages:"
-	optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss
-}

diff --git a/sci-biology/biopython/files/biopython-1.67-pull-884.patch b/sci-biology/biopython/files/biopython-1.67-pull-884.patch
deleted file mode 100644
index f2a2537..0000000
--- a/sci-biology/biopython/files/biopython-1.67-pull-884.patch
+++ /dev/null
@@ -1,87 +0,0 @@
---- Bio/SeqRecord.py.old	2016-06-08 15:27:00.000000000 +0200
-+++ Bio/SeqRecord.py	2016-07-22 17:48:19.620712535 +0200
-@@ -292,19 +292,28 @@
-         >>> sub_record.letter_annotations = {}
-         >>> sub_record.letter_annotations
-         {}
-+
-+        Note that if replacing the record's sequence with a sequence of a
-+        different length you must first clear the letter_annotations dict.
-         """)
- 
-     def _set_seq(self, value):
-         # TODO - Add a deprecation warning that the seq should be write only?
-         if self._per_letter_annotations:
--            # TODO - Make this a warning? Silently empty the dictionary?
--            raise ValueError("You must empty the letter annotations first!")
--        self._seq = value
--        try:
--            self._per_letter_annotations = _RestrictedDict(length=len(self.seq))
--        except AttributeError:
--            # e.g. seq is None
--            self._per_letter_annotations = _RestrictedDict(length=0)
-+            if len(self) != len(value):
-+                # TODO - Make this a warning? Silently empty the dictionary?
-+                raise ValueError("You must empty the letter annotations first!")
-+            else:
-+                # Leave the existing per letter annotations unchanged:
-+                self._seq = value
-+        else:
-+            self._seq = value
-+            # Reset the (empty) letter annotations dict with new length:
-+            try:
-+                self._per_letter_annotations = _RestrictedDict(length=len(self.seq))
-+            except AttributeError:
-+                # e.g. seq is None
-+                self._per_letter_annotations = _RestrictedDict(length=0)
- 
-     seq = property(fget=lambda self: self._seq,
-                    fset=_set_seq,
-@@ -427,10 +436,17 @@
-             if self.seq is None:
-                 raise ValueError("If the sequence is None, we cannot slice it.")
-             parent_length = len(self)
--            answer = self.__class__(self.seq[index],
--                                    id=self.id,
--                                    name=self.name,
--                                    description=self.description)
-+            from BioSQL.BioSeq import DBSeqRecord
-+            if isinstance(self, DBSeqRecord):
-+                answer = SeqRecord(self.seq[index],
-+                                        id=self.id,
-+                                        name=self.name,
-+                                        description=self.description)
-+            else:
-+                answer = self.__class__(self.seq[index],
-+                                        id=self.id,
-+                                        name=self.name,
-+                                        description=self.description)
-             # TODO - The description may no longer apply.
-             # It would be safer to change it to something
-             # generic like "edited" or the default value.
---- Tests/test_SeqRecord.py.old	2016-06-08 15:27:00.000000000 +0200
-+++ Tests/test_SeqRecord.py	2016-07-22 17:48:45.401428898 +0200
-@@ -72,6 +72,23 @@
-         except (TypeError, ValueError) as e:
-             pass
- 
-+    def test_replacing_seq(self):
-+        """Replacing .seq if .letter_annotation present."""
-+        rec = SeqRecord(Seq("ACGT", generic_dna),
-+                        id="Test", name="Test", description="Test",
-+                        letter_annotations={"example": [1, 2, 3, 4]})
-+        try:
-+            rec.seq = Seq("ACGTACGT", generic_dna)
-+            self.fail("Changing .seq length with letter_annotations present should fail!")
-+        except ValueError as e:
-+            self.assertEqual(str(e), "You must empty the letter annotations first!")
-+        # Check we can replace IF the length is the same
-+        self.assertEqual(str(rec.seq), "ACGT")
-+        self.assertEqual(rec.letter_annotations, {"example": [1, 2, 3, 4]})
-+        rec.seq = Seq("NNNN" , generic_dna)
-+        self.assertEqual(str(rec.seq), "NNNN")
-+        self.assertEqual(rec.letter_annotations, {"example": [1, 2, 3, 4]})
-+
-     def test_valid_id(self):
-         with self.assertRaises(TypeError):
-             SeqRecord(Seq("ACGT", generic_dna), id=dict())

diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml
deleted file mode 100644
index 959160f..0000000
--- a/sci-biology/biopython/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@g.o</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>