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-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata>