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commit: 8ffc5a1942e322e42d57a77eb5d89a9a15501ae9 |
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Author: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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AuthorDate: Mon Jan 2 21:51:34 2017 +0000 |
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Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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CommitDate: Mon Jan 2 22:09:05 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8ffc5a19 |
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|
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sci-biology/biopython: Drop old |
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|
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Package-Manager: Portage-2.3.3, Repoman-2.3.1 |
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Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> |
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|
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sci-biology/biopython/Manifest | 2 - |
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sci-biology/biopython/biopython-1.65.ebuild | 56 ---------------------- |
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sci-biology/biopython/biopython-1.66.ebuild | 56 ---------------------- |
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.../files/biopython-1.65-test-fix-backport.patch | 40 ---------------- |
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4 files changed, 154 deletions(-) |
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|
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diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest |
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index 9e5a8d9..415ede8 100644 |
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--- a/sci-biology/biopython/Manifest |
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+++ b/sci-biology/biopython/Manifest |
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@@ -1,3 +1 @@ |
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-DIST biopython-1.65.tar.gz 12641342 SHA256 463cc81db84e9bfcdfb15629511c81ed556a6c0287e670dbfe80f03c65d2a88e SHA512 2a9c6a89d0279374c243938d13bfdd6f2b124a08afbfb0c262e1e4827c48a141fb9941f4cdb960f76b523f0ac152095a8c6ea566d9b469ce9daf8a7e7993f7af WHIRLPOOL 40757938c0eb7e30c9609ef5aa2d397fa21ad92cd20c9b6300cde1b381a0e6c21e4ebb7f4d25bf02651789437d7d86341154b907ccc0007759c17939f2e29da2 |
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-DIST biopython-1.66.tar.gz 13724754 SHA256 5178ea3b343b1d8710f39205386093e5369ed653aa020e1b0c4b7622a59346c1 SHA512 6bb01f1058728f957527447df82ffbb9027e74564e81c8308b3404d033a0f12fef50da05b343bd4c4eae98508931eedc9c4bc23b2efdf36bbb49f1557fa52d71 WHIRLPOOL 0cfe3f4829ec72afa466b17cf6745cc334105713ebeeb06019e2df94acc1289aeb07a7bba70a50afeae00de90c48d2455a1af8cf26f916ceb4c0ab92a4a05fbd |
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DIST biopython-1.68.tar.gz 14445813 SHA256 d1dc09d1ddc8e90833f507cf09f80fa9ee1537d319058d1c44fe9c09be3d0c1f SHA512 0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69 WHIRLPOOL 9348354d0063efe0f9051f46e3be60540c5df21a43c094d74e64d37279736921d890cd639c904336eb21b2996e9948b8a050017b77569d2333ac80aa5b8bf156 |
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|
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diff --git a/sci-biology/biopython/biopython-1.65.ebuild b/sci-biology/biopython/biopython-1.65.ebuild |
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deleted file mode 100644 |
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index 64bb66c..00000000 |
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--- a/sci-biology/biopython/biopython-1.65.ebuild |
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+++ /dev/null |
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@@ -1,56 +0,0 @@ |
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-# Copyright 1999-2015 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Id$ |
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- |
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-EAPI=5 |
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- |
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-PYTHON_COMPAT=( python2_7 python3_4 pypy ) |
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- |
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-inherit distutils-r1 eutils |
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- |
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-DESCRIPTION="Python modules for computational molecular biology" |
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-HOMEPAGE="http://www.biopython.org/ https://pypi.python.org/pypi/biopython/" |
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-SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz" |
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- |
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-LICENSE="HPND" |
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-SLOT="0" |
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-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" |
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-IUSE="" |
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- |
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-RDEPEND=" |
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- dev-python/matplotlib[$(python_gen_usedep 'python*')] |
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- dev-python/networkx[$(python_gen_usedep 'python*')] |
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- dev-python/numpy[$(python_gen_usedep 'python*')] |
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- dev-python/rdflib[$(python_gen_usedep 'python*')] |
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- dev-python/pygraphviz[$(python_gen_usedep 'python2*')] |
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- dev-python/reportlab[$(python_gen_usedep 'python*')] |
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- media-gfx/pydot[$(python_gen_usedep 'python2*')] |
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- " |
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-DEPEND="${RDEPEND} |
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- sys-devel/flex" |
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- |
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-DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) |
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- |
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-PATCHES=( "${FILESDIR}"/${P}-test-fix-backport.patch ) |
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- |
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-python_test() { |
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- [[ ${EPYTHON} == pypy ]] && return |
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- cd Tests || die |
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- ${PYTHON} run_tests.py || die |
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-} |
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- |
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-python_install_all() { |
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- distutils-r1_python_install_all |
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- |
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- dodir /usr/share/${PN} |
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- cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die |
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-} |
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- |
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-pkg_postinst() { |
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- elog "For database support you need to install:" |
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- optfeature "MySQL" dev-python/mysql-python |
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- optfeature "PostGreSQL" dev-python/psycopg |
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- echo |
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- elog "Some applications need extra packages:" |
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- optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss |
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-} |
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|
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diff --git a/sci-biology/biopython/biopython-1.66.ebuild b/sci-biology/biopython/biopython-1.66.ebuild |
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deleted file mode 100644 |
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index 1e6a2a4..00000000 |
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--- a/sci-biology/biopython/biopython-1.66.ebuild |
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+++ /dev/null |
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@@ -1,56 +0,0 @@ |
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-# Copyright 1999-2016 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Id$ |
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- |
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-EAPI=5 |
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- |
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-PYTHON_COMPAT=( python2_7 python3_{4,5} pypy ) |
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- |
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-inherit distutils-r1 eutils |
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- |
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-DESCRIPTION="Python modules for computational molecular biology" |
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-HOMEPAGE="http://www.biopython.org/ https://pypi.python.org/pypi/biopython/" |
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-SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz" |
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- |
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-LICENSE="HPND" |
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-SLOT="0" |
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-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" |
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-IUSE="" |
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- |
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-RDEPEND=" |
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- dev-python/matplotlib[$(python_gen_usedep 'python*')] |
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- dev-python/networkx[$(python_gen_usedep 'python*')] |
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- dev-python/numpy[$(python_gen_usedep 'python*')] |
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- dev-python/rdflib[$(python_gen_usedep 'python*')] |
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- dev-python/pygraphviz[$(python_gen_usedep 'python2*')] |
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- dev-python/reportlab[$(python_gen_usedep 'python*')] |
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- media-gfx/pydot[$(python_gen_usedep 'python2*')] |
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- " |
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-DEPEND="${RDEPEND} |
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- sys-devel/flex" |
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- |
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-DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) |
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- |
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-python_test() { |
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- distutils_install_for_testing |
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- cp -r "${S}"/{Doc,Tests} "${TEST_DIR}"/lib/ || die |
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- cd "${TEST_DIR}"/lib/Tests || die |
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- rm ./test_BioSQL_psycopg2.py ./test_BioSQL_MySQLdb.py ./test_BioSQL_mysql_connector.py || die |
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- ${PYTHON} run_tests.py --offline --verbose || die |
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-} |
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- |
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-python_install_all() { |
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- distutils-r1_python_install_all |
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- |
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- dodir /usr/share/${PN} |
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- cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die |
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-} |
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- |
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-pkg_postinst() { |
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- elog "For database support you need to install:" |
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- optfeature "MySQL" dev-python/mysql-python |
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- optfeature "PostGreSQL" dev-python/psycopg |
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- echo |
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- elog "Some applications need extra packages:" |
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- optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss |
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-} |
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|
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diff --git a/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch b/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch |
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deleted file mode 100644 |
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index 2efdef9..00000000 |
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--- a/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch |
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+++ /dev/null |
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@@ -1,40 +0,0 @@ |
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-From 08c72f8778a87701586a03dffcce33c7589bc6d7 Mon Sep 17 00:00:00 2001 |
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-From: Peter Cock <p.j.a.cock@××××××××××.com> |
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-Date: Sun, 18 Jan 2015 02:07:54 +0000 |
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-Subject: [PATCH] Clearer error message; update failing test. |
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- |
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-One of the orchid examples now returns different enough |
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-results that the test was failing. The new error message |
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-makes it much easier to pick another positive example to |
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-add to the the white-list. |
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---- |
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- Tests/test_NCBI_qblast.py | 9 +++++---- |
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- 1 file changed, 5 insertions(+), 4 deletions(-) |
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- |
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-diff --git a/Tests/test_NCBI_qblast.py b/Tests/test_NCBI_qblast.py |
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-index 88bfe61..19f7b35 100644 |
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---- a/Tests/test_NCBI_qblast.py |
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-+++ b/Tests/test_NCBI_qblast.py |
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-@@ -66,7 +66,7 @@ def test_orchid_est(self): |
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- AGCCATGGATTTCTCAGAAGAAAATGATTATACTTCTTAATCAGGCAACTGATATTATCAATTTATGGCA |
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- GCAGAGTGGTGGCTCCTTGTCCCAGCAGCAGTAATTACTTTTTTTTCTCTTTTTGTTTCCAAATTAAGAA |
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- ACATTAGTATCATATGGCTATTTGCTCAATTGCAGATTTCTTTCTTTTGTGAATG""", |
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-- 0.0000001, None, ["21554275", "18409071", "296087288"]) |
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-+ 0.0000001, None, ["21554275", "18409071", "296087288", "566183510"]) |
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- |
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- def run_qblast(self, program, database, query, e_value, entrez_filter, expected_hits): |
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- try: |
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-@@ -120,9 +120,10 @@ def run_qblast(self, program, database, query, e_value, entrez_filter, expected_ |
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- print("Update this test to have some redundancy...") |
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- for alignment in record.alignments: |
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- print(alignment.hit_id) |
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-- assert found_result, "Missing all of %s in alignments" \ |
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-- % ", ".join(expected_hits) |
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-- self.assertTrue(found_result) |
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-+ self.assertTrue(found_result, |
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-+ "Missing all expected hits (%s), instead have: %s" |
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-+ % (", ".join(expected_hits), |
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-+ ", ".join(a.hit_id for a in record.alignments))) |
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- |
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- # Check the expected result(s) are found in the descriptions |
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- if expected_hits is None: |