commit: 8ffc5a1942e322e42d57a77eb5d89a9a15501ae9 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Mon Jan 2 21:51:34 2017 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Mon Jan 2 22:09:05 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8ffc5a19
sci-biology/biopython: Drop old Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> sci-biology/biopython/Manifest | 2 - sci-biology/biopython/biopython-1.65.ebuild | 56 ---------------------- sci-biology/biopython/biopython-1.66.ebuild | 56 ---------------------- .../files/biopython-1.65-test-fix-backport.patch | 40 ---------------- 4 files changed, 154 deletions(-) diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index 9e5a8d9..415ede8 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1,3 +1 @@ -DIST biopython-1.65.tar.gz 12641342 SHA256 463cc81db84e9bfcdfb15629511c81ed556a6c0287e670dbfe80f03c65d2a88e SHA512 2a9c6a89d0279374c243938d13bfdd6f2b124a08afbfb0c262e1e4827c48a141fb9941f4cdb960f76b523f0ac152095a8c6ea566d9b469ce9daf8a7e7993f7af WHIRLPOOL 40757938c0eb7e30c9609ef5aa2d397fa21ad92cd20c9b6300cde1b381a0e6c21e4ebb7f4d25bf02651789437d7d86341154b907ccc0007759c17939f2e29da2 -DIST biopython-1.66.tar.gz 13724754 SHA256 5178ea3b343b1d8710f39205386093e5369ed653aa020e1b0c4b7622a59346c1 SHA512 6bb01f1058728f957527447df82ffbb9027e74564e81c8308b3404d033a0f12fef50da05b343bd4c4eae98508931eedc9c4bc23b2efdf36bbb49f1557fa52d71 WHIRLPOOL 0cfe3f4829ec72afa466b17cf6745cc334105713ebeeb06019e2df94acc1289aeb07a7bba70a50afeae00de90c48d2455a1af8cf26f916ceb4c0ab92a4a05fbd DIST biopython-1.68.tar.gz 14445813 SHA256 d1dc09d1ddc8e90833f507cf09f80fa9ee1537d319058d1c44fe9c09be3d0c1f SHA512 0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69 WHIRLPOOL 9348354d0063efe0f9051f46e3be60540c5df21a43c094d74e64d37279736921d890cd639c904336eb21b2996e9948b8a050017b77569d2333ac80aa5b8bf156 diff --git a/sci-biology/biopython/biopython-1.65.ebuild b/sci-biology/biopython/biopython-1.65.ebuild deleted file mode 100644 index 64bb66c..00000000 --- a/sci-biology/biopython/biopython-1.65.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 python3_4 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="${RDEPEND} - sys-devel/flex" - -DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) - -PATCHES=( "${FILESDIR}"/${P}-test-fix-backport.patch ) - -python_test() { - [[ ${EPYTHON} == pypy ]] && return - 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 -} - -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/biopython-1.66.ebuild b/sci-biology/biopython/biopython-1.66.ebuild deleted file mode 100644 index 1e6a2a4..00000000 --- a/sci-biology/biopython/biopython-1.66.ebuild +++ /dev/null @@ -1,56 +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_{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="${RDEPEND} - sys-devel/flex" - -DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) - -python_test() { - distutils_install_for_testing - cp -r "${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-1.65-test-fix-backport.patch b/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch deleted file mode 100644 index 2efdef9..00000000 --- a/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch +++ /dev/null @@ -1,40 +0,0 @@ -From 08c72f8778a87701586a03dffcce33c7589bc6d7 Mon Sep 17 00:00:00 2001 -From: Peter Cock <p.j.a.c...@googlemail.com> -Date: Sun, 18 Jan 2015 02:07:54 +0000 -Subject: [PATCH] Clearer error message; update failing test. - -One of the orchid examples now returns different enough -results that the test was failing. The new error message -makes it much easier to pick another positive example to -add to the the white-list. ---- - Tests/test_NCBI_qblast.py | 9 +++++---- - 1 file changed, 5 insertions(+), 4 deletions(-) - -diff --git a/Tests/test_NCBI_qblast.py b/Tests/test_NCBI_qblast.py -index 88bfe61..19f7b35 100644 ---- a/Tests/test_NCBI_qblast.py -+++ b/Tests/test_NCBI_qblast.py -@@ -66,7 +66,7 @@ def test_orchid_est(self): - AGCCATGGATTTCTCAGAAGAAAATGATTATACTTCTTAATCAGGCAACTGATATTATCAATTTATGGCA - GCAGAGTGGTGGCTCCTTGTCCCAGCAGCAGTAATTACTTTTTTTTCTCTTTTTGTTTCCAAATTAAGAA - ACATTAGTATCATATGGCTATTTGCTCAATTGCAGATTTCTTTCTTTTGTGAATG""", -- 0.0000001, None, ["21554275", "18409071", "296087288"]) -+ 0.0000001, None, ["21554275", "18409071", "296087288", "566183510"]) - - def run_qblast(self, program, database, query, e_value, entrez_filter, expected_hits): - try: -@@ -120,9 +120,10 @@ def run_qblast(self, program, database, query, e_value, entrez_filter, expected_ - print("Update this test to have some redundancy...") - for alignment in record.alignments: - print(alignment.hit_id) -- assert found_result, "Missing all of %s in alignments" \ -- % ", ".join(expected_hits) -- self.assertTrue(found_result) -+ self.assertTrue(found_result, -+ "Missing all expected hits (%s), instead have: %s" -+ % (", ".join(expected_hits), -+ ", ".join(a.hit_id for a in record.alignments))) - - # Check the expected result(s) are found in the descriptions - if expected_hits is None:
