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From: "Justin Lecher" <jlec@gentoo.org>
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Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/biopython/files/, sci-biology/biopython/
X-VCS-Repository: repo/gentoo
X-VCS-Files: sci-biology/biopython/Manifest sci-biology/biopython/biopython-1.65.ebuild sci-biology/biopython/biopython-1.66.ebuild sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch
X-VCS-Directories: sci-biology/biopython/ sci-biology/biopython/files/
X-VCS-Committer: jlec
X-VCS-Committer-Name: Justin Lecher
X-VCS-Revision: 8ffc5a1942e322e42d57a77eb5d89a9a15501ae9
X-VCS-Branch: master
Date: Mon, 2 Jan 2017 22:09:13 +0000 (UTC)
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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.cock@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: