proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

4 files changed, 102 insertions, 0 deletions

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
new file mode 100644
index 000000000000..e835e2490342
--- /dev/null
+++ b/sci-biology/biopython/Manifest
@@ -0,0 +1 @@
+DIST biopython-1.65.tar.gz 12641342 SHA256 463cc81db84e9bfcdfb15629511c81ed556a6c0287e670dbfe80f03c65d2a88e SHA512 2a9c6a89d0279374c243938d13bfdd6f2b124a08afbfb0c262e1e4827c48a141fb9941f4cdb960f76b523f0ac152095a8c6ea566d9b469ce9daf8a7e7993f7af WHIRLPOOL 40757938c0eb7e30c9609ef5aa2d397fa21ad92cd20c9b6300cde1b381a0e6c21e4ebb7f4d25bf02651789437d7d86341154b907ccc0007759c17939f2e29da2
diff --git a/sci-biology/biopython/biopython-1.65.ebuild b/sci-biology/biopython/biopython-1.65.ebuild
new file mode 100644
index 000000000000..9c23f0bd0635
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.65.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} pypy )
+
+inherit distutils-r1 eutils
+
+DESCRIPTION="Python modules for computational molecular biology"
+HOMEPAGE="http://www.biopython.org/ http://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/files/biopython-1.65-test-fix-backport.patch b/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch
new file mode 100644
index 000000000000..2efdef97d799
--- /dev/null
+++ b/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch
@@ -0,0 +1,40 @@
+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:
diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/biopython/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>