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

6 files changed, 164 insertions, 0 deletions

diff --git a/sci-chemistry/acpype/Manifest b/sci-chemistry/acpype/Manifest
new file mode 100644
index 000000000000..e1cd9723b479
--- /dev/null
+++ b/sci-chemistry/acpype/Manifest
@@ -0,0 +1,3 @@
+DIST acpype-366.tar.xz 539408 SHA256 f0c77abea0a5680ecbbecadc1a95c8f851159b7c84d079f6f527336d447e1e9d
+DIST acpype-374.tar.xz 521076 SHA256 60a15d1c29ba3254a17c0792ae859444641e7a9375bd24cdd8baccc27920fde3 SHA512 99915299b32878e2139f67503260b491e05f8a592c37c5668e5aea3414822965827a91e09578264cfb48684decbadfb60c833706b756ff277ffde8b15159391e WHIRLPOOL b4e59eec36438eb2ee6d05183a6f08200213923ff50fbff1377cd976c8e39cc24429eb727d890028af2b5b5ad90428c70a10821ae20b50f7fc494ff9163322a8
+DIST acpype-389.tar.xz 524460 SHA256 4fd4036308cd81a480beaa56ae65b43a8c5ee3bbfc64b07b4d0b6649602f529a SHA512 0fbcb83ae8306d6bcc1cfd921d70c67a15e14c443453ab8c4cfd7082c15b95599801abbe31a46313674aa4841c5cd5499b69cc080221acc2793dc808df247987 WHIRLPOOL 21c8ee51c651c7a519716c818b0febd5fd62384aeeb6a5ce0f8dcf877181edba75fdd15be0d5a158b5a22d051765fb231c7c10038b8da1bcd98bede848057e95
diff --git a/sci-chemistry/acpype/acpype-366.ebuild b/sci-chemistry/acpype/acpype-366.ebuild
new file mode 100644
index 000000000000..01a804da9cba
--- /dev/null
+++ b/sci-chemistry/acpype/acpype-366.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=3
+
+inherit eutils python
+PYTHON_DEPEND="2:2.5"
+
+DESCRIPTION="AnteChamber PYthon Parser interfacE"
+HOMEPAGE="http://code.google.com/p/acpype/"
+SRC_URI="mirror://gentoo/${P}.tar.xz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE=""
+
+DEPEND="sci-chemistry/ambertools"
+RDEPEND="${DEPEND}"
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	epatch "${FILESDIR}/${PN}.patch"
+	python_convert_shebangs -r 2 .
+}
+
+src_install() {
+	newbin ${PN}.py ${PN}
+	newbin CcpnToAcpype.py CcpnToAcpype
+	dodoc NOTE.txt README.txt
+	insinto /usr/share/${PN}
+	doins -r ffamber_additions test
+}
diff --git a/sci-chemistry/acpype/acpype-374.ebuild b/sci-chemistry/acpype/acpype-374.ebuild
new file mode 100644
index 000000000000..56036152102c
--- /dev/null
+++ b/sci-chemistry/acpype/acpype-374.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+PYTHON_DEPEND="2:2.5"
+
+inherit python
+
+DESCRIPTION="AnteChamber PYthon Parser interfacE"
+HOMEPAGE="http://code.google.com/p/acpype/"
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE=""
+
+DEPEND="sci-chemistry/ambertools"
+RDEPEND="${DEPEND}"
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	python_convert_shebangs -r 2 .
+}
+
+src_install() {
+	newbin ${PN}.py ${PN}
+	newbin CcpnToAcpype.py CcpnToAcpype
+	dodoc NOTE.txt README.txt
+	insinto /usr/share/${PN}
+	doins -r ffamber_additions test
+}
diff --git a/sci-chemistry/acpype/acpype-389.ebuild b/sci-chemistry/acpype/acpype-389.ebuild
new file mode 100644
index 000000000000..6ff35e1fcc47
--- /dev/null
+++ b/sci-chemistry/acpype/acpype-389.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit python-r1
+
+DESCRIPTION="AnteChamber PYthon Parser interfacE"
+HOMEPAGE="http://code.google.com/p/acpype/"
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="
+	${PYTHON_DEPS}
+	sci-chemistry/ambertools"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	sed \
+		-e '1s:^:#!/usr/bin/python\n\n:g' \
+		-i CcpnToAcpype.py || die
+}
+
+src_install() {
+	python_parallel_foreach_impl python_newscript ${PN}.py ${PN}
+	python_parallel_foreach_impl python_newscript CcpnToAcpype.py CcpnToAcpype
+	dodoc NOTE.txt README.txt
+	insinto /usr/share/${PN}
+	doins -r ffamber_additions test
+}
diff --git a/sci-chemistry/acpype/files/acpype.patch b/sci-chemistry/acpype/files/acpype.patch
new file mode 100644
index 000000000000..9354527cc8a9
--- /dev/null
+++ b/sci-chemistry/acpype/files/acpype.patch
@@ -0,0 +1,37 @@
+Index: acpype.py
+===================================================================
+--- acpype.py	(revision 366)
++++ acpype.py	(working copy)
+@@ -3020,32 +3020,6 @@
+         acMol2FileName = '%s_%s_%s.mol2' % (base, chargeType, atomType)
+         self.acMol2FileName = acMol2FileName
+         self.charmmBase = '%s_CHARMM' % base
+-        # check for which version of antechamber
+-        if 'amber10' in self.acExe:
+-            if qprog == 'sqm':
+-                self.printWarn("SQM is not implemented in AmberTools 1.2")
+-                self.printWarn("Setting mopac for antechamber")
+-                qprog = 'mopac'
+-            elif qprog == 'divcon':
+-                if not os.path.exists(os.path.join(os.path.dirname(self.acExe), qprog)):
+-                    self.printWarn("DIVCON is not installed")
+-                    self.printWarn("Setting mopac for antechamber")
+-                    qprog = 'mopac'
+-        elif 'amber11' in self.acExe:
+-            if qprog == 'divcon':
+-                self.printWarn("DIVCON is not implemented in AmberTools 1.3 anymore")
+-                self.printWarn("Setting sqm for antechamber")
+-                qprog = 'sqm'
+-            elif qprog == 'mopac':
+-                if not os.path.exists(os.path.join(os.path.dirname(self.acExe), qprog)):
+-                    self.printWarn("MOPAC is not installed")
+-                    self.printWarn("Setting sqm for antechamber")
+-                    return None
+-                    qprog = 'sqm'
+-        else:
+-            self.printWarn("Old version of antechamber. Strongly consider upgrading to AmberTools")
+-            self.printWarn("Setting mopac for antechamber")
+-            qprog = 'mopac'
+         self.qFlag = qDict[qprog]
+         self.outTopols = [outTopol]
+         if outTopol == 'all':
diff --git a/sci-chemistry/acpype/metadata.xml b/sci-chemistry/acpype/metadata.xml
new file mode 100644
index 000000000000..13ef0bf5a17c
--- /dev/null
+++ b/sci-chemistry/acpype/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>alexxy@gentoo.org</email>
+    <name>Alexey Shvetsov</name>
+  </maintainer>
+</pkgmetadata>