Version Bump; Move to new python eclasses

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-chemistry/autodock/ChangeLog b/sci-chemistry/autodock/ChangeLog
index 9ffe85a823b2a5122ddb43c63aa8f681e49536a5..93c2e1bef953d4af619d01eb44a93fc589a8d112 100644 (file)
--- a/sci-chemistry/autodock/ChangeLog
+++ b/sci-chemistry/autodock/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/autodock
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/autodock/ChangeLog,v 1.9 2011/06/26 09:00:41 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/autodock/ChangeLog,v 1.10 2015/03/13 11:04:23 jlec Exp $
+
+*autodock-4.2.6 (13 Mar 2015)
+
+  13 Mar 2015; Justin Lecher <jlec@gentoo.org> +autodock-4.2.6.ebuild,
+  +files/autodock-4.2.6-buildsystem.patch, autodock-4.2.3-r1.ebuild,
+  metadata.xml:
+  Version Bump; Move to new python eclasses
 
   26 Jun 2011; Justin Lecher <jlec@gentoo.org> autodock-4.2.3-r1.ebuild:
   Straight out QA issues
@@ -41,4 +48,3 @@
   +autodock-4.0.1.ebuild:
   Initial import. Thanks to Luc Grenier <lgrenier@rsvs.ulaval.ca> for his
   ebuild and for testing the package.
-

diff --git a/sci-chemistry/autodock/Manifest b/sci-chemistry/autodock/Manifest
index 52922697b1c8f6049d281bd583e1911441ffdf45..1d1366cf4d71de54d42500e483f1ac6ceacc68f6 100644 (file)
--- a/sci-chemistry/autodock/Manifest
+++ b/sci-chemistry/autodock/Manifest
@@ -1,15 +1,30 @@
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+Hash: SHA512
 
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+EBUILD autodock-4.2.3-r1.ebuild 1992 SHA256 13f990158e2e5f3edb5eec03bd3e94affbaa41be072b0b49c536faf2a6b07424 SHA512 479290f4290c89b4a36605b2ed64c742d889c7824f9a0d2098a6dc6589714ae3fcde80e399fee754902be8bee1045e3a94454346c856e61f441c0557f071a159 WHIRLPOOL d58fec6185507e680f4cc7241d46e98bd09a0220aee5e38b98954607f449c8a81ef70a8fa1f2e90d27288dc65f60ce42b34c6c5ddc1eb4acfec82949c72c912e
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diff --git a/sci-chemistry/autodock/autodock-4.2.3-r1.ebuild b/sci-chemistry/autodock/autodock-4.2.3-r1.ebuild
index a3f213286ec6f7bd4b5cfd523497ae1e24e21bd2..9b30e285af3285c65ffcda0b8d61df25b9bbef5b 100644 (file)
--- a/sci-chemistry/autodock/autodock-4.2.3-r1.ebuild
+++ b/sci-chemistry/autodock/autodock-4.2.3-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/autodock/autodock-4.2.3-r1.ebuild,v 1.3 2011/06/26 09:00:41 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/autodock/autodock-4.2.3-r1.ebuild,v 1.4 2015/03/13 11:04:23 jlec Exp $
 
 EAPI=3
 

diff --git a/sci-chemistry/autodock/autodock-4.2.6.ebuild b/sci-chemistry/autodock/autodock-4.2.6.ebuild
new file mode 100644 (file)
index 0000000..9b987ef
--- /dev/null
+++ b/sci-chemistry/autodock/autodock-4.2.6.ebuild
@@ -0,0 +1,102 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/autodock/autodock-4.2.6.ebuild,v 1.1 2015/03/13 11:04:23 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools eutils python-any-r1 versionator
+
+MY_PN="autodocksuite"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="A suite of automated docking tools"
+HOMEPAGE="http://autodock.scripps.edu/"
+SRC_URI="http://autodock.scripps.edu/downloads/autodock-registration/tars/dist$(delete_all_version_separators)/${MY_P}-src.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="examples openmp test"
+
+RDEPEND=""
+DEPEND="test? ( ${PYTHON_DEPS} )"
+
+S="${WORKDIR}/src"
+
+PATCHES=(
+       "${FILESDIR}"/${P}-buildsystem.patch
+)
+
+src_prepare() {
+       local i
+
+       epatch ${PATCHES[@]}
+
+       sed \
+               -e "s/\tcsh/\tsh/" \
+               -i auto{dock,grid}/Makefile.am || die
+       for i in autodock autogrid; do
+               pushd $i &>/dev/null
+               eautoreconf
+               popd &>/dev/null
+       done
+}
+
+src_configure() {
+       local i
+       for i in autodock autogrid; do
+               pushd $i &>/dev/null
+               econf $(use_enable openmp)
+               popd &>/dev/null
+       done
+}
+
+src_compile() {
+       emake -C autodock
+       emake -C autogrid
+}
+
+src_test() {
+       elog "Testing autodock"
+       cd "${S}/autodock/Tests" || die
+       cp ../*.dat . || die
+       ${EPYTHON} test_autodock4.py || die "AutoDock tests failed."
+       einfo "Testing autogrid"
+       cd "${S}/autogrid/Tests" || die
+       ${EPYTHON} test_autogrid4.py || die "AutoGrid tests failed."
+}
+
+src_install() {
+       if use openmp; then
+               newbin autodock/autodock4.omp ${PN}4
+               dobin autogrid/autogrid4
+       else
+               dobin autodock/autodock4 autogrid/autogrid4
+       fi
+
+       insinto /usr/share/${PN}
+       doins -r \
+               autodock/{AD4_parameters.dat,AD4_PARM99.dat} \
+               $(usex examples "autodoc/EXAMPLES" "")
+
+       DOCS=(
+               RELEASENOTES
+               autodock/{AUTHORS,README}
+               autodock/USERGUIDES/AutoDock4.{0,1,2}_UserGuide.doc
+               autodock/USERGUIDES/AutoDock4.2_UserGuide.pdf
+       )
+       einstalldocs
+}
+
+pkg_postinst() {
+       elog "The AutoDock development team requests all users to fill out the"
+       elog "registration form at:"
+       echo
+       elog "\thttp://autodock.scripps.edu/downloads/autodock-registration"
+       echo
+       elog "The number of unique users of AutoDock is used by Prof. Arthur J."
+       elog "Olson and the Scripps Research Institude to support grant"
+       elog "applications."
+}

diff --git a/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch
new file mode 100644 (file)
index 0000000..ae44ffe
--- /dev/null
+++ b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch
@@ -0,0 +1,44 @@
+ src/autodock/Makefile.am | 6 +++---
+ src/autogrid/Makefile.am | 4 ++--
+ 2 files changed, 5 insertions(+), 5 deletions(-)
+
+diff --git a/src/autodock/Makefile.am b/src/autodock/Makefile.am
+index 799a3c4..911897b 100644
+--- a/src/autodock/Makefile.am
++++ b/src/autodock/Makefile.am
+@@ -459,7 +459,8 @@ endif
+ 
+ BUILT_SOURCES = $(autodock4_SOURCES) default_parameters.h
+ 
+-AM_CXXFLAGS = -O3 # Agressive optimization
++AM_CXXFLAGS =
++#AM_CXXFLAGS = -O3 # Agressive optimization
+ #AM_CXXFLAGS = -g # debug
+ 
+     # if gnu c++ compiler
+@@ -488,8 +489,7 @@ endif
+ AM_CPPFLAGS = -DNOSQRT \
+             -DUSE_DOUBLE \
+               -DUSE_8A_NBCUTOFF \
+-            -DUSE_INT_AS_FOURBYTELONG \
+-            -O3
++            -DUSE_INT_AS_FOURBYTELONG
+ # AM_LDFLAGS = -g # -g is MP debug
+ 
+ 
+diff --git a/src/autogrid/Makefile.am b/src/autogrid/Makefile.am
+index b531099..b78b380 100644
+--- a/src/autogrid/Makefile.am
++++ b/src/autogrid/Makefile.am
+@@ -94,9 +94,9 @@ autogrid4_SOURCES = main.cpp \
+ BUILT_SOURCES = default_parameters.h
+ 
+ 
+-AM_CFLAGS = -Wall -O3 # All warnings, Agressive optimization
++AM_CFLAGS = -Wall # All warnings, Agressive optimization
+ 
+-AM_CPPFLAGS = -Wall -O3 -I $(srcdir) -I$(srcdir)/../autodock # All warnings, Agressive optimization
++AM_CPPFLAGS = -Wall -I $(srcdir) -I$(srcdir)/../autodock # All warnings, Agressive optimization
+ AM_CPPFLAGS += -Wno-write-strings # increase compatibility with pre 4.x compilers for string handling
+ #  M Pique - add USE_8A_NBCUTOFF
+ AM_CPPFLAGS += -DUSE_8A_NBCUTOFF

diff --git a/sci-chemistry/autodock/metadata.xml b/sci-chemistry/autodock/metadata.xml
index e42d0af60f426ab88c9ae496408729e5aaa728e1..51fdedab1b3844b82077be28af7b25ad5d5ca54d 100644 (file)
--- a/sci-chemistry/autodock/metadata.xml
+++ b/sci-chemistry/autodock/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-       <herd>sci-chemistry</herd>
+  <herd>sci-chemistry</herd>
 </pkgmetadata>