Merge branch 'SoapZaNet-master'

* SoapZaNet-master: (34 commits)
  sci-biology/embassy-meme: Bump eclass, Drop old
  empty package
  empty package
  sci-biology/embassy-mse: Bump eclass, drop old
  sci-biology/embassy-iprscan: Bump eclass, Drop old
  sci-biology/embassy-phylipnew: Bump eclass, drop old
  sci-biology/embassy-hmmer: Bump eclass, Drop old
  sci-biology/embassy-signature: Bump eclass, drop old
  sci-biology/embassy-esim4: Bump eclass, Drop old
  sci-biology/embassy-structure: Bump eclass, drop old
  sci-biology/embassy-emnu: Bump eclass, Drop old
  sci-biology/embassy-topo: Bump eclass, drop old
  sci-biology/embassy-domsearch: Bump eclass, Drop old
  sci-biology/embassy-vienna: Bump eclass, drop old
  sci-biology/embassy-domalign: Bump eclass, Drop old
  sci-biology/embassy-domainatrix: Bump eclass, Drop old
  sci-biology/embassy-clustalomega: Bump eclass
  sci-biology/embassy-cbstools: Bump eclass, Drop old
  sci-biology/embassy: Drop old
  sci-biology/emboss: Drop old
  ...

1 files changed, 49 insertions, 40 deletions

diff --git a/eclass/emboss.eclass b/eclass/emboss-r1.eclass
index aff93dfd2..b185802da 100644
--- a/eclass/emboss.eclass
+++ b/eclass/emboss-r1.eclass
@@ -1,27 +1,25 @@
-# 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/eclass/embassy.eclass,v 1.17 2008/11/03 22:17:50 ribosome Exp $
+# $Header: $
 
-# Creator of the original eclass
-# Author Olivier Fisette <ofisette@gmail.com>
-#
-# Author of the next generation eclass
-# Justin Lecher <jlec@gentoo.org>
-
-# @ECLASS: emboss.eclass
+# @ECLASS: emboss-r1.eclass
 # @MAINTAINER:
 # sci-biology@gentoo.org
 # jlec@gentoo.org
+# ted.tanberry@gmail.com
+# @AUTHOR:
+# Original author: Author Olivier Fisette <ofisette@gmail.com>
+# Next gen author: Justin Lecher <jlec@gentoo.org>
+# Next gen author: Ted Tanberry <ted.tanberry@gmail.com>
 # @BLURB: Use this to easy install EMBOSS and EMBASSY programs (EMBOSS add-ons).
 # @DESCRIPTION:
-# The inheriting ebuild must set EAPI=4 and provide EBO_DESCRIPTION before the inherit line.
+# The inheriting ebuild must set at least EAPI=5 and provide EBO_DESCRIPTION before the inherit line.
 # KEYWORDS should be set. Additionally "(R|P)DEPEND"encies and other standard
 # ebuild variables can be extended (FOO+=" bar").
-# Default installation of following DOCS="AUTHORS ChangeLog NEWS README"
 #
 # Example:
 #
-# EAPI="4"
+# EAPI="5"
 #
 # EBO_DESCRIPTION="applications from the CBS group"
 #
@@ -37,22 +35,21 @@
 #
 # Defaults to the upstream name of the module.
 
-# @ECLASS-VARIABLE: EBO_EAUTORECONF
-# @DESCRIPTION:
-# Set to 'no', if you don't want eautoreconf to be run after patching.
-: ${EBO_EAUTORECONF:=yes}
-
 # @ECLASS-VARIABLE: EBO_EXTRA_ECONF
 # @DEFAULT_UNSET
 # @DESCRIPTION:
 # Extra config options passed to econf, similar to EXTRA_ECONF.
 
 case ${EAPI:-0} in
-	4) ;;
-	*) die "this eclass doesn't support < EAPI 4" ;;
+	5) ;;
+	*) die "this eclass doesn't support < EAPI 5" ;;
 esac
 
-inherit autotools eutils
+if [[ -f "${FILESDIR}"/${P}_fix-build-system.patch ]]; then
+	AUTOTOOLS_AUTORECONF=1
+fi
+
+inherit autotools-utils eutils flag-o-matic
 
 HOMEPAGE="http://emboss.sourceforge.net/"
 LICENSE="LGPL-2 GPL-2"
@@ -73,6 +70,7 @@ DEPEND="
 RDEPEND="${DEPEND}"
 
 if [[ ${PN} == embassy-* ]]; then
+	EMBASSY_PACKAGE=yes
 	# The EMBASSY package name, retrieved from the inheriting ebuild's name
 	EN=${PN:8}
 	# The full name and version of the EMBASSY package (excluding the Gentoo
@@ -86,19 +84,25 @@ if [[ ${PN} == embassy-* ]]; then
 	S="${WORKDIR}"/${EF}
 fi
 
-DOCS="AUTHORS ChangeLog NEWS README"
-
 # @FUNCTION: emboss_src_prepare
 # @DESCRIPTION:
-# Does following things
+# Does the following things
 #
-#  1. Patches with "${FILESDIR}"/${PF}.patch, if present
-#  2. Runs eautoreconf, unless EBO_EAUTORECONF is set to no
+#  1. Patches with "${FILESDIR}"/${P}_fix-build-system.patch, if present,
+#     and eventually runs eautoreconf in autotools-utils
+#  2. Patches with "${FILESDIR}"/${PF}.patch, if present
+#  3. Applies ${PATCHES[@]} via autotools-utils.eclass
 #
 
-emboss_src_prepare() {
-	[[ -f ${FILESDIR}/${PF}.patch ]] && epatch "${FILESDIR}"/${PF}.patch
-	[[ ${EBO_EAUTORECONF} == yes ]] && eautoreconf
+emboss-r1_src_prepare() {
+	if [[ -f "${FILESDIR}"/${P}_fix-build-system.patch ]]; then
+		mv configure.{in,ac} || die
+		epatch "${FILESDIR}"/${P}_fix-build-system.patch
+	fi
+
+	[[ -f "${FILESDIR}"/${PF}.patch ]] && epatch "${FILESDIR}"/${PF}.patch
+
+	autotools-utils_src_prepare
 }
 
 # @FUNCTION: emboss_src_configure
@@ -117,19 +121,24 @@ emboss_src_prepare() {
 #  --docdir="${EPREFIX}/usr/share/doc/${PF}"
 #  ${EBO_EXTRA_ECONF}
 
-emboss_src_configure() {
-	econf \
-		$(use_with X x) \
-		$(use_with png pngdriver) \
-		$(use_with pdf hpdf) \
-		$(use_with mysql mysql) \
-		$(use_with postgres postgresql) \
-		$(use_enable static-libs static) \
-		--enable-large \
-		--without-java \
-		--enable-systemlibs \
-		--docdir="${EPREFIX}/usr/share/doc/${PF}" \
+emboss-r1_src_configure() {
+	local myeconfargs=(
+		$(use_with X x)
+		$(use_with png pngdriver "${EPREFIX}/usr")
+		$(use_with pdf hpdf "${EPREFIX}/usr")
+		$(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config")
+		$(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config")
+		--enable-large
+		--without-java
+		--enable-systemlibs
+		--docdir="${EPREFIX}/usr/share/doc/${PF}"
 		${EBO_EXTRA_ECONF}
+	)
+
+	[[ ${EMBASSY_PACKAGE} == yes ]] && \
+		append-cppflags "-I${EPREFIX}/usr/include/emboss"
+
+	autotools-utils_src_configure
 }
 
 EXPORT_FUNCTIONS src_prepare src_configure