[gentoo-commits] proj/sci:master commit in: eclass/, sci-biology/emboss/, sci-biology/emboss/files/

["Justin Lecher" <jlec@gentoo.org>]

commit:     1f18e25a472d14585102cdf0fc2819fdf8090bc0
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb  4 07:56:01 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb  4 08:05:57 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1f18e25a

Rename eclass to compensate API changes

* Require at least EAPI=5
* Clean tiny bits

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 eclass/{emboss.eclass => emboss-r1.eclass} | 28 ++++++++++--------------
 sci-biology/emboss/emboss-6.6.0.ebuild     | 25 +++++++++-------------
 sci-biology/emboss/files/README.gentoo     | 34 ++++++++++++++++++++++++++++++
 3 files changed, 55 insertions(+), 32 deletions(-)

diff --git a/eclass/emboss.eclass b/eclass/emboss-r1.eclass
similarity index 85%
rename from eclass/emboss.eclass
rename to eclass/emboss-r1.eclass
index 3ba65bb..b185802 100644
--- a/eclass/emboss.eclass
+++ b/eclass/emboss-r1.eclass
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-# @ECLASS: emboss.eclass
+# @ECLASS: emboss-r1.eclass
 # @MAINTAINER:
 # sci-biology@gentoo.org
 # jlec@gentoo.org
@@ -13,14 +13,13 @@
 # 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 at least 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=()
 #
 # Example:
 #
-# EAPI="4"
+# EAPI="5"
 #
 # EBO_DESCRIPTION="applications from the CBS group"
 #
@@ -42,8 +41,8 @@
 # Extra config options passed to econf, similar to EXTRA_ECONF.
 
 case ${EAPI:-0} in
-	4|5) ;;
-	*) die "this eclass doesn't support < EAPI 4" ;;
+	5) ;;
+	*) die "this eclass doesn't support < EAPI 5" ;;
 esac
 
 if [[ -f "${FILESDIR}"/${P}_fix-build-system.patch ]]; then
@@ -85,26 +84,23 @@ if [[ ${PN} == embassy-* ]]; then
 	S="${WORKDIR}"/${EF}
 fi
 
-DOCS=()
-
 # @FUNCTION: emboss_src_prepare
 # @DESCRIPTION:
 # Does the following things
 #
 #  1. Patches with "${FILESDIR}"/${P}_fix-build-system.patch, if present,
 #     and eventually runs eautoreconf in autotools-utils
-#  2. Patches with "${WORKDIR}"/${P}-upstream-r1.patch, if ${EBO_PATCH} is set
-#  3. Patches with "${FILESDIR}"/${PF}.patch, if present
+#  2. Patches with "${FILESDIR}"/${PF}.patch, if present
+#  3. Applies ${PATCHES[@]} via autotools-utils.eclass
 #
 
-emboss_src_prepare() {
+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
 
-	[[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream-r1.patch
-	[[ -f ${FILESDIR}/${PF}.patch ]] && epatch "${FILESDIR}"/${PF}.patch
+	[[ -f "${FILESDIR}"/${PF}.patch ]] && epatch "${FILESDIR}"/${PF}.patch
 
 	autotools-utils_src_prepare
 }
@@ -125,14 +121,13 @@ emboss_src_prepare() {
 #  --docdir="${EPREFIX}/usr/share/doc/${PF}"
 #  ${EBO_EXTRA_ECONF}
 
-emboss_src_configure() {
+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")
-		$(use_enable static-libs static)
 		--enable-large
 		--without-java
 		--enable-systemlibs
@@ -140,9 +135,8 @@ emboss_src_configure() {
 		${EBO_EXTRA_ECONF}
 	)
 
-	if [[ ${EMBASSY_PACKAGE} == yes ]]; then
+	[[ ${EMBASSY_PACKAGE} == yes ]] && \
 		append-cppflags "-I${EPREFIX}/usr/include/emboss"
-	fi
 
 	autotools-utils_src_configure
 }

diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild
index 7ac75b6..59285d7 100644
--- a/sci-biology/emboss/emboss-6.6.0.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild
@@ -4,10 +4,7 @@
 
 EAPI=5
 
-inherit autotools-utils emboss eutils
-
-EBO_PATCH=""
-EBOV=${PV}
+inherit autotools-utils emboss-r1 eutils readme.gentoo
 
 DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
 SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
@@ -25,38 +22,36 @@ PDEPEND+="
 		sci-biology/rebase
 		)"
 
-S="${WORKDIR}"/EMBOSS-${EBOV}
-
-EBO_EXTRA_ECONF="--includedir=${EPREFIX}/usr/include/emboss"
+S="${WORKDIR}"/EMBOSS-${PV}
 
 DOCS=( ChangeLog AUTHORS NEWS THANKS FAQ )
+
 PATCHES=(
-	"${FILESDIR}/${P}_FORTIFY_SOURCE-fix.patch"
-	"${FILESDIR}/${P}_plplot-declarations.patch"
-	"${FILESDIR}/${P}_qa-implicit-declarations.patch"
+	"${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch
+	"${FILESDIR}"/${P}_plplot-declarations.patch
+	"${FILESDIR}"/${P}_qa-implicit-declarations.patch
 )
 
 src_install() {
 	# Use autotools-utils_* to remove useless *.la files
 	autotools-utils_src_install
 
-	sed -e "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
-	dodoc README.Gentoo
+	readme.gentoo_create_doc
 
 	# Install env file for setting libplplot and acd files path.
-	cat <<- EOF > 22emboss
+	cat > 22emboss <<- EOF
 		# ACD files location
 		EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
 		EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
 	EOF
 	doenvd 22emboss
 
-	# Remove useless dummy files from the image.
+	# Remove useless dummy files
 	find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files."
 
 	# Move the provided codon files to a different directory. This will avoid
 	# user confusion and file collisions on case-insensitive file systems (see
-	# bug #115446). This change is documented in "README.Gentoo".
+	# bug #115446). This change is documented in "README.gentoo".
 	mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
 			die "Failed to move CODON directory."
 }

diff --git a/sci-biology/emboss/files/README.gentoo b/sci-biology/emboss/files/README.gentoo
new file mode 100644
index 0000000..d1879bd
--- /dev/null
+++ b/sci-biology/emboss/files/README.gentoo
@@ -0,0 +1,34 @@
+Administrating EMBOSS on Gentoo systems
+=======================================
+
+
+Codon data files location
+-------------------------
+
+The codon data files that are distributed with EMBOSS are installed in the
+``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual
+``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between
+these codon files and those installed with the CUTG database. The names of
+these files sometimes vary only by their case. Having both sets of files in
+the same directory is also impossible on systems such as MacOSX, where the
+root filesystem is case insensitive. If you do not have the CUTG database
+installed and want to use the codon files distributed with EMBOSS, you can
+symlink the ``CODONS.orig`` directory to ``CODONS``::
+
+	# cd ${EPREFIX}/usr/share/EMBOSS/data
+	# ln -s CODONS.orig CODONS
+
+
+Restriction enzymes equivalence file location
+---------------------------------------------
+
+The restriction enzymes equivalence file distributed with EMBOSS is installed
+as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual
+``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file
+collision with the equivalence file provided by the Rebase database. If you do
+not have the Rebase database installed and want to use the equivalence file
+distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to
+``embossre.equ``::
+
+	# cd ${EPREFIX}/usr/share/EMBOSS/data
+	# ln -s embossre.equ.orig embossre.equ