[gentoo-commits] proj/sci:master commit in: sci-biology/exonerate-gff3/files/, sci-biology/exonerate-gff3/

[gentoo-commits] proj/sci:master commit in: sci-biology/exonerate-gff3/files/, sci-biology/exonerate-gff3/

[Martin Mokrejs]

commit:     88a8a7c98513e17af66a583de1bc0b5ad414771c
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 30 19:20:56 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 30 19:20:56 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=88a8a7c9

sci-biology/exonerate-gff3: an improved version of exonerate-2.2.0 with GFF3 format output support

 sci-biology/exonerate-gff3/ChangeLog               | 12 +++++
 .../exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild  | 53 ++++++++++++++++++++++
 .../files/exonerate-gff3-2.2.0-asneeded.patch      | 15 ++++++
 sci-biology/exonerate-gff3/metadata.xml            |  9 ++++
 4 files changed, 89 insertions(+)

diff --git a/sci-biology/exonerate-gff3/ChangeLog b/sci-biology/exonerate-gff3/ChangeLog
new file mode 100644
index 0000000..fc492c8
--- /dev/null
+++ b/sci-biology/exonerate-gff3/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/exonerate-gff3
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*exonerate-gff3-2.2.0-r1 (30 Mar 2015)
+
+  30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +exonerate-gff3-2.2.0-r1.ebuild, +files/exonerate-gff3-2.2.0-asneeded.patch,
+  +metadata.xml:
+  sci-biology/exonerate-gff3: an improved version of exonerate-2.2.0 with GFF3
+  format output support
+

diff --git a/sci-biology/exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild b/sci-biology/exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild
new file mode 100644
index 0000000..fd24728
--- /dev/null
+++ b/sci-biology/exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/exonerate/exonerate-2.2.0-r1.ebuild,v 1.5 2013/01/25 16:24:50 jlec Exp $
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils toolchain-funcs git-r3
+
+DESCRIPTION="exonerate-2.2.0 with patches to add GFF3 formatted output"
+HOMEPAGE="https://github.com/hotdogee/exonerate-gff3"
+EGIT_REPO_URI="https://github.com/hotdogee/exonerate-gff3.git"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="utils test threads"
+
+REQUIRED_USE="test? ( utils )"
+
+# block with sci-biology/exonerate , maybe the best would be to change SRC_URI in sci-biology/exonerate
+DEPEND="
+	!sci-biology/exonerate
+	dev-libs/glib:2"
+RDEPEND="${DEPEND}"
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+PATCHES=( "${FILESDIR}"/${P}-asneeded.patch )
+
+src_prepare() {
+	tc-export CC
+	sed \
+		-e 's: -O3 -finline-functions::g' \
+		-i configure.in || die
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	local myeconfargs=(
+		$(use_enable utils utilities)
+		$(use_enable threads pthreads)
+		--enable-largefile
+		--enable-glib2
+	)
+	autotools-utils_src_configure
+}
+
+src_install() {
+	autotools-utils_src_install
+	doman doc/man/man1/*.1
+}

diff --git a/sci-biology/exonerate-gff3/files/exonerate-gff3-2.2.0-asneeded.patch b/sci-biology/exonerate-gff3/files/exonerate-gff3-2.2.0-asneeded.patch
new file mode 100644
index 0000000..3268055
--- /dev/null
+++ b/sci-biology/exonerate-gff3/files/exonerate-gff3-2.2.0-asneeded.patch
@@ -0,0 +1,15 @@
+Fix build with --as-needed
+
+https://bugs.gentoo.org/268094
+
+--- configure.in
++++ configure.in
+@@ -289,7 +289,7 @@
+ if test "$enable_pthreads" = yes; then
+     echo "Using PTHREADS"
+     CFLAGS="$CFLAGS -DUSE_PTHREADS"
+-    LDFLAGS="$LDFLAGS -lpthread"
++    LIBS="$LIBS -lpthread"
+ elif test "$enable_pthreads" = no; then
+     echo "Not using pthreads"
+ else

diff --git a/sci-biology/exonerate-gff3/metadata.xml b/sci-biology/exonerate-gff3/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/exonerate-gff3/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-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>

[gentoo-commits] proj/sci:master commit in: sci-biology/exonerate-gff3/files/, sci-biology/exonerate-gff3/

[Andrew Ammerlaan]

commit:     3f11f39cd3669f9328b7599254b12c8a2bf4ea7d
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 24 14:24:32 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 24 14:24:32 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3f11f39c

sci-biology/exonerate-gff3: EAPI bump

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 .../exonerate-gff3/exonerate-gff3-9999.ebuild      | 29 ++++++++--------------
 .../files/exonerate-gff3-9999-asneeded.patch       | 15 -----------
 2 files changed, 10 insertions(+), 34 deletions(-)

diff --git a/sci-biology/exonerate-gff3/exonerate-gff3-9999.ebuild b/sci-biology/exonerate-gff3/exonerate-gff3-9999.ebuild
index cc0ba0118..3ca71c262 100644
--- a/sci-biology/exonerate-gff3/exonerate-gff3-9999.ebuild
+++ b/sci-biology/exonerate-gff3/exonerate-gff3-9999.ebuild
@@ -1,23 +1,20 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils toolchain-funcs git-r3
+inherit toolchain-funcs git-r3
 
 DESCRIPTION="exonerate-2.2.0 with patches to add GFF3 formatted output"
 HOMEPAGE="https://github.com/hotdogee/exonerate-gff3"
-SRC_URI=""
 EGIT_REPO_URI="https://github.com/hotdogee/exonerate-gff3.git"
 
 LICENSE="GPL-3"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
+
 IUSE="utils test threads"
 RESTRICT="!test? ( test )"
-
 REQUIRED_USE="test? ( utils )"
 
 # block with sci-biology/exonerate , maybe the best would be to change SRC_URI in sci-biology/exonerate
@@ -26,10 +23,6 @@ DEPEND="
 	dev-libs/glib:2"
 RDEPEND="${DEPEND}"
 
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-PATCHES=( "${FILESDIR}"/${P}-asneeded.patch )
-
 src_prepare() {
 	tc-export CC
 	sed \
@@ -37,20 +30,18 @@ src_prepare() {
 		-i configure.in || die
 	# we patch the configure.in file like sci-biology/exonerate:gentoo does, though it is ugly hack
 	# mv configure.in configure.ac
-	autotools-utils_src_prepare
+	default
 }
 
 src_configure() {
-	local myeconfargs=(
-		$(use_enable utils utilities)
-		$(use_enable threads pthreads)
-		--enable-largefile
+	econf \
+		$(use_enable utils utilities) \
+		$(use_enable threads pthreads) \
+		--enable-largefile \
 		--enable-glib2
-	)
-	autotools-utils_src_configure
 }
 
 src_install() {
-	autotools-utils_src_install
+	default
 	doman doc/man/man1/*.1
 }

diff --git a/sci-biology/exonerate-gff3/files/exonerate-gff3-9999-asneeded.patch b/sci-biology/exonerate-gff3/files/exonerate-gff3-9999-asneeded.patch
deleted file mode 100644
index 3268055cd..000000000
--- a/sci-biology/exonerate-gff3/files/exonerate-gff3-9999-asneeded.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Fix build with --as-needed
-
-https://bugs.gentoo.org/268094
-
---- configure.in
-+++ configure.in
-@@ -289,7 +289,7 @@
- if test "$enable_pthreads" = yes; then
-     echo "Using PTHREADS"
-     CFLAGS="$CFLAGS -DUSE_PTHREADS"
--    LDFLAGS="$LDFLAGS -lpthread"
-+    LIBS="$LIBS -lpthread"
- elif test "$enable_pthreads" = no; then
-     echo "Not using pthreads"
- else