[gentoo-commits] proj/sci:master commit in: dev-perl/Bio-EnsEMBL/

[gentoo-commits] proj/sci:master commit in: dev-perl/Bio-EnsEMBL/

[Martin Mokrejs]

commit:     38ef4fac3f1c8bfb5044571b268200a0a1488969
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec  2 22:52:44 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec  2 22:52:44 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=38ef4fac

dev-perl/Bio-EnsEMBL: new package to provide EnsEMBL Perl API

This is needed by sci-biology/ensembl-tools, do not miss the
official installation procedure at
http://www.ensembl.org/info/docs/api/api_installation.html

Package-Manager: portage-2.3.2

 dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild | 35 ++++++++++++++++++++++++++++
 dev-perl/Bio-EnsEMBL/metadata.xml            | 12 ++++++++++
 2 files changed, 47 insertions(+)

diff --git a/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild b/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
new file mode 100644
index 0000000..73e3a47
--- /dev/null
+++ b/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+MODULE_AUTHOR=""
+inherit perl-module
+
+DESCRIPTION="EnsEMBL Perl API aka ensembl-api exposing Bio::EnsEMBL::Registry"
+SRC_URI="ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz"
+
+#LICENSE="|| ( Artistic GPL-1+ )"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+src_install(){
+	perl_set_version
+	insinto "${VENDOR_LIB}" # do not add "${PN}" so the the PERL path starts with Bio/
+	find . -name t | xargs rm -rf || die
+	find . -name test.pl | xargs rm -f || die
+	find . -name \*.example | xargs rm -f || die
+	find . -name \*.json | xargs rm -f || die
+	find . -name README* | xargs rm -rf || die
+	find . -name \*.conf | xargs rm -f || die
+	find . -name travisci | xargs rm -rf || die
+	find . -name sql | xargs rm -rf || die
+	find . -name modules | while read d; do pushd "$d"; doins -r *; popd; done || die
+}

diff --git a/dev-perl/Bio-EnsEMBL/metadata.xml b/dev-perl/Bio-EnsEMBL/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/dev-perl/Bio-EnsEMBL/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>

[gentoo-commits] proj/sci:master commit in: dev-perl/Bio-EnsEMBL/

[Andrew Ammerlaan]

commit:     e8d6f21dd913f9ee527d6ad59726980f8967e05f
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Jan 16 10:48:48 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Jan 16 10:48:48 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e8d6f21d

dev-perl/Bio-EnsEMBL: re-gen manifest

upstream has no releases, so this will have to
be re-genned from time to time

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild b/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
index d4910ad68..80014f94f 100644
--- a/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
+++ b/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
@@ -1,21 +1,18 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 MODULE_AUTHOR=""
 inherit perl-module
 
 DESCRIPTION="EnsEMBL Perl API aka ensembl-api exposing Bio::EnsEMBL::Registry"
+HOMEPAGE="https://www.ensembl.org/index.html"
 SRC_URI="ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz"
 
-#LICENSE="|| ( Artistic GPL-1+ )"
+LICENSE="Apache-2.0"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}"
 
 S="${WORKDIR}"
 

[gentoo-commits] proj/sci:master commit in: dev-perl/Bio-EnsEMBL/

[Andrew Ammerlaan]

commit:     70d12c8b741e74bfdc4b5125c3b178703e3ed6f2
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 18:53:33 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 18:53:33 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=70d12c8b

dev-perl/Bio-EnsEMBL: use perl_domodule

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild b/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
index 80014f94f..f2d7c6a54 100644
--- a/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
+++ b/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
@@ -18,7 +18,6 @@ S="${WORKDIR}"
 
 src_install(){
 	perl_set_version
-	insinto "${VENDOR_LIB}" # do not add "${PN}" so the the PERL path starts with Bio/
 	find . -name t | xargs rm -rf || die
 	find . -name test.pl | xargs rm -f || die
 	find . -name \*.example | xargs rm -f || die
@@ -27,5 +26,5 @@ src_install(){
 	find . -name \*.conf | xargs rm -f || die
 	find . -name travisci | xargs rm -rf || die
 	find . -name sql | xargs rm -rf || die
-	find . -name modules | while read d; do pushd "$d"; doins -r *; popd; done || die
+	find . -name modules | while read d; do pushd "$d"; perl_domodule -r *; popd; done || die
 }

[gentoo-commits] proj/sci:master commit in: dev-perl/Bio-EnsEMBL/

[Andrew Ammerlaan]

commit:     fbff3b23c7b848ac245aec24083b8eccbd4e03a4
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 24 14:42:29 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon Jan 24 14:42:29 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fbff3b23

dev-perl/Bio-EnsEMBL: remove fundamentally broken package

how is this even supposed to work?

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild | 30 ----------------------------
 dev-perl/Bio-EnsEMBL/metadata.xml            | 12 -----------
 2 files changed, 42 deletions(-)

diff --git a/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild b/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
deleted file mode 100644
index f2d7c6a54..000000000
--- a/dev-perl/Bio-EnsEMBL/Bio-EnsEMBL-9999.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MODULE_AUTHOR=""
-inherit perl-module
-
-DESCRIPTION="EnsEMBL Perl API aka ensembl-api exposing Bio::EnsEMBL::Registry"
-HOMEPAGE="https://www.ensembl.org/index.html"
-SRC_URI="ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS=""
-
-S="${WORKDIR}"
-
-src_install(){
-	perl_set_version
-	find . -name t | xargs rm -rf || die
-	find . -name test.pl | xargs rm -f || die
-	find . -name \*.example | xargs rm -f || die
-	find . -name \*.json | xargs rm -f || die
-	find . -name README* | xargs rm -rf || die
-	find . -name \*.conf | xargs rm -f || die
-	find . -name travisci | xargs rm -rf || die
-	find . -name sql | xargs rm -rf || die
-	find . -name modules | while read d; do pushd "$d"; perl_domodule -r *; popd; done || die
-}

diff --git a/dev-perl/Bio-EnsEMBL/metadata.xml b/dev-perl/Bio-EnsEMBL/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/dev-perl/Bio-EnsEMBL/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>