[gentoo-commits] proj/sci:master commit in: sci-biology/jtreeview/, profiles/

[gentoo-commits] proj/sci:master commit in: sci-biology/jtreeview/, profiles/

[Andrew Ammerlaan]

commit:     26212fea17cb62e4fc20bb50e26d47e63c511b0d
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 12:54:55 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 12:55:06 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=26212fea

sci-biology/jtreeview: fix fetch, fix build, EAPI bump

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

 profiles/package.mask                              |  1 -
 ...eview-1.1.6.4.ebuild => jtreeview-1.2.0.ebuild} | 25 +++++++--------
 sci-biology/jtreeview/jtreeview-9999.ebuild        | 37 +++++++++-------------
 3 files changed, 27 insertions(+), 36 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index b6e454b48..31c424659 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -72,4 +72,3 @@ sci-biology/hydra-sv
 sci-biology/ICC
 sci-biology/IMAGE
 sci-biology/jannovar
-sci-biology/jtreeview

diff --git a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild b/sci-biology/jtreeview/jtreeview-1.2.0.ebuild
similarity index 57%
rename from sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
rename to sci-biology/jtreeview/jtreeview-1.2.0.ebuild
index e89e14cf0..34a6ae178 100644
--- a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
+++ b/sci-biology/jtreeview/jtreeview-1.2.0.ebuild
@@ -1,29 +1,28 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit java-pkg-2 java-ant-2 eutils perl-module
-
-S="${WORKDIR}"/TreeView-1.1.6r4-src
+inherit perl-module java-pkg-2 java-ant-2
 
 DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
 HOMEPAGE="http://jtreeview.sourceforge.net/" # no https
 SRC_URI="
-	https://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-src.tar.gz
-	https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz"
-#http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-bin.tar.gz
+	https://sourceforge.net/projects/jtreeview/files/jtreeview/${PV}/TreeView-${PV}-src.tar.gz
+	https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz
+"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="" # resulting java binary does not execute for me
-IUSE=""
+KEYWORDS="~amd64"
 
-DEPEND=">virtual/jdk-1.5:*
+DEPEND=">virtual/jdk-1.7:*
 	dev-java/nanoxml"
 RDEPEND="${DEPEND}
-	>=virtual/jre-1.5:*"
+	>=virtual/jre-1.7:*"
+
+S="${WORKDIR}/TreeView-${PV}-src"
+JAVA_PKG_BSFIX_NAME="${S}"
 
 # TODO: use xltproc to create docs following TreeView-1.1.6r4-src/doc/README
 

diff --git a/sci-biology/jtreeview/jtreeview-9999.ebuild b/sci-biology/jtreeview/jtreeview-9999.ebuild
index 159448ab7..0b95e7cb3 100644
--- a/sci-biology/jtreeview/jtreeview-9999.ebuild
+++ b/sci-biology/jtreeview/jtreeview-9999.ebuild
@@ -1,38 +1,31 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit java-pkg-2 git-r3
+inherit perl-module java-pkg-2 java-ant-2 git-r3
 
 DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
-HOMEPAGE="http://jtreeview.sourceforge.net
-	https://bitbucket.org/TreeView3Dev/treeview3" # no https
+HOMEPAGE="http://jtreeview.sourceforge.net/" # no https
 EGIT_REPO_URI="https://bitbucket.org/TreeView3Dev/treeview3.git"
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS="" # builds and executes fines
-IUSE=""
+KEYWORDS=""
 
 DEPEND=">virtual/jdk-1.7:*"
 RDEPEND="${DEPEND}
 	>=virtual/jre-1.7:*"
 
-src_prepare(){
-	chmod u+x ./gradle* || die
-	eapply_user
-}
-
-src_compile(){
-	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
-	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-	# make jure SDK-1.8 is available, JRE-1.8 is not enough
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
-}
-
 src_install(){
-	cd build/libs || die
-	java-pkg_dojar *.jar
-	java-pkg_dolauncher ${PN}
+	java-pkg_dojar TreeView.jar
+	java-pkg_dolauncher ${PN} TreeView.jar
+	cd ../helper-scripts-0.0.2 || die
+	perl_set_version
+	insinto "${VENDOR_LIB}"
+	doins *.pm
+	dobin *.pl
+	insinto /usr/share/"${PN}"/examples
+	doins blues.color
+	newdoc README README.helper-scripts
 }