* [gentoo-commits] proj/sci:master commit in: sci-biology/imagej/files/, sci-biology/imagej/
@ 2017-03-15 21:38 Martin Mokrejs
0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2017-03-15 21:38 UTC (permalink / raw
To: gentoo-commits
commit: 395c7e7490baf0d7a6e6550fd47d966c285dc171
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 15 21:38:28 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 15 21:38:28 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=395c7e74
sci-biology/imagej: new package
Ebuild taken over from https://bugs.gentoo.org/show_bug.cgi?id=112275
src_compile screams about:
>>> Compiling source in /scratch/var/tmp/portage/sci-biology/imagej-1.51k/work/source ...
!!! ERROR: Package jython was not found!
but it builds fine using Apache ant.
ImageJ2 is using maven as a build system ( https://imagej.net/ImageJ2 )
Package-Manager: Portage-2.3.3, Repoman-2.3.1
.../imagej/files/AutoThresholder.java.patch | 10 ++
sci-biology/imagej/imagej-1.51k.ebuild | 132 +++++++++++++++++++++
sci-biology/imagej/metadata.xml | 15 +++
3 files changed, 157 insertions(+)
diff --git a/sci-biology/imagej/files/AutoThresholder.java.patch b/sci-biology/imagej/files/AutoThresholder.java.patch
new file mode 100644
index 000000000..97c893244
--- /dev/null
+++ b/sci-biology/imagej/files/AutoThresholder.java.patch
@@ -0,0 +1,10 @@
+--- imagej-1.51k/work/source/ij/process/AutoThresholder.java.ori 2017-03-15 22:33:45.843801175 +0100
++++ imagej-1.51k/work/source/ij/process/AutoThresholder.java 2017-03-15 22:33:55.104053480 +0100
+@@ -650,7 +650,6 @@
+ }
+ // The threshold is the minimum between the two peaks.
+ for (int i=1; i<255; i++) {
+- //IJ.log(" "+i+" "+iHisto[i]);
+ if (iHisto[i-1] > iHisto[i] && iHisto[i+1] >= iHisto[i]) {
+ threshold = i;
+ break;
diff --git a/sci-biology/imagej/imagej-1.51k.ebuild b/sci-biology/imagej/imagej-1.51k.ebuild
new file mode 100644
index 000000000..0467973e4
--- /dev/null
+++ b/sci-biology/imagej/imagej-1.51k.ebuild
@@ -0,0 +1,132 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=6
+
+inherit java-pkg-2 java-ant-2 eutils versionator
+
+MY_PN="ij"
+MY_PV=$(delete_all_version_separators)
+
+# NOTE:
+# as plugins are regularly lagging behind, we use the pack released for previous
+# version instead. Change to present version locally if you are sure proper
+# version has been released.
+# see https://bugs.gentoo.org/show_bug.cgi?id=112275
+IJ_PV=$(expr ${MY_PV::3} - 1)
+
+DESCRIPTION="Image Processing and Analysis in Java"
+HOMEPAGE="http://rsb.info.nih.gov/ij/"
+
+SRC_URI="http://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
+ http://rsb.info.nih.gov/ij/images/ImageJ.png
+ plugins? ( http://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )"
+# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins
+# plugins? ( http://rsb.info.nih.gov/ij/download/zips/${MY_PN}${IJ_PV}.zip )"
+
+RESTRICT=""
+LICENSE="public-domain"
+SLOT="0"
+
+KEYWORDS=""
+
+IUSE="doc plugins debug"
+
+RDEPEND=">=virtual/jre-1.6:*
+ dev-java/java-config
+ dev-java/jython"
+DEPEND=">=virtual/jdk-1.6:*
+ dev-java/ant-core
+ ${RDEPEND}"
+
+S=${WORKDIR}/source
+IJ_S=${WORKDIR}/ImageJ
+
+src_prepare() {
+ cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die
+
+ if ! use debug ; then
+ sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die
+ fi
+ epatch "${FILESDIR}"/AutoThresholder.java.patch
+ eapply_user
+}
+
+# in src_compile we get: !!! ERROR: Package jython was not found!
+# TODO: overwrite calls to jython ? See
+# ij/plugin/frame/Editor.java
+# plugin/PlugInInterpreter.java
+# plugin/Macro_Runner.java
+
+src_compile() {
+ local antflags="build"
+ use doc && antflags="${antflags} javadocs"
+
+ ant ${antflags} || die "ant build failed"
+
+ # Max memory usage depends on available memory and CPU type
+ MEM=$(grep MemTotal ${EPREFIX}/proc/meminfo | cut -d':' -f2 | grep -o [0-9]*)
+ IJ_MAX_MEM=$(expr ${MEM} / 1024)
+ if use x86 && $IJ_MAX_MEM -gt 2048 ; then
+ IJ_MAX_MEM=2048
+ fi
+ # build finished, generate startup wrapper
+ cat <<EOF > "${T}/${PN}"
+#!${EPREFIX}/bin/bash
+IJ_LIB=${EPREFIX}/usr/share/${PN}/lib
+if !([ "\${IJ_HOME}" ]) ; then
+ IJ_HOME=\${HOME}
+fi
+if [ -d \${IJ_HOME}/plugins ] ; then
+ IJ_PLG=\${IJ_HOME}
+else
+ IJ_PLG=${EPREFIX}/usr/share/${PN}/lib
+fi
+if !([ "\$IJ_MEM" ]) ; then
+ IJ_MEM=${IJ_MAX_MEM}
+fi
+if !([ "\$IJ_CP" ]) ; then
+ IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar
+else
+ IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar:\${IJ_CP}
+fi
+\$(java-config --java) \\
+ -Xmx\${IJ_MEM}m -Dswing.aatext=true \\
+ -Dawt.useSystemAAFontSettings=on\\
+ -cp \${IJ_CP} \\
+ -Duser.home=\${IJ_HOME} \\
+ -Dplugins.dir=\${IJ_PLG} \\
+ ij.ImageJ "\$@"
+EOF
+}
+
+src_install() {
+ java-pkg_dojar *.jar
+ dobin "${T}/${PN}"
+
+ if use plugins ; then
+ cp -R "${IJ_S}"/plugins "${ED}"/usr/share/"${PN}"/lib/
+ cp -R "${IJ_S}"/macros "${ED}"/usr/share/"${PN}"/lib/
+ fi
+
+ use doc && java-pkg_dohtml -r "${WORKDIR}"/api
+
+ insinto /usr/share/pixmaps
+ doins "${WORKDIR}/${PN}".png
+ make_desktop_entry "${PN}" ImageJ "${PN}".png Graphics
+}
+
+pkg_postinst() {
+ einfo ""
+ einfo "You can configure the path of a folder, which contains \"plugins\" directory and IJ_Prefs.txt,"
+ einfo "by setting the environmental variable, \$IJ_HOME."
+ einfo "Default setting is \$IJ_HOME=\${HOME}, i.e. \${HOME}/plugins and \${HOME}/IJ_Prefs.txt."
+ einfo ""
+ einfo "You can also configure the memory size by setting the environmental variable, \$IJ_MEM,"
+ einfo "and the class path by setting the environmental variable, \$IJ_CP."
+ einfo ""
+ einfo "If you want to use much more plugins, please see http://rsb.info.nih.gov/ij/plugins/index.html"
+ einfo "and add *.class files to \$IJ_HOME/plugins folder"
+ einfo ""
+}
diff --git a/sci-biology/imagej/metadata.xml b/sci-biology/imagej/metadata.xml
new file mode 100644
index 000000000..4f14b2e58
--- /dev/null
+++ b/sci-biology/imagej/metadata.xml
@@ -0,0 +1,15 @@
+<?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>
+ <use>
+ <flag name="plugins">Install additional plugins</flag>
+ </use>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/imagej/files/, sci-biology/imagej/
@ 2021-01-26 15:02 Andrew Ammerlaan
0 siblings, 0 replies; 2+ messages in thread
From: Andrew Ammerlaan @ 2021-01-26 15:02 UTC (permalink / raw
To: gentoo-commits
commit: 2bb3e74a499bc39723588d1affa29204bf82a78f
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 26 15:00:08 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 26 15:00:08 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2bb3e74a
sci-biology/imagej: version bump, EAPI bump, add keywords
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
.../imagej/files/AutoThresholder.java.patch | 10 -----
.../{imagej-1.51k.ebuild => imagej-1.53g.ebuild} | 49 ++++++++--------------
2 files changed, 18 insertions(+), 41 deletions(-)
diff --git a/sci-biology/imagej/files/AutoThresholder.java.patch b/sci-biology/imagej/files/AutoThresholder.java.patch
deleted file mode 100644
index 97c893244..000000000
--- a/sci-biology/imagej/files/AutoThresholder.java.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- imagej-1.51k/work/source/ij/process/AutoThresholder.java.ori 2017-03-15 22:33:45.843801175 +0100
-+++ imagej-1.51k/work/source/ij/process/AutoThresholder.java 2017-03-15 22:33:55.104053480 +0100
-@@ -650,7 +650,6 @@
- }
- // The threshold is the minimum between the two peaks.
- for (int i=1; i<255; i++) {
-- //IJ.log(" "+i+" "+iHisto[i]);
- if (iHisto[i-1] > iHisto[i] && iHisto[i+1] >= iHisto[i]) {
- threshold = i;
- break;
diff --git a/sci-biology/imagej/imagej-1.51k.ebuild b/sci-biology/imagej/imagej-1.53g.ebuild
similarity index 71%
rename from sci-biology/imagej/imagej-1.51k.ebuild
rename to sci-biology/imagej/imagej-1.53g.ebuild
index 57b46c045..6c9fdf736 100644
--- a/sci-biology/imagej/imagej-1.51k.ebuild
+++ b/sci-biology/imagej/imagej-1.53g.ebuild
@@ -1,47 +1,41 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-inherit java-pkg-2 java-ant-2 eutils versionator
+inherit java-pkg-2 java-ant-2 desktop
MY_PN="ij"
-MY_PV=$(delete_all_version_separators)
-
-# NOTE:
-# as plugins are regularly lagging behind, we use the pack released for previous
-# version instead. Change to present version locally if you are sure proper
-# version has been released.
-# see https://bugs.gentoo.org/show_bug.cgi?id=112275
-# https://github.com/imagej/imagej1/issues/28
-IJ_PV=$((${MY_PV::3}-1))
+MY_PV=${PV//.}
+IJ_PV=${MY_PV::-1}
DESCRIPTION="Image Processing and Analysis in Java"
-HOMEPAGE="http://rsb.info.nih.gov/ij/"
+HOMEPAGE="https://imagej.nih.gov/ij/"
-SRC_URI="http://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
- http://rsb.info.nih.gov/ij/images/ImageJ.png
- plugins? ( http://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )"
+SRC_URI="https://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
+ https://rsb.info.nih.gov/ij/images/ImageJ.png
+ plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )"
# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins
# plugins? ( http://rsb.info.nih.gov/ij/download/zips/${MY_PN}${IJ_PV}.zip )"
-RESTRICT=""
LICENSE="public-domain" # http://imagej.net/disclaimer.html
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
IUSE="doc plugins debug"
-RDEPEND=">=virtual/jre-1.6:*
+RDEPEND="
+ >=virtual/jre-1.7:*
dev-java/java-config
- dev-java/jython"
-DEPEND=">=virtual/jdk-1.6:*
+"
+DEPEND="${RDEPEND}
+ >=virtual/jdk-1.7:*
dev-java/ant-core
app-arch/unzip
- ${RDEPEND}"
+"
-S=${WORKDIR}/source
+S="${WORKDIR}/source"
IJ_S=${WORKDIR}/ImageJ
src_prepare() {
@@ -50,16 +44,9 @@ src_prepare() {
if ! use debug ; then
sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die
fi
- epatch "${FILESDIR}"/AutoThresholder.java.patch
- eapply_user
+ default
}
-# in src_compile we get: !!! ERROR: Package jython was not found!
-# TODO: overwrite calls to jython ? See
-# ij/plugin/frame/Editor.java
-# plugin/PlugInInterpreter.java
-# plugin/Macro_Runner.java
-
src_compile() {
local antflags="build"
use doc && antflags="${antflags} javadocs"
@@ -115,7 +102,7 @@ src_install() {
insinto /usr/share/pixmaps
doins "${WORKDIR}/${PN}".png
- make_desktop_entry "${PN}" ImageJ "${PN}".png Graphics
+ make_desktop_entry "${PN}" ImageJ "${PN}" Graphics
}
pkg_postinst() {
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2021-01-26 15:02 Andrew Ammerlaan
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