[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2024-06-17 Thread Andrew Ammerlaan
commit: 6f4847c6f5bc771f45f8d4dc3106679ce4c760d1
Author: Israel Hernandez  gmail  com>
AuthorDate: Sun Jun 16 18:25:24 2024 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Mon Jun 17 12:28:04 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6f4847c6

sci-biology/imagej: ant-core deprecated

Signed-off-by: IAHMCOL  thejabberwocky.net>

This commit removes dev-java/ant-core from dependencies
This has been deprecated, and it gets automatically used with ant2

Latest updates had depclean  dev-java/ant-core, and the packages still builds 
after dependency removal

see:
https://packages.gentoo.org/packages/dev-java/ant-core
Closes: https://github.com/gentoo/sci/pull/1275
Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-biology/imagej/{imagej-1.54i.ebuild => imagej-1.54i-r1.ebuild} | 1 -
 sci-biology/imagej/imagej-.ebuild  | 1 -
 2 files changed, 2 deletions(-)

diff --git a/sci-biology/imagej/imagej-1.54i.ebuild 
b/sci-biology/imagej/imagej-1.54i-r1.ebuild
similarity index 99%
rename from sci-biology/imagej/imagej-1.54i.ebuild
rename to sci-biology/imagej/imagej-1.54i-r1.ebuild
index ec98393df..f95167bcd 100644
--- a/sci-biology/imagej/imagej-1.54i.ebuild
+++ b/sci-biology/imagej/imagej-1.54i-r1.ebuild
@@ -50,7 +50,6 @@ DEPEND="
 "
 
 BDEPEND="
-   dev-java/ant-core
app-arch/unzip
 "
 

diff --git a/sci-biology/imagej/imagej-.ebuild 
b/sci-biology/imagej/imagej-.ebuild
index ec98393df..f95167bcd 100644
--- a/sci-biology/imagej/imagej-.ebuild
+++ b/sci-biology/imagej/imagej-.ebuild
@@ -50,7 +50,6 @@ DEPEND="
 "
 
 BDEPEND="
-   dev-java/ant-core
app-arch/unzip
 "
 



[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2024-06-10 Thread Andrew Ammerlaan
commit: f9718d14356d6ac995991a9e02331b40d97204d8
Author: Israel Hernandez  gmail  com>
AuthorDate: Sun Jun  9 18:59:06 2024 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Mon Jun 10 06:58:57 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f9718d14

sci-biology/imagej: add 1.54i, drop 1.54h

Signed-off-by: IAHMCOL  thejabberwocky.net>

* This PR bumps imagej to version 1.54i
* This PR, also, redirects the icon to the new URL. Old URL hosted on the nih
became disabled
Closes: https://github.com/gentoo/sci/pull/1272

Signed-off-by: Andrew Ammerlaan  gentoo.org>

 .../imagej/{imagej-1.54h-r1.ebuild => imagej-1.54i.ebuild}| 8 
 sci-biology/imagej/imagej-.ebuild | 8 
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/sci-biology/imagej/imagej-1.54h-r1.ebuild 
b/sci-biology/imagej/imagej-1.54i.ebuild
similarity index 94%
rename from sci-biology/imagej/imagej-1.54h-r1.ebuild
rename to sci-biology/imagej/imagej-1.54i.ebuild
index 0252d6613..ec98393df 100644
--- a/sci-biology/imagej/imagej-1.54h-r1.ebuild
+++ b/sci-biology/imagej/imagej-1.54i.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -11,12 +11,12 @@ IJ_PV="154" #plugins now available for 154
 DESCRIPTION="Image Processing and Analysis in Java"
 
 HOMEPAGE="
-   https://imagej.nih.gov/ij/
+   https://imagej.net/software/imagej/
https://github.com/imagej
 "
 
 SRC_URI="
-   https://imagej.nih.gov/ij/images/ImageJ.png
+   https://imagej.net/media/icons/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
 
@@ -55,7 +55,7 @@ BDEPEND="
 "
 
 src_prepare() {
-   cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die
+   cp "${DISTDIR}"/imagej.png "${WORKDIR}/${PN}.png" || die
 
if [[ ${PV} ==  ]]; then
   if use plugins ; then

diff --git a/sci-biology/imagej/imagej-.ebuild 
b/sci-biology/imagej/imagej-.ebuild
index 0252d6613..ec98393df 100644
--- a/sci-biology/imagej/imagej-.ebuild
+++ b/sci-biology/imagej/imagej-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -11,12 +11,12 @@ IJ_PV="154" #plugins now available for 154
 DESCRIPTION="Image Processing and Analysis in Java"
 
 HOMEPAGE="
-   https://imagej.nih.gov/ij/
+   https://imagej.net/software/imagej/
https://github.com/imagej
 "
 
 SRC_URI="
-   https://imagej.nih.gov/ij/images/ImageJ.png
+   https://imagej.net/media/icons/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
 
@@ -55,7 +55,7 @@ BDEPEND="
 "
 
 src_prepare() {
-   cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die
+   cp "${DISTDIR}"/imagej.png "${WORKDIR}/${PN}.png" || die
 
if [[ ${PV} ==  ]]; then
   if use plugins ; then



[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2023-12-20 Thread Andrew Ammerlaan
commit: c5701b9a123d9cf9ebdf13570b3b92cabae54fc2
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Wed Dec 20 09:46:29 2023 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Wed Dec 20 09:46:29 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c5701b9a

sci-biology/imagej: revbump 1.54h

Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-biology/imagej/{imagej-1.54h.ebuild => imagej-1.54h-r1.ebuild} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-biology/imagej/imagej-1.54h.ebuild 
b/sci-biology/imagej/imagej-1.54h-r1.ebuild
similarity index 100%
rename from sci-biology/imagej/imagej-1.54h.ebuild
rename to sci-biology/imagej/imagej-1.54h-r1.ebuild



[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2023-12-20 Thread Andrew Ammerlaan
commit: be482279cf5432b33ae455e27c427919392a8764
Author: Israel Hernandez  gmail  com>
AuthorDate: Tue Dec 19 16:02:53 2023 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Wed Dec 20 09:46:02 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=be482279

sci-biology/imagej: bump version imagej sources and plugins

* ImageJ version bump 1.53t to 1.54g from NIH sources
* plugins version bump 153 to 154

Signed-off-by: IAHMCOL  thejabberwocky.net>
Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-biology/imagej/{imagej-1.53t.ebuild => imagej-1.54g.ebuild} | 2 --
 sci-biology/imagej/imagej-1.54h.ebuild  | 4 ++--
 sci-biology/imagej/imagej-.ebuild   | 4 ++--
 3 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/sci-biology/imagej/imagej-1.53t.ebuild 
b/sci-biology/imagej/imagej-1.54g.ebuild
similarity index 94%
rename from sci-biology/imagej/imagej-1.53t.ebuild
rename to sci-biology/imagej/imagej-1.54g.ebuild
index 952eff08b..4bf6db8d9 100644
--- a/sci-biology/imagej/imagej-1.53t.ebuild
+++ b/sci-biology/imagej/imagej-1.54g.ebuild
@@ -15,8 +15,6 @@ HOMEPAGE="https://imagej.nih.gov/ij/;
 SRC_URI="https://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
https://imagej.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 )"
 
 LICENSE="public-domain" # http://imagej.net/disclaimer.html
 SLOT="0"

diff --git a/sci-biology/imagej/imagej-1.54h.ebuild 
b/sci-biology/imagej/imagej-1.54h.ebuild
index 33a10b0e4..0252d6613 100644
--- a/sci-biology/imagej/imagej-1.54h.ebuild
+++ b/sci-biology/imagej/imagej-1.54h.ebuild
@@ -6,7 +6,7 @@ EAPI=8
 inherit java-pkg-2 java-ant-2 desktop
 
 MY_PN="ij"
-IJ_PV="153" #plugins not currently available under 154
+IJ_PV="154" #plugins now available for 154
 
 DESCRIPTION="Image Processing and Analysis in Java"
 
@@ -59,7 +59,7 @@ src_prepare() {
 
if [[ ${PV} ==  ]]; then
   if use plugins ; then
- unpack "${MY_PN}${IJ_PV}.zip"
+ unpack "${MY_PN}${IJ_PV}.zip"
   fi
fi
 

diff --git a/sci-biology/imagej/imagej-.ebuild 
b/sci-biology/imagej/imagej-.ebuild
index 33a10b0e4..0252d6613 100644
--- a/sci-biology/imagej/imagej-.ebuild
+++ b/sci-biology/imagej/imagej-.ebuild
@@ -6,7 +6,7 @@ EAPI=8
 inherit java-pkg-2 java-ant-2 desktop
 
 MY_PN="ij"
-IJ_PV="153" #plugins not currently available under 154
+IJ_PV="154" #plugins now available for 154
 
 DESCRIPTION="Image Processing and Analysis in Java"
 
@@ -59,7 +59,7 @@ src_prepare() {
 
if [[ ${PV} ==  ]]; then
   if use plugins ; then
- unpack "${MY_PN}${IJ_PV}.zip"
+ unpack "${MY_PN}${IJ_PV}.zip"
   fi
fi
 



[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2023-12-20 Thread Andrew Ammerlaan
commit: 9d05db0ba02b6bf5638da71761558eaa5b7face4
Author: Israel Hernandez  gmail  com>
AuthorDate: Tue Dec 19 19:32:27 2023 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Wed Dec 20 09:46:06 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9d05db0b

sci-biology/imagej: drop 1.54g

Signed-off-by: IAHMCOL  thejabberwocky.net>
Closes: https://github.com/gentoo/sci/pull/1227
Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-biology/imagej/imagej-1.54g.ebuild | 120 -
 1 file changed, 120 deletions(-)

diff --git a/sci-biology/imagej/imagej-1.54g.ebuild 
b/sci-biology/imagej/imagej-1.54g.ebuild
deleted file mode 100644
index 4bf6db8d9..0
--- a/sci-biology/imagej/imagej-1.54g.ebuild
+++ /dev/null
@@ -1,120 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit java-pkg-2 java-ant-2 desktop
-
-MY_PN="ij"
-MY_PV=${PV//.}
-IJ_PV=${MY_PV::-1}
-
-DESCRIPTION="Image Processing and Analysis in Java"
-HOMEPAGE="https://imagej.nih.gov/ij/;
-
-SRC_URI="https://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
-   https://imagej.nih.gov/ij/images/ImageJ.png
-   plugins? ( 
https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )"
-
-LICENSE="public-domain" # http://imagej.net/disclaimer.html
-SLOT="0"
-
-KEYWORDS="~amd64"
-
-IUSE="doc plugins debug"
-
-RDEPEND="
-   >=virtual/jre-1.7:*
-   dev-java/java-config
-"
-DEPEND="${RDEPEND}
-   >=virtual/jdk-1.7:*
-"
-BDEPEND="
-   dev-java/ant-core
-   app-arch/unzip
-"
-
-S="${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">:' "${S}"/build.xml || die
-   fi
-   default
-}
-
-src_compile() {
-   local antflags="build"
-   use doc && antflags="${antflags} javadocs"
-
-   ant ${antflags} || die  "ant build failed"
-
-   # Max memory usage depends on available memory and CPU type
-   MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*)
-   IJ_MAX_MEM=$(expr ${MEM} / 1024)
-   if use x86 && $IJ_MAX_MEM -gt 2048 ; then
-   IJ_MAX_MEM=2048
-   fi
-   # build finished, generate startup wrapper
-   cat < "${T}/${PN}"
-#!${EPREFIX}/bin/bash
-IJ_LIB=${EPREFIX}/usr/share/${PN}/lib
-if !([ "\${IJ_HOME}" ]) ; then
-   IJ_HOME=\${HOME}/.imagej
-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}" 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}/.imagej, i.e. 
\${HOME}/.imagej/plugins and \${HOME}/.imagej/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 ""
-}



[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2023-12-19 Thread Andrew Ammerlaan
commit: 4e29aee84176d30527862de23b0fe7c5c049c70c
Author: Israel Hernandez  gmail  com>
AuthorDate: Mon Dec 18 23:21:17 2023 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Tue Dec 19 09:04:20 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4e29aee8

sci-biology/imagej: add 1.54h, drop 1.54f

Signed-off-by: IAHMCOL  thejabberwocky.net>
Closes: https://github.com/gentoo/sci/pull/1224
Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-biology/imagej/{imagej-1.54f.ebuild => imagej-1.54h.ebuild} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-biology/imagej/imagej-1.54f.ebuild 
b/sci-biology/imagej/imagej-1.54h.ebuild
similarity index 100%
rename from sci-biology/imagej/imagej-1.54f.ebuild
rename to sci-biology/imagej/imagej-1.54h.ebuild



[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2023-08-17 Thread Andrew Ammerlaan
commit: 2d9c80a90fcc0affb4f85daba6fcfef4b2831b64
Author: Israel Hernandez  gmail  com>
AuthorDate: Thu Aug 17 19:20:50 2023 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Thu Aug 17 19:27:27 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2d9c80a9

sci-biology/imagej: add 1.54f, drop 1.54d

Signed-off-by: IAHMCOL  thejabberwocky.net>
Closes: https://github.com/gentoo/sci/pull/1213
Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-biology/imagej/{imagej-1.54d.ebuild => imagej-1.54f.ebuild} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-biology/imagej/imagej-1.54d.ebuild 
b/sci-biology/imagej/imagej-1.54f.ebuild
similarity index 100%
rename from sci-biology/imagej/imagej-1.54d.ebuild
rename to sci-biology/imagej/imagej-1.54f.ebuild



[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2023-07-09 Thread Andrew Ammerlaan
commit: f6ee8374ed488f3621b2193345c0039cd73d06e9
Author: Israel Hernandez  gmail  com>
AuthorDate: Sat Jul  8 18:23:30 2023 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Sun Jul  9 18:58:21 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f6ee8374

sci-biology/imagej: Add unstable git versions

Signed-off-by: IAHMCOL  thejabberwocky.net>
Co-authored-by: Andrew Ammerlaan  gentoo.org>
Closes: https://github.com/gentoo/sci/pull/1198
Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-biology/imagej/imagej-1.53t.ebuild |  2 +
 .../{imagej-1.53t.ebuild => imagej-1.54d.ebuild}   | 50 --
 .../{imagej-1.53t.ebuild => imagej-.ebuild}| 50 --
 sci-biology/imagej/metadata.xml|  3 ++
 4 files changed, 79 insertions(+), 26 deletions(-)

diff --git a/sci-biology/imagej/imagej-1.53t.ebuild 
b/sci-biology/imagej/imagej-1.53t.ebuild
index d2959e18c..952eff08b 100644
--- a/sci-biology/imagej/imagej-1.53t.ebuild
+++ b/sci-biology/imagej/imagej-1.53t.ebuild
@@ -31,6 +31,8 @@ RDEPEND="
 "
 DEPEND="${RDEPEND}
>=virtual/jdk-1.7:*
+"
+BDEPEND="
dev-java/ant-core
app-arch/unzip
 "

diff --git a/sci-biology/imagej/imagej-1.53t.ebuild 
b/sci-biology/imagej/imagej-1.54d.ebuild
similarity index 82%
copy from sci-biology/imagej/imagej-1.53t.ebuild
copy to sci-biology/imagej/imagej-1.54d.ebuild
index d2959e18c..33a10b0e4 100644
--- a/sci-biology/imagej/imagej-1.53t.ebuild
+++ b/sci-biology/imagej/imagej-1.54d.ebuild
@@ -6,22 +6,36 @@ EAPI=8
 inherit java-pkg-2 java-ant-2 desktop
 
 MY_PN="ij"
-MY_PV=${PV//.}
-IJ_PV=${MY_PV::-1}
+IJ_PV="153" #plugins not currently available under 154
 
 DESCRIPTION="Image Processing and Analysis in Java"
-HOMEPAGE="https://imagej.nih.gov/ij/;
 
-SRC_URI="https://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
+HOMEPAGE="
+   https://imagej.nih.gov/ij/
+   https://github.com/imagej
+"
+
+SRC_URI="
https://imagej.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 )"
 
-LICENSE="public-domain" # http://imagej.net/disclaimer.html
-SLOT="0"
+if [[ ${PV} ==  ]]; then
+   inherit git-r3
+   EGIT_REPO_URI="https://github.com/imagej/ImageJ;
+   IJ_S="${S}/ImageJ"
+else
+   SRC_URI+="
+   
https://github.com/imagej/ImageJ/archive/refs/tags/v${PV}.tar.gz -> 
${P}.gh.tar.gz
+   "
+   S="${WORKDIR}/ImageJ-${PV}"
+   IJ_S="${WORKDIR}/ImageJ"
+   KEYWORDS="~amd64"
+fi
+
+LICENSE="public-domain"
 
-KEYWORDS="~amd64"
+SLOT="0"
 
 IUSE="doc plugins debug"
 
@@ -29,18 +43,26 @@ RDEPEND="
>=virtual/jre-1.7:*
dev-java/java-config
 "
-DEPEND="${RDEPEND}
+
+DEPEND="
+   ${RDEPEND}
>=virtual/jdk-1.7:*
+"
+
+BDEPEND="
dev-java/ant-core
app-arch/unzip
 "
 
-S="${WORKDIR}/source"
-IJ_S=${WORKDIR}/ImageJ
-
 src_prepare() {
cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die
 
+   if [[ ${PV} ==  ]]; then
+  if use plugins ; then
+ unpack "${MY_PN}${IJ_PV}.zip"
+  fi
+   fi
+
if ! use debug ; then
sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die
fi
@@ -56,9 +78,11 @@ src_compile() {
# Max memory usage depends on available memory and CPU type
MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*)
IJ_MAX_MEM=$(expr ${MEM} / 1024)
+
if use x86 && $IJ_MAX_MEM -gt 2048 ; then
-   IJ_MAX_MEM=2048
+  IJ_MAX_MEM=2048
fi
+
# build finished, generate startup wrapper
cat < "${T}/${PN}"
 #!${EPREFIX}/bin/bash

diff --git a/sci-biology/imagej/imagej-1.53t.ebuild 
b/sci-biology/imagej/imagej-.ebuild
similarity index 82%
copy from sci-biology/imagej/imagej-1.53t.ebuild
copy to sci-biology/imagej/imagej-.ebuild
index d2959e18c..33a10b0e4 100644
--- a/sci-biology/imagej/imagej-1.53t.ebuild
+++ b/sci-biology/imagej/imagej-.ebuild
@@ -6,22 +6,36 @@ EAPI=8
 inherit java-pkg-2 java-ant-2 desktop
 
 MY_PN="ij"
-MY_PV=${PV//.}
-IJ_PV=${MY_PV::-1}
+IJ_PV="153" #plugins not currently available under 154
 
 DESCRIPTION="Image Processing and Analysis in Java"
-HOMEPAGE="https://imagej.nih.gov/ij/;
 
-SRC_URI="https://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
+HOMEPAGE="
+   https://imagej.nih.gov/ij/
+   https://github.com/imagej
+"
+
+SRC_URI="
https://imagej.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? ( 

[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2023-07-03 Thread Andrew Ammerlaan
commit: 5cf6be39e39840cc88e4dfa86ed372ff85736e95
Author: Israel Hernandez  gmail  com>
AuthorDate: Sun Jul  2 21:43:21 2023 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Mon Jul  3 08:10:08 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5cf6be39

sci-biology/imagej: bump to 1.53t

Closes: https://github.com/gentoo/sci/pull/1197
Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-biology/imagej/{imagej-1.53g.ebuild => imagej-1.53t.ebuild} | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/imagej/imagej-1.53g.ebuild 
b/sci-biology/imagej/imagej-1.53t.ebuild
similarity index 97%
rename from sci-biology/imagej/imagej-1.53g.ebuild
rename to sci-biology/imagej/imagej-1.53t.ebuild
index 6c9fdf736..d2959e18c 100644
--- a/sci-biology/imagej/imagej-1.53g.ebuild
+++ b/sci-biology/imagej/imagej-1.53t.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 inherit java-pkg-2 java-ant-2 desktop
 
@@ -13,7 +13,7 @@ DESCRIPTION="Image Processing and Analysis in Java"
 HOMEPAGE="https://imagej.nih.gov/ij/;
 
 SRC_URI="https://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
-   https://rsb.info.nih.gov/ij/images/ImageJ.png
+   https://imagej.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 )"



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

2021-01-26 Thread Andrew Ammerlaan
commit: 2bb3e74a499bc39723588d1affa29204bf82a78f
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Tue Jan 26 15:00:08 2021 +
Commit: Andrew Ammerlaan  riseup  net>
CommitDate: Tue Jan 26 15:00:08 2021 +
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  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..0
--- 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() {



[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2021-01-19 Thread Andrew Ammerlaan
commit: 595d87fc830c18593784b5634cff7139d17028e3
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Tue Jan 19 16:21:31 2021 +
Commit: Andrew Ammerlaan  riseup  net>
CommitDate: Tue Jan 19 16:21:31 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=595d87fc

sci-biology/imagej: depend on app-arch/unzip

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

 sci-biology/imagej/imagej-1.51k.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/imagej/imagej-1.51k.ebuild 
b/sci-biology/imagej/imagej-1.51k.ebuild
index 931aef0bc..57b46c045 100644
--- a/sci-biology/imagej/imagej-1.51k.ebuild
+++ b/sci-biology/imagej/imagej-1.51k.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -38,6 +38,7 @@ RDEPEND=">=virtual/jre-1.6:*
dev-java/jython"
 DEPEND=">=virtual/jdk-1.6:*
dev-java/ant-core
+   app-arch/unzip
${RDEPEND}"
 
 S=${WORKDIR}/source



[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2017-09-07 Thread David Seifert
commit: db6c1666f10c9df6f91a38a45fcba0da7424cdfd
Author: David Seifert  gentoo  org>
AuthorDate: Thu Sep  7 20:28:36 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Thu Sep  7 20:28:36 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=db6c1666

sci-biology/imagej: Do not call external programs in global scope

Closes: https://bugs.gentoo.org/show_bug.cgi?id=630214
Package-Manager: Portage-2.3.8, Repoman-2.3.3

 sci-biology/imagej/imagej-1.51k.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/imagej/imagej-1.51k.ebuild 
b/sci-biology/imagej/imagej-1.51k.ebuild
index 2681665f5..931aef0bc 100644
--- a/sci-biology/imagej/imagej-1.51k.ebuild
+++ b/sci-biology/imagej/imagej-1.51k.ebuild
@@ -14,7 +14,7 @@ MY_PV=$(delete_all_version_separators)
 # version has been released.
 # see https://bugs.gentoo.org/show_bug.cgi?id=112275
 # https://github.com/imagej/imagej1/issues/28
-IJ_PV=$(expr ${MY_PV::3} - 1)
+IJ_PV=$((${MY_PV::3}-1))
 
 DESCRIPTION="Image Processing and Analysis in Java"
 HOMEPAGE="http://rsb.info.nih.gov/ij/;



[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2017-03-16 Thread Martin Mokrejs
commit: ce9dbd43bb73dc4b69fdc4ccf1cfd38e5485b029
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Mar 16 10:51:20 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar 16 10:51:20 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ce9dbd43

sci-biology/imagej: adjust einfo message accordingly

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/imagej/imagej-1.51k.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/imagej/imagej-1.51k.ebuild 
b/sci-biology/imagej/imagej-1.51k.ebuild
index 845fc48cb..2681665f5 100644
--- a/sci-biology/imagej/imagej-1.51k.ebuild
+++ b/sci-biology/imagej/imagej-1.51k.ebuild
@@ -121,7 +121,7 @@ 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 "Default setting is \$IJ_HOME=\${HOME}/.imagej, i.e. 
\${HOME}/.imagej/plugins and \${HOME}/.imagej/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."



[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2017-03-16 Thread Martin Mokrejs
commit: 7124d48942d4162762b188a131a5f1f186e1f460
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Mar 16 10:49:15 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar 16 10:49:15 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7124d489

sci-biology/imagej: change default IJ_HOME value to $HOME/.imagej

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/imagej/imagej-1.51k.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/imagej/imagej-1.51k.ebuild 
b/sci-biology/imagej/imagej-1.51k.ebuild
index 26a5ab0b7..845fc48cb 100644
--- a/sci-biology/imagej/imagej-1.51k.ebuild
+++ b/sci-biology/imagej/imagej-1.51k.ebuild
@@ -76,7 +76,7 @@ src_compile() {
 #!${EPREFIX}/bin/bash
 IJ_LIB=${EPREFIX}/usr/share/${PN}/lib
 if !([ "\${IJ_HOME}" ]) ; then
-   IJ_HOME=\${HOME}
+   IJ_HOME=\${HOME}/.imagej
 fi
 if [ -d \${IJ_HOME}/plugins ] ; then
IJ_PLG=\${IJ_HOME}



[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/

2017-03-16 Thread Martin Mokrejs
commit: 11a62943a13d8d1837f530fa234480991589a501
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Mar 16 10:35:06 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar 16 10:35:06 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=11a62943

sci-biology/imagej: there is no separate /proc/meminfo in EPREFIXed hosts

Add link to github issue. Remove CVS header line.

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/imagej/imagej-1.51k.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/imagej/imagej-1.51k.ebuild 
b/sci-biology/imagej/imagej-1.51k.ebuild
index 0467973e4..26a5ab0b7 100644
--- a/sci-biology/imagej/imagej-1.51k.ebuild
+++ b/sci-biology/imagej/imagej-1.51k.ebuild
@@ -1,6 +1,5 @@
 # Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: $
 
 EAPI=6
 
@@ -14,6 +13,7 @@ MY_PV=$(delete_all_version_separators)
 # version instead. Change to present version locally if you are sure proper
 # version has been released.
 # see https://bugs.gentoo.org/show_bug.cgi?id=112275
+# https://github.com/imagej/imagej1/issues/28
 IJ_PV=$(expr ${MY_PV::3} - 1)
 
 DESCRIPTION="Image Processing and Analysis in Java"
@@ -26,7 +26,7 @@ 
SRC_URI="http://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
 #  plugins? ( 
http://rsb.info.nih.gov/ij/download/zips/${MY_PN}${IJ_PV}.zip )"
 
 RESTRICT=""
-LICENSE="public-domain"
+LICENSE="public-domain" # http://imagej.net/disclaimer.html
 SLOT="0"
 
 KEYWORDS=""
@@ -66,7 +66,7 @@ src_compile() {
ant ${antflags} || die  "ant build failed"
 
# Max memory usage depends on available memory and CPU type
-   MEM=$(grep MemTotal ${EPREFIX}/proc/meminfo | cut -d':' -f2 | grep -o 
[0-9]*)
+   MEM=$(grep MemTotal /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



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

2017-03-15 Thread Martin Mokrejs
commit: 395c7e7490baf0d7a6e6550fd47d966c285dc171
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Wed Mar 15 21:38:28 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Wed Mar 15 21:38:28 2017 +
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 0..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 0..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 && $IJ_MAX_MEM -gt 2048 ; then
+   IJ_MAX_MEM=2048
+   fi
+   # build finished, generate startup wrapper
+   cat < "${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\\
+