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

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

[Martin Mokrejs]

commit:     11a62943a13d8d1837f530fa234480991589a501
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 16 10:35:06 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 16 10:35:06 2017 +0000
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/

[Martin Mokrejs]

commit:     7124d48942d4162762b188a131a5f1f186e1f460
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 16 10:49:15 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 16 10:49:15 2017 +0000
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/

[Martin Mokrejs]

commit:     ce9dbd43bb73dc4b69fdc4ccf1cfd38e5485b029
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 16 10:51:20 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 16 10:51:20 2017 +0000
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/

[David Seifert]

commit:     db6c1666f10c9df6f91a38a45fcba0da7424cdfd
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Sep  7 20:28:36 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Sep  7 20:28:36 2017 +0000
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/

[Andrew Ammerlaan]

commit:     595d87fc830c18593784b5634cff7139d17028e3
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:21:31 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:21:31 2021 +0000
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 <andrewammerlaan <AT> 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/

[Andrew Ammerlaan]

commit:     5cf6be39e39840cc88e4dfa86ed372ff85736e95
Author:     Israel Hernandez <israel.a.hernandez <AT> gmail <DOT> com>
AuthorDate: Sun Jul  2 21:43:21 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon Jul  3 08:10:08 2023 +0000
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 <andrewammerlaan <AT> 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/

[Andrew Ammerlaan]

commit:     f6ee8374ed488f3621b2193345c0039cd73d06e9
Author:     Israel Hernandez <israel.a.hernandez <AT> gmail <DOT> com>
AuthorDate: Sat Jul  8 18:23:30 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sun Jul  9 18:58:21 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f6ee8374

sci-biology/imagej: Add unstable git versions

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

 sci-biology/imagej/imagej-1.53t.ebuild             |  2 +
 .../{imagej-1.53t.ebuild => imagej-1.54d.ebuild}   | 50 ++++++++++++++++------
 .../{imagej-1.53t.ebuild => imagej-9999.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 [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/imagej/ImageJ"
+	IJ_S="${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 [[ ${PV} == 9999 ]]; then
+	   if use plugins ; then
+	      unpack "${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 && $IJ_MAX_MEM -gt 2048 ; then
-		IJ_MAX_MEM=2048
+	   IJ_MAX_MEM=2048
 	fi
+
 	# build finished, generate startup wrapper
 	cat <<EOF > "${T}/${PN}"
 #!${EPREFIX}/bin/bash

diff --git a/sci-biology/imagej/imagej-1.53t.ebuild b/sci-biology/imagej/imagej-9999.ebuild
similarity index 82%
copy from sci-biology/imagej/imagej-1.53t.ebuild
copy to sci-biology/imagej/imagej-9999.ebuild
index d2959e18c..33a10b0e4 100644
--- a/sci-biology/imagej/imagej-1.53t.ebuild
+++ b/sci-biology/imagej/imagej-9999.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 [[ ${PV} == 9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/imagej/ImageJ"
+	IJ_S="${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 [[ ${PV} == 9999 ]]; then
+	   if use plugins ; then
+	      unpack "${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 && $IJ_MAX_MEM -gt 2048 ; then
-		IJ_MAX_MEM=2048
+	   IJ_MAX_MEM=2048
 	fi
+
 	# build finished, generate startup wrapper
 	cat <<EOF > "${T}/${PN}"
 #!${EPREFIX}/bin/bash

diff --git a/sci-biology/imagej/metadata.xml b/sci-biology/imagej/metadata.xml
index ca2867d8c..8b8ebd7d9 100644
--- a/sci-biology/imagej/metadata.xml
+++ b/sci-biology/imagej/metadata.xml
@@ -12,4 +12,7 @@
 	<use>
 		<flag name="plugins">Install additional plugins</flag>
 	</use>
+	<upstream>
+		<remote-id type="github">imagej/ImageJ</remote-id>
+	</upstream>
 </pkgmetadata>

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

[Andrew Ammerlaan]

commit:     2d9c80a90fcc0affb4f85daba6fcfef4b2831b64
Author:     Israel Hernandez <israel.a.hernandez <AT> gmail <DOT> com>
AuthorDate: Thu Aug 17 19:20:50 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Aug 17 19:27:27 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2d9c80a9

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

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

[Andrew Ammerlaan]

commit:     4e29aee84176d30527862de23b0fe7c5c049c70c
Author:     Israel Hernandez <israel.a.hernandez <AT> gmail <DOT> com>
AuthorDate: Mon Dec 18 23:21:17 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Dec 19 09:04:20 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4e29aee8

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

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

[Andrew Ammerlaan]

commit:     c5701b9a123d9cf9ebdf13570b3b92cabae54fc2
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Dec 20 09:46:29 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Dec 20 09:46:29 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c5701b9a

sci-biology/imagej: revbump 1.54h

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> 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/

[Andrew Ammerlaan]

commit:     9d05db0ba02b6bf5638da71761558eaa5b7face4
Author:     Israel Hernandez <israel.a.hernandez <AT> gmail <DOT> com>
AuthorDate: Tue Dec 19 19:32:27 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Dec 20 09:46:06 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9d05db0b

sci-biology/imagej: drop 1.54g

Signed-off-by: IAHMCOL <IAHMCOL <AT> thejabberwocky.net>
Closes: https://github.com/gentoo/sci/pull/1227
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> 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..000000000
--- 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 && $IJ_MAX_MEM -gt 2048 ; then
-		IJ_MAX_MEM=2048
-	fi
-	# build finished, generate startup wrapper
-	cat <<EOF > "${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/

[Andrew Ammerlaan]

commit:     be482279cf5432b33ae455e27c427919392a8764
Author:     Israel Hernandez <israel.a.hernandez <AT> gmail <DOT> com>
AuthorDate: Tue Dec 19 16:02:53 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Dec 20 09:46:02 2023 +0000
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 <IAHMCOL <AT> thejabberwocky.net>
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> 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-9999.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 [[ ${PV} == 9999 ]]; then
 	   if use plugins ; then
-	      unpack "${MY_PN}${IJ_PV}.zip"
+		  unpack "${MY_PN}${IJ_PV}.zip"
 	   fi
 	fi
 

diff --git a/sci-biology/imagej/imagej-9999.ebuild b/sci-biology/imagej/imagej-9999.ebuild
index 33a10b0e4..0252d6613 100644
--- a/sci-biology/imagej/imagej-9999.ebuild
+++ b/sci-biology/imagej/imagej-9999.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 [[ ${PV} == 9999 ]]; then
 	   if use plugins ; then
-	      unpack "${MY_PN}${IJ_PV}.zip"
+		  unpack "${MY_PN}${IJ_PV}.zip"
 	   fi
 	fi
 

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

[Andrew Ammerlaan]

commit:     f9718d14356d6ac995991a9e02331b40d97204d8
Author:     Israel Hernandez <israel.a.hernandez <AT> gmail <DOT> com>
AuthorDate: Sun Jun  9 18:59:06 2024 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon Jun 10 06:58:57 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f9718d14

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

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

 .../imagej/{imagej-1.54h-r1.ebuild => imagej-1.54i.ebuild}        | 8 ++++----
 sci-biology/imagej/imagej-9999.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} == 9999 ]]; then
 	   if use plugins ; then

diff --git a/sci-biology/imagej/imagej-9999.ebuild b/sci-biology/imagej/imagej-9999.ebuild
index 0252d6613..ec98393df 100644
--- a/sci-biology/imagej/imagej-9999.ebuild
+++ b/sci-biology/imagej/imagej-9999.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} == 9999 ]]; then
 	   if use plugins ; then

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

[Andrew Ammerlaan]

commit:     6f4847c6f5bc771f45f8d4dc3106679ce4c760d1
Author:     Israel Hernandez <israel.a.hernandez <AT> gmail <DOT> com>
AuthorDate: Sun Jun 16 18:25:24 2024 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon Jun 17 12:28:04 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6f4847c6

sci-biology/imagej: ant-core deprecated

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

 sci-biology/imagej/{imagej-1.54i.ebuild => imagej-1.54i-r1.ebuild} | 1 -
 sci-biology/imagej/imagej-9999.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-9999.ebuild b/sci-biology/imagej/imagej-9999.ebuild
index ec98393df..f95167bcd 100644
--- a/sci-biology/imagej/imagej-9999.ebuild
+++ b/sci-biology/imagej/imagej-9999.ebuild
@@ -50,7 +50,6 @@ DEPEND="
 "
 
 BDEPEND="
-	dev-java/ant-core
 	app-arch/unzip
 "