[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/
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/
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/
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/
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}${IJ_PV}.zip" fi fi
[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/
commit: 9d05db0ba02b6bf5638da71761558eaa5b7face4 Author: Israel Hernandez gmail com> AuthorDate: Tue Dec 19 19:32:27 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Wed Dec 20 09:46:06 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9d05db0b sci-biology/imagej: drop 1.54g Signed-off-by: IAHMCOL thejabberwocky.net> Closes: https://github.com/gentoo/sci/pull/1227 Signed-off-by: Andrew Ammerlaan gentoo.org> sci-biology/imagej/imagej-1.54g.ebuild | 120 - 1 file changed, 120 deletions(-) diff --git a/sci-biology/imagej/imagej-1.54g.ebuild b/sci-biology/imagej/imagej-1.54g.ebuild deleted file mode 100644 index 4bf6db8d9..0 --- a/sci-biology/imagej/imagej-1.54g.ebuild +++ /dev/null @@ -1,120 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit java-pkg-2 java-ant-2 desktop - -MY_PN="ij" -MY_PV=${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/
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/
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/
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 $IJ_HOME/plugins -# plugins? (
[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/
commit: 5cf6be39e39840cc88e4dfa86ed372ff85736e95 Author: Israel Hernandez gmail com> AuthorDate: Sun Jul 2 21:43:21 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Mon Jul 3 08:10:08 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5cf6be39 sci-biology/imagej: bump to 1.53t Closes: https://github.com/gentoo/sci/pull/1197 Signed-off-by: Andrew Ammerlaan gentoo.org> sci-biology/imagej/{imagej-1.53g.ebuild => imagej-1.53t.ebuild} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/sci-biology/imagej/imagej-1.53g.ebuild b/sci-biology/imagej/imagej-1.53t.ebuild similarity index 97% rename from sci-biology/imagej/imagej-1.53g.ebuild rename to sci-biology/imagej/imagej-1.53t.ebuild index 6c9fdf736..d2959e18c 100644 --- a/sci-biology/imagej/imagej-1.53g.ebuild +++ b/sci-biology/imagej/imagej-1.53t.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 java-ant-2 desktop @@ -13,7 +13,7 @@ DESCRIPTION="Image Processing and Analysis in Java" HOMEPAGE="https://imagej.nih.gov/ij/; SRC_URI="https://imagej.nih.gov/ij/download/src/${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}${IJ_PV}.zip )"
[gentoo-commits] proj/sci:master commit in: sci-biology/imagej/files/, sci-biology/imagej/
commit: 2bb3e74a499bc39723588d1affa29204bf82a78f Author: Andrew Ammerlaan riseup net> AuthorDate: Tue Jan 26 15:00:08 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Tue Jan 26 15:00:08 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2bb3e74a sci-biology/imagej: version bump, EAPI bump, add keywords Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> .../imagej/files/AutoThresholder.java.patch| 10 - .../{imagej-1.51k.ebuild => imagej-1.53g.ebuild} | 49 -- 2 files changed, 18 insertions(+), 41 deletions(-) diff --git a/sci-biology/imagej/files/AutoThresholder.java.patch b/sci-biology/imagej/files/AutoThresholder.java.patch deleted file mode 100644 index 97c893244..0 --- a/sci-biology/imagej/files/AutoThresholder.java.patch +++ /dev/null @@ -1,10 +0,0 @@ imagej-1.51k/work/source/ij/process/AutoThresholder.java.ori 2017-03-15 22:33:45.843801175 +0100 -+++ imagej-1.51k/work/source/ij/process/AutoThresholder.java 2017-03-15 22:33:55.104053480 +0100 -@@ -650,7 +650,6 @@ - } - // The threshold is the minimum between the two peaks. - for (int i=1; i<255; i++) { -- //IJ.log(" "+i+" "+iHisto[i]); - if (iHisto[i-1] > iHisto[i] && iHisto[i+1] >= iHisto[i]) { - threshold = i; - break; diff --git a/sci-biology/imagej/imagej-1.51k.ebuild b/sci-biology/imagej/imagej-1.53g.ebuild similarity index 71% rename from sci-biology/imagej/imagej-1.51k.ebuild rename to sci-biology/imagej/imagej-1.53g.ebuild index 57b46c045..6c9fdf736 100644 --- a/sci-biology/imagej/imagej-1.51k.ebuild +++ b/sci-biology/imagej/imagej-1.53g.ebuild @@ -1,47 +1,41 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -inherit java-pkg-2 java-ant-2 eutils versionator +inherit java-pkg-2 java-ant-2 desktop MY_PN="ij" -MY_PV=$(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/
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/
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/
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/
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/
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/
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\\ +