[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/jmol/files/12.0.45/, sci-chemistry/jmol/files/, profiles/, ...

[Michał Górny]

commit:     1c1e7716d83e31e0ea116ddcab30807b2cdc0d5b
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 14 15:44:20 2019 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sat Sep 14 15:44:20 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1c1e7716

sci-chemistry/jmol: Remove last-rited pkg

Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 profiles/package.mask                              |   1 -
 sci-chemistry/jmol/Manifest                        |   3 -
 .../jmol/files/12.0.45/jmol-manifest.patch         |  96 ------
 sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch | 313 -------------------
 sci-chemistry/jmol/files/caffeine.xyz              |  26 --
 sci-chemistry/jmol/files/index.html                |  14 -
 sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch | 330 ---------------------
 sci-chemistry/jmol/jmol-12.0.45-r1.ebuild          | 100 -------
 sci-chemistry/jmol/jmol-12.2.27-r1.ebuild          |  98 ------
 sci-chemistry/jmol/metadata.xml                    |  15 -
 10 files changed, 996 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 0de8a394f4f..feef25289e3 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -1117,7 +1117,6 @@ app-text/jpdftweak
 dev-util/deskzilla
 media-sound/tuxguitar
 sci-mathematics/isabelle
-sci-chemistry/jmol
 
 # Michał Górny <mgorny@g.o> (2019-08-14)
 # No longer builds.  Homepage is gone, and its keep-alive fork is also

diff --git a/sci-chemistry/jmol/Manifest b/sci-chemistry/jmol/Manifest
deleted file mode 100644
index f2869dc0d9a..00000000000
--- a/sci-chemistry/jmol/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST Jmol-12.0.45-full.tar.gz 26501382 BLAKE2B 68db22b79ecfca719ac4dc6e971e5f3fbfc1c66cd669ea5e823e18da0fca28279afaf9cc8999398849df9d718a6efcbd975f913c62e0b558de5b785f63d62045 SHA512 b0e999335c039e5bde5e261c076f3eb75dd0c33a351445d5c086995d32b3fd03795b3a11dc57a06bf8ac39e74945f3c9f4547ecfbf18b56d827b9a42f5208c11
-DIST Jmol-12.2.27-full.tar.gz 29493780 BLAKE2B 8e4dc9334348847fe0b54baea1c0575d70a2e564a194474e8e007ec6dc60fdb46a8d139f5dad1686b32f23a4be11a76dfc6578e015d65a532a891bf24425c20e SHA512 a8608e64dc06b6d3b0cb7e911f0a224456a65bdc15c51d6b420ee6abf8d82cdcec9f54f6b1a51cfe032e2e074f173f50a88bcff783311de19ce9b95ad990ebca
-DIST jmol-selfSignedCertificate.store.tar 10240 BLAKE2B 04dc1504bc751d2a9829b12fe64f851885d308ffee170cffc871d59552d46bff8ab211e5bdb4ed00b596b3882a359669bf4ebf170cca37d518d76f140294d1e6 SHA512 2c3e9d1183a0b174273346d0fba0729caa415ef53fe01629a4c47daa2393c9e18ca3f57984911e6340197429cf0ee581c64bb9b6072db902102976030d9f2c23

diff --git a/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch b/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch
deleted file mode 100644
index 3b43c219d94..00000000000
--- a/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch
+++ /dev/null
@@ -1,96 +0,0 @@
-diff -aurN jmol-11.0.3-orig/manifest/applet0.txt jmol-11.0.3/manifest/applet0.txt
---- jmol-11.0.3-orig/manifest/applet0.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet0.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,6 @@
-+Main-Class: JmolApplet
-+Sealed: true
-+
-+Name: org/jmol/api/
-+Sealed: false
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet1.txt jmol-11.0.3/manifest/applet1.txt
---- jmol-11.0.3-orig/manifest/applet1.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet1.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,6 @@
-+Name: org/jmol/api/
-+Sealed: false
-+
-+Name: org/jmol/applet/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet2.txt jmol-11.0.3/manifest/applet2.txt
---- jmol-11.0.3-orig/manifest/applet2.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet2.txt	2007-05-16 01:56:19.000000000 -0500
-@@ -0,0 +1,3 @@
-+Name: javax/vecmath/
-+
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet3.txt jmol-11.0.3/manifest/applet3.txt
---- jmol-11.0.3-orig/manifest/applet3.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet3.txt	2007-05-16 01:56:47.000000000 -0500
-@@ -0,0 +1,4 @@
-+
-+Name: org/jmol/g3d/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet4.txt jmol-11.0.3/manifest/applet4.txt
---- jmol-11.0.3-orig/manifest/applet4.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet4.txt	2007-05-16 01:57:05.000000000 -0500
-@@ -0,0 +1,4 @@
-+
-+Name: org/jmol/adapter/smarter/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet5.txt jmol-11.0.3/manifest/applet5.txt
---- jmol-11.0.3-orig/manifest/applet5.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet5.txt	2007-05-16 01:57:23.000000000 -0500
-@@ -0,0 +1,4 @@
-+Name: org/openscience/jmol/ui/
-+Sealed: true
-+
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet6.txt jmol-11.0.3/manifest/applet6.txt
---- jmol-11.0.3-orig/manifest/applet6.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet6.txt	2007-05-16 01:57:46.000000000 -0500
-@@ -0,0 +1,4 @@
-+
-+Name: org/jmol/viewer/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/appletMain.txt jmol-11.0.3/manifest/appletMain.txt
---- jmol-11.0.3-orig/manifest/appletMain.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/appletMain.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,5 @@
-+Manifest-Version: 1.0
-+Sealed: true
-+
-+Name: org/jmol/api/
-+Sealed: false
-diff -aurN jmol-11.0.3-orig/manifest/appletMonolithic.txt jmol-11.0.3/manifest/appletMonolithic.txt
---- jmol-11.0.3-orig/manifest/appletMonolithic.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/appletMonolithic.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,7 @@
-+Main-Class: JmolApplet
-+Sealed: true
-+
-+Name: org/jmol/api/
-+Sealed: false
-+
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet.txt jmol-11.0.3/manifest/applet.txt
---- jmol-11.0.3-orig/manifest/applet.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,2 @@
-+Manifest-Version: 1.0
-+Sealed: true
-\ No newline at end of file
-diff -aurN jmol-11.0.3-orig/manifest/application.txt jmol-11.0.3/manifest/application.txt
---- jmol-11.0.3-orig/manifest/application.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/application.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1 @@
-+Main-Class: org.openscience.jmol.app.Jmol
-diff -aurN jmol-11.0.3-orig/manifest/jvxl.txt jmol-11.0.3/manifest/jvxl.txt
---- jmol-11.0.3-orig/manifest/jvxl.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/jvxl.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1 @@
-+Main-Class: org.openscience.jvxl.Jvxl

diff --git a/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch b/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch
deleted file mode 100644
index c1b22e83c61..00000000000
--- a/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch
+++ /dev/null
@@ -1,313 +0,0 @@
---- build.xml	2011-02-25 12:59:43.000000000 -0600
-+++ build.xml.new	2011-02-27 12:16:02.398959959 -0600
-@@ -110,10 +110,6 @@
-           <srcfiles dir="doc/source"
-                     includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>
-         </uptodate>
--        <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>
--        </uptodate>
-       </and>
-     </condition>
- 
-@@ -123,14 +119,6 @@
-           <srcfiles dir="doc/source"
-                     includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />
-         </uptodate>
--        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />
--        </uptodate>
--        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />
--        </uptodate>
-       </and>
-     </condition>
-     
-@@ -140,14 +128,6 @@
-           <srcfiles dir="doc/source"
-                     includes="JmolDevelopersGuide.docbook.xml"/>
-         </uptodate>
--        <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolDevelopersGuide_fr.docbook.xml"/>
--        </uptodate>
--        <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolDevelopersGuide_de.docbook.xml"/>
--        </uptodate>
-       </and>
-     </condition>
- 
-@@ -157,14 +137,6 @@
-           <srcfiles dir="doc/source"
-                     includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>
-         </uptodate>
--        <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>
--        </uptodate>
--        <uptodate targetfile="build/doc/JmolAppletGuide_de.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolAppletGuide_de.docbook.xml"/>
--        </uptodate>
-       </and>
-     </condition>
- 
-@@ -385,17 +357,12 @@
-   </target>
- 
-   <target name="jar" id="jar"
--          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">
-+          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">
-     <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >
-       <fileset dir="build/doc/JmolUserGuide">
-         <include name="**/*.html" />
-       </fileset>
-     </copy>
--    <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >
--      <fileset dir="build/doc/JmolUserGuide_fr">
--        <include name="**/*.html" />
--      </fileset>
--    </copy>
-     <copy todir="${classes.dir}/org/openscience/jmol/Data" >
-       <fileset dir="build/doc/JmolHistory">
-         <include name="**/*.html" />
-@@ -587,18 +554,6 @@
-       <fileset dir="${appletjars.dir}" includes="**/*"/>
-     </jar>
- 
--    <for list="${all.JmolApplet.languages}" delimiter=","
--         param="current.Jmol.language">
--      <sequential>
--        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
--             manifest="manifest/applet_i18n.txt" >
--          <fileset dir="${applet.classes.dir}">
--            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
--          </fileset>
--        </jar>
--      </sequential>
--    </for>
--
-     <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
-       <fileset dir="${applet.classes.dir}">
-         <include name="org/jmol/minimize/**" />
-@@ -712,7 +667,6 @@
-         <include name="org/jmol/bspt/**" />
-         <include name="org/jmol/g3d/**" />
-         <include name="org/jmol/geodesic/**" />
--        <include name="org/jmol/i18n/**" />
-         <include name="org/jmol/modelset/**" />
-         <include name="org/jmol/script/**" />
-         <include name="org/jmol/shape/**" />
-@@ -738,7 +692,6 @@
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
--        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
-       </indexjars>
-     </jar>
-     <!-- changes to this must be replicated below for the signed applet -->
-@@ -851,16 +804,6 @@
-              keystore="selfSignedCertificate/selfSignedCertificate.store"
-              storepass="selfSignedCertificate" alias="selfSignedCertificate" />
- 
--    <for list="${all.JmolApplet.languages}" delimiter=","
--         param="current.Jmol.language">
--      <sequential>
--      	<signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
--                 signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n_@{current.Jmol.language}.jar"
--                 keystore="selfSignedCertificate/selfSignedCertificate.store"
--                 storepass="selfSignedCertificate" alias="selfSignedCertificate" />
--      </sequential>
--    </for>
--
-     <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
-     <!-- this one must be treated specially because of jar indexing
-          we cannot simply rename the jar file, because the index has
-@@ -906,7 +849,6 @@
-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />
--        <fileset dir="${jmol.applet.build.dir}" includes="JmolAppletSigned0_i18n_*.jar" />
-       </indexjars>
-     </jar>
-     <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
-@@ -944,18 +886,6 @@
- 	      </fileset>
- 	    </jar>
- 
--	    <for list="${all.JmolApplet.languages}" delimiter=","
--	         param="current.Jmol.language">
--	      <sequential>
--	        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
--	             manifest="manifest/applet_i18n.txt" >
--	          <fileset dir="${applet.classes.dir}">
--	            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
--	          </fileset>
--	        </jar>
--	      </sequential>
--	    </for>
--
- 	    <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
- 	      <fileset dir="${applet.classes.dir}">
- 	        <include name="org/jmol/minimize/**" />
-@@ -1069,7 +999,6 @@
- 	        <include name="org/jmol/bspt/**" />
- 	        <include name="org/jmol/g3d/**" />
- 	        <include name="org/jmol/geodesic/**" />
--	        <include name="org/jmol/i18n/**" />
- 	        <include name="org/jmol/modelset/**" />
- 	        <include name="org/jmol/script/**" />
- 	        <include name="org/jmol/shape/**" />
-@@ -1095,7 +1024,6 @@
- 	        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
- 	        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
- 	        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
--	        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
- 	      </indexjars>
- 	    </jar>
- 	    <!-- changes to this must be replicated below for the signed applet -->
-@@ -1104,7 +1032,7 @@
- 	  </target>
- 
- 	<target name="dist" id="dist"
--          depends="doc,main-i18n,main,signed-applet">
-+          depends="doc,main,signed-applet">
-     <!-- first build binary distribution -->
-     <delete dir="build/dist/jmol-${version}"/>
-     <mkdir dir="build/dist/jmol-${version}"/>
-@@ -1163,7 +1091,6 @@
-       <fileset dir=".">
-         <include name="applet.classes" />
-         <include name="build.xml" />
--        <include name="build-i18n.xml" />
-       </fileset>
-     </copy>
- 
-@@ -1246,7 +1173,6 @@
-       <fileset dir=".">
-         <include name="apisio.classes" />
-         <include name="build.xml" />
--        <include name="build-i18n.xml" />
-       </fileset>
-     </copy>
- 
-@@ -1342,7 +1268,7 @@
-   <target name="xclean" id="xclean">
-   </target>
- 
--  <target name="spotless" id="spotless" depends="clean,spotless-i18n">
-+  <target name="spotless" id="spotless" depends="clean">
-     <delete dir="build"/>
-     <delete dir="${javadoc.dir}"/>
-     <delete dir="packaging/rpm/dist"/>
-@@ -1406,16 +1332,6 @@
-       <arg value="../../../doc/source/JmolGuide.docbook.xml" />
-       <arg value="../../${docbook-xsl}/html/chunk.xsl" />
-     </java>
--    <echo message="Generating user's guide (fr)" />
--    <mkdir dir="build/doc/JmolUserGuide_fr" />
--    <java fork="true" dir="build/doc/JmolUserGuide_fr"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <jvmarg value="${proxyHost}" />
--      <jvmarg value="${proxyPort}" />
--      <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />
--      <arg value="../../${docbook-xsl}/html/chunk.xsl" />
--    </java>
-   </target>
- 
-   <target name="jmolHistory" id="jmolHistory"
-@@ -1430,26 +1346,6 @@
-       <arg value="../../../doc/source/JmolHistory.xml" />
-       <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
-     </java>
--    <echo message="Generating history of changes (fr)" />
--    <java fork="true" dir="build/doc/JmolHistory"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <arg value="-o" />
--      <arg value="ChangeLog_fr.html" />
--      <arg value="../../../doc/source/JmolHistory_fr.xml" />
--      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
--      <arg value="lang=fr" />
--    </java>
--    <echo message="Generating history of changes (nl)" />
--    <java fork="true" dir="build/doc/JmolHistory"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <arg value="-o" />
--      <arg value="ChangeLog_nl.html" />
--      <arg value="../../../doc/source/JmolHistory_nl.xml" />
--      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
--      <arg value="lang=nl" />
--    </java>
-   </target>
- 
-   <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"
-@@ -1463,24 +1359,6 @@
-       <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />
-       <arg value="../${docbook-xsl}/html/docbook.xsl" />
-     </java>
--    <echo message="Generating developer's guide (fr)" />
--    <java fork="true" dir="build/doc"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <arg value="-o" />
--      <arg value="JmolDevelopersGuide_fr.html" />
--      <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />
--      <arg value="../${docbook-xsl}/html/docbook.xsl" />
--    </java>
--    <echo message="Generating developer's guide (de)" />
--    <java fork="true" dir="build/doc"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <arg value="-o" />
--      <arg value="JmolDevelopersGuide_de.html" />
--      <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />
--      <arg value="../${docbook-xsl}/html/docbook.xsl" />
--    </java>
-   </target>
- 
-   <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
-@@ -1494,24 +1372,6 @@
-       <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
-       <arg value="../${docbook-xsl}/html/docbook.xsl" />
-     </java>
--    <echo message="Generating applet guide (fr)" />
--    <java fork="true" dir="build/doc"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <arg value="-o" />
--      <arg value="JmolAppletGuide_fr.html" />
--      <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />
--      <arg value="../${docbook-xsl}/html/docbook.xsl" />
--    </java>
--    <echo message="Generating applet guide (de)" />
--    <java fork="true" dir="build/doc"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <arg value="-o" />
--      <arg value="JmolAppletGuide_de.html" />
--      <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />
--      <arg value="../${docbook-xsl}/html/docbook.xsl" />
--    </java>
-   </target>
- 
-   <target name="test" id="test" depends="main,compile-tests">
-@@ -1543,12 +1403,4 @@
-     <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />
-   </target>
- 
--  <!-- i18n stuff -->
--  <target name="main-i18n" depends="classes">
--    <ant antfile="tools/build-i18n.xml" target="main-i18n"/>
--  </target>
--  <target name="spotless-i18n">
--    <ant antfile="tools/build-i18n.xml" target="spotless-i18n"/>
--  </target>
--
- </project>

diff --git a/sci-chemistry/jmol/files/caffeine.xyz b/sci-chemistry/jmol/files/caffeine.xyz
deleted file mode 100644
index f0325b049f3..00000000000
--- a/sci-chemistry/jmol/files/caffeine.xyz
+++ /dev/null
@@ -1,26 +0,0 @@
-24
-Caffeine
-H      -3.3804130    -1.1272367     0.5733036
-N       0.9668296    -1.0737425    -0.8198227
-C       0.0567293     0.8527195     0.3923156
-N      -1.3751742    -1.0212243    -0.0570552
-C      -1.2615018     0.2590713     0.5234135
-C      -0.3068337    -1.6836331    -0.7169344
-C       1.1394235     0.1874122    -0.2700900
-N       0.5602627     2.0839095     0.8251589
-O      -0.4926797    -2.8180554    -1.2094732
-C      -2.6328073    -1.7303959    -0.0060953
-O      -2.2301338     0.7988624     1.0899730
-H       2.5496990     2.9734977     0.6229590
-C       2.0527432    -1.7360887    -1.4931279
-H      -2.4807715    -2.7269528     0.4882631
-H      -3.0089039    -1.9025254    -1.0498023
-H       2.9176101    -1.8481516    -0.7857866
-H       2.3787863    -1.1211917    -2.3743655
-H       1.7189877    -2.7489920    -1.8439205
-C      -0.1518450     3.0970046     1.5348347
-C       1.8934096     2.1181245     0.4193193
-N       2.2861252     0.9968439    -0.2440298
-H      -0.1687028     4.0436553     0.9301094
-H       0.3535322     3.2979060     2.5177747
-H      -1.2074498     2.7537592     1.7203047

diff --git a/sci-chemistry/jmol/files/index.html b/sci-chemistry/jmol/files/index.html
deleted file mode 100644
index 35a5d49217e..00000000000
--- a/sci-chemistry/jmol/files/index.html
+++ /dev/null
@@ -1,14 +0,0 @@
-<html>
-  <head>
-    <title>Jmol Test Page</title>
-      <div align="center"> <b>All the Sugar and Twice the Caffeine.</b> <br><br>
-      <script src="./Jmol.js"></script>
-  </head>
-  <body>
-    <script>
-      jmolInitialize("./"); // REQUIRED
-      jmolApplet(400, "load ./caffeine.xyz");
-    </script></div>
-  </body>
-</html>
-

diff --git a/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch
deleted file mode 100644
index 0a43faaf653..00000000000
--- a/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch
+++ /dev/null
@@ -1,330 +0,0 @@
---- orig-build.xml	2012-05-31 13:42:43.943062427 -0500
-+++ build.xml	2012-05-31 14:01:01.691982062 -0500
-@@ -52,8 +52,6 @@
- 
-   <property file="proxy.properties" />
- 
--  <import file="tools/build-i18n.xml"/>
--
-   <path id="project.class.path">
-     <fileset dir="${lib.dir}">
-       <include name="*.jar" />
-@@ -111,10 +109,6 @@
-           <srcfiles dir="doc/source"
-                     includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>
-         </uptodate>
--        <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>
--        </uptodate>
-       </and>
-     </condition>
- 
-@@ -124,14 +118,6 @@
-           <srcfiles dir="doc/source"
-                     includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />
-         </uptodate>
--        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />
--        </uptodate>
--        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />
--        </uptodate>
-       </and>
-     </condition>
-     
-@@ -141,14 +127,6 @@
-           <srcfiles dir="doc/source"
-                     includes="JmolDevelopersGuide.docbook.xml"/>
-         </uptodate>
--        <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolDevelopersGuide_fr.docbook.xml"/>
--        </uptodate>
--        <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolDevelopersGuide_de.docbook.xml"/>
--        </uptodate>
-       </and>
-     </condition>
- 
-@@ -158,14 +136,6 @@
-           <srcfiles dir="doc/source"
-                     includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>
-         </uptodate>
--        <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>
--        </uptodate>
--        <uptodate targetfile="build/doc/JmolAppletGuide_de.html">
--          <srcfiles dir="doc/source"
--                    includes="JmolAppletGuide_de.docbook.xml"/>
--        </uptodate>
-       </and>
-     </condition>
- 
-@@ -388,17 +358,12 @@
-   </target>
- 
-   <target name="jar" id="jar"
--          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">
-+          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">
-     <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >
-       <fileset dir="build/doc/JmolUserGuide">
-         <include name="**/*.html" />
-       </fileset>
-     </copy>
--    <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >
--      <fileset dir="build/doc/JmolUserGuide_fr">
--        <include name="**/*.html" />
--      </fileset>
--    </copy>
-     <copy todir="${classes.dir}/org/openscience/jmol/Data" >
-       <fileset dir="build/doc/JmolHistory">
-         <include name="**/*.html" />
-@@ -603,18 +568,6 @@
-       <fileset dir="${appletjars.dir}" includes="**/*"/>
-     </jar>
- 
--    <for list="${all.JmolApplet.languages}" delimiter=","
--         param="current.Jmol.language">
--      <sequential>
--        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
--             manifest="manifest/applet_i18n.txt" >
--          <fileset dir="${applet.classes.dir}">
--            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
--          </fileset>
--        </jar>
--      </sequential>
--    </for>
--
-     <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
-       <fileset dir="${applet.classes.dir}">
-         <include name="org/jmol/minimize/**" />
-@@ -729,7 +682,6 @@
-         <include name="org/jmol/constant/**" />
-         <include name="org/jmol/g3d/**" />
-         <include name="org/jmol/geodesic/**" />
--        <include name="org/jmol/i18n/**" />
-         <include name="org/jmol/modelset/**" />
-         <include name="org/jmol/script/**" />
-         <include name="org/jmol/shape/**" />
-@@ -755,7 +707,6 @@
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
--        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
-       </indexjars>
-     </jar>
-     <!-- changes to this must be replicated below for the signed applet -->
-@@ -868,16 +819,6 @@
-              keystore="selfSignedCertificate/selfSignedCertificate.store"
-              storepass="selfSignedCertificate" alias="selfSignedCertificate" />
- 
--    <for list="${all.JmolApplet.languages}" delimiter=","
--         param="current.Jmol.language">
--      <sequential>
--      	<signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
--                 signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n_@{current.Jmol.language}.jar"
--                 keystore="selfSignedCertificate/selfSignedCertificate.store"
--                 storepass="selfSignedCertificate" alias="selfSignedCertificate" />
--      </sequential>
--    </for>
--
-     <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
-     <!-- this one must be treated specially because of jar indexing
-          we cannot simply rename the jar file, because the index has
-@@ -905,7 +846,6 @@
- 		<include name="org/jmol/shape/**" />
- 		<include name="org/jmol/viewer/**" />
- 		<include name="org/jmol/util/**" />
--		<include name="org/jmol/i18n/**" />
-       </fileset>    	
-       <indexjars>
-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Console.jar" />
-@@ -924,7 +864,6 @@
-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />
--        <fileset dir="${jmol.applet.build.dir}" includes="JmolAppletSigned0_i18n_*.jar" />
-       </indexjars>
-     </jar>
-     <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
-@@ -963,18 +902,6 @@
-       </fileset>
-     </jar>
- 
--    <for list="${all.JmolApplet.languages}" delimiter=","
--         param="current.Jmol.language">
--      <sequential>
--        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
--             manifest="manifest/applet_i18n.txt" >
--          <fileset dir="${applet.classes.dir}">
--            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
--          </fileset>
--        </jar>
--      </sequential>
--    </for>
--
-     <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
-       <fileset dir="${applet.classes.dir}">
-         <include name="org/jmol/minimize/**" />
-@@ -1088,7 +1015,6 @@
-         <include name="org/jmol/constant/**" />
-         <include name="org/jmol/g3d/**" />
-         <include name="org/jmol/geodesic/**" />
--        <include name="org/jmol/i18n/**" />
-         <include name="org/jmol/modelset/**" />
-         <include name="org/jmol/script/**" />
-         <include name="org/jmol/shape/**" />
-@@ -1114,7 +1040,6 @@
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
--        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
-       </indexjars>
-     </jar>
-     <!-- changes to this must be replicated below for the signed applet -->
-@@ -1123,7 +1048,7 @@
-   </target>
- 
-   <target name="dist" id="dist"
--          depends="doc,main-i18n,main,signed-applet">
-+          depends="doc,main,signed-applet">
-     <!-- first build binary distribution -->
-     <delete dir="build/dist/jmol-${version}"/>
-     <mkdir dir="build/dist/jmol-${version}"/>
-@@ -1183,7 +1108,6 @@
-       <fileset dir=".">
-         <include name="applet.classes" />
-         <include name="build.xml" />
--        <include name="build-i18n.xml" />
-       </fileset>
-     </copy>
- 
-@@ -1278,7 +1202,6 @@
-       <fileset dir=".">
-         <include name="apisio.classes" />
-         <include name="build.xml" />
--        <include name="build-i18n.xml" />
-       </fileset>
-     </copy>
- 
-@@ -1374,7 +1297,7 @@
-   <target name="xclean" id="xclean">
-   </target>
- 
--  <target name="spotless" id="spotless" depends="clean,spotless-i18n">
-+  <target name="spotless" id="spotless" depends="clean">
-     <delete dir="build"/>
-     <delete dir="${javadoc.dir}"/>
-     <delete dir="packaging/rpm/dist"/>
-@@ -1438,16 +1361,6 @@
-       <arg value="../../../doc/source/JmolGuide.docbook.xml" />
-       <arg value="../../${docbook-xsl}/html/chunk.xsl" />
-     </java>
--    <echo message="Generating user's guide (fr)" />
--    <mkdir dir="build/doc/JmolUserGuide_fr" />
--    <java fork="true" dir="build/doc/JmolUserGuide_fr"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <jvmarg value="${proxyHost}" />
--      <jvmarg value="${proxyPort}" />
--      <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />
--      <arg value="../../${docbook-xsl}/html/chunk.xsl" />
--    </java>
-   </target>
- 
-   <target name="jmolHistory" id="jmolHistory"
-@@ -1462,26 +1375,6 @@
-       <arg value="../../../doc/source/JmolHistory.xml" />
-       <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
-     </java>
--    <echo message="Generating history of changes (fr)" />
--    <java fork="true" dir="build/doc/JmolHistory"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <arg value="-o" />
--      <arg value="ChangeLog_fr.html" />
--      <arg value="../../../doc/source/JmolHistory_fr.xml" />
--      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
--      <arg value="lang=fr" />
--    </java>
--    <echo message="Generating history of changes (nl)" />
--    <java fork="true" dir="build/doc/JmolHistory"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <arg value="-o" />
--      <arg value="ChangeLog_nl.html" />
--      <arg value="../../../doc/source/JmolHistory_nl.xml" />
--      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
--      <arg value="lang=nl" />
--    </java>
-   </target>
- 
-   <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"
-@@ -1495,24 +1388,6 @@
-       <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />
-       <arg value="../${docbook-xsl}/html/docbook.xsl" />
-     </java>
--    <echo message="Generating developer's guide (fr)" />
--    <java fork="true" dir="build/doc"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <arg value="-o" />
--      <arg value="JmolDevelopersGuide_fr.html" />
--      <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />
--      <arg value="../${docbook-xsl}/html/docbook.xsl" />
--    </java>
--    <echo message="Generating developer's guide (de)" />
--    <java fork="true" dir="build/doc"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <arg value="-o" />
--      <arg value="JmolDevelopersGuide_de.html" />
--      <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />
--      <arg value="../${docbook-xsl}/html/docbook.xsl" />
--    </java>
-   </target>
- 
-   <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
-@@ -1526,24 +1401,6 @@
-       <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
-       <arg value="../${docbook-xsl}/html/docbook.xsl" />
-     </java>
--    <echo message="Generating applet guide (fr)" />
--    <java fork="true" dir="build/doc"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <arg value="-o" />
--      <arg value="JmolAppletGuide_fr.html" />
--      <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />
--      <arg value="../${docbook-xsl}/html/docbook.xsl" />
--    </java>
--    <echo message="Generating applet guide (de)" />
--    <java fork="true" dir="build/doc"
--          classname="com.icl.saxon.StyleSheet"
--          classpath="${lib.dir}/saxon.jar" >
--      <arg value="-o" />
--      <arg value="JmolAppletGuide_de.html" />
--      <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />
--      <arg value="../${docbook-xsl}/html/docbook.xsl" />
--    </java>
-   </target>
- 
-   <target name="test" id="test" depends="main,compile-tests">
-@@ -1575,12 +1432,4 @@
-     <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />
-   </target>
- 
--  <!-- i18n stuff -->
--  <target name="main-i18n" depends="classes">
--    <ant antfile="tools/build-i18n.xml" target="main-i18n"/>
--  </target>
--  <target name="spotless-i18n">
--    <ant antfile="tools/build-i18n.xml" target="spotless-i18n"/>
--  </target>
--
- </project>

diff --git a/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild
deleted file mode 100644
index 589cc469b42..00000000000
--- a/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-WEBAPP_OPTIONAL="yes"
-
-inherit eutils webapp java-pkg-2 java-ant-2
-
-MY_P=Jmol
-
-DESCRIPTION="Java molecular viever for 3-D chemical structures"
-HOMEPAGE="http://jmol.sourceforge.net/"
-SRC_URI="
-	mirror://sourceforge/${PN}/${MY_P}-${PV}-full.tar.gz
-	https://dev.gentoo.org/~jlec/distfiles/${PN}-selfSignedCertificate.store.tar"
-
-WEBAPP_MANUAL_SLOT="yes"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-LICENSE="LGPL-2.1"
-IUSE="client-only vhosts"
-
-COMMON_DEP="
-	dev-java/commons-cli:1
-	dev-java/itext:0
-	sci-libs/jmol-acme:0
-	sci-libs/vecmath-objectclub:0"
-
-RDEPEND=">=virtual/jre-1.4
-	${COMMON_DEP}"
-DEPEND=">=virtual/jdk-1.4
-	!client-only? ( ${WEBAPP_DEPEND} )
-	${COMMON_DEP}"
-
-pkg_setup() {
-	use client-only || webapp_pkg_setup
-	java-pkg-2_pkg_setup
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}/${PN}-nointl.patch \
-		"${FILESDIR}"/${PV}/${PN}-manifest.patch
-
-	mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory."
-	cp "${WORKDIR}"/selfSignedCertificate.store "${S}"/selfSignedCertificate/ \
-		|| die "Failed to install Cert file."
-
-	rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die
-	cd "${S}/jars"
-
-# We still have to use netscape.jar on amd64 until a nice way to include plugin.jar comes along.
-	if use amd64; then
-		mv -v netscape.jar netscape.tempjar || die "Failed to move netscape.jar."
-		rm -v *.jar *.tar.gz || die "Failed to remove jars."
-		mv -v netscape.tempjar netscape.jar || die "Failed to move netscape.tempjar."
-	fi
-
-	java-pkg_jar-from vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar
-	java-pkg_jar-from itext iText.jar itext-1.4.5.jar
-	java-pkg_jar-from jmol-acme jmol-acme.jar Acme.jar
-	java-pkg_jar-from commons-cli-1 commons-cli.jar commons-cli-1.0.jar
-
-	mkdir -p "${S}/build/appjars" || die
-}
-
-src_compile() {
-	# prevent absorbing dep's classes
-	eant -Dlibjars.uptodate=true main
-}
-
-src_install() {
-	java-pkg_dojar build/Jmol.jar
-	dohtml -r  build/doc/* || die "Failed to install html docs."
-	dodoc *.txt doc/*license* || die "Failed to install licenses."
-
-	java-pkg_dolauncher ${PN} --main org.openscience.jmol.app.Jmol \
-		--java_args "-Xmx512m"
-
-	if ! use client-only ; then
-		webapp_src_preinst
-		cp Jmol.js build/Jmol.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-		cp build/JmolApplet*.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-		cp applet.classes "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-		cp -r build/classes/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-		cp -r build/appletjars/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-		cp "${FILESDIR}"/caffeine.xyz "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-		cp "${FILESDIR}"/index.html "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-
-		webapp_src_install
-	fi
-}
-
-pkg_postinst() {
-	use client-only || webapp_pkg_postinst
-}
-
-pkg_prerm() {
-	use client-only || webapp_pkg_prerm
-}

diff --git a/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild b/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild
deleted file mode 100644
index a109067c1d7..00000000000
--- a/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild
+++ /dev/null
@@ -1,98 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-WEBAPP_OPTIONAL="yes"
-
-inherit eutils webapp java-pkg-2 java-ant-2
-
-MY_P=Jmol
-
-DESCRIPTION="Java molecular viever for 3-D chemical structures"
-HOMEPAGE="http://jmol.sourceforge.net/"
-SRC_URI="
-	mirror://sourceforge/${PN}/${MY_P}-${PV}-full.tar.gz
-	https://dev.gentoo.org/~jlec/distfiles/${PN}-selfSignedCertificate.store.tar"
-
-LICENSE="LGPL-2.1"
-KEYWORDS="~amd64 ~x86"
-IUSE="+client-only vhosts"
-
-WEBAPP_MANUAL_SLOT="yes"
-SLOT="0"
-
-COMMON_DEP="
-	dev-java/commons-cli:1
-	dev-java/itext:0
-	sci-libs/jmol-acme:0
-	sci-libs/vecmath-objectclub:0
-	sci-libs/naga"
-RDEPEND=">=virtual/jre-1.5
-	${COMMON_DEP}"
-DEPEND=">=virtual/jdk-1.5
-	dev-java/saxon:6.5
-	!client-only? ( ${WEBAPP_DEPEND} )
-	${COMMON_DEP}"
-
-pkg_setup() {
-	use client-only || webapp_pkg_setup
-	java-pkg-2_pkg_setup
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-nointl.patch
-
-	rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die
-	cd "${S}/jars"
-
-# We still have to use netscape.jar on amd64 until a nice way to include plugin.jar comes along.
-	if use amd64; then
-		mv -v netscape.jar netscape.tempjar || die "Failed to move netscape.jar."
-		rm -v *.jar *.tar.gz || die "Failed to remove jars."
-		mv -v netscape.tempjar netscape.jar || die "Failed to move netscape.tempjar."
-	fi
-
-	java-pkg_jar-from vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar
-	java-pkg_jar-from itext iText.jar itext-1.4.5.jar
-	java-pkg_jar-from jmol-acme jmol-acme.jar Acme.jar
-	java-pkg_jar-from commons-cli-1 commons-cli.jar commons-cli-1.0.jar
-	java-pkg_jar-from naga
-	java-pkg_jar-from --build-only saxon-6.5 saxon.jar
-
-	mkdir -p "${S}/build/appjars" || die
-}
-
-src_compile() {
-	# prevent absorbing dep's classes
-	eant -Dlibjars.uptodate=true main
-}
-
-src_install() {
-	java-pkg_dojar build/Jmol.jar
-	dohtml -r  build/doc/* || die "Failed to install html docs."
-	dodoc *.txt doc/*license* || die "Failed to install licenses."
-
-	java-pkg_dolauncher ${PN} --main org.openscience.jmol.app.Jmol \
-		--java_args "-Xmx512m"
-
-	if ! use client-only ; then
-		webapp_src_preinst
-		cp Jmol.js build/Jmol.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-		cp build/JmolApplet*.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-		cp applet.classes "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-		cp -r build/classes/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-		cp -r build/appletjars/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-		cp "${FILESDIR}"/caffeine.xyz "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-		cp "${FILESDIR}"/index.html "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
-
-		webapp_src_install
-	fi
-}
-
-pkg_postinst() {
-	use client-only || webapp_pkg_postinst
-}
-
-pkg_prerm() {
-	use client-only || webapp_pkg_prerm
-}

diff --git a/sci-chemistry/jmol/metadata.xml b/sci-chemistry/jmol/metadata.xml
deleted file mode 100644
index 888f06b55ce..00000000000
--- a/sci-chemistry/jmol/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@g.o</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <use>
-    <flag name="client-only">Install the viewer only, no applet files for httpd
-    </flag>
-  </use>
-  <upstream>
-    <remote-id type="sourceforge">jmol</remote-id>
-  </upstream>
-</pkgmetadata>