Import Debian changes 0.7.0-6

elki (0.7.0-6) unstable; urgency=medium

  * Add missing libsvm3-java dependency (Thanks, Tomas Barton)
    Unfortunately, debian-maven-helper does not automatically add this,
    because the libsvm3-java package does not include a pom.
  * Use find_jars to locate batik, which resolves problems with batik 1.7
    (When using the /usr/bin/elki commands - please upgrade to batik 1.8
     or adjust your classpath if you see the error
     NoClassDefFoundError: org/apache/batik/dom/anim/AnimationTarget)
  * Require libbatik-java >= 1.8 for building, 1.7 lacks pom data.
  * Remove execute bit from all files in source jars, not just .java files.
  * Add fop (libfop-java) to the classpath, for eps, pdf, ps export.
  * Suggest libfop-java instead of making it an "alternative" to batik

7 files changed, 301 insertions, 7 deletions

diff --git a/debian/changelog b/debian/changelog
index 594a6a2e..23679db7 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,19 @@
+elki (0.7.0-6) unstable; urgency=medium
+
+  * Add missing libsvm3-java dependency (Thanks, Tomas Barton)
+    Unfortunately, debian-maven-helper does not automatically add this,
+    because the libsvm3-java package does not include a pom.
+  * Use find_jars to locate batik, which resolves problems with batik 1.7
+    (When using the /usr/bin/elki commands - please upgrade to batik 1.8
+     or adjust your classpath if you see the error
+     NoClassDefFoundError: org/apache/batik/dom/anim/AnimationTarget)
+  * Require libbatik-java >= 1.8 for building, 1.7 lacks pom data.
+  * Remove execute bit from all files in source jars, not just .java files.
+  * Add fop (libfop-java) to the classpath, for eps, pdf, ps export.
+  * Suggest libfop-java instead of making it an "alternative" to batik
+
+ -- Erich Schubert <erich@debian.org>  Fri, 08 Jan 2016 18:02:39 +0100
+
 elki (0.7.0-5) unstable; urgency=low
 
   * Cherry-pick important bug fixes from upstream.
diff --git a/debian/control b/debian/control
index 617a131a..0a6c09dc 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,8 @@ Section: science
 Priority: extra
 Maintainer: Erich Schubert <erich@debian.org>
 Build-Depends: debhelper (>= 9), openjdk-7-jdk | java7-sdk, maven-debian-helper (>= 1.5),
- libbatik-java, libsvm3-java, libtrove3-java, libxmlgraphics-commons-java, maven (>= 3),
+ libbatik-java (>= 1.8), libxmlgraphics-commons-java,
+ libsvm3-java, libtrove3-java, maven (>= 3),
  libmaven-antrun-plugin-java (>= 1.7), libmaven-antrun-plugin-java (<< 1.8),
  libmaven-compiler-plugin-java (>= 3.2), libmaven-compiler-plugin-java (<< 3.3),
  libmaven-exec-plugin-java (>= 1.1.1), libmaven-exec-plugin-java (<< 1.2),
@@ -11,14 +12,14 @@ Build-Depends: debhelper (>= 9), openjdk-7-jdk | java7-sdk, maven-debian-helper
  libmaven-resources-plugin-java (>= 2.6), libmaven-resources-plugin-java (<< 2.7),
  libmaven-source-plugin-java (>= 2.4), libmaven-source-plugin-java (<< 2.5),
  libsurefire-java (>= 2.17), libsurefire-java (<< 2.18), junit4,
- openjdk-7-doc | default-jdk-doc
+ default-jdk-doc
 Standards-Version: 3.9.6
 Homepage: http://elki.dbs.ifi.lmu.de/
 
 Package: elki
 Architecture: all
-Depends: default-jre (>= 2:1.7) | java7-runtime, ${misc:Depends}, ${maven:Depends}, fop | libbatik-java
-Suggests: elki-dev, ${maven:OptionalDepends}
+Depends: default-jre (>= 2:1.7) | java7-runtime, ${misc:Depends}, ${maven:Depends}, libbatik-java, libsvm3-java
+Suggests: elki-dev, libfop-java, ${maven:OptionalDepends}
 Description: Data mining algorithm development framework
  ELKI: "Environment for Developing KDD-Applications Supported by
  Index-Structures" is a development framework for data mining algorithms
diff --git a/debian/extra/elki b/debian/extra/elki
index c0319c9d..447d3769 100644
--- a/debian/extra/elki
+++ b/debian/extra/elki
@@ -3,6 +3,9 @@
 
 find_java_runtime openjdk8 oracle8 java8 openjdk7 oracle7 java7
 
-find_jars elki /usr/share/elki/addons/*.jar libsvm3
+find_jars elki /usr/share/elki/addons/*.jar libsvm3 batik-all
+
+# FOP is not strictly required
+find_jars fop 2> /dev/null
 
 run_java de.lmu.ifi.dbs.elki.application.ELKILauncher "$@"
diff --git a/debian/extra/elki-cli b/debian/extra/elki-cli
index 9872aaf9..43f9d6f0 100644
--- a/debian/extra/elki-cli
+++ b/debian/extra/elki-cli
@@ -3,6 +3,9 @@
 
 find_java_runtime openjdk8 oracle8 java8 openjdk7 oracle7 java7
 
-find_jars elki /usr/share/elki/addons/*.jar libsvm3
+find_jars elki /usr/share/elki/addons/*.jar libsvm3 batik-all
+
+# FOP is not strictly required
+find_jars fop 2> /dev/null
 
 run_java de.lmu.ifi.dbs.elki.application.KDDCLIApplication "$@"
diff --git a/debian/patches/javadoc-encoding.patch b/debian/patches/javadoc-encoding.patch
index f91dbcde..fcb60b12 100644
--- a/debian/patches/javadoc-encoding.patch
+++ b/debian/patches/javadoc-encoding.patch
@@ -25,3 +25,39 @@ Index: elki-0.7.0/pom.xml
  				</configuration>
  			</plugin>
  		</plugins>
+Index: elki-0.7.0/addons/batikvis/pom.xml
+===================================================================
+--- elki-0.7.0.orig/addons/batikvis/pom.xml
++++ elki-0.7.0/addons/batikvis/pom.xml
+@@ -1,3 +1,4 @@
++<?xml version='1.0' encoding='UTF-8'?>
+ <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ 	<modelVersion>4.0.0</modelVersion>
+Index: elki-0.7.0/addons/libsvm/pom.xml
+===================================================================
+--- elki-0.7.0.orig/addons/libsvm/pom.xml
++++ elki-0.7.0/addons/libsvm/pom.xml
+@@ -1,3 +1,4 @@
++<?xml version='1.0' encoding='UTF-8'?>
+ <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ 	<modelVersion>4.0.0</modelVersion>
+Index: elki-0.7.0/addons/tutorial/pom.xml
+===================================================================
+--- elki-0.7.0.orig/addons/tutorial/pom.xml
++++ elki-0.7.0/addons/tutorial/pom.xml
+@@ -1,3 +1,4 @@
++<?xml version='1.0' encoding='UTF-8'?>
+ <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ 	<modelVersion>4.0.0</modelVersion>
+Index: elki-0.7.0/elki/pom.xml
+===================================================================
+--- elki-0.7.0.orig/elki/pom.xml
++++ elki-0.7.0/elki/pom.xml
+@@ -1,3 +1,4 @@
++<?xml version='1.0' encoding='UTF-8'?>
+ <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ 	<modelVersion>4.0.0</modelVersion>
diff --git a/debian/patches/repeatable-documentation.patch b/debian/patches/repeatable-documentation.patch
index a7562c62..da33b86b 100644
--- a/debian/patches/repeatable-documentation.patch
+++ b/debian/patches/repeatable-documentation.patch
@@ -77,3 +77,238 @@ index 7d448fc..3b9f029 100644
          documentReferencesWiki(refs, refstreamW);
          refstreamW.flush();
          refstreamW.close();
+commit 03b1d86f6101ce74ac7318720cf5679b3a4ea4b2
+Author: Erich Schubert <schube@dbs.ifi.lmu.de>
+Date:   Fri Jan 8 16:17:43 2016 +0100
+
+    Stricter sorting of references.
+
+diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentReferences.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentReferences.java
+index 3b9f029..04b6a89 100644
+--- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentReferences.java
++++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentReferences.java
+@@ -330,7 +330,28 @@ public class DocumentReferences {
+       @Override
+       public int compare(Pair<Reference, TreeSet<Object>> p1, Pair<Reference, TreeSet<Object>> p2) {
+         final Object o1 = p1.second.first(), o2 = p2.second.first();
+-        return COMPARATOR.compare(o1, o2);
++        int c = COMPARATOR.compare(o1, o2);
++        if(c == 0) {
++          Reference r1 = p1.first, r2 = p2.first;
++          c = compareNull(r1.title(), r2.title());
++          c = (c != 0) ? c : compareNull(r1.authors(), r2.authors());
++          c = (c != 0) ? c : compareNull(r1.booktitle(), r2.booktitle());
++        }
++        return c;
++      }
++
++      /**
++       * Null-tolerant String comparison.
++       * 
++       * @param s1 First string
++       * @param s2 Second string
++       * @return Order
++       */
++      private int compareNull(String s1, String s2) {
++        return (s1 == s2) ? 0 //
++        : (s1 == null) ? -1 //
++        : (s2 == null) ? +1 //
++        : s1.compareTo(s2);
+       }
+     });
+     return refs;
+
+commit a24a37a0c6410a5373d1bd25811d62ff96f5cdc8
+Author: Erich Schubert <schube@dbs.ifi.lmu.de>
+Date:   Fri Jan 8 16:19:26 2016 +0100
+
+    Stricter sorting of parameter occurrences.
+
+diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentParameters.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentParameters.java
+index cdbad00..90a6ec9 100644
+--- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentParameters.java
++++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentParameters.java
+@@ -724,9 +724,18 @@ public class DocumentParameters {
+     Element maindl = htmldoc.createElement(HTMLUtil.HTML_DL_TAG);
+     body.appendChild(maindl);
+ 
+-    List<OptionID> opts = new ArrayList<>(byopt.keySet());
+-    Collections.sort(opts, new SortByOption());
++    final Comparator<OptionID> osort = new SortByOption();
++    final Comparator<Class<?>> csort = new ELKIServiceScanner.ClassSorter();
++    Comparator<Pair<Parameter<?>, Class<?>>> psort = new Comparator<Pair<Parameter<?>, Class<?>>>() {
++      @Override
++      public int compare(Pair<Parameter<?>, Class<?>> o1, Pair<Parameter<?>, Class<?>> o2) {
++        int c = osort.compare(o1.first.getOptionID(), o2.first.getOptionID());
++        return (c != 0) ? c : csort.compare(o1.second, o2.second);
++      }
++    };
+ 
++    List<OptionID> opts = new ArrayList<>(byopt.keySet());
++    Collections.sort(opts, osort);
+     for(OptionID oid : opts) {
+       final Parameter<?> firstopt = byopt.get(oid).get(0).getFirst();
+       // DT = definition term
+@@ -791,7 +800,9 @@ public class DocumentParameters {
+         optdd.appendChild(p);
+       }
+       optdd.appendChild(classesul);
+-      for(Pair<Parameter<?>, Class<?>> clinst : byopt.get(oid)) {
++      List<Pair<Parameter<?>, Class<?>>> plist = byopt.get(oid);
++      Collections.sort(plist, psort);
++      for(Pair<Parameter<?>, Class<?>> clinst : plist) {
+         // DT definition term: option name, in TT for typewriter optics
+         Element classli = htmldoc.createElement(HTMLUtil.HTML_LI_TAG);
+ 
+
+commit 83cb0dbda65e1e1f72d1cd9ba9c9cd66ea5fb3d0
+Author: Erich Schubert <schube@dbs.ifi.lmu.de>
+Date:   Fri Jan 8 15:25:24 2016 +0100
+
+    Fix getDefaultValueAsString() for ListParameter subclasses.
+
+diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentParameters.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentParameters.java
+index 90a6ec9..4b9a5e0 100644
+--- a/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentParameters.java
++++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/application/internal/DocumentParameters.java
+@@ -1039,8 +1039,7 @@ public class DocumentParameters {
+         p.appendChild(htmldoc.createTextNode("use global random seed"));
+       }
+       else {
+-        Object def = par.getDefaultValue();
+-        p.appendChild(htmldoc.createTextNode(def.toString()));
++        p.appendChild(htmldoc.createTextNode(par.getDefaultValueAsString()));
+       }
+       optdd.appendChild(p);
+     }
+@@ -1069,8 +1068,7 @@ public class DocumentParameters {
+       out.print("use global random seed");
+     }
+     else {
+-      Object def = par.getDefaultValue();
+-      out.print(def.toString());
++      out.print(par.getDefaultValueAsString());
+     }
+     out.println();
+   }
+diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ClassListParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ClassListParameter.java
+index d9d1a3a..f4f70a4 100644
+--- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ClassListParameter.java
++++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/ClassListParameter.java
+@@ -96,6 +96,23 @@ public class ClassListParameter<C> extends ListParameter<ClassListParameter<C>,
+     return buf.toString();
+   }
+ 
++  @Override
++  public String getDefaultValueAsString() {
++    StringBuilder buf = new StringBuilder();
++    final String defPackage = restrictionClass.getPackage().getName() + ".";
++    for(Class<? extends C> c : getDefaultValue()) {
++      if(buf.length() > 0) {
++        buf.append(LIST_SEP);
++      }
++      String name = c.getName();
++      if(name.startsWith(defPackage)) {
++        name = name.substring(defPackage.length());
++      }
++      buf.append(name);
++    }
++    return buf.toString();
++  }
++
+   @SuppressWarnings("unchecked")
+   @Override
+   protected List<Class<? extends C>> parseValue(Object obj) throws ParameterException {
+diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleListParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleListParameter.java
+index 074bb0e..e8a59cb 100644
+--- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleListParameter.java
++++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/DoubleListParameter.java
+@@ -60,6 +60,11 @@ public class DoubleListParameter extends ListParameter<DoubleListParameter, doub
+   }
+ 
+   @Override
++  public String getDefaultValueAsString() {
++    return FormatUtil.format(getDefaultValue(), LIST_SEP);
++  }
++
++  @Override
+   protected double[] parseValue(Object obj) throws ParameterException {
+     if(obj instanceof double[]) {
+       return double[].class.cast(obj);
+diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/FileListParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/FileListParameter.java
+index e5f1b02..02b397f 100644
+--- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/FileListParameter.java
++++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/FileListParameter.java
+@@ -89,6 +89,20 @@ public class FileListParameter extends ListParameter<FileListParameter, List<Fil
+     return buf.toString();
+   }
+ 
++  @Override
++  public String getDefaultValueAsString() {
++    StringBuilder buf = new StringBuilder();
++    List<File> val = getDefaultValue();
++    Iterator<File> veciter = val.iterator();
++    while(veciter.hasNext()) {
++      buf.append(veciter.next());
++      if (veciter.hasNext()) {
++        buf.append(LIST_SEP);
++      }
++    }
++    return buf.toString();
++  }
++
+   @SuppressWarnings("unchecked")
+   @Override
+   protected List<File> parseValue(Object obj) throws ParameterException {
+diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/IntListParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/IntListParameter.java
+index 756dbb9..0f2306e 100644
+--- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/IntListParameter.java
++++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/IntListParameter.java
+@@ -70,6 +70,21 @@ public class IntListParameter extends ListParameter<IntListParameter, int[]> {
+   }
+ 
+   @Override
++  public String getDefaultValueAsString() {
++    int[] val = getDefaultValue();
++    if(val.length == 0) {
++      return "";
++    }
++    StringBuilder buf = new StringBuilder();
++    buf.append(val[0]);
++    for(int i = 1; i < val.length; i++) {
++      buf.append(LIST_SEP);
++      buf.append(val[i]);
++    }
++    return buf.toString();
++  }
++
++  @Override
+   protected int[] parseValue(Object obj) throws ParameterException {
+     if(obj instanceof int[]) {
+       return (int[]) obj;
+diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/VectorListParameter.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/VectorListParameter.java
+index b6d999f..815611a 100644
+--- a/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/VectorListParameter.java
++++ b/elki/src/main/java/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameters/VectorListParameter.java
+@@ -122,6 +122,21 @@ public class VectorListParameter extends ListParameter<VectorListParameter, List
+     return buf.toString();
+   }
+ 
++  @Override
++  public String getDefaultValueAsString() {
++    StringBuilder buf = new StringBuilder();
++    List<Vector> val = getDefaultValue();
++    Iterator<Vector> valiter = val.iterator();
++    while(valiter.hasNext()) {
++      buf.append(FormatUtil.format(valiter.next().getArrayRef(), LIST_SEP));
++      // Append separation character
++      if(valiter.hasNext()) {
++        buf.append(VECTOR_SEP);
++      }
++    }
++    return buf.toString();
++  }
++
+   @SuppressWarnings("unchecked")
+   @Override
+   protected List<Vector> parseValue(Object obj) throws ParameterException {
diff --git a/debian/rules b/debian/rules
index 7c7e06db..85c68c10 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,7 +11,7 @@ MVN=/usr/share/maven/bin/mvn -Dmaven.repo.local=$(REPO)
 
 override_dh_auto_configure:
 	# Remove unneded executable bits:
-	find -type f -name "*.java" -executable -exec chmod -x {} \+
+	find elki addons data -type f -executable -exec chmod -x {} \+
 	dh_auto_configure -O--buildsystem=maven
 
 #build: