merge from test-ci

.gitlab-ci.yml

+image: maven:latest
+
+#workflow:
+#  rules:
+#    - if: $CI_COMMIT_TAG
+
+variables:
+  MAVEN_CLI_OPTS: "-s .m2/settings.xml --batch-mode"
+  MAVEN_OPTS: "-Dmaven.repo.local=.m2/repository"
+
+stages:
+  - build
+  - package
+  - test
+  - deploy
+  - release
+
+cache:
+  paths:
+    - .m2/repository
+    - build/
+
+build-job:
+  stage: build
+  script:
+    - echo "Building Artifact"
+    - mvn $MAVEN_CLI_OPTS clean compile
+  artifacts:
+    when: on_success
+    expire_in: 1 hour
+    paths:
+      - build/
+
+package-job:
+  stage: package
+  dependencies:
+    - build-job
+  script:
+    - echo "Packaging the code"
+    - mvn $MAVEN_CLI_OPTS package -Dmaven.test.skip=true
+  artifacts:
+    paths:
+      - build/
+
+test-job:
+  stage: test
+  dependencies:
+    - build-job
+  script:
+    - echo "Checking files"
+    - mvn clean verify
+  artifacts:
+    when: on_success
+    expire_in: 1 hour
+    paths:
+      - build/
+
+deploy-job:
+  stage: deploy
+  #only:
+    #- test-ci
+  dependencies:
+    - package-job
+  script:
+    - echo "Deploy artifact to the Nexus"
+    - mvn $MAVEN_CLI_OPTS deploy
+  artifacts:
+    when: on_success
+    expire_in: 1 hour
+    paths:
+      - build/*.jar
+
+#release-job:
+#  stage: release
+#  #only:
+#    #- releases
+#  dependencies:
+#    - deploy-job
+#  script:
+#    - "/tools/maven-release"
\ No newline at end of file

.m2/settings.xml

+<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
+          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+          xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
+                              https://maven.apache.org/xsd/settings-1.0.0.xsd">
+    <servers>
+        <server>
+            <id>icy-prod</id>
+            <username>${env.MAVEN_REPO_USER}</username>
+            <password>${env.MAVEN_REPO_PASS}</password>
+        </server>
+    </servers>
+</settings>
\ No newline at end of file

pom.xml

@@ -198,6 +198,7 @@
                     <archive>
                         <manifest>
                             <classpathLayoutType>custom</classpathLayoutType>
+                            <!--suppress UnresolvedMavenProperty -->
                             <customClasspathLayout>$${artifact.artifactId}.$${artifact.extension}</customClasspathLayout>
                             <addClasspath>true</addClasspath>
                             <classpathPrefix>lib/</classpathPrefix>
@@ -210,6 +211,35 @@
                     </archive>
                 </configuration>
             </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+                <version>3.2.0</version>
+                <executions>
+                    <execution>
+                        <id>attach-javadocs</id>
+                        <goals>
+                            <goal>jar</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-source-plugin</artifactId>
+                <version>3.2.0</version>
+                <executions>
+                    <execution>
+                        <id>attach-sources</id>
+                        <phase>verify</phase>
+                        <goals>
+                            <goal>jar-no-fork</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
     </build>
 
@@ -390,7 +420,8 @@
     <distributionManagement>
         <repository>
             <id>icy-prod</id>
-            <url>https://icy-nexus.pasteur.fr/repository/icy-core/</url>
+            <!--suppress UnresolvedMavenProperty -->
+            <url>${env.MAVEN_REPO_URL}/icy-core/</url>
         </repository>
         <snapshotRepository>
             <id>icy-dev</id>

src/main/java/icy/canvas/Canvas2D.java

@@ -2070,7 +2070,7 @@ public class Canvas2D extends IcyCanvas2D implements ROITaskListener
     final CanvasMap canvasMap;
 
     /**
-     * GUI & setting
+     * GUI & setting
      */
     IcyToggleButton zoomFitCanvasButton;
     Color bgColor;

src/main/java/icy/canvas/IcyCanvas.java

@@ -90,7 +90,7 @@ import plugins.kernel.canvas.Canvas2DPlugin;
 import plugins.kernel.canvas.VtkCanvasPlugin;
 
 /**
- * @author Fabrice de Chaumont & Stephane Dallongeville<br>
+ * @author Fabrice de Chaumont &amp; Stephane Dallongeville<br>
  *         <br>
  *         An IcyCanvas is a basic Canvas used into the viewer. It contains a visual representation
  *         of the sequence and provides some facilities as basic transformation and view
@@ -576,7 +576,7 @@ public abstract class IcyCanvas extends JPanel
     }
 
     /**
-     * Called by the viewer when canvas is closed to release some resources.<br/>
+     * Called by the viewer when canvas is closed to release some resources.<br>
      * Be careful to not restore previous state here (as the colormap) because generally <code>shutdown</code> is called
      * <b>after</b> the creation of the other canvas.
      */
@@ -815,7 +815,7 @@ public abstract class IcyCanvas extends JPanel
     }
 
     /**
-     * Returns all layers attached to this canvas.<br/>
+     * Returns all layers attached to this canvas.<br>
      * 
      * @param sorted
      *        If <code>true</code> the returned list is sorted on the layer priority.<br>
@@ -858,7 +858,7 @@ public abstract class IcyCanvas extends JPanel
     }
 
     /**
-     * Returns all layers attached to this canvas.<br/>
+     * Returns all layers attached to this canvas.<br>
      * The returned list is sorted on the layer priority.<br>
      * Sort operation is cached so the method could take sometime when cache need to be rebuild.
      */
@@ -890,7 +890,7 @@ public abstract class IcyCanvas extends JPanel
 
     /**
      * Returns all visible layers (visible property set to <code>true</code>) attached to this
-     * canvas.<br/>
+     * canvas.<br>
      * The list is sorted on the layer priority.
      */
     public ArrayList<Layer> getVisibleLayers()
@@ -4207,7 +4207,7 @@ public abstract class IcyCanvas extends JPanel
     }
 
     /**
-     * Remove the layer for the specified {@link Overlay} from the canvas.<br/>
+     * Remove the layer for the specified {@link Overlay} from the canvas.<br>
      * Returns <code>true</code> if the method succeed.
      */
     public boolean removeLayer(Overlay overlay)

src/main/java/icy/canvas/Layer.java

@@ -236,7 +236,7 @@ public class Layer implements OverlayListener, Comparable<Layer>
 
     /**
      * Returns <code>true</code> if the layer can be freely removed from the Canvas where it
-     * appears and <code>false</code> otherwise.<br/>
+     * appears and <code>false</code> otherwise.<br>
      * 
      * @see Overlay#getCanBeRemoved()
      */
@@ -246,7 +246,7 @@ public class Layer implements OverlayListener, Comparable<Layer>
     }
 
     /**
-     * Set the <code>canBeRemoved</code> property.<br/>
+     * Set the <code>canBeRemoved</code> property.<br>
      * Set it to false if you want to prevent the layer to be removed from the Canvas where it
      * appears.
      * 

src/main/java/icy/common/CollapsibleEvent.java

@@ -4,7 +4,7 @@
 package icy.common;
 
 /**
- * Collapsible interface for collapsible event used by UpdateEventHandler.<br/>
+ * Collapsible interface for collapsible event used by UpdateEventHandler.<br>
  * As we use HashMap to store these events, so we rely on Object.equals(..) and
  * Object.hashcode() implementation for these events.
  * 
@@ -16,19 +16,21 @@ public interface CollapsibleEvent
      * Collapse current object/event with specified one.
      * 
      * @return <code>false</code> if collapse operation failed (object are not 'equals')
+     * @param event event
      */
     public boolean collapse(CollapsibleEvent event);
 
     /**
-     * Returns <code>true</code> if the current event is equivalent to the specified one.<br/>
+     * @return Returns <code>true</code> if the current event is equivalent to the specified one.<br>
      * We want event to override {@link Object#equals(Object)} method as we use an HashMap to store
      * these event
      * in the {@link UpdateEventHandler} class.
+     * @param event event
      */
     public boolean equals(Object event);
 
     /**
-     * Returns hash code for current event. It should respect the default {@link Object#hashCode()}
+     * @return Returns hash code for current event. It should respect the default {@link Object#hashCode()}
      * contract.
      */
     public int hashCode();

src/main/java/icy/common/exception/TooLargeArrayException.java

@@ -4,7 +4,7 @@
 package icy.common.exception;
 
 /**
- * Exception when trying to allocate a too large array (length > 2^31)
+ * Exception when trying to allocate a too large array (length > 2^31)
  * 
  * @author Stephane
  */

src/main/java/icy/common/listener/ChangeListener.java

@@ -29,6 +29,7 @@ public interface ChangeListener
 {
     /**
      * fire changed event
+     * @param event collapsible
      */
     public void onChanged(CollapsibleEvent event);
 }

src/main/java/icy/file/FileUtil.java

@@ -68,7 +68,7 @@ public class FileUtil
 
     /**
      * Transform any system specific path in java generic path form.<br>
-     * Ex: "C:\windows" --> "C:/windows"
+     * Ex: "C:\windows" --&gt; "C:/windows"
      */
     public static String getGenericPath(String path)
     {
@@ -100,9 +100,9 @@ public class FileUtil
     /**
      * Change path extension.<br>
      * Ex : setExtension(path, ".dat")<br>
-     * "c:\temp" --> "c:\temp.dat"
-     * "c:\file.out" --> "c:\file.dat"
-     * "" --> ""
+     * "c:\temp" --&gt; "c:\temp.dat"
+     * "c:\file.out" --&gt; "c:\file.dat"
+     * "" --&gt; ""
      */
     public static String setExtension(String path, String extension)
     {
@@ -371,10 +371,10 @@ public class FileUtil
     /**
      * Return drive / mount point from specified path<br>
      * <br>
-     * getDrive("D:/temp/file.txt") --> "D:"<br>
-     * getDrive("D:/temp") --> "D:"<br>
-     * getDrive("C:file.txt") --> "C:"<br>
-     * getDrive("file.txt") --> ""<br>
+     * getDrive("D:/temp/file.txt") --&gt; "D:"<br>
+     * getDrive("D:/temp") --&gt; "D:"<br>
+     * getDrive("C:file.txt") --&gt; "C:"<br>
+     * getDrive("file.txt") --&gt; ""<br>
      */
     public static String getDrive(String path)
     {
@@ -393,16 +393,16 @@ public class FileUtil
     /**
      * Returns directory information from specified path<br>
      * <br>
-     * getDirectory("/file.txt", true) --> "/"<br>
-     * getDirectory("D:/temp/file.txt", true) --> "D:/temp/"<br>
-     * getDirectory("D:/temp/", true) --> "D:/temp/"<br>
-     * getDirectory("D:/temp/", false) --> "D:/temp"<br>
-     * getDirectory("D:/temp", true) --> "D:/"<br>
-     * getDirectory("D:/temp", false) --> "D:"<br>
-     * getDirectory("C:file.txt") --> "C:"<br>
-     * getDirectory("file.txt") --> ""<br>
-     * getDirectory("file") --> ""<br>
-     * getDirectory(null) --> ""
+     * getDirectory("/file.txt", true) --&gt; "/"<br>
+     * getDirectory("D:/temp/file.txt", true) --&gt; "D:/temp/"<br>
+     * getDirectory("D:/temp/", true) --&gt; "D:/temp/"<br>
+     * getDirectory("D:/temp/", false) --&gt; "D:/temp"<br>
+     * getDirectory("D:/temp", true) --&gt; "D:/"<br>
+     * getDirectory("D:/temp", false) --&gt; "D:"<br>
+     * getDirectory("C:file.txt") --&gt; "C:"<br>
+     * getDirectory("file.txt") --&gt; ""<br>
+     * getDirectory("file") --&gt; ""<br>
+     * getDirectory(null) --&gt; ""
      */
     public static String getDirectory(String path, boolean wantSeparator)
     {
@@ -425,14 +425,14 @@ public class FileUtil
     /**
      * Return directory information from specified path<br>
      * <br>
-     * getDirectory("/file.txt") --> "/"<br>
-     * getDirectory("D:/temp/file.txt") --> "D:/temp/"<br>
-     * getDirectory("D:/temp/") --> "D:/temp/"<br>
-     * getDirectory("D:/temp") --> "D:/"<br>
-     * getDirectory("C:file.txt") --> "C:"<br>
-     * getDirectory("file.txt") --> ""<br>
-     * getDirectory("file") --> ""<br>
-     * getDirectory(null) --> ""
+     * getDirectory("/file.txt") --&gt; "/"<br>
+     * getDirectory("D:/temp/file.txt") --&gt; "D:/temp/"<br>
+     * getDirectory("D:/temp/") --&gt; "D:/temp/"<br>
+     * getDirectory("D:/temp") --&gt; "D:/"<br>
+     * getDirectory("C:file.txt") --&gt; "C:"<br>
+     * getDirectory("file.txt") --&gt; ""<br>
+     * getDirectory("file") --&gt; ""<br>
+     * getDirectory(null) --&gt; ""
      */
     public static String getDirectory(String path)
     {
@@ -442,11 +442,11 @@ public class FileUtil
     /**
      * Return filename information from specified path.<br>
      * <br>
-     * getFileName("/file.txt") --> "file.txt"<br>
-     * getFileName("D:/temp/file.txt") --> "file.txt"<br>
-     * getFileName("C:file.txt") --> "file.txt"<br>
-     * getFileName("file.txt") --> "file.txt"<br>
-     * getFileName(null) --> ""
+     * getFileName("/file.txt") --&gt; "file.txt"<br>
+     * getFileName("D:/temp/file.txt") --&gt; "file.txt"<br>
+     * getFileName("C:file.txt") --&gt; "file.txt"<br>
+     * getFileName("file.txt") --&gt; "file.txt"<br>
+     * getFileName(null) --&gt; ""
      */
     public static String getFileName(String path)
     {
@@ -457,11 +457,11 @@ public class FileUtil
      * Return filename information from specified path.<br>
      * Filename's extension is returned depending the withExtension flag value<br>
      * <br>
-     * getFileName("/file.txt") --> "file(.txt)"<br>
-     * getFileName("D:/temp/file.txt") --> "file(.txt)"<br>
-     * getFileName("C:file.txt") --> "file(.txt)"<br>
-     * getFileName("file.txt") --> "file(.txt)"<br>
-     * getFileName(null) --> ""
+     * getFileName("/file.txt") --&gt; "file(.txt)"<br>
+     * getFileName("D:/temp/file.txt") --&gt; "file(.txt)"<br>
+     * getFileName("C:file.txt") --&gt; "file(.txt)"<br>
+     * getFileName("file.txt") --&gt; "file(.txt)"<br>
+     * getFileName(null) --&gt; ""
      */
     public static String getFileName(String path, boolean withExtension)
     {
@@ -502,11 +502,11 @@ public class FileUtil
      * Return filename extension information from specified path<br>
      * Dot character is returned depending the withDot flag value<br>
      * <br>
-     * getFileExtension("/file.txt") --> "(.)txt)"<br>
-     * getFileExtension("D:/temp/file.txt.old") --> "(.)old"<br>
-     * getFileExtension("C:/win/dir2/file") --> ""<br>
-     * getFileExtension(".txt") --> "(.)txt)"<br>
-     * getFileExtension(null) --> ""
+     * getFileExtension("/file.txt") --&gt; "(.)txt)"<br>
+     * getFileExtension("D:/temp/file.txt.old") --&gt; "(.)old"<br>
+     * getFileExtension("C:/win/dir2/file") --&gt; ""<br>
+     * getFileExtension(".txt") --&gt; "(.)txt)"<br>
+     * getFileExtension(null) --&gt; ""
      */
     public static String getFileExtension(String path, boolean withDot)
     {

src/main/java/icy/file/Loader.java

@@ -76,7 +76,7 @@ import plugins.kernel.importer.LociImporterPlugin;
 /**
  * Sequence / Image loader class.
  * 
- * @author Fabrice de Chaumont & Stephane
+ * @author Fabrice de Chaumont & Stephane
  */
 public class Loader
 {
@@ -866,7 +866,7 @@ public class Loader
     }
 
     /**
-     * Check if we can open the given image plane resolution (XY size < 2^31).<br>
+     * Check if we can open the given image plane resolution (XY size &lt; 2^31).<br>
      * If the image plane is too large the method throw an exception with an informative error
      * message about the encountered limitation.
      * 
@@ -881,7 +881,7 @@ public class Loader
      * @param messageSuffix
      *        message suffix for the exception if wanted
      * @throws UnsupportedOperationException
-     *         if the XY plane size is >= 2^31 pixels
+     *         if the XY plane size is &gt;= 2^31 pixels
      * @return the number of pixels of the image plane
      */
     public static long checkOpeningPlane(int resolution, int sizeX, int sizeY, String messageSuffix)
@@ -903,7 +903,7 @@ public class Loader
     /**
      * Check if we have enough resource to open the image defined by the given size information and
      * wanted resolution.<br>
-     * If the image is too large to be displayed at full resolution (XY plane size > 2^31) or if we
+     * If the image is too large to be displayed at full resolution (XY plane size &gt; 2^31) or if we
      * don't have enough
      * memory to store the whole image the method throw an exception with an informative error
      * message about the
@@ -928,7 +928,7 @@ public class Loader
      * @param messageSuffix
      *        message suffix for the exception if wanted
      * @throws UnsupportedOperationException
-     *         if the XY plane size is >= 2^31 pixels
+     *         if the XY plane size is &gt;= 2^31 pixels
      * @throws OutOfMemoryError
      *         if there is not enough memory to open the image
      */
@@ -961,7 +961,7 @@ public class Loader
     /**
      * Check if we have enough resource to open the image defined by the given metadata information, series index and
      * wanted resolution.<br>
-     * If the image is too large to be displayed at full resolution (XY plane size > 2^31) or if we* don't have enough
+     * If the image is too large to be displayed at full resolution (XY plane size &gt; 2^31) or if we* don't have enough
      * memory to store the whole image the method throw an exception with an informative error message about the
      * encountered limitation.
      * 
@@ -981,7 +981,7 @@ public class Loader
      * @param messageSuffix
      *        message suffix for the exception if wanted
      * @throws UnsupportedOperationException
-     *         if the XY plane size is >= 2^31 pixels
+     *         if the XY plane size is &gt;= 2^31 pixels
      * @throws OutOfMemoryError
      *         if there is not enough memory to open the image
      */
@@ -996,7 +996,7 @@ public class Loader
     /**
      * Check if we have enough resource to open the image defined by the given metadata information, series index and
      * wanted resolution.<br>
-     * If the image is too large to be displayed at full resolution (XY plane size > 2^31) or if we don't have enough
+     * If the image is too large to be displayed at full resolution (XY plane size &gt; 2^31) or if we don't have enough
      * memory to store the whole image the method throw an exception with an informative error message about the
      * encountered limitation.
      * 
@@ -1012,7 +1012,7 @@ public class Loader
      * @param messageSuffix
      *        message suffix for the exception if wanted
      * @throws UnsupportedOperationException
-     *         if the XY plane size is >= 2^31 pixels
+     *         if the XY plane size is &gt;= 2^31 pixels
      * @throws OutOfMemoryError
      *         if there is not enough memory to open the image
      */

src/main/java/icy/file/Saver.java

@@ -61,7 +61,7 @@ import ome.xml.meta.OMEXMLMetadata;
  * When sequence is saved as multiple file the following naming convention is used :<br>
  * <code>filename-tttt-zzzz</code>
  * 
- * @author Stephane & Fab
+ * @author Stephane &amp; Fab
  */
 public class Saver
 {

src/main/java/icy/file/SequenceFileImporter.java

@@ -65,8 +65,10 @@ public interface SequenceFileImporter extends SequenceIdImporter
      *        Path of the image file to open.
      * @param flags
      *        operation flag:<br>
+     *        <ul>
      *        <li>{@link #FLAG_METADATA_MINIMUM} = load minimum metadata informations</li>
      *        <li>{@link #FLAG_METADATA_ALL} = load all metadata informations</li>
+     *        </ul>
      * @return <code>true</code> if the operation has succeeded and <code>false</code> otherwise.
      */
     @Override

src/main/java/icy/file/SequenceFileSticher.java

@@ -38,7 +38,7 @@ import ome.xml.meta.OMEXMLMetadata;
 import plugins.kernel.importer.LociImporterPlugin;
 
 /**
- * This class is an utility class aim to help in grouping a list of <i>file path</id> representing image to form a complete and valid Sequence.
+ * This class is an utility class aim to help in grouping a list of <i>file path</i> representing image to form a complete and valid Sequence.
  * 
  * @author Stephane
  */

src/main/java/icy/file/xml/XMLPersistent.java

@@ -26,12 +26,14 @@ import org.w3c.dom.Node;
 public interface XMLPersistent
 {
     /**
-     * LOAD
+     * @return LOAD
+     * @param node node
      */
     public boolean loadFromXML(Node node);
 
     /**
-     * SAVE
+     * @return SAVE
+     * @param node node
      */
     public boolean saveToXML(Node node);
 

src/main/java/icy/gui/component/CheckTabbedPane.java

@@ -166,7 +166,7 @@ public class CheckTabbedPane extends JTabbedPane
      * @return true if tab component at <code>index</code> is checked, false
      *         otherwise
      * @exception IndexOutOfBoundsException
-     *            if index is out of range (index < 0 || index >= tab count)
+     *            if index is out of range (index &lt; 0 || index &gt;= tab count)
      * @see #setTabChecked(int, boolean)
      */
     public boolean isTabChecked(int index)
@@ -182,7 +182,7 @@ public class CheckTabbedPane extends JTabbedPane
      * @param value
      *        the check state
      * @exception IndexOutOfBoundsException
-     *            if index is out of range (index < 0 || index >= tab count)
+     *            if index is out of range (index &lt; 0 || index &gt;= tab count)
      * @see #isTabChecked(int)
      */
     public void setTabChecked(int index, boolean value)