dev-java/fits: Version bump and import to the science overlay

(Portage version: 2.1.10.56/git/Linux x86_64, unsigned Manifest commit)

4 files changed, 488 insertions, 0 deletions

diff --git a/dev-java/fits/files/01-Use-getResource-to-access-CompressTest-data-for-unit.patch b/dev-java/fits/files/01-Use-getResource-to-access-CompressTest-data-for-unit.patch
new file mode 100644
index 000000000..389c233d1
--- /dev/null
+++ b/dev-java/fits/files/01-Use-getResource-to-access-CompressTest-data-for-unit.patch
@@ -0,0 +1,137 @@
+diff --git a/src/nom/tam/fits/test/CompressTest.java b/src/nom/tam/fits/test/CompressTest.java
+index dd3aad0..c6d953e 100644
+--- a/src/nom/tam/fits/test/CompressTest.java
++++ b/src/nom/tam/fits/test/CompressTest.java
+@@ -54,58 +54,57 @@ public class CompressTest {
+ 
+     @Test
+     public void testStream() throws Exception {
+-        InputStream is;
++        String is;
+ 
+-        is = new FileInputStream("test.fits");
++        is = "test.fits";
+         assertEquals("Stream1", 300, streamRead(is, false, false));
+ 
+-        is = new FileInputStream("test.fits.Z");
++        is = "test.fits.Z";
+         assertEquals("Stream2", 300, streamRead(is, false, false));
+ 
+-        is = new FileInputStream("test.fits.gz");
++        is = "test.fits.gz";
+         assertEquals("Stream3", 300, streamRead(is, false, false));
+ 
+-        is = new FileInputStream("test.fits");
++        is = "test.fits";
+         assertEquals("Stream4", 300, streamRead(is, false, true));
+ 
+-        is = new FileInputStream("test.fits.Z");
++        is = "test.fits.Z";
+         assertEquals("Stream5", 300, streamRead(is, false, true));
+ 
+-        is = new FileInputStream("test.fits.gz");
++        is = "test.fits.gz";
+         assertEquals("Stream6", 300, streamRead(is, false, true));
+ 
+-
+-        is = new FileInputStream("test.fits.Z");
++        is = "test.fits.Z";
+         assertEquals("Stream7", 300, streamRead(is, true, true));
+ 
+-        is = new FileInputStream("test.fits.gz");
++        is = "test.fits.gz";
+         assertEquals("Stream8", 300, streamRead(is, true, true));
+ 
+-        is = new FileInputStream("test.fits.bz2");
++        is = "test.fits.bz2";
+         assertEquals("Stream9", 300, streamRead(is, true, true));
+     }
+ 
+     @Test
+     public void testFile() throws Exception {
+-        File is = new File("test.fits");
++        String is = "test.fits";
+         assertEquals("File1", 300, fileRead(is, false, false));
+ 
+-        is = new File("test.fits.Z");
++        is = "test.fits.Z";
+         assertEquals("File2", 300, fileRead(is, false, false));
+ 
+-        is = new File("test.fits.gz");
++        is = "test.fits.gz";
+         assertEquals("File3", 300, fileRead(is, false, false));
+ 
+-        is = new File("test.fits");
++        is = "test.fits";
+         assertEquals("File4", 300, fileRead(is, false, true));
+ 
+-        is = new File("test.fits.Z");
++        is = "test.fits.Z";
+         assertEquals("File7", 300, fileRead(is, true, true));
+ 
+-        is = new File("test.fits.gz");
++        is = "test.fits.gz";
+         assertEquals("File8", 300, fileRead(is, true, true));
+ 
+-        is = new File("test.fits.bz2");
++        is = "test.fits.bz2";
+         assertEquals("File9", 300, fileRead(is, true, true));
+     }
+ 
+@@ -131,7 +130,6 @@ public class CompressTest {
+ 
+         is = "test.fits.bz2";
+         assertEquals("String8", 300, stringRead(is, true, true));
+-
+     }
+ 
+     @Test
+@@ -158,13 +156,9 @@ public class CompressTest {
+         assertEquals("String8", 300, urlRead(is, true, true));
+     }
+ 
+-    int urlRead(String is, boolean comp, boolean useComp)
++    int urlRead(String filename, boolean comp, boolean useComp)
+             throws Exception {
+-        File fil = new File(is);
+-
+-        String path = fil.getCanonicalPath();
+-        URL u = new URL("file://" + path);
+-
++        URL u = CompressTest.class.getResource(filename);
+         Fits f;
+         if (useComp) {
+             f = new Fits(u, comp);
+@@ -176,8 +170,9 @@ public class CompressTest {
+         return total(data);
+     }
+ 
+-    int streamRead(InputStream is, boolean comp, boolean useComp)
++    int streamRead(String filename, boolean comp, boolean useComp)
+             throws Exception {
++        InputStream is = CompressTest.class.getResourceAsStream(filename);
+         Fits f;
+         if (useComp) {
+             f = new Fits(is, comp);
+@@ -190,8 +185,9 @@ public class CompressTest {
+         return total(data);
+     }
+ 
+-    int fileRead(File is, boolean comp, boolean useComp)
++    int fileRead(String filename, boolean comp, boolean useComp)
+             throws Exception {
++        File is = new File(CompressTest.class.getResource(filename).getPath());
+         Fits f;
+         if (useComp) {
+             f = new Fits(is, comp);
+@@ -203,8 +199,9 @@ public class CompressTest {
+         return total(data);
+     }
+ 
+-    int stringRead(String is, boolean comp, boolean useComp)
++    int stringRead(String filename, boolean comp, boolean useComp)
+             throws Exception {
++        String is = CompressTest.class.getResource(filename).getPath();
+         Fits f;
+         if (useComp) {
+             f = new Fits(is, comp);
diff --git a/dev-java/fits/files/02-Update-ArrayFuncsTest.java-to-JUnit-4.patch b/dev-java/fits/files/02-Update-ArrayFuncsTest.java-to-JUnit-4.patch
new file mode 100644
index 000000000..c9cd02d55
--- /dev/null
+++ b/dev-java/fits/files/02-Update-ArrayFuncsTest.java-to-JUnit-4.patch
@@ -0,0 +1,223 @@
+From b9edd6a86e66d354b0c1d010125246d8359cbb37 Mon Sep 17 00:00:00 2001
+From: W. Trevor King <wking@drexel.edu>
+Date: Fri, 7 Oct 2011 03:44:18 -0400
+Subject: [PATCH 7/8] Update ArrayFuncsTest.java to JUnit-4.
+
+---
+ src/nom/tam/util/test/ArrayFuncsTest.java |   44 +++++++++++++++++++---------
+ 1 files changed, 30 insertions(+), 14 deletions(-)
+
+diff --git a/src/nom/tam/util/test/ArrayFuncsTest.java b/src/nom/tam/util/test/ArrayFuncsTest.java
+index df5efb0..7ad8e51 100644
+--- a/src/nom/tam/util/test/ArrayFuncsTest.java
++++ b/src/nom/tam/util/test/ArrayFuncsTest.java
+@@ -6,6 +6,12 @@
+  */

+ package nom.tam.util.test;

+ 

++import org.junit.Test;

++import static org.junit.Assert.assertEquals;

++import static org.junit.Assert.assertTrue;

++import static org.junit.Assert.assertFalse;

++import static org.junit.Assert.assertSame;

++import static org.junit.Assert.assertNotSame;

+ import junit.framework.*;

+ import java.lang.reflect.*;

+ import java.util.Arrays;

+@@ -15,21 +21,12 @@ import nom.tam.util.ArrayFuncs;
+  *

+  * @author Thomas McGlynn

+  */

+-public class ArrayFuncsTest extends TestCase {

+-

+-    public ArrayFuncsTest(String testName) {

+-        super(testName);

+-    }

+-

+-    protected void setUp() throws Exception {

+-    }

+-

+-    protected void tearDown() throws Exception {

+-    }

++public class ArrayFuncsTest {

+ 

+     /**

+      * Test of computeSize method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testComputeSize() {

+         System.out.println("computeSize");

+ 

+@@ -58,6 +55,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of nElements method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testNElements() {

+         System.out.println("nElements");

+ 

+@@ -72,6 +70,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of deepClone method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testDeepClone() {

+         int[][] test = {{0, 1}, {2, 3}, {4, 5}};

+         int[][] result = (int[][]) nom.tam.util.ArrayFuncs.deepClone(test);

+@@ -96,6 +95,7 @@ public class ArrayFuncsTest extends TestCase {
+         }

+ 

+         public boolean equals(Object x) {

++	    System.out.println("checking equality");

+             return (x instanceof CloneTest)

+                     && (((CloneTest) x).value == this.value);

+         }

+@@ -104,6 +104,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of genericClone method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testGenericClone() {

+         System.out.println("genericClone");

+ 

+@@ -126,6 +127,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of copyArray method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testCopyArray() {

+         System.out.println("copyArray");

+ 

+@@ -138,6 +140,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of getDimensions method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testGetDimensions() {

+         System.out.println("getDimensions");

+ 

+@@ -157,6 +160,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of getBaseArray method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testGetBaseArray() {

+ 

+         int[][][] test = new int[2][3][4];

+@@ -169,6 +173,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of getBaseClass method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testGetBaseClass() {

+         System.out.println("getBaseClass");

+ 

+@@ -179,6 +184,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of getBaseLength method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testGetBaseLength() {

+ 

+         assertEquals(ArrayFuncs.getBaseLength(new int[2][3]), 4);

+@@ -195,6 +201,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of generateArray method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testGenerateArray() {

+         System.out.println("generateArray");

+ 

+@@ -213,6 +220,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of testPattern method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testTestPattern() {

+         System.out.println("testPattern");

+ 

+@@ -229,6 +237,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of flatten method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testFlatten() {

+         System.out.println("flatten");

+ 

+@@ -241,6 +250,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of curl method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testCurl() {

+         System.out.println("curl");

+ 

+@@ -259,6 +269,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of mimicArray method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testMimicArray() {

+         System.out.println("mimicArray");

+ 

+@@ -273,6 +284,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of convertArray method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testConvertArray() {

+         System.out.println("convertArray");

+ 

+@@ -286,7 +298,7 @@ public class ArrayFuncsTest extends TestCase {
+ 

+         newType = int.class;

+         int[][] ires = (int[][]) ArrayFuncs.convertArray(array, newType, true);

+-        assertEquals(array, ires);

++        assertSame(array, ires);

+ 

+         ires = (int[][]) ArrayFuncs.convertArray(array, newType, false);

+         assertNotSame(array, ires);

+@@ -296,6 +308,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of copyInto method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testCopyInto() {

+         System.out.println("copyInto");

+ 

+@@ -304,13 +317,14 @@ public class ArrayFuncsTest extends TestCase {
+ 

+         ArrayFuncs.copyInto(x, y);

+ 

+-        assertEquals((double) x[0][0], y[0][0]);

+-        assertEquals((double) x[1][2], y[1][2]);

++        assertEquals((double) x[0][0], y[0][0], 0.01);

++        assertEquals((double) x[1][2], y[1][2], 0.01);

+     }

+ 

+     /**

+      * Test of arrayEquals method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testArrayEquals() {

+         System.out.println("arrayEquals");

+ 

+@@ -331,6 +345,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of doubleArrayEquals method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testDoubleArrayEquals() {

+ 

+         double x[] = {1, 2, 3};

+@@ -349,6 +364,7 @@ public class ArrayFuncsTest extends TestCase {
+     /**

+      * Test of floatArrayEquals method, of class nom.tam.util.ArrayFuncs.

+      */

++    @Test

+     public void testFloatArrayEquals() {

+         float x[] = {1f, 2f, 3f};

+         float y[] = {1f, 2f, 3f};

+-- 
+1.7.3.1.104.gc752e
+
diff --git a/dev-java/fits/files/README.Gentoo b/dev-java/fits/files/README.Gentoo
new file mode 100644
index 000000000..62c238cdd
--- /dev/null
+++ b/dev-java/fits/files/README.Gentoo
@@ -0,0 +1,44 @@
+I have been unable to track down a source repository for fits, so this
+ebuild straps a build system onto source unpacked from a source JAR.
+Not the greatest solution, but it's the best I can come up with.  I've
+also had trouble figuring out who holds copyright and what the
+licensing terms are.  If you find more authoritative information, let
+me know!
+
+Authors (listed with the first release note to mention them):
+  Tom McGlynn <thomas.a.mcglynn@nasa.gov> [1,12]
+  Jens Knudstrup [2]
+  Alan Brighton [2]
+  R.J. Mathar [3]
+  Jorgo Bakker [3]
+  Laurent Michel [3]
+  R. Mathar [4]
+  Guillame Belanger [4]
+  A. Kovacs [5]
+  Javier Diaz [6]
+  Juan Carlos Segovia [7]
+  Thomas Granzer [7]
+  L. Michel [8]
+  Mark Taylor [9]
+  Laurent Bourges [10]
+  V. Forchi [11]
+
+From [11]:
+
+> [The] build procedure for FITS library has been changed. The library
+> is now stored as a NetBeans project and the standard NetBeans build
+> script has been modified to generate the fits.jar and fits_src.jar.
+
+
+[1]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v0.9/NOTES/NOTE.v091
+[2]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v0.9/NOTES/NOTE.v093
+[3]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v0.9/NOTES/NOTE.v099
+[4]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v0.9/NOTES/NOTE.v099.1
+[5]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v0.9/NOTES/NOTE.v099.5
+[6]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v100.1
+[7]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v101.0
+[8]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v102.0
+[9]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v104.0
+[10]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v105.0
+[11]: http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v105.1
+[12]: http://asd.gsfc.nasa.gov/Thomas.McGlynn/
diff --git a/dev-java/fits/files/build.xml b/dev-java/fits/files/build.xml
new file mode 100644
index 000000000..d8aa41b85
--- /dev/null
+++ b/dev-java/fits/files/build.xml
@@ -0,0 +1,84 @@
+<?xml version="1.0"?>
+<project name="fits" default="all" basedir=".">
+  <target name="init" description="Sets build properties">
+    <!-- package configuration -->
+    <property name="package.version" value="devel"/>
+    <!-- directory locations -->
+    <property name="src" value="${basedir}/src"/>
+    <property name="build" value="${basedir}/build"/>
+    <property name="doc" value="${basedir}/doc"/>
+    <property name="doc.api" value="${doc}/api"/>
+    <!-- external dependencies -->
+    <property name="junit.jar" value="junit.jar"/>
+    <!-- classpaths -->
+    <path id="project.class.path">
+    </path>
+    <path id="build.class.path">
+      <pathelement location="${junit.jar}"/>
+    </path>
+    <path id="test.class.path">
+      <pathelement location="${build}"/>
+    </path>
+  </target>
+  <target name="all" depends="jar,javadoc"
+          description="Pseudo-target that builds JAR and Javadoc">
+  </target>
+  <target name="build" depends="init"
+          description="Compiles the classes">
+    <mkdir dir="${build}"/>
+    <javac destdir="${build}" srcdir="${src}" debug="true"
+           deprecation="true" includeantruntime="false">
+      <classpath refid="project.class.path"/>
+      <classpath refid="build.class.path"/>
+      <!--compilerarg line="-Xlint:unchecked"/-->
+    </javac>
+    <copy todir="${build}">
+      <mappedresources>
+        <fileset dir="${src}" includes="**/test/test.fits*"/>
+        <globmapper from="*" to="*"/>
+      </mappedresources>
+    </copy>
+  </target>
+  <target name="test" depends="build">
+    <junit>
+      <classpath refid="project.class.path" />
+      <classpath refid="test.class.path"/>
+      <formatter type="brief" usefile="false" />
+      <batchtest>
+        <fileset dir="${build}">
+          <include name="**/test/*.class" />
+          <exclude name="**/*$*.class" />
+        </fileset>
+      </batchtest>
+    </junit>
+  </target>
+  <target name="javadoc" depends="init"
+          description="Generates Javadoc API documentation">
+    <mkdir dir="${doc.api}"/>
+    <javadoc packagenames="*"
+             sourcepath="${src}" destdir="${doc.api}"
+             author="true"       version="true"
+             use="true"          private="true">
+      <classpath refid="project.class.path" />
+      <classpath refid="build.class.path"/>
+    </javadoc>
+  </target>
+  <target name="jar" depends="build"
+          description="Builds a project JAR file">
+    <jar basedir="${build}" jarfile="${build}/fits.jar">
+      <manifest>
+        <attribute name="Version" value="${package.version}"/>
+      </manifest>
+    </jar>
+  </target>
+  <target name="clean" depends="init"
+          description="Erase all generated files and dirs">
+    <delete dir="${build}" verbose="true"/>
+    <delete dir="${doc}/api" verbose="true"/>
+    <delete verbose="true">
+        <fileset dir="${basedir}" includes="*.fits"/>
+        <fileset dir="${basedir}" includes="*.fil"/>
+        <fileset dir="${basedir}" includes="*.hdr"/>
+    </delete>
+  </target>
+</project>