[med-svn] [Git][med-team/libsis-base-java][master] 10 commits: New upstream version 18.09~pre1+git20180928.45fbd31+dfsg
Andreas Tille
gitlab at salsa.debian.org
Tue Oct 27 19:56:34 GMT 2020
Andreas Tille pushed to branch master at Debian Med / libsis-base-java
Commits:
1a7b930d by Andreas Tille at 2020-10-27T20:51:16+01:00
New upstream version 18.09~pre1+git20180928.45fbd31+dfsg
- - - - -
a209f59d by Andreas Tille at 2020-10-27T20:51:16+01:00
routine-update: New upstream version
- - - - -
917eb148 by Andreas Tille at 2020-10-27T20:51:17+01:00
Update upstream source from tag 'upstream/18.09_pre1+git20180928.45fbd31+dfsg'
Update to upstream version '18.09~pre1+git20180928.45fbd31+dfsg'
with Debian dir 7801051a85aa1d66757c8e7ee7d17d1652b0b4da
- - - - -
cee0017e by Andreas Tille at 2020-10-27T20:51:17+01:00
routine-update: Standards-Version: 4.5.0
- - - - -
01252290 by Andreas Tille at 2020-10-27T20:51:17+01:00
routine-update: debhelper-compat 13
- - - - -
de95cb61 by Andreas Tille at 2020-10-27T20:51:53+01:00
routine-update: Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
66dced7f by Andreas Tille at 2020-10-27T20:51:53+01:00
routine-update: Remove trailing whitespace in debian/copyright
- - - - -
25d10f57 by Andreas Tille at 2020-10-27T20:51:54+01:00
routine-update: Remove trailing whitespace in debian/rules
- - - - -
ede788a7 by Andreas Tille at 2020-10-27T20:51:54+01:00
routine-update: Add salsa-ci file
- - - - -
06b41fe6 by Andreas Tille at 2020-10-27T20:51:54+01:00
routine-update: Rules-Requires-Root: no
- - - - -
15 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- debian/rules
- + debian/salsa-ci.yml
- source/java/ch/systemsx/cisd/base/mdarray/MDAbstractArray.java
- source/java/ch/systemsx/cisd/base/mdarray/MDByteArray.java
- source/java/ch/systemsx/cisd/base/mdarray/MDDoubleArray.java
- source/java/ch/systemsx/cisd/base/mdarray/MDFloatArray.java
- source/java/ch/systemsx/cisd/base/mdarray/MDIntArray.java
- source/java/ch/systemsx/cisd/base/mdarray/MDLongArray.java
- source/java/ch/systemsx/cisd/base/mdarray/MDShortArray.java
- source/java/ch/systemsx/cisd/base/utilities/NativeLibraryUtilities.java
- sourceTest/java/ch/systemsx/cisd/base/mdarray/MDArrayTests.java
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+libsis-base-java (18.09~pre1+git20180928.45fbd31+dfsg-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine-
+ update)
+ * Remove trailing whitespace in debian/copyright (routine-update)
+ * Remove trailing whitespace in debian/rules (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Tue, 27 Oct 2020 20:51:16 +0100
+
libsis-base-java (18.09~pre1+git20180827.fe4953e+dfsg-1) unstable; urgency=medium
* Temporarily use Git HEAD since latest HEAD is needed to package
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
Andreas Tille <tille at debian.org>
Section: java
Priority: optional
-Build-Depends: debhelper (>= 11),
+Build-Depends: debhelper-compat (= 13),
default-jdk,
javahelper,
libcommons-lang3-java,
@@ -13,10 +13,11 @@ Build-Depends: debhelper (>= 11),
testng,
libtool,
procps
-Standards-Version: 4.2.1
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/libsis-base-java
Vcs-Git: https://salsa.debian.org/med-team/libsis-base-java.git
Homepage: https://sissource.ethz.ch/sispub/base
+Rules-Requires-Root: no
Package: libsis-base-java
Architecture: all
=====================================
debian/copyright
=====================================
@@ -15,16 +15,16 @@ Files: source/c/*
Copyright: 1988-2004, the Board of Trustees of the University of Illinois.
2007-2018, Center for Information Sciences and Databases, ETH Zurich, Switzerland.
License: hdf5
- Contributors to the library: National Center for Supercomputing
- Applications (NCSA) at the University of Illinois, Lawrence
- Livermore Nationall Laboratory (LLNL), Sandia National Laboratories (SNL),
- Los Alamos National Laboratory (LANL). Fortner Software, Unidata
- Program Center (netCDF), The Independent JPEG Group (JPEG),
- Jean-loup Gailly and Mark Adler ($gzip), and Digital Equipment
+ Contributors to the library: National Center for Supercomputing
+ Applications (NCSA) at the University of Illinois, Lawrence
+ Livermore Nationall Laboratory (LLNL), Sandia National Laboratories (SNL),
+ Los Alamos National Laboratory (LANL). Fortner Software, Unidata
+ Program Center (netCDF), The Independent JPEG Group (JPEG),
+ Jean-loup Gailly and Mark Adler ($gzip), and Digital Equipment
Corporation (DEC). Macintosh support contributed by Gregory L. Guerin.
Center for Information Sciences and Databases, ETH Zurich, Switzerland
.
- This work was supported in part by a Cooperative Agreement with
+ This work was supported in part by a Cooperative Agreement with
NASA under NASA grant NAG 5-2040 and NAG NCC5-599.
.
Redistribution and use in source and binary forms, with or without
@@ -58,7 +58,7 @@ License: hdf5
advised of the possibility of such damage.
.
--------------------------------------------------------------------------
- Portions of HDF5 were developed with support from the University of
+ Portions of HDF5 were developed with support from the University of
California, Lawrence Livermore National Laboratory (UC LLNL).
The following statement applies to those portions of the product
and must be retained in any redistribution of source code, binaries,
@@ -66,25 +66,25 @@ License: hdf5
.
This work was partially produced at the University of California,
Lawrence Livermore National Laboratory (UC LLNL) under contract no.
- W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy
- (DOE) and The Regents of the University of California (University)
+ W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy
+ (DOE) and The Regents of the University of California (University)
for the operation of UC LLNL.
.
DISCLAIMER:
- This work was prepared as an account of work sponsored by an agency
- of the United States Government. Neither the United States
- Government nor the University of California nor any of their
- employees, makes any warranty, express or implied, or assumes any
- liability or responsibility for the accuracy, completeness, or
- usefulness of any information, apparatus, product, or process
+ This work was prepared as an account of work sponsored by an agency
+ of the United States Government. Neither the United States
+ Government nor the University of California nor any of their
+ employees, makes any warranty, express or implied, or assumes any
+ liability or responsibility for the accuracy, completeness, or
+ usefulness of any information, apparatus, product, or process
disclosed, or represents that its use would not infringe privately-
- owned rights. Reference herein to any specific commercial products,
- process, or service by trade name, trademark, manufacturer, or
- otherwise, does not necessarily constitute or imply its endorsement,
- recommendation, or favoring by the United States Government or the
- University of California. The views and opinions of authors
- expressed herein do not necessarily state or reflect those of the
- United States Government or the University of California, and shall
+ owned rights. Reference herein to any specific commercial products,
+ process, or service by trade name, trademark, manufacturer, or
+ otherwise, does not necessarily constitute or imply its endorsement,
+ recommendation, or favoring by the United States Government or the
+ University of California. The views and opinions of authors
+ expressed herein do not necessarily state or reflect those of the
+ United States Government or the University of California, and shall
not be used for advertising or product endorsement purposes.
--------------------------------------------------------------------------
=====================================
debian/rules
=====================================
@@ -29,7 +29,7 @@ override_dh_auto_clean:
if test -e source/c/Makefile; then cd source/c; make clean; fi
rm -f source/c/AUTHORS source/c/NEWS source/c/README source/c/ChangeLog
rm -rf source/c/configure* source/c/Makefile* source/c/autom4te.cache source/c/.deps
- rm -rf src lib build *.jar test .classpath libs
+ rm -rf src lib build *.jar test .classpath libs
#find test -name '*.class' -delete
dh_auto_clean
@@ -41,7 +41,9 @@ override_dh_auto_build:
cd source/c ; ./configure && make
override_dh_auto_test-arch:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
dh_auto_test -a
mkdir test ; cp -r source/java/ch test ; cp -r sourceTest/java/ch test
jh_build sis-base-test.jar test
LC_ALL=C java -Djava.library.path=source/c/.libs -classpath sis-base-test.jar ch.systemsx.cisd.base.AllTests
+endif
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
source/java/ch/systemsx/cisd/base/mdarray/MDAbstractArray.java
=====================================
@@ -105,6 +105,14 @@ public abstract class MDAbstractArray<T> implements Serializable,
}
}
+ protected MDAbstractArray(MDAbstractArray<T> template)
+ {
+ this.dimensions = template.dimensions.clone();
+ this.hyperRowLength = template.hyperRowLength;
+ this.capacityHyperRows = template.capacityHyperRows;
+ this.size = template.size;
+ }
+
protected int computeHyperRowLength(@SuppressWarnings("hiding")
int[] dimensions)
{
=====================================
source/java/ch/systemsx/cisd/base/mdarray/MDByteArray.java
=====================================
@@ -153,6 +153,15 @@ public final class MDByteArray extends MDAbstractArray<Byte>
}
}
+ /**
+ * Creates an independent copy (clone) of the <var>template</var> provided.
+ */
+ public MDByteArray(MDByteArray template)
+ {
+ super(template);
+ this.flattenedArray = template.flattenedArray.clone();
+ }
+
private static int[] getDimensions(byte[][] matrix)
{
assert matrix != null;
@@ -373,4 +382,10 @@ public final class MDByteArray extends MDAbstractArray<Byte>
}
}
+ @Override
+ public MDByteArray clone()
+ {
+ return new MDByteArray(this);
+ }
+
}
=====================================
source/java/ch/systemsx/cisd/base/mdarray/MDDoubleArray.java
=====================================
@@ -153,6 +153,15 @@ public final class MDDoubleArray extends MDAbstractArray<Double>
}
}
+ /**
+ * Creates an independent copy (clone) of the <var>template</var> provided.
+ */
+ public MDDoubleArray(MDDoubleArray template)
+ {
+ super(template);
+ this.flattenedArray = template.flattenedArray.clone();
+ }
+
private static int[] getDimensions(double[][] matrix)
{
assert matrix != null;
@@ -373,4 +382,10 @@ public final class MDDoubleArray extends MDAbstractArray<Double>
}
}
+ @Override
+ public MDDoubleArray clone()
+ {
+ return new MDDoubleArray(this);
+ }
+
}
=====================================
source/java/ch/systemsx/cisd/base/mdarray/MDFloatArray.java
=====================================
@@ -153,6 +153,15 @@ public final class MDFloatArray extends MDAbstractArray<Float>
}
}
+ /**
+ * Creates an independent copy (clone) of the <var>template</var> provided.
+ */
+ public MDFloatArray(MDFloatArray template)
+ {
+ super(template);
+ this.flattenedArray = template.flattenedArray.clone();
+ }
+
private static int[] getDimensions(float[][] matrix)
{
assert matrix != null;
@@ -373,4 +382,10 @@ public final class MDFloatArray extends MDAbstractArray<Float>
}
}
+ @Override
+ public MDFloatArray clone()
+ {
+ return new MDFloatArray(this);
+ }
+
}
=====================================
source/java/ch/systemsx/cisd/base/mdarray/MDIntArray.java
=====================================
@@ -153,6 +153,15 @@ public final class MDIntArray extends MDAbstractArray<Integer>
}
}
+ /**
+ * Creates an independent copy (clone) of the <var>template</var> provided.
+ */
+ public MDIntArray(MDIntArray template)
+ {
+ super(template);
+ this.flattenedArray = template.flattenedArray.clone();
+ }
+
private static int[] getDimensions(int[][] matrix)
{
assert matrix != null;
@@ -373,4 +382,10 @@ public final class MDIntArray extends MDAbstractArray<Integer>
}
}
+ @Override
+ public MDIntArray clone()
+ {
+ return new MDIntArray(this);
+ }
+
}
=====================================
source/java/ch/systemsx/cisd/base/mdarray/MDLongArray.java
=====================================
@@ -153,6 +153,15 @@ public final class MDLongArray extends MDAbstractArray<Long>
}
}
+ /**
+ * Creates an independent copy (clone) of the <var>template</var> provided.
+ */
+ public MDLongArray(MDLongArray template)
+ {
+ super(template);
+ this.flattenedArray = template.flattenedArray.clone();
+ }
+
private static int[] getDimensions(long[][] matrix)
{
assert matrix != null;
@@ -373,4 +382,10 @@ public final class MDLongArray extends MDAbstractArray<Long>
}
}
+ @Override
+ public MDLongArray clone()
+ {
+ return new MDLongArray(this);
+ }
+
}
=====================================
source/java/ch/systemsx/cisd/base/mdarray/MDShortArray.java
=====================================
@@ -153,6 +153,15 @@ public final class MDShortArray extends MDAbstractArray<Short>
}
}
+ /**
+ * Creates an independent copy (clone) of the <var>template</var> provided.
+ */
+ public MDShortArray(MDShortArray template)
+ {
+ super(template);
+ this.flattenedArray = template.flattenedArray.clone();
+ }
+
private static int[] getDimensions(short[][] matrix)
{
assert matrix != null;
@@ -373,4 +382,10 @@ public final class MDShortArray extends MDAbstractArray<Short>
}
}
+ @Override
+ public MDShortArray clone()
+ {
+ return new MDShortArray(this);
+ }
+
}
=====================================
source/java/ch/systemsx/cisd/base/utilities/NativeLibraryUtilities.java
=====================================
@@ -102,7 +102,7 @@ import java.util.zip.ZipFile;
* mandatory locks make this impossible). This is the 'auto mode' and thus the simplest way of using this utility class for the user of your
* program.</li>
* <li>Finally, if no appropriate structure is found in the classpath, {@link #loadNativeLibrary(String)} will fall back to the Java default method of
- * loading JNI libraries via {@link System#loadLibrary()}. This may require the Java property <code>java.library.path</code> to be set and it may
+ * loading JNI libraries via {@link System#loadLibrary(String)}. This may require the Java property <code>java.library.path</code> to be set and it may
* require the library to follow a platform specific naming convention for the native shared library file.</li>
* </ol>
*
=====================================
sourceTest/java/ch/systemsx/cisd/base/mdarray/MDArrayTests.java
=====================================
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.base.mdarray;
+import static org.testng.Assert.assertNotSame;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
@@ -288,6 +289,34 @@ public class MDArrayTests
}
}
+ @Test
+ public void testCloneMDArray()
+ {
+ final float[][] matrix1 = new float[][]
+ {
+ { 1f, 2f, 3f, 4f },
+ { 5f, 6f, 7f, 8f },
+ { 9f, 10f, 11f, 12f } };
+ final MDFloatArray array = new MDFloatArray(matrix1);
+ final MDFloatArray array2 = array.clone();
+ assertNotSame(array2.getAsFlatArray(), array.getAsFlatArray());
+ assertNotSame(array2.dimensions, array.dimensions);
+ assertEquals(array2.hyperRowLength, array.hyperRowLength);
+ assertEquals(array2.capacityHyperRows, array.capacityHyperRows);
+ assertEquals(array2.size, array.size);
+ assertEquals(2, array2.rank());
+ assertEquals(12, array2.size());
+ assertEquals(3, array2.size(0));
+ assertEquals(4, array2.size(1));
+ assertEquals(7f, array2.get(1, 2));
+ final float[][] matrix2 = array2.toMatrix();
+ assertEquals(matrix1.length, matrix2.length);
+ for (int i = 0; i < matrix1.length; ++i)
+ {
+ assertTrue(Arrays.equals(matrix1[i], matrix2[i]));
+ }
+ }
+
public static void main(String[] args) throws Throwable
{
System.out.println(BuildAndEnvironmentInfo.INSTANCE);
View it on GitLab: https://salsa.debian.org/med-team/libsis-base-java/-/compare/761e4ec437fe15156fc8ffcd7c3a97004129aaef...06b41fe61b18f8b53186216351909409b67c3aad
--
View it on GitLab: https://salsa.debian.org/med-team/libsis-base-java/-/compare/761e4ec437fe15156fc8ffcd7c3a97004129aaef...06b41fe61b18f8b53186216351909409b67c3aad
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