Merge pull request #140 from jamesmudd/prepare-v0.5.3

Prepare v0.5.3

Author: jamesmudd

Diff for: CHANGES.md

@@ -1,5 +1,11 @@
 # jHDF Change Log
 
+## v0.5.3
+- Add support for chunked v4 datasets with b-tree chunk indexing
+- Improve exceptions for unsupported b-tree records
+- Improve test coverage
+- Upgrade to Gradle 6.0.1
+
 ## v0.5.2
 - Fix https://github.com/jamesmudd/jhdf/issues/124 String padding not handled correctly.
 - Fix https://github.com/jamesmudd/jhdf/issues/132 Multi dimensional fixed length string datasets read incorrectly.

Diff for: jhdf/build.gradle

@@ -26,7 +26,7 @@ plugins {
 
 // Variables
 group = 'io.jhdf'
-version = '0.5.2'
+version = '0.5.3'
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
 // Set source encoding to UTF-8

Diff for: jhdf/src/main/java/io/jhdf/dataset/chunked/ChunkedDatasetBase.java

@@ -112,7 +112,10 @@ private boolean partOfChunkIsOutsideDataset(final int chunkInternalOffsetIndex,
     /**
      * Calculates the linear offsets into the dataset for each of the chunks internal offsets. It can be thought of as
      * only doing this do the first chunk as to calculate the offsets required for any other chunk you need to add
-     * the inital linear offset of that chunk to each of these values.
+     * the initial linear offset of that chunk to each of these values.
+     *
+     * @param chunkInternalOffsets a chunk offset
+     * @return offset in the dataset
      */
     protected int[] getDataOffsets(int[] chunkInternalOffsets) {
 
@@ -165,6 +168,8 @@ public ByteBuffer getDataBuffer() {
 
     /**
      * Gets the number of linear steps to move for one step in the corresponding dimension
+     *
+     * @return array of the number of linear step to move for one step in each dimension
      */
     private int[] getDimensionLinearOffsets() {
         int dimLength = getDimensions().length;
@@ -181,6 +186,10 @@ private int[] getDimensionLinearOffsets() {
 
     /**
      * Gets the offsets inside a chunk where a contiguous run of data starts.
+     *
+     * @param chunkDimensions the dimensions of each chunk
+     * @param elementSize number of bytes in a an dataset element
+     * @return an array of locations inside the chunk where contiguous data starts
      */
     protected int[] getChunkInternalOffsets(int[] chunkDimensions, int elementSize) {
         final int fastestChunkDim = chunkDimensions[chunkDimensions.length - 1];
@@ -198,6 +207,9 @@ protected int[] getChunkInternalOffsets(int[] chunkDimensions, int elementSize)
     /**
      * A partial chunk is one that is not completely inside the dataset. i.e. some of its contents are not part of the
      * dataset
+     *
+     * @param chunk The chunk to test
+     * @return true if this is a partial chunk
      */
     private boolean isPartialChunk(Chunk chunk) {
         final int[] datasetDims = getDimensions();