Merge pull request #64 from jamesmudd/prepare-v0.4.0

Prepare v0.4.0
jamesmudd · Mar 11, 2019 · 828d071 · 828d071
2 parents 4af166c + 40901ff
commit 828d071
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diff --git a/CHANGES.md b/CHANGES.md
@@ -2,6 +2,16 @@
 
 Please note this project is still in pre-release development.
 
+## v0.4.0
+- Add support for accessing attributes (see [Attribute.java](jhdf/src/main/java/io/jhdf/api/Attribute.java))
+- Add support for scalar datasets
+- Add support for empty datasets
+- Add support for files with user blocks
+- Fix bug where "old" style groups containing soft links could not be opened
+- Fix bug reading unsigned numbers from "awkward" buffer sizes
+- Lots of minor code cleanup and refactoring
+- Improvements to tests and coverage
+
 ## v0.3.2
 - Fix bug when fixed size string datasets contain strings of exactly that size.
 - Fix bug where >1D fixed size datasets could not be read

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018 James Mudd
+Copyright (c) 2019 James Mudd
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/jhdf/build.gradle b/jhdf/build.gradle
@@ -16,7 +16,7 @@ plugins {
 
 // Varibles
 group = 'io.jhdf'
-version = '0.3.2'
+version = '0.4.0'
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
 

diff --git a/jhdf/src/main/java/io/jhdf/AbstractNode.java b/jhdf/src/main/java/io/jhdf/AbstractNode.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 import static java.util.stream.Collectors.toMap;
@@ -159,4 +168,4 @@ public Map<String, Attribute> getAttributes() {
 	public Attribute getAttribute(String name) {
 		return getAttributes().get(name);
 	}
-}
+}
diff --git a/jhdf/src/main/java/io/jhdf/AttributeImpl.java b/jhdf/src/main/java/io/jhdf/AttributeImpl.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 import static org.apache.commons.lang3.ClassUtils.primitiveToWrapper;

diff --git a/jhdf/src/main/java/io/jhdf/Constants.java b/jhdf/src/main/java/io/jhdf/Constants.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 public final class Constants {

diff --git a/jhdf/src/main/java/io/jhdf/FractalHeap.java b/jhdf/src/main/java/io/jhdf/FractalHeap.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 import static io.jhdf.Constants.UNDEFINED_ADDRESS;

diff --git a/jhdf/src/main/java/io/jhdf/GlobalHeap.java b/jhdf/src/main/java/io/jhdf/GlobalHeap.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 import static io.jhdf.Utils.createSubBuffer;

diff --git a/jhdf/src/main/java/io/jhdf/GroupImpl.java b/jhdf/src/main/java/io/jhdf/GroupImpl.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 import java.nio.ByteBuffer;

diff --git a/jhdf/src/main/java/io/jhdf/GroupSymbolTableNode.java b/jhdf/src/main/java/io/jhdf/GroupSymbolTableNode.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 import static java.nio.ByteOrder.LITTLE_ENDIAN;

diff --git a/jhdf/src/main/java/io/jhdf/HdfFile.java b/jhdf/src/main/java/io/jhdf/HdfFile.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 import java.io.File;

diff --git a/jhdf/src/main/java/io/jhdf/HdfFileChannel.java b/jhdf/src/main/java/io/jhdf/HdfFileChannel.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 import static java.nio.ByteOrder.LITTLE_ENDIAN;

diff --git a/jhdf/src/main/java/io/jhdf/LocalHeap.java b/jhdf/src/main/java/io/jhdf/LocalHeap.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 import java.nio.ByteBuffer;

diff --git a/jhdf/src/main/java/io/jhdf/ObjectHeader.java b/jhdf/src/main/java/io/jhdf/ObjectHeader.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 import static io.jhdf.Utils.readBytesAsUnsignedInt;

diff --git a/jhdf/src/main/java/io/jhdf/Superblock.java b/jhdf/src/main/java/io/jhdf/Superblock.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 import static io.jhdf.Utils.toHex;

diff --git a/jhdf/src/main/java/io/jhdf/SymbolTableEntry.java b/jhdf/src/main/java/io/jhdf/SymbolTableEntry.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 import static io.jhdf.Utils.toHex;

diff --git a/jhdf/src/main/java/io/jhdf/Utils.java b/jhdf/src/main/java/io/jhdf/Utils.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf;
 
 import static java.nio.ByteOrder.LITTLE_ENDIAN;

diff --git a/jhdf/src/main/java/io/jhdf/api/Attribute.java b/jhdf/src/main/java/io/jhdf/api/Attribute.java
@@ -1,5 +1,29 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
+/*
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see LICENSE file
+ */
 package io.jhdf.api;
 
+/**
+ * Interface for HDF5 attributes. Attributes can be attached to {@link Group}s
+ * or {@link Dataset}s. They contain metadata about that object.
+ * 
+ * @author James Mudd
+ */
 public interface Attribute {
 
 	/**

diff --git a/jhdf/src/main/java/io/jhdf/api/Dataset.java b/jhdf/src/main/java/io/jhdf/api/Dataset.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf.api;
 
 import io.jhdf.object.message.DataLayout;
@@ -86,4 +95,4 @@ public interface Dataset extends Node {
 	 */
 	Class<?> getJavaType();
 
-}
+}
diff --git a/jhdf/src/main/java/io/jhdf/api/Group.java b/jhdf/src/main/java/io/jhdf/api/Group.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf.api;
 
 import java.util.Map;

diff --git a/jhdf/src/main/java/io/jhdf/api/Link.java b/jhdf/src/main/java/io/jhdf/api/Link.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf.api;
 
 public interface Link extends Node {

diff --git a/jhdf/src/main/java/io/jhdf/api/Node.java b/jhdf/src/main/java/io/jhdf/api/Node.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf.api;
 
 import java.io.File;

diff --git a/jhdf/src/main/java/io/jhdf/api/NodeType.java b/jhdf/src/main/java/io/jhdf/api/NodeType.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf.api;
 
 public enum NodeType {

diff --git a/jhdf/src/main/java/io/jhdf/api/package-info.java b/jhdf/src/main/java/io/jhdf/api/package-info.java
@@ -1,6 +1,15 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 /**
  * The API classes for accessing HDF5 files using the jHDF library.
  * 
  * @author James Mudd
  */
-package io.jhdf.api;
+package io.jhdf.api;
diff --git a/jhdf/src/main/java/io/jhdf/btree/BTreeV1.java b/jhdf/src/main/java/io/jhdf/btree/BTreeV1.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf.btree;
 
 import java.nio.ByteBuffer;
@@ -116,4 +125,4 @@ public long getAddress() {
 
 	public abstract List<Long> getChildAddresses();
 
-}
+}
diff --git a/jhdf/src/main/java/io/jhdf/btree/BTreeV1Data.java b/jhdf/src/main/java/io/jhdf/btree/BTreeV1Data.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf.btree;
 
 import static java.util.stream.Collectors.toList;
@@ -165,4 +174,4 @@ public List<Long> getChildAddresses() {
 			return childAddresses;
 		}
 	}
-}
+}
diff --git a/jhdf/src/main/java/io/jhdf/btree/BTreeV1Group.java b/jhdf/src/main/java/io/jhdf/btree/BTreeV1Group.java
@@ -1,3 +1,12 @@
+/*******************************************************************************
+ * This file is part of jHDF. A pure Java library for accessing HDF5 files.
+ * 
+ * http://jhdf.io
+ * 
+ * Copyright 2019 James Mudd
+ * 
+ * MIT License see 'LICENSE' file
+ ******************************************************************************/
 package io.jhdf.btree;
 
 import java.nio.ByteBuffer;