Merge pull request #537 from jamesmudd/prepare-v0.7.0

Prepare v0.7.0-alpha
jamesmudd · Jan 31, 2024 · c428099 · c428099
2 parents 1392d9f + 72b1932
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,9 @@
 # jHDF Change Log
 
+## v0.7.0-alpha
+- Add initial HDF5 writing support! https://github.com/jamesmudd/jhdf/issues/354. Special thanks to [@thadguidry](https://github.com/thadguidry) for sponsoring this work. See [WriteHdf5.java](jhdf/src/main/java/io/jhdf/examples/WriteHdf5.java) for example usage.
+- Build and dependency updates
+
 ##  v0.6.10
 - Add support for files containing superblock extensions https://github.com/jamesmudd/jhdf/issues/462
 - Build and dependency updates

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # jHDF - Pure Java HDF5 library
 [![jHDF CI](https://github.com/jamesmudd/jhdf/actions/workflows/ci.yml/badge.svg)](https://github.com/jamesmudd/jhdf/actions/workflows/ci.yml) [![Coverage](https://sonarcloud.io/api/project_badges/measure?project=jamesmudd_jhdf&metric=coverage)](https://sonarcloud.io/dashboard?id=jamesmudd_jhdf) [![Maven Central](https://img.shields.io/maven-central/v/io.jhdf/jhdf.svg?label=Maven%20Central)](https://search.maven.org/artifact/io.jhdf/jhdf) [![Javadocs](http://javadoc.io/badge/io.jhdf/jhdf.svg)](http://javadoc.io/doc/io.jhdf/jhdf) [![JetBrains Supported](https://img.shields.io/badge/supported-project.svg?label=&colorA=grey&colorB=orange&logo=data%3Aimage%2Fsvg%2Bxml%3Bbase64%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%2BPHBhdGggZmlsbD0iI0ZGRkZGRiIgZD0iTTYuOCwxaDMuNGMwLjgsMCwxLjUsMC4yLDEuOSwwLjZjMC4zLDAuMywwLjUsMC43LDAuNSwxLjJsMCwwYzAsMC44LTAuNCwxLjMtMSwxLjZDMTIuNSw0LjgsMTMsNS4zLDEzLDYuMmwwLDBjMCwxLjMtMS4xLDItMi43LDJINi44VjF6IE0xMSwzLjFjMC0wLjUtMC40LTAuNy0xLTAuN0g4LjR2MS41aDEuNUMxMC42LDMuOSwxMSwzLjcsMTEsMy4xTDExLDMuMXogTTEwLjIsNS4zSDguNHYxLjZoMS45YzAuNywwLDEuMS0wLjIsMS4xLTAuOGwwLDBDMTEuNCw1LjYsMTEuMSw1LjMsMTAuMiw1LjN6Ii8%2BPHJlY3QgeD0iMSIgeT0iMTIiIGZpbGw9IiNGRkZGRkYiIHdpZHRoPSI3IiBoZWlnaHQ9IjEiLz48L3N2Zz4%3D)](https://www.jetbrains.com/?from=jhdf) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3996097.svg)](https://doi.org/10.5281/zenodo.3996097)
 
-This project is a pure Java implementation for accessing HDF5 files. It is written from the file format specification and is not using any HDF Group code, it is *not* a wrapper around the C libraries. The file format specification is available from the HDF Group [here](https://portal.hdfgroup.org/display/HDF5/File+Format+Specification). More information on the format is available on [Wikipedia](https://en.wikipedia.org/wiki/Hierarchical_Data_Format).
+This project is a pure Java implementation for accessing HDF5 files. It is written from the file format specification and is not using any HDF Group code, it is *not* a wrapper around the C libraries. The file format specification is available from the HDF Group [here](https://docs.hdfgroup.org/hdf5/v1_10/_f_m_t3.html). More information on the format is available on [Wikipedia](https://en.wikipedia.org/wiki/Hierarchical_Data_Format).
 
 The intention is to make a clean Java API to access HDF5 data. Currently, the project is targeting HDF5 read-only compatibility. For progress see the [change log](CHANGES.md). Java 8, 11 and 17 are officially supported.
 

diff --git a/jhdf/build.gradle b/jhdf/build.gradle
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */
@@ -27,7 +27,7 @@ plugins {
 
 // Variables
 group = 'io.jhdf'
-version = '0.6.10'
+version = '0.7.0-alpha'
 
 compileJava {
     sourceCompatibility = "1.8"
@@ -158,6 +158,10 @@ publishing {
                     developerConnection = 'scm:git:git://github.com/jamesmudd/jhdf.git'
                     url = 'https://github.com/jamesmudd/jhdf.git'
                 }
+                issueManagement {
+                    system = 'github'
+                    url = 'https://github.com/jamesmudd/jhdf/issues'
+                }
             }
         }
     }

diff --git a/jhdf/config/checkstyle/header.txt b/jhdf/config/checkstyle/header.txt
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */
diff --git a/jhdf/gradle.properties b/jhdf/gradle.properties
@@ -3,7 +3,7 @@
 #
 # http://jhdf.io
 #
-# Copyright (c) 2023 James Mudd
+# Copyright (c) 2024 James Mudd
 #
 # MIT License see 'LICENSE' file
 #-------------------------------------------------------------------------------

diff --git a/jhdf/settings.gradle b/jhdf/settings.gradle
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/jmh/java/io/jhdf/benchmarks/MemoryMapBenchmark.java b/jhdf/src/jmh/java/io/jhdf/benchmarks/MemoryMapBenchmark.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/AbstractNode.java b/jhdf/src/main/java/io/jhdf/AbstractNode.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/AbstractWritableNode.java b/jhdf/src/main/java/io/jhdf/AbstractWritableNode.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/AttributeImpl.java b/jhdf/src/main/java/io/jhdf/AttributeImpl.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/BufferBuilder.java b/jhdf/src/main/java/io/jhdf/BufferBuilder.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/CommittedDatatype.java b/jhdf/src/main/java/io/jhdf/CommittedDatatype.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/Constants.java b/jhdf/src/main/java/io/jhdf/Constants.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/FractalHeap.java b/jhdf/src/main/java/io/jhdf/FractalHeap.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/GlobalHeap.java b/jhdf/src/main/java/io/jhdf/GlobalHeap.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/GroupImpl.java b/jhdf/src/main/java/io/jhdf/GroupImpl.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/GroupSymbolTableNode.java b/jhdf/src/main/java/io/jhdf/GroupSymbolTableNode.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/HdfFile.java b/jhdf/src/main/java/io/jhdf/HdfFile.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/LocalHeap.java b/jhdf/src/main/java/io/jhdf/LocalHeap.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/ObjectHeader.java b/jhdf/src/main/java/io/jhdf/ObjectHeader.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/Superblock.java b/jhdf/src/main/java/io/jhdf/Superblock.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/SymbolTableEntry.java b/jhdf/src/main/java/io/jhdf/SymbolTableEntry.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/Utils.java b/jhdf/src/main/java/io/jhdf/Utils.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/WritableDatasetImpl.java b/jhdf/src/main/java/io/jhdf/WritableDatasetImpl.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/WritableGroupImpl.java b/jhdf/src/main/java/io/jhdf/WritableGroupImpl.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/WritableHdfFile.java b/jhdf/src/main/java/io/jhdf/WritableHdfFile.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */
@@ -42,11 +42,10 @@ public class WritableHdfFile implements WritableGroup, AutoCloseable {
 	private final FileChannel fileChannel;
 	private final Superblock.SuperblockV2V3 superblock;
 	private final HdfFileChannel hdfFileChannel;
-	private ObjectHeader.ObjectHeaderV2 rootGroupObjectHeader;
-
 	private final WritableGroup rootGroup;
 
-	public WritableHdfFile(Path path) {
+	WritableHdfFile(Path path) {
+		logger.warn("Writing files is in alpha. Check files carefully!");
 		logger.info("Writing HDF5 file to [{}]", path.toAbsolutePath());
 		this.path = path;
 		try {
@@ -58,24 +57,7 @@ public WritableHdfFile(Path path) {
 		this.hdfFileChannel = new HdfFileChannel(this.fileChannel, this.superblock);
 
 		this.rootGroup = new WritableGroupImpl(null, "/");
-//		createRootGroup();
-//		try {
-//			hdfFileChannel.write(superblock.toBuffer(), 0L);
-//			long endOfFile = rootGroup.write(hdfFileChannel, ROOT_GROUP_ADDRESS);
-////			hdfFileChannel.write(rootGroup.(), ROOT_GROUP_ADDRESS);
-//			hdfFileChannel.write(ByteBuffer.wrap(new byte[]{1}), 250);
-//		} catch (IOException e) {
-//			throw new HdfWritingExcpetion("Failed to write superblock", e);
-//		}
-	}
-
-//	private void createRootGroup() {
-//		List<Message> messages = new ArrayList<>();
-//		messages.add(LinkInfoMessage.createBasic());
-//		messages.add(GroupInfoMessage.createBasic());
-//		messages.add(NilMessage.create());
-//		this.rootGroupObjectHeader = new ObjectHeader.ObjectHeaderV2(ROOT_GROUP_ADDRESS, messages);
-//	}
+	}
 
 	@Override
 	public void close() {

diff --git a/jhdf/src/main/java/io/jhdf/api/Attribute.java b/jhdf/src/main/java/io/jhdf/api/Attribute.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */
@@ -12,7 +12,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see LICENSE file
  */

diff --git a/jhdf/src/main/java/io/jhdf/api/Dataset.java b/jhdf/src/main/java/io/jhdf/api/Dataset.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/api/Group.java b/jhdf/src/main/java/io/jhdf/api/Group.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/api/Link.java b/jhdf/src/main/java/io/jhdf/api/Link.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/api/Node.java b/jhdf/src/main/java/io/jhdf/api/Node.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/api/NodeType.java b/jhdf/src/main/java/io/jhdf/api/NodeType.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/api/WritableGroup.java b/jhdf/src/main/java/io/jhdf/api/WritableGroup.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/api/WritableNode.java b/jhdf/src/main/java/io/jhdf/api/WritableNode.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/api/WritiableDataset.java b/jhdf/src/main/java/io/jhdf/api/WritiableDataset.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */

diff --git a/jhdf/src/main/java/io/jhdf/api/dataset/ChunkedDataset.java b/jhdf/src/main/java/io/jhdf/api/dataset/ChunkedDataset.java
@@ -3,7 +3,7 @@
  *
  * http://jhdf.io
  *
- * Copyright (c) 2023 James Mudd
+ * Copyright (c) 2024 James Mudd
  *
  * MIT License see 'LICENSE' file
  */