Key value interface, attribute paths, attribute caching

.github/workflows/build-main.yml

@@ -9,7 +9,10 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
 
     steps:
       - uses: actions/checkout@v2

.github/workflows/platform-test.yml

@@ -0,0 +1,30 @@
+name: test
+
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - "*-[0-9]+.*"
+  pull_request:
+    branches:
+      - master
+  workflow_dispatch:
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Java
+        uses: actions/setup-java@v2
+        with:
+          java-version: '8'
+          distribution: 'zulu'
+          cache: 'maven'
+      - name: Maven Test
+        run: mvn -B clean test --file pom.xml

.gitignore

@@ -16,3 +16,6 @@ hs_err_pid*
 .classpath
 .project
 .settings
+
+.idea
+*.iml

LICENSE.md

@@ -1,6 +1,6 @@
 ## BSD 2-Clause License
 
-Copyright (c) 2017-2020, Stephan Saalfeld
+Copyright (c) 2017-2023, Stephan Saalfeld
 
 All rights reserved.
 

README.md

@@ -1,4 +1,4 @@
-# N5 [![Build Status](https://travis-ci.com/saalfeldlab/n5.svg?branch=master)](https://travis-ci.com/saalfeldlab/n5) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6578231.svg)](https://doi.org/10.5281/zenodo.6578231)
+# N5 [![Build Status](https://travis-ci.com/saalfeldlab/n5.svg?branch=master)](https://travis-ci.com/saalfeldlab/n5)
 
 The N5 API specifies the primitive operations needed to store large chunked n-dimensional tensors, and arbitrary meta-data in a hierarchy of groups similar to HDF5.
 
@@ -16,7 +16,7 @@ Chunked datasets can be sparse, i.e. empty chunks do not need to be stored.
 
 ## File-system specification
 
-*version 2.5.2-SNAPSHOT*
+*version 2.6.1*
 
 N5 group is not a single file but simply a directory on the file system.  Meta-data is stored as a JSON file per each group/ directory.  Tensor datasets can be chunked and chunks are stored as individual files.  This enables parallel reading and writing on a cluster.
 

doc/LICENSE.md

@@ -1,6 +1,6 @@
 ## BSD 2-Clause License
 
-Copyright (c) @project.inceptionYear@-2020, Stephan Saalfeld
+Copyright (c) @project.inceptionYear@-@current.year@, Stephan Saalfeld
 
 All rights reserved.
 

doc/README.md

@@ -16,7 +16,7 @@ Chunked datasets can be sparse, i.e. empty chunks do not need to be stored.
 
 ## File-system specification
 
-*version @project.version@*
+*version @n5-spec.version@*
 
 N5 group is not a single file but simply a directory on the file system.  Meta-data is stored as a JSON file per each group/ directory.  Tensor datasets can be chunked and chunks are stored as individual files.  This enables parallel reading and writing on a cluster.
 

pom.xml

@@ -5,13 +5,13 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>31.1.0</version>
+		<version>34.0.0</version>
 		<relativePath />
 	</parent>
 
 	<groupId>org.janelia.saalfeldlab</groupId>
 	<artifactId>n5</artifactId>
-	<version>2.5.2-SNAPSHOT</version>
+	<version>3.0.0-SNAPSHOT</version>
 
 	<name>N5</name>
 	<description>Not HDF5</description>
@@ -105,6 +105,11 @@
 		<cisd.jhdf5.version>19.04.0</cisd.jhdf5.version>
 
 		<commons-collections4.version>4.2</commons-collections4.version>
+
+		<maven-enforcer-plugin.version>3.0.0-M3</maven-enforcer-plugin.version>
+		<jacoco-maven-plugin.version>0.8.6</jacoco-maven-plugin.version>
+
+		<n5-spec.version>2.6.1</n5-spec.version>
 	</properties>
 
 	<dependencies>
@@ -145,7 +150,6 @@
 		<dependency>
 			<groupId>cisd</groupId>
 			<artifactId>jhdf5</artifactId>
-			<version>${cisd.jhdf5.version}</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
@@ -174,6 +178,23 @@
 	<build>
 		<pluginManagement>
 			<plugins>
+				<plugin>
+					<groupId>org.codehaus.mojo</groupId>
+					<artifactId>build-helper-maven-plugin</artifactId>
+					<executions>
+						<execution>
+							<id>timestamp-property</id>
+							<goals>
+								<goal>timestamp-property</goal>
+							</goals>
+							<phase>validate</phase>
+							<configuration>
+								<name>current.year</name>
+								<pattern>yyyy</pattern>
+							</configuration>
+						</execution>
+					</executions>
+				</plugin>
 				<plugin>
 					<artifactId>maven-resources-plugin</artifactId>
 					<executions>

src/main/java/org/janelia/saalfeldlab/n5/AbstractDataBlock.java

@@ -29,6 +29,7 @@
  * Abstract base class for {@link DataBlock} implementations.
  *
  * @param <T>
+ *            the block data type
  *
  * @author Stephan Saalfeld
  */

src/main/java/org/janelia/saalfeldlab/n5/BlockReader.java

@@ -40,8 +40,15 @@ public interface BlockReader {
 	 * Reads a {@link DataBlock} from an {@link InputStream}.
 	 *
 	 * @param dataBlock
+	 *            the data block
 	 * @param in
+	 *            the input stream
+	 * @param <T>
+	 *            the block data type
+	 * @param <B>
+	 *            the block type
 	 * @throws IOException
+	 *             the exception
 	 */
 	public <T, B extends DataBlock<T>> void read(final B dataBlock, final InputStream in) throws IOException;
 }

src/main/java/org/janelia/saalfeldlab/n5/BlockWriter.java

@@ -40,8 +40,13 @@ public interface BlockWriter {
 	 * Writes a {@link DataBlock} into an {@link OutputStream}.
 	 *
 	 * @param dataBlock
+	 *            the data block
 	 * @param out
+	 *            the output stream
+	 * @param <T>
+	 *            the block data type
 	 * @throws IOException
+	 *             the exception
 	 */
 	public <T> void write(final DataBlock<T> dataBlock, final OutputStream out) throws IOException;
 }

src/main/java/org/janelia/saalfeldlab/n5/ByteArrayDataBlock.java

@@ -46,10 +46,10 @@ public void readData(final ByteBuffer buffer) {
 		if (buffer.array() != getData())
 			buffer.get(getData());
 	}
-	
+
 	@Override
 	public int getNumElements() {
-		
+
 		return data.length;
 	}
 }

src/main/java/org/janelia/saalfeldlab/n5/Bzip2Compression.java

@@ -74,4 +74,14 @@ public Bzip2Compression getWriter() {
 
 		return this;
 	}
+
+	@Override
+	public boolean equals(final Object other) {
+
+		if (other == null || other.getClass() != Bzip2Compression.class)
+			return false;
+		else
+			return blockSize == ((Bzip2Compression)other).blockSize;
+	}
+
 }