Merge branch 'master' into wip/codecsShards

.github/setup.sh

@@ -1,3 +1,10 @@
 #!/bin/sh
 curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/main/ci-setup-github-actions.sh
 sh ci-setup-github-actions.sh
+
+# Let the Linux build handle artifact deployment.
+if [ "$(uname)" != Linux ]
+then
+  echo "No deploy -- non-Linux build"
+  echo "NO_DEPLOY=1" >> $GITHUB_ENV
+fi

.github/workflows/build-main.yml → .github/workflows/build.yml

@@ -6,6 +6,9 @@ on:
       - master
     tags:
       - "*-[0-9]+.*"
+  pull_request:
+    branches:
+      - master
 
 jobs:
   build:
@@ -24,8 +27,10 @@ jobs:
           cache: 'maven'
       - name: Set up CI environment
         run: .github/setup.sh
+        shell: bash
       - name: Execute the build
         run: .github/build.sh
+        shell: bash
         env:
           GPG_KEY_NAME: ${{ secrets.GPG_KEY_NAME }}
           GPG_PASSPHRASE: ${{ secrets.GPG_PASSPHRASE }}

LICENSE.md

@@ -1,6 +1,6 @@
 ## BSD 2-Clause License
 
-Copyright (c) 2017-2024, Stephan Saalfeld
+Copyright (c) 2017-2025, Stephan Saalfeld
 
 All rights reserved.
 

README.md

@@ -22,7 +22,7 @@ N5 group is not a single file but simply a directory on the file system.  Meta-d
 
 1. All directories of the file system are N5 groups.
 2. A JSON file `attributes.json` in a directory contains arbitrary attributes.  A group without attributes may not have an `attributes.json` file.
-3. The version of this specification is 1.0.0 and is stored in the "n5" attribute of the root group "/".
+3. The version of this specification is 4.0.0 and is stored in the "n5" attribute of the root group "/".
 4. A dataset is a group with the mandatory attributes:
    * dimensions (e.g. [100, 200, 300]),
    * blockSize (e.g. [64, 64, 64]),
@@ -38,7 +38,7 @@ N5 group is not a single file but simply a directory on the file system.  Meta-d
      * xz with parameters
        * preset (integer, default 6).
 
-   Custom compression schemes with arbitrary parameters can be added using [compression annotations](#extensible-compression-schemes), e.g. [N5 Blosc](https://github.com/saalfeldlab/n5-blosc).
+   Custom compression schemes with arbitrary parameters can be added using [compression annotations](#extensible-compression-schemes), e.g. [N5 Blosc](https://github.com/saalfeldlab/n5-blosc) and [N5 ZStandard](https://github.com/JaneliaSciComp/n5-zstandard/).
 5. Chunks are stored in a directory hierarchy that enumerates their positive integer position in the chunk grid (e.g. `0/4/1/7` for chunk grid position p=(0, 4, 1, 7)).
 6. Datasets are sparse, i.e. there is no guarantee that all chunks of a dataset exist.
 7. Chunks cannot be larger than 2GB (2<sup>31</sup>Bytes).
@@ -134,4 +134,3 @@ Custom compression schemes can be implemented using the annotation discovery mec
 HDF5 is a great format that provides a wealth of conveniences that I do not want to miss.  It's inefficiency for parallel writing, however, limit its applicability for handling of very large n-dimensional data.
 
 N5 uses the native filesystem of the target platform and JSON files to specify basic and custom meta-data as attributes.  It aims at preserving the convenience of HDF5 where possible but doesn't try too hard to be a full replacement.
-Please do not take this project too seriously, we will see where it will get us and report back when more data is available.

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>org.janelia.saalfeldlab</groupId>
 	<artifactId>n5</artifactId>
-	<version>3.3.1-SNAPSHOT</version>
+	<version>3.3.2-SNAPSHOT</version>
 
 	<name>N5</name>
 	<description>Not HDF5</description>

src/main/java/org/janelia/saalfeldlab/n5/N5Reader.java

@@ -565,10 +565,9 @@ default String[] deepList(
 		final LinkedBlockingQueue<Future<String>> datasetFutures = new LinkedBlockingQueue<>();
 		deepListHelper(this, normalPathName, false, filter, executor, datasetFutures);
 
-		datasetFutures.poll().get(); // skip self
 		while (!datasetFutures.isEmpty()) {
 			final String result = datasetFutures.poll().get();
-			if (result != null)
+			if (result != null && !result.equals(normalPathName))
 				results.add(result.substring(normalPathName.length() + groupSeparator.length()));
 		}