Merge branch 'master' into flatlaf

# Conflicts: # pom.xml # src/main/java/org/janelia/saalfeldlab/View.java
saalfeldlab · Sep 3, 2024 · be65582 · be65582
2 parents 9c3e5b9 + 4613089
commit be65582
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diff --git a/.travis/build.sh → .github/build.sh b/.travis/build.sh → .github/build.sh
@@ -1,3 +1,3 @@
 #!/bin/sh
-curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/master/travis-build.sh
-sh travis-build.sh
+curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/main/ci-build.sh
+sh ci-build.sh
diff --git a/.github/setup.sh b/.github/setup.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/main/ci-setup-github-actions.sh
+sh ci-setup-github-actions.sh
diff --git a/.github/workflows/build-main.yml b/.github/workflows/build-main.yml
@@ -0,0 +1,32 @@
+name: build
+
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - "*-[0-9]+.*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Java
+        uses: actions/setup-java@v2
+        with:
+          java-version: '8'
+          distribution: 'zulu'
+          cache: 'maven'
+      - name: Set up CI environment
+        run: .github/setup.sh
+      - name: Execute the build
+        run: .github/build.sh
+        env:
+          GPG_KEY_NAME: ${{ secrets.GPG_KEY_NAME }}
+          GPG_PASSPHRASE: ${{ secrets.GPG_PASSPHRASE }}
+          MAVEN_USER: ${{ secrets.MAVEN_USER }}
+          MAVEN_PASS: ${{ secrets.MAVEN_PASS }}
+          OSSRH_PASS: ${{ secrets.OSSRH_PASS }}
+          SIGNING_ASC: ${{ secrets.SIGNING_ASC }}
diff --git a/.github/workflows/build-pr.yml b/.github/workflows/build-pr.yml
@@ -0,0 +1,23 @@
+name: build PR
+
+on:
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Java
+        uses: actions/setup-java@v2
+        with:
+          java-version: '8'
+          distribution: 'zulu'
+          cache: 'maven'
+      - name: Set up CI environment
+        run: .github/setup.sh
+      - name: Execute the build
+        run: .github/build.sh
diff --git a/.travis.yml b/.travis.yml
diff --git a/README.md b/README.md
@@ -1,4 +1,7 @@
-# n5-utils [![Build Status](https://travis-ci.com/saalfeldlab/n5-utils.svg?branch=master)](https://travis-ci.com/saalfeldlab/n5-utils)
+[![Build Status](https://github.com/saalfeldlab/n5-utils/actions/workflows/build-main.yml/badge.svg)](https://github.com/saalfeldlab/n5-utils/actions/workflows/build-main.yml)
+
+# n5-utils
+
 Simple standalone BigDataViewer for multiple N5 (or HDF5) datasets
 or mipmap pyramids and also a copy, rechunking, and recompressing
 tool for N5 and HDF5.

diff --git a/install b/install
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-VERSION="0.0.6-SNAPSHOT"
+VERSION="0.0.7-SNAPSHOT"
 INSTALL_DIR=${1:-$(pwd)}
 
 echo "Installing into $INSTALL_DIR"
@@ -48,7 +48,7 @@ echo 'java \' >> n5-view-cosem
 echo "  -Xmx${MEM}g \\" >> n5-view-cosem
 if [[ $(java -version 2>&1 | grep version) =~ 1.8 ]]
 	then
-		echo '  -XX:+UseConcMarkSweepGC \' >> n5-view
+		echo '  -XX:+UseConcMarkSweepGC \' >> n5-view-cosem
 fi
 echo -n '  -cp $JAR:' >> n5-view-cosem
 echo -n $(cat cp.txt) >> n5-view-cosem
@@ -64,7 +64,7 @@ echo 'java \' >> n5-copy
 echo "  -Xmx${MEM}g \\" >> n5-copy
 if [[ $(java -version 2>&1 | grep version) =~ 1.8 ]]
 	then
-		echo '  -XX:+UseConcMarkSweepGC \' >> n5-view
+		echo '  -XX:+UseConcMarkSweepGC \' >> n5-copy
 fi
 echo -n '  -cp $JAR:' >> n5-copy
 echo -n $(cat cp.txt) >> n5-copy
@@ -80,7 +80,7 @@ echo 'java \' >> n5-equals
 echo "  -Xmx${MEM}g \\" >> n5-equals
 if [[ $(java -version 2>&1 | grep version) =~ 1.8 ]]
 	then
-		echo '  -XX:+UseConcMarkSweepGC \' >> n5-view
+		echo '  -XX:+UseConcMarkSweepGC \' >> n5-equals
 fi
 echo -n '  -cp $JAR:' >> n5-equals
 echo -n $(cat cp.txt) >> n5-equals

diff --git a/pom.xml b/pom.xml
@@ -7,15 +7,16 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>31.1.0</version>
+		<version>37.0.0</version>
 	</parent>
 
 	<groupId>org.janelia.saalfeldlab</groupId>
 	<artifactId>n5-utils</artifactId>
-	<version>0.0.6-SNAPSHOT</version>
+	<version>0.0.7-SNAPSHOT</version>
 
 	<name>N5 Utils</name>
-	<description>simple standalone BigDataViewer for multiple N5 (or HDF5) datasets.</description>
+	<description>simple standalone BigDataViewer for multiple N5 (or HDF5)
+		datasets.</description>
 	<url>https://github.com/saalfeldlab/n5-utils</url>
 	<inceptionYear>2017</inceptionYear>
 	<organization>
@@ -105,8 +106,8 @@
 		<url>https://github.com/saalfeldlab/n5-utils/issues</url>
 	</issueManagement>
 	<ciManagement>
-		<system>Travis CI</system>
-		<url>https://travis-ci.com/saalfeldlab/n5-utils</url>
+		<system>GitHub Actions</system>
+		<url>https://github.com/saalfeldlab/n5-utils/actions</url>
 	</ciManagement>
 
 	<properties>
@@ -117,27 +118,21 @@
 		<license.copyrightOwners>Stephan Saalfeld</license.copyrightOwners>
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
-		<releaseProfiles>deploy-to-scijava</releaseProfiles>
+		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 
-		<!-- TODO remove when pom-scijava-base is updated -->
-		<scijava.jvm.version>8</scijava.jvm.version>
-		<scijava.jvm.build.version>[1.8.0-101,)</scijava.jvm.build.version>
-
-		<maven-enforcer-plugin.version>3.0.0-M3</maven-enforcer-plugin.version>
-		<jacoco-maven-plugin.version>0.8.6</jacoco-maven-plugin.version>
-
-		<enforcer.skip>true</enforcer.skip>
-		<bigdataviewer-core.version>10.3.2-SNAPSHOT</bigdataviewer-core.version>
-		<bigdataviewer-vistools.version>1.0.0-beta-30-SNAPSHOT</bigdataviewer-vistools.version>
-		<n5.version>2.4.0</n5.version>
-		<n5-imglib2.version>3.5.1</n5-imglib2.version>
-		<n5-hdf5.version>1.2.0</n5-hdf5.version>
-		<n5-aws-s3.version>3.2.0</n5-aws-s3.version>
-		<n5-blosc.version>1.1.0</n5-blosc.version>
-		<n5-zarr.version>0.0.6</n5-zarr.version>
+		<n5.version>3.2.0</n5.version>
+		<n5-aws-s3.version>4.2.0</n5-aws-s3.version>
+		<n5-blosc.version>1.1.1</n5-blosc.version>
+		<n5-google-cloud.version>4.1.0</n5-google-cloud.version>
+		<n5-hdf5.version>2.2.0</n5-hdf5.version>
+		<n5-ij.version>4.2.1</n5-ij.version>
+		<n5-imglib2.version>7.0.0</n5-imglib2.version>
 		<n5-jpeg.version>0.0.1-beta1</n5-jpeg.version>
-		<n5-google-cloud>3.3.1</n5-google-cloud>
-		<ui-behaviour.version>2.0.5</ui-behaviour.version>
+		<n5-universe.version>1.6.0</n5-universe.version>
+		<n5-viewer_fiji.version>6.1.1</n5-viewer_fiji.version>
+		<n5-zarr.version>1.3.4</n5-zarr.version>
+		<n5-zstandard.version>1.0.2</n5-zstandard.version>
+		<imagej-legacy.version>1.2.2</imagej-legacy.version>
 	</properties>
 
 	<dependencies>
@@ -170,6 +165,11 @@
 			<groupId>org.janelia.saalfeldlab</groupId>
 			<artifactId>n5-hdf5</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>net.imglib2</groupId>
+			<artifactId>imglib2-algorithm-gpl</artifactId>
+		</dependency>
+
 		<dependency>
 			<groupId>org.janelia.saalfeldlab</groupId>
 			<artifactId>n5-aws-s3</artifactId>
@@ -223,6 +223,14 @@
 			<artifactId>n5-jpeg</artifactId>
 			<version>${n5-jpeg.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-universe</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>cisd</groupId>
+			<artifactId>jhdf5</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>com.formdev</groupId>
 			<artifactId>flatlaf</artifactId>

diff --git a/src/main/java/org/janelia/saalfeldlab/Copy.java b/src/main/java/org/janelia/saalfeldlab/Copy.java
@@ -119,7 +119,6 @@
  */
 package org.janelia.saalfeldlab;
 
-import java.io.IOException;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -129,12 +128,12 @@
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 
-import org.janelia.saalfeldlab.N5Factory.N5Options;
 import org.janelia.saalfeldlab.n5.Bzip2Compression;
 import org.janelia.saalfeldlab.n5.Compression;
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
 import org.janelia.saalfeldlab.n5.GzipCompression;
 import org.janelia.saalfeldlab.n5.Lz4Compression;
+import org.janelia.saalfeldlab.n5.N5Exception;
 import org.janelia.saalfeldlab.n5.N5Reader;
 import org.janelia.saalfeldlab.n5.N5Writer;
 import org.janelia.saalfeldlab.n5.RawCompression;
@@ -143,6 +142,7 @@
 import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Writer;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
 import org.janelia.saalfeldlab.n5.jpeg.JPEGCompression;
+import org.janelia.saalfeldlab.n5.universe.N5Factory;
 
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.type.NativeType;
@@ -236,7 +236,7 @@ protected void reorderIfNecessary(final long[] array) {
 			reorder(array);
 	}
 
-	protected <T extends NativeType<T>> void copyDataset(final String datasetName) throws IOException, InterruptedException, ExecutionException {
+	protected <T extends NativeType<T>> void copyDataset(final String datasetName) throws InterruptedException, ExecutionException {
 
 		System.out.println(datasetName);
 
@@ -272,8 +272,7 @@ protected <T extends NativeType<T>> void copyDataset(final String datasetName) t
 		copyAttributes(datasetName);
 	}
 
-	protected void copyAttributes(final String groupName)
-			throws IOException {
+	protected void copyAttributes(final String groupName) {
 
 		System.out.println("  attributes:");
 
@@ -291,14 +290,14 @@ protected void copyAttributes(final String groupName)
 
 				try {
 					n5Writer.setAttribute(groupName, key, n5Reader.getAttribute(groupName, key, clazz));
-				} catch (final IOException e) {
+				} catch (final N5Exception e) {
 					e.printStackTrace(System.err);
 				}
 			}
 		});
 	}
 
-	protected <T extends NativeType<T>> void copyGroup(final String groupName) throws IOException, InterruptedException, ExecutionException {
+	protected <T extends NativeType<T>> void copyGroup(final String groupName) throws InterruptedException, ExecutionException {
 
 		System.out.println(groupName);
 
@@ -315,7 +314,7 @@ protected <T extends NativeType<T>> void copyGroup(final String groupName) throw
 	}
 
 	@Override
-	public Void call() throws IOException, InterruptedException, ExecutionException {
+	public Void call() throws InterruptedException, ExecutionException {
 
 		blockSize = blockSizeString == null ? null : parseCSIntArray(blockSizeString);
 
@@ -349,8 +348,14 @@ public Void call() throws IOException, InterruptedException, ExecutionException
 			}
 		}
 
-		n5Reader = N5Factory.createN5Reader(new N5Options(inputContainerPath, blockSize, compression));
-		n5Writer = N5Factory.createN5Writer(new N5Options(outputContainerPath, blockSize, compression));
+		final N5Factory n5Factory = new N5Factory()
+				.hdf5DefaultBlockSize(blockSize)
+				.zarrDimensionSeparator(".")
+				.zarrMapN5Attributes(false)
+				.zarrMergeAttributes(false);
+
+		n5Reader = n5Factory.openReader(inputContainerPath);
+		n5Writer = n5Factory.openWriter(outputContainerPath);
 
 		if (groupNames == null)
 			copyGroup("");

diff --git a/src/main/java/org/janelia/saalfeldlab/Equals.java b/src/main/java/org/janelia/saalfeldlab/Equals.java
@@ -119,15 +119,15 @@
  */
 package org.janelia.saalfeldlab;
 
-import java.io.IOException;
 import java.util.Arrays;
 import java.util.concurrent.Callable;
 import java.util.concurrent.ExecutionException;
 
-import org.janelia.saalfeldlab.N5Factory.N5Options;
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
+import org.janelia.saalfeldlab.n5.N5Exception;
 import org.janelia.saalfeldlab.n5.N5Reader;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
+import org.janelia.saalfeldlab.n5.universe.N5Factory;
 
 import net.imglib2.Cursor;
 import net.imglib2.RandomAccessibleInterval;
@@ -179,18 +179,18 @@ protected <T extends Type<T>> Boolean datasetEquals() {
 
 			return equals;
 		}
-		catch (final IOException e) {
+		catch (final N5Exception e) {
 
 			return false;
 		}
 	}
 
 
 	@Override
-	public Boolean call() throws IOException, InterruptedException, ExecutionException {
+	public Boolean call() throws InterruptedException, ExecutionException {
 
-		n5Reader1 = N5Factory.createN5Reader(new N5Options(inputContainerPath1, null, null));
-		n5Reader2 = N5Factory.createN5Reader(new N5Options(inputContainerPath2, null, null));
+		n5Reader1 = new N5Factory().openReader(inputContainerPath1);
+		n5Reader2 = new N5Factory().openReader(inputContainerPath2);
 
 		return datasetEquals();
 	}