Chore: reformat codebase

.gitignore

@@ -4,7 +4,9 @@ target/
 !**/src/test/**/target/
 
 ### IntelliJ IDEA ###
-.idea/
+.idea/*
+!.idea/codeStyles/
+!.idea/codeStyles/**
 *.iws
 *.iml
 *.ipr
@@ -43,4 +45,4 @@ build/
 /main.py
 /pyproject.toml
 /uv.lock
-**/__pycache__
+**/__pycache__

README.md

@@ -3,6 +3,7 @@
 This repository contains a Java implementation of Zarr version 2 and 3.
 
 ## Usage
+
 ```java
 import dev.zarr.zarrjava.store.FilesystemStore;
 import dev.zarr.zarrjava.store.HttpStore;
@@ -11,40 +12,54 @@ import dev.zarr.zarrjava.v3.DataType;
 import dev.zarr.zarrjava.v3.Group;
 
 Group hierarchy = Group.open(
-    new HttpStore("https://static.webknossos.org/data/zarr_v3")
-        .resolve("l4_sample")
+        new HttpStore("https://static.webknossos.org/data/zarr_v3")
+                .resolve("l4_sample")
 );
 Group color = (Group) hierarchy.get("color");
 Array array = (Array) color.get("1");
 ucar.ma2.Array outArray = array.read(
-    new long[]{0, 3073, 3073, 513}, // offset
-    new int[]{1, 64, 64, 64} // shape
+        new long[]{0, 3073, 3073, 513}, // offset
+        new int[]{1, 64, 64, 64} // shape
 );
 
 Array array = Array.create(
-    new FilesystemStore("/path/to/zarr").resolve("array"),
-    Array.metadataBuilder()
-        .withShape(1, 4096, 4096, 1536)
-        .withDataType(DataType.UINT32)
-        .withChunkShape(1, 1024, 1024, 1024)
-        .withFillValue(0)
-        .withCodecs(c -> c.withSharding(new int[]{1, 32, 32, 32}, c1 -> c1.withBlosc()))
-        .build()
+        new FilesystemStore("/path/to/zarr").resolve("array"),
+        Array.metadataBuilder()
+                .withShape(1, 4096, 4096, 1536)
+                .withDataType(DataType.UINT32)
+                .withChunkShape(1, 1024, 1024, 1024)
+                .withFillValue(0)
+                .withCodecs(c -> c.withSharding(new int[]{1, 32, 32, 32}, c1 -> c1.withBlosc()))
+                .build()
 );
 ucar.ma2.Array data = ucar.ma2.Array.factory(ucar.ma2.DataType.UINT, new int[]{1, 1024, 1024, 1024});
-array.write(
-    new long[]{0, 0, 0, 0}, // offset
-    data
+array.
+
+write(
+    new long[] {
+    0, 0, 0, 0
+}, // offset
+data
 );
 ```
+
 ## Development Start-Guide
 
 ### Run Tests Locally
-To be able to run the tests locally, make sure to have `python3.11` and `uv` installed. 
+
+To be able to run the tests locally, make sure to have `python3.11` and `uv` installed.
 
 Furthermore, you will need the `l4_sample` test data:
 
 `curl https://static.webknossos.org/data/zarr_v3/l4_sample.zip -o testdata/l4_sample.zip
 && cd testdata
 && unzip l4_sample.zip
 `
+
+### Code Style & Formatting
+
+This project uses IntelliJ IDEA default Java formatting
+
+Before submitting changes, please run:
+
+- IntelliJ: `Reformat Code` and `Optimize Imports`

pom.xml

@@ -194,10 +194,10 @@
                 <version>3.5.0</version>
                 <executions>
                     <execution>
-                    <id>attach-javadoc</id>
-                    <goals>
-                        <goal>jar</goal>
-                    </goals>
+                        <id>attach-javadoc</id>
+                        <goals>
+                            <goal>jar</goal>
+                        </goals>
                     </execution>
                 </executions>
                 <configuration>
@@ -210,14 +210,14 @@
                 <version>1.6</version>
                 <executions>
                     <execution>
-                    <id>sign-artifacts</id>
-                    <phase>verify</phase>
-                    <goals>
-                        <goal>sign</goal>
-                    </goals>
-                    <configuration>
-                        <keyname>9F88D86AD9A0D91E</keyname>
-                    </configuration>
+                        <id>sign-artifacts</id>
+                        <phase>verify</phase>
+                        <goals>
+                            <goal>sign</goal>
+                        </goals>
+                        <configuration>
+                            <keyname>9F88D86AD9A0D91E</keyname>
+                        </configuration>
                     </execution>
                 </executions>
             </plugin>

src/main/java/dev/zarr/zarrjava/ZarrException.java

@@ -2,11 +2,11 @@
 
 public class ZarrException extends Exception {
 
-  public ZarrException(String message, Throwable cause) {
-    super(message, cause);
-  }
+    public ZarrException(String message, Throwable cause) {
+        super(message, cause);
+    }
 
-  public ZarrException(String message) {
-    super(message);
-  }
+    public ZarrException(String message) {
+        super(message);
+    }
 }

src/main/java/dev/zarr/zarrjava/core/Array.java

@@ -1,12 +1,12 @@
 package dev.zarr.zarrjava.core;
 
 import dev.zarr.zarrjava.ZarrException;
+import dev.zarr.zarrjava.core.codec.CodecPipeline;
 import dev.zarr.zarrjava.store.FilesystemStore;
 import dev.zarr.zarrjava.store.StoreHandle;
 import dev.zarr.zarrjava.utils.IndexingUtils;
 import dev.zarr.zarrjava.utils.MultiArrayUtils;
 import dev.zarr.zarrjava.utils.Utils;
-import dev.zarr.zarrjava.core.codec.CodecPipeline;
 import ucar.ma2.InvalidRangeException;
 
 import javax.annotation.Nonnull;
@@ -21,7 +21,6 @@
 public abstract class Array extends AbstractNode {
 
     protected CodecPipeline codecPipeline;
-    public abstract ArrayMetadata metadata();
 
     protected Array(StoreHandle storeHandle) throws ZarrException {
         super(storeHandle);
@@ -47,7 +46,8 @@ public static Array open(StoreHandle storeHandle) throws IOException, ZarrExcept
             throw new ZarrException("No Zarr array found at the specified location.");
         }
     }
-     /**
+
+    /**
      * Opens an existing Zarr array at a specified storage location. Automatically detects the Zarr version.
      *
      * @param path the storage location of the Zarr array
@@ -69,6 +69,8 @@ public static Array open(String path) throws IOException, ZarrException {
         return open(Paths.get(path));
     }
 
+    public abstract ArrayMetadata metadata();
+
     /**
      * Writes a ucar.ma2.Array into the Zarr array at a specified offset. The shape of the Zarr array
      * needs be large enough for the write.
@@ -94,32 +96,32 @@ public void write(long[] offset, ucar.ma2.Array array, boolean parallel) {
             chunkStream = chunkStream.parallel();
         }
         chunkStream.forEach(
-            chunkCoords -> {
-                try {
-                    final IndexingUtils.ChunkProjection chunkProjection =
-                        IndexingUtils.computeProjection(chunkCoords, metadata.shape, chunkShape, offset,
-                            shape
-                        );
-
-                    ucar.ma2.Array chunkArray;
-                    if (IndexingUtils.isFullChunk(chunkProjection.chunkOffset, chunkProjection.shape,
-                        chunkShape
-                    )) {
-                        chunkArray = array.sectionNoReduce(chunkProjection.outOffset,
-                            chunkProjection.shape,
-                            null
-                        );
-                    } else {
-                        chunkArray = readChunk(chunkCoords);
-                        MultiArrayUtils.copyRegion(array, chunkProjection.outOffset, chunkArray,
-                            chunkProjection.chunkOffset, chunkProjection.shape
-                        );
+                chunkCoords -> {
+                    try {
+                        final IndexingUtils.ChunkProjection chunkProjection =
+                                IndexingUtils.computeProjection(chunkCoords, metadata.shape, chunkShape, offset,
+                                        shape
+                                );
+
+                        ucar.ma2.Array chunkArray;
+                        if (IndexingUtils.isFullChunk(chunkProjection.chunkOffset, chunkProjection.shape,
+                                chunkShape
+                        )) {
+                            chunkArray = array.sectionNoReduce(chunkProjection.outOffset,
+                                    chunkProjection.shape,
+                                    null
+                            );
+                        } else {
+                            chunkArray = readChunk(chunkCoords);
+                            MultiArrayUtils.copyRegion(array, chunkProjection.outOffset, chunkArray,
+                                    chunkProjection.chunkOffset, chunkProjection.shape
+                            );
+                        }
+                        writeChunk(chunkCoords, chunkArray);
+                    } catch (ZarrException | InvalidRangeException e) {
+                        throw new RuntimeException(e);
                     }
-                    writeChunk(chunkCoords, chunkArray);
-                } catch (ZarrException | InvalidRangeException e) {
-                    throw new RuntimeException(e);
-                }
-            });
+                });
 
     }
 
@@ -246,7 +248,7 @@ boolean chunkIsInArray(long[] chunkCoords) {
         final int[] chunkShape = metadata().chunkShape();
         for (int dimIdx = 0; dimIdx < metadata().ndim(); dimIdx++) {
             if (chunkCoords[dimIdx] < 0
-                || chunkCoords[dimIdx] * chunkShape[dimIdx] >= metadata().shape[dimIdx]) {
+                    || chunkCoords[dimIdx] * chunkShape[dimIdx] >= metadata().shape[dimIdx]) {
                 return false;
             }
         }
@@ -282,47 +284,47 @@ public ucar.ma2.Array read(final long[] offset, final int[] shape, final boolean
         }
 
         final ucar.ma2.Array outputArray = ucar.ma2.Array.factory(metadata.dataType().getMA2DataType(),
-            shape);
+                shape);
         Stream<long[]> chunkStream = Arrays.stream(IndexingUtils.computeChunkCoords(metadata.shape, chunkShape, offset, shape));
         if (parallel) {
             chunkStream = chunkStream.parallel();
         }
         chunkStream.forEach(
-            chunkCoords -> {
-                try {
-                    final IndexingUtils.ChunkProjection chunkProjection =
-                        IndexingUtils.computeProjection(chunkCoords, metadata.shape, chunkShape, offset,
-                            shape
-                        );
-
-                    if (chunkIsInArray(chunkCoords)) {
-                        MultiArrayUtils.copyRegion(metadata.allocateFillValueChunk(),
-                            chunkProjection.chunkOffset, outputArray, chunkProjection.outOffset,
-                            chunkProjection.shape
-                        );
-                    }
-
-                    final String[] chunkKeys = metadata.chunkKeyEncoding().encodeChunkKey(chunkCoords);
-                    final StoreHandle chunkHandle = storeHandle.resolve(chunkKeys);
-                    if (!chunkHandle.exists()) {
-                        return;
+                chunkCoords -> {
+                    try {
+                        final IndexingUtils.ChunkProjection chunkProjection =
+                                IndexingUtils.computeProjection(chunkCoords, metadata.shape, chunkShape, offset,
+                                        shape
+                                );
+
+                        if (chunkIsInArray(chunkCoords)) {
+                            MultiArrayUtils.copyRegion(metadata.allocateFillValueChunk(),
+                                    chunkProjection.chunkOffset, outputArray, chunkProjection.outOffset,
+                                    chunkProjection.shape
+                            );
+                        }
+
+                        final String[] chunkKeys = metadata.chunkKeyEncoding().encodeChunkKey(chunkCoords);
+                        final StoreHandle chunkHandle = storeHandle.resolve(chunkKeys);
+                        if (!chunkHandle.exists()) {
+                            return;
+                        }
+                        if (codecPipeline.supportsPartialDecode()) {
+                            final ucar.ma2.Array chunkArray = codecPipeline.decodePartial(chunkHandle,
+                                    Utils.toLongArray(chunkProjection.chunkOffset), chunkProjection.shape);
+                            MultiArrayUtils.copyRegion(chunkArray, new int[metadata.ndim()], outputArray,
+                                    chunkProjection.outOffset, chunkProjection.shape
+                            );
+                        } else {
+                            MultiArrayUtils.copyRegion(readChunk(chunkCoords), chunkProjection.chunkOffset,
+                                    outputArray, chunkProjection.outOffset, chunkProjection.shape
+                            );
+                        }
+
+                    } catch (ZarrException e) {
+                        throw new RuntimeException(e);
                     }
-                    if (codecPipeline.supportsPartialDecode()) {
-                        final ucar.ma2.Array chunkArray = codecPipeline.decodePartial(chunkHandle,
-                            Utils.toLongArray(chunkProjection.chunkOffset), chunkProjection.shape);
-                        MultiArrayUtils.copyRegion(chunkArray, new int[metadata.ndim()], outputArray,
-                            chunkProjection.outOffset, chunkProjection.shape
-                        );
-                    } else {
-                        MultiArrayUtils.copyRegion(readChunk(chunkCoords), chunkProjection.chunkOffset,
-                            outputArray, chunkProjection.outOffset, chunkProjection.shape
-                        );
-                    }
-
-                } catch (ZarrException e) {
-                    throw new RuntimeException(e);
-                }
-            });
+                });
         return outputArray;
     }