Merge pull request #3 from scalableminds/publishing-preparation

Publishing preparation

Author: joshmoore

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: '22'
+          java-version: '11'
           distribution: 'temurin'
           cache: maven
 
@@ -38,11 +38,6 @@ jobs:
           python -m venv venv_zarrita
           if [ "${{ runner.os }}" = "Windows" ]; then venv_zarrita/Scripts/pip install zarrita; else venv_zarrita/bin/pip install zarrita; fi
 
-      - name: Download blosc jar
-        run: |
-          mkdir -p ../blosc-java/target
-          curl https://static.webknossos.org/misc/blosc-java-0.1-1.21.4-SNAPSHOT.jar -o ../blosc-java/target/blosc-java-0.1-1.21.4-SNAPSHOT.jar
-
       - name: Download testdata
         run: |
           mkdir testoutput

.github/workflows/deploy.yml

@@ -29,8 +29,29 @@ jobs:
           # Verify gpg secret key
           gpg --list-secret-keys --keyid-format LONG
 
+      # Begin copy from ci.yml. Refactor?
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install zarrita
+        run: |
+          python -m venv venv_zarrita
+          if [ "${{ runner.os }}" = "Windows" ]; then venv_zarrita/Scripts/pip install zarrita; else venv_zarrita/bin/pip install zarrita; fi
+
+      - name: Download testdata
+        run: |
+          mkdir testoutput
+          curl https://static.webknossos.org/data/zarr_v3/l4_sample.zip -o testdata/l4_sample.zip
+          cd testdata
+          unzip l4_sample.zip
+
+      # End copy from ci.yml
+
       - name: Publish package
-        run: mvn --batch-mode deploy
+        run: mvn --batch-mode deploy -DargLine="-Xmx6g"
         env:
           MAVEN_USERNAME: ${{ secrets.OSSRH_USERNAME }}
           MAVEN_PASSWORD: ${{ secrets.OSSRH_TOKEN }}

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>dev.zarr</groupId>
     <artifactId>zarr-java</artifactId>
-    <version>0.0.1</version>
+    <version>0.0.2</version>
 
     <name>zarr-java</name>
 
@@ -42,8 +42,7 @@
     </developers>
 
     <properties>
-        <maven.compiler.source>8</maven.compiler.source>
-        <maven.compiler.target>8</maven.compiler.target>
+        <maven.compiler.release>8</maven.compiler.release>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <jackson.version>2.14.2</jackson.version>
         <aws.version>1.12.477</aws.version>
@@ -147,6 +146,53 @@
                     <useSystemClassLoader>false</useSystemClassLoader>
                 </configuration>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.13.0</version>
+                <configuration>
+                    <release>${maven.compiler.release}</release>
+                    <encoding>UTF-8</encoding>
+                    <excludes>
+                        <exclude>.gitignore</exclude>
+                        <exclude>temp/**</exclude>
+                    </excludes>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-source-plugin</artifactId>
+                <version>3.1.0</version>
+                <executions>
+                    <execution>
+                        <phase>verify</phase>
+                        <goals>
+                            <goal>jar</goal>
+                        </goals>
+                        <configuration>
+                            <excludes>
+                                <exclude>temp.**</exclude>
+                            </excludes>
+                        </configuration>
+                    </execution>
+                </executions>
+                <configuration>
+                    <excludeResources>true</excludeResources>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-resources-plugin</artifactId>
+                <version>3.1.0</version>
+                <configuration>
+                    <encoding>UTF-8</encoding>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>build-helper-maven-plugin</artifactId>
+                <version>1.10</version>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-javadoc-plugin</artifactId>

src/test/java/dev/zarr/zarrjava/ZarrTest.java

@@ -14,7 +14,6 @@
 import dev.zarr.zarrjava.v3.*;
 import dev.zarr.zarrjava.v3.codec.CodecBuilder;
 import dev.zarr.zarrjava.v3.codec.core.TransposeCodec;
-import jdk.jshell.spi.ExecutionControl;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
@@ -30,6 +29,7 @@
 import java.nio.file.Paths;
 import java.util.Arrays;
 import java.util.Comparator;
+import java.util.HashMap;
 import java.util.Map;
 import java.util.stream.Stream;
 
@@ -150,13 +150,16 @@ public void testWriteReadWithZarrita(String codec, String codecParam) throws Exc
         int[] testData = new int[16 * 16 * 16];
         Arrays.setAll(testData, p -> p);
 
+        Map<String, Object> attributes = new HashMap<>();
+        attributes.put("test_key", "test_value");
+
         StoreHandle storeHandle = new FilesystemStore(TESTOUTPUT).resolve("write_to_zarrita", codec, codecParam);
         ArrayMetadataBuilder builder = Array.metadataBuilder()
                 .withShape(16, 16, 16)
                 .withDataType(DataType.UINT32)
                 .withChunkShape(2, 4, 8)
                 .withFillValue(0)
-                .withAttributes(Map.of("test_key", "test_value"));
+                .withAttributes(attributes);
 
         switch (codec) {
             case "blosc":
@@ -425,8 +428,11 @@ public void testV3FillValue() throws ZarrException {
     public void testV3Group() throws IOException, ZarrException {
         FilesystemStore fsStore = new FilesystemStore(TESTOUTPUT);
 
+        Map<String, Object> attributes = new HashMap<>();
+        attributes.put("hello", "world");
+
         Group group = Group.create(fsStore.resolve("testgroup"));
-        Group group2 = group.createGroup("test2", Map.of("hello", "world"));
+        Group group2 = group.createGroup("test2", attributes);
         Array array = group2.createArray("array", b ->
                 b.withShape(10, 10)
                         .withDataType(DataType.UINT8)