Add cli wrapper (#45)

* add cli wrapper

* Add pull request trigger to conformance workflow

* fix pom dependencies

* print array

* use fork for debugging

* add zstd to v2

* update zarr-cli version to 0.0.10 in conformance tests

* update zarr-cli path in conformance tests

* set dynamic JAR path for conformance tests

* Improve JAR path handling in conformance workflow

- Use GITHUB_ENV instead of GITHUB_OUTPUT for better compatibility
- Add verification step to ensure JAR exists before running tests
- Add human-readable confirmation message

* set conformance tests back to Bisaloo/zarr-conformance-tests@main

* Revert "set conformance tests back to Bisaloo/zarr-conformance-tests@main"

This reverts commit 592731e.

* remove debug statements

* Update conformance test action to not use fork

* fix version v0.0.2 of Bisaloo/zarr-conformance-tests

Co-authored-by: Hugo Gruson <hugo.gruson@protonmail.com>

* fix imports

---------

Co-authored-by: Hugo Gruson <hugo.gruson@protonmail.com>

Author: brokkoli71

.github/workflows/conformance.yml

@@ -0,0 +1,39 @@
+name: Zarr Conformance Tests
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '17 3 * * 0'
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  conformance-tests:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: '11'
+          distribution: 'temurin'
+          cache: maven
+
+      - name: Build
+        run: mvn package -DskipTests
+
+      - name: Prepare JAR for testing
+        run: |
+          # Find the JAR
+          JAR_PATH=$(ls target/zarr-java-*.jar | grep -v original | grep -v javadoc | grep -v sources | head -1)
+          FULL_JAR_PATH="${GITHUB_WORKSPACE}/${JAR_PATH}"
+          echo "JAR_PATH=${FULL_JAR_PATH}" >> $GITHUB_ENV
+          echo "Found JAR at: ${FULL_JAR_PATH}"
+
+      - name: Run Conformance Tests
+        uses: Bisaloo/zarr-conformance-tests@v0.0.2
+        with:
+          zarr-cli: "java -jar ${{ env.JAR_PATH }}"

pom.xml

@@ -132,6 +132,12 @@
             <artifactId>commons-compress</artifactId>
             <version>1.28.0</version>
         </dependency>
+
+        <dependency>
+            <groupId>info.picocli</groupId>
+            <artifactId>picocli</artifactId>
+            <version>4.7.6</version>
+        </dependency>
     </dependencies>
 
     <repositories>
@@ -246,6 +252,26 @@
                     <tokenAuth>true</tokenAuth>
                 </configuration>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>3.5.0</version>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>shade</goal>
+                        </goals>
+                        <configuration>
+                            <transformers>
+                                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                    <mainClass>dev.zarr.zarrjava.cli.Main</mainClass>
+                                </transformer>
+                            </transformers>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
     </build>
 </project>

src/main/java/dev/zarr/zarrjava/cli/Main.java

@@ -0,0 +1,44 @@
+package dev.zarr.zarrjava.cli;
+
+import dev.zarr.zarrjava.core.Array;
+import picocli.CommandLine;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Option;
+
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.concurrent.Callable;
+
+@Command(name = "zarr-java-cli", mixinStandardHelpOptions = true, version = "1.0", description = "CLI wrapper for zarr-java conformance tests.")
+public class Main implements Callable<Integer> {
+
+    @Option(names = { "--array_path" }, description = "Path to the Zarr array", required = true)
+    private String arrayPath;
+
+    @Override
+    public Integer call() throws Exception {
+        try {
+            Path path = Paths.get(arrayPath);
+            // Attempt to open the array. This should throw if the array is invalid or
+            // cannot be opened.
+            Array array = Array.open(path);
+
+            // Read the entire array
+            ucar.ma2.Array data = array.read();
+
+            // Print the array values using ucar.ma2.Array's string representation.
+            System.out.println(data.toString());
+
+            return 0;
+        } catch (Exception e) {
+            System.err.println("Failed to open array at " + arrayPath);
+            e.printStackTrace();
+            return 1;
+        }
+    }
+
+    public static void main(String[] args) {
+        int exitCode = new CommandLine(new Main()).execute(args);
+        System.exit(exitCode);
+    }
+}