TEMPORARILYHE PROJECT TO BE ABLE TO USE IT

pom.xml

@@ -120,7 +120,6 @@
 		<dependency>
 			<groupId>org.yaml</groupId>
 			<artifactId>snakeyaml</artifactId>
-			<version>2.0</version>
 		</dependency>
 		<dependency>
 			<groupId>net.imglib2</groupId>
@@ -131,20 +130,17 @@
 			<artifactId>jackson-dataformat-msgpack</artifactId>
 			<version>0.9.5</version>
 		</dependency>
-		<dependency>
-			<groupId>org.apposed</groupId>
-			<artifactId>appose</artifactId>
-			<version>0.1.1-SNAPSHOT</version>
-		</dependency>
-		<!--<dependency>
-            <groupId>org.msgpack</groupId>
-            <artifactId>jackson-dataformat-msgpack</artifactId>
-            <version>0.9.0</version>
-    	</dependency> -->
 		<dependency>
 			<groupId>net.java.dev.jna</groupId>
-			<artifactId>jna</artifactId>
+			<artifactId>jna-platform</artifactId>
 			<version>5.13.0</version>
 		</dependency>
+		<!-- APPOSE DEPS-->
+		<dependency>
+		    <groupId>org.apache.commons</groupId>
+		    <artifactId>commons-compress</artifactId>
+		    <version>1.24.0</version>
+		<!-- APPOSE DEPS-->
+		</dependency>
 	</dependencies>
 </project>

src/main/java/io/bioimage/modelrunner/apposed/appose/Appose.java

@@ -0,0 +1,182 @@
+/*-
+ * #%L
+ * Appose: multi-language interprocess cooperation with shared memory.
+ * %%
+ * Copyright (C) 2023 Appose developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package io.bioimage.modelrunner.apposed.appose;
+
+import java.io.File;
+
+/**
+ * Appose is a library for interprocess cooperation with shared memory. The
+ * guiding principles are <em>simplicity</em> and <em>efficiency</em>.
+ * <p>
+ * Appose was written to enable <strong>easy execution of Python-based deep
+ * learning from Java without copying tensors</strong>, but its utility extends
+ * beyond that. The steps for using Appose are:
+ * </p>
+ * <ol>
+ * <li>Build an {@link Environment} with the dependencies you need.</li>
+ * <li>Create a {@link Service} linked to a <em>worker</em>, which runs in its
+ * own process.</li>
+ * <li>Execute scripts on the worker by launching {@link Service.Task
+ * Tasks}.</li>
+ * <li>Receive status updates from the task asynchronously
+ * {@link Service.Task#listen via callbacks}.</li>
+ * </ol>
+ * <h2>Examples</h2>
+ * <ul>
+ * <li>TODO - move the below code somewhere linkable, for succinctness
+ * here.</li>
+ * </ul>
+ * <p>
+ * Here is a very simple example written in Java:
+ * </p>
+ * 
+ * <pre>{@code
+ * Environment env = Appose.conda("/path/to/environment.yml").build();
+ * Service python = env.python();
+ * Task task = python.task("""
+ *     5 + 6
+ *     """);
+ * task.start().waitFor();
+ * Object result = task.outputs.get("result");
+ * assertEquals(11, result);
+ * }</pre>
+ * <p>
+ * And here is an example using a few more of Appose's features:
+ * </p>
+ * 
+ * <pre>{@code
+ * Environment env = Appose.conda("/path/to/environment.yml").build();
+ * Service python = env.python();
+ * Task golden_ratio = python.task("""
+ *     # Approximate the golden ratio using the Fibonacci sequence.
+ *     previous = 0
+ *     current = 1
+ *     for i in range(iterations):
+ *         if task.cancel_requested:
+ *             task.cancel()
+ *             break
+ *         task.status(current=i, maximum=iterations)
+ *         v = current
+ *         current += previous
+ *         previous = v
+ *     task.outputs["numer"] = current
+ *     task.outputs["denom"] = previous
+ *     """);
+ * task.listen(event -> {
+ *     switch (event.responseType) {
+ *         case UPDATE:
+ *             System.out.println("Progress: " + task.current + "/" + task.maximum);
+ *             break;
+ *         case COMPLETION:
+ *             long numer = (Long) task.outputs["numer"];
+ *             long denom = (Long) task.outputs["denom"];
+ *             double ratio = (double) numer / denom;
+ *             System.out.println("Task complete. Result: " + numer + "/" + denom + " =~ " + ratio);
+ *             break;
+ *         case CANCELATION:
+ *             System.out.println("Task canceled");
+ *             break;
+ *         case FAILURE:
+ *             System.out.println("Task failed: " + task.error);
+ *             break;
+ *     }
+ * });
+ * task.start();
+ * Thread.sleep(1000);
+ * if (!task.status.isFinished()) {
+ *     // Task is taking too long; request a cancelation.
+ *     task.cancel();
+ * }
+ * task.waitFor();
+ * }</pre>
+ * <p>
+ * Of course, the above examples could have been done all in Java. But hopefully
+ * they hint at the possibilities of easy cross-language integration.
+ * </p>
+ * <h2>Workers</h2>
+ * <p>
+ * A <em>worker</em> is a separate process created by Appose to do asynchronous
+ * computation on behalf of the calling process. The calling process interacts
+ * with a worker via its associated {@link Service}.
+ * </p>
+ * <p>
+ * Appose comes with built-in support for two worker implementations:
+ * {@code python_worker} to run Python scripts, and {@link GroovyWorker}
+ * to run Groovy scripts. These workers can be created easily by invoking
+ * the {@link Environment#python} and {@link Environment#groovy} methods
+ * respectively.
+ * </p>
+ * <p>
+ * But Appose is compatible with any program that abides by the
+ * <em>Appose worker process contract</em>:
+ * </p>
+ * <ol>
+ * <li>The worker must accept requests in Appose's request format on its
+ * standard input (stdin) stream.</li>
+ * <li>The worker must issue responses in Appose's response format on its
+ * standard output (stdout) stream.</li>
+ * </ol>
+ * <p>
+ * TODO - write up the request and response formats in detail here!
+ * JSON, one line per request/response.
+ * </p>
+ * 
+ * @author Curtis Rueden
+ */
+public class Appose {
+
+	public static Builder base(File directory) {
+		return new Builder().base(directory);
+	}
+
+	public static Builder base(String directory) {
+		return base(new File(directory));
+	}
+
+	public static Builder java(String vendor, String version) {
+		return new Builder().java(vendor, version);
+	}
+
+	public static Builder conda(File environmentYaml) {
+		return new Builder().conda(environmentYaml);
+	}
+
+	public static Environment system() {
+		return system(new File("."));
+	}
+
+	public static Environment system(File directory) {
+		return new Builder().base(directory).useSystemPath().build();
+	}
+
+	public static Environment system(String directory) {
+		return system(new File(directory));
+	}
+}

src/main/java/io/bioimage/modelrunner/apposed/appose/Builder.java

@@ -0,0 +1,112 @@
+/*-
+ * #%L
+ * Appose: multi-language interprocess cooperation with shared memory.
+ * %%
+ * Copyright (C) 2023 Appose developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package io.bioimage.modelrunner.apposed.appose;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.nio.file.Paths;
+
+import org.apache.commons.compress.archivers.ArchiveException;
+
+public class Builder {
+
+
+	public Environment build() {
+		String base = baseDir.getPath();
+		boolean useSystemPath = systemPath;
+
+		// TODO Build the thing!~
+		// Hash the state to make a base directory name.
+		// - Construct conda environment from condaEnvironmentYaml.
+		// - Download and unpack JVM of the given vendor+version.
+		// - Populate ${baseDirectory}/jars with Maven artifacts?
+
+		try {
+			Conda conda = new Conda(Conda.BASE_PATH);
+			String envName = "appose";
+			if (conda.getEnvironmentNames().contains( envName )) {
+				// TODO: Should we update it? For now, we just use it.
+			}
+			else {
+				conda.create(envName, "-f", condaEnvironmentYaml.getAbsolutePath());
+			}
+		} catch (IOException e) {
+			throw new RuntimeException(e);
+		} catch (InterruptedException e) {
+			throw new RuntimeException(e);
+		} catch (ArchiveException e) {
+			throw new RuntimeException(e);
+		} catch (URISyntaxException e) {
+			throw new RuntimeException(e);
+		}
+
+		return new Environment() {
+			@Override public String base() { return base; }
+			@Override public boolean useSystemPath() { return useSystemPath; }
+		};
+	}
+
+	// -- Configuration --
+
+	private boolean systemPath;
+
+	public Builder useSystemPath() {
+		systemPath = true;
+		return this;
+	}
+
+	private File baseDir;
+
+	public Builder base(File directory) {
+		baseDir = directory;
+		return this;
+	}
+
+	// -- Conda --
+
+	private File condaEnvironmentYaml;
+
+	public Builder conda(File environmentYaml) {
+		this.condaEnvironmentYaml = environmentYaml;
+		return this;
+	}
+
+	// -- Java --
+
+	private String javaVendor;
+	private String javaVersion;
+
+	public Builder java(String vendor, String version) {
+		this.javaVendor = vendor;
+		this.javaVersion = version;
+		return this;
+	}
+}