add java docs

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

@@ -134,9 +134,9 @@
  * </p>
  * <p>
  * Appose comes with built-in support for two worker implementations:
- * {@code python_worker} to run Python scripts, and {@link GroovyWorker}
+ * {@code python_worker} to run Python scripts,
  * to run Groovy scripts. These workers can be created easily by invoking
- * the {@link Environment#python} and {@link Environment#groovy} methods
+ * the {@link Environment#python} methods
  * respectively.
  * </p>
  * <p>

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

@@ -146,8 +146,8 @@ private ProcessBuilder getBuilder( final boolean isInheritIO )
 	 *             If the current thread is interrupted by another thread while it
 	 *             is waiting, then the wait is ended and an InterruptedException is
 	 *             thrown.
-	 * @throws ArchiveException 
-	 * @throws URISyntaxException 
+	 * @throws ArchiveException if there is any error decompressing the micromamba files
+	 * @throws URISyntaxException if the micromamba install link is wrong or does not work or there is no internet connection
 	 */
 	public Conda() throws IOException, InterruptedException, ArchiveException, URISyntaxException
 	{
@@ -178,8 +178,8 @@ public Conda() throws IOException, InterruptedException, ArchiveException, URISy
 	 *             If the current thread is interrupted by another thread while it
 	 *             is waiting, then the wait is ended and an InterruptedException is
 	 *             thrown.
-	 * @throws ArchiveException 
-	 * @throws URISyntaxException 
+	 * @throws ArchiveException if there is any error decompressing the micromamba files
+	 * @throws URISyntaxException if the micromamba install link is wrong or does not work or there is no internet connection
 	 */
 	public Conda( final String rootdir ) throws IOException, InterruptedException, ArchiveException, URISyntaxException
 	{
@@ -784,6 +784,8 @@ public void runConda(Consumer<String> consumer, final String... args ) throws Ru
 	 *            One or more arguments for the Conda command.
 	 * @throws IOException
 	 *             If an I/O error occurs.
+	 * @throws RuntimeException
+	 *             If the Conda command does not run properly
 	 * @throws InterruptedException
 	 *             If the current thread is interrupted by another thread while it
 	 *             is waiting, then the wait is ended and an InterruptedException is
@@ -876,6 +878,15 @@ public List< String > getEnvironmentNames() throws IOException
 		return envs;
 	}
 
+	/**
+	 * TODO
+	 * Check whether an environment has the wanted deps installed
+	 * @param envDir
+	 * 	directory of the environment
+	 * @param dependencies
+	 * 	lsit of wanted deps
+	 * @return true if the wanted deps are installed or false otherwise
+	 */
 	public static boolean checkDependenciesInEnv(String envDir, List<String> dependencies) {
 		if (!(new File(envDir).isDirectory()))
 			return false;
@@ -884,6 +895,13 @@ public static boolean checkDependenciesInEnv(String envDir, List<String> depende
 		return false;
 	}
 
+	/**
+	 * TODO
+	 * Check the environment defined by this yaml file exists
+	 * @param envYaml
+	 * 	path to the Conda/Mamba env yaml file
+	 * @return	true if it exists and false otherwise
+	 */
 	public boolean checkEnvFromYamlExists(String envYaml) {
 		if (envYaml == null || new File(envYaml).isFile() == false 
 				|| (envYaml.endsWith(".yaml") && envYaml.endsWith(".yml"))) {

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

@@ -57,7 +57,6 @@ public interface Environment {
 	 * </p>
 	 * 
 	 * @return The newly created service.
-	 * @see #groovy To create a service for Groovy script execution.
 	 * @throws IOException If something goes wrong starting the worker process.
 	 */
 	default Service python() throws IOException {
@@ -125,7 +124,6 @@ default Service java(String mainClass, List<String> classPath,
 	 * @param args Command line arguments to pass to the worker process
 	 *          (e.g. <code>{"-v", "--enable-everything"}</code>.
 	 * @return The newly created service.
-	 * @see #groovy To create a service for Groovy script execution.
 	 * @see #python() To create a service for Python script execution.
 	 * @throws IOException If something goes wrong starting the worker process.
 	 */

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

@@ -93,9 +93,9 @@ public static void unBZip2(File source, File destination) throws FileNotFoundExc
 	 * 
 	 * @param inputFile     the input .tar file
 	 * @param outputDir     the output directory file. 
-	 * @throws IOException 
-	 * @throws FileNotFoundException
-	 * @throws ArchiveException 
+	 * @throws IOException reding, writting or creating the target or source files
+	 * @throws FileNotFoundException if the file that needs to be untared is not found
+	 * @throws ArchiveException  if there is any error decompressing the tar file
 	 */
 	public static void unTar(final File inputFile, final File outputDir) throws FileNotFoundException, IOException, ArchiveException {
 
@@ -126,6 +126,15 @@ public static void unTar(final File inputFile, final File outputDir) throws File
 
 	}
 
+	/**
+	 * Example main method
+	 * @param args
+	 * 	no args are required
+	 * @throws FileNotFoundException if some file is not found
+	 * @throws IOException if there is any error reading or writting
+	 * @throws ArchiveException if there is any error decompressing
+	 * @throws URISyntaxException if the url is wrong or there is no internet connection
+	 */
 	public static void main(String[] args) throws FileNotFoundException, IOException, ArchiveException, URISyntaxException {
 		String url = Conda.MICROMAMBA_URL;
 		final File tempFile = File.createTempFile( "miniconda", ".tar.bz2" );
@@ -156,11 +165,9 @@ public static void main(String[] args) throws FileNotFoundException, IOException
 	 * has been redirected
 	 * @param url
 	 * 	original url. Connecting to that url must give a 301, 302 or 303 response code
-	 * @param conn
-	 * 	connection to the url
 	 * @return the redirected url
-	 * @throws MalformedURLException 
-	 * @throws URISyntaxException 
+	 * @throws MalformedURLException if the url does not fulfil the requirements for an url to be correct
+	 * @throws URISyntaxException if the url is incorrect or there is no internet connection
 	 */
 	public static URL redirectedURL(URL url) throws MalformedURLException, URISyntaxException {
 		int statusCode;