Serialization Overhaul (#81)

* overhaul serizalition code

* unify access to Input(De)Serializers behind facades to leverage the default methods for various input/output channels
* drop implicit buffering/decompressing as this should be decided where the stream are constructed (user-land)
* remove/cleanup the (now) unused code

* taf cleanups

* fix wording

CHANGELOG.md

@@ -28,17 +28,20 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
   * The `Visualization` factory has been moved from the `automata-core` artifact to the `automata-api` artifact. Furthermore, the previous `DummyVP` has been replaced with a `NoopVP` that does not show a swing window anymore when no proper VisualizationProvider is configured but instead logs an error message. This allows us to drop the `java.desktop` (module) dependency for headless setups and only require it in actual visualizers (DOT, JUNG, etc.).
 * The `DirectPowersetDTS` class has been renamed to `PowersetView`.
 * The `FormatException` is now a checked exception because we can [reasonably expect clients to recover from this error](https://docs.oracle.com/javase/tutorial/essential/exceptions/runtime.html). Furthermore, all parsing-related code has been aligned to use the `FormatException` instead of leaking implementation details (such as the `ParseException`s generated by JavaCC).
+* The serializers have been overhauled to allow for better integration of custom automaton types (especially when parsing). Some of the changes introduce new factory methods which may require some refactoring but the previous functionality is still available. As a part of this streamlining, many parsers no longer automatically un-compress or buffer the input streams to reduce overhead. The need for this can be determined best where the streams are created (in user-land).
 
 ### Removed
 
 * `SimpleTS#getSuccessors(S state, Iterable<? extends I> input)` has been removed. In order to traverse a (non-deterministic) transition system, use `TransitionSystem#powersetView` instead.
 * The `net.automatalib:automata-serialization-core` artifact has been dropped. Its contents are now part of the `net.automatalib:automata-api` artifact.
+* `TAFParseDiagnosticListener` has been removed. Reporting is now done via (slf4j) logging.
 
 ### Fixed
 
 * Fixed a bug in `SBAs#toCFMPS` which would allow the returned view to reach a final node on a non-return symbol.
 * Fixed (another) inconsistency bug in `Incremental*DAGBuilder`s.
 * The `AUTParser` now correctly reads non-deterministic automata.
+* The `TAFParsers` now correctly support wildcard transition definitions for DFAs.
 
 
 ## [0.11.0](https://github.com/LearnLib/automatalib/releases/tag/automatalib-0.11.0) - 2023-11-06

api/src/main/java/module-info.java

@@ -66,7 +66,6 @@
     exports net.automatalib.graph.visualization;
     exports net.automatalib.modelchecking;
     exports net.automatalib.serialization;
-    exports net.automatalib.serialization.automaton;
     exports net.automatalib.ts;
     exports net.automatalib.ts.acceptor;
     exports net.automatalib.ts.modal;

api/src/main/java/net/automatalib/serialization/InputModelSerializer.java

@@ -18,6 +18,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.nio.charset.StandardCharsets;
 
 import net.automatalib.alphabet.Alphabet;
 import net.automatalib.common.util.IOUtil;
@@ -35,7 +36,8 @@
 public interface InputModelSerializer<I, M extends SimpleTS<?, I>> extends ModelSerializer<InputModelData<I, M>> {
 
     /**
-     * Writes the model to the given output stream.
+     * Writes the model to the given output stream. If the format is a textual one, the output is typically encoded in
+     * {@link StandardCharsets#UTF_8 UTF-8}.
      * <p>
      * Note: the output stream will <b>not</b> be closed.
      *
@@ -52,7 +54,8 @@ public interface InputModelSerializer<I, M extends SimpleTS<?, I>> extends Model
     void writeModel(OutputStream os, M model, Alphabet<I> alphabet) throws IOException;
 
     /**
-     * Writes the model to the given file.
+     * Writes the model to the given file. If the format is a textual one, the output is typically encoded in
+     * {@link StandardCharsets#UTF_8 UTF-8}.
      *
      * @param f
      *         the file to write to

api/src/main/java/net/automatalib/serialization/ModelDeserializer.java

@@ -20,6 +20,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URL;
+import java.nio.charset.StandardCharsets;
 
 import net.automatalib.common.util.IOUtil;
 import net.automatalib.exception.FormatException;
@@ -33,7 +34,8 @@
 public interface ModelDeserializer<M> {
 
     /**
-     * Reads the contents from the given input stream and de-serializes it into a model instance.
+     * Reads the contents from the given input stream and de-serializes it into a model instance. If the format is a
+     * textual one, the input stream is typically interpreted in {@link StandardCharsets#UTF_8 UTF-8}.
      * <p>
      * Note: the input stream will <b>not</b> be closed.
      *
@@ -50,7 +52,8 @@ public interface ModelDeserializer<M> {
     M readModel(InputStream is) throws IOException, FormatException;
 
     /**
-     * Reads the contents from the given URL and de-serializes it into a model instance.
+     * Reads the contents from the given URL and de-serializes it into a model instance. If the format is a textual one,
+     * the input stream is typically interpreted in {@link StandardCharsets#UTF_8 UTF-8}.
      *
      * @param url
      *         the url to read data from
@@ -69,7 +72,8 @@ default M readModel(URL url) throws IOException, FormatException {
     }
 
     /**
-     * Reads the contents from the given file and de-serializes it into a model instance.
+     * Reads the contents from the given file and de-serializes it into a model instance. If the format is a textual
+     * one, the input stream is typically interpreted in {@link StandardCharsets#UTF_8 UTF-8}.
      *
      * @param f
      *         the file to read data from
@@ -88,7 +92,8 @@ default M readModel(File f) throws IOException, FormatException {
     }
 
     /**
-     * Reads the contents from the given byte buffer and de-serializes it into a model instance.
+     * Reads the contents from the given byte buffer and de-serializes it into a model instance. If the format is a
+     * textual one, the input stream is typically interpreted in {@link StandardCharsets#UTF_8 UTF-8}.
      *
      * @param buf
      *         the buffer to read data from

api/src/main/java/net/automatalib/serialization/ModelSerializer.java

@@ -18,6 +18,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.nio.charset.StandardCharsets;
 
 import net.automatalib.common.util.IOUtil;
 
@@ -30,7 +31,8 @@
 public interface ModelSerializer<M> {
 
     /**
-     * Writes the model to the given output stream.
+     * Writes the model to the given output stream. If the format is a textual one, the output is typically encoded in
+     * {@link StandardCharsets#UTF_8 UTF-8}.
      * <p>
      * Note: the output stream will <b>not</b> be closed.
      *
@@ -45,7 +47,8 @@ public interface ModelSerializer<M> {
     void writeModel(OutputStream os, M model) throws IOException;
 
     /**
-     * Writes the model to the given file.
+     * Writes the model to the given file. If the format is a textual one, the output is typically encoded in
+     * {@link StandardCharsets#UTF_8 UTF-8}.
      *
      * @param f
      *         the file to write to