- * In BEAST3, bounds are derived from the parameter's domain and are never written to the - * state file. The expected format is therefore always bound-free: + * The XML node's {@code id} attribute is set on {@code param} directly; the node's text + * content is the full {@link #paramToString(StateNode)} output, which still begins with the + * parameter ID. In BEAST 3, bounds are derived from the domain at runtime and are never + * written to the state file. Expected formats: *
Two distinct concerns are kept as separate methods on purpose: + *
Individual test classes are responsible for naming their own XML/JSON files.
+ */
+public class XMLPathUtil {
+
+ private static final String EXAMPLES_CLASSPATH = "beast.base/examples";
+
+ /**
+ * Returns the absolute path to the beast.base examples directory.
+ * Resolves via the test classpath (works on any machine or CI runner),
+ * falling back to {@code user.dir} if the resource is not found.
+ */
+ public static String resolveExamplesDir() {
+ URL url = XMLPathUtil.class.getClassLoader().getResource(EXAMPLES_CLASSPATH);
+ if (url != null) {
+ try {
+ return new File(url.toURI()).getAbsolutePath();
+ } catch (URISyntaxException e) {
+ // fall through to user.dir fallback
+ }
+ }
+ return System.getProperty("user.dir") + "/" + EXAMPLES_CLASSPATH;
+ }
+
+ /**
+ * Creates the {@code ./test/} output directory if absent and sets
+ * {@code file.name.prefix=test/} so BEAST logger output is written there.
+ * Call from {@code @BeforeEach} in each integration test class.
+ */
+ public static void setUpOutputDir() {
+ setUpOutputDir("");
+ }
+
+ /**
+ * Creates {@code ./test/ Note: {@code file.name.prefix} is a JVM-wide system property. Callers that
+ * mutate it must declare {@code @ResourceLock("beast.logger.globals")} so JUnit 5's
+ * parallel scheduler serializes them; see {@code junit-platform.properties} for the
+ * full list of affected classes.
+ */
+ public static void setUpOutputDir(String subdir) {
+ String path = subdir == null || subdir.isEmpty() ? "test/" : "test/" + subdir + "/";
+ File dir = new File("./" + path);
+ if (!dir.exists())
+ dir.mkdirs();
+ System.setProperty("file.name.prefix", path);
+ }
+}
diff --git a/beast-base/src/test/java/test/beast/integration/XMLProducerTest.java b/beast-base/src/test/java/test/beast/integration/XMLProducerTest.java
index a4bbeef0..cd9ea584 100644
--- a/beast-base/src/test/java/test/beast/integration/XMLProducerTest.java
+++ b/beast-base/src/test/java/test/beast/integration/XMLProducerTest.java
@@ -1,12 +1,5 @@
package test.beast.integration;
-import java.io.File;
-import java.io.FilenameFilter;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.jupiter.api.Test;
-
import beast.base.core.BEASTInterface;
import beast.base.evolution.datatype.Nucleotide;
import beast.base.inference.Logger;
@@ -14,7 +7,13 @@
import beast.base.parser.XMLParser;
import beast.base.parser.XMLProducer;
import beast.base.util.Randomizer;
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import org.junit.jupiter.api.Test;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.util.ArrayList;
+import java.util.List;
+
import static org.junit.jupiter.api.Assertions.assertTrue;
public class XMLProducerTest {
@@ -34,9 +33,12 @@ public class XMLProducerTest {
@Test
public void test_ThatNexusExamplesProduces() {
try {
- String dirName = System.getProperty("user.dir") + "/beast.base/examples/nexus";
+ // Delegate to XMLPathUtil so classpath resolution and user.dir fallback
+ // logic lives in one place; nexus/ is a subdirectory of examples/.
+ String dirName = new File(XMLPathUtil.resolveExamplesDir(), "nexus").getAbsolutePath();
System.out.println("Test Nexus Examples in " + dirName);
File exampleDir = new File(dirName);
+ assertTrue(exampleDir.exists(), "Nexus example directory does not exist: " + dirName);
String[] exampleFiles = exampleDir.list(new FilenameFilter() {
@Override
public boolean accept(File dir, String name) {
diff --git a/beast-fx/pom.xml b/beast-fx/pom.xml
index 0886aa28..e7b955b3 100644
--- a/beast-fx/pom.xml
+++ b/beast-fx/pom.xml
@@ -102,10 +102,12 @@
--add-reads beast.fx=ALL-UNNAMED
--add-reads beast.base=ALL-UNNAMED
--add-reads beast.pkgmgmt=ALL-UNNAMED
+ --add-exports javafx.base/com.sun.javafx.logging=ALL-UNNAMED
--add-exports javafx.graphics/com.sun.glass.ui=ALL-UNNAMED
- --add-exports javafx.graphics/com.sun.glass.ui.monocle=ALL-UNNAMED
--add-exports javafx.graphics/com.sun.javafx.application=ALL-UNNAMED
+ --add-exports javafx.graphics/com.sun.javafx.util=ALL-UNNAMED
--add-opens javafx.graphics/com.sun.glass.ui=ALL-UNNAMED
+ --add-opens javafx.graphics/com.sun.javafx.application=ALL-UNNAMED