From bdf24a3259f995e8b89349359b9ca150f7b0a7f2 Mon Sep 17 00:00:00 2001
From: walterxie <walter@cs.auckland.ac.nz>
Date: Wed, 17 Jan 2024 17:57:50 +1300
Subject: [PATCH] fix unit tests #109 #112

---
 .github/workflows/lphybeast.yml                    |  2 +-
 .../src/test/java/lphybeast/H5N1TutorialTest.java  | 14 ++++++++------
 .../src/test/java/lphybeast/RSV2TutorialTest.java  | 10 +++++-----
 .../java/lphybeast/SkylinePlotsTutorialTest.java   | 10 ++++++----
 4 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/lphybeast.yml b/.github/workflows/lphybeast.yml
index 587ae5c..548e90a 100644
--- a/.github/workflows/lphybeast.yml
+++ b/.github/workflows/lphybeast.yml
@@ -75,7 +75,7 @@ jobs:
         working-directory: ./LPhyBeast
         # only available in lphy at the moment
         # temp disable test because of github issue
-        run: ./gradlew build -x test
+        run: ./gradlew build
 
       - name: Publish unit test results
         uses: EnricoMi/publish-unit-test-result-action@v2
diff --git a/lphybeast/src/test/java/lphybeast/H5N1TutorialTest.java b/lphybeast/src/test/java/lphybeast/H5N1TutorialTest.java
index 7b930f1..0052b6e 100644
--- a/lphybeast/src/test/java/lphybeast/H5N1TutorialTest.java
+++ b/lphybeast/src/test/java/lphybeast/H5N1TutorialTest.java
@@ -124,15 +124,17 @@ public void testDPG() {
         assertTrue(xml.contains("BitFlipOperator") && xml.contains("parameter=\"@I\""), "I.bitFlip Operator" );
 
         // 6 ScaleOperator, incl. tree
-        assertEquals(6, xml.split("ScaleOperator", -1).length - 1, "ScaleOperator" );
+        assertEquals(6, xml.split("BactrianScaleOperator", -1).length - 1,
+                "BactrianScaleOperator" );
 
-        assertTrue(xml.contains("Exchange") && xml.contains("SubtreeSlide") && xml.contains("Uniform") &&
-                xml.contains("WilsonBalding"), "Tree Operator" );
+        assertTrue(xml.contains("Exchange") && xml.contains("BactrianSubtreeSlide") &&
+                xml.contains("BactrianNodeOperator") && xml.contains("WilsonBalding"), "Tree Operator" );
 
-        assertTrue(xml.contains("UpDownOperator") &&
-                xml.contains("<up") && xml.contains("<down"), "UpDownOperator" );
+        assertTrue(xml.contains("BactrianUpDownOperator") &&
+                xml.contains("<up") && xml.contains("<down"), "BactrianUpDownOperator" );
         // 3 DeltaExchangeOperator
-        assertEquals(3, xml.split("DeltaExchangeOperator", -1).length - 1, "DeltaExchangeOperator");
+        assertEquals(3, xml.split("BactrianDeltaExchangeOperator", -1).length - 1,
+                "BactrianDeltaExchangeOperator");
 
         assertTrue(xml.contains("chainLength=\"1000000\"") && xml.contains("logEvery=\"500\"") &&
                 xml.contains("fileName=\"" + fileStem + ".log\"") && xml.contains("fileName=\"" + fileStem + ".trees\""),
diff --git a/lphybeast/src/test/java/lphybeast/RSV2TutorialTest.java b/lphybeast/src/test/java/lphybeast/RSV2TutorialTest.java
index 2d15af3..74dac8d 100644
--- a/lphybeast/src/test/java/lphybeast/RSV2TutorialTest.java
+++ b/lphybeast/src/test/java/lphybeast/RSV2TutorialTest.java
@@ -88,15 +88,15 @@ public void testRSV2() {
         assertEquals(3,xml.split("ThreadedTreeLikelihood", -1).length - 1, "Tree Likelihood" );
 
         // 5 ScaleOperator, incl. tree
-        assertEquals(5, xml.split("ScaleOperator", -1).length - 1, "ScaleOperator" );
+        assertEquals(5, xml.split("BactrianScaleOperator", -1).length - 1, "BactrianScaleOperator" );
 
-        assertTrue(xml.contains("Exchange") && xml.contains("SubtreeSlide") && xml.contains("Uniform") &&
+        assertTrue(xml.contains("Exchange") && xml.contains("BactrianSubtreeSlide") && xml.contains("BactrianNodeOperator") &&
                 xml.contains("WilsonBalding"), "Tree Operator" );
 
-        assertTrue(xml.contains("UpDownOperator") &&
-                xml.contains("<up") && xml.contains("<down"), "UpDownOperator" );
+        assertTrue(xml.contains("BactrianUpDownOperator") &&
+                xml.contains("<up") && xml.contains("<down"), "BactrianUpDownOperator" );
         // 4 DeltaExchangeOperator
-        assertEquals(4, xml.split("DeltaExchangeOperator", -1).length - 1, "DeltaExchangeOperator");
+        assertEquals(4, xml.split("BactrianDeltaExchangeOperator", -1).length - 1, "BactrianDeltaExchangeOperator");
 
         assertTrue(xml.contains("chainLength=\"1000000\"") && xml.contains("logEvery=\"500\"") &&
                 xml.contains("fileName=\"" + fileStem + ".log\"") && xml.contains("fileName=\"" + fileStem + ".trees\""),
diff --git a/lphybeast/src/test/java/lphybeast/SkylinePlotsTutorialTest.java b/lphybeast/src/test/java/lphybeast/SkylinePlotsTutorialTest.java
index d85d1c3..cad72ff 100644
--- a/lphybeast/src/test/java/lphybeast/SkylinePlotsTutorialTest.java
+++ b/lphybeast/src/test/java/lphybeast/SkylinePlotsTutorialTest.java
@@ -83,13 +83,15 @@ public void testBS() {
         assertTrue(xml.contains("gammaCategoryCount=\"4\"") && xml.contains("shape=\"@gamma\""), "SiteModel" );
 
         // 4 ScaleOperator, incl. tree
-        assertEquals(4, xml.split("ScaleOperator", -1).length - 1, "ScaleOperator" );
+        assertEquals(4, xml.split("BactrianScaleOperator", -1).length - 1,
+                "BactrianScaleOperator" );
 
-        assertTrue(xml.contains("Exchange") && xml.contains("SubtreeSlide") && xml.contains("Uniform") &&
-                xml.contains("WilsonBalding"), "Tree Operator" );
+        assertTrue(xml.contains("Exchange") && xml.contains("BactrianSubtreeSlide") &&
+                xml.contains("BactrianNodeOperator") && xml.contains("WilsonBalding"), "Tree Operator" );
 
        // 3 DeltaExchangeOperator
-        assertEquals(3, xml.split("DeltaExchangeOperator", -1).length - 1, "DeltaExchangeOperator");
+        assertEquals(3, xml.split("BactrianDeltaExchangeOperator", -1).length - 1,
+                "BactrianDeltaExchangeOperator");
 
         assertTrue(xml.contains("chainLength=\"1000000\"") && xml.contains("logEvery=\"500\"") &&
                 xml.contains("fileName=\"" + fileStem + ".log\"") && xml.contains("fileName=\"" + fileStem + ".trees\"") &&