enable tests #12

.github/workflows/maven.yml

@@ -0,0 +1,51 @@
+# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-maven
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: LPhyBeast test
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout LPhyBeastExt
+        uses: actions/checkout@v4
+      - name: Checkout LPhy
+        uses: actions/checkout@v4
+        with:
+          repository: LinguaPhylo/linguaPhylo
+      - name: Checkout LPhy
+        uses: actions/checkout@v4
+        with:
+          repository: LinguaPhylo/LPhyBeast
+
+      - name: Set up JDK 17
+        uses: actions/setup-java@v3
+        with:
+          java-version: '17'
+          distribution: 'temurin'
+          cache: maven
+
+      - name: Clean
+        run: mvn clean
+        # -B,--batch-mode   Run in non-interactive (batch) mode (disables output color)
+      - name: Test with Maven
+        run: mvn -B test --file pom.xml
+
+      - name: Publish unit test results
+        uses: EnricoMi/publish-unit-test-result-action@v2
+        if: always()
+        with:
+          files: ./LPhyBeast/*/target/surefire-reports/**/*.xml

lphybeast-mascot/src/test/java/mascot/lphybeast/H3N2TutorialTest.java

@@ -5,6 +5,7 @@
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
@@ -24,9 +25,12 @@ public class H3N2TutorialTest {
 
     @BeforeEach
     public void setUp() {
-        // load lphybeast-ext/build/lphybeast/version.xml
+        // load ../LPhyBeast/version.xml
         Path lphybeastDir = Paths.get(UserDir.getUserDir().toAbsolutePath().getParent().toString(),
-                "lphybeast-ext","build","lphybeast");
+                "..","LPhyBeast");
+        if (!Files.exists(lphybeastDir))
+            throw new IllegalArgumentException("Cannot locate LPhyBeast Dir : " + lphybeastDir);
+
         TestUtils.loadServices(lphybeastDir.toString());
         // load mascot/version.xml
         Path parentDir = UserDir.getUserDir().toAbsolutePath();

lphybeast-mm/src/test/java/mm/lphybeast/tobeast/generators/LewisMKToBEASTTest.java

@@ -5,6 +5,7 @@
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
@@ -26,10 +27,12 @@ public class LewisMKToBEASTTest {
 
     @BeforeEach
     public void setUp() {
-        // load lphybeast-ext/build/lphybeast/version.xml
+        // load ../LPhyBeast/version.xml
         Path lphybeastDir = Paths.get(UserDir.getUserDir().toAbsolutePath().getParent().toString(),
-                "lphybeast-ext","build","lphybeast");
-        TestUtils.loadServices(lphybeastDir.toString());
+                "..","LPhyBeast");
+        if (!Files.exists(lphybeastDir))
+            throw new IllegalArgumentException("Cannot locate LPhyBeast Dir : " + lphybeastDir);
+
         // load mm/version.xml
         Path parentDir = UserDir.getUserDir().toAbsolutePath();
         TestUtils.loadServices(parentDir.toString());

lphybeast-sa/src/test/java/sa/lphybeast/tobeast/generators/FossilBirthDeathTreeToBEASTTest.java

@@ -5,6 +5,7 @@
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
@@ -27,9 +28,12 @@ class FossilBirthDeathTreeToBEASTTest {
 
     @BeforeEach
     public void setUp() {
-        // load lphybeast-ext/build/lphybeast/version.xml
+        // load ../LPhyBeast/version.xml
         Path lphybeastDir = Paths.get(UserDir.getUserDir().toAbsolutePath().getParent().toString(),
-                "lphybeast-ext","build","lphybeast");
+                "..","LPhyBeast");
+        if (!Files.exists(lphybeastDir))
+            throw new IllegalArgumentException("Cannot locate LPhyBeast Dir : " + lphybeastDir);
+
         TestUtils.loadServices(lphybeastDir.toString());
         // load sa/version.xml
         Path parentDir = UserDir.getUserDir().toAbsolutePath();

lphybeast-sa/src/test/java/sa/lphybeast/tobeast/generators/SimFBDAgeToBEASTTest.java

@@ -5,6 +5,7 @@
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
@@ -24,9 +25,12 @@ class SimFBDAgeToBEASTTest {
 
     @BeforeEach
     public void setUp() {
-        // load lphybeast-ext/build/lphybeast/version.xml
+        // load ../LPhyBeast/version.xml
         Path lphybeastDir = Paths.get(UserDir.getUserDir().toAbsolutePath().getParent().toString(),
-                "lphybeast-ext","build","lphybeast");
+                "..","LPhyBeast");
+        if (!Files.exists(lphybeastDir))
+            throw new IllegalArgumentException("Cannot locate LPhyBeast Dir : " + lphybeastDir);
+
         TestUtils.loadServices(lphybeastDir.toString());
         // load sa/version.xml
         Path parentDir = UserDir.getUserDir().toAbsolutePath();