change persist default option to root

.github/workflows/publish-javadoc.yml

@@ -0,0 +1,39 @@
+name: Publish Javadoc
+
+on:
+  push:
+    branches:
+      - develop  # Only publish when pushing to develop branch
+
+jobs:
+  publish-javadoc:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write  # Needed to push to the javadoc branch
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up JDK 19
+        uses: actions/setup-java@v3
+        with:
+          java-version: '19'
+          distribution: 'temurin'
+          cache: maven
+
+      - name: Build (optional if Javadoc needs compiled sources)
+        run: mvn -B compile --file pom.xml
+
+      - name: Generate Javadoc
+        run: mvn javadoc:javadoc --file pom.xml
+
+      - name: Deploy Javadoc to branch
+        uses: MathieuSoysal/Javadoc-publisher.yml@v3.0.2
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          javadoc-branch: javadoc
+          java-version: 19
+          target-folder: javadoc
+          project: maven
+

src/main/java/simpaths/data/CallEMLight.java

@@ -10,7 +10,7 @@ public class CallEMLight {
 
     //-------------------------------------------------------------------------------------------------------------
     /**
-     *	CALLING EUROMOD LIGHT IN THIS SIMULATION RUN TO GIVE THE USER THE OPPORTUNITY TO CREATE EUROMOD OUTPUT POPULATION from which to generate population of households and persons after tax & benefit treatment
+     *	CALLING EUROMOD LIGHT IN THIS SIMULATION RUN TO GIVE THE USER THE OPPORTUNITY TO CREATE EUROMOD OUTPUT POPULATION from which to generate population of households and persons after tax and benefit treatment
      **/
     //-------------------------------------------------------------------------------------------------------------
 

src/main/java/simpaths/data/CallEUROMOD.java

@@ -11,7 +11,7 @@ public class CallEUROMOD {
 
 	//-------------------------------------------------------------------------------------------------------------
     /**
-    *	CALLING EUROMOD IN THIS SIMULATION RUN TO GIVE THE USER THE OPPORTUNITY TO CREATE EUROMOD OUTPUT POPULATION from which to generate population of households and persons after tax & benefit treatment 
+    *	CALLING EUROMOD IN THIS SIMULATION RUN TO GIVE THE USER THE OPPORTUNITY TO CREATE EUROMOD OUTPUT POPULATION from which to generate population of households and persons after tax and benefit treatment
     **/
     //-------------------------------------------------------------------------------------------------------------    		
 	public static void run() {

src/main/java/simpaths/data/ScenarioTable.java

@@ -28,7 +28,6 @@ public class ScenarioTable extends JPanel implements ActionListener {
     /**
      *
      *  CONSTRUCTOR TO INITIATE TABLE
-     * @param title
      * @param columnNames
      * @param data
      *

src/main/java/simpaths/experiment/SimPathsMultiRun.java

@@ -85,15 +85,16 @@ public static void main(String[] args) {
 			} else {
 				countryString = "United Kingdom";
 			}
+		    country = Country.getCountryFromNameString(countryString);
 			String valueYear = lastDatabaseCountryAndYear.getValue(country.toString()).toString();
 			startYear = Integer.parseInt(valueYear);
 		} catch (NullPointerException e) {
 			System.out.println("No last database country and year found.");
 			countryString = "United Kingdom";
+		    country = Country.getCountryFromNameString(countryString);
 			startYear = 2019;
 		}
 
-		country = Country.getCountryFromNameString(countryString);
 
 		if (innovationArgs!=null)
 			updateLocalParameters(innovationArgs);
@@ -178,7 +179,7 @@ private static boolean parseCommandLineArgs(String[] args) {
 				"\n - root: persist to root output folder (input/)" +
 				"\n - run: persist to run output folder (output/[yyyymmdd_seed]/input/)" +
 				"\n - none: do not write/read processed dataset.\n" +
-				"(default: `run` - multirun copy in output folder)");
+				"(default: `root` - persist to root folder for further runs)");
 		persistRoot.setArgName("persist");
 		options.addOption(persistRoot);
 
@@ -241,9 +242,9 @@ private static boolean parseCommandLineArgs(String[] args) {
 						persist_root = false;
 						break;
 					default:
-						System.out.println("Persist option `" + cmd.getOptionValue("P") + "` not recognised. Valid values: `none`, `root`, `run`. Persisting processed data to run folder");
+						System.out.println("Persist option `" + cmd.getOptionValue("P") + "` not recognised. Valid values: `none`, `root`, `run`. Persisting processed data to root folder");
 						persist_population = true;
-						persist_root = false;
+						persist_root = true;
 				}
 
 			if (cmd.hasOption("f")) {

src/main/java/simpaths/model/taxes/database/TaxDonorDataParser.java

@@ -28,8 +28,8 @@
 /**
  *
  * CLASS TO MANAGE TRANSLATION OF CSV DATA FROM EUROMOD TO DATABASE FOR DONORS USED TO IMPUTE TAX AND BENEFIT PAYMENTS
- * csv data are processed and saved to the DONORPERSON_<country code> table in the relational database. These data
- * are used as working variables to construct the DONORTAXUNIT_<country code> table, which is then used exclusively \
+ * csv data are processed and saved to the DONORPERSON_country code table in the relational database. These data
+ * are used as working variables to construct the DONORTAXUNIT_country code table, which is then used exclusively \
  * for imputing tax and benefit payments, drawing heavily on SQL calls made via Hibernate
  *
  */
@@ -421,7 +421,6 @@ public static String stringAppender(Collection<String> strings) {
      * output .txt files, picking up the relevant columns for each EUROMOD policy scenario, that
      * will eventually be parsed into the JAS-mine input database.
      *
-     * @return The name of the created CSV file (without the .csv extension)
      *
      */
     public static void constructAggregateTaxDonorPopulationCSVfile(Country country, boolean showGui) {