Merge branch 'master' into developParkingSearch

.github/dependabot.yml

@@ -4,7 +4,11 @@ updates:
     directory: "/"
     schedule:
       interval: "daily"
+
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       interval: "daily"
+    groups:
+      github-actions:
+        patterns: ["*"]

.github/workflows/codeql.yml

@@ -0,0 +1,49 @@
+name: CodeQL
+
+on:
+  push:
+    branches: 'master'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: 'ubuntu-latest'
+    timeout-minutes: 360
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup Java
+        uses: actions/setup-java@v3
+        with:
+          java-version: 17
+          distribution: 'zulu'
+          cache: 'maven'
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: 'java'
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+
+          # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+          # queries: security-extended,security-and-quality
+
+
+      # Autobuild attempts to build any compiled languages (C/C++, C#, Go, Java, or Swift).
+      # If this step fails, then you should remove it and run the build manually (see below)
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v2
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: "/language:java"

.github/workflows/deploy-on-pr-merge.yaml

@@ -10,8 +10,8 @@ on:
 jobs:
   deploy-snapshot:
     name: deploy PR-labelled version
-    # for PR-labelled deployment -- only if closed by merging
-    if: github.event_name == 'push' || github.event.pull_request.merged == true
+    # only if PR closed by merging
+    if: github.event.pull_request.merged == true
 
     runs-on: ubuntu-latest
 
@@ -25,7 +25,7 @@ jobs:
           java-version: 17
           distribution: 'zulu'
           cache: 'maven'
-          server-id: ${{ github.event_name == 'push' && 'matsim-snapshots' || 'matsim-releases' }} #choose mvn repo
+          server-id: 'matsim-releases'
           server-username: MAVEN_USERNAME
           server-password: MAVEN_PASSWORD
 
@@ -43,5 +43,10 @@ jobs:
           MAVEN_USERNAME: ${{ secrets.REPOMATSIM_USERNAME }}
           MAVEN_PASSWORD: ${{ secrets.REPOMATSIM_TOKEN }}
 
+      - name: Submit Dependency Graph
+        # Generate a complete dependency graph and submit the graph to the GitHub repository.
+        # The goal is to improve security alerts from dependabot, because dependabot is not able to compute the complete dependency graph.
+        uses: advanced-security/maven-dependency-submission-action@v3
+
     env:
       MAVEN_OPTS: -Xmx2g

.github/workflows/verify-push.yaml

@@ -55,9 +55,9 @@ jobs:
           - contribs/socnetsim
           - contribs/sumo
           - contribs/pseudosimulation
+          - contribs/railsim
           - contribs/roadpricing
           - contribs/analysis
-          - contribs/eventsBasedPTRouter
           - contribs/hybridsim
           - contribs/informed-mode-choice
           - contribs/otfvis

benchmark/src/main/java/org/matsim/benchmark/Benchmark.java

@@ -32,7 +32,7 @@ public class Benchmark {
 	public static void main(String[] args) throws IOException {
 		Config config = ConfigUtils.loadConfig(IOUtils.extendUrl(ExamplesUtils.getTestScenarioURL("benchmark"), "config.xml"));
 		Controler ctl = new Controler(config);
-        ctl.getConfig().controler().setCreateGraphs(false);
+        ctl.getConfig().controller().setCreateGraphs(false);
         ctl.run();
 	}
 

contribs/README.md

@@ -41,6 +41,7 @@ The MATSim core development team cannot make any guarantee that these extensions
 | [parking](parking/README.md)                                             | Parking infrastructure and supply constraints
 | [protobuf](protobuf/README.md)                                           | Protocol buffer implementation and converter for the MATSim event infrastructure
 | [pseudosimulation](pseudosimulation/README.md)                           | Pseudo-simulation to speed-up simulation times
+| [railsim](railsim/README.md)                                             | A large-scale hybrid micro- and mesoscopic simulation approach for railway operation
 | [roadpricing](roadpricing/README.md)                                     | Functionality to simulate different road-pricing scenarios in MATSim
 | [shared_mobility](shared_mobility/README.md)                             | Simulate human-driven shared mobility (i.e., micromobility)
 | [signals](signals/README.md)                                             | Simulate traffic lights microscopically

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/AccessibilityComputationNairobiLandUseLocalCopy.java

@@ -39,26 +39,26 @@
  */
 class AccessibilityComputationNairobiLandUseLocalCopy {
 	public static final Logger LOG = LogManager.getLogger(AccessibilityComputationNairobiLandUseLocalCopy.class);
-	
+
 	public static void main(String[] args) {
 		int tileSize_m = 500;
 		boolean push2Geoserver = false; // Set true for run on server
 		boolean createQGisOutput = true; // Set false for run on server
-		
+
 		final Config config = ConfigUtils.createConfig(new AccessibilityConfigGroup());
-		
+
 		Envelope envelope = new Envelope(246000, 271000, 9853000, 9863000); // Central part of Nairobi
 		String scenarioCRS = "EPSG:21037"; // EPSG:21037 = Arc 1960 / UTM zone 37S, for Nairobi, Kenya
-		
+
 		config.network().setInputFile("../nairobi/data/nairobi/input/2015-10-15_network.xml");
 		config.facilities().setInputFile("../nairobi/data/land_use/Nairobi_LU_2010/facilities.xml");
 		String runId = "ke_nairobi_landuse_hexagons_" + tileSize_m;
-		config.controler().setOutputDirectory("../nairobi/data/nairobi/output/" + runId + "_lcpt_par4_car_tr-7_500/");
-		config.controler().setRunId(runId);
-		
-		config.controler().setOverwriteFileSetting(OverwriteFileSetting.deleteDirectoryIfExists);
-		config.controler().setLastIteration(0);
-		
+		config.controller().setOutputDirectory("../nairobi/data/nairobi/output/" + runId + "_lcpt_par4_car_tr-7_500/");
+		config.controller().setRunId(runId);
+
+		config.controller().setOverwriteFileSetting(OverwriteFileSetting.deleteDirectoryIfExists);
+		config.controller().setLastIteration(0);
+
 		AccessibilityConfigGroup acg = ConfigUtils.addOrGetModule(config, AccessibilityConfigGroup.class);
 		acg.setAreaOfAccessibilityComputation(AreaOfAccesssibilityComputation.fromBoundingBoxHexagons);
 		acg.setEnvelope(envelope);
@@ -69,17 +69,17 @@ public static void main(String[] args) {
 		acg.setOutputCrs(scenarioCRS);
 
 		//acg.setUseParallelization(false);
-		
+
 		ConfigUtils.setVspDefaults(config);
-		
+
 		final Scenario scenario = ScenarioUtils.loadScenario(config);
-		
+
 //		final List<String> activityTypes = Arrays.asList(new String[]{"educational", "commercial", "industrial", "recreational", "water_body"});
 		final List<String> activityTypes = Arrays.asList(new String[]{"educational"});
 		final ActivityFacilities densityFacilities = AccessibilityUtils.createFacilityForEachLink(Labels.DENSITIY, scenario.getNetwork());
-		
+
 		final Controler controler = new Controler(scenario);
-		
+
 		for (String activityType : activityTypes) {
 			AccessibilityModule module = new AccessibilityModule();
 			module.setConsideredActivityType(activityType);
@@ -88,17 +88,17 @@ public static void main(String[] args) {
 			module.setCreateQGisOutput(createQGisOutput);
 			controler.addOverridingModule(module);
 		}
-		
+
 		controler.run();
-		
+
 		if (createQGisOutput) {
 			final Integer range = 9; // In the current implementation, this must always be 9
 			final Double lowerBound = -3.5; // (upperBound - lowerBound) ideally nicely divisible by (range - 2)
 			final Double upperBound = 3.5;
 			final int populationThreshold = (int) (10 / (1000/tileSize_m * 1000/tileSize_m)); // People per km^2 or roads (?)
-			
+
 			String osName = System.getProperty("os.name");
-			String workingDirectory = config.controler().getOutputDirectory();
+			String workingDirectory = config.controller().getOutputDirectory();
 			for (String actType : activityTypes) {
 				String actSpecificWorkingDirectory = workingDirectory + actType + "/";
 				for (Modes4Accessibility mode : acg.getIsComputingMode()) {

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/AccessibilityComputationShutdownListener.java

@@ -30,11 +30,10 @@
 import org.matsim.api.core.v01.Id;
 import org.matsim.api.core.v01.Scenario;
 import org.matsim.api.core.v01.TransportMode;
-import org.matsim.api.core.v01.network.Node;
 import org.matsim.contrib.accessibility.utils.AggregationObject;
 import org.matsim.contrib.accessibility.utils.ProgressBar;
 import org.matsim.core.config.ConfigUtils;
-import org.matsim.core.config.groups.PlanCalcScoreConfigGroup;
+import org.matsim.core.config.groups.ScoringConfigGroup;
 import org.matsim.core.controler.events.ShutdownEvent;
 import org.matsim.core.controler.listener.ShutdownListener;
 import org.matsim.core.gbl.Gbl;
@@ -58,9 +57,9 @@ final class AccessibilityComputationShutdownListener implements ShutdownListener
 	private final ArrayList<FacilityDataExchangeInterface> zoneDataExchangeListeners = new ArrayList<>();
 
 	private AccessibilityConfigGroup acg;
-	private final PlanCalcScoreConfigGroup cnScoringGroup;
+	private final ScoringConfigGroup cnScoringGroup;
+
 
-
 	public AccessibilityComputationShutdownListener(Scenario scenario, ActivityFacilities measuringPoints, ActivityFacilities opportunities,
 										   String outputDirectory) {
 	    this.measuringPoints = measuringPoints;
@@ -69,7 +68,7 @@ public AccessibilityComputationShutdownListener(Scenario scenario, ActivityFacil
 		this.outputDirectory = outputDirectory;
 
 		this.acg = ConfigUtils.addOrGetModule(scenario.getConfig(), AccessibilityConfigGroup.GROUP_NAME, AccessibilityConfigGroup.class);
-		this.cnScoringGroup = scenario.getConfig().planCalcScore();
+		this.cnScoringGroup = scenario.getConfig().scoring();
 
 		if (cnScoringGroup.getOrCreateModeParams(TransportMode.car).getMarginalUtilityOfDistance() != 0.) {
 			LOG.error("Marginal utility of distance for car different from zero, but not used in accessibility computations");
@@ -241,10 +240,10 @@ private void writeCSVFile(String adaptedOutputDirectory) {
 			writer.writeField(facility.getCoord().getX());
 			writer.writeField(facility.getCoord().getY());
 			writer.writeField(tuple.getSecond());
-			
+
 			for (String mode : getModes() ) {
 				final double value = accessibilitiesMap.get(tuple).get(mode);
-				if (!Double.isNaN(value)) { 
+				if (!Double.isNaN(value)) {
 					writer.writeField(value) ;
 				} else {
 					writer.writeField(Double.NaN) ;

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/AccessibilityFromEvents.java

@@ -58,7 +58,7 @@ private AccessibilityFromEvents( Scenario scenario, String eventsFile, List<Faci
 	public void run() {
 		LinkedHashMap<String, TravelTime> map = new LinkedHashMap<>(  ) ;
 		EventsManager events = EventsUtils.createEventsManager();
-		for( String mode : scenario.getConfig().plansCalcRoute().getNetworkModes() ){
+		for( String mode : scenario.getConfig().routing().getNetworkModes() ){
 			TravelTimeCalculator.Builder builder = new TravelTimeCalculator.Builder( scenario.getNetwork() );
 			builder.setCalculateLinkTravelTimes( true );
 			builder.setCalculateLinkToLinkTravelTimes( false );
@@ -74,7 +74,7 @@ public void run() {
 				install( new ScenarioByInstanceModule( scenario ) ) ;
 				install( new TripRouterModule() ) ;
 				install( new TimeInterpretationModule() );
-				for( String mode : getConfig().plansCalcRoute().getNetworkModes() ){
+				for( String mode : getConfig().routing().getNetworkModes() ){
 					addTravelTimeBinding( mode ).toInstance( map.get(mode) );
 				}
 				install( new TravelDisutilityModule() ) ;

contribs/accessibility/src/main/java/org/matsim/contrib/accessibility/AccessibilityModule.java

@@ -139,7 +139,7 @@ public ControlerListener get() {
 				}
 				AccessibilityUtils.assignAdditionalFacilitiesDataToMeasurePoint(measuringPoints, measurePointGeometryMap, additionalFacs);
 
-				String outputDirectory = scenario.getConfig().controler().getOutputDirectory() + "/" + activityType;
+				String outputDirectory = scenario.getConfig().controller().getOutputDirectory() + "/" + activityType;
 				AccessibilityComputationShutdownListener accessibilityShutdownListener = new AccessibilityComputationShutdownListener(scenario, measuringPoints, opportunities, outputDirectory);
 
 //				for (Modes4Accessibility mode : acg.getIsComputingMode()) {
@@ -150,14 +150,14 @@ public ControlerListener get() {
 						final TravelDisutilityFactory travelDisutilityFactory = travelDisutilityFactories.get(TransportMode.car);
 						Gbl.assertNotNull(travelDisutilityFactory);
 						calculator = new NetworkModeAccessibilityExpContributionCalculator(mode, new FreeSpeedTravelTime(), travelDisutilityFactory, scenario);
-					} else if ( config.plansCalcRoute().getNetworkModes().contains( mode ) ) {
+					} else if ( config.routing().getNetworkModes().contains( mode ) ) {
 						final TravelTime nwModeTravelTime = travelTimes.get(mode);
 						Gbl.assertNotNull(nwModeTravelTime);
 						final TravelDisutilityFactory nwModeTravelDisutility = travelDisutilityFactories.get(mode);
 						Gbl.assertNotNull( nwModeTravelDisutility );
 						calculator = new NetworkModeAccessibilityExpContributionCalculator(mode, nwModeTravelTime, nwModeTravelDisutility, scenario);
 					} else if ( TransportMode.pt.equals( mode ) ){
-						calculator = new SwissRailRaptorAccessibilityContributionCalculator( mode, config.planCalcScore(), scenario );
+						calculator = new SwissRailRaptorAccessibilityContributionCalculator( mode, config.scoring(), scenario );
 					} else if ( Modes4Accessibility.matrixBasedPt.name().equals( mode ) ) {
 						throw new RuntimeException("currently not supported because implementation not consistent with guice grapher.  kai, sep'19") ;
 //						calculator = new LeastCostPathCalculatorAccessibilityContributionCalculator(
@@ -175,7 +175,7 @@ public ControlerListener get() {
 						if ( travelDisutilityFactory==null ) {
 							throw new RuntimeException("mode=" + mode + "; travelDisutilityFactory is null!") ;
 						}
-						calculator = new TripRouterAccessibilityContributionCalculator(mode, tripRouter, config.planCalcScore(), scenario,
+						calculator = new TripRouterAccessibilityContributionCalculator(mode, tripRouter, config.scoring(), scenario,
 							  travelTime, travelDisutilityFactory );
 					}
 
@@ -195,7 +195,7 @@ public ControlerListener get() {
 					}
 					Set <String> additionalFacInfo = additionalFacs.keySet();
 					accessibilityShutdownListener.addFacilityDataExchangeListener(new GeoserverUpdater(acg.getOutputCrs(),
-							config.controler().getRunId() + "_" + activityType, measurePointGeometryMap, additionalFacInfo,
+							config.controller().getRunId() + "_" + activityType, measurePointGeometryMap, additionalFacInfo,
 							outputDirectory, pushing2Geoserver, createQGisOutput));
 				}