Merge branch 'master' into freespeed-model

# Conflicts:
#	contribs/sumo/src/test/java/org/matsim/contrib/sumo/SumoNetworkConverterTest.java

.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/code-coverage.yaml

@@ -12,10 +12,10 @@ jobs:
 
     steps:
       - name: Checkout git repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Java
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 17
           distribution: 'zulu'

.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@v4
+        with:
+          java-version: 17
+          distribution: 'zulu'
+          cache: 'maven'
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        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@v3
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3
+        with:
+          category: "/language:java"

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

@@ -10,22 +10,22 @@ 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
 
     steps:
       - name: Checkout git repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Java
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           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/deploy-on-release-created.yaml

@@ -11,10 +11,10 @@ jobs:
 
     steps:
       - name: Checkout git repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Java
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 17
           distribution: 'zulu'

.github/workflows/deploy-weekly.yaml

@@ -12,10 +12,10 @@ jobs:
 
     steps:
       - name: Checkout git repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Java
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 17
           distribution: 'zulu'

.github/workflows/full-integration.yaml

@@ -1,6 +1,7 @@
 name: full-integration
 
 on:
+  workflow_dispatch:
   schedule:
     - cron: '30 0 * * *' # daily at 0:30 UTC
 
@@ -13,18 +14,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest]
+        os: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
       - name: Prepare git
         # turn off CRLF conversion (necessary on Windows)
         run: git config --global core.autocrlf false
 
       - name: Checkout git repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Java
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 17
           distribution: 'zulu'

.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
@@ -70,7 +70,7 @@ jobs:
 
     steps:
       - name: Checkout git repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Detect changes against master
         # we only want to build matsim (module) if changes are not limited to contribs
@@ -84,7 +84,7 @@ jobs:
 
       - name: Setup Java
         if: ${{matrix.module != 'matsim' || steps.detect-changes.outputs.outside-contribs == 'true'}}
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 17
           distribution: 'zulu'

benchmark/pom.xml

@@ -41,8 +41,12 @@
 			<version>16.0-SNAPSHOT</version>
 		</dependency>
 		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter-engine</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter</artifactId>
 		</dependency>
 	</dependencies>
 

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/pom.xml

@@ -52,7 +52,7 @@
 		<dependency>
 			<groupId>org.openstreetmap.osmosis</groupId>
 			<artifactId>osmosis-core</artifactId>
-			<version>0.48.3</version>
+			<version>${osmosis.version}</version>
 			<exclusions>
 				<!-- needed to compile in IntelliJ with Eclipse compiler -->
 				<!-- see: https://bugs.eclipse.org/bugs/show_bug.cgi?id=536928 -->
@@ -65,7 +65,7 @@
 		<dependency>
 			<groupId>org.openstreetmap.osmosis</groupId>
 			<artifactId>osmosis-xml</artifactId>
-			<version>0.48.3</version>
+			<version>${osmosis.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>org.matsim.contrib</groupId>

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() ) ;