From 9df4464b2254f8c1ceb9626987666c33ed6b1674 Mon Sep 17 00:00:00 2001
From: Travis Uhrig <travisformayor@users.noreply.github.com>
Date: Wed, 25 Mar 2026 09:42:18 -0600
Subject: [PATCH 1/3] fix: add missing full local build deps

---
 dataModels/pom.xml | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/dataModels/pom.xml b/dataModels/pom.xml
index 405e768c1..85104059f 100644
--- a/dataModels/pom.xml
+++ b/dataModels/pom.xml
@@ -24,7 +24,7 @@
 		<repository>
 			<id>osgeo</id>
 			<name>osgeo</name>
-			<url>http://download.osgeo.org/webdav/geotools/</url>
+			<url>https://download.osgeo.org/webdav/geotools/</url>
 		</repository>
 		<repository>
 			<id>alfresco</id>
@@ -82,6 +82,27 @@
 			<version>1.7-SNAPSHOT</version>
 		</dependency>
 
+		<dependency>
+			<groupId>org.apache.httpcomponents</groupId>
+			<artifactId>httpclient</artifactId>
+			<version>4.5.3</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.httpcomponents</groupId>
+			<artifactId>httpcore</artifactId>
+			<version>4.4.6</version>
+		</dependency>
+		<dependency>
+			<groupId>com.google.code.gson</groupId>
+			<artifactId>gson</artifactId>
+			<version>2.7</version>
+		</dependency>
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+			<version>18.0</version>
+		</dependency>
+
 		<dependency>
 			<groupId>net.sf.trove4j</groupId>
 			<artifactId>trove4j</artifactId>

From 17c876e1b0d96905a76994c9dbc9e9a6e6eb4294 Mon Sep 17 00:00:00 2001
From: Travis Uhrig <travisformayor@users.noreply.github.com>
Date: Wed, 25 Mar 2026 09:43:00 -0600
Subject: [PATCH 2/3] fix: update .gitignore for java sdkman

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 92006f752..ebf91cd50 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,6 +13,7 @@ bin/iBioSim.jar
 .settings/
 **/.project
 /.metadata/
+.sdkmanrc
 
 # intellij artefacts
 out

From e2d8b7a5a00f99090d0b203ba34a016f1a9354b4 Mon Sep 17 00:00:00 2001
From: Travis Uhrig <travisformayor@users.noreply.github.com>
Date: Thu, 26 Mar 2026 20:19:42 -0600
Subject: [PATCH 3/3] fix: filter unread progress stdout noise in headless mode

---
 .../main/java/edu/utah/ece/async/ibiosim/analysis/Run.java    | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java b/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java
index 3b4a41381..9435f989c 100644
--- a/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java
+++ b/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java
@@ -876,9 +876,11 @@ public void run () {
 				  String line = br.readLine ();
 				  if (line == null) break;
 				  if (name.equals("stdin")) {
+					  boolean isProgress = false;
 					  try {
 						  if (line.contains("Time")) {
 							  time = Double.parseDouble(line.substring(line.indexOf('=') + 1, line.length()));
+							  isProgress = true;
 							  if (oldTime > time) {
 								  runNum++;
 							  }
@@ -900,7 +902,7 @@ public void run () {
 					  if (parent!=null) {
 						  message.setInteger(prog);
 						  parent.send(RequestType.REQUEST_PROGRESS, message);
-					  } else{
+					  } else if (!isProgress) {
 						  System.out.println(line);
 					  }
 				  } else {