Fix headless stdout flooding

[travisformayor]

Running simulations through SynBioSuite can fail with ERR_CHILD_PROCESS_STDIO_MAXBUFFER when reb2sac progress output overflows Node.js's buffer in iBioSim-API. In headless mode, Run.java dumps every progress line (Time=X) to stdout, but nothing downstream uses them, they just accumulate until the buffer overflows.

• Skip System.out.println for lines successfully parsed as progress updates. Diagnostic output (warnings, errors) still prints.
• GUI path is unchanged, progress still goes through parent.send().
• Add explicit transitive deps to dataModels/pom.xml so the module builds standalone.
• Fix http to https for osgeo Maven repo URL.
• Ignore .sdkmanrc in .gitignore.

[Copilot]

Pull request overview

This PR reduces headless simulation failures caused by excessive child-process output by suppressing reb2sac progress-line printing in headless mode, while keeping GUI progress reporting unchanged. It also updates build/infra metadata so modules build more reliably and use secure repository URLs.

Changes:

• Suppress stdout printing of successfully parsed Time=... progress lines when running headless (no parent), while still printing non-progress diagnostics.
• Add explicit dependencies to dataModels/pom.xml to support standalone builds and update the osgeo repository URL to HTTPS.
• Ignore .sdkmanrc in .gitignore.

Reviewed changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated 3 comments.

File	Description
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java	Avoids printing progress lines to stdout in headless mode to prevent buffer flooding.
dataModels/pom.xml	Adds explicit dependencies for standalone builds and switches osgeo repo URL to HTTPS.
.gitignore	Ignores .sdkmanrc.

Comments suppressed due to low confidence (1)

analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java:901

• Progress detection uses line.contains("Time") and then unconditionally attempts substring(line.indexOf('=') + 1, ...). If a non-progress diagnostic line contains the word "Time" but not the expected Time=... format, this will throw and e.printStackTrace() will emit a stack trace per line, which can still flood stderr in headless runs. Tighten the condition (e.g., require Time= prefix / regex with = present) and avoid printing full stack traces in this hot loop (log once or include the offending line in a concise message).

						  if (line.contains("Time")) {
							  time = Double.parseDouble(line.substring(line.indexOf('=') + 1, line.length()));
							  isProgress = true;
							  if (oldTime > time) {
								  runNum++;
							  }
							  oldTime = time;
							  time += (runNum * properties.getSimulationProperties().getTimeLimit());
							  double d = ((time * 100) / runTime);
							  String s = d + "";
							  double decimal = Double.parseDouble(s.substring(s.indexOf('.'), s.length()));
							  if (decimal >= 0.5) {
								  prog = (int) (Math.ceil(d));
							  } else {
								  prog = (int) (d);
							  }
						  }
					  }
					  catch (Exception e) {
						  e.printStackTrace();
					  }

---

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[Copilot]

httpclient already brings in a compatible httpcore transitively. Declaring httpcore explicitly here is redundant unless you're intentionally overriding the transitive version; if you do need to pin it, it would help to add a brief comment explaining why. Otherwise consider removing the direct httpcore dependency to reduce version-locking and future maintenance overhead.

Suggested change

	<groupId>org.apache.httpcomponents</groupId>
	<artifactId>httpcore</artifactId>
	<version>4.4.6</version>
	</dependency>
	<dependency>

[Copilot]

The newly added dependency versions (gson 2.7 and guava 18.0) are quite old and are commonly flagged by vulnerability scanners / have many fixes in newer releases. If there isn't a compatibility constraint forcing these versions, consider upgrading to more recent releases (or centralizing the versions in the parent POM) to reduce security and maintenance risk.

Suggested change

	<version>2.7</version>
	</dependency>
	<dependency>
	<groupId>com.google.guava</groupId>
	<artifactId>guava</artifactId>
	<version>18.0</version>
	<version>2.10.1</version>
	</dependency>
	<dependency>
	<groupId>com.google.guava</groupId>
	<artifactId>guava</artifactId>
	<version>32.1.3-jre</version>

[Copilot]

In the non-GUI path (parent == null), progress lines are now suppressed, but in the GUI path you still call parent.send(REQUEST_PROGRESS, ...) for every line read, even when the line wasn't parsed as a progress update (prog remains stale). This can create unnecessary IPC traffic and repeated identical progress events. Consider sending REQUEST_PROGRESS only when a progress update was successfully parsed (e.g., gate the send on isProgress).

Suggested change

	message.setInteger(prog);
	parent.send(RequestType.REQUEST_PROGRESS, message);
	if (isProgress) {
	message.setInteger(prog);
	parent.send(RequestType.REQUEST_PROGRESS, message);
	}