From f3c256a1b8ff23a012e200b31ebce540055ec777 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Mon, 15 Jan 2024 15:36:56 -0600
Subject: [PATCH 1/2] Unset "help" flag on "-p" option

This should fix unexpected behavior when "-p" is used with other (potentially invalid) options.
---
 src/main/java/com/glencoesoftware/bioformats2raw/Converter.java | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
index 03240ad..4cc96d5 100644
--- a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
+++ b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -401,7 +401,6 @@ public void setLogLevel(String level) {
   @Option(
     names = {"-p", "--progress"},
     description = "Print progress bars during conversion",
-    help = true,
     defaultValue = "false"
   )
   public void setProgressBars(boolean useProgressBars) {

From 699ee76616fdfa3a6de6304967add0fb765350a2 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Mon, 15 Jan 2024 15:38:14 -0600
Subject: [PATCH 2/2] Add explicit "--help" option

---
 .../bioformats2raw/Converter.java             | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
index 4cc96d5..1e72ccc 100644
--- a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
+++ b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -138,6 +138,7 @@ public class Converter implements Callable<Integer> {
   private volatile String logLevel;
   private volatile boolean progressBars = false;
   private volatile boolean printVersion = false;
+  private volatile boolean help = false;
 
   private volatile int maxWorkers;
   private volatile int maxCachedTiles;
@@ -423,6 +424,21 @@ public void setPrintVersionOnly(boolean versionOnly) {
     printVersion = versionOnly;
   }
 
+  /**
+   * Configure whether to print help and exit without converting.
+   *
+   * @param helpOnly whether or not to print help and exit
+   */
+  @Option(
+    names = "--help",
+    description = "Print usage information and exit",
+    usageHelp = true,
+    defaultValue = "false"
+  )
+  public void setHelp(boolean helpOnly) {
+    help = helpOnly;
+  }
+
   /**
    * Set the maximum number of workers to use for converting tiles.
    * Defaults to 4 or the number of detected CPUs, whichever is smaller.
@@ -917,6 +933,13 @@ public boolean getPrintVersionOnly() {
     return printVersion;
   }
 
+  /**
+   * @return true if only usage info is displayed
+   */
+  public boolean getHelp() {
+    return help;
+  }
+
   /**
    * @return maximum number of worker threads
    */
@@ -1094,6 +1117,10 @@ public Integer call() throws Exception {
         LoggerFactory.getLogger(Logger.ROOT_LOGGER_NAME);
     root.setLevel(Level.toLevel(logLevel));
 
+    if (help) {
+      return -1;
+    }
+
     if (printVersion) {
       String version = Optional.ofNullable(
         this.getClass().getPackage().getImplementationVersion()