From 7ed567fbad1e16b1d349ee8e6343dc58907b26da Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Tue, 21 Mar 2023 22:01:20 +0700
Subject: [PATCH] Make the `--help` or `-h` options working when mandatory
 options are declared

Former-commit-id: db502ff81dcf20449d126978fcebf890edb814ae
---
 pkg/obioptions/options.go | 27 +++++++++++++++------------
 1 file changed, 15 insertions(+), 12 deletions(-)

diff --git a/pkg/obioptions/options.go b/pkg/obioptions/options.go
index 8212bb7..1ba683b 100644
--- a/pkg/obioptions/options.go
+++ b/pkg/obioptions/options.go
@@ -41,8 +41,22 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 
 		remaining, err := options.Parse(args[1:])
 
+		if options.Called("help") {
+			fmt.Fprint(os.Stderr, options.Help())
+			os.Exit(1)
+		}
+
+		log.SetLevel(log.InfoLevel)
+		if options.Called("debug") {
+			log.SetLevel(log.DebugLevel)
+			log.Debugln("Switch to debug level logging")
+		}
+
+		// Handle user errors
 		if err != nil {
-			log.Fatalf("Error on the commande line : %v",err)
+			fmt.Fprintf(os.Stderr, "ERROR: %s\n\n", err)
+			fmt.Fprint(os.Stderr, options.Help(getoptions.HelpSynopsis))
+			os.Exit(1)
 		}
 
 		// Setup the maximum number of CPU usable by the program
@@ -59,17 +73,6 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 			log.Printf("No singleton option set")
 		}
 
-		if options.Called("help") {
-			fmt.Fprint(os.Stderr, options.Help())
-			os.Exit(1)
-		}
-
-		log.SetLevel(log.InfoLevel)
-		if options.Called("debug") {
-			log.SetLevel(log.DebugLevel)
-			log.Debugln("Switch to debug level logging")
-		}
-
 		return options, remaining
 	}
 }