add help argument for detailed help. See #73. Fix #145. See #148.

doc/source/usage.rst

@@ -22,7 +22,7 @@ Here you can see the command-line usage instructions for the main looper command
 
 	>looper --help
 
-	version: 0.6.0-rc2
+	version: 0.6.0-dev
 	usage: looper [-h] [-V] {run,summarize,destroy,check,clean} ...
 	
 	looper - Loop through samples and submit pipelines.
@@ -41,11 +41,12 @@ Here you can see the command-line usage instructions for the main looper command
 	  -V, --version         show program's version number and exit
 	
 	For subcommand-specific options, type: 'looper <subcommand> -h'
-	https://github.com/epigen/looper
+	https://github.com/epigen/looper For debug options, type: 'looper -h
+	--details'
 	
 	
 	>looper run --help
-	version: 0.6.0-rc2
+	version: 0.6.0-dev
 	usage: looper run [-h] [-t TIME_DELAY] [--ignore-flags] [--compute COMPUTE]
 	                  [--env ENV] [--limit LIMIT] [--file-checks] [-d]
 	                  [--sp SUBPROJECT]
@@ -73,7 +74,7 @@ Here you can see the command-line usage instructions for the main looper command
 	
 	
 	>looper summarize --help
-	version: 0.6.0-rc2
+	version: 0.6.0-dev
 	usage: looper summarize [-h] [--file-checks] [-d] [--sp SUBPROJECT]
 	                        config_file
 	
@@ -89,7 +90,7 @@ Here you can see the command-line usage instructions for the main looper command
 	
 	
 	>looper destroy --help
-	version: 0.6.0-rc2
+	version: 0.6.0-dev
 	usage: looper destroy [-h] [--file-checks] [-d] [--sp SUBPROJECT] config_file
 	
 	positional arguments:
@@ -104,7 +105,7 @@ Here you can see the command-line usage instructions for the main looper command
 	
 	
 	>looper check --help
-	version: 0.6.0-rc2
+	version: 0.6.0-dev
 	usage: looper check [-h] [--file-checks] [-d] [--sp SUBPROJECT] config_file
 	
 	positional arguments:
@@ -119,7 +120,7 @@ Here you can see the command-line usage instructions for the main looper command
 	
 	
 	>looper clean --help
-	version: 0.6.0-rc2
+	version: 0.6.0-dev
 	usage: looper clean [-h] [--file-checks] [-d] [--sp SUBPROJECT] config_file
 	
 	positional arguments:
@@ -131,3 +132,34 @@ Here you can see the command-line usage instructions for the main looper command
 	  -d, --dry-run    Don't actually submit the project/subproject.
 	  --sp SUBPROJECT  Name of subproject to use, as designated in the project's
 	                   configuration file
+	
+	
+	>looper --details --help
+	version: 0.6.0-dev
+	usage: looper [-h] [-V] [--logfile LOGFILE] [--verbosity {0,1,2,3,4}]
+	              [--logging-level LOGGING_LEVEL] [--dbg]
+	              {run,summarize,destroy,check,clean} ...
+	
+	looper - Loop through samples and submit pipelines.
+	
+	positional arguments:
+	  {run,summarize,destroy,check,clean}
+	    run                 Main Looper function: Submit jobs for samples.
+	    summarize           Summarize statistics of project samples.
+	    destroy             Remove all files of the project.
+	    check               Checks flag status of current runs.
+	    clean               Runs clean scripts to remove intermediate files of
+	                        already processed jobs.
+	
+	optional arguments:
+	  -h, --help            show this help message and exit
+	  -V, --version         show program's version number and exit
+	  --logfile LOGFILE     Optional output file for looper logs (default: None)
+	  --verbosity {0,1,2,3,4}
+	                        Choose level of verbosity (default: None)
+	  --logging-level LOGGING_LEVEL
+	                        Set logging level (default: None)
+	  --dbg                 Turn on debug mode (default: False)
+	
+	For subcommand-specific options, type: 'looper <subcommand> -h'
+	https://github.com/epigen/looper

looper/_version.py

@@ -1 +1 @@
-__version__ = "0.6.0-rc2"
+__version__ = "0.6.0-dev"

looper/looper.py

@@ -47,8 +47,19 @@ def parse_arguments():
 
     description = "%(prog)s - Loop through samples and submit pipelines."
     epilog = "For subcommand-specific options, type: '%(prog)s <subcommand> -h'"
+
     epilog += "\nhttps://github.com/epigen/looper"
 
+    preparser = argparse.ArgumentParser(add_help=False)
+    preparser.add_argument("--details", action="store_true", default=False)
+    args, remaining_args = preparser.parse_known_args()
+    if args.details:
+        # Showing detailed help.
+        suppress_details = False
+    else:
+        suppress_details = argparse.SUPPRESS
+        epilog += "\n  For debug options, type: '%(prog)s -h --details'"
+
     parser = VersionInHelpParser(
         description=description, epilog=epilog,
         formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -57,16 +68,16 @@ def parse_arguments():
 
     # Logging control
     parser.add_argument("--logfile",
-                        help=argparse.SUPPRESS)
+                        help=suppress_details or "Optional output file for looper logs")
     parser.add_argument("--verbosity",
                         type=int,
                         choices=range(len(_LEVEL_BY_VERBOSITY)),
-                        help=argparse.SUPPRESS)
+                        help=suppress_details or "Choose level of verbosity")
     parser.add_argument("--logging-level",
-                        help=argparse.SUPPRESS)
+                        help=suppress_details or "Set logging level")
     parser.add_argument("--dbg",
                         action="store_true",
-                        help=argparse.SUPPRESS)
+                        help=suppress_details or "Turn on debug mode")
 
     subparsers = parser.add_subparsers(dest="command")
 

update-usage-docs.sh

@@ -1,6 +1,6 @@
 looper --help > USAGE.temp 2>&1
 
-for cmd in run summarize destroy check clean; do
+for cmd in run summarize destroy check clean "--details"; do
 	echo $cmd
 	echo -e "\n\n>looper $cmd --help" >> USAGE.temp
 	looper $cmd --help >> USAGE.temp 2>&1