From c139422e786c5f559689375632d6bd8faa3783cb Mon Sep 17 00:00:00 2001
From: Guillaume Poirier-Morency <poirigui@msl.ubc.ca>
Date: Fri, 13 Oct 2023 10:08:15 -0700
Subject: [PATCH] Add documentation for CLI options

---
 bioluigi/cli.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/bioluigi/cli.py b/bioluigi/cli.py
index 3964374..0096a15 100755
--- a/bioluigi/cli.py
+++ b/bioluigi/cli.py
@@ -139,13 +139,13 @@ def main():
 
 @main.command()
 @click.argument('task_glob', required=False)
-@click.option('--status', multiple=True)
-@click.option('--user', multiple=True)
-@click.option('--summary', is_flag=True)
-@click.option('--detailed', is_flag=True)
-@click.option('--extract-id', is_flag=True)
-@click.option('--extract-parameter')
-@click.option('--no-limit', is_flag=True)
+@click.option('--status', multiple=True, help='Filter tasks by status.')
+@click.option('--user', multiple=True, help='Filter tasks by submitted.')
+@click.option('--summary', is_flag=True, help='Produce a summary output for each task.')
+@click.option('--detailed', is_flag=True, help='Produce a detailed output for each task.')
+@click.option('--extract-id', is_flag=True, help='Extract the task ID.')
+@click.option('--extract-parameter', help='Extract the given parameter.')
+@click.option('--no-limit', is_flag=True, help='Do not limit the number of tasks retrieved.')
 def list(task_glob, status, user, summary, detailed, extract_id, extract_parameter, no_limit):
     """
     List all tasks that match the given pattern and filters.
@@ -232,9 +232,9 @@ def show(task_id):
 
 @main.command()
 @click.argument('task_id')
-@click.option('--forgive', is_flag=True)
-@click.option('--recursive', is_flag=True)
-def reenable(task_id, forgive, recursive):
+@click.option('--recursive', is_flag=True, help='Reenable all the dependencies of a task.')
+@click.option('--forgive', is_flag=True, help='Forgive the task once it\'s been reenabled.')
+def reenable(task_id, recursive, forgive):
     """
     Reenable a disabled task.
     """
@@ -256,7 +256,7 @@ def reenable(task_id, forgive, recursive):
 
 @main.command()
 @click.argument('task_id')
-@click.option('--recursive', is_flag=True)
+@click.option('--recursive', is_flag=True, help='Forgive all the dependencies of a task.')
 def forgive(task_id, recursive):
     """
     Forgive a failed task.