This is not well documented, but you can call your command functions directly, and thus can run the code in a debugger:

Sample Code:

import click

@click.command()
@click.option('--my_arg', default=1, help='a number')
def my_command(my_arg):
    click.echo("my_arg='%d'" % my_arg)

if __name__ == '__main__':
    my_command(['--my_arg', '3'])

Result:

my_arg='3'

I'm a couple years late to the party, but in case anyone else comes here looking for an answer like I just did:

Calling your function with CliRunner.invoke() will return a "Result" object with an "exc_info" attribute. You can feed that to traceback.print_exception() like so:

runner = CliRunner()
result = runner.invoke(my_command)
traceback.print_exception(*result.exc_info)

The setup.py generates:

• console_script.exe
• console_script-script.py

from cmdline:

console_app --help

expands out to the IDE configuration cmd:

python <absolute path to>\console_app-script.py --help

Tested in PyCharm 2018.2 - you can set and hit breakpoints and preserve the expected cmdline/arg paradigm.