Given I have code like this:
columns = ['col1', 'col2', 'col3', 'col4']
@click.option('--columns', is_flag=False, 
  default=columns, show_default=True, metavar='<columns>', type=click.Choice(columns), 
  help='Sets target columns', multiple=True)
Then I can call my app like this:
./myapp --columns=col1
However, how to make this work with multiple items separated by comma, like so:
./myapp --columns=col1,col3
My goal is to retrieve the passed values from an resulting columns array ['col1', 'col3'].
I do NOT want to pass the option multiple times.
The multiple keyword in click.option is so you can pass the same option multiple times, e.g. --columns=col1 --columns=col2. Instead you can accept a string for columns and then extract and validate the columns yourself:
cols = ['col1', 'col2', 'col3', 'col4']
@click.option('--columns', is_flag=False, default=','.join(cols), show_default=True,
              metavar='<columns>', type=click.STRING, help='Sets target columns')
@click.command()
def main(columns):
    # split columns by ',' and remove whitespace
    columns = [c.strip() for c in columns.split(',')]
    # validate passed columns
    for c in columns:
        if c not in cols:
            raise click.BadOptionUsage("%s is not an available column." % c)
    print(columns)
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