It seems to be as simple as this: if the -n (the Parallel Execution flag) is used, any PythonInteractiveActions that use the built-in input() function fail with EOFError: EOF when reading a line.

Consider the following task (python3.6):

def task_copy_bpipe_config():
    # Filepaths
    in_template = ROOT / 'pipeline/bpipe.config.template'
    out_template = ROOT / 'pipeline/bpipe.config'

    def action():
        # Prompt for user input
        queue = input('What queueing system do you use? "slurm", "torque", "pbspro", or "none" (no queueing system) are accepted.')
        options = {'slurm', "torque", "pbspro", "none"}
        if queue not in options:
            raise Exception(f'Queueing system must be one of: {", ".join(options)}')
        account = input('What account name do you want to use when running jobs in this system?') if not queue == 'none' else ''

        # Write out the new config file
        template = Template(in_template.read_text())
        out_template.write_text(template.render({
            'queue': queue,
            'account': account
        })) 

    return {
        'actions': [PythonInteractiveAction(action)],
        'targets': [out_template],
        'uptodate': [True]
    }   

When run with -n set, it fails as follows:

(python) ubuntu@michael-xl:/mnt/cpipe_install_test$ doit -n 1 install
-- generate_pipeline_id
-- copy_main_config
What queueing system do you use? "slurm", "torque", "pbspro", or "none" (no queueing system) are accepted..  copy_bpipe_config
########################################
TaskError - taskid:copy_bpipe_config
PythonAction Error
Traceback (most recent call last):
  File "/mnt/cpipe_install_test/tools/python/lib/python3.6/site-packages/doit/tools.py", line 218, in execute
    returned_value = self.py_callable(*self.args, **kwargs)
  File "/mnt/cpipe_install_test/dodo.py", line 123, in action
    queue = input('What queueing system do you use? "slurm", "torque", "pbspro", or "none" (no queueing system) are accepted.')
EOFError: EOF when reading a line

When run without -n set, it succeeds, and prompts the user:

(python) ubuntu@michael-xl:/mnt/cpipe_install_test$ doit install
-- generate_pipeline_id
-- copy_main_config
.  copy_bpipe_config
What queueing system do you use? "slurm", "torque", "pbspro", or "none" (no queueing system) are accepted.