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Given that what you see when you run your test_pyems.py is the result of energyplus --help, I think your test_pyems.py is calling api.runtime.run_energyplus with incorrect arguments.

An example would be:

import sys
sys.path.insert(0, '/usr/local/EnergyPlus-9-4-0/')
from pyenergyplus.api import EnergyPlusAPI

api = EnergyPlusAPI()
state = api.state_manager.new_state()

# Register any callbacks
def callback_function(state_arguments):
    pass

api.runtime.callback_begin_zone_timestep_after_init_heat_balance(state, callback_function)
api.runtime.run_energyplus(state,
    [
        '-w', '/usr/local/EnergyPlus-9-4-0/WeatherData/USA_CO_Golden-NREL.724666_TMY3.epw',
        '-d', 'out',
        'myfile.idf'
    ]
)

I have an example notebook on Github on jmarrec/OpenStudio_to_EnergyPlusAPI, and you can find a few on the E+ repo in tst/EnergyPlus/api, for example tst/EnergyPlus/api/TestRuntime.py