def test_setup_env():
arguments = [spike_times_file_name,
'--settings-file', 'tests/settings/test_utils.yaml']
task, spike_times, spike_times_optimization, spike_times_validation, \
analysis_file, csv_stats_file, csv_histdep_data_file, csv_auto_MI_data_file, \
analysis_num, settings = parse_arguments(arguments,
defined_tasks,
defined_estimation_methods)
estimator_env.spike_times = spike_times
estimator_env.settings = settings
def test_argument_parser():
arguments = [
spike_times_file_name, '--settings-file',
'tests/settings/test_utils.yaml'
]
task, spike_times, spike_times_optimization, spike_times_validation, \
analysis_file, csv_stats_file, csv_histdep_data_file, csv_auto_MI_data_file, \
analysis_num, settings = parse_arguments(arguments,
defined_tasks,
defined_estimation_methods)
assert task == "full-analysis"
assert np.isclose(spike_times, estimator_env.spike_times).all()
assert utl.get_hash(spike_times) == utl.get_hash(estimator_env.spike_times)
assert type(analysis_file) == h5py.File
for f in [csv_stats_file, csv_histdep_data_file, csv_auto_MI_data_file]:
p = Path(f.name)
assert p.is_file()
assert settings["embedding_past_range_set"] == exp.embedding_past_range_set
assert settings[
"embedding_number_of_bins_set"] == exp.embedding_number_of_bins_set
assert settings[
"embedding_scaling_exponent_set"] == exp.embedding_scaling_exponent_set
assert settings["estimation_method"] == exp.estimation_method
estimator_env.spike_times_optimization = spike_times_optimization
estimator_env.spike_times_validation = spike_times_validation
estimator_env.analysis_file = analysis_file
estimator_env.csv_stats_file = csv_stats_file
estimator_env.csv_histdep_data_file = csv_histdep_data_file
estimator_env.csv_auto_MI_data_file = csv_auto_MI_data_file
estimator_env.analysis_num = analysis_num
estimator_env.settings = settings
# assert error catching
# no arguments
arguments = []
with pytest.raises(SystemExit) as pytest_e:
task, spike_times, spike_times_optimization, spike_times_validation, \
analysis_file, csv_stats_file, csv_histdep_data_file, csv_auto_MI_data_file, \
analysis_num, settings = parse_arguments(arguments,
defined_tasks,
defined_estimation_methods)
assert pytest_e.type == SystemExit
assert pytest_e.value.code == 2 # might want to remove this line
# wrong task (non-existing spike times file)
arguments = ['tests/asdfg.dat']
with pytest.raises(SystemExit) as pytest_e:
task, spike_times, spike_times_optimization, spike_times_validation, \
analysis_file, csv_stats_file, csv_histdep_data_file, csv_auto_MI_data_file, \
analysis_num, settings = parse_arguments(arguments,
defined_tasks,
defined_estimation_methods)
assert pytest_e.type == SystemExit
assert pytest_e.value.code == EXIT_FAILURE
# wrong task (too short -> not unique, could be confidence-intervals or csv-files)
arguments = [
spike_times_file_name, '-t', 'c', '--settings-file',
'tests/settings/test_utils.yaml'
]
with pytest.raises(SystemExit) as pytest_e:
task, spike_times, spike_times_optimization, spike_times_validation, \
analysis_file, csv_stats_file, csv_histdep_data_file, csv_auto_MI_data_file, \
analysis_num, settings = parse_arguments(arguments,
defined_tasks,
defined_estimation_methods)
assert pytest_e.type == SystemExit
assert pytest_e.value.code == EXIT_FAILURE
# max number of bins d too large, has to be < 63
arguments = [
spike_times_file_name, '--settings-file',
'tests/settings/test_max_num_bins.yaml'
]
with pytest.raises(SystemExit) as pytest_e:
task, spike_times, spike_times_optimization, spike_times_validation, \
analysis_file, csv_stats_file, csv_histdep_data_file, csv_auto_MI_data_file, \
analysis_num, settings = parse_arguments(arguments,
defined_tasks,
defined_estimation_methods)
assert pytest_e.type == SystemExit
assert pytest_e.value.code == EXIT_FAILURE