mobspy/debugging_script.py at main · ROBACON/mobspy · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
from test_script import *
from test_ode_syntax import *
import sys

# This is here because pytest is too slow - so it's a faster test that avoid the collection step.
# Pytest is used in the GitHub while pushing
# This script is oriented towards fast debugging and development
# Also in the future, it might be nice to add an automated way to get the test names
test_list = [
    test_model_1,
    test_model_2,
    test_model_3,
    test_model_4,
    test_model_5,
    test_model_6,
    test_model_7,
    test_orthogonal_spaces,
    test_average_value,
    test_hybrid_sim,
    test_concatenated_simulation,
    test_event_type,
    test_reacting_species_event,
    test_unit_event_test,
    test_reaction_deactivation,
    test_double_rate,
    test_single_rate,
    test_triple_rate,
    test_stochastic_event_duration,
    test_logic_operator_syntax,
    test_stack_position,
    test_empty_arguments,
    test_conditional_between_meta_species,
    test_conditional_between_meta_species_2,
    test_event_reaction_not_allowed,
    test_all,
    test_2_all,
    test_error_mult,
    test_set_counts,
    test_bool_error,
    test_event_all,
    test_one_value_concatenation_sim,
    test_crash_after_modification,
    test_unit_bi_dimension,
    test_bi_dimensional_rates,
    test_dimension_in_function_only,
    test_multiple_simulation_counts,
    test_string_events_assignment,
    test_plotting,
    test_volume_after_sim,
    test_shared_parameter_name,
    test_set_counts_parameters,
    test_repeated_parameters,
    test_initial_expression,
    test_wrong_dimension_error,
    test_more_than_used,
    zero_rate_test,
    test_wrong_rate,
    test_conversion_outside,
    test_first_characteristic_in_reacting_species,
    test_model_reference,
    test_sbml_generation,
    test_multi_sim_sbml,
    test_inline_comment,
    test_with_statement_any_and_species_characteristics,
    test_with_statement_on_any_and_event,
    test_matching_characteristic_rate,
    test_changes_after_compilation,
    test_proper_unit_context_exit,
    test_run_args,
    test_unit_args,
    test_multi_parameters_in_run,
    test_output_concentration_in_multi_sim,
    test_parameter_operation_in_rate,
    test_multi_parameter_with_expression,
    test_double_parameters_with_units,
    test_parameters_with_units,
    test_convert_back_parameter,
    test_numpy_in_expression_function,
    test_numpy_in_rates,
    test_numpy_in_counts,
    test_numpy_in_set_counts,
    test_multi_methods_plot,
    test_unit_x_conversion,
    test_Silicon_valley,
    test_replacing_species_name_in_expression,
    test_basic_assignment,
    test_all_asgn_ops,
    text_complex_assignments,
    text_assign_context_exit,
    text_even_more_complex_assignments,
    test_assign_context_complex,
    test_assign_context_constant,
    test_duration_with_run,
    test_rev,
    test_dimensionless_count,
    test_assignment_similar_species,
    test_blocked_names,
    test_blocked_names_2,
    test_update_parameter_for_multi_model,
    test_update_parameter_through_str,
    test_update_multiple_parameters_in_expression,
    test_update_parameter_with_unit,
    test_species_value_modification,
    test_all_value_modification,
    test_new_reversible_reaction_notation,
    test_2D_reaction_with_units,
    test_parameters_as_initial_values,
    test_parameters_in_lambda_expression,
    test_ode_syntax_basic,
    test_ode_syntax_two_species,
    test_ode_applied_to_species,
    test_ode_neg_test,
    test_ode_compartments,
    test_ode_complex_expressions,
    test_ode_inheritance,
    test_ode_with_functions,
    test_ode_neg,
]

# test_no_species_in_asg
# test_illegal_unit_op_in_assignment
# temporary_test_removal = [test_parameter_fit_with_units, test_multiple_runs_fit, test_simple_fit]
test_remov = [test_antimony_compose_model_gen, test_antimony_model]
sub_test = test_list


# sub_test = [test_parameters_with_sbml]
def perform_tests():
    any_failed = False
    failed_tests = []
    for test in sub_test:
        try:
            test()
            print(f"Test {test} passed")
        except:
            message = "\033[91m" + f"Test {test} failed" + "\033[0m"
            print(message, file=sys.stderr)
            any_failed = True
            failed_tests.append(message)
    if any_failed:
        print()
        print("The following tests failed", file=sys.stderr)
        for t in failed_tests:
            print(t, file=sys.stderr)

        assert False


perform_tests()