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KarrLab/wc_sim

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Showing 107 of 141 total issues

Function populations_to_concentrations has 7 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def populations_to_concentrations(self, time, species, populations, dynamic_model, concentrations,
Severity: Major
Found in wc_sim/species_populations.py - About 50 mins to fix

    Function verify_model has 7 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def verify_model(self, num_discrete_stochastic_runs=None, discard_run_results=True, plot_file=None,
    Severity: Major
    Found in wc_sim/testing/verify.py - About 50 mins to fix

      Function __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __init__(self, verification_dir, case_name, ssa_model_file, ssa_settings, hybrid_model_file, hybrid_settings):
      Severity: Major
      Found in wc_sim/testing/verify.py - About 50 mins to fix

        Function concentrations_to_populations has 7 arguments (exceeds 4 allowed). Consider refactoring.
        Open

            def concentrations_to_populations(self, time, species, concentrations, dynamic_model, populations,
        Severity: Major
        Found in wc_sim/species_populations.py - About 50 mins to fix

          Function __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def __init__(self, id, dynamic_model, reactions, species, dynamic_compartments,
          Severity: Major
          Found in wc_sim/submodels/testing/deterministic_simulation_algorithm.py - About 50 mins to fix

            Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
            Open

                def __init__(self, time, method, species, last_population, population_decrease, delta_time=None):
            Severity: Minor
            Found in wc_sim/multialgorithm_errors.py - About 45 mins to fix

              Function sim_hyb has 6 arguments (exceeds 4 allowed). Consider refactoring.
              Open

              def sim_hyb(rxns, rate_params, init_species, init_time, max_time, checkpoint_period):
              Severity: Minor
              Found in examples/transcription_translation_hybrid_model/run_with_custom_code.py - About 45 mins to fix

                Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                    def __init__(self, id, dynamic_model, reactions, species, dynamic_compartments,
                Severity: Minor
                Found in wc_sim/submodels/nrm.py - About 45 mins to fix

                  Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                      def __init__(self, id, dynamic_model, reactions, species, dynamic_compartments, local_species_population):
                  Severity: Minor
                  Found in wc_sim/submodels/dynamic_submodel.py - About 45 mins to fix

                    Function run_multialg has 6 arguments (exceeds 4 allowed). Consider refactoring.
                    Open

                        def run_multialg(self, cases, ode_time_step_factors=None, tolerances=False, verbose=None,
                    Severity: Minor
                    Found in wc_sim/testing/verify.py - About 45 mins to fix

                      Function annotate_heatmap has 6 arguments (exceeds 4 allowed). Consider refactoring.
                      Open

                      def annotate_heatmap(im, data=None, valfmt="{x:.2f}",
                      Severity: Minor
                      Found in wc_sim/testing/analyze_tolerances.py - About 45 mins to fix

                        Function sim_ode has 6 arguments (exceeds 4 allowed). Consider refactoring.
                        Open

                        def sim_ode(rxns, rate_params, init_species, init_time, max_time, checkpoint_period):
                        Severity: Minor
                        Found in examples/transcription_translation_hybrid_model/run_with_custom_code.py - About 45 mins to fix

                          Function sim_ssa has 6 arguments (exceeds 4 allowed). Consider refactoring.
                          Open

                          def sim_ssa(rxns, rate_params, init_species, init_time, max_time, checkpoint_period):
                          Severity: Minor
                          Found in examples/transcription_translation_hybrid_model/run_with_custom_code.py - About 45 mins to fix

                            Function _record_result has 6 arguments (exceeds 4 allowed). Consider refactoring.
                            Open

                                def _record_result(self, case_type_name, case_num, result_type, duration, **kwargs):
                            Severity: Minor
                            Found in wc_sim/testing/verify.py - About 45 mins to fix

                              Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
                              Open

                                  def __init__(self, name, checkpoint_period, checkpoint_dir, local_species_population,
                              Severity: Minor
                              Found in wc_sim/multialgorithm_checkpointing.py - About 45 mins to fix

                                Consider simplifying this complex logical expression.
                                Open

                                        if (2 < num_species or 1 < num_reactions or
            (0 < num_reactions and num_species == 0) or
                (rate_law_type == RateLawType.product_pop and num_species != 2)):
            raise ValueError("invalid combination of num_species ({}), num_reactions ({}), rate_law_type ({})".format(
                num_species, num_reactions, rate_law_type.name))
                                Severity: Major
                                Found in wc_sim/testing/make_models.py - About 40 mins to fix

                                  Function func has 5 arguments (exceeds 4 allowed). Consider refactoring.
                                  Open

                                      def func(ys, time, species_ids, rxns, rate_params):
                                  Severity: Minor
                                  Found in examples/transcription_translation_hybrid_model/run_with_custom_code.py - About 35 mins to fix

                                    Function init_cell_state_species has 5 arguments (exceeds 4 allowed). Consider refactoring.
                                    Open

                                        def init_cell_state_species(self, species_id, population, molecular_weight, cont_submodel_ids=None):
                                    Severity: Minor
                                    Found in wc_sim/species_populations.py - About 35 mins to fix

                                      Function __init__ has 5 arguments (exceeds 4 allowed). Consider refactoring.
                                      Open

                                          def __init__(self, dynamic_model, local_species_population, wc_lang_model, wc_lang_expression):
                                      Severity: Minor
                                      Found in wc_sim/dynamic_components.py - About 35 mins to fix

                                        Function __init__ has 5 arguments (exceeds 4 allowed). Consider refactoring.
                                        Open

                                            def __init__(self, dynamic_model, local_species_population, wc_lang_model, value):
                                        Severity: Minor
                                        Found in wc_sim/dynamic_components.py - About 35 mins to fix
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