Sign upLogin

KarrLab/wc_sim

View on GitHub
Star

Showing 107 of 141 total issues

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

          def __init__(self, name=None, initial_population=None, molecular_weights=None,
      Severity: Major
      Found in wc_sim/species_populations.py - About 50 mins to fix

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

        def plot_expected_vs_simulated(dynamic_model,
        Severity: Major
        Found in wc_sim/testing/utils.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 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 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 __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 _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 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 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 __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

                              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

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

                                      def read_into_array(self, time, species, populations, round=True):
                                  Severity: Minor
                                  Found in wc_sim/species_populations.py - About 35 mins to fix

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

                                        def adjust_continuously(self, time, cont_submodel_id, population_slopes, time_step=None):
                                    Severity: Minor
                                    Found in wc_sim/species_populations.py - About 35 mins to fix

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

                                          def get_population(self, time, interpolate=None, round=None, temporary_mode=False):
                                      Severity: Minor
                                      Found in wc_sim/species_populations.py - About 35 mins to fix

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

                                            def continuous_adjustment(self, time, cont_submodel_id, population_slope, time_step=None):
                                        Severity: Minor
                                        Found in wc_sim/species_populations.py - About 35 mins to fix
                                          Severity
                                          Category
                                          Status
                                          Source
                                          Language