Sign upLogin

KarrLab/wc_model_gen

View on GitHub
Star

Showing 341 of 341 total issues

Avoid deeply nested control flow statements.
Open

                        if comp.distribution_init_concentration.mean!=0.0:
                            kcat.value = shared_vmax/comp.distribution_init_concentration.mean*\
                                kcat_adjustment_factor                                    
                            kcat.comments = 'Value imputed based on FVA bound value ' +\
                                'and adjusted with a factor of {}'.format(kcat_adjustment_factor)
Severity: Major
Found in wc_model_gen/eukaryote/metabolism.py - About 45 mins to fix

    Similar blocks of code found in 13 locations. Consider refactoring.
    Open

                init_reaction.participants.append(metabolites['h'][
                translation_compartment.id].species_coefficients.get_or_create(coefficient=5))
    Severity: Major
    Found in wc_model_gen/eukaryote/translation_translocation.py and 12 other locations - About 45 mins to fix
    wc_model_gen/eukaryote/transcription.py on lines 439..440
    wc_model_gen/eukaryote/transcription.py on lines 442..443
    wc_model_gen/eukaryote/transcription.py on lines 445..446
    wc_model_gen/eukaryote/transcription.py on lines 448..449
    wc_model_gen/eukaryote/transcription.py on lines 451..452
    wc_model_gen/eukaryote/translation_translocation.py on lines 358..359
    wc_model_gen/eukaryote/translation_translocation.py on lines 360..361
    wc_model_gen/eukaryote/translation_translocation.py on lines 362..363
    wc_model_gen/eukaryote/translation_translocation.py on lines 371..372
    wc_model_gen/eukaryote/translation_translocation.py on lines 373..374
    wc_model_gen/eukaryote/translation_translocation.py on lines 375..376
    wc_model_gen/eukaryote/translation_translocation.py on lines 377..378

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 35.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Avoid deeply nested control flow statements.
    Open

                            if trna_obs not in self._modifiers:
                            self._modifiers.append(trna_obs)
                        trna = trna_obs.expression.species.get_one(compartment=cytosol)
    Severity: Major
    Found in wc_model_gen/prokaryote/translation.py - About 45 mins to fix

      Avoid deeply nested control flow statements.
      Open

                              if codon == 'ATG':
                            aa = model.species_types.get_one(id='met').species.get_one(compartment=cytosol)
                        elif codon == 'ACT' or codon == 'ACC' or codon == 'ACA' or codon == 'ACG':
                            aa = model.species_types.get_one(id='thr').species.get_one(compartment=cytosol)
                        elif codon == 'ATT' or codon == 'ATC' or codon == 'ATA':
      Severity: Major
      Found in wc_model_gen/prokaryote/translation.py - About 45 mins to fix

        Function run has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
        Open

            def run(self):
        self.gen_compartments()

        self.gen_parameters()
        self.clean_and_validate_options()
        Severity: Minor
        Found in wc_model_gen/prokaryote/initalize_model.py - About 45 mins to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        Avoid deeply nested control flow statements.
        Open

                                if serine_coefficient:
                            old_coef = serine_coefficient.coefficient
                            el_reaction.participants.remove(serine_coefficient)
                            el_reaction.participants.add(
                                serine_species.species_coefficients.get_or_create(
        Severity: Major
        Found in wc_model_gen/eukaryote/translation_translocation.py - About 45 mins to fix

          Avoid deeply nested control flow statements.
          Open

                                  if cplx_species.compartment in conc_per_comp:
                            conc_per_comp[cplx_species.compartment] += stoic * \
                                cplx_species.distribution_init_concentration.mean
                        else:        
                            conc_per_comp[cplx_species.compartment] = stoic * \
          Severity: Major
          Found in wc_model_gen/eukaryote/translation_translocation.py - About 45 mins to fix

            Avoid deeply nested control flow statements.
            Open

                                    if subunit_id not in gvar.transcript_ntp_usage:
                            seq = subunit.species_type.get_seq()
                            gvar.transcript_ntp_usage[subunit.species_type.id] = {
                                'A': seq.upper().count('A'),
                                'C': seq.upper().count('C'),
            Severity: Major
            Found in wc_model_gen/eukaryote/initialize_model.py - About 45 mins to fix

              Similar blocks of code found in 13 locations. Consider refactoring.
              Open

                          init_reaction.participants.append(metabolites['gtp'][
                translation_compartment.id].species_coefficients.get_or_create(coefficient=-2))
              Severity: Major
              Found in wc_model_gen/eukaryote/translation_translocation.py and 12 other locations - About 45 mins to fix
              wc_model_gen/eukaryote/transcription.py on lines 439..440
              wc_model_gen/eukaryote/transcription.py on lines 442..443
              wc_model_gen/eukaryote/transcription.py on lines 445..446
              wc_model_gen/eukaryote/transcription.py on lines 448..449
              wc_model_gen/eukaryote/transcription.py on lines 451..452
              wc_model_gen/eukaryote/translation_translocation.py on lines 358..359
              wc_model_gen/eukaryote/translation_translocation.py on lines 360..361
              wc_model_gen/eukaryote/translation_translocation.py on lines 369..370
              wc_model_gen/eukaryote/translation_translocation.py on lines 371..372
              wc_model_gen/eukaryote/translation_translocation.py on lines 373..374
              wc_model_gen/eukaryote/translation_translocation.py on lines 375..376
              wc_model_gen/eukaryote/translation_translocation.py on lines 377..378

              Duplicated Code

              Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

              Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

              When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

              Tuning

              This issue has a mass of 35.

              We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

              The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

              If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

              See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

              Refactorings

              Further Reading

              Similar blocks of code found in 2 locations. Consider refactoring.
              Open

                                      el_reaction.participants.append(metabolites['ppi'][
                            translation_compartment.id].species_coefficients.get_or_create(
              Severity: Minor
              Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 45 mins to fix
              wc_model_gen/eukaryote/translation_translocation.py on lines 426..427

              Duplicated Code

              Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

              Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

              When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

              Tuning

              This issue has a mass of 35.

              We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

              The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

              If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

              See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

              Refactorings

              Further Reading

              Avoid deeply nested control flow statements.
              Open

                                      if species.distribution_init_concentration:
                            if species.distribution_init_concentration.mean:    
                                param.value = beta * species.distribution_init_concentration.mean \
                                    / Avogadro.value / species.compartment.init_volume.mean
                                param.comments = 'The value was assumed to be {} times the concentration of {} in {}'.format(
              Severity: Major
              Found in wc_model_gen/eukaryote/complexation.py - About 45 mins to fix

                Avoid deeply nested control flow statements.
                Open

                                        if model_compl_species.distribution_init_concentration:
                            param.value = self._effective_dissociation_constant['{}[{}]'.format(
                                complex_st_id, compl_compartment_id)] * model_compl_species.distribution_init_concentration.mean
                        else:
                            param.value = self._effective_dissociation_constant['{}[{}]'.format(
                Severity: Major
                Found in wc_model_gen/eukaryote/complexation.py - About 45 mins to fix

                  Avoid deeply nested control flow statements.
                  Open

                                          for part in prot_deg_reaction.participants:
                            if part.species.id in met_requirement:
                                met_requirement[part.species.id] += -part.coefficient * prot_concentration * \
                                    doubling_time / prot_half_life
                  Severity: Major
                  Found in wc_model_gen/eukaryote/metabolism.py - About 45 mins to fix

                    Similar blocks of code found in 13 locations. Consider refactoring.
                    Open

                                    init_reaction.participants.append(metabolites['adp'][
                    transcription_compartment.id].species_coefficients.get_or_create(
                    Severity: Major
                    Found in wc_model_gen/eukaryote/transcription.py and 12 other locations - About 45 mins to fix
                    wc_model_gen/eukaryote/transcription.py on lines 439..440
                    wc_model_gen/eukaryote/transcription.py on lines 442..443
                    wc_model_gen/eukaryote/transcription.py on lines 448..449
                    wc_model_gen/eukaryote/transcription.py on lines 451..452
                    wc_model_gen/eukaryote/translation_translocation.py on lines 358..359
                    wc_model_gen/eukaryote/translation_translocation.py on lines 360..361
                    wc_model_gen/eukaryote/translation_translocation.py on lines 362..363
                    wc_model_gen/eukaryote/translation_translocation.py on lines 369..370
                    wc_model_gen/eukaryote/translation_translocation.py on lines 371..372
                    wc_model_gen/eukaryote/translation_translocation.py on lines 373..374
                    wc_model_gen/eukaryote/translation_translocation.py on lines 375..376
                    wc_model_gen/eukaryote/translation_translocation.py on lines 377..378

                    Duplicated Code

                    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                    Tuning

                    This issue has a mass of 35.

                    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                    Refactorings

                    Further Reading

                    Avoid deeply nested control flow statements.
                    Open

                                            if aa_coefficient:
                            old_coef = aa_coefficient.coefficient
                            el_reaction.participants.remove(aa_coefficient)
                            el_reaction.participants.add(
                                aa_species.species_coefficients.get_or_create(
                    Severity: Major
                    Found in wc_model_gen/eukaryote/translation_translocation.py - About 45 mins to fix

                      Similar blocks of code found in 12 locations. Consider refactoring.
                      Open

                              Avogadro = model.parameters.get_or_create(
            id='Avogadro',
            type=None,
            value=scipy.constants.Avogadro,
            units=unit_registry.parse_units('molecule mol^-1'))
                      Severity: Major
                      Found in wc_model_gen/eukaryote/complexation.py and 11 other locations - About 40 mins to fix
                      wc_model_gen/eukaryote/transcription.py on lines 1095..1099
                      wc_model_gen/eukaryote/translation_translocation.py on lines 1387..1391
                      wc_model_gen/prokaryote/protein_degradation.py on lines 131..135
                      wc_model_gen/prokaryote/rna_degradation.py on lines 107..111
                      wc_model_gen/prokaryote/transcription.py on lines 105..109
                      wc_model_gen/prokaryote/translation.py on lines 167..171
                      wc_model_gen/utils.py on lines 210..214
                      wc_model_gen/utils.py on lines 255..259
                      wc_model_gen/utils.py on lines 343..347
                      wc_model_gen/utils.py on lines 432..436
                      wc_model_gen/utils.py on lines 514..518

                      Duplicated Code

                      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                      Tuning

                      This issue has a mass of 34.

                      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                      Refactorings

                      Further Reading

                      Similar blocks of code found in 12 locations. Consider refactoring.
                      Open

                              Avogadro = model.parameters.get_or_create(
            id='Avogadro',
            type=None,
            value=scipy.constants.Avogadro,
            units=unit_registry.parse_units('molecule mol^-1'))
                      Severity: Major
                      Found in wc_model_gen/prokaryote/translation.py and 11 other locations - About 40 mins to fix
                      wc_model_gen/eukaryote/complexation.py on lines 363..367
                      wc_model_gen/eukaryote/transcription.py on lines 1095..1099
                      wc_model_gen/eukaryote/translation_translocation.py on lines 1387..1391
                      wc_model_gen/prokaryote/protein_degradation.py on lines 131..135
                      wc_model_gen/prokaryote/rna_degradation.py on lines 107..111
                      wc_model_gen/prokaryote/transcription.py on lines 105..109
                      wc_model_gen/utils.py on lines 210..214
                      wc_model_gen/utils.py on lines 255..259
                      wc_model_gen/utils.py on lines 343..347
                      wc_model_gen/utils.py on lines 432..436
                      wc_model_gen/utils.py on lines 514..518

                      Duplicated Code

                      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                      Tuning

                      This issue has a mass of 34.

                      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                      Refactorings

                      Further Reading

                      Similar blocks of code found in 12 locations. Consider refactoring.
                      Open

                          avogadro = model.parameters.get_or_create(
        id='Avogadro',
        type=None,
        value=scipy.constants.Avogadro,
        units=unit_registry.parse_units('molecule mol^-1'))
                      Severity: Major
                      Found in wc_model_gen/utils.py and 11 other locations - About 40 mins to fix
                      wc_model_gen/eukaryote/complexation.py on lines 363..367
                      wc_model_gen/eukaryote/transcription.py on lines 1095..1099
                      wc_model_gen/eukaryote/translation_translocation.py on lines 1387..1391
                      wc_model_gen/prokaryote/protein_degradation.py on lines 131..135
                      wc_model_gen/prokaryote/rna_degradation.py on lines 107..111
                      wc_model_gen/prokaryote/transcription.py on lines 105..109
                      wc_model_gen/prokaryote/translation.py on lines 167..171
                      wc_model_gen/utils.py on lines 210..214
                      wc_model_gen/utils.py on lines 255..259
                      wc_model_gen/utils.py on lines 343..347
                      wc_model_gen/utils.py on lines 514..518

                      Duplicated Code

                      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                      Tuning

                      This issue has a mass of 34.

                      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                      Refactorings

                      Further Reading

                      Similar blocks of code found in 2 locations. Consider refactoring.
                      Open

                                      ntp_count = {k:v+add_seq[k] for k,v in ntp_count.items()}
                      Severity: Minor
                      Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 40 mins to fix
                      wc_model_gen/eukaryote/transcription.py on lines 354..354

                      Duplicated Code

                      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                      Tuning

                      This issue has a mass of 34.

                      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                      Refactorings

                      Further Reading

                      Similar blocks of code found in 2 locations. Consider refactoring.
                      Open

                                          add_seq = {k:v+add_count[k] for k,v in add_seq.items()}
                      Severity: Minor
                      Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 40 mins to fix
                      wc_model_gen/eukaryote/transcription.py on lines 492..492

                      Duplicated Code

                      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                      Tuning

                      This issue has a mass of 34.

                      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                      Refactorings

                      Further Reading

                      Severity
                      Category
                      Status
                      Source
                      Language