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BjornFJohansson/pydna

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scripts/gel/gel_old.py

Summary

Maintainability
F
3 wks
Test Coverage

File gel_old.py has 1496 lines of code (exceeds 250 allowed). Consider refactoring.
Open

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# doctest: +NORMALIZE_WHITESPACE
# doctest: +SKIP
Severity: Major
Found in scripts/gel/gel_old.py - About 3 days to fix

    Function gelplot_imshow has a Cognitive Complexity of 57 (exceeds 5 allowed). Consider refactoring.
    Open

    def gelplot_imshow(
    distances,
    bandwidths,
    intensities,
    lanes,
    Severity: Minor
    Found in scripts/gel/gel_old.py - About 1 day 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

    Function run has a Cognitive Complexity of 39 (exceeds 5 allowed). Consider refactoring.
    Open

        def run(
        self,
        till_len=0.75,  # percent of gel_len
        till_time=None,  # hours
        exposure=0.5,  # [0-1]
    Severity: Minor
    Found in scripts/gel/gel_old.py - About 5 hrs 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

    Function run has 89 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        def run(
        self,
        till_len=0.75,  # percent of gel_len
        till_time=None,  # hours
        exposure=0.5,  # [0-1]
    Severity: Major
    Found in scripts/gel/gel_old.py - About 3 hrs to fix

      Function run has 20 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def run(
      Severity: Major
      Found in scripts/gel/gel_old.py - About 2 hrs to fix

        Function gelplot_imshow has 20 arguments (exceeds 4 allowed). Consider refactoring.
        Open

        def gelplot_imshow(
        Severity: Major
        Found in scripts/gel/gel_old.py - About 2 hrs to fix

          Function gelplot_imshow has 54 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

          def gelplot_imshow(
    distances,
    bandwidths,
    intensities,
    lanes,
          Severity: Major
          Found in scripts/gel/gel_old.py - About 2 hrs to fix

            Function assign_quantitiesB has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
            Open

            def assign_quantitiesB(samples, maxdef=Q_(150, "ng")):
    """
    Assigns quantities (masses in nanograms) to the DNA fragments without
    corresponding quantity assuming a linear relationship between the DNA
    length (in basepairs) and its mass. As if the fragments originated in
            Severity: Minor
            Found in scripts/gel/gel_old.py - About 1 hr 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

            Function ferguson_to_mu0 has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
            Open

            def ferguson_to_mu0(
    field,
    Tvals,
    DNAvals,
    dataset,
            Severity: Minor
            Found in scripts/gel/gel_old.py - About 1 hr 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

            Function __init__ has 32 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

                def __init__(
        self,
        samples,  # list of lists of Dseqrecords
        names=None,
        percentgel=Q_(1.0, "(g/(100 mL))*100"),  # agar/buffer
            Severity: Minor
            Found in scripts/gel/gel_old.py - About 1 hr to fix

              Function __init__ has 10 arguments (exceeds 4 allowed). Consider refactoring.
              Open

                  def __init__(
              Severity: Major
              Found in scripts/gel/gel_old.py - About 1 hr to fix

                Function vWBRfit has 8 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                def vWBRfit(
                Severity: Major
                Found in scripts/gel/gel_old.py - About 1 hr to fix

                  Function ferguson_to_mu0 has 8 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                  def ferguson_to_mu0(
                  Severity: Major
                  Found in scripts/gel/gel_old.py - About 1 hr to fix

                    Function _to_units has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
                    Open

                    def _to_units(quantity, units, var_name=None):
    """Asserts that the quantity has the proper dimensions
    (inferred from the default units) if the quantity is an instance of
    pint.unit.Quantity or assigns the default units if it's not.
    """
                    Severity: Minor
                    Found in scripts/gel/gel_old.py - About 55 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

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

                    def size_to_mobility(
                    Severity: Major
                    Found in scripts/gel/gel_old.py - About 50 mins to fix

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

                      def reduced_field(eta, a, mu0, E, kB, T):
                      Severity: Minor
                      Found in scripts/gel/gel_old.py - About 45 mins to fix

                        Avoid deeply nested control flow statements.
                        Open

                                            if forYI <= Itol or pxlYfor == pxl_y:
                        forwdYstop = True
    # Background color
    if noise is None or noise <= 0:
                        Severity: Major
                        Found in scripts/gel/gel_old.py - About 45 mins to fix

                          Avoid deeply nested control flow statements.
                          Open

                                              if pxlYbck < len(rgb_arr):
                        rgb_arr[pxlYbck, from_x:to_x] += bckYI
                    pxlYbck -= 1
                          Severity: Major
                          Found in scripts/gel/gel_old.py - About 45 mins to fix

                            Avoid deeply nested control flow statements.
                            Open

                                                if bckYI <= Itol or pxlYbck == -1:
                        bckwdYstop = True
                if not forwdYstop:
                            Severity: Major
                            Found in scripts/gel/gel_old.py - About 45 mins to fix

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

                              def reduced_field_Kuhn(eta, l, mu0, E, kB, T):
                              Severity: Minor
                              Found in scripts/gel/gel_old.py - About 45 mins to fix

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

                                def Zimm_g(Nbp, DRouse, qeff, mu0, kB, T):
                                Severity: Minor
                                Found in scripts/gel/gel_old.py - About 45 mins to fix

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

                                  def pore_size(gamma, muL, mu0, lp, b):
                                  Severity: Minor
                                  Found in scripts/gel/gel_old.py - About 35 mins to fix

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

                                    def diffusion_coefficient(Nbp, N_lim1, N_lim2, N_lim3, args):
                                    Severity: Minor
                                    Found in scripts/gel/gel_old.py - About 35 mins to fix

                                      Function flatten has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
                                      Open

                                      def flatten(List):
    if List == []:
        return List
    flatL = []
    for elem in List:
                                      Severity: Minor
                                      Found in scripts/gel/gel_old.py - About 35 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

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

                                          for i in range(nlanes):
        bandlength = bandlengths[i]
        center = lane_centers[i]
        x = center - bandlength / 2.0
        for j in range(len(lanes[i])):
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 2 days to fix
                                      scripts/gel/gel2.py on lines 525..548

                                      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 270.

                                      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

                                                      if N < N_lim3:
                    # Ogston-Zimm
                    L = contour_length(Nbp, b)  # (m)
                    Rg = radius_gyration(L, lp)  # (m)
                    D0 = free_solution(kB, temperature, eta, Rg)  # (m^2/s)
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 1 day to fix
                                      scripts/gel/gel_old.py on lines 550..566

                                      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 173.

                                      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

                                          if N < N_lim3:
        # Ogston-Zimm
        L = contour_length(Nbp, b)
        Rg = radius_gyration(L, lp)
        D0 = free_solution(kB, T, eta, Rg)
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 1 day to fix
                                      scripts/gel/gel_old.py on lines 1573..1589

                                      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 173.

                                      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

                                          for l in range(len(DNAvals)):
        not_nan = _np.logical_not(_np.isnan(ln_mu_LxT[l]))
        if sum(not_nan) > 1:
            # (enough points for linear regression)
            gradient, intercept, r_value, p_value, std_err = _stats.linregress(Tvals[not_nan], ln_mu_LxT[l][not_nan])
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 7 hrs to fix
                                      scripts/gel/gel2.py on lines 279..289

                                      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 121.

                                      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

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

                                          for i in range(nlanes):
        ctr = lane_centers[i]
        wx = wellx[i]
        wy = welly[i]
        ax1.fill_between(
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 6 hrs to fix
                                      scripts/gel/gel2.py on lines 513..521

                                      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 108.

                                      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

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

                                          if noise is None or noise <= 0:
        rgb_arr += back_col
    else:
        bckg = _np.random.normal(back_col, noise, (len(rgb_arr), len(rgb_arr[0])))
        rgb_arr += bckg[:, :, _np.newaxis]
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 4 hrs to fix
                                      scripts/gel/gel2.py on lines 473..477

                                      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 80.

                                      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

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

                                          vWBR = lambda L, muS, muL, gamma: (1 / muS + (1 / muL - 1 / muS) * (1 - _np.exp(-L / gamma))) ** -1
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 4 hrs to fix
                                      scripts/gel/gel2.py on lines 245..245

                                      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 78.

                                      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

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

                                          return (lp * L / 3 * (1 - lp / L + lp / L * _np.exp(-L / lp))) ** (1 / 2)
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 4 hrs to fix
                                      scripts/gel/gel2.py on lines 174..174

                                      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 77.

                                      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

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

                                      Ogston_Rouse = lambda Nbp, kB, T, a, eta, b, l: kB * T * a**3 / (eta * b**2 * l**2 * Nbp**2)
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 4 hrs to fix
                                      scripts/gel/gel2.py on lines 182..182

                                      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 77.

                                      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

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

                                          minorLocator = _FixedLocator(
        [j / 10.0 for k in range(0, int(gel_len + 1) * 10, 10) for j in range(1 + k, 10 + k, 1)]
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 3 hrs to fix
                                      scripts/gel/gel2.py on lines 502..503

                                      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 68.

                                      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

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

                                          if len(lregr_stats) > 0:
        # Free solution mobility determination
        ln_mu0 = _np.mean([row[1] for row in lregr_stats])  # mean of intercepts
        mu0 = _np.exp(ln_mu0)  # cm^2/(V.seg)
    else:
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 2 hrs to fix
                                      scripts/gel/gel2.py on lines 292..297

                                      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 56.

                                      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

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

                                          cursor_args = dict(
        display="multiple",
        draggable=True,
        hover=False,
        bbox=dict(fc="white"),
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 2 hrs to fix
                                      scripts/gel/gel2.py on lines 564..571

                                      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 52.

                                      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

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

                                          an1 = _plt.annotate(
        title,
        xy=(0, 0),
        xytext=(xlim + 0.4, (gel_len + max(welly)) / 2.0),
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 2 hrs to fix
                                      scripts/gel/gel2.py on lines 555..558

                                      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 52.

                                      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

                                      def reduced_field_Kuhn(eta, l, mu0, E, kB, T):
    return eta * l**2 * mu0 * E / (kB * T)
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 2 hrs to fix
                                      scripts/gel/gel_old.py on lines 421..422

                                      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 50.

                                      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

                                      def reduced_field(eta, a, mu0, E, kB, T):
    return eta * a**2 * mu0 * E / (kB * T)
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 2 hrs to fix
                                      scripts/gel/gel_old.py on lines 425..426

                                      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 50.

                                      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

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

                                          return FWTM * _np.sqrt(2 * _np.log(2)) / _np.sqrt(2 * _np.log(10))
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 1 hr to fix
                                      scripts/gel/gel2.py on lines 188..188

                                      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 49.

                                      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

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

                                          return hgt * _np.exp(-((x - ctr) ** 2) / (2 * dev**2))
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 1 hr to fix
                                      scripts/gel/gel2.py on lines 185..185

                                      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 47.

                                      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

                                      def Nbp_to_N(Nbp, a, b, l):
    return Nbp * (b / l) * (l / a) ** 2  # number of occupied pores
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 1 hr to fix
                                      scripts/gel/gel_old.py on lines 463..464

                                      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 42.

                                      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

                                      def N_to_Nbp(N, a, b, l):
    return N * (l / b) * (a / l) ** 2  # number of base pairs (bp)
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 1 hr to fix
                                      scripts/gel/gel_old.py on lines 467..468

                                      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 42.

                                      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

                                          return lambda L: 1 / (beta + alpha * (1 - _np.exp(-L / gamma)))
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 1 hr to fix
                                      scripts/gel/gel2.py on lines 159..159

                                      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 41.

                                      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

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

                                              intensities = [[(1 - back_col) / satI * fragI for fragI in lane] for lane in raw_Is]
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 1 hr to fix
                                      scripts/gel/gel2.py on lines 402..402

                                      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 39.

                                      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

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

                                              bandwidths0 = [mobs * time0[l] * field for l, mobs in enumerate(mobilities)]
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 1 other location - About 1 hr to fix
                                      scripts/gel/gel2.py on lines 374..374

                                      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 38.

                                      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

                                          E_space = list(_np.linspace(minE.magnitude, maxE.magnitude, divsE)) * ureg(str(minE.units))
                                      Severity: Minor
                                      Found in scripts/gel/gel_old.py and 1 other location - About 55 mins to fix
                                      scripts/gel/gel_old.py on lines 1760..1760

                                      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 37.

                                      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

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

                                          return (gamma * muL * lp * b / mu0) ** (1 / 2)
                                      Severity: Minor
                                      Found in scripts/gel/gel_old.py and 1 other location - About 55 mins to fix
                                      scripts/gel/gel2.py on lines 305..305

                                      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 37.

                                      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

                                          T_space = list(_np.linspace(minT.magnitude, maxT.magnitude, divsT)) * ureg(str(minT.units))
                                      Severity: Minor
                                      Found in scripts/gel/gel_old.py and 1 other location - About 55 mins to fix
                                      scripts/gel/gel_old.py on lines 1756..1756

                                      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 37.

                                      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 4 locations. Consider refactoring.
                                      Open

                                                          if pxlYbck < len(rgb_arr):
                        rgb_arr[pxlYbck, from_x:to_x] += bckYI
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 3 other locations - About 40 mins to fix
                                      scripts/gel/gel2.py on lines 449..450
                                      scripts/gel/gel2.py on lines 459..460
                                      scripts/gel/gel_old.py on lines 1014..1015

                                      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 4 locations. Consider refactoring.
                                      Open

                                                  if pxlYmid < len(rgb_arr):  # band within gel frontiers
                rgb_arr[pxlYmid, from_x:to_x] += midI
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 3 other locations - About 40 mins to fix
                                      scripts/gel/gel2.py on lines 449..450
                                      scripts/gel/gel2.py on lines 459..460
                                      scripts/gel/gel_old.py on lines 1024..1025

                                      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

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

                                              from_x = int(round(((distXmid - bandlength / 2.0) * res).magnitude))
                                      Severity: Minor
                                      Found in scripts/gel/gel_old.py and 1 other location - About 35 mins to fix
                                      scripts/gel/gel2.py on lines 434..434

                                      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 33.

                                      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

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

                                          return kB * T / (6 * _np.pi * eta * Rh)
                                      Severity: Minor
                                      Found in scripts/gel/gel_old.py and 1 other location - About 35 mins to fix
                                      scripts/gel/gel2.py on lines 179..179

                                      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 33.

                                      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 5 locations. Consider refactoring.
                                      Open

                                          datasets[name]["muL"] = temp_dset["muL"] * ureg("1.0E-8 m**2/(V*s)")
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 4 other locations - About 35 mins to fix
                                      scripts/gel/gel_old.py on lines 348..348
                                      scripts/gel/gel_old.py on lines 349..349
                                      scripts/gel/gel_old.py on lines 350..350
                                      scripts/gel/gel_old.py on lines 352..352

                                      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 33.

                                      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 5 locations. Consider refactoring.
                                      Open

                                          datasets[name]["gamma"] = temp_dset["gamma"] * ureg("kbp")
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 4 other locations - About 35 mins to fix
                                      scripts/gel/gel_old.py on lines 348..348
                                      scripts/gel/gel_old.py on lines 349..349
                                      scripts/gel/gel_old.py on lines 350..350
                                      scripts/gel/gel_old.py on lines 351..351

                                      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 33.

                                      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

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

                                              to_x = int(round(((distXmid + bandlength / 2.0) * res).magnitude))
                                      Severity: Minor
                                      Found in scripts/gel/gel_old.py and 1 other location - About 35 mins to fix
                                      scripts/gel/gel2.py on lines 435..435

                                      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 33.

                                      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 5 locations. Consider refactoring.
                                      Open

                                          datasets[name]["T"] = temp_dset["T"] * ureg("(g/(100 mL))*100")
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 4 other locations - About 35 mins to fix
                                      scripts/gel/gel_old.py on lines 348..348
                                      scripts/gel/gel_old.py on lines 350..350
                                      scripts/gel/gel_old.py on lines 351..351
                                      scripts/gel/gel_old.py on lines 352..352

                                      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 33.

                                      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 5 locations. Consider refactoring.
                                      Open

                                          datasets[name]["E"] = temp_dset["E"] * ureg("V/cm")
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 4 other locations - About 35 mins to fix
                                      scripts/gel/gel_old.py on lines 349..349
                                      scripts/gel/gel_old.py on lines 350..350
                                      scripts/gel/gel_old.py on lines 351..351
                                      scripts/gel/gel_old.py on lines 352..352

                                      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 33.

                                      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 5 locations. Consider refactoring.
                                      Open

                                          datasets[name]["muS"] = temp_dset["muS"] * ureg("1.0E-8 m**2/(V*s)")
                                      Severity: Major
                                      Found in scripts/gel/gel_old.py and 4 other locations - About 35 mins to fix
                                      scripts/gel/gel_old.py on lines 348..348
                                      scripts/gel/gel_old.py on lines 349..349
                                      scripts/gel/gel_old.py on lines 351..351
                                      scripts/gel/gel_old.py on lines 352..352

                                      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 33.

                                      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

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