update black formatting to version 24.1.1

burnman/classes/averaging_schemes.py

@@ -9,7 +9,6 @@
 
 
 class AveragingScheme(object):
-
     """
     Base class defining an interface for determining average
     elastic properties of a rock.  Given a list of volume
@@ -144,7 +143,6 @@ def average_heat_capacity_p(self, fractions, c_p):
 
 
 class VoigtReussHill(AveragingScheme):
-
     """
     Class for computing the Voigt-Reuss-Hill average for elastic properties.
     This derives from :class:`burnman.averaging_schemes.averaging_scheme`,
@@ -218,7 +216,6 @@ def average_shear_moduli(self, volumes, bulk_moduli, shear_moduli):
 
 
 class Voigt(AveragingScheme):
-
     """
     Class for computing the Voigt (iso-strain) bound for elastic properties.
     This derives from :class:`burnman.averaging_schemes.averaging_scheme`,
@@ -277,7 +274,6 @@ def average_shear_moduli(self, volumes, bulk_moduli, shear_moduli):
 
 
 class Reuss(AveragingScheme):
-
     """
     Class for computing the Reuss (iso-stress) bound for elastic properties.
     This derives from :class:`burnman.averaging_schemes.averaging_scheme`,
@@ -336,7 +332,6 @@ def average_shear_moduli(self, volumes, bulk_moduli, shear_moduli):
 
 
 class HashinShtrikmanUpper(AveragingScheme):
-
     """
     Class for computing the upper Hashin-Shtrikman bound for elastic properties.
     This derives from :class:`burnman.averaging_schemes.averaging_scheme`,
@@ -423,7 +418,6 @@ def average_shear_moduli(self, volumes, bulk_moduli, shear_moduli):
 
 
 class HashinShtrikmanLower(AveragingScheme):
-
     """
     Class for computing the lower Hashin-Shtrikman bound for elastic properties.
     This derives from :class:`burnman.averaging_schemes.averaging_scheme`,
@@ -510,7 +504,6 @@ def average_shear_moduli(self, volumes, bulk_moduli, shear_moduli):
 
 
 class HashinShtrikmanAverage(AveragingScheme):
-
     """
     Class for computing arithmetic mean of the Hashin-Shtrikman bounds on
     elastic properties.

burnman/classes/combinedmineral.py

@@ -14,7 +14,6 @@
 
 
 class CombinedMineral(Mineral):
-
     """
     This is the base class for endmembers constructed from a
     linear combination of other minerals.

burnman/classes/composite.py

@@ -38,7 +38,6 @@ def check_pairs(phases, fractions):
 
 # static composite of minerals/composites
 class Composite(Material):
-
     """
     Base class for a composite material.
     The static phases can be minerals or materials,

burnman/classes/elasticsolutionmodel.py

@@ -26,7 +26,6 @@
 
 
 class ElasticSolutionModel(object):
-
     """
     This is the base class for an Elastic solution model, intended for use
     in defining solutions and performing thermodynamic calculations
@@ -216,7 +215,6 @@ def excess_partial_pressures(self, volume, temperature, molar_fractions):
 
 
 class ElasticMechanicalSolution(ElasticSolutionModel):
-
     """
     An extremely simple class representing a mechanical solution model.
     A mechanical solution experiences no interaction between endmembers.
@@ -251,7 +249,6 @@ def excess_partial_entropies(self, volume, temperature, molar_fractions):
 
 
 class ElasticIdealSolution(ElasticSolutionModel):
-
     """
     A class representing an ideal solution model.
     Calculates the excess Helmholtz energy and entropy due to configurational
@@ -382,7 +379,6 @@ def _ideal_activities(self, molar_fractions):
 
 
 class ElasticAsymmetricRegularSolution(ElasticIdealSolution):
-
     """
     Solution model implementing the asymmetric regular solution model
     formulation as described in :cite:`HP2003`.
@@ -510,7 +506,6 @@ def pressure_hessian(self, volume, temperature, molar_fractions):
 
 
 class ElasticSymmetricRegularSolution(ElasticAsymmetricRegularSolution):
-
     """
     Solution model implementing the symmetric regular solution model.
     This is a special case of the
@@ -536,7 +531,6 @@ def __init__(
 
 
 class ElasticSubregularSolution(ElasticIdealSolution):
-
     """
     Solution model implementing the subregular solution model formulation
     as described in :cite:`HW1989`. The excess conconfigurational

burnman/classes/material.py

@@ -14,7 +14,6 @@
 # TODO: When we require Python 3.8+, replace with
 # functools.cached_property decorator
 class cached_property(property):
-
     """A decorator that converts a function into a lazy property.  The
     function wrapped is called the first time to retrieve the result
     and then that calculated result is used the next time you access
@@ -87,7 +86,6 @@ def get(self, obj):
 
 
 class Material(object):
-
     """
     Base class for all materials. The main functionality is unroll() which
     returns a list of objects of type :class:`~burnman.Mineral` and their molar

burnman/classes/mineral.py

@@ -15,7 +15,6 @@
 
 
 class Mineral(Material):
-
     """
     This is the base class for all minerals. States of the mineral
     can only be queried after setting the pressure and temperature

burnman/classes/mineral_helpers.py

@@ -168,7 +168,6 @@ def debug_print(self, indent=""):
 
 
 class HelperSpinTransition(Composite):
-
     """
     Helper class that makes a mineral that switches between two materials
     (for low and high spin) based on some transition pressure [Pa]

burnman/classes/solutionmodel.py

@@ -128,7 +128,6 @@ def inverseish(x, eps=1.0e-5):
 
 
 class SolutionModel(object):
-
     """
     This is the base class for a solution model,  intended for use
     in defining solutions and performing thermodynamic calculations
@@ -326,7 +325,6 @@ def VoverKT_excess(self):
 
 
 class MechanicalSolution(SolutionModel):
-
     """
     An extremely simple class representing a mechanical solution model.
     A mechanical solution experiences no interaction between endmembers.
@@ -372,7 +370,6 @@ def activities(self, pressure, temperature, molar_fractions):
 
 
 class IdealSolution(SolutionModel):
-
     """
     A class representing an ideal solution model.
     Calculates the excess gibbs free energy and entropy due to configurational
@@ -511,7 +508,6 @@ def activities(self, pressure, temperature, molar_fractions):
 
 
 class AsymmetricRegularSolution(IdealSolution):
-
     """
     Solution model implementing the asymmetric regular solution model
     formulation as described in :cite:`HP2003`.
@@ -657,7 +653,6 @@ def activities(self, pressure, temperature, molar_fractions):
 
 
 class SymmetricRegularSolution(AsymmetricRegularSolution):
-
     """
     Solution model implementing the symmetric regular solution model.
     This is a special case of the
@@ -683,7 +678,6 @@ def __init__(
 
 
 class SubregularSolution(IdealSolution):
-
     """
     Solution model implementing the subregular solution model formulation
     as described in :cite:`HW1989`. The excess nonconfigurational

burnman/eos/birch_murnaghan.py

@@ -114,7 +114,6 @@ def shear_modulus_third_order(volume, params):
 
 
 class BirchMurnaghanBase(eos.EquationOfState):
-
     """
     Base class for the isothermal Birch Murnaghan equation of state.  This is third order in strain, and
     has no temperature dependence.  However, the shear modulus is sometimes fit to a second order
@@ -258,7 +257,6 @@ def validate_parameters(self, params):
 
 
 class BM3(BirchMurnaghanBase):
-
     """
     Third order Birch Murnaghan isothermal equation of state.
     This uses the third order expansion for shear modulus.
@@ -269,7 +267,6 @@ def __init__(self):
 
 
 class BM2(BirchMurnaghanBase):
-
     """
     Third order Birch Murnaghan isothermal equation of state.
     This uses the second order expansion for shear modulus.

burnman/eos/birch_murnaghan_4th.py

@@ -81,7 +81,6 @@ def birch_murnaghan_fourth(x, params):
 
 
 class BM4(eos.EquationOfState):
-
     """
     Base class for the isothermal Birch Murnaghan equation of state.  This is fourth order in strain, and
     has no temperature dependence.

burnman/eos/cork.py

@@ -34,7 +34,6 @@ def cork_variables(cork, cork_P, cork_T, temperature):
 
 
 class CORK(eos.EquationOfState):
-
     """
     Class for the CoRK equation of state detailed in :cite:`HP1991`. The
     CoRK EoS is a simple virial-type extension to the modified Redlich-Kwong

burnman/eos/dks_solid.py

@@ -61,7 +61,6 @@ def _delta_pressure(
 
 
 class DKS_S(eos.EquationOfState):
-
     """
     Base class for the finite strain solid equation of state detailed
     in :cite:`deKoker2013` (supplementary materials).

burnman/eos/equation_of_state.py

@@ -5,7 +5,6 @@
 
 
 class EquationOfState(object):
-
     """
     This class defines the interface for an equation of state
     that a mineral uses to determine its properties at a

burnman/eos/hp.py

@@ -17,7 +17,6 @@
 
 
 class HP_TMT(eos.EquationOfState):
-
     """
     Base class for the thermal equation of state based on
     the generic modified Tait equation of state (class MT),
@@ -395,7 +394,6 @@ def validate_parameters(self, params):
 
 
 class HP_TMTL(eos.EquationOfState):
-
     """
     Base class for the thermal equation of state
     described in :cite:`HP1998`, but with the Modified Tait as the static part,
@@ -668,7 +666,6 @@ def validate_parameters(self, params):
 
 
 class HP98(eos.EquationOfState):
-
     """
     Base class for the thermal equation of state
     described in :cite:`HP1998`.

burnman/eos/mie_grueneisen_debye.py

@@ -16,7 +16,6 @@
 
 
 class MGDBase(eos.EquationOfState):
-
     """
     Base class for a generic finite-strain Mie-Grueneisen-Debye
     equation of state.  References for this can be found in many
@@ -304,7 +303,6 @@ def validate_parameters(self, params):
 
 
 class MGD3(MGDBase):
-
     """
     MGD equation of state with third order finite strain expansion for the
     shear modulus (this should be preferred, as it is more thermodynamically
@@ -316,7 +314,6 @@ def __init__(self):
 
 
 class MGD2(MGDBase):
-
     """
     MGD equation of state with second order finite strain expansion for the
     shear modulus.  In general, this should not be used, but sometimes

burnman/eos/modified_tait.py

@@ -92,7 +92,6 @@ def intVdP(pressure, params):
 
 
 class MT(eos.EquationOfState):
-
     """
     Base class for the generic modified Tait equation of state.
     References for this can be found in :cite:`HC1974`

burnman/eos/morse_potential.py

@@ -75,7 +75,6 @@ def volume(pressure, params):
 
 
 class Morse(eos.EquationOfState):
-
     """
     Class for the isothermal Morse Potential equation of state
     detailed in :cite:`Stacey1981`.

burnman/eos/murnaghan.py

@@ -39,7 +39,6 @@ def intVdP(pressure, V_0, K_0, Kprime_0):
 
 
 class Murnaghan(eos.EquationOfState):
-
     """
     Base class for the isothermal Murnaghan equation of state,
     as described in :cite:`Murnaghan1944`.

burnman/eos/reciprocal_kprime.py

@@ -124,7 +124,6 @@ def shear_modulus(pressure, params):
 
 
 class RKprime(eos.EquationOfState):
-
     """
     Class for the isothermal reciprocal K-prime equation of state
     detailed in :cite:`StaceyDavis2004`.  This equation of state is

burnman/eos/slb.py

@@ -63,7 +63,6 @@ def _delta_pressure(
 
 
 class SLBBase(eos.EquationOfState):
-
     """
     Base class for the finite strain-Mie-Grueneiesen-Debye equation of state
     detailed in :cite:`Stixrude2005`.  For the most part the equations are
@@ -468,7 +467,6 @@ def validate_parameters(self, params):
 
 
 class SLB3(SLBBase):
-
     """
     SLB equation of state with third order finite strain expansion for the
     shear modulus (this should be preferred, as it is more thermodynamically
@@ -480,7 +478,6 @@ def __init__(self):
 
 
 class SLB2(SLBBase):
-
     """
     SLB equation of state with second order finite strain expansion for the
     shear modulus.  In general, this should not be used, but sometimes

burnman/eos/vinet.py

@@ -56,7 +56,6 @@ def volume(pressure, params):
 
 
 class Vinet(eos.EquationOfState):
-
     """
     Base class for the isothermal Vinet equation of state.
     References for this equation of state are :cite:`vinet1986`

burnman/minerals/Murakami_2013.py

@@ -36,7 +36,6 @@ def __init__(self):
 
 
 class wuestite(Mineral):
-
     """
     Murakami 2013 and references therein
     """

burnman/minerals/other.py

@@ -130,7 +130,6 @@ def __init__(self):
 
 
 class Speziale_fe_periclase_HS(Mineral):
-
     """
     Speziale et al. 2007, Mg#=83
     """
@@ -151,7 +150,6 @@ def __init__(self):
 
 
 class Speziale_fe_periclase_LS(Mineral):
-
     """
     Speziale et al. 2007, Mg#=83
     """
@@ -172,7 +170,6 @@ def __init__(self):
 
 
 class Liquid_Fe_Anderson(Mineral):
-
     """
     Anderson & Ahrens, 1994 JGR
     """
@@ -190,7 +187,6 @@ def __init__(self):
 
 
 class Fe_Dewaele(Mineral):
-
     """
     Dewaele et al., 2006, Physical Review Letters
     """

burnman/tools/equilibration.py

@@ -644,9 +644,11 @@ def get_equilibration_parameters(assemblage, composition, free_compositional_vec
         prm.free_compositional_vectors = np.array(
             [
                 [
-                    free_compositional_vectors[i][e]
-                    if e in free_compositional_vectors[i]
-                    else 0.0
+                    (
+                        free_compositional_vectors[i][e]
+                        if e in free_compositional_vectors[i]
+                        else 0.0
+                    )
                     for e in assemblage.elements
                 ]
                 for i in range(n_free_compositional_vectors)

contrib/CHRU2014/helper_solid_solution.py

@@ -12,7 +12,6 @@
 
 
 class HelperSolidSolution(burnman.Mineral):
-
     """
     This material is deprecated!
 

contrib/CHRU2014/paper_uncertain.py

@@ -28,7 +28,6 @@
 
 
 class my_perovskite(burnman.Mineral):
-
     """
     based on Stixrude & Lithgow-Bertelloni 2011 and references therein
     """

contrib/anisotropic_eos/tools.py

@@ -42,9 +42,11 @@ def print_table_for_mineral_constants_2(mineral, param_list, indices):
         row = [f"{i}", f"{j}"]
         row.extend(
             [
-                f"{constants[ci, i]:.4e}"
-                if constants[ci, i] != 0 and constants[ci, i] != 1
-                else "-"
+                (
+                    f"{constants[ci, i]:.4e}"
+                    if constants[ci, i] != 0 and constants[ci, i] != 1
+                    else "-"
+                )
                 for i in range(len(param_list))
             ]
         )

examples/example_user_input_material.py

@@ -81,7 +81,7 @@ def __init__(self):
                 # See Stixrude & Lithgow-Bertelloni, 2005 for values
                 "q_0": 0.917,  # isotropic strain derivative of gruneisen
                 # parameter. Values in Stixrude & Lithgow-Bertelloni, 2005
-                "eta_s_0": 3.0  # full strain derivative of gruneisen parameter
+                "eta_s_0": 3.0,  # full strain derivative of gruneisen parameter
                 # parameter. Values in Stixrude & Lithgow-Bertelloni, 2005
             }
             burnman.Mineral.__init__(self)

misc/gen_doc.py

@@ -1,4 +1,5 @@
 """ generates a list with the examples """
+
 from __future__ import absolute_import
 from __future__ import print_function
 

tests/test_averaging.py

@@ -9,7 +9,6 @@
 
 
 class mypericlase(burnman.Mineral):
-
     """
     Stixrude & Lithgow-Bertelloni 2005 and references therein
     """

tests/test_debye.py

@@ -6,7 +6,6 @@
 
 
 class mypericlase(burnman.Mineral):
-
     """
     Stixrude & Lithgow-Bertelloni 2005 and references therein
     """

tests/test_eos.py

@@ -11,7 +11,6 @@
 
 
 class mypericlase(burnman.Mineral):
-
     """
     Stixrude & Lithgow-Bertelloni 2005 and references therein
     """
@@ -36,7 +35,6 @@ def __init__(self):
 
 
 class Fe_Dewaele(burnman.Mineral):
-
     """
     Dewaele et al., 2006, Physical Review Letters
     """
@@ -54,7 +52,6 @@ def __init__(self):
 
 
 class Liquid_Fe_Anderson(burnman.Mineral):
-
     """
     Anderson & Ahrens, 1994 JGR
     """
@@ -72,7 +69,6 @@ def __init__(self):
 
 
 class outer_core_rkprime(burnman.Mineral):
-
     """
     Stacey and Davis, 2004 PEPI (Table 5)
     """
@@ -90,7 +86,6 @@ def __init__(self):
 
 
 class periclase_morse(burnman.Mineral):
-
     """
     Periclase parameters from SLB dataset (which uses BM3)
     """

tests/test_geotherm.py

@@ -6,7 +6,6 @@
 
 
 class mypericlase(burnman.Mineral):
-
     """
     Stixrude & Lithgow-Bertelloni 2005 and references therein
     """

tests/test_material.py

@@ -7,11 +7,9 @@
 
 
 class test_material_name(BurnManTest):
-
     """test Material.name and that we can edit and override it in Mineral"""
 
     class min_no_name(burnman.Mineral):
-
         """
         Stixrude & Lithgow-Bertelloni 2005 and references therein
         """
@@ -36,7 +34,6 @@ def __init__(self):
             burnman.Mineral.__init__(self)
 
     class min_with_name(burnman.Mineral):
-
         """
         Stixrude & Lithgow-Bertelloni 2005 and references therein
         """
@@ -62,7 +59,6 @@ def __init__(self):
             burnman.Mineral.__init__(self)
 
     class min_with_name_manually(burnman.Mineral):
-
         """
         Stixrude & Lithgow-Bertelloni 2005 and references therein
         """