Merge pull request #567 from bobmyhill/python_3.12

enable python 3.12

.github/workflows/main.yml

@@ -10,7 +10,7 @@ jobs:
 
  strategy:
  matrix:
- python-versions: ['3.11']
+ python-versions: ['3.12']
 
  steps:
  - uses: actions/checkout@v2
@@ -38,7 +38,7 @@ jobs:
 
  strategy:
  matrix:
- python-versions: ['3.8', '3.9', '3.10', '3.11']
+ python-versions: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
  steps:
  - uses: actions/checkout@v2

burnman/eos/aa.py

@@ -20,24 +20,24 @@ class AA(eos.EquationOfState):
  which gives volume as a function of pressure,
  coupled with the thermodynamic identity:
 
- :math:`-\partial E/ \partial V |_S = P`.
+ :math:`-\\partial E/ \\partial V |_S = P`.
 
  The temperature along the isentrope is calculated via
 
- :math:`\partial (\ln T)/\partial (\ln \\rho) |_S = \gamma`
+ :math:`\\partial (\\ln T)/\\partial (\\ln \\rho) |_S = \\gamma`
 
  which gives:
 
- :math:`T_S/T_0 = \exp(\int( \gamma/\\rho ) d \\rho)`
+ :math:`T_S/T_0 = \\exp(\\int( \\gamma/\\rho ) d \\rho)`
 
  The thermal effect on internal energy is calculated at constant volume
  using expressions for the kinetic, electronic and potential contributions
  to the volumetric heat capacity, which can then be integrated with respect
  to temperature:
 
- :math:`\partial E/\partial T |_V = C_V`
+ :math:`\\partial E/\\partial T |_V = C_V`
 
- :math:`\partial E/\partial S |_V = T`
+ :math:`\\partial E/\\partial S |_V = T`
 
  We note that :cite:`AA1994` also include a detailed description
  of the Gruneisen parameter as a function of volume and energy (Equation 15),
@@ -50,16 +50,16 @@ class AA(eos.EquationOfState):
  1) As energy and entropy are defined by the equation of state at any
  temperature and volume, pressure can be found by via the expression:
 
- :math:`\partial E/\partial V |_S = P`
+ :math:`\\partial E/\\partial V |_S = P`
 
  2) The Grueneisen parameter can now be determined as
- :math:`\gamma = V \partial P/\partial E |_V`
+ :math:`\\gamma = V \\partial P/\\partial E |_V`
 
  To reiterate: away from the reference isentrope, the Grueneisen parameter
  calculated using these expressions is *not* equal to the
  (thermodynamically inconsistent) analytical expression given by :cite:`AA1994`.
 
- A final note: the expression for :math:`\Lambda` (Equation 17).
+ A final note: the expression for :math:`\\Lambda` (Equation 17).
  does not reproduce Figure 5. We assume here that the figure matches the model
  actually used by :cite:`AA1994`, which has the form:
  :math:`F(-325.23 + 302.07 (\\rho/\\rho_0) + 30.45 (\\rho/\\rho_0)^{0.4})`.
@@ -249,7 +249,7 @@ def pressure(self, temperature, volume, params):
  E1 = self._isentropic_energy_change(volume, params) - params['E_0']
  E2 = E1 + dE
 
- # Integrate at constant volume (V \int dP = \int gr dE)
+ # Integrate at constant volume (V \\int dP = \\int gr dE)
  dP = (params['grueneisen_0']*(E2 - E1) +
  (0.5*params['grueneisen_prime'] *
  np.power(params['V_0']/volume, params['grueneisen_n']) *

burnman/eos/birch_murnaghan.py

@@ -153,13 +153,13 @@ def shear_modulus(self, pressure, temperature, volume, params):
 
  def entropy(self, pressure, temperature, volume, params):
  """
- Returns the molar entropy :math:`\mathcal{S}` of the mineral. :math:`[J/K/mol]`
+ Returns the molar entropy :math:`\\mathcal{S}` of the mineral. :math:`[J/K/mol]`
  """
  return 0.0
 
  def molar_internal_energy(self, pressure, temperature, volume, params):
  """
- Returns the internal energy :math:`\mathcal{E}` of the mineral. :math:`[J/mol]`
+ Returns the internal energy :math:`\\mathcal{E}` of the mineral. :math:`[J/mol]`
  """
  x = np.power(volume / params["V_0"], -1.0 / 3.0)
  x2 = x * x
@@ -184,7 +184,7 @@ def molar_internal_energy(self, pressure, temperature, volume, params):
 
  def gibbs_free_energy(self, pressure, temperature, volume, params):
  """
- Returns the Gibbs free energy :math:`\mathcal{G}` of the mineral. :math:`[J/mol]`
+ Returns the Gibbs free energy :math:`\\mathcal{G}` of the mineral. :math:`[J/mol]`
  """
  # G = int VdP = [PV] - int PdV = E + PV
 

burnman/eos/birch_murnaghan_4th.py

@@ -116,13 +116,13 @@ def shear_modulus(self, pressure, temperature, volume, params):
 
  def entropy(self, pressure, temperature, volume, params):
  """
- Returns the molar entropy :math:`\mathcal{S}` of the mineral. :math:`[J/K/mol]`
+ Returns the molar entropy :math:`\\mathcal{S}` of the mineral. :math:`[J/K/mol]`
  """
  return 0.0
 
  def molar_internal_energy(self, pressure, temperature, volume, params):
  """
- Returns the internal energy :math:`\mathcal{E}` of the mineral. :math:`[J/mol]`
+ Returns the internal energy :math:`\\mathcal{E}` of the mineral. :math:`[J/mol]`
  """
  x = np.power(volume / params["V_0"], -1.0 / 3.0)
  x2 = x * x
@@ -157,7 +157,7 @@ def molar_internal_energy(self, pressure, temperature, volume, params):
 
  def gibbs_free_energy(self, pressure, temperature, volume, params):
  """
- Returns the Gibbs free energy :math:`\mathcal{G}` of the mineral. :math:`[J/mol]`
+ Returns the Gibbs free energy :math:`\\mathcal{G}` of the mineral. :math:`[J/mol]`
  """
  # G = int VdP = [PV] - int PdV = E + PV
 

burnman/eos/modified_tait.py

@@ -137,13 +137,13 @@ def shear_modulus(self, pressure, temperature, volume, params):
 
  def entropy(self, pressure, temperature, volume, params):
  """
- Returns the molar entropy :math:`\mathcal{S}` of the mineral. :math:`[J/K/mol]`
+ Returns the molar entropy :math:`\\mathcal{S}` of the mineral. :math:`[J/K/mol]`
  """
  return 0.0
 
  def molar_internal_energy(self, pressure, temperature, volume, params):
  """
- Returns the internal energy :math:`\mathcal{E}` of the mineral. :math:`[J/mol]`
+ Returns the internal energy :math:`\\mathcal{E}` of the mineral. :math:`[J/mol]`
  """
 
  return (
@@ -153,7 +153,7 @@ def molar_internal_energy(self, pressure, temperature, volume, params):
 
  def gibbs_free_energy(self, pressure, temperature, volume, params):
  """
- Returns the Gibbs free energy :math:`\mathcal{G}` of the mineral. :math:`[J/mol]`
+ Returns the Gibbs free energy :math:`\\mathcal{G}` of the mineral. :math:`[J/mol]`
  """
  # G = int VdP = [PV] - int PdV = E + PV
  a, b, c = tait_constants(params)

burnman/eos/morse_potential.py

@@ -111,13 +111,13 @@ def shear_modulus(self, pressure, temperature, volume, params):
 
  def entropy(self, pressure, temperature, volume, params):
  """
- Returns the molar entropy :math:`\mathcal{S}` of the mineral. :math:`[J/K/mol]`
+ Returns the molar entropy :math:`\\mathcal{S}` of the mineral. :math:`[J/K/mol]`
  """
  return 0.0
 
  def molar_internal_energy(self, pressure, temperature, volume, params):
  """
- Returns the internal energy :math:`\mathcal{E}` of the mineral. :math:`[J/mol]`
+ Returns the internal energy :math:`\\mathcal{E}` of the mineral. :math:`[J/mol]`
  """
 
  x = (params["Kprime_0"] - 1) * (1 - np.power(volume / params["V_0"], 1.0 / 3.0))
@@ -134,7 +134,7 @@ def molar_internal_energy(self, pressure, temperature, volume, params):
 
  def gibbs_free_energy(self, pressure, temperature, volume, params):
  """
- Returns the Gibbs free energy :math:`\mathcal{G}` of the mineral. :math:`[J/mol]`
+ Returns the Gibbs free energy :math:`\\mathcal{G}` of the mineral. :math:`[J/mol]`
  """
  return (
  self.molar_internal_energy(pressure, temperature, volume, params)

burnman/eos/murnaghan.py

@@ -76,14 +76,14 @@ def shear_modulus(self, pressure, temperature, volume, params):
 
  def entropy(self, pressure, temperature, volume, params):
  """
- Returns the molar entropy :math:`\mathcal{S}` of the mineral.
+ Returns the molar entropy :math:`\\mathcal{S}` of the mineral.
  :math:`[J/K/mol]`
  """
  return 0.0
 
  def molar_internal_energy(self, pressure, temperature, volume, params):
  """
- Returns the internal energy :math:`\mathcal{E}` of the mineral.
+ Returns the internal energy :math:`\\mathcal{E}` of the mineral.
  :math:`[J/mol]`
  """
  return energy(
@@ -92,7 +92,7 @@ def molar_internal_energy(self, pressure, temperature, volume, params):
 
  def gibbs_free_energy(self, pressure, temperature, volume, params):
  """
- Returns the Gibbs free energy :math:`\mathcal{G}` of the mineral.
+ Returns the Gibbs free energy :math:`\\mathcal{G}` of the mineral.
  :math:`[J/mol]`
  """
  # G = E + PV

burnman/eos/reciprocal_kprime.py

@@ -136,11 +136,11 @@ class RKprime(eos.EquationOfState):
  unstable at negative pressures, so should not be trusted to provide
  a good *HT-LP* equation of state using a thermal pressure
  formulation. The negative root of :math:`dP/dK`
- can be found at :math:`K/P = K'_{\infty} - K'_0`,
+ can be found at :math:`K/P = K'_{\\infty} - K'_0`,
  which corresponds to a bulk modulus of
- :math:`K = K_0 ( 1 - K'_{\infty}/K'_0 )^{K'_0/K'_{\infty}}`
+ :math:`K = K_0 ( 1 - K'_{\\infty}/K'_0 )^{K'_0/K'_{\\infty}}`
  and a volume of
- :math:`V = V_0 ( K'_0 / (K'_0 - K'_{\infty}) )^{K'_0/{K'}^2_{\infty}} \exp{(-1/K'_{\infty})}`.
+ :math:`V = V_0 ( K'_0 / (K'_0 - K'_{\\infty}) )^{K'_0/{K'}^2_{\\infty}} \\exp{(-1/K'_{\\infty})}`.
 
  This equation of state has no temperature dependence.
  """
@@ -196,7 +196,7 @@ def shear_modulus(self, pressure, temperature, volume, params):
 
  def entropy(self, pressure, temperature, volume, params):
  """
- Returns the molar entropy :math:`\mathcal{S}` of the mineral. :math:`[J/K/mol]`
+ Returns the molar entropy :math:`\\mathcal{S}` of the mineral. :math:`[J/K/mol]`
  """
  return 0.0
 
@@ -228,7 +228,7 @@ def _intVdP(self, xi, params):
 
  def gibbs_free_energy(self, pressure, temperature, volume, params):
  """
- Returns the Gibbs free energy :math:`\mathcal{G}` of the mineral. :math:`[J/mol]`
+ Returns the Gibbs free energy :math:`\\mathcal{G}` of the mineral. :math:`[J/mol]`
  """
  # G = E0 + int VdP (when S = 0)
  K = self.isothermal_bulk_modulus(pressure, temperature, volume, params)
@@ -241,7 +241,7 @@ def gibbs_free_energy(self, pressure, temperature, volume, params):
 
  def molar_internal_energy(self, pressure, temperature, volume, params):
  """
- Returns the internal energy :math:`\mathcal{E}` of the mineral. :math:`[J/mol]`
+ Returns the internal energy :math:`\\mathcal{E}` of the mineral. :math:`[J/mol]`
  """
  # E = G - PV (+ TS)
  return (
@@ -276,7 +276,7 @@ def grueneisen_parameter(self, pressure, temperature, volume, params):
  def validate_parameters(self, params):
  """
  Check for existence and validity of the parameters.
- The value for :math:`K'_{\infty}` is thermodynamically bounded
+ The value for :math:`K'_{\\infty}` is thermodynamically bounded
  between 5/3 and :math:`K'_0` :cite:`StaceyDavis2004`.
  """
 

burnman/eos/vinet.py

@@ -95,13 +95,13 @@ def shear_modulus(self, pressure, temperature, volume, params):
 
  def entropy(self, pressure, temperature, volume, params):
  """
- Returns the molar entropy :math:`\mathcal{S}` of the mineral. :math:`[J/K/mol]`
+ Returns the molar entropy :math:`\\mathcal{S}` of the mineral. :math:`[J/K/mol]`
  """
  return 0.0
 
  def molar_internal_energy(self, pressure, temperature, volume, params):
  """
- Returns the internal energy :math:`\mathcal{E}` of the mineral. :math:`[J/mol]`
+ Returns the internal energy :math:`\\mathcal{E}` of the mineral. :math:`[J/mol]`
  """
  x = pow(volume / params["V_0"], 1.0 / 3.0)
  eta = (3.0 / 2.0) * (params["Kprime_0"] - 1.0)
@@ -118,7 +118,7 @@ def molar_internal_energy(self, pressure, temperature, volume, params):
 
  def gibbs_free_energy(self, pressure, temperature, volume, params):
  """
- Returns the Gibbs free energy :math:`\mathcal{G}` of the mineral. :math:`[J/mol]`
+ Returns the Gibbs free energy :math:`\\mathcal{G}` of the mineral. :math:`[J/mol]`
  """
  # G = int VdP = [PV] - int PdV = E + PV
 

burnman/utils/chemistry.py

@@ -449,7 +449,7 @@ def process_solution_chemistry(solution_model):
  )
 
  solution_model.empty_formula = re.sub(
- "([\[]).*?([\]])", "\g<1>\g<2>", solution_model.formulas[0]
+ "([\\[]).*?([\\]])", "\\g<1>\\g<2>", solution_model.formulas[0]
  )
  split_empty = solution_model.empty_formula.split("[")
  solution_model.general_formula = split_empty[0]

burnman/utils/geotherm.py

@@ -102,7 +102,7 @@ def adiabatic(pressures, T0, rock):
  pressure. A good first guess is provided by integrating:
 
  .. math::
- \\frac{\partial T}{\partial P} = \\frac{ \\gamma T}{ K_s }
+ \\frac{\\partial T}{\\partial P} = \\frac{ \\gamma T}{ K_s }
 
  where :math:`\\gamma` is the Grueneisen parameter and :math:`K_s` is
  the adiabatic bulk modulus.

burnman/utils/misc.py

@@ -105,7 +105,7 @@ def pretty_print_table(table, use_tabs=False):
  """
  if use_tabs:
  for r in table:
- print("\t".join(r).replace("_", "\_"))
+ print("\t".join(r).replace("_", "\\_"))
  return
 
  def col_width(table, colidx):

contrib/CHRU2014/paper_benchmark.py

@@ -115,24 +115,24 @@ def check_slb_fig7_txt():
  )
  gr_comp[i] = (forsterite.grueneisen_parameter - gr[i]) / gr[i]
 
- plt.plot(temperature, rho_comp, label=r"$\rho$")
+ plt.plot(temperature, rho_comp, label=r"$\\rho$")
  plt.plot(temperature, Kt_comp, label=r"$K_S$")
  plt.plot(temperature, Ks_comp, label=r"$K_T$")
  plt.plot(temperature, G_comp, label=r"$G$")
  plt.plot(temperature, VS_comp, label=r"$V_S$")
  plt.plot(temperature, VP_comp, label=r"$V_P$")
- plt.plot(temperature, VB_comp, label=r"$V_\phi$")
+ plt.plot(temperature, VB_comp, label=r"$V_\\phi$")
  plt.plot(temperature, vol_comp, label=r"$V$")
- plt.plot(temperature, alpha_comp, label=r"$\alpha$")
+ plt.plot(temperature, alpha_comp, label=r"$\\alpha$")
  plt.plot(temperature, Cp_comp, label=r"$c_P$")
- plt.plot(temperature, gr_comp, label=r"$\gamma$")
+ plt.plot(temperature, gr_comp, label=r"$\\gamma$")
 
  plt.xlim([0, 2200])
  plt.ylim([-0.002, 0.002])
  plt.yticks([-0.002, -0.001, 0, 0.001, 0.002])
  plt.xticks([0, 800, 1600, 2200])
  plt.xlabel("Temperature (K)")
- plt.ylabel("Difference (\%)")
+ plt.ylabel("Difference (\\%)")
  plt.legend(loc="lower center", prop=prop, ncol=4)
  if "RUNNING_TESTS" not in globals():
  plt.savefig("benchmark1.pdf", bbox_inches="tight")

contrib/CHRU2014/paper_onefit.py

@@ -65,16 +65,16 @@ def output_rock(rock, file_handle):
  for ph in rock.staticphases:
  if isinstance(ph.mineral, HelperSolidSolution):
  for mineral in ph.mineral.endmembers:
- file_handle.write("\t" + mineral.to_string() + "\n")
+ file_handle.write("\\t" + mineral.to_string() + "\\n")
  for key in mineral.params:
  file_handle.write(
- "\t\t" + key + ": " + str(mineral.params[key]) + "\n"
+ "\\t\\t" + key + ": " + str(mineral.params[key]) + "\\n"
  )
  else:
- file_handle.write("\t" + ph.mineral.to_string() + "\n")
+ file_handle.write("\\t" + ph.mineral.to_string() + "\\n")
  for key in ph.mineral.params:
  file_handle.write(
- "\t\t" + key + ": " + str(ph.mineral.params[key]) + "\n"
+ "\\t\\t" + key + ": " + str(ph.mineral.params[key]) + "\\n"
  )
 
 
@@ -351,7 +351,7 @@ def array_to_rock(arr, names):
  figsize = (6, 5)
  prop = {"size": 12}
  plt.rc("text", usetex=True)
- plt.rcParams["text.latex.preamble"] = r"\usepackage{relsize}"
+ plt.rcParams["text.latex.preamble"] = r"\\usepackage{relsize}"
  plt.rc("font", family="sans-serif")
  figure = plt.figure(dpi=100, figsize=figsize)
 
@@ -436,7 +436,7 @@ def array_to_rock(arr, names):
  )
 
  plt.xlabel("Pressure (GPa)")
- plt.ylabel("Velocities (km/s) and Density ($\cdot 10^3$ kg/m$^3$)")
+ plt.ylabel("Velocities (km/s) and Density ($\\cdot 10^3$ kg/m$^3$)")
  plt.legend(bbox_to_anchor=(1.0, 0.9), prop={"size": 12})
  plt.xlim(25, 135)
  # plt.ylim(6,11)