Ruff-style

PyCO2SYS/api/__init__.py

@@ -2,8 +2,8 @@
 # Copyright (C) 2020--2024  Matthew P. Humphreys et al.  (GNU GPLv3)
 """Alternative APIs for executing the main CO2SYS function."""
 
+from ..engine import _CO2SYS, CO2SYS
 from . import ezio
-from ..engine import CO2SYS, _CO2SYS
 
 
 def CO2SYS_wrap(
@@ -114,9 +114,10 @@ def CO2SYS_wrap(
     system parameters. Note that output variables are labelled as the original
     CO2SYS output names, and not the wrapper inputs.
     """
-    from autograd import numpy as np
     import inspect
+
     import pandas as pd
+    from autograd import numpy as np
 
     try:
         import xarray as xr
@@ -177,8 +178,9 @@ def printv(*args, **kwargs):
         df = pd.DataFrame(params, index=np.arange(max(sizes)))
     except ValueError:
         raise UserWarning(
-            "Your inputs must be length of 1 or n (sizes shown below)"
-            ":\n {}".format(str(sizes))
+            "Your inputs must be length of 1 or n (sizes shown below)" ":\n {}".format(
+                str(sizes)
+            )
         )
 
     # DEFINE PARAMETER TYPES

PyCO2SYS/buffers.py

@@ -2,8 +2,8 @@
 # Copyright (C) 2020--2024  Matthew P. Humphreys et al.  (GNU GPLv3)
 """Calculate various buffer factors of the marine carbonate system."""
 
-import jax
 from jax import numpy as np
+
 from . import solubility, solve
 from .meta import egrad
 

PyCO2SYS/constants.py

@@ -4,7 +4,6 @@
 
 from autograd import numpy as np
 
-
 RGasConstant_DOEv2 = 83.1451  # ml bar-1 K-1 mol-1, DOEv2 (always used by default)
 RGasConstant_DOEv3 = 83.14472  # ml bar-1 K-1 mol-1, DOEv3 (never used in PyCO2SYS)
 RGasConstant_CODATA2018 = 83.14462618  # 10^-1 J mol^-1 K^-1 (available from v1.4.1)

PyCO2SYS/convert.py

@@ -26,8 +26,11 @@
 fCO2_to_CO2aq
     Convert CO2 fugacity to aqueous content.
 """
+
 import copy
+
 from jax import numpy as np
+
 from . import constants
 
 

PyCO2SYS/engine/__init__.py

@@ -3,6 +3,7 @@
 """Helpers for the main CO2SYS program."""
 
 from autograd import numpy as np
+
 from .. import convert, equilibria, salts, solve
 from . import nd, system
 

PyCO2SYS/engine/nd.py

@@ -3,7 +3,9 @@
 """Carbonate system solving in N dimensions."""
 
 import itertools
+
 from autograd import numpy as np
+
 from .. import convert, equilibria, salts, solve, uncertainty, upsilon
 
 # Define function input keys that should be converted to floats

PyCO2SYS/engine/system.py

@@ -1,10 +1,12 @@
 # PyCO2SYS: marine carbonate system calculations in Python.
 # Copyright (C) 2020--2024  Matthew P. Humphreys et al.  (GNU GPLv3)
 import itertools
+
 import networkx as nx
-from jax import numpy as np
 import numpy as onp
+from jax import numpy as np
 from matplotlib import pyplot as plt
+
 from .. import (
     bio,
     buffers,
@@ -29,11 +31,17 @@
     "k_CO2_1atm": equilibria.p1atm.k_CO2_W74,
     "k_H2S_total_1atm": equilibria.p1atm.k_H2S_total_YM95,
     # pH scale conversion factors at 1 atm
-    "free_to_sws_1atm": lambda total_fluoride, total_sulfate, k_HF_free_1atm, k_HSO4_free_1atm: convert.pH_free_to_sws(
+    "free_to_sws_1atm": lambda total_fluoride,
+    total_sulfate,
+    k_HF_free_1atm,
+    k_HSO4_free_1atm: convert.pH_free_to_sws(
         total_fluoride, total_sulfate, k_HF_free_1atm, k_HSO4_free_1atm
     ),
     "nbs_to_sws": convert.pH_nbs_to_sws,  # because fH doesn't get pressure-corrected
-    "tot_to_sws_1atm": lambda total_fluoride, total_sulfate, k_HF_free_1atm, k_HSO4_free_1atm: convert.pH_tot_to_sws(
+    "tot_to_sws_1atm": lambda total_fluoride,
+    total_sulfate,
+    k_HF_free_1atm,
+    k_HSO4_free_1atm: convert.pH_tot_to_sws(
         total_fluoride, total_sulfate, k_HF_free_1atm, k_HSO4_free_1atm
     ),
     # Equilibrium constants at 1 atm and on the seawater pH scale
@@ -491,7 +499,7 @@
     ),
     2: dict(
         k_BOH3_nbs_1atm=equilibria.p1atm.k_BOH3_nbs_LTB69,
-        k_BOH3_sws_1atm=lambda k_BOH3_total_1atm, nbs_to_sws: (
+        k_BOH3_sws_1atm=lambda k_BOH3_nbs_1atm, nbs_to_sws: (
             k_BOH3_nbs_1atm * nbs_to_sws
         ),
     ),
@@ -902,7 +910,6 @@ def _assemble(self, icase, values):
         return graph, funcs, values
 
     def _get(self, parameters, graph, funcs, values, save_steps, verbose):
-
         def printv(*args, **kwargs):
             if verbose:
                 print(*args, **kwargs)
@@ -1252,7 +1259,7 @@ def get_grad(self, var_of, var_wrt):
     def get_grads(self, vars_of, vars_wrt):
         for var_of in vars_of:
             for var_wrt in vars_wrt:
-                get_grad(var_of, var_wrt)
+                self.get_grad(var_of, var_wrt)
 
     def get_values_original(self):
         return {k: self.values[k] for k in self.nodes_original}

PyCO2SYS/equilibria/__init__.py

@@ -3,8 +3,9 @@
 """Calculate equilibrium constants from temperature, salinity and pressure."""
 
 from autograd import numpy as np
-from . import p1atm, pcx
+
 from .. import constants, convert, gas, solubility
+from . import p1atm, pcx, pressured
 
 
 def prepare(temperature, pressure, equilibria):

PyCO2SYS/equilibria/p1atm.py

@@ -143,7 +143,9 @@
     Carbonic acid dissociation constants following PLR18.
     Used when opt_k_carbonic = 18.
 """
+
 from jax import numpy as np
+
 from .. import convert
 
 
@@ -1388,7 +1390,7 @@ def k_H2CO3_sws_MGH06(temperature, salinity):
     B_1 = -530.123 * salinity**0.5 - 6.103 * salinity
     C_1 = -2.06950 * salinity**0.5
     pK1 = A_1 + B_1 / TempK + C_1 * np.log(TempK) + pK1_0  # pK1 sigma = 0.0054
-    return 10.0 ** -(pK1)
+    return 10.0**-(pK1)
 
 
 def k_HCO3_sws_MGH06(temperature, salinity):
@@ -1413,7 +1415,7 @@ def k_HCO3_sws_MGH06(temperature, salinity):
     B_2 = -772.483 * salinity**0.5 - 20.051 * salinity
     C_2 = -3.3336 * salinity**0.5
     pK2 = A_2 + B_2 / TempK + C_2 * np.log(TempK) + pK2_0  # pK2 sigma = 0.011
-    return 10.0 ** -(pK2)
+    return 10.0**-(pK2)
 
 
 def k_H2CO3_sws_M10(temperature, salinity):

PyCO2SYS/equilibria/pcx.py

@@ -56,6 +56,7 @@
 factor_k_CO2
     Calculate the pressure-correction factor for k_CO2 following W74 eq. 5.
 """
+
 # Original notes from CO2SYS-MATLAB regarding pressure corrections:
 # ****************************************************************************
 # Correct dissociation constants for pressure
@@ -127,6 +128,7 @@
 #       Kappas are in cm3/mole/bar
 # ****************************************************************************
 from jax import numpy as np
+
 from .. import convert
 
 

PyCO2SYS/gas.py

@@ -14,6 +14,7 @@
 """
 
 from jax import numpy as np
+
 from . import convert
 
 

PyCO2SYS/meta.py

@@ -1,6 +1,7 @@
 # PyCO2SYS: marine carbonate system calculations in Python.
 # Copyright (C) 2020--2024  Matthew P. Humphreys et al.  (GNU GPLv3)
 """Define metadata about PyCO2SYS."""
+
 import jax
 from jax import numpy as np
 
@@ -44,9 +45,7 @@ def hello():
    Lasciate ogni speranza, voi ch' entrate!
                                     Dante, Inferno iii, 9
                                     sign on the entrance gates of hell
-""".format(
-            version_xyz
-        )
+""".format(version_xyz)
     )  # (All hope abandon, ye who enter here!)
 
 

PyCO2SYS/solubility.py

@@ -3,6 +3,7 @@
 """Calculate saturation states of soluble solids."""
 
 from autograd import numpy as np
+
 from . import convert
 
 

PyCO2SYS/uncertainty.py

@@ -3,7 +3,9 @@
 """Propagate uncertainties through marine carbonate system calculations."""
 
 import copy
+
 from autograd import numpy as np
+
 from . import engine
 
 # Default uncertainties in pK values following OEDG18

PyCO2SYS/upsilon.py

@@ -1,6 +1,7 @@
 # PyCO2SYS: marine carbonate system calculations in Python.
 # Copyright (C) 2020--2024  Matthew P. Humphreys et al.  (GNU GPLv3)
 from jax import numpy as np
+
 from . import constants
 
 bh_TOG93_H24 = 28995  # J / mol