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Santiso-Group · Dec 23, 2024 · 742c602 · 742c602
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diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -80,7 +80,7 @@ jobs:
       - name: Flake8
         shell: bash -l {0}
         run: |
-          python -m flake8 despasito --count --ignore=E741,W503 --max-line-length=92 --show-source --statistics
+          python -m flake8 despasito --count --ignore=E741,W503 --max-line-length=120 --per-file-ignores="__init__.py:F401" --show-source --statistics
 
   paper:
     runs-on: ubuntu-latest

diff --git a/despasito/__init__.py b/despasito/__init__.py
@@ -53,9 +53,7 @@ def initiate_logger(console=None, log_file=None, verbose=30):
     # Set up logging to console
     if console and handler_console is None:
         console_handler = logging.StreamHandler()  # sys.stderr
-        console_handler.setFormatter(
-            logging.Formatter("[%(levelname)s](%(name)s): %(message)s")
-        )
+        console_handler.setFormatter(logging.Formatter("[%(levelname)s](%(name)s): %(message)s"))
         console_handler.setLevel(verbose)
         logger.addHandler(console_handler)
     elif console:
@@ -75,10 +73,7 @@ def initiate_logger(console=None, log_file=None, verbose=30):
 
         log_file_handler = logging.handlers.RotatingFileHandler(log_file)
         log_file_handler.setFormatter(
-            logging.Formatter(
-                "%(asctime)s [%(levelname)s](%(name)s:%(funcName)s:%(lineno)d): "
-                + "%(message)s"
-            )
+            logging.Formatter("%(asctime)s [%(levelname)s](%(name)s:%(funcName)s:%(lineno)d): " + "%(message)s")
         )
         log_file_handler.setLevel(verbose)
         logger.addHandler(log_file_handler)

diff --git a/despasito/__main__.py b/despasito/__main__.py
@@ -27,19 +27,15 @@
     os.remove(args.logFile)
 log_file_handler = logging.handlers.RotatingFileHandler(args.logFile)
 log_file_handler.setFormatter(
-    logging.Formatter(
-        "%(asctime)s [%(levelname)s](%(name)s:%(funcName)s:%(lineno)d): %(message)s"
-    )
+    logging.Formatter("%(asctime)s [%(levelname)s](%(name)s:%(funcName)s:%(lineno)d): %(message)s")
 )
 log_file_handler.setLevel(args.verbose)
 logger.addHandler(log_file_handler)
 
 if args.console:
     # Set up logging to console
     console_handler = logging.StreamHandler()  # sys.stderr
-    console_handler.setFormatter(
-        logging.Formatter("[%(levelname)s](%(name)s): %(message)s")
-    )
+    console_handler.setFormatter(logging.Formatter("[%(levelname)s](%(name)s): %(message)s"))
     console_handler.setLevel(args.verbose)
     logger.addHandler(console_handler)
 

diff --git a/despasito/_version.py b/despasito/_version.py
@@ -1 +1 @@
-__version__ = "0.3.0+16.gcc3fbe0.dirty"
+__version__ = "0.3.0+28.ge5ffa36.dirty"
diff --git a/despasito/equations_of_state/__init__.py b/despasito/equations_of_state/__init__.py
@@ -25,19 +25,15 @@ def __init__(self, numba=True, cython=False, python=False):
 
     def __str__(self):
 
-        string = "Compilation: numba {}, cython {}, python {}".format(
-            self.numba, self.cython, self.python
-        )
+        string = "Compilation: numba {}, cython {}, python {}".format(self.numba, self.cython, self.python)
 
         return string
 
 
 logger = logging.getLogger(__name__)
 
 
-def initiate_eos(
-    eos="saft.gamma_mie", numba=True, cython=False, python=False, **kwargs
-):
+def initiate_eos(eos="saft.gamma_mie", numba=True, cython=False, python=False, **kwargs):
     """
     Interface between the user and our library of equations of state (EOS).
 
@@ -69,39 +65,29 @@ def initiate_eos(
 
     kwargs["method_stat"] = method_stat(numba=numba, cython=cython, python=python)
 
-    factory_families = [
-        "saft"
-    ]  # Eos families in this list have a general object with a factory to import
+    factory_families = ["saft"]  # Eos families in this list have a general object with a factory to import
     # relevant modules
 
     logger.info("Using EOS: {}".format(eos))
 
     try:
         eos_fam, eos_type = eos.split(".")
     except Exception:
-        raise ValueError(
-            "Input should be in the form EOSfamily.EOSname (e.g. saft.gamme_mie)."
-        )
+        raise ValueError("Input should be in the form EOSfamily.EOSname (e.g. saft.gamme_mie).")
 
     class_name = "EosType"
     try:
         if eos_fam in factory_families:
-            eos_module = import_module(
-                "." + eos_fam, package="despasito.equations_of_state." + eos_fam
-            )
+            eos_module = import_module("." + eos_fam, package="despasito.equations_of_state." + eos_fam)
             kwargs["saft_name"] = eos_type
 
         else:
-            eos_module = import_module(
-                "." + eos_type, package="despasito.equations_of_state." + eos_fam
-            )
+            eos_module = import_module("." + eos_type, package="despasito.equations_of_state." + eos_fam)
         eos_class = getattr(eos_module, class_name)
     except AttributeError:
         raise ImportError(
             "Based on your input, '{}', we expect the class, {}, in a module, {},"
-            " found in the package, {}, which indicates the EOS family.".format(
-                eos, class_name, eos_type, eos_fam
-            )
+            " found in the package, {}, which indicates the EOS family.".format(eos, class_name, eos_type, eos_fam)
         )
     instance = eos_class(**kwargs)
 

diff --git a/despasito/equations_of_state/combining_rule_types.py b/despasito/equations_of_state/combining_rule_types.py
@@ -82,11 +82,7 @@ def volumetric_geometric_mean(beadA, beadB, parameter, weighting_parameters=[]):
 
     tmp1 = np.sqrt(beadA[parameter] * beadB[parameter])
     param2 = weighting_parameters[0]
-    tmp2 = (
-        np.sqrt((beadA[param2] ** 3) * (beadB[param2] ** 3))
-        * 8
-        / ((beadA[param2] + beadB[param2]) ** 3)
-    )
+    tmp2 = np.sqrt((beadA[param2] ** 3) * (beadB[param2] ** 3)) * 8 / ((beadA[param2] + beadB[param2]) ** 3)
     return tmp1 * tmp2
 
 
@@ -115,9 +111,9 @@ def weighted_mean(beadA, beadB, parameter, weighting_parameters=[]):
     """
 
     param2 = weighting_parameters[0]
-    parameter12 = (
-        beadA[parameter] * beadA[param2] + beadB[parameter] * beadB[param2]
-    ) / (beadA[param2] + beadB[param2])
+    parameter12 = (beadA[parameter] * beadA[param2] + beadB[parameter] * beadB[param2]) / (
+        beadA[param2] + beadB[param2]
+    )
 
     return parameter12
 
@@ -173,23 +169,15 @@ def square_well_berthelot(beadA, beadB, parameter, weighting_parameters=[]):
     param2, param3 = weighting_parameters[0], weighting_parameters[1]
 
     tmp1 = np.sqrt(beadA[parameter] * beadB[parameter])
-    tmp2 = (
-        np.sqrt((beadA[param2] ** 3) * (beadB[param2] ** 3))
-        * 8
-        / ((beadA[param2] + beadB[param2]) ** 3)
-    )
+    tmp2 = np.sqrt((beadA[param2] ** 3) * (beadB[param2] ** 3)) * 8 / ((beadA[param2] + beadB[param2]) ** 3)
 
     param3_12 = weighted_mean(beadA, beadB, param3, weighting_parameters=[param2])
-    tmp3 = np.sqrt((beadA[param3] ** 3 - 1) * (beadB[param3] ** 3 - 1)) / (
-        param3_12**3 - 1
-    )
+    tmp3 = np.sqrt((beadA[param3] ** 3 - 1) * (beadB[param3] ** 3 - 1)) / (param3_12**3 - 1)
 
     return tmp1 * tmp2 * tmp3
 
 
-def multipole(
-    beadA, beadB, parameter, temperature=None, mode="curve fit", scaled=False
-):
+def multipole(beadA, beadB, parameter, temperature=None, mode="curve fit", scaled=False):
     r"""
     Calculates cross interaction parameter with the multipole combining rules from
     the plug-in `MAPSCI <https://github.com/jaclark5/mapsci>`_.
@@ -239,17 +227,13 @@ def multipole(
             tmp[key]["sigma"] = value["sigma"] * 10  # convert from nm to angstroms
 
         if mode == "curve fit":
-            dict_cross, _ = mr.extended_combining_rules_fitting(
-                tmp, temperature, shape_factor_scale=shape_factor_scale
-            )
+            dict_cross, _ = mr.extended_combining_rules_fitting(tmp, temperature, shape_factor_scale=shape_factor_scale)
         elif mode == "analytical":
             dict_cross, _ = mr.extended_combining_rules_analytical(
                 tmp, temperature, shape_factor_scale=shape_factor_scale
             )
         else:
-            raise ValueError(
-                "Multipole mixing rule must be either 'curve fit' or 'analytical'."
-            )
+            raise ValueError("Multipole mixing rule must be either 'curve fit' or 'analytical'.")
         output = dict_cross["beadA"]["beadB"]
     else:
         logger.warning("Temperature is None, using geometric mean.")

diff --git a/despasito/equations_of_state/cubic/peng_robinson.py b/despasito/equations_of_state/cubic/peng_robinson.py
@@ -94,25 +94,14 @@ def __init__(self, **kwargs):
         self._test_critical = [False for _ in self.beads]
         self._test_parameters = [False for _ in self.beads]
         for i, bead in enumerate(self.beads):
-            if (
-                "omega" in self.bead_library[bead]
-                and "kappa" not in self.bead_library[bead]
-            ):
+            if "omega" in self.bead_library[bead] and "kappa" not in self.bead_library[bead]:
                 self._test_kappa[i] = True
 
-            self._test_critical[i] = (
-                "Tc" in self.bead_library[bead] and "Pc" in self.bead_library[bead]
-            )
-            self._test_parameters[i] = (
-                "ai" in self.bead_library[bead] and "bi" in self.bead_library[bead]
-            )
+            self._test_critical[i] = "Tc" in self.bead_library[bead] and "Pc" in self.bead_library[bead]
+            self._test_parameters[i] = "ai" in self.bead_library[bead] and "bi" in self.bead_library[bead]
 
             if not self._test_critical[i] and not self._test_parameters[i]:
-                raise ValueError(
-                    "Either 'Tc' or 'Pc' was not provided for component: {}".format(
-                        bead
-                    )
-                )
+                raise ValueError("Either 'Tc' or 'Pc' was not provided for component: {}".format(bead))
 
         # Cross interaction parameters
         if "cross_library" in kwargs:
@@ -155,9 +144,7 @@ def _calc_temp_dependent_parameters(self, T):
         for i, bead in enumerate(self.beads):
             if "kappa" in self.bead_library[bead]:
                 self.eos_dict["alpha"][i] = (
-                    1
-                    + self.bead_library[bead]["kappa"]
-                    * (1 - np.sqrt(T / self.bead_library[bead]["Tc"]))
+                    1 + self.bead_library[bead]["kappa"] * (1 - np.sqrt(T / self.bead_library[bead]["Tc"]))
                 ) ** 2
             else:
                 self.eos_dict["alpha"][i] = 1.0
@@ -235,11 +222,8 @@ def pressure(self, rho, T, xi):
         elif not isinstance(rho, np.ndarray):
             rho = np.array(rho)
 
-        P = constants.R * self.T * rho / (
-            1 - self.eos_dict["bij"] * rho
-        ) - rho**2 * self.eos_dict["aij"] / (
-            (1 + self.eos_dict["bij"] * rho)
-            + rho * self.eos_dict["bij"] * (1 - self.eos_dict["bij"] * rho)
+        P = constants.R * self.T * rho / (1 - self.eos_dict["bij"] * rho) - rho**2 * self.eos_dict["aij"] / (
+            (1 + self.eos_dict["bij"] * rho) + rho * self.eos_dict["bij"] * (1 - self.eos_dict["bij"] * rho)
         )
 
         return P
@@ -296,11 +280,7 @@ def fugacity_coefficient(self, P, rho, xi, T):
         A = self.eos_dict["aij"] * P / tmp_RT**2
 
         sqrt2 = np.sqrt(2.0)
-        tmp1 = (
-            A
-            / (2.0 * sqrt2 * B)
-            * np.log((Z + (1 + sqrt2) * B) / (Z + (1 - sqrt2) * B))
-        )
+        tmp1 = A / (2.0 * sqrt2 * B) * np.log((Z + (1 + sqrt2) * B) / (Z + (1 - sqrt2) * B))
         tmp3 = Bi * (Z - 1) / B - np.log(Z - B)
         tmp2 = np.zeros(len(xi))
 
@@ -363,15 +343,8 @@ def update_parameter(self, param_name, bead_names, param_value):
             Value of parameter
         """
 
-        if (
-            param_name in ["ai", "bi"]
-            and self._test_critical[self.beads.index(bead_names[0])]
-        ):
-            raise ValueError(
-                "Bead, {}, initialized with critical properties, not ai and bi".format(
-                    bead_names[0]
-                )
-            )
+        if param_name in ["ai", "bi"] and self._test_critical[self.beads.index(bead_names[0])]:
+            raise ValueError("Bead, {}, initialized with critical properties, not ai and bi".format(bead_names[0]))
         super().update_parameter(param_name, bead_names, param_value)
 
     def parameter_refresh(self):
@@ -384,10 +357,7 @@ def parameter_refresh(self):
         """
 
         for i, bead in enumerate(self.beads):
-            if (
-                "omega" in self.bead_library[bead]
-                and "kappa" not in self.bead_library[bead]
-            ):
+            if "omega" in self.bead_library[bead] and "kappa" not in self.bead_library[bead]:
                 self.bead_library[bead]["kappa"] = (
                     0.37464
                     + 1.54226 * self.bead_library[bead]["omega"]
@@ -396,14 +366,10 @@ def parameter_refresh(self):
 
             if self._test_critical[i] and not self._test_parameters[i]:
                 self.bead_library[bead]["ai"] = (
-                    0.45723553
-                    * (constants.R * self.bead_library[bead]["Tc"]) ** 2
-                    / self.bead_library[bead]["Pc"]
+                    0.45723553 * (constants.R * self.bead_library[bead]["Tc"]) ** 2 / self.bead_library[bead]["Pc"]
                 )
                 self.bead_library[bead]["bi"] = 0.07779607 * (
-                    constants.R
-                    * self.bead_library[bead]["Tc"]
-                    / self.bead_library[bead]["Pc"]
+                    constants.R * self.bead_library[bead]["Tc"] / self.bead_library[bead]["Pc"]
                 )
 
             parameters = ["ai", "bi"]

diff --git a/despasito/equations_of_state/eos_toolbox.py b/despasito/equations_of_state/eos_toolbox.py
@@ -40,9 +40,7 @@ def remove_insignificant_components(xi_old, massi_old):
     return xi_new, massi_new
 
 
-def partial_density_central_difference(
-    xi, rho, T, func, step_size=1e-2, log_method=False
-):
+def partial_density_central_difference(xi, rho, T, func, step_size=1e-2, log_method=False):
     """
     Take the derivative of a dependent variable calculated with a given function
     using the central difference method.
@@ -164,9 +162,7 @@ def calc_massi(molecular_composition, bead_library, beads):
             if "mass" in bead_library[bead]:
                 massi[i] += molecular_composition[i, k] * bead_library[bead]["mass"]
             else:
-                raise ValueError(
-                    "The mass for bead, {}, was not provided.".format(bead)
-                )
+                raise ValueError("The mass for bead, {}, was not provided.".format(bead))
 
     return massi
 
@@ -205,9 +201,7 @@ def extract_property(prop, bead_library, beads, default=None):
             prop_array[i] = bead_library[bead][prop]
         else:
             if default is None:
-                raise ValueError(
-                    "The property {} for bead, {}, was not provided.".format(prop, bead)
-                )
+                raise ValueError("The property {} for bead, {}, was not provided.".format(prop, bead))
             else:
                 prop_array[i] = default
 
@@ -249,8 +243,7 @@ def check_bead_parameters(bead_library0, parameter_defaults):
                     )
                 else:
                     raise ValueError(
-                        "Parameter, {}, should have been defined for parametrized "
-                        "group, {}.".format(parameter, bead)
+                        "Parameter, {}, should have been defined for parametrized " "group, {}.".format(parameter, bead)
                     )
 
     return bead_library
@@ -299,27 +292,14 @@ def cross_interaction_from_dict(beads, bead_library, combining_dict, cross_libra
         for j, beadname2 in enumerate(beads):
             if j > i:
                 for key in combining_dict:
-                    if (
-                        cross_library.get(beadname, {})
-                        .get(beadname2, {})
-                        .get(key, None)
-                        is not None
-                    ):
+                    if cross_library.get(beadname, {}).get(beadname2, {}).get(key, None) is not None:
                         output[key][i, j] = cross_library[beadname][beadname2][key]
-                    elif (
-                        cross_library.get(beadname2, {})
-                        .get(beadname, {})
-                        .get(key, None)
-                        is not None
-                    ):
+                    elif cross_library.get(beadname2, {}).get(beadname, {}).get(key, None) is not None:
                         output[key][i, j] = cross_library[beadname2][beadname][key]
                     else:
                         try:
                             tmp = combining_rules(
-                                bead_library[beadname],
-                                bead_library[beadname2],
-                                key,
-                                **combining_dict[key]
+                                bead_library[beadname], bead_library[beadname2], key, **combining_dict[key]
                             )
                         except Exception:
                             raise ValueError(
@@ -369,9 +349,7 @@ def construct_dummy_bead_library(input_dict, keys=None):
             keys = [str(x) for x in range(len(input_dict[parameter]))]
             flag = True
         if len(keys) != len(input_dict[parameter]):
-            raise ValueError(
-                "Number of keys is not equal to the number of quantities given"
-            )
+            raise ValueError("Number of keys is not equal to the number of quantities given")
 
         for i, bead in enumerate(keys):
             if bead not in output:
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		__version__ = "0.3.0+16.gcc3fbe0.dirty"
		__version__ = "0.3.0+28.ge5ffa36.dirty"