invoke format

toughio/__init__.py

@@ -2,8 +2,8 @@
 from .__about__ import __version__
 from ._helpers import convert_labels
 from ._io import (
-    ElementOutput,
     ConnectionOutput,
+    ElementOutput,
     read_input,
     read_output,
     read_table,

toughio/_io/__init__.py

@@ -2,7 +2,7 @@
 from .input import read as read_input
 from .input import register as register_input
 from .input import write as write_input
-from .output import ElementOutput, ConnectionOutput
+from .output import ConnectionOutput, ElementOutput
 from .output import read as read_output
 from .output import register as register_output
 from .output import write as write_output

toughio/_io/h5/_write.py

@@ -2,7 +2,7 @@
 
 import h5py
 
-from ..output import ElementOutput, ConnectionOutput
+from ..output import ConnectionOutput, ElementOutput
 from ..output import read as read_output
 from ..table import read as read_table
 

toughio/_io/output/__init__.py

@@ -1,5 +1,5 @@
 from . import csv, petrasim, save, tecplot, tough
-from ._common import ElementOutput, ConnectionOutput
+from ._common import ConnectionOutput, ElementOutput
 from ._helpers import read, register, write
 
 __all__ = [

toughio/_io/output/_common.py

@@ -1,5 +1,5 @@
-from abc import ABC, abstractmethod
 import logging
+from abc import ABC, abstractmethod
 
 import numpy as np
 
@@ -24,13 +24,13 @@ def __init__(self, time, data, labels=None):
     def __getitem__(self):
         """Slice output."""
         pass
-    
+
     @abstractmethod
     def index(self):
         """Get index of element or connection."""
         if self.labels is None:
             raise AttributeError()
-        
+
     @property
     def n_data(self):
         """Return number of data points."""
@@ -40,31 +40,31 @@ def n_data(self):
     def time(self):
         """Return time step (in seconds)."""
         return self._time
-    
+
     @time.setter
     def time(self, value):
         self._time = value
-    
+
     @property
     def data(self):
         """Return data arrays."""
         return self._data
-    
+
     @data.setter
     def data(self, value):
         self._data = value
-    
+
     @property
     def labels(self):
         """Return labels."""
         return self._labels
-    
+
     @labels.setter
     def labels(self, value):
         if value is not None:
             if len(value) != self.n_data:
                 raise ValueError()
-            
+
             self._labels = list(value)
 
         else:
@@ -84,14 +84,14 @@ def __init__(self, time, data, labels=None):
             Data arrays.
         labels : sequence of str or None, default, None
             Labels of elements.
-        
+
         """
         super().__init__(time, data, labels)
 
     def __getitem__(self, islice):
         """
         Slice element output.
-        
+
         Parameters
         ----------
         islice : int, str, slice, sequence of int or sequence of str
@@ -101,26 +101,26 @@ def __getitem__(self, islice):
         -------
         dict or :class:`toughio.ElementOutput`
             Sliced element outputs.
-        
+
         """
         if self.labels is None:
             raise AttributeError()
-        
+
         if np.ndim(islice) == 0:
             if isinstance(islice, slice):
                 islice = np.arange(self.n_data)[islice]
 
             else:
                 islice = self.index(islice) if isinstance(islice, str) else islice
-            
+
                 return {k: v[islice] for k, v in self.data.items()}
-        
+
         elif np.ndim(islice) == 1:
             islice = [self.index(i) if isinstance(i, str) else i for i in islice]
 
         else:
             raise ValueError()
-        
+
         return ElementOutput(
             self.time,
             {k: v[islice] for k, v in self.data.items()},
@@ -130,7 +130,7 @@ def __getitem__(self, islice):
     def index(self, label):
         """
         Get index of element.
-        
+
         Parameters
         ----------
         label : str
@@ -140,10 +140,10 @@ def index(self, label):
         -------
         int
             Index of element.
-        
+
         """
         super().index()
-        
+
         return self.labels.index(label)
 
 
@@ -160,14 +160,14 @@ def __init__(self, time, data, labels=None):
             Data arrays.
         labels : sequence of str or None, default, None
             Labels of connections.
-        
+
         """
         super().__init__(time, data, labels)
 
     def __getitem__(self, islice):
         """
         Slice connection output.
-        
+
         Parameters
         ----------
         islice : int, str, slice, sequence of int or sequence of str
@@ -177,15 +177,16 @@ def __getitem__(self, islice):
         -------
         dict or :class:`toughio.ConnectionOutput`
             Sliced connection outputs.
-        
+
         """
         if self.labels is None:
             raise AttributeError()
-        
+
         if np.ndim(islice) == 0:
             if isinstance(islice, str):
                 islice = [
-                    i for i, (label1, label2) in enumerate(self.labels)
+                    i
+                    for i, (label1, label2) in enumerate(self.labels)
                     if label1 == islice or label2 == islice
                 ]
 
@@ -194,13 +195,13 @@ def __getitem__(self, islice):
 
             else:
                 return {k: v[islice] for k, v in self.data.items()}
-        
+
         elif np.ndim(islice) <= 2:
             islice = [self.index(*i) if np.ndim(i) == 1 else i for i in islice]
 
         else:
             raise ValueError()
-        
+
         return ConnectionOutput(
             self.time,
             {k: v[islice] for k, v in self.data.items()},
@@ -210,7 +211,7 @@ def __getitem__(self, islice):
     def index(self, label1, label2):
         """
         Get index of connection.
-        
+
         Parameters
         ----------
         label1 : str
@@ -222,7 +223,7 @@ def index(self, label1, label2):
         -------
         int
             Index of connection.
-        
+
         """
         super().index()
         labels = ["".join(label) for label in self.labels]
@@ -240,7 +241,11 @@ def to_output(file_type, labels_order, headers, times, labels, data):
             "data": {k: v for k, v in zip(headers, np.transpose(data_))},
         }
 
-        output = ElementOutput(**kwargs) if file_type == "element" else ConnectionOutput(**kwargs)
+        output = (
+            ElementOutput(**kwargs)
+            if file_type == "element"
+            else ConnectionOutput(**kwargs)
+        )
         outputs.append(output)
 
     # Some older versions of TOUGH3 have duplicate connection outputs when running in parallel

toughio/_io/output/_helpers.py

@@ -184,5 +184,5 @@ def get_output_type(filename):
             else:
                 file_format = "element"
                 file_type = None
-            
+
     return file_type, file_format

toughio/_io/output/csv/_csv.py

@@ -1,5 +1,5 @@
 from ...._common import open_file
-from .._common import to_output, ElementOutput
+from .._common import ElementOutput, to_output
 
 __all__ = [
     "read",
@@ -58,7 +58,7 @@ def read(filename, file_type, labels_order=None, time_steps=None):
         if any(i < 0 for i in time_steps):
             n_steps = _count_time_steps(filename)
             time_steps = [i if i >= 0 else n_steps + i for i in time_steps]
-        
+
         time_steps = set(time_steps)
 
     with open_file(filename, "r") as f:
@@ -115,7 +115,7 @@ def _read_csv(f, file_type, time_steps=None):
 
             else:
                 labels[-1].append([l.replace('"', "").strip() for l in line[:ilab]])
-            
+
             data[-1].append([float(l.strip()) for l in line[ilab:]])
 
         line = f.readline()

toughio/_io/output/petrasim/_petrasim.py

@@ -1,7 +1,7 @@
 import numpy as np
 
 from ...._common import open_file
-from .._common import to_output, ElementOutput
+from .._common import ElementOutput, to_output
 
 __all__ = [
     "read",
@@ -37,7 +37,7 @@ def read(filename, file_type, labels_order=None, time_steps=None):
         if any(i < 0 for i in time_steps):
             n_steps = _count_time_steps(filename)
             time_steps = [i if i >= 0 else n_steps + i for i in time_steps]
-        
+
         time_steps = set(time_steps)
 
     with open_file(filename, "r") as f:
@@ -122,9 +122,7 @@ def write(filename, output):
             if isinstance(out, ElementOutput)
             else ["TIME [sec]", "ELEM1", "ELEM2", "INDEX"]
         )
-        record = ",".join(
-            f"{header:>18}" for header in headers_ + headers
-        )
+        record = ",".join(f"{header:>18}" for header in headers_ + headers)
         f.write(f"{record}\n")
 
         # Data

toughio/_io/output/save/_save.py

@@ -30,7 +30,7 @@ def read(filename, file_type=None, labels_order=None, time_steps=None):
 
     """
     parameters = tough.read(filename)
-    
+
     data = [v["values"] for v in parameters["initial_conditions"].values()]
     data = {f"X{i + 1}": x for i, x in enumerate(np.transpose(data))}
     data["porosity"] = np.array(

toughio/_io/output/tecplot/_tecplot.py

@@ -56,7 +56,7 @@ def read(filename, file_type, labels_order=None, time_steps=None):
         if any(i < 0 for i in time_steps):
             n_steps = _count_time_steps(filename)
             time_steps = [i if i >= 0 else n_steps + i for i in time_steps]
-        
+
         time_steps = set(time_steps)
 
     with open_file(filename, "r") as f:
@@ -93,7 +93,7 @@ def read_buffer(f, time_steps=None):
 
             if "I" not in zone:
                 raise ValueError()
-            
+
             else:
                 t_step += 1
 

toughio/_io/output/tough/_tough.py

@@ -39,7 +39,7 @@ def read(filename, file_type, labels_order=None, time_steps=None):
         if any(i < 0 for i in time_steps):
             n_steps = _count_time_steps(filename)
             time_steps = [i if i >= 0 else n_steps + i for i in time_steps]
-        
+
         time_steps = set(time_steps)
 
     with open_file(filename, "r") as f:
@@ -110,7 +110,7 @@ def _read_table(f, file_type, time_steps=None):
 
             if not (time_steps is None or t_step in time_steps):
                 continue
-            
+
             # Read time step in following line
             line = next(f).strip()
             times.append(float(line.split()[0]))

toughio/_mesh/_mesh.py

@@ -490,13 +490,15 @@ def read_output(
 
         """
         from .. import read_output
-        from .._io.output._common import ElementOutput, ConnectionOutput
+        from .._io.output._common import ConnectionOutput, ElementOutput
 
         if not isinstance(time_step, int):
             raise TypeError()
 
         if isinstance(file_or_output, str):
-            out = read_output(file_or_output, time_steps=time_step, connection=connection)[0]
+            out = read_output(
+                file_or_output, time_steps=time_step, connection=connection
+            )[0]
 
         else:
             out = file_or_output