Update to PEP8

cadet/__init__.py

@@ -2,5 +2,5 @@
 
 __version__ = "0.14.1"
 
-from .cadet import H5
 from .cadet import Cadet
+from .cadet import H5

cadet/cadet.py

@@ -1,8 +1,9 @@
+import warnings
+
 from addict import Dict
 
-import warnings
 with warnings.catch_warnings():
-    warnings.filterwarnings("ignore",category=FutureWarning)
+    warnings.filterwarnings("ignore", category=FutureWarning)
     import h5py
 import numpy
 import subprocess
@@ -17,6 +18,7 @@
 
 from cadet.cadet_dll import CadetDLL
 
+
 class H5():
     pp = pprint.PrettyPrinter(indent=4)
 
@@ -117,10 +119,12 @@ def __setitem__(self, key, value):
                 obj = obj[i]
         obj[parts[-1]] = value
 
+
 def is_dll(value):
     suffix = Path(value).suffix
     return suffix in {'.so', '.dll'}
 
+
 class CadetMeta(type):
     _cadet_runner_class = None
     _is_file_class = None
@@ -144,7 +148,7 @@ def __init__(cls):
             del cls._cadet_runner_class
 
         if is_dll(value):
-            cls._cadet_runner_class  = CadetDLL(value)
+            cls._cadet_runner_class = CadetDLL(value)
             cls._is_file_class = False
         else:
             cls._cadet_runner_class = CadetFile(value)
@@ -154,8 +158,9 @@ def __init__(cls):
     def cadet_path(cls):
         del cls._cadet_runner_class
 
+
 class Cadet(H5, metaclass=CadetMeta):
-    #cadet_path must be set in order for simulations to run
+    # cadet_path must be set in order for simulations to run
     def __init__(self, *data):
         super().__init__(*data)
         self._cadet_runner = None
@@ -188,7 +193,7 @@ def cadet_path(self, value):
             del self._cadet_runner
 
         if is_dll(value):
-            self._cadet_runner  = CadetDLL(value)
+            self._cadet_runner = CadetDLL(value)
             self._is_file = False
         else:
             self._cadet_runner = CadetFile(value)
@@ -209,14 +214,14 @@ def load_results(self):
         if runner is not None:
             runner.load_results(self)
 
-    def run(self, timeout = None, check=None):
+    def run(self, timeout=None, check=None):
         data = self.cadet_runner.run(simulation=self.root.input, filename=self.filename, timeout=timeout, check=check)
-        #self.return_information = data
+        # self.return_information = data
         return data
 
-    def run_load(self, timeout = None, check=None, clear=True):
+    def run_load(self, timeout=None, check=None, clear=True):
         data = self.cadet_runner.run(simulation=self.root.input, filename=self.filename, timeout=timeout, check=check)
-        #self.return_information = data
+        # self.return_information = data
         self.load_results()
         if clear:
             self.clear()
@@ -227,14 +232,15 @@ def clear(self):
         if runner is not None:
             runner.clear()
 
+
 class CadetFile:
 
     def __init__(self, cadet_path):
         self.cadet_path = cadet_path
 
-    def run(self, filename = None, simulation=None, timeout = None, check=None):
+    def run(self, filename=None, simulation=None, timeout=None, check=None):
         if filename is not None:
-            data = subprocess.run([self.cadet_path, filename], timeout = timeout, check=check, capture_output=True)
+            data = subprocess.run([self.cadet_path, filename], timeout=timeout, check=check, capture_output=True)
             return data
         else:
             print("Filename must be set before run can be used")
@@ -245,9 +251,10 @@ def clear(self):
     def load_results(self, sim):
         sim.load(paths=["/meta", "/output"], update=True)
 
+
 def convert_from_numpy(data, func):
     ans = Dict()
-    for key_original,item in data.items():
+    for key_original, item in data.items():
         key = func(key_original)
         if isinstance(item, numpy.ndarray):
             item = item.tolist()
@@ -264,18 +271,20 @@ def convert_from_numpy(data, func):
             ans[key] = item
     return ans
 
-def recursively_load_dict( data, func):
+
+def recursively_load_dict(data, func):
     ans = Dict()
-    for key_original,item in data.items():
+    for key_original, item in data.items():
         key = func(key_original)
         if isinstance(item, dict):
             ans[key] = recursively_load_dict(item, func)
         else:
             ans[key] = item
     return ans
 
+
 def set_path(obj, path, value):
-    "paths need to be broken up so that subobjects are correctly made"
+    """paths need to be broken up so that subobjects are correctly made"""
     path = path.split('/')
     path = [i for i in path if i]
 
@@ -285,7 +294,8 @@ def set_path(obj, path, value):
 
     temp[path[-1]] = value
 
-def recursively_load( h5file, path, func, paths):
+
+def recursively_load(h5file, path, func, paths):
     ans = Dict()
     if paths is not None:
         for path in paths:
@@ -306,8 +316,8 @@ def recursively_load( h5file, path, func, paths):
                 ans[key] = recursively_load(h5file, local_path + '/', func, None)
     return ans
 
-def recursively_save(h5file, path, dic, func):
 
+def recursively_save(h5file, path, dic, func):
     if not isinstance(path, str):
         raise ValueError("path must be a string")
     if not isinstance(h5file, h5py._hl.files.File):