Merge pull request #40 from CASCI-lab/style-and-formatting-patch1

format, style, and fixed some unused args

cana/__init__.py

@@ -1,19 +1,21 @@
-__package__ = 'cana'
-__title__ = u'CANAlization: Control & Redundancy in Boolean Networks'
-__description__ = u'This package implements a series of methods used to study control, canalization and redundancy in Boolean networks.'
+__package__ = "cana"
+__title__ = "CANAlization: Control & Redundancy in Boolean Networks"
+__description__ = "This package implements a series of methods used to study control, canalization and redundancy in Boolean networks."
 
-__author__ = """\n""".join([
-    'Rion Brattig Correia <rionbr@gmail.com>',
-    'Alex Gates <ajgates42@gmail.com>',
-    'Xuan Wang <xw47@indiana.edu>',
-    'Thomas Parmer <tjparmer@indiana.edu>',
-    'Etienne Nzabarushimana <enzabaru@indiana.edu>',
-    'Luis M. Rocha <rocha@indiana.edu>'
-])
+__author__ = """\n""".join(
+    [
+        "Rion Brattig Correia <rionbr@gmail.com>",
+        "Alex Gates <ajgates42@gmail.com>",
+        "Xuan Wang <xw47@indiana.edu>",
+        "Thomas Parmer <tjparmer@indiana.edu>",
+        "Etienne Nzabarushimana <enzabaru@indiana.edu>",
+        "Luis M. Rocha <rocha@indiana.edu>",
+    ]
+)
 
-__copyright__ = u'2021, Correia, R. B., Gates, A., Rocha, L. M.'
+__copyright__ = "2021, Correia, R. B., Gates, A., Rocha, L. M."
 
-__version__ = '0.2.0'
-__release__ = '0.2.0'
+__version__ = "0.2.0"
+__release__ = "0.2.0"
 #
-__all__ = ['boolean_network', 'boolean_node']
+__all__ = ["boolean_network", "boolean_node"]

cana/base.py

@@ -1,18 +1,22 @@
-import warnings
 import functools
+import warnings
 
 
 def deprecated(func):
     """This is a decorator which can be used to mark functions as deprecated.
     It will result in a warning being emitted when the function is used.
     """
+
     @functools.wraps(func)
     def new_func(*args, **kwargs):
         warnings.warn_explicit(
-            "You've called a deprecated function. Maybe this function needs updating to the new package. {}".format(func.__name__),
+            "You've called a deprecated function. Maybe this function needs updating to the new package. {}".format(
+                func.__name__
+            ),
             category=DeprecationWarning,
             filename=func.func_code.co_filename,
-            lineno=func.func_code.co_firstlineno + 1
+            lineno=func.func_code.co_firstlineno + 1,
         )
         return func(*args, **kwargs)
+
     return new_func

cana/bns/__init__.py

@@ -28,6 +28,7 @@
 import os
 import subprocess
 import tempfile
+
 from cana.utils import binstate_to_statenum
 
 _path = os.path.dirname(os.path.realpath(__file__))
@@ -53,41 +54,45 @@ def attractors(cnet, bnspath=_path, cleanup=True):
     # If string, Creates a Temporary File to be supplied to BNS
     elif isinstance(cnet, str):
         tmp = tempfile.NamedTemporaryFile(delete=cleanup)
-        with open(tmp.name, 'w') as openfile:
+        with open(tmp.name, "w") as openfile:
             openfile.write(cnet)
         tmp.file.close()
         file = tmp.name
     else:
-        raise TypeError('The cnet input should be either a file to a .cnet file or a string containing the .cnet content')
+        raise TypeError(
+            "The cnet input should be either a file to a .cnet file or a string containing the .cnet content"
+        )
 
-    cmd = [os.path.join(_path, 'bns'), file]
+    cmd = [os.path.join(bnspath, "bns"), file]
     attractors = list()
 
     try:
         p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 
         current_attractor = []
-        for i, line in enumerate(p.stdout):
+        for _, line in enumerate(p.stdout):
             # Strip line
-            cleanline = line.decode('ascii').strip().replace('\n', '')
+            cleanline = line.decode("ascii").strip().replace("\n", "")
 
-            if 'Attractor' in cleanline:
+            if "Attractor" in cleanline:
                 attractors.append(current_attractor)
                 current_attractor = []
-            elif 'Node' in cleanline and 'assumed to be constant' in cleanline:
+            elif "Node" in cleanline and "assumed to be constant" in cleanline:
                 pass
-            elif 'Total' in cleanline:
+            elif "Total" in cleanline:
                 pass
-            elif 'Start searching for all atractors.' in cleanline:
+            elif "Start searching for all atractors." in cleanline:
                 pass
-            elif 'Depth' in cleanline:
+            elif "Depth" in cleanline:
                 pass
-            elif 'average' in cleanline:
+            elif "average" in cleanline:
                 pass
             elif len(cleanline) > 0:
                 current_attractor.append(binstate_to_statenum(cleanline))
 
     except OSError:
-        print("'BNS' could not be found! You must have it compiled or download the binary for your system from the 'bns' website (https://people.kth.se/~dubrova/bns.html).")
+        print(
+            "'BNS' could not be found! You must have it compiled or download the binary for your system from the 'bns' website (https://people.kth.se/~dubrova/bns.html)."
+        )
 
     return attractors