bmtool 0.7.0.6.4__py3-none-any.whl → 0.7.1__py3-none-any.whl

bmtool/util/commands.py

@@ -1,53 +1,122 @@
-from os import system, name
-import click
-import logging
-import os
-import questionary
+import glob
 import json
-import tempfile
+import os
 import shutil
-import glob
+import tempfile
+from os import name, system
 
-from clint.textui import puts, colored, indent
+import click
+import questionary
+from clint.textui import colored
 
 from .util import load_config
 
-@click.group('util')
-@click.option('-c', '--config', type=click.Path(), default='./simulation_config.json', help='Configuration file to use, default: "simulation_config.json"')
+
+@click.group("util")
+@click.option(
+    "-c",
+    "--config",
+    type=click.Path(),
+    default="./simulation_config.json",
+    help='Configuration file to use, default: "simulation_config.json"',
+)
 @click.pass_context
 def cli(ctx, config):
-    config_path = os.path.abspath(os.path.expanduser(config)).replace("\\","/")
+    config_path = os.path.abspath(os.path.expanduser(config)).replace("\\", "/")
 
     ctx.obj["config"] = config_path
 
     if not os.path.exists(config_path):
-        #click.echo(colored.red("Config file not found: " + config))
+        # click.echo(colored.red("Config file not found: " + config))
         pass
 
+
 def check_neuron_installed(confirm=True):
     try:
-        import neuron
+        import importlib.util
+
+        if importlib.util.find_spec("neuron") is None:
+            raise ModuleNotFoundError("neuron module not found")
     except ModuleNotFoundError as e:
         print("Error: Python NEURON was not found.")
         if not confirm or not questionary.confirm("Do you want to continue anyway? ").ask():
             return False
     return True
 
-@click.group('cell', help="Access various utilities for manipulating your cell")
-@click.option('--hoc-folder', type=click.STRING, default=None, help="override the default cell picker from the simulation config hoc location")
-@click.option('--mod-folder', type=click.STRING, default=None, help="override the default simulation config mod file location")
-@click.option('--template', type=click.STRING, default=None, help="supply template name and skip interactive mode question")
-@click.option('--hoc', type=click.STRING, default=None, help="loads a single hoc file, best for directories with multiple NON-Template hoc files, specify --hoc TEMPLATE_FILE.hoc")
-@click.option('--prefab',type=click.BOOL,default=False,is_flag=True,help="Downloads a set of pre-defined cells to the current directory")
-@click.option('--prefab-repo', type=click.STRING, default="https://github.com/tjbanks/bmtool-cell-prefab", help="Override the github repository URL to download pre-defined cells from (default: https://github.com/tjbanks/bmtool-cell-prefab)")
-@click.option('--prefab-branch', type=click.STRING, default="master", help="Override the github repository branch (default: master)")
-@click.option('--prefab-refresh',type=click.BOOL,default=False,is_flag=True,help="Delete cached cells directory and re-download from prefab repository (WARNING: deletes everything in the folder)")
-@click.option('--prefab-no-compile',type=click.BOOL,default=False,is_flag=True,help="Don't attempt to (re-)compile prefab cell mod files")
+
+@click.group("cell", help="Access various utilities for manipulating your cell")
+@click.option(
+    "--hoc-folder",
+    type=click.STRING,
+    default=None,
+    help="override the default cell picker from the simulation config hoc location",
+)
+@click.option(
+    "--mod-folder",
+    type=click.STRING,
+    default=None,
+    help="override the default simulation config mod file location",
+)
+@click.option(
+    "--template",
+    type=click.STRING,
+    default=None,
+    help="supply template name and skip interactive mode question",
+)
+@click.option(
+    "--hoc",
+    type=click.STRING,
+    default=None,
+    help="loads a single hoc file, best for directories with multiple NON-Template hoc files, specify --hoc TEMPLATE_FILE.hoc",
+)
+@click.option(
+    "--prefab",
+    type=click.BOOL,
+    default=False,
+    is_flag=True,
+    help="Downloads a set of pre-defined cells to the current directory",
+)
+@click.option(
+    "--prefab-repo",
+    type=click.STRING,
+    default="https://github.com/tjbanks/bmtool-cell-prefab",
+    help="Override the github repository URL to download pre-defined cells from (default: https://github.com/tjbanks/bmtool-cell-prefab)",
+)
+@click.option(
+    "--prefab-branch",
+    type=click.STRING,
+    default="master",
+    help="Override the github repository branch (default: master)",
+)
+@click.option(
+    "--prefab-refresh",
+    type=click.BOOL,
+    default=False,
+    is_flag=True,
+    help="Delete cached cells directory and re-download from prefab repository (WARNING: deletes everything in the folder)",
+)
+@click.option(
+    "--prefab-no-compile",
+    type=click.BOOL,
+    default=False,
+    is_flag=True,
+    help="Don't attempt to (re-)compile prefab cell mod files",
+)
 @click.pass_context
-def cell(ctx,hoc_folder,mod_folder,template,hoc,prefab,prefab_repo,prefab_branch,prefab_refresh,prefab_no_compile):
-  
+def cell(
+    ctx,
+    hoc_folder,
+    mod_folder,
+    template,
+    hoc,
+    prefab,
+    prefab_repo,
+    prefab_branch,
+    prefab_refresh,
+    prefab_no_compile,
+):
     if not check_neuron_installed():
-        return   
+        return
 
     hoc_template_file = None
     prefab_dict = None
@@ -59,49 +128,58 @@ def cell(ctx,hoc_folder,mod_folder,template,hoc,prefab,prefab_repo,prefab_branch
     prefab_location = ""
 
     dl = False
-    if prefab: # User has elected to use prefab cells
-        if os.path.exists("./"+prefab_dict_file): #If the current directory contains the repository continue
+    if prefab:  # User has elected to use prefab cells
+        if os.path.exists(
+            "./" + prefab_dict_file
+        ):  # If the current directory contains the repository continue
             prefab_location = "./"
 
-            #mod_folder = "./" + os.path.relpath("./").replace("\\","/")
-            #hoc_folder = "./" + os.path.relpath("./").replace("\\","/")
-            #hoc_template_file = prefab_template_file
+            # mod_folder = "./" + os.path.relpath("./").replace("\\","/")
+            # hoc_folder = "./" + os.path.relpath("./").replace("\\","/")
+            # hoc_template_file = prefab_template_file
             if prefab_refresh:
-                click.echo(colored.red("Refresh selected -- Change directory to parent directory (cd ..) and re-run to refresh"))
-
-        else: # Check if current directory contains the repository
+                click.echo(
+                    colored.red(
+                        "Refresh selected -- Change directory to parent directory (cd ..) and re-run to refresh"
+                    )
+                )
 
+        else:  # Check if current directory contains the repository
             if os.path.exists("./" + prefab_directory + "/" + prefab_dict_file):
                 if prefab_refresh:
-                    shutil.rmtree("./"+prefab_directory)
+                    shutil.rmtree("./" + prefab_directory)
                     dl = True
-            else: # The folder/file we're looking for doesn't exist
+            else:  # The folder/file we're looking for doesn't exist
                 dl = True
 
-            if dl: # Download the repo
+            if dl:  # Download the repo
                 click.echo(colored.green("Downloading premade cells from " + prefab_zip_url))
-                import requests, zipfile, io
+                import io
+                import zipfile
+
+                import requests
+
                 r = requests.get(prefab_zip_url)
                 z = zipfile.ZipFile(io.BytesIO(r.content))
                 z.extractall()
-                
-            prefab_location = "./" + os.path.relpath(prefab_directory).replace("\\","/")
-  
-            
-        with open(os.path.join(prefab_location,prefab_dict_file), 'r') as f:
+
+            prefab_location = "./" + os.path.relpath(prefab_directory).replace("\\", "/")
+
+        with open(os.path.join(prefab_location, prefab_dict_file), "r") as f:
             prefab_dict = json.load(f)
 
-        
         prefab_cells = prefab_dict.get("cells") or []
-        
+
         if not template:
-            template = questionary.select(
-            "Select a cell:",
-            choices=prefab_cells).ask()
+            template = questionary.select("Select a cell:", choices=prefab_cells).ask()
 
-        mod_folder = prefab_location + "/" + prefab_cells.get(template).get("mod_folder").replace("\\","/")
-        hoc_folder = prefab_location + "/" + prefab_cells.get(template).get("hoc_folder").replace("\\","/")
-        hoc_template_file =  prefab_cells.get(template).get("hoc_template_file").replace("\\","/")
+        mod_folder = (
+            prefab_location + "/" + prefab_cells.get(template).get("mod_folder").replace("\\", "/")
+        )
+        hoc_folder = (
+            prefab_location + "/" + prefab_cells.get(template).get("hoc_folder").replace("\\", "/")
+        )
+        hoc_template_file = prefab_cells.get(template).get("hoc_template_file").replace("\\", "/")
 
         if not prefab_no_compile:
             click.echo(colored.green("Compiling mod files..."))
@@ -113,43 +191,53 @@ def cell(ctx,hoc_folder,mod_folder,template,hoc,prefab,prefab_repo,prefab_branch
             if not ret:
                 click.echo(colored.green("COMPILATION COMPLETE"))
             else:
-                click.echo(colored.red("nrnivmodl may not have been run, execute nrnivmodl or mknrndll manually in the `")+colored.green(os.path.abspath(mod_folder))+colored.red("` folder then press enter... SKIP THIS IF YOU HAVE ALREADY COMPILED"))
+                click.echo(
+                    colored.red(
+                        "nrnivmodl may not have been run, execute nrnivmodl or mknrndll manually in the `"
+                    )
+                    + colored.green(os.path.abspath(mod_folder))
+                    + colored.red(
+                        "` folder then press enter... SKIP THIS IF YOU HAVE ALREADY COMPILED"
+                    )
+                )
                 input()
-            
+
     else:
         if hoc:
             if not hoc_folder:
-                hoc_folder = './'
+                hoc_folder = "./"
             if not mod_folder:
-                mod_folder = './'
+                mod_folder = "./"
             hoc_template_file = hoc
         elif not hoc_folder or not mod_folder:
             try:
-                cfg = load_config(ctx.obj['config'])
+                cfg = load_config(ctx.obj["config"])
                 if not hoc_folder:
-                    hoc_folder = cfg['components']['templates_dir']
+                    hoc_folder = cfg["components"]["templates_dir"]
                 if not mod_folder:
-                    mod_folder = cfg['components']['mechanisms_dir']  
+                    mod_folder = cfg["components"]["mechanisms_dir"]
             except Exception as e:
-                #lazy way of passing cases where sim config is not found and template provided
+                # lazy way of passing cases where sim config is not found and template provided
                 if not hoc_folder:
                     print("Setting hoc folder to ./")
-                    hoc_folder = '.'
+                    hoc_folder = "."
                 if not mod_folder:
                     print("Setting mod folder to ./")
-                    mod_folder = '.'
+                    mod_folder = "."
 
     ctx.obj["hoc_folder"] = hoc_folder
     ctx.obj["mod_folder"] = mod_folder
     ctx.obj["hoc_template_file"] = hoc_template_file
     ctx.obj["cell_template"] = template
     ctx.obj["prefab"] = prefab_dict
-    
+
     return
 
+
 cli.add_command(cell)
 
-class Builder():
+
+class Builder:
     def __init__(self):
         self.title = ""
         self._options = {}
@@ -157,14 +245,14 @@ class Builder():
         return
 
     def run(self):
-        def clear(): 
-            # for windows 
-            if name == 'nt': 
-                _ = system('cls') 
-            # for mac and linux(here, os.name is 'posix') 
-            else: 
-                _ = system('clear') 
-                
+        def clear():
+            # for windows
+            if name == "nt":
+                _ = system("cls")
+            # for mac and linux(here, os.name is 'posix')
+            else:
+                _ = system("clear")
+
         prompter = self
         while prompter:
             clear()
@@ -174,36 +262,35 @@ class Builder():
         return
 
     def prompt(self):
-        options = list(self._options.keys()) 
-        options_ind = [str(i+1)+") "+op for i,op in enumerate(options)]
+        options = list(self._options.keys())
+        options_ind = [str(i + 1) + ") " + op for i, op in enumerate(options)]
         if bool(self._exit_option):
-            exit_option = list(self._exit_option.keys()) 
-            exit_option_ind = [str(i)+") "+op for i,op in enumerate(exit_option)]#should only be one
+            exit_option = list(self._exit_option.keys())
+            exit_option_ind = [
+                str(i) + ") " + op for i, op in enumerate(exit_option)
+            ]  # should only be one
             options = options + exit_option
             options_ind = options_ind + exit_option_ind
-        
-        selected = questionary.select(
-        self.title,
-        choices=options_ind).ask()
+
+        selected = questionary.select(self.title, choices=options_ind).ask()
 
         selected = options[options_ind.index(selected)]
-        
+
         if self._exit_option.get(selected):
             _prompt = self._exit_option[selected][0]()
         else:
             _prompt = self._options[selected][0]()
         return _prompt
 
-    def register(self, text, handler,args=None,is_exit=False):
+    def register(self, text, handler, args=None, is_exit=False):
         if is_exit:
             self._exit_option.clear()
-            self._exit_option[text] = (handler,args) 
+            self._exit_option[text] = (handler, args)
         else:
-            self._options[text] = (handler,args)
+            self._options[text] = (handler, args)
         return
 
 
-
 class BaseBuilder(Builder):
     def __init__(self, ctg):
         super(BaseBuilder, self).__init__()
@@ -213,31 +300,33 @@ class BaseBuilder(Builder):
         return
 
     def register_all(self):
-
         def new_window():
-            return WindowBuilder(self,self.ctg)
-        
+            return WindowBuilder(self, self.ctg)
+
         def print_ctx():
             print("Not currently implemented")
             print("Press enter to continue...")
             input()
             return self
-        
+
         def write_to_hoc():
-            #print("Enter the name of the file you wish to write: (eg: cellgui.hoc)")
-            filename = questionary.text("Enter the name of the file you wish to write: (eg: cellgui.hoc)",default="cellgui.hoc").ask()
+            # print("Enter the name of the file you wish to write: (eg: cellgui.hoc)")
+            filename = questionary.text(
+                "Enter the name of the file you wish to write: (eg: cellgui.hoc)",
+                default="cellgui.hoc",
+            ).ask()
             self.ctg.write_hoc(filename)
             print("Done. Press enter to continue...")
             input()
             return self
 
         def set_tstop():
-            tstop = questionary.text("Set tstop (ms): )",default=str(self.ctg.tstop)).ask()
+            tstop = questionary.text("Set tstop (ms): )", default=str(self.ctg.tstop)).ask()
             self.ctg.tstop = tstop
             return self
 
         def set_v_init():
-            v_init = questionary.text("Set v_init (mV): )",default=str(self.ctg.v_init)).ask()
+            v_init = questionary.text("Set v_init (mV): )", default=str(self.ctg.v_init)).ask()
             self.ctg.v_init = v_init
             return self
 
@@ -249,8 +338,9 @@ class BaseBuilder(Builder):
         self.register("Set tstop", set_tstop)
         self.register("Set v_init", set_v_init)
         self.register("Write to HOC executable", write_to_hoc)
-        self.register("Finish and Display", finished ,is_exit=True)
- 
+        self.register("Finish and Display", finished, is_exit=True)
+
+
 class WindowBuilder(Builder):
     def __init__(self, parent, ctg):
         super(WindowBuilder, self).__init__()
@@ -262,22 +352,22 @@ class WindowBuilder(Builder):
         return
 
     def register_all(self):
-
         def set_title():
             print("Type the new title for this window")
-            self.ctg.set_title(self.window_index,input())
+            self.ctg.set_title(self.window_index, input())
             self.title = self.ctg.get_title(self.window_index)
             return self
-        
+
         def new_column():
-            return ColumnBuilder(self,self.ctg)
-        
+            return ColumnBuilder(self, self.ctg)
+
         def finished():
             return self.parent
 
         self.register("Add Column", new_column)
         self.register("Set Window Title", set_title)
-        self.register("Finish Window", finished ,is_exit=True)
+        self.register("Finish Window", finished, is_exit=True)
+
 
 class ColumnBuilder(Builder):
     def __init__(self, parent, ctg):
@@ -285,69 +375,68 @@ class ColumnBuilder(Builder):
         self.parent = parent
         self.ctg = ctg
         self.column_index = ctg.add_column(self.parent.window_index)
-        self.title = "Window " + str(self.parent.window_index+1) + " Column " + str(self.column_index+1)
+        self.title = (
+            "Window " + str(self.parent.window_index + 1) + " Column " + str(self.column_index + 1)
+        )
         self.register_all()
         return
 
     def register_all(self):
-        
         def new_widget():
             print("Not currently implemented")
             print("Press enter to continue...")
             input()
             return self
-        
+
         def new_plot_widget():
-            return PlotWidgetBuilder(self,self.ctg)
-        
+            return PlotWidgetBuilder(self, self.ctg)
+
         def new_controlmenu_widget():
             from .neuron.celltuner import ControlMenuWidget
+
             widget = ControlMenuWidget()
-            self.ctg.add_widget(self.parent.window_index, self.column_index,widget)
+            self.ctg.add_widget(self.parent.window_index, self.column_index, widget)
             print("Done. Press enter to continue...")
             input()
             return self
 
         def new_pointmenu_widget():
-            return PointMenuWidgetBuilder(self,self.ctg)
+            return PointMenuWidgetBuilder(self, self.ctg)
 
         def new_secmenu_widget():
-            return SecMenuWidgetBuilder(self,self.ctg)
+            return SecMenuWidgetBuilder(self, self.ctg)
 
         def finished():
             return self.parent
 
-        #self.register("Add Widget", new_widget)
+        # self.register("Add Widget", new_widget)
         self.register("Add Plot Widget", new_plot_widget)
         self.register("Add Control Menu Widget (Init & Run)", new_controlmenu_widget)
         self.register("Add SecMenu Widget (Section Variables)", new_secmenu_widget)
         self.register("Add Point Menu Widget (Current Clamp, Netstim)", new_pointmenu_widget)
-        self.register("Finish Column", finished ,is_exit=True)
+        self.register("Finish Column", finished, is_exit=True)
+
 
 class SecMenuWidgetBuilder(Builder):
     def __init__(self, parent, ctg):
         super(SecMenuWidgetBuilder, self).__init__()
 
-        from .neuron.celltuner import SecMenuWidget
-
         self.parent = parent
         self.ctg = ctg
-        self.title =  "(Section Menu Widget)"
+        self.title = "(Section Menu Widget)"
         self.register_all()
         return
 
     def register_all(self):
-        
         def select():
             from .neuron.celltuner import SecMenuWidget
+
             cell_options = []
             cell_options_obj = []
             cell_options.append(self.ctg.template.hname())
             cell_options_obj.append(self.ctg.template)
-            
-            cell_selected = questionary.select(
-            "Select the Cell",
-            choices=cell_options).ask()
+
+            cell_selected = questionary.select("Select the Cell", choices=cell_options).ask()
 
             section_options = []
             section_options_obj = []
@@ -356,45 +445,47 @@ class SecMenuWidgetBuilder(Builder):
             section_options = [s.hname() for s in section_options_obj]
 
             section_selected = questionary.select(
-            "Select the Section",
-            choices=section_options).ask()
+                "Select the Section", choices=section_options
+            ).ask()
 
             section_selected_obj = section_options_obj[section_options.index(section_selected)]
-            section_location = questionary.text("Enter recording location (default:0.5): ",default="0.5").ask()
+            section_location = questionary.text(
+                "Enter recording location (default:0.5): ", default="0.5"
+            ).ask()
+
+            self.widget = SecMenuWidget(section_selected_obj, x=float(section_location))
+            self.widget_index = self.ctg.add_widget(
+                self.parent.parent.window_index, self.parent.column_index, self.widget
+            )
 
-            self.widget = SecMenuWidget(section_selected_obj,x=float(section_location))
-            self.widget_index = self.ctg.add_widget(self.parent.parent.window_index, self.parent.column_index,self.widget)
-        
             return self.parent
 
         def finish():
             return self.parent
 
         self.register("Select Section", select)
-        self.register("Return without adding widget", finish ,is_exit=True)
+        self.register("Return without adding widget", finish, is_exit=True)
         return
 
+
 class PointMenuWidgetBuilder(Builder):
     def __init__(self, parent, ctg):
         super(PointMenuWidgetBuilder, self).__init__()
 
         self.parent = parent
         self.ctg = ctg
-        self.title =  "(Point Menu Widget)"
+        self.title = "(Point Menu Widget)"
         self.register_all()
         return
 
     def register_all(self):
-
         def select_section_location():
             cell_options = []
             cell_options_obj = []
             cell_options.append(self.ctg.template.hname())
             cell_options_obj.append(self.ctg.template)
-            
-            cell_selected = questionary.select(
-            "Select the Cell",
-            choices=cell_options).ask()
+
+            cell_selected = questionary.select("Select the Cell", choices=cell_options).ask()
 
             section_options = []
             section_options_obj = []
@@ -403,67 +494,113 @@ class PointMenuWidgetBuilder(Builder):
             section_options = [s.hname() for s in section_options_obj]
 
             section_selected = questionary.select(
-            "Select the Section",
-            choices=section_options).ask()
+                "Select the Section", choices=section_options
+            ).ask()
 
             section_selected_obj = section_options_obj[section_options.index(section_selected)]
-            section_location = questionary.text("Enter location (default:0.5): ",default="0.5").ask()
+            section_location = questionary.text(
+                "Enter location (default:0.5): ", default="0.5"
+            ).ask()
 
             return section_selected_obj, section_location
 
         def new_clamp():
             from .neuron.celltuner import PointMenuWidget
-            
+
             section_selected_obj, section_location = select_section_location()
 
-            delay = float(questionary.text("Enter default iclamp delay (default:0): ",default="0").ask())
-            dur = float(questionary.text("Enter default iclamp duration (default:100): ",default="100").ask())
-            amp = float(questionary.text("Enter default iclamp amp(mA) (default:1): ",default="1").ask())            
+            delay = float(
+                questionary.text("Enter default iclamp delay (default:0): ", default="0").ask()
+            )
+            dur = float(
+                questionary.text(
+                    "Enter default iclamp duration (default:100): ", default="100"
+                ).ask()
+            )
+            amp = float(
+                questionary.text("Enter default iclamp amp(mA) (default:1): ", default="1").ask()
+            )
 
             self.widget = PointMenuWidget(None)
-            iclamp = self.widget.iclamp(section_selected_obj(float(section_location)),dur,amp,delay)
+            iclamp = self.widget.iclamp(
+                section_selected_obj(float(section_location)), dur, amp, delay
+            )
             self.ctg.register_iclamp(iclamp)
-            self.widget_index = self.ctg.add_widget(self.parent.parent.window_index, self.parent.column_index,self.widget)
+            self.widget_index = self.ctg.add_widget(
+                self.parent.parent.window_index, self.parent.column_index, self.widget
+            )
 
             return self.parent
 
         def new_netstim():
             from .neuron.celltuner import PointMenuWidget
+
             section_selected_obj, section_location = select_section_location()
 
             notlisted = "Synapse not listed"
 
             synapse_options = self.ctg.mechanism_point_processes[:]
-            synapse_options = synapse_options + ["AlphaSynapse","Exp2Syn","ExpSyn"] #Builtins
+            synapse_options = synapse_options + ["AlphaSynapse", "Exp2Syn", "ExpSyn"]  # Builtins
             synapse_options.append(notlisted)
 
             synapse_selected = questionary.select(
-            "Select the Synapse type from the most likely options",
-            choices=synapse_options).ask()
+                "Select the Synapse type from the most likely options", choices=synapse_options
+            ).ask()
 
             if synapse_selected == notlisted:
                 synapse_options = [i for i in self.ctg.get_all_h_hocobjects()]
                 synapse_selected = questionary.select(
-                "Select the Synapse (ALL HOCOBJECTS)",
-                choices=synapse_options).ask()
-
-            interval = int(questionary.text("Enter default netstim interval (ms (mean) time between spikes): ",default="50").ask())
-            number = int(questionary.text("Enter default netstim number of events ((average) number of spikes): ",default="10").ask())
-            start = int(questionary.text("Enter default netstim start (ms (most likely) start time of first spike): ",default="0").ask())
-            noise = float(questionary.text("Enter default netstim noise (range 0 to 1. Fractional randomness.): ",default="0").ask())
-            weight = float(questionary.text("Enter default netcon weight (range 0 to 1. Default: 1): ",default="1").ask())
-            
+                    "Select the Synapse (ALL HOCOBJECTS)", choices=synapse_options
+                ).ask()
+
+            interval = int(
+                questionary.text(
+                    "Enter default netstim interval (ms (mean) time between spikes): ", default="50"
+                ).ask()
+            )
+            number = int(
+                questionary.text(
+                    "Enter default netstim number of events ((average) number of spikes): ",
+                    default="10",
+                ).ask()
+            )
+            start = int(
+                questionary.text(
+                    "Enter default netstim start (ms (most likely) start time of first spike): ",
+                    default="0",
+                ).ask()
+            )
+            noise = float(
+                questionary.text(
+                    "Enter default netstim noise (range 0 to 1. Fractional randomness.): ",
+                    default="0",
+                ).ask()
+            )
+            weight = float(
+                questionary.text(
+                    "Enter default netcon weight (range 0 to 1. Default: 1): ", default="1"
+                ).ask()
+            )
+
             self.widget = PointMenuWidget(None)
             self.widget_extra = PointMenuWidget(None)
-            synapse = self.widget_extra.synapse(section_selected_obj,section_location,synapse_selected)
-            netstim,netcon = self.widget.netstim(interval,number,start,noise,target=synapse,weight=weight)
+            synapse = self.widget_extra.synapse(
+                section_selected_obj, section_location, synapse_selected
+            )
+            netstim, netcon = self.widget.netstim(
+                interval, number, start, noise, target=synapse, weight=weight
+            )
             self.ctg.register_netstim(netstim)
             self.ctg.register_netcon(netcon)
             self.ctg.register_synapse(synapse)
 
-            self.widget_index_extra = self.ctg.add_widget(self.parent.parent.window_index, self.parent.column_index,self.widget_extra)
-            self.widget_index = self.ctg.add_widget(self.parent.parent.window_index, self.parent.column_index,self.widget)
-            
+            self.widget_index_extra = self.ctg.add_widget(
+                self.parent.parent.window_index, self.parent.column_index, self.widget_extra
+            )
+            self.widget_index = self.ctg.add_widget(
+                self.parent.parent.window_index, self.parent.column_index, self.widget
+            )
+
             return self.parent
 
         def finish():
@@ -471,9 +608,10 @@ class PointMenuWidgetBuilder(Builder):
 
         self.register("Add Netstim to Cell and Insert Widgets", new_netstim)
         self.register("Add Current Clamp to Cell and Insert Widget", new_clamp)
-        self.register("Finished", finish ,is_exit=True)        
+        self.register("Finished", finish, is_exit=True)
         return
 
+
 class PlotWidgetBuilder(Builder):
     def __init__(self, parent, ctg):
         super(PlotWidgetBuilder, self).__init__()
@@ -483,331 +621,482 @@ class PlotWidgetBuilder(Builder):
         self.parent = parent
         self.ctg = ctg
         self.widget = PlotWidget(tstop=self.ctg.tstop)
-        self.widget_index = ctg.add_widget(self.parent.parent.window_index, self.parent.column_index,self.widget)
-        self.title = "Window " + str(self.parent.parent.window_index + 1) + " Column " + \
-            str(self.parent.column_index + 1) + " Widget " + str(self.widget_index) + " (Plot Widget)"
+        self.widget_index = ctg.add_widget(
+            self.parent.parent.window_index, self.parent.column_index, self.widget
+        )
+        self.title = (
+            "Window "
+            + str(self.parent.parent.window_index + 1)
+            + " Column "
+            + str(self.parent.column_index + 1)
+            + " Widget "
+            + str(self.widget_index)
+            + " (Plot Widget)"
+        )
         self.register_all()
         return
 
     def register_all(self):
-            
         def new_expression():
-            obj_options = ["Cell","Quick - Template Cell.soma Membrane Voltage (0.5)"]
+            obj_options = ["Cell", "Quick - Template Cell.soma Membrane Voltage (0.5)"]
             obj_selected = questionary.select(
-            "Select the object type to plot",
-            choices=obj_options).ask()
+                "Select the object type to plot", choices=obj_options
+            ).ask()
             if obj_selected == obj_options[0]:
-                
                 cell_options = []
                 cell_options_obj = []
                 cell_options.append(self.ctg.template.hname())
                 cell_options_obj.append(self.ctg.template)
-                
-                cell_selected = questionary.select(
-                "Select the Cell",
-                choices=cell_options).ask()
+
+                cell_selected = questionary.select("Select the Cell", choices=cell_options).ask()
 
                 section_options = []
                 section_options_obj = []
                 all_sections = self.ctg.all_sections()
-                section_options_obj = [s for s in all_sections if s.hname().startswith(cell_selected)]
+                section_options_obj = [
+                    s for s in all_sections if s.hname().startswith(cell_selected)
+                ]
                 section_options = [s.hname() for s in section_options_obj]
 
                 section_selected = questionary.select(
-                "Select the Section",
-                choices=section_options).ask()
+                    "Select the Section", choices=section_options
+                ).ask()
 
                 section_selected_obj = section_options_obj[section_options.index(section_selected)]
-                section_location = questionary.text("Enter recording location (default:0.5): ",default="0.5").ask()
-                
-                mechs = [mech.name() for mech in section_selected_obj(float(section_location)) if not mech.name().endswith("_ion")]            
+                section_location = questionary.text(
+                    "Enter recording location (default:0.5): ", default="0.5"
+                ).ask()
+
+                mechs = [
+                    mech.name()
+                    for mech in section_selected_obj(float(section_location))
+                    if not mech.name().endswith("_ion")
+                ]
 
                 variable_options = []
-                variable_options.append("v") # builtin voltage variable
+                variable_options.append("v")  # builtin voltage variable
                 for mech in mechs:
                     if self.ctg.mechanism_dict.get(mech):
                         ranges = self.ctg.mechanism_dict[mech]["NEURON"]["RANGE"]
                         variable_options = variable_options + [rng + "_" + mech for rng in ranges]
 
                 variables_selected = questionary.checkbox(
-                "Select the Variables",
-                choices=variable_options).ask()
+                    "Select the Variables", choices=variable_options
+                ).ask()
+
+                # sec_text = self.ctg.root_sec.hname().split('.')[-1]+"(.5)"
+                # self.widget.add_expr(self.ctg.root_sec(0.5)._ref_v,sec_text,hoc_text="%s.soma.v(0.5)",hoc_text_obj=self.ctg.template)
 
-                #sec_text = self.ctg.root_sec.hname().split('.')[-1]+"(.5)"
-                #self.widget.add_expr(self.ctg.root_sec(0.5)._ref_v,sec_text,hoc_text="%s.soma.v(0.5)",hoc_text_obj=self.ctg.template)
-                
                 for variable_selected in variables_selected:
-                    #sec_var_ref = exec("section_selected_obj(float(section_location))."+variable_selected)
-                    sec_var_ref = getattr(section_selected_obj(float(section_location)),"_ref_"+variable_selected)
-                    sec_text = section_selected_obj.hname().split('.')[-1]+"("+section_location+")."+variable_selected
-                    sec_hoc_text = section_selected.split('.')[-1]
-                    hoc_text = "%s." + sec_hoc_text +"."+ variable_selected + "(" + section_location +")"
+                    # sec_var_ref = exec("section_selected_obj(float(section_location))."+variable_selected)
+                    sec_var_ref = getattr(
+                        section_selected_obj(float(section_location)), "_ref_" + variable_selected
+                    )
+                    sec_text = (
+                        section_selected_obj.hname().split(".")[-1]
+                        + "("
+                        + section_location
+                        + ")."
+                        + variable_selected
+                    )
+                    sec_hoc_text = section_selected.split(".")[-1]
+                    hoc_text = (
+                        "%s."
+                        + sec_hoc_text
+                        + "."
+                        + variable_selected
+                        + "("
+                        + section_location
+                        + ")"
+                    )
                     hoc_text_obj = cell_selected
-                    
-                    self.widget.add_expr(sec_var_ref,sec_text,hoc_text=hoc_text,hoc_text_obj=hoc_text_obj)
 
-                #import pdb;pdb.set_trace()
+                    self.widget.add_expr(
+                        sec_var_ref, sec_text, hoc_text=hoc_text, hoc_text_obj=hoc_text_obj
+                    )
+
+                # import pdb;pdb.set_trace()
 
             elif obj_selected == obj_options[1]:
-                sec_text = self.ctg.root_sec.hname().split('.')[-1]+"(.5)"
-                self.widget.add_expr(self.ctg.root_sec(0.5)._ref_v,sec_text,hoc_text="%s.soma.v(0.5)",hoc_text_obj=self.ctg.template)
+                sec_text = self.ctg.root_sec.hname().split(".")[-1] + "(.5)"
+                self.widget.add_expr(
+                    self.ctg.root_sec(0.5)._ref_v,
+                    sec_text,
+                    hoc_text="%s.soma.v(0.5)",
+                    hoc_text_obj=self.ctg.template,
+                )
                 print("Captured. Press enter to continue...")
                 input()
             return self
-        
+
         def finished():
             return self.parent
 
         self.register("Add Expression", new_expression)
-        self.register("Finish Widget", finished ,is_exit=True)
-
-@cell.command('tune', help="Creates a NEURON GUI window with everything you need to tune a cell")
-@click.option('--easy', type=click.BOOL, default=None, is_flag=True, help="Builds a simple GUI with no walkthrough")
-@click.option('--builder', type=click.BOOL, default=None, is_flag=True, help="A commandline walkthrough for building your own GUI")
-@click.option('--write-hoc', type=click.STRING, default=None, help="write a standalone hoc file for your GUI, supply filename")
-@click.option('--hide', type=click.BOOL, default=False, is_flag=True, help="hide the interface that shows automatically after building the GUI")
-@click.option('--title',type=click.STRING,default=None)
-@click.option('--tstop',type=click.INT,default=250)
-@click.option('--debug', type=click.BOOL, default=False, is_flag=True, help="Print debug messages and errors")
+        self.register("Finish Widget", finished, is_exit=True)
+
+
+@cell.command("tune", help="Creates a NEURON GUI window with everything you need to tune a cell")
+@click.option(
+    "--easy",
+    type=click.BOOL,
+    default=None,
+    is_flag=True,
+    help="Builds a simple GUI with no walkthrough",
+)
+@click.option(
+    "--builder",
+    type=click.BOOL,
+    default=None,
+    is_flag=True,
+    help="A commandline walkthrough for building your own GUI",
+)
+@click.option(
+    "--write-hoc",
+    type=click.STRING,
+    default=None,
+    help="write a standalone hoc file for your GUI, supply filename",
+)
+@click.option(
+    "--hide",
+    type=click.BOOL,
+    default=False,
+    is_flag=True,
+    help="hide the interface that shows automatically after building the GUI",
+)
+@click.option("--title", type=click.STRING, default=None)
+@click.option("--tstop", type=click.INT, default=250)
+@click.option(
+    "--debug", type=click.BOOL, default=False, is_flag=True, help="Print debug messages and errors"
+)
 @click.pass_context
-def cell_tune(ctx,easy,builder,write_hoc,hide,title,tstop,debug):#, title, populations, group_by, save_file):
+def cell_tune(
+    ctx, easy, builder, write_hoc, hide, title, tstop, debug
+):  # , title, populations, group_by, save_file):
     print("Loading...")
-    from .neuron.celltuner import CellTunerGUI, PlotWidget, ControlMenuWidget, SecMenuWidget
+    from .neuron.celltuner import CellTunerGUI, ControlMenuWidget, PlotWidget, SecMenuWidget
 
     hoc_folder = ctx.obj["hoc_folder"]
     mod_folder = ctx.obj["mod_folder"]
     hoc_template_file = ctx.obj["hoc_template_file"]
     template = ctx.obj["cell_template"]
 
-    ctg = CellTunerGUI(hoc_folder,mod_folder,title=title,print_debug=debug)
+    ctg = CellTunerGUI(hoc_folder, mod_folder, title=title, print_debug=debug)
     hoc_templates = ctg.get_templates(hoc_template_file=hoc_template_file)
-    
+
     # Cell selector
     if not template:
-        template = questionary.select(
-        "Select a cell:",
-        choices=hoc_templates).ask()
+        template = questionary.select("Select a cell:", choices=hoc_templates).ask()
 
     ctg.load_template(template)
     if not title:
-        title = template + " - Cell Configurator - Interface generated by BMTool (https://github.com/tjbanks/bmtool)"
+        title = (
+            template
+            + " - Cell Configurator - Interface generated by BMTool (https://github.com/tjbanks/bmtool)"
+        )
 
     # Mode selector
     if easy is None and builder is None:
         easy = questionary.confirm("Use pre-built interface? (no for advanced mode) ").ask()
-    
+
     if easy:
-        #Window 1
+        # Window 1
         window_index = ctg.add_window(title=title)
-        #Column 1
+        # Column 1
         column_index = ctg.add_column(window_index)
         plot_widget = PlotWidget(tstop=tstop)
-        sec_text = ctg.root_sec.hname().split('.')[-1]+"(.5)"
-        plot_widget.add_expr(ctg.root_sec(0.5)._ref_v,sec_text)
-        ctg.add_widget(window_index,column_index,plot_widget)
-        
+        sec_text = ctg.root_sec.hname().split(".")[-1] + "(.5)"
+        plot_widget.add_expr(ctg.root_sec(0.5)._ref_v, sec_text)
+        ctg.add_widget(window_index, column_index, plot_widget)
+
         if len(ctg.sections) > 1:
             plot_widget = PlotWidget(tstop=tstop)
             for sec in ctg.sections:
-                sec_text = sec.hname().split('.')[-1]+"(.5)"
-                plot_widget.add_expr(sec(0.5)._ref_v,sec_text)
-            ctg.add_widget(window_index,column_index,plot_widget)
-        
-        #Column 2
+                sec_text = sec.hname().split(".")[-1] + "(.5)"
+                plot_widget.add_expr(sec(0.5)._ref_v, sec_text)
+            ctg.add_widget(window_index, column_index, plot_widget)
+
+        # Column 2
         column_index = ctg.add_column(window_index)
-        for i in range(len(ctg.sections)):#regular iteration was acting funny
-            #import pdb;pdb.set_trace()
+        for i in range(len(ctg.sections)):  # regular iteration was acting funny
+            # import pdb;pdb.set_trace()
             sec_menu_widget = SecMenuWidget(ctg.sections[i])
-            ctg.add_widget(window_index,column_index,sec_menu_widget)
+            ctg.add_widget(window_index, column_index, sec_menu_widget)
 
-        #Column 3
+        # Column 3
         column_index = ctg.add_column(window_index)
         control_widget = ControlMenuWidget()
-        ctg.add_widget(window_index,column_index,control_widget)
-        iclamp_widget, iclamp = ctg.new_IClamp_Widget(ctg.sections[0](0.5),200,0.1,25)
-        ctg.add_widget(window_index,column_index,iclamp_widget)
-        
-    else:        
+        ctg.add_widget(window_index, column_index, control_widget)
+        iclamp_widget, iclamp = ctg.new_IClamp_Widget(ctg.sections[0](0.5), 200, 0.1, 25)
+        ctg.add_widget(window_index, column_index, iclamp_widget)
+
+    else:
         cmd_builder = BaseBuilder(ctg)
         cmd_builder.run()
-        
 
     # Section selector
-    #section_names = ctg.get_section_names()
+    # section_names = ctg.get_section_names()
 
-    #sections_selected = questionary.checkbox(
+    # sections_selected = questionary.checkbox(
     #'Select sections you want to configure (each will recieve a window):',
-    #choices=section_names).ask()
+    # choices=section_names).ask()
 
     # Display selector
-    #displays_available = ['Voltages', 'Currents', 'Conductances', 'FIR']
-    #inputs_available = ['Current Clamp', 'Spike Input']
-    #configuration_available = ['Parameter']
+    # displays_available = ['Voltages', 'Currents', 'Conductances', 'FIR']
+    # inputs_available = ['Current Clamp', 'Spike Input']
+    # configuration_available = ['Parameter']
 
-    #Do you want to select which currents to plot?
-    #import pdb;pdb.set_trace()
+    # Do you want to select which currents to plot?
+    # import pdb;pdb.set_trace()
     if write_hoc:
         ctg.write_hoc(write_hoc)
 
     if not hide:
         ctg.show()
 
-@cell.command('fi', help="Creates a NEURON GUI window with FI curve and passive properties")
-#@click.option('--easy', type=click.BOOL, default=None, is_flag=True, help="override the default simulation config mod file location")
-#@click.option('--write-hoc', type=click.STRING, default=None, help="write a standalone hoc file for your GUI, supply filename")
-#@click.option('--hide', type=click.BOOL, default=False, is_flag=True, help="hide the interface that shows automatically after building the GUI")
-@click.option('--title',type=click.STRING,default=None)
-@click.option('--min-pa',type=click.INT,default=0,help="Min pA for injection")
-@click.option('--max-pa',type=click.INT,default=1000,help="Max pA for injection")
-@click.option('--passive-delay',type=click.INT,default=650,help="Wait n ms before determining steadystate value (default: 650)")
-@click.option('--increment',type=click.FLOAT,default=100,help="Increment the injection by [i] pA")
-@click.option('--tstart',type=click.INT,default=150, help="Injection start time")
-@click.option('--tdur',type=click.INT,default=1000,help="Duration of injection default:1000ms")
-@click.option('--advanced',type=click.BOOL,default=False,is_flag=True,help="Interactive dialog to select injection and recording points")
+
+@cell.command("fi", help="Creates a NEURON GUI window with FI curve and passive properties")
+# @click.option('--easy', type=click.BOOL, default=None, is_flag=True, help="override the default simulation config mod file location")
+# @click.option('--write-hoc', type=click.STRING, default=None, help="write a standalone hoc file for your GUI, supply filename")
+# @click.option('--hide', type=click.BOOL, default=False, is_flag=True, help="hide the interface that shows automatically after building the GUI")
+@click.option("--title", type=click.STRING, default=None)
+@click.option("--min-pa", type=click.INT, default=0, help="Min pA for injection")
+@click.option("--max-pa", type=click.INT, default=1000, help="Max pA for injection")
+@click.option(
+    "--passive-delay",
+    type=click.INT,
+    default=650,
+    help="Wait n ms before determining steadystate value (default: 650)",
+)
+@click.option(
+    "--increment", type=click.FLOAT, default=100, help="Increment the injection by [i] pA"
+)
+@click.option("--tstart", type=click.INT, default=150, help="Injection start time")
+@click.option("--tdur", type=click.INT, default=1000, help="Duration of injection default:1000ms")
+@click.option(
+    "--advanced",
+    type=click.BOOL,
+    default=False,
+    is_flag=True,
+    help="Interactive dialog to select injection and recording points",
+)
 @click.pass_context
-def cell_fir(ctx,title,min_pa,max_pa,passive_delay,increment,tstart,tdur,advanced):#, title, populations, group_by, save_file):
-    
-    from .neuron.celltuner import CellTunerGUI, TextWidget, PlotWidget, ControlMenuWidget, SecMenuWidget, FICurveWidget
+def cell_fir(
+    ctx, title, min_pa, max_pa, passive_delay, increment, tstart, tdur, advanced
+):  # , title, populations, group_by, save_file):
+    from .neuron.celltuner import (
+        CellTunerGUI,
+        FICurveWidget,
+        PlotWidget,
+        TextWidget,
+    )
 
     hoc_folder = ctx.obj["hoc_folder"]
     mod_folder = ctx.obj["mod_folder"]
     hoc_template_file = ctx.obj["hoc_template_file"]
     template = ctx.obj["cell_template"]
 
-    tstop = tstart+tdur
+    tstop = tstart + tdur
 
-    ctg = CellTunerGUI(hoc_folder,mod_folder,tstop=tstop,skip_load_mod=True)
+    ctg = CellTunerGUI(hoc_folder, mod_folder, tstop=tstop, skip_load_mod=True)
     hoc_templates = ctg.get_templates(hoc_template_file=hoc_template_file)
-    
+
     # Cell selector
     if not template:
-        template = questionary.select(
-        "Select a cell:",
-        choices=hoc_templates).ask()
+        template = questionary.select("Select a cell:", choices=hoc_templates).ask()
 
     ctg.load_template(template)
     if not title:
-        title = template + " - Cell FI Curve - Interface generated by BMTool (https://github.com/tjbanks/bmtool)"
-        #ctg.set_title(title)
-    
+        title = (
+            template
+            + " - Cell FI Curve - Interface generated by BMTool (https://github.com/tjbanks/bmtool)"
+        )
+        # ctg.set_title(title)
+
     inj_sec = ctg.root_sec.hname()
     rec_sec = ctg.root_sec.hname()
 
-    inj_loc = "0.5"    
+    inj_loc = "0.5"
     rec_loc = "0.5"
-    
+
     if advanced:
         inj_sec = questionary.select(
-            "Select the current injection segment: ",
-            choices=ctg.get_section_names()
+            "Select the current injection segment: ", choices=ctg.get_section_names()
         ).ask()
         inj_loc = questionary.text("Enter current injection segment location (eg:0.5): ").ask()
         rec_sec = questionary.select(
-            "Select the recording segment: ",
-            choices=ctg.get_section_names()
+            "Select the recording segment: ", choices=ctg.get_section_names()
         ).ask()
         rec_loc = questionary.text("Enter recording segment location (eg:0.5): ").ask()
-        
-    
-    rec_sec_split = rec_sec.split('.')[-1]
-    inj_sec_split = inj_sec.split('.')[-1]
-
-    click.echo("Using section " + colored.green(inj_sec_split + "("+inj_loc+")") + " for injection")
-    click.echo("Using section " + colored.green(rec_sec_split + "("+rec_loc+")") + " for recording")
-    
-    #Window 1
-    window_index = ctg.add_window(title=title,width=800,height=650)
-    #Column 1
+
+    rec_sec_split = rec_sec.split(".")[-1]
+    inj_sec_split = inj_sec.split(".")[-1]
+
+    click.echo(
+        "Using section " + colored.green(inj_sec_split + "(" + inj_loc + ")") + " for injection"
+    )
+    click.echo(
+        "Using section " + colored.green(rec_sec_split + "(" + rec_loc + ")") + " for recording"
+    )
+
+    # Window 1
+    window_index = ctg.add_window(title=title, width=800, height=650)
+    # Column 1
     column_index = ctg.add_column(window_index)
-    fir_widget = FICurveWidget(template,i_increment=increment,i_start=min_pa,i_stop=max_pa,tstart=tstart,tdur=tdur,passive_delay=passive_delay,
-        record_sec=rec_sec_split, record_loc=rec_loc, inj_sec=inj_sec_split, inj_loc=inj_loc)
+    fir_widget = FICurveWidget(
+        template,
+        i_increment=increment,
+        i_start=min_pa,
+        i_stop=max_pa,
+        tstart=tstart,
+        tdur=tdur,
+        passive_delay=passive_delay,
+        record_sec=rec_sec_split,
+        record_loc=rec_loc,
+        inj_sec=inj_sec_split,
+        inj_loc=inj_loc,
+    )
 
-    
     plot_widget = PlotWidget(tstop=ctg.tstop)
-    plot_widget.add_expr(eval("fir_widget.passive_cell." + rec_sec_split + "("+ rec_loc+")._ref_v"),str(round(float(fir_widget.passive_amp),2)))
-    for cell,amp in zip(fir_widget.cells, fir_widget.amps):
-        plot_widget.add_expr(eval("cell." + rec_sec_split + "("+ rec_loc+")._ref_v"),str(round(float(amp),2)))
-
-    ctg.add_widget(window_index,column_index,fir_widget)
-    ctg.add_widget(window_index,column_index,plot_widget)
-
-    #Column 2
-    #column_index = ctg.add_column(window_index)
-    #control_widget = ControlMenuWidget()
-    #ctg.add_widget(window_index,column_index,control_widget)
-    
+    plot_widget.add_expr(
+        eval("fir_widget.passive_cell." + rec_sec_split + "(" + rec_loc + ")._ref_v"),
+        str(round(float(fir_widget.passive_amp), 2)),
+    )
+    for cell, amp in zip(fir_widget.cells, fir_widget.amps):
+        plot_widget.add_expr(
+            eval("cell." + rec_sec_split + "(" + rec_loc + ")._ref_v"), str(round(float(amp), 2))
+        )
+
+    ctg.add_widget(window_index, column_index, fir_widget)
+    ctg.add_widget(window_index, column_index, plot_widget)
+
+    # Column 2
+    # column_index = ctg.add_column(window_index)
+    # control_widget = ControlMenuWidget()
+    # ctg.add_widget(window_index,column_index,control_widget)
+
     text_widget = TextWidget()
     text_widget.set_to_fir_passive(fir_widget)
     ctg.add_widget(window_index, column_index, text_widget)
 
-    ctg.show(auto_run=True,on_complete=text_widget.update_fir_passive)
-
-#https://www.youtube.com/watch?v=MkzeOmkOUHM
-
-@cell.command('vhsegbuild', help="Alturki et al. (2016) V1/2 Automated Segregation Interface, simplify tuning by separating channel activation AUTO BUILD EXPERIMENT")
-@click.option('--title',type=click.STRING,default=None)
-@click.option('--tstop',type=click.INT,default=1150)
-@click.option('--outhoc',type=click.STRING,default="segmented_template.hoc",help="Specify the file you want the modified cell template written to")
-@click.option('--outfolder',type=click.STRING,default="./",help="Specify the directory you want the modified cell template and mod files written to (default: _seg)")
-@click.option('--outappend',type=click.BOOL,default=False,is_flag=True,help="Append out instead of overwriting (default: False)")
-#@click.option('--skipmod',type=click.BOOL,default=False,is_flag=True,help="Skip new mod file generation")
-@click.option('--debug',type=click.BOOL,default=False,is_flag=True,help="Print all debug statements")
-@click.option('--build',type=click.BOOL,default=False,is_flag=True,help="Build must be run before viewing GUI")
-@click.option('--fminpa',type=click.INT,default=0,help="Starting FIR Curve amps (default: 0)")
-@click.option('--fmaxpa',type=click.INT,default=1000,help="Ending FIR Curve amps (default: 1000)")
-@click.option('--fincrement',type=click.INT,default=100,help="Increment the FIR Curve amps by supplied pA (default: 100)")
-
+    ctg.show(auto_run=True, on_complete=text_widget.update_fir_passive)
+
+
+# https://www.youtube.com/watch?v=MkzeOmkOUHM
+
+
+@cell.command(
+    "vhsegbuild",
+    help="Alturki et al. (2016) V1/2 Automated Segregation Interface, simplify tuning by separating channel activation AUTO BUILD EXPERIMENT",
+)
+@click.option("--title", type=click.STRING, default=None)
+@click.option("--tstop", type=click.INT, default=1150)
+@click.option(
+    "--outhoc",
+    type=click.STRING,
+    default="segmented_template.hoc",
+    help="Specify the file you want the modified cell template written to",
+)
+@click.option(
+    "--outfolder",
+    type=click.STRING,
+    default="./",
+    help="Specify the directory you want the modified cell template and mod files written to (default: _seg)",
+)
+@click.option(
+    "--outappend",
+    type=click.BOOL,
+    default=False,
+    is_flag=True,
+    help="Append out instead of overwriting (default: False)",
+)
+# @click.option('--skipmod',type=click.BOOL,default=False,is_flag=True,help="Skip new mod file generation")
+@click.option(
+    "--debug", type=click.BOOL, default=False, is_flag=True, help="Print all debug statements"
+)
+@click.option(
+    "--build",
+    type=click.BOOL,
+    default=False,
+    is_flag=True,
+    help="Build must be run before viewing GUI",
+)
+@click.option("--fminpa", type=click.INT, default=0, help="Starting FIR Curve amps (default: 0)")
+@click.option(
+    "--fmaxpa", type=click.INT, default=1000, help="Ending FIR Curve amps (default: 1000)"
+)
+@click.option(
+    "--fincrement",
+    type=click.INT,
+    default=100,
+    help="Increment the FIR Curve amps by supplied pA (default: 100)",
+)
 @click.pass_context
-def cell_vhsegbuild(ctx,title,tstop,outhoc,outfolder,outappend,debug,build,fminpa,fmaxpa,fincrement):
+def cell_vhsegbuild(
+    ctx, title, tstop, outhoc, outfolder, outappend, debug, build, fminpa, fmaxpa, fincrement
+):
     click.echo(colored.red("EXPERIMENTAL - UNLIKELY TO WORK"))
     if not build:
         click.echo(colored.red("BE SURE TO RUN `vhseg --build` FOR YOUR CELL FIRST!"))
-    from .neuron.celltuner import CellTunerGUI, TextWidget, PlotWidget, ControlMenuWidget, SecMenuWidget, FICurveWidget,PointMenuWidget, MultiSecMenuWidget
-    from .neuron.celltuner import VoltagePlotWidget, SegregationSelectorWidget, SegregationPassiveWidget, SegregationFIRFitWidget, AutoVInitWidget
+    from .neuron.celltuner import (
+        AutoVInitWidget,
+        CellTunerGUI,
+        ControlMenuWidget,
+        FICurveWidget,
+        MultiSecMenuWidget,
+        PlotWidget,
+        PointMenuWidget,
+        SegregationFIRFitWidget,
+        SegregationPassiveWidget,
+        SegregationSelectorWidget,
+        TextWidget,
+        VoltagePlotWidget,
+    )
+
     hoc_folder = ctx.obj["hoc_folder"]
     mod_folder = ctx.obj["mod_folder"]
     hoc_template_file = ctx.obj["hoc_template_file"]
     template = ctx.obj["cell_template"]
 
     if build:
-        ctg = CellTunerGUI(hoc_folder,mod_folder,tstop=tstop,print_debug=debug)
+        ctg = CellTunerGUI(hoc_folder, mod_folder, tstop=tstop, print_debug=debug)
     else:
-        #template = template + "Seg" #Likely not the best way to do it
-        #slm = True if os.path.abspath("./"+outfolder) == os.path.abspath(mod_folder) else False
-        ctg = CellTunerGUI("./"+outfolder,"./"+outfolder,tstop=tstop,print_debug=debug)#,skip_load_mod=slm)
+        # template = template + "Seg" #Likely not the best way to do it
+        # slm = True if os.path.abspath("./"+outfolder) == os.path.abspath(mod_folder) else False
+        ctg = CellTunerGUI(
+            "./" + outfolder, "./" + outfolder, tstop=tstop, print_debug=debug
+        )  # ,skip_load_mod=slm)
         pass
-        #ctg.load_template(template,hoc_template_file=outhoc)
+        # ctg.load_template(template,hoc_template_file=outhoc)
 
-    
-    if build:  
+    if build:
         # Cell selector
         hoc_templates = ctg.get_templates(hoc_template_file=hoc_template_file)
         if not template:
-            template = questionary.select(
-            "Select a cell:",
-            choices=hoc_templates).ask()
+            template = questionary.select("Select a cell:", choices=hoc_templates).ask()
 
         ctg.load_template(template)
     else:
         # Cell selector
         hoc_templates = ctg.get_templates(hoc_template_file=outhoc)
         if not template:
-            template = questionary.select(
-            "Select a cell:",
-            choices=hoc_templates).ask()
-        
-        ctg.load_template(template,hoc_template_file=outhoc)
-   
+            template = questionary.select("Select a cell:", choices=hoc_templates).ask()
+
+        ctg.load_template(template, hoc_template_file=outhoc)
+
     if not title:
-        title = template + " - V1/2 Segregation - Interface generated by BMTool (https://github.com/tjbanks/bmtool)"
-    #import pdb;pdb.set_trace()
+        title = (
+            template
+            + " - V1/2 Segregation - Interface generated by BMTool (https://github.com/tjbanks/bmtool)"
+        )
+    # import pdb;pdb.set_trace()
     sec = ctg.root_sec.hname()
-    sec_split = sec.split('.')[-1]
+    sec_split = sec.split(".")[-1]
     click.echo("Using section " + colored.green(sec_split))
-    
+
     if build:
         # Carry out the segregation method
-        fpath = os.path.abspath('./'+outfolder)
+        fpath = os.path.abspath("./" + outfolder)
         if not os.path.exists(fpath):
             try:
                 os.mkdir(fpath)
@@ -815,19 +1104,20 @@ def cell_vhsegbuild(ctx,title,tstop,outhoc,outfolder,outappend,debug,build,fminp
                 print("Creation of the directory %s failed" % fpath)
 
         mechs_processed = ctg.seg_mechs(folder=fpath)
-        template = ctg.seg_template(os.path.join(fpath,outhoc),mechs_processed)
+        template = ctg.seg_template(os.path.join(fpath, outhoc), mechs_processed)
         click.echo(colored.green("COMPILING MOD FILES"))
 
         cwd = os.getcwd()
 
-        if os.path.abspath(mod_folder) != cwd: #The mod files will get loaded already
-            import glob, shutil
+        if os.path.abspath(mod_folder) != cwd:  # The mod files will get loaded already
+            import glob
+            import shutil
 
             files = glob.iglob(os.path.join(mod_folder, "*.mod"))
             for file in files:
                 if os.path.isfile(file):
                     shutil.copy2(file, fpath)
-                
+
         os.chdir(fpath)
         ret = os.system("nrnivmodl")
         os.chdir(cwd)
@@ -835,31 +1125,35 @@ def cell_vhsegbuild(ctx,title,tstop,outhoc,outfolder,outappend,debug,build,fminp
         if not ret:
             click.echo(colored.green("COMPILATION COMPLETE"))
         else:
-            click.echo(colored.red("nrnivmodl may not have been run, execute nrnivmodl or mknrndll manually in the `")+colored.green(fpath)+colored.red("` folder then press enter..."))
+            click.echo(
+                colored.red(
+                    "nrnivmodl may not have been run, execute nrnivmodl or mknrndll manually in the `"
+                )
+                + colored.green(fpath)
+                + colored.red("` folder then press enter...")
+            )
             input()
             click.echo(colored.green("Done... remove the `--build` flag and re-run."))
         return
     else:
-        #template = template + "Seg" #Likely not the best way to do it
-        #slm = True if os.path.abspath("./"+outfolder) == os.path.abspath(mod_folder) else False
-        #ctg = CellTunerGUI("./"+outfolder,"./"+outfolder,tstop=tstop,print_debug=debug,skip_load_mod=slm)
+        # template = template + "Seg" #Likely not the best way to do it
+        # slm = True if os.path.abspath("./"+outfolder) == os.path.abspath(mod_folder) else False
+        # ctg = CellTunerGUI("./"+outfolder,"./"+outfolder,tstop=tstop,print_debug=debug,skip_load_mod=slm)
         pass
-        #ctg.load_template(template,hoc_template_file=outhoc)
+        # ctg.load_template(template,hoc_template_file=outhoc)
 
     do_others = False
     if ctg.other_sec:
-        do_others = questionary.confirm("Show other sections? (default: No)",default=False).ask()
+        do_others = questionary.confirm("Show other sections? (default: No)", default=False).ask()
     selected_segments = []
     if do_others:
-        choices = [s.name().split('.')[-1] for s in ctg.other_sec]
+        choices = [s.name().split(".")[-1] for s in ctg.other_sec]
         selected_segments = questionary.checkbox(
-            'Select other sections (space bar to select):',
-            choices=choices).ask()
-        
-    
+            "Select other sections (space bar to select):", choices=choices
+        ).ask()
 
     section_selected = "soma"
-    #FIR Properties
+    # FIR Properties
     min_pa = fminpa
     max_pa = fmaxpa
     increment = fincrement
@@ -867,13 +1161,15 @@ def cell_vhsegbuild(ctx,title,tstop,outhoc,outfolder,outappend,debug,build,fminp
     tdur = 1000
     inj_sec = ctg.root_sec.hname()
     rec_sec = ctg.root_sec.hname()
-    inj_loc = "0.5"    
+    inj_loc = "0.5"
     rec_loc = "0.5"
-    rec_sec_split = rec_sec.split('.')[-1]
-    inj_sec_split = inj_sec.split('.')[-1]
+    rec_sec_split = rec_sec.split(".")[-1]
+    inj_sec_split = inj_sec.split(".")[-1]
 
-    if tstop < tstart+tdur:
-        print("tstop must be greater than " + str(tstart+tdur) + " due to FIR injection properties")
+    if tstop < tstart + tdur:
+        print(
+            "tstop must be greater than " + str(tstart + tdur) + " due to FIR injection properties"
+        )
         print("Exiting")
         return
     # Current Clamp properties
@@ -881,8 +1177,18 @@ def cell_vhsegbuild(ctx,title,tstop,outhoc,outfolder,outappend,debug,build,fminp
     dur = 1000
     amp = 0.2
 
-    fir_widget = FICurveWidget(template,i_increment=increment,i_start=min_pa,i_stop=max_pa,tstart=tstart,tdur=tdur,
-        record_sec=rec_sec_split, record_loc=rec_loc, inj_sec=inj_sec_split, inj_loc=inj_loc)
+    fir_widget = FICurveWidget(
+        template,
+        i_increment=increment,
+        i_start=min_pa,
+        i_stop=max_pa,
+        tstart=tstart,
+        tdur=tdur,
+        record_sec=rec_sec_split,
+        record_loc=rec_loc,
+        inj_sec=inj_sec_split,
+        inj_loc=inj_loc,
+    )
     other_cells = fir_widget.cells + [fir_widget.passive_cell]
 
     for segment in selected_segments:
@@ -890,116 +1196,198 @@ def cell_vhsegbuild(ctx,title,tstop,outhoc,outfolder,outappend,debug,build,fminp
         # Column 1
         column_index = ctg.add_column(window_index)
         plot_widget = PlotWidget(tstop=tstop)
-        sec_text = segment+"(.5)"
-        cellsec = eval('ctg.template.'+section_selected)
-        plot_widget.add_expr(cellsec(0.5)._ref_v,sec_text)
+        sec_text = segment + "(.5)"
+        cellsec = eval("ctg.template." + section_selected)
+        plot_widget.add_expr(cellsec(0.5)._ref_v, sec_text)
 
-        ctg.add_widget(window_index,column_index,plot_widget)
+        ctg.add_widget(window_index, column_index, plot_widget)
 
         widget = ControlMenuWidget()
-        ctg.add_widget(window_index,column_index,widget)
+        ctg.add_widget(window_index, column_index, widget)
 
         # Column 2
         column_index = ctg.add_column(window_index)
-        widget = MultiSecMenuWidget(ctg.root_sec.cell(), other_cells,segment,ctg.mechanism_dict)
-        ctg.add_widget(window_index,column_index,widget)
-    
+        widget = MultiSecMenuWidget(ctg.root_sec.cell(), other_cells, segment, ctg.mechanism_dict)
+        ctg.add_widget(window_index, column_index, widget)
 
-    #Window 1
+    # Window 1
     window_index = ctg.add_window(title=title)
 
-    #Column 1
+    # Column 1
     column_index = ctg.add_column(window_index)
 
     plot_widget = PlotWidget(tstop=tstop)
-    sec_text = ctg.root_sec.hname().split('.')[-1]+"(.5)"
-
-    plot_widget.add_expr(ctg.root_sec(0.5)._ref_v,sec_text)
-    plot_widget.add_expr(eval("fir_widget.passive_cell." + rec_sec_split + "("+ rec_loc+")._ref_v"),"Passive @"+str(int(fir_widget.passive_amp*1e3))+"pA")
-    ctg.add_widget(window_index,column_index,plot_widget)
+    sec_text = ctg.root_sec.hname().split(".")[-1] + "(.5)"
 
-    ctg.add_widget(window_index,column_index,fir_widget)
+    plot_widget.add_expr(ctg.root_sec(0.5)._ref_v, sec_text)
+    plot_widget.add_expr(
+        eval("fir_widget.passive_cell." + rec_sec_split + "(" + rec_loc + ")._ref_v"),
+        "Passive @" + str(int(fir_widget.passive_amp * 1e3)) + "pA",
+    )
+    ctg.add_widget(window_index, column_index, plot_widget)
 
-    
+    ctg.add_widget(window_index, column_index, fir_widget)
 
-    plot_widget = VoltagePlotWidget(ctg.root_sec.cell(),section="soma")
+    plot_widget = VoltagePlotWidget(ctg.root_sec.cell(), section="soma")
     plot_widget.add_act_inf(ctg.mechanism_dict)
-    ctg.add_widget(window_index,column_index,plot_widget)
-    
+    ctg.add_widget(window_index, column_index, plot_widget)
 
-    #Column 2
+    # Column 2
     column_index = ctg.add_column(window_index)
-    
-    #import pdb;pdb.set_trace()
-    widget = MultiSecMenuWidget(ctg.root_sec.cell(), other_cells,section_selected,ctg.mechanism_dict)
 
-    #for cell,amp in zip(fir_widget.cells, fir_widget.amps):
-        #plot_widget.add_expr(eval("cell." + rec_sec_split + "("+ rec_loc+")._ref_v"),str(round(float(amp),2)))
-    widget_index = ctg.add_widget(window_index, column_index,widget) 
-    #widget = SecMenuWidget(ctg.root_sec,x=float(inj_loc))
-    #widget_index = ctg.add_widget(window_index, column_index,widget) 
+    # import pdb;pdb.set_trace()
+    widget = MultiSecMenuWidget(
+        ctg.root_sec.cell(), other_cells, section_selected, ctg.mechanism_dict
+    )
 
-    #Column 3
+    # for cell,amp in zip(fir_widget.cells, fir_widget.amps):
+    # plot_widget.add_expr(eval("cell." + rec_sec_split + "("+ rec_loc+")._ref_v"),str(round(float(amp),2)))
+    widget_index = ctg.add_widget(window_index, column_index, widget)
+    # widget = SecMenuWidget(ctg.root_sec,x=float(inj_loc))
+    # widget_index = ctg.add_widget(window_index, column_index,widget)
+
+    # Column 3
     column_index = ctg.add_column(window_index)
     widget = ControlMenuWidget()
-    ctg.add_widget(window_index,column_index,widget)
-              
+    ctg.add_widget(window_index, column_index, widget)
 
     widget = PointMenuWidget(None)
-    iclamp = widget.iclamp(ctg.root_sec(float(inj_loc)),dur,amp,delay)
+    iclamp = widget.iclamp(ctg.root_sec(float(inj_loc)), dur, amp, delay)
     ctg.register_iclamp(iclamp)
-    widget_index = ctg.add_widget(window_index, column_index,widget)
+    widget_index = ctg.add_widget(window_index, column_index, widget)
 
     text_widget = TextWidget()
-    text_widget.set_to_fir_passive(fir_widget,print_calc=False,print_fi=False)
-    widget_index = ctg.add_widget(window_index, column_index,text_widget)
+    text_widget.set_to_fir_passive(fir_widget, print_calc=False, print_fi=False)
+    widget_index = ctg.add_widget(window_index, column_index, text_widget)
 
     vinit_widget = AutoVInitWidget(fir_widget)
-    widget_index = ctg.add_widget(window_index, column_index,vinit_widget)
+    widget_index = ctg.add_widget(window_index, column_index, vinit_widget)
 
-    #Column 4
+    # Column 4
     column_index = ctg.add_column(window_index)
-    
-    widget = SegregationSelectorWidget(ctg.root_sec.cell(), other_cells,section_selected,ctg.mechanism_dict,all_sec=True)
-    ctg.add_widget(window_index,column_index,widget)
 
-    widget = SegregationPassiveWidget(fir_widget,ctg.root_sec.cell(), other_cells,section_selected,ctg.mechanism_dict)
-    ctg.add_widget(window_index,column_index,widget)
+    widget = SegregationSelectorWidget(
+        ctg.root_sec.cell(), other_cells, section_selected, ctg.mechanism_dict, all_sec=True
+    )
+    ctg.add_widget(window_index, column_index, widget)
+
+    widget = SegregationPassiveWidget(
+        fir_widget, ctg.root_sec.cell(), other_cells, section_selected, ctg.mechanism_dict
+    )
+    ctg.add_widget(window_index, column_index, widget)
 
     widget = SegregationFIRFitWidget(fir_widget)
-    ctg.add_widget(window_index,column_index,widget)
+    ctg.add_widget(window_index, column_index, widget)
 
-    ctg.show(auto_run=True,on_complete_fih=text_widget.update_fir_passive,run_count=2)
+    ctg.show(auto_run=True, on_complete_fih=text_widget.update_fir_passive, run_count=2)
 
     return
 
-@cell.command('vhseg', help="Alturki et al. (2016) V1/2 Automated Segregation Interface, simplify tuning by separating channel activation")
-@click.option('--title',type=click.STRING,default=None)
-@click.option('--tstop',type=click.INT,default=1150)
-#@click.option('--outhoc',type=click.STRING,default="segmented_template.hoc",help="Specify the file you want the modified cell template written to")
-#@click.option('--outfolder',type=click.STRING,default="./",help="Specify the directory you want the modified cell template and mod files written to (default: _seg)")
-#@click.option('--outappend',type=click.BOOL,default=False,is_flag=True,help="Append out instead of overwriting (default: False)")
-#@click.option('--skipmod',type=click.BOOL,default=False,is_flag=True,help="Skip new mod file generation")
-@click.option('--debug',type=click.BOOL,default=False,is_flag=True,help="Print all debug statements")
-@click.option('--fminpa',type=click.INT,default=0,help="Starting FI Curve amps (default: 0)")
-@click.option('--fmaxpa',type=click.INT,default=1000,help="Ending FI Curve amps (default: 1000)")
-@click.option('--passive-delay',type=click.INT,default=650,help="Wait n ms before determining steadystate value (default: 650)")
-@click.option('--fincrement',type=click.INT,default=100,help="Increment the FIR Curve amps by supplied pA (default: 100)")
-@click.option('--infvars',type=click.STRING,default=None,help="Specify the inf variables to plot, skips the wizard. (Comma separated, eg: inf_mech,minf_mech2,ninf_mech2)")
-@click.option('--segvars',type=click.STRING,default=None,help="Specify the segregation variables to globally set, skips the wizard. (Comma separated, eg: mseg_mech,nseg_mech2)")
-@click.option('--eleak',type=click.STRING,default=None,help="Specify the eleak var manually")
-@click.option('--gleak',type=click.STRING,default=None,help="Specify the gleak var manually")
-@click.option('--othersec',type=click.STRING,default=None,help="Specify other sections that a window should be generated for (Comma separated, eg: dend[0],dend[1])")
-@click.option('--clampsec',type=click.STRING,default=None,help="Specify sections that a current clamp should be attached. Root section will always have a clamp. (Comma separated, eg: dend[0],dend[1])")
-@click.option('--synsec',type=click.STRING,default=None,help="Specify sections that a synapse should be attached. Exp2Syn default, unless --syntype specified. (Comma separated, eg: dend[0],dend[1])")
-@click.option('--syntype',type=click.STRING,default="Exp2Syn",help="Specify the synapse mechanism that will be attached to the cell (Single type)")
-@click.option('--synloc',type=click.STRING,default="0.5",help="Specify the synapse location (Default: 0.5)")
+
+@cell.command(
+    "vhseg",
+    help="Alturki et al. (2016) V1/2 Automated Segregation Interface, simplify tuning by separating channel activation",
+)
+@click.option("--title", type=click.STRING, default=None)
+@click.option("--tstop", type=click.INT, default=1150)
+# @click.option('--outhoc',type=click.STRING,default="segmented_template.hoc",help="Specify the file you want the modified cell template written to")
+# @click.option('--outfolder',type=click.STRING,default="./",help="Specify the directory you want the modified cell template and mod files written to (default: _seg)")
+# @click.option('--outappend',type=click.BOOL,default=False,is_flag=True,help="Append out instead of overwriting (default: False)")
+# @click.option('--skipmod',type=click.BOOL,default=False,is_flag=True,help="Skip new mod file generation")
+@click.option(
+    "--debug", type=click.BOOL, default=False, is_flag=True, help="Print all debug statements"
+)
+@click.option("--fminpa", type=click.INT, default=0, help="Starting FI Curve amps (default: 0)")
+@click.option("--fmaxpa", type=click.INT, default=1000, help="Ending FI Curve amps (default: 1000)")
+@click.option(
+    "--passive-delay",
+    type=click.INT,
+    default=650,
+    help="Wait n ms before determining steadystate value (default: 650)",
+)
+@click.option(
+    "--fincrement",
+    type=click.INT,
+    default=100,
+    help="Increment the FIR Curve amps by supplied pA (default: 100)",
+)
+@click.option(
+    "--infvars",
+    type=click.STRING,
+    default=None,
+    help="Specify the inf variables to plot, skips the wizard. (Comma separated, eg: inf_mech,minf_mech2,ninf_mech2)",
+)
+@click.option(
+    "--segvars",
+    type=click.STRING,
+    default=None,
+    help="Specify the segregation variables to globally set, skips the wizard. (Comma separated, eg: mseg_mech,nseg_mech2)",
+)
+@click.option("--eleak", type=click.STRING, default=None, help="Specify the eleak var manually")
+@click.option("--gleak", type=click.STRING, default=None, help="Specify the gleak var manually")
+@click.option(
+    "--othersec",
+    type=click.STRING,
+    default=None,
+    help="Specify other sections that a window should be generated for (Comma separated, eg: dend[0],dend[1])",
+)
+@click.option(
+    "--clampsec",
+    type=click.STRING,
+    default=None,
+    help="Specify sections that a current clamp should be attached. Root section will always have a clamp. (Comma separated, eg: dend[0],dend[1])",
+)
+@click.option(
+    "--synsec",
+    type=click.STRING,
+    default=None,
+    help="Specify sections that a synapse should be attached. Exp2Syn default, unless --syntype specified. (Comma separated, eg: dend[0],dend[1])",
+)
+@click.option(
+    "--syntype",
+    type=click.STRING,
+    default="Exp2Syn",
+    help="Specify the synapse mechanism that will be attached to the cell (Single type)",
+)
+@click.option(
+    "--synloc", type=click.STRING, default="0.5", help="Specify the synapse location (Default: 0.5)"
+)
 @click.pass_context
-def cell_vhseg(ctx,title,tstop,debug,fminpa,fmaxpa,passive_delay,fincrement,infvars,segvars,eleak,gleak,othersec,clampsec,synsec,syntype,synloc):
-    
-    from .neuron.celltuner import CellTunerGUI, TextWidget, PlotWidget, ControlMenuWidget, SecMenuWidget, FICurveWidget,PointMenuWidget, MultiSecMenuWidget
-    from .neuron.celltuner import VoltagePlotWidget, SegregationSelectorWidget, SegregationPassiveWidget, SegregationFIRFitWidget, AutoVInitWidget, SingleButtonWidget
-    from .util import tk_email_input, send_mail, popupmsg
+def cell_vhseg(
+    ctx,
+    title,
+    tstop,
+    debug,
+    fminpa,
+    fmaxpa,
+    passive_delay,
+    fincrement,
+    infvars,
+    segvars,
+    eleak,
+    gleak,
+    othersec,
+    clampsec,
+    synsec,
+    syntype,
+    synloc,
+):
+    from .neuron.celltuner import (
+        AutoVInitWidget,
+        CellTunerGUI,
+        ControlMenuWidget,
+        FICurveWidget,
+        MultiSecMenuWidget,
+        PlotWidget,
+        PointMenuWidget,
+        SegregationFIRFitWidget,
+        SegregationPassiveWidget,
+        SegregationSelectorWidget,
+        SingleButtonWidget,
+        TextWidget,
+        VoltagePlotWidget,
+    )
+    from .util import popupmsg, send_mail, tk_email_input
 
     hoc_folder = ctx.obj["hoc_folder"]
     mod_folder = ctx.obj["mod_folder"]
@@ -1007,31 +1395,35 @@ def cell_vhseg(ctx,title,tstop,debug,fminpa,fmaxpa,passive_delay,fincrement,infv
     template = ctx.obj["cell_template"]
     prefab_dict = ctx.obj["prefab"]
     prefab_dictvh = None
-    
-    ctg = CellTunerGUI(hoc_folder,mod_folder,tstop=tstop,print_debug=debug)
-    
-    
+
+    ctg = CellTunerGUI(hoc_folder, mod_folder, tstop=tstop, print_debug=debug)
+
     # Cell selector
     hoc_templates = ctg.get_templates(hoc_template_file=hoc_template_file)
     if not template:
-        template = questionary.select(
-        "Select a cell:",
-        choices=hoc_templates).ask()
-    
+        template = questionary.select("Select a cell:", choices=hoc_templates).ask()
+
     ctg.load_template(template)
 
     original_cell_values = ctg.get_current_cell_values()
 
-    if prefab_dict and prefab_dict.get("cells") and prefab_dict["cells"].get(template) and prefab_dict["cells"][template].get("vhseg"):
+    if (
+        prefab_dict
+        and prefab_dict.get("cells")
+        and prefab_dict["cells"].get(template)
+        and prefab_dict["cells"][template].get("vhseg")
+    ):
         prefab_dictvh = prefab_dict["cells"][template]["vhseg"]
 
     if not title:
-        title = template + " - V1/2 - Interface generated by BMTool (https://github.com/tjbanks/bmtool)"
-    #import pdb;pdb.set_trace()
+        title = (
+            template + " - V1/2 - Interface generated by BMTool (https://github.com/tjbanks/bmtool)"
+        )
+    # import pdb;pdb.set_trace()
     sec = ctg.root_sec.hname()
-    sec_split = sec.split('.')[-1]
+    sec_split = sec.split(".")[-1]
     click.echo("Using section " + colored.green(sec_split))
-    
+
     selected_segments = []
 
     if prefab_dictvh and prefab_dictvh.get("othersec"):
@@ -1040,104 +1432,101 @@ def cell_vhseg(ctx,title,tstop,debug,fminpa,fmaxpa,passive_delay,fincrement,infv
     else:
         do_others = False
         if ctg.other_sec:
-
             if othersec:
                 do_others = True
             else:
-                do_others = questionary.confirm("Show other sections? (default: No)",default=False).ask()
+                do_others = questionary.confirm(
+                    "Show other sections? (default: No)", default=False
+                ).ask()
 
-        
         if do_others:
             if othersec:
                 selected_segments = othersec.split(",")
             else:
-                choices = [s.name().split('.')[-1] for s in ctg.other_sec]
+                choices = [s.name().split(".")[-1] for s in ctg.other_sec]
                 selected_segments = questionary.checkbox(
-                    'Select other sections (space bar to select):',
-                    choices=choices).ask()
-        
+                    "Select other sections (space bar to select):", choices=choices
+                ).ask()
+
     section_selected = sec_split
-    
-    #cellsec = getattr(ctg.template,section_selected)
-    cellsec = eval('ctg.template.'+section_selected)
+
+    # cellsec = getattr(ctg.template,section_selected)
+    cellsec = eval("ctg.template." + section_selected)
 
     mechs = [mech.name() for mech in cellsec(0.5) if not mech.name().endswith("_ion")]
     ions = [mech.name() for mech in cellsec(0.5) if mech.name().endswith("_ion")]
     cellmechvars = []
-    
+
     for mech in mechs:
-        if hasattr(cellsec(0.5),mech):
-            mechobj = getattr(cellsec(0.5),mech)
+        if hasattr(cellsec(0.5), mech):
+            mechobj = getattr(cellsec(0.5), mech)
         else:
             print(mech + " not found on " + cellsec.name())
             continue
-        
-        attribs = [at for at in dir(mechobj) if not at.startswith("__") and at !="name"]
+
+        attribs = [at for at in dir(mechobj) if not at.startswith("__") and at != "name"]
         for attrib in attribs:
-            ref = attrib+"_"+mech
-            if hasattr(cellsec(0.5),ref):
+            ref = attrib + "_" + mech
+            if hasattr(cellsec(0.5), ref):
                 cellmechvars.append(ref)
 
     for ion in ions:
-        if hasattr(cellsec(0.5),ion):
-            ionobj = getattr(cellsec(0.5),ion)
+        if hasattr(cellsec(0.5), ion):
+            ionobj = getattr(cellsec(0.5), ion)
         else:
             print(ion + " not found on " + cellsec.name())
             continue
-        attribs = [at for at in dir(ionobj) if not at.startswith("__") and at !="name"]
+        attribs = [at for at in dir(ionobj) if not at.startswith("__") and at != "name"]
         for attrib in attribs:
             ref = attrib
-            if hasattr(cellsec(0.5),ref):
+            if hasattr(cellsec(0.5), ref):
                 cellmechvars.append(ref)
 
-    #Puts the best matches at the top
-    inf_choices = [s for s in cellmechvars if "inf" in s.lower()] + [s for s in cellmechvars if not "inf" in s.lower()]
-    seg_choices = [s for s in cellmechvars if "seg" in s.lower()] + [s for s in cellmechvars if not "seg" in s.lower()]
+    # Puts the best matches at the top
+    inf_choices = [s for s in cellmechvars if "inf" in s.lower()] + [
+        s for s in cellmechvars if "inf" not in s.lower()
+    ]
+    seg_choices = [s for s in cellmechvars if "seg" in s.lower()] + [
+        s for s in cellmechvars if "seg" not in s.lower()
+    ]
     from neuron import h
+
     globalvars = dir(h)
     list_global_text = "** More ** (Shows unselected global [MANY]) (current selection retained)"
-    
+
     if prefab_dictvh and prefab_dictvh.get("infvars"):
         infvars = prefab_dictvh["infvars"]
-        
+
     else:
         if infvars:
             infvars = infvars.split(",")
         else:
-            question_text = 'Select inf variables to plot (with respect to membrane potential) (space bar to select): '
+            question_text = "Select inf variables to plot (with respect to membrane potential) (space bar to select): "
             inf_choices = inf_choices + [list_global_text]
-            infvars = questionary.checkbox(
-                question_text,
-                choices=inf_choices).ask()
+            infvars = questionary.checkbox(question_text, choices=inf_choices).ask()
             if list_global_text in infvars:
                 infvars.remove(list_global_text)
-                global_choices =  [c for c in globalvars if c not in infvars]
-                globalinfvars = questionary.checkbox(
-                question_text,
-                choices=global_choices).ask()
+                global_choices = [c for c in globalvars if c not in infvars]
+                globalinfvars = questionary.checkbox(question_text, choices=global_choices).ask()
                 infvars = infvars + globalinfvars
 
     if prefab_dictvh and prefab_dictvh.get("segvars"):
         segvars = prefab_dictvh["segvars"]
-        
+
     else:
         if segvars:
             segvars = segvars.split(",")
         else:
-            question_text = 'Select segregation variables [OR VARIABLES YOU WANT TO CHANGE ON ALL SEGMENTS at the same time] (space bar to select):'
+            question_text = "Select segregation variables [OR VARIABLES YOU WANT TO CHANGE ON ALL SEGMENTS at the same time] (space bar to select):"
             seg_choices = seg_choices + [list_global_text]
-            segvars = questionary.checkbox(
-                question_text,
-                choices=seg_choices).ask()
+            segvars = questionary.checkbox(question_text, choices=seg_choices).ask()
             if list_global_text in segvars:
                 segvars.remove(list_global_text)
-                global_choices =  [c for c in globalvars if c not in segvars]
-                globalsegvars = questionary.checkbox(
-                question_text,
-                choices=global_choices).ask()
+                global_choices = [c for c in globalvars if c not in segvars]
+                globalsegvars = questionary.checkbox(question_text, choices=global_choices).ask()
                 segvars = segvars + globalsegvars
 
-    #clampsec,synsec,syntype
+    # clampsec,synsec,syntype
     clampme = []
     synme = []
     if selected_segments:
@@ -1145,12 +1534,18 @@ def cell_vhseg(ctx,title,tstop,debug,fminpa,fmaxpa,passive_delay,fincrement,infv
             clampme = prefab_dictvh["clampsec"]
         else:
             if not clampsec:
-                do_clamps = questionary.confirm("Attach a current clamp to other section? (root section ["+section_selected+"] automatically attached) (default: No)",default=False).ask()        
+                do_clamps = questionary.confirm(
+                    "Attach a current clamp to other section? (root section ["
+                    + section_selected
+                    + "] automatically attached) (default: No)",
+                    default=False,
+                ).ask()
 
                 if do_clamps:
                     clampme = questionary.checkbox(
-                    'Select other sections to attach a current clamp to (space bar to select):',
-                    choices=selected_segments).ask()
+                        "Select other sections to attach a current clamp to (space bar to select):",
+                        choices=selected_segments,
+                    ).ask()
             else:
                 clampme = clampsec.split(",")
 
@@ -1158,15 +1553,21 @@ def cell_vhseg(ctx,title,tstop,debug,fminpa,fmaxpa,passive_delay,fincrement,infv
             clampme = prefab_dictvh["synsec"]
         else:
             if not synsec:
-                do_syns = questionary.confirm("Attach a synapse to other section? (root section ["+section_selected+"] automatically attached) (default: No)",default=False).ask()        
+                do_syns = questionary.confirm(
+                    "Attach a synapse to other section? (root section ["
+                    + section_selected
+                    + "] automatically attached) (default: No)",
+                    default=False,
+                ).ask()
 
                 if do_syns:
                     synme = questionary.checkbox(
-                    'Select sections to attach an artifical synapse (space bar to select):',
-                    choices=selected_segments).ask()
+                        "Select sections to attach an artifical synapse (space bar to select):",
+                        choices=selected_segments,
+                    ).ask()
             else:
                 synme = synsec.split(",")
-        
+
     if prefab_dictvh and prefab_dictvh.get("eleak"):
         eleak = prefab_dictvh["eleak"]
 
@@ -1178,8 +1579,8 @@ def cell_vhseg(ctx,title,tstop,debug,fminpa,fmaxpa,passive_delay,fincrement,infv
 
     if prefab_dictvh and prefab_dictvh.get("synloc"):
         synloc = prefab_dictvh["synloc"]
-    
-    #FIR Properties
+
+    # FIR Properties
     min_pa = fminpa
     max_pa = fmaxpa
     increment = fincrement
@@ -1187,13 +1588,15 @@ def cell_vhseg(ctx,title,tstop,debug,fminpa,fmaxpa,passive_delay,fincrement,infv
     tdur = 1000
     inj_sec = ctg.root_sec.hname()
     rec_sec = ctg.root_sec.hname()
-    inj_loc = "0.5"    
+    inj_loc = "0.5"
     rec_loc = "0.5"
-    rec_sec_split = rec_sec.split('.')[-1]
-    inj_sec_split = inj_sec.split('.')[-1]
+    rec_sec_split = rec_sec.split(".")[-1]
+    inj_sec_split = inj_sec.split(".")[-1]
 
-    if tstop < tstart+tdur:
-        print("tstop must be greater than " + str(tstart+tdur) + " due to FIR injection properties")
+    if tstop < tstart + tdur:
+        print(
+            "tstop must be greater than " + str(tstart + tdur) + " due to FIR injection properties"
+        )
         print("Exiting")
         return
     # Current Clamp properties
@@ -1201,8 +1604,19 @@ def cell_vhseg(ctx,title,tstop,debug,fminpa,fmaxpa,passive_delay,fincrement,infv
     dur = 1000
     amp = 0.2
 
-    fir_widget = FICurveWidget(template,i_increment=increment,i_start=min_pa,i_stop=max_pa,tstart=tstart,tdur=tdur,passive_delay=passive_delay,
-        record_sec=rec_sec_split, record_loc=rec_loc, inj_sec=inj_sec_split, inj_loc=inj_loc)
+    fir_widget = FICurveWidget(
+        template,
+        i_increment=increment,
+        i_start=min_pa,
+        i_stop=max_pa,
+        tstart=tstart,
+        tdur=tdur,
+        passive_delay=passive_delay,
+        record_sec=rec_sec_split,
+        record_loc=rec_loc,
+        inj_sec=inj_sec_split,
+        inj_loc=inj_loc,
+    )
     other_cells = fir_widget.cells + [fir_widget.passive_cell]
 
     for segment in selected_segments:
@@ -1213,90 +1627,104 @@ def cell_vhseg(ctx,title,tstop,debug,fminpa,fmaxpa,passive_delay,fincrement,infv
         # Column 1
         column_index = ctg.add_column(window_index)
         plot_widget = PlotWidget(tstop=tstop)
-        sec_text = segment+"(.5)"
-        cellsec = eval('ctg.template.'+segment)
-        plot_widget.add_expr(cellsec(0.5)._ref_v,sec_text,hoc_text="%s."+segment+".v(0.5)",hoc_text_obj=ctg.template)
+        sec_text = segment + "(.5)"
+        cellsec = eval("ctg.template." + segment)
+        plot_widget.add_expr(
+            cellsec(0.5)._ref_v,
+            sec_text,
+            hoc_text="%s." + segment + ".v(0.5)",
+            hoc_text_obj=ctg.template,
+        )
 
-        ctg.add_widget(window_index,column_index,plot_widget)
+        ctg.add_widget(window_index, column_index, plot_widget)
 
         if segment in clampme:
             widget = PointMenuWidget(None)
-            iclamp = widget.iclamp(cellsec(float(inj_loc)),0,0,0)
+            iclamp = widget.iclamp(cellsec(float(inj_loc)), 0, 0, 0)
             ctg.register_iclamp(iclamp)
-            widget_index = ctg.add_widget(window_index, column_index,widget)
-            
-        
+            widget_index = ctg.add_widget(window_index, column_index, widget)
+
         widget = ControlMenuWidget()
-        ctg.add_widget(window_index,column_index,widget)
+        ctg.add_widget(window_index, column_index, widget)
 
         # Column 2
         column_index = ctg.add_column(window_index)
-        widget = MultiSecMenuWidget(ctg.root_sec.cell(), other_cells,segment,ctg.mechanism_dict)
-        ctg.add_widget(window_index,column_index,widget)
+        widget = MultiSecMenuWidget(ctg.root_sec.cell(), other_cells, segment, ctg.mechanism_dict)
+        ctg.add_widget(window_index, column_index, widget)
 
         if segment in synme:
             column_index = ctg.add_column(window_index)
 
-            interval = 50 #int(questionary.text("Enter default netstim interval (ms (mean) time between spikes): ",default="50").ask())
-            number = 0 #int(questionary.text("Enter default netstim number of events ((average) number of spikes): ",default="10").ask())
-            start = 0 #int(questionary.text("Enter default netstim start (ms (most likely) start time of first spike): ",default="0").ask())
-            noise = 0 #float(questionary.text("Enter default netstim noise (range 0 to 1. Fractional randomness.): ",default="0").ask())
-            weight = 1 #float(questionary.text("Enter default netcon weight (range 0 to 1. Default: 1): ",default="1").ask())
-            
+            interval = 50  # int(questionary.text("Enter default netstim interval (ms (mean) time between spikes): ",default="50").ask())
+            number = 0  # int(questionary.text("Enter default netstim number of events ((average) number of spikes): ",default="10").ask())
+            start = 0  # int(questionary.text("Enter default netstim start (ms (most likely) start time of first spike): ",default="0").ask())
+            noise = 0  # float(questionary.text("Enter default netstim noise (range 0 to 1. Fractional randomness.): ",default="0").ask())
+            weight = 1  # float(questionary.text("Enter default netcon weight (range 0 to 1. Default: 1): ",default="1").ask())
+
             widget = PointMenuWidget(None)
             widget_extra = PointMenuWidget(None)
-            synapse = widget_extra.synapse(eval("ctg.template."+segment),synloc,syntype)
-            netstim,netcon = widget.netstim(interval,number,start,noise,target=synapse,weight=weight)
+            synapse = widget_extra.synapse(eval("ctg.template." + segment), synloc, syntype)
+            netstim, netcon = widget.netstim(
+                interval, number, start, noise, target=synapse, weight=weight
+            )
             ctg.register_netstim(netstim)
             ctg.register_netcon(netcon)
             ctg.register_synapse(synapse)
 
             widget_index_extra = ctg.add_widget(window_index, column_index, widget_extra)
             widget_index = ctg.add_widget(window_index, column_index, widget)
-    
 
-    #Window 1
+    # Window 1
     window_index = ctg.add_window(title=title)
 
-    #Column 1
+    # Column 1
     column_index = ctg.add_column(window_index)
 
     plot_widget = PlotWidget(tstop=tstop)
-    sec_text = ctg.root_sec.hname().split('.')[-1]+"(.5)"
+    sec_text = ctg.root_sec.hname().split(".")[-1] + "(.5)"
+
+    plot_widget.add_expr(
+        ctg.root_sec(0.5)._ref_v,
+        sec_text,
+        hoc_text="%s." + section_selected + ".v(0.5)",
+        hoc_text_obj=ctg.template,
+    )
+    plot_widget.add_expr(
+        eval("fir_widget.passive_cell." + rec_sec_split + "(" + rec_loc + ")._ref_v"),
+        "Passive @" + str(int(fir_widget.passive_amp * 1e3)) + "pA",
+    )
+    ctg.add_widget(window_index, column_index, plot_widget)
+
+    ctg.add_widget(window_index, column_index, fir_widget)
+
+    plot_widget = VoltagePlotWidget(ctg.root_sec.cell(), section=section_selected)
+    plot_widget.add_act_inf(variables=infvars)  # ctg.mechanism_dict)
+    ctg.add_widget(window_index, column_index, plot_widget)
+
+    # Column 2
+    column_index = ctg.add_column(window_index)
 
-    plot_widget.add_expr(ctg.root_sec(0.5)._ref_v,sec_text,hoc_text="%s."+section_selected+".v(0.5)",hoc_text_obj=ctg.template)
-    plot_widget.add_expr(eval("fir_widget.passive_cell." + rec_sec_split + "("+ rec_loc+")._ref_v"),"Passive @"+str(int(fir_widget.passive_amp*1e3))+"pA")
-    ctg.add_widget(window_index,column_index,plot_widget)
+    # import pdb;pdb.set_trace()
+    widget = MultiSecMenuWidget(
+        ctg.root_sec.cell(), other_cells, section_selected, ctg.mechanism_dict
+    )
 
-    ctg.add_widget(window_index,column_index,fir_widget)
+    # for cell,amp in zip(fir_widget.cells, fir_widget.amps):
+    # plot_widget.add_expr(eval("cell." + rec_sec_split + "("+ rec_loc+")._ref_v"),str(round(float(amp),2)))
+    widget_index = ctg.add_widget(window_index, column_index, widget)
+    # widget = SecMenuWidget(ctg.root_sec,x=float(inj_loc))
+    # widget_index = ctg.add_widget(window_index, column_index,widget)
 
-    plot_widget = VoltagePlotWidget(ctg.root_sec.cell(),section=section_selected)
-    plot_widget.add_act_inf(variables=infvars)#ctg.mechanism_dict)
-    ctg.add_widget(window_index,column_index,plot_widget)
-    
+    interval = 50  # int(questionary.text("Enter default netstim interval (ms (mean) time between spikes): ",default="50").ask())
+    number = 0  # int(questionary.text("Enter default netstim number of events ((average) number of spikes): ",default="10").ask())
+    start = 0  # int(questionary.text("Enter default netstim start (ms (most likely) start time of first spike): ",default="0").ask())
+    noise = 0  # float(questionary.text("Enter default netstim noise (range 0 to 1. Fractional randomness.): ",default="0").ask())
+    weight = 1  # float(questionary.text("Enter default netcon weight (range 0 to 1. Default: 1): ",default="1").ask())
 
-    #Column 2
-    column_index = ctg.add_column(window_index)
-    
-    #import pdb;pdb.set_trace()
-    widget = MultiSecMenuWidget(ctg.root_sec.cell(), other_cells,section_selected,ctg.mechanism_dict)
-
-    #for cell,amp in zip(fir_widget.cells, fir_widget.amps):
-        #plot_widget.add_expr(eval("cell." + rec_sec_split + "("+ rec_loc+")._ref_v"),str(round(float(amp),2)))
-    widget_index = ctg.add_widget(window_index, column_index,widget) 
-    #widget = SecMenuWidget(ctg.root_sec,x=float(inj_loc))
-    #widget_index = ctg.add_widget(window_index, column_index,widget) 
-
-    interval = 50 #int(questionary.text("Enter default netstim interval (ms (mean) time between spikes): ",default="50").ask())
-    number = 0 #int(questionary.text("Enter default netstim number of events ((average) number of spikes): ",default="10").ask())
-    start = 0 #int(questionary.text("Enter default netstim start (ms (most likely) start time of first spike): ",default="0").ask())
-    noise = 0 #float(questionary.text("Enter default netstim noise (range 0 to 1. Fractional randomness.): ",default="0").ask())
-    weight = 1 #float(questionary.text("Enter default netcon weight (range 0 to 1. Default: 1): ",default="1").ask())
-    
     widget = PointMenuWidget(None)
     widget_extra = PointMenuWidget(None)
-    synapse = widget_extra.synapse(eval("ctg.template."+section_selected),synloc,syntype)
-    netstim,netcon = widget.netstim(interval,number,start,noise,target=synapse,weight=weight)
+    synapse = widget_extra.synapse(eval("ctg.template." + section_selected), synloc, syntype)
+    netstim, netcon = widget.netstim(interval, number, start, noise, target=synapse, weight=weight)
     ctg.register_netstim(netstim)
     ctg.register_netcon(netcon)
     ctg.register_synapse(synapse)
@@ -1304,59 +1732,64 @@ def cell_vhseg(ctx,title,tstop,debug,fminpa,fmaxpa,passive_delay,fincrement,infv
     widget_index_extra = ctg.add_widget(window_index, column_index, widget_extra)
     widget_index = ctg.add_widget(window_index, column_index, widget)
 
-    #Column 3
+    # Column 3
     column_index = ctg.add_column(window_index)
     widget = ControlMenuWidget()
-    ctg.add_widget(window_index,column_index,widget)
-              
+    ctg.add_widget(window_index, column_index, widget)
 
     widget = PointMenuWidget(None)
-    iclamp = widget.iclamp(ctg.root_sec(float(inj_loc)),dur,amp,delay)
+    iclamp = widget.iclamp(ctg.root_sec(float(inj_loc)), dur, amp, delay)
     ctg.register_iclamp(iclamp)
-    widget_index = ctg.add_widget(window_index, column_index,widget)
+    widget_index = ctg.add_widget(window_index, column_index, widget)
 
     text_widget = TextWidget()
-    text_widget.set_to_fir_passive(fir_widget,print_calc=False,print_fi=False)
-    widget_index = ctg.add_widget(window_index, column_index,text_widget)
+    text_widget.set_to_fir_passive(fir_widget, print_calc=False, print_fi=False)
+    widget_index = ctg.add_widget(window_index, column_index, text_widget)
 
     vinit_widget = AutoVInitWidget(fir_widget)
-    widget_index = ctg.add_widget(window_index, column_index,vinit_widget)
-
-    
+    widget_index = ctg.add_widget(window_index, column_index, vinit_widget)
 
     def email_func():
         addr = tk_email_input()
         if addr is not None:
-            usernotes = tk_email_input(title="Usernotes",prompt="Enter any notes you want to include with the email. Click cancel for no notes, and send.")
+            usernotes = tk_email_input(
+                title="Usernotes",
+                prompt="Enter any notes you want to include with the email. Click cancel for no notes, and send.",
+            )
             experiment_hoc = "run_experiment.hoc"
             changed_cell_values = ctg.get_current_cell_values(change_dict=original_cell_values)
-            ctg.write_hoc(experiment_hoc,mechanism_dir="./",template_dir="./", val_set={ctg.template:changed_cell_values})
+            ctg.write_hoc(
+                experiment_hoc,
+                mechanism_dir="./",
+                template_dir="./",
+                val_set={ctg.template: changed_cell_values},
+            )
             report_file = write_report(exp_hoc=experiment_hoc)
-            template_zip = template+".zip"
+            template_zip = template + ".zip"
 
             dirpath = tempfile.mkdtemp()
 
-            for file in glob.glob(os.path.join(hoc_folder,"*.hoc")):
-                shutil.copy2(file,dirpath)
-            for file in glob.glob(os.path.join(mod_folder,"*.mod")):
-                shutil.copy2(file,dirpath)
-            
-            mod_mod_folder = os.path.join(mod_folder,"modfiles")
+            for file in glob.glob(os.path.join(hoc_folder, "*.hoc")):
+                shutil.copy2(file, dirpath)
+            for file in glob.glob(os.path.join(mod_folder, "*.mod")):
+                shutil.copy2(file, dirpath)
+
+            mod_mod_folder = os.path.join(mod_folder, "modfiles")
             if os.path.exists(mod_mod_folder):
-                for file in glob.glob(os.path.join(mod_mod_folder,"*.mod")):
-                    shutil.copy2(file,dirpath)
-            
-            shutil.copy2(experiment_hoc,dirpath)
-            shutil.copy2(report_file,dirpath)
-            shutil.make_archive(template,"zip",dirpath)
+                for file in glob.glob(os.path.join(mod_mod_folder, "*.mod")):
+                    shutil.copy2(file, dirpath)
+
+            shutil.copy2(experiment_hoc, dirpath)
+            shutil.copy2(report_file, dirpath)
+            shutil.make_archive(template, "zip", dirpath)
             shutil.rmtree(dirpath)
 
             if usernotes is not None:
                 usernotes = "User notes: " + usernotes
             else:
                 usernotes = ""
-            
-            message_subject = "Your \"" + template + "\" Model from Cyneuro.org"
+
+            message_subject = 'Your "' + template + '" Model from Cyneuro.org'
             message_text = """
 Dear BMTool User,
 
@@ -1364,7 +1797,7 @@ Thank you for using bmtool. Your "{}" model cell is enclosed in the attached zip
 
 1. You'll need to have NEURON installed (https://neuron.yale.edu/)
 2. Unzip the {} file.
-3. Compile the .mod files using `mknrndll` (Windows) or `nrnivmodl` (Mac/Linux), included with NEURON. 
+3. Compile the .mod files using `mknrndll` (Windows) or `nrnivmodl` (Mac/Linux), included with NEURON.
 4. Finally, double click the `{}` file to view the user interface.
 
 {}
@@ -1376,63 +1809,84 @@ Cyneuro.org
 BMTool
 https://github.com/tjbanks/bmtool
 
-            """.format(template,template_zip, experiment_hoc,usernotes)
-        
-            send_mail("BMTool@cyneuro.org",[addr],message_subject,message_text,files=[os.path.abspath(template_zip)])
+            """.format(template, template_zip, experiment_hoc, usernotes)
+
+            send_mail(
+                "BMTool@cyneuro.org",
+                [addr],
+                message_subject,
+                message_text,
+                files=[os.path.abspath(template_zip)],
+            )
 
             os.remove(experiment_hoc)
             os.remove(report_file)
             os.remove(template_zip)
 
-
     def save_func():
         experiment_hoc = "run_experiment.hoc"
         write_report(experiment_hoc)
         changed_cell_values = ctg.get_current_cell_values(change_dict=original_cell_values)
-        ctg.write_hoc(experiment_hoc,val_set={ctg.template:changed_cell_values})
-        popupmsg("Saved to " + os.path.abspath("./"+experiment_hoc))
+        ctg.write_hoc(experiment_hoc, val_set={ctg.template: changed_cell_values})
+        popupmsg("Saved to " + os.path.abspath("./" + experiment_hoc))
 
-    emailer_widget = SingleButtonWidget("Email this model",email_func)
-    widget_index = ctg.add_widget(window_index, column_index,emailer_widget)
+    emailer_widget = SingleButtonWidget("Email this model", email_func)
+    widget_index = ctg.add_widget(window_index, column_index, emailer_widget)
 
-    save_widget = SingleButtonWidget("Save Hoc GUI with parameters",save_func)
-    widget_index = ctg.add_widget(window_index, column_index,save_widget)
+    save_widget = SingleButtonWidget("Save Hoc GUI with parameters", save_func)
+    widget_index = ctg.add_widget(window_index, column_index, save_widget)
 
-    #Column 4
+    # Column 4
     column_index = ctg.add_column(window_index)
-    
-    widget = SegregationSelectorWidget(ctg.root_sec.cell(), other_cells,section_selected,ctg.mechanism_dict,all_sec=True,variables=segvars)
-    ctg.add_widget(window_index,column_index,widget)
 
-    segpassivewidget = SegregationPassiveWidget(fir_widget,ctg.root_sec.cell(), other_cells,section_selected,ctg.mechanism_dict,gleak_var=gleak,eleak_var=eleak)
-    ctg.add_widget(window_index,column_index,segpassivewidget)
+    widget = SegregationSelectorWidget(
+        ctg.root_sec.cell(),
+        other_cells,
+        section_selected,
+        ctg.mechanism_dict,
+        all_sec=True,
+        variables=segvars,
+    )
+    ctg.add_widget(window_index, column_index, widget)
+
+    segpassivewidget = SegregationPassiveWidget(
+        fir_widget,
+        ctg.root_sec.cell(),
+        other_cells,
+        section_selected,
+        ctg.mechanism_dict,
+        gleak_var=gleak,
+        eleak_var=eleak,
+    )
+    ctg.add_widget(window_index, column_index, segpassivewidget)
 
     widget = SegregationFIRFitWidget(fir_widget)
-    ctg.add_widget(window_index,column_index,widget)
-
+    ctg.add_widget(window_index, column_index, widget)
 
     def write_report(exp_hoc=""):
         report_file = "Report and Instructions.txt"
 
-        uvrest = str(round(fir_widget.v_rest,2))
+        uvrest = str(round(fir_widget.v_rest, 2))
         if segpassivewidget.v_rest:
-            uvrest = str(round(segpassivewidget.v_rest.val,2))
-        
-        urin = str(round(fir_widget.r_in/1e6,2))
+            uvrest = str(round(segpassivewidget.v_rest.val, 2))
+
+        urin = str(round(fir_widget.r_in / 1e6, 2))
         if segpassivewidget.r_in:
-            urin = str(round(segpassivewidget.r_in.val,2))
+            urin = str(round(segpassivewidget.r_in.val, 2))
 
-        utau = str(round(fir_widget.tau,2))
+        utau = str(round(fir_widget.tau, 2))
         if segpassivewidget.tau:
-            utau = str(round(segpassivewidget.tau.val,2))
+            utau = str(round(segpassivewidget.tau.val, 2))
 
-        vrest = str(round(fir_widget.v_rest,2))
-        rin = str(round(fir_widget.r_in/1e6,2))
-        tau = str(round(fir_widget.tau,2))
+        vrest = str(round(fir_widget.v_rest, 2))
+        rin = str(round(fir_widget.r_in / 1e6, 2))
+        tau = str(round(fir_widget.tau, 2))
 
-        spikes = [str(round(i,0)) for i in fir_widget.plenvec]
+        spikes = [str(round(i, 0)) for i in fir_widget.plenvec]
         amps = fir_widget.amps
-        ficurve = " | ".join("["+str(round(a*1e3,0))+" pA]:"+n for a,n in zip(amps,spikes))
+        ficurve = " | ".join(
+            "[" + str(round(a * 1e3, 0)) + " pA]:" + n for a, n in zip(amps, spikes)
+        )
 
         report_text = """
 Report generated by BMTool (https://github.com/tjbanks/bmtool)
@@ -1440,7 +1894,7 @@ Report generated by BMTool (https://github.com/tjbanks/bmtool)
 Thank you for using bmtool to model your "{}" cell. To view your cell:
 
 1. You'll need to have NEURON installed (https://neuron.yale.edu/)
-2. Compile the .mod files using `mknrndll` (Windows) or `nrnivmodl` (Mac/Linux), included with NEURON. 
+2. Compile the .mod files using `mknrndll` (Windows) or `nrnivmodl` (Mac/Linux), included with NEURON.
 3. Finally, double click the `{}` file to view the user interface.
 
 Cell template: {}
@@ -1459,29 +1913,27 @@ V_rest = {} (mV)
 R_in = {} (MOhms)
 tau = {} (ms)
 
-FI Curve: 
+FI Curve:
 {}
 
 Cell values:
 
-""".format(template,exp_hoc,template,uvrest,urin,utau,vrest,rin,tau,ficurve)
+""".format(template, exp_hoc, template, uvrest, urin, utau, vrest, rin, tau, ficurve)
         changed_cell_values = ctg.get_current_cell_values()
 
-        with open(report_file,"w+") as f:
+        with open(report_file, "w+") as f:
             f.write(report_text)
-            for sec,vals in changed_cell_values.items():
-                f.write(sec+"\n")
-                for key,val in vals.items():
-                    f.write("\t" + key + " = " + str(round(val,6)) + "\n")
+            for sec, vals in changed_cell_values.items():
+                f.write(sec + "\n")
+                for key, val in vals.items():
+                    f.write("\t" + key + " = " + str(round(val, 6)) + "\n")
 
         return report_file
 
-
-    ctg.show(auto_run=True,on_complete_fih=text_widget.update_fir_passive,run_count=2)
-
-    
+    ctg.show(auto_run=True, on_complete_fih=text_widget.update_fir_passive, run_count=2)
 
     return
 
+
 if __name__ == "__main__":
-    cli()
+    cli()