diff --git a/openad/app/main.py b/openad/app/main.py
index 578ad34b..9e4c6c04 100644
--- a/openad/app/main.py
+++ b/openad/app/main.py
@@ -21,6 +21,7 @@
 from openad.gui.ws_server import ws_server  # Web socket server for gui - experimental
 from openad.helpers.output import output_table
 from openad.helpers.plugins import display_plugin_overview
+from openad.helpers.history import init_history, update_history_file, add_history_entry
 
 # Core
 import openad.core.help as openad_help
@@ -508,27 +509,11 @@ def do_help(self, inp, display_info=True, starts_with_only=False, disable_catego
 
     def preloop(self):
         """CMD class called function: Preloop is called by cmd to get an update the history file each History File"""
-        if readline and os.path.exists(self.histfile):
-            # note history files can get corrupted so using try to compensate
-            try:
-                readline.read_history_file(self.histfile)
-            except Exception:  # pylint: disable=broad-exception-caught # do not need to know exception
-                # Create history file in case it doesn't exist yet.
-                # - - -
-                # To trigger:
-                # >> create new workspace foobar
-                # >> ctrl+c
-                # (Reboot)
-                readline.write_history_file(self.histfile)
+        init_history(self)
 
     def postloop(self):
         """CMD class called function: Post loop is called by cmd to get an update the history file"""
-        readline.set_history_length(self.histfile_size)
-        readline.write_history_file(self.histfile)
-
-    def add_history(self, inp):
-        """CMD class called function: adds history file"""
-        readline.add_history(inp)
+        update_history_file(self)
 
     def complete(self, text, state):
         """CMD class called function:
@@ -748,10 +733,6 @@ def emptyline(self):
     def default(self, line):
         """Default method call on hitting of the return Key, it tries to parse and execute the statements."""
 
-        # Prevent the history from growing too large
-        if readline.get_current_history_length() > self.histfile_size:
-            readline.remove_history_item(0)
-
         inp = line  # assigning line to input value
 
         x = None
@@ -1031,7 +1012,6 @@ def api_remote(
     """
 
     global MAGIC_PROMPT
-    # GLOBAL_SETTINGS["display"] = "notebook"
 
     initialise()
 
@@ -1066,14 +1046,7 @@ def api_remote(
             set_context(magic_prompt, x)
 
     magic_prompt.api_variables = api_var_list
-    # We now manage history. The history sometimes gets corrupted through no fault of ours.
-    # If so, we just reset it.
-    try:
-        readline.read_history_file(magic_prompt.histfile)
-    except Exception:  # pylint: disable=broad-exception-caught # could be a number of errors
-        readline.add_history("")
-        readline.write_history_file(magic_prompt.histfile)
-        readline.read_history_file(magic_prompt.histfile)
+
     for i in arguments:
         inp = inp + a_space + i
         a_space = " "
@@ -1105,9 +1078,8 @@ def api_remote(
         # Note, may be possible add code completion here #revisit
         else:
             magic_prompt.preloop()
-            magic_prompt.add_history(inp)
+            add_history_entry(magic_prompt, inp)
             magic_prompt.postloop()
-            readline.write_history_file(magic_prompt.histfile)
 
             result = magic_prompt.default(inp)
 
@@ -1171,7 +1143,7 @@ def cmd_line():
                 and command_line.settings["context"] == words[2 + word_increment].upper()
             ):
                 command_line.preloop()
-                command_line.add_history(str(" ".join(words[3 + word_increment :])).strip())
+                add_history_entry(command_line, str(" ".join(words[3 + word_increment :])).strip())
                 command_line.postloop()
                 result = command_line.default(str(" ".join(words[3 + word_increment :])).strip())
         else:
@@ -1179,7 +1151,7 @@ def cmd_line():
             # Note, may be possible add code completion here #revisit
 
             command_line.preloop()
-            command_line.add_history(inp[+increment:].strip())
+            add_history_entry(command_line, inp[+increment:].strip())
             command_line.postloop()
             result = command_line.default(inp[+increment:].strip())
         command_line.do_exit("dummy do not remove")
diff --git a/openad/core/lang_runs.py b/openad/core/lang_runs.py
index 9efdb838..043c9734 100644
--- a/openad/core/lang_runs.py
+++ b/openad/core/lang_runs.py
@@ -7,6 +7,7 @@
 
 # Global variables
 from openad.app.global_var_lib import GLOBAL_SETTINGS
+from openad.helpers.history import update_history_file
 
 # Helpers
 from openad.helpers.output import output_text, output_error, output_success, output_table
@@ -23,7 +24,7 @@ def _create_workspace_dir_if_nonexistent(cmd_pointer, dir_name):
 def save_run(cmd_pointer, parser):
     """Saves a Run"""
     _create_workspace_dir_if_nonexistent(cmd_pointer, "_runs")
-    readline.write_history_file(cmd_pointer.histfile)
+    update_history_file(cmd_pointer)
 
     # f =_meta_workspaces+'/'+ cmd_pointer.settings['workspace'].upper()+'/.cmd_history'
     runlist = []
@@ -111,9 +112,6 @@ def display_run(cmd_pointer, parser):
     # Create _runs directory if it does not exist yet.
     _create_workspace_dir_if_nonexistent(cmd_pointer, "_runs")
 
-    # import readline
-    # readline.write_history_file(cmd_pointer.histfile)  # @Phil, I put this back but it was commented out
-
     # Read the run file.
     commands = []
     run_file_path = (
diff --git a/openad/core/lang_workspaces.py b/openad/core/lang_workspaces.py
index aa34894e..966ec89e 100644
--- a/openad/core/lang_workspaces.py
+++ b/openad/core/lang_workspaces.py
@@ -3,8 +3,6 @@
 import os
 from time import sleep
 
-import readline
-
 # Core
 from openad.core.lang_sessions_and_registry import write_registry, update_main_registry_env_var
 
@@ -16,12 +14,13 @@
 from openad.helpers.output_msgs import msg
 from openad.helpers.general import other_sessions_exist, user_input
 from openad.helpers.spinner import spinner
+from openad.helpers.history import clear_memory_history, init_history
 
 
 # Sets the current workspace from the fgiven workspaces available
 def set_workspace(cmd_pointer, parser):
     """Sets the current Workspace"""
-    readline.write_history_file(cmd_pointer.histfile)
+
     current_workspace_name = cmd_pointer.settings["workspace"].upper()
     new_workspace_name = parser["Workspace_Name"].upper()
     if new_workspace_name not in cmd_pointer.settings["workspaces"]:
@@ -29,19 +28,17 @@ def set_workspace(cmd_pointer, parser):
 
     elif new_workspace_name == current_workspace_name:
         return output_warning(msg("warn_workspace_already_active", new_workspace_name))
+
+    # New workspace
     else:
         cmd_pointer.settings["workspace"] = new_workspace_name
         write_registry(cmd_pointer.settings, cmd_pointer)
         cmd_pointer.histfile = os.path.expanduser(cmd_pointer.workspace_path(new_workspace_name) + "/.cmd_history")
-        readline.clear_history()
 
-        try:  # Open history file if not corrupt
-            if readline and os.path.exists(cmd_pointer.histfile):
-                readline.read_history_file(cmd_pointer.histfile)
-        except Exception:
-            readline.write_history_file(cmd_pointer.histfile)
+        # Switch history
+        clear_memory_history(cmd_pointer)
+        init_history(cmd_pointer)
 
-        readline.write_history_file(cmd_pointer.histfile)
         return output_success(msg("success_workspace_set", new_workspace_name))
 
 
@@ -131,11 +128,9 @@ def remove_workspace(cmd_pointer, parser):
 
 def create_workspace(cmd_pointer, parser):
     """Creates a Workspace"""
-    # Make sure existing workspace history file is saved.
-    readline.write_history_file(cmd_pointer.histfile)
+
     cmd_pointer.refresh_vector = True
     cmd_pointer.refresh_train = True
-
     cmd_pointer.settings["env_vars"]["refresh_help_ai"] = True
     update_main_registry_env_var(cmd_pointer, "refresh_help_ai", True)
 
@@ -167,7 +162,7 @@ def create_workspace(cmd_pointer, parser):
         cmd_pointer.settings["descriptions"][workspace_name] = description
         write_registry(cmd_pointer.settings, cmd_pointer, True)  # Create registry
         write_registry(cmd_pointer.settings, cmd_pointer)  # Create session registry
-    except Exception as err:
+    except Exception as err:  # pylint: disable=broad-exception-caught
         return output_error(msg("err_workspace_description", err))
 
     # Create workspace.
@@ -198,16 +193,17 @@ def create_workspace(cmd_pointer, parser):
         if not os.path.exists(dir_path):
             os.mkdir(dir_path)
         else:
-            # This currently happens when you remove a workspace and then try to recreate it.
-            # @Phil - we probably should move or archive the workspace folder when removing the workspace.
+            # When you remove a workspace and then recreate it
             os.chdir(dir_path)
             error_creating_dir = msg("warn_workspace_folder_already_exists", workspace_name)
+
         # Main and session registry writes
         write_registry(cmd_pointer.settings, cmd_pointer, True)
         write_registry(cmd_pointer.settings, cmd_pointer)
 
-        readline.clear_history()
-        readline.write_history_file(cmd_pointer.histfile)
+        # Switch history
+        clear_memory_history(cmd_pointer)
+
         # raise ValueError('This is a test error.\n') @later this causes the app to break permamenently.
     except Exception as err:
         error_other = msg("err_workspace_create", err)
diff --git a/openad/helpers/general.py b/openad/helpers/general.py
index 505d77f3..eb5dcfc7 100644
--- a/openad/helpers/general.py
+++ b/openad/helpers/general.py
@@ -29,7 +29,7 @@ def refresh_prompt(settings):
 def is_notebook_mode():
     """Return True if we are running inside a Jupyter Notebook or Jupyter Lab."""
     try:
-        get_ipython()  # pylint: disable=undefined-variable
+        get_ipython()  # pylint: disable=undefined-variable # noqa: F821
         return True
     except Exception:  # pylint: disable=broad-exception-caught
         return False
@@ -191,7 +191,7 @@ def load_module_from_path(module_name, file_path):
         sys.modules[module_name] = module
         spec.loader.exec_module(module)
         return module
-    except Exception as err:
+    except Exception:
         # Silent fail - only enable this for debugging
         # output_error(f"load_module_from_path('{module_name}', {file_path})\n<soft>{err}</soft>")
         return None
@@ -201,7 +201,7 @@ def load_module_from_path(module_name, file_path):
 def print_separator(style=None, width=None, return_val=False):
     from openad.app.global_var_lib import GLOBAL_SETTINGS
 
-    if GLOBAL_SETTINGS["display"] == "terminal" or GLOBAL_SETTINGS["display"] == None:
+    if GLOBAL_SETTINGS["display"] == "terminal" or GLOBAL_SETTINGS["display"] is None:
         cli_width = get_print_width(full=True)
         width = cli_width if not width or cli_width < width else width
         if style:
@@ -439,19 +439,3 @@ async def _loop(text="", i=0, line_length=0):
     # _loop(text=text) # Sync
     asyncio.run(_loop(text=text))
     sys.stdout.write("\033[?25h")  # Show cursor
-
-
-# NOT USED
-# Clear the current line.
-# Couldn't get this to work, because I can't clear the buffer.
-# As a result, (eg.) when you try ctrl-c twice with n answer,
-# the second time it will have the first time's response in the buffer,
-# causing it to mess up the layout.
-def clear_current_line():
-    buffer = readline.get_line_buffer()
-    line_length = len(buffer)
-    readline.clear_history()
-    eraser = "\b \b" * line_length
-    sys.stdout.write(eraser)
-    # readline.insert_text(' ')
-    # print(len(buffer), buffer)
diff --git a/openad/helpers/history.py b/openad/helpers/history.py
new file mode 100644
index 00000000..328e313e
--- /dev/null
+++ b/openad/helpers/history.py
@@ -0,0 +1,84 @@
+import os
+import readline
+from openad.helpers.output import output_text, output_error, output_success
+
+DEBUG_HIST = False
+
+
+def init_history(cmd_pointer):
+    """
+    Load history content from the .cmd_history file:
+    - On startup
+    - When switching workspaces
+    """
+    readline.set_history_length(cmd_pointer.histfile_size)
+    if readline and os.path.exists(cmd_pointer.histfile):
+        try:
+            is_startup = readline.get_current_history_length() == 0
+            if is_startup:
+                readline.read_history_file(cmd_pointer.histfile)
+                if DEBUG_HIST:
+                    output_success(f"load_history_file: {cmd_pointer.histfile}", return_val=False)
+        except Exception as err:  # pylint: disable=broad-exception-caught
+            if DEBUG_HIST:
+                output_error(["load_history_file", err], return_val=False)
+    elif DEBUG_HIST:
+        output_error(
+            [
+                f"load_history_file - .cmd_history not found in {cmd_pointer.settings['workspace']}",
+                cmd_pointer.histfile,
+            ],
+            return_val=False,
+        )
+
+
+def clear_memory_history(cmd_pointer):
+    """
+    Clear the in-memory history without removing the history file.
+    Used when switching workspaces.
+
+    Workaround needed because readline doesn't let you clear in-memory
+    history without also deleting the history file.
+    """
+    try:
+        readline.write_history_file(cmd_pointer.histfile + "--temp")
+        readline.clear_history()
+        os.remove(cmd_pointer.histfile + "--temp")
+    except Exception as err:  # pylint: disable=broad-exception-caught
+        if DEBUG_HIST:
+            output_error(["refresh_history", err], return_val=False)
+
+
+def add_history_entry(cmd_pointer, inp):
+    """
+    Add the current command to the in-memory history.
+    This is called when a command is executed.
+    """
+    try:
+        # Ignore super long commands
+        if len(str(str(inp).strip())) < int(4096):
+            readline.add_history(str(str(inp).strip()))
+
+        # Cap the in-memory history
+        # Without this, it will keep on growing until you switch workspaces or restart kernel
+        if readline.get_current_history_length() > cmd_pointer.histfile_size:
+            readline.remove_history_item(0)
+
+        if DEBUG_HIST:
+            output_text(f"add_history_entry #{cmd_pointer.histfile_size}: {inp}", return_val=False)
+    except Exception as err:  # pylint: disable=broad-exception-caught
+        if DEBUG_HIST:
+            output_error(["add_history_entry", err], return_val=False)
+
+
+def update_history_file(cmd_pointer):
+    """
+    Write in-memory history to disk.
+    """
+    try:
+        readline.write_history_file(cmd_pointer.histfile)
+        if DEBUG_HIST:
+            output_text(f"update_history_file: {cmd_pointer.histfile}", return_val=False)
+    except Exception as err:  # pylint: disable=broad-exception-caught
+        if DEBUG_HIST:
+            output_error(["update_history_file", err], return_val=False)
diff --git a/openad/helpers/spinner.py b/openad/helpers/spinner.py
index b8f95bd3..d6ca351a 100644
--- a/openad/helpers/spinner.py
+++ b/openad/helpers/spinner.py
@@ -26,12 +26,10 @@
 
 
 class Spinner(Halo):
-
     def __init__(self):
-
         # Fancy spinner, but requires more CPU, blocking the main thread
         # To do: see if separating thread for spinner resolves this
-        wave_spinner = {
+        wave_spinner = {  # noqa: F841
             "interval": 700,
             "frames": [
                 "▉▋▍▎▏▏",
diff --git a/openad/user_toolkits/RXN/fn_reactions/fn_predict_retro.py b/openad/user_toolkits/RXN/fn_reactions/fn_predict_retro.py
index 1e2abd8a..baf79fd1 100644
--- a/openad/user_toolkits/RXN/fn_reactions/fn_predict_retro.py
+++ b/openad/user_toolkits/RXN/fn_reactions/fn_predict_retro.py
@@ -261,7 +261,7 @@ def predict_retro(inputs: dict, cmd_pointer):
                 "",
                 return_val=False,
             )
-            if num_results < 4 or GLOBAL_SETTINGS["display"] == "api"::
+            if num_results < 4 or GLOBAL_SETTINGS["display"] == "api":
                 results[str(index)] = {"confidence": tree["confidence"], "reactions": []}
 
             output_text(
@@ -273,7 +273,7 @@ def predict_retro(inputs: dict, cmd_pointer):
             )
 
             for reaction in collect_reactions_from_retrosynthesis(tree):
-                if num_results < 4 or GLOBAL_SETTINGS["display"] == "api"::
+                if num_results < 4 or GLOBAL_SETTINGS["display"] == "api":
                     results[str(index)]["reactions"].append(reactions_text[i])
                 output_text("<green> Reaction: </green>" + reactions_text[i], return_val=False)
                 i = i + 1