From b7c3ec8fcca2d973333a0c2671c7727a274966ac Mon Sep 17 00:00:00 2001
From: Daniel Pastor Ramirez <daniel.ramirezecheme@ucalgary.ca>
Date: Tue, 5 Mar 2024 11:27:38 -0700
Subject: [PATCH] include "typer[all]" dependency

---
 bin/prolint2                   | 25 +++----------------------
 prolint2/server/chord_utils.py |  1 -
 setup.py                       |  2 +-
 3 files changed, 4 insertions(+), 24 deletions(-)

diff --git a/bin/prolint2 b/bin/prolint2
index 4bc30be..52e1412 100755
--- a/bin/prolint2
+++ b/bin/prolint2
@@ -37,7 +37,7 @@ class OrderCommands(TyperGroup):
 # Creating the parser
 prolint2 = typer.Typer(
     help="[blue]Command-line version of the ProLint v.2 library.[/blue] :sparkles:",
-    epilog="[blue]Have fun analyzing lipid-protein interactions![/blue] :stuck_out_tongue_winking_eye:",
+    epilog="[blue]Have fun analyzing lipid-protein interactions![/blue] ",
     rich_markup_mode="rich",
     add_completion=False,
     cls=OrderCommands,
@@ -46,9 +46,7 @@ prolint2 = typer.Typer(
 
 
 # creating the run command
-@prolint2.command(
-    epilog="[blue]Have fun analyzing lipid-protein interactions![/blue] :stuck_out_tongue_winking_eye:"
-)
+@prolint2.command(epilog="[blue]Have fun analyzing lipid-protein interactions![/blue] ")
 def run(
     structure: Annotated[
         pathlib.Path,
@@ -108,9 +106,7 @@ def run(
 
 
 # creating the dashboard command
-@prolint2.command(
-    epilog="[blue]Have fun analyzing lipid-protein interactions![/blue] :stuck_out_tongue_winking_eye:"
-)
+@prolint2.command(epilog="[blue]Have fun analyzing lipid-protein interactions![/blue] ")
 def dashboard(
     structure: Annotated[
         pathlib.Path,
@@ -188,20 +184,5 @@ def dashboard(
         sys.exit()
 
 
-@prolint2.command(
-    epilog="[blue]Have fun analyzing lipid-protein interactions![/blue] :stuck_out_tongue_winking_eye:"
-)
-def plot(
-    contacts: Annotated[
-        pathlib.Path,
-        typer.Argument(
-            show_default=False,
-            help='path to the structure/topology file (E.g.: "coordinates.gro").',
-        ),
-    ],
-):
-    """[blue]ProLint v.2: Plotting paper quality graphs to visualize lipid-protein interactions.[/blue] :sparkles:"""
-
-
 if __name__ == "__main__":
     prolint2()
diff --git a/prolint2/server/chord_utils.py b/prolint2/server/chord_utils.py
index 4ca0758..abc6337 100644
--- a/prolint2/server/chord_utils.py
+++ b/prolint2/server/chord_utils.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-from inspect import ArgSpec
 import numpy as np
 from itertools import combinations
 from prolint2.server.utils import calculate_contact_intervals
diff --git a/setup.py b/setup.py
index b136507..07dbc98 100644
--- a/setup.py
+++ b/setup.py
@@ -55,7 +55,7 @@
         "pandas",
         "mdanalysis",
         "bottle",
-        "typer",
+        "typer[all]",
         "requests",
     ],  # Required packages, pulls from pip if needed; do not use for Conda deployment
     platforms=[