cleaned up logic in tip to tip distances function

phykit/services/tree/tip_to_tip_distance.py

@@ -1,4 +1,5 @@
 import sys
+from typing import Dict
 
 from Bio.Phylo.BaseTree import TreeMixin
 
@@ -12,21 +13,23 @@ def __init__(self, args) -> None:
     def run(self):
         tree_zero = self.read_tree_file()
 
-        # determine is leaves exists
         self.check_leaves(tree_zero, self.tip_1, self.tip_2)
 
-        # print distance
         print(round(TreeMixin.distance(tree_zero, self.tip_1, self.tip_2), 4))
 
     def check_leaves(self, tree_zero, tip_1, tip_2):
         leaf1 = TreeMixin.find_any(tree_zero, tip_1)
-        if (bool(leaf1)) == False:
+        if not bool(leaf1):
             print(tip_1, "not on tree\nExiting...")
             sys.exit()
         leaf2 = TreeMixin.find_any(tree_zero, tip_2)
-        if (bool(leaf2)) == False:
+        if not bool(leaf2):
             print(tip_2, "not on tree\nExiting...")
             sys.exit()
 
-    def process_args(self, args):
-        return dict(tree_file_path=args.tree_zero, tip_1=args.tip_1, tip_2=args.tip_2)
+    def process_args(self, args) -> Dict[str, str]:
+        return dict(
+            tree_file_path=args.tree_zero,
+            tip_1=args.tip_1,
+            tip_2=args.tip_2,
+        )

tests/integration/tree/test_tip_to_tip_distance_integration.py

@@ -1,9 +1,7 @@
-import pytest
-import sys
-from math import isclose
 from mock import patch, call
 from pathlib import Path
-from textwrap import dedent
+import pytest
+import sys
 
 from phykit.phykit import Phykit
 
@@ -96,4 +94,4 @@ def test_tip_to_tip_distance_bad_file_path(self, mocked_print):
             Phykit()
 
         assert pytest_wrapped_e.type == SystemExit
-        assert pytest_wrapped_e.value.code == 2
+        assert pytest_wrapped_e.value.code == 2