minor fixes

tests/test_parsing.py

@@ -1,12 +1,14 @@
 import re
 import string
-import pytest
-from hypothesis import settings, HealthCheck, given, strategies as st
 from pathlib import Path
 
+import pytest
+from hypothesis import HealthCheck, given, settings
+from hypothesis import strategies as st
+
 from kimmdy import parsing
-from kimmdy.utils import get_gmx_dir
 from kimmdy.constants import AA3
+from kimmdy.utils import get_gmx_dir
 
 
 ## test topology parser
@@ -40,6 +42,7 @@ def test_doubleparse_urea(arranged_tmp_path):
 def test_ff_includes_with_gmxdir(arranged_tmp_path):
     top_dict = parsing.read_top(Path("urea.top"))
     gmx_dir = get_gmx_dir("gmx")
+    assert gmx_dir is not None, "gmx dir not found"
     tip3_dict = parsing.read_top(gmx_dir / "top" / "amber99.ff" / "tip3p.itp")
 
     assert top_dict["atomtypes"]

tests/test_recipe.py

@@ -128,9 +128,9 @@ def test_place_initialization():
     assert m2 != m3
 
     with pytest.raises(TypeError):
-        recipe.Place(ix_to_place=1)
+        recipe.Place(ix_to_place=1)  # type: ignore
     with pytest.raises(ValueError):
-        recipe.Place(id_to_place=1, new_coords=(0, 0, 0))
+        recipe.Place(id_to_place=1, new_coords=(0, 0, 0))  # type: ignore
 
 
 def test_relax_initialization():

tests/test_topology.py

@@ -331,7 +331,8 @@ def test_del_atom_hexala(self, hexala_top_fix, atomindex):
         for a_del in angles_to_delete:
             assert None in [update.get(a) for a in a_del]
         for a_up in angles_to_update:
-            new = top.angles[tuple([update.get(a) for a in a_up])]
+            k1, k2, k3 = [update[a] for a in a_up]
+            new = top.angles[k1, k2, k3]
             old = hexala_top_fix.angles[a_up]
             assert old.ai == rev_update.get(new.ai)
             assert old.aj == rev_update.get(new.aj)
@@ -341,7 +342,8 @@ def test_del_atom_hexala(self, hexala_top_fix, atomindex):
         for pd_del in pd_to_delete:
             assert None in tuple([update.get(a) for a in pd_del])
         for pd_up in pd_to_update:
-            new = top.proper_dihedrals[tuple([update.get(a) for a in pd_up])]
+            k1, k2, k3, k4 = [update[a] for a in pd_up]
+            new = top.proper_dihedrals[k1, k2, k3, k4]
             old = hexala_top_fix.proper_dihedrals[pd_up]
             assert old.ai == rev_update.get(new.ai)
             assert old.aj == rev_update.get(new.aj)
@@ -360,7 +362,8 @@ def test_del_atom_hexala(self, hexala_top_fix, atomindex):
         for id_del in id_to_delete:
             assert None in tuple([update.get(a) for a in id_del])
         for id_up in id_to_update:
-            new = top.improper_dihedrals[tuple([update.get(a) for a in id_up])]
+            k1, k2, k3, k4 = [update[a] for a in id_up]
+            new = top.improper_dihedrals[k1, k2, k3, k4]
             old = hexala_top_fix.improper_dihedrals[id_up]
             assert old.ai == rev_update.get(new.ai)
             assert old.aj == rev_update.get(new.aj)
@@ -637,9 +640,10 @@ def test_top_update_dict(self, raw_hexala_top_fix):
         assert raw["moleculetype_Protein"]["content"][0] == ["Protein", "3"]
         assert top.top["moleculetype_Reactive"]["content"][0] == ["Reactive", "3"]
         for section in ["atoms", "bonds", "angles", "dihedrals", "pairs"]:
-            top.top["moleculetype_Reactive"]["subsections"][section]["content"] == raw[
-                "moleculetype_Protein"
-            ]["subsections"][section]["content"]
+            assert (
+                top.top["moleculetype_Reactive"]["subsections"][section]["content"]
+                == raw["moleculetype_Protein"]["subsections"][section]["content"]
+            )
 
     def test_top_properties(self, hexala_top_fix):
         top = deepcopy(hexala_top_fix)