Fix lint issues SCMSUITE-8674 SO--

interfaces/molecule/packmol.py

@@ -282,9 +282,8 @@ def run(self):
                         structure.molecule.write(structure_fname)
                     input_file.write(structure.get_input_block(structure_fname, tolerance=self.tolerance))
 
-            my_input = open(input_fname, "r")
-            saferun(self.executable, stdin=my_input, stdout=subprocess.DEVNULL)
-            my_input.close()
+            with open(input_fname) as my_input:
+                saferun(self.executable, stdin=my_input, stdout=subprocess.DEVNULL)
 
             if not os.path.exists(output_fname):
                 raise PackMolError("Packmol failed. It may work if you try a lower density.")

unit_tests/conftest.py

@@ -2,8 +2,6 @@
 from unittest.mock import patch, MagicMock
 from pathlib import Path
 
-from scm.plams.mol.molecule import Molecule
-
 
 @pytest.fixture(autouse=True)
 def config():

unit_tests/test_identify.py

@@ -1,9 +1,7 @@
 import pytest
-import numpy as np
 
 from scm.plams.tools.periodic_table import PT
 from scm.plams.mol.molecule import Molecule
-from scm.plams.mol.identify import reorder, get_graph, find_permutation
 
 PT.set_connectors("Mg", 4)
 

unit_tests/test_molecule_interfaces.py

@@ -262,33 +262,36 @@ def five_water(self):
 
     def test_packmol(self, five_water, plams_mols):
         # Packmol requires calling AMS, so mock out the call to the executable and return an expected xyz
-        with get_mock_open_function(lambda f: f.endswith("output.xyz"), five_water), patch(
-            "os.path.exists", return_value=True
-        ), patch("scm.plams.interfaces.molecule.packmol.saferun") as mock_saferun:
-            input_mol = plams_mols["water"]
-
-            # Packmol has a lot of internal function calls, so even returning successfully is pretty good
-            # But also sanity-check the temporary input files passed to AMS
-            def read_input_file(*args, **kwargs):
-                # Intercept the tmp input files and check they are as expected
-                content = kwargs["stdin"].read()
-                assert int(re.search(r"number (\d+)", content).group(1)) == 5
-
-                structure_file = re.search(r"structure\s+([/\w\d-]+)", content).group(1)
-                with open(f"{structure_file}.xyz") as f:
-                    s = f.read()
-                assert (
-                    s
-                    == """3
+        with get_mock_open_function(lambda f: f.endswith("output.xyz"), five_water):
+            with patch("os.path.exists", return_value=True):
+                with patch("scm.plams.interfaces.molecule.packmol.saferun") as mock_saferun:
+                    input_mol = plams_mols["water"]
+
+                    # Packmol has a lot of internal function calls, so even returning successfully is pretty good
+                    # But also sanity-check the temporary input files passed to AMS
+                    def read_input_file(*args, **kwargs):
+                        # Intercept the tmp input files and check they are as expected
+                        input_file = kwargs["stdin"]
+                        content = input_file.read()
+                        assert int(re.search(r"number (\d+)", content).group(1)) == 5
+
+                        print(content)
+
+                        structure_file_name = re.search(r"structure\s+([\\:/\w\d-]+)", content).group(1)
+                        with open(f"{structure_file_name}.xyz") as structure_file:
+                            s = structure_file.read()
+                        assert (
+                            s
+                            == """3
 
          O       0.06692105       0.06692105       0.00000000
          H       1.01204160      -0.07896265       0.00000000
          H      -0.07896265       1.01204160       0.00000000
 """
-                )
+                        )
 
-            mock_saferun.side_effect = read_input_file
-            mols = packmol(input_mol, n_atoms=15, density=1.0, executable="mock_exe")
+                    mock_saferun.side_effect = read_input_file
+                    mols = packmol(input_mol, n_atoms=15, density=1.0, executable="mock_exe")
 
-        # And assert on the number of returned molecules
-        assert len(mols) == 15
+                    # And assert on the number of returned molecules
+                    assert len(mols) == 15