setting up packmol tests

mdagent/tools/base_tools/preprocess_tools/packing.py

@@ -67,7 +67,7 @@ def __init__(
     ):
         self.path_registry = path_registry
         self.molecules = []
-        self.file_number = 1
+        self.file_number = file_number
         self.file_description = file_description
         self.final_name = None
 

tests/test_packing.py

@@ -0,0 +1,44 @@
+import os
+
+import pytest
+
+from mdagent.tools.base_tools.preprocess_tools.packing import Molecule, PackmolBox
+from mdagent.utils import PathRegistry
+
+
+@pytest.fixture
+def get_registry():
+    return PathRegistry()
+
+
+@pytest.fixture
+def packmolbox(get_registry):
+    return PackmolBox(get_registry)
+
+
+@pytest.fixture
+def dummy_molecule():
+    return Molecule(
+        filename="water", file_id=100, number_of_molecules=2, instructions=None
+    )
+
+
+def test_add_molecule(packmolbox, dummy_molecule):
+    initial_length = len(packmolbox.molecules)
+    packmolbox.add_molecule(dummy_molecule)
+    assert len(packmolbox.molecules) == initial_length + 1
+
+
+def test_generate_input_header(packmolbox):
+    packmolbox.generate_input_header()
+    # assert file packmol.inp exists
+    assert os.path.isfile("packmol.inp")
+    os.remove("packmol.inp")
+
+
+def test_generate_input(packmolbox, dummy_molecule):
+    packmolbox.add_molecule(dummy_molecule)
+    output = packmolbox.generate_input()
+    assert "structure water" in output
+    assert "number 2" in output
+    assert "end structure" in output