reorganized tool-existing related tests

tests/test_fxns.py → tests/test_analysis_fxns.py

@@ -4,12 +4,7 @@
 
 import pytest
 
-from mdagent.tools.base_tools import (
-    CleaningTools,
-    SimulationFunctions,
-    VisFunctions,
-    get_pdb,
-)
+from mdagent.tools.base_tools.analysis_tools import VisFunctions
 from mdagent.tools.base_tools.analysis_tools.plot_tools import plot_data, process_csv
 from mdagent.utils import PathRegistry
 
@@ -33,34 +28,12 @@ def path_to_cif():
     os.chdir(original_cwd)
 
 
-@pytest.fixture
-def cleaning_fxns():
-    return CleaningTools()
-
-
-# Test simulation tools
-@pytest.fixture
-def sim_fxns():
-    return SimulationFunctions()
-
-
-# Test visualization tools
-@pytest.fixture
-def vis_fxns():
-    return VisFunctions()
-
-
-# Test MD utility tools
-@pytest.fixture
-def fibronectin():
-    return "fibronectin pdb"
-
-
 @pytest.fixture
 def get_registry():
     return PathRegistry()
 
 
+# Plot tools
 def test_process_csv():
     mock_csv_content = "Time,Value1,Value2\n1,10,20\n2,15,25"
     mock_reader = MagicMock()
@@ -114,6 +87,12 @@ def test_plot_data():
         assert "All plots failed due to non-numeric data." in str(excinfo.value)
 
 
+# Visualization tools
+@pytest.fixture
+def vis_fxns():
+    return VisFunctions()
+
+
 @pytest.mark.skip(reason="molrender is not pip installable")
 def test_run_molrender(path_to_cif, vis_fxns):
     result = vis_fxns.run_molrender(path_to_cif)
@@ -123,49 +102,3 @@ def test_run_molrender(path_to_cif, vis_fxns):
 def test_create_notebook(path_to_cif, vis_fxns, get_registry):
     result = vis_fxns.create_notebook(path_to_cif, get_registry)
     assert result == "Visualization Complete"
-
-
-def test_add_hydrogens_and_remove_water(path_to_cif, cleaning_fxns, get_registry):
-    result = cleaning_fxns._add_hydrogens_and_remove_water(path_to_cif, get_registry)
-    assert "Cleaned File" in result  # just want to make sur the function ran
-
-
-@patch("os.path.exists")
-@patch("os.listdir")
-def test_extract_parameters_path(mock_listdir, mock_exists, sim_fxns, get_registry):
-    # Test when parameters.json exists
-    mock_exists.return_value = True
-    assert sim_fxns._extract_parameters_path() == "simulation_parameters_summary.json"
-    mock_exists.assert_called_once_with("simulation_parameters_summary.json")
-    mock_exists.reset_mock()  # Reset the mock for the next scenario
-
-    # Test when parameters.json does not exist, but some_parameters.json does
-    mock_exists.return_value = False
-    mock_listdir.return_value = ["some_parameters.json", "other_file.txt"]
-    assert sim_fxns._extract_parameters_path() == "some_parameters.json"
-
-    # Test when no appropriate file exists
-    mock_listdir.return_value = ["other_file.json", "other_file.txt"]
-    with pytest.raises(ValueError) as e:
-        sim_fxns._extract_parameters_path()
-    assert str(e.value) == "No parameters.json file found in directory."
-
-
-@patch(
-    "builtins.open",
-    new_callable=mock_open,
-    read_data='{"param1": "value1", "param2": "value2"}',
-)
-@patch("json.load")
-def test_setup_simulation_from_json(mock_json_load, mock_file_open, sim_fxns):
-    # Define the mock behavior for json.load
-    mock_json_load.return_value = {"param1": "value1", "param2": "value2"}
-    params = sim_fxns._setup_simulation_from_json("test_file.json")
-    mock_file_open.assert_called_once_with("test_file.json", "r")
-    mock_json_load.assert_called_once()
-    assert params == {"param1": "value1", "param2": "value2"}
-
-
-def test_getpdb(fibronectin, get_registry):
-    name = get_pdb(fibronectin, get_registry)
-    assert name.endswith(".pdb")

tests/test_preprocess_fxns.py

@@ -0,0 +1,52 @@
+import os
+
+import pytest
+
+from mdagent.tools.base_tools.preprocess_tools import CleaningTools, get_pdb
+from mdagent.utils import PathRegistry
+
+# Test functions in preprocess tools
+
+
+@pytest.fixture
+def get_registry():
+    return PathRegistry()
+
+
+@pytest.fixture
+def path_to_cif():
+    # Save original working directory
+    original_cwd = os.getcwd()
+
+    # Change current working directory to the directory where the CIF file is located
+    tests_dir = os.path.dirname(os.path.abspath(__file__))
+    os.chdir(tests_dir)
+
+    # Yield the filename only
+    filename_only = "3pqr.cif"
+    yield filename_only
+
+    # Restore original working directory after the test is done
+    os.chdir(original_cwd)
+
+
+# test get pdb file
+@pytest.fixture
+def fibronectin():
+    return "fibronectin pdb"
+
+
+def test_getpdb(fibronectin, get_registry):
+    name = get_pdb(fibronectin, get_registry)
+    assert name.endswith(".pdb")
+
+
+# test cleaning functions
+@pytest.fixture
+def cleaning_fxns():
+    return CleaningTools()
+
+
+def test_add_hydrogens_and_remove_water(path_to_cif, cleaning_fxns, get_registry):
+    result = cleaning_fxns._add_hydrogens_and_remove_water(path_to_cif, get_registry)
+    assert "Cleaned File" in result  # just want to make sur the function ran

tests/test_sim_fxns.py

@@ -0,0 +1,48 @@
+from unittest.mock import mock_open, patch
+
+import pytest
+
+from mdagent.tools.base_tools.simulation_tools import SimulationFunctions
+
+# Test functions in simulation tools
+
+
+@pytest.fixture
+def sim_fxns():
+    return SimulationFunctions()
+
+
+@patch("os.path.exists")
+@patch("os.listdir")
+def test_extract_parameters_path(mock_listdir, mock_exists, sim_fxns):
+    # Test when parameters.json exists
+    mock_exists.return_value = True
+    assert sim_fxns._extract_parameters_path() == "simulation_parameters_summary.json"
+    mock_exists.assert_called_once_with("simulation_parameters_summary.json")
+    mock_exists.reset_mock()  # Reset the mock for the next scenario
+
+    # Test when parameters.json does not exist, but some_parameters.json does
+    mock_exists.return_value = False
+    mock_listdir.return_value = ["some_parameters.json", "other_file.txt"]
+    assert sim_fxns._extract_parameters_path() == "some_parameters.json"
+
+    # Test when no appropriate file exists
+    mock_listdir.return_value = ["other_file.json", "other_file.txt"]
+    with pytest.raises(ValueError) as e:
+        sim_fxns._extract_parameters_path()
+    assert str(e.value) == "No parameters.json file found in directory."
+
+
+@patch(
+    "builtins.open",
+    new_callable=mock_open,
+    read_data='{"param1": "value1", "param2": "value2"}',
+)
+@patch("json.load")
+def test_setup_simulation_from_json(mock_json_load, mock_file_open, sim_fxns):
+    # Define the mock behavior for json.load
+    mock_json_load.return_value = {"param1": "value1", "param2": "value2"}
+    params = sim_fxns._setup_simulation_from_json("test_file.json")
+    mock_file_open.assert_called_once_with("test_file.json", "r")
+    mock_json_load.assert_called_once()
+    assert params == {"param1": "value1", "param2": "value2"}