rearranged tests to subfiles

tests/test_analysis_tools.py

@@ -0,0 +1,128 @@
+import os
+from unittest.mock import MagicMock, mock_open, patch
+
+import pytest
+
+from mdagent.tools.base_tools import VisFunctions
+from mdagent.tools.base_tools.analysis_tools.plot_tools import PlottingTools
+from mdagent.utils import PathRegistry
+
+
+@pytest.fixture
+def get_registry():
+    return PathRegistry()
+
+
+@pytest.fixture
+def plotting_tools(get_registry):
+    return PlottingTools(get_registry)
+
+
+@pytest.fixture
+def vis_fxns(get_registry):
+    return VisFunctions(get_registry)
+
+
+@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)
+
+
+def test_process_csv(plotting_tools):
+    mock_csv_content = "Time,Value1,Value2\n1,10,20\n2,15,25"
+    mock_reader = MagicMock()
+    mock_reader.fieldnames = ["Time", "Value1", "Value2"]
+    mock_reader.__iter__.return_value = iter(
+        [
+            {"Time": "1", "Value1": "10", "Value2": "20"},
+            {"Time": "2", "Value1": "15", "Value2": "25"},
+        ]
+    )
+    plotting_tools.file_path = "mock_file.csv"
+    plotting_tools.file_name = "mock_file.csv"
+    with patch("builtins.open", mock_open(read_data=mock_csv_content)):
+        with patch("csv.DictReader", return_value=mock_reader):
+            plotting_tools.process_csv()
+
+    assert plotting_tools.headers == ["Time", "Value1", "Value2"]
+    assert len(plotting_tools.matched_headers) == 1
+    assert plotting_tools.matched_headers[0][1] == "Time"
+    assert len(plotting_tools.data) == 2
+    assert (
+        plotting_tools.data[0]["Time"] == "1"
+        and plotting_tools.data[0]["Value1"] == "10"
+    )
+
+
+def test_plot_data(plotting_tools):
+    # Test successful plot generation
+    data_success = [
+        {"Time": "1", "Value1": "10", "Value2": "20"},
+        {"Time": "2", "Value1": "15", "Value2": "25"},
+    ]
+    headers = ["Time", "Value1", "Value2"]
+    matched_headers = [(0, "Time")]
+
+    with patch("matplotlib.pyplot.figure"), patch("matplotlib.pyplot.plot"), patch(
+        "matplotlib.pyplot.xlabel"
+    ), patch("matplotlib.pyplot.ylabel"), patch("matplotlib.pyplot.title"), patch(
+        "matplotlib.pyplot.savefig"
+    ), patch(
+        "matplotlib.pyplot.close"
+    ):
+        plotting_tools.data = data_success
+        plotting_tools.headers = headers
+        plotting_tools.matched_headers = matched_headers
+        created_plots = plotting_tools.plot_data()
+        assert "time_vs_value1.png" in created_plots
+        assert "time_vs_value2.png" in created_plots
+
+    # Test failure due to non-numeric data
+    data_failure = [
+        {"Time": "1", "Value1": "A", "Value2": "B"},
+        {"Time": "2", "Value1": "C", "Value2": "D"},
+    ]
+
+    plotting_tools.data = data_failure
+    plotting_tools.headers = headers
+    plotting_tools.matched_headers = matched_headers
+
+    with pytest.raises(Exception) as excinfo:
+        plotting_tools.plot_data()
+        assert "All plots failed due to non-numeric data." in str(excinfo.value)
+
+
+@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)
+    assert result == "Visualization created"
+
+
+def test_find_png(vis_fxns):
+    vis_fxns.starting_files = os.listdir(".")
+    test_file = "test_image.png"
+    with open(test_file, "w") as f:
+        f.write("")
+    png_files = vis_fxns._find_png()
+    assert test_file in png_files
+
+    os.remove(test_file)
+
+
+def test_create_notebook(path_to_cif, vis_fxns):
+    result = vis_fxns.create_notebook(path_to_cif)
+    path_to_notebook = path_to_cif.split(".")[0] + "_vis.ipynb"
+    os.remove(path_to_notebook)
+    assert result == "Visualization Complete"