improve test coverage

.gitignore

@@ -6,4 +6,5 @@ _version.py
 .tox
 venv
 build
-.coverage
+.coverage
+*.zarr/

src/tests/test_export.py

@@ -1,19 +1,210 @@
-from zarr_tools import convert, __main__
-import numpy as np
-import dask.array as da
+import json
 import os
 import shutil
+from unittest.mock import MagicMock, Mock, patch
+
+import dask.array as da
+import numpy as np
+import pytest
+
+from zarr_tools import __main__, convert
+
 
 def test_convert():
 
-    data = np.zeros((15,3,2**12, 2**12), dtype="uint16")
+    data = np.zeros((15, 3, 2**12, 2**12), dtype="uint16")
     path = "test.zarr"
-    convert.to_zarr(
-        da.from_array(data),
-        path = path,
-        steps=3
-    )
+    convert.to_zarr(da.from_array(data), path=path, steps=3)
     for i in range(3):
-        assert da.from_zarr(os.path.join(path, str(i))).shape[-1] == 2**(12-i)
-
-    shutil.rmtree(path)
+        assert da.from_zarr(os.path.join(path, str(i))).shape[-1] == 2 ** (
+            12 - i
+        )
+
+    shutil.rmtree(path)
+
+
+def test_convert_dry_run():
+    """Test dry_run mode in to_zarr"""
+    data = np.zeros((2, 3, 128, 128), dtype="uint16")
+    path = "test_dry_run.zarr"
+
+    # Run with dry_run=True
+    result = convert.to_zarr(
+        da.from_array(data), path=path, steps=2, dry_run=True
+    )
+
+    # Verify the path is returned but nothing is saved
+    assert result == path
+    # Directory might be created but should be empty or minimal
+    if os.path.exists(path):
+        shutil.rmtree(path)
+
+
+def test_convert_with_custom_channel_axis():
+    """Test to_zarr with custom channel_axis"""
+    data = np.zeros((2, 3, 128, 128), dtype="uint16")
+    path = "test_custom_channel.zarr"
+
+    result = convert.to_zarr(
+        da.from_array(data), path=path, steps=2, channel_axis=0
+    )
+
+    assert result == path
+    assert os.path.exists(path)
+
+    shutil.rmtree(path)
+
+
+def test_save_metadata():
+    """Test save_metadata function"""
+    output = "test_metadata.zarr"
+    os.makedirs(output, exist_ok=True)
+
+    # Create a mock ND2File object
+    mock_nd2 = Mock()
+    mock_nd2.custom_data = {
+        "test_key": "test_value",
+        "NDControlV1_0": {"existing": "data"},
+    }
+
+    meta_path = __main__.save_metadata(mock_nd2, output)
+
+    assert os.path.exists(meta_path)
+    assert meta_path == os.path.join(output, ".metadata")
+
+    # Verify the metadata was written correctly
+    with open(meta_path) as f:
+        saved_meta = json.load(f)
+        assert "test_key" in saved_meta
+        assert saved_meta["test_key"] == "test_value"
+
+    shutil.rmtree(output)
+
+
+def test_save_metadata_type_error():
+    """Test save_metadata with non-serializable data"""
+    output = "test_metadata_error.zarr"
+    os.makedirs(output, exist_ok=True)
+
+    # Create a mock ND2File with non-serializable data
+    mock_nd2 = Mock()
+    mock_nd2.custom_data = {
+        "non_serializable": lambda x: x  # Function cannot be JSON serialized
+    }
+
+    with pytest.raises(TypeError):
+        __main__.save_metadata(mock_nd2, output)
+
+    shutil.rmtree(output)
+
+
+def test_get_lut():
+    """Test get_lut function"""
+    mock_nd2 = Mock()
+    mock_nd2.sizes = {"C": 2}
+    mock_nd2.custom_data = {
+        "LUTDataV1_0": {
+            "LutParam": {
+                "CompLutParam": {
+                    "00": {"MinSrc": [100], "MaxSrc": [1000]},
+                    "01": {"MinSrc": [200], "MaxSrc": [2000]},
+                }
+            }
+        }
+    }
+
+    lut = __main__.get_lut(mock_nd2)
+
+    assert lut is not None
+    assert len(lut) == 2
+    assert lut[0] == [100, 1000]
+    assert lut[1] == [200, 2000]
+
+
+def test_get_lut_missing_data():
+    """Test get_lut with missing LUT data"""
+    mock_nd2 = Mock()
+    mock_nd2.sizes = {"C": 2}
+    mock_nd2.custom_data = {}
+
+    lut = __main__.get_lut(mock_nd2)
+
+    assert lut is None
+
+
+@patch("zarr_tools.__main__.nd2.ND2File")
+def test_main(mock_nd2_class):
+    """Test main function"""
+    # Create a mock ND2File instance
+    mock_nd2_instance = MagicMock()
+    mock_nd2_instance.sizes = {"C": 2, "Y": 128, "X": 128}
+    mock_data = da.zeros((2, 128, 128), dtype="uint16")
+    mock_nd2_instance.to_dask.return_value = mock_data
+    mock_nd2_instance.custom_data = {
+        "LUTDataV1_0": {
+            "LutParam": {
+                "CompLutParam": {
+                    "00": {"MinSrc": [0], "MaxSrc": [100]},
+                    "01": {"MinSrc": [0], "MaxSrc": [100]},
+                }
+            }
+        }
+    }
+
+    mock_nd2_class.return_value = mock_nd2_instance
+
+    # Create a temporary nd2 file path (doesn't need to exist due to mocking)
+    nd2_path = "test_file.nd2"
+    output_path = "test_output.zarr"
+
+    with pytest.raises(SystemExit) as exc_info:
+        __main__.main(nd2_path, output=output_path, steps=2, dry_run=True)
+
+    assert exc_info.value.code == 0
+    mock_nd2_class.assert_called_once_with(nd2_path)
+
+
+@patch("zarr_tools.__main__.nd2.ND2File")
+def test_main_no_channel_axis(mock_nd2_class):
+    """Test main function without channel axis"""
+    mock_nd2_instance = MagicMock()
+    mock_nd2_instance.sizes = {"Y": 128, "X": 128}  # No 'C' dimension
+    mock_data = da.zeros((128, 128), dtype="uint16")
+    mock_nd2_instance.to_dask.return_value = mock_data
+    mock_nd2_instance.custom_data = {}
+
+    mock_nd2_class.return_value = mock_nd2_instance
+
+    nd2_path = "test_file_no_channel.nd2"
+
+    with pytest.raises(SystemExit) as exc_info:
+        __main__.main(nd2_path, steps=2, dry_run=True)
+
+    assert exc_info.value.code == 0
+
+
+@patch("zarr_tools.__main__.nd2.ND2File")
+@patch("zarr_tools.__main__.save_metadata")
+def test_main_metadata_save_fails(mock_save_metadata, mock_nd2_class):
+    """Test main function when metadata saving fails"""
+    # Create a mock ND2File instance
+    mock_nd2_instance = MagicMock()
+    mock_nd2_instance.sizes = {"C": 2, "Y": 128, "X": 128}
+    mock_data = da.zeros((2, 128, 128), dtype="uint16")
+    mock_nd2_instance.to_dask.return_value = mock_data
+    mock_nd2_instance.custom_data = {}
+
+    mock_nd2_class.return_value = mock_nd2_instance
+
+    # Make save_metadata raise an exception
+    mock_save_metadata.side_effect = Exception("Metadata save failed")
+
+    nd2_path = "test_file_metadata_fail.nd2"
+    output_path = "test_output_metadata_fail.zarr"
+
+    # The main function should catch the exception and exit normally
+    with pytest.raises(SystemExit) as exc_info:
+        __main__.main(nd2_path, output=output_path, steps=2, dry_run=True)
+
+    assert exc_info.value.code == 0
+    mock_save_metadata.assert_called_once()