convert the rest of the test case to pytest

tests/unit/tools/test_generate_ion_image.py

@@ -1,5 +1,4 @@
-import unittest
-from unittest.mock import MagicMock, patch, ANY
+from unittest.mock import MagicMock, ANY
 
 import numpy as np
 import pytest
@@ -69,78 +68,74 @@ def test_generate_channel_values(mocker, mock_generate: GenerateIonImage, mock_p
     )
 
 
-class TestGenerateIonImage(unittest.TestCase):
-    def setUp(self) -> None:
-        self.mock_parallel_config = MagicMock(name="mock_parallel_config")
-        self.mock_generate = GenerateIonImage(parallel_config=self.mock_parallel_config)
-
-    @patch.object(GenerateIonImage, "_compute_for_mz_ranges")
-    @patch.object(ReadSpectraParallel, "from_config")
-    @patch("depiction.tools.generate_ion_image.MultiChannelImage")
-    def test_generate_range_images_for_file(
-        self, mock_multi_channel_image, mock_from_config, method_compute_for_mz_ranges
-    ) -> None:
-        mock_input_file = MagicMock(name="input_file", spec=["coordinates_2d"])
-        mock_mz_ranges = MagicMock(name="mz_ranges", spec=[])
-
-        result = self.mock_generate.generate_range_images_for_file(
-            input_file=mock_input_file,
-            mz_ranges=mock_mz_ranges,
-            channel_names=None,
-        )
-        mock_from_config.assert_called_once_with(self.mock_parallel_config)
-        mock_parallelize = mock_from_config.return_value
-        mock_parallelize.map_chunked.assert_called_once_with(
-            read_file=mock_input_file,
-            operation=method_compute_for_mz_ranges,
-            bind_args=dict(mz_ranges=mock_mz_ranges),
-            reduce_fn=ANY,
-        )
-        # check that the reduce_fn is behaving as expected
-        reduce_fn = mock_parallelize.map_chunked.call_args[1]["reduce_fn"]
-        reduced = reduce_fn([np.array([[1], [2]]), np.array([[3], [4]])])
-        np.testing.assert_array_equal(np.array([[1], [2], [3], [4]]), reduced)
-
-        mock_multi_channel_image.from_numpy_sparse.assert_called_once_with(
-            values=mock_parallelize.map_chunked.return_value,
-            coordinates=mock_input_file.coordinates_2d,
-            channel_names=None,
-            bg_value=np.nan,
-        )
-        self.assertEqual(mock_multi_channel_image.from_numpy_sparse.return_value, result)
-
-    def test_compute_for_mz_ranges(self) -> None:
-        mock_reader = MagicMock(name="reader")
-        mock_reader.get_spectrum.side_effect = {
-            7: (np.array([1, 2, 3, 4, 4.2]), np.array([0, 0, 1, 1, 1])),
-            11: (np.array([1, 2, 3, 4, 4.2]), np.array([1, 1, 1, 0, 0])),
-        }.__getitem__
-        mz_ranges = [(1, 3), (3, 4)]
-
-        result = GenerateIonImage._compute_for_mz_ranges(reader=mock_reader, mz_ranges=mz_ranges, spectra_ids=[7, 11])
-
-        self.assertTupleEqual((2, 2), result.shape)
-        np.testing.assert_array_equal([1.0, 2.0], result[0])
-        np.testing.assert_array_equal([3.0, 1.0], result[1])
-
-    def test_compute_channels_chunk(self) -> None:
-        mock_reader = MagicMock(name="reader")
-        mock_reader.get_spectrum.side_effect = {
-            7: (np.array([1, 2, 3, 4, 4.2]), np.array([0, 0, 1, 1, 1])),
-            11: (np.array([1, 2, 3, 4, 4.2]), np.array([1, 1, 1, 0, 0])),
-        }.__getitem__
-        mz_values = [1, 3, 4]
-        tol = [0.5, 0.5, 0.5]
-        spectra_ids = [7, 11]
-
-        result = GenerateIonImage._compute_channels_chunk(
-            reader=mock_reader, spectra_ids=spectra_ids, mz_values=mz_values, tol_values=tol
-        )
-
-        self.assertTupleEqual((2, 3), result.shape)
-        np.testing.assert_array_equal([0, 1, 2], result[0])
-        np.testing.assert_array_equal([1, 1, 0], result[1])
+def test_compute_for_mz_ranges() -> None:
+    mock_reader = MagicMock(name="reader")
+    mock_reader.get_spectrum.side_effect = {
+        7: (np.array([1, 2, 3, 4, 4.2]), np.array([0, 0, 1, 1, 1])),
+        11: (np.array([1, 2, 3, 4, 4.2]), np.array([1, 1, 1, 0, 0])),
+    }.__getitem__
+    mz_ranges = [(1, 3), (3, 4)]
+
+    result = GenerateIonImage._compute_for_mz_ranges(reader=mock_reader, mz_ranges=mz_ranges, spectra_ids=[7, 11])
+
+    assert result.shape == (2, 2)
+    np.testing.assert_array_equal([1.0, 2.0], result[0])
+    np.testing.assert_array_equal([3.0, 1.0], result[1])
+
+
+def test_compute_channels_chunk() -> None:
+    mock_reader = MagicMock(name="reader")
+    mock_reader.get_spectrum.side_effect = {
+        7: (np.array([1, 2, 3, 4, 4.2]), np.array([0, 0, 1, 1, 1])),
+        11: (np.array([1, 2, 3, 4, 4.2]), np.array([1, 1, 1, 0, 0])),
+    }.__getitem__
+    mz_values = [1, 3, 4]
+    tol = [0.5, 0.5, 0.5]
+    spectra_ids = [7, 11]
+
+    result = GenerateIonImage._compute_channels_chunk(
+        reader=mock_reader, spectra_ids=spectra_ids, mz_values=mz_values, tol_values=tol
+    )
+
+    assert result.shape == (2, 3)
+    np.testing.assert_array_equal([0, 1, 2], result[0])
+    np.testing.assert_array_equal([1, 1, 0], result[1])
+
+
+def test_generate_range_images_for_file(mocker, mock_generate: GenerateIonImage, mock_parallel_config) -> None:
+    mock_from_config = mocker.patch.object(ReadSpectraParallel, "from_config")
+    method_compute_for_mz_ranges = mocker.patch.object(GenerateIonImage, "_compute_for_mz_ranges")
+    mock_multi_channel_image = mocker.patch("depiction.tools.generate_ion_image.MultiChannelImage")
+
+    mock_input_file = MagicMock(name="input_file", spec=["coordinates_2d"])
+    mock_mz_ranges = MagicMock(name="mz_ranges", spec=[])
+
+    result = mock_generate.generate_range_images_for_file(
+        input_file=mock_input_file,
+        mz_ranges=mock_mz_ranges,
+        channel_names=None,
+    )
+    mock_from_config.assert_called_once_with(mock_parallel_config)
+    mock_parallelize = mock_from_config.return_value
+    mock_parallelize.map_chunked.assert_called_once_with(
+        read_file=mock_input_file,
+        operation=method_compute_for_mz_ranges,
+        bind_args=dict(mz_ranges=mock_mz_ranges),
+        reduce_fn=ANY,
+    )
+    # check that the reduce_fn is behaving as expected
+    reduce_fn = mock_parallelize.map_chunked.call_args[1]["reduce_fn"]
+    reduced = reduce_fn([np.array([[1], [2]]), np.array([[3], [4]])])
+    np.testing.assert_array_equal(np.array([[1], [2], [3], [4]]), reduced)
+
+    mock_multi_channel_image.from_numpy_sparse.assert_called_once_with(
+        values=mock_parallelize.map_chunked.return_value,
+        coordinates=mock_input_file.coordinates_2d,
+        channel_names=None,
+        bg_value=np.nan,
+    )
+    assert result == mock_multi_channel_image.from_numpy_sparse.return_value
 
 
 if __name__ == "__main__":
-    unittest.main()
+    pytest.main()