modernize

tests/unit/spectrum/peak_filtering/test_chain_filters.py

@@ -1,75 +1,76 @@
-import unittest
-from unittest.mock import MagicMock
+import pytest
+from pytest_mock import MockerFixture
 
 from depiction.spectrum.peak_filtering import ChainFilters
 
 
-class TestChainFilters(unittest.TestCase):
-    def setUp(self) -> None:
-        self.mock_filter_1 = MagicMock(name="mock_filter_1")
-        self.mock_filter_2 = MagicMock(name="mock_filter_2")
-        self.chain_filters = ChainFilters(
-            filters=[
-                self.mock_filter_1,
-                self.mock_filter_2,
-            ]
-        )
+@pytest.fixture()
+def mock_filter_1(mocker: MockerFixture):
+    return mocker.MagicMock(name="mock_filter_1")
 
-    def test_filter_index_peaks(self) -> None:
-        self.mock_filter_1.filter_index_peaks.return_value = [1, 2, 3]
-        self.mock_filter_2.filter_index_peaks.return_value = [2, 3]
-        mock_spectrum_mz_arr = MagicMock(name="mock_spectrum_mz_arr")
-        mock_spectrum_int_arr = MagicMock(name="mock_spectrum_int_arr")
-        peak_idx_arr = [1, 2, 3, 4]
 
-        result_peak_idx_arr = self.chain_filters.filter_index_peaks(
-            spectrum_mz_arr=mock_spectrum_mz_arr,
-            spectrum_int_arr=mock_spectrum_int_arr,
-            peak_idx_arr=peak_idx_arr,
-        )
+@pytest.fixture()
+def mock_filter_2(mocker: MockerFixture):
+    return mocker.MagicMock(name="mock_filter_2")
 
-        self.assertEqual(result_peak_idx_arr, [2, 3])
-        self.mock_filter_1.filter_index_peaks.assert_called_once_with(
-            mock_spectrum_mz_arr,
-            mock_spectrum_int_arr,
-            peak_idx_arr,
-        )
-        self.mock_filter_2.filter_index_peaks.assert_called_once_with(
-            mock_spectrum_mz_arr,
-            mock_spectrum_int_arr,
-            [1, 2, 3],
-        )
 
-    def test_filter_peaks(self) -> None:
-        self.mock_filter_1.filter_peaks.return_value = ([1, 2, 3], [4, 5, 6])
-        self.mock_filter_2.filter_peaks.return_value = ([2, 3], [5, 6])
-        mock_spectrum_mz_arr = MagicMock(name="mock_spectrum_mz_arr")
-        mock_spectrum_int_arr = MagicMock(name="mock_spectrum_int_arr")
-        peak_mz_arr = [1, 2, 3, 4]
-        peak_int_arr = [4, 5, 6, 7]
+@pytest.fixture()
+def chain_filters(mock_filter_1, mock_filter_2):
+    return ChainFilters(filters=[mock_filter_1, mock_filter_2])
 
-        result_peak_mz_arr, result_peak_int_arr = self.chain_filters.filter_peaks(
-            spectrum_mz_arr=mock_spectrum_mz_arr,
-            spectrum_int_arr=mock_spectrum_int_arr,
-            peak_mz_arr=peak_mz_arr,
-            peak_int_arr=peak_int_arr,
-        )
 
-        self.assertEqual(result_peak_mz_arr, [2, 3])
-        self.assertEqual(result_peak_int_arr, [5, 6])
-        self.mock_filter_1.filter_peaks.assert_called_once_with(
-            mock_spectrum_mz_arr,
-            mock_spectrum_int_arr,
-            peak_mz_arr,
-            peak_int_arr,
-        )
-        self.mock_filter_2.filter_peaks.assert_called_once_with(
-            mock_spectrum_mz_arr,
-            mock_spectrum_int_arr,
-            [1, 2, 3],
-            [4, 5, 6],
-        )
+def test_filter_index_peaks(mocker, mock_filter_1, mock_filter_2, chain_filters) -> None:
+    mock_filter_1.filter_index_peaks.return_value = [1, 2, 3]
+    mock_filter_2.filter_index_peaks.return_value = [2, 3]
+    mock_spectrum_mz_arr = mocker.MagicMock(name="mock_spectrum_mz_arr")
+    mock_spectrum_int_arr = mocker.MagicMock(name="mock_spectrum_int_arr")
+    peak_idx_arr = [1, 2, 3, 4]
 
+    result_peak_idx_arr = chain_filters.filter_index_peaks(
+        spectrum_mz_arr=mock_spectrum_mz_arr,
+        spectrum_int_arr=mock_spectrum_int_arr,
+        peak_idx_arr=peak_idx_arr,
+    )
 
-if __name__ == "__main__":
-    unittest.main()
+    assert result_peak_idx_arr == [2, 3]
+    mock_filter_1.filter_index_peaks.assert_called_once_with(
+        mock_spectrum_mz_arr,
+        mock_spectrum_int_arr,
+        peak_idx_arr,
+    )
+    mock_filter_2.filter_index_peaks.assert_called_once_with(
+        mock_spectrum_mz_arr,
+        mock_spectrum_int_arr,
+        [1, 2, 3],
+    )
+
+
+def test_filter_peaks(mocker, mock_filter_1, mock_filter_2, chain_filters) -> None:
+    mock_filter_1.filter_peaks.return_value = ([1, 2, 3], [4, 5, 6])
+    mock_filter_2.filter_peaks.return_value = ([2, 3], [5, 6])
+    mock_spectrum_mz_arr = mocker.MagicMock(name="mock_spectrum_mz_arr")
+    mock_spectrum_int_arr = mocker.MagicMock(name="mock_spectrum_int_arr")
+    peak_mz_arr = [1, 2, 3, 4]
+    peak_int_arr = [4, 5, 6, 7]
+
+    result_peak_mz_arr, result_peak_int_arr = chain_filters.filter_peaks(
+        spectrum_mz_arr=mock_spectrum_mz_arr,
+        spectrum_int_arr=mock_spectrum_int_arr,
+        peak_mz_arr=peak_mz_arr,
+        peak_int_arr=peak_int_arr,
+    )
+
+    assert result_peak_mz_arr == [2, 3]
+    assert result_peak_int_arr == [5, 6]
+    mock_filter_1.filter_peaks.assert_called_once_with(
+        mock_spectrum_mz_arr,
+        mock_spectrum_int_arr,
+        peak_mz_arr,
+        peak_int_arr,
+    )
+    mock_filter_2.filter_peaks.assert_called_once_with(
+        mock_spectrum_mz_arr,
+        mock_spectrum_int_arr,
+        [1, 2, 3],
+        [4, 5, 6],
+    )