Update similarity.py to improve test coverage to 99%

selector/measures/tests/test_similarity.py

@@ -0,0 +1,154 @@
+# -*- coding: utf-8 -*-
+#
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
+#
+# This file is part of Selector.
+#
+# Selector is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 3
+# of the License, or (at your option) any later version.
+#
+# Selector is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>
+#
+# --
+"""Test Similarity Module."""
+
+import numpy as np
+import pytest
+
+from selector.measures.similarity import (
+    pairwise_similarity_bit,
+    tanimoto,
+    modified_tanimoto,
+    scaled_similarity_matrix,
+    similarity_index,
+)
+
+
+def test_tanimoto_value():
+    """Check correctness of Tanimoto similarity formula."""
+    a = np.array([1, 0, 1])
+    b = np.array([1, 1, 0])
+    result = tanimoto(a, b)
+    assert pytest.approx(result) == 1 / 3
+
+
+def test_tanimoto_error():
+    """Check tanimoto raises error for invalid input format."""
+    with pytest.raises(ValueError):
+        tanimoto(np.array([[1, 2]]), np.array([1, 2]))
+
+
+def test_tanimoto_shape_mismatch():
+    """Check tanimoto raises error when vector shapes differ."""
+    with pytest.raises(ValueError):
+        tanimoto(np.array([1, 2]), np.array([1, 2, 3]))
+
+
+def test_modified_all_zero():
+    """Check modified tanimoto handles zero vectors safely."""
+    a = np.zeros(5)
+    b = np.zeros(5)
+    assert isinstance(modified_tanimoto(a, b), float)
+
+
+def test_modified_partial_case():
+    """Check modified tanimoto returns valid float for partial overlap."""
+    a = np.array([1, 0, 1, 0])
+    b = np.array([1, 1, 0, 0])
+    result = modified_tanimoto(a, b)
+    assert isinstance(result, float)
+
+
+def test_invalid_metric():
+    """Check pairwise_similarity_bit rejects invalid metric name."""
+    X = np.array([[1, 0], [0, 1]])
+    with pytest.raises(ValueError):
+        pairwise_similarity_bit(X, "wrong")
+
+
+def test_pairwise_similarity_valid():
+    """Check pairwise similarity returns correct matrix shape."""
+    X = np.array([[1, 0], [0, 1]])
+    result = pairwise_similarity_bit(X, "tanimoto")
+    assert result.shape == (2, 2)
+
+
+def test_pairwise_invalid_dimension():
+    """Check pairwise_similarity_bit rejects 1D input."""
+    X = np.array([1, 0, 1])
+    with pytest.raises(ValueError):
+        pairwise_similarity_bit(X, "tanimoto")
+
+
+def test_scaled_identity():
+    """Check scaled similarity preserves identity matrix."""
+    X = np.eye(3)
+    assert np.allclose(scaled_similarity_matrix(X), X)
+
+
+def test_scaled_general_case():
+    """Check scaled similarity preserves matrix shape."""
+    X = np.array([[2.0, 1.0], [1.0, 3.0]])
+    result = scaled_similarity_matrix(X)
+    assert result.shape == X.shape
+
+
+def test_scaled_not_square():
+    """Check scaled similarity rejects non-square matrix."""
+    X = np.array([[1, 2, 3], [4, 5, 6]])
+    with pytest.raises(ValueError):
+        scaled_similarity_matrix(X)
+
+
+def test_scaled_invalid_values():
+    """Check scaled similarity rejects invalid diagonal values."""
+    X = np.array([[0, 1], [1, 2]])
+    with pytest.raises(ValueError):
+        scaled_similarity_matrix(X)
+
+
+def test_similarity_invalid():
+    """Check similarity_index rejects invalid method name."""
+    x = np.array([1, 0])
+    y = np.array([0, 1])
+    with pytest.raises(ValueError):
+        similarity_index(x, y, "bad")
+
+
+def test_similarity_shape_mismatch():
+    """Check similarity_index rejects mismatched vector shapes."""
+    x = np.array([1, 0, 1])
+    y = np.array([1, 0])
+    with pytest.raises(ValueError):
+        similarity_index(x, y, "RR")
+
+
+def test_similarity_dimension_error():
+    """Check similarity_index rejects 2D input."""
+    x = np.array([[1, 0]])
+    y = np.array([1, 0])
+    with pytest.raises(ValueError):
+        similarity_index(x, y, "RR")
+
+
+@pytest.mark.parametrize(
+    "idx",
+    ["AC", "BUB", "CT1", "CT2", "Fai", "Gle", "Ja", "JT", "RT", "RR", "SM", "SS1", "SS2"]
+)
+def test_similarity_all_indices(idx):
+    """Check all similarity index methods return float."""
+    x = np.array([1, 0, 1])
+    y = np.array([1, 1, 0])
+    result = similarity_index(x, y, idx)
+    assert isinstance(result, float)