distclassipy 0.2.0a0__py3-none-any.whl → 0.2.2a1__py3-none-any.whl

distclassipy/distances.py

@@ -48,1437 +48,1517 @@ import numpy as np
 
 import scipy
 
+# Default epsilon value to avoid division by zero
+EPSILON = np.finfo(float).eps
+_ALL_METRICS = [
+    "euclidean",
+    "braycurtis",
+    "canberra",
+    "cityblock",
+    "chebyshev",
+    "clark",
+    "correlation",
+    "cosine",
+    "hellinger",
+    "jaccard",
+    "lorentzian",
+    "marylandbridge",
+    "meehl",
+    "motyka",
+    "soergel",
+    "wave_hedges",
+    "kulczynski",
+    "add_chisq",
+    "acc",
+    "chebyshev_min",
+    "czekanowski",
+    "dice",
+    "divergence",
+    "google",
+    "gower",
+    "jeffreys",
+    "jensenshannon_divergence",
+    "jensen_difference",
+    "kumarjohnson",
+    "matusita",
+    "minkowski",
+    "penroseshape",
+    "prob_chisq",
+    "ruzicka",
+    "sorensen",
+    "squared_chisq",
+    "squaredchord",
+    "squared_euclidean",
+    "taneja",
+    "tanimoto",
+    "topsoe",
+    "vicis_symmetric_chisq",
+    "vicis_wave_hedges",
+]
+
+
+def euclidean(u, v, w=None):
+    """Calculate the Euclidean distance between two vectors.
+
+    The Euclidean distance is the "ordinary" straight-line distance between two
+    points in Euclidean space.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Euclidean distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return scipy.spatial.distance.euclidean(u, v, w)
+
+
+def braycurtis(u, v, w=None):
+    """Calculate the Bray-Curtis distance between two vectors.
+
+    The Bray-Curtis distance is a measure of dissimilarity between two non-negative
+    vectors, often used in ecology to measure the compositional dissimilarity
+    between two sites based on counts of species at both sites. It is closely
+    related to the Sørensen distance and is also known as Bray-Curtis
+    dissimilarity.
+
+    Notes
+    -----
+        When used for comparing two probability density functions (pdfs),
+        the Bray-Curtis distance equals the Cityblock distance divided by 2.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Bray-Curtis distance between the two vectors.
+
+    References
+    ----------
+        1. Bray JR, Curtis JT (1957) An ordination of the upland forest of
+           southern Wisconsin. Ecological Monographs, 27, 325-349.
+        2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4), 300-307.
+        3. https://en.wikipedia.org/wiki/Bray–Curtis_dissimilarity
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return scipy.spatial.distance.braycurtis(u, v, w)
+
+
+def canberra(u, v, w=None):
+    """Calculate the Canberra distance between two vectors.
+
+    The Canberra distance is a weighted version of the Manhattan distance, used
+    in numerical analysis.
+
+    Notes
+    -----
+        When `u[i]` and `v[i]` are 0 for given i, then the fraction 0/0 = 0
+        is used in the calculation.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Canberra distance between the two vectors.
 
-class Distance:
-    """A class to calculate various distance metrics between vectors.
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return scipy.spatial.distance.canberra(u, v, w)
 
-    This class provides methods to compute different types of distances between
-    two vectors, such as Euclidean, Manhattan, Canberra, and other statistical
-    distances. Each method takes two vectors as input and returns the calculated
-    distance. The class can handle both numpy arrays and lists, converting them
-    internally to numpy arrays for computation.
 
-    Attributes
+def cityblock(u, v, w=None):
+    """Calculate the Cityblock (Manhattan) distance between two vectors.
+
+    Parameters
     ----------
-    epsilon : float, optional
-        A small value to avoid division by zero errors in certain distance
-        calculations. Default is the machine precision for float data type.
+    - u, v: Input vectors between which the distance is to be calculated.
 
-    Methods
+    Returns
     -------
-    acc(u, v)
-        Returns the average of Cityblock/Manhattan and Chebyshev distances.
-    add_chisq(u, v)
-        Returns the Additive Symmetric Chi-square distance.
-    (Other methods are not listed here for brevity)
-
-    Examples
-    --------
-    >>> dist = Distance()
-    >>> u = [1, 2, 3]
-    >>> v = [4, 5, 6]
-    >>> print(dist.acc(u, v))
-    5.0
+    - The Cityblock distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4):300-307.
+
+    Synonyms:
+        City block distance
+        Manhattan distance
+        Rectilinear distance
+        Taxicab norm
+
+    Notes
+    -----
+        Cityblock distance between two probability density functions
+        (pdfs) equals:
+        1. Non-intersection distance multiplied by 2.
+        2. Gower distance multiplied by vector length.
+        3. Bray-Curtis distance multiplied by 2.
+        4. Google distance multiplied by 2.
     """
+    u, v = np.asarray(u), np.asarray(v)
+    return scipy.spatial.distance.cityblock(u, v, w)
+
+
+def chebyshev(u, v, w=None):
+    """Calculate the Chebyshev distance between two vectors.
+
+    The Chebyshev distance is a metric defined on a vector space where the distance
+    between two vectors
+    is the greatest of their differences along any coordinate dimension.
+
+    Synonyms:
+        Chessboard distance
+        King-move metric
+        Maximum value distance
+        Minimax approximation
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Chebyshev distance between the two vectors.
 
-    def __init__(self, epsilon=None):
-        """Initialize the Distance class with an optional epsilon value.
-
-        Parameters
-        ----------
-        - epsilon: A small value to avoid division by zero errors.
-        """
-        self.epsilon = np.finfo(float).eps if not epsilon else epsilon
-
-    def euclidean(self, u, v, w=None):
-        """Calculate the Euclidean distance between two vectors.
-
-        The Euclidean distance is the "ordinary" straight-line distance between two
-        points in Euclidean space.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Euclidean distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return scipy.spatial.distance.euclidean(u, v, w)
-
-    def braycurtis(self, u, v, w=None):
-        """Calculate the Bray-Curtis distance between two vectors.
-
-        The Bray-Curtis distance is a measure of dissimilarity between two non-negative
-        vectors, often used in ecology to measure the compositional dissimilarity
-        between two sites based on counts of species at both sites. It is closely
-        related to the Sørensen distance and is also known as Bray-Curtis
-        dissimilarity.
-
-        Notes
-        -----
-            When used for comparing two probability density functions (pdfs),
-            the Bray-Curtis distance equals the Cityblock distance divided by 2.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Bray-Curtis distance between the two vectors.
-
-        References
-        ----------
-            1. Bray JR, Curtis JT (1957) An ordination of the upland forest of
-               southern Wisconsin. Ecological Monographs, 27, 325-349.
-            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-            3. https://en.wikipedia.org/wiki/Bray–Curtis_dissimilarity
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return scipy.spatial.distance.braycurtis(u, v, w)
-
-    def canberra(self, u, v, w=None):
-        """Calculate the Canberra distance between two vectors.
-
-        The Canberra distance is a weighted version of the Manhattan distance, used
-        in numerical analysis.
-
-        Notes
-        -----
-            When `u[i]` and `v[i]` are 0 for given i, then the fraction 0/0 = 0
-            is used in the calculation.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Canberra distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return scipy.spatial.distance.canberra(u, v, w)
-
-    def cityblock(self, u, v, w=None):
-        """Calculate the Cityblock (Manhattan) distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Cityblock distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4):300-307.
-
-        Synonyms:
-            City block distance
-            Manhattan distance
-            Rectilinear distance
-            Taxicab norm
-
-        Notes
-        -----
-            Cityblock distance between two probability density functions
-            (pdfs) equals:
-            1. Non-intersection distance multiplied by 2.
-            2. Gower distance multiplied by vector length.
-            3. Bray-Curtis distance multiplied by 2.
-            4. Google distance multiplied by 2.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return scipy.spatial.distance.cityblock(u, v, w)
-
-    def chebyshev(self, u, v, w=None):
-        """Calculate the Chebyshev distance between two vectors.
-
-        The Chebyshev distance is a metric defined on a vector space where the distance
-        between two vectors
-        is the greatest of their differences along any coordinate dimension.
-
-        Synonyms:
-            Chessboard distance
-            King-move metric
-            Maximum value distance
-            Minimax approximation
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Chebyshev distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return scipy.spatial.distance.chebyshev(u, v, w)
-
-    def correlation(self, u, v, w=None, centered=True):
-        """Calculate the Pearson correlation distance between two vectors.
-
-        Returns a distance value between 0 and 2.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Pearson correlation distance between the two vectors.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        if len(u) < 2 or len(v) < 2:
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return scipy.spatial.distance.chebyshev(u, v, w)
+
+
+def correlation(u, v, w=None, centered=True):
+    """Calculate the Pearson correlation distance between two vectors.
+
+    Returns a distance value between 0 and 2.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Pearson correlation distance between the two vectors.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    if len(u) < 2 or len(v) < 2:
+        warnings.warn(
+            "Pearson correlation requires vectors of length at least 2.",
+            RuntimeWarning,
+        )
+        d = 0
+    else:
+        d = scipy.spatial.distance.correlation(u, v, w, centered)
+        if np.isnan(d) and (
+            np.allclose(u - np.mean(u), 0) or np.allclose(v - np.mean(v), 0)
+        ):
             warnings.warn(
-                "Pearson correlation requires vectors of length at least 2.",
+                "One of the vectors is constant; correlation is set to 0",
                 RuntimeWarning,
             )
             d = 0
-        else:
-            d = scipy.spatial.distance.correlation(u, v, w, centered)
-            if np.isnan(d) and (
-                np.allclose(u - np.mean(u), 0) or np.allclose(v - np.mean(v), 0)
-            ):
-                warnings.warn(
-                    "One of the vectors is constant; correlation is set to 0",
-                    RuntimeWarning,
-                )
-                d = 0
-        return d
-
-    def cosine(self, u, v, w=None):
-        """Calculate the cosine distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The cosine distance between the two vectors.
-
-        References
-        ----------
-            1. SciPy.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return scipy.spatial.distance.cosine(u, v, w)
-
-    def clark(self, u, v):
-        """Calculate the Clark distance between two vectors.
-
-        The Clark distance equals the square root of half of the divergence.
-
-        Notes
-        -----
-            When `u[i]` and `v[i]` are 0 for given i, then the fraction 0/0 = 0
-            is used in the calculation.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Clark distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        with np.errstate(divide="ignore", invalid="ignore"):
-            return np.sqrt(np.nansum(np.power(np.abs(u - v) / (u + v), 2)))
-
-    def hellinger(self, u, v):
-        """Calculate the Hellinger distance between two vectors.
-
-        The Hellinger distance is a measure of similarity between two probability
-        distributions.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Hellinger distance between the two vectors.
-
-        Notes
-        -----
-            This implementation produces values two times larger than values
-            obtained by Hellinger distance described in Wikipedia and also
-            in https://gist.github.com/larsmans/3116927.
-
-        References
-        ----------
-           1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-              Measures between Probability Density Functions. International
-              Journal of Mathematical Models and Methods in Applied Sciences.
-              1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
+    return d
+
+
+def cosine(u, v, w=None):
+    """Calculate the cosine distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The cosine distance between the two vectors.
+
+    References
+    ----------
+        1. SciPy.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return scipy.spatial.distance.cosine(u, v, w)
+
+
+def clark(u, v):
+    """Calculate the Clark distance between two vectors.
+
+    The Clark distance equals the square root of half of the divergence.
+
+    Notes
+    -----
+        When `u[i]` and `v[i]` are 0 for given i, then the fraction 0/0 = 0
+        is used in the calculation.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Clark distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    with np.errstate(divide="ignore", invalid="ignore"):
+        return np.sqrt(np.nansum(np.power(np.abs(u - v) / (u + v), 2)))
+
+
+def hellinger(u, v):
+    """Calculate the Hellinger distance between two vectors.
+
+    The Hellinger distance is a measure of similarity between two probability
+    distributions.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Hellinger distance between the two vectors.
+
+    Notes
+    -----
+        This implementation produces values two times larger than values
+        obtained by Hellinger distance described in Wikipedia and also
+        in https://gist.github.com/larsmans/3116927.
+
+    References
+    ----------
+       1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+          Measures between Probability Density Functions. International
+          Journal of Mathematical Models and Methods in Applied Sciences.
+          1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    # Clip negative values to zero for valid sqrt
+    with np.errstate(divide="ignore", invalid="ignore"):
+        u = np.clip(u, a_min=0, a_max=None)
+        v = np.clip(v, a_min=0, a_max=None)
         return np.sqrt(2 * np.sum((np.sqrt(u) - np.sqrt(v)) ** 2))
 
-    def jaccard(self, u, v):
-        """Calculate the Jaccard distance between two vectors.
-
-        The Jaccard distance measures dissimilarity between sample sets.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Jaccard distance between the two vectors.
-
-        References
-        ----------
-           1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-              Measures between Probability Density Functions. International
-              Journal of Mathematical Models and Methods in Applied Sciences.
-              1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        uv = np.dot(u, v)
-        return 1 - (uv / (np.dot(u, u) + np.dot(v, v) - uv))
-
-    def lorentzian(self, u, v):
-        """Calculate the Lorentzian distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Lorentzian distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4):300-307.
-
-        Notes
-        -----
-            One (1) is added to guarantee the non-negativity property and to
-            eschew the log of zero.
-        """
-        u, v = np.asarray(u), np.asarray(v)
+
+def jaccard(u, v):
+    """Calculate the Jaccard distance between two vectors.
+
+    The Jaccard distance measures dissimilarity between sample sets.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Jaccard distance between the two vectors.
+
+    References
+    ----------
+       1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+          Measures between Probability Density Functions. International
+          Journal of Mathematical Models and Methods in Applied Sciences.
+          1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    uv = np.dot(u, v)
+    return 1 - (uv / (np.dot(u, u) + np.dot(v, v) - uv))
+
+
+def lorentzian(u, v):
+    """Calculate the Lorentzian distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Lorentzian distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4):300-307.
+
+    Notes
+    -----
+        One (1) is added to guarantee the non-negativity property and to
+        eschew the log of zero.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    with np.errstate(divide="ignore", invalid="ignore"):
         return np.sum(np.log(np.abs(u - v) + 1))
 
-    def marylandbridge(self, u, v):
-        """Calculate the Maryland Bridge distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Maryland Bridge distance between the two vectors.
-
-        References
-        ----------
-            1. Deza M, Deza E (2009) Encyclopedia of Distances.
-               Springer-Verlag Berlin Heidelberg. 1-590.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        uvdot = np.dot(u, v)
-        return 1 - (uvdot / np.dot(u, u) + uvdot / np.dot(v, v)) / 2
-
-    def meehl(self, u, v):
-        """Calculate the Meehl distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Meehl distance between the two vectors.
-
-        Notes
-        -----
-            Added by SC.
-
-        References
-        ----------
-            1. Deza M. and Deza E. (2013) Encyclopedia of Distances.
-               Berlin, Heidelberg: Springer Berlin Heidelberg.
-               https://doi.org/10.1007/978-3-642-30958-8.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-
-        xi = u[:-1]
-        yi = v[:-1]
-        xiplus1 = np.roll(u, 1)[:-1]
-        yiplus1 = np.roll(v, 1)[:-1]
-
-        with np.errstate(divide="ignore", invalid="ignore"):
-            return np.nansum((xi - yi - xiplus1 + yiplus1) ** 2)
-
-    def motyka(self, u, v):
-        """Calculate the Motyka distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Motyka distance between the two vectors.
-
-        Notes
-        -----
-            The distance between identical vectors is not equal to 0 but 0.5.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return np.sum(np.maximum(u, v)) / np.sum(u + v)
-
-    def soergel(self, u, v):
-        """Calculate the Soergel distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Soergel distance between the two vectors.
-
-        Notes
-        -----
-            Equals Tanimoto distance.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return np.sum(np.abs(u - v)) / np.sum(np.maximum(u, v))
-
-    def wave_hedges(self, u, v):
-        """Calculate the Wave Hedges distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Wave Hedges distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        with np.errstate(divide="ignore", invalid="ignore"):
-            u_v = abs(u - v)
-            uvmax = np.maximum(u, v)
-            return np.sum(np.where(((u_v != 0) & (uvmax != 0)), u_v / uvmax, 0))
-
-    def kulczynski(self, u, v):
-        """Calculate the Kulczynski distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Kulczynski distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4):300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return np.sum(np.abs(u - v)) / np.sum(np.minimum(u, v))
-
-    def add_chisq(self, u, v):
-        """Compute the Additive Symmetric Chi-square distance between two vectors.
-
-        The Additive Symmetric Chi-square distance is a measure that
-        can be used to compare two vectors. This function calculates it based
-        on the input vectors u and v.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Additive Symmetric Chi-square distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions.
-               International Journal of Mathematical Models and Methods in
-               Applied Sciences.
-               vol. 1(4), pp. 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        uvmult = u * v
-        with np.errstate(divide="ignore", invalid="ignore"):
-            return np.sum(np.where(uvmult != 0, ((u - v) ** 2 * (u + v)) / uvmult, 0))
-
-    # NOTE: THE FOLLOWING DISTANCES HAVE NOT BEEN TESTED EXTENSIVELY AND ARE
-    # CURRENTLY IN ALPHA AND SO HAVE BEEN COMMENTED
-
-    def acc(self, u, v):
-        """Calculate the average of Cityblock and Chebyshev distance.
-
-        This function computes the ACC distance, also known as the
-        Average distance, between two vectors u and v. It is the average of the
-        Cityblock (or Manhattan) and Chebyshev distances.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The ACC distance between the two vectors.
-
-        References
-        ----------
-            1. Krause EF (2012) Taxicab Geometry An Adventure in Non-Euclidean
-               Geometry. Dover Publications.
-            2. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               vol. 1(4), pp. 300-307.
-        """
-        return (self.cityblock(u, v) + self.chebyshev(u, v)) / 2
-
-    # def bhattacharyya(self, u, v):
-    #     """
-    #     Calculate the Bhattacharyya distance between two vectors.
-
-    #     Returns a distance value between 0 and 1.
-
-    #     Parameters
-    #     ----------
-    #     - u, v: Input vectors between which the distance is to be calculated.
-
-    #     Returns
-    #     -------
-    #     - The Bhattacharyya distance between the two vectors.
-
-    #     References
-    #     ----------
-    #         1. Bhattacharyya A (1947) On a measure of divergence between two
-    #            statistical populations defined by probability distributions,
-    #            Bull. Calcutta Math. Soc., 35, 99–109.
-    #         2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-    #            Measures between Probability Density Functions. International
-    #            Journal of Mathematical Models and Methods in Applied Sciences.
-    #            1(4), 300-307.
-    #         3. https://en.wikipedia.org/wiki/Bhattacharyya_distance
-    #     """
-    #     u, v = np.asarray(u), np.asarray(v)
-    #     return -np.log(np.sum(np.sqrt(u * v)))
-
-    def chebyshev_min(self, u, v):
-        """Calculate the minimum value distance between two vectors.
-
-        This measure represents a custom approach by Zielezinski to distance
-        measurement, focusing on the minimum absolute difference.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The minimum value distance between the two vectors.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return np.amin(np.abs(u - v))
-
-    def czekanowski(self, u, v):
-        """Calculate the Czekanowski distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Czekanowski distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return np.sum(np.abs(u - v)) / np.sum(u + v)
-
-    def dice(self, u, v):
-        """Calculate the Dice dissimilarity between two vectors.
-
-        Synonyms:
-            Sorensen distance
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Dice dissimilarity between the two vectors.
-
-        References
-        ----------
-            1. Dice LR (1945) Measures of the amount of ecologic association
-               between species. Ecology. 26, 297-302.
-            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        u_v = u - v
-        return np.dot(u_v, u_v) / (np.dot(u, u) + np.dot(v, v))
-
-    def divergence(self, u, v):
-        """Calculate the divergence between two vectors.
-
-        Divergence equals squared Clark distance multiplied by 2.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The divergence between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        with np.errstate(invalid="ignore"):
-            return 2 * np.nansum(np.power(u - v, 2) / np.power(u + v, 2))
-
-    def google(self, u, v):
-        """Calculate the Normalized Google Distance (NGD) between two vectors.
-
-        NGD is a measure of similarity derived from the number of hits returned by the
-        Google search engine for a given set of keywords.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Normalized Google Distance between the two vectors.
-
-        Notes
-        -----
-            When used for comparing two probability density functions (pdfs),
-            Google distance equals half of Cityblock distance.
-
-        References
-        ----------
-            1. Lee & Rashid (2008) Information Technology, ITSim 2008.
-               doi:10.1109/ITSIM.2008.4631601.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        x = float(np.sum(u))
-        y = float(np.sum(v))
-        summin = float(np.sum(np.minimum(u, v)))
-        return (max([x, y]) - summin) / ((x + y) - min([x, y]))
-
-    def gower(self, u, v):
-        """Calculate the Gower distance between two vectors.
-
-        The Gower distance equals the Cityblock distance divided by the vector length.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Gower distance between the two vectors.
-
-        References
-        ----------
-            1. Gower JC. (1971) General Coefficient of Similarity
-               and Some of Its Properties, Biometrics 27, 857-874.
-            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return np.sum(np.abs(u - v)) / u.size
-
-    def jeffreys(self, u, v):
-        """Calculate the Jeffreys divergence between two vectors.
-
-        The Jeffreys divergence is a symmetric version of the Kullback-Leibler
-        divergence.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the divergence is to be calculated.
-
-        Returns
-        -------
-        - The Jeffreys divergence between the two vectors.
-
-        References
-        ----------
-            1. Jeffreys H (1946) An Invariant Form for the Prior Probability
-               in Estimation Problems. Proc.Roy.Soc.Lon., Ser. A 186, 453-461.
-            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        # Add epsilon to zeros in vectors to avoid division
-        # by 0 and/or log of 0. Alternatively, zeros in the
-        # vectors could be ignored or masked (see below).
-        # u = ma.masked_where(u == 0, u)
-        # v = ma.masked_where(v == 0, u)
-        u = np.where(u == 0, self.epsilon, u)
-        v = np.where(v == 0, self.epsilon, v)
-        return np.sum((u - v) * np.log(u / v))
-
-    def jensenshannon_divergence(self, u, v):
-        """Calculate the Jensen-Shannon divergence between two vectors.
-
-        The Jensen-Shannon divergence is a symmetric and finite measure of similarity
-        between two probability distributions.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the divergence is to be calculated.
-
-        Returns
-        -------
-        - The Jensen-Shannon divergence between the two vectors.
-
-        References
-        ----------
-            1. Lin J. (1991) Divergence measures based on the Shannon entropy.
-               IEEE Transactions on Information Theory, 37(1):145–151.
-            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        Comments:
-            Equals Jensen difference in Sung-Hyuk (2007):
-            u = np.where(u==0, self.epsilon, u)
-            v = np.where(v==0, self.epsilon, v)
-            el1 = (u * np.log(u) + v * np.log(v)) / 2
-            el2 = (u + v)/2
-            el3 = np.log(el2)
-            return np.sum(el1 - el2 * el3)
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        u = np.where(u == 0, self.epsilon, u)
-        v = np.where(v == 0, self.epsilon, v)
-        dl = u * np.log(2 * u / (u + v))
-        dr = v * np.log(2 * v / (u + v))
+
+def marylandbridge(u, v):
+    """Calculate the Maryland Bridge distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Maryland Bridge distance between the two vectors.
+
+    References
+    ----------
+        1. Deza M, Deza E (2009) Encyclopedia of Distances.
+           Springer-Verlag Berlin Heidelberg. 1-590.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    uvdot = np.dot(u, v)
+    return 1 - (uvdot / np.dot(u, u) + uvdot / np.dot(v, v)) / 2
+
+
+def meehl(u, v):
+    """Calculate the Meehl distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Meehl distance between the two vectors.
+
+    Notes
+    -----
+        Added by SC.
+
+    References
+    ----------
+        1. Deza M. and Deza E. (2013) Encyclopedia of Distances.
+           Berlin, Heidelberg: Springer Berlin Heidelberg.
+           https://doi.org/10.1007/978-3-642-30958-8.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+
+    xi = u[:-1]
+    yi = v[:-1]
+    xiplus1 = np.roll(u, 1)[:-1]
+    yiplus1 = np.roll(v, 1)[:-1]
+
+    with np.errstate(divide="ignore", invalid="ignore"):
+        return np.nansum((xi - yi - xiplus1 + yiplus1) ** 2)
+
+
+def motyka(u, v):
+    """Calculate the Motyka distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Motyka distance between the two vectors.
+
+    Notes
+    -----
+        The distance between identical vectors is not equal to 0 but 0.5.
+
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return np.sum(np.maximum(u, v)) / np.sum(u + v)
+
+
+def soergel(u, v):
+    """Calculate the Soergel distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Soergel distance between the two vectors.
+
+    Notes
+    -----
+        Equals Tanimoto distance.
+
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return np.sum(np.abs(u - v)) / np.sum(np.maximum(u, v))
+
+
+def wave_hedges(u, v):
+    """Calculate the Wave Hedges distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Wave Hedges distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4), 300-307
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    with np.errstate(divide="ignore", invalid="ignore"):
+        u_v = abs(u - v)
+        uvmax = np.maximum(u, v)
+        return np.sum(np.where(((u_v != 0) & (uvmax != 0)), u_v / uvmax, 0))
+
+
+def kulczynski(u, v):
+    """Calculate the Kulczynski distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Kulczynski distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4):300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return np.sum(np.abs(u - v)) / np.sum(np.minimum(u, v))
+
+
+def add_chisq(u, v):
+    """Compute the Additive Symmetric Chi-square distance between two vectors.
+
+    The Additive Symmetric Chi-square distance is a measure that
+    can be used to compare two vectors. This function calculates it based
+    on the input vectors u and v.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Additive Symmetric Chi-square distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions.
+           International Journal of Mathematical Models and Methods in
+           Applied Sciences.
+           vol. 1(4), pp. 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    uvmult = u * v
+    with np.errstate(divide="ignore", invalid="ignore"):
+        return np.sum(np.where(uvmult != 0, ((u - v) ** 2 * (u + v)) / uvmult, 0))
+
+
+# NOTE: THE FOLLOWING DISTANCES HAVE NOT BEEN TESTED EXTENSIVELY AND ARE
+# CURRENTLY IN ALPHA AND SO HAVE BEEN COMMENTED
+
+
+def acc(u, v):
+    """Calculate the average of Cityblock and Chebyshev distance.
+
+    This function computes the ACC distance, also known as the
+    Average distance, between two vectors u and v. It is the average of the
+    Cityblock (or Manhattan) and Chebyshev distances.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The ACC distance between the two vectors.
+
+    References
+    ----------
+        1. Krause EF (2012) Taxicab Geometry An Adventure in Non-Euclidean
+           Geometry. Dover Publications.
+        2. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           vol. 1(4), pp. 300-307.
+    """
+    return (cityblock(u, v) + chebyshev(u, v)) / 2
+
+
+# def bhattacharyya(u, v):
+#     """
+#     Calculate the Bhattacharyya distance between two vectors.
+
+#     Returns a distance value between 0 and 1.
+
+#     Parameters
+#     ----------
+#     - u, v: Input vectors between which the distance is to be calculated.
+
+#     Returns
+#     -------
+#     - The Bhattacharyya distance between the two vectors.
+
+#     References
+#     ----------
+#         1. Bhattacharyya A (1947) On a measure of divergence between two
+#            statistical populations defined by probability distributions,
+#            Bull. Calcutta Math. Soc., 35, 99–109.
+#         2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+#            Measures between Probability Density Functions. International
+#            Journal of Mathematical Models and Methods in Applied Sciences.
+#            1(4), 300-307.
+#         3. https://en.wikipedia.org/wiki/Bhattacharyya_distance
+#     """
+#     u, v = np.asarray(u), np.asarray(v)
+#     with np.errstate(divide="ignore", invalid="ignore"):
+#         return -np.log(np.sum(np.sqrt(u * v)))
+
+
+def chebyshev_min(u, v):
+    """Calculate the minimum value distance between two vectors.
+
+    This measure represents a custom approach by Zielezinski to distance
+    measurement, focusing on the minimum absolute difference.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The minimum value distance between the two vectors.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return np.amin(np.abs(u - v))
+
+
+def czekanowski(u, v):
+    """Calculate the Czekanowski distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Czekanowski distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return np.sum(np.abs(u - v)) / np.sum(u + v)
+
+
+def dice(u, v):
+    """Calculate the Dice dissimilarity between two vectors.
+
+    Synonyms:
+        Sorensen distance
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Dice dissimilarity between the two vectors.
+
+    References
+    ----------
+        1. Dice LR (1945) Measures of the amount of ecologic association
+           between species. Ecology. 26, 297-302.
+        2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    u_v = u - v
+    return np.dot(u_v, u_v) / (np.dot(u, u) + np.dot(v, v))
+
+
+def divergence(u, v):
+    """Calculate the divergence between two vectors.
+
+    Divergence equals squared Clark distance multiplied by 2.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The divergence between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+           Measures between Probability Density Functions. International
+           Journal of Mathematical Models and Methods in Applied Sciences.
+           1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    with np.errstate(invalid="ignore"):
+        return 2 * np.nansum(np.power(u - v, 2) / np.power(u + v, 2))
+
+
+def google(u, v):
+    """Calculate the Normalized Google Distance (NGD) between two vectors.
+
+    NGD is a measure of similarity derived from the number of hits returned by the
+    Google search engine for a given set of keywords.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Normalized Google Distance between the two vectors.
+
+    Notes
+    -----
+        When used for comparing two probability density functions (pdfs),
+        Google distance equals half of Cityblock distance.
+
+    References
+    ----------
+        1. Lee & Rashid (2008) Information Technology, ITSim 2008.
+            doi:10.1109/ITSIM.2008.4631601.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    x = float(np.sum(u))
+    y = float(np.sum(v))
+    summin = float(np.sum(np.minimum(u, v)))
+    return (max([x, y]) - summin) / ((x + y) - min([x, y]))
+
+
+def gower(u, v):
+    """Calculate the Gower distance between two vectors.
+
+    The Gower distance equals the Cityblock distance divided by the vector length.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Gower distance between the two vectors.
+
+    References
+    ----------
+        1. Gower JC. (1971) General Coefficient of Similarity
+            and Some of Its Properties, Biometrics 27, 857-874.
+        2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return np.sum(np.abs(u - v)) / u.size
+
+
+def jeffreys(u, v):
+    """Calculate the Jeffreys divergence between two vectors.
+
+    The Jeffreys divergence is a symmetric version of the Kullback-Leibler
+    divergence.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the divergence is to be calculated.
+
+    Returns
+    -------
+    - The Jeffreys divergence between the two vectors.
+
+    References
+    ----------
+        1. Jeffreys H (1946) An Invariant Form for the Prior Probability
+            in Estimation Problems. Proc.Roy.Soc.Lon., Ser. A 186, 453-461.
+        2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    # Add epsilon to zeros in vectors to avoid division
+    # by 0 and/or log of 0. Alternatively, zeros in the
+    # vectors could be ignored or masked (see below).
+    # u = ma.masked_where(u == 0, u)
+    # v = ma.masked_where(v == 0, u)
+    with np.errstate(divide="ignore", invalid="ignore"):
+        u[u == 0] = EPSILON
+        v[v == 0] = EPSILON
+        # Clip negative values to zero for valid log
+        udivv = np.clip(u / v, a_min=EPSILON, a_max=None)
+        return np.sum((u - v) * np.log(udivv))
+
+
+def jensenshannon_divergence(u, v):
+    """Calculate the Jensen-Shannon divergence between two vectors.
+
+    The Jensen-Shannon divergence is a symmetric and finite measure of similarity
+    between two probability distributions.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the divergence is to be calculated.
+
+    Returns
+    -------
+    - The Jensen-Shannon divergence between the two vectors.
+
+    References
+    ----------
+        1. Lin J. (1991) Divergence measures based on the Shannon entropy.
+            IEEE Transactions on Information Theory, 37(1):145–151.
+        2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4), 300-307.
+    Comments:
+        Equals Jensen difference in Sung-Hyuk (2007):
+        u = np.where(u==0, EPSILON, u)
+        v = np.where(v==0, EPSILON, v)
+        el1 = (u * np.log(u) + v * np.log(v)) / 2
+        el2 = (u + v)/2
+        el3 = np.log(el2)
+        return np.sum(el1 - el2 * el3)
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    with np.errstate(divide="ignore", invalid="ignore"):
+        # Clip negative values to zero for valid log
+        u[u == 0] = EPSILON
+        v[v == 0] = EPSILON
+
+        term1 = np.clip(2 * u / (u + v), a_min=EPSILON, a_max=None)
+        term2 = np.clip(2 * v / (u + v), a_min=EPSILON, a_max=None)
+
+        dl = u * np.log(term1)
+        dr = v * np.log(term2)
         return (np.sum(dl) + np.sum(dr)) / 2
 
-    def jensen_difference(self, u, v):
-        """Calculate the Jensen difference between two vectors.
 
-        The Jensen difference is considered similar to the Jensen-Shannon divergence.
+def jensen_difference(u, v):
+    """Calculate the Jensen difference between two vectors.
 
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
+    The Jensen difference is considered similar to the Jensen-Shannon divergence.
 
-        Returns
-        -------
-        - The Jensen difference between the two vectors.
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Jensen difference between the two vectors.
+
+    Notes
+    -----
+        1. Equals half of Topsøe distance
+        2. Equals squared jensenshannon_distance.
 
-        Notes
-        -----
-            1. Equals half of Topsøe distance
-            2. Equals squared jensenshannon_distance.
 
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
 
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        u = np.where(u == 0, self.epsilon, u)
-        v = np.where(v == 0, self.epsilon, v)
+    with np.errstate(divide="ignore", invalid="ignore"):
+        # Clip negative values to eps for valid log
+        u = np.clip(u, EPSILON, None)
+        v = np.clip(v, EPSILON, None)
         el1 = (u * np.log(u) + v * np.log(v)) / 2
-        el2 = (u + v) / 2
+        el2 = np.clip((u + v) / 2, a_min=EPSILON, a_max=None)
         return np.sum(el1 - el2 * np.log(el2))
 
-    def kumarjohnson(self, u, v):
-        """Calculate the Kumar-Johnson distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Kumar-Johnson distance between the two vectors.
-
-        References
-        ----------
-            1. Kumar P, Johnson A. (2005) On a symmetric divergence measure
-               and information inequalities, Journal of Inequalities in pure
-               and applied Mathematics. 6(3).
-            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4):300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        uvmult = u * v
-        with np.errstate(divide="ignore", invalid="ignore"):
-            numer = np.power(u**2 - v**2, 2)
-            denom = 2 * np.power(uvmult, 3 / 2)
-            return np.sum(np.where(uvmult != 0, numer / denom, 0))
-
-    def matusita(self, u, v):
-        """Calculate the Matusita distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Matusita distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4):300-307.
-
-        Notes
-        -----
-            Equals square root of Squared-chord distance.
-        """
-        u, v = np.asarray(u), np.asarray(v)
+
+def kumarjohnson(u, v):
+    """Calculate the Kumar-Johnson distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Kumar-Johnson distance between the two vectors.
+
+    References
+    ----------
+        1. Kumar P, Johnson A. (2005) On a symmetric divergence measure
+            and information inequalities, Journal of Inequalities in pure
+            and applied Mathematics. 6(3).
+        2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4):300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    uvmult = u * v
+    with np.errstate(divide="ignore", invalid="ignore"):
+        numer = np.power(u**2 - v**2, 2)
+        denom = 2 * np.power(uvmult, 3 / 2)
+        return np.sum(np.where(uvmult != 0, numer / denom, 0))
+
+
+def matusita(u, v):
+    """Calculate the Matusita distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Matusita distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4):300-307.
+
+    Notes
+    -----
+        Equals square root of Squared-chord distance.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    with np.errstate(divide="ignore", invalid="ignore"):
         return np.sqrt(np.sum((np.sqrt(u) - np.sqrt(v)) ** 2))
 
-    def minkowski(self, u, v, p=2):
-        """Calculate the Minkowski distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-        - p: The order of the norm of the difference.
-
-        Returns
-        -------
-        - The Minkowski distance between the two vectors.
-
-        Notes
-        -----
-            When p goes to infinite, the Chebyshev distance is derived.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-                Measures between Probability Density Functions. International
-                Journal of Mathematical Models and Methods in Applied Sciences.
-                1(4):300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return np.linalg.norm(u - v, ord=p)
-
-    def penroseshape(self, u, v):
-        """Calculate the Penrose shape distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Penrose shape distance between the two vectors.
-
-        References
-        ----------
-            1. Deza M, Deza E (2009) Encyclopedia of Distances.
-               Springer-Verlag Berlin Heidelberg. 1-590.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        umu = np.mean(u)
-        vmu = np.mean(v)
+
+def minkowski(u, v, p=2):
+    """Calculate the Minkowski distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+    - p: The order of the norm of the difference.
+
+    Returns
+    -------
+    - The Minkowski distance between the two vectors.
+
+    Notes
+    -----
+        When p goes to infinite, the Chebyshev distance is derived.
+
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4):300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return np.linalg.norm(u - v, ord=p)
+
+
+def penroseshape(u, v):
+    """Calculate the Penrose shape distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Penrose shape distance between the two vectors.
+
+    References
+    ----------
+        1. Deza M, Deza E (2009) Encyclopedia of Distances.
+            Springer-Verlag Berlin Heidelberg. 1-590.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    umu = np.mean(u)
+    vmu = np.mean(v)
+    with np.errstate(divide="ignore", invalid="ignore"):
         return np.sqrt(np.sum(((u - umu) - (v - vmu)) ** 2))
 
-    def prob_chisq(self, u, v):
-        """Calculate the Probabilistic chi-square distance between two vectors.
 
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
+def prob_chisq(u, v):
+    """Calculate the Probabilistic chi-square distance between two vectors.
 
-        Returns
-        -------
-        - The Probabilistic chi-square distance between the two vectors.
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
 
-        Notes
-        -----
-            Added by SC.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        uvsum = u + v
-        with np.errstate(divide="ignore", invalid="ignore"):
-            return 2 * np.sum(np.where(uvsum != 0, (u - v) ** 2 / uvsum, 0))
-
-    def ruzicka(self, u, v):
-        """Calculate the Ruzicka distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Ruzicka distance between the two vectors.
-
-        Notes
-        -----
-            Added by SC.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        den = np.sum(np.maximum(u, v))
-
-        return 1 - np.sum(np.minimum(u, v)) / den
-
-    def sorensen(self, u, v):
-        """Calculate the Sorensen distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Sorensen distance between the two vectors.
-
-        Notes
-        -----
-            The Sorensen distance equals the Manhattan distance divided by the sum of
-            the two vectors.
-
-            Added by SC.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return np.sum(np.abs(u - v)) / np.sum(u + v)
-
-    def squared_chisq(self, u, v):
-        """Calculate the Squared chi-square distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Squared chi-square distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        uvsum = u + v
-        with np.errstate(divide="ignore", invalid="ignore"):
-            return np.sum(np.where(uvsum != 0, (u - v) ** 2 / uvsum, 0))
-
-    def squaredchord(self, u, v):
-        """Calculate the Squared-chord distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Squared-chord distance between the two vectors.
-
-        References
-        ----------
-            1. Gavin DG et al. (2003) A statistical approach to evaluating
-               distance metrics and analog assignments for pollen records.
-               Quaternary Research 60:356–367.
-            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-
-        Notes
-        -----
-            Equals to squared Matusita distance.
-        """
-        u, v = np.asarray(u), np.asarray(v)
+    Returns
+    -------
+    - The Probabilistic chi-square distance between the two vectors.
+
+    Notes
+    -----
+        Added by SC.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    uvsum = u + v
+    with np.errstate(divide="ignore", invalid="ignore"):
+        return 2 * np.sum(np.where(uvsum != 0, (u - v) ** 2 / uvsum, 0))
+
+
+def ruzicka(u, v):
+    """Calculate the Ruzicka distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Ruzicka distance between the two vectors.
+
+    Notes
+    -----
+        Added by SC.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    den = np.sum(np.maximum(u, v))
+
+    return 1 - np.sum(np.minimum(u, v)) / den
+
+
+def sorensen(u, v):
+    """Calculate the Sorensen distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Sorensen distance between the two vectors.
+
+    Notes
+    -----
+        The Sorensen distance equals the Manhattan distance divided by the sum of
+        the two vectors.
+
+        Added by SC.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return np.sum(np.abs(u - v)) / np.sum(u + v)
+
+
+def squared_chisq(u, v):
+    """Calculate the Squared chi-square distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Squared chi-square distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    uvsum = u + v
+    with np.errstate(divide="ignore", invalid="ignore"):
+        return np.sum(np.where(uvsum != 0, (u - v) ** 2 / uvsum, 0))
+
+
+def squaredchord(u, v):
+    """Calculate the Squared-chord distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Squared-chord distance between the two vectors.
+
+    References
+    ----------
+        1. Gavin DG et al. (2003) A statistical approach to evaluating
+            distance metrics and analog assignments for pollen records.
+            Quaternary Research 60:356–367.
+        2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4), 300-307.
+
+    Notes
+    -----
+        Equals to squared Matusita distance.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    with np.errstate(divide="ignore", invalid="ignore"):
         return np.sum((np.sqrt(u) - np.sqrt(v)) ** 2)
 
-    def squared_euclidean(self, u, v):
-        """Calculate the Squared Euclidean distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Squared Euclidean distance between the two vectors.
-
-        References
-        ----------
-            1. Gavin DG et al. (2003) A statistical approach to evaluating
-               distance metrics and analog assignments for pollen records.
-               Quaternary Research 60:356–367.
-            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-
-        Notes
-        -----
-            Equals to squared Euclidean distance.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        return np.dot((u - v), (u - v))
-
-    def taneja(self, u, v):
-        """Calculate the Taneja distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Taneja distance between the two vectors.
-
-        References
-        ----------
-            1. Taneja IJ. (1995), New Developments in Generalized Information
-               Measures, Chapter in: Advances in Imaging and Electron Physics,
-               Ed. P.W. Hawkes, 91, 37-135.
-            2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        u = np.where(u == 0, self.epsilon, u)
-        v = np.where(v == 0, self.epsilon, v)
+
+def squared_euclidean(u, v):
+    """Calculate the Squared Euclidean distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Squared Euclidean distance between the two vectors.
+
+    References
+    ----------
+        1. Gavin DG et al. (2003) A statistical approach to evaluating
+            distance metrics and analog assignments for pollen records.
+            Quaternary Research 60:356–367.
+        2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4), 300-307.
+
+    Notes
+    -----
+        Equals to squared Euclidean distance.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    return np.dot((u - v), (u - v))
+
+
+def taneja(u, v):
+    """Calculate the Taneja distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Taneja distance between the two vectors.
+
+    References
+    ----------
+        1. Taneja IJ. (1995), New Developments in Generalized Information
+            Measures, Chapter in: Advances in Imaging and Electron Physics,
+            Ed. P.W. Hawkes, 91, 37-135.
+        2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    with np.errstate(divide="ignore", invalid="ignore"):
+        u[u == 0] = EPSILON
+        v[v == 0] = EPSILON
         uvsum = u + v
-        return np.sum((uvsum / 2) * np.log(uvsum / (2 * np.sqrt(u * v))))
-
-    def tanimoto(self, u, v):
-        """Calculate the Tanimoto distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Tanimoto distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-
-        Notes
-        -----
-            Equals Soergel distance.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        # return np.sum(abs(u-v)) / np.sum(np.maximum(u, v))
-        usum = np.sum(u)
-        vsum = np.sum(v)
-        minsum = np.sum(np.minimum(u, v))
-        return (usum + vsum - 2 * minsum) / (usum + vsum - minsum)
-
-    def topsoe(self, u, v):
-        """Calculate the Topsøe distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Topsøe distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-
-        Notes
-        -----
-            Equals two times Jensen-Shannon divergence.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        u = np.where(u == 0, self.epsilon, u)
-        v = np.where(v == 0, self.epsilon, v)
-        dl = u * np.log(2 * u / (u + v))
-        dr = v * np.log(2 * v / (u + v))
+        logarg = np.clip(uvsum / (2 * np.sqrt(u * v)), a_min=EPSILON, a_max=None)
+        return np.sum((uvsum / 2) * np.log(logarg))
+
+
+def tanimoto(u, v):
+    """Calculate the Tanimoto distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Tanimoto distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4), 300-307.
+
+    Notes
+    -----
+        Equals Soergel distance.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    # return np.sum(abs(u-v)) / np.sum(np.maximum(u, v))
+    usum = np.sum(u)
+    vsum = np.sum(v)
+    minsum = np.sum(np.minimum(u, v))
+    return (usum + vsum - 2 * minsum) / (usum + vsum - minsum)
+
+
+def topsoe(u, v):
+    """Calculate the Topsøe distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Topsøe distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4), 300-307.
+
+    Notes
+    -----
+        Equals two times Jensen-Shannon divergence.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    with np.errstate(divide="ignore", invalid="ignore"):
+        u[u == 0] = EPSILON
+        v[v == 0] = EPSILON
+        logarg1 = np.clip(2 * u / (u + v), a_min=EPSILON, a_max=None)
+        logarg2 = np.clip(2 * v / (u + v), a_min=EPSILON, a_max=None)
+        dl = u * np.log(logarg1)
+        dr = v * np.log(logarg2)
         return np.sum(dl + dr)
 
-    def vicis_symmetric_chisq(self, u, v):
-        """Calculate the Vicis Symmetric chi-square distance.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Vicis Symmetric chi-square distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        with np.errstate(divide="ignore", invalid="ignore"):
-            u_v = (u - v) ** 2
-            uvmin = np.minimum(u, v) ** 2
-            return np.sum(np.where(uvmin != 0, u_v / uvmin, 0))
-
-    def vicis_wave_hedges(self, u, v):
-        """Calculate the Vicis-Wave Hedges distance between two vectors.
-
-        Parameters
-        ----------
-        - u, v: Input vectors between which the distance is to be calculated.
-
-        Returns
-        -------
-        - The Vicis-Wave Hedges distance between the two vectors.
-
-        References
-        ----------
-            1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
-               Measures between Probability Density Functions. International
-               Journal of Mathematical Models and Methods in Applied Sciences.
-               1(4), 300-307.
-        """
-        u, v = np.asarray(u), np.asarray(v)
-        with np.errstate(divide="ignore", invalid="ignore"):
-            u_v = abs(u - v)
-            uvmin = np.minimum(u, v)
-            return np.sum(np.where(uvmin != 0, u_v / uvmin, 0))
-
-    # def fidelity(self, u, v):
-    #     """
-    #     Calculate the fidelity distance between two vectors.
-
-    #     The fidelity distance measures the similarity between two probability
-    #     distributions.
-
-    #     Parameters
-    #     ----------
-    #     - u, v: Input vectors between which the distance is to be calculated.
-
-    #     Returns
-    #     -------
-    #     - The fidelity distance between the two vectors.
-
-    #     Notes
-    #     -----
-    #         Added by SC.
-    #     """
-    #     u, v = np.asarray(u), np.asarray(v)
-    #     return 1 - (np.sum(np.sqrt(u * v)))
-
-    # # NEEDS CHECKING
-    # # def harmonicmean(self, u, v):
-    # #     """
-    # #     Harmonic mean distance.
-    # #     Notes:
-    # #         Added by SC.
-    # #     """
-    # #     u, v = np.asarray(u), np.asarray(v)
-    # #     return 1 - 2.0 * np.sum(u * v / (u + v))
-
-    #     # def inner(self, u, v):
-    #     #     """
-    #     #     Calculate the inner product distance between two vectors.
-
-    #     #     The inner product distance is a measure of
-    #     #     similarity between two vectors,
-    #     #     based on their inner product.
-
-    #     #     Parameters
-    #     #     ----------
-    #     #     - u, v: Input vectors between which the distance is to be calculated.
-
-    #     #     Returns
-    #     #     -------
-    #     #     - The inner product distance between the two vectors.
-
-    #     #     Notes
-    #     #     -----
-    #     #         Added by SC.
-    #     #     """
-    #     #     u, v = np.asarray(u), np.asarray(v)
-    #     #     return 1 - np.dot(u, v)
-
-    # def k_divergence(self, u, v):
-    #     """Calculate the K divergence between two vectors.
-
-    #     Parameters
-    #     ----------
-    #     - u, v: Input vectors between which the divergence is to be calculated.
-
-    #     Returns
-    #     -------
-    #     - The K divergence between the two vectors.
-
-    #     References
-    #     ----------
-    #         1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-    #            Measures between Probability Density Functions. International
-    #            Journal of Mathematical Models and Methods in Applied Sciences.
-    #            1(4), 300-307.
-    #     """
-    #     u, v = np.asarray(u), np.asarray(v)
-    #     u = np.where(u == 0, self.epsilon, u)
-    #     v = np.where(v == 0, self.epsilon, v)
-    #     return np.sum(u * np.log(2 * u / (u + v)))
-
-    # def kl_divergence(self, u, v):
-    #     """Calculate the Kullback-Leibler divergence between two vectors.
-
-    #     The Kullback-Leibler divergence measures the difference between two
-    #     probability distributions.
-
-    #     Parameters
-    #     ----------
-    #     - u, v: Input vectors between which the divergence is to be calculated.
-
-    #     Returns
-    #     -------
-    #     - The Kullback-Leibler divergence between the two vectors.
-
-    #     References
-    #     ----------
-    #         1. Kullback S, Leibler RA (1951) On information and sufficiency.
-    #            Ann. Math. Statist. 22:79–86
-    #         2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-    #            Measures between Probability Density Functions. International
-    #            Journal of Mathematical Models and Methods in Applied Sciences.
-    #            1(4):300-307.
-    #     """
-    #     u, v = np.asarray(u), np.asarray(v)
-    #     u = np.where(u == 0, self.epsilon, u)
-    #     v = np.where(v == 0, self.epsilon, v)
-    #     return np.sum(u * np.log(u / v))
-
-    # def max_symmetric_chisq(self, u, v):
-    #     """Calculate the maximum symmetric chi-square distance.
-
-    #     Parameters
-    #     ----------
-    #     - u, v: Input vectors between which the distance is to be calculated.
-
-    #     Returns
-    #     -------
-    #     - The maximum symmetric chi-square distance between the two vectors.
-
-    #     References
-    #     ----------
-    #         1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-    #            Measures between Probability Density Functions. International
-    #            Journal of Mathematical Models and Methods in Applied Sciences.
-    #            1(4):300-307.
-    #     """
-    #     u, v = np.asarray(u), np.asarray(v)
-    #     return max(self.neyman_chisq(u, v), self.pearson_chisq(u, v))
-
-    # def min_symmetric_chisq(self, u, v):
-    #     """Calculate the minimum symmetric chi-square distance.
-
-    #     Parameters
-    #     ----------
-    #     - u, v: Input vectors between which the distance is to be calculated.
-
-    #     Returns
-    #     -------
-    #     - The minimum symmetric chi-square distance between the two vectors.
-
-    #     Notes
-    #     -----
-    #         Added by SC.
-    #     """
-    #     u, v = np.asarray(u), np.asarray(v)
-    #     return min(self.neyman_chisq(u, v), self.pearson_chisq(u, v))
-
-    # def neyman_chisq(self, u, v):
-    #     """Calculate the Neyman chi-square distance between two vectors.
-
-    #     Parameters
-    #     ----------
-    #     - u, v: Input vectors between which the distance is to be calculated.
-
-    #     Returns
-    #     -------
-    #     - The Neyman chi-square distance between the two vectors.
-
-    #     References
-    #     ----------
-    #         1. Neyman J (1949) Contributions to the theory of the chi^2 test.
-    #            In Proceedings of the First Berkley Symposium on Mathematical
-    #            Statistics and Probability.
-    #         2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-    #            Measures between Probability Density Functions. International
-    #            Journal of Mathematical Models and Methods in Applied Sciences.
-    #            1(4), 300-307.
-    #     """
-    #     u, v = np.asarray(u), np.asarray(v)
-    #     with np.errstate(divide="ignore", invalid="ignore"):
-    #         return np.sum(np.where(u != 0, (u - v) ** 2 / u, 0))
-
-    # def pearson_chisq(self, u, v):
-    #     """Calculate the Pearson chi-square divergence between two vectors.
-
-    #     Parameters
-    #     ----------
-    #     - u, v: Input vectors between which the divergence is to be calculated.
-
-    #     Returns
-    #     -------
-    #     - The Pearson chi-square divergence between the two vectors.
-
-    #     References
-    #     ----------
-    #         1. Pearson K. (1900) On the Criterion that a given system of
-    #            deviations from the probable in the case of correlated system
-    #            of variables is such that it can be reasonable supposed to have
-    #            arisen from random sampling, Phil. Mag. 50, 157-172.
-    #         2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-    #            Measures between Probability Density Functions. International
-    #            Journal of Mathematical Models and Methods in Applied Sciences.
-    #            1(4), 300-307.
-
-    #     Notes
-    #     -----
-    #         Pearson chi-square divergence is asymmetric.
-    #     """
-    #     u, v = np.asarray(u), np.asarray(v)
-    #     with np.errstate(divide="ignore", invalid="ignore"):
-    #         return np.sum(np.where(v != 0, (u - v) ** 2 / v, 0))
-
-    # def nonintersection(self, u, v):
-    #     """
-    #     Calculate the Nonintersection distance between two vectors.
-
-    #     Parameters
-    #     ----------
-    #     - u, v: Input vectors between which the distance is to be calculated.
-
-    #     Returns
-    #     -------
-    #     - The Nonintersection distance between the two vectors.
-
-    #     References
-    #     ----------
-    #         1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
-    #             Measures between Probability Density Functions. International
-    #             Journal of Mathematical Models and Methods in Applied Sciences.
-    #             1(4), 300-307.
-
-    #     Notes
-    #     -----
-    #         When used for comparing two probability density functions (pdfs),
-    #         Nonintersection distance equals half of Cityblock distance.
-    #     """
-    #     u, v = np.asarray(u), np.asarray(v)
-    #     return 1 - np.sum(np.minimum(u, v))
+
+def vicis_symmetric_chisq(u, v):
+    """Calculate the Vicis Symmetric chi-square distance.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Vicis Symmetric chi-square distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4), 300-307
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    with np.errstate(divide="ignore", invalid="ignore"):
+        u_v = (u - v) ** 2
+        uvmin = np.minimum(u, v) ** 2
+        return np.sum(np.where(uvmin != 0, u_v / uvmin, 0))
+
+
+def vicis_wave_hedges(u, v):
+    """Calculate the Vicis-Wave Hedges distance between two vectors.
+
+    Parameters
+    ----------
+    - u, v: Input vectors between which the distance is to be calculated.
+
+    Returns
+    -------
+    - The Vicis-Wave Hedges distance between the two vectors.
+
+    References
+    ----------
+        1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
+            Measures between Probability Density Functions. International
+            Journal of Mathematical Models and Methods in Applied Sciences.
+            1(4), 300-307.
+    """
+    u, v = np.asarray(u), np.asarray(v)
+    with np.errstate(divide="ignore", invalid="ignore"):
+        u_v = abs(u - v)
+        uvmin = np.minimum(u, v)
+        return np.sum(np.where(uvmin != 0, u_v / uvmin, 0))
+
+
+# def fidelity(u, v):
+#     """
+#     Calculate the fidelity distance between two vectors.
+
+#     The fidelity distance measures the similarity between two probability
+#     distributions.
+
+#     Parameters
+#     ----------
+#     - u, v: Input vectors between which the distance is to be calculated.
+
+#     Returns
+#     -------
+#     - The fidelity distance between the two vectors.
+
+#     Notes
+#     -----
+#         Added by SC.
+#     """
+#     u, v = np.asarray(u), np.asarray(v)
+#     return 1 - (np.sum(np.sqrt(u * v)))
+
+# # NEEDS CHECKING
+# # def harmonicmean(u, v):
+# #     """
+# #     Harmonic mean distance.
+# #     Notes:
+# #         Added by SC.
+# #     """
+# #     u, v = np.asarray(u), np.asarray(v)
+# #     return 1 - 2.0 * np.sum(u * v / (u + v))
+
+#     # def inner(u, v):
+#     #     """
+#     #     Calculate the inner product distance between two vectors.
+
+#     #     The inner product distance is a measure of
+#     #     similarity between two vectors,
+#     #     based on their inner product.
+
+#     #     Parameters
+#     #     ----------
+#     #     - u, v: Input vectors between which the distance is to be calculated.
+
+#     #     Returns
+#     #     -------
+#     #     - The inner product distance between the two vectors.
+
+#     #     Notes
+#     #     -----
+#     #         Added by SC.
+#     #     """
+#     #     u, v = np.asarray(u), np.asarray(v)
+#     #     return 1 - np.dot(u, v)
+
+# def k_divergence(u, v):
+#     """Calculate the K divergence between two vectors.
+
+#     Parameters
+#     ----------
+#     - u, v: Input vectors between which the divergence is to be calculated.
+
+#     Returns
+#     -------
+#     - The K divergence between the two vectors.
+
+#     References
+#     ----------
+#         1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+#            Measures between Probability Density Functions. International
+#            Journal of Mathematical Models and Methods in Applied Sciences.
+#            1(4), 300-307.
+#     """
+#     u, v = np.asarray(u), np.asarray(v)
+#     u[u == 0] = EPSILON
+#     v[v == 0] = EPSILON
+#     with np.errstate(divide="ignore", invalid="ignore"):
+#         return np.sum(u * np.log(2 * u / (u + v)))
+
+# def kl_divergence(u, v):
+#     """Calculate the Kullback-Leibler divergence between two vectors.
+
+#     The Kullback-Leibler divergence measures the difference between two
+#     probability distributions.
+
+#     Parameters
+#     ----------
+#     - u, v: Input vectors between which the divergence is to be calculated.
+
+#     Returns
+#     -------
+#     - The Kullback-Leibler divergence between the two vectors.
+
+#     References
+#     ----------
+#         1. Kullback S, Leibler RA (1951) On information and sufficiency.
+#            Ann. Math. Statist. 22:79–86
+#         2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+#            Measures between Probability Density Functions. International
+#            Journal of Mathematical Models and Methods in Applied Sciences.
+#            1(4):300-307.
+#     """
+#     u, v = np.asarray(u), np.asarray(v)
+#     u[u == 0] = EPSILON
+#     v[v == 0] = EPSILON
+#     with np.errstate(divide="ignore", invalid="ignore"):
+#         return np.sum(u * np.log(u / v))
+
+# def max_symmetric_chisq(u, v):
+#     """Calculate the maximum symmetric chi-square distance.
+
+#     Parameters
+#     ----------
+#     - u, v: Input vectors between which the distance is to be calculated.
+
+#     Returns
+#     -------
+#     - The maximum symmetric chi-square distance between the two vectors.
+
+#     References
+#     ----------
+#         1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+#            Measures between Probability Density Functions. International
+#            Journal of Mathematical Models and Methods in Applied Sciences.
+#            1(4):300-307.
+#     """
+#     u, v = np.asarray(u), np.asarray(v)
+#     return max(neyman_chisq(u, v), pearson_chisq(u, v))
+
+# def min_symmetric_chisq(u, v):
+#     """Calculate the minimum symmetric chi-square distance.
+
+#     Parameters
+#     ----------
+#     - u, v: Input vectors between which the distance is to be calculated.
+
+#     Returns
+#     -------
+#     - The minimum symmetric chi-square distance between the two vectors.
+
+#     Notes
+#     -----
+#         Added by SC.
+#     """
+#     u, v = np.asarray(u), np.asarray(v)
+#     return min(neyman_chisq(u, v), pearson_chisq(u, v))
+
+# def neyman_chisq(u, v):
+#     """Calculate the Neyman chi-square distance between two vectors.
+
+#     Parameters
+#     ----------
+#     - u, v: Input vectors between which the distance is to be calculated.
+
+#     Returns
+#     -------
+#     - The Neyman chi-square distance between the two vectors.
+
+#     References
+#     ----------
+#         1. Neyman J (1949) Contributions to the theory of the chi^2 test.
+#            In Proceedings of the First Berkley Symposium on Mathematical
+#            Statistics and Probability.
+#         2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+#            Measures between Probability Density Functions. International
+#            Journal of Mathematical Models and Methods in Applied Sciences.
+#            1(4), 300-307.
+#     """
+#     u, v = np.asarray(u), np.asarray(v)
+#     with np.errstate(divide="ignore", invalid="ignore"):
+#         return np.sum(np.where(u != 0, (u - v) ** 2 / u, 0))
+
+# def pearson_chisq(u, v):
+#     """Calculate the Pearson chi-square divergence between two vectors.
+
+#     Parameters
+#     ----------
+#     - u, v: Input vectors between which the divergence is to be calculated.
+
+#     Returns
+#     -------
+#     - The Pearson chi-square divergence between the two vectors.
+
+#     References
+#     ----------
+#         1. Pearson K. (1900) On the Criterion that a given system of
+#            deviations from the probable in the case of correlated system
+#            of variables is such that it can be reasonable supposed to have
+#            arisen from random sampling, Phil. Mag. 50, 157-172.
+#         2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+#            Measures between Probability Density Functions. International
+#            Journal of Mathematical Models and Methods in Applied Sciences.
+#            1(4), 300-307.
+
+#     Notes
+#     -----
+#         Pearson chi-square divergence is asymmetric.
+#     """
+#     u, v = np.asarray(u), np.asarray(v)
+#     with np.errstate(divide="ignore", invalid="ignore"):
+#         return np.sum(np.where(v != 0, (u - v) ** 2 / v, 0))
+
+# def nonintersection(u, v):
+#     """
+#     Calculate the Nonintersection distance between two vectors.
+
+#     Parameters
+#     ----------
+#     - u, v: Input vectors between which the distance is to be calculated.
+
+#     Returns
+#     -------
+#     - The Nonintersection distance between the two vectors.
+
+#     References
+#     ----------
+#         1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
+#             Measures between Probability Density Functions. International
+#             Journal of Mathematical Models and Methods in Applied Sciences.
+#             1(4), 300-307.
+
+#     Notes
+#     -----
+#         When used for comparing two probability density functions (pdfs),
+#         Nonintersection distance equals half of Cityblock distance.
+#     """
+#     u, v = np.asarray(u), np.asarray(v)
+#     return 1 - np.sum(np.minimum(u, v))