[ENH] Adapter for Scipy Distributions (#287)

Fixes #227 

#### What does this implement/fix? Explain your changes.
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A clear and concise description of what you have implemented.
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- Adapter for Scipy distributions
- Fisk Distribution using Scipy Adapter
- Poisson Distribution using Scipy Adapter

skpro/distributions/adapters/scipy/__init__.py

@@ -1,6 +1,7 @@
 """Adapters for probability distribution objects, scipy facing."""
 # copyright: skpro developers, BSD-3-Clause License (see LICENSE file)
 
+from skpro.distributions.adapters.scipy._distribution import _ScipyAdapter
 from skpro.distributions.adapters.scipy._empirical import empirical_from_discrete
 
-__all__ = ["empirical_from_discrete"]
+__all__ = ["empirical_from_discrete", "_ScipyAdapter"]

skpro/distributions/adapters/scipy/_distribution.py

@@ -0,0 +1,109 @@
+# copyright: skpro developers, BSD-3-Clause License (see LICENSE file)
+"""Adapter for Scipy Distributions."""
+
+__author__ = ["malikrafsan"]
+
+from typing import Union
+
+import pandas as pd
+from scipy.stats import rv_continuous, rv_discrete
+
+from skpro.distributions.base import BaseDistribution
+
+__all__ = ["_ScipyAdapter"]
+
+
+class _ScipyAdapter(BaseDistribution):
+    """Adapter for scipy distributions.
+
+    This class is an adapter for scipy distributions. It provides a common
+    interface for all scipy distributions. The class is abstract
+    and should not be instantiated directly.
+    """
+
+    _distribution_attr = "_dist"
+    _tags = {
+        "object_type": ["distribution", "scipy_distribution_adapter"],
+    }
+
+    def __init__(self, index=None, columns=None):
+        obj = self._get_scipy_object()
+        setattr(self, self._distribution_attr, obj)
+        super().__init__(index, columns)
+
+    def _get_scipy_object(self) -> Union[rv_continuous, rv_discrete]:
+        """Abstract method to get the scipy distribution object.
+
+        Should import the scipy distribution object and return it.
+        """
+        raise NotImplementedError("abstract method")
+
+    def _get_scipy_param(self):
+        """Abstract method to get the scipy distribution parameters.
+
+        Should return a tuple with two elements: a list of positional arguments (args)
+        and a dictionary of keyword arguments (kwds).
+        """
+        raise NotImplementedError("abstract method")
+
+    def _mean(self):
+        obj: Union[rv_continuous, rv_discrete] = getattr(self, self._distribution_attr)
+        args, kwds = self._get_scipy_param()
+        return obj.mean(*args, **kwds)
+
+    def _var(self):
+        obj: Union[rv_continuous, rv_discrete] = getattr(self, self._distribution_attr)
+        args, kwds = self._get_scipy_param()
+        return obj.var(*args, **kwds)
+
+    def _pdf(self, x: pd.DataFrame):
+        obj: Union[rv_continuous, rv_discrete] = getattr(self, self._distribution_attr)
+        if isinstance(obj, rv_discrete):
+            return 0
+
+        args, kwds = self._get_scipy_param()
+        return obj.pdf(x, *args, **kwds)
+
+    def _log_pdf(self, x: pd.DataFrame):
+        obj: Union[rv_continuous, rv_discrete] = getattr(self, self._distribution_attr)
+        if isinstance(obj, rv_discrete):
+            return 0
+
+        args, kwds = self._get_scipy_param()
+        return obj.logpdf(x, *args, **kwds)
+
+    def _cdf(self, x: pd.DataFrame):
+        obj: Union[rv_continuous, rv_discrete] = getattr(self, self._distribution_attr)
+        args, kwds = self._get_scipy_param()
+        return obj.cdf(x, *args, **kwds)
+
+    def _ppf(self, p: pd.DataFrame):
+        obj: Union[rv_continuous, rv_discrete] = getattr(self, self._distribution_attr)
+        args, kwds = self._get_scipy_param()
+        return obj.ppf(p, *args, **kwds)
+
+    def _pmf(self, x: pd.DataFrame):
+        """Return the probability mass function evaluated at x."""
+        obj: Union[rv_continuous, rv_discrete] = getattr(self, self._distribution_attr)
+        if isinstance(obj, rv_continuous):
+            return 0
+
+        args, kwds = self._get_scipy_param()
+        return obj.pmf(x, *args, **kwds)
+
+    def pmf(self, x: pd.DataFrame):
+        """Return the probability mass function evaluated at x."""
+        return self._boilerplate("_pmf", x=x)
+
+    def _log_pmf(self, x: pd.DataFrame):
+        """Return the log of the probability mass function evaluated at x."""
+        obj: Union[rv_continuous, rv_discrete] = getattr(self, self._distribution_attr)
+        if isinstance(obj, rv_continuous):
+            return 0
+
+        args, kwds = self._get_scipy_param()
+        return obj.logpmf(x, *args, **kwds)
+
+    def log_pmf(self, x: pd.DataFrame):
+        """Return the log of the probability mass function evaluated at x."""
+        return self._boilerplate("_log_pmf", x=x)

skpro/distributions/adapters/scipy/tests/test_scipy_adapters.py

@@ -2,6 +2,12 @@
 
 import numpy as np
 import pandas as pd
+import pytest
+from skbase.testing import QuickTester
+
+from skpro.tests.test_all_estimators import BaseFixtureGenerator, PackageConfig
+
+__author__ = ["fkiraly", "malikrafsan"]
 
 
 def test_empirical_from_discrete():
@@ -40,3 +46,82 @@ def test_empirical_from_discrete():
     )
     assert np.all(emp2.spl.index == expected_idx)
     assert np.all(emp2.spl.columns == ["abc"])
+
+
+class ScipyDistributionFixtureGenerator(BaseFixtureGenerator):
+    """Fixture generator for scipy distributions adapter.
+
+    Fixtures parameterized
+    ----------------------
+    object_class: object inheriting from BaseObject
+        ranges over object classes not excluded by EXCLUDE_OBJECTS, EXCLUDED_TESTS
+    object_instance: instance of object inheriting from BaseObject
+        ranges over object classes not excluded by EXCLUDE_OBJECTS, EXCLUDED_TESTS
+        instances are generated by create_test_instance class method
+    """
+
+    object_type_filter = "scipy_distribution_adapter"
+
+
+class TestScipyAdapter(PackageConfig, ScipyDistributionFixtureGenerator, QuickTester):
+    """Test the scipy adapter."""
+
+    METHOD_TESTS = {
+        "NO_PARAMS": [("mean", "mean"), ("var", "var")],
+        "X_PARAMS": [("cdf", "cdf"), ("ppf", "ppf")],
+        "CONTINUOUS": [("pdf", "pdf"), ("log_pdf", "logpdf")],
+        "DISCRETE": [("pmf", "pmf"), ("log_pmf", "logpmf")],
+    }
+
+    X_VALUES = [0.1, 0.5, 0.99]
+
+    @pytest.mark.parametrize("method,scipy_method", METHOD_TESTS["NO_PARAMS"])
+    def test_method_no_params(self, object_instance, method, scipy_method):
+        """Test method that doesn't need additional parameters."""
+        res = getattr(object_instance, method)()
+        params = object_instance._get_scipy_param()
+        scipy_obj = object_instance._get_scipy_object()
+
+        scipy_res = getattr(scipy_obj, scipy_method)(*params[0], **params[1])
+
+        assert np.allclose(res, scipy_res)
+
+    @pytest.mark.parametrize("method,scipy_method", METHOD_TESTS["X_PARAMS"])
+    @pytest.mark.parametrize("x", X_VALUES)
+    def test_method_with_x_params(self, object_instance, method, scipy_method, x):
+        """Test method that needs x as parameter."""
+        res = getattr(object_instance, method)(x)
+        params = object_instance._get_scipy_param()
+        scipy_obj = object_instance._get_scipy_object()
+
+        scipy_res = getattr(scipy_obj, scipy_method)(x, *params[0], **params[1])
+
+        assert np.allclose(res, scipy_res)
+
+    @pytest.mark.parametrize("method,scipy_method", METHOD_TESTS["CONTINUOUS"])
+    @pytest.mark.parametrize("x", X_VALUES)
+    def test_method_continuous_dist(self, object_instance, method, scipy_method, x):
+        """Test continuous distribution method."""
+        res = getattr(object_instance, method)(x)
+        if object_instance._tags["distr:measuretype"] != "continuous":
+            scipy_res = 0
+        else:
+            params = object_instance._get_scipy_param()
+            scipy_obj = object_instance._get_scipy_object()
+            scipy_res = getattr(scipy_obj, scipy_method)(x, *params[0], **params[1])
+
+        assert np.allclose(res, scipy_res)
+
+    @pytest.mark.parametrize("method,scipy_method", METHOD_TESTS["DISCRETE"])
+    @pytest.mark.parametrize("x", X_VALUES)
+    def test_method_discrete_dist(self, object_instance, method, scipy_method, x):
+        """Test discrete distribution method."""
+        res = getattr(object_instance, method)(x)
+        if object_instance._tags["distr:measuretype"] != "discrete":
+            scipy_res = 0
+        else:
+            params = object_instance._get_scipy_param()
+            scipy_obj = object_instance._get_scipy_object()
+            scipy_res = getattr(scipy_obj, scipy_method)(x, *params[0], **params[1])
+
+        assert np.allclose(res, scipy_res)

skpro/distributions/fisk.py

@@ -1,15 +1,15 @@
 # copyright: skpro developers, BSD-3-Clause License (see LICENSE file)
 """Log-logistic aka Fisk probability distribution."""
 
-__author__ = ["fkiraly"]
+__author__ = ["fkiraly", "malikrafsan"]
 
 import pandas as pd
-from scipy.stats import fisk
+from scipy.stats import fisk, rv_continuous
 
-from skpro.distributions.base import BaseDistribution
+from skpro.distributions.adapters.scipy import _ScipyAdapter
 
 
-class Fisk(BaseDistribution):
+class Fisk(_ScipyAdapter):
     r"""Fisk distribution, aka log-logistic distribution.
 
     The Fisk distribution is parametrized by a scale parameter :math:`\alpha`
@@ -47,109 +47,14 @@ def __init__(self, alpha=1, beta=1, index=None, columns=None):
 
         super().__init__(index=index, columns=columns)
 
-    def _mean(self):
-        """Return expected value of the distribution.
+    def _get_scipy_object(self) -> rv_continuous:
+        return fisk
 
-        Returns
-        -------
-        2D np.ndarray, same shape as ``self``
-            expected value of distribution (entry-wise)
-        """
+    def _get_scipy_param(self):
         alpha = self._bc_params["alpha"]
         beta = self._bc_params["beta"]
 
-        mean_arr = fisk.mean(scale=alpha, c=beta)
-        return mean_arr
-
-    def _var(self):
-        r"""Return element/entry-wise variance of the distribution.
-
-        Returns
-        -------
-        2D np.ndarray, same shape as ``self``
-            variance of the distribution (entry-wise)
-        """
-        alpha = self._bc_params["alpha"]
-        beta = self._bc_params["beta"]
-
-        var_arr = fisk.var(scale=alpha, c=beta)
-        return var_arr
-
-    def _pdf(self, x):
-        """Probability density function.
-
-        Parameters
-        ----------
-        x : 2D np.ndarray, same shape as ``self``
-            values to evaluate the pdf at
-
-        Returns
-        -------
-        2D np.ndarray, same shape as ``self``
-            pdf values at the given points
-        """
-        alpha = self._bc_params["alpha"]
-        beta = self._bc_params["beta"]
-
-        pdf_arr = fisk.pdf(x, scale=alpha, c=beta)
-        return pdf_arr
-
-    def _log_pdf(self, x):
-        """Logarithmic probability density function.
-
-        Parameters
-        ----------
-        x : 2D np.ndarray, same shape as ``self``
-            values to evaluate the pdf at
-
-        Returns
-        -------
-        2D np.ndarray, same shape as ``self``
-            log pdf values at the given points
-        """
-        alpha = self._bc_params["alpha"]
-        beta = self._bc_params["beta"]
-
-        lpdf_arr = fisk.logpdf(x, scale=alpha, c=beta)
-        return lpdf_arr
-
-    def _cdf(self, x):
-        """Cumulative distribution function.
-
-        Parameters
-        ----------
-        x : 2D np.ndarray, same shape as ``self``
-            values to evaluate the cdf at
-
-        Returns
-        -------
-        2D np.ndarray, same shape as ``self``
-            cdf values at the given points
-        """
-        alpha = self._bc_params["alpha"]
-        beta = self._bc_params["beta"]
-
-        cdf_arr = fisk.cdf(x, scale=alpha, c=beta)
-        return cdf_arr
-
-    def _ppf(self, p):
-        """Quantile function = percent point function = inverse cdf.
-
-        Parameters
-        ----------
-        p : 2D np.ndarray, same shape as ``self``
-            values to evaluate the ppf at
-
-        Returns
-        -------
-        2D np.ndarray, same shape as ``self``
-            ppf values at the given points
-        """
-        alpha = self._bc_params["alpha"]
-        beta = self._bc_params["beta"]
-
-        icdf_arr = fisk.ppf(p, scale=alpha, c=beta)
-        return icdf_arr
+        return [], {"c": beta, "scale": alpha}
 
     @classmethod
     def get_test_params(cls, parameter_set="default"):