Merge pull request #374 from sebp/Finesim97-pipeline_scale_fix

Expose _predict_risk_score in Pipeline

sksurv/__init__.py

@@ -6,6 +6,8 @@
 from sklearn.pipeline import Pipeline, _final_estimator_has
 from sklearn.utils.metaestimators import available_if
 
+from .util import property_available_if
+
 
 def _get_version(name):
     try:
@@ -125,9 +127,15 @@ def predict_survival_function(self, X, **kwargs):
     return self.steps[-1][-1].predict_survival_function(Xt, **kwargs)
 
 
+@property_available_if(_final_estimator_has("_predict_risk_score"))
+def _predict_risk_score(self):
+    return self.steps[-1][-1]._predict_risk_score
+
+
 def patch_pipeline():
     Pipeline.predict_survival_function = predict_survival_function
     Pipeline.predict_cumulative_hazard_function = predict_cumulative_hazard_function
+    Pipeline._predict_risk_score = _predict_risk_score
 
 
 try:

sksurv/util.py

@@ -259,3 +259,63 @@ def safe_concat(objs, *args, **kwargs):
         concatenated[name] = pd.Categorical(concatenated[name], **params)
 
     return concatenated
+
+
+class _PropertyAvailableIfDescriptor:
+    """Implements a conditional property using the descriptor protocol based on the property decorator.
+
+    The corresponding class in scikit-learn (`_AvailableIfDescriptor`) only supports callables.
+    This class adopts the property decorator as described in the descriptor guide in the offical Python documentation.
+
+    See also
+    --------
+    https://docs.python.org/3/howto/descriptor.html
+        Descriptor HowTo Guide
+
+    :class:`sklearn.utils.available_if._AvailableIfDescriptor`
+        The original class in scikit-learn.
+    """
+
+    def __init__(self, check, fget, doc=None):
+        self.check = check
+        self.fget = fget
+        if doc is None and fget is not None:
+            doc = fget.__doc__
+        self.__doc__ = doc
+        self._name = ""
+
+    def __set_name__(self, owner, name):
+        self._name = name
+
+    def __get__(self, obj, objtype=None):
+        if obj is None:
+            return self
+
+        attr_err = AttributeError(f"This {obj!r} has no attribute {self._name!r}")
+        if not self.check(obj):
+            raise attr_err
+
+        if self.fget is None:
+            raise AttributeError(f"property '{self._name}' has no getter")
+        return self.fget(obj)
+
+
+def property_available_if(check):
+    """A property attribute that is available only if check returns a truthy value.
+
+    Only supports getting an attribute value, setting or deleting an attribute value are not supported.
+
+    Parameters
+    ----------
+    check : callable
+        When passed the object of the decorated method, this should return
+        `True` if the property attribute is available, and either return `False`
+        or raise an `AttributeError` if not available.
+
+    Returns
+    -------
+    callable
+        Callable makes the decorated property available if `check` returns
+        `True`, otherwise the decorated property is unavailable.
+    """
+    return lambda fn: _PropertyAvailableIfDescriptor(check=check, fget=fn)

tests/test_aft.py

@@ -1,7 +1,9 @@
 import numpy as np
 from numpy.testing import assert_array_almost_equal
 import pytest
+from sklearn.pipeline import make_pipeline
 
+from sksurv.base import SurvivalAnalysisMixin
 from sksurv.linear_model import IPCRidge
 from sksurv.testing import assert_cindex_almost_equal
 
@@ -51,3 +53,21 @@ def test_predict(make_whas500):
         )
 
         assert model.score(x_test, y_test) == 0.66925817946226107
+
+    @staticmethod
+    def test_pipeline_score(make_whas500):
+        whas500 = make_whas500()
+        pipe = make_pipeline(IPCRidge())
+        pipe.fit(whas500.x[:400], whas500.y[:400])
+
+        x_test = whas500.x[400:]
+        y_test = whas500.y[400:]
+        p = pipe.predict(x_test)
+        assert_cindex_almost_equal(
+            y_test["fstat"],
+            y_test["lenfol"],
+            -p,
+            (0.66925817946226107, 2066, 1021, 0, 1),
+        )
+
+        assert SurvivalAnalysisMixin.score(pipe, x_test, y_test) == 0.66925817946226107

tests/test_util.py

@@ -8,7 +8,7 @@
 import pytest
 
 from sksurv.testing import FixtureParameterFactory
-from sksurv.util import Surv, safe_concat
+from sksurv.util import Surv, _PropertyAvailableIfDescriptor, property_available_if, safe_concat
 
 
 class ConcatCasesFactory(FixtureParameterFactory):
@@ -369,3 +369,37 @@ def test_from_dataframe(args, expected, expected_error):
 
     if expected is not None:
         assert_array_equal(y, expected)
+
+
+def test_cond_avail_property():
+    class WithCondProp:
+        def __init__(self, val):
+            self.avail = False
+            self._prop = val
+
+        @property_available_if(lambda self: self.avail)
+        def prop(self):
+            return self._prop
+
+        no_prop = _PropertyAvailableIfDescriptor(lambda self: self.avail, fget=None)
+
+    testval = 43
+    msg = "has no attribute 'prop'"
+
+    assert WithCondProp.prop is not None
+
+    test_obj = WithCondProp(testval)
+    with pytest.raises(AttributeError, match=msg):
+        _ = test_obj.prop
+    assert test_obj.avail is False
+
+    test_obj.avail = True
+    assert test_obj.prop == testval
+
+    test_obj.avail = False
+    with pytest.raises(AttributeError, match=msg):
+        _ = test_obj.prop
+
+    test_obj.avail = True
+    with pytest.raises(AttributeError, match="has no getter"):
+        _ = test_obj.no_prop