Merge pull request #159 from lucasimi/feature/scikit-learn-compatibility

Feature/scikit learn compatibility

Author: lucasimi

src/tdamapper/_common.py

@@ -3,6 +3,8 @@
 """
 import warnings
 
+import numpy as np
+
 
 def warn_deprecated(deprecated, substitute):
     msg = f'{deprecated} is deprecated and will be removed in a future version. Use {substitute} instead.'
@@ -17,6 +19,52 @@ def warn_user(msg):
     warnings.warn(msg, UserWarning, stacklevel=2)
 
 
+class EstimatorMixin:
+
+    def _is_sparse(self, X):
+        # simple alternative use scipy.sparse.issparse
+        return hasattr(X, 'toarray')
+
+    def _validate_X_y(self, X, y):
+        if self._is_sparse(X):
+            raise ValueError('Sparse data not supported.')
+
+        X = np.asarray(X)
+        y = np.asarray(y)
+
+        if X.size == 0:
+            msg = f'0 feature(s) (shape={X.shape}) while a minimum of 1 is required.'
+            raise ValueError(msg)
+
+        if y.size == 0:
+            msg = f'0 feature(s) (shape={y.shape}) while a minimum of 1 is required.'
+            raise ValueError(msg)
+
+        if X.ndim == 1:
+            raise ValueError('1d-arrays not supported.')
+
+        if np.iscomplexobj(X) or np.iscomplexobj(y):
+            raise ValueError('Complex data not supported.')
+
+        if X.dtype == np.object_:
+            X = np.array(X, dtype=float)
+
+        if y.dtype == np.object_:
+            y = np.array(y, dtype=float)
+
+        if np.isnan(X).any() or np.isinf(X).any() or \
+                np.isnan(y).any() or np.isinf(y).any():
+            raise ValueError('NaNs or infinite values not supported.')
+
+        return X, y
+
+    def fit(self, X, y=None):
+        X, y = self._validate_X_y(X, y)
+        res = super().fit(X, y)
+        self.n_features_in_ = X.shape[1]
+        return res
+
+
 class ParamsMixin:
     """
     Mixin to add setters and getters for public parameters, compatible with

src/tdamapper/clustering.py

@@ -4,7 +4,12 @@
 
 from tdamapper.core import mapper_connected_components, TrivialCover
 import tdamapper.core
-from tdamapper._common import ParamsMixin, clone, warn_deprecated
+from tdamapper._common import (
+    ParamsMixin,
+    EstimatorMixin,
+    clone,
+    warn_deprecated,
+)
 
 
 class TrivialClustering(tdamapper.core.TrivialClustering):
@@ -33,7 +38,34 @@ def __init__(self, clustering=None, verbose=True):
         super().__init__(clustering, verbose)
 
 
-class MapperClustering(ParamsMixin):
+class _MapperClustering:
+
+    def __init__(self, cover=None, clustering=None, n_jobs=1):
+        self.cover = cover
+        self.clustering = clustering
+        self.n_jobs = n_jobs
+
+    def fit(self, X, y=None):
+        cover = TrivialCover() if self.cover is None \
+            else self.cover
+        cover = clone(cover)
+        clustering = TrivialClustering() if self.clustering is None \
+            else self.clustering
+        clustering = clone(clustering)
+        n_jobs = self.n_jobs
+        y = X if y is None else y
+        itm_lbls = mapper_connected_components(
+            X,
+            y,
+            cover,
+            clustering,
+            n_jobs=n_jobs,
+        )
+        self.labels_ = [itm_lbls[i] for i, _ in enumerate(X)]
+        return self
+
+
+class MapperClustering(EstimatorMixin, _MapperClustering, ParamsMixin):
     """
     A clustering algorithm based on the Mapper graph.
 
@@ -60,25 +92,4 @@ class MapperClustering(ParamsMixin):
     """
 
     def __init__(self, cover=None, clustering=None, n_jobs=1):
-        self.cover = cover
-        self.clustering = clustering
-        self.n_jobs = n_jobs
-
-    def fit(self, X, y=None):
-        cover = TrivialCover() if self.cover is None \
-            else self.cover
-        cover = clone(cover)
-        clustering = TrivialClustering() if self.clustering is None \
-            else self.clustering
-        clustering = clone(clustering)
-        n_jobs = self.n_jobs
-        y = X if y is None else y
-        itm_lbls = mapper_connected_components(
-            X,
-            y,
-            cover,
-            clustering,
-            n_jobs=n_jobs,
-        )
-        self.labels_ = [itm_lbls[i] for i, _ in enumerate(X)]
-        return self
+        super().__init__(cover=cover, clustering=clustering, n_jobs=n_jobs)

src/tdamapper/core.py

@@ -33,7 +33,7 @@
 from joblib import Parallel, delayed
 
 from tdamapper.utils.unionfind import UnionFind
-from tdamapper._common import ParamsMixin, clone
+from tdamapper._common import ParamsMixin, EstimatorMixin, clone
 
 
 ATTR_IDS = 'ids'
@@ -364,7 +364,53 @@ def apply(self, X):
         yield list(range(0, len(X)))
 
 
-class MapperAlgorithm(ParamsMixin):
+class _MapperAlgorithm:
+
+    def __init__(
+        self,
+        cover=None,
+        clustering=None,
+        failsafe=True,
+        verbose=True,
+        n_jobs=1,
+    ):
+        self.cover = cover
+        self.clustering = clustering
+        self.failsafe = failsafe
+        self.verbose = verbose
+        self.n_jobs = n_jobs
+
+    def fit(self, X, y=None):
+        self.__cover = TrivialCover() if self.cover is None \
+            else self.cover
+        self.__clustering = TrivialClustering() if self.clustering is None \
+            else self.clustering
+        self.__verbose = self.verbose
+        self.__failsafe = self.failsafe
+        if self.__failsafe:
+            self.__clustering = FailSafeClustering(
+                clustering=self.__clustering,
+                verbose=self.__verbose,
+            )
+        self.__cover = clone(self.__cover)
+        self.__clustering = clone(self.__clustering)
+        self.__n_jobs = self.n_jobs
+        y = X if y is None else y
+        self.graph_ = mapper_graph(
+            X,
+            y,
+            self.__cover,
+            self.__clustering,
+            n_jobs=self.__n_jobs,
+        )
+        return self
+
+    def fit_transform(self, X, y):
+        self.fit(X, y)
+        return self.graph_
+
+
+class MapperAlgorithm(EstimatorMixin, _MapperAlgorithm, ParamsMixin):
     """
     A class for creating and analyzing Mapper graphs.
 
@@ -412,11 +458,13 @@ def __init__(
         verbose=True,
         n_jobs=1,
     ):
-        self.cover = cover
-        self.clustering = clustering
-        self.failsafe = failsafe
-        self.verbose = verbose
-        self.n_jobs = n_jobs
+        super().__init__(
+            cover=cover,
+            clustering=clustering,
+            failsafe=failsafe,
+            verbose=verbose,
+            n_jobs=n_jobs,
+        )
 
     def fit(self, X, y=None):
         """
@@ -431,29 +479,7 @@ def fit(self, X, y=None):
         :type y: array-like of shape (n, k) or list-like of length n
         :return: The object itself.
         """
-        self.__cover = TrivialCover() if self.cover is None \
-            else self.cover
-        self.__clustering = TrivialClustering() if self.clustering is None \
-            else self.clustering
-        self.__verbose = self.verbose
-        self.__failsafe = self.failsafe
-        if self.__failsafe:
-            self.__clustering = FailSafeClustering(
-                clustering=self.__clustering,
-                verbose=self.__verbose,
-            )
-        self.__cover = clone(self.__cover)
-        self.__clustering = clone(self.__clustering)
-        self.__n_jobs = self.n_jobs
-        y = X if y is None else y
-        self.graph_ = mapper_graph(
-            X,
-            y,
-            self.__cover,
-            self.__clustering,
-            n_jobs=self.__n_jobs,
-        )
-        return self
+        return super().fit(X, y)
 
     def fit_transform(self, X, y):
         """
@@ -469,8 +495,7 @@ def fit_transform(self, X, y):
         :return: The Mapper graph.
         :rtype: :class:`networkx.Graph`
         """
-        self.fit(X, y)
-        return self.graph_
+        return super().fit_transform(X, y)
 
 
 class FailSafeClustering(ParamsMixin):

tests/test_unit_sklearn.py

@@ -3,7 +3,6 @@
 
 import numpy as np
 
-
 from sklearn.utils.estimator_checks import check_estimator
 
 from tdamapper.core import MapperAlgorithm
@@ -21,57 +20,6 @@ def euclidean(x, y):
     return np.linalg.norm(x - y)
 
 
-class ValidationMixin:
-
-    def _is_sparse(self, X):
-        # in alternative use scipy.sparse.issparse
-        return hasattr(X, 'toarray')
-
-    def _validate_X_y(self, X, y):
-        if self._is_sparse(X):
-            raise ValueError('Sparse data not supported.')
-
-        if X.size == 0:
-            msg = f'0 feature(s) (shape={X.shape}) while a minimum of 1 is required.'
-            raise ValueError(msg)
-
-        if y.size == 0:
-            msg = f'0 feature(s) (shape={y.shape}) while a minimum of 1 is required.'
-            raise ValueError(msg)
-
-        if X.ndim == 1:
-            raise ValueError('1d-arrays not supported.')
-
-        if np.iscomplexobj(X) or np.iscomplexobj(y):
-            raise ValueError('Complex data not supported.')
-
-        if X.dtype == np.object_:
-            X = np.array(X, dtype=float)
-
-        if y.dtype == np.object_:
-            y = np.array(y, dtype=float)
-
-        if np.isnan(X).any() or np.isinf(X).any() or \
-           np.isnan(y).any() or np.isinf(y).any():
-            raise ValueError('NaNs or infinite values not supported.')
-
-        return X, y
-
-    def fit(self, X, y=None):
-        X, y = self._validate_X_y(X, y)
-        res = super().fit(X, y)
-        self.n_features_in_ = X.shape[1]
-        return res
-
-
-class MapperEstimator(ValidationMixin, MapperAlgorithm):
-    pass
-
-
-class MapperClusteringEstimator(ValidationMixin, MapperClustering):
-    pass
-
-
 class TestSklearn(unittest.TestCase):
 
     setup_logging()
@@ -83,25 +31,25 @@ def run_tests(self, estimator):
             check(est)
 
     def test_trivial(self):
-        est = MapperEstimator()
+        est = MapperAlgorithm()
         self.run_tests(est)
 
     def test_ball(self):
-        est = MapperEstimator(cover=BallCover(metric=euclidean))
+        est = MapperAlgorithm(cover=BallCover(metric=euclidean))
         self.run_tests(est)
 
     def test_knn(self):
-        est = MapperEstimator(cover=KNNCover(metric=euclidean))
+        est = MapperAlgorithm(cover=KNNCover(metric=euclidean))
         self.run_tests(est)
 
     def test_cubical(self):
-        est = MapperEstimator(cover=CubicalCover())
+        est = MapperAlgorithm(cover=CubicalCover())
         self.run_tests(est)
 
     def test_clustering_trivial(self):
-        est = MapperClusteringEstimator()
+        est = MapperClustering()
         self.run_tests(est)
 
     def test_clustering_ball(self):
-        est = MapperClusteringEstimator(cover=BallCover(metric=euclidean))
+        est = MapperClustering(cover=BallCover(metric=euclidean))
         self.run_tests(est)