Miscellaneous typos and code cleaning

examples/pcovc/KPCovC_Comparison.py

@@ -105,7 +105,7 @@
     t_train = model.fit_transform(X_train_scaled, y_train)
     t_test = model.transform(X_test_scaled)
 
-    ax.scatter(t_test[:, 0], t_test[:, 1], alpha=alpha_d, cmap=cm_bright, c=y_test)
+    ax.scatter(t_test[:, 0], t_test[:, 1], alpha=alpha_p, cmap=cm_bright, c=y_test)
     ax.scatter(t_train[:, 0], t_train[:, 1], cmap=cm_bright, c=y_train)
 
     ax.set_title(models[model])
@@ -197,20 +197,16 @@
 models = {
     LogisticRegressionCV(random_state=random_state): {
         "kernel_params": {"kernel": "rbf", "gamma": 12},
-        "title": "Logistic Regression",
     },
     RidgeClassifierCV(): {
         "kernel_params": {"kernel": "rbf", "gamma": 1},
-        "title": "Ridge Classifier",
         "eps": 0.40,
     },
     LinearSVC(random_state=random_state): {
         "kernel_params": {"kernel": "rbf", "gamma": 15},
-        "title": "Support Vector Classification",
     },
     SGDClassifier(random_state=random_state): {
         "kernel_params": {"kernel": "rbf", "gamma": 15},
-        "title": "SGD Classifier",
         "eps": 10,
     },
 }

src/skmatter/decomposition/_kernel_pcovc.py

@@ -24,8 +24,8 @@
 class KernelPCovC(LinearClassifierMixin, _BaseKPCov):
     r"""Kernel Principal Covariates Classification (KPCovC).
 
-    KPCovC is a modification on the PrincipalCovariates Classification
-    proposed in [Jorgensen2025]_.  It determines  a latent-space projection
+    KPCovC is a modification on the Principal Covariates Classification
+    proposed in [Jorgensen2025]_. It determines a latent-space projection
     :math:`\mathbf{T}` which minimizes a combined loss in supervised and unsupervised
     tasks in the reproducing kernel Hilbert space (RKHS).
 
@@ -272,7 +272,7 @@ def fit(self, X, Y, W=None):
         check_classification_targets(Y)
         self.classes_ = np.unique(Y)
 
-        super().fit(X)
+        super()._set_fit_params(X)
 
         K = self._get_kernel(X)
 
@@ -314,14 +314,13 @@ def fit(self, X, Y, W=None):
 
             # Check if classifier is fitted; if not, fit with precomputed K
             self.z_classifier_ = check_cl_fit(classifier, K, Y)
-            W = self.z_classifier_.coef_.T.reshape(K.shape[1], -1)
+            W = self.z_classifier_.coef_.T
 
         else:
             # If precomputed, use default classifier to predict Y from T
             classifier = LogisticRegression(max_iter=500)
             if W is None:
                 W = LogisticRegression().fit(K, Y).coef_.T
-                W = W.reshape(K.shape[1], -1)
 
         Z = K @ W
 
@@ -440,7 +439,7 @@ def decision_function(self, X=None, T=None):
             if self.center:
                 K = self.centerer_.transform(K)
 
-            # Or self.classifier_.decision_function(K @ self.pxt_)
+            # Or self.classifier_.decision_function(K @ self.pkt_)
             return K @ self.pkz_ + self.classifier_.intercept_
 
         else:

src/skmatter/decomposition/_kernel_pcovr.py

@@ -242,7 +242,7 @@ def fit(self, X, Y, W=None):
         """
         X, Y = validate_data(self, X, Y, y_numeric=True, multi_output=True)
 
-        super().fit(X)
+        super()._set_fit_params(X)
 
         K = self._get_kernel(X)
 

src/skmatter/decomposition/_kpcov.py

@@ -74,10 +74,12 @@ def _get_kernel(self, X, Y=None):
             X, Y, metric=self.kernel, filter_params=True, n_jobs=self.n_jobs, **params
         )
 
-    def fit(self, X):
-        """Contains the common functionality for the KPCovR and KPCovC fit methods,
-        but leaves the rest of the functionality to the subclass.
-        """
+    @abstractmethod
+    def fit(self, X, Y):
+        """Fit the model with X and Y. Subclasses should implement this method."""
+
+    def _set_fit_params(self, X):
+        """Initializes common fit parameters for PCovR and PCovC."""
         self.X_fit_ = X.copy()
 
         if self.n_components is None:

src/skmatter/decomposition/_pcov.py

@@ -48,10 +48,12 @@ def __init__(
         self.random_state = random_state
         self.whiten = whiten
 
-    def fit(self, X):
-        """Contains the common functionality for the PCovR and PCovC fit methods,
-        but leaves the rest of the functionality to the subclass.
-        """
+    @abstractmethod
+    def fit(self, X, Y):
+        """Fit the model with X and Y. Subclasses should implement this method."""
+
+    def _set_fit_params(self, X):
+        """Initializes common fit parameters for PCovR and PCovC."""
         # saved for inverse transformations from the latent space,
         # should be zero in the case that the features have been properly centered
         self.mean_ = np.mean(X, axis=0)

src/skmatter/decomposition/_pcovc.py

@@ -97,11 +97,11 @@ class PCovC(LinearClassifierMixin, _BasePCov):
         Must be of range [0.0, infinity).
 
     space: {'feature', 'sample', 'auto'}, default='auto'
-        whether to compute the PCovC in `sample` or `feature` space
-        default=`sample` when :math:`{n_{samples} < n_{features}}` and
-        `feature` when :math:`{n_{features} < n_{samples}}`
+        whether to compute the PCovC in ``sample`` or ``feature`` space.
+        The default is equal to ``sample`` when :math:`{n_{samples} < n_{features}}`
+        and ``feature`` when :math:`{n_{features} < n_{samples}}`
 
-     classifier: `estimator object` or `precomputed`, default=None
+    classifier: ``estimator object`` or ``precomputed``, default=None
         classifier for computing :math:`{\mathbf{Z}}`. The classifier should be
         one of the following:
 
@@ -144,9 +144,9 @@ class PCovC(LinearClassifierMixin, _BasePCov):
         Must be of range [0.0, infinity).
 
     space: {'feature', 'sample', 'auto'}, default='auto'
-        whether to compute the PCovC in `sample` or `feature` space
-        default=`sample` when :math:`{n_{samples} < n_{features}}` and
-        `feature` when :math:`{n_{features} < n_{samples}}`
+        whether to compute the PCovC in ``sample`` or ``feature`` space.
+        The default is equal to ``sample`` when :math:`{n_{samples} < n_{features}}`
+        and ``feature`` when :math:`{n_{features} < n_{samples}}`
 
     n_components_ : int
         The estimated number of components, which equals the parameter
@@ -160,7 +160,7 @@ class PCovC(LinearClassifierMixin, _BasePCov):
         The linear classifier fit between :math:`\mathbf{X}` and :math:`\mathbf{Y}`.
 
     classifier_ : estimator object
-        The linear classifier fit between :math:`\mathbf{T}` and  :math:`\mathbf{Y}`.
+        The linear classifier fit between :math:`\mathbf{T}` and :math:`\mathbf{Y}`.
 
     pxt_ : ndarray of size :math:`({n_{features}, n_{components}})`
         the projector, or weights, from the input space :math:`\mathbf{X}`
@@ -254,15 +254,15 @@ def fit(self, X, Y, W=None):
             Training data, where n_samples is the number of samples.
 
         W : numpy.ndarray, shape (n_features, n_classes)
-            Classification weights, optional when classifier = `precomputed`. If
+            Classification weights, optional when classifier is ``precomputed``. If
             not passed, it is assumed that the weights will be taken from a
             linear classifier fit between :math:`\mathbf{X}` and :math:`\mathbf{Y}`
         """
         X, Y = validate_data(self, X, Y, y_numeric=False)
         check_classification_targets(Y)
         self.classes_ = np.unique(Y)
 
-        super().fit(X)
+        super()._set_fit_params(X)
 
         compatible_classifiers = (
             LogisticRegression,
@@ -291,14 +291,13 @@ def fit(self, X, Y, W=None):
                 classifier = self.classifier
 
             self.z_classifier_ = check_cl_fit(classifier, X, Y)
-            W = self.z_classifier_.coef_.T.reshape(X.shape[1], -1)
+            W = self.z_classifier_.coef_.T
 
         else:
             # If precomputed, use default classifier to predict Y from T
             classifier = LogisticRegression()
             if W is None:
                 W = LogisticRegression().fit(X, Y).coef_.T
-                W = W.reshape(X.shape[1], -1)
 
         Z = X @ W
 

src/skmatter/decomposition/_pcovr.py

@@ -88,9 +88,9 @@ class PCovR(RegressorMixin, MultiOutputMixin, _BasePCov):
         range [0.0, infinity).
 
     space: {'feature', 'sample', 'auto'}, default='auto'
-        whether to compute the PCovR in `sample` or `feature` space default=`sample`
-        when :math:`{n_{samples} < n_{features}}` and `feature` when
-        :math:`{n_{features} < n_{samples}}`
+        whether to compute the PCovC in ``sample`` or ``feature`` space.
+        The default is equal to ``sample`` when :math:`{n_{samples} < n_{features}}`
+        and ``feature`` when :math:`{n_{features} < n_{samples}}`
 
     regressor: {`Ridge`, `RidgeCV`, `LinearRegression`, `precomputed`}, default=None
         regressor for computing approximated :math:`{\mathbf{\hat{Y}}}`. The regressor
@@ -126,9 +126,9 @@ class PCovR(RegressorMixin, MultiOutputMixin, _BasePCov):
         Must be of range [0.0, infinity).
 
     space: {'feature', 'sample', 'auto'}, default='auto'
-        whether to compute the PCovR in `sample` or `feature` space default=`sample`
-        when :math:`{n_{samples} < n_{features}}` and `feature` when
-        :math:`{n_{features} < n_{samples}}`
+        whether to compute the PCovR in ``sample`` or ``feature`` space.
+        The default is equal to ``sample`` when :math:`{n_{samples} < n_{features}}`
+        and ``feature`` when :math:`{n_{features} < n_{samples}}`
 
     n_components_ : int
         The estimated number of components, which equals the parameter n_components, or
@@ -227,11 +227,12 @@ def fit(self, X, Y, W=None):
             regressed form of the properties, :math:`{\mathbf{\hat{Y}}}`.
 
         W : numpy.ndarray, shape (n_features, n_properties)
-            Regression weights, optional when regressor= `precomputed`. If not
+            Regression weights, optional when regressor is ``precomputed``. If not
             passed, it is assumed that `W = np.linalg.lstsq(X, Y, self.tol)[0]`
         """
         X, Y = validate_data(self, X, Y, y_numeric=True, multi_output=True)
-        super().fit(X)
+
+        super()._set_fit_params(X)
 
         compatible_regressors = (LinearRegression, Ridge, RidgeCV)
 
@@ -414,7 +415,7 @@ def score(self, X, y, T=None):
             Negative sum of the loss in reconstructing X from the latent-space
             projection T and the loss in predicting Y from the latent-space projection T
         """
-        X, y = validate_data(self, X, y, reset=False)
+        X, y = validate_data(self, X, y, multi_output=True, reset=False)
 
         if T is None:
             T = self.transform(X)

tests/test_kernel_pcovc.py

@@ -160,22 +160,17 @@ def test_Z_shape(self):
         kpcovc.fit(self.X, self.Y)
 
         # Shape (n_samples, ) for binary classifcation
-        Z = kpcovc.decision_function(self.X)
+        Z_binary = kpcovc.decision_function(self.X)
 
-        self.assertTrue(Z.ndim == 1)
-        self.assertTrue(Z.shape[0] == self.X.shape[0])
-
-        # Modify Y so that it now contains three classes
-        Y_multiclass = self.Y.copy()
-        Y_multiclass[0] = 2
-        kpcovc.fit(self.X, Y_multiclass)
-        n_classes = len(np.unique(Y_multiclass))
+        self.assertEqual(Z_binary.ndim, 1)
+        self.assertEqual(Z_binary.shape[0], self.X.shape[0])
 
         # Shape (n_samples, n_classes) for multiclass classification
-        Z = kpcovc.decision_function(self.X)
+        kpcovc.fit(self.X, np.random.randint(0, 3, size=self.X.shape[0]))
+        Z_multi = kpcovc.decision_function(self.X)
 
-        self.assertTrue(Z.ndim == 2)
-        self.assertTrue((Z.shape[0], Z.shape[1]) == (self.X.shape[0], n_classes))
+        self.assertEqual(Z_multi.ndim, 2)
+        self.assertEqual(Z_multi.shape, (self.X.shape[0], len(kpcovc.classes_)))
 
     def test_decision_function(self):
         """Check that KPCovC's decision_function works when only T is
@@ -225,11 +220,11 @@ def test_prefit_classifier(self):
         kpcovc = KernelPCovC(mixing=0.5, classifier=classifier, **kernel_params)
         kpcovc.fit(self.X, self.Y)
 
-        Z_classifier = classifier.decision_function(K).reshape(K.shape[0], -1)
-        W_classifier = classifier.coef_.T.reshape(K.shape[1], -1)
+        Z_classifier = classifier.decision_function(K)
+        W_classifier = classifier.coef_.T
 
-        Z_kpcovc = kpcovc.z_classifier_.decision_function(K).reshape(K.shape[0], -1)
-        W_kpcovc = kpcovc.z_classifier_.coef_.T.reshape(K.shape[1], -1)
+        Z_kpcovc = kpcovc.z_classifier_.decision_function(K)
+        W_kpcovc = kpcovc.z_classifier_.coef_.T
 
         self.assertTrue(np.allclose(Z_classifier, Z_kpcovc))
         self.assertTrue(np.allclose(W_classifier, W_kpcovc))
@@ -273,40 +268,37 @@ def test_none_classifier(self):
         self.assertTrue(kpcovc.classifier_ is not None)
 
     def test_incompatible_coef_shape(self):
-        kernel_params = {"kernel": "rbf", "gamma": 0.1, "degree": 3, "coef0": 0}
-
-        K = pairwise_kernels(self.X, metric="rbf", filter_params=True, **kernel_params)
-
-        # Modify Y to be multiclass
-        Y_multiclass = self.Y.copy()
-        Y_multiclass[0] = 2
+        kernel_params = {"kernel": "sigmoid", "gamma": 0.1, "degree": 3, "coef0": 0}
+        K = pairwise_kernels(
+            self.X, metric="sigmoid", filter_params=True, **kernel_params
+        )
 
-        classifier1 = LinearSVC()
-        classifier1.fit(K, Y_multiclass)
-        kpcovc1 = self.model(mixing=0.5, classifier=classifier1, **kernel_params)
+        cl_multi = LinearSVC()
+        cl_multi.fit(K, np.random.randint(0, 3, size=self.X.shape[0]))
+        kpcovc_binary = self.model(mixing=0.5, classifier=cl_multi)
 
         # Binary classification shape mismatch
         with self.assertRaises(ValueError) as cm:
-            kpcovc1.fit(self.X, self.Y)
+            kpcovc_binary.fit(self.X, self.Y)
         self.assertEqual(
             str(cm.exception),
             "For binary classification, expected classifier coefficients "
             "to have shape (1, %d) but got shape %r"
-            % (K.shape[1], classifier1.coef_.shape),
+            % (K.shape[1], cl_multi.coef_.shape),
         )
 
-        classifier2 = LinearSVC()
-        classifier2.fit(K, self.Y)
-        kpcovc2 = self.model(mixing=0.5, classifier=classifier2)
+        cl_binary = LinearSVC()
+        cl_binary.fit(K, self.Y)
+        kpcovc_multi = self.model(mixing=0.5, classifier=cl_binary)
 
         # Multiclass classification shape mismatch
         with self.assertRaises(ValueError) as cm:
-            kpcovc2.fit(self.X, Y_multiclass)
+            kpcovc_multi.fit(self.X, np.random.randint(0, 3, size=self.X.shape[0]))
         self.assertEqual(
             str(cm.exception),
             "For multiclass classification, expected classifier coefficients "
             "to have shape (%d, %d) but got shape %r"
-            % (len(np.unique(Y_multiclass)), K.shape[1], classifier2.coef_.shape),
+            % (len(kpcovc_multi.classes_), K.shape[1], cl_binary.coef_.shape),
         )
 
     def test_precomputed_classification(self):
@@ -316,7 +308,7 @@ def test_precomputed_classification(self):
         classifier = LogisticRegression()
         classifier.fit(K, self.Y)
 
-        W = classifier.coef_.T.reshape(K.shape[1], -1)
+        W = classifier.coef_.T
         kpcovc1 = self.model(mixing=0.5, classifier="precomputed", **kernel_params)
         kpcovc1.fit(self.X, self.Y, W)
         t1 = kpcovc1.transform(self.X)