DOC fixes references issues given by sphinx (scikit-learn#27432)

Author: glemaitre

doc/modules/classes.rst

@@ -10,6 +10,23 @@ function raw specifications may not be enough to give full guidelines on their
 uses.
 For reference on concepts repeated across the API, see :ref:`glossary`.
 
+:mod:`sklearn`: Settings and information tools
+==============================================
+
+.. automodule:: sklearn
+    :no-members:
+    :no-inherited-members:
+
+.. currentmodule:: sklearn
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
+   config_context
+   get_config
+   set_config
+   show_versions
 
 :mod:`sklearn.base`: Base classes and utility functions
 =======================================================
@@ -51,10 +68,6 @@ Functions
    base.clone
    base.is_classifier
    base.is_regressor
-   config_context
-   get_config
-   set_config
-   show_versions
 
 .. _calibration_ref:
 
@@ -150,7 +163,7 @@ details.
 .. currentmodule:: sklearn
 
 .. autosummary::
-    :toctree: generated
+    :toctree: generated/
     :template: class.rst
 
     compose.ColumnTransformer
@@ -355,7 +368,7 @@ Samples generator
 .. currentmodule:: sklearn
 
 .. autosummary::
-   :toctree: generated
+   :toctree: generated/
    :template: class.rst
 
    discriminant_analysis.LinearDiscriminantAnalysis
@@ -592,7 +605,14 @@ From text
   gaussian_process.GaussianProcessClassifier
   gaussian_process.GaussianProcessRegressor
 
-Kernels:
+Kernels
+-------
+
+.. automodule:: sklearn.gaussian_process.kernels
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
 
 .. autosummary::
   :toctree: generated/
@@ -687,7 +707,7 @@ Plotting
    isotonic.IsotonicRegression
 
 .. autosummary::
-   :toctree: generated
+   :toctree: generated/
    :template: function.rst
 
    isotonic.check_increasing
@@ -865,9 +885,14 @@ Miscellaneous
 
 .. autosummary::
    :toctree: generated/
-   :template: function.rst
+   :template: classes.rst
 
    linear_model.PassiveAggressiveRegressor
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
    linear_model.enet_path
    linear_model.lars_path
    linear_model.lars_path_gram
@@ -1266,7 +1291,7 @@ Visualization
 .. currentmodule:: sklearn
 
 .. autosummary::
-    :toctree: generated
+    :toctree: generated/
     :template: class.rst
 
     multiclass.OneVsRestClassifier
@@ -1608,62 +1633,224 @@ Plotting
    :toctree: generated/
    :template: function.rst
 
-   utils.arrayfuncs.min_pos
    utils.as_float_array
    utils.assert_all_finite
+   utils.deprecated
+   utils.estimator_html_repr
+   utils.gen_batches
+   utils.gen_even_slices
+   utils.indexable
+   utils.murmurhash3_32
+   utils.resample
+   utils._safe_indexing
+   utils.safe_mask
+   utils.safe_sqr
+   utils.shuffle
+
+Input and parameter validation
+------------------------------
+
+.. automodule:: sklearn.utils.validation
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
    utils.check_X_y
    utils.check_array
    utils.check_scalar
    utils.check_consistent_length
    utils.check_random_state
+   utils.validation.check_is_fitted
+   utils.validation.check_memory
+   utils.validation.check_symmetric
+   utils.validation.column_or_1d
+   utils.validation.has_fit_parameter
+
+Utilities used in meta-estimators
+---------------------------------
+
+.. automodule:: sklearn.utils.metaestimators
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
+   utils.metaestimators.available_if
+
+Utilities to handle weights based on class labels
+-------------------------------------------------
+
+.. automodule:: sklearn.utils.class_weight
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
    utils.class_weight.compute_class_weight
    utils.class_weight.compute_sample_weight
-   utils.deprecated
-   utils.estimator_checks.check_estimator
-   utils.estimator_checks.parametrize_with_checks
-   utils.estimator_html_repr
+
+Utilities to deal with multiclass target in classifiers
+-------------------------------------------------------
+
+.. automodule:: sklearn.utils.multiclass
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
+   utils.multiclass.type_of_target
+   utils.multiclass.is_multilabel
+   utils.multiclass.unique_labels
+
+Utilities for optimal mathematical operations
+---------------------------------------------
+
+.. automodule:: sklearn.utils.extmath
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
    utils.extmath.safe_sparse_dot
    utils.extmath.randomized_range_finder
    utils.extmath.randomized_svd
    utils.extmath.fast_logdet
    utils.extmath.density
    utils.extmath.weighted_mode
-   utils.gen_batches
-   utils.gen_even_slices
-   utils.graph.single_source_shortest_path_length
-   utils.indexable
-   utils.metaestimators.available_if
-   utils.multiclass.type_of_target
-   utils.multiclass.is_multilabel
-   utils.multiclass.unique_labels
-   utils.murmurhash3_32
-   utils.resample
-   utils._safe_indexing
-   utils.safe_mask
-   utils.safe_sqr
-   utils.shuffle
+
+Utilities to work with sparse matrices and arrays
+-------------------------------------------------
+
+.. automodule:: sklearn.utils.sparsefuncs
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
    utils.sparsefuncs.incr_mean_variance_axis
    utils.sparsefuncs.inplace_column_scale
    utils.sparsefuncs.inplace_row_scale
    utils.sparsefuncs.inplace_swap_row
    utils.sparsefuncs.inplace_swap_column
    utils.sparsefuncs.mean_variance_axis
    utils.sparsefuncs.inplace_csr_column_scale
+
+.. automodule:: sklearn.utils.sparsefuncs_fast
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
    utils.sparsefuncs_fast.inplace_csr_row_normalize_l1
    utils.sparsefuncs_fast.inplace_csr_row_normalize_l2
+
+Utilities to work with graphs
+-----------------------------
+
+.. automodule:: sklearn.utils.graph
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
+   utils.graph.single_source_shortest_path_length
+
+Utilities for random sampling
+-----------------------------
+
+.. automodule:: sklearn.utils.random
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
    utils.random.sample_without_replacement
-   utils.validation.check_is_fitted
-   utils.validation.check_memory
-   utils.validation.check_symmetric
-   utils.validation.column_or_1d
-   utils.validation.has_fit_parameter
+
+
+Utilities to operate on arrays
+------------------------------
+
+.. automodule:: sklearn.utils.arrayfuncs
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
+   utils.arrayfuncs.min_pos
+
+Metadata routing
+----------------
+
+.. automodule:: sklearn.utils.metadata_routing
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
    utils.metadata_routing.get_routing_for_object
+   utils.metadata_routing.process_routing
+
+.. autosummary::
+   :toctree: generated/
+   :template: class.rst
+
    utils.metadata_routing.MetadataRouter
    utils.metadata_routing.MetadataRequest
    utils.metadata_routing.MethodMapping
-   utils.metadata_routing.process_routing
 
-Specific utilities to list scikit-learn components:
+Scikit-learn object discovery
+-----------------------------
+
+.. automodule:: sklearn.utils.discovery
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
 
 .. autosummary::
    :toctree: generated/
@@ -1673,7 +1860,30 @@ Specific utilities to list scikit-learn components:
    utils.discovery.all_displays
    utils.discovery.all_functions
 
-Utilities from joblib:
+Scikit-learn compatibility checker
+----------------------------------
+
+.. automodule:: sklearn.utils.estimator_checks
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
+   utils.estimator_checks.check_estimator
+   utils.estimator_checks.parametrize_with_checks
+
+Utilities for parallel computing
+--------------------------------
+
+.. automodule:: sklearn.utils.parallel
+   :no-members:
+   :no-inherited-members:
+
+.. currentmodule:: sklearn
 
 .. autosummary::
    :toctree: generated/