scikit-base 0.8.3__tar.gz → 0.10.0__tar.gz

{scikit_base-0.8.3/scikit_base.egg-info → scikit_base-0.10.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-base
-Version: 0.8.3
+Version: 0.10.0
 Summary: Base classes for sklearn-like parametric objects
 Author-email: sktime developers <sktime.toolbox@gmail.com>
 Maintainer: Franz Király
@@ -114,7 +114,7 @@ Requires-Dist: scikit-learn>=0.24.0; extra == "test"
 `skbase` provides base classes for creating scikit-learn-like parametric objects,
 along with tools to make it easier to build your own packages that follow these design patterns.
 
-:rocket: Version 0.8.3 is now available. Check out our
+:rocket: Version 0.10.0 is now available. Check out our
 [release notes](https://skbase.readthedocs.io/en/latest/changelog.html).
 
 | Overview | |

{scikit_base-0.8.3 → scikit_base-0.10.0}/README.md

@@ -7,7 +7,7 @@
 `skbase` provides base classes for creating scikit-learn-like parametric objects,
 along with tools to make it easier to build your own packages that follow these design patterns.
 
-:rocket: Version 0.8.3 is now available. Check out our
+:rocket: Version 0.10.0 is now available. Check out our
 [release notes](https://skbase.readthedocs.io/en/latest/changelog.html).
 
 | Overview | |

{scikit_base-0.8.3 → scikit_base-0.10.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "scikit-base"
-version = "0.8.3"
+version = "0.10.0"
 description = "Base classes for sklearn-like parametric objects"
 authors = [
     {name = "sktime developers", email = "sktime.toolbox@gmail.com"},

{scikit_base-0.8.3 → scikit_base-0.10.0/scikit_base.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-base
-Version: 0.8.3
+Version: 0.10.0
 Summary: Base classes for sklearn-like parametric objects
 Author-email: sktime developers <sktime.toolbox@gmail.com>
 Maintainer: Franz Király
@@ -114,7 +114,7 @@ Requires-Dist: scikit-learn>=0.24.0; extra == "test"
 `skbase` provides base classes for creating scikit-learn-like parametric objects,
 along with tools to make it easier to build your own packages that follow these design patterns.
 
-:rocket: Version 0.8.3 is now available. Check out our
+:rocket: Version 0.10.0 is now available. Check out our
 [release notes](https://skbase.readthedocs.io/en/latest/changelog.html).
 
 | Overview | |

{scikit_base-0.8.3 → scikit_base-0.10.0}/skbase/__init__.py

@@ -6,4 +6,4 @@
 The included functionality makes it easy to reuse scikit-learn and
 sktime design principles in your project.
 """
-__version__: str = "0.8.3"
+__version__: str = "0.10.0"

{scikit_base-0.8.3 → scikit_base-0.10.0}/skbase/base/_base.py

@@ -31,8 +31,8 @@ Tag inspection and setter methods
     set/clone dynamic tags        - clone_tags(estimator, tag_names=None)
 
 Blueprinting: resetting and cloning, post-init state with same hyper-parameters
-    reset estimator to post-init  - reset()
-    cloneestimator (copy&reset)   - clone()
+    reset object to post-init  - reset()
+    clone object (copy&reset)  - clone()
 
 Testing with default parameters methods
     getting default parameters (all sets)         - get_test_params()
@@ -144,10 +144,10 @@ class BaseObject(_FlagManager):
         return self
 
     def clone(self):
-        """Obtain a clone of the object with same hyper-parameters.
+        """Obtain a clone of the object with same hyper-parameters and config.
 
         A clone is a different object without shared references, in post-init state.
-        This function is equivalent to returning sklearn.clone of self.
+        This function is equivalent to returning ``sklearn.clone`` of ``self``.
 
         Raises
         ------
@@ -197,7 +197,7 @@ class BaseObject(_FlagManager):
         for p in parameters:
             if p.kind == p.VAR_POSITIONAL:
                 raise RuntimeError(
-                    "scikit-learn compatible estimators should always "
+                    "scikit-base compatible classes should always "
                     "specify their parameters in the signature"
                     " of their __init__ (no varargs)."
                     " %s with constructor %s doesn't "
@@ -290,7 +290,7 @@ class BaseObject(_FlagManager):
     def set_params(self, **params):
         """Set the parameters of this object.
 
-        The method works on simple estimators as well as on composite objects.
+        The method works on simple skbase objects as well as on composite objects.
         Parameter key strings ``<component>__<parameter>`` can be used for composites,
         i.e., objects that contain other objects, to access ``<parameter>`` in
         the component ``<component>``.
@@ -333,7 +333,7 @@ class BaseObject(_FlagManager):
                 valid_params[key] = value
 
         # all matched params have now been set
-        # reset estimator to clean post-init state with those params
+        # reset object to clean post-init state with those params
         self.reset()
 
         # recurse in components
@@ -460,7 +460,7 @@ class BaseObject(_FlagManager):
         )
 
     def get_tags(self):
-        """Get tags from estimator class and dynamic tag overrides.
+        """Get tags from skbase class and dynamic tag overrides.
 
         Returns
         -------
@@ -472,7 +472,7 @@ class BaseObject(_FlagManager):
         return self._get_flags(flag_attr_name="_tags")
 
     def get_tag(self, tag_name, tag_value_default=None, raise_error=True):
-        """Get tag value from estimator class and dynamic tag overrides.
+        """Get tag value from object class and dynamic tag overrides.
 
         Parameters
         ----------
@@ -523,11 +523,11 @@ class BaseObject(_FlagManager):
         return self
 
     def clone_tags(self, estimator, tag_names=None):
-        """Clone tags from another estimator as dynamic override.
+        """Clone tags from another object as dynamic override.
 
         Parameters
         ----------
-        estimator : estimator inheriting from :class:BaseEstimator
+        estimator : An instance of :class:BaseObject or derived class
         tag_names : str or list of str, default = None
             Names of tags to clone. If None then all tags in estimator are used
             as `tag_names`.
@@ -582,7 +582,7 @@ class BaseObject(_FlagManager):
 
     @classmethod
     def get_test_params(cls, parameter_set="default"):
-        """Return testing parameter settings for the estimator.
+        """Return testing parameter settings for the skbase object.
 
         Parameters
         ----------
@@ -605,7 +605,7 @@ class BaseObject(_FlagManager):
         # if non-default parameters are required, but none have been found, raise error
         if len(params_without_defaults) > 0:
             raise ValueError(
-                f"Estimator: {cls} has parameters without default values, "
+                f"skbase object {cls} has parameters without default values, "
                 f"but these are not set in get_test_params. "
                 f"Please set them in get_test_params, or provide default values. "
                 f"Also see the respective extension template, if applicable."
@@ -618,7 +618,7 @@ class BaseObject(_FlagManager):
 
     @classmethod
     def create_test_instance(cls, parameter_set="default"):
-        """Construct Estimator instance if possible.
+        """Construct an instance of the class, using first test parameter set.
 
         Parameters
         ----------
@@ -904,18 +904,18 @@ class BaseObject(_FlagManager):
     def set_random_state(self, random_state=None, deep=True, self_policy="copy"):
         """Set random_state pseudo-random seed parameters for self.
 
-        Finds ``random_state`` named parameters via ``estimator.get_params``,
+        Finds ``random_state`` named parameters via ``self.get_params``,
         and sets them to integers derived from ``random_state`` via ``set_params``.
         These integers are sampled from chain hashing via ``sample_dependent_seed``,
         and guarantee pseudo-random independence of seeded random generators.
 
-        Applies to ``random_state`` parameters in ``estimator`` depending on
-        ``self_policy``, and remaining component estimators
+        Applies to ``random_state`` parameters in ``self``, depending on
+        ``self_policy``, and remaining component objects
         if and only if ``deep=True``.
 
         Note: calls ``set_params`` even if ``self`` does not have a ``random_state``,
         or none of the components have a ``random_state`` parameter.
-        Therefore, ``set_random_state`` will reset any ``scikit-base`` estimator,
+        Therefore, ``set_random_state`` will reset any ``scikit-base`` object,
         even those without a ``random_state`` parameter.
 
         Parameters
@@ -925,15 +925,18 @@ class BaseObject(_FlagManager):
             integers. Pass int for reproducible output across multiple function calls.
 
         deep : bool, default=True
-            Whether to set the random state in sub-estimators.
-            If False, will set only ``self``'s ``random_state`` parameter, if exists.
-            If True, will set ``random_state`` parameters in sub-estimators as well.
+            Whether to set the random state in skbase object valued parameters, i.e.,
+            component estimators.
+
+            * If False, will set only ``self``'s ``random_state`` parameter, if exists.
+            * If True, will set ``random_state`` parameters in component objects
+              as well.
 
         self_policy : str, one of {"copy", "keep", "new"}, default="copy"
 
-            * "copy" : ``estimator.random_state`` is set to input ``random_state``
-            * "keep" : ``estimator.random_state`` is kept as is
-            * "new" : ``estimator.random_state`` is set to a new random state,
+            * "copy" : ``self.random_state`` is set to input ``random_state``
+            * "keep" : ``self.random_state`` is kept as is
+            * "new" : ``self.random_state`` is set to a new random state,
             derived from input ``random_state``, and in general different from it
 
         Returns
@@ -985,7 +988,21 @@ class TagAliaserMixin:
 
     @classmethod
     def get_class_tags(cls):
-        """Get class tags from estimator class and all its parent classes.
+        """Get class tags from class, with tag level inheritance from parent classes.
+
+        Every ``scikit-base`` compatible class has a set of tags,
+        which are used to store metadata about the object.
+
+        This is a class method, and retrieves tags applicable to the class,
+        with tag level overrides in the following order of decreasing priority:
+
+        1. class tags of the class, of which the object is an instance
+        2. class tags of all parent classes, in method resolution order
+
+        Instances can override these tags depending on hyper-parameters.
+
+        To retrieve tags with potential instance overrides, use
+        the ``get_tags`` method instead.
 
         Returns
         -------
@@ -1000,7 +1017,22 @@ class TagAliaserMixin:
 
     @classmethod
     def get_class_tag(cls, tag_name, tag_value_default=None):
-        """Get tag value from estimator class (only class tags).
+        """Get class tag value from class, with tag level inheritance from parents.
+
+        Every ``scikit-base`` compatible class has a set of tags,
+        which are used to store metadata about the object.
+
+        This is a class method, and retrieves the value of a tag applicable
+        to the class,
+        with tag level overrides in the following order of decreasing priority:
+
+        1. class tags of the class, of which the object is an instance
+        2. class tags of all parent classes, in method resolution order
+
+        Instances can override these tags depending on hyper-parameters.
+
+        To retrieve tag values with potential instance overrides, use
+        the ``get_tag`` method instead.
 
         Parameters
         ----------
@@ -1021,7 +1053,17 @@ class TagAliaserMixin:
         )
 
     def get_tags(self):
-        """Get tags from estimator class and dynamic tag overrides.
+        """Get tags from instance, with tag level inheritance and overrides.
+
+        Every ``scikit-base`` compatible object has a set of tags,
+        which are used to store metadata about the object.
+
+        This method retrieves all tags as a dictionary, with tag level overrides in the
+        following order of decreasing priority:
+
+        1. dynamic tags set at construction, e.g., dependent on hyper-parameters
+        2. class tags of the class, of which the object is an instance
+        3. class tags of all parent classes, in method resolution order
 
         Returns
         -------
@@ -1035,7 +1077,17 @@ class TagAliaserMixin:
         return collected_tags
 
     def get_tag(self, tag_name, tag_value_default=None, raise_error=True):
-        """Get tag value from estimator class and dynamic tag overrides.
+        """Get tag value from instance, with tag level inheritance and overrides.
+
+        Every ``scikit-base`` compatible object has a set of tags,
+        which are used to store metadata about the object.
+
+        This method retrieves the value of a single tag, with tag level overrides in the
+        following order of decreasing priority:
+
+        1. dynamic tags set at construction, e.g., dependent on hyper-parameters
+        2. class tags of the class, of which the object is an instance
+        3. class tags of all parent classes, in method resolution order
 
         Parameters
         ----------
@@ -1231,19 +1283,13 @@ class BaseEstimator(BaseObject):
         if not deep:
             return fitted_params
 
-        def sh(x):
-            """Shorthand to remove all underscores at end of a string."""
-            if x.endswith("_"):
-                return sh(x[:-1])
-            else:
-                return x
-
         # add all nested parameters from components that are skbase BaseEstimator
         c_dict = self._components()
         for c, comp in c_dict.items():
             if isinstance(comp, BaseEstimator) and comp._is_fitted:
                 c_f_params = comp.get_fitted_params(deep=deep)
-                c_f_params = {f"{sh(c)}__{k}": v for k, v in c_f_params.items()}
+                c = c.rstrip("_")
+                c_f_params = {f"{c}__{k}": v for k, v in c_f_params.items()}
                 fitted_params.update(c_f_params)
 
         # add all nested parameters from components that are sklearn estimators
@@ -1256,7 +1302,8 @@ class BaseEstimator(BaseObject):
             for c, comp in old_new_params.items():
                 if isinstance(comp, self.GET_FITTED_PARAMS_NESTING):
                     c_f_params = self._get_fitted_params_default(comp)
-                    c_f_params = {f"{sh(c)}__{k}": v for k, v in c_f_params.items()}
+                    c = c.rstrip("_")
+                    c_f_params = {f"{c}__{k}": v for k, v in c_f_params.items()}
                     new_params.update(c_f_params)
             fitted_params.update(new_params)
             old_new_params = new_params.copy()
@@ -1384,7 +1431,8 @@ def _clone(estimator, *, safe=True):
     found in :ref:`randomness`.
     """
     estimator_type = type(estimator)
-    # XXX: not handling dictionaries
+    if estimator_type is dict:
+        return {k: _clone(v, safe=safe) for k, v in estimator.items()}
     if estimator_type in (list, tuple, set, frozenset):
         return estimator_type([_clone(e, safe=safe) for e in estimator])
     elif not hasattr(estimator, "get_params") or isinstance(estimator, type):

{scikit_base-0.8.3 → scikit_base-0.10.0}/skbase/lookup/_lookup.py

@@ -203,46 +203,16 @@ def _filter_by_tags(obj, tag_filter=None, as_dataframe=True):
     if not hasattr(obj, "get_class_tag"):
         return False
 
-    klass_tags = obj.get_class_tags().keys()
-
-    # todo 0.9.0: remove the warning message
-    # i.e., this message and all warnings referring to it
-    warn_msg = (
-        "The meaning of filter_tags arguments in all_objects of type str "
-        "and iterable of str will change from scikit-base 0.9.0. "
-        "Currently, str or iterable of str arguments select objects that possess the "
-        "tag(s) with the specified name, of any value. "
-        "From 0.9.0 onwards, str or iterable of str "
-        "will select objects that possess the tag with the specified name, "
-        "with the value True (boolean). See scikit-base issue #326 for the rationale "
-        "behind this change. "
-        "To retain previous behaviour, that is, "
-        "to select objects that possess the tag with the specified name, of any value, "
-        "use a dict with the tag name as key, and re.Pattern('*?') as value. "
-        "That is, from re import Pattern, and pass {tag_name: Pattern('*?')} "
-        "as filter_tags, and similarly with multiple tag names. "
-    )
-
     # case: tag_filter is string
     if isinstance(tag_filter, str):
-        # todo 0.9.0: reomove this warning
-        warnings.warn(warn_msg, DeprecationWarning, stacklevel=2)
-        # todo 0.9.0: replace this line
-        return tag_filter in klass_tags
-        # by this line
-        # tag_filter = {tag_filter: True}
+        tag_filter = {tag_filter: True}
 
     # case: tag_filter is iterable of str but not dict
     # If a iterable of strings is provided, check that all are in the returned tag_dict
     if isinstance(tag_filter, Iterable) and not isinstance(tag_filter, dict):
         if not all(isinstance(t, str) for t in tag_filter):
             raise ValueError(f"{type_msg} {tag_filter}")
-        # todo 0.9.0: reomove this warning
-        warnings.warn(warn_msg, DeprecationWarning, stacklevel=2)
-        # todo 0.9.0: replace this line
-        return all(tag in klass_tags for tag in tag_filter)
-        # by this line
-        # tag_filter = {tag: True for tag in tag_filter}
+        tag_filter = dict.fromkeys(tag_filter, True)
 
     # case: tag_filter is dict
     # check that all keys are str
@@ -712,8 +682,6 @@ def get_package_metadata(
     return module_info
 
 
-# todo 0.9.0: change docstring to reflect handling of filter_tags
-# in case of str or iterable of str
 def all_objects(
     object_types=None,
     filter_tags=None,
@@ -760,7 +728,9 @@ def all_objects(
         Filter used to determine if ``klass`` has tag or expected tag values.
 
         - If a str or list of strings is provided, the return will be filtered
-          to keep classes that have all the tag(s) specified by the strings.
+          to keep classes that have all the tag(s) specified by the strings,
+          with the tag value being True.
+
         - If a dict is provided, the return will be filtered to keep exactly the classes
           where tags satisfy all the filter conditions specified by ``filter_tags``.
           Filter conditions are as follows, for ``tag_name: search_value`` pairs in

{scikit_base-0.8.3 → scikit_base-0.10.0}/skbase/lookup/tests/test_lookup.py

@@ -35,6 +35,7 @@ from skbase.tests.conftest import (
     SKBASE_PUBLIC_CLASSES_BY_MODULE,
     SKBASE_PUBLIC_FUNCTIONS_BY_MODULE,
     SKBASE_PUBLIC_MODULES,
+    ClassWithABTrue,
     Parent,
 )
 from skbase.tests.mock_package.test_mock_package import (
@@ -374,18 +375,18 @@ def test_filter_by_tags():
     assert _filter_by_tags(NotABaseObject) is True
 
     # Check when tag_filter is a str and present in the class
-    assert _filter_by_tags(Parent, tag_filter="A") is True
+    assert _filter_by_tags(ClassWithABTrue, tag_filter="A") is True
     # Check when tag_filter is str and not present in the class
-    assert _filter_by_tags(BaseObject, tag_filter="A") is False
+    assert _filter_by_tags(Parent, tag_filter="A") is False
 
     # Test functionality when tag present and object doesn't have tag interface
     assert _filter_by_tags(NotABaseObject, tag_filter="A") is False
 
     # Test functionality where tag_filter is Iterable of str
     # all tags in iterable are in the class
-    assert _filter_by_tags(Parent, ("A", "B", "C")) is True
+    assert _filter_by_tags(ClassWithABTrue, ("A", "B")) is True
     # Some tags in iterable are in class and others aren't
-    assert _filter_by_tags(Parent, ("A", "B", "C", "D", "E")) is False
+    assert _filter_by_tags(ClassWithABTrue, ("A", "B", "C", "D", "E")) is False
 
     # Test functionality where tag_filter is Dict[str, Any]
     # All keys in dict are in tag_filter and values all match

{scikit_base-0.8.3 → scikit_base-0.10.0}/skbase/testing/test_all_objects.py

@@ -736,9 +736,13 @@ class TestAllObjects(BaseFixtureGenerator, QuickTester):
             assert not obj_clone.is_fitted
 
     def test_repr(self, object_instance):
-        """Check we can call repr."""
+        """Check that __repr__ call to instance does not raise exceptions."""
         repr(object_instance)
 
+    def test_repr_html(self, object_instance):
+        """Check that _repr_html_ call to instance does not raise exceptions."""
+        object_instance._repr_html_()
+
     def test_constructor(self, object_class):
         """Check that the constructor has sklearn compatible signature and behaviour.
 

{scikit_base-0.8.3 → scikit_base-0.10.0}/skbase/tests/conftest.py

@@ -314,3 +314,19 @@ class Child(Parent):
     def some_other_method(self):
         """To be implemented in the child class."""
         pass
+
+
+# Fixture class for testing tag system, child overrides tags
+class ClassWithABTrue(Parent):
+    """Child class that sets A, B tags to True."""
+
+    _tags = {"A": True, "B": True}
+    __author__ = ["fkiraly", "RNKuhns"]
+
+    def some_method(self):
+        """Child class' implementation."""
+        pass
+
+    def some_other_method(self):
+        """To be implemented in the child class."""
+        pass

{scikit_base-0.8.3 → scikit_base-0.10.0}/skbase/utils/dependencies/_dependencies.py

@@ -11,14 +11,12 @@ from packaging.specifiers import InvalidSpecifier, Specifier, SpecifierSet
 from packaging.version import InvalidVersion, Version
 
 
-# todo 0.10.0: remove suppress_import_stdout argument
 def _check_soft_dependencies(
     *packages,
     package_import_alias="deprecated",
     severity="error",
     obj=None,
     msg=None,
-    suppress_import_stdout="deprecated",
 ):
     """Check if required soft dependencies are installed and raise error or warning.
 
@@ -68,22 +66,6 @@ def _check_soft_dependencies(
     -------
     boolean - whether all packages are installed, only if no exception is raised
     """
-    # todo 0.10.0: remove this warning
-    if suppress_import_stdout != "deprecated":
-        warnings.warn(
-            "In skbase _check_soft_dependencies, the suppress_import_stdout argument "
-            "is deprecated and no longer has any effect. "
-            "The argument will be removed in version 0.10.0, so users of the "
-            "_check_soft_dependencies utility should not pass this argument anymore. "
-            "The _check_soft_dependencies utility also no longer causes imports, "
-            "hence no stdout "
-            "output is created from imports, for any setting of the "
-            "suppress_import_stdout argument. If you wish to import packages "
-            "and make use of stdout prints, import the package directly instead.",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-
     if len(packages) == 1 and isinstance(packages[0], (tuple, list)):
         packages = packages[0]
     if not all(isinstance(x, str) for x in packages):