Merge branch 'main' into pre-commit-ci-update-config

.github/workflows/test.yml

@@ -114,7 +114,7 @@ jobs:
       - name: Generate Pytest coverage report
         shell: bash -l {0}
         run: |
-          pytest --cov=./ --cov-report=xml
+          python -m pytest
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3

docs/source/api_reference.rst

@@ -19,7 +19,7 @@ additional details.
 Base Classes
 ============
 
-.. currentmodule:: skbase
+.. currentmodule:: skbase.base
 
 .. autosummary::
     :toctree: api_reference/auto_generated/
@@ -33,7 +33,7 @@ Base Classes
 Object Retrieval
 ================
 
-.. currentmodule:: skbase
+.. currentmodule:: skbase.lookup
 
 .. autosummary::
     :toctree: api_reference/auto_generated/
@@ -42,6 +42,18 @@ Object Retrieval
     all_objects
     get_package_metadata
 
+.. _obj_validation:
+
+Object Validation and Comparison
+================================
+
+.. currentmodule:: skbase.validate
+
+.. autosummary::
+    :toctree: api_reference/auto_generated/
+    :template: function.rst
+
+
 .. _obj_testing:
 
 Testing

docs/source/user_documentation/user_guide.rst

@@ -27,6 +27,7 @@ that ``skbase`` provides, see the :ref:`api_ref`.
    user_guide/overview
    user_guide/base_classes
    user_guide/lookup
+   user_guide/validate
    user_guide/testing
 
 
@@ -77,6 +78,20 @@ that ``skbase`` provides, see the :ref:`api_ref`.
 
     ---
 
+    Validation and Comparison
+    ^^^^^^^^^^^^^^^^^^^^^^^^^
+
+    Tools for validating and comparing ``BaseObject``-s.
+
+    +++
+
+    .. link-button:: user_guide/validate
+            :type: ref
+            :text: Validation and Comparison
+            :classes: btn-block btn-secondary stretched-link
+
+    ---
+
     Testing
     ^^^^^^^
 

pyproject.toml

@@ -3,7 +3,7 @@ name = "skbase"
 version = "0.2.0"
 description = "Base classes for sklearn-like parametric objects"
 authors = [
-    {name = "Franz Kiraly", email = "f.kiraly@ucl.ac.uk"},
+    {name = "Franz Király", email = "f.kiraly@ucl.ac.uk"},
     {name = "Markus Löning"},
     {name = "Ryan Kuhns", email = "rk.skbase@gmail.com"},
 ]
@@ -85,6 +85,8 @@ test = [
     "coverage",
     "pytest-cov",
     "safety",
+    "numpy",
+    "scipy",
 ]
 
 [project.urls]
@@ -97,19 +99,22 @@ download = "https://pypi.org/project/skbase/#files"
 file = "LICENSE"
 
 [build-system]
-requires = ["setuptools", "wheel", "toml", "build"]
+requires = ["setuptools>61", "wheel", "toml", "build"]
 build-backend = "setuptools.build_meta"
 
 [tool.pytest.ini_options]
 # ignore certain folders
 addopts = [
     "--doctest-modules",
     "--ignore=docs",
+    "--cov=.",
+    "--cov-report=xml",
+    "--cov-report=html",
 ]
 
 [tool.isort]
 profile = "black"
-src_paths = ["isort", "test"]
+src_paths = ["skbase/*"]
 multi_line_output = 3
 known_first_party = ["skbase"]
 
@@ -134,3 +139,20 @@ ignore_path = ["docs/_build", "docs/source/api_reference/auto_generated"]
 
 [tool.bandit]
 exclude_dirs = ["*/tests/*", "*/testing/*"]
+
+[tool.setuptools]
+zip-safe = true
+
+[tool.setuptools.package-data]
+sktime = [
+    "*.csv",
+    "*.csv.gz",
+    "*.arff",
+    "*.arff.gz",
+    "*.txt",
+    "*.ts",
+    "*.tsv",
+]
+
+[tool.setuptools.packages.find]
+exclude = ["tests", "tests.*"]

skbase/__init__.py

@@ -6,18 +6,37 @@
 The included functionality makes it easy to re-use scikit-learn and
 sktime design principles in your project.
 """
+import warnings
+from typing import List
 
-__version__ = "0.2.0"
+from skbase.base import BaseEstimator, BaseMetaEstimator, BaseObject
+from skbase.base._meta import _HeterogenousMetaEstimator
+from skbase.lookup import all_objects, get_package_metadata
 
-__author__ = ["mloning", "RNKuhns", "fkiraly"]
-__all__ = [
+__version__: str = "0.2.0"
+
+__author__: List[str] = ["mloning", "RNKuhns", "fkiraly"]
+__all__: List[str] = [
     "BaseObject",
     "BaseEstimator",
+    "BaseMetaEstimator",
     "_HeterogenousMetaEstimator",
     "all_objects",
     "get_package_metadata",
 ]
 
-from skbase._base import BaseEstimator, BaseObject
-from skbase._lookup import all_objects, get_package_metadata
-from skbase._meta import _HeterogenousMetaEstimator
+warnings.warn(
+    " ".join(
+        [
+            "Importing from the `skbase` module is deprecated as of version 0.3.0.",
+            "Ability to import from `skbase` will be removed in version 0.5.0.",
+            "Import BaseObject, BaseEstimator, and HeterogenousMetaEstimator",
+            "from skbase.base. Import lookup functionality ",
+            "(all_objects, get_package_metadata) from skbase.lookup.",
+            "_HeterogenousMetaEstimator has been depracated as of version 0.3.0.",
+            "Functionality is available as part of BaseMetaEstimator.",
+            "_HeterogenousMetaEstimator will be removed in version 0.5.0.",
+        ]
+    ),
+    DeprecationWarning,
+)

skbase/_exceptions.py

@@ -6,8 +6,16 @@
 """Custom exceptions used in ``skbase``."""
 from typing import List
 
-__author__: List[str] = ["mloning", "rnkuhns"]
-__all__: List[str] = ["NotFittedError"]
+__author__: List[str] = ["fkiraly", "mloning", "rnkuhns"]
+__all__: List[str] = ["FixtureGenerationError", "NotFittedError"]
+
+
+class FixtureGenerationError(Exception):
+    """Raised when a fixture fails to generate."""
+
+    def __init__(self, fixture_name="", err=None):
+        self.fixture_name = fixture_name
+        super().__init__(f"fixture {fixture_name} failed to generate. {err}")
 
 
 class NotFittedError(ValueError, AttributeError):

skbase/base/__init__.py

@@ -0,0 +1,19 @@
+#!/usr/bin/env python3 -u
+# -*- coding: utf-8 -*-
+# copyright: skbase developers, BSD-3-Clause License (see LICENSE file)
+""":mod:`skbase.base` contains base classes for creating parametric objects.
+
+The included functionality makes it easy to re-use scikit-learn and
+sktime design principles in your project.
+"""
+from typing import List
+
+from skbase.base._base import BaseEstimator, BaseObject
+from skbase.base._meta import BaseMetaEstimator
+
+__author__: List[str] = ["mloning", "RNKuhns", "fkiraly"]
+__all__: List[str] = [
+    "BaseObject",
+    "BaseEstimator",
+    "BaseMetaEstimator",
+]

skbase/_base.py → skbase/base/_base.py

@@ -52,20 +52,20 @@ class name: BaseEstimator
     fitted state flag       - is_fitted (property)
     fitted state check      - check_is_fitted (raises error if not is_fitted)
 """
-
-__author__ = ["mloning", "RNKuhns", "fkiraly"]
-__all__ = ["BaseEstimator", "BaseObject"]
-
 import inspect
 import warnings
 from collections import defaultdict
 from copy import deepcopy
+from typing import List
 
 from sklearn import clone
 from sklearn.base import BaseEstimator as _BaseEstimator
 
 from skbase._exceptions import NotFittedError
 
+__author__: List[str] = ["mloning", "RNKuhns", "fkiraly"]
+__all__: List[str] = ["BaseEstimator", "BaseObject"]
+
 
 class BaseObject(_BaseEstimator):
     """Base class for parametric objects with sktime style tag interface.
@@ -427,7 +427,7 @@ def get_test_params(cls, parameter_set="default"):
         """
         # if non-default parameters are required, but none have been found, raise error
         if hasattr(cls, "_required_parameters"):
-            required_parameters = getattr(cls, "required_parameters", [])
+            required_parameters = getattr(cls, "_required_parameters", [])
             if len(required_parameters) > 0:
                 raise ValueError(
                     f"Estimator: {cls} requires "
@@ -466,13 +466,8 @@ def create_test_instance(cls, parameter_set="default"):
         else:
             params = cls.get_test_params()
 
-        if isinstance(params, list):
-            if isinstance(params[0], dict):
-                params = params[0]
-            else:
-                raise TypeError(
-                    "get_test_params should either return a dict or list of dict."
-                )
+        if isinstance(params, list) and isinstance(params[0], dict):
+            params = params[0]
         elif isinstance(params, dict):
             pass
         else:
@@ -853,6 +848,6 @@ def check_is_fitted(self):
         """
         if not self.is_fitted:
             raise NotFittedError(
-                f"This instance of {self.__class__.__name__} has not "
-                f"been fitted yet; please call `fit` first."
+                f"This instance of {self.__class__.__name__} has not been fitted yet. "
+                f"Please call `fit` first."
             )