Merged main, resolved conflict

.github/workflows/test.yml

@@ -68,8 +68,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
-        os: [ubuntu-latest, windows-latest, macOS-13]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
@@ -107,8 +107,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
-        os: [ubuntu-latest, windows-latest, macOS-13]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4

.github/workflows/wheels.yml

@@ -34,8 +34,8 @@ jobs:
     strategy:
       fail-fast: false  # to not fail all combinations if just one fail
       matrix:
-        os: [ubuntu-latest, macOS-13]
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        os: [ubuntu-latest, macOS-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4
@@ -66,7 +66,7 @@ jobs:
       fail-fast: false  # to not fail all combinations if just one fail
       matrix:
         os: [windows-latest]
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4

README.md

@@ -1,6 +1,6 @@
 <a href="https://skpro.readthedocs.io/en/latest"><img src="https://github.com/sktime/skpro/blob/main/docs/source/images/skpro-banner.png" width="500" align="right" /></a>
 
-:rocket: **Version 2.5.0 out now!** [Read the release notes here.](https://skpro.readthedocs.io/en/latest/changelog.html).
+:rocket: **Version 2.7.0 out now!** [Read the release notes here.](https://skpro.readthedocs.io/en/latest/changelog.html).
 
 `skpro` is a library for supervised probabilistic prediction in python.
 It provides `scikit-learn`-like, `scikit-base` compatible interfaces to:

docs/source/_static/switcher.json

@@ -5,7 +5,22 @@
     "url": "https://skpro.readthedocs.io/en/latest/"
   },
   {
-    "name": "2.5.0 (stable)",
+    "name": "2.7.0 (stable)",
+    "version": "stable",
+    "url": "https://skpro.readthedocs.io/en/v2.7.0/"
+  },
+  {
+    "name": "2.6.0",
+    "version": "stable",
+    "url": "https://skpro.readthedocs.io/en/v2.6.0/"
+  },
+  {
+    "name": "2.5.1",
+    "version": "stable",
+    "url": "https://skpro.readthedocs.io/en/v2.5.1/"
+  },
+  {
+    "name": "2.5.0",
     "version": "stable",
     "url": "https://skpro.readthedocs.io/en/v2.5.0/"
   },

docs/source/api_reference/regression.rst

@@ -44,6 +44,19 @@ Model selection and tuning
 
     evaluate
 
+Online learning
+---------------
+
+.. currentmodule:: skpro.regression.online
+
+.. autosummary::
+    :toctree: auto_generated/
+    :template: class.rst
+
+    OnlineRefit
+    OnlineRefitEveryN
+    OnlineDontRefit
+
 Reduction - adding ``predict_proba``
 ------------------------------------
 

docs/source/changelog.rst

@@ -16,6 +16,120 @@ For planned changes and upcoming releases, see roadmap in the
 `issue tracker <https://github.com/sktime/skpro/issues>`_.
 
 
+[2.7.0] - 2024-10-08
+====================
+
+Maintenance release with ``python 3.13`` support.
+
+Also contains:
+
+* new ``update`` unified interface point for probabilistic regressors,
+  to enable online learning and Bayesian updates in models
+* dependency updates
+
+Dependency changes
+~~~~~~~~~~~~~~~~~~
+
+* ``skpro`` is now compatible with ``python 3.13``.
+* ``scikit-base`` bounds have been updated to ``>=0.6.1,<0.12.0``.
+* ``polars`` (data container soft dependency) bounds have been updated to ``<1.10.0``.
+* dead (unimported) soft dependencies have been removed: ``attrs``, ``tabulate``, ``uncertainties``.
+
+Core interface changes
+~~~~~~~~~~~~~~~~~~~~~~
+
+Probabilistic regressors and time-to-event predictors now have an ``update`` method.
+The ``update`` method is the unified interface point for incremental fitting strategies,
+such as online learning, efficient re-fit strategies, or Bayesian updates.
+
+Whether a non-trivial ``update`` method is implemented depends on the specific estimator,
+this can be inspected via the ``capability:update`` tag of the estimator.
+
+Estimators without a dedicated ``update`` method, that is, those with
+``capability:update=False``, implement the trivial ``update`` where no update
+is performed, with the internal estimator state remaining unchanged.
+
+Enhancements
+~~~~~~~~~~~~
+
+* [ENH] online update capability for probabilistic regressors (:pr:`462`) :user:`fkiraly`
+* [ENH] online refitting strategy after N data points (:pr:`469`) :user:`fkiraly`
+* [ENH] ``datatypes`` examples - docstrings, deepcopy (:pr:`466`) :user:`fkiraly`
+* [ENH] sync proba predict utils with ``sktime`` (:pr:`465`) :user:`fkiraly`
+* [ENH] minor refactor - remove unnecessary `__init__` methods in `datatypes` module (:pr:`475`) :user:`fkiraly`
+
+Maintenance
+~~~~~~~~~~~
+
+* [MNT] ``python 3.13`` support, add ``3.13`` to CI test matrix (:pr:`471`) :user:`fkiraly`
+* [MNT] differential testing - handle non-package changes in ``pyproject.toml`` (:pr:`472`) :user:`fkiraly`
+* [MNT] change macos runners to ``macos-latest`` version (:pr:`477`) :user:`fkiraly`
+* [MNT] [Dependabot](deps): Update ``scikit-base`` requirement from ``<0.10.0,>=0.6.1`` to ``>=0.6.1,<0.12.0`` (:pr:`468`) :user:`dependabot[bot]`
+* [MNT] [Dependabot](deps): Update ``polars`` requirement from ``<1.7.0`` to ``<1.10.0`` (:pr:`473`) :user:`dependabot[bot]`
+
+
+[2.6.0] - 2024-09-08
+====================
+
+Maintenance release with scheduled deprecations and updates.
+
+Dependency changes
+~~~~~~~~~~~~~~~~~~
+
+* ``numpy`` bounds have been updated to ``>=1.21.0,<2.2``.
+* ``scikit-base`` bounds have been updated to ``>=0.6.1,<0.10.0``.
+
+Enhancements
+~~~~~~~~~~~~
+
+* [ENH] refactor ``datatypes`` mtypes - checkers, converters (:pr:`392`) :user:`fkiraly`
+* [ENH] refactor ``datatypes`` mtypes - example fixtures (:pr:`458`) :user:`fkiraly`
+
+Maintenance
+~~~~~~~~~~~
+
+* [MNT] [Dependabot](deps): Update ``scikit-base`` requirement from ``<0.9.0,>=0.6.1`` to ``>=0.6.1,<0.10.0`` (:pr:`454`) :user:`dependabot[bot]`
+* [MNT] [Dependabot](deps): Update ``numpy`` requirement from ``<2.1,>=1.21.0`` to ``>=1.21.0,<2.2`` (:pr:`453`) :user:`dependabot[bot]`
+
+
+[2.5.1] - 2024-09-07
+====================
+
+Minor feature and bugfix release.
+
+Dependency changes
+~~~~~~~~~~~~~~~~~~
+
+* ``polars`` (data container and parallelization back-end) bounds have been updated to ``<1.7.0``
+
+Enhancements
+~~~~~~~~~~~~
+
+* [ENH] Polars adapter enhancements (:pr:`449`) :user:`julian-fong`
+
+Maintenance
+~~~~~~~~~~~
+
+* [MNT] [Dependabot](deps): Update polars requirement from ``<1.5.0`` to ``<1.7.0`` (:pr:`456`) :user:`dependabot[bot]`
+
+Fixes
+~~~~~
+
+* [BUG] changelog utility: fix termination condition to retrieve merged PR (:pr:`448`) :user:`fkiraly`
+* [BUG] Update ``skpro.utils.git_diff`` to fix issue with encoding  (:pr:`452`) :user:`julian-fong`
+* [BUG] fix variance bug in ``DummyProbaRegressor`` (:pr:`455`) :user:`fkiraly`
+
+Documentation
+~~~~~~~~~~~~~
+
+* [DOC] minor updates to ``README.md`` (:pr:`451`) :user:`fkiraly`
+
+Contributors
+~~~~~~~~~~~~
+
+:user:`fkiraly`,
+:user:`julian-fong`
+
 [2.5.0] - 2024-08-02
 ====================
 

pyproject.toml

@@ -1,15 +1,15 @@
 [project]
 name = "skpro"
-version = "2.5.0"
-description = "A unified framework for probability distributions and probabilistic supervised regression"
+version = "2.7.0"
+description = "A unified framework for tabular probabilistic regression, time-to-event prediction, and probability distributions in python"
 authors = [
-    {name = "skpro developers", email = "sktime.[email protected]"},
+    {name = "skpro developers", email = "info@sktime.net"},
     {name = "Franz Király"},
     {name = "Frithjof Gressmann"},
     {name = "Vitaly Davydov"},
 ]
 maintainers = [
-    {name = "skpro developers", email = "sktime.[email protected]"},
+    {name = "skpro developers", email = "info@sktime.net"},
 ]
 readme = "README.md"
 keywords = [
@@ -35,29 +35,29 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
-requires-python = ">=3.9,<3.13"
+requires-python = ">=3.9,<3.14"
 dependencies = [
-    "numpy>=1.21.0,<2.1",
+    "numpy>=1.21.0,<2.2",
     "pandas>=1.1.0,<2.3.0",
     "packaging",
-    "scikit-base>=0.6.1,<0.9.0",
+    "scikit-base>=0.6.1,<0.12.0",
     "scikit-learn>=0.24.0,<1.6.0",
     "scipy<2.0.0,>=1.2.0",
 ]
 
 [project.optional-dependencies]
 all_extras = [
-    "attrs",
     "cyclic-boosting>=1.4.0; python_version < '3.12'",
-    "distfit",
-    "lifelines<0.30.0",
-    "mapie",
+    "distfit; python_version < '3.13'",
+    "lifelines<0.30.0; python_version < '3.13'",
+    "mapie; python_version < '3.13'",
     "matplotlib>=3.3.2",
-    "ngboost<0.6.0",
-    "polars<1.5.0",
+    "ngboost<0.6.0; python_version < '3.13'",
+    "polars<1.10.0",
     "pyarrow<14.0.0; python_version < '3.12'",
-    "scikit-survival<0.24.0",
+    "scikit-survival<0.24.0; python_version < '3.13'",
     "statsmodels>=0.12.1",
     "tabulate",
     "uncertainties",
@@ -89,7 +89,7 @@ docs = [
     "sphinx!=7.2.0,<9.0.0",
     "sphinx-design<0.7.0",
     "sphinx-issues<5.0.0",
-    "sphinx-gallery<0.18.0",
+    "sphinx-gallery<0.19.0",
     "sphinx-panels",
     "tabulate",
 ]

skpro/__init__.py

@@ -1,6 +1,6 @@
 """skpro."""
 
-__version__ = "2.5.0"
+__version__ = "2.7.0"
 
 __all__ = ["show_versions"]
 

skpro/base/_base.py

@@ -36,7 +36,7 @@ def __init__(self):
         py39_or_higher = SpecifierSet(">=3.9")
         sys_version = sys.version.split(" ")[0]
 
-        # todo 2.6.0 - check whether python 3.8 eol is reached.
+        # todo 2.8.0 - check whether python 3.8 eol is reached.
         # If yes, remove this msg.
         if sys_version not in py39_or_higher:
             warn(

skpro/datatypes/_base/__init__.py

@@ -0,0 +1,5 @@
+"""Base module for datatypes."""
+
+from skpro.datatypes._base._base import BaseConverter, BaseDatatype, BaseExample
+
+__all__ = ["BaseConverter", "BaseDatatype", "BaseExample"]