diff --git a/README.md b/README.md index bb6c38de3..2a7d26524 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -:rocket: **Version 2.4.1 out now!** [Read the release notes here.](https://skpro.readthedocs.io/en/latest/changelog.html). +:rocket: **Version 2.4.2 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: diff --git a/docs/source/_static/switcher.json b/docs/source/_static/switcher.json index 1f3e59858..26f61a636 100644 --- a/docs/source/_static/switcher.json +++ b/docs/source/_static/switcher.json @@ -5,7 +5,12 @@ "url": "https://skpro.readthedocs.io/en/latest/" }, { - "name": "2.4.1 (stable)", + "name": "2.4.2 (stable)", + "version": "stable", + "url": "https://skpro.readthedocs.io/en/v2.4.2/" + }, + { + "name": "2.4.1", "version": "stable", "url": "https://skpro.readthedocs.io/en/v2.4.1/" }, diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index ab7a119be..9a8b2dca6 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -2,7 +2,7 @@ Changelog ========= -All notable changes to this project beginning with version 0.1.0 will be +All notable changes to this project beginning with version 1.0.0 are documented in this file. The format is based on `Keep a Changelog `_ and we adhere to `Semantic Versioning `_. The source @@ -16,6 +16,71 @@ For planned changes and upcoming releases, see roadmap in the `issue tracker `_. +[2.4.2] - 2024-08-02 +==================== + +Highlights +~~~~~~~~~~ + +* Multiclass classification reduction using Histograms (:pr:`410`) :user:`ShreeshaM07` +* ``DummyProbaRegressor`` - probabilistic dummy regressor (:pr:`437`) :user:`julian-fong` +* new probability distributions interfaced: Inverse Gamma, Truncated Normal (:pr:`415`, :pr:`421`) :user:`meraldoantonio`, :user:`ShreeshaM07` +* various ``numpy 2`` compatibility fixes (:pr:`414`, :pr:`436`) :user:`ShreeshaM07`, :user:`fkiraly` + +Enhancements +~~~~~~~~~~~~ + +Data types, checks, conversions +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +* [ENH] Syncing datatypes module ``_check.py`` and ``_convert.py`` with ``sktime`` (:pr:`432`) :user:`julian-fong` + +Probability distributions +^^^^^^^^^^^^^^^^^^^^^^^^^ + +* [ENH] Inverse Gamma distribution (:pr:`415`) :user:`meraldoantonio` +* [ENH] Truncated Normal distribution (:pr:`421`) :user:`ShreeshaM07` + +Probabilistic regression +^^^^^^^^^^^^^^^^^^^^^^^^ + +* [ENH] Multiclass classification reduction using Histograms (:pr:`410`) :user:`ShreeshaM07` +* [ENH] ``DummyProbaRegressor`` - probabilistic dummy regressor (:pr:`437`) :user:`julian-fong` + +Test framework +^^^^^^^^^^^^^^ + +* [ENH] differential testing for CI tests (:pr:`435`) :user:`fkiraly` + +Fixes +~~~~~ + +Probability distributions +^^^^^^^^^^^^^^^^^^^^^^^^^ + +* [BUG] Histogram Distribution: address ``np.broadcast_arrays`` deprecation of writable return in ``numpy 2.0.0`` (:pr:`414`) :user:`ShreeshaM07` + +Maintenance +~~~~~~~~~~~ + +* [MNT] [Dependabot](deps): Update scikit-survival requirement from ``<0.23.0`` to ``<0.24.0`` (:pr:`419`) :user:`dependabot[bot]` +* [MNT] [Dependabot](deps): Update polars requirement from ``<0.21.0`` to ``<1.1.0`` (:pr:`418`) :user:`dependabot[bot]` +* [MNT] [Dependabot](deps): Update polars requirement from ``<1.1.0`` to ``<1.2.0`` (:pr:`420`) :user:`dependabot[bot]` +* [MNT] [Dependabot](deps): Update polars requirement from ``<1.2.0`` to ``<1.3.0`` (:pr:`425`) :user:`dependabot[bot]` +* [MNT] [Dependabot](deps): Update sphinx-gallery requirement from ``<0.17.0`` to ``<0.18.0`` (:pr:`431`) :user:`dependabot[bot]` +* [MNT] [Dependabot](deps): Update sphinx requirement from ``!=7.2.0,<8.0.0`` to ``!=7.2.0,<9.0.0`` (:pr:`438`) :user:`dependabot[bot]` +* [MNT] sync differential testing utilities with ``sktime`` (:pr:`434`) :user:`fkiraly` +* [MNT] fix ``numpy 2`` incompatibility of ``Pareto`` distribution (:pr:`436`) :user:`fkiraly` + +Contributors +~~~~~~~~~~~~ + +:user:`fkiraly`, +:user:`julian-fong`, +:user:`meraldoantonio`, +:user:`ShreeshaM07` + + [2.4.1] - 2024-06-26 ==================== @@ -34,7 +99,7 @@ Dependency changes * ``numpy`` bounds have been updated to ``>=1.21.0,<2.1.0``. Contents --------- +~~~~~~~~ * [MNT] increase ``numpy`` bound to ``numpy < 2.1``, ``numpy 2`` compatibility (:pr:`393`) :user:`fkiraly` @@ -45,7 +110,7 @@ Contents ==================== Highlights ----------- +~~~~~~~~~~ * ``GLM`` now supports multiple ``distributions`` and ``link`` function (:pr:`384`) :user:`ShreeshaM07` @@ -62,7 +127,7 @@ Enhancements ~~~~~~~~~~~~ Probability distributions -~~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^^ * [ENH] mean-scale family of distributions, composite (:pr:`282`) :user:`fkiraly` * [ENH] Half Normal Distribution (:pr:`363`) :user:`SaiRevanth25` @@ -73,13 +138,13 @@ Probability distributions * [ENH] Pareto distribution (:pr:`396`) :user:`sukjingitsit` Probabilistic regression -~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^ * [ENH] ``GLM`` with multiple ``distributions`` and ``link`` function support (:pr:`384`) :user:`ShreeshaM07` * [ENH] interval width and area under calibration curve metrics (:pr:`391`) :user:`fkiraly` Test framework -~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^ * [ENH] Tests for polars support for estimators (:pr:`370`) :user:`julian-fong` @@ -87,13 +152,13 @@ Fixes ~~~~~ Probability distributions -~~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^^ * [BUG] fix ``test_methods_p`` logic when ``shuffle`` is ``True`` (:pr:`381`) :user:`ShreeshaM07` * [BUG] ensure ``index`` and ``columns`` are taken into account in broadcasting if ``bc_params`` are set (:pr:`403`) :user:`fkiraly` Probabilistic regression -~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^ * [BUG] bugfix when ``None`` was specified for ``max_iter`` parameter in sklearn regressors (:pr:`386`) :user:`julian-fong` @@ -201,7 +266,7 @@ Contributors ==================== Highlights ----------- +~~~~~~~~~~ * new tutorial notebooks for survival prediction and probability distributions (:pr:`303`, :pr:`305`) :user:`fkiraly` * interface to ``ngboost`` probabilistic regressor and survival predictor (:pr:`215`, :pr:`301`, :pr:`309`, :pr:`332`) :user:`ShreeshaM07` @@ -290,7 +355,7 @@ Enhancements ~~~~~~~~~~~~ Probability distributions -~~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^^ * [ENH] probability distributions - boilerplate refactor (:pr:`265`) :user:`fkiraly` * [ENH] probability distributions: convenience feature to coerce ``index`` and ``columns`` to ``pd.Index`` (:pr:`276`) :user:`fkiraly` @@ -319,7 +384,7 @@ Probability distributions * [ENH] improved defaults for ``BaseDistribution`` ``_mean``, ``_var``, and ``_energy_x`` (:pr:`330`) :user:`fkiraly` Probabilistic regression -~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^ * [ENH] interface to ``ngboost`` (:pr:`215`) :user:`ShreeshaM07` * [ENH] interfacing Poisson regressor from sklearn (:pr:`213`) :user:`nilesh05apr` @@ -334,7 +399,7 @@ Survival and time-to-event prediction * [ENH] in ``ConditionUncensored`` reducer, ensure coercion to float of ``C`` (:pr:`318`) :user:`fkiraly` Test framework -~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^ * [MNT] faster collection of differential tests through caching, test if pyproject change (:pr:`296`) :user:`fkiraly` @@ -342,7 +407,7 @@ Fixes ~~~~~ Probability distributions -~~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^^ * [BUG] bugfixes for distribution base class default methods (:pr:`281`) :user:`fkiraly` * [BUG] fix ``Empirical`` index to be ``pd.MultiIndex`` for hierarchical data index (:pr:`286`) :user:`fkiraly` @@ -401,7 +466,7 @@ Contributors ==================== Highlights ----------- +~~~~~~~~~~ * ``lifelines`` predictive survival regressors are available as ``skpro`` estimators: accelerated failure time (Fisk, Log-normal, Weibull), CoxPH variants, @@ -418,7 +483,7 @@ Core interface changes ~~~~~~~~~~~~~~~~~~~~~~ Probability distributions -~~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^^ * Probability distributions (``BaseDistribution``) now have a ``len`` method, which returns the number of number of rows of the distribution, this is the same @@ -427,10 +492,10 @@ Probability distributions Such distributions implement ``pmf`` and ``log_pmf`` methods. Enhancements ------------- +~~~~~~~~~~~~ Probability distributions -~~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^^ * [ENH] Log-normal probability distribution (:pr:`218`) :user:`bhavikar` * [ENH] Poisson distribution (:pr:`226`) :user:`fkiraly` @@ -445,7 +510,7 @@ Probability distributions * [ENH] Fisk distribution aka log-logistic distribution (:pr:`259`) :user:`fkiraly` Probabilistic regression -~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^ * [ENH] ``GLMRegressor`` using statsmodels ``GLM`` with Gaussian link (:pr:`222`) :user:`julian-fong` * [ENH] added test parameters for probabilistic metrics (:pr:`234`) :user:`fkiraly` @@ -459,34 +524,34 @@ Survival and time-to-event prediction * [ENH] log-logistic/Fisk AFT model from ``lifelines`` (:pr:`260`) :user:`fkiraly` Test framework -~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^ * [ENH] refactor test scenario creation to be lazy rather than on module load (:pr:`245`) :user:`fkiraly` Fixes ------ +~~~~~ Probability distributions -~~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^^ * [BUG] bugfixes to QPD distributions - ``QPD_U``, ``QPD_S`` (:pr:`194`) :user:`fkiraly` * [BUG] fixes to lognormal distribution (:pr:`261`) :user:`fkiraly` Documentation -------------- +~~~~~~~~~~~~~ * [DOC] documentation improvement for probabilistic metrics (:pr:`234`) :user:`fkiraly` * [DOC] add :user:`julian-fong` to ``all-contributorsrc`` (:pr:`238`) :user:`fkiraly` * [DOC] docstring with mathematical description for ``QPD_Empirical`` (:pr:`253`) :user:`fkiraly` Maintenance ------------ +~~~~~~~~~~~ * [MNT] fix version pointer in readthedocs ``json`` (:pr:`225`) :user:`fkiraly` * [MNT] fix broken api source links in latest docs version (:pr:`243`) :user:`duydl` Contributors ------------- +~~~~~~~~~~~~ :user:`bhavikar`, :user:`duydl`, @@ -501,7 +566,7 @@ Contributors Minor bugfix and maintenance release. Contents --------- +~~~~~~~~ * [ENH] migrate tests of distribution prediction metrics to ``skbase`` class (:pr:`208`) :user:`fkiraly` @@ -514,7 +579,7 @@ Contents ==================== Highlights ----------- +~~~~~~~~~~ * interface to ``cyclic_boosting`` package (:pr:`144`) :user:`setoguchi-naoki`, :user:`FelixWick` * framework support for probabilistic survival/time-to-event prediction with right censored data (:pr:`157`) :user:`fkiraly` @@ -543,7 +608,7 @@ BaseObject and base framework abstract parallelization backend in ``sktime``. Probabilistic regression -~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^ * all probabilistic regressors now accept an argument ``C`` in ``fit``, to pass censoring information. This is for API compatibility with survival @@ -577,7 +642,7 @@ Survival and time-to-event prediction information. Enhancements ------------- +~~~~~~~~~~~~ BaseObject and base framework ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -586,13 +651,13 @@ BaseObject and base framework (:pr:`187`) :user:`fkiraly` Probability distributions -~~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^^ * [ENH] Johnson Quantile-Parameterized Distributions (QPD) with bounded and unbounded mode (:pr:`144`) :user:`setoguchi-naoki`, :user:`FelixWick` Probabilistic regression -~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^ * [ENH] Cyclic boosting interface (:pr:`144`) :user:`setoguchi-naoki`, :user:`FelixWick` * [ENH] abstract parallelization backend, refactor of ``evaluate`` and tuners, @@ -609,10 +674,10 @@ Survival and time-to-event prediction (:pr:`198`) :user:`fkiraly` Fixes ------ +~~~~~ Probabilistic regression -~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^ * [BUG] fix API non-compliance in ``sklearn`` variance prediction adapter (:pr:`192`) :user:`fkiraly` * [BUG] fix defaulting logic for ``_predict_interval`` and ``_predict_quantiles`` when only ``_predict_var`` is implemented (:pr:`191`) :user:`fkiraly` @@ -620,18 +685,18 @@ Probabilistic regression * [BUG] fix fallback for ``pdfnorm`` method, add metrics to tests (:pr:`204`) :user:`fkiraly` Test framework -~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^ * [BUG] fix lookup for specialized test classes (:pr:`189`) :user:`fkiraly` Documentation -------------- +~~~~~~~~~~~~~ * [DOC] API reference for performance metrics (:pr:`206`) :user:`fkiraly` * [DOC] README update for 2.2.0 (:pr:`207`) :user:`fkiraly` Maintenance ------------ +~~~~~~~~~~~ * [MNT] [Dependabot](deps): Bump styfle/cancel-workflow-action from ``0.12.0`` to ``0.12.1`` (:pr:`183`) :user:`dependabot` * [MNT] skip ``CyclicBoosting`` and QPD tests until #189 failures are resolved (:pr:`193`) :user:`fkiraly` @@ -640,7 +705,7 @@ Maintenance * [MNT] [Dependabot](deps): Bump pre-commit/action from ``3.0.0`` to ``3.0.1`` (:pr:`202`) :user:`dependabot` Contributors ------------- +~~~~~~~~~~~~ :user:`FelixWick`, :user:`fkiraly`, @@ -677,13 +742,13 @@ Probabilistic regression interface. Enhancements ------------- +~~~~~~~~~~~~ * [ENH] in ``BaseRegressorProba.fit``, use ``"feature_names"`` metadata field to store feature names and write to ``self`` in ``fit`` (:pr:`180`) :user:`dependabot` Maintenance ------------ +~~~~~~~~~~~ * [MNT] [Dependabot](deps): Bump ``actions/dependency-review-action`` from 3 to 4 (:pr:`178`) :user:`dependabot` @@ -699,7 +764,7 @@ Maintenance ==================== Highlights ----------- +~~~~~~~~~~ * ``sklearn`` based probabilistic regressors - Gaussian processes, Bayesian linear regression (:pr:`166`) :user:`fkiraly` * ``SklearnProbaReg`` - general interface adapter to ``sklearn`` regressors with variance prediction model (:pr:`163`) :user:`fkiraly` @@ -711,21 +776,21 @@ Dependency changes * ``polars`` (data container soft dependency) bounds have been updated to allow python 3.12. Enhancements ------------- +~~~~~~~~~~~~ Data types, checks, conversions -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * [ENH] ``n_features`` and ``feature_names`` metadata field for table mtypes (:pr:`150`) :user:`fkiraly` * [ENH] ``check_is_mtype`` dict type return, improved input check error messages in ``BaseRegressorProba`` (:pr:`151`) :user:`fkiraly` Probability distributions -~~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^^ * [ENH] adapter from ``scipy`` ``rv_discrete`` to ``skpro`` ``Empirical`` (:pr:`155`) :user:`fkiraly` Probabilistic regression -~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^ * [ENH] ``sklearn`` wrappers to str-coerce columns of ``pd.DataFrame`` before passing (:pr:`148`) :user:`fkiraly` * [ENH] clean up copy-paste leftovers in ``BaseProbaRegressor`` (:pr:`156`) :user:`fkiraly` @@ -734,26 +799,26 @@ Probabilistic regression * [ENH] interfacing all concrete ``sklearn`` probabilistic regressors (:pr:`166`) :user:`fkiraly` Test framework -~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^ * [ENH] scenario tests for mixed ``pandas`` column index types (:pr:`145`) :user:`fkiraly` * [ENH] scitype inference utility, test class register, test class test condition (:pr:`159`) :user:`fkiraly` Fixes ------ +~~~~~ Probabilistic regression -~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^ * [BUG] in probabilistic regressors, ensure correct index treatment if ``X: pd.DataFrame`` and ``y: np.ndarray`` are passed (:pr:`146`) :user:`fkiraly` Documentation -------------- +~~~~~~~~~~~~~ * [DOC] update ``AUTHORS.rst`` file (:pr:`147`) :user:`fkiraly` Maintenance ------------ +~~~~~~~~~~~ * [MNT] [Dependabot](deps): Bump ``actions/upload-artifact`` from 3 to 4 (:pr:`154`) :user:`dependabot` * [MNT] [Dependabot](deps): Bump ``actions/download-artifact`` from 3 to 4 (:pr:`153`) :user:`dependabot` @@ -769,7 +834,7 @@ Maintenance ==================== Highlights ----------- +~~~~~~~~~~ * probabilistic regressor: multiple quantile regression (:pr:`108`) :user:`Ram0nB` * probabilistic regressor: interface to ``MapieRegressor`` from ``mapie`` package @@ -777,15 +842,15 @@ Highlights * framework support for ``polars`` via mtypes (:pr:`130`) :user:`fkiraly` Enhancements ------------- +~~~~~~~~~~~~ Data types, checks, conversions -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * [ENH] ``polars`` mtypes for data tables (:pr:`130`) :user:`fkiraly` Probabilistic regression -~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^ * [ENH] probabilistic regressors - input checks and support for more input types (:pr:`129`) :user:`fkiraly` @@ -793,7 +858,7 @@ Probabilistic regression * [ENH] interface ``MapieRegressor`` from ``mapie`` (:pr:`136`) :user:`fkiraly` Test framework -~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^ * [ENH] integrate ``check_estimator`` with ``TestAllEstimators`` and ``TestAllRegressors`` for python command line estimator testing @@ -801,7 +866,7 @@ Test framework * [ENH] improved conditional testing (:pr:`140`) :user:`fkiraly` Documentation -------------- +~~~~~~~~~~~~~ * [DOC] fix math in ``plotting`` docstrings (:pr:`121`) :user:`fkiraly` * [DOC] improved probabilistic tabular regressor extension template @@ -809,21 +874,21 @@ Documentation * [DOC] typo fixes in regression extension template (:pr:`139`) :user:`fkiraly` Maintenance ------------ +~~~~~~~~~~~ * [MNT] point readthedocs ``json`` switcher variable to GitHub (:pr:`125`) :user:`fkiraly` * [MNT] change test OS versions to latest (:pr:`126`) :user:`fkiraly` Fixes ------ +~~~~~ * [BUG] fix test fixture generation logic (:pr:`142`) :user:`fkiraly` * [BUG] fix retrieval in ``all_objects`` if ``filter_tags`` is provided (:pr:`141`) :user:`fkiraly` Contributors ------------- +~~~~~~~~~~~~ :user:`fkiraly`, :user:`Ram0nB` @@ -834,7 +899,7 @@ Contributors Python 3.12 compatibility release. Contents --------- +~~~~~~~~ * [MNT] [Dependabot](deps-dev): Update ``numpy`` requirement from ``<1.25,>=1.21.0`` to ``>=1.21.0,<1.27`` (:pr:`118`) :user:`dependabot` @@ -847,17 +912,17 @@ Contents Release with minor maintenance actions and enhancements. Enhancements ------------- +~~~~~~~~~~~~ * [ENH] basic "test all estimators" suite (:pr:`89`) :user:`fkiraly` Documentation -------------- +~~~~~~~~~~~~~ * [DOC] improvements to notebook 1 (:pr:`106`) :user:`fkiraly` Maintenance ------------ +~~~~~~~~~~~ * [MNT] address deprecation of ``skbase.testing.utils.deep_equals`` (:pr:`111`) :user:`fkiraly` @@ -887,7 +952,7 @@ Contributions, bug reports, and feature requests are welcome on the `issue track or on the `community Discord `_. Contributors ------------- +~~~~~~~~~~~~ :user:`Alex-JG3`, :user:`fkiraly`, :user:`frthjf` diff --git a/pyproject.toml b/pyproject.toml index 9a1349ab2..08ff335e0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "skpro" -version = "2.4.1" +version = "2.4.2" description = "A unified framework for probability distributions and probabilistic supervised regression" authors = [ {name = "skpro developers", email = "sktime.toolbox@gmail.com"}, diff --git a/skpro/__init__.py b/skpro/__init__.py index 49d2f2e57..31b4fcb2d 100644 --- a/skpro/__init__.py +++ b/skpro/__init__.py @@ -1,6 +1,6 @@ """skpro.""" -__version__ = "2.4.1" +__version__ = "2.4.2" __all__ = ["show_versions"]