From 56f15bd6409d169316ea76d0552491b79be021a3 Mon Sep 17 00:00:00 2001 From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com> Date: Wed, 11 Dec 2024 11:14:28 +0800 Subject: [PATCH] MNT align with sklearn 1.6 --- fastcan/_fastcan.py | 5 +- fastcan/_narx.py | 95 +- meson.build | 2 +- pixi.lock | 4678 +++++++++++++++++-------------------------- pyproject.toml | 11 +- tests/test_narx.py | 8 +- 6 files changed, 1882 insertions(+), 2917 deletions(-) diff --git a/fastcan/_fastcan.py b/fastcan/_fastcan.py index ff5d760..b5e99cd 100644 --- a/fastcan/_fastcan.py +++ b/fastcan/_fastcan.py @@ -12,7 +12,7 @@ from sklearn.utils import check_array, check_consistent_length from sklearn.utils._openmp_helpers import _openmp_effective_n_threads from sklearn.utils._param_validation import Interval -from sklearn.utils.validation import check_is_fitted +from sklearn.utils.validation import check_is_fitted, validate_data from ._cancorr_fast import _forward_search # type: ignore @@ -162,7 +162,8 @@ def fit(self, X, y): "dtype": float, "force_writeable": True, } - X, y = self._validate_data( + X, y = validate_data( + self, X=X, y=y, multi_output=True, diff --git a/fastcan/_narx.py b/fastcan/_narx.py index 49562a4..de6f476 100644 --- a/fastcan/_narx.py +++ b/fastcan/_narx.py @@ -13,7 +13,11 @@ from sklearn.linear_model import LinearRegression from sklearn.utils import check_array, check_consistent_length, column_or_1d from sklearn.utils._param_validation import Interval, StrOptions, validate_params -from sklearn.utils.validation import check_is_fitted +from sklearn.utils.validation import ( + _check_sample_weight, + check_is_fitted, + validate_data, +) from ._fastcan import FastCan from ._refine import refine @@ -52,7 +56,7 @@ def make_time_shift_features(X, ids): [5., 3., 4.], [7., 5., 6.]]) """ - X = check_array(X, ensure_2d=True, dtype=float, force_all_finite="allow-nan") + X = check_array(X, ensure_2d=True, dtype=float, ensure_all_finite="allow-nan") ids = check_array(ids, ensure_2d=True, dtype=int) n_samples = X.shape[0] n_outputs = ids.shape[0] @@ -177,7 +181,7 @@ def make_poly_features(X, ids): [ 1., 5., 25., 6.], [ 1., 7., 49., 8.]]) """ - X = check_array(X, ensure_2d=True, dtype=float, force_all_finite="allow-nan") + X = check_array(X, ensure_2d=True, dtype=float, ensure_all_finite="allow-nan") ids = check_array(ids, ensure_2d=True, dtype=int) n_samples = X.shape[0] n_outputs, degree = ids.shape @@ -269,7 +273,7 @@ def _mask_missing_value(*arr): return tuple([x[mask_nomissing] for x in arr]) -class Narx(BaseEstimator, RegressorMixin): +class Narx(RegressorMixin, BaseEstimator): """Nonlinear Autoregressive eXogenous model. For example, a (polynomial) Narx model is like y(t) = y(t-1)*u(t-1) + u(t-1)^2 + u(t-2) + 1.5 @@ -374,10 +378,11 @@ def __init__( @validate_params( { "coef_init": [None, StrOptions({"one_step_ahead"}), "array-like"], + "sample_weight": ["array-like", None], }, prefer_skip_nested_validation=True, ) - def fit(self, X, y, coef_init=None, **params): + def fit(self, X, y, sample_weight=None, coef_init=None, **params): """ Fit narx model. @@ -389,6 +394,10 @@ def fit(self, X, y, coef_init=None, **params): y : array-like of shape (n_samples,) Target values. Will be cast to X's dtype if necessary. + sample_weight : array-like of shape (n_samples,), default=None + Individual weights for each sample, which are used for a One-Step-Ahead + Narx. + coef_init : array-like of shape (n_terms,), default=None The initial values of coefficients and intercept for optimization. When `coef_init` is None, the model will be a One-Step-Ahead Narx. @@ -410,9 +419,15 @@ def fit(self, X, y, coef_init=None, **params): self : object Fitted Estimator. """ - X = self._validate_data(X, dtype=float, force_all_finite="allow-nan") + X = validate_data( + self, + X, + dtype=float, + ensure_all_finite="allow-nan", + ) y = column_or_1d(y, dtype=float, warn=True) check_consistent_length(X, y) + sample_weight = _check_sample_weight(sample_weight, X) if self.time_shift_ids is None: self.time_shift_ids_ = make_time_shift_ids( @@ -467,9 +482,11 @@ def fit(self, X, y, coef_init=None, **params): time_shift_vars = make_time_shift_features(xy_hstack, self.time_shift_ids_) poly_terms = make_poly_features(time_shift_vars, self.poly_ids_) # Remove missing values - poly_terms_masked, y_masked = _mask_missing_value(poly_terms, y) + poly_terms_masked, y_masked, sample_weight_masked = _mask_missing_value( + poly_terms, y, sample_weight + ) - osa_narx.fit(poly_terms_masked, y_masked) + osa_narx.fit(poly_terms_masked, y_masked, sample_weight_masked) if coef_init is None: self.coef_ = osa_narx.coef_ self.intercept_ = osa_narx.intercept_ @@ -545,7 +562,7 @@ def _predict(expression, X, y_init, coef, intercept, max_delay): else: y_hat[k] = expression(X, y_hat, coef, intercept, k) if np.any(y_hat[k] > 1e20): - y_hat[k:] = np.inf + y_hat[k:] = 1e20 return y_hat return y_hat @@ -564,7 +581,7 @@ def _residual( y_masked, y_hat_masked = _mask_missing_value(y, y_hat) - return (y_masked - y_hat_masked).flatten() + return y_masked - y_hat_masked @validate_params( { @@ -591,7 +608,7 @@ def predict(self, X, y_init=None): """ check_is_fitted(self) - X = self._validate_data(X, reset=False, force_all_finite="allow-nan") + X = validate_data(self, X, reset=False, ensure_all_finite="allow-nan") if y_init is None: y_init = np.zeros(self.max_delay_) else: @@ -613,8 +630,10 @@ def predict(self, X, y_init=None): self.max_delay_, ) - def _more_tags(self): - return {"allow_nan": True} + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.allow_nan = True + return tags @validate_params( @@ -718,14 +737,13 @@ def _get_term_str(term_id): ], "include_zero_delay": [None, "array-like"], "static_indices": [None, "array-like"], - "eta": ["boolean"], - "verbose": ["verbose"], - "drop": [ + "refine_verbose": ["verbose"], + "refine_drop": [ None, Interval(Integral, 1, None, closed="left"), StrOptions({"all"}), ], - "max_iter": [ + "refine_max_iter": [ None, Interval(Integral, 1, None, closed="left"), ], @@ -741,10 +759,10 @@ def make_narx( *, include_zero_delay=None, static_indices=None, - eta=False, - verbose=1, - drop=None, - max_iter=None, + refine_verbose=1, + refine_drop=None, + refine_max_iter=None, + **params, ): """Find `time_shift_ids` and `poly_ids` for a Narx model. @@ -775,19 +793,20 @@ def make_narx( If the corresponding include_zero_delay of the static features is False, the static feature will be excluded from candidate features. - eta : bool, default=False - Whether to use eta-cosine method. + refine_verbose : int, default=1 + The verbosity level of refine. - verbose : int, default=1 - The verbosity level. - - drop : int or "all", default=None + refine_drop : int or "all", default=None The number of the selected features dropped for the consequencing reselection. If `drop` is None, no refining will be performed. - max_iter : int, default=None + refine_max_iter : int, default=None The maximum number of valid iterations in the refining process. + **params : dict + Keyword arguments passed to + `fastcan.FastCan`. + Returns ------- narx : Narx @@ -818,7 +837,8 @@ def make_narx( ... static_indices=[1], ... eta=True, ... verbose=0, - ... drop=1) + ... refine_verbose=0, + ... refine_drop=1) >>> print(f"{mean_squared_error(y, narx.fit(X, y).predict(X)):.4f}") 0.0289 >>> print_narx(narx) @@ -830,7 +850,7 @@ def make_narx( | X[k-1,0]*X[k-3,0] | 1.999 | | X[k-2,0]*X[k-0,1] | 1.527 | """ - X = check_array(X, dtype=float, ensure_2d=True, force_all_finite="allow-nan") + X = check_array(X, dtype=float, ensure_2d=True, ensure_all_finite="allow-nan") y = column_or_1d(y, dtype=float) check_consistent_length(X, y) @@ -838,12 +858,14 @@ def make_narx( n_features = X.shape[1] if include_zero_delay is None: - include_zero_delay = [True] * n_features + [False] + _include_zero_delay = [True] * n_features + [False] + else: + _include_zero_delay = include_zero_delay + [False] time_shift_ids_all = make_time_shift_ids( n_features=xy_hstack.shape[1], max_delay=max_delay, - include_zero_delay=include_zero_delay, + include_zero_delay=_include_zero_delay, ) time_shift_ids_all = np.delete( @@ -867,11 +889,12 @@ def make_narx( csf = FastCan( n_features_to_select, - eta=eta, - verbose=0, + **params, ).fit(poly_terms_masked, y_masked) - if drop is not None: - indices, _ = refine(csf, drop=drop, max_iter=max_iter, verbose=verbose) + if refine_drop is not None: + indices, _ = refine( + csf, drop=refine_drop, max_iter=refine_max_iter, verbose=refine_verbose + ) support = np.zeros(shape=csf.n_features_in_, dtype=bool) support[indices] = True else: diff --git a/meson.build b/meson.build index d836371..522ef8a 100644 --- a/meson.build +++ b/meson.build @@ -1,7 +1,7 @@ project( 'fastcan', 'c', 'cython', - version: '0.2.7', + version: '0.3.0', license: 'MIT', meson_version: '>= 1.1.0', default_options: [ diff --git a/pixi.lock b/pixi.lock index dbad1be..be62b15 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,4 +1,4 @@ -version: 5 +version: 6 environments: default: channels: @@ -9,18 +9,18 @@ environments: linux-64: - 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Beta", @@ -23,6 +23,7 @@ classifiers = [ "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", "Programming Language :: Python :: Implementation :: CPython", ] @@ -55,7 +56,7 @@ python-build = "*" uv = "*" [build-system] -requires = ["meson-python>=0.16.0", "Cython>=3.0.10", "scikit-learn>=1.5.0"] +requires = ["meson-python>=0.16.0", "Cython>=3.0.10", "scikit-learn>=1.6.0"] build-backend = "mesonpy" [tool.pixi.project] @@ -79,11 +80,11 @@ compilers = "*" [tool.pixi.host-dependencies] meson-python = ">=0.16.0" cython = ">=3.0.10" -scikit-learn = ">=1.5.0" +scikit-learn = ">=1.6.0" [tool.pixi.dependencies] python = ">=3.12.0" -scikit-learn = ">=1.5.0" +scikit-learn = ">=1.6.0" [tool.pixi.tasks] time-h = "python -m timeit -n 5 -s 'import numpy as np; from fastcan import FastCan; X = np.random.rand(3000, 100); y = np.random.rand(3000, 20)' 's = FastCan(100, verbose=0).fit(X, y)'" diff --git a/tests/test_narx.py b/tests/test_narx.py index ef5f9ed..4c8e062 100644 --- a/tests/test_narx.py +++ b/tests/test_narx.py @@ -50,7 +50,7 @@ def test_narx(nan): assert narx_default.poly_ids.shape[0] ==\ params["n_features_to_select"] - params["include_zero_delay"] = [False, True, False] + params["include_zero_delay"] = [False, True] narx_0_delay = make_narx(X=X, y=y, **params) time_shift_ids = narx_0_delay.time_shift_ids time_ids_u0 = time_shift_ids[time_shift_ids[:, 0] == 0] @@ -67,8 +67,8 @@ def test_narx(nan): if time_ids_u1.size != 0: assert time_ids_u1[0, 1] == 0 - params["drop"] = 1 - params["max_iter"] = 10 + params["refine_drop"] = 1 + params["refine_max_iter"] = 10 narx_drop = make_narx(X=X, y=y, **params) assert np.any( narx_drop.poly_ids !=\ @@ -124,5 +124,3 @@ def test_narx(nan): poly_ids = make_poly_ids(time_shift_ids.shape[0]+1, 2) with pytest.raises(ValueError, match=r"The element x of poly_ids should .*"): narx_osa = Narx(time_shift_ids=time_shift_ids, poly_ids=poly_ids).fit(X, y) - -test_narx(True)