diff --git a/dynamo/preprocessing/deprecated.py b/dynamo/preprocessing/deprecated.py index 16488ee3c..f9fca44b9 100644 --- a/dynamo/preprocessing/deprecated.py +++ b/dynamo/preprocessing/deprecated.py @@ -130,7 +130,7 @@ def _hat_matrix_legacy(X: np.ndarray, W: np.ndarray) -> np.ndarray: @deprecated def cook_dist(*args, **kwargs): - _cook_dist_legacy(*args, **kwargs) + return _cook_dist_legacy(*args, **kwargs) def _cook_dist_legacy(model: sm.Poisson, X: np.ndarray, good: npt.ArrayLike) -> np.ndarray: @@ -522,7 +522,7 @@ def _calc_mean_var_dispersion_sparse_legacy( @deprecated def calc_sz_factor_legacy(*args, **kwargs): - _calc_sz_factor_legacy(*args, **kwargs) + return _calc_sz_factor_legacy(*args, **kwargs) def _calc_sz_factor_legacy( @@ -657,7 +657,7 @@ def _calc_sz_factor_legacy( @deprecated def normalize_cell_expr_by_size_factors(*args, **kwargs): - _normalize_cell_expr_by_size_factors_legacy(*args, **kwargs) + return _normalize_cell_expr_by_size_factors_legacy(*args, **kwargs) def _normalize_cell_expr_by_size_factors_legacy( @@ -784,7 +784,7 @@ def _normalize_cell_expr_by_size_factors_legacy( @deprecated def filter_cells_legacy(*args, **kwargs): - _filter_cells_legacy(*args, **kwargs) + return _filter_cells_legacy(*args, **kwargs) def _filter_cells_legacy( @@ -875,7 +875,7 @@ def _filter_cells_legacy( @deprecated def filter_genes_by_outliers_legacy(*args, **kwargs): - _filter_genes_by_outliers_legacy(*args, **kwargs) + return _filter_genes_by_outliers_legacy(*args, **kwargs) def _filter_genes_by_outliers_legacy( @@ -990,7 +990,7 @@ def _filter_genes_by_outliers_legacy( @deprecated def recipe_monocle(*args, **kwargs): - _recipe_monocle_legacy(*args, **kwargs) + return _recipe_monocle_legacy(*args, **kwargs) def _recipe_monocle_legacy( @@ -1613,7 +1613,7 @@ def _recipe_monocle_legacy( @deprecated def recipe_velocyto(*args, **kwargs): - _recipe_velocyto_legacy(*args, **kwargs) + return _recipe_velocyto_legacy(*args, **kwargs) def _recipe_velocyto_legacy( @@ -1747,7 +1747,7 @@ def _recipe_velocyto_legacy( @deprecated def select_genes_monocle_legacy(*args, **kwargs): - _select_genes_monocle_legacy(*args, **kwargs) + return _select_genes_monocle_legacy(*args, **kwargs) def _select_genes_monocle_legacy( diff --git a/dynamo/tools/deprecated.py b/dynamo/tools/deprecated.py index 850bfe003..7bad129b0 100644 --- a/dynamo/tools/deprecated.py +++ b/dynamo/tools/deprecated.py @@ -54,7 +54,7 @@ def wrapper(*args, **kwargs): # deprecated _dynamics_deprecated.py @deprecated def _dynamics(*args, **kwargs): - _dynamics_legacy(*args, **kwargs) + return _dynamics_legacy(*args, **kwargs) def _dynamics_legacy( @@ -72,7 +72,7 @@ def _dynamics_legacy( concat_data=False, log_unnormalized=True, one_shot_method="combined", -): +) -> AnnData: """Inclusive model of expression dynamics considers splicing, metabolic labeling and protein translation. It supports learning high-dimensional velocity vector samples for droplet based (10x, inDrop, drop-seq, etc), scSLAM-seq, NASC-seq sci-fate, scNT-seq or cite-seq datasets. @@ -379,7 +379,7 @@ def fbar(x_a, x_i, a, b): # deprecated dynamo_bk.py @deprecated def sol_u(*args, **kwargs): - _sol_u_legacy(*args, **kwargs) + return _sol_u_legacy(*args, **kwargs) def _sol_u_legacy(t, u0, alpha, beta): @@ -388,7 +388,7 @@ def _sol_u_legacy(t, u0, alpha, beta): @deprecated def sol_s_dynamo_bk(*args, **kwargs): - _sol_s_dynamo_bk_legacy(*args, **kwargs) + return _sol_s_dynamo_bk_legacy(*args, **kwargs) def _sol_s_dynamo_bk_legacy(t, s0, u0, alpha, beta, gamma): @@ -400,7 +400,7 @@ def _sol_s_dynamo_bk_legacy(t, s0, u0, alpha, beta, gamma): @deprecated def fit_gamma_labelling_dynamo_bk(*args, **kwargs): - _fit_gamma_labelling_dynamo_bk_legacy(*args, **kwargs) + return _fit_gamma_labelling_dynamo_bk_legacy(*args, **kwargs) def _fit_gamma_labelling_dynamo_bk_legacy(t, l, mode=None, lbound=None): @@ -427,7 +427,7 @@ def _fit_gamma_labelling_dynamo_bk_legacy(t, l, mode=None, lbound=None): @deprecated def fit_alpha_dynamo_bk_labelling(*args, **kwargs): - _fit_alpha_labelling_dynamo_bk_legacy(*args, **kwargs) + return _fit_alpha_labelling_dynamo_bk_legacy(*args, **kwargs) def _fit_alpha_labelling_dynamo_bk_legacy(t, u, gamma, mode=None): @@ -456,7 +456,7 @@ def _fit_alpha_labelling_dynamo_bk_legacy(t, u, gamma, mode=None): @deprecated def fit_gamma_splicing_dynamo_bk(*args, **kwargs): - _fit_gamma_splicing_dynamo_bk_legacy(*args, **kwargs) + return _fit_gamma_splicing_dynamo_bk_legacy(*args, **kwargs) def _fit_gamma_splicing_dynamo_bk_legacy(t, s, beta, u0, bounds=(0, np.inf)): @@ -471,7 +471,7 @@ def _fit_gamma_splicing_dynamo_bk_legacy(t, s, beta, u0, bounds=(0, np.inf)): @deprecated def fit_gamma_dynamo_bk(*args, **kwargs): - _fit_gamma_dynamo_bk_legacy(*args, **kwargs) + return _fit_gamma_dynamo_bk_legacy(*args, **kwargs) def _fit_gamma_dynamo_bk_legacy(u, s): @@ -485,7 +485,7 @@ def _fit_gamma_dynamo_bk_legacy(u, s): # deprecated dynamo_fitting.py @deprecated def sol_s_dynamo_fitting(*args, **kwargs): - _sol_s_dynamo_fitting_legacy(*args, **kwargs) + return _sol_s_dynamo_fitting_legacy(*args, **kwargs) def _sol_s_dynamo_fitting_legacy(t, s0, u0, alpha, beta, gamma): @@ -503,7 +503,7 @@ def _sol_s_dynamo_fitting_legacy(t, s0, u0, alpha, beta, gamma): @deprecated def sol_p_dynamo_fitting(*args, **kwargs): - _sol_p_dynamo_fitting_legacy(*args, **kwargs) + return _sol_p_dynamo_fitting_legacy(*args, **kwargs) def _sol_p_dynamo_fitting_legacy(t, p0, s0, u0, alpha, beta, gamma, eta, gamma_p): @@ -518,7 +518,7 @@ def _sol_p_dynamo_fitting_legacy(t, p0, s0, u0, alpha, beta, gamma, eta, gamma_p @deprecated def sol_ode_dynamo_fitting(*args, **kwargs): - _sol_ode_dynamo_fitting_legacy(*args, **kwargs) + return _sol_ode_dynamo_fitting_legacy(*args, **kwargs) def _sol_ode_dynamo_fitting_legacy(x, t, alpha, beta, gamma, eta, gamma_p): @@ -531,7 +531,7 @@ def _sol_ode_dynamo_fitting_legacy(x, t, alpha, beta, gamma, eta, gamma_p): @deprecated def sol_num_dynamo_fitting(args, kwargs): - _sol_num_dynamo_fitting_legacy(*args, **kwargs) + return _sol_num_dynamo_fitting_legacy(*args, **kwargs) def _sol_num_dynamo_fitting_legacy(t, p0, s0, u0, alpha, beta, gamma, eta, gamma_p): @@ -545,7 +545,7 @@ def _sol_num_dynamo_fitting_legacy(t, p0, s0, u0, alpha, beta, gamma, eta, gamma @deprecated def fit_gamma_labelling_dynamo_fitting(*args, **kwargs): - _fit_gamma_labelling_dynamo_fitting_legacy(*args, **kwargs) + return _fit_gamma_labelling_dynamo_fitting_legacy(*args, **kwargs) def _fit_gamma_labelling_dynamo_fitting_legacy(t, l, mode=None, lbound=None): @@ -588,7 +588,7 @@ def _fit_gamma_labelling_dynamo_fitting_legacy(t, l, mode=None, lbound=None): @deprecated def fit_beta_lsq_dynamo_fitting(*args, **kwargs): - _fit_beta_lsq_dynamo_fitting_legacy(*args, **kwargs) + return _fit_beta_lsq_dynamo_fitting_legacy(*args, **kwargs) def _fit_beta_lsq_dynamo_fitting_legacy(t, l, bounds=(0, np.inf), fix_l0=False, beta_0=None): @@ -611,7 +611,7 @@ def _fit_beta_lsq_dynamo_fitting_legacy(t, l, bounds=(0, np.inf), fix_l0=False, @deprecated def fit_alpha_labelling_dynamo_fitting(*args, **kwargs): - _fit_alpha_labelling_dynamo_fitting_legacy(*args, **kwargs) + return _fit_alpha_labelling_dynamo_fitting_legacy(*args, **kwargs) def _fit_alpha_labelling_dynamo_fitting_legacy(t, u, gamma, mode=None): @@ -640,7 +640,7 @@ def _fit_alpha_labelling_dynamo_fitting_legacy(t, u, gamma, mode=None): @deprecated def fit_alpha_synthesis_dynamo_fitting(*args, **kwargs): - _fit_alpha_synthesis_dynamo_fitting_legacy(*args, **kwargs) + return _fit_alpha_synthesis_dynamo_fitting_legacy(*args, **kwargs) def _fit_alpha_synthesis_dynamo_fitting_legacy(t, u, beta, mode=None): @@ -655,7 +655,7 @@ def _fit_alpha_synthesis_dynamo_fitting_legacy(t, u, beta, mode=None): @deprecated def fit_gamma_splicing_dynamo_fitting(*args, **kwargs): - _fit_gamma_splicing_dynamo_fitting_legacy(*args, **kwargs) + return _fit_gamma_splicing_dynamo_fitting_legacy(*args, **kwargs) def _fit_gamma_splicing_dynamo_fitting_legacy(t, s, beta, u0, bounds=(0, np.inf), fix_s0=False): @@ -677,7 +677,7 @@ def _fit_gamma_splicing_dynamo_fitting_legacy(t, s, beta, u0, bounds=(0, np.inf) @deprecated def fit_gamma_dynamo_fitting(*args, **kwargs): - _fit_gamma_dynamo_fitting_legacy(*args, **kwargs) + return _fit_gamma_dynamo_fitting_legacy(*args, **kwargs) def _fit_gamma_dynamo_fitting_legacy(u, s):