Merge pull request #663 from Sichao25/deprecated

Add missing return value to deprecated functions

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(

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):