Convert submodules to namespace packages

improves import performance and circular dependency issues

src/pyliger/__init__.py

@@ -1,17 +1,19 @@
-from .clustering import leiden_cluster, louvain_cluster
-from .factorization import iNMF_HALS, online_iNMF, optimize_ALS
-from .plotting import (
-    plot_by_dataset_and_cluster,
-    plot_gene,
-    plot_gene_loadings,
-    plot_spatial,
-)
-from .preprocessing import (
-    create_liger,
-    make_feature_matrix,
-    normalize,
-    scale_not_center,
-    select_genes,
-)
+from .clustering._leiden import leiden_cluster
+from .clustering._louvain import louvain_cluster
+from .factorization._iNMF_HALS import iNMF_HALS
+from .factorization._online_iNMF import online_iNMF
+from .factorization._iNMF_ANLS import optimize_ALS
+from .plotting._dataset_cluster import plot_by_dataset_and_cluster
+from .plotting._gene import plot_gene
+from .plotting._gene_loadings import plot_gene_loadings
+from .plotting._spatial import plot_spatial
+from .preprocessing._initialization import create_liger
+from .preprocessing._select_genes import select_genes
+from .preprocessing._normalization import normalize
+from .preprocessing._scale import scale_not_center
+from .preprocessing._cal_feature import make_feature_matrix
 from .read_write import read_10X, read_10X_h5, read_10X_visium
-from .tools import quantile_norm, run_umap, run_wilcoxon
+from .tools._quantile_norm import quantile_norm
+from .tools._umap import run_umap
+from .tools._wilcoxon import run_wilcoxon
+from .pyliger import Liger

src/pyliger/clustering/_leiden.py

@@ -1,7 +1,12 @@
 import leidenalg
 import numpy as np
 
-from ._utilities import _assign_cluster, build_igraph, compute_snn, run_knn
+from pyliger.clustering._utilities import (
+    _assign_cluster,
+    build_igraph,
+    compute_snn,
+    run_knn,
+)
 
 
 def leiden_cluster(

src/pyliger/clustering/_louvain.py

@@ -1,7 +1,12 @@
 import louvain
 import numpy as np
 
-from ._utilities import _assign_cluster, build_igraph, compute_snn, run_knn
+from pyliger.clustering._utilities import (
+    _assign_cluster,
+    build_igraph,
+    compute_snn,
+    run_knn,
+)
 
 
 def louvain_cluster(

src/pyliger/clustering/__init__.py → src/pyliger/clustering/todo.py

@@ -1,7 +1,3 @@
-from ._leiden import leiden_cluster
-from ._louvain import louvain_cluster
-
-
 #####TODO
 def imputeKNN(
     liger_object, reference, queries, knn_k=20, weight=True, norm=True, scale=False

src/pyliger/factorization/_iNMF_ANLS.py

@@ -1,7 +1,7 @@
 import numpy as np
 from tqdm import tqdm
 
-from ._utilities import nnlsm_blockpivot
+from pyliger.factorization._utilities import nnlsm_blockpivot
 
 
 def optimize_ALS(

src/pyliger/factorization/_iNMF_HALS.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-from ._utilities import (
+from pyliger.factorization._utilities import (
     _init_H,
     _init_V,
     _init_W,

src/pyliger/factorization/_online_iNMF.py

@@ -3,11 +3,11 @@
 from scipy.sparse import vstack
 from tqdm import tqdm
 
-from .._utilities import _h5_idx_generator
-from ..preprocessing._initialization import _initialization_online
-from ..preprocessing._normalization import _normalize_online
-from ..preprocessing._scale import _scale_online
-from ._utilities import (
+from pyliger._utilities import _h5_idx_generator
+from pyliger.preprocessing._initialization import _initialization_online
+from pyliger.preprocessing._normalization import _normalize_online
+from pyliger.preprocessing._scale import _scale_online
+from pyliger.factorization._utilities import (
     _init_V_online,
     _init_W,
     _update_V_HALS,

src/pyliger/factorization/_utilities.py

@@ -3,7 +3,7 @@
 import scipy.linalg as sla
 import scipy.sparse as sps
 
-from .._utilities import _h5_idx_generator
+from pyliger._utilities import _h5_idx_generator
 
 
 def nonneg(x, eps=1e-16):

src/pyliger/factorization/__init__.py → src/pyliger/factorization/todo.py

@@ -1,6 +1,3 @@
-from ._iNMF_ANLS import optimize_ALS
-from ._iNMF_HALS import iNMF_HALS
-from ._online_iNMF import online_iNMF
 
 #######################################################################################
 #### Factorization TODO

src/pyliger/plotting/_gene.py

@@ -21,7 +21,7 @@
 )
 from sklearn.preprocessing import scale
 
-from ._utilities import get_gene_values
+from pyliger.plotting._utilities import get_gene_values
 
 
 def plot_gene(

src/pyliger/plotting/_gene_loadings.py

@@ -18,7 +18,8 @@
 )
 from tqdm import tqdm
 
-from ..tools import calc_dataset_specificity, get_factor_markers
+from pyliger.tools._marker import get_factor_markers
+from pyliger.tools._metrics import calc_dataset_specificity
 
 
 def plot_gene_loadings(

src/pyliger/plotting/_spatial.py

@@ -13,7 +13,7 @@
     ylim,
 )
 
-from ._utilities import get_gene_values
+from pyliger.plotting._utilities import get_gene_values
 
 
 def plot_spatial(

src/pyliger/plotting/__init__.py → src/pyliger/plotting/todo.py

@@ -1,11 +1,4 @@
 # from ._qc import plot_qc
-import numpy as np
-
-from ._dataset_cluster import plot_by_dataset_and_cluster
-from ._gene import plot_gene
-from ._gene_loadings import plot_gene_loadings
-from ._go import plot_go_term
-from ._spatial import plot_spatial
 
 
 ###############TODO

src/pyliger/preprocessing/_initialization.py

@@ -4,8 +4,8 @@
 import numpy as np
 from scipy.sparse import csr_matrix
 
-from .._utilities import _h5_idx_generator, _merge_sparse_data_all, _remove_missing_obs
-from ..pyliger import Liger
+from pyliger._utilities import _h5_idx_generator, _merge_sparse_data_all, _remove_missing_obs
+from pyliger.pyliger import Liger
 
 
 def create_liger(

src/pyliger/preprocessing/_normalization.py

@@ -5,8 +5,8 @@
 import numpy as np
 from sklearn.preprocessing import normalize as sp_normalize
 
-from .._utilities import _h5_idx_generator, _remove_missing_obs
-from ..pyliger import Liger
+from pyliger._utilities import _h5_idx_generator, _remove_missing_obs
+from pyliger.pyliger import Liger
 
 PARRENT_PATH = Path(__file__).parent
 

src/pyliger/preprocessing/_scale.py

@@ -5,7 +5,7 @@
 from scipy.sparse import csr_matrix
 from sklearn.utils.sparsefuncs import inplace_column_scale
 
-from .._utilities import _h5_idx_generator
+from pyliger._utilities import _h5_idx_generator
 
 
 def scale_not_center(

src/pyliger/preprocessing/_select_genes.py

@@ -8,7 +8,7 @@
 from scipy.stats import norm
 from sklearn.utils.sparsefuncs import mean_variance_axis
 
-from .._utilities import _h5_idx_generator
+from pyliger._utilities import _h5_idx_generator
 
 
 def select_genes(

src/pyliger/tools/_marker.py

@@ -3,8 +3,8 @@
 from scipy.sparse import vstack
 from sklearn.preprocessing import scale
 
-from ..tools import _wilcoxon, calc_dataset_specificity
-
+from pyliger.tools import _wilcoxon
+from pyliger.tools._metrics import calc_dataset_specificity
 
 # Find shared and dataset-specific markers
 def get_factor_markers(

src/pyliger/tools/__init__.py → src/pyliger/tools/todo.py

@@ -1,10 +1,3 @@
-from ._go import run_GO_analysis
-from ._marker import get_factor_markers
-from ._metrics import calc_dataset_specificity
-from ._quantile_norm import quantile_norm
-from ._umap import run_umap
-from ._wilcoxon import _wilcoxon, run_wilcoxon
-
 #######################################################################################
 #### Conversion/Transformation TODO