prepare release for 1.0.9 (1.0.1 tomorrow)

Author: Xiaojieqiu

docs/source/conf.py

@@ -82,7 +82,7 @@
 author = "Xiaojie Qiu, Yan Zhang, Ke Ni"
 
 # The full version, including alpha/beta/rc tags
-release = "1.0.0"
+release = "1.0.9"
 
 # -- General configuration ---------------------------------------------------
 

dynamo/preprocessing/__init__.py

@@ -10,10 +10,7 @@
     filter_cells_by_outliers,
     filter_cells_legacy,
     filter_genes_by_clusters_,
-)
-from .preprocess import filter_genes_by_outliers
-from .preprocess import filter_genes_by_outliers as filter_genes
-from .preprocess import (
+    filter_genes_by_outliers,
     get_svr_filter,
     highest_frac_genes,
     normalize_cell_expr_by_size_factors_legacy,
@@ -35,7 +32,10 @@
     top_pca_genes,
 )
 
+filter_cells = filter_cells_by_outliers
+filter_genes = filter_genes_by_outliers
 log1p = log1p_adata
+normalize_cells = normalize_cell_expr_by_size_factors
 
 from .preprocess_monocle_utils import estimate_dispersion, top_table
 from .Preprocessor import Preprocessor

setup.py

@@ -12,7 +12,7 @@
 if __name__ == "__main__":
     setup(
         name="dynamo-release",
-        version="v1.0.0",
+        version="v1.0.9",
         python_requires=">=3.7",
         install_requires=[l.strip() for l in Path("requirements.txt").read_text("utf-8").splitlines()],  # 'yt>=3.5.1',
         extras_require={