update

.readthedocs.yml

@@ -9,6 +9,6 @@ sphinx:
   configuration: docs/source/conf.py
 
 python:
-    version: 3.6
+    version: 3.7
     install:
         - requirements: docs/requirements.txt

docs/requirements.txt

@@ -13,7 +13,7 @@ pandas>=0.25.1
 scipy>=1.0
 scikit-learn>=0.19.1
 cvxopt>=1.2.3
-anndata==0.7.5
+anndata>=0.7.6
 loompy>=3.0.5
 matplotlib>=3.1.0
 trimap>=1.0.11
@@ -28,4 +28,4 @@ seaborn>=0.9.0
 colorcet>=2.0.1
 tqdm
 python-igraph>=0.7.1
-pynndescent>=0.4.8
+pynndescent>=0.5.2

dynamo/preprocessing/utils.py

@@ -218,10 +218,11 @@ def cook_dist(model, X, good):
 
 # ---------------------------------------------------------------------------------------------------
 # preprocess utilities
-def filter_genes_by_pattern(adata: anndata.AnnData,
-                            patterns: tuple = ('MT-', 'RPS', 'RPL', 'MRPS', 'MRPL', 'ERCC-'),
-                            drop_genes: bool = False
-                            ) -> Union[anndata.AnnData, None]:
+def filter_genes_by_pattern(
+        adata: anndata.AnnData,
+        patterns: tuple = ('MT-', 'RPS', 'RPL', 'MRPS', 'MRPL', 'ERCC-'),
+        drop_genes: bool = False,
+) -> Union[list, None]:
     """Utility function to filter mitochondria, ribsome protein and ERCC spike-in genes, etc."""
     logger = LoggerManager.gen_logger("dynamo-utils")
 

pyproject.toml

@@ -4,24 +4,24 @@ build-backend = 'flit.buildapi'
 
 [tool.flit.metadata]
 module = 'dynamo'
-author = 'Xiaojie Qiu, Yan Zhang'
+author = 'Xiaojie Qiu, Yan Zhang, Ke Ni'
 author-email = '[email protected]'
 home-page = 'https://github.com/aristoteleo/dynamo-release'
 license = 'BSD'
 description-file = 'README.md'
-requires-python = '>=3.6'
+requires-python = '>=3.7'
 requires = ['numpy>=1.18.1',
             'pandas>=0.25.1',
             'scipy>=1.0',
             'scikit-learn>=0.19.1',
             'cvxopt>=1.2.3',
-            'anndata>=0.7.4',
+            'anndata>=0.7.6',
             'loompy>=3.0.5',
             'matplotlib>=3.1.0',
             'trimap>=1.0.11',
             'setuptools',
             'numdifftools>=0.9.39',
-            'umap-learn>=0.4.3',
+            'umap-learn>=0.5.1',
             'hdbscan>=0.8.26',
             'PATSY>=0.5.1',
             'statsmodels>=0.9.0',
@@ -30,7 +30,7 @@ requires = ['numpy>=1.18.1',
             'colorcet>=2.0.1',
             'tqdm',
             'python-igraph>=0.7.1',
-            'pynndescent>=0.4.8',
+            'pynndescent>=0.5.2',
             'joblib',
             'setuptools']
 requires-extra = { doc = ['docutils'], test = ['pytest', 'sympy>=1.4'], spatial = ['pysal>2.0.0'], dimension_reduction = ['fitsne>=1.0.1'], bigdata_visualization = ["datashader>=0.9.0", "bokeh>=1.4.0", "holoviews>=1.9.2"] }

requirements.txt

@@ -3,7 +3,7 @@ pandas>=0.25.1
 scipy>=1.0
 scikit-learn>=0.19.1
 cvxopt>=1.2.3
-anndata==0.7.5
+anndata>=0.7.6
 loompy>=3.0.5
 matplotlib>=3.1.0
 trimap>=1.0.11
@@ -18,6 +18,6 @@ seaborn>=0.9.0
 colorcet>=2.0.1
 tqdm
 python-igraph>=0.7.1
-pynndescent>=0.4.8
+pynndescent>=0.5.2
 pre-commit
 networkx

sinfo-requirements.txt

@@ -1,4 +1,4 @@
-anndata==0.7.5
+anndata>=0.7.6
 scanpy==1.6.0
 sinfo==0.3.1
 IPython==7.20.0