rebase

apis/python/README-dev.md

@@ -1,6 +1,8 @@
 * Most things are configured using GitHub Actions at `../../.github/workflows`
 * Pre-push suggestions:
   * `black .`
+  * `isort .`
+  * `flake8`
   * `python -m pytest tests`
 * PyPI:
   * https://pypi.org/project/tiledbsc/

apis/python/src/tiledbsc/annotation_dataframe.py

@@ -1,3 +1,4 @@
+import logging
 from typing import List, Optional, Set, Tuple
 
 import numpy as np

apis/python/src/tiledbsc/annotation_matrix.py

@@ -1,3 +1,4 @@
+import logging
 from typing import Optional, Tuple
 
 import pandas as pd

apis/python/src/tiledbsc/annotation_matrix_group.py

@@ -1,3 +1,4 @@
+import logging
 import os
 from typing import Dict, List, Optional
 

apis/python/src/tiledbsc/annotation_pairwise_matrix_group.py

@@ -1,3 +1,4 @@
+import logging
 import os
 from typing import Dict, List, Optional
 
@@ -136,7 +137,7 @@ def to_dict_of_csr(
             grp = tiledb.Group(self.uri, mode="r", ctx=self._ctx)
         except tiledb.TileDBError:
             pass
-        if grp == None:
+        if grp is None:
             logging.info(f"{self._indent}{self.uri} not found")
             return {}
 

apis/python/src/tiledbsc/assay_matrix.py

@@ -1,3 +1,4 @@
+import logging
 import math
 import time
 from typing import Optional, Tuple, Union

apis/python/src/tiledbsc/io.py

@@ -1,3 +1,5 @@
+import logging
+
 import anndata as ad
 import scanpy
 import tiledb

apis/python/src/tiledbsc/raw_group.py

@@ -1,3 +1,4 @@
+import logging
 from typing import Optional
 
 import anndata as ad

apis/python/src/tiledbsc/soma.py

@@ -1,9 +1,9 @@
+import logging
 import os
 from typing import Dict, List, Optional
 
 import pandas as pd
 import tiledb
-import logging
 
 from .annotation_dataframe import AnnotationDataFrame
 from .annotation_matrix_group import AnnotationMatrixGroup

apis/python/src/tiledbsc/soma_collection.py

@@ -1,3 +1,4 @@
+import logging
 from typing import List, Optional
 
 import tiledb

apis/python/src/tiledbsc/tiledb_group.py

@@ -1,3 +1,4 @@
+import logging
 from typing import Dict, List, Optional
 
 import tiledb

apis/python/src/tiledbsc/tiledb_object.py

@@ -1,4 +1,3 @@
-import os
 from typing import Dict, List, Optional
 
 import tiledb

apis/python/src/tiledbsc/uns_array.py

@@ -1,3 +1,4 @@
+import logging
 from typing import Optional
 
 import numpy as np

apis/python/src/tiledbsc/uns_group.py

@@ -1,3 +1,4 @@
+import logging
 import os
 from typing import Dict, List, Optional
 

apis/python/tools/ingestor

@@ -14,6 +14,7 @@ URIs will be supported.
 """
 
 import argparse
+import logging
 import os
 import shutil
 import sys
@@ -24,8 +25,6 @@ import tiledbsc
 import tiledbsc.io
 import tiledbsc.util
 
-import logging
-
 
 # ================================================================
 def main():

apis/python/tools/outgestor

@@ -16,6 +16,7 @@
 import argparse
 import os
 import sys
+import logging
 
 import tiledb