From 46da39b8f1a0010126fb8f7ef6d1360e70425c25 Mon Sep 17 00:00:00 2001
From: John Kerl <kerl.john.r@gmail.com>
Date: Thu, 23 Jun 2022 17:51:06 -0400
Subject: [PATCH] rebase

---
 apis/python/README-dev.md                                    | 2 ++
 apis/python/src/tiledbsc/annotation_dataframe.py             | 1 +
 apis/python/src/tiledbsc/annotation_matrix.py                | 1 +
 apis/python/src/tiledbsc/annotation_matrix_group.py          | 1 +
 apis/python/src/tiledbsc/annotation_pairwise_matrix_group.py | 3 ++-
 apis/python/src/tiledbsc/assay_matrix.py                     | 1 +
 apis/python/src/tiledbsc/io.py                               | 2 ++
 apis/python/src/tiledbsc/raw_group.py                        | 1 +
 apis/python/src/tiledbsc/soma.py                             | 2 +-
 apis/python/src/tiledbsc/soma_collection.py                  | 1 +
 apis/python/src/tiledbsc/tiledb_group.py                     | 1 +
 apis/python/src/tiledbsc/tiledb_object.py                    | 1 -
 apis/python/src/tiledbsc/uns_array.py                        | 1 +
 apis/python/src/tiledbsc/uns_group.py                        | 1 +
 apis/python/tools/ingestor                                   | 3 +--
 apis/python/tools/outgestor                                  | 1 +
 16 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/apis/python/README-dev.md b/apis/python/README-dev.md
index 5a59d3596d..78967ed2de 100644
--- a/apis/python/README-dev.md
+++ b/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/
diff --git a/apis/python/src/tiledbsc/annotation_dataframe.py b/apis/python/src/tiledbsc/annotation_dataframe.py
index 9a0ff4927a..7baf6e57d3 100644
--- a/apis/python/src/tiledbsc/annotation_dataframe.py
+++ b/apis/python/src/tiledbsc/annotation_dataframe.py
@@ -1,3 +1,4 @@
+import logging
 from typing import List, Optional, Set, Tuple
 
 import numpy as np
diff --git a/apis/python/src/tiledbsc/annotation_matrix.py b/apis/python/src/tiledbsc/annotation_matrix.py
index 9f51fb1db4..153edff490 100644
--- a/apis/python/src/tiledbsc/annotation_matrix.py
+++ b/apis/python/src/tiledbsc/annotation_matrix.py
@@ -1,3 +1,4 @@
+import logging
 from typing import Optional, Tuple
 
 import pandas as pd
diff --git a/apis/python/src/tiledbsc/annotation_matrix_group.py b/apis/python/src/tiledbsc/annotation_matrix_group.py
index c00c7e0659..917fc9cabf 100644
--- a/apis/python/src/tiledbsc/annotation_matrix_group.py
+++ b/apis/python/src/tiledbsc/annotation_matrix_group.py
@@ -1,3 +1,4 @@
+import logging
 import os
 from typing import Dict, List, Optional
 
diff --git a/apis/python/src/tiledbsc/annotation_pairwise_matrix_group.py b/apis/python/src/tiledbsc/annotation_pairwise_matrix_group.py
index 3794103e7f..100d79a622 100644
--- a/apis/python/src/tiledbsc/annotation_pairwise_matrix_group.py
+++ b/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 {}
 
diff --git a/apis/python/src/tiledbsc/assay_matrix.py b/apis/python/src/tiledbsc/assay_matrix.py
index 0954876e49..ceb0bdddbd 100644
--- a/apis/python/src/tiledbsc/assay_matrix.py
+++ b/apis/python/src/tiledbsc/assay_matrix.py
@@ -1,3 +1,4 @@
+import logging
 import math
 import time
 from typing import Optional, Tuple, Union
diff --git a/apis/python/src/tiledbsc/io.py b/apis/python/src/tiledbsc/io.py
index 9694146dec..6d7723a3e4 100644
--- a/apis/python/src/tiledbsc/io.py
+++ b/apis/python/src/tiledbsc/io.py
@@ -1,3 +1,5 @@
+import logging
+
 import anndata as ad
 import scanpy
 import tiledb
diff --git a/apis/python/src/tiledbsc/raw_group.py b/apis/python/src/tiledbsc/raw_group.py
index 0f4ec1cc7f..b466bb66ed 100644
--- a/apis/python/src/tiledbsc/raw_group.py
+++ b/apis/python/src/tiledbsc/raw_group.py
@@ -1,3 +1,4 @@
+import logging
 from typing import Optional
 
 import anndata as ad
diff --git a/apis/python/src/tiledbsc/soma.py b/apis/python/src/tiledbsc/soma.py
index d85e6d5db5..64480c4777 100644
--- a/apis/python/src/tiledbsc/soma.py
+++ b/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
diff --git a/apis/python/src/tiledbsc/soma_collection.py b/apis/python/src/tiledbsc/soma_collection.py
index b00908c5a9..fd9554e097 100644
--- a/apis/python/src/tiledbsc/soma_collection.py
+++ b/apis/python/src/tiledbsc/soma_collection.py
@@ -1,3 +1,4 @@
+import logging
 from typing import List, Optional
 
 import tiledb
diff --git a/apis/python/src/tiledbsc/tiledb_group.py b/apis/python/src/tiledbsc/tiledb_group.py
index f8cb9f99fd..1367d24312 100644
--- a/apis/python/src/tiledbsc/tiledb_group.py
+++ b/apis/python/src/tiledbsc/tiledb_group.py
@@ -1,3 +1,4 @@
+import logging
 from typing import Dict, List, Optional
 
 import tiledb
diff --git a/apis/python/src/tiledbsc/tiledb_object.py b/apis/python/src/tiledbsc/tiledb_object.py
index e4b99c7c36..d2e10566e3 100644
--- a/apis/python/src/tiledbsc/tiledb_object.py
+++ b/apis/python/src/tiledbsc/tiledb_object.py
@@ -1,4 +1,3 @@
-import os
 from typing import Dict, List, Optional
 
 import tiledb
diff --git a/apis/python/src/tiledbsc/uns_array.py b/apis/python/src/tiledbsc/uns_array.py
index 9ae919bc1a..fe0fe20ed3 100644
--- a/apis/python/src/tiledbsc/uns_array.py
+++ b/apis/python/src/tiledbsc/uns_array.py
@@ -1,3 +1,4 @@
+import logging
 from typing import Optional
 
 import numpy as np
diff --git a/apis/python/src/tiledbsc/uns_group.py b/apis/python/src/tiledbsc/uns_group.py
index efca287032..4b84321ec2 100644
--- a/apis/python/src/tiledbsc/uns_group.py
+++ b/apis/python/src/tiledbsc/uns_group.py
@@ -1,3 +1,4 @@
+import logging
 import os
 from typing import Dict, List, Optional
 
diff --git a/apis/python/tools/ingestor b/apis/python/tools/ingestor
index c0ff16204d..9858b7f780 100755
--- a/apis/python/tools/ingestor
+++ b/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():
diff --git a/apis/python/tools/outgestor b/apis/python/tools/outgestor
index 6c6d2f4d60..ae55856ffb 100755
--- a/apis/python/tools/outgestor
+++ b/apis/python/tools/outgestor
@@ -16,6 +16,7 @@
 import argparse
 import os
 import sys
+import logging
 
 import tiledb