Merge pull request #203 from d33bs/sqlite-read-performance

SQLite Utils: clean_like_nulls and More!
cytomining · Jun 9, 2022 · 3a69511 · 3a69511
2 parents 02d0522 + 6e9eab4
commit 3a69511
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Showing 6 changed files with 995 additions and 3 deletions.
diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
@@ -7,7 +7,7 @@ on:
   push:
     branches: [ master ]
   pull_request:
-    branches: [ master ]
+    branches: [ master, develop ]
 
 jobs:
   build:

diff --git a/pycytominer/cyto_utils/__init__.py b/pycytominer/cyto_utils/__init__.py
@@ -34,3 +34,12 @@
     aggregate_fields_count,
     aggregate_image_features,
 )
+from .sqlite import (
+    clean_like_nulls,
+    collect_columns,
+    contains_conflicting_aff_storage_class,
+    contains_str_like_null,
+    engine_from_str,
+    update_columns_to_nullable,
+    update_values_like_null_to_null,
+)
diff --git a/pycytominer/cyto_utils/cells.py b/pycytominer/cyto_utils/cells.py
@@ -16,6 +16,7 @@
     extract_image_features,
     aggregate_fields_count,
     aggregate_image_features,
+    engine_from_str,
 )
 
 default_compartments = get_default_compartments()
@@ -148,7 +149,7 @@ def __init__(
             self.set_subsample_n(self.subsample_n)
 
         # Connect to sqlite engine
-        self.engine = create_engine(self.sql_file)
+        self.engine = engine_from_str(self.sql_file)
         self.conn = self.engine.connect()
 
         # Throw an error if both subsample_frac and subsample_n is set