Reconcile v0.3.5 with changes in branch 0.3.4 (#135)

* Move database connection from `into` to `seed`, close connection

* Update setup.py

* Update setup.cfg

* Update conf.py

* Update setup.py

* bump cfg version

* formatting

---------

Co-authored-by: Beth Cimini <[email protected]>

Author: d33bs

cytominer_database/ingest.py

@@ -47,6 +47,7 @@
 import tempfile
 import sqlalchemy.exc
 from sqlalchemy import create_engine
+from sqlalchemy.pool import NullPool
 
 import cytominer_database.utils
 
@@ -58,7 +59,7 @@ def __format__(name, header):
     return "{}_{}".format(name, header)
 
 
-def into(input, output, name, identifier, skip_table_prefix=False):
+def into(input, output, name, identifier, con, skip_table_prefix=False):
     """Ingest a CSV file into a table in a database.
 
     :param input: Input CSV file.
@@ -132,6 +133,9 @@ def seed(source, target, config_path, skip_image_prefix=True):
     # list the subdirectories that contain CSV files
     directories = sorted(list(cytominer_database.utils.find_directories(source)))
 
+    engine = create_engine(target, poolclass=NullPool)
+    con = engine.connect()
+    
     for directory in directories:
         # get the image CSV and the CSVs for each of the compartments
         try:
@@ -158,7 +162,8 @@ def seed(source, target, config_path, skip_image_prefix=True):
                 output=target,
                 name=name.capitalize(),
                 identifier=identifier,
-                skip_table_prefix=skip_image_prefix,
+                con=con,
+                skip_table_prefix=skip_image_prefix
             )
         except sqlalchemy.exc.DatabaseError as e:
             click.echo(e)
@@ -173,4 +178,6 @@ def seed(source, target, config_path, skip_image_prefix=True):
                 output=target,
                 name=name.capitalize(),
                 identifier=identifier,
+                con=con
             )
+    con.close()

setup.cfg

@@ -11,4 +11,4 @@ testpaths =
 
 [build_sphinx]
 project = 'cytominer_database'
-version = 0.3.3
+version = 0.3.5