build(deps): bump sqlalchemy from 1.4.52 to 2.0.36; move to sqlalchem…

…y.text for queries (#469)

* build(deps): bump sqlalchemy from 1.4.52 to 2.0.36

Bumps [sqlalchemy](https://github.com/sqlalchemy/sqlalchemy) from 1.4.52 to 2.0.36.
- [Release notes](https://github.com/sqlalchemy/sqlalchemy/releases)
- [Changelog](https://github.com/sqlalchemy/sqlalchemy/blob/main/CHANGES.rst)
- [Commits](https://github.com/sqlalchemy/sqlalchemy/commits)

---
updated-dependencies:
- dependency-name: sqlalchemy
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

* use sqlalchemy.text for queries

* remove sqlalchemy uber warning

Co-Authored-By: Ken Brewer <kenibrewer@users.noreply.github.com>

* reupdate lockfile

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: d33bs <dave.bunten@cuanschutz.edu>
Co-authored-by: Ken Brewer <kenibrewer@users.noreply.github.com>

.github/workflows/integration-test.yml

@@ -91,10 +91,6 @@ jobs:
     runs-on: ${{ matrix.os }}
     env:
       OS: ${{ matrix.os }}
-      # This is needed to avoid a warning from SQLAlchemy
-      # https://sqlalche.me/e/b8d9
-      # We can remove this once we upgrade to SQLAlchemy >= 2.0
-      SQLALCHEMY_SILENCE_UBER_WARNING: "1"
     if: github.event_name != 'schedule'
     steps:
       - name: Checkout repo

pycytominer/cyto_utils/cells.py

@@ -18,7 +18,7 @@
     output,
     provide_linking_cols_feature_name_update,
 )
-from sqlalchemy import create_engine
+from sqlalchemy import create_engine, text
 
 default_compartments = get_default_compartments()
 default_linking_cols = get_default_linking_cols()
@@ -420,12 +420,12 @@ def get_subsample(self, df=None, compartment="cells", rename_col=True):
 
     def count_sql_table_rows(self, table):
         """Count total number of rows for a table."""
-        (num_rows,) = next(self.conn.execute(f"SELECT COUNT(*) FROM {table}"))
+        (num_rows,) = next(self.conn.execute(text(f"SELECT COUNT(*) FROM {table}")))
         return num_rows
 
     def get_sql_table_col_names(self, table):
         """Get column names from the database."""
-        ptr = self.conn.execute(f"SELECT * FROM {table} LIMIT 1").cursor
+        ptr = self.conn.execute(text(f"SELECT * FROM {table} LIMIT 1")).cursor
         col_names = [obj[0] for obj in ptr.description]
 
         return col_names
@@ -476,8 +476,7 @@ def load_compartment(self, compartment):
 
         # Query database for selected columns of chosen compartment
         columns = ", ".join(meta_cols + feat_cols)
-        query = f"select {columns} from {compartment}"
-        query_result = self.conn.execute(query)
+        query_result = self.conn.execute(text(f"select {columns} from {compartment}"))
 
         # Load data row by row for both meta information and features
         for i, row in enumerate(query_result):

pyproject.toml

@@ -51,7 +51,7 @@ numpy = ">=1.16.5"
 scipy = ">=1.5"
 pandas = ">=1.2.0"
 scikit-learn = ">=0.21.2"
-sqlalchemy = ">=1.3.6, <2"
+sqlalchemy = ">=1.3.6,<3"
 pyarrow = ">=8.0.0"
 
 # Extra dependencies for cell_locations