Move to pandas>=2 and sqlalchemy>=2

pyproject.toml

@@ -1,3 +1,6 @@
+[project]
+name = "dwclib"
+
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
@@ -14,10 +17,10 @@ repository = "https://github.com/larib-data/dwclib"
 [tool.poetry.dependencies]
 python = ">=3.8,<4"
 numpy = "^1"
-pandas = ">=1.4,<3"
+pandas = ">=2.2.0"
 dask = ">=2023"
-SQLAlchemy = "~1.4"
-platformdirs = "^3.0.0"
+SQLAlchemy = ">=2.0.25"
+platformdirs = ">=4.2.0"
 
 [tool.poetry.dev-dependencies]
 flake8 = "^4.0.1"

src/dwclib/alerts/alerts.py

@@ -45,8 +45,8 @@ def run_alerts_query(
 
 
 def build_alerts_query(engine, dtbegin, dtend, patientids):
-    dbmeta = MetaData(bind=engine)
-    at = Table('Alert_', dbmeta, schema='_Export', autoload=True, autoload_with=engine)
+    dbmeta = MetaData()
+    at = Table('Alert_', dbmeta, schema='_Export', autoload_with=engine)
 
     aq = select(
         at.c.AlertId,

src/dwclib/common/numerics.py

@@ -30,12 +30,12 @@ def run_numerics_query(
 
 
 def build_numerics_query(engine, dtbegin, dtend, patientids, labels, sublabels):
-    dbmeta = MetaData(bind=engine)
+    dbmeta = MetaData()
     nnt = Table(
-        'Numeric_', dbmeta, schema='_Export', autoload=True, autoload_with=engine
+        'Numeric_', dbmeta, schema='_Export', autoload_with=engine
     )
     nvt = Table(
-        'NumericValue_', dbmeta, schema='_Export', autoload=True, autoload_with=engine
+        'NumericValue_', dbmeta, schema='_Export', autoload_with=engine
     )
 
     nn = select(nnt.c.TimeStamp, nnt.c.Id, nnt.c.Label, nnt.c.SubLabel)

src/dwclib/common/waves.py

@@ -19,10 +19,10 @@ def run_waves_query(uri, dtbegin, dtend, patientid, labels):
 
 
 def build_waves_query(engine, dtbegin, dtend, patientid, labels):
-    dbmeta = MetaData(bind=engine)
-    wwt = Table('Wave_', dbmeta, schema='_Export', autoload=True, autoload_with=engine)
+    dbmeta = MetaData()
+    wwt = Table('Wave_', dbmeta, schema='_Export', autoload_with=engine)
     wst = Table(
-        'WaveSample_', dbmeta, schema='_Export', autoload=True, autoload_with=engine
+        'WaveSample_', dbmeta, schema='_Export', autoload_with=engine
     )
 
     ww = select(

src/dwclib/enumerations/enumerations.py

@@ -66,9 +66,9 @@ def run_enumerations_query(
 
 
 def build_enumerations_query(engine, dtbegin, dtend, patientids, labels):
-    dbmeta = MetaData(bind=engine)
-    eet = Table('Enumeration_', dbmeta, schema='_Export', autoload=True, autoload_with=engine)
-    evt = Table('EnumerationValue_', dbmeta, schema='_Export', autoload=True, autoload_with=engine)
+    dbmeta = MetaData()
+    eet = Table('Enumeration_', dbmeta, schema='_Export', autoload_with=engine)
+    evt = Table('EnumerationValue_', dbmeta, schema='_Export', autoload_with=engine)
 
     ee = select(eet.c.TimeStamp, eet.c.Id, eet.c.Label)
     ee = ee.with_hint(eet, 'WITH (NOLOCK)')

src/dwclib/patients/patients.py

@@ -113,7 +113,7 @@ def build_query(
     numericsublabels,
 ):
     pgdb = create_engine(uri)
-    pgmeta = MetaData(bind=pgdb)
+    pgmeta = MetaData()
 
     t_patients = Table('patients', pgmeta, autoload_with=pgdb)
     p = t_patients.c
@@ -136,7 +136,7 @@ def build_query(
         t_patients = select(fields).cte()  # Replace Patients table with CTE
         p = t_patients.c
 
-    q = select([t_patients, pl.numericlabels, pl.numericsublabels, pl.wavelabels])
+    q = select(t_patients, pl.numericlabels, pl.numericsublabels, pl.wavelabels)
     q = q.select_from(t_patients.join(t_patientlabels, pl.patientid == p.patientid, isouter=True))
     if patientid:
         q = q.where(p.patientid == patientid)