Update sqlalchemy version

- Updates implicitly converted scalar queries in orf and junctions.
- Removes "threadlocal" strategy from the engine connection parameters in xml_serialiser.py as this is not supported.

Fixes #388

Mikado/serializers/blast_serializer/xml_serialiser.py

@@ -30,7 +30,7 @@ def xml_pickler(configuration, filename, default_header,
                 cache=None,
                 max_target_seqs=10):
     valid, _, exc = BlastOpener(filename).sniff(default_header=default_header)
-    engine = connect(configuration, strategy="threadlocal")
+    engine = connect(configuration)
     session = Session(bind=engine)
 
     if not valid:

Mikado/serializers/junction.py

@@ -75,7 +75,7 @@ class Junction(DBBASE):
         "junction_index", "chrom_id", "junction_start", "junction_end"), {"extend_existing": True})
 
     chrom_object = relationship(Chrom, uselist=False)
-    chrom = column_property(select([Chrom.name]).where(chrom_id == Chrom.chrom_id))
+    chrom = column_property(select([Chrom.name]).where(chrom_id == Chrom.chrom_id).scalar_subquery())
 
     def __init__(self, junction_start, junction_end, name, strand, score, chrom_id):
         """

Mikado/serializers/orf.py

@@ -60,7 +60,7 @@ class Orf(DBBASE):
                                 backref=backref("orfs"), lazy="joined", innerjoin=True)
 
     query = column_property(select([Query.query_name]).where(
-        Query.query_id == query_id))
+        Query.query_id == query_id).scalar_subquery())
 
     def __init__(self, bed12_object, query_id):
         if not isinstance(bed12_object, bed12.BED12):

requirements.txt

@@ -12,8 +12,8 @@ pysam>=0.15.3
 pyyaml>=5.1.2
 scipy>=1.3.1
 snakemake>=5.7.0
-sqlalchemy>=1.3.9,<1.4.0
-sqlalchemy-utils>=0.34.1
+sqlalchemy>=1.4.0
+sqlalchemy-utils>=0.37
 tabulate>=0.8.5
 pytest>=5.4.1
 python-rapidjson>=1.0.0