Merge pull request #26 from Ensembl/jalvarez/bugfixes

Several bugfixes following the latest additions and better testing

src/ensembl/utils/__init__.py

@@ -14,7 +14,7 @@
 # limitations under the License.
 """Ensembl Python general-purpose utils library."""
 
-__version__ = "0.4.4"
+__version__ = "0.5.0"
 
 __all__ = [
     "StrPath",

src/ensembl/utils/database/unittestdb.py

@@ -126,17 +126,16 @@ def _load_schema_and_data(
 
             # Load the schema
             if metadata:
-                self.dbc.create_all_tables(metadata)
+                metadata.create_all(conn)
             elif dump_dir:
-                dump_dir_path = Path(dump_dir)
-                with open(dump_dir_path / "table.sql", "r") as schema:
+                with Path(dump_dir, "table.sql").open("r") as schema:
                     for query in "".join(schema.readlines()).split(";"):
                         if query.strip():
                             conn.execute(text(query))
 
             # And import any available data for each table
             if dump_dir:
-                for tsv_file in dump_dir_path.glob("*.txt"):
+                for tsv_file in Path(dump_dir).glob("*.txt"):
                     table = tsv_file.stem
                     self._load_data(conn, table, tsv_file)
 

src/ensembl/utils/plugin.py

@@ -190,7 +190,9 @@ def test_method(..., test_dbs: dict[str, UnitTestDB], ...):
     """
     databases = {}
     for argument in request.param:
-        src = Path(argument["src"])
+        src = argument.get("src", None)
+        if src is not None:
+            src = Path(src)
         name = argument.get("name", None)
         key = name if name else src.name
         databases[key] = db_factory(src=src, name=name, metadata=argument.get("metadata"))