Store position attribute as Array type

The list of position attributes has now been replaced with a single
attribute, which can be an Array. Postgre will store the array directly,
SQLite will create one column for each element.

This commit also tightens the requirements for optional arguments
passed to the graph databases and simplifies the meta-data checks.

There is now also documentation on the allowed read/write modes and
checks for the passed arguments.

funlib/persistence/graphs/pgsql_graph_database.py

@@ -14,7 +14,7 @@
 class PgSQLGraphDatabase(SQLGraphDataBase):
     def __init__(
         self,
-        position_attributes: list[str],
+        position_attribute: str,
         db_name: str,
         db_host: str = "localhost",
         db_user: Optional[str] = None,
@@ -62,8 +62,8 @@ def __init__(
         self.cur = self.connection.cursor()
 
         super().__init__(
-            position_attributes,
             mode=mode,
+            position_attribute=position_attribute,
             directed=directed,
             total_roi=total_roi,
             nodes_table=nodes_table,
@@ -86,10 +86,8 @@ def _drop_tables(self) -> None:
         self._commit()
 
     def _create_tables(self) -> None:
-        columns = self.position_attributes + list(self.node_attrs.keys())
-        types = [self.__sql_type(float) + " NOT NULL"] * len(
-            self.position_attributes
-        ) + list([self.__sql_type(t) for t in self.node_attrs.values()])
+        columns = self.node_attrs.keys()
+        types = [self.__sql_type(t) for t in self.node_attrs.values()]
         column_types = [f"{c} {t}" for c, t in zip(columns, types)]
         self.__exec(
             f"CREATE TABLE IF NOT EXISTS "
@@ -100,7 +98,7 @@ def _create_tables(self) -> None:
         )
         self.__exec(
             f"CREATE INDEX IF NOT EXISTS pos_index ON "
-            f"{self.nodes_table_name}({','.join(self.position_attributes)})"
+            f"{self.nodes_table_name}({self.position_attribute})"
         )
 
         columns = list(self.edge_attrs.keys())
@@ -139,6 +137,7 @@ def _read_metadata(self) -> Optional[dict[str, Any]]:
         return None
 
     def _select_query(self, query) -> Iterable[Any]:
+        print(query)
         self.__exec(query)
         return self.cur