Added additional test for fully automatic typing based on sequence

src/automlst/cli/aggregated.py

@@ -1,6 +1,6 @@
 from os import path
 from typing import Any, AsyncGenerator, AsyncIterable, Iterable, Sequence
-from automlst.engine.data.MLST import MLSTProfile
+from automlst.engine.data.mlst import MLSTProfile
 from automlst.engine.data.genomics import NamedString
 from automlst.engine.local.abif import read_abif
 from automlst.engine.local.fasta import read_fasta

src/automlst/engine/local/csv.py

@@ -3,7 +3,7 @@ from io import TextIOWrapper
 from os import PathLike
 from typing import AsyncIterable, Iterable, Mapping, Sequence, Union
 
-from automlst.engine.data.MLST import Allele, MLSTProfile
+from automlst.engine.data.mlst import Allele, MLSTProfile
 
 
 def loci_alleles_variants_from_loci(alleles_map: Mapping[str, Sequence[Allele]]):

src/automlst/engine/remote/databases/institutpasteur/mlst.py

@@ -3,7 +3,7 @@ from contextlib import AbstractAsyncContextManager
 import re
 from typing import Any, AsyncGenerator, AsyncIterable, Generator, Iterable, Sequence, Union
 from aiohttp import ClientSession, ClientTimeout
-from automlst.engine.data.MLST import Allele, MLSTProfile
+from automlst.engine.data.mlst import Allele, MLSTProfile
 from automlst.engine.data.genomics import NamedString
 
 class InstitutPasteurProfiler(AbstractAsyncContextManager):

src/automlst/engine/remote/databases/mlst.py

@@ -4,7 +4,7 @@ from typing import AsyncGenerator, AsyncIterable, Generator, Iterable, Mapping,
 
 from aiohttp import ClientSession
 
-from automlst.engine.data.MLST import Allele, MLSTProfile
+from automlst.engine.data.mlst import Allele, MLSTProfile
 
 MLST_DATABASES = [
     "https://bigsdb.pasteur.fr/api/db",

src/automlst/engine/remote/databases/pubmlst/mlst.py

@@ -3,7 +3,7 @@ from contextlib import AbstractAsyncContextManager
 import re
 from typing import Any, AsyncGenerator, AsyncIterable, Generator, Iterable, Mapping, Sequence, Union
 from aiohttp import ClientSession, ClientTimeout
-from automlst.engine.data.MLST import Allele, MLSTProfile
+from automlst.engine.data.mlst import Allele, MLSTProfile
 from automlst.engine.data.genomics import NamedString
 from automlst.engine.remote.databases.mlst import MLSTProfiler