Refactored code layout

tests/automlst/engine/local/test_abif.py

@@ -1,12 +1,8 @@
 import os
 
-from automlst.engine.local.abif import read_abif, reference_consensus_assembly
+from automlst.engine.data.local.abif import read_abif
 
 async def test_load_sanger_sequence_has_data():
     assert os.path.exists("tests/resources/1I1_F_P1815443_047.ab1")
     result_data = await read_abif("tests/resources/1I1_F_P1815443_047.ab1")
     assert result_data is not None
-
-async def test_consensus_assembly_with_ncbi():
-    consensus = reference_consensus_assembly("ON685494.1", [await read_abif("tests/resources/1I1_F_P1815443_047.ab1"), await read_abif("tests/resources/1I1_R_P1815443_094.ab1")])
-    # TODO complete implementing this

tests/automlst/engine/remote/databases/ncbi/test_genbank.py

@@ -1,5 +0,0 @@
-from automlst.engine.remote.databases.ncbi.genbank import fetch_ncbi_genbank
-
-
-async def test_fetch_ncbi_genbank_with_id_works():
-    assert len((await fetch_ncbi_genbank("CP011448.1")).sequence) > 0 

tests/automlst/engine/remote/databases/test_bigsdb.py

@@ -3,10 +3,10 @@ import re
 from typing import Collection, Sequence, Union
 from Bio import SeqIO
 import pytest
-from automlst.engine.data.genomics import NamedString
-from automlst.engine.data.mlst import Allele, MLSTProfile
+from automlst.engine.data.structures.genomics import NamedString
+from automlst.engine.data.structures.mlst import Allele, MLSTProfile
 from automlst.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException
-from automlst.engine.remote.databases.bigsdb import BIGSdbIndex, BIGSdbMLSTProfiler
+from automlst.engine.data.remote.databases.bigsdb import BIGSdbIndex, BIGSdbMLSTProfiler
 
 def gene_scrambler(gene: str, mutation_site_count: Union[int, float], alphabet: Sequence[str] = ["A", "T", "C", "G"]):
     rand = random.Random(gene)