Ruff check and format

dscript/commands/evaluate.py

@@ -26,8 +26,8 @@ from tqdm import tqdm
 
 from dscript.loading import LoadingPool
 
-from ..utils import log
 from ..fasta import parse_dict
+from ..utils import log
 
 matplotlib.use("Agg")
 

dscript/fasta.py

@@ -1,8 +1,9 @@
 import os
 
-from loguru import logger
-from biotite.sequence.io import fasta
 from biotite import InvalidFileError
+from biotite.sequence.io import fasta
+from loguru import logger
+
 
 def parse_dict(f: str):
     """
@@ -24,6 +25,7 @@ def parse_dict(f: str):
 
     return seq_dict
 
+
 def parse(f: str):
     """
     Parse a FASTA file and return a tuple of sequence names and sequences.
@@ -78,7 +80,7 @@ def parse_directory(directory, extension=".seq"):
         - list of str: Sequences.
     :rtype: (list of str, list of str)
     """
-    
+
     names = []
     sequences = []
 

dscript/tests/test_language_model.py

@@ -1,16 +1,15 @@
 import os
 import shutil
-from sre_parse import parse
 import subprocess as sp
 import tempfile
 
 from loguru import logger
 
+from dscript.fasta import parse
 from dscript.language_model import (
     embed_from_fasta,
     lm_embed,
 )
-from dscript.fasta import parse
 
 
 class TestLanguageModel: