dayhoff-tools 1.1.27__tar.gz → 1.1.29__tar.gz

{dayhoff_tools-1.1.27 → dayhoff_tools-1.1.29}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.1.27
+Version: 1.1.29
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com
@@ -34,6 +34,7 @@ Requires-Dist: sqlalchemy (>=2.0.40,<3.0.0) ; extra == "full"
 Requires-Dist: toml (>=0.10)
 Requires-Dist: torch (>=2.4.0) ; extra == "embedders"
 Requires-Dist: tqdm (>=4.67.1) ; extra == "embedders"
+Requires-Dist: tqdm (>=4.67.1) ; extra == "full"
 Requires-Dist: transformers (==4.36.2) ; extra == "full"
 Requires-Dist: transformers (>=4.36.2) ; extra == "embedders"
 Requires-Dist: typer (>=0.9.0)

{dayhoff_tools-1.1.27 → dayhoff_tools-1.1.29}/dayhoff_tools/deployment/processors.py

@@ -7,8 +7,6 @@ import subprocess
 from abc import ABC, abstractmethod
 from pathlib import Path
 
-from dayhoff_tools.fasta import subset_fasta
-
 logger = logging.getLogger(__name__)
 
 
@@ -442,9 +440,12 @@ class MMSeqsProfileProcessor(Processor):
                         writer = csv.writer(csvfile)
                         writer.writerow(m8_columns)
                 else:
-                    with open(intermediate_results_m8_file, "r") as m8file, open(
-                        intermediate_results_as_csv_file, "w", newline=""
-                    ) as csvfile:
+                    with (
+                        open(intermediate_results_m8_file, "r") as m8file,
+                        open(
+                            intermediate_results_as_csv_file, "w", newline=""
+                        ) as csvfile,
+                    ):
                         writer = csv.writer(csvfile)
                         writer.writerow(m8_columns)
                         for line in m8file:

{dayhoff_tools-1.1.27 → dayhoff_tools-1.1.29}/dayhoff_tools/fasta.py

@@ -8,7 +8,7 @@ import sqlite3
 import time
 from functools import partial
 from pathlib import Path
-from typing import Any, Dict, Iterator, List, Optional, Set, Tuple, Union
+from typing import Dict, Iterator, List, Optional, Set, Tuple, Union
 
 import requests
 from Bio import SeqIO

{dayhoff_tools-1.1.27 → dayhoff_tools-1.1.29}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "dayhoff-tools"
-version = "1.1.27"
+version = "1.1.29"
 description = "Common tools for all the repos at Dayhoff Labs"
 authors = [
     {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}
@@ -34,6 +34,7 @@ full = [
     "sqlalchemy (>=2.0.40,<3.0.0)",
     "transformers==4.36.2",
     "sentencepiece>=0.2.0",
+    "tqdm>=4.67.1",
 ]
 embedders = [
     "biopython>=1.85",