Swap black and isort for ruff

.pre-commit-config.yaml

@@ -13,15 +13,11 @@ repos:
       - id: check-toml
       - id: check-json
       - id: check-added-large-files
-  - repo: local
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.4.4
     hooks:
-      - id: black
-        name: black
-        entry: poetry run black
-        language: system
-        types: [file, python]
-      - id: isort
-        name: isort
-        entry: poetry run isort
-        language: system
-        types: [file, python]
+      # Run the linter.
+      - id: ruff
+      # Run the formatter.
+      - id: ruff-format

pyproject.toml

@@ -16,10 +16,7 @@ agr-blast-service-configuration = {git = "https://github.com/alliance-genome/agr
 typer = "^0.12.3"
 biopython = "^1.83"
 tqdm = "^4.66.4"
-
-[tool.poetry.group.dev.dependencies]
-black = "^24.4.2"
-isort = "^5.13.2"
+ruff = "^0.4.4"
 
 [build-system]
 requires = ["poetry-core"]

src/blast_db_configuration/__main__.py

@@ -105,7 +105,7 @@ def generate(
         desc="Processing organisms",
         unit="organism",
     ):
-        logger.debug(f"Processing %s %s", genus, species)
+        logger.debug("Processing %s %s", genus, species)
         if genus == "Drosophila" and species == "melanogaster":
             all_dbs.extend(create_dmel_metadata(dmel_annot_release))
         else:

src/blast_db_configuration/db_metadata.py

@@ -1,6 +1,5 @@
 import logging
 import urllib.request
-from typing import Optional
 
 import agr_blast_service_configuration.schemas.metadata as blast_metadata_schema
 

src/blast_db_configuration/ncbi/genomes.py

@@ -1,7 +1,6 @@
 import ftplib
 import logging
 import re
-import urllib.error
 from pathlib import Path
 from functools import cache
 from ftplib import FTP
@@ -56,7 +55,7 @@ def get_current_genome_assembly_files(
     :param file_regex: Regular expression to match files (default: None)
     :return: Tuple of (genome assembly directory, genome assembly file, md5 checksum file)
     """
-    if type(organism_group) is str:
+    if isinstance(organism_group, str):
         organism_group = OrganismGroup(organism_group)
 
     path = f"/genomes/refseq/{organism_group}/{genus}_{species.replace(' ', '_')}/latest_assembly_versions"

src/blast_db_configuration/ncbi/taxonomy.py

@@ -15,7 +15,7 @@ def get_taxonomy_id(genus: str, species: str) -> Optional[int]:
     :return: NCBI taxonomy ID.
     """
     try:
-        logger.debug(f"Searching for %s %s", genus, species)
+        logger.debug("Searching for %s %s", genus, species)
         handle = Entrez.esearch(db="taxonomy", term=f"{genus} {species}[SCIN]")
         record = Entrez.read(handle)
         num_results = int(record["Count"])