From Black to Ruff

.pre-commit-config.yaml

@@ -1,11 +1,7 @@
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
-    hooks:
-    -   id: check-yaml
-    -   id: end-of-file-fixer
-    -   id: trailing-whitespace
--   repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-    -   id: black
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.4
+  hooks:
+    - id: ruff
+      args: [ --fix ]
+    - id: ruff-format

README.md

@@ -264,5 +264,6 @@ cd hostile
 conda env create -y -f environment.yml
 conda activate hostile
 pip install --editable '.[dev]'
+pre-commit install
 pytest
 ```

src/hostile/__init__.py

@@ -1,2 +1,3 @@
 """Accurate host read removal"""
+
 __version__ = "1.1.0"

src/hostile/aligner.py

@@ -112,7 +112,7 @@ def gen_clean_cmd(
         count_after_path = out_dir / f"{fastq_stem}.reads_out.txt"
         if not force and fastq_out_path.exists():
             raise FileExistsError(
-                f"Output file already exists. Use --force to overwrite"
+                "Output file already exists. Use --force to overwrite"
             )
         filter_cmd = " | samtools view -hF 4 -" if invert else " | samtools view -f 4 -"
         reorder_cmd = " | samtools sort -n -O sam -@ 6 -m 1G" if reorder else ""
@@ -175,7 +175,7 @@ def gen_paired_clean_cmd(
         count_after_path = out_dir / f"{fastq1_stem}.reads_out.txt"
         if not force and (fastq1_out_path.exists() or fastq2_out_path.exists()):
             raise FileExistsError(
-                f"Output files already exist. Use --force to overwrite"
+                "Output files already exist. Use --force to overwrite"
             )
         filter_cmd = (
             " | samtools view -hF 12 -" if invert else " | samtools view -f 12 -"

src/hostile/util.py

@@ -31,7 +31,7 @@ def choose_default_thread_count(cpu_count: int) -> int:
 
 CWD = Path.cwd()
 CACHE_DIR = (
-    Path(os.environ.get("HOSTILE_CACHE_DIR"))
+    Path(os.environ.get("HOSTILE_CACHE_DIR", ""))
     if os.environ.get("HOSTILE_CACHE_DIR")
     else Path(user_data_dir("hostile", "Bede Constantinides"))
 )

tests/test_all.py

@@ -284,7 +284,7 @@ def test_paired_rename():
 
 def test_with_and_without_force():
     shutil.rmtree(out_dir, ignore_errors=True)
-    stats = lib.clean_paired_fastqs(
+    lib.clean_paired_fastqs(
         fastqs=[
             (
                 data_dir / "tuberculosis_1_2.fastq.gz",
@@ -297,7 +297,7 @@ def test_with_and_without_force():
         out_dir=out_dir,
     )
     with pytest.raises(FileExistsError):
-        stats = lib.clean_paired_fastqs(
+        lib.clean_paired_fastqs(
             fastqs=[
                 (
                     data_dir / "tuberculosis_1_2.fastq.gz",
@@ -313,7 +313,7 @@ def test_with_and_without_force():
 
 
 def test_no_rename():
-    stats = lib.clean_paired_fastqs(
+    lib.clean_paired_fastqs(
         fastqs=[
             (
                 data_dir / "tuberculosis_1_2.fastq.gz",
@@ -334,7 +334,7 @@ def test_no_rename():
 
 def test_broken_fastq_path():
     with pytest.raises(FileNotFoundError):
-        stats = lib.clean_fastqs(
+        lib.clean_fastqs(
             fastqs=[Path("invalid_path.fastq.gz")],
             aligner=lib.ALIGNER.bowtie2,
             index=data_dir / "sars-cov-2/sars-cov-2",
@@ -603,7 +603,7 @@ def test_invert_paired_2():
 
 
 def test_minimap2_reordering_linux():
-    stats = lib.clean_paired_fastqs(
+    lib.clean_paired_fastqs(
         fastqs=[
             (
                 data_dir / "sars-cov-2_1_1.fastq",
@@ -676,6 +676,7 @@ def test_fixing_empty_fastqs_single():
         force=True,
     )
     run(f"gzip -dc {stats[0]['fastq1_out_path']}")
+    shutil.rmtree(out_dir, ignore_errors=True)
 
 
 def test_fixing_empty_fastqs_paired():
@@ -699,7 +700,7 @@ def test_fixing_empty_fastqs_paired():
 def test_mismatched_number_of_reads_bowtie2():
     """This has caused sinister errors in the wild, yet is handled gracefully here"""
     with pytest.raises(subprocess.CalledProcessError):
-        stats = lib.clean_paired_fastqs(
+        lib.clean_paired_fastqs(
             fastqs=[
                 (
                     data_dir / "sars-cov-2_100_1.fastq.gz",
@@ -711,15 +712,15 @@ def test_mismatched_number_of_reads_bowtie2():
             out_dir=out_dir,
             force=True,
         )
-        shutil.rmtree(out_dir, ignore_errors=True)
+    shutil.rmtree(out_dir, ignore_errors=True)
 
 
 def test_offline_invalid_standard_index_name():
     with pytest.raises(FileNotFoundError):
-        stats = lib.clean_fastqs(
+        lib.clean_fastqs(
             fastqs=[data_dir / "sars-cov-2_1_1.fastq"],
             index="invalid_index_name",
             out_dir=out_dir,
             offline=True,
         )
-        shutil.rmtree(out_dir, ignore_errors=True)
+    shutil.rmtree(out_dir, ignore_errors=True)