checks

Author: telatin

run_checks.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+set -e
+
+echo "================================"
+echo "Running code quality checks..."
+echo "================================"
+echo ""
+
+echo "📝 Checking code formatting with black..."
+black --check src/ tests/
+echo "✓ Black formatting check passed"
+echo ""
+
+echo "🔍 Linting code with ruff..."
+ruff check src/ tests/
+echo "✓ Ruff linting passed"
+echo ""
+
+echo "🧪 Running tests with coverage..."
+pytest --cov=votuderep --cov-report=term-missing --cov-report=xml -v
+echo "✓ All tests passed"
+echo ""
+
+echo "================================"
+echo "✅ All checks passed!"
+echo "================================"

src/votuderep/cli.py

@@ -1,7 +1,6 @@
 """Main CLI interface for votuderep using rich-click."""
 
 import sys
-from typing import Optional
 
 import rich_click as click
 from rich.console import Console

src/votuderep/commands/derep.py

@@ -3,7 +3,6 @@
 import os
 import shutil
 import tempfile
-from pathlib import Path
 
 import rich_click as click
 from rich.console import Console
@@ -179,7 +178,7 @@ def derep(
             progress.update(task4, completed=True)
 
         # Success message
-        console.print(f"\n[bold green]Success![/bold green]")
+        console.print("\n[bold green]Success![/bold green]")
         console.print(f"Wrote {num_written} dereplicated sequences to: [bold]{output}[/bold]")
 
         if keep:

src/votuderep/commands/filter.py

@@ -1,7 +1,5 @@
 """Filter command for filtering FASTA files using CheckV metrics."""
 
-import sys
-
 import rich_click as click
 from rich.console import Console
 
@@ -145,7 +143,7 @@ def filter_cmd(
         )
 
         # Success message (to stderr so it doesn't interfere with stdout output)
-        console.print(f"\n[bold green]Success![/bold green]")
+        console.print("\n[bold green]Success![/bold green]")
         console.print(f"Filtered {num_written} sequences")
 
         if output:

src/votuderep/core/__pycache__/blast.cpython-310.pyc

@@ -1,8 +1,6 @@
 """BLAST operations for vOTU dereplication."""
 
 import subprocess
-from pathlib import Path
-from typing import Optional
 
 from ..utils.logging import get_logger
 from ..utils.validators import VotuDerepError

src/votuderep/core/__pycache__/dereplication.cpython-310.pyc

@@ -1,10 +1,8 @@
 """ANI calculation and clustering for vOTU dereplication."""
 
 import gzip
-from pathlib import Path
 from typing import Iterator, Dict, List, Tuple, Set
 
-import numpy as np
 
 from ..utils.logging import get_logger
 from ..utils.io import read_fasta
@@ -259,8 +257,7 @@ def cluster_by_ani(
         for line in handle:
             fields = line.strip().split("\t")
             qname, tname = fields[0], fields[1]
-            num_alns, ani, qcov, tcov = (
-                int(fields[2]),
+            ani, qcov, tcov = (
                 float(fields[3]),
                 float(fields[4]),
                 float(fields[5]),

src/votuderep/core/__pycache__/filtering.cpython-310.pyc

@@ -1,6 +1,5 @@
 """Filtering sequences based on CheckV quality metrics."""
 
-from pathlib import Path
 from typing import Set, Optional
 
 import pandas as pd