add integration test

Author: Laurenz0908

.gitignore

@@ -2,3 +2,5 @@ build/
 guacamole.egg-info/
 dist/
 guacamole_bio.egg-info/
+__pycache__/
+tests/test_out_pytest/

tests/test_integration.py

@@ -0,0 +1,94 @@
+import pytest
+import subprocess
+import os
+import shutil
+import pandas as pd
+import numpy as np
+import bz2
+import sys
+
+@pytest.fixture(scope="module")
+def demo_env():
+    """
+    Sets up the test environment
+    """
+    project_root = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+    demo_dir = os.path.join(project_root, "demo_data")
+    out_dir = os.path.join(project_root, "tests/test_out_pytest")
+
+    if os.path.exists(out_dir):
+        shutil.rmtree(out_dir)
+    os.makedirs(out_dir)
+
+    files_to_decompress = [
+        "SRR12996245.1pct.kraken",
+        "SRR12996245.1pct_1.fastq",
+        "SRR12996245.1pct_2.fastq"
+    ]
+
+    print(f"\n[Setup] Preparing test data in {out_dir}...")
+
+    for filename in files_to_decompress:
+        source_bz2 = os.path.join(demo_dir, filename + ".bz2")
+        dest_file = os.path.join(out_dir, filename)
+        
+        if os.path.exists(source_bz2):
+            with bz2.open(source_bz2, "rb") as f_in, open(dest_file, "wb") as f_out:
+                shutil.copyfileobj(f_in, f_out)
+        else:
+            pytest.fail(f"Required source file missing: {source_bz2}")
+
+    # Yield paths so the test function knows where things are
+    yield {'out': out_dir, 'demo': demo_dir}
+
+def test_guacamole_metrics(demo_env):
+    """
+    Runs guacamole and asserts efficiency and abundance ranges.
+    """
+    out_dir = demo_env['out']
+    demo_dir = demo_env['demo']
+    output_file_name = "SRR12996245.1pct.guaca"
+
+    # Construct command
+    cmd = [
+        sys.executable, "-m", "guacamole.guacamole",
+        "--output", output_file_name,
+        "--kraken_report", os.path.join(demo_dir, "SRR12996245.1pct_report.txt"),
+        "--kraken_file", os.path.join(out_dir, "SRR12996245.1pct.kraken"),
+        "--read_files", os.path.join(out_dir, "SRR12996245.1pct_1.fastq"), os.path.join(out_dir, "SRR12996245.1pct_2.fastq"),
+        "--kraken_db", os.path.join(demo_dir, "demo_db"),
+        "--read_len", "150",
+        "--fragment_len", "400",
+        "--length_correction", "True",
+        "--threshold", "5",
+        "--plot", "False"
+    ]
+
+    # Run Guacamole
+    result = subprocess.run(
+        cmd, cwd=out_dir, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True
+    )
+    
+    # Assert successful run
+    assert result.returncode == 0, f"Command failed with stderr: {result.stderr}"
+
+    # 1. Check Efficiencies (50% - 70%)
+    eff_path = os.path.join(out_dir, "efficiencies.txt")
+    assert os.path.exists(eff_path), "efficiencies.txt was not created"
+    
+    efficiencies = np.loadtxt(eff_path)
+    max_eff = np.argmax(efficiencies)
+    
+    assert 20 <= max_eff <= 30, f"Max efficiency {max_eff:.2f} is out of range [20, 30]"
+
+    # 2. Check Abundances (4% - 12%)
+    guaca_path = os.path.join(out_dir, output_file_name)
+    assert os.path.exists(guaca_path), f"{output_file_name} was not created"
+
+    df = pd.read_csv(guaca_path, sep="\t")
+    abundances = df['GuaCAMOLE_estimate']
+
+    # Vectorized check (faster and cleaner than a loop)
+    assert (np.sum(abundances) == pytest.approx(1.0, abs=0.01)), f"Sum of abundances is not 1: {np.sum(abundances)}"
+    assert (abundances >= 0.03).all(), f"Some abundances are < 4%:\n{df[abundances < 0.04]}"
+    assert (abundances <= 0.12).all(), f"Some abundances are > 12%:\n{df[abundances > 0.12]}"