PyEvoMotion 0.1.1__py3-none-any.whl → 0.1.2__py3-none-any.whl

share/run_parallel_analysis.py

@@ -0,0 +1,196 @@
+#!/usr/bin/env python3
+"""
+Parallel execution script for running multiple PyEvoMotion analyses.
+
+This script runs the UK and USA analyses multiple times to assess
+reproducibility and variance due to nonlinear fitting randomness.
+Results are saved in separate subdirectories for each run.
+
+Usage:
+    python run_parallel_analysis.py [batch_name] [num_runs] [max_workers]
+    
+Examples:
+    python run_parallel_analysis.py batch2           # Run batch2 with 5 runs
+    python run_parallel_analysis.py batch3 10        # Run batch3 with 10 runs
+    python run_parallel_analysis.py batch4 5 4       # Run batch4 with 5 runs, max 4 parallel workers
+"""
+
+import os
+import sys
+import subprocess
+from pathlib import Path
+from concurrent.futures import ProcessPoolExecutor, as_completed
+
+
+def run_analysis(country: str, run_number: int, base_output_dir: Path) -> tuple[str, int, bool]:
+    """
+    Run a single PyEvoMotion analysis for UK or USA dataset.
+    
+    :param country: Either "UK" or "USA"
+    :type country: str
+    :param run_number: The run number for this batch
+    :type run_number: int
+    :param base_output_dir: Base directory for output files
+    :type base_output_dir: Path
+    :return: Tuple of (country, run_number, success_status)
+    :rtype: tuple[str, int, bool]
+    """
+    # Create output directory for this specific run
+    output_dir = base_output_dir / f"{country}_run{run_number}"
+    output_dir.mkdir(parents=True, exist_ok=True)
+    
+    # Output file prefix (without extension - PyEvoMotion will add suffixes)
+    output_prefix = output_dir / f"fig{country}"
+    
+    # Build the command
+    cmd = [
+        "PyEvoMotion",
+        f"tests/data/test3/test3{country}.fasta",
+        f"share/figdata{country}.tsv",
+        str(output_prefix),
+        "-k", "total",
+        "-dt", "7D",
+        "-dr", "2020-10-01..2021-08-01",
+        "-ep",
+        "-xj",
+    ]
+    
+    print(f"Starting {country} run {run_number}...")
+    
+    try:
+        # Run the command
+        result = subprocess.run(
+            cmd,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            text=True,
+            check=True
+        )
+        
+        print(f"Completed {country} run {run_number}")
+        
+        # Optionally save stdout/stderr to log files
+        log_file = output_dir / "run.log"
+        with open(log_file, 'w') as f:
+            f.write(f"Command: {' '.join(cmd)}\n")
+            f.write("\n=== STDOUT ===\n")
+            f.write(result.stdout)
+            f.write("\n=== STDERR ===\n")
+            f.write(result.stderr)
+        
+        return (country, run_number, True)
+        
+    except subprocess.CalledProcessError as e:
+        print(f"ERROR in {country} run {run_number}: {e}")
+        
+        # Save error log
+        error_log = output_dir / "error.log"
+        with open(error_log, 'w') as f:
+            f.write(f"Command: {' '.join(cmd)}\n")
+            f.write(f"\nReturn code: {e.returncode}\n")
+            f.write("\n=== STDOUT ===\n")
+            f.write(e.stdout if e.stdout else "No stdout")
+            f.write("\n=== STDERR ===\n")
+            f.write(e.stderr if e.stderr else "No stderr")
+        
+        return (country, run_number, False)
+    except Exception as e:
+        print(f"UNEXPECTED ERROR in {country} run {run_number}: {e}")
+        return (country, run_number, False)
+
+
+def main():
+    """
+    Main execution function for parallel batch analysis.
+    
+    Runs UK and USA PyEvoMotion analyses multiple times in parallel to assess
+    reproducibility. Results are saved to batch subdirectories with configurable
+    parallelism and run counts via command line arguments.
+    """
+    
+    # Parse command line arguments
+    batch_name = sys.argv[1] if len(sys.argv) > 1 else "batch1"
+    num_runs = int(sys.argv[2]) if len(sys.argv) > 2 else 5
+    max_workers = int(sys.argv[3]) if len(sys.argv) > 3 else os.cpu_count()
+    
+    # Configuration
+    NUM_RUNS = num_runs
+    COUNTRIES = ["UK", "USA"]
+    BASE_OUTPUT_DIR = Path(f"share/test-runs/{batch_name}")
+    
+    # Check if directory already exists and warn user
+    if BASE_OUTPUT_DIR.exists():
+        existing_files = list(BASE_OUTPUT_DIR.glob("*"))
+        if existing_files:
+            print(f"WARNING: {BASE_OUTPUT_DIR} already exists with {len(existing_files)} items!")
+            response = input("Continue anyway? This may overwrite existing files. [y/N]: ")
+            if response.lower() != 'y':
+                print("Aborted.")
+                return
+    
+    # Create base output directory
+    BASE_OUTPUT_DIR.mkdir(parents=True, exist_ok=True)
+    print(f"Created output directory: {BASE_OUTPUT_DIR}")
+    print(f"Batch name: {batch_name}")
+    
+    # Generate all tasks (combinations of country and run number)
+    tasks = [
+        (country, run_num)
+        for country in COUNTRIES
+        for run_num in range(1, NUM_RUNS + 1)
+    ]
+    
+    print(f"\nTotal number of tasks: {len(tasks)}")
+    print(f"Running {NUM_RUNS} runs for each of {COUNTRIES}")
+    print(f"Max parallel workers: {max_workers}")
+    print(f"Output will be saved to: {BASE_OUTPUT_DIR}/")
+    print("\nStarting parallel execution...\n")
+    
+    # Run tasks in parallel
+    # Use max_workers to control parallelism (None = number of CPUs)
+    # Adjust this if you want to limit parallel processes
+    
+    results = []
+    with ProcessPoolExecutor(max_workers=max_workers) as executor:
+        # Submit all tasks
+        future_to_task = {
+            executor.submit(run_analysis, country, run_num, BASE_OUTPUT_DIR): (country, run_num)
+            for country, run_num in tasks
+        }
+        
+        # Collect results as they complete
+        for future in as_completed(future_to_task):
+            country, run_num, success = future.result()
+            results.append((country, run_num, success))
+    
+    # Print summary
+    print("\n" + "="*60)
+    print("EXECUTION SUMMARY")
+    print("="*60)
+    
+    successful = [r for r in results if r[2]]
+    failed = [r for r in results if not r[2]]
+    
+    print(f"\nTotal runs: {len(results)}")
+    print(f"Successful: {len(successful)}")
+    print(f"Failed: {len(failed)}")
+    
+    if failed:
+        print("\nFailed runs:")
+        for country, run_num, _ in failed:
+            print(f"  - {country} run {run_num}")
+    
+    print(f"\nAll results saved to: {BASE_OUTPUT_DIR}/")
+    print("\nDirectory structure:")
+    for country in COUNTRIES:
+        for run_num in range(1, NUM_RUNS + 1):
+            run_dir = BASE_OUTPUT_DIR / f"{country}_run{run_num}"
+            status = "✓" if (country, run_num, True) in results else "✗"
+            print(f"  {status} {run_dir}/")
+    
+    print("\n" + "="*60)
+
+
+if __name__ == "__main__":
+    main()
+

pyevomotion-0.1.1.dist-info/RECORD

@@ -1,31 +0,0 @@
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-PyEvoMotion/core/__init__.py,sha256=1I-NkFFh6ljLgB_mqQVFLNvCrVKEHLVxa_5dsv3ihWQ,450
-PyEvoMotion/core/base.py,sha256=0NQ0njPIFn9sL4PdymWE3LYcOmrl3LyCsMDRtAPCRVM,16851
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-PyEvoMotion/utils.py,sha256=Ye3eL1RXZOZzzs2KZy0R45u06DOtLYo-zqE45tN2t7g,2859
-share/anomalous_diffusion.pdf,sha256=yBjHK1dzyx1akaOjmQ8ogWhH1QUWXqCTdUHlXMhtwug,19384
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-share/figdataUSA.tsv,sha256=z5yaIwcyfLo7Wr5ioE-x6_qXg9IhT_CmAJxcLTfP4jA,827811
-share/figure.pdf,sha256=9D2gy7fr-LC52kRfD09aZP8Z8jmY_7K8IhigzIgAK5U,24194
-share/generate_sequences_from_synthdata.py,sha256=_2IdMgcOB7SxAq30iypA-VypSmZyZmMhA8otKQnkfAw,3443
-share/mafft_install.sh,sha256=pCw70UsKkkNXUsZMwQlQ2b4zSXFrBA7jAj9iOfGLzUw,1007
-share/manuscript_figure.py,sha256=G61puV4VjfTgXbokD380aSB0C4Wo9HEJ8y3kw0_Z-TQ,24474
-share/synth_figure.pdf,sha256=2hckyY0Uie16yn3YH5B1LE2lakOJGLzSbF6GHelvSEE,26350
-share/uk_time_windows.pdf,sha256=U1zAMRgZxvfpfMr2ahUqHGYSxPVoDRQTGJSF96NJFck,35022
-share/weekly_size.pdf,sha256=9hn6U8IBWQvZTR8hNLo3r3Kb4hwB7awxlt31_clcHjA,14602
-pyevomotion-0.1.1.dist-info/METADATA,sha256=jgRSgfXK41_APjXUKNA41jggW_bGx9zYxnULz1B1ulQ,7833
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