"""
Main analysis script for code metrics analysis project.
Orchestrates data collection, analysis, and visualization.
"""
import pandas as pd
import numpy as np
import json
from pathlib import Path
from typing import Optional, Dict
from concurrent.futures import ThreadPoolExecutor, as_completed
from github_client import GitHubClient
from code_analyzer import CodeAnalyzer
from data_collector import DataCollector
from statistical_analysis import StatisticalAnalyzer
from visualizer import Visualizer
from config import (
    MAX_REPOSITORIES, MIN_STARS, EXCLUDE_DIRS, 
    OUTPUT_DIR, FIGURES_DIR, SIGNIFICANCE_LEVEL, CONFIDENCE_LEVEL,
    CURATED_REPOSITORIES, MAX_WORKERS, PARALLEL_REPOS, PARALLEL_FILES,
    USE_EXISTING_METRICS, RAW_METRICS_FILE, FOCUSED_MODE
)


def main():
    """Main analysis pipeline."""
    print("=" * 80)
    print("Code Metrics Analysis Pipeline")
    print("=" * 80)
    
    # Create output directories
    Path(OUTPUT_DIR).mkdir(exist_ok=True)
    Path(FIGURES_DIR).mkdir(exist_ok=True)
    
    # Initialize components
    print("\n1. Initializing components...")
    stat_analyzer = StatisticalAnalyzer(
        significance_level=SIGNIFICANCE_LEVEL,
        confidence_level=CONFIDENCE_LEVEL
    )
    visualizer = Visualizer(output_dir=FIGURES_DIR)
    
    # Check if we should use existing metrics
    raw_metrics_path = Path(RAW_METRICS_FILE)
    use_existing = USE_EXISTING_METRICS and raw_metrics_path.exists()
    
    if use_existing:
        print(f"\n2. Loading existing raw metrics from {RAW_METRICS_FILE}...")
        try:
            df = pd.read_csv(raw_metrics_path)
            print(f"  ✓ Loaded {len(df)} file metrics from existing data")
            all_metrics = df.to_dict('records')
            repo_summaries = []  # We don't have repo summaries from CSV
        except Exception as e:
            print(f"  ✗ Error loading existing metrics: {e}")
            print("  Falling back to data collection...")
            use_existing = False
    
    if not use_existing:
        # Initialize data collection components
        github_client = GitHubClient()
        code_analyzer = CodeAnalyzer(exclude_dirs=EXCLUDE_DIRS)
        data_collector = DataCollector(code_analyzer)
        
        # Use curated list of popular Python repositories
        print("\n2. Using curated list of popular Python repositories...")
        repositories_to_analyze = CURATED_REPOSITORIES[:MAX_REPOSITORIES]
        print(f"Selected {len(repositories_to_analyze)} repositories:")
        for owner, repo_name in repositories_to_analyze:
            print(f"  - {owner}/{repo_name}")
        
        # Collect data from repositories (parallelized)
        print("\n3. Collecting data from repositories...")
        all_metrics = []
        repo_summaries = []
        
        def process_repository(owner: str, repo_name: str) -> Optional[Dict]:
            """Process a single repository and return results."""
            try:
                print(f"  Processing {owner}/{repo_name}...")
                
                # Get repository info for stars count
                try:
                    repo_info = github_client.get_repository_info(owner, repo_name)
                    stars = repo_info.get('stargazers_count', 0)
                except:
                    stars = 0
                
                repo_data = data_collector.collect_repository_data(
                    owner, repo_name, 
                    parallel_files=PARALLEL_FILES, 
                    max_workers=MAX_WORKERS
                )
                
                if repo_data and repo_data['code_metrics']:
                    print(f"  ✓ {owner}/{repo_name}: {len(repo_data['code_metrics'])} files, {repo_data['total_fixes']} fixes")
                    return {
                        'metrics': repo_data['code_metrics'],
                        'summary': {
                            'owner': owner,
                            'repo': repo_name,
                            'files_analyzed': len(repo_data['code_metrics']),
                            'total_fixes': repo_data['total_fixes'],
                            'stars': stars
                        }
                    }
                else:
                    print(f"  ✗ {owner}/{repo_name}: No data collected")
                    return None
            except Exception as e:
                print(f"  ✗ {owner}/{repo_name}: Error - {e}")
                import traceback
                traceback.print_exc()
                return None
        
        if PARALLEL_REPOS and len(repositories_to_analyze) > 1:
            # Process repositories in parallel
            print(f"  Processing {len(repositories_to_analyze)} repositories in parallel...")
            with ThreadPoolExecutor(max_workers=min(len(repositories_to_analyze), MAX_WORKERS or 4)) as executor:
                futures = {executor.submit(process_repository, owner, repo_name): (owner, repo_name) 
                          for owner, repo_name in repositories_to_analyze}
                
                for future in as_completed(futures):
                    owner, repo_name = futures[future]
                    try:
                        result = future.result()
                        if result:
                            all_metrics.extend(result['metrics'])
                            repo_summaries.append(result['summary'])
                    except Exception as e:
                        print(f"  ✗ {owner}/{repo_name}: Failed - {e}")
        else:
            # Sequential processing
            for i, (owner, repo_name) in enumerate(repositories_to_analyze, 1):
                print(f"\n[{i}/{len(repositories_to_analyze)}] Processing {owner}/{repo_name}...")
                result = process_repository(owner, repo_name)
                if result:
                    all_metrics.extend(result['metrics'])
                    repo_summaries.append(result['summary'])
        
        if not all_metrics:
            print("\nNo metrics collected. Exiting.")
            return
        
        # Convert to DataFrame
        print("\n4. Preparing data for analysis...")
        df = stat_analyzer.prepare_dataframe(all_metrics)
        print(f"Total files analyzed: {len(df)}")
        print(f"Columns: {list(df.columns)}")
        
        # Save raw data
        df.to_csv(Path(OUTPUT_DIR) / 'raw_metrics.csv', index=False)
        print(f"  ✓ Saved raw metrics to {OUTPUT_DIR}/raw_metrics.csv")
    else:
        # Already have DataFrame from CSV
        print("\n3. Preparing data for analysis...")
        df = stat_analyzer.prepare_dataframe(all_metrics)
        print(f"Total files analyzed: {len(df)}")
        print(f"Columns: {list(df.columns)}")
    
    if len(df) == 0:
        print("\nNo metrics available for analysis. Exiting.")
        return
    
    # Statistical Analysis
    step_num = "4" if use_existing else "5"
    print(f"\n{step_num}. Performing statistical analysis...")
    
    if FOCUSED_MODE:
        print("  [FOCUSED MODE: Regression and Hypothesis Testing Only]")
        
        # Regression analysis
        print("  - Regression analysis...")
        complexity_features = [
            'loc', 'cyclomatic_complexity', 'cognitive_complexity',
            'max_complexity', 'avg_complexity', 'max_inheritance_depth'
        ]
        regression_results = stat_analyzer.regression_analysis(
            df, complexity_features, target='fix_count'
        )
        
        # Hypothesis testing - t-tests
        print("  - T-test analysis...")
        t_test_results = stat_analyzer.t_test_analysis(df)
        
        # Hypothesis testing - z-tests
        print("  - Z-test analysis...")
        z_test_results = stat_analyzer.z_test_analysis(df)
        
        # Hypothesis testing - module comparisons (ANOVA)
        print("  - Hypothesis testing (ANOVA)...")
        hypothesis_results = stat_analyzer.hypothesis_testing(df)
        
        # Confidence intervals for key metrics
        print("  - Confidence intervals...")
        ci_results = stat_analyzer.confidence_intervals(
            df, ['cyclomatic_complexity', 'cognitive_complexity', 'loc', 'fix_count']
        )
        
        # Initialize empty results for skipped analyses
        correlation_results = {}
        var_cov_results = {}
        pivot_results = {}
        distribution_results = {}
    else:
        # Full analysis mode
        # Correlation analysis
        print("  - Correlation analysis...")
        correlation_results = stat_analyzer.correlation_analysis(df)
        
        # Regression analysis
        print("  - Regression analysis...")
        complexity_features = [
            'loc', 'cyclomatic_complexity', 'cognitive_complexity',
            'max_complexity', 'avg_complexity', 'max_inheritance_depth'
        ]
        regression_results = stat_analyzer.regression_analysis(
            df, complexity_features, target='fix_count'
        )
        
        # Hypothesis testing
        print("  - Hypothesis testing...")
        hypothesis_results = stat_analyzer.hypothesis_testing(df)
        
        # T-test analysis
        print("  - T-test analysis...")
        t_test_results = stat_analyzer.t_test_analysis(df)
        
        # Z-test analysis
        print("  - Z-test analysis...")
        z_test_results = stat_analyzer.z_test_analysis(df)
        
        # Confidence intervals
        print("  - Confidence intervals...")
        ci_results = stat_analyzer.confidence_intervals(
            df, ['cyclomatic_complexity', 'cognitive_complexity', 'loc', 'fix_count']
        )
        
        # Variance-covariance analysis
        print("  - Variance-covariance analysis...")
        var_cov_results = stat_analyzer.variance_covariance_analysis(df)
        
        # Pivot table analysis
        print("  - Pivot table analysis...")
        pivot_results = stat_analyzer.pivot_table_analysis(df)
        
        # Discrete distribution analysis
        print("  - Discrete distribution analysis...")
        distribution_results = stat_analyzer.discrete_distribution_analysis(df)
    
    # Save analysis results
    step_num = "5" if use_existing else "6"
    print(f"\n{step_num}. Saving analysis results...")
    results = {
        'correlation_analysis': correlation_results,
        'regression_analysis': regression_results,
        'hypothesis_testing': hypothesis_results,
        't_test_analysis': t_test_results if 't_test_results' in locals() else {},
        'z_test_analysis': z_test_results if 'z_test_results' in locals() else {},
        'confidence_intervals': ci_results,
        'variance_covariance': var_cov_results,
        'pivot_tables': {k: v.to_dict() if isinstance(v, pd.DataFrame) else v 
                        for k, v in pivot_results.items()},
        'distribution_analysis': distribution_results,
        'repository_summaries': repo_summaries,
        'analysis_mode': 'focused' if FOCUSED_MODE else 'full'
    }
    
    # Convert numpy types to native Python types for JSON serialization
    def convert_to_serializable(obj):
        if isinstance(obj, (np.integer, np.floating)):
            return float(obj)
        elif isinstance(obj, np.ndarray):
            return obj.tolist()
        elif isinstance(obj, dict):
            return {k: convert_to_serializable(v) for k, v in obj.items()}
        elif isinstance(obj, list):
            return [convert_to_serializable(item) for item in obj]
        elif isinstance(obj, pd.DataFrame):
            return obj.to_dict()
        return obj
    
    results_serializable = convert_to_serializable(results)
    
    with open(Path(OUTPUT_DIR) / 'analysis_results.json', 'w') as f:
        json.dump(results_serializable, f, indent=2, default=str)
    print(f"  ✓ Saved analysis results to {OUTPUT_DIR}/analysis_results.json")
    
    # Create visualizations
    print("\n" + ("6" if use_existing else "7") + ". Creating visualizations...")
    
    if FOCUSED_MODE:
        print("  [FOCUSED MODE: Regression visualizations only]")
        
        # Scatter plots for key relationships
        print("  - Scatter plots...")
        visualizer.plot_complexity_vs_issues_scatter(
            df, 'loc', 'fix_count',
            'loc_vs_fixes.png'
        )
        visualizer.plot_complexity_vs_issues_scatter(
            df, 'cognitive_complexity', 'fix_count',
            'cognitive_complexity_vs_fixes.png'
        )
        
        # Regression results
        if regression_results:
            print("  - Regression results...")
            visualizer.plot_regression_results(regression_results)
    else:
        # Full visualization mode
        # Correlation heatmap
        print("  - Correlation heatmap...")
        visualizer.plot_correlation_heatmap(
            df,
            complexity_cols=['loc', 'cyclomatic_complexity', 'cognitive_complexity', 
                           'max_complexity', 'avg_complexity'],
            issue_cols=['fix_count', 'total_fixes']
        )
        
        # Scatter plots
        print("  - Scatter plots...")
        visualizer.plot_complexity_vs_issues_scatter(
            df, 'cyclomatic_complexity', 'fix_count',
            'cyclomatic_complexity_vs_fixes.png'
        )
        visualizer.plot_complexity_vs_issues_scatter(
            df, 'cognitive_complexity', 'fix_count',
            'cognitive_complexity_vs_fixes.png'
        )
        visualizer.plot_complexity_vs_issues_scatter(
            df, 'loc', 'fix_count',
            'loc_vs_fixes.png'
        )
        
        # Module comparison
        print("  - Module comparison...")
        visualizer.plot_module_complexity_comparison(
            df, 'cyclomatic_complexity'
        )
        
        # Distribution analysis
        print("  - Distribution analysis...")
        visualizer.plot_distribution_analysis(df, 'cyclomatic_complexity')
        visualizer.plot_distribution_analysis(df, 'fix_count', 
                                             'fix_distribution.png')
        
        # Regression results
        if regression_results:
            print("  - Regression results...")
            visualizer.plot_regression_results(regression_results)
    
    print(f"  ✓ Saved visualizations to {FIGURES_DIR}/")
    
    # Print summary statistics
    step_num = "7" if use_existing else "8"
    print(f"\n{step_num}. Summary Statistics")
    print("=" * 80)
    print(f"\nTotal files analyzed: {len(df)}")
    if repo_summaries:
        print(f"Total repositories: {len(repo_summaries)}")
    
    print("\nComplexity Metrics (Mean ± Std):")
    for metric in ['loc', 'cyclomatic_complexity', 'cognitive_complexity', 
                   'max_complexity', 'avg_complexity']:
        if metric in df.columns:
            mean_val = df[metric].mean()
            std_val = df[metric].std()
            print(f"  {metric:30s}: {mean_val:8.2f} ± {std_val:8.2f}")
    
    print("\nFix Metrics (Mean ± Std):")
    for metric in ['fix_count', 'total_fixes']:
        if metric in df.columns:
            mean_val = df[metric].mean()
            std_val = df[metric].std()
            print(f"  {metric:30s}: {mean_val:8.2f} ± {std_val:8.2f}")
    
    if not FOCUSED_MODE:
        print("\nSignificant Correlations:")
        sig_corr = correlation_results.get('significant_correlations', {})
        if sig_corr:
            for metric, corr_value in list(sig_corr.items())[:10]:
                print(f"  {metric}: {corr_value:.3f}")
        else:
            print("  None found")
    
    if regression_results:
        print(f"\nRegression Analysis:")
        print(f"  R²: {regression_results.get('r_squared', 0):.3f}")
        print(f"  RMSE: {regression_results.get('rmse', 0):.3f}")
        if regression_results.get('significant_features'):
            print(f"  Significant features: {regression_results['significant_features']}")
    
    # T-test results
    if 't_test_results' in locals() and t_test_results:
        print(f"\nT-Test Results (High-fix vs Low-fix files):")
        for metric, result in t_test_results.items():
            if 'error' not in result:
                sig_marker = "***" if result.get('significant') else ""
                print(f"  {metric}:")
                print(f"    t-statistic: {result.get('t_statistic', 0):.3f}")
                print(f"    p-value: {result.get('p_value', 1):.4f} {sig_marker}")
                print(f"    High-fix mean: {result.get('high_fix_mean', 0):.2f}")
                print(f"    Low-fix mean: {result.get('low_fix_mean', 0):.2f}")
    
    # Z-test results
    if 'z_test_results' in locals() and z_test_results:
        print(f"\nZ-Test Results (High-fix vs Low-fix files):")
        for metric, result in z_test_results.items():
            if 'error' not in result:
                sig_marker = "***" if result.get('significant') else ""
                print(f"  {metric}:")
                print(f"    z-statistic: {result.get('z_statistic', 0):.3f}")
                print(f"    p-value: {result.get('p_value', 1):.4f} {sig_marker}")
                print(f"    Mean difference: {result.get('mean_difference', 0):.2f}")
                print(f"    95% CI: [{result.get('ci_lower', 0):.2f}, {result.get('ci_upper', 0):.2f}]")
    
    # Hypothesis testing results
    if hypothesis_results:
        print(f"\nHypothesis Testing (ANOVA/Kruskal-Wallis):")
        for test_name, result in list(hypothesis_results.items())[:5]:
            if isinstance(result, dict) and 'p_value' in result:
                sig_marker = "***" if result.get('significant') else ""
                print(f"  {test_name}: p={result.get('p_value', 1):.4f} {sig_marker}")
    
    print("\n" + "=" * 80)
    print("Analysis complete!")
    print(f"Results saved to: {OUTPUT_DIR}/")
    print(f"Figures saved to: {FIGURES_DIR}/")
    print("=" * 80)
    
    # Cleanup (only if we collected data)
    if not use_existing:
        data_collector.cleanup()


if __name__ == '__main__':
    main()