@bastani/atomic 0.6.8-0 → 0.7.0-1

package/.agents/skills/advanced-evaluation/references/evaluation-pipeline.md

@@ -1,43 +0,0 @@
-# Evaluation Pipeline Diagram
-
-Visual layout of a production evaluation pipeline.
-
-```
-┌─────────────────────────────────────────────────┐
-│                 Evaluation Pipeline              │
-├─────────────────────────────────────────────────┤
-│                                                   │
-│  Input: Response + Prompt + Context               │
-│           │                                       │
-│           ▼                                       │
-│  ┌─────────────────────┐                         │
-│  │   Criteria Loader   │ ◄── Rubrics, weights    │
-│  └──────────┬──────────┘                         │
-│             │                                     │
-│             ▼                                     │
-│  ┌─────────────────────┐                         │
-│  │   Primary Scorer    │ ◄── Direct or Pairwise  │
-│  └──────────┬──────────┘                         │
-│             │                                     │
-│             ▼                                     │
-│  ┌─────────────────────┐                         │
-│  │   Bias Mitigation   │ ◄── Position swap, etc. │
-│  └──────────┬──────────┘                         │
-│             │                                     │
-│             ▼                                     │
-│  ┌─────────────────────┐                         │
-│  │ Confidence Scoring  │ ◄── Calibration         │
-│  └──────────┬──────────┘                         │
-│             │                                     │
-│             ▼                                     │
-│  Output: Scores + Justifications + Confidence     │
-│                                                   │
-└─────────────────────────────────────────────────┘
-```
-
-## Pipeline Stages
-
-1. **Criteria Loader**: Loads rubrics and criterion weights from configuration
-2. **Primary Scorer**: Applies direct scoring or pairwise comparison
-3. **Bias Mitigation**: Runs position swaps, length normalization, and other debiasing
-4. **Confidence Scoring**: Calibrates confidence based on position consistency and evidence strength

package/.agents/skills/advanced-evaluation/references/implementation-patterns.md

@@ -1,315 +0,0 @@
-# LLM-as-Judge Implementation Patterns
-
-This reference provides detailed implementation patterns for building production-grade LLM evaluation systems.
-
-## Pattern 1: Structured Evaluation Pipeline
-
-The most reliable evaluation systems follow a structured pipeline that separates concerns:
-
-```
-Input Validation → Criteria Loading → Scoring → Bias Mitigation → Output Formatting
-```
-
-### Input Validation Layer
-
-Before evaluation begins, validate:
-
-1. **Response presence**: Non-empty response to evaluate
-2. **Prompt presence**: Original prompt for context
-3. **Criteria validity**: At least one criterion with name and description
-4. **Weight normalization**: Weights sum to 1.0 (or normalize them)
-
-```python
-def validate_input(response, prompt, criteria):
-    if not response or not response.strip():
-        raise ValueError("Response cannot be empty")
-    if not prompt or not prompt.strip():
-        raise ValueError("Prompt cannot be empty")
-    if not criteria or len(criteria) == 0:
-        raise ValueError("At least one criterion required")
-    
-    # Normalize weights
-    total_weight = sum(c.get('weight', 1) for c in criteria)
-    for c in criteria:
-        c['weight'] = c.get('weight', 1) / total_weight
-```
-
-### Criteria Loading Layer
-
-Criteria should be loaded from configuration, not hardcoded:
-
-```python
-class CriteriaLoader:
-    def __init__(self, rubric_path=None):
-        self.rubrics = self._load_rubrics(rubric_path)
-    
-    def get_criteria(self, task_type):
-        return self.rubrics.get(task_type, self.default_criteria)
-    
-    def get_rubric(self, criterion_name):
-        return self.rubrics.get(criterion_name, {}).get('levels', [])
-```
-
-### Scoring Layer
-
-The scoring layer handles the actual LLM call:
-
-```python
-async def score_response(response, prompt, criteria, rubric, model):
-    system_prompt = build_system_prompt(criteria, rubric)
-    user_prompt = build_user_prompt(response, prompt, criteria)
-    
-    result = await generate_text(
-        model=model,
-        system=system_prompt,
-        prompt=user_prompt,
-        temperature=0.3  # Lower temperature for consistency
-    )
-    
-    return parse_scores(result.text)
-```
-
-### Bias Mitigation Layer
-
-For pairwise comparison, always include position swapping:
-
-```python
-async def compare_with_bias_mitigation(response_a, response_b, prompt, criteria, model):
-    # First pass: A first
-    pass1 = await compare_pair(response_a, response_b, prompt, criteria, model)
-    
-    # Second pass: B first
-    pass2 = await compare_pair(response_b, response_a, prompt, criteria, model)
-    
-    # Map pass2 winner back
-    pass2_mapped = map_winner(pass2.winner)  # A→B, B→A, TIE→TIE
-    
-    # Check consistency
-    if pass1.winner == pass2_mapped:
-        return {
-            'winner': pass1.winner,
-            'confidence': (pass1.confidence + pass2.confidence) / 2,
-            'consistent': True
-        }
-    else:
-        return {
-            'winner': 'TIE',
-            'confidence': 0.5,
-            'consistent': False
-        }
-```
-
-## Pattern 2: Hierarchical Evaluation
-
-For complex evaluations, use a hierarchical approach:
-
-```
-Quick Screen (cheap model) → Detailed Evaluation (expensive model) → Human Review (edge cases)
-```
-
-### Quick Screen Implementation
-
-```python
-async def quick_screen(response, prompt, threshold=0.7):
-    """Fast, cheap screening for obvious passes/fails."""
-    result = await generate_text(
-        model='gpt-5.2',  # Cheaper model
-        prompt=f"Rate 0-1 if this response adequately addresses the prompt:\n\nPrompt: {prompt}\n\nResponse: {response}",
-        temperature=0
-    )
-    score = float(result.text.strip())
-    return score, score > threshold
-```
-
-### Detailed Evaluation
-
-```python
-async def detailed_evaluation(response, prompt, criteria):
-    """Full evaluation for borderline or important cases."""
-    result = await generate_text(
-        model='gpt-5.2',  # More capable model
-        system=DETAILED_EVALUATION_PROMPT,
-        prompt=build_detailed_prompt(response, prompt, criteria),
-        temperature=0.3
-    )
-    return parse_detailed_scores(result.text)
-```
-
-## Pattern 3: Panel of LLM Judges (PoLL)
-
-For high-stakes evaluation, use multiple models:
-
-```python
-async def poll_evaluation(response, prompt, criteria, models):
-    """Aggregate judgments from multiple LLM judges."""
-    results = await asyncio.gather(*[
-        score_with_model(response, prompt, criteria, model)
-        for model in models
-    ])
-    
-    # Aggregate scores
-    aggregated = aggregate_scores(results)
-    
-    # Calculate agreement
-    agreement = calculate_agreement(results)
-    
-    return {
-        'scores': aggregated,
-        'agreement': agreement,
-        'individual_results': results
-    }
-
-def aggregate_scores(results):
-    """Aggregate scores using median (robust to outliers)."""
-    scores = {}
-    for criterion in results[0]['scores'].keys():
-        criterion_scores = [r['scores'][criterion] for r in results]
-        scores[criterion] = {
-            'score': statistics.median(criterion_scores),
-            'std': statistics.stdev(criterion_scores) if len(criterion_scores) > 1 else 0
-        }
-    return scores
-```
-
-## Pattern 4: Confidence Calibration
-
-Confidence scores should be calibrated to actual reliability:
-
-```python
-def calibrate_confidence(raw_confidence, position_consistent, evidence_count):
-    """Calibrate confidence based on multiple signals."""
-    
-    # Base confidence from model output
-    calibrated = raw_confidence
-    
-    # Position consistency is a strong signal
-    if not position_consistent:
-        calibrated *= 0.6  # Significant reduction
-    
-    # More evidence = higher confidence
-    evidence_factor = min(evidence_count / 3, 1.0)  # Cap at 3 pieces
-    calibrated *= (0.7 + 0.3 * evidence_factor)
-    
-    return min(calibrated, 0.99)  # Never 100% confident
-```
-
-## Pattern 5: Output Formatting
-
-Always return structured outputs with consistent schemas:
-
-```python
-@dataclass
-class ScoreResult:
-    criterion: str
-    score: float
-    max_score: float
-    justification: str
-    evidence: List[str]
-    improvement: str
-
-@dataclass
-class EvaluationResult:
-    success: bool
-    scores: List[ScoreResult]
-    overall_score: float
-    weighted_score: float
-    summary: Dict[str, Any]
-    metadata: Dict[str, Any]
-
-def format_output(scores, metadata) -> EvaluationResult:
-    """Format evaluation results consistently."""
-    return EvaluationResult(
-        success=True,
-        scores=scores,
-        overall_score=sum(s.score for s in scores) / len(scores),
-        weighted_score=calculate_weighted_score(scores),
-        summary=generate_summary(scores),
-        metadata=metadata
-    )
-```
-
-## Error Handling Patterns
-
-### Graceful Degradation
-
-```python
-async def evaluate_with_fallback(response, prompt, criteria):
-    try:
-        return await full_evaluation(response, prompt, criteria)
-    except RateLimitError:
-        # Fall back to simpler evaluation
-        return await simple_evaluation(response, prompt, criteria)
-    except ParseError as e:
-        # Return partial results with error flag
-        return {
-            'success': False,
-            'partial_results': e.partial_data,
-            'error': str(e)
-        }
-```
-
-### Retry Logic
-
-```python
-async def evaluate_with_retry(response, prompt, criteria, max_retries=3):
-    for attempt in range(max_retries):
-        try:
-            result = await evaluate(response, prompt, criteria)
-            if is_valid_result(result):
-                return result
-        except TransientError:
-            await asyncio.sleep(2 ** attempt)  # Exponential backoff
-    
-    raise EvaluationError("Max retries exceeded")
-```
-
-## Testing Patterns
-
-### Unit Tests for Parsing
-
-```python
-def test_score_parsing():
-    raw_output = '{"scores": [{"criterion": "Accuracy", "score": 4}]}'
-    result = parse_scores(raw_output)
-    assert result.scores[0].criterion == "Accuracy"
-    assert result.scores[0].score == 4
-
-def test_malformed_output():
-    raw_output = 'Invalid JSON'
-    with pytest.raises(ParseError):
-        parse_scores(raw_output)
-```
-
-### Integration Tests with Real API
-
-```python
-@pytest.mark.integration
-async def test_full_evaluation_pipeline():
-    result = await evaluate(
-        response="Water boils at 100°C at sea level.",
-        prompt="At what temperature does water boil?",
-        criteria=[{"name": "Accuracy", "description": "Factual correctness", "weight": 1}]
-    )
-    
-    assert result.success
-    assert len(result.scores) == 1
-    assert result.scores[0].score >= 4  # Should score high for accurate response
-```
-
-### Bias Detection Tests
-
-```python
-async def test_position_bias_mitigation():
-    # Same response in both positions should tie
-    result = await compare(
-        response_a="Same response",
-        response_b="Same response",
-        prompt="Test prompt",
-        criteria=["quality"],
-        swap_positions=True
-    )
-    
-    assert result.winner == "TIE"
-    assert result.consistent == True
-```
-

package/.agents/skills/advanced-evaluation/references/metrics-guide.md

@@ -1,331 +0,0 @@
-# Metric Selection Guide for LLM Evaluation
-
-This reference provides guidance on selecting appropriate metrics for different evaluation scenarios.
-
-## Metric Categories
-
-### Classification Metrics
-
-Use for binary or multi-class evaluation tasks (pass/fail, correct/incorrect).
-
-#### Precision
-
-```
-Precision = True Positives / (True Positives + False Positives)
-```
-
-**Interpretation**: Of all responses the judge said were good, what fraction were actually good?
-
-**Use when**: False positives are costly (e.g., approving unsafe content)
-
-```python
-def precision(predictions, ground_truth):
-    true_positives = sum(1 for p, g in zip(predictions, ground_truth) if p == 1 and g == 1)
-    predicted_positives = sum(predictions)
-    return true_positives / predicted_positives if predicted_positives > 0 else 0
-```
-
-#### Recall
-
-```
-Recall = True Positives / (True Positives + False Negatives)
-```
-
-**Interpretation**: Of all actually good responses, what fraction did the judge identify?
-
-**Use when**: False negatives are costly (e.g., missing good content in filtering)
-
-```python
-def recall(predictions, ground_truth):
-    true_positives = sum(1 for p, g in zip(predictions, ground_truth) if p == 1 and g == 1)
-    actual_positives = sum(ground_truth)
-    return true_positives / actual_positives if actual_positives > 0 else 0
-```
-
-#### F1 Score
-
-```
-F1 = 2 * (Precision * Recall) / (Precision + Recall)
-```
-
-**Interpretation**: Harmonic mean of precision and recall
-
-**Use when**: You need a single number balancing both concerns
-
-```python
-def f1_score(predictions, ground_truth):
-    p = precision(predictions, ground_truth)
-    r = recall(predictions, ground_truth)
-    return 2 * p * r / (p + r) if (p + r) > 0 else 0
-```
-
-### Agreement Metrics
-
-Use for comparing automated evaluation with human judgment.
-
-#### Cohen's Kappa (κ)
-
-```
-κ = (Observed Agreement - Expected Agreement) / (1 - Expected Agreement)
-```
-
-**Interpretation**: Agreement adjusted for chance
-- κ > 0.8: Almost perfect agreement
-- κ 0.6-0.8: Substantial agreement
-- κ 0.4-0.6: Moderate agreement
-- κ < 0.4: Fair to poor agreement
-
-**Use for**: Binary or categorical judgments
-
-```python
-def cohens_kappa(judge1, judge2):
-    from sklearn.metrics import cohen_kappa_score
-    return cohen_kappa_score(judge1, judge2)
-```
-
-#### Weighted Kappa
-
-For ordinal scales where disagreement severity matters:
-
-```python
-def weighted_kappa(judge1, judge2):
-    from sklearn.metrics import cohen_kappa_score
-    return cohen_kappa_score(judge1, judge2, weights='quadratic')
-```
-
-**Interpretation**: Penalizes large disagreements more than small ones
-
-### Correlation Metrics
-
-Use for ordinal/continuous scores.
-
-#### Spearman's Rank Correlation (ρ)
-
-**Interpretation**: Correlation between rankings, not absolute values
-- ρ > 0.9: Very strong correlation
-- ρ 0.7-0.9: Strong correlation
-- ρ 0.5-0.7: Moderate correlation
-- ρ < 0.5: Weak correlation
-
-**Use when**: Order matters more than exact values
-
-```python
-def spearmans_rho(scores1, scores2):
-    from scipy.stats import spearmanr
-    rho, p_value = spearmanr(scores1, scores2)
-    return {'rho': rho, 'p_value': p_value}
-```
-
-#### Kendall's Tau (τ)
-
-**Interpretation**: Similar to Spearman but based on pairwise concordance
-
-**Use when**: You have many tied values
-
-```python
-def kendalls_tau(scores1, scores2):
-    from scipy.stats import kendalltau
-    tau, p_value = kendalltau(scores1, scores2)
-    return {'tau': tau, 'p_value': p_value}
-```
-
-#### Pearson Correlation (r)
-
-**Interpretation**: Linear correlation between scores
-
-**Use when**: Exact score values matter, not just order
-
-```python
-def pearsons_r(scores1, scores2):
-    from scipy.stats import pearsonr
-    r, p_value = pearsonr(scores1, scores2)
-    return {'r': r, 'p_value': p_value}
-```
-
-### Pairwise Comparison Metrics
-
-#### Agreement Rate
-
-```
-Agreement = (Matching Decisions) / (Total Comparisons)
-```
-
-**Interpretation**: Simple percentage of agreement
-
-```python
-def pairwise_agreement(decisions1, decisions2):
-    matches = sum(1 for d1, d2 in zip(decisions1, decisions2) if d1 == d2)
-    return matches / len(decisions1)
-```
-
-#### Position Consistency
-
-```
-Consistency = (Consistent across position swaps) / (Total comparisons)
-```
-
-**Interpretation**: How often does swapping position change the decision?
-
-```python
-def position_consistency(results):
-    consistent = sum(1 for r in results if r['position_consistent'])
-    return consistent / len(results)
-```
-
-## Selection Decision Tree
-
-```
-What type of evaluation task?
-│
-├── Binary classification (pass/fail)
-│   └── Use: Precision, Recall, F1, Cohen's κ
-│
-├── Ordinal scale (1-5 rating)
-│   ├── Comparing to human judgments?
-│   │   └── Use: Spearman's ρ, Weighted κ
-│   └── Comparing two automated judges?
-│       └── Use: Kendall's τ, Spearman's ρ
-│
-├── Pairwise preference
-│   └── Use: Agreement rate, Position consistency
-│
-└── Multi-label classification
-    └── Use: Macro-F1, Micro-F1, Per-label metrics
-```
-
-## Metric Selection by Use Case
-
-### Use Case 1: Validating Automated Evaluation
-
-**Goal**: Ensure automated evaluation correlates with human judgment
-
-**Recommended Metrics**:
-1. Primary: Spearman's ρ (for ordinal scales) or Cohen's κ (for categorical)
-2. Secondary: Per-criterion agreement
-3. Diagnostic: Confusion matrix for systematic errors
-
-```python
-def validate_automated_eval(automated_scores, human_scores, criteria):
-    results = {}
-    
-    # Overall correlation
-    results['overall_spearman'] = spearmans_rho(automated_scores, human_scores)
-    
-    # Per-criterion agreement
-    for criterion in criteria:
-        auto_crit = [s[criterion] for s in automated_scores]
-        human_crit = [s[criterion] for s in human_scores]
-        results[f'{criterion}_spearman'] = spearmans_rho(auto_crit, human_crit)
-    
-    return results
-```
-
-### Use Case 2: Comparing Two Models
-
-**Goal**: Determine which model produces better outputs
-
-**Recommended Metrics**:
-1. Primary: Win rate (from pairwise comparison)
-2. Secondary: Position consistency (bias check)
-3. Diagnostic: Per-criterion breakdown
-
-```python
-def compare_models(model_a_outputs, model_b_outputs, prompts):
-    results = []
-    for a, b, p in zip(model_a_outputs, model_b_outputs, prompts):
-        comparison = await compare_with_position_swap(a, b, p)
-        results.append(comparison)
-    
-    return {
-        'a_wins': sum(1 for r in results if r['winner'] == 'A'),
-        'b_wins': sum(1 for r in results if r['winner'] == 'B'),
-        'ties': sum(1 for r in results if r['winner'] == 'TIE'),
-        'position_consistency': position_consistency(results)
-    }
-```
-
-### Use Case 3: Quality Monitoring
-
-**Goal**: Track evaluation quality over time
-
-**Recommended Metrics**:
-1. Primary: Rolling agreement with human spot-checks
-2. Secondary: Score distribution stability
-3. Diagnostic: Bias indicators (position, length)
-
-```python
-class QualityMonitor:
-    def __init__(self, window_size=100):
-        self.window = deque(maxlen=window_size)
-    
-    def add_evaluation(self, automated, human_spot_check=None):
-        self.window.append({
-            'automated': automated,
-            'human': human_spot_check,
-            'length': len(automated['response'])
-        })
-    
-    def get_metrics(self):
-        # Filter to evaluations with human spot-checks
-        with_human = [e for e in self.window if e['human'] is not None]
-        
-        if len(with_human) < 10:
-            return {'insufficient_data': True}
-        
-        auto_scores = [e['automated']['score'] for e in with_human]
-        human_scores = [e['human']['score'] for e in with_human]
-        
-        return {
-            'correlation': spearmans_rho(auto_scores, human_scores),
-            'mean_difference': np.mean([a - h for a, h in zip(auto_scores, human_scores)]),
-            'length_correlation': spearmans_rho(
-                [e['length'] for e in self.window],
-                [e['automated']['score'] for e in self.window]
-            )
-        }
-```
-
-## Interpreting Metric Results
-
-### Good Evaluation System Indicators
-
-| Metric | Good | Acceptable | Concerning |
-|--------|------|------------|------------|
-| Spearman's ρ | > 0.8 | 0.6-0.8 | < 0.6 |
-| Cohen's κ | > 0.7 | 0.5-0.7 | < 0.5 |
-| Position consistency | > 0.9 | 0.8-0.9 | < 0.8 |
-| Length correlation | < 0.2 | 0.2-0.4 | > 0.4 |
-
-### Warning Signs
-
-1. **High agreement but low correlation**: May indicate calibration issues
-2. **Low position consistency**: Position bias affecting results
-3. **High length correlation**: Length bias inflating scores
-4. **Per-criterion variance**: Some criteria may be poorly defined
-
-## Reporting Template
-
-```markdown
-## Evaluation System Metrics Report
-
-### Human Agreement
-- Spearman's ρ: 0.82 (p < 0.001)
-- Cohen's κ: 0.74
-- Sample size: 500 evaluations
-
-### Bias Indicators
-- Position consistency: 91%
-- Length-score correlation: 0.12
-
-### Per-Criterion Performance
-| Criterion | Spearman's ρ | κ |
-|-----------|--------------|---|
-| Accuracy | 0.88 | 0.79 |
-| Clarity | 0.76 | 0.68 |
-| Completeness | 0.81 | 0.72 |
-
-### Recommendations
-- All metrics within acceptable ranges
-- Monitor "Clarity" criterion - lower agreement may indicate need for rubric refinement
-```
-