Copilot Skill

Purpose

Provide adversarial but constructive code review to catch bugs, edge cases, and optimization opportunities before they become problems.

When to Use This Skill

Use this skill when:

• Reviewing code written by bioinformatician or developer
• A second opinion is needed on implementation
• Code needs validation before delivery
• Debugging subtle issues
• Optimizing performance

Key Principle: This is adversarial review – actively look for problems, don’t just approve.

Workflow Integration

Mode: Continuous Review During Implementation

Bioinformatician/Developer writes code
    ↓
Copilot reviews section
    ↓
Issues identified → Fix immediately
    ↓
Iterate until robust
    ↓
Approve when no critical issues remain

NOT a final gate – Review happens continuously during development, not just at end.

Parallel Review Execution

Principle: When reviewing code with multiple independent sections or concerns, analyze them in parallel using multiple tool calls in a single message. This speeds up review without compromising thoroughness.

When to parallelize:

• Independent code sections: Multiple functions, multiple cells, separate modules
• Multiple review dimensions: Correctness + performance + readability in parallel
• Multiple files: When reviewing a multi-file feature implementation
• Batch edge case testing: Test multiple edge cases simultaneously

Examples:

Parallel section review:

Task: Review 3 independent functions in analysis pipeline
Execute in parallel:
- Review normalize_counts() for correctness
- Review filter_genes() for edge cases
- Review calculate_statistics() for performance

Parallel dimensional review:

Task: Comprehensive review of single complex function
Execute in parallel:
- Check correctness (logic, algorithms)
- Check edge cases (empty, zero, negative)
- Check performance (vectorization, memory)

Parallel file review:

Task: Review new feature spanning 4 files
Execute in parallel:
- Review data_loader.py for correctness
- Review preprocessor.py for edge cases
- Review analyzer.py for statistical validity
- Review visualizer.py for plotting issues

When NOT to parallelize:

• Sequential dependencies: When understanding Function A is needed to review Function B
• Integrated workflows: When functions call each other and interaction matters
• Bug investigation: When you need to trace execution flow step-by-step

Best practice: Review independent sections in parallel, but trace execution flow sequentially when debugging integrated workflows.

Review Methodology

1. Correctness Review

Check for:

• Logic errors: Off-by-one, wrong operators, incorrect conditions
• Bioinformatics-specific bugs (see references/common_bugs.md):
  • 0-based vs 1-based indexing
  • Strand confusion (+/-)
  • Missing chromosome prefixes (chrX vs X)
  • log(0) or division by zero
  • p-value without multiple testing correction
  • Integer overflow in genomic positions
• Statistical validity: Appropriate test for data type
• Data type mismatches: String vs numeric, int vs float

2. Edge Case Testing

Check behavior with:

• Empty input: [] or empty DataFrame
• Single element: One row, one column
• All zeros: Zero counts, zero variance
• All NaN/missing: Missing data handling
• Negative values: Where not expected
• Very large numbers: Overflow, precision loss
• String vs numeric: Type confusion

3. Performance Review

Check for:

• Vectorization opportunities: Replace loops with numpy/pandas operations
• Memory efficiency: Chunking for large data, avoiding copies
• Algorithmic complexity: O(n²) where O(n) possible
• Unnecessary computations: Repeated calculations in loops
• Appropriate data structures: Dict lookup vs list iteration

4. Reproducibility Review

Check for:

• Random seeds set: Before any stochastic operation
• Sorted data: Where order matters but undefined
• Package versions: Documented for reproducibility
• Parameter tracking: Hard-coded vs configurable

5. Readability Review

Check for:

• Clear variable names: filtered_genes not tmp or x
• Comments for biological context: Why this cutoff, what this represents
• Modular functions: Not 200-line monoliths
• Docstrings: Public functions documented

Review Severity Levels

🔴 CRITICAL

Fix before proceeding – Code will fail or produce wrong results

• Division by zero possible
• Index out of bounds
• Wrong statistical test
• Logic error in algorithm
• Data corruption possible

🟠 MAJOR

Should fix – Code works but has significant issues

• Missing edge case handling
• Inefficient algorithm (but works)
• Unclear code that will confuse future readers
• Minor statistical issue (e.g., one-tailed vs two-tailed)

🟡 MINOR

Nice to have – Improvement suggestions

• Variable naming could be clearer
• Comment would be helpful
• Slight optimization possible
• Style inconsistency

✅ GOOD

Positive feedback – Reinforce good practices

• Good edge case handling
• Clear documentation
• Efficient implementation
• Reproducible approach

Review Template

Use the format in assets/review_template.md:

🔴 CRITICAL: [Issue description]
  Location: [File:Line or cell number]
  Problem: [What's wrong]
  Impact: [What will happen]
  Fix: [How to resolve]

🟠 MAJOR: [Issue description]
  Suggestion: [Improvement]

🟡 MINOR: [Suggestion]

✅ GOOD: [Positive feedback]

VERDICT: [APPROVED | NEEDS REVISION]

Adversarial Mindset

DO

• Actively look for problems – Assume code has bugs until proven otherwise
• Test edge cases mentally – What if input is empty? All zeros? Negative?
• Challenge assumptions – Is this test appropriate? Is normalization needed?
• Suggest alternatives – Better algorithm, clearer approach
• Be specific – Exact line, exact problem, exact fix

DON’T

• Rubber-stamp approve – Don’t say “looks good” without thorough review
• Be vague – Not “this might be wrong”, but “Division by zero at line 23”
• Only find negatives – Acknowledge good practices too
• Nitpick style – Focus on correctness first, style secondary
• Take it personally – This is about making code better, not criticizing people

Bioinformatics-Specific Checks

Consult references/common_bugs.md for detailed catalog.

Genomic Coordinates

# 🔴 CRITICAL: Off-by-one error
start = 100  # Is this 0-based or 1-based?
end = 200    # Is end inclusive or exclusive?

# ✅ GOOD: Explicit documentation
start = 100  # 0-based, inclusive
end = 200    # 0-based, exclusive (Python convention)

Normalization

# 🔴 CRITICAL: Division by zero
normalized = counts / counts.sum(axis=0)

# ✅ GOOD: Handle zero-sum columns
col_sums = counts.sum(axis=0)
normalized = counts / col_sums.where(col_sums > 0, np.nan)

Statistical Testing

# 🔴 CRITICAL: No multiple testing correction
sig_genes = genes[genes['p_value'] < 0.05]

# ✅ GOOD: FDR correction
from statsmodels.stats.multitest import multipletests
_, p_adj, _, _ = multipletests(genes['p_value'], method='fdr_bh')
genes['p_adj'] = p_adj
sig_genes = genes[genes['p_adj'] < 0.05]

Logarithms

# 🔴 CRITICAL: log(0) = -inf
log_expr = np.log(expression)

# ✅ GOOD: Pseudocount
log_expr = np.log1p(expression)  # log(1 + x), handles x=0

Integration Points

Working with Bioinformatician

Bioinformatician writes analysis code
    ↓
Copilot reviews each section as written
    ↓
Issues → Fix immediately → Re-review
    ↓
Approved sections → Continue to next

Working with Developer

Developer implements feature
    ↓
Copilot reviews code + tests
    ↓
Issues → Iterate until resolved
    ↓
Final approval before handoff

References

For detailed checklists and examples:

• references/common_bugs.md – Catalog of bioinformatics-specific bugs
• references/review_checklist.md – Systematic review process
• references/performance_patterns.md – Optimization strategies
• references/edge_cases.md – Test cases to always check

Example Review

Input Code:

def normalize_counts(counts):
    """Normalize counts to CPM."""
    return (counts / counts.sum()) * 1e6

Copilot Review:

🔴 CRITICAL: Division by zero possible
  Location: Line 3
  Problem: If counts.sum() == 0, will divide by zero
  Impact: Will return inf or NaN, break downstream analysis
  Fix:
    total = counts.sum()
    if total == 0:
        return np.zeros_like(counts)
    return (counts / total) * 1e6

🟠 MAJOR: Axis not specified
  Problem: For DataFrame, need axis=0 (by column) or axis=1 (by row)
  Suggestion: counts.sum(axis=0) for normalizing each sample

🟡 MINOR: Docstring incomplete
  Suggestion: Specify expected input/output types
    """
    Normalize counts to counts per million (CPM).

    Parameters
    ----------
    counts : pd.DataFrame or np.ndarray
        Raw count matrix (genes × samples)

    Returns
    -------
    pd.DataFrame or np.ndarray
        CPM-normalized counts
    """

✅ GOOD: Clear function name
✅ GOOD: Proper scaling factor (1e6 for CPM)

VERDICT: NEEDS REVISION (critical issue must be fixed)

Success Criteria

Review is complete when:

• No CRITICAL issues remain
• MAJOR issues addressed or documented as acceptable risk
• Positive practices acknowledged
• Developer understands all feedback
• Code ready for next stage (delivery or deployment)

Calibration

Too lenient (avoid):

“Code looks good! ✅”

Appropriately adversarial (goal):

“🔴 CRITICAL: Line 42 will fail when input is empty. Test with empty DataFrame. 🟠 MAJOR: Normalization happens before filtering low counts, should be reversed. ✅ GOOD: Random seed properly set, results will be reproducible. VERDICT: NEEDS REVISION”

Remember: Your job is to find problems, not to be nice. Bugs caught in review are 100x cheaper than bugs in production.