Python Rust Package Methods Check

Python/Rust Package Methods Check

Review changed Python, Rust, or mixed-language scientific software with emphasis on methodological correctness, numerical robustness, package behavior, tests, and documentation.

Use this for:

• Python packages
• Rust crates
• Python bindings to Rust, C, C++, or Fortran
• scientific CLI tools
• simulation code
• numerical methods
• statistical estimators
• bioinformatics pipelines
• pre-PR review before merging

Do not focus mainly on formatting unless formatting affects correctness, maintainability, or user-facing behavior.

1. Scientific and statistical correctness

Ask:

• What is the target quantity?
• What is observed versus inferred?
• What is an input, hyperparameter, estimator, posterior quantity, diagnostic, or output?
• Are assumptions stated and consistent with the implementation?
• Are transformations, offsets, links, scales, and parameterizations handled correctly?
• Are probability, log-probability, likelihood, loss, and objective functions clearly distinguished?
• Are quantities returned on the intended scale?
• Are uncertainty-related quantities labeled and computed correctly?
• Are defaults scientifically defensible?
• Are preprocessing, filtering, normalization, pseudocounts, or thresholds hiding assumptions?

2. Numerical robustness

Check for:

• unstable subtraction, division, exponentiation, or log operations
• underflow and overflow
• division by zero or near-zero values
• unguarded log, exp, softmax, logsumexp, sigmoid, or likelihood calculations
• singular, ill-conditioned, or non-positive-definite matrix operations
• incorrect dtype behavior, integer division, precision loss, or silent casting
• incorrect handling of NaN, Inf, None, missing values, or masked arrays
• poor behavior for small sample sizes, sparse data, rare events, extreme counts, heavy tails, or skewed distributions
• boundary cases such as empty arrays, one-row inputs, one-column inputs, all-zero rows, ties, duplicate IDs, and one-level factors

For Rust specifically, also check:

• panic risk from unwrap, expect, indexing, slicing, or unchecked assumptions
• misuse of Result, Option, or error propagation
• unsafe blocks and whether they are justified
• ownership, borrowing, cloning, and allocation patterns that may affect correctness or performance
• numeric conversions using as that may truncate, overflow, or lose precision
• parallel code for race conditions or nondeterministic outputs

For Python specifically, also check:

• mutable default arguments
• shape/broadcasting bugs
• pandas index alignment bugs
• dtype coercion
• chained assignment
• hidden global state
• random seed behavior
• inconsistent NumPy, pandas, Polars, PyTorch, JAX, or SciPy array semantics

3. API and package behavior

Ask:

• Are public and private APIs separated clearly?
• Are names, arguments, defaults, and return values coherent?
• Are argument checks early and informative?
• Are error messages actionable?
• Is backward compatibility preserved where reasonable?
• Are dependencies necessary and minimal?
• Are examples safe, fast, and reproducible?
• Are CLI arguments documented and stable?
• Are outputs deterministic when they should be?
• Are files written only where the user expects?

For Python packages, check:

• pyproject.toml
• package layout
• imports
• optional dependencies
• type hints
• tests
• wheels/build behavior
• CLI entry points

For Rust crates, check:

• Cargo.toml
• feature flags
• public API exports
• examples
• docs
• benchmarks
• tests
• error types

4. Tests

Propose the smallest tests that would catch real breakage.

Prefer:

• one minimal regression test over broad rewrites
• edge-case tests for boundary inputs
• deterministic tests for random algorithms
• property-style checks when exact values are hard to specify
• numerical tolerance checks with justified tolerances
• cross-language consistency tests for Python/Rust bindings

Do not suggest large test rewrites unless the current tests cannot detect the risk.

5. Performance

Flag performance only when it affects usability, scalability, or correctness.

Check:

• avoidable quadratic or cubic complexity
• unnecessary copies
• repeated parsing or repeated allocation
• slow loops that should be vectorized or moved to Rust
• memory growth with large matrices, count tables, sparse arrays, or simulation grids
• parallelization that increases memory more than expected

6. Documentation

Flag documentation that no longer matches behavior:

• README
• docstrings
• examples
• vignettes/tutorials
• CLI help
• changelog
• API reference
• mathematical notation
• default values
• output schema

Output format

Return exactly these sections:

Summary

2-4 sentences on what changed and the main risk.

Major issues

For each issue, give:

• Issue
• Why it matters
• Smallest fix

Suggested tests

List minimal tests to add or update.

Documentation updates

List docs, examples, or CLI help that should be updated.

Performance or scalability concerns

Only include concerns that matter for realistic use.

Nice-to-have improvements

Optional cleanup that is not required for correctness.

Behavior:

• Be skeptical about scientific correctness, not just syntax.
• Prefer the smallest correct patch.
• Distinguish correctness issues from maintainability issues.
• If uncertain, say exactly what is uncertain.
• Review first; do not start editing unless explicitly asked.