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…hanges

- Updated `Cargo.toml` and `Cargo.lock` to reflect the new version and improved dependencies.
- Enhanced the library's description to highlight its production-ready features, including numerical stability and comprehensive diagnostics.
- Introduced a new `CHANGELOG.md` to document significant changes and improvements in version 0.3.0.
- Added a new example for improved Gaussian mean estimation, showcasing enhanced diagnostics and validation tests.
- Implemented structured error handling with the new `FugueError` type for better debugging and user feedback.
- Refactored inference algorithms to include a Diminishing Adaptation strategy for MCMC, ensuring theoretical soundness and improved performance.
- Added numerical utilities for stable computations and enhanced existing distributions with parameter validation.
- Comprehensive tests for numerical stability and distribution correctness to ensure robustness under extreme conditions.
- Updated README.md to provide a comprehensive overview of Fugue, highlighting its production-ready features and extensive capabilities.
- Added detailed sections on library features, quick start instructions, core concepts, and validation/testing methodologies.
- Introduced a new example for Bayesian linear regression, demonstrating practical usage and enhanced diagnostics.
- Improved formatting and organization of existing examples for better clarity and usability.
- Refactored code in example files to ensure consistency and adherence to best practices.
- Updated CHANGELOG.md to reflect major academic improvements, performance optimizations, and new features in version 0.3.0.
- Removed the deprecated AdaptiveScales struct from the codebase, encouraging users to transition to DiminishingAdaptation for better theoretical properties.
- Enhanced various modules with improved parameter validation and error handling for robustness.
- Updated README.md to introduce the new type-safe distribution system, highlighting its benefits and key improvements.
- Added a new section demonstrating type-safe usage of Bernoulli, Poisson, and Categorical distributions with natural return types.
- Introduced a new example file `fully_type_safe.rs` showcasing the type-safe distribution system in action.
- Refactored existing examples to utilize type-safe boolean comparisons and improved clarity in probabilistic modeling.
- Enhanced documentation across various modules to reflect changes in distribution handling and type safety.
- Updated distribution constructors (e.g., Normal, Bernoulli, Poisson) to utilize safe constructors with validation, ensuring parameters are checked for correctness.
- Refactored examples and tests to demonstrate the new type-safe distribution system, improving clarity and usability.
- Enhanced README.md to reflect changes in distribution handling and provide examples of safe usage.
- Introduced a new test suite for validating distribution constructors and their parameters, ensuring robustness against invalid inputs.
- Improved error handling in the core library to provide clearer feedback on parameter validation failures
@alexnodeland alexnodeland requested a review from Copilot August 22, 2025 21:23
@alexnodeland alexnodeland self-assigned this Aug 22, 2025

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- Updated `Cargo.toml` to include `criterion` for benchmarking and added a new `memory_benchmarks` file for performance testing of memory management optimizations.
- Enhanced `Cargo.lock` with new dependencies including `criterion`, `ciborium`, and others to support the latest features and improvements.
- Refactored `TraceBuilder` and `TracePool` in `memory.rs` to improve memory allocation efficiency and added statistics tracking for the trace pool.
- Introduced various benchmarks to evaluate the performance of memory management strategies, including trace building and pooling efficiency.
- Introduced a new benchmark suite for MCMC algorithms in `benches/mcmc_benchmarks.rs`, focusing on performance improvements and diagnostics.
- Updated `Cargo.toml` to include the new `mcmc_benchmarks` benchmark group.
- Modified the `DiminishingAdaptation` struct in `mcmc_utils.rs` to store scales and their cached logarithms, optimizing performance during adaptation updates.
- Enhanced the `get_scale` and `update` methods to utilize cached logarithmic values, reducing computational overhead.
- Updated the Metropolis-Hastings algorithm to utilize type-safe proposal strategies, ensuring that proposals respect the original types of parameters (e.g., bool, u64, usize).
- Introduced new proposal strategies (GaussianWalkProposal, FlipProposal, DiscreteWalkProposal, UniformCategoricalProposal) to improve proposal generation based on value types.
- Enhanced documentation to clarify the limitations of the current implementation regarding distribution-aware proposals, particularly for bounded distributions like Beta.
- Added comprehensive tests to validate the type safety of the MCMC implementation, ensuring that types are preserved across various parameter types during sampling.
- Improved the proposal function to leverage the new strategy traits, enhancing numerical stability and type safety in the proposal process.
- Updated `mcmc_benchmarks.rs` to enhance readability and maintainability by reorganizing imports and formatting code.
- Improved the performance benchmarks for DiminishingAdaptation and MCMC diagnostics, ensuring thorough testing of adaptation strategies.
- Refactored memory benchmarks in `memory_benchmarks.rs` for consistency and clarity, including adjustments to address patterns and trace pool efficiency.
- Enhanced the `mcmc_utils.rs` file by cleaning up unnecessary whitespace and ensuring consistent formatting across functions.
- Updated tests in `type_safe_mh_tests.rs` to validate type safety and proposal strategies, ensuring robust performance across various parameter types.
…testing, and benchmarking

- Added core dependencies: `rand`, `rand_distr`, and `libm`.
- Introduced CLI dependency: `clap` with derive feature.
- Included testing dependency: `proptest`.
- Added benchmarking dependency: `criterion` with HTML reports feature.
- Introduced a comprehensive documentation style guide to ensure consistency across the Fugue repository, covering module structure, common patterns, performance considerations, and maintenance guidelines.
- Added a standardized README template for modules, outlining essential sections such as overview, quick start, components, usage examples, and design principles to facilitate uniform documentation practices.
- Enhanced existing README files in core, inference, and runtime modules with improved structure and clarity, aligning with the new style guide.
- Introduced a comprehensive error handling framework in the `error.rs` module, featuring structured error types with rich context information for better debugging.
- Added `ErrorCode` and `ErrorCategory` enums for programmatic error categorization and handling.
- Enhanced `FugueError` to include error codes and context, improving the clarity of error messages.
- Implemented helper methods and macros for convenient error creation and context management.
- Updated distribution constructors and validation methods to utilize the new error handling system, ensuring consistent error reporting across the library.
- Added extensive tests to validate the new error handling features, including error codes, context information, and helper macros.
- Introduced a Makefile to streamline development tasks, including targets for testing, coverage reports, linting, and code formatting.
- Added commands for generating coverage reports using cargo-tarpaulin and cleaning build artifacts.
- Updated .gitignore to exclude coverage reports and profiling files, ensuring a cleaner repository.
- Enhanced README with CI badge and Codecov integration for better visibility of test coverage and continuous integration status.
@alexnodeland alexnodeland requested a review from Copilot August 23, 2025 01:16
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Pull Request Overview

This pull request aims to "refactor/productionize" the Fugue probabilistic programming library by adding comprehensive test coverage across multiple modules. The changes focus on expanding the test suite to cover previously untested functionality, improving error handling validation, and ensuring robustness of inference algorithms.

Key changes include:

  • Addition of 13 new comprehensive test modules covering VI inference, validation framework, type safety, SMC methods, runtime interpreters, and more
  • Enhanced error handling tests with specific error codes and validation scenarios
  • Extensive numerical stability and edge case testing

Reviewed Changes

Copilot reviewed 64 out of 66 changed files in this pull request and generated 7 comments.

Show a summary per file
File Description
tests/vi_inference_tests.rs Tests for Variational Inference methods including ELBO estimation and mean-field guides
tests/validation_framework_tests.rs Tests for statistical validation framework with KS tests and conjugate model validation
tests/type_safety_tests.rs Comprehensive type safety tests for distribution constructors and trace accessors
tests/type_safe_mh_tests.rs Tests for type-safe Metropolis-Hastings implementation across different data types
tests/test_utils.rs Shared test utilities including helper functions, models, and statistical tools
tests/smc_inference_tests.rs Tests for Sequential Monte Carlo inference methods and particle filtering
tests/runtime_interpreter_tests.rs Tests for runtime interpreters and handlers with mixed types and edge cases
tests/property_tests.rs Updated property-based tests to use new distribution constructors
tests/numerical_utilities_tests.rs Comprehensive tests for numerical utilities like log_sum_exp and log_gamma
tests/numerical_stability_tests.rs Tests validating numerical stability under extreme conditions
tests/layout_tests.rs Updated to use new distribution constructor pattern
tests/integration_examples.rs Integration tests mirroring examples directory functionality
tests/inference_tests.rs Updated to use new distribution constructor pattern
tests/extended_distribution_tests.rs Updated distribution tests using natural type system
tests/enhanced_error_handling_tests.rs Tests for enhanced error handling system with error codes and categories
tests/distribution_tests.rs Updated basic distribution tests
tests/diagnostics_tests.rs Comprehensive tests for MCMC diagnostics and parameter summaries
tests/core_tests.rs Updated core functionality tests
tests/comprehensive_error_tests.rs Extensive error handling validation tests

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@alexnodeland alexnodeland marked this pull request as ready for review August 23, 2025 01:48
@alexnodeland alexnodeland merged commit a6d0695 into develop Aug 23, 2025
@alexnodeland alexnodeland deleted the refactor/productionize branch August 28, 2025 21:53
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2 participants