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…xamples and detailed descriptions
… and descriptions
… add detailed examples
…hance struct descriptions
…ns and structures
… loading functions
…opology functions
TKanX
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Pull request overview
This PR successfully establishes the complete public API surface and comprehensive documentation for dreid-forge, transforming it into a production-ready crate. The changes include thorough RustDoc coverage for all public types and functions, two substantial documentation guides (README and ARCHITECTURE), and a flattened module structure that greatly improves API ergonomics.
Key Changes
- Public API Definition: Flattened module structure with all core types re-exported at the crate root for convenient access
- Comprehensive Documentation: Added module-level docs, type-level docs with examples, and function-level docs for every public item
- Documentation Guides: Created feature-rich README with pipeline visualization and practical examples, plus detailed ARCHITECTURE guide with diagrams and algorithm descriptions
Reviewed changes
Copilot reviewed 22 out of 22 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
src/lib.rs |
Added extensive crate-level documentation with Quick Start example and re-exported all public API types from internal modules |
src/model/*.rs |
Added module and type documentation for atoms, bonds, systems, metadata, topology, and chemical primitives with usage examples |
src/io/mod.rs |
Documented all I/O types, reader/writer interfaces, and configuration structs with practical examples |
src/io/util.rs |
Added documentation for internal conversion utilities between dreid-forge and bio-forge data models |
src/io/error.rs |
Documented error variants with detailed descriptions of error sources and context |
src/io/bgf/writer.rs |
Added documentation for BGF file writer with usage example |
src/io/lammps/writer.rs |
Documented LAMMPS output generation with configuration examples and updated test to use struct literal syntax |
src/forge/*.rs |
Added comprehensive documentation for parameterization pipeline stages, configuration types, and internal modules |
README.md |
Created project README with highlights, pipeline diagram, dependency table, and two complete usage examples |
ARCHITECTURE.md |
Created 945-line architecture guide with Mermaid diagrams, algorithm descriptions, and internal design documentation |
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TKanX
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feature/7-finalize-public-api-surface-implement-complete-rustdoc-documentation-and-create-readme-with-architecture-guide
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Summary:
Established the definitive public API surface for
dreid-forgeand implemented complete RustDoc coverage for all exported modules. Transforms the library into a consumer-ready crate by flattening the module structure for better ergonomics and providing extensive high-level documentation. It includes a detailed Architecture guide with diagrams, a feature-rich README, and updates to core dependencies to their latest versions.Changes:
Defined Public API Surface:
src/lib.rsto export a flat, ergonomic API, re-exporting core types frommodel,io, andforgeto the crate root.Implemented High-Level Documentation:
README.mdfeaturing project highlights, pipeline visualization (Mermaid), and practical usage examples for parameterizing small molecules and processing PDB files.ARCHITECTURE.md, a comprehensive guide detailing the system overview, I/O layer architecture, Forge pipeline stages, algorithmic deep dives (QEq, Torsion Rules), and error handling strategies.Added RustDoc Coverage:
///) for all public structs, enums, and functions.ForgeConfig,System,BioReader, andLammpsConfig.forge::intermediate,forge::paramgen) to assist future contributors.