[pull] master from JuliaDiff:master #5
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Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v4...v5) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]>
…ons/checkout-5 Bump actions/checkout from 4 to 5
- Document epsilon computation functions with mathematical details - Add comprehensive JVPCache struct and constructor documentation - Document setindex overloads and utility functions (_vec, _mat) - Add docstrings for sparse Jacobian internal functions - Document Hessian utility functions and cache helpers - Include examples, parameter descriptions, and implementation notes 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
Formatted all modified source files using JuliaFormatter with SciMLStyle: - Fixed indentation and spacing consistency - Standardized function parameter alignment - Applied consistent code style throughout 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
- Added finite_difference_jvp and finite_difference_jvp! to docs - Added JVPCache documentation section - Included explanation of JVP functionality and use cases - Documentation now builds cleanly without warnings 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
- Split single API page into organized category pages: - Overview (api.md) - Quick start and navigation - Derivatives - Single/multi-point derivative functions - Gradients - Gradient computation with detailed notes - Jacobians - Jacobian matrices including sparse support - Hessians - Hessian matrices with mathematical background - JVP - Jacobian-vector products for efficient directional derivatives - Utilities - Internal functions and helpers - Updated pages.jl with hierarchical documentation structure - Enhanced each page with category-specific guidance and examples - Improved navigation with cross-references between sections - Documentation builds successfully with clean sidebar organization 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
- Moved API reference content to index page (generated from make.jl) - Removed separate API reference page level from navigation - Reorganized all pages to show summaries before docstrings - Updated pages.jl to have flat navigation structure - All category pages now appear directly in sidebar - Index page contains comprehensive API guidance and navigation Documentation structure now follows: - Home (with API reference) → Category pages directly - Each page: Summary/Notes → Functions → Cache 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
- Removed API reference content from index page generation - Index page now contains only README and reproducibility content - Clean documentation structure with direct category navigation - Documentation builds successfully with minimal warnings 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
- Created comprehensive "Step Size Selection" page covering: - Mathematical theory of optimal step sizes - Error analysis (truncation vs round-off) - Adaptive step sizing algorithms - Special cases for complex step and sparse Jacobians - Renamed "Utilities" to "Internal Utilities" with complete coverage of: - Array utilities (_vec, _mat, setindex overloads) - Hessian utilities (_hessian_inplace, mutable_zeromatrix) - Sparse Jacobian internals (_make_Ji, _colorediteration!) - Performance optimizations and sparsity detection - Cache resize functions and error handling - Updated pages.jl navigation structure - Documentation builds cleanly with proper organization 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
…-docstrings Add comprehensive API documentation and restructure docs organization
- Moved fx0 computation outside the loop in finite_difference_gradient! - Optimizes function evaluations from 2N to N+1 for forward differences - Maintains compatibility with both cached and uncached function values - Simplifies logic by eliminating conditional branches in the main loop Fixes #202 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
…evaluation Fix repeated evaluation of fx0 in forward gradient computation
…cer.jl` and `SparseMatrixColorings.jl`
Update Docs: Replace `SparseDiffTools.jl` with `SparseConnectivityTracer.jl` and `SparseMatrixColorings.jl`
Feature introduced in Pkg.jl v1.11
Use consistent spacing and alignment for type annotations and default values
Update documentation infrastructure and minor formatting
Update finitedifftests.jl for non-allocating
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