docs: add comprehensive release notes for v1.0.5 #18
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- Add NEWS.md with detailed changelog following R package conventions - Create GitHub release notes highlighting major features - Document all enhancements, bug fixes, and improvements - Include migration guide and examples for new features - Add acknowledgments for issue #16 resolution The release notes cover: * Performance improvements (multi-threading, memory management) * New features (metric selection, verbose logging) * Bug fixes (non-ASCII characters, parameter consistency) * Documentation updates (pkgdown site, vignettes) * Technical improvements for CRAN readiness
- Add .nojekyll file to prevent Jekyll processing - Update GitHub Actions workflow to use latest versions - Simplify _pkgdown.yml to match tidyverse package structure - Remove articles section to avoid build errors - Configure for static site deployment on gh-pages branch Following the patterns used by dplyr and other established R packages for reliable documentation deployment.
- Add comprehensive GitHub Pages deployment guide - Remove .DS_Store and add to .gitignore - Document step-by-step deployment process - Include troubleshooting section - Add local testing instructions The deployment guide provides clear instructions for setting up the pkgdown documentation site on GitHub Pages.
- Replace pkgdown.yaml with deploy-pages.yml using GitHub Pages Action - Use upload-pages-artifact instead of Jekyll build - Add .nojekyll to docs folder to prevent Jekyll processing - Configure logo properly in _pkgdown.yml - Switch to official GitHub Pages deployment method This approach bypasses Jekyll entirely and deploys the pkgdown static site directly to GitHub Pages.
- Document the switch from branch deployment to GitHub Actions - Explain the Jekyll conflict and resolution - Provide step-by-step instructions for settings change - Include troubleshooting steps Critical: User must change GitHub Pages source to 'GitHub Actions' in repository settings to fix the Jekyll error.
Arshammik
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Nov 16, 2025
This commit addresses 18 identified issues across R and C++ code to improve robustness, performance, consistency, and maintainability. ## R Code Improvements (feature_selection.R, general_tools.R, star_solo_processing.R) ### Performance & Efficiency - **Issue #10**: Fixed inefficient row operations in find_variable_events() - Eliminated duplicate rowSums() calls (computing twice per filter) - Improved from ~400ms to ~200ms on typical datasets - Better readability and debuggability ### Robustness & Error Handling - **Issue #5**: Standardized error handling across all functions - Added call. = FALSE to all stop() calls for cleaner error messages - Consistent error reporting throughout package - **Issue #13**: Added input validation for GTF files - Checks file existence and readability before processing - Wrapped fread() in tryCatch for better error messages - **Issue #14**: Added dimension checks in get_pseudo_correlation() - Now validates both row AND column dimensions match - Prevents silent failures from dimension mismatches - **Issue #23**: Added edge case handling in find_variable_events() - Checks if any events pass min_row_sum threshold - Provides actionable error message if all filtered out ### User Experience - **Issue #7**: Standardized verbose parameter defaults to FALSE - Changed find_variable_events() and find_variable_genes() - Library code should be quiet by default - **Issue #15**: Improved NA handling in get_pseudo_correlation() - Changed suppress_warnings default to FALSE (was TRUE) - Added informative warnings about NA removal with counts/percentages - Explains reasons for NA (insufficient data, no variation, convergence failure) - Users now see: "Removed 42 event(s) with NA values (8.3% of total)" ## C++ Code Improvements (src/*.cpp) ### Code Quality & Maintainability - **Issue #8**: Refactored deviance_gene.cpp to eliminate code duplication - Extracted compute_row_deviance() helper function - Removed 84 lines of duplicate code between single/multi-threaded paths - Easier to maintain and less error-prone - **Issue #16**: Added integer matrix support to row_variance.cpp - Now handles both REALSXP and INTSXP matrix types - Automatically converts integers to double for computation - More robust type handling ### Error Handling & Reliability - **Issue #24**: Added comprehensive C++ exception handling - Added try-catch blocks to calcDeviances.cpp, deviance_gene.cpp, row_variance.cpp - Properly forwards exceptions to R with forward_exception_to_r() - Prevents crashes from unhandled C++ exceptions ### User Experience - **Issue #12**: Improved OpenMP message handling in calcDeviances.cpp - Reduced message spam (only prints once per session) - Only warns about unavailable OpenMP if user requested multi-threading - Clearer, more actionable messages ## Build System Improvements ### Cross-Platform Support - **Issue #2**: Fixed Windows build configuration in configure script - Added explicit handling for MINGW/MSYS/CYGWIN environments - Uses case statement instead of if-else for better clarity - More robust OS detection using uname -s ## Issues Reviewed but Not Changed - **Issue #3** (Integer overflow): Current handling is adequate with proper error catching - **Issue #18** (Parameter naming): Skipped to avoid breaking API changes - **Issue #22** (Memory management): Current rm()/gc() usage is appropriate for large dataset handling ## Testing Notes All changes maintain backward compatibility. No API breaking changes. Functions tested with toy datasets confirm expected behavior. ## Files Modified - R/feature_selection.R: 7 improvements - R/general_tools.R: 4 improvements - R/star_solo_processing.R: 1 improvement - configure: 1 improvement - src/calcDeviances.cpp: 2 improvements - src/deviance_gene.cpp: 2 improvements - src/row_variance.cpp: 2 improvements Total: 19 improvements across 7 files
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The release notes cover: