                        Changes in version 1.2.5                        

  - breaking:
    
      - inferCSN now keeps the inference core only: inferCSN(),
        single_network(), fit_greedy_l0(), fit_greedy_l0_batch(),
        network_format(), and filter_sort_matrix().

  - func:
    
      - Added a backward-deletion refinement pass to the batch greedy-L0
        solver (fit_greedy_l0_batch()), removing predictors that no
        longer improve BIC after forward selection, which avoids
        over-selecting the support near perfect fits.
      - Group numerically tied deletion evidence against a fixed group
        maximum using a relative tolerance of 1e-12 when computing
        signed ordinal weights.
      - Added direct-QR regression checks for batch coefficients, BIC,
        deletion evidence, and near-perfect-fit behavior.
      - Cell preprocessing (meta_cells() and subsampling()) now lives in
        multiCSN; call multiCSN::meta_cells() or multiCSN::subsampling()
        instead.

  - deps:
    
      - Remove unused gtools and RTransferEntropy suggestions.
      - Drop plotting and evaluation dependencies (ggplot2, thisplot,
        patchwork, precrec, pROC).
      - Remove RANN, igraph, irlba, and proxy from this package after
        moving cell preprocessing to multiCSN. Drop scatter-only and
        network-plot Suggests (ggExtra, ggpointdensity, ggpubr,
        RColorBrewer, viridis, ggnetwork, ggraph, dplyr, purrr,
        ComplexHeatmap, circlize, gganimate, network, plotly,
        tidygraph).

  - ci:
    
      - Fixed failing package CI checks.
      - Removed unused dev/config_attachment.yaml.

                        Changes in version 1.2.4                        

  - breaking:
    
      - Replaced fit_srm() with the greedy-L0 interfaces fit_greedy_l0()
        and fit_greedy_l0_batch().
      - Replaced the legacy regularization, cross-validation, and
        subsampling arguments of inferCSN() with pseudotime,
        max_support_size, lag_fraction, and lag_steps.

  - func:
    
      - Added static and pseudotime-ordered network inference for dense
        and sparse matrices, including multi-branch pseudotime and
        deterministic parallel output.
      - Added early-precision, signed-edge, motif, path, and cross-run
        stability metrics.
      - Extended plot_network_heatmap() with aligned multi-network
        layouts, performance labels, and ground-truth cell borders.

  - deps:
    
      - Removed L0Learn and added thisplot for plotting support.

  - ci:
    
      - Added R-hub platform checks and manual CRAN release checks, and
        updated checkout actions to v5.

  - docs:
    
      - Updated generated documentation, examples, example datasets, and
        the pkgdown reference index.

                        Changes in version 1.2.3                        

  - func:
    
      - Optimize check_parameters() for check input parameters.

  - docs:
    
      - Updated documentation across multiple functions.

                        Changes in version 1.2.2                        

  - func:
    
      - Removed network_sift() and weight_sift() functions.
      - Removed S4 method for data.frame.

  - docs:
    
      - Updated documentation across multiple functions.

                        Changes in version 1.2.1                        

  - func:
    
      - Fixed warning on Windows platform for better compatibility.

  - docs:
    
      - Updated documentation across multiple functions.

                 Changes in version 1.2.0 (2025-10-16)                  

  - func:
    
      - Removed srm related functions and files.
      - Removed RcppArmadillo dependency.
      - Removed Makevars files for simplified build process.
      - Reorganized package structure by moving and removing files.

  - refactor:
    
      - Updated package template structure.
      - Cleaned up package dependencies and build configuration.

  - docs:
    
      - Updated package logo.
      - Improved documentation formatting.

                        Changes in version 1.1.9                        

  - func:
    
      - Enhanced logo printing functionality.

  - docs:
    
      - Updated documentation across multiple functions.

                        Changes in version 1.1.8                        

  - func:
    
      - Added inferCSN_logo() function for displaying package logo.
      - Added new parameters for log_message() function.
      - Modified .cores_detect() function for better CPU core detection.
      - Removed PKG_LIBS from Makevars and Makevars.win files.
      - Moved utility functions to thisutils package.

  - refactor:
    
      - Updated pkgdown webpage theme.
      - Fixed warnings and errors in GCC compilation.
      - Optimized document structure.

  - docs:
    
      - Added examples in README.
      - Updated package description.
      - Updated renv configuration files.

                 Changes in version 1.1.7 (2025-03-30)                  

  - func:
      - Added sparse_cov_cor() function for sparse covariance and
        correlation computation.
      - Removed deprecated sparseCovCor function.
      - Updated documentation for sparse_cor() function.

                 Changes in version 1.1.6 (2025-03-27)                  

  - func:
    
      - Fixed error in table_to_matrix() function.
      - Optimized performance for matrix operations.

  - bugs:
    
      - Fixed error in pkgdown build process.

  - docs:
    
      - Added example for calculate_accuracy() function.
      - Modified examples for plot_network_heatmap() function.
      - Updated badge display.
      - Updated ProjectId.

                        Changes in version 1.1.3                        

  - func:
    
      - Added new network evaluation functions for assessing network
        quality.
      - Updated import records for better dependency management.

  - docs:
    
      - Edited documentation for multiple functions.
      - Modified documentation for plot_network_heatmap() function.
      - Updated test-coverage.yaml file.
      - Renamed files for better organization.

  - refactor:
    
      - Added check workflow for automated testing.
      - Modified import statements.

                        Changes in version 1.1.2                        

  - func:
    
      - Renamed fit_sparse_regression() to fit_srm() for shorter
        function name.
      - Modified parameters for multiple functions.

  - docs:
    
      - Updated package logo.
      - Updated badge display.

                        Changes in version 1.1.1                        

  - func:
      - Renamed function fit_sparse_regression() to fit_srm().

                        Changes in version 1.1.0                        

  - func:
      - Modified algorithm parameter to non-exported for internal use.

                        Changes in version 1.0.9                        

  - func:
    
      - Added new utility functions including %s%, matrix_to_table(),
        pearson_correlation(), simulate_sparse_matrix(),
        plot_coefficients(), split_indices(), subsampling_fun(), and
        weight_sift().
      - Added new C++ functions including network_format(),
        prepare_calculate_metrics() for improved performance.
      - Added CITATION file for proper citation.
      - Renamed function from percent_samples to subsampling.
      - Imported native R pipe operator |> for better compatibility with
        R >= 4.1.0.

  - refactor:
    
      - Renamed function %s% to %ss%.
      - Renamed functions to calculate_metrics().
      - Modified structure of sparse_regression() output.
      - Modified normalization method implementation.
      - Updated log_message() function.
      - Improved documentation across multiple functions.

  - bugs:
    
      - Fixed multiple coding style issues.
      - Fixed error in various functions.
      - Fixed warning when package installation.
      - Fixed download badge display.

  - docs:
    
      - Optimized function documentation.
      - Updated .gitignore.
      - Updated packages record information.

  - deps:
    
      - Deleted suggests packages that are no longer needed.
      - Deleted useless packages from dependencies.

                 Changes in version 1.0.8 (2024-08-24)                  

  - func:
    
      - Added log_message() function for consistent logging across
        package.
      - Added export of log_message() for user access.
      - Modified documentation for multiple functions.

  - deps:
    
      - Added import of cli package for better message formatting.
      - Modified Imports section.
      - Removed exports for internal functions.

  - docs:
    
      - Updated README.
      - Improved documentation consistency.

  - refactor:
    
      - Coding style improvements.

                        Changes in version 1.0.7                        

  - func:
    
      - Removed export of prepare_network_data() as internal function.
      - Modified documentation for multiple functions.

  - bugs:
    
      - Fixed error for normalization() when setting method to softmax.

                        Changes in version 1.0.6                        

  - func:
    
      - Added new visualization functions: plot_embedding() and
        plot_weight_distribution().
      - Added new parameters for plot_weight_distribution().
      - Added asMatrixParallel() for parallel matrix operations.
      - Added RcppParallel support for improved performance.
      - Added PKG_LIBS information in Makevars.
      - Added new function check_sparsity() for sparsity checking.
      - Added new global variables.
      - Renamed performance_evaluation functions.
      - Renamed files and functions for better organization.
      - Support for sparse matrix operations.
      - Updated R version requirement.
      - Reduced computation complexity for better performance.
      - Removed export of check_parameters().

  - bugs:
    
      - Fixed error for .weight_sift().
      - Fixed error and improved coding style in plot_scatter().
      - Fixed document issues.

  - docs:
    
      - Modified documentation for multiple functions.
      - Modified examples, parameters, and documentation.
      - Updated renv files.
      - Updated Makevars files.
      - Updated document for some parameters.

  - refactor:
    
      - Coding style improvements.
      - Renamed functions and files.

                 Changes in version 1.0.5 (2024-06-26)                  

  - func:
    
      - Added entropy to filter edges in network.
      - Added new function as_matrix() for matrix conversion.
      - Added new function plot_scatter() for scatter plot
        visualization.
      - Added new parameter for plot_scatter().
      - Added new function network_sift() for network filtering (renamed
        from previous version).
      - Added new functions: r_square(), plot_contrast_networks(),
        plot_dynamic_networks().
      - Added new function map_parallel() and parallelize_fun() for
        parallel processing.
      - Added .softmax() function.
      - Added new parameter heatmap_size_lock for network.heatmap().
      - Modified S4 method for inferCSN.
      - Removed dynamic.networks, contrast.networks functions
        (renamed/replaced).
      - Renamed net.format to network_format().
      - Renamed dynamic.networks to plot_static_networks().
      - Fixed errors and added new parameters for network_sift().
      - Deleted unnecessary functions.
      - Modified import functions and packages.
      - Using as_matrix() instead of as.matrix() for better performance.

  - deps:
    
      - Removed progress package and added pbapply package.
      - Added new packages for enhanced functionality.
      - Updated imports.

  - bugs:
    
      - Fixed error in check.parameters().
      - Fixed multiple errors.
      - Fixed warning.
      - Fixed note info.

  - docs:
    
      - Updated badges.
      - Modified examples.
      - Updated _pkgdown.yml.
      - Modified examples and figure style.
      - Updated renv file.
      - Modified parameter description of functions.
      - Updated .gitignore.
      - Updated README.

  - refactor:
    
      - Coding style improvements across multiple files.
      - Improved function organization.

                 Changes in version 1.0.3 (2024-04-17)                  

  - func:
    
      - Added new function weight_filter() for filtering weights.
      - Added new parameters for network.heatmap().
      - Set crossweight example to \dontrun{} for CRAN compatibility.

  - docs:
    
      - Updated NAMESPACE and import records.

                        Changes in version 1.0.2                        

  - func:
    
      - Added new function normalization() for data normalization.
      - Added new function crossweight() for cross-weight analysis.
      - Added new function crossweight_params().
      - Added new function extract_net() (later deleted).
      - Added new example data example_meta_data.
      - Updated crossweight and related functions.
      - Updated example data.
      - Added new parameters for calculate.gene.rank().
      - Renamed function to filter_sort.matrix to handle CRAN warning.
      - Renamed multiple functions for consistency.
      - Deleted function extract_net().

  - bugs:
    
      - Fixed error when sample.
      - Fixed multiple errors.
      - Fixed pkgdown error.

  - docs:
    
      - Updated README.
      - Updated crossweight.Rd.
      - Updated _pkgdown.yml.
      - Updated NAMESPACE.
      - Updated renv.lock.
      - Modified examples.
      - Formatted progress information.

  - refactor:
    
      - Fixed coding style issues.

                 Changes in version 1.0.1 (2024-03-15)                  

  - func:
    
      - Added new function filter.sort.matrix() for efficient matrix
        filtering and sorting.
      - Optimized memory consumption for handling large datasets.
      - Modified function used to handle data.
      - Modified parameter k_folds.
      - Modified parameter regulators_num.
      - Renamed multiple functions for consistency:
        calculate.gene.rank(), sub.model.fit(), model.fit(),
        single.network().
      - Added examples for multiple functions including
        network.heatmap(), dynamic.networks().
      - Added new parameter for net.format().
      - Modified some functions for better performance.
      - Fixed error code.

  - bugs:
    
      - Fixed multiple errors.

  - docs:
    
      - Updated README with improved examples.
      - Updated _pkgdown.yml.
      - Updated .gitignore.
      - Updated cran_release.R.
      - Updated .Rbuildignore.
      - Modified parameter information.
      - Added test examples for table_to_matrix().
      - Updated logo.svg.

  - refactor:
    
      - Removed test files.
      - Updated NAMESPACE.
      - Updated renv file.
      - Added examples throughout.

                 Changes in version 1.0.0 (2024-02-09)                  

  - feat:
    
      - First major release of inferCSN package.
      - Core functionality for inferring cell-specific gene regulatory
        networks.
      - Sparse regression-based network inference algorithm.
      - Support for single-cell RNA-seq data.
      - Network visualization and analysis functions.
      - Performance evaluation metrics.

  - docs:
    
      - Complete documentation for all exported functions.
      - Comprehensive README with usage examples.
      - Package website with pkgdown.

                 Changes in version 0.99.9 (2024-01-10)                 

  - func:
    
      - Updated table_to_matrix.cpp for improved performance.
      - Updated version to 0.99.9 in preparation for CRAN submission.

  - docs:
    
      - Updated cran_release.R.
      - Fixed example information.
      - Added new function and renamed files.

                 Changes in version 0.99.8 (2023-12-04)                 

  - func:
    
      - Updated inferCSN() function with improvements.
      - Updated C++ functions for better performance.
      - Updated and formatted code across multiple files.
      - Updated example data.

  - bugs:
    
      - Fixed pkgdown error.

  - docs:
    
      - Fixed error and modified documentation.
      - Updated renv.lock.
      - Updated requirements.sh.

                 Changes in version 0.99.7 (2023-10-30)                 

  - func:
    
      - Fixed error when compiling on CentOS system.
      - Updated requirements.sh.

  - refactor:
    
      - Version update for CRAN submission preparation.

                        Changes in version 0.1.1                        

  - func:
    
      - Initial package development.
      - Basic sparse regression implementation.
      - C++ integration for performance.

  - docs:
    
      - Basic documentation structure.
      - Initial README.

                        Changes in version 0.1.0                        

  - feat:
      - Initial version.
