Changelog

Fixed missing package dependencies in DESCRIPTION: added cli, cowplot, reshape2, and broom to Imports.
Removed pheatmap, R6, and clisymbols from Imports (unused); moved evoverse.datasets to Suggests.
Replaced deprecated dplyr::progress_estimated() (removed in dplyr 1.0.0) with cli::cli_progress_bar() in revolver_fit, revolver_cluster, remove_drivers, and utils_jackknife.
Removed require() call inside plot_patient_oncoprint (non-standard in package code).
Fixed typos in DESCRIPTION description field.
Fixed incorrect install URL in README.md.
Updated GitHub Actions workflows to current versions (actions/checkout@v4, r-lib/actions/*@v2).
Fixed duplicate @param x roxygen entries in compute_clone_trees and compute_mutation_trees; added missing @return and @param documentation.
Fixed revolver_cluster example referencing non-existent revolver_evo_distance().
Added ^old_vignette$ to .Rbuildignore.
Removed large commented-out dead code block from revolver_jackknife.R.
Updated Date to 2026-06-29.

Re-coding of all the internal structure of the cohorts using tibbles and in general the tidy data paradigm;
New interface to access the data, based on ad hoc getter functions;
All plotting functions have been re-implemented using ggplot to gain more flexibility, and remove the PDF jamming routines;
Clone trees from CCF data have been extracted and included in a new dedicated package caravagn.github.io/ctree;
Added a NEWS.md file to track changes to the package.

Bugs fixing, and removal of the actual code taken from CloneEvol to increase clarity and improve performance.
jamPDF is now associated to an option (default = FALSE) to increase compatibility with MS Windows systems.

revolver 1.0.1