greatR 1.0.0

Rewrote registration pipeline from scratch, deprecating unnecessary, and redundant auxiliary functions.
Added L-BFGS-B and Nelder-Mead (now default) optimisation methods to {greatR}.
Switched to manual calculation of log likelihood via calc_loglik() instead of stats::logLik().
Reduced computation time up to 1000 times, (x30 speed-up from package rewrite, and x35 speed-up from switching default optimisation method).
Removed {dplyr}, {magrittr}, {purrr}, {rlang}, and {stringr} as package dependencies.
Added {neldermead} as a package depedency.
Updated list of exported functions:
- register()
- summarise_registration()
- get_approximate_stretch()
- plot_registration_results()
- plot_heatmap()
- calculate_distance()

Improvements

Simplified parameters of main register() function, and added scaling_method.
Simplified structure of output object of register().
Simplfied parameters of summarise_registration(), plot_registration_results(), plot_heatmap(), calculate_distance() to simply require results object from register(), vastly simplifing usage.
Improved messages, errors, and progress indicators with {cli}.
Added correct pluralisation in {cli} messages.
Rewrote unit tests to use {data.table} exclusively for data manipulation.
Added unit tests for calc_loglik_H1(), calc_loglik_H2(), calc_overlapping_percent(), calculate_distance(), cross_join(), get_search_space_limits_from_params(), get_search_space_limits(), objective_fun(), optimise(), plot_heatmap(), plot_registration_results(), preprocess_data(), register_manually(), register(), summary_registration(), validate_params().

Fixed match_names() call when validating accession names in register()
Fixed use of deprecated aes_string() by parsing timepoint_var using !!ggplot2::sym() call.
Fixed preds left join in plot_registration_results().
Fixed issue in plot_registration_results() not working when all genes are unregistered with type = "registered".
Fixed calculation of time_delta in preprocess_data() to ensure it's grouped by gene_id and accession (not just accession).