Changes in version 1.3.0 (2026-03-31) - MODERNISATION: Replace %>% pipes with native |> pipe throughout. - MODERNISATION: Remove magrittr dependency; replace set_rownames()/set_colnames() with base R assignments. - MODERNISATION: Replace deprecated dplyr::do() with reframe(). - MODERNISATION: Replace deprecated mutate_at() with mutate(across()). - FIX: Add missing "id" to globalVariables() to silence R CMD check NOTE about no visible binding for global variable id. - FIX: Replace relative cross-vignette URLs (../create_ti_method_xxx) with proper file-relative links to silence R CMD check NOTE. - MINOR CHANGE: Update GitHub Actions workflows to use actions/checkout@v6 and actions/upload-artifact@v7. - MINOR CHANGE: Add pkgdown.yaml GitHub Actions workflow for website deployment. Changes in version 1.2.5 (2025-11-26) - BUG FIX convert_definition(): Fix for purrr having deprecated invoke in favour of exec (PR #166). Changes in version 1.2.4 (2023-07-19) - Resubmission after babelwhale was removed from CRAN. - MINOR CHANGE: Added @return documentation to all functions. Changes in version 1.2.3 (2023-03-01) - MINOR CHANGE: Fixes to metadata (documentation, citation entry, broken links). - MINOR CHANGE: Use alternative method for checking whether dynmethods is installed. Changes in version 1.2.2 (2021-03-23) - MAJOR CHANGE convert_milestone_percentages_to_progressions(): Rewrite implementation to attain significant speedup. - MINOR CHANGE infer_trajectory(): Infer command (Rscript/python) from file extension if possible and avoid using shebang to execute script, because R CMD check for R 4.0 puts Rscript and R dummy executables on the path before R CMD check. This means #!/usr/bin/env Rscript does not work anymore. - MINOR CHANGE add_feature_importance(): Add a function for adding feature importance scores to a trajectory. - BUG FIX project_waypoints(): Rename milestone waypoints such that the names are unique. - BUG FIX infer_trajectory(): Fix error message printing. - BUG FIX: dyndimred is used conditionally. - BUG FIX: wrap_expression() and add_expression(): Do not override feature_info when it already exists in dataset. Changes in version 1.2.1 (2020-05-14) - BUG FIX project_trajectory(): Correctly pass parameters. - MINOR CHANGES select_waypoints(): Do not recompute waypoints if trajectory already contains some. - MINOR CHANGES convert_progressions_to_milestone_percentages(): Solve tapply issues ahead of dplyr 1.0 release. Changes in version 1.2.0 (2020-03-09) - FUNCTIONALITY: Improved RNA velocity handling. Not all features need to be present in the projected expression, allowing integration with standard velocyto.R pipelines. - BUG FIX calculate_pseudotime(): Fix pseudotime calculation on branching trajectories (#139). - BUG FIX flip_edges(): Also flip dimred_segment_progressions if available. - BUG FIX add_root(): Fix rooting for some linear trajectories (#149) - MINOR CHANGES: Allow a named vector for groups_id prior information (#154) - MINOR CHANGES: Moved orient_topology_to_velocity() to scvelo R package. - BUG FIX simplify_trajectory(): handle dimred_milestones and dimred_segments values (#153). - BUG FIX add_dimred(): Do not execute example of dyndimred if is not installed. Changes in version 1.1.4 (2019-10-11) First CRAN release! - BUG FIX: Fixed #142 where the error message was truncated - DOCUMENTATION: Added examples to all functions. Changes in version 1.1.3 - MINOR CHANGE add_dimred(): Add a separate argument for specifying the projected dimred rather than expecting the projected dimred to be passed as additional columns in dimred. - BUG FIX: Fix for dynverse/dyno#52, do specify whether or not to use optional priors when passed. Changes in version 1.1.2 - FEATURE: Add leaves_n as prior information Changes in version 1.1.1 - BUG FIX: Fixed bug for directed geodesic distances with disconnected gra phs, dynverse/dynplot#37 Changes in version 1.1 - FEATURE: RNA velocity data can now be included in the wrapper - FEATURE: RNA velocity projected expression can now be given to methods - FEATURE: Added orient_topology_to_velocity() to orient the edges of a trajectory based on the velocity vectors - FEATURE: calculate_geodesic_distances() now has a directed parameter, with which you can calculate directed geodesic distances. Unreachable cells will receive an infinite distance - FEATURE: Added projected_trajectory() (ported from dynplot). add_dimred() will now by default also add a projection of the trajectory to the data Changes in version 1.0.1 - MINOR CHANGE: infer_trajectory(..., debug = TRUE) will now return commands for both entering the container and running the dyncli::main() function inside the container - MINOR CHANGE: Make create_ti_method_definition() actually work - DOCUMENTATION: Added examples for each trajectory wrapper - DOCUMENTATION: Added vignette discussing wrapper types - DOCUMENTATION: Added vignette discussing create_ti_method_definition() - BUG FIX: Fixed bug where sink() was not removed after interruption Changes in version 1.0.0 - MAJOR CHANGE: Add support for Singularity 3.0, drop support for previous releases of Singularity and singularity-hub. - MAJOR CHANGE: dynwrap now always works with sparse count and expression matrices - FEATURE: Add create_ti_method_definition() to create a definition from a local script. - DOCUMENTATION: Major update of all documentation for dynbenchmark publication - MINOR CHANGE: Rename compute_tented_geodesic_distances() to calculate_geodesic_distances() - MINOR CHANGE: Harmonisation of function arguments to either dataset or trajectory Changes in version 0.3.1.2 - BUG FIX: simplify_replace_edges() would sometimes swap edges in milestone network around, but forget invert percentages. - BUG FIX: Close sinks when interupting the R process - MINOR CHANGE: Work with new babelwhale, which includes support for singularity 3.0 Changes in version 0.3.1.1 - CLEAN UP: Removed helper functions that are not required any more: get_env_or_null(), read_rds_or_null() and print_processx(). - MINOR CHANGE: remove requirement that milestone_ids and cell_ids cannot overlap Changes in version 0.3.1 - HOTFIX: Use utils::data() to get access to priors. Changes in version 0.3.0 - MINOR CHANGE: Added metadata on the different wrapper types implemented in dynwrap. - CLEAN UP: Removed plot_fun argument from create_ti_method(). - MINOR CHANGE: Replaced mc_cores with more flexible map_fun. - MINOR CHANGE: Renamed create_ti_method() to create_ti_method_r(), and create_ti_method_with_container() to create_ti_method_container(). - CLEAN UP: Drastically reworked create_ti_method_r() and create_ti_method_container(), and the underlying functions for executing a method on a dataset. - CLEAN UP: Remove parse_parameter_definition() and thereby dependency on ParamHelpers. Changes in version 0.2.0 - BUG FIX: Fixed incorrect calculation of milestone percentage during trajectory simplification. Occurs only in a rare edge case, namely when the order of the milestones in the milestone network is very different from the order of the milestone ids (0475e94). - BUG FIX: Fixed suggested dependencies not being installed in the dynwrap containers (#100). - FEATURE REMOVAL: Removed feather data format because it's not being used and creates dependency issues every now and again. - BUG FIX: devtools:::shim_system.file() has been moved to pkgload:::shim_system.file(). - TESTING: Solved issue with the unit tests by not using any helpers. - MINOR CHANGE: Have docker images build from dynwrap@devel. - BUG FIX: Remove option(echo = FALSE) from .Rprofile in recipes because some packages directly rely on standard output from R, so printing the command wreaks havoc. Changes in version 0.1.0 - INITIAL RELEASE: dynwrap, functionality for containerised trajectory inference. - Wrap the input data of a trajectory inference method, such as expression and prior information - Run a trajectory inference method in R, in a docker container or a singularity container - Wrap the output of a trajectory inference method, such as the pseudotime, a clustering or a branch network, and convert it into a common trajectory model - Further postprocess the trajectory model, such as labelling the milestones and rooting the trajectory