Resubmission after babelwhale was removed from CRAN.
MINOR CHANGE: Added @return documentation to all functions.
MINOR CHANGE: Fixes to metadata (documentation, citation entry, broken links).
MINOR CHANGE: Use alternative method for checking whether dynmethods is installed.
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.
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.
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.
First CRAN release!
BUG FIX: Fixed #142 where the error message was truncated
DOCUMENTATION: Added examples to all functions.
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.
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
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
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
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
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
utils::data() to get access to priors.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.
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.