Changelog

Source: NEWS.md

GiottoUtils 0.2.5 (2025/05/21)

New

• str_reformat() for print post-processing with strwrap()

Enhancement

• Improve fallbacks for print_list()

GiottoUtils 0.2.4 (2025/05/06)

Changes

• deprecate fread_colmatch() in favor of read_colmatch()

New

• str_abbreviate() for shortening long strings for printing

Enhancement

• More ergonomic ref selection for suite_install()
• R4.1.0 branch can now be used as a ref for suite_install()
• read_colmatch() now uses {arrow} for faster .csv filtering, enhanced with automated schema detection performed through data.table::fread()
• dry_run param for suite_install() to preview install commands
• vmsg() logging can now be ephemerally diverted to other files

Bug Fixes

• package_check() error when checking with a provided github repo and a version number
• package_check() error when checking packages with “.” characters

GiottoUtils 0.2.3 (2025/01/17)

New

• handle_errors() for catching errors with call. = FALSE to avoid console locking in complex calls

Enhancement

• package_check() now supports version checks of the style repository = "pip:XXXXX>=A.B.C" (reported as warnings)

GiottoUtils 0.2.2 (2024/12/09)

Enhancement

• lapply_flex() BiocParallel method added.
• warning added when sequential evaluation is used with lapply_flex(). Silenceable through options("giotto.warn_sequential" = FALSE)
• vlim, slim, seed params for getRainbowColors() to allow more diverse palettes

GiottoUtils 0.2.1 (2024/11/4)

New

• suite_packages() for reporting the names of Giotto Suite modules
• suite_install() for installing specific branches of Giotto Suite

GiottoUtils 0.2.0 (2024/10/26)

Breaking change

• R version requirement is now 4.4.1

New

• gwith_package(), gwith_options(), gwith_seed() for setting temporary conditions for eval
• handle_warnings() for graceful warning handling

GiottoUtils 0.1.12 (2024/09/27)

New

• pbar() and with_pbar() as progress reporting utils. These are wrappers around progressr functionalities.
• reexports of fromJSON() and read_json() from jsonlite.
• melt_matrix() to emulate reshape2::melt.matrix() (deprecated package) for most use cases in Giotto.

GiottoUtils 0.1.11 (2024/08/22)

New

• py_active_env() utility function for detecting any active python environment without initializing

Enhancement

• package_check() now works for pip github installs
• package_check() now reports which conda environment is being activated and what python version it is.

GiottoUtils 0.1.10 (2024/07/26)

New

• dir_manifest() for creating a named list of files within a directory. Mostly wraps list.files()

GiottoUtils 0.1.9 (2024/07/12)

New

• deprecate_param() utility function for streamlining code
• print_list() for pretty printing of list-like objects
• from_scipy_sparse() for conversion from scipy csr and csc to Matrix dgCMatrix and dgRMatrix

Changes

• newer github version checking refactored into new_github_ver_avail()

GiottoUtils 0.1.8 (2024/05/22)

New

• wrap_txtf() variant of wrap_txt() that uses sprintf() formatting
• init_option() for setting an option if it does not exist

Enhancement

• dt_to_matrix() can now chunk the conversion to Matrix to avoid memory issues
• get_args_list() now has a keep param that allows selection of which collected args to keep

GiottoUtils 0.1.6 (2024/02/26)

New

• %null%, %na%, and %none% infix operators for setting a default value when an object is, respectively, NULL, NA, or length of 0.
• local_seed() for transiently setting a seed only for the duration of a function

GiottoUtils 0.1.5 (2024/02/11)

Bug Fixes

• str_locate2() now works with vectorized inputs like the stringr counterpart
• str_locate2() no-matches now properly return NA_integer_ instead of negative values

New

• to_scipy_sparse() conversion of R matrices to scipy sparse representations

GiottoUtils 0.1.4 (2024/02/05)

Enhancement

• new seed param for getDistinctColors() that allows the ordering of the distinct colors to be changed.
• package_check() now allows more than one package to be checked using repo:location notation.

GiottoUtils 0.1.3

Added

• Add: mixedsort() and mixedorder() from gtools

GiottoUtils 0.1.2 (2024/01/02)

Added

• Add: getMonochromeColors() basic color palette function. Useful for image colorization.

GiottoUtils 0.1.1 (2023/12/16)

Breaking changes

• Remove checkmate reexports
• Remove deprecated flex_lapply()
• Rename guard_against_notgiotto() to assert_giotto()
• Rename set_row_order_dt() to dt_set_row_order()
• Rename dcast_dt_string() to dt_dcast_string()
• Rename sort_combine_two_DT_columns() to dt_sort_combine_two_columns()
• Rename DT_removeNA() to dt_remove_na()
• Rename assert_DT() to assert_dt()

Added

• Add gstop() as a framework for sending module specific error messages
• Add str_locate2() (implementation of stringr::str_locate() in base R)
• Add str_vector() for pretty printing a vector as a string
• Add: str_bracket(), str_parenth(), str_quote(), str_double_quote() convenience functions
• Move: get_prev_fname(), get_args(), and get_prev_call() to this package
• Add get_prev_call()
• Move basic color palettes getDistinctColors() and getRainbowColors() to this package
• Add: RColorBrewer to suggests for getDistinctColors()

Changes

• improvements to assert_giotto()

GiottoUtils 0.1.0 (2023/11/29)

Initial release