Changes in version 0.2.9 New - package_check() gains on_missing ("error", "warning", "message" or "none") for what to do when a package is missing, and once = TRUE to show a warning or message once per session. An installed package below a requested version is reported at the same level ("error" still reports it as a warning) - package_check() accepts repository = "r-universe:owner/package". The install message points at that owner's r-universe (with CRAN for dependencies), which serves binaries where an install from GitHub would compile from source Changes - package_check() returns FALSE when a package is missing and on_missing is not "error". It returned TRUE before, so if (package_check(x, optional = TRUE)) never skipped its body for a missing package - package_check(optional) is deprecated in favour of on_missing. TRUE maps to "message" and FALSE to "error" - package_check() with several packages, one of them missing and given a version request, now reports the install instructions. It errored in packageVersion() instead - suite_install(install_arrow = TRUE) builds arrow in a fresh library. Its dependencies now come from CRAN (only r-universe was searched before, so they were not found and the build failed with a warning), and the install stops with an error if the result still lacks zstd - suite_install() installs tilework from its dev branch until tilework 1.0.1 is on CRAN. main lacks the tile-edge fix (drieslab/tilework#5): without it, a point or polygon on the top or right edge of the data can fall outside every tile and be dropped from a GiottoDisk store Changes in version 0.2.7 New - keep_awake() and gwith_awake() hold a system sleep assertion during long computations (caffeinate on macOS, systemd-inhibit on Linux, no-op elsewhere). A sleep part-way through a run inflates wall-clock timings while CPU and memory counters look normal Enhancement - suite_install() accepts "tilework" and "arrow" as modules under any ref, and adds both automatically for GiottoDisk - install_arrow param for suite_install(). arrow needs zstd support for 10x parquet files, and the source build from r-universe is slow, so a missing or zstd-less arrow errors with the install command unless install_arrow = TRUE (install) or FALSE (skip) Changes in version 0.2.6 Enhancement - "disk" ref for suite_install() installs the on-disk build set (gsource branches + GiottoDisk) - GiottoDisk is now recognized as a Giotto Suite extension module - suite_install() installs GiottoData from its R4.1.0 branch for the R4.4.0 and R4.1.0 refs. The default branch requires R (>= 4.3.0), so it could not be installed under the R4.1.0 ref at all Changes in version 0.2.5 New - str_reformat() for print post-processing with strwrap() Enhancement - Improve fallbacks for print_list() Changes in version 0.2.4 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 Changes in version 0.2.3 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) Changes in version 0.2.2 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 Changes in version 0.2.1 New - suite_packages() for reporting the names of Giotto Suite modules - suite_install() for installing specific branches of Giotto Suite Changes in version 0.2.0 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 Changes in version 0.1.12 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. Changes in version 0.1.11 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. Changes in version 0.1.10 New - dir_manifest() for creating a named list of files within a directory. Mostly wraps list.files() Changes in version 0.1.9 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() Changes in version 0.1.8 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 Changes in version 0.1.6 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 Changes in version 0.1.5 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 Changes in version 0.1.4 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. Changes in version 0.1.3 Added - Add: mixedsort() and mixedorder() from gtools Changes in version 0.1.2 Added - Add: getMonochromeColors() basic color palette function. Useful for image colorization. Changes in version 0.1.1 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() Changes in version 0.1.0 Initial release