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Version 0.6

AcidBase 0.6.0 (2022-04-29)

Major changes:

  • Updated minimum R dependency version to 4.2
  • Reduced the number of strong dependencies, migrating AcidCLI, stats, and utils to Suggests from Imports.

Minor changes:

  • Improved formatting consistency using styler package.

AcidBase 0.6.1 (2022-05-02)

New functions:

  • Migrated gitCurrentBranch and gitDefaultBranch from r-koopa here.

Minor changes:

  • shell: Added returnStdout argument, which helps parse stdout.
  • fileExt: Added option to override default extPattern match.

AcidBase 0.6.2 (2022-05-20)

Minor changes:

  • Updated package to use testthat 3e and updated lintr checks.
  • fileExt: Added pattern formal, which lets us override compressed file handling in other packages.
  • compress: Improved handling of ZIP files, to no longer rely on internal setwd call. Now using withr::with_dir temporary approach instead.
  • compress and decompress: Reformatted internal code to pass lintr checks.
  • forceDetach: Simplify internal code using a for loop.
  • Now using Map internally instead of mapply.

AcidBase 0.6.3 (2022-05-31)

Minor changes:

  • Improved internal consistency of normalizePath calls, using platform fsep for winslash, similar to conventions used in realpath. This helps improve consistency of messages and file path output on Windows.
  • Fixed unit test compatibility on Windows.

AcidBase 0.6.4 (2022-06-02)

New functions:

  • tempdir2: Temporary directory generator that improves upon base R tempdir conventions, ensuring that a new unique directory is created per call.
  • unlink2: Hardened variant of unlink that provides better file system compatibility with Windows. Function will intentionally error if file or directory does not exist on disk.

AcidBase 0.6.5 (2022-06-08)

Minor changes:

  • unlink2: Added assert check to ensure files and/or directories are successfully deleted. Calls file.exists internally, which checks both files and directories.

AcidBase 0.6.6 (2022-08-24)

Minor changes:

  • requireNamespaces: Made error message regarding NAMESPACE more informative. Now indicates that user needs to install a missing package.
  • Miscellaneous documentation updates, based on roxygen2 changes.

AcidBase 0.6.7 (2022-09-06)

Minor changes:

  • shell: Added support for env, which allows for environment variable definition inside the child process. Refer to processx::run and system2 for details.

AcidBase 0.6.8 (2022-10-20)

New functions:

  • truncateString: Simple utility function that smartly adds ellipsis (...) when necessary to a long character string. Don’t want to export this as truncate, which is defined in base R for connections.

Minor changes:

  • shell: Improved interactive printing and error message handling. The function now attempts to automatically handle ~ character, when defined at the beginning of an argument.

AcidBase 0.6.9 (2022-11-21)

New functions:

  • euclidean: Calculate Euclidean distance of two numeric vectors.
  • zscore: Calculate Z score for an input numeric vector or matrix. Note that matrix method defaults to row-wise scaling, defined by MARGIN argument. This convention is intended to match recommended R defaults, and also to work as expected with sample (columns) x gene (rows) matrix, commonly used for gene expression in SummarizedExperiment class objects.

AcidBase 0.6.10 (2023-01-30)

Minor changes:

  • Deprecated minorVersion in favor of majorMinorVersion, which improves legibility. Added asserts against "" and NA input. Improved code coverage and support for input of a major version alone here (e.g. "1" instead of "1.0").
  • Now using requireNamespaces instead of requireNamespace consistently across the package, to improve error messages.

AcidBase 0.6.11 (2023-02-07)

Minor changes:

  • requireNamespaces: Migrated this function to goalie. Still reexporting this function in the NAMESPACE, but that likely will change with a future update.

AcidBase 0.6.12 (2023-02-09)

Minor changes:

  • Removed requireNamespaces as a reexport.

AcidBase 0.6.13 (2023-04-12)

New functions:

  • matchNested: Match recursively across columns for DataFrame method, and per element for list method. This is very useful for quick matching of cancer cell line name variants (Cellosaurus) and gene name aliases (HGNC, NCBI in AcidGenomes).

Minor changes:

  • Removed defunct matchArgsToDoCall from NAMESPACE.

AcidBase 0.6.14 (2023-04-26)

New functions:

  • Now re-exporting new quietly function from goalie.

AcidBase 0.6.15 (2023-04-26)

Minor changes:

  • Renamed all class definitions to DFrame from DataFrame.

AcidBase 0.6.16 (2023-05-16)

New functions:

  • cpus: Return the number of total CPUs available.
  • ram: Return the amount of total or free ram, in GB by default.

Minor changes:

  • initDir is now vectorized and supports multiple directories.

AcidBase 0.6.17 (2023-07-27)

Minor changes:

  • pasteURL now automatically encodes URLs via utils::URLencode. This is helpful for improving consistent handling of complex URLs. We ran into differences in handling between httr and httr2 for URLs containing spaces. Note that goalie isURL will now return FALSE for non-encoded URLs.

AcidBase 0.6.18 (2023-08-01)

New functions:

  • randomString: Random string generator.

Minor changes:

  • tempdir2: Now calls randomString internally to generate a unique temporary directory that is simpler and performs more consistently across platforms.

AcidBase 0.6.19 (2023-08-23)

Minor changes:

  • showHeader: Improved header for S4 DFrame, which contains rows and columns. For classes that extend Annotated but don’t support dim, still returns legacy length information.
  • Removed forceDetach function, as it is no longer used in any other Acid Genomics packages.

AcidBase 0.6.20 (2023-09-08)

New functions:

  • keepOnlyAtomicCols: New utility function that removes complex non-atomic columns (e.g. list) from a DFrame or data.frame class object.

AcidBase 0.6.21 (2023-09-11)

Minor changes:

  • euclidean: Reworked so that generic no longer requires y. We have modified this downstream in the pending DepMapAnalysis package update.

AcidBase 0.6.22 (2023-09-13)

New functions:

  • strsplit2: This function works like base strsplit but consistently splits into a character matrix for easier extraction of values. Works like stringi and stringr variants but designed to be as simple as possible without requiring a non-base R dependency.

AcidBase 0.6.23 (2023-09-19)

Minor changes:

  • pasteURL: Hardened against unwanted recycling, which is allowed in base paste but undesirable here. Also added an assert check to ensure that URL is always returning, containing "://". This edge case can happen when user uses function with protocol set to "none". Also added support for input of a character vector as the first argument alone, which can be useful for passing in variables.