NEWS.md

Release notes

AcidBase 0.7.3 (2023-12-15)

New functions:

• matchAll: Variant of base match() that returns all positional matches of x in table, instead of only returning the first match. Differs from base match() in that the function always errors on any match failures instead of returning NA.
• notDupes: Works like dupes(), but only returns values that are not duplicated.

AcidBase 0.7.2 (2023-11-10)

Minor changes:

• shell: Set print argument to TRUE by default, rather than interactive(), which improves console output during scripts invoked by Rscript instead of running directly in an R session.
• Updated lintr checks.

AcidBase 0.7.1 (2023-10-06)

Minor changes:

• showHeader: Improved edge case handling of DFrameList class.

AcidBase 0.7.0 (2023-09-29)

New functions:

• dupes: Return unique values that result in TRUE via base duplicated. See also goalie::isDuplicate for details.
• pkgCacheDir: Return the directory path for a package's file cache.
• strExtract: Base R variant of stringi::stri_extract_first.
• strExtractAll: Base R variant of stringi::stri_extract_all.
• strMatch: Base R variant of stringi::stri_match_first.
• strMatchAll: Base R variant of stringi::stri_match_all.
• strPad: Base R variant of stringr::str_pad.
• strRemoveEmpty: Base R variant of stringi::stri_remove_empty.
• strReplaceNa: Base R variant of stringi::stri_replace_na.
• strSplit: Base R variant of stringi::str_split_fixed.

Major changes:

• Now enforcing strict camel case naming of all functions.
• Renamed pasteURL to pasteUrl.
• Renamed strsplit to strSplit (note case).

Minor changes:

• headtail: Now returns character instead of printing to the console.
• matchNested: Simplified internal code by using lengths.
• showSlotInfo: Reworked internal code.

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.

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 0.6.21 (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 0.6.20 (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 0.6.19 (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 0.6.18 (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 0.6.17 (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 0.6.16 (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 0.6.15 (2023-04-26)

Minor changes:

• Renamed all class definitions to DFrame from DataFrame.

AcidBase 0.6.14 (2023-04-26)

New functions:

• Now re-exporting new quietly function from goalie.

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 0.6.12 (2023-02-09)

Minor changes:

• Removed requireNamespaces as a reexport.

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 0.6.10 (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 0.6.9 (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 0.6.8 (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 0.6.7 (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 0.6.6 (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 0.6.5 (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 0.6.4 (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 0.6.3 (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 0.6.2 (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 0.6.1 (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 0.6.0 (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 0.5.0 (2022-03-11)

Minor changes:

• Ordered S4 method exports alphabetically by class, where applicable.
• compress / decompress: Simplified default formals and documentation. User can no longer set remove or overwrite globally with "acid.compress.remove" or "acid.overwrite", respectively.
• Removed formalsList from NAMESPACE, in favor of a reworked approach across packages that previously inherited these values (in development).
• printString: Improved and cleaned up documentation.
• Updated working examples to use DataFrame object instead of DFrame, where applicable. This requires an update to AcidTest package.
• compress: Bug fix for ZIP file compression handling outside of working directory. Incorrectly used basename argument internally. Unfortunately need to change the working directory internally to get this working correctly.

AcidBase 0.4.5 (2021-09-08)

Minor changes:

• Cleaned up the NAMESPACE a bit, removing some deprecated functions: metadataBlacklist (in favor of metadataDenylist) and bapply, which should only be defined in goalie package.
• Reexporting tar from untils package alongside untar, for consistency.

AcidBase 0.4.4 (2021-09-03)

Minor changes:

• parentDirectory: Added support for handling URLs.

AcidBase 0.4.3 (2021-08-23)

New functions:

• collapseToPathString: Previously used internally, now exporting so we can use in koopa dependency package.

AcidBase 0.4.2 (2021-08-19)

New functions:

• parentDirectory (parentDir): Allows for each return of nested parent directories, similar to approach used in koopa shell package (parent_dir).

Minor changes:

• realpath: Now keeps track of names, if defined.

AcidBase 0.4.1 (2021-08-18)

Minor changes:

• shell Added some more useful options for subprocess handling and logging: wd, stdoutFile, stderrFile, as well as stderrToStdout.

AcidBase 0.4.0 (2021-08-18)

New functions:

• Added new system path modifier functions, based on code previously defined in koopa shell package: addToPathStart, addToPathEnd, removeFromPath.
• Also added some useful path string parsing functions: splitPathString and uniquePathString.

Major changes:

• shell: Reworked internal code to handoff to processx::run instead of using base::system2. Simplified console output handling using a single print argument.

AcidBase 0.3.16 (2021-08-13)

Minor changes:

• Reworked package to use AcidCLI for improved error messages, which are now called via abort instead of stop internally.

AcidBase 0.3.15 (2021-08-04)

New functions:

• simpleClass: Added utility function for simple class checks, primarily intended for unit testing with testthat package.

AcidBase 0.3.14 (2021-06-20)

Minor changes:

• standardizeCall: Updated handling of dots handoff to match.call in R 4.1.
• Now importing median and quantile functions from AcidGenerics, which use S4 defined in IRanges, rather than the base version defined in stats.

AcidBase 0.3.13 (2021-03-02)

Minor changes:

• Including data and median as reexports.

AcidBase 0.3.12 (2021-03-01)

Minor changes:

• Added install.packages as a reexport, which is used by r-koopa.
• Also including head and tail as reexports.

AcidBase 0.3.11 (2021-02-25)

Minor changes:

• Deprecating metadataBlacklist in favor of metadataDenylist.

AcidBase 0.3.10 (2021-02-23)

Minor changes:

• Migrated printString back here from goalie package.
• showHeader now checks for packageVersion inside of metadata as default instead of version.

AcidBase 0.3.9 (2021-02-21)

Minor changes:

• Reexporting URLencode from utils, which is used downstream in Cellosaurus package.

AcidBase 0.3.8 (2021-02-17)

Minor changes:

• Including formula and untar as reexports, which are used in the WormBase package.

AcidBase 0.3.7 (2021-02-12)

Minor changes:

• Including download.file as a reexport from utils.

AcidBase 0.3.6 (2021-02-11)

Minor changes:

• Now reexporting all functions used in other Acid Genomics packages defined in base/recommended R packages here, including: grDevices, grid, methods, and stats, utils.

AcidBase 0.3.5 (2021-02-04)

Major changes:

• Migrated geometricMean and sem methods from basejump.
• Migrated showHeader from basejump.
• Migrated coerceToList from basejump.
• Migrated log ratio functions from basejump.
• Migrated intersection functions from basejump.

Minor changes:

• Made matchArgsToDoCall function defunct. Doesn't always evaluate arguments correctly when called inside nested functions or complex S4 stacks.

AcidBase 0.3.4 (2021-01-28)

New functions:

• Added classContains utility function.

AcidBase 0.3.3 (2021-01-21)

Minor changes:

• pasteURL: Added support for rsync as a protocol. Using this in future update in AcidGenomes package for downloading from UCSC server.

AcidBase 0.3.2 (2021-01-15)

Minor changes:

• Removed sampleId from metadataBlacklist global.
• pasteURL now supports "s3" as a protocol value.

AcidBase 0.3.1 (2021-01-06)

Minor changes:

• Now importing new AcidCLI package, to improve CLI messages.

AcidBase 0.3.0 (2021-01-06)

Major changes:

• Reworked internal function organization a bit, handing off some functions back into the goalie package.
• Now that goalie doesn't depend on AcidBase, we can import and use the superior assert checks defined in the package.

AcidBase 0.2.6 (2020-12-15)

Minor changes:

• download: Function now recursively creates destination file parent directory if necessary.
• pasteURL: Now defaulting to no protocol (e.g. "https") by default. This makes pasting of an existing URL with subdirectories easier.

AcidBase 0.2.5 (2020-12-10)

New functions:

• Added download, which acts as a hardened wrapper for utils::download.file. Annoying, download.file returns status codes but does not intentionally error on any unsuccessful downloads. Our wrapper ensures that R always errors on any file download issue. It also sets a longer timeout internally, to avoid any potential issues with the timeout option being defined in Rprofile.

Bug fixes

• compress and decompress were found to potentially generate integer overflow warnings on very large files, due to R using 32-bit integers. This issue has been resolving by ensuring the internal nbytes counter is set as numeric instead. See related Stack Overflow post for details on integer overflows in R.
• sem: Requires AsIs class support, to work inside dplyr summarize calls.
• Now need to import BiocGenerics, for proper import of AsIs S4 class, which is an oldClass of the S3 class.

AcidBase 0.2.4 (2020-11-24)

New functions:

• sem: Added support for standard error of the mean calculation.

AcidBase 0.2.3 (2020-10-07)

• Fixed reference to AcidPlots package, renamed from previous "acidplots".

AcidBase 0.2.2 (2020-10-07)

New functions:

• Migrated headtail atomic, matrix, and data.frame methods here from basejump. The methods that work on S4 objects, such as DataFrame, Matrix, GRanges, and SummarizedExperiment are still defined in basejump.
• showSlotInfo: Migrated from basejump, so we can use in AcidGenomes.

AcidBase 0.2.1 (2020-10-06)

New functions:

• Added forceDetach, previously used internally inside basejump.
• Updated documentation to inherit from AcidRoxygen instead of acidroxygen.

AcidBase 0.2.0 (2020-10-06)

Major changes:

• Renamed package from acidbase to AcidBase.

acidbase 0.1.14 (2020-08-25)

Minor changes:

• Migrated some globals previously exported in basejump.
• Updated formalsList to consolidate params from basejump.

acidbase 0.1.13 (2020-08-11)

Minor changes:

• Bug fix for realpath file path resolution using ...

acidbase 0.1.12 (2020-08-09)

Major changes:

• Migrated parseArgs and positionalArgs out of package.

acidbase 0.1.11 (2020-07-24)

Minor changes:

• Maintenance release, increasing minimum R dependency to 4.0.

acidbase 0.1.10 (2020-07-07)

Minor changes:

• formalsList: Added acid.import.make.names global.

acidbase 0.1.9 (2020-05-09)

Minor changes:

• positionalArgs: Function now intentionally errors when no positional arguments are defined.

acidbase 0.1.8 (2020-05-05)

Minor changes:

• shell: The args argument has been changed to "" by default so that only command argument is required as input.

acidbase 0.1.7 (2020-04-09)

New functions:

• majorVersion, minorVersion, sanitizeVersion: Additional version utilites that help extraction major and minor release versions. sanitizeVersion helps strip extra characters at the end of version strings commonly found in the return of some shell commands (e.g. via --version command).
• shell: Wrapper for base system2 function.

acidbase 0.1.6 (2020-04-08)

New functions:

• parseArgs and positionalArgs: Migrated these functions previously defined inside koopa shell bootloader package.
• requireNamespaces: Parameterized variant of requireNamespace that allows for easy loading of multiple package namespaces in a single call.

acidbase 0.1.5 (2020-01-28)

Minor changes:

• Documentation fixes to pass CRAN release checks.
• Switched license from MIT to GPL-3.

acidbase 0.1.4 (2020-01-19)

New functions:

• compress, decompress: Added dynamic file compression/decompression support for GZ, BZ2, XZ, and ZIP files. Inspired by approach used in R.utils compressFile and decompressFile.

Minor changes:

• fileDepth: Updated unit test to work reliably on macOS.

acidbase 0.1.3 (2020-01-10)

Minor changes:

• standardizeCall: Removed extra unnecessary assert check.

acidbase 0.1.2 (2019-12-05)

New functions:

• Added new fileDepth function.

acidbase 0.1.1 (2019-10-22)

Minor changes:

• Migrated realpath from brio package. Reworked slightly to not depend on any assert checks from goalie package. Now this function essentially wraps normalizePath but provides a more informative error message.
• basenameSansExt: Minor tweak to ensure that files without an extension still return basename as expected.

acidbase 0.1.0 (2019-10-21)

• Initial release.