NEWS.md

In acidgenomics/goalie: Assertive Check Functions

Release notes

goalie 0.7.7 (2023-12-04)

Minor changes:

• isOrganism: Added support for full latin with three names, such as "Canis lupus familiaris".

goalie 0.7.6 (2023-11-28)

Minor changes:

• quietly: Now correctly closes sink connection on error.

goalie 0.7.5 (2023-11-03)

New functions:

• isAwsS3Uri: Check if the input contains AWS S3 URIs.
• isExistingAwsS3Uri: Check if the input contains AWS S3 URIs that exist.

goalie 0.7.4 (2023-10-25)

Minor changes:

• Updated suggested packages so automated build checks pass. This required adding BiocGenerics and memuse, which is used by AcidBase::ram.

goalie 0.7.3 (2023-10-06)

Minor changes:

• hasDims, hasRows, hasCols: Add edge case support for DFrameList class, which uses dims instead of dim, nrows instead of nrow, and ncols instead of ncol.

goalie 0.7.2 (2023-10-06)

Major changes:

• Remove import requirement of utils package.
• quietly now uses base R sink instead of utils::capture.output.

goalie 0.7.1 (2023-10-04)

Minor changes:

• Remove length checks for set comparisons.

goalie 0.7.0 (2023-10-03)

Major changes:

• Reworked primary goalie class to only accept unnamed input and unnamed cause attribute. Hardened validity checks to error if names are attempted to be passed through. This required updating some internal bapply calls to set USE.NAMES as FALSE.
• Vectorized checks should now always return the same length as the input.
• Now enforcing strict camel case for function names.
• Renamed hasCPU to hasCpu.
• Renamed hasGitHubPAT to hasGithubPat.
• Renamed hasRAM to hasRam.
• Renamed isGGScale to isGgscale.
• Renamed isMacOS to isMacos.
• Renamed isRStudio to isRstudio.
• Renamed isExistingURL to isExistingUrl, and other variants.
• Renamed isURL to isUrl, and other variants.

Minor changes:

• No longer using getNameInParent approach, which makes functions cleaner.

goalie 0.6.18 (2023-09-19)

New functions:

• isDuplicate: Variant of base duplicated that returns TRUE for all observed duplicated values in a vector. Differs from base duplicated, which only starts to return TRUE on the second observed value.
• allAreIntegerish: Added an additional scalar variant of isIntegerish.

Minor changes:

• hasDims, hasRows, hasCols: Now support n argument for checking expected dimensions. Note that for hasDims, this needs to be length 2. Integerish values (e.g. 1 instead of 1L) are supported, but direct input of integer is recommended.
• isExistingURL: Now checks for libcurl support in R session.

goalie 0.6.17 (2023-09-15)

Minor changes:

• isAnExistingURL: Reworked engine back to use base R via curlGetHeaders function. Returns FALSE for status codes >= 400 for both HTTP(S) and FTP. No longer need to include RCurl as a suggested package.

goalie 0.6.16 (2023-09-15)

Minor changes:

• isAnExistingURL: Reworked internal code to use RCurl::url.exists instead of a direct connection check, as this is more reliable for returning FALSE for some offline servers, such as the Ensembl FTP server, which has stability issues.
• Now using requireNamespaces instead of requireNamespace consistently internally in the package.

goalie 0.6.15 (2023-08-24)

New functions:

• Added isExistingURL variants of isURL, which check if the connection is active and that the URL actually exists, rather than whether it is merely formatted correctly. Also added isAnExistingURL and allAreExistingURLs variants, similar to the simpler isURL checks. The internal logic of this check was ported from the previous hasInternet function, but speed up to use a try call with a faster timeout.

Major changes:

• hasInternet has been reworked to simply wrap isAnExistingURL with a call to check if the Bioconductor website is up.

goalie 0.6.14 (2023-08-10)

New functions:

• hasCPU: Does the current machine have a sufficient number of CPU cores?
• hasRAM: Does the current machine have sufficient memory (in GB)?

goalie 0.6.13 (2023-07-27)

Minor changes:

• isURL now returns FALSE for non-encoded URLs (e.g. containing spaces, other invalid characters). This helps protect against unwanted input into httr2 engine for REST API calls. Refer to utils::URLencode for encoding checks.

goalie 0.6.12 (2023-07-24)

New functions:

• isTximport: New check function to perform validity checks on tximport list return, which isn't currently classed.

Minor changes:

• Updated lintr checks to be compatible with new release.

goalie 0.6.11 (2023-07-13)

New functions:

• isTempFile / isATempFile / allAreTempFiles: Check functions to determine if a file exists on disk as a temporary file, defined by tempfile. Checks directory path internally against tempdir return. This function will be used in pipette update for compressed file cleanup during import calls.

Minor changes:

• Now requiring R 4.3 / Bioconductor 3.17.

goalie 0.6.10 (2023-05-31)

Minor changes:

• compressExtPattern: Updated to ensure that maching is case insensitive.
• Relaxed suggested package dependencies.

goalie 0.6.9 (2023-04-26)

New functions:

• quietly: Useful expression wrapper that suppresses all warnings, messages, and console output. Now used internally in requireNamespaces to suppress unwanted warnings from some Bioconductor packages, such as AnnotationHub, which now masks utils in the 3.17 release.

Minor changes:

• validateClasses: Improved assert check for input of empty list.

goalie 0.6.8 (2023-01-12)

New functions:

• requireNamespaces: Migrated this useful base function from AcidBase package here to goalie instead, as this is often used inside of assert checks.

Minor changes:

• hasNoDuplicates: Improve support for Rle handling. Note that S4Vectors currently doesn't define a duplicated method for Rle, so we have to work around this at the moment.

goalie 0.6.7 (2022-12-14)

New functions:

• isIntegerish: New check function that will also return true for vector-like classes, including factor and S4 Rle.

Minor changes:

• hasRownames: Should now return TRUE for data.frame with integer row names out of order. This is useful for matrix export method defined in pipette package.
• Added support for S4 Rle class handling in isSubset, areDisjointSets, areIntersectingSets, areSetEqual.
• Removed unused skip_on_docker test function.

goalie 0.6.6 (2022-10-18)

New functions:

• isVSCode: Check if R session is running inside of Visual Studio Code.

goalie 0.6.5 (2022-10-18)

Minor changes:

• Using isSubset in place of %in% where possible.
• isInstalled: Now calling .packages internally instead of checking rownames on installed.packages return.
• hasDuplicates, hasNoDuplicates: Hardened internal calls to anyDuplicated to check whether values return non-zero or not.
• isCleanSystemLibrary: NAMESPACE fix for installed.packages call.

goalie 0.6.4 (2022-05-31)

Minor changes:

• isGitRepo: Return with classed cause in the event that Git is not installed.

goalie 0.6.3 (2022-05-13)

Minor changes:

• Reworked package to support new lintr and testthat releases.
• Now using Map internally instead of mapply, as recommended by lintr.

goalie 0.6.2 (2022-05-09)

Minor changes:

• validateClasses: Reworked internal code to use isAny, to allowing "or" checking for multiple acceptable class types. Currently needed to update validity checks against sessionInfo (utils package) vs. session_info (sessioninfo package) in our S4 classes that extend SummarizedExperiment.

goalie 0.6.1 (2022-04-29)

Minor changes:

• Updated R dependency to 4.2.

goalie 0.6.0 (2022-03-11)

Major changes:

• assert: Engine will use AcidCLI::abort if installed, to return richer error messages in the console. Also improved named message handling, similar to stopifnot conventions.
• Updated minimum R version dependency to 4.1, matching Bioconductor 3.14.

Minor changes:

• Improved some cause attributes to use better CLI formatting.
• Migrated some check functions from pointillism / AcidSingleCell packages: hasClusters, hasMultipleSamples, and isBiocParallelParam.
• Migrated isDark check here from AcidPlots package.
• Updated pkgdown website to use bootstrap 5 template.

goalie 0.5.5 (2021-09-21)

Minor changes:

• isDockerEnabled: Bug fix for properly checking successful status on internal docker info call via system2.

goalie 0.5.4 (2021-08-22)

Minor changes:

• isInstalled: Added support for lib argument, which allows the user to check whether an R package is installed in a specific package library. Defaults to checking against all libraries, calling installed.packages internally. This is a non-breaking change.

goalie 0.5.3 (2021-08-19)

New functions:

• isCondaEnabled: Scalar check to determine if Conda is active inside of the current R session. Evaluates CONDA_DEFAULT_ENV and CONDA_SHLVL system environment variables internally.
• isDockerEnabled: Scalar check to determine if Docker is installed and is actively running on the current machine.
• isGitRepo: Vectorized checks for the existence of Git repositories. This is a little tricky to check inside of CI, so may need to think of a more clever approach for code coverage in the future.

Minor changes:

• assert, validate: Improved cause return when attribute is set from internal falseFromVector call. This was detected when isSystemCommand was not returning the expected program name in the assert call.
• falseFromVector: Improved internal cause attribute handling for scalars.
• Reworked no coverage exclusions with nocov, for platform- and configuration- specific checks.

goalie 0.5.2 (2021-07-19)

Minor changes:

• isAURL: Improve setting of cause attribute when string is encoded. Bug fix is applied internally to falseFromVector, which passes false to internal sprintf call.
• Got package coverage back to 100%.

goalie 0.5.1 (2021-03-09)

Minor changes:

• Miscellaneous documentation updates, to pass build checks.

goalie 0.5.0 (2021-02-23)

Major changes:

• Reworked internal engine to redefine the goalie class as an S4 instead of an S3. This allows us to provide better validity checks with setValidity.
• Reworked internal handling of cause attribute, to provide better compatibility inside of R Markdown renders.

goalie 0.4.14 (2021-01-06)

Minor changes:

• isOrganism: Added nullOK argument.

goalie 0.4.13 (2021-01-06)

New functions:

• isOrganism: New assert check to verify that user precisely entered expected organism format of <genus> <species> (e.g. "Homo sapiens"). Case sensitivity and spaces are required here.

goalie 0.4.12 (2021-01-04)

Minor changes:

• Migrated some base functions that were previously defined in AcidBase, so we can pin the dependencies to base R only: compressExtPattern, extPattern, printString, safeDeparse, shorten, toNames.

goalie 0.4.11 (2020-11-05)

Minor changes:

• Decreased the number of suggested packages, removing DelayedArray and DelayedMatrixStats. These packages were called internally but basically never used in practice inside the hasNonzeroRowsAndCols check function. DelayedArray can have some HDF5-related build issues on some machines, so removing it as a suggested package makes goalie easier to install consistently across platforms.

goalie 0.4.10 (2020-10-29)

New functions:

• isDevel: Check if session is running inside R-devel. Internally checks against R.version.string.
• isBiocDevel: Check if Bioconductor installation is under development. Requires BiocManager and yaml packages, which have been added to "Suggests".

goalie 0.4.9 (2020-10-06)

• Updated dependency package names (e.g. AcidBase).

goalie 0.4.8 (2020-08-12)

New functions:

• Migrated isCleanSystemLibrary here from bb8.

Minor changes:

• Switched vignette back to default instead of using BiocStyle.

goalie 0.4.7 (2020-08-11)

New functions:

• isPackageVersion: Migrated check that was previously defined in koopa.
• isVanilla: Check if R session is running with --vanilla flag enabled.

goalie 0.4.6 (2020-07-24)

Minor changes:

• Maintenance release, increasing minimum R dependency to 4.0.

goalie 0.4.5 (2020-06-26)

New functions:

• isSymlink, isASymlink, allAreSymlinks: Added logical check functions for symbolic links. Note that these functions won't work on Windows.

goalie 0.4.4 (2020-04-12)

New functions:

• isRStudio: Checks whether current R session is running inside RStudio.

Minor changes:

• Now setting cause attribute on failure for: isLinux, isMacOS, isUnix, and isWindows.

goalie 0.4.3 (2020-04-08)

New functions:

Migrated some functions that were previously defined in the koopa package:

• hasGitHubPAT: Check if the user has a GitHUB personal access token (PAT) defined as GITHUB_PAT environment variable.
• isMacOS, isLinux, isUnix, isWindows. The Linux, Unix, and Windows checks are new but inspired by the macOS check from koopa.
• isSystemCommand (previously named isCommand in koopa). This check will look to see if a system (shell) command is available.

Minor changes:

• isDocker: Hardened the check function to look at /proc/1/cgroup.

goalie 0.4.2 (2020-01-28)

Minor changes:

• Switched license from MIT to GPL-3.

goalie 0.4.1 (2019-12-09)

Minor changes:

• hasRownames: Improved internal check for integer (sequence) row names for data.frame class, which previously returned TRUE unexpectedly if the rows are reordered or subset. Now this function uses an internal grepl check via allAreMatchingRegex, which hardens this check, and now should always return FALSE for soft NULL row names in data.frame class.

goalie 0.4.0 (2019-10-22)

The increase in version number here denotes new import of acidbase package.

Major changes:

• Migrated base (system) functions to new low-level acidbase package. Some of these functions are not specific to an assert check engine and should be defined in a separate package.

New functions:

• Added assert checks, based on file extension: isCompressedFile, isACompressedFile, allAreCompressedFiles. These perform similarly to isFile but also check to see if the file extension contains a compression format (e.g. bz2, gz, xz, zip).

goalie 0.3.12 (2019-10-21)

New functions:

• isFileSystemCaseSensitive: Checks whether file system is case sensitive (TRUE) or insensitive (FALSE). Linux tends to default to case sensitive, where as macOS and Windows default to case insensitive. Note that case insensitive file systems can lead to issues with Git repos. This check will be incorporated into a new rename mode for syntactic naming functions in a future release.

goalie 0.3.11 (2019-10-18)

Minor changes:

• Improved consistency of scalar and vector print messages.

goalie 0.3.10 (2019-10-10)

Minor changes:

• toNames: Bug fix for na.omit return causing assert check to fail because class returns FALSE for is.vector check but TRUE for is.atomic.
• isIntegerish now returns logical vector for na.omit return. This supports isScalarIntegerish and isInt check functions.

goalie 0.3.9 (2019-10-04)

New functions:

• nElements: Return the number of elements in an object. Previously this was defined internally in the package but is generally useful.

Minor changes:

• hasElements: No longer requiring the n argument. The function now performs similarly to hasLength.
• isEmpty and isNonEmpty are now soft deprecated. isEmpty is defined in the Bioconductor S4Vectors package, and we don't want to mask in interactive scripting sessions.
• is2: No longer exported, since this function isn't really intended for use outside of the package. Refer to isAll or isAny checks instead.

goalie 0.3.8 (2019-09-15)

Minor changes:

• isGGScale: Update aes argument to support American "color" pass-in in addition to British "colour" spelling.

Minor changes:

• Switched to consistent use of "color" instead of "colour" in documentation, working examples, and unit tests.

goalie 0.3.7 (2019-09-06)

Minor changes:

• hasInternet: Now allowing a user to check a specific URL, using the url argument. Currently defaults to Bioconductor.

goalie 0.3.6 (2019-08-27)

Updated R dependency to 3.6.

Minor changes:

• appendToBody: Now allowing pass-in of multiple values as a list. The list must contains call elements.
• hasNonzeroRowsAndCols: Renamed function, improving consistency with generic defined in bioverbs. Also added support for DelayedMatrix, improving consistency with basejump nonzeroRowsAndCols function.

goalie 0.3.5 (2019-08-13)

Minor changes:

• isURL now returns true on url class input.
• Improved message consistency.

goalie 0.3.4 (2019-08-12)

New functions:

• hasMetrics, hasSubset: New functions that were previously used internally in basejump. Requires S4Vectors / SummarizedExperiment.

goalie 0.3.3 (2019-08-11)

Minor changes:

• validNames: Bug fix and improvement for function, clearly showing position where names are invalid.

goalie 0.3.2 (2019-08-10)

New functions:

• Now exporting toNames, which was previously used internally by the package. Improved handling in this function for floating points. Also now using toNames more consistently internally to sanitize names for cause return.

Minor changes:

• standardizeCall: Now returns with default arguments included. Can disable using defaults = FALSE.
• matchArgsToDoCall: Tweaked internal code slightly based on standardizeCall update.
• Updated messages to use quotes more consistently.
• Improved vector name handling for cause return.

goalie 0.3.1 (2019-08-05)

Minor changes:

• Improved documentation consistency, using shared params defined in new AcidRoxygen package. This will be used across the basejump packages in a forthcoming update.

goalie 0.3.0 (2019-07-29)

Version bump, reflecting start of a new release series.

Minor changes:

• Hardened hasColnames, hasDimnames, hasNames, hasRownames, hasValidDimnames, and hasValidNames against invalid objects that don't return either a value or NULL. This can happen in rare cases with invalid SummarizedExperiment objects (e.g. bcb_invalid object in bcbioRNASeq tests).

goalie 0.2.19 (2019-07-21)

Minor changes:

• Improved full line comments to use "##" instead of "#", as recommended by current Bioconductor coding style.

goalie 0.2.18 (2019-07-18)

New functions:

• Added isDocker and skip_on_docker functions for improved conditional testing inside Docker R images.

goalie 0.2.17 (2019-07-15)

Major changes:

• Tweaked the internal code slightly for assert and validate to match the new conventions used in stopifnot for R 3.6 release. This should be completely backward compatible and transparency, but file an issue if you run into any unexpected bugs with this change.
• Improved n argument handling in hasElements checks. Previously this didn't return scalar consistently and could cause some build check issues to pop up in R 3.6, which are now fixed.
• Removed support for R 3.4 and no longer need to import backports.

Minor changes:

• No longer exporting extractLocal and hasLocal. These are currently only used by MethodDefinition utility functions defined here in the goalie package.
• Improved code coverage back up to 100%.
• Improved the documentation file names.

goalie 0.2.16 (2019-05-04)

Minor changes:

• Improved pkgdown NEWS configuration.
• Improved Travis Docker configuration.
• Initial commit of draft vignette.
• Improved comments regarding call standardization and name handling inside assert function.

goalie 0.2.15 (2019-04-22)

Minor changes:

• Bug fix for name handling in assert and validate calls. Now using unname internally to prevent unexpected errors with named logical vectors.

goalie 0.2.14 (2019-04-02)

Minor changes:

• standardizeCall: Improved isNonNegative assert check by wrapping in unname call, to keep backward compatibility with R 3.4.
• Improved code coverage, getting closer to 100%.

goalie 0.2.13 (2019-03-31)

Minor changes:

• Overhauled and improved assert checks.
• Miscellaneous bug fixes for assert checks.

goalie 0.2.12 (2019-03-22)

Minor changes:

• Migrated domain to Acid Genomics.

goalie 0.2.11 (2019-03-17)

Minor changes:

• isDirectory, isFile: Now return with cause attribute set on failure.
• Updated assert checks and reworked comments to pass lintr checks.

goalie 0.2.10 (2019-03-10)

Minor changes:

• isSubset: Improved cause message, which would error using internal deparse call on long vectors.

goalie 0.2.9 (2019-02-25)

Minor changes:

• Needed to tweak internal code in assignToBody to fix backports handling of ...elt for R 3.4.
• hasAccess: Needed to add uname call internally for R 3.4 backward compatibility, for checks that rely upon isTRUE to return TRUE, as expected. The handling of this situation has changed in R 3.5.

goalie 0.2.8 (2019-02-11)

Minor changes:

• Bioconda unit tests revealed that ...elt approach used in assert isn't backward compatible with R 3.4. The backports package was added as a dependency, which provides legacy support for ...elt in R 3.4. This is called internally inside .onLoad specifically for R releases prior to 3.5.

goalie 0.2.7 (2019-02-11)

Minor changes:

• assert: traceback argument is disabled by default. Note that this can be enabled globally using options(goalie.traceback = TRUE), which can be useful for code debugging in some situations.
• isSubset: Improved cause message if user attempts to pass in NULL for either x or y arguments.
• hasNonZeroRowsAndCols: Fixed typo in internal code that didn't check using hasCols properly.
• isFlag: Improved cause message if user passes in NA.

goalie 0.2.6 (2019-01-22)

New functions:

• Migrated printString from basejump package.

goalie 0.2.5 (2019-01-15)

Minor changes:

• isADirectory, isAFile: Added nullOK argument support.

goalie 0.2.4 (2019-01-06)

New functions:

• New exports: allAreDirectories, allAreFiles, which return scalar.

Minor changes:

• Documentation improvements.

goalie 0.2.3 (2019-01-04)

New functions:

• Migrated some low-level functions from basejump that are useful for assertive checks: matchArgsToDoCall, standardizeCall, and the MethodDefinition family, which includes methodFunction, methodFormals, hasLocal, extractLocal. These will get re-exported in basejump.

Minor changes:

• Reorganized base engine function files, getting rid of the base- prefix.
• Added conditional NULL support where applicable, with nullOK formal. Applies to isInt, isNumber, isString, for example.
• General documentation improvements.

goalie 0.2.2 (2018-12-22)

Major changes:

• assert: Added msg formal. Improved error message when a user inputs check functions that don't return boolean.
• capitalize: Simplified documentation, referring the user to the documentation provided in syntactic package.
• falseFromVector: Newly exported function.
• isInRange family: Added scalar variants for all vectorized functions.
• Improved scalar return consistency in functions where applicable, using falseFromVector internally.

goalie 0.2.1 (2018-12-20)

Major changes:

• The approach to the package update is heavily influenced by the conventions defined in the assertive package. In goalie, I'm attempting to create a minimal assert check engine that behaves similar to stopifnot, but with more informative error messages. This approach is inspired by the assertthat package, but neither assertive or assertthat are working quite right for my needs.
• Overhauled the assert and validate engines, re-writing the code from scratch based on the internal code of stopifnot.
• Reworked all assertive check functions to reduce the number of dependencies. Now the package is lean and mean, only importing methods and utils into the NAMESPACE.
• Assertive checks now return as goalie class in addition to logical.

goalie 0.2.0 (2018-12-12)

Major changes:

• Removed all assert* functions in favor of a simpler, assertthat style approach using assert for all checks. The package will export check functions that return logical, typically logical(1) (boolean flag) for most checks. These checks can then be wrapped in assert or validate (for S4 class validity checks) calls.

goalie 0.1.2 (2018-11-21)

Minor changes:

• isDir and isFile now import R.utils::isDirectory and R.utils::isFile.

goalie 0.1.1 (2018-11-14)

Minor changes:

• areUniqueGeneNames now returns boolean as expected.
• Improved error message for assertAreUniqueGeneNames.

goalie 0.1.0 (2018-11-11)

• Initial release, migrating assertive check functions from basejump package.

acidgenomics/goalie documentation built on Dec. 11, 2023, 11:36 p.m.