NEWS.md

In acidgenomics/syntactic: Syntactically Valid Names

Release notes

syntactic 0.7.1 (2023-10-27)

Minor changes:

• autopadZeros: Fix to improve sprintf return consistency on Linux. Need to use %d instead of %s with integer to improve return consistency.

syntactic 0.7.0 (2023-10-03)

Major changes:

• Starting a new release series, based on changes in other Acid Genomics dependency packages.
• Improved some edge case handling of word boundaries for syntactic engine. Added code coverage for these.

Minor changes:

• makeNames now works without stringi package installed.
• Updated assert checks for rename mode.

syntactic 0.6.6 (2023-04-28)

Minor changes:

• makeNames: Added additional regular expression pattern matching of micro character, coercing to "u".

syntactic 0.6.5 (2023-04-12)

Minor changes:

• makeNames: Fixed accidental sanitization of " - " to "_minus_".
• Improved smart mode coverage in makeNames.
• Removed deprecated aliases: camel, snake, upperCamel.

syntactic 0.6.4 (2023-02-06)

Minor changes:

• Smart rename mode now strips single quotes, which are often problematic word boundaries in file names.
• syntacticRename: Now defaults to using smart engine internally. Also added support for dryRun mode, which will be accessible via CLI using --dry-run in next koopa update. Improved to and from file path return and code coverage.

syntactic 0.6.3 (2022-06-10)

Minor changes:

• syntacticRename: Harden against single quotes breaking CLI alert messages, due to internal glue parser. See related issue.

syntactic 0.6.2 (2022-06-02)

Minor changes:

• Hardened working examples and unit tests to use tempdir2 and unlink2 from AcidBase update.

syntactic 0.6.1 (2022-05-23)

Minor changes:

• Updated lintr and testthat checks.

syntactic 0.6.0 (2022-04-29)

Major changes:

• Updated minimum R dependency to 4.2.
• Reduced the number of strong dependencies, migrating AcidBase, AcidCLI, stringi, and stringr to Suggests instead of Imports.

syntactic 0.5.2 (2022-03-23)

Minor changes:

• autopadZeros: Improved regular expression matching in cases where additional numbers are present in string.

syntactic 0.5.1 (2022-03-11)

Minor changes:

• Updated R dependency to 4.1, matching Bioconductor 3.14.
• Increased verbosity of setMethod calls.

syntactic 0.5.0 (2021-08-24)

Major changes:

• Reworked rename approach in package. Now defining a main syntacticRename function that supports kebabCase, snakeCase, camelCase, and upperCamelCase. Rename functionality has been removed from individual S4 character methods designed for syntactic string functions (e.g. camelCase). This approach makes these commonly used functions less complicated, and the behavior is more consistent with the other S4 methods defined in other packages (e.g. SummarizedExperiment in AcidExperiment).

Minor changes:

• Now importing AcidCLI package, for more informative messages and errors, where applicable.

syntactic 0.4.5 (2021-03-03)

Minor changes:

• Tweaked rules slightly to improve capitalization rules around numbers for camel case in strict mode.

syntacitc 0.4.4 (2021-01-21)

Major changes:

• camelCase and upperCamelCase now default to strict = TRUE, which enforces stricter but simpler camel case syntax by default. This converts "gene_id" to "geneId" instead of "geneID" by default, which is now the preferred convention for metadata columns across the Acid Genomics packages.

Minor changes:

• Single quotation marks are now stripped automatically when smart = TRUE (recommended by default).

syntactic 0.4.3 (2020-10-06)

Minor changes:

• Updated dependencies to use renamed AcidBase, AcidGenerics, and AcidRoxygen packages.

syntactic 0.4.2 (2020-07-24)

Minor changes:

• Maintenance release updating minimum R dependency to 4.0.

syntactic 0.4.1 (2020-07-09)

Minor changes:

• Added additional regular expression to catch "10uM" and "uM" edge cases in names that weren't sanitizing to "um" for snake case, as expected.

syntactic 0.4.0 (2020-07-08)

Reworked the internal code and improved default handling for makeNames. Our makeNames variant behaves a bit differently from base R make.names. By default, it returns unique values and sanitizes using underscores (_) rather than periods (.), which are easier to read and more compatible across programming languages and in file names.

Now all syntactic naming functions, including snakeCase, camelCase, and dottedCase internally pass through to makeNames. We have added some edge case handlers that are now enabled by default in all of these functions, including automatic detection of +/-, % (converts to percent) and some other useful defaults for bioinformatics. These can be disabled by setting smart = FALSE.

This release should be fully backward compatible and non-breaking with previous syntactic functions, but the version has been increased to denote the change in the internal code handling.

syntactic 0.3.10 (2020-06-15)

New functions:

• autopadZeros: Migrated character method previously defined in basejump. Also defined support for integer class objects. Improved padding support of integer strings and hardened function against partial padding matches.

syntactic 0.3.9 (2020-04-07)

Minor changes:

• Rename mode now checks for "_" prefix and will skip the file rename. This is particularly useful for avoiding issues with files such as _pkgdown.yml.

syntactic 0.3.8 (2020-02-25)

Minor changes:

• Rename mode now includes a helpful message showing the original file name and modified target name. This convention matches Perl File::Rename module.

syntactic 0.3.7 (2020-02-02)

Minor changes:

• camelCase: Bug fix for strict = TRUE not working as expected in rename mode (rename = TRUE).
• Switched license from MIT to GPL-3.
• Renamed package title to conform to CRAN requirements.

syntactic 0.3.6 (2020-01-27)

Major changes:

• Migrated S4 generics to acidgenerics package.

Minor changes:

• Fix to perserve extension case (e.g. "R", "Rmd") for files in rename mode.

Deprecations:

• Deprecated camel in favor of camelCase.
• Deprecated dotted in favor of dottedCase.
• Deprecated kebab in favor of kebabCase.
• Deprecated snake in favor of snakeCase.
• Deprecated upperCamel in favor of upperCamelCase.

syntactic 0.3.5 (2020-01-14)

Minor changes:

• Syntactic naming functions now check for "&" and convert to "and". This behavior can be disabled by setting smart = FALSE.
• Accented characters are now coerced to plain letters by default internally via stringi::stri_trans_general. This behavior can be disabled by setting smart = FALSE.

syntactic 0.3.4 (2019-12-08)

Minor changes:

• Fixed expected handling of file rename mode on case insensitive file systems. Had to rework the internal code to loop across the files and directories, using an apply call internally.

syntactic 0.3.3 (2019-12-05)

Major changes:

• Added recursive file rename support.

Minor changes:

• Improved handling of " - ", avoiding return of "minus" in file rename mode.
• File extension is automatically converted to lowercase when applicable.

syntactic 0.3.2 (2019-10-22)

File rename mode support.

camelCase, kebabCase, snakeCase, and upperCamelCase now support file rename mode (rename = TRUE). This works on either case-sensitive (Linux) or case-insensitive (macOS, Windows) file systems. Files and directories are supported, including files outside of the current working directory.

I recommend using either kebabCase or snakeCase for files.

When renaming with files beginning with a number, prefix = TRUE will prefix the file with an "x", similar to the behavior in make.names. This can be disabled by settingprefix = FALSE. Smart acronyms and other features can also be disabled by setting smart = FALSE.

This code will be called internally in the upcoming koopa update.

syntactic 0.3.1 (2019-10-08)

Minor changes:

• Now allowing prefix = FALSE for camelCase, dottedCase, kebabCase, snakeCase, and upperCamelCase. This override allows the user to disable automatic "X" prefix defined by make.names internally for input that begins with a syntactically invalid character, such as a number (R-specific) or a non-alphanumeric. We're now allowing this override so we can pass to new camel-case, kebab-case, and snake-case shell scripts defined in koopa.
• Also now allowing smart = FALSE, which disables smart mode handling of mixed case acronyms (e.g. "RNAi", "mRNA"), numeric delims/decimals ("," "."), special characters that can represent words ("+"/"-"; plus/minus), etc. Enabled by default and strongly recommended. Added a new override mode for some edge cases with our new shell methods defined in koopa.
• Migrated character code coverage methods back here from basejump.
• Simplifed code coverage, removing usage of parameterized tests that depend on patrick package.

syntactic 0.3.0 (2019-09-25)

Major changes:

• Migrated non-character S4 methods to basejump package, to keep syntactic very lightweight and fast. Defining only the character methods here allows the package to start up very quickly, and improves shell scripting calls defined in the koopa bootloader package.

syntactic 0.2.6 (2019-09-13)

Minor changes:

• Improved handling of "+", "-", and "/" in character vectors. This update is particularly useful for handling examples such as "dox+" and "vector +/- treatment".

syntactic 0.2.5 (2019-09-09)

Minor changes:

• Migrated S4 generics here from bioverbs package, because they're not really "biological" per se. I consolidated the generics here in case we need to submit syntactic to CRAN rather than Bioconductor.
• Removed S4 generic methods for mcolnames. I'll add this into basejump directly instead.
• Improved documentation consistency and added timestamps.

syntactic 0.2.4 (2019-08-27)

Minor changes:

• Updated R dependency to 3.6.

syntactic 0.2.3 (2019-08-11)

Minor changes:

• Documentation improvements.
• Updated basejump dependencies.

syntactic 0.2.2 (2019-07-29)

Minor changes:

• Renamed label to makeLabel and title to makeTitle, so we don't mask any functions in the graphics package.

syntactic 0.2.1 (2019-07-28)

New functions:

• makeWords: Take a syntactic name vector and reformat to character strings containing words separated by spaces.
• label: Generates a character string suitable for plot axis labels. Uses the new makeWords function internally.
• title: Generate a sentence case string suitable for plot titles.

syntactic 0.2.0 (2019-07-22)

Major changes:

• Renamed case functions. camel to camelCase; kebab to kebabCase; snake to snakeCase; upperCamel to upperCamelCase.

Minor changes:

• Updated naming consistency of internal S4 functions.
• Updated basejump dependencies.

syntactic 0.1.10 (2019-07-12)

Minor changes:

• Updated R dependency to 3.5.

syntactic 0.1.9 (2019-04-25)

Minor changes:

• S4 generic reexport documentation fixes.

syntactic 0.1.8 (2019-03-29)

Minor changes:

• Bug fixes for SummarizedExperiment method support in syntactic functions. Added method suport for snake, which was missing, and forgot to import SummarizedExperiment as a class.
• 100% code coverage!

syntactic 0.1.7 (2019-03-28)

Minor changes:

• Added SummarizedExperiment methods for syntactic naming functions, which reenables support for rownames and colnames arguments.
• Switched to using AcidTest package for example test data.

syntactic 0.1.6 (2019-03-22)

Minor changes:

• Migrated code to Acid Genomics.

syntactic 0.1.5 (2019-02-25)

New functions:

• kebab: Added character vector method support for kebab case.

Minor changes:

• Improved internal code to remove dependency on magrittr pipe.

syntactic 0.1.4 (2019-02-11)

Minor changes:

• Converted capitalize to S4 method that dispatches on character vectors.

syntactic 0.1.3 (2019-01-23)

Minor changes:

• Split out imports into imports.R file, to match conventions used in the other basejump subpackages.
• Added pkgdown website.

syntactic 0.1.2 (2019-01-05)

Minor changes:

• Matrix NAMESPACE fix.
• Documentation improvements.

syntactic 0.1.1 (2019-01-04)

Minor changes:

• Added back Matrix S4 class method support.

syntactic 0.1.0 (2019-01-01)

Initial release. Migrated syntactic name functions from basejump package here to form a more compact package that is easier to unit test.

acidgenomics/syntactic documentation built on Oct. 28, 2023, 7:12 a.m.