pipette 0.4.0 (2020-01-19)

Major changes

  • Renamed package from brio to pipette, in preparation of CRAN submission.
  • export: Reworked internal methods to use new compress and decompress functions defined in acidbase package.
  • localOrRemoteFile: Reworked to use new decompress defined in acidbase internally, with improved tempfile handling.
  • Migrated coercion methods and other utitilies from the now archived transformer package: atomize, coerceToList, droplevels, decode, encode, factorize, matchRowNameColumn, and metadata2.

Minor changes

  • Switched to using cli package for improved messages.

pipette 0.4.1 (2020-01-28)

Minor changes

  • Switched license from MIT to GPL-3.
  • Ensure that coerce method is reexported – thanks @dpryan79 for catching this issue in basejump.

pipette 0.4.2 (2020-04-10)

Minor changes

  • droplevels: Ensuring S4 generic variant defined in S4Vectors package gets reexported and masks base S3 generic. This helps avoid a C stack usage issue that has popped up in the latest version of R.
  • import: Fix for importing JSON files without extension. Can now declare using the format argument. This fix was needed to import GitHub JSON URLs inside new installGitHub function defined in bb8 package.

pipette 0.4.3 (2020-04-15)

Minor changes

  • import: Bug fix for format argument erroring on some supported file types.

pipette 0.4.4 (2020-05-12)

Major changes

  • import and export functions now default to using vroom engine instead of data.table. Internally, these now call vroom and vroom_write. We noticed that the data.table fwrite function in particular can have issues writing many files on AWS EC2 instances, resulting in a stack imbalance. The vroom package seems to be more stable currently.

Minor changes

  • loadData, saveData: Switched to using cli_alert instead of cli_text internally for status messages.

pipette 0.4.5 (2020-05-18)

Minor changes

  • import: Now setting delim internally for vroom import call, to handle single column data frame import. Otherwise vroom will warn about failing to detect expected delimiter.

pipette 0.4.6 (2020-06-11)

Minor changes

  • import: Added support for skip argument, which allows the user to skip a certain number of lines in the input.
  • import and export of source code lines now uses readr package internally (read_lines and write_lines) instead of base readLines and writeLines.

pipette 0.4.7 (2020-07-07)

Minor changes

  • import Hardened Excel input to intentionally error on any warnings returned by internal read_excel call, which is too liberal in coercing data types, in my opinion.
  • import: Switched XLS parser from gdata (no longer updated) back to readxl, which is more actively developed.
  • import: Added makeNames argument, to override default internal handling. This allows the user to apply snake case and/or camel case formatting automatically with this argument.

pipette 0.4.8 (2020-07-24)

Minor changes

  • export: Improved messaages to include full output path.
  • Increased minimum R dependency to 4.0.

pipette 0.4.9 (2020-07-27)

Minor changes

  • Decreased data.table dependency from 1.13.0 back to 1.12.8, so we can build successfully on bioconda.

pipette 0.4.10 (2020-08-03)

Minor changes

  • Relax name checks for import.

pipette 0.4.11 (2020-08-11)

Minor changes

  • export: Ensuring that full directory path is always resolved in message.
  • Miscellaneous message improvements, related to internal toString handling.

pipette 0.4.12 (2020-08-13)

Minor changes

  • import: Improved messages to always resolve full path to import directory.
  • Bug fix for AppVeyor CI config.

pipette 0.4.13 (2020-08-18)

Minor changes

  • export: Now dropping non-atomic columns (e.g. Entrez ID list column) from data frames automatically prior to export. Previously, the allAreAtomic assert check was called automatically and would error on non-atomics.

pipette 0.4.14 (2020-09-14)

Minor changes

  • sanitizeNA: Added support for “N/A” string, which is present in some Excel spreadsheets.

pipette 0.4.15 (2020-10-06)

New functions

  • cacheURL: Utility function for easy package file caching using BiocFileCache package internally.

Minor changes

  • Updated Acid Genomics package dependencies.

pipette 0.4.16 (2020-10-06)

New functions

  • getURLDirList: Migrated this function from previous definition in basejump, so we can inherit inside new AcidGenomes package.

Minor changes

  • cacheURL: Added package argument, so other packages that use this function will automatically inherit the current package, as expected.

pipette 0.4.17 (2020-10-09)

New functions

  • Migrated transmit here from basejump.

pipette 0.4.18 (2020-10-09)

Minor changes

  • Bug fix for breaking change in readr v1.4 release. In the write_* functions, including write_lines and write_csv, the path argument has been renamed to file. Now requiring readr v1.4+ in pipette.

pipette 0.4.19 (2020-10-12)

Minor changes

  • transmit: Added download argument support, to optionally return matching URLs without downloading. This is useful for handing off to cacheURL function for caching files inside of packages with BiocFileCache.