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Version 0.5

pipette 0.5.0 (2021-01-13)

Major changes:

  • import: Improved internal engine support for plain text delimited (e.g. CSV, TSV) files and source code lines. The vroom engine remains enabled by default but data.table, readr, and base R are consistently supported for import of either delimited files or source code lines.
  • export: Added supported for base R export of CSV and TSV files. Internal engine consistency has been improved for character and matrix/data.frame methods. Note that character method currently falls back to using readr’s write_lines function instead of attempting to use the vroom package by default.

pipette 0.5.1 (2021-01-13)

Minor changes:

  • naStrings: Now including lowercase NA variants, which are seen in some files on RefSeq FTP server.
  • sanitizeNA: Updated to also match lowercase NA patterns.

pipette 0.5.2 (2021-01-15)

Minor changes:

  • cacheURL: Improved message. Now only showing when file gets cached into package cache via BiocFileCache. Now defaults to caching into BiocFileCache directory instead of pipette.
  • Now exporting useful rbindlist function from data.table.
  • Renamed matchRowNameColumn to matchRownameColumn (note case).

pipette 0.5.3 (2021-02-03)

New functions:

  • Added md5 and sha256 functions, that use the digest package internally. Previously these were defined in the AcidGenomes package, but have migrated here for file management consistency.

Major changes:

  • cacheURL: Fix bug that resulted in different remote URLs with the same base name being cached as the same object internally by BiocFileCache. Now URLs should always be cached uniquely.

Minor changes:

  • Migrated test data from “tests.acidgenomics.com” to “r.acidgenomics.com/testdata”.
  • Added droplevels method for DataFrame.

pipette 0.5.4 (2021-02-09)

Minor changes:

  • Reexporting some additional functions and classes from GenomicRanges, IRanges, Matrix, and S4Vectors that we can inherit in basejump.

pipette 0.5.5 (2021-02-11)

Minor changes:

  • Including more reexports of useful S4 classes and functions defined in IRanges that we will reexport in basejump: CharacterList, FactorList, IntegerList, LogicalList, NumericList, RleList.

pipette 0.5.6 (2021-02-11)

Minor changes:

  • Reexporting additional useful functions and classes from IRanges, including AtomicList virtual class.
  • Migrated S4Vectors reexports to AcidGenerics, including Annotated, Factor, Factor, LLint, and RectangularData classes.

pipette 0.5.7 (2021-02-12)

Minor changes:

  • Minor rework and simplification of NAMESPACE, inheriting from AcidGenerics and AcidBase when possible.

pipette 0.5.9 (2021-02-12)

Minor changes:

  • Migrated IRanges reexports to AcidGenerics.

pipette 0.5.10 (2021-02-17)

Minor changes:

  • Include CompressedGRangesList from GenomicRanges as a reexport.

pipette 0.5.11 (2021-02-19)

Minor changes:

  • as.DataFrame: Restrict list-based coercion to list and SimpleList (instead of List virtual class).

pipette 0.5.12 (2021-02-22)

Minor changes:

  • Including seqnames as a reexport, which is defined in GenomeInfoDb via GenomicRanges.

pipette 0.5.13 (2021-03-04)

Minor changes:

  • import: Hardened importer against unexpected mismatch when user attempts to manually define column names via colnames argument. Some importers such as vroom are currently too liberal about mismatches.

pipette 0.5.14 (2021-03-17)

Major changes:

  • Switched the default engine back to data.table package for import and export functions.

Minor changes:

  • Improved consistency of arguments for internal engines (base, data.table, readr, and vroom) for import and export of delimited files.
  • Base engine now uses read.table and write.table instead of read.csv and write.csv for CSV files.
  • The optional readr engine now uses read_delim and write_delim, similar to the update for base engine.
  • Improved code coverage of base engine for import/export.

pipette 0.5.15 (2021-04-27)

Minor changes:

  • cacheURL now internally calls BiocFileCache and rappdirs as suggested packages, rather than direct imports. This helps keep the package a bit lighter and improve loading times, as BiocFileCache currently calls a number of heavy dependencies, including dplyr.
  • The checksum functions md5 and sha256 now call digest internally as a suggested package, rather than a direct import.

pipette 0.5.16 (2021-05-18)

Minor changes:

  • Documentation updates, to pass build checks without warnings on R 4.1 and Bioconductor 3.13.

pipette 0.5.17 (2021-05-18)

Major changes:

  • as.DataFrame: Updated list to DataFrame coercion support that is compatible with Bioconductor 3.13 release update.
  • cacheURL: Now using tools::R_user_dir instead of rappdirs::user_cache_dir internally. This matches the conventions used in Bioconductor 3.13 (e.g. AnnotationHub and BiocFileCache).

pipette 0.5.18 (2021-05-18)

Minor changes:

  • decode / encode: Reworked internal code slightly to provide compatibility with S4Vectors update in Bioconductor 3.13.