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NEWS.md

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restez (development version)

restez 2.1.5

(2025-03-07)

BUG FIXES

  • gb_sequence_get() now ensures that accessions are returned in same order as query (#64), thanks @krlmlr

  • tests no longer use with_mock() (#63), thanks @hadley

  • Fix bug where a very long sequence record crashed db_create() (#60), thanks @btupper

restez 2.1.4

(2023-10-25)

BUG FIXES

  • Fix bug in test due to update to duckdb (#55)

restez 2.1.3

(2022-11-09)

BUG FIXES

  • Fix error in processing GenBank release notes that arose in GenBank release 252 (#47)

restez 2.1.2

(2022-09-05)

BUG FIXES

  • Fix spelling errors (4c0f9e48fb3e4d3351a4282d121b26f24d4241f1)
  • Fix broken links (fddb4c2508975fe5bf5588da6aae5aca15f82a61)
  • Other minor fixes for submission to CRAN (43795b48d6fa4ef4c7485dc0f1675d6a2e4fa574, 325b74ff3193bb94e9062bb6114a30b709324ca8)

restez 2.1.1

(2022-09-05)

BUG FIXES

  • Fix incorrect warning about max_tries (#45)

restez 2.1.0

(2022-08-31)

BUG FIXES

  • Fixed bug where restez_status() did not show correct file size (#32)
  • Fixed frequent appearance of "Database is garbage-collected" warning (#33)
  • Skip scanning of gzipped file if zgrep is not detected (3de4f95985c9e857eba276c323625c5c32461155)

DOCUMENTATION

  • Add "Accession filter" to "Tips and Tricks" (1e30498f91b7efd765fb24243df686e10ee16977)
  • Use markdown syntax for roxygen2 (ded1466af50562b88fa1bd349fdadbc1081495d3)

NEW FEATURES

  • Change use of restez_connect() and restez_disconnect(): they are no longer user-facing, and instead get run internally for each instance of connecting to the local database. Also, connection to DB is made in read-only mode, which should allow for multiple simultaneous processes to access the DB (#33, #35)
  • Add ncbi_acc_get() to enable easier querying of GenBank accession numbers (#37, #43)
  • Add max_tries argument to db_download() to automatically re-try download in the event of a drop in internet connectivity (#36, #42)
  • Add dnabin argument to gb_sequence_get() to return sequences in ape DNAbin format (#38, #44)

restez 2.0.0

(2022-07-07)

BUG FIXES

  • Migrate to duckdb (#18, #26)

DOCUMENTATION

  • Update to correct github repo (#28)

NEW FEATURES

  • Add option to connect to database in read-only mode (91b85f6dd24153c16be1cf74a712e5349e31c679)

OTHER

  • Switch CI from travis to github actions (9cc52e888accf489310b604b2636ffbfd0acecd7)

restez 1.1.0

(2022-06-03)

BUG FIXES

  • Fix bug where single extremely long sequence caused db_create() to die (#14)

NEW FEATURES

  • Add ability to filter database by accession number upon creation (#25)

OTHER

restez 1.0.1

(2019-01-07)

BUG FIXES

  • Check internet connection in mainland China

restez 1.0.0

(2018-11-27)

OTHER

  • Post-review version of restez released.
  • Download and query parts of GenBank from within R