NEWS.md

In TIBHannover/BacDiveR: Programmatic Interface For The Bacterial Diversity Metadatabase by DSMZ

Unreleased

Added

Changed

Deprecated

Removed

Fixed

Security

BacDiveR 0.9.1

Fixed

• Expose a previously silent download error (#110; Thanks to @jfy133!)

Changed

• Repair outdated links in documentation
• Improve some code sections in minor ways

BacDiveR 0.9.0

All notable changes to this project will be documented in this file. The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Changed

• NEW API: The deprecations announced in v0.8.0 are now completed: The bd_retrieve() family of functions has replaced retrieve_data() and retrieve_search_results() has been renamed to bd_retrieve_by_search(), see #96. Please update scripts and other downstream code that use BacDiveR.
• purrr is no longer an imported / required dependency, but only suggested due to use in the introductory vignette, see #98.

BacDiveR 0.8.1

Changed

• Warning message about no data being found is more informative now
• Documentation to follow BacDive's database updates
• Use pandoc 2.7.2 to generate the website

BacDiveR 0.8.0

Added

• NEW API: The bd_retrieve() family of functions will replace retrieve_data() soon. It consists of bd_retrieve(id = …), bd_retrieve_by_culture(collectionno = …), bd_retrieve_by_sequence(accession = …) and bd_retrieve_taxon(name = …) which is more auto-complete-friendly and should help avoid the internal need to sanitise inputs.

Deprecated

• retrieve_data() has been replaced as described above.
• retrieve_search_results() has been renamed to bd_retrieve_by_search().
• Both old functions will be removed in the next major version. Please update your BacDiveR-using scripts and other downstream code.

BacDiveR 0.7.4

Fixed

• A bug in the test suite.

BacDiveR 0.7.3

Changed

• Warnings, errors and message are now more concisely/informatively/strongly worded.

BacDiveR 0.7.2

Changed

• retrieve_data & retrieve_search_results() now validate all inputs (fix #71 & #78)

BacDiveR 0.7.1

Changed

• The combined use of a) RCurl for downloading JSON-encoded data from BacDive with b) jsonlite for converting the download into an R objects was plagued by some whitespace escaping problems. This spawned a custom repair solution, adding accidental complexity. That swamp is now drained by use of httr.

BacDiveR 0.7.0

Added

• A vignette section about mass-downloading datasets.

Changed

• Instead of stopping with an error if a search returns no results, BacDiveR now only warns about this case and returns an empty list (#93).
• Estimated download times are now reported before all downloads longer than ca. 30 seconds (#84).

BacDiveR 0.6.1

Fixed

• Errors caused by comparing against a NULL (#91; Thanks to @jotech!)

BacDiveR 0.6.0

Added

• The vignette Logic-Checking BacDive Datasets

Changed

• retrieve_search_results() now returns NULL when no results are found, in order to ease integration of datasets into testthat tests.

BacDiveR 0.5.1

Fixed

• Another JSON whitespace escaping bug (#91; Thanks to @jotech!)

BacDiveR 0.5.0

Added

• Syncing of release versions to Zenodo, starting with 10.5281/zenodo.1308061

Changed

• The JSON downloads are no longer purged of all space characters pre-emptively to prevent jsonlite from complaining about invalid encoding (#43). Instead, only \r, \n and \t are repaired to \\r, \\n and \\t, which jsonlite expects. This leads to different output (newline & tabs, where previously only spaces occurred)! Thus, if you are parsing BacDiveR output in any way, you may need to adjust that. Because I consider this unlikely given the "maturing" status, and because no API surface was changed, I don't consider this a major change in the SemVer.org sense.

BacDiveR 0.4.2

Fixed

• Install errors are now warnings and better advise about fixing them (#62)

BacDiveR 0.4.1

Changed

• Don't run all function docu examples, and limit their output on the reference pages (see #52)

BacDiveR 0.4.0

Added

• This changelog (see #41)
• retrieve_search_results(), see #61
• Architecture Decision records, see #53 & /docs/arch/adr-*.md

Changed

• retrieve_data() now downloads the dataset(s) by default, not only the ID(s), see #54 & #59
• Datasets in the aggregated (large) list are now named according to their bacdive_IDs (see #47). Before, the lists were only numbered with 1, 2, 3, etc.

BacDiveR 0.3.1

Fixed

• An error in the download of a single dataset found through its culture collection number (see #45)

Added

• Usable example / vignette in the README.md file (see #16)

TIBHannover/BacDiveR documentation built on June 2, 2022, 2:51 p.m.