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 0.7.3
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
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
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
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)