bold 0.9.0
==========

### MINOR IMPROVEMENTS

* improved test coverage (#58)
* allow curl options to be passed into `bold_identify_parents()` (#64)
* fix instructions in README for package `sangerseqR` - instructions depend on which version of R is being used (#65) thanks @KevCaz

### BUG FIXES

* fixes in package for `_R_CHECK_LENGTH_1_LOGIC2_` (#57)
* `bold_identify()` fix: ampersands needed to be escaped (#62) thanks @devonorourke


bold 0.8.6
==========

### MINOR IMPROVEMENTS

* tests that make HTTP requests now use package `vcr` to cache responses, speeds up tests significantly, and no longer relies on an internet connection (#55) (#56)
* `bold_seq()`: sometimes on large requests, the BOLD servers time out, and give back partial output but don't indicate that there was an error. We catch this kind of error now, throw a message for the user, and the function gives back the partial output given by the server. Also added to the documentation for `bold_seq()` and in the README that if you run into this problem try to do many queries that will result in smaller set of results instead of one or fewer larger queries (#52) (#53)
* `bold_seq()`: remove return characters (`\r` and `\n`) from sequences (#54)


bold 0.8.0
==========

### MINOR IMPROVEMENTS

* link to taxize bookdown book in readme and vignette (#51)
* `bold_identify_parents()` gains many new parameters (`taxid`, `taxon`, `tax_rank`, `tax_division`, `parentid`, `parentname`, `taxonrep`, `specimenrecords`) to filter parents based on any of a number of fields - should solve problem where multiple parents found for a single taxon, often in different kingdoms (#50)
* add note in docs of `bold_identify()` that the function uses `lapply` internally, so queries with lots of sequences can take a long time

### BUG FIXES

* fix `bold_specimens()`: use `rawToChar()` on raw bytes instead of `parse()` from `crul` (#47)

bold 0.5.0
==========

### NEW FEATURES

* Now using BOLD's v4 API throughout the package. This was essentially
just a change of the BASE URL for each request (#30) 
* Now using `crul` for HTTP requests. Only really affects users in that
specifying curl options works slightly differenlty (#42) 

### BUG FIXES 

* `marker` parameter in `bold_seqspec` was and maybe still is not working, 
in the sense that using the parameter doesn't always limit results to the 
marker you specify. Not really fixed - watch out for it, and filter after you
get results back to get markers you want. (#25) 
* Fixed bug in `bold_identify_parents` - was failing when no match for a
parent name. (#41) thx @VascoElbrecht  
* `tsv` results were erroring in `bold_specimens` and other fxns (#46) - fixed
by switching to new BOLD v4 API (#30)

### MINOR IMPROVEMENTS

* Namespace calls to base pkgs for `stats` and `utils` - replaced 
`is` with `inherits` (#39) 



bold 0.4.0
==========

### NEW FEATURES

* New function `bold_identify_parents()` to add taxonomic information
to the output of `bold_identif()`. We take the taxon names from `bold_identify`
output, and use `bold_tax_name` to get the taxonomic ID, passing it to 
`bold_tax_id` to get the parent names, then attaches those to the input data. 
There are two options given what you put for the `wide` parameter. If `TRUE`
you get data.frames of the same dimensions with parent rank name and ID 
as new columns (for each name going up the hierarchy) - while if `FALSE` 
you get a long data.frame. thanks @dougwyu for inspiring this (#36) 

### MINOR IMPROVEMENTS

* replace `xml2::xml_find_one` with `xml2::xml_find_first` (#33)
* Fix description of `db` options in `bold_identify` man file - 
COX1 and COX1_SPECIES were switched (#37) thanks for pointing that out 
@dougwyu

### BUG FIXES

* Fix to `bold_tax_id` for when some elements returned from the BOLD 
API were empty/`NULL` (#32) thanks @fmichonneau !!


bold 0.3.5
==========

### MINOR IMPROVEMENTS

* Added more tests to the test suite (#28)

### BUG FIXES

* Fixed a bug in an internal data parser (#27)

bold 0.3.4
==========

### NEW FEATURES

* Added a code of conduct

### MINOR IMPROVEMENTS

* Switched to `xml2` from `XML` as the XML parser for this package (#26)
* Fixes to `bold_trace()` to create dir and tar file when it doesn't
already exist

### BUG FIXES

* Fixed odd problem where sometimes resulting data from HTTP request
was garbled on `content(x, "text")`, so now using `rawToChar(content(x))`,
which works (#24)


bold 0.3.0
==========

### MINOR IMPROVEMENTS

* Explicitly import non-base R functions (#22)
* Better package level manual file


bold 0.2.6
==========

### MINOR IMPROVEMENTS

* `sangerseqR` package now in Suggests for reading trace files, and is only used in `bold_trace()`
function.
* General code tidying, reduction of code duplication.
* `bold_trace()` gains two new parameters: `overwrite` to choose whether to overwrite an existing
file of the same name or not, `progress` to show a progress bar for downloading or not.
* `bold_trace()` gains a print method to show a tidy summary of the trace file downloaded.

### BUG FIXES

* Fixed similar bugs in `bold_tax_name()` (#17) and `bold_tax_id()` (#18) in which species that were missing from the BOLD database returned empty arrays but 200 status codes. Parsing those as failed attempts now. Also fixes problem in taxize in `bold_search()` that use these two functions.

bold 0.2.0
==========

### NEW FEATURES

* Package gains two new functions for working with the BOLD taxonomy APIs: `bold_tax_name()` and `bold_tax_id()`, which search for taxonomic data from BOLD using either names or BOLD identifiers, respectively. (#11)
* Two new packages in Imports: `jsonlite` and `reshape`.

### MINOR IMPROVEMENTS

* Added new taxonomy API functions to the vignette (#14)
* Added reference URLS to all function doc files to allow easy reference for the appropriate API docs.
* `callopts` parameter changed to `...` throughout the package, so that passing on options to `httr::GET` is done via named parameters, e.g., `config=verbose()`. (#13)
* Added examples of doing curl debugging throughout man pages.


bold 0.1.2
==========

### MINOR IMPROVEMENTS

* Improved the vignette (#8)
* Added small function to print helpful message when user inputs no parameters or zero length parameter values.

### BUG FIXES

* Fixed some broken tests with the new `httr` (v0.4) (#9), and added a few more tests (#7)


bold 0.1.0
==========

### NEW FEATURES

* released to CRAN
