Add changelog, contribution guide & templates

.Rbuildignore

@@ -7,3 +7,4 @@
 ^README\.Rmd$
 ^docs$
 ^figure/
+^\.github$

.github/CONTRIBUTING.md

@@ -0,0 +1,55 @@
+# Contributing to BacDiveR
+
+This outlines how to propose a change to BacDiveR. Because this project should 
+be to developed according to the needs of BacDive users, please in particular 
+feel free to up- or down-vote existing issues, pull requests or comments. 
+Thumbs-up and -down reactions will inform which issues to prioritise.
+
+
+### Improving texts
+
+Small typos or grammatical errors in documentation may be edited directly using
+the GitHub web interface, so long as the changes are made in the _source_ file.
+
+*  YES: you edit a roxygen comment in an `.R` file below `R/` or any `.Rmd` file.
+*  NO: you edit an `.Rd` file below `man/`.
+
+When in doubt, please proceed with:
+
+
+### Filing issues (also see the [`ISSUE_TEMPLATE.md`
+]((https://github.com/katrinleinweber/BacDiveR/blob/master/.github/ISSUE_TEMPLATE.md))
+
+Please don't hesitate to open an [issue][issues] if you:
+
+a) want to ask a question,
+
+a) suggest a new feature, 
+
+a) found a bug. Illustrating it with a [minimal, reproducible example][reprex] 
+is extremely helpful for fixing it ;-) 
+
+a) in other cases, such as wanting to discuss sending a substantial pull request.
+
+Please spend a few minutes searching the [existing issues (also the closed ones)
+][issues], though. What you want to write might have been already ;-)
+
+[issues]: https://github.com/katrinleinweber/BacDiveR/issues/
+[reprex]: https://www.tidyverse.org/help/#reprex
+
+
+### Sending pull requests (also see the [`PULL_REQUEST_TEMPLATE.md
+`]((https://github.com/katrinleinweber/BacDiveR/blob/master/.github/PULL_REQUEST_TEMPLATE.md))
+
+Contributions through pull requests are welcome, and will be replied to within 1 
+or 2 (non-holi)days.
+
+*  We recommend that you create a Git branch for each PR, preferably with an issue number prepended to the [branch name][bn].
+*  New code should follow RStudio's style guide. Select code & press `Shift`+`CTRL`/`CMD`+`A` (or go to the "Code Tools" menu > "Reformat Code").
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with
+[Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/markdown.html), 
+for documentation.  
+*  We use [testthat](https://cran.r-project.org/package=testthat). Contributions
+with test cases included are easier to accept.  
+
+[bn]: https://github.com/katrinleinweber/BacDiveR/branches

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,36 @@
+<!-- Please start with a brief description what this issue is about. Are you 
+reporting a problem, asking a question, requesting a new feature, starting a 
+discussion, etc.? Anything is welcome :-) -->
+
+I have a question: 
+
+<!-- When reporting a bug, please include a [minimal reproducible example (AKA a 
+reprex)](http://reprex.tidyverse.org/). If you've never heard of that, please 
+read: [tidyverse.org/help/#reprex](https://www.tidyverse.org/help/#reprex).
+-->
+
+I noticed the following problem....
+
+```r
+# Please insert a repr(oducible )ex(ample) here
+```
+
+<!-- When requesting a new feature, please explain why it would be useful, and 
+how you would like to use it. A user story is a helpful way of phrasing such a
+request, see https://en.wikipedia.org/wiki/User_story#Examples -->
+
+I suggest to add a feature. As a ...your role..., I would like to see 
+...functionality..., in order to....
+
+<!-- In any case, please mark the relevant boxes below (with an x). Striking out
+irrelevant lines with ~~ ... ~~ is fine :-) -->
+
+##### I have...
+
+- [ ] ... ensured that I have installed the [latest release version
+](https://github.com/katrinleinweber/BacDiveR/releases) and this issue pertains
+to it, not to an old version.
+- [ ] ... spent a few minutes [searching the existing issues
+](https://github.com/katrinleinweber/BacDiveR/issues?utf8=%E2%9C%93&q=all).
+
+<!-- Thank you :-)   I'll try to reply to this within one week. -->

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,24 @@
+<!-- Please start with a brief summary. If it's trivial, "See diff" and deleting 
+the rest of the template text is fine :-) -->
+
+See diff ;-)
+
+<!-- If your PR includes more substantial changes, please explain them above and
+then mark the relevant boxes below (with an x). Striking out irrelevant lines
+with ~~...~~ is fine :-) -->
+
+##### I have...
+
+- [ ] ... run `testthat::auto_test_package()` and saw now errors.
+- [ ] ... added/updated tests to `/tests/testthat/` for new features or bug-fixes.
+- [ ] ... updated the [changelog / `NEWS.md`
+](https://github.com/katrinleinweber/BacDiveR/blob/master/NEWS.md) in the 
+`Unreleased` section, if my PR introduces user-facing changes.
+- [ ] ... incremented the minor or patch version number in [`DESCRIPTION`
+](https://github.com/katrinleinweber/BacDiveR/blob/master/DESCRIPTION), if my PR
+is a new feature or a bug-fix.
+- [ ] ...read (at least) the [`LICENCSE` (short version)
+](https://github.com/katrinleinweber/BacDiveR/tree/master/LICENSE) and agreed 
+that it will apply to my contribution as well. 
+
+<!-- Thank you! -->

Makefile

@@ -0,0 +1,13 @@
+all: docu vignettes site
+
+check: docu
+	Rscript -e "devtools::check(document = FALSE)"
+
+docu: vignettes
+	Rscript -e "devtools::document(); roxygen2::roxygenise()"
+
+site: docu
+	Rscript -e "pkgdown::build_site()"
+
+vignettes:
+	Rscript -e "knitr::knit(list.files(path = "vignettes", pattern = "*.Rmd$", full.names = TRUE))"

NEWS.md

@@ -0,0 +1,40 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## Unreleased
+
+### Added
+
+- `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 
+
+## [0.4.0] - 2018-04-27
+
+### Added
+
+- This changelog (see #41)
+
+### Changed
+
+- Datasets in the aggregated (large) list are now named according to their 
+`bacdive_ID`s (see #47). Before, the list were only numbered with `1`, `2`, `3`,
+etc.
+
+## [0.3.1] - 2018-03-24
+
+### Fixed
+
+- An error in the download of a single dataset found through it's culture collection number (see #45)
+
+### Added
+
+- Usable example / vignette in the README.md file (see #16)
+

R/construct_url.R

@@ -12,7 +12,7 @@ construct_url <- function(searchTerm,
       searchType,
       "/",
       searchTerm,
-      "/?format=json"
+      "/", "?format=json"
     )
   )
 }

R/retrieve_data.R

@@ -15,12 +15,6 @@
 #'
 #' @export
 #' @examples retrieve_data(searchTerm = "Bacillus subtilis subtilis")
-#'   # This returns a numeric vector of IDs. To download all the corresponding
-#'   # data, use:
-#'   retrieve_data("Bacillus subtilis subtilis")
-#'
-#'   # In case the `searchTerm` is unambiguous already, the data download will
-#'   # procede automatically:
 #'   retrieve_data(searchTerm = "DSM 319", searchType = "culturecollectionno")
 #'   retrieve_data(searchTerm = "AJ000733", searchType = "sequence")
 #'   retrieve_data(searchTerm = 717, searchType = "bacdive_id")
@@ -63,17 +57,17 @@ retrieve_data <- function(searchTerm,
 download <-
   function(URL,
            userpwd = paste(get_credentials(), collapse = ":")) {
-    gsub(
-      pattern = "[[:space:]]+",
-      replacement = " ",
-      perl = TRUE,
-      # Prevent "lexical error: invalid character inside string."
-      # https://github.com/jeroen/jsonlite/issues/47
+  gsub(
+    pattern = "[[:space:]]+",
+    replacement = " ",
+    perl = TRUE,
+    # Prevent "lexical error: invalid character inside string."
+    # https://github.com/jeroen/jsonlite/issues/47
       RCurl::getURL(URL,
-                    userpwd = userpwd,
+    userpwd = userpwd,
                     httpauth = 1L)
-    )
-  }
+  )
+}
 
 
 #' Aggregate BacDive-IDs from a Paged List of Retrieved URLs