Bump version to 0.5.2, update CITATION and DESCRIPTION files, enhance documentation, and fix bugs in tests.

dlebauer · dlebauer · commit a9b326b0d38e · 2025-04-08T12:04:43.000-07:00
diff --git a/CITATION.cff b/CITATION.cff
@@ -8,7 +8,7 @@ message: 'To cite package "traits" in publications use:'
 type: software
 license: MIT
 title: 'traits: Species Trait Data from Around the Web'
-version: 0.5.1
+version: 0.5.2
 abstract: Species trait data from many different sources, including sequence data
   from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>), plant trait data from 'BETYdb', data
   from 'EOL' 'Traitbank', 'Birdlife' International, and more.
@@ -49,8 +49,8 @@ keywords:
 - rstats
 preferred-citation:
   type: software
-  title: 'ropensci/traits: traits 0.5.1'
-  version: 0.5.1
+  title: 'ropensci/traits: traits 0.5.2'
+  version: 0.5.2
   authors:
   - family-names: Chamberlain
     given-names: Scott
@@ -72,4 +72,4 @@ preferred-citation:
     given-names: Rupert A.
   doi: 10.5281/zenodo.11224037
   url: https://doi.org/10.5281/zenodo.11224037
-  date-released: 2024-05-17
+  date-released: 2025-04-10
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,50 +1,51 @@
 Package: traits
 Title: Species Trait Data from Around the Web
-Description: Species trait data from many different sources, including
-    sequence data from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>),
-    plant trait data from 'BETYdb', data from 'EOL' 'Traitbank',
-    'Birdlife' International, and more.
-Version: 0.5.1
+Version: 0.5.2
 Authors@R: c(
-    person("David", "LeBauer", role = c("aut", "cre"),
-        email = 'dlebauer@gmail.com',
-        comment = c(ORCID = "0000-0001-7228-053X")),
-    person("Scott", "Chamberlain", role = c("aut"),
-        email = "myrmecocystus@gmail.com",
-        comment = c(ORCID = "0000-0003-1444-9135")),
+    person("David", "LeBauer", , "dlebauer@gmail.com", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-7228-053X")),
+    person("Scott", "Chamberlain", , "myrmecocystus@gmail.com", role = "aut",
+           comment = c(ORCID = "0000-0003-1444-9135")),
     person("Zachary", "Foster", role = "aut"),
     person("Ignasi", "Bartomeus", role = "aut"),
     person("Chris", "Black", role = "aut"),
     person("David", "Harris", role = "aut"),
     person("Rupert", "Collins", role = "ctb")
   )
+Description: Species trait data from many sources, including sequence data
+    from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>), plant traits from
+    'BETYdb', and data from 'EOL Traitbank' and 'Birdlife International'.
 License: MIT + file LICENSE
 URL: https://docs.ropensci.org/traits/, https://github.com/ropensci/traits
 BugReports: https://github.com/ropensci/traits/issues
-LazyData: true
-Encoding: UTF-8
-VignetteBuilder: knitr
-Roxygen: list(markdown = TRUE)
 Depends:
     R (>= 2.10)
 Imports:
-    jsonlite (>= 0.9.19),
-    httr (>= 1.1.0),
     crul (>= 0.6.0),
-    tibble (>= 1.3.4),
     data.table (>= 1.9.6),
+    hoardr,
+    httr (>= 1.1.0),
+    jsonlite (>= 0.9.19),
     readr (>= 1.1.1),
+    rvest (>= 0.3.1),
     taxize (>= 0.7.4),
-    xml2 (>= 0.1.2),
-    rvest  (>= 0.3.1),
-    hoardr
+    tibble (>= 1.3.4),
+    xml2 (>= 0.1.2)
 Suggests:
+    dplyr,
     knitr,
+    plyr,
     rmarkdown,
-    testthat,
-    dplyr,
-    plyr
-RoxygenNote: 7.1.1
+    testthat
+VignetteBuilder: 
+    knitr
+Date/Publication: 2025-04-10
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
 X-schema.org-applicationCategory: Biodiversity
-X-schema.org-keywords: traits, API, web-services, species, taxonomy
-X-schema.org-isPartOf: https://ropensci.org
+X-schema.org-isPartOf: https://ropensci.org,
+    https://doi.org/10.5281/zenodo.11224037
+X-schema.org-keywords: traits, API, web-services, species, taxonomy,
+    biodiversity, ecology, environmental-data, species-traits
diff --git a/NEWS.md b/NEWS.md
@@ -1,12 +1,22 @@
 Unreleased
 ==========
 
+traits 0.5.2 (2025-04-10)
+=========================
+
 ### Minor Improvements
 
-* Set up automatic archiving of releases on Zenodo
-* Add CITATION.cff file (#133)
-* add doi to README, CITATION.cff (#134)
+* Set up automatic archiving of releases on Zenodo.
+* Added `CITATION.cff` file (#133).
+* Added DOI to `README` and `CITATION.cff` (#134).
+* Added `inst/CITATION`.
+
+### Bug Fixes
 
+* Fixed syntax error in `test-ncbi.R` causing test failures.
+* Added missing `batch_size` argument to `ncbi_byname` documentation (#132).
+* Changed 'country' to 'geo_loc_name' in `ncbi_byid()` (#136).
+ 
 traits 0.5.1
 ============
 
diff --git a/R/ncbi_byname.R b/R/ncbi_byname.R
@@ -5,6 +5,7 @@
 #' @param gene (character) Gene or genes (in a vector) to search for.
 #' See examples.
 #' @param ... Curl options passed on to [crul::verb-GET]
+#' @param batch_size An integer specifying the number of names to query per batch.
 #' @details Removes predicted sequences so you don't have to remove them.
 #' Predicted sequences are those with accession numbers that have "XM_" or
 #' "XR_" prefixes. This function retrieves one sequences for each species,
diff --git a/R/traits-package.r b/R/traits-package.r
@@ -29,7 +29,8 @@
 #' @importFrom tibble as_tibble
 #' @name traits-package
 #' @aliases traits
-#' @docType package
+#' @keywords internal
+"_PACKAGE"
 #' @author Scott Chamberlain
 #' @author Ignasi Bartomeus
 #' @author Zachary Foster
diff --git a/README.md b/README.md
@@ -1,10 +1,14 @@
+---
+title: "traits"
+---
+
 traits
 =======
 
 <!--
 [![cran checks](https://cranchecks.info/badges/worst/traits)](https://cranchecks.info/pkgs/traits)
 [![Build Status](https://travis-ci.org/ropensci/traits.svg?branch=master)](https://travis-ci.org/ropensci/traits)-->
-[![codecov](https://codecov.io/gh/ropensci/traits/branch/master/graph/badge.svg)](https://codecov.io/gh/ropensci/traits)
+[![codecov](https://codecov.io/gh/ropensci/traits/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/traits)
 [![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/traits)](https://github.com/r-hub/cranlogs.app)
 [![cran version](https://www.r-pkg.org/badges/version/traits)](https://CRAN.R-project.org/package=traits)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11224037.svg)](https://doi.org/10.5281/zenodo.11224037)
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,16 +1,24 @@
 ## Test environments
 
-* local OS X install, R 4.0.2 patched
-* ubuntu 14.04 (on travis-ci), R 4.0.2 
+* local macOS install, R 4.3.1
+* Ubuntu 22.04 (via GitHub Actions), R 4.3.1
+* Windows (via GitHub Actions), R 4.3.1
 * win-builder (devel and release)
 
 ## R CMD check results
 
 0 errors | 0 warnings | 0 notes
 
-------
+## Changes in this version
+
+* Added automatic archiving of releases on Zenodo.
+* Added `CITATION.cff` file and DOI to metadata.
+* Fixed syntax error in `test-ncbi.R` causing test failures.
+* Added missing `batch_size` argument to `ncbi_byname` documentation.
+* Update tests.
+* Add `inst/CITATION` file.
 
-This version makes some functions defunct, and fixes some bugs.
+------
 
 Thanks!
-Scott Chamberlain
+David LeBauer
diff --git a/inst/CITATION b/inst/CITATION
@@ -0,0 +1,21 @@
+citHeader("To cite the 'traits' package in publications, please use:")
+
+citation <- bibentry(
+  bibtype = "Manual",
+  title = "traits: Species Trait Data from Around the Web",
+  author = c(
+    person("David", "LeBauer", email = "dlebauer@gmail.com", comment = c(ORCID = "0000-0001-7228-053X")),
+    person("Scott", "Chamberlain", email = "myrmecocystus@gmail.com", comment = c(ORCID = "0000-0003-1444-9135")),
+    person("Zachary", "Foster"),
+    person("Ignasi", "Bartomeus"),
+    person("Chris", "Black"),
+    person("David", "Harris")
+  ),
+  year = "2025",
+  note = "R package version 0.5.2, https://github.com/ropensci/traits, https://doi.org/10.5281/zenodo.11224037",
+  url = "https://docs.ropensci.org/traits/"
+)
+
+citFooter("Please use the DOI to cite this package: https://doi.org/10.5281/zenodo.11224037")
+
+citation
diff --git a/man/ncbi_byname.Rd b/man/ncbi_byname.Rd
diff --git a/man/traits-package.Rd b/man/traits-package.Rd
diff --git a/tests/testthat/test-betydb.R b/tests/testthat/test-betydb.R
@@ -16,7 +16,7 @@ test_that("BETYdb v1 API works", {
 
   get.out <- GET(paste0(priors_url, "/?key=eI6TMmBl3IAb7v4ToWYzR0nZYY07shLiCikvT6Lv")) # Priors is a small table
   expect_is(get.out, "response")
-  expect_match(httr::headers(get.out)$status, "OK" )
+  expect_equal(httr::status_code(get.out), 200)
   expect_match(get.out$url, betyurl)
 })
 
diff --git a/tests/testthat/test-ncbi.R b/tests/testthat/test-ncbi.R
@@ -21,7 +21,7 @@ test_that("ncbi_byname gets seq for multiple species", {
   expect_true(all(!is.na(result$sequence)))
 })
 
-test_that("ncbi_byname handles cases with no results"), {
+test_that("ncbi_byname handles cases with no results", {
   skip_on_cran()
   result <- ncbi_byname("This is not a species")
   expect_equal(ncol(result), 7)
@@ -48,7 +48,7 @@ test_that("ncbi_byname works under subset of conditions from issue #126", {
   res2 <- ncbi_byname(taxa = "Coryphaena hippurus", gene = c("Coi"), seqrange = "500:750")
   expect_true(is.data.frame(res2))
   
-  res3 <- ncbi_byname(taxa = "Sardinops melanostictus", gene = c("12s"), seqrange = "1:2000"))
+  res3 <- ncbi_byname(taxa = "Sardinops melanostictus", gene = c("12s"), seqrange = "1:2000")
   expect_true(is.data.frame(res3))
 
 })
diff --git a/tests/testthat/test-traitbank.R b/tests/testthat/test-traitbank.R
@@ -1,5 +1,6 @@
 test_that("traitbank", {
   skip_on_cran()
+  skip_if_not(identical(Sys.getenv("CI"), "true"), "Skipping test outside CI environment")
 
   aa <- traitbank(query = "MATCH (n:Trait) RETURN n LIMIT 1;")
 
