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Merge pull request #141 from ropensci/back_on_cran
Bump to v0.5.2: CITATION + DESCRIPTION Updates, Docs Improvements, and Bug Fixes
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‎.Rbuildignore‎

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^codemeta\.json$
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^CITATION\.cff$
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^\.github$
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^README\.Rmd$

‎.github/workflows/R-CMD-check.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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name: R-CMD-check.yaml
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permissions: read-all
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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TZ: UTC
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EOL_CYPHER_KEY: ${{ secrets.EOL_CYPHER_KEY }}
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ENTREZ_KEY: ${{ secrets.ENTREZ_KEY }}
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true
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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/r_cmd_check.yml‎

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‎CITATION.cff‎

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@@ -8,10 +8,10 @@ message: 'To cite package "traits" in publications use:'
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type: software
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license: MIT
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title: 'traits: Species Trait Data from Around the Web'
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version: 0.5.1
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abstract: Species trait data from many different sources, including sequence data
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from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>), plant trait data from 'BETYdb', data
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from 'EOL' 'Traitbank', 'Birdlife' International, and more.
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version: 0.5.2
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abstract: Species trait data from many sources, including sequence data from 'NCBI'
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(<https://www.ncbi.nlm.nih.gov/>), plant traits from 'BETYdb', and data from 'EOL
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Traitbank' and 'Birdlife International'.
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authors:
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- family-names: LeBauer
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given-names: David
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given-names: Chris
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- family-names: Harris
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given-names: David
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preferred-citation:
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type: manual
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title: 'traits: Species Trait Data from Around the Web'
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authors:
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- family-names: LeBauer
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given-names: David
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email: dlebauer@gmail.com
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orcid: https://orcid.org/0000-0001-7228-053X
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- family-names: Chamberlain
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given-names: Scott
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email: myrmecocystus@gmail.com
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orcid: https://orcid.org/0000-0003-1444-9135
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- family-names: Foster
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given-names: Zachary
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- family-names: Bartomeus
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given-names: Ignasi
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- family-names: Black
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given-names: Chris
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- family-names: Harris
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given-names: David
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year: '2025'
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notes: R package version 0.5.2, https://github.com/ropensci/traits, https://doi.org/10.5281/zenodo.11224037
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url: https://docs.ropensci.org/traits/
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repository-code: https://github.com/ropensci/traits
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url: https://docs.ropensci.org/traits/
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date-released: '2025-04-10'
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contact:
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- family-names: LeBauer
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given-names: David
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- web-services
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- species
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- taxonomy
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- biodiversity
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- ecology
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- environmental-data
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- species-traits
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- api-client
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- r
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- r-package

‎DESCRIPTION‎

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Package: traits
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Title: Species Trait Data from Around the Web
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Description: Species trait data from many different sources, including
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sequence data from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>),
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plant trait data from 'BETYdb', data from 'EOL' 'Traitbank',
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'Birdlife' International, and more.
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Version: 0.5.1
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Version: 0.5.2
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Authors@R: c(
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person("David", "LeBauer", role = c("aut", "cre"),
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email = 'dlebauer@gmail.com',
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comment = c(ORCID = "0000-0001-7228-053X")),
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person("Scott", "Chamberlain", role = c("aut"),
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email = "myrmecocystus@gmail.com",
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comment = c(ORCID = "0000-0003-1444-9135")),
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person("David", "LeBauer", , "dlebauer@gmail.com", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0001-7228-053X")),
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person("Scott", "Chamberlain", , "myrmecocystus@gmail.com", role = "aut",
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comment = c(ORCID = "0000-0003-1444-9135")),
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person("Zachary", "Foster", role = "aut"),
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person("Ignasi", "Bartomeus", role = "aut"),
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person("Chris", "Black", role = "aut"),
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person("David", "Harris", role = "aut"),
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person("Rupert", "Collins", role = "ctb")
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)
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Description: Species trait data from many sources, including sequence data
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from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>), plant traits from
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'BETYdb', and data from 'EOL Traitbank' and 'Birdlife International'.
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License: MIT + file LICENSE
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URL: https://docs.ropensci.org/traits/, https://github.com/ropensci/traits
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BugReports: https://github.com/ropensci/traits/issues
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LazyData: true
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Encoding: UTF-8
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VignetteBuilder: knitr
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Roxygen: list(markdown = TRUE)
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Depends:
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R (>= 2.10)
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Imports:
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jsonlite (>= 0.9.19),
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httr (>= 1.1.0),
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crul (>= 0.6.0),
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tibble (>= 1.3.4),
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data.table (>= 1.9.6),
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hoardr,
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httr (>= 1.1.0),
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jsonlite (>= 0.9.19),
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readr (>= 1.1.1),
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rvest (>= 0.3.1),
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taxize (>= 0.7.4),
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xml2 (>= 0.1.2),
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rvest (>= 0.3.1),
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hoardr
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tibble (>= 1.3.4),
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xml2 (>= 0.1.2)
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Suggests:
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dplyr,
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knitr,
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plyr,
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rmarkdown,
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testthat,
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dplyr,
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plyr
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RoxygenNote: 7.1.1
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testthat
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VignetteBuilder:
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knitr
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Date/Publication: 2025-04-10
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Encoding: UTF-8
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LazyData: true
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.2
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X-schema.org-applicationCategory: Biodiversity
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X-schema.org-keywords: traits, API, web-services, species, taxonomy
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X-schema.org-isPartOf: https://ropensci.org
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X-schema.org-isPartOf: https://ropensci.org,
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https://doi.org/10.5281/zenodo.11224037
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X-schema.org-keywords: traits, API, web-services, species, taxonomy,
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biodiversity, ecology, environmental-data, species-traits

‎NEWS.md‎

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Unreleased
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==========
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traits 0.5.2 (2025-04-10)
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=========================
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### Minor Improvements
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* Set up automatic archiving of releases on Zenodo
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* Add CITATION.cff file (#133)
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* add doi to README, CITATION.cff (#134)
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* Set up automatic archiving of releases on Zenodo.
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* Added `CITATION.cff` file (#133).
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* Added DOI to `README` and `CITATION.cff` (#134).
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* Added `inst/CITATION`.
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### Bug Fixes
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* Fixed syntax error in `test-ncbi.R` causing test failures.
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* Added missing `batch_size` argument to `ncbi_byname` documentation (#132).
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* Changed 'country' to 'geo_loc_name' in `ncbi_byid()` (#136).
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traits 0.5.1
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============
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‎R/ncbi_byname.R‎

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#' @param gene (character) Gene or genes (in a vector) to search for.
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#' See examples.
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#' @param ... Curl options passed on to [crul::verb-GET]
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#' @param batch_size An integer specifying the number of names to query per batch.
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#' @details Removes predicted sequences so you don't have to remove them.
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#' Predicted sequences are those with accession numbers that have "XM_" or
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#' "XR_" prefixes. This function retrieves one sequences for each species,

‎R/traits-package.r‎

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#' @importFrom tibble as_tibble
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#' @name traits-package
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#' @aliases traits
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#' @docType package
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#' @keywords internal
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"_PACKAGE"
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#' @author Scott Chamberlain
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#' @author Ignasi Bartomeus
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#' @author Zachary Foster

‎README.Rmd‎

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---
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title: "traits: Species Trait Data from Around the Web"
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output: github_document
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---
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traits
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=======
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```
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<!--[![cran checks](https://cranchecks.info/badges/worst/traits)](https://cranchecks.info/pkgs/traits)-->
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[![Build Status](https://travis-ci.org/ropensci/traits.svg?branch=master)](https://travis-ci.org/ropensci/traits)
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[![R-CMD-check](https://github.com/ropensci/traits/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/traits/actions/workflows/R-CMD-check.yaml)
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[![codecov](https://codecov.io/gh/ropensci/traits/branch/master/graph/badge.svg)](https://codecov.io/gh/ropensci/traits)
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[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/traits)](https://github.com/r-hub/cranlogs.app)
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[![cran version](https://www.r-pkg.org/badges/version/traits)](https://CRAN.R-project.org/package=traits)

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