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base repository: ropensci/traits
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Commits on Aug 31, 2015

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Commits on Sep 11, 2015

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Commits on May 29, 2016

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  2. added url parameter to betydb functions to support queries of differe…

    …nt hosts in the betydb network
    dlebauer committed May 29, 2016
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Commits on May 31, 2016

  1. Merge pull request #75 from dlebauer/master

    Add url parameter to betydb functions
    sckott committed May 31, 2016
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Commits on Aug 25, 2016

  1. Update betydb.R

    dlebauer authored Aug 25, 2016
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  2. Merge pull request #78 from dlebauer/patch-2

    Provide api endpoints in betydb fn documentation
    sckott authored Aug 25, 2016
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Commits on Jan 3, 2017

  1. eol traitbank updated to reflect current API results

    - function ‘trait bank’:
        * checks for correct structure of returned object
        * prints message if structure mismatches expectation
        * always returns same object structure (potentially with empty
    elements)
    
    - unit tests:
        * function ‘check_traitbank’
        * file ‘test-traitbank.R’
    dschlaep committed Jan 3, 2017
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  2. Merge pull request #80 from dschlaep/updated_eol_traitbank_api

    eol traitbank updated to reflect current API results
    sckott authored Jan 3, 2017
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Commits on Jan 26, 2017

  1. tidy ncbi_byname and namespace setNames call #81

    and make sure empty data.frame col classes match those of when data is found
    bump dev version
    sckott committed Jan 26, 2017
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Commits on Feb 1, 2017

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  2. Provide null default for betydb_http auth

    If no auth info is provided, betydb_auth will use a default API key-- no need to pass the NULLs in by hand.
    infotroph committed Feb 1, 2017
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  6. New function betydb_query

    infotroph committed Feb 1, 2017
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  8. add header

    infotroph committed Feb 1, 2017
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  9. New Bety API: allow nested lists in single-item functions

    N.B. this changes return type of betydb_{trait, specie, citation, site}: Were dataframes, now lists as was documented
    infotroph committed Feb 1, 2017
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Commits on Feb 2, 2017

  1. use betydb_query in betydb_search

    All existing functions should now work with API v1.
    infotroph committed Feb 2, 2017
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Commits on Feb 3, 2017

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Commits on Feb 6, 2017

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Commits on Feb 7, 2017

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  2. Fix broken build

    replaces #85
    dlebauer authored Feb 7, 2017
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  3. Merge pull request #86 from dlebauer/patch-4

    Fix broken build
    sckott authored Feb 7, 2017
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  4. Merge pull request #82 from infotroph/betydb_refactor

    Refactor Betydb functions to support new API
    sckott authored Feb 7, 2017
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Commits on Feb 23, 2017

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  3. merge makeurl functions

    infotroph committed Feb 23, 2017
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  4. whitespace fixes

    infotroph committed Feb 23, 2017
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Commits on Feb 24, 2017

  1. add user and pwd to betydb_query

    Security issue! When passed in ..., username and password were treated
    as query arguments and appended to the URL. Fixed by adding them as named arguments.
    infotroph committed Feb 24, 2017
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Commits on Mar 16, 2017

  1. Link to query docs

    infotroph committed Mar 16, 2017
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  2. Merge pull request #88 from infotroph/traits-cleanup

    BETY cleanup
    sckott authored Mar 16, 2017
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Commits on Mar 21, 2017

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  2. update man files for new roxygen2 version, force new pkg version

    bump pkg de vresion
    sckott committed Mar 21, 2017
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Commits on Apr 12, 2017

  1. Merge pull request #3 from ropensci/master

    update fork
    dlebauer authored Apr 12, 2017
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Commits on Apr 13, 2017

  1. adding ability to page through queries that return many many results …

    …in order to prevent 504 timeout errors
    dlebauer committed Apr 13, 2017
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Commits on Apr 14, 2017

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  4. reduced default paging limit further

    Merge branch 'master' of https://github.com/dlebauer/traits
    
    Conflicts:
    	tests/testthat/test-betydb.R
    dlebauer committed Apr 14, 2017
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  5. fixed broken tests

    dlebauer committed Apr 14, 2017
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Commits on Apr 17, 2017

  1. ensure iterations are correctly used when per_call_limit is not default

    updated tests to use smaller per-call limit
    dlebauer committed Apr 17, 2017
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  2. betydb fns: handle results w/ no counts in warning

    change warning to message
    tests: fixed errors testing API responses
    dlebauer committed Apr 17, 2017
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Commits on Apr 18, 2017

  1. Merge pull request #1 from dlebauer/master

    recent changes to allow paging
    dlebauer authored Apr 18, 2017
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  2. addressed comments by @infotroph

    better opts handling
    change from `expect_true(grepl ...` to `expect_match`
    dlebauer committed Apr 18, 2017
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Showing with 3,175 additions and 3,351 deletions.
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  101. +29 −0 revdep/README.md
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  105. +24 −0 tests/testthat/helper-traits.R
  106. +134 −13 tests/testthat/test-betydb.R
  107. +25 −0 tests/testthat/test-traitbank.R
  108. +0 −21 traits.Rproj
  109. +45 −142 vignettes/betydb.Rmd
  110. +14 −9 inst/vign/betydb.Rmd → vignettes/betydb.Rmd.og
  111. +287 −0 vignettes/traits.Rmd
  112. +83 −0 vignettes/traits.Rmd.og
  113. +0 −469 vignettes/traits_intro.Rmd
10 changes: 8 additions & 2 deletions .Rbuildignore
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@@ -9,7 +9,13 @@ inst/stuff/
^.*\.Rproj$
^\.Rproj\.user$
README.Rmd
NEWS.md
cran-comments.md
inst/readmecache
inst/vign/vigncache
vignettes/cache
.github
^CODE_OF_CONDUCT\.md$
^cran-comments\.md$
^revdep$
^codemeta\.json$
^CITATION\.cff$
^\.github$
16 changes: 16 additions & 0 deletions .github/CONTRIBUTING.md
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# CONTRIBUTING #

### Bugs?

* Submit an issue on the [Issues page](https://github.com/ropensci/traits/issues)

### Code contributions

* Fork this repo to your Github account
* Clone your version on your account down to your machine from your account, e.g,. `git clone https://github.com/<yourgithubusername>/traits.git`
* Make sure to track progress upstream (i.e., on our version of `traits` at `ropensci/traits`) by doing `git remote add upstream https://github.com/ropensci/traits.git`. Before making changes make sure to pull changes in from upstream by doing either `git fetch upstream` then merge later or `git pull upstream` to fetch and merge in one step
* Make your changes (bonus points for making changes on a new feature branch)
* Push up to your account
* Submit a pull request to home base at `ropensci/traits`

### Also, check out our [discussion forum](https://discuss.ropensci.org)
12 changes: 12 additions & 0 deletions .github/issue_template.md
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<!-- If authentication is involved: do not share your username/password, or api keys/tokens in this issue - most likely the maintainer will have their own equivalent key -->

<!-- Do not share screen shots of code. Share actual code in text format. -->

<!-- If this issue relates to usage of the package, whether a question, bug or similar, along with your query, please paste your devtools::session_info() or sessionInfo() into the code block below, AND include a reproducible example (consider using a "reprex" https://cran.rstudio.com/web/packages/reprex/). If not, delete all this and proceed :) -->

<details> <summary><strong>Session Info</strong></summary>

```r

```
</details>
16 changes: 16 additions & 0 deletions .github/pull_request_template.md
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<!--- Provide a general summary of your changes in the Title above -->

## Description
<!--- Describe your changes in detail -->

## Related Issue
<!--- if this closes an issue make sure include e.g., "fix #4"
or similar - or if just relates to an issue make sure to mention
it like "#4" -->

## Example
<!--- if introducing a new feature or changing behavior of existing
methods/functions, include an example if possible to do in brief form -->

<!--- Did you remember to include tests? Unless you're just changing
grammar, please include new tests for your change -->
27 changes: 27 additions & 0 deletions .github/workflows/r_cmd_check.yml
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name: R CMD check

on:
push:
branches:
- main
pull_request:
branches:
- main
jobs:
check:
runs-on: ubuntu-latest
env:
_R_CHECK_CRAN_INCOMING_: false
steps:
- name: Set up R
uses: r-lib/actions/setup-r@v2
with:
r-version: '4.3.1'

- name: Install dependencies
run: |
install.packages('devtools')
devtools::install_deps(dependencies = TRUE)
- name: Check
run: R CMD check --no-manual --as-cran
59 changes: 59 additions & 0 deletions .github/workflows/update-citation-cff.yaml
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# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# The action runs when:
# - A new release is published
# - The DESCRIPTION or inst/CITATION are modified
# - Can be run manually
# For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
on:
release:
types: [published]
push:
branches: [master, main]
paths:
- DESCRIPTION
- inst/CITATION
workflow_dispatch:

name: Update CITATION.cff

jobs:
update-citation-cff:
runs-on: macos-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v3
- uses: r-lib/actions/setup-r@v2
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: |
any::cffr
any::V8
- name: Update CITATION.cff
run: |
library(cffr)
# Customize with your own code
# See https://docs.ropensci.org/cffr/articles/cffr.html
# Write your own keys
mykeys <- list()
# Create your CITATION.cff file
cff_write(keys = mykeys, dependencies = FALSE)
shell: Rscript {0}

- name: Commit results
run: |
git config --local user.name "github-actions[bot]"
git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
git add CITATION.cff
git commit -m 'Update CITATION.cff' || echo "No changes to commit"
git push origin || echo "No changes to commit"
5 changes: 5 additions & 0 deletions .gitignore
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.Rproj.user
plantatt.pdf
inst/PLANTATT_19_Nov_08/*
inst/vign/vigncache
revdep/checks.noindex
revdep/data.sqlite
revdep/library.noindex
vignettes/cache
4 changes: 4 additions & 0 deletions .travis.yml
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@@ -1,6 +1,10 @@
language: r
sudo: false
cache: packages
dist: trusty

r_github_packages:
- jimhester/covr

after_success:
- Rscript -e 'covr::codecov()'
75 changes: 75 additions & 0 deletions CITATION.cff
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# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------

cff-version: 1.2.0
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
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.
authors:
- family-names: LeBauer
given-names: David
email: dlebauer@gmail.com
orcid: https://orcid.org/0000-0001-7228-053X
- family-names: Chamberlain
given-names: Scott
email: myrmecocystus@gmail.com
orcid: https://orcid.org/0000-0003-1444-9135
- family-names: Foster
given-names: Zachary
- family-names: Bartomeus
given-names: Ignasi
- family-names: Black
given-names: Chris
- family-names: Harris
given-names: David
repository: https://CRAN.R-project.org/package=traits
repository-code: https://github.com/ropensci/traits
url: https://docs.ropensci.org/traits/
contact:
- family-names: LeBauer
given-names: David
email: dlebauer@gmail.com
orcid: https://orcid.org/0000-0001-7228-053X
keywords:
- traits
- API
- web-services
- species
- taxonomy
- api-client
- r
- r-package
- rstats
preferred-citation:
type: software
title: 'ropensci/traits: traits 0.5.1'
version: 0.5.1
authors:
- family-names: Chamberlain
given-names: Scott
- family-names: LeBauer
given-names: David
- family-names: Black
given-names: Chris
- family-names: Harris
given-names: David J.
- family-names: Bartomeus
given-names: Ignasi
- family-names: Foster
given-names: Zachary
- family-names: Salmon
given-names: Maëlle
- family-names: Heyek
given-names: Nick
- family-names: Collins
given-names: Rupert A.
doi: 10.5281/zenodo.11224037
url: https://doi.org/10.5281/zenodo.11224037
date-released: 2024-05-17
53 changes: 31 additions & 22 deletions DESCRIPTION
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@@ -1,41 +1,50 @@
Package: traits
Title: Species Trait Data from Around the Web
Description: Species trait data from many different sources, including
sequence data from 'NCBI', plant trait data from 'BETYdb', invasive species
data from the Global Invasive Species Database and 'EOL', 'Traitbank' data
from 'EOL', Coral traits data from http://coraltraits.org, 'nativity' status
('Flora Europaea' or 'ITIS'), and 'Birdlife' International.
Version: 0.2.0
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
Authors@R: c(
person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com"),
person("Zachary", "Foster", role = "aut", email = "zacharyfoster1989@gmail.com"),
person("Ignasi", "Bartomeus", role = "aut", email = "nacho.bartomeus@gmail.com"),
person("David", "LeBauer", role = "aut", email = "dlebauer@gmail.com"),
person("David", "Harris", role = "aut", email = "davharris@ucdavis.edu")
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("Zachary", "Foster", role = "aut"),
person("Ignasi", "Bartomeus", role = "aut"),
person("Chris", "Black", role = "aut"),
person("David", "Harris", role = "aut"),
person("Rupert", "Collins", role = "ctb")
)
License: MIT + file LICENSE
URL: https://github.com/ropensci/traits
BugReports: http://www.github.com/ropensci/traits/issues
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:
methods,
stats,
utils,
jsonlite (>= 0.9.19),
httr (>= 1.1.0),
dplyr (>= 0.4.3),
crul (>= 0.6.0),
tibble (>= 1.3.4),
data.table (>= 1.9.6),
readr (>= 0.2.2),
readr (>= 1.1.1),
taxize (>= 0.7.4),
xml2 (>= 0.1.2),
rvest (>= 0.3.1)
rvest (>= 0.3.1),
hoardr
Suggests:
roxygen2 (>= 5.0.1),
knitr,
rmarkdown,
testthat,
plyr,
covr
RoxygenNote: 5.0.1
dplyr,
plyr
RoxygenNote: 7.1.1
X-schema.org-applicationCategory: Biodiversity
X-schema.org-keywords: traits, API, web-services, species, taxonomy
X-schema.org-isPartOf: https://ropensci.org
2 changes: 1 addition & 1 deletion LICENSE
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
YEAR: 2016
YEAR: 2020
COPYRIGHT HOLDER: Scott Chamberlain
45 changes: 37 additions & 8 deletions Makefile
Original file line number Diff line number Diff line change
@@ -1,10 +1,39 @@
all: move rmd2md
PACKAGE := $(shell grep '^Package:' DESCRIPTION | sed -E 's/^Package:[[:space:]]+//')
RSCRIPT = Rscript --no-init-file

move:
cp inst/vign/betydb.md vignettes;\
cp inst/vign/traits_intro.md vignettes
vign:
cd vignettes;\
${RSCRIPT} -e "Sys.setenv(NOT_CRAN='true'); knitr::knit('traits.Rmd.og', output = 'traits.Rmd')";\
cd ..

rmd2md:
cd vignettes;\
mv betydb.md betydb.Rmd;\
mv traits_intro.md traits_intro.Rmd
vign_bety:
cd vignettes;\
${RSCRIPT} -e "Sys.setenv(NOT_CRAN='true'); knitr::knit('betydb.Rmd.og', output = 'betydb.Rmd')";\
cd ..

install: doc build
R CMD INSTALL . && rm *.tar.gz

build:
R CMD build .

doc:
${RSCRIPT} -e "devtools::document()"

eg:
${RSCRIPT} -e "devtools::run_examples(run = TRUE)"

check: build
_R_CHECK_CRAN_INCOMING_=FALSE R CMD CHECK --as-cran --no-manual `ls -1tr ${PACKAGE}*gz | tail -n1`
@rm -f `ls -1tr ${PACKAGE}*gz | tail -n1`
@rm -rf ${PACKAGE}.Rcheck

test:
${RSCRIPT} -e 'devtools::test()'

readme:
${RSCRIPT} -e 'knitr::knit("README.Rmd")'

check_windows:
${RSCRIPT} -e "devtools::check_win_devel(); devtools::check_win_release()"

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