From 631d45cabfcfb052ab74dc69eeb11eea847f9bef Mon Sep 17 00:00:00 2001 From: Geoff Ower Date: Wed, 14 Feb 2024 13:36:59 -0600 Subject: [PATCH] Update name --- CONTRIBUTING.md | 4 ++-- DESCRIPTION | 8 +++---- LICENSE | 2 +- LICENSE.md | 4 ++-- Makefile | 2 +- NEWS.md | 2 +- R/http.R | 2 +- ...nWorks-package.R => rtaxonworks-package.R} | 6 ++--- README.Rmd | 22 +++++++++--------- README.md | 23 ++++++++++--------- codemeta.json | 12 +++++----- .../{RTaxonWorks.Rmd => rtaxonworks.Rmd} | 10 ++++---- ...{RTaxonWorks.Rmd.og => rtaxonworks.Rmd.og} | 10 ++++---- 13 files changed, 54 insertions(+), 53 deletions(-) rename R/{RTaxonWorks-package.R => rtaxonworks-package.R} (80%) rename vignettes/{RTaxonWorks.Rmd => rtaxonworks.Rmd} (72%) rename vignettes/{RTaxonWorks.Rmd.og => rtaxonworks.Rmd.og} (75%) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 09b2aca..a59040a 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -6,9 +6,9 @@ Install the package dependencies: install.packages('devtools', 'roxygen2', 'profvis', 'httr2', 'vcr') ``` -Install the development version of the RTaxonWorks package: +Install the development version of the rtaxonworks package: ```{r eval=FALSE} -remotes::install_github("SpeciesFileGroup/RTaxonWorks") +remotes::install_github("SpeciesFileGroup/rtaxonworks") ``` diff --git a/DESCRIPTION b/DESCRIPTION index 6bd378c..7d158cc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,4 +1,4 @@ -Package: RTaxonWorks +Package: rtaxonworks Type: Package Title: TaxonWorks Client Description: Client for TaxonWorks @@ -11,9 +11,9 @@ Authors@R: c(person("Geoff", "Ower", role = c("aut", "cre"), email = "gdower@illinois.edu", comment = c(ORCID = "0000-0002-9770-2345")), person(given = "Species File Group", role = "fnd", comment = "https://speciesfilegroup.org/")) -License: MIT + file LICENSE -URL: https://docs.ropensci.org/rtaxonworks/ (docs), https://github.com/SpeciesFileGroup/RTaxonWorks -BugReports: https://github.com/SpeciesFileGroup/RTaxonWorks/issues +License: NCSA +URL: https://docs.ropensci.org/rtaxonworks/ (docs), https://github.com/SpeciesFileGroup/rtaxonworks +BugReports: https://github.com/SpeciesFileGroup/rtaxonworks/issues Roxygen: list(markdown = TRUE) Encoding: UTF-8 Language: en-US diff --git a/LICENSE b/LICENSE index 6143ee2..6ff6ce8 100644 --- a/LICENSE +++ b/LICENSE @@ -2,7 +2,7 @@ Copyright © 2023 Species File Group. All rights reserved. Developed by: Species File Group Illinois Natural History Survey -https://github.com/SpeciesFileGroup/RTaxonWorks +https://github.com/SpeciesFileGroup/rtaxonworks Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal with the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: diff --git a/LICENSE.md b/LICENSE.md index dc8b789..6ff6ce8 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -2,12 +2,12 @@ Copyright © 2023 Species File Group. All rights reserved. Developed by: Species File Group Illinois Natural History Survey -https://github.com/SpeciesFileGroup/RTaxonWorks +https://github.com/SpeciesFileGroup/rtaxonworks Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal with the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimers in the documentation and/or other materials provided with the distribution. - Neither the names of , nor the names of its contributors may be used to endorse or promote products derived from this Software without specific prior written permission. + Neither the names of Species File Group, Illinois Natural History Survey, Prairie Research Institute, University of Illinois, nor the names of its contributors may be used to endorse or promote products derived from this Software without specific prior written permission. THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE. \ No newline at end of file diff --git a/Makefile b/Makefile index 070ac18..9857613 100644 --- a/Makefile +++ b/Makefile @@ -32,7 +32,7 @@ test: vign: cd vignettes;\ - ${RSCRIPT} -e "Sys.setenv(NOT_CRAN='true'); knitr::knit('RTaxonWorks.Rmd.og', output = 'RTaxonWorks.Rmd')";\ + ${RSCRIPT} -e "Sys.setenv(NOT_CRAN='true'); knitr::knit('rtaxonworks.Rmd.og', output = 'rtaxonworks.Rmd')";\ cd .. # update api spec and params in functions diff --git a/NEWS.md b/NEWS.md index e3d0498..c7ea708 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -RTaxonWorks 0.0.1 +rtaxonworks 0.0.1 ========== ### NEW FEATURES diff --git a/R/http.R b/R/http.R index a5750dc..f7133c0 100644 --- a/R/http.R +++ b/R/http.R @@ -43,7 +43,7 @@ serialize <- function(params) { tw_ua <- function(on_gh_actions = FALSE) { versions <- c(paste0("r-curl/", utils::packageVersion("curl")), paste0("httr2/", utils::packageVersion("httr2")), - sprintf("SpeciesFileGroup(RTaxonWorks/%s)", utils::packageVersion("RTaxonWorks"))) + sprintf("SpeciesFileGroup(rtaxonworks/%s)", utils::packageVersion("rtaxonworks"))) if (on_gh_actions) versions <- c(versions, "GitHub Actions") paste0(versions, collapse = " ") } diff --git a/R/RTaxonWorks-package.R b/R/rtaxonworks-package.R similarity index 80% rename from R/RTaxonWorks-package.R rename to R/rtaxonworks-package.R index 914f15f..483b23e 100644 --- a/R/RTaxonWorks-package.R +++ b/R/rtaxonworks-package.R @@ -1,12 +1,12 @@ -#' @title RTaxonWorks +#' @title rtaxonworks #' @description TaxonWorks Client #' @note TW API docs: https://api.taxonworks.org/ #' @importFrom httr2 request req_perform resp_body_json #' @importFrom tibble tibble #' @importFrom jsonlite fromJSON #' @importFrom data.table setDF rbindlist -#' @name RTaxonWorks-package -#' @aliases RTaxonWorks +#' @name rtaxonworks-package +#' @aliases rtaxonworks #' @docType package #' @keywords package #' @author Geoff Ower diff --git a/README.Rmd b/README.Rmd index 2259a33..d282cb1 100644 --- a/README.Rmd +++ b/README.Rmd @@ -1,4 +1,4 @@ -RTaxonWorks +rtaxonworks ==== ```{r echo=FALSE} @@ -13,12 +13,12 @@ knitr::opts_chunk$set( [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) -[![cran checks](https://cranchecks.info/badges/worst/RTaxonWorks)](https://cranchecks.info/pkgs/RTaxonWorks) -[![R-CMD-check](https://github.com/SpeciesFileGroup/RTaxonWorks/workflows/R-CMD-check/badge.svg)](https://github.com/SpeciesFileGroup/RTaxonWorks/actions) -[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/RTaxonWorks)](https://github.com/r-hub/cranlogs.app) -[![cran version](https://www.r-pkg.org/badges/version/RTaxonWorks)](https://cran.r-project.org/package=RTaxonWorks) +[![cran checks](https://cranchecks.info/badges/worst/rtaxonworks)](https://cranchecks.info/pkgs/rtaxonworks) +[![R-CMD-check](https://github.com/SpeciesFileGroup/rtaxonworks/workflows/R-CMD-check/badge.svg)](https://github.com/SpeciesFileGroup/rtaxonworks/actions) +[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/rtaxonworks)](https://github.com/r-hub/cranlogs.app) +[![cran version](https://www.r-pkg.org/badges/version/rtaxonworks)](https://cran.r-project.org/package=rtaxonworks) -`RTaxonWorks` is an R client for the [TaxonWorks](https://taxonworks.org) API. Code follow the spirit/approach of the Gem [rcol](https://github.com/sckott/rcol), and indeed much of the wrapping utility is copied 1:1 from that repo, thanks [@sckott](https://github.com/sckott). +`rtaxonworks` is an R client for the [TaxonWorks](https://taxonworks.org) API. Code follow the spirit/approach of the Gem [rcol](https://github.com/sckott/rcol), and indeed much of the wrapping utility is copied 1:1 from that repo, thanks [@sckott](https://github.com/sckott). Package documentation: https://docs.taxonworks.org/r @@ -31,19 +31,19 @@ Package documentation: https://docs.taxonworks.org/r ## Installation ```{r eval=FALSE} -install.packages("RTaxonWorks") +install.packages("rtaxonworks") ``` Load the package ```{r} -library("RTaxonWorks") +library("rtaxonworks") ``` Dev version ## Contributing -Bug reports and pull requests are welcome on GitHub at https://github.com/SpeciesFileGroup/RTaxonWorks. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [code of conduct](https://github.com/SpeciesFileGroup/RTaxonWorks/blob/main/CODE_OF_CONDUCT.md). +Bug reports and pull requests are welcome on GitHub at https://github.com/SpeciesFileGroup/rtaxonworks. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [code of conduct](https://github.com/SpeciesFileGroup/rtaxonworks/blob/main/CODE_OF_CONDUCT.md). ## Development @@ -51,8 +51,8 @@ Please read the [CONTRIBUTING guide](CONTRIBUTING.md) for instructions on how to ## License -The gem is available as open source under the terms of the [NCSA/Illinois](https://github.com/SpeciesFileGroup/RTaxonWorks/blob/main/LICENSE.txt) license. You can learn more about the NCSA license on [Wikipedia](https://en.wikipedia.org/wiki/University_of_Illinois/NCSA_Open_Source_License) and compare it with other open source licenses at the [Open Source Initiative](https://opensource.org/license/uoi-ncsa-php/). +The gem is available as open source under the terms of the [NCSA/Illinois](https://github.com/SpeciesFileGroup/rtaxonworks/blob/main/LICENSE.txt) license. You can learn more about the NCSA license on [Wikipedia](https://en.wikipedia.org/wiki/University_of_Illinois/NCSA_Open_Source_License) and compare it with other open source licenses at the [Open Source Initiative](https://opensource.org/license/uoi-ncsa-php/). ## Code of Conduct -Everyone interacting in the RTaxonWorks project's codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/SpeciesFileGroup/RTaxonWorks/blob/main/CODE_OF_CONDUCT.md). +Everyone interacting in the rtaxonworks project's codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/SpeciesFileGroup/rtaxonworks/blob/main/CODE_OF_CONDUCT.md). diff --git a/README.md b/README.md index c1b0907..cbc4fc1 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -RTaxonWorks +rtaxonworks ==== @@ -6,12 +6,12 @@ RTaxonWorks [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) -[![cran checks](https://cranchecks.info/badges/worst/RTaxonWorks)](https://cranchecks.info/pkgs/RTaxonWorks) -[![R-CMD-check](https://github.com/SpeciesFileGroup/RTaxonWorks/workflows/R-CMD-check/badge.svg)](https://github.com/SpeciesFileGroup/RTaxonWorks/actions) -[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/RTaxonWorks)](https://github.com/r-hub/cranlogs.app) -[![cran version](https://www.r-pkg.org/badges/version/RTaxonWorks)](https://cran.r-project.org/package=RTaxonWorks) +[![cran checks](https://cranchecks.info/badges/worst/rtaxonworks)](https://cranchecks.info/pkgs/rtaxonworks) +[![R-CMD-check](https://github.com/SpeciesFileGroup/rtaxonworks/workflows/R-CMD-check/badge.svg)](https://github.com/SpeciesFileGroup/rtaxonworks/actions) +[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/rtaxonworks)](https://github.com/r-hub/cranlogs.app) +[![cran version](https://www.r-pkg.org/badges/version/rtaxonworks)](https://cran.r-project.org/package=rtaxonworks) -`RTaxonWorks` is an R client for the [TaxonWorks](https://taxonworks.org) API. Code follow the spirit/approach of the Gem [rcol](https://github.com/sckott/rcol), and indeed much of the wrapping utility is copied 1:1 from that repo, thanks [@sckott](https://github.com/sckott). +`rtaxonworks` is an R client for the [TaxonWorks](https://taxonworks.org) API. Code follow the spirit/approach of the Gem [rcol](https://github.com/sckott/rcol), and indeed much of the wrapping utility is copied 1:1 from that repo, thanks [@sckott](https://github.com/sckott). Package documentation: https://docs.taxonworks.org/r @@ -25,20 +25,21 @@ Package documentation: https://docs.taxonworks.org/r ```r -install.packages("RTaxonWorks") +install.packages("rtaxonworks") ``` Load the package ```r -library("RTaxonWorks") +library("rtaxonworks") +#> Error in library("rtaxonworks"): there is no package called 'rtaxonworks' ``` Dev version ## Contributing -Bug reports and pull requests are welcome on GitHub at https://github.com/SpeciesFileGroup/RTaxonWorks. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [code of conduct](https://github.com/SpeciesFileGroup/RTaxonWorks/blob/main/CODE_OF_CONDUCT.md). +Bug reports and pull requests are welcome on GitHub at https://github.com/SpeciesFileGroup/rtaxonworks. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [code of conduct](https://github.com/SpeciesFileGroup/rtaxonworks/blob/main/CODE_OF_CONDUCT.md). ## Development @@ -46,8 +47,8 @@ Please read the [CONTRIBUTING guide](CONTRIBUTING.md) for instructions on how to ## License -The gem is available as open source under the terms of the [NCSA/Illinois](https://github.com/SpeciesFileGroup/RTaxonWorks/blob/main/LICENSE.txt) license. You can learn more about the NCSA license on [Wikipedia](https://en.wikipedia.org/wiki/University_of_Illinois/NCSA_Open_Source_License) and compare it with other open source licenses at the [Open Source Initiative](https://opensource.org/license/uoi-ncsa-php/). +The gem is available as open source under the terms of the [NCSA/Illinois](https://github.com/SpeciesFileGroup/rtaxonworks/blob/main/LICENSE.txt) license. You can learn more about the NCSA license on [Wikipedia](https://en.wikipedia.org/wiki/University_of_Illinois/NCSA_Open_Source_License) and compare it with other open source licenses at the [Open Source Initiative](https://opensource.org/license/uoi-ncsa-php/). ## Code of Conduct -Everyone interacting in the RTaxonWorks project's codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/SpeciesFileGroup/RTaxonWorks/blob/main/CODE_OF_CONDUCT.md). +Everyone interacting in the rtaxonworks project's codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/SpeciesFileGroup/rtaxonworks/blob/main/CODE_OF_CONDUCT.md). diff --git a/codemeta.json b/codemeta.json index bec0d02..4fb79a9 100644 --- a/codemeta.json +++ b/codemeta.json @@ -4,12 +4,12 @@ "http://schema.org" ], "@type": "SoftwareSourceCode", - "identifier": "RTaxonWorks", + "identifier": "rtaxonworks", "description": "Client for TaxonWorks\n (); a web application for managing biodiversity data, in particular taxonomic data. TaxonWorks is a Rails application, and this package provides an R interface to the TaxonWorks API.", - "name": "RTaxonWorks: TaxonWorks Client", - "codeRepository": "https://github.com/SpeciesFileGroup/RTaxonWorks", + "name": "rtaxonworks: TaxonWorks Client", + "codeRepository": "https://github.com/SpeciesFileGroup/rtaxonworks", "relatedLink": "https://api.taxonworks.org", - "issueTracker": "https://github.com/SpeciesFileGroup/RTaxonWorks/issues", + "issueTracker": "https://github.com/SpeciesFileGroup/rtaxonworks/issues", "license": "https://spdx.org/licenses/NCSA", "version": "0.0.1", "programmingLanguage": { @@ -135,8 +135,8 @@ "applicationCategory": "Biology", "isPartOf": "https://taxonworks.org", "keywords": ["biology", "science", "API", "web", "api-client", "taxonomy", "species", "rstats", "r"], - "releaseNotes": "https://github.com/SpeciesFileGroup/RTaxonWorks/blob/master/NEWS.md", - "readme": "https://github.com/SpeciesFileGroup/RTaxonWorks/blob/master/README.md", + "releaseNotes": "https://github.com/SpeciesFileGroup/rtaxonworks/blob/master/NEWS.md", + "readme": "https://github.com/SpeciesFileGroup/rtaxonworks/blob/master/README.md", "fileSize": "212.515KB", "provider": { "@id": "https://cran.r-project.org", diff --git a/vignettes/RTaxonWorks.Rmd b/vignettes/rtaxonworks.Rmd similarity index 72% rename from vignettes/RTaxonWorks.Rmd rename to vignettes/rtaxonworks.Rmd index b32eeb4..5ccbdc5 100644 --- a/vignettes/RTaxonWorks.Rmd +++ b/vignettes/rtaxonworks.Rmd @@ -1,5 +1,5 @@ --- -title: "RTaxonWorks" +title: "rtaxonworks" author: "Geoff Ower" date: "2024-02-12" output: @@ -8,14 +8,14 @@ output: toc_float: true theme: readable vignette: > - %\VignetteIndexEntry{Introduction to RTaxonWorks} + %\VignetteIndexEntry{Introduction to rtaxonworks} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- -`RTaxonWorks` is a R client for the TaxonWorks API +`rtaxonworks` is a R client for the TaxonWorks API Package documentation: https://docs.taxonworks.org/r @@ -31,10 +31,10 @@ The following are a few examples. ```r -remotes::install_github("SpeciesFileGroup/RTaxonWorks") +remotes::install_github("SpeciesFileGroup/rtaxonworks") ``` ```r -library("RTaxonWorks") +library("rtaxonworks") ``` diff --git a/vignettes/RTaxonWorks.Rmd.og b/vignettes/rtaxonworks.Rmd.og similarity index 75% rename from vignettes/RTaxonWorks.Rmd.og rename to vignettes/rtaxonworks.Rmd.og index 30fc50b..9d25ac2 100644 --- a/vignettes/RTaxonWorks.Rmd.og +++ b/vignettes/rtaxonworks.Rmd.og @@ -1,5 +1,5 @@ --- -title: "RTaxonWorks" +title: "rtaxonworks" author: "Geoff Ower" date: "`r Sys.Date()`" output: @@ -8,7 +8,7 @@ output: toc_float: true theme: readable vignette: > - %\VignetteIndexEntry{Introduction to RTaxonWorks} + %\VignetteIndexEntry{Introduction to rtaxonworks} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- @@ -20,7 +20,7 @@ knitr::opts_chunk$set( ) ``` -`RTaxonWorks` is a R client for the TaxonWorks API +`rtaxonworks` is a R client for the TaxonWorks API Package documentation: https://docs.taxonworks.org/r @@ -35,9 +35,9 @@ The following are a few examples. ## Installation ```{r eval=FALSE} -remotes::install_github("SpeciesFileGroup/RTaxonWorks") +remotes::install_github("SpeciesFileGroup/rtaxonworks") ``` ```{r} -library("RTaxonWorks") +library("rtaxonworks") ```