From f59e20d289a2271df3d458c0a1ef7ccae234ba95 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Tue, 27 Aug 2024 14:10:31 -0600 Subject: [PATCH 1/6] update: add R-CMD-CHECK badge --- README.Rmd | 4 ++++ README.md | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/README.Rmd b/README.Rmd index 42eba5a..65f6812 100644 --- a/README.Rmd +++ b/README.Rmd @@ -4,6 +4,10 @@ output: github_document + + [![R-CMD-check](https://github.com/nationalparkservice/NPSdataverse/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nationalparkservice/NPSdataverse/actions/workflows/R-CMD-check.yaml) + + ```{r, include = FALSE} knitr::opts_chunk$set( collapse = TRUE, diff --git a/README.md b/README.md index 2c79809..212f067 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,10 @@ + +[![R-CMD-check](https://github.com/nationalparkservice/NPSdataverse/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nationalparkservice/NPSdataverse/actions/workflows/R-CMD-check.yaml) + + # NPSdataverse Image diagraming NPSdataverse and its consituent packages using hexicons A hexicon of NPSdataverse points to the hexicons for the 4 NPS-maintained packages that load with the NPSdataverse: QCkit, EMLeditor, DPchecker, and NPSutils. The key external packages EML and EMLassemblyline that also load are included in a text box. From c86c5144b18638f9470d4783cfefc4f6142c43f5 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Tue, 27 Aug 2024 14:11:01 -0600 Subject: [PATCH 2/6] delete _pkgdown.yml which was causing github.io pages to not render properly. --- _pkgdown.yml | 4 ---- 1 file changed, 4 deletions(-) delete mode 100644 _pkgdown.yml diff --git a/_pkgdown.yml b/_pkgdown.yml deleted file mode 100644 index 48e011e..0000000 --- a/_pkgdown.yml +++ /dev/null @@ -1,4 +0,0 @@ -url: https://github.com/nationalparkservice/NPSdataverse -template: - bootstrap: 5 - From 6ca52faae6a7f2ef3a50485905f38d964708ae93 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Tue, 27 Aug 2024 14:11:22 -0600 Subject: [PATCH 3/6] update via devtools::document and pkgdown::build_site_gihub_pages --- .github/.gitignore | 1 + .github/workflows/R-CMD-check.yaml | 68 +++++++ DESCRIPTION | 5 +- NAMESPACE | 1 + R/NPSdataverse-package.R | 7 + docs/404.html | 112 +++++++---- docs/LICENSE-text.html | 96 ++++++---- docs/LICENSE.html | 89 +++++---- docs/articles/NPSdataverse.html | 120 +++++++----- docs/articles/index.html | 91 +++++---- docs/authors.html | 107 ++++++----- docs/index.html | 129 ++++++++----- docs/news/index.html | 107 ++++++----- docs/paper.html | 96 ++++++---- docs/pkgdown.js | 176 +++++++----------- docs/pkgdown.yml | 5 +- docs/reference/NPSdataverse_packages.html | 110 ++++++----- docs/reference/detach_NPSdataverse.html | 112 ++++++----- .../dot-print_cust_package_deps.html | 112 ++++++----- docs/reference/dot-update_git_repos.html | 108 ++++++----- docs/reference/index.html | 141 +++++++------- docs/reference/is_online.html | 116 +++++++----- docs/sitemap.xml | 31 +-- man/NPSdataverse-package.Rd | 29 +++ man/figures/lifecycle-deprecated.svg | 21 +++ man/figures/lifecycle-experimental.svg | 21 +++ man/figures/lifecycle-stable.svg | 29 +++ man/figures/lifecycle-superseded.svg | 21 +++ 28 files changed, 1273 insertions(+), 788 deletions(-) create mode 100644 .github/.gitignore create mode 100644 .github/workflows/R-CMD-check.yaml create mode 100644 R/NPSdataverse-package.R create mode 100644 man/NPSdataverse-package.Rd create mode 100644 man/figures/lifecycle-deprecated.svg create mode 100644 man/figures/lifecycle-experimental.svg create mode 100644 man/figures/lifecycle-stable.svg create mode 100644 man/figures/lifecycle-superseded.svg diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..b38e8d3 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,68 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +# fix linux build fails: +# https://forum.posit.co/t/libraptor2-dev-depends-libcurl4-gnutls-dev-but-it-is-not-installable-in-r-lib-actions-setup-r-dependencies-v2/181572/4 +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +name: R-CMD-check.yaml + +permissions: read-all + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + PKG_SYSREQS: false + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - name: dependencies on Linux + if: runner.os == 'Linux' + run: sudo apt-get install -y make pandoc git libssl-dev libgdal-dev gdal-bin libgeos-dev libproj-dev libsqlite3-dev libicu-dev libudunits2-dev librdf0-dev libxml2-dev libfreetype6-dev libjpeg-dev libpng-dev libtiff-dev libfontconfig1-dev libfribidi-dev libharfbuzz-dev libcurl4-gnutls-dev + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::pkgdown, local::. + needs: website + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/DESCRIPTION b/DESCRIPTION index 672fde1..e0db07f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -16,7 +16,7 @@ Description: Loads a suite of R packages for creating and manipulating data pack License: CC0 Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Imports: cli, crayon, @@ -28,7 +28,8 @@ Imports: QCkit (>= 0.1.0), rstudioapi, utils, - remotes + remotes, + lifecycle Remotes: nationalparkservice/DPchecker, nationalparkservice/EMLeditor, diff --git a/NAMESPACE b/NAMESPACE index cbb4f1f..397a97c 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -3,3 +3,4 @@ export(NPSdataverse_packages) export(detach_NPSdataverse) export(is_online) +importFrom(lifecycle,deprecated) diff --git a/R/NPSdataverse-package.R b/R/NPSdataverse-package.R new file mode 100644 index 0000000..425b3c1 --- /dev/null +++ b/R/NPSdataverse-package.R @@ -0,0 +1,7 @@ +#' @keywords internal +"_PACKAGE" + +## usethis namespace: start +#' @importFrom lifecycle deprecated +## usethis namespace: end +NULL diff --git a/docs/404.html b/docs/404.html index 68ba20f..4420d9c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -4,73 +4,103 @@ - + Page not found (404) • NPSdataverse - - - - - + + + + + + + - - Skip to contents - - -
-
-
+
+
+

Page not found (404)

-
Content not found. Please use links in the navbar. -
+
+ + +
-
-

Developed by Robert Baker, Judd Patterson, Joe DeVivo.

+ +
+

+

Developed by Robert Baker, Judd Patterson, Joe DeVivo.

-
-

Site built with pkgdown 2.1.0.

+
+

+

Site built with pkgdown 2.1.0.

-
+
+ diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index d55509b..a449eb8 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -1,54 +1,78 @@ -License • NPSdataverse - Skip to contents - - -
-
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+License • NPSdataverse + + +
+
+ + + +
+
+

License

- 
YEAR: 2022
 COPYRIGHT HOLDER: NPSdataverse authors
-
+
+ -
-

Developed by Robert Baker, Judd Patterson, Joe DeVivo.

-
-

Site built with pkgdown 2.1.0.

+ + +
+

Developed by Robert Baker, Judd Patterson, Joe DeVivo.

+
+ +
+

Site built with pkgdown 2.1.0.

-
+
+ diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 48217ac..1d07125 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -1,36 +1,52 @@ -CC0 1.0 Universal • NPSdataverse - Skip to contents - - -
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- +
+
+

CC0 1.0 Universal

- Source: LICENSE.md
@@ -68,19 +84,26 @@

Statement of Purpose

+
+ -
+ diff --git a/docs/articles/NPSdataverse.html b/docs/articles/NPSdataverse.html index ff2f769..f4966a3 100644 --- a/docs/articles/NPSdataverse.html +++ b/docs/articles/NPSdataverse.html @@ -4,84 +4,110 @@ - + NPSdataverse • NPSdataverse - - - - - + + + + + + + - - Skip to contents - - -
- - + +
+ -
-
-

NPSdataverse

+
+
+
+

NPSdataverse

- Source: vignettes/NPSdataverse.Rmd -
NPSdataverse.Rmd
+ Source: vignettes/NPSdataverse.Rmd + + 
 devtools::install_github("nationalparkservice/NPSdataverse")
-library(NPSdataverse)
-
+library(NPSdataverse)
+
+ + +
-
-

Developed by Robert Baker, Judd Patterson, Joe DeVivo.

+
+

+

Developed by Robert Baker, Judd Patterson, Joe DeVivo.

-
-

Site built with pkgdown 2.1.0.

+
+

+

Site built with pkgdown 2.1.0.

-
+
+ diff --git a/docs/articles/index.html b/docs/articles/index.html index c61137e..6ddeb4a 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -1,56 +1,75 @@ -Articles • NPSdataverse - Skip to contents - - -
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+Articles • NPSdataverse + + +
+
+ + + +
+
+

Articles

All vignettes

-
+

NPSdataverse
-
+
+ -
-

Developed by Robert Baker, Judd Patterson, Joe DeVivo.

+
+

Developed by Robert Baker, Judd Patterson, Joe DeVivo.

-
-

Site built with pkgdown 2.1.0.

+
+

Site built with pkgdown 2.1.0.

-
+
+ diff --git a/docs/authors.html b/docs/authors.html index 6b21a5b..d446155 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,39 +1,55 @@ -Authors and Citation • NPSdataverse - Skip to contents - - -
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Authors and Citation

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Authors and Citation

+
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Authors

  • Robert Baker. Author, maintainer. @@ -48,37 +64,42 @@

    Authors

+
+
+

Citation

+ Source: DESCRIPTION +
+
-
-

Citation

-

Source: DESCRIPTION

-

Baker R, Patterson J, DeVivo J (2024). +

Baker R, Patterson J, DeVivo J (2024). NPSdataverse: Tools and Packages for Data and Metadata Manipulation. -R package version 0.1.0, https://github.com/nationalparkservice/NPSdataverse. +R package version 0.1.0, https://github.com/nationalparkservice/NPSdataverse.

- 
@Manual{,
+    
@Manual{,
   title = {NPSdataverse: Tools and Packages for Data and Metadata Manipulation},
   author = {Robert Baker and Judd Patterson and Joe DeVivo},
   year = {2024},
   note = {R package version 0.1.0},
   url = {https://github.com/nationalparkservice/NPSdataverse},
 }

-
-
+
+ + + -
-

Developed by Robert Baker, Judd Patterson, Joe DeVivo.

+
+

Developed by Robert Baker, Judd Patterson, Joe DeVivo.

-
-

Site built with pkgdown 2.1.0.

+
+

Site built with pkgdown 2.1.0.

-
+
+ diff --git a/docs/index.html b/docs/index.html index 6c21ae8..2a86848 100644 --- a/docs/index.html +++ b/docs/index.html @@ -4,53 +4,76 @@ - + Tools and Packages for Data and Metadata Manipulation • NPSdataverse - - - - - - + + + + + + + - - Skip to contents - - -
-
-
+

NPSdataverse

-

Image diagraming NPSdataverse and its consituent packages using hexicons A hexicon of NPSdataverse points to the hexicons for the 4 NPS-maintained packages that load with the NPSdataverse: QCkit, EMLeditor, DPchecker, and NPSutils. The key external packages EML and EMLassemblyline that also load are included in a text box. NPSdataverse loads a suite of R packages for creating, manipulating, and accessing data packages including interacting with DataStore. This is an early version of the NPSdataverse. Please request enhancements and bug fixes through Issues.

+

Image diagraming NPSdataverse and its consituent packages using hexicons A hexicon of NPSdataverse points to the hexicons for the 4 NPS-maintained packages that load with the NPSdataverse: QCkit, EMLeditor, DPchecker, and NPSutils. The key external packages EML and EMLassemblyline that also load are included in a text box. NPSdataverse loads a suite of R packages for creating, manipulating, and accessing data packages including interacting with DataStore. This is an early version of the NPSdataverse. Please request enhancements and bug fixes through Issues.

Installation

@@ -109,7 +132,7 @@

Trouble shooting installation

Updating NPSdataverse packages

-

Many of the NPSdataverse packages are in a phase of rapid development. When you load the NPSdataverse (using library(NPSdataverse)), if you are online, NPSdataverse will check for new versions of the packages stored on GitHub (all the packages except r/EML). NPSdataverse will tell you if all your packages are up to date. Conversely if any of the NPSdataverse packages need to be updated, NPSdataverse will indicate which packages need updating and how to perform the updates. If you do not get any notices about whether your packages are up to date or not, then the NPSdataverse package itself needs to be updated. See Installation for instructions on how to update the NPSdataverse package.

+

Many of the NPSdataverse packages are in a phase of rapid development. When you load the NPSdataverse (using library(NPSdataverse)), if you are online, NPSdataverse will check for new versions of the packages stored on GitHub (all the packages except r/EML). NPSdataverse will tell you if all your packages are up to date. Conversely if any of the NPSdataverse packages need to be updated, NPSdataverse will indicate which packages need updating and how to perform the updates. If you do not get any notices about whether your packages are up to date or not, then the NPSdataverse package itself needs to be updated. See Installation for instructions on how to update the NPSdataverse package.

Creating data packages @@ -121,11 +144,15 @@

Creating data packagesThis will open a new file on that you can edit to generate EML metadata for your data package. See the web pages associated with EMLeditor for additional information, instructions, and examples.

-
+
-
-

Developed by Robert Baker, Judd Patterson, Joe DeVivo.

+
+

+

Developed by Robert Baker, Judd Patterson, Joe DeVivo.

-
-

Site built with pkgdown 2.1.0.

+
+

+

Site built with pkgdown 2.1.0.

-
+
+ diff --git a/docs/news/index.html b/docs/news/index.html index 3c4d57a..25d4d54 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,74 +1,97 @@ -Changelog • NPSdataverse - Skip to contents - - -
-
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+Changelog • NPSdataverse + + +
+
+ + + +
+
+
+

Changelog

+ Source: NEWS.md
-

NPSdataverse 0.1.0

+

NPSdataverse 0.1.0

2024-08-19 * Reduce github.com API rate limits by only hitting API in interactive session.

2024-07-26 * Updated license from MIT to CC0. * Start paper.md for JOSS * Add paper.bib for JOSS

-

NPSdataverse 0.0.2

+

NPSdataverse 0.0.2

2024-01-02

  • Added function ability to load NPSdataverse (using library()) when offline
  • Now dynamically checks for github username rather than hardcoding in NPS
  • Fixed operands so that updates actually get checked
-

NPSdataverse 0.0.1

+

NPSdataverse 0.0.1

2023-09-12

  • updated version to be in line with forthcoming versioning guidance
  • updated documentation to assist in install/updating
  • updated updateR.R to tell the user not only when data packages are out of date but also when they are all up to date upon loading NPSdataverse.
-

NPSdataverse 0.0.0.9000

+

NPSdataverse 0.0.0.9000

  • Added a NEWS.md file to track changes to the package.
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+ -
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Developed by Robert Baker, Judd Patterson, Joe DeVivo.

-
-

Site built with pkgdown 2.1.0.

+ +
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Developed by Robert Baker, Judd Patterson, Joe DeVivo.

+
+ +
+

Site built with pkgdown 2.1.0.

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+
+ diff --git a/docs/paper.html b/docs/paper.html index 3a685e0..d6d10f7 100644 --- a/docs/paper.html +++ b/docs/paper.html @@ -1,36 +1,52 @@ -Summary • NPSdataverse - Skip to contents - - -
-
-
+Summary • NPSdataverse + + +
+
+ + + +
+
+

Summary

- Source: paper.md
@@ -70,18 +86,26 @@

References +

+ +
+ -
+ diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 9757bf9..6f0eee4 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -2,43 +2,83 @@ (function($) { $(function() { - $('nav.navbar').headroom(); + $('.navbar-fixed-top').headroom(); - Toc.init({ - $nav: $("#toc"), - $scope: $("main h2, main h3, main h4, main h5, main h6") + $('body').css('padding-top', $('.navbar').height() + 10); + $(window).resize(function(){ + $('body').css('padding-top', $('.navbar').height() + 10); }); - if ($('#toc').length) { - $('body').scrollspy({ - target: '#toc', - offset: $("nav.navbar").outerHeight() + 1 - }); + $('[data-toggle="tooltip"]').tooltip(); + + var cur_path = paths(location.pathname); + var links = $("#navbar ul li a"); + var max_length = -1; + var pos = -1; + for (var i = 0; i < links.length; i++) { + if (links[i].getAttribute("href") === "#") + continue; + // Ignore external links + if (links[i].host !== location.host) + continue; + + var nav_path = paths(links[i].pathname); + + var length = prefix_length(nav_path, cur_path); + if (length > max_length) { + max_length = length; + pos = i; + } } - // Activate popovers - $('[data-bs-toggle="popover"]').popover({ - container: 'body', - html: true, - trigger: 'focus', - placement: "top", - sanitize: false, - }); + // Add class to parent
  • , and enclosing
  • if in dropdown + if (pos >= 0) { + var menu_anchor = $(links[pos]); + menu_anchor.parent().addClass("active"); + menu_anchor.closest("li.dropdown").addClass("active"); + } + }); - $('[data-bs-toggle="tooltip"]').tooltip(); + function paths(pathname) { + var pieces = pathname.split("/"); + pieces.shift(); // always starts with / + + var end = pieces[pieces.length - 1]; + if (end === "index.html" || end === "") + pieces.pop(); + return(pieces); + } + + // Returns -1 if not found + function prefix_length(needle, haystack) { + if (needle.length > haystack.length) + return(-1); + + // Special case for length-0 haystack, since for loop won't run + if (haystack.length === 0) { + return(needle.length === 0 ? 0 : -1); + } + + for (var i = 0; i < haystack.length; i++) { + if (needle[i] != haystack[i]) + return(i); + } + + return(haystack.length); + } /* Clipboard --------------------------*/ function changeTooltipMessage(element, msg) { - var tooltipOriginalTitle=element.getAttribute('data-bs-original-title'); - element.setAttribute('data-bs-original-title', msg); + var tooltipOriginalTitle=element.getAttribute('data-original-title'); + element.setAttribute('data-original-title', msg); $(element).tooltip('show'); - element.setAttribute('data-bs-original-title', tooltipOriginalTitle); + element.setAttribute('data-original-title', tooltipOriginalTitle); } if(ClipboardJS.isSupported()) { $(document).ready(function() { - var copyButton = ""; + var copyButton = ""; $("div.sourceCode").addClass("hasCopyButton"); @@ -49,106 +89,20 @@ $('.btn-copy-ex').tooltip({container: 'body'}); // Initialize clipboard: - var clipboard = new ClipboardJS('[data-clipboard-copy]', { + var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { text: function(trigger) { return trigger.parentNode.textContent.replace(/\n#>[^\n]*/g, ""); } }); - clipboard.on('success', function(e) { + clipboardBtnCopies.on('success', function(e) { changeTooltipMessage(e.trigger, 'Copied!'); e.clearSelection(); }); - clipboard.on('error', function(e) { + clipboardBtnCopies.on('error', function() { changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); }); - }); } - - /* Search marking --------------------------*/ - var url = new URL(window.location.href); - var toMark = url.searchParams.get("q"); - var mark = new Mark("main#main"); - if (toMark) { - mark.mark(toMark, { - accuracy: { - value: "complementary", - limiters: [",", ".", ":", "/"], - } - }); - } - - /* Search --------------------------*/ - /* Adapted from https://github.com/rstudio/bookdown/blob/2d692ba4b61f1e466c92e78fd712b0ab08c11d31/inst/resources/bs4_book/bs4_book.js#L25 */ - // Initialise search index on focus - var fuse; - $("#search-input").focus(async function(e) { - if (fuse) { - return; - } - - $(e.target).addClass("loading"); - var response = await fetch($("#search-input").data("search-index")); - var data = await response.json(); - - var options = { - keys: ["what", "text", "code"], - ignoreLocation: true, - threshold: 0.1, - includeMatches: true, - includeScore: true, - }; - fuse = new Fuse(data, options); - - $(e.target).removeClass("loading"); - }); - - // Use algolia autocomplete - var options = { - autoselect: true, - debug: true, - hint: false, - minLength: 2, - }; - var q; -async function searchFuse(query, callback) { - await fuse; - - var items; - if (!fuse) { - items = []; - } else { - q = query; - var results = fuse.search(query, { limit: 20 }); - items = results - .filter((x) => x.score <= 0.75) - .map((x) => x.item); - if (items.length === 0) { - items = [{dir:"Sorry 😿",previous_headings:"",title:"No results found.",what:"No results found.",path:window.location.href}]; - } - } - callback(items); -} - $("#search-input").autocomplete(options, [ - { - name: "content", - source: searchFuse, - templates: { - suggestion: (s) => { - if (s.title == s.what) { - return `${s.dir} >
    ${s.title}
    `; - } else if (s.previous_headings == "") { - return `${s.dir} >
    ${s.title}
    > ${s.what}`; - } else { - return `${s.dir} >
    ${s.title}
    > ${s.previous_headings} > ${s.what}`; - } - }, - }, - }, - ]).on('autocomplete:selected', function(event, s) { - window.location.href = s.path + "?q=" + q + "#" + s.id; - }); - }); })(window.jQuery || window.$) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 6ba25f2..ee45558 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,7 +3,4 @@ pkgdown: 2.1.0 pkgdown_sha: ~ articles: NPSdataverse: NPSdataverse.html -last_built: 2024-08-19T17:22Z -urls: - reference: https://github.com/nationalparkservice/NPSdataverse/reference - article: https://github.com/nationalparkservice/NPSdataverse/articles +last_built: 2024-08-27T20:07Z diff --git a/docs/reference/NPSdataverse_packages.html b/docs/reference/NPSdataverse_packages.html index f5d74d9..6e1b1b0 100644 --- a/docs/reference/NPSdataverse_packages.html +++ b/docs/reference/NPSdataverse_packages.html @@ -1,70 +1,90 @@ -List all packages imported by NPSdataverse — NPSdataverse_packages • NPSdataverse - Skip to contents - - -
    -
    -
    +List all packages imported by NPSdataverse — NPSdataverse_packages • NPSdataverse + + +
    +
    + + + +
    +
    +
    +

    List all packages imported by NPSdataverse

    + Source: R/attach.R +
    -
    +

    List all packages imported by NPSdataverse

    -
    -

    Usage

    + 
    NPSdataverse_packages()
    -
    -

    Examples

    +
    +

    Examples

    NPSdataverse_packages()
 #>  [1] "cli"             "crayon"          "DPchecker"       "EML"            
 #>  [5] "EMLassemblyline" "EMLeditor"       "NPSutils"        "QCkit"          
-#>  [9] "rstudioapi"      "utils"           "remotes"        
+#>  [9] "rstudioapi"      "utils"           "remotes"         "lifecycle"
    -
    +
    + +
    • -
    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +
    +

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    -
    -

    Site built with pkgdown 2.1.0.

    +
    +

    Site built with pkgdown 2.1.0.

    -
    +
    + diff --git a/docs/reference/detach_NPSdataverse.html b/docs/reference/detach_NPSdataverse.html index 65e7cfc..7b26b30 100644 --- a/docs/reference/detach_NPSdataverse.html +++ b/docs/reference/detach_NPSdataverse.html @@ -1,73 +1,93 @@ -Detach all loaded packages — detach_NPSdataverse • NPSdataverse - Skip to contents - - -
    -
    -
    +Detach all loaded packages — detach_NPSdataverse • NPSdataverse + + +
    +
    + + + +
    +
    +
    +

    Detach all loaded packages

    + Source: R/attach.R +
    -
    +

    Detach all loaded packages

    -
    -

    Usage

    + 
    detach_NPSdataverse()
    -
    -

    Value

    +
    +

    Value

    invisilble

    -
    -

    Examples

    +
    +

    Examples

    if (FALSE) { # \dontrun{
 detach_NPSdataverse()
 } # }
    -
    +
    + +
    -
    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +
    +

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    -
    -

    Site built with pkgdown 2.1.0.

    +
    +

    Site built with pkgdown 2.1.0.

    -
    +
    + diff --git a/docs/reference/dot-print_cust_package_deps.html b/docs/reference/dot-print_cust_package_deps.html index 1e0a4cc..f09742f 100644 --- a/docs/reference/dot-print_cust_package_deps.html +++ b/docs/reference/dot-print_cust_package_deps.html @@ -1,50 +1,66 @@ -Custom print function for github repos to update — .print_cust_package_deps • NPSdataverse - Skip to contents - - -
    -
    -
    +Custom print function for github repos to update — .print_cust_package_deps • NPSdataverse + + +
    +
    + + + +
    +
    +
    +

    Custom print function for github repos to update

    + Source: R/updateR.R +
    -
    +

    formats print table for custom printing package dependencies in need to updating. Derived from remotes:::print.package_deps().

    -
    -

    Usage

    + 
    .print_cust_package_deps(x, show_ok = FALSE, ...)
    -
    -

    Arguments

    +
    +

    Arguments

    x
    @@ -59,24 +75,28 @@

    Arguments -

    Value

    +
    +

    Value

    printed text to console

    -

    +
    + + -
    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +
    +

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    -
    -

    Site built with pkgdown 2.1.0.

    +
    +

    Site built with pkgdown 2.1.0.

    -
    +
    + diff --git a/docs/reference/dot-update_git_repos.html b/docs/reference/dot-update_git_repos.html index c75f7de..d5c17ff 100644 --- a/docs/reference/dot-update_git_repos.html +++ b/docs/reference/dot-update_git_repos.html @@ -1,66 +1,86 @@ -Update info for git repos in NPSdataverse — .update_git_repos • NPSdataverse - Skip to contents - - -
    -
    -
    +Update info for git repos in NPSdataverse — .update_git_repos • NPSdataverse + + +
    +
    + + + +
    +
    +
    +

    Update info for git repos in NPSdataverse

    + Source: R/updateR.R +
    -
    +

    .update_git_repos() determines which of the NPSdataverse packages from github need to be updated and provides instructions on how to do so.

    -
    -

    Usage

    + 
    .update_git_repos()
    -
    -

    Value

    +
    +

    Value

    dataframe

    -
    +
    + + -
    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +
    +

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    -
    -

    Site built with pkgdown 2.1.0.

    +
    +

    Site built with pkgdown 2.1.0.

    -
    +
    + diff --git a/docs/reference/index.html b/docs/reference/index.html index d8aaae0..7a4f750 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,79 +1,88 @@ -Package index • NPSdataverse - Skip to contents - - -
    -
    -
    - -

    Package index

    +Package index • NPSdataverse + + +
    +
    +
    +
    +

    Reference

    +
    - -
    List all packages imported by NPSdataverse
    -
    -
    + + + + + + + +
    +

    All functions

    +

    +
    +

    detach_NPSdataverse()

    +

    Detach all loaded packages

    +

    is_online()

    +

    Check internet connectivity

    +

    NPSdataverse_packages()

    +

    List all packages imported by NPSdataverse

    + + + -
    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +
    +

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    -
    -

    Site built with pkgdown 2.1.0.

    +
    +

    Site built with pkgdown 2.1.0.

    -
    +
    + diff --git a/docs/reference/is_online.html b/docs/reference/is_online.html index dd9f23a..052cf5d 100644 --- a/docs/reference/is_online.html +++ b/docs/reference/is_online.html @@ -1,80 +1,100 @@ -Check internet connectivity — is_online • NPSdataverse - Skip to contents - - -
    -
    -
    +Check internet connectivity — is_online • NPSdataverse + + +
    +
    + + + +
    +
    +
    +

    Check internet connectivity

    + Source: R/attach.R +
    -
    +

    Checks whether the system can ping github.com. Adapted from:https://stackoverflow.com/questions/5076593/how-to-determine-if-you-have-an-internet-connection-in-r

    -
    -

    Usage

    + 
    is_online(site = "https://github.com/")
    -
    -

    Arguments

    +
    +

    Arguments

    site

    string defaults to https://github.com

    -
    -

    Value

    +
    +

    Value

    logical

    -
    -

    Examples

    +
    +

    Examples

    is_online()
 #> [1] TRUE
    -
    +
    + + -
    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +
    +

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    -
    -

    Site built with pkgdown 2.1.0.

    +
    +

    Site built with pkgdown 2.1.0.

    -
    +
    + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index f2a112b..f2436e8 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,18 +1,19 @@ -https://github.com/nationalparkservice/NPSdataverse/404.html -https://github.com/nationalparkservice/NPSdataverse/articles/index.html -https://github.com/nationalparkservice/NPSdataverse/articles/NPSdataverse.html -https://github.com/nationalparkservice/NPSdataverse/authors.html -https://github.com/nationalparkservice/NPSdataverse/index.html -https://github.com/nationalparkservice/NPSdataverse/LICENSE-text.html -https://github.com/nationalparkservice/NPSdataverse/LICENSE.html -https://github.com/nationalparkservice/NPSdataverse/news/index.html -https://github.com/nationalparkservice/NPSdataverse/paper.html -https://github.com/nationalparkservice/NPSdataverse/reference/detach_NPSdataverse.html -https://github.com/nationalparkservice/NPSdataverse/reference/dot-print_cust_package_deps.html -https://github.com/nationalparkservice/NPSdataverse/reference/dot-update_git_repos.html -https://github.com/nationalparkservice/NPSdataverse/reference/index.html -https://github.com/nationalparkservice/NPSdataverse/reference/is_online.html -https://github.com/nationalparkservice/NPSdataverse/reference/NPSdataverse_packages.html +/404.html +/articles/index.html +/articles/NPSdataverse.html +/authors.html +/index.html +/LICENSE-text.html +/LICENSE.html +/news/index.html +/paper.html +/reference/detach_NPSdataverse.html +/reference/dot-print_cust_package_deps.html +/reference/dot-update_git_repos.html +/reference/index.html +/reference/is_online.html +/reference/NPSdataverse-package.html +/reference/NPSdataverse_packages.html diff --git a/man/NPSdataverse-package.Rd b/man/NPSdataverse-package.Rd new file mode 100644 index 0000000..cdd7ecf --- /dev/null +++ b/man/NPSdataverse-package.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/NPSdataverse-package.R +\docType{package} +\name{NPSdataverse-package} +\alias{NPSdataverse} +\alias{NPSdataverse-package} +\title{NPSdataverse: Tools and Packages for Data and Metadata Manipulation} +\description{ +Loads a suite of R packages for creating and manipulating data packages including interacting with DataStore. +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/nationalparkservice/NPSdataverse} + \item Report bugs at \url{https://github.com/nationalparkservice/NPSdataverse/issues} +} + +} +\author{ +\strong{Maintainer}: Robert Baker \email{robert_baker@nps.gov} (\href{https://orcid.org/0000-0001-7591-5035}{ORCID}) + +Authors: +\itemize{ + \item Judd Patterson \email{Judd_Patterson@nps.gov} (\href{https://orcid.org/0000-0002-0951-7917}{ORCID}) + \item Joe DeVivo \email{Joe_DeVivo@nps.gov} (\href{https://orcid.org/0000-0002-0414-7865}{ORCID}) +} + +} +\keyword{internal} diff --git a/man/figures/lifecycle-deprecated.svg b/man/figures/lifecycle-deprecated.svg new file mode 100644 index 0000000..b61c57c --- /dev/null +++ b/man/figures/lifecycle-deprecated.svg @@ -0,0 +1,21 @@ + + lifecycle: deprecated + + + + + + + + + + + + + + + lifecycle + + deprecated + + diff --git a/man/figures/lifecycle-experimental.svg b/man/figures/lifecycle-experimental.svg new file mode 100644 index 0000000..5d88fc2 --- /dev/null +++ b/man/figures/lifecycle-experimental.svg @@ -0,0 +1,21 @@ + + lifecycle: experimental + + + + + + + + + + + + + + + lifecycle + + experimental + + diff --git a/man/figures/lifecycle-stable.svg b/man/figures/lifecycle-stable.svg new file mode 100644 index 0000000..9bf21e7 --- /dev/null +++ b/man/figures/lifecycle-stable.svg @@ -0,0 +1,29 @@ + + lifecycle: stable + + + + + + + + + + + + + + + + lifecycle + + + + stable + + + diff --git a/man/figures/lifecycle-superseded.svg b/man/figures/lifecycle-superseded.svg new file mode 100644 index 0000000..db8d757 --- /dev/null +++ b/man/figures/lifecycle-superseded.svg @@ -0,0 +1,21 @@ + + lifecycle: superseded + + + + + + + + + + + + + + + lifecycle + + superseded + + From 560c57992f7a5cef1a516a285ea7a01b6754bfaf Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Tue, 27 Aug 2024 15:08:15 -0600 Subject: [PATCH 4/6] updated via usethis::use_github_actions() --- .Rbuildignore | 1 + .github/workflows/R-CMD-check.yaml | 17 ++++------------- 2 files changed, 5 insertions(+), 13 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index ca8575e..d154c3f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -5,3 +5,4 @@ ^_pkgdown\.yml$ ^docs$ ^pkgdown$ +^\.github$ diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index b38e8d3..c5ab1df 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -44,24 +44,15 @@ jobs: http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true - - uses: r-lib/actions/setup-r@v2 - with: - use-public-rspm: true - - - name: dependencies on Linux - if: runner.os == 'Linux' - run: sudo apt-get install -y make pandoc git libssl-dev libgdal-dev gdal-bin libgeos-dev libproj-dev libsqlite3-dev libicu-dev libudunits2-dev librdf0-dev libxml2-dev libfreetype6-dev libjpeg-dev libpng-dev libtiff-dev libfontconfig1-dev libfribidi-dev libharfbuzz-dev libcurl4-gnutls-dev - - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: any::pkgdown, local::. - needs: website - - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: any::rcmdcheck needs: check + - name: dependencies on Linux + if: runner.os == 'Linux' + run: sudo apt-get install -y make pandoc git libjq-dev libssl-dev libgdal-dev gdal-bin libgeos-dev libproj-dev libsqlite3-dev libicu-dev libudunits2-dev librdf0-dev libxml2-dev libfreetype6-dev libjpeg-dev libpng-dev libtiff-dev libfontconfig1-dev libfribidi-dev libharfbuzz-dev libcurl4-gnutls-dev + - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true From c707ca82690478b2a4b69914eec7f549e981bbb9 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Tue, 27 Aug 2024 15:13:38 -0600 Subject: [PATCH 5/6] update readme: use pak for installation instead of devtools. --- README.Rmd | 4 ++-- README.md | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.Rmd b/README.Rmd index 65f6812..a43e93d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -36,8 +36,8 @@ NPSdataverse loads a suite of R packages for creating, manipulating, and accessi You can install the development version of NPSdataverse from [GitHub](https://github.com/) with: ``` r -# install.packages("devtools") -devtools::install_github("nationalparkservice/NPSdataverse") +# install.packages("pak") +pak::pkg_install("nationalparkservice/NPSdataverse") ``` NPSdataverse will install the following R packages: diff --git a/README.md b/README.md index 212f067..57731ad 100644 --- a/README.md +++ b/README.md @@ -20,8 +20,8 @@ You can install the development version of NPSdataverse from [GitHub](https://github.com/) with: ``` r -# install.packages("devtools") -devtools::install_github("nationalparkservice/NPSdataverse") +# install.packages("pak") +pak::pkg_install("nationalparkservice/NPSdataverse") ``` NPSdataverse will install the following R packages: From d7bb0fbf196277084b4c3479503a1257403fdd35 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Tue, 27 Aug 2024 15:17:01 -0600 Subject: [PATCH 6/6] updated with pkgdown::build_site_github_pages --- docs/index.html | 4 ++-- docs/pkgdown.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/index.html b/docs/index.html index 2a86848..ca263fa 100644 --- a/docs/index.html +++ b/docs/index.html @@ -79,8 +79,8 @@

    InstallationGitHub with:

    -# install.packages("devtools")
-devtools::install_github("nationalparkservice/NPSdataverse")
    +# install.packages("pak") +pak::pkg_install("nationalparkservice/NPSdataverse")

    NPSdataverse will install the following R packages:

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index ee45558..b265579 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,4 +3,4 @@ pkgdown: 2.1.0 pkgdown_sha: ~ articles: NPSdataverse: NPSdataverse.html -last_built: 2024-08-27T20:07Z +last_built: 2024-08-27T21:12Z