Merge pull request #144 from NCEAS/gha-repair

GitHub Action Repair

.Rbuildignore

@@ -1,6 +1,7 @@
 ^Meta$
 ^doc$
 ^docs$
+^dev$
 ^_pkgdown\.yml$
 ^.*\.Rproj$
 ^\.Rproj\.user$

.github/workflows/R-CMD-check.yaml

@@ -1,35 +1,54 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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
 on:
   push:
-    branches:
-      - dev
-      - main
+    branches: [main, master]
   pull_request:
-    branches:
-      - dev
-      - main
+    branches: [main, master]
 
 name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    runs-on: macOS-latest
+    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@v2
-      - uses: r-lib/actions/setup-pandoc@v1
-      - uses: r-lib/actions/setup-r@v1
+      - 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
-      - name: Install udunits
-        run: brew install udunits
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-        shell: Rscript {0}
-      - name: Check
-        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
-        shell: Rscript {0}
+
+      - name: dependencies on Linux
+        if: runner.os == 'Linux'
+        run: sudo apt-get install -y libcurl4-gnutls-dev libicu-dev libjq-dev libnode-dev librdf0-dev libssl-dev libxml2-dev make pandoc
+
+      - 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

.github/workflows/pkgdown.yaml

@@ -1,8 +1,10 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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
 on:
   push:
     branches: [main, master]
+  pull_request:
+    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
@@ -12,27 +14,41 @@ name: pkgdown
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      PKG_SYSREQS: false
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - name: Install udunit2
-        run: sudo apt-get install libudunits2-dev
+      - name: dependencies on Linux
+        if: runner.os == 'Linux'
+        run: sudo apt-get install -y make libicu-dev libxml2-dev libssl-dev pandoc librdf0-dev libnode-dev libcurl4-gnutls-dev
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: pkgdown
+          extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Deploy package
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          Rscript -e 'pkgdown::deploy_to_branch(github_pages = (branch == "gh-pages"), new_process = FALSE)'
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -1,9 +1,17 @@
-Meta/
-doc/
+# Background R stuff
 .Rproj.user
 .Rhistory
 .RData
 .Ruserdata
 .httr-oauth
-.DS_Store
+
+# R project
+*.Rproj
+
+# Certain folders
+Meta/
+doc/
 docs/
+
+# Ignore Mac file
+.DS_Store

DESCRIPTION

@@ -2,7 +2,6 @@ Package: metajam
 Type: Package
 Title: Easily Download Data and Metadata from 'DataONE'
 Version: 0.2.3
-Date: 2020-10-14
 Authors@R: c(
               person("Julien", "Brun", 
                  email = "[email protected]", 
@@ -15,6 +14,11 @@ Authors@R: c(
               person("Mitchell", "Maier", 
                  comment= c(ORCID = "0000-0001-6955-0535"), 
                  role = "aut"),
+              person("Nicholas", "Lyon",
+                 email = "[email protected]",
+                 comment = c(ORCID = "0000-0003-3905-1078",
+                     "https://njlyon0.github.io/"),
+                 role = "ctb"),
               person("Nathan", "Hwangbo", 
                  email = "[email protected]", 
                  comment= c(ORCID = "0000-0002-3777-0821"),
@@ -32,13 +36,19 @@ Authors@R: c(
                  comment = c(ORCID = "0000-0002-6388-0901"),
                  role = "ctb")
               )
-Maintainer: Julien Brun <brun@nceas.ucsb.edu>
+Maintainer: Julien Brun <jb160@ucsb.edu>
 Description: A set of tools to foster the development of reproducible analytical workflow by simplifying the download of data and 
     metadata from 'DataONE' (<https://www.dataone.org>) and easily importing this information into R.
 License: Apache License (== 2.0)
-URL: https://github.com/nceas/metajam,
-    https://nceas.github.io/metajam/
+Encoding: UTF-8
+Language: en-US
+RoxygenNote: 7.2.3
+SystemRequirements: Mac OSX: redland (>= 1.0.14) ; Linux: librdf0 (>= 1.0.14),
+    librdf0-dev (>= 1.0.14)
+URL: https://nceas.github.io/metajam/
 BugReports: https://github.com/nceas/metajam/issues
+Depends:
+    R (>= 3.1.1)
 Imports:
     dataone,
     dplyr,
@@ -51,13 +61,9 @@ Imports:
     stringr,
     tibble,
     tidyr,
-    rlang
+    XML
 Suggests:
-    testthat,
     knitr,
     rmarkdown,
-    udunits2
-Encoding: UTF-8
+    testthat
 VignetteBuilder: knitr
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1

NAMESPACE

@@ -15,12 +15,12 @@ importFrom(dataone,query)
 importFrom(emld,as_emld)
 importFrom(lubridate,ymd_hms)
 importFrom(purrr,"%||%")
-importFrom(rlang,.data)
 importFrom(stats,setNames)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_extract)
 importFrom(stringr,str_trim)
 importFrom(tibble,enframe)
 importFrom(tidyr,pivot_wider)
+importFrom(tidyr,spread)
 importFrom(tools,file_path_sans_ext)
 importFrom(utils,URLdecode)

R/check_version.R

@@ -1,9 +1,9 @@
-#' Check PID version
+#' @title Check PID version
 #'
-#' This function takes an identifier and checks to see if it has been obsoleted.
+#' @description This function takes an identifier and checks to see if it has been obsoleted.
 #'
 #' @param pid (character) The persistent identifier of a data, metadata, or resource map object on a DataONE member node.
-#' @param formatType (character) Optional. The format type to return (one of data, metadata, or resource).
+#' @param formatType (character) Optional. The format type to return (one of 'data', 'metadata', or 'resource').
 #'
 #' @return (data.frame) A data frame of object version PIDs and related information.
 #'
@@ -32,28 +32,28 @@
 
 check_version <- function(pid, formatType = NULL) {
 
-  if (!all(is.character(pid), all(nchar(pid) > 0))) {
-    stop("Argument 'pids' must be character class with non-zero number of characters.")
-  }
-  if (!is.null(formatType) && !all(is.character(formatType), length(formatType) == 1, formatType %in% c("data", "metadata", "resource"))) {
+  # Error out for missing pids
+  if(all(is.character(pid), nchar(pid) > 0) != TRUE)
+    stop("Argument 'pid' must be character class with non-zero number of characters.")
+
+  # Error out for missing / unsupported `formatType` specification
+  if(is.null(formatType) != TRUE & all(is.character(formatType), length(formatType) == 1, formatType %in% c("data", "metadata", "resource")) != TRUE)
     stop("Argument 'formatType' should either be NULL or one of 'data', 'metadata', or 'resource'.")
-  }
 
+  # Query DataONE for the specified `pid`
   while (nchar(pid) > 5) {
     results <- suppressMessages(
-      dataone::query(dataone::CNode(),
-                     list(q = sprintf('identifier:"%s"', pid),
-                          fl = "identifier, dateUploaded, formatType, obsoletedBy, resourceMap"),
+      dataone::query(x = dataone::CNode(),
+                     solrQuery = list(q = sprintf('identifier:"%s"', pid),
+                                      fl = "identifier, dateUploaded, formatType, obsoletedBy, resourceMap"),
                      as = "data.frame")
     )
-    #if results is null or empty dataframe, remove part of the URI
+    # If results is null or empty dataframe, remove part of the URI
     if (is.null(results) || nrow(results) == 0) {
-      pid <- gsub("^[^/=]+[/=]*", "", pid)
+      pid <- gsub(pattern = "^[^/=]+[/=]*", replacement = "", x = pid)
 
-    } else {
-      #what to do if multiple are returned
-      break
-    }
+      # If multiple are returned, break
+    } else { break }
   }
 
   # filter out extra types (resource map/etc with similar pid)
@@ -66,16 +66,12 @@ check_version <- function(pid, formatType = NULL) {
     stop("No matching identifiers were found.")
   } else if (nrow(results) == 1) {
     if (is.null(results$obsoletedBy) || is.na(results$obsoletedBy)) {
-      message("\n",
-              results$identifier,
-              "\nis the latest version for identifier\n",
-              pid)
+      message(results$identifier, " is the latest version for the provided persistent identifier")
     } else {
       warning("The identifier has been obsoleted by ", results$obsoletedBy)
     }
   } else {
     warning("Several identifiers are associated with ", pid)
   }
 
-  return(results)
-}
+  return(results) }