Remove rgdal dependency (#19)

ropensci-archive · Jan 15, 2024 · 710494f · 710494f
1 parent cfd96ed
commit 710494f
Show file tree

Hide file tree

Showing 16 changed files with 205 additions and 253 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -7,3 +7,4 @@ vignettes/rdefra_vignette.Rmd.orig
 vignettes/precompile.R
 _pkgdown.yml
 ^\.github$
+^rdefra\.Rproj$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,18 +1,10 @@
-# NOTE: This workflow is overkill for most R packages
-# check-standard.yaml is likely a better choice
-# usethis::use_github_action("check-standard") will install it.
-#
-# 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:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -26,78 +18,32 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: '3.6'}
-          - {os: ubuntu-18.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.1.0 (ubuntu-18.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
-        id: install-r
+      - 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-pandoc@v1
-
-      - name: Install pak and query dependencies
-        run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
-        shell: Rscript {0}
-
-      - name: Install dependencies
-        run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -1,49 +1,32 @@
+# 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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: lint
 
 jobs:
   lint:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          use-public-rspm: true
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("lintr")
-        shell: Rscript {0}
-
-      - name: Install package
-        run: R CMD INSTALL .
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
 
       - name: Lint
         run: lintr::lint_package()
         shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,48 +1,50 @@
+# 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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
 
-      - name: Query dependencies
+      - name: Test coverage
         run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
+      - name: Show testthat output
+        if: always()
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,13 +1,13 @@
 Package: rdefra
-Title: Retrieve Data from the UK AIR Database
-Version: 0.3.9
+Title: Interact with the UK AIR Pollution Database from DEFRA
+Version: 0.3.9.9000
 Authors@R: c(person(given = "Cheryl",
                     family = "Lim",
-                    role = c("aut", "cre"),
+                    role = c("aut"),
                     email = "[email protected]"),
              person(given = "Claudia",
                     family = "Vitolo",
-                    role = c("aut"),
+                    role = c("aut", "cre"),
                     email = "[email protected]",
                     comment = c(ORCID = "0000-0002-4252-1176", "Claudia is the original creator of the package")),
              person("Andrew", "Russell", role = c("ctb"),
@@ -22,7 +22,6 @@ Authors@R: c(person(given = "Cheryl",
              person("Hao", "Zhu", role = c("ctb"),
                     comment = "Hao Zhu reviewed the package for rOpenSci, see
                     https://github.com/ropensci/software-review/issues/68"))
-Maintainer: Claudia Vitolo <[email protected]>
 URL: https://docs.ropensci.org/rdefra/, https://github.com/ropensci/rdefra
 BugReports: https://github.com/ropensci/rdefra/issues
 Description: This packages allows to retrieve air pollution data from the Air
@@ -33,12 +32,11 @@ Description: This packages allows to retrieve air pollution data from the Air
   The package is described in Vitolo et al. (2016) "rdefra: Interact with the
   UK AIR Pollution Database from DEFRA" <doi:10.21105/joss.00051>.
 Depends: R (>= 3.5.0)
-Imports: lubridate, tibble, httr, xml2, dplyr, sf, rgdal, curl
+Imports: lubridate, tibble, httr, xml2, dplyr, sf, curl
 Suggests: testthat, rmarkdown, knitr, ggplot2, zoo
-SystemRequirements: GDAL
 VignetteBuilder: knitr
 LazyData: true
 Encoding: UTF-8
 License: GPL-3
-Repository: CRAN
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
+Roxygen: list(markdown = TRUE)
diff --git a/NAMESPACE b/NAMESPACE
@@ -7,7 +7,6 @@ export(ukair_catalogue)
 export(ukair_get_coordinates)
 export(ukair_get_hourly_data)
 export(ukair_get_site_id)
-import(rgdal)
 importFrom(curl,has_internet)
 importFrom(dplyr,bind_rows)
 importFrom(httr,GET)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+rdefra (development)
+==============
+
+Remove dependency on rgdal.
+
 rdefra 0.3.8
 ==============
 

diff --git a/R/rdefra-package.R b/R/rdefra-package.R
@@ -1,15 +1,7 @@
-#' rdefra: Interact with the UK AIR Pollution Database from DEFRA
-#'
-#' The R package rdefra allows to retrieve air pollution data from the Air
-#' Information Resource (UK-AIR) of the Department for Environment, Food and
-#' Rural Affairs in the United Kingdom (see \url{https://uk-air.defra.gov.uk/}).
-#' UK-AIR does not provide public APIs for programmatic access to data,
-#' therefore this package scrapes the HTML pages to get relevant information.
-#'
-#' @name rdefra
-#' @docType package
-#'
-#' @import rgdal
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
 #' @importFrom curl has_internet
 #' @importFrom httr GET content http_error set_config config
 #' @importFrom utils read.csv
@@ -18,7 +10,7 @@
 #' @importFrom tibble as_tibble
 #' @importFrom dplyr bind_rows
 #' @importFrom sf st_as_sf st_transform st_coordinates
-#'
+## usethis namespace: end
 NULL
 
 #' List of all the DEFRA air quality monitoring stations with complete
@@ -28,8 +20,6 @@ NULL
 #' installed in the UK and operated by DEFRA networks (as per February 2016).
 #' As the network expands, metadata for new stations will be added.
 #'
-#' @usage data("stations")
-#'
 #' @format A data frame with 6561 observations on the following 14 variables.
 #' \describe{
 #'   \item{\code{UK.AIR.ID}}{ID reference for monitoring stations}
@@ -54,7 +44,7 @@ NULL
 #'   \item{\code{SiteID}}{Site ID, used to retrieve time series data.}
 #' }
 #'
-#' @keywords datasets
-#'
 #' @source \url{https://uk-air.defra.gov.uk/}
+#' @examples
+#' stations
 "stations"
diff --git a/R/ukair_get_site_id.R b/R/ukair_get_site_id.R
@@ -1,6 +1,6 @@
 #' Get site identification numbers for DEFRA stations
 #'
-#' @description Given the UK AIR ID (from the \code{ukair_catalogue()}), this
+#' @description Given the UK AIR ID (from [ukair_catalogue()]), this
 #' function fetches the catalogue of monitoring stations from DEFRA's website.
 #'
 #' @param id_s An alphanumeric string (or vector of strings) containing the UK