Merge pull request #108 from r-spatialecology/main

v2.0

.github/workflows/Deploy-pkgdown.yaml

@@ -1,33 +1,43 @@
-# 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, development]
-    tags: ['*']
+  workflow_dispatch:
 
-name: Deploy-pkgdown
+name: deploy-pkgdown
 
 jobs:
   deploy-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 }}
     steps:
       - uses: actions/checkout@v2
 
-      - 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
+          extra-repositories: 'http://packages.ropensci.org'
 
-      - 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(new_process = FALSE, clean = TRUE)'
+      - 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

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

@@ -1,13 +1,12 @@
-# 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: [CRAN, main, development]
   pull_request:
     branches: [CRAN, main]
 
-name: R-CMD-check
+name: r-cmd-check
 
 jobs:
   r-cmd-check:
@@ -31,34 +30,20 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Install spatial dependencies
-        if: runner.os == 'macOS'
-        run: |
-          brew install gdal
-          brew install proj
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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
+          extra-repositories: 'http://packages.ropensci.org'
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
-
-      - uses: r-lib/actions/check-r-package@v1
-
-      - 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: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

.github/workflows/Render-README.yaml

@@ -1,13 +1,13 @@
-# 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:
     paths: ['README.Rmd']
 
-name: Render-README
+name: render-rmarkdown
 
 jobs:
-  render-readme:
+  render-rmarkdown:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -17,21 +17,19 @@ jobs:
         with:
           fetch-depth: 0
 
-      - 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-dependencies@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
-          extra-packages: rmarkdown
+          extra-repositories: 'http://packages.ropensci.org'
 
-      - name: Render README files
-        run: Rscript -e 'rmarkdown::render("README.Rmd")'
+      - uses: r-lib/actions/setup-renv@v2
 
-      - name: Commit README
+      - name: Render Rmarkdown files and Commit Results
         run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Actions"
-          git add README.md man/figures/README-*
-          git commit -m "Re-build README.md" || echo "No changes to commit"
+          RMD_PATH=($(git diff --name-only ${{ github.event.before }} ${{ github.sha }} | grep '[.]Rmd$'))
+          Rscript -e 'for (f in commandArgs(TRUE)) if (file.exists(f)) rmarkdown::render(f)' ${RMD_PATH[*]}
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git commit ${RMD_PATH[*]/.Rmd/.md} -m 'Re-build Rmarkdown files' || echo "No changes to commit"
           git push origin || echo "No changes to commit"

.github/workflows/Test-coverage.yaml

@@ -1,12 +1,12 @@
-# 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: [CRAN, main, development]
   pull_request:
     branches: [CRAN, main]
 
-name: Test-coverage
+name: test-coverage
 
 jobs:
   test-coverage:
@@ -18,14 +18,16 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: 'http://packages.ropensci.org'
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: covr
+          extra-packages: any::covr
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: covr::codecov(quiet = FALSE)
         shell: Rscript {0}

DESCRIPTION

@@ -51,7 +51,7 @@ Suggests:
     sf,
     spatstat (>= 2.0.0),
     testthat (>= 2.1.0)
-Remotes: ropensci/getCRUCLdata
+Additional_repositories: http://packages.ropensci.org
 VignetteBuilder: knitr
 Encoding: UTF-8
 LazyData: true

NEWS.md

@@ -1,7 +1,10 @@
 # shar 2.0
-* Using `terra` instead of `raster`
-* Adding `pack_randomized()` and `unpack_randomized()` due to `terra` saving behavior
-* Naming raster values "layer"
+* Improvements
+  * Using `terra` instead of `raster`
+* Bugfixes
+  * Naming raster values "layer"
+* New functionality
+  * Adding `pack_randomized()` and `unpack_randomized()` due to `terra` saving behavior
 
 # shar 1.3.2
 * Improvements

R/onLoad.R

@@ -0,0 +1,11 @@
+.onLoad <- function(libname, pkgname) {
+
+  repos <- getOption("repos")
+
+  repos["getCRUCLdata"] <- "http://packages.ropensci.org"
+
+  options(repos = repos)
+
+  invisible(repos)
+
+}

codecov.yml

@@ -1,12 +1,8 @@
 comment: false
 
 coverage:
-  status:
-    project:
-      default:
-        target: 80%
-        threshold: 1%
-    patch:
-      default:
-        target: 80%
-        threshold: 1%
+  precision: 2
+  round: nearest
+  range: 70..100
+  target: 80%
+  threshold: 5%

cran-comments.md

@@ -1,7 +1,8 @@
 For details changes, please see NEWS.md.
 
-## shar 1.4
-Update dependencies
+## shar 2.0
+* Replace `raster` with `terra` and several code changes related to this
+* Fixed issue of earlier submission "Unknown, possibly misspelled, fields in DESCRIPTION: 'Remotes'"
 
 ## shar 1.3.2
 Improvements of existing functions and spatstat update
@@ -66,9 +67,9 @@ which is together alreadyv more than 10 min which is the CRAN threshold for a pa
 * Renamed package from `SHAR` to `shar`
 
 ## Test environments
-* Windows 10, R 3.5.1
-* macOS Mojave, R 3.5.1
-* https://win-builder.r-project.org (devel and release)
+* macOS-latest,   R: 'release'
+* windows-latest, R: 'release'
+* ubuntu-latest,  R: 'release'
 
 ## R CMD check results
 0 errors | 0 warnings | 0 note