Merge pull request #266 from r-spatialecology/main

Update lsm 1.5.5
r-spatialecology · Oct 31, 2022 · b5f0cf2 · b5f0cf2
2 parents ee2d9ca + c2b2390
commit b5f0cf2
Show file tree

Hide file tree

Showing 298 changed files with 1,025 additions and 1,016 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -22,3 +22,4 @@ vignettes/articles
 ^pkgdown
 ^\.github$
 test_data/
+^CODE_OF_CONDUCT\.md$
diff --git a/.github/workflows/Deploy-pkgdown.yaml b/.github/workflows/Deploy-pkgdown.yaml
@@ -1,48 +1,45 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - CRAN
-      - main
-    tags:
-      -'*'
+    branches: [CRAN, main]
+    tags: ['*']
 
 name: Deploy-pkgdown
 
 jobs:
   deploy-pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
-      - uses: r-lib/actions/setup-pandoc@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}
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@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-
+          extra-packages: any::pkgdown, any::bench, any::dplyr, any::landscapetools, any::purrr, any::stars, local::.
+          needs: website
 
       - name: Install dependencies
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
+         install.packages(c("remotes"))
+         remotes::install_version(package = "SDMTools", version = "1.1-221.2")
         shell: Rscript {0}
 
-      - name: Install package
-        run: R CMD INSTALL .
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
 
-      - name: Deploy package
-        run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,14 +1,11 @@
-# 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/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+
 on:
   push:
-    branches:
-      - CRAN
-      - main
+    branches: [CRAN, main, development]
   pull_request:
-    branches:
-      - CRAN
-      - main
+    branches: [CRAN, main]
 
 name: R-CMD-check
 
@@ -23,61 +20,40 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'release'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
-      - uses: r-lib/actions/setup-pandoc@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}
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Restore R package cache
-        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 spatial dependencies
+        if: runner.os == 'macOS'
+        run: |
+          brew install gdal
+          brew install proj
 
-      - name: Install system dependencies
+      - name : Install libudunits2
         if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+        run: sudo apt-get install libudunits2-dev
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
+      - 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: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          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
diff --git a/.github/workflows/Render-README.yaml b/.github/workflows/Render-README.yaml
@@ -1,39 +1,37 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - CRAN
-      - main
-    paths:
-      - README.Rmd
+    paths: ["README.Rmd"]
 
 name: Render-README
 
 jobs:
   render-readme:
-    name: Render README
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
-      - uses: r-lib/actions/setup-pandoc@v1
+      - name: Checkout repo
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
 
-      - name: Install rmarkdown, remotes, and the local package
-        run: |
-          install.packages("remotes")
-          remotes::install_cran("rmarkdown")
-          remotes::install_cran("landscapetools")
-          remotes::install_local(".")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rmarkdown, any::landscapemetrics, any::landscapetools
 
-      - name: Render README
+      - name: Render README files
         run: Rscript -e 'rmarkdown::render("README.Rmd")'
 
-      - name: Commit results
+      - name: Commit README
         run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Actions"
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
           git add README.md man/figures/README-*
           git commit -m "Re-build README.md" || echo "No changes to commit"
           git push origin || echo "No changes to commit"
diff --git a/.github/workflows/Test-coverage.yaml b/.github/workflows/Test-coverage.yaml
@@ -1,45 +1,33 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+
 on:
   push:
-    branches:
-      - CRAN
-      - main
+    branches: [CRAN, main, development]
+  pull_request:
+    branches: [CRAN, main]
 
 name: Test-coverage
 
 jobs:
   test-coverage:
     if: "!contains(github.event.commits[0].message, '[skip-ci]')"
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
-
-      - uses: r-lib/actions/setup-pandoc@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: Restore R package cache
-        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("covr")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::stars
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: covr::codecov(quiet = FALSE)
         shell: Rscript {0}
diff --git a/.github/workflows/Write-codemeta.yaml b/.github/workflows/Write-codemeta.yaml
@@ -0,0 +1,35 @@
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+
+on:
+  push:
+    paths: ['DESCRIPTION']
+
+name: Write-codemeta
+
+jobs:
+  render-readme:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::codemeta
+
+      - name: Write codemeta file
+        run: Rscript -e 'codemeta::write_codemeta()'
+
+      - name: Commit codemeta file
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add codemeta.json
+          git commit -m "Re-write codemeta.json" || echo "No changes to commit"
+          git push origin || echo "No changes to commit"