Merge pull request #218 from r-spatialecology/master

Update v1.5.1

.Rbuildignore

@@ -1,7 +1,6 @@
 ^CRAN-RELEASE$
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.travis\.yml$
 ^README.*$
 ^NOTES.*$
 ^notes.*$
@@ -15,10 +14,10 @@
 ^CONTRIBUTING.*$
 ^LICENSE.*$
 ^data-raw$
-^appveyor\.yml$
 vignettes/articles
 ^codemeta\.json$
 ^tic\.R$
 ^vignettes/articles$
 ^\.httr-oauth$
 ^pkgdown
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/Deploy-pkgdown.yaml

@@ -0,0 +1,55 @@
+on:
+  push:
+    branches:
+      - CRAN
+      - master
+
+name: Deploy-pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-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: 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
+        run: |
+          install.packages("remotes")
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("pkgdown", type = "binary")
+          remotes::install_cran("patchwork")
+          remotes::install_cran("tidyverse")
+          remotes::install_version("SDMTools", version = "1.1-221.2")
+          remotes::install_cran("NLMR")
+          remotes::install_cran("landscapetools")
+          remotes::install_cran("bench")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - 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)'

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

@@ -0,0 +1,83 @@
+# 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
+on:
+  push:
+    branches:
+      - CRAN
+      - master
+  pull_request:
+    branches:
+      - CRAN
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      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"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    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}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        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 system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/Render-README.yaml

@@ -0,0 +1,33 @@
+on:
+  push:
+    paths:
+      - README.Rmd
+
+name: Render-README
+
+jobs:
+  render:
+    name: Render README
+    runs-on: macOS-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: Install rmarkdown, remotes, and the local package
+        run: |
+          install.packages("remotes")
+          remotes::install_local(".")
+          remotes::install_cran("rmarkdown")
+          remotes::install_cran("landscapetools")
+        shell: Rscript {0}
+      - name: Render README
+        run: Rscript -e 'rmarkdown::render("README.Rmd")'
+      - name: 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.Rmd' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"

.github/workflows/Test-coverage.yaml

@@ -0,0 +1,48 @@
+on:
+  push:
+    branches:
+      - CRAN
+      - master
+  pull_request:
+    branches:
+      - CRAN
+      - master
+
+name: Test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: macOS-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: 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
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

CONTRIBUTING.md

@@ -14,14 +14,14 @@ We appreciate any contribution and collaboration.
 
 ### Code contributions
 
-* Fork this repo to your Github account
-* Clone your version on your account down to your machine from your account, e.g,. `git clone https://github.com/r-spatialecology/landscapemetrics.git`
-* Make sure to track progress upstream (i.e., on our version of `landscapemetrics` at `r-spatialecology/landscapemetrics`) by doing `git remote add upstream https://github.com/r-spatialecology/landscapemetrics.git`. 
-Before making changes make sure to pull changes in from upstream by doing either `git fetch upstream` then merge later or `git pull upstream` to fetch and merge in one step
-* Make your changes (bonus points for making changes on a new branch)
-* If you alter package functionality at all (e.g., the code itself, not just documentation) please do write some tests to cover the new functionality
-* Push up to your account
-* Submit a pull request to home base at `r-spatialecology/landscapemetrics`
+1. Fork this repo to your GitHub account
+2. Clone your version to your machine, e.g., `git clone https://github.com/r-spatialecology/landscapemetrics.git`
+3. Make sure to track progress upstream (i.e., our version of `landscapemetrics` at `r-spatialecology/landscapemetrics`) by doing `git remote add upstream https://github.com/r-spatialecology/landscapemetrics.git`
+Before making any changes, make sure to pull changes in from upstream by either doing `git fetch upstream` then merge later, or `git pull upstream` to fetch and merge in one step
+4. Make your changes (bonus points for making changes on a new branch)
+5. If you alter package functionality at all (e.g., the code itself, not just documentation) please do write some tests to cover the new functionality.
+6. Push changes to your account
+7. Submit a pull request to the master branch at `r-spatialecology/landscapemetrics`
 
 ### Questions? Get in touch: [[email protected]](mailto:[email protected]) or [[email protected]](mailto:[email protected])
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: landscapemetrics
 Title: Landscape Metrics for Categorical Map Patterns
-Version: 1.5.0
+Version: 1.5.1
 Authors@R: c(person("Maximillian H.K.", "Hesselbarth",
              role = c("aut", "cre"),
              email = "[email protected]",

NEWS.md

@@ -1,3 +1,9 @@
+# landscapemetrics 1.5.1
+* Improvements
+    * Use GitHub actions
+* Bugfixes
+ * Bug in `lsm_c_lsi`, `lsm_c_nlsi`, `lsm_l_lsi` not using cell surfaces
+
 # landscapemetrics 1.5.0
 * Improvements
     * Improved internal understandment of input classes