Merge branch 'master' into terra

ropensci · Oct 4, 2024 · d8b1111 · d8b1111
2 parents f75a390 + 196dbfd
commit d8b1111
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -18,3 +18,4 @@ man-roxygen
 ^\.github$
 ^vignettes/articles$
 ^CRAN-RELEASE$
+figure/
diff --git a/.github/workflows/Deploy-pkgdown.yaml b/.github/workflows/Deploy-pkgdown.yaml
@@ -16,19 +16,36 @@ jobs:
     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
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: pkgdown
+          extra-packages: |
+            RandomFields=?ignore
+            any::pkgdown
+            any::XML
           needs: website
 
-      - name: Deploy package
+      - name: Install additional package dependencies
         run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+          repos.orig <- getOption('repos')
+          options(repos = c(PE = "https://predictiveecology.r-universe.dev")) ## TODO: use ropensci universe
+          pak::pkg_install("RandomFields")
+          options(repos = repos.orig)
+        shell: Rscript {0}
+
+      - 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/github-pages-deploy-action@4.1.4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -30,20 +30,31 @@ jobs:
     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:
+          extra-repositories: 'https://predictiveecology.r-universe.dev' ## TODO: use ropensci universe
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: |
+            RandomFields=?ignore
+            any::rcmdcheck
+            any::XML
+
+      - name: Install additional package dependencies
+        run: |
+          repos.orig <- getOption('repos')
+          options(repos = c(PE = "https://predictiveecology.r-universe.dev")) ## TODO: use ropensci universe
+          pak::pkg_install("RandomFields")
+          options(repos = repos.orig)
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/check-r-package@v2
 
-      - uses: r-lib/actions/check-r-package@v1
-
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true

diff --git a/.github/workflows/Render-readme.yaml b/.github/workflows/Render-readme.yaml
@@ -17,13 +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@v2
+        with:
+          extra-repositories: 'https://predictiveecology.r-universe.dev' ## TODO: use ropensci universe
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rmarkdown
+          extra-packages: |
+            RandomFields=?ignore
+            any::rmarkdown
+            any::XML
 
       - name: Render README files
         run: Rscript -e 'rmarkdown::render("README.Rmd")'

diff --git a/.github/workflows/Test-coverage.yaml b/.github/workflows/Test-coverage.yaml
@@ -19,13 +19,16 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
+          extra-repositories: 'https://predictiveecology.r-universe.dev' ## TODO: use ropensci universe
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: covr
+          extra-packages: |
+            any::covr
+            any::XML
 
       - name: Test coverage
         run: covr::codecov()

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: codemeta
+
+      - name: Write codemeta file
+        run: Rscript -e 'codemeta::write_codemeta()'
+
+      - name: Commit codemeta file
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          git add codemeta.json
+          git commit -m "Re-write codemeta.json" || echo "No changes to commit"
+          git push origin || echo "No changes to commit"
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,65 +1,82 @@
-Package: NLMR
 Type: Package
+Package: NLMR
 Title: Simulating Neutral Landscape Models
-Version: 1.1
-Authors@R: c(person("Marco", "Sciaini", email = "marco.sciaini@posteo.net", role = c("aut", "cre"), comment = c(ORCID = '0000-0002-3042-5435')), 
-    person("Matthias", "Fritsch", email = "matthias.fritsch@forst.uni-goettingen.de", role = "aut"), 
-    person("Maximilian", "Hesselbarth", email = "mhk.hesselbarth@gmail.com", role = "aut"),
-    person("Craig", "Simpkins", email = "simpkinscraig063@gmail.com",
-       role =  "aut", comment = c(ORCID = '0000-0003-3212-1379')),
-    person("Cédric", "Scherer", email = "cedricphilippscherer@gmail.com", 
-       role =  c("aut"), comment = c(ORCID = '0000-0003-0465-2543')),
-    person("Sebastian", "Hanß", role = "aut", comment = c(ORCID = '0000-0002-3990-4897')), 
+Version: 1.1.1
+Authors@R: c(
+    person("Marco", "Sciaini", , "marco.sciaini@posteo.net", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-3042-5435")),
+    person("Matthias", "Fritsch", , "matthias.fritsch@forst.uni-goettingen.de", role = "aut"),
+    person("Maximilian", "Hesselbarth", , "mhk.hesselbarth@gmail.com", role = "aut"),
+    person("Craig", "Simpkins", , "simpkinscraig063@gmail.com", role = "aut",
+           comment = c(ORCID = "0000-0003-3212-1379")),
+    person("Cédric", "Scherer", , "cedricphilippscherer@gmail.com", role = "aut",
+           comment = c(ORCID = "0000-0003-0465-2543")),
+    person("Sebastian", "Hanß", role = "aut",
+           comment = c(ORCID = "0000-0002-3990-4897")),
     person("Laura", "Graham", role = "rev",
-       comment = "Laura reviewed the package for rOpenSci, see 
-                  https://github.com/ropensci/onboarding/issues/188"),
+           comment = "Laura reviewed the package for rOpenSci, see \n                  https://github.com/ropensci/onboarding/issues/188"),
     person("Jeffrey", "Hollister", role = "rev",
-       comment = "Jeffrey reviewed the package for rOpenSci, see 
-                  https://github.com/ropensci/onboarding/issues/188"))
+           comment = "Jeffrey reviewed the package for rOpenSci, see \n                  https://github.com/ropensci/onboarding/issues/188")
+  )
 Maintainer: Marco Sciaini <marco.sciaini@posteo.net>
 Description: Provides neutral landscape models (<doi:10.1007/BF02275262>,
-    <http://sci-hub.tw/10.1007/bf02275262>).  
-    Neutral landscape models range from "hard" 
-    neutral models (completely random distributed), to "soft" neutral models 
-    (definable spatial characteristics) and generate landscape patterns that are 
-    independent of ecological processes.
-    Thus, these patterns can be used as null models in landscape ecology. 'NLMR' 
-    combines a large number of algorithms from other published software for 
-    simulating neutral landscapes. The simulation results are obtained in a
-    spatial data format (raster* objects from the 'raster' package) and can,
-    therefore, be used in any sort of raster data operation that is performed 
-    with standard observation data.                                                                                                  
+    <http://sci-hub.tw/10.1007/bf02275262>).  Neutral landscape models
+    range from "hard" neutral models (completely random distributed), to
+    "soft" neutral models (definable spatial characteristics) and generate
+    landscape patterns that are independent of ecological processes.
+    Thus, these patterns can be used as null models in landscape ecology.
+    'NLMR' combines a large number of algorithms from other published
+    software for simulating neutral landscapes. The simulation results are
+    obtained in a spatial data format (raster* objects from the 'raster'
+    package) and can, therefore, be used in any sort of raster data
+    operation that is performed with standard observation data.
 License: GPL-3
-Encoding: UTF-8
-LazyData: true
-ByteCompile: true
+URL: https://ropensci.github.io/NLMR/
+BugReports: https://github.com/ropensci/NLMR/issues/
 Depends:
     R (>= 3.1.0)
-SystemRequirements: C++11
-Roxygen: list(roclets = c("rd", "namespace", "collate"))
-RoxygenNote: 7.1.1
 Imports: 
     checkmate,
     dplyr,
-    RandomFields,
+    fasterize,
     raster,
-    spatstat.core,
+    Rcpp,
+    sf,
+    spatstat.random,
     spatstat.geom,
-    igraph,
     stats,
     tibble,
-    fasterize,
-    sf,
     Rcpp,
     terra
-URL: https://ropensci.github.io/NLMR/
-BugReports: https://github.com/ropensci/NLMR/issues/
 Suggests:
-    testthat,
-    covr,
+    ggplot2,
+    highcharter,
     knitr,
+    kableExtra,
+    landscapemetrics,
+    landscapetools,
+    magrittr,
+    pals,
+    plotly,
+    purrr,
+    RandomFields,
+    RandomFieldsUtils,
+    rasterVis,
+    rayshader,
+    rgl,
     rmarkdown,
-    lintr,
-    landscapetools
-LinkingTo: Rcpp
-VignetteBuilder: knitr
+    testthat,
+    viridis
+LinkingTo: 
+    Rcpp
+VignetteBuilder: 
+    knitr
+Additional_repositories: https://predictiveecology.r-universe.dev/
+ByteCompile: true
+Config/Needs/website: bindrcpp, igraph, landscapemetrics, rasterVis, pals,
+    rgl, viridis, plotly, rayshader
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(roclets = c("rd", "namespace", "collate"))
+RoxygenNote: 7.2.1
+SystemRequirements: C++11
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,11 @@
-____________________________________________________________________________________
+## NLMR 1.1.1 Release Notes
+
+- Adding onload function and help for users that dont have `RandomFields`
+
+## NLMR 1.1.0.9000 Release Notes
+
+- move `RandomFields` and `RandomFieldsUtils` to Suggests and use AdditionalRepositories to provide these packages since they are no longer available from CRAN (with #95)
+
 ## NLMR 0.4.2 Release Notes
 
 - Bugfix in nlm_mosaicfield to rely on new version of RandomFields

diff --git a/NLMR.Rproj b/NLMR.Rproj
@@ -12,6 +12,12 @@ Encoding: UTF-8
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
 
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace
+
+QuitChildProcessesOnExit: Yes
diff --git a/R/NLMR.R b/R/NLMR.R
@@ -13,6 +13,7 @@
 #'
 #' @useDynLib NLMR, .registration=TRUE
 #' @importFrom Rcpp sourceCpp
+#' @keywords internal
 # nocov start
 # nolint start
 "_PACKAGE"

diff --git a/R/nlm_fbm.R b/R/nlm_fbm.R
@@ -52,14 +52,16 @@
 #'
 #' @export
 #'
-
 nlm_fbm <- function(ncol,
                     nrow,
                     resolution = 1,
                     fract_dim = 1,
                     user_seed = NULL,
                     rescale = TRUE,
                     ...) {
+
+  hasData()
+
   # Check function arguments ----
   checkmate::assert_count(ncol, positive = TRUE)
   checkmate::assert_count(nrow, positive = TRUE)
@@ -105,4 +107,5 @@ nlm_fbm <- function(ncol,
   }
 
   return(fbm_raster)
+
 }
diff --git a/R/nlm_gaussianfield.R b/R/nlm_gaussianfield.R
@@ -50,7 +50,6 @@
 #'
 #' @export
 #'
-
 nlm_gaussianfield <- function(ncol,
                               nrow,
                               resolution = 1,
@@ -61,6 +60,8 @@ nlm_gaussianfield <- function(ncol,
                               user_seed = NULL,
                               rescale = TRUE) {
 
+  hasData()
+
   # Check function arguments ----
   checkmate::assert_count(ncol, positive = TRUE)
   checkmate::assert_count(nrow, positive = TRUE)