Merge pull request #110 from r-spatialecology/main

Update v2.0.1

Author: mhesselbarth

.Rbuildignore

@@ -1,18 +1,15 @@
-^CRAN-RELEASE$
-^.*\.Rproj$
-^\.Rproj\.user$
-^README.*$
-^cran-comments\.md$
-^docs$
-^CODE_OF_CONDUCT.*$
-^vignettes/articles$
+codecov.yml
+codemeta.json
+CODE_OF_CONDUCT.md
+CONTRIBUTING.md
+cran-comments.md
+data-raw
+docs
+LICENSE.md
+pkgdown
+README.Rmd
+README.md
+shar.Rproj
 vignettes/articles
-^data-raw$
-^_pkgdown\.yml$
-^codecov\.yml$
-^CONTRIBUTING.*$
-^pkgdown$
-^\.github$
-^LICENSE\.md$
-^CRAN-SUBMISSION$
-^CODE_OF_CONDUCT\.md$
+.github
+_pkgdown.yml

.github/workflows/Deploy-pkgdown.yaml

@@ -1,35 +1,41 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2-branch/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
 
 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: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - 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@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: any::pkgdown, any::ggplot2, any::future, any::future.apply,
+                          any::patchwork, any::rgbif, any::rgdal, any::rnaturalearth,
+                          any::rnaturalearthdata, any::sf, local::.
           needs: website
 
+      - name: Install getCRUCLdata
+        run: install.packages('getCRUCLdata', repos = 'http://packages.ropensci.org', typ = 'source')
+        shell: Rscript {0}
+
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}

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

@@ -1,18 +1,18 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2-branch/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]
+  workflow_dispatch:
 
 name: r-cmd-check
 
 jobs:
   r-cmd-check:
     if: "!contains(github.event.commits[0].message, '[skip-ci]')"
     runs-on: ${{ matrix.config.os }}
-
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
     strategy:
@@ -28,7 +28,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -37,7 +37,6 @@ jobs:
           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@v2
         with:

.github/workflows/Render-README.yaml

@@ -1,35 +1,39 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2-branch/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    paths: ['README.Rmd']
+    paths: ["README.Rmd"]
+  workflow_dispatch:
 
-name: render-rmarkdown
+name: render-readme
 
 jobs:
-  render-rmarkdown:
+  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: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          extra-repositories: 'http://packages.ropensci.org'
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rmarkdown, any::spatstat, any::terra
 
-      - uses: r-lib/actions/setup-renv@v2
+      - name: Render README files
+        run: Rscript -e 'rmarkdown::render("README.Rmd")'
 
-      - name: Render Rmarkdown files and Commit Results
+      - name: Commit README
         run: |
-          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 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"

.github/workflows/Test-coverage.yaml

@@ -1,27 +1,28 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2-branch/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]
+  workflow_dispatch:
 
 name: test-coverage
 
 jobs:
   test-coverage:
     if: "!contains(github.event.commits[0].message, '[skip-ci]')"
     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@v2
         with:
           use-public-rspm: true
-          extra-repositories: 'http://packages.ropensci.org'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

.github/workflows/Write-codemeta.yaml

@@ -0,0 +1,36 @@
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+
+on:
+  push:
+    paths: ['DESCRIPTION']
+  workflow_dispatch:
+
+name: write-codemeta
+
+jobs:
+  write-codemeta:
+    runs-on: ubuntu-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install codemeta
+        run: Rscript -e 'install.packages("codemeta")'
+
+      - name: Write codemeta file
+        run: Rscript -e 'codemeta::write_codemeta()'
+
+      - name: Commit codemeta file
+        run: |
+          git config --local user.name "$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"

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: shar
 Title: Species-Habitat Associations
-Version: 2.0.0
-Authors@R: c(person("Maximillian H.K.", "Hesselbarth", email = "[email protected]",
+Version: 2.0.1
+Authors@R: c(person("Maximilian H.K.", "Hesselbarth", email = "[email protected]",
              role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1125-9918")),
              person("Marco", "Sciaini", email = "[email protected]",
              role = "aut", comment = c(ORCID = "0000-0002-3042-5435")), 
@@ -11,7 +11,7 @@ Authors@R: c(person("Maximillian H.K.", "Hesselbarth", email = "mhk.hesselbarth@
              person("Thomas", "Etherington", email = "[email protected]",
              role = "ctb", comment = c(ORCID = "0000-0002-3187-075X"))
              )
-Maintainer: Maximillian H.K. Hesselbarth <[email protected]>
+Maintainer: Maximilian H.K. Hesselbarth <[email protected]>
 Description:
   Analyse species-habitat associations in R. Therefore, information about the location 
   of the species (as a point pattern) is needed together with environmental conditions 
@@ -37,18 +37,8 @@ RoxygenNote: 7.2.1
 Suggests:
     covr,
     dplyr,
-    getCRUCLdata,
-    ggplot2,
-    future,
-    future.apply,
     knitr,
-    patchwork,
-    rgbif,
-    rgdal,
     rmarkdown,
-    rnaturalearth, 
-    rnaturalearthdata,
-    sf,
     spatstat (>= 2.0.0),
     testthat (>= 2.1.0)
 Additional_repositories: http://packages.ropensci.org

NEWS.md

@@ -1,3 +1,9 @@
+# shar 2.0.1
+* Improvements
+  * Better approach for external repo
+* Various
+  * Fixing typo in maintainer name
+
 # shar 2.0.0
 * Improvements
   * Using `terra` instead of `raster`

R/onLoad.R

@@ -1,5 +1,7 @@
 ---
-output: github_document
+output: 
+    github_document:
+      html_preview: false
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
@@ -15,6 +17,8 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 
+Last updated: `r Sys.Date()`
+
 | CI | Development | CRAN | License |
 |----|-------------|------|---------|
 | [![R-CMD-check](https://github.com/r-spatialecology/shar/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/r-spatialecology/shar/actions/workflows/R-CMD-check.yaml) | [![Project Status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) | [![CRAN status](https://www.r-pkg.org/badges/version/shar)](https://cran.r-project.org/package=shar) |[![JOSS](https://joss.theoj.org/papers/1b786c028a5425858cb0e5428bd9173b/status.svg)](https://joss.theoj.org/papers/1b786c028a5425858cb0e5428bd9173b) |
@@ -43,8 +47,7 @@ install.packages("shar")
 And the development version from [GitHub](https://github.com/r-spatialecology/shar) with:
 
 ```{r install-github, eval = FALSE}
-install.packages("remotes")
-
+# install.packages("remotes")
 remotes::install_github("r-spatialecology/shar")
 ```
 
@@ -98,7 +101,7 @@ Of course, there are several utility functions. For example, you can plot the su
 plot(reconstruction, what = "pp")
 ```
 
-Another utility functions allows to calculate the differences between the observed pattern and the randomized patterns (also called energy using summary functions). 
+Another utility function allows to calculate the differences between the observed pattern and the randomized patterns (also called energy using summary functions). 
 
 ```{r calculate-energy, message = FALSE}
 calculate_energy(reconstruction, return_mean = TRUE)
@@ -114,7 +117,6 @@ Furthermore, please be aware that due to the randomization of the null model dat
 torus_trans <- unpack_randomized(torus_trans)
 ```
 
-
 ```{r results}
 significance_level <- 0.01
 
@@ -129,7 +131,7 @@ Contributions to **shar** are highly welcomed and appreciated. This includes any
 
 Please note that the **shar** package is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.
 
-To see how to contribute to this project, please see the [Contributing guidelines](CONTRIBUTING.md).
+To contribute to this project, please see the [Contributing guidelines](CONTRIBUTING.md).
 
 ### References