sync update with r ecosystems

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

@@ -0,0 +1,51 @@
+# 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, master]
+  pull_request:
+
+name: R-CMD-check
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -8,7 +8,7 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown.yaml
+name: pkgdown
 
 permissions: read-all
 

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -27,15 +27,15 @@ Description: Use the spatial association marginal contributions derived from spa
 License: GPL-3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 URL: https://stscl.github.io/cisp/, https://github.com/stscl/cisp
 BugReports: https://github.com/stscl/cisp/issues
 Depends: 
     R (>= 4.1.0)
 Imports: 
     dplyr,
     forcats,
-    gdverse (>= 1.3-2),
+    gdverse (>= 1.5),
     ggplot2,
     ggraph,
     igraph,
@@ -48,7 +48,8 @@ Imports:
     tidyr
 Suggests: 
     knitr,
-    rmarkdown
+    rmarkdown,
+    spEDM
 Remotes:
     stscl/gdverse
 VignetteBuilder: knitr

README.Rmd

@@ -21,6 +21,7 @@ knitr::opts_chunk$set(
 [![DownloadsAll](https://badgen.net/cran/dt/cisp?color=orange)](https://CRAN.R-project.org/package=cisp)
 [![DownloadsMonth](https://cranlogs.r-pkg.org/badges/cisp)](https://CRAN.R-project.org/package=cisp)
 [![R-universe](https://stscl.r-universe.dev/badges/cisp?color=cyan)](https://stscl.r-universe.dev/cisp)
+[![R-CMD-check](https://github.com/stscl/cisp/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/stscl/cisp/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 **A Correlation Indicator Based on Spatial Patterns**

README.md

@@ -11,6 +11,7 @@ stable](https://img.shields.io/badge/lifecycle-stable-cyan.svg)](https://lifecyc
 [![DownloadsAll](https://badgen.net/cran/dt/cisp?color=orange)](https://CRAN.R-project.org/package=cisp)
 [![DownloadsMonth](https://cranlogs.r-pkg.org/badges/cisp)](https://CRAN.R-project.org/package=cisp)
 [![R-universe](https://stscl.r-universe.dev/badges/cisp?color=cyan)](https://stscl.r-universe.dev/cisp)
+[![R-CMD-check](https://github.com/stscl/cisp/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/stscl/cisp/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 **A Correlation Indicator Based on Spatial Patterns**