Added Cole's start on a documentation

afsc-assessments · Feb 29, 2024 · 59ee46c · 59ee46c
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Showing 20 changed files with 148 additions and 31 deletions.
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,8 +1,10 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
+    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
@@ -12,24 +14,35 @@ name: pkgdown
 jobs:
   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 }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - 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: any::pkgdown, local::.
           needs: website
 
-      - name: Deploy package
-        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)'
+      - 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@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/R/runSPM.R b/R/runSPM.R
@@ -6,6 +6,7 @@
 #'
 #' @param dirname A string specifying the directory in which to run the SPM analysis.
 #' @param ctrl Optional control settings for the SPM analysis. If NULL, default settings are used.
+#' @param run Logical. If TRUE, the SPM analysis is run. If FALSE, the function only reads the results from `spm_detail.csv`.
 #' @return A data frame containing the results from `spm_detail.csv`.
 #' @importFrom readr read_csv
 #' @examples

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,4 +1,6 @@
-url: ~
+url: http://afsc-assessments.github.io/spmR/
 template:
   bootstrap: 5
+development:
+  mode: auto
 
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/00-spm-example.html b/docs/articles/00-spm-example.html
diff --git a/docs/articles/01-Background.html b/docs/articles/01-Background.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,8 +1,9 @@
-pandoc: 3.1.2
+pandoc: 3.1.12.1
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   00-spm-example: 00-spm-example.html
   01-Background: 01-Background.html
-last_built: 2024-02-28T22:59Z
+  02-MoreDoc: 02-MoreDoc.html
+last_built: 2024-02-29T02:42Z
 
diff --git a/docs/reference/dat2list.html b/docs/reference/dat2list.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/list2dat.html b/docs/reference/list2dat.html