updates to remove dependencies on the HiddenSemiMarkov package

Author: lasy

.github/workflows/pkgdown.yaml

@@ -1,48 +1,49 @@
+# 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
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    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: r-lib/actions/setup-r@v1
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - 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}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@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: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
-        shell: Rscript {0}
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install package
-        run: R CMD INSTALL .
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
 
-      - 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)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -3,29 +3,25 @@ Type: Package
 Title: PMDD and MRMD Diagnoses Following The Carolina Premenstrual Assessment Scoring System (C-PASS)
 Version: 0.1.0
 Authors@R: c(
-    person("Laura", "Symul", email = "[email protected]",role = c("aut", "cre","ccp")),
+    person("Laura", "Symul", email = "[email protected]",role = c("aut", "cre","ccp")),
     person("Tory", "Eisenlohr-Moul", email = "[email protected]", role = c("aut","ccp"))
     )
-Maintainer: Laura Symul <[email protected]>
+Maintainer: Laura Symul <[email protected]>
 Description: This package is an implementation of the C-PASS (Carolina Premenstrual Assessment Scoring System) procedure for the diagnosis of PMDD (Pre-Menstrual Dysphoric Disorder) and MRMD (Menstrually Related Mood Disorder). For a full description of this procedure, refer to Tory A. Eisenlohr-Moul et al., 2017, American Journal of Psychiatry.
     In addition to the implementation of the procedure, this package also provides multiple options for the visualization of the reported symptoms and diagnoses.
 License: CC BY 4.0
 URL: https://lasy.github.io/cpass/
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.2
 Imports: 
     magrittr,
+    tidyr,
     ggplot2,
     dplyr,
-    ggthemes,
     cowplot,
     purrr,
-    tidyr,
-    stringr,
-    ggpubr
-Remotes:
-    lasy/HiddenSemiMarkov
+    stringr
 Depends: 
     R (>= 2.10)
 Suggests: 

NAMESPACE

@@ -12,7 +12,6 @@ export(simulate_cycle)
 export(supported_data_format)
 import(dplyr)
 import(ggplot2)
-import(magrittr)
 import(tidyr)
 importFrom(magrittr,"%>%")
 importFrom(purrr,map_dfr)