Merge pull request #6 from UCD-SERG/fixing-pkgdown

Fixing pkgdown

.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@v3
 
-      - 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 "[email protected]"
-          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/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -5,15 +5,13 @@ Version: 0.1.0.9000
 Date: 2022-03-29
 Authors@R: c(
   person(given = "Peter", family = "Teunis", email = "[email protected]", role = c("aut", "cph"), comment = "Author of the method and original code."),
-  person(given = "Jan", family = "van Eijkeren", role = c("ctb"), comment = "Author of the method and original code."), 
-  person(given = "Daniel", family = "Lewandowski", email = "[email protected]", role = c("ctb"), comment = "Creator of the `seroincidence` R package."), 
-  person(given = "Chantal", family = "Quinten", email = "[email protected]", role = c("ctb")),
-  person(given = "Kristen", family = "Aiemjoy", email = "[email protected]", role = c("aut", "ctb")),
-  person(given = "Douglas Ezra", family = "Morrison", email = "[email protected]", role = c("aut", "ctb", "cre"), comment = "Package maintainer."))
+  person(given = "Kristina", family = "Lai", role = c("aut")), 
+  person(given = "Kristen", family = "Aiemjoy", email = "[email protected]", role = c("aut")),
+  person(given = "Douglas Ezra", family = "Morrison", email = "[email protected]", role = c("aut", "cre")))
 Description: Translates antibody levels measured in a (cross-sectional)
   population sample into an estimate of the frequency with which
   seroconversions (infections) occur in the sampled population.
-  Fork of the "seroincidence" package v2.0.0 on CRAN (https://cran.r-project.org/web/packages/seroincidence/index.html)
+  Forked from the "seroincidence" package v2.0.0 on CRAN (https://cran.r-project.org/web/packages/seroincidence/index.html)
 Depends: R (>= 2.10)
 License: GPL-3
 Imports: 
@@ -32,7 +30,7 @@ Suggests:
 VignetteBuilder: knitr
 LazyData: true
 Encoding: UTF-8
-URL: https://github.com/UCD-SEG/serocalculator, https://ucd-seg.github.io/serocalculator/
+URL: https://github.com/UCD-SERG/serocalculator, https://ucd-serg.github.io/serocalculator/
 RoxygenNote: 7.2.3
 NeedsCompilation: no
 LinkingTo: 

README.md

@@ -1,29 +1,29 @@
-serocalculator package
-=====================
-
-------------------------------------------------------------------------
-
-<!-- badges: start -->
-[![R-CMD-check](https://github.com/UCD-SERG/serocalculator/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/UCD-SERG/serocalculator/actions/workflows/R-CMD-check.yaml)
-<!-- badges: end -->
-
-Antibody levels measured in a (cross–sectional) population sample can be
-translated into an estimate of the frequency with which seroconversions
-(infections) occur in the sampled population. Formulated simply: the
-presence of many high titres indicates that many subjects likely
-experienced infection recently, while low titres indicate a low
-frequency of infections in the sampled population.
-
-The serocalculator script was designed to use the longitudinal
-response characteristics by means of a set of parameters characterizing
-the longitudinal response of the selected serum antibodies.
-
-## Installation
-
-You can install the development version from
-[GitHub](https://github.com/) with:
-
-``` r
-install.packages("devtools")
-devtools::install_github("ucd-seg/serocalculator")
-```
+serocalculator package
+=====================
+
+------------------------------------------------------------------------
+
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/UCD-SERG/serocalculator/workflows/R-CMD-check/badge.svg)](https://github.com/UCD-SERG/serocalculator/actions)
+<!-- badges: end -->
+
+Antibody levels measured in a (cross–sectional) population sample can be
+translated into an estimate of the frequency with which seroconversions
+(infections) occur in the sampled population. Formulated simply: the
+presence of many high titres indicates that many subjects likely
+experienced infection recently, while low titres indicate a low
+frequency of infections in the sampled population.
+
+The serocalculator script was designed to use the longitudinal
+response characteristics by means of a set of parameters characterizing
+the longitudinal response of the selected serum antibodies.
+
+## Installation
+
+You can install the development version from
+[GitHub](https://github.com/) with:
+
+``` r
+install.packages("devtools")
+devtools::install_github("ucd-serg/serocalculator")
+```

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: https://ucd-seg.github.io/serocalculator/
+url: https://ucd-serg.github.io/serocalculator/
 template:
   bootstrap: 5