From 190ab71b1e13d0dbfa331558644ec11d2f701dae Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Fri, 4 Feb 2022 21:20:43 +0200
Subject: [PATCH] Squashed commit of the following:

commit 14e112c23d49ad94699627f3baaff11731a2221f
Author: Sam Abbott <contact@samabbott.co.uk>
Date:   Fri Feb 4 15:50:18 2022 +0000

    add github to vscode tools for dev environmenth

commit a851c753dd3e0ce58b5043497afd27d5503eeb46
Author: Sam Abbott <contact@samabbott.co.uk>
Date:   Fri Feb 4 15:43:07 2022 +0000

    switch to preferably template for website
---
 .devcontainer/devcontainer.json |  3 +-
 .github/workflows/pkgdown.yaml  | 53 +++++++++++++++++++++++++++++++++
 .pre-commit-config.yaml         |  4 +--
 DESCRIPTION                     |  4 ++-
 NEWS.md                         |  1 +
 5 files changed, 61 insertions(+), 4 deletions(-)
 create mode 100644 .github/workflows/pkgdown.yaml

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 6717a1de..66b4b139 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -21,7 +21,8 @@
 		"shan.code-settings-sync",
 		"searking.preview-vscode",
 		"tht13.html-preview-vscode",
-		"formulahendry.code-runner"
+		"formulahendry.code-runner",
+		"github.vscode-pull-request-github"
 	],
 
 	// Use 'forwardPorts' to make a list of ports inside the container available locally.
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 00000000..8d695bc1
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,53 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+    tags: ['*']
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: n1hility/cancel-previous-runs@v2
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-r@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@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: |
+          install.packages(c("remotes", "curl"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_github("r-lib/pkgdown")
+          remotes::install_github("amirmasoudabdol/preferably", type = "source")
+        shell: Rscript {0}
+        
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - 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)'
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 008fa328..f35a2100 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.1.3.9014
+    rev: v0.2.2.9009
     hooks: 
     -   id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]    
@@ -45,7 +45,7 @@ repos:
     -   id: no-browser-statement
     -   id: deps-in-desc
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.1.0
     hooks: 
     -   id: check-added-large-files
         args: ['--maxkb=800']
diff --git a/DESCRIPTION b/DESCRIPTION
index 91b47f8e..2acdb0e3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -107,7 +107,6 @@ Suggests:
     ggspatial,
     knitr,
     mockery,
-    pkgdown,
     rmarkdown,
     RSocrata,
     rvest,
@@ -119,6 +118,9 @@ Suggests:
 VignetteBuilder:
     knitr
 Config/testthat/edition: 3
+Config/Needs/website: 
+    r-lib/pkgdown,
+    amirmasoudabdol/preferably
 Encoding: UTF-8
 Language: en-gb
 LazyData: true
diff --git a/NEWS.md b/NEWS.md
index 4a270315..16faffd2 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -12,6 +12,7 @@ This release is currently under development
 * Change the data source for Switzerland to draw data from the Swiss Federal Office of Public Health (FOPH)
 * Updated the package logo to include the newly supported data sets.
 * Reduced the number of package dependencies (@bisaloo and @RichardMN)
+
 ## Bug fixes
 
 - Fixed a bug in the data sourced from Germany so that instead of treating it as a line list of individuals it is treated as a relatively finely resolved count data which needs to be summed up (by @sbfnk).