From 3c6086c5b274d300106e3a97e63da4acd6273349 Mon Sep 17 00:00:00 2001
From: James McMahon <james.mcmahon@phs.scot>
Date: Wed, 24 Aug 2022 15:40:17 +0100
Subject: [PATCH 01/14] Update the R-CMD-check workflow

I've renamed and re-written the R-CMD-check workflow to be more consistent.

It is now based on the r-lib v2 action examples and runs against a collection of R versions to represent the PHS current and future potential setup
---
 .Rbuildignore                      |  1 +
 .github/.gitignore                 |  1 +
 .github/workflows/R-CMD-check.yaml | 54 +++++++++++++++++++
 .github/workflows/phsopendata.yml  | 85 ------------------------------
 README.Rmd                         |  2 +-
 README.md                          | 85 ++++++++++++++++--------------
 6 files changed, 102 insertions(+), 126 deletions(-)
 create mode 100644 .github/.gitignore
 create mode 100644 .github/workflows/R-CMD-check.yaml
 delete mode 100644 .github/workflows/phsopendata.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index 588683b..c16d1c6 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,4 @@
 ^phsopendata\.Rproj$
 ^\.Rproj\.user$
 ^README\.Rmd$
+^\.github$
diff --git a/.github/.gitignore b/.github/.gitignore
new file mode 100644
index 0000000..2d19fc7
--- /dev/null
+++ b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 0000000..60199e5
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,54 @@
+# 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]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    continue-on-error: ${{ matrix.config.must_pass }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+            # Windows
+          - {os: windows-latest, r: 'release', must_pass: true}
+            # Use 3.6 to trigger usage of RTools35
+          - {os: windows-latest, r: '3.6', must_pass: true}
+            # Linux
+          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release', must_pass: false}
+          - {os: ubuntu-latest, r: 'release', must_pass: true}
+          - {os: ubuntu-latest, r: 'oldrel-1', must_pass: true}
+          - {os: ubuntu-latest, r: 'oldrel-2', must_pass: true}
+          - {os: ubuntu-latest, r: '3.6.1', must_pass: true}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - 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
diff --git a/.github/workflows/phsopendata.yml b/.github/workflows/phsopendata.yml
deleted file mode 100644
index cea7ca2..0000000
--- a/.github/workflows/phsopendata.yml
+++ /dev/null
@@ -1,85 +0,0 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
-on:
-  push:
-    branches:
-      - main
-      - master
-  pull_request:
-    branches:
-      - main
-      - master
-
-name: R-CMD-check
-
-jobs:
-  R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$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 system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
diff --git a/README.Rmd b/README.Rmd
index d66733d..c796acc 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -16,7 +16,7 @@ knitr::opts_chunk$set(
 # phsopendata
 
 <!-- badges: start -->
-[![R build status](https://github.com/Public-Health-Scotland/phsopendata/workflows/R-CMD-check/badge.svg)](https://github.com/Public-Health-Scotland/phsopendata/actions)
+[![R-CMD-check](https://github.com/Public-Health-Scotland/phsopendata/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Public-Health-Scotland/phsopendata/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 `phsopendata` contains functions to interact with open data from the [Scottish Health and Social Care Open Data platform](https://www.opendata.nhs.scot/) via the CKAN API. 
diff --git a/README.md b/README.md
index f8ea467..7f872cf 100644
--- a/README.md
+++ b/README.md
@@ -1,21 +1,20 @@
+
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-phsopendata
-===========
+# phsopendata
 
 <!-- badges: start -->
 
-[![R build
-status](https://github.com/Public-Health-Scotland/phsopendata/workflows/R-CMD-check/badge.svg)](https://github.com/Public-Health-Scotland/phsopendata/actions)
+[![R-CMD-check](https://github.com/Public-Health-Scotland/phsopendata/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Public-Health-Scotland/phsopendata/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 `phsopendata` contains functions to interact with open data from the
 [Scottish Health and Social Care Open Data
 platform](https://www.opendata.nhs.scot/) via the CKAN API.
 
--   `get-resource` extracts a single resource from an open dataset by
+  - `get-resource` extracts a single resource from an open dataset by
     resource id
--   `get-dataset` extracts multiple resources from an open dataset by
+  - `get-dataset` extracts multiple resources from an open dataset by
     dataset name
 
 For extracting metadata and search functionality, we recommend using the
@@ -26,60 +25,65 @@ For extracting metadata and search functionality, we recommend using the
 RStudio. However, depending on firewall settings, proxy use may need to
 be configured with `use_proxy()`.
 
-Installation
-------------
+## Installation
 
 You need to install `phsopendata` from GitHub, which requires a package
 like `remotes` or `devtools`.
 
 Using `remotes` you run this to install the package:
 
-    remotes::install_github("Public-Health-Scotland/phsopendata",
-      upgrade = "never"
-    )
+``` r
+remotes::install_github("Public-Health-Scotland/phsopendata",
+  upgrade = "never"
+)
+```
 
-Examples
---------
+## Examples
 
 ### Downloading a data table with `get_resource()`
 
 To extract a specific resource, you will need it’s unique identifier -
 resource id. This can be found in the dataset metadata, the URL of a
-resource’s page on
-<a href="https://www.opendata.nhs.scot/" class="uri">https://www.opendata.nhs.scot/</a>,
-or extracted using `ckanr::package_show`.
+resource’s page on <https://www.opendata.nhs.scot/>, or extracted using
+`ckanr::package_show`.
 
-    library(phsopendata)
+``` r
+library(phsopendata)
 
-    # define a resource ID
-    res_id <- "a794d603-95ab-4309-8c92-b48970478c14"
+# define a resource ID
+res_id <- "a794d603-95ab-4309-8c92-b48970478c14"
 
-    # download the data from the CKAN database
-    data <- get_resource(res_id = "a794d603-95ab-4309-8c92-b48970478c14")
+# download the data from the CKAN database
+data <- get_resource(res_id = "a794d603-95ab-4309-8c92-b48970478c14")
+```
 
 ### Querying/filtering data with `get_resource()`
 
 You can define a row limit with the `rows` argument to get the first *N*
 rows of a table.
 
-    # get first 100 rows
-    get_resource(
-      res_id = "a794d603-95ab-4309-8c92-b48970478c14",
-      rows = 100
-    )
+``` r
+# get first 100 rows
+get_resource(
+  res_id = "a794d603-95ab-4309-8c92-b48970478c14",
+  rows = 100
+)
+```
 
 You can use `col_select` and `row_filters` to query the data server-side
 (i.e., the data is filtered before it is downloaded to your machine).
 
-    # get first 100 rows
-    get_resource(
-      res_id = "a794d603-95ab-4309-8c92-b48970478c14",
-      col_select = c("GPPracticeName", "TelephoneNumber"),
-      row_filters = list(
-        HB = "S08000017",
-        Dispensing = "Y"
-      )
-    )
+``` r
+# get first 100 rows
+get_resource(
+  res_id = "a794d603-95ab-4309-8c92-b48970478c14",
+  col_select = c("GPPracticeName", "TelephoneNumber"),
+  row_filters = list(
+    HB = "S08000017",
+    Dispensing = "Y"
+  )
+)
+```
 
 ### Downloading multiple tables with `get_dataset()`
 
@@ -93,12 +97,13 @@ from:
 [opendata.nhs.scot/dataset/*gp-practice-populations*](https://www.opendata.nhs.scot/dataset/gp-practice-populations),
 so the dataset name will be gp-practice-populations.
 
-    # if max_resources is not set, all resources will be returned by default. 
-    # Here we pull 10 rows from the first 2 resources only
-    get_dataset("gp-practice-populations", max_resources = 2, rows = 10)
+``` r
+# if max_resources is not set, all resources will be returned by default. 
+# Here we pull 10 rows from the first 2 resources only
+get_dataset("gp-practice-populations", max_resources = 2, rows = 10)
+```
 
-Contributing to phsopendata
----------------------------
+## Contributing to phsopendata
 
 At present, this package is maintained by [David
 Aikman](https://github.com/daikman).

From bda241bd50888e1e68bd3c9ba626311bb414b361 Mon Sep 17 00:00:00 2001
From: runner <runner@Mac-1661352101890.local>
Date: Wed, 24 Aug 2022 14:43:49 +0000
Subject: [PATCH 02/14] Re-build README.Rmd

---
 README.md | 82 ++++++++++++++++++++++++++-----------------------------
 1 file changed, 38 insertions(+), 44 deletions(-)

diff --git a/README.md b/README.md
index 7f872cf..9310e07 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
-
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# phsopendata
+phsopendata
+===========
 
 <!-- badges: start -->
 
@@ -12,9 +12,9 @@
 [Scottish Health and Social Care Open Data
 platform](https://www.opendata.nhs.scot/) via the CKAN API.
 
-  - `get-resource` extracts a single resource from an open dataset by
+-   `get-resource` extracts a single resource from an open dataset by
     resource id
-  - `get-dataset` extracts multiple resources from an open dataset by
+-   `get-dataset` extracts multiple resources from an open dataset by
     dataset name
 
 For extracting metadata and search functionality, we recommend using the
@@ -25,65 +25,60 @@ For extracting metadata and search functionality, we recommend using the
 RStudio. However, depending on firewall settings, proxy use may need to
 be configured with `use_proxy()`.
 
-## Installation
+Installation
+------------
 
 You need to install `phsopendata` from GitHub, which requires a package
 like `remotes` or `devtools`.
 
 Using `remotes` you run this to install the package:
 
-``` r
-remotes::install_github("Public-Health-Scotland/phsopendata",
-  upgrade = "never"
-)
-```
+    remotes::install_github("Public-Health-Scotland/phsopendata",
+      upgrade = "never"
+    )
 
-## Examples
+Examples
+--------
 
 ### Downloading a data table with `get_resource()`
 
 To extract a specific resource, you will need it’s unique identifier -
 resource id. This can be found in the dataset metadata, the URL of a
-resource’s page on <https://www.opendata.nhs.scot/>, or extracted using
-`ckanr::package_show`.
+resource’s page on
+<a href="https://www.opendata.nhs.scot/" class="uri">https://www.opendata.nhs.scot/</a>,
+or extracted using `ckanr::package_show`.
 
-``` r
-library(phsopendata)
+    library(phsopendata)
 
-# define a resource ID
-res_id <- "a794d603-95ab-4309-8c92-b48970478c14"
+    # define a resource ID
+    res_id <- "a794d603-95ab-4309-8c92-b48970478c14"
 
-# download the data from the CKAN database
-data <- get_resource(res_id = "a794d603-95ab-4309-8c92-b48970478c14")
-```
+    # download the data from the CKAN database
+    data <- get_resource(res_id = "a794d603-95ab-4309-8c92-b48970478c14")
 
 ### Querying/filtering data with `get_resource()`
 
 You can define a row limit with the `rows` argument to get the first *N*
 rows of a table.
 
-``` r
-# get first 100 rows
-get_resource(
-  res_id = "a794d603-95ab-4309-8c92-b48970478c14",
-  rows = 100
-)
-```
+    # get first 100 rows
+    get_resource(
+      res_id = "a794d603-95ab-4309-8c92-b48970478c14",
+      rows = 100
+    )
 
 You can use `col_select` and `row_filters` to query the data server-side
 (i.e., the data is filtered before it is downloaded to your machine).
 
-``` r
-# get first 100 rows
-get_resource(
-  res_id = "a794d603-95ab-4309-8c92-b48970478c14",
-  col_select = c("GPPracticeName", "TelephoneNumber"),
-  row_filters = list(
-    HB = "S08000017",
-    Dispensing = "Y"
-  )
-)
-```
+    # get first 100 rows
+    get_resource(
+      res_id = "a794d603-95ab-4309-8c92-b48970478c14",
+      col_select = c("GPPracticeName", "TelephoneNumber"),
+      row_filters = list(
+        HB = "S08000017",
+        Dispensing = "Y"
+      )
+    )
 
 ### Downloading multiple tables with `get_dataset()`
 
@@ -97,13 +92,12 @@ from:
 [opendata.nhs.scot/dataset/*gp-practice-populations*](https://www.opendata.nhs.scot/dataset/gp-practice-populations),
 so the dataset name will be gp-practice-populations.
 
-``` r
-# if max_resources is not set, all resources will be returned by default. 
-# Here we pull 10 rows from the first 2 resources only
-get_dataset("gp-practice-populations", max_resources = 2, rows = 10)
-```
+    # if max_resources is not set, all resources will be returned by default. 
+    # Here we pull 10 rows from the first 2 resources only
+    get_dataset("gp-practice-populations", max_resources = 2, rows = 10)
 
-## Contributing to phsopendata
+Contributing to phsopendata
+---------------------------
 
 At present, this package is maintained by [David
 Aikman](https://github.com/daikman).

From 4beaaaa159e9aec3848bc96883b1b6c2e7aaa597 Mon Sep 17 00:00:00 2001
From: James McMahon <james.mcmahon@phs.scot>
Date: Wed, 24 Aug 2022 15:45:08 +0100
Subject: [PATCH 03/14] Add test coverage workflow and infrastructure

This workflow will check and report test coverage to codecov.io
---
 .Rbuildignore                        |  1 +
 .github/workflows/test-coverage.yaml | 31 ++++++++++++++++++++++++++++
 DESCRIPTION                          |  1 +
 README.Rmd                           |  1 +
 README.md                            |  2 ++
 codecov.yml                          | 14 +++++++++++++
 6 files changed, 50 insertions(+)
 create mode 100644 .github/workflows/test-coverage.yaml
 create mode 100644 codecov.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index c16d1c6..04c793c 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 ^README\.Rmd$
 ^\.github$
+^codecov\.yml$
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..4b65418
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,31 @@
+# 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]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: covr::codecov(quiet = FALSE)
+        shell: Rscript {0}
diff --git a/DESCRIPTION b/DESCRIPTION
index 1b03080..82b66dd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -20,6 +20,7 @@ Imports:
     cli,
     xml2
 Suggests: 
+    covr,
     testthat (>= 3.0.0)
 Encoding: UTF-8
 LazyData: true
diff --git a/README.Rmd b/README.Rmd
index c796acc..96b452e 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -17,6 +17,7 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/Public-Health-Scotland/phsopendata/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Public-Health-Scotland/phsopendata/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/Public-Health-Scotland/phsopendata/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Public-Health-Scotland/phsopendata?branch=master)
 <!-- badges: end -->
 
 `phsopendata` contains functions to interact with open data from the [Scottish Health and Social Care Open Data platform](https://www.opendata.nhs.scot/) via the CKAN API. 
diff --git a/README.md b/README.md
index 9310e07..059abaf 100644
--- a/README.md
+++ b/README.md
@@ -6,6 +6,8 @@ phsopendata
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/Public-Health-Scotland/phsopendata/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Public-Health-Scotland/phsopendata/actions/workflows/R-CMD-check.yaml)
+[![Codecov test
+coverage](https://codecov.io/gh/Public-Health-Scotland/phsopendata/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Public-Health-Scotland/phsopendata?branch=master)
 <!-- badges: end -->
 
 `phsopendata` contains functions to interact with open data from the
diff --git a/codecov.yml b/codecov.yml
new file mode 100644
index 0000000..04c5585
--- /dev/null
+++ b/codecov.yml
@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true

From bf69d1970e8f2e7dd799e618225e2b4e7dd9447d Mon Sep 17 00:00:00 2001
From: James McMahon <james.mcmahon@phs.scot>
Date: Wed, 24 Aug 2022 15:47:11 +0100
Subject: [PATCH 04/14] Add pkgdown workflow and infrastructure

This will build the package documentation, Readme and vignettes into a website on a new branch `gh_pages` this can be deployed to GitHub pages with the right permissions.
---
 .Rbuildignore                  |  3 +++
 .github/workflows/pkgdown.yaml | 46 ++++++++++++++++++++++++++++++++++
 .gitignore                     |  1 +
 DESCRIPTION                    |  2 ++
 _pkgdown.yml                   |  4 +++
 5 files changed, 56 insertions(+)
 create mode 100644 .github/workflows/pkgdown.yaml
 create mode 100644 _pkgdown.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index 04c793c..e87d948 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -3,3 +3,6 @@
 ^README\.Rmd$
 ^\.github$
 ^codecov\.yml$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 0000000..0b26021
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,46 @@
+# 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:
+
+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 }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - 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@4.1.4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.gitignore b/.gitignore
index 807ea25..c2f15ec 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 .Rproj.user
 .Rhistory
 .RData
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
index 82b66dd..cc7c00e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,3 +27,5 @@ LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
 Config/testthat/edition: 3
+URL: https://github.com/Public-Health-Scotland/phsopendata
+BugReports: https://github.com/Public-Health-Scotland/phsopendata/issues
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 0000000..d71acfb
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,4 @@
+url: ~
+template:
+  bootstrap: 5
+

From e73f5af0f8ee70334fb2e84e19f979c6bec5422a Mon Sep 17 00:00:00 2001
From: James McMahon <james.mcmahon@phs.scot>
Date: Wed, 24 Aug 2022 15:49:06 +0100
Subject: [PATCH 05/14] Add an action to style the package

This will run whenever a relevant filetype is modified and style the package with `styler` to the tidyverse style.

All the changes will be only cosmetic but will ensure consistency.
---
 .github/workflows/style.yaml | 68 ++++++++++++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 .github/workflows/style.yaml

diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml
new file mode 100644
index 0000000..f0bb30c
--- /dev/null
+++ b/.github/workflows/style.yaml
@@ -0,0 +1,68 @@
+# 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:
+    paths: ["**.[rR]", "**.[rR]md", "**.[rR]markdown", "**.[rR]nw"]
+  pull_request:
+    paths: ["**.[rR]", "**.[rR]md", "**.[rR]markdown", "**.[rR]nw"]
+
+name: Style
+
+jobs:
+  style:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::styler
+          needs: styler
+
+      - name: Enable styler cache
+        run: styler::cache_activate()
+        shell: Rscript {0}
+
+      - name: Determine cache location
+        id: styler-location
+        run: |
+          cat(
+            "##[set-output name=location;]",
+            styler::cache_info(format = "tabular")$location,
+            "\n",
+            sep = ""
+          )
+        shell: Rscript {0}
+
+      - name: Cache styler
+        uses: actions/cache@v2
+        with:
+          path: ${{ steps.styler-location.outputs.location }}
+          key: ${{ runner.os }}-styler-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-styler-
+            ${{ runner.os }}-
+
+      - name: Style
+        run: styler::style_pkg(filetype = c(".R", ".Rmd", ".Rmarkdown", ".Rnw"))
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add R/\*
+          git commit -m "Style code" || echo "No changes to commit"
+          git pull --ff-only
+          git push origin

From 12a7437e8723732c26bab295cf5e4fc95f9874d7 Mon Sep 17 00:00:00 2001
From: Moohan <Moohan@users.noreply.github.com>
Date: Wed, 24 Aug 2022 14:52:02 +0000
Subject: [PATCH 06/14] Style code

---
 R/check_dataset_name.R   |  7 ++++---
 R/check_res_id.R         | 10 ++++++----
 R/dump_download.R        |  4 ++--
 R/error_check.R          | 15 +++++++++------
 R/parse_col_select.R     |  5 ++---
 R/parse_error.R          |  2 --
 R/parse_row_filters.R    | 15 +++++++++------
 R/phs_GET.R              |  4 ++--
 R/request_url.R          |  7 ++++---
 R/suggest_dataset_name.R |  5 ++---
 R/use_dump_check.R       |  7 ++++---
 11 files changed, 44 insertions(+), 37 deletions(-)

diff --git a/R/check_dataset_name.R b/R/check_dataset_name.R
index eb9ae91..0dc8648 100644
--- a/R/check_dataset_name.R
+++ b/R/check_dataset_name.R
@@ -11,15 +11,16 @@ check_dataset_name <- function(dataset_name) {
   # Has only lowercase alphanum or hyphens inbetween
   dataset_name_regex <- "^[a-z0-9][a-z0-9\\-]+?[a-z0-9]$"
 
-  if (!inherits(dataset_name, "character"))
+  if (!inherits(dataset_name, "character")) {
     cli::cli_abort(c(
       "The dataset name supplied {.var {dataset_name}} is invalid.",
       "x" = "dataset_name must be of type character.",
       "i" = "You supplied a {.cls {class(dataset_name)[0]}} value."
     ))
+  }
 
 
-  if (!grepl(dataset_name_regex, dataset_name))
+  if (!grepl(dataset_name_regex, dataset_name)) {
     cli::cli_abort(c(
       "The dataset name supplied {.var {dataset_name}} is invalid",
       "x" = "dataset_name must be in dash-case
@@ -27,5 +28,5 @@ check_dataset_name <- function(dataset_name) {
       "i" = "You can find dataset names in the URL
       of a dataset's page on {.url www.opendata.nhs.scot}."
     ))
-
+  }
 }
diff --git a/R/check_res_id.R b/R/check_res_id.R
index c449fca..5692600 100644
--- a/R/check_res_id.R
+++ b/R/check_res_id.R
@@ -9,28 +9,30 @@
 check_res_id <- function(res_id) {
 
   # check res_id is single value
-  if (length(res_id) > 1)
+  if (length(res_id) > 1) {
     cli::cli_abort(c(
       "Argument {.var res_id} must be of length 1.",
       i = "You supplied a res_id with a length of {length(res_id)}",
       x = "`get_resource` does not currently support
       requests for multiple resources simultaneously."
     ))
+  }
 
   # check res_id is character
-  if (!inherits(res_id, "character"))
+  if (!inherits(res_id, "character")) {
     cli::cli_abort(c(
       "Argument {.var res_id} must be of type character",
       i = "You supplied a {.var res_id} with type  {.cls {class(res_id)[1]}}"
     ))
+  }
 
   # check regex pattern
   res_id_regex <-
     "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"
-  if (!grepl(res_id_regex, res_id))
+  if (!grepl(res_id_regex, res_id)) {
     cli::cli_abort(c(
       "Argument {.var res_id} is in an invalid format.",
       i = "You can find a resource's ID in the URL of it's page on {.url www.opendata.nhs.scot}."
     ))
-
+  }
 }
diff --git a/R/dump_download.R b/R/dump_download.R
index 4c9d7e3..8cf4270 100644
--- a/R/dump_download.R
+++ b/R/dump_download.R
@@ -11,12 +11,12 @@ dump_download <- function(res_id) {
   )
 
   # if content is a web page
-  if ("xml_document" %in% class(content))
+  if ("xml_document" %in% class(content)) {
     cli::cli_abort(c(
       "Can't find resource with ID {.var {res_id}} in datastore."
     ))
+  }
 
   # return data
   return(content[, -1])
-
 }
diff --git a/R/error_check.R b/R/error_check.R
index 6802376..f1dc6b0 100644
--- a/R/error_check.R
+++ b/R/error_check.R
@@ -6,17 +6,21 @@ error_check <- function(content) {
 
   # if content is not a list,
   # stop for content (a string describing an error)
-  if (!is.list(content)) cli::cli_abort(c(
-    "API error",
-    x = content
-  ))
+  if (!is.list(content)) {
+    cli::cli_abort(c(
+      "API error",
+      x = content
+    ))
+  }
 
   # if there is no error status/message in the content,
   # break out of the function
   is_error <- suppressWarnings(
     !is.null(content$error)
   )
-  if (!is_error) return()
+  if (!is_error) {
+    return()
+  }
 
   # generate error message and stop
   error_text <- parse_error(content$error)
@@ -24,5 +28,4 @@ error_check <- function(content) {
     "API error.",
     x = error_text
   ))
-
 }
diff --git a/R/parse_col_select.R b/R/parse_col_select.R
index c0980dd..82232b2 100644
--- a/R/parse_col_select.R
+++ b/R/parse_col_select.R
@@ -4,12 +4,11 @@
 #' @param col_select a character vector identifying the columns to select.
 #' @return a character string
 parse_col_select <- function(col_select) {
-
-  if (is.null(col_select))
+  if (is.null(col_select)) {
     return(NULL)
+  }
 
   return(
     paste0(col_select, collapse = ",")
   )
-
 }
diff --git a/R/parse_error.R b/R/parse_error.R
index 1cc9f07..353d91a 100644
--- a/R/parse_error.R
+++ b/R/parse_error.R
@@ -14,13 +14,11 @@ parse_error <- function(error) {
 
   # special case for validation errors
   if (error_type == "Validation Error") {
-
     error_output <- paste0(names(error[1][1]), ": ", error[1][[1]])
 
     # translate message for package users
     error_output <- sub("fields", "col_select", error_output)
     error_output <- sub("q", "row_filters", error_output)
-
   }
 
   # special case for SQL validation errors
diff --git a/R/parse_row_filters.R b/R/parse_row_filters.R
index 1cc8ce4..756dca2 100644
--- a/R/parse_row_filters.R
+++ b/R/parse_row_filters.R
@@ -5,18 +5,20 @@
 parse_row_filters <- function(row_filters) {
 
   # exit function if no filters
-  if (is.null(row_filters))
+  if (is.null(row_filters)) {
     return(NULL)
+  }
 
   # check if any filters in list have length > 1
   too_many <- sapply(row_filters, length) > 1
 
-  if (any(too_many))
+  if (any(too_many)) {
     cli::cli_abort(c(
       "Invalid input for {.var row_filters}",
       i = "{names(row_filters)[which(too_many)]} in {.var row_filters} has too many values. ",
       x = "The {.var row_filters} list must only contain vectors of length 1."
     ))
+  }
 
   # check if any items in the list/vector have the same name
   # find number of unique names
@@ -26,19 +28,20 @@ parse_row_filters <- function(row_filters) {
   # if same, all names are unique
   unique_names <- n_u_row_filters == n_row_filters
 
-  if (!unique_names)
+  if (!unique_names) {
     cli::cli_abort(c(
       "Invalid input for {.var row_filters}",
       x = "One or more elements in {.var row_filters} have the same name.",
       i = "Only one filter per field is currently supported by `get_resource`."
     ))
+  }
 
   filter_body <- paste0(
-    '"', names(row_filters), '":"', row_filters, '"', collapse = ","
+    '"', names(row_filters), '":"', row_filters, '"',
+    collapse = ","
   )
 
   return(
-    paste0('{', filter_body, '}')
+    paste0("{", filter_body, "}")
   )
-
 }
diff --git a/R/phs_GET.R b/R/phs_GET.R
index d7fd156..99a6fe1 100644
--- a/R/phs_GET.R
+++ b/R/phs_GET.R
@@ -19,11 +19,12 @@ phs_GET <- function(action, query, verbose = FALSE) {
   )
 
   # Check for response from server
-  if (!inherits(response, "response"))
+  if (!inherits(response, "response")) {
     cli::cli_abort(c(
       "Can't connect to the CKAN server.",
       i = "Check your network/proxy settings."
     ))
+  }
 
   # extract content from HTTP response
   content <- httr::content(
@@ -35,5 +36,4 @@ phs_GET <- function(action, query, verbose = FALSE) {
 
   if (verbose) cat("GET request successful.\n")
   return(content)
-
 }
diff --git a/R/request_url.R b/R/request_url.R
index 7aa65b0..ba2e866 100644
--- a/R/request_url.R
+++ b/R/request_url.R
@@ -8,23 +8,24 @@ request_url <- function(action, query) {
 
   # check action is valid
   valid_actions <- c("datastore_search", "datastore_search_sql", "dump", "package_show", "package_list")
-  if (!(action %in% valid_actions))
+  if (!(action %in% valid_actions)) {
     cli::cli_abort(c(
       "API call failed.",
       x = "Invalid {.var action} argument in request."
     ))
+  }
 
   # return dump URL
-  if (action == "dump")
+  if (action == "dump") {
     return(paste0(
       "https://www.opendata.nhs.scot/datastore/dump/",
       query, "?bom=true"
     ))
+  }
 
   # return standard API endpoint (i.e., not dump)
   return(paste0(
     "https://www.opendata.nhs.scot/api/3/action/",
     action, "?", query
   ))
-
 }
diff --git a/R/suggest_dataset_name.R b/R/suggest_dataset_name.R
index f1dd34b..0a61cbe 100644
--- a/R/suggest_dataset_name.R
+++ b/R/suggest_dataset_name.R
@@ -4,7 +4,6 @@
 #' @param dataset_name a string to be matched against valid dataset names
 #'
 suggest_dataset_name <- function(dataset_name) {
-
   content <- phs_GET("package_list", "")
 
   dataset_names <- unlist(content$result)
@@ -13,13 +12,14 @@ suggest_dataset_name <- function(dataset_name) {
   string_distances <- stringdist::stringdist(dataset_name, dataset_names)
 
   # if min distance is too big, abort
-  if (min(string_distances) > 10)
+  if (min(string_distances) > 10) {
     cli::cli_abort(c(
       "Can't find the dataset name
       {.var {dataset_name}}, or a close match.",
       i = "Find a dataset's name in the URL
       of it's page on {.url www.opendata.nhs.scot.}"
     ))
+  }
 
   # find closet match
   closest_match <- dataset_names[which.min(string_distances)]
@@ -29,5 +29,4 @@ suggest_dataset_name <- function(dataset_name) {
     "Can't find the dataset name {.var {dataset_name}}.",
     "i" = "Did you mean '{closest_match}'?"
   ))
-
 }
diff --git a/R/use_dump_check.R b/R/use_dump_check.R
index 632d96b..b6cf714 100644
--- a/R/use_dump_check.R
+++ b/R/use_dump_check.R
@@ -21,7 +21,7 @@ use_dump_check <- function(query, rows) {
   # if user queried the data
   queried <- !is.null(query$q) || !is.null(query$filter) || !is.null(query$fields)
 
-  if (queried && use_dump)
+  if (queried && use_dump) {
     cli::cli_warn(c(
       "Invalid combination of {.var rows}, {.var row_filters}
       and/or {.var col_select}.",
@@ -29,12 +29,13 @@ use_dump_check <- function(query, rows) {
       AND query its rows/columns.",
       i = "ALL rows and columns of the resource will be downloaded."
     ))
+  }
 
   # warn users if they haven't queried
   # the data but have requested rows > 99999
 
   if (is.null(rows)) rows <- 0
-  if (!queried && rows > 99999)
+  if (!queried && rows > 99999) {
     cli::cli_warn(c(
       "Getting all rows of resource.",
       i = "All rows will be returned if you
@@ -42,8 +43,8 @@ use_dump_check <- function(query, rows) {
       i = "You set {.var rows} to
       {format(rows, big.mark = ',', scientific = FALSE)}"
     ))
+  }
 
 
   return(use_dump)
 }
-

From dd3ccec46366dd9aff97b6d52b6ec62a4a13ebe9 Mon Sep 17 00:00:00 2001
From: James McMahon <james.mcmahon@phs.scot>
Date: Wed, 24 Aug 2022 15:50:30 +0100
Subject: [PATCH 07/14] Add an action to document the package

Will run when any files in the `R` directory are modified and ensure the package documentation is up to date.
---
 .github/workflows/document.yaml | 44 +++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 .github/workflows/document.yaml

diff --git a/.github/workflows/document.yaml b/.github/workflows/document.yaml
new file mode 100644
index 0000000..9a772c0
--- /dev/null
+++ b/.github/workflows/document.yaml
@@ -0,0 +1,44 @@
+# 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:
+    paths: ["R/**"]
+  pull_request:
+    paths: ["R/**"]
+
+name: Document
+
+jobs:
+  document:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: roxygen2
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE
+          git commit -m "Update documentation" || echo "No changes to commit"
+          git pull --ff-only
+          git push origin

From 856307776becfaff869b8d21df2665f1042ee9a8 Mon Sep 17 00:00:00 2001
From: James McMahon <james.mcmahon@phs.scot>
Date: Wed, 24 Aug 2022 15:51:09 +0100
Subject: [PATCH 08/14] Add an action to lint the package

It will run on any push or pull and add annotiations to the commit / PR with suggestions from `lintr` which provides best practice.
---
 .github/workflows/lint.yaml | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 .github/workflows/lint.yaml

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
new file mode 100644
index 0000000..381410b
--- /dev/null
+++ b/.github/workflows/lint.yaml
@@ -0,0 +1,30 @@
+# 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]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}

From 9fcdafb0b6b41312fbab5396965ff382e24a9eeb Mon Sep 17 00:00:00 2001
From: James McMahon <james.mcmahon@phs.scot>
Date: Wed, 24 Aug 2022 16:35:21 +0100
Subject: [PATCH 09/14] Setup infrastructure for pkgdown -> GitHub pages

I realised that I did actually have permissions
---
 DESCRIPTION  | 3 ++-
 _pkgdown.yml | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index cc7c00e..47c0117 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,5 +27,6 @@ LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
 Config/testthat/edition: 3
-URL: https://github.com/Public-Health-Scotland/phsopendata
+URL: https://github.com/Public-Health-Scotland/phsopendata,
+    https://public-health-scotland.github.io/phsopendata/
 BugReports: https://github.com/Public-Health-Scotland/phsopendata/issues
diff --git a/_pkgdown.yml b/_pkgdown.yml
index d71acfb..0dcfc08 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -1,4 +1,4 @@
-url: ~
+url: https://public-health-scotland.github.io/phsopendata/
 template:
   bootstrap: 5
 

From 713f15ec05efcd10968e2a0c4f3fcd04c6169178 Mon Sep 17 00:00:00 2001
From: James McMahon <james.mcmahon@phs.scot>
Date: Thu, 6 Oct 2022 16:18:14 +0100
Subject: [PATCH 10/14] use stefanzweifel action to commit

---
 .github/workflows/style.yaml | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml
index f0bb30c..4419ac4 100644
--- a/.github/workflows/style.yaml
+++ b/.github/workflows/style.yaml
@@ -59,10 +59,6 @@ jobs:
         shell: Rscript {0}
 
       - name: Commit and push changes
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          git add R/\*
-          git commit -m "Style code" || echo "No changes to commit"
-          git pull --ff-only
-          git push origin
+        uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          commit_message: "Style code"

From 110e476baf41ebfecdef49ed0cb43767ec79db8d Mon Sep 17 00:00:00 2001
From: James McMahon <james.mcmahon@phs.scot>
Date: Thu, 6 Oct 2022 16:19:16 +0100
Subject: [PATCH 11/14] Use stefanzweifel to commit change

---
 .github/workflows/document.yaml | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/document.yaml b/.github/workflows/document.yaml
index 9a772c0..4d00aff 100644
--- a/.github/workflows/document.yaml
+++ b/.github/workflows/document.yaml
@@ -35,10 +35,6 @@ jobs:
         shell: Rscript {0}
 
       - name: Commit and push changes
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          git add man/\* NAMESPACE
-          git commit -m "Update documentation" || echo "No changes to commit"
-          git pull --ff-only
-          git push origin
+        uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          commit_message: "Update documentation"

From 7484b8e5281cf3c98c87ec79af13d716586ef503 Mon Sep 17 00:00:00 2001
From: James McMahon <james.mcmahon@phs.scot>
Date: Tue, 2 May 2023 16:03:50 +0100
Subject: [PATCH 12/14] Update actions to the latest examples from r-lib

(https://github.com/r-lib/actions/blob/v2/examples/README.md)[]
---
 .github/workflows/R-CMD-check.yaml   |  7 +++++--
 .github/workflows/document.yaml      | 14 +++++++------
 .github/workflows/lint.yaml          |  2 +-
 .github/workflows/pkgdown.yaml       |  6 ++++--
 .github/workflows/style.yaml         | 31 ++++++++++++++++++----------
 .github/workflows/test-coverage.yaml | 23 +++++++++++++++++++--
 6 files changed, 59 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 60199e5..2ae07d5 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -26,7 +26,10 @@ jobs:
           - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release', must_pass: false}
           - {os: ubuntu-latest, r: 'release', must_pass: true}
           - {os: ubuntu-latest, r: 'oldrel-1', must_pass: true}
-          - {os: ubuntu-latest, r: 'oldrel-2', must_pass: true}
+          - {os: ubuntu-latest, r: 'oldrel-2', must_pass: false}
+            # Vesions in use on PHS PWB
+          - {os: ubuntu-latest, r: '4.0.2', must_pass: true}
+          - {os: ubuntu-latest, r: '4.1.2', must_pass: true}
           - {os: ubuntu-latest, r: '3.6.1', must_pass: true}
 
     env:
@@ -34,7 +37,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
diff --git a/.github/workflows/document.yaml b/.github/workflows/document.yaml
index 4d00aff..6c118dd 100644
--- a/.github/workflows/document.yaml
+++ b/.github/workflows/document.yaml
@@ -3,8 +3,6 @@
 on:
   push:
     paths: ["R/**"]
-  pull_request:
-    paths: ["R/**"]
 
 name: Document
 
@@ -15,7 +13,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
@@ -35,6 +33,10 @@ jobs:
         shell: Rscript {0}
 
       - name: Commit and push changes
-        uses: stefanzweifel/git-auto-commit-action@v4
-        with:
-          commit_message: "Update documentation"
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE DESCRIPTION
+          git commit -m "Update documentation" || echo "No changes to commit"
+          git pull --ff-only
+          git push origin
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index 381410b..24d656d 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 0b26021..ed7650c 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -19,8 +19,10 @@ jobs:
       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@v2
 
@@ -39,7 +41,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@4.1.4
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
         with:
           clean: false
           branch: gh-pages
diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml
index 4419ac4..37c986e 100644
--- a/.github/workflows/style.yaml
+++ b/.github/workflows/style.yaml
@@ -2,9 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    paths: ["**.[rR]", "**.[rR]md", "**.[rR]markdown", "**.[rR]nw"]
-  pull_request:
-    paths: ["**.[rR]", "**.[rR]md", "**.[rR]markdown", "**.[rR]nw"]
+    paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown", "**.[rR]nw", "**.[rR]profile"]
 
 name: Style
 
@@ -15,7 +13,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
@@ -27,7 +25,7 @@ jobs:
       - name: Install dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::styler
+          extra-packages: any::styler, any::roxygen2
           needs: styler
 
       - name: Enable styler cache
@@ -38,15 +36,17 @@ jobs:
         id: styler-location
         run: |
           cat(
-            "##[set-output name=location;]",
+            "location=",
             styler::cache_info(format = "tabular")$location,
             "\n",
+            file = Sys.getenv("GITHUB_OUTPUT"),
+            append = TRUE,
             sep = ""
           )
         shell: Rscript {0}
 
       - name: Cache styler
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ steps.styler-location.outputs.location }}
           key: ${{ runner.os }}-styler-${{ github.sha }}
@@ -55,10 +55,19 @@ jobs:
             ${{ runner.os }}-
 
       - name: Style
-        run: styler::style_pkg(filetype = c(".R", ".Rmd", ".Rmarkdown", ".Rnw"))
+        run: styler::style_pkg()
         shell: Rscript {0}
 
       - name: Commit and push changes
-        uses: stefanzweifel/git-auto-commit-action@v4
-        with:
-          commit_message: "Style code"
+        run: |
+          if FILES_TO_COMMIT=($(git diff-index --name-only ${{ github.sha }} \
+              | egrep --ignore-case '\.(R|[qR]md|Rmarkdown|Rnw|Rprofile)$'))
+          then
+            git config --local user.name "$GITHUB_ACTOR"
+            git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+            git commit ${FILES_TO_COMMIT[*]} -m "Style code"
+            git pull --ff-only
+            git push origin
+          else
+            echo "No changes to commit."
+          fi
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 4b65418..2c5bb50 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -27,5 +27,24 @@ jobs:
           needs: coverage
 
       - name: Test coverage
-        run: covr::codecov(quiet = FALSE)
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

From 6a0c9f1cc637fee8db8e1a62160ca1ad3b947c53 Mon Sep 17 00:00:00 2001
From: Moohan <Moohan@users.noreply.github.com>
Date: Thu, 30 Nov 2023 12:29:00 +0000
Subject: [PATCH 13/14] Update documentation

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d4f2410..02cf416 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -25,7 +25,7 @@ Suggests:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Config/testthat/edition: 3
 URL: https://github.com/Public-Health-Scotland/phsopendata,
     https://public-health-scotland.github.io/phsopendata/

From e5234f7e835adf81e6b9b7a762101f985a5a6647 Mon Sep 17 00:00:00 2001
From: James McMahon <james.mcmahon@phs.scot>
Date: Thu, 30 Nov 2023 12:36:14 +0000
Subject: [PATCH 14/14] Update to use latest examples (again)

Also simplify the R CMD check
---
 .github/workflows/R-CMD-check.yaml   | 21 +++++++++++----------
 .github/workflows/render-README.yml  | 10 ++++++----
 .github/workflows/style.yaml         |  2 +-
 .github/workflows/test-coverage.yaml |  2 +-
 4 files changed, 19 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 2ae07d5..138d69c 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -11,26 +11,27 @@ name: R-CMD-check
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
+
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-    continue-on-error: ${{ matrix.config.must_pass }}
 
     strategy:
       fail-fast: false
       matrix:
         config:
             # Windows
-          - {os: windows-latest, r: 'release', must_pass: true}
+          - {os: windows-latest, r: 'release'}
             # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6', must_pass: true}
+          - {os: windows-latest, r: '3.6'}
             # Linux
-          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release', must_pass: false}
-          - {os: ubuntu-latest, r: 'release', must_pass: true}
-          - {os: ubuntu-latest, r: 'oldrel-1', must_pass: true}
-          - {os: ubuntu-latest, r: 'oldrel-2', must_pass: false}
+          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest, r: 'release'}
+            # Mac OS
+          - {os: macos-latest,   r: 'release'}
+
             # Vesions in use on PHS PWB
-          - {os: ubuntu-latest, r: '4.0.2', must_pass: true}
-          - {os: ubuntu-latest, r: '4.1.2', must_pass: true}
-          - {os: ubuntu-latest, r: '3.6.1', must_pass: true}
+          - {os: ubuntu-latest, r: '4.0.2'}
+          - {os: ubuntu-latest, r: '4.1.2'}
+          - {os: ubuntu-latest, r: '3.6.1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/render-README.yml b/.github/workflows/render-README.yml
index 49b2b1e..42a57c7 100644
--- a/.github/workflows/render-README.yml
+++ b/.github/workflows/render-README.yml
@@ -6,18 +6,20 @@ on:
 jobs:
   render:
     name: Render README
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-pandoc@v2
       - name: Install rmarkdown
         run: Rscript -e 'install.packages("rmarkdown")'
       - name: Render README
         run: Rscript -e 'rmarkdown::render("README.Rmd", output_format = "md_document")'
       - name: Commit results
         run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
           git commit README.md -m 'Re-build README.Rmd' || echo "No changes to commit"
           git push origin || echo "No changes to commit"
diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml
index 37c986e..bee3e48 100644
--- a/.github/workflows/style.yaml
+++ b/.github/workflows/style.yaml
@@ -65,7 +65,7 @@ jobs:
           then
             git config --local user.name "$GITHUB_ACTOR"
             git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-            git commit ${FILES_TO_COMMIT[*]} -m "Style code"
+            git commit ${FILES_TO_COMMIT[*]} -m "Style code (GHA)"
             git pull --ff-only
             git push origin
           else
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 2c5bb50..27d4528 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -31,7 +31,7 @@ jobs:
           covr::codecov(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
         shell: Rscript {0}