Improve gh pages and rendering of Vignettes

.github/workflows/pkgdown.yaml

@@ -39,8 +39,7 @@ 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
         with:
-          clean: false
           branch: gh-pages
           folder: docs

.github/workflows/render_readme.yaml

@@ -0,0 +1,51 @@
+# Name of the workflow
+name: render-readme
+
+# Controls when the action will run. Triggers include:
+#
+# - button trigger from github action page
+# - on changes to readme.Rmd
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - 'README.Rmd'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  render-readme:
+    runs-on: macos-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repos
+        uses: actions/checkout@v3
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rmarkdown, local::.
+
+      - name: Compile the readme
+        run: |
+          rmarkdown::render("README.Rmd")
+        shell: Rscript {0}
+
+      - name: Commit files
+        run: |
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git add README.md 
+          git diff-index --quiet HEAD || git commit -m "Automatic readme update"
+          git status -sb | grep -q ahead && git push origin

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: scoringutils
 Title: Utilities for Scoring and Assessing Predictions
-Version: 1.2.0
+Version: 1.2.1
 Language: en-GB
 Authors@R: c(
     person(given = "Nikos",

NEWS.md

@@ -1,3 +1,12 @@
+# scoringutils 1.2.1
+
+## Package updates
+- This minor update fixes a few issues related to gh actions and the vignettes displayed at epiforecasts.io/scoringutils. It
+  - gets rid of the preferably package in _pkgdown.yml. The theme had a toggle between light and dark theme that didn't work properly
+  - updates the gh pages deploy action to v4 and also cleans up files when triggered
+  - introduces a gh action to automatically render the Readme from Readme.Rmd
+  - removes links to vignettes that have been renamed
+
 # scoringutils 1.2.0
 
 This major release contains a range of new features and bug fixes that have been introduced in minor releases since `1.1.0`. The most important changes are:

R/score.R

@@ -31,7 +31,7 @@
 #' contributing a pull request.
 #'
 #' For additional help and examples, check out the [Getting Started
-#' Vignette](https://epiforecasts.io/scoringutils/articles/getting-started.html)
+#' Vignette](https://epiforecasts.io/scoringutils/articles/scoringutils.html)
 #' as well as the paper [Evaluating Forecasts with scoringutils in
 #' R](https://arxiv.org/abs/2205.07090).
 #'

README.Rmd

@@ -30,7 +30,7 @@ library(knitr)
 
 The `scoringutils` package provides a collection of metrics and proper scoring rules and aims to make it simple to score probabilistic forecasts against the true observed values. 
 
-You can find additional information and examples in the papers [Evaluating Forecasts with scoringutils in R](https://arxiv.org/abs/2205.07090) [Scoring epidemiological forecasts on transformed scales](https://www.medrxiv.org/content/10.1101/2023.01.23.23284722v1) as well as the Vignettes ([Getting started](https://epiforecasts.io/scoringutils/articles/getting-started.html), [Details on the metrics implemented](https://epiforecasts.io/scoringutils/articles/metric-details.html) and [Scoring forecasts directly](https://epiforecasts.io/scoringutils/articles/scoring-forecasts-directly.html)).
+You can find additional information and examples in the papers [Evaluating Forecasts with scoringutils in R](https://arxiv.org/abs/2205.07090) [Scoring epidemiological forecasts on transformed scales](https://www.medrxiv.org/content/10.1101/2023.01.23.23284722v1) as well as the Vignettes ([Getting started](https://epiforecasts.io/scoringutils/articles/scoringutils.html), [Details on the metrics implemented](https://epiforecasts.io/scoringutils/articles/metric-details.html) and [Scoring forecasts directly](https://epiforecasts.io/scoringutils/articles/scoring-forecasts-directly.html)).
 
 The `scoringutils` package offers convenient automated forecast evaluation through the function `score()`. The function operates on data.frames (it uses `data.table` internally for speed and efficiency) and can easily be integrated in a workflow based on `dplyr` or `data.table`. It also provides experienced users with a set of reliable lower-level scoring metrics operating on vectors/matrices they can build upon in other applications. In addition it implements a wide range of flexible plots designed to cover many use cases.
 

README.md

@@ -22,7 +22,7 @@ R](https://arxiv.org/abs/2205.07090) [Scoring epidemiological forecasts
 on transformed
 scales](https://www.medrxiv.org/content/10.1101/2023.01.23.23284722v1)
 as well as the Vignettes ([Getting
-started](https://epiforecasts.io/scoringutils/articles/getting-started.html),
+started](https://epiforecasts.io/scoringutils/articles/scoringutils.html),
 [Details on the metrics
 implemented](https://epiforecasts.io/scoringutils/articles/metric-details.html)
 and [Scoring forecasts
@@ -186,8 +186,8 @@ example_quantile %>%
 #> 5:  epiforecasts-EpiNow2       Cases     log   6.005778e-01    0.1066329
 #> 6:  epiforecasts-EpiNow2       Cases natural   1.443844e+04 5664.3779484
 #>    underprediction overprediction coverage_deviation        bias    ae_median
-#> 1:    3.521964e-01      0.3804607        -0.10940217  0.09726563 1.185905e+00
-#> 2:    1.028497e+04   7702.9836957        -0.10940217  0.09726563 3.208048e+04
+#> 1:    3.521964e-01      0.3804607        -0.10940217  0.09726562 1.185905e+00
+#> 2:    1.028497e+04   7702.9836957        -0.10940217  0.09726562 3.208048e+04
 #> 3:    1.356563e-01      0.3132561        -0.09785326 -0.05640625 7.410484e-01
 #> 4:    4.237177e+03   3650.0047554        -0.09785326 -0.05640625 1.770795e+04
 #> 5:    1.858699e-01      0.3080750        -0.06660326 -0.07890625 7.656591e-01

_pkgdown.yml

@@ -1,9 +1,8 @@
 url: https://epiforecasts.io/scoringutils/
 template:
   bootstrap: 5
-  package: preferably
-  params:
-    toggle: manual
+  bslib:
+    font_weight_base : 300
   twitter:
     creator: "@nikosbosse"
     card: summary_large_image