Merge branch 'main' into release-1.5.0

Author: sbfnk

.github/workflows/R-CMD-as-cran-check.yaml

@@ -33,14 +33,15 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: https://mc-stan.org/r-packages/
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: NA
           extra-packages: |
             rcmdcheck
             rmarkdown
-            stan-dev/cmdstanr
+            cmdstanr
             testthat
 
       - name: Install cmdstan

.github/workflows/R-CMD-check.yaml

@@ -54,6 +54,7 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
+          extra-repositories: https://mc-stan.org/r-packages/
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -62,7 +63,7 @@ jobs:
             dplyr
             rmarkdown
             rcmdcheck
-            stan-dev/cmdstanr
+            cmdstanr
             testthat
 
       - name: Install cmdstan

.github/workflows/lint-only-changed-files.yaml

@@ -18,14 +18,16 @@ jobs:
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
+        with:
+          extra-repositories: https://mc-stan.org/r-packages/
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: NA
           extra-packages: |
             here
             usethis
-            stan-dev/cmdstanr
+            cmdstanr
             any::gh
             any::lintr
             any::purrr

.github/workflows/render-readme.yaml

@@ -1,40 +1,61 @@
+name: render-readme
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
 on:
   workflow_dispatch:
   push:
-    paths:
-      - .github/workflows/render-readme.yaml
-      - 'README.Rmd'
+    branches:
+      - main
 
 jobs:
   render-readme:
-    runs-on: ubuntu-latest
+    runs-on: macos-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout repos
+        uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          dependencies: NA
-          extra-packages: |
-            any::pkgdown
-            local::.
+          extra-packages: any::rmarkdown, any::allcontributors
+
+      - name: Update contributors
+        if: github.ref == 'refs/heads/main'
+        run: allcontributors::add_contributors(format = "text")
+        shell: Rscript {0}
 
       - name: Compile the readme
         run: |
           rmarkdown::render("README.Rmd")
         shell: Rscript {0}
 
-      - name: Commit files
-        run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Action"
-          git add README.md man/figures/
-          git diff-index --quiet HEAD || git commit -m "Automatic readme update"
-          git push origin || echo "No changes to push"
+      - name: Upload README.md as an artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: readme
+          path: README.md
+
+      - name: Create Pull Request
+        if: github.ref == 'refs/heads/main'
+        uses: peter-evans/create-pull-request@v6
+        with:
+          commit-message: "Automatic README update"
+          title: "Update README"
+          body: "This is an automated pull request to update the README."
+          branch: "update-readme-${{ github.run_number }}"
+          labels: "documentation"
+          add-paths: |
+            README.Rmd
+            README.md
+          token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/stan-model-benchmark.yaml

@@ -24,14 +24,15 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: https://mc-stan.org/r-packages/
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           packages: |
             local::.
             here
             purrr
-            stan-dev/cmdstanr
+            cmdstanr
 
       - name: Install cmdstan
         run: |

.github/workflows/test-coverage.yaml

@@ -23,13 +23,14 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: https://mc-stan.org/r-packages/
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: NA
           extra-packages: |
             covr
-            stan-dev/cmdstanr
+            cmdstanr
             testthat
 
       - name: Install cmdstan

DESCRIPTION

@@ -6,7 +6,7 @@ Version: 1.4.9000
 Authors@R: 
     c(person(given = "Sam",
              family = "Abbott",
-             role = c("aut", "cre"),
+             role = c("aut"),
              email = "[email protected]",
              comment = c(ORCID = "0000-0001-8057-8037")),
       person(given = "Joel",
@@ -80,7 +80,7 @@ Authors@R:
              role = "aut"),
       person(given = "Sebastian",
              family = "Funk",
-             role = "aut",
+             role = c("aut", "cre"),
              email = "[email protected]",
              comment = c(ORCID = "0000-0002-2842-3406"))
     )

NEWS.md

@@ -1,5 +1,8 @@
 # EpiNow2 1.5.0
 
+This release comes with a change of maintainer, from @seabbs to @sbfnk.
+This is to reflect who will handle the upcoming CRAN submission, but is not expected to lead to a change in workflows.
+
 ## Major changes
 
 * Delay discretisation is now based on a two-day censoring window (with uniform probability in between), based on recommendations in [Park et al, medRxiv, 2024](https://doi.org/10.1101/2024.01.12.24301247). By @sbfnk in #518 and reviewed by @jamesmbaazam.

README.Rmd

@@ -153,3 +153,5 @@ A simple example of using the package to estimate a national Rt for Covid-19 can
 We welcome all contributions. If you have identified an issue with the package,
 you can file an issue [here](https://github.com/epiforecasts/EpiNow2/issues). We also welcome additions and extensions to the underlying model either in the form of options or improvements. If you wish to contribute in any form, please follow the
 [package contributing guide](https://github.com/epiforecasts/EpiNow2/blob/main/.github/CONTRIBUTING.md).
+
+## Contributors