Adding r pkgs github infrastructure (QoL)

.Rbuildignore

@@ -7,3 +7,8 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+
+# Tech stack
+^\.devcontainer$
+^\.vscode$
+^\.github$

.devcontainer/.vscode/settings.json

@@ -0,0 +1,4 @@
+{
+    "r.plot.useHttpgd": true,
+    "r.alwaysUseActiveTerminal": true
+}

.devcontainer/Containerfile

@@ -0,0 +1,43 @@
+FROM ghcr.io/rocker-org/devcontainer/r-ver:4.5
+
+# Architecture-specific variable (built in Docker BuildKit)
+ARG TARGETARCH
+
+# Runtime dependency for R package 'fs' (provides libuv.so.1)
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends libuv1t64 && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install quarto-cli and the orange-book extension
+RUN wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.9.35/quarto-1.9.35-linux-${TARGETARCH}.deb && \
+    dpkg -i quarto-1.9.35-linux-${TARGETARCH}.deb && \
+    rm quarto-1.9.35-linux-${TARGETARCH}.deb
+
+# Adding R packages
+RUN install2.r --error fable \
+    fabletools \
+    progressr \
+    feasts \
+    tsibble \
+    dplyr \
+    tidyr \
+    ggplot2 \
+    distributional \
+    epidatr \
+    rlang \
+    EpiEstim \
+    projections \
+    incidence \
+    jsonlite \
+    baselinenowcast \
+    DiagrammeR \
+    knitr \
+    rmarkdown \
+    devtools \
+    pipetime \
+    fable.prophet \
+    testthat
+
+RUN installGithub.r hubverse-org/hubEvals
+
+CMD ["bash"]

.devcontainer/devcontainer.json

@@ -0,0 +1,42 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/cpp
+{
+	"name": "ACCIDDA - acciddasuite",
+	"build": {
+		"dockerfile": "Containerfile"
+	},
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"reditorsupport.r",
+				"rdebugger.r-debugger",
+				"quarto.quarto",
+				"tianyishi.rmarkdown",
+				"github.vscode-github-actions",
+				"ms-vscode.live-server"
+			]
+		}
+	},
+	"mounts": [
+        // Mount the .vscode configuration into the container
+        "source=${localWorkspaceFolder}/.devcontainer/.vscode,target=/workspaces/${localWorkspaceFolderBasename}/.vscode,type=bind,consistency=cached"
+    ],
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	"features": {
+			"ghcr.io/devcontainers/features/github-cli:1": {
+					"version": "2.68.1"
+			}
+	},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "gcc -v",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	"remoteUser": "root"
+}

.github/workflows/copilot-setup-steps.yml

@@ -0,0 +1,42 @@
+name: "Copilot Setup Steps"
+
+# Automatically run the setup steps when they are changed to allow for easy validation, and
+# allow manual testing through the repository's "Actions" tab
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  pull_request:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+
+jobs:
+  # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+
+    # Set the permissions to the lowest permissions possible needed for your steps.
+    # Copilot will be given its own token for its operations.
+    permissions:
+      # If you want to clone the repository as part of your setup steps, for example to install dependencies, you'll need the `contents: read` permission. If you don't clone the repository in your setup steps, Copilot will do this for you automatically after the steps complete.
+      contents: read
+
+    # You can define any steps you want, and they will run before the agent starts.
+    # If you do not check out your code, Copilot will do this for you.
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+          needs: check

.github/workflows/coverage.yaml

@@ -0,0 +1,39 @@
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: Coverage
+
+jobs:
+  coverage:
+    runs-on: ubuntu-latest
+    name: Coverage
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2.9.0
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::covr
+          needs: check
+
+      - name: Running coverage
+        run: |
+          # Files to exclude
+          files <- list.files("inst/", full.names = TRUE, recursive = TRUE)
+
+          # Run coverage
+          covr::codecov(
+            line_exclusions = as.list(files),
+            token = Sys.getenv("CODECOV_TOKEN")
+            )
+        shell: Rscript {0}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/pkgdown.yaml

@@ -10,7 +10,9 @@ on:
 
 name: pkgdown.yaml
 
-permissions: read-all
+permissions:
+  read-all:
+  pull-requests: write
 
 jobs:
   pkgdown:
@@ -40,6 +42,23 @@ jobs:
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
+      # Upload artifact for PR preview (only for pull requests)
+      - name: Upload PR artifact
+        if: github.event_name == 'pull_request'
+        uses: actions/upload-artifact@v4
+        with:
+          name: pkgdown-site
+          path: docs
+
+      # Post comment with link to artifact on PRs
+      - name: Post artifact link to PR
+        if: github.event_name == 'pull_request'
+        uses: CDCgov/cfa-actions/post-artifact@v1.2.0
+        with:
+          artifact-name: pkgdown-site
+          gh-token: ${{ secrets.GITHUB_TOKEN }}
+          message: 'Thank you for your contribution @${{ github.actor }} :rocket:! The pkgdown site preview is ready for review :point_right: [Download here]({ artifact-url }) :point_left:!'
+
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
         uses: JamesIves/github-pages-deploy-action@v4.5.0

.github/workflows/r.yml

@@ -0,0 +1,99 @@
+# 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
+#
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check-final
+
+env:
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          # - {os: macOS-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: windows-latest, r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - 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: quarto-dev/quarto-actions/setup@v2.2.0
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tinytex: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          install-quarto: false
+          install-pandoc: false
+          extra-packages:
+            any::rcmdcheck
+            any::testthat
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        if: ${{ matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release' }}
+        with:
+          args: 'c("--as-cran", "--no-manual")'
+          upload-snapshots: false
+          upload-results: false
+          check-dir: '"check"'
+          error-on: '"warning"'
+
+      - uses: r-lib/actions/check-r-package@v2
+        if: ${{ matrix.config.os != 'windows-latest' && (matrix.config.os != 'ubuntu-latest' || matrix.config.r != 'release') }}
+        with:
+          upload-snapshots: false
+          upload-results: false
+          check-dir: '"check"'
+          error-on: '"warning"'
+
+      - name: Check package (Windows)
+        if: ${{ matrix.config.os == 'windows-latest' }}
+        run: |
+          R.exe CMD build .
+          R.exe CMD check --no-manual (Get-Item acciddasuite_*.tar.gz).Name
+        shell: pwsh
+
+      - name: Build the package
+        if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') }}
+        run: R CMD build .
+
+      - uses: actions/upload-artifact@v4
+        if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') }}
+        with:
+          name: acciddasuite-built-package-${{ matrix.config.os }}-${{ matrix.config.r }}
+          path: acciddasuite_*.tar.gz
+          retention-days: 7
+

.gitignore

@@ -13,3 +13,5 @@ docs
 .Ruserdata
 
 **/*.quarto_ipynb
+.vscode/
+*.html

README.Rmd

@@ -4,6 +4,13 @@ output: github_document
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
+```{=markdown}
+[![R-CMD-check](https://github.com/ACCIDDA/acciddasuite/actions/workflows/r.yml/badge.svg)](https://github.com/ACCIDDA/acciddasuite/actions/workflows/r.yml)
+[![codecov](https://codecov.io/gh/ACCIDDA/acciddasuite/graph/badge.svg?token=ZB8FVLI7GN)](https://app.codecov.io/gh/ACCIDDA/acciddasuite)
+[![status](https://tinyverse.netlify.app/badge/acciddasuite)](https://CRAN.R-project.org/package=acciddasuite)
+```
+<!-- badges: end -->
+
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,

README.md

@@ -1,6 +1,12 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
+[![R-CMD-check](https://github.com/ACCIDDA/acciddasuite/actions/workflows/r.yml/badge.svg)](https://github.com/ACCIDDA/acciddasuite/actions/workflows/r.yml)
+[![codecov](https://codecov.io/gh/ACCIDDA/acciddasuite/graph/badge.svg?token=ZB8FVLI7GN)](https://app.codecov.io/gh/ACCIDDA/acciddasuite)
+[![status](https://tinyverse.netlify.app/badge/acciddasuite)](https://CRAN.R-project.org/package=acciddasuite)
+
+<!-- badges: end -->
+
 # acciddasuite <a href="https://accidda.github.io/acciddasuite/"><img src="man/figures/logo.png" align="right" height="139" alt="acciddasuite website" /></a>
 
 <!-- badges: start -->
@@ -48,6 +54,20 @@ fcast <- example_data |>
   )
 #> ℹ Using max_delay = 12 from data
 #> ℹ Truncating from max_delay = 12 to 4.
+#> Warning: 1 error encountered for ARIMA
+#> [1]
+#> ℹ Some rows containing NA values may be removed. This is fine if not
+#> unexpected.
+#> ℹ Some rows containing NA values may be removed. This is fine if not
+#> unexpected.
+#> Warning: 1 error encountered for ARIMA
+#> [1] 
+#> 
+#> 1 error encountered for ARIMA
+#> [1] 
+#> 
+#> 1 error encountered for ARIMA
+#> [1]
 ```
 
 ``` r