Copilot instructions

.github/actions/r-check-env/action.yaml

@@ -0,0 +1,32 @@
+name: "Setup R check environment"
+description: "Common R environment (Pandoc, system libs, R, renv) for R CMD check and Copilot"
+
+runs:
+  using: "composite"
+  steps:
+    - name: Setup Pandoc
+      uses: r-lib/actions/setup-pandoc@v2
+
+    - name: Install system libraries (Linux only)
+      if: runner.os == 'Linux'
+      shell: bash
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y \
+          cmake \
+          libcurl4-openssl-dev \
+          libgit2-dev libssh2-1-dev libssl-dev \
+          libfontconfig1-dev libfreetype6-dev libharfbuzz-dev libfribidi-dev \
+          libpng-dev libtiff5-dev libjpeg-dev libcairo2-dev \
+          libx11-dev \
+          libxml2-dev
+
+    - name: Setup R
+      uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: renv          # pick R version from renv.lock
+        Ncpus: 6
+        use-public-rspm: true    # faster Linux binaries
+
+    - name: Setup renv
+      uses: r-lib/actions/setup-renv@v2

.github/copilot-instructions.md

@@ -0,0 +1,41 @@
+# Copilot Instructions
+
+## Goal
+Maintain passing CI (lint, unit tests, R CMD check).
+Automatically fix failing tests and re-run until green.
+
+## Stack
+R (≥4.2.2), Shiny, renv, testthat (edition 3), lintr, GitHub Actions.
+
+## Code and Naming Conventions
+- Use native pipe |>, line length ≤80 and indent of 4 spaces.
+- Ideally, the body of a function/module fits within 50 lines and
+  should rarely exceed 100 lines. If it does, consider refactoring.
+- Document all functions with roxygen2 headers. The header should end
+  with an @noRd tag unless they are @export ed.
+- Maintain file naming consistent with existing structure.
+
+## Test Practices
+- Add tests for new logic immediately.
+- Name tests: tests/testthat/test_<source>.R
+- Individual files can be tested via devtools::test(filter = <source>.R).
+- Use mockery for external deps.
+- If a test fails: inspect, patch code or tests, and
+  re-run devtools::test(filter = <source>.R).
+
+#### Full check (= “green CI pipeline”)
+
+When working on an issue, *before* creating a Pull Request,
+you MUST follow these steps:
+
+1) `lintr::lint_package()` — fix all lints.
+2) `devtools::test()` — fix failing tests.
+3) `rcmdcheck::rcmdcheck(args='--no-manual', error_on='warning')` — fix all errors/warnings.
+
+Target in step 3: **0 errors / 0 warnings** (notes preferably 0).
+
+If you are unable to fix all issues within **45 minutes**,
+commit your latest changes, then stop, and do *not* open a PR.
+
+## Commit Messages
+Conventional commits (feat:, fix:, test:, refactor:, docs:).

.github/workflows/ci.yaml

@@ -28,10 +28,12 @@ jobs:
           r-version: renv          # pick R version from renv.lock
           Ncpus: 6
           use-public-rspm: true
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::lintr
           needs: lintr
+
       - name: Lint
         shell: Rscript {0}
         run: |
@@ -62,37 +64,13 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
+
     steps:
       - uses: actions/checkout@v4
         with:
           lfs: true
 
-      # Pandoc for rmarkdown/knitr/pkgdown/vignettes
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Install system libraries
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y \
-            cmake \
-            libcurl4-openssl-dev \
-            libgit2-dev libssh2-1-dev libssl-dev \
-            libfontconfig1-dev libfreetype6-dev libharfbuzz-dev libfribidi-dev \
-            libpng-dev libtiff5-dev libjpeg-dev libcairo2-dev \
-            libx11-dev \
-            libxml2-dev
-
-      - name: Setup R
-        uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: renv          # pick R version from renv.lock
-          Ncpus: 6
-          use-public-rspm: true    # faster Linux binaries
-          # working-directory: .   # set if renv.lock is not at repo root
-
-      - name: Setup renv
-        uses: r-lib/actions/setup-renv@v2
+      - uses: ./.github/actions/r-check-env
 
       - name: R CMD check with renv-pinned deps
         shell: Rscript {0}
@@ -106,7 +84,6 @@ jobs:
           TESTTHAT_CPUS: 6
           _R_CHECK_LIMIT_CORES_: FALSE   # allow more than 2 cores
 
-
       - name: R CMD check against current CRAN
         uses: r-lib/actions/check-r-package@v2
         with:

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

@@ -0,0 +1,26 @@
+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. In addition, the setup steps
+# are run each time before Copilot starts working independently from below filters.
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  pull_request:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+
+
+jobs:
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - uses: ./.github/actions/r-check-env