From 709db064ebeb365e3ff01e4b3e6784ee394913ad Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 8 Sep 2025 09:13:19 +0000
Subject: [PATCH 1/4] Initial plan


From 693bb6f46d46aedb62022fee8c99a6fd381910b0 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 8 Sep 2025 09:47:47 +0000
Subject: [PATCH 2/4] Update copilot instructions with validated build and
 configuration details

Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>
---
 .github/copilot-instructions.md | 70 ++++++++++++++++++++++++++++-----
 1 file changed, 61 insertions(+), 9 deletions(-)

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index fd2379980..ba3869a58 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -94,6 +94,15 @@ TreeTools contains core functionality for tree and split manipulation, designed
   R -e "devtools::build_vignettes(install = FALSE)"
   ```
 
+### Key Dependencies
+**Critical**: TreeDist requires these packages to build successfully:
+- `ape` (>= 5.0) - Phylogenetic analysis package
+- `TreeTools` (>= 1.16) - Core tree manipulation (large dependency, 10+ min install)
+- `Rdpack` (>= 0.7) - Bibliography and citation support  
+- `shinyjs` - Interactive web applications
+- `colorspace` - Color space manipulation
+- `Rcpp` (>= 1.0.8) - C++ integration (must install before TreeTools)
+
 ## Validation
 
 **CRITICAL: Always run the full test suite before proposing changes**
@@ -112,10 +121,34 @@ TreeTools contains core functionality for tree and split manipulation, designed
   ```bash
   R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < memcheck/tests.R
   ```
+  **Note**: Memory check scripts available in `memcheck/` directory:
+  - `memcheck/tests.R` - Run test suite with valgrind
+  - `memcheck/all.R` - Run tests, examples, and build vignettes with memory checking
 
 ## Validation Scenarios
 After making code changes, validate functionality by testing core phylogenetic tree operations:
 
+### Essential Pre-commit Validation Steps
+1. **Install core dependencies first**:
+   ```bash
+   sudo R -e "install.packages(c('ape', 'colorspace', 'Rdpack', 'shinyjs', 'TreeTools'), repos='https://cran.r-project.org/', dependencies=TRUE)"
+   ```
+
+2. **Basic build test** (quick validation):
+   ```bash
+   R CMD build . --no-build-vignettes
+   ```
+
+3. **Run linting** (expects GitHub Actions format):
+   ```bash
+   R -e "lintr::lint_dir('.')"
+   ```
+
+4. **Load package for testing**:
+   ```bash
+   R -e "devtools::load_all()"
+   ```
+
 
 ## Time Expectations & Critical Warnings
 - **R startup**: ~0.1 seconds
@@ -130,9 +163,9 @@ After making code changes, validate functionality by testing core phylogenetic t
 
 ## Repository Structure
 ### Key Directories
-- `R/` - R source code (59 R files with 500+ exported functions)
-- `src/` - C++ source code requiring compilation (17 C++ files, SystemRequirements: C++17)
-- `tests/testthat/` - Test suite (61+ test files)
+- `R/` - R source code (31 R files with 500+ exported functions)
+- `src/` - C++ source code requiring compilation (14 C++ files, SystemRequirements: C++17)
+- `tests/testthat/` - Test suite (30+ test files)
 - `benchmark/` - Performance benchmarking (10+ benchmark files)  
 - `man/` - Generated documentation (do not edit manually)
 - `vignettes/` - Package tutorials and documentation
@@ -142,9 +175,9 @@ After making code changes, validate functionality by testing core phylogenetic t
 ### Important Files
 - `DESCRIPTION` - Package metadata, dependencies, and system requirements
 - `NAMESPACE` - Generated by roxygen2 (do not edit manually)
-- `.lintr` - Code style configuration (follows Google R style guide)
 - `NEWS.md` - Version history (update for user-facing changes)
 - `tests/testthat.R` - Test runner entry point
+- **Note**: No `.lintr` file exists - linting uses default configuration with GitHub Actions output format
 
 ## Common Tasks
 ### After Making Changes
@@ -179,9 +212,28 @@ After making code changes, validate functionality by testing core phylogenetic t
 - Missing or inadequate documentation
 - Missing test coverage for new code
 
+### CI/CD Workflows Available
+- **R-CMD-check.yml**: Comprehensive checks on Windows, macOS, Ubuntu across R versions
+- **benchmark.yml**: Performance regression testing triggered on PRs
+- **memcheck.yml**: Memory checking with valgrind (runs `tests`, `examples`, `vignettes`)
+- **ASan.yml**: Address sanitizer checks
+- **RcppDeepState.yml**: Deep testing of C++ code
+- **pkgdown.yml**: Documentation site generation
+- **revdepcheck.yml**: Downstream dependency validation
+
 ## Troubleshooting
-- If package won't build: check that all system dependencies are installed
-- If tests fail after C++ changes: rebuild package completely
-- If documentation is missing: run `devtools::document()`
-- If benchmarks fail: performance regressions may need investigation
-- Memory issues: use valgrind checking for C++ code validation
+### Common Build Issues
+- **Missing dependencies**: Install system packages first: `sudo apt install -y libcurl4-openssl-dev libssl-dev libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev`
+- **Rdpack warnings**: These are normal when `Rdpack` isn't installed but don't prevent building
+- **Package won't build**: Install core dependencies: `ape`, `colorspace`, `Rdpack`, `shinyjs`, `TreeTools`
+- **TreeTools installation fails**: This is a large dependency - allow 10+ minutes for compilation
+- **Tests fail after C++ changes**: rebuild package completely with `R CMD build .`
+- **Documentation warnings**: Run `devtools::document()` to regenerate documentation
+- **Benchmarks fail**: Performance regressions may need investigation
+- **Memory issues**: Use valgrind checking for C++ code validation
+
+### System Requirements Validation
+- R version 4.0+ required (tested with R 4.3.3)
+- C++17 compiler support required
+- Minimum 2GB RAM recommended for building with dependencies
+- Allow 60+ minutes for full dependency installation from scratch

From 97835dc4ac9fc1bb31e5b1b9f7d2fb368d679c07 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 8 Sep 2025 10:54:51 +0100
Subject: [PATCH 3/4] Create .lintr

---
 .lintr | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 .lintr

diff --git a/.lintr b/.lintr
new file mode 100644
index 000000000..d6f9bf143
--- /dev/null
+++ b/.lintr
@@ -0,0 +1,3 @@
+linters: linters_with_defaults(
+    object_name_linter(styles = c("CamelCase", "camelCase", "snake_case", "dotted.case"))
+  )

From f095db57ee911a682e48ab192eaffb51844f29d0 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 8 Sep 2025 10:57:40 +0100
Subject: [PATCH 4/4] Update copilot-instructions.md

---
 .github/copilot-instructions.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index ba3869a58..6d4ce5004 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -97,11 +97,11 @@ TreeTools contains core functionality for tree and split manipulation, designed
 ### Key Dependencies
 **Critical**: TreeDist requires these packages to build successfully:
 - `ape` (>= 5.0) - Phylogenetic analysis package
-- `TreeTools` (>= 1.16) - Core tree manipulation (large dependency, 10+ min install)
+- `Rcpp` (>= 1.0.8) - C++ integration (must install before TreeTools)
+- `TreeTools` (>= 1.16) - Core tree manipulation (large dependency)
 - `Rdpack` (>= 0.7) - Bibliography and citation support  
 - `shinyjs` - Interactive web applications
 - `colorspace` - Color space manipulation
-- `Rcpp` (>= 1.0.8) - C++ integration (must install before TreeTools)
 
 ## Validation
 
@@ -177,7 +177,8 @@ After making code changes, validate functionality by testing core phylogenetic t
 - `NAMESPACE` - Generated by roxygen2 (do not edit manually)
 - `NEWS.md` - Version history (update for user-facing changes)
 - `tests/testthat.R` - Test runner entry point
-- **Note**: No `.lintr` file exists - linting uses default configuration with GitHub Actions output format
+- `inst/_pkgdown.yml` - template for online documentation.
+    (Check that new functions are registered here, ideally using `@family`)
 
 ## Common Tasks
 ### After Making Changes
@@ -217,8 +218,7 @@ After making code changes, validate functionality by testing core phylogenetic t
 - **benchmark.yml**: Performance regression testing triggered on PRs
 - **memcheck.yml**: Memory checking with valgrind (runs `tests`, `examples`, `vignettes`)
 - **ASan.yml**: Address sanitizer checks
-- **RcppDeepState.yml**: Deep testing of C++ code
-- **pkgdown.yml**: Documentation site generation
+- **pkgdown.yml**: Documentation site generation.
 - **revdepcheck.yml**: Downstream dependency validation
 
 ## Troubleshooting