Fix runtime errors and improve robustness in host configs and scripts

- Fix KeyError in julia.nix when Project.toml lacks deps table
- Fix incorrect uv args in python.nix (remove --run + --add-flags combination)
- Remove redundant 'uv add ipython' from sync branch in python.nix
- Fix relative paths in project-scripts.nix (./scripts -> ../scripts)
- Fix initProject.sh to check file existence before git add
- Add RVER validation in updateDeps.sh with proper error handling
- Add tool availability checks in updateDeps.sh (uv, julia, devenv)
- Add flake.nix backup before modification in updateDeps.sh
- Ensure updateDeps.sh runs from repository root

Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>

templates/rde/scripts/initProject.sh

@@ -44,15 +44,24 @@ fi
 # Initialize git
 if [[ ! -d ".git" ]]; then
   git init
-  echo "✓ Initialized Git repository and added: flake.nix, flake.lock"
+  echo "✓ Initialized Git repository"
 fi
-# Check if files are already staged/tracked before adding
-if ! git diff --cached --name-only | grep -q "flake.nix\|flake.lock" &&
-   ! git ls-files --error-unmatch flake.nix flake.lock >/dev/null 2>&1; then
-  echo "✓ Adding flake.nix, flake.lock to Git repository"
-  git add flake.nix flake.lock
-else
-  echo "✓ flake.nix, flake.lock already tracked/staged in Git"
+
+# Check if files exist and are not already staged/tracked before adding
+if [[ -f "flake.nix" ]] && ! git diff --cached --name-only 2>/dev/null | grep -q "flake.nix" &&
+   ! git ls-files --error-unmatch flake.nix >/dev/null 2>&1; then
+  echo "✓ Adding flake.nix to Git repository"
+  git add flake.nix
+elif [[ -f "flake.nix" ]]; then
+  echo "✓ flake.nix already tracked/staged in Git"
+fi
+
+if [[ -f "flake.lock" ]] && ! git diff --cached --name-only 2>/dev/null | grep -q "flake.lock" &&
+   ! git ls-files --error-unmatch flake.lock >/dev/null 2>&1; then
+  echo "✓ Adding flake.lock to Git repository"
+  git add flake.lock
+elif [[ -f "flake.lock" ]]; then
+  echo "✓ flake.lock already tracked/staged in Git"
 fi
 # Create .gitignore
 if [[ ! -f ".gitignore" ]]; then

templates/rde/scripts/updateDeps.sh

@@ -3,30 +3,77 @@ set -euo pipefail
 
 echo "🔄 Updating project dependencies..."
 
+# Ensure we're in the repository root
+if [[ ! -f "flake.nix" ]]; then
+  # Try to find git root
+  if git rev-parse --show-toplevel >/dev/null 2>&1; then
+    cd "$(git rev-parse --show-toplevel)"
+    if [[ ! -f "flake.nix" ]]; then
+      echo "❌ Error: flake.nix not found in repository root"
+      exit 1
+    fi
+  else
+    echo "❌ Error: Not in a git repository and flake.nix not found"
+    exit 1
+  fi
+fi
+
 # Fetch latest R version from rstats-on-nix
 # This command chain: downloads CSV, extracts last line, gets 4th field (date), removes quotes
-RVER=$( wget -qO- 'https://raw.githubusercontent.com/ropensci/rix/refs/heads/main/inst/extdata/available_df.csv' | tail -n 1 | head -n 1 | cut -d',' -f4 | tr -d '"' ) &&\
+echo "📡 Fetching latest R version from rstats-on-nix..."
+RVER=$( wget -qO- 'https://raw.githubusercontent.com/ropensci/rix/refs/heads/main/inst/extdata/available_df.csv' | tail -n 1 | head -n 1 | cut -d',' -f4 | tr -d '"' )
+
+# Validate RVER matches YYYY-MM-DD format
+if [[ ! "$RVER" =~ ^[0-9]{4}-[0-9]{2}-[0-9]{2}$ ]]; then
+  echo "❌ Error: Failed to fetch valid R version date. Got: '$RVER'"
+  exit 1
+fi
+
+echo "✅ R date is $RVER"
+
+# Create backup of flake.nix before modifying
+cp flake.nix flake.nix.backup
 
 # Update rixpkgs date in flake.nix
-sed -i  "s|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}\";|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/$RVER\";|" flake.nix
-echo "✅ R date is $RVER"
+if sed -i "s|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}\";|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/$RVER\";|" flake.nix; then
+  echo "✅ Updated rixpkgs date in flake.nix"
+  rm flake.nix.backup
+else
+  echo "⚠️  Warning: Failed to update flake.nix, restoring backup"
+  mv flake.nix.backup flake.nix
+fi
 
 nix flake update
 echo "✅ Flake inputs updated"
 
+# Update Python dependencies if pyproject.toml exists and uv is available
 if [[ -f "pyproject.toml" ]]; then
-  uv sync --upgrade
-  echo "✅ Python dependencies updated"
+  if command -v uv >/dev/null 2>&1; then
+    uv sync --upgrade
+    echo "✅ Python dependencies updated"
+  else
+    echo "ℹ️  pyproject.toml found but uv command not available, skipping Python update"
+  fi
 fi
 
+# Update Julia dependencies if Project.toml exists and julia is available
 if [[ -f "Project.toml" ]]; then
-  @defaultPackageName@-jl -e "using Pkg; Pkg.update()"
-  echo "✅ Julia dependencies updated"
+  if command -v @defaultPackageName@-jl >/dev/null 2>&1; then
+    @defaultPackageName@-jl -e "using Pkg; Pkg.update()"
+    echo "✅ Julia dependencies updated"
+  else
+    echo "ℹ️  Project.toml found but @defaultPackageName@-jl command not available, skipping Julia update"
+  fi
 fi
 
+# Update devenv dependencies if devenv.nix exists and devenv is available
 if [[ -f "devenv.nix" ]]; then
-  devenv update
-  echo "✅ Devenv dependencies updated"
+  if command -v devenv >/dev/null 2>&1; then
+    devenv update
+    echo "✅ Devenv dependencies updated"
+  else
+    echo "ℹ️  devenv.nix found but devenv command not available, skipping devenv update"
+  fi
 fi
 
 echo "🎉 All dependencies updated!"