added better using statements

Author: Aoife

assets/scripts/add_notebook_links.sh

@@ -28,16 +28,19 @@ find _site/tutorials _site/usage _site/developers -name "index.html" 2>/dev/null
             relative_path="${html_file#_site/}"
             relative_path="${relative_path%/index.html}"
 
+            # Extract notebook name from parent folder
+            notebook_name=$(basename "$relative_path")
+
             # Construct Colab URL
             if [ -n "$COLAB_PATH_PREFIX" ]; then
                 colab_url="https://colab.research.google.com/github/${COLAB_REPO}/blob/${COLAB_BRANCH}/${COLAB_PATH_PREFIX}/${relative_path}/index.ipynb"
             else
                 colab_url="https://colab.research.google.com/github/${COLAB_REPO}/blob/${COLAB_BRANCH}/${relative_path}/index.ipynb"
             fi
 
-            # Insert both download and Colab links AFTER the "Report an issue" link
-            # The download="index.ipynb" attribute forces browser to download instead of navigate
-            perl -i -pe 's|(<a href="[^"]*issues/new"[^>]*><i class="bi[^"]*"></i>Report an issue</a></li>)|$1<li><a href="index.ipynb" class="toc-action" download="index.ipynb"><i class="bi bi-journal-code"></i>'"$DOWNLOAD_TEXT"'</a></li><li><a href="'"$colab_url"'" class="toc-action" target="_blank" rel="noopener"><i class="bi bi-google"></i>'"$COLAB_TEXT"'</a></li>|g' "$html_file"
+            # Insert both download and Colab links BEFORE the "Edit this page" link
+            # The download attribute forces browser to download with custom filename instead of navigate
+            perl -i -pe 's|(<li><a href="[^"]*edit[^"]*"[^>]*><i class="bi[^"]*"></i>Edit this page</a></li>)|<li><a href="index.ipynb" class="toc-action" download="'"$notebook_name"'.ipynb"><i class="bi bi-journal-code"></i>'"$DOWNLOAD_TEXT"'</a></li><li><a href="'"$colab_url"'" class="toc-action" target="_blank" rel="noopener"><i class="bi bi-google"></i>'"$COLAB_TEXT"'</a></li>$1|g' "$html_file"
             echo "  ✓ Added notebook links to $html_file"
         fi
     fi

assets/scripts/qmd_to_ipynb.py

@@ -16,6 +16,28 @@ def __init__(self, qmd_path: str):
         self.qmd_path = Path(qmd_path)
         self.cells: List[Dict[str, Any]] = []
         self.kernel_name = "julia"  # Default kernel
+        self.packages: set = set()  # Track packages found in using statements
+
+    def _extract_packages_from_line(self, line: str) -> None:
+        """Extract package names from a 'using' statement and add to self.packages."""
+        line = line.strip()
+        if not line.startswith('using '):
+            return
+
+        # Remove 'using ' prefix and any trailing semicolon/whitespace
+        remainder = line[6:].rstrip(';').strip()
+
+        # Handle 'using Package: item1, item2' format - extract just the package name
+        if ':' in remainder:
+            package = remainder.split(':')[0].strip()
+            if package and package != 'Pkg':
+                self.packages.add(package)
+        else:
+            # Handle 'using Package1, Package2, ...' format
+            packages = [pkg.strip() for pkg in remainder.split(',')]
+            for pkg in packages:
+                if pkg and pkg != 'Pkg':
+                    self.packages.add(pkg)
 
     def parse(self) -> None:
         """Parse the .qmd file and extract cells."""
@@ -113,6 +135,11 @@ def _add_markdown_cell(self, lines: List[str]) -> None:
 
     def _add_code_cell(self, lines: List[str], lang: str) -> None:
         """Add a code cell."""
+        # Extract packages from Julia code cells
+        if lang == 'julia':
+            for line in lines:
+                self._extract_packages_from_line(line)
+
         content = '\n'.join(lines)
 
         # For non-Julia code blocks (like dot/graphviz), add as markdown with code formatting
@@ -141,12 +168,19 @@ def to_notebook(self) -> Dict[str, Any]:
         # Add package activation cell at the top for Julia notebooks
         cells = self.cells
         if self.kernel_name.startswith("julia"):
+            # Build the source code for the setup cell
+            pkg_source_lines = ["using Pkg; Pkg.activate(; temp=true)"]
+
+            # Add Pkg.add() calls for each package found in the document
+            for package in sorted(self.packages):
+                pkg_source_lines.append(f'Pkg.add("{package}")')
+
             pkg_cell = {
                 "cell_type": "code",
                 "execution_count": None,
                 "metadata": {},
                 "outputs": [],
-                "source": "using Pkg; Pkg.activate(; temp=true)"
+                "source": "\n".join(pkg_source_lines)
             }
             cells = [pkg_cell] + self.cells