rxiv-maker 1.16.5__tar.gz → 1.16.7__tar.gz

{rxiv_maker-1.16.5 → rxiv_maker-1.16.7}/.gitignore

@@ -52,7 +52,6 @@ output.txt
 *~
 
 # Claude Code configuration
-CLAUDE.md
 .claude
 
 # Byte-compiled / optimized / DLL files
@@ -316,6 +315,7 @@ GEMINI.md
 !CHANGELOG.md
 !CONTRIBUTING.md
 !CODE_OF_CONDUCT.md
+!CLAUDE.md
 !docs/**/*.md
 !EXAMPLE_MANUSCRIPT/**/*.md
 !MANUSCRIPT/**/*.md
@@ -330,7 +330,6 @@ GEMINI.md
 todo*.md
 DOCKER_ACCELERATION.md
 GEMINI.md
-CLAUDE.md
 output.md
 
 # Temporary analysis files
@@ -394,4 +393,4 @@ rxivdraft/MANUSCRIPT/2025__antónio_d_brito_et_al__rxiv.pdf
 .gemini/
 .gemini-clipboard/
 gha-creds-*.json
-fatetracking/MANUSCRIPT/.rxiv_cache
+fatetracking/MANUSCRIPT/.rxiv_cache

{rxiv_maker-1.16.5 → rxiv_maker-1.16.7}/CHANGELOG.md

@@ -7,6 +7,37 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.16.7] - 2025-12-18
+
+### Changed
+
+- **Upgrade Workflow Centralization**: Migrated to henriqueslab-updater v1.2.0 for centralized upgrade management
+  - Simplified upgrade command implementation from 165 to 53 lines (68% reduction)
+  - Created custom `RxivUpgradeNotifier` implementing `UpgradeNotifier` protocol
+  - Integrated with existing changelog parser for rich change summaries with breaking change highlighting
+  - Maintains backward compatibility with all existing flags (`--yes`, `--check-only`)
+  - Reduces code duplication across HenriquesLab CLI tools
+  - Provides consistent upgrade UX across all HenriquesLab projects
+
+## [1.16.6] - 2025-12-17
+
+### Fixed
+
+- **Check Installation Guidance**: Improved fresh install experience
+  - Updated `rxiv check-installation` next steps to guide users on downloading example manuscript
+  - Replaced assumption of existing manuscript with `rxiv get-rxiv-preprint` guidance
+  - Enhanced user onboarding for first-time users
+
+- **Mermaid Diagram Error Messages**: Enhanced error reporting for figure generation
+  - Distinguished between timeout, HTTP errors (400/503/429), and network failures
+  - Shows specific error reasons: "syntax error or diagram too complex" for 400, "service timeout" for 503
+  - Improved diagnostic information for troubleshooting diagram rendering issues
+
+- **Heading Validation False Positives**: Fixed validator treating Python comments as markdown headings
+  - Modified `_validate_headings()` to exclude `{{py:exec}}` code blocks from heading analysis
+  - Prevents false positives where Python `# comments` were flagged as H1 markdown headings
+  - Applies existing content protection mechanism to heading validation
+
 ## [1.16.5] - 2025-12-15
 
 ### Fixed

{rxiv_maker-1.16.5 → rxiv_maker-1.16.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.16.5
+Version: 1.16.7
 Summary: Write scientific preprints in Markdown. Generate publication-ready PDFs efficiently.
 Project-URL: Homepage, https://github.com/HenriquesLab/rxiv-maker
 Project-URL: Documentation, https://github.com/HenriquesLab/rxiv-maker#readme
@@ -27,7 +27,7 @@ Requires-Python: >=3.10
 Requires-Dist: click>=8.0.0
 Requires-Dist: crossref-commons>=0.0.7
 Requires-Dist: gitpython>=3.1.0
-Requires-Dist: henriqueslab-updater>=1.1.3
+Requires-Dist: henriqueslab-updater>=1.2.0
 Requires-Dist: latex2mathml>=3.78.0
 Requires-Dist: matplotlib>=3.7.0
 Requires-Dist: numpy>=1.24.0
@@ -358,9 +358,14 @@ rxiv config --non-interactive  # Show current settings
 
 ### Maintenance
 ```bash
-rxiv upgrade               # Upgrade to latest version
-rxiv changelog             # View changelog and release notes
-rxiv changelog --recent 5  # View last 5 versions
+# Upgrade commands (auto-detects Homebrew, pip, uv, pipx)
+rxiv upgrade                 # Interactive upgrade with confirmation
+rxiv upgrade --yes           # Upgrade without confirmation
+rxiv upgrade --check-only    # Check for updates only
+
+# Changelog and version information
+rxiv changelog               # View changelog and release notes
+rxiv changelog --recent 5    # View last 5 versions
 ```
 
 > **💡 CI/Automation Note:** All interactive commands support non-interactive mode or configuration files for use in CI/CD pipelines and automated workflows. Use `--non-interactive` flag or configure via `~/.rxiv-maker/config` for non-TTY environments.

{rxiv_maker-1.16.5 → rxiv_maker-1.16.7}/README.md

@@ -281,9 +281,14 @@ rxiv config --non-interactive  # Show current settings
 
 ### Maintenance
 ```bash
-rxiv upgrade               # Upgrade to latest version
-rxiv changelog             # View changelog and release notes
-rxiv changelog --recent 5  # View last 5 versions
+# Upgrade commands (auto-detects Homebrew, pip, uv, pipx)
+rxiv upgrade                 # Interactive upgrade with confirmation
+rxiv upgrade --yes           # Upgrade without confirmation
+rxiv upgrade --check-only    # Check for updates only
+
+# Changelog and version information
+rxiv changelog               # View changelog and release notes
+rxiv changelog --recent 5    # View last 5 versions
 ```
 
 > **💡 CI/Automation Note:** All interactive commands support non-interactive mode or configuration files for use in CI/CD pipelines and automated workflows. Use `--non-interactive` flag or configure via `~/.rxiv-maker/config` for non-TTY environments.

{rxiv_maker-1.16.5 → rxiv_maker-1.16.7}/pyproject.toml

@@ -53,7 +53,7 @@ dependencies = [
     "GitPython>=3.1.0",
     "prompt_toolkit>=3.0.0",
     # Update checking
-    "henriqueslab-updater>=1.1.3",
+    "henriqueslab-updater>=1.2.0",
 ]
 
 [project.urls]

rxiv_maker-1.16.7/src/docs/api/README.md

@@ -0,0 +1,4 @@
+# API Documentation
+
+Welcome to the API documentation for rxiv-maker.
+

rxiv_maker-1.16.7/src/docs/api/index.md

@@ -0,0 +1,4 @@
+# API Documentation
+
+Welcome to the API documentation for rxiv-maker.
+

{rxiv_maker-1.16.5 → rxiv_maker-1.16.7}/src/rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.16.5"
+__version__ = "1.16.7"

rxiv_maker-1.16.7/src/rxiv_maker/cli/commands/upgrade.py

@@ -0,0 +1,52 @@
+"""Upgrade command for rxiv-maker CLI."""
+
+import sys
+
+import click
+from henriqueslab_updater import handle_upgrade_workflow
+from rich.console import Console
+
+from ... import __version__
+from ...utils.install_detector import detect_install_method
+from ...utils.rich_upgrade_notifier import RxivUpgradeNotifier
+
+console = Console()
+
+
+@click.command()
+@click.option("--yes", "-y", is_flag=True, help="Skip confirmation prompt")
+@click.option("--check-only", "-c", is_flag=True, help="Only check for updates, don't upgrade")
+@click.pass_context
+def upgrade(ctx: click.Context, yes: bool, check_only: bool) -> None:
+    """Upgrade rxiv-maker to the latest version.
+
+    This command automatically detects how rxiv-maker was installed
+    (Homebrew, pip, uv, pipx, etc.) and runs the appropriate upgrade command.
+
+    Examples:
+        rxiv upgrade              # Check and upgrade with confirmation
+        rxiv upgrade --yes        # Upgrade without confirmation
+        rxiv upgrade --check-only # Only check for updates
+    """
+    # Handle development installations specially
+    install_method = detect_install_method()
+    if install_method == "dev":
+        console.print("⚠️  Development installation detected", style="yellow")
+        console.print("   To update, pull the latest changes from git:", style="yellow")
+        console.print("   [cyan]cd <repo> && git pull && uv sync[/cyan]", style="yellow")
+        sys.exit(0)
+
+    # Use centralized upgrade workflow
+    notifier = RxivUpgradeNotifier(console)
+    success, error = handle_upgrade_workflow(
+        package_name="rxiv-maker",
+        current_version=__version__,
+        check_only=check_only,
+        skip_confirmation=yes,
+        notifier=notifier,
+        github_org="HenriquesLab",
+        github_repo="rxiv-maker",
+    )
+
+    if not success and error:
+        sys.exit(1)

{rxiv_maker-1.16.5 → rxiv_maker-1.16.7}/src/rxiv_maker/cli/framework/utility_commands.py

@@ -187,13 +187,16 @@ class CheckInstallationCommand(BaseCommand):
         """Show next steps after dependency check."""
         if not missing_results:
             self.console.print("\n🚀 Next steps:", style="blue")
-            self.console.print("  • Test PDF generation: rxiv pdf ../manuscript-rxiv-maker/MANUSCRIPT")
+            self.console.print("  • Get example manuscript: rxiv get-rxiv-preprint")
+            self.console.print("  • Navigate to manuscript: cd manuscript-rxiv-maker/MANUSCRIPT")
+            self.console.print("  • Generate PDF: rxiv pdf")
             return
 
         self.console.print("\n🔧 Next steps:", style="blue")
         self.console.print("  • Install missing dependencies shown above")
         self.console.print("  • Re-run: rxiv check-installation")
-        self.console.print("  • Test PDF generation: rxiv pdf ../manuscript-rxiv-maker/MANUSCRIPT")
+        self.console.print("  • Get example manuscript: rxiv get-rxiv-preprint")
+        self.console.print("  • Generate PDF: cd manuscript-rxiv-maker/MANUSCRIPT && rxiv pdf")
 
     def _show_basic_results(self, results: dict) -> None:
         """Show basic installation results."""

{rxiv_maker-1.16.5 → rxiv_maker-1.16.7}/src/rxiv_maker/engines/operations/generate_figures.py

@@ -250,31 +250,95 @@ class FigureGenerator:
                         response = get_with_retry(mermaid_url, max_attempts=5, timeout=30)
                     else:
                         response = requests.get(mermaid_url, timeout=30)
-                except Exception:
-                    # If retry fails, fall back to placeholder
-                    return self._create_fallback_mermaid_diagram(input_file, output_file)
+                except requests.Timeout:
+                    # Timeout - likely diagram too complex or service slow
+                    return self._create_fallback_mermaid_diagram(
+                        input_file, output_file, reason="timeout", details="30s timeout exceeded"
+                    )
+                except requests.HTTPError as e:
+                    # HTTP error (400, 503, etc.) - extract status code
+                    status_code = e.response.status_code if hasattr(e, "response") else "unknown"
+                    if status_code == 400:
+                        details = "syntax error or diagram too complex"
+                    elif status_code == 503:
+                        details = "service timeout (diagram too complex)"
+                    else:
+                        details = f"HTTP {status_code}"
+                    return self._create_fallback_mermaid_diagram(
+                        input_file, output_file, reason="http_error", details=details
+                    )
+                except Exception as e:
+                    # Network or other error during request
+                    error_msg = str(e)
+                    # Try to extract status code from error message if it's there
+                    if "400" in error_msg:
+                        details = "syntax error or diagram too complex"
+                    elif "503" in error_msg:
+                        details = "service timeout (diagram too complex)"
+                    elif "429" in error_msg:
+                        details = "rate limit exceeded"
+                    else:
+                        details = "connection error"
+                    return self._create_fallback_mermaid_diagram(
+                        input_file, output_file, reason="network_error", details=details
+                    )
 
                 if response.status_code == 200:
                     with open(output_file, "wb") as f:
                         f.write(response.content)
                     return True
                 else:
-                    print(f"mermaid.ink service returned status {response.status_code}")
-                    print(
-                        "💡 Tip: If this is a syntax error, check your Mermaid diagram at https://www.mermaidchart.com/"
+                    # Determine failure reason from status code
+                    if response.status_code == 400:
+                        reason_msg = "syntax error or diagram too complex"
+                    elif response.status_code == 429:
+                        reason_msg = "rate limit exceeded"
+                    elif response.status_code == 503:
+                        reason_msg = "service timeout (diagram too complex)"
+                    elif response.status_code >= 500:
+                        reason_msg = "service unavailable"
+                    else:
+                        reason_msg = f"HTTP {response.status_code}"
+
+                    return self._create_fallback_mermaid_diagram(
+                        input_file, output_file, reason="http_error", details=reason_msg
                     )
-                    return self._create_fallback_mermaid_diagram(input_file, output_file)
             else:
-                print("requests library not available for Mermaid generation")
-                return self._create_fallback_mermaid_diagram(input_file, output_file)
+                return self._create_fallback_mermaid_diagram(
+                    input_file, output_file, reason="no_requests_lib", details="requests library not available"
+                )
 
         except Exception as e:
-            print(f"mermaid.ink service error: {e}")
-            print("💡 Tip: Check your Mermaid diagram syntax at https://www.mermaidchart.com/")
-            return self._create_fallback_mermaid_diagram(input_file, output_file)
+            return self._create_fallback_mermaid_diagram(
+                input_file, output_file, reason="unexpected_error", details=str(e)
+            )
+
+    def _create_fallback_mermaid_diagram(
+        self, input_file: Path, output_file: Path, reason: str = "unknown", details: str = "service unavailable"
+    ) -> bool:
+        """Create a fallback placeholder diagram when Mermaid service is unavailable.
+
+        Args:
+            input_file: Source mermaid file
+            output_file: Output file path
+            reason: Failure reason category (timeout, http_error, network_error, etc.)
+            details: Detailed error message
+
+        Returns:
+            True if placeholder was created successfully
+        """
+        # Generate user-friendly warning message based on failure reason
+        if reason == "timeout":
+            warning_msg = f"diagram rendering timed out ({details})"
+        elif reason == "http_error":
+            warning_msg = f"{details}"
+        elif reason == "network_error":
+            warning_msg = f"network error: {details}"
+        elif reason == "no_requests_lib":
+            warning_msg = "requests library not available"
+        else:
+            warning_msg = f"{details}"
 
-    def _create_fallback_mermaid_diagram(self, input_file: Path, output_file: Path) -> bool:
-        """Create a fallback placeholder diagram when Mermaid service is unavailable."""
         try:
             if self.output_format.lower() == "svg":
                 # Create SVG placeholder
@@ -294,6 +358,7 @@ class FigureGenerator:
 </svg>"""
                 with open(output_file, "w", encoding="utf-8") as f:
                     f.write(svg_content)
+                print(f"⚠️  Created placeholder SVG for {input_file.name} ({warning_msg})")
                 return True
             elif self.output_format.lower() == "png":
                 # Create minimal PNG placeholder (1x1 white pixel)
@@ -303,7 +368,7 @@ class FigureGenerator:
                 )
                 with open(output_file, "wb") as f:
                     f.write(png_data)
-                print(f"⚠️  Created placeholder PNG for {input_file.name} (mermaid.ink unavailable)")
+                print(f"⚠️  Created placeholder PNG for {input_file.name} ({warning_msg})")
                 return True
             elif self.output_format.lower() == "pdf":
                 # Create minimal PDF placeholder
@@ -374,20 +439,83 @@ startxref
 """
                 with open(output_file, "w", encoding="utf-8") as f:
                     f.write(pdf_content)
-                print(f"⚠️  Created placeholder PDF for {input_file.name} (mermaid.ink unavailable)")
+                print(f"⚠️  Created placeholder PDF for {input_file.name} ({warning_msg})")
                 return True
             else:
                 # Fallback for other formats - create text file with warning
                 with open(output_file.with_suffix(".txt"), "w", encoding="utf-8") as f:
                     f.write(f"Mermaid diagram placeholder for {input_file.name}\n")
-                    f.write("mermaid.ink service unavailable - diagram generation failed\n")
+                    f.write(f"Reason: {warning_msg}\n")
                     f.write("\n💡 Tip: Check your Mermaid diagram syntax at https://www.mermaidchart.com/\n")
-                print(f"⚠️  Created text placeholder for {input_file.name} (mermaid.ink unavailable)")
+                print(f"⚠️  Created text placeholder for {input_file.name} ({warning_msg})")
                 return True
         except Exception as e:
             print(f"Failed to create fallback diagram: {e}")
             return False
 
+    def validate_mermaid_diagram(self, mmd_file: Path) -> tuple[bool, str, dict]:
+        """Validate a Mermaid diagram for mermaid.ink compatibility.
+
+        Args:
+            mmd_file: Path to .mmd file
+
+        Returns:
+            Tuple of (is_valid, message, details_dict)
+            - is_valid: True if diagram will render successfully
+            - message: Human-readable validation result
+            - details_dict: Dict with complexity metrics and suggestions
+        """
+        if not requests:
+            return False, "requests library not available for validation", {}
+
+        try:
+            # Read and analyze the diagram
+            with open(mmd_file, "r", encoding="utf-8") as f:
+                content = f.read().strip()
+
+            # Analyze complexity
+            details = {
+                "file_size": len(content),
+                "line_count": content.count("\n") + 1,
+                "subgraph_count": content.count("subgraph"),
+                "node_count": len(re.findall(r"\w+\[", content)),
+                "class_def_count": content.count("classDef"),
+            }
+
+            # Check for known problematic patterns
+            warnings = []
+            if details["file_size"] > 2500:
+                warnings.append(f"Large diagram ({details['file_size']} chars, limit ~2500)")
+            if details["subgraph_count"] > 5:
+                warnings.append(f"Many subgraphs ({details['subgraph_count']}, limit ~5)")
+            if details["class_def_count"] > 6:
+                warnings.append(f"Heavy styling ({details['class_def_count']} classes, limit ~6)")
+
+            # Test with mermaid.ink
+            encoded = base64.b64encode(content.encode("utf-8")).decode("ascii")
+            test_url = f"https://mermaid.ink/svg/{encoded}"  # Use SVG for faster testing
+
+            try:
+                response = requests.get(test_url, timeout=10)
+                if response.status_code == 200:
+                    if warnings:
+                        msg = f"✓ Valid (but complex: {', '.join(warnings)})"
+                        return True, msg, details
+                    return True, "✓ Valid and will render successfully", details
+                elif response.status_code == 400:
+                    return False, "✗ Syntax error or too complex for mermaid.ink", details
+                elif response.status_code == 503:
+                    return False, "✗ Diagram too complex (service timeout)", details
+                else:
+                    return False, f"✗ HTTP {response.status_code}", details
+            except requests.Timeout:
+                return False, "✗ Validation timeout (diagram likely too complex)", details
+            except Exception as e:
+                return False, f"✗ Network error: {str(e)[:50]}", details
+
+        except Exception as e:
+            return False, f"✗ Error reading diagram: {str(e)[:50]}", {}
+
     def _execute_python_files(self, progress=None, task_id=None, use_rich: bool = True):
         """Execute Python scripts to generate figures using local Python."""
         py_files = list(self.figures_dir.glob("*.py"))

rxiv_maker-1.16.7/src/rxiv_maker/utils/rich_upgrade_notifier.py

@@ -0,0 +1,162 @@
+"""Rich console adapter for upgrade notifications in rxiv-maker."""
+
+import click
+from rich.console import Console
+
+
+class RxivUpgradeNotifier:
+    """Adapt Rich console to UpgradeNotifier protocol for rxiv-maker.
+
+    Integrates with rxiv-maker's changelog parser to show rich change summaries.
+    """
+
+    def __init__(self, console: Console):
+        """Initialize with Rich console instance.
+
+        Args:
+            console: Rich Console instance for styled output
+        """
+        self.console = console
+
+    def show_checking(self) -> None:
+        """Show 'checking for updates' message."""
+        self.console.print("🔍 Checking for updates...", style="blue")
+
+    def show_version_check(self, current: str, latest: str, available: bool) -> None:
+        """Show version check results.
+
+        Args:
+            current: Current installed version
+            latest: Latest available version
+            available: Whether an update is available
+        """
+        if available:
+            self.console.print(
+                f"📦 Update available: [cyan]v{current}[/cyan] → [green bold]v{latest}[/green bold]",
+                style="yellow",
+            )
+        else:
+            self.console.print(
+                f"✅ You already have the latest version ([cyan]v{current}[/cyan])",
+                style="green",
+            )
+
+    def show_update_info(self, current: str, latest: str, release_url: str) -> None:
+        """Show update available information with changelog integration.
+
+        Args:
+            current: Current version
+            latest: Latest version
+            release_url: URL to release notes
+        """
+        # Import here to avoid circular dependencies
+        from .changelog_parser import fetch_and_format_changelog
+
+        # Fetch and display changelog
+        summary, error = fetch_and_format_changelog(
+            current_version=current,
+            latest_version=latest,
+            highlights_per_version=3,
+        )
+
+        if summary and not error:
+            self.console.print("\n📋 What's changing:", style="bold blue")
+            # Display changelog - format_summary returns rich-formatted text
+            # Parse and display with proper styling
+            for line in summary.split("\n"):
+                if line.startswith("⚠️"):
+                    # Highlight breaking changes prominently
+                    self.console.print(line, style="bold red")
+                elif "What's New:" in line or "What's changing:" in line:
+                    self.console.print(line, style="bold cyan")
+                elif line.strip().startswith("v"):
+                    # Version headers
+                    self.console.print(line, style="bold yellow")
+                elif line.strip().startswith(("✨", "🔄", "🐛", "🗑️", "🔒", "📝")):
+                    # Change items with emojis
+                    self.console.print(f"   {line.strip()}", style="white")
+                elif line.strip().startswith("•"):
+                    # Breaking change items
+                    self.console.print(f"   {line.strip()}", style="yellow")
+                elif line.strip():
+                    self.console.print(f"   {line}", style="dim")
+        else:
+            # Fallback if changelog unavailable
+            self.console.print(
+                f"\nView release notes: [link]{release_url}[/link]",
+                style="blue",
+            )
+
+    def show_installer_info(self, friendly_name: str, command: str) -> None:
+        """Show detected installer information.
+
+        Args:
+            friendly_name: Human-readable installer name
+            command: The upgrade command that will be executed
+        """
+        self.console.print()
+        self.console.print(
+            f"🔍 Detected installation method: [bold]{friendly_name}[/bold]",
+            style="blue",
+        )
+        self.console.print(f"📦 Running: [yellow]{command}[/yellow]")
+
+    def show_success(self, version: str) -> None:
+        """Show successful upgrade message.
+
+        Args:
+            version: Version that was successfully installed
+        """
+        self.console.print()
+        self.console.print("✅ Upgrade completed successfully!", style="green bold")
+        self.console.print(f"   Now running: [green]v{version}[/green]")
+        self.console.print()
+        self.console.print("   Run [blue]'rxiv --version'[/blue] to verify the installation", style="dim")
+
+    def show_error(self, error: str | None) -> None:
+        """Show upgrade error message.
+
+        Args:
+            error: Error message or None
+        """
+        self.console.print()
+        self.console.print("❌ Upgrade failed", style="red bold")
+        if error:
+            self.console.print(f"   {error}", style="red")
+
+    def show_manual_instructions(self, install_method: str) -> None:
+        """Show manual upgrade instructions.
+
+        Args:
+            install_method: The detected installation method
+        """
+        self.console.print("\n💡 Try running manually:", style="yellow bold")
+
+        if install_method == "homebrew":
+            self.console.print("   [cyan]brew update && brew upgrade rxiv-maker[/cyan]")
+        elif install_method == "pipx":
+            self.console.print("   [cyan]pipx upgrade rxiv-maker[/cyan]")
+        elif install_method == "uv":
+            self.console.print("   [cyan]uv tool upgrade rxiv-maker[/cyan]")
+        elif install_method == "dev":
+            self.console.print("   [cyan]cd <repo> && git pull && uv sync[/cyan]", style="dim")
+        else:
+            self.console.print("   [cyan]pip install --upgrade rxiv-maker[/cyan]")
+            self.console.print("   [dim]# Or with --user flag:[/dim]")
+            self.console.print("   [cyan]pip install --upgrade --user rxiv-maker[/cyan]")
+
+    def confirm_upgrade(self, version: str) -> bool:
+        """Prompt user for confirmation using click.
+
+        Args:
+            version: Version to upgrade to
+
+        Returns:
+            True if user confirms, False otherwise
+        """
+        try:
+            self.console.print()
+            return click.confirm(f"Upgrade rxiv-maker to v{version}?", default=True)
+        except (KeyboardInterrupt, EOFError):
+            self.console.print("\n⚠️  Upgrade cancelled.", style="yellow")
+            return False

{rxiv_maker-1.16.5 → rxiv_maker-1.16.7}/src/rxiv_maker/validators/syntax_validator.py

@@ -854,8 +854,17 @@ class SyntaxValidator(BaseValidator):
         heading_texts = {}
         previous_level = 0
 
-        for line_num, line in enumerate(lines, 1):
-            match = heading_pattern.match(line)
+        # Protect code blocks (including {{py:exec}}) from being treated as headings
+        content = "\n".join(lines)
+        protected_content = self._protect_validation_sensitive_content(content)
+        protected_lines = protected_content.split("\n")
+
+        for line_num, (original_line, protected_line) in enumerate(zip(lines, protected_lines, strict=False), 1):
+            # Skip protected code blocks (they might contain # comments)
+            if "XXPROTECTEDCODEXX" in protected_line:
+                continue
+
+            match = heading_pattern.match(protected_line)
             if match:
                 hashes = match.group(1)
                 heading_text = match.group(2).strip()
@@ -904,7 +913,7 @@ class SyntaxValidator(BaseValidator):
                             f"Heading hierarchy skips levels: {previous_level} → {level}",
                             file_path=file_path,
                             line_number=line_num,
-                            context=line.strip(),
+                            context=original_line.strip(),
                             suggestion=(
                                 f"Consider using {'#' * (previous_level + 1)} instead of {'#' * level}.\n"
                                 f"   Skipping heading levels (e.g., ## to ####) makes document structure unclear."
@@ -927,7 +936,7 @@ class SyntaxValidator(BaseValidator):
                                 f"Standard section '{heading_text}' using level 1 heading (#)",
                                 file_path=file_path,
                                 line_number=line_num,
-                                context=line.strip(),
+                                context=original_line.strip(),
                                 suggestion=(
                                     f"Change to level 2 heading: ## {heading_text}\n"
                                     f"   Level 1 (#) should only be used for the document title.\n"