rxiv-maker 1.16.5__py3-none-any.whl → 1.16.7__py3-none-any.whl

rxiv_maker/__version__.py

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

rxiv_maker/cli/commands/upgrade.py

@@ -1,68 +1,18 @@
 """Upgrade command for rxiv-maker CLI."""
 
-import subprocess  # nosec B404 - needed for executing upgrade commands
 import sys
 
 import click
-from henriqueslab_updater import force_update_check
+from henriqueslab_updater import handle_upgrade_workflow
 from rich.console import Console
 
 from ... import __version__
-from ...utils.changelog_parser import fetch_and_format_changelog
-from ...utils.install_detector import detect_install_method, get_friendly_install_name, get_upgrade_command
-from ..interactive import prompt_confirm
+from ...utils.install_detector import detect_install_method
+from ...utils.rich_upgrade_notifier import RxivUpgradeNotifier
 
 console = Console()
 
 
-def _display_changelog(console: Console, current_version: str, latest_version: str) -> None:
-    """Display changelog summary for version range.
-
-    Args:
-        console: Rich console for output
-        current_version: Current installed version
-        latest_version: Latest available version
-    """
-    console.print("\n📋 What's changing:", style="bold blue")
-
-    # Fetch changelog summary
-    summary, error = fetch_and_format_changelog(
-        current_version=current_version,
-        latest_version=latest_version,
-        highlights_per_version=3,
-    )
-
-    if error:
-        console.print("   Unable to fetch changelog details", style="dim yellow")
-        console.print(
-            f"   View online: https://github.com/henriqueslab/rxiv-maker/releases/tag/v{latest_version}",
-            style="dim blue",
-        )
-        return
-
-    if summary:
-        # Display the changelog with proper formatting
-        for line in summary.split("\n"):
-            if line.startswith("⚠️"):
-                # Highlight breaking changes prominently
-                console.print(line, style="bold red")
-            elif line.startswith("What's New:"):
-                console.print(line, style="bold cyan")
-            elif line.startswith("  v"):
-                # Version headers
-                console.print(line, style="bold yellow")
-            elif line.strip().startswith(("✨", "🔄", "🐛", "🗑️", "🔒", "📝")):
-                # Change items
-                console.print(f"   {line.strip()}", style="white")
-            elif line.strip().startswith("•"):
-                # Breaking change items
-                console.print(f"   {line.strip()}", style="yellow")
-            elif line.strip():
-                console.print(f"   {line}", style="dim")
-    else:
-        console.print("   No detailed changelog available", style="dim")
-
-
 @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")
@@ -72,93 +22,31 @@ def upgrade(ctx: click.Context, yes: bool, check_only: bool) -> None:
 
     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
     """
-    # Detect installation method
+    # Handle development installations specially
     install_method = detect_install_method()
-    install_name = get_friendly_install_name(install_method)
-
-    console.print(f"🔍 Detected installation method: {install_name}", style="blue")
-
-    # Handle development installations
     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("   cd <repo> && git pull && uv sync", style="yellow")
+        console.print("   [cyan]cd <repo> && git pull && uv sync[/cyan]", style="yellow")
         sys.exit(0)
 
-    # Check for updates
-    console.print("🔍 Checking for updates...", style="blue")
-    try:
-        update_available, latest_version = force_update_check()
-
-        if not update_available:
-            console.print(f"✅ You already have the latest version ({__version__})", style="green")
-            sys.exit(0)
-
-        console.print(f"📦 Update available: {__version__} → {latest_version}", style="green")
-
-        # Fetch and display changelog
-        _display_changelog(console, __version__, latest_version)
-
-        if check_only:
-            upgrade_cmd = get_upgrade_command(install_method)
-            console.print(f"\n   Run: {upgrade_cmd}", style="blue")
-            sys.exit(0)
-
-    except Exception as e:
-        console.print(f"⚠️  Could not check for updates: {e}", style="yellow")
-        console.print("   Proceeding with upgrade attempt...", style="yellow")
-        latest_version = "latest"
-
-    # Get upgrade command
-    upgrade_cmd = get_upgrade_command(install_method)
-
-    # Show confirmation
-    if not yes:
-        console.print(f"\n📦 About to run: {upgrade_cmd}", style="blue")
-        if not prompt_confirm("Do you want to continue?", default=True):
-            console.print("❌ Upgrade cancelled", style="yellow")
-            sys.exit(0)
-
-    # Execute upgrade command directly
-    console.print("\n🚀 Upgrading rxiv-maker...", style="blue")
-    console.print(f"   Running: {upgrade_cmd}", style="dim")
-
-    try:
-        # Split command for safer execution without shell=True
-        import shlex
-
-        cmd_parts = shlex.split(upgrade_cmd)
-        result = subprocess.run(
-            cmd_parts,
-            check=True,
-            capture_output=False,
-            timeout=300,
-        )  # nosec B603 - upgrade_cmd comes from trusted install_detector module
-        success = result.returncode == 0
-        error = None
-    except subprocess.CalledProcessError as e:
-        success = False
-        error = f"Command failed with exit code {e.returncode}"
-    except subprocess.TimeoutExpired:
-        success = False
-        error = "Upgrade timed out after 5 minutes"
-    except Exception as e:
-        success = False
-        error = str(e)
-
-    if success:
-        console.print("\n✅ Upgrade completed successfully!", style="green")
-        console.print("   Run 'rxiv --version' to verify the installation", style="blue")
+    # 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",
+    )
 
-        # Show what's new in the upgraded version
-        if latest_version != "latest":
-            console.print(f"\n🎉 What's new in v{latest_version}:", style="bold green")
-            console.print(
-                f"   View full changelog: https://github.com/henriqueslab/rxiv-maker/releases/tag/v{latest_version}",
-                style="blue",
-            )
-    else:
-        console.print(f"\n❌ Upgrade failed: {error}", style="red")
-        console.print(f"   Try running manually: {upgrade_cmd}", style="yellow")
+    if not success and error:
         sys.exit(1)

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/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/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/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"

{rxiv_maker-1.16.5.dist-info → rxiv_maker-1.16.7.dist-info}/METADATA

@@ -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.dist-info → rxiv_maker-1.16.7.dist-info}/RECORD

@@ -1,5 +1,5 @@
 rxiv_maker/__init__.py,sha256=p04JYC5ZhP6dLXkoWVlKNyiRvsDE1a4C88f9q4xO3tA,3268
-rxiv_maker/__version__.py,sha256=scH9t8S4Yy0pZ0rKdWKP1B1m1lQmPo9FwrixAZxLlR0,51
+rxiv_maker/__version__.py,sha256=--L7TPRaASOQ9_Gb1AzwOD0jIisWKuGJB7fbHOHsoFs,51
 rxiv_maker/rxiv_maker_cli.py,sha256=9Lu_mhFPXwx5jzAR6StCNxwCm_fkmP5qiOYdNuh_AwI,120
 rxiv_maker/validate.py,sha256=AIzgP59KbCQJqC9WIGfUdVv0xI6ud9g1fFznQkaGz5Q,9373
 rxiv_maker/cli/__init__.py,sha256=Jw0DTFUSofN-02xpVrt1UUzRcgH5NNd-GPNidhmNwpU,77
@@ -29,7 +29,7 @@ rxiv_maker/cli/commands/repos.py,sha256=SQ9nuhSkyHKFPYn_TrOxyQoGdDRI-OBOgUSGJpRu
 rxiv_maker/cli/commands/repos_search.py,sha256=6sUMvyHlHEX1p88hPtu0_Hf8z6JpOinJ53l9ZI-rirc,7743
 rxiv_maker/cli/commands/setup.py,sha256=9ue4bDETpSPGVkWFDfpuTDsysax5-QKGxmt42Gb7oeU,2294
 rxiv_maker/cli/commands/track_changes.py,sha256=omf_77A7htRSa8naUEPTTtUTxrSwMpzHFOuU0j1xAJw,1163
-rxiv_maker/cli/commands/upgrade.py,sha256=VJ1snYyLGrb5-snF4olfsMwfQsuKkAbXEr8aQ88WYYE,6349
+rxiv_maker/cli/commands/upgrade.py,sha256=UpdqEQwbNYmDMbSrYGv_pVd-7u8PPT3US5RVENhKK4w,1852
 rxiv_maker/cli/commands/validate.py,sha256=3JghFQevJvQDQII4p_QWbQXMEUyDpM-t9-WxtaT4edo,1629
 rxiv_maker/cli/commands/version.py,sha256=VMlfSxxsrZH02d24MXLUDZfHBW39yZRpWxUpMhQ-X0Y,2737
 rxiv_maker/cli/framework/__init__.py,sha256=4FPXdP8J6v4eeEn46mwY0VtnwxjR1jnW_kTrXykQlQs,2704
@@ -38,7 +38,7 @@ rxiv_maker/cli/framework/cache_commands.py,sha256=J91UYLTsLTRoNdzuhAbNL2bJJovYYf
 rxiv_maker/cli/framework/config_commands.py,sha256=a1uOQkCCw3d4qlro3OwHIorcoNg03T_R4-HbfVb-hmQ,19336
 rxiv_maker/cli/framework/content_commands.py,sha256=RilxKeG2c1m2fu0CtWAvP3cGh11DGx9P-nh2kIewAg4,22596
 rxiv_maker/cli/framework/decorators.py,sha256=fh085e3k1CaLSMoZevt8hvgnEuejrf-mcNS-dwXoY_A,10365
-rxiv_maker/cli/framework/utility_commands.py,sha256=_P_KwjlyiNS-vVboU-DqkHynGPqzXyoZRWGmLMLTnOs,26214
+rxiv_maker/cli/framework/utility_commands.py,sha256=drIAc1TAYpne76gj7SZeZhPozVAY5uL9GFPVT_Ez0-E,26437
 rxiv_maker/cli/framework/workflow_commands.py,sha256=CFa3c5oJMmy9cUZxTAU97eKC6YrOljzerSAMrywjbKw,29684
 rxiv_maker/config/defaults.py,sha256=vHyLGVxe5-z9TLxu5f6NhquPvqQkER_KZv_j1I4_dHQ,3055
 rxiv_maker/config/validator.py,sha256=9XDPfo_YgasGt6NLkl6HIhaGh1fr6XsFNiXU2DSsivw,38299
@@ -96,7 +96,7 @@ rxiv_maker/engines/operations/build_manager.py,sha256=TAX4-r8HjraAzzvQuIt0CNlvWL
 rxiv_maker/engines/operations/cleanup.py,sha256=RfbXif0neEVMlprFIHWyvQh6kwghalcesY3t-69Iwsw,18095
 rxiv_maker/engines/operations/fix_bibliography.py,sha256=ZD8uO4YCxDCMWH4WtBSDc4TOMgM383fcLgsCCW0yK60,22428
 rxiv_maker/engines/operations/generate_docs.py,sha256=8d_oVYUuRRqTuYN1KnJKqM5Ydp4_yt52ntBv8gUoRVk,11223
-rxiv_maker/engines/operations/generate_figures.py,sha256=3oIuS0wryO9WpPZ3UD2qm0YscNidTOEiO4_Jd6r3SmY,32842
+rxiv_maker/engines/operations/generate_figures.py,sha256=YeKzH6qVsuPGjtCsvWugLJoys6y73xTyO7Y5g30KM20,38730
 rxiv_maker/engines/operations/generate_preprint.py,sha256=wpKDAu2RLJ4amSdhX5GZ7hU-iTsTRt4etcEA7AZYp04,2662
 rxiv_maker/engines/operations/prepare_arxiv.py,sha256=cd0JN5IO-Wy9T8ab75eibyaA8_K8Gpwrz2F-95OMnx4,21551
 rxiv_maker/engines/operations/setup_environment.py,sha256=gERuThHTldH0YqgXn85995deHBP6csY1ZhCNgU6-vFg,12691
@@ -165,6 +165,7 @@ rxiv_maker/utils/performance.py,sha256=EBDVNshSaeG7Nu-GCZtRAzTunGn4z_Bb2jEck045b
 rxiv_maker/utils/platform.py,sha256=DCD3gvm7_DBcT67gGIXhTDV5mPrBjWrL7R2JdsmIgng,17773
 rxiv_maker/utils/python_execution_reporter.py,sha256=l3hqLXtGAg_wKUlkikK1oaHPeBpoCkj3iR6i1fc11ys,10606
 rxiv_maker/utils/retry.py,sha256=aNsuc7HuxMwG4yubgX0GxIEZ0iF6_4lACusVMc0ZSXA,11026
+rxiv_maker/utils/rich_upgrade_notifier.py,sha256=aMqkx9l_2KtEiwVFdhOU4oqsAgdWQ86LuqWN4k_cTA0,6365
 rxiv_maker/utils/text_utils.py,sha256=ntovIx7qXB0LWO9OmCu7-rqTSfyEvthrTjYEJTbmZ_U,1972
 rxiv_maker/utils/tips.py,sha256=XHgbJkyFjYt5Pz-Rdz_yCjnRLguxIsHwdFmNSg323NA,8078
 rxiv_maker/utils/title_sync.py,sha256=C7NT80DgBJrS70mil6b7ghcZyKR2n5_MNlC6Yli_dXM,15094
@@ -180,15 +181,15 @@ rxiv_maker/validators/latex_error_parser.py,sha256=crk3NAniLBp2iABP4lxts7gvCEg6K
 rxiv_maker/validators/math_validator.py,sha256=LcRIGAv47OsPfOg4E48l2vKN1Q7lHAeduNN5MFMLQGE,27669
 rxiv_maker/validators/pdf_validator.py,sha256=YU4WRPeTEOtvBlquFEtZrG9p_WjlN5nnCByTSRAvWyw,21530
 rxiv_maker/validators/reference_validator.py,sha256=UqvsEa3kVOBkbGMo24fXpFVUtpN1feIf9MfDQIraQZs,15868
-rxiv_maker/validators/syntax_validator.py,sha256=H7JK3H116nI9f_3uzAS_RlIsbcbgajhpoU5T2aGh46w,43098
+rxiv_maker/validators/syntax_validator.py,sha256=hHpKVKky3UiA1ZylA6jJVP3DN47LgaSSJCK2PPA-8BA,43599
 rxiv_maker/validators/doi/__init__.py,sha256=NqATXseuS0zVNns56RvFe8TdqgvueY0Rbw2Pjozlajc,494
 rxiv_maker/validators/doi/api_clients.py,sha256=tqdYUq8LFgRIO0tWfcenwmy2uO-IB1-GMvBfF3lP7-0,21763
 rxiv_maker/validators/doi/metadata_comparator.py,sha256=euqHhKP5sHQAdZbdoAahUn6YqJqOfXIOobNgAqFHlN8,11533
 rxiv_maker/tex/template.tex,sha256=zrJ3aFfu8j9zkg1l375eE9w-j42P3rz16wMD3dSgi1I,1354
 rxiv_maker/tex/style/rxiv_maker_style.bst,sha256=jbVqrJgAm6F88cow5vtZuPBwwmlcYykclTm8RvZIo6Y,24281
 rxiv_maker/tex/style/rxiv_maker_style.cls,sha256=F2qtnS9mI6SwOIaVH76egXZkB2_GzbH4gCTG_ZcfCDQ,24253
-rxiv_maker-1.16.5.dist-info/METADATA,sha256=2U4BcFzbnYaEhzXTOgtUCk13H5w_J_RyoCZ5lQQjaGE,17950
-rxiv_maker-1.16.5.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rxiv_maker-1.16.5.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
-rxiv_maker-1.16.5.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
-rxiv_maker-1.16.5.dist-info/RECORD,,
+rxiv_maker-1.16.7.dist-info/METADATA,sha256=6O761FLD317XmFqsnlCerTogrcC1Kq4wUJW9xnz4psM,18177
+rxiv_maker-1.16.7.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rxiv_maker-1.16.7.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
+rxiv_maker-1.16.7.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
+rxiv_maker-1.16.7.dist-info/RECORD,,