rxiv-maker 1.16.6__tar.gz → 1.16.7__tar.gz

{rxiv_maker-1.16.6 → 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

{rxiv_maker-1.16.6 → rxiv_maker-1.16.7}/CHANGELOG.md

@@ -7,6 +7,18 @@ 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

{rxiv_maker-1.16.6 → rxiv_maker-1.16.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.16.6
+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-1.16.6 → 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-1.16.6 → 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-1.16.6 → rxiv_maker-1.16.7}/src/rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.16.6"
+__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-1.16.7/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-1.16.7/tests/unit/test_rich_upgrade_notifier.py

@@ -0,0 +1,206 @@
+"""Tests for RxivUpgradeNotifier."""
+
+from unittest.mock import Mock, patch
+
+from rich.console import Console
+
+from src.rxiv_maker.utils.rich_upgrade_notifier import RxivUpgradeNotifier
+
+
+class TestRxivUpgradeNotifier:
+    """Test RxivUpgradeNotifier functionality."""
+
+    def setup_method(self):
+        """Set up test environment."""
+        self.console = Mock(spec=Console)
+        self.notifier = RxivUpgradeNotifier(self.console)
+
+    def test_show_checking(self):
+        """Test show_checking displays checking message."""
+        self.notifier.show_checking()
+
+        self.console.print.assert_called_once()
+        call_args = self.console.print.call_args[0]
+        assert "Checking for updates" in call_args[0]
+
+    def test_show_version_check_update_available(self):
+        """Test version check with update available."""
+        self.notifier.show_version_check("1.0.0", "1.1.0", True)
+
+        assert self.console.print.called
+        # Check that output mentions update available
+        call_text = str(self.console.print.call_args)
+        assert "1.0.0" in call_text and "1.1.0" in call_text
+
+    def test_show_version_check_no_update(self):
+        """Test version check with no update."""
+        self.notifier.show_version_check("1.0.0", "1.0.0", False)
+
+        assert self.console.print.called
+        call_text = str(self.console.print.call_args)
+        assert "latest version" in call_text
+
+    @patch("src.rxiv_maker.utils.changelog_parser.fetch_and_format_changelog")
+    def test_show_update_info_with_changelog(self, mock_fetch):
+        """Test update info with changelog integration."""
+        mock_fetch.return_value = ("✨ Added new feature\n🐛 Fixed bug", None)
+
+        self.notifier.show_update_info("1.0.0", "1.1.0", "https://github.com/...")
+
+        mock_fetch.assert_called_once_with(
+            current_version="1.0.0",
+            latest_version="1.1.0",
+            highlights_per_version=3,
+        )
+        assert self.console.print.called
+
+    @patch("src.rxiv_maker.utils.changelog_parser.fetch_and_format_changelog")
+    def test_show_update_info_changelog_error(self, mock_fetch):
+        """Test update info when changelog unavailable."""
+        mock_fetch.return_value = (None, "Network error")
+
+        self.notifier.show_update_info("1.0.0", "1.1.0", "https://github.com/...")
+
+        # Should show release URL as fallback
+        assert self.console.print.called
+        calls_text = " ".join(str(call) for call in self.console.print.call_args_list)
+        assert "release notes" in calls_text.lower() or "github.com" in calls_text
+
+    @patch("src.rxiv_maker.utils.changelog_parser.fetch_and_format_changelog")
+    def test_show_update_info_breaking_changes(self, mock_fetch):
+        """Test that breaking changes are highlighted prominently."""
+        mock_fetch.return_value = (
+            "⚠️ Breaking changes:\n• Removed old API\n✨ Added new feature",
+            None,
+        )
+
+        self.notifier.show_update_info("1.0.0", "2.0.0", "https://github.com/...")
+
+        # Verify breaking changes are printed with bold red style
+        calls = self.console.print.call_args_list
+        # Find calls with breaking change indicator
+        breaking_calls = [c for c in calls if "⚠️" in str(c)]
+        assert len(breaking_calls) > 0
+
+    def test_show_installer_info(self):
+        """Test installer info display."""
+        self.notifier.show_installer_info("Homebrew", "brew update && brew upgrade rxiv-maker")
+
+        assert self.console.print.called
+        calls_text = " ".join(str(call) for call in self.console.print.call_args_list)
+        assert "Homebrew" in calls_text
+        assert "brew" in calls_text
+
+    def test_show_success(self):
+        """Test success message display."""
+        self.notifier.show_success("1.1.0")
+
+        assert self.console.print.called
+        # Check for success indicators
+        calls_text = " ".join(str(call) for call in self.console.print.call_args_list)
+        assert "success" in calls_text.lower() or "✅" in calls_text
+        assert "1.1.0" in calls_text
+
+    def test_show_error_with_message(self):
+        """Test error message display with error text."""
+        self.notifier.show_error("Installation failed")
+
+        assert self.console.print.called
+        calls_text = " ".join(str(call) for call in self.console.print.call_args_list)
+        assert "failed" in calls_text.lower() or "❌" in calls_text
+        assert "Installation failed" in calls_text
+
+    def test_show_error_without_message(self):
+        """Test error message display without error text."""
+        self.notifier.show_error(None)
+
+        assert self.console.print.called
+        calls_text = " ".join(str(call) for call in self.console.print.call_args_list)
+        assert "failed" in calls_text.lower() or "❌" in calls_text
+
+    def test_show_manual_instructions_homebrew(self):
+        """Test manual instructions for Homebrew."""
+        self.notifier.show_manual_instructions("homebrew")
+
+        assert self.console.print.called
+        calls_text = " ".join(str(call) for call in self.console.print.call_args_list)
+        assert "brew" in calls_text
+
+    def test_show_manual_instructions_pipx(self):
+        """Test manual instructions for pipx."""
+        self.notifier.show_manual_instructions("pipx")
+
+        assert self.console.print.called
+        calls_text = " ".join(str(call) for call in self.console.print.call_args_list)
+        assert "pipx" in calls_text
+
+    def test_show_manual_instructions_uv(self):
+        """Test manual instructions for uv."""
+        self.notifier.show_manual_instructions("uv")
+
+        assert self.console.print.called
+        calls_text = " ".join(str(call) for call in self.console.print.call_args_list)
+        assert "uv tool" in calls_text
+
+    def test_show_manual_instructions_pip(self):
+        """Test manual instructions for pip."""
+        self.notifier.show_manual_instructions("pip")
+
+        assert self.console.print.called
+        calls_text = " ".join(str(call) for call in self.console.print.call_args_list)
+        assert "pip install" in calls_text
+
+    def test_show_manual_instructions_dev(self):
+        """Test manual instructions for dev installation."""
+        self.notifier.show_manual_instructions("dev")
+
+        assert self.console.print.called
+        calls_text = " ".join(str(call) for call in self.console.print.call_args_list)
+        assert "git pull" in calls_text
+
+    @patch("src.rxiv_maker.utils.rich_upgrade_notifier.click.confirm")
+    def test_confirm_upgrade_accepted(self, mock_confirm):
+        """Test user confirms upgrade."""
+        mock_confirm.return_value = True
+
+        result = self.notifier.confirm_upgrade("1.1.0")
+
+        assert result is True
+        mock_confirm.assert_called_once()
+        # Check that version is in the confirmation prompt
+        call_args = mock_confirm.call_args[0]
+        assert "1.1.0" in call_args[0]
+
+    @patch("src.rxiv_maker.utils.rich_upgrade_notifier.click.confirm")
+    def test_confirm_upgrade_declined(self, mock_confirm):
+        """Test user declines upgrade."""
+        mock_confirm.return_value = False
+
+        result = self.notifier.confirm_upgrade("1.1.0")
+
+        assert result is False
+        mock_confirm.assert_called_once()
+
+    @patch("src.rxiv_maker.utils.rich_upgrade_notifier.click.confirm")
+    def test_confirm_upgrade_keyboard_interrupt(self, mock_confirm):
+        """Test keyboard interrupt during confirmation."""
+        mock_confirm.side_effect = KeyboardInterrupt()
+
+        result = self.notifier.confirm_upgrade("1.1.0")
+
+        assert result is False
+        # Check that cancellation message was shown
+        assert self.console.print.called
+        calls_text = " ".join(str(call) for call in self.console.print.call_args_list)
+        assert "cancel" in calls_text.lower()
+
+    @patch("src.rxiv_maker.utils.rich_upgrade_notifier.click.confirm")
+    def test_confirm_upgrade_eof_error(self, mock_confirm):
+        """Test EOF error during confirmation."""
+        mock_confirm.side_effect = EOFError()
+
+        result = self.notifier.confirm_upgrade("1.1.0")
+
+        assert result is False
+        # Check that cancellation message was shown
+        assert self.console.print.called

rxiv_maker-1.16.7/tests/unit/test_upgrade_command.py

@@ -0,0 +1,134 @@
+"""Tests for the upgrade command."""
+
+from unittest.mock import patch
+
+from click.testing import CliRunner
+
+from src.rxiv_maker.cli.commands.upgrade import upgrade
+
+# Patch paths for the upgrade module
+PATCH_PATH_DETECT = "src.rxiv_maker.cli.commands.upgrade.detect_install_method"
+PATCH_PATH_WORKFLOW = "src.rxiv_maker.cli.commands.upgrade.handle_upgrade_workflow"
+
+
+class TestUpgradeCommand:
+    """Test upgrade command functionality."""
+
+    def setup_method(self):
+        """Set up test environment."""
+        self.runner = CliRunner()
+
+    @patch(PATCH_PATH_DETECT)
+    def test_upgrade_dev_installation_warning(self, mock_detect):
+        """Test that dev installations show a warning and exit."""
+        mock_detect.return_value = "dev"
+
+        result = self.runner.invoke(upgrade)
+
+        assert result.exit_code == 0
+        assert "Development installation detected" in result.output
+        assert "git pull" in result.output
+
+    @patch(PATCH_PATH_DETECT)
+    @patch(PATCH_PATH_WORKFLOW)
+    def test_upgrade_success(self, mock_workflow, mock_detect):
+        """Test successful upgrade."""
+        mock_detect.return_value = "pip"
+        mock_workflow.return_value = (True, None)
+
+        result = self.runner.invoke(upgrade, ["--yes"])
+
+        assert result.exit_code == 0
+        mock_workflow.assert_called_once()
+        # Verify workflow called with correct parameters
+        call_args = mock_workflow.call_args
+        assert call_args[1]["package_name"] == "rxiv-maker"
+        assert call_args[1]["skip_confirmation"] is True
+        assert call_args[1]["check_only"] is False
+
+    @patch(PATCH_PATH_DETECT)
+    @patch(PATCH_PATH_WORKFLOW)
+    def test_upgrade_check_only(self, mock_workflow, mock_detect):
+        """Test --check-only flag."""
+        mock_detect.return_value = "pip"
+        mock_workflow.return_value = (True, None)
+
+        result = self.runner.invoke(upgrade, ["--check-only"])
+
+        assert result.exit_code == 0
+        call_args = mock_workflow.call_args
+        assert call_args[1]["check_only"] is True
+
+    @patch(PATCH_PATH_DETECT)
+    @patch(PATCH_PATH_WORKFLOW)
+    def test_upgrade_without_yes_flag(self, mock_workflow, mock_detect):
+        """Test upgrade without --yes flag (interactive mode)."""
+        mock_detect.return_value = "pip"
+        mock_workflow.return_value = (True, None)
+
+        result = self.runner.invoke(upgrade)
+
+        assert result.exit_code == 0
+        call_args = mock_workflow.call_args
+        assert call_args[1]["skip_confirmation"] is False
+
+    @patch(PATCH_PATH_DETECT)
+    @patch(PATCH_PATH_WORKFLOW)
+    def test_upgrade_failure(self, mock_workflow, mock_detect):
+        """Test failed upgrade."""
+        mock_detect.return_value = "pip"
+        mock_workflow.return_value = (False, "Network error")
+
+        result = self.runner.invoke(upgrade, ["--yes"])
+
+        assert result.exit_code == 1
+
+    @patch(PATCH_PATH_DETECT)
+    @patch(PATCH_PATH_WORKFLOW)
+    def test_upgrade_homebrew(self, mock_workflow, mock_detect):
+        """Test upgrade with Homebrew installation."""
+        mock_detect.return_value = "homebrew"
+        mock_workflow.return_value = (True, None)
+
+        result = self.runner.invoke(upgrade, ["--yes"])
+
+        assert result.exit_code == 0
+        mock_workflow.assert_called_once()
+
+    @patch(PATCH_PATH_DETECT)
+    @patch(PATCH_PATH_WORKFLOW)
+    def test_upgrade_uv(self, mock_workflow, mock_detect):
+        """Test upgrade with uv installation."""
+        mock_detect.return_value = "uv"
+        mock_workflow.return_value = (True, None)
+
+        result = self.runner.invoke(upgrade, ["--yes"])
+
+        assert result.exit_code == 0
+        mock_workflow.assert_called_once()
+
+    @patch(PATCH_PATH_DETECT)
+    @patch(PATCH_PATH_WORKFLOW)
+    def test_upgrade_pipx(self, mock_workflow, mock_detect):
+        """Test upgrade with pipx installation."""
+        mock_detect.return_value = "pipx"
+        mock_workflow.return_value = (True, None)
+
+        result = self.runner.invoke(upgrade, ["--yes"])
+
+        assert result.exit_code == 0
+        mock_workflow.assert_called_once()
+
+    @patch(PATCH_PATH_DETECT)
+    @patch(PATCH_PATH_WORKFLOW)
+    def test_upgrade_github_params(self, mock_workflow, mock_detect):
+        """Test that GitHub organization and repo are passed correctly."""
+        mock_detect.return_value = "pip"
+        mock_workflow.return_value = (True, None)
+
+        result = self.runner.invoke(upgrade, ["--yes"])
+
+        assert result.exit_code == 0
+        call_args = mock_workflow.call_args
+        assert call_args[1]["github_org"] == "HenriquesLab"
+        assert call_args[1]["github_repo"] == "rxiv-maker"