rxiv-maker 1.16.0__tar.gz → 1.16.2__tar.gz

{rxiv_maker-1.16.0 → rxiv_maker-1.16.2}/CHANGELOG.md

@@ -7,7 +7,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-## [1.16.0] - 2025-12-14
+## [1.16.2] - 2025-12-15
+
+### Changed
+- **Non-Interactive Init Command**: Made `rxiv init` fully non-interactive for reliable automated testing
+  - Removed all interactive prompts (overwrite confirmation, manuscript details)
+  - Always uses sensible defaults for title, author, email, ORCID, and affiliation
+  - Fails immediately with clear error message if directory exists without `--force` flag
+  - `--no-interactive` flag hidden but maintained for backward compatibility
+  - Updated documentation to clearly state non-interactive behavior
+
+### Fixed
+- **Error Messages**: Improved `CommandExecutionError` handling to display clean error messages to stderr
+- **Import Fix**: Updated upgrade command to import `force_update_check` from `henriqueslab-updater` package
+
+### Testing
+- Added comprehensive test suite with 26 tests covering all init command edge cases
+- All tests passing: 26 new tests + 4 existing integration tests (30/30 total)
+
+## [1.16.1] - 2025-12-15
 
 ### Added
 - **Configurable bibliography author name format**: New `bibliography_author_format` configuration option to control how author names appear in both PDF and DOCX bibliography sections
@@ -22,6 +40,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - New BibTeX style generator: `src/rxiv_maker/utils/bst_generator.py` for dynamic .bst file generation
 - Added `00_CONFIG.yml` to `ConfigManager` search paths for better backward compatibility with legacy manuscript configurations
 
+## [1.16.0] - 2025-12-14
+
+### Changed
+- **Update Checker Modernization**: Migrated to `henriqueslab-updater` package for centralized update checking
+  - Removed internal update_checker.py, install_detector.py, homebrew_checker.py, and changelog_parser.py
+  - Now uses `henriqueslab-updater>=1.0.0` with RichNotifier and ChangelogPlugin
+  - Enhanced update notifications with changelog highlights (up to 3 per version)
+  - Maintains same user experience with improved code maintainability
+  - Reduces code duplication across HenriquesLab packages
+
+### Dependencies
+- Added `henriqueslab-updater>=1.0.0` dependency
+
 ## [1.15.9] - 2025-12-09
 
 ### Added

{rxiv_maker-1.16.0 → rxiv_maker-1.16.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.16.0
+Version: 1.16.2
 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
@@ -27,6 +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>=1.0.0
 Requires-Dist: latex2mathml>=3.78.0
 Requires-Dist: matplotlib>=3.7.0
 Requires-Dist: numpy>=1.24.0

{rxiv_maker-1.16.0 → rxiv_maker-1.16.2}/pyproject.toml

@@ -52,6 +52,8 @@ dependencies = [
     # Repository management dependencies
     "GitPython>=3.1.0",
     "prompt_toolkit>=3.0.0",
+    # Update checking
+    "henriqueslab-updater>=1.0.0",
 ]
 
 [project.urls]

{rxiv_maker-1.16.0 → rxiv_maker-1.16.2}/src/rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.16.0"
+__version__ = "1.16.2"

{rxiv_maker-1.16.0 → rxiv_maker-1.16.2}/src/rxiv_maker/cli/commands/init.py

@@ -8,7 +8,7 @@ from ..framework import InitCommand
 @click.command(context_settings={"help_option_names": ["-h", "--help"]})
 @click.argument("manuscript_path", type=click.Path(), required=False)
 @click.option("--force", "-f", is_flag=True, help="Force overwrite existing files")
-@click.option("--no-interactive", is_flag=True, help="Skip interactive prompts and use defaults")
+@click.option("--no-interactive", is_flag=True, hidden=True, help="Deprecated (command is always non-interactive)")
 @click.option(
     "--validate", is_flag=True, help="Run validation after initialization to ensure template builds correctly"
 )
@@ -25,6 +25,9 @@ def init(
     **MANUSCRIPT_PATH**: Directory to create for your manuscript.
     Defaults to MANUSCRIPT/
 
+    This command is fully non-interactive and uses sensible defaults for all values.
+    You can customize the manuscript details by editing 00_CONFIG.yml after initialization.
+
     Creates all required files including configuration, main content, supplementary
     information, bibliography, and figure directory with example scripts.
 
@@ -45,10 +48,6 @@ def init(
     **Initialize and validate template builds correctly:**
 
         $ rxiv init --validate
-
-    **Non-interactive initialization:**
-
-        $ rxiv init --no-interactive
     """
     # Use centralized InitCommand framework - eliminates 250+ lines of boilerplate!
     command = InitCommand()

{rxiv_maker-1.16.0 → rxiv_maker-1.16.2}/src/rxiv_maker/cli/commands/upgrade.py

@@ -5,12 +5,12 @@ import subprocess
 import sys
 
 import click
+from henriqueslab_updater import force_update_check
 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 ...utils.update_checker import force_update_check
 from ..interactive import prompt_confirm
 
 console = Console()

{rxiv_maker-1.16.0 → rxiv_maker-1.16.2}/src/rxiv_maker/cli/framework/base.py

@@ -210,6 +210,9 @@ class BaseCommand(ABC):
             return self.execute_operation(**kwargs)
 
         except CommandExecutionError as e:
+            # Print error message to stderr before exiting
+            error_console = Console(stderr=True)
+            error_console.print(f"❌ Error: {e}", style="red")
             sys.exit(e.exit_code)
         except KeyboardInterrupt:
             self.handle_keyboard_interrupt(operation_name)

{rxiv_maker-1.16.0 → rxiv_maker-1.16.2}/src/rxiv_maker/cli/framework/workflow_commands.py

@@ -50,44 +50,26 @@ class InitCommand(BaseCommand):
 
         Args:
             force: Force overwrite existing files
-            no_interactive: Skip interactive prompts
+            no_interactive: Deprecated (command is always non-interactive)
             validate: Run validation after initialization
             template: Template type to use (default, minimal, journal, preprint)
         """
-        from rich.prompt import Prompt
-
         # Get manuscript path from raw path (set during setup_common_options)
         manuscript_path = self.raw_manuscript_path
 
         manuscript_dir = Path(manuscript_path)
 
-        # Check if directory exists
+        # Check if directory exists and fail if --force not used
         if manuscript_dir.exists() and not force:
-            if not no_interactive:
-                overwrite = Prompt.ask(
-                    f"Directory '{manuscript_path}' already exists. Overwrite?", choices=["y", "n"], default="n"
-                )
-                if overwrite == "n":
-                    self.console.print("❌ Initialization cancelled", style="yellow")
-                    return
-            else:
-                raise CommandExecutionError(f"Directory '{manuscript_path}' already exists. Use --force to overwrite.")
+            raise CommandExecutionError(f"Directory '{manuscript_path}' already exists. Use --force to overwrite.")
 
-        # Get user information if interactive (BEFORE progress bar)
+        # Always use default values (non-interactive mode only)
         title = "Your Manuscript Title"
         author_name = "Your Name"
         author_email = "your.email@example.com"
         author_orcid = "0000-0000-0000-0000"
         author_affiliation = "Your Institution"
 
-        if not no_interactive:
-            self.console.print("\n📝 Enter manuscript details (press Enter for defaults):")
-            title = Prompt.ask("Title", default=title)
-            author_name = Prompt.ask("Author name", default=author_name)
-            author_email = Prompt.ask("Author email", default=author_email)
-            author_orcid = Prompt.ask("Author ORCID", default=author_orcid)
-            author_affiliation = Prompt.ask("Author affiliation", default=author_affiliation)
-
         with self.create_progress() as progress:
             task = progress.add_task(f"Initializing manuscript (template: {template})...", total=2)
 

{rxiv_maker-1.16.0 → rxiv_maker-1.16.2}/src/rxiv_maker/cli/main.py

@@ -4,10 +4,15 @@
 import os
 
 import rich_click as click
+from henriqueslab_updater import (
+    ChangelogPlugin,
+    RichNotifier,
+    check_for_updates_async_background,
+    show_update_notification,
+)
 from rich.console import Console
 
 from .. import __version__
-from ..utils.update_checker import check_for_updates_async, show_update_notification
 from . import commands
 from .commands.check_installation import check_installation
 
@@ -143,8 +148,18 @@ class UpdateCheckGroup(click.Group):
     def invoke(self, ctx):
         """Invoke command and handle update checking."""
         try:
-            # Start update check in background (non-blocking)
-            check_for_updates_async()
+            # Start update check in background (non-blocking) with RichNotifier and ChangelogPlugin
+            check_for_updates_async_background(
+                package_name="rxiv-maker",
+                current_version=__version__,
+                notifier=RichNotifier(color_scheme="blue"),
+                plugins=[
+                    ChangelogPlugin(
+                        changelog_url="https://raw.githubusercontent.com/HenriquesLab/rxiv-maker/main/CHANGELOG.md",
+                        highlights_per_version=3,
+                    ),
+                ],
+            )
 
             # Invoke the actual command
             result = super().invoke(ctx)

{rxiv_maker-1.16.0 → rxiv_maker-1.16.2}/src/rxiv_maker/engines/operations/track_changes.py

@@ -499,7 +499,7 @@ class TrackChangesManager:
             # Copy tag figures to output/Figures_tag
             tag_figures_src = target_manuscript_dir / "FIGURES"
             tag_figures_dst = self.output_dir / "Figures_tag"
-            
+
             if tag_figures_src.exists():
                 if tag_figures_dst.exists():
                     shutil.rmtree(tag_figures_dst)