rxiv-maker 1.16.1__tar.gz → 1.16.3__tar.gz

{rxiv_maker-1.16.1 → rxiv_maker-1.16.3}/CHANGELOG.md

@@ -7,6 +7,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.16.3] - 2025-12-15
+
+### Fixed
+- **BibTeX Style Template Resolution**: Fixed `.bst` template file path resolution in `bst_generator.py`
+  - Corrected path traversal to properly locate template files in both installed and development environments
+  - Added fallback locations for robust template detection
+  - Eliminates "Template .bst file not found" warnings during PDF generation with custom bibliography formats
+  - Improved error messages to show all searched locations when template is not found
+
+## [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

{rxiv_maker-1.16.1 → rxiv_maker-1.16.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.16.1
+Version: 1.16.3
 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

{rxiv_maker-1.16.1 → rxiv_maker-1.16.3}/src/docs/api/README.md

@@ -16,6 +16,8 @@ Welcome to the API documentation for rxiv-maker.
 - [utils.citation_utils.py](utils_citation_utils.py.md)
 - [utils.email_encoder.py](utils_email_encoder.py.md)
 - [utils.github.py](utils_github.py.md)
+- [utils.homebrew_checker.py](utils_homebrew_checker.py.md)
+- [utils.install_detector.py](utils_install_detector.py.md)
 - [utils.operation_ids.py](utils_operation_ids.py.md)
 - [utils.platform.py](utils_platform.py.md)
 - [utils.python_execution_reporter.py](utils_python_execution_reporter.py.md)

rxiv_maker-1.16.3/src/docs/api/homebrew_checker.py.md

@@ -0,0 +1,99 @@
+<!-- markdownlint-disable -->
+
+<a href="https://github.com/henriqueslab/rxiv-maker/blob/main/src/src/rxiv_maker/utils/homebrew_checker.py#L0"><img align="right" style="float:right;" src="https://img.shields.io/badge/-source-cccccc?style=flat-square"></a>
+
+# <kbd>module</kbd> `homebrew_checker.py`
+Homebrew update checker for rxiv-maker. 
+
+Checks if a newer version is available via Homebrew. 
+
+Note: Before upgrading with Homebrew, always run 'brew update' first to fetch the latest formulae. 
+
+**Global Variables**
+---------------
+- **HOMEBREW_TAP**
+- **FORMULA_NAME**
+- **FORMULA_URL**
+
+---
+
+<a href="https://github.com/henriqueslab/rxiv-maker/blob/main/src/src/rxiv_maker/utils/homebrew_checker.py#L21"><img align="right" style="float:right;" src="https://img.shields.io/badge/-source-cccccc?style=flat-square"></a>
+
+## <kbd>function</kbd> `check_brew_outdated`
+
+```python
+check_brew_outdated(
+    package: str = 'rxiv-maker',
+    timeout: int = 5
+) → Optional[Tuple[str, str]]
+```
+
+Check if package is outdated using `brew outdated` command. 
+
+
+
+**Args:**
+ 
+ - <b>`package`</b>:  Package name to check 
+ - <b>`timeout`</b>:  Command timeout in seconds 
+
+
+
+**Returns:**
+ Tuple of (current_version, latest_version) if outdated, None otherwise Returns None if brew is not installed or command fails 
+
+
+---
+
+<a href="https://github.com/henriqueslab/rxiv-maker/blob/main/src/src/rxiv_maker/utils/homebrew_checker.py#L63"><img align="right" style="float:right;" src="https://img.shields.io/badge/-source-cccccc?style=flat-square"></a>
+
+## <kbd>function</kbd> `check_formula_github`
+
+```python
+check_formula_github(
+    formula_url: str = 'https://raw.githubusercontent.com/henriqueslab/homebrew-formulas/main/Formula/rxiv-maker.rb',
+    timeout: int = 5
+) → Optional[str]
+```
+
+Check the latest version from the GitHub formula file. 
+
+
+
+**Args:**
+ 
+ - <b>`formula_url`</b>:  URL to the formula Ruby file 
+ - <b>`timeout`</b>:  Request timeout in seconds 
+
+
+
+**Returns:**
+ Latest version string if found, None otherwise 
+
+
+---
+
+<a href="https://github.com/henriqueslab/rxiv-maker/blob/main/src/src/rxiv_maker/utils/homebrew_checker.py#L99"><img align="right" style="float:right;" src="https://img.shields.io/badge/-source-cccccc?style=flat-square"></a>
+
+## <kbd>function</kbd> `check_homebrew_update`
+
+```python
+check_homebrew_update(current_version: str) → Optional[Tuple[bool, str]]
+```
+
+Check if a Homebrew update is available. 
+
+Tries brew outdated command first, falls back to GitHub formula. 
+
+
+
+**Args:**
+ 
+ - <b>`current_version`</b>:  Current installed version 
+
+
+
+**Returns:**
+ Tuple of (has_update, latest_version) if check succeeds, None on failure 
+
+

{rxiv_maker-1.16.1 → rxiv_maker-1.16.3}/src/docs/api/index.md

@@ -16,6 +16,8 @@ Welcome to the API documentation for rxiv-maker.
 - [utils.citation_utils.py](utils_citation_utils.py.md)
 - [utils.email_encoder.py](utils_email_encoder.py.md)
 - [utils.github.py](utils_github.py.md)
+- [utils.homebrew_checker.py](utils_homebrew_checker.py.md)
+- [utils.install_detector.py](utils_install_detector.py.md)
 - [utils.operation_ids.py](utils_operation_ids.py.md)
 - [utils.platform.py](utils_platform.py.md)
 - [utils.python_execution_reporter.py](utils_python_execution_reporter.py.md)

rxiv_maker-1.16.3/src/docs/api/install_detector.py.md

@@ -0,0 +1,81 @@
+<!-- markdownlint-disable -->
+
+<a href="https://github.com/henriqueslab/rxiv-maker/blob/main/src/src/rxiv_maker/utils/install_detector.py#L0"><img align="right" style="float:right;" src="https://img.shields.io/badge/-source-cccccc?style=flat-square"></a>
+
+# <kbd>module</kbd> `install_detector.py`
+Installation method detection for rxiv-maker. 
+
+Detects how rxiv-maker was installed (Homebrew, pipx, uv, pip, etc.) to provide appropriate upgrade instructions. 
+
+
+---
+
+<a href="https://github.com/henriqueslab/rxiv-maker/blob/main/src/src/rxiv_maker/utils/install_detector.py#L15"><img align="right" style="float:right;" src="https://img.shields.io/badge/-source-cccccc?style=flat-square"></a>
+
+## <kbd>function</kbd> `detect_install_method`
+
+```python
+detect_install_method() → Literal['homebrew', 'pipx', 'uv', 'pip-user', 'pip', 'dev', 'unknown']
+```
+
+Detect how rxiv-maker was installed. 
+
+
+
+**Returns:**
+ 
+ - <b>`Installation method`</b>:  homebrew, pipx, uv, pip-user, pip, dev, or unknown 
+
+
+---
+
+<a href="https://github.com/henriqueslab/rxiv-maker/blob/main/src/src/rxiv_maker/utils/install_detector.py#L84"><img align="right" style="float:right;" src="https://img.shields.io/badge/-source-cccccc?style=flat-square"></a>
+
+## <kbd>function</kbd> `get_upgrade_command`
+
+```python
+get_upgrade_command(
+    install_method: Literal['homebrew', 'pipx', 'uv', 'pip-user', 'pip', 'dev', 'unknown']
+) → str
+```
+
+Get the appropriate upgrade command for the installation method. 
+
+
+
+**Args:**
+ 
+ - <b>`install_method`</b>:  The detected installation method 
+
+
+
+**Returns:**
+ Upgrade command string 
+
+
+---
+
+<a href="https://github.com/henriqueslab/rxiv-maker/blob/main/src/src/rxiv_maker/utils/install_detector.py#L106"><img align="right" style="float:right;" src="https://img.shields.io/badge/-source-cccccc?style=flat-square"></a>
+
+## <kbd>function</kbd> `get_friendly_install_name`
+
+```python
+get_friendly_install_name(
+    install_method: Literal['homebrew', 'pipx', 'uv', 'pip-user', 'pip', 'dev', 'unknown']
+) → str
+```
+
+Get a user-friendly name for the installation method. 
+
+
+
+**Args:**
+ 
+ - <b>`install_method`</b>:  The detected installation method 
+
+
+
+**Returns:**
+ Friendly name string 
+
+

{rxiv_maker-1.16.1 → rxiv_maker-1.16.3}/src/rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.16.1"
+__version__ = "1.16.3"

{rxiv_maker-1.16.1 → rxiv_maker-1.16.3}/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-1.16.1 → rxiv_maker-1.16.3}/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-1.16.1 → rxiv_maker-1.16.3}/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-1.16.1 → rxiv_maker-1.16.3}/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-1.16.1 → rxiv_maker-1.16.3}/src/rxiv_maker/utils/bst_generator.py

@@ -50,12 +50,29 @@ def generate_bst_file(format_type: str, output_dir: Path) -> Path:
     format_string = BST_FORMAT_MAP[format_type]
 
     # Find the template .bst file in the package
-    # The template is located at src/tex/style/rxiv_maker_style.bst
-    package_root = Path(__file__).parent.parent.parent
-    template_path = package_root / "tex" / "style" / "rxiv_maker_style.bst"
-
-    if not template_path.exists():
-        raise FileNotFoundError(f"Template .bst file not found at: {template_path}")
+    # Try multiple locations for development and installed configurations
+    possible_template_paths = [
+        # Installed package location (site-packages/rxiv_maker/tex/style/)
+        Path(__file__).parent.parent / "tex" / "style" / "rxiv_maker_style.bst",
+        # Development location (src/tex/style/)
+        Path(__file__).parent.parent.parent / "tex" / "style" / "rxiv_maker_style.bst",
+        # Alternative development location
+        Path(__file__).parent.parent.parent.parent / "src" / "tex" / "style" / "rxiv_maker_style.bst",
+    ]
+
+    template_path = None
+    for path in possible_template_paths:
+        if path.exists():
+            template_path = path
+            break
+
+    if template_path is None:
+        searched_paths = "\n".join(f"  - {p}" for p in possible_template_paths)
+        raise FileNotFoundError(
+            f"Template .bst file not found.\n"
+            f"Searched locations:\n{searched_paths}\n"
+            f"This may indicate a corrupted installation."
+        )
 
     # Read the template file
     try: