rxiv-maker 1.15.9__py3-none-any.whl → 1.16.0__py3-none-any.whl

rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.15.9"
+__version__ = "1.16.0"

rxiv_maker/config/defaults.py

@@ -10,6 +10,8 @@ from typing import Any, Dict
 DEFAULT_CONFIG: Dict[str, Any] = {
     # Citation configuration
     "citation_style": "numbered",  # or "author-date"
+    # Bibliography author name format
+    "bibliography_author_format": "lastname_firstname",  # Options: lastname_initials, lastname_firstname, firstname_lastname
     # Figures configuration
     "figures": {
         "directory": "FIGURES",

rxiv_maker/config/validator.py

@@ -391,6 +391,10 @@ class ConfigValidator:
                     },
                     "bibliography": {"type": "string"},
                     "citation_style": {"type": "string", "enum": ["numbered", "author-date"]},
+                    "bibliography_author_format": {
+                        "type": "string",
+                        "enum": ["lastname_initials", "lastname_firstname", "firstname_lastname"],
+                    },
                     "enable_inline_doi_resolution": {"type": "boolean"},
                     "language": {"type": "string", "enum": ["en", "es", "pt", "fr", "de"]},
                     "license": {"type": "string"},

rxiv_maker/converters/citation_processor.py

@@ -158,10 +158,10 @@ def process_citations_in_text(text: MarkdownContent, citation_style: str = "numb
     # Match email-like patterns: word@word.word or @word.word (domain patterns)
     text = re.sub(r"(\w+@[\w.-]+\.\w+|@[\w.-]+\.\w+)", protect_email, text)
 
-    # Handle single citations like @citation_key (but not figure/equation references)
+    # Handle single citations like @citation_key (but not cross-references)
     # Allow alphanumeric, underscore, and hyphen in citation keys
-    # Exclude figure and equation references by not matching @fig: or @eq: patterns
-    text = re.sub(r"@(?!fig:|eq:)([a-zA-Z0-9_-]+)", rf"\\{inline_cmd}{{\1}}", text)
+    # Exclude all cross-references by not matching @word: patterns (@fig:, @sfig:, @snote:, @tbl:, etc.)
+    text = re.sub(r"@(?![a-zA-Z]+:)([a-zA-Z0-9_-]+)", rf"\\{inline_cmd}{{\1}}", text)
 
     # Restore protected email patterns
     for i, pattern in enumerate(email_patterns):
@@ -194,16 +194,29 @@ def extract_citations_from_text(text: MarkdownContent) -> list[CitationKey]:
     """
     citations: list[CitationKey] = []
 
+    # First, remove content inside backticks (inline code) to avoid extracting example citations
+    # This prevents `@key` or `@Knuth...` from being treated as actual citations
+    backtick_patterns = []
+
+    def protect_backticks(match):
+        backtick_patterns.append(match.group(0))
+        return f"__BACKTICK_PATTERN_{len(backtick_patterns) - 1}__"
+
+    # Match both single backticks `...` and triple backticks ```...```
+    text_cleaned = re.sub(r"`[^`]+`", protect_backticks, text)
+    text_cleaned = re.sub(r"```.*?```", protect_backticks, text_cleaned, flags=re.DOTALL)
+
     # Find bracketed multiple citations
-    bracketed_matches = re.findall(r"\[(@[^]]+)\]", text)
+    bracketed_matches = re.findall(r"\[(@[^]]+)\]", text_cleaned)
     for match in bracketed_matches:
         for cite in match.split(";"):
             clean_cite = cite.strip().lstrip("@").strip()
             if clean_cite and clean_cite not in citations:
                 citations.append(clean_cite)
 
-    # Find single citations (excluding figure and equation references)
-    single_matches = re.findall(r"@(?!fig:|eq:)([a-zA-Z0-9_-]+)", text)
+    # Find single citations (excluding all cross-references like @fig:, @sfig:, @snote:, @tbl:, etc.)
+    # Exclude any pattern that looks like @word: (cross-reference format)
+    single_matches = re.findall(r"@(?![a-zA-Z]+:)([a-zA-Z0-9_-]+)", text_cleaned)
     for cite in single_matches:
         if cite not in citations:
             citations.append(cite)

rxiv_maker/core/managers/config_manager.py

@@ -38,6 +38,7 @@ class ConfigManager:
         # Configuration search paths (in order of priority)
         # Only search in manuscript directory, no global home directory configs
         self.config_paths = [
+            self.base_dir / "00_CONFIG.yml",  # Legacy manuscript config (first priority)
             self.base_dir / "rxiv.yml",
             self.base_dir / "rxiv.yaml",
             self.base_dir / ".rxiv.yml",

rxiv_maker/core/managers/unified_config_manager.py

@@ -39,6 +39,7 @@ CONFIG_SCOPE_MAP = {
     "output": ConfigScope.MANUSCRIPT,
     "figures": ConfigScope.MANUSCRIPT,
     "bibliography": ConfigScope.MANUSCRIPT,
+    "bibliography_author_format": ConfigScope.MANUSCRIPT,
     "validation": ConfigScope.MANUSCRIPT,
     "cache": ConfigScope.MANUSCRIPT,
     "acknowledge_rxiv_maker": ConfigScope.MANUSCRIPT,

rxiv_maker/engines/operations/build_manager.py

@@ -781,8 +781,30 @@ class BuildManager:
         self.log("Copying style files...", "STEP")
 
         try:
-            # Use centralized path manager method for style file copying
-            copied_files = self.path_manager.copy_style_files_to_output()
+            # Generate custom .bst file with author name format preference
+            from ...core.managers.config_manager import ConfigManager
+            from ...utils.bst_generator import generate_bst_file
+
+            # Load config to get bibliography author format
+            config_manager = ConfigManager(base_dir=self.path_manager.manuscript_path)
+            config = config_manager.load_config()
+            author_format = config.get("bibliography_author_format", "lastname_firstname")
+
+            # Generate custom .bst file directly to output directory
+            try:
+                output_dir = self.path_manager.output_dir
+                generate_bst_file(author_format, output_dir)
+                self.log(f"Generated custom .bst file with format: {author_format}", "INFO")
+            except Exception as e:
+                self.log(f"Failed to generate custom .bst file: {e}. Using default.", "WARNING")
+                # If generation failed, copy the default .bst
+                copied_files = self.path_manager.copy_style_files_to_output()
+                for copied_file in copied_files:
+                    self.log(f"Copied {copied_file.name} to output directory", "INFO")
+                return True
+
+            # Copy only .cls file (not .bst since we generated a custom one)
+            copied_files = self.path_manager.copy_style_files_to_output(style_files=["rxiv_maker_style.cls"])
 
             for copied_file in copied_files:
                 self.log(f"Copied {copied_file.name} to output directory", "INFO")
@@ -897,10 +919,12 @@ class BuildManager:
                             verbose=self.verbose,
                         )
                         success = tracker.generate_change_tracked_pdf()
-                        
+
                         if self.performance_tracker:
-                            self.performance_tracker.end_operation("complete_build", metadata={"result": "success" if success else "failure"})
-                        
+                            self.performance_tracker.end_operation(
+                                "complete_build", metadata={"result": "success" if success else "failure"}
+                            )
+
                         op.add_metadata("build_successful", success)
                         op.add_metadata("track_changes", True)
                         return success

rxiv_maker/engines/operations/generate_preprint.py

@@ -34,7 +34,7 @@ def generate_preprint(output_dir, yaml_metadata, manuscript_path=None):
     manuscript_md = find_manuscript_md(manuscript_path)
 
     # Process all template replacements
-    template_content = process_template_replacements(template_content, yaml_metadata, str(manuscript_md))
+    template_content = process_template_replacements(template_content, yaml_metadata, str(manuscript_md), output_dir)
 
     # Extract manuscript name using centralized logic (PathManager handles this via write_manuscript_output)
     # The write_manuscript_output function now uses PathManager internally for consistent name extraction

rxiv_maker/exporters/docx_exporter.py

@@ -11,6 +11,7 @@ from pathlib import Path
 from typing import Any, Dict
 
 from ..core.logging_config import get_logger
+from ..core.managers.config_manager import ConfigManager
 from ..core.path_manager import PathManager
 from ..processors.yaml_processor import extract_yaml_metadata
 from ..utils.bibliography_parser import parse_bib_file
@@ -44,6 +45,11 @@ class DocxExporter:
         self.resolve_dois = resolve_dois
         self.include_footnotes = include_footnotes
 
+        # Load config to get author name format preference
+        config_manager = ConfigManager(base_dir=Path(manuscript_path))
+        config = config_manager.load_config()
+        self.author_format = config.get("bibliography_author_format", "lastname_firstname")
+
         # Components
         self.citation_mapper = CitationMapper()
         self.content_processor = DocxContentProcessor()
@@ -317,7 +323,7 @@ class DocxExporter:
             #     doi = self._resolve_doi_from_metadata(entry)
 
             # Format entry (full format for DOCX bibliography)
-            formatted = format_bibliography_entry(entry, doi, slim=False)
+            formatted = format_bibliography_entry(entry, doi, slim=False, author_format=self.author_format)
 
             bibliography[number] = {"key": key, "entry": entry, "doi": doi, "formatted": formatted}
 

rxiv_maker/exporters/docx_writer.py

@@ -146,14 +146,23 @@ class DocxWriter:
 
         # Collect unique affiliations and build mapping
         all_affiliations = []
-        affiliation_map = {}  # Maps affiliation string to number
+        affiliation_map = {}  # Maps affiliation shortname to number
+
+        # Get full affiliation details from metadata
+        affiliation_details = {a.get("shortname"): a for a in metadata.get("affiliations", [])}
 
         for author in authors:
             author_affils = author.get("affiliations", [])
-            for affil in author_affils:
-                if affil not in affiliation_map:
-                    affiliation_map[affil] = len(affiliation_map) + 1
-                    all_affiliations.append(affil)
+            for affil_shortname in author_affils:
+                if affil_shortname not in affiliation_map:
+                    affiliation_map[affil_shortname] = len(affiliation_map) + 1
+                    # Look up full affiliation info
+                    affil_info = affiliation_details.get(affil_shortname, {})
+                    full_name = affil_info.get("full_name", affil_shortname)
+                    location = affil_info.get("location", "")
+                    # Format: "Full Name, Location" or just "Full Name" if no location
+                    affil_text = f"{full_name}, {location}" if location else full_name
+                    all_affiliations.append(affil_text)
 
         # Add authors with superscript affiliation numbers
         if authors:

rxiv_maker/processors/template_processor.py

@@ -298,8 +298,20 @@ def generate_keywords(yaml_metadata):
     return result
 
 
-def generate_bibliography(yaml_metadata):
-    """Generate LaTeX bibliography section from YAML metadata."""
+def generate_bibliography(yaml_metadata, output_dir=None):
+    """Generate LaTeX bibliography section from YAML metadata.
+
+    Args:
+        yaml_metadata: Manuscript metadata dictionary
+        output_dir: Output directory for generated files (optional)
+
+    Returns:
+        LaTeX bibliography command string
+    """
+    from pathlib import Path
+
+    from ..utils.bst_generator import generate_bst_file
+
     bibliography_config = yaml_metadata.get("bibliography", "03_REFERENCES")
 
     # Handle both dict and string formats for backward compatibility
@@ -312,11 +324,34 @@ def generate_bibliography(yaml_metadata):
     if bibliography.endswith(".bib"):
         bibliography = bibliography[:-4]
 
+    # Generate custom .bst file with author name format preference
+    if output_dir:
+        author_format = yaml_metadata.get("bibliography_author_format", "lastname_firstname")
+        try:
+            output_path = Path(output_dir)
+            generate_bst_file(author_format, output_path)
+        except Exception as e:
+            # Log warning but don't fail - fall back to default .bst
+            import logging
+
+            logger = logging.getLogger(__name__)
+            logger.warning(f"Failed to generate custom .bst file: {e}. Using default.")
+
     return f"\\bibliography{{{bibliography}}}"
 
 
-def process_template_replacements(template_content, yaml_metadata, article_md):
-    """Process all template replacements with metadata and content."""
+def process_template_replacements(template_content, yaml_metadata, article_md, output_dir=None):
+    """Process all template replacements with metadata and content.
+
+    Args:
+        template_content: LaTeX template content
+        yaml_metadata: Manuscript metadata dictionary
+        article_md: Article markdown content
+        output_dir: Output directory for generated files (optional)
+
+    Returns:
+        Processed template content with all replacements
+    """
     # Process draft watermark based on status field
     is_draft = False
     if "status" in yaml_metadata:
@@ -424,7 +459,7 @@ def process_template_replacements(template_content, yaml_metadata, article_md):
     template_content = template_content.replace("<PY-RPL:KEYWORDS>", keywords_section)
 
     # Generate bibliography section
-    bibliography_section = generate_bibliography(yaml_metadata)
+    bibliography_section = generate_bibliography(yaml_metadata, output_dir)
     template_content = template_content.replace("<PY-RPL:BIBLIOGRAPHY>", bibliography_section)
 
     # Extract content sections from markdown

rxiv_maker/services/manuscript_service.py

@@ -221,7 +221,7 @@ class ManuscriptService(BaseService):
 
             # Process template with metadata
             processed_content = process_template_replacements(
-                template_content, metadata.raw, str(metadata.manuscript_path)
+                template_content, metadata.raw, str(metadata.manuscript_path), output_dir
             )
 
             # Write output

rxiv_maker/templates/registry.py

@@ -154,6 +154,9 @@ citation_style: "numbered"
 #
 # methods_placement: "after_bibliography"  # Options: "inline", "after_results", "after_bibliography"
 # acknowledge_rxiv_maker: true
+#
+# # Bibliography author name format (applies to both PDF and DOCX):
+# bibliography_author_format: "lastname_firstname"  # Options: "lastname_initials" (Smith, J.A.), "lastname_firstname" (Smith, John A.), "firstname_lastname" (John A. Smith)
 """
 
     def _get_default_main_template(self) -> str:

rxiv_maker/utils/author_name_formatter.py

@@ -0,0 +1,311 @@
+"""Author name parsing and formatting utilities.
+
+This module provides functionality to parse, format, and transform author names
+between different bibliographic citation formats.
+
+Supported formats:
+- lastname_initials: "Smith, J.A."
+- lastname_firstname: "Smith, John A."
+- firstname_lastname: "John A. Smith"
+"""
+
+import re
+from typing import Dict
+
+
+def extract_initials(given_name: str) -> str:
+    """Extract initials from a given name.
+
+    Args:
+        given_name: Given name(s), which may include first and middle names
+
+    Returns:
+        Formatted initials with periods
+
+    Examples:
+        >>> extract_initials("John Alan")
+        'J.A.'
+        >>> extract_initials("J. A.")
+        'J.A.'
+        >>> extract_initials("Jean-Paul")
+        'J.-P.'
+        >>> extract_initials("John")
+        'J.'
+    """
+    if not given_name or not given_name.strip():
+        return ""
+
+    given_name = given_name.strip()
+
+    # Handle hyphenated names specially (e.g., "Jean-Paul" → "J.-P.")
+    if "-" in given_name:
+        # Remove periods first, then split on hyphen
+        cleaned = given_name.replace(".", "").strip()
+        parts = cleaned.split("-")
+        initials = "-".join(part[0].upper() + "." for part in parts if part and part.strip())
+        return initials
+
+    # Remove periods and split on whitespace to handle multi-word names
+    cleaned = given_name.replace(".", "").strip()
+    words = cleaned.split()
+
+    if not words:
+        return ""
+
+    # Handle concatenated initials like "JA" → "J.A."
+    # If we have a single "word" with multiple uppercase letters, treat each as an initial
+    if len(words) == 1 and len(words[0]) > 1:
+        word = words[0]
+        # Check if it looks like concatenated initials (all or mostly uppercase)
+        uppercase_count = sum(1 for c in word if c.isupper())
+        if uppercase_count >= len(word) * 0.8:  # 80% or more uppercase
+            # Treat each uppercase letter as an initial
+            initials = [c.upper() + "." for c in word if c.isupper()]
+            return "".join(initials) if initials else ""
+
+    # Extract first letter from each word
+    initials = []
+    for word in words:
+        if word and word[0].isalpha():
+            initials.append(word[0].upper() + ".")
+
+    return "".join(initials) if initials else ""
+
+
+def parse_author_name(name_str: str) -> Dict[str, str]:
+    """Parse an author name into components.
+
+    Handles both "LastName, FirstName MiddleName" and "FirstName MiddleName LastName" formats.
+
+    Args:
+        name_str: Author name string to parse
+
+    Returns:
+        Dictionary with keys: first, middle, last, suffix, von
+        Empty strings for missing components
+
+    Examples:
+        >>> parse_author_name("Smith, John A.")
+        {'first': 'John', 'middle': 'A.', 'last': 'Smith', 'suffix': '', 'von': ''}
+        >>> parse_author_name("von Neumann, John")
+        {'first': 'John', 'middle': '', 'last': 'von Neumann', 'suffix': '', 'von': 'von'}
+        >>> parse_author_name("Martin, James Jr.")
+        {'first': 'James', 'middle': '', 'last': 'Martin', 'suffix': 'Jr.', 'von': ''}
+        >>> parse_author_name("John A. Smith")
+        {'first': 'John', 'middle': 'A.', 'last': 'Smith', 'suffix': '', 'von': ''}
+    """
+    if not name_str or not name_str.strip():
+        return {"first": "", "middle": "", "last": "", "suffix": "", "von": ""}
+
+    name_str = name_str.strip()
+
+    # Common suffixes to detect
+    suffixes = ["Jr.", "Jr", "Sr.", "Sr", "II", "III", "IV", "V"]
+
+    # Check for "LastName, FirstName" format (comma indicates this format)
+    if "," in name_str:
+        # Split by comma
+        parts = [p.strip() for p in name_str.split(",", 1)]
+        last_part = parts[0]
+        given_part = parts[1] if len(parts) > 1 else ""
+
+        # Check if last part of given_part is a suffix
+        suffix = ""
+        if given_part:
+            given_words = given_part.split()
+            if given_words and given_words[-1] in suffixes:
+                suffix = given_words[-1]
+                given_part = " ".join(given_words[:-1])
+
+        # Parse given names (first + middle)
+        given_words = given_part.split() if given_part else []
+        first = given_words[0] if given_words else ""
+        middle = " ".join(given_words[1:]) if len(given_words) > 1 else ""
+
+        # Check for von/van prefix in last name
+        von = ""
+        last_words = last_part.split()
+        if last_words and last_words[0].lower() in ["von", "van", "de", "del", "della", "di"]:
+            von = last_words[0]
+            # Keep von as part of last name
+            last = last_part
+        else:
+            last = last_part
+
+        return {
+            "first": first,
+            "middle": middle,
+            "last": last,
+            "suffix": suffix,
+            "von": von,
+        }
+    else:
+        # "FirstName MiddleName LastName" format
+        words = name_str.split()
+
+        if not words:
+            return {"first": "", "middle": "", "last": "", "suffix": "", "von": ""}
+
+        # Check if last word is a suffix
+        suffix = ""
+        if words[-1] in suffixes:
+            suffix = words[-1]
+            words = words[:-1]
+
+        if not words:
+            return {"first": "", "middle": "", "last": "", "suffix": suffix, "von": ""}
+
+        # Single name (e.g., "Plato")
+        if len(words) == 1:
+            return {
+                "first": "",
+                "middle": "",
+                "last": words[0],
+                "suffix": suffix,
+                "von": "",
+            }
+
+        # Check for von/van prefix
+        von = ""
+        von_idx = None
+        for i, word in enumerate(words[:-1]):  # Don't check last word
+            if word.lower() in ["von", "van", "de", "del", "della", "di"]:
+                von = word
+                von_idx = i
+                break
+
+        if von_idx is not None:
+            # Everything before von is first/middle, von + rest is last
+            first = words[0] if von_idx > 0 else ""
+            middle = " ".join(words[1:von_idx]) if von_idx > 1 else ""
+            last = " ".join(words[von_idx:])
+        else:
+            # Standard: First [Middle...] Last
+            first = words[0]
+            middle = " ".join(words[1:-1]) if len(words) > 2 else ""
+            last = words[-1]
+
+        return {
+            "first": first,
+            "middle": middle,
+            "last": last,
+            "suffix": suffix,
+            "von": von,
+        }
+
+
+def format_author_name(author_parts: Dict[str, str], format_type: str) -> str:
+    """Format an author name according to the specified format.
+
+    Args:
+        author_parts: Dictionary with author name components (from parse_author_name)
+        format_type: One of "lastname_initials", "lastname_firstname", "firstname_lastname"
+
+    Returns:
+        Formatted author name string
+
+    Examples:
+        >>> parts = {'first': 'John', 'middle': 'A.', 'last': 'Smith', 'suffix': '', 'von': ''}
+        >>> format_author_name(parts, "lastname_initials")
+        'Smith, J.A.'
+        >>> format_author_name(parts, "lastname_firstname")
+        'Smith, John A.'
+        >>> format_author_name(parts, "firstname_lastname")
+        'John A. Smith'
+    """
+    first = author_parts.get("first", "").strip()
+    middle = author_parts.get("middle", "").strip()
+    last = author_parts.get("last", "").strip()
+    suffix = author_parts.get("suffix", "").strip()
+
+    # Build given name (first + middle)
+    given_parts = []
+    if first:
+        given_parts.append(first)
+    if middle:
+        given_parts.append(middle)
+    given_name = " ".join(given_parts)
+
+    # Handle single-name authors (e.g., "Plato")
+    if not given_name and last:
+        return last
+
+    if not last:
+        return given_name  # Fallback if no last name
+
+    # Format based on type
+    if format_type == "lastname_initials":
+        # Extract initials from given name
+        initials = extract_initials(given_name)
+        if initials:
+            result = f"{last}, {initials}"
+        else:
+            result = last
+    elif format_type == "lastname_firstname":
+        if given_name:
+            result = f"{last}, {given_name}"
+        else:
+            result = last
+    elif format_type == "firstname_lastname":
+        if given_name:
+            result = f"{given_name} {last}"
+        else:
+            result = last
+    else:
+        # Default to lastname_firstname
+        if given_name:
+            result = f"{last}, {given_name}"
+        else:
+            result = last
+
+    # Add suffix if present
+    if suffix:
+        if format_type in ["lastname_initials", "lastname_firstname"]:
+            result = f"{result}, {suffix}"
+        else:
+            result = f"{result} {suffix}"
+
+    return result
+
+
+def format_author_list(authors_str: str, format_type: str) -> str:
+    """Format a list of authors separated by 'and'.
+
+    Note: Caller should clean LaTeX commands from authors_str before calling this function.
+
+    Args:
+        authors_str: String of authors separated by " and " (should be LaTeX-cleaned)
+        format_type: One of "lastname_initials", "lastname_firstname", "firstname_lastname"
+
+    Returns:
+        Formatted author list joined by " and "
+
+    Examples:
+        >>> format_author_list("Smith, John and Jones, Mary A.", "lastname_initials")
+        'Smith, J. and Jones, M.A.'
+        >>> format_author_list("Smith, John A. and Jones, Mary", "firstname_lastname")
+        'John A. Smith and Mary Jones'
+    """
+    if not authors_str or not authors_str.strip():
+        return ""
+
+    # Split by " and " (BibTeX standard separator)
+    # Handle potential variations: "and", " and ", " and  "
+    author_list = re.split(r"\s+and\s+", authors_str)
+
+    # Parse and format each author
+    formatted_authors = []
+    for author in author_list:
+        author = author.strip()
+        if not author:
+            continue
+
+        # Parse the name
+        author_parts = parse_author_name(author)
+
+        # Format according to specified type
+        formatted = format_author_name(author_parts, format_type)
+        formatted_authors.append(formatted)
+
+    # Join with " and "
+    return " and ".join(formatted_authors)

rxiv_maker/utils/bst_generator.py

@@ -0,0 +1,119 @@
+"""BibTeX style file generator for custom author name formatting.
+
+This module generates custom .bst files with different author name format strings
+to support lastname_initials, lastname_firstname, and firstname_lastname formats.
+"""
+
+import re
+from pathlib import Path
+from typing import Dict
+
+from ..core.logging_config import get_logger
+
+logger = get_logger()
+
+# BibTeX format string mapping
+# BibTeX format codes:
+# ff = full first name, f = first initial
+# vv = von part, ll = last name, jj = junior part
+BST_FORMAT_MAP: Dict[str, str] = {
+    "lastname_initials": "{vv~}{ll}{, f.}",  # Smith, J.A.
+    "lastname_firstname": "{ff~}{vv~}{ll}{, jj}",  # Smith, John A. (current default)
+    "firstname_lastname": "{ff~}{vv~}{ll}",  # John A. Smith
+}
+
+
+def generate_bst_file(format_type: str, output_dir: Path) -> Path:
+    """Generate a custom .bst file with the specified author name format.
+
+    Args:
+        format_type: One of "lastname_initials", "lastname_firstname", "firstname_lastname"
+        output_dir: Directory where the generated .bst file should be written
+
+    Returns:
+        Path to the generated .bst file
+
+    Raises:
+        ValueError: If format_type is not recognized
+        FileNotFoundError: If template .bst file cannot be found
+        IOError: If .bst file cannot be written
+
+    Example:
+        >>> output_path = generate_bst_file("lastname_initials", Path("./output"))
+        >>> # Creates ./output/rxiv_maker_style.bst with lastname, initials format
+    """
+    if format_type not in BST_FORMAT_MAP:
+        valid_formats = ", ".join(BST_FORMAT_MAP.keys())
+        raise ValueError(f"Invalid format_type '{format_type}'. Must be one of: {valid_formats}")
+
+    # Get the format string for this format type
+    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}")
+
+    # Read the template file
+    try:
+        with open(template_path, "r", encoding="utf-8") as f:
+            bst_content = f.read()
+    except IOError as e:
+        raise IOError(f"Failed to read template .bst file: {e}") from e
+
+    # Replace the format string on line 222
+    # The line looks like: s nameptr "{ff~}{vv~}{ll}{, jj}" format.name$ 't :=
+    # We need to replace the format string in quotes
+    pattern = r'(s\s+nameptr\s+")([^"]+)("\s+format\.name\$)'
+    replacement = rf"\1{format_string}\3"
+
+    modified_content, num_subs = re.subn(pattern, replacement, bst_content)
+
+    if num_subs == 0:
+        logger.warning("No format string pattern found in .bst file. The .bst file may have been modified.")
+        # Still write the file but log a warning
+    elif num_subs > 1:
+        logger.warning(
+            f"Found {num_subs} format string patterns in .bst file. Expected only 1. All have been replaced."
+        )
+
+    # Create output directory if it doesn't exist
+    output_dir = Path(output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    # Write the generated .bst file
+    output_path = output_dir / "rxiv_maker_style.bst"
+    try:
+        with open(output_path, "w", encoding="utf-8") as f:
+            f.write(modified_content)
+    except IOError as e:
+        raise IOError(f"Failed to write generated .bst file: {e}") from e
+
+    logger.debug(f"Generated .bst file with format '{format_type}' at: {output_path}")
+
+    return output_path
+
+
+def get_bst_format_string(format_type: str) -> str:
+    """Get the BibTeX format string for a given format type.
+
+    Args:
+        format_type: One of "lastname_initials", "lastname_firstname", "firstname_lastname"
+
+    Returns:
+        BibTeX format string
+
+    Raises:
+        ValueError: If format_type is not recognized
+
+    Example:
+        >>> get_bst_format_string("lastname_initials")
+        '{vv~}{ll}{, f.}'
+    """
+    if format_type not in BST_FORMAT_MAP:
+        valid_formats = ", ".join(BST_FORMAT_MAP.keys())
+        raise ValueError(f"Invalid format_type '{format_type}'. Must be one of: {valid_formats}")
+    return BST_FORMAT_MAP[format_type]

rxiv_maker/utils/docx_helpers.py

@@ -14,6 +14,8 @@ from typing import Optional
 
 from PIL import Image
 
+from rxiv_maker.utils.author_name_formatter import format_author_list
+
 from ..utils.bibliography_parser import BibEntry
 
 
@@ -39,7 +41,12 @@ def remove_yaml_header(content: str) -> str:
     return content
 
 
-def format_bibliography_entry(entry: BibEntry, doi: Optional[str] = None, slim: bool = False) -> str:
+def format_bibliography_entry(
+    entry: BibEntry,
+    doi: Optional[str] = None,
+    slim: bool = False,
+    author_format: str = "lastname_firstname",
+) -> str:
     """Format a bibliography entry for display.
 
     Full format: Author (Year). Title. Journal Volume(Number): Pages. DOI (if provided)
@@ -50,6 +57,7 @@ def format_bibliography_entry(entry: BibEntry, doi: Optional[str] = None, slim:
         entry: Bibliography entry to format
         doi: DOI string (optional)
         slim: If True, use slim format (LastName, Year)
+        author_format: Format for author names - "lastname_initials", "lastname_firstname", "firstname_lastname"
 
     Returns:
         Formatted bibliography string
@@ -69,8 +77,9 @@ def format_bibliography_entry(entry: BibEntry, doi: Optional[str] = None, slim:
     author = entry.fields.get("author", "Unknown Author")
     year = entry.fields.get("year", "n.d.")
 
-    # Clean LaTeX commands from author names
+    # Clean LaTeX commands from author names and format according to specified style
     author = clean_latex_commands(author)
+    author = format_author_list(author, author_format)
 
     if slim:
         # Slim format: First author last name, Year

{rxiv_maker-1.15.9.dist-info → rxiv_maker-1.16.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.15.9
+Version: 1.16.0
 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
@@ -201,6 +201,7 @@ rxiv pdf
 - BibTeX integration with `[@citation]` syntax
 - Automatic bibliography generation
 - **Multiple citation styles**: Choose between numbered `[1, 2]` or author-date `(Smith, 2024)` citations
+- **Configurable author name formatting**: Format bibliography as `Smith, J.A.` or `Smith, John A.` or `John A. Smith`
 - **Inline DOI resolution**: Paste DOIs directly in text `10.1038/...` and auto-convert to citations
 - CrossRef/DataCite DOI validation and metadata fetching
 

{rxiv_maker-1.15.9.dist-info → rxiv_maker-1.16.0.dist-info}/RECORD

@@ -1,5 +1,5 @@
 rxiv_maker/__init__.py,sha256=p04JYC5ZhP6dLXkoWVlKNyiRvsDE1a4C88f9q4xO3tA,3268
-rxiv_maker/__version__.py,sha256=Jie3UBhYYz9xfwQlIZS6rCw1H9FHwp9v16l4VwSxKVc,51
+rxiv_maker/__version__.py,sha256=0b3_5IT4Rl1KTRqfSivXOu2oAnVS0q_ptEV7xe5L9Yo,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
@@ -40,10 +40,10 @@ rxiv_maker/cli/framework/content_commands.py,sha256=RilxKeG2c1m2fu0CtWAvP3cGh11D
 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/workflow_commands.py,sha256=GbK1Wv4cTQfCiOyukn_R3q3IUqKvLk8MMK1vOXW3PaE,30556
-rxiv_maker/config/defaults.py,sha256=UYktZW3fTx9gs7uoP419nePYN-gXddAw1QMZCbZD9Mk,2891
-rxiv_maker/config/validator.py,sha256=TOp5nI_ma-eEmv2LNWB40IRXhBXHE43zfIL3g5GIJIY,38083
+rxiv_maker/config/defaults.py,sha256=vHyLGVxe5-z9TLxu5f6NhquPvqQkER_KZv_j1I4_dHQ,3055
+rxiv_maker/config/validator.py,sha256=9XDPfo_YgasGt6NLkl6HIhaGh1fr6XsFNiXU2DSsivw,38299
 rxiv_maker/converters/__init__.py,sha256=d7WGsRwWqRQWO117IkKDP0Ap0ERiK0N2-dXHInye3_A,685
-rxiv_maker/converters/citation_processor.py,sha256=1wYca1sZ8-Aw6ajS_N4d1BGoQmzg5agkfej9BOOHW5Q,8198
+rxiv_maker/converters/citation_processor.py,sha256=Y4JpSvoqYU4GnqYC5bnB0Zn0OMTAR_FG3G8hWkgQj0o,8917
 rxiv_maker/converters/code_processor.py,sha256=ZFkJsqJ4nYUiDGtLeV7yWgOWUZNUXIFaBxZOPq88UrU,9324
 rxiv_maker/converters/comment_processor.py,sha256=Tlem4btYqMmfRf5AM5s6ZbB_pZPvkFpACz8XsLNVl50,7845
 rxiv_maker/converters/custom_command_processor.py,sha256=89wkIKP2It89qhXPBxiK-ib3Wwb5bKYsVf8E6BBRTlk,23467
@@ -79,25 +79,25 @@ rxiv_maker/core/cache/doi_cache.py,sha256=lw_ouHlfKNzg4zDMAOEUDhsFLfm88rWcPYBVyj
 rxiv_maker/core/cache/secure_cache_utils.py,sha256=EejPWvxw_mUPqO0TRBHYYTsLXWZEUH1qykEfBwgpkcc,18000
 rxiv_maker/core/managers/__init__.py,sha256=sh4ZuZH4YrAu4XTiN9ky1-tQQASKiSTY0udJJAzDRcU,950
 rxiv_maker/core/managers/cache_manager.py,sha256=8btUaRDYPOrUynHWBMz7RVeS9xcpUoyhemFNUi8NqpQ,21893
-rxiv_maker/core/managers/config_manager.py,sha256=dqruhoi3r_0eyV65LD6RZRY4afamqKvBzqoUQfUcYeE,18739
+rxiv_maker/core/managers/config_manager.py,sha256=DdM-3_mfrjHFkPQ2vOmpQnXaoSJU-ianVwUvCEIwZss,18829
 rxiv_maker/core/managers/dependency_manager.py,sha256=DwVRcvk4JcZGzYc-K6ue7aGfw8fSnne50pPI_8Arlzw,25800
 rxiv_maker/core/managers/execution_manager.py,sha256=cEDS0KyWBHf_N74Fc8MC4VRXxmEcaz_DJtyWO5-o628,29585
 rxiv_maker/core/managers/file_manager.py,sha256=SVRnP1JQoGCAms3E7iSpOp_RG60P36Qk9HGAmJDaFvE,18641
 rxiv_maker/core/managers/install_manager.py,sha256=8HChOfbm5-uXsksKMDqmgrYNMJJtyDoL2RDNpbFwhwc,15533
 rxiv_maker/core/managers/state_manager.py,sha256=vqcg5aiAh9NvUJDiV7wTgU2EIGS-qAgZ50n4Xcuo49A,17713
-rxiv_maker/core/managers/unified_config_manager.py,sha256=qOn6cQ8UE8Th4GIq1Bmp4fqpwDUgJ2DDwUA2D__u-ug,12529
+rxiv_maker/core/managers/unified_config_manager.py,sha256=fqoL9-qwixdBOw4kZ3iFZ06nG9nxkUl-Ckc8hxYwxmo,12587
 rxiv_maker/core/managers/validation_manager.py,sha256=wqmYJUybgAX5dJRe6S9lG7tShLWjYOmARIhR0xygHVM,29948
 rxiv_maker/core/managers/workflow_manager.py,sha256=WJehwdVZpaWgjk0SbvRb5AdHIK_b5FQTKFF12bv90HY,27082
 rxiv_maker/data/tips.yaml,sha256=PZvLH4L-keJko1BOvnP_aQpvNVOQ20t6OcPLF1vTWzg,4739
 rxiv_maker/engines/__init__.py,sha256=FiVpmWADcXzP2w_tQk9E4KEABGtsoXniPE7TFk-mwkY,1075
 rxiv_maker/engines/operations/__init__.py,sha256=m0es7aH_qVqAGk6CLS6SMo3ZNL2F_gLrM_wLY1shDR4,1292
 rxiv_maker/engines/operations/add_bibliography.py,sha256=eIYbZRmRFHPm09svhnrsgIjjzt3Imc1U3h4eeEj-D1M,20511
-rxiv_maker/engines/operations/build_manager.py,sha256=jS1KPMNkIWcoevos3PMBq7izjo5D3lLdrfYqLOk05y4,43733
+rxiv_maker/engines/operations/build_manager.py,sha256=TAX4-r8HjraAzzvQuIt0CNlvWLo5pF40I7BRuIxZZRc,45022
 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=f9IjZD2_nK-kD8RLRugRuXMslDgx4857f3AqLGRJFrY,11084
 rxiv_maker/engines/operations/generate_figures.py,sha256=3oIuS0wryO9WpPZ3UD2qm0YscNidTOEiO4_Jd6r3SmY,32842
-rxiv_maker/engines/operations/generate_preprint.py,sha256=EtWSL1-LGm8N61_CLABSswgvVw61haEx8m4727pdzgM,2650
+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
 rxiv_maker/engines/operations/track_changes.py,sha256=XMU1x31nwLIwbi1lwYJn333O7Tx9llQfBv8yY9O_Dww,24734
@@ -106,8 +106,8 @@ rxiv_maker/engines/operations/validate_pdf.py,sha256=qyrtL752Uap3i6ntQheY570soVj
 rxiv_maker/exporters/__init__.py,sha256=NcTD1SDb8tTgsHhCS1A7TVEZncyWbDRTa6sJIdLqcsE,350
 rxiv_maker/exporters/docx_citation_mapper.py,sha256=Qp3IEqrR6lQGQPQ4JeGdOCWeg97XBbVCKdX1gtX9XfY,4584
 rxiv_maker/exporters/docx_content_processor.py,sha256=3srXfq4lC_FJpTAfu-WB930WheSm6rCy-vNUtFlsflY,23878
-rxiv_maker/exporters/docx_exporter.py,sha256=v1XSKfXHUOHxj2tEv3IFBVv9mN1p8RIIrkqHDs9Unxo,14792
-rxiv_maker/exporters/docx_writer.py,sha256=LAlhwZXjN1xDMa-ocX4FpHYp-IX-pn9qjPpd4t_IMaM,41284
+rxiv_maker/exporters/docx_exporter.py,sha256=i2G_AF-Co4AOD6ZdRzDZ7VgcJLdCmxu-Fn3SykvBywQ,15152
+rxiv_maker/exporters/docx_writer.py,sha256=qI_0JklqAxF_TUHxO3wPopZpJ44O2qYjMPOptrnU0XM,41915
 rxiv_maker/install/__init__.py,sha256=kAB6P-12IKg_K1MQ-uzeC5IR11O2cNxj0t_2JMhooZs,590
 rxiv_maker/install/dependency_handlers/__init__.py,sha256=NN9dP1usXpYgLpSw0uEnJ6ugX2zefihVjdyDdm1k-cE,231
 rxiv_maker/install/dependency_handlers/latex.py,sha256=xopSJxYkg3D63rH7RoVLN-Ykl87AZqhlUrrG3m6LoWo,3304
@@ -127,7 +127,7 @@ rxiv_maker/manuscript_utils/figure_utils.py,sha256=FsNtMiA1IOHeA6gQsENmAWLZSAvPp
 rxiv_maker/processors/__init__.py,sha256=8UmaeFkbPfcwAL5MnhN2DcOA2k8iuJu0B5dDA6_pmnA,720
 rxiv_maker/processors/author_processor.py,sha256=jC4qZ9M_GADelkp1v8pk46ESUf4DNraXLfMYGhn_7ZM,10016
 rxiv_maker/processors/markdown_preprocessor.py,sha256=Ez_2lhSFEdJY0CS2SKJJESRfnmSdMq4s0jP2nlFSKN8,11228
-rxiv_maker/processors/template_processor.py,sha256=xOgPmHOtkPsbBf9Dh4xYELYfz_dqZM9ezbg_dy4_LTw,28834
+rxiv_maker/processors/template_processor.py,sha256=mX8L19Evo9c8DvcdvSdtFHGaGGrQseVsF1CKfj_WYow,30024
 rxiv_maker/processors/yaml_processor.py,sha256=SSXHpwY1Cw81IDN4x40UFtosz-T9l29oh-CZpusmlYo,11499
 rxiv_maker/scripts/__init__.py,sha256=nKsDmj6UAc90uC6sKd-V6O80OMYjAl4Uha9zF_6ayX0,154
 rxiv_maker/scripts/custom_doc_generator.py,sha256=pMkdTI8a4qG8Z3gFUJtPwRuu2i0ioW3pKfs22es0KCk,6311
@@ -136,20 +136,22 @@ rxiv_maker/services/__init__.py,sha256=8PtucdpuVrO6OmzvW4AyaWXKlQpdErIDeCLlXpKEM
 rxiv_maker/services/base.py,sha256=iCfX8yGyCFTNIQf4tPblQzlc4-LFMv-H7p9I3Qc2LT0,5484
 rxiv_maker/services/build_service.py,sha256=0irCnWoYw-0tagwNiNxAwDxlqgS_qpOvSCpc5EJ85I0,2120
 rxiv_maker/services/configuration_service.py,sha256=MCKWFLkMA9hi7wQE5xPpH6KxO6QiWpogrl1ivFRL00o,3899
-rxiv_maker/services/manuscript_service.py,sha256=ZrTnZBcFY-iIxk-2pw3JiVf0mhSMo7BuiFzJHLdga4k,11292
+rxiv_maker/services/manuscript_service.py,sha256=wev9gBTbKbcypQMmoKvR7gh2Ha1nRuvRdkrFJcmr3Io,11304
 rxiv_maker/services/publication_service.py,sha256=0p8yQ1jrY3RHwCkzTEl_sAbWYTafRk-NaTqHWZW3_dg,1740
 rxiv_maker/services/validation_service.py,sha256=eWg14NqJu6LzyJBgeXkTaVZAlX4wYFX8ZEvSR5hMx7U,14619
 rxiv_maker/templates/__init__.py,sha256=UTet1pYPkPdgvrLw-wwaY-PAgdjGJasAi_hdyIh0J8s,562
 rxiv_maker/templates/manager.py,sha256=HlI7Qb52866Okf4k1aRh0fUy9heOSNGjMQJtrCdL3Xk,6131
-rxiv_maker/templates/registry.py,sha256=NA88HsCpwDmsNVilp_dAcQOQtsQ96GyIK1FGfH6ScVo,12749
+rxiv_maker/templates/registry.py,sha256=L8M7M9Yhf2P0SQEghmCXufWfsGQhaW1TYjdkUw-wvDw,12993
 rxiv_maker/tex/python_execution_section.tex,sha256=pHz6NGfZN4ViBo6rInUO5FAuk81sV_Ppqszrvl00w_4,2218
 rxiv_maker/utils/__init__.py,sha256=4ya5VR8jqRqUChlnUeMeeetOuWV-gIvjPwcE1u_1OnI,1540
+rxiv_maker/utils/author_name_formatter.py,sha256=UjvarbyQm89EUIYqckygx3g37o-EcNyvipBtY8GJDxs,10222
 rxiv_maker/utils/bibliography_checksum.py,sha256=Jh4VILSpGQ5KJ9UBCUb7oFy6lZ9_ncXD87vEXxw5jbY,10270
 rxiv_maker/utils/bibliography_parser.py,sha256=WZIQoEpVwdbLmbkw9FdkVgoLE5GX7itqnzPnEEb_fFU,6846
+rxiv_maker/utils/bst_generator.py,sha256=EHNhMT0Tq6YXUh2TfpGwOzYaarAyjEsAeeJ4H4np7Og,4313
 rxiv_maker/utils/changelog_parser.py,sha256=WCDp9Iy6H6_3nC6FB7RLt6i00zuCyvU17sCU4e3pqCY,11954
 rxiv_maker/utils/citation_utils.py,sha256=spIgVxPAN6jPvoG-eOE00rVX_buUGKnUjP1Fhz31sl4,5134
 rxiv_maker/utils/dependency_checker.py,sha256=EdyIvk-W_bhC1DJCpFw5ePhjEU74C9j7RYMm06unBMA,14366
-rxiv_maker/utils/docx_helpers.py,sha256=QUKTyhhVakovoEOhDMpC8j-H2InTkjuVhNHciKpBgUY,12519
+rxiv_maker/utils/docx_helpers.py,sha256=jhxkrU80JjDJXDE3gNfsJt9PqLyByYDfymY_Jm9ZqoI,12860
 rxiv_maker/utils/doi_resolver.py,sha256=8_oy5cTtklm1GCKXpn509yqYsu4P5gYbMjtfQ8dRgFA,10253
 rxiv_maker/utils/email_encoder.py,sha256=QMD5JbGNu68gD8SBdGHfNY8uCgbMzEcmzE1TCYDMgWY,5139
 rxiv_maker/utils/figure_checksum.py,sha256=PWgh2QAErNnnQCV-t-COACQXKICUaggAAIxhgHLCGNM,10748
@@ -185,8 +187,8 @@ rxiv_maker/validators/doi/metadata_comparator.py,sha256=euqHhKP5sHQAdZbdoAahUn6Y
 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-1.15.9.dist-info/METADATA,sha256=pRVBi_qnjSNaLZl3Lz7D0RsNJ4gaMp3SnFxp-4e-TA8,19656
-rxiv_maker-1.15.9.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
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