rxiv-maker 1.16.8__py3-none-any.whl → 1.18.0__py3-none-any.whl

rxiv_maker/utils/docx_helpers.py

@@ -7,6 +7,7 @@ This module provides utility functions for DOCX generation including:
 - PDF to image conversion
 """
 
+import html
 import io
 import logging
 import re
@@ -201,124 +202,18 @@ def clean_latex_commands(text: str) -> str:
         >>> clean_latex_commands("Griffi{\\'e}")
         'Griffié'
     """
+    # First, handle escaped HTML entities from BibTeX (\&\#233 -> &#233)
+    text = text.replace("\\&\\#", "&#")
+    text = text.replace("\\&#", "&#")  # Handle partially escaped variants
+
+    # Then decode HTML entities (é -> é, á -> á, … -> …, etc.)
+    text = html.unescape(text)
+
     # Convert LaTeX accent commands to Unicode
-    # Handle both with and without backslashes (BibTeX parser may strip them)
-    # Also handle variant forms where backslash is replaced with the literal character
-    accent_map = {
-        # Acute accents (é, á, í, ó, ú) - use non-raw strings for single backslash
-        "\\'e": "é",
-        "{\\'e}": "é",
-        "{'e}": "é",
-        "{'é}": "é",
-        "\\'a": "á",
-        "{\\'a}": "á",
-        "{'a}": "á",
-        "{'á}": "á",
-        "\\'i": "í",
-        "{\\'i}": "í",
-        "{'i}": "í",
-        "{'í}": "í",
-        "'{\\i}": "í",  # Acute on dotless i
-        "\\'o": "ó",
-        "{\\'o}": "ó",
-        "{'o}": "ó",
-        "{'ó}": "ó",
-        "'{o}": "ó",  # Acute o (variant without backslash)
-        "\\'u": "ú",
-        "{\\'u}": "ú",
-        "{'u}": "ú",
-        "{'ú}": "ú",
-        # Uppercase acute accents
-        "\\'E": "É",
-        "{\\'E}": "É",
-        "{'E}": "É",
-        "\\'A": "Á",
-        "{\\'A}": "Á",
-        "{'A}": "Á",
-        "\\'I": "Í",
-        "{\\'I}": "Í",
-        "{'I}": "Í",
-        "'{\\I}": "Í",  # Acute on uppercase dotless I
-        "\\'O": "Ó",
-        "{\\'O}": "Ó",
-        "{'O}": "Ó",
-        "'{O}": "Ó",
-        "\\'U": "Ú",
-        "{\\'U}": "Ú",
-        "{'U}": "Ú",
-        # Umlaut/diaeresis (ë, ä, ï, ö, ü)
-        '\\"e': "ë",
-        '{\\"e}': "ë",
-        '{"e}': "ë",
-        '{"ë}': "ë",
-        '\\"a': "ä",
-        '{\\"a}': "ä",
-        '{"a}': "ä",
-        '{"ä}': "ä",
-        '\\"i': "ï",
-        '{\\"i}': "ï",
-        '{"i}': "ï",
-        '{"ï}': "ï",
-        '\\"o': "ö",
-        '{\\"o}': "ö",
-        '{"o}': "ö",
-        '{"ö}': "ö",
-        '\\"u': "ü",
-        '{\\"u}': "ü",
-        '{"u}': "ü",
-        '{"ü}': "ü",
-        # Grave accents (è, à)
-        "\\`e": "è",
-        "{\\`e}": "è",
-        "{`e}": "è",
-        "{`è}": "è",
-        "\\`a": "à",
-        "{\\`a}": "à",
-        "{`a}": "à",
-        "{`à}": "à",
-        # Circumflex (ê, â)
-        "\\^e": "ê",
-        "{\\^e}": "ê",
-        "{^e}": "ê",
-        "{^ê}": "ê",
-        "\\^a": "â",
-        "{\\^a}": "â",
-        "{^a}": "â",
-        "{^â}": "â",
-        # Tilde (ñ, ã, õ)
-        "\\~n": "ñ",
-        "{\\~n}": "ñ",
-        "{~n}": "ñ",
-        "{~ñ}": "ñ",
-        "~{n}": "ñ",
-        "\\~a": "ã",
-        "{\\~a}": "ã",
-        "{~a}": "ã",
-        "~{a}": "ã",  # Tilde on a (variant)
-        "{~ã}": "ã",
-        "\\~o": "õ",
-        "{\\~o}": "õ",
-        "{~o}": "õ",
-        "~{o}": "õ",  # Tilde on o (variant)
-        "{~õ}": "õ",
-        # Uppercase tilde
-        "\\~N": "Ñ",
-        "{\\~N}": "Ñ",
-        "~{N}": "Ñ",
-        "\\~A": "Ã",
-        "{\\~A}": "Ã",
-        "~{A}": "Ã",
-        "\\~O": "Õ",
-        "{\\~O}": "Õ",
-        "~{O}": "Õ",
-        # Cedilla (ç)
-        "\\c{c}": "ç",
-        "{\\c{c}}": "ç",
-        "{\\c{ç}}": "ç",
-    }
-
-    for latex_cmd, unicode_char in accent_map.items():
-        text = text.replace(latex_cmd, unicode_char)
+    # Uses centralized accent map from accent_character_map module
+    from .accent_character_map import clean_latex_accents
+
+    text = clean_latex_accents(text)
 
     # Remove common formatting commands but keep their content
     text = re.sub(r"\\textbf\{([^}]+)\}", r"\1", text)
@@ -338,7 +233,37 @@ def clean_latex_commands(text: str) -> str:
     # Remove lone backslashes
     text = re.sub(r"\\(?![a-zA-Z])", "", text)
 
-    return text
+    # Remove braces around single characters or short words (common BibTeX artifact)
+    # This handles cases like {P} or {n} that appear after HTML entity decoding issues
+    text = re.sub(r"\{([A-Za-z]{1,3})\}", r"\1", text)
+
+    # Remove unmatched opening braces at start of words (e.g., "{Sperr" -> "Sperr")
+    text = re.sub(r"\{([A-Za-z])", r"\1", text)
+
+    # Remove unmatched closing braces at end of words or after accented characters (e.g., "Team}" -> "Team", "Pé}" -> "Pé")
+    text = re.sub(r"([A-Za-zÀ-ÿ])\}", r"\1", text)
+
+    # Remove isolated braces (opening or closing)
+    text = re.sub(r"\{(?![A-Za-z])", "", text)  # Opening brace not followed by letter
+    text = re.sub(r"(?<![A-Za-z])\}", "", text)  # Closing brace not preceded by letter
+
+    # Fix common malformed author name patterns from bad BibTeX encoding
+    # Pattern: "Pé and Rez, Fernando" -> "Pérez, Fernando" (very short word with accent + capitalized word + comma)
+    # Only match if first word is 2-4 chars and ends with accented character
+    def fix_name_case(match):
+        part1, part2 = match.group(1), match.group(2)
+        # Lowercase the second part since it's continuation of first name
+        return f"{part1}{part2.lower()},"
+
+    text = re.sub(r"\b([A-ZÀ-Ÿ][à-ÿ]{1,3}) and ([A-Z][a-z]+),", fix_name_case, text)
+    # Pattern: "Damiá and n and" -> "Damián and" (word ending in accent + isolated letter + " and")
+    text = re.sub(r"\b([A-ZÀ-Ÿ][a-zà-ÿ]+[à-ÿ]) and ([a-zà-ÿ])\s+and\s+", r"\1\2 and ", text)
+
+    # Clean up any remaining empty braces or double spaces
+    text = re.sub(r"\{\}", "", text)
+    text = re.sub(r"\s+", " ", text)
+
+    return text.strip()
 
 
 def truncate_text(text: str, max_length: int = 100, suffix: str = "...") -> str:

rxiv_maker/utils/label_extractor.py

@@ -0,0 +1,185 @@
+r"""Label extraction utilities for manuscript processing.
+
+This module provides centralized label extraction for figures, tables, equations,
+and supplementary elements. Used by both DOCX export and LaTeX processing to
+create consistent numbering across formats.
+
+Examples:
+    >>> extractor = LabelExtractor()
+    >>> content = "![Figure](img.png)\\n{#fig:results}"
+    >>> fig_map = extractor.extract_figure_labels(content)
+    >>> fig_map
+    {'results': 1}
+r
+"""
+
+import re
+from typing import Dict, Tuple
+
+
+class LabelExtractor:
+    r"""Extract and map reference labels from markdown content."""
+
+    @staticmethod
+    def extract_figure_labels(content: str) -> Dict[str, int]:
+        r"""Extract main figure labels and create number mapping.
+
+        Finds patterns like: ![...](...)\\n{#fig:label}
+
+        Args:
+            content: Markdown content to scan
+
+        Returns:
+            Dict mapping label names to sequential numbers
+
+        Examples:
+            >>> extractor = LabelExtractor()
+            >>> content = "![](a.png)\\n{#fig:first}\\n\\n![](b.png)\\n{#fig:second}"
+            >>> extractor.extract_figure_labels(content)
+            {'first': 1, 'second': 2}
+        r
+        """
+        # Pattern: Image markdown followed by {#fig:label}
+        # Allow hyphens and underscores in label names
+        labels = re.findall(r"!\[[^\]]*\]\([^)]+\)\s*\n\s*\{#fig:([\w-]+)", content)
+        return {label: i + 1 for i, label in enumerate(labels)}
+
+    @staticmethod
+    def extract_supplementary_figure_labels(content: str) -> Dict[str, int]:
+        r"""Extract supplementary figure labels and create number mapping.
+
+        Finds patterns like: ![...](...)\\n{#sfig:label}
+
+        Args:
+            content: Markdown content to scan
+
+        Returns:
+            Dict mapping label names to sequential numbers
+
+        Examples:
+            >>> extractor = LabelExtractor()
+            >>> content = "![](s1.png)\\n{#sfig:methods}\\n\\n![](s2.png)\\n{#sfig:data}"
+            >>> extractor.extract_supplementary_figure_labels(content)
+            {'methods': 1, 'data': 2}
+        r
+        """
+        # Pattern: Image markdown followed by {#sfig:label}
+        labels = re.findall(r"!\[[^\]]*\]\([^)]+\)\s*\n\s*\{#sfig:([\w-]+)", content)
+        return {label: i + 1 for i, label in enumerate(labels)}
+
+    @staticmethod
+    def extract_supplementary_table_labels(content: str) -> Dict[str, int]:
+        r"""Extract supplementary table labels and create number mapping.
+
+        Finds both markdown format {#stable:label} and LaTeX format \\label{stable:label}.
+        Prefers LaTeX labels if both are present (matches PDF behavior).
+
+        Args:
+            content: Markdown/LaTeX content to scan
+
+        Returns:
+            Dict mapping label names to sequential numbers
+
+        Examples:
+            >>> extractor = LabelExtractor()
+            >>> content = "{#stable:params}\\n\\n{#stable:results}"
+            >>> extractor.extract_supplementary_table_labels(content)
+            {'params': 1, 'results': 2}
+        r
+        """
+        # Extract both markdown and LaTeX formats
+        markdown_labels = re.findall(r"\{#stable:([\w-]+)\}", content)
+        latex_labels = re.findall(r"\\label\{stable:([\w-]+)\}", content)
+
+        # Prefer LaTeX labels (matches PDF behavior), fall back to markdown
+        table_labels = latex_labels if latex_labels else markdown_labels
+
+        # Remove duplicates while preserving order
+        seen = set()
+        unique_labels = [label for label in table_labels if not (label in seen or seen.add(label))]
+
+        return {label: i + 1 for i, label in enumerate(unique_labels)}
+
+    @staticmethod
+    def extract_supplementary_note_labels(content: str) -> Dict[str, int]:
+        r"""Extract supplementary note labels and create number mapping.
+
+        Finds patterns like: {#snote:label}
+
+        Args:
+            content: Markdown content to scan
+
+        Returns:
+            Dict mapping label names to sequential numbers
+
+        Examples:
+            >>> extractor = LabelExtractor()
+            >>> content = "{#snote:methods}\\n\\n{#snote:analysis}"
+            >>> extractor.extract_supplementary_note_labels(content)
+            {'methods': 1, 'analysis': 2}
+        r
+        """
+        labels = re.findall(r"\{#snote:([\w-]+)\}", content)
+        return {label: i + 1 for i, label in enumerate(labels)}
+
+    @staticmethod
+    def extract_equation_labels(content: str) -> Dict[str, int]:
+        r"""Extract equation labels and create number mapping.
+
+        Finds patterns like: {#eq:label}
+
+        Args:
+            content: Markdown content to scan
+
+        Returns:
+            Dict mapping label names to sequential numbers
+
+        Examples:
+            >>> extractor = LabelExtractor()
+            >>> content = "{#eq:energy}\\n\\n{#eq:momentum}"
+            >>> extractor.extract_equation_labels(content)
+            {'energy': 1, 'momentum': 2}
+        r
+        """
+        labels = re.findall(r"\{#eq:([\w-]+)\}", content)
+        return {label: i + 1 for i, label in enumerate(labels)}
+
+    @staticmethod
+    def extract_all_labels(
+        main_content: str, si_content: str = ""
+    ) -> Tuple[Dict[str, int], Dict[str, int], Dict[str, int], Dict[str, int], Dict[str, int]]:
+        r"""Extract all label types from content.
+
+        Convenience method to extract all label types at once. Supplementary
+        elements are extracted from SI content if provided, otherwise from main content.
+
+        Args:
+            main_content: Main manuscript content
+            si_content: Supplementary information content (optional)
+
+        Returns:
+            Tuple of (figure_map, sfig_map, stable_map, snote_map, eq_map)
+
+        Examples:
+            >>> extractor = LabelExtractor()
+            >>> main = "![](fig.png)\\n{#fig:main}\\n{#eq:formula}"
+            >>> si = "![](sfig.png)\\n{#sfig:extra}"
+            >>> fig, sfig, stable, snote, eq = extractor.extract_all_labels(main, si)
+            >>> (fig, sfig, eq)
+            ({'main': 1}, {'extra': 1}, {'formula': 1})
+        r
+        """
+        extractor = LabelExtractor()
+
+        # Main figures and equations from main content
+        figure_map = extractor.extract_figure_labels(main_content)
+        equation_map = extractor.extract_equation_labels(main_content)
+
+        # Supplementary elements from SI content if provided, else main content
+        content_for_si = si_content if si_content else main_content
+
+        sfig_map = extractor.extract_supplementary_figure_labels(content_for_si)
+        stable_map = extractor.extract_supplementary_table_labels(content_for_si)
+        snote_map = extractor.extract_supplementary_note_labels(content_for_si)
+
+        return figure_map, sfig_map, stable_map, snote_map, equation_map

rxiv_maker/utils/pdf_splitter.py

@@ -0,0 +1,116 @@
+"""PDF splitting utilities for separating main and SI sections."""
+
+import logging
+from pathlib import Path
+from typing import Optional, Tuple
+
+from pypdf import PdfReader, PdfWriter
+
+logger = logging.getLogger(__name__)
+
+
+def find_si_start_page(pdf_path: Path) -> Optional[int]:
+    """Find the page number where Supplementary Information starts.
+
+    Args:
+        pdf_path: Path to the PDF file
+
+    Returns:
+        Page number (0-indexed) where SI starts, or None if not found
+    """
+    try:
+        reader = PdfReader(pdf_path)
+
+        # Search for common SI markers
+        si_markers = [
+            "Supplementary Information",
+            "Supplementary Material",
+            "Supplementary Data",
+            "Supporting Information",
+            "SI APPENDIX",
+            "SUPPLEMENTARY FIGURES",
+            "Supplementary Methods",
+        ]
+
+        for page_num, page in enumerate(reader.pages):
+            try:
+                text = page.extract_text()
+
+                # Check for SI markers (case-insensitive)
+                text_upper = text.upper()
+                for marker in si_markers:
+                    if marker.upper() in text_upper:
+                        logger.info(f"Found SI marker '{marker}' on page {page_num + 1}")
+                        return page_num
+
+            except Exception as e:
+                logger.debug(f"Could not extract text from page {page_num}: {e}")
+                continue
+
+        logger.warning("Could not find SI start marker in PDF")
+        return None
+
+    except Exception as e:
+        logger.error(f"Error finding SI start: {e}")
+        return None
+
+
+def split_pdf(
+    pdf_path: Path,
+    si_start_page: Optional[int] = None,
+) -> Tuple[Optional[Path], Optional[Path]]:
+    """Split PDF into main and SI sections.
+
+    Args:
+        pdf_path: Path to the PDF file to split
+        si_start_page: Page number (0-indexed) where SI starts. If None, will auto-detect.
+
+    Returns:
+        Tuple of (main_pdf_path, si_pdf_path). Either may be None if splitting fails.
+    """
+    try:
+        # Auto-detect SI start if not provided
+        if si_start_page is None:
+            si_start_page = find_si_start_page(pdf_path)
+
+        if si_start_page is None:
+            logger.warning("Cannot split PDF: SI start page not found")
+            return None, None
+
+        reader = PdfReader(pdf_path)
+        total_pages = len(reader.pages)
+
+        if si_start_page >= total_pages:
+            logger.error(f"SI start page {si_start_page} exceeds total pages {total_pages}")
+            return None, None
+
+        # Generate output paths
+        stem = pdf_path.stem
+        parent = pdf_path.parent
+
+        main_path = parent / f"{stem}__main.pdf"
+        si_path = parent / f"{stem}__si.pdf"
+
+        # Create main PDF (pages before SI)
+        main_writer = PdfWriter()
+        for page_num in range(si_start_page):
+            main_writer.add_page(reader.pages[page_num])
+
+        with open(main_path, "wb") as f:
+            main_writer.write(f)
+        logger.info(f"Created main PDF: {main_path} ({si_start_page} pages)")
+
+        # Create SI PDF (pages from SI onwards)
+        si_writer = PdfWriter()
+        for page_num in range(si_start_page, total_pages):
+            si_writer.add_page(reader.pages[page_num])
+
+        with open(si_path, "wb") as f:
+            si_writer.write(f)
+        logger.info(f"Created SI PDF: {si_path} ({total_pages - si_start_page} pages)")
+
+        return main_path, si_path
+
+    except Exception as e:
+        logger.error(f"Error splitting PDF: {e}")
+        return None, None

{rxiv_maker-1.16.8.dist-info → rxiv_maker-1.18.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.16.8
+Version: 1.18.0
 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
@@ -56,6 +56,7 @@ Requires-Dist: mypy>=1.0; extra == 'dev'
 Requires-Dist: nbstripout>=0.7.1; extra == 'dev'
 Requires-Dist: nox>=2023.0.0; extra == 'dev'
 Requires-Dist: pre-commit>=4.2.0; extra == 'dev'
+Requires-Dist: pypdf2>=3.0.0; extra == 'dev'
 Requires-Dist: pytest-asyncio>=0.21.0; extra == 'dev'
 Requires-Dist: pytest-benchmark>=4.0.0; extra == 'dev'
 Requires-Dist: pytest-clarity>=1.0.0; extra == 'dev'

{rxiv_maker-1.16.8.dist-info → rxiv_maker-1.18.0.dist-info}/RECORD

@@ -1,5 +1,5 @@
 rxiv_maker/__init__.py,sha256=p04JYC5ZhP6dLXkoWVlKNyiRvsDE1a4C88f9q4xO3tA,3268
-rxiv_maker/__version__.py,sha256=FDIQKkG-uf-zpYYZrGmwOD83CED6k3EcIvKFr382p-g,51
+rxiv_maker/__version__.py,sha256=MVd3J-jKwgAFkETITQ9sUCvhAdXfezvIvUmYNFYviSc,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
@@ -11,7 +11,7 @@ rxiv_maker/cli/main.py,sha256=AwqEcq46MPu8T72iqO39RWemtiD7WiAeUkfxACMUdgs,8697
 rxiv_maker/cli/commands/__init__.py,sha256=jp_dRdPBJNhgZxA7ccAplbtESUBtb81k-boLA5yi3Fg,1396
 rxiv_maker/cli/commands/arxiv.py,sha256=nlAS36lgTNjd6Hn1cdporXFZskf7-Jl-fZLvjxc6gjo,1245
 rxiv_maker/cli/commands/bibliography.py,sha256=3a4gNtY7Lvd5-mwIj-vCD5WwRDgMqPT37tJETthKYKA,2956
-rxiv_maker/cli/commands/build.py,sha256=yjbntR-KxyNzXoBNPAlUKVjQavo5CAmtl_jZSfASjgo,3289
+rxiv_maker/cli/commands/build.py,sha256=v513o3duOD9YvKUoOTggqshqQzwD4THBVIAClJTnx60,3525
 rxiv_maker/cli/commands/cache_management.py,sha256=y58QsuSjzCz_IhY6iXnir8OoblHW5ZBMqItfnfjTP-Y,4577
 rxiv_maker/cli/commands/changelog.py,sha256=OzEay8E8sWfXagjXyWiKwfE-OC9UKokWB7mbINp36t4,8461
 rxiv_maker/cli/commands/check_installation.py,sha256=D_ewz_hGZTqOr_V4eWfnQHOsePTlY1WD3O6XTSpjGNM,1232
@@ -39,11 +39,11 @@ rxiv_maker/cli/framework/config_commands.py,sha256=a1uOQkCCw3d4qlro3OwHIorcoNg03
 rxiv_maker/cli/framework/content_commands.py,sha256=RilxKeG2c1m2fu0CtWAvP3cGh11DGx9P-nh2kIewAg4,22596
 rxiv_maker/cli/framework/decorators.py,sha256=fh085e3k1CaLSMoZevt8hvgnEuejrf-mcNS-dwXoY_A,10365
 rxiv_maker/cli/framework/utility_commands.py,sha256=drIAc1TAYpne76gj7SZeZhPozVAY5uL9GFPVT_Ez0-E,26437
-rxiv_maker/cli/framework/workflow_commands.py,sha256=CFa3c5oJMmy9cUZxTAU97eKC6YrOljzerSAMrywjbKw,29684
+rxiv_maker/cli/framework/workflow_commands.py,sha256=Csls8VGmNCWPjpY9PMfdIAdzDhD_ZmSfRkhdcUihzpk,32699
 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=Y4JpSvoqYU4GnqYC5bnB0Zn0OMTAR_FG3G8hWkgQj0o,8917
+rxiv_maker/converters/citation_processor.py,sha256=8nllASY5K-pCT2jgU1bpLXNRR-SPqWWBIxDy8BR6_5M,9083
 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
@@ -79,7 +79,7 @@ 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=DdM-3_mfrjHFkPQ2vOmpQnXaoSJU-ianVwUvCEIwZss,18829
+rxiv_maker/core/managers/config_manager.py,sha256=G1hlKNqwFO5i3Epq3XDI3awEYowhi_E7TczfMnLzDBQ,18894
 rxiv_maker/core/managers/dependency_manager.py,sha256=qtUR4sQD2x1zv4Fi77d6ThwPx9eHZ9_ZyNy0hRpIKKQ,26308
 rxiv_maker/core/managers/execution_manager.py,sha256=cEDS0KyWBHf_N74Fc8MC4VRXxmEcaz_DJtyWO5-o628,29585
 rxiv_maker/core/managers/file_manager.py,sha256=SVRnP1JQoGCAms3E7iSpOp_RG60P36Qk9HGAmJDaFvE,18641
@@ -104,10 +104,10 @@ rxiv_maker/engines/operations/track_changes.py,sha256=jJZ-XnTFx8TMvcnX8_9D7ydc0G
 rxiv_maker/engines/operations/validate.py,sha256=OVmtRVtG-r1hoA8IqYaNC-ijN1a5ixM3X5Z8Gda-O2M,17142
 rxiv_maker/engines/operations/validate_pdf.py,sha256=qyrtL752Uap3i6ntQheY570soVjFZRJe8ANrw5AvHFs,5899
 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=Q18TuZCbx6fzAs1f9G2A9h5N2Gw5qhCrL7a2NKXizg8,18672
-rxiv_maker/exporters/docx_writer.py,sha256=CW2Xu9-vpuEct9344bM8ofGkCiWlAYijoXVzZ7MQZ6g,43460
+rxiv_maker/exporters/docx_citation_mapper.py,sha256=oSy1LglLvxlmhO18bzl3EInA2PleE8nXqEgQIIRVzwE,5170
+rxiv_maker/exporters/docx_content_processor.py,sha256=FoOaF9BoEpZEF3HG3pzFZFgYbYKwbgRNwkOyURZ8XtI,27895
+rxiv_maker/exporters/docx_exporter.py,sha256=7HYgQSGE_7xl3PTMSPKXIW6yHg-b3MU9ASXG-rKVSXo,21456
+rxiv_maker/exporters/docx_writer.py,sha256=252nqO1_ItJzCiuvsrpVdlU4VbLVMSh5FvFpo4k2GtI,56510
 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
@@ -141,17 +141,21 @@ rxiv_maker/services/publication_service.py,sha256=0p8yQ1jrY3RHwCkzTEl_sAbWYTafRk
 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=mRKUhuNg1VWzryEV-l6tD2pmdQG6b_JDh3_jtrR_K48,16200
+rxiv_maker/templates/registry.py,sha256=XHO3sQBRulsTsYUmP9R3K6RxnYMAehqrY-MoPgGaexE,16206
 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/accent_character_map.py,sha256=L8BDiUH3IPCZ_pQzfsnlY0KkJpbyNpf3nQy4DBUdczE,3484
+rxiv_maker/utils/author_affiliation_processor.py,sha256=UdUsMvRMXtjfJ8g2u6fge1MlgZPciWVu_zPnoSjhNDk,5604
 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=m69JWMIvf9eRiHcaWB-8D3DQCDO8flVIYbOBMuzV-F0,6097
 rxiv_maker/utils/changelog_parser.py,sha256=WCDp9Iy6H6_3nC6FB7RLt6i00zuCyvU17sCU4e3pqCY,11954
+rxiv_maker/utils/citation_range_formatter.py,sha256=1Zb_csGOEWR8YIHWPqLSCzNEs0ogw49Q86BAm9KglrI,3619
 rxiv_maker/utils/citation_utils.py,sha256=spIgVxPAN6jPvoG-eOE00rVX_buUGKnUjP1Fhz31sl4,5134
+rxiv_maker/utils/comment_filter.py,sha256=LcT5EgdvOwP82Gn-zt0Z3iU8_6XL9Cpt87eBOlMHl7o,1522
 rxiv_maker/utils/dependency_checker.py,sha256=EdyIvk-W_bhC1DJCpFw5ePhjEU74C9j7RYMm06unBMA,14366
-rxiv_maker/utils/docx_helpers.py,sha256=rNNnz3mhXymrTgQR4bZDnGwpUFylWVpfpJnY0bWnl30,13635
+rxiv_maker/utils/docx_helpers.py,sha256=xE1PnXjoUaX33GlbW4w7yQq_563MvFkhXBbvrmch-40,12708
 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
@@ -159,7 +163,9 @@ rxiv_maker/utils/file_helpers.py,sha256=qy3CqX6PkfiFSR2XKwASfx038VOnfnnVQL1wGPy2
 rxiv_maker/utils/github.py,sha256=jFzwdI6OPG7Q5w5iOPWUC-OqFqE65UscaGZLs6npGGw,15341
 rxiv_maker/utils/homebrew_checker.py,sha256=tyqnYMxxyONN-1krEJk8sYGOv-FhJZGgkvBny7xSZvI,3978
 rxiv_maker/utils/install_detector.py,sha256=4Ir_ZAM-wrarxBkup7WuUYcT48t0P2c9IeTDWkp_q4w,3869
+rxiv_maker/utils/label_extractor.py,sha256=xQpWieDvBdQNpJBHVXpP-wA083LH68NAF4k1MVDm5T4,6816
 rxiv_maker/utils/operation_ids.py,sha256=dH9m7OGRrk2EG5abnJFF_1KPQ80lLZLcZD_KYaT9GwI,6083
+rxiv_maker/utils/pdf_splitter.py,sha256=aDyMMg7bxQOWpZIvjLX9SR8BsIibL0ngSlrrryXEy5I,3601
 rxiv_maker/utils/pdf_utils.py,sha256=MwT5RSnQ3OJHuFDQ_OP6BOcB-h6HfF618t6-j5icnyk,4253
 rxiv_maker/utils/performance.py,sha256=EBDVNshSaeG7Nu-GCZtRAzTunGn4z_Bb2jEck045bxo,8169
 rxiv_maker/utils/platform.py,sha256=DCD3gvm7_DBcT67gGIXhTDV5mPrBjWrL7R2JdsmIgng,17773
@@ -187,9 +193,9 @@ rxiv_maker/validators/doi/api_clients.py,sha256=tqdYUq8LFgRIO0tWfcenwmy2uO-IB1-G
 rxiv_maker/validators/doi/metadata_comparator.py,sha256=euqHhKP5sHQAdZbdoAahUn6YqJqOfXIOobNgAqFHlN8,11533
 rxiv_maker/tex/template.tex,sha256=zrJ3aFfu8j9zkg1l375eE9w-j42P3rz16wMD3dSgi1I,1354
 rxiv_maker/tex/style/rxiv_maker_style.bst,sha256=jbVqrJgAm6F88cow5vtZuPBwwmlcYykclTm8RvZIo6Y,24281
-rxiv_maker/tex/style/rxiv_maker_style.cls,sha256=F2qtnS9mI6SwOIaVH76egXZkB2_GzbH4gCTG_ZcfCDQ,24253
-rxiv_maker-1.16.8.dist-info/METADATA,sha256=3GydBaQKqwL3nUaxEPdNRRobVMhmb7hRvJW7e5qQ_gc,18177
-rxiv_maker-1.16.8.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rxiv_maker-1.16.8.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
-rxiv_maker-1.16.8.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
-rxiv_maker-1.16.8.dist-info/RECORD,,
+rxiv_maker/tex/style/rxiv_maker_style.cls,sha256=6VDmZE0uvYWog6rcYi2K_NIM9-Pgjx9AFdRg_sTheK0,24374
+rxiv_maker-1.18.0.dist-info/METADATA,sha256=uJSb2e2tMW1eUvob2E8iKM5kJAVZsILejVNbG_Uitto,18222
+rxiv_maker-1.18.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rxiv_maker-1.18.0.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
+rxiv_maker-1.18.0.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
+rxiv_maker-1.18.0.dist-info/RECORD,,