rxiv-maker 1.17.0__py3-none-any.whl → 1.18.1__py3-none-any.whl

rxiv_maker/exporters/docx_writer.py

@@ -4,6 +4,7 @@ This module handles the actual generation of DOCX files using python-docx,
 writing structured content with formatting, citations, and references.
 """
 
+import base64
 from pathlib import Path
 from typing import Any, Dict, Optional
 
@@ -11,11 +12,12 @@ from docx import Document
 from docx.enum.text import WD_ALIGN_PARAGRAPH, WD_COLOR_INDEX
 from docx.oxml import OxmlElement
 from docx.oxml.ns import qn
-from docx.shared import Inches, Pt
+from docx.shared import Pt, RGBColor
 from latex2mathml.converter import convert as latex_to_mathml
 from lxml import etree
 
 from ..core.logging_config import get_logger
+from ..utils.author_affiliation_processor import AuthorAffiliationProcessor
 from ..utils.docx_helpers import convert_pdf_to_image
 
 logger = get_logger()
@@ -57,6 +59,8 @@ class DocxWriter:
         metadata: Optional[Dict[str, Any]] = None,
         table_map: Optional[Dict[str, int]] = None,
         figures_at_end: bool = False,
+        hide_highlighting: bool = False,
+        hide_comments: bool = False,
     ) -> Path:
         """Write DOCX file from structured content.
 
@@ -69,6 +73,8 @@ class DocxWriter:
             metadata: Document metadata (title, authors, affiliations)
             table_map: Mapping from table labels to numbers (for supplementary tables)
             figures_at_end: Place main figures at end before SI/bibliography
+            hide_highlighting: Disable colored highlighting on references and citations
+            hide_comments: Exclude all comments (block and inline) from output
 
         Returns:
             Path to created DOCX file
@@ -77,8 +83,13 @@ class DocxWriter:
         self.bibliography = bibliography
         self.include_footnotes = include_footnotes
         self.table_map = table_map or {}
+        self.hide_highlighting = hide_highlighting
+        self.hide_comments = hide_comments
         doc = Document()
 
+        # Set default font to Arial for entire document
+        self._set_default_font(doc, "Arial")
+
         # Add title and author information if metadata provided
         if metadata:
             self._add_title_page(doc, metadata)
@@ -123,14 +134,18 @@ class DocxWriter:
         # Add collected main figures at the end (before bibliography)
         if figures_at_end and collected_main_figures:
             doc.add_page_break()
-            doc.add_heading("Figures", level=1)
+            heading = doc.add_heading("Figures", level=1)
+            for run in heading.runs:
+                run.font.color.rgb = RGBColor(0, 0, 0)  # Ensure black text
             for section, fig_num in collected_main_figures:
                 self._add_figure(doc, section, figure_number=fig_num, is_supplementary=False)
 
         # Add bibliography section at the end
         if include_footnotes and bibliography:
             doc.add_page_break()
-            doc.add_heading("Bibliography", level=1)
+            heading = doc.add_heading("Bibliography", level=1)
+            for run in heading.runs:
+                run.font.color.rgb = RGBColor(0, 0, 0)  # Ensure black text
 
             # Add numbered bibliography entries
             for num in sorted(bibliography.keys()):
@@ -144,12 +159,12 @@ class DocxWriter:
                 # Add formatted bibliography text (without DOI - added separately below)
                 para.add_run(bib_entry["formatted"])
 
-                # Add DOI as hyperlink with yellow highlighting if present
+                # Add DOI as hyperlink with yellow highlighting if present (unless hide_highlighting is enabled)
                 if bib_entry.get("doi"):
                     doi = bib_entry["doi"]
                     doi_url = f"https://doi.org/{doi}" if not doi.startswith("http") else doi
                     para.add_run("\nDOI: ")
-                    self._add_hyperlink(para, doi_url, doi_url, highlight=True)
+                    self._add_hyperlink(para, doi_url, doi_url, highlight=not self.hide_highlighting)
 
                 # Add spacing between entries
                 para.paragraph_format.space_after = Pt(6)
@@ -158,6 +173,38 @@ class DocxWriter:
         doc.save(str(output_path))
         return output_path
 
+    def _set_default_font(self, doc: Document, font_name: str):
+        """Set the default font for the entire document.
+
+        Args:
+            doc: Document object
+            font_name: Font name to use (e.g., "Arial", "Times New Roman")
+        """
+        # Set font on Normal style (base style for most content)
+        style = doc.styles["Normal"]
+        font = style.font
+        font.name = font_name
+        font.size = Pt(10)  # Default body font size
+
+        # Also set on heading styles to ensure consistency
+        for i in range(1, 10):
+            try:
+                heading_style = doc.styles[f"Heading {i}"]
+                heading_style.font.name = font_name
+            except KeyError:
+                # Heading style doesn't exist, skip
+                pass
+
+    def _apply_highlight(self, run, color: WD_COLOR_INDEX):
+        """Apply highlight color to a run, unless highlighting is disabled.
+
+        Args:
+            run: The run object to apply highlighting to
+            color: The WD_COLOR_INDEX color to apply
+        """
+        if not self.hide_highlighting:
+            run.font.highlight_color = color
+
     def _add_title_page(self, doc: Document, metadata: Dict[str, Any]):
         """Add title, author and affiliation information.
 
@@ -193,27 +240,16 @@ class DocxWriter:
         if not authors:
             return  # Nothing more to add
 
-        # Collect unique affiliations and build mapping
-        all_affiliations = []
-        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_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
+        # Process author and affiliation metadata using centralized processor
+        processor = AuthorAffiliationProcessor()
+        processed = processor.process(metadata)
+
+        affiliation_map = processed["affiliation_map"]
+        ordered_affiliations = processed["ordered_affiliations"]
+        cofirst_authors = processed["cofirst_authors"]
+        corresponding_authors = processed["corresponding_authors"]
+
+        # Add authors with superscript affiliation numbers and corresponding author markers
         if authors:
             author_para = doc.add_paragraph()
             for i, author in enumerate(authors):
@@ -231,25 +267,94 @@ class DocxWriter:
                     sup_run = author_para.add_run(",".join(affil_nums))
                     sup_run.font.superscript = True
 
+                # Add co-first author marker (dagger) if applicable
+                is_cofirst = author.get("co_first_author", False)
+                if is_cofirst:
+                    cofirst_run = author_para.add_run("†")
+                    cofirst_run.font.superscript = True
+
+                # Add corresponding author marker (asterisk) if applicable
+                is_corresponding = author.get("corresponding_author", False)
+                if is_corresponding:
+                    corr_run = author_para.add_run("*")
+                    corr_run.font.superscript = True
+
             author_para.paragraph_format.space_after = Pt(8)
 
         # Add affiliations
-        if all_affiliations:
-            for i, affil_text in enumerate(all_affiliations, start=1):
+        if ordered_affiliations:
+            for affil_num, _affil_shortname, affil_text in ordered_affiliations:
                 affil_para = doc.add_paragraph()
 
                 # Add superscript number
-                num_run = affil_para.add_run(str(i))
+                num_run = affil_para.add_run(str(affil_num))
                 num_run.font.superscript = True
+                num_run.font.size = Pt(8)
 
                 # Add affiliation text
-                affil_para.add_run(f" {affil_text}")
+                affil_run = affil_para.add_run(f" {affil_text}")
+                affil_run.font.size = Pt(8)
                 affil_para.paragraph_format.space_after = Pt(4)
-                affil_para.runs[1].font.size = Pt(10)
 
             # Extra space after last affiliation
             affil_para.paragraph_format.space_after = Pt(12)
 
+        # Add co-first author information if any (already extracted by processor)
+        if cofirst_authors:
+            cofirst_para = doc.add_paragraph()
+            cofirst_marker = cofirst_para.add_run("†")
+            cofirst_marker.font.superscript = True
+            cofirst_marker.font.size = Pt(8)
+
+            cofirst_label = cofirst_para.add_run(" These authors contributed equally: ")
+            cofirst_label.font.size = Pt(8)
+
+            for i, author in enumerate(cofirst_authors):
+                if i > 0:
+                    sep_run = cofirst_para.add_run(", ")
+                    sep_run.font.size = Pt(8)
+
+                name = author.get("name", "")
+                name_run = cofirst_para.add_run(name)
+                name_run.font.size = Pt(8)
+
+            cofirst_para.paragraph_format.space_after = Pt(12)
+
+        # Add corresponding author information if any (already extracted by processor)
+        if corresponding_authors:
+            corr_para = doc.add_paragraph()
+            corr_marker = corr_para.add_run("*")
+            corr_marker.font.superscript = True
+            corr_marker.font.size = Pt(8)
+
+            corr_label = corr_para.add_run(" Correspondence: ")
+            corr_label.font.size = Pt(8)
+
+            for i, author in enumerate(corresponding_authors):
+                if i > 0:
+                    sep_run = corr_para.add_run("; ")
+                    sep_run.font.size = Pt(8)
+
+                name = author.get("name", "")
+                email = author.get("email", "")
+
+                # Decode email if it's base64 encoded
+                if not email:
+                    email64 = author.get("email64", "")
+                    if email64:
+                        try:
+                            email = base64.b64decode(email64).decode("utf-8")
+                        except Exception:
+                            email = ""
+
+                if email:
+                    info_run = corr_para.add_run(f"{name} ({email})")
+                else:
+                    info_run = corr_para.add_run(name)
+                info_run.font.size = Pt(8)
+
+            corr_para.paragraph_format.space_after = Pt(12)
+
     def _add_section(
         self,
         doc: Document,
@@ -278,7 +383,8 @@ class DocxWriter:
         elif section_type == "code_block":
             self._add_code_block(doc, section)
         elif section_type == "comment":
-            self._add_comment(doc, section)
+            if not self.hide_comments:
+                self._add_comment(doc, section)
         elif section_type == "figure":
             self._add_figure(doc, section)
         elif section_type == "table":
@@ -304,6 +410,7 @@ class DocxWriter:
         run = para.add_run(text)
         run.bold = True
         run.font.size = Pt(12)
+        run.font.color.rgb = RGBColor(0, 0, 0)  # Ensure black text
 
     def _add_heading(self, doc: Document, section: Dict[str, Any]):
         """Add heading to document.
@@ -314,7 +421,10 @@ class DocxWriter:
         """
         level = section["level"]
         text = section["text"]
-        doc.add_heading(text, level=level)
+        heading = doc.add_heading(text, level=level)
+        # Ensure heading text is black (not blue)
+        for run in heading.runs:
+            run.font.color.rgb = RGBColor(0, 0, 0)  # Explicitly set to black
 
     def _add_paragraph(
         self,
@@ -371,9 +481,9 @@ class DocxWriter:
             if run_data.get("xref"):
                 # Use color based on xref type (fig, sfig, stable, eq, etc.)
                 xref_type = run_data.get("xref_type", "cite")
-                run.font.highlight_color = self.get_xref_color(xref_type)
+                self._apply_highlight(run, self.get_xref_color(xref_type))
             if run_data.get("highlight_yellow"):
-                run.font.highlight_color = WD_COLOR_INDEX.YELLOW
+                self._apply_highlight(run, WD_COLOR_INDEX.YELLOW)
 
         elif run_data["type"] == "hyperlink":
             # Add hyperlink with yellow highlighting
@@ -387,18 +497,19 @@ class DocxWriter:
             self._add_inline_equation(paragraph, latex_content)
 
         elif run_data["type"] == "inline_comment":
-            # Add inline comment with gray highlighting
-            comment_text = run_data["text"]
-            run = paragraph.add_run(f"[Comment: {comment_text}]")
-            run.font.highlight_color = WD_COLOR_INDEX.GRAY_25
-            run.italic = True
-            run.font.size = Pt(10)
+            # Add inline comment with gray highlighting (unless hide_comments is enabled)
+            if not self.hide_comments:
+                comment_text = run_data["text"]
+                run = paragraph.add_run(f"[Comment: {comment_text}]")
+                self._apply_highlight(run, WD_COLOR_INDEX.GRAY_25)
+                run.italic = True
+                run.font.size = Pt(10)
 
         elif run_data["type"] == "citation":
             cite_num = run_data["number"]
             # Add citation as [NN] inline with yellow highlighting
             run = paragraph.add_run(f"[{cite_num}]")
-            run.font.highlight_color = WD_COLOR_INDEX.YELLOW
+            self._apply_highlight(run, WD_COLOR_INDEX.YELLOW)
             run.font.size = Pt(10)
 
     def _add_list(self, doc: Document, section: Dict[str, Any]):
@@ -436,12 +547,12 @@ class DocxWriter:
                     if run_data.get("xref"):
                         # Use color based on xref type
                         xref_type = run_data.get("xref_type", "cite")
-                        run.font.highlight_color = self.get_xref_color(xref_type)
+                        self._apply_highlight(run, self.get_xref_color(xref_type))
                     if run_data.get("highlight_yellow"):
-                        run.font.highlight_color = WD_COLOR_INDEX.YELLOW
+                        self._apply_highlight(run, WD_COLOR_INDEX.YELLOW)
                         run.font.size = Pt(10)
                     if run_data.get("highlight_yellow"):
-                        run.font.highlight_color = WD_COLOR_INDEX.YELLOW
+                        self._apply_highlight(run, WD_COLOR_INDEX.YELLOW)
                 elif run_data["type"] == "hyperlink":
                     text = run_data.get("text", "")
                     url = run_data.get("url", "")
@@ -451,18 +562,19 @@ class DocxWriter:
                     latex_content = run_data.get("latex", "")
                     self._add_inline_equation(paragraph, latex_content)
                 elif run_data["type"] == "inline_comment":
-                    # Add inline comment with gray highlighting
-                    comment_text = run_data["text"]
-                    run = paragraph.add_run(f"[Comment: {comment_text}]")
-                    run.font.highlight_color = WD_COLOR_INDEX.GRAY_25
-                    run.italic = True
-                    run.font.size = Pt(10)
+                    # Add inline comment with gray highlighting (unless hide_comments is enabled)
+                    if not self.hide_comments:
+                        comment_text = run_data["text"]
+                        run = paragraph.add_run(f"[Comment: {comment_text}]")
+                        self._apply_highlight(run, WD_COLOR_INDEX.GRAY_25)
+                        run.italic = True
+                        run.font.size = Pt(10)
                 elif run_data["type"] == "citation":
                     cite_num = run_data["number"]
                     run = paragraph.add_run(f"[{cite_num}]")
                     run.bold = True
                     run.font.size = Pt(10)
-                    run.font.highlight_color = WD_COLOR_INDEX.YELLOW
+                    self._apply_highlight(run, WD_COLOR_INDEX.YELLOW)
 
     def _add_code_block(self, doc: Document, section: Dict[str, Any]):
         """Add code block to document.
@@ -495,7 +607,7 @@ class DocxWriter:
 
         # Add comment text with light gray highlighting to distinguish from colored xrefs
         run = paragraph.add_run(f"[Comment: {comment_text}]")
-        run.font.highlight_color = WD_COLOR_INDEX.GRAY_25
+        self._apply_highlight(run, WD_COLOR_INDEX.GRAY_25)
         run.italic = True
         run.font.size = Pt(10)
 
@@ -577,9 +689,22 @@ class DocxWriter:
                     img_width, img_height = img.size
                     aspect_ratio = img_width / img_height
 
-                # Page dimensions with margins (Letter size: 8.5 x 11 inches, 1 inch margins)
-                max_width = Inches(6.5)  # 8.5 - 2*1
-                max_height = Inches(9)  # 11 - 2*1
+                # Calculate available width from document section settings
+                # Get the current section to read actual page dimensions and margins
+                section = doc.sections[-1]  # Use the most recent section
+
+                # Page width minus left and right margins
+                available_width = section.page_width - section.left_margin - section.right_margin
+
+                # Page height minus top and bottom margins
+                available_height = section.page_height - section.top_margin - section.bottom_margin
+
+                # Convert available width to Inches for comparison
+                max_width = available_width
+                max_height = available_height
+
+                # Calculate aspect ratio thresholds
+                page_aspect_ratio = available_width / available_height
 
                 # Add figure centered
                 # Note: add_picture() creates a paragraph automatically, but we need to add it explicitly
@@ -588,7 +713,7 @@ class DocxWriter:
                 fig_para.alignment = WD_ALIGN_PARAGRAPH.CENTER
 
                 # Calculate optimal size maintaining aspect ratio
-                if aspect_ratio > (6.5 / 9):  # Wide image - constrain by width
+                if aspect_ratio > page_aspect_ratio:  # Wide image - constrain by width
                     run = fig_para.add_run()
                     run.add_picture(img_source, width=max_width)
                 else:  # Tall image - constrain by height
@@ -625,11 +750,11 @@ class DocxWriter:
                 else:
                     run = caption_para.add_run(f"Fig. {figure_number}. ")
                 run.bold = True
-                run.font.size = Pt(7)
+                run.font.size = Pt(8)
             else:
                 run = caption_para.add_run("Figure: ")
                 run.bold = True
-                run.font.size = Pt(7)
+                run.font.size = Pt(8)
 
             # Parse and add caption with inline formatting
             # Import the processor to parse inline formatting
@@ -642,7 +767,7 @@ class DocxWriter:
                 if run_data["type"] == "text":
                     text = run_data["text"]
                     run = caption_para.add_run(text)
-                    run.font.size = Pt(7)
+                    run.font.size = Pt(8)
 
                     # Apply formatting
                     if run_data.get("bold"):
@@ -658,26 +783,27 @@ class DocxWriter:
                     if run_data.get("xref"):
                         # Use color based on xref type
                         xref_type = run_data.get("xref_type", "cite")
-                        run.font.highlight_color = self.get_xref_color(xref_type)
+                        self._apply_highlight(run, self.get_xref_color(xref_type))
                     if run_data.get("highlight_yellow"):
-                        run.font.highlight_color = WD_COLOR_INDEX.YELLOW
+                        self._apply_highlight(run, WD_COLOR_INDEX.YELLOW)
                 elif run_data["type"] == "inline_equation":
                     # Add inline equation as Office Math
                     latex_content = run_data.get("latex", "")
                     self._add_inline_equation(caption_para, latex_content)
                 elif run_data["type"] == "inline_comment":
-                    # Add inline comment with gray highlighting
-                    comment_text = run_data["text"]
-                    run = caption_para.add_run(f"[Comment: {comment_text}]")
-                    run.font.highlight_color = WD_COLOR_INDEX.GRAY_25
-                    run.italic = True
-                    run.font.size = Pt(7)
+                    # Add inline comment with gray highlighting (unless hide_comments is enabled)
+                    if not self.hide_comments:
+                        comment_text = run_data["text"]
+                        run = caption_para.add_run(f"[Comment: {comment_text}]")
+                        self._apply_highlight(run, WD_COLOR_INDEX.GRAY_25)
+                        run.italic = True
+                        run.font.size = Pt(8)
                 elif run_data["type"] == "citation":
                     cite_num = run_data["number"]
                     run = caption_para.add_run(f"[{cite_num}]")
                     run.bold = True
-                    run.font.size = Pt(7)
-                    run.font.highlight_color = WD_COLOR_INDEX.YELLOW
+                    run.font.size = Pt(8)
+                    self._apply_highlight(run, WD_COLOR_INDEX.YELLOW)
 
             # Add spacing after figure (reduced from 12 to 6 for compactness)
             caption_para.paragraph_format.space_after = Pt(6)
@@ -752,7 +878,7 @@ class DocxWriter:
                             if run_data.get("xref"):
                                 # Use color based on xref type
                                 xref_type = run_data.get("xref_type", "cite")
-                                run.font.highlight_color = self.get_xref_color(xref_type)
+                                self._apply_highlight(run, self.get_xref_color(xref_type))
 
         # Add table caption if present
         caption = section.get("caption")
@@ -775,7 +901,7 @@ class DocxWriter:
                     # Fallback if label not in map
                     run = caption_para.add_run("Supp. Table: ")
                 run.bold = True
-                run.font.size = Pt(7)
+                run.font.size = Pt(8)
             elif label and label.startswith("table:"):
                 # Extract label name for main tables
                 label_name = label.split(":", 1)[1] if ":" in label else label
@@ -786,7 +912,7 @@ class DocxWriter:
                 else:
                     run = caption_para.add_run("Table: ")
                 run.bold = True
-                run.font.size = Pt(7)
+                run.font.size = Pt(8)
 
             # Parse and add caption with inline formatting
             caption_runs = processor._parse_inline_formatting(caption, {})
@@ -794,7 +920,7 @@ class DocxWriter:
                 if run_data["type"] == "text":
                     text = run_data["text"]
                     run = caption_para.add_run(text)
-                    run.font.size = Pt(7)
+                    run.font.size = Pt(8)
                     if run_data.get("bold"):
                         run.bold = True
                     if run_data.get("italic"):
@@ -810,7 +936,7 @@ class DocxWriter:
                     if run_data.get("xref"):
                         # Use color based on xref type
                         xref_type = run_data.get("xref_type", "cite")
-                        run.font.highlight_color = self.get_xref_color(xref_type)
+                        self._apply_highlight(run, self.get_xref_color(xref_type))
 
             # Add spacing after table (reduced from 12 to 6 for compactness)
             caption_para.paragraph_format.space_after = Pt(6)

rxiv_maker/processors/template_processor.py

@@ -639,6 +639,16 @@ def process_template_replacements(template_content, yaml_metadata, article_md, o
         acknowledgements_block = ""
     template_content = template_content.replace("<PY-RPL:ACKNOWLEDGEMENTS-BLOCK>", acknowledgements_block)
 
+    # Funding
+    funding = content_sections.get("funding", "").strip()
+    if funding:
+        funding_block = f"""\\begin{{funding}}
+{funding}
+\\end{{funding}}"""
+    else:
+        funding_block = ""
+    template_content = template_content.replace("<PY-RPL:FUNDING-BLOCK>", funding_block)
+
     # Competing Interests
     competing_interests = content_sections.get("competing_interests", "").strip()
     if competing_interests:

rxiv_maker/templates/registry.py

@@ -190,9 +190,29 @@ Interpret your results in the context of existing literature and theory. Discuss
 
 Summarize your key findings and their significance. Reinforce the main contributions of your work and their broader impact on the field. Keep this section concise but impactful, leaving readers with a clear understanding of what your research has accomplished and why it matters.
 
-## References
+## Data Availability
 
-Citations are automatically formatted from 03_REFERENCES.bib. Reference works using citation keys like [@smith2023] for single citations or [@smith2023; @johnson2022] for multiple citations.
+Describe where the data supporting the findings of this study are available. Include repository names, accession numbers, DOIs, or URLs. If data are available upon request, state this clearly with contact information.
+
+## Code Availability
+
+Provide information about the availability of code, software, or algorithms used in this study. Include repository URLs (e.g., GitHub), software package names with version numbers, and any licensing information.
+
+## Author Contributions
+
+Describe the specific contributions of each author to the work. Use initials to identify authors and describe their roles (e.g., "A.B. and C.D. designed the study. A.B. performed experiments. C.D. analyzed data. All authors contributed to writing the manuscript.").
+
+## Acknowledgements
+
+Acknowledge individuals, groups, or organizations that contributed to the work but do not meet authorship criteria. This may include technical assistance, discussions, or provision of materials.
+
+## Funding
+
+Provide information about funding sources, grant numbers, and supporting organizations. If no external funding was received, state "This research received no external funding."
+
+## Competing Interests
+
+The authors declare no competing interests.
 """
 
     def _get_default_supplementary_template(self) -> str:
@@ -353,10 +373,6 @@ Organize your content with additional sections as needed.
 ## Conclusions
 
 Summarize your conclusions.
-
-## References
-
-Add citations using [@ref_key].
 """
 
     def _get_minimal_supplementary_template(self) -> str:
@@ -436,9 +452,29 @@ Suggest future research directions.
 
 Summarize key conclusions.
 
-## References
+## Data Availability
+
+Describe where the data supporting the findings of this study are available. Include repository names, accession numbers, DOIs, or URLs. If data are available upon request, state this clearly with contact information.
+
+## Code Availability
 
-[@ref]
+Provide information about the availability of code, software, or algorithms used in this study. Include repository URLs (e.g., GitHub), software package names with version numbers, and any licensing information.
+
+## Author Contributions
+
+Describe the specific contributions of each author to the work. Use initials to identify authors and describe their roles (e.g., "A.B. and C.D. designed the study. A.B. performed experiments. C.D. analyzed data. All authors contributed to writing the manuscript.").
+
+## Acknowledgements
+
+Acknowledge individuals, groups, or organizations that contributed to the work but do not meet authorship criteria. This may include technical assistance, discussions, or provision of materials.
+
+## Funding
+
+Provide information about funding sources, grant numbers, and supporting organizations. If no external funding was received, state "This research received no external funding."
+
+## Competing Interests
+
+The authors declare no competing interests.
 """
 
     # Preprint template methods
@@ -485,13 +521,17 @@ Links to data repositories, code, and protocols for reproducibility.
 
 Detailed author contribution statements.
 
-## Competing Interests
+## Acknowledgements
 
-Declaration of competing interests.
+Acknowledge individuals, groups, or organizations that contributed to the work but do not meet authorship criteria. This may include technical assistance, discussions, or provision of materials.
 
-## References
+## Funding
 
-[@ref]
+Provide information about funding sources, grant numbers, and supporting organizations. If no external funding was received, state "This research received no external funding."
+
+## Competing Interests
+
+Declaration of competing interests.
 """
 
 

rxiv_maker/tex/template.tex

@@ -48,6 +48,8 @@
 
 <PY-RPL:ACKNOWLEDGEMENTS-BLOCK>
 
+<PY-RPL:FUNDING-BLOCK>
+
 <PY-RPL:COMPETING-INTERESTS-BLOCK>
 
 \begin{exauthor}