rxiv-maker 1.18.0__tar.gz → 1.18.2__tar.gz

{rxiv_maker-1.18.0 → rxiv_maker-1.18.2}/CHANGELOG.md

@@ -7,7 +7,56 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-## [1.18.0] - 2025-12-23
+## [1.18.2] - 2026-01-06
+
+### Fixed
+
+- **Table Caption Parser Enhancement**: Improved robustness of table caption detection
+  - Flexible whitespace handling: Parser now skips blank lines and HTML comments between tables and captions
+  - Cross-reference support: Table captions can now include references to figures, tables, and equations
+  - Dynamic line-skipping logic: Intelligently determines how many lines to skip based on actual content
+  - Fixes issues where captions separated from tables by comments or extra whitespace were not detected
+
+## [1.18.1] - 2024-12-24
+
+### Added
+
+- **Complete Template Sections**: All standard manuscript sections now included by default in `rxiv init`
+  - Data Availability: Repository information and DOI guidance
+  - Code Availability: GitHub links, software versions, licensing details
+  - Author Contributions: Role descriptions with author initials
+  - Acknowledgements: Non-author contributors and assistance
+  - Funding: Grant information and funding declarations
+  - Competing Interests: Conflict of interest statements
+  - Ensures manuscripts include all sections required by most journals
+
+### Changed
+
+- **Template Standardization**: Consistent section structure across all template types
+  - Journal template now includes all standard sections (Data/Code Availability, Author Contributions, Acknowledgements)
+  - Preprint template now includes Acknowledgements section
+  - All templates use same section ordering for consistency
+
+### Fixed
+
+- **Funding Section in PDF**: Funding section now correctly appears in generated PDFs
+  - Added `<PY-RPL:FUNDING-BLOCK>` placeholder to LaTeX template
+  - Added funding block generation logic to template processor
+  - Funding environment was defined in style file but not used in pipeline
+- **DOCX Figure Width**: Figures no longer exceed text line width in DOCX output
+  - Changed from hardcoded 6.5" width to dynamic calculation from document dimensions
+  - Calculates available width from page width minus left/right margins
+  - Ensures figures fit properly regardless of page size or margin settings
+- **Template Clarity**: Removed confusing "References" heading from all templates
+  - Eliminates confusion between manual References heading and auto-generated Bibliography section
+  - Users no longer see duplicate or conflicting reference-related headings
+
+### Documentation
+
+- Template placeholder text provides clear guidance on what content to include in each section
+- Section ordering follows standard scientific manuscript structure
+
+## [1.18.0] - 2024-12-23
 
 ### Added
 

{rxiv_maker-1.18.0 → rxiv_maker-1.18.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.18.0
+Version: 1.18.2
 Summary: Write scientific preprints in Markdown. Generate publication-ready PDFs efficiently.
 Project-URL: Homepage, https://github.com/HenriquesLab/rxiv-maker
 Project-URL: Documentation, https://github.com/HenriquesLab/rxiv-maker#readme

{rxiv_maker-1.18.0 → rxiv_maker-1.18.2}/src/rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.18.0"
+__version__ = "1.18.2"

{rxiv_maker-1.18.0 → rxiv_maker-1.18.2}/src/rxiv_maker/converters/table_processor.py

@@ -139,9 +139,9 @@ def convert_tables_to_latex(
                     result_lines.pop()  # Remove caption line
 
             # Check for new format table caption after the table
-            new_format_caption, table_id, rotation_angle = _parse_table_caption(lines, i)
-            if new_format_caption:
-                i += 2  # Skip blank line and caption line
+            new_format_caption, table_id, rotation_angle, lines_to_skip = _parse_table_caption(lines, i)
+            if new_format_caption and lines_to_skip:
+                i += lines_to_skip  # Skip blank lines, comments, and caption line
 
             # Generate LaTeX table with the processed caption
             latex_table = generate_latex_table(
@@ -844,39 +844,68 @@ def _is_table_row(line: str) -> bool:
     return "|" in line and line.startswith("|") and line.endswith("|")
 
 
-def _parse_table_caption(lines: list[str], i: int) -> tuple[str | None, str | None, int | None]:
-    """Parse table caption in new format after table."""
+def _parse_table_caption(lines: list[str], i: int) -> tuple[str | None, str | None, int | None, int | None]:
+    """Parse table caption in new format after table.
+
+    Returns:
+        tuple of (caption, table_id, rotation_angle, lines_to_skip)
+        lines_to_skip indicates how many lines after position i should be skipped
+    """
     new_format_caption = None
     table_id = None
     rotation_angle = None
+    lines_to_skip = None
 
-    if (
-        i < len(lines)
-        and lines[i].strip() == ""
-        and i + 1 < len(lines)
-        and re.match(r"^\{#[a-zA-Z0-9_:-]+.*\}\s*\*\*.*\*\*", lines[i + 1].strip())
-    ):
-        # Found new format caption, parse it
-        caption_line = lines[i + 1].strip()
-
-        # Parse caption with optional attributes like rotate=90
-        caption_match = re.match(r"^\{#([a-zA-Z0-9_:-]+)([^}]*)\}\s*(.+)$", caption_line)
-        if caption_match:
-            table_id = caption_match.group(1)
-            attributes_str = caption_match.group(2).strip()
-            caption_text = caption_match.group(3)
-
-            # Extract rotation attribute if present
-            if attributes_str:
-                rotation_match = re.search(r"rotate=(\d+)", attributes_str)
-                if rotation_match:
-                    rotation_angle = int(rotation_match.group(1))
-
-            # Process caption text to handle markdown formatting
-            new_format_caption = re.sub(r"\*\*([^*]+)\*\*", r"\\textbf{\1}", caption_text)
-            new_format_caption = re.sub(r"\*([^*]+)\*", r"\\textit{\1}", new_format_caption)
-
-    return new_format_caption, table_id, rotation_angle
+    # Look ahead for caption, skipping blank lines and HTML comments
+    # Search up to 5 lines ahead to be flexible
+    search_limit = min(i + 5, len(lines))
+
+    for offset in range(search_limit - i):
+        check_line = lines[i + offset].strip()
+
+        # Skip blank lines and HTML comments
+        if check_line == "" or (check_line.startswith("<!--") and check_line.endswith("-->")):
+            continue
+
+        # Check if this is a new-format caption
+        if re.match(r"^\{#[a-zA-Z0-9_:-]+.*\}\s*\*\*.*\*\*", check_line):
+            caption_line = check_line
+
+            # Parse caption with optional attributes like rotate=90
+            caption_match = re.match(r"^\{#([a-zA-Z0-9_:-]+)([^}]*)\}\s*(.+)$", caption_line)
+            if caption_match:
+                table_id = caption_match.group(1)
+                attributes_str = caption_match.group(2).strip()
+                caption_text = caption_match.group(3)
+
+                # Extract rotation attribute if present
+                if attributes_str:
+                    rotation_match = re.search(r"rotate=(\d+)", attributes_str)
+                    if rotation_match:
+                        rotation_angle = int(rotation_match.group(1))
+
+                # Process caption text to handle markdown formatting
+                new_format_caption = re.sub(r"\*\*([^*]+)\*\*", r"\\textbf{\1}", caption_text)
+                new_format_caption = re.sub(r"\*([^*]+)\*", r"\\textit{\1}", new_format_caption)
+
+                # Convert cross-references (figures, tables, equations) in caption
+                from .figure_processor import (
+                    convert_equation_references_to_latex,
+                    convert_figure_references_to_latex,
+                )
+
+                new_format_caption = convert_figure_references_to_latex(new_format_caption)
+                new_format_caption = convert_table_references_to_latex(new_format_caption)
+                new_format_caption = convert_equation_references_to_latex(new_format_caption)
+
+                # Return how many lines to skip (all lines from i to caption, inclusive)
+                lines_to_skip = offset + 1
+                break
+        else:
+            # Found a non-blank, non-comment, non-caption line - stop searching
+            break
+
+    return new_format_caption, table_id, rotation_angle, lines_to_skip
 
 
 def _split_table_row_respecting_backticks(row: str) -> list[str]:

{rxiv_maker-1.18.0 → rxiv_maker-1.18.2}/src/rxiv_maker/exporters/docx_writer.py

@@ -12,7 +12,7 @@ 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, RGBColor
+from docx.shared import Pt, RGBColor
 from latex2mathml.converter import convert as latex_to_mathml
 from lxml import etree
 
@@ -689,9 +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
@@ -700,7 +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

{rxiv_maker-1.18.0 → rxiv_maker-1.18.2}/src/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-1.18.0 → rxiv_maker-1.18.2}/src/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-1.18.0 → rxiv_maker-1.18.2}/src/tex/template.tex

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

{rxiv_maker-1.18.0 → rxiv_maker-1.18.2}/tests/cli/test_changelog_command.py

@@ -27,6 +27,12 @@ def sample_changelog():
     # Include current version to match __version__
     return """# Changelog
 
+## [v1.18.2] - 2026-01-06
+
+### Fixed
+- Table caption parser enhancement with flexible whitespace handling
+- Cross-reference support in table captions
+
 ## [v1.18.0] - 2025-12-23
 
 ### Added
@@ -144,7 +150,7 @@ class TestChangelogCommand:
         """Test --breaking-only flag."""
         mock_fetch.return_value = sample_changelog
 
-        result = runner.invoke(changelog, ["--recent", "7", "--breaking-only"])
+        result = runner.invoke(changelog, ["--recent", "8", "--breaking-only"])
 
         assert result.exit_code == 0
         # Should show v1.12.0 which has breaking changes
@@ -199,7 +205,7 @@ class TestChangelogCommand:
         mock_fetch.return_value = sample_changelog
 
         # Use the latest version to ensure no versions after it
-        result = runner.invoke(changelog, ["--since", "v1.18.0"])
+        result = runner.invoke(changelog, ["--since", "v1.18.2"])
 
         assert result.exit_code == 0
         output = strip_ansi(result.output)