rxiv-maker 1.18.0__py3-none-any.whl → 1.18.2__py3-none-any.whl

rxiv_maker/__version__.py

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

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/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/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}

{rxiv_maker-1.18.0.dist-info → rxiv_maker-1.18.2.dist-info}/METADATA

@@ -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.dist-info → rxiv_maker-1.18.2.dist-info}/RECORD

@@ -1,5 +1,5 @@
 rxiv_maker/__init__.py,sha256=p04JYC5ZhP6dLXkoWVlKNyiRvsDE1a4C88f9q4xO3tA,3268
-rxiv_maker/__version__.py,sha256=MVd3J-jKwgAFkETITQ9sUCvhAdXfezvIvUmYNFYviSc,51
+rxiv_maker/__version__.py,sha256=r1DNB3JWDHXSSJtFwhx61DHqp-syX6loJLs-YmN6FEQ,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
@@ -55,7 +55,7 @@ rxiv_maker/converters/md2tex.py,sha256=eO0gMjINrFmefJZARCEQO0ACmLgVE5mAccR_Fqz8z
 rxiv_maker/converters/python_executor.py,sha256=YMJO7A-re8EOCQjy-PKryFFBoxddK3g9R1VuaH2MfYY,37369
 rxiv_maker/converters/section_processor.py,sha256=7znzb_FYH2sCYH336l5J1ZdRaQv-ycdCN79RpI3Tc-w,5706
 rxiv_maker/converters/supplementary_note_processor.py,sha256=8wzQw2kN0Afg0iB7hPFdeWiDlDsFhhTkcRTvwCXIvjc,6689
-rxiv_maker/converters/table_processor.py,sha256=chicOshkX20NleRTgdOkx8cuwCBITcrsFXHOByUKXAU,38431
+rxiv_maker/converters/table_processor.py,sha256=0sCtDVlQwLcAC8_dJMijgVb7DCmtannCyDgWNJ35-KE,39869
 rxiv_maker/converters/text_formatters.py,sha256=pa2kVAqyPkGh5LViL5Iqqjjqw1ixB0GKBZJloaVBVi0,42816
 rxiv_maker/converters/types.py,sha256=mTLXVTBGfEi2dp_U2maSE7kZQFz_lfmLDQjlMAeU9lE,885
 rxiv_maker/converters/url_processor.py,sha256=xoZrgz7kgRtMzSay_14ZpYEwK9uXj3YloQW9K-G8LAc,6586
@@ -107,7 +107,7 @@ rxiv_maker/exporters/__init__.py,sha256=NcTD1SDb8tTgsHhCS1A7TVEZncyWbDRTa6sJIdLq
 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/exporters/docx_writer.py,sha256=JvNVprMqdvvDGf65ESsEqf7-A33G1D9Kd0Zi2Q4gmbw,57145
 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=mX8L19Evo9c8DvcdvSdtFHGaGGrQseVsF1CKfj_WYow,30024
+rxiv_maker/processors/template_processor.py,sha256=V47kh5zyiZDPNXBfNkQeyU5r-3MBHM3UMWAjcfgs11s,30316
 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
@@ -141,7 +141,7 @@ 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=XHO3sQBRulsTsYUmP9R3K6RxnYMAehqrY-MoPgGaexE,16206
+rxiv_maker/templates/registry.py,sha256=GikYKBBUSzzT0yeI8W8EZYVo40B9wtseNVGTLsAJGKY,18800
 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
@@ -191,11 +191,11 @@ rxiv_maker/validators/syntax_validator.py,sha256=hHpKVKky3UiA1ZylA6jJVP3DN47LgaS
 rxiv_maker/validators/doi/__init__.py,sha256=NqATXseuS0zVNns56RvFe8TdqgvueY0Rbw2Pjozlajc,494
 rxiv_maker/validators/doi/api_clients.py,sha256=tqdYUq8LFgRIO0tWfcenwmy2uO-IB1-GMvBfF3lP7-0,21763
 rxiv_maker/validators/doi/metadata_comparator.py,sha256=euqHhKP5sHQAdZbdoAahUn6YqJqOfXIOobNgAqFHlN8,11533
-rxiv_maker/tex/template.tex,sha256=zrJ3aFfu8j9zkg1l375eE9w-j42P3rz16wMD3dSgi1I,1354
+rxiv_maker/tex/template.tex,sha256=_tPtxrurn3sKTt9Kfa44lPdPyT44vHbDUOGqldU9r2s,1378
 rxiv_maker/tex/style/rxiv_maker_style.bst,sha256=jbVqrJgAm6F88cow5vtZuPBwwmlcYykclTm8RvZIo6Y,24281
 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,,
+rxiv_maker-1.18.2.dist-info/METADATA,sha256=OqROaCqeuMSX45OfafGdLjR5Q_Y-XxaC__NboFz_z54,18222
+rxiv_maker-1.18.2.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rxiv_maker-1.18.2.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
+rxiv_maker-1.18.2.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
+rxiv_maker-1.18.2.dist-info/RECORD,,