rxiv-maker 1.19.0__py3-none-any.whl → 1.19.1__py3-none-any.whl

rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.19.0"
+__version__ = "1.19.1"

rxiv_maker/converters/md2tex.py

@@ -185,7 +185,7 @@ def convert_markdown_to_latex(
 
     # Post-processing: catch any remaining unconverted headers
     # This is a safety net in case some headers weren't converted properly
-    content = re.sub(r"^### (.+)$", r"\\subsubsection{\1}", content, flags=re.MULTILINE)
+    content = re.sub(r"^### (.+)$", r"\\subsubsection{\1}\n\n", content, flags=re.MULTILINE)
 
     # Process supplementary note references BEFORE citations
     # (for both main and supplementary content)
@@ -457,26 +457,26 @@ def _process_tables_with_protection(
 
 
 def _convert_headers(content: LatexContent, is_supplementary: bool = False) -> LatexContent:
-    """Convert markdown headers to LaTeX sections."""
+    """Convert markdown headers to LaTeX sections with proper spacing."""
     if is_supplementary:
         # For supplementary content, use \\section* for the first header
         # to avoid "Note 1:" prefix
         # First, find the first # header and replace it with \section*
-        content = re.sub(r"^# (.+)$", r"\\section*{\1}", content, flags=re.MULTILINE, count=1)
+        content = re.sub(r"^# (.+)$", r"\\section*{\1}\n\n", content, flags=re.MULTILINE, count=1)
         # Then replace any remaining # headers with regular \section
-        content = re.sub(r"^# (.+)$", r"\\section{\1}", content, flags=re.MULTILINE)
+        content = re.sub(r"^# (.+)$", r"\\section{\1}\n\n", content, flags=re.MULTILINE)
     else:
-        content = re.sub(r"^# (.+)$", r"\\section{\1}", content, flags=re.MULTILINE)
+        content = re.sub(r"^# (.+)$", r"\\section{\1}\n\n", content, flags=re.MULTILINE)
 
-    content = re.sub(r"^## (.+)$", r"\\subsection{\1}", content, flags=re.MULTILINE)
+    content = re.sub(r"^## (.+)$", r"\\subsection{\1}\n\n", content, flags=re.MULTILINE)
 
     # For supplementary content, ### headers are handled by the
     # supplementary note processor
     # For non-supplementary content, convert all ### headers normally
     if not is_supplementary:
-        content = re.sub(r"^### (.+)$", r"\\subsubsection{\1}", content, flags=re.MULTILINE)
+        content = re.sub(r"^### (.+)$", r"\\subsubsection{\1}\n\n", content, flags=re.MULTILINE)
 
-    content = re.sub(r"^#### (.+)$", r"\\paragraph{\1}", content, flags=re.MULTILINE)
+    content = re.sub(r"^#### (.+)$", r"\\paragraph{\1}\n\n", content, flags=re.MULTILINE)
     return content
 
 

rxiv_maker/engines/operations/prepare_biorxiv.py

@@ -23,13 +23,15 @@ def encode_html_entities(text: str) -> str:
 
     bioRxiv's TSV upload requires special characters to be encoded as HTML entities.
     For example, "António" becomes "António", "Åbo" becomes "Åbo".
+    Characters without named entities use numeric references (e.g., "č" -> "č").
 
     Args:
         text: Text that may contain Unicode characters
 
     Returns:
         Text with Unicode characters converted to HTML entities
-        (e.g., "António" -> "António", "Åbo" -> "Åbo")
+        (e.g., "António" -> "António", "Åbo" -> "Åbo",
+        "Vaitkevičiūtė" -> "Vaitkevičiūtė")
 
     Examples:
         >>> encode_html_entities("António")
@@ -38,6 +40,8 @@ def encode_html_entities(text: str) -> str:
         'Åbo'
         >>> encode_html_entities("José García")
         'José García'
+        >>> encode_html_entities("Vaitkevičiūtė")
+        'Vaitkevičiūtė'
     """
     if not text:
         return text
@@ -50,13 +54,19 @@ def encode_html_entities(text: str) -> str:
         if ord(char) > 127:
             char_to_entity[char] = f"&{entity_name};"
 
-    # Convert each character to HTML entity if it has one
+    # Convert each character to HTML entity (named or numeric)
     result = []
     for char in text:
-        if char in char_to_entity:
+        char_code = ord(char)
+        if char_code <= 127:
+            # Basic ASCII - keep as-is
+            result.append(char)
+        elif char in char_to_entity:
+            # Has named entity - use it
             result.append(char_to_entity[char])
         else:
-            result.append(char)
+            # No named entity - use numeric character reference
+            result.append(f"&#{char_code};")
 
     return "".join(result)
 

rxiv_maker/tex/style/rxiv_maker_style.cls

@@ -418,7 +418,7 @@
   {\sffamily\small\bfseries\itshape}
   {\thesubsubsection.}
   {0.5em}
-  {#1. }
+  {#1.\enskip}
   []
 \titleformat{\paragraph}[runin]
   {\sffamily\small\bfseries}
@@ -427,7 +427,7 @@
   {#1}
 \titlespacing*{\section}{0pc}{1.5ex \@plus2pt \@minus1pt}{2pt}
 \titlespacing*{\subsection}{0pc}{1.2ex \@plus2pt \@minus1pt}{1pt}
-\titlespacing*{\subsubsection}{0pc}{1ex \@plus1pt \@minus0.5pt}{1pt}
+\titlespacing*{\subsubsection}{0pc}{1ex \@plus1pt \@minus0.5pt}{8pt}
 \titlespacing*{\paragraph}{0pc}{0.8ex \@plus1pt \@minus0.5pt}{8pt}
 
 %% Figure caption style

{rxiv_maker-1.19.0.dist-info → rxiv_maker-1.19.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.19.0
+Version: 1.19.1
 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-1.19.0.dist-info → rxiv_maker-1.19.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
 rxiv_maker/__init__.py,sha256=p04JYC5ZhP6dLXkoWVlKNyiRvsDE1a4C88f9q4xO3tA,3268
-rxiv_maker/__version__.py,sha256=s7-5Jsk7L8O8kxknnMqV6RyUG2rsUkOD8DjGMhagzNo,51
+rxiv_maker/__version__.py,sha256=1asCY_t8ZrspO60Mj4f6F7xZwm107oYPswgQnlvSKek,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
@@ -52,7 +52,7 @@ rxiv_maker/converters/figure_processor.py,sha256=xA7Z7-H4q4cPLAqlCjlcv4v_cYI-fLT
 rxiv_maker/converters/html_processor.py,sha256=n4AfjipeSi6uFpDtLiZb4GQYOQzYF_HD_FqdDXk84dY,5879
 rxiv_maker/converters/list_processor.py,sha256=QTt22XrkR5ESO12jvY0hCSFjagoCk2Htrc5bZ4kqon4,6430
 rxiv_maker/converters/math_processor.py,sha256=fwna-YFEbLFdsq6kllKAeAHv_6WS6rQn8R5JbeR1QQI,8324
-rxiv_maker/converters/md2tex.py,sha256=eO0gMjINrFmefJZARCEQO0ACmLgVE5mAccR_Fqz8zl4,21395
+rxiv_maker/converters/md2tex.py,sha256=rDaSvQyfpuu7zkQOGrrXcAKnuSbQOIiRAvBM_hlIS1M,21443
 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
@@ -100,7 +100,7 @@ rxiv_maker/engines/operations/generate_docs.py,sha256=8d_oVYUuRRqTuYN1KnJKqM5Ydp
 rxiv_maker/engines/operations/generate_figures.py,sha256=YeKzH6qVsuPGjtCsvWugLJoys6y73xTyO7Y5g30KM20,38730
 rxiv_maker/engines/operations/generate_preprint.py,sha256=wpKDAu2RLJ4amSdhX5GZ7hU-iTsTRt4etcEA7AZYp04,2662
 rxiv_maker/engines/operations/prepare_arxiv.py,sha256=cd0JN5IO-Wy9T8ab75eibyaA8_K8Gpwrz2F-95OMnx4,21551
-rxiv_maker/engines/operations/prepare_biorxiv.py,sha256=-Ok4iwnLsgNk6xJ9HSk74_7UBammJRTF3r8ISy_qDjc,13858
+rxiv_maker/engines/operations/prepare_biorxiv.py,sha256=X0U0UdFhTYldUMKjBJbu9IUL1xH8taIecmpC27HqndM,14353
 rxiv_maker/engines/operations/setup_environment.py,sha256=gERuThHTldH0YqgXn85995deHBP6csY1ZhCNgU6-vFg,12691
 rxiv_maker/engines/operations/track_changes.py,sha256=jJZ-XnTFx8TMvcnX8_9D7ydc0G01S1PnckLkxHRTX1g,24722
 rxiv_maker/engines/operations/validate.py,sha256=OVmtRVtG-r1hoA8IqYaNC-ijN1a5ixM3X5Z8Gda-O2M,17142
@@ -195,9 +195,9 @@ 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=_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-1.19.0.dist-info/METADATA,sha256=cM3QcAip52NGWPYbS5RqFTaP1Q3L6nsN6z0UmBt6YT4,18432
-rxiv_maker-1.19.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rxiv_maker-1.19.0.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
-rxiv_maker-1.19.0.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
-rxiv_maker-1.19.0.dist-info/RECORD,,
+rxiv_maker/tex/style/rxiv_maker_style.cls,sha256=sMYmXtCZB6rEdZKqnY8f3-Jh6ku_3eZNKMcpNbQF-JQ,24380
+rxiv_maker-1.19.1.dist-info/METADATA,sha256=ieFzn7Auj1L10FzS-PRbY569MADJqhXj_OmJXiNDVmU,18432
+rxiv_maker-1.19.1.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rxiv_maker-1.19.1.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
+rxiv_maker-1.19.1.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
+rxiv_maker-1.19.1.dist-info/RECORD,,