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

rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.16.8"
+__version__ = "1.18.0"

rxiv_maker/cli/commands/build.py

@@ -30,6 +30,7 @@ from ..framework import BuildCommand
 @click.option("--keep-output", is_flag=True, help="Preserve existing output directory (default: clear before build)")
 @click.option("--docx", is_flag=True, help="Also export to DOCX format for collaborative review")
 @click.option("--resolve-dois", "-r", is_flag=True, help="Attempt to resolve missing DOIs (when using --docx)")
+@click.option("--split-si", is_flag=True, help="Split PDF into main and SI sections (__main.pdf and __si.pdf)")
 @click.option("--verbose", "-v", is_flag=True, help="Enable verbose output")
 @click.option("--quiet", "-q", is_flag=True, help="Suppress non-essential output")
 @click.option("--debug", "-d", is_flag=True, help="Enable debug output")
@@ -49,6 +50,7 @@ def build(
     keep_output: bool,
     docx: bool,
     resolve_dois: bool,
+    split_si: bool,
     verbose: bool,
     quiet: bool,
     debug: bool,
@@ -81,6 +83,10 @@ def build(
 
         $ rxiv pdf --docx --resolve-dois
 
+    **Split PDF into main and SI sections:**
+
+        $ rxiv pdf --split-si
+
     **Force regenerate all figures:**
 
         $ rxiv pdf --force-figures
@@ -108,6 +114,7 @@ def build(
         keep_output=keep_output,
         docx=docx,
         resolve_dois=resolve_dois,
+        split_si=split_si,
         debug=debug or verbose,
         quiet=quiet,
         container_mode=container_mode,

rxiv_maker/cli/framework/workflow_commands.py

@@ -30,8 +30,10 @@ class InitCommand(BaseCommand):
         self.engine = "local"  # Only local engine is supported
 
         # Store manuscript path without PathManager validation since we're creating the directory
+        # NOTE: For init command, we should NOT use environment variable MANUSCRIPT_PATH
+        # as it's meant for finding existing manuscripts, not determining where to initialize
         if manuscript_path is None:
-            manuscript_path = EnvironmentManager.get_manuscript_path() or "MANUSCRIPT"
+            manuscript_path = "MANUSCRIPT"
 
         # Store the raw path for use in execute_operation
         self.raw_manuscript_path = manuscript_path
@@ -142,6 +144,7 @@ class BuildCommand(BaseCommand):
         keep_output: bool = False,
         docx: bool = False,
         resolve_dois: bool = False,
+        split_si: bool = False,
         debug: bool = False,
         quiet: bool = False,
         container_mode: Optional[str] = None,
@@ -156,6 +159,7 @@ class BuildCommand(BaseCommand):
             keep_output: Preserve existing output directory
             docx: Also export to DOCX format
             resolve_dois: Attempt to resolve missing DOIs (for DOCX export)
+            split_si: Split PDF into main and SI sections
             debug: Enable debug output
             quiet: Suppress non-critical warnings
             container_mode: Container behavior mode
@@ -223,6 +227,10 @@ class BuildCommand(BaseCommand):
             if docx:
                 self._export_docx(resolve_dois=resolve_dois, quiet=quiet, debug=debug)
 
+            # Split PDF if requested
+            if split_si:
+                self._split_pdf(pdf_path, quiet=quiet, debug=debug)
+
             # Show helpful tips after successful build
             self._show_build_tips()
 
@@ -252,11 +260,69 @@ class BuildCommand(BaseCommand):
                 self.console.print(f"[green]✅ DOCX exported:[/green] {docx_path}")
 
         except Exception as e:
-            self.console.print(f"[yellow]⚠️  DOCX export failed:[/yellow] {e}", err=True)
+            self.console.print(f"[yellow]⚠️  DOCX export failed:[/yellow] {e}")
+            if debug:
+                import traceback
+
+                self.console.print(f"[dim]{traceback.format_exc()}[/dim]")
+
+    def _split_pdf(self, pdf_path: Path, quiet: bool = False, debug: bool = False) -> None:
+        """Split PDF into main and SI sections after successful PDF build.
+
+        Args:
+            pdf_path: Path to the generated PDF
+            quiet: Suppress non-essential output
+            debug: Enable debug output
+        """
+        try:
+            from ...processors.yaml_processor import extract_yaml_metadata
+            from ...utils.file_helpers import find_manuscript_md
+            from ...utils.pdf_splitter import split_pdf
+            from ...utils.pdf_utils import get_custom_pdf_filename
+
+            if not quiet:
+                self.console.print("\n[cyan]✂️  Splitting PDF into main and SI sections...[/cyan]")
+
+            # Split the PDF
+            main_path, si_path = split_pdf(pdf_path)
+
+            if main_path and si_path:
+                # Extract metadata to generate custom filename
+                manuscript_md = find_manuscript_md(str(self.path_manager.manuscript_path))
+                yaml_metadata = extract_yaml_metadata(str(manuscript_md))
+
+                # Get base filename (e.g., "2025__saraiva_et_al__rxiv.pdf")
+                base_filename = get_custom_pdf_filename(yaml_metadata)
+                base_name = base_filename.replace(".pdf", "")
+
+                # Generate final filenames with __main and __si suffixes
+                main_filename = f"{base_name}__main.pdf"
+                si_filename = f"{base_name}__si.pdf"
+
+                # Copy split files to manuscript directory
+                final_main_path = self.path_manager.manuscript_path / main_filename
+                final_si_path = self.path_manager.manuscript_path / si_filename
+
+                shutil.copy2(main_path, final_main_path)
+                shutil.copy2(si_path, final_si_path)
+
+                if not quiet:
+                    self.console.print("[green]✅ PDF split successfully:[/green]")
+                    self.console.print(f"   📄 Main: {final_main_path}")
+                    self.console.print(f"   📄 SI: {final_si_path}")
+            elif main_path is None and si_path is None:
+                if not quiet:
+                    self.console.print("[yellow]⚠️  Could not split PDF: SI section marker not found[/yellow]")
+            else:
+                if not quiet:
+                    self.console.print("[yellow]⚠️  PDF splitting partially failed[/yellow]")
+
+        except Exception as e:
+            self.console.print(f"[yellow]⚠️  PDF splitting failed:[/yellow] {e}")
             if debug:
                 import traceback
 
-                self.console.print(f"[dim]{traceback.format_exc()}[/dim]", err=True)
+                self.console.print(f"[dim]{traceback.format_exc()}[/dim]")
 
     def _show_build_tips(self) -> None:
         """Show helpful tips after successful PDF build."""

rxiv_maker/converters/citation_processor.py

@@ -202,9 +202,11 @@ def extract_citations_from_text(text: MarkdownContent) -> list[CitationKey]:
         backtick_patterns.append(match.group(0))
         return f"__BACKTICK_PATTERN_{len(backtick_patterns) - 1}__"
 
-    # Match both single backticks `...` and triple backticks ```...```
-    text_cleaned = re.sub(r"`[^`]+`", protect_backticks, text)
-    text_cleaned = re.sub(r"```.*?```", protect_backticks, text_cleaned, flags=re.DOTALL)
+    # IMPORTANT: Match triple backticks FIRST, then single backticks
+    # This prevents the single-backtick pattern from matching across triple-backtick blocks
+    # (e.g., from a ` before ```latex to the first ` inside the code block)
+    text_cleaned = re.sub(r"```.*?```", protect_backticks, text, flags=re.DOTALL)
+    text_cleaned = re.sub(r"`[^`]+`", protect_backticks, text_cleaned)
 
     # Find bracketed multiple citations
     bracketed_matches = re.findall(r"\[(@[^]]+)\]", text_cleaned)

rxiv_maker/core/managers/config_manager.py

@@ -343,6 +343,7 @@ class ConfigManager:
             "bibliography": {"file": "03_REFERENCES.bib", "style": "nature"},
             "citation_style": "numbered",
             "enable_inline_doi_resolution": False,
+            "docx": {"hide_si": False, "figures_at_end": False},
             "cache": {"enabled": True, "ttl_hours": 24},
             "version": "1.0",
             "acknowledge_rxiv_maker": True,

rxiv_maker/exporters/docx_citation_mapper.py

@@ -8,11 +8,26 @@ import re
 from typing import Dict, List
 
 from ..converters.citation_processor import extract_citations_from_text
+from ..utils.citation_range_formatter import format_citation_ranges
 
 
 class CitationMapper:
     """Maps citation keys to sequential numbers for DOCX export."""
 
+    @staticmethod
+    def _format_citation_ranges(text: str) -> str:
+        """Format consecutive citations as ranges.
+
+        Uses centralized citation range formatter from utils module.
+
+        Args:
+            text: Text with numbered citations
+
+        Returns:
+            Text with consecutive citations formatted as ranges
+        """
+        return format_citation_ranges(text)
+
     def create_mapping(self, citations: List[str]) -> Dict[str, int]:
         """Create citation key → number mapping.
 
@@ -121,4 +136,7 @@ class CitationMapper:
         for i, pattern in enumerate(email_patterns):
             text = text.replace(f"__EMAIL_PATTERN_{i}__", pattern)
 
+        # Format consecutive citations as ranges (e.g., [1][2][3] -> [1-3])
+        text = self._format_citation_ranges(text)
+
         return text

rxiv_maker/exporters/docx_content_processor.py

@@ -7,6 +7,8 @@ DOCX generation with python-docx.
 import re
 from typing import Any, Dict, List, Optional
 
+from ..utils.comment_filter import is_metadata_comment
+
 
 class DocxContentProcessor:
     """Parses markdown content into structured format for DOCX writing."""
@@ -55,10 +57,38 @@ class DocxContentProcessor:
                 i += 1
                 continue
 
-            # Skip HTML/markdown comments
+            # Parse HTML/markdown comments (single-line and multi-line)
+            # Skip informational/metadata comments (those starting with "Note:")
             if line.strip().startswith("<!--"):
-                i += 1
-                continue
+                # Check if it's a single-line comment
+                if line.strip().endswith("-->"):
+                    # Single-line comment
+                    comment_text = line.strip()[4:-3].strip()
+                    # Skip metadata comments (e.g., "note that...", "Comment: ...")
+                    if comment_text and not is_metadata_comment(comment_text):
+                        sections.append({"type": "comment", "text": comment_text})
+                    i += 1
+                    continue
+                else:
+                    # Multi-line comment - collect all lines until -->
+                    comment_lines = [line.strip()[4:]]  # Remove <!--
+                    i += 1
+                    while i < len(lines):
+                        if lines[i].strip().endswith("-->"):
+                            # Last line of comment
+                            comment_lines.append(lines[i].strip()[:-3])  # Remove -->
+                            i += 1
+                            break
+                        else:
+                            comment_lines.append(lines[i].strip())
+                            i += 1
+
+                    # Join and add comment
+                    comment_text = " ".join(comment_lines).strip()
+                    # Skip metadata comments (e.g., "note that...", "Comment: ...")
+                    if comment_text and not is_metadata_comment(comment_text):
+                        sections.append({"type": "comment", "text": comment_text})
+                    continue
 
             # Skip LaTeX commands like <clearpage>
             if line.strip().startswith("<") and line.strip().endswith(">") and " " not in line.strip():
@@ -335,18 +365,21 @@ class DocxContentProcessor:
         runs = []
 
         # Find all formatting markers, links, and citations
-        # Pattern to match: <<HIGHLIGHT_YELLOW>>text<</HIGHLIGHT_YELLOW>>, <<XREF>>text<</XREF>>, [text](url), **bold**, __underlined__, *italic*, _italic_, `code`, $math$, [number]
+        # Pattern to match: <<HIGHLIGHT_YELLOW>>text<</HIGHLIGHT_YELLOW>>, <<XREF:type>>text<</XREF>>, <!-- comment -->, [text](url), **bold**, __underlined__, *italic*, _italic_, ~subscript~, ^superscript^, `code`, $math$, [number]
         pattern = re.compile(
             r"(<<HIGHLIGHT_YELLOW>>([^<]+)<</HIGHLIGHT_YELLOW>>)"  # Yellow highlight (must be first)
-            r"|(<<XREF>>([^<]+)<</XREF>>)"  # Cross-reference
+            r"|(<<XREF:(\w+)>>([^<]+)<</XREF>>)"  # Cross-reference with type
+            r"|(<!--\s*(.+?)\s*-->)"  # HTML comments (inline)
             r"|(\[([^\]]+)\]\(([^)]+)\))"  # Markdown link [text](url) (before citations)
             r"|(\*\*([^*]+)\*\*)"  # Bold
             r"|(__([^_]+)__)"  # Underline with double underscores (must come before single underscore)
             r"|(\*([^*]+)\*)"  # Italic with asterisks
             r"|(_([^_]+)_)"  # Italic with underscores
+            r"|(~([^~]+)~)"  # Subscript
+            r"|(\^([^^]+)\^)"  # Superscript
             r"|(`([^`]+)`)"  # Code
             r"|(\$([^\$]+)\$)"  # Inline math
-            r"|(\[(\d+(?:,\s*\d+)*)\])"  # Citation numbers
+            r"|(\[(\d+(?:[-,]\s*\d+)*)\])"  # Citation numbers (supports both ranges [1-3] and lists [1, 2])
         )
 
         last_end = 0
@@ -378,67 +411,99 @@ class DocxContentProcessor:
                     if run["type"] == "text":
                         run["highlight_yellow"] = True
                     runs.append(run)
-            elif match.group(3):  # Cross-reference
+            elif match.group(3):  # Cross-reference with type
                 runs.append(
                     {
                         "type": "text",
-                        "text": match.group(4),
+                        "text": match.group(5),  # Text is now in group 5
                         "bold": False,
                         "italic": False,
                         "underline": False,
                         "code": False,
                         "xref": True,
+                        "xref_type": match.group(4),  # Type is in group 4
                     }
                 )
-            elif match.group(5):  # Markdown link [text](url)
+            elif match.group(6):  # Inline HTML comment
+                comment_text = match.group(7).strip()
+                # Skip metadata comments (e.g., "note that...", "Comment: ...")
+                if comment_text and not is_metadata_comment(comment_text):
+                    runs.append({"type": "inline_comment", "text": comment_text})
+            elif match.group(8):  # Markdown link [text](url)
                 runs.append(
                     {
                         "type": "hyperlink",
-                        "text": match.group(6),
-                        "url": match.group(7),
+                        "text": match.group(9),
+                        "url": match.group(10),
                     }
                 )
-            elif match.group(8):  # Bold
+            elif match.group(11):  # Bold
                 # Recursively parse inner text for underline/italic/other formatting
-                inner_text = match.group(9)
+                inner_text = match.group(12)
                 inner_runs = self._parse_inline_formatting(inner_text, citation_map)
                 # Add bold to all inner runs
                 for run in inner_runs:
                     if run["type"] == "text":
                         run["bold"] = True
                     runs.append(run)
-            elif match.group(10):  # Underline
+            elif match.group(13):  # Underline
                 # Recursively parse inner text for bold/italic/other formatting
-                inner_text = match.group(11)
+                inner_text = match.group(14)
                 inner_runs = self._parse_inline_formatting(inner_text, citation_map)
                 # Add underline to all inner runs
                 for run in inner_runs:
                     if run["type"] == "text":
                         run["underline"] = True
                     runs.append(run)
-            elif match.group(12):  # Italic with asterisks
+            elif match.group(15):  # Italic with asterisks
                 # Recursively parse inner text for bold/underline/other formatting
-                inner_text = match.group(13)
+                inner_text = match.group(16)
                 inner_runs = self._parse_inline_formatting(inner_text, citation_map)
                 # Add italic to all inner runs
                 for run in inner_runs:
                     if run["type"] == "text":
                         run["italic"] = True
                     runs.append(run)
-            elif match.group(14):  # Italic with underscores
+            elif match.group(17):  # Italic with underscores
                 # Recursively parse inner text for bold/underline/other formatting
-                inner_text = match.group(15)
+                inner_text = match.group(18)
                 inner_runs = self._parse_inline_formatting(inner_text, citation_map)
                 # Add italic to all inner runs
                 for run in inner_runs:
                     if run["type"] == "text":
                         run["italic"] = True
                     runs.append(run)
-            elif match.group(16):  # Code
+            elif match.group(19):  # Subscript
                 runs.append(
                     {
                         "type": "text",
-                        "text": match.group(17),
+                        "text": match.group(20),
+                        "bold": False,
+                        "italic": False,
+                        "underline": False,
+                        "code": False,
+                        "xref": False,
+                        "subscript": True,
+                    }
+                )
+            elif match.group(21):  # Superscript
+                runs.append(
+                    {
+                        "type": "text",
+                        "text": match.group(22),
+                        "bold": False,
+                        "italic": False,
+                        "underline": False,
+                        "code": False,
+                        "xref": False,
+                        "superscript": True,
+                    }
+                )
+            elif match.group(23):  # Code
+                runs.append(
+                    {
+                        "type": "text",
+                        "text": match.group(24),
                         "bold": False,
                         "italic": False,
                         "underline": False,
@@ -446,14 +511,23 @@ class DocxContentProcessor:
                         "xref": False,
                     }
                 )
-            elif match.group(18):  # Inline math
-                runs.append({"type": "inline_equation", "latex": match.group(19)})
-            elif match.group(20):  # Citation
-                # Parse citation numbers (may be multiple: [1, 2, 3])
-                numbers_str = match.group(21)
-                numbers = [int(n.strip()) for n in numbers_str.split(",")]
-                for num in numbers:
-                    runs.append({"type": "citation", "number": num})
+            elif match.group(25):  # Inline math
+                runs.append({"type": "inline_equation", "latex": match.group(26)})
+            elif match.group(27):  # Citation
+                # Keep citation as formatted text with yellow highlighting
+                # The citation mapper has already formatted ranges (e.g., [1-3], [1, 4-6, 8])
+                citation_text = match.group(0)  # Full match including brackets
+                runs.append(
+                    {
+                        "type": "text",
+                        "text": citation_text,
+                        "bold": False,
+                        "italic": False,
+                        "underline": False,
+                        "code": False,
+                        "highlight_yellow": True,  # Highlight citations in yellow
+                    }
+                )
 
             last_end = match.end()
 
@@ -516,6 +590,7 @@ class DocxContentProcessor:
         # Look ahead for caption line (skip empty lines)
         caption = ""
         label = ""
+        is_supplementary = False  # Default to main figure
         next_i = start_idx + 1
 
         # Skip empty lines to find caption
@@ -529,6 +604,9 @@ class DocxContentProcessor:
 
             # Check for {#fig:label ...} or {#sfig:label ...} **Caption**
             if next_line and (next_line.startswith("{#fig:") or next_line.startswith("{#sfig:")):
+                # Detect if it's a supplementary figure
+                is_supplementary = next_line.startswith("{#sfig:")
+
                 # Extract label if present
                 label_match = re.match(r"\{#s?fig:(\w+)[^}]*\}", next_line)
                 if label_match:
@@ -572,6 +650,7 @@ class DocxContentProcessor:
             "alt": alt_text,
             "caption": caption,
             "label": label,
+            "is_supplementary": is_supplementary,
         }, next_i
 
     def _parse_table(self, lines: List[str], start_idx: int) -> tuple[Optional[Dict[str, Any]], int]:
@@ -626,7 +705,8 @@ class DocxContentProcessor:
         if i < len(lines):
             caption_line = lines[i].strip()
             # Match {#stable:label} Caption or {#table:label} Caption
-            caption_match = re.match(r"^\{#(stable|table):(\w+)\}\s*(.+)$", caption_line)
+            # Allow hyphens and underscores in label names (e.g., "tool-comparison")
+            caption_match = re.match(r"^\{#(stable|table):([\w-]+)\}\s*(.+)$", caption_line)
             if caption_match:
                 label = f"{caption_match.group(1)}:{caption_match.group(2)}"
                 caption = caption_match.group(3).strip()