rxiv-maker 1.18.5__tar.gz → 1.19.1__tar.gz

{rxiv_maker-1.18.5 → rxiv_maker-1.19.1}/.gitignore

@@ -394,3 +394,8 @@ rxivdraft/MANUSCRIPT/2025__antónio_d_brito_et_al__rxiv.pdf
 .gemini-clipboard/
 gha-creds-*.json
 fatetracking/MANUSCRIPT/.rxiv_cache
+
+# Claude-mem context (override negations above)
+**/CLAUDE.md
+
+**/*.docx

{rxiv_maker-1.18.5 → rxiv_maker-1.19.1}/CHANGELOG.md

@@ -7,6 +7,51 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.19.1] - 2026-02-05
+
+### Fixed
+
+- **bioRxiv Character Encoding**: Enhanced HTML entity encoding to handle all Unicode characters
+  - Now uses numeric character references (e.g., `č` for č) for characters without named HTML entities
+  - Properly encodes Lithuanian characters (č, ū, ė) and other special characters
+  - Example: "Vaitkevičiūtė" → "Vaitkevičiūtė"
+  - Ensures bioRxiv TSV files handle international author names correctly
+
+- **LaTeX Section Spacing**: Fixed spacing issues in PDF output for section headers
+  - Added proper blank lines (`\n\n`) after all LaTeX section commands in markdown conversion
+  - Increased spacing after `\subsubsection` titles from 1pt to 8pt in LaTeX class file
+  - Changed subsubsection title format to use `\enskip` for consistent visual spacing
+  - Fixes runin format issue where text appeared to run directly into section titles
+  - Example fix: "Manuscripts.A central" → "Manuscripts. A central" (with visible space)
+
+## [1.19.0] - 2026-02-05
+
+### Added
+
+- **bioRxiv Submission Package Command**: New `rxiv biorxiv` command generates complete submission package
+  - Generates bioRxiv author template (TSV format) with HTML entity encoding for special characters
+  - Includes manuscript PDF, source files (TeX, figures, bibliography)
+  - Creates ZIP archive ready for bioRxiv upload
+  - Supports custom submission directory and ZIP filename options
+  - HTML entity encoding for accented characters (António → António, Åbo → Åbo)
+  - Automatic handling of multiple corresponding authors (keeps last one)
+  - Command options: `--biorxiv-dir`, `--zip-filename`, `--no-zip`
+
+### Changed
+
+- **Code Architecture**: Centralized common submission logic in BaseCommand
+  - Refactored ArxivCommand and BioRxivCommand to share common patterns
+  - Added `_clear_output_directory()`, `_ensure_pdf_built()`, `_set_submission_defaults()` helper methods
+  - Eliminated ~64 lines of duplicated code between commands
+  - Improved maintainability and consistency across submission commands
+
+### Fixed
+
+- **bioRxiv Character Encoding**: Special characters now properly encoded as HTML entities
+  - Previously stripped accents to ASCII (António → Antonio)
+  - Now preserves original characters using HTML entities (António → António)
+  - Complies with bioRxiv's TSV import requirements for international author names
+
 ## [1.18.5] - 2026-02-05
 
 ### Fixed

{rxiv_maker-1.18.5 → rxiv_maker-1.19.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.18.5
+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-1.18.5 → rxiv_maker-1.19.1}/src/rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.18.5"
+__version__ = "1.19.1"

{rxiv_maker-1.18.5 → rxiv_maker-1.19.1}/src/rxiv_maker/cli/commands/__init__.py

@@ -2,6 +2,7 @@
 
 from .arxiv import arxiv
 from .bibliography import bibliography
+from .biorxiv import biorxiv
 from .build import build as pdf
 from .cache_management import cache_group as cache
 from .changelog import changelog
@@ -29,6 +30,7 @@ from .version import version
 __all__ = [
     "arxiv",
     "bibliography",
+    "biorxiv",
     "cache",
     "changelog",
     "config",

rxiv_maker-1.19.1/src/rxiv_maker/cli/commands/biorxiv.py

@@ -0,0 +1,51 @@
+"""bioRxiv submission package generation command."""
+
+import rich_click as click
+
+from ..framework.workflow_commands import BioRxivCommand
+
+
+@click.command(context_settings={"help_option_names": ["-h", "--help"]})
+@click.argument("manuscript_path", type=click.Path(exists=True, file_okay=False), required=False)
+@click.option("--output-dir", "-o", default="output", help="Output directory for generated files")
+@click.option(
+    "--biorxiv-dir",
+    "-b",
+    help="Custom bioRxiv submission directory (default: output/biorxiv_submission)",
+)
+@click.option(
+    "--zip-filename",
+    "-z",
+    help="Custom ZIP filename (default: {manuscript}_biorxiv.zip)",
+)
+@click.option(
+    "--no-zip",
+    is_flag=True,
+    help="Don't create ZIP file (only create submission directory)",
+)
+@click.pass_context
+def biorxiv(ctx, manuscript_path, output_dir, biorxiv_dir, zip_filename, no_zip):
+    r"""Generate bioRxiv submission package.
+
+    Creates a complete submission package including:
+    - bioRxiv author template (TSV file)
+    - Manuscript PDF
+    - Source files (TeX, figures, bibliography)
+    - ZIP file for upload
+
+    \b
+    Example:
+        rxiv biorxiv                           # Full package with ZIP
+        rxiv biorxiv --no-zip                  # Package without ZIP
+        rxiv biorxiv -b custom_dir             # Custom submission directory
+        rxiv biorxiv -z my_submission.zip      # Custom ZIP filename
+    """
+    command = BioRxivCommand()
+    return command.run(
+        ctx,
+        manuscript_path=manuscript_path,
+        output_dir=output_dir,
+        biorxiv_dir=biorxiv_dir,
+        zip_filename=zip_filename,
+        no_zip=no_zip,
+    )

{rxiv_maker-1.18.5 → rxiv_maker-1.19.1}/src/rxiv_maker/cli/framework/base.py

@@ -162,6 +162,97 @@ class BaseCommand(ABC):
         if suggestion:
             self.console.print(f"💡 {suggestion}", style="yellow")
 
+    def _clear_output_directory(self) -> None:
+        """Clear and recreate the output directory.
+
+        Raises:
+            CommandExecutionError: If path_manager is not initialized
+        """
+        import shutil
+
+        if not self.path_manager:
+            raise CommandExecutionError("Path manager not initialized")
+
+        if self.path_manager.output_dir.exists():
+            shutil.rmtree(self.path_manager.output_dir)
+        self.path_manager.output_dir.mkdir(parents=True, exist_ok=True)
+
+    def _ensure_pdf_built(self, progress_task=None, quiet: bool = True) -> None:
+        """Ensure PDF is built, building it if necessary.
+
+        Args:
+            progress_task: Optional progress task to update
+            quiet: Whether to suppress build output
+
+        Raises:
+            CommandExecutionError: If path_manager is not initialized or build fails
+        """
+        from ...engines.operations.build_manager import BuildManager
+
+        if not self.path_manager:
+            raise CommandExecutionError("Path manager not initialized")
+
+        pdf_filename = f"{self.path_manager.manuscript_name}.pdf"
+        pdf_path = self.path_manager.output_dir / pdf_filename
+
+        if not pdf_path.exists():
+            if progress_task:
+                progress_task.update(description="Building PDF first...")
+
+            build_manager = BuildManager(
+                manuscript_path=str(self.path_manager.manuscript_path),
+                output_dir=str(self.path_manager.output_dir),
+                verbose=self.verbose,
+                quiet=quiet,
+            )
+
+            try:
+                success = build_manager.build()
+                if not success:
+                    raise CommandExecutionError("PDF build failed")
+            except Exception as e:
+                raise CommandExecutionError(f"Failed to build PDF: {e}") from e
+
+    def _set_submission_defaults(
+        self,
+        submission_type: str,
+        submission_dir: Optional[str] = None,
+        zip_filename: Optional[str] = None,
+    ) -> tuple[str, str]:
+        """Set default paths for submission directories and ZIP files.
+
+        Args:
+            submission_type: Type of submission ("arxiv" or "biorxiv")
+            submission_dir: Custom submission directory path (optional)
+            zip_filename: Custom ZIP filename (optional)
+
+        Returns:
+            Tuple of (submission_dir, zip_filename) with defaults applied
+
+        Raises:
+            CommandExecutionError: If path_manager is not initialized
+        """
+        from pathlib import Path
+
+        if not self.path_manager:
+            raise CommandExecutionError("Path manager not initialized")
+
+        manuscript_output_dir = str(self.path_manager.output_dir)
+
+        # Set default submission directory
+        if submission_dir is None:
+            submission_dir = str(Path(manuscript_output_dir) / f"{submission_type}_submission")
+
+        # Set default ZIP filename
+        if zip_filename is None:
+            manuscript_name = self.path_manager.manuscript_name
+            if submission_type == "arxiv":
+                zip_filename = str(Path(manuscript_output_dir) / "for_arxiv.zip")
+            else:
+                zip_filename = str(Path(manuscript_output_dir) / f"{manuscript_name}_{submission_type}.zip")
+
+        return submission_dir, zip_filename
+
     @abstractmethod
     def execute_operation(self, **kwargs) -> Any:
         """Execute the main command operation.

{rxiv_maker-1.18.5 → rxiv_maker-1.19.1}/src/rxiv_maker/cli/framework/workflow_commands.py

@@ -366,46 +366,25 @@ class ArxivCommand(BaseCommand):
             no_zip: Don't create zip file
         """
         import sys
-        from pathlib import Path
 
-        from rxiv_maker.engines.operations.build_manager import BuildManager
         from rxiv_maker.engines.operations.prepare_arxiv import main as prepare_arxiv_main
 
-        if self.path_manager is None:
-            raise CommandExecutionError("Path manager not initialized")
-
+        # Set defaults using shared helper
+        arxiv_dir, zip_filename = self._set_submission_defaults("arxiv", arxiv_dir, zip_filename)
         manuscript_output_dir = str(self.path_manager.output_dir)
 
-        # Set defaults using PathManager
-        if arxiv_dir is None:
-            arxiv_dir = str(Path(manuscript_output_dir) / "arxiv_submission")
-        if zip_filename is None:
-            zip_filename = str(Path(manuscript_output_dir) / "for_arxiv.zip")
-
         with self.create_progress() as progress:
-            # Clear output directory first (similar to PDF command)
+            # Clear output directory using shared helper
             task = progress.add_task("Clearing output directory...", total=None)
-            if self.path_manager.output_dir.exists():
-                shutil.rmtree(self.path_manager.output_dir)
-            self.path_manager.output_dir.mkdir(parents=True, exist_ok=True)
+            self._clear_output_directory()
 
-            # First, ensure PDF is built
+            # Ensure PDF is built using shared helper
             progress.update(task, description="Checking PDF exists...")
-            pdf_filename = f"{self.path_manager.manuscript_name}.pdf"
-            pdf_path = self.path_manager.output_dir / pdf_filename
-
-            if not pdf_path.exists():
-                progress.update(task, description="Building PDF first...")
-                build_manager = BuildManager(
-                    manuscript_path=str(self.path_manager.manuscript_path),
-                    output_dir=str(self.path_manager.output_dir),
-                    verbose=self.verbose,
-                    quiet=False,
-                )
-                success = build_manager.run()
-                if not success:
-                    self.error_message("PDF build failed. Cannot prepare arXiv package.")
-                    raise CommandExecutionError("PDF build failed")
+            try:
+                self._ensure_pdf_built(progress_task=task, quiet=False)
+            except CommandExecutionError:
+                self.error_message("PDF build failed. Cannot prepare arXiv package.")
+                raise
 
             # Prepare arXiv package
             progress.update(task, description="Preparing arXiv package...")
@@ -524,6 +503,95 @@ class ArxivCommand(BaseCommand):
         return year, first_author
 
 
+class BioRxivCommand(BaseCommand):
+    """BioRxiv command implementation for generating submission package."""
+
+    def execute_operation(
+        self,
+        output_dir: str = "output",
+        biorxiv_dir: Optional[str] = None,
+        zip_filename: Optional[str] = None,
+        no_zip: bool = False,
+    ) -> None:
+        """Execute bioRxiv submission package preparation.
+
+        Args:
+            output_dir: Output directory for generated files
+            biorxiv_dir: Custom bioRxiv submission directory path
+            zip_filename: Custom zip filename
+            no_zip: Don't create zip file
+        """
+        from pathlib import Path
+
+        from ...engines.operations.prepare_biorxiv import (
+            BioRxivAuthorError,
+            create_biorxiv_zip,
+            generate_biorxiv_author_tsv,
+            prepare_biorxiv_package,
+        )
+
+        # Set defaults using shared helper
+        biorxiv_dir, zip_filename = self._set_submission_defaults("biorxiv", biorxiv_dir, zip_filename)
+
+        with self.create_progress() as progress:
+            # Clear output directory using shared helper
+            task = progress.add_task("Clearing output directory...", total=None)
+            self._clear_output_directory()
+
+            # Ensure PDF is built using shared helper
+            progress.update(task, description="Checking PDF exists...")
+            self._ensure_pdf_built(progress_task=task, quiet=True)
+
+            # Generate bioRxiv author template TSV
+            progress.update(task, description="Generating bioRxiv author template...")
+            output_path = self.path_manager.output_dir
+            tsv_file = output_path / "biorxiv_authors.tsv"
+
+            try:
+                generate_biorxiv_author_tsv(
+                    config_path=self.path_manager.get_config_file_path(),
+                    output_path=tsv_file,
+                )
+            except BioRxivAuthorError as e:
+                progress.update(task, completed=True)
+                raise CommandExecutionError(f"Failed to generate bioRxiv template: {e}") from e
+
+            # Prepare bioRxiv submission package
+            progress.update(task, description="Preparing bioRxiv submission package...")
+            try:
+                biorxiv_path = prepare_biorxiv_package(
+                    manuscript_path=self.path_manager.manuscript_path,
+                    output_dir=self.path_manager.output_dir,
+                    biorxiv_dir=Path(biorxiv_dir),
+                )
+            except Exception as e:
+                progress.update(task, completed=True)
+                raise CommandExecutionError(f"Failed to prepare bioRxiv package: {e}") from e
+
+            # Create ZIP file if requested
+            zip_path = None
+            if not no_zip:
+                progress.update(task, description="Creating ZIP package...")
+                try:
+                    zip_path = create_biorxiv_zip(
+                        biorxiv_path=biorxiv_path,
+                        zip_filename=zip_filename,
+                        manuscript_path=self.path_manager.manuscript_path,
+                    )
+                except Exception as e:
+                    progress.update(task, completed=True)
+                    raise CommandExecutionError(f"Failed to create ZIP: {e}") from e
+
+            progress.update(task, completed=True)
+
+            # Show success message
+            self.console.print("\n[green]✅ bioRxiv submission package ready![/green]")
+            self.console.print(f"   📁 Package directory: {biorxiv_path}")
+            if zip_path:
+                self.console.print(f"   📦 ZIP file: {zip_path}")
+            self.console.print("\n📤 Upload to: https://submit.biorxiv.org/")
+
+
 class TrackChangesCommand(BaseCommand):
     """Track changes command implementation using the framework."""
 

{rxiv_maker-1.18.5 → rxiv_maker-1.19.1}/src/rxiv_maker/cli/main.py

@@ -60,7 +60,7 @@ click.rich_click.COMMAND_GROUPS = {
         },
         {
             "name": "Workflow Commands",
-            "commands": ["get-rxiv-preprint", "arxiv", "track-changes", "setup"],
+            "commands": ["get-rxiv-preprint", "arxiv", "biorxiv", "track-changes", "setup"],
         },
         {
             "name": "Configuration",
@@ -252,6 +252,7 @@ main.add_command(commands.docx)
 main.add_command(commands.figures)
 main.add_command(commands.get_rxiv_preprint, name="get-rxiv-preprint")
 main.add_command(commands.arxiv)
+main.add_command(commands.biorxiv)
 main.add_command(commands.init)
 main.add_command(commands.bibliography)
 main.add_command(commands.track_changes)

{rxiv_maker-1.18.5 → rxiv_maker-1.19.1}/src/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