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Merged
paxcalpt merged 1 commit into from
Feb 5, 2026
Merged

feat: add bioRxiv submission package command (v1.19.0) #291

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5 changes: 5 additions & 0 deletions .gitignore
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Expand Up @@ -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
28 changes: 28 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,34 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## [Unreleased]

## [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
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2 changes: 1 addition & 1 deletion src/rxiv_maker/__version__.py
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@@ -1,3 +1,3 @@
"""Version information."""

__version__ = "1.18.5"
__version__ = "1.19.0"
2 changes: 2 additions & 0 deletions src/rxiv_maker/cli/commands/__init__.py
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Expand Up @@ -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
Expand Down Expand Up @@ -29,6 +30,7 @@
__all__ = [
"arxiv",
"bibliography",
"biorxiv",
"cache",
"changelog",
"config",
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51 changes: 51 additions & 0 deletions src/rxiv_maker/cli/commands/biorxiv.py
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"""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,
)
91 changes: 91 additions & 0 deletions src/rxiv_maker/cli/framework/base.py
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Expand Up @@ -162,6 +162,97 @@ def error_message(self, message: str, suggestion: Optional[str] = None) -> None:
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.
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130 changes: 99 additions & 31 deletions src/rxiv_maker/cli/framework/workflow_commands.py
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Expand Up @@ -366,46 +366,25 @@ def execute_operation(
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...")
Expand Down Expand Up @@ -524,6 +503,95 @@ def _extract_author_and_year(self, config_path: Path) -> tuple[str, str]:
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."""

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3 changes: 2 additions & 1 deletion src/rxiv_maker/cli/main.py
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Expand Up @@ -60,7 +60,7 @@
},
{
"name": "Workflow Commands",
"commands": ["get-rxiv-preprint", "arxiv", "track-changes", "setup"],
"commands": ["get-rxiv-preprint", "arxiv", "biorxiv", "track-changes", "setup"],
},
{
"name": "Configuration",
Expand Down Expand Up @@ -252,6 +252,7 @@ def main(
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)
Expand Down
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