Scitex Writer
LaTeX manuscript compilation with automatic versioning, diff generation, and MCP server for AI assistants. Part of SciTeX.
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SciTeX Writer
scitex.ai Β· docs Β· pip install scitex-writer
LaTeX compilation system for scientific manuscripts with automatic versioning, diff generation, and cross-platform reproducibility.
Part of the SciTeX ecosystem β empowers both human researchers and AI agents.
Problem and Solution
| # | Problem | Solution |
|---|---|---|
| 1 | LaTeX compilation is fragile -- bib, figs, tables, cross-refs, supplement each have their own failure mode | scitex writer compile -- one command runs bibtex β latex β bibtex β latex twice; handles supplement + revision diffs |
| 2 | Figures drift from manuscript -- author renumbers a figure; half the references go stale; \ref{} silently prints ?? | Reference check + float-order audit -- writer_check_references + writer_check_float_order catch dangling \ref{} before submission |
| 3 | Manuscript claims uncheckable -- a paper asserts "t(58) = 2.34, p = .021"; reviewer has no way to verify | Clew-backed claims -- writer_add_claim binds each assertion to a source session + file hash; writer_render_claims exposes the verification DAG |
Demo
Β Β
Light mode (default) and dark mode (--dark-mode)
Demo video with AI agent
Installation
# LaTeX dependencies (Ubuntu/Debian)
sudo apt-get install texlive-latex-extra latexdiff parallel imagemagick ghostscript
# LaTeX dependencies (macOS)
brew install texlive latexdiff parallel imagemagick ghostscript
# Python package + MCP server
pip install scitex-writer
Quick Start
git clone https://github.com/ywatanabe1989/scitex-writer.git my-paper
cd my-paper && make manuscript # or: ./compile.sh manuscript
Part of SciTeX
scitex-writer is part of SciTeX. Install via
the umbrella with pip install scitex[writer] to use as
scitex.writer (Python) or scitex writer ... (CLI).
Four Freedoms for Research
- The freedom to run your research anywhere β your machine, your terms.
- The freedom to study how every step works β from raw data to final manuscript.
- The freedom to redistribute your workflows, not just your papers.
- The freedom to modify any module and share improvements with the community.
AGPL-3.0 β because we believe research infrastructure deserves the same freedoms as the software it runs on.
Problem
LaTeX compilation for scientific manuscripts is painful:
- Environment inconsistency β "It compiles on my machine" is not a solution when collaborating across Linux, macOS, WSL2, and HPC clusters.
- Manual figure conversion β Converting between PNG, SVG, PDF, Mermaid, and TIFF formats by hand wastes time and introduces errors.
- No version tracking β Generating tracked-change diffs between revisions requires manual
latexdiffinvocations and careful file management. - Fragmented tooling β Separate workflows for compilation, bibliography management, table formatting, and submission packaging.
- AI agents cannot help β Without a programmatic interface, AI assistants have no way to compile or manage manuscripts.
Solution
SciTeX Writer solves each of these problems:
- Container-based reproducible compilation β Consistent builds across all platforms via Docker, Singularity, or native installation with automatic engine selection (Tectonic, latexmk, or 3-pass).
- Automatic asset conversion β Figures and tables are converted in parallel from source formats (PNG, SVG, comma-separated values (CSV), Mermaid) to LaTeX-ready output.
- Built-in version tracking with diff generation β Every compilation archives the previous version and generates a
latexdiffdocument automatically. - Unified interface β One tool for compilation, bibliography deduplication, figure/table management, and arXiv export packaging.
- 39 Model Context Protocol (MCP) tools for AI agents β AI assistants can compile, edit, and manage manuscripts programmatically.
Architecture
flowchart TB
subgraph Surfaces["Surfaces (user-facing)"]
CLI["CLI<br/><code>_cli/</code>"]
MCP["MCP Tools<br/><code>_mcp/</code>"]
Web["Django Editor + Viewer<br/><code>_django/</code>"]
Ports["Optional Bridges<br/><code>_ports/</code>"]
end
subgraph Engines["Engines (pure functions)"]
Compile["Compile<br/><code>_compile/</code>"]
Bib["Bibliography<br/><code>bib.py</code>"]
Claim["Claims<br/><code>claim.py</code>"]
Export["Export / arXiv<br/><code>export/</code>"]
Migrate["Migration<br/><code>migration/</code>"]
end
subgraph Model["Project model (source of truth)"]
DC["<code>_dataclasses/</code><br/>(immutable manuscript view)"]
Proj["<code>_project/</code>"]
Utils["<code>_utils/</code>"]
end
Surfaces --> Engines
Engines --> Model
Ports -.optional.-> Scholar["scitex-scholar<br/>(SCHOLAR_AVAILABLE)"]
Ports -.optional.-> Figrecipe["figrecipe / clew / stats"]
scitex-writer is layered in three concentric rings:
| Ring | Modules | Role |
|---|---|---|
| Project model | _dataclasses/, _project/, _utils/ | Immutable view of a manuscript's tree, config, and contents β the source of truth every other layer reads. |
| Engines | _compile/, bib.py, claim.py, export/, migration/ | Pure functions that operate on the project model β LaTeX compilation, BibTeX ops, claim rendering, arXiv export. No UI, no I/O assumptions beyond paths. |
| Surfaces | _cli/, _mcp/, _django/, _ports/ | Four user-facing interfaces (CLI, MCP tools for AI agents, Django web editor, optional bridges to scitex-scholar/figrecipe/clew). Each delegates to the engines; they never bypass them. |
The _django editor + viewer ship the same code that runs locally and on scitex.ai/apps/writer/ (no separate cloud-side implementation). Optional sibling integrations (_ports/scholar.py, etc.) follow the *_AVAILABLE flag pattern from scitex-python β if the peer isn't installed, the bridge degrades silently.
See Four Interfaces below for usage details per surface.
Four Interfaces
| Interface | For | Description |
|---|---|---|
| Python API | Human researchers | import scitex_writer as sw |
| Command-Line Interface (CLI) Commands | Terminal users | scitex-writer compile, scitex-writer bib |
| MCP Tools | AI agents | 39 tools for Claude/GPT integration |
| Skills | AI agent discovery | Workflow guides for capabilities and patterns |
Python API
Compile β Build PDFs
import scitex_writer as sw
sw.compile.manuscript("./my-paper") # Full compile
sw.compile.manuscript("./my-paper", draft=True) # Fast draft mode
sw.compile.supplementary("./my-paper")
sw.compile.revision("./my-paper", track_changes=True)
Export β arXiv Submission
sw.export.manuscript("./my-paper") # arXiv-ready tarball
sw.export.manuscript("./my-paper", output_dir="/tmp") # Custom output dir
Tables/Figures/Bib β Create, Read, Update, Delete (CRUD) Operations
# Tables
sw.tables.list("./my-paper")
sw.tables.add("./my-paper", "results", "a,b\n1,2", "Results summary")
sw.tables.remove("./my-paper", "results")
# Figures
sw.figures.list("./my-paper")
sw.figures.add("./my-paper", "fig01", "./plot.png", "My figure")
sw.figures.remove("./my-paper", "fig01")
# Bibliography
sw.bib.list_files("./my-paper")
sw.bib.add("./my-paper", "@article{Smith2024, title={...}}")
sw.bib.merge("./my-paper") # Merge + deduplicate
Guidelines β Introduction, Methods, Results, and Discussion (IMRAD) Writing Tips
sw.guidelines.get("abstract")
sw.guidelines.build("abstract", draft="Your draft...")
sw.guidelines.list_sections() # ['abstract', 'introduction', 'methods', 'discussion', 'proofread']
Prompts β AI2 Asta
from scitex_writer import generate_asta
result = generate_asta("./my-paper", search_type="related")
GUI β Browser-based Editor
sw.gui("./my-paper") # Launch editor
sw.gui("./my-paper", port=8080, dark_mode=True) # Custom options
CLI Commands
scitex-writer --help # Show all commands
# Compile - Build PDFs
scitex-writer compile manuscript # Compile manuscript
scitex-writer compile manuscript --draft # Fast single-pass
scitex-writer compile supplementary # Compile supplementary
scitex-writer compile revision # Compile revision letter
# Export - arXiv submission
scitex-writer export manuscript # Package for arXiv upload
# Bibliography - Reference management
scitex-writer bib list-files # List .bib files
scitex-writer bib list-entries # List all entries
scitex-writer bib get Smith2024 # Get specific entry
scitex-writer bib add '@article{...}' # Add entry
scitex-writer bib remove Smith2024 # Remove entry
scitex-writer bib merge # Merge and deduplicate
# Tables - CSV to LaTeX management
scitex-writer tables list # List tables
scitex-writer tables add results data.csv "Caption"
scitex-writer tables remove results
# Figures - Image management
scitex-writer figures list # List figures
scitex-writer figures add fig01 plot.png "Caption"
scitex-writer figures remove fig01
# Guidelines - IMRAD writing tips
scitex-writer guidelines list # List available sections
scitex-writer guidelines abstract # Get abstract guidelines
scitex-writer guidelines abstract -d draft.tex # Build prompt with draft
# Prompts - AI2 Asta integration
scitex-writer prompts asta # Generate related papers prompt
scitex-writer prompts asta -t coauthors # Find collaborators
# MCP server management
scitex-writer mcp list-tools # List all MCP tools (markdown)
scitex-writer mcp doctor # Check server health
scitex-writer mcp installation # Show Claude Desktop config
scitex-writer mcp start # Start MCP server
# GUI - Browser-based editor
scitex-writer gui # Launch editor (current dir)
scitex-writer gui ./my-paper # Open specific project
scitex-writer gui --port 8080 --no-browser # Custom port, no auto-open
MCP Tools β 39 tools for AI Agents
Turn AI agents into autonomous manuscript compilers.
| Category | Tools | Description |
|---|---|---|
| project | 4 | Clone, info, PDF paths, document types |
| compile | 4 | Manuscript, supplementary, revision, content |
| tables | 5 | CSV to LaTeX, list/add/remove tables |
| figures | 5 | Convert, render PDF, list/add/remove |
| bib | 6 | List files/entries, CRUD, merge/dedupe |
| guidelines | 3 | List, get, build with draft |
| prompts | 1 | AI2 Asta prompt generation |
| export | 1 | arXiv-ready tarball packaging |
| claim | 6 | Traceable scientific assertions |
| migration | 2 | Overleaf import/export |
| update | 1 | Template update from upstream |
Claude Desktop (~/.config/Claude/claude_desktop_config.json):
{
"mcpServers": {
"scitex-writer": {
"command": "scitex-writer",
"args": ["mcp", "start"]
}
}
}
Skills β for AI Agent Discovery
Skills provide workflow-oriented guides that AI agents query to discover capabilities and usage patterns.
scitex-writer skills list # List available skill pages
scitex-writer skills get SKILL # Show main skill page
scitex-dev skills export --package scitex-writer # Export to Claude Code
| Skill | Content |
|---|---|
quick-start | Basic manuscript workflow |
compilation | Compile manuscript, supplementary, revision |
bibliography | BibTeX management, enrichment |
figures-and-tables | Figure/table insertion and conversion |
claims | Claim tracking and rendering |
cli-reference | CLI commands |
mcp-tools | MCP tools for AI agents |
writing-attitude | Evidence requirements, scientific standards |
writing-figures-stats | Figure rules, statistical reporting |
writing-proofreading | Proofreading corrections, language rules |
writing-abstract | Abstract template with 7-section structure |
writing-introduction | Introduction template with 8-section structure |
writing-methods | Methods template with reproducibility guidelines |
writing-discussion | Discussion template with 5-section structure |
audit-paper | Comprehensive pre-submission manuscript audit |
Additional Interfaces
Shell Scripts / Make β Direct compilation without Python.
make manuscript # Compile manuscript
make supplementary # Compile supplementary
make revision # Compile revision
make all # Compile all documents
make manuscript-export # Package for arXiv submission
make clean # Remove build artifacts
./compile.sh manuscript --draft # Fast single-pass
./compile.sh manuscript --no-figs # Skip figures
./compile.sh manuscript --dark-mode # Dark mode (Monaco theme)
./compile.sh manuscript --watch # Hot-reload
SCITEX_WRITER_DARK_MODE=true make manuscript
GUI Editor β Standalone browser-based editor with file tree, PDF preview, and compilation controls.
Β Β
pip install scitex-writer[editor]
scitex-writer gui # Current directory
scitex-writer gui ./my-paper # Specific project
scitex-writer gui --port 8080 # Custom port
Output Structure
./scitex-writer/
βββ 00_shared/ # Shared resources across all documents
β βββ title.tex / authors.tex / keywords.tex / journal_name.tex
β βββ bib_files/ # Multiple .bib files (auto-merged and deduplicated)
β βββ latex_styles/ # Common LaTeX configurations
β βββ templates/ # LaTeX document templates
βββ 01_manuscript/ # Main manuscript
β βββ contents/ # abstract, introduction, methods, results, discussion
β β βββ figures/ # Figure captions + media
β β βββ tables/ # Table captions + CSV data
β βββ archive/ # Version history (gitignored)
β βββ manuscript.tex # Compiled LaTeX
β βββ manuscript_diff.tex # Change-tracked version
β βββ manuscript.pdf # Output PDF
βββ 02_supplementary/ # Supplementary materials (same structure)
βββ 03_revision/ # Revision response letter
β βββ contents/ # editor/, reviewer1/, reviewer2/
βββ config/ # config_manuscript.yaml
βββ scripts/ # containers, installation, shell, python
Features
Details
| Feature | Description |
|---|---|
| Separated Files | Modular sections (abstract, intro, methods, results, discussion) |
| Built-in Templates | Pre-configured manuscript, supplementary materials, and revision |
| Bibliography | Multi-file with auto-deduplication, 20+ citation styles |
| Assets | Parallel figure/table processing (PNG, PDF, SVG, Mermaid, CSV) |
| GUI Editor | Browser-based editor with PDF preview (scitex-writer gui) |
| Dark Mode | Monaco/VS Code dark theme for comfortable reading (--dark-mode) |
| Multi-Engine | Auto-selects best engine (Tectonic 1-3s, latexmk 3-6s, 3-pass 12-18s) |
| Cross-Platform | Linux, macOS, WSL2, Docker, Singularity, HPC clusters |
Usage
PDF Compilation
# Basic compilation
./scripts/shell/compile_manuscript.sh # Manuscript
./scripts/shell/compile_supplementary.sh # Supplementary
./scripts/shell/compile_revision.sh # Revision letter
# Performance options
./scripts/shell/compile_manuscript.sh --draft # Fast single-pass
./scripts/shell/compile_manuscript.sh --no-figs # Skip figures
./scripts/shell/compile_manuscript.sh --no-tables # Skip tables
./scripts/shell/compile_manuscript.sh --no-diff # Skip diff generation
# Engine selection
./scripts/shell/compile_manuscript.sh --engine tectonic # Fastest
./scripts/shell/compile_manuscript.sh --engine latexmk # Standard
./scripts/shell/compile_manuscript.sh --engine 3pass # Most compatible
# Development
./scripts/shell/compile_manuscript.sh --watch # Hot-reload on file changes
./scripts/shell/compile_manuscript.sh --clean # Remove cache
Figures
-
Place media files in
01_manuscript/contents/figures/caption_and_media/:01_example_figure.png 01_example_figure.tex # Caption file -
Caption file format (
01_example_figure.tex):%% Figure caption \caption{Your figure caption here. Explain panels (A, B, C) if applicable.} \label{fig:example_figure_01} -
Supported formats: PNG, JPEG, PDF, SVG, TIFF, Mermaid (.mmd)
-
Figures auto-compile and include in
FINAL.tex
Tables
-
Place CSV + caption in
01_manuscript/contents/tables/caption_and_media/:01_example_table.csv 01_example_table.tex # Caption file -
CSV auto-converts to LaTeX table format
-
Caption file format (
01_example_table.tex):%% Table caption \caption{Your table caption. Define abbreviations used.} \label{tab:example_table_01}
References
Organize references in multiple .bib files - they auto-merge with deduplication:
00_shared/bib_files/
βββ methods_refs.bib # Method-related references
βββ field_background.bib # Background literature
βββ my_papers.bib # Your own publications
Change citation style in config/config_manuscript.yaml:
unsrtnat(numbered, order of citation)plainnat(numbered, alphabetical)apalike(author-year, APA style)IEEEtran(IEEE format)naturemag(Nature style)
Documentation
Details
| Guide | Description |
|---|---|
| Installation | Setup for all environments |
| Quick Start | Common workflows |
| Content Creation | Writing manuscripts |
| Bibliography | Reference management |
| Architecture | Technical details |
