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<a href="https://scitex.ai">
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# SciTeX Writer
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<a href="https://scitex.ai">scitex.ai</a> · <a href="https://scitex-writer.readthedocs.io/">docs</a> · <code>uv pip install scitex-writer[all]</code>
</p>
---
**LaTeX compilation system for scientific manuscripts with automatic versioning, diff generation, and cross-platform reproducibility.**
Part of the [SciTeX](https://scitex.ai) ecosystem — 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 → latex → bibtex → 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
<p align="center">
<img src="docs/demo-manuscript-light.png" alt="Light Mode" width="380"/>
<img src="docs/demo-manuscript-dark.png" alt="Dark Mode" width="380"/>
</p>
<p align="center">
<em>Light mode (default) and dark mode (<code>--dark-mode</code>)</em>
</p>
<p align="center">
<a href="https://scitex.ai/demos/watch/scitex-writer/">
<img src="examples/scitex-writer-v2.2.0-demo-thumbnail.png" alt="Demo Video" width="600"/>
</a>
</p>
<p align="center">
<em>Demo video with AI agent</em>
</p>
## Installation
```bash
# 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
```bash
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**](https://scitex.ai). Install via
the umbrella with `pip install scitex[writer]` to use as
`scitex.writer` (Python) or `scitex writer ...` (CLI).
>Four Freedoms for Research
>
>0. The freedom to **run** your research anywhere — your machine, your terms.
>1. The freedom to **study** how every step works — from raw data to final manuscript.
>2. The freedom to **redistribute** your workflows, not just your papers.
>3. The freedom to **modify** any module and share improvements with the community.
>
>AGPL-3.0 — 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** — "It compiles on my machine" is not a solution when collaborating across Linux, macOS, WSL2, and HPC clusters.
- **Manual figure conversion** — Converting between PNG, SVG, PDF, Mermaid, and TIFF formats by hand wastes time and introduces errors.
- **No version tracking** — Generating tracked-change diffs between revisions requires manual `latexdiff` invocations and careful file management.
- **Fragmented tooling** — Separate workflows for compilation, bibliography management, table formatting, and submission packaging.
- **AI agents cannot help** — 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** — Consistent builds across all platforms via Docker, Singularity, or native installation with automatic engine selection (Tectonic, latexmk, or 3-pass).
- **Automatic asset conversion** — 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** — Every compilation archives the previous version and generates a `latexdiff` document automatically.
- **Unified interface** — One tool for compilation, bibliography deduplication, figure/table management, and arXiv export packaging.
- **44 Model Context Protocol (MCP) tools for AI agents** — AI assistants can compile, edit, and manage manuscripts programmatically.
## Architecture
```mermaid
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 — the source of truth every other layer reads. |
| **Engines** | `_compile/`, `bib.py`, `claim.py`, `export/`, `migration/` | Pure functions that operate on the project model — 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` — if the peer isn't installed, the bridge degrades silently.
See [`Four Interfaces`](#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 | 44 tools for Claude/GPT integration |
| **Skills** | AI agent discovery | Workflow guides for capabilities and patterns |
<details open>
<summary><strong>Python API</strong></summary>
**Compile** — Build PDFs
```python
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** — arXiv Submission
```python
sw.export.manuscript("./my-paper") # arXiv-ready tarball
sw.export.manuscript("./my-paper", output_dir="/tmp") # Custom output dir
```
**Tables/Figures/Bib** — Create, Read, Update, Delete (CRUD) Operations
```python
# 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** — Introduction, Methods, Results, and Discussion (IMRAD) Writing Tips
```python
sw.guidelines.get("abstract")
sw.guidelines.build("abstract", draft="Your draft...")
sw.guidelines.list_sections() # ['abstract', 'introduction', 'methods', 'discussion', 'proofread']
```
**Prompts** — AI2 Asta
```python
from scitex_writer import generate_asta
result = generate_asta("./my-paper", search_type="related")
```
**GUI** — Browser-based Editor
```python
sw.gui("./my-paper") # Launch editor
sw.gui("./my-paper", port=8080, dark_mode=True) # Custom options
```
</details>
<details>
<summary><strong>CLI Commands</strong></summary>
```bash
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
# Checks - Pre-submission validation
scitex-writer check-references # Cross-refs, citations, labels, duplicate headings
scitex-writer check-limits # Section word limits + reference cap (config-driven)
# Update - Sync engine files from the template
scitex-writer update-project # Preview drifted engine files (safe; pass --yes to apply)
# 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 install # 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
```
</details>
<details>
<summary><strong>MCP Tools — 44 tools for AI Agents</strong></summary>
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 | 6 | CSV to LaTeX, list/add/remove, archive |
| figures | 6 | Convert, render PDF, list/add/remove, archive |
| 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 |
| checks | 2 | Reference integrity, float order |
| skills | 2 | List and retrieve skill pages |
| update | 1 | Engine-file sync with drift detection |
**Claude Desktop** (`~/.config/Claude/claude_desktop_config.json`):
```json
{
"mcpServers": {
"scitex-writer": {
"command": "scitex-writer",
"args": ["mcp", "start"]
}
}
}
```
> **[Full MCP tool reference](./docs/MCP_TOOLS.md)**
</details>
<details>
<summary><strong>Skills — for AI Agent Discovery</strong></summary>
<br>
Skills provide workflow-oriented guides that AI agents query to discover capabilities and usage patterns.
```bash
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 |
</details>
<details>
<summary><strong>Additional Interfaces</strong></summary>
**Shell Scripts / Make** — Direct compilation without Python.
```bash
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** — Standalone browser-based editor with file tree, PDF preview, and compilation controls.
<p align="center">
<img src="docs/demo-gui-light.png" alt="GUI Light Mode" width="380"/>
<img src="docs/demo-gui-dark.png" alt="GUI Dark Mode" width="380"/>
</p>
```bash
pip install scitex-writer[editor]
scitex-writer gui # Current directory
scitex-writer gui ./my-paper # Specific project
scitex-writer gui --port 8080 # Custom port
```
</details>
<details>
<summary><strong>Output Structure</strong></summary>
```
./scitex-writer/
├── 00_shared/ # Shared resources across all documents
│ ├── title.tex / authors.tex / keywords.tex / journal_name.tex
│ ├── bib_files/ # Multiple .bib files (auto-merged and deduplicated)
│ ├── latex_styles/ # Common LaTeX configurations
│ └── templates/ # LaTeX document templates
├── 01_manuscript/ # Main manuscript
│ ├── contents/ # abstract, introduction, methods, results, discussion
│ │ ├── figures/ # Figure captions + media
│ │ └── tables/ # Table captions + CSV data
│ ├── archive/ # Version history (gitignored)
│ ├── manuscript.tex # Compiled LaTeX
│ ├── manuscript_diff.tex # Change-tracked version
│ └── manuscript.pdf # Output PDF
├── 02_supplementary/ # Supplementary materials (same structure)
├── 03_revision/ # Revision response letter
│ └── contents/ # editor/, reviewer1/, reviewer2/
├── config/ # config_manuscript.yaml
└── scripts/ # containers, installation, shell, python
```
</details>
## Features
<details>
<summary><strong>Details</strong></summary>
| 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`) |
| **Section Limits** | Word caps per IMRAD section + reference cap, checked before compile |
| **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 |
</details>
## Usage
<details>
<summary><strong>PDF Compilation</strong></summary>
```bash
# 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
```
</details>
<details>
<summary><strong>Figures</strong></summary>
1. Place media files in `01_manuscript/contents/figures/caption_and_media/`:
```
01_example_figure.png
01_example_figure.tex # Caption file
```
2. Caption file format (`01_example_figure.tex`):
```latex
%% Figure caption
\caption{Your figure caption here. Explain panels (A, B, C) if applicable.}
\label{fig:example_figure_01}
```
3. Supported formats: PNG, JPEG, PDF, SVG, TIFF, Mermaid (.mmd)
4. Figures auto-compile and include in `FINAL.tex`
</details>
<details>
<summary><strong>Tables</strong></summary>
1. Place CSV + caption in `01_manuscript/contents/tables/caption_and_media/`:
```
01_example_table.csv
01_example_table.tex # Caption file
```
2. CSV auto-converts to LaTeX table format
3. Caption file format (`01_example_table.tex`):
```latex
%% Table caption
\caption{Your table caption. Define abbreviations used.}
\label{tab:example_table_01}
```
</details>
<details>
<summary><strong>References</strong></summary>
Organize references in multiple `.bib` files - they auto-merge with deduplication:
```bash
00_shared/bib_files/
├── methods_refs.bib # Method-related references
├── field_background.bib # Background literature
└── 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)
</details>
## Documentation
<details>
<summary><strong>Details</strong></summary>
| Guide | Description |
|-------|-------------|
| [Installation](docs/01_GUIDE_INSTALLATION.md) | Setup for all environments |
| [Quick Start](docs/01_GUIDE_QUICK_START.md) | Common workflows |
| [Content Creation](docs/01_GUIDE_CONTENT_CREATION.md) | Writing manuscripts |
| [Bibliography](docs/01_GUIDE_BIBLIOGRAPHY.md) | Reference management |
| [Architecture](docs/02_ARCHITECTURE_IMPLEMENTATION.md) | Technical details |
</details>
---
<p align="center">
<a href="https://scitex.ai" target="_blank"><img src="docs/scitex-icon-navy-inverted.png" alt="SciTeX" width="40"/></a>
<br>
AGPL-3.0
</p>
<!-- EOF -->
MCP Config
Below is the configuration for this MCP Server. You can copy it directly to Cursor or other MCP clients.
mcp.json
Connection Info
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