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Tools"],"sub_categories":["GitHub Actions"],"readme":"\u003c!-- ---\n!-- File: README.md\n!-- --- --\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://scitex.ai\"\u003e\n    \u003cimg src=\"docs/scitex-logo-banner.png\" alt=\"SciTeX Writer\" width=\"400\"\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\n# SciTeX Writer\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://badge.fury.io/py/scitex-writer\"\u003e\u003cimg src=\"https://badge.fury.io/py/scitex-writer.svg\" alt=\"PyPI version\"\u003e\u003c/a\u003e\n  \u003ca href=\"https://pypi.org/project/scitex-writer/\"\u003e\u003cimg src=\"https://img.shields.io/pypi/pyversions/scitex-writer.svg\" alt=\"Python Versions\"\u003e\u003c/a\u003e\n  \u003ca href=\"https://scitex-writer.readthedocs.io/\"\u003e\u003cimg src=\"https://readthedocs.org/projects/scitex-writer/badge/?version=latest\" alt=\"Documentation\"\u003e\u003c/a\u003e\n  \u003ca href=\"https://github.com/ywatanabe1989/scitex-writer/blob/main/LICENSE\"\u003e\u003cimg src=\"https://img.shields.io/github/license/ywatanabe1989/scitex-writer\" alt=\"License\"\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://scitex.ai\"\u003escitex.ai\u003c/a\u003e · \u003ca href=\"https://scitex-writer.readthedocs.io/\"\u003edocs\u003c/a\u003e · \u003ccode\u003epip install scitex-writer\u003c/code\u003e\n\u003c/p\u003e\n\n---\n\n**LaTeX compilation system for scientific manuscripts with automatic versioning, diff generation, and cross-platform reproducibility.**\n\nPart of the [SciTeX](https://scitex.ai) ecosystem — empowers both human researchers and AI agents.\n\n## Preview\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"docs/demo-manuscript-light.png\" alt=\"Light Mode\" width=\"380\"/\u003e\n  \u0026nbsp;\u0026nbsp;\n  \u003cimg src=\"docs/demo-manuscript-dark.png\" alt=\"Dark Mode\" width=\"380\"/\u003e\n\u003c/p\u003e\n\u003cp align=\"center\"\u003e\n  \u003cem\u003eLight mode (default) and dark mode (\u003ccode\u003e--dark-mode\u003c/code\u003e)\u003c/em\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://scitex.ai/demos/watch/scitex-writer/\"\u003e\n    \u003cimg src=\"examples/scitex-writer-v2.2.0-demo-thumbnail.png\" alt=\"Demo Video\" width=\"600\"/\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\u003cp align=\"center\"\u003e\n  \u003cem\u003eDemo video with AI agent\u003c/em\u003e\n\u003c/p\u003e\n\n## Installation\n\n```bash\n# LaTeX dependencies (Ubuntu/Debian)\nsudo apt-get install texlive-latex-extra latexdiff parallel imagemagick ghostscript\n\n# LaTeX dependencies (macOS)\nbrew install texlive latexdiff parallel imagemagick ghostscript\n\n# Python package + MCP server\npip install scitex-writer\n```\n\n## Quick Start\n\n```bash\ngit clone https://github.com/ywatanabe1989/scitex-writer.git my-paper\ncd my-paper \u0026\u0026 make manuscript   # or: ./compile.sh manuscript\n```\n\n## Problem\n\nLaTeX compilation for scientific manuscripts is painful:\n\n- **Environment inconsistency** — \"It compiles on my machine\" is not a solution when collaborating across Linux, macOS, WSL2, and HPC clusters.\n- **Manual figure conversion** — Converting between PNG, SVG, PDF, Mermaid, and TIFF formats by hand wastes time and introduces errors.\n- **No version tracking** — Generating tracked-change diffs between revisions requires manual `latexdiff` invocations and careful file management.\n- **Fragmented tooling** — Separate workflows for compilation, bibliography management, table formatting, and submission packaging.\n- **AI agents cannot help** — Without a programmatic interface, AI assistants have no way to compile or manage manuscripts.\n\n## Solution\n\nSciTeX Writer solves each of these problems:\n\n- **Container-based reproducible compilation** — Consistent builds across all platforms via Docker, Singularity, or native installation with automatic engine selection (Tectonic, latexmk, or 3-pass).\n- **Automatic asset conversion** — Figures and tables are converted in parallel from source formats (PNG, SVG, comma-separated values (CSV), Mermaid) to LaTeX-ready output.\n- **Built-in version tracking with diff generation** — Every compilation archives the previous version and generates a `latexdiff` document automatically.\n- **Unified interface** — One tool for compilation, bibliography deduplication, figure/table management, and arXiv export packaging.\n- **39 Model Context Protocol (MCP) tools for AI agents** — AI assistants can compile, edit, and manage manuscripts programmatically.\n\n## Four Interfaces\n\n| Interface | For | Description |\n|-----------|-----|-------------|\n| **Python API** | Human researchers | `import scitex_writer as sw` |\n| **Command-Line Interface (CLI) Commands** | Terminal users | `scitex-writer compile`, `scitex-writer bib` |\n| **MCP Tools** | AI agents | 39 tools for Claude/GPT integration |\n| **Skills** | AI agent discovery | Workflow guides for capabilities and patterns |\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cstrong\u003ePython API\u003c/strong\u003e\u003c/summary\u003e\n\n**Compile** — Build PDFs\n\n```python\nimport scitex_writer as sw\n\nsw.compile.manuscript(\"./my-paper\")                    # Full compile\nsw.compile.manuscript(\"./my-paper\", draft=True)       # Fast draft mode\nsw.compile.supplementary(\"./my-paper\")\nsw.compile.revision(\"./my-paper\", track_changes=True)\n```\n\n**Export** — arXiv Submission\n\n```python\nsw.export.manuscript(\"./my-paper\")                     # arXiv-ready tarball\nsw.export.manuscript(\"./my-paper\", output_dir=\"/tmp\")  # Custom output dir\n```\n\n**Tables/Figures/Bib** — Create, Read, Update, Delete (CRUD) Operations\n\n```python\n# Tables\nsw.tables.list(\"./my-paper\")\nsw.tables.add(\"./my-paper\", \"results\", \"a,b\\n1,2\", \"Results summary\")\nsw.tables.remove(\"./my-paper\", \"results\")\n\n# Figures\nsw.figures.list(\"./my-paper\")\nsw.figures.add(\"./my-paper\", \"fig01\", \"./plot.png\", \"My figure\")\nsw.figures.remove(\"./my-paper\", \"fig01\")\n\n# Bibliography\nsw.bib.list_files(\"./my-paper\")\nsw.bib.add(\"./my-paper\", \"@article{Smith2024, title={...}}\")\nsw.bib.merge(\"./my-paper\")  # Merge + deduplicate\n```\n\n**Guidelines** — Introduction, Methods, Results, and Discussion (IMRAD) Writing Tips\n\n```python\nsw.get_guideline(\"abstract\")\nsw.build_guideline(\"abstract\", draft=\"Your draft...\")\nsw.list_guidelines()  # ['abstract', 'introduction', 'methods', 'discussion', 'proofread']\n```\n\n**Prompts** — AI2 Asta\n\n```python\nfrom scitex_writer import generate_asta\nresult = generate_asta(\"./my-paper\", search_type=\"related\")\n```\n\n**GUI** — Browser-based Editor\n\n```python\nsw.gui(\"./my-paper\")                              # Launch editor\nsw.gui(\"./my-paper\", port=8080, dark_mode=True)  # Custom options\n```\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cstrong\u003eCLI Commands\u003c/strong\u003e\u003c/summary\u003e\n\n```bash\nscitex-writer --help                           # Show all commands\n\n# Compile - Build PDFs\nscitex-writer compile manuscript               # Compile manuscript\nscitex-writer compile manuscript --draft       # Fast single-pass\nscitex-writer compile supplementary            # Compile supplementary\nscitex-writer compile revision                 # Compile revision letter\n\n# Export - arXiv submission\nscitex-writer export manuscript               # Package for arXiv upload\n\n# Bibliography - Reference management\nscitex-writer bib list-files                   # List .bib files\nscitex-writer bib list-entries                 # List all entries\nscitex-writer bib get Smith2024                # Get specific entry\nscitex-writer bib add '@article{...}'          # Add entry\nscitex-writer bib remove Smith2024             # Remove entry\nscitex-writer bib merge                        # Merge and deduplicate\n\n# Tables - CSV to LaTeX management\nscitex-writer tables list                      # List tables\nscitex-writer tables add results data.csv \"Caption\"\nscitex-writer tables remove results\n\n# Figures - Image management\nscitex-writer figures list                     # List figures\nscitex-writer figures add fig01 plot.png \"Caption\"\nscitex-writer figures remove fig01\n\n# Guidelines - IMRAD writing tips\nscitex-writer guidelines list                  # List available sections\nscitex-writer guidelines abstract              # Get abstract guidelines\nscitex-writer guidelines abstract -d draft.tex # Build prompt with draft\n\n# Prompts - AI2 Asta integration\nscitex-writer prompts asta                     # Generate related papers prompt\nscitex-writer prompts asta -t coauthors        # Find collaborators\n\n# MCP server management\nscitex-writer mcp list-tools                   # List all MCP tools (markdown)\nscitex-writer mcp doctor                       # Check server health\nscitex-writer mcp installation                 # Show Claude Desktop config\nscitex-writer mcp start                        # Start MCP server\n\n# GUI - Browser-based editor\nscitex-writer gui                              # Launch editor (current dir)\nscitex-writer gui ./my-paper                   # Open specific project\nscitex-writer gui --port 8080 --no-browser     # Custom port, no auto-open\n```\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cstrong\u003eMCP Tools — 39 tools for AI Agents\u003c/strong\u003e\u003c/summary\u003e\n\nTurn AI agents into autonomous manuscript compilers.\n\n| Category | Tools | Description |\n|----------|-------|-------------|\n| project | 4 | Clone, info, PDF paths, document types |\n| compile | 4 | Manuscript, supplementary, revision, content |\n| tables | 5 | CSV to LaTeX, list/add/remove tables |\n| figures | 5 | Convert, render PDF, list/add/remove |\n| bib | 6 | List files/entries, CRUD, merge/dedupe |\n| guidelines | 3 | List, get, build with draft |\n| prompts | 1 | AI2 Asta prompt generation |\n| export | 1 | arXiv-ready tarball packaging |\n| claim | 6 | Traceable scientific assertions |\n| migration | 2 | Overleaf import/export |\n| update | 1 | Template update from upstream |\n\n**Claude Desktop** (`~/.config/Claude/claude_desktop_config.json`):\n\n```json\n{\n  \"mcpServers\": {\n    \"scitex-writer\": {\n      \"command\": \"scitex-writer\",\n      \"args\": [\"mcp\", \"start\"]\n    }\n  }\n}\n```\n\n\u003e **[Full MCP tool reference](./docs/MCP_TOOLS.md)**\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cstrong\u003eSkills — for AI Agent Discovery\u003c/strong\u003e\u003c/summary\u003e\n\n\u003cbr\u003e\n\nSkills provide workflow-oriented guides that AI agents query to discover capabilities and usage patterns.\n\n```bash\nscitex-writer skills list              # List available skill pages\nscitex-writer skills get SKILL         # Show main skill page\nscitex-dev skills export --package scitex-writer  # Export to Claude Code\n```\n\n| Skill | Content |\n|-------|---------|\n| `quick-start` | Basic manuscript workflow |\n| `compilation` | Compile manuscript, supplementary, revision |\n| `bibliography` | BibTeX management, enrichment |\n| `figures-and-tables` | Figure/table insertion and conversion |\n| `claims` | Claim tracking and rendering |\n| `cli-reference` | CLI commands |\n| `mcp-tools` | MCP tools for AI agents |\n| `writing-attitude` | Evidence requirements, scientific standards |\n| `writing-figures-stats` | Figure rules, statistical reporting |\n| `writing-proofreading` | Proofreading corrections, language rules |\n| `writing-abstract` | Abstract template with 7-section structure |\n| `writing-introduction` | Introduction template with 8-section structure |\n| `writing-methods` | Methods template with reproducibility guidelines |\n| `writing-discussion` | Discussion template with 5-section structure |\n| `audit-paper` | Comprehensive pre-submission manuscript audit |\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cstrong\u003eAdditional Interfaces\u003c/strong\u003e\u003c/summary\u003e\n\n**Shell Scripts / Make** — Direct compilation without Python.\n\n```bash\nmake manuscript              # Compile manuscript\nmake supplementary           # Compile supplementary\nmake revision                # Compile revision\nmake all                     # Compile all documents\nmake manuscript-export       # Package for arXiv submission\nmake clean                   # Remove build artifacts\n./compile.sh manuscript --draft       # Fast single-pass\n./compile.sh manuscript --no-figs     # Skip figures\n./compile.sh manuscript --dark-mode   # Dark mode (Monaco theme)\n./compile.sh manuscript --watch       # Hot-reload\nSCITEX_WRITER_DARK_MODE=true make manuscript\n```\n\n**GUI Editor** — Standalone browser-based editor with file tree, PDF preview, and compilation controls.\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"docs/demo-gui-light.png\" alt=\"GUI Light Mode\" width=\"380\"/\u003e\n  \u0026nbsp;\u0026nbsp;\n  \u003cimg src=\"docs/demo-gui-dark.png\" alt=\"GUI Dark Mode\" width=\"380\"/\u003e\n\u003c/p\u003e\n\n```bash\npip install scitex-writer[editor]\nscitex-writer gui                    # Current directory\nscitex-writer gui ./my-paper         # Specific project\nscitex-writer gui --port 8080        # Custom port\n```\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cstrong\u003eOutput Structure\u003c/strong\u003e\u003c/summary\u003e\n\n```\n./scitex-writer/\n├── 00_shared/                  # Shared resources across all documents\n│   ├── title.tex / authors.tex / keywords.tex / journal_name.tex\n│   ├── bib_files/              # Multiple .bib files (auto-merged and deduplicated)\n│   ├── latex_styles/           # Common LaTeX configurations\n│   └── templates/              # LaTeX document templates\n├── 01_manuscript/              # Main manuscript\n│   ├── contents/               # abstract, introduction, methods, results, discussion\n│   │   ├── figures/            # Figure captions + media\n│   │   └── tables/             # Table captions + CSV data\n│   ├── archive/                # Version history (gitignored)\n│   ├── manuscript.tex          # Compiled LaTeX\n│   ├── manuscript_diff.tex     # Change-tracked version\n│   └── manuscript.pdf          # Output PDF\n├── 02_supplementary/           # Supplementary materials (same structure)\n├── 03_revision/                # Revision response letter\n│   └── contents/               # editor/, reviewer1/, reviewer2/\n├── config/                     # config_manuscript.yaml\n└── scripts/                    # containers, installation, shell, python\n```\n\n\u003c/details\u003e\n\n## Features\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cstrong\u003eDetails\u003c/strong\u003e\u003c/summary\u003e\n\n| Feature                | Description                                                           |\n|------------------------|-----------------------------------------------------------------------|\n| **Separated Files**    | Modular sections (abstract, intro, methods, results, discussion)      |\n| **Built-in Templates** | Pre-configured manuscript, supplementary materials, and revision      |\n| **Bibliography**       | Multi-file with auto-deduplication, 20+ citation styles               |\n| **Assets**             | Parallel figure/table processing (PNG, PDF, SVG, Mermaid, CSV)        |\n| **GUI Editor**         | Browser-based editor with PDF preview (`scitex-writer gui`)           |\n| **Dark Mode**          | Monaco/VS Code dark theme for comfortable reading (`--dark-mode`)     |\n| **Multi-Engine**       | Auto-selects best engine (Tectonic 1-3s, latexmk 3-6s, 3-pass 12-18s) |\n| **Cross-Platform**     | Linux, macOS, WSL2, Docker, Singularity, HPC clusters                 |\n\n\u003c/details\u003e\n\n## Usage\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cstrong\u003ePDF Compilation\u003c/strong\u003e\u003c/summary\u003e\n\n```bash\n# Basic compilation\n./scripts/shell/compile_manuscript.sh          # Manuscript\n./scripts/shell/compile_supplementary.sh       # Supplementary\n./scripts/shell/compile_revision.sh            # Revision letter\n\n# Performance options\n./scripts/shell/compile_manuscript.sh --draft      # Fast single-pass\n./scripts/shell/compile_manuscript.sh --no-figs    # Skip figures\n./scripts/shell/compile_manuscript.sh --no-tables  # Skip tables\n./scripts/shell/compile_manuscript.sh --no-diff    # Skip diff generation\n\n# Engine selection\n./scripts/shell/compile_manuscript.sh --engine tectonic  # Fastest\n./scripts/shell/compile_manuscript.sh --engine latexmk   # Standard\n./scripts/shell/compile_manuscript.sh --engine 3pass     # Most compatible\n\n# Development\n./scripts/shell/compile_manuscript.sh --watch  # Hot-reload on file changes\n./scripts/shell/compile_manuscript.sh --clean  # Remove cache\n```\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cstrong\u003eFigures\u003c/strong\u003e\u003c/summary\u003e\n\n1. Place media files in `01_manuscript/contents/figures/caption_and_media/`:\n   ```\n   01_example_figure.png\n   01_example_figure.tex  # Caption file\n   ```\n\n2. Caption file format (`01_example_figure.tex`):\n   ```latex\n   %% Figure caption\n   \\caption{Your figure caption here. Explain panels (A, B, C) if applicable.}\n   \\label{fig:example_figure_01}\n   ```\n\n3. Supported formats: PNG, JPEG, PDF, SVG, TIFF, Mermaid (.mmd)\n\n4. Figures auto-compile and include in `FINAL.tex`\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cstrong\u003eTables\u003c/strong\u003e\u003c/summary\u003e\n\n1. Place CSV + caption in `01_manuscript/contents/tables/caption_and_media/`:\n   ```\n   01_example_table.csv\n   01_example_table.tex  # Caption file\n   ```\n\n2. CSV auto-converts to LaTeX table format\n\n3. Caption file format (`01_example_table.tex`):\n   ```latex\n   %% Table caption\n   \\caption{Your table caption. Define abbreviations used.}\n   \\label{tab:example_table_01}\n   ```\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cstrong\u003eReferences\u003c/strong\u003e\u003c/summary\u003e\n\nOrganize references in multiple `.bib` files - they auto-merge with deduplication:\n\n```bash\n00_shared/bib_files/\n├── methods_refs.bib      # Method-related references\n├── field_background.bib  # Background literature\n└── my_papers.bib         # Your own publications\n```\n\nChange citation style in `config/config_manuscript.yaml`:\n- `unsrtnat` (numbered, order of citation)\n- `plainnat` (numbered, alphabetical)\n- `apalike` (author-year, APA style)\n- `IEEEtran` (IEEE format)\n- `naturemag` (Nature style)\n\n\u003c/details\u003e\n\n## Documentation\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cstrong\u003eDetails\u003c/strong\u003e\u003c/summary\u003e\n\n| Guide | Description |\n|-------|-------------|\n| [Installation](docs/01_GUIDE_INSTALLATION.md) | Setup for all environments |\n| [Quick Start](docs/01_GUIDE_QUICK_START.md) | Common workflows |\n| [Content Creation](docs/01_GUIDE_CONTENT_CREATION.md) | Writing manuscripts |\n| [Bibliography](docs/01_GUIDE_BIBLIOGRAPHY.md) | Reference management |\n| [Architecture](docs/02_ARCHITECTURE_IMPLEMENTATION.md) | Technical details |\n\n\u003c/details\u003e\n\n## Part of SciTeX\n\nSciTeX Writer is part of [SciTeX](https://scitex.ai). When used inside the orchestrator package `scitex`, synergy between modules enables end-to-end scientific workflows — from data analysis through publication-ready manuscripts.\n\nThe SciTeX ecosystem follows the **Four Freedoms** for researchers, inspired by [the Free Software Definition](https://www.gnu.org/philosophy/free-sw.en.html):\n\n0. **Use** — Run the software for any research purpose\n1. **Study** — Examine how it works and adapt it to your needs\n2. **Share** — Distribute copies to fellow researchers\n3. **Improve** — Enhance the software and share improvements with the community\n\n---\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://scitex.ai\" target=\"_blank\"\u003e\u003cimg src=\"docs/scitex-icon-navy-inverted.png\" alt=\"SciTeX\" width=\"40\"/\u003e\u003c/a\u003e\n  \u003cbr\u003e\n  AGPL-3.0\n\u003c/p\u003e\n\n\u003c!-- EOF --\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fywatanabe1989%2Fscitex-writer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fywatanabe1989%2Fscitex-writer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fywatanabe1989%2Fscitex-writer/lists"}