13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps,โฆ
Local document and PDF parsing that returns spatial text with bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; running OCR on scans; producing layout-preserved JSON for RAG; batch-ingesting folders of papers; or rendering pages to PNG for
Claude Code
$ npx -y skills add K-Dense-AI/scientific-agent-skills --skill liteparse --agent claude-code
Codex
$ npx skills add K-Dense-AI/scientific-agent-skills --skill liteparse -a codex -y
Cursor
$ npx skills add K-Dense-AI/scientific-agent-skills --skill liteparse -a cursor -y
Gemini CLI
$ npx skills add K-Dense-AI/scientific-agent-skills --skill liteparse -a gemini-cli -y
GitHub Copilot
$ npx skills add K-Dense-AI/scientific-agent-skills --skill liteparse -a github-copilot -y
OpenCode
$ npx skills add K-Dense-AI/scientific-agent-skills --skill liteparse -a opencode -y
Windsurf
$ npx skills add K-Dense-AI/scientific-agent-skills --skill liteparse -a windsurf -y
name: liteparse description: Local document and PDF parsing that returns spatial text with bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; running OCR on scans; producing layout-preserved JSON for RAG; batch-ingesting folders of papers; or rendering pages to PNG for multimodal agents. Distinguishing capabilities are spatial text boxes, Markdown, page raster output, and local parsing with optional custom HTTP OCR. license: Apache-2.0 allowed-tools: Read Write Edit Bash compatibility: Python 3.10+ with liteparse 2.15.0. LibreOffice required for Office formats; images convert natively. Tesseract is bundled but missing language data downloads on first use. Optional HTTP OCR requires network access and server-specific authentication. metadata: version: "1.6" last-reviewed: "2026-10-01" upstream-version: "2.15.0" skill-author: K-Dense Inc.
LiteParse is an open-source document parser (Rust core, Python/Node bindings) for **local, layout-aware text extraction**. It produces layout text, structured JSON, or heuristic Markdown. Spatial text items may span several words; Python `emit_word_boxes=True` adds word boxes when needed.
**Verified release:** Python **liteparse 2.15.0** (September 29, 2026); CLI and synthetic local PDF/image fixtures tested on Python 3.13. Node/Rust examples below are source-checked and illustrative. Images convert through bundled Rust libraries, not ImageMagick. No cloud account is needed, but missing Tesseract language data can download from GitHub and an explicitly configured HTTP OCR service receives document images.
For parser selection vs MarkItDown, PDF manipulation libraries, or LlamaParse, see `references/choosing_a_parser.md`.
Use LiteParse when you need:
| Task | Use instead | |------|-------------| | Markdown for LLM ingestion (EPUB, audio, YouTube, HTML) | `markitdown` skill | | Merge/split PDFs, forms, watermarks, rotation | A PDF manipulation library such as `pypdf` | | Dense tables, handwriting, production cloud pipelines | [LlamaParse](https://developers.llamaindex.ai/llamaparse/parse/) (cloud; sign up separately) |
uv pip install "liteparse==2.15.0"
This installs the Python bindings and the **`lit`** CLI. Verify:
lit --help python -c "import liteparse; print(liteparse.__version__)"
**Optional system tool** (for Office inputs):
PNG, JPEG, TIFF, WebP, SVG and other supported images convert natively.
Install commands are in `references/ocr_and_formats.md`.
**Node.js / TypeScript** (optional): `npm i @llamaindex/liteparse@2.15.0` โ see `references/api_reference.md`.
---
from liteparse import LiteParse
parser = LiteParse(quiet=True)
result = parser.parse("paper.pdf")
print(result.text)
for page in result.pages:
print(f"Page {page.page_num}: {len(page.text_items)} items")# Layout-preserved text (default) lit parse paper.pdf # Structured JSON with bounding boxes lit parse paper.pdf --format json -o paper.json # Heuristic Markdown, including headings, tables and links lit parse paper.pdf --format markdown -o paper.md # Disable OCR on text-native PDFs (faster) lit parse paper.pdf --no-ocr
---
Best for quick full-document text or feeding chunkers that do not need coordinates.
parser = LiteParse(ocr_enabled=True, quiet=True)
result = parser.parse("document.pdf")
full_text = result.textlit parse document.pdf -o output.txt
Use when building layout-aware RAG, highlighting source regions, or joining text with screenshots.
from liteparse import LiteParse
parser = LiteParse(output_format="json", quiet=True)
result = parser.parse("document.pdf")
# Programmatic access
for page in result.pages:
for item in page.text_items:
bbox = (item.x, item.y, item.width, item.height)
# item.text, item.confidence, item.font_name, item.font_sizelit parse document.pdf --format json -o document.json
JSON field layout: `references/output_formats.md`.
parser = LiteParse(target_pages="1-5,10,15-20", quiet=True)
result = parser.parse("long_paper.pdf")lit parse long_paper.pdf --target-pages "1-5,10"
Useful for uploads, S3 downloads, or piping remote PDFs.
with open("document.pdf", "rb") as f:
result = parser.parse(f.read())curl -sL https://example.com/report.pdf | lit parse -
Screenshots capture visual content that text extraction alone misses (figures, complex tables, handwriting).
from pathlib import Path
parser = LiteParse(dpi=150, quiet=True)
shots = parser.screenshot("document.pdf", page_numbers=[1, 2, 3])
out = Path("screenshots")
out.mkdir(exist_ok=True)
for s in shots:
(out / f"page_{s.page_num}.png").write_bytes(s.image_bytes)lit screenshot document.pdf --target-pages "1,3,5" -o ./screenshots lit screenshot document.pdf --dpi 300 -o ./screenshots
Combine **JSON parse + screenshots** when an agent needs both coordinates and pixels for the same
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