visual-parser 2.0.4__tar.gz → 2.2.0__tar.gz

visual_parser-2.2.0/LICENSE

@@ -0,0 +1,201 @@
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visual_parser-2.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: visual-parser
+Version: 2.2.0
+Summary: Standalone Visual-RAG PDF Parser - text extraction and Vision-LLM figure descriptions to JSONL
+Author: Zavier N. Ndum
+Author-email: zavier.ndum@tamu.edu
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/SmartLabNuclear/RADIANT_LLM
+Project-URL: Repository, https://github.com/SmartLabNuclear/RADIANT_LLM
+Project-URL: Docker Hub, https://hub.docker.com/r/zev94/radiant-llm
+Keywords: pdf,rag,nougat,vision-llm,ocr,document-parsing,jsonl,knowledge-base
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Text Processing :: Markup
+Classifier: Intended Audience :: Science/Research
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: PyMuPDF>=1.23.0
+Requires-Dist: Pillow>=10.0.0
+Requires-Dist: torch>=2.1.0
+Requires-Dist: transformers>=4.38.0
+Requires-Dist: huggingface-hub>=0.36.0
+Requires-Dist: langchain-community>=0.0.20
+Requires-Dist: langchain>=0.1.0
+Requires-Dist: langchain-text-splitters>=0.0.1
+Requires-Dist: openai>=1.14.0
+Requires-Dist: google-generativeai>=0.5.0
+Requires-Dist: requests>=2.31.0
+Requires-Dist: python-dotenv>=1.0.0
+Requires-Dist: tqdm>=4.66.0
+Requires-Dist: nltk>=3.8
+Requires-Dist: python-Levenshtein>=0.20
+Provides-Extra: ocr
+Requires-Dist: pytesseract>=0.3.10; extra == "ocr"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Dynamic: license-file
+
+# visual-parser (Standalone Visual-RAG PDF Ingestion)
+
+![Python 3.10+](https://img.shields.io/badge/Python-3.10%2B-brightgreen.svg)
+![PyTorch](https://img.shields.io/badge/PyTorch-2.1%2B-ee4c2c.svg)
+![LangChain](https://img.shields.io/badge/LangChain-0.1%2B-1C3C3C.svg)
+![CUDA](https://img.shields.io/badge/CUDA-optional-76B900.svg)
+
+`visual-parser` converts PDFs into a multi-modal JSONL knowledge base (text chunks, figure descriptions, metadata). It was extracted from [RADIANT-LLM](https://github.com/SmartLabNuclear/RADIANT_LLM) as a standalone PDF-ingestion tool, independent of any chatbot.
+
+1) Run `visual-parser` on curated PDFs to generate JSONL KB files.
+2) Point any downstream RAG system at the generated KB — RADIANT-LLM, AutoSAM, and AutoFLUKA all consume the identical JSONL/registry format, so the same KB works with any of them without re-parsing.
+
+## Table of Contents
+
+- [Outputs (JSONL KB)](#outputs-jsonl-kb)
+- [API Keys (.env)](#api-keys-env)
+- [Install and Run](#install-and-run)
+  - [Via pip](#via-pip)
+  - [Via Docker](#via-docker)
+  - [From source](#from-source)
+- [Common configuration flags](#common-configuration-flags)
+- [Local Ollama vision provider](#local-ollama-vision-provider)
+- [Citation](#citation)
+- [License](#license)
+
+## Outputs (JSONL KB)
+
+By default, the pipeline writes:
+- `01_chunks_kb.jsonl`: chunked text extracted from PDFs (Nougat by default).
+- `02_visuals_kb.jsonl`: figure/page visual descriptions (Vision LLM).
+- `03_metadata_kb.jsonl`: document metadata rows (title/author/etc.).
+
+Alongside the KB, the pipeline also writes two bookkeeping files: `04_processed_pdfs.txt` (tracks which PDFs have already been processed, so re-runs skip them unless `--rebuild`) and `05_pipeline.log` (run log at the verbosity set by `--log-level`, default `ERROR`).
+
+## API Keys (.env)
+
+Provide at least one provider:
+- `OPENAI_API_KEY` (OpenAI)
+- `GEMINI_API_KEY` (Gemini)
+
+Set these via a `.env` file (checked, in order: `~/.config/visual-parser/.env`, a `.env` in the current directory, `$VISUAL_PARSER_ENV_FILE` if set) or as regular OS environment variables (e.g. `setx` on Windows).
+
+Optional:
+- `HF_TOKEN` (for gated Hugging Face models)
+- `PORTKEY_API_KEY` + `PORTKEY_OPENAI_PROVIDER_SLUG` — routes OpenAI-family calls (vision LLM + `--list-models`) through a [Portkey](https://portkey.ai) gateway instead of OpenAI directly. Only takes effect when `OPENAI_API_KEY` is absent/empty; direct OpenAI wins when both are set. Set `VISUAL_PARSER_FORCE_PORTKEY=true` to force Portkey even when `OPENAI_API_KEY` is set at the OS/system level.
+
+## Install and Run
+
+Three ways to run `visual-parser`, in order of setup effort: [pip install](#via-pip), [Docker](#via-docker), or [from source](#from-source). All three share the identical CLI and flags — see [Common configuration flags](#common-configuration-flags).
+
+### Via pip
+
+```bash
+pip install visual-parser
+```
+
+Check the install:
+
+```bash
+visual-parser --version
+```
+
+Run against a folder of PDFs:
+
+```bash
+visual-parser --input-dir /path/to/pdfs --output-dir /path/to/pdfs
+```
+
+#### GPU acceleration
+
+`--text-mode nougat` (the default) uses a CUDA GPU automatically when one is available (`torch.cuda.is_available()`). A plain `pip install visual-parser` (or `pip install torch`) installs PyPI's default CPU-only torch wheel, even on a GPU machine. Install the matching CUDA build from PyTorch's index instead:
+
+```bash
+pip install torch --index-url https://download.pytorch.org/whl/cu130
+```
+
+Use `cu130` or newer, not `cu126` — `cu126` only covers compute capability up to `sm_90` (Hopper); on a newer GPU (e.g. Blackwell, `sm_120`), `torch.cuda.is_available()` still reports `True` but the first kernel launch fails. `cu130` covers Blackwell and every architecture `cu126` covered, and requires an r580+ NVIDIA driver. Pick the exact tag for your driver at [pytorch.org/get-started](https://pytorch.org/get-started/locally/) if `cu130` doesn't apply. Reinstalling `visual-parser` afterward does not downgrade this back to CPU. Verify with:
+
+```bash
+python -c "import torch; print(torch.cuda.is_available(), torch.cuda.get_device_name(0) if torch.cuda.is_available() else None)"
+```
+
+### Via Docker
+
+Prebuilt images are on **[zev94/radiant-llm](https://hub.docker.com/r/zev94/radiant-llm)** under the **visual-parser** tags:
+
+| Tag | Description |
+|-----|-------------|
+| `visual-parser-latest` | Always latest build (rolling) |
+| `visual-parser-2.1.0` | Pinned release |
+| `visual-parser-2.0` | Pinned release |
+| `visual-parser-1.0.2` | Legacy |
+| `visual-parser-1.0` | Legacy — v1.0.0, stale |
+
+#### Install Docker
+
+Docker Desktop (Windows/macOS) or Docker Engine (Linux).
+
+#### Pull the image
+
+```bash
+docker pull zev94/radiant-llm:visual-parser-latest
+```
+
+#### Run (input and output on the same mounted folder)
+
+Windows PowerShell:
+```powershell
+docker run --rm --env-file .env `
+  -v "C:\path\to\pdfs:/data" `
+  zev94/radiant-llm:visual-parser-latest `
+  --input-dir /data --output-dir /data
+```
+
+Linux / WSL:
+```bash
+docker run --rm --env-file .env \
+  -v "/path/to/pdfs:/data" \
+  zev94/radiant-llm:visual-parser-latest \
+  --input-dir /data --output-dir /data
+```
+
+#### Run (separate output directory)
+
+Windows PowerShell:
+```powershell
+docker run --rm --env-file .env `
+  -v "C:\path\to\pdfs:/data" `
+  -v "C:\path\to\out:/out" `
+  zev94/radiant-llm:visual-parser-latest `
+  --input-dir /data --output-dir /out
+```
+
+#### GPU acceleration
+
+Add `--gpus all` to any run command above to use an NVIDIA GPU instead of CPU for `--text-mode nougat` (the default). Works out of the box with Docker Desktop's WSL2 backend; no extra `nvidia-container-toolkit` install needed on most machines. Omit it (or run on a machine with no GPU) to fall back to CPU automatically.
+
+Requires an NVIDIA driver supporting CUDA 13.0+ (r580 or newer) on the host — check with `nvidia-smi`; update from [nvidia.com/Download](https://www.nvidia.com/Download/index.aspx) if it reports an older version. Without it, `torch.cuda.is_available()` still reports `True`, but the first Nougat inference call fails with `CUDA error: no kernel image is available`:
+
+```powershell
+docker run --rm --gpus all --env-file .env `
+  -v "C:\path\to\pdfs:/data" `
+  zev94/radiant-llm:visual-parser-latest `
+  --input-dir /data --output-dir /data
+```
+
+#### Troubleshooting: GPU not detected
+
+- Confirm the host sees the GPU at all: `nvidia-smi` (run from WSL if on Windows).
+- Confirm the driver supports CUDA 13.0+: check the `CUDA Version` line in that output — needs to read 13.0 or higher (roughly r580+). Update from [nvidia.com/Download](https://www.nvidia.com/Download/index.aspx) if it reads lower.
+- Confirm Docker can reach the GPU: `docker run --rm --gpus all nvidia/cuda:12.2.0-base-ubuntu22.04 nvidia-smi`.
+- If Docker Desktop's WSL2 backend still doesn't see the GPU after a driver update, restart the WSL VM: `wsl --shutdown`, then restart Docker Desktop.
+
+#### Offline install (legacy .tar)
+
+```powershell
+docker load -i .\visual-parser_2.1.0.tar
+docker images   # use the tag printed by Docker
+```
+
+#### Model overrides (optional)
+
+Default vision model is **GPT-5.4** when using `--vision-provider gpt`. Override on the command line (works identically via Docker or a plain CLI install):
+
+```powershell
+docker run --rm --env-file .env -v "C:\path\to\pdfs:/data" `
+  zev94/radiant-llm:visual-parser-latest `
+  --input-dir /data --output-dir /data --vision-model gpt-5.6
+```
+
+### From source
+
+Clone the repository and install dependencies directly, without packaging:
+
+```bash
+git clone https://github.com/SmartLabNuclear/RADIANT_LLM.git
+cd RADIANT_LLM/Visual-Parser
+pip install -r requirements.txt
+```
+
+Run the top-level script:
+
+```bash
+python visual-parser.py --input-dir ./my_pdfs
+```
+
+or as a module:
+
+```bash
+python -m visual_parser --input-dir ./my_pdfs
+```
+
+Both use the same CLI and flags as [Via pip](#via-pip). GPU acceleration follows the same rule: a plain `pip install -r requirements.txt` also resolves to the CPU-only torch wheel by default — see [GPU acceleration](#gpu-acceleration) under Via pip for the CUDA-build install command.
+
+## Common configuration flags
+
+Full flag list via `--help` — Docker:
+
+```bash
+docker run --rm zev94/radiant-llm:visual-parser-latest --help
+```
+
+or plain CLI:
+
+```bash
+visual-parser --help
+```
+
+For copy-paste Docker examples (vision presets, text modes, workers, rebuild), see [`docker-usage-examples.md`](docker-usage-examples.md).
+
+Paths:
+- `--input-dir` / `-i` (required unless `--list-models` is given)
+- `--output-dir` / `-o` (default: same as input)
+
+Text extraction:
+- `--text-mode nougat|lightweight` (default: `nougat`)
+- `--nougat-model facebook/nougat-small`
+- `--chunk-size 500`
+- `--chunk-overlap 100`
+
+Vision LLM:
+- `--vision-provider gpt|gemini|ollama` (default: `gpt`) — see [Local Ollama vision provider](#local-ollama-vision-provider) for the `ollama` option
+- `--vision-model gpt-5.6` (or `gpt-4o`, `gemini-2.5-flash`, etc. — run `--list-models` for what's actually live on your account; omit entirely for `ollama` to auto-select)
+- `--vision-detail low|high|auto` (default: `low`)
+- `--reasoning-effort minimal|none|low|medium|high|xhigh` (default: `medium`)
+- `--metadata-pages 2`
+- `--vision-context-pages 0` — include N adjacent pages (before and after) as context in each figure-description call, to help with figures/captions that span a page break. 0 (default) is today's single-page behavior; more context pages means more tokens per call
+
+Performance / misc:
+- `--max-workers 4`
+- `--rebuild` (reprocess everything; ignore `04_processed_pdfs.txt`)
+- `--skip-text` (skip text extraction and resume only the vision steps; use after an interrupted run)
+- `--list-models` — print the live, currently-available vision models for whichever provider(s) you have a key configured for, then exit (no PDF processing). Reflects Portkey's catalog too when that's active.
+- `--version` / `-V`
+- `--log-level DEBUG|INFO|WARNING|ERROR` (default: `ERROR`)
+
+## Local Ollama vision provider
+
+`--vision-provider ollama` runs figure description and metadata extraction against a locally-pulled model served by [Ollama](https://ollama.com), instead of a cloud API — no API key needed, no per-call cost.
+
+```bash
+visual-parser --input-dir /path/to/pdfs --vision-provider ollama
+```
+
+Omit `--vision-model` and the largest locally-pulled, vision-capable model that fits in currently-free GPU VRAM is auto-selected (logged to the console/`05_pipeline.log` as it's picked). To use a specific model instead, pass it explicitly:
+
+```bash
+visual-parser --input-dir /path/to/pdfs --vision-provider ollama --vision-model qwen2.5-vl:32b
+```
+
+Auto-selection:
+- Pull at least one vision-capable model first: `ollama pull llava` (or any other vision-capable tag).
+- Vision capability is detected via Ollama's reported model capabilities, falling back to a name heuristic (`llava`, `vision`, `-vl`, `pixtral`, `moondream`, `minicpm-v`, `bakllava`) on older Ollama versions that don't report it.
+- The selection budget is 85% of currently-free VRAM (not total VRAM) — this correctly leaves room for whatever else is already resident (e.g. Nougat's model during the same pipeline run) and for the model's own KV-cache/context overhead, which isn't included in its on-disk size.
+- If no CUDA GPU is visible to the process at all — including the case of running in a Docker container without `--gpus all` while Ollama runs on the host with a real GPU — CPU-only Ollama is treated as a legitimate setup: auto-selection falls back to the smallest pulled vision-capable model instead of refusing, printing a clear warning that it's running CPU-only and will be slow. Pass an explicit `--vision-model` to pick a different one.
+- If a real GPU *is* visible but no vision-capable model fits the free-VRAM budget, that case stays strict — auto-selection raises an error asking for an explicit `--vision-model`, rather than silently falling back to heavy CPU offload.
+
+Reachability: checks `OLLAMA_BASE_URL` (if set) → `http://localhost:11434` → `http://host.docker.internal:11434` (the containerized case). On Docker Desktop (Windows/macOS) the container reaches a host-installed Ollama automatically; on native Linux Docker Engine, add `--add-host=host.docker.internal:host-gateway` to the `docker run` command, or set `OLLAMA_BASE_URL` directly.
+
+---
+
+## Citation
+
+If you use RADIANT-LLM or the accompanying evaluation materials, please cite the journal article:
+
+```bibtex
+@article{ndum2026retrieval,
+  title={A retrieval-augmented, domain-intelligent agentic framework for reliable decision support in safety-critical nuclear engineering},
+  author={Ndum, Zavier Ndum and Tao, Jian and Ford, John and Yim, Mansung and Liu, Yang},
+  journal={Reliability Engineering \& System Safety},
+  pages={113057},
+  year={2026},
+  publisher={Elsevier}
+}
+```
+
+Journal: *Reliability Engineering & System Safety* (2026), article 113057
+Preprint: https://arxiv.org/abs/2604.22755
+
+---
+
+## License
+
+Copyright 2026 Zavier N. Ndum
+
+This project is licensed under the Apache License 2.0, the same license as its parent project, [RADIANT-LLM](https://github.com/SmartLabNuclear/RADIANT_LLM). See the [LICENSE](https://github.com/SmartLabNuclear/RADIANT_LLM/blob/main/LICENSE) file in the RADIANT_LLM repository, or the `LICENSE` file bundled with this package, for the full license text.