deepresearch-flow 0.2.1__py3-none-any.whl → 0.4.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- deepresearch_flow/cli.py +2 -0
- deepresearch_flow/paper/config.py +15 -0
- deepresearch_flow/paper/db.py +193 -0
- deepresearch_flow/paper/db_ops.py +1939 -0
- deepresearch_flow/paper/llm.py +2 -0
- deepresearch_flow/paper/web/app.py +46 -3320
- deepresearch_flow/paper/web/constants.py +23 -0
- deepresearch_flow/paper/web/filters.py +255 -0
- deepresearch_flow/paper/web/handlers/__init__.py +14 -0
- deepresearch_flow/paper/web/handlers/api.py +217 -0
- deepresearch_flow/paper/web/handlers/pages.py +334 -0
- deepresearch_flow/paper/web/markdown.py +549 -0
- deepresearch_flow/paper/web/static/css/main.css +857 -0
- deepresearch_flow/paper/web/static/js/detail.js +406 -0
- deepresearch_flow/paper/web/static/js/index.js +266 -0
- deepresearch_flow/paper/web/static/js/outline.js +58 -0
- deepresearch_flow/paper/web/static/js/stats.js +39 -0
- deepresearch_flow/paper/web/templates/base.html +43 -0
- deepresearch_flow/paper/web/templates/detail.html +332 -0
- deepresearch_flow/paper/web/templates/index.html +114 -0
- deepresearch_flow/paper/web/templates/stats.html +29 -0
- deepresearch_flow/paper/web/templates.py +85 -0
- deepresearch_flow/paper/web/text.py +68 -0
- deepresearch_flow/recognize/cli.py +157 -3
- deepresearch_flow/recognize/organize.py +58 -0
- deepresearch_flow/translator/__init__.py +1 -0
- deepresearch_flow/translator/cli.py +451 -0
- deepresearch_flow/translator/config.py +19 -0
- deepresearch_flow/translator/engine.py +959 -0
- deepresearch_flow/translator/fixers.py +451 -0
- deepresearch_flow/translator/placeholder.py +62 -0
- deepresearch_flow/translator/prompts.py +116 -0
- deepresearch_flow/translator/protector.py +291 -0
- deepresearch_flow/translator/segment.py +180 -0
- deepresearch_flow-0.4.0.dist-info/METADATA +327 -0
- {deepresearch_flow-0.2.1.dist-info → deepresearch_flow-0.4.0.dist-info}/RECORD +40 -13
- deepresearch_flow-0.2.1.dist-info/METADATA +0 -424
- {deepresearch_flow-0.2.1.dist-info → deepresearch_flow-0.4.0.dist-info}/WHEEL +0 -0
- {deepresearch_flow-0.2.1.dist-info → deepresearch_flow-0.4.0.dist-info}/entry_points.txt +0 -0
- {deepresearch_flow-0.2.1.dist-info → deepresearch_flow-0.4.0.dist-info}/licenses/LICENSE +0 -0
- {deepresearch_flow-0.2.1.dist-info → deepresearch_flow-0.4.0.dist-info}/top_level.txt +0 -0
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Metadata-Version: 2.4
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Name: deepresearch-flow
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Version: 0.4.0
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Summary: Workflow tools for paper extraction, review, and research automation.
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Author-email: DengQi <dengqi935@gmail.com>
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License: MIT License
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Copyright (c) 2025 DengQi
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Project-URL: Homepage, https://github.com/nerdneilsfield/ai-deepresearch-flow
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Project-URL: Repository, https://github.com/nerdneilsfield/ai-deepresearch-flow
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Project-URL: Issues, https://github.com/nerdneilsfield/ai-deepresearch-flow/issues
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Keywords: research,papers,pdf,ocr,llm,workflow
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Classifier: Development Status :: 3 - Alpha
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Classifier: Intended Audience :: Science/Research
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3 :: Only
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Classifier: Topic :: Scientific/Engineering :: Information Analysis
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Requires-Python: >=3.12
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: anthropic>=0.28.0
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Requires-Dist: click>=8.1.7
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Requires-Dist: coloredlogs>=15.0.1
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Requires-Dist: dashscope>=1.20.0
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Requires-Dist: google-auth>=2.0.0
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Requires-Dist: google-genai>=0.5.0
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Requires-Dist: httpx>=0.27.0
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Requires-Dist: jinja2>=3.1.3
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Requires-Dist: json-repair>=0.31.0
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Requires-Dist: jsonschema>=4.21.1
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Requires-Dist: markdown-it-py>=3.0.0
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Requires-Dist: mdit-py-plugins>=0.4.0
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Requires-Dist: pypdf>=3.0.0
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Requires-Dist: pybtex>=0.24.0
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Requires-Dist: rich>=13.7.1
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Requires-Dist: rumdl>=0.0.214
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Requires-Dist: starlette>=0.37.2
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Requires-Dist: tqdm>=4.66.4
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Requires-Dist: uvicorn>=0.27.1
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Dynamic: license-file
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<p align="center">
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<img src=".github/assets/logo.png" width="140" alt="ai-deepresearch-flow logo" />
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</p>
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<h3 align="center">ai-deepresearch-flow</h3>
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<p align="center">
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<em>From documents to deep research insight — automatically.</em>
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</p>
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<p align="center">
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<a href="README.md">English</a> | <a href="README_ZH.md">中文</a>
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</p>
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<p align="center">
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<a href="https://github.com/nerdneilsfield/ai-deepresearch-flow/actions">
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<img src="https://img.shields.io/github/actions/workflow/status/nerdneilsfield/ai-deepresearch-flow/push-to-pypi.yml?style=flat-square" />
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</a>
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<a href="https://pypi.org/project/deepresearch-flow/">
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<img src="https://img.shields.io/pypi/v/deepresearch-flow?style=flat-square" />
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</a>
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<a href="https://pypi.org/project/deepresearch-flow/">
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<img src="https://img.shields.io/pypi/pyversions/deepresearch-flow?style=flat-square" />
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</a>
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<a href="https://hub.docker.com/r/nerdneils/deepresearch-flow">
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<img src="https://img.shields.io/docker/v/nerdneils/deepresearch-flow?style=flat-square" />
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</a>
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<a href="https://ghcr.io/nerdneilsfield/deepresearch-flow">
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<img src="https://img.shields.io/badge/ghcr.io-nerdneilsfield%2Fdeepresearch-flow-0f172a?style=flat-square" />
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</a>
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<a href="https://github.com/nerdneilsfield/ai-deepresearch-flow/blob/main/LICENSE">
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<img src="https://img.shields.io/github/license/nerdneilsfield/ai-deepresearch-flow?style=flat-square" />
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</a>
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<a href="https://github.com/nerdneilsfield/ai-deepresearch-flow/stargazers">
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<img src="https://img.shields.io/github/stars/nerdneilsfield/ai-deepresearch-flow?style=flat-square" />
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</a>
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<a href="https://pypi.org/project/deepresearch-flow">
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<img alt="PyPI - Version" src="https://img.shields.io/pypi/v/deepresearch-flow">
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</a>
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<a href="https://github.com/nerdneilsfield/ai-deepresearch-flow/issues">
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<img src="https://img.shields.io/github/issues/nerdneilsfield/ai-deepresearch-flow?style=flat-square" />
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</a>
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</p>
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---
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## The Core Pain Points
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- **OCR Chaos**: Raw markdown from OCR tools is often broken -- tables drift, formulas break, and references are non-clickable.
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- **Translation Nightmares**: Translating technical papers often destroys code blocks, LaTeX formulas, and table structures.
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- **Information Overload**: Extracting structured insights (authors, venues, summaries) from hundreds of PDFs manually is impossible.
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- **Context Switching**: Managing PDFs, summaries, and translations in different windows kills focus.
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## The Solution
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DeepResearch Flow provides a unified pipeline to **Repair**, **Translate**, **Extract**, and **Serve** your research library.
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## Key Features
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- **Smart Extraction**: Turn unstructured Markdown into schema-enforced JSON (summaries, metadata, Q&A) using LLMs (OpenAI, Claude, Gemini, etc.).
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- **Precision Translation**: Translate OCR Markdown to Chinese/Japanese (`.zh.md`, `.ja.md`) while **freezing** formulas, code, tables, and references. No more broken layout.
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- **Local Knowledge DB**: A high-performance local Web UI to browse papers with **Split View** (Source vs. Translated vs. Summary), full-text search, and multi-dimensional filtering.
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- **Coverage Compare**: Compare JSON/PDF/Markdown/Translated datasets to find missing artifacts and export CSV reports.
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- **OCR Post-Processing**: Automatically fix broken references (`[1]` -> `[^1]`), merge split paragraphs, and standardize layouts.
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---
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## Quick Start
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### 1) Installation
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```bash
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# Recommended: using uv for speed
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uv pip install deepresearch-flow
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# Or standard pip
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pip install deepresearch-flow
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```
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### 2) Configuration
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Set up your LLM providers. We support OpenAI, Claude, Gemini, Ollama, and more.
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```bash
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cp config.example.toml config.toml
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# Edit config.toml to add your API keys (e.g., env:OPENAI_API_KEY)
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```
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### 3) The "Zero to Hero" Workflow
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#### Step 1: Extract Insights
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Scan a folder of markdown files and extract structured summaries.
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```bash
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uv run deepresearch-flow paper extract \
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--input ./docs \
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--model openai/gpt-4o-mini \
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--prompt-template deep_read
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```
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#### Step 2: Translate Safely
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Translate papers to Chinese, protecting LaTeX and tables.
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```bash
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uv run deepresearch-flow translator translate \
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--input ./docs \
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--target-lang zh \
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--model openai/gpt-4o-mini \
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--fix-level moderate
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```
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#### Step 3: Serve Your Database
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Launch a local UI to read and manage your papers.
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```bash
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uv run deepresearch-flow paper db serve \
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--input paper_infos.json \
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--md-root ./docs \
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--md-translated-root ./docs \
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--host 127.0.0.1
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```
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---
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## Comprehensive Guide
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<details>
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<summary><strong>1. Translator: OCR-Safe Translation</strong></summary>
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The translator module is built for scientific documents. It uses a node-based architecture to ensure stability.
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- Structure Protection: automatically detects and "freezes" code blocks, LaTeX (`$$...$$`), HTML tables, and images before sending text to the LLM.
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- OCR Repair: use `--fix-level` to merge broken paragraphs and convert text references (`[1]`) to clickable Markdown footnotes (`[^1]`).
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- Context-Aware: supports retries for failed chunks and falls back gracefully.
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```bash
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# Translate with structure protection and OCR repairs
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uv run deepresearch-flow translator translate \
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--input ./paper.md \
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--target-lang ja \
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--fix-level aggressive \
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--model claude/claude-3-5-sonnet-20240620
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```
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</details>
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<details>
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<summary><strong>2. Paper Extract: Structured Knowledge</strong></summary>
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Turn loose markdown files into a queryable database.
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- Templates: built-in prompts like `simple`, `eight_questions`, and `deep_read` guide the LLM to extract specific insights.
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- Async and throttled: precise control over concurrency (`--max-concurrency`) and rate limits (`--sleep-every`).
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- Incremental: skips already processed files; resumes from where you left off.
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```bash
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uv run deepresearch-flow paper extract \
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--input ./library \
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--output paper_data.json \
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--template-dir ./my-custom-prompts \
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--max-concurrency 10
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```
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</details>
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<details>
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<summary><strong>3. Database and UI: Your Personal ArXiv</strong></summary>
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The db serve command creates a local research station.
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- Split View: read the original PDF/Markdown on the left and the Summary/Translation on the right.
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- Full Text Search: search by title, author, year, or content tags (`tag:fpga year:2023..2024`).
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- Stats: visualize publication trends and keyword frequencies.
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- PDF Viewer: built-in PDF.js viewer prevents cross-origin issues with local files.
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```bash
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uv run deepresearch-flow paper db serve \
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--input paper_infos.json \
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--pdf-root ./pdfs \
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--cache-dir .cache/db
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```
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</details>
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<details>
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<summary><strong>4. Paper DB Compare: Coverage Audit</strong></summary>
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Compare two datasets (A/B) to find missing PDFs, markdowns, translations, or JSON items, with match metadata.
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```bash
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uv run deepresearch-flow paper db compare \
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--input-a ./a.json \
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--md-root-b ./md_root \
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--output-csv ./compare.csv
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# Compare translated markdowns by language
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uv run deepresearch-flow paper db compare \
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--md-translated-root-a ./translated_a \
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--md-translated-root-b ./translated_b \
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--lang zh
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```
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</details>
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<details>
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<summary><strong>5. Recognize: OCR Post-Processing</strong></summary>
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Tools to clean up raw outputs from OCR engines like MinerU.
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```bash
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--input ./mineru_outputs \
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--fix
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# Fix and format existing markdown outputs
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--input ./ocr_md \
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--output ./ocr_md_fixed
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# Fix in place
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--in-place
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</details>
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---
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## Docker Support
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Don't want to manage Python environments?
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```bash
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```
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## Configuration
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The config.toml is your control center. It supports:
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- Multiple Providers: mix and match OpenAI, DeepSeek (DashScope), Gemini, Claude, and Ollama.
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- Environment Variables: keep secrets safe using `env:VAR_NAME` syntax.
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See `config.example.toml` for a full reference.
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---
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<p align="center">
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Built with love for the Open Science community.
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</p>
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