deepresearch-flow 0.2.1__py3-none-any.whl → 0.4.0__py3-none-any.whl

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Files changed (41) hide show
  1. deepresearch_flow/cli.py +2 -0
  2. deepresearch_flow/paper/config.py +15 -0
  3. deepresearch_flow/paper/db.py +193 -0
  4. deepresearch_flow/paper/db_ops.py +1939 -0
  5. deepresearch_flow/paper/llm.py +2 -0
  6. deepresearch_flow/paper/web/app.py +46 -3320
  7. deepresearch_flow/paper/web/constants.py +23 -0
  8. deepresearch_flow/paper/web/filters.py +255 -0
  9. deepresearch_flow/paper/web/handlers/__init__.py +14 -0
  10. deepresearch_flow/paper/web/handlers/api.py +217 -0
  11. deepresearch_flow/paper/web/handlers/pages.py +334 -0
  12. deepresearch_flow/paper/web/markdown.py +549 -0
  13. deepresearch_flow/paper/web/static/css/main.css +857 -0
  14. deepresearch_flow/paper/web/static/js/detail.js +406 -0
  15. deepresearch_flow/paper/web/static/js/index.js +266 -0
  16. deepresearch_flow/paper/web/static/js/outline.js +58 -0
  17. deepresearch_flow/paper/web/static/js/stats.js +39 -0
  18. deepresearch_flow/paper/web/templates/base.html +43 -0
  19. deepresearch_flow/paper/web/templates/detail.html +332 -0
  20. deepresearch_flow/paper/web/templates/index.html +114 -0
  21. deepresearch_flow/paper/web/templates/stats.html +29 -0
  22. deepresearch_flow/paper/web/templates.py +85 -0
  23. deepresearch_flow/paper/web/text.py +68 -0
  24. deepresearch_flow/recognize/cli.py +157 -3
  25. deepresearch_flow/recognize/organize.py +58 -0
  26. deepresearch_flow/translator/__init__.py +1 -0
  27. deepresearch_flow/translator/cli.py +451 -0
  28. deepresearch_flow/translator/config.py +19 -0
  29. deepresearch_flow/translator/engine.py +959 -0
  30. deepresearch_flow/translator/fixers.py +451 -0
  31. deepresearch_flow/translator/placeholder.py +62 -0
  32. deepresearch_flow/translator/prompts.py +116 -0
  33. deepresearch_flow/translator/protector.py +291 -0
  34. deepresearch_flow/translator/segment.py +180 -0
  35. deepresearch_flow-0.4.0.dist-info/METADATA +327 -0
  36. {deepresearch_flow-0.2.1.dist-info → deepresearch_flow-0.4.0.dist-info}/RECORD +40 -13
  37. deepresearch_flow-0.2.1.dist-info/METADATA +0 -424
  38. {deepresearch_flow-0.2.1.dist-info → deepresearch_flow-0.4.0.dist-info}/WHEEL +0 -0
  39. {deepresearch_flow-0.2.1.dist-info → deepresearch_flow-0.4.0.dist-info}/entry_points.txt +0 -0
  40. {deepresearch_flow-0.2.1.dist-info → deepresearch_flow-0.4.0.dist-info}/licenses/LICENSE +0 -0
  41. {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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+
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+ Copyright (c) 2025 DengQi
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+
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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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+
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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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+
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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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+
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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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+
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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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+
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+ <h3 align="center">ai-deepresearch-flow</h3>
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+
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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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+
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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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+
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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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+ ---
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+
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+ ## The Core Pain Points
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+
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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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+
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+ ## The Solution
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+
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+ DeepResearch Flow provides a unified pipeline to **Repair**, **Translate**, **Extract**, and **Serve** your research library.
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+
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+ ## Key Features
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+
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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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+ ---
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+
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+ ## Quick Start
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+
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+ ### 1) Installation
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+
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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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+
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+ # Or standard pip
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+ pip install deepresearch-flow
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+ ```
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+
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+ ### 2) Configuration
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+
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+ Set up your LLM providers. We support OpenAI, Claude, Gemini, Ollama, and more.
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+
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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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+
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+ ### 3) The "Zero to Hero" Workflow
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+
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+ #### Step 1: Extract Insights
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+
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+ Scan a folder of markdown files and extract structured summaries.
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+
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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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+
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+ #### Step 2: Translate Safely
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+
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+ Translate papers to Chinese, protecting LaTeX and tables.
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+
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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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+
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+ #### Step 3: Serve Your Database
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+
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+ Launch a local UI to read and manage your papers.
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+
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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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+ ---
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+
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+ ## Comprehensive Guide
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+
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+ <details>
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+ <summary><strong>1. Translator: OCR-Safe Translation</strong></summary>
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+
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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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+
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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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+
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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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+
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+ </details>
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+
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+ <details>
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+ <summary><strong>2. Paper Extract: Structured Knowledge</strong></summary>
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+
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+ Turn loose markdown files into a queryable database.
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+
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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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+
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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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+
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+ </details>
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+
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+ <details>
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+ <summary><strong>3. Database and UI: Your Personal ArXiv</strong></summary>
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+
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+ The db serve command creates a local research station.
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+
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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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+
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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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+
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+ </details>
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+
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+ <details>
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+ <summary><strong>4. Paper DB Compare: Coverage Audit</strong></summary>
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+
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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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+
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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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+
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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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+
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+ </details>
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+
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+ <details>
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+ <summary><strong>5. Recognize: OCR Post-Processing</strong></summary>
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+
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+ Tools to clean up raw outputs from OCR engines like MinerU.
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+
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+ - Embed Images: convert local image links to Base64 for a portable single-file Markdown.
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+ - Unpack Images: extract Base64 images back to files.
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+ - Organize: flatten nested OCR output directories.
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+ - Fix: apply OCR fixes and rumdl formatting during organize, or as a standalone step.
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+
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+ ```bash
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+ uv run deepresearch-flow recognize md embed --input ./raw_ocr --output ./clean_md
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+ ```
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+
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+ ```bash
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+ # Organize MinerU output and apply OCR fixes
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+ uv run deepresearch-flow recognize organize \
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+ --input ./mineru_outputs \
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+ --output-simple ./ocr_md \
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+ --fix
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+
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+ # Fix and format existing markdown outputs
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+ uv run deepresearch-flow recognize fix \
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+ --input ./ocr_md \
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+ --output ./ocr_md_fixed
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+
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+ # Fix in place
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+ uv run deepresearch-flow recognize fix \
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+ --input ./ocr_md \
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+ --in-place
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+ ```
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+
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+ </details>
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+
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+ ---
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+
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+ ## Docker Support
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+
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+ Don't want to manage Python environments?
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+
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+ ```bash
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+ docker run --rm -v $(pwd):/app -it ghcr.io/nerdneilsfield/deepresearch-flow --help
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+ ```
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+
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+ ## Configuration
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+
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+ The config.toml is your control center. It supports:
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+
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+ - Multiple Providers: mix and match OpenAI, DeepSeek (DashScope), Gemini, Claude, and Ollama.
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+ - Model Routing: explicit routing to specific models (`--model provider/model_name`).
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+ - Environment Variables: keep secrets safe using `env:VAR_NAME` syntax.
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+
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+ See `config.example.toml` for a full reference.
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+
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+ ---
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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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- deepresearch_flow/paper/llm.py,sha256=R4rmFoYnGq_JiQODr4Jzk5j8U-j2NSYUXex6eR-WHXg,3929
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  deepresearch_flow/paper/web/pdfjs/build/pdf.js.map,sha256=W0nwVFY4inhYxz1raDU6NZ6-rNA21FxLj13txVAqbm4,1434098
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