academic-refchecker 2.0.18__tar.gz → 2.0.19__tar.gz

academic_refchecker-2.0.19/PKG-INFO

@@ -0,0 +1,366 @@
+Metadata-Version: 2.4
+Name: academic-refchecker
+Version: 2.0.19
+Summary: A comprehensive tool for validating reference accuracy in academic papers
+Author-email: Mark Russinovich <markrussinovich@hotmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/markrussinovich/refchecker
+Project-URL: Repository, https://github.com/markrussinovich/refchecker
+Project-URL: Bug Tracker, https://github.com/markrussinovich/refchecker/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests>=2.25.0
+Requires-Dist: beautifulsoup4>=4.9.0
+Requires-Dist: pypdf>=5.0.0
+Requires-Dist: arxiv>=1.4.0
+Requires-Dist: python-dateutil>=2.8.0
+Requires-Dist: tqdm>=4.60.0
+Requires-Dist: colorama>=0.4.4
+Requires-Dist: fuzzywuzzy>=0.18.0
+Requires-Dist: python-Levenshtein>=0.12.0
+Requires-Dist: pandas<2.4.0,>=1.3.0
+Requires-Dist: numpy<2.0.0,>=1.22.4
+Requires-Dist: pdfplumber>=0.6.0
+Requires-Dist: bibtexparser>=1.4.0
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=2.0.0; extra == "dev"
+Requires-Dist: black>=21.0.0; extra == "dev"
+Requires-Dist: isort>=5.0.0; extra == "dev"
+Requires-Dist: flake8>=3.9.0; extra == "dev"
+Requires-Dist: mypy>=0.910; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=4.0.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=0.5.0; extra == "docs"
+Provides-Extra: llm
+Requires-Dist: openai>=1.0.0; extra == "llm"
+Requires-Dist: anthropic>=0.7.0; extra == "llm"
+Requires-Dist: google-generativeai>=0.3.0; extra == "llm"
+Provides-Extra: optional
+Requires-Dist: lxml>=4.6.0; extra == "optional"
+Requires-Dist: selenium>=4.0.0; extra == "optional"
+Requires-Dist: pikepdf>=5.0.0; extra == "optional"
+Requires-Dist: nltk>=3.6.0; extra == "optional"
+Requires-Dist: scikit-learn>=1.0.0; extra == "optional"
+Requires-Dist: joblib>=1.1.0; extra == "optional"
+Provides-Extra: vllm
+Requires-Dist: vllm>=0.3.0; extra == "vllm"
+Requires-Dist: huggingface_hub>=0.17.0; extra == "vllm"
+Requires-Dist: torch>=2.0.0; extra == "vllm"
+Provides-Extra: webui
+Requires-Dist: fastapi>=0.100.0; extra == "webui"
+Requires-Dist: uvicorn[standard]>=0.22.0; extra == "webui"
+Requires-Dist: pydantic>=2.0.0; extra == "webui"
+Requires-Dist: aiosqlite>=0.19.0; extra == "webui"
+Requires-Dist: httpx>=0.24.0; extra == "webui"
+Requires-Dist: cryptography>=42.0.0; extra == "webui"
+Requires-Dist: pymupdf>=1.23.0; extra == "webui"
+Requires-Dist: Pillow>=9.0.0; extra == "webui"
+Requires-Dist: python-multipart>=0.0.6; extra == "webui"
+Dynamic: license-file
+
+# RefChecker
+
+Validate reference accuracy in academic papers. Useful for authors checking bibliographies and reviewers ensuring citations are authentic. RefChecker verifies citations against Semantic Scholar, OpenAlex, and CrossRef.
+
+*Built by Mark Russinovich with AI assistants (Cursor, GitHub Copilot, Claude Code). [Watch the deep dive video](https://www.youtube.com/watch?v=n929Alz-fjo).*
+
+## Contents
+
+- [Quick Start](#quick-start)
+- [Features](#features)
+- [Sample Output](#sample-output)
+- [Install](#install)
+- [Run](#run)
+- [Output](#output)
+- [Configure](#configure)
+- [Docker](#docker)
+- [Local Database](#local-database)
+- [Testing](#testing)
+- [License](#license)
+
+## Quick Start
+
+### Web UI (Docker)
+
+```bash
+docker run -p 8000:8000 ghcr.io/markrussinovich/refchecker:latest
+```
+
+Open **http://localhost:8000** in your browser.
+
+### Web UI (pip)
+
+```bash
+pip install academic-refchecker[llm,webui]
+refchecker-webui
+```
+
+### CLI (pip)
+
+```bash
+pip install academic-refchecker[llm]
+academic-refchecker --paper 1706.03762
+academic-refchecker --paper /path/to/paper.pdf
+```
+
+> **Performance**: Set `SEMANTIC_SCHOLAR_API_KEY` for 1-2s per reference vs 5-10s without.
+
+## Features
+
+- **Multiple formats**: ArXiv papers, PDFs, LaTeX, text files
+- **LLM-powered extraction**: OpenAI, Anthropic, Google, Azure, vLLM
+- **Multi-source verification**: Semantic Scholar, OpenAlex, CrossRef
+- **Comprehensive checks**: Titles, authors, years, venues, DOIs, ArXiv IDs
+- **Smart matching**: Handles formatting variations (BERT vs B-ERT, pre-trained vs pretrained)
+- **Detailed reports**: Errors, warnings, corrected references
+
+## Sample Output
+
+**Web UI**
+
+![RefChecker Web UI](assets/webui.png)
+
+**CLI**
+
+```
+📄 Processing: Attention Is All You Need
+   URL: https://arxiv.org/abs/1706.03762
+
+[1/45] Neural machine translation in linear time
+       Nal Kalchbrenner et al. | 2017
+       ⚠️  Warning: Year mismatch: cited '2017', actual '2016'
+
+[2/45] Effective approaches to attention-based neural machine translation
+       Minh-Thang Luong et al. | 2015
+       ❌ Error: First author mismatch: cited 'Minh-Thang Luong', actual 'Thang Luong'
+
+[3/45] Deep Residual Learning for Image Recognition
+       Kaiming He et al. | 2016 | https://doi.org/10.1109/CVPR.2016.91
+       ❌ Error: DOI mismatch: cited '10.1109/CVPR.2016.91', actual '10.1109/CVPR.2016.90'
+
+============================================================
+📋 SUMMARY
+📚 Total references processed: 68
+❌ Total errors: 55  ⚠️ Total warnings: 16  ❓ Unverified: 15
+```
+
+## Install
+
+### PyPI (Recommended)
+
+```bash
+pip install academic-refchecker[llm,webui]  # Web UI + CLI + LLM providers
+pip install academic-refchecker             # CLI only
+```
+
+### From Source (Development)
+
+```bash
+git clone https://github.com/markrussinovich/refchecker.git && cd refchecker
+python -m venv .venv && source .venv/bin/activate
+pip install -e ".[llm,webui]"
+```
+
+**Requirements:** Python 3.7+ (3.10+ recommended). Node.js 18+ is only needed for Web UI development.
+
+## Run
+
+### Web UI
+
+The Web UI shows live progress, history, and export (including corrected values).
+
+```bash
+refchecker-webui --port 8000
+```
+
+#### Development (frontend)
+
+```bash
+cd web-ui
+npm install
+npm start
+```
+
+Open **http://localhost:5173**.
+
+Alternative (separate servers):
+
+```bash
+# Terminal 1
+python -m uvicorn backend.main:app --reload --port 8000
+
+# Terminal 2
+cd web-ui
+npm run dev
+```
+
+Verify the backend is running:
+
+```bash
+curl http://localhost:8000/
+```
+
+Web UI documentation: see [web-ui/README.md](web-ui/README.md).
+
+### CLI
+
+```bash
+# ArXiv (ID or URL)
+academic-refchecker --paper 1706.03762
+academic-refchecker --paper https://arxiv.org/abs/1706.03762
+
+# Local files
+academic-refchecker --paper paper.pdf
+academic-refchecker --paper paper.tex
+academic-refchecker --paper paper.txt
+academic-refchecker --paper refs.bib
+
+# Faster/offline verification (local DB)
+academic-refchecker --paper paper.pdf --db-path semantic_scholar_db/semantic_scholar.db
+
+# Save results
+academic-refchecker --paper 1706.03762 --output-file errors.txt
+```
+
+## Output
+
+RefChecker reports these result types:
+
+| Type | Description | Examples |
+|------|-------------|----------|
+| ❌ **Error** | Critical issues needing correction | Author/title/DOI mismatches, incorrect ArXiv IDs |
+| ⚠️ **Warning** | Minor issues to review | Year differences, venue variations |
+| ℹ️ **Suggestion** | Recommended improvements | Add missing ArXiv/DOI URLs, small metadata fixes |
+| ❓ **Unverified** | Could not verify against any source | Rare publications, preprints |
+
+Verified references include discovered URLs (Semantic Scholar, ArXiv, DOI). Suggestions are non-blocking improvements.
+
+<details>
+<summary>Detailed examples</summary>
+
+```
+❌ Error: First author mismatch: cited 'T. Xie', actual 'Zhao Xu'
+❌ Error: DOI mismatch: cited '10.5555/3295222.3295349', actual '10.48550/arXiv.1706.03762'
+⚠️ Warning: Year mismatch: cited '2024', actual '2023'
+ℹ️ Suggestion: Add ArXiv URL https://arxiv.org/abs/1706.03762
+❓ Could not verify: Llama guard (M. A. Research, 2024)
+```
+
+</details>
+
+## Configure
+
+### LLM
+
+LLM-powered extraction improves accuracy with complex bibliographies. Claude Sonnet 4 performs best; GPT-4o may hallucinate DOIs.
+
+| Provider | Env Variable | Example Model |
+|----------|--------------|---------------|
+| Anthropic | `ANTHROPIC_API_KEY` | `claude-sonnet-4-20250514` |
+| OpenAI | `OPENAI_API_KEY` | `gpt-4o` |
+| Google | `GOOGLE_API_KEY` | `gemini-2.5-flash` |
+| Azure | `AZURE_OPENAI_API_KEY` | `gpt-4` |
+| vLLM | (local) | `meta-llama/Llama-3.1-8B-Instruct` |
+
+```bash
+export ANTHROPIC_API_KEY=your_key
+academic-refchecker --paper 1706.03762 --llm-provider anthropic
+
+academic-refchecker --paper paper.pdf --llm-provider openai --llm-model gpt-4o
+academic-refchecker --paper paper.pdf --llm-provider vllm --llm-model meta-llama/Llama-3.1-8B-Instruct
+```
+
+#### Local models (vLLM)
+
+There is no separate “GPU Docker image”. For local inference, install the vLLM extra and run an OpenAI-compatible vLLM server:
+
+```bash
+pip install "academic-refchecker[vllm]"
+python scripts/start_vllm_server.py --model meta-llama/Llama-3.1-8B-Instruct --port 8001
+academic-refchecker --paper paper.pdf --llm-provider vllm --llm-endpoint http://localhost:8001/v1
+```
+
+### Command Line
+
+```bash
+--paper PAPER              # ArXiv ID, URL, or file path
+--llm-provider PROVIDER    # openai, anthropic, google, azure, vllm
+--llm-model MODEL          # Override default model
+--db-path PATH             # Local database for offline verification
+--output-file [PATH]       # Save results (default: reference_errors.txt)
+--debug                    # Verbose output
+```
+
+### Environment Variables
+
+```bash
+# LLM
+export REFCHECKER_LLM_PROVIDER=anthropic
+export ANTHROPIC_API_KEY=your_key           # Also: OPENAI_API_KEY, GOOGLE_API_KEY
+
+# Performance
+export SEMANTIC_SCHOLAR_API_KEY=your_key    # Higher rate limits / faster verification
+```
+
+## Docker
+
+Pre-built images are published to GitHub Container Registry.
+
+```bash
+docker run -p 8000:8000 \
+       -e ANTHROPIC_API_KEY=your_key \
+       -v refchecker-data:/app/data \
+       ghcr.io/markrussinovich/refchecker:latest
+```
+
+Docker Compose:
+
+```bash
+git clone https://github.com/markrussinovich/refchecker.git && cd refchecker
+cp .env.example .env  # Add your API keys
+docker compose up -d
+```
+
+| Tag | Description | Arch | Size |
+|-----|-------------|------|------|
+| `latest` | RefChecker (Web UI + API-based LLM support) | amd64, arm64 | ~800MB |
+
+## Local Database
+
+For offline verification or faster processing:
+
+```bash
+python scripts/download_db.py \
+  --field "computer science" \
+  --start-year 2020 --end-year 2024
+
+academic-refchecker --paper paper.pdf --db-path semantic_scholar_db/semantic_scholar.db
+```
+
+## Testing
+
+490+ tests covering unit, integration, and end-to-end scenarios.
+
+```bash
+pytest tests/                    # All tests
+pytest tests/unit/              # Unit only
+pytest --cov=src tests/         # With coverage
+```
+
+See [tests/README.md](tests/README.md) for details.
+
+## License
+
+MIT License - see [LICENSE](LICENSE).

academic_refchecker-2.0.19/README.md

@@ -0,0 +1,294 @@
+# RefChecker
+
+Validate reference accuracy in academic papers. Useful for authors checking bibliographies and reviewers ensuring citations are authentic. RefChecker verifies citations against Semantic Scholar, OpenAlex, and CrossRef.
+
+*Built by Mark Russinovich with AI assistants (Cursor, GitHub Copilot, Claude Code). [Watch the deep dive video](https://www.youtube.com/watch?v=n929Alz-fjo).*
+
+## Contents
+
+- [Quick Start](#quick-start)
+- [Features](#features)
+- [Sample Output](#sample-output)
+- [Install](#install)
+- [Run](#run)
+- [Output](#output)
+- [Configure](#configure)
+- [Docker](#docker)
+- [Local Database](#local-database)
+- [Testing](#testing)
+- [License](#license)
+
+## Quick Start
+
+### Web UI (Docker)
+
+```bash
+docker run -p 8000:8000 ghcr.io/markrussinovich/refchecker:latest
+```
+
+Open **http://localhost:8000** in your browser.
+
+### Web UI (pip)
+
+```bash
+pip install academic-refchecker[llm,webui]
+refchecker-webui
+```
+
+### CLI (pip)
+
+```bash
+pip install academic-refchecker[llm]
+academic-refchecker --paper 1706.03762
+academic-refchecker --paper /path/to/paper.pdf
+```
+
+> **Performance**: Set `SEMANTIC_SCHOLAR_API_KEY` for 1-2s per reference vs 5-10s without.
+
+## Features
+
+- **Multiple formats**: ArXiv papers, PDFs, LaTeX, text files
+- **LLM-powered extraction**: OpenAI, Anthropic, Google, Azure, vLLM
+- **Multi-source verification**: Semantic Scholar, OpenAlex, CrossRef
+- **Comprehensive checks**: Titles, authors, years, venues, DOIs, ArXiv IDs
+- **Smart matching**: Handles formatting variations (BERT vs B-ERT, pre-trained vs pretrained)
+- **Detailed reports**: Errors, warnings, corrected references
+
+## Sample Output
+
+**Web UI**
+
+![RefChecker Web UI](assets/webui.png)
+
+**CLI**
+
+```
+📄 Processing: Attention Is All You Need
+   URL: https://arxiv.org/abs/1706.03762
+
+[1/45] Neural machine translation in linear time
+       Nal Kalchbrenner et al. | 2017
+       ⚠️  Warning: Year mismatch: cited '2017', actual '2016'
+
+[2/45] Effective approaches to attention-based neural machine translation
+       Minh-Thang Luong et al. | 2015
+       ❌ Error: First author mismatch: cited 'Minh-Thang Luong', actual 'Thang Luong'
+
+[3/45] Deep Residual Learning for Image Recognition
+       Kaiming He et al. | 2016 | https://doi.org/10.1109/CVPR.2016.91
+       ❌ Error: DOI mismatch: cited '10.1109/CVPR.2016.91', actual '10.1109/CVPR.2016.90'
+
+============================================================
+📋 SUMMARY
+📚 Total references processed: 68
+❌ Total errors: 55  ⚠️ Total warnings: 16  ❓ Unverified: 15
+```
+
+## Install
+
+### PyPI (Recommended)
+
+```bash
+pip install academic-refchecker[llm,webui]  # Web UI + CLI + LLM providers
+pip install academic-refchecker             # CLI only
+```
+
+### From Source (Development)
+
+```bash
+git clone https://github.com/markrussinovich/refchecker.git && cd refchecker
+python -m venv .venv && source .venv/bin/activate
+pip install -e ".[llm,webui]"
+```
+
+**Requirements:** Python 3.7+ (3.10+ recommended). Node.js 18+ is only needed for Web UI development.
+
+## Run
+
+### Web UI
+
+The Web UI shows live progress, history, and export (including corrected values).
+
+```bash
+refchecker-webui --port 8000
+```
+
+#### Development (frontend)
+
+```bash
+cd web-ui
+npm install
+npm start
+```
+
+Open **http://localhost:5173**.
+
+Alternative (separate servers):
+
+```bash
+# Terminal 1
+python -m uvicorn backend.main:app --reload --port 8000
+
+# Terminal 2
+cd web-ui
+npm run dev
+```
+
+Verify the backend is running:
+
+```bash
+curl http://localhost:8000/
+```
+
+Web UI documentation: see [web-ui/README.md](web-ui/README.md).
+
+### CLI
+
+```bash
+# ArXiv (ID or URL)
+academic-refchecker --paper 1706.03762
+academic-refchecker --paper https://arxiv.org/abs/1706.03762
+
+# Local files
+academic-refchecker --paper paper.pdf
+academic-refchecker --paper paper.tex
+academic-refchecker --paper paper.txt
+academic-refchecker --paper refs.bib
+
+# Faster/offline verification (local DB)
+academic-refchecker --paper paper.pdf --db-path semantic_scholar_db/semantic_scholar.db
+
+# Save results
+academic-refchecker --paper 1706.03762 --output-file errors.txt
+```
+
+## Output
+
+RefChecker reports these result types:
+
+| Type | Description | Examples |
+|------|-------------|----------|
+| ❌ **Error** | Critical issues needing correction | Author/title/DOI mismatches, incorrect ArXiv IDs |
+| ⚠️ **Warning** | Minor issues to review | Year differences, venue variations |
+| ℹ️ **Suggestion** | Recommended improvements | Add missing ArXiv/DOI URLs, small metadata fixes |
+| ❓ **Unverified** | Could not verify against any source | Rare publications, preprints |
+
+Verified references include discovered URLs (Semantic Scholar, ArXiv, DOI). Suggestions are non-blocking improvements.
+
+<details>
+<summary>Detailed examples</summary>
+
+```
+❌ Error: First author mismatch: cited 'T. Xie', actual 'Zhao Xu'
+❌ Error: DOI mismatch: cited '10.5555/3295222.3295349', actual '10.48550/arXiv.1706.03762'
+⚠️ Warning: Year mismatch: cited '2024', actual '2023'
+ℹ️ Suggestion: Add ArXiv URL https://arxiv.org/abs/1706.03762
+❓ Could not verify: Llama guard (M. A. Research, 2024)
+```
+
+</details>
+
+## Configure
+
+### LLM
+
+LLM-powered extraction improves accuracy with complex bibliographies. Claude Sonnet 4 performs best; GPT-4o may hallucinate DOIs.
+
+| Provider | Env Variable | Example Model |
+|----------|--------------|---------------|
+| Anthropic | `ANTHROPIC_API_KEY` | `claude-sonnet-4-20250514` |
+| OpenAI | `OPENAI_API_KEY` | `gpt-4o` |
+| Google | `GOOGLE_API_KEY` | `gemini-2.5-flash` |
+| Azure | `AZURE_OPENAI_API_KEY` | `gpt-4` |
+| vLLM | (local) | `meta-llama/Llama-3.1-8B-Instruct` |
+
+```bash
+export ANTHROPIC_API_KEY=your_key
+academic-refchecker --paper 1706.03762 --llm-provider anthropic
+
+academic-refchecker --paper paper.pdf --llm-provider openai --llm-model gpt-4o
+academic-refchecker --paper paper.pdf --llm-provider vllm --llm-model meta-llama/Llama-3.1-8B-Instruct
+```
+
+#### Local models (vLLM)
+
+There is no separate “GPU Docker image”. For local inference, install the vLLM extra and run an OpenAI-compatible vLLM server:
+
+```bash
+pip install "academic-refchecker[vllm]"
+python scripts/start_vllm_server.py --model meta-llama/Llama-3.1-8B-Instruct --port 8001
+academic-refchecker --paper paper.pdf --llm-provider vllm --llm-endpoint http://localhost:8001/v1
+```
+
+### Command Line
+
+```bash
+--paper PAPER              # ArXiv ID, URL, or file path
+--llm-provider PROVIDER    # openai, anthropic, google, azure, vllm
+--llm-model MODEL          # Override default model
+--db-path PATH             # Local database for offline verification
+--output-file [PATH]       # Save results (default: reference_errors.txt)
+--debug                    # Verbose output
+```
+
+### Environment Variables
+
+```bash
+# LLM
+export REFCHECKER_LLM_PROVIDER=anthropic
+export ANTHROPIC_API_KEY=your_key           # Also: OPENAI_API_KEY, GOOGLE_API_KEY
+
+# Performance
+export SEMANTIC_SCHOLAR_API_KEY=your_key    # Higher rate limits / faster verification
+```
+
+## Docker
+
+Pre-built images are published to GitHub Container Registry.
+
+```bash
+docker run -p 8000:8000 \
+       -e ANTHROPIC_API_KEY=your_key \
+       -v refchecker-data:/app/data \
+       ghcr.io/markrussinovich/refchecker:latest
+```
+
+Docker Compose:
+
+```bash
+git clone https://github.com/markrussinovich/refchecker.git && cd refchecker
+cp .env.example .env  # Add your API keys
+docker compose up -d
+```
+
+| Tag | Description | Arch | Size |
+|-----|-------------|------|------|
+| `latest` | RefChecker (Web UI + API-based LLM support) | amd64, arm64 | ~800MB |
+
+## Local Database
+
+For offline verification or faster processing:
+
+```bash
+python scripts/download_db.py \
+  --field "computer science" \
+  --start-year 2020 --end-year 2024
+
+academic-refchecker --paper paper.pdf --db-path semantic_scholar_db/semantic_scholar.db
+```
+
+## Testing
+
+490+ tests covering unit, integration, and end-to-end scenarios.
+
+```bash
+pytest tests/                    # All tests
+pytest tests/unit/              # Unit only
+pytest --cov=src tests/         # With coverage
+```
+
+See [tests/README.md](tests/README.md) for details.
+
+## License
+
+MIT License - see [LICENSE](LICENSE).