bibguard 0.2.0__tar.gz

bibguard-0.2.0/.claude/commands/bibguard.md

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+Run the bibguard citation verification tool on a .bib file.
+
+Usage: /bibguard <bib-file> [--tex <tex-file>] [--fix]
+
+Instructions:
+1. Parse the user's arguments. The first argument is the .bib file path. Optional: --tex for cross-audit, --fix to generate auto-corrected .bib.
+2. Run the verification:
+   ```
+   bibguard <bib-file> [--tex <tex-file>] [--out /tmp/refcheck_report.md] [--fix /tmp/refcheck_fixed.bib]
+   ```
+   If `bibguard` is not on PATH, use: `python -m bibguard.cli <bib-file> ...`
+3. Read the output report and present results to the user.
+4. For any WARN or FAIL entries:
+   - Summarize what went wrong (phantom DOI, author mismatch, not found, etc.)
+   - For phantom_doi / phantom_arxiv FAILs: these are likely hallucinated references. Search the web to find the correct reference or confirm it doesn't exist.
+   - For other WARNs: check if the reference needs correction (wrong year, venue mismatch, etc.)
+5. If --fix was used, show the auto-fix diff.
+
+$ARGUMENTS

bibguard-0.2.0/.codex/skills/bibguard/SKILL.md

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+---
+name: bibguard
+description: Run citation verification on a .bib file. Detects hallucinated references, phantom DOIs, author mismatches, and retracted papers. Use when user asks to check, verify, or validate references/citations in a paper.
+---
+
+# bibguard: Citation Verification
+
+Run the bibguard tool to verify references in a .bib file.
+
+## Usage
+
+```
+bibguard <bib-file> [--tex <tex-file>] [--out report.md] [--fix fixed.bib] [--json]
+```
+
+If `bibguard` is not on PATH, use: `pip install bibguard && bibguard <bib-file>`
+
+## Instructions
+
+1. Parse the user's request. Identify the .bib file path and any optional flags.
+2. Run verification: `bibguard <bib-file> --out /tmp/refcheck_report.md`
+3. Read the output report and present results.
+4. For FAIL entries:
+   - **phantom_doi / phantom_arxiv**: The identifier has valid format but doesn't resolve. This is the strongest hallucination signal. Search the web to find the correct reference.
+   - **verification (NO API MATCH)**: Not found in any database. May be hallucinated or have a very different title.
+   - **retraction**: Paper has been retracted.
+5. For WARN entries: Check if venue/year/author mismatches need correction.
+6. If `--fix` was used, show what was auto-corrected.
+
+## Arguments
+
+$ARGUMENTS

bibguard-0.2.0/.cursor/rules/bibguard.md

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+---
+description: Citation verification for academic papers using bibguard
+globs: ["*.bib", "*.tex"]
+---
+
+# bibguard Integration
+
+When the user asks to verify, check, or validate references in a .bib file, use the `bibguard` CLI tool.
+
+## Setup
+
+```bash
+pip install bibguard
+```
+
+## Commands
+
+```bash
+# Basic verification
+bibguard references.bib
+
+# With TeX cross-audit
+bibguard references.bib --tex main.tex
+
+# Save report + auto-fix
+bibguard references.bib --out report.md --fix fixed.bib
+
+# JSON output for programmatic use
+bibguard references.bib --json --out report.json
+```
+
+## Interpreting Results
+
+- **FAIL (phantom_doi/phantom_arxiv)**: Identifier looks valid but doesn't resolve. Strongest hallucination signal. Search the web to find the correct reference or confirm it's fabricated.
+- **FAIL (NO API MATCH)**: Not found in any of 5 databases. Likely hallucinated or title differs significantly.
+- **FAIL (retraction)**: Paper has been retracted.
+- **WARN**: Metadata mismatch (venue, year, author count). Usually needs human review.
+- **OK**: Verified against at least one source.
+
+Exit code 1 means at least one FAIL was found.

bibguard-0.2.0/.gitignore

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+__pycache__/
+*.pyc
+*.pyo
+*.egg-info/
+dist/
+build/
+.venv/
+.env
+*.egg
+.pytest_cache/
+.coverage
+htmlcov/
+.mypy_cache/

bibguard-0.2.0/CHANGELOG.md

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+# Changelog
+
+## [0.2.0] - 2026-03-24
+
+### Changed
+- Renamed from `ref-check` to `bibguard` (PyPI name conflict)
+- Upgraded to Apache 2.0 license
+- Improved CLI output: emoji status, timing, fail summary
+- Improved Markdown report: grouped by severity, compact OK entries
+- Modular package structure (sources/, parsers/)
+
+### Added
+- 58-case golden benchmark (`tests/bench_golden.py`)
+- GitHub Pages landing page
+- AI assistant skills: Claude Code, OpenAI Codex, Cursor
+- CONTRIBUTORS.md with detailed attribution
+- CHANGELOG.md
+- `py.typed` marker (PEP 561)
+- `--json` output mode for CI pipelines
+- Bilingual README (English + Chinese)
+
+### Benchmark
+- Hallucination recall: 100% (14/14)
+- Chimera detection: 100% (5/5)
+- Runtime: 95s for 58 entries
+
+## [0.1.0] - 2026-03-24
+
+Initial release (as `ref-check`, not published to PyPI).
+
+- 5-source cascade: arXiv, Crossref, DBLP, Semantic Scholar, OpenAlex
+- Phantom DOI/arXiv detection with kill-shot logic
+- TeX cross-audit, duplicate detection, auto-fix
+- CLI and Python API

bibguard-0.2.0/CONTRIBUTORS.md

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+# Contributors
+
+## Geoffrey Wang ([@GeoffreyWang1117](https://github.com/GeoffreyWang1117))
+- Project creator and lead developer
+- System architecture: 5-source cascade verification design
+- Core algorithms: phantom-ID detection, kill-shot logic, author-guard search
+- Early implementation: BibTeX parsing, API query modules, field matching heuristics
+- Benchmark design: golden test set curation (58 cases across 4 categories)
+- Extracted from [IntegriRef](https://github.com/GeoffreyWang1117/IntegriRef) L0 layer
+
+## Claude (Anthropic)
+- Code optimization: modular refactoring from single-file to package structure
+- Output formatting: CLI progress display, Markdown report generation
+- Packaging: pyproject.toml, cross-platform skill definitions
+- Documentation: README, benchmark analysis, contributor attribution
+- Model: Claude Opus 4.6 (1M context)

bibguard-0.2.0/LICENSE

@@ -0,0 +1,191 @@
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+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
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+      has been advised of the possibility of such damages.
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+   9. Accepting Warranty or Additional Liability. While redistributing
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bibguard-0.2.0/PKG-INFO

@@ -0,0 +1,302 @@
+Metadata-Version: 2.4
+Name: bibguard
+Version: 0.2.0
+Summary: Detect hallucinated and broken citations in academic papers
+Project-URL: Homepage, https://geoffreywang1117.github.io/bibguard/
+Project-URL: Repository, https://github.com/GeoffreyWang1117/bibguard
+Project-URL: Issues, https://github.com/GeoffreyWang1117/bibguard/issues
+Project-URL: Changelog, https://github.com/GeoffreyWang1117/bibguard/blob/main/CHANGELOG.md
+Author-email: Geoffrey Wang <geoffreywang1117@gmail.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: academic,bibguard,bibtex,citation,hallucination,integrity,latex,reference,scholarly,verification
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Text Processing :: Markup :: LaTeX
+Classifier: Typing :: Typed
+Requires-Python: >=3.9
+Requires-Dist: bibtexparser<2,>=1.4
+Requires-Dist: requests>=2.28
+Provides-Extra: all
+Requires-Dist: pymupdf>=1.23; extra == 'all'
+Requires-Dist: rapidfuzz>=3.0; extra == 'all'
+Provides-Extra: dev
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: pytest>=7.0; extra == 'dev'
+Provides-Extra: fast
+Requires-Dist: rapidfuzz>=3.0; extra == 'fast'
+Provides-Extra: pdf
+Requires-Dist: pymupdf>=1.23; extra == 'pdf'
+Description-Content-Type: text/markdown
+
+# bibguard
+
+[![PyPI version](https://img.shields.io/pypi/v/bibguard)](https://pypi.org/project/bibguard/)
+[![Python](https://img.shields.io/pypi/pyversions/bibguard)](https://pypi.org/project/bibguard/)
+[![License](https://img.shields.io/badge/license-Apache%202.0-blue)](LICENSE)
+[![Tests](https://img.shields.io/badge/tests-58%20cases-green)]()
+
+**Detect hallucinated and broken citations in academic papers.**
+
+One command to verify every reference in your `.bib` file against five scholarly databases. Catches phantom DOIs, fabricated arXiv IDs, author mismatches, retracted papers, and AI-hallucinated citations.
+
+```bash
+pip install bibguard
+bibguard paper.bib
+```
+
+[Landing Page](https://geoffreywang1117.github.io/bibguard/) | [PyPI](https://pypi.org/project/bibguard/) | [Changelog](CHANGELOG.md)
+
+---
+
+## Why
+
+Large language models hallucinate citations. Copy-paste errors corrupt metadata. Retracted papers slip through review. `bibguard` catches these problems **before** submission.
+
+- **5 sources**: arXiv, Crossref, DBLP, Semantic Scholar, OpenAlex
+- **Phantom ID detection**: Valid-format DOI/arXiv that doesn't resolve = hallucination signal
+- **Kill-shot logic**: A phantom ID cannot be overridden by a similar search result
+- **TeX cross-audit**: Find `\cite{key}` with no `.bib` entry, and orphan entries never cited
+- **Duplicate detection**: Flag near-identical entries with different keys
+- **Auto-fix**: Generate a corrected `.bib` with missing DOIs and eprint IDs filled in
+- **Zero heavy dependencies**: Core requires only `requests` + `bibtexparser`
+
+## Install
+
+```bash
+pip install bibguard            # minimal
+pip install bibguard[fast]      # + RapidFuzz for better title matching
+pip install bibguard[all]       # + RapidFuzz + PyMuPDF for PDF parsing
+```
+
+Requires Python 3.9+.
+
+## Usage
+
+### CLI
+
+```bash
+# Basic: verify all entries in a .bib file
+bibguard references.bib
+
+# With TeX cross-audit (finds phantom \cite and orphan entries)
+bibguard references.bib --tex main.tex
+
+# Save report + auto-fix
+bibguard references.bib --tex main.tex --out report.md --fix fixed.bib
+
+# JSON output (for CI pipelines)
+bibguard references.bib --json --out report.json
+```
+
+### Python API
+
+```python
+from bibguard import verify_bib, verify_entry
+
+# Verify entire .bib file
+results, report = verify_bib("references.bib", tex_path="main.tex")
+for r in results:
+    if r.overall != "OK":
+        print(f"{r.overall}: {r.key} -- {r.title}")
+
+# Verify a single entry
+from bibguard.parsers.bibtex import parse_bib
+entries = parse_bib("references.bib")
+result = verify_entry(entries[0])
+print(result.overall, result.checks)
+```
+
+### Exit codes
+
+| Code | Meaning |
+|------|---------|
+| 0 | All entries OK or WARN |
+| 1 | At least one FAIL (hallucination, phantom ID, no match, or retraction) |
+| 2 | Input error (file not found) |
+
+Use in CI: `bibguard references.bib || echo "Citation issues found"`
+
+## How it works
+
+```
+Input (.bib)
+  |
+  v
+Parse entries (bibtexparser)
+  |
+  v
+For each entry:
+  1. arXiv lookup (by arXiv ID)        -- direct ID resolution
+  2. Crossref lookup (by DOI)           -- direct ID resolution
+  3. Phantom ID detection               -- valid format but doesn't resolve?
+  4. DBLP search (by title + author)    -- with author disambiguation
+  5. Semantic Scholar search             -- fallback + citation count
+  6. OpenAlex search                     -- fallback for non-CS / old papers
+  |
+  v
+Post-processing:
+  - Source-aware status (confirmed source overrides noisy cross-checks)
+  - Kill-shot: phantom ID overrides search-confirmed status
+  - Suggested fixes (missing DOI, eprint)
+  |
+  v
+Report (Markdown / JSON)
+  + TeX cross-audit (phantom refs, orphan entries)
+  + Duplicate detection
+  + Auto-fixed .bib
+```
+
+## Benchmark
+
+Tested on a 58-case golden test set (`tests/golden_benchmark.bib`). Reproduce with `python tests/bench_golden.py`.
+
+| Category | Metric | Result |
+|----------|--------|--------|
+| **Hallucinated** (14 fabricated + 1 control) | Detected as FAIL | **14/14 (100%)** |
+| | Detected as >= WARN | **15/15 (100%)** |
+| **Chimera** (5 mixed-metadata) | Detected as >= WARN | **5/5 (100%)** |
+| **Real papers** (10 legitimate) | Clean pass (OK) | 4/10 (40%) |
+| | False positive (FAIL) | 1/10 (10%) |
+| **Retracted** (28 retractions) | Any issue flagged | 19/28 (68%) |
+| **Runtime** | 58 entries | **95s (~1.6s/entry)** |
+
+**Notes:**
+- The 1 false-positive FAIL is a 1962 book with no DOI — a known edge case for API-based verification.
+- WARN on real papers are mostly venue/author-count mismatches — reviewable by humans.
+- All 14 truly fabricated citations are caught at FAIL level.
+
+For semantic NLI, citation graph analysis, and Bayesian risk scoring, see [IntegriRef](https://github.com/GeoffreyWang1117/IntegriRef).
+
+## AI Coding Assistant Integration
+
+bibguard ships with skill/rule definitions for major AI coding assistants. The AI runs verification, analyzes FAIL entries, and searches the web to find correct references.
+
+### Claude Code
+
+```bash
+mkdir -p ~/.claude/commands
+curl -o ~/.claude/commands/bibguard.md \
+  https://raw.githubusercontent.com/GeoffreyWang1117/bibguard/main/.claude/commands/bibguard.md
+```
+Then use `/bibguard paper.bib` in Claude Code.
+
+### OpenAI Codex CLI
+
+```bash
+mkdir -p ~/.codex/skills/bibguard
+curl -o ~/.codex/skills/bibguard/SKILL.md \
+  https://raw.githubusercontent.com/GeoffreyWang1117/bibguard/main/.codex/skills/bibguard/SKILL.md
+```
+
+### Cursor
+
+```bash
+mkdir -p .cursor/rules
+curl -o .cursor/rules/bibguard.md \
+  https://raw.githubusercontent.com/GeoffreyWang1117/bibguard/main/.cursor/rules/bibguard.md
+```
+
+### Any other assistant
+
+bibguard is a standard CLI tool. Any AI assistant that can run shell commands can use it:
+```
+bibguard paper.bib --json --out report.json
+```
+
+## Optional dependencies
+
+| Package | Purpose | Install |
+|---------|---------|---------|
+| `rapidfuzz` | Better title matching (token_set_ratio) | `pip install bibguard[fast]` |
+| `pymupdf` | PDF reference extraction (no GROBID needed) | `pip install bibguard[pdf]` |
+
+## API sources
+
+| Source | Lookup method | Coverage |
+|--------|--------------|----------|
+| arXiv | ID resolution | CS, Physics, Math, ... |
+| Crossref | DOI resolution | 150M+ records |
+| DBLP | Title search | CS papers (gold standard) |
+| Semantic Scholar | Title search | 200M+ papers |
+| OpenAlex | Title search | 250M+ works (all disciplines) |
+
+All queries respect rate limits. No API keys required.
+
+## Contributing
+
+Issues and PRs welcome. To run tests:
+
+```bash
+git clone https://github.com/GeoffreyWang1117/bibguard.git
+cd bibguard
+pip install -e ".[dev]"
+pytest
+```
+
+## Related
+
+- [IntegriRef](https://github.com/GeoffreyWang1117/IntegriRef) -- Full L0-L4 verification stack with semantic NLI (93.5% accuracy), citation graph analysis, and Bayesian risk scoring
+- [Rebiber](https://github.com/yuchenlin/rebiber) -- Normalize BibTeX with DBLP/ACL Anthology
+
+## Contributors
+
+See [CONTRIBUTORS.md](CONTRIBUTORS.md) for detailed attribution.
+
+- **Geoffrey Wang** — Architecture, core algorithms, phantom-ID detection, kill-shot logic, benchmark design
+- **Claude (Anthropic)** — Modular refactoring, output formatting, packaging, documentation
+
+## License
+
+Apache License 2.0. See [LICENSE](LICENSE) for details.
+
+---
+
+<details>
+<summary><strong>中文说明</strong></summary>
+
+# bibguard — 学术论文引用幻觉检测工具
+
+**一行命令，检测论文中的虚假引用。**
+
+大语言模型会"幻觉"出格式正确但根本不存在的参考文献。bibguard 用 5 个学术数据库（arXiv、Crossref、DBLP、Semantic Scholar、OpenAlex）交叉验证你的 `.bib` 文件。
+
+```bash
+pip install bibguard
+bibguard paper.bib
+```
+
+### 核心能力
+
+- **幽灵 DOI / arXiv ID 检测** — 格式正确但不存在 = 最强幻觉信号
+- **Kill-shot 逻辑** — 幽灵 ID 不会被相似论文的搜索结果覆盖
+- **TeX 交叉审计** — 检测 `\cite{key}` 在 `.bib` 中无定义，以及定义了但从未引用的条目
+- **自动修复** — 补全缺失的 DOI 和 eprint 字段
+- **极轻依赖** — 仅需 `requests` + `bibtexparser`
+
+### 基准测试 (58 条公开测试集)
+
+| 类别 | 指标 | 结果 |
+|------|------|------|
+| AI 幻觉引用 (14 条) | 检出率 (FAIL) | **100%** |
+| 元数据嵌合体 (5 条) | 检出率 (>=WARN) | **100%** |
+| 真实论文 (10 条) | 假阳率 (FAIL) | 10% (1 本 1962 年书籍) |
+| 运行时间 | 58 条 | 95 秒 |
+
+### AI 编程助手集成
+
+支持 Claude Code (`/bibguard`)、OpenAI Codex、Cursor 自动触发。
+
+### 深度验证
+
+bibguard 是 L0（存在性验证）层。如需语义 NLI 验证 (93.5%)、引文图谱异常检测、贝叶斯风险评分，请使用 [IntegriRef](https://github.com/GeoffreyWang1117/IntegriRef)。
+
+</details>