### Install CiteCheck CLI from Source

Source: https://github.com/color4-alt/citecheck/blob/main/README.md

Alternatively, you can install the CiteCheck CLI directly from its source repository. This method involves cloning the repository and then installing it using pip in editable mode, with optional support for PDF and development dependencies.

```bash
git clone https://github.com/color4-alt/CiteCheck.git
```

```bash
cd CiteCheck
```

```bash
pip install -e ".[pdf,dev]"
```

--------------------------------

### Install CiteCheck with PDF Support

Source: https://github.com/color4-alt/citecheck/blob/main/GEMINI.md

Install CiteCheck with the necessary dependencies for PDF file support.

```bash
pip install CiteCheck[pdf]
```

--------------------------------

### Clone and Install CiteCheck

Source: https://github.com/color4-alt/citecheck/blob/main/README.md

Commands to clone the CiteCheck repository and install it in editable mode with development dependencies.

```bash
# Clone
git clone https://github.com/color4-alt/CiteCheck.git
cd CiteCheck

# Install in editable mode with dev dependencies
pip install -e ".[dev]"
```

--------------------------------

### Install CiteCheck Python Package

Source: https://github.com/color4-alt/citecheck/blob/main/GEMINI.md

Install the core CiteCheck Python package using pip.

```bash
pip install CiteCheck
```

--------------------------------

### Install CiteCheck Skill via Agent

Source: https://github.com/color4-alt/citecheck/blob/main/README.md

The easiest way to install CiteCheck as a skill for your coding agent is to ask the agent directly. This command will prompt the agent to clone the repository into the correct skill directory.

```bash
Install this skill for me: https://github.com/color4-alt/CiteCheck
```

--------------------------------

### Install CiteCheck Package

Source: https://github.com/color4-alt/citecheck/blob/main/skills/citecheck/SKILL.md

Install the CiteCheck Python package using pip. Include the `[pdf]` extra for PDF support.

```bash
pip install CiteCheck
```

```bash
pip install CiteCheck[pdf]
```

--------------------------------

### Install and Test CiteCheck

Source: https://github.com/color4-alt/citecheck/blob/main/CLAUDE.md

Installs the CiteCheck package in editable mode with development dependencies and runs the pytest suite.

```bash
pip install -e ".[dev]"
pytest tests/
```

--------------------------------

### Invoke CiteCheck Skill with File Reference

Source: https://github.com/color4-alt/citecheck/blob/main/README.md

When CiteCheck is installed as a skill, you can invoke it using natural language or a slash command followed by a file or directory path. The agent will then handle the citation verification process.

```bash
/citation-verification @main.tex
```

```bash
/citation-verification @paper.pdf
```

```bash
/citation-verification @path/to/latex_project/
```

--------------------------------

### Run Tests and Formatting Checks

Source: https://github.com/color4-alt/citecheck/blob/main/README.md

Commands to execute the test suite and apply code formatting and linting using pytest, black, and ruff.

```bash
# Run tests
pytest tests/ -v

# Format & lint
black src/ tests/
ruff check src/ tests/
```

--------------------------------

### CiteCheck Workflow Overview

Source: https://github.com/color4-alt/citecheck/blob/main/README.md

This diagram outlines the six-step workflow of CiteCheck, from parsing input documents to generating a final report.

```text
Input (LaTeX / PDF)
    │
    ▼
┌─────────────────┐
│ 1. Parse Paper  │  ← Extract refs, citations, body text
└────────┬────────┘
         │
    ┌────┴────┐
    ▼         ▼
┌────────┐ ┌─────────────┐
│ LaTeX  │ │ PDF Fallback │
│(.bib)  │ │ (PyMuPDF)    │
└────────┘ └─────────────┘
         │
         ▼
┌─────────────────┐
│ 2. Format Check │  ← Validate BibTeX fields, types, venues
└────────┬────────┘
         │
         ▼
┌─────────────────────┐
│ 3. Queryability     │  ← Crossref → Semantic Scholar → OpenAlex → PubMed → arXiv → dblp → Google Scholar → WebSearch
└────────┬────────────┘
         │
         ▼
┌─────────────────────┐
│ 4. Thematic Match   │  ← Skill: agent reasoning | CLI: heuristic/LLM
└────────┬────────────┘
         │
         ▼
┌─────────────────────┐
│ 5. Semantic Match   │  ← Skill: agent reasoning | CLI: heuristic/LLM
└────────┬────────────┘
         │
         ▼
┌─────────────────────┐
│ 6. Generate Report  │  ← Markdown report with findings
└─────────────────────┘
```

--------------------------------

### Verify Queryability of Citations with Citecheck

Source: https://github.com/color4-alt/citecheck/blob/main/skills/citecheck/examples/example-latex-verification.md

Run citecheck again to verify the extracted references against external databases like Crossref and Semantic Scholar. This command skips semantic checks and outputs a report on queryability.

```bash
citecheck ./latex_paper/ --skip-semantic -o verified_report.md
```

--------------------------------

### Run CiteCheck CLI on LaTeX Project

Source: https://github.com/color4-alt/citecheck/blob/main/README.md

The primary way to use the CiteCheck CLI is by providing the path to a LaTeX project directory. This allows CiteCheck to process all associated .tex and .bib files for citation verification.

```bash
citecheck path/to/latex_project/
```

--------------------------------

### Queryability Verification

Source: https://github.com/color4-alt/citecheck/blob/main/skills/citecheck/examples/example-pdf-verification.md

Verify extracted references against external databases like Crossref and Semantic Scholar using the citecheck CLI. This command skips semantic analysis and outputs a report on verification status.

```bash
citecheck paper.pdf --skip-semantic -o verified_report.md
```

--------------------------------

### Run CiteCheck CLI with External LLM for Matching

Source: https://github.com/color4-alt/citecheck/blob/main/README.md

CiteCheck can optionally use an external LLM for semantic matching by providing an API key. If no API key is provided, it falls back to heuristic-based matching.

```bash
citecheck main.tex --api-key $OPENAI_API_KEY
```

--------------------------------

### Test LaTeX Source Parsing with CiteCheck

Source: https://github.com/color4-alt/citecheck/blob/main/AGENTS.md

Use this command to test the parsing of LaTeX source files. It skips verification and semantic checks, outputting results to a temporary Markdown file. Observe the expected counts for parsed references, citation markers, format issues, and uncited lists.

```bash
# From inside CiteCheck/
cd CiteCheck

# 1. Test LaTeX source parsing
citecheck ../latex_paper/main.tex --skip-verification --skip-semantic -o /tmp/test_latex.md

# Expected baseline:
#   - 19 references parsed
#   - 18 citation markers detected
#   - 7 format issues (preprints, wrong entry type, missing author, future year)
#   - Uncited list: only [3] touvron2023llama
```

--------------------------------

### Parse LaTeX Paper with CiteCheck CLI

Source: https://github.com/color4-alt/citecheck/blob/main/skills/citecheck/SKILL.md

Use this command to parse a LaTeX project directory or a single LaTeX file. The `--skip-verification` and `--skip-semantic` flags are required when used in Skill mode.

```bash
citecheck path/to/latex_project/ --skip-verification --skip-semantic -o parsed_report.md
```

```bash
citecheck main.tex --skip-verification --skip-semantic -o parsed_report.md
```

--------------------------------

### Test PDF Fallback Parsing with CiteCheck

Source: https://github.com/color4-alt/citecheck/blob/main/AGENTS.md

Use this command to test CiteCheck's fallback parsing of PDF files. This command also skips verification and semantic checks. Note that PDF parsing may yield fewer parsed references due to limitations in extracting metadata.

```bash
# 2. Test PDF fallback parsing
citecheck ../latex_paper/main.pdf --skip-verification --skip-semantic -o /tmp/test_pdf.md

# Expected baseline:
#   - 18 references parsed (PDF loses incomplete entry metadata)
#   - 18 citation markers detected
#   - 0 format issues (PDF parser has limited format checking)
```

--------------------------------

### CiteCheck Project Structure

Source: https://github.com/color4-alt/citecheck/blob/main/README.md

This outlines the directory and file structure of the CiteCheck project, including source code, skill definitions, and documentation.

```text
CiteCheck/
├── skills/citecheck/SKILL.md      ← Agent skill entry (cross-platform)
├── .claude-plugin/plugin.json     ← Claude Code marketplace metadata
├── .codex-plugin/plugin.json      ← Codex CLI marketplace metadata
├── CLAUDE.md                      ← Project context for Claude Code
├── AGENTS.md                      ← Project context for Codex / generic agents
├── GEMINI.md                      ← Project context for Gemini CLI
├── src/citecheck/                 ← Python CLI source
│   ├── cli.py
│   ├── parser.py
│   ├── bibtex_parser.py
│   ├── pdf_parser.py
│   ├── verifier.py
│   ├── matcher.py
│   ├── models.py
│   └── reporter.py
├── references/                    ← Skill reference docs
│   ├── format-check-rules.md
│   ├── api-reference.md
│   ├── thematic-scoring-prompt.md
│   └── semantic-matching-prompt.md
├── tests/
├── examples/
└── README.md / README.zh.md
```

--------------------------------

### Run CiteCheck CLI on PDF with Output File

Source: https://github.com/color4-alt/citecheck/blob/main/README.md

CiteCheck can process PDF files as a fallback, although LaTeX is preferred. The '-o' option allows you to specify a custom output path for the report.

```bash
citecheck paper.pdf -o report.md
```

--------------------------------

### Run CiteCheck CLI on Single LaTeX File

Source: https://github.com/color4-alt/citecheck/blob/main/README.md

You can also run CiteCheck on a single .tex file. This is useful for verifying citations within a specific document.

```bash
citecheck main.tex
```

--------------------------------

### Run CiteCheck CLI in Offline Mode

Source: https://github.com/color4-alt/citecheck/blob/main/README.md

To perform citation verification without making any online requests to databases like Crossref or Semantic Scholar, use the '--skip-verification' flag. This mode relies solely on local parsing and formatting checks.

```bash
citecheck main.tex --skip-verification
```

--------------------------------

### Suggested Fix for Reference [4]

Source: https://github.com/color4-alt/citecheck/blob/main/examples/example_report.md

This BibTeX entry provides a corrected format for reference [4], addressing issues like preprint source and year mismatch. Use this to update your bibliography.

```bibtex
@article{krithara2023bioasq,
  title={BioASQ-QA: A manually curated corpus for Biomedical Question Answering},
  author={Krithara, Anastasia and Nentidis, Anastasios and Bougiatiotis, Konstantinos and Paliouras, Georgios},
  journal={Scientific Data},
  volume={10},
  pages={170},
  year={2023},
  doi={10.1038/s41597-023-02068-4}
}
```

--------------------------------

### Suggested Fix for Reference [8]

Source: https://github.com/color4-alt/citecheck/blob/main/examples/example_report.md

This BibTeX entry offers a corrected format for reference [8], resolving the incorrect entry type and missing DOI/URL. Apply this to fix the citation.

```bibtex
@article{tsatsaronis2015overview,
  title={An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition},
  author={Tsatsaronis, George and Balikas, Georgios and Malakasiotis, Prodromos and others},
  journal={BMC Bioinformatics},
  volume={16},
  pages={138},
  year={2015},
  doi={10.1186/s12859-015-0564-6}
}
```

--------------------------------

### Parse LaTeX Paper with Citecheck

Source: https://github.com/color4-alt/citecheck/blob/main/skills/citecheck/examples/example-latex-verification.md

Use the citecheck CLI to parse a LaTeX paper, extracting references and detecting in-text citations. This command skips verification and semantic checks to focus on parsing.

```bash
citecheck ./latex_paper/ --skip-verification --skip-semantic -o parsed_report.md
```

--------------------------------

### Parse Paper PDF

Source: https://github.com/color4-alt/citecheck/blob/main/skills/citecheck/examples/example-pdf-verification.md

Use the citecheck CLI to parse a PDF paper, extracting references and detecting in-text citations. This command skips verification and semantic checks, focusing solely on initial parsing.

```bash
citecheck paper.pdf --skip-verification --skip-semantic -o parsed_report.md
```

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