opencode-skills-antigravity 1.0.39 → 1.0.41

package/bundled-skills/hugging-face-paper-publisher/scripts/paper_manager.py

@@ -0,0 +1,606 @@
+#!/usr/bin/env -S uv run
+# /// script
+# requires-python = ">=3.10"
+# dependencies = [
+#     "huggingface_hub",
+#     "pyyaml",
+#     "requests",
+#     "python-dotenv",
+# ]
+# ///
+"""
+Paper Manager for Hugging Face Hub
+Manages paper indexing, linking, authorship, and article creation.
+"""
+
+import argparse
+import os
+import sys
+import re
+import json
+from pathlib import Path
+from typing import Optional, List, Dict, Any
+from datetime import datetime
+
+try:
+    from huggingface_hub import HfApi, hf_hub_download, get_token
+    import yaml
+    import requests
+    from dotenv import load_dotenv
+except ImportError as e:
+    print(f"Error: Missing required dependency: {e}")
+    print("Tip: run this script with `uv run scripts/paper_manager.py ...`.")
+    sys.exit(1)
+
+# Load environment variables
+load_dotenv()
+
+
+class PaperManager:
+    """Manages paper publishing operations on Hugging Face Hub."""
+
+    def __init__(self, hf_token: Optional[str] = None):
+        """Initialize Paper Manager with HF token."""
+        self.token = hf_token or os.getenv("HF_TOKEN") or get_token()
+        if not self.token:
+            print("Warning: No HF_TOKEN found. Some operations will fail.")
+        self.api = HfApi(token=self.token)
+
+    def index_paper(self, arxiv_id: str) -> Dict[str, Any]:
+        """
+        Index a paper on Hugging Face from arXiv.
+
+        Args:
+            arxiv_id: arXiv identifier (e.g., "2301.12345")
+
+        Returns:
+            dict: Status information
+        """
+        # Clean and validate arXiv ID
+        try:
+            arxiv_id = self._clean_arxiv_id(arxiv_id)
+        except ValueError as e:
+            print(f"Error: {e}")
+            return {"status": "error", "message": str(e)}
+
+        print(f"Indexing paper {arxiv_id} on Hugging Face...")
+
+        # Check if paper exists
+        paper_url = f"https://huggingface.co/papers/{arxiv_id}"
+
+        try:
+            response = requests.get(paper_url, timeout=10)
+            if response.status_code == 200:
+                print(f"✓ Paper already indexed at {paper_url}")
+                return {"status": "exists", "url": paper_url}
+            else:
+                print(f"Paper not indexed. Visit {paper_url} to trigger indexing.")
+                print("The paper will be automatically indexed when you first visit the URL.")
+                return {"status": "not_indexed", "url": paper_url, "action": "visit_url"}
+        except requests.RequestException as e:
+            print(f"Error checking paper status: {e}")
+            return {"status": "error", "message": str(e)}
+
+    def check_paper(self, arxiv_id: str) -> Dict[str, Any]:
+        """
+        Check if a paper exists on Hugging Face.
+
+        Args:
+            arxiv_id: arXiv identifier
+
+        Returns:
+            dict: Paper status and metadata
+        """
+        try:
+            arxiv_id = self._clean_arxiv_id(arxiv_id)
+        except ValueError as e:
+            return {"exists": False, "error": str(e)}
+        paper_url = f"https://huggingface.co/papers/{arxiv_id}"
+
+        try:
+            response = requests.get(paper_url, timeout=10)
+            if response.status_code == 200:
+                return {
+                    "exists": True,
+                    "url": paper_url,
+                    "arxiv_id": arxiv_id,
+                    "arxiv_url": f"https://arxiv.org/abs/{arxiv_id}"
+                }
+            else:
+                return {
+                    "exists": False,
+                    "arxiv_id": arxiv_id,
+                    "index_url": paper_url,
+                    "message": f"Visit {paper_url} to index this paper"
+                }
+        except requests.RequestException as e:
+            return {"exists": False, "error": str(e)}
+
+    def link_paper_to_repo(
+        self,
+        repo_id: str,
+        arxiv_id: str,
+        repo_type: str = "model",
+        citation: Optional[str] = None,
+        create_pr: bool = False
+    ) -> Dict[str, Any]:
+        """
+        Link a paper to a model/dataset/space repository.
+
+        Args:
+            repo_id: Repository identifier (e.g., "username/repo-name")
+            arxiv_id: arXiv identifier
+            repo_type: Type of repository ("model", "dataset", or "space")
+            citation: Optional full citation text
+            create_pr: Create a PR instead of direct commit
+
+        Returns:
+            dict: Operation status
+        """
+        try:
+            arxiv_id = self._clean_arxiv_id(arxiv_id)
+        except ValueError as e:
+            print(f"Error: {e}")
+            return {"status": "error", "message": str(e)}
+
+        print(f"Linking paper {arxiv_id} to {repo_type} {repo_id}...")
+
+        try:
+            # Download current README
+            readme_path = hf_hub_download(
+                repo_id=repo_id,
+                filename="README.md",
+                repo_type=repo_type,
+                token=self.token
+            )
+
+            with open(readme_path, 'r', encoding='utf-8') as f:
+                content = f.read()
+
+            # Parse or create YAML frontmatter
+            updated_content = self._add_paper_to_readme(content, arxiv_id, citation)
+
+            # Upload updated README
+            commit_message = f"Add paper reference: arXiv:{arxiv_id}"
+
+            if create_pr:
+                # Create PR (not implemented in basic version)
+                print("PR creation not yet implemented. Committing directly.")
+
+            self.api.upload_file(
+                path_or_fileobj=updated_content.encode('utf-8'),
+                path_in_repo="README.md",
+                repo_id=repo_id,
+                repo_type=repo_type,
+                commit_message=commit_message,
+                token=self.token
+            )
+
+            paper_url = f"https://huggingface.co/papers/{arxiv_id}"
+            repo_url = f"https://huggingface.co/{repo_id}"
+
+            print(f"✓ Successfully linked paper to repository")
+            print(f"  Paper: {paper_url}")
+            print(f"  Repo: {repo_url}")
+
+            return {
+                "status": "success",
+                "paper_url": paper_url,
+                "repo_url": repo_url,
+                "arxiv_id": arxiv_id
+            }
+
+        except Exception as e:
+            print(f"Error linking paper: {e}")
+            return {"status": "error", "message": str(e)}
+
+    def _add_paper_to_readme(
+        self,
+        content: str,
+        arxiv_id: str,
+        citation: Optional[str] = None
+    ) -> str:
+        """
+        Add paper reference to README content.
+
+        Args:
+            content: Current README content
+            arxiv_id: arXiv identifier
+            citation: Optional citation text
+
+        Returns:
+            str: Updated README content
+        """
+        arxiv_url = f"https://arxiv.org/abs/{arxiv_id}"
+        hf_paper_url = f"https://huggingface.co/papers/{arxiv_id}"
+
+        # Check if YAML frontmatter exists
+        yaml_pattern = r'^---\s*\n(.*?)\n---\s*\n'
+        match = re.match(yaml_pattern, content, re.DOTALL)
+
+        if match:
+            # YAML exists, check if paper already referenced
+            if arxiv_id in content:
+                print(f"Paper {arxiv_id} already referenced in README")
+                return content
+
+            # Add to existing content (after YAML)
+            yaml_end = match.end()
+            before = content[:yaml_end]
+            after = content[yaml_end:]
+        else:
+            # No YAML, add minimal frontmatter
+            yaml_content = "---\n---\n\n"
+            before = yaml_content
+            after = content
+
+        # Add paper reference section with boundary markers
+        paper_section = "\n<!-- paper-manager:start -->\n"
+        paper_section += f"## Paper\n\n"
+        paper_section += f"This {'model' if 'model' in content.lower() else 'work'} is based on research presented in:\n\n"
+        paper_section += f"**[View on arXiv]({arxiv_url})** | "
+        paper_section += f"**[View on Hugging Face]({hf_paper_url})**\n\n"
+
+        if citation:
+            safe_citation = self._sanitize_text(citation)
+            paper_section += f"### Citation\n\n```bibtex\n{safe_citation}\n```\n\n"
+
+        paper_section += "<!-- paper-manager:end -->\n"
+
+        # Insert after YAML, before main content
+        updated_content = before + paper_section + after
+
+        return updated_content
+
+    def create_research_article(
+        self,
+        template: str,
+        title: str,
+        output: str,
+        authors: Optional[str] = None,
+        abstract: Optional[str] = None
+    ) -> Dict[str, Any]:
+        """
+        Create a research article from template.
+
+        Args:
+            template: Template name ("standard", "modern", "arxiv", "ml-report")
+            title: Paper title
+            output: Output filename
+            authors: Comma-separated author names
+            abstract: Abstract text
+
+        Returns:
+            dict: Creation status
+        """
+        print(f"Creating research article with '{template}' template...")
+
+        # Load template
+        template_dir = Path(__file__).parent.parent / "templates"
+        template_file = template_dir / f"{template}.md"
+
+        if not template_file.exists():
+            return {
+                "status": "error",
+                "message": f"Template '{template}' not found at {template_file}"
+            }
+
+        with open(template_file, 'r', encoding='utf-8') as f:
+            template_content = f.read()
+
+        # Prepare safe values for different contexts
+        date_str = datetime.now().strftime("%Y-%m-%d")
+        safe_title_body = self._sanitize_text(title)
+        authors_val = authors if authors else "Your Name"
+        safe_authors_body = self._sanitize_text(authors_val)
+        abstract_val = abstract if abstract else "Abstract to be written..."
+        safe_abstract_body = self._sanitize_text(abstract_val)
+
+        # Split frontmatter from body for context-aware escaping
+        fm_pattern = r'^(---\s*\n)(.*?\n)(---\s*\n)'
+        fm_match = re.match(fm_pattern, template_content, re.DOTALL)
+
+        if fm_match:
+            fm_open, fm_body, fm_close = fm_match.group(1), fm_match.group(2), fm_match.group(3)
+            body = template_content[fm_match.end():]
+
+            # YAML-escape values in frontmatter
+            fm_body = fm_body.replace("{{TITLE}}", self._escape_yaml_value(title))
+            fm_body = fm_body.replace("{{AUTHORS}}", self._escape_yaml_value(authors_val))
+            fm_body = fm_body.replace("{{DATE}}", date_str)
+
+            # Sanitize values in body
+            body = body.replace("{{TITLE}}", safe_title_body)
+            body = body.replace("{{AUTHORS}}", safe_authors_body)
+            body = body.replace("{{ABSTRACT}}", safe_abstract_body)
+            body = body.replace("{{DATE}}", date_str)
+
+            content = fm_open + fm_body + fm_close + body
+        else:
+            # No frontmatter — sanitize everything
+            content = template_content.replace("{{TITLE}}", safe_title_body)
+            content = content.replace("{{DATE}}", date_str)
+            content = content.replace("{{AUTHORS}}", safe_authors_body)
+            content = content.replace("{{ABSTRACT}}", safe_abstract_body)
+
+        # Write output
+        with open(output, 'w', encoding='utf-8') as f:
+            f.write(content)
+
+        print(f"✓ Research article created at {output}")
+
+        return {
+            "status": "success",
+            "output": output,
+            "template": template
+        }
+
+    def get_arxiv_info(self, arxiv_id: str) -> Dict[str, Any]:
+        """
+        Fetch paper information from arXiv API.
+
+        Args:
+            arxiv_id: arXiv identifier
+
+        Returns:
+            dict: Paper metadata
+        """
+        try:
+            arxiv_id = self._clean_arxiv_id(arxiv_id)
+        except ValueError as e:
+            return {"error": str(e)}
+        api_url = f"https://export.arxiv.org/api/query?id_list={arxiv_id}"
+
+        try:
+            response = requests.get(api_url, timeout=10)
+            response.raise_for_status()
+
+            # Parse XML response (simplified)
+            content = response.text
+
+            # Extract basic info with regex (proper XML parsing would be better)
+            title_match = re.search(r'<title>(.*?)</title>', content, re.DOTALL)
+            authors_matches = re.findall(r'<name>(.*?)</name>', content)
+            summary_match = re.search(r'<summary>(.*?)</summary>', content, re.DOTALL)
+
+            # Sanitize all text extracted from the external API
+            raw_title = title_match.group(1).strip() if title_match else None
+            raw_authors = authors_matches[1:] if len(authors_matches) > 1 else []
+            raw_abstract = summary_match.group(1).strip() if summary_match else None
+
+            return {
+                "arxiv_id": arxiv_id,
+                "title": self._sanitize_text(raw_title) if raw_title else None,
+                "authors": [self._sanitize_text(a) for a in raw_authors],
+                "abstract": self._sanitize_text(raw_abstract) if raw_abstract else None,
+                "arxiv_url": f"https://arxiv.org/abs/{arxiv_id}",
+                "pdf_url": f"https://arxiv.org/pdf/{arxiv_id}.pdf"
+            }
+        except Exception as e:
+            return {"error": str(e)}
+
+    def generate_citation(
+        self,
+        arxiv_id: str,
+        format: str = "bibtex"
+    ) -> str:
+        """
+        Generate citation for a paper.
+
+        Args:
+            arxiv_id: arXiv identifier
+            format: Citation format ("bibtex", "apa", "mla")
+
+        Returns:
+            str: Formatted citation
+        """
+        try:
+            arxiv_id = self._clean_arxiv_id(arxiv_id)
+        except ValueError as e:
+            return f"Error: {e}"
+
+        info = self.get_arxiv_info(arxiv_id)
+
+        if "error" in info:
+            return f"Error fetching paper info: {info['error']}"
+
+        if format == "bibtex":
+            # Generate BibTeX citation
+            key = f"arxiv{arxiv_id.replace('.', '_')}"
+            raw_authors = " and ".join(info.get("authors", ["Unknown"]))
+            raw_title = info.get("title", "Untitled")
+            year = arxiv_id.split(".")[0][:2]  # Extract year from ID (simplified)
+            year = f"20{year}" if int(year) < 50 else f"19{year}"
+
+            # Escape BibTeX structural characters in untrusted values
+            safe_title = raw_title.replace('{', r'\{').replace('}', r'\}')
+            safe_authors = raw_authors.replace('{', r'\{').replace('}', r'\}')
+
+            citation = f"""@article{{{key},
+  title={{{safe_title}}},
+  author={{{safe_authors}}},
+  journal={{arXiv preprint arXiv:{arxiv_id}}},
+  year={{{year}}}
+}}"""
+            return citation
+
+        return f"Format '{format}' not yet implemented"
+
+    # Patterns for valid arXiv IDs
+    _ARXIV_ID_MODERN = re.compile(r'^\d{4}\.\d{4,5}(v\d+)?$')
+    _ARXIV_ID_LEGACY = re.compile(r'^[a-zA-Z\-]+/\d{7}(v\d+)?$')
+
+    @staticmethod
+    def _clean_arxiv_id(arxiv_id: str) -> str:
+        """Clean, normalize, and validate arXiv ID.
+
+        Raises:
+            ValueError: If the cleaned ID does not match a valid arXiv format.
+        """
+        # Remove common prefixes and whitespace
+        arxiv_id = arxiv_id.strip()
+        arxiv_id = re.sub(r'^(arxiv:|arXiv:)', '', arxiv_id, flags=re.IGNORECASE)
+        arxiv_id = re.sub(r'https?://arxiv\.org/(abs|pdf)/', '', arxiv_id)
+        arxiv_id = arxiv_id.replace('.pdf', '')
+
+        # Validate format
+        if not (PaperManager._ARXIV_ID_MODERN.match(arxiv_id)
+                or PaperManager._ARXIV_ID_LEGACY.match(arxiv_id)):
+            raise ValueError(
+                f"Invalid arXiv ID: {arxiv_id!r}. "
+                "Expected format: YYMM.NNNNN[vN] or category/YYMMNNN[vN]"
+            )
+
+        return arxiv_id
+
+    @staticmethod
+    def _escape_yaml_value(value: str) -> str:
+        """Escape a string for safe use as a YAML scalar value.
+
+        Wraps in double quotes and escapes internal quotes and backslashes
+        to prevent YAML injection via crafted titles/authors.
+        """
+        value = value.replace('\\', '\\\\').replace('"', '\\"')
+        return f'"{value}"'
+
+    @staticmethod
+    def _sanitize_text(text: str) -> str:
+        """Sanitize untrusted text for safe inclusion in Markdown/YAML output.
+
+        Normalizes whitespace, strips control characters, and neutralizes
+        markdown code-fence breakout and YAML document delimiters.
+        """
+        # Remove control characters (keep newlines and tabs)
+        text = re.sub(r'[\x00-\x08\x0b\x0c\x0e-\x1f\x7f]', '', text)
+        # Normalize whitespace runs (collapse multiple spaces/tabs, preserve single newlines)
+        text = re.sub(r'[^\S\n]+', ' ', text)
+        text = re.sub(r'\n{3,}', '\n\n', text)
+        # Neutralize markdown code fence breakout
+        text = text.replace('```', r'\`\`\`')
+        # Neutralize YAML document delimiters at line start
+        text = re.sub(r'^---', r'\\---', text, flags=re.MULTILINE)
+        return text.strip()
+
+
+def main():
+    """Main CLI entry point."""
+    parser = argparse.ArgumentParser(
+        description="Paper Manager for Hugging Face Hub",
+        formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    subparsers = parser.add_subparsers(dest="command", help="Command to execute")
+
+    # Index command
+    index_parser = subparsers.add_parser("index", help="Index a paper from arXiv")
+    index_parser.add_argument("--arxiv-id", required=True, help="arXiv paper ID")
+
+    # Check command
+    check_parser = subparsers.add_parser("check", help="Check if paper exists")
+    check_parser.add_argument("--arxiv-id", required=True, help="arXiv paper ID")
+
+    # Link command
+    link_parser = subparsers.add_parser("link", help="Link paper to repository")
+    link_parser.add_argument("--repo-id", required=True, help="Repository ID")
+    link_parser.add_argument("--repo-type", default="model", choices=["model", "dataset", "space"])
+    link_parser.add_argument("--arxiv-id", help="Single arXiv ID")
+    link_parser.add_argument("--arxiv-ids", help="Comma-separated arXiv IDs")
+    link_parser.add_argument("--citation", help="Full citation text")
+    link_parser.add_argument("--create-pr", action="store_true", help="Create PR instead of direct commit")
+
+    # Create command
+    create_parser = subparsers.add_parser("create", help="Create research article")
+    create_parser.add_argument("--template", required=True, help="Template name")
+    create_parser.add_argument("--title", required=True, help="Paper title")
+    create_parser.add_argument("--output", required=True, help="Output filename")
+    create_parser.add_argument("--authors", help="Comma-separated authors")
+    create_parser.add_argument("--abstract", help="Abstract text")
+
+    # Info command
+    info_parser = subparsers.add_parser("info", help="Get paper information")
+    info_parser.add_argument("--arxiv-id", required=True, help="arXiv paper ID")
+    info_parser.add_argument("--format", default="json", choices=["json", "text"])
+
+    # Citation command
+    citation_parser = subparsers.add_parser("citation", help="Generate citation")
+    citation_parser.add_argument("--arxiv-id", required=True, help="arXiv paper ID")
+    citation_parser.add_argument("--format", default="bibtex", choices=["bibtex", "apa", "mla"])
+
+    # Search command
+    search_parser = subparsers.add_parser("search", help="Search papers")
+    search_parser.add_argument("--query", required=True, help="Search query")
+
+    args = parser.parse_args()
+
+    if not args.command:
+        parser.print_help()
+        sys.exit(1)
+
+    # Initialize manager
+    manager = PaperManager()
+
+    # Execute command
+    if args.command == "index":
+        result = manager.index_paper(args.arxiv_id)
+        print(json.dumps(result, indent=2))
+
+    elif args.command == "check":
+        result = manager.check_paper(args.arxiv_id)
+        print(json.dumps(result, indent=2))
+
+    elif args.command == "link":
+        arxiv_ids = []
+        if args.arxiv_id:
+            arxiv_ids.append(args.arxiv_id)
+        if args.arxiv_ids:
+            arxiv_ids.extend([id.strip() for id in args.arxiv_ids.split(",")])
+
+        if not arxiv_ids:
+            print("Error: Must provide --arxiv-id or --arxiv-ids")
+            sys.exit(1)
+
+        for arxiv_id in arxiv_ids:
+            result = manager.link_paper_to_repo(
+                repo_id=args.repo_id,
+                arxiv_id=arxiv_id,
+                repo_type=args.repo_type,
+                citation=args.citation,
+                create_pr=args.create_pr
+            )
+            print(json.dumps(result, indent=2))
+
+    elif args.command == "create":
+        result = manager.create_research_article(
+            template=args.template,
+            title=args.title,
+            output=args.output,
+            authors=args.authors,
+            abstract=args.abstract
+        )
+        print(json.dumps(result, indent=2))
+
+    elif args.command == "info":
+        result = manager.get_arxiv_info(args.arxiv_id)
+        if args.format == "json":
+            print(json.dumps(result, indent=2))
+        else:
+            if "error" in result:
+                print(f"Error: {result['error']}")
+            else:
+                print(f"Title: {result.get('title')}")
+                print(f"Authors: {', '.join(result.get('authors', []))}")
+                print(f"arXiv URL: {result.get('arxiv_url')}")
+                print(f"\nAbstract:\n{result.get('abstract')}")
+
+    elif args.command == "citation":
+        citation = manager.generate_citation(args.arxiv_id, args.format)
+        print(citation)
+
+    elif args.command == "search":
+        print(f"Searching for: {args.query}")
+        print("Search functionality coming soon!")
+        print(f"Visit: https://huggingface.co/papers?search={args.query}")
+
+
+if __name__ == "__main__":
+    main()