clearai-dsh 0.3.0 → 0.4.0

package/presets/clearai/template/skills/literature-review/scripts/generate_pdf.py

@@ -1,176 +0,0 @@
-#!/usr/bin/env python3
-"""
-PDF Generation Script for Literature Reviews
-Converts markdown files to professionally formatted PDFs with proper styling.
-"""
-
-import subprocess
-import sys
-import os
-from pathlib import Path
-
-def generate_pdf(
-    markdown_file: str,
-    output_pdf: str = None,
-    citation_style: str = "apa",
-    template: str = None,
-    toc: bool = True,
-    number_sections: bool = True
-) -> bool:
-    """
-    Generate a PDF from a markdown file using pandoc.
-
-    Args:
-        markdown_file: Path to the markdown file
-        output_pdf: Path for output PDF (defaults to same name as markdown)
-        citation_style: Citation style (apa, nature, chicago, etc.)
-        template: Path to custom LaTeX template
-        toc: Include table of contents
-        number_sections: Number the sections
-
-    Returns:
-        True if successful, False otherwise
-    """
-
-    # Verify markdown file exists
-    if not os.path.exists(markdown_file):
-        print(f"Error: Markdown file not found: {markdown_file}")
-        return False
-
-    # Set default output path
-    if output_pdf is None:
-        output_pdf = Path(markdown_file).with_suffix('.pdf')
-
-    # Check if pandoc is installed
-    try:
-        subprocess.run(['pandoc', '--version'], capture_output=True, check=True)
-    except (subprocess.CalledProcessError, FileNotFoundError):
-        print("Error: pandoc is not installed.")
-        print("Install with: brew install pandoc (macOS) or apt-get install pandoc (Linux)")
-        return False
-
-    # Build pandoc command
-    cmd = [
-        'pandoc',
-        markdown_file,
-        '-o', str(output_pdf),
-        '--pdf-engine=xelatex',  # Better Unicode support
-        '-V', 'geometry:margin=1in',
-        '-V', 'fontsize=11pt',
-        '-V', 'colorlinks=true',
-        '-V', 'linkcolor=blue',
-        '-V', 'urlcolor=blue',
-        '-V', 'citecolor=blue',
-    ]
-
-    # Add table of contents
-    if toc:
-        cmd.extend(['--toc', '--toc-depth=3'])
-
-    # Add section numbering
-    if number_sections:
-        cmd.append('--number-sections')
-
-    # Add citation processing if bibliography exists
-    bib_file = Path(markdown_file).with_suffix('.bib')
-    if bib_file.exists():
-        cmd.extend([
-            '--citeproc',
-            '--bibliography', str(bib_file),
-            '--csl', f'{citation_style}.csl' if not citation_style.endswith('.csl') else citation_style
-        ])
-
-    # Add custom template if provided
-    if template and os.path.exists(template):
-        cmd.extend(['--template', template])
-
-    # Execute pandoc
-    try:
-        print(f"Generating PDF: {output_pdf}")
-        print(f"Command: {' '.join(cmd)}")
-        result = subprocess.run(cmd, capture_output=True, text=True, check=True)
-        print(f"✓ PDF generated successfully: {output_pdf}")
-        return True
-    except subprocess.CalledProcessError as e:
-        print(f"Error generating PDF:")
-        print(f"STDOUT: {e.stdout}")
-        print(f"STDERR: {e.stderr}")
-        return False
-
-def check_dependencies():
-    """Check if required dependencies are installed."""
-    dependencies = {
-        'pandoc': 'pandoc --version',
-        'xelatex': 'xelatex --version'
-    }
-
-    missing = []
-    for name, cmd in dependencies.items():
-        try:
-            subprocess.run(cmd.split(), capture_output=True, check=True)
-            print(f"✓ {name} is installed")
-        except (subprocess.CalledProcessError, FileNotFoundError):
-            print(f"✗ {name} is NOT installed")
-            missing.append(name)
-
-    if missing:
-        print("\n" + "="*60)
-        print("Missing dependencies:")
-        for dep in missing:
-            if dep == 'pandoc':
-                print("  - pandoc: brew install pandoc (macOS) or apt-get install pandoc (Linux)")
-            elif dep == 'xelatex':
-                print("  - xelatex: brew install --cask mactex (macOS) or apt-get install texlive-xetex (Linux)")
-        return False
-
-    return True
-
-def main():
-    """Command-line interface."""
-    if len(sys.argv) < 2:
-        print("Usage: python generate_pdf.py <markdown_file> [output_pdf] [--citation-style STYLE]")
-        print("\nOptions:")
-        print("  --citation-style STYLE    Citation style (default: apa)")
-        print("  --no-toc                  Disable table of contents")
-        print("  --no-numbers              Disable section numbering")
-        print("  --check-deps              Check if dependencies are installed")
-        sys.exit(1)
-
-    # Check dependencies mode
-    if '--check-deps' in sys.argv:
-        check_dependencies()
-        sys.exit(0)
-
-    # Parse arguments
-    markdown_file = sys.argv[1]
-    output_pdf = sys.argv[2] if len(sys.argv) > 2 and not sys.argv[2].startswith('--') else None
-
-    citation_style = 'apa'
-    toc = True
-    number_sections = True
-
-    # Parse optional flags
-    if '--citation-style' in sys.argv:
-        idx = sys.argv.index('--citation-style')
-        if idx + 1 < len(sys.argv):
-            citation_style = sys.argv[idx + 1]
-
-    if '--no-toc' in sys.argv:
-        toc = False
-
-    if '--no-numbers' in sys.argv:
-        number_sections = False
-
-    # Generate PDF
-    success = generate_pdf(
-        markdown_file,
-        output_pdf,
-        citation_style=citation_style,
-        toc=toc,
-        number_sections=number_sections
-    )
-
-    sys.exit(0 if success else 1)
-
-if __name__ == "__main__":
-    main()

package/presets/clearai/template/skills/literature-review/scripts/generate_schematic.py

@@ -1,139 +0,0 @@
-#!/usr/bin/env python3
-"""
-Scientific schematic generation using Nano Banana 2.
-
-Generate any scientific diagram by describing it in natural language.
-Nano Banana 2 handles everything automatically with smart iterative refinement.
-
-Smart iteration: Only regenerates if quality is below threshold for your document type.
-Quality review: Uses Gemini 3.1 Pro Preview for professional scientific evaluation.
-
-Usage:
-    # Generate for journal paper (highest quality threshold)
-    python generate_schematic.py "CONSORT flowchart" -o flowchart.png --doc-type journal
-    
-    # Generate for presentation (lower threshold, faster)
-    python generate_schematic.py "Transformer architecture" -o transformer.png --doc-type presentation
-    
-    # Generate for poster
-    python generate_schematic.py "MAPK signaling pathway" -o pathway.png --doc-type poster
-"""
-
-import argparse
-import os
-import subprocess
-import sys
-from pathlib import Path
-
-
-def main():
-    """Command-line interface."""
-    parser = argparse.ArgumentParser(
-        description="Generate scientific schematics using AI with smart iterative refinement",
-        formatter_class=argparse.RawDescriptionHelpFormatter,
-        epilog="""
-How it works:
-  Simply describe your diagram in natural language
-  Nano Banana 2 generates it automatically with:
-  - Smart iteration (only regenerates if quality is below threshold)
-  - Quality review by Gemini 3.1 Pro Preview
-  - Document-type aware quality thresholds
-  - Publication-ready output
-
-Document Types (quality thresholds):
-  journal      8.5/10  - Nature, Science, peer-reviewed journals
-  conference   8.0/10  - Conference papers
-  thesis       8.0/10  - Dissertations, theses
-  grant        8.0/10  - Grant proposals
-  preprint     7.5/10  - arXiv, bioRxiv, etc.
-  report       7.5/10  - Technical reports
-  poster       7.0/10  - Academic posters
-  presentation 6.5/10  - Slides, talks
-  default      7.5/10  - General purpose
-
-Examples:
-  # Generate for journal paper (strict quality)
-  python generate_schematic.py "CONSORT participant flow" -o flowchart.png --doc-type journal
-  
-  # Generate for poster (moderate quality)
-  python generate_schematic.py "Transformer architecture" -o arch.png --doc-type poster
-  
-  # Generate for slides (faster, lower threshold)
-  python generate_schematic.py "System diagram" -o system.png --doc-type presentation
-  
-  # Custom max iterations
-  python generate_schematic.py "Complex pathway" -o pathway.png --iterations 2
-  
-  # Verbose output
-  python generate_schematic.py "Circuit diagram" -o circuit.png -v
-
-Environment Variables:
-  OPENROUTER_API_KEY    Required for AI generation
-        """
-    )
-    
-    parser.add_argument("prompt", 
-                       help="Description of the diagram to generate")
-    parser.add_argument("-o", "--output", required=True,
-                       help="Output file path")
-    parser.add_argument("--doc-type", default="default",
-                       choices=["journal", "conference", "poster", "presentation",
-                               "report", "grant", "thesis", "preprint", "default"],
-                       help="Document type for quality threshold (default: default)")
-    parser.add_argument("--iterations", type=int, default=2,
-                       help="Maximum refinement iterations (default: 2, max: 2)")
-    parser.add_argument("--api-key", 
-                       help="OpenRouter API key (or use OPENROUTER_API_KEY env var)")
-    parser.add_argument("-v", "--verbose", action="store_true",
-                       help="Verbose output")
-    
-    args = parser.parse_args()
-    
-    # Check for API key
-    api_key = args.api_key or os.getenv("OPENROUTER_API_KEY")
-    if not api_key:
-        print("Error: OPENROUTER_API_KEY environment variable not set")
-        print("\nFor AI generation, you need an OpenRouter API key.")
-        print("Get one at: https://openrouter.ai/keys")
-        print("\nSet it with:")
-        print("  export OPENROUTER_API_KEY='your_api_key'")
-        print("\nOr use --api-key flag")
-        sys.exit(1)
-    
-    # Find AI generation script
-    script_dir = Path(__file__).parent
-    ai_script = script_dir / "generate_schematic_ai.py"
-    
-    if not ai_script.exists():
-        print(f"Error: AI generation script not found: {ai_script}")
-        sys.exit(1)
-    
-    # Build command
-    cmd = [sys.executable, str(ai_script), args.prompt, "-o", args.output]
-    
-    if args.doc_type != "default":
-        cmd.extend(["--doc-type", args.doc_type])
-    
-    # Enforce max 2 iterations
-    iterations = min(args.iterations, 2)
-    if iterations != 2:
-        cmd.extend(["--iterations", str(iterations)])
-    
-    if args.verbose:
-        cmd.append("-v")
-    
-    # Execute — pass API key via environment to avoid exposure in process listings
-    try:
-        env = os.environ.copy()
-        if api_key:
-            env["OPENROUTER_API_KEY"] = api_key
-        result = subprocess.run(cmd, check=False, env=env)
-        sys.exit(result.returncode)
-    except Exception as e:
-        print(f"Error executing AI generation: {e}")
-        sys.exit(1)
-
-
-if __name__ == "__main__":
-    main()
-