clearai-dsh 0.1.0

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

@@ -0,0 +1,176 @@
+#!/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

@@ -0,0 +1,139 @@
+#!/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()
+