scientific-writer 2.2.1__py3-none-any.whl → 2.2.3__py3-none-any.whl

scientific_writer/.claude/skills/markitdown/assets/example_usage.md

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+# MarkItDown Example Usage
+
+This document provides practical examples of using MarkItDown in various scenarios.
+
+## Basic Examples
+
+### 1. Simple File Conversion
+
+```python
+from markitdown import MarkItDown
+
+md = MarkItDown()
+
+# Convert a PDF
+result = md.convert("research_paper.pdf")
+print(result.text_content)
+
+# Convert a Word document
+result = md.convert("manuscript.docx")
+print(result.text_content)
+
+# Convert a PowerPoint
+result = md.convert("presentation.pptx")
+print(result.text_content)
+```
+
+### 2. Save to File
+
+```python
+from markitdown import MarkItDown
+
+md = MarkItDown()
+result = md.convert("document.pdf")
+
+with open("output.md", "w", encoding="utf-8") as f:
+    f.write(result.text_content)
+```
+
+### 3. Convert from Stream
+
+```python
+from markitdown import MarkItDown
+
+md = MarkItDown()
+
+with open("document.pdf", "rb") as f:
+    result = md.convert_stream(f, file_extension=".pdf")
+    print(result.text_content)
+```
+
+## Scientific Workflows
+
+### Convert Research Papers
+
+```python
+from markitdown import MarkItDown
+from pathlib import Path
+
+md = MarkItDown()
+
+# Convert all papers in a directory
+papers_dir = Path("research_papers/")
+output_dir = Path("markdown_papers/")
+output_dir.mkdir(exist_ok=True)
+
+for paper in papers_dir.glob("*.pdf"):
+    result = md.convert(str(paper))
+    
+    # Save with original filename
+    output_file = output_dir / f"{paper.stem}.md"
+    output_file.write_text(result.text_content)
+    
+    print(f"Converted: {paper.name}")
+```
+
+### Extract Tables from Excel
+
+```python
+from markitdown import MarkItDown
+
+md = MarkItDown()
+
+# Convert Excel to Markdown tables
+result = md.convert("experimental_data.xlsx")
+
+# The result contains Markdown-formatted tables
+print(result.text_content)
+
+# Save for further processing
+with open("data_tables.md", "w") as f:
+    f.write(result.text_content)
+```
+
+### Process Presentation Slides
+
+```python
+from markitdown import MarkItDown
+from openai import OpenAI
+
+# With AI descriptions for images
+client = OpenAI()
+md = MarkItDown(
+    llm_client=client,
+    llm_model="anthropic/claude-sonnet-4.5",
+    llm_prompt="Describe this scientific slide, focusing on data and key findings"
+)
+
+result = md.convert("conference_talk.pptx")
+
+# Save with metadata
+output = f"""# Conference Talk
+
+{result.text_content}
+"""
+
+with open("talk_notes.md", "w") as f:
+    f.write(output)
+```
+
+## AI-Enhanced Conversions
+
+### Detailed Image Descriptions
+
+```python
+from markitdown import MarkItDown
+from openai import OpenAI
+
+# Initialize OpenRouter client
+client = OpenAI(
+    api_key="your-openrouter-api-key",
+    base_url="https://openrouter.ai/api/v1"
+)
+
+# Scientific diagram analysis
+scientific_prompt = """
+Analyze this scientific figure. Describe:
+- Type of visualization (graph, microscopy, diagram, etc.)
+- Key data points and trends
+- Axes, labels, and legends
+- Scientific significance
+Be technical and precise.
+"""
+
+md = MarkItDown(
+    llm_client=client,
+    llm_model="anthropic/claude-sonnet-4.5",  # recommended for scientific vision
+    llm_prompt=scientific_prompt
+)
+
+# Convert paper with figures
+result = md.convert("paper_with_figures.pdf")
+print(result.text_content)
+```
+
+### Different Prompts for Different Files
+
+```python
+from markitdown import MarkItDown
+from openai import OpenAI
+
+# Initialize OpenRouter client
+client = OpenAI(
+    api_key="your-openrouter-api-key",
+    base_url="https://openrouter.ai/api/v1"
+)
+
+# Scientific papers - use Claude for technical analysis
+scientific_md = MarkItDown(
+    llm_client=client,
+    llm_model="anthropic/claude-sonnet-4.5",
+    llm_prompt="Describe scientific figures with technical precision"
+)
+
+# Presentations - use GPT-4o for visual understanding
+presentation_md = MarkItDown(
+    llm_client=client,
+    llm_model="anthropic/claude-sonnet-4.5",
+    llm_prompt="Summarize slide content and key visual elements"
+)
+
+# Use appropriate instance for each file
+paper_result = scientific_md.convert("research.pdf")
+slides_result = presentation_md.convert("talk.pptx")
+```
+
+## Batch Processing
+
+### Process Multiple Files
+
+```python
+from markitdown import MarkItDown
+from pathlib import Path
+
+md = MarkItDown()
+
+files_to_convert = [
+    "paper1.pdf",
+    "data.xlsx",
+    "presentation.pptx",
+    "notes.docx"
+]
+
+for file in files_to_convert:
+    try:
+        result = md.convert(file)
+        output = Path(file).stem + ".md"
+        
+        with open(output, "w") as f:
+            f.write(result.text_content)
+        
+        print(f"✓ {file} -> {output}")
+    except Exception as e:
+        print(f"✗ Error converting {file}: {e}")
+```
+
+### Parallel Processing
+
+```python
+from markitdown import MarkItDown
+from pathlib import Path
+from concurrent.futures import ThreadPoolExecutor
+
+def convert_file(filepath):
+    md = MarkItDown()
+    result = md.convert(filepath)
+    
+    output = Path(filepath).stem + ".md"
+    with open(output, "w") as f:
+        f.write(result.text_content)
+    
+    return filepath, output
+
+files = list(Path("documents/").glob("*.pdf"))
+
+with ThreadPoolExecutor(max_workers=4) as executor:
+    results = executor.map(convert_file, [str(f) for f in files])
+    
+    for input_file, output_file in results:
+        print(f"Converted: {input_file} -> {output_file}")
+```
+
+## Integration Examples
+
+### Literature Review Pipeline
+
+```python
+from markitdown import MarkItDown
+from pathlib import Path
+import json
+
+md = MarkItDown()
+
+# Convert papers and create metadata
+papers_dir = Path("literature/")
+output_dir = Path("literature_markdown/")
+output_dir.mkdir(exist_ok=True)
+
+catalog = []
+
+for paper in papers_dir.glob("*.pdf"):
+    result = md.convert(str(paper))
+    
+    # Save Markdown
+    md_file = output_dir / f"{paper.stem}.md"
+    md_file.write_text(result.text_content)
+    
+    # Store metadata
+    catalog.append({
+        "title": result.title or paper.stem,
+        "source": paper.name,
+        "markdown": str(md_file),
+        "word_count": len(result.text_content.split())
+    })
+
+# Save catalog
+with open(output_dir / "catalog.json", "w") as f:
+    json.dump(catalog, f, indent=2)
+```
+
+### Data Extraction Pipeline
+
+```python
+from markitdown import MarkItDown
+import re
+
+md = MarkItDown()
+
+# Convert Excel data to Markdown
+result = md.convert("experimental_results.xlsx")
+
+# Extract tables (Markdown tables start with |)
+tables = []
+current_table = []
+in_table = False
+
+for line in result.text_content.split('\n'):
+    if line.strip().startswith('|'):
+        in_table = True
+        current_table.append(line)
+    elif in_table:
+        if current_table:
+            tables.append('\n'.join(current_table))
+            current_table = []
+        in_table = False
+
+# Process each table
+for i, table in enumerate(tables):
+    print(f"Table {i+1}:")
+    print(table)
+    print("\n" + "="*50 + "\n")
+```
+
+### YouTube Transcript Analysis
+
+```python
+from markitdown import MarkItDown
+
+md = MarkItDown()
+
+# Get transcript
+video_url = "https://www.youtube.com/watch?v=VIDEO_ID"
+result = md.convert(video_url)
+
+# Save transcript
+with open("lecture_transcript.md", "w") as f:
+    f.write(f"# Lecture Transcript\n\n")
+    f.write(f"**Source**: {video_url}\n\n")
+    f.write(result.text_content)
+```
+
+## Error Handling
+
+### Robust Conversion
+
+```python
+from markitdown import MarkItDown
+from pathlib import Path
+import logging
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+md = MarkItDown()
+
+def safe_convert(filepath):
+    """Convert file with error handling."""
+    try:
+        result = md.convert(filepath)
+        output = Path(filepath).stem + ".md"
+        
+        with open(output, "w") as f:
+            f.write(result.text_content)
+        
+        logger.info(f"Successfully converted {filepath}")
+        return True
+    
+    except FileNotFoundError:
+        logger.error(f"File not found: {filepath}")
+        return False
+    
+    except ValueError as e:
+        logger.error(f"Invalid file format for {filepath}: {e}")
+        return False
+    
+    except Exception as e:
+        logger.error(f"Unexpected error converting {filepath}: {e}")
+        return False
+
+# Use it
+files = ["paper.pdf", "data.xlsx", "slides.pptx"]
+results = [safe_convert(f) for f in files]
+
+print(f"Successfully converted {sum(results)}/{len(files)} files")
+```
+
+## Advanced Use Cases
+
+### Custom Metadata Extraction
+
+```python
+from markitdown import MarkItDown
+import re
+from datetime import datetime
+
+md = MarkItDown()
+
+def convert_with_metadata(filepath):
+    result = md.convert(filepath)
+    
+    # Extract metadata from content
+    metadata = {
+        "file": filepath,
+        "title": result.title,
+        "converted_at": datetime.now().isoformat(),
+        "word_count": len(result.text_content.split()),
+        "char_count": len(result.text_content)
+    }
+    
+    # Try to find author
+    author_match = re.search(r'(?:Author|By):\s*(.+?)(?:\n|$)', result.text_content)
+    if author_match:
+        metadata["author"] = author_match.group(1).strip()
+    
+    # Create formatted output
+    output = f"""---
+title: {metadata['title']}
+author: {metadata.get('author', 'Unknown')}
+source: {metadata['file']}
+converted: {metadata['converted_at']}
+words: {metadata['word_count']}
+---
+
+{result.text_content}
+"""
+    
+    return output, metadata
+
+# Use it
+content, meta = convert_with_metadata("paper.pdf")
+print(meta)
+```
+
+### Format-Specific Processing
+
+```python
+from markitdown import MarkItDown
+from pathlib import Path
+
+md = MarkItDown()
+
+def process_by_format(filepath):
+    path = Path(filepath)
+    result = md.convert(filepath)
+    
+    if path.suffix == '.pdf':
+        # Add PDF-specific metadata
+        output = f"# PDF Document: {path.stem}\n\n"
+        output += result.text_content
+    
+    elif path.suffix == '.xlsx':
+        # Add table count
+        table_count = result.text_content.count('|---')
+        output = f"# Excel Data: {path.stem}\n\n"
+        output += f"**Tables**: {table_count}\n\n"
+        output += result.text_content
+    
+    elif path.suffix == '.pptx':
+        # Add slide count
+        slide_count = result.text_content.count('## Slide')
+        output = f"# Presentation: {path.stem}\n\n"
+        output += f"**Slides**: {slide_count}\n\n"
+        output += result.text_content
+    
+    else:
+        output = result.text_content
+    
+    return output
+
+# Use it
+content = process_by_format("presentation.pptx")
+print(content)
+```
+