From 5b52a8dd236726213b814f6a29ebbc00675b06be Mon Sep 17 00:00:00 2001 From: Vinayak Agarwal Date: Mon, 5 Jan 2026 13:06:20 -0800 Subject: [PATCH] Remove test scripts and summary files --- .../references/IMPLEMENTATION_SUMMARY.md | 641 ------------------ .../markitdown/references/SKILL_SUMMARY.md | 307 --------- .../scripts/test_ai_generation.py | 243 ------- 3 files changed, 1191 deletions(-) delete mode 100644 scientific-skills/clinical-reports/references/IMPLEMENTATION_SUMMARY.md delete mode 100644 scientific-skills/markitdown/references/SKILL_SUMMARY.md delete mode 100644 scientific-skills/scientific-schematics/scripts/test_ai_generation.py diff --git a/scientific-skills/clinical-reports/references/IMPLEMENTATION_SUMMARY.md b/scientific-skills/clinical-reports/references/IMPLEMENTATION_SUMMARY.md deleted file mode 100644 index 1068b6b..0000000 --- a/scientific-skills/clinical-reports/references/IMPLEMENTATION_SUMMARY.md +++ /dev/null @@ -1,641 +0,0 @@ -# Clinical Reports Skill - Implementation Summary - -## ๐Ÿ“Š Overview - -Successfully implemented a comprehensive clinical reports skill for the Claude Scientific Writer project. - -**Implementation Date**: November 4, 2025 -**Total Files Created**: 30 -**Total Lines of Code/Documentation**: 11,577 -**Status**: โœ… Complete and tested - ---- - -## ๐Ÿ“‚ Structure - -``` -.claude/skills/clinical-reports/ -โ”œโ”€โ”€ README.md (Quick start guide) -โ”œโ”€โ”€ SKILL.md (Main skill definition - 1,089 lines) -โ”œโ”€โ”€ references/ (8 comprehensive guides) -โ”‚ โ”œโ”€โ”€ case_report_guidelines.md (571 lines) -โ”‚ โ”œโ”€โ”€ diagnostic_reports_standards.md (531 lines) -โ”‚ โ”œโ”€โ”€ clinical_trial_reporting.md (694 lines) -โ”‚ โ”œโ”€โ”€ patient_documentation.md (745 lines) -โ”‚ โ”œโ”€โ”€ regulatory_compliance.md (578 lines) -โ”‚ โ”œโ”€โ”€ medical_terminology.md (589 lines) -โ”‚ โ”œโ”€โ”€ data_presentation.md (531 lines) -โ”‚ โ””โ”€โ”€ peer_review_standards.md (586 lines) -โ”œโ”€โ”€ assets/ (12 professional templates) -โ”‚ โ”œโ”€โ”€ case_report_template.md (353 lines) -โ”‚ โ”œโ”€โ”€ soap_note_template.md (254 lines) -โ”‚ โ”œโ”€โ”€ history_physical_template.md (244 lines) -โ”‚ โ”œโ”€โ”€ discharge_summary_template.md (338 lines) -โ”‚ โ”œโ”€โ”€ consult_note_template.md (249 lines) -โ”‚ โ”œโ”€โ”€ radiology_report_template.md (317 lines) -โ”‚ โ”œโ”€โ”€ pathology_report_template.md (261 lines) -โ”‚ โ”œโ”€โ”€ lab_report_template.md (349 lines) -โ”‚ โ”œโ”€โ”€ clinical_trial_sae_template.md (437 lines) -โ”‚ โ”œโ”€โ”€ clinical_trial_csr_template.md (304 lines) -โ”‚ โ”œโ”€โ”€ quality_checklist.md (301 lines) -โ”‚ โ””โ”€โ”€ hipaa_compliance_checklist.md (367 lines) -โ””โ”€โ”€ scripts/ (8 validation tools) - โ”œโ”€โ”€ validate_case_report.py (198 lines) - โ”œโ”€โ”€ check_deidentification.py (250 lines) - โ”œโ”€โ”€ validate_trial_report.py (95 lines) - โ”œโ”€โ”€ format_adverse_events.py (120 lines) - โ”œโ”€โ”€ generate_report_template.py (159 lines) - โ”œโ”€โ”€ extract_clinical_data.py (97 lines) - โ”œโ”€โ”€ compliance_checker.py (88 lines) - โ””โ”€โ”€ terminology_validator.py (125 lines) -``` - ---- - -## โœ… Completed Deliverables - -### 1. Main Skill File โœ“ - -**SKILL.md** (1,089 lines) -- YAML frontmatter with name and description -- Comprehensive overview and usage guidelines -- Four major sections (case reports, diagnostic, trials, patient docs) -- CARE guidelines implementation -- ICH-E3 and CONSORT compliance -- HIPAA privacy and de-identification -- Regulatory compliance (FDA, ICH-GCP) -- Medical terminology standards -- Quality assurance principles -- Integration with other skills -- Complete workflows and checklists - -### 2. Reference Documentation โœ“ - -**8 comprehensive reference files (total 4,825 lines)** - -1. **case_report_guidelines.md** (571 lines) - - Complete CARE checklist (17 items) - - Journal-specific requirements - - De-identification best practices - - Privacy and ethics guidelines - - Literature search strategies - - Submission process - -2. **diagnostic_reports_standards.md** (531 lines) - - ACR radiology standards - - Structured reporting (BI-RADS, Lung-RADS, LI-RADS, PI-RADS) - - CAP pathology protocols - - Synoptic reporting elements - - Laboratory reporting (CLSI) - - LOINC coding - - Critical value reporting - -3. **clinical_trial_reporting.md** (694 lines) - - ICH-E3 complete structure - - CONSORT guidelines - - SAE reporting requirements - - MedDRA coding - - DSMB procedures - - Regulatory timelines - - Causality assessment methods - -4. **patient_documentation.md** (745 lines) - - SOAP note structure - - H&P comprehensive template - - Discharge summary requirements - - ROS (Review of Systems) - - Documentation standards - - Billing considerations - -5. **regulatory_compliance.md** (578 lines) - - HIPAA Privacy Rule - - 18 HIPAA identifiers - - Safe Harbor de-identification - - 21 CFR Part 11 (electronic records) - - ICH-GCP principles - - FDA regulations - - EU CTR requirements - -6. **medical_terminology.md** (589 lines) - - SNOMED-CT - - LOINC codes - - ICD-10-CM - - CPT codes - - Standard abbreviations - - "Do Not Use" list (Joint Commission) - - Anatomical terminology - - Laboratory units and conversions - - Grading/staging systems - -7. **data_presentation.md** (531 lines) - - Clinical tables design - - Demographics tables - - Adverse events tables - - CONSORT flow diagrams - - Kaplan-Meier curves - - Forest plots - - Statistical presentation - - Software recommendations - -8. **peer_review_standards.md** (586 lines) - - Review criteria for clinical manuscripts - - CARE guideline compliance - - CONSORT compliance - - STARD guidelines - - STROBE guidelines - - Statistical assessment - - Writing quality evaluation - -### 3. Professional Templates โœ“ - -**12 templates (total 3,574 lines)** - -All templates include: -- Complete structure with all required sections -- Placeholder text with examples -- Formatting guidelines -- Checklists for completeness -- Regulatory compliance notes -- Best practices - -**Templates created:** -1. Case report (CARE-compliant) -2. SOAP note (progress documentation) -3. History & Physical -4. Discharge summary -5. Consultation note -6. Radiology report -7. Pathology report (with synoptic reporting) -8. Laboratory report -9. SAE report (serious adverse event) -10. CSR outline (ICH-E3) -11. Quality checklist -12. HIPAA compliance checklist - -### 4. Validation Scripts โœ“ - -**8 Python scripts (total 1,132 lines)** - -All scripts include: -- Command-line interface -- JSON output option -- Error handling -- Help documentation -- Executable permissions set - -**Scripts created:** -1. **validate_case_report.py** - CARE compliance checker - - Validates 12+ CARE requirements - - Checks word count (1500-3500) - - Verifies references present - - Scans for HIPAA identifiers - - Generates compliance report - -2. **check_deidentification.py** - HIPAA identifier scanner - - Detects all 18 HIPAA identifiers - - Severity classification (Critical/High/Medium) - - Age compliance checking (>89 aggregation) - - Detailed violation reporting - -3. **validate_trial_report.py** - ICH-E3 structure validator - - Checks 15 ICH-E3 sections - - Calculates compliance rate - - Pass/fail determination - -4. **format_adverse_events.py** - AE table generator - - Converts CSV to formatted markdown tables - - Calculates percentages - - Grouped by treatment arm - - Publication-ready output - -5. **generate_report_template.py** - Interactive template generator - - Lists all 10 template types - - Interactive selection mode - - Command-line mode - - Automatic file copying - -6. **extract_clinical_data.py** - Data extraction tool - - Extracts vital signs - - Parses demographics - - Extracts medications - - JSON output - -7. **compliance_checker.py** - Regulatory compliance - - HIPAA compliance checks - - GCP compliance checks - - FDA compliance checks - - Pattern-based validation - -8. **terminology_validator.py** - Medical terminology validation - - "Do Not Use" abbreviation detection - - Ambiguous abbreviation flagging - - ICD-10 code detection - - Severity classification - ---- - -## ๐ŸŽฏ Key Features Implemented - -### Complete Coverage - -โœ… **Clinical Case Reports** -- CARE guidelines (all 17 checklist items) -- De-identification (18 HIPAA identifiers) -- Informed consent documentation -- Timeline creation -- Journal-specific formatting - -โœ… **Diagnostic Reports** -- Radiology (ACR standards, Lung-RADS, BI-RADS, LI-RADS, PI-RADS) -- Pathology (CAP synoptic reporting, TNM staging) -- Laboratory (LOINC coding, critical values, reference ranges) - -โœ… **Clinical Trial Reports** -- SAE reporting (7-day, 15-day timelines) -- ICH-E3 Clinical Study Reports (15 sections) -- CONSORT compliance -- MedDRA coding -- Causality assessment (WHO-UMC, Naranjo) - -โœ… **Patient Documentation** -- SOAP notes (S-O-A-P structure) -- History & Physical (13 components) -- Discharge summaries (10 required elements) -- Consultation notes - -### Regulatory Compliance - -โœ… **HIPAA** -- Safe Harbor de-identification -- 18 identifier removal -- Privacy protection -- Breach notification - -โœ… **FDA** -- 21 CFR Part 11 (electronic records) -- 21 CFR Part 50 (informed consent) -- 21 CFR Part 56 (IRB standards) -- 21 CFR Part 312 (IND regulations) - -โœ… **ICH-GCP** -- Good Clinical Practice principles -- Essential documents -- Source documentation -- Record retention - -### Medical Standards - -โœ… **Terminology** -- SNOMED-CT -- LOINC -- ICD-10-CM -- CPT codes -- RxNorm - -โœ… **Professional Organizations** -- ACR (American College of Radiology) -- CAP (College of American Pathologists) -- CLSI (Clinical Laboratory Standards Institute) -- JCAHO (Joint Commission) - ---- - -## ๐Ÿ”— Integration - -### With Existing Skills - -The clinical-reports skill integrates with: -- โœ… `scientific-writing` - Medical writing principles -- โœ… `peer-review` - Quality assessment -- โœ… `citation-management` - Literature references -- โœ… `research-grants` - Clinical trial protocols - -### MCP System - -- โœ… Skill accessible via MCP find_helpful_skills -- โœ… Compatible with existing skill structure -- โœ… Follows established patterns -- โœ… Auto-loaded by the system - ---- - -## ๐Ÿ“ Documentation Updates - -### Files Updated - -1. โœ… **README.md** - - Added clinical reports to features - - Added example command - - Added to document types table - - Updated "What's New" section - -2. โœ… **docs/SKILLS.md** - - Added Section 6: Clinical Reports (comprehensive) - - Renumbered subsequent sections (7-14) - - Added example usage for all report types - - Included all templates, references, and scripts - -3. โœ… **docs/FEATURES.md** - - Added Clinical Reports section - - Listed 4 report types - - Added key features - - Included usage examples - -4. โœ… **CHANGELOG.md** - - Added [Unreleased] section - - Documented new clinical-reports skill - - Listed all components and features - - Noted documentation updates - -5. โœ… **clinical-reports/README.md** (New) - - Quick start guide - - Template usage examples - - Script usage instructions - - Best practices - - Integration information - ---- - -## โœจ Highlights - -### Templates from Real-World Sources - -Templates based on: -- โœ… BMJ Case Reports (CARE guidelines) -- โœ… Journal of Osteopathic Medicine -- โœ… ACR radiology standards -- โœ… CAP pathology protocols -- โœ… ICH-E3 clinical study reports -- โœ… FDA guidance documents -- โœ… Academic medical centers - -### Comprehensive Reference Materials - -- 8 reference files totaling **4,825 lines** -- Covers all major standards and guidelines -- Includes practical examples throughout -- Cross-referenced between files -- Professional organization standards - -### Robust Validation Tools - -- 8 Python scripts totaling **1,132 lines** -- All executable and tested -- JSON output for automation -- Human-readable reports -- Error handling included - -### Professional Quality - -- Medical accuracy verified against standards -- Regulatory compliance built-in -- Industry-standard formatting -- Professional medical terminology -- Evidence-based best practices - ---- - -## ๐Ÿงช Testing - -### Verified - -โœ… Directory structure created correctly -โœ… All 30 files present -โœ… Scripts executable (chmod +x) -โœ… Template generator script functional -โœ… MCP skill discovery working -โœ… Integration with existing skills -โœ… Documentation updated across project - -### Script Tests - -โœ… **generate_report_template.py** - Lists all 10 template types correctly -โœ… File paths resolve properly -โœ… Python syntax valid (no import errors expected) -โœ… Command-line arguments work - ---- - -## ๐Ÿ“š Statistics - -### Content Breakdown - -| Category | Count | Lines | -|----------|-------|-------| -| Main skill file | 1 | 1,089 | -| Reference files | 8 | 4,825 | -| Template files | 12 | 3,574 | -| Python scripts | 8 | 1,132 | -| README | 1 | 197 | -| **Total** | **30** | **11,817** | - -### Reference Files Statistics - -| File | Lines | Coverage | -|------|-------|----------| -| patient_documentation.md | 745 | SOAP, H&P, discharge | -| clinical_trial_reporting.md | 694 | ICH-E3, CONSORT, SAE | -| medical_terminology.md | 589 | SNOMED, LOINC, ICD-10 | -| peer_review_standards.md | 586 | Review criteria | -| regulatory_compliance.md | 578 | HIPAA, FDA, GCP | -| case_report_guidelines.md | 571 | CARE guidelines | -| data_presentation.md | 531 | Tables, figures | -| diagnostic_reports_standards.md | 531 | ACR, CAP, CLSI | - -### Template Files Statistics - -| Template | Lines | Purpose | -|----------|-------|---------| -| clinical_trial_sae_template.md | 437 | Adverse event reporting | -| hipaa_compliance_checklist.md | 367 | Privacy verification | -| case_report_template.md | 353 | Journal case reports | -| lab_report_template.md | 349 | Laboratory results | -| discharge_summary_template.md | 338 | Hospital discharge | -| radiology_report_template.md | 317 | Imaging reports | -| clinical_trial_csr_template.md | 304 | Study reports | -| quality_checklist.md | 301 | QA for all types | -| pathology_report_template.md | 261 | Surgical pathology | -| soap_note_template.md | 254 | Progress notes | -| consult_note_template.md | 249 | Consultations | -| history_physical_template.md | 244 | H&P examination | - ---- - -## ๐Ÿš€ Usage Examples - -### Generate a Clinical Case Report - -```bash -# Interactive template generation -python scripts/generate_report_template.py -# Select: 1 (case_report) - -# Or via CLI -> Create a clinical case report for unusual presentation of acute appendicitis -``` - -### Validate Reports - -```bash -# Check CARE compliance -python scripts/validate_case_report.py my_report.md - -# Check de-identification -python scripts/check_deidentification.py my_report.md - -# Check trial report structure -python scripts/validate_trial_report.py my_csr.md -``` - -### Generate Documentation - -```bash -# SOAP note -> Create a SOAP note for follow-up diabetes visit - -# Discharge summary -> Generate discharge summary for CHF patient - -# SAE report -> Write serious adverse event report for clinical trial -``` - ---- - -## ๐Ÿ“‹ Standards Covered - -### Medical Standards -- โœ… CARE (CAse REport) guidelines -- โœ… ACR (American College of Radiology) -- โœ… CAP (College of American Pathologists) -- โœ… CLSI (Clinical Laboratory Standards Institute) -- โœ… CONSORT (clinical trial reporting) -- โœ… STARD (diagnostic accuracy) -- โœ… STROBE (observational studies) -- โœ… PRISMA (systematic reviews) - -### Regulatory Standards -- โœ… HIPAA Privacy Rule -- โœ… FDA 21 CFR Part 11 (electronic records) -- โœ… FDA 21 CFR Part 50 (informed consent) -- โœ… FDA 21 CFR Part 56 (IRB) -- โœ… FDA 21 CFR Part 312 (IND) -- โœ… ICH-E3 (clinical study reports) -- โœ… ICH-E6 (GCP) -- โœ… EU CTR 536/2014 - -### Coding Systems -- โœ… SNOMED-CT (clinical terms) -- โœ… LOINC (lab observations) -- โœ… ICD-10-CM (diagnoses) -- โœ… CPT (procedures) -- โœ… RxNorm (medications) -- โœ… MedDRA (adverse events) - ---- - -## ๐ŸŽ“ Educational Value - -### Learning Resources - -Each reference file serves as: -- Comprehensive learning material -- Quick reference guide -- Implementation checklist -- Best practices repository - -### Skill Development - -Supports development of: -- Medical writing skills -- Clinical documentation -- Regulatory knowledge -- Quality assurance -- Privacy compliance - ---- - -## ๐Ÿ”„ Next Steps - -### For Users - -1. Use the skill via CLI: `scientific-writer` -2. Generate templates: `python scripts/generate_report_template.py` -3. Validate reports before submission -4. Follow CARE/ICH-E3/HIPAA guidelines - -### For Developers - -1. Skill is ready for use in production -2. Scripts can be extended with additional features -3. Templates can be customized for specific institutions -4. Reference files can be updated as standards evolve - -### Future Enhancements (Optional) - -- [ ] Add institutional-specific templates -- [ ] Integrate with EHR systems -- [ ] Add more validation rules -- [ ] Create web-based template generator -- [ ] Add support for additional languages -- [ ] Integrate with medical terminology APIs - ---- - -## โœ… Quality Assurance - -### Code Quality -โœ… Python scripts follow PEP 8 style -โœ… Comprehensive error handling -โœ… Command-line argument parsing -โœ… JSON output for automation -โœ… Human-readable reports -โœ… Executable permissions set - -### Documentation Quality -โœ… Clear structure and organization -โœ… Comprehensive coverage -โœ… Real-world examples -โœ… Professional medical terminology -โœ… Cross-referenced between files -โœ… Consistent formatting - -### Template Quality -โœ… Based on professional standards -โœ… Complete with all required elements -โœ… Placeholder text with examples -โœ… Checklists included -โœ… Regulatory notes -โœ… Best practices documented - ---- - -## ๐Ÿ“– Documentation Summary - -| Document | Status | Content | -|----------|--------|---------| -| README.md (main) | โœ… Updated | Added clinical reports to features and examples | -| docs/SKILLS.md | โœ… Updated | Added Section 6 with full documentation | -| docs/FEATURES.md | โœ… Updated | Added clinical reports section with examples | -| CHANGELOG.md | โœ… Updated | Added [Unreleased] section documenting new skill | -| clinical-reports/README.md | โœ… Created | Quick start guide for the skill | -| clinical-reports/SKILL.md | โœ… Created | Main skill definition (1,089 lines) | - ---- - -## ๐ŸŽ‰ Success Metrics - -- โœ… 100% of planned deliverables completed -- โœ… All templates based on real-world standards -- โœ… Comprehensive regulatory compliance coverage -- โœ… Fully functional validation tools -- โœ… Complete integration with existing skills -- โœ… Professional-quality documentation -- โœ… Ready for immediate use - ---- - -**Implementation completed successfully on November 4, 2025** - -The clinical-reports skill is now fully integrated into the Claude Scientific Writer project and ready for use! - diff --git a/scientific-skills/markitdown/references/SKILL_SUMMARY.md b/scientific-skills/markitdown/references/SKILL_SUMMARY.md deleted file mode 100644 index 33612d3..0000000 --- a/scientific-skills/markitdown/references/SKILL_SUMMARY.md +++ /dev/null @@ -1,307 +0,0 @@ -# MarkItDown Skill - Creation Summary - -## Overview - -A comprehensive skill for using Microsoft's MarkItDown tool has been created for the Claude Scientific Writer. This skill enables conversion of 15+ file formats to Markdown, optimized for LLM processing and scientific workflows. - -## What Was Created - -### Core Documentation - -1. **SKILL.md** (Main skill file) - - Complete guide to MarkItDown - - Quick start examples - - All supported formats - - Advanced features (AI, Azure DI) - - Best practices - - Use cases and examples - -2. **README.md** - - Skill overview - - Key features - - Quick reference - - Integration guide - -3. **QUICK_REFERENCE.md** - - Cheat sheet for common tasks - - Quick syntax reference - - Common commands - - Troubleshooting tips - -4. **INSTALLATION_GUIDE.md** - - Step-by-step installation - - System dependencies - - Virtual environment setup - - Optional features - - Troubleshooting - -### Reference Documentation - -Located in `references/`: - -1. **api_reference.md** - - Complete API documentation - - Class and method references - - Custom converter development - - Plugin system - - Error handling - - Breaking changes guide - -2. **file_formats.md** - - Detailed format-specific guides - - 15+ supported formats - - Format capabilities and limitations - - Best practices per format - - Example outputs - -### Utility Scripts - -Located in `scripts/`: - -1. **batch_convert.py** - - Parallel batch conversion - - Multi-format support - - Recursive directory search - - Progress tracking - - Error reporting - - Command-line interface - -2. **convert_with_ai.py** - - AI-enhanced conversions - - Predefined prompt types (scientific, medical, data viz, etc.) - - Custom prompt support - - Multiple model support - - OpenRouter integration (advanced vision models) - -3. **convert_literature.py** - - Scientific literature conversion - - Metadata extraction from filenames - - Year-based organization - - Automatic index generation - - JSON catalog creation - - Front matter support - -### Assets - -Located in `assets/`: - -1. **example_usage.md** - - 20+ practical examples - - Basic conversions - - Scientific workflows - - AI-enhanced processing - - Batch operations - - Error handling patterns - - Integration examples - -### License - -- **LICENSE.txt** - MIT License from Microsoft - -## Skill Structure - -``` -.claude/skills/markitdown/ -โ”œโ”€โ”€ SKILL.md # Main skill documentation -โ”œโ”€โ”€ README.md # Skill overview -โ”œโ”€โ”€ QUICK_REFERENCE.md # Quick reference guide -โ”œโ”€โ”€ INSTALLATION_GUIDE.md # Installation instructions -โ”œโ”€โ”€ SKILL_SUMMARY.md # This file -โ”œโ”€โ”€ LICENSE.txt # MIT License -โ”œโ”€โ”€ references/ -โ”‚ โ”œโ”€โ”€ api_reference.md # Complete API docs -โ”‚ โ””โ”€โ”€ file_formats.md # Format-specific guides -โ”œโ”€โ”€ scripts/ -โ”‚ โ”œโ”€โ”€ batch_convert.py # Batch conversion utility -โ”‚ โ”œโ”€โ”€ convert_with_ai.py # AI-enhanced conversion -โ”‚ โ””โ”€โ”€ convert_literature.py # Literature conversion -โ””โ”€โ”€ assets/ - โ””โ”€โ”€ example_usage.md # Practical examples -``` - -## Capabilities - -### File Format Support - -- **Documents**: PDF, DOCX, PPTX, XLSX, XLS, EPUB -- **Images**: JPEG, PNG, GIF, WebP (with OCR) -- **Audio**: WAV, MP3 (with transcription) -- **Web**: HTML, YouTube URLs -- **Data**: CSV, JSON, XML -- **Archives**: ZIP files -- **Email**: Outlook MSG files - -### Advanced Features - -1. **AI Enhancement via OpenRouter** - - Access to 100+ AI models through OpenRouter - - Multiple preset prompts (scientific, medical, data viz) - - Custom prompt support - - Default: Advanced vision model (best for scientific vision) - - Choose best model for each task - -2. **Azure Integration** - - Azure Document Intelligence for complex PDFs - - Enhanced layout understanding - - Better table extraction - -3. **Batch Processing** - - Parallel conversion with configurable workers - - Recursive directory processing - - Progress tracking and error reporting - - Format-specific organization - -4. **Scientific Workflows** - - Literature conversion with metadata - - Automatic index generation - - Year-based organization - - Citation-friendly output - -## Integration with Scientific Writer - -The skill has been added to the Scientific Writer's skill catalog: - -- **Location**: `.claude/skills/markitdown/` -- **Skill Number**: #5 in Document Manipulation Skills -- **SKILLS.md**: Updated with complete skill description - -### Usage Examples - -``` -> Convert all PDFs in the literature folder to Markdown -> Convert this PowerPoint presentation to Markdown with AI-generated descriptions -> Extract tables from this Excel file -> Transcribe this lecture recording -``` - -## Scripts Usage - -### Batch Convert -```bash -python scripts/batch_convert.py input_dir/ output_dir/ --extensions .pdf .docx --workers 4 -``` - -### AI-Enhanced Convert -```bash -export OPENROUTER_API_KEY="sk-or-v1-..." -python scripts/convert_with_ai.py paper.pdf output.md \ - --model anthropic/claude-sonnet-4.5 \ - --prompt-type scientific -``` - -### Literature Convert -```bash -python scripts/convert_literature.py papers/ markdown/ --organize-by-year --create-index -``` - -## Key Features - -1. **Token-Efficient Output**: Markdown optimized for LLM processing -2. **Comprehensive Format Support**: 15+ file types -3. **AI Enhancement**: Detailed image descriptions via OpenAI -4. **OCR Support**: Extract text from scanned documents -5. **Audio Transcription**: Speech-to-text for audio files -6. **YouTube Support**: Video transcript extraction -7. **Plugin System**: Extensible architecture -8. **Batch Processing**: Efficient parallel conversion -9. **Error Handling**: Robust error management -10. **Scientific Focus**: Optimized for research workflows - -## Installation - -```bash -# Full installation -pip install 'markitdown[all]' - -# Selective installation -pip install 'markitdown[pdf,docx,pptx,xlsx]' -``` - -## Quick Start - -```python -from markitdown import MarkItDown - -# Basic usage -md = MarkItDown() -result = md.convert("document.pdf") -print(result.text_content) - -# With AI via OpenRouter -from openai import OpenAI -client = OpenAI( - api_key="your-openrouter-api-key", - base_url="https://openrouter.ai/api/v1" -) -md = MarkItDown( - llm_client=client, - llm_model="anthropic/claude-sonnet-4.5" # or openai/gpt-4o -) -result = md.convert("presentation.pptx") -``` - -## Documentation Files - -| File | Purpose | Lines | -|------|---------|-------| -| SKILL.md | Main documentation | 400+ | -| api_reference.md | API documentation | 500+ | -| file_formats.md | Format guides | 600+ | -| example_usage.md | Practical examples | 500+ | -| batch_convert.py | Batch conversion | 200+ | -| convert_with_ai.py | AI conversion | 200+ | -| convert_literature.py | Literature conversion | 250+ | -| QUICK_REFERENCE.md | Quick reference | 300+ | -| INSTALLATION_GUIDE.md | Installation guide | 300+ | - -**Total**: ~3,000+ lines of documentation and code - -## Use Cases - -1. **Literature Review**: Convert research papers to Markdown for analysis -2. **Data Extraction**: Extract tables from Excel/PDF for processing -3. **Presentation Processing**: Convert slides with AI descriptions -4. **Document Analysis**: Prepare documents for LLM consumption -5. **Lecture Transcription**: Convert audio recordings to text -6. **YouTube Analysis**: Extract video transcripts -7. **Archive Processing**: Batch convert document collections - -## Next Steps - -1. Install MarkItDown: `pip install 'markitdown[all]'` -2. Read `QUICK_REFERENCE.md` for common tasks -3. Try example scripts in `scripts/` directory -4. Explore `SKILL.md` for comprehensive guide -5. Check `example_usage.md` for practical examples - -## Resources - -- **MarkItDown GitHub**: https://github.com/microsoft/markitdown -- **PyPI**: https://pypi.org/project/markitdown/ -- **OpenRouter**: https://openrouter.ai (AI model access) -- **OpenRouter API Keys**: https://openrouter.ai/keys -- **OpenRouter Models**: https://openrouter.ai/models -- **License**: MIT (Microsoft Corporation) -- **Python**: 3.10+ required -- **Skill Location**: `.claude/skills/markitdown/` - -## Success Criteria - -โœ… Comprehensive skill documentation created -โœ… Complete API reference provided -โœ… Format-specific guides included -โœ… Utility scripts implemented -โœ… Practical examples documented -โœ… Installation guide created -โœ… Quick reference guide added -โœ… Integration with Scientific Writer complete -โœ… SKILLS.md updated -โœ… Scripts made executable -โœ… MIT License included - -## Skill Status - -**Status**: โœ… Complete and Ready to Use - -The MarkItDown skill is fully integrated into the Claude Scientific Writer and ready for use. All documentation, scripts, and examples are in place. - diff --git a/scientific-skills/scientific-schematics/scripts/test_ai_generation.py b/scientific-skills/scientific-schematics/scripts/test_ai_generation.py deleted file mode 100644 index 0c4db82..0000000 --- a/scientific-skills/scientific-schematics/scripts/test_ai_generation.py +++ /dev/null @@ -1,243 +0,0 @@ -#!/usr/bin/env python3 -""" -Test script to verify AI generation implementation. - -This script performs dry-run tests without making actual API calls. -It verifies: -1. Script structure and imports -2. Class initialization -3. Method signatures -4. Error handling -5. Command-line interface - -Usage: - python test_ai_generation.py -""" - -import sys -import os -from pathlib import Path - -# Add scripts directory to path -scripts_dir = Path(__file__).parent / "scripts" -sys.path.insert(0, str(scripts_dir)) - -def test_imports(): - """Test that all required modules can be imported.""" - print("Testing imports...") - try: - from generate_schematic_ai import ScientificSchematicGenerator - print("โœ“ generate_schematic_ai imports successfully") - return True - except ImportError as e: - print(f"โœ— Import failed: {e}") - return False - -def test_class_structure(): - """Test class initialization and structure.""" - print("\nTesting class structure...") - try: - from generate_schematic_ai import ScientificSchematicGenerator - - # Test initialization with dummy key - generator = ScientificSchematicGenerator(api_key="test_key", verbose=False) - print("โœ“ Class initializes successfully") - - # Check required methods exist - required_methods = [ - 'generate_image', - 'review_image', - 'improve_prompt', - 'generate_iterative' - ] - - for method in required_methods: - if not hasattr(generator, method): - print(f"โœ— Missing method: {method}") - return False - print(f"โœ“ Method exists: {method}") - - # Check attributes - if not hasattr(generator, 'api_key'): - print("โœ— Missing attribute: api_key") - return False - print("โœ“ Attribute exists: api_key") - - if not hasattr(generator, 'image_model'): - print("โœ— Missing attribute: image_model") - return False - print(f"โœ“ Image model: {generator.image_model}") - - if not hasattr(generator, 'review_model'): - print("โœ— Missing attribute: review_model") - return False - print(f"โœ“ Review model: {generator.review_model}") - - return True - except Exception as e: - print(f"โœ— Class structure test failed: {e}") - return False - -def test_error_handling(): - """Test error handling for missing API key.""" - print("\nTesting error handling...") - try: - from generate_schematic_ai import ScientificSchematicGenerator - - # Clear environment variable - old_key = os.environ.get("OPENROUTER_API_KEY") - if old_key: - del os.environ["OPENROUTER_API_KEY"] - - # Try to initialize without key - try: - generator = ScientificSchematicGenerator() - print("โœ— Should have raised ValueError for missing API key") - return False - except ValueError as e: - if "OPENROUTER_API_KEY" in str(e): - print("โœ“ Correctly raises ValueError for missing API key") - else: - print(f"โœ— Wrong error message: {e}") - return False - - # Restore environment variable - if old_key: - os.environ["OPENROUTER_API_KEY"] = old_key - - return True - except Exception as e: - print(f"โœ— Error handling test failed: {e}") - return False - -def test_wrapper_script(): - """Test wrapper script structure.""" - print("\nTesting wrapper script...") - try: - import generate_schematic - print("โœ“ generate_schematic imports successfully") - - # Check main functions exist - if not hasattr(generate_schematic, 'main'): - print("โœ— Missing function: main") - return False - print("โœ“ Function exists: main") - - return True - except Exception as e: - print(f"โœ— Wrapper script test failed: {e}") - return False - -def test_prompt_engineering(): - """Test prompt construction.""" - print("\nTesting prompt engineering...") - try: - from generate_schematic_ai import ScientificSchematicGenerator - - generator = ScientificSchematicGenerator(api_key="test_key", verbose=False) - - # Test improve_prompt method - original = "Create a flowchart" - critique = "Add more spacing between boxes" - improved = generator.improve_prompt(original, critique, 2) - - if not improved: - print("โœ— improve_prompt returned empty string") - return False - - if original not in improved: - print("โœ— Improved prompt doesn't include original") - return False - - if critique not in improved: - print("โœ— Improved prompt doesn't include critique") - return False - - if "ITERATION 2" not in improved: - print("โœ— Improved prompt doesn't include iteration number") - return False - - print("โœ“ Prompt engineering works correctly") - print(f" Original length: {len(original)} chars") - print(f" Improved length: {len(improved)} chars") - - return True - except Exception as e: - print(f"โœ— Prompt engineering test failed: {e}") - return False - -def test_file_paths(): - """Test that all required files exist.""" - print("\nTesting file structure...") - - base_dir = Path(__file__).parent - required_files = [ - "scripts/generate_schematic_ai.py", - "scripts/generate_schematic.py", - "SKILL.md", - "README.md" - ] - - all_exist = True - for file_path in required_files: - full_path = base_dir / file_path - if full_path.exists(): - print(f"โœ“ {file_path}") - else: - print(f"โœ— Missing: {file_path}") - all_exist = False - - return all_exist - -def main(): - """Run all tests.""" - print("="*60) - print("Scientific Schematics AI Generation - Verification Tests") - print("="*60) - - tests = [ - ("File Structure", test_file_paths), - ("Imports", test_imports), - ("Class Structure", test_class_structure), - ("Error Handling", test_error_handling), - ("Wrapper Script", test_wrapper_script), - ("Prompt Engineering", test_prompt_engineering), - ] - - results = [] - for test_name, test_func in tests: - try: - result = test_func() - results.append((test_name, result)) - except Exception as e: - print(f"\nโœ— Test '{test_name}' crashed: {e}") - results.append((test_name, False)) - - # Summary - print("\n" + "="*60) - print("Test Summary") - print("="*60) - - passed = sum(1 for _, result in results if result) - total = len(results) - - for test_name, result in results: - status = "โœ“ PASS" if result else "โœ— FAIL" - print(f"{status}: {test_name}") - - print(f"\nTotal: {passed}/{total} tests passed") - - if passed == total: - print("\nโœ“ All tests passed! Implementation verified.") - print("\nNext steps:") - print("1. Set OPENROUTER_API_KEY environment variable") - print("2. Test with actual API call:") - print(" python scripts/generate_schematic.py 'test diagram' -o test.png") - return 0 - else: - print(f"\nโœ— {total - passed} test(s) failed. Please review errors above.") - return 1 - -if __name__ == "__main__": - sys.exit(main()) -