academic-document-checker 0.4.1b1__tar.gz

academic_document_checker-0.4.1b1/LICENSE

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+MIT License
+
+Copyright (c) 2024 Academic Document Checker Team
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

academic_document_checker-0.4.1b1/MANIFEST.in

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+include README.md
+include LICENSE
+include requirements.txt
+include requirements-dev.txt
+recursive-include src/doc_checker/profiles *.yaml
+recursive-include templates *.html
+recursive-include config *.yaml

academic_document_checker-0.4.1b1/PKG-INFO

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+Metadata-Version: 2.4
+Name: academic-document-checker
+Version: 0.4.1b1
+Summary: Rule-based academic document checker with optional AI enhancement (coming in v1.5+)
+Author: Academic Document Checker Team
+License: MIT
+Project-URL: Homepage, https://github.com/darmsc/Academic_Document_Checker
+Project-URL: Documentation, https://github.com/darmsc/Academic_Document_Checker#readme
+Project-URL: Repository, https://github.com/darmsc/Academic_Document_Checker
+Project-URL: Issues, https://github.com/darmsc/Academic_Document_Checker/issues
+Keywords: academic,document,checker,thesis,medical,journal,validation
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Education
+Classifier: Topic :: Text Processing :: Linguistic
+Classifier: Topic :: Scientific/Engineering
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click>=8.0
+Requires-Dist: python-docx>=0.8.11
+Requires-Dist: PyYAML>=6.0
+Requires-Dist: rich>=13.0
+Requires-Dist: jinja2>=3.1
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: pytest-benchmark>=4.0; extra == "dev"
+Requires-Dist: pytest-mock>=3.10; extra == "dev"
+Requires-Dist: black>=23.0; extra == "dev"
+Requires-Dist: flake8>=6.0; extra == "dev"
+Requires-Dist: mypy>=1.0; extra == "dev"
+Provides-Extra: ai
+Requires-Dist: openai>=1.0; extra == "ai"
+Requires-Dist: anthropic>=0.20; extra == "ai"
+Provides-Extra: medical
+Requires-Dist: language-tool-python>=2.7; extra == "medical"
+Requires-Dist: pyspellchecker>=0.7.0; extra == "medical"
+Provides-Extra: all
+Requires-Dist: academic-document-checker[ai,dev,medical]; extra == "all"
+Dynamic: license-file
+
+# Academic Document Checker
+
+> A Python CLI tool that automatically validates academic documents (Word, PDF, and more) with profile-based checking for PhD theses, medical journals, and more.
+
+## What Does It Do?
+
+The Academic Document Checker analyzes your Word documents and provides comprehensive feedback on:
+
+- ✅ **Structure** - Required sections, heading hierarchy, organization
+- ✅ **Formatting** - Word counts, figure limits, citation style
+- ✅ **Citations** - Format validation, orphaned references, completeness
+- ✅ **Grammar** - Academic tone, passive voice, sentence complexity
+- ✅ **Style** - Writing quality, clarity, domain-specific requirements
+
+## Why Use This Tool?
+
+### For PhD Students
+- Ensure your thesis meets institutional requirements before submission
+- Catch structural and formatting issues early
+- Validate citation completeness and consistency
+- Get feedback on academic writing style
+
+### For Medical Researchers
+- Check compliance with journal-specific guidelines (Lancet, NEJM, BMJ)
+- Validate CONSORT/STROBE/PRISMA checklist items
+- Ensure proper medical terminology usage
+- Meet strict word and reference limits
+
+### For Academic Supervisors
+- Standardize quality expectations across students
+- Quickly identify common issues in student work
+- Provide consistent, objective feedback
+- Save time on structural reviews
+
+## Quick Start
+
+### Installation
+
+```bash
+pip install academic-document-checker
+```
+
+### Basic Usage
+
+```bash
+# Check a PhD thesis
+doc-checker check thesis.docx --profile phd-thesis
+
+# Check a medical journal manuscript
+doc-checker check manuscript.docx --profile lancet
+
+# Generate HTML report
+doc-checker check thesis.docx --profile phd-thesis --format html --output report.html
+```
+
+### Example Output
+
+```
+📄 Checking: thesis.docx
+📋 Profile: PhD Thesis
+
+Structure Analysis:
+  ✓ All required sections present
+  ❌ Missing: "List of Abbreviations"
+  ⚠️  Section order: "Discussion" should come before "Conclusion"
+
+Formatting:
+  ✓ Abstract: 287 words (limit: 500)
+  ❌ Total words: 38,450 (minimum: 40,000)
+  ✓ References: 67 (minimum: 50)
+
+Citations:
+  ⚠️  3 citations not found in references
+  ⚠️  5 references never cited in text
+  ✓ Citation format is consistent (APA)
+
+Grammar & Style:
+  ⚠️  Passive voice: 28% (recommended: <25%)
+  ⚠️  12 sentences exceed 40 words
+  💡 Consider more active voice in Discussion section
+
+Summary: 2 errors, 7 warnings, 1 suggestion
+```
+
+## Profile System
+
+The tool uses **profiles** to adapt checking rules for different document types:
+
+### Available Profiles
+
+| Profile | Best For | Key Features |
+|---------|----------|--------------|
+| **generic** | General academic papers | Basic structure, flexible formatting |
+| **phd-thesis** | Doctoral dissertations | 15+ required sections, 40k+ words, comprehensive |
+| **medical-journal** | Medical research papers | IMRAD structure, clinical guidelines, medical terms |
+| **lancet** | The Lancet submissions | 3000 word limit, 30 references, strict formatting |
+| **nejm** | NEJM submissions | 2700 word limit, 40 references, NEJM style |
+| **bmj** | BMJ submissions | 4000 word limit, patient involvement, BMJ boxes |
+| **grant-proposal** | Generic grant applications | Aims, budget, significance, innovation sections |
+| **nih** | NIH grant applications | NIH-specific sections, page limits, review criteria |
+| **nsf** | NSF grant applications | Broader impacts, intellectual merit requirements |
+
+### Profile Inheritance
+
+Profiles build on each other to avoid duplication:
+
+```
+Generic Publication
+├── PhD Thesis
+├── Medical Journal
+│   ├── The Lancet
+│   ├── NEJM
+│   ├── BMJ
+│   └── Custom Journals...
+└── Grant Proposal
+    ├── NIH
+    ├── NSF
+    └── Custom Grants...
+```
+
+## Features
+
+### 1. Multi-Format Support
+Works with Word documents (.docx), plain text (.txt), and Markdown (.md) out of the box.
+PDF and LaTeX support is planned for a future release.
+
+```bash
+# Word document
+doc-checker check thesis.docx --profile phd-thesis
+
+# Markdown
+doc-checker check thesis.md --profile phd-thesis
+
+# Plain text
+doc-checker check thesis.txt --profile phd-thesis
+
+# Future formats (planned)
+doc-checker check thesis.pdf --profile phd-thesis
+```
+
+### 2. Multi-Profile Support
+Choose the right profile for your document type. Each profile has specific requirements and validation rules.
+
+```bash
+doc-checker profiles --list
+doc-checker check document.docx --profile phd-thesis
+```
+
+### 3. Comprehensive Checking
+- **Structure**: Required sections, heading hierarchy, numbering
+- **Formatting**: Word limits, figure counts, spacing requirements
+- **Citations**: Format detection, completeness, consistency
+- **Grammar**: Academic tone, passive voice, sentence length
+- **Style**: Writing quality, clarity, domain-specific standards
+
+### 4. Multiple Output Formats
+```bash
+# Terminal output (default)
+doc-checker check thesis.docx --profile phd-thesis
+
+# HTML report
+doc-checker check thesis.docx --profile phd-thesis --format html --output report.html
+
+# JSON output (for automation)
+doc-checker check thesis.docx --profile phd-thesis --format json --output results.json
+```
+
+### 5. Custom Profiles
+Create profiles for your institution or specific needs:
+
+```bash
+# Create new profile
+doc-checker profile create my-university --extends phd-thesis
+
+# Validate custom profile
+doc-checker profile validate my-profile.yaml
+```
+
+### 6. AI Enhancement (Roadmap)
+
+⚠️ **Coming in Future Releases** - AI features are planned but not yet implemented.
+
+The tool will support three AI options in future versions:
+
+#### v1.5 (Target: Q3 2026) - Cloud AI
+- **Providers**: OpenAI (ChatGPT), Anthropic (Claude)
+- **Cost**: $0.10-$0.50 per document
+- **Quality**: Excellent
+- **Privacy**: Document sent to provider's servers
+- **Use case**: Best for final review before submission
+
+#### v2.0 (Target: Q4 2026) - Local AI  
+- **Provider**: Ollama (runs on your computer)
+- **Cost**: Free
+- **Quality**: Good
+- **Privacy**: Completely private, offline
+- **Use case**: Budget-friendly, sensitive documents
+
+#### v2.5 (Target: Q1 2027) - Fine-Tuned Models
+- **Provider**: Custom models via Ollama/Hugging Face
+- **Cost**: Free (after training)
+- **Quality**: Excellent for specific domains
+- **Privacy**: Completely private, offline
+- **Use case**: Institution-specific requirements
+
+**Current Version (v1.0)**: Rule-based checking only (no AI required)
+
+See [`plans/UPDATED_PROJECT_PLAN_v2.0.md`](plans/UPDATED_PROJECT_PLAN_v2.0.md) for detailed AI strategy.
+
+## Documentation
+
+### Planning Documents
+- **[Project Plan (v2.0)](plans/UPDATED_PROJECT_PLAN_v2.0.md)** - Consolidated project plan with all specifications
+  - Technical architecture
+  - Development roadmap
+  - Testing strategy
+  - AI enhancement strategy
+  - ICMJE/COPE compliance
+  - Profile specifications
+
+### User Guides (Coming Soon)
+- User Guide - How to use the tool effectively
+- Creating Custom Profiles - Build your own profiles
+- Medical Guidelines - Understanding clinical reporting standards
+- Configuration Reference - All configuration options
+
+## Command Reference
+
+### Checking Documents
+
+```bash
+# Basic check
+doc-checker check <file> --profile <profile-name>
+
+# Multiple files
+doc-checker check chapter*.docx --merge
+
+# Custom configuration
+doc-checker check <file> --config custom-rules.yaml
+
+# Specify output
+doc-checker check <file> --format html --output report.html
+
+# Set severity threshold
+doc-checker check <file> --severity error
+
+# Ignore sections
+doc-checker check <file> --ignore "Acknowledgements,Appendices"
+```
+
+### Managing Profiles
+
+```bash
+# List available profiles
+doc-checker profiles --list
+
+# Show profile details
+doc-checker profile show phd-thesis
+
+# Create custom profile
+doc-checker profile create <name> --extends <parent-profile>
+
+# Validate profile
+doc-checker profile validate <profile-file>
+
+# Compare profiles
+doc-checker profile diff <profile1> <profile2>
+```
+
+### Configuration
+
+```bash
+# Initialize configuration
+doc-checker init
+
+# Show current configuration
+doc-checker config --show
+
+# Set default profile
+doc-checker config set default-profile phd-thesis
+```
+
+## Configuration File
+
+Create a `.doc-checker.yaml` file in your project:
+
+```yaml
+# Default profile to use
+default_profile: "phd-thesis"
+
+# Citation style preference
+citation_style: "apa"
+
+# Custom dictionary
+custom_dictionary:
+  - "bioinformatics"
+  - "proteomics"
+  - "metabolomics"
+
+# Ignore patterns
+ignore_sections:
+  - "Acknowledgements"
+  - "Dedication"
+
+# Severity threshold
+severity: "warning"  # Only show warnings and errors
+
+# Output preferences
+output:
+  format: "html"
+  include_suggestions: true
+  show_line_numbers: true
+
+# AI enhancement (optional)
+ai:
+  enabled: false
+  provider: "openai"
+  model: "gpt-4"
+  api_key: "${OPENAI_API_KEY}"  # Use environment variable
+```
+
+## Requirements
+
+- Python 3.8 or higher
+- Supported document formats: `.docx` (Word), `.md` (Markdown), `.txt` (plain text)
+- Internet connection only required for optional AI features (planned for v1.5+)
+- Future format support planned: PDF, LaTeX, RTF
+
+## Development Status & Release Plan
+
+### Current Status
+🚀 **v0.4.1-beta** — Bug fixes, improved citation handling, and integration tests complete
+📅 **Next Milestone**: v1.0.0 Public Release (Target: Q2 2026)
+
+### Release Roadmap
+
+#### v1.0 - Rule-Based Core (Target: Q2 2026) 🎯 CURRENT FOCUS
+**Status**: Final Polish & Documentation
+
+**Completed**:
+- ✅ Phase 1: Foundation & Core Architecture
+- ✅ Phase 2: Core Analyzers (Structure, Formatting, Citations)
+- ✅ Phase 3: Medical & PhD Profiles (ICMJE/COPE Compliance)
+- ✅ Phase 3b: Grant Proposal Profiles (NIH, NSF)
+- ✅ MVP Stage 1: Verification & Testing Foundation (70%+ coverage)
+- ✅ MVP Stage 2: Sample Documents Creation (4 complete datasets)
+- ✅ MVP Stage 3: Integration Testing & Bug Fixes (135 tests, 0 failures)
+
+**In Progress**:
+- 🔄 Phase 4: User Documentation
+
+**Features**:
+- Complete rule-based document checking
+- Structure, formatting, citations, grammar analysis
+- ICMJE/COPE compliance validation
+- HTML, JSON, Terminal, JUnit reports
+- Multiple profiles (PhD thesis, medical journals, generic)
+- CI/CD integration support
+- Comprehensive documentation
+
+**No AI required** - Fast, free, works offline
+
+---
+
+#### v1.5 - Cloud AI Integration (Target: Q3 2026)
+**Status**: Planned for 8 weeks after v1.0 release
+
+**Scope**:
+- ⏳ Phase 5: Cloud AI Integration (Weeks 16-23)
+
+**New Features**:
+- Optional `--ai-enhance` flag
+- OpenAI (GPT-4) integration
+- Anthropic (Claude) integration
+- Cost estimation and tracking
+- AI-powered content quality analysis
+- Semantic citation validation
+- Context-aware writing suggestions
+
+**Requires**: User-provided API key, internet connection
+
+---
+
+#### v2.0 - Local AI Support (Target: Q4 2026)
+**Status**: Planned for 6 weeks after v1.5 release
+
+**Scope**:
+- ⏳ Phase 6: Local AI Support (Weeks 24-29)
+
+**New Features**:
+- Ollama integration
+- Local LLM support (Llama 3, Mistral, etc.)
+- `--ai-provider local` option
+- Model management CLI (`doc-checker ai models`)
+- Completely offline AI analysis
+- Zero API costs
+
+**Requires**: Ollama installed, 8GB+ RAM, 5-10GB disk space
+
+---
+
+#### v2.5 - Fine-Tuned Models (Target: Q1 2027)
+**Status**: Planned for 12+ weeks after v2.0 release
+
+**Scope**:
+- ⏳ Phase 7: Fine-Tuned Models (Weeks 30-41+)
+
+**New Features**:
+- Pre-trained domain-specific models:
+  - `medical-v1` - Medical journal manuscripts
+  - `phd-thesis-v1` - PhD dissertations
+  - `generic-academic-v1` - General academic papers
+- Hugging Face model distribution
+- Custom model fine-tuning scripts
+- Institution-specific model support
+- Fine-tuning documentation and guides
+
+**Requires**: Same as v2.0
+
+---
+
+#### v3.0+ - Future Enhancements
+- PDF document support
+- Markdown and LaTeX support
+- Multi-language support
+- Collaborative checking
+- Web interface
+- **Profile Governance & Accreditation System** (see [`plans/profile-governance-strategy.md`](plans/profile-governance-strategy.md))
+
+---
+
+See [`plans/UPDATED_PROJECT_PLAN_v2.0.md`](plans/UPDATED_PROJECT_PLAN_v2.0.md) for detailed roadmap.
+
+## Contributing
+
+Contributions are welcome! Here's how you can help:
+
+- **Add profiles** - Create profiles for specific journals or institutions
+- **Improve analyzers** - Enhance existing checks or add new ones
+- **Write documentation** - Improve guides and examples
+- **Report bugs** - Open issues for problems you encounter
+- **Suggest features** - Share ideas for improvements
+
+## Technology Stack
+
+- **Python 3.8+** - Core language
+- **Click/Typer** - CLI framework
+- **python-docx** - Word document parsing
+- **LanguageTool** - Grammar checking
+- **Rich** - Terminal output
+- **Jinja2** - Report generation
+- **pytest** - Testing
+- **Future**: PyPDF2/pdfplumber (PDF), python-markdown (Markdown), pylatex (LaTeX)
+
+## License
+
+[MIT](LICENSE)
+
+## Support
+
+- **Issues**: [GitHub Issues](https://github.com/darmsc/Academic_Document_Checker/issues)
+- **Discussions**: [GitHub Discussions](https://github.com/darmsc/Academic_Document_Checker/discussions)
+- **Documentation**: [Full documentation](https://github.com/darmsc/Academic_Document_Checker/docs)
+
+## Acknowledgements
+
+This tool is designed to help academic writers produce high-quality documents. It complements, but does not replace, human review and editorial judgment.
+
+---
+
+**Status**: Active Development - Phase 4 | **Current Version**: 0.4.1-beta | **Target v1.0**: Q2 2026 | **Last Updated**: April 2026