Update 2026-01-28 20:20:23

Dockerfile

@@ -1,6 +1,18 @@
 FROM python:3.9-slim
-   WORKDIR /app
-   COPY requirements.txt .
-   RUN pip install --no-cache-dir -r requirements.txt
-   COPY . .
-   CMD ["python", "app.py"]
+
+WORKDIR /app
+
+# Copy requirements
+COPY requirements.txt .
+
+# Install dependencies
+RUN pip install --no-cache-dir -r requirements.txt
+
+# Copy application
+COPY . .
+
+# Expose port (HF Spaces uses 7860)
+EXPOSE 7860
+
+# Run Flask app
+CMD ["python", "app.py"]

README.md

@@ -1,205 +1,21 @@
-# Reference Management System - Flask Application
-
-A web-based application for processing, enriching, and managing BibTeX references. Users paste their BibTeX entries, apply optional processing steps, view results, and save to a local database.
-
-## Features
-
-- **Paste & Process**: Directly input BibTeX entries without needing files
-- **Crossref Enrichment**: Fetch updated metadata from Crossref API
-- **Journal Abbreviations**: Apply LTWA abbreviations using local `ltwa.txt` file
-- **Acronym Protection**: Wrap acronyms in braces to preserve LaTeX capitalization
-- **Database Storage**: Save all versions to SQLite database
-- **Multiple Export Formats**: Export as CSV or BibTeX file
-- **Database Management**: View, delete, and manage stored references
-- **Real-time Statistics**: Track total entries, types, and years
-
-## Installation
-
-### Requirements
-- Python 3.8+
-- pip
-
-### Setup Steps
-
-1. **Install Dependencies**
-   ```bash
-   pip install -r requirements.txt
-   ```
-
-2. **Add Journal Abbreviations (Optional)**
-   - Place `ltwa.txt` in the same directory as `app.py`
-   - Format: Tab-separated values
-     ```
-     Journal Full Name	Abbrev
-     Nature Biotechnology	Nat Biotechnol
-     ```
-
-3. **Run the Application**
-   ```bash
-   python app.py
-   ```
-   - Open browser to `http://localhost:5000`
-
-## Usage
-
-### Basic Workflow
-
-1. **Paste BibTeX**
-   - Copy your BibTeX entries into the input area
-   - Supports multiple entries
-
-2. **Select Processing Options**
-   - ✅ **Enrich with Crossref**: Query Crossref API (3-5 sec per entry)
-   - ✅ **Apply Journal Abbreviations**: Requires ltwa.txt file
-   - ✅ **Protect Acronyms**: Wraps multi-uppercase words in braces
-   - ✅ **Save to Database**: Store for later access
-
-3. **Process & View Results**
-   - Click "Process References"
-   - View in three formats: Table, BibTeX, JSON
-   - Results include metadata, similarity scores, multiple BibTeX versions
-
-4. **Manage & Export**
-   - View database entries with statistics
-   - Delete individual entries
-   - Export all data as CSV or BibTeX
-
-### Processing Options Explained
-
-#### Enrich with Crossref
-- Queries Crossref API for each reference
-- Fetches complete metadata and BibTeX
-- Shows title similarity percentage (95%+ uses Crossref data)
-- Slower but most accurate for published papers
-
-#### Journal Abbreviations
-- **Requires**: `ltwa.txt` file in app directory
-- Replaces full journal names with standard abbreviations
-- Essential for formatting journal names correctly
-
-#### Protect Acronyms
-- Wraps acronyms/multi-uppercase words in braces: `{RNN}`, `{LSTM}`
-- Prevents LaTeX from lowercasing acronyms in titles
-- Applied to title, booktitle, and journal fields
-
-#### Save to Database
-- Stores original and all processed versions
-- Preserves session/import date
-- Enables future bulk exports
-
-## Database Structure
-
-The SQLite database (`refs_management.db`) includes:
-
-| Column | Purpose |
-|--------|---------|
-| id | Primary key |
-| key | BibTeX citation key |
-| type | Entry type (article, book, etc.) |
-| authors | Author names |
-| title | Paper/book title |
-| journal_booktitle | Journal or conference name |
-| year | Publication year |
-| bibtex | Original user-provided BibTeX |
-| crossref_bibtex | Crossref API fetched version |
-| crossref_bibtex_abbrev | With journal abbreviations |
-| crossref_bibtex_protected | With protected acronyms |
-| title_similarity | Crossref match percentage |
-| imported_date | When imported |
-
-## API Endpoints
-
-### Process References
-- **POST** `/api/process`
-- **Body**: 
-  ```json
-  {
-    "bibtex_content": "...",
-    "enrich": true,
-    "abbreviate": true,
-    "protect": true,
-    "save_to_db": true
-  }
-  ```
-
-### Database Management
-- **GET** `/api/database/entries` - List all entries
-- **DELETE** `/api/database/delete/<key>` - Delete entry
-- **GET** `/api/database/export` - Export CSV
-- **GET** `/api/database/export-bibtex` - Export BibTeX
-
-### Statistics
-- **GET** `/api/stats` - Database statistics
-
-## File Structure
-
-```
-.
-├── app.py                 # Flask application
-├── templates/
-│   └── index.html        # Web interface
-├── requirements.txt      # Python dependencies
-├── refs_management.db    # Database (created automatically)
-└── ltwa.txt             # Journal abbreviations (optional)
+---
+title: Reference Management System
+emoji: 📚
+colorFrom: blue
+colorTo: purple
+sdk: docker
+app_file: app.py
+pinned: false
+---
 ```
 
-## Example BibTeX Input
-
-```bibtex
-@article{Smith2024,
-  author = {Smith, John and Doe, Jane},
-  title = {Machine Learning for Natural Language Processing},
-  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
-  year = {2024},
-  volume = {46},
-  pages = {1234-1250}
-}
+Then keep your existing documentation below it.
 
-@book{Johnson2023,
-  author = {Johnson, Michael},
-  title = {Deep Learning Fundamentals},
-  publisher = {Academic Press},
-  year = {2023}
-}
+Final repo should have:
 ```
-
-## Troubleshooting
-
-### "No journal abbreviations found"
-- Ensure `ltwa.txt` is in the same directory as `app.py`
-- Verify tab-separated format
-
-### Crossref enrichment is slow
-- Normal behavior (API rate limiting)
-- Average: 3-5 seconds per entry
-- Results cached in database
-
-### Database not updating
-- Check `refs_management.db` permissions
-- Ensure "Save to Database" option is checked
-
-### Port 5000 already in use
-- Change in app.py: `app.run(debug=True, port=5001)`
-
-## Performance Notes
-
-- **Crossref API**: ~3-5 seconds per reference (rate-limited)
-- **Batch processing**: Process 10 references in ~30-50 seconds
-- **Database**: Handles 1000+ entries efficiently
-
-## Future Enhancements
-
-- Multiple database tables for different projects
-- BibTeX key normalization
-- Duplicate detection
-- Advanced search/filtering
-- Batch upload capability
-
-## Support
-
-For issues with the Crossref API, visit: https://crossref.org
-For journal abbreviation standards: https://www.nlm.nih.gov/bsd/ltwa_mainpage.html
-
-## License
-
-This application is provided as-is for reference management purposes.
+app.py
+requirements.txt
+Dockerfile
+.gitattributes
+README.md (with HF header)
+templates/index.html