bgc-viewer 0.1.0__tar.gz

bgc_viewer-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
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+.eggs/
+lib/
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+parts/
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+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
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+.coverage
+.coverage.*
+.cache
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+coverage.xml
+*.cover
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+.hypothesis/
+.pytest_cache/
+
+# Translations
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+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
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+ENV/
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+# Spyder project settings
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+# Rope project settings
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+Thumbs.db
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+# Custom
+data/

bgc_viewer-0.1.0/LICENSE

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bgc_viewer-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: bgc-viewer
+Version: 0.1.0
+Summary: A Flask server for Biosynthetic Gene Cluster analysis
+Author-email: Your Name <your.email@example.com>
+License: Apache-2.0
+License-File: LICENSE
+Requires-Python: >=3.8.1
+Requires-Dist: flask-cors>=4.0.0
+Requires-Dist: flask>=2.3.0
+Requires-Dist: python-dotenv>=1.0.1
+Requires-Dist: waitress>=3.0.0
+Provides-Extra: dev
+Requires-Dist: black>=23.0.0; extra == 'dev'
+Requires-Dist: build>=0.10.0; extra == 'dev'
+Requires-Dist: flake8>=6.0.0; extra == 'dev'
+Requires-Dist: mypy>=1.0.0; extra == 'dev'
+Requires-Dist: pytest>=7.0.0; extra == 'dev'
+Requires-Dist: twine>=4.0.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# BGC-Viewer
+
+!!Work-in-progress!!
+
+A viewer for BGC data.
+
+
+## Project Structure
+
+```
+bgc-viewer/
+├── bgc_viewer/
+│   ├── __init__.py
+│   ├── app.py              # Main Flask application
+│   ├── static/
+│   │   └── style.css       # Styling
+│   │   └── app.js          # Frontend JavaScript
+│   └── templates/
+│       └── index.html      # Main HTML template
+├── data/
+│   └── custom_data.json    # Optional custom data file
+├── tests/
+│   └── test_app.py         # Test files
+├── pyproject.toml          # Project configuration
+├── README.md
+└── .gitignore
+```
+
+## Setup
+
+### Prerequisites
+
+- Python 3.8+
+- [uv](https://github.com/astral-sh/uv) package manager
+
+### Installation
+
+1. Clone or create the project directory:
+   ```bash
+   mkdir bgc-viewer
+   cd bgc-viewer
+   ```
+
+2. Create the project structure and files (as shown above)
+
+3. Initialize the project with uv:
+   ```bash
+   uv venv
+   source .venv/bin/activate  # On Windows: .venv\Scripts\activate
+   uv pip install -e .
+   ```
+
+4. For development dependencies:
+   ```bash
+   uv pip install -e ".[dev]"
+   ```
+
+## Usage
+
+### Running the Server
+
+```bash
+# Using the console script
+serve
+
+# Or directly with Python
+python -m bgc_viewer.app
+
+# Or with environment variables
+FLASK_DEBUG=true PORT=8000 serve
+```
+
+The server will start on `http://localhost:5005` by default.
+
+### API Endpoints
+
+- `GET /` - Main HTML page with interactive API tester
+- `GET /api/data` - Get all custom data
+- `GET /api/users` - Get user list
+- `GET /api/users/<id>` - Get specific user
+- `GET /api/stats` - Get application statistics
+- `GET /api/health` - Health check endpoint
+
+### Testing the API
+
+Visit `http://localhost:5005` in your browser to access the interactive API tester, or use curl:
+
+```bash
+# Get all data
+curl http://localhost:5005/api/data
+
+# Get users
+curl http://localhost:5005/api/users
+
+# Get specific user
+curl http://localhost:5005/api/users/1
+
+# Health check
+curl http://localhost:5005/api/health
+```
+
+## Development
+
+### Code Formatting
+
+```bash
+# Format code
+uv run black bgc_viewer/
+
+# Lint code
+uv run flake8 bgc_viewer/
+
+# Type checking
+uv run mypy bgc_viewer/
+```
+
+### Testing
+
+```bash
+# Run tests
+uv run pytest
+
+# Run tests with coverage
+uv run pytest --cov=bgc_viewer
+```
+
+### Adding Custom Data
+
+1. Create a `data/custom_data.json` file with your data structure
+2. Modify the `load_custom_data()` function in `app.py` to read from your data source
+3. Update the API endpoints to serve your custom data
+
+## Customization
+
+### Adding New Endpoints
+
+1. Add new route functions to `app.py`
+2. Update the HTML template to include new endpoints
+3. Add corresponding JavaScript functions if needed
+
+### Styling
+
+Modify `static/css/style.css` to customize the appearance of the web interface.
+
+### Frontend Behavior
+
+Update `static/js/app.js` to add new interactive features.
+
+## Environment Variables
+
+Environment variables can be set to change the configuration of the viewer.
+A convenient way to change them is to put a file called `.env` in the directory from
+which you are running the application.
+
+- `BGCV_HOST` - Server host (default: localhost)
+- `BGCV_PORT` - Server port (default: 5005)
+- `BGCV_DEBUG_MODE` - Enable dev/debug mode (default: False)
+
+## License
+
+Apache 2.0

bgc_viewer-0.1.0/README.md

@@ -0,0 +1,161 @@
+# BGC-Viewer
+
+!!Work-in-progress!!
+
+A viewer for BGC data.
+
+
+## Project Structure
+
+```
+bgc-viewer/
+├── bgc_viewer/
+│   ├── __init__.py
+│   ├── app.py              # Main Flask application
+│   ├── static/
+│   │   └── style.css       # Styling
+│   │   └── app.js          # Frontend JavaScript
+│   └── templates/
+│       └── index.html      # Main HTML template
+├── data/
+│   └── custom_data.json    # Optional custom data file
+├── tests/
+│   └── test_app.py         # Test files
+├── pyproject.toml          # Project configuration
+├── README.md
+└── .gitignore
+```
+
+## Setup
+
+### Prerequisites
+
+- Python 3.8+
+- [uv](https://github.com/astral-sh/uv) package manager
+
+### Installation
+
+1. Clone or create the project directory:
+   ```bash
+   mkdir bgc-viewer
+   cd bgc-viewer
+   ```
+
+2. Create the project structure and files (as shown above)
+
+3. Initialize the project with uv:
+   ```bash
+   uv venv
+   source .venv/bin/activate  # On Windows: .venv\Scripts\activate
+   uv pip install -e .
+   ```
+
+4. For development dependencies:
+   ```bash
+   uv pip install -e ".[dev]"
+   ```
+
+## Usage
+
+### Running the Server
+
+```bash
+# Using the console script
+serve
+
+# Or directly with Python
+python -m bgc_viewer.app
+
+# Or with environment variables
+FLASK_DEBUG=true PORT=8000 serve
+```
+
+The server will start on `http://localhost:5005` by default.
+
+### API Endpoints
+
+- `GET /` - Main HTML page with interactive API tester
+- `GET /api/data` - Get all custom data
+- `GET /api/users` - Get user list
+- `GET /api/users/<id>` - Get specific user
+- `GET /api/stats` - Get application statistics
+- `GET /api/health` - Health check endpoint
+
+### Testing the API
+
+Visit `http://localhost:5005` in your browser to access the interactive API tester, or use curl:
+
+```bash
+# Get all data
+curl http://localhost:5005/api/data
+
+# Get users
+curl http://localhost:5005/api/users
+
+# Get specific user
+curl http://localhost:5005/api/users/1
+
+# Health check
+curl http://localhost:5005/api/health
+```
+
+## Development
+
+### Code Formatting
+
+```bash
+# Format code
+uv run black bgc_viewer/
+
+# Lint code
+uv run flake8 bgc_viewer/
+
+# Type checking
+uv run mypy bgc_viewer/
+```
+
+### Testing
+
+```bash
+# Run tests
+uv run pytest
+
+# Run tests with coverage
+uv run pytest --cov=bgc_viewer
+```
+
+### Adding Custom Data
+
+1. Create a `data/custom_data.json` file with your data structure
+2. Modify the `load_custom_data()` function in `app.py` to read from your data source
+3. Update the API endpoints to serve your custom data
+
+## Customization
+
+### Adding New Endpoints
+
+1. Add new route functions to `app.py`
+2. Update the HTML template to include new endpoints
+3. Add corresponding JavaScript functions if needed
+
+### Styling
+
+Modify `static/css/style.css` to customize the appearance of the web interface.
+
+### Frontend Behavior
+
+Update `static/js/app.js` to add new interactive features.
+
+## Environment Variables
+
+Environment variables can be set to change the configuration of the viewer.
+A convenient way to change them is to put a file called `.env` in the directory from
+which you are running the application.
+
+- `BGCV_HOST` - Server host (default: localhost)
+- `BGCV_PORT` - Server port (default: 5005)
+- `BGCV_DEBUG_MODE` - Enable dev/debug mode (default: False)
+
+## License
+
+Apache 2.0

bgc_viewer-0.1.0/bgc_viewer/__init__.py

@@ -0,0 +1,11 @@
+"""
+My Flask App - A simple Flask server with API endpoints
+"""
+
+__version__ = "0.1.0"
+__author__ = "Your Name"
+__email__ = "your.email@example.com"
+
+from .app import app
+
+__all__ = ["app"]