seagliderOG1

This repository converts Seaglider basestation files (pSSSDDDD*.nc) into OG1 format for standardized oceanographic glider data.

Code is based on votoutils.

Installation

Recommended: Using pip

For most users, pip installation is the simplest approach:

# Install from PyPI (when available)
pip install seagliderOG1

# Or install from source
pip install git+https://github.com/ocean-uhh/seagliderOG1.git

Development setup

For contributors and developers:

# Clone the repository
git clone https://github.com/ocean-uhh/seagliderOG1.git
cd seagliderOG1

# Install dependencies and package in development mode
pip install -r requirements-dev.txt
pip install -e .

Alternative: Using conda/micromamba

If you prefer conda environments:

# Using conda
conda env create -f environment.yml
conda activate TEST

# Using micromamba (faster)
micromamba env create -f environment.yml
micromamba activate TEST

Package Structure

Scripts within the seagliderOG1 package are organized by functionality:

• readers.py - Reads basestation files (*.nc) from server or local directory
• writers.py - Writes OG1 *.nc files to output directory (default: data/)
• plotters.py - Basic plotting and data visualization functions
• convertOG1.py - Main conversion logic from basestation to OG1 format
• vocabularies.py - Vocabulary translation mappings for OG1 compliance
• tools.py - User-facing utility functions
• utilities.py - Internal helper functions for data processing

Configuration

The seagliderOG1/config/ directory contains YAML files that define OG1 format specifications:

• OG1_global_attrs.yaml - Global attributes for OG1 format
• OG1_var_names.yaml - Variable name mappings
• OG1_sensor_attrs.yaml - Sensor attribute definitions
• OG1_vocab_attrs.yaml - Vocabulary attribute mappings
• OG1_author.yaml - Author information template
• mission_yaml.yaml - Mission configuration template

Usage

Basic conversion

from seagliderOG1 import convertOG1, readers

# Load basestation files
datasets = readers.load_basestation_files("path/to/basestation/files/")

# Convert to OG1 format
og1_dataset, variable_list = convertOG1.convert_to_OG1(datasets)

# Save result
from seagliderOG1 import writers
writers.save_dataset(og1_dataset, "output_file.nc")

Examples

See the notebooks/ directory for detailed examples:

• demo.ipynb - Basic usage demonstration
• dev_notebooks/ - Development and troubleshooting notebooks

Development

Running tests

pytest                    # Run all tests
pytest -v                 # Verbose output
pytest tests/test_*.py    # Run specific test file

Code quality

black .                   # Format code
ruff check --fix          # Lint and auto-fix
pre-commit run --all-files # Run all pre-commit hooks

Building documentation

cd docs
make clean html

Dependencies

The project uses different dependency files for different use cases:

• requirements.txt - Core runtime dependencies (recommended for most users)
• requirements-dev.txt - Additional development tools (testing, documentation, code quality)
• environment.yml - Complete conda/micromamba environment (alternative for conda users)

Core dependencies

• xarray & netCDF4 - NetCDF file handling and data manipulation
• numpy, pandas - Numerical operations and data structures
• gsw - Seawater property calculations (TEOS-10)
• matplotlib - Plotting and visualization
• pooch - Data downloading and caching

Contributing

1. Fork the repository
2. Create a feature branch (git checkout -b feature/amazing-feature)
3. Make your changes
4. Run tests and ensure they pass
5. Commit your changes (git commit -m 'Add amazing feature')
6. Push to the branch (git push origin feature/amazing-feature)
7. Open a Pull Request

Status

This project is under active development. Collaborations and contributions are welcome!

License

See LICENSE for details.