v2

sophy v2 release notes

• New data transformation workflow
  • Make a Jupyter notebook which reads unmodified dataset and outputs modified dataset
  • transformations/README.md has more details
  • Also see transform_template.ipynb as a starting point for any transformation
• Added build.py
  • Builds the database (xlsx and db versions) using modified datasets
  • Creates log file with diagnostics
    • Includes debug logs from other packages such as geopandas and pyworms
  • WoRMS caching
    • Script stores result of WoRMS queries in _cache/worms.json for improved runtime of build.py
• Added AMT cruise data to sophy
  • Transformation done in amt.ipynb
• SQL schema updates
  • Now include HPLC data in main sample table
  • New metadata table
    • Holds units, description, data type, and more
• Updated sophy_example.ipynb with new examples for using the database
• Updated sophybook with newer sophy_example and removed old notebooks
• Improved documentation of util scripts and transform notebooks