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Collection of Python functions for working with oceanography data processing and analysis.

Maintained by the Oceanography section at the Norwegian Polar Institute.

Supported by the project HiAOOS.

Last release,0.0.2-beta:

DOI

Note: This library was until recently called oceanograpy

In active development.

CORE FUNCTIONALITY
Submodules
  • file: Converting to and from various file format (e.g. read CTD .cnv data to xarray/netCDF)
  • data: Data post-processing and QC (e.g. CTD post-processing)
  • metadata: Handling and standardizing metadata according to CF conventions
  • plots*: Various tools to help make nice (matplotlib) figures
  • map: Tools for making maps
  • geo: Geographical calculations (coordinate transformations, point-to-point distances etc)
  • ocean: Oceanography-specific tools (e.g. (*) vertical modes, turner angles, wkb scaling, geostrophical calculations)
  • calc: Various useful functions for numerical calculations.
  • util: Various backend support functions and wrappers for xarray functionality.
  • signal: Filtering, spectral analysis, etc.

* Not implemented

GENERAL PRINCIPLES

Note: These are aspirational guidelines and not always adhered to in the current code structure. We will try to get there!

Code
  • Written in Python (>=3.8).
  • Tailored for use in a [Jupyter] notebook environment.
  • Data and metadata should be stored in [xarray(https://docs.xarray.dev/en/stable/)] Datasets.
    • Intermediate operations using, e.g., numpy or pandas objects are fine, but the end user should only interact with Datasets.
  • Code should adhere to PEP8 style guide, and all functions should have docstrings.
  • All functionality should have associated pytest tests.
    • Unit tests of individual functions are found in tests/unit_tests/. Its directory structure and contents should mirror that of src/kval.
    • Tests of more complex functionality (e.g. processing pipelines using multiple modules) should be put in tests/functional_tests/.
    • A collection of sample data to be used in testing is found in tests/test_data/. Should aim to cover a wide range of input data, but we also don't want this to become too bulky - try to keep file size to a minimum.
Metadata
  • All operations that modify data should be recorded in the file metadata.
  • Wherever possibly, and at as early a stage as possible, all available useful metadata should be added to Datasets.
  • Metadata formatting should adhere to CF and ACDD conventions, supplemented by:
Project
  • The project is maintained by the Oceanography section at the Norwegian Polar Institute.
    • External contributions (pull requests, issues, whatever) are very welcome!
  • We will attempt to follow the guidelines from the Scientific Python Library Development Guide.
  • Releases will be published relatively often, whenever a new functionality has been added. Releases will be archived on zenodo and given a DOI.
Contributing

Pull requests, issues, etc are very welcome!

[Something about branches here]

[Something about python style, test suite]

RELEASE NOTES

  • 0.1.0 (in development):

    • Refactoring of large parts of the code for structure, clarity and efficiency.
    • Complete reproducability and self-documentation in the CTD processing functionality.
    • Adding mooring processing functionality
      • Functionality for parsing moored CTD sensors (RBR and SBE)
      • Functionality for basic processing source file -> CF-NetCDF
    • Test suite (comprehensive but not entirely complete)
    • Decluttering the repo bringing it down from its currently bloated state.
    • Reasonably useful documentation wit hnotebook examples (readthedocs).
    • Possibly: release to PyPi and conda-forge.

  • Changes tabled but not planned included in 0.1.0

    • Removal of NPI-specific content.

  • 0.0.2:

    • Name change from oceanograpy to kval.
    • Introduction of test suite.
    • Other minor changes.

  • 0.0.1:

    • Initial release.
    • Functionality tailored for CTD processing.