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:

---

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:
  • OceanSITES
  • 2021 NPI NetCDF guidelines

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.