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](https://peps.python.org/pep-0008/) style guide, and all functions should have docstrings.
- All functionality should have associated [pytest](https://docs.pytest.org/en/7.4.x/) 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](http://cfconventions.org/) and [ACDD](https://wiki.esipfed.org/Attribute_Convention_for_Data_Discovery_1-3) conventions, supplemented by:
- [OceanSITES](http://www.oceansites.org/docs/oceansites_data_format_reference_manual_20140917.pdf)
- [2021 NPI NetCDF guidelines](https://gitlab.com/npolar/netcdf-creator/-/blob/main/docs/netcdf_standard_npi.pdf?ref_type=heads)
###### Project
- The project is maintained by the Oceanography section at the [Norwegian Polar Institute](www.npolar.no/en).
- External contributions (pull requests, issues, whatever) are very welcome!
- We will attempt to follow the guidelines from the
[Scientific Python Library Development Guide](https://learn.scientific-python.org/development/).
- *Releases* will be published relatively often, whenever a new functionality has been added.
Releases will be archived on [zenodo](www.zenodo.org) 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.