xnemogcm 0.4.2

Interface to open NEMO global circulation model output dataset and create a xgcm grid.

xnemogcm

Interface to open NEMO ocean global circulation model output dataset and create a xgcm grid. NEMO 3.6, 4.0, and 4.2.0 are tested and supported. Any version between 3.6 and 4.2.0 should work, but in case of trouble, please open an issue.

Usage

from pathlib import Path
from xnemogcm import open_nemo_and_domain_cfg

ds = open_nemo_and_domain_cfg(
    nemo_files='/path/to/output/files',
    domcfg_files='/path/to/domain_cfg/mesh_mask/files'
)

# Interface with xgcm
from xnemogcm import get_metrics
import xgcm
grid = xgcm.Grid(ds, metrics=get_metrics(ds), periodic=False)

See the example directory for some jupyter notebook examples. xnemocgm is able to process xarray.Datasets (e.g. they could be retrieved from a remote server), and can get information of the variables grid points with multiple options (see example/open_process_files.ipynb.

Note

xnemogcm is capable or recombining the domain_cfg and mesh_mask files output by multiple processors, the recombining tool from the NEMO toolbox is thus not needed here, see the example/recombing_mesh_mask_domain_cfg.ipynb

Installation

Installation via pip:

pip3 install xnemogcm

Installation via conda:

conda install -c conda-forge xnemogcm

Requirements for dev

We use poetry to set up a virtual environment containing all needed packages to run xnemogcm and the tests. To install all the dependencies, type poetry install --with test,dev after cloning the directory. This will create a new virtual environment. Typing poetry shell in the package directory will activate the virtual environment.

About test data

Test data are based on the GYRE configuration, and produced by another repository: rcaneill/xnemogcm_test_data. Testing is built in a way that it is quite easy to add other nemo version to test.

About notebooks examples

Sources for the notebooks are located in src_example. This is where to add / modify the examples. A github action is set to automatically build the notebook according to the latest version of the code, and publish them to example when commiting to master branch.

What's new

v0.4.2 (2023-08-07)

• Allow additional dimension names occurring when variables on inner grid are diagnosed, e.g. x_grid_U_inner or x_grid_U.
• Add coordinates into the DataArrays
• Add some standard names and units in domcfg

v0.4.1 (2023-03-29)

• Allow to open files if time bounds are missing
• Minor bug correction for nemo 3.6
• Add nemo 3.6 and 4.2.0 test data
• Update code to support nemo 3.6 and 4.2.0

v0.4.0 (2022-12-08)

• Optimize speed
• Add option to decode grid type from attributes
• Shift from pipenv and setupy.py to poetry
• Refactor data test to allow testing of multiple version of NEMO

v0.3.4 (2021-06-15)

• Adding some example
• Bug fixes
• Add option to compute extra scale factors

v0.3.2 - v0.3.3 (2021-05-05)

• By default adds the lat/lon/depth variables of domcfg as coordinates

v0.3.1 (2021-05-04)

• Minor bug fix when merging
• better squeezing of time in domcfg + nemo v3.6 compatibility

v0.3.0 (2021-04-13)

• Cleaning the backend
• Removing the saving options (that were useless and confusing)
• Minor bug fixes
• Tested with realistic regional configuration

v0.2.3 (2021-03-15)

• Support for surface only files
• Reshaping the data files for the tests (dev)