metyanc 0.1.4

Yet another NetCDF checker

This command-line program checks that a NetCDF file conforms to a pre-defined specification. It checks if the file contains the specified dimensions and variables; that the dimensions are of the correct size; that the variables have values within range; and that the variables have certain attributes.

Example use

python yanc.py\
   --ncfile http://thredds.met.no/thredds/dodsC/meps25files/meps_det_pp_2_5km_latest.nc \
   --template templates/meps_det_pp_2_5km.yml

Template

Yanc checks the NetCDF file against specifications in a template file. The template understands the following structure:

dimensions:
- name: time
    length: 15
- name: x
    min_length: 10
    max_length: 20

variables:
- name: air_temperature
  min: 200
  max: 400
  units: K
  '% missing': 10
  missing_timesteps: [0,1,2]

All attributes are optional, and yanc will not check dimensions/variables/min/max/etc when not specified. Dimensions can be checked for an exact length (by using the work ‘length’) or a range of lengths (inclusively, by using ‘min_length’ and ‘max_length’).

Neither ‘dimensions’ nor ‘variables’ are required to be present in the file.

Installation

The easiest way to install yanc is using pip:

pip install metyanc

To install from source, install like this:

pip install -r requirements.txt
python setup.py install

Return codes

The program returns 0 if the file is valid. Otherwise a non-zero code is returned. If the template file is missing or contains invalid YAML, or if the NetCDF file does not exist or is invalid NetCDF, then a non-zero code is returned.

Missing values

By default, variables are not allowed to have missing values. To allow a missing values, the ‘% missing’ can be added, which means the test will fail if there the percentage of missing values exceeds the allowed value. Some variables (such as precipitation_amount) will have have missing values on the first timestep. Data in timesteps specified by missing_timesteps will not count towards the percentage missing.

For example, the following requires the precipitation_amount variable to have no missing values except for the first time step:

variables:
- name: precipitation_amount
  units: m
  '% missing': 0
  missing_timesteps: 0

missing_timesteps can also be an array like this:

variables:
- name: precipitation_amount
  units: m
  '% missing': 0
  missing_timesteps: [0, 1, 2]

Testing

Running “make test” runs some quick unittests. Running “make testop” checks that the current operational files conform to specifications. This can take 10-15 minutes.