ugrid-checks 0.1.2

Check netcdf files for conformance with UGRID specifications

ugrid-checks

Version : 0.1.2

A utility to check netcdf files to the UGRID specification.

It tests files against the UGRID conformance rules, and can also produce a summary of the mesh content of a file.

• Installation
• Command Line : checking
  • Basic usage
  • Controlling checks
• Command Line : structure analysis
• List of Conformance Rules and codes
• Limitations
• Python API
• Runtime Requirements
• Known Issues
• Changelog

Installation

Available on PyPI.

To install:

> pip install ugrid-checker

Command Line : checking

$ ugrid-checker -h
usage: ugrid-checker [-h] [-q] [-e] [-s] [--nonmesh] [-i IGNORE] [-v] file

Check a netcdf-CF file for conformance to the UGRID conventions.

positional arguments:
  file                  File to check.

optional arguments:
  -h, --help            show this help message and exit
  -q, --quiet           don't print a checking report if there were no
                        problems
  -e, --errorsonly      ignore all warnings ("Axxx"= advise codes), and only
                        report errors ("Rxxx"= require codes).
  -s, --summary         print a summary of UGRID mesh information found in the
                        file
  --nonmesh             include a list of non-mesh variables in the summary
  -i IGNORE, --ignore IGNORE
                        a list of errorcodes to ignore.
  -v, --version         print version information
$

Basic usage

$ ugrid-checker data_C4.nc

UGRID conformance checks complete.

No problems found.

Done.
$

$ ugrid-checker data_C4_warn_error.nc 

UGRID conformance checks complete.

List of checker messages :
  *** FAIL R106 : Mesh variable "topology" attribute 'face_coordinates' refers to a variable "longitude", but there is no such variable in the dataset.
  *** FAIL R108 : Mesh variable "topology" has face_coordinates="latitude longitude", which is not a list of variables in the dataset.
  ... WARN A304 : Mesh connectivity variable "face_nodes" of mesh "topology" has a '_FillValue' attribute, which should not be present on a "face_node_connectivity" connectivity.

Total of 3 problems logged :
  2 Rxxx requirement failures
  1 Axxx advisory recommendation warnings

Done.
$

Controlling checks

The -e / --errorsonly option checks only against the requirements (aka "errors"), and skips the recommendations (aka "warnings").

The -i / --ignore option skips particular checks according to their Axxx/Rxxx codes.
See List of codes.

Example:

$ ugrid-checker data_C4_warn_error.nc --errorsonly --ignore r106,r108

Ignoring codes:
  R106, R108

UGRID conformance checks complete.

No problems found.

Done.
$

Command line : structure analysis

The -s / --summary option prints a summary of a file's mesh content.

$ ugrid-checker data_C4.nc --summary --quiet

File mesh structure
-------------------
Meshes
    "topology"
        node("num_node")
            coordinates : "node_lat", "node_lon"
        face("dim0")
            face_node_connectivity : "face_nodes"
            coordinates : "latitude", "longitude"

Mesh Data Variables
    "sample_data"
        mesh : "topology"
        location : "face"

$

List of Conformance Rules and codes

All the error/warning codes used are defined in the UGRID conformance rules. Each has an identifying code : "Rxxx" for requirements or "Axxx" for advisory rules.

See the list here : UGRID Draft Conformance Rules

Note : these are currently only available in this preliminary draft version, not yet accepted into the UGRID spec.

Limitations

No data value checks

At present, none of the rules which test actual data values in variables are implemented.

• For example : A305 -- "a connectivity that contains missing indices should have a _Fillvalue property"

It is intended that these checks will be added later, enabled by a new flag such as --datachecks

No 3-D / Volume support

The draft conformance rules do not currently cover 3-d meshes, so neither does the checker code. There is also an ongoing discussion whether it is needed to "fix" this feature, or even to remove it in a future release of UGRID. See this developer discusssion.
Alternatively, this can be added in future.

Python API

The checker is provided as an importable module "ugrid_checks".

Running the module directly calls the command-line interface,
e.g. $ python -m ugrid_checks file.nc is the same as $ ugrid-checker file.nc.

Within Python, the module can be used like this :

>>> from ugrid_checks.check import check_dataset
>>> print(check_dataset.__doc__)

    Run UGRID conformance checks on a file.

    Optionally print a result summary.
    Optionally ignore errors below a logging level.
    Returns a checker object with a file analysis and checking log records.

    Parameters
    ----------
    file : string, Path or :class:`NcFileSummary`
        path to, or representation of a netcdf input file
    print_summary : bool, default=True
        print a results summary at the end
    omit_advisories : bool, default False
        If set, log only 'requirements' Rxxx statements, and ignore the
        advisory 'Axxx' ones.
    ignore_codes : list(str) or None, default None
        A list of error codes to ignore.

    Returns
    -------
    checker : Checker
        A checker for the file.

    
>>>
>>> checker = check_dataset('data_C4_warn.nc', print_summary=False)
>>> 
>>> type(checker)
<class 'ugrid_checks.check.Checker'>
>>>
>>> print(checker.checking_report())
UGRID conformance checks complete.

List of checker messages :
  ... WARN A304 : Mesh connectivity variable "face_nodes" of mesh "topology" has a '_FillValue' attribute, which should not be present on a "face_node_connectivity" connectivity.

Total of 1 problems logged :
  0 Rxxx requirement failures
  1 Axxx advisory recommendation warnings

Done.
>>> 
>>> print(checker.structure_report())
Meshes
    "topology"
        node("num_node")
            coordinates : "node_lat", "node_lon"
        face("dim0")
            face_node_connectivity : "face_nodes"
            coordinates : "latitude", "longitude"

Mesh Data Variables
    "sample_data"
        mesh : "topology"
        location : "face"
>>>

For the time being, there is no built API documentation : Please refer to code docstrings for more detail.

Runtime Requirements

• Python >= 3.7
• netCDF4

Known Issues

• none known

Raising Issues

Please create an issue in : https://github.com/pp-mo/ugrid-checks

Changelog

• TODO: move to separate file ?

• v0.1.2

  • release 2022-02-27
    • #36 fix to A304
      allow face-node-connectivity to have a _FillValue, as this is used for flexible 2d meshes.

• v0.1.1

  • release 2022-02-24
    • #23 structure-report bugfixes :
      • report optional connectivities, which were previously missing
      • report location-index-sets, which previously used to error
    • #26 corrected statement codes :
      Some statements in the range R109-R112 were being reported with the wrong statement code

• v0.1.0

  • release 2022-02-09