pyExodiff - pure python exodiff

pyexodiff compares two Exodus II files to determine whether they are identical. It is intended as a python replacement of the Exodiff utility, allowing two Exodus II files to be compared without the need to install SEACAS.

Setup

pyexodiff requires the following python packages to be installed:

• numpy
• netCDF4
• argparse
• re

These can be installed using pip if they are not already installed

pip install numpy

for example.

Two additional python package are required to run the test script:

• pytest
• pyYAML

Again, these can be installed using

pip install pytest

for example.

Usage

pyexodiff can be used as a standalone utility to compare two Exoduss II files on the commandline using

./pyexodiff.py file1 file2

If the two Exodus II files are identical, pyexodiff reports that they are the same:

$ pyexodiff.py test/simple_cube.e test/simple_cube.e

pyexodiff: files are identical

If the files are different, however, pyexodiff will report that they are not identical and will provide a brief summary of the differences.

For example, if the dimensions of the Exodus II files are different, then pyexodiff will report the difference:

$  pyexodiff.py test/simple_cube.e test/simple_cube_missing_prop.e

pyexodiff: difference summary:

Dimensions:
    num_elem_var is different: file1 size is 6; file2 size is 5
    num_sset_var is different: file1 size is 6; file2 size is 5
  Variables:
      name_elem_var is different: variable poro not in both files
      name_sset_var is different: variable poro not in both files

pyexodiff: files are different

If the variables of both files are not equal (to within the given tolerances), then pyexodiff will print out the maximum difference for each variable that is different as well as its position (node or element id):

$ pyexodiff.py test/simple_cube.e test/simple_cube_incorrect_coordx.e

pyexodiff: difference summary:

Variables:
    coordx is different:
      max absolute diff 1.0000e+00 at position 12
      max relative diff 6.6667e-01 at position 12

pyexodiff: files are different

pyexodiff can also be used as a module in a python script using

from pyexodiff import exodiff

diff = exodiff(file1, file2, atol, rtol)

to return a dictionary of the differences.

In this case, the pyexodiff repository should be added to the PYTHONPATH environment variable

export PYTHONPATH=$PYTHONPATH:/path/to/pyexodiff

Commandline options

Some parameters can be overwritten using the commandline options.

$ pyexodiff.py --help

usage: pyexodiff.py [-h] [--rtol RTOL] [--atol ATOL] file1 file2

Compares two Exodus II files

positional arguments:
  file1
  file2

optional arguments:
  -h, --help   show this help message and exit
  --rtol RTOL  Relative tolerance (default: 1e-06)
  --atol ATOL  Absolute tolerance (default: 1e-06)
  -q, --quiet  Quiet mode (only prints final message) (default: False)

Test suite

pyexodiff includes a python script run_tests.py which uses the pytest framework to run the included tests. The test suite can be run using

./run_tests.py

New tests can be added anywhere within the test directory. The test harness recurses through this directory and all subdirectories looking for all instances of a tests file. This YAML file contains the details of each test in that directory.

The tests file syntax is basic YAML, and looks like:

simple_cube:
  file1: simple_cube.e
  file2: simple_cube.e

In this example, the test harness will run

pyexodiff simple_cube.e simple_cube.e

and determine whether the two files are identical.

The test harness can also test for expected error messages. For example, the following block in a tests file

simple_cube_missing_prop:
  file1: simple_cube.e
  file2: simple_cube_missing_prop.e
  expected_error: variable poro not in both files

will run

pyexodiff simple_cube.e simple_cube_missing_prop.e

and then check that the error message contains the string variable poro not in both files.

Each tests files can contain multiple individual tests. When pytest runs the test suite, the top-level label for each individual test in the tests file (for example, the labels simple_cube and missing_specgrid in the above examples) will be printed to the commandline, along with the status of each test run.

The test suite is run automatically on all pull requests to ensure that pyexodiff continues to work as expected.

Contributors

pyexodiff has been developed by

• Chris Green, CSIRO (cpgr)

New contributions are welcome, using the pull request feature of GitHub.

Feature requests/ bug reports

Any feature requests or bug reports should be made using the issues feature of GitHub. Pull requests are always welcome!