test_suite

Tabulating Validation Test Results on the SBML Test Suite

The process_test_suite.py script is designed to evaluate SBML files using the pyneuroml library.

It currently runs three validation tests:

1. Standard SBML validation.
2. SBML validation with strict unit checks.
3. SEDML validation, where SEDML files are assumed to have the same base filename as the SBML files but with a -sedml.xml extension instead of .xml.

The output is a markdown file containing a simple table of the results obtained on each file, where each test result is recorded as either a pass or FAIL.

Run the Validation Script

Navigate to the test_suite directory and run for example

 python process_test_suite.py --cases 00001 00002 00011 --sbml-level_version l1v2 --output-file results_00001_00002_00011.md

or to run all test cases using the highest SBML versions available navigate to the test_suite directory and run (overwrites results.md)

 python process_test_suite.py 

Test specific cases

Navigate to the test_suite directory and run for example

test_test_suite_compatibility_biosimulators.py --cases 00006 01280 --sbml-level_version highest

or to run test cases 00001 and 01186 (tested in this repository) using the highest SBML versions available navigate to the test_suite directory and run

test_test_suite_compatibility_biosimulators.py 

Command Line Options

• --limit
  Description: Limits the number of test cases processed.
  Usage: --limit <number>
  Default: 0 (no limit)

• --cases
  Description: List specific cases to process.
  Usage: --cases <list>
  Default: [] (no limit)

• --suite-path
  Description: Specifies the path to the directory containing the test suite files.
  Usage: --suite-path <path>
  Default: . (current directory)

• --sbml-level_version
  Description: String that specifies the level and version of files to select for processing (e.g., 'l3v2').
  Usage: --sbml-level_version <string>
  Default: highest

• --suite-url-base
  Description: Base URL for the online test case files to include as links in the results. Set to an empty string to disable links.
  Usage: --suite-url-base <url>
  Default: https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic

process_test_suite only

• --skip
  Description: Skip cases listed.
  Usage: --skip <list>
  Default: [] (no skip)

• --output-file
  Description: Specifies the path to the output file where the results will be written.
  Usage: --output-file <file path>
  Default: results.md