memote.suite.api

Programmatically interact with the memote test suite.

Module Contents

Functions

validate_model(path) Validate a model structurally and optionally store results as JSON.
test_model(model, sbml_version=None, results=False, pytest_args=None, exclusive=None, skip=None, experimental=None, solver_timeout=10) Test a model and optionally store results as JSON.
snapshot_report(result, config=None, html=True) Generate a snapshot report from a result set and configuration.
history_report(history, config=None, html=True) Test a model and save a history report.
diff_report(diff_results, config=None, html=True) Generate a diff report from a result set and configuration.
memote.suite.api.validate_model(path)[source]

Validate a model structurally and optionally store results as JSON.

Parameters:
path

Path to model file.

Returns:
tuple
cobra.Model

The metabolic model under investigation.

tuple

A tuple reporting on the SBML level, version, and FBC package version used (if any) in the SBML document.

dict

A simple dictionary containing a list of errors and warnings.

memote.suite.api.test_model(model, sbml_version=None, results=False, pytest_args=None, exclusive=None, skip=None, experimental=None, solver_timeout=10)[source]

Test a model and optionally store results as JSON.

Parameters:
model : cobra.Model

The metabolic model under investigation.

sbml_version: tuple, optional

A tuple reporting on the level, version, and FBC use of the SBML file.

results : bool, optional

Whether to return the results in addition to the return code.

pytest_args : list, optional

Additional arguments for the pytest suite.

exclusive : iterable, optional

Names of test cases or modules to run and exclude all others. Takes precedence over skip.

skip : iterable, optional

Names of test cases or modules to skip.

solver_timeout: int, optional

Timeout in seconds to set on the mathematical optimization solver (default 10).

Returns:
int

The return code of the pytest suite.

memote.Result, optional

A nested dictionary structure that contains the complete test results.

memote.suite.api.snapshot_report(result, config=None, html=True)[source]

Generate a snapshot report from a result set and configuration.

Parameters:
result : memote.MemoteResult

Nested dictionary structure as returned from the test suite.

config : dict, optional

The final test report configuration (default None).

html : bool, optional

Whether to render the report as full HTML or JSON (default True).

memote.suite.api.history_report(history, config=None, html=True)[source]

Test a model and save a history report.

Parameters:
history : memote.HistoryManager

The manager grants access to previous results.

config : dict, optional

The final test report configuration.

html : bool, optional

Whether to render the report as full HTML or JSON (default True).

memote.suite.api.diff_report(diff_results, config=None, html=True)[source]

Generate a diff report from a result set and configuration.

Parameters:
diff_results : iterable of memote.MemoteResult

Nested dictionary structure as returned from the test suite.

config : dict, optional

The final test report configuration (default None).

html : bool, optional

Whether to render the report as full HTML or JSON (default True).