memote

(me)tabolic (mo)del (te)sts.

The memote Python package is a community-driven effort towards a standardized genome-scale metabolic model test suite.

Package Contents

Classes

MemoteResult Collect the metabolic model test suite results.
ResultManager Manage storage of results to JSON files.
RepoResultManager Manage storage of results to JSON files.
SQLResultManager Manage storage of results to a database.
HistoryManager Manage access to results in the commit history of a git repository.
ReportConfiguration Collect the metabolic model test suite results.
Report Determine the abstract report interface.
SnapshotReport Render a one-time report from the given model results.
HistoryReport Render a rich report using the git repository history.
DiffReport Render a report displaying the results of two or more models side-by-side.
MemoteExtension Provide an absolute path to a file.

Functions

get_versions() Get version information or return default if unable to do so.
show_versions() Print formatted dependency information to stdout.
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.
diff_report(diff_results, config=None, html=True) Generate a diff report from a result set and configuration.
history_report(history, config=None, html=True) Test a model and save a history report.
memote.__author__ = Moritz E. Beber[source]
memote.__email__ = midnighter@posteo.net[source]
memote.get_versions()[source]

Get version information or return default if unable to do so.

memote.__version__[source]
memote.show_versions()[source]

Print formatted dependency information to stdout.

memote.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.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.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.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).
memote.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).
class memote.MemoteResult(*args, **kwargs)

Bases: dict

Collect the metabolic model test suite results.

static add_environment_information(meta)

Record environment information.

class memote.ResultManager(**kwargs)

Bases: object

Manage storage of results to JSON files.

store(self, result, filename, pretty=True)

Write a result to the given file.

Parameters:
result : memote.MemoteResult

The dictionary structure of results.

filename : str or pathlib.Path

Store results directly to the given filename.

pretty : bool, optional

Whether (default) or not to write JSON in a more legible format.
load(self, filename)

Load a result from the given JSON file.

class memote.RepoResultManager(repository, location, **kwargs)

Bases: memote.suite.results.result_manager.ResultManager

Manage storage of results to JSON files.

Results are stored to and loaded from a specific location (directory) and enriched with git commit meta information.

record_git_info(self, commit=None)

Record git meta information.

Parameters:
commit : str, optional

Unique hexsha of the desired commit.
Returns:
GitInfo

Git commit meta information.
get_filename(self, git_info)

Create a filename from the storage directory and the commit hash.

Parameters:
git_info : GitInfo

A named tuple with git meta information.
Returns:
str

The path to the file where the result of the current commit is stored.
static add_git(meta, git_info)

Enrich the result meta information with commit data.

store(self, result, commit=None, **kwargs)

Store a result in a JSON file attaching git meta information.

Parameters:
result : memote.MemoteResult

The dictionary structure of results.

commit : str, optional

Unique hexsha of the desired commit.

kwargs

Passed to parent function.
load(self, commit=None)

Load a result from the storage directory.

class memote.SQLResultManager(**kwargs)

Bases: memote.suite.results.repo_result_manager.RepoResultManager

Manage storage of results to a database.

store(self, result, commit=None, **kwargs)

Store a result in a JSON file attaching git meta information.

Parameters:
result : memote.MemoteResult

The dictionary structure of results.

commit : str, optional

Unique hexsha of the desired commit.

kwargs

Passed to parent function.
load(self, commit=None)

Load a result from the database.

class memote.HistoryManager(repository, manager, **kwargs)

Bases: object

Manage access to results in the commit history of a git repository.

Attributes:
manager : memote.RepoResultManager

The manager for accessing individual results.

current : str

The name of the currently active branch.
build_branch_structure(self, model, skip)

Inspect and record the repo’s branches and their history.

iter_branches(self)

Iterate over branch names and their commit histories.

iter_commits(self)

Iterate over all commit hashes in the repository.

load_history(self, model, skip=('gh-pages', ))

Load the entire results history into memory.

Could be a bad idea in a far future.

get_result(self, commit, default=None)

Return an individual result from the history if it exists.

__contains__(self, commit)

Test for the existence of a result for a commit.

class memote.ReportConfiguration(*args, **kwargs)

Bases: dict

Collect the metabolic model test suite results.

classmethod load(cls, filename=None)

Load a test report configuration.

merge(self, other)

Merge a custom configuration.

class memote.Report(result, configuration, **kwargs)

Bases: object

Determine the abstract report interface.

Attributes:
result : memote.MemoteResult

The dictionary structure of results.

configuration : memote.MemoteConfiguration

A memote configuration structure.
render_json(self, pretty=False)

Render the report results as JSON.

Parameters:
pretty : bool, optional

Whether to format the resulting JSON in a more legible way ( default False).
render_html(self)

Render an HTML report.

get_configured_tests(self)

Get tests explicitly configured.

determine_miscellaneous_tests(self)

Identify tests not explicitly configured in test organization.

List them as an additional card called Misc, which is where they will now appear in the report.

compute_score(self)

Calculate the overall test score using the configuration.

memote.LOGGER
class memote.SnapshotReport(**kwargs)

Bases: memote.suite.reporting.report.Report

Render a one-time report from the given model results.

Attributes:
result : memote.MemoteResult

The dictionary structure of results.

configuration : memote.MemoteConfiguration

A memote configuration structure.
class memote.HistoryReport(history, configuration, **kwargs)

Bases: memote.suite.reporting.report.Report

Render a rich report using the git repository history.

Attributes:
configuration : memote.MemoteConfiguration

A memote configuration structure.
collect_history(self)

Build the structure of results in terms of a commit history.

class memote.DiffReport(diff_results, configuration, **kwargs)

Bases: memote.suite.reporting.report.Report

Render a report displaying the results of two or more models side-by-side.

Attributes:
diff_results : python.Dictionary

The dictionary structure of memote.MemoteResult objects.

configuration : memote.MemoteConfiguration

A memote configuration structure.
format_and_score_diff_data(self, diff_results)

Reformat the api results to work with the front-end.

class memote.MemoteExtension(environment)[source]

Bases: jinja2.ext.Extension

Provide an absolute path to a file.

tags
static normalize(filename)

Return an absolute path of the given file name.