# -*- coding: utf-8 -*-
# Copyright 2017 Novo Nordisk Foundation Center for Biosustainability,
# Technical University of Denmark.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Programmatically interact with the memote test suite."""
from __future__ import absolute_import
import io
import logging
try:
import simplejson as json
except ImportError:
import json
import pytest
from six import iteritems
from memote.suite import TEST_DIRECTORY
from memote.suite.collect import ResultCollectionPlugin
from memote.suite.reporting.reports import SnapshotReport, HistoryReport
__all__ = ("test_model", "snapshot_report", "diff_report", "history_report")
LOGGER = logging.getLogger(__name__)
[docs]def test_model(model, filename=None, results=False, pytest_args=None,
exclusive=None, skip=None, solver=None, custom=(None, None)):
"""
Test a model and optionally store results as JSON.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
filename : str or pathlib.Path, optional
A filename if JSON output of the results is desired.
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.
custom : tuple, optional
A tuple with the absolute path to a directory that contains custom test
modules at index 0 and the absolute path to the corresponding config
file at index 1.
Returns
-------
int
The return code of the pytest suite.
dict, optional
A nested dictionary structure that contains the complete test results.
"""
if pytest_args is None:
pytest_args = ["--tb", "short", TEST_DIRECTORY]
elif not any(a.startswith("--tb") for a in pytest_args):
pytest_args.extend(["--tb", "short"])
if TEST_DIRECTORY not in pytest_args:
pytest_args.append(TEST_DIRECTORY)
LOGGER.debug("%s", str(custom))
if custom != (None, None):
custom_test_path, custom_config = custom
pytest_args.append(custom_test_path)
plugin = ResultCollectionPlugin(model, exclusive=exclusive, skip=skip,
custom_config=custom_config)
LOGGER.info("#" * 50)
LOGGER.info("%s", plugin.custom_config)
LOGGER.info("#" * 50)
else:
plugin = ResultCollectionPlugin(model, exclusive=exclusive, skip=skip)
code = pytest.main(pytest_args, plugins=[plugin])
if filename is not None:
with open(filename, "w") as file_h:
LOGGER.info("Writing JSON output '%s'.", filename)
try:
json.dump(plugin.results, file_h, sort_keys=True, indent=4,
separators=(",", ": "))
except TypeError:
# Log information to easily find the culprit.
json_types = (type(None), int, float, str, list, dict)
for name, annotation in iteritems(plugin.results["tests"]):
data = annotation.get("data")
try:
for key, value in iteritems(data):
if not isinstance(value, json_types):
LOGGER.debug(
" %s - %s: %s", name, key, type(
value)
)
except AttributeError:
if not isinstance(data, json_types):
LOGGER.debug(" %s: %s", name, type(data))
if results:
return code, plugin.results
else:
return code
[docs]def snapshot_report(results, filename):
"""
Test a model and save a basic report.
Parameters
----------
results : dict
Nested dictionary structure as returned from the test suite.
filename : str or pathlib.Path
A filename for the HTML report.
"""
report = SnapshotReport(results)
LOGGER.info("Writing basic report '%s'.", filename)
with io.open(filename, "w") as file_h:
file_h.write(report.render_html())
[docs]def history_report(repository, directory, filename, index="hash"):
"""
Test a model and save a history report.
Parameters
----------
repository : git.Repo, optional
An instance of the working directory git repository.
directory : str or pathlib.Path
Use the JSON files in the directory that correspond to this git branch's
commit history to generate the report.
filename : str or pathlib.Path
A filename for the HTML report.
index : {"hash", "time"}, optional
The default horizontal axis type for all plots.
"""
report = HistoryReport(repository, directory, index=index)
LOGGER.info("Writing history report '%s'.", filename)
with io.open(filename, "w") as file_h:
file_h.write(report.render_html())
[docs]def diff_report():
u"""Coming soon™."""
raise NotImplementedError(u"Coming soon™.")
