schrodinger.application.matsci.mstest module¶

Unit test related functions/classes.

schrodinger.application.matsci.mstest.assert_same_struct(struct1, struct2, target_rmsd=0.0, decimal=1, msg=None)¶

Assert that two structures are almost same.

Parameters

struct1 (structure.Structure) – First structure
struct2 (structure.Structure) – Second structure
target_rmsd (float) – Target RMSD for two structures
decimal (int) – The number of decimal places used for comparing the two RMSD floats. In unittest needs to be set fairly loosely so that the tests pass on different OSs
msg (str or None) – message shown if failure occurs

Raises

AssertionError – when the two struct are not equal within given tolerance

schrodinger.application.matsci.mstest.mmexception_side_effect()¶

Get an MmException object that can be used as a side effect

Return type: mm.MmException
Returns: returns an mm.MmException object that can be used as a side effect for Mocks

class schrodinger.application.matsci.mstest.MSTestCase(*args, **kwargs)¶

Bases: unittest.case.TestCase

__init__(*args, **kwargs)¶: See parent for documentation. When using addTypeEqualityFunc for a new object, always add it to assertAlmostEqual.

numpy_equal(actual, desired, msg=None)¶: Call numpy equal

assertStructEqual(struct1, struct2, msg=None)¶

Assert that two structures are equivalent.

Parameters

struct1 (structure.Structure) – First structure
struct2 (structure.Structure) – Second structure
msg (str or None) – message shown if failure occurs

Raises

AssertionError – when the two structures are not same.

assertStructAlmostEqual(struct1, struct2, target_rmsd=0.0, decimal=1, msg=None)¶

Assert that two structures are almost same.

Parameters

struct1 (structure.Structure) – First structure
struct2 (structure.Structure) – Second structure
target_rmsd (float) – Target RMSD for two structures
decimal (int) – The number of decimal places used for comparing the two RMSD floats. In unittest needs to be set fairly loosely so that the tests pass on different OSs
msg (str or None) – message shown if failure occurs

Raises

AssertionError – when the two struct are not equal within given tolerance

assertAlmostEqual(actual, desired, decimal=6, msg=None, places=None)¶

Override assertAlmostEqual with numpy testing assert_almost_equal. Add functionality to test structure and dictionaries as well.

Parameters

actual (array_like or dict or structure.Structure) – the object to check
desired (array_like or dict or structure.Structure) – the expected object
msg (str or None) – message shown if failure occurs
decimal (int) – desired precision
places (int) – Provided for compatibility with unittest API, which uses the places keyword rather than decimal. If given, will override the decimal value

typeTest(obj_type, actual, desired, msg)¶

Check if actual and desired are of given type.

Parameters

obj_type (any class) – Object type to check actual and desired is of
actual (any class) – the actual object to check the type of
desired (any class) – the desired object to check the type of

Return bool

True if type of actual and desired is obj_type else False

getCallResult(mocked_function, index=None, key=None, call_number=None, msg=None)¶

Get the value for the passed argument for the mocked function

Parameters

mocked_function (unittest.mock.MagicMock) – mocked function which was called
index (int) – 0-based index of the argument to compare.
argument (str) – Name of the keyword argument
call_number (int) – Index of the call made to the function. None means the most recent call, calls are indexed starting at 1.
msg (str or None) – message shown if failure occurs

Return list or tuple or dict or set or frozenset or str

value for the passed argument for the mocked function

Raises

AssertionError – the mocked fuction was not called with input index or argument.

assertCallEqual(actual, mocked_function, index=None, argument=None, call_number=None, msg=None)¶

Check if the actual value is equal to value that the mocked fuction was called with.

Parameters

actual – actual value of the mock call to compare to
mocked_function (unittest.mock.MagicMock) – mocked function which was called
index (int) – index of the argument to compare
argument (str) – name of the keyword argument
call_number (int or None) – Number of the call made to the function. If none the last call will be taken and 1 will be oldest (first) call
msg (str or None) – message shown if failure occurs

Raises

AssertionError – If actual value is not equal to value that the mocked fuction was called with or the fuction was not called with input index/argument.

assertCallNotEqual(actual, mocked_function, index=None, argument=None, call_number=None, msg=None)¶

Check if the actual value is not equal to value that the mocked fuction was called with.

Parameters

actual – actual value of the mock call to compare to
mocked_function (unittest.mock.MagicMock) – mocked function which was called
index (int) – Index of the argument to compare
argument (str) – Name of the keyword argument
call_number (int or None) – Number of the call made to the function. If none the last call will be taken and 1 will be oldest (first) call
msg (str or None) – message shown if failure occurs

Raises

AssertionError – If actual value is equal to value that the mocked fuction was called with or the fuction was not called with input index/argument.

assertCallIn(actual, mocked_function, index=None, argument=None, call_number=None, msg=None)¶

Check if the actual value is in the container that the mocked fuction was called with.

Parameters

actual – value to check if it was in the call argument
mocked_function (unittest.mock.MagicMock) – mocked function which was called
index (int) – Index of the argument to compare
argument (str) – Name of the keyword argument
call_number (int or None) – Number of the call made to the function. If none the last call will be taken and 1 will be oldest (first) call
msg (str or None) – message shown if failure occurs

Raises

AssertionError – If actual value is not in to value that the mocked fuction was called with or the fuction was not called with input index/argument.

assertCallNotIn(actual, mocked_function, index=None, argument=None, call_number=None, msg=None)¶

Check if the actual value is not in the container that the mocked fuction was called with.

Parameters

actual – value to check if it was not in the call argument
mocked_function (unittest.mock.MagicMock) – mocked function which was called
index (int) – Index of the argument to compare
argument (str) – Name of the keyword argument
call_number (int or None) – Number of the call made to the function. If none the last call will be taken and 1 will be oldest (first) call

Raises

AssertionError – If actual value is not in to value that the mocked fuction was called with or the fuction was not called with input index/argument.

assertCallAlmostEqual(actual, mocked_function, index=None, argument=None, call_number=None, msg=None, decimal=6)¶

Check if the actual value is equal to value that the mocked fuction was called with.

Parameters

actual (list or tuple or dict or set or frozenset or str) – actual value of the mock call to compare to
mocked_function (unittest.mock.MagicMock) – mocked function which was called
index (int) – Index of the argument to compare
argument (str) – Name of the keyword argument
call_number (int or None) – Number of the call made to the function. If none the last call will be taken and 1 will be oldest (first) call
msg (str or None) – message shown if failure occurs
decimal (int) – desired precision

Raises

AssertionError – If actual value is not equal (within the decimal places) to value that the mocked fuction was called with or the fuction was not called with input index/argument.

assertCalledTimes(times, mocked_function, msg=None)¶

Check if the mocked fuction was called passed number of times

Parameters

times (int) – number of times mocked_function was called
mocked_function (unittest.mock.MagicMock) – mocked function which was called
msg (str or None) – message shown if failure occurs

Raises

AssertionError – If the mocked fuction was not called the passed amount of time

assertFlag(cmd, flag, value=None, is_in=True)¶

Check that an expected flag is in (or not in) the command line list and also check the value of that flag. Note that the language used here is for the command line, but this function works for any sequence where one might want to simultaneously check the ith and i+1th values together.

Examples:: self.assertFlag(cmd, ‘-gpu’) self.assertFlag(cmd, ‘-HOST’, value=’bolt_personal:5’) self.assertFlag(cmd, ‘-nosystem’, is_in=False)

Parameters

cmd (list) – The list to check
flag – The item to check if it is in cmd (may be any type)
value – If given, the item following flag will be checked to see if it is equal to value.
is_in (bool) – If true, checks if flag is in cmd. If False, checks that flag is not in cmd, and value is ignored.

Raises

AssertionError – If flag violates the is_in setting, or if value is given and does not match the item after flag.

assertTableContentsEqual(table, expected_contents, expected_column_headers=None)¶

Assert that the actual table contents match the expected ones. Optionally checks table headers too.

Parameters

table (QtWidgets.QTableWidget) – The table to get actual contents from
expected_contents (list) – List of lists containing the desired data in the table. Each inner list has the contents of a row.
expected_column_headers (list) – If not None, the column headers in the table will be compared with this list

Raises

AssertionError – If the contents are not equal

assertStageEqual(stage1, stage2)¶

Assert that the two desmond stages are equal.

Parameters

stage1 (sea.Map) – first stage
stage2 (sea.Map) – Second stage

Raises

AssertionError – If the contents are not equal

classmethod addClassCleanup(function, /, *args, **kwargs)¶: Same as addCleanup, except the cleanup items are called even if setUpClass fails (unlike tearDownClass).

addCleanup(function, /, *args, **kwargs)¶

Add a function, with arguments, to be called when the test is completed. Functions added are called on a LIFO basis and are called after tearDown on test failure or success.

Cleanup items are called even if setUp fails (unlike tearDown).

addTypeEqualityFunc(typeobj, function)¶

Add a type specific assertEqual style function to compare a type.

This method is for use by TestCase subclasses that need to register their own type equality functions to provide nicer error messages.

Args:

typeobj: The data type to call this function on when both values: are of the same type in assertEqual().
function: The callable taking two arguments and an optional: msg= argument that raises self.failureException with a useful error message when the two arguments are not equal.

assertAlmostEquals(**kwargs)¶

assertCountEqual(first, second, msg=None)¶

Asserts that two iterables have the same elements, the same number of times, without regard to order.

self.assertEqual(Counter(list(first)),
Counter(list(second)))

Example:

[0, 1, 1] and [1, 0, 1] compare equal.

[0, 0, 1] and [0, 1] compare unequal.

assertDictContainsSubset(subset, dictionary, msg=None)¶: Checks whether dictionary is a superset of subset.

assertDictEqual(d1, d2, msg=None)¶

assertEqual(first, second, msg=None)¶: Fail if the two objects are unequal as determined by the ‘==’ operator.

assertEquals(**kwargs)¶

assertFalse(expr, msg=None)¶: Check that the expression is false.

assertGreater(a, b, msg=None)¶: Just like self.assertTrue(a > b), but with a nicer default message.

assertGreaterEqual(a, b, msg=None)¶: Just like self.assertTrue(a >= b), but with a nicer default message.

assertIn(member, container, msg=None)¶: Just like self.assertTrue(a in b), but with a nicer default message.

assertIs(expr1, expr2, msg=None)¶: Just like self.assertTrue(a is b), but with a nicer default message.

assertIsInstance(obj, cls, msg=None)¶: Same as self.assertTrue(isinstance(obj, cls)), with a nicer default message.

assertIsNone(obj, msg=None)¶: Same as self.assertTrue(obj is None), with a nicer default message.

assertIsNot(expr1, expr2, msg=None)¶: Just like self.assertTrue(a is not b), but with a nicer default message.

assertIsNotNone(obj, msg=None)¶: Included for symmetry with assertIsNone.

assertLess(a, b, msg=None)¶: Just like self.assertTrue(a < b), but with a nicer default message.

assertLessEqual(a, b, msg=None)¶: Just like self.assertTrue(a <= b), but with a nicer default message.

assertListEqual(list1, list2, msg=None)¶

A list-specific equality assertion.

Args:: list1: The first list to compare. list2: The second list to compare. msg: Optional message to use on failure instead of a list of

differences.

assertLogs(logger=None, level=None)¶

Fail unless a log message of level level or higher is emitted on logger_name or its children. If omitted, level defaults to INFO and logger defaults to the root logger.

This method must be used as a context manager, and will yield a recording object with two attributes: output and records. At the end of the context manager, the output attribute will be a list of the matching formatted log messages and the records attribute will be a list of the corresponding LogRecord objects.

Example:

with self.assertLogs('foo', level='INFO') as cm:
    logging.getLogger('foo').info('first message')
    logging.getLogger('foo.bar').error('second message')
self.assertEqual(cm.output, ['INFO:foo:first message',
                             'ERROR:foo.bar:second message'])

assertMultiLineEqual(first, second, msg=None)¶: Assert that two multi-line strings are equal.

assertNotAlmostEqual(first, second, places=None, msg=None, delta=None)¶

Fail if the two objects are equal as determined by their difference rounded to the given number of decimal places (default 7) and comparing to zero, or by comparing that the difference between the two objects is less than the given delta.

Note that decimal places (from zero) are usually not the same as significant digits (measured from the most significant digit).

Objects that are equal automatically fail.

assertNotAlmostEquals(**kwargs)¶

assertNotEqual(first, second, msg=None)¶: Fail if the two objects are equal as determined by the ‘!=’ operator.

assertNotEquals(**kwargs)¶

assertNotIn(member, container, msg=None)¶: Just like self.assertTrue(a not in b), but with a nicer default message.

assertNotIsInstance(obj, cls, msg=None)¶: Included for symmetry with assertIsInstance.

assertNotRegex(text, unexpected_regex, msg=None)¶: Fail the test if the text matches the regular expression.

assertNotRegexpMatches(**kwargs)¶

assertRaises(expected_exception, *args, **kwargs)¶

Fail unless an exception of class expected_exception is raised by the callable when invoked with specified positional and keyword arguments. If a different type of exception is raised, it will not be caught, and the test case will be deemed to have suffered an error, exactly as for an unexpected exception.

If called with the callable and arguments omitted, will return a context object used like this:

with self.assertRaises(SomeException):
    do_something()

An optional keyword argument ‘msg’ can be provided when assertRaises is used as a context object.

The context manager keeps a reference to the exception as the ‘exception’ attribute. This allows you to inspect the exception after the assertion:

with self.assertRaises(SomeException) as cm:
    do_something()
the_exception = cm.exception
self.assertEqual(the_exception.error_code, 3)

assertRaisesRegex(expected_exception, expected_regex, *args, **kwargs)¶

Asserts that the message in a raised exception matches a regex.

Args:

expected_exception: Exception class expected to be raised. expected_regex: Regex (re.Pattern object or string) expected

to be found in error message.

args: Function to be called and extra positional args. kwargs: Extra kwargs. msg: Optional message used in case of failure. Can only be used

when assertRaisesRegex is used as a context manager.

assertRaisesRegexp(**kwargs)¶

assertRegex(text, expected_regex, msg=None)¶: Fail the test unless the text matches the regular expression.

assertRegexpMatches(**kwargs)¶

assertSequenceEqual(seq1, seq2, msg=None, seq_type=None)¶

An equality assertion for ordered sequences (like lists and tuples).

For the purposes of this function, a valid ordered sequence type is one which can be indexed, has a length, and has an equality operator.

Args:

seq1: The first sequence to compare. seq2: The second sequence to compare. seq_type: The expected datatype of the sequences, or None if no

datatype should be enforced.

msg: Optional message to use on failure instead of a list of: differences.

assertSetEqual(set1, set2, msg=None)¶

A set-specific equality assertion.

Args:: set1: The first set to compare. set2: The second set to compare. msg: Optional message to use on failure instead of a list of

differences.

assertSetEqual uses ducktyping to support different types of sets, and is optimized for sets specifically (parameters must support a difference method).

assertTrue(expr, msg=None)¶: Check that the expression is true.

assertTupleEqual(tuple1, tuple2, msg=None)¶

A tuple-specific equality assertion.

Args:: tuple1: The first tuple to compare. tuple2: The second tuple to compare. msg: Optional message to use on failure instead of a list of

differences.

assertWarns(expected_warning, *args, **kwargs)¶

Fail unless a warning of class warnClass is triggered by the callable when invoked with specified positional and keyword arguments. If a different type of warning is triggered, it will not be handled: depending on the other warning filtering rules in effect, it might be silenced, printed out, or raised as an exception.

If called with the callable and arguments omitted, will return a context object used like this:

with self.assertWarns(SomeWarning):
    do_something()

An optional keyword argument ‘msg’ can be provided when assertWarns is used as a context object.

The context manager keeps a reference to the first matching warning as the ‘warning’ attribute; similarly, the ‘filename’ and ‘lineno’ attributes give you information about the line of Python code from which the warning was triggered. This allows you to inspect the warning after the assertion:

with self.assertWarns(SomeWarning) as cm:
    do_something()
the_warning = cm.warning
self.assertEqual(the_warning.some_attribute, 147)

assertWarnsRegex(expected_warning, expected_regex, *args, **kwargs)¶

Asserts that the message in a triggered warning matches a regexp. Basic functioning is similar to assertWarns() with the addition that only warnings whose messages also match the regular expression are considered successful matches.

Args:

expected_warning: Warning class expected to be triggered. expected_regex: Regex (re.Pattern object or string) expected

to be found in error message.

args: Function to be called and extra positional args. kwargs: Extra kwargs. msg: Optional message used in case of failure. Can only be used

when assertWarnsRegex is used as a context manager.

assert_(**kwargs)¶

countTestCases()¶

debug()¶: Run the test without collecting errors in a TestResult

defaultTestResult()¶

classmethod doClassCleanups()¶: Execute all class cleanup functions. Normally called for you after tearDownClass.

doCleanups()¶: Execute all cleanup functions. Normally called for you after tearDown.

fail(msg=None)¶: Fail immediately, with the given message.

failIf(**kwargs)¶

failIfAlmostEqual(**kwargs)¶

failIfEqual(**kwargs)¶

failUnless(**kwargs)¶

failUnlessAlmostEqual(**kwargs)¶

failUnlessEqual(**kwargs)¶

failUnlessRaises(**kwargs)¶

failureException¶: alias of AssertionError

id()¶

longMessage = True¶

maxDiff = 640¶

run(result=None)¶

setUp()¶: Hook method for setting up the test fixture before exercising it.

classmethod setUpClass()¶: Hook method for setting up class fixture before running tests in the class.

shortDescription()¶

Returns a one-line description of the test, or None if no description has been provided.

The default implementation of this method returns the first line of the specified test method’s docstring.

skipTest(reason)¶: Skip this test.

subTest(msg=<object object>, **params)¶: Return a context manager that will return the enclosed block of code in a subtest identified by the optional message and keyword parameters. A failure in the subtest marks the test case as failed but resumes execution at the end of the enclosed block, allowing further test code to be executed.

tearDown()¶: Hook method for deconstructing the test fixture after testing it.

classmethod tearDownClass()¶: Hook method for deconstructing the class fixture after running all tests in the class.

schrodinger.application.matsci.mstest.matsci_scripts_testfile(path)¶

Get the full path to the test file at mmshare/python/test/matsci/path

Parameters: path (str) – Relative path of file
Return type: str
Returns: Full path to file

schrodinger.application.matsci.mstest.matsci_application_testfile(path)¶

Get the full path to the test file at mmshare/python/test/application/matsci/path

Parameters: path (str) – Relative path of file
Return type: str
Returns: Full path to file

schrodinger.application.matsci.mstest.load_structure(filename)¶

Load the first structure from the given file in the testfile directory where structures are stored

Parameters: filename (str) – The name of the structure file
Return type: structure.Structure
Returns: The first structure in filename

schrodinger.application.matsci.mstest.mock_json_load_from_fh(module, contents_dict)¶

Context manager to mock json.load on a file handle in the given module and return the given contents dictionary.

Parameters

module (module) – the module using open and json
contents_dict (dict) – the contents dictionary

schrodinger.application.matsci.mstest.set_wa_dont_show_on_screen(widget)¶

Sets WA_DontShowOnScreen attribute to True for the given widget

Parameters: widget (QWidget) – The widget whose WA_DontShowOnScreen attribute is to be set.

schrodinger.application.matsci.mstest.ms_use_rdkit_ff_helper(state)¶

Yield with MS_USE_RDKIT feature flag set to state.

Parameters: state (bool) – Whether feature flag should be enabled or disabled