deepchem.models.tests package

Submodules

deepchem.models.tests.test_api module

Integration tests for singletask vector feature models.

class deepchem.models.tests.test_api.TestAPI(methodName='runTest')[source]

Bases: unittest.case.TestCase

Test top-level API for ML models.

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.

Parameters:
  • 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.
assertAlmostEqual(first, second, places=None, msg=None, delta=None)

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

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

If the two objects compare equal then they will automatically compare almost equal.

assertAlmostEquals(*args, **kwargs)
assertCountEqual(first, second, msg=None)

An unordered sequence comparison asserting that the same elements, regardless of order. If the same element occurs more than once, it verifies that the elements occur the same number of times.

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(*args, **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.

Parameters:
  • 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 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(*args, **kwargs)
assertNotEqual(first, second, msg=None)

Fail if the two objects are equal as determined by the ‘!=’ operator.

assertNotEquals(*args, **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(*args, **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.

Parameters:
  • 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(*args, **kwargs)
assertRegex(text, expected_regex, msg=None)

Fail the test unless the text matches the regular expression.

assertRegexpMatches(*args, **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.

Parameters:
  • 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.

Parameters:
  • 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.

Parameters:
  • 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.

Parameters:
  • 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_(*args, **kwargs)
countTestCases()
debug()

Run the test without collecting errors in a TestResult

defaultTestResult()
doCleanups()

Execute all cleanup functions. Normally called for you after tearDown.

fail(msg=None)

Fail immediately, with the given message.

failIf(*args, **kwargs)
failIfAlmostEqual(*args, **kwargs)
failIfEqual(*args, **kwargs)
failUnless(*args, **kwargs)
failUnlessAlmostEqual(*args, **kwargs)
failUnlessEqual(*args, **kwargs)
failUnlessRaises(*args, **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.

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.

tearDownClass()

Hook method for deconstructing the class fixture after running all tests in the class.

test_singletask_sklearn_rf_ECFP_regression_API()[source]

Test of singletask RF ECFP regression API.

test_singletask_sklearn_rf_RDKIT_descriptor_regression_API()[source]

Test of singletask RF RDKIT-descriptor regression API.

test_singletask_sklearn_rf_user_specified_regression_API()[source]

Test of singletask RF USF regression API.

test_singletask_tg_mlp_ECFP_classification_API()[source]

Test of TensorGraph singletask deepchem classification API.

deepchem.models.tests.test_generalize module

Tests to make sure deepchem models can fit models on easy datasets.

class deepchem.models.tests.test_generalize.TestGeneralize(methodName='runTest')[source]

Bases: unittest.case.TestCase

Test that models can learn generalizable models on simple datasets.

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.

Parameters:
  • 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.
assertAlmostEqual(first, second, places=None, msg=None, delta=None)

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

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

If the two objects compare equal then they will automatically compare almost equal.

assertAlmostEquals(*args, **kwargs)
assertCountEqual(first, second, msg=None)

An unordered sequence comparison asserting that the same elements, regardless of order. If the same element occurs more than once, it verifies that the elements occur the same number of times.

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(*args, **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.

Parameters:
  • 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 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(*args, **kwargs)
assertNotEqual(first, second, msg=None)

Fail if the two objects are equal as determined by the ‘!=’ operator.

assertNotEquals(*args, **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(*args, **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.

Parameters:
  • 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(*args, **kwargs)
assertRegex(text, expected_regex, msg=None)

Fail the test unless the text matches the regular expression.

assertRegexpMatches(*args, **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.

Parameters:
  • 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.

Parameters:
  • 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.

Parameters:
  • 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.

Parameters:
  • 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_(*args, **kwargs)
countTestCases()
debug()

Run the test without collecting errors in a TestResult

defaultTestResult()
doCleanups()

Execute all cleanup functions. Normally called for you after tearDown.

fail(msg=None)

Fail immediately, with the given message.

failIf(*args, **kwargs)
failIfAlmostEqual(*args, **kwargs)
failIfEqual(*args, **kwargs)
failUnless(*args, **kwargs)
failUnlessAlmostEqual(*args, **kwargs)
failUnlessEqual(*args, **kwargs)
failUnlessRaises(*args, **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.

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.

tearDownClass()

Hook method for deconstructing the class fixture after running all tests in the class.

test_sklearn_multitask_regression()[source]

Test that sklearn models can learn on simple multitask regression.

test_sklearn_regression()[source]

Test that sklearn models can learn on simple regression datasets.

test_sklearn_transformed_regression()[source]

Test that sklearn models can learn on simple transformed regression datasets.

test_xgboost_classification()[source]

Test that sklearn models can learn on simple classification datasets.

test_xgboost_multitask_regression()[source]

Test that xgboost models can learn on simple multitask regression. This test is not actually slow – but cannot currently run on Ubuntu 14.04 with Tensorflow 1.4.0

See Discussion Here https://github.com/deepchem/deepchem/issues/960

test_xgboost_regression()[source]

This test is not actually slow – but cannot currently run on Ubuntu 14.04 with Tensorflow 1.4.0

See Discussion Here https://github.com/deepchem/deepchem/issues/960

deepchem.models.tests.test_multitask module

Integration tests for multitask datasets.

class deepchem.models.tests.test_multitask.TestMultitask(methodName='runTest')[source]

Bases: unittest.case.TestCase

Sanity tests for multitask data.

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.

Parameters:
  • 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.
assertAlmostEqual(first, second, places=None, msg=None, delta=None)

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

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

If the two objects compare equal then they will automatically compare almost equal.

assertAlmostEquals(*args, **kwargs)
assertCountEqual(first, second, msg=None)

An unordered sequence comparison asserting that the same elements, regardless of order. If the same element occurs more than once, it verifies that the elements occur the same number of times.

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(*args, **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.

Parameters:
  • 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 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(*args, **kwargs)
assertNotEqual(first, second, msg=None)

Fail if the two objects are equal as determined by the ‘!=’ operator.

assertNotEquals(*args, **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(*args, **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.

Parameters:
  • 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(*args, **kwargs)
assertRegex(text, expected_regex, msg=None)

Fail the test unless the text matches the regular expression.

assertRegexpMatches(*args, **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.

Parameters:
  • 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.

Parameters:
  • 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.

Parameters:
  • 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.

Parameters:
  • 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_(*args, **kwargs)
countTestCases()
debug()

Run the test without collecting errors in a TestResult

defaultTestResult()
doCleanups()

Execute all cleanup functions. Normally called for you after tearDown.

fail(msg=None)

Fail immediately, with the given message.

failIf(*args, **kwargs)
failIfAlmostEqual(*args, **kwargs)
failIfEqual(*args, **kwargs)
failUnless(*args, **kwargs)
failUnlessAlmostEqual(*args, **kwargs)
failUnlessEqual(*args, **kwargs)
failUnlessRaises(*args, **kwargs)
failureException

alias of AssertionError

id()
longMessage = True
maxDiff = 640
run(result=None)
setUp()[source]
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.

tearDownClass()

Hook method for deconstructing the class fixture after running all tests in the class.

test_multitask_data()[source]

Test that data associated with a tasks stays associated with it.

test_multitask_order()[source]

Test that order of tasks in multitask datasets is preserved.

deepchem.models.tests.test_overfit module

Tests to make sure deepchem models can overfit on tiny datasets.

class deepchem.models.tests.test_overfit.TestOverfit(methodName='runTest')[source]

Bases: tensorflow.python.framework.test_util.TensorFlowTestCase

Test that models can overfit simple datasets.

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.

Parameters:
  • 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.
assertAllClose(a, b, rtol=1e-06, atol=1e-06)

Asserts that two numpy arrays, or dicts of same, have near values.

This does not support nested dicts.

Parameters:
  • a – The expected numpy ndarray (or anything can be converted to one), or dict of same. Must be a dict iff b is a dict.
  • b – The actual numpy ndarray (or anything can be converted to one), or dict of same. Must be a dict iff a is a dict.
  • rtol – relative tolerance.
  • atol – absolute tolerance.
Raises:

ValueError – if only one of a and b is a dict.

assertAllCloseAccordingToType(a, b, rtol=1e-06, atol=1e-06, float_rtol=1e-06, float_atol=1e-06, half_rtol=0.001, half_atol=0.001, bfloat16_rtol=0.01, bfloat16_atol=0.01)

Like assertAllClose, but also suitable for comparing fp16 arrays.

In particular, the tolerance is reduced to 1e-3 if at least one of the arguments is of type float16.

Parameters:
  • a – the expected numpy ndarray or anything can be converted to one.
  • b – the actual numpy ndarray or anything can be converted to one.
  • rtol – relative tolerance.
  • atol – absolute tolerance.
  • float_rtol – relative tolerance for float32.
  • float_atol – absolute tolerance for float32.
  • half_rtol – relative tolerance for float16.
  • half_atol – absolute tolerance for float16.
  • bfloat16_rtol – relative tolerance for bfloat16.
  • bfloat16_atol – absolute tolerance for bfloat16.
assertAllEqual(a, b)

Asserts that two numpy arrays have the same values.

Parameters:
  • a – the expected numpy ndarray or anything can be converted to one.
  • b – the actual numpy ndarray or anything can be converted to one.
assertAlmostEqual(first, second, places=None, msg=None, delta=None)

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

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

If the two objects compare equal then they will automatically compare almost equal.

assertAlmostEquals(*args, **kwargs)
assertArrayNear(farray1, farray2, err)

Asserts that two float arrays are near each other.

Checks that for all elements of farray1 and farray2 |f1 - f2| < err. Asserts a test failure if not.

Parameters:
  • farray1 – a list of float values.
  • farray2 – a list of float values.
  • err – a float value.
assertCountEqual(first, second, msg=None)

An unordered sequence comparison asserting that the same elements, regardless of order. If the same element occurs more than once, it verifies that the elements occur the same number of times.

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.
assertDeviceEqual(device1, device2)

Asserts that the two given devices are the same.

Parameters:
  • device1 – A string device name or TensorFlow DeviceSpec object.
  • device2 – A string device name or TensorFlow DeviceSpec object.
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(*args, **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.

assertItemsEqual(first, second, msg=None)

An unordered sequence comparison asserting that the same elements, regardless of order. If the same element occurs more than once, it verifies that the elements occur the same number of times.

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.
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.

Parameters:
  • 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.

assertNDArrayNear(ndarray1, ndarray2, err)

Asserts that two numpy arrays have near values.

Parameters:
  • ndarray1 – a numpy ndarray.
  • ndarray2 – a numpy ndarray.
  • err – a float. The maximum absolute difference allowed.
assertNear(f1, f2, err, msg=None)

Asserts that two floats are near each other.

Checks that |f1 - f2| < err and asserts a test failure if not.

Parameters:
  • f1 – A float value.
  • f2 – A float value.
  • err – A float value.
  • msg – An optional string message to append to the failure message.
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 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(*args, **kwargs)
assertNotEqual(first, second, msg=None)

Fail if the two objects are equal as determined by the ‘!=’ operator.

assertNotEquals(*args, **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(*args, **kwargs)
assertProtoEquals(expected_message_maybe_ascii, message)

Asserts that message is same as parsed expected_message_ascii.

Creates another prototype of message, reads the ascii message into it and then compares them using self._AssertProtoEqual().

Parameters:
  • expected_message_maybe_ascii – proto message in original or ascii form.
  • message – the message to validate.
assertProtoEqualsVersion(expected, actual, producer=24, min_consumer=0)
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)
assertRaisesOpError(expected_err_re_or_predicate)
assertRaisesRegex(expected_exception, expected_regex, *args, **kwargs)

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

Parameters:
  • 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(expected_exception, expected_regex, *args, **kwargs)

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

Parameters:
  • 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.
assertRaisesWithPredicateMatch(exception_type, expected_err_re_or_predicate)

Returns a context manager to enclose code expected to raise an exception.

If the exception is an OpError, the op stack is also included in the message predicate search.

Parameters:
  • exception_type – The expected type of exception that should be raised.
  • expected_err_re_or_predicate – If this is callable, it should be a function of one argument that inspects the passed-in exception and returns True (success) or False (please fail the test). Otherwise, the error message is expected to match this regular expression partially.
Returns:

A context manager to surround code that is expected to raise an exception.

assertRegex(text, expected_regex, msg=None)

Fail the test unless the text matches the regular expression.

assertRegexpMatches(*args, **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.

Parameters:
  • 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.

Parameters:
  • 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).

assertShapeEqual(np_array, tf_tensor)

Asserts that a Numpy ndarray and a TensorFlow tensor have the same shape.

Parameters:
  • np_array – A Numpy ndarray or Numpy scalar.
  • tf_tensor – A Tensor.
Raises:

TypeError – If the arguments have the wrong type.

assertStartsWith(actual, expected_start, msg=None)

Assert that actual.startswith(expected_start) is True.

Parameters:
  • actual – str
  • expected_start – str
  • msg – Optional message to report on failure.
assertTrue(expr, msg=None)

Check that the expression is true.

assertTupleEqual(tuple1, tuple2, msg=None)

A tuple-specific equality assertion.

Parameters:
  • 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.

Parameters:
  • 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_(*args, **kwargs)
checkedThread(target, args=None, kwargs=None)

Returns a Thread wrapper that asserts ‘target’ completes successfully.

This method should be used to create all threads in test cases, as otherwise there is a risk that a thread will silently fail, and/or assertions made in the thread will not be respected.

Parameters:
  • target – A callable object to be executed in the thread.
  • args – The argument tuple for the target invocation. Defaults to ().
  • kwargs – A dictionary of keyword arguments for the target invocation. Defaults to {}.
Returns:

A wrapper for threading.Thread that supports start() and join() methods.

countTestCases()
debug()

Run the test without collecting errors in a TestResult

defaultTestResult()
doCleanups()

Execute all cleanup functions. Normally called for you after tearDown.

evaluate(tensors)

Evaluates tensors and returns numpy values.

Parameters:tensors – A Tensor or a nested list/tuple of Tensors.
Returns:tensors numpy values.
fail(msg=None)

Fail immediately, with the given message.

failIf(*args, **kwargs)
failIfAlmostEqual(*args, **kwargs)
failIfEqual(*args, **kwargs)
failUnless(*args, **kwargs)
failUnlessAlmostEqual(*args, **kwargs)
failUnlessEqual(*args, **kwargs)
failUnlessRaises(*args, **kwargs)
failureException

alias of AssertionError

get_temp_dir()

Returns a unique temporary directory for the test to use.

If you call this method multiple times during in a test, it will return the same folder. However, across different runs the directories will be different. This will ensure that across different runs tests will not be able to pollute each others environment. If you need multiple unique directories within a single test, you should use tempfile.mkdtemp as follows:

tempfile.mkdtemp(dir=self.get_temp_dir()):
Returns:string, the path to the unique temporary directory created for this test.
id()
longMessage = True
maxDiff = 640
run(result=None)
setUp()[source]
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()
tearDownClass()

Hook method for deconstructing the class fixture after running all tests in the class.

test_ANI_multitask_regression_overfit()[source]

Test ANI-1 regression overfits tiny data.

test_BP_symmetry_function_overfit()[source]

Test ANI-1 regression overfits tiny data.

test_IRV_multitask_classification_overfit()[source]

Test IRV classifier overfits tiny data.

test_MPNN_singletask_regression_overfit()[source]

Test MPNN overfits tiny data.

test_classification_overfit()[source]

Test that TensorGraph models can overfit simple classification datasets.

test_fittransform_regression_overfit()[source]

Test that TensorGraph FitTransform models can overfit simple regression datasets.

test_multitask_classification_overfit()[source]

Test TensorGraph multitask overfits tiny data.

test_multitask_regression_overfit()[source]

Test TensorGraph multitask overfits tiny data.

test_regression_overfit()[source]

Test that TensorGraph models can overfit simple regression datasets.

test_session(graph=None, config=None, use_gpu=False, force_gpu=False)

Returns a TensorFlow Session for use in executing tests.

This method should be used for all functional tests.

This method behaves different than session.Session: for performance reasons test_session will by default (if graph is None) reuse the same session across tests. This means you may want to either call the function reset_default_graph() before tests, or if creating an explicit new graph, pass it here (simply setting it with as_default() won’t do it), which will trigger the creation of a new session.

Use the use_gpu and force_gpu options to control where ops are run. If force_gpu is True, all ops are pinned to /device:GPU:0. Otherwise, if use_gpu is True, TensorFlow tries to run as many ops on the GPU as possible. If both force_gpu and `use_gpu are False, all ops are pinned to the CPU.

Example: ```python class MyOperatorTest(test_util.TensorFlowTestCase):

def testMyOperator(self):
with self.test_session(use_gpu=True):

valid_input = [1.0, 2.0, 3.0, 4.0, 5.0] result = MyOperator(valid_input).eval() self.assertEqual(result, [1.0, 2.0, 3.0, 5.0, 8.0] invalid_input = [-1.0, 2.0, 7.0] with self.assertRaisesOpError(“negative input not supported”):

MyOperator(invalid_input).eval()

```

Parameters:
  • graph – Optional graph to use during the returned session.
  • config – An optional config_pb2.ConfigProto to use to configure the session.
  • use_gpu – If True, attempt to run as many ops as possible on GPU.
  • force_gpu – If True, pin all ops to /device:GPU:0.
Returns:

A Session object that should be used as a context manager to surround the graph building and execution code in a test case.

test_skewed_classification_overfit()[source]

Test TensorGraph models can overfit 0/1 datasets with few actives.

test_skewed_missing_classification_overfit()[source]

TG, skewed data, few actives

Test TensorGraph models overfit 0/1 datasets with missing data and few actives. This is intended to be as close to singletask MUV datasets as possible.

test_sklearn_classification_overfit()[source]

Test that sklearn models can overfit simple classification datasets.

test_sklearn_multitask_classification_overfit()[source]

Test SKLearn singletask-to-multitask overfits tiny data.

test_sklearn_multitask_regression_overfit()[source]

Test SKLearn singletask-to-multitask overfits tiny regression data.

test_sklearn_regression_overfit()[source]

Test that sklearn models can overfit simple regression datasets.

test_sklearn_skewed_classification_overfit()[source]

Test sklearn models can overfit 0/1 datasets with few actives.

test_tensorgraph_DAG_singletask_regression_overfit()[source]

Test DAG regressor multitask overfits tiny data.

test_tensorgraph_DTNN_multitask_regression_overfit()[source]

Test deep tensor neural net overfits tiny data.

test_tensorgraph_weave_singletask_classification_overfit()[source]

Test weave model overfits tiny data.

test_tensorgraph_weave_singletask_regression_overfit()[source]

Test weave model overfits tiny data.

test_textCNN_singletask_classification_overfit()[source]

Test textCNN model overfits tiny data.

test_textCNN_singletask_regression_overfit()[source]

Test textCNN model overfits tiny data.

test_tf_progressive_regression_overfit()[source]

Test tf progressive multitask overfits tiny data.

test_tf_robust_multitask_classification_overfit()[source]

Test tf robust multitask overfits tiny data.

test_tf_robust_multitask_regression_overfit()[source]

Test tf robust multitask overfits tiny data.

deepchem.models.tests.test_predict module

Tests that deepchem models make deterministic predictions.

class deepchem.models.tests.test_predict.TestPredict(methodName='runTest')[source]

Bases: tensorflow.python.framework.test_util.TensorFlowTestCase

Test that models make deterministic predictions

These tests guard against failures like having dropout turned on at test time.

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.

Parameters:
  • 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.
assertAllClose(a, b, rtol=1e-06, atol=1e-06)

Asserts that two numpy arrays, or dicts of same, have near values.

This does not support nested dicts.

Parameters:
  • a – The expected numpy ndarray (or anything can be converted to one), or dict of same. Must be a dict iff b is a dict.
  • b – The actual numpy ndarray (or anything can be converted to one), or dict of same. Must be a dict iff a is a dict.
  • rtol – relative tolerance.
  • atol – absolute tolerance.
Raises:

ValueError – if only one of a and b is a dict.

assertAllCloseAccordingToType(a, b, rtol=1e-06, atol=1e-06, float_rtol=1e-06, float_atol=1e-06, half_rtol=0.001, half_atol=0.001, bfloat16_rtol=0.01, bfloat16_atol=0.01)

Like assertAllClose, but also suitable for comparing fp16 arrays.

In particular, the tolerance is reduced to 1e-3 if at least one of the arguments is of type float16.

Parameters:
  • a – the expected numpy ndarray or anything can be converted to one.
  • b – the actual numpy ndarray or anything can be converted to one.
  • rtol – relative tolerance.
  • atol – absolute tolerance.
  • float_rtol – relative tolerance for float32.
  • float_atol – absolute tolerance for float32.
  • half_rtol – relative tolerance for float16.
  • half_atol – absolute tolerance for float16.
  • bfloat16_rtol – relative tolerance for bfloat16.
  • bfloat16_atol – absolute tolerance for bfloat16.
assertAllEqual(a, b)

Asserts that two numpy arrays have the same values.

Parameters:
  • a – the expected numpy ndarray or anything can be converted to one.
  • b – the actual numpy ndarray or anything can be converted to one.
assertAlmostEqual(first, second, places=None, msg=None, delta=None)

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

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

If the two objects compare equal then they will automatically compare almost equal.

assertAlmostEquals(*args, **kwargs)
assertArrayNear(farray1, farray2, err)

Asserts that two float arrays are near each other.

Checks that for all elements of farray1 and farray2 |f1 - f2| < err. Asserts a test failure if not.

Parameters:
  • farray1 – a list of float values.
  • farray2 – a list of float values.
  • err – a float value.
assertCountEqual(first, second, msg=None)

An unordered sequence comparison asserting that the same elements, regardless of order. If the same element occurs more than once, it verifies that the elements occur the same number of times.

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.
assertDeviceEqual(device1, device2)

Asserts that the two given devices are the same.

Parameters:
  • device1 – A string device name or TensorFlow DeviceSpec object.
  • device2 – A string device name or TensorFlow DeviceSpec object.
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(*args, **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.

assertItemsEqual(first, second, msg=None)

An unordered sequence comparison asserting that the same elements, regardless of order. If the same element occurs more than once, it verifies that the elements occur the same number of times.

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.
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.

Parameters:
  • 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.

assertNDArrayNear(ndarray1, ndarray2, err)

Asserts that two numpy arrays have near values.

Parameters:
  • ndarray1 – a numpy ndarray.
  • ndarray2 – a numpy ndarray.
  • err – a float. The maximum absolute difference allowed.
assertNear(f1, f2, err, msg=None)

Asserts that two floats are near each other.

Checks that |f1 - f2| < err and asserts a test failure if not.

Parameters:
  • f1 – A float value.
  • f2 – A float value.
  • err – A float value.
  • msg – An optional string message to append to the failure message.
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 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(*args, **kwargs)
assertNotEqual(first, second, msg=None)

Fail if the two objects are equal as determined by the ‘!=’ operator.

assertNotEquals(*args, **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(*args, **kwargs)
assertProtoEquals(expected_message_maybe_ascii, message)

Asserts that message is same as parsed expected_message_ascii.

Creates another prototype of message, reads the ascii message into it and then compares them using self._AssertProtoEqual().

Parameters:
  • expected_message_maybe_ascii – proto message in original or ascii form.
  • message – the message to validate.
assertProtoEqualsVersion(expected, actual, producer=24, min_consumer=0)
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)
assertRaisesOpError(expected_err_re_or_predicate)
assertRaisesRegex(expected_exception, expected_regex, *args, **kwargs)

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

Parameters:
  • 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(expected_exception, expected_regex, *args, **kwargs)

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

Parameters:
  • 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.
assertRaisesWithPredicateMatch(exception_type, expected_err_re_or_predicate)

Returns a context manager to enclose code expected to raise an exception.

If the exception is an OpError, the op stack is also included in the message predicate search.

Parameters:
  • exception_type – The expected type of exception that should be raised.
  • expected_err_re_or_predicate – If this is callable, it should be a function of one argument that inspects the passed-in exception and returns True (success) or False (please fail the test). Otherwise, the error message is expected to match this regular expression partially.
Returns:

A context manager to surround code that is expected to raise an exception.

assertRegex(text, expected_regex, msg=None)

Fail the test unless the text matches the regular expression.

assertRegexpMatches(*args, **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.

Parameters:
  • 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.

Parameters:
  • 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).

assertShapeEqual(np_array, tf_tensor)

Asserts that a Numpy ndarray and a TensorFlow tensor have the same shape.

Parameters:
  • np_array – A Numpy ndarray or Numpy scalar.
  • tf_tensor – A Tensor.
Raises:

TypeError – If the arguments have the wrong type.

assertStartsWith(actual, expected_start, msg=None)

Assert that actual.startswith(expected_start) is True.

Parameters:
  • actual – str
  • expected_start – str
  • msg – Optional message to report on failure.
assertTrue(expr, msg=None)

Check that the expression is true.

assertTupleEqual(tuple1, tuple2, msg=None)

A tuple-specific equality assertion.

Parameters:
  • 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.

Parameters:
  • 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_(*args, **kwargs)
checkedThread(target, args=None, kwargs=None)

Returns a Thread wrapper that asserts ‘target’ completes successfully.

This method should be used to create all threads in test cases, as otherwise there is a risk that a thread will silently fail, and/or assertions made in the thread will not be respected.

Parameters:
  • target – A callable object to be executed in the thread.
  • args – The argument tuple for the target invocation. Defaults to ().
  • kwargs – A dictionary of keyword arguments for the target invocation. Defaults to {}.
Returns:

A wrapper for threading.Thread that supports start() and join() methods.

countTestCases()
debug()

Run the test without collecting errors in a TestResult

defaultTestResult()
doCleanups()

Execute all cleanup functions. Normally called for you after tearDown.

evaluate(tensors)

Evaluates tensors and returns numpy values.

Parameters:tensors – A Tensor or a nested list/tuple of Tensors.
Returns:tensors numpy values.
fail(msg=None)

Fail immediately, with the given message.

failIf(*args, **kwargs)
failIfAlmostEqual(*args, **kwargs)
failIfEqual(*args, **kwargs)
failUnless(*args, **kwargs)
failUnlessAlmostEqual(*args, **kwargs)
failUnlessEqual(*args, **kwargs)
failUnlessRaises(*args, **kwargs)
failureException

alias of AssertionError

get_temp_dir()

Returns a unique temporary directory for the test to use.

If you call this method multiple times during in a test, it will return the same folder. However, across different runs the directories will be different. This will ensure that across different runs tests will not be able to pollute each others environment. If you need multiple unique directories within a single test, you should use tempfile.mkdtemp as follows:

tempfile.mkdtemp(dir=self.get_temp_dir()):
Returns:string, the path to the unique temporary directory created for this test.
id()
longMessage = True
maxDiff = 640
run(result=None)
setUp()[source]
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()
tearDownClass()

Hook method for deconstructing the class fixture after running all tests in the class.

test_session(graph=None, config=None, use_gpu=False, force_gpu=False)

Returns a TensorFlow Session for use in executing tests.

This method should be used for all functional tests.

This method behaves different than session.Session: for performance reasons test_session will by default (if graph is None) reuse the same session across tests. This means you may want to either call the function reset_default_graph() before tests, or if creating an explicit new graph, pass it here (simply setting it with as_default() won’t do it), which will trigger the creation of a new session.

Use the use_gpu and force_gpu options to control where ops are run. If force_gpu is True, all ops are pinned to /device:GPU:0. Otherwise, if use_gpu is True, TensorFlow tries to run as many ops on the GPU as possible. If both force_gpu and `use_gpu are False, all ops are pinned to the CPU.

Example: ```python class MyOperatorTest(test_util.TensorFlowTestCase):

def testMyOperator(self):
with self.test_session(use_gpu=True):

valid_input = [1.0, 2.0, 3.0, 4.0, 5.0] result = MyOperator(valid_input).eval() self.assertEqual(result, [1.0, 2.0, 3.0, 5.0, 8.0] invalid_input = [-1.0, 2.0, 7.0] with self.assertRaisesOpError(“negative input not supported”):

MyOperator(invalid_input).eval()

```

Parameters:
  • graph – Optional graph to use during the returned session.
  • config – An optional config_pb2.ConfigProto to use to configure the session.
  • use_gpu – If True, attempt to run as many ops as possible on GPU.
  • force_gpu – If True, pin all ops to /device:GPU:0.
Returns:

A Session object that should be used as a context manager to surround the graph building and execution code in a test case.

deepchem.models.tests.test_reload module

Test reload for trained models.

class deepchem.models.tests.test_reload.TestReload(methodName='runTest')[source]

Bases: unittest.case.TestCase

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.

Parameters:
  • 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.
assertAlmostEqual(first, second, places=None, msg=None, delta=None)

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

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

If the two objects compare equal then they will automatically compare almost equal.

assertAlmostEquals(*args, **kwargs)
assertCountEqual(first, second, msg=None)

An unordered sequence comparison asserting that the same elements, regardless of order. If the same element occurs more than once, it verifies that the elements occur the same number of times.

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(*args, **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.

Parameters:
  • 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 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(*args, **kwargs)
assertNotEqual(first, second, msg=None)

Fail if the two objects are equal as determined by the ‘!=’ operator.

assertNotEquals(*args, **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(*args, **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.

Parameters:
  • 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(*args, **kwargs)
assertRegex(text, expected_regex, msg=None)

Fail the test unless the text matches the regular expression.

assertRegexpMatches(*args, **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.

Parameters:
  • 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.

Parameters:
  • 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.

Parameters:
  • 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.

Parameters:
  • 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_(*args, **kwargs)
countTestCases()
debug()

Run the test without collecting errors in a TestResult

defaultTestResult()
doCleanups()

Execute all cleanup functions. Normally called for you after tearDown.

fail(msg=None)

Fail immediately, with the given message.

failIf(*args, **kwargs)
failIfAlmostEqual(*args, **kwargs)
failIfEqual(*args, **kwargs)
failUnless(*args, **kwargs)
failUnlessAlmostEqual(*args, **kwargs)
failUnlessEqual(*args, **kwargs)
failUnlessRaises(*args, **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.

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.

tearDownClass()

Hook method for deconstructing the class fixture after running all tests in the class.

test_sklearn_reload()[source]

Test that trained model can be reloaded correctly.

deepchem.models.tests.test_singletask_to_multitask module

Testing singletask-to-multitask.

class deepchem.models.tests.test_singletask_to_multitask.TestSingletasktoMultitask(methodName='runTest')[source]

Bases: unittest.case.TestCase

Test top-level API for singletask_to_multitask ML models.

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.

Parameters:
  • 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.
assertAlmostEqual(first, second, places=None, msg=None, delta=None)

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

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

If the two objects compare equal then they will automatically compare almost equal.

assertAlmostEquals(*args, **kwargs)
assertCountEqual(first, second, msg=None)

An unordered sequence comparison asserting that the same elements, regardless of order. If the same element occurs more than once, it verifies that the elements occur the same number of times.

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(*args, **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.

Parameters:
  • 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 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(*args, **kwargs)
assertNotEqual(first, second, msg=None)

Fail if the two objects are equal as determined by the ‘!=’ operator.

assertNotEquals(*args, **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(*args, **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.

Parameters:
  • 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(*args, **kwargs)
assertRegex(text, expected_regex, msg=None)

Fail the test unless the text matches the regular expression.

assertRegexpMatches(*args, **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.

Parameters:
  • 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.

Parameters:
  • 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.

Parameters:
  • 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.

Parameters:
  • 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_(*args, **kwargs)
countTestCases()
debug()

Run the test without collecting errors in a TestResult

defaultTestResult()
doCleanups()

Execute all cleanup functions. Normally called for you after tearDown.

fail(msg=None)

Fail immediately, with the given message.

failIf(*args, **kwargs)
failIfAlmostEqual(*args, **kwargs)
failIfEqual(*args, **kwargs)
failUnless(*args, **kwargs)
failUnlessAlmostEqual(*args, **kwargs)
failUnlessEqual(*args, **kwargs)
failUnlessRaises(*args, **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.

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.

tearDownClass()

Hook method for deconstructing the class fixture after running all tests in the class.

test_to_singletask()[source]

Test that to_singletask works.

Module contents