lsst.utils.tests Namespace Reference

Classes
class	ExecutablesTestCase
class	MemoryTestCase
class	TestCase

Functions
def	init ()
def	sort_tests (tests)
def	suiteClassWrapper (tests)
def	getTempFilePath (ext, expectOutput=True)
def	inTestCase (func)
def	debugger (exceptions)
def	plotImageDiff (lhs, rhs, bad=None, diff=None, plotFileName=None)
def	assertFloatsAlmostEqual (testCase, lhs, rhs, rtol=sys.float_info.epsilon, atol=sys.float_info.epsilon, relTo=None, printFailures=True, plotOnFailure=False, plotFileName=None, invert=False, msg=None)
def	assertFloatsNotEqual (testCase, lhs, rhs, kwds)
def	assertFloatsEqual (testCase, lhs, rhs, kwargs)

Variables
	psutil
	open_files

Function Documentation

assertFloatsAlmostEqual()

def lsst.utils.tests.assertFloatsAlmostEqual	(		testCase,
			lhs,
			rhs,
			rtol = sys.float_info.epsilon,
			atol = sys.float_info.epsilon,
			relTo = None,
			printFailures = True,
			plotOnFailure = False,
			plotFileName = None,
			invert = False,
			msg = None
	)

Highly-configurable floating point comparisons for scalars and arrays.

The test assertion will fail if all elements ``lhs`` and ``rhs`` are not
equal to within the tolerances specified by ``rtol`` and ``atol``.
More precisely, the comparison is:

``abs(lhs - rhs) <= relTo*rtol OR abs(lhs - rhs) <= atol``

If ``rtol`` or ``atol`` is `None`, that term in the comparison is not
performed at all.

When not specified, ``relTo`` is the elementwise maximum of the absolute
values of ``lhs`` and ``rhs``.  If set manually, it should usually be set
to either ``lhs`` or ``rhs``, or a scalar value typical of what is
expected.

Parameters
----------
testCase : `unittest.TestCase`
    Instance the test is part of.
lhs : scalar or array-like
    LHS value(s) to compare; may be a scalar or array-like of any
    dimension.
rhs : scalar or array-like
    RHS value(s) to compare; may be a scalar or array-like of any
    dimension.
rtol : `float`, optional
    Relative tolerance for comparison; defaults to double-precision
    epsilon.
atol : `float`, optional
    Absolute tolerance for comparison; defaults to double-precision
    epsilon.
relTo : `float`, optional
    Value to which comparison with rtol is relative.
printFailures : `bool`, optional
    Upon failure, print all inequal elements as part of the message.
plotOnFailure : `bool`, optional
    Upon failure, plot the originals and their residual with matplotlib.
    Only 2-d arrays are supported.
plotFileName : `str`, optional
    Filename to save the plot to.  If `None`, the plot will be displayed in
    a window.
invert : `bool`, optional
    If `True`, invert the comparison and fail only if any elements *are*
    equal. Used to implement `~lsst.utils.tests.assertFloatsNotEqual`,
    which should generally be used instead for clarity.
msg : `str`, optional
    String to append to the error message when assert fails.

Raises
------
AssertionError
    The values are not almost equal.

Definition at line 532 of file tests.py.

                            plotFileName=None, invert=False, msg=None):
    """Highly-configurable floating point comparisons for scalars and arrays.

    The test assertion will fail if all elements ``lhs`` and ``rhs`` are not
    equal to within the tolerances specified by ``rtol`` and ``atol``.
    More precisely, the comparison is:

    ``abs(lhs - rhs) <= relTo*rtol OR abs(lhs - rhs) <= atol``

    If ``rtol`` or ``atol`` is `None`, that term in the comparison is not
    performed at all.

    When not specified, ``relTo`` is the elementwise maximum of the absolute
    values of ``lhs`` and ``rhs``.  If set manually, it should usually be set
    to either ``lhs`` or ``rhs``, or a scalar value typical of what is
    expected.

    Parameters
    ----------
    testCase : `unittest.TestCase`
        Instance the test is part of.
    lhs : scalar or array-like
        LHS value(s) to compare; may be a scalar or array-like of any
        dimension.
    rhs : scalar or array-like
        RHS value(s) to compare; may be a scalar or array-like of any
        dimension.
    rtol : `float`, optional
        Relative tolerance for comparison; defaults to double-precision
        epsilon.
    atol : `float`, optional
        Absolute tolerance for comparison; defaults to double-precision
        epsilon.
    relTo : `float`, optional
        Value to which comparison with rtol is relative.
    printFailures : `bool`, optional
        Upon failure, print all inequal elements as part of the message.
    plotOnFailure : `bool`, optional
        Upon failure, plot the originals and their residual with matplotlib.
        Only 2-d arrays are supported.
    plotFileName : `str`, optional
        Filename to save the plot to.  If `None`, the plot will be displayed in
        a window.
    invert : `bool`, optional
        If `True`, invert the comparison and fail only if any elements *are*
        equal. Used to implement `~lsst.utils.tests.assertFloatsNotEqual`,
        which should generally be used instead for clarity.
    msg : `str`, optional
        String to append to the error message when assert fails.

    Raises
    ------
    AssertionError
        The values are not almost equal.
    """
    if not numpy.isfinite(lhs).all():
        testCase.fail("Non-finite values in lhs")
    if not numpy.isfinite(rhs).all():
        testCase.fail("Non-finite values in rhs")
    diff = lhs - rhs
    absDiff = numpy.abs(lhs - rhs)
    if rtol is not None:
        if relTo is None:
            relTo = numpy.maximum(numpy.abs(lhs), numpy.abs(rhs))
        else:
            relTo = numpy.abs(relTo)
        bad = absDiff > rtol*relTo
        if atol is not None:
            bad = numpy.logical_and(bad, absDiff > atol)
    else:
        if atol is None:
            raise ValueError("rtol and atol cannot both be None")
        bad = absDiff > atol
    failed = numpy.any(bad)
    if invert:
        failed = not failed
        bad = numpy.logical_not(bad)
        cmpStr = "=="
        failStr = "are the same"
    else:
        cmpStr = "!="
        failStr = "differ"
    errMsg = []
    if failed:
        if numpy.isscalar(bad):
            if rtol is None:
                errMsg = ["%s %s %s; diff=%s with atol=%s"
                          % (lhs, cmpStr, rhs, absDiff, atol)]
            elif atol is None:
                errMsg = ["%s %s %s; diff=%s/%s=%s with rtol=%s"
                          % (lhs, cmpStr, rhs, absDiff, relTo, absDiff/relTo, rtol)]
            else:
                errMsg = ["%s %s %s; diff=%s/%s=%s with rtol=%s, atol=%s"
                          % (lhs, cmpStr, rhs, absDiff, relTo, absDiff/relTo, rtol, atol)]
        else:
            errMsg = ["%d/%d elements %s with rtol=%s, atol=%s"
                      % (bad.sum(), bad.size, failStr, rtol, atol)]
            if plotOnFailure:
                if len(lhs.shape) != 2 or len(rhs.shape) != 2:
                    raise ValueError("plotOnFailure is only valid for 2-d arrays")
                try:
                    plotImageDiff(lhs, rhs, bad, diff=diff, plotFileName=plotFileName)
                except ImportError:
                    errMsg.append("Failure plot requested but matplotlib could not be imported.")
            if printFailures:
                # Make sure everything is an array if any of them are, so we can treat
                # them the same (diff and absDiff are arrays if either rhs or lhs is),
                # and we don't get here if neither is.
                if numpy.isscalar(relTo):
                    relTo = numpy.ones(bad.shape, dtype=float) * relTo
                if numpy.isscalar(lhs):
                    lhs = numpy.ones(bad.shape, dtype=float) * lhs
                if numpy.isscalar(rhs):
                    rhs = numpy.ones(bad.shape, dtype=float) * rhs
                if rtol is None:
                    for a, b, diff in zip(lhs[bad], rhs[bad], absDiff[bad]):
                        errMsg.append("%s %s %s (diff=%s)" % (a, cmpStr, b, diff))
                else:
                    for a, b, diff, rel in zip(lhs[bad], rhs[bad], absDiff[bad], relTo[bad]):
                        errMsg.append("%s %s %s (diff=%s/%s=%s)" % (a, cmpStr, b, diff, rel, diff/rel))

    if msg is not None:
        errMsg.append(msg)
    testCase.assertFalse(failed, msg="\n".join(errMsg))


@inTestCase

assertFloatsEqual()

def lsst.utils.tests.assertFloatsEqual	(		testCase,
			lhs,
			rhs,
			kwargs
	)

Assert that lhs == rhs (both numeric types, whether scalar or array).

See `~lsst.utils.tests.assertFloatsAlmostEqual` (called with
``rtol=atol=0``) for more information.

Parameters
----------
testCase : `unittest.TestCase`
    Instance the test is part of.
lhs : scalar or array-like
    LHS value(s) to compare; may be a scalar or array-like of any
    dimension.
rhs : scalar or array-like
    RHS value(s) to compare; may be a scalar or array-like of any
    dimension.

Raises
------
AssertionError
    The values are not equal.

Definition at line 686 of file tests.py.

def assertFloatsEqual(testCase, lhs, rhs, **kwargs):
    """
    Assert that lhs == rhs (both numeric types, whether scalar or array).

    See `~lsst.utils.tests.assertFloatsAlmostEqual` (called with
    ``rtol=atol=0``) for more information.

    Parameters
    ----------
    testCase : `unittest.TestCase`
        Instance the test is part of.
    lhs : scalar or array-like
        LHS value(s) to compare; may be a scalar or array-like of any
        dimension.
    rhs : scalar or array-like
        RHS value(s) to compare; may be a scalar or array-like of any
        dimension.

    Raises
    ------
    AssertionError
        The values are not equal.
    """
    return assertFloatsAlmostEqual(testCase, lhs, rhs, rtol=0, atol=0, **kwargs)

assertFloatsNotEqual()

def lsst.utils.tests.assertFloatsNotEqual	(		testCase,
			lhs,
			rhs,
			kwds
	)

Fail a test if the given floating point values are equal to within the
given tolerances.

See `~lsst.utils.tests.assertFloatsAlmostEqual` (called with
``rtol=atol=0``) for more information.

Parameters
----------
testCase : `unittest.TestCase`
    Instance the test is part of.
lhs : scalar or array-like
    LHS value(s) to compare; may be a scalar or array-like of any
    dimension.
rhs : scalar or array-like
    RHS value(s) to compare; may be a scalar or array-like of any
    dimension.

Raises
------
AssertionError
    The values are almost equal.

Definition at line 659 of file tests.py.

def assertFloatsNotEqual(testCase, lhs, rhs, **kwds):
    """Fail a test if the given floating point values are equal to within the
    given tolerances.

    See `~lsst.utils.tests.assertFloatsAlmostEqual` (called with
    ``rtol=atol=0``) for more information.

    Parameters
    ----------
    testCase : `unittest.TestCase`
        Instance the test is part of.
    lhs : scalar or array-like
        LHS value(s) to compare; may be a scalar or array-like of any
        dimension.
    rhs : scalar or array-like
        RHS value(s) to compare; may be a scalar or array-like of any
        dimension.

    Raises
    ------
    AssertionError
        The values are almost equal.
    """
    return assertFloatsAlmostEqual(testCase, lhs, rhs, invert=True, **kwds)


@inTestCase

debugger()

def lsst.utils.tests.debugger

(

exceptions

)

Decorator to enter the debugger when there's an uncaught exception

To use, just slap a ``@debugger()`` on your function.

You may provide specific exception classes to catch as arguments to
the decorator function, e.g.,
``@debugger(RuntimeError, NotImplementedError)``.
This defaults to just `AssertionError`, for use on `unittest.TestCase`
methods.

Code provided by "Rosh Oxymoron" on StackOverflow:
http://stackoverflow.com/questions/4398967/python-unit-testing-automatically-running-the-debugger-when-a-test-fails

Notes
-----
Consider using ``pytest --pdb`` instead of this decorator.

Definition at line 430 of file tests.py.

def debugger(*exceptions):
    """Decorator to enter the debugger when there's an uncaught exception

    To use, just slap a ``@debugger()`` on your function.

    You may provide specific exception classes to catch as arguments to
    the decorator function, e.g.,
    ``@debugger(RuntimeError, NotImplementedError)``.
    This defaults to just `AssertionError`, for use on `unittest.TestCase`
    methods.

    Code provided by "Rosh Oxymoron" on StackOverflow:
    http://stackoverflow.com/questions/4398967/python-unit-testing-automatically-running-the-debugger-when-a-test-fails

    Notes
    -----
    Consider using ``pytest --pdb`` instead of this decorator.
    """
    if not exceptions:
        exceptions = (AssertionError, )

    def decorator(f):
        @functools.wraps(f)
        def wrapper(*args, **kwargs):
            try:
                return f(*args, **kwargs)
            except exceptions:
                import sys
                import pdb
                pdb.post_mortem(sys.exc_info()[2])
        return wrapper
    return decorator

getTempFilePath()

def lsst.utils.tests.getTempFilePath	(		ext,
			expectOutput = True
	)

Return a path suitable for a temporary file and try to delete the
file on success

If the with block completes successfully then the file is deleted,
if possible; failure results in a printed warning.
If a file is remains when it should not, a RuntimeError exception is
raised. This exception is also raised if a file is not present on context
manager exit when one is expected to exist.
If the block exits with an exception the file if left on disk so it can be
examined. The file name has a random component such that nested context
managers can be used with the same file suffix.

Parameters
----------

ext : `str`
    File name extension, e.g. ``.fits``.
expectOutput : `bool`, optional
    If `True`, a file should be created within the context manager.
    If `False`, a file should not be present when the context manager
    exits.

Returns
-------
`str`
    Path for a temporary file. The path is a combination of the caller's
    file path and the name of the top-level function

Notes
-----
::

    # file tests/testFoo.py
    import unittest
    import lsst.utils.tests
    class FooTestCase(unittest.TestCase):
        def testBasics(self):
            self.runTest()

        def runTest(self):
            with lsst.utils.tests.getTempFilePath(".fits") as tmpFile:
                # if tests/.tests exists then
                # tmpFile = "tests/.tests/testFoo_testBasics.fits"
                # otherwise tmpFile = "testFoo_testBasics.fits"
                ...
                # at the end of this "with" block the path tmpFile will be
                # deleted, but only if the file exists and the "with"
                # block terminated normally (rather than with an exception)
    ...

Definition at line 317 of file tests.py.

def getTempFilePath(ext, expectOutput=True):
    """Return a path suitable for a temporary file and try to delete the
    file on success

    If the with block completes successfully then the file is deleted,
    if possible; failure results in a printed warning.
    If a file is remains when it should not, a RuntimeError exception is
    raised. This exception is also raised if a file is not present on context
    manager exit when one is expected to exist.
    If the block exits with an exception the file if left on disk so it can be
    examined. The file name has a random component such that nested context
    managers can be used with the same file suffix.

    Parameters
    ----------

    ext : `str`
        File name extension, e.g. ``.fits``.
    expectOutput : `bool`, optional
        If `True`, a file should be created within the context manager.
        If `False`, a file should not be present when the context manager
        exits.

    Returns
    -------
    `str`
        Path for a temporary file. The path is a combination of the caller's
        file path and the name of the top-level function

    Notes
    -----
    ::

        # file tests/testFoo.py
        import unittest
        import lsst.utils.tests
        class FooTestCase(unittest.TestCase):
            def testBasics(self):
                self.runTest()

            def runTest(self):
                with lsst.utils.tests.getTempFilePath(".fits") as tmpFile:
                    # if tests/.tests exists then
                    # tmpFile = "tests/.tests/testFoo_testBasics.fits"
                    # otherwise tmpFile = "testFoo_testBasics.fits"
                    ...
                    # at the end of this "with" block the path tmpFile will be
                    # deleted, but only if the file exists and the "with"
                    # block terminated normally (rather than with an exception)
        ...
    """
    stack = inspect.stack()
    # get name of first function in the file
    for i in range(2, len(stack)):
        frameInfo = inspect.getframeinfo(stack[i][0])
        if i == 2:
            callerFilePath = frameInfo.filename
            callerFuncName = frameInfo.function
        elif callerFilePath == frameInfo.filename:
            # this function called the previous function
            callerFuncName = frameInfo.function
        else:
            break

    callerDir, callerFileNameWithExt = os.path.split(callerFilePath)
    callerFileName = os.path.splitext(callerFileNameWithExt)[0]
    outDir = os.path.join(callerDir, ".tests")
    if not os.path.isdir(outDir):
        outDir = ""
    prefix = "%s_%s-" % (callerFileName, callerFuncName)
    outPath = tempfile.mktemp(dir=outDir, suffix=ext, prefix=prefix)
    if os.path.exists(outPath):
        # There should not be a file there given the randomizer. Warn and remove.
        # Use stacklevel 3 so that the warning is reported from the end of the with block
        warnings.warn("Unexpectedly found pre-existing tempfile named %r" % (outPath,),
                      stacklevel=3)
        try:
            os.remove(outPath)
        except OSError:
            pass

    yield outPath

    fileExists = os.path.exists(outPath)
    if expectOutput:
        if not fileExists:
            raise RuntimeError("Temp file expected named {} but none found".format(outPath))
    else:
        if fileExists:
            raise RuntimeError("Unexpectedly discovered temp file named {}".format(outPath))
    # Try to clean up the file regardless
    if fileExists:
        try:
            os.remove(outPath)
        except OSError as e:
            # Use stacklevel 3 so that the warning is reported from the end of the with block
            warnings.warn("Warning: could not remove file %r: %s" % (outPath, e), stacklevel=3)

init()

def lsst.utils.tests.init

(

)

Initialize the memory tester and file descriptor leak tester.

Definition at line 64 of file tests.py.

def init():
    """Initialize the memory tester and file descriptor leak tester."""
    global open_files
    # Reset the list of open files
    open_files = _get_open_files()

inTestCase()

def lsst.utils.tests.inTestCase

(

func

)

A decorator to add a free function to our custom TestCase class, while also
making it available as a free function.

Definition at line 422 of file tests.py.

def inTestCase(func):
    """A decorator to add a free function to our custom TestCase class, while also
    making it available as a free function.
    """
    setattr(TestCase, func.__name__, func)
    return func

plotImageDiff()

def lsst.utils.tests.plotImageDiff	(		lhs,
			rhs,
			bad = None,
			diff = None,
			plotFileName = None
	)

Plot the comparison of two 2-d NumPy arrays.

Parameters
----------
lhs : `numpy.ndarray`
    LHS values to compare; a 2-d NumPy array
rhs : `numpy.ndarray`
    RHS values to compare; a 2-d NumPy array
bad : `numpy.ndarray`
    A 2-d boolean NumPy array of values to emphasize in the plots
diff : `numpy.ndarray`
    difference array; a 2-d NumPy array, or None to show lhs-rhs
plotFileName : `str`
    Filename to save the plot to.  If None, the plot will be displayed in
    a window.

Notes
-----
This method uses `matplotlib` and imports it internally; it should be
wrapped in a try/except block within packages that do not depend on
`matplotlib` (including `~lsst.utils`).

Definition at line 464 of file tests.py.

def plotImageDiff(lhs, rhs, bad=None, diff=None, plotFileName=None):
    """Plot the comparison of two 2-d NumPy arrays.

    Parameters
    ----------
    lhs : `numpy.ndarray`
        LHS values to compare; a 2-d NumPy array
    rhs : `numpy.ndarray`
        RHS values to compare; a 2-d NumPy array
    bad : `numpy.ndarray`
        A 2-d boolean NumPy array of values to emphasize in the plots
    diff : `numpy.ndarray`
        difference array; a 2-d NumPy array, or None to show lhs-rhs
    plotFileName : `str`
        Filename to save the plot to.  If None, the plot will be displayed in
        a window.

    Notes
    -----
    This method uses `matplotlib` and imports it internally; it should be
    wrapped in a try/except block within packages that do not depend on
    `matplotlib` (including `~lsst.utils`).
    """
    from matplotlib import pyplot
    if diff is None:
        diff = lhs - rhs
    pyplot.figure()
    if bad is not None:
        # make an rgba image that's red and transparent where not bad
        badImage = numpy.zeros(bad.shape + (4,), dtype=numpy.uint8)
        badImage[:, :, 0] = 255
        badImage[:, :, 1] = 0
        badImage[:, :, 2] = 0
        badImage[:, :, 3] = 255*bad
    vmin1 = numpy.minimum(numpy.min(lhs), numpy.min(rhs))
    vmax1 = numpy.maximum(numpy.max(lhs), numpy.max(rhs))
    vmin2 = numpy.min(diff)
    vmax2 = numpy.max(diff)
    for n, (image, title) in enumerate([(lhs, "lhs"), (rhs, "rhs"), (diff, "diff")]):
        pyplot.subplot(2, 3, n + 1)
        im1 = pyplot.imshow(image, cmap=pyplot.cm.gray, interpolation='nearest', origin='lower',
                            vmin=vmin1, vmax=vmax1)
        if bad is not None:
            pyplot.imshow(badImage, alpha=0.2, interpolation='nearest', origin='lower')
        pyplot.axis("off")
        pyplot.title(title)
        pyplot.subplot(2, 3, n + 4)
        im2 = pyplot.imshow(image, cmap=pyplot.cm.gray, interpolation='nearest', origin='lower',
                            vmin=vmin2, vmax=vmax2)
        if bad is not None:
            pyplot.imshow(badImage, alpha=0.2, interpolation='nearest', origin='lower')
        pyplot.axis("off")
        pyplot.title(title)
    pyplot.subplots_adjust(left=0.05, bottom=0.05, top=0.92, right=0.75, wspace=0.05, hspace=0.05)
    cax1 = pyplot.axes([0.8, 0.55, 0.05, 0.4])
    pyplot.colorbar(im1, cax=cax1)
    cax2 = pyplot.axes([0.8, 0.05, 0.05, 0.4])
    pyplot.colorbar(im2, cax=cax2)
    if plotFileName:
        pyplot.savefig(plotFileName)
    else:
        pyplot.show()


@inTestCase

sort_tests()

def lsst.utils.tests.sort_tests

(

tests

)

Sort supplied test suites such that MemoryTestCases are at the end.

`lsst.utils.tests.MemoryTestCase` tests should always run after any other
tests in the module.

Parameters
----------
tests : sequence
    Sequence of test suites.

Returns
-------
suite : `unittest.TestSuite`
    A combined `~unittest.TestSuite` with
    `~lsst.utils.tests.MemoryTestCase` at the end.

Definition at line 71 of file tests.py.

def sort_tests(tests):
    """Sort supplied test suites such that MemoryTestCases are at the end.

    `lsst.utils.tests.MemoryTestCase` tests should always run after any other
    tests in the module.

    Parameters
    ----------
    tests : sequence
        Sequence of test suites.

    Returns
    -------
    suite : `unittest.TestSuite`
        A combined `~unittest.TestSuite` with
        `~lsst.utils.tests.MemoryTestCase` at the end.
    """

    suite = unittest.TestSuite()
    memtests = []
    for test_suite in tests:
        try:
            # Just test the first test method in the suite for MemoryTestCase
            # Use loop rather than next as it is possible for a test class
            # to not have any test methods and the Python community prefers
            # for loops over catching a StopIteration exception.
            bases = None
            for method in test_suite:
                bases = inspect.getmro(method.__class__)
                break
            if bases is not None and MemoryTestCase in bases:
                memtests.append(test_suite)
            else:
                suite.addTests(test_suite)
        except TypeError:
            if isinstance(test_suite, MemoryTestCase):
                memtests.append(test_suite)
            else:
                suite.addTest(test_suite)
    suite.addTests(memtests)
    return suite

suiteClassWrapper()

def lsst.utils.tests.suiteClassWrapper

(

tests

)

Definition at line 114 of file tests.py.

def suiteClassWrapper(tests):
    return unittest.TestSuite(sort_tests(tests))


# Replace the suiteClass callable in the defaultTestLoader
# so that we can reorder the test ordering. This will have
# no effect if no memory test cases are found.
unittest.defaultTestLoader.suiteClass = suiteClassWrapper

Variable Documentation

open_files

lsst.utils.tests.open_files

Definition at line 47 of file tests.py.

psutil

lsst.utils.tests.psutil

Definition at line 44 of file tests.py.

---

Generated on Sat Nov 16 2019 09:15:53 for LSSTApplications by   1.8.13