test/__init__.py

"""@namespace IMP::test
   @brief Methods and classes for testing the IMP kernel and modules.
   @ingroup python
"""

import re
import math
import sys
import os
import tempfile
import random
import IMP
import time
import types
import shutil
import difflib
import pprint
import unittest
from unittest.util import safe_repr
import datetime
import pickle
import contextlib
import subprocess
from pathlib import Path


# Expose some unittest decorators for convenience
expectedFailure = unittest.expectedFailure
skip = unittest.skip
skipIf = unittest.skipIf
skipUnless = unittest.skipUnless


def unstable(test_item):
    """Mark a test as 'unstable', i.e. that it fails randomly.

       'unstable' tests are tests that do not reliably pass or fail, such
       as 'science' tests that perform some sort of stochastic sampling or
       optimization and then assert on the results. This decorator can be
       used to mark such tests. They are skipped by default. To run the
       tests anyway, set the IMP_UNSTABLE_TESTS environment variable."""
    reason = "unstable test; enable by setting $IMP_UNSTABLE_TESTS"
    tf = unittest.skipUnless('IMP_UNSTABLE_TESTS' in os.environ, reason)
    return tf(test_item)


class _TempDir:
    def __init__(self, dir=None):
        self.tmpdir = tempfile.mkdtemp(dir=dir)

    def __del__(self):
        shutil.rmtree(self.tmpdir, ignore_errors=True)


@contextlib.contextmanager
def temporary_working_directory():
    """Simple context manager to run in a temporary directory.
       While the context manager is active (within the 'with' block)
       the current working directory is set to a temporary directory.
       When the context manager exists, the working directory is reset
       and the temporary directory deleted."""
    origdir = os.getcwd()
    tmpdir = tempfile.mkdtemp()
    os.chdir(tmpdir)
    yield tmpdir
    os.chdir(origdir)
    shutil.rmtree(tmpdir, ignore_errors=True)


@contextlib.contextmanager
def temporary_directory(dir=None):
    """Simple context manager to make a temporary directory.
       The temporary directory has the same lifetime as the context manager
       (i.e. it is created at the start of the 'with' block, and deleted
       at the end of the block).
       @param dir If given, the temporary directory is made as a subdirectory
                  of that directory, rather than in the default temporary
                  directory location (e.g. /tmp)
       @return the full path to the temporary directory.
    """
    tmpdir = tempfile.mkdtemp(dir=dir)
    yield tmpdir
    shutil.rmtree(tmpdir, ignore_errors=True)


def numerical_derivative(func, val, step):
    """Calculate the derivative of the single-value function `func` at
       point `val`. The derivative is calculated using simple finite
       differences starting with the given `step`; Richardson extrapolation
       is then used to extrapolate the derivative at step=0."""
    maxsteps = 50
    con = 1.4
    safe = 2.0
    err = 1.0e30
    f1 = func(val + step)
    f2 = func(val - step)
    # create first element in triangular matrix d of derivatives
    d = [[(f1 - f2) / (2.0 * step)]]
    retval = None
    for i in range(1, maxsteps):
        d.append([0.] * (i + 1))
        step /= con
        f1 = func(val + step)
        f2 = func(val - step)
        d[i][0] = (f1 - f2) / (2.0 * step)
        fac = con * con
        for j in range(1, i + 1):
            d[i][j] = (d[i][j-1] * fac - d[i-1][j-1]) / (fac - 1.)
            fac *= con * con
            errt = max(abs(d[i][j] - d[i][j-1]),
                       abs(d[i][j] - d[i-1][j-1]))
            if errt <= err:
                err = errt
                retval = d[i][j]
        if abs(d[i][i] - d[i-1][i-1]) >= safe * err:
            break
    if retval is None:
        raise ValueError("Cannot calculate numerical derivative")
    return retval


def xyz_numerical_derivatives(sf, xyz, step):
    """Calculate the x,y and z derivatives of the scoring function `sf`
       on the `xyz` particle. The derivatives are approximated numerically
       using the numerical_derivatives() function."""
    class _XYZDerivativeFunc:
        def __init__(self, sf, xyz, basis_vector):
            self._xyz = xyz
            self._sf = sf
            self._basis_vector = basis_vector
            self._starting_coordinates = xyz.get_coordinates()

        def __call__(self, val):
            self._xyz.set_coordinates(self._starting_coordinates +
                                      self._basis_vector * val)
            return self._sf.evaluate(False)

    return tuple([IMP.test.numerical_derivative(
                  _XYZDerivativeFunc(sf, xyz, IMP.algebra.Vector3D(*x)),
                  0, 0.01)
                  for x in ((1, 0, 0), (0, 1, 0), (0, 0, 1))])


class TestCase(unittest.TestCase):
    """Super class for IMP test cases.
       This provides a number of useful IMP-specific methods on top of
       the standard Python `unittest.TestCase` class.
       Test scripts should generally contain a subclass of this class,
       conventionally called `Tests` (this makes it easier to run an
       individual test from the command line) and use IMP::test::main()
       as their main function."""

    # Provide assert(Not)Regex for Python 2 users (assertRegexMatches is
    # deprecated in Python 3)
    if not hasattr(unittest.TestCase, 'assertRegex'):
        assertRegex = unittest.TestCase.assertRegexpMatches
        assertNotRegex = unittest.TestCase.assertNotRegexpMatches

    def __init__(self, *args, **keys):
        super().__init__(*args, **keys)
        self._progname = Path(sys.argv[0]).absolute()

    def setUp(self):
        self.__check_level = IMP.get_check_level()
        # Turn on expensive runtime checks while running the test suite:
        IMP.set_check_level(IMP.USAGE_AND_INTERNAL)
        # python ints are bigger than C++ ones, so we need to make sure it fits
        # otherwise python throws fits
        IMP.random_number_generator.seed(hash(time.time()) % 2**30)

    def tearDown(self):
        # Restore original check level
        IMP.set_check_level(self.__check_level)
        # Clean up any temporary files
        if hasattr(self, '_tmpdir'):
            del self._tmpdir

    def get_input_file_name(self, filename):
        """Get the full name of an input file in the top-level
           test directory."""
        if self.__module__ == '__main__':
            testdir = self._progname
        else:
            testdir = Path(sys.modules[self.__module__].__file__)
        for p in testdir.parents:
            input = p / "input"
            if input.is_dir():
                ret = input / filename
                if not ret.exists():
                    raise IOError("Test input file %s does not exist" % ret)
                return str(ret)
        raise IOError("No test input directory found")

    def open_input_file(self, filename, mode='rb'):
        """Open and return an input file in the top-level test directory."""
        return open(self.get_input_file_name(filename), mode)

    def get_tmp_file_name(self, filename):
        """Get the full name of an output file in the tmp directory.
           The directory containing this file will be automatically
           cleaned up when the test completes."""
        if not hasattr(self, '_tmpdir'):
            self._tmpdir = _TempDir(os.environ.get('IMP_TMP_DIR'))
        tmpdir = self._tmpdir.tmpdir
        return str(Path(tmpdir) / filename)

    def get_magnitude(self, vector):
        """Get the magnitude of a list of floats"""
        return sum(x*x for x in vector)**.5

    def assertRaisesUsageException(self, c, *args, **keys):
        """Assert that the given callable object raises UsageException.
           This differs from unittest's assertRaises in that the test
           is skipped in fast mode (where usage checks are turned off)."""
        if IMP.get_check_level() >= IMP.USAGE:
            return self.assertRaises(IMP.UsageException, c, *args, **keys)

    def assertRaisesInternalException(self, c, *args, **keys):
        """Assert that the given callable object raises InternalException.
           This differs from unittest's assertRaises in that the test
           is skipped in fast mode (where internal checks are turned off)."""
        if IMP.get_check_level() >= IMP.USAGE_AND_INTERNAL:
            return self.assertRaises(IMP.InternalException, c, *args, **keys)

    def assertNotImplemented(self, c, *args, **keys):
        """Assert that the given callable object is not implemented."""
        return self.assertRaises(IMP.InternalException, c, *args, **keys)

    def assertXYZDerivativesInTolerance(self, sf, xyz, tolerance=0,
                                        percentage=0):
        """Assert that x,y,z analytical derivatives match numerical within
           a tolerance, or a percentage (of the analytical value), whichever
           is larger. `sf` should be a ScoringFunction or Restraint."""
        sf.evaluate(True)
        derivs = xyz.get_derivatives()
        num_derivs = xyz_numerical_derivatives(sf, xyz, 0.01)
        pct = percentage / 100.0
        self.assertAlmostEqual(
            self.get_magnitude(derivs-num_derivs), 0,
            delta=tolerance+percentage*self.get_magnitude(num_derivs),
            msg="Don't match "+str(derivs) + str(num_derivs))
        self.assertAlmostEqual(derivs[0], num_derivs[0],
                               delta=max(tolerance, abs(derivs[0]) * pct))
        self.assertAlmostEqual(derivs[1], num_derivs[1],
                               delta=max(tolerance, abs(derivs[1]) * pct))
        self.assertAlmostEqual(derivs[2], num_derivs[2],
                               delta=max(tolerance, abs(derivs[2]) * pct))

    def assertNumPyArrayEqual(self, numpy_array, exp_array):
        """Fail if the given numpy array doesn't match expected"""
        if IMP.IMP_KERNEL_HAS_NUMPY:
            import numpy.testing
            self.assertIsInstance(numpy_array, numpy.ndarray)
            numpy.testing.assert_array_equal(numpy_array, exp_array)
        else:
            self.assertEqual(numpy_array, exp_array)

    def assertSequenceAlmostEqual(self, first, second, places=None, msg=None,
                                  delta=None):
        """Fail if the difference between any two items in the two sequences
           are exceed the specified number of places or delta. See
           `assertAlmostEqual`.
        """
        if delta is not None and places is not None:
            raise TypeError("specify delta or places not both")

        ftype = type(first)
        ftypename = ftype.__name__
        stype = type(second)
        stypename = stype.__name__
        if ftype != stype:
            raise self.failureException(
                'Sequences are of different types: %s != %s' % (
                    ftypename, stypename))

        try:
            flen = len(first)
        except (NotImplementedError, TypeError):
            raise self.failureException(
                'First %s has no length' % (ftypename))
        try:
            slen = len(second)
        except (NotImplementedError, TypeError):
            raise self.failureException(
                'Second %s has no length' % (stypename))

        if flen != slen:
            raise self.failureException(
                'Sequences have non equal lengths: %d != %d' % (flen, slen))

        differing = None
        for i in range(min(flen, slen)):
            differing = '%ss differ: %s != %s\n' % (
                    ftypename.capitalize(), safe_repr(first),
                    safe_repr(second))

            try:
                f = first[i]
            except (TypeError, IndexError, NotImplementedError):
                differing += ('\nUnable to index element %d of first %s\n' %
                              (i, ftypename))
                break

            try:
                s = second[i]
            except (TypeError, IndexError, NotImplementedError):
                differing += ('\nUnable to index element %d of second %s\n' %
                              (i, stypename))
                break

            try:
                self.assertAlmostEqual(
                    f, s, places=places, msg=msg, delta=delta)
            except (TypeError, ValueError, NotImplementedError,
                    AssertionError):
                differing += (
                    "\nFirst differing element "
                    "%d:\n%s\n%s\n") % (i, safe_repr(f), safe_repr(s))
                break
        else:
            return

        standardMsg = differing
        diffMsg = '\n' + '\n'.join(
            difflib.ndiff(pprint.pformat(first).splitlines(),
                          pprint.pformat(second).splitlines()))
        standardMsg = self._truncateMessage(standardMsg, diffMsg)
        msg = self._formatMessage(msg, standardMsg)
        raise self.failureException(msg)

    def _read_cmake_cfg(self, cmake_cfg):
        """Parse IMPConfig.cmake and extract info on the C++ compiler"""
        cxx = flags = sysroot = None
        includes = []
        with open(cmake_cfg) as fh:
            for line in fh:
                if line.startswith('set(IMP_CXX_COMPILER '):
                    cxx = line.split('"')[1]
                elif line.startswith('set(IMP_CXX_FLAGS '):
                    flags = line.split('"')[1]
                elif line.startswith('set(IMP_OSX_SYSROOT '):
                    sysroot = line.split('"')[1]
                elif line.startswith('SET(Boost_INCLUDE_DIR '):
                    includes.append(line.split('"')[1])
                elif line.startswith('SET(EIGEN3_INCLUDE_DIR '):
                    includes.append(line.split('"')[1])
                elif line.startswith('SET(cereal_INCLUDE_DIRS '):
                    includes.append(line.split('"')[1])
        return cxx, flags, includes, sysroot

    def assertCompileFails(self, headers, body):
        """Test that the given C++ code fails to compile with a static
           assertion."""
        if sys.platform == 'win32':
            self.skipTest("No support for Windows yet")
        libdir = os.path.dirname(IMP.__file__)
        cmake_cfg = os.path.join(libdir, '..', '..', 'IMPConfig.cmake')
        if not os.path.exists(cmake_cfg):
            self.skipTest("cannot find IMPConfig.cmake")
        cxx, flags, includes, sysroot = self._read_cmake_cfg(cmake_cfg)
        # On Mac we need to point to the SDK
        if sys.platform == 'darwin' and sysroot:
            flags = flags + " -isysroot" + sysroot
        includes.append(os.path.join(libdir, '..', '..', 'include'))
        include = " ".join("-I" + inc for inc in includes)
        with temporary_directory() as tmpdir:
            fname = os.path.join(tmpdir, 'test.cpp')
            with open(fname, 'w') as fh:
                for h in headers:
                    fh.write("#include <%s>\n" % h)
                fh.write("\nint main() {\n" + body + "\n  return 0;\n}\n")
            cmdline = "%s %s %s %s" % (cxx, flags, include, fname)
            print(cmdline)
            p = subprocess.Popen(cmdline, shell=True,
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE,
                                 universal_newlines=True)
            out, err = p.communicate()
            self.assertIn('error: static assertion failed', err)

    def create_point_particle(self, model, x, y, z):
        """Make a particle with optimizable x, y and z attributes, and
           add it to the model."""
        p = IMP.Particle(model)
        p.add_attribute(IMP.FloatKey("x"), x, True)
        p.add_attribute(IMP.FloatKey("y"), y, True)
        p.add_attribute(IMP.FloatKey("z"), z, True)
        return p

    def probabilistic_check(self, testcall, chance_of_failure):
        """Help handle a test which is expected to fail some fraction of
        the time. The test is run multiple times and an exception
        is thrown only if it fails too many times.
        @note Use of this function should be avoided. If there is a corner
              case that results in a test 'occasionally' failing, write a
              new test specifically for that corner case and assert that
              it fails consistently (and remove the corner case from the
              old test).
        """
        prob = chance_of_failure
        tries = 1
        while prob > .001:
            tries += 1
            prob = prob*chance_of_failure
        for i in range(0, tries):
            try:
                eval(testcall)
            except:  # noqa: E722
                pass
            else:
                return
        eval(testcall)
        raise AssertionError("Too many failures")

    def failure_probability(self, testcall):
        """Estimate how likely a given block of code is to raise an
        AssertionError."""
        failures = 0
        tries = 0.0
        while failures < 10 and tries < 1000:
            try:
                eval(testcall)
            except:  # noqa: E722
                failures += 1
            tries = tries+1
        return failures/tries

    def randomize_particles(self, particles, deviation):
        """Randomize the xyz coordinates of a list of particles"""
        # Note: cannot use XYZ here since that pulls in IMP.core
        xkey = IMP.FloatKey("x")
        ykey = IMP.FloatKey("y")
        zkey = IMP.FloatKey("z")
        for p in particles:
            p.set_value(xkey, random.uniform(-deviation, deviation))
            p.set_value(ykey, random.uniform(-deviation, deviation))
            p.set_value(zkey, random.uniform(-deviation, deviation))

    def particle_distance(self, p1, p2):
        """Return distance between two given particles"""
        xkey = IMP.FloatKey("x")
        ykey = IMP.FloatKey("y")
        zkey = IMP.FloatKey("z")
        dx = p1.get_value(xkey) - p2.get_value(xkey)
        dy = p1.get_value(ykey) - p2.get_value(ykey)
        dz = p1.get_value(zkey) - p2.get_value(zkey)
        return math.sqrt(dx*dx + dy*dy + dz*dz)

    def check_unary_function_deriv(self, func, lb, ub, step):
        """Check the unary function func's derivatives against numerical
           approximations between lb and ub"""
        for f in [lb + i * step for i in range(1, int((ub-lb)/step))]:
            (v, d) = func.evaluate_with_derivative(f)
            da = numerical_derivative(func.evaluate, f, step / 10.)
            self.assertAlmostEqual(d, da, delta=max(abs(.1 * d), 0.01))

    def check_unary_function_min(self, func, lb, ub, step, expected_fmin):
        """Make sure that the minimum of the unary function func over the
           range between lb and ub is at expected_fmin"""
        fmin, vmin = lb, func.evaluate(lb)
        for f in [lb + i * step for i in range(1, int((ub-lb)/step))]:
            v = func.evaluate(f)
            if v < vmin:
                fmin, vmin = f, v
        self.assertAlmostEqual(fmin, expected_fmin, delta=step)

    def check_standard_object_methods(self, obj):
        """Check methods that every IMP::Object class should have"""
        obj.set_was_used(True)
        # Test get_from static method
        cls = type(obj)
        self.assertIsNotNone(cls.get_from(obj))
        self.assertRaises(ValueError, cls.get_from, IMP.Model())
        # Test __str__ and __repr__
        self.assertIsInstance(str(obj), str)
        self.assertIsInstance(repr(obj), str)
        # Test get_version_info()
        verinf = obj.get_version_info()
        self.assertIsInstance(verinf, IMP.VersionInfo)
        # Test SWIG thisown flag
        o = obj.thisown
        obj.thisown = o

    def create_particles_in_box(self, model, num=10,
                                lb=[0, 0, 0],
                                ub=[10, 10, 10]):
        """Create a bunch of particles in a box"""
        import IMP.algebra
        lbv = IMP.algebra.Vector3D(lb[0], lb[1], lb[2])
        ubv = IMP.algebra.Vector3D(ub[0], ub[1], ub[2])
        ps = []
        for i in range(0, num):
            v = IMP.algebra.get_random_vector_in(
                IMP.algebra.BoundingBox3D(lbv, ubv))
            p = self.create_point_particle(model, v[0], v[1], v[2])
            ps.append(p)
        return ps

    def _get_type(self, module, name):
        return eval('type('+module+"."+name+')')

    def assertValueObjects(self, module, exceptions_list):
        "Check that all the C++ classes in the module are values or objects."
        all = dir(module)
        ok = set(exceptions_list + module._value_types + module._object_types
                 + module._raii_types + module._plural_types)

        bad = []
        for name in all:
            if self._get_type(module.__name__, name) == type \
                    and not name.startswith("_"):
                if name.find("SwigPyIterator") != -1:
                    continue
                # Exclude Python-only classes
                if not eval('hasattr(%s.%s, "__swig_destroy__")'
                            % (module.__name__, name)):
                    continue
                if name in ok:
                    continue
                bad.append(name)
        self.assertEqual(
            len(bad), 0,
            "All IMP classes should be labeled as values or objects to get "
            "memory management correct in Python. The following are not:\n%s\n"
            "Please add an IMP_SWIG_OBJECT or IMP_SWIG_VALUE call to the "
            "Python wrapper, or if the class has a good reason to be "
            "neither, add the name to the value_object_exceptions list in "
            "the IMPModuleTest call." % str(bad))
        for e in exceptions_list:
            self.assertTrue(
                e not in module._value_types + module._object_types
                + module._raii_types + module._plural_types,
                "Value/Object exception "+e+" is not an exception")

    def _check_spelling(self, word, words):
        """Check that the word is spelled correctly"""
        if "words" not in dir(self):
            with open(IMP.test.get_data_path("linux.words"), "r") as fh:
                wordlist = fh.read().split("\n")
            # why is "all" missing on my mac?
            custom_words = ["info", "prechange", "int", "ints", "optimizeds",
                            "graphviz", "voxel", "voxels", "endian", 'rna',
                            'dna', "xyzr", "pdbs", "fft", "ccc", "gaussian"]
            # Exclude some common alternative spellings - we want to
            # be consistent
            exclude_words = set(["adapter", "grey"])
            self.words = set(wordlist+custom_words) - exclude_words
        if self.words:
            for i in "0123456789":
                if i in word:
                    return True
            if word in words:
                return True
            if word in self.words:
                return True
            else:
                return False
        else:
            return True

    def assertClassNames(self, module, exceptions, words):
        """Check that all the classes in the module follow the IMP
           naming conventions."""
        all = dir(module)
        misspelled = []
        bad = []
        cc = re.compile("([A-Z][a-z]*)")
        for name in all:
            if self._get_type(module.__name__, name) == type \
                    and not name.startswith("_"):
                if name.find("SwigPyIterator") != -1:
                    continue
                for t in re.findall(cc, name):
                    if not self._check_spelling(t.lower(), words):
                        misspelled.append(t.lower())
                        bad.append(name)

        self.assertEqual(
            len(bad), 0,
            "All IMP classes should be properly spelled. The following "
            "are not: %s.\nMisspelled words: %s. Add words to the "
            "spelling_exceptions variable of the IMPModuleTest if needed."
            % (str(bad), ", ".join(set(misspelled))))

        for name in all:
            if self._get_type(module.__name__, name) == type \
                    and not name.startswith("_"):
                if name.find("SwigPyIterator") != -1:
                    continue
                if name.find('_') != -1:
                    bad.append(name)
                if name.lower == name:
                    bad.append(name)
                for t in re.findall(cc, name):
                    if not self._check_spelling(t.lower(), words):
                        print("misspelled %s in %s" % (t, name))
                        bad.append(name)
        self.assertEqual(
            len(bad), 0,
            "All IMP classes should have CamelCase names. The following "
            "do not: %s." % "\n".join(bad))

    def _check_function_name(self, prefix, name, verbs, all, exceptions, words,
                             misspelled):
        if prefix:
            fullname = prefix+"."+name
        else:
            fullname = name
        old_exceptions = [
            'unprotected_evaluate', "unprotected_evaluate_if_good",
            "unprotected_evaluate_if_below",
            'unprotected_evaluate_moved', "unprotected_evaluate_moved_if_good",
            "unprotected_evaluate_moved_if_below",
            "after_evaluate", "before_evaluate", "has_attribute",
            "decorate_particle", "particle_is_instance"]
        if name in old_exceptions:
            return []
        if fullname in exceptions:
            return []
        if name.endswith("swigregister"):
            return []
        if name.lower() != name:
            if name[0].lower() != name[0] and name.split('_')[0] in all:
                # static methods
                return []
            else:
                return [fullname]
        tokens = name.split("_")
        if tokens[0] not in verbs:
            return [fullname]
        for t in tokens:
            if not self._check_spelling(t, words):
                misspelled.append(t)
                print("misspelled %s in %s" % (t, name))
                return [fullname]
        return []

    def _static_method(self, module, prefix, name):
        """For static methods of the form Foo.bar SWIG creates free functions
           named Foo_bar. Exclude these from spelling checks since the method
           Foo.bar has already been checked."""
        if prefix is None and '_' in name:
            modobj = eval(module)
            cls, meth = name.split('_', 1)
            if hasattr(modobj, cls):
                clsobj = eval(module + '.' + cls)
                if hasattr(clsobj, meth):
                    return True

    def _check_function_names(self, module, prefix, names, verbs, all,
                              exceptions, words, misspelled):
        bad = []
        for name in names:
            typ = self._get_type(module, name)
            if name.startswith("_") or name == "weakref_proxy":
                continue
            if typ in (types.BuiltinMethodType, types.MethodType) \
                    or (typ == types.FunctionType and  # noqa: E721
                        not self._static_method(module, prefix, name)):
                bad.extend(self._check_function_name(prefix, name, verbs, all,
                                                     exceptions, words,
                                                     misspelled))
            if typ == type and "SwigPyIterator" not in name:
                members = eval("dir("+module+"."+name+")")
                bad.extend(self._check_function_names(module+"."+name,
                                                      name, members, verbs, [],
                                                      exceptions, words,
                                                      misspelled))
        return bad

    def assertFunctionNames(self, module, exceptions, words):
        """Check that all the functions in the module follow the IMP
           naming conventions."""
        all = dir(module)
        verbs = set(["add", "remove", "get", "set", "evaluate", "compute",
                     "show", "create", "destroy", "push", "pop", "write",
                     "read", "do", "show", "load", "save", "reset", "accept",
                     "reject", "clear", "handle", "update", "apply",
                     "optimize", "reserve", "dump", "propose", "setup",
                     "teardown", "visit", "find", "run", "swap", "link",
                     "validate", "erase", "check"])
        misspelled = []
        bad = self._check_function_names(module.__name__, None, all, verbs,
                                         all, exceptions, words, misspelled)
        message = ("All IMP methods and functions should have lower case "
                   "names separated by underscores and beginning with a "
                   "verb, preferably one of ['add', 'remove', 'get', 'set', "
                   "'create', 'destroy']. Each of the words should be a "
                   "properly spelled English word. The following do not "
                   "(given our limited list of verbs that we check for):\n"
                   "%(bad)s\nIf there is a good reason for them not to "
                   "(eg it does start with a verb, just one with a meaning "
                   "that is not covered by the normal list), add them to the "
                   "function_name_exceptions variable in the "
                   "standards_exceptions file. Otherwise, please fix. "
                   "The current verb list is %(verbs)s"
                   % {"bad": "\n".join(bad), "verbs": verbs})
        if len(misspelled) > 0:
            message += "\nMisspelled words: " + ", ".join(set(misspelled)) \
                       + ". Add words to the spelling_exceptions variable " \
                       + "of the standards_exceptions file if needed."
        self.assertEqual(len(bad), 0, message)

    def assertShow(self, modulename, exceptions):
        """Check that all the classes in modulename have a show method"""
        all = dir(modulename)
        if hasattr(modulename, '_raii_types'):
            excludes = frozenset(
                modulename._raii_types + modulename._plural_types)
        else:
            # Python-only modules don't have these two lists
            excludes = frozenset()
        not_found = []
        for f in all:
            # Exclude SWIG C global variables object
            if f == 'cvar':
                continue
            # Exclude Python-only classes; they are all showable
            if not eval('hasattr(%s.%s, "__swig_destroy__")'
                        % (modulename.__name__, f)):
                continue
            if self._get_type(modulename.__name__, f) == type \
                    and not f.startswith("_") \
                    and not f.endswith("_swigregister")\
                    and f not in exceptions\
                    and not f.endswith("Temp") and not f.endswith("Iterator")\
                    and not f.endswith("Exception") and\
                    f not in excludes:
                if not hasattr(getattr(modulename, f), 'show'):
                    not_found.append(f)
        self.assertEqual(
            len(not_found), 0,
            "All IMP classes should support show and __str__. The following "
            "do not:\n%s\n If there is a good reason for them not to, add "
            "them to the show_exceptions variable in the IMPModuleTest "
            "call. Otherwise, please fix." % "\n".join(not_found))
        for e in exceptions:
            self.assertIn(e, all,
                          "Show exception "+e+" is not a class in module")
            self.assertTrue(not hasattr(getattr(modulename, e), 'show'),
                            "Exception "+e+" is not really a show exception")

    def run_example(self, filename):
        """Run the named example script.
           @return a dictionary of all the script's global variables.
                   This can be queried in a test case to make sure
                   the example performed correctly."""
        class _FatalError(Exception):
            pass

        # Add directory containing the example to sys.path, so it can import
        # other Python modules in the same directory
        path, name = os.path.split(filename)
        oldsyspath = sys.path[:]
        olssysargv = sys.argv[:]
        sys.path.insert(0, path)
        sys.argv = [filename]
        vars = {}
        try:
            exec(open(filename).read(), vars)
        # Catch sys.exit() called from within the example; a non-zero exit
        # value should cause the test case to fail
        except SystemExit as e:
            if e.code != 0 and e.code is not None:
                raise _FatalError(
                    "Example exit with code %s" % str(e.code))
        finally:
            # Restore sys.path
            sys.path = oldsyspath
            sys.argv = olssysargv

        return _ExecDictProxy(vars)

    def run_python_module(self, module, args):
        """Run a Python module as if with "python -m <modname>",
           with the given list of arguments as sys.argv.

           If module is an already-imported Python module, run its 'main'
           function and return the result.

           If module is a string, run the module in a subprocess and return
           a subprocess.Popen-like object containing the child stdin,
           stdout and stderr.
        """
        def mock_setup_from_argv(*args, **kwargs):
            # do-nothing replacement for boost command line parser
            pass
        if type(module) == type(os):  # noqa: E721
            mod = module
        else:
            mod = __import__(module, {}, {}, [''])
        modpath = mod.__file__
        if modpath.endswith('.pyc'):
            modpath = modpath[:-1]
        if type(module) == type(os):  # noqa: E721
            old_sys_argv = sys.argv
            # boost parser doesn't like being called multiple times per process
            old_setup = IMP.setup_from_argv
            IMP.setup_from_argv = mock_setup_from_argv
            try:
                sys.argv = [modpath] + args
                return module.main()
            finally:
                IMP.setup_from_argv = old_setup
                sys.argv = old_sys_argv
        else:
            return _SubprocessWrapper(sys.executable, [modpath] + args)

    def check_runnable_python_module(self, module):
        """Check a Python module designed to be runnable with 'python -m'
           to make sure it supports standard command line options."""
        # --help should return with exit 0, no errors
        r = self.run_python_module(module, ['--help'])
        out, err = r.communicate()
        self.assertEqual(r.returncode, 0)
        self.assertNotEqual(err, "")
        self.assertEqual(out, "")


class _ExecDictProxy:
    """exec returns a Python dictionary, which contains IMP objects, other
       Python objects, as well as base Python modules (such as sys and
       __builtins__). If we just delete this dictionary, it is entirely
       possible that base Python modules are removed from the dictionary
       *before* some IMP objects. This will prevent the IMP objects' Python
       destructors from running properly, so C++ objects will not be
       cleaned up. This class proxies the base dict class, and on deletion
       attempts to remove keys from the dictionary in an order that allows
       IMP destructors to fire."""
    def __init__(self, d):
        self._d = d

    def __del__(self):
        # Try to release example objects in a sensible order
        module_type = type(IMP)
        d = self._d
        for k in d.keys():
            if type(d[k]) != module_type:  # noqa: E721
                del d[k]

    for meth in ['__contains__', '__getitem__', '__iter__', '__len__',
                 'get', 'has_key', 'items', 'keys', 'values']:
        exec("def %s(self, *args, **keys): "
             "return self._d.%s(*args, **keys)" % (meth, meth))


class _TestResult(unittest.TextTestResult):

    def __init__(self, stream=None, descriptions=None, verbosity=None):
        super().__init__(stream, descriptions, verbosity)
        self.all_tests = []

    def stopTestRun(self):
        if 'IMP_TEST_DETAIL_DIR' in os.environ:
            # Various parts of the IMP build pipeline use Python 3.6,
            # which predates pickle protocol 5
            protocol = min(pickle.HIGHEST_PROTOCOL, 4)
            fname = (Path(os.environ['IMP_TEST_DETAIL_DIR'])
                     / Path(sys.argv[0]).name)
            # In Wine builds, we may have cd'd to a different drive, e.g. C:
            # in which case we will no longer be able to see /tmp. In this
            # case, try to disambiguate by adding a drive.
            if not fname.exists():
                fname = Path("Z:") / fname
            with open(str(fname), 'wb') as fh:
                pickle.dump(self.all_tests, fh, protocol)
        super().stopTestRun()

    def startTest(self, test):
        super().startTest(test)
        test.start_time = datetime.datetime.now()

    def _test_finished(self, test, state, detail=None):
        if hasattr(test, 'start_time'):
            delta = datetime.datetime.now() - test.start_time
            try:
                pv = delta.total_seconds()
            except AttributeError:
                pv = (float(delta.microseconds)
                      + (delta.seconds
                         + delta.days * 24 * 3600) * 10**6) / 10**6
            if pv > 1:
                self.stream.write("in %.3fs ... " % pv)
        else:
            # If entire test was skipped, startTest() may not have been
            # called, in which case start_time won't be set
            pv = 0
        if detail is not None and not isinstance(detail, str):
            detail = self._exc_info_to_string(detail, test)
        test_doc = self.getDescription(test)
        test_name = test.id()
        if test_name.startswith('__main__.'):
            test_name = test_name[9:]
        self.all_tests.append({'name': test_name,
                               'docstring': test_doc,
                               'time': pv, 'state': state, 'detail': detail})

    def addSuccess(self, test):
        self._test_finished(test, 'OK')
        super().addSuccess(test)

    def addError(self, test, err):
        self._test_finished(test, 'ERROR', err)
        super().addError(test, err)

    def addFailure(self, test, err):
        self._test_finished(test, 'FAIL', err)
        super().addFailure(test, err)

    def addSkip(self, test, reason):
        self._test_finished(test, 'SKIP', reason)
        super().addSkip(test, reason)

    def addExpectedFailure(self, test, err):
        self._test_finished(test, 'EXPFAIL', err)
        super().addExpectedFailure(test, err)

    def addUnexpectedSuccess(self, test):
        self._test_finished(test, 'UNEXPSUC')
        super().addUnexpectedSuccess(test)

    def getDescription(self, test):
        doc_first_line = test.shortDescription()
        if self.descriptions and doc_first_line:
            return doc_first_line
        else:
            return str(test)


class _TestRunner(unittest.TextTestRunner):
    def _makeResult(self):
        return _TestResult(self.stream, self.descriptions, self.verbosity)


def main(*args, **keys):
    """Run a set of tests; similar to unittest.main().
       Obviates the need to separately import the 'unittest' module, and
       ensures that main() is from the same unittest module that the
       IMP.test testcases are. In addition, turns on some extra checks
       (e.g. trying to use deprecated code will cause an exception
       to be thrown)."""
    import IMP
    IMP.set_deprecation_exceptions(True)
    return unittest.main(testRunner=_TestRunner, *args, **keys)


class _SubprocessWrapper(subprocess.Popen):
    def __init__(self, app, args, cwd=None):
        # For (non-Python) applications to work on Windows, the
        # PATH must include the directory containing built DLLs
        if sys.platform == 'win32' and app != sys.executable:
            # Hack to find the location of build/lib/
            libdir = os.environ['PYTHONPATH'].split(';')[0]
            env = os.environ.copy()
            env['PATH'] += ';' + libdir
        else:
            env = None
        super().__init__([app]+list(args),
                         stdin=subprocess.PIPE,
                         stdout=subprocess.PIPE,
                         stderr=subprocess.PIPE, env=env, cwd=cwd,
                         universal_newlines=True)


class ApplicationTestCase(TestCase):
    """Super class for simple IMP application test cases"""
    def _get_application_file_name(self, filename):
        # If we ran from run-all-tests.py, it set an env variable for us with
        # the top-level test directory
        if sys.platform == 'win32':
            filename += '.exe'
        return filename

    def run_application(self, app, args, cwd=None):
        """Run an application with the given list of arguments.
           @return a subprocess.Popen-like object containing the child stdin,
                   stdout and stderr.
        """
        filename = self._get_application_file_name(app)
        if sys.platform == 'win32':
            # Cannot rely on PATH on wine builds, so use full pathname
            return _SubprocessWrapper(os.path.join(os.environ['IMP_BIN_DIR'],
                                                   filename), args, cwd=cwd)
        else:
            return _SubprocessWrapper(filename, args, cwd=cwd)

    def run_python_application(self, app, args):
        """Run a Python application with the given list of arguments.
           The Python application should be self-runnable (i.e. it should
           be executable and with a #! on the first line).
           @return a subprocess.Popen-like object containing the child stdin,
                   stdout and stderr.
        """
        # Handle platforms where /usr/bin/python doesn't work
        if sys.executable != '/usr/bin/python' and 'IMP_BIN_DIR' in os.environ:
            return _SubprocessWrapper(
                sys.executable,
                [os.path.join(os.environ['IMP_BIN_DIR'], app)] + args)
        else:
            return _SubprocessWrapper(app, args)

    def import_python_application(self, app):
        """Import an installed Python application, rather than running it.
           This is useful to directly test components of the application.
           @return the Python module object."""
        import importlib.machinery
        import importlib.util
        name = os.path.splitext(app)[0]
        if name in sys.modules:
            return sys.modules[name]
        pathname = os.path.join(os.environ['IMP_BIN_DIR'], app)
        loader = importlib.machinery.SourceFileLoader(name, pathname)
        spec = importlib.util.spec_from_loader(name, loader)
        module = importlib.util.module_from_spec(spec)
        sys.modules[name] = module
        spec.loader.exec_module(module)
        return module

    def run_script(self, app, args):
        """Run an application with the given list of arguments.
           @return a subprocess.Popen-like object containing the child stdin,
                   stdout and stderr.
        """
        return _SubprocessWrapper(sys.executable, [app]+args)

    def assertApplicationExitedCleanly(self, ret, error):
        """Assert that the application exited cleanly (return value = 0)."""
        if ret < 0:
            raise OSError("Application exited with signal %d\n" % -ret
                          + error)
        else:
            self.assertEqual(
                ret, 0,
                "Application exited uncleanly, with exit code %d\n" % ret
                + error)

    def read_shell_commands(self, doxfile):
        """Read and return a set of shell commands from a doxygen file.
           Each command is assumed to be in a \code{.sh}...\endcode block.
           The doxygen file is specified relative to the test file itself.
           This is used to make sure the commands shown in an application
           example actually work (the testcase can also check the resulting
           files for correctness)."""
        def win32_normpath(p):
            # Sometimes Windows can read Unix-style paths, but sometimes it
            # gets confused... so normalize all paths to be sure
            return " ".join([os.path.normpath(x) for x in p.split()])

        def fix_win32_command(cmd):
            # Make substitutions so a Unix shell command works on Windows
            if cmd.startswith('cp -r '):
                return 'xcopy /E ' + win32_normpath(cmd[6:])
            elif cmd.startswith('cp '):
                return 'copy ' + win32_normpath(cmd[3:])
            else:
                return cmd
        d = os.path.dirname(sys.argv[0])
        doc = os.path.join(d, doxfile)
        inline = False
        cmds = []
        example_path = os.path.abspath(IMP.get_example_path('..'))
        with open(doc) as fh:
            for line in fh.readlines():
                if '\code{.sh}' in line:
                    inline = True
                elif '\endcode' in line:
                    inline = False
                elif inline:
                    cmds.append(line.rstrip('\r\n').replace(
                                  '<imp_example_path>', example_path))
        if sys.platform == 'win32':
            cmds = [fix_win32_command(x) for x in cmds]
        return cmds

    def run_shell_command(self, cmd):
        "Print and run a shell command, as returned by read_shell_commands()"
        print(cmd)
        p = subprocess.call(cmd, shell=True)
        if p != 0:
            raise OSError("%s failed with exit value %d" % (cmd, p))


class RefCountChecker:
    """Check to make sure the number of C++ object references is as expected"""

    def __init__(self, testcase):
        # Make sure no director objects are hanging around; otherwise these
        # may be unexpectedly garbage collected later, decreasing the
        # live object count
        IMP._director_objects.cleanup()
        self.__testcase = testcase
        if IMP.get_check_level() >= IMP.USAGE_AND_INTERNAL:
            self.__basenum = IMP.Object.get_number_of_live_objects()
            self.__names = IMP.get_live_object_names()

    def assert_number(self, expected):
        "Make sure that the number of references matches the expected value."
        t = self.__testcase
        IMP._director_objects.cleanup()
        if IMP.get_check_level() >= IMP.USAGE_AND_INTERNAL:
            newnames = [x for x in IMP.get_live_object_names()
                        if x not in self.__names]
            newnum = IMP.Object.get_number_of_live_objects()-self.__basenum
            t.assertEqual(newnum, expected,
                          "Number of objects don't match: "
                          + str(newnum) + " != " + str(expected) + " found "
                          + str(newnames))


class DirectorObjectChecker:
    """Check to make sure the number of director references is as expected"""

    def __init__(self, testcase):
        IMP._director_objects.cleanup()
        self.__testcase = testcase
        self.__basenum = IMP._director_objects.get_object_count()

    def assert_number(self, expected, force_cleanup=True):
        """Make sure that the number of references matches the expected value.
           If force_cleanup is set, clean up any unused references first before
           doing the assertion.
        """
        t = self.__testcase
        if force_cleanup:
            IMP._director_objects.cleanup()
        t.assertEqual(IMP._director_objects.get_object_count()
                      - self.__basenum, expected)


# Make sure that the IMP binary directory (build/bin) is in the PATH, if
# we're running under wine (the imppy.sh script normally ensures this, but
# wine overrides the PATH). This is needed so that tests of imported Python
# applications can successfully spawn C++ applications (e.g. idock.py tries
# to run recompute_zscore.exe). build/lib also needs to be in the PATH, since
# that's how Windows locates dependent DLLs such as libimp.dll.
if sys.platform == 'win32' and 'PYTHONPATH' in os.environ \
   and 'IMP_BIN_DIR' in os.environ:
    libdir = os.environ['PYTHONPATH'].split(';')[0]
    bindir = os.environ['IMP_BIN_DIR']
    path = os.environ['PATH']
    if libdir not in path or bindir not in path:
        os.environ['PATH'] = bindir + ';' + libdir + ';' + path


__version__ = "20260825.develop.6701db5d00"

def get_module_version():
    '''Return the version of this module, as a string'''
    return "20260825.develop.6701db5d00"

def get_module_name():
    '''Return the fully-qualified name of this module'''
    return "IMP::test"

def get_data_path(fname):
    '''Return the full path to one of this module's data files'''
    import IMP
    return IMP._get_module_data_path("test", fname)

def get_example_path(fname):
    '''Return the full path to one of this module's example files'''
    import IMP
    return IMP._get_module_example_path("test", fname)