10 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17 def swig_import_helper():
19 pkg = __name__.rpartition(
'.')[0]
20 mname =
'.'.join((pkg,
'_IMP_test')).lstrip(
'.')
22 return importlib.import_module(mname)
24 return importlib.import_module(
'_IMP_test')
25 _IMP_test = swig_import_helper()
26 del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28 def swig_import_helper():
29 from os.path
import dirname
33 fp, pathname, description = imp.find_module(
'_IMP_test', [dirname(__file__)])
39 _mod = imp.load_module(
'_IMP_test', fp, pathname, description)
43 _IMP_test = swig_import_helper()
44 del swig_import_helper
47 del _swig_python_version_info
49 _swig_property = property
54 import builtins
as __builtin__
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59 if (name ==
"thisown"):
60 return self.this.own(value)
62 if type(value).__name__ ==
'SwigPyObject':
63 self.__dict__[name] = value
65 method = class_type.__swig_setmethods__.get(name,
None)
67 return method(self, value)
69 object.__setattr__(self, name, value)
71 raise AttributeError(
"You cannot add attributes to %s" % self)
74 def _swig_setattr(self, class_type, name, value):
75 return _swig_setattr_nondynamic(self, class_type, name, value, 0)
78 def _swig_getattr(self, class_type, name):
79 if (name ==
"thisown"):
80 return self.this.own()
81 method = class_type.__swig_getmethods__.get(name,
None)
84 raise AttributeError(
"'%s' object has no attribute '%s'" % (class_type.__name__, name))
89 strthis =
"proxy of " + self.this.__repr__()
90 except __builtin__.Exception:
92 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
95 def _swig_setattr_nondynamic_method(set):
96 def set_attr(self, name, value):
97 if (name ==
"thisown"):
98 return self.this.own(value)
99 if hasattr(self, name)
or (name ==
"this"):
100 set(self, name, value)
102 raise AttributeError(
"You cannot add attributes to %s" % self)
108 weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110 weakref_proxy =
lambda x: x
113 class IMP_TEST_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_TEST_SwigPyIterator class."""
116 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
118 def __init__(self, *args, **kwargs):
119 raise AttributeError(
"No constructor defined - class is abstract")
120 __repr__ = _swig_repr
121 __swig_destroy__ = _IMP_test.delete_IMP_TEST_SwigPyIterator
122 __del__ =
lambda self:
None
125 """value(IMP_TEST_SwigPyIterator self) -> PyObject *"""
126 return _IMP_test.IMP_TEST_SwigPyIterator_value(self)
131 incr(IMP_TEST_SwigPyIterator self, size_t n=1) -> IMP_TEST_SwigPyIterator
132 incr(IMP_TEST_SwigPyIterator self) -> IMP_TEST_SwigPyIterator
134 return _IMP_test.IMP_TEST_SwigPyIterator_incr(self, n)
139 decr(IMP_TEST_SwigPyIterator self, size_t n=1) -> IMP_TEST_SwigPyIterator
140 decr(IMP_TEST_SwigPyIterator self) -> IMP_TEST_SwigPyIterator
142 return _IMP_test.IMP_TEST_SwigPyIterator_decr(self, n)
145 def distance(self, x):
146 """distance(IMP_TEST_SwigPyIterator self, IMP_TEST_SwigPyIterator x) -> ptrdiff_t"""
147 return _IMP_test.IMP_TEST_SwigPyIterator_distance(self, x)
151 """equal(IMP_TEST_SwigPyIterator self, IMP_TEST_SwigPyIterator x) -> bool"""
152 return _IMP_test.IMP_TEST_SwigPyIterator_equal(self, x)
156 """copy(IMP_TEST_SwigPyIterator self) -> IMP_TEST_SwigPyIterator"""
157 return _IMP_test.IMP_TEST_SwigPyIterator_copy(self)
161 """next(IMP_TEST_SwigPyIterator self) -> PyObject *"""
162 return _IMP_test.IMP_TEST_SwigPyIterator_next(self)
166 """__next__(IMP_TEST_SwigPyIterator self) -> PyObject *"""
167 return _IMP_test.IMP_TEST_SwigPyIterator___next__(self)
171 """previous(IMP_TEST_SwigPyIterator self) -> PyObject *"""
172 return _IMP_test.IMP_TEST_SwigPyIterator_previous(self)
175 def advance(self, n):
176 """advance(IMP_TEST_SwigPyIterator self, ptrdiff_t n) -> IMP_TEST_SwigPyIterator"""
177 return _IMP_test.IMP_TEST_SwigPyIterator_advance(self, n)
181 """__eq__(IMP_TEST_SwigPyIterator self, IMP_TEST_SwigPyIterator x) -> bool"""
182 return _IMP_test.IMP_TEST_SwigPyIterator___eq__(self, x)
186 """__ne__(IMP_TEST_SwigPyIterator self, IMP_TEST_SwigPyIterator x) -> bool"""
187 return _IMP_test.IMP_TEST_SwigPyIterator___ne__(self, x)
190 def __iadd__(self, n):
191 """__iadd__(IMP_TEST_SwigPyIterator self, ptrdiff_t n) -> IMP_TEST_SwigPyIterator"""
192 return _IMP_test.IMP_TEST_SwigPyIterator___iadd__(self, n)
195 def __isub__(self, n):
196 """__isub__(IMP_TEST_SwigPyIterator self, ptrdiff_t n) -> IMP_TEST_SwigPyIterator"""
197 return _IMP_test.IMP_TEST_SwigPyIterator___isub__(self, n)
200 def __add__(self, n):
201 """__add__(IMP_TEST_SwigPyIterator self, ptrdiff_t n) -> IMP_TEST_SwigPyIterator"""
202 return _IMP_test.IMP_TEST_SwigPyIterator___add__(self, n)
205 def __sub__(self, *args):
207 __sub__(IMP_TEST_SwigPyIterator self, ptrdiff_t n) -> IMP_TEST_SwigPyIterator
208 __sub__(IMP_TEST_SwigPyIterator self, IMP_TEST_SwigPyIterator x) -> ptrdiff_t
210 return _IMP_test.IMP_TEST_SwigPyIterator___sub__(self, *args)
214 IMP_TEST_SwigPyIterator_swigregister = _IMP_test.IMP_TEST_SwigPyIterator_swigregister
215 IMP_TEST_SwigPyIterator_swigregister(IMP_TEST_SwigPyIterator)
223 IMP_DEBUG = _IMP_test.IMP_DEBUG
224 IMP_RELEASE = _IMP_test.IMP_RELEASE
225 IMP_SILENT = _IMP_test.IMP_SILENT
226 IMP_PROGRESS = _IMP_test.IMP_PROGRESS
227 IMP_TERSE = _IMP_test.IMP_TERSE
228 IMP_VERBOSE = _IMP_test.IMP_VERBOSE
229 IMP_MEMORY = _IMP_test.IMP_MEMORY
230 IMP_NONE = _IMP_test.IMP_NONE
231 IMP_USAGE = _IMP_test.IMP_USAGE
232 IMP_INTERNAL = _IMP_test.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_test.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_test.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_test.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_test.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_test.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_test.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_test.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_test.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_test.IMPKERNEL_SHOW_WARNINGS
244 class _DirectorObjects(object):
245 """@internal Simple class to keep references to director objects
246 to prevent premature deletion."""
249 def register(self, obj):
250 """Take a reference to a director object; will only work for
251 refcounted C++ classes"""
252 if hasattr(obj,
'get_ref_count'):
253 self._objects.append(obj)
255 """Only drop our reference and allow cleanup by Python if no other
256 Python references exist (we hold 3 references: one in self._objects,
257 one in x, and one in the argument list for getrefcount) *and* no
258 other C++ references exist (the Python object always holds one)"""
259 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
260 or x.get_ref_count() > 1]
264 def get_object_count(self):
265 """Get number of director objects (useful for testing only)"""
266 return len(self._objects)
267 _director_objects = _DirectorObjects()
269 class _ostream(object):
270 """Proxy of C++ std::ostream class."""
272 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
274 def __init__(self, *args, **kwargs):
275 raise AttributeError(
"No constructor defined")
276 __repr__ = _swig_repr
278 def write(self, osa_buf):
279 """write(_ostream self, char const * osa_buf)"""
280 return _IMP_test._ostream_write(self, osa_buf)
282 _ostream_swigregister = _IMP_test._ostream_swigregister
283 _ostream_swigregister(_ostream)
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_test.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_test.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_test.IMP_HAS_NOEXCEPT
289 IMP_TEST_HAS_BOOST_FILESYSTEM = _IMP_test.IMP_TEST_HAS_BOOST_FILESYSTEM
290 IMP_TEST_HAS_BOOST_PROGRAMOPTIONS = _IMP_test.IMP_TEST_HAS_BOOST_PROGRAMOPTIONS
291 IMP_TEST_HAS_BOOST_RANDOM = _IMP_test.IMP_TEST_HAS_BOOST_RANDOM
292 IMP_TEST_HAS_BOOST_SYSTEM = _IMP_test.IMP_TEST_HAS_BOOST_SYSTEM
293 IMPTEST_SHOW_WARNINGS = _IMP_test.IMPTEST_SHOW_WARNINGS
296 """@namespace IMP::test
297 @brief Methods and classes for testing the IMP kernel and modules.
311 from .
import _compat_python
312 from ._compat_python
import unittest2
329 def __load_unittest_package():
331 for modname, fromlist
in ((
'unittest', []),
335 u = __import__(modname, {}, {}, fromlist)
336 if hasattr(u,
'skip'):
339 errors.append(
"'%s' does not have the 'skip' decorator" \
341 except ImportError
as e:
342 errors.append(str(e))
344 return _compat_python.unittest2
345 raise ImportError(
"IMP.test requires a newer version of Python's unittest "
346 "package than is available. Either upgrade to a new "
347 "enough Python (at least 2.7 or 3.2) or install the "
348 "unittest2 package. Encountered errors: %s" \
350 unittest = __load_unittest_package()
353 expectedFailure = unittest.expectedFailure
355 skipIf = unittest.skipIf
356 skipUnless = unittest.skipUnless
360 """Simple RAII-style class to run in a temporary directory.
361 When the object is created, the temporary directory is created
362 and becomes the current working directory. When the object goes out
363 of scope, the working directory is reset and the temporary directory
366 self.origdir = os.getcwd()
367 self.tmpdir = tempfile.mkdtemp()
368 os.chdir(self.tmpdir)
370 os.chdir(self.origdir)
371 shutil.rmtree(self.tmpdir, ignore_errors=
True)
373 @contextlib.contextmanager
375 """Simple context manager to run in a temporary directory.
376 While the context manager is active (within the 'with' block)
377 the current working directory is set to a temporary directory.
378 When the context manager exists, the working directory is reset
379 and the temporary directory deleted."""
380 origdir = os.getcwd()
381 tmpdir = tempfile.mkdtemp()
385 shutil.rmtree(tmpdir, ignore_errors=
True)
389 """Simple RAII-style class to make a temporary directory. When the object
390 is created, the temporary directory is created. When the object goes
391 out of scope, the temporary directory is deleted."""
392 def __init__(self, dir=None):
393 self.tmpdir = tempfile.mkdtemp(dir=dir)
395 shutil.rmtree(self.tmpdir, ignore_errors=
True)
397 class _TempDir(object):
398 def __init__(self, dir=None):
399 self.tmpdir = tempfile.mkdtemp(dir=dir)
401 shutil.rmtree(self.tmpdir, ignore_errors=
True)
403 @contextlib.contextmanager
405 """Simple context manager to make a temporary directory.
406 The temporary directory has the same lifetime as the context manager
407 (i.e. it is created at the start of the 'with' block, and deleted
408 at the end of the block).
409 @param dir If given, the temporary directory is made as a subdirectory
410 of that directory, rather than in the default temporary
411 directory location (e.g. /tmp)
412 @return the full path to the temporary directory.
414 tmpdir = tempfile.mkdtemp(dir=dir)
416 shutil.rmtree(tmpdir, ignore_errors=
True)
419 """Calculate the derivative of the single-value function `func` at
420 point `val`. The derivative is calculated using simple finite
421 differences starting with the given `step`; Richardson extrapolation
422 is then used to extrapolate the derivative at step=0."""
427 f1 = func(val + step)
428 f2 = func(val - step)
430 d = [[(f1 - f2) / (2.0 * step)]]
432 for i
in range(1, maxsteps):
433 d.append([0.] * (i + 1))
435 f1 = func(val + step)
436 f2 = func(val - step)
437 d[i][0] = (f1 - f2) / (2.0 * step)
439 for j
in range(1, i + 1):
440 d[i][j] = (d[i][j-1] * fac - d[i-1][j-1]) / (fac - 1.)
442 errt = max(abs(d[i][j] - d[i][j-1]),
443 abs(d[i][j] - d[i-1][j-1]))
447 if abs(d[i][i] - d[i-1][i-1]) >= safe * err:
450 raise ValueError(
"Cannot calculate numerical derivative")
455 """Calculate the x,y and z derivatives of the scoring function `sf`
456 on the `xyz` particle. The derivatives are approximated numerically
457 using the numerical_derivatives() function."""
458 class _XYZDerivativeFunc(object):
459 def __init__(self, sf, xyz, basis_vector):
462 self._basis_vector = basis_vector
463 self._starting_coordinates = xyz.get_coordinates()
465 def __call__(self, val):
466 self._xyz.set_coordinates(self._starting_coordinates + \
467 self._basis_vector * val)
468 return self._sf.evaluate(
False)
472 for x
in ((1,0,0), (0,1,0), (0,0,1))])
476 """Super class for IMP test cases.
477 This provides a number of useful IMP-specific methods on top of
478 the standard Python `unittest.TestCase` class.
479 Test scripts should generally contain a subclass of this class,
480 conventionally called `Tests` (this makes it easier to run an
481 individual test from the commane line) and use IMP::test::main()
482 as their main function."""
484 def __init__(self, *args, **keys):
485 unittest.TestCase.__init__(self, *args, **keys)
486 self._progname = os.path.abspath(sys.argv[0])
494 IMP.random_number_generator.seed(hash(time.time())%2**30)
500 if hasattr(self,
'_tmpdir'):
504 """Get the full name of an input file in the top-level
506 testdir = os.path.dirname(self._progname)
507 dirs = testdir.split(os.path.sep)
508 for i
in range(len(dirs), 0, -1):
509 input = os.path.sep.join(dirs[:i] + [
'input'])
510 if os.path.isdir(input):
511 ret = os.path.join(input, filename)
512 if not os.path.exists(ret):
513 raise IOError(
"Test input file "+ret+
" does not exist")
515 raise IOError(
"No test input directory found")
518 """Open and return an input file in the top-level test directory."""
522 """Get the full name of an output file in the tmp directory.
523 The directory containing this file will be automatically
524 cleaned up when the test completes."""
525 if not hasattr(self,
'_tmpdir'):
526 self._tmpdir = _TempDir(os.environ[
'IMP_TMP_DIR'])
527 tmpdir = self._tmpdir.tmpdir
528 return os.path.join(tmpdir, filename)
531 """Get the magnitude of a list of floats"""
532 return sum([x*x
for x
in vector], 0)**.5
535 """Assert that the given callable object raises UsageException.
536 This differs from unittest's assertRaises in that the test
537 is skipped in fast mode (where usage checks are turned off)."""
542 """Assert that the given callable object raises InternalException.
543 This differs from unittest's assertRaises in that the test
544 is skipped in fast mode (where internal checks are turned off)."""
549 """Assert that the given callable object is not implemented."""
554 """Assert that x,y,z analytical derivatives match numerical within
555 a tolerance, or a percentage (of the analytical value), whichever
556 is larger. `sf` should be a ScoringFunction or Restraint,
557 although for backwards compatibility a Model is also accepted."""
559 derivs = xyz.get_derivatives()
561 pct = percentage / 100.0
562 self.assertAlmostEqual(self.
get_magnitude(derivs-num_derivs),0,
564 msg=
"Don't match "+str(derivs) + str(num_derivs))
565 self.assertAlmostEqual(derivs[0], num_derivs[0],
566 delta=max(tolerance, abs(derivs[0]) * pct))
567 self.assertAlmostEqual(derivs[1], num_derivs[1],
568 delta=max(tolerance, abs(derivs[1]) * pct))
569 self.assertAlmostEqual(derivs[2], num_derivs[2],
570 delta=max(tolerance, abs(derivs[2]) * pct))
573 """Make a particle with optimizable x, y and z attributes, and
574 add it to the model."""
582 """Help handle a test which is expected to fail some fraction of
583 the time. The test is run multiple times and an exception
584 is thrown only if it fails too many times.
585 @note Use of this function should be avoided. If there is a corner
586 case that results in a test 'occasionally' failing, write a
587 new test specifically for that corner case and assert that
588 it fails consistently (and remove the corner case from the
591 prob=chance_of_failure
595 prob= prob*chance_of_failure
596 for i
in range(0, tries):
604 raise AssertError(
"Too many failures")
607 """Estimate how likely a given block of code is to raise an
611 while failures < 10
and tries <1000:
617 return failures/tries
620 """Randomize the xyz coordinates of a list of particles"""
626 p.set_value(xkey, random.uniform(-deviation, deviation))
627 p.set_value(ykey, random.uniform(-deviation, deviation))
628 p.set_value(zkey, random.uniform(-deviation, deviation))
631 """Return distance between two given particles"""
635 dx = p1.get_value(xkey) - p2.get_value(xkey)
636 dy = p1.get_value(ykey) - p2.get_value(ykey)
637 dz = p1.get_value(zkey) - p2.get_value(zkey)
638 return math.sqrt(dx*dx + dy*dy + dz*dz)
641 """Check the unary function func's derivatives against numerical
642 approximations between lb and ub"""
643 for f
in [lb + i * step
for i
in range(1, int((ub-lb)/step))]:
644 (v,d)= func.evaluate_with_derivative(f)
646 self.assertAlmostEqual(d, da, delta=max(abs(.1 *d), 0.01))
649 """Make sure that the minimum of the unary function func over the
650 range between lb and ub is at expected_fmin"""
651 fmin, vmin = lb, func.evaluate(lb)
652 for f
in [lb + i * step
for i
in range(1, int((ub-lb)/step))]:
656 self.assertAlmostEqual(fmin, expected_fmin, delta=step)
659 """Check methods that every IMP::Object class should have"""
660 obj.set_was_used(
True)
663 self.assertIsNotNone(cls.get_from(obj))
664 self.assertRaises(ValueError, cls.get_from,
IMP.Model())
666 self.assertIsInstance(str(obj), str)
667 self.assertIsInstance(repr(obj), str)
669 verinf = obj.get_version_info()
678 """Create a bunch of particles in a box"""
683 for i
in range(0,num):
688 def _get_type(self, module, name):
689 return eval(
'type('+module+
"."+name+
')')
691 "Check that all the C++ classes in the module are values or objects."
693 ok = set(exceptions_list + module._value_types + module._object_types + module._raii_types + module._plural_types)
697 if self._get_type(module.__name__, name)==type
and not name.startswith(
"_"):
698 if name.find(
"SwigPyIterator") != -1:
701 if not eval(
'hasattr(%s.%s, "__swig_destroy__")' \
702 % (module.__name__, name)):
707 message=
"All IMP classes should be labeled as values or objects to get memory management correct in Python. The following are not:\n%s\nPlease 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." \
709 self.assertEqual(len(bad), 0, message)
710 for e
in exceptions_list:
711 self.assertTrue(e
not in module._value_types
712 + module._object_types
714 + module._plural_types,
715 "Value/Object exception "+e+
" is not an exception")
717 def _check_spelling(self, word, words):
718 """Check that the word is spelled correctly"""
719 if "words" not in dir(self):
721 wordlist= fh.read().split("\n")
723 custom_words=[
"info",
"prechange",
"int",
"ints",
"optimizeds",
"graphviz",
724 "voxel",
"voxels",
"endian",
'rna',
'dna',
725 "xyzr",
"pdbs",
"fft",
"ccc",
"gaussian"]
728 exclude_words = set([
"adapter",
"grey"])
729 self.words=set(wordlist+custom_words) - exclude_words
731 for i
in "0123456789":
736 if word
in self.words:
743 """Check that all the classes in the module follow the IMP
744 naming conventions."""
748 cc=re.compile(
"([A-Z][a-z]*)")
750 if self._get_type(module.__name__, name)==type
and not name.startswith(
"_"):
751 if name.find(
"SwigPyIterator") != -1:
753 for t
in re.findall(cc, name):
754 if not self._check_spelling(t.lower(), words):
755 misspelled.append(t.lower())
758 self.assertEqual(len(bad), 0,
759 "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." \
760 % (str(bad),
", ".join(set(misspelled))))
763 if self._get_type(module.__name__, name)==type
and not name.startswith(
"_"):
764 if name.find(
"SwigPyIterator") != -1:
766 if name.find(
'_') != -1:
768 if name.lower== name:
770 for t
in re.findall(cc, name):
771 if not self._check_spelling(t.lower(), words):
772 print(
"misspelled %s in %s" % (t, name))
774 message=
"All IMP classes should have CamelCase names. The following do not: %s." \
776 self.assertEqual(len(bad), 0, message)
778 def _check_function_name(self, prefix, name, verbs, all, exceptions, words,
781 fullname=prefix+
"."+name
784 old_exceptions=[
'unprotected_evaluate',
"unprotected_evaluate_if_good",
785 "unprotected_evaluate_if_below",
786 "after_evaluate",
"before_evaluate",
"has_attribute",
787 "decorate_particle",
"particle_is_instance"]
788 if name
in old_exceptions:
791 if fullname
in exceptions:
793 if name.endswith(
"swigregister"):
795 if name.lower() != name:
796 if name[0].lower() != name[0]
and name.split(
'_')[0]
in all:
801 tokens= name.split(
"_")
802 if tokens[0]
not in verbs:
805 if not self._check_spelling(t, words):
807 print(
"misspelled %s in %s" % (t, name))
811 def _static_method(self, module, prefix, name):
812 """For static methods of the form Foo.bar SWIG creates free functions
813 named Foo_bar. Exclude these from spelling checks since the method
814 Foo.bar has already been checked."""
815 if prefix
is None and '_' in name:
816 modobj = eval(module)
817 cls, meth = name.split(
'_', 1)
818 if hasattr(modobj, cls):
819 clsobj = eval(module +
'.' + cls)
820 if hasattr(clsobj, meth):
823 def _check_function_names(self, module, prefix, names, verbs, all,
824 exceptions, words, misspelled):
827 typ = self._get_type(module, name)
828 if name.startswith(
"_")
or name ==
"weakref_proxy":
830 if typ
in (types.BuiltinMethodType, types.MethodType) \
831 or (typ == types.FunctionType
and \
832 not self._static_method(module, prefix, name)):
833 bad.extend(self._check_function_name(prefix, name, verbs, all,
836 if typ == type
and "SwigPyIterator" not in name:
837 members=eval(
"dir("+module+
"."+name+
")")
838 bad.extend(self._check_function_names(module+
"."+name,
839 name, members, verbs, [],
845 """Check that all the functions in the module follow the IMP
846 naming conventions."""
848 verbs=set([
"add",
"remove",
"get",
"set",
"evaluate",
"compute",
"show",
"create",
"destroy",
849 "push",
"pop",
"write",
"read",
"do",
"show",
"load",
"save",
"reset",
851 "clear",
"handle",
"update",
"apply",
"optimize",
"reserve",
"dump",
852 "propose",
"setup",
"teardown",
"visit",
"find",
"run",
"swap",
"link",
855 bad=self._check_function_names(module.__name__,
None, all, verbs, all, exceptions, words, misspelled)
856 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" \
857 % {
"bad":
"\n".join(bad),
"verbs":verbs}
858 if len(misspelled) > 0:
859 message +=
"\nMisspelled words: " +
", ".join(set(misspelled)) \
860 +
". Add words to the spelling_exceptions variable " \
861 +
"of the standards_exceptions file if needed."
862 self.assertEqual(len(bad), 0, message)
866 """Check that all the classes in modulename have a show method"""
874 if not eval(
'hasattr(%s.%s, "__swig_destroy__")' \
875 % (modulename.__name__, f)):
877 if self._get_type(modulename.__name__, f) == type \
878 and not f.startswith(
"_") \
879 and not f.endswith(
"_swigregister")\
880 and f
not in exceptions\
881 and not f.endswith(
"Temp")
and not f.endswith(
"Iterator")\
882 and not f.endswith(
"Exception")
and\
883 f
not in modulename._raii_types
and \
884 f
not in modulename._plural_types:
885 if not hasattr(getattr(modulename, f),
'show'):
887 message=
"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." \
888 %
"\n".join(not_found)
889 self.assertEqual(len(not_found), 0, message)
891 self.assertIn(e, all,
"Show exception "+e+
" is not a class in module")
892 self.assertTrue(
not hasattr(getattr(modulename, e),
'show'),
893 "Exception "+e+
" is not really a show exception")
896 """Run the named example script.
897 @return a dictionary of all the script's global variables.
898 This can be queried in a test case to make sure
899 the example performed correctly."""
904 path, name = os.path.split(filename)
905 oldsyspath = sys.path[:]
906 olssysargv= sys.argv[:]
907 sys.path.insert(0, path)
912 exec(open(filename).read(), vars)
915 except SystemExit
as e:
916 if e.code != 0
and e.code
is not None:
917 raise _FatalError(
"Example exit with code %s" % str(e.code))
921 sys.path = oldsyspath
924 return _ExecDictProxy(vars)
927 """Run a Python module as if with "python -m <modname>",
928 with the given list of arguments as sys.argv.
930 If module is an already-imported Python module, run its 'main'
931 function and return the result.
933 If module is a string, run the module in a subprocess and return
934 a subprocess.Popen-like object containing the child stdin,
937 if type(module) == type(os):
940 mod = __import__(module, {}, {}, [
''])
941 modpath = mod.__file__
942 if modpath.endswith(
'.pyc'):
943 modpath = modpath[:-1]
944 if type(module) == type(os):
945 old_sys_argv = sys.argv
947 IMP.OptionParser._use_boost_parser =
False
949 sys.argv = [modpath] + args
952 IMP.OptionParser._use_boost_parser =
True
953 sys.argv = old_sys_argv
955 return _SubprocessWrapper(sys.executable, [modpath] + args)
958 """Check a Python module designed to be runnable with 'python -m'
959 to make sure it supports standard command line options."""
962 out, err = r.communicate()
963 self.assertEqual(r.returncode, 0)
964 self.assertNotEqual(err,
"")
965 self.assertEqual(out,
"")
968 class _ExecDictProxy(object):
969 """exec returns a Python dictionary, which contains IMP objects, other
970 Python objects, as well as base Python modules (such as sys and
971 __builtins__). If we just delete this dictionary, it is entirely
972 possible that base Python modules are removed from the dictionary
973 *before* some IMP objects. This will prevent the IMP objects' Python
974 destructors from running properly, so C++ objects will not be
975 cleaned up. This class proxies the base dict class, and on deletion
976 attempts to remove keys from the dictionary in an order that allows
977 IMP destructors to fire."""
978 def __init__(self, d):
982 module_type = type(IMP)
985 if type(d[k]) != module_type:
988 for meth
in [
'__contains__',
'__getitem__',
'__iter__',
'__len__',
989 'get',
'has_key',
'items',
'keys',
'values']:
990 exec(
"def %s(self, *args, **keys): "
991 "return self._d.%s(*args, **keys)" % (meth, meth))
994 class _TestResult(unittest.TextTestResult):
996 def __init__(self, stream=None, descriptions=None, verbosity=None):
997 super(_TestResult, self).__init__(stream, descriptions, verbosity)
1000 def stopTestRun(self):
1001 if 'IMP_TEST_DETAIL_DIR' in os.environ:
1002 fname = os.path.join(os.environ[
'IMP_TEST_DETAIL_DIR'],
1003 os.path.basename(sys.argv[0]))
1004 with open(fname,
'wb')
as fh:
1005 pickle.dump(self.all_tests, fh, -1)
1006 super(_TestResult, self).stopTestRun()
1008 def startTest(self, test):
1009 super(_TestResult, self).startTest(test)
1010 test.start_time=datetime.datetime.now()
1012 def _test_finished(self, test, state, detail=None):
1013 delta = datetime.datetime.now() - test.start_time
1015 pv= delta.total_seconds()
1016 except AttributeError:
1017 pv = (float(delta.microseconds) \
1018 + (delta.seconds + delta.days * 24 * 3600) * 10**6) / 10**6
1020 self.stream.write(
"in %.3fs ... " % pv)
1021 if detail
is not None and not isinstance(detail, str):
1022 detail = self._exc_info_to_string(detail, test)
1023 test_doc = self.getDescription(test)
1024 test_name = test.id()
1025 if test_name.startswith(
'__main__.'):
1026 test_name = test_name[9:]
1027 self.all_tests.append({
'name': test_name,
1028 'docstring': test_doc,
1029 'time': pv,
'state': state,
'detail': detail})
1031 def addSuccess(self, test):
1032 self._test_finished(test,
'OK')
1033 super(_TestResult, self).addSuccess(test)
1035 def addError(self, test, err):
1036 self._test_finished(test,
'ERROR', err)
1037 super(_TestResult, self).addError(test, err)
1039 def addFailure(self, test, err):
1040 self._test_finished(test,
'FAIL', err)
1041 super(_TestResult, self).addFailure(test, err)
1043 def addSkip(self, test, reason):
1044 self._test_finished(test,
'SKIP', reason)
1045 super(_TestResult, self).addSkip(test, reason)
1047 def addExpectedFailure(self, test, err):
1048 self._test_finished(test,
'EXPFAIL', err)
1049 super(_TestResult, self).addExpectedFailure(test, err)
1051 def addUnexpectedSuccess(self, test):
1052 self._test_finished(test,
'UNEXPSUC')
1053 super(_TestResult, self).addUnexpectedSuccess(test)
1055 def getDescription(self, test):
1056 doc_first_line = test.shortDescription()
1057 if self.descriptions
and doc_first_line:
1058 return doc_first_line
1063 class _TestRunner(unittest.TextTestRunner):
1064 def _makeResult(self):
1065 return _TestResult(self.stream, self.descriptions, self.verbosity)
1069 """Run a set of tests; similar to unittest.main().
1070 Obviates the need to separately import the 'unittest' module, and
1071 ensures that main() is from the same unittest module that the
1072 IMP.test testcases are. In addition, turns on some extra checks
1073 (e.g. trying to use deprecated code will cause an exception
1077 return unittest.main(testRunner=_TestRunner, *args, **keys)
1080 class _SubprocessWrapper(subprocess.Popen):
1081 def __init__(self, app, args):
1084 if sys.platform ==
'win32' and app != sys.executable:
1086 libdir = os.environ[
'PYTHONPATH'].split(
';')[0]
1087 env = os.environ.copy()
1088 env[
'PATH'] +=
';' + libdir
1091 subprocess.Popen.__init__(self, [app]+list(args),
1092 stdin=subprocess.PIPE,
1093 stdout=subprocess.PIPE,
1094 stderr=subprocess.PIPE, env=env,
1095 universal_newlines=
True)
1099 """Super class for simple IMP application test cases"""
1100 def _get_application_file_name(self, filename):
1103 if sys.platform ==
'win32':
1111 """Run an application with the given list of arguments.
1112 @return a subprocess.Popen-like object containing the child stdin,
1115 filename = self._get_application_file_name(app)
1116 if sys.platform ==
'win32':
1118 return _SubprocessWrapper(os.path.join(os.environ[
'IMP_BIN_DIR'],
1121 return _SubprocessWrapper(filename, args)
1124 """Run a Python application with the given list of arguments.
1125 The Python application should be self-runnable (i.e. it should
1126 be executable and with a #! on the first line).
1127 @return a subprocess.Popen-like object containing the child stdin,
1131 if sys.executable !=
'/usr/bin/python' and 'IMP_BIN_DIR' in os.environ:
1132 return _SubprocessWrapper(sys.executable,
1133 [os.path.join(os.environ[
'IMP_BIN_DIR'], app)] + args)
1135 return _SubprocessWrapper(app, args)
1138 """Import an installed Python application, rather than running it.
1139 This is useful to directly test components of the application.
1140 @return the Python module object."""
1142 import importlib.machinery
1146 name = os.path.splitext(app)[0]
1147 pathname = os.path.join(os.environ[
'IMP_BIN_DIR'], app)
1149 return importlib.machinery.SourceFileLoader(name,
1150 pathname).load_module()
1152 return imp.load_source(name, pathname)
1155 """Run an application with the given list of arguments.
1156 @return a subprocess.Popen-like object containing the child stdin,
1159 return _SubprocessWrapper(sys.executable, [app]+args)
1162 """Assert that the application exited cleanly (return value = 0)."""
1164 raise OSError(
"Application exited with signal %d\n" % -ret\
1167 self.assertEqual(ret, 0,
1168 "Application exited uncleanly, with exit code %d\n" % ret\
1172 """Read and return a set of shell commands from a doxygen file.
1173 Each command is assumed to be in a \code{.sh}...\endcode block.
1174 The doxygen file is specified relative to the test file itself.
1175 This is used to make sure the commands shown in an application
1176 example actually work (the testcase can also check the resulting
1177 files for correctness)."""
1178 def win32_normpath(p):
1181 return " ".join([os.path.normpath(x)
for x
in p.split()])
1182 def fix_win32_command(cmd):
1184 if cmd.startswith(
'cp -r '):
1185 return 'xcopy /E ' + win32_normpath(cmd[6:])
1186 elif cmd.startswith(
'cp '):
1187 return 'copy ' + win32_normpath(cmd[3:])
1190 d = os.path.dirname(sys.argv[0])
1191 doc = os.path.join(d, doxfile)
1195 with open(doc)
as fh:
1196 for line
in fh.readlines():
1197 if '\code{.sh}' in line:
1199 elif '\endcode' in line:
1202 cmds.append(line.rstrip(
'\r\n').replace(
1203 '<imp_example_path>', example_path))
1204 if sys.platform ==
'win32':
1205 cmds = [fix_win32_command(x)
for x
in cmds]
1209 "Print and run a shell command, as returned by read_shell_commands()"
1212 p = subprocess.call(cmd, shell=
True)
1214 raise OSError(
"%s failed with exit value %d" % (cmd, p))
1218 """Check to make sure the number of C++ object references is as expected"""
1220 def __init__(self, testcase):
1224 IMP._director_objects.cleanup()
1225 self.__testcase = testcase
1227 self.__basenum = IMP.Object.get_number_of_live_objects()
1231 "Make sure that the number of references matches the expected value."
1233 IMP._director_objects.cleanup()
1236 newnum=IMP.Object.get_number_of_live_objects()-self.__basenum
1237 t.assertEqual(newnum, expected,
1238 "Number of objects don't match: "\
1240 +
" != "+ str(expected) +
" found "+\
1246 """Check to make sure the number of director references is as expected"""
1248 def __init__(self, testcase):
1249 IMP._director_objects.cleanup()
1250 self.__testcase = testcase
1251 self.__basenum = IMP._director_objects.get_object_count()
1254 """Make sure that the number of references matches the expected value.
1255 If force_cleanup is set, clean up any unused references first before
1256 doing the assertion.
1260 IMP._director_objects.cleanup()
1261 t.assertEqual(IMP._director_objects.get_object_count() \
1262 - self.__basenum, expected)
1270 if sys.platform ==
'win32' and 'PYTHONPATH' in os.environ \
1271 and 'IMP_BIN_DIR' in os.environ:
1272 libdir = os.environ[
'PYTHONPATH'].split(
';')[0]
1273 bindir = os.environ[
'IMP_BIN_DIR']
1274 path = os.environ[
'PATH']
1275 if libdir
not in path
or bindir
not in path:
1276 os.environ[
'PATH'] = bindir +
';' + libdir +
';' + path
1279 def get_module_version():
1280 """get_module_version() -> std::string const"""
1281 return _IMP_test.get_module_version()
1284 """get_example_path(std::string fname) -> std::string"""
1285 return _IMP_test.get_example_path(fname)
1288 """get_data_path(std::string fname) -> std::string"""
1289 return _IMP_test.get_data_path(fname)
1291 from .
import _version_check
1292 _version_check.check_version(get_module_version())
1293 __version__ = get_module_version()
def run_python_module
Run a Python module as if with "python -m <modname>", with the given list of arguments as sys...
def temporary_working_directory
Simple context manager to run in a temporary directory.
def assertApplicationExitedCleanly
Assert that the application exited cleanly (return value = 0).
CheckLevel get_check_level()
Get the current audit mode.
def import_python_application
Import an installed Python application, rather than running it.
def open_input_file
Open and return an input file in the top-level test directory.
def run_application
Run an application with the given list of arguments.
def randomize_particles
Randomize the xyz coordinates of a list of particles.
A general exception for an internal error in IMP.
def main
Run a set of tests; similar to unittest.main().
An exception for an invalid usage of IMP.
Super class for simple IMP application test cases.
def assertRaisesInternalException
Assert that the given callable object raises InternalException.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
def assert_number
Make sure that the number of references matches the expected value.
Check to make sure the number of director references is as expected.
def assertShow
Check that all the classes in modulename have a show method.
def run_shell_command
Print and run a shell command, as returned by read_shell_commands()
def assertRaisesUsageException
Assert that the given callable object raises UsageException.
Vector3D get_random_vector_in(const Cylinder3D &c)
Generate a random vector in a cylinder with uniform density.
Class for storing model, its restraints, constraints, and particles.
def run_python_application
Run a Python application with the given list of arguments.
def assert_number
Make sure that the number of references matches the expected value.
Simple RAII-style class to run in a temporary directory.
Strings get_live_object_names()
Return the names of all live objects.
def check_standard_object_methods
Check methods that every IMP::Object class should have.
def particle_distance
Return distance between two given particles.
def check_unary_function_deriv
Check the unary function func's derivatives against numerical approximations between lb and ub...
def get_tmp_file_name
Get the full name of an output file in the tmp directory.
Version and module information for Objects.
def run_example
Run the named example script.
def get_magnitude
Get the magnitude of a list of floats.
void set_deprecation_exceptions(bool tf)
Toggle whether an exception is thrown when a deprecated method is used.
def check_unary_function_min
Make sure that the minimum of the unary function func over the range between lb and ub is at expected...
def probabilistic_test
Help handle a test which is expected to fail some fraction of the time.
def create_particles_in_box
Create a bunch of particles in a box.
def deprecated_object
Python decorator to mark a class as deprecated.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
def assertNotImplemented
Assert that the given callable object is not implemented.
The general base class for IMP exceptions.
def numerical_derivative
Calculate the derivative of the single-value function func at point val.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
def xyz_numerical_derivatives
Calculate the x,y and z derivatives of the scoring function sf on the xyz particle.
def failure_probability
Estimate how likely a given block of code is to raise an AssertionError.
def assertClassNames
Check that all the classes in the module follow the IMP naming conventions.
def create_point_particle
Make a particle with optimizable x, y and z attributes, and add it to the model.
Class to handle individual particles of a Model object.
def read_shell_commands
Read and return a set of shell commands from a doxygen file.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Check to make sure the number of C++ object references is as expected.
Simple RAII-style class to make a temporary directory.
def assertFunctionNames
Check that all the functions in the module follow the IMP naming conventions.
def assertValueObjects
Check that all the C++ classes in the module are values or objects.
Super class for IMP test cases.
def assertXYZDerivativesInTolerance
Assert that x,y,z analytical derivatives match numerical within a tolerance, or a percentage (of the ...
def temporary_directory
Simple context manager to make a temporary directory.
def run_script
Run an application with the given list of arguments.
def get_input_file_name
Get the full name of an input file in the top-level test directory.
def check_runnable_python_module
Check a Python module designed to be runnable with 'python -m' to make sure it supports standard comm...
void set_check_level(CheckLevel tf)
Control runtime checks in the code.