def test_angelapreference():
# check default args
pref = angelaPreference(1. / 3, 'docs')
assert not pref.validator(1)
assert pref.docs == 'docs'
assert pref.default == 1. / 3
assert pref.representor(pref.default) == repr(1. / 3)
def test_str_repr():
# Just test whether str and repr do not throw an error and return something
gp = angelaGlobalPreferences()
gp.register_preferences('main',
'main category',
name=angelaPreference(True, 'some preference'))
assert len(str(gp))
assert len(repr(gp))
assert len(str(gp.main))
assert len(repr(gp.main))
def test_preference_name_checking():
'''
Test that you cannot set illegal preference names.
'''
gp = angelaGlobalPreferences()
# Name that starts with an underscore
with pytest.raises(PreferenceError):
gp.register_preferences('dummy',
'dummy doc',
_notalegalname=angelaPreference(
True, 'some preference'))
# Name that clashes with a method name
with pytest.raises(PreferenceError):
gp.register_preferences('dummy',
'dummy doc',
update=angelaPreference(
True, 'some preference'))
gp.register_preferences('a',
'dummy doc',
b=angelaPreference(True, 'some preference'))
#Trying to register a subcategory that would shadow a preference
with pytest.raises(PreferenceError):
gp.register_preferences('a.b',
'dummy doc',
name=angelaPreference(True, 'some preference'))
gp.register_preferences('b.c',
'dummy doc',
name=angelaPreference(True, 'some preference'))
#Trying to register a preference that clashes with an existing category
with pytest.raises(PreferenceError):
gp.register_preferences('b',
'dummy doc',
c=angelaPreference(True, 'some preference'))
'ERROR': logging.ERROR,
'WARNING': logging.WARNING,
'INFO': logging.INFO,
'DEBUG': logging.DEBUG,
'DIAGNOSTIC': DIAGNOSTIC}
logging.addLevelName(DIAGNOSTIC, 'DIAGNOSTIC')
if 'logging' not in prefs.pref_register:
# Duplicate import of this module can happen when the documentation is built
prefs.register_preferences('logging', 'Logging system preferences',
delete_log_on_exit=angelaPreference(
default=True,
docs='''
Whether to delete the log and script file on exit.
If set to ``True`` (the default), log files (and the copy of the main
script) will be deleted after the angela process has exited, unless an
uncaught exception occurred. If set to ``False``, all log files will be
kept.
''',
),
file_log_level=angelaPreference(
default='DIAGNOSTIC',
docs='''
What log level to use for the log written to the log file.
In case file logging is activated (see `logging.file_log`), which log
level should be used for logging. Has to be one of CRITICAL, ERROR,
WARNING, INFO, DEBUG or DIAGNOSTIC.
''',
validator=log_level_validator),
get_numpy_dtype)
from ...targets import codegen_targets
from ...cpp_prefs import get_compiler_and_args
from .extension_manager import cython_extension_manager
__all__ = ['CythonCodeObject']
logger = get_logger(__name__)
# Preferences
prefs.register_preferences(
'codegen.runtime.cython',
'Cython runtime codegen preferences',
multiprocess_safe=angelaPreference(default=True,
docs='''
Whether to use a lock file to prevent simultaneous write access
to cython .pyx and .so files.
'''),
cache_dir=angelaPreference(
default=None,
validator=lambda x: x is None or isinstance(x, str),
docs='''
Location of the cache directory for Cython files. By default,
will be stored in a ``angela_extensions`` subdirectory
where Cython inline stores its temporary files
(the result of ``get_cython_cache_dir()``).
'''),
delete_source_files=angelaPreference(default=True,
docs='''
Whether to delete source files after compiling. The Cython
source files can take a significant amount of disk space, and
def test_angelaglobalpreferences():
# test that pre-setting a nonexistent preference in a subsequently
# existing base name raises an error at the correct point
gp = angelaGlobalPreferences()
# This shouldn't work, in user code only registered preferences can be set
with pytest.raises(PreferenceError):
gp.__setitem__('a.b', 5)
# This uses the method that is used when reading preferences from a file
gp._set_preference('a.b', 5)
gp._set_preference('a.c', 5)
with pytest.raises(PreferenceError):
gp.register_preferences('a',
'docs for a',
b=angelaPreference(5, 'docs for b'))
# test that post-setting a nonexistent preference in an existing base
# name raises an error
gp = angelaGlobalPreferences()
gp.register_preferences('a',
'docs for a',
b=angelaPreference(5, 'docs for b'))
with pytest.raises(PreferenceError):
gp.__setitem__('a.c', 5)
# Test pre and post-setting some correct names but valid and invalid values
gp = angelaGlobalPreferences()
gp._set_preference('a.b', 5)
gp.register_preferences(
'a',
'docs for a',
b=angelaPreference(5, 'docs for b'),
c=angelaPreference(1 * volt, 'docs for c'),
d=angelaPreference(0, 'docs for d', validator=lambda x: x >= 0),
e=angelaPreference(float64,
'docs for e',
representor=lambda x: x.__name__),
)
assert gp['a.c'] == 1 * volt
gp['a.c'] = 2 * volt
with pytest.raises(PreferenceError):
gp.__setitem__('a.c', 3 * amp)
gp['a.d'] = 2.0
with pytest.raises(PreferenceError):
gp.__setitem__('a.d', -1)
gp['a.e'] = float32
with pytest.raises(PreferenceError):
gp.__setitem__('a.e', 0)
# test backup and restore
gp._backup()
gp['a.d'] = 10
assert gp['a.d'] == 10
gp._restore()
assert gp['a.d'] == 2.0
# test that documentation and as_file generation runs without error, but
# don't test for values because we might change the organisation of it
assert len(gp.get_documentation())
gp.as_file
gp.defaults_as_file
# test that reading a preference file works as expected
pref_file = StringIO('''
# a comment
a.b = 10
[a]
c = 5*volt
d = 1
e = float64
''')
gp.read_preference_file(pref_file)
assert gp['a.b'] == 10
assert gp['a.c'] == 5 * volt
assert gp['a.d'] == 1
assert gp['a.e'] == float64
# test that reading a badly formatted prefs file fails
pref_file = StringIO('''
[a
b = 10
''')
with pytest.raises(PreferenceError):
gp.read_preference_file(pref_file)
# test that reading a well formatted prefs file with an invalid value fails
pref_file = StringIO('''
a.b = 'oh no, not a string'
''')
with pytest.raises(PreferenceError):
gp.read_preference_file(pref_file)
# assert that writing the prefs to a file and loading them gives the
# same values
gp = angelaGlobalPreferences()
gp.register_preferences(
'a',
'docs for a',
b=angelaPreference(5, 'docs for b'),
)
gp._backup()
gp['a.b'] = 10
str_modified = gp.as_file
str_defaults = gp.defaults_as_file
gp['a.b'] = 15
gp.read_preference_file(StringIO(str_modified))
assert gp['a.b'] == 10
gp.read_preference_file(StringIO(str_defaults))
assert gp['a.b'] == 5
# check that load_preferences works, but nothing about its values
gp = angelaGlobalPreferences()
gp.load_preferences()
from angela2.core.functions import Function
from ...codeobject import CodeObject, constant_or_scalar, check_compiler_kwds
from ...templates import Templater
from ...generators.numpy_generator import NumpyCodeGenerator
from ...targets import codegen_targets
__all__ = ['NumpyCodeObject']
# Preferences
prefs.register_preferences('codegen.runtime.numpy',
'Numpy runtime codegen preferences',
discard_units=angelaPreference(default=False,
docs='''
Whether to change the namespace of user-specifed functions to remove
units.
'''))
class LazyArange(Iterable):
'''
A class that can be used as a `~numpy.arange` replacement (with an implied
step size of 1) but does not actually create an array of values until
necessary. It is somewhat similar to the ``range()`` function in Python 3,
but does not use a generator. It is tailored to a special use case, the
``_vectorisation_idx`` variable in numpy templates, and not meant for
general use. The ``_vectorisation_idx`` is used for stateless function
calls such as ``rand()`` and for the numpy codegen target determines the
number of values produced by such a call. This will often be the number of
neurons or synapses, and this class avoids creating a new array of that size
def test_preference_name_access():
'''
Test various ways of accessing preferences
'''
gp = angelaGlobalPreferences()
gp.register_preferences('main',
'main category',
name=angelaPreference(True, 'some preference'))
gp.register_preferences('main.sub',
'subcategory',
name2=angelaPreference(True, 'some preference'))
gp.register_preferences('main.sub_no_pref',
'subcategory without preference')
gp.register_preferences('main.sub_no_pref.sub',
'deep subcategory',
name=angelaPreference(True, 'some preference'))
# Keyword based access
assert gp['main.name']
assert gp['main.sub.name2']
assert gp['main.sub_no_pref.sub.name']
gp['main.name'] = False
gp['main.sub.name2'] = False
gp['main.sub_no_pref.sub.name'] = False
# Attribute based access
assert not gp.main.name # we set it to False above
assert not gp.main.sub.name2
assert not gp.main.sub_no_pref.sub.name
gp.main.name = True
gp.main.sub.name2 = True
gp.main.sub_no_pref.sub.name = True
# Mixed access
assert gp.main['name']
assert gp['main'].name
assert gp.main['sub'].name2
assert gp['main'].sub['name2']
# Accessing categories
assert isinstance(gp['main'], angelaGlobalPreferencesView)
assert isinstance(gp['main.sub'], angelaGlobalPreferencesView)
assert isinstance(gp.main, angelaGlobalPreferencesView)
assert isinstance(gp.main.sub, angelaGlobalPreferencesView)
# Setting categories shouldn't work
with pytest.raises(PreferenceError):
gp.__setitem__('main', None)
with pytest.raises(PreferenceError):
gp.__setattr__('main', None)
with pytest.raises(PreferenceError):
gp.main.__setitem__('sub', None)
with pytest.raises(PreferenceError):
gp.main.__setattr__('sub', None)
# Neither should deleting categories or preferences
with pytest.raises(PreferenceError):
gp.__delitem__('main')
with pytest.raises(PreferenceError):
gp.__delattr__('main')
with pytest.raises(PreferenceError):
gp.main.__delitem__('name')
with pytest.raises(PreferenceError):
gp.main.__delattr__('name')
with pytest.raises(PreferenceError):
gp.main.__delitem__('sub')
with pytest.raises(PreferenceError):
gp.main.__delattr__('sub')
#Errors for accessing non-existing preferences
with pytest.raises(KeyError):
gp['main.doesnotexist']
with pytest.raises(KeyError):
gp['nonexisting.name']
with pytest.raises(KeyError):
gp.main.doesnotexist
with pytest.raises(KeyError):
gp.nonexisting.name
# Check dictionary functionality
for name, value in gp.items():
assert gp[name] == value
for name, value in gp.main.items():
assert gp.main[name] == value
assert len(gp) == 3 # three preferences in total
assert len(gp['main']) == 3 # all preferences are in the main category
assert len(gp['main.sub']) == 1 # one preference in main.sub
assert 'main.name' in gp
assert 'name' in gp['main']
assert 'name2' in gp['main.sub']
assert not 'name' in gp['main.sub']
gp['main.name'] = True
gp.update({'main.name': False})
assert not gp['main.name']
gp.main.update({'name': True})
assert gp['main.name']
# Class based functionality
assert 'main' in dir(gp)
assert 'sub' in dir(gp.main)
assert 'name' in dir(gp.main)
# Check that the fiddling with getattr and setattr did not destroy the
# access to standard attributes
assert len(gp.prefs)
assert gp.main._basename == 'main'
'has to be existing directory' % (val)))
if any(not os.path.isfile(os.path.join(val, 'gsl', filename))
for filename in ['gsl_odeiv2.h', 'gsl_errno.h', 'gsl_matrix.h']):
raise PreferenceError(('Illegal value for GSL directory: %s, '
'has to contain gsl_odeiv2.h, gsl_errno.h '
'and gsl_matrix.h' % (val)))
return True
prefs.register_preferences(
'GSL',
'Directory containing GSL code',
directory=angelaPreference(
validator=valid_gsl_dir,
docs=
("Set path to directory containing GSL header files (gsl_odeiv2.h etc.)"
"\nIf this directory is already in Python's include (e.g. because of "
"conda installation), this path can be set to None."),
default=None))
class GSLCodeGenerator(object):
'''
GSL code generator.
Notes
-----
Approach is to first let the already existing code generator for a target
language do the bulk of the translating from abstract_code to actual code.
This generated code is slightly adapted to render it GSL compatible.
The most critical part here is that the vector_code that is normally
elif dtype == numpy.bool_ or dtype is bool:
dtype = 'char'
else:
raise ValueError("dtype " + str(dtype) + " not known.")
return dtype
# Preferences
prefs.register_preferences(
'codegen.generators.cpp',
'C++ codegen preferences',
restrict_keyword=angelaPreference(
default='__restrict',
docs='''
The keyword used for the given compiler to declare pointers as restricted.
This keyword is different on different compilers, the default works for
gcc and MSVS.
''',
),
flush_denormals=angelaPreference(
default=False,
docs='''
Adds code to flush denormals to zero.
The code is gcc and architecture specific, so may not compile on all
platforms. The code, for reference is::
#define CSR_FLUSH_TO_ZERO (1 << 15)
unsigned csr = __builtin_ia32_stmxcsr();
csr |= CSR_FLUSH_TO_ZERO;
msvc_arch_flag = '/arch:SSE'
if 'sse2' in flags:
msvc_arch_flag = '/arch:SSE2'
if 'avx' in flags:
msvc_arch_flag = '/arch:AVX'
if 'avx2' in flags:
msvc_arch_flag = '/arch:AVX2'
# Preferences
prefs.register_preferences(
'codegen.cpp',
'C++ compilation preferences',
compiler = angelaPreference(
default='',
docs='''
Compiler to use (uses default if empty)
Should be gcc or msvc.
'''
),
extra_compile_args=angelaPreference(
default=None,
validator=lambda v: True,
docs='''
Extra arguments to pass to compiler (if None, use either
``extra_compile_args_gcc`` or ``extra_compile_args_msvc``).
'''
),
extra_compile_args_gcc=angelaPreference(
default=['-w', '-O3', '-ffast-math', '-fno-finite-math-only', '-march=native', '-std=c++11'],
docs='''
Extra compile arguments to pass to GCC compiler
__all__ = []
def dtype_repr(dtype):
return dtype.__name__
def default_float_dtype_validator(dtype):
return dtype in [float32, float64]
prefs.register_preferences('core', 'Core angela preferences',
default_float_dtype=angelaPreference(
default=float64,
docs='''
Default dtype for all arrays of scalars (state variables, weights, etc.).
''',
representor=dtype_repr,
validator=default_float_dtype_validator,
),
default_integer_dtype=angelaPreference(
default=int32,
docs='''
Default dtype for all arrays of integer scalars.
''',
representor=dtype_repr,
),
outdated_dependency_error=angelaPreference(
default=True,
docs='''
Whether to raise an error for outdated dependencies (``True``) or just
a warning (``False``).
from .codeobject import CodeObject
# Preferences
prefs.register_preferences(
'codegen',
'Code generation preferences',
target=angelaPreference(
default='auto',
docs='''
Default target for code generation.
Can be a string, in which case it should be one of:
* ``'auto'`` the default, automatically chose the best code generation
target available.
* ``'cython'``, uses the Cython package to generate C++ code. Needs a
working installation of Cython and a C++ compiler.
* ``'numpy'`` works on all platforms and doesn't need a C compiler but
is often less efficient.
Or it can be a ``CodeObject`` class.
''',
validator=lambda target: isinstance(target, str) or issubclass(
target, CodeObject),
),
string_expression_target=angelaPreference(
default='numpy',
docs='''
Default target for the evaluation of string expressions (e.g. when
indexing state variables). Should normally not be changed from the
default numpy target, because the overhead of compiling code is not