def _show_system_info(self):
nose = import_nose()
import numpy
print("NumPy version %s" % numpy.__version__)
relaxed_strides = numpy.ones((10, 1), order="C").flags.f_contiguous
print("NumPy relaxed strides checking option:", relaxed_strides)
npdir = os.path.dirname(numpy.__file__)
print("NumPy is installed in %s" % npdir)
if 'scipy' in self.package_name:
import scipy
print("SciPy version %s" % scipy.__version__)
spdir = os.path.dirname(scipy.__file__)
print("SciPy is installed in %s" % spdir)
pyversion = sys.version.replace('\n', '')
print("Python version %s" % pyversion)
print("nose version %d.%d.%d" % nose.__versioninfo__)
python类__file__()的实例源码
def _show_system_info(self):
nose = import_nose()
import numpy
print("NumPy version %s" % numpy.__version__)
relaxed_strides = numpy.ones((10, 1), order="C").flags.f_contiguous
print("NumPy relaxed strides checking option:", relaxed_strides)
npdir = os.path.dirname(numpy.__file__)
print("NumPy is installed in %s" % npdir)
if 'scipy' in self.package_name:
import scipy
print("SciPy version %s" % scipy.__version__)
spdir = os.path.dirname(scipy.__file__)
print("SciPy is installed in %s" % spdir)
pyversion = sys.version.replace('\n', '')
print("Python version %s" % pyversion)
print("nose version %d.%d.%d" % nose.__versioninfo__)
def check_biopython(raise_exception_on_fail=False):
# Unpatched Bio.PDB requires md5, which was missing in PyMOL1.2/1.3
# because its Python2.5 was not linked against OpenSSL libraries
if not raise_exception_on_fail:
try:
import Bio.PDB, Bio, Bio.Phylo # Phylo was missing in PyMOL1.5
from Bio.Align.Applications import ClustalwCommandline # This was missing in PyMOL 1.4.
from Bio.Align.Applications import MuscleCommandline
return Bio.__version__, Bio.__file__
except:
return "",""
else:
import Bio.PDB, Bio, Bio.Phylo
from Bio.Align.Applications import ClustalwCommandline
from Bio.Align.Applications import MuscleCommandline
return Bio.__version__, Bio.__file__
def find_systemwide_lib(lib_name):
"""
Check if a systemwide Python library can be imported in PyMOL.
"""
lib_path = ""
if sys.platform in ("linux2", "darwin"):
try:
# lib_file = subprocess.check_output(["/usr/bin/python2", "-Ec", "import %s; print %s.__file__" % (lib_name, lib_name)]).rstrip()
r = subprocess.Popen("/usr/bin/python2 -Ec 'import %s; print %s.__file__'" % (lib_name, lib_name),
stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True
).communicate()
lib_file = r[0].rstrip()
if lib_file:
lib_path = os.path.split(os.path.dirname(lib_file))[0]
except:
pass
return lib_path
def check_importable_modeller():
"""
Checks if systemwide MODELLER can be imported. If it can be imported, returns its version.
"""
try:
import modeller, _modeller
import modeller.automodel
from modeller.scripts import complete_pdb
if hasattr(_modeller,"mod_short_version_get"):
hasmodeller=_modeller.mod_short_version_get()
else:
hasmodeller=[e.lower()[8:].strip("-") for e in os.path.realpath(
os.path.dirname(modeller.__file__)).split(os.sep) if e.lower(
).startswith("modeller") and len(e)>8][0]
if not hasmodeller:
hasmodeller="unknown"
except:
hasmodeller=""
return hasmodeller
def _show_system_info(self):
nose = import_nose()
import numpy
print("NumPy version %s" % numpy.__version__)
relaxed_strides = numpy.ones((10, 1), order="C").flags.f_contiguous
print("NumPy relaxed strides checking option:", relaxed_strides)
npdir = os.path.dirname(numpy.__file__)
print("NumPy is installed in %s" % npdir)
if 'scipy' in self.package_name:
import scipy
print("SciPy version %s" % scipy.__version__)
spdir = os.path.dirname(scipy.__file__)
print("SciPy is installed in %s" % spdir)
pyversion = sys.version.replace('\n', '')
print("Python version %s" % pyversion)
print("nose version %d.%d.%d" % nose.__versioninfo__)
def _show_system_info(self):
nose = import_nose()
import numpy
print("NumPy version %s" % numpy.__version__)
relaxed_strides = numpy.ones((10, 1), order="C").flags.f_contiguous
print("NumPy relaxed strides checking option:", relaxed_strides)
npdir = os.path.dirname(numpy.__file__)
print("NumPy is installed in %s" % npdir)
if 'scipy' in self.package_name:
import scipy
print("SciPy version %s" % scipy.__version__)
spdir = os.path.dirname(scipy.__file__)
print("SciPy is installed in %s" % spdir)
pyversion = sys.version.replace('\n', '')
print("Python version %s" % pyversion)
print("nose version %d.%d.%d" % nose.__versioninfo__)
def test_warning_calls():
# combined "ignore" and stacklevel error
base = Path(numpy.__file__).parent
for path in base.rglob("*.py"):
if base / "testing" in path.parents:
continue
if path == base / "__init__.py":
continue
if path == base / "random" / "__init__.py":
continue
# use tokenize to auto-detect encoding on systems where no
# default encoding is defined (e.g. LANG='C')
with tokenize.open(str(path)) as file:
tree = ast.parse(file.read())
FindFuncs(path).visit(tree)
def _show_system_info(self):
nose = import_nose()
import numpy
print("NumPy version %s" % numpy.__version__)
relaxed_strides = numpy.ones((10, 1), order="C").flags.f_contiguous
print("NumPy relaxed strides checking option:", relaxed_strides)
npdir = os.path.dirname(numpy.__file__)
print("NumPy is installed in %s" % npdir)
if 'scipy' in self.package_name:
import scipy
print("SciPy version %s" % scipy.__version__)
spdir = os.path.dirname(scipy.__file__)
print("SciPy is installed in %s" % spdir)
pyversion = sys.version.replace('\n', '')
print("Python version %s" % pyversion)
print("nose version %d.%d.%d" % nose.__versioninfo__)
def _show_system_info(self):
nose = import_nose()
import numpy
print("NumPy version %s" % numpy.__version__)
relaxed_strides = numpy.ones((10, 1), order="C").flags.f_contiguous
print("NumPy relaxed strides checking option:", relaxed_strides)
npdir = os.path.dirname(numpy.__file__)
print("NumPy is installed in %s" % npdir)
if 'scipy' in self.package_name:
import scipy
print("SciPy version %s" % scipy.__version__)
spdir = os.path.dirname(scipy.__file__)
print("SciPy is installed in %s" % spdir)
pyversion = sys.version.replace('\n', '')
print("Python version %s" % pyversion)
print("nose version %d.%d.%d" % nose.__versioninfo__)
def get_include():
"""
Return the directory that contains the NumPy \\*.h header files.
Extension modules that need to compile against NumPy should use this
function to locate the appropriate include directory.
Notes
-----
When using ``distutils``, for example in ``setup.py``.
::
import numpy as np
...
Extension('extension_name', ...
include_dirs=[np.get_include()])
...
"""
import numpy
if numpy.show_config is None:
# running from numpy source directory
d = os.path.join(os.path.dirname(numpy.__file__), 'core', 'include')
else:
# using installed numpy core headers
import numpy.core as core
d = os.path.join(os.path.dirname(core.__file__), 'include')
return d
def get_path_from_frame(frame, parent_path=None):
"""Return path of the module given a frame object from the call stack.
Returned path is relative to parent_path when given,
otherwise it is absolute path.
"""
# First, try to find if the file name is in the frame.
try:
caller_file = eval('__file__', frame.f_globals, frame.f_locals)
d = os.path.dirname(os.path.abspath(caller_file))
except NameError:
# __file__ is not defined, so let's try __name__. We try this second
# because setuptools spoofs __name__ to be '__main__' even though
# sys.modules['__main__'] might be something else, like easy_install(1).
caller_name = eval('__name__', frame.f_globals, frame.f_locals)
__import__(caller_name)
mod = sys.modules[caller_name]
if hasattr(mod, '__file__'):
d = os.path.dirname(os.path.abspath(mod.__file__))
else:
# we're probably running setup.py as execfile("setup.py")
# (likely we're building an egg)
d = os.path.abspath('.')
# hmm, should we use sys.argv[0] like in __builtin__ case?
if parent_path is not None:
d = rel_path(d, parent_path)
return d or '.'
def get_npy_pkg_dir():
"""Return the path where to find the npy-pkg-config directory."""
# XXX: import here for bootstrapping reasons
import numpy
d = os.path.join(os.path.dirname(numpy.__file__),
'core', 'lib', 'npy-pkg-config')
return d
def __init__(self, package=None, raise_warnings="release", depth=0):
# Back-compat: 'None' used to mean either "release" or "develop"
# depending on whether this was a release or develop version of
# numpy. Those semantics were fine for testing numpy, but not so
# helpful for downstream projects like scipy that use
# numpy.testing. (They want to set this based on whether *they* are a
# release or develop version, not whether numpy is.) So we continue to
# accept 'None' for back-compat, but it's now just an alias for the
# default "release".
if raise_warnings is None:
raise_warnings = "release"
package_name = None
if package is None:
f = sys._getframe(1 + depth)
package_path = f.f_locals.get('__file__', None)
if package_path is None:
raise AssertionError
package_path = os.path.dirname(package_path)
package_name = f.f_locals.get('__name__', None)
elif isinstance(package, type(os)):
package_path = os.path.dirname(package.__file__)
package_name = getattr(package, '__name__', None)
else:
package_path = str(package)
self.package_path = package_path
# Find the package name under test; this name is used to limit coverage
# reporting (if enabled).
if package_name is None:
package_name = get_package_name(package_path)
self.package_name = package_name
# Set to "release" in constructor in maintenance branches.
self.raise_warnings = raise_warnings
def get_include():
"""
Return the directory that contains the NumPy \\*.h header files.
Extension modules that need to compile against NumPy should use this
function to locate the appropriate include directory.
Notes
-----
When using ``distutils``, for example in ``setup.py``.
::
import numpy as np
...
Extension('extension_name', ...
include_dirs=[np.get_include()])
...
"""
import numpy
if numpy.show_config is None:
# running from numpy source directory
d = os.path.join(os.path.dirname(numpy.__file__), 'core', 'include')
else:
# using installed numpy core headers
import numpy.core as core
d = os.path.join(os.path.dirname(core.__file__), 'include')
return d
def get_path_from_frame(frame, parent_path=None):
"""Return path of the module given a frame object from the call stack.
Returned path is relative to parent_path when given,
otherwise it is absolute path.
"""
# First, try to find if the file name is in the frame.
try:
caller_file = eval('__file__', frame.f_globals, frame.f_locals)
d = os.path.dirname(os.path.abspath(caller_file))
except NameError:
# __file__ is not defined, so let's try __name__. We try this second
# because setuptools spoofs __name__ to be '__main__' even though
# sys.modules['__main__'] might be something else, like easy_install(1).
caller_name = eval('__name__', frame.f_globals, frame.f_locals)
__import__(caller_name)
mod = sys.modules[caller_name]
if hasattr(mod, '__file__'):
d = os.path.dirname(os.path.abspath(mod.__file__))
else:
# we're probably running setup.py as execfile("setup.py")
# (likely we're building an egg)
d = os.path.abspath('.')
# hmm, should we use sys.argv[0] like in __builtin__ case?
if parent_path is not None:
d = rel_path(d, parent_path)
return d or '.'
def get_npy_pkg_dir():
"""Return the path where to find the npy-pkg-config directory."""
# XXX: import here for bootstrapping reasons
import numpy
d = os.path.join(os.path.dirname(numpy.__file__),
'core', 'lib', 'npy-pkg-config')
return d
def __init__(self, package=None, raise_warnings="release", depth=0):
# Back-compat: 'None' used to mean either "release" or "develop"
# depending on whether this was a release or develop version of
# numpy. Those semantics were fine for testing numpy, but not so
# helpful for downstream projects like scipy that use
# numpy.testing. (They want to set this based on whether *they* are a
# release or develop version, not whether numpy is.) So we continue to
# accept 'None' for back-compat, but it's now just an alias for the
# default "release".
if raise_warnings is None:
raise_warnings = "release"
package_name = None
if package is None:
f = sys._getframe(1 + depth)
package_path = f.f_locals.get('__file__', None)
if package_path is None:
raise AssertionError
package_path = os.path.dirname(package_path)
package_name = f.f_locals.get('__name__', None)
elif isinstance(package, type(os)):
package_path = os.path.dirname(package.__file__)
package_name = getattr(package, '__name__', None)
else:
package_path = str(package)
self.package_path = package_path
# Find the package name under test; this name is used to limit coverage
# reporting (if enabled).
if package_name is None:
package_name = get_package_name(package_path)
self.package_name = package_name
# Set to "release" in constructor in maintenance branches.
self.raise_warnings = raise_warnings
def check_numpy():
try: # check numpy
import numpy
return numpy.__version__, numpy.__file__
except:
return "",""
misc_util.py 文件源码
项目：PyDataLondon29-EmbarrassinglyParallelDAWithAWSLambda
作者: SignalMedia
项目源码
文件源码
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def get_path_from_frame(frame, parent_path=None):
"""Return path of the module given a frame object from the call stack.
Returned path is relative to parent_path when given,
otherwise it is absolute path.
"""
# First, try to find if the file name is in the frame.
try:
caller_file = eval('__file__', frame.f_globals, frame.f_locals)
d = os.path.dirname(os.path.abspath(caller_file))
except NameError:
# __file__ is not defined, so let's try __name__. We try this second
# because setuptools spoofs __name__ to be '__main__' even though
# sys.modules['__main__'] might be something else, like easy_install(1).
caller_name = eval('__name__', frame.f_globals, frame.f_locals)
__import__(caller_name)
mod = sys.modules[caller_name]
if hasattr(mod, '__file__'):
d = os.path.dirname(os.path.abspath(mod.__file__))
else:
# we're probably running setup.py as execfile("setup.py")
# (likely we're building an egg)
d = os.path.abspath('.')
# hmm, should we use sys.argv[0] like in __builtin__ case?
if parent_path is not None:
d = rel_path(d, parent_path)
return d or '.'
misc_util.py 文件源码
项目：PyDataLondon29-EmbarrassinglyParallelDAWithAWSLambda
作者: SignalMedia
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def get_npy_pkg_dir():
"""Return the path where to find the npy-pkg-config directory."""
# XXX: import here for bootstrapping reasons
import numpy
d = os.path.join(os.path.dirname(numpy.__file__),
'core', 'lib', 'npy-pkg-config')
return d
nosetester.py 文件源码
项目：PyDataLondon29-EmbarrassinglyParallelDAWithAWSLambda
作者: SignalMedia
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def __init__(self, package=None, raise_warnings=None):
if raise_warnings is None and (
not hasattr(np, '__version__') or '.dev0' in np.__version__):
raise_warnings = "develop"
elif raise_warnings is None:
raise_warnings = "release"
package_name = None
if package is None:
f = sys._getframe(1)
package_path = f.f_locals.get('__file__', None)
if package_path is None:
raise AssertionError
package_path = os.path.dirname(package_path)
package_name = f.f_locals.get('__name__', None)
elif isinstance(package, type(os)):
package_path = os.path.dirname(package.__file__)
package_name = getattr(package, '__name__', None)
else:
package_path = str(package)
self.package_path = package_path
# Find the package name under test; this name is used to limit coverage
# reporting (if enabled).
if package_name is None:
package_name = get_package_name(package_path)
self.package_name = package_name
# Set to "release" in constructor in maintenance branches.
self.raise_warnings = raise_warnings
nosetester.py 文件源码
项目：PyDataLondon29-EmbarrassinglyParallelDAWithAWSLambda
作者: SignalMedia
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def _test_argv(self, label, verbose, extra_argv):
''' Generate argv for nosetest command
Parameters
----------
label : {'fast', 'full', '', attribute identifier}, optional
see ``test`` docstring
verbose : int, optional
Verbosity value for test outputs, in the range 1-10. Default is 1.
extra_argv : list, optional
List with any extra arguments to pass to nosetests.
Returns
-------
argv : list
command line arguments that will be passed to nose
'''
argv = [__file__, self.package_path, '-s']
if label and label != 'full':
if not isinstance(label, basestring):
raise TypeError('Selection label should be a string')
if label == 'fast':
label = 'not slow'
argv += ['-A', label]
argv += ['--verbosity', str(verbose)]
# When installing with setuptools, and also in some other cases, the
# test_*.py files end up marked +x executable. Nose, by default, does
# not run files marked with +x as they might be scripts. However, in
# our case nose only looks for test_*.py files under the package
# directory, which should be safe.
argv += ['--exe']
if extra_argv:
argv += extra_argv
return argv
def get_include():
"""
Return the directory that contains the NumPy \\*.h header files.
Extension modules that need to compile against NumPy should use this
function to locate the appropriate include directory.
Notes
-----
When using ``distutils``, for example in ``setup.py``.
::
import numpy as np
...
Extension('extension_name', ...
include_dirs=[np.get_include()])
...
"""
import numpy
if numpy.show_config is None:
# running from numpy source directory
d = os.path.join(os.path.dirname(numpy.__file__), 'core', 'include')
else:
# using installed numpy core headers
import numpy.core as core
d = os.path.join(os.path.dirname(core.__file__), 'include')
return d
def get_path_from_frame(frame, parent_path=None):
"""Return path of the module given a frame object from the call stack.
Returned path is relative to parent_path when given,
otherwise it is absolute path.
"""
# First, try to find if the file name is in the frame.
try:
caller_file = eval('__file__', frame.f_globals, frame.f_locals)
d = os.path.dirname(os.path.abspath(caller_file))
except NameError:
# __file__ is not defined, so let's try __name__. We try this second
# because setuptools spoofs __name__ to be '__main__' even though
# sys.modules['__main__'] might be something else, like easy_install(1).
caller_name = eval('__name__', frame.f_globals, frame.f_locals)
__import__(caller_name)
mod = sys.modules[caller_name]
if hasattr(mod, '__file__'):
d = os.path.dirname(os.path.abspath(mod.__file__))
else:
# we're probably running setup.py as execfile("setup.py")
# (likely we're building an egg)
d = os.path.abspath('.')
# hmm, should we use sys.argv[0] like in __builtin__ case?
if parent_path is not None:
d = rel_path(d, parent_path)
return d or '.'
def get_npy_pkg_dir():
"""Return the path where to find the npy-pkg-config directory."""
# XXX: import here for bootstrapping reasons
import numpy
d = os.path.join(os.path.dirname(numpy.__file__),
'core', 'lib', 'npy-pkg-config')
return d
def __init__(self, package=None, raise_warnings=None):
if raise_warnings is None and (
not hasattr(np, '__version__') or '.dev0' in np.__version__):
raise_warnings = "develop"
elif raise_warnings is None:
raise_warnings = "release"
package_name = None
if package is None:
f = sys._getframe(1)
package_path = f.f_locals.get('__file__', None)
if package_path is None:
raise AssertionError
package_path = os.path.dirname(package_path)
package_name = f.f_locals.get('__name__', None)
elif isinstance(package, type(os)):
package_path = os.path.dirname(package.__file__)
package_name = getattr(package, '__name__', None)
else:
package_path = str(package)
self.package_path = package_path
# Find the package name under test; this name is used to limit coverage
# reporting (if enabled).
if package_name is None:
package_name = get_package_name(package_path)
self.package_name = package_name
# Set to "release" in constructor in maintenance branches.
self.raise_warnings = raise_warnings
def get_include():
"""
Return the directory that contains the NumPy \\*.h header files.
Extension modules that need to compile against NumPy should use this
function to locate the appropriate include directory.
Notes
-----
When using ``distutils``, for example in ``setup.py``.
::
import numpy as np
...
Extension('extension_name', ...
include_dirs=[np.get_include()])
...
"""
import numpy
if numpy.show_config is None:
# running from numpy source directory
d = os.path.join(os.path.dirname(numpy.__file__), 'core', 'include')
else:
# using installed numpy core headers
import numpy.core as core
d = os.path.join(os.path.dirname(core.__file__), 'include')
return d
def get_path_from_frame(frame, parent_path=None):
"""Return path of the module given a frame object from the call stack.
Returned path is relative to parent_path when given,
otherwise it is absolute path.
"""
# First, try to find if the file name is in the frame.
try:
caller_file = eval('__file__', frame.f_globals, frame.f_locals)
d = os.path.dirname(os.path.abspath(caller_file))
except NameError:
# __file__ is not defined, so let's try __name__. We try this second
# because setuptools spoofs __name__ to be '__main__' even though
# sys.modules['__main__'] might be something else, like easy_install(1).
caller_name = eval('__name__', frame.f_globals, frame.f_locals)
__import__(caller_name)
mod = sys.modules[caller_name]
if hasattr(mod, '__file__'):
d = os.path.dirname(os.path.abspath(mod.__file__))
else:
# we're probably running setup.py as execfile("setup.py")
# (likely we're building an egg)
d = os.path.abspath('.')
# hmm, should we use sys.argv[0] like in __builtin__ case?
if parent_path is not None:
d = rel_path(d, parent_path)
return d or '.'
def get_npy_pkg_dir():
"""Return the path where to find the npy-pkg-config directory."""
# XXX: import here for bootstrapping reasons
import numpy
d = os.path.join(os.path.dirname(numpy.__file__),
'core', 'lib', 'npy-pkg-config')
return d
