def which(command, env=None):
"""Get the full path to a command.
Parameters
----------
command: str
The command name or path.
env: dict, optional
The environment variables, defaults to `os.environ`.
"""
env = env or os.environ
path = env.get('PATH') or os.defpath
command_with_path = _which(command, path=path)
# Allow nodejs as an alias to node.
if command == 'node' and not command_with_path:
command = 'nodejs'
command_with_path = _which('nodejs', path=path)
if not command_with_path:
if command in ['nodejs', 'node', 'npm']:
msg = 'Please install nodejs 5+ and npm before continuing installation. nodejs may be installed using conda or directly from the nodejs website.'
raise ValueError(msg)
raise ValueError('The command was not found or was not ' +
'executable: %s.' % command)
return command_with_path
def which(command, env=None):
"""Get the full path to a command.
Parameters
----------
command: str
The command name or path.
env: dict, optional
The environment variables, defaults to `os.environ`.
"""
env = env or os.environ
path = env.get('PATH') or os.defpath
command_with_path = _which(command, path=path)
# Allow nodejs as an alias to node.
if command == 'node' and not command_with_path:
command = 'nodejs'
command_with_path = _which('nodejs', path=path)
if not command_with_path:
if command in ['nodejs', 'node', 'npm']:
msg = 'Please install Node.js and npm before continuing installation. You may be able to install Node.js from your package manager, from conda, or directly from the Node.js website (https://nodejs.org).'
raise ValueError(msg)
raise ValueError('The command was not found or was not ' +
'executable: %s.' % command)
return os.path.abspath(command_with_path)
def __init__(self, sequence, database=None, executable='jackhmmer', **kwargs):
# Empty container for parsed/validated sequences
self.sequences = []
self.database = database
# Setup logging with module name
self.logger = logging.getLogger(__name__)
# Iterate over kwargs and define defaults if not user-provided
_defaults = {'evalue': 1E-20,
'ncpus': 2,
'niter': 5,
'mock': False}
for kwarg in _defaults:
kwarg_val = kwargs.get(kwarg)
if not kwarg_val:
kwarg_val = _defaults[kwarg]
setattr(self, kwarg, kwarg_val)
# Validate sequence data and locate executable
self.__validate(sequence)
if not _which(executable):
raise OSError("HMMER executable not found in PATH: '{}'".format(executable))
def get_external_executable(_exec):
_exec_path = _which(_exec)
if _exec_path:
return _exec_path
else:
sys.exit("Required executable '{}' not found on this system. "
"Please install or add to PATH".format(_exec))
def change_wallpaper(path: str):
file = _which("feh")
if file is None:
# I did the checking here not to seem we don't support i3
print("feh not found, you need it to set the background in i3.")
_exit(0)
_system(f'feh --bg-fill "{path}"')
def _check_binary():
"""
Make sure that the `gsutil` cli is present
"""
if not _which(GCSProxy._GS_UTIL_CLI):
raise _FlyteUserException(
"gsutil (gcloud cli) not found! Please install.")
def get_external_executable(_exec):
_exec_path = _which(_exec)
if _exec_path:
return _exec_path
else:
sys.exit("Required executable '{}' not found on this system. "
"Please install or add to PATH".format(_exec))
def _maybe_register(executable, **kw):
if _which(executable):
return _partial(register_terminal, **kw)
else:
def wrapper(fn, *args, **kwargs):
return fn
return wrapper
def which(file, mode=os.F_OK | os.X_OK):
"""A wrapper around shutil.which() that searches a predictable set of
paths and is more verbose about what is happening. See get_path()
for more information.
"""
path = get_path()
rv = _which(file, mode, path)
if rv:
debug2("which() found '%s' at %s" % (file, rv))
else:
debug2("which() could not find '%s' in %s" % (file, path))
return rv
def which(*args, **kw):
# Wrapper to which() to use lazy import for 'import shutil'
global _which
if _which is None:
try:
# Python 3.3
from shutil import which as _which
except ImportError:
# Backport shutil.which() from Python 3.6,
# comments/docstring stripped
def _which(cmd, mode=os.F_OK | os.X_OK, path=None):
def _access_check(fn, mode):
return (os.path.exists(fn) and os.access(fn, mode)
and not os.path.isdir(fn))
if os.path.dirname(cmd):
if _access_check(cmd, mode):
return cmd
return None
if path is None:
path = os.environ.get("PATH", os.defpath)
if not path:
return None
path = path.split(os.pathsep)
if sys.platform == "win32":
if os.curdir not in path:
path.insert(0, os.curdir)
pathext = os.environ.get("PATHEXT", "").split(os.pathsep)
if any(cmd.lower().endswith(ext.lower())
for ext in pathext):
files = [cmd]
else:
files = [cmd + ext for ext in pathext]
else:
files = [cmd]
seen = set()
for dir in path:
normdir = os.path.normcase(dir)
if normdir not in seen:
seen.add(normdir)
for thefile in files:
name = os.path.join(dir, thefile)
if _access_check(name, mode):
return name
return None
return _which(*args, **kw)
def which(cmd):
"""Return full path to specified command, or raise OSError if missing."""
try:
# For Python 3
from shutil import which as _which
except ImportError:
# For Python 2
from backports.shutil_which import which as _which
full_path = _which(cmd)
if full_path is None:
raise OSError('Cannot find {!r} in $PATH'.format(cmd))
log.debug('which %r => %r', cmd, full_path)
return full_path
def which(*args, **kw):
# Wrapper to which() to use lazy import for 'import shutil'
global _which
if _which is None:
try:
# Python 3.3
from shutil import which as _which
except ImportError:
# Backport shutil.which() from Python 3.6,
# comments/docstring stripped
def _which(cmd, mode=os.F_OK | os.X_OK, path=None):
def _access_check(fn, mode):
return (os.path.exists(fn) and os.access(fn, mode)
and not os.path.isdir(fn))
if os.path.dirname(cmd):
if _access_check(cmd, mode):
return cmd
return None
if path is None:
path = os.environ.get("PATH", os.defpath)
if not path:
return None
path = path.split(os.pathsep)
if sys.platform == "win32":
if os.curdir not in path:
path.insert(0, os.curdir)
pathext = os.environ.get("PATHEXT", "").split(os.pathsep)
if any(cmd.lower().endswith(ext.lower()) for ext in pathext):
files = [cmd]
else:
files = [cmd + ext for ext in pathext]
else:
files = [cmd]
seen = set()
for dir in path:
normdir = os.path.normcase(dir)
if normdir not in seen:
seen.add(normdir)
for thefile in files:
name = os.path.join(dir, thefile)
if _access_check(name, mode):
return name
return None
return _which(*args, **kw)
def which(cmd, mode=os.F_OK | os.X_OK, path=None, **kwargs):
"""Given a command, mode, and a PATH string, return the path which
conforms to the given mode on the PATH, or None if there is no such
file.
`mode` defaults to ``os.F_OK | os.X_OK``. `path` defaults to the result
of ``os.environ.get("PATH")``, or can be overridden with a custom search
path.
Backported from :py:func:`shutil.which`
(`<https://docs.python.org/3.3/library/shutil.html#shutil.which>`_),
available in Python 3.3.
"""
kwargs.update({'mode': mode, 'path': path})
global _which
if _which is not None:
return _which(cmd, **kwargs)
return _which_backport(cmd, **kwargs)
def which(cmd, mode=os.F_OK | os.X_OK, path=None, **kwargs):
"""Given a command, mode, and a PATH string, return the path which
conforms to the given mode on the PATH, or None if there is no such
file.
`mode` defaults to ``os.F_OK | os.X_OK``. `path` defaults to the result
of ``os.environ.get("PATH")``, or can be overridden with a custom search
path.
Backported from :py:func:`shutil.which`
(`<https://docs.python.org/3.3/library/shutil.html#shutil.which>`_),
available in Python 3.3.
"""
kwargs.update({'mode': mode, 'path': path})
global _which
if _which is not None:
return _which(cmd, **kwargs)
return _which_backport(cmd, **kwargs)
def bash_command_exists(bash_command_name):
"""Check whether `name` is on PATH and marked as executable.
"""
return _which(bash_command_name) is not None
def which(binary):
path = _which(binary)
if path:
realpath = os.path.realpath(path)
return realpath
return None
def which(binary):
path = _which(binary)
if path:
realpath = os.path.realpath(path)
return realpath
return None
def _check_binary():
"""
Make sure that the AWS cli is present
"""
if not _which(AwsS3Proxy._AWS_CLI):
raise _FlyteUserException('AWS CLI not found at Please install.')