Source code for astropy.utils.misc

# Licensed under a 3-clause BSD style license - see LICENSE.rst
A "grab bag" of relatively small general-purpose utilities that don't have
a clear module/package to live in.

import abc
import contextlib
import difflib
import inspect
import json
import locale
import os
import re
import signal
import sys
import threading
import traceback
import unicodedata
from collections import OrderedDict, defaultdict
from contextlib import contextmanager

from astropy.utils.decorators import deprecated

__all__ = [

# Because they are deprecated.
__doctest_skip__ = ["OrderedDescriptor", "OrderedDescriptorContainer"]

    "File {} already exists. If you mean to replace it "
    'then use the argument "overwrite=True".'
# A useful regex for tests.
    r"File .* already exists\. If you mean to "
    r"replace it then use the argument "

[docs] def isiterable(obj): """Returns `True` if the given object is iterable.""" try: iter(obj) return True except TypeError: return False
[docs] def indent(s, shift=1, width=4): """Indent a block of text. The indentation is applied to each line.""" indented = "\n".join(" " * (width * shift) + l if l else "" for l in s.splitlines()) if s[-1] == "\n": indented += "\n" return indented
class _DummyFile: """A noop writeable object.""" def write(self, s): pass
[docs] @contextlib.contextmanager def silence(): """A context manager that silences sys.stdout and sys.stderr.""" old_stdout = sys.stdout old_stderr = sys.stderr sys.stdout = _DummyFile() sys.stderr = _DummyFile() yield sys.stdout = old_stdout sys.stderr = old_stderr
[docs] def format_exception(msg, *args, **kwargs): """Fill in information about the exception that occurred. Given an exception message string, uses new-style formatting arguments ``{filename}``, ``{lineno}``, ``{func}`` and/or ``{text}`` to fill in information about the exception that occurred. For example: try: 1/0 except: raise ZeroDivisionError( format_except('A divide by zero occurred in {filename} at ' 'line {lineno} of function {func}.')) Any additional positional or keyword arguments passed to this function are also used to format the message. .. note:: This uses `sys.exc_info` to gather up the information needed to fill in the formatting arguments. Since `sys.exc_info` is not carried outside a handled exception, it's not wise to use this outside of an ``except`` clause - if it is, this will substitute '<unknown>' for the 4 formatting arguments. """ tb = traceback.extract_tb(sys.exc_info()[2], limit=1) if len(tb) > 0: filename, lineno, func, text = tb[0] else: filename = lineno = func = text = "<unknown>" return msg.format( *args, filename=filename, lineno=lineno, func=func, text=text, **kwargs )
[docs] class NumpyRNGContext: """ A context manager (for use with the ``with`` statement) that will seed the numpy random number generator (RNG) to a specific value, and then restore the RNG state back to whatever it was before. This is primarily intended for use in the astropy testing suit, but it may be useful in ensuring reproducibility of Monte Carlo simulations in a science context. Parameters ---------- seed : int The value to use to seed the numpy RNG Examples -------- A typical use case might be:: with NumpyRNGContext(<some seed value you pick>): from numpy import random randarr = random.randn(100) ... run your test using `randarr` ... #Any code using numpy.random at this indent level will act just as it #would have if it had been before the with statement - e.g. whatever #the default seed is. """ def __init__(self, seed): self.seed = seed def __enter__(self): from numpy import random self.startstate = random.get_state() random.seed(self.seed) def __exit__(self, exc_type, exc_value, traceback): from numpy import random random.set_state(self.startstate)
[docs] def find_api_page(obj, version=None, openinbrowser=True, timeout=None): """ Determines the URL of the API page for the specified object, and optionally open that page in a web browser. .. note:: You must be connected to the internet for this to function even if ``openinbrowser`` is `False`, unless you provide a local version of the documentation to ``version`` (e.g., ``file:///path/to/docs``). Parameters ---------- obj The object to open the docs for or its fully-qualified name (as a str). version : str The doc version - either a version number like '0.1', 'dev' for the development/latest docs, or a URL to point to a specific location that should be the *base* of the documentation. Defaults to latest if you are on aren't on a release, otherwise, the version you are on. openinbrowser : bool If `True`, the `webbrowser` package will be used to open the doc page in a new web browser window. timeout : number, optional The number of seconds to wait before timing-out the query to the astropy documentation. If not given, the default python stdlib timeout will be used. Returns ------- url : str The loaded URL Raises ------ ValueError If the documentation can't be found """ import webbrowser from zlib import decompress from import get_readable_fileobj if ( not isinstance(obj, str) and hasattr(obj, "__module__") and hasattr(obj, "__name__") ): obj = obj.__module__ + "." + obj.__name__ elif inspect.ismodule(obj): obj = obj.__name__ if version is None: from astropy import version if version.release: version = "v" + version.version else: version = "dev" if "://" in version: if version.endswith("index.html"): baseurl = version[:-10] elif version.endswith("/"): baseurl = version else: baseurl = version + "/" elif version == "dev" or version == "latest": baseurl = "" else: baseurl = f"{version}/" # Custom request headers; see # url = baseurl + "objects.inv" headers = {"User-Agent": f"Astropy/{version}"} with get_readable_fileobj( url, encoding="binary", remote_timeout=timeout, http_headers=headers ) as uf: oiread = # need to first read/remove the first four lines, which have info before # the compressed section with the actual object inventory idx = -1 headerlines = [] for _ in range(4): oldidx = idx idx = oiread.index(b"\n", oldidx + 1) headerlines.append(oiread[(oldidx + 1) : idx].decode("utf-8")) # intersphinx version line, project name, and project version ivers, proj, vers, compr = headerlines if "The remainder of this file is compressed using zlib" not in compr: raise ValueError( f"The file downloaded from {baseurl}objects.inv does not seem to be" "the usual Sphinx objects.inv format. Maybe it " "has changed?" ) compressed = oiread[(idx + 1) :] decompressed = decompress(compressed).decode("utf-8") resurl = None for l in decompressed.strip().splitlines(): ls = l.split() name = ls[0] loc = ls[3] if loc.endswith("$"): loc = loc[:-1] + name if name == obj: resurl = baseurl + loc break if resurl is None: raise ValueError(f"Could not find the docs for the object {obj}") elif openinbrowser: return resurl
def signal_number_to_name(signum): """ Given an OS signal number, returns a signal name. If the signal number is unknown, returns ``'UNKNOWN'``. """ # Since these numbers and names are platform specific, we use the # builtin signal module and build a reverse mapping. signal_to_name_map = { k: v for v, k in signal.__dict__.items() if v.startswith("SIG") } return signal_to_name_map.get(signum, "UNKNOWN") if sys.platform == "win32": import ctypes def _has_hidden_attribute(filepath): """ Returns True if the given filepath has the hidden attribute on MS-Windows. Based on a post here: """ if isinstance(filepath, bytes): filepath = filepath.decode(sys.getfilesystemencoding()) try: attrs = ctypes.windll.kernel32.GetFileAttributesW(filepath) result = bool(attrs & 2) and attrs != -1 except AttributeError: result = False return result else: def _has_hidden_attribute(filepath): return False
[docs] def is_path_hidden(filepath): """ Determines if a given file or directory is hidden. Parameters ---------- filepath : str The path to a file or directory Returns ------- hidden : bool Returns `True` if the file is hidden """ name = os.path.basename(os.path.abspath(filepath)) if isinstance(name, bytes): is_dotted = name.startswith(b".") else: is_dotted = name.startswith(".") return is_dotted or _has_hidden_attribute(filepath)
[docs] def walk_skip_hidden(top, onerror=None, followlinks=False): """ A wrapper for `os.walk` that skips hidden files and directories. This function does not have the parameter ``topdown`` from `os.walk`: the directories must always be recursed top-down when using this function. See Also -------- os.walk : For a description of the parameters """ for root, dirs, files in os.walk( top, topdown=True, onerror=onerror, followlinks=followlinks ): # These lists must be updated in-place so os.walk will skip # hidden directories dirs[:] = [d for d in dirs if not is_path_hidden(d)] files[:] = [f for f in files if not is_path_hidden(f)] yield root, dirs, files
[docs] class JsonCustomEncoder(json.JSONEncoder): """Support for data types that JSON default encoder does not do. This includes: * Numpy array or number * Complex number * Set * Bytes * astropy.UnitBase * astropy.Quantity Examples -------- >>> import json >>> import numpy as np >>> from astropy.utils.misc import JsonCustomEncoder >>> json.dumps(np.arange(3), cls=JsonCustomEncoder) '[0, 1, 2]' """
[docs] def default(self, obj): import numpy as np from astropy import units as u if isinstance(obj, u.Quantity): return dict(value=obj.value, unit=obj.unit.to_string()) if isinstance(obj, (np.number, np.ndarray)): return obj.tolist() elif isinstance(obj, complex): return [obj.real, obj.imag] elif isinstance(obj, set): return list(obj) elif isinstance(obj, bytes): # pragma: py3 return obj.decode() elif isinstance(obj, (u.UnitBase, u.FunctionUnitBase)): if obj == u.dimensionless_unscaled: obj = "dimensionless_unit" else: return obj.to_string() return json.JSONEncoder.default(self, obj)
def strip_accents(s): """ Remove accents from a Unicode string. This helps with matching "ångström" to "angstrom", for example. """ return "".join( c for c in unicodedata.normalize("NFD", s) if unicodedata.category(c) != "Mn" ) def did_you_mean(s, candidates, n=3, cutoff=0.8, fix=None): """ When a string isn't found in a set of candidates, we can be nice to provide a list of alternatives in the exception. This convenience function helps to format that part of the exception. Parameters ---------- s : str candidates : sequence of str or dict of str keys n : int The maximum number of results to include. See `difflib.get_close_matches`. cutoff : float In the range [0, 1]. Possibilities that don't score at least that similar to word are ignored. See `difflib.get_close_matches`. fix : callable A callable to modify the results after matching. It should take a single string and return a sequence of strings containing the fixed matches. Returns ------- message : str Returns the string "Did you mean X, Y, or Z?", or the empty string if no alternatives were found. """ if isinstance(s, str): s = strip_accents(s) s_lower = s.lower() # Create a mapping from the lower case name to all capitalization # variants of that name. candidates_lower = {} for candidate in candidates: candidate_lower = candidate.lower() candidates_lower.setdefault(candidate_lower, []) candidates_lower[candidate_lower].append(candidate) # The heuristic here is to first try "singularizing" the word. If # that doesn't match anything use difflib to find close matches in # original, lower and upper case. if s_lower.endswith("s") and s_lower[:-1] in candidates_lower: matches = [s_lower[:-1]] else: matches = difflib.get_close_matches( s_lower, candidates_lower, n=n, cutoff=cutoff ) if len(matches): capitalized_matches = set() for match in matches: capitalized_matches.update(candidates_lower[match]) matches = capitalized_matches if fix is not None: mapped_matches = [] for match in matches: mapped_matches.extend(fix(match)) matches = mapped_matches matches = list(set(matches)) matches = sorted(matches) if len(matches) == 1: matches = matches[0] else: matches = ", ".join(matches[:-1]) + " or " + matches[-1] return f"Did you mean {matches}?" return "" _ordered_descriptor_deprecation_message = """\ The {func} {obj_type} is deprecated and may be removed in a future version. You can replace its functionality with a combination of the __init_subclass__ and __set_name__ magic methods introduced in Python 3.6. See for recipes on how to replicate their functionality. """
[docs] @deprecated("4.3", _ordered_descriptor_deprecation_message) class OrderedDescriptor(metaclass=abc.ABCMeta): """ Base class for descriptors whose order in the class body should be preserved. Intended for use in concert with the `OrderedDescriptorContainer` metaclass. Subclasses of `OrderedDescriptor` must define a value for a class attribute called ``_class_attribute_``. This is the name of a class attribute on the *container* class for these descriptors, which will be set to an `~collections.OrderedDict` at class creation time. This `~collections.OrderedDict` will contain a mapping of all class attributes that were assigned instances of the `OrderedDescriptor` subclass, to the instances themselves. See the documentation for `OrderedDescriptorContainer` for a concrete example. Optionally, subclasses of `OrderedDescriptor` may define a value for a class attribute called ``_name_attribute_``. This should be the name of an attribute on instances of the subclass. When specified, during creation of a class containing these descriptors, the name attribute on each instance will be set to the name of the class attribute it was assigned to on the class. .. note:: Although this class is intended for use with *descriptors* (i.e. classes that define any of the ``__get__``, ``__set__``, or ``__delete__`` magic methods), this base class is not itself a descriptor, and technically this could be used for classes that are not descriptors too. However, use with descriptors is the original intended purpose. """ # This id increments for each OrderedDescriptor instance created, so they # are always ordered in the order they were created. Class bodies are # guaranteed to be executed from top to bottom. Not sure if this is # thread-safe though. _nextid = 1 @property @abc.abstractmethod def _class_attribute_(self): """ Subclasses should define this attribute to the name of an attribute on classes containing this subclass. That attribute will contain the mapping of all instances of that `OrderedDescriptor` subclass defined in the class body. If the same descriptor needs to be used with different classes, each with different names of this attribute, multiple subclasses will be needed. """ _name_attribute_ = None """ Subclasses may optionally define this attribute to specify the name of an attribute on instances of the class that should be filled with the instance's attribute name at class creation time. """ def __init__(self, *args, **kwargs): # The _nextid attribute is shared across all subclasses so that # different subclasses of OrderedDescriptors can be sorted correctly # between themselves self.__order = OrderedDescriptor._nextid OrderedDescriptor._nextid += 1 super().__init__() def __lt__(self, other): """ Defined for convenient sorting of `OrderedDescriptor` instances, which are defined to sort in their creation order. """ if isinstance(self, OrderedDescriptor) and isinstance(other, OrderedDescriptor): try: return self.__order < other.__order except AttributeError: raise RuntimeError( f"Could not determine ordering for {self} and {other}; at least " "one of them is not calling super().__init__ in its " "__init__." ) else: return NotImplemented
[docs] @deprecated("4.3", _ordered_descriptor_deprecation_message) class OrderedDescriptorContainer(type): """ Classes should use this metaclass if they wish to use `OrderedDescriptor` attributes, which are class attributes that "remember" the order in which they were defined in the class body. Every subclass of `OrderedDescriptor` has an attribute called ``_class_attribute_``. For example, if we have .. code:: python class ExampleDecorator(OrderedDescriptor): _class_attribute_ = '_examples_' Then when a class with the `OrderedDescriptorContainer` metaclass is created, it will automatically be assigned a class attribute ``_examples_`` referencing an `~collections.OrderedDict` containing all instances of ``ExampleDecorator`` defined in the class body, mapped to by the names of the attributes they were assigned to. When subclassing a class with this metaclass, the descriptor dict (i.e. ``_examples_`` in the above example) will *not* contain descriptors inherited from the base class. That is, this only works by default with decorators explicitly defined in the class body. However, the subclass *may* define an attribute ``_inherit_decorators_`` which lists `OrderedDescriptor` classes that *should* be added from base classes. See the examples section below for an example of this. Examples -------- >>> from astropy.utils import OrderedDescriptor, OrderedDescriptorContainer >>> class TypedAttribute(OrderedDescriptor): ... \"\"\" ... Attributes that may only be assigned objects of a specific type, ... or subclasses thereof. For some reason we care about their order. ... \"\"\" ... ... _class_attribute_ = 'typed_attributes' ... _name_attribute_ = 'name' ... # A default name so that instances not attached to a class can ... # still be repr'd; useful for debugging ... name = '<unbound>' ... ... def __init__(self, type): ... # Make sure not to forget to call the super __init__ ... super().__init__() ... self.type = type ... ... def __get__(self, obj, objtype=None): ... if obj is None: ... return self ... if in obj.__dict__: ... return obj.__dict__[] ... else: ... raise AttributeError( ... ... def __set__(self, obj, value): ... if not isinstance(value, self.type): ... raise ValueError('{0}.{1} must be of type {2!r}'.format( ... obj.__class__.__name__,, self.type)) ... obj.__dict__[] = value ... ... def __delete__(self, obj): ... if in obj.__dict__: ... del obj.__dict__[] ... else: ... raise AttributeError( ... ... def __repr__(self): ... if isinstance(self.type, tuple) and len(self.type) > 1: ... typestr = '({0})'.format( ... ', '.join(t.__name__ for t in self.type)) ... else: ... typestr = self.type.__name__ ... return '<{0}(name={1}, type={2})>'.format( ... self.__class__.__name__,, typestr) ... Now let's create an example class that uses this ``TypedAttribute``:: >>> class Point2D(metaclass=OrderedDescriptorContainer): ... x = TypedAttribute((float, int)) ... y = TypedAttribute((float, int)) ... ... def __init__(self, x, y): ... self.x, self.y = x, y ... >>> p1 = Point2D(1.0, 2.0) >>> p1.x 1.0 >>> p1.y 2.0 >>> p2 = Point2D('a', 'b') # doctest: +IGNORE_EXCEPTION_DETAIL Traceback (most recent call last): ... ValueError: Point2D.x must be of type (float, int>) We see that ``TypedAttribute`` works more or less as advertised, but there's nothing special about that. Let's see what `OrderedDescriptorContainer` did for us:: >>> Point2D.typed_attributes OrderedDict([('x', <TypedAttribute(name=x, type=(float, int))>), ('y', <TypedAttribute(name=y, type=(float, int))>)]) If we create a subclass, it does *not* by default add inherited descriptors to ``typed_attributes``:: >>> class Point3D(Point2D): ... z = TypedAttribute((float, int)) ... >>> Point3D.typed_attributes OrderedDict([('z', <TypedAttribute(name=z, type=(float, int))>)]) However, if we specify ``_inherit_descriptors_`` from ``Point2D`` then it will do so:: >>> class Point3D(Point2D): ... _inherit_descriptors_ = (TypedAttribute,) ... z = TypedAttribute((float, int)) ... >>> Point3D.typed_attributes OrderedDict([('x', <TypedAttribute(name=x, type=(float, int))>), ('y', <TypedAttribute(name=y, type=(float, int))>), ('z', <TypedAttribute(name=z, type=(float, int))>)]) .. note:: Hopefully it is clear from these examples that this construction also allows a class of type `OrderedDescriptorContainer` to use multiple different `OrderedDescriptor` classes simultaneously. """ _inherit_descriptors_ = () def __init__(cls, cls_name, bases, members): descriptors = defaultdict(list) seen = set() inherit_descriptors = () descr_bases = {} for mro_cls in cls.__mro__: for name, obj in mro_cls.__dict__.items(): if name in seen: # Checks if we've already seen an attribute of the given # name (if so it will override anything of the same name in # any base class) continue seen.add(name) if not isinstance(obj, OrderedDescriptor) or ( inherit_descriptors and not isinstance(obj, inherit_descriptors) ): # The second condition applies when checking any # subclasses, to see if we can inherit any descriptors of # the given type from subclasses (by default inheritance is # disabled unless the class has _inherit_descriptors_ # defined) continue if obj._name_attribute_ is not None: setattr(obj, obj._name_attribute_, name) # Don't just use the descriptor's class directly; instead go # through its MRO and find the class on which _class_attribute_ # is defined directly. This way subclasses of some # OrderedDescriptor *may* override _class_attribute_ and have # its own _class_attribute_, but by default all subclasses of # some OrderedDescriptor are still grouped together # TODO: It might be worth clarifying this in the docs if obj.__class__ not in descr_bases: for obj_cls_base in obj.__class__.__mro__: if "_class_attribute_" in obj_cls_base.__dict__: descr_bases[obj.__class__] = obj_cls_base descriptors[obj_cls_base].append((obj, name)) break else: # Make sure to put obj first for sorting purposes obj_cls_base = descr_bases[obj.__class__] descriptors[obj_cls_base].append((obj, name)) if not getattr(mro_cls, "_inherit_descriptors_", False): # If _inherit_descriptors_ is undefined then we don't inherit # any OrderedDescriptors from any of the base classes, and # there's no reason to continue through the MRO break else: inherit_descriptors = mro_cls._inherit_descriptors_ for descriptor_cls, instances in descriptors.items(): instances.sort() instances = OrderedDict((key, value) for value, key in instances) setattr(cls, descriptor_cls._class_attribute_, instances) super().__init__(cls_name, bases, members)
LOCALE_LOCK = threading.Lock() @contextmanager def _set_locale(name): """ Context manager to temporarily set the locale to ``name``. An example is setting locale to "C" so that the C strtod() function will use "." as the decimal point to enable consistent numerical string parsing. Note that one cannot nest multiple _set_locale() context manager statements as this causes a threading lock. This code taken from Parameters ---------- name : str Locale name, e.g. "C" or "fr_FR". """ name = str(name) with LOCALE_LOCK: saved = locale.setlocale(locale.LC_ALL) if saved == name: # Don't do anything if locale is already the requested locale yield else: try: locale.setlocale(locale.LC_ALL, name) yield finally: locale.setlocale(locale.LC_ALL, saved) set_locale = deprecated("4.0")(_set_locale) set_locale.__doc__ = """Deprecated version of :func:`_set_locale` above. See """
[docs] def dtype_bytes_or_chars(dtype): """ Parse the number out of a dtype.str value like '<U5' or '<f8'. See #5819 for discussion on the need for this function for getting the number of characters corresponding to a string dtype. Parameters ---------- dtype : numpy dtype object Input dtype Returns ------- bytes_or_chars : int or None Bits (for numeric types) or characters (for string types) """ match ="(\d+)$", dtype.str) out = int( if match else None return out
def _hungry_for(option): # pragma: no cover """ Open browser loaded with ``option`` options near you. *Disclaimers: Payments not included. Astropy is not responsible for any liability from using this function.* .. note:: Accuracy depends on your browser settings. """ import webbrowser"{option}+near+me") def pizza(): # pragma: no cover """``/pizza``.""" _hungry_for("pizza") def coffee(is_adam=False, is_brigitta=False): # pragma: no cover """``/coffee``.""" if is_adam and is_brigitta: raise ValueError("There can be only one!") if is_adam: option = "fresh+third+wave+coffee" elif is_brigitta: option = "decent+espresso" else: option = "coffee" _hungry_for(option)