two version of R2R are here HEAD master

4 files changed, 725 insertions, 0 deletions

diff --git a/.venv/lib/python3.12/site-packages/numpy/_utils/__init__.py b/.venv/lib/python3.12/site-packages/numpy/_utils/__init__.py
new file mode 100644
index 00000000..388dd917
--- /dev/null
+++ b/.venv/lib/python3.12/site-packages/numpy/_utils/__init__.py
@@ -0,0 +1,29 @@
+"""
+This is a module for defining private helpers which do not depend on the
+rest of NumPy.
+
+Everything in here must be self-contained so that it can be
+imported anywhere else without creating circular imports.
+If a utility requires the import of NumPy, it probably belongs
+in ``numpy.core``.
+"""
+
+from ._convertions import asunicode, asbytes
+
+
+def set_module(module):
+    """Private decorator for overriding __module__ on a function or class.
+
+    Example usage::
+
+        @set_module('numpy')
+        def example():
+            pass
+
+        assert example.__module__ == 'numpy'
+    """
+    def decorator(func):
+        if module is not None:
+            func.__module__ = module
+        return func
+    return decorator
diff --git a/.venv/lib/python3.12/site-packages/numpy/_utils/_convertions.py b/.venv/lib/python3.12/site-packages/numpy/_utils/_convertions.py
new file mode 100644
index 00000000..ab15a8ba
--- /dev/null
+++ b/.venv/lib/python3.12/site-packages/numpy/_utils/_convertions.py
@@ -0,0 +1,18 @@
+"""
+A set of methods retained from np.compat module that
+are still used across codebase.
+"""
+
+__all__ = ["asunicode", "asbytes"]
+
+
+def asunicode(s):
+    if isinstance(s, bytes):
+        return s.decode('latin1')
+    return str(s)
+
+
+def asbytes(s):
+    if isinstance(s, bytes):
+        return s
+    return str(s).encode('latin1')
diff --git a/.venv/lib/python3.12/site-packages/numpy/_utils/_inspect.py b/.venv/lib/python3.12/site-packages/numpy/_utils/_inspect.py
new file mode 100644
index 00000000..9a874a71
--- /dev/null
+++ b/.venv/lib/python3.12/site-packages/numpy/_utils/_inspect.py
@@ -0,0 +1,191 @@
+"""Subset of inspect module from upstream python
+
+We use this instead of upstream because upstream inspect is slow to import, and
+significantly contributes to numpy import times. Importing this copy has almost
+no overhead.
+
+"""
+import types
+
+__all__ = ['getargspec', 'formatargspec']
+
+# ----------------------------------------------------------- type-checking
+def ismethod(object):
+    """Return true if the object is an instance method.
+
+    Instance method objects provide these attributes:
+        __doc__         documentation string
+        __name__        name with which this method was defined
+        im_class        class object in which this method belongs
+        im_func         function object containing implementation of method
+        im_self         instance to which this method is bound, or None
+
+    """
+    return isinstance(object, types.MethodType)
+
+def isfunction(object):
+    """Return true if the object is a user-defined function.
+
+    Function objects provide these attributes:
+        __doc__         documentation string
+        __name__        name with which this function was defined
+        func_code       code object containing compiled function bytecode
+        func_defaults   tuple of any default values for arguments
+        func_doc        (same as __doc__)
+        func_globals    global namespace in which this function was defined
+        func_name       (same as __name__)
+
+    """
+    return isinstance(object, types.FunctionType)
+
+def iscode(object):
+    """Return true if the object is a code object.
+
+    Code objects provide these attributes:
+        co_argcount     number of arguments (not including * or ** args)
+        co_code         string of raw compiled bytecode
+        co_consts       tuple of constants used in the bytecode
+        co_filename     name of file in which this code object was created
+        co_firstlineno  number of first line in Python source code
+        co_flags        bitmap: 1=optimized | 2=newlocals | 4=*arg | 8=**arg
+        co_lnotab       encoded mapping of line numbers to bytecode indices
+        co_name         name with which this code object was defined
+        co_names        tuple of names of local variables
+        co_nlocals      number of local variables
+        co_stacksize    virtual machine stack space required
+        co_varnames     tuple of names of arguments and local variables
+        
+    """
+    return isinstance(object, types.CodeType)
+
+# ------------------------------------------------ argument list extraction
+# These constants are from Python's compile.h.
+CO_OPTIMIZED, CO_NEWLOCALS, CO_VARARGS, CO_VARKEYWORDS = 1, 2, 4, 8
+
+def getargs(co):
+    """Get information about the arguments accepted by a code object.
+
+    Three things are returned: (args, varargs, varkw), where 'args' is
+    a list of argument names (possibly containing nested lists), and
+    'varargs' and 'varkw' are the names of the * and ** arguments or None.
+
+    """
+
+    if not iscode(co):
+        raise TypeError('arg is not a code object')
+
+    nargs = co.co_argcount
+    names = co.co_varnames
+    args = list(names[:nargs])
+
+    # The following acrobatics are for anonymous (tuple) arguments.
+    # Which we do not need to support, so remove to avoid importing
+    # the dis module.
+    for i in range(nargs):
+        if args[i][:1] in ['', '.']:
+            raise TypeError("tuple function arguments are not supported")
+    varargs = None
+    if co.co_flags & CO_VARARGS:
+        varargs = co.co_varnames[nargs]
+        nargs = nargs + 1
+    varkw = None
+    if co.co_flags & CO_VARKEYWORDS:
+        varkw = co.co_varnames[nargs]
+    return args, varargs, varkw
+
+def getargspec(func):
+    """Get the names and default values of a function's arguments.
+
+    A tuple of four things is returned: (args, varargs, varkw, defaults).
+    'args' is a list of the argument names (it may contain nested lists).
+    'varargs' and 'varkw' are the names of the * and ** arguments or None.
+    'defaults' is an n-tuple of the default values of the last n arguments.
+
+    """
+
+    if ismethod(func):
+        func = func.__func__
+    if not isfunction(func):
+        raise TypeError('arg is not a Python function')
+    args, varargs, varkw = getargs(func.__code__)
+    return args, varargs, varkw, func.__defaults__
+
+def getargvalues(frame):
+    """Get information about arguments passed into a particular frame.
+
+    A tuple of four things is returned: (args, varargs, varkw, locals).
+    'args' is a list of the argument names (it may contain nested lists).
+    'varargs' and 'varkw' are the names of the * and ** arguments or None.
+    'locals' is the locals dictionary of the given frame.
+    
+    """
+    args, varargs, varkw = getargs(frame.f_code)
+    return args, varargs, varkw, frame.f_locals
+
+def joinseq(seq):
+    if len(seq) == 1:
+        return '(' + seq[0] + ',)'
+    else:
+        return '(' + ', '.join(seq) + ')'
+
+def strseq(object, convert, join=joinseq):
+    """Recursively walk a sequence, stringifying each element.
+
+    """
+    if type(object) in [list, tuple]:
+        return join([strseq(_o, convert, join) for _o in object])
+    else:
+        return convert(object)
+
+def formatargspec(args, varargs=None, varkw=None, defaults=None,
+                  formatarg=str,
+                  formatvarargs=lambda name: '*' + name,
+                  formatvarkw=lambda name: '**' + name,
+                  formatvalue=lambda value: '=' + repr(value),
+                  join=joinseq):
+    """Format an argument spec from the 4 values returned by getargspec.
+
+    The first four arguments are (args, varargs, varkw, defaults).  The
+    other four arguments are the corresponding optional formatting functions
+    that are called to turn names and values into strings.  The ninth
+    argument is an optional function to format the sequence of arguments.
+
+    """
+    specs = []
+    if defaults:
+        firstdefault = len(args) - len(defaults)
+    for i in range(len(args)):
+        spec = strseq(args[i], formatarg, join)
+        if defaults and i >= firstdefault:
+            spec = spec + formatvalue(defaults[i - firstdefault])
+        specs.append(spec)
+    if varargs is not None:
+        specs.append(formatvarargs(varargs))
+    if varkw is not None:
+        specs.append(formatvarkw(varkw))
+    return '(' + ', '.join(specs) + ')'
+
+def formatargvalues(args, varargs, varkw, locals,
+                    formatarg=str,
+                    formatvarargs=lambda name: '*' + name,
+                    formatvarkw=lambda name: '**' + name,
+                    formatvalue=lambda value: '=' + repr(value),
+                    join=joinseq):
+    """Format an argument spec from the 4 values returned by getargvalues.
+
+    The first four arguments are (args, varargs, varkw, locals).  The
+    next four arguments are the corresponding optional formatting functions
+    that are called to turn names and values into strings.  The ninth
+    argument is an optional function to format the sequence of arguments.
+
+    """
+    def convert(name, locals=locals,
+                formatarg=formatarg, formatvalue=formatvalue):
+        return formatarg(name) + formatvalue(locals[name])
+    specs = [strseq(arg, convert, join) for arg in args]
+
+    if varargs:
+        specs.append(formatvarargs(varargs) + formatvalue(locals[varargs]))
+    if varkw:
+        specs.append(formatvarkw(varkw) + formatvalue(locals[varkw]))
+    return '(' + ', '.join(specs) + ')'
diff --git a/.venv/lib/python3.12/site-packages/numpy/_utils/_pep440.py b/.venv/lib/python3.12/site-packages/numpy/_utils/_pep440.py
new file mode 100644
index 00000000..73d0afb5
--- /dev/null
+++ b/.venv/lib/python3.12/site-packages/numpy/_utils/_pep440.py
@@ -0,0 +1,487 @@
+"""Utility to compare pep440 compatible version strings.
+
+The LooseVersion and StrictVersion classes that distutils provides don't
+work; they don't recognize anything like alpha/beta/rc/dev versions.
+"""
+
+# Copyright (c) Donald Stufft and individual contributors.
+# All rights reserved.
+
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+
+#     1. Redistributions of source code must retain the above copyright notice,
+#        this list of conditions and the following disclaimer.
+
+#     2. Redistributions in binary form must reproduce the above copyright
+#        notice, this list of conditions and the following disclaimer in the
+#        documentation and/or other materials provided with the distribution.
+
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+
+import collections
+import itertools
+import re
+
+
+__all__ = [
+    "parse", "Version", "LegacyVersion", "InvalidVersion", "VERSION_PATTERN",
+]
+
+
+# BEGIN packaging/_structures.py
+
+
+class Infinity:
+    def __repr__(self):
+        return "Infinity"
+
+    def __hash__(self):
+        return hash(repr(self))
+
+    def __lt__(self, other):
+        return False
+
+    def __le__(self, other):
+        return False
+
+    def __eq__(self, other):
+        return isinstance(other, self.__class__)
+
+    def __ne__(self, other):
+        return not isinstance(other, self.__class__)
+
+    def __gt__(self, other):
+        return True
+
+    def __ge__(self, other):
+        return True
+
+    def __neg__(self):
+        return NegativeInfinity
+
+
+Infinity = Infinity()
+
+
+class NegativeInfinity:
+    def __repr__(self):
+        return "-Infinity"
+
+    def __hash__(self):
+        return hash(repr(self))
+
+    def __lt__(self, other):
+        return True
+
+    def __le__(self, other):
+        return True
+
+    def __eq__(self, other):
+        return isinstance(other, self.__class__)
+
+    def __ne__(self, other):
+        return not isinstance(other, self.__class__)
+
+    def __gt__(self, other):
+        return False
+
+    def __ge__(self, other):
+        return False
+
+    def __neg__(self):
+        return Infinity
+
+
+# BEGIN packaging/version.py
+
+
+NegativeInfinity = NegativeInfinity()
+
+_Version = collections.namedtuple(
+    "_Version",
+    ["epoch", "release", "dev", "pre", "post", "local"],
+)
+
+
+def parse(version):
+    """
+    Parse the given version string and return either a :class:`Version` object
+    or a :class:`LegacyVersion` object depending on if the given version is
+    a valid PEP 440 version or a legacy version.
+    """
+    try:
+        return Version(version)
+    except InvalidVersion:
+        return LegacyVersion(version)
+
+
+class InvalidVersion(ValueError):
+    """
+    An invalid version was found, users should refer to PEP 440.
+    """
+
+
+class _BaseVersion:
+
+    def __hash__(self):
+        return hash(self._key)
+
+    def __lt__(self, other):
+        return self._compare(other, lambda s, o: s < o)
+
+    def __le__(self, other):
+        return self._compare(other, lambda s, o: s <= o)
+
+    def __eq__(self, other):
+        return self._compare(other, lambda s, o: s == o)
+
+    def __ge__(self, other):
+        return self._compare(other, lambda s, o: s >= o)
+
+    def __gt__(self, other):
+        return self._compare(other, lambda s, o: s > o)
+
+    def __ne__(self, other):
+        return self._compare(other, lambda s, o: s != o)
+
+    def _compare(self, other, method):
+        if not isinstance(other, _BaseVersion):
+            return NotImplemented
+
+        return method(self._key, other._key)
+
+
+class LegacyVersion(_BaseVersion):
+
+    def __init__(self, version):
+        self._version = str(version)
+        self._key = _legacy_cmpkey(self._version)
+
+    def __str__(self):
+        return self._version
+
+    def __repr__(self):
+        return "<LegacyVersion({0})>".format(repr(str(self)))
+
+    @property
+    def public(self):
+        return self._version
+
+    @property
+    def base_version(self):
+        return self._version
+
+    @property
+    def local(self):
+        return None
+
+    @property
+    def is_prerelease(self):
+        return False
+
+    @property
+    def is_postrelease(self):
+        return False
+
+
+_legacy_version_component_re = re.compile(
+    r"(\d+ | [a-z]+ | \.| -)", re.VERBOSE,
+)
+
+_legacy_version_replacement_map = {
+    "pre": "c", "preview": "c", "-": "final-", "rc": "c", "dev": "@",
+}
+
+
+def _parse_version_parts(s):
+    for part in _legacy_version_component_re.split(s):
+        part = _legacy_version_replacement_map.get(part, part)
+
+        if not part or part == ".":
+            continue
+
+        if part[:1] in "0123456789":
+            # pad for numeric comparison
+            yield part.zfill(8)
+        else:
+            yield "*" + part
+
+    # ensure that alpha/beta/candidate are before final
+    yield "*final"
+
+
+def _legacy_cmpkey(version):
+    # We hardcode an epoch of -1 here. A PEP 440 version can only have an epoch
+    # greater than or equal to 0. This will effectively put the LegacyVersion,
+    # which uses the defacto standard originally implemented by setuptools,
+    # as before all PEP 440 versions.
+    epoch = -1
+
+    # This scheme is taken from pkg_resources.parse_version setuptools prior to
+    # its adoption of the packaging library.
+    parts = []
+    for part in _parse_version_parts(version.lower()):
+        if part.startswith("*"):
+            # remove "-" before a prerelease tag
+            if part < "*final":
+                while parts and parts[-1] == "*final-":
+                    parts.pop()
+
+            # remove trailing zeros from each series of numeric parts
+            while parts and parts[-1] == "00000000":
+                parts.pop()
+
+        parts.append(part)
+    parts = tuple(parts)
+
+    return epoch, parts
+
+
+# Deliberately not anchored to the start and end of the string, to make it
+# easier for 3rd party code to reuse
+VERSION_PATTERN = r"""
+    v?
+    (?:
+        (?:(?P<epoch>[0-9]+)!)?                           # epoch
+        (?P<release>[0-9]+(?:\.[0-9]+)*)                  # release segment
+        (?P<pre>                                          # pre-release
+            [-_\.]?
+            (?P<pre_l>(a|b|c|rc|alpha|beta|pre|preview))
+            [-_\.]?
+            (?P<pre_n>[0-9]+)?
+        )?
+        (?P<post>                                         # post release
+            (?:-(?P<post_n1>[0-9]+))
+            |
+            (?:
+                [-_\.]?
+                (?P<post_l>post|rev|r)
+                [-_\.]?
+                (?P<post_n2>[0-9]+)?
+            )
+        )?
+        (?P<dev>                                          # dev release
+            [-_\.]?
+            (?P<dev_l>dev)
+            [-_\.]?
+            (?P<dev_n>[0-9]+)?
+        )?
+    )
+    (?:\+(?P<local>[a-z0-9]+(?:[-_\.][a-z0-9]+)*))?       # local version
+"""
+
+
+class Version(_BaseVersion):
+
+    _regex = re.compile(
+        r"^\s*" + VERSION_PATTERN + r"\s*$",
+        re.VERBOSE | re.IGNORECASE,
+    )
+
+    def __init__(self, version):
+        # Validate the version and parse it into pieces
+        match = self._regex.search(version)
+        if not match:
+            raise InvalidVersion("Invalid version: '{0}'".format(version))
+
+        # Store the parsed out pieces of the version
+        self._version = _Version(
+            epoch=int(match.group("epoch")) if match.group("epoch") else 0,
+            release=tuple(int(i) for i in match.group("release").split(".")),
+            pre=_parse_letter_version(
+                match.group("pre_l"),
+                match.group("pre_n"),
+            ),
+            post=_parse_letter_version(
+                match.group("post_l"),
+                match.group("post_n1") or match.group("post_n2"),
+            ),
+            dev=_parse_letter_version(
+                match.group("dev_l"),
+                match.group("dev_n"),
+            ),
+            local=_parse_local_version(match.group("local")),
+        )
+
+        # Generate a key which will be used for sorting
+        self._key = _cmpkey(
+            self._version.epoch,
+            self._version.release,
+            self._version.pre,
+            self._version.post,
+            self._version.dev,
+            self._version.local,
+        )
+
+    def __repr__(self):
+        return "<Version({0})>".format(repr(str(self)))
+
+    def __str__(self):
+        parts = []
+
+        # Epoch
+        if self._version.epoch != 0:
+            parts.append("{0}!".format(self._version.epoch))
+
+        # Release segment
+        parts.append(".".join(str(x) for x in self._version.release))
+
+        # Pre-release
+        if self._version.pre is not None:
+            parts.append("".join(str(x) for x in self._version.pre))
+
+        # Post-release
+        if self._version.post is not None:
+            parts.append(".post{0}".format(self._version.post[1]))
+
+        # Development release
+        if self._version.dev is not None:
+            parts.append(".dev{0}".format(self._version.dev[1]))
+
+        # Local version segment
+        if self._version.local is not None:
+            parts.append(
+                "+{0}".format(".".join(str(x) for x in self._version.local))
+            )
+
+        return "".join(parts)
+
+    @property
+    def public(self):
+        return str(self).split("+", 1)[0]
+
+    @property
+    def base_version(self):
+        parts = []
+
+        # Epoch
+        if self._version.epoch != 0:
+            parts.append("{0}!".format(self._version.epoch))
+
+        # Release segment
+        parts.append(".".join(str(x) for x in self._version.release))
+
+        return "".join(parts)
+
+    @property
+    def local(self):
+        version_string = str(self)
+        if "+" in version_string:
+            return version_string.split("+", 1)[1]
+
+    @property
+    def is_prerelease(self):
+        return bool(self._version.dev or self._version.pre)
+
+    @property
+    def is_postrelease(self):
+        return bool(self._version.post)
+
+
+def _parse_letter_version(letter, number):
+    if letter:
+        # We assume there is an implicit 0 in a pre-release if there is
+        # no numeral associated with it.
+        if number is None:
+            number = 0
+
+        # We normalize any letters to their lower-case form
+        letter = letter.lower()
+
+        # We consider some words to be alternate spellings of other words and
+        # in those cases we want to normalize the spellings to our preferred
+        # spelling.
+        if letter == "alpha":
+            letter = "a"
+        elif letter == "beta":
+            letter = "b"
+        elif letter in ["c", "pre", "preview"]:
+            letter = "rc"
+        elif letter in ["rev", "r"]:
+            letter = "post"
+
+        return letter, int(number)
+    if not letter and number:
+        # We assume that if we are given a number but not given a letter,
+        # then this is using the implicit post release syntax (e.g., 1.0-1)
+        letter = "post"
+
+        return letter, int(number)
+
+
+_local_version_seperators = re.compile(r"[\._-]")
+
+
+def _parse_local_version(local):
+    """
+    Takes a string like abc.1.twelve and turns it into ("abc", 1, "twelve").
+    """
+    if local is not None:
+        return tuple(
+            part.lower() if not part.isdigit() else int(part)
+            for part in _local_version_seperators.split(local)
+        )
+
+
+def _cmpkey(epoch, release, pre, post, dev, local):
+    # When we compare a release version, we want to compare it with all of the
+    # trailing zeros removed. So we'll use a reverse the list, drop all the now
+    # leading zeros until we come to something non-zero, then take the rest,
+    # re-reverse it back into the correct order, and make it a tuple and use
+    # that for our sorting key.
+    release = tuple(
+        reversed(list(
+            itertools.dropwhile(
+                lambda x: x == 0,
+                reversed(release),
+            )
+        ))
+    )
+
+    # We need to "trick" the sorting algorithm to put 1.0.dev0 before 1.0a0.
+    # We'll do this by abusing the pre-segment, but we _only_ want to do this
+    # if there is no pre- or a post-segment. If we have one of those, then
+    # the normal sorting rules will handle this case correctly.
+    if pre is None and post is None and dev is not None:
+        pre = -Infinity
+    # Versions without a pre-release (except as noted above) should sort after
+    # those with one.
+    elif pre is None:
+        pre = Infinity
+
+    # Versions without a post-segment should sort before those with one.
+    if post is None:
+        post = -Infinity
+
+    # Versions without a development segment should sort after those with one.
+    if dev is None:
+        dev = Infinity
+
+    if local is None:
+        # Versions without a local segment should sort before those with one.
+        local = -Infinity
+    else:
+        # Versions with a local segment need that segment parsed to implement
+        # the sorting rules in PEP440.
+        # - Alphanumeric segments sort before numeric segments
+        # - Alphanumeric segments sort lexicographically
+        # - Numeric segments sort numerically
+        # - Shorter versions sort before longer versions when the prefixes
+        #   match exactly
+        local = tuple(
+            (i, "") if isinstance(i, int) else (-Infinity, i)
+            for i in local
+        )
+
+    return epoch, release, pre, post, dev, local