finalizare 1.0
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"""
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External, bundled dependencies.
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"""
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"""Vendoered from
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https://github.com/pypa/packaging/blob/main/packaging/_structures.py
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"""
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# Copyright (c) Donald Stufft and individual contributors.
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# All rights reserved.
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|
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# 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.
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||||
|
||||
|
||||
class InfinityType:
|
||||
def __repr__(self) -> str:
|
||||
return "Infinity"
|
||||
|
||||
def __hash__(self) -> int:
|
||||
return hash(repr(self))
|
||||
|
||||
def __lt__(self, other: object) -> bool:
|
||||
return False
|
||||
|
||||
def __le__(self, other: object) -> bool:
|
||||
return False
|
||||
|
||||
def __eq__(self, other: object) -> bool:
|
||||
return isinstance(other, self.__class__)
|
||||
|
||||
def __ne__(self, other: object) -> bool:
|
||||
return not isinstance(other, self.__class__)
|
||||
|
||||
def __gt__(self, other: object) -> bool:
|
||||
return True
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||||
|
||||
def __ge__(self, other: object) -> bool:
|
||||
return True
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||||
|
||||
def __neg__(self: object) -> "NegativeInfinityType":
|
||||
return NegativeInfinity
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||||
|
||||
|
||||
Infinity = InfinityType()
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||||
|
||||
|
||||
class NegativeInfinityType:
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||||
def __repr__(self) -> str:
|
||||
return "-Infinity"
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||||
|
||||
def __hash__(self) -> int:
|
||||
return hash(repr(self))
|
||||
|
||||
def __lt__(self, other: object) -> bool:
|
||||
return True
|
||||
|
||||
def __le__(self, other: object) -> bool:
|
||||
return True
|
||||
|
||||
def __eq__(self, other: object) -> bool:
|
||||
return isinstance(other, self.__class__)
|
||||
|
||||
def __ne__(self, other: object) -> bool:
|
||||
return not isinstance(other, self.__class__)
|
||||
|
||||
def __gt__(self, other: object) -> bool:
|
||||
return False
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||||
|
||||
def __ge__(self, other: object) -> bool:
|
||||
return False
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||||
|
||||
def __neg__(self: object) -> InfinityType:
|
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return Infinity
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||||
|
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|
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NegativeInfinity = NegativeInfinityType()
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@@ -0,0 +1,535 @@
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"""Vendoered from
|
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https://github.com/pypa/packaging/blob/main/packaging/version.py
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"""
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# Copyright (c) Donald Stufft and individual contributors.
|
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# 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.
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import collections
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import itertools
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import re
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import warnings
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from typing import Callable, Iterator, List, Optional, SupportsInt, Tuple, Union
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from ._structures import Infinity, InfinityType, NegativeInfinity, NegativeInfinityType
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__all__ = ["parse", "Version", "LegacyVersion", "InvalidVersion", "VERSION_PATTERN"]
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InfiniteTypes = Union[InfinityType, NegativeInfinityType]
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PrePostDevType = Union[InfiniteTypes, Tuple[str, int]]
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SubLocalType = Union[InfiniteTypes, int, str]
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LocalType = Union[
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NegativeInfinityType,
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Tuple[
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Union[
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SubLocalType,
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Tuple[SubLocalType, str],
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Tuple[NegativeInfinityType, SubLocalType],
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],
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...,
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],
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]
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CmpKey = Tuple[
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int, Tuple[int, ...], PrePostDevType, PrePostDevType, PrePostDevType, LocalType
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]
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LegacyCmpKey = Tuple[int, Tuple[str, ...]]
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VersionComparisonMethod = Callable[
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[Union[CmpKey, LegacyCmpKey], Union[CmpKey, LegacyCmpKey]], bool
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]
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_Version = collections.namedtuple(
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"_Version", ["epoch", "release", "dev", "pre", "post", "local"]
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)
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def parse(version: str) -> Union["LegacyVersion", "Version"]:
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"""Parse the given version from a string to an appropriate class.
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Parameters
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----------
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version : str
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Version in a string format, eg. "0.9.1" or "1.2.dev0".
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Returns
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-------
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version : :class:`Version` object or a :class:`LegacyVersion` object
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Returned class depends on the given version: if is a valid
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PEP 440 version or a legacy version.
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"""
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try:
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return Version(version)
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except InvalidVersion:
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return LegacyVersion(version)
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class InvalidVersion(ValueError):
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"""
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An invalid version was found, users should refer to PEP 440.
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"""
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class _BaseVersion:
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_key: Union[CmpKey, LegacyCmpKey]
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def __hash__(self) -> int:
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return hash(self._key)
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# Please keep the duplicated `isinstance` check
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# in the six comparisons hereunder
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# unless you find a way to avoid adding overhead function calls.
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def __lt__(self, other: "_BaseVersion") -> bool:
|
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if not isinstance(other, _BaseVersion):
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return NotImplemented
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||||
|
||||
return self._key < other._key
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||||
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def __le__(self, other: "_BaseVersion") -> bool:
|
||||
if not isinstance(other, _BaseVersion):
|
||||
return NotImplemented
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||||
|
||||
return self._key <= other._key
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def __eq__(self, other: object) -> bool:
|
||||
if not isinstance(other, _BaseVersion):
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||||
return NotImplemented
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||||
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return self._key == other._key
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||||
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def __ge__(self, other: "_BaseVersion") -> bool:
|
||||
if not isinstance(other, _BaseVersion):
|
||||
return NotImplemented
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||||
|
||||
return self._key >= other._key
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||||
|
||||
def __gt__(self, other: "_BaseVersion") -> bool:
|
||||
if not isinstance(other, _BaseVersion):
|
||||
return NotImplemented
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||||
|
||||
return self._key > other._key
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||||
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||||
def __ne__(self, other: object) -> bool:
|
||||
if not isinstance(other, _BaseVersion):
|
||||
return NotImplemented
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||||
|
||||
return self._key != other._key
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||||
|
||||
|
||||
class LegacyVersion(_BaseVersion):
|
||||
def __init__(self, version: str) -> None:
|
||||
self._version = str(version)
|
||||
self._key = _legacy_cmpkey(self._version)
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||||
|
||||
warnings.warn(
|
||||
"Creating a LegacyVersion has been deprecated and will be "
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||||
"removed in the next major release",
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DeprecationWarning,
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)
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||||
def __str__(self) -> str:
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||||
return self._version
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|
||||
def __repr__(self) -> str:
|
||||
return f"<LegacyVersion('{self}')>"
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@property
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||||
def public(self) -> str:
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return self._version
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@property
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def base_version(self) -> str:
|
||||
return self._version
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||||
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||||
@property
|
||||
def epoch(self) -> int:
|
||||
return -1
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@property
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||||
def release(self) -> None:
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||||
return None
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||||
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||||
@property
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||||
def pre(self) -> None:
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||||
return None
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||||
|
||||
@property
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||||
def post(self) -> None:
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||||
return None
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||||
|
||||
@property
|
||||
def dev(self) -> None:
|
||||
return None
|
||||
|
||||
@property
|
||||
def local(self) -> None:
|
||||
return None
|
||||
|
||||
@property
|
||||
def is_prerelease(self) -> bool:
|
||||
return False
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||||
|
||||
@property
|
||||
def is_postrelease(self) -> bool:
|
||||
return False
|
||||
|
||||
@property
|
||||
def is_devrelease(self) -> bool:
|
||||
return False
|
||||
|
||||
|
||||
_legacy_version_component_re = re.compile(r"(\d+ | [a-z]+ | \.| -)", re.VERBOSE)
|
||||
|
||||
_legacy_version_replacement_map = {
|
||||
"pre": "c",
|
||||
"preview": "c",
|
||||
"-": "final-",
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||||
"rc": "c",
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||||
"dev": "@",
|
||||
}
|
||||
|
||||
|
||||
def _parse_version_parts(s: str) -> Iterator[str]:
|
||||
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: str) -> LegacyCmpKey:
|
||||
|
||||
# We hardcode an epoch of -1 here. A PEP 440 version can only have a 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
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||||
|
||||
# This scheme is taken from pkg_resources.parse_version setuptools prior to
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||||
# it's adoption of the packaging library.
|
||||
parts: List[str] = []
|
||||
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)
|
||||
|
||||
return epoch, tuple(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: str) -> None:
|
||||
|
||||
# Validate the version and parse it into pieces
|
||||
match = self._regex.search(version)
|
||||
if not match:
|
||||
raise InvalidVersion(f"Invalid version: '{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) -> str:
|
||||
return f"<Version('{self}')>"
|
||||
|
||||
def __str__(self) -> str:
|
||||
parts = []
|
||||
|
||||
# Epoch
|
||||
if self.epoch != 0:
|
||||
parts.append(f"{self.epoch}!")
|
||||
|
||||
# Release segment
|
||||
parts.append(".".join(str(x) for x in self.release))
|
||||
|
||||
# Pre-release
|
||||
if self.pre is not None:
|
||||
parts.append("".join(str(x) for x in self.pre))
|
||||
|
||||
# Post-release
|
||||
if self.post is not None:
|
||||
parts.append(f".post{self.post}")
|
||||
|
||||
# Development release
|
||||
if self.dev is not None:
|
||||
parts.append(f".dev{self.dev}")
|
||||
|
||||
# Local version segment
|
||||
if self.local is not None:
|
||||
parts.append(f"+{self.local}")
|
||||
|
||||
return "".join(parts)
|
||||
|
||||
@property
|
||||
def epoch(self) -> int:
|
||||
_epoch: int = self._version.epoch
|
||||
return _epoch
|
||||
|
||||
@property
|
||||
def release(self) -> Tuple[int, ...]:
|
||||
_release: Tuple[int, ...] = self._version.release
|
||||
return _release
|
||||
|
||||
@property
|
||||
def pre(self) -> Optional[Tuple[str, int]]:
|
||||
_pre: Optional[Tuple[str, int]] = self._version.pre
|
||||
return _pre
|
||||
|
||||
@property
|
||||
def post(self) -> Optional[int]:
|
||||
return self._version.post[1] if self._version.post else None
|
||||
|
||||
@property
|
||||
def dev(self) -> Optional[int]:
|
||||
return self._version.dev[1] if self._version.dev else None
|
||||
|
||||
@property
|
||||
def local(self) -> Optional[str]:
|
||||
if self._version.local:
|
||||
return ".".join(str(x) for x in self._version.local)
|
||||
else:
|
||||
return None
|
||||
|
||||
@property
|
||||
def public(self) -> str:
|
||||
return str(self).split("+", 1)[0]
|
||||
|
||||
@property
|
||||
def base_version(self) -> str:
|
||||
parts = []
|
||||
|
||||
# Epoch
|
||||
if self.epoch != 0:
|
||||
parts.append(f"{self.epoch}!")
|
||||
|
||||
# Release segment
|
||||
parts.append(".".join(str(x) for x in self.release))
|
||||
|
||||
return "".join(parts)
|
||||
|
||||
@property
|
||||
def is_prerelease(self) -> bool:
|
||||
return self.dev is not None or self.pre is not None
|
||||
|
||||
@property
|
||||
def is_postrelease(self) -> bool:
|
||||
return self.post is not None
|
||||
|
||||
@property
|
||||
def is_devrelease(self) -> bool:
|
||||
return self.dev is not None
|
||||
|
||||
@property
|
||||
def major(self) -> int:
|
||||
return self.release[0] if len(self.release) >= 1 else 0
|
||||
|
||||
@property
|
||||
def minor(self) -> int:
|
||||
return self.release[1] if len(self.release) >= 2 else 0
|
||||
|
||||
@property
|
||||
def micro(self) -> int:
|
||||
return self.release[2] if len(self.release) >= 3 else 0
|
||||
|
||||
|
||||
def _parse_letter_version(
|
||||
letter: str, number: Union[str, bytes, SupportsInt]
|
||||
) -> Optional[Tuple[str, int]]:
|
||||
|
||||
if letter:
|
||||
# We consider there to be an implicit 0 in a pre-release if there is
|
||||
# not a 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 if we are given a number, but we are not given a letter
|
||||
# then this is using the implicit post release syntax (e.g. 1.0-1)
|
||||
letter = "post"
|
||||
|
||||
return letter, int(number)
|
||||
|
||||
return None
|
||||
|
||||
|
||||
_local_version_separators = re.compile(r"[\._-]")
|
||||
|
||||
|
||||
def _parse_local_version(local: str) -> Optional[LocalType]:
|
||||
"""
|
||||
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_separators.split(local)
|
||||
)
|
||||
return None
|
||||
|
||||
|
||||
def _cmpkey(
|
||||
epoch: int,
|
||||
release: Tuple[int, ...],
|
||||
pre: Optional[Tuple[str, int]],
|
||||
post: Optional[Tuple[str, int]],
|
||||
dev: Optional[Tuple[str, int]],
|
||||
local: Optional[Tuple[SubLocalType]],
|
||||
) -> CmpKey:
|
||||
|
||||
# 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 not a 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: PrePostDevType = NegativeInfinity
|
||||
# Versions without a pre-release (except as noted above) should sort after
|
||||
# those with one.
|
||||
elif pre is None:
|
||||
_pre = Infinity
|
||||
else:
|
||||
_pre = pre
|
||||
|
||||
# Versions without a post segment should sort before those with one.
|
||||
if post is None:
|
||||
_post: PrePostDevType = NegativeInfinity
|
||||
|
||||
else:
|
||||
_post = post
|
||||
|
||||
# Versions without a development segment should sort after those with one.
|
||||
if dev is None:
|
||||
_dev: PrePostDevType = Infinity
|
||||
|
||||
else:
|
||||
_dev = dev
|
||||
|
||||
if local is None:
|
||||
# Versions without a local segment should sort before those with one.
|
||||
_local: LocalType = NegativeInfinity
|
||||
else:
|
||||
# Versions with a local segment need that segment parsed to implement
|
||||
# the sorting rules in PEP440.
|
||||
# - Alpha numeric segments sort before numeric segments
|
||||
# - Alpha numeric 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 (NegativeInfinity, i) for i in local
|
||||
)
|
||||
|
||||
return epoch, _release, _pre, _post, _dev, _local
|
||||
Vendored
BIN
Binary file not shown.
Vendored
BIN
Binary file not shown.
+1
@@ -0,0 +1 @@
|
||||
from ._laplacian import laplacian
|
||||
BIN
Binary file not shown.
BIN
Binary file not shown.
+557
@@ -0,0 +1,557 @@
|
||||
"""
|
||||
This file is a copy of the scipy.sparse.csgraph._laplacian module from SciPy 1.12
|
||||
|
||||
scipy.sparse.csgraph.laplacian supports sparse arrays only starting from Scipy 1.12,
|
||||
see https://github.com/scipy/scipy/pull/19156. This vendored file can be removed as
|
||||
soon as Scipy 1.12 becomes the minimum supported version.
|
||||
|
||||
Laplacian of a compressed-sparse graph
|
||||
"""
|
||||
|
||||
# License: BSD 3 clause
|
||||
|
||||
import numpy as np
|
||||
from scipy.sparse import issparse
|
||||
from scipy.sparse.linalg import LinearOperator
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Graph laplacian
|
||||
def laplacian(
|
||||
csgraph,
|
||||
normed=False,
|
||||
return_diag=False,
|
||||
use_out_degree=False,
|
||||
*,
|
||||
copy=True,
|
||||
form="array",
|
||||
dtype=None,
|
||||
symmetrized=False,
|
||||
):
|
||||
"""
|
||||
Return the Laplacian of a directed graph.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
csgraph : array_like or sparse matrix, 2 dimensions
|
||||
Compressed-sparse graph, with shape (N, N).
|
||||
normed : bool, optional
|
||||
If True, then compute symmetrically normalized Laplacian.
|
||||
Default: False.
|
||||
return_diag : bool, optional
|
||||
If True, then also return an array related to vertex degrees.
|
||||
Default: False.
|
||||
use_out_degree : bool, optional
|
||||
If True, then use out-degree instead of in-degree.
|
||||
This distinction matters only if the graph is asymmetric.
|
||||
Default: False.
|
||||
copy : bool, optional
|
||||
If False, then change `csgraph` in place if possible,
|
||||
avoiding doubling the memory use.
|
||||
Default: True, for backward compatibility.
|
||||
form : 'array', or 'function', or 'lo'
|
||||
Determines the format of the output Laplacian:
|
||||
|
||||
* 'array' is a numpy array;
|
||||
* 'function' is a pointer to evaluating the Laplacian-vector
|
||||
or Laplacian-matrix product;
|
||||
* 'lo' results in the format of the `LinearOperator`.
|
||||
|
||||
Choosing 'function' or 'lo' always avoids doubling
|
||||
the memory use, ignoring `copy` value.
|
||||
Default: 'array', for backward compatibility.
|
||||
dtype : None or one of numeric numpy dtypes, optional
|
||||
The dtype of the output. If ``dtype=None``, the dtype of the
|
||||
output matches the dtype of the input csgraph, except for
|
||||
the case ``normed=True`` and integer-like csgraph, where
|
||||
the output dtype is 'float' allowing accurate normalization,
|
||||
but dramatically increasing the memory use.
|
||||
Default: None, for backward compatibility.
|
||||
symmetrized : bool, optional
|
||||
If True, then the output Laplacian is symmetric/Hermitian.
|
||||
The symmetrization is done by ``csgraph + csgraph.T.conj``
|
||||
without dividing by 2 to preserve integer dtypes if possible
|
||||
prior to the construction of the Laplacian.
|
||||
The symmetrization will increase the memory footprint of
|
||||
sparse matrices unless the sparsity pattern is symmetric or
|
||||
`form` is 'function' or 'lo'.
|
||||
Default: False, for backward compatibility.
|
||||
|
||||
Returns
|
||||
-------
|
||||
lap : ndarray, or sparse matrix, or `LinearOperator`
|
||||
The N x N Laplacian of csgraph. It will be a NumPy array (dense)
|
||||
if the input was dense, or a sparse matrix otherwise, or
|
||||
the format of a function or `LinearOperator` if
|
||||
`form` equals 'function' or 'lo', respectively.
|
||||
diag : ndarray, optional
|
||||
The length-N main diagonal of the Laplacian matrix.
|
||||
For the normalized Laplacian, this is the array of square roots
|
||||
of vertex degrees or 1 if the degree is zero.
|
||||
|
||||
Notes
|
||||
-----
|
||||
The Laplacian matrix of a graph is sometimes referred to as the
|
||||
"Kirchhoff matrix" or just the "Laplacian", and is useful in many
|
||||
parts of spectral graph theory.
|
||||
In particular, the eigen-decomposition of the Laplacian can give
|
||||
insight into many properties of the graph, e.g.,
|
||||
is commonly used for spectral data embedding and clustering.
|
||||
|
||||
The constructed Laplacian doubles the memory use if ``copy=True`` and
|
||||
``form="array"`` which is the default.
|
||||
Choosing ``copy=False`` has no effect unless ``form="array"``
|
||||
or the matrix is sparse in the ``coo`` format, or dense array, except
|
||||
for the integer input with ``normed=True`` that forces the float output.
|
||||
|
||||
Sparse input is reformatted into ``coo`` if ``form="array"``,
|
||||
which is the default.
|
||||
|
||||
If the input adjacency matrix is not symmetric, the Laplacian is
|
||||
also non-symmetric unless ``symmetrized=True`` is used.
|
||||
|
||||
Diagonal entries of the input adjacency matrix are ignored and
|
||||
replaced with zeros for the purpose of normalization where ``normed=True``.
|
||||
The normalization uses the inverse square roots of row-sums of the input
|
||||
adjacency matrix, and thus may fail if the row-sums contain
|
||||
negative or complex with a non-zero imaginary part values.
|
||||
|
||||
The normalization is symmetric, making the normalized Laplacian also
|
||||
symmetric if the input csgraph was symmetric.
|
||||
|
||||
References
|
||||
----------
|
||||
.. [1] Laplacian matrix. https://en.wikipedia.org/wiki/Laplacian_matrix
|
||||
|
||||
Examples
|
||||
--------
|
||||
>>> import numpy as np
|
||||
>>> from scipy.sparse import csgraph
|
||||
|
||||
Our first illustration is the symmetric graph
|
||||
|
||||
>>> G = np.arange(4) * np.arange(4)[:, np.newaxis]
|
||||
>>> G
|
||||
array([[0, 0, 0, 0],
|
||||
[0, 1, 2, 3],
|
||||
[0, 2, 4, 6],
|
||||
[0, 3, 6, 9]])
|
||||
|
||||
and its symmetric Laplacian matrix
|
||||
|
||||
>>> csgraph.laplacian(G)
|
||||
array([[ 0, 0, 0, 0],
|
||||
[ 0, 5, -2, -3],
|
||||
[ 0, -2, 8, -6],
|
||||
[ 0, -3, -6, 9]])
|
||||
|
||||
The non-symmetric graph
|
||||
|
||||
>>> G = np.arange(9).reshape(3, 3)
|
||||
>>> G
|
||||
array([[0, 1, 2],
|
||||
[3, 4, 5],
|
||||
[6, 7, 8]])
|
||||
|
||||
has different row- and column sums, resulting in two varieties
|
||||
of the Laplacian matrix, using an in-degree, which is the default
|
||||
|
||||
>>> L_in_degree = csgraph.laplacian(G)
|
||||
>>> L_in_degree
|
||||
array([[ 9, -1, -2],
|
||||
[-3, 8, -5],
|
||||
[-6, -7, 7]])
|
||||
|
||||
or alternatively an out-degree
|
||||
|
||||
>>> L_out_degree = csgraph.laplacian(G, use_out_degree=True)
|
||||
>>> L_out_degree
|
||||
array([[ 3, -1, -2],
|
||||
[-3, 8, -5],
|
||||
[-6, -7, 13]])
|
||||
|
||||
Constructing a symmetric Laplacian matrix, one can add the two as
|
||||
|
||||
>>> L_in_degree + L_out_degree.T
|
||||
array([[ 12, -4, -8],
|
||||
[ -4, 16, -12],
|
||||
[ -8, -12, 20]])
|
||||
|
||||
or use the ``symmetrized=True`` option
|
||||
|
||||
>>> csgraph.laplacian(G, symmetrized=True)
|
||||
array([[ 12, -4, -8],
|
||||
[ -4, 16, -12],
|
||||
[ -8, -12, 20]])
|
||||
|
||||
that is equivalent to symmetrizing the original graph
|
||||
|
||||
>>> csgraph.laplacian(G + G.T)
|
||||
array([[ 12, -4, -8],
|
||||
[ -4, 16, -12],
|
||||
[ -8, -12, 20]])
|
||||
|
||||
The goal of normalization is to make the non-zero diagonal entries
|
||||
of the Laplacian matrix to be all unit, also scaling off-diagonal
|
||||
entries correspondingly. The normalization can be done manually, e.g.,
|
||||
|
||||
>>> G = np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]])
|
||||
>>> L, d = csgraph.laplacian(G, return_diag=True)
|
||||
>>> L
|
||||
array([[ 2, -1, -1],
|
||||
[-1, 2, -1],
|
||||
[-1, -1, 2]])
|
||||
>>> d
|
||||
array([2, 2, 2])
|
||||
>>> scaling = np.sqrt(d)
|
||||
>>> scaling
|
||||
array([1.41421356, 1.41421356, 1.41421356])
|
||||
>>> (1/scaling)*L*(1/scaling)
|
||||
array([[ 1. , -0.5, -0.5],
|
||||
[-0.5, 1. , -0.5],
|
||||
[-0.5, -0.5, 1. ]])
|
||||
|
||||
Or using ``normed=True`` option
|
||||
|
||||
>>> L, d = csgraph.laplacian(G, return_diag=True, normed=True)
|
||||
>>> L
|
||||
array([[ 1. , -0.5, -0.5],
|
||||
[-0.5, 1. , -0.5],
|
||||
[-0.5, -0.5, 1. ]])
|
||||
|
||||
which now instead of the diagonal returns the scaling coefficients
|
||||
|
||||
>>> d
|
||||
array([1.41421356, 1.41421356, 1.41421356])
|
||||
|
||||
Zero scaling coefficients are substituted with 1s, where scaling
|
||||
has thus no effect, e.g.,
|
||||
|
||||
>>> G = np.array([[0, 0, 0], [0, 0, 1], [0, 1, 0]])
|
||||
>>> G
|
||||
array([[0, 0, 0],
|
||||
[0, 0, 1],
|
||||
[0, 1, 0]])
|
||||
>>> L, d = csgraph.laplacian(G, return_diag=True, normed=True)
|
||||
>>> L
|
||||
array([[ 0., -0., -0.],
|
||||
[-0., 1., -1.],
|
||||
[-0., -1., 1.]])
|
||||
>>> d
|
||||
array([1., 1., 1.])
|
||||
|
||||
Only the symmetric normalization is implemented, resulting
|
||||
in a symmetric Laplacian matrix if and only if its graph is symmetric
|
||||
and has all non-negative degrees, like in the examples above.
|
||||
|
||||
The output Laplacian matrix is by default a dense array or a sparse matrix
|
||||
inferring its shape, format, and dtype from the input graph matrix:
|
||||
|
||||
>>> G = np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]]).astype(np.float32)
|
||||
>>> G
|
||||
array([[0., 1., 1.],
|
||||
[1., 0., 1.],
|
||||
[1., 1., 0.]], dtype=float32)
|
||||
>>> csgraph.laplacian(G)
|
||||
array([[ 2., -1., -1.],
|
||||
[-1., 2., -1.],
|
||||
[-1., -1., 2.]], dtype=float32)
|
||||
|
||||
but can alternatively be generated matrix-free as a LinearOperator:
|
||||
|
||||
>>> L = csgraph.laplacian(G, form="lo")
|
||||
>>> L
|
||||
<3x3 _CustomLinearOperator with dtype=float32>
|
||||
>>> L(np.eye(3))
|
||||
array([[ 2., -1., -1.],
|
||||
[-1., 2., -1.],
|
||||
[-1., -1., 2.]])
|
||||
|
||||
or as a lambda-function:
|
||||
|
||||
>>> L = csgraph.laplacian(G, form="function")
|
||||
>>> L
|
||||
<function _laplace.<locals>.<lambda> at 0x0000012AE6F5A598>
|
||||
>>> L(np.eye(3))
|
||||
array([[ 2., -1., -1.],
|
||||
[-1., 2., -1.],
|
||||
[-1., -1., 2.]])
|
||||
|
||||
The Laplacian matrix is used for
|
||||
spectral data clustering and embedding
|
||||
as well as for spectral graph partitioning.
|
||||
Our final example illustrates the latter
|
||||
for a noisy directed linear graph.
|
||||
|
||||
>>> from scipy.sparse import diags, random
|
||||
>>> from scipy.sparse.linalg import lobpcg
|
||||
|
||||
Create a directed linear graph with ``N=35`` vertices
|
||||
using a sparse adjacency matrix ``G``:
|
||||
|
||||
>>> N = 35
|
||||
>>> G = diags(np.ones(N-1), 1, format="csr")
|
||||
|
||||
Fix a random seed ``rng`` and add a random sparse noise to the graph ``G``:
|
||||
|
||||
>>> rng = np.random.default_rng()
|
||||
>>> G += 1e-2 * random(N, N, density=0.1, random_state=rng)
|
||||
|
||||
Set initial approximations for eigenvectors:
|
||||
|
||||
>>> X = rng.random((N, 2))
|
||||
|
||||
The constant vector of ones is always a trivial eigenvector
|
||||
of the non-normalized Laplacian to be filtered out:
|
||||
|
||||
>>> Y = np.ones((N, 1))
|
||||
|
||||
Alternating (1) the sign of the graph weights allows determining
|
||||
labels for spectral max- and min- cuts in a single loop.
|
||||
Since the graph is undirected, the option ``symmetrized=True``
|
||||
must be used in the construction of the Laplacian.
|
||||
The option ``normed=True`` cannot be used in (2) for the negative weights
|
||||
here as the symmetric normalization evaluates square roots.
|
||||
The option ``form="lo"`` in (2) is matrix-free, i.e., guarantees
|
||||
a fixed memory footprint and read-only access to the graph.
|
||||
Calling the eigenvalue solver ``lobpcg`` (3) computes the Fiedler vector
|
||||
that determines the labels as the signs of its components in (5).
|
||||
Since the sign in an eigenvector is not deterministic and can flip,
|
||||
we fix the sign of the first component to be always +1 in (4).
|
||||
|
||||
>>> for cut in ["max", "min"]:
|
||||
... G = -G # 1.
|
||||
... L = csgraph.laplacian(G, symmetrized=True, form="lo") # 2.
|
||||
... _, eves = lobpcg(L, X, Y=Y, largest=False, tol=1e-3) # 3.
|
||||
... eves *= np.sign(eves[0, 0]) # 4.
|
||||
... print(cut + "-cut labels:\\n", 1 * (eves[:, 0]>0)) # 5.
|
||||
max-cut labels:
|
||||
[1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1]
|
||||
min-cut labels:
|
||||
[1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
|
||||
|
||||
As anticipated for a (slightly noisy) linear graph,
|
||||
the max-cut strips all the edges of the graph coloring all
|
||||
odd vertices into one color and all even vertices into another one,
|
||||
while the balanced min-cut partitions the graph
|
||||
in the middle by deleting a single edge.
|
||||
Both determined partitions are optimal.
|
||||
"""
|
||||
if csgraph.ndim != 2 or csgraph.shape[0] != csgraph.shape[1]:
|
||||
raise ValueError("csgraph must be a square matrix or array")
|
||||
|
||||
if normed and (
|
||||
np.issubdtype(csgraph.dtype, np.signedinteger)
|
||||
or np.issubdtype(csgraph.dtype, np.uint)
|
||||
):
|
||||
csgraph = csgraph.astype(np.float64)
|
||||
|
||||
if form == "array":
|
||||
create_lap = _laplacian_sparse if issparse(csgraph) else _laplacian_dense
|
||||
else:
|
||||
create_lap = (
|
||||
_laplacian_sparse_flo if issparse(csgraph) else _laplacian_dense_flo
|
||||
)
|
||||
|
||||
degree_axis = 1 if use_out_degree else 0
|
||||
|
||||
lap, d = create_lap(
|
||||
csgraph,
|
||||
normed=normed,
|
||||
axis=degree_axis,
|
||||
copy=copy,
|
||||
form=form,
|
||||
dtype=dtype,
|
||||
symmetrized=symmetrized,
|
||||
)
|
||||
if return_diag:
|
||||
return lap, d
|
||||
return lap
|
||||
|
||||
|
||||
def _setdiag_dense(m, d):
|
||||
step = len(d) + 1
|
||||
m.flat[::step] = d
|
||||
|
||||
|
||||
def _laplace(m, d):
|
||||
return lambda v: v * d[:, np.newaxis] - m @ v
|
||||
|
||||
|
||||
def _laplace_normed(m, d, nd):
|
||||
laplace = _laplace(m, d)
|
||||
return lambda v: nd[:, np.newaxis] * laplace(v * nd[:, np.newaxis])
|
||||
|
||||
|
||||
def _laplace_sym(m, d):
|
||||
return (
|
||||
lambda v: v * d[:, np.newaxis]
|
||||
- m @ v
|
||||
- np.transpose(np.conjugate(np.transpose(np.conjugate(v)) @ m))
|
||||
)
|
||||
|
||||
|
||||
def _laplace_normed_sym(m, d, nd):
|
||||
laplace_sym = _laplace_sym(m, d)
|
||||
return lambda v: nd[:, np.newaxis] * laplace_sym(v * nd[:, np.newaxis])
|
||||
|
||||
|
||||
def _linearoperator(mv, shape, dtype):
|
||||
return LinearOperator(matvec=mv, matmat=mv, shape=shape, dtype=dtype)
|
||||
|
||||
|
||||
def _laplacian_sparse_flo(graph, normed, axis, copy, form, dtype, symmetrized):
|
||||
# The keyword argument `copy` is unused and has no effect here.
|
||||
del copy
|
||||
|
||||
if dtype is None:
|
||||
dtype = graph.dtype
|
||||
|
||||
graph_sum = np.asarray(graph.sum(axis=axis)).ravel()
|
||||
graph_diagonal = graph.diagonal()
|
||||
diag = graph_sum - graph_diagonal
|
||||
if symmetrized:
|
||||
graph_sum += np.asarray(graph.sum(axis=1 - axis)).ravel()
|
||||
diag = graph_sum - graph_diagonal - graph_diagonal
|
||||
|
||||
if normed:
|
||||
isolated_node_mask = diag == 0
|
||||
w = np.where(isolated_node_mask, 1, np.sqrt(diag))
|
||||
if symmetrized:
|
||||
md = _laplace_normed_sym(graph, graph_sum, 1.0 / w)
|
||||
else:
|
||||
md = _laplace_normed(graph, graph_sum, 1.0 / w)
|
||||
if form == "function":
|
||||
return md, w.astype(dtype, copy=False)
|
||||
elif form == "lo":
|
||||
m = _linearoperator(md, shape=graph.shape, dtype=dtype)
|
||||
return m, w.astype(dtype, copy=False)
|
||||
else:
|
||||
raise ValueError(f"Invalid form: {form!r}")
|
||||
else:
|
||||
if symmetrized:
|
||||
md = _laplace_sym(graph, graph_sum)
|
||||
else:
|
||||
md = _laplace(graph, graph_sum)
|
||||
if form == "function":
|
||||
return md, diag.astype(dtype, copy=False)
|
||||
elif form == "lo":
|
||||
m = _linearoperator(md, shape=graph.shape, dtype=dtype)
|
||||
return m, diag.astype(dtype, copy=False)
|
||||
else:
|
||||
raise ValueError(f"Invalid form: {form!r}")
|
||||
|
||||
|
||||
def _laplacian_sparse(graph, normed, axis, copy, form, dtype, symmetrized):
|
||||
# The keyword argument `form` is unused and has no effect here.
|
||||
del form
|
||||
|
||||
if dtype is None:
|
||||
dtype = graph.dtype
|
||||
|
||||
needs_copy = False
|
||||
if graph.format in ("lil", "dok"):
|
||||
m = graph.tocoo()
|
||||
else:
|
||||
m = graph
|
||||
if copy:
|
||||
needs_copy = True
|
||||
|
||||
if symmetrized:
|
||||
m += m.T.conj()
|
||||
|
||||
w = np.asarray(m.sum(axis=axis)).ravel() - m.diagonal()
|
||||
if normed:
|
||||
m = m.tocoo(copy=needs_copy)
|
||||
isolated_node_mask = w == 0
|
||||
w = np.where(isolated_node_mask, 1, np.sqrt(w))
|
||||
m.data /= w[m.row]
|
||||
m.data /= w[m.col]
|
||||
m.data *= -1
|
||||
m.setdiag(1 - isolated_node_mask)
|
||||
else:
|
||||
if m.format == "dia":
|
||||
m = m.copy()
|
||||
else:
|
||||
m = m.tocoo(copy=needs_copy)
|
||||
m.data *= -1
|
||||
m.setdiag(w)
|
||||
|
||||
return m.astype(dtype, copy=False), w.astype(dtype)
|
||||
|
||||
|
||||
def _laplacian_dense_flo(graph, normed, axis, copy, form, dtype, symmetrized):
|
||||
if copy:
|
||||
m = np.array(graph)
|
||||
else:
|
||||
m = np.asarray(graph)
|
||||
|
||||
if dtype is None:
|
||||
dtype = m.dtype
|
||||
|
||||
graph_sum = m.sum(axis=axis)
|
||||
graph_diagonal = m.diagonal()
|
||||
diag = graph_sum - graph_diagonal
|
||||
if symmetrized:
|
||||
graph_sum += m.sum(axis=1 - axis)
|
||||
diag = graph_sum - graph_diagonal - graph_diagonal
|
||||
|
||||
if normed:
|
||||
isolated_node_mask = diag == 0
|
||||
w = np.where(isolated_node_mask, 1, np.sqrt(diag))
|
||||
if symmetrized:
|
||||
md = _laplace_normed_sym(m, graph_sum, 1.0 / w)
|
||||
else:
|
||||
md = _laplace_normed(m, graph_sum, 1.0 / w)
|
||||
if form == "function":
|
||||
return md, w.astype(dtype, copy=False)
|
||||
elif form == "lo":
|
||||
m = _linearoperator(md, shape=graph.shape, dtype=dtype)
|
||||
return m, w.astype(dtype, copy=False)
|
||||
else:
|
||||
raise ValueError(f"Invalid form: {form!r}")
|
||||
else:
|
||||
if symmetrized:
|
||||
md = _laplace_sym(m, graph_sum)
|
||||
else:
|
||||
md = _laplace(m, graph_sum)
|
||||
if form == "function":
|
||||
return md, diag.astype(dtype, copy=False)
|
||||
elif form == "lo":
|
||||
m = _linearoperator(md, shape=graph.shape, dtype=dtype)
|
||||
return m, diag.astype(dtype, copy=False)
|
||||
else:
|
||||
raise ValueError(f"Invalid form: {form!r}")
|
||||
|
||||
|
||||
def _laplacian_dense(graph, normed, axis, copy, form, dtype, symmetrized):
|
||||
if form != "array":
|
||||
raise ValueError(f'{form!r} must be "array"')
|
||||
|
||||
if dtype is None:
|
||||
dtype = graph.dtype
|
||||
|
||||
if copy:
|
||||
m = np.array(graph)
|
||||
else:
|
||||
m = np.asarray(graph)
|
||||
|
||||
if dtype is None:
|
||||
dtype = m.dtype
|
||||
|
||||
if symmetrized:
|
||||
m += m.T.conj()
|
||||
np.fill_diagonal(m, 0)
|
||||
w = m.sum(axis=axis)
|
||||
if normed:
|
||||
isolated_node_mask = w == 0
|
||||
w = np.where(isolated_node_mask, 1, np.sqrt(w))
|
||||
m /= w
|
||||
m /= w[:, np.newaxis]
|
||||
m *= -1
|
||||
_setdiag_dense(m, 1 - isolated_node_mask)
|
||||
else:
|
||||
m *= -1
|
||||
_setdiag_dense(m, w)
|
||||
|
||||
return m.astype(dtype, copy=False), w.astype(dtype, copy=False)
|
||||
@@ -0,0 +1,6 @@
|
||||
# Do not collect any tests in externals. This is more robust than using
|
||||
# --ignore because --ignore needs a path and it is not convenient to pass in
|
||||
# the externals path (very long install-dependent path in site-packages) when
|
||||
# using --pyargs
|
||||
def pytest_ignore_collect(path, config):
|
||||
return True
|
||||
Reference in New Issue
Block a user