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232,700 | nerdvegas/rez | src/rezplugins/build_system/custom.py | CustomBuildSystem.build | def build(self, context, variant, build_path, install_path, install=False,
build_type=BuildType.local):
"""Perform the build.
Note that most of the func args aren't used here - that's because this
info is already passed to the custom build command via environment
variables... | python | def build(self, context, variant, build_path, install_path, install=False,
build_type=BuildType.local):
"""Perform the build.
Note that most of the func args aren't used here - that's because this
info is already passed to the custom build command via environment
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232,701 | nerdvegas/rez | src/rezplugins/release_vcs/hg.py | HgReleaseVCS._create_tag_highlevel | def _create_tag_highlevel(self, tag_name, message=None):
"""Create a tag on the toplevel repo if there is no patch repo,
or a tag on the patch repo and bookmark on the top repo if there is a
patch repo
Returns a list where each entry is a dict for each bookmark or tag
created, w... | python | def _create_tag_highlevel(self, tag_name, message=None):
"""Create a tag on the toplevel repo if there is no patch repo,
or a tag on the patch repo and bookmark on the top repo if there is a
patch repo
Returns a list where each entry is a dict for each bookmark or tag
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232,702 | nerdvegas/rez | src/rezplugins/release_vcs/hg.py | HgReleaseVCS._create_tag_lowlevel | def _create_tag_lowlevel(self, tag_name, message=None, force=True,
patch=False):
"""Create a tag on the toplevel or patch repo
If the tag exists, and force is False, no tag is made. If force is True,
and a tag exists, but it is a direct ancestor of the current commi... | python | def _create_tag_lowlevel(self, tag_name, message=None, force=True,
patch=False):
"""Create a tag on the toplevel or patch repo
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232,703 | nerdvegas/rez | src/rezplugins/release_vcs/hg.py | HgReleaseVCS.is_ancestor | def is_ancestor(self, commit1, commit2, patch=False):
"""Returns True if commit1 is a direct ancestor of commit2, or False
otherwise.
This method considers a commit to be a direct ancestor of itself"""
result = self.hg("log", "-r", "first(%s::%s)" % (commit1, commit2),
... | python | def is_ancestor(self, commit1, commit2, patch=False):
"""Returns True if commit1 is a direct ancestor of commit2, or False
otherwise.
This method considers a commit to be a direct ancestor of itself"""
result = self.hg("log", "-r", "first(%s::%s)" % (commit1, commit2),
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232,704 | nerdvegas/rez | src/rez/utils/patching.py | get_patched_request | def get_patched_request(requires, patchlist):
"""Apply patch args to a request.
For example, consider:
>>> print get_patched_request(["foo-5", "bah-8.1"], ["foo-6"])
["foo-6", "bah-8.1"]
>>> print get_patched_request(["foo-5", "bah-8.1"], ["^bah"])
["foo-5"]
The following ... | python | def get_patched_request(requires, patchlist):
"""Apply patch args to a request.
For example, consider:
>>> print get_patched_request(["foo-5", "bah-8.1"], ["foo-6"])
["foo-6", "bah-8.1"]
>>> print get_patched_request(["foo-5", "bah-8.1"], ["^bah"])
["foo-5"]
The following ... | [
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>>> print get_patched_request(["foo-5", "bah-8.1"], ["^bah"])
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232,705 | nerdvegas/rez | src/support/shotgun_toolkit/rez_app_launch.py | AppLaunch.execute | def execute(self, app_path, app_args, version, **kwargs):
"""
The execute functon of the hook will be called to start the required application
:param app_path: (str) The path of the application executable
:param app_args: (str) Any arguments the application may require
:param ve... | python | def execute(self, app_path, app_args, version, **kwargs):
"""
The execute functon of the hook will be called to start the required application
:param app_path: (str) The path of the application executable
:param app_args: (str) Any arguments the application may require
:param ve... | [
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232,706 | nerdvegas/rez | src/support/shotgun_toolkit/rez_app_launch.py | AppLaunch.check_rez | def check_rez(self, strict=True):
"""
Checks to see if a Rez package is available in the current environment.
If it is available, add it to the system path, exposing the Rez Python API
:param strict: (bool) If True, raise an error if Rez is not available as a package.
... | python | def check_rez(self, strict=True):
"""
Checks to see if a Rez package is available in the current environment.
If it is available, add it to the system path, exposing the Rez Python API
:param strict: (bool) If True, raise an error if Rez is not available as a package.
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232,707 | nerdvegas/rez | src/rezplugins/release_vcs/svn.py | get_last_changed_revision | def get_last_changed_revision(client, url):
"""
util func, get last revision of url
"""
try:
svn_entries = client.info2(url,
pysvn.Revision(pysvn.opt_revision_kind.head),
recurse=False)
if not svn_entries:
... | python | def get_last_changed_revision(client, url):
"""
util func, get last revision of url
"""
try:
svn_entries = client.info2(url,
pysvn.Revision(pysvn.opt_revision_kind.head),
recurse=False)
if not svn_entries:
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232,708 | nerdvegas/rez | src/rezplugins/release_vcs/svn.py | get_svn_login | def get_svn_login(realm, username, may_save):
"""
provide svn with permissions. @TODO this will have to be updated to take
into account automated releases etc.
"""
import getpass
print "svn requires a password for the user %s:" % username
pwd = ''
while not pwd.strip():
pwd = ge... | python | def get_svn_login(realm, username, may_save):
"""
provide svn with permissions. @TODO this will have to be updated to take
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"""
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print "svn requires a password for the user %s:" % username
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232,709 | nerdvegas/rez | src/rez/vendor/pygraph/readwrite/markup.py | read | def read(string):
"""
Read a graph from a XML document and return it. Nodes and edges specified in the input will
be added to the current graph.
@type string: string
@param string: Input string in XML format specifying a graph.
@rtype: graph
@return: Graph
"""
dom = parseS... | python | def read(string):
"""
Read a graph from a XML document and return it. Nodes and edges specified in the input will
be added to the current graph.
@type string: string
@param string: Input string in XML format specifying a graph.
@rtype: graph
@return: Graph
"""
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232,710 | nerdvegas/rez | src/rez/vendor/pygraph/readwrite/markup.py | read_hypergraph | def read_hypergraph(string):
"""
Read a graph from a XML document. Nodes and hyperedges specified in the input will be added
to the current graph.
@type string: string
@param string: Input string in XML format specifying a graph.
@rtype: hypergraph
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... | python | def read_hypergraph(string):
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@type string: string
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232,711 | nerdvegas/rez | src/rez/utils/diff_packages.py | diff_packages | def diff_packages(pkg1, pkg2=None):
"""Invoke a diff editor to show the difference between the source of two
packages.
Args:
pkg1 (`Package`): Package to diff.
pkg2 (`Package`): Package to diff against. If None, the next most recent
package version is used.
"""
if pkg2 i... | python | def diff_packages(pkg1, pkg2=None):
"""Invoke a diff editor to show the difference between the source of two
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Args:
pkg1 (`Package`): Package to diff.
pkg2 (`Package`): Package to diff against. If None, the next most recent
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232,712 | nerdvegas/rez | src/rez/cli/_util.py | sigint_handler | def sigint_handler(signum, frame):
"""Exit gracefully on ctrl-C."""
global _handled_int
if not _handled_int:
_handled_int = True
if not _env_var_true("_REZ_QUIET_ON_SIG"):
print >> sys.stderr, "Interrupted by user"
sigbase_handler(signum, frame) | python | def sigint_handler(signum, frame):
"""Exit gracefully on ctrl-C."""
global _handled_int
if not _handled_int:
_handled_int = True
if not _env_var_true("_REZ_QUIET_ON_SIG"):
print >> sys.stderr, "Interrupted by user"
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232,713 | nerdvegas/rez | src/rez/cli/_util.py | sigterm_handler | def sigterm_handler(signum, frame):
"""Exit gracefully on terminate."""
global _handled_term
if not _handled_term:
_handled_term = True
if not _env_var_true("_REZ_QUIET_ON_SIG"):
print >> sys.stderr, "Terminated by user"
sigbase_handler(signum, frame) | python | def sigterm_handler(signum, frame):
"""Exit gracefully on terminate."""
global _handled_term
if not _handled_term:
_handled_term = True
if not _env_var_true("_REZ_QUIET_ON_SIG"):
print >> sys.stderr, "Terminated by user"
sigbase_handler(signum, frame) | [
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232,714 | nerdvegas/rez | src/rez/cli/_util.py | LazyArgumentParser.format_help | def format_help(self):
"""Sets up all sub-parsers when help is requested."""
if self._subparsers:
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if isinstance(action, LazySubParsersAction):
for parser_name, parser in action._name_parser_map.iteritems():
... | python | def format_help(self):
"""Sets up all sub-parsers when help is requested."""
if self._subparsers:
for action in self._subparsers._actions:
if isinstance(action, LazySubParsersAction):
for parser_name, parser in action._name_parser_map.iteritems():
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232,715 | nerdvegas/rez | src/rez/utils/formatting.py | is_valid_package_name | def is_valid_package_name(name, raise_error=False):
"""Test the validity of a package name string.
Args:
name (str): Name to test.
raise_error (bool): If True, raise an exception on failure
Returns:
bool.
"""
is_valid = PACKAGE_NAME_REGEX.match(name)
if raise_error and ... | python | def is_valid_package_name(name, raise_error=False):
"""Test the validity of a package name string.
Args:
name (str): Name to test.
raise_error (bool): If True, raise an exception on failure
Returns:
bool.
"""
is_valid = PACKAGE_NAME_REGEX.match(name)
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232,716 | nerdvegas/rez | src/rez/utils/formatting.py | expand_abbreviations | def expand_abbreviations(txt, fields):
"""Expand abbreviations in a format string.
If an abbreviation does not match a field, or matches multiple fields, it
is left unchanged.
Example:
>>> fields = ("hey", "there", "dude")
>>> expand_abbreviations("hello {d}", fields)
'hello d... | python | def expand_abbreviations(txt, fields):
"""Expand abbreviations in a format string.
If an abbreviation does not match a field, or matches multiple fields, it
is left unchanged.
Example:
>>> fields = ("hey", "there", "dude")
>>> expand_abbreviations("hello {d}", fields)
'hello d... | [
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232,717 | nerdvegas/rez | src/rez/utils/formatting.py | dict_to_attributes_code | def dict_to_attributes_code(dict_):
"""Given a nested dict, generate a python code equivalent.
Example:
>>> d = {'foo': 'bah', 'colors': {'red': 1, 'blue': 2}}
>>> print dict_to_attributes_code(d)
foo = 'bah'
colors.red = 1
colors.blue = 2
Returns:
str.
... | python | def dict_to_attributes_code(dict_):
"""Given a nested dict, generate a python code equivalent.
Example:
>>> d = {'foo': 'bah', 'colors': {'red': 1, 'blue': 2}}
>>> print dict_to_attributes_code(d)
foo = 'bah'
colors.red = 1
colors.blue = 2
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str.
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232,718 | nerdvegas/rez | src/rez/utils/formatting.py | columnise | def columnise(rows, padding=2):
"""Print rows of entries in aligned columns."""
strs = []
maxwidths = {}
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for i, e in enumerate(row):
se = str(e)
nse = len(se)
w = maxwidths.get(i, -1)
if nse > w:
maxwidths[i] = nse... | python | def columnise(rows, padding=2):
"""Print rows of entries in aligned columns."""
strs = []
maxwidths = {}
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for i, e in enumerate(row):
se = str(e)
nse = len(se)
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232,719 | nerdvegas/rez | src/rez/utils/formatting.py | print_colored_columns | def print_colored_columns(printer, rows, padding=2):
"""Like `columnise`, but with colored rows.
Args:
printer (`colorize.Printer`): Printer object.
Note:
The last entry in each row is the row color, or None for no coloring.
"""
rows_ = [x[:-1] for x in rows]
colors = [x[-1] fo... | python | def print_colored_columns(printer, rows, padding=2):
"""Like `columnise`, but with colored rows.
Args:
printer (`colorize.Printer`): Printer object.
Note:
The last entry in each row is the row color, or None for no coloring.
"""
rows_ = [x[:-1] for x in rows]
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232,720 | nerdvegas/rez | src/rez/utils/formatting.py | expanduser | def expanduser(path):
"""Expand '~' to home directory in the given string.
Note that this function deliberately differs from the builtin
os.path.expanduser() on Linux systems, which expands strings such as
'~sclaus' to that user's homedir. This is problematic in rez because the
string '~packagename... | python | def expanduser(path):
"""Expand '~' to home directory in the given string.
Note that this function deliberately differs from the builtin
os.path.expanduser() on Linux systems, which expands strings such as
'~sclaus' to that user's homedir. This is problematic in rez because the
string '~packagename... | [
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232,721 | nerdvegas/rez | src/rez/utils/formatting.py | as_block_string | def as_block_string(txt):
"""Return a string formatted as a python block comment string, like the one
you're currently reading. Special characters are escaped if necessary.
"""
import json
lines = []
for line in txt.split('\n'):
line_ = json.dumps(line)
line_ = line_[1:-1].rstri... | python | def as_block_string(txt):
"""Return a string formatted as a python block comment string, like the one
you're currently reading. Special characters are escaped if necessary.
"""
import json
lines = []
for line in txt.split('\n'):
line_ = json.dumps(line)
line_ = line_[1:-1].rstri... | [
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232,722 | nerdvegas/rez | src/rez/utils/formatting.py | StringFormatMixin.format | def format(self, s, pretty=None, expand=None):
"""Format a string.
Args:
s (str): String to format, eg "hello {name}"
pretty (bool): If True, references to non-string attributes such as
lists are converted to basic form, with characters such as
br... | python | def format(self, s, pretty=None, expand=None):
"""Format a string.
Args:
s (str): String to format, eg "hello {name}"
pretty (bool): If True, references to non-string attributes such as
lists are converted to basic form, with characters such as
br... | [
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232,723 | nerdvegas/rez | src/rez/vendor/version/version.py | Version.copy | def copy(self):
"""Returns a copy of the version."""
other = Version(None)
other.tokens = self.tokens[:]
other.seps = self.seps[:]
return other | python | def copy(self):
"""Returns a copy of the version."""
other = Version(None)
other.tokens = self.tokens[:]
other.seps = self.seps[:]
return other | [
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232,724 | nerdvegas/rez | src/rez/vendor/version/version.py | Version.trim | def trim(self, len_):
"""Return a copy of the version, possibly with less tokens.
Args:
len_ (int): New version length. If >= current length, an
unchanged copy of the version is returned.
"""
other = Version(None)
other.tokens = self.tokens[:len_]
... | python | def trim(self, len_):
"""Return a copy of the version, possibly with less tokens.
Args:
len_ (int): New version length. If >= current length, an
unchanged copy of the version is returned.
"""
other = Version(None)
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232,725 | nerdvegas/rez | src/rez/vendor/version/version.py | VersionRange.union | def union(self, other):
"""OR together version ranges.
Calculates the union of this range with one or more other ranges.
Args:
other: VersionRange object (or list of) to OR with.
Returns:
New VersionRange object representing the union.
"""
if no... | python | def union(self, other):
"""OR together version ranges.
Calculates the union of this range with one or more other ranges.
Args:
other: VersionRange object (or list of) to OR with.
Returns:
New VersionRange object representing the union.
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232,726 | nerdvegas/rez | src/rez/vendor/version/version.py | VersionRange.intersection | def intersection(self, other):
"""AND together version ranges.
Calculates the intersection of this range with one or more other ranges.
Args:
other: VersionRange object (or list of) to AND with.
Returns:
New VersionRange object representing the intersection, or... | python | def intersection(self, other):
"""AND together version ranges.
Calculates the intersection of this range with one or more other ranges.
Args:
other: VersionRange object (or list of) to AND with.
Returns:
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232,727 | nerdvegas/rez | src/rez/vendor/version/version.py | VersionRange.inverse | def inverse(self):
"""Calculate the inverse of the range.
Returns:
New VersionRange object representing the inverse of this range, or
None if there is no inverse (ie, this range is the any range).
"""
if self.is_any():
return None
else:
... | python | def inverse(self):
"""Calculate the inverse of the range.
Returns:
New VersionRange object representing the inverse of this range, or
None if there is no inverse (ie, this range is the any range).
"""
if self.is_any():
return None
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232,728 | nerdvegas/rez | src/rez/vendor/version/version.py | VersionRange.split | def split(self):
"""Split into separate contiguous ranges.
Returns:
A list of VersionRange objects. For example, the range "3|5+" will
be split into ["3", "5+"].
"""
ranges = []
for bound in self.bounds:
range = VersionRange(None)
... | python | def split(self):
"""Split into separate contiguous ranges.
Returns:
A list of VersionRange objects. For example, the range "3|5+" will
be split into ["3", "5+"].
"""
ranges = []
for bound in self.bounds:
range = VersionRange(None)
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232,729 | nerdvegas/rez | src/rez/vendor/version/version.py | VersionRange.as_span | def as_span(cls, lower_version=None, upper_version=None,
lower_inclusive=True, upper_inclusive=True):
"""Create a range from lower_version..upper_version.
Args:
lower_version: Version object representing lower bound of the range.
upper_version: Version object rep... | python | def as_span(cls, lower_version=None, upper_version=None,
lower_inclusive=True, upper_inclusive=True):
"""Create a range from lower_version..upper_version.
Args:
lower_version: Version object representing lower bound of the range.
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232,730 | nerdvegas/rez | src/rez/vendor/version/version.py | VersionRange.from_version | def from_version(cls, version, op=None):
"""Create a range from a version.
Args:
version: Version object. This is used as the upper/lower bound of
the range.
op: Operation as a string. One of 'gt'/'>', 'gte'/'>=', lt'/'<',
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"""Create a range from a version.
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version: Version object. This is used as the upper/lower bound of
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232,731 | nerdvegas/rez | src/rez/vendor/version/version.py | VersionRange.from_versions | def from_versions(cls, versions):
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Args:
versions: List of Version objects.
Returns:
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"""Create a range from a list of versions.
This method creates a range that contains only the given versions and
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Args:
versions: List of Version objects.
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232,732 | nerdvegas/rez | src/rez/vendor/version/version.py | VersionRange.to_versions | def to_versions(self):
"""Returns exact version ranges as Version objects, or None if there
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"""
versions = []
for bound in self.bounds:
if bound.lower.inclusive and bound.upper.inclusive \
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"""Returns exact version ranges as Version objects, or None if there
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"""
versions = []
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if bound.lower.inclusive and bound.upper.inclusive \
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232,733 | nerdvegas/rez | src/rez/vendor/version/version.py | VersionRange.contains_version | def contains_version(self, version):
"""Returns True if version is contained in this range."""
if len(self.bounds) < 5:
# not worth overhead of binary search
for bound in self.bounds:
i = bound.version_containment(version)
if i == 0:
... | python | def contains_version(self, version):
"""Returns True if version is contained in this range."""
if len(self.bounds) < 5:
# not worth overhead of binary search
for bound in self.bounds:
i = bound.version_containment(version)
if i == 0:
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232,734 | nerdvegas/rez | src/rez/vendor/version/version.py | VersionRange.iter_intersecting | def iter_intersecting(self, iterable, key=None, descending=False):
"""Like `iter_intersect_test`, but returns intersections only.
Returns:
An iterator that returns items from `iterable` that intersect.
"""
return _ContainsVersionIterator(self, iterable, key, descending,
... | python | def iter_intersecting(self, iterable, key=None, descending=False):
"""Like `iter_intersect_test`, but returns intersections only.
Returns:
An iterator that returns items from `iterable` that intersect.
"""
return _ContainsVersionIterator(self, iterable, key, descending,
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232,735 | nerdvegas/rez | src/rez/vendor/version/version.py | VersionRange.iter_non_intersecting | def iter_non_intersecting(self, iterable, key=None, descending=False):
"""Like `iter_intersect_test`, but returns non-intersections only.
Returns:
An iterator that returns items from `iterable` that don't intersect.
"""
return _ContainsVersionIterator(self, iterable, key, de... | python | def iter_non_intersecting(self, iterable, key=None, descending=False):
"""Like `iter_intersect_test`, but returns non-intersections only.
Returns:
An iterator that returns items from `iterable` that don't intersect.
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232,736 | nerdvegas/rez | src/rez/vendor/version/version.py | VersionRange.span | def span(self):
"""Return a contiguous range that is a superset of this range.
Returns:
A VersionRange object representing the span of this range. For
example, the span of "2+<4|6+<8" would be "2+<8".
"""
other = VersionRange(None)
bound = _Bound(self.bou... | python | def span(self):
"""Return a contiguous range that is a superset of this range.
Returns:
A VersionRange object representing the span of this range. For
example, the span of "2+<4|6+<8" would be "2+<8".
"""
other = VersionRange(None)
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232,737 | nerdvegas/rez | src/rez/vendor/version/version.py | VersionRange.visit_versions | def visit_versions(self, func):
"""Visit each version in the range, and apply a function to each.
This is for advanced usage only.
If `func` returns a `Version`, this call will change the versions in
place.
It is possible to change versions in a way that is nonsensical - for
... | python | def visit_versions(self, func):
"""Visit each version in the range, and apply a function to each.
This is for advanced usage only.
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232,738 | getsentry/raven-python | raven/transport/http.py | HTTPTransport.send | def send(self, url, data, headers):
"""
Sends a request to a remote webserver using HTTP POST.
"""
req = urllib2.Request(url, headers=headers)
try:
response = urlopen(
url=req,
data=data,
timeout=self.timeout,
... | python | def send(self, url, data, headers):
"""
Sends a request to a remote webserver using HTTP POST.
"""
req = urllib2.Request(url, headers=headers)
try:
response = urlopen(
url=req,
data=data,
timeout=self.timeout,
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232,739 | getsentry/raven-python | raven/contrib/django/views.py | extract_auth_vars | def extract_auth_vars(request):
"""
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"""
if request.META.get('HTTP_X_SENTRY_AUTH', '').startswith('Sentry'):
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elif request.META.get('HTTP_AU... | python | def extract_auth_vars(request):
"""
raven-js will pass both Authorization and X-Sentry-Auth depending on the browser
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"""
if request.META.get('HTTP_X_SENTRY_AUTH', '').startswith('Sentry'):
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232,740 | getsentry/raven-python | raven/events.py | Exception._get_value | def _get_value(self, exc_type, exc_value, exc_traceback):
"""
Convert exception info to a value for the values list.
"""
stack_info = get_stack_info(
iter_traceback_frames(exc_traceback),
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capture_locals=self.client.capture_l... | python | def _get_value(self, exc_type, exc_value, exc_traceback):
"""
Convert exception info to a value for the values list.
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232,741 | getsentry/raven-python | raven/breadcrumbs.py | record | def record(message=None, timestamp=None, level=None, category=None,
data=None, type=None, processor=None):
"""Records a breadcrumb for all active clients. This is what integration
code should use rather than invoking the `captureBreadcrumb` method
on a specific client.
"""
if timestamp i... | python | def record(message=None, timestamp=None, level=None, category=None,
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232,742 | getsentry/raven-python | raven/breadcrumbs.py | ignore_logger | def ignore_logger(name_or_logger, allow_level=None):
"""Ignores a logger during breadcrumb recording.
"""
def handler(logger, level, msg, args, kwargs):
if allow_level is not None and \
level >= allow_level:
return False
return True
register_special_log_handler(nam... | python | def ignore_logger(name_or_logger, allow_level=None):
"""Ignores a logger during breadcrumb recording.
"""
def handler(logger, level, msg, args, kwargs):
if allow_level is not None and \
level >= allow_level:
return False
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232,743 | getsentry/raven-python | raven/utils/serializer/manager.py | Serializer.transform | def transform(self, value, **kwargs):
"""
Primary function which handles recursively transforming
values via their serializers
"""
if value is None:
return None
objid = id(value)
if objid in self.context:
return '<...>'
self.contex... | python | def transform(self, value, **kwargs):
"""
Primary function which handles recursively transforming
values via their serializers
"""
if value is None:
return None
objid = id(value)
if objid in self.context:
return '<...>'
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232,744 | getsentry/raven-python | raven/contrib/tornado/__init__.py | AsyncSentryClient.send | def send(self, auth_header=None, callback=None, **data):
"""
Serializes the message and passes the payload onto ``send_encoded``.
"""
message = self.encode(data)
return self.send_encoded(message, auth_header=auth_header, callback=callback) | python | def send(self, auth_header=None, callback=None, **data):
"""
Serializes the message and passes the payload onto ``send_encoded``.
"""
message = self.encode(data)
return self.send_encoded(message, auth_header=auth_header, callback=callback) | [
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232,745 | getsentry/raven-python | raven/contrib/tornado/__init__.py | AsyncSentryClient._send_remote | def _send_remote(self, url, data, headers=None, callback=None):
"""
Initialise a Tornado AsyncClient and send the request to the sentry
server. If the callback is a callable, it will be called with the
response.
"""
if headers is None:
headers = {}
re... | python | def _send_remote(self, url, data, headers=None, callback=None):
"""
Initialise a Tornado AsyncClient and send the request to the sentry
server. If the callback is a callable, it will be called with the
response.
"""
if headers is None:
headers = {}
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232,746 | getsentry/raven-python | raven/contrib/tornado/__init__.py | SentryMixin.get_sentry_data_from_request | def get_sentry_data_from_request(self):
"""
Extracts the data required for 'sentry.interfaces.Http' from the
current request being handled by the request handler
:param return: A dictionary.
"""
return {
'request': {
'url': self.request.full_u... | python | def get_sentry_data_from_request(self):
"""
Extracts the data required for 'sentry.interfaces.Http' from the
current request being handled by the request handler
:param return: A dictionary.
"""
return {
'request': {
'url': self.request.full_u... | [
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232,747 | getsentry/raven-python | raven/base.py | Client.get_public_dsn | def get_public_dsn(self, scheme=None):
"""
Returns a public DSN which is consumable by raven-js
>>> # Return scheme-less DSN
>>> print client.get_public_dsn()
>>> # Specify a scheme to use (http or https)
>>> print client.get_public_dsn('https')
"""
if s... | python | def get_public_dsn(self, scheme=None):
"""
Returns a public DSN which is consumable by raven-js
>>> # Return scheme-less DSN
>>> print client.get_public_dsn()
>>> # Specify a scheme to use (http or https)
>>> print client.get_public_dsn('https')
"""
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232,748 | getsentry/raven-python | raven/base.py | Client.capture | def capture(self, event_type, data=None, date=None, time_spent=None,
extra=None, stack=None, tags=None, sample_rate=None,
**kwargs):
"""
Captures and processes an event and pipes it off to SentryClient.send.
To use structured data (interfaces) with capture:
... | python | def capture(self, event_type, data=None, date=None, time_spent=None,
extra=None, stack=None, tags=None, sample_rate=None,
**kwargs):
"""
Captures and processes an event and pipes it off to SentryClient.send.
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232,749 | getsentry/raven-python | raven/base.py | Client._log_failed_submission | def _log_failed_submission(self, data):
"""
Log a reasonable representation of an event that should have been sent
to Sentry
"""
message = data.pop('message', '<no message value>')
output = [message]
if 'exception' in data and 'stacktrace' in data['exception']['va... | python | def _log_failed_submission(self, data):
"""
Log a reasonable representation of an event that should have been sent
to Sentry
"""
message = data.pop('message', '<no message value>')
output = [message]
if 'exception' in data and 'stacktrace' in data['exception']['va... | [
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232,750 | getsentry/raven-python | raven/base.py | Client.send_encoded | def send_encoded(self, message, auth_header=None, **kwargs):
"""
Given an already serialized message, signs the message and passes the
payload off to ``send_remote``.
"""
client_string = 'raven-python/%s' % (raven.VERSION,)
if not auth_header:
timestamp = tim... | python | def send_encoded(self, message, auth_header=None, **kwargs):
"""
Given an already serialized message, signs the message and passes the
payload off to ``send_remote``.
"""
client_string = 'raven-python/%s' % (raven.VERSION,)
if not auth_header:
timestamp = tim... | [
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232,751 | getsentry/raven-python | raven/base.py | Client.captureQuery | def captureQuery(self, query, params=(), engine=None, **kwargs):
"""
Creates an event for a SQL query.
>>> client.captureQuery('SELECT * FROM foo')
"""
return self.capture(
'raven.events.Query', query=query, params=params, engine=engine,
**kwargs) | python | def captureQuery(self, query, params=(), engine=None, **kwargs):
"""
Creates an event for a SQL query.
>>> client.captureQuery('SELECT * FROM foo')
"""
return self.capture(
'raven.events.Query', query=query, params=params, engine=engine,
**kwargs) | [
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232,752 | getsentry/raven-python | raven/base.py | Client.captureBreadcrumb | def captureBreadcrumb(self, *args, **kwargs):
"""
Records a breadcrumb with the current context. They will be
sent with the next event.
"""
# Note: framework integration should not call this method but
# instead use the raven.breadcrumbs.record_breadcrumb function
... | python | def captureBreadcrumb(self, *args, **kwargs):
"""
Records a breadcrumb with the current context. They will be
sent with the next event.
"""
# Note: framework integration should not call this method but
# instead use the raven.breadcrumbs.record_breadcrumb function
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232,753 | getsentry/raven-python | raven/transport/registry.py | TransportRegistry.register_scheme | def register_scheme(self, scheme, cls):
"""
It is possible to inject new schemes at runtime
"""
if scheme in self._schemes:
raise DuplicateScheme()
urlparse.register_scheme(scheme)
# TODO (vng): verify the interface of the new class
self._schemes[sche... | python | def register_scheme(self, scheme, cls):
"""
It is possible to inject new schemes at runtime
"""
if scheme in self._schemes:
raise DuplicateScheme()
urlparse.register_scheme(scheme)
# TODO (vng): verify the interface of the new class
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232,754 | getsentry/raven-python | raven/contrib/flask.py | Sentry.get_http_info | def get_http_info(self, request):
"""
Determine how to retrieve actual data by using request.mimetype.
"""
if self.is_json_type(request.mimetype):
retriever = self.get_json_data
else:
retriever = self.get_form_data
return self.get_http_info_with_re... | python | def get_http_info(self, request):
"""
Determine how to retrieve actual data by using request.mimetype.
"""
if self.is_json_type(request.mimetype):
retriever = self.get_json_data
else:
retriever = self.get_form_data
return self.get_http_info_with_re... | [
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232,755 | getsentry/raven-python | raven/conf/__init__.py | setup_logging | def setup_logging(handler, exclude=EXCLUDE_LOGGER_DEFAULTS):
"""
Configures logging to pipe to Sentry.
- ``exclude`` is a list of loggers that shouldn't go to Sentry.
For a typical Python install:
>>> from raven.handlers.logging import SentryHandler
>>> client = Sentry(...)
>>> setup_logg... | python | def setup_logging(handler, exclude=EXCLUDE_LOGGER_DEFAULTS):
"""
Configures logging to pipe to Sentry.
- ``exclude`` is a list of loggers that shouldn't go to Sentry.
For a typical Python install:
>>> from raven.handlers.logging import SentryHandler
>>> client = Sentry(...)
>>> setup_logg... | [
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>>> from raven.handlers.logging import SentryHandler
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>>> setup_logging(SentryHandler(client))
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232,756 | getsentry/raven-python | raven/utils/stacks.py | to_dict | def to_dict(dictish):
"""
Given something that closely resembles a dictionary, we attempt
to coerce it into a propery dictionary.
"""
if hasattr(dictish, 'iterkeys'):
m = dictish.iterkeys
elif hasattr(dictish, 'keys'):
m = dictish.keys
else:
raise ValueError(dictish)
... | python | def to_dict(dictish):
"""
Given something that closely resembles a dictionary, we attempt
to coerce it into a propery dictionary.
"""
if hasattr(dictish, 'iterkeys'):
m = dictish.iterkeys
elif hasattr(dictish, 'keys'):
m = dictish.keys
else:
raise ValueError(dictish)
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232,757 | getsentry/raven-python | raven/utils/stacks.py | slim_frame_data | def slim_frame_data(frames, frame_allowance=25):
"""
Removes various excess metadata from middle frames which go beyond
``frame_allowance``.
Returns ``frames``.
"""
frames_len = 0
app_frames = []
system_frames = []
for frame in frames:
frames_len += 1
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"""
Removes various excess metadata from middle frames which go beyond
``frame_allowance``.
Returns ``frames``.
"""
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232,758 | getsentry/raven-python | raven/contrib/webpy/utils.py | get_data_from_request | def get_data_from_request():
"""Returns request data extracted from web.ctx."""
return {
'request': {
'url': '%s://%s%s' % (web.ctx['protocol'], web.ctx['host'], web.ctx['path']),
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'method': web.ctx.method,
'data': web.data(),... | python | def get_data_from_request():
"""Returns request data extracted from web.ctx."""
return {
'request': {
'url': '%s://%s%s' % (web.ctx['protocol'], web.ctx['host'], web.ctx['path']),
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232,759 | getsentry/raven-python | raven/contrib/django/resolver.py | get_regex | def get_regex(resolver_or_pattern):
"""Utility method for django's deprecated resolver.regex"""
try:
regex = resolver_or_pattern.regex
except AttributeError:
regex = resolver_or_pattern.pattern.regex
return regex | python | def get_regex(resolver_or_pattern):
"""Utility method for django's deprecated resolver.regex"""
try:
regex = resolver_or_pattern.regex
except AttributeError:
regex = resolver_or_pattern.pattern.regex
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232,760 | getsentry/raven-python | raven/utils/basic.py | once | def once(func):
"""Runs a thing once and once only."""
lock = threading.Lock()
def new_func(*args, **kwargs):
if new_func.called:
return
with lock:
if new_func.called:
return
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new_func.called = True
... | python | def once(func):
"""Runs a thing once and once only."""
lock = threading.Lock()
def new_func(*args, **kwargs):
if new_func.called:
return
with lock:
if new_func.called:
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232,761 | getsentry/raven-python | raven/contrib/django/utils.py | get_host | def get_host(request):
"""
A reimplementation of Django's get_host, without the
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"""
# We try three options, in order of decreasing preference.
if settings.USE_X_FORWARDED_HOST and (
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host = request.META['HTTP... | python | def get_host(request):
"""
A reimplementation of Django's get_host, without the
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"""
# We try three options, in order of decreasing preference.
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232,762 | getsentry/raven-python | raven/contrib/django/models.py | install_middleware | def install_middleware(middleware_name, lookup_names=None):
"""
Install specified middleware
"""
if lookup_names is None:
lookup_names = (middleware_name,)
# default settings.MIDDLEWARE is None
middleware_attr = 'MIDDLEWARE' if getattr(settings,
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"""
Install specified middleware
"""
if lookup_names is None:
lookup_names = (middleware_name,)
# default settings.MIDDLEWARE is None
middleware_attr = 'MIDDLEWARE' if getattr(settings,
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232,763 | sebp/scikit-survival | sksurv/meta/base.py | _fit_and_score | def _fit_and_score(est, x, y, scorer, train_index, test_index, parameters, fit_params, predict_params):
"""Train survival model on given data and return its score on test data"""
X_train, y_train = _safe_split(est, x, y, train_index)
train_params = fit_params.copy()
# Training
est.set_params(**para... | python | def _fit_and_score(est, x, y, scorer, train_index, test_index, parameters, fit_params, predict_params):
"""Train survival model on given data and return its score on test data"""
X_train, y_train = _safe_split(est, x, y, train_index)
train_params = fit_params.copy()
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232,764 | sebp/scikit-survival | sksurv/linear_model/coxnet.py | CoxnetSurvivalAnalysis._interpolate_coefficients | def _interpolate_coefficients(self, alpha):
"""Interpolate coefficients by calculating the weighted average of coefficient vectors corresponding to
neighbors of alpha in the list of alphas constructed during training."""
exact = False
coef_idx = None
for i, val in enumerate(self.... | python | def _interpolate_coefficients(self, alpha):
"""Interpolate coefficients by calculating the weighted average of coefficient vectors corresponding to
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exact = False
coef_idx = None
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232,765 | sebp/scikit-survival | sksurv/linear_model/coxnet.py | CoxnetSurvivalAnalysis.predict | def predict(self, X, alpha=None):
"""The linear predictor of the model.
Parameters
----------
X : array-like, shape = (n_samples, n_features)
Test data of which to calculate log-likelihood from
alpha : float, optional
Constant that multiplies the penalty... | python | def predict(self, X, alpha=None):
"""The linear predictor of the model.
Parameters
----------
X : array-like, shape = (n_samples, n_features)
Test data of which to calculate log-likelihood from
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232,766 | sebp/scikit-survival | sksurv/meta/ensemble_selection.py | BaseEnsembleSelection._create_base_ensemble | def _create_base_ensemble(self, out, n_estimators, n_folds):
"""For each base estimator collect models trained on each fold"""
ensemble_scores = numpy.empty((n_estimators, n_folds))
base_ensemble = numpy.empty_like(ensemble_scores, dtype=numpy.object)
for model, fold, score, est in out:
... | python | def _create_base_ensemble(self, out, n_estimators, n_folds):
"""For each base estimator collect models trained on each fold"""
ensemble_scores = numpy.empty((n_estimators, n_folds))
base_ensemble = numpy.empty_like(ensemble_scores, dtype=numpy.object)
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232,767 | sebp/scikit-survival | sksurv/meta/ensemble_selection.py | BaseEnsembleSelection._create_cv_ensemble | def _create_cv_ensemble(self, base_ensemble, idx_models_included, model_names=None):
"""For each selected base estimator, average models trained on each fold"""
fitted_models = numpy.empty(len(idx_models_included), dtype=numpy.object)
for i, idx in enumerate(idx_models_included):
mod... | python | def _create_cv_ensemble(self, base_ensemble, idx_models_included, model_names=None):
"""For each selected base estimator, average models trained on each fold"""
fitted_models = numpy.empty(len(idx_models_included), dtype=numpy.object)
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232,768 | sebp/scikit-survival | sksurv/meta/ensemble_selection.py | BaseEnsembleSelection._get_base_estimators | def _get_base_estimators(self, X):
"""Takes special care of estimators using custom kernel function
Parameters
----------
X : array, shape = (n_samples, n_features)
Samples to pre-compute kernel matrix from.
Returns
-------
base_estimators : list
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"""Takes special care of estimators using custom kernel function
Parameters
----------
X : array, shape = (n_samples, n_features)
Samples to pre-compute kernel matrix from.
Returns
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base_estimators : list
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232,769 | sebp/scikit-survival | sksurv/meta/ensemble_selection.py | BaseEnsembleSelection._restore_base_estimators | def _restore_base_estimators(self, kernel_cache, out, X, cv):
"""Restore custom kernel functions of estimators for predictions"""
train_folds = {fold: train_index for fold, (train_index, _) in enumerate(cv)}
for idx, fold, _, est in out:
if idx in kernel_cache:
if no... | python | def _restore_base_estimators(self, kernel_cache, out, X, cv):
"""Restore custom kernel functions of estimators for predictions"""
train_folds = {fold: train_index for fold, (train_index, _) in enumerate(cv)}
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232,770 | sebp/scikit-survival | sksurv/meta/ensemble_selection.py | BaseEnsembleSelection._fit_and_score_ensemble | def _fit_and_score_ensemble(self, X, y, cv, **fit_params):
"""Create a cross-validated model by training a model for each fold with the same model parameters"""
fit_params_steps = self._split_fit_params(fit_params)
folds = list(cv.split(X, y))
# Take care of custom kernel functions
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"""Create a cross-validated model by training a model for each fold with the same model parameters"""
fit_params_steps = self._split_fit_params(fit_params)
folds = list(cv.split(X, y))
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232,771 | sebp/scikit-survival | sksurv/meta/ensemble_selection.py | BaseEnsembleSelection.fit | def fit(self, X, y=None, **fit_params):
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----------
X : array-like, shape = (n_samples, n_features)
Training data.
y : array-like, optional
Target data if base estimators are supervised.
Returns
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"""Fit ensemble of models
Parameters
----------
X : array-like, shape = (n_samples, n_features)
Training data.
y : array-like, optional
Target data if base estimators are supervised.
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232,772 | sebp/scikit-survival | sksurv/io/arffwrite.py | writearff | def writearff(data, filename, relation_name=None, index=True):
"""Write ARFF file
Parameters
----------
data : :class:`pandas.DataFrame`
DataFrame containing data
filename : string or file-like object
Path to ARFF file or file-like object. In the latter case,
the handle is ... | python | def writearff(data, filename, relation_name=None, index=True):
"""Write ARFF file
Parameters
----------
data : :class:`pandas.DataFrame`
DataFrame containing data
filename : string or file-like object
Path to ARFF file or file-like object. In the latter case,
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232,773 | sebp/scikit-survival | sksurv/io/arffwrite.py | _write_header | def _write_header(data, fp, relation_name, index):
"""Write header containing attribute names and types"""
fp.write("@relation {0}\n\n".format(relation_name))
if index:
data = data.reset_index()
attribute_names = _sanitize_column_names(data)
for column, series in data.iteritems():
... | python | def _write_header(data, fp, relation_name, index):
"""Write header containing attribute names and types"""
fp.write("@relation {0}\n\n".format(relation_name))
if index:
data = data.reset_index()
attribute_names = _sanitize_column_names(data)
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232,774 | sebp/scikit-survival | sksurv/io/arffwrite.py | _sanitize_column_names | def _sanitize_column_names(data):
"""Replace illegal characters with underscore"""
new_names = {}
for name in data.columns:
new_names[name] = _ILLEGAL_CHARACTER_PAT.sub("_", name)
return new_names | python | def _sanitize_column_names(data):
"""Replace illegal characters with underscore"""
new_names = {}
for name in data.columns:
new_names[name] = _ILLEGAL_CHARACTER_PAT.sub("_", name)
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232,775 | sebp/scikit-survival | sksurv/io/arffwrite.py | _write_data | def _write_data(data, fp):
"""Write the data section"""
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"""Write the data section"""
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232,776 | sebp/scikit-survival | sksurv/meta/stacking.py | Stacking.fit | def fit(self, X, y=None, **fit_params):
"""Fit base estimators.
Parameters
----------
X : array-like, shape = (n_samples, n_features)
Training data.
y : array-like, optional
Target data if base estimators are supervised.
Returns
-------
... | python | def fit(self, X, y=None, **fit_params):
"""Fit base estimators.
Parameters
----------
X : array-like, shape = (n_samples, n_features)
Training data.
y : array-like, optional
Target data if base estimators are supervised.
Returns
-------
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232,777 | sebp/scikit-survival | sksurv/column.py | standardize | def standardize(table, with_std=True):
"""
Perform Z-Normalization on each numeric column of the given table.
Parameters
----------
table : pandas.DataFrame or numpy.ndarray
Data to standardize.
with_std : bool, optional, default: True
If ``False`` data is only centered and not... | python | def standardize(table, with_std=True):
"""
Perform Z-Normalization on each numeric column of the given table.
Parameters
----------
table : pandas.DataFrame or numpy.ndarray
Data to standardize.
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232,778 | sebp/scikit-survival | sksurv/column.py | encode_categorical | def encode_categorical(table, columns=None, **kwargs):
"""
Encode categorical columns with `M` categories into `M-1` columns according
to the one-hot scheme.
Parameters
----------
table : pandas.DataFrame
Table with categorical columns to encode.
columns : list-like, optional, defa... | python | def encode_categorical(table, columns=None, **kwargs):
"""
Encode categorical columns with `M` categories into `M-1` columns according
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table : pandas.DataFrame
Table with categorical columns to encode.
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232,779 | sebp/scikit-survival | sksurv/column.py | categorical_to_numeric | def categorical_to_numeric(table):
"""Encode categorical columns to numeric by converting each category to
an integer value.
Parameters
----------
table : pandas.DataFrame
Table with categorical columns to encode.
Returns
-------
encoded : pandas.DataFrame
Table with ca... | python | def categorical_to_numeric(table):
"""Encode categorical columns to numeric by converting each category to
an integer value.
Parameters
----------
table : pandas.DataFrame
Table with categorical columns to encode.
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232,780 | sebp/scikit-survival | sksurv/util.py | check_y_survival | def check_y_survival(y_or_event, *args, allow_all_censored=False):
"""Check that array correctly represents an outcome for survival analysis.
Parameters
----------
y_or_event : structured array with two fields, or boolean array
If a structured array, it must contain the binary event indicator
... | python | def check_y_survival(y_or_event, *args, allow_all_censored=False):
"""Check that array correctly represents an outcome for survival analysis.
Parameters
----------
y_or_event : structured array with two fields, or boolean array
If a structured array, it must contain the binary event indicator
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232,781 | sebp/scikit-survival | sksurv/util.py | check_arrays_survival | def check_arrays_survival(X, y, **kwargs):
"""Check that all arrays have consistent first dimensions.
Parameters
----------
X : array-like
Data matrix containing feature vectors.
y : structured array with two fields
A structured array containing the binary event indicator
a... | python | def check_arrays_survival(X, y, **kwargs):
"""Check that all arrays have consistent first dimensions.
Parameters
----------
X : array-like
Data matrix containing feature vectors.
y : structured array with two fields
A structured array containing the binary event indicator
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232,782 | sebp/scikit-survival | sksurv/util.py | Surv.from_arrays | def from_arrays(event, time, name_event=None, name_time=None):
"""Create structured array.
Parameters
----------
event : array-like
Event indicator. A boolean array or array with values 0/1.
time : array-like
Observed time.
name_event : str|None
... | python | def from_arrays(event, time, name_event=None, name_time=None):
"""Create structured array.
Parameters
----------
event : array-like
Event indicator. A boolean array or array with values 0/1.
time : array-like
Observed time.
name_event : str|None
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232,783 | sebp/scikit-survival | sksurv/util.py | Surv.from_dataframe | def from_dataframe(event, time, data):
"""Create structured array from data frame.
Parameters
----------
event : object
Identifier of column containing event indicator.
time : object
Identifier of column containing time.
data : pandas.DataFrame
... | python | def from_dataframe(event, time, data):
"""Create structured array from data frame.
Parameters
----------
event : object
Identifier of column containing event indicator.
time : object
Identifier of column containing time.
data : pandas.DataFrame
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232,784 | sebp/scikit-survival | sksurv/ensemble/survival_loss.py | CoxPH.update_terminal_regions | def update_terminal_regions(self, tree, X, y, residual, y_pred,
sample_weight, sample_mask,
learning_rate=1.0, k=0):
"""Least squares does not need to update terminal regions.
But it has to update the predictions.
"""
# upd... | python | def update_terminal_regions(self, tree, X, y, residual, y_pred,
sample_weight, sample_mask,
learning_rate=1.0, k=0):
"""Least squares does not need to update terminal regions.
But it has to update the predictions.
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232,785 | sebp/scikit-survival | sksurv/setup.py | build_from_c_and_cpp_files | def build_from_c_and_cpp_files(extensions):
"""Modify the extensions to build from the .c and .cpp files.
This is useful for releases, this way cython is not required to
run python setup.py install.
"""
for extension in extensions:
sources = []
for sfile in extension.sources:
... | python | def build_from_c_and_cpp_files(extensions):
"""Modify the extensions to build from the .c and .cpp files.
This is useful for releases, this way cython is not required to
run python setup.py install.
"""
for extension in extensions:
sources = []
for sfile in extension.sources:
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232,786 | sebp/scikit-survival | sksurv/svm/survival_svm.py | SurvivalCounter._count_values | def _count_values(self):
"""Return dict mapping relevance level to sample index"""
indices = {yi: [i] for i, yi in enumerate(self.y) if self.status[i]}
return indices | python | def _count_values(self):
"""Return dict mapping relevance level to sample index"""
indices = {yi: [i] for i, yi in enumerate(self.y) if self.status[i]}
return indices | [
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232,787 | sebp/scikit-survival | sksurv/svm/survival_svm.py | BaseSurvivalSVM._create_optimizer | def _create_optimizer(self, X, y, status):
"""Samples are ordered by relevance"""
if self.optimizer is None:
self.optimizer = 'avltree'
times, ranks = y
if self.optimizer == 'simple':
optimizer = SimpleOptimizer(X, status, self.alpha, self.rank_ratio, timeit=sel... | python | def _create_optimizer(self, X, y, status):
"""Samples are ordered by relevance"""
if self.optimizer is None:
self.optimizer = 'avltree'
times, ranks = y
if self.optimizer == 'simple':
optimizer = SimpleOptimizer(X, status, self.alpha, self.rank_ratio, timeit=sel... | [
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232,788 | sebp/scikit-survival | sksurv/svm/survival_svm.py | BaseSurvivalSVM._argsort_and_resolve_ties | def _argsort_and_resolve_ties(time, random_state):
"""Like numpy.argsort, but resolves ties uniformly at random"""
n_samples = len(time)
order = numpy.argsort(time, kind="mergesort")
i = 0
while i < n_samples - 1:
inext = i + 1
while inext < n_samples and... | python | def _argsort_and_resolve_ties(time, random_state):
"""Like numpy.argsort, but resolves ties uniformly at random"""
n_samples = len(time)
order = numpy.argsort(time, kind="mergesort")
i = 0
while i < n_samples - 1:
inext = i + 1
while inext < n_samples and... | [
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232,789 | sebp/scikit-survival | sksurv/linear_model/aft.py | IPCRidge.fit | def fit(self, X, y):
"""Build an accelerated failure time model.
Parameters
----------
X : array-like, shape = (n_samples, n_features)
Data matrix.
y : structured array, shape = (n_samples,)
A structured array containing the binary event indicator
... | python | def fit(self, X, y):
"""Build an accelerated failure time model.
Parameters
----------
X : array-like, shape = (n_samples, n_features)
Data matrix.
y : structured array, shape = (n_samples,)
A structured array containing the binary event indicator
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232,790 | sebp/scikit-survival | sksurv/linear_model/coxph.py | BreslowEstimator.fit | def fit(self, linear_predictor, event, time):
"""Compute baseline cumulative hazard function.
Parameters
----------
linear_predictor : array-like, shape = (n_samples,)
Linear predictor of risk: `X @ coef`.
event : array-like, shape = (n_samples,)
Contain... | python | def fit(self, linear_predictor, event, time):
"""Compute baseline cumulative hazard function.
Parameters
----------
linear_predictor : array-like, shape = (n_samples,)
Linear predictor of risk: `X @ coef`.
event : array-like, shape = (n_samples,)
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232,791 | sebp/scikit-survival | sksurv/linear_model/coxph.py | CoxPHOptimizer.nlog_likelihood | def nlog_likelihood(self, w):
"""Compute negative partial log-likelihood
Parameters
----------
w : array, shape = (n_features,)
Estimate of coefficients
Returns
-------
loss : float
Average negative partial log-likelihood
"""
... | python | def nlog_likelihood(self, w):
"""Compute negative partial log-likelihood
Parameters
----------
w : array, shape = (n_features,)
Estimate of coefficients
Returns
-------
loss : float
Average negative partial log-likelihood
"""
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232,792 | sebp/scikit-survival | sksurv/linear_model/coxph.py | CoxPHOptimizer.update | def update(self, w, offset=0):
"""Compute gradient and Hessian matrix with respect to `w`."""
time = self.time
x = self.x
exp_xw = numpy.exp(offset + numpy.dot(x, w))
n_samples, n_features = x.shape
gradient = numpy.zeros((1, n_features), dtype=float)
hessian = n... | python | def update(self, w, offset=0):
"""Compute gradient and Hessian matrix with respect to `w`."""
time = self.time
x = self.x
exp_xw = numpy.exp(offset + numpy.dot(x, w))
n_samples, n_features = x.shape
gradient = numpy.zeros((1, n_features), dtype=float)
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232,793 | sebp/scikit-survival | sksurv/linear_model/coxph.py | CoxPHSurvivalAnalysis.fit | def fit(self, X, y):
"""Minimize negative partial log-likelihood for provided data.
Parameters
----------
X : array-like, shape = (n_samples, n_features)
Data matrix
y : structured array, shape = (n_samples,)
A structured array containing the binary even... | python | def fit(self, X, y):
"""Minimize negative partial log-likelihood for provided data.
Parameters
----------
X : array-like, shape = (n_samples, n_features)
Data matrix
y : structured array, shape = (n_samples,)
A structured array containing the binary even... | [
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232,794 | sebp/scikit-survival | sksurv/nonparametric.py | _compute_counts | def _compute_counts(event, time, order=None):
"""Count right censored and uncensored samples at each unique time point.
Parameters
----------
event : array
Boolean event indicator.
time : array
Survival time or time of censoring.
order : array or None
Indices to order ... | python | def _compute_counts(event, time, order=None):
"""Count right censored and uncensored samples at each unique time point.
Parameters
----------
event : array
Boolean event indicator.
time : array
Survival time or time of censoring.
order : array or None
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Survival time or time of censoring.
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232,795 | sebp/scikit-survival | sksurv/nonparametric.py | _compute_counts_truncated | def _compute_counts_truncated(event, time_enter, time_exit):
"""Compute counts for left truncated and right censored survival data.
Parameters
----------
event : array
Boolean event indicator.
time_start : array
Time when a subject entered the study.
time_exit : array
... | python | def _compute_counts_truncated(event, time_enter, time_exit):
"""Compute counts for left truncated and right censored survival data.
Parameters
----------
event : array
Boolean event indicator.
time_start : array
Time when a subject entered the study.
time_exit : array
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Time when a subject entered the study.
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Time when a subject left the study due to an
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232,796 | sebp/scikit-survival | sksurv/nonparametric.py | kaplan_meier_estimator | def kaplan_meier_estimator(event, time_exit, time_enter=None, time_min=None):
"""Kaplan-Meier estimator of survival function.
Parameters
----------
event : array-like, shape = (n_samples,)
Contains binary event indicators.
time_exit : array-like, shape = (n_samples,)
Contains event... | python | def kaplan_meier_estimator(event, time_exit, time_enter=None, time_min=None):
"""Kaplan-Meier estimator of survival function.
Parameters
----------
event : array-like, shape = (n_samples,)
Contains binary event indicators.
time_exit : array-like, shape = (n_samples,)
Contains event... | [
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Contains event/censoring times.
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232,797 | sebp/scikit-survival | sksurv/nonparametric.py | nelson_aalen_estimator | def nelson_aalen_estimator(event, time):
"""Nelson-Aalen estimator of cumulative hazard function.
Parameters
----------
event : array-like, shape = (n_samples,)
Contains binary event indicators.
time : array-like, shape = (n_samples,)
Contains event/censoring times.
Returns
... | python | def nelson_aalen_estimator(event, time):
"""Nelson-Aalen estimator of cumulative hazard function.
Parameters
----------
event : array-like, shape = (n_samples,)
Contains binary event indicators.
time : array-like, shape = (n_samples,)
Contains event/censoring times.
Returns
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Contains binary event indicators.
time : array-like, shape = (n_samples,)
Contains event/censoring times.
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232,798 | sebp/scikit-survival | sksurv/nonparametric.py | ipc_weights | def ipc_weights(event, time):
"""Compute inverse probability of censoring weights
Parameters
----------
event : array, shape = (n_samples,)
Boolean event indicator.
time : array, shape = (n_samples,)
Time when a subject experienced an event or was censored.
Returns
-------... | python | def ipc_weights(event, time):
"""Compute inverse probability of censoring weights
Parameters
----------
event : array, shape = (n_samples,)
Boolean event indicator.
time : array, shape = (n_samples,)
Time when a subject experienced an event or was censored.
Returns
-------... | [
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232,799 | sebp/scikit-survival | sksurv/nonparametric.py | SurvivalFunctionEstimator.fit | def fit(self, y):
"""Estimate survival distribution from training data.
Parameters
----------
y : structured array, shape = (n_samples,)
A structured array containing the binary event indicator
as first field, and time of event or time of censoring as
... | python | def fit(self, y):
"""Estimate survival distribution from training data.
Parameters
----------
y : structured array, shape = (n_samples,)
A structured array containing the binary event indicator
as first field, and time of event or time of censoring as
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