SYMBOL INDEX (985 symbols across 71 files)

FILE: doc/sphinxext/docscrape.py
  class Reader (line 12) | class Reader:
    method __init__ (line 15) | def __init__(self, data):
    method __getitem__ (line 29) | def __getitem__(self, n):
    method reset (line 32) | def reset(self):  # noqa: D102
    method read (line 35) | def read(self):  # noqa: D102
    method seek_next_non_empty_line (line 43) | def seek_next_non_empty_line(self):  # noqa: D102
    method eof (line 50) | def eof(self):  # noqa: D102
    method read_to_condition (line 53) | def read_to_condition(self, condition_func):  # noqa: D102
    method read_to_next_empty_line (line 63) | def read_to_next_empty_line(self):  # noqa: D102
    method read_to_next_unindented_line (line 71) | def read_to_next_unindented_line(self):  # noqa: D102
    method peek (line 77) | def peek(self, n=0):  # noqa: D102
    method is_empty (line 83) | def is_empty(self):  # noqa: D102
  class NumpyDocString (line 87) | class NumpyDocString(collections.abc.Mapping):  # noqa: D101
    method __init__ (line 88) | def __init__(self, docstring, config={}):  # noqa: B006
    method __getitem__ (line 114) | def __getitem__(self, key):
    method __setitem__ (line 117) | def __setitem__(self, key, val):
    method __iter__ (line 123) | def __iter__(self):
    method __len__ (line 126) | def __len__(self):
    method _is_at_section (line 129) | def _is_at_section(self):
    method _strip (line 143) | def _strip(self, doc):
    method _read_to_next_section (line 156) | def _read_to_next_section(self):
    method _read_sections (line 167) | def _read_sections(self):
    method _parse_param_list (line 179) | def _parse_param_list(self, content):
    method _parse_see_also (line 202) | def _parse_see_also(self, content):
    method _parse_index (line 257) | def _parse_index(self, section, content):
    method _parse_summary (line 276) | def _parse_summary(self):
    method _parse (line 297) | def _parse(self):
    method _str_header (line 335) | def _str_header(self, name, symbol='-'):
    method _str_indent (line 338) | def _str_indent(self, doc, indent=4):
    method _str_signature (line 344) | def _str_signature(self):
    method _str_summary (line 350) | def _str_summary(self):
    method _str_extended_summary (line 356) | def _str_extended_summary(self):
    method _str_param_list (line 362) | def _str_param_list(self, name):
    method _str_section (line 375) | def _str_section(self, name):
    method _str_see_also (line 383) | def _str_see_also(self, func_role):
    method _str_index (line 409) | def _str_index(self):
    method __str__ (line 419) | def __str__(self, func_role=''):
  function indent (line 443) | def indent(str, indent=4):  # noqa: A002, D103
  function dedent_lines (line 451) | def dedent_lines(lines):
  function header (line 456) | def header(text, style='-'):  # noqa: D103
  class FunctionDoc (line 460) | class FunctionDoc(NumpyDocString):  # noqa: D101
    method __init__ (line 461) | def __init__(self, func, role='func', doc=None, config={}):  # noqa: B006
    method get_func (line 483) | def get_func(self):  # noqa: D102
    method __str__ (line 491) | def __str__(self):
  class ClassDoc (line 508) | class ClassDoc(NumpyDocString):  # noqa: D101
    method __init__ (line 511) | def __init__(self, cls, doc=None, modulename='', func_doc=FunctionDoc,...
    method methods (line 549) | def methods(self):  # noqa: D102
    method properties (line 563) | def properties(self):  # noqa: D102
    method _is_show_member (line 578) | def _is_show_member(self, name):

FILE: doc/sphinxext/docscrape_sphinx.py
  class SphinxDocString (line 10) | class SphinxDocString(NumpyDocString):  # noqa: D101
    method __init__ (line 11) | def __init__(self, docstring, config={}):  # noqa: B006
    method _str_header (line 16) | def _str_header(self, name, symbol='`'):
    method _str_field_list (line 19) | def _str_field_list(self, name):
    method _str_indent (line 22) | def _str_indent(self, doc, indent=4):
    method _str_signature (line 28) | def _str_signature(self):
    method _str_summary (line 35) | def _str_summary(self):
    method _str_extended_summary (line 38) | def _str_extended_summary(self):
    method _str_param_list (line 41) | def _str_param_list(self, name):
    method _obj (line 54) | def _obj(self):
    method _str_member_list (line 61) | def _str_member_list(self, name):
    method _str_section (line 101) | def _str_section(self, name):
    method _str_see_also (line 111) | def _str_see_also(self, func_role):
    method _str_warnings (line 119) | def _str_warnings(self):
    method _str_index (line 126) | def _str_index(self):
    method _str_references (line 142) | def _str_references(self):
    method _str_examples (line 164) | def _str_examples(self):
    method __str__ (line 177) | def __str__(self, indent=0, func_role='obj'):
  class SphinxFunctionDoc (line 196) | class SphinxFunctionDoc(SphinxDocString, FunctionDoc):  # noqa: D101
    method __init__ (line 197) | def __init__(self, obj, doc=None, config={}):  # noqa: B006
  class SphinxClassDoc (line 202) | class SphinxClassDoc(SphinxDocString, ClassDoc):  # noqa: D101
    method __init__ (line 203) | def __init__(self, obj, doc=None, func_doc=None, config={}):  # noqa: ...
  class SphinxObjDoc (line 208) | class SphinxObjDoc(SphinxDocString):  # noqa: D101
    method __init__ (line 209) | def __init__(self, obj, doc=None, config={}):  # noqa: B006
  function get_doc_object (line 214) | def get_doc_object(obj, what=None, doc=None, config={}):  # noqa: B006, ...

FILE: doc/sphinxext/github.py
  function make_link_node (line 24) | def make_link_node(rawtext, app, type, slug, options):  # noqa: A002
  function ghissue_role (line 51) | def ghissue_role(name, rawtext, text, lineno, inliner, options={}, conte...
  function ghuser_role (line 94) | def ghuser_role(name, rawtext, text, lineno, inliner, options={}, conten...
  function ghcommit_role (line 116) | def ghcommit_role(name, rawtext, text, lineno, inliner, options={}, cont...
  function setup (line 147) | def setup(app):

FILE: doc/sphinxext/math_dollar.py
  function dollars_to_math (line 4) | def dollars_to_math(source):
  function process_dollars (line 55) | def process_dollars(app, docname, source):  # noqa: D103
  function mathdollar_docstrings (line 59) | def mathdollar_docstrings(app, what, name, obj, options, lines):  # noqa...
  function setup (line 63) | def setup(app):  # noqa: D103

FILE: doc/sphinxext/numpydoc.py
  function mangle_docstrings (line 32) | def mangle_docstrings(app, what, name, obj, options, lines, reference_of...
  function mangle_signature (line 81) | def mangle_signature(app, what, name, obj, options, sig, retann):  # noq...
  function setup (line 100) | def setup(app, get_doc_object_=get_doc_object):  # noqa: D103
  class ManglingDomainBase (line 129) | class ManglingDomainBase:  # noqa: D101
    method __init__ (line 132) | def __init__(self, *a, **kw):
    method wrap_mangling_directives (line 136) | def wrap_mangling_directives(self):  # noqa: D102
  class NumpyPythonDomain (line 141) | class NumpyPythonDomain(ManglingDomainBase, PythonDomain):  # noqa: D101
  class NumpyCDomain (line 155) | class NumpyCDomain(ManglingDomainBase, CDomain):  # noqa: D101
  function wrap_mangling_directive (line 166) | def wrap_mangling_directive(base_directive, objtype):  # noqa: D103

FILE: src/bids/_version.py
  function get_keywords (line 23) | def get_keywords() -> Dict[str, str]:
  class VersioneerConfig (line 36) | class VersioneerConfig:
  function get_config (line 47) | def get_config() -> VersioneerConfig:
  class NotThisMethod (line 61) | class NotThisMethod(Exception):
  function register_vcs_handler (line 69) | def register_vcs_handler(vcs: str, method: str) -> Callable:  # decorator
  function run_command (line 80) | def run_command(
  function versions_from_parentdir (line 128) | def versions_from_parentdir(
  function git_get_keywords (line 157) | def git_get_keywords(versionfile_abs: str) -> Dict[str, str]:
  function git_versions_from_keywords (line 185) | def git_versions_from_keywords(
  function git_pieces_from_vcs (line 253) | def git_pieces_from_vcs(
  function plus_or_dot (line 390) | def plus_or_dot(pieces: Dict[str, Any]) -> str:
  function render_pep440 (line 397) | def render_pep440(pieces: Dict[str, Any]) -> str:
  function render_pep440_branch (line 422) | def render_pep440_branch(pieces: Dict[str, Any]) -> str:
  function pep440_split_post (line 452) | def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]:
  function render_pep440_pre (line 462) | def render_pep440_pre(pieces: Dict[str, Any]) -> str:
  function render_pep440_post (line 486) | def render_pep440_post(pieces: Dict[str, Any]) -> str:
  function render_pep440_post_branch (line 513) | def render_pep440_post_branch(pieces: Dict[str, Any]) -> str:
  function render_pep440_old (line 542) | def render_pep440_old(pieces: Dict[str, Any]) -> str:
  function render_git_describe (line 564) | def render_git_describe(pieces: Dict[str, Any]) -> str:
  function render_git_describe_long (line 584) | def render_git_describe_long(pieces: Dict[str, Any]) -> str:
  function render (line 604) | def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]:
  function get_versions (line 640) | def get_versions() -> Dict[str, Any]:

FILE: src/bids/cli.py
  class Either (line 17) | class Either(click.ParamType):
    method __init__ (line 51) | def __init__(self, *types):
    method name (line 55) | def name(self):  # noqa: D102
    method convert (line 59) | def convert(self, value, param, ctx):  # noqa: D102
  class PathOrRegex (line 70) | class PathOrRegex(click.ParamType):
    method convert (line 75) | def convert(self, value, param, ctx):  # noqa: D102
  function cli (line 85) | def cli():
  function layout (line 144) | def layout(
  function upgrade (line 191) | def upgrade(root):
  function upgrade_dataset_description (line 222) | def upgrade_dataset_description(description):
  function upgrade_filenames (line 255) | def upgrade_filenames(root, description):  # noqa: D103
  function model_report (line 300) | def model_report(

FILE: src/bids/config.py
  function set_option (line 23) | def set_option(key, value):
  function set_options (line 47) | def set_options(**kwargs):
  function get_option (line 58) | def get_option(key):
  function from_file (line 70) | def from_file(filenames, error_on_missing=True):
  function reset_options (line 89) | def reset_options(update_from_file=False):
  function _update_from_standard_locations (line 103) | def _update_from_standard_locations():

FILE: src/bids/conftest.py
  function config_paths (line 25) | def config_paths():  # noqa: D103
  function extension_initial_dot (line 32) | def extension_initial_dot():  # noqa: D103
  function mock_config (line 39) | def mock_config(config_paths, extension_initial_dot):  # noqa: D103
  function bids_examples (line 49) | def bids_examples():  # noqa: D103
  function tests_dir (line 65) | def tests_dir():  # noqa: D103

FILE: src/bids/due.py
  class InactiveDueCreditCollector (line 28) | class InactiveDueCreditCollector:
    method _donothing (line 31) | def _donothing(self, *args, **kwargs):
    method dcite (line 35) | def dcite(self, *args, **kwargs):
    method __repr__ (line 46) | def __repr__(self):
  function _donothing_func (line 50) | def _donothing_func(*args, **kwargs):

FILE: src/bids/exceptions.py
  class PyBIDSError (line 8) | class PyBIDSError(Exception):
  class ConfigError (line 12) | class ConfigError(ValueError, PyBIDSError):
  class NoMatchError (line 16) | class NoMatchError(ValueError, PyBIDSError):
  class BIDSEntityError (line 20) | class BIDSEntityError(AttributeError, PyBIDSError):
  class TargetError (line 24) | class TargetError(ValueError, PyBIDSError):
  class BIDSValidationError (line 28) | class BIDSValidationError(ValueError, PyBIDSError):
  class BIDSDerivativesValidationError (line 32) | class BIDSDerivativesValidationError(BIDSValidationError):
  class BIDSConflictingValuesError (line 36) | class BIDSConflictingValuesError(BIDSValidationError):
  class BIDSChildDatasetError (line 40) | class BIDSChildDatasetError(ValueError, PyBIDSError):

FILE: src/bids/external/inflect.py
  class UnknownClassicalModeError (line 70) | class UnknownClassicalModeError(Exception):
  class BadNumValueError (line 74) | class BadNumValueError(Exception):
  class BadChunkingOptionError (line 78) | class BadChunkingOptionError(Exception):
  class NumOutOfRangeError (line 82) | class NumOutOfRangeError(Exception):
  class BadUserDefinedPatternError (line 86) | class BadUserDefinedPatternError(Exception):
  class BadRcFileError (line 90) | class BadRcFileError(Exception):
  class BadGenderError (line 94) | class BadGenderError(Exception):
  function print3 (line 101) | def print3(txt: str) -> None:
  function enclose (line 106) | def enclose(s: str) -> str:
  function joinstem (line 110) | def joinstem(cutpoint: Optional[int] = 0, words: Optional[Iterable[str]]...
  function bysize (line 127) | def bysize(words: Iterable[str]) -> Dict[int, set]:
  function make_pl_si_lists (line 144) | def make_pl_si_lists(
  function get_si_pron (line 1696) | def get_si_pron(thecase, word, gender) -> str:
  class Words (line 2023) | class Words(str):
    method __init__ (line 2029) | def __init__(self, orig) -> None:
  class engine (line 2036) | class engine:
    method __init__ (line 2037) | def __init__(self) -> None:
    method _number_args (line 2051) | def _number_args(self):
    method _number_args (line 2055) | def _number_args(self, val):
    method __getattr__ (line 2073) | def __getattr__(self, meth):
    method defnoun (line 2079) | def defnoun(self, singular: str, plural: str) -> int:
    method defverb (line 2090) | def defverb(self, s1: str, p1: str, s2: str, p2: str, s3: str, p3: str...
    method defadj (line 2106) | def defadj(self, singular: str, plural: str) -> int:
    method defa (line 2116) | def defa(self, pattern: str) -> int:
    method defan (line 2125) | def defan(self, pattern: str) -> int:
    method checkpat (line 2134) | def checkpat(self, pattern: Optional[str]) -> None:
    method checkpatplural (line 2146) | def checkpatplural(self, pattern: str) -> None:
    method ud_match (line 2152) | def ud_match(self, word: str, wordlist: List[str]) -> Optional[str]:
    method classical (line 2164) | def classical(self, **kwargs) -> None:
    method num (line 2198) | def num(
    method gender (line 2220) | def gender(self, gender: str) -> None:
    method _get_value_from_ast (line 2237) | def _get_value_from_ast(self, obj):
    method _string_to_substitute (line 2259) | def _string_to_substitute(
    method inflect (line 2291) | def inflect(self, text: str) -> str:
    method postprocess (line 2330) | def postprocess(self, orig: str, inflected) -> str:
    method partition_word (line 2360) | def partition_word(self, text: str) -> Tuple[str, str, str]:
    method plural (line 2367) | def plural(self, text: str, count: Optional[Union[str, int]] = None) -...
    method plural_noun (line 2390) | def plural_noun(self, text: str, count: Optional[Union[str, int]] = No...
    method plural_verb (line 2408) | def plural_verb(self, text: str, count: Optional[Union[str, int]] = No...
    method plural_adj (line 2429) | def plural_adj(self, text: str, count: str = None) -> str:
    method compare (line 2447) | def compare(self, word1: str, word2: str) -> Union[str, bool]:
    method compare_nouns (line 2465) | def compare_nouns(self, word1: str, word2: str) -> Union[str, bool]:
    method compare_verbs (line 2480) | def compare_verbs(self, word1: str, word2: str) -> Union[str, bool]:
    method compare_adjs (line 2495) | def compare_adjs(self, word1: str, word2: str) -> Union[str, bool]:
    method singular_noun (line 2510) | def singular_noun(
    method _plequal (line 2551) | def _plequal(self, word1: str, word2: str, pl) -> Union[str, bool]:  #...
    method _pl_reg_plurals (line 2577) | def _pl_reg_plurals(self, pair: str, stems: str, end1: str, end2: str)...
    method _pl_check_plurals_N (line 2581) | def _pl_check_plurals_N(self, word1: str, word2: str) -> bool:
    method _pl_check_plurals_adj (line 2614) | def _pl_check_plurals_adj(self, word1: str, word2: str) -> bool:
    method get_count (line 2627) | def get_count(self, count: Optional[Union[str, int]] = None) -> Union[...
    method _plnoun (line 2648) | def _plnoun(  # noqa: C901
    method _handle_prepositional_phrase (line 2940) | def _handle_prepositional_phrase(cls, phrase, transform, sep):
    method _find_pivot (line 2966) | def _find_pivot(words, candidates):
    method _pl_special_verb (line 2975) | def _pl_special_verb(  # noqa: C901
    method _pl_general_verb (line 3057) | def _pl_general_verb(
    method _pl_special_adjective (line 3081) | def _pl_special_adjective(
    method _sinoun (line 3118) | def _sinoun(  # noqa: C901
    method a (line 3445) | def a(self, text: str, count: int = 1) -> str:
    method _indef_article (line 3470) | def _indef_article(self, word: str, count: int) -> str:  # noqa: C901
    method no (line 3521) | def no(self, text: str, count: Optional[Union[int, str]] = None) -> str:
    method present_participle (line 3558) | def present_participle(self, word: str) -> str:
    method ordinal (line 3576) | def ordinal(self, num: Union[int, str]) -> str:  # noqa: C901
    method millfn (line 3617) | def millfn(self, ind: int = 0) -> str:
    method unitfn (line 3623) | def unitfn(self, units: int, mindex: int = 0) -> str:
    method tenfn (line 3626) | def tenfn(self, tens, units, mindex=0) -> str:
    method hundfn (line 3638) | def hundfn(self, hundreds: int, tens: int, units: int, mindex: int) ->...
    method group1sub (line 3650) | def group1sub(self, mo: Match) -> str:
    method group1bsub (line 3659) | def group1bsub(self, mo: Match) -> str:
    method group2sub (line 3666) | def group2sub(self, mo: Match) -> str:
    method group3sub (line 3675) | def group3sub(self, mo: Match) -> str:
    method hundsub (line 3693) | def hundsub(self, mo: Match) -> str:
    method tensub (line 3700) | def tensub(self, mo: Match) -> str:
    method unitsub (line 3703) | def unitsub(self, mo: Match) -> str:
    method enword (line 3706) | def enword(self, num: str, group: int) -> str:
    method number_to_words (line 3735) | def number_to_words(  # noqa: C901
    method join (line 3886) | def join(

FILE: src/bids/layout/db.py
  function get_database_file (line 15) | def get_database_file(path):  # noqa: D103
  class ConnectionManager (line 25) | class ConnectionManager:  # noqa: D101
    method __init__ (line 26) | def __init__(self, database_path=None, reset_database=False, config=No...
    method _get_engine (line 45) | def _get_engine(self, database_file):
    method exists (line 99) | def exists(cls, database_path):  # noqa: D102
    method reset_database (line 102) | def reset_database(self, init_args, config):  # noqa: D102
    method save_database (line 114) | def save_database(self, database_path, replace_connection=True):
    method session (line 149) | def session(self):  # noqa: D102
    method layout_info (line 156) | def layout_info(self):  # noqa: D102
    method reset_session (line 159) | def reset_session(self):

FILE: src/bids/layout/index.py
  function _regexfy (line 18) | def _regexfy(patt, root=None):
  function _extract_entities (line 30) | def _extract_entities(bidsfile, entities):
  function _check_path_matches_patterns (line 41) | def _check_path_matches_patterns(path, patterns, root=None):
  function _validate_path (line 62) | def _validate_path(path, incl_patt=None, excl_patt=None, root=None):
  class BIDSLayoutIndexer (line 70) | class BIDSLayoutIndexer:
    method __init__ (line 111) | def __init__(
    method __call__ (line 136) | def __call__(self, layout):  # noqa: D102
    method session (line 160) | def session(self):  # noqa: D102
    method _validate_file (line 163) | def _validate_file(self, f):
    method _index_dir (line 188) | def _index_dir(self, path, config, force=None):
    method _index_file (line 269) | def _index_file(self, abs_fn, entities):
    method _index_metadata (line 289) | def _index_metadata(self):
  function _resolve_intent (line 531) | def _resolve_intent(intent: str, root: Path, subject: str) -> str | None:

FILE: src/bids/layout/layout.py
  function call (line 39) | def call(func, *args, **kwargs):
  class Sentinel (line 46) | class Sentinel:
    method __repr__ (line 47) | def __repr__(self):
  class RemovedOption (line 52) | class RemovedOption(Sentinel):
  class BIDSLayout (line 56) | class BIDSLayout:
    method __init__ (line 116) | def __init__(
    method root (line 220) | def root(self):  # noqa: D102
    method __getattr__ (line 223) | def __getattr__(self, key):
    method __repr__ (line 246) | def __repr__(self):
    method _in_scope (line 280) | def _in_scope(self, scope):
    method _get_layouts_in_scope (line 306) | def _get_layouts_in_scope(self, scope):
    method _sanitize_query_dtypes (line 320) | def _sanitize_query_dtypes(self, entities):
    method session (line 342) | def session(self):  # noqa: D102
    method config (line 347) | def config(self):  # noqa: D102
    method entities (line 351) | def entities(self):
    method files (line 356) | def files(self):
    method load (line 361) | def load(cls, database_path):
    method save (line 375) | def save(self, database_path, replace_connection=True):
    method get_entities (line 409) | def get_entities(self, scope='all', metadata=None):
    method _find_directories_for_entity_using_schema (line 444) | def _find_directories_for_entity_using_schema(self, entity_name, resul...
    method _build_path_from_schema_rules (line 468) | def _build_path_from_schema_rules(self, entities, directory_rules):
    method get_files (line 528) | def get_files(self, scope='all'):
    method clone (line 553) | def clone(self):
    method parse_file_entities (line 557) | def parse_file_entities(
    method _get_derivative_dirs (line 598) | def _get_derivative_dirs(self, paths):
    method add_derivatives (line 610) | def add_derivatives(self, path, parent_database_path=None, **kwargs):
    method to_df (line 666) | def to_df(self, metadata=False, **filters):
    method get (line 715) | def get(  # noqa: D417
    method get_file (line 915) | def get_file(self, filename, scope='all'):
    method _build_file_query (line 941) | def _build_file_query(self, **kwargs):
    method get_collections (line 1012) | def get_collections(
    method get_metadata (line 1068) | def get_metadata(self, path, include_entities=False, scope='all'):
    method get_dataset_description (line 1113) | def get_dataset_description(self, scope='self', all_=False):
    method get_nearest (line 1140) | def get_nearest(  # noqa: D417
    method get_bvec (line 1250) | def get_bvec(self, path, **kwargs):
    method get_bval (line 1255) | def get_bval(self, path, **kwargs):
    method get_fieldmap (line 1260) | def get_fieldmap(self, path, return_list=False):
    method _get_fieldmaps (line 1281) | def _get_fieldmaps(self, path):
    method get_tr (line 1322) | def get_tr(self, derivatives=False, **filters):
    method build_path (line 1360) | def build_path(
    method copy_files (line 1457) | def copy_files(
    method write_to_file (line 1504) | def write_to_file(  # noqa: D417
  class Query (line 1572) | class Query(enum.Enum):

FILE: src/bids/layout/models.py
  class LayoutInfo (line 34) | class LayoutInfo(Base):
    method __init__ (line 44) | def __init__(self, **kwargs):
    method _init_on_load (line 59) | def _init_on_load(self):
    method _sanitize_init_args (line 70) | def _sanitize_init_args(self, kwargs):
    method __repr__ (line 95) | def __repr__(self):
  class Config (line 99) | class Config(Base):
    method __init__ (line 128) | def __init__(self, name, entities=None, default_path_patterns=None, se...
    method _init_on_load (line 146) | def _init_on_load(self):
    method load (line 150) | def load(cls, config, session=None):
    method _from_schema (line 201) | def _from_schema(cls, schema_version=None, session=None):
    method _extract_entity_names_from_rules (line 280) | def _extract_entity_names_from_rules(cls, bids_schema):
    method _create_entities_from_schema (line 305) | def _create_entities_from_schema(cls, entity_names, entity_values, bid...
    method _extract_entity_values_from_rules (line 367) | def _extract_entity_values_from_rules(cls, bids_schema, entity_names):
    method __repr__ (line 396) | def __repr__(self):
  class BIDSFile (line 400) | class BIDSFile(Base):
    method __init__ (line 428) | def __init__(self, filename):
    method _path (line 435) | def _path(self):
    method _dirname (line 439) | def _dirname(self):
    method __repr__ (line 442) | def __repr__(self):
    method __fspath__ (line 445) | def __fspath__(self):
    method relpath (line 450) | def relpath(self):
    method get_associations (line 455) | def get_associations(self, kind=None, include_parents=False):
    method get_metadata (line 503) | def get_metadata(self):
    method get_entities (line 509) | def get_entities(self, metadata=False, values='tags'):
    method copy (line 548) | def copy(self, path_patterns, symbolic_link=False, root=None, conflict...
  class BIDSDataFile (line 594) | class BIDSDataFile(BIDSFile):
    method get_df (line 603) | def get_df(self, include_timing=True, adjust_onset=False, enforce_dtyp...
  class BIDSImageFile (line 662) | class BIDSImageFile(BIDSFile):
    method get_image (line 671) | def get_image(self, **kwargs):
  class BIDSJSONFile (line 686) | class BIDSJSONFile(BIDSFile):
    method get_dict (line 695) | def get_dict(self):
    method get_json (line 705) | def get_json(self):
  class Entity (line 711) | class Entity(Base):
    method __init__ (line 744) | def __init__(self, name, pattern=None, mandatory=False, directory=None...
    method __repr__ (line 756) | def __repr__(self):
    method _init_on_load (line 760) | def _init_on_load(self):
    method __iter__ (line 771) | def __iter__(self):
    method __deepcopy__ (line 774) | def __deepcopy__(self, memo):
    method match_file (line 792) | def match_file(self, f):
    method unique (line 812) | def unique(self):
    method count (line 816) | def count(self, files=False):
    method _astype (line 833) | def _astype(self, val):
  class Tag (line 848) | class Tag(Base):
    method __init__ (line 889) | def __init__(self, file, entity, value, dtype=None, is_metadata=False):
    method __repr__ (line 904) | def __repr__(self):
    method _init_on_load (line 909) | def _init_on_load(self):
  function _create_tag_dict (line 921) | def _create_tag_dict(file, entity, value, dtype=None, is_metadata=False):
  class FileAssociation (line 950) | class FileAssociation(Base):  # noqa: D101
  class DerivativeDatasets (line 967) | class DerivativeDatasets(UserDict):  # noqa: D101
    method __getitem__ (line 968) | def __getitem__(self, key):
    method get_pipeline (line 991) | def get_pipeline(self, pipeline):  # noqa: D102

FILE: src/bids/layout/tests/conftest.py
  function layout_7t_trt (line 11) | def layout_7t_trt(tests_dir):
  function layout_ds005 (line 16) | def layout_ds005(tests_dir):
  function layout_ds005_no_validate (line 21) | def layout_ds005_no_validate(tests_dir):
  function layout_ds117 (line 26) | def layout_ds117(tests_dir):
  function layout_ds005_derivs (line 31) | def layout_ds005_derivs(tests_dir):
  function layout_ds005_deriv_dummy_vxxx (line 40) | def layout_ds005_deriv_dummy_vxxx(tests_dir):
  function layout_ds005_deriv_both_dummies (line 49) | def layout_ds005_deriv_both_dummies(tests_dir):
  function db_dir (line 59) | def db_dir(tmpdir_factory):
  function layout_ds005_multi_derivs (line 65) | def layout_ds005_multi_derivs(tests_dir, request, db_dir):
  function layout_ds005_deriv_name_collision (line 77) | def layout_ds005_deriv_name_collision(tests_dir, request):
  function layout_synthetic (line 88) | def layout_synthetic(tests_dir, request, db_dir):
  function layout_synthetic_nodb (line 95) | def layout_synthetic_nodb(tests_dir, request, db_dir):
  function temporary_dataset (line 101) | def temporary_dataset(tmp_path, tests_dir):

FILE: src/bids/layout/tests/test_db.py
  function test_get_database_file (line 7) | def test_get_database_file(tmp_path):

FILE: src/bids/layout/tests/test_layout.py
  function test_layout_init (line 28) | def test_layout_init(layout_7t_trt):
  function test_index_metadata (line 44) | def test_index_metadata(tests_dir, index_metadata, filters, result, mock...
  function test_config_filename (line 58) | def test_config_filename(tests_dir, config_type):
  function test_layout_repr (line 66) | def test_layout_repr(layout_7t_trt):
  function test_invalid_dataset_description (line 70) | def test_invalid_dataset_description(tests_dir, tmp_path):
  function test_layout_repr_overshadow_run (line 79) | def test_layout_repr_overshadow_run(tests_dir, tmp_path):
  function test_load_description (line 103) | def test_load_description(layout_7t_trt):
  function test_get_file (line 110) | def test_get_file(layout_ds005_derivs):
  class TestDerivativeAsRoot (line 149) | class TestDerivativeAsRoot:
    method test_dataset_without_datasettype_parsed_as_raw (line 150) | def test_dataset_without_datasettype_parsed_as_raw(self, tests_dir):
    method test_derivative_indexing_forced_with_is_derivative (line 160) | def test_derivative_indexing_forced_with_is_derivative(self, tests_dir):
    method test_forced_derivative_indexing_fails_validation (line 169) | def test_forced_derivative_indexing_fails_validation(self, tests_dir):
    method test_dataset_missing_generatedby_fails_validation (line 177) | def test_dataset_missing_generatedby_fails_validation(self, tests_dir):
    method test_correctly_formatted_derivative_loads_as_derivative (line 183) | def test_correctly_formatted_derivative_loads_as_derivative(self, test...
    method test_derivative_datasets_load_with_no_validation (line 195) | def test_derivative_datasets_load_with_no_validation(self, tests_dir, ...
  function test_get_metadata (line 201) | def test_get_metadata(layout_7t_trt):
  function test_get_metadata2 (line 208) | def test_get_metadata2(layout_7t_trt):
  function test_get_metadata3 (line 215) | def test_get_metadata3(layout_7t_trt):
  function test_get_metadata4 (line 227) | def test_get_metadata4(layout_ds005):
  function test_get_metadata_error2 (line 234) | def test_get_metadata_error2(layout_7t_trt):
  function test_get_metadata_meg (line 250) | def test_get_metadata_meg(layout_ds117):
  function test_get_metadata5 (line 269) | def test_get_metadata5(layout_7t_trt):
  function test_get_metadata_via_bidsfile (line 278) | def test_get_metadata_via_bidsfile(layout_7t_trt):
  function test_metadata_equivalence (line 289) | def test_metadata_equivalence(layout_7t_trt):
  function test_get_metadata_error (line 315) | def test_get_metadata_error(layout_7t_trt):
  function test_get_with_bad_target (line 331) | def test_get_with_bad_target(layout_7t_trt):
  function test_get_bvals_bvecs (line 342) | def test_get_bvals_bvecs(layout_ds005):
  function test_get_subjects (line 351) | def test_get_subjects(layout_7t_trt):
  function test_get_fieldmap (line 357) | def test_get_fieldmap(layout_7t_trt):
  function test_get_fieldmap2 (line 365) | def test_get_fieldmap2(layout_7t_trt):
  function test_bids_json (line 373) | def test_bids_json(layout_7t_trt):
  function test_get_return_type_dir (line 380) | def test_get_return_type_dir(layout_7t_trt):
  function test_get_val_none (line 390) | def test_get_val_none(layout_7t_trt, acq):
  function test_get_val_enum_any (line 400) | def test_get_val_enum_any(layout_7t_trt):
  function test_get_val_enum_any_optional (line 411) | def test_get_val_enum_any_optional(layout_7t_trt, layout_ds005):
  function test_get_return_sorted (line 428) | def test_get_return_sorted(layout_7t_trt):
  function test_ignore_files (line 437) | def test_ignore_files(tests_dir, layout_ds005):
  function test_force_index (line 455) | def test_force_index(tests_dir, layout_ds005):
  function test_nested_include_exclude (line 467) | def test_nested_include_exclude(tests_dir):
  function test_nested_include_exclude_with_regex (line 579) | def test_nested_include_exclude_with_regex(tests_dir):
  function test_layout_with_derivs (line 639) | def test_layout_with_derivs(tests_dir, layout_ds005_derivs):
  function test_accessing_deriv_by_pipeline_name_is_deprecated (line 653) | def test_accessing_deriv_by_pipeline_name_is_deprecated(layout_ds005_der...
  function test_cant_access_nonexistant_deriv_by_key (line 660) | def test_cant_access_nonexistant_deriv_by_key(layout_ds005_deriv_dummy_v...
  function test_accessing_deriv_by_pipeline_name_via_method (line 665) | def test_accessing_deriv_by_pipeline_name_via_method(layout_ds005_deriv_...
  function test_cant_get_nonexistant_deriv_via_method (line 671) | def test_cant_get_nonexistant_deriv_via_method(layout_ds005_deriv_dummy_...
  function test_cant_get_deriv_with_duplicate_pipeline_via_method (line 676) | def test_cant_get_deriv_with_duplicate_pipeline_via_method(layout_ds005_...
  function test_layout_with_multi_derivs (line 681) | def test_layout_with_multi_derivs(tests_dir, layout_ds005_multi_derivs):
  function test_layout_with_conflicting_deriv_folders (line 697) | def test_layout_with_conflicting_deriv_folders(tests_dir):
  function test_query_derivatives (line 705) | def test_query_derivatives(layout_ds005_derivs):
  function test_restricted_words_in_path (line 724) | def test_restricted_words_in_path(tests_dir, tmpdir):
  function test_derivative_getters (line 738) | def test_derivative_getters(tests_dir):
  function test_get_tr (line 746) | def test_get_tr(layout_7t_trt):
  function test_get_nonhashable_metadata (line 765) | def test_get_nonhashable_metadata(layout_ds117):
  function test_to_df (line 785) | def test_to_df(layout_ds117):
  function test_parse_file_entities_from_layout (line 815) | def test_parse_file_entities_from_layout(layout_synthetic):
  function test_deriv_indexing (line 851) | def test_deriv_indexing(tests_dir):
  function test_path_arguments (line 867) | def test_path_arguments(tests_dir):
  function test_layout_in_scope (line 882) | def test_layout_in_scope(layout_ds005, layout_ds005_derivs):
  function test_get_layouts_in_scope (line 895) | def test_get_layouts_in_scope(layout_ds005_multi_derivs):
  function test_get_dataset_description (line 907) | def test_get_dataset_description(layout_ds005_multi_derivs):
  function test_indexed_file_associations (line 919) | def test_indexed_file_associations(layout_7t_trt):
  function test_layout_save (line 951) | def test_layout_save(tests_dir, tmp_path, layout_7t_trt):
  function test_indexing_tag_conflict (line 960) | def test_indexing_tag_conflict(tests_dir):
  function test_get_with_wrong_dtypes (line 968) | def test_get_with_wrong_dtypes(layout_7t_trt):
  function test_get_with_regex_search (line 982) | def test_get_with_regex_search(layout_7t_trt):
  function test_get_with_regex_search_bad_dtype (line 1013) | def test_get_with_regex_search_bad_dtype(layout_7t_trt):
  function test_get_with_invalid_filters (line 1031) | def test_get_with_invalid_filters(layout_ds005):
  function test_get_with_query_constants_in_match_list (line 1055) | def test_get_with_query_constants_in_match_list(layout_ds005):
  function test_get_non_run_entity_with_query_constants_in_match_list (line 1068) | def test_get_non_run_entity_with_query_constants_in_match_list(layout_ds...
  function test_query_constants_work_on_extension (line 1081) | def test_query_constants_work_on_extension(layout_ds005_no_validate):
  function test_load_layout (line 1093) | def test_load_layout(layout_synthetic_nodb, db_dir):
  function test_load_layout_config_not_overwritten (line 1106) | def test_load_layout_config_not_overwritten(layout_synthetic_nodb, tmpdir):
  function test_padded_run_roundtrip (line 1134) | def test_padded_run_roundtrip(layout_ds005):
  function test_indexer_patterns (line 1155) | def test_indexer_patterns(fname):
  function test_symlinks_in_path (line 1191) | def test_symlinks_in_path(tests_dir, tmp_path):
  function test_ignore_dotfiles (line 1209) | def test_ignore_dotfiles(temporary_dataset):
  function test_empty_directory (line 1234) | def test_empty_directory(temporary_dataset):
  function test_intended_for (line 1256) | def test_intended_for(temporary_dataset, intent):
  function test_get_return_type_dir_with_schema_datatype (line 1270) | def test_get_return_type_dir_with_schema_datatype(layout_7t_trt):
  function test_get_return_type_dir_with_legacy_config_no_template (line 1286) | def test_get_return_type_dir_with_legacy_config_no_template():
  function test_bids_sort (line 1327) | def test_bids_sort(layout_7t_trt):

FILE: src/bids/layout/tests/test_layout_on_examples.py
  function test_layout_on_examples_with_derivatives (line 32) | def test_layout_on_examples_with_derivatives(dataset, nb_files, bids_exa...
  function test_layout_on_examples_no_derivatives (line 67) | def test_layout_on_examples_no_derivatives(dataset, nb_files, bids_examp...

FILE: src/bids/layout/tests/test_models.py
  function create_session (line 29) | def create_session():
  function sample_bidsfile (line 37) | def sample_bidsfile(tmpdir):
  function subject_entity (line 45) | def subject_entity():
  function test_layoutinfo_init (line 55) | def test_layoutinfo_init():
  function test_entity_initialization (line 73) | def test_entity_initialization():
  function test_entity_init_all_args (line 82) | def test_entity_init_all_args(subject_entity):
  function test_entity_init_with_bad_dtype (line 90) | def test_entity_init_with_bad_dtype():
  function test_entity_matches (line 96) | def test_entity_matches(tmpdir):
  function test_entity_deepcopy (line 105) | def test_entity_deepcopy(subject_entity):
  function test_file_associations (line 113) | def test_file_associations():
  function test_tag_init (line 135) | def test_tag_init(sample_bidsfile, subject_entity):
  function test_tag_dtype (line 142) | def test_tag_dtype(sample_bidsfile, subject_entity):
  function test_entity_add_file (line 157) | def test_entity_add_file(sample_bidsfile):
  function test_config_init_with_args (line 167) | def test_config_init_with_args():
  function test_load_existing_config (line 181) | def test_load_existing_config():
  function test_bidsfile_get_df_from_tsv_gz (line 203) | def test_bidsfile_get_df_from_tsv_gz(layout_synthetic):
  function test_bidsdatafile_enforces_dtype (line 221) | def test_bidsdatafile_enforces_dtype(layout_synthetic):
  function test_bidsimagefile_get_image (line 233) | def test_bidsimagefile_get_image():
  function test_bidsjsonfile (line 242) | def test_bidsjsonfile(layout_synthetic):
  function test_bidsfile_get_metadata (line 253) | def test_bidsfile_get_metadata(layout_synthetic):
  function test_bidsfile_get_entities (line 259) | def test_bidsfile_get_entities(layout_synthetic):
  function test_bidsfile_relpath (line 288) | def test_bidsfile_relpath(layout_synthetic):
  function test_bidsfile_fspath (line 296) | def test_bidsfile_fspath(sample_bidsfile):

FILE: src/bids/layout/tests/test_path_building.py
  function layout (line 13) | def layout():
  function test_path_building_pet (line 18) | def test_path_building_pet(layout):
  function test_bold_construction (line 29) | def test_bold_construction(layout):
  function test_invalid_file_construction (line 39) | def test_invalid_file_construction(layout):
  function test_failed_file_construction (line 49) | def test_failed_file_construction(layout):
  function test_insufficient_entities (line 57) | def test_insufficient_entities(layout, strict, validate):
  function test_path_building_on_derivative_examples (line 84) | def test_path_building_on_derivative_examples(dataset, bids_examples):
  function test_path_building_in_raw_scope (line 133) | def test_path_building_in_raw_scope(dataset, bids_examples):
  function test_path_building_on_examples_with_meg_ds_folder (line 144) | def test_path_building_on_examples_with_meg_ds_folder(dataset, scope, bi...

FILE: src/bids/layout/tests/test_remote_bids.py
  function test_layout_on_s3_datasets_no_derivatives (line 23) | def test_layout_on_s3_datasets_no_derivatives(dataset, nb_files):

FILE: src/bids/layout/tests/test_rootpath.py
  function test_strroot_pos (line 19) | def test_strroot_pos():
  function test_strroot_neg (line 23) | def test_strroot_neg():
  function test_pathroot_pos (line 28) | def test_pathroot_pos():
  function test_pathroot_neg (line 32) | def test_pathroot_neg():

FILE: src/bids/layout/tests/test_schema_config.py
  class TestSchemaConfig (line 8) | class TestSchemaConfig:
    method test_load_bids_schema_basic (line 11) | def test_load_bids_schema_basic(self):
    method test_schema_entity_patterns (line 28) | def test_schema_entity_patterns(self):
    method test_schema_version_tracking (line 50) | def test_schema_version_tracking(self):
    method test_schema_version_parameter (line 60) | def test_schema_version_parameter(self):
    method test_invalid_schema_version (line 70) | def test_invalid_schema_version(self):
    method test_entity_generation (line 76) | def test_entity_generation(self):
    method test_schema_directory_query (line 115) | def test_schema_directory_query(self):

FILE: src/bids/layout/tests/test_schema_pattern_validation.py
  class TestSchemaAccuracy (line 8) | class TestSchemaAccuracy:
    method test_extension_patterns_match_schema (line 11) | def test_extension_patterns_match_schema(self):
    method test_suffix_patterns_match_schema (line 64) | def test_suffix_patterns_match_schema(self):
    method test_datatype_patterns_match_schema (line 116) | def test_datatype_patterns_match_schema(self):
    method test_entity_format_patterns_match_schema (line 157) | def test_entity_format_patterns_match_schema(self):
    method test_no_hardcoded_values (line 184) | def test_no_hardcoded_values(self):

FILE: src/bids/layout/tests/test_schema_version_differences.py
  class TestSchemaVersionDifferences (line 11) | class TestSchemaVersionDifferences:
    method test_entity_parsing_version_differences (line 14) | def test_entity_parsing_version_differences(self):
    method test_motion_datatype_evolution (line 46) | def test_motion_datatype_evolution(self):
    method test_schema_version_metadata_differences (line 81) | def test_schema_version_metadata_differences(self):

FILE: src/bids/layout/tests/test_schema_vs_json_config.py
  class TestConfigCompatibility (line 8) | class TestConfigCompatibility:
    method test_core_entities_present_in_both_configs (line 11) | def test_core_entities_present_in_both_configs(self):
    method test_schema_entities_are_superset_of_valid_old_entities (line 25) | def test_schema_entities_are_superset_of_valid_old_entities(self):
    method test_new_suffixes_compatible_with_old_pattern (line 48) | def test_new_suffixes_compatible_with_old_pattern(self):
    method test_new_extensions_compatible_with_old_pattern (line 68) | def test_new_extensions_compatible_with_old_pattern(self):
    method test_datatype_coverage_matches (line 107) | def test_datatype_coverage_matches(self):
    method test_functional_filename_parsing_compatibility (line 140) | def test_functional_filename_parsing_compatibility(self):
    method test_new_config_parses_schema_compliant_filenames (line 182) | def test_new_config_parses_schema_compliant_filenames(self):
    method test_pattern_structure_similarity (line 208) | def test_pattern_structure_similarity(self):
    method test_config_names_and_metadata (line 232) | def test_config_names_and_metadata(self):
    method _extract_suffixes_from_pattern (line 253) | def _extract_suffixes_from_pattern(self, pattern):
    method _extract_extensions_from_pattern (line 267) | def _extract_extensions_from_pattern(self, pattern):
    method _extract_datatypes_from_pattern (line 289) | def _extract_datatypes_from_pattern(self, pattern):
    method _parse_filename_entities (line 303) | def _parse_filename_entities(self, filename, config):
    method _map_entity_name_old_to_new (line 315) | def _map_entity_name_old_to_new(self, new_entity_name):

FILE: src/bids/layout/tests/test_utils.py
  function test_bidsmetadata_class (line 16) | def test_bidsmetadata_class():
  function test_parse_file_entities (line 25) | def test_parse_file_entities(mock_config):
  function test_parse_degenerate_files (line 73) | def test_parse_degenerate_files(mock_config, filename, target):
  function test_add_config_paths (line 77) | def test_add_config_paths():
  function test_PaddedInt_array_comparisons (line 91) | def test_PaddedInt_array_comparisons():
  function test_PaddedInt_dataframe_behavior (line 108) | def test_PaddedInt_dataframe_behavior():

FILE: src/bids/layout/tests/test_validation.py
  function testvalidator (line 14) | def testvalidator():
  function test_layout_with_validation (line 18) | def test_layout_with_validation():

FILE: src/bids/layout/tests/test_writing.py
  function writable_file (line 18) | def writable_file(tmpdir):
  function tmp_bids (line 39) | def tmp_bids(tmpdir_factory):
  function layout (line 51) | def layout(tmp_bids):
  class TestWritableFile (line 59) | class TestWritableFile:
    method test_parse_pattern_re (line 60) | def test_parse_pattern_re(self):
    method test_build_path (line 104) | def test_build_path(self, writable_file):
    method test_strict_build_path (line 199) | def test_strict_build_path(self):
    method test_build_file (line 207) | def test_build_file(self, writable_file, tmp_bids, caplog):
  class TestWritableLayout (line 251) | class TestWritableLayout:
    method test_write_files (line 252) | def test_write_files(self, tmp_bids, layout):
    method test_write_to_file (line 290) | def test_write_to_file(self, tmp_bids, layout):
    method test_write_to_file_defaults (line 302) | def test_write_to_file_defaults(self, tmp_bids, layout):
    method test_build_file_from_layout (line 327) | def test_build_file_from_layout(self, tmpdir, layout):

FILE: src/bids/layout/utils.py
  class BIDSMetadata (line 10) | class BIDSMetadata(dict):
    method __init__ (line 13) | def __init__(self, source_file):
    method __getitem__ (line 17) | def __getitem__(self, key):
  class PaddedInt (line 24) | class PaddedInt(int):
    method __init__ (line 66) | def __init__(self, val):
    method __eq__ (line 69) | def __eq__(self, val):
    method __str__ (line 78) | def __str__(self):
    method __repr__ (line 81) | def __repr__(self):
    method __format__ (line 84) | def __format__(self, format_spec):
    method __hash__ (line 95) | def __hash__(self):
  function parse_file_entities (line 99) | def parse_file_entities(filename, entities=None, config=None, include_un...
  function add_config_paths (line 152) | def add_config_paths(**kwargs):

FILE: src/bids/layout/validation.py
  function validate_root (line 40) | def validate_root(root, validate):  # noqa: D103
  function validate_derivative_path (line 97) | def validate_derivative_path(path, **kwargs):  # noqa: D103
  function _sort_patterns (line 127) | def _sort_patterns(patterns, root):
  function validate_indexing_args (line 141) | def validate_indexing_args(ignore, force_index, root):  # noqa: D103

FILE: src/bids/layout/writing.py
  function build_path (line 19) | def build_path(entities, path_patterns, strict=False):
  function write_to_file (line 205) | def write_to_file(
  function _expand_options (line 299) | def _expand_options(value):
  function _expand_entities (line 319) | def _expand_entities(entities):

FILE: src/bids/modeling/auto_model.py
  function _make_passthrough_contrast (line 8) | def _make_passthrough_contrast(level, model_type='glm', test='t'):
  function auto_model (line 22) | def auto_model(layout, scan_length=None, one_vs_rest=False):

FILE: src/bids/modeling/hrf.py
  function _gamma_difference_hrf (line 14) | def _gamma_difference_hrf(
  function spm_hrf (line 66) | def spm_hrf(tr, oversampling=50, time_length=32.0, onset=0.0):
  function glover_hrf (line 89) | def glover_hrf(tr, oversampling=50, time_length=32.0, onset=0.0):
  function spm_time_derivative (line 122) | def spm_time_derivative(tr, oversampling=50, time_length=32.0, onset=0.0):
  function glover_time_derivative (line 154) | def glover_time_derivative(tr, oversampling=50, time_length=32.0, onset=...
  function spm_dispersion_derivative (line 186) | def spm_dispersion_derivative(tr, oversampling=50, time_length=32.0, ons...
  function glover_dispersion_derivative (line 218) | def glover_dispersion_derivative(tr, oversampling=50, time_length=32.0, ...
  function _sample_condition (line 268) | def _sample_condition(exp_condition, frame_times, oversampling=50, min_o...
  function _resample_regressor (line 341) | def _resample_regressor(hr_regressor, hr_frame_times, frame_times):
  function _orthogonalize (line 365) | def _orthogonalize(X):
  function _regressor_names (line 393) | def _regressor_names(con_name, hrf_model, fir_delays=None):
  function _hrf_kernel (line 421) | def _hrf_kernel(hrf_model, tr, oversampling=50, fir_delays=None):
  function compute_regressor (line 483) | def compute_regressor(

FILE: src/bids/modeling/model_spec.py
  class ModelSpec (line 10) | class ModelSpec(metaclass=ABCMeta):
    method from_df (line 14) | def from_df(self, df, model, metadata=None):
  class GLMMSpec (line 19) | class GLMMSpec(ModelSpec):
    method __init__ (line 56) | def __init__(
    method __repr__ (line 83) | def __repr__(self):
    method set_priors (line 86) | def set_priors(self, fixed=None, random=None):  # noqa: D102
    method build_fixed_terms (line 89) | def build_fixed_terms(self, X):
    method build_variance_components (line 107) | def build_variance_components(self, Z, groups=None, sigma=None, names=...
    method add_term (line 144) | def add_term(self, term):
    method X (line 158) | def X(self):
    method Z (line 166) | def Z(self):
    method fixed_terms (line 177) | def fixed_terms(self):
    method variance_components (line 182) | def variance_components(self):
    method from_df (line 187) | def from_df(cls, df, model, metadata=None, formula=None):
  class MetaAnalysisSpec (line 268) | class MetaAnalysisSpec(GLMMSpec):  # noqa: D101
  class Term (line 272) | class Term:
    method __init__ (line 290) | def __init__(self, name, values, categorical=False, prior=None, metada...
  class VarComp (line 298) | class VarComp(Term):
    method __init__ (line 317) | def __init__(self, name, values, prior=None, metadata=None):
    method dummies_to_vec (line 322) | def dummies_to_vec(dummies):
  class Prior (line 344) | class Prior:
    method __init__ (line 363) | def __init__(self, name, **kwargs):

FILE: src/bids/modeling/report/base.py
  function _build_node_dict (line 17) | def _build_node_dict(node, all_entities):
  function _build_report_dict (line 78) | def _build_report_dict(graph):
  function _write_report (line 105) | def _write_report(report_dict, out_dir, template_path=None):
  function generate_report (line 133) | def generate_report(model, dataset_path, derivatives, output_dir, scan_l...

FILE: src/bids/modeling/report/utils.py
  function node_report (line 9) | def node_report(node_output):
  function est_vif (line 32) | def est_vif(desmat):  # noqa: D417
  function get_eff_reg_vif (line 60) | def get_eff_reg_vif(desmat, contrast_def):  # noqa: D417
  function generate_contrast_matrix (line 104) | def generate_contrast_matrix(contrasts, cols):  # noqa: D417
  function get_all_contrast_vif (line 128) | def get_all_contrast_vif(node_output):  # noqa: D417
  function deroot (line 152) | def deroot(val, root):  # noqa: D103
  function snake_to_camel (line 167) | def snake_to_camel(string):  # noqa: D103
  function displayify (line 172) | def displayify(contrast_name):  # noqa: D103
  function to_alphanum (line 178) | def to_alphanum(string):

FILE: src/bids/modeling/report/viz.py
  function plot_corr_matrix (line 5) | def plot_corr_matrix(dm_wide):  # noqa: D103
  function melt_dm (line 38) | def melt_dm(dm):  # noqa: D103
  function plot_design_matrix (line 43) | def plot_design_matrix(dm_wide, scale=False, timecourse=True):  # noqa: ...

FILE: src/bids/modeling/statsmodels.py
  function validate_model (line 23) | def validate_model(model, *, stacklevel=2):  # noqa: D417
  class BIDSStatsModelsGraph (line 95) | class BIDSStatsModelsGraph:
    method __init__ (line 110) | def __init__(self, layout, model):
    method __repr__ (line 119) | def __repr__(self):
    method __getitem__ (line 122) | def __getitem__(self, key):
    method root_node (line 127) | def root_node(self):
    method _load_model (line 132) | def _load_model(model, validate=True):
    method _load_nodes (line 144) | def _load_nodes(model):
    method _load_edges (line 152) | def _load_edges(model, nodes):
    method get_node (line 174) | def get_node(self, name):
    method load_collections (line 192) | def load_collections(self, nodes=None, drop_na=False, **kwargs):  # no...
    method write_graph (line 225) | def write_graph(self, dotfilename='graph.dot', format='png', pipe=Fals...
    method run_graph (line 256) | def run_graph(self, entities=None, **kwargs):
  function _run_node_recursive (line 274) | def _run_node_recursive(node, inputs=None, filters=None, **kwargs):
  class BIDSStatsModelsNode (line 293) | class BIDSStatsModelsNode:
    method __init__ (line 328) | def __init__(
    method __repr__ (line 367) | def __repr__(self):
    method _build_groups (line 371) | def _build_groups(objects, group_by):
    method run (line 467) | def run(
    method add_child (line 584) | def add_child(self, edge):
    method add_parent (line 595) | def add_parent(self, edge):
    method add_collections (line 606) | def add_collections(self, collections):
    method get_collections (line 623) | def get_collections(self, **filters):
  function expand_wildcards (line 646) | def expand_wildcards(selectors, pool):  # noqa: D103
  class BIDSStatsModelsNodeOutput (line 655) | class BIDSStatsModelsNodeOutput:
    method __init__ (line 706) | def __init__(
    method _collections_to_dfs (line 826) | def _collections_to_dfs(self, collections, *, collection_history=False):
    method _inputs_to_df (line 885) | def _inputs_to_df(self, inputs):
    method _build_contrasts (line 892) | def _build_contrasts(self, unique_in_contrast=None):
    method X (line 979) | def X(self):
    method __repr__ (line 983) | def __repr__(self):

FILE: src/bids/modeling/tests/test_automodel.py
  function model (line 13) | def model():
  function test_automodel_valid (line 22) | def test_automodel_valid(model):
  function test_automodel_runs (line 30) | def test_automodel_runs(model):
  function test_auto_model_graph (line 48) | def test_auto_model_graph(model):

FILE: src/bids/modeling/tests/test_hrf.py
  function test_duplicate_onsets (line 6) | def test_duplicate_onsets():

FILE: src/bids/modeling/tests/test_model_spec.py
  function collection (line 14) | def collection():
  function test_df_to_model_spec (line 26) | def test_df_to_model_spec(collection):
  function test_glmmspec_empty_init (line 45) | def test_glmmspec_empty_init():
  function test_fixed_term_init (line 55) | def test_fixed_term_init():
  function test_var_comp_init (line 62) | def test_var_comp_init():

FILE: src/bids/modeling/tests/test_statsmodels.py
  function graph (line 22) | def graph():
  function graph_intercept (line 32) | def graph_intercept():
  function graph_nodummy (line 42) | def graph_nodummy():
  function test_load_collections_types (line 51) | def test_load_collections_types(graph):
  function test_write_graph (line 60) | def test_write_graph(graph, tmp_path):
  function test_repr (line 69) | def test_repr(graph):
  function test_manual_intercept (line 82) | def test_manual_intercept(graph_intercept):
  function test_first_level_sparse_design_matrix (line 101) | def test_first_level_sparse_design_matrix(graph):
  function test_incremental_data_loading (line 120) | def test_incremental_data_loading():
  function test_step_get_collections (line 130) | def test_step_get_collections(graph):
  function test_contrast_info (line 136) | def test_contrast_info(graph):
  function test_contrast_dummy_vs_explicit (line 152) | def test_contrast_dummy_vs_explicit(graph, graph_nodummy):
  function test_get_run_level_model_spec (line 181) | def test_get_run_level_model_spec(graph):
  function test_entire_graph_smoketest (line 193) | def test_entire_graph_smoketest(graph):
  function test_expand_wildcards (line 274) | def test_expand_wildcards():
  function test_interceptonly_runlevel_error (line 292) | def test_interceptonly_runlevel_error():
  function test_missing_value_fill (line 300) | def test_missing_value_fill():

FILE: src/bids/modeling/tests/test_transformations.py
  function collection (line 32) | def collection():
  function sparse_run_variable_with_missing_values (line 49) | def sparse_run_variable_with_missing_values():
  function test_convolve_multi (line 58) | def test_convolve_multi(collection):
  function test_convolve (line 66) | def test_convolve(collection):
  function test_convolve_oversampling (line 88) | def test_convolve_oversampling(collection):
  function test_convolve_impulse (line 133) | def test_convolve_impulse():
  function test_rename (line 144) | def test_rename(collection):
  function test_product (line 157) | def test_product(collection):
  function test_sum (line 164) | def test_sum(collection):
  function test_scale (line 178) | def test_scale(collection, sparse_run_variable_with_missing_values):
  function test_demean (line 206) | def test_demean(collection):
  function test_orthogonalize_dense (line 214) | def test_orthogonalize_dense(collection):
  function test_orthogonalize_sparse (line 247) | def test_orthogonalize_sparse(collection):
  function test_split (line 263) | def test_split(collection):
  function test_resample_dense (line 316) | def test_resample_dense(collection):
  function test_threshold (line 337) | def test_threshold(collection):
  function test_assign (line 357) | def test_assign(collection):
  function test_assign_multiple (line 382) | def test_assign_multiple(collection):
  function test_copy (line 401) | def test_copy(collection):
  function test_expand_variable_names (line 407) | def test_expand_variable_names(collection):
  function test_factor (line 423) | def test_factor(collection):
  function test_filter (line 471) | def test_filter(collection):
  function test_replace (line 486) | def test_replace(collection):
  function test_select (line 505) | def test_select(collection):
  function test_delete (line 512) | def test_delete(collection):
  function test_and (line 520) | def test_and(collection):
  function test_or (line 535) | def test_or(collection):
  function test_not (line 547) | def test_not(collection):
  function test_dropna (line 555) | def test_dropna(sparse_run_variable_with_missing_values):
  function test_group (line 567) | def test_group(collection):
  function test_resample (line 584) | def test_resample(collection):
  function test_Lag (line 609) | def test_Lag():

FILE: src/bids/modeling/transformations/base.py
  class Transformation (line 20) | class Transformation(metaclass=ABCMeta):  # noqa: D101
    method __new__ (line 100) | def __new__(cls, collection, variables, *args, **kwargs):  # noqa: D102
    method _setup (line 105) | def _setup(self, collection, variables, *args, **kwargs):
    method _expand_variable_groups (line 140) | def _expand_variable_groups(self):
    method _expand_variable_names (line 148) | def _expand_variable_names(self):
    method _clone_variables (line 176) | def _clone_variables(self):
    method _check_categorical_variables (line 200) | def _check_categorical_variables(self):
    method _densify_variables (line 221) | def _densify_variables(self):
    method transform (line 236) | def transform(self):  # noqa: D102
    method _transform (line 350) | def _transform(self, **kwargs):
    method _preprocess (line 353) | def _preprocess(self, col):
    method _postprocess (line 356) | def _postprocess(self, col):
    method _align_variables (line 359) | def _align_variables(self, variables):
  class TransformationOutput (line 427) | class TransformationOutput:  # noqa: D101
  class TransformerManager (line 436) | class TransformerManager:
    method __init__ (line 453) | def __init__(self, default=None, keep_history=True):
    method _sanitize_name (line 461) | def _sanitize_name(self, name):
    method register (line 475) | def register(self, name, func):
    method transform (line 489) | def transform(self, collection, transformations):

FILE: src/bids/modeling/transformations/compute.py
  function _fractional_gcd (line 16) | def _fractional_gcd(vals, res=0.001):
  class Convolve (line 23) | class Convolve(Transformation):
    method _transform (line 52) | def _transform(self, var, model='spm', derivative=False, dispersion=Fa...
  class Demean (line 121) | class Demean(Transformation):  # noqa: D101
    method _transform (line 122) | def _transform(self, data):
  class Orthogonalize (line 126) | class Orthogonalize(Transformation):  # noqa: D101
    method _transform (line 133) | def _transform(self, var, other):
  class Product (line 147) | class Product(Transformation):  # noqa: D101
    method _transform (line 153) | def _transform(self, data):
  class Scale (line 158) | class Scale(Transformation):
    method _transform (line 182) | def _transform(self, data, demean=True, rescale=True, replace_na=None):
  class Sum (line 201) | class Sum(Transformation):  # noqa: D101
    method _transform (line 208) | def _transform(self, data, weights=None):
  class Threshold (line 223) | class Threshold(Transformation):
    method _transform (line 252) | def _transform(self, data, threshold=0.0, binarize=False, above=True, ...
  class And_ (line 263) | class And_(Transformation):
    method _transform (line 279) | def _transform(self, dfs):
  class Not (line 284) | class Not(Transformation):
    method _transform (line 298) | def _transform(self, var):
  class Or_ (line 302) | class Or_(Transformation):
    method _transform (line 318) | def _transform(self, dfs):
  class Lag (line 323) | class Lag(Transformation):
    method _transform (line 376) | def _transform(self, var, shift=1, order=3, mode='nearest', constant=0...

FILE: src/bids/modeling/transformations/munge.py
  class Assign (line 21) | class Assign(Transformation):
    method _transform (line 31) | def _transform(self, input, target, input_attr='amplitude', target_att...
  class Copy (line 78) | class Copy(Transformation):
    method _transform (line 92) | def _transform(self, col):
  class Delete (line 97) | class Delete(Transformation):
    method _transform (line 113) | def _transform(self, variables):
  class DropNA (line 120) | class DropNA(Transformation):  # noqa: D101
    method _transform (line 126) | def _transform(self, var):
  class Factor (line 133) | class Factor(Transformation):  # noqa: D101
    method _transform (line 139) | def _transform(self, var, constraint='none', ref_level=None, sep='.'):
  class Filter (line 175) | class Filter(Transformation):
    method _transform (line 185) | def _transform(self, var, query, by=None):
  class Group (line 211) | class Group(Transformation):
    method _transform (line 219) | def _transform(self, variables, name):
  class Rename (line 227) | class Rename(Transformation):
    method _transform (line 242) | def _transform(self, var):
  class Replace (line 249) | class Replace(Transformation):
    method _transform (line 257) | def _transform(self, var, replace, attribute='value'):
  class Select (line 270) | class Select(Transformation):
    method _transform (line 287) | def _transform(self, variables):
  class Split (line 291) | class Split(Transformation):
    method _transform (line 310) | def _transform(self, var, by):
  class ToDense (line 336) | class ToDense(Transformation):
    method _transform (line 343) | def _transform(self, var, sampling_rate=10):
  class Resample (line 347) | class Resample(Transformation):
    method _transform (line 354) | def _transform(self, var, sampling_rate=10):

FILE: src/bids/reports/conftest.py
  function testlayout (line 11) | def testlayout(tests_dir):
  function config_file (line 17) | def config_file():  # noqa: D103
  function testconfig (line 24) | def testconfig(config_file):  # noqa: D103
  function _unsupported_files (line 29) | def _unsupported_files():

FILE: src/bids/reports/parameters.py
  function describe_slice_timing (line 16) | def describe_slice_timing(img, metadata: dict) -> str:
  function describe_repetition_time (line 28) | def describe_repetition_time(metadata: dict):
  function describe_func_duration (line 35) | def describe_func_duration(n_vols: int, tr) -> str:
  function describe_duration (line 42) | def describe_duration(files) -> str:
  function describe_multiband_factor (line 67) | def describe_multiband_factor(metadata) -> str:
  function describe_echo_times (line 76) | def describe_echo_times(files):
  function describe_echo_times_fmap (line 105) | def describe_echo_times_fmap(files):
  function describe_image_size (line 133) | def describe_image_size(img):
  function describe_inplane_accel (line 157) | def describe_inplane_accel(metadata: dict) -> str:
  function describe_flip_angle (line 166) | def describe_flip_angle(metadata: dict) -> str:
  function describe_dmri_directions (line 171) | def describe_dmri_directions(img):
  function describe_bvals (line 176) | def describe_bvals(bval_file) -> str:
  function describe_pe_direction (line 190) | def describe_pe_direction(metadata: dict, config: dict) -> str:
  function describe_intendedfor_targets (line 197) | def describe_intendedfor_targets(metadata: dict, layout) -> str:
  function get_slice_info (line 244) | def get_slice_info(slice_times) -> str:
  function describe_sequence (line 286) | def describe_sequence(metadata: dict, config: dict):
  function get_size_str (line 319) | def get_size_str(img):

FILE: src/bids/reports/parsing.py
  function func_info (line 16) | def func_info(layout, files, config):
  function anat_info (line 81) | def anat_info(layout, files, config):
  function dwi_info (line 140) | def dwi_info(layout, files, config):
  function fmap_info (line 203) | def fmap_info(layout, files, config):
  function general_acquisition_info (line 258) | def general_acquisition_info(metadata):
  function final_paragraph (line 282) | def final_paragraph(metadata):
  function parse_files (line 310) | def parse_files(layout, data_files, sub, config):
  function _parse_files (line 331) | def _parse_files(layout, data_files, sub, config, *, stacklevel=3):

FILE: src/bids/reports/report.py
  class BIDSReport (line 10) | class BIDSReport:
    method __init__ (line 45) | def __init__(self, layout, config=None):
    method generate_from_files (line 65) | def generate_from_files(self, files):
    method generate (line 136) | def generate(self, **kwargs):
    method _report_subject (line 182) | def _report_subject(self, subject, **kwargs):  # noqa: D417

FILE: src/bids/reports/tests/test_parameters.py
  function testimg (line 8) | def testimg(testlayout):
  function testdiffimg (line 20) | def testdiffimg(testlayout):
  function testmeta (line 31) | def testmeta():
  function testmeta_light (line 43) | def testmeta_light():
  function test_describe_sequence (line 71) | def test_describe_sequence(
  function test_describe_pe_direction (line 96) | def test_describe_pe_direction(pe_direction, expected, testconfig):
  function test_describe_bvals_smoke (line 103) | def test_describe_bvals_smoke(testlayout):
  function test_describe_echo_times_smoke (line 119) | def test_describe_echo_times_smoke(testlayout):
  function test_describe_echo_times_fmap (line 134) | def test_describe_echo_times_fmap(testlayout):
  function test_describe_repetition_time_smoke (line 150) | def test_describe_repetition_time_smoke(testmeta):
  function test_describe_func_duration_smoke (line 158) | def test_describe_func_duration_smoke():
  function test_describe_multiband_factor_smoke (line 169) | def test_describe_multiband_factor_smoke(testmeta, testmeta_light):
  function test_describe_inplane_accel_smoke (line 183) | def test_describe_inplane_accel_smoke(testmeta, testmeta_light):
  function test_describe_flip_angle_smoke (line 197) | def test_describe_flip_angle_smoke(testmeta):
  function test_get_slice_info (line 214) | def test_get_slice_info(slice_times, expected):
  function test_describe_slice_timing (line 219) | def test_describe_slice_timing(testimg, testmeta, testmeta_light):
  function test_get_size_str (line 229) | def test_get_size_str(testimg):
  function test_describe_image_size (line 239) | def test_describe_image_size(testimg):
  function test_describe_dmri_directions (line 249) | def test_describe_dmri_directions(testdiffimg):
  function test_describe_intendedfor_targets (line 255) | def test_describe_intendedfor_targets(testmeta_light, testlayout):

FILE: src/bids/reports/tests/test_parsing.py
  function testmeta (line 9) | def testmeta():
  function test_anat_info_smoke (line 14) | def test_anat_info_smoke(testlayout, testconfig):
  function test_dwi_info_smoke (line 30) | def test_dwi_info_smoke(testlayout, testconfig):
  function test_fmap_info_smoke (line 46) | def test_fmap_info_smoke(testlayout, testconfig):
  function test_func_info_smoke (line 63) | def test_func_info_smoke(testlayout, testconfig):
  function test_general_acquisition_info_smoke (line 80) | def test_general_acquisition_info_smoke(testmeta):
  function test_final_paragraph_smoke (line 89) | def test_final_paragraph_smoke(testmeta):
  function test_parse_files_smoke (line 98) | def test_parse_files_smoke(testlayout, testconfig):

FILE: src/bids/reports/tests/test_report.py
  function test_report_init (line 7) | def test_report_init(testlayout):
  function test_report_gen (line 13) | def test_report_gen(testlayout):
  function test_report_gen_from_files (line 20) | def test_report_gen_from_files(testlayout):
  function test_report_subject (line 30) | def test_report_subject(testlayout):
  function test_report_session (line 39) | def test_report_session(testlayout):
  function test_report_file_config (line 48) | def test_report_file_config(testlayout, config_file):
  function test_report_dict_config (line 55) | def test_report_dict_config(testlayout, testconfig):

FILE: src/bids/reports/utils.py
  function reminder (line 12) | def reminder():
  function remove_duplicates (line 17) | def remove_duplicates(seq):
  function num_to_str (line 27) | def num_to_str(num):
  function list_to_str (line 38) | def list_to_str(lst):

FILE: src/bids/tests/test_cli.py
  function runner (line 12) | def runner():
  function test_cli_entrypoint (line 16) | def test_cli_entrypoint(runner):
  function test_validate_multiple (line 28) | def test_validate_multiple():
  function test_layout (line 37) | def test_layout(runner, tmp_path):

FILE: src/bids/tests/test_config.py
  function test_load_from_standard_paths (line 13) | def test_load_from_standard_paths():
  function test_set_option (line 41) | def test_set_option():
  function test_extension_initial_dot (line 59) | def test_extension_initial_dot(mock_config):

FILE: src/bids/tests/utils.py
  function get_test_data_path (line 6) | def get_test_data_path():

FILE: src/bids/utils.py
  class frozendict (line 13) | class frozendict(_frozendict):
    method __repr__ (line 16) | def __repr__(self):
  function listify (line 21) | def listify(obj):
  function hashablefy (line 28) | def hashablefy(obj):
  function matches_entities (line 38) | def matches_entities(obj, entities, strict=False):
  function natural_sort (line 55) | def natural_sort(l, field=None):  # noqa: E741
  function convert_JSON (line 69) | def convert_JSON(j):
  function splitext (line 106) | def splitext(path):
  function make_bidsfile (line 121) | def make_bidsfile(filename):
  function collect_associated_files (line 141) | def collect_associated_files(layout, files, extra_entities=()):  # noqa:...
  function validate_multiple (line 183) | def validate_multiple(val, retval=None):
  function entity_indices (line 199) | def entity_indices(schema_spec=None):  # noqa: D103
  function bids_sort (line 209) | def bids_sort(unsorted: dict, schema_spec=None):

FILE: src/bids/variables/collections.py
  function _pandas_3_0 (line 26) | def _pandas_3_0():
  function _pandas_3_0_options (line 46) | def _pandas_3_0_options():
  class BIDSVariableCollection (line 62) | class BIDSVariableCollection:
    method __init__ (line 81) | def __init__(self, variables, name=None):
    method merge_variables (line 125) | def merge_variables(variables, **kwargs):  # noqa: D417
    method to_df (line 148) | def to_df(self, variables=None, format='wide', fillna=np.nan, entities...
    method from_df (line 234) | def from_df(cls, data, entities=None, source='contrast'):  # noqa: D417
    method clone (line 261) | def clone(self):
    method _index_entities (line 271) | def _index_entities(self):
    method __getitem__ (line 292) | def __getitem__(self, var):
    method __setitem__ (line 300) | def __setitem__(self, var, obj):
    method match_variables (line 313) | def match_variables(self, pattern, return_type='name', match_type='uni...
    method __repr__ (line 348) | def __repr__(self):
  class BIDSRunVariableCollection (line 352) | class BIDSRunVariableCollection(BIDSVariableCollection):
    method __init__ (line 372) | def __init__(self, variables, sampling_rate=None):
    method get_dense_variables (line 381) | def get_dense_variables(self, variables=None):
    method get_sparse_variables (line 391) | def get_sparse_variables(self, variables=None):
    method all_dense (line 401) | def all_dense(self):  # noqa: D102
    method all_sparse (line 404) | def all_sparse(self):  # noqa: D102
    method _get_sampling_rate (line 407) | def _get_sampling_rate(self, sampling_rate):
    method _densify_and_resample (line 445) | def _densify_and_resample(
    method to_dense (line 494) | def to_dense(  # noqa: D417
    method resample (line 541) | def resample(
    method to_df (line 582) | def to_df(
  function merge_collections (line 674) | def merge_collections(collections, sampling_rate='highest', output_level...

FILE: src/bids/variables/entities.py
  class Node (line 15) | class Node:
    method __init__ (line 27) | def __init__(self, level, entities):
    method add_variable (line 36) | def add_variable(self, variable):
  class RunNode (line 52) | class RunNode(Node):
    method __init__ (line 72) | def __init__(self, entities, image_file, duration, repetition_time, n_...
    method get_info (line 79) | def get_info(self):  # noqa: D102
  class RunInfo (line 93) | class RunInfo(RunInfo_):
  class NodeIndex (line 102) | class NodeIndex:
    method __init__ (line 105) | def __init__(self):
    method get_collections (line 110) | def get_collections(self, unit, names=None, merge=False, sampling_rate...
    method get_nodes (line 172) | def get_nodes(self, level=None, entities=None, strict=False):
    method create_node (line 237) | def create_node(self, level, entities, *args, **kwargs):
    method get_or_create_node (line 271) | def get_or_create_node(self, level, entities, *args, **kwargs):

FILE: src/bids/variables/io.py
  function load_variables (line 18) | def load_variables(  # noqa: D417
  function _get_nvols (line 110) | def _get_nvols(img_f):
  function _load_time_variables (line 132) | def _load_time_variables(  # noqa: D417
  function _load_tsv_variables (line 425) | def _load_tsv_variables(  # noqa: D417

FILE: src/bids/variables/tests/test_collections.py
  function run_coll (line 13) | def run_coll():
  function run_coll_bad_length (line 23) | def run_coll_bad_length():
  function run_coll_list (line 33) | def run_coll_list():
  function run_coll_derivs (line 42) | def run_coll_derivs():
  function test_run_variable_collection_init (line 52) | def test_run_variable_collection_init(run_coll):
  function test_run_variable_collection_sparse_variable_accessors (line 61) | def test_run_variable_collection_sparse_variable_accessors(run_coll):
  function test_run_variable_collection_dense_variable_accessors (line 70) | def test_run_variable_collection_dense_variable_accessors(run_coll):
  function test_run_variable_collection_get_sampling_rate (line 82) | def test_run_variable_collection_get_sampling_rate(run_coll):
  function test_resample_run_variable_collection (line 99) | def test_resample_run_variable_collection(run_coll):
  function test_run_variable_collection_to_df_all_sparse_vars (line 125) | def test_run_variable_collection_to_df_all_sparse_vars(run_coll):
  function test_run_variable_collection_to_df_all_dense_vars (line 183) | def test_run_variable_collection_to_df_all_dense_vars(run_coll):
  function test_run_variable_collection_bad_length_to_df_all_dense_vars (line 250) | def test_run_variable_collection_bad_length_to_df_all_dense_vars(run_col...
  function test_run_variable_collection_to_df_mixed_vars (line 286) | def test_run_variable_collection_to_df_mixed_vars(run_coll):
  function test_merge_collections (line 311) | def test_merge_collections(run_coll, run_coll_list):
  function test_get_collection_entities (line 319) | def test_get_collection_entities(run_coll_list):
  function test_match_variables (line 335) | def test_match_variables(run_coll):
  function test_n_variables (line 346) | def test_n_variables(run_coll_derivs):

FILE: src/bids/variables/tests/test_entities.py
  function layout1 (line 12) | def layout1():
  function layout2 (line 19) | def layout2():
  function test_run (line 25) | def test_run(layout1):
  function test_get_or_create_node (line 36) | def test_get_or_create_node(layout1):
  function test_get_nodes (line 62) | def test_get_nodes(layout1):
  function test_get_collections_merged (line 76) | def test_get_collections_merged(layout1):
  function test_get_collections_unmerged (line 87) | def test_get_collections_unmerged(layout2):

FILE: src/bids/variables/tests/test_io.py
  function layout1 (line 12) | def layout1():
  function synthetic (line 19) | def synthetic(request):
  function test_load_events (line 30) | def test_load_events(layout1):
  function test_load_participants (line 44) | def test_load_participants(layout1):
  function test_load_synthetic_dataset (line 62) | def test_load_synthetic_dataset(synthetic):

FILE: src/bids/variables/tests/test_variables.py
  function generate_DEV (line 17) | def generate_DEV(name='test', sr=20, duration=480):
  function layout1 (line 30) | def layout1():
  function layout2 (line 37) | def layout2():
  function test_dense_event_variable_init (line 43) | def test_dense_event_variable_init():
  function test_dense_event_variable_resample (line 52) | def test_dense_event_variable_resample():
  function test_merge_wrapper (line 59) | def test_merge_wrapper():
  function test_sparse_run_variable_to_dense (line 68) | def test_sparse_run_variable_to_dense(layout1):
  function test_sparse_run_variable_to_dense_default_sr (line 88) | def test_sparse_run_variable_to_dense_default_sr(layout1):
  function test_merge_densified_variables (line 111) | def test_merge_densified_variables(layout1):
  function test_densify_merged_variables (line 128) | def test_densify_merged_variables(layout1):
  function test_merge_simple_variables (line 149) | def test_merge_simple_variables(layout2):
  function test_merge_sparse_run_variables (line 160) | def test_merge_sparse_run_variables(layout1):
  function test_merge_dense_run_variables (line 170) | def test_merge_dense_run_variables(layout2):
  function test_simple_variable_to_df (line 179) | def test_simple_variable_to_df(layout1):
  function test_sparse_run_variable_to_df (line 183) | def test_sparse_run_variable_to_df(layout1):
  function test_dense_run_variable_to_df (line 187) | def test_dense_run_variable_to_df(layout2):
  function test_filter_simple_variable (line 191) | def test_filter_simple_variable(layout2):
  function test_resampling_edge_case (line 211) | def test_resampling_edge_case(tmpdir, TR, nvols):
  function test_downsampling (line 232) | def test_downsampling(tmpdir):

FILE: src/bids/variables/variables.py
  class BIDSVariable (line 16) | class BIDSVariable(metaclass=ABCMeta):
    method __init__ (line 24) | def __init__(self, name, values, source):
    method __repr__ (line 30) | def __repr__(self):
    method clone (line 33) | def clone(self, data=None, **kwargs):
    method filter (line 71) | def filter(self, filters=None, query=None, strict=False, inplace=False):
    method merge (line 127) | def merge(cls, variables, name=None, **kwargs):
    method _merge (line 168) | def _merge(cls, variables, name, **kwargs):
    method get_grouper (line 171) | def get_grouper(self, groupby='run'):
    method apply (line 190) | def apply(self, func, groupby='run', *args, **kwargs):
    method to_df (line 208) | def to_df(self, condition=True, entities=True, **kwargs):  # noqa: D417
    method _extract_entities (line 237) | def _extract_entities(self):
  class SimpleVariable (line 269) | class SimpleVariable(BIDSVariable):
    method __init__ (line 291) | def __init__(self, name, data, source, **kwargs):
    method split (line 300) | def split(self, grouper):
    method _merge (line 333) | def _merge(cls, variables, name, **kwargs):
    method select_rows (line 339) | def select_rows(self, rows):
  class SparseRunVariable (line 356) | class SparseRunVariable(SimpleVariable):
    method __init__ (line 380) | def __init__(self, name, data, run_info, source, **kwargs):
    method get_duration (line 392) | def get_duration(self):
    method to_dense (line 396) | def to_dense(self, sampling_rate=None):
    method _extract_entities (line 468) | def _extract_entities(self):
    method _merge (line 478) | def _merge(cls, variables, name, **kwargs):
  class DenseRunVariable (line 483) | class DenseRunVariable(BIDSVariable):
    method __init__ (line 503) | def __init__(self, name, values, run_info, source, sampling_rate):
    method split (line 519) | def split(self, grouper):
    method _build_entity_index (line 547) | def _build_entity_index(self, run_info, sampling_rate, match_vol=False):
    method resample (line 583) | def resample(self, sampling_rate, inplace=False, kind='linear'):
    method to_df (line 627) | def to_df(self, condition=True, entities=True, timing=True, sampling_r...
    method _merge (line 655) | def _merge(cls, variables, name, sampling_rate=None, **kwargs):
  function merge_variables (line 682) | def merge_variables(variables, **kwargs):
  function _resample (line 730) | def _resample(y, new_sr, old_sr, new_num, kind='linear'):

FILE: tools/check_noqa_budget.py
  function git (line 16) | def git(*args: str) -> str:
  function tracked_python_files (line 20) | def tracked_python_files(ref: str) -> list[str]:
  function file_content_at_ref (line 25) | def file_content_at_ref(ref: str, path: str) -> str:
  function count_noqa_in_text (line 29) | def count_noqa_in_text(text: str) -> int:
  function count_noqa_at_ref (line 33) | def count_noqa_at_ref(ref: str) -> int:
  function main (line 45) | def main() -> int:

FILE: tools/prep_zenodo.py
  function decommify (line 15) | def decommify(name):