sequence stringlengths 492 15.9k | code stringlengths 75 8.58k |
|---|---|
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:get_dummy_dynamic_run; 3, parameters; 3, 4; 3, 5; 4, identifier:nsamples; 5, dictionary_splat_pattern; 5, 6; 6, identifier:kwargs; 7, block; 7, 8; 7, 18; 7, 28; 7, 38; 7, 48; 7, 58; 7, 71; 7, 94; 7, 114; 7, 125; 7, 148; 7, 171; 7, 182; 7, 193; ... | def get_dummy_dynamic_run(nsamples, **kwargs):
seed = kwargs.pop('seed', False)
ndim = kwargs.pop('ndim', 2)
nthread_init = kwargs.pop('nthread_init', 2)
nthread_dyn = kwargs.pop('nthread_dyn', 3)
logl_range = kwargs.pop('logl_range', 1)
if kwargs:
raise TypeError('Unexpected **kwargs: {... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:get_dates_for_project; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:project; 6, block; 6, 7; 6, 18; 6, 22; 6, 88; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:file_re; 10, call; 10, 11; 10, 14; 11, at... | def get_dates_for_project(self, project):
file_re = re.compile(r'^%s_([0-9]{8})\.json$' % project)
all_dates = []
for f in os.listdir(self.cache_path):
if not os.path.isfile(os.path.join(self.cache_path, f)):
continue
m = file_re.match(f)
if m ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 12; 2, function_name:insort_event_right; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 4, identifier:self; 5, identifier:event; 6, default_parameter; 6, 7; 6, 8; 7, identifier:lo; 8, integer:0; 9, default_parameter; 9, 10; 9, 11; 10, identifier:hi; 11, None; 12, block; 1... | def insort_event_right(self, event, lo=0, hi=None):
if lo < 0:
raise ValueError('lo must be non-negative')
if hi is None:
hi = len(self.queue)
while lo < hi:
mid = (lo + hi) // 2
if event[0] < self.queue[mid][0]:
hi = mid
else:
lo = mid + 1
self.queue.insert... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:getMd5Checksum; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 27; 5, 44; 5, 57; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:references; 9, call; 9, 10; 9, 11; 10, identifier:sorted; 11, argument_list; 1... | def getMd5Checksum(self):
references = sorted(
self.getReferences(),
key=lambda ref: ref.getMd5Checksum())
checksums = ''.join([ref.getMd5Checksum() for ref in references])
md5checksum = hashlib.md5(checksums).hexdigest()
return md5checksum |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 13; 2, function_name:knn_impute_few_observed; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 10; 4, identifier:X; 5, identifier:missing_mask; 6, identifier:k; 7, default_parameter; 7, 8; 7, 9; 8, identifier:verbose; 9, False; 10, default_parameter; 10, 11; 10, 12; 11, ... | def knn_impute_few_observed(
X, missing_mask, k, verbose=False, print_interval=100):
start_t = time.time()
n_rows, n_cols = X.shape
missing_mask_column_major = np.asarray(missing_mask, order="F")
observed_mask_column_major = ~missing_mask_column_major
X_column_major = X.copy(order="F")
X... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:_sort_converters; 3, parameters; 3, 4; 3, 5; 4, identifier:cls; 5, default_parameter; 5, 6; 5, 7; 6, identifier:app_ready; 7, False; 8, block; 8, 9; 8, 11; 8, 21; 9, expression_statement; 9, 10; 10, string:'''Sorts the converter functions'''; 1... | def _sort_converters(cls, app_ready=False):
'''Sorts the converter functions'''
cls._sorting_enabled = cls._sorting_enabled or app_ready
if cls._sorting_enabled:
for converter in cls.converters:
converter.prepare_sort_key()
cls.converters.sort(key=attrgett... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:prepare_sort_key; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 8; 5, 80; 6, expression_statement; 6, 7; 7, string:'''
Triggered by view_function._sort_converters when our sort key should be created.
This can't be ... | def prepare_sort_key(self):
'''
Triggered by view_function._sort_converters when our sort key should be created.
This can't be called in the constructor because Django models might not be ready yet.
'''
if isinstance(self.convert_type, str):
try:
app_n... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 12; 2, function_name:sort_key_for_numeric_suffixes; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:path; 5, default_parameter; 5, 6; 5, 7; 6, identifier:sep; 7, string:'.'; 8, default_parameter; 8, 9; 8, 10; 9, identifier:suffix_index; 10, unary_operator:-; 10, 11... | def sort_key_for_numeric_suffixes(path, sep='.', suffix_index=-2):
chunks = path.split(sep)
if chunks[suffix_index].isdigit():
return sep.join(chunks[:suffix_index] + chunks[suffix_index+1:]), int(chunks[suffix_index])
return path, 0 |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:_get_query; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:cursor; 6, block; 6, 7; 6, 9; 6, 27; 6, 45; 6, 56; 7, expression_statement; 7, 8; 8, string:'''
Query tempalte for source Solr, sorts by id by default.
'... | def _get_query(self, cursor):
'''
Query tempalte for source Solr, sorts by id by default.
'''
query = {'q':'*:*',
'sort':'id desc',
'rows':self._rows,
'cursorMark':cursor}
if self._date_field:
query['sort'] = "{... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:url_params; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:request; 5, default_parameter; 5, 6; 5, 7; 6, identifier:except_params; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:as_is; 10, False; 11, block; 11, 12; 11, 20; 11, 24; 1... | def url_params(request, except_params=None, as_is=False):
if not request.GET:
return ''
params = []
for key, value in request.GET.items():
if except_params and key not in except_params:
for v in request.GET.getlist(key):
params.append('%s=%s' % (key, urlquote(v)))... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:compose; 3, parameters; 3, 4; 4, list_splat_pattern; 4, 5; 5, identifier:funcs; 6, block; 6, 7; 7, if_statement; 7, 8; 7, 14; 7, 38; 7, 73; 7, 86; 7, 98; 8, comparison_operator:==; 8, 9; 8, 13; 9, call; 9, 10; 9, 11; 10, identifier:len; 11, arg... | def compose(*funcs):
if len(funcs) == 2: f0,f1=funcs; return lambda *a,**kw: f0(f1(*a,**kw))
elif len(funcs) == 3: f0,f1,f2=funcs; return lambda *a,**kw: f0(f1(f2(*a,**kw)))
elif len(funcs) == 0: return lambda x:x
elif len(funcs) == 1: return funcs[0]
else:
def composed(*args,**kwargs):
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:_sort_lines; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 11; 8, attribute; 8, 9; 8, 10; 9, identifier:self; 10, identifier:_valid_lines; 11, call; 11, 12; 11, 13; 12, identifie... | def _sort_lines(self):
self._valid_lines = sorted(
self._valid_lines,
key=lambda line: line.accept_date,
) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:_sort_and_trim; 3, parameters; 3, 4; 3, 5; 4, identifier:data; 5, default_parameter; 5, 6; 5, 7; 6, identifier:reverse; 7, False; 8, block; 8, 9; 8, 13; 8, 21; 8, 39; 9, expression_statement; 9, 10; 10, assignment; 10, 11; 10, 12; 11, identifie... | def _sort_and_trim(data, reverse=False):
threshold = 10
data_list = data.items()
data_list = sorted(
data_list,
key=lambda data_info: data_info[1],
reverse=reverse,
)
return data_list[:threshold] |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:get_queryset; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 8; 5, 20; 5, 29; 5, 38; 6, expression_statement; 6, 7; 7, string:'''Apply Datatables sort and search criterion to QuerySet'''; 8, expression_statement; 8, 9; 9, assignmen... | def get_queryset(self):
'''Apply Datatables sort and search criterion to QuerySet'''
qs = super(DatatablesView, self).get_queryset()
qs = self.global_search(qs)
qs = self.column_search(qs)
return qs.order_by(*self.get_orders()) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:rangify; 3, parameters; 3, 4; 4, identifier:number_list; 5, block; 5, 6; 5, 12; 5, 16; 5, 24; 5, 57; 5, 66; 6, if_statement; 6, 7; 6, 9; 7, not_operator; 7, 8; 8, identifier:number_list; 9, block; 9, 10; 10, return_statement; 10, 11; 11, identi... | def rangify(number_list):
if not number_list:
return number_list
ranges = []
range_start = prev_num = number_list[0]
for num in number_list[1:]:
if num != (prev_num + 1):
ranges.append((range_start, prev_num))
range_start = num
prev_num = num
ranges.ap... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 13; 2, function_name:get_solver; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:name; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:refresh; 10, False; 11, dictionary_splat_pattern; 11, 12; 1... | def get_solver(self, name=None, refresh=False, **filters):
_LOGGER.debug("Requested a solver that best matches feature filters=%r", filters)
if name is not None:
filters.setdefault('name', name)
if not filters and self.default_solver:
filters = self.default_solver
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:find_germanet_xml_files; 3, parameters; 3, 4; 4, identifier:xml_path; 5, block; 5, 6; 5, 8; 5, 28; 5, 55; 5, 70; 5, 79; 5, 102; 5, 117; 5, 153; 5, 180; 5, 195; 5, 204; 5, 230; 5, 245; 5, 254; 5, 263; 6, expression_statement; 6, 7; 7, string:'''... | def find_germanet_xml_files(xml_path):
'''
Globs the XML files contained in the given directory and sorts
them into sections for import into the MongoDB database.
Arguments:
- `xml_path`: the path to the directory containing the GermaNet
XML files
'''
xml_files = sorted(glob.glob(os.pa... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 31; 2, function_name:iter_org_issues; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 3, 18; 3, 21; 3, 24; 3, 28; 4, identifier:self; 5, identifier:name; 6, default_parameter; 6, 7; 6, 8; 7, identifier:filter; 8, string:''; 9, default_parameter; 9, 10; 9, 11;... | def iter_org_issues(self, name, filter='', state='', labels='', sort='',
direction='', since=None, number=-1, etag=None):
url = self._build_url('orgs', name, 'issues')
params = issue_params(filter, state, labels, sort, direction, since)
return self._iter(int(number), url,... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 21; 2, function_name:iter_repos; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 18; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:type; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:sort; 10, None; 11, default_parameter; 11, 12... | def iter_repos(self, type=None, sort=None, direction=None, number=-1,
etag=None):
url = self._build_url('user', 'repos')
params = {}
if type in ('all', 'owner', 'public', 'private', 'member'):
params.update(type=type)
if sort in ('created', 'updated', 'push... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 21; 2, function_name:iter_starred; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 18; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:login; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:sort; 10, None; 11, default_parameter; 11,... | def iter_starred(self, login=None, sort=None, direction=None, number=-1,
etag=None):
if login:
return self.user(login).iter_starred(sort, direction)
params = {'sort': sort, 'direction': direction}
self._remove_none(params)
url = self._build_url('user', 's... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 25; 2, function_name:search_code; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 3, 18; 3, 22; 4, identifier:self; 5, identifier:query; 6, default_parameter; 6, 7; 6, 8; 7, identifier:sort; 8, None; 9, default_parameter; 9, 10; 9, 11; 10, identifier:order; 1... | def search_code(self, query, sort=None, order=None, per_page=None,
text_match=False, number=-1, etag=None):
params = {'q': query}
headers = {}
if sort == 'indexed':
params['sort'] = sort
if sort and order in ('asc', 'desc'):
params['order'] = o... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 25; 2, function_name:search_issues; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 3, 18; 3, 22; 4, identifier:self; 5, identifier:query; 6, default_parameter; 6, 7; 6, 8; 7, identifier:sort; 8, None; 9, default_parameter; 9, 10; 9, 11; 10, identifier:order;... | def search_issues(self, query, sort=None, order=None, per_page=None,
text_match=False, number=-1, etag=None):
params = {'q': query}
headers = {}
if sort in ('comments', 'created', 'updated'):
params['sort'] = sort
if order in ('asc', 'desc'):
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 25; 2, function_name:search_users; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 3, 18; 3, 22; 4, identifier:self; 5, identifier:query; 6, default_parameter; 6, 7; 6, 8; 7, identifier:sort; 8, None; 9, default_parameter; 9, 10; 9, 11; 10, identifier:order; ... | def search_users(self, query, sort=None, order=None, per_page=None,
text_match=False, number=-1, etag=None):
params = {'q': query}
headers = {}
if sort in ('followers', 'repositories', 'joined'):
params['sort'] = sort
if order in ('asc', 'desc'):
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 18; 2, function_name:iter_starred; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 15; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:sort; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:direction; 10, None; 11, default_parameter; 11, 12... | def iter_starred(self, sort=None, direction=None, number=-1, etag=None):
from .repos import Repository
params = {'sort': sort, 'direction': direction}
self._remove_none(params)
url = self.starred_urlt.expand(owner=None, repo=None)
return self._iter(int(number), url, Repository, p... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 15; 2, function_name:iter_forks; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 12; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:sort; 7, string:''; 8, default_parameter; 8, 9; 8, 10; 9, identifier:number; 10, unary_operator:-; 10, 11; 11, integer:1; 1... | def iter_forks(self, sort='', number=-1, etag=None):
url = self._build_url('forks', base_url=self._api)
params = {}
if sort in ('newest', 'oldest', 'watchers'):
params = {'sort': sort}
return self._iter(int(number), url, Repository, params, etag) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 36; 2, function_name:iter_issues; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 17; 3, 20; 3, 23; 3, 26; 3, 29; 3, 33; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:milestone; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:stat... | def iter_issues(self,
milestone=None,
state=None,
assignee=None,
mentioned=None,
labels=None,
sort=None,
direction=None,
since=None,
number=... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 21; 2, function_name:iter_milestones; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 18; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:state; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:sort; 10, None; 11, default_parameter; ... | def iter_milestones(self, state=None, sort=None, direction=None,
number=-1, etag=None):
url = self._build_url('milestones', base_url=self._api)
accepted = {'state': ('open', 'closed'),
'sort': ('due_date', 'completeness'),
'direction': ('as... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 27; 2, function_name:iter_pulls; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 17; 3, 20; 3, 24; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:state; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:head; 10, None; 11, default_pa... | def iter_pulls(self, state=None, head=None, base=None, sort='created',
direction='desc', number=-1, etag=None):
url = self._build_url('pulls', base_url=self._api)
params = {}
if state and state.lower() in ('all', 'open', 'closed'):
params['state'] = state.lower()
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 21; 2, function_name:iter_user_repos; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 18; 4, identifier:login; 5, default_parameter; 5, 6; 5, 7; 6, identifier:type; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:sort; 10, None; 11, default_parameter; ... | def iter_user_repos(login, type=None, sort=None, direction=None, number=-1,
etag=None):
if login:
return gh.iter_user_repos(login, type, sort, direction, number, etag)
return iter([]) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:sort_descendants; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:attr; 7, string:"name"; 8, block; 8, 9; 8, 23; 9, expression_statement; 9, 10; 10, assignment; 10, 11; 10, 12; 11, identifier:node2... | def sort_descendants(self, attr="name"):
node2content = self.get_cached_content(store_attr=attr, container_type=list)
for n in self.traverse():
if not n.is_leaf():
n.children.sort(key=lambda x: str(sorted(node2content[x]))) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:collect_backups; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:location; 6, block; 6, 7; 6, 11; 6, 18; 6, 26; 6, 32; 6, 192; 6, 207; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:backups; 10, list:[]; 1... | def collect_backups(self, location):
backups = []
location = coerce_location(location)
logger.info("Scanning %s for backups ..", location)
location.ensure_readable()
for entry in natsort(location.context.list_entries(location.directory)):
match = TIMESTAMP_PATTERN.sea... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 14; 2, function_name:prepare_bam; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 8; 3, 11; 4, identifier:job; 5, identifier:uuid; 6, identifier:url; 7, identifier:config; 8, default_parameter; 8, 9; 8, 10; 9, identifier:paired_url; 10, None; 11, default_parameter; 11, ... | def prepare_bam(job, uuid, url, config, paired_url=None, rg_line=None):
if config.run_bwa:
get_bam = job.wrapJobFn(setup_and_run_bwakit,
uuid,
url,
rg_line,
config,
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:alignment; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:job; 5, identifier:ids; 6, identifier:input_args; 7, identifier:sample; 8, block; 8, 9; 8, 15; 8, 25; 8, 31; 8, 37; 8, 45; 8, 59; 8, 78; 8, 92; 8, 137; 8, 168; 8, 202; 8, 236; 8, 2... | def alignment(job, ids, input_args, sample):
uuid, urls = sample
work_dir = job.fileStore.getLocalTempDir()
output_dir = input_args['output_dir']
key_path = input_args['ssec']
cores = multiprocessing.cpu_count()
return_input_paths(job, work_dir, ids, 'ref.fa', 'ref.fa.amb', 'ref.fa.ann',
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:bamsort_and_index; 3, parameters; 3, 4; 3, 5; 4, identifier:job; 5, identifier:job_vars; 6, block; 6, 7; 6, 13; 6, 23; 6, 29; 6, 39; 6, 51; 6, 64; 6, 73; 6, 89; 6, 105; 6, 118; 6, 139; 6, 156; 6, 173; 7, expression_statement; 7, 8; 8, assignmen... | def bamsort_and_index(job, job_vars):
input_args, ids = job_vars
work_dir = job.fileStore.getLocalTempDir()
sudo = input_args['sudo']
rg_alignments = return_input_paths(job, work_dir, ids, 'rg_alignments.bam')
output = os.path.join(work_dir, 'sorted.bam')
cmd1 = ['sort', docker_path(rg_alignment... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:sort_bam_by_reference; 3, parameters; 3, 4; 3, 5; 4, identifier:job; 5, identifier:job_vars; 6, block; 6, 7; 6, 13; 6, 23; 6, 36; 6, 48; 6, 52; 6, 72; 6, 113; 6, 119; 6, 177; 6, 195; 6, 205; 6, 212; 6, 225; 6, 245; 6, 262; 7, expression_stateme... | def sort_bam_by_reference(job, job_vars):
input_args, ids = job_vars
work_dir = job.fileStore.getLocalTempDir()
sorted_bam, sorted_bai = return_input_paths(job, work_dir, ids, 'sorted.bam', 'sorted.bam.bai')
output = os.path.join(work_dir, 'sort_by_ref.bam')
ref_seqs = []
handle = subprocess.Pop... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 4; 2, function_name:main; 3, parameters; 4, block; 4, 5; 4, 11; 4, 20; 4, 28; 4, 121; 5, expression_statement; 5, 6; 6, assignment; 6, 7; 6, 8; 7, identifier:parser; 8, call; 8, 9; 8, 10; 9, identifier:build_parser; 10, argument_list; 11, expression_statement; 11,... | def main():
parser = build_parser()
Job.Runner.addToilOptions(parser)
args = parser.parse_args()
inputs = {'config': args.config,
'config_fastq': args.config_fastq,
'input': args.input,
'unc.bed': args.unc,
'hg19.transcripts.fa': args.fasta,
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:fourier_series; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:self; 5, identifier:pars; 6, identifier:x; 7, identifier:order; 8, block; 8, 9; 8, 15; 8, 77; 9, expression_statement; 9, 10; 10, assignment; 10, 11; 10, 12; 11, identifier:su... | def fourier_series(self, pars, x, order):
sum = pars[0]
for i in range(order):
sum += pars[i * 2 + 1] * np.sin(2 * np.pi * (i + 1) * x) \
+ pars[i * 2 + 2] * np.cos(2 * np.pi * (i + 1) * x)
return sum |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:slope_percentile; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:self; 5, identifier:date; 6, identifier:mag; 7, block; 7, 8; 7, 27; 7, 46; 7, 57; 7, 63; 7, 69; 7, 75; 7, 85; 7, 95; 8, expression_statement; 8, 9; 9, assignment; 9, 10; 9, 11; 10... | def slope_percentile(self, date, mag):
date_diff = date[1:] - date[:len(date) - 1]
mag_diff = mag[1:] - mag[:len(mag) - 1]
index = np.where(mag_diff != 0.)
date_diff = date_diff[index]
mag_diff = mag_diff[index]
slope = date_diff / mag_diff
percentile_10 = np.perc... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:number_aware_alphabetical_cmp; 3, parameters; 3, 4; 3, 5; 4, identifier:str1; 5, identifier:str2; 6, block; 6, 7; 6, 55; 6, 65; 6, 75; 6, 89; 6, 93; 6, 125; 6, 152; 7, function_definition; 7, 8; 7, 9; 7, 11; 8, function_name:flatten_tokens; 9, ... | def number_aware_alphabetical_cmp(str1, str2):
def flatten_tokens(tokens):
l = []
for token in tokens:
if isinstance(token, str):
for char in token:
l.append(char)
else:
assert isinstance(token, float)
l.appe... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:sort_members; 3, parameters; 3, 4; 3, 5; 4, identifier:tup; 5, identifier:names; 6, block; 6, 7; 6, 30; 6, 53; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 12; 9, pattern_list; 9, 10; 9, 11; 10, identifier:scalars; 11, identifier:tupl... | def sort_members(tup, names):
scalars, tuples = partition(lambda x: not is_tuple_node(tup.member[x].value), names)
unbound, bound = partition(lambda x: tup.member[x].value.is_unbound(), scalars)
return usorted(unbound) + usorted(bound), usorted(tuples) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:sort_schemas; 3, parameters; 3, 4; 4, identifier:schemas; 5, block; 5, 6; 5, 60; 6, function_definition; 6, 7; 6, 8; 6, 10; 7, function_name:keyfun; 8, parameters; 8, 9; 9, identifier:v; 10, block; 10, 11; 10, 24; 11, expression_statement; 11, ... | def sort_schemas(schemas):
def keyfun(v):
x = SQL_SCHEMA_REGEXP.match(v).groups()
return (int(x[0]), x[1], int(x[2]) if x[2] else None,
x[3] if x[3] else 'zzz', int(x[4]))
return sorted(schemas, key=keyfun) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:sort_nodes; 3, parameters; 3, 4; 3, 5; 4, identifier:dom; 5, identifier:cmp_func; 6, block; 6, 7; 6, 13; 7, expression_statement; 7, 8; 8, call; 8, 9; 8, 12; 9, attribute; 9, 10; 9, 11; 10, identifier:dom; 11, identifier:normalize; 12, argument... | def sort_nodes(dom, cmp_func):
dom.normalize()
for node in list(walk_dom(dom, elements_only=True)):
prev_sib = node.previousSibling
while prev_sib and cmp_func(prev_sib, node) == 1:
node.parentNode.insertBefore(node, prev_sib)
prev_sib = node.previousSibling |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 1, 7; 2, function_name:currentdir; 3, parameters; 3, 4; 4, identifier:self; 5, type; 5, 6; 6, identifier:str; 7, block; 7, 8; 7, 99; 8, if_statement; 8, 9; 8, 14; 9, comparison_operator:is; 9, 10; 9, 13; 10, attribute; 10, 11; 10, 12; 11, identifier:self; 12, i... | def currentdir(self) -> str:
if self._currentdir is None:
directories = self.availabledirs.folders
if len(directories) == 1:
self.currentdir = directories[0]
elif self.DEFAULTDIR in directories:
self.currentdir = self.DEFAULTDIR
els... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 1, 7; 2, function_name:zip_currentdir; 3, parameters; 3, 4; 4, identifier:self; 5, type; 5, 6; 6, None; 7, block; 7, 8; 7, 48; 8, with_statement; 8, 9; 8, 21; 9, with_clause; 9, 10; 10, with_item; 10, 11; 11, as_pattern; 11, 12; 11, 19; 12, call; 12, 13; 12, 16... | def zip_currentdir(self) -> None:
with zipfile.ZipFile(f'{self.currentpath}.zip', 'w') as zipfile_:
for filepath, filename in zip(self.filepaths, self.filenames):
zipfile_.write(filename=filepath, arcname=filename)
del self.currentdir |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 1, 11; 2, function_name:keywords; 3, parameters; 3, 4; 4, identifier:self; 5, type; 5, 6; 6, generic_type; 6, 7; 6, 8; 7, identifier:Set; 8, type_parameter; 8, 9; 9, type; 9, 10; 10, identifier:str; 11, block; 11, 12; 12, return_statement; 12, 13; 13, call; 13,... | def keywords(self) -> Set[str]:
return set(keyword for device in self
for keyword in device.keywords if
keyword not in self._shadowed_keywords) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 1, 11; 2, function_name:variables; 3, parameters; 3, 4; 4, identifier:self; 5, type; 5, 6; 6, generic_type; 6, 7; 6, 8; 7, identifier:Set; 8, type_parameter; 8, 9; 9, type; 9, 10; 10, identifier:str; 11, block; 11, 12; 11, 24; 11, 39; 12, expression_statement; ... | def variables(self) -> Set[str]:
variables: Set[str] = set()
for connection in self.__connections:
variables.update(connection.variables)
return variables |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 1, 23; 2, function_name:model2subs2seqs; 3, parameters; 3, 4; 4, identifier:self; 5, type; 5, 6; 6, generic_type; 6, 7; 6, 8; 7, identifier:Dict; 8, type_parameter; 8, 9; 8, 11; 9, type; 9, 10; 10, identifier:str; 11, type; 11, 12; 12, generic_type; 12, 13; 12,... | def model2subs2seqs(self) -> Dict[str, Dict[str, List[str]]]:
model2subs2seqs = collections.defaultdict(
lambda: collections.defaultdict(list))
for model in self.find('sequences'):
model_name = strip(model.tag)
if model_name == 'node':
continue
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 1, 17; 2, function_name:subs2seqs; 3, parameters; 3, 4; 4, identifier:self; 5, type; 5, 6; 6, generic_type; 6, 7; 6, 8; 7, identifier:Dict; 8, type_parameter; 8, 9; 8, 11; 9, type; 9, 10; 10, identifier:str; 11, type; 11, 12; 12, generic_type; 12, 13; 12, 14; 1... | def subs2seqs(self) -> Dict[str, List[str]]:
subs2seqs = collections.defaultdict(list)
nodes = find(self.find('sequences'), 'node')
if nodes is not None:
for seq in nodes:
subs2seqs['node'].append(strip(seq.tag))
return subs2seqs |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 4; 1, 10; 2, function_name:get_modelnames; 3, parameters; 4, type; 4, 5; 5, generic_type; 5, 6; 5, 7; 6, identifier:List; 7, type_parameter; 7, 8; 8, type; 8, 9; 9, identifier:str; 10, block; 10, 11; 11, return_statement; 11, 12; 12, call; 12, 13; 12, 14; 13, iden... | def get_modelnames() -> List[str]:
return sorted(str(fn.split('.')[0])
for fn in os.listdir(models.__path__[0])
if (fn.endswith('.py') and (fn != '__init__.py'))) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 1, 15; 2, function_name:toys; 3, parameters; 3, 4; 4, identifier:self; 5, type; 5, 6; 6, generic_type; 6, 7; 6, 8; 7, identifier:Tuple; 8, type_parameter; 8, 9; 8, 13; 9, type; 9, 10; 10, attribute; 10, 11; 10, 12; 11, identifier:timetools; 12, identifier:TOY; ... | def toys(self) -> Tuple[timetools.TOY, ...]:
return tuple(toy for (toy, _) in self) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 1, 8; 2, function_name:collect_variables; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:selections; 6, type; 6, 7; 7, None; 8, block; 8, 9; 9, expression_statement; 9, 10; 10, call; 10, 11; 10, 14; 11, attribute; 11, 12; 11, 13; 12, identifier:se... | def collect_variables(self, selections) -> None:
self.insert_variables(self.device2target, self.targetspecs, selections) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 1, 8; 2, function_name:collect_variables; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:selections; 6, type; 6, 7; 7, None; 8, block; 8, 9; 8, 18; 9, expression_statement; 9, 10; 10, call; 10, 11; 10, 16; 11, attribute; 11, 12; 11, 15; 12, call; ... | def collect_variables(self, selections) -> None:
super().collect_variables(selections)
self.insert_variables(self.device2base, self.basespecs, selections) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 14; 2, function_name:save_controls; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:parameterstep; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:simulationstep; 10, None; 11, default_parameter... | def save_controls(self, parameterstep=None, simulationstep=None,
auxfiler=None):
self.elements.save_controls(parameterstep=parameterstep,
simulationstep=simulationstep,
auxfiler=auxfiler) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:variables; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 13; 5, 28; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:variables; 9, call; 9, 10; 9, 11; 10, identifier:set; 11, argument_list; 11, 12; 12, list:... | def variables(self):
variables = set([])
for node in self.nodes:
variables.add(node.variable)
return sorted(variables) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 1, 15; 2, function_name:sort_timeplaceentries; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:self; 5, identifier:timeentry; 6, identifier:placeentry; 7, type; 7, 8; 8, generic_type; 8, 9; 8, 10; 9, identifier:Tuple; 10, type_parameter; 10, 11; 10, 13; 11, type... | def sort_timeplaceentries(self, timeentry, placeentry) -> Tuple[Any, Any]:
if self._timeaxis:
return placeentry, timeentry
return timeentry, placeentry |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 4; 1, 16; 2, function_name:prepare_io_example_1; 3, parameters; 4, type; 4, 5; 5, generic_type; 5, 6; 5, 7; 6, identifier:Tuple; 7, type_parameter; 7, 8; 7, 12; 8, type; 8, 9; 9, attribute; 9, 10; 9, 11; 10, identifier:devicetools; 11, identifier:Nodes; 12, type; ... | def prepare_io_example_1() -> Tuple[devicetools.Nodes, devicetools.Elements]:
from hydpy import TestIO
TestIO.clear()
from hydpy.core.filetools import SequenceManager
hydpy.pub.sequencemanager = SequenceManager()
with TestIO():
hydpy.pub.sequencemanager.inputdirpath = 'inputpath'
hyd... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 29; 2, function_name:comparison_table; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 17; 3, 20; 3, 23; 3, 26; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:caption; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:label; 10, stri... | def comparison_table(self, caption=None, label="tab:model_comp", hlines=True,
aic=True, bic=True, dic=True, sort="bic", descending=True):
if sort == "bic":
assert bic, "You cannot sort by BIC if you turn it off"
if sort == "aic":
assert aic, "You cannot s... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:_initDevClasses; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 12; 5, 18; 5, 24; 5, 28; 5, 32; 5, 45; 5, 153; 5, 165; 5, 177; 5, 181; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 11; 8, attribute; 8, 9; 8, 10; 9, identif... | def _initDevClasses(self):
self._devClassTree = {}
self._partitionTree = {}
self._mapDevType = {}
basedevs = []
otherdevs = []
if self._mapMajorDevclass is None:
self._initBlockMajorMap()
for dev in self._diskStats:
stats = self._diskStats[... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 10; 2, function_name:zdiffstore; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:self; 5, identifier:dest; 6, identifier:keys; 7, default_parameter; 7, 8; 7, 9; 8, identifier:withscores; 9, False; 10, block; 10, 11; 10, 13; 10, 23; 10, 30; 11, expression_stat... | def zdiffstore(self, dest, keys, withscores=False):
'''Compute the difference of multiple sorted.
The difference of sets specified by ``keys`` into a new sorted set
in ``dest``.
'''
keys = (dest,) + tuple(keys)
wscores = 'withscores' if withscores else ''
r... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 19; 2, function_name:places_within_radius; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 17; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:place; 7, None; 8, default_parameter; 8, 9; 8, 10; 9, identifier:latitude; 10, None; 11, default_pa... | def places_within_radius(
self, place=None, latitude=None, longitude=None, radius=0, **kwargs
):
kwargs['withdist'] = True
kwargs['withcoord'] = True
kwargs['withhash'] = False
kwargs.setdefault('sort', 'ASC')
unit = kwargs.setdefault('unit', 'km')
if place is... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:naturalize_person; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:string; 6, block; 6, 7; 6, 20; 6, 34; 6, 44; 6, 48; 6, 52; 6, 56; 6, 60; 6, 69; 6, 103; 6, 165; 6, 178; 6, 187; 7, expression_statement; 7, 8; 8, assignment; 8, 9; ... | def naturalize_person(self, string):
suffixes = [
'Jr', 'Jr.', 'Sr', 'Sr.',
'I', 'II', 'III', 'IV', 'V',
]
suffixes = suffixes + [s.lower() for s in suffixes]
particles = [
'Le', 'La',
'Von', 'Van... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:get_countries; 3, parameters; 3, 4; 4, identifier:self; 5, block; 5, 6; 5, 36; 5, 40; 5, 66; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:qs; 9, call; 9, 10; 9, 34; 10, attribute; 10, 11; 10, 32; 10, 33; 11, call; 11,... | def get_countries(self):
qs = Venue.objects.values('country') \
.exclude(country='') \
.distinct() \
.order_by('country')
countries = []
for c in qs:
countries.append({
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 13; 2, function_name:fit; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 10; 4, identifier:self; 5, identifier:t; 6, identifier:y; 7, default_parameter; 7, 8; 7, 9; 8, identifier:dy; 9, integer:1; 10, default_parameter; 10, 11; 10, 12; 11, identifier:presorted; 12, Fal... | def fit(self, t, y, dy=1, presorted=False):
self.t, self.y, self.dy = self._validate_inputs(t, y, dy, presorted)
self._fit(self.t, self.y, self.dy)
return self |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:validate_inputs; 3, parameters; 3, 4; 3, 6; 4, list_splat_pattern; 4, 5; 5, identifier:arrays; 6, dictionary_splat_pattern; 6, 7; 7, identifier:kwargs; 8, block; 8, 9; 8, 19; 8, 29; 8, 46; 8, 60; 8, 103; 9, expression_statement; 9, 10; 10, assi... | def validate_inputs(*arrays, **kwargs):
arrays = np.broadcast_arrays(*arrays)
sort_by = kwargs.pop('sort_by', None)
if kwargs:
raise ValueError("unrecognized arguments: {0}".format(kwargs.keys()))
if arrays[0].ndim != 1:
raise ValueError("Input arrays should be one-dimensional.")
if ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 10; 2, function_name:multinterp; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:x; 5, identifier:y; 6, identifier:xquery; 7, default_parameter; 7, 8; 7, 9; 8, identifier:slow; 9, False; 10, block; 10, 11; 10, 27; 10, 33; 10, 39; 10, 51; 10, 70; 11, expressio... | def multinterp(x, y, xquery, slow=False):
x, y, xquery = map(np.asarray, (x, y, xquery))
assert x.ndim == 1
assert xquery.ndim == 1
assert y.shape == x.shape + xquery.shape
xquery = np.clip(xquery, x.min(), x.max())
if slow:
from scipy.interpolate import interp1d
return np.array(... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 12; 2, function_name:check_valid_time_and_sort; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 4, identifier:df; 5, identifier:timescol; 6, default_parameter; 6, 7; 6, 8; 7, identifier:days; 8, integer:5; 9, default_parameter; 9, 10; 9, 11; 10, identifier:warning; 11, Tru... | def check_valid_time_and_sort(df, timescol, days=5, warning=True):
timediff = (df[timescol].max() - df[timescol].min()).days
if timediff < days:
return df.sort_values(timescol).reset_index(drop=True).reset_index()
else:
if warning:
sys.stderr.write(
"\nWarning: da... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 18; 2, function_name:list_anime_series; 3, parameters; 3, 4; 3, 5; 3, 10; 3, 15; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:sort; 7, attribute; 7, 8; 7, 9; 8, identifier:META; 9, identifier:SORT_ALPHA; 10, default_parameter; 10, 11; 10, 12... | def list_anime_series(self, sort=META.SORT_ALPHA, limit=META.MAX_SERIES, offset=0):
result = self._android_api.list_series(
media_type=ANDROID.MEDIA_TYPE_ANIME,
filter=sort,
limit=limit,
offset=offset)
return result |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 18; 2, function_name:list_drama_series; 3, parameters; 3, 4; 3, 5; 3, 10; 3, 15; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:sort; 7, attribute; 7, 8; 7, 9; 8, identifier:META; 9, identifier:SORT_ALPHA; 10, default_parameter; 10, 11; 10, 12... | def list_drama_series(self, sort=META.SORT_ALPHA, limit=META.MAX_SERIES, offset=0):
result = self._android_api.list_series(
media_type=ANDROID.MEDIA_TYPE_DRAMA,
filter=sort,
limit=limit,
offset=offset)
return result |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 19; 2, function_name:list_media; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 11; 3, 16; 4, identifier:self; 5, identifier:series; 6, default_parameter; 6, 7; 6, 8; 7, identifier:sort; 8, attribute; 8, 9; 8, 10; 9, identifier:META; 10, identifier:SORT_DESC; 11, default_par... | def list_media(self, series, sort=META.SORT_DESC, limit=META.MAX_MEDIA, offset=0):
params = {
'sort': sort,
'offset': offset,
'limit': limit,
}
params.update(self._get_series_query_dict(series))
result = self._android_api.list_media(**params)
r... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:solve_sort; 3, parameters; 3, 4; 3, 5; 4, identifier:expr; 5, identifier:vars; 6, block; 6, 7; 6, 24; 6, 30; 6, 50; 6, 62; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:lhs_values; 10, call; 10, 11; 10, 14; 11, attrib... | def solve_sort(expr, vars):
lhs_values = repeated.getvalues(__solve_for_repeated(expr.lhs, vars)[0])
sort_expression = expr.rhs
def _key_func(x):
return solve(sort_expression, __nest_scope(expr.lhs, vars, x)).value
results = ordered.ordered(lhs_values, key_func=_key_func)
return Result(repea... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:expression; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:previous_precedence; 7, integer:0; 8, block; 8, 9; 8, 17; 9, expression_statement; 9, 10; 10, assignment; 10, 11; 10, 12; 11, identifier:... | def expression(self, previous_precedence=0):
lhs = self.atom()
return self.operator(lhs, previous_precedence) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:application; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:func; 6, block; 6, 7; 6, 17; 6, 53; 6, 62; 6, 85; 6, 96; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:start; 10, attribute; 10, 11; 10, 16; 11... | def application(self, func):
start = self.tokens.matched.start
if self.tokens.accept(common_grammar.rparen):
return ast.Apply(func, start=start, end=self.tokens.matched.end,
source=self.original)
arguments = [self.expression()]
while self.tokens.a... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:value_eq; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:other; 6, block; 6, 7; 6, 20; 6, 34; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:self_sorted; 10, call; 10, 11; 10, 14; 11, attribute; 11, 12; 1... | def value_eq(self, other):
self_sorted = ordered.ordered(self.getvalues())
other_sorted = ordered.ordered(repeated.getvalues(other))
return self_sorted == other_sorted |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:merge; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:a_intervals; 5, identifier:b_intervals; 6, identifier:op; 7, block; 7, 8; 7, 20; 7, 32; 7, 48; 7, 53; 7, 58; 7, 62; 7, 66; 7, 70; 7, 82; 7, 177; 8, expression_statement; 8, 9; 9, assignment;... | def merge(a_intervals, b_intervals, op):
a_endpoints = a_intervals.flatten().tolist()
b_endpoints = b_intervals.flatten().tolist()
sentinel = max(a_endpoints[-1], b_endpoints[-1]) + 1
a_endpoints += [sentinel]
b_endpoints += [sentinel]
a_index = 0
b_index = 0
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:check_bam; 3, parameters; 3, 4; 3, 5; 4, identifier:bam; 5, default_parameter; 5, 6; 5, 7; 6, identifier:samtype; 7, string:"bam"; 8, block; 8, 9; 8, 16; 8, 26; 8, 58; 8, 89; 8, 143; 9, expression_statement; 9, 10; 10, call; 10, 11; 10, 14; 11,... | def check_bam(bam, samtype="bam"):
ut.check_existance(bam)
samfile = pysam.AlignmentFile(bam, "rb")
if not samfile.has_index():
pysam.index(bam)
samfile = pysam.AlignmentFile(bam, "rb")
logging.info("Nanoget: No index for bam file could be found, created index.")
if not samfile.h... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 21; 2, function_name:get_input; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 9; 3, 12; 3, 15; 3, 18; 4, identifier:source; 5, identifier:files; 6, default_parameter; 6, 7; 6, 8; 7, identifier:threads; 8, integer:4; 9, default_parameter; 9, 10; 9, 11; 10, identifier:readtyp... | def get_input(source, files, threads=4, readtype="1D",
combine="simple", names=None, barcoded=False):
proc_functions = {
'fastq': ex.process_fastq_plain,
'fasta': ex.process_fasta,
'bam': ex.process_bam,
'summary': ex.process_summary,
'fastq_rich': ex.process_fa... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:validate_wavelengths; 3, parameters; 3, 4; 4, identifier:wavelengths; 5, block; 5, 6; 5, 36; 5, 49; 5, 58; 5, 87; 5, 96; 5, 145; 6, if_statement; 6, 7; 6, 14; 6, 30; 7, call; 7, 8; 7, 9; 8, identifier:isinstance; 9, argument_list; 9, 10; 9, 11;... | def validate_wavelengths(wavelengths):
if isinstance(wavelengths, u.Quantity):
units.validate_wave_unit(wavelengths.unit)
wave = wavelengths.value
else:
wave = wavelengths
if np.isscalar(wave):
wave = [wave]
wave = np.asarray(wave)
if np.any(wave <= 0):
raise ... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:heapify; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:key; 7, identifier:__marker; 8, block; 8, 9; 9, if_statement; 9, 10; 9, 15; 9, 44; 10, comparison_operator:is; 10, 11; 10, 12; 11, identifie... | def heapify(self, key=__marker):
if key is self.__marker:
n = len(self._heap)
for pos in reversed(range(n//2)):
self._sink(pos)
else:
try:
pos = self._position[key]
except KeyError:
raise KeyError(key)
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 29; 1, 31; 2, function_name:__update_display_items_model; 3, parameters; 3, 4; 3, 5; 3, 11; 3, 21; 4, identifier:self; 5, typed_parameter; 5, 6; 5, 7; 6, identifier:display_items_model; 7, type; 7, 8; 8, attribute; 8, 9; 8, 10; 9, identifier:ListModel; 10, identif... | def __update_display_items_model(self, display_items_model: ListModel.FilteredListModel, data_group: typing.Optional[DataGroup.DataGroup], filter_id: typing.Optional[str]) -> None:
with display_items_model.changes():
if data_group is not None:
display_items_model.container = data_gro... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:sort_by_date_key; 3, parameters; 3, 4; 4, identifier:data_item; 5, block; 5, 6; 6, return_statement; 6, 7; 7, expression_list; 7, 8; 7, 25; 7, 28; 8, conditional_expression:if; 8, 9; 8, 19; 8, 22; 9, binary_operator:+; 9, 10; 9, 13; 10, attribu... | def sort_by_date_key(data_item):
return data_item.title + str(data_item.uuid) if data_item.is_live else str(), data_item.date_for_sorting, str(data_item.uuid) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 19; 2, function_name:open_mfbpchdataset; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 3, 17; 4, identifier:paths; 5, default_parameter; 5, 6; 5, 7; 6, identifier:concat_dim; 7, string:'time'; 8, default_parameter; 8, 9; 8, 10; 9, identifier:compat; 10, string:'n... | def open_mfbpchdataset(paths, concat_dim='time', compat='no_conflicts',
preprocess=None, lock=None, **kwargs):
from xarray.backends.api import _MultiFileCloser
dask = kwargs.pop('dask', False)
if not dask:
raise ValueError("Reading multiple files without dask is not supported"... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:_get_archive_filelist; 3, parameters; 3, 4; 4, identifier:filename; 5, block; 5, 6; 5, 10; 5, 88; 5, 100; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:names; 9, list:[]; 10, if_statement; 10, 11; 10, 17; 10, 42; 10, 7... | def _get_archive_filelist(filename):
names = []
if tarfile.is_tarfile(filename):
with tarfile.open(filename) as tar_file:
names = sorted(tar_file.getnames())
elif zipfile.is_zipfile(filename):
with zipfile.ZipFile(filename) as zip_file:
names = sorted(zip_file.namelis... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 10; 2, function_name:pbar_strings; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:files; 5, default_parameter; 5, 6; 5, 7; 6, identifier:desc; 7, string:''; 8, dictionary_splat_pattern; 8, 9; 9, identifier:kwargs; 10, block; 10, 11; 11, return_statement; 11, 12; 1... | def pbar_strings(files, desc='', **kwargs):
return tqdm(
sorted(files, key=lambda s: s.lower()),
desc=('<' + str(datetime.now().strftime("%Y-%m-%d %H:%M:%S")) + '> ' +
desc),
dynamic_ncols=True,
**kwargs) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:sort_func; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:key; 6, block; 6, 7; 6, 18; 6, 29; 6, 40; 7, if_statement; 7, 8; 7, 15; 8, comparison_operator:==; 8, 9; 8, 10; 9, identifier:key; 10, attribute; 10, 11; 10, 14; 11, attrib... | def sort_func(self, key):
if key == self._KEYS.TIME:
return 'aaa'
if key == self._KEYS.DATA:
return 'zzy'
if key == self._KEYS.SOURCE:
return 'zzz'
return key |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:sort_func; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:key; 6, block; 6, 7; 6, 18; 6, 29; 7, if_statement; 7, 8; 7, 15; 8, comparison_operator:==; 8, 9; 8, 10; 9, identifier:key; 10, attribute; 10, 11; 10, 14; 11, attribute; 11... | def sort_func(self, key):
if key == self._KEYS.VALUE:
return 'aaa'
if key == self._KEYS.SOURCE:
return 'zzz'
return key |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:sort_func; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:key; 6, block; 6, 7; 6, 18; 6, 29; 6, 40; 6, 51; 6, 62; 6, 73; 6, 84; 7, if_statement; 7, 8; 7, 15; 8, comparison_operator:==; 8, 9; 8, 10; 9, identifier:key; 10, attribute... | def sort_func(self, key):
if key == self._KEYS.SCHEMA:
return 'aaa'
if key == self._KEYS.NAME:
return 'aab'
if key == self._KEYS.SOURCES:
return 'aac'
if key == self._KEYS.ALIAS:
return 'aad'
if key == self._KEYS.MODELS:
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:sort_func; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:key; 6, block; 6, 7; 6, 18; 6, 29; 6, 40; 7, if_statement; 7, 8; 7, 15; 8, comparison_operator:==; 8, 9; 8, 10; 9, identifier:key; 10, attribute; 10, 11; 10, 14; 11, attrib... | def sort_func(self, key):
if key == self._KEYS.TIME:
return 'aaa'
if key == self._KEYS.MODEL:
return 'zzy'
if key == self._KEYS.SOURCE:
return 'zzz'
return key |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:TypeFactory; 3, parameters; 3, 4; 4, identifier:type_; 5, block; 5, 6; 5, 21; 5, 40; 6, if_statement; 6, 7; 6, 18; 7, boolean_operator:and; 7, 8; 7, 13; 8, call; 8, 9; 8, 10; 9, identifier:isinstance; 10, argument_list; 10, 11; 10, 12; 11, iden... | def TypeFactory(type_):
if isinstance(type_, type) and issubclass(type_, Type):
return type_
for x in __types__:
if x.represents(type_):
return x.get(type_)
raise UnknownType(type_) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:get_sorted_dependencies; 3, parameters; 3, 4; 4, identifier:service_model; 5, block; 5, 6; 5, 21; 5, 33; 5, 60; 5, 77; 6, expression_statement; 6, 7; 7, assignment; 7, 8; 7, 9; 8, identifier:app_models; 9, call; 9, 10; 9, 11; 10, identifier:lis... | def get_sorted_dependencies(service_model):
app_models = list(service_model._meta.app_config.get_models())
dependencies = {model: set() for model in app_models}
relations = (
relation
for model in app_models
for relation in model._meta.related_objects
if relation.on_delete in... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:format_time_and_value_to_segment_list; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 8; 4, identifier:time_and_value_list; 5, identifier:segments_count; 6, identifier:start_timestamp; 7, identifier:end_timestamp; 8, default_parameter; 8, 9; 8, 10;... | def format_time_and_value_to_segment_list(time_and_value_list, segments_count, start_timestamp,
end_timestamp, average=False):
segment_list = []
time_step = (end_timestamp - start_timestamp) / segments_count
for i in range(segments_count):
segment_start_time... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:get_api_root_view; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:api_urls; 7, None; 8, block; 8, 9; 8, 15; 8, 25; 8, 47; 8, 154; 9, expression_statement; 9, 10; 10, assignment; 10, 11; 10, 12; 11... | def get_api_root_view(self, api_urls=None):
api_root_dict = OrderedDict()
list_name = self.routes[0].name
for prefix, viewset, basename in self.registry:
api_root_dict[prefix] = list_name.format(basename=basename)
class APIRootView(views.APIView):
_ignore_model_pe... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:get_default_base_name; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:viewset; 6, block; 6, 7; 6, 16; 6, 41; 7, expression_statement; 7, 8; 8, assignment; 8, 9; 8, 10; 9, identifier:queryset; 10, call; 10, 11; 10, 12; 11, identifi... | def get_default_base_name(self, viewset):
queryset = getattr(viewset, 'queryset', None)
if queryset is not None:
get_url_name = getattr(queryset.model, 'get_url_name', None)
if get_url_name is not None:
return get_url_name()
return super(SortedDefaultRoute... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:sort_dict; 3, parameters; 3, 4; 3, 5; 4, identifier:d; 5, default_parameter; 5, 6; 5, 7; 6, identifier:desc; 7, True; 8, block; 8, 9; 8, 31; 9, expression_statement; 9, 10; 10, assignment; 10, 11; 10, 12; 11, identifier:sort; 12, call; 12, 13; ... | def sort_dict(d, desc=True):
sort = sorted(d.items(), key=lambda x: x[1], reverse=desc)
return OrderedDict(sort) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 23; 2, function_name:_tupleCompare; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 17; 3, 20; 4, identifier:tuple1; 5, identifier:ineq; 6, identifier:tuple2; 7, default_parameter; 7, 8; 7, 9; 8, identifier:eq; 9, lambda; 9, 10; 9, 13; 10, lambda_parameters; 10, 11; 10,... | def _tupleCompare(tuple1, ineq, tuple2,
eq=lambda a,b: (a==b),
ander=AND,
orer=OR):
orholder = []
for limit in range(len(tuple1)):
eqconstraint = [
eq(elem1, elem2) for elem1, elem2 in zip(tuple1, tuple2)[:limit]]
ineqconstraint = in... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 10; 2, function_name:get_datasets; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:self; 5, default_parameter; 5, 6; 5, 7; 6, identifier:query; 7, string:'*:*'; 8, dictionary_splat_pattern; 8, 9; 9, identifier:kwargs; 10, block; 10, 11; 11, return_statement; 11, 12... | def get_datasets(self, query='*:*', **kwargs):
return hdx.data.dataset.Dataset.search_in_hdx(query=query,
configuration=self.configuration,
fq='organization:%s' % self.data['name'], **kwargs) |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:get_all_organization_names; 3, parameters; 3, 4; 3, 7; 4, default_parameter; 4, 5; 4, 6; 5, identifier:configuration; 6, None; 7, dictionary_splat_pattern; 7, 8; 8, identifier:kwargs; 9, block; 9, 10; 9, 19; 9, 25; 10, expression_statement; 10,... | def get_all_organization_names(configuration=None, **kwargs):
organization = Organization(configuration=configuration)
organization['id'] = 'all organizations'
return organization._write_to_hdx('list', kwargs, 'id') |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 16; 2, function_name:search_in_hdx; 3, parameters; 3, 4; 3, 5; 3, 8; 3, 11; 3, 14; 4, identifier:cls; 5, default_parameter; 5, 6; 5, 7; 6, identifier:query; 7, string:'*:*'; 8, default_parameter; 8, 9; 8, 10; 9, identifier:configuration; 10, None; 11, default_para... | def search_in_hdx(cls, query='*:*', configuration=None, page_size=1000, **kwargs):
dataset = Dataset(configuration=configuration)
total_rows = kwargs.get('rows', cls.max_int)
start = kwargs.get('start', 0)
all_datasets = None
attempts = 0
while attempts < cls.max_attempts... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 18; 1, 22; 2, function_name:sort_dict; 3, parameters; 3, 4; 3, 8; 3, 13; 4, typed_parameter; 4, 5; 4, 6; 5, identifier:d; 6, type; 6, 7; 7, identifier:dict; 8, typed_default_parameter; 8, 9; 8, 10; 8, 12; 9, identifier:by; 10, type; 10, 11; 11, identifier:str; 12,... | def sort_dict(d: dict, by: str = 'key',
allow_duplicates: bool = True) -> collections.OrderedDict:
if by == 'key':
i = 0
elif by == 'value':
values = list(d.values())
if len(values) != len(set(values)) and not allow_duplicates:
duplicates = find_duplicates(value... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:get_all_users; 3, parameters; 3, 4; 3, 7; 4, default_parameter; 4, 5; 4, 6; 5, identifier:configuration; 6, None; 7, dictionary_splat_pattern; 7, 8; 8, identifier:kwargs; 9, block; 9, 10; 9, 19; 9, 25; 9, 36; 9, 42; 9, 75; 10, expression_statem... | def get_all_users(configuration=None, **kwargs):
user = User(configuration=configuration)
user['id'] = 'all users'
result = user._write_to_hdx('list', kwargs, 'id')
users = list()
if result:
for userdict in result:
user = User(userdict, configuration=c... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:fromkeys; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:cls; 5, identifier:iterable; 6, default_parameter; 6, 7; 6, 8; 7, identifier:value; 8, None; 9, block; 9, 10; 9, 28; 10, if_statement; 10, 11; 10, 16; 11, not_operator; 11, 12; 12, call; ... | def fromkeys(cls, iterable, value=None):
if not callable(value):
return cls(dict.fromkeys(iterable, value))
return cls((key, value(key)) for key in iterable) |
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