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value | func_code_url stringlengths 87 315 |
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kislyuk/aegea | aegea/packages/github3/repos/repo.py | Repository.release | def release(self, id):
"""Get a single release.
:param int id: (required), id of release
:returns: :class:`Release <github3.repos.release.Release>`
"""
json = None
if int(id) > 0:
url = self._build_url('releases', str(id), base_url=self._api)
json... | python | def release(self, id):
"""Get a single release.
:param int id: (required), id of release
:returns: :class:`Release <github3.repos.release.Release>`
"""
json = None
if int(id) > 0:
url = self._build_url('releases', str(id), base_url=self._api)
json... | [
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kislyuk/aegea | aegea/packages/github3/repos/repo.py | Repository.remove_collaborator | def remove_collaborator(self, login):
"""Remove collaborator ``login`` from the repository.
:param str login: (required), login name of the collaborator
:returns: bool
"""
resp = False
if login:
url = self._build_url('collaborators', login, base_url=self._api... | python | def remove_collaborator(self, login):
"""Remove collaborator ``login`` from the repository.
:param str login: (required), login name of the collaborator
:returns: bool
"""
resp = False
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kislyuk/aegea | aegea/packages/github3/repos/repo.py | Repository.tag | def tag(self, sha):
"""Get an annotated tag.
http://learn.github.com/p/tagging.html
:param str sha: (required), sha of the object for this tag
:returns: :class:`Tag <github3.git.Tag>`
"""
json = None
if sha:
url = self._build_url('git', 'tags', sha, ... | python | def tag(self, sha):
"""Get an annotated tag.
http://learn.github.com/p/tagging.html
:param str sha: (required), sha of the object for this tag
:returns: :class:`Tag <github3.git.Tag>`
"""
json = None
if sha:
url = self._build_url('git', 'tags', sha, ... | [
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kislyuk/aegea | aegea/packages/github3/repos/repo.py | Repository.tree | def tree(self, sha):
"""Get a tree.
:param str sha: (required), sha of the object for this tree
:returns: :class:`Tree <github3.git.Tree>`
"""
json = None
if sha:
url = self._build_url('git', 'trees', sha, base_url=self._api)
json = self._json(sel... | python | def tree(self, sha):
"""Get a tree.
:param str sha: (required), sha of the object for this tree
:returns: :class:`Tree <github3.git.Tree>`
"""
json = None
if sha:
url = self._build_url('git', 'trees', sha, base_url=self._api)
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kislyuk/aegea | aegea/packages/github3/repos/repo.py | Repository.update_label | def update_label(self, name, color, new_name=''):
"""Update the label ``name``.
:param str name: (required), name of the label
:param str color: (required), color code
:param str new_name: (optional), new name of the label
:returns: bool
"""
label = self.label(na... | python | def update_label(self, name, color, new_name=''):
"""Update the label ``name``.
:param str name: (required), name of the label
:param str color: (required), color code
:param str new_name: (optional), new name of the label
:returns: bool
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kislyuk/aegea | aegea/packages/github3/repos/repo.py | Repository.weekly_commit_count | def weekly_commit_count(self):
"""Returns the total commit counts.
The dictionary returned has two entries: ``all`` and ``owner``. Each
has a fifty-two element long list of commit counts. (Note: ``all``
includes the owner.) ``d['all'][0]`` will be the oldest week,
``d['all'][51]... | python | def weekly_commit_count(self):
"""Returns the total commit counts.
The dictionary returned has two entries: ``all`` and ``owner``. Each
has a fifty-two element long list of commit counts. (Note: ``all``
includes the owner.) ``d['all'][0]`` will be the oldest week,
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kislyuk/aegea | aegea/instance_ctl.py | rename | def rename(args):
"""Supply two names: Existing instance name or ID, and new name to assign to the instance."""
old_name, new_name = args.names
add_tags(resources.ec2.Instance(resolve_instance_id(old_name)), Name=new_name, dry_run=args.dry_run) | python | def rename(args):
"""Supply two names: Existing instance name or ID, and new name to assign to the instance."""
old_name, new_name = args.names
add_tags(resources.ec2.Instance(resolve_instance_id(old_name)), Name=new_name, dry_run=args.dry_run) | [
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kislyuk/aegea | aegea/packages/github3/repos/deployment.py | Deployment.create_status | def create_status(self, state, target_url='', description=''):
"""Create a new deployment status for this deployment.
:param str state: (required), The state of the status. Can be one of
``pending``, ``success``, ``error``, or ``failure``.
:param str target_url: The target URL to as... | python | def create_status(self, state, target_url='', description=''):
"""Create a new deployment status for this deployment.
:param str state: (required), The state of the status. Can be one of
``pending``, ``success``, ``error``, or ``failure``.
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kislyuk/aegea | aegea/packages/github3/repos/deployment.py | Deployment.iter_statuses | def iter_statuses(self, number=-1, etag=None):
"""Iterate over the deployment statuses for this deployment.
:param int number: (optional), the number of statuses to return.
Default: -1, returns all statuses.
:param str etag: (optional), the ETag header value from the last time
... | python | def iter_statuses(self, number=-1, etag=None):
"""Iterate over the deployment statuses for this deployment.
:param int number: (optional), the number of statuses to return.
Default: -1, returns all statuses.
:param str etag: (optional), the ETag header value from the last time
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kislyuk/aegea | aegea/packages/github3/gists/history.py | GistHistory.get_gist | def get_gist(self):
"""Retrieve the gist at this version.
:returns: :class:`Gist <github3.gists.gist.Gist>`
"""
from .gist import Gist
json = self._json(self._get(self._api), 200)
return Gist(json, self) | python | def get_gist(self):
"""Retrieve the gist at this version.
:returns: :class:`Gist <github3.gists.gist.Gist>`
"""
from .gist import Gist
json = self._json(self._get(self._api), 200)
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kislyuk/aegea | aegea/packages/github3/git.py | Reference.update | def update(self, sha, force=False):
"""Update this reference.
:param str sha: (required), sha of the reference
:param bool force: (optional), force the update or not
:returns: bool
"""
data = {'sha': sha, 'force': force}
json = self._json(self._patch(self._api, ... | python | def update(self, sha, force=False):
"""Update this reference.
:param str sha: (required), sha of the reference
:param bool force: (optional), force the update or not
:returns: bool
"""
data = {'sha': sha, 'force': force}
json = self._json(self._patch(self._api, ... | [
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kislyuk/aegea | aegea/packages/github3/git.py | Tree.recurse | def recurse(self):
"""Recurse into the tree.
:returns: :class:`Tree <Tree>`
"""
json = self._json(self._get(self._api, params={'recursive': '1'}),
200)
return Tree(json, self._session) if json else None | python | def recurse(self):
"""Recurse into the tree.
:returns: :class:`Tree <Tree>`
"""
json = self._json(self._get(self._api, params={'recursive': '1'}),
200)
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kislyuk/aegea | aegea/util/printing.py | format_table | def format_table(table, column_names=None, column_specs=None, max_col_width=32, auto_col_width=False):
"""
Table pretty printer. Expects tables to be given as arrays of arrays::
print(format_table([[1, "2"], [3, "456"]], column_names=['A', 'B']))
"""
orig_col_args = dict(column_names=column_nam... | python | def format_table(table, column_names=None, column_specs=None, max_col_width=32, auto_col_width=False):
"""
Table pretty printer. Expects tables to be given as arrays of arrays::
print(format_table([[1, "2"], [3, "456"]], column_names=['A', 'B']))
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kislyuk/aegea | aegea/aegea_config.py | get | def get(args):
"""Get an Aegea configuration parameter by name"""
from . import config
for key in args.key.split("."):
config = getattr(config, key)
print(json.dumps(config)) | python | def get(args):
"""Get an Aegea configuration parameter by name"""
from . import config
for key in args.key.split("."):
config = getattr(config, key)
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kislyuk/aegea | aegea/aegea_config.py | set | def set(args):
"""Set an Aegea configuration parameter to a given value"""
from . import config, tweak
class ConfigSaver(tweak.Config):
@property
def config_files(self):
return [config.config_files[2]]
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"""Set an Aegea configuration parameter to a given value"""
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kislyuk/aegea | aegea/packages/github3/api.py | authorize | def authorize(login, password, scopes, note='', note_url='', client_id='',
client_secret='', two_factor_callback=None):
"""Obtain an authorization token for the GitHub API.
:param str login: (required)
:param str password: (required)
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kislyuk/aegea | aegea/packages/github3/api.py | iter_following | def iter_following(username, number=-1, etag=None):
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:param str username: (required), login of the user
:param int number: (optional), number of users being followed by username
to return. Default: -1, return all of them
:param str etag: (optional), ETag ... | python | def iter_following(username, number=-1, etag=None):
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kislyuk/aegea | aegea/packages/github3/api.py | iter_repo_issues | def iter_repo_issues(owner, repository, milestone=None, state=None,
assignee=None, mentioned=None, labels=None, sort=None,
direction=None, since=None, number=-1, etag=None):
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kislyuk/aegea | aegea/packages/github3/api.py | iter_user_repos | def iter_user_repos(login, type=None, sort=None, direction=None, number=-1,
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"""List public repositories for the specified ``login``.
.. versionadded:: 0.6
.. note:: This replaces github3.iter_repos
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:param str type: (optional), accepted ... | python | def iter_user_repos(login, type=None, sort=None, direction=None, number=-1,
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kislyuk/aegea | aegea/packages/github3/api.py | markdown | def markdown(text, mode='', context='', raw=False):
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:param str text: (required), the text of the document to render
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kislyuk/aegea | aegea/packages/github3/api.py | search_repositories | def search_repositories(query, sort=None, order=None, per_page=None,
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"""Find repositories via various criteria.
.. warning::
You will only be able to make 5 calls with this or other search
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kislyuk/aegea | aegea/ls.py | limits | def limits(args):
"""
Describe limits in effect on your AWS account. See also https://console.aws.amazon.com/ec2/v2/home#Limits:
"""
# https://aws.amazon.com/about-aws/whats-new/2014/06/19/amazon-ec2-service-limits-report-now-available/
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kislyuk/aegea | aegea/packages/github3/issues/issue.py | Issue.add_labels | def add_labels(self, *args):
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:param str args: (required), names of the labels you wish to add
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url = self._build_url('labels', base_url=self._api)
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:param str args: (required), names of the labels you wish to add
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kislyuk/aegea | aegea/packages/github3/issues/issue.py | Issue.assign | def assign(self, login):
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json = None
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kislyuk/aegea | aegea/packages/github3/issues/issue.py | Issue.iter_comments | def iter_comments(self, number=-1):
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:returns: iterator of
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url = self._build_url('comments'... | python | def iter_comments(self, number=-1):
"""Iterate over the comments on this issue.
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kislyuk/aegea | aegea/packages/github3/issues/issue.py | Issue.remove_label | def remove_label(self, name):
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url = self._build_url('labels', name, base_url=self._api)
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kislyuk/aegea | aegea/packages/github3/issues/issue.py | Issue.replace_labels | def replace_labels(self, labels):
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kislyuk/aegea | aegea/packages/github3/issues/issue.py | Issue.reopen | def reopen(self):
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"""
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number = self.milestone.number if self.milestone else None
labels = [str(l) for l in self.labels]
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"""Re-open a closed issue.
:returns: bool
"""
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kislyuk/aegea | aegea/packages/github3/models.py | GitHubObject._strptime | def _strptime(self, time_str):
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if time_str:
# Parse UTC string into naive datetime, then add timezone
dt = datetime.strptime(time_str, __timeformat__)
return dt.replace(tz... | python | def _strptime(self, time_str):
"""Convert an ISO 8601 formatted string in UTC into a
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kislyuk/aegea | aegea/packages/github3/models.py | GitHubCore._iter | def _iter(self, count, url, cls, params=None, etag=None):
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:param int url: First URL to start with
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kislyuk/aegea | aegea/packages/github3/models.py | GitHubCore.ratelimit_remaining | def ratelimit_remaining(self):
"""Number of requests before GitHub imposes a ratelimit.
:returns: int
"""
json = self._json(self._get(self._github_url + '/rate_limit'), 200)
core = json.get('resources', {}).get('core', {})
self._remaining = core.get('remaining', 0)
... | python | def ratelimit_remaining(self):
"""Number of requests before GitHub imposes a ratelimit.
:returns: int
"""
json = self._json(self._get(self._github_url + '/rate_limit'), 200)
core = json.get('resources', {}).get('core', {})
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kislyuk/aegea | aegea/packages/github3/models.py | GitHubCore.refresh | def refresh(self, conditional=False):
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kislyuk/aegea | aegea/packages/github3/models.py | BaseComment.edit | def edit(self, body):
"""Edit this comment.
:param str body: (required), new body of the comment, Markdown
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:returns: bool
"""
if body:
json = self._json(self._patch(self._api,
data=dumps({'body': body})), 200)
... | python | def edit(self, body):
"""Edit this comment.
:param str body: (required), new body of the comment, Markdown
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:returns: bool
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if body:
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quantmind/dynts | dynts/formatters/tsplot.py | toplot | def toplot(ts,
filename=None,
grid=True,
legend=True,
pargs=(),
**kwargs):
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fig = plt.figure()
ax = fig.add_subplot(111)
dates = list(ts.dates())
ax.plot(dates, ts.values(), *pargs)
ax.grid(grid)
# ro... | python | def toplot(ts,
filename=None,
grid=True,
legend=True,
pargs=(),
**kwargs):
'''To plot formatter'''
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ax = fig.add_subplot(111)
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doakey3/DashTable | dashtable/dashutils/check_table.py | check_table | def check_table(table):
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----------
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doakey3/DashTable | dashtable/dashutils/get_span.py | get_span | def get_span(spans, row, column):
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Parameters
----------
spans : list of lists of lists
A list containing spans, which are lists of [row, column] pairs
that define where a span is inside a table.
Returns
-------
span : ... | python | def get_span(spans, row, column):
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doakey3/DashTable | dashtable/html2data/find_unassigned_table_cell.py | find_unassigned_table_cell | def find_unassigned_table_cell(table):
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table : list of lists of str
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table : list of lists of str
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quantmind/dynts | dynts/backends/np.py | Numpy.insert | def insert(self, dte, values):
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if not self:
self._date = np.array([dte])
self._data = np.array([values])
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# search for the date
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'''insert *values* at date *dte*.'''
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eaton-lab/toytree | toytree/etemini.py | _translate_nodes | def _translate_nodes(root, *nodes):
"""
Convert node names into node instances...
"""
#name2node = {[n, None] for n in nodes if type(n) is str}
name2node = dict([[n, None] for n in nodes if type(n) is str])
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"""
Convert node names into node instances...
"""
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eaton-lab/toytree | toytree/etemini.py | TreeNode.add_feature | def add_feature(self, pr_name, pr_value):
""" Add or update a node's feature. """
setattr(self, pr_name, pr_value)
self.features.add(pr_name) | python | def add_feature(self, pr_name, pr_value):
""" Add or update a node's feature. """
setattr(self, pr_name, pr_value)
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eaton-lab/toytree | toytree/etemini.py | TreeNode.add_features | def add_features(self, **features):
""" Add or update several features. """
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self.features.add(fname) | python | def add_features(self, **features):
""" Add or update several features. """
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eaton-lab/toytree | toytree/etemini.py | TreeNode.del_feature | def del_feature(self, pr_name):
""" Permanently deletes a node's feature."""
if hasattr(self, pr_name):
delattr(self, pr_name)
self.features.remove(pr_name) | python | def del_feature(self, pr_name):
""" Permanently deletes a node's feature."""
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eaton-lab/toytree | toytree/etemini.py | TreeNode.add_child | def add_child(self, child=None, name=None, dist=None, support=None):
"""
Adds a new child to this node. If child node is not suplied
as an argument, a new node instance will be created.
Parameters
----------
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the node instance to be added as a... | python | def add_child(self, child=None, name=None, dist=None, support=None):
"""
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eaton-lab/toytree | toytree/etemini.py | TreeNode.remove_child | def remove_child(self, child):
"""
Removes a child from this node (parent and child
nodes still exit but are no longer connected).
"""
try:
self.children.remove(child)
except ValueError as e:
raise TreeError("child not found")
else:
... | python | def remove_child(self, child):
"""
Removes a child from this node (parent and child
nodes still exit but are no longer connected).
"""
try:
self.children.remove(child)
except ValueError as e:
raise TreeError("child not found")
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eaton-lab/toytree | toytree/etemini.py | TreeNode.add_sister | def add_sister(self, sister=None, name=None, dist=None):
"""
Adds a sister to this node. If sister node is not supplied
as an argument, a new TreeNode instance will be created and
returned.
"""
if self.up == None:
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"""
Adds a sister to this node. If sister node is not supplied
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"""
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eaton-lab/toytree | toytree/etemini.py | TreeNode.remove_sister | def remove_sister(self, sister=None):
"""
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If a sister node is not supplied, the first sister will be deleted
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:return: The nod... | python | def remove_sister(self, sister=None):
"""
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eaton-lab/toytree | toytree/etemini.py | TreeNode.delete | def delete(self, prevent_nondicotomic=True, preserve_branch_length=False):
"""
Deletes node from the tree structure. Notice that this method
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that children from the deleted node are transferred to the
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eaton-lab/toytree | toytree/etemini.py | TreeNode.detach | def detach(self):
"""
Detachs this node (and all its descendants) from its parent
and returns the referent to itself.
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"""
Detachs this node (and all its descendants) from its parent
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eaton-lab/toytree | toytree/etemini.py | TreeNode.prune | def prune(self, nodes, preserve_branch_length=False):
"""
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internal nodes. The minimum number of nodes that conserve the
topological relationships among the requested nodes will be
retained. Root node is always... | python | def prune(self, nodes, preserve_branch_length=False):
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eaton-lab/toytree | toytree/etemini.py | TreeNode.get_sisters | def get_sisters(self):
""" Returns an indepent list of sister nodes."""
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return [ch for ch in self.up.children if ch != self]
else:
return [] | python | def get_sisters(self):
""" Returns an indepent list of sister nodes."""
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eaton-lab/toytree | toytree/etemini.py | TreeNode.iter_leaves | def iter_leaves(self, is_leaf_fn=None):
""" Returns an iterator over the leaves under this node."""
for n in self.traverse(strategy="preorder", is_leaf_fn=is_leaf_fn):
if not is_leaf_fn:
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yield n
else:
if is_leaf_... | python | def iter_leaves(self, is_leaf_fn=None):
""" Returns an iterator over the leaves under this node."""
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eaton-lab/toytree | toytree/etemini.py | TreeNode.iter_leaf_names | def iter_leaf_names(self, is_leaf_fn=None):
"""Returns an iterator over the leaf names under this node."""
for n in self.iter_leaves(is_leaf_fn=is_leaf_fn):
yield n.name | python | def iter_leaf_names(self, is_leaf_fn=None):
"""Returns an iterator over the leaf names under this node."""
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eaton-lab/toytree | toytree/etemini.py | TreeNode.iter_descendants | def iter_descendants(self, strategy="levelorder", is_leaf_fn=None):
""" Returns an iterator over all descendant nodes."""
for n in self.traverse(strategy=strategy, is_leaf_fn=is_leaf_fn):
if n is not self:
yield n | python | def iter_descendants(self, strategy="levelorder", is_leaf_fn=None):
""" Returns an iterator over all descendant nodes."""
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eaton-lab/toytree | toytree/etemini.py | TreeNode.get_descendants | def get_descendants(self, strategy="levelorder", is_leaf_fn=None):
""" Returns a list of all (leaves and internal) descendant nodes."""
return [n for n in self.iter_descendants(
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eaton-lab/toytree | toytree/etemini.py | TreeNode.traverse | def traverse(self, strategy="levelorder", is_leaf_fn=None):
""" Returns an iterator to traverse tree under this node.
Parameters:
-----------
strategy:
set the way in which tree will be traversed. Possible
values are: "preorder" (first parent and then c... | python | def traverse(self, strategy="levelorder", is_leaf_fn=None):
""" Returns an iterator to traverse tree under this node.
Parameters:
-----------
strategy:
set the way in which tree will be traversed. Possible
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eaton-lab/toytree | toytree/etemini.py | TreeNode.iter_prepostorder | def iter_prepostorder(self, is_leaf_fn=None):
"""
Iterate over all nodes in a tree yielding every node in both
pre and post order. Each iteration returns a postorder flag
(True if node is being visited in postorder) and a node
instance.
"""
to_visit = [self]
... | python | def iter_prepostorder(self, is_leaf_fn=None):
"""
Iterate over all nodes in a tree yielding every node in both
pre and post order. Each iteration returns a postorder flag
(True if node is being visited in postorder) and a node
instance.
"""
to_visit = [self]
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eaton-lab/toytree | toytree/etemini.py | TreeNode._iter_descendants_levelorder | def _iter_descendants_levelorder(self, is_leaf_fn=None):
""" Iterate over all desdecendant nodes."""
tovisit = deque([self])
while len(tovisit) > 0:
node = tovisit.popleft()
yield node
if not is_leaf_fn or not is_leaf_fn(node):
tovisit.extend(n... | python | def _iter_descendants_levelorder(self, is_leaf_fn=None):
""" Iterate over all desdecendant nodes."""
tovisit = deque([self])
while len(tovisit) > 0:
node = tovisit.popleft()
yield node
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eaton-lab/toytree | toytree/etemini.py | TreeNode._iter_descendants_preorder | def _iter_descendants_preorder(self, is_leaf_fn=None):
""" Iterator over all descendant nodes. """
to_visit = deque()
node = self
while node is not None:
yield node
if not is_leaf_fn or not is_leaf_fn(node):
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""" Iterator over all descendant nodes. """
to_visit = deque()
node = self
while node is not None:
yield node
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eaton-lab/toytree | toytree/etemini.py | TreeNode.iter_ancestors | def iter_ancestors(self):
"""
Iterates over the list of all ancestor nodes from
current node to the current tree root.
"""
node = self
while node.up is not None:
yield node.up
node = node.up | python | def iter_ancestors(self):
"""
Iterates over the list of all ancestor nodes from
current node to the current tree root.
"""
node = self
while node.up is not None:
yield node.up
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eaton-lab/toytree | toytree/etemini.py | TreeNode.write | def write(self,
features=None,
outfile=None,
format=0,
is_leaf_fn=None,
format_root_node=False,
dist_formatter=None,
support_formatter=None,
name_formatter=None):
"""
Returns the newick representation of current node. Several
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features=None,
outfile=None,
format=0,
is_leaf_fn=None,
format_root_node=False,
dist_formatter=None,
support_formatter=None,
name_formatter=None):
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Returns the newick representation of current node. Several
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eaton-lab/toytree | toytree/etemini.py | TreeNode.get_tree_root | def get_tree_root(self):
""" Returns the absolute root node of current tree structure."""
root = self
while root.up is not None:
root = root.up
return root | python | def get_tree_root(self):
""" Returns the absolute root node of current tree structure."""
root = self
while root.up is not None:
root = root.up
return root | [
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eaton-lab/toytree | toytree/etemini.py | TreeNode.get_common_ancestor | def get_common_ancestor(self, *target_nodes, **kargs):
"""
Returns the first common ancestor between this node and a given
list of 'target_nodes'.
**Examples:**
t = tree.Tree("(((A:0.1, B:0.01):0.001, C:0.0001):1.0[&&NHX:name=common], (D:0.00001):0.000001):2.0[&&NHX:name=root]... | python | def get_common_ancestor(self, *target_nodes, **kargs):
"""
Returns the first common ancestor between this node and a given
list of 'target_nodes'.
**Examples:**
t = tree.Tree("(((A:0.1, B:0.01):0.001, C:0.0001):1.0[&&NHX:name=common], (D:0.00001):0.000001):2.0[&&NHX:name=root]... | [
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eaton-lab/toytree | toytree/etemini.py | TreeNode.iter_search_nodes | def iter_search_nodes(self, **conditions):
"""
Search nodes in an interative way. Matches are being yield as
they are being found. This avoids to scan the full tree
topology before returning the first matches. Useful when
dealing with huge trees.
"""
for n in self... | python | def iter_search_nodes(self, **conditions):
"""
Search nodes in an interative way. Matches are being yield as
they are being found. This avoids to scan the full tree
topology before returning the first matches. Useful when
dealing with huge trees.
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eaton-lab/toytree | toytree/etemini.py | TreeNode.search_nodes | def search_nodes(self, **conditions):
"""
Returns the list of nodes matching a given set of conditions.
**Example:**
tree.search_nodes(dist=0.0, name="human")
"""
matching_nodes = []
for n in self.iter_search_nodes(**conditions):
matching_nodes.append(... | python | def search_nodes(self, **conditions):
"""
Returns the list of nodes matching a given set of conditions.
**Example:**
tree.search_nodes(dist=0.0, name="human")
"""
matching_nodes = []
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eaton-lab/toytree | toytree/etemini.py | TreeNode.get_distance | def get_distance(self, target, target2=None, topology_only=False):
"""
Returns the distance between two nodes. If only one target is
specified, it returns the distance bewtween the target and the
current node.
Parameters:
-----------
target:
a no... | python | def get_distance(self, target, target2=None, topology_only=False):
"""
Returns the distance between two nodes. If only one target is
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eaton-lab/toytree | toytree/etemini.py | TreeNode.get_farthest_node | def get_farthest_node(self, topology_only=False):
"""
Returns the node's farthest descendant or ancestor node, and the
distance to it.
:argument False topology_only: If set to True, distance
between nodes will be referred to the number of nodes
between them. In other... | python | def get_farthest_node(self, topology_only=False):
"""
Returns the node's farthest descendant or ancestor node, and the
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eaton-lab/toytree | toytree/etemini.py | TreeNode.get_farthest_leaf | def get_farthest_leaf(self, topology_only=False, is_leaf_fn=None):
"""
Returns node's farthest descendant node (which is always a leaf), and the
distance to it.
:argument False topology_only: If set to True, distance
between nodes will be referred to the number of nodes
... | python | def get_farthest_leaf(self, topology_only=False, is_leaf_fn=None):
"""
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eaton-lab/toytree | toytree/etemini.py | TreeNode.get_midpoint_outgroup | def get_midpoint_outgroup(self):
"""
Returns the node that divides the current tree into two
distance-balanced partitions.
"""
# Gets the farthest node to the current root
root = self.get_tree_root()
nA, r2A_dist = root.get_farthest_leaf()
nB, A2B_dist = ... | python | def get_midpoint_outgroup(self):
"""
Returns the node that divides the current tree into two
distance-balanced partitions.
"""
# Gets the farthest node to the current root
root = self.get_tree_root()
nA, r2A_dist = root.get_farthest_leaf()
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eaton-lab/toytree | toytree/etemini.py | TreeNode.populate | def populate(self,
size,
names_library=None,
reuse_names=False,
random_branches=False,
branch_range=(0, 1),
support_range=(0, 1)):
"""
Generates a random topology by populating current node.
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reuse_names=False,
random_branches=False,
branch_range=(0, 1),
support_range=(0, 1)):
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eaton-lab/toytree | toytree/etemini.py | TreeNode.set_outgroup | def set_outgroup(self, outgroup):
"""
Sets a descendant node as the outgroup of a tree. This function
can be used to root a tree or even an internal node.
Parameters:
-----------
outgroup:
a node instance within the same tree structure that will be
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"""
Sets a descendant node as the outgroup of a tree. This function
can be used to root a tree or even an internal node.
Parameters:
-----------
outgroup:
a node instance within the same tree structure that will be
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eaton-lab/toytree | toytree/etemini.py | TreeNode.unroot | def unroot(self):
"""
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any other internal node. It will convert a split into a
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"""
if len(self.children)==2:
if n... | python | def unroot(self):
"""
Unroots current node. This function is expected to be used on
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eaton-lab/toytree | toytree/etemini.py | TreeNode._asciiArt | def _asciiArt(self, char1='-', show_internal=True, compact=False, attributes=None):
"""
Returns the ASCII representation of the tree.
Code based on the PyCogent GPL project.
"""
if not attributes:
attributes = ["name"]
# toytree edit:
# remove... | python | def _asciiArt(self, char1='-', show_internal=True, compact=False, attributes=None):
"""
Returns the ASCII representation of the tree.
Code based on the PyCogent GPL project.
"""
if not attributes:
attributes = ["name"]
# toytree edit:
# remove... | [
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eaton-lab/toytree | toytree/etemini.py | TreeNode.get_ascii | def get_ascii(self, show_internal=True, compact=False, attributes=None):
"""
Returns a string containing an ascii drawing of the tree.
Parameters:
-----------
show_internal:
include internal edge names.
compact:
use exactly one line per ... | python | def get_ascii(self, show_internal=True, compact=False, attributes=None):
"""
Returns a string containing an ascii drawing of the tree.
Parameters:
-----------
show_internal:
include internal edge names.
compact:
use exactly one line per ... | [
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eaton-lab/toytree | toytree/etemini.py | TreeNode.ladderize | def ladderize(self, direction=0):
"""
Sort the branches of a given tree (swapping children nodes)
according to the size of each partition.
"""
if not self.is_leaf():
n2s = {}
for n in self.get_children():
s = n.ladderize(direction=direction... | python | def ladderize(self, direction=0):
"""
Sort the branches of a given tree (swapping children nodes)
according to the size of each partition.
"""
if not self.is_leaf():
n2s = {}
for n in self.get_children():
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eaton-lab/toytree | toytree/etemini.py | TreeNode.sort_descendants | def sort_descendants(self, attr="name"):
"""
This function sort the branches of a given tree by
considerening node names. After the tree is sorted, nodes are
labeled using ascendent numbers. This can be used to ensure
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... | python | def sort_descendants(self, attr="name"):
"""
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eaton-lab/toytree | toytree/etemini.py | TreeNode.get_cached_content | def get_cached_content(self, store_attr=None, container_type=set, _store=None):
"""
Returns a dictionary pointing to the preloaded content of each
internal node under this tree. Such a dictionary is intended
to work as a cache for operations that require many traversal
operations... | python | def get_cached_content(self, store_attr=None, container_type=set, _store=None):
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eaton-lab/toytree | toytree/etemini.py | TreeNode.robinson_foulds | def robinson_foulds(self,
t2,
attr_t1="name",
attr_t2="name",
unrooted_trees=False,
expand_polytomies=False,
polytomy_size_limit=5,
skip_large_polytomies=False,
correct_by_polytomy_size=False,
min_support_t1=0.0,
min_support_t2=0.0):
... | python | def robinson_foulds(self,
t2,
attr_t1="name",
attr_t2="name",
unrooted_trees=False,
expand_polytomies=False,
polytomy_size_limit=5,
skip_large_polytomies=False,
correct_by_polytomy_size=False,
min_support_t1=0.0,
min_support_t2=0.0):
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eaton-lab/toytree | toytree/etemini.py | TreeNode.iter_edges | def iter_edges(self, cached_content=None):
"""
Iterate over the list of edges of a tree. Each egde is represented as a
tuple of two elements, each containing the list of nodes separated by
the edge.
"""
if not cached_content:
cached_content = self.get_cached_c... | python | def iter_edges(self, cached_content=None):
"""
Iterate over the list of edges of a tree. Each egde is represented as a
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eaton-lab/toytree | toytree/etemini.py | TreeNode.get_topology_id | def get_topology_id(self, attr="name"):
"""
Returns the unique ID representing the topology of the current tree.
Two trees with the same topology will produce the same id. If trees are
unrooted, make sure that the root node is not binary or use the
tree.unroot() function before ... | python | def get_topology_id(self, attr="name"):
"""
Returns the unique ID representing the topology of the current tree.
Two trees with the same topology will produce the same id. If trees are
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eaton-lab/toytree | toytree/etemini.py | TreeNode.check_monophyly | def check_monophyly(self,
values,
target_attr,
ignore_missing=False,
unrooted=False):
"""
Returns True if a given target attribute is monophyletic under
this node for the provided set of values.
If not all values are represented in the current tree
... | python | def check_monophyly(self,
values,
target_attr,
ignore_missing=False,
unrooted=False):
"""
Returns True if a given target attribute is monophyletic under
this node for the provided set of values.
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eaton-lab/toytree | toytree/etemini.py | TreeNode.get_monophyletic | def get_monophyletic(self, values, target_attr):
"""
Returns a list of nodes matching the provided monophyly
criteria. For a node to be considered a match, all
`target_attr` values within and node, and exclusively them,
should be grouped.
:param values: a set of values f... | python | def get_monophyletic(self, values, target_attr):
"""
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eaton-lab/toytree | toytree/etemini.py | TreeNode.expand_polytomies | def expand_polytomies(self,
map_attr="name",
polytomy_size_limit=5,
skip_large_polytomies=False):
"""
Given a tree with one or more polytomies, this functions returns the
list of all trees (in newick format) resulting from the combination of
all possible solutio... | python | def expand_polytomies(self,
map_attr="name",
polytomy_size_limit=5,
skip_large_polytomies=False):
"""
Given a tree with one or more polytomies, this functions returns the
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.. warning:
Please note that the number of of possible binary trees grows
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eaton-lab/toytree | toytree/etemini.py | TreeNode.resolve_polytomy | def resolve_polytomy(self,
default_dist=0.0,
default_support=0.0,
recursive=True):
"""
Resolve all polytomies under current node by creating an
arbitrary dicotomic structure among the affected nodes. This
function randomly modifies current tree topology and shou... | python | def resolve_polytomy(self,
default_dist=0.0,
default_support=0.0,
recursive=True):
"""
Resolve all polytomies under current node by creating an
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doakey3/DashTable | dashtable/simple2data/truncate_empty_lines.py | truncate_empty_lines | def truncate_empty_lines(lines):
"""
Removes all empty lines from above and below the text.
We can't just use text.strip() because that would remove the leading
space for the table.
Parameters
----------
lines : list of str
Returns
-------
lines : list of str
The text ... | python | def truncate_empty_lines(lines):
"""
Removes all empty lines from above and below the text.
We can't just use text.strip() because that would remove the leading
space for the table.
Parameters
----------
lines : list of str
Returns
-------
lines : list of str
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quantmind/dynts | dynts/lib/fallback/dates.py | jstimestamp_slow | def jstimestamp_slow(dte):
'''Convert a date or datetime object into a javsacript timestamp'''
year, month, day, hour, minute, second = dte.timetuple()[:6]
days = date(year, month, 1).toordinal() - _EPOCH_ORD + day - 1
hours = days*24 + hour
minutes = hours*60 + minute
seconds = minutes*60... | python | def jstimestamp_slow(dte):
'''Convert a date or datetime object into a javsacript timestamp'''
year, month, day, hour, minute, second = dte.timetuple()[:6]
days = date(year, month, 1).toordinal() - _EPOCH_ORD + day - 1
hours = days*24 + hour
minutes = hours*60 + minute
seconds = minutes*60... | [
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quantmind/dynts | dynts/lib/fallback/dates.py | jstimestamp | def jstimestamp(dte):
'''Convert a date or datetime object into a javsacript timestamp.'''
days = date(dte.year, dte.month, 1).toordinal() - _EPOCH_ORD + dte.day - 1
hours = days*24
if isinstance(dte,datetime):
hours += dte.hour
minutes = hours*60 + dte.minute
second... | python | def jstimestamp(dte):
'''Convert a date or datetime object into a javsacript timestamp.'''
days = date(dte.year, dte.month, 1).toordinal() - _EPOCH_ORD + dte.day - 1
hours = days*24
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minutes = hours*60 + dte.minute
second... | [
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doakey3/DashTable | dashtable/html2rst.py | html2rst | def html2rst(html_string, force_headers=False, center_cells=False,
center_headers=False):
"""
Convert a string or html file to an rst table string.
Parameters
----------
html_string : str
Either the html string, or the filepath to the html
force_headers : bool
Make ... | python | def html2rst(html_string, force_headers=False, center_cells=False,
center_headers=False):
"""
Convert a string or html file to an rst table string.
Parameters
----------
html_string : str
Either the html string, or the filepath to the html
force_headers : bool
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Either the html string, or the filepath to the html
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Make the first row become headers, whether or not they are
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doakey3/DashTable | dashtable/dashutils/make_span.py | make_span | def make_span(row, column, extra_rows, extra_columns):
"""
Create a list of rows and columns that will make up a span
Parameters
----------
row : int
The row of the first cell in the span
column : int
The column of the first cell in the span
extra_rows : int
The numb... | python | def make_span(row, column, extra_rows, extra_columns):
"""
Create a list of rows and columns that will make up a span
Parameters
----------
row : int
The row of the first cell in the span
column : int
The column of the first cell in the span
extra_rows : int
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doakey3/DashTable | dashtable/data2rst/make_cell.py | make_cell | def make_cell(table, span, widths, heights, use_headers):
"""
Convert the contents of a span of the table to a grid table cell
Parameters
----------
table : list of lists of str
The table of rows containg strings to convert to a grid table
span : list of lists of int
list of [ro... | python | def make_cell(table, span, widths, heights, use_headers):
"""
Convert the contents of a span of the table to a grid table cell
Parameters
----------
table : list of lists of str
The table of rows containg strings to convert to a grid table
span : list of lists of int
list of [ro... | [
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inveniosoftware/invenio-db | invenio_db/ext.py | InvenioDB.init_app | def init_app(self, app, **kwargs):
"""Initialize application object."""
self.init_db(app, **kwargs)
app.config.setdefault('ALEMBIC', {
'script_location': pkg_resources.resource_filename(
'invenio_db', 'alembic'
),
'version_locations': [
... | python | def init_app(self, app, **kwargs):
"""Initialize application object."""
self.init_db(app, **kwargs)
app.config.setdefault('ALEMBIC', {
'script_location': pkg_resources.resource_filename(
'invenio_db', 'alembic'
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'version_locations': [
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inveniosoftware/invenio-db | invenio_db/ext.py | InvenioDB.init_db | def init_db(self, app, entry_point_group='invenio_db.models', **kwargs):
"""Initialize Flask-SQLAlchemy extension."""
# Setup SQLAlchemy
app.config.setdefault(
'SQLALCHEMY_DATABASE_URI',
'sqlite:///' + os.path.join(app.instance_path, app.name + '.db')
)
ap... | python | def init_db(self, app, entry_point_group='invenio_db.models', **kwargs):
"""Initialize Flask-SQLAlchemy extension."""
# Setup SQLAlchemy
app.config.setdefault(
'SQLALCHEMY_DATABASE_URI',
'sqlite:///' + os.path.join(app.instance_path, app.name + '.db')
)
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inveniosoftware/invenio-db | invenio_db/ext.py | InvenioDB.init_versioning | def init_versioning(self, app, database, versioning_manager=None):
"""Initialize the versioning support using SQLAlchemy-Continuum."""
try:
pkg_resources.get_distribution('sqlalchemy_continuum')
except pkg_resources.DistributionNotFound: # pragma: no cover
default_versio... | python | def init_versioning(self, app, database, versioning_manager=None):
"""Initialize the versioning support using SQLAlchemy-Continuum."""
try:
pkg_resources.get_distribution('sqlalchemy_continuum')
except pkg_resources.DistributionNotFound: # pragma: no cover
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doakey3/DashTable | dashtable/html2data/extract_table.py | extract_table | def extract_table(html_string, row_count, column_count):
"""
Convert an html string to data table
Parameters
----------
html_string : str
row_count : int
column_count : int
Returns
-------
data_table : list of lists of str
"""
try:
from bs4 import BeautifulSoup
... | python | def extract_table(html_string, row_count, column_count):
"""
Convert an html string to data table
Parameters
----------
html_string : str
row_count : int
column_count : int
Returns
-------
data_table : list of lists of str
"""
try:
from bs4 import BeautifulSoup
... | [
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data_table : list of lists of str | [
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