repository_name stringclasses 316
values | func_path_in_repository stringlengths 6 223 | func_name stringlengths 1 134 | language stringclasses 1
value | func_code_string stringlengths 57 65.5k | func_documentation_string stringlengths 1 46.3k | split_name stringclasses 1
value | func_code_url stringlengths 91 315 | called_functions listlengths 1 156 ⌀ | enclosing_scope stringlengths 2 1.48M |
|---|---|---|---|---|---|---|---|---|---|
inveniosoftware/invenio-records-files | invenio_records_files/api.py | FilesIterator.rename | python | def rename(self, old_key, new_key):
assert new_key not in self
assert old_key != new_key
file_ = self[old_key]
old_data = self.filesmap[old_key]
# Create a new version with the new name
obj = ObjectVersion.create(
bucket=self.bucket, key=new_key,
... | Rename a file.
:param old_key: Old key that holds the object.
:param new_key: New key that will hold the object.
:returns: The object that has been renamed. | train | https://github.com/inveniosoftware/invenio-records-files/blob/c410eba986ea43be7e97082d5dcbbdc19ccec39c/invenio_records_files/api.py#L195-L218 | null | class FilesIterator(object):
"""Iterator for files."""
def __init__(self, record, bucket=None, file_cls=None):
"""Initialize iterator."""
self._it = None
self.record = record
self.model = record.model
self.file_cls = file_cls or FileObject
self.bucket = bucket
... |
inveniosoftware/invenio-records-files | invenio_records_files/api.py | FilesIterator.dumps | python | def dumps(self, bucket=None):
return [
self.file_cls(o, self.filesmap.get(o.key, {})).dumps()
for o in sorted_files_from_bucket(bucket or self.bucket, self.keys)
] | Serialize files from a bucket.
:param bucket: Instance of files
:class:`invenio_files_rest.models.Bucket`. (Default:
``self.bucket``)
:returns: List of serialized files. | train | https://github.com/inveniosoftware/invenio-records-files/blob/c410eba986ea43be7e97082d5dcbbdc19ccec39c/invenio_records_files/api.py#L220-L231 | [
"def sorted_files_from_bucket(bucket, keys=None):\n \"\"\"Return files from bucket sorted by given keys.\n\n :param bucket: :class:`~invenio_files_rest.models.Bucket` containing the\n files.\n :param keys: Keys order to be used.\n :returns: Sorted list of bucket items.\n \"\"\"\n keys = key... | class FilesIterator(object):
"""Iterator for files."""
def __init__(self, record, bucket=None, file_cls=None):
"""Initialize iterator."""
self._it = None
self.record = record
self.model = record.model
self.file_cls = file_cls or FileObject
self.bucket = bucket
... |
inveniosoftware/invenio-records-files | invenio_records_files/api.py | FilesMixin.files | python | def files(self):
if self.model is None:
raise MissingModelError()
records_buckets = RecordsBuckets.query.filter_by(
record_id=self.id).first()
if not records_buckets:
bucket = self._create_bucket()
if not bucket:
return None
... | Get files iterator.
:returns: Files iterator. | train | https://github.com/inveniosoftware/invenio-records-files/blob/c410eba986ea43be7e97082d5dcbbdc19ccec39c/invenio_records_files/api.py#L263-L282 | null | class FilesMixin(object):
"""Implement files attribute for Record models.
.. note::
Implement ``_create_bucket()`` in subclass to allow files property
to automatically create a bucket in case no bucket is present.
"""
file_cls = FileObject
"""File class used to generate the instance... |
inveniosoftware/invenio-records-files | invenio_records_files/api.py | FilesMixin.files | python | def files(self, data):
current_files = self.files
if current_files:
raise RuntimeError('Can not update existing files.')
for key in data:
current_files[key] = data[key] | Set files from data. | train | https://github.com/inveniosoftware/invenio-records-files/blob/c410eba986ea43be7e97082d5dcbbdc19ccec39c/invenio_records_files/api.py#L285-L291 | null | class FilesMixin(object):
"""Implement files attribute for Record models.
.. note::
Implement ``_create_bucket()`` in subclass to allow files property
to automatically create a bucket in case no bucket is present.
"""
file_cls = FileObject
"""File class used to generate the instance... |
inveniosoftware/invenio-records-files | invenio_records_files/api.py | Record.delete | python | def delete(self, force=False):
if force:
RecordsBuckets.query.filter_by(
record=self.model,
bucket=self.files.bucket
).delete()
return super(Record, self).delete(force) | Delete a record and also remove the RecordsBuckets if necessary.
:param force: True to remove also the
:class:`~invenio_records_files.models.RecordsBuckets` object.
:returns: Deleted record. | train | https://github.com/inveniosoftware/invenio-records-files/blob/c410eba986ea43be7e97082d5dcbbdc19ccec39c/invenio_records_files/api.py#L297-L309 | null | class Record(_Record, FilesMixin):
"""Define API for files manipulation using ``FilesMixin``."""
|
inveniosoftware/invenio-records-files | invenio_records_files/models.py | RecordsBuckets.create | python | def create(cls, record, bucket):
rb = cls(record=record, bucket=bucket)
db.session.add(rb)
return rb | Create a new RecordsBuckets and adds it to the session.
:param record: Record used to relate with the ``Bucket``.
:param bucket: Bucket used to relate with the ``Record``.
:returns: The :class:`~invenio_records_files.models.RecordsBuckets`
object created. | train | https://github.com/inveniosoftware/invenio-records-files/blob/c410eba986ea43be7e97082d5dcbbdc19ccec39c/invenio_records_files/models.py#L48-L58 | null | class RecordsBuckets(db.Model):
"""Relationship between Records and Buckets."""
__tablename__ = 'records_buckets'
record_id = db.Column(
UUIDType,
db.ForeignKey(RecordMetadata.id),
primary_key=True,
nullable=False,
# NOTE no unique constrain for better future ...
... |
inveniosoftware/invenio-records-files | invenio_records_files/utils.py | sorted_files_from_bucket | python | def sorted_files_from_bucket(bucket, keys=None):
keys = keys or []
total = len(keys)
sortby = dict(zip(keys, range(total)))
values = ObjectVersion.get_by_bucket(bucket).all()
return sorted(values, key=lambda x: sortby.get(x.key, total)) | Return files from bucket sorted by given keys.
:param bucket: :class:`~invenio_files_rest.models.Bucket` containing the
files.
:param keys: Keys order to be used.
:returns: Sorted list of bucket items. | train | https://github.com/inveniosoftware/invenio-records-files/blob/c410eba986ea43be7e97082d5dcbbdc19ccec39c/invenio_records_files/utils.py#L19-L31 | null | # -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2016-2019 CERN.
#
# Invenio is free software; you can redistribute it and/or modify it
# under the terms of the MIT License; see LICENSE file for more details.
"""Implementention of various utility functions."""
from __future__ import absolute_... |
inveniosoftware/invenio-records-files | invenio_records_files/utils.py | record_file_factory | python | def record_file_factory(pid, record, filename):
try:
if not (hasattr(record, 'files') and record.files):
return None
except MissingModelError:
return None
try:
return record.files[filename]
except KeyError:
return None | Get file from a record.
:param pid: Not used. It keeps the function signature.
:param record: Record which contains the files.
:param filename: Name of the file to be returned.
:returns: File object or ``None`` if not found. | train | https://github.com/inveniosoftware/invenio-records-files/blob/c410eba986ea43be7e97082d5dcbbdc19ccec39c/invenio_records_files/utils.py#L34-L51 | null | # -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2016-2019 CERN.
#
# Invenio is free software; you can redistribute it and/or modify it
# under the terms of the MIT License; see LICENSE file for more details.
"""Implementention of various utility functions."""
from __future__ import absolute_... |
inveniosoftware/invenio-records-files | invenio_records_files/utils.py | file_download_ui | python | def file_download_ui(pid, record, _record_file_factory=None, **kwargs):
_record_file_factory = _record_file_factory or record_file_factory
# Extract file from record.
fileobj = _record_file_factory(
pid, record, kwargs.get('filename')
)
if not fileobj:
abort(404)
obj = fileobj.... | File download view for a given record.
Plug this method into your ``RECORDS_UI_ENDPOINTS`` configuration:
.. code-block:: python
RECORDS_UI_ENDPOINTS = dict(
recid=dict(
# ...
route='/records/<pid_value/files/<filename>',
view_imp='invenio_r... | train | https://github.com/inveniosoftware/invenio-records-files/blob/c410eba986ea43be7e97082d5dcbbdc19ccec39c/invenio_records_files/utils.py#L54-L101 | null | # -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2016-2019 CERN.
#
# Invenio is free software; you can redistribute it and/or modify it
# under the terms of the MIT License; see LICENSE file for more details.
"""Implementention of various utility functions."""
from __future__ import absolute_... |
inveniosoftware/invenio-records-files | invenio_records_files/links.py | default_bucket_link_factory | python | def default_bucket_link_factory(pid):
try:
record = Record.get_record(pid.get_assigned_object())
bucket = record.files.bucket
return url_for('invenio_files_rest.bucket_api',
bucket_id=bucket.id, _external=True)
except AttributeError:
return None | Factory for record bucket generation. | train | https://github.com/inveniosoftware/invenio-records-files/blob/c410eba986ea43be7e97082d5dcbbdc19ccec39c/invenio_records_files/links.py#L16-L25 | null | # -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2016-2019 CERN.
#
# Invenio is free software; you can redistribute it and/or modify it
# under the terms of the MIT License; see LICENSE file for more details.
"""Link for file bucket creation."""
from flask import url_for
from .api import Rec... |
tmoerman/arboreto | arboreto/core.py | to_tf_matrix | python | def to_tf_matrix(expression_matrix,
gene_names,
tf_names):
tuples = [(index, gene) for index, gene in enumerate(gene_names) if gene in tf_names]
tf_indices = [t[0] for t in tuples]
tf_matrix_names = [t[1] for t in tuples]
return expression_matrix[:, tf_indices], tf_m... | :param expression_matrix: numpy matrix. Rows are observations and columns are genes.
:param gene_names: a list of gene names. Each entry corresponds to the expression_matrix column with same index.
:param tf_names: a list of transcription factor names. Should be a subset of gene_names.
:return: tuple of:
... | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/core.py#L85-L102 | null | """
Core functional building blocks, composed in a Dask graph for distributed computation.
"""
import numpy as np
import pandas as pd
import logging
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor, ExtraTreesRegressor
from dask import delayed
from dask.dataframe import from_delayed
from ... |
tmoerman/arboreto | arboreto/core.py | fit_model | python | def fit_model(regressor_type,
regressor_kwargs,
tf_matrix,
target_gene_expression,
early_stop_window_length=EARLY_STOP_WINDOW_LENGTH,
seed=DEMON_SEED):
regressor_type = regressor_type.upper()
assert tf_matrix.shape[0] == len(target_gene_expr... | :param regressor_type: string. Case insensitive.
:param regressor_kwargs: a dictionary of key-value pairs that configures the regressor.
:param tf_matrix: the predictor matrix (transcription factor matrix) as a numpy array.
:param target_gene_expression: the target (y) gene expression to predict in function... | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/core.py#L105-L141 | [
"def is_sklearn_regressor(regressor_type):\n \"\"\"\n :param regressor_type: string. Case insensitive.\n :return: whether the regressor type is a scikit-learn regressor, following the scikit-learn API.\n \"\"\"\n return regressor_type.upper() in SKLEARN_REGRESSOR_FACTORY.keys()\n",
"def do_sklearn_... | """
Core functional building blocks, composed in a Dask graph for distributed computation.
"""
import numpy as np
import pandas as pd
import logging
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor, ExtraTreesRegressor
from dask import delayed
from dask.dataframe import from_delayed
from ... |
tmoerman/arboreto | arboreto/core.py | to_feature_importances | python | def to_feature_importances(regressor_type,
regressor_kwargs,
trained_regressor):
if is_oob_heuristic_supported(regressor_type, regressor_kwargs):
n_estimators = len(trained_regressor.estimators_)
denormalized_importances = trained_regressor.fea... | Motivation: when the out-of-bag improvement heuristic is used, we cancel the effect of normalization by dividing
by the number of trees in the regression ensemble by multiplying again by the number of trees used.
This enables prioritizing links that were inferred in a regression where lots of
:param regre... | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/core.py#L144-L166 | [
"def is_oob_heuristic_supported(regressor_type, regressor_kwargs):\n \"\"\"\n :param regressor_type: on\n :param regressor_kwargs:\n :return: whether early stopping heuristic based on out-of-bag improvement is supported.\n\n \"\"\"\n return \\\n regressor_type.upper() == 'GBM' and \\\n ... | """
Core functional building blocks, composed in a Dask graph for distributed computation.
"""
import numpy as np
import pandas as pd
import logging
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor, ExtraTreesRegressor
from dask import delayed
from dask.dataframe import from_delayed
from ... |
tmoerman/arboreto | arboreto/core.py | to_meta_df | python | def to_meta_df(trained_regressor,
target_gene_name):
n_estimators = len(trained_regressor.estimators_)
return pd.DataFrame({'target': [target_gene_name], 'n_estimators': [n_estimators]}) | :param trained_regressor: the trained model from which to extract the meta information.
:param target_gene_name: the name of the target gene.
:return: a Pandas DataFrame containing side information about the regression. | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/core.py#L169-L178 | null | """
Core functional building blocks, composed in a Dask graph for distributed computation.
"""
import numpy as np
import pandas as pd
import logging
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor, ExtraTreesRegressor
from dask import delayed
from dask.dataframe import from_delayed
from ... |
tmoerman/arboreto | arboreto/core.py | to_links_df | python | def to_links_df(regressor_type,
regressor_kwargs,
trained_regressor,
tf_matrix_gene_names,
target_gene_name):
def pythonic():
# feature_importances = trained_regressor.feature_importances_
feature_importances = to_feature_importances(r... | :param regressor_type: string. Case insensitive.
:param regressor_kwargs: dict of key-value pairs that configures the regressor.
:param trained_regressor: the trained model from which to extract the feature importances.
:param tf_matrix_gene_names: the list of names corresponding to the columns of the tf_ma... | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/core.py#L181-L212 | [
"def is_sklearn_regressor(regressor_type):\n \"\"\"\n :param regressor_type: string. Case insensitive.\n :return: whether the regressor type is a scikit-learn regressor, following the scikit-learn API.\n \"\"\"\n return regressor_type.upper() in SKLEARN_REGRESSOR_FACTORY.keys()\n",
"def is_xgboost_... | """
Core functional building blocks, composed in a Dask graph for distributed computation.
"""
import numpy as np
import pandas as pd
import logging
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor, ExtraTreesRegressor
from dask import delayed
from dask.dataframe import from_delayed
from ... |
tmoerman/arboreto | arboreto/core.py | clean | python | def clean(tf_matrix,
tf_matrix_gene_names,
target_gene_name):
if target_gene_name not in tf_matrix_gene_names:
clean_tf_matrix = tf_matrix
else:
clean_tf_matrix = np.delete(tf_matrix, tf_matrix_gene_names.index(target_gene_name), 1)
clean_tf_names = [tf for tf in tf_mat... | :param tf_matrix: numpy array. The full transcription factor matrix.
:param tf_matrix_gene_names: the full list of transcription factor names, corresponding to the tf_matrix columns.
:param target_gene_name: the target gene to remove from the tf_matrix and tf_names.
:return: a tuple of (matrix, names) equal... | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/core.py#L215-L235 | null | """
Core functional building blocks, composed in a Dask graph for distributed computation.
"""
import numpy as np
import pandas as pd
import logging
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor, ExtraTreesRegressor
from dask import delayed
from dask.dataframe import from_delayed
from ... |
tmoerman/arboreto | arboreto/core.py | retry | python | def retry(fn, max_retries=10, warning_msg=None, fallback_result=None):
nr_retries = 0
result = fallback_result
for attempt in range(max_retries):
try:
result = fn()
except Exception as cause:
nr_retries += 1
msg_head = '' if warning_msg is None else rep... | Minimalistic retry strategy to compensate for failures probably caused by a thread-safety bug in scikit-learn:
* https://github.com/scikit-learn/scikit-learn/issues/2755
* https://github.com/scikit-learn/scikit-learn/issues/7346
:param fn: the function to retry.
:param max_retries: the maximum number o... | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/core.py#L238-L267 | [
"def blue_skies():\n return 1\n",
"def i_will_never_work():\n raise ValueError('never')\n",
"def i_procrastinate(self):\n self.attempts += 1\n\n if self.attempts == 3:\n return 1\n else:\n raise ValueError('later')\n",
"def fn():\n (clean_tf_matrix, clean_tf_matrix_gene_names) ... | """
Core functional building blocks, composed in a Dask graph for distributed computation.
"""
import numpy as np
import pandas as pd
import logging
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor, ExtraTreesRegressor
from dask import delayed
from dask.dataframe import from_delayed
from ... |
tmoerman/arboreto | arboreto/core.py | infer_partial_network | python | def infer_partial_network(regressor_type,
regressor_kwargs,
tf_matrix,
tf_matrix_gene_names,
target_gene_name,
target_gene_expression,
include_meta=False,
... | Ties together regressor model training with regulatory links and meta data extraction.
:param regressor_type: string. Case insensitive.
:param regressor_kwargs: dict of key-value pairs that configures the regressor.
:param tf_matrix: numpy matrix. The feature matrix X to use for the regression.
:param ... | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/core.py#L270-L323 | [
"def retry(fn, max_retries=10, warning_msg=None, fallback_result=None):\n \"\"\"\n Minimalistic retry strategy to compensate for failures probably caused by a thread-safety bug in scikit-learn:\n * https://github.com/scikit-learn/scikit-learn/issues/2755\n * https://github.com/scikit-learn/scikit-learn/... | """
Core functional building blocks, composed in a Dask graph for distributed computation.
"""
import numpy as np
import pandas as pd
import logging
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor, ExtraTreesRegressor
from dask import delayed
from dask.dataframe import from_delayed
from ... |
tmoerman/arboreto | arboreto/core.py | target_gene_indices | python | def target_gene_indices(gene_names,
target_genes):
if isinstance(target_genes, list) and len(target_genes) == 0:
return []
if isinstance(target_genes, str) and target_genes.upper() == 'ALL':
return list(range(len(gene_names)))
elif isinstance(target_genes, int):
... | :param gene_names: list of gene names.
:param target_genes: either int (the top n), 'all', or a collection (subset of gene_names).
:return: the (column) indices of the target genes in the expression_matrix. | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/core.py#L326-L357 | null | """
Core functional building blocks, composed in a Dask graph for distributed computation.
"""
import numpy as np
import pandas as pd
import logging
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor, ExtraTreesRegressor
from dask import delayed
from dask.dataframe import from_delayed
from ... |
tmoerman/arboreto | arboreto/core.py | create_graph | python | def create_graph(expression_matrix,
gene_names,
tf_names,
regressor_type,
regressor_kwargs,
client,
target_genes='all',
limit=None,
include_meta=False,
early_stop_wind... | Main API function. Create a Dask computation graph.
Note: fixing the GC problems was fixed by 2 changes: [1] and [2] !!!
:param expression_matrix: numpy matrix. Rows are observations and columns are genes.
:param gene_names: list of gene names. Each entry corresponds to the expression_matrix column with s... | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/core.py#L364-L450 | [
"def to_tf_matrix(expression_matrix,\n gene_names,\n tf_names):\n \"\"\"\n :param expression_matrix: numpy matrix. Rows are observations and columns are genes.\n :param gene_names: a list of gene names. Each entry corresponds to the expression_matrix column with same index.\... | """
Core functional building blocks, composed in a Dask graph for distributed computation.
"""
import numpy as np
import pandas as pd
import logging
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor, ExtraTreesRegressor
from dask import delayed
from dask.dataframe import from_delayed
from ... |
tmoerman/arboreto | arboreto/core.py | EarlyStopMonitor.window_boundaries | python | def window_boundaries(self, current_round):
lo = max(0, current_round - self.window_length + 1)
hi = current_round + 1
return lo, hi | :param current_round:
:return: the low and high boundaries of the estimators window to consider. | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/core.py#L462-L471 | null | class EarlyStopMonitor:
def __init__(self, window_length=EARLY_STOP_WINDOW_LENGTH):
"""
:param window_length: length of the window over the out-of-bag errors.
"""
self.window_length = window_length
def __call__(self, current_round, regressor, _):
"""
Implement... |
tmoerman/arboreto | arboreto/algo.py | grnboost2 | python | def grnboost2(expression_data,
gene_names=None,
tf_names='all',
client_or_address='local',
early_stop_window_length=EARLY_STOP_WINDOW_LENGTH,
limit=None,
seed=None,
verbose=False):
return diy(expression_data=expressio... | Launch arboreto with [GRNBoost2] profile.
:param expression_data: one of:
* a pandas DataFrame (rows=observations, columns=genes)
* a dense 2D numpy.ndarray
* a sparse scipy.sparse.csc_matrix
:param gene_names: optional list of gene names (strings). Required when a (dense or sp... | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/algo.py#L10-L41 | [
"def diy(expression_data,\n regressor_type,\n regressor_kwargs,\n gene_names=None,\n tf_names='all',\n client_or_address='local',\n early_stop_window_length=EARLY_STOP_WINDOW_LENGTH,\n limit=None,\n seed=None,\n verbose=False):\n \"\"\"\n :param e... | """
Top-level functions.
"""
import pandas as pd
from distributed import Client, LocalCluster
from arboreto.core import create_graph, SGBM_KWARGS, RF_KWARGS, EARLY_STOP_WINDOW_LENGTH
def genie3(expression_data,
gene_names=None,
tf_names='all',
client_or_address='local',
l... |
tmoerman/arboreto | arboreto/algo.py | genie3 | python | def genie3(expression_data,
gene_names=None,
tf_names='all',
client_or_address='local',
limit=None,
seed=None,
verbose=False):
return diy(expression_data=expression_data, regressor_type='RF', regressor_kwargs=RF_KWARGS,
gene_names=gen... | Launch arboreto with [GENIE3] profile.
:param expression_data: one of:
* a pandas DataFrame (rows=observations, columns=genes)
* a dense 2D numpy.ndarray
* a sparse scipy.sparse.csc_matrix
:param gene_names: optional list of gene names (strings). Required when a (dense or spars... | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/algo.py#L44-L73 | [
"def diy(expression_data,\n regressor_type,\n regressor_kwargs,\n gene_names=None,\n tf_names='all',\n client_or_address='local',\n early_stop_window_length=EARLY_STOP_WINDOW_LENGTH,\n limit=None,\n seed=None,\n verbose=False):\n \"\"\"\n :param e... | """
Top-level functions.
"""
import pandas as pd
from distributed import Client, LocalCluster
from arboreto.core import create_graph, SGBM_KWARGS, RF_KWARGS, EARLY_STOP_WINDOW_LENGTH
def grnboost2(expression_data,
gene_names=None,
tf_names='all',
client_or_address='local',
... |
tmoerman/arboreto | arboreto/algo.py | diy | python | def diy(expression_data,
regressor_type,
regressor_kwargs,
gene_names=None,
tf_names='all',
client_or_address='local',
early_stop_window_length=EARLY_STOP_WINDOW_LENGTH,
limit=None,
seed=None,
verbose=False):
if verbose:
print('preparin... | :param expression_data: one of:
* a pandas DataFrame (rows=observations, columns=genes)
* a dense 2D numpy.ndarray
* a sparse scipy.sparse.csc_matrix
:param regressor_type: string. One of: 'RF', 'GBM', 'ET'. Case insensitive.
:param regressor_kwargs: a dictionary of key-value pa... | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/algo.py#L76-L142 | [
"def create_graph(expression_matrix,\n gene_names,\n tf_names,\n regressor_type,\n regressor_kwargs,\n client,\n target_genes='all',\n limit=None,\n include_meta=False,\n e... | """
Top-level functions.
"""
import pandas as pd
from distributed import Client, LocalCluster
from arboreto.core import create_graph, SGBM_KWARGS, RF_KWARGS, EARLY_STOP_WINDOW_LENGTH
def grnboost2(expression_data,
gene_names=None,
tf_names='all',
client_or_address='local',
... |
tmoerman/arboreto | arboreto/algo.py | _prepare_client | python | def _prepare_client(client_or_address):
if client_or_address is None or str(client_or_address).lower() == 'local':
local_cluster = LocalCluster(diagnostics_port=None)
client = Client(local_cluster)
def close_client_and_local_cluster(verbose=False):
if verbose:
p... | :param client_or_address: one of:
* None
* verbatim: 'local'
* string address
* a Client instance
:return: a tuple: (Client instance, shutdown callback function).
:raises: ValueError if no valid client input was provided. | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/algo.py#L145-L191 | null | """
Top-level functions.
"""
import pandas as pd
from distributed import Client, LocalCluster
from arboreto.core import create_graph, SGBM_KWARGS, RF_KWARGS, EARLY_STOP_WINDOW_LENGTH
def grnboost2(expression_data,
gene_names=None,
tf_names='all',
client_or_address='local',
... |
tmoerman/arboreto | arboreto/algo.py | _prepare_input | python | def _prepare_input(expression_data,
gene_names,
tf_names):
if isinstance(expression_data, pd.DataFrame):
expression_matrix = expression_data.as_matrix()
gene_names = list(expression_data.columns)
else:
expression_matrix = expression_data
ass... | Wrangle the inputs into the correct formats.
:param expression_data: one of:
* a pandas DataFrame (rows=observations, columns=genes)
* a dense 2D numpy.ndarray
* a sparse scipy.sparse.csc_matrix
:param gene_names: optional list... | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/algo.py#L194-L231 | null | """
Top-level functions.
"""
import pandas as pd
from distributed import Client, LocalCluster
from arboreto.core import create_graph, SGBM_KWARGS, RF_KWARGS, EARLY_STOP_WINDOW_LENGTH
def grnboost2(expression_data,
gene_names=None,
tf_names='all',
client_or_address='local',
... |
tmoerman/arboreto | arboreto/utils.py | load_tf_names | python | def load_tf_names(path):
with open(path) as file:
tfs_in_file = [line.strip() for line in file.readlines()]
return tfs_in_file | :param path: the path of the transcription factor list file.
:return: a list of transcription factor names read from the file. | train | https://github.com/tmoerman/arboreto/blob/3ff7b6f987b32e5774771751dea646fa6feaaa52/arboreto/utils.py#L6-L15 | null | """
Utility functions.
"""
|
TadLeonard/tfatool | tfatool/sync.py | up_down_by_arrival | python | def up_down_by_arrival(*filters, local_dir=".",
remote_dir=DEFAULT_REMOTE_DIR):
local_monitor = watch_local_files(*filters, local_dir=local_dir)
remote_monitor = watch_remote_files(*filters, remote_dir=remote_dir)
_, lfile_set = next(local_monitor)
_, rfile_set = next(remote_monit... | Monitors a local directory and a remote FlashAir directory and
generates sets of new files to be uploaded or downloaded.
Sets to upload are generated in a tuple
like (Direction.up, {...}), while download sets to download
are generated in a tuple like (Direction.down, {...}). The generator yields
bef... | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/sync.py#L83-L115 | [
"def watch_local_files(*filters, local_dir=\".\"):\n list_local = partial(list_local_files, *filters, local_dir=local_dir)\n old_files = new_files = set(list_local())\n while True:\n yield new_files - old_files, new_files\n old_files = new_files\n new_files = set(list_local())\n",
"d... | import logging
import os
import threading
import time
from enum import Enum
from functools import partial
from pathlib import Path
from urllib.parse import urljoin
import arrow
import requests
import tqdm
from . import command, upload
from .info import URL, DEFAULT_REMOTE_DIR
from .info import RawFileInfo, SimpleFil... |
TadLeonard/tfatool | tfatool/sync.py | up_by_arrival | python | def up_by_arrival(*filters, local_dir=".", remote_dir=DEFAULT_REMOTE_DIR):
local_monitor = watch_local_files(*filters, local_dir=local_dir)
_, file_set = next(local_monitor)
_notify_sync_ready(len(file_set), local_dir, remote_dir)
for new_arrivals, file_set in local_monitor:
yield Direction.up, ... | Monitors a local directory and
generates sets of new files to be uploaded to FlashAir.
Sets to upload are generated in a tuple like (Direction.up, {...}).
The generator yields before each upload actually takes place. | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/sync.py#L118-L131 | [
"def watch_local_files(*filters, local_dir=\".\"):\n list_local = partial(list_local_files, *filters, local_dir=local_dir)\n old_files = new_files = set(list_local())\n while True:\n yield new_files - old_files, new_files\n old_files = new_files\n new_files = set(list_local())\n",
"d... | import logging
import os
import threading
import time
from enum import Enum
from functools import partial
from pathlib import Path
from urllib.parse import urljoin
import arrow
import requests
import tqdm
from . import command, upload
from .info import URL, DEFAULT_REMOTE_DIR
from .info import RawFileInfo, SimpleFil... |
TadLeonard/tfatool | tfatool/sync.py | down_by_arrival | python | def down_by_arrival(*filters, local_dir=".", remote_dir=DEFAULT_REMOTE_DIR):
remote_monitor = watch_remote_files(*filters, remote_dir=remote_dir)
_, file_set = next(remote_monitor)
_notify_sync_ready(len(file_set), remote_dir, local_dir)
for new_arrivals, file_set in remote_monitor:
if new_arriv... | Monitors a remote FlashAir directory and generates sets of
new files to be downloaded from FlashAir.
Sets to download are generated in a tuple like (Direction.down, {...}).
The generator yields AFTER each download actually takes place. | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/sync.py#L134-L147 | [
"def watch_remote_files(*filters, remote_dir=\".\"):\n command.memory_changed() # clear change status to start\n list_remote = partial(command.list_files,\n *filters, remote_dir=remote_dir)\n old_files = new_files = set(list_remote())\n while True:\n yield new_files - ol... | import logging
import os
import threading
import time
from enum import Enum
from functools import partial
from pathlib import Path
from urllib.parse import urljoin
import arrow
import requests
import tqdm
from . import command, upload
from .info import URL, DEFAULT_REMOTE_DIR
from .info import RawFileInfo, SimpleFil... |
TadLeonard/tfatool | tfatool/sync.py | down_by_time | python | def down_by_time(*filters, remote_dir=DEFAULT_REMOTE_DIR, local_dir=".", count=1):
files = command.list_files(*filters, remote_dir=remote_dir)
most_recent = sorted(files, key=lambda f: f.datetime)
to_sync = most_recent[-count:]
_notify_sync(Direction.down, to_sync)
down_by_files(to_sync[::-1], local... | Sync most recent file by date, time attribues | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/sync.py#L164-L170 | [
"def _notify_sync(direction, files):\n logger.info(\"{:d} files to {:s}:\\n{}\".format(\n len(files), direction,\n \"\\n\".join(\" \" + f.filename for f in files)))\n",
"def down_by_files(to_sync, local_dir=\".\"):\n \"\"\"Sync a given list of files from `command.list_files` to `local_dir` di... | import logging
import os
import threading
import time
from enum import Enum
from functools import partial
from pathlib import Path
from urllib.parse import urljoin
import arrow
import requests
import tqdm
from . import command, upload
from .info import URL, DEFAULT_REMOTE_DIR
from .info import RawFileInfo, SimpleFil... |
TadLeonard/tfatool | tfatool/sync.py | down_by_name | python | def down_by_name(*filters, remote_dir=DEFAULT_REMOTE_DIR, local_dir=".", count=1):
files = command.list_files(*filters, remote_dir=remote_dir)
greatest = sorted(files, key=lambda f: f.filename)
to_sync = greatest[-count:]
_notify_sync(Direction.down, to_sync)
down_by_files(to_sync[::-1], local_dir=l... | Sync files whose filename attribute is highest in alphanumeric order | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/sync.py#L173-L179 | [
"def _notify_sync(direction, files):\n logger.info(\"{:d} files to {:s}:\\n{}\".format(\n len(files), direction,\n \"\\n\".join(\" \" + f.filename for f in files)))\n",
"def down_by_files(to_sync, local_dir=\".\"):\n \"\"\"Sync a given list of files from `command.list_files` to `local_dir` di... | import logging
import os
import threading
import time
from enum import Enum
from functools import partial
from pathlib import Path
from urllib.parse import urljoin
import arrow
import requests
import tqdm
from . import command, upload
from .info import URL, DEFAULT_REMOTE_DIR
from .info import RawFileInfo, SimpleFil... |
TadLeonard/tfatool | tfatool/sync.py | _write_file_safely | python | def _write_file_safely(local_path, fileinfo, response):
try:
_write_file(local_path, fileinfo, response)
except BaseException as e:
logger.warning("{} interrupted writing {} -- "
"cleaning up partial file".format(
e.__class__.__name__, local_path))
... | attempts to stream a remote file into a local file object,
removes the local file if it's interrupted by any error | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/sync.py#L215-L225 | null | import logging
import os
import threading
import time
from enum import Enum
from functools import partial
from pathlib import Path
from urllib.parse import urljoin
import arrow
import requests
import tqdm
from . import command, upload
from .info import URL, DEFAULT_REMOTE_DIR
from .info import RawFileInfo, SimpleFil... |
TadLeonard/tfatool | tfatool/sync.py | up_by_files | python | def up_by_files(to_sync, remote_dir=DEFAULT_REMOTE_DIR, remote_files=None):
if remote_files is None:
remote_files = command.map_files_raw(remote_dir=remote_dir)
for local_file in to_sync:
_sync_local_file(local_file, remote_dir, remote_files) | Sync a given list of local files to `remote_dir` dir | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/sync.py#L289-L294 | [
"def _sync_local_file(local_file_info, remote_dir, remote_files):\n local_name = local_file_info.filename\n local_size = local_file_info.size\n if local_name in remote_files:\n remote_file_info = remote_files[local_name]\n remote_size = remote_file_info.size\n if local_size == remote_s... | import logging
import os
import threading
import time
from enum import Enum
from functools import partial
from pathlib import Path
from urllib.parse import urljoin
import arrow
import requests
import tqdm
from . import command, upload
from .info import URL, DEFAULT_REMOTE_DIR
from .info import RawFileInfo, SimpleFil... |
TadLeonard/tfatool | tfatool/sync.py | up_by_time | python | def up_by_time(*filters, local_dir=".", remote_dir=DEFAULT_REMOTE_DIR, count=1):
remote_files = command.map_files_raw(remote_dir=remote_dir)
local_files = list_local_files(*filters, local_dir=local_dir)
most_recent = sorted(local_files, key=lambda f: f.datetime)
to_sync = most_recent[-count:]
_notif... | Sync most recent file by date, time attribues | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/sync.py#L297-L304 | [
"def _notify_sync(direction, files):\n logger.info(\"{:d} files to {:s}:\\n{}\".format(\n len(files), direction,\n \"\\n\".join(\" \" + f.filename for f in files)))\n",
"def up_by_files(to_sync, remote_dir=DEFAULT_REMOTE_DIR, remote_files=None):\n \"\"\"Sync a given list of local files to `re... | import logging
import os
import threading
import time
from enum import Enum
from functools import partial
from pathlib import Path
from urllib.parse import urljoin
import arrow
import requests
import tqdm
from . import command, upload
from .info import URL, DEFAULT_REMOTE_DIR
from .info import RawFileInfo, SimpleFil... |
TadLeonard/tfatool | tfatool/sync.py | up_by_name | python | def up_by_name(*filters, local_dir=".", remote_dir=DEFAULT_REMOTE_DIR, count=1):
remote_files = command.map_files_raw(remote_dir=remote_dir)
local_files = list_local_files(*filters, local_dir=local_dir)
greatest = sorted(local_files, key=lambda f: f.filename)
to_sync = greatest[-count:]
_notify_sync... | Sync files whose filename attribute is highest in alphanumeric order | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/sync.py#L307-L314 | [
"def _notify_sync(direction, files):\n logger.info(\"{:d} files to {:s}:\\n{}\".format(\n len(files), direction,\n \"\\n\".join(\" \" + f.filename for f in files)))\n",
"def up_by_files(to_sync, remote_dir=DEFAULT_REMOTE_DIR, remote_files=None):\n \"\"\"Sync a given list of local files to `re... | import logging
import os
import threading
import time
from enum import Enum
from functools import partial
from pathlib import Path
from urllib.parse import urljoin
import arrow
import requests
import tqdm
from . import command, upload
from .info import URL, DEFAULT_REMOTE_DIR
from .info import RawFileInfo, SimpleFil... |
TadLeonard/tfatool | tfatool/sync.py | _upload_file_safely | python | def _upload_file_safely(fileinfo, remote_dir):
try:
upload.upload_file(fileinfo.path, remote_dir=remote_dir)
except BaseException as e:
logger.warning("{} interrupted writing {} -- "
"cleaning up partial remote file".format(
e.__class__.__name__, fil... | attempts to upload a local file to FlashAir,
tries to remove the remote file if interrupted by any error | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/sync.py#L344-L354 | null | import logging
import os
import threading
import time
from enum import Enum
from functools import partial
from pathlib import Path
from urllib.parse import urljoin
import arrow
import requests
import tqdm
from . import command, upload
from .info import URL, DEFAULT_REMOTE_DIR
from .info import RawFileInfo, SimpleFil... |
TadLeonard/tfatool | tfatool/config.py | config | python | def config(param_map, mastercode=DEFAULT_MASTERCODE):
pmap = {Config.mastercode: mastercode}
pmap.update(param_map)
processed_params = dict(_process_params(pmap))
return processed_params | Takes a dictionary of {Config.key: value} and
returns a dictionary of processed keys and values to be used in the
construction of a POST request to FlashAir's config.cgi | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/config.py#L8-L15 | [
"def _process_params(params):\n for param, value in params.items():\n assert param in Config, \"Invalid param: {}\".format(param)\n yield param.value, value_validators[param](value)\n"
] | import logging
from functools import partial
from . import cgi
from .info import URL, DEFAULT_MASTERCODE
from .info import WifiMode, WifiModeOnBoot, ModeValue, DriveMode, Config
def _process_params(params):
for param, value in params.items():
assert param in Config, "Invalid param: {}".format(param)
... |
TadLeonard/tfatool | tfatool/config.py | post | python | def post(param_map, url=URL):
prepped_request = _prep_post(url=url, **param_map)
return cgi.send(prepped_request) | Posts a `param_map` created with `config` to
the FlashAir config.cgi entrypoint | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/config.py#L24-L28 | null | import logging
from functools import partial
from . import cgi
from .info import URL, DEFAULT_MASTERCODE
from .info import WifiMode, WifiModeOnBoot, ModeValue, DriveMode, Config
def config(param_map, mastercode=DEFAULT_MASTERCODE):
"""Takes a dictionary of {Config.key: value} and
returns a dictionary of proce... |
TadLeonard/tfatool | tfatool/config.py | _validate_timeout | python | def _validate_timeout(seconds: float):
val = int(seconds * 1000)
assert 60000 <= val <= 4294967294, "Bad value: {}".format(val)
return val | Creates an int from 60000 to 4294967294 that represents a
valid millisecond wireless LAN timeout | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/config.py#L48-L53 | null | import logging
from functools import partial
from . import cgi
from .info import URL, DEFAULT_MASTERCODE
from .info import WifiMode, WifiModeOnBoot, ModeValue, DriveMode, Config
def config(param_map, mastercode=DEFAULT_MASTERCODE):
"""Takes a dictionary of {Config.key: value} and
returns a dictionary of proce... |
TadLeonard/tfatool | tfatool/util.py | parse_datetime | python | def parse_datetime(datetime_input):
date_els, time_els = _split_datetime(datetime_input)
date_vals = _parse_date(date_els)
time_vals = _parse_time(time_els)
vals = tuple(date_vals) + tuple(time_vals)
return arrow.get(*vals) | The arrow library is sadly not good enough to parse
certain date strings. It even gives unexpected results for partial
date strings such as '2015-01' or just '2015', which I think
should be seen as 'the first moment of 2014'.
This function should overcome those limitations. | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/util.py#L7-L17 | [
"def _split_datetime(datetime_input):\n dt_input = datetime_input.split(\" \")\n if len(dt_input) == 1:\n dt_input.append(\"\")\n date_input, time_input = dt_input\n if \":\" in date_input:\n date_input, time_input = time_input, date_input\n if not date_input:\n date_input = arro... | import arrow
from itertools import groupby
from operator import attrgetter, itemgetter
def _split_datetime(datetime_input):
dt_input = datetime_input.split(" ")
if len(dt_input) == 1:
dt_input.append("")
date_input, time_input = dt_input
if ":" in date_input:
date_input, time_input =... |
TadLeonard/tfatool | tfatool/upload.py | _encode_time | python | def _encode_time(mtime: float):
dt = arrow.get(mtime)
dt = dt.to("local")
date_val = ((dt.year - 1980) << 9) | (dt.month << 5) | dt.day
secs = dt.second + dt.microsecond / 10**6
time_val = (dt.hour << 11) | (dt.minute << 5) | math.floor(secs / 2)
return (date_val << 16) | time_val | Encode a mtime float as a 32-bit FAT time | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/upload.py#L84-L91 | null | import math
import os
import arrow
from functools import partial
from . import cgi
from .info import DEFAULT_REMOTE_DIR, DEFAULT_MASTERCODE, URL
from .info import WriteProtectMode, Upload, ResponseCode
from requests import RequestException
def upload_file(local_path: str, url=URL, remote_dir=DEFAULT_REMOTE_DIR):
... |
TadLeonard/tfatool | tfatool/command.py | memory_changed | python | def memory_changed(url=URL):
response = _get(Operation.memory_changed, url)
try:
return int(response.text) == 1
except ValueError:
raise IOError("Likely no FlashAir connection, "
"memory changed CGI command failed") | Returns True if memory has been written to, False otherwise | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/command.py#L46-L53 | [
"def _get(operation: Operation, url=URL, **params):\n \"\"\"HTTP GET of the FlashAir command.cgi entrypoint\"\"\"\n prepped_request = _prep_get(operation, url=url, **params)\n return cgi.send(prepped_request)\n"
] | import logging
import arrow
from pathlib import PurePosixPath
from collections import namedtuple
from . import cgi
from .info import URL, DEFAULT_REMOTE_DIR
from .info import WifiMode, WifiModeOnBoot, ModeValue, Operation
from .info import FileInfo, RawFileInfo
logger = logging.getLogger(__name__)
################... |
TadLeonard/tfatool | tfatool/command.py | _get | python | def _get(operation: Operation, url=URL, **params):
prepped_request = _prep_get(operation, url=url, **params)
return cgi.send(prepped_request) | HTTP GET of the FlashAir command.cgi entrypoint | train | https://github.com/TadLeonard/tfatool/blob/12da2807b5fb538c5317ef255d846b32ceb174d0/tfatool/command.py#L147-L150 | [
"def _prep_get(operation: Operation, url=URL, **params):\n params.update(op=int(operation)) # op param required\n return cgi.prep_get(cgi.Entrypoint.command, url=url, **params)\n"
] | import logging
import arrow
from pathlib import PurePosixPath
from collections import namedtuple
from . import cgi
from .info import URL, DEFAULT_REMOTE_DIR
from .info import WifiMode, WifiModeOnBoot, ModeValue, Operation
from .info import FileInfo, RawFileInfo
logger = logging.getLogger(__name__)
################... |
python-astrodynamics/spacetrack | shovel/docs.py | watch | python | def watch():
# Start with a clean build
sphinx_build['-b', 'html', '-E', 'docs', 'docs/_build/html'] & FG
handler = ShellCommandTrick(
shell_command='sphinx-build -b html docs docs/_build/html',
patterns=['*.rst', '*.py'],
ignore_patterns=['_build/*'],
ignore_directories=['... | Renerate documentation when it changes. | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/shovel/docs.py#L18-L31 | null | # coding: utf-8
from __future__ import absolute_import, division, print_function
import os
from shutil import rmtree
from plumbum import FG
from plumbum.cmd import pandoc, sphinx_build
from shovel import task
from watchdog.observers import Observer
from watchdog.tricks import ShellCommandTrick
from watchdog.watchmedo... |
python-astrodynamics/spacetrack | shovel/docs.py | gen | python | def gen(skipdirhtml=False):
docs_changelog = 'docs/changelog.rst'
check_git_unchanged(docs_changelog)
pandoc('--from=markdown', '--to=rst', '--output=' + docs_changelog, 'CHANGELOG.md')
if not skipdirhtml:
sphinx_build['-b', 'dirhtml', '-W', '-E', 'docs', 'docs/_build/dirhtml'] & FG
sphinx_b... | Generate html and dirhtml output. | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/shovel/docs.py#L35-L42 | null | # coding: utf-8
from __future__ import absolute_import, division, print_function
import os
from shutil import rmtree
from plumbum import FG
from plumbum.cmd import pandoc, sphinx_build
from shovel import task
from watchdog.observers import Observer
from watchdog.tricks import ShellCommandTrick
from watchdog.watchmedo... |
python-astrodynamics/spacetrack | shovel/_helpers.py | check_git_unchanged | python | def check_git_unchanged(filename, yes=False):
if check_staged(filename):
s = 'There are staged changes in {}, overwrite? [y/n] '.format(filename)
if yes or input(s) in ('y', 'yes'):
return
else:
raise RuntimeError('There are staged changes in '
... | Check git to avoid overwriting user changes. | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/shovel/_helpers.py#L7-L22 | [
"def check_staged(filename=None):\n \"\"\"Check if there are 'changes to be committed' in the index.\"\"\"\n retcode, _, stdout = git['diff-index', '--quiet', '--cached', 'HEAD',\n filename].run(retcode=None)\n if retcode == 1:\n return True\n elif retcode == 0:\n ... | # coding: utf-8
from __future__ import absolute_import, division, print_function
from plumbum.cmd import git
def check_staged(filename=None):
"""Check if there are 'changes to be committed' in the index."""
retcode, _, stdout = git['diff-index', '--quiet', '--cached', 'HEAD',
fi... |
python-astrodynamics/spacetrack | shovel/_helpers.py | check_staged | python | def check_staged(filename=None):
retcode, _, stdout = git['diff-index', '--quiet', '--cached', 'HEAD',
filename].run(retcode=None)
if retcode == 1:
return True
elif retcode == 0:
return False
else:
raise RuntimeError(stdout) | Check if there are 'changes to be committed' in the index. | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/shovel/_helpers.py#L25-L34 | null | # coding: utf-8
from __future__ import absolute_import, division, print_function
from plumbum.cmd import git
def check_git_unchanged(filename, yes=False):
"""Check git to avoid overwriting user changes."""
if check_staged(filename):
s = 'There are staged changes in {}, overwrite? [y/n] '.format(filen... |
python-astrodynamics/spacetrack | spacetrack/aio.py | _raise_for_status | python | async def _raise_for_status(response):
try:
response.raise_for_status()
except aiohttp.ClientResponseError as exc:
reason = response.reason
spacetrack_error_msg = None
try:
json = await response.json()
if isinstance(json, Mapping):
space... | Raise an appropriate error for a given response.
Arguments:
response (:py:class:`aiohttp.ClientResponse`): The API response.
Raises:
:py:class:`aiohttp.web_exceptions.HTTPException`: The appropriate
error for the response's status.
This function was taken from the aslack project and m... | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/spacetrack/aio.py#L349-L409 | null | # coding: utf-8
from __future__ import absolute_import, division, print_function
import asyncio
import ssl
import time
from collections.abc import AsyncIterator, Mapping
import aiohttp
import aiohttp.web_exceptions
import requests.certs
from aiohttp.helpers import parse_mimetype
from .base import AuthenticationError... |
python-astrodynamics/spacetrack | spacetrack/aio.py | AsyncSpaceTrackClient.generic_request | python | async def generic_request(self, class_, iter_lines=False, iter_content=False,
controller=None, parse_types=False, **kwargs):
if iter_lines and iter_content:
raise ValueError('iter_lines and iter_content cannot both be True')
if 'format' in kwargs and parse_type... | Generic Space-Track query coroutine.
The request class methods use this method internally; the public
API is as follows:
.. code-block:: python
st.tle_publish(*args, **st)
st.basicspacedata.tle_publish(*args, **st)
st.file(*args, **st)
st.filesh... | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/spacetrack/aio.py#L70-L213 | [
"def _stringify_predicate_value(value):\n \"\"\"Convert Python objects to Space-Track compatible strings\n\n - Booleans (``True`` -> ``'true'``)\n - Sequences (``[25544, 34602]`` -> ``'25544,34602'``)\n - dates/datetimes (``date(2015, 12, 23)`` -> ``'2015-12-23'``)\n - ``None`` -> ``'null-val'``\n ... | class AsyncSpaceTrackClient(SpaceTrackClient):
"""Asynchronous SpaceTrack client class.
This class should be considered experimental.
It must be closed by calling
:meth:`~spacetrack.aio.AsyncSpaceTrackClient.close`. Alternatively,
instances of this class can be used as a context manager.
Para... |
python-astrodynamics/spacetrack | spacetrack/aio.py | AsyncSpaceTrackClient._download_predicate_data | python | async def _download_predicate_data(self, class_, controller):
await self.authenticate()
url = ('{0}{1}/modeldef/class/{2}'
.format(self.base_url, controller, class_))
resp = await self._ratelimited_get(url)
await _raise_for_status(resp)
resp_json = await resp.j... | Get raw predicate information for given request class, and cache for
subsequent calls. | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/spacetrack/aio.py#L242-L256 | [
"async def _raise_for_status(response):\n \"\"\"Raise an appropriate error for a given response.\n\n Arguments:\n response (:py:class:`aiohttp.ClientResponse`): The API response.\n\n Raises:\n :py:class:`aiohttp.web_exceptions.HTTPException`: The appropriate\n error for the response's stat... | class AsyncSpaceTrackClient(SpaceTrackClient):
"""Asynchronous SpaceTrack client class.
This class should be considered experimental.
It must be closed by calling
:meth:`~spacetrack.aio.AsyncSpaceTrackClient.close`. Alternatively,
instances of this class can be used as a context manager.
Para... |
python-astrodynamics/spacetrack | spacetrack/operators.py | _stringify_predicate_value | python | def _stringify_predicate_value(value):
if isinstance(value, bool):
return str(value).lower()
elif isinstance(value, Sequence) and not isinstance(value, six.string_types):
return ','.join(_stringify_predicate_value(x) for x in value)
elif isinstance(value, datetime.datetime):
return v... | Convert Python objects to Space-Track compatible strings
- Booleans (``True`` -> ``'true'``)
- Sequences (``[25544, 34602]`` -> ``'25544,34602'``)
- dates/datetimes (``date(2015, 12, 23)`` -> ``'2015-12-23'``)
- ``None`` -> ``'null-val'`` | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/spacetrack/operators.py#L45-L64 | null | # coding: utf-8
from __future__ import absolute_import, division, print_function
import datetime
import six
try:
from collections.abc import Sequence
except ImportError:
from collections import Sequence
def greater_than(value):
"""``'>value'``."""
return '>' + _stringify_predicate_value(value)
de... |
python-astrodynamics/spacetrack | spacetrack/base.py | _iter_content_generator | python | def _iter_content_generator(response, decode_unicode):
for chunk in response.iter_content(100 * 1024, decode_unicode=decode_unicode):
if decode_unicode:
# Replace CRLF newlines with LF, Python will handle
# platform specific newlines if written to file.
chunk = chunk.repl... | Generator used to yield 100 KiB chunks for a given response. | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/spacetrack/base.py#L640-L649 | null | # coding: utf-8
from __future__ import absolute_import, division, print_function
import datetime as dt
import re
import threading
import time
import weakref
from collections import OrderedDict
from functools import partial
import requests
from logbook import Logger
from ratelimiter import RateLimiter
from represent i... |
python-astrodynamics/spacetrack | spacetrack/base.py | _iter_lines_generator | python | def _iter_lines_generator(response, decode_unicode):
pending = None
for chunk in _iter_content_generator(response, decode_unicode=decode_unicode):
if pending is not None:
chunk = pending + chunk
lines = chunk.splitlines()
if lines and lines[-1] and chunk and lines[-1][-1]... | Iterates over the response data, one line at a time. When
stream=True is set on the request, this avoids reading the
content at once into memory for large responses.
The function is taken from :meth:`requests.models.Response.iter_lines`, but
modified to use our :func:`~spacetrack.base._iter_content_ge... | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/spacetrack/base.py#L652-L683 | [
"def _iter_content_generator(response, decode_unicode):\n \"\"\"Generator used to yield 100 KiB chunks for a given response.\"\"\"\n for chunk in response.iter_content(100 * 1024, decode_unicode=decode_unicode):\n if decode_unicode:\n # Replace CRLF newlines with LF, Python will handle\n ... | # coding: utf-8
from __future__ import absolute_import, division, print_function
import datetime as dt
import re
import threading
import time
import weakref
from collections import OrderedDict
from functools import partial
import requests
from logbook import Logger
from ratelimiter import RateLimiter
from represent i... |
python-astrodynamics/spacetrack | spacetrack/base.py | _raise_for_status | python | def _raise_for_status(response):
http_error_msg = ''
if 400 <= response.status_code < 500:
http_error_msg = '%s Client Error: %s for url: %s' % (
response.status_code, response.reason, response.url)
elif 500 <= response.status_code < 600:
http_error_msg = '%s Server Error: %s ... | Raises stored :class:`HTTPError`, if one occurred.
This is the :meth:`requests.models.Response.raise_for_status` method,
modified to add the response from Space-Track, if given. | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/spacetrack/base.py#L686-L719 | null | # coding: utf-8
from __future__ import absolute_import, division, print_function
import datetime as dt
import re
import threading
import time
import weakref
from collections import OrderedDict
from functools import partial
import requests
from logbook import Logger
from ratelimiter import RateLimiter
from represent i... |
python-astrodynamics/spacetrack | spacetrack/base.py | SpaceTrackClient.generic_request | python | def generic_request(self, class_, iter_lines=False, iter_content=False,
controller=None, parse_types=False, **kwargs):
r"""Generic Space-Track query.
The request class methods use this method internally; the public
API is as follows:
.. code-block:: python
... | r"""Generic Space-Track query.
The request class methods use this method internally; the public
API is as follows:
.. code-block:: python
st.tle_publish(*args, **kw)
st.basicspacedata.tle_publish(*args, **kw)
st.file(*args, **kw)
st.fileshare.fi... | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/spacetrack/base.py#L245-L402 | [
"def _stringify_predicate_value(value):\n \"\"\"Convert Python objects to Space-Track compatible strings\n\n - Booleans (``True`` -> ``'true'``)\n - Sequences (``[25544, 34602]`` -> ``'25544,34602'``)\n - dates/datetimes (``date(2015, 12, 23)`` -> ``'2015-12-23'``)\n - ``None`` -> ``'null-val'``\n ... | class SpaceTrackClient(object):
"""SpaceTrack client class.
Parameters:
identity: Space-Track username.
password: Space-Track password.
For more information, refer to the `Space-Track documentation`_.
.. _`Space-Track documentation`: https://www.space-track.org/documentation
#... |
python-astrodynamics/spacetrack | spacetrack/base.py | SpaceTrackClient._ratelimited_get | python | def _ratelimited_get(self, *args, **kwargs):
with self._ratelimiter:
resp = self.session.get(*args, **kwargs)
# It's possible that Space-Track will return HTTP status 500 with a
# query rate limit violation. This can happen if a script is cancelled
# before it has finished s... | Perform get request, handling rate limiting. | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/spacetrack/base.py#L415-L441 | null | class SpaceTrackClient(object):
"""SpaceTrack client class.
Parameters:
identity: Space-Track username.
password: Space-Track password.
For more information, refer to the `Space-Track documentation`_.
.. _`Space-Track documentation`: https://www.space-track.org/documentation
#... |
python-astrodynamics/spacetrack | spacetrack/base.py | SpaceTrackClient._find_controller | python | def _find_controller(self, class_):
for controller, classes in self.request_controllers.items():
if class_ in classes:
return controller
else:
raise ValueError('Unknown request class {!r}'.format(class_)) | Find first controller that matches given request class.
Order is specified by the keys of
``SpaceTrackClient.request_controllers``
(:class:`~collections.OrderedDict`) | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/spacetrack/base.py#L479-L490 | null | class SpaceTrackClient(object):
"""SpaceTrack client class.
Parameters:
identity: Space-Track username.
password: Space-Track password.
For more information, refer to the `Space-Track documentation`_.
.. _`Space-Track documentation`: https://www.space-track.org/documentation
#... |
python-astrodynamics/spacetrack | spacetrack/base.py | SpaceTrackClient._download_predicate_data | python | def _download_predicate_data(self, class_, controller):
self.authenticate()
url = ('{0}{1}/modeldef/class/{2}'
.format(self.base_url, controller, class_))
logger.debug(requests.utils.requote_uri(url))
resp = self._ratelimited_get(url)
_raise_for_status(resp)
... | Get raw predicate information for given request class, and cache for
subsequent calls. | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/spacetrack/base.py#L492-L507 | [
"def _raise_for_status(response):\n \"\"\"Raises stored :class:`HTTPError`, if one occurred.\n\n This is the :meth:`requests.models.Response.raise_for_status` method,\n modified to add the response from Space-Track, if given.\n \"\"\"\n\n http_error_msg = ''\n\n if 400 <= response.status_code < 50... | class SpaceTrackClient(object):
"""SpaceTrack client class.
Parameters:
identity: Space-Track username.
password: Space-Track password.
For more information, refer to the `Space-Track documentation`_.
.. _`Space-Track documentation`: https://www.space-track.org/documentation
#... |
python-astrodynamics/spacetrack | spacetrack/base.py | SpaceTrackClient.get_predicates | python | def get_predicates(self, class_, controller=None):
if class_ not in self._predicates:
if controller is None:
controller = self._find_controller(class_)
else:
classes = self.request_controllers.get(controller, None)
if classes is None:
... | Get full predicate information for given request class, and cache
for subsequent calls. | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/spacetrack/base.py#L509-L529 | [
"def _find_controller(self, class_):\n \"\"\"Find first controller that matches given request class.\n\n Order is specified by the keys of\n ``SpaceTrackClient.request_controllers``\n (:class:`~collections.OrderedDict`)\n \"\"\"\n for controller, classes in self.request_controllers.items():\n ... | class SpaceTrackClient(object):
"""SpaceTrack client class.
Parameters:
identity: Space-Track username.
password: Space-Track password.
For more information, refer to the `Space-Track documentation`_.
.. _`Space-Track documentation`: https://www.space-track.org/documentation
#... |
python-astrodynamics/spacetrack | spacetrack/base.py | _ControllerProxy.get_predicates | python | def get_predicates(self, class_):
return self.client.get_predicates(
class_=class_, controller=self.controller) | Proxy ``get_predicates`` to client with stored request
controller. | train | https://github.com/python-astrodynamics/spacetrack/blob/18f63b7de989a31b983d140a11418e01bd6fd398/spacetrack/base.py#L632-L637 | null | class _ControllerProxy(object):
"""Proxies request class methods with a preset request controller."""
def __init__(self, client, controller):
# The client will cache _ControllerProxy instances, so only store
# a weak reference to it.
self.client = weakref.proxy(client)
self.contr... |
howl-anderson/MicroTokenizer | MicroTokenizer/tokenizer_loader.py | TokenizerLoader.create_tokenizer | python | def create_tokenizer(self, name, config=dict()):
if name not in self.factories:
raise KeyError(Errors.E002.format(name=name))
factory = self.factories[name]
return factory(self, **config) | Create a pipeline component from a factory.
name (unicode): Factory name to look up in `Language.factories`.
config (dict): Configuration parameters to initialise component.
RETURNS (callable): Pipeline component. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/tokenizer_loader.py#L44-L54 | null | class TokenizerLoader(object):
Defaults = BaseDefaults
factories = {
'max_match_forward_tokenizer': lambda nlp, **cfg: MaxMatchForwardTokenizer(**cfg),
'max_match_backward_tokenizer': lambda nlp, **cfg: MaxMatchBackwardTokenizer(**cfg),
'max_match_bidirectional_tokenizer': lambda nlp, *... |
howl-anderson/MicroTokenizer | MicroTokenizer/errors.py | add_codes | python | def add_codes(err_cls):
class ErrorsWithCodes(object):
def __getattribute__(self, code):
msg = getattr(err_cls, code)
return '[{code}] {msg}'.format(code=code, msg=msg)
return ErrorsWithCodes() | Add error codes to string messages via class attribute names. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/errors.py#L9-L15 | null | # coding: utf8
from __future__ import unicode_literals
import os
import warnings
import inspect
@add_codes
class Warnings(object):
W001 = ("As of spaCy v2.0, the keyword argument `path=` is deprecated. "
"You can now call spacy.load with the path as its first argument, "
"and the model's... |
howl-anderson/MicroTokenizer | MicroTokenizer/errors.py | _warn | python | def _warn(message, warn_type='user'):
w_id = message.split('[', 1)[1].split(']', 1)[0] # get ID from string
if warn_type in SPACY_WARNING_TYPES and w_id not in SPACY_WARNING_IGNORE:
category = WARNINGS[warn_type]
stack = inspect.stack()[-1]
with warnings.catch_warnings():
if... | message (unicode): The message to display.
category (Warning): The Warning to show. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/errors.py#L314-L326 | null | # coding: utf8
from __future__ import unicode_literals
import os
import warnings
import inspect
def add_codes(err_cls):
"""Add error codes to string messages via class attribute names."""
class ErrorsWithCodes(object):
def __getattribute__(self, code):
msg = getattr(err_cls, code)
... |
howl-anderson/MicroTokenizer | MicroTokenizer/cli_command/download.py | download | python | def download(model=None, direct=False, *pip_args):
if model is None:
model = about.__default_corpus__
if direct:
dl = download_model('{m}/{m}.tar.gz#egg={m}'.format(m=model), pip_args)
else:
shortcuts = get_json(about.__shortcuts__, "available shortcuts")
model_name = shortc... | Download compatible model from default download path using pip. Model
can be shortcut, model name or, if --direct flag is set, full model name
with version. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/cli_command/download.py#L22-L53 | [
"def get_version(model, comp):\n model = model.rsplit('.dev', 1)[0]\n if model not in comp:\n prints(Messages.M007.format(name=model, version=about.__version__),\n title=Messages.M005, exits=1)\n return comp[model][0]\n",
"def prints(*texts, **kwargs):\n \"\"\"Print formatted mess... | # coding: utf8
from __future__ import unicode_literals
import plac
import requests
import os
import subprocess
import sys
from MicroTokenizer.cli_command._messages import Messages
from MicroTokenizer.cli_command.link import link
from MicroTokenizer.util import prints, get_package_path
from MicroTokenizer import about... |
howl-anderson/MicroTokenizer | MicroTokenizer/cli_command/link.py | link | python | def link(origin, link_name, force=False, model_path=None):
if util.is_package(origin):
model_path = util.get_package_path(origin)
else:
model_path = Path(origin) if model_path is None else Path(model_path)
if not model_path.exists():
prints(Messages.M009.format(path=path2str(model_pa... | Create a symlink for models within the spacy/data directory. Accepts
either the name of a pip package, or the local path to the model data
directory. Linking models allows loading them via spacy.load(link_name). | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/cli_command/link.py#L17-L53 | [
"def is_package(name):\n \"\"\"Check if string maps to a package installed via pip.\n\n name (unicode): Name of package.\n RETURNS (bool): True if installed package, False if not.\n \"\"\"\n name = name.lower() # compare package name against lowercase name\n packages = pkg_resources.working_set.b... | # coding: utf8
from __future__ import unicode_literals
import plac
from pathlib import Path
from ._messages import Messages
from ..compat import symlink_to, path2str
from ..util import prints
from .. import util
@plac.annotations(
origin=("package name or local path to model", "positional", None, str),
link... |
howl-anderson/MicroTokenizer | MicroTokenizer/util.py | load_model_from_path | python | def load_model_from_path(model_path, meta=False, **overrides):
from .tokenizer_loader import TokenizerLoader
if not meta:
meta = get_model_meta(model_path)
tokenizer_loader = TokenizerLoader(meta=meta, **overrides)
tokenizers = meta.get('tokenizers', [])
disable = overrides.get('disable', [... | Load a model from a data directory path. Creates Language class with
pipeline from meta.json and then calls from_disk() with path. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/util.py#L101-L120 | [
"def get_model_meta(path):\n \"\"\"Get model meta.json from a directory path and validate its contents.\n\n path (unicode or Path): Path to model directory.\n RETURNS (dict): The model's meta data.\n \"\"\"\n model_path = ensure_path(path)\n if not model_path.exists():\n raise IOError(Error... | # coding: utf8
from __future__ import unicode_literals, print_function
import functools
import importlib
import random
import sys
import textwrap
import ujson
from pathlib import Path
import numpy.random
import pkg_resources
import regex as re
from .compat import import_file
from .compat import path2str, basestring_... |
howl-anderson/MicroTokenizer | MicroTokenizer/util.py | is_package | python | def is_package(name):
name = name.lower() # compare package name against lowercase name
packages = pkg_resources.working_set.by_key.keys()
for package in packages:
if package.lower().replace('-', '_') == name:
return True
return False | Check if string maps to a package installed via pip.
name (unicode): Name of package.
RETURNS (bool): True if installed package, False if not. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/util.py#L159-L170 | null | # coding: utf8
from __future__ import unicode_literals, print_function
import functools
import importlib
import random
import sys
import textwrap
import ujson
from pathlib import Path
import numpy.random
import pkg_resources
import regex as re
from .compat import import_file
from .compat import path2str, basestring_... |
howl-anderson/MicroTokenizer | MicroTokenizer/util.py | decaying | python | def decaying(start, stop, decay):
def clip(value):
return max(value, stop) if (start > stop) else min(value, stop)
nr_upd = 1.
while True:
yield clip(start * 1./(1. + decay * nr_upd))
nr_upd += 1 | Yield an infinite series of linearly decaying values. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/util.py#L272-L279 | [
"def clip(value):\n return max(value, stop) if (start > stop) else min(value, stop)\n"
] | # coding: utf8
from __future__ import unicode_literals, print_function
import functools
import importlib
import random
import sys
import textwrap
import ujson
from pathlib import Path
import numpy.random
import pkg_resources
import regex as re
from .compat import import_file
from .compat import path2str, basestring_... |
howl-anderson/MicroTokenizer | MicroTokenizer/util.py | read_json | python | def read_json(location):
location = ensure_path(location)
with location.open('r', encoding='utf8') as f:
return ujson.load(f) | Open and load JSON from file.
location (Path): Path to JSON file.
RETURNS (dict): Loaded JSON content. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/util.py#L311-L319 | [
"def ensure_path(path):\n \"\"\"Ensure string is converted to a Path.\n\n path: Anything. If string, it's converted to Path.\n RETURNS: Path or original argument.\n \"\"\"\n if isinstance(path, basestring_):\n return Path(path)\n else:\n return path\n"
] | # coding: utf8
from __future__ import unicode_literals, print_function
import functools
import importlib
import random
import sys
import textwrap
import ujson
from pathlib import Path
import numpy.random
import pkg_resources
import regex as re
from .compat import import_file
from .compat import path2str, basestring_... |
howl-anderson/MicroTokenizer | MicroTokenizer/util.py | get_raw_input | python | def get_raw_input(description, default=False):
additional = ' (default: %s)' % default if default else ''
prompt = ' %s%s: ' % (description, additional)
user_input = input_(prompt)
return user_input | Get user input from the command line via raw_input / input.
description (unicode): Text to display before prompt.
default (unicode or False/None): Default value to display with prompt.
RETURNS (unicode): User input. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/util.py#L322-L332 | null | # coding: utf8
from __future__ import unicode_literals, print_function
import functools
import importlib
import random
import sys
import textwrap
import ujson
from pathlib import Path
import numpy.random
import pkg_resources
import regex as re
from .compat import import_file
from .compat import path2str, basestring_... |
howl-anderson/MicroTokenizer | MicroTokenizer/util.py | print_table | python | def print_table(data, title=None):
if isinstance(data, dict):
data = list(data.items())
tpl_row = ' {:<15}' * len(data[0])
table = '\n'.join([tpl_row.format(l, unicode_(v)) for l, v in data])
if title:
print('\n \033[93m{}\033[0m'.format(title))
print('\n{}\n'.format(table)) | Print data in table format.
data (dict or list of tuples): Label/value pairs.
title (unicode or None): Title, will be printed above. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/util.py#L355-L367 | null | # coding: utf8
from __future__ import unicode_literals, print_function
import functools
import importlib
import random
import sys
import textwrap
import ujson
from pathlib import Path
import numpy.random
import pkg_resources
import regex as re
from .compat import import_file
from .compat import path2str, basestring_... |
howl-anderson/MicroTokenizer | MicroTokenizer/util.py | print_markdown | python | def print_markdown(data, title=None):
def excl_value(value):
# contains path, i.e. personal info
return isinstance(value, basestring_) and Path(value).exists()
if isinstance(data, dict):
data = list(data.items())
markdown = ["* **{}:** {}".format(l, unicode_(v))
for ... | Print data in GitHub-flavoured Markdown format for issues etc.
data (dict or list of tuples): Label/value pairs.
title (unicode or None): Title, will be rendered as headline 2. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/util.py#L370-L386 | null | # coding: utf8
from __future__ import unicode_literals, print_function
import functools
import importlib
import random
import sys
import textwrap
import ujson
from pathlib import Path
import numpy.random
import pkg_resources
import regex as re
from .compat import import_file
from .compat import path2str, basestring_... |
howl-anderson/MicroTokenizer | MicroTokenizer/util.py | prints | python | def prints(*texts, **kwargs):
exits = kwargs.get('exits', None)
title = kwargs.get('title', None)
title = '\033[93m{}\033[0m\n'.format(_wrap(title)) if title else ''
message = '\n\n'.join([_wrap(text) for text in texts])
print('\n{}{}\n'.format(title, message))
if exits is not None:
sys.... | Print formatted message (manual ANSI escape sequences to avoid
dependency)
*texts (unicode): Texts to print. Each argument is rendered as paragraph.
**kwargs: 'title' becomes coloured headline. exits=True performs sys exit. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/util.py#L389-L402 | [
"def _wrap(text, wrap_max=80, indent=4):\n \"\"\"Wrap text at given width using textwrap module.\n\n text (unicode): Text to wrap. If it's a Path, it's converted to string.\n wrap_max (int): Maximum line length (indent is deducted).\n indent (int): Number of spaces for indentation.\n RETURNS (unicode... | # coding: utf8
from __future__ import unicode_literals, print_function
import functools
import importlib
import random
import sys
import textwrap
import ujson
from pathlib import Path
import numpy.random
import pkg_resources
import regex as re
from .compat import import_file
from .compat import path2str, basestring_... |
howl-anderson/MicroTokenizer | MicroTokenizer/util.py | _wrap | python | def _wrap(text, wrap_max=80, indent=4):
indent = indent * ' '
wrap_width = wrap_max - len(indent)
if isinstance(text, Path):
text = path2str(text)
return textwrap.fill(text, width=wrap_width, initial_indent=indent,
subsequent_indent=indent, break_long_words=False,
... | Wrap text at given width using textwrap module.
text (unicode): Text to wrap. If it's a Path, it's converted to string.
wrap_max (int): Maximum line length (indent is deducted).
indent (int): Number of spaces for indentation.
RETURNS (unicode): Wrapped text. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/util.py#L405-L419 | [
"path2str = lambda path: str(path)\n"
] | # coding: utf8
from __future__ import unicode_literals, print_function
import functools
import importlib
import random
import sys
import textwrap
import ujson
from pathlib import Path
import numpy.random
import pkg_resources
import regex as re
from .compat import import_file
from .compat import path2str, basestring_... |
howl-anderson/MicroTokenizer | MicroTokenizer/util.py | escape_html | python | def escape_html(text):
text = text.replace('&', '&')
text = text.replace('<', '<')
text = text.replace('>', '>')
text = text.replace('"', '"')
return text | Replace <, >, &, " with their HTML encoded representation. Intended to
prevent HTML errors in rendered displaCy markup.
text (unicode): The original text.
RETURNS (unicode): Equivalent text to be safely used within HTML. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/util.py#L433-L444 | null | # coding: utf8
from __future__ import unicode_literals, print_function
import functools
import importlib
import random
import sys
import textwrap
import ujson
from pathlib import Path
import numpy.random
import pkg_resources
import regex as re
from .compat import import_file
from .compat import path2str, basestring_... |
howl-anderson/MicroTokenizer | MicroTokenizer/compat.py | normalize_string_keys | python | def normalize_string_keys(old):
new = {}
for key, value in old.items():
if isinstance(key, bytes_):
new[key.decode('utf8')] = value
else:
new[key] = value
return new | Given a dictionary, make sure keys are unicode strings, not bytes. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/compat.py#L78-L86 | null | # coding: utf8
from __future__ import unicode_literals
import sys
import ujson
import itertools
import locale
try:
import cPickle as pickle
except ImportError:
import pickle
try:
import copy_reg
except ImportError:
import copyreg as copy_reg
pickle = pickle
copy_reg = copy_reg
izip = getattr(itertoo... |
howl-anderson/MicroTokenizer | MicroTokenizer/compat.py | locale_escape | python | def locale_escape(string, errors='replace'):
'''
Mangle non-supported characters, for savages with ascii terminals.
'''
encoding = locale.getpreferredencoding()
string = string.encode(encoding, errors).decode('utf8')
return string | Mangle non-supported characters, for savages with ascii terminals. | train | https://github.com/howl-anderson/MicroTokenizer/blob/41bbe9c31d202b4f751ad5201d343ad1123b42b5/MicroTokenizer/compat.py#L102-L108 | null | # coding: utf8
from __future__ import unicode_literals
import sys
import ujson
import itertools
import locale
try:
import cPickle as pickle
except ImportError:
import pickle
try:
import copy_reg
except ImportError:
import copyreg as copy_reg
pickle = pickle
copy_reg = copy_reg
izip = getattr(itertoo... |
jmvrbanac/Specter | specter/reporting/dots.py | DotsReporter.print_error | python | def print_error(self, wrapper):
level = 0
parent = wrapper.parent
while parent:
print_test_msg(parent.name, level, TestStatus.FAIL, self.use_color)
level += 1
parent = parent.parent
print_test_msg(wrapper.name, level, TestStatus.FAIL, self.use_color)
... | A crude way of output the errors for now. This needs to be
cleaned up into something better. | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/reporting/dots.py#L29-L53 | [
"def print_expects(test_case, level, use_color=True, use_unicode=True):\n # Print expects\n for expect in test_case.expects:\n mark = u'\\u2718'\n if not use_unicode:\n mark = 'x'\n\n status = TestStatus.FAIL\n if expect.success:\n status = TestStatus.PASS\n ... | class DotsReporter(AbstractConsoleReporter, AbstractParallelReporter):
def __init__(self):
super(DotsReporter, self).__init__()
self.total = 0
self.failed_tests = []
self.use_color = True
def get_name(self):
return _('Dots Reporter')
def subscribe_to_spec(self, spe... |
jmvrbanac/Specter | specter/runner.py | SpecterRunner.combine_coverage_reports | python | def combine_coverage_reports(self, omit, parallel):
tmp_cov = coverage.coverage(omit=omit, data_suffix=parallel)
tmp_cov.load()
tmp_cov.combine()
tmp_cov.save() | Method to force the combination of parallel coverage reports. | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/runner.py#L120-L125 | null | class SpecterRunner(object):
DESCRIPTION = _('Specter is a spec-based testing library to help '
'facilitate BDD in Python.')
def __init__(self):
super(SpecterRunner, self).__init__()
self.coverage = None
self.suite_scanner = None
self.arg_parser = ArgumentPar... |
jmvrbanac/Specter | specter/spec.py | CaseWrapper.serialize | python | def serialize(self):
expects = [exp.serialize() for exp in self.expects]
converted_dict = {
'id': self.id,
'name': self.pretty_name,
'raw_name': self.name,
'doc': self.doc,
'error': self.error,
'skipped': self.skipped,
'... | Serializes the CaseWrapper object for collection.
Warning, this will only grab the available information.
It is strongly that you only call this once all specs and
tests have completed. | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/spec.py#L53-L76 | [
"def remove_empty_entries_from_dict(input_dict):\n return {k: v for k, v in six.iteritems(input_dict) if v is not None}\n"
] | class CaseWrapper(TimedObject):
def __init__(self, case_func, parent, execute_kwargs=None, metadata={}):
super(CaseWrapper, self).__init__()
self.id = str(uuid.uuid4())
self.case_func = case_func
self.expects = []
self.parent = parent
self.failed = None
self.e... |
jmvrbanac/Specter | specter/spec.py | Describe.serialize | python | def serialize(self):
cases = [case.serialize() for key, case in six.iteritems(self.cases)]
specs = [spec.serialize() for spec in self.describes]
converted_dict = {
'id': self.id,
'name': self.name,
'class_path': self.real_class_path,
'doc': self.... | Serializes the Spec/Describe object for collection.
Warning, this will only grab the available information.
It is strongly that you only call this once all specs and
tests have completed. | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/spec.py#L280-L299 | null | class Describe(EventDispatcher):
__FIXTURE__ = False
#: List of methods to be called after every test
hooks = ()
def __init__(self, parent=None):
super(Describe, self).__init__()
self.id = str(uuid.uuid4())
wrappers = self.__wrappers__
self.parent = parent
self.... |
jmvrbanac/Specter | specter/spec.py | Describe._run_hooks | python | def _run_hooks(self):
for hook in self.hooks:
getattr(self, hook)(self._state) | Calls any registered hooks providing the current state. | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/spec.py#L301-L304 | null | class Describe(EventDispatcher):
__FIXTURE__ = False
#: List of methods to be called after every test
hooks = ()
def __init__(self, parent=None):
super(Describe, self).__init__()
self.id = str(uuid.uuid4())
wrappers = self.__wrappers__
self.parent = parent
self.... |
jmvrbanac/Specter | specter/reporting/__init__.py | ReporterPluginManager.subscribe_all_to_spec | python | def subscribe_all_to_spec(self, spec):
for reporter in self.reporters:
if self.can_use_reporter(reporter, self.parallel):
reporter.subscribe_to_spec(spec) | Will automatically not subscribe reporters that are not parallel
or serial depending on the current mode. | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/reporting/__init__.py#L77-L83 | [
"def can_use_reporter(self, reporter, parallel):\n can_use = False\n if parallel:\n if isinstance(reporter, AbstractParallelReporter):\n can_use = True\n else:\n if isinstance(reporter, AbstractSerialReporter):\n can_use = True\n return can_use\n"
] | class ReporterPluginManager(object):
def __init__(self, parallel=False):
self.reporters = []
self.load_reporters()
self.parallel = parallel
def get_console_reporters(self):
return [reporter for reporter in self.reporters
if issubclass(type(reporter), AbstractCon... |
jmvrbanac/Specter | specter/reporting/console.py | ConsoleReporter.output | python | def output(self, msg, indent, status=None):
color = None
if self.use_color:
color = get_color_from_status(status)
print_indent_msg(msg, indent, color) | Alias for print_indent_msg with color determined by status. | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/reporting/console.py#L139-L144 | [
"def get_color_from_status(status):\n color = None\n if status == TestStatus.PASS:\n color = ConsoleColors.GREEN\n elif status == TestStatus.SKIP:\n color = ConsoleColors.YELLOW\n elif status == TestStatus.INCOMPLETE:\n color = ConsoleColors.MAGENTA\n elif status is not None:\n ... | class ConsoleReporter(AbstractConsoleReporter, AbstractSerialReporter):
""" Simple BDD Style console reporter. """
def __init__(self, output_docstrings=False, use_color=True):
super(ConsoleReporter, self).__init__()
self.use_color = use_color
self.use_unicode = True
self.test_to... |
jmvrbanac/Specter | specter/util.py | get_real_last_traceback | python | def get_real_last_traceback(exception):
traceback_blocks = []
_n, _n, exc_traceback = sys.exc_info()
tb_list = get_all_tracebacks(exc_traceback)[1:]
# Remove already captured tracebacks
# TODO(jmv): This must be a better way of doing this. Need to revisit.
tb_list = [tb for tb in tb_list if tb ... | An unfortunate evil... All because Python's traceback cannot
determine where my executed code is coming from... | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/util.py#L155-L183 | [
"def get_numbered_source(lines, line_num, starting_line=0):\n try:\n center = (line_num - starting_line) - 1\n start = center - 2 if center - 2 > 0 else 0\n end = center + 2 if center + 2 <= len(lines) else len(lines)\n\n orig_src_lines = [line.rstrip('\\n') for line in lines[start:en... | import ast
import inspect
import re
import itertools
import sys
import six
from specter.vendor.ast_decompiler import decompile
try:
import __builtin__
except ImportError:
import builtins as __builtin__
CAPTURED_TRACEBACKS = []
class ExpectParams(object):
types_with_args = [
'equal',
'al... |
jmvrbanac/Specter | specter/vendor/ast_decompiler.py | decompile | python | def decompile(ast, indentation=4, line_length=100, starting_indentation=0):
decompiler = Decompiler(
indentation=indentation,
line_length=line_length,
starting_indentation=starting_indentation,
)
return decompiler.run(ast) | Decompiles an AST into Python code.
Arguments:
- ast: code to decompile, using AST objects as generated by the standard library ast module
- indentation: indentation level of lines
- line_length: if lines become longer than this length, ast_decompiler will try to break them up
(but it will not ne... | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/vendor/ast_decompiler.py#L94-L110 | [
"def run(self, ast):\n self.visit(ast)\n if self.current_line:\n self.lines.append(''.join(self.current_line))\n self.current_line = []\n return ''.join(self.lines)\n"
] | """
Vendored Project: AST Decompiler
Package: ast-decompiler
Version: 0.2
Author: Jelle Zijlstra
License: Apache v2
Project: https://github.com/JelleZijlstra/ast_decompiler
"""
import ast
from contextlib import contextmanager
import sys
try:
_basestring = basestring
_long = long
PY3 = False
except NameErr... |
jmvrbanac/Specter | specter/vendor/ast_decompiler.py | Decompiler.write_expression_list | python | def write_expression_list(self, nodes, separator=', ', allow_newlines=True, need_parens=True,
final_separator_if_multiline=True):
first = True
last_line = len(self.lines)
current_line = list(self.current_line)
for node in nodes:
if first:
... | Writes a list of nodes, separated by separator.
If allow_newlines, will write the expression over multiple lines if necessary to say within
max_line_length. If need_parens, will surround the expression with parentheses in this case.
If final_separator_if_multiline, will write a separator at the... | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/vendor/ast_decompiler.py#L164-L208 | [
"def visit(self, node):\n self.node_stack.append(node)\n try:\n return super(Decompiler, self).visit(node)\n finally:\n if self.node_stack:\n self.node_stack.pop()\n",
"def write(self, code):\n assert isinstance(code, _basestring), 'invalid code %r' % code\n self.current_li... | class Decompiler(ast.NodeVisitor):
def __init__(self, indentation, line_length, starting_indentation):
self.lines = []
self.current_line = []
self.current_indentation = starting_indentation
self.node_stack = []
self.indentation = indentation
self.max_line_length = lin... |
jmvrbanac/Specter | specter/expect.py | expect | python | def expect(obj, caller_args=[]):
line, module = get_module_and_line('__spec__')
src_params = ExpectParams(line, module)
expect_obj = ExpectAssert(
obj,
src_params=src_params,
caller_args=caller_args
)
_add_expect_to_wrapper(expect_obj)
return expect_obj | Primary method for test assertions in Specter
:param obj: The evaluated target object
:param caller_args: Is only used when using expecting a raised Exception | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/expect.py#L202-L217 | [
"def get_module_and_line(use_child_attr=None):\n last_frame = inspect.currentframe()\n\n steps = 2\n for i in range(steps):\n last_frame = last_frame.f_back\n\n self = module = last_frame.f_locals['self']\n # Use an attr instead of self\n if use_child_attr:\n module = getattr(self, u... | import functools
import inspect
# Making sure we support 2.7 and 3+
try:
from types import ClassType as ClassObjType
except ImportError:
from types import ModuleType as ClassObjType
from specter import _
from specter.spec import (CaseWrapper, FailedRequireException,
TestSkippedExcepti... |
jmvrbanac/Specter | specter/expect.py | require | python | def require(obj, caller_args=[]):
line, module = get_module_and_line('__spec__')
src_params = ExpectParams(line, module)
require_obj = RequireAssert(
obj,
src_params=src_params,
caller_args=caller_args
)
_add_expect_to_wrapper(require_obj)
return require_obj | Primary method for test assertions in Specter
:param obj: The evaluated target object
:param caller_args: Is only used when using expecting a raised Exception | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/expect.py#L220-L235 | [
"def get_module_and_line(use_child_attr=None):\n last_frame = inspect.currentframe()\n\n steps = 2\n for i in range(steps):\n last_frame = last_frame.f_back\n\n self = module = last_frame.f_locals['self']\n # Use an attr instead of self\n if use_child_attr:\n module = getattr(self, u... | import functools
import inspect
# Making sure we support 2.7 and 3+
try:
from types import ClassType as ClassObjType
except ImportError:
from types import ModuleType as ClassObjType
from specter import _
from specter.spec import (CaseWrapper, FailedRequireException,
TestSkippedExcepti... |
jmvrbanac/Specter | specter/expect.py | skip | python | def skip(reason):
def decorator(test_func):
if not isinstance(test_func, (type, ClassObjType)):
func_data = None
if test_func.__name__ == 'DECORATOR_ONCALL':
# Call down and save the results
func_data = test_func()
@functools.wraps(test_fu... | The skip decorator allows for you to always bypass a test.
:param reason: Expects a string | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/expect.py#L238-L259 | null | import functools
import inspect
# Making sure we support 2.7 and 3+
try:
from types import ClassType as ClassObjType
except ImportError:
from types import ModuleType as ClassObjType
from specter import _
from specter.spec import (CaseWrapper, FailedRequireException,
TestSkippedExcepti... |
jmvrbanac/Specter | specter/expect.py | skip_if | python | def skip_if(condition, reason=None):
if condition:
return skip(reason)
def wrapper(func):
return func
return wrapper | The skip_if decorator allows for you to bypass a test on conditions
:param condition: Expects a boolean
:param reason: Expects a string | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/expect.py#L262-L273 | [
"def skip(reason):\n \"\"\"The skip decorator allows for you to always bypass a test.\n\n :param reason: Expects a string\n \"\"\"\n def decorator(test_func):\n if not isinstance(test_func, (type, ClassObjType)):\n func_data = None\n if test_func.__name__ == 'DECORATOR_ONCAL... | import functools
import inspect
# Making sure we support 2.7 and 3+
try:
from types import ClassType as ClassObjType
except ImportError:
from types import ModuleType as ClassObjType
from specter import _
from specter.spec import (CaseWrapper, FailedRequireException,
TestSkippedExcepti... |
jmvrbanac/Specter | specter/expect.py | incomplete | python | def incomplete(test_func):
if not isinstance(test_func, (type, ClassObjType)):
@functools.wraps(test_func)
def skip_wrapper(*args, **kwargs):
raise TestIncompleteException(test_func, _('Test is incomplete'))
return skip_wrapper | The incomplete decorator behaves much like a normal skip; however,
tests that are marked as incomplete get tracked under a different metric.
This allows for you to create a skeleton around all of your features and
specifications, and track what tests have been written and what
tests are left outstanding... | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/expect.py#L276-L294 | null | import functools
import inspect
# Making sure we support 2.7 and 3+
try:
from types import ClassType as ClassObjType
except ImportError:
from types import ModuleType as ClassObjType
from specter import _
from specter.spec import (CaseWrapper, FailedRequireException,
TestSkippedExcepti... |
jmvrbanac/Specter | specter/expect.py | metadata | python | def metadata(**key_value_pairs):
def onTestFunc(func):
def DECORATOR_ONCALL(*args, **kwargs):
return (func, key_value_pairs)
return DECORATOR_ONCALL
return onTestFunc | The metadata decorator allows for you to tag specific tests with
key/value data for run-time processing or reporting. The common use case
is to use metadata to tag a test as a positive or negative test type.
.. code-block:: python
# Example of using the metadata decorator
@metadata(type='n... | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/expect.py#L297-L313 | null | import functools
import inspect
# Making sure we support 2.7 and 3+
try:
from types import ClassType as ClassObjType
except ImportError:
from types import ModuleType as ClassObjType
from specter import _
from specter.spec import (CaseWrapper, FailedRequireException,
TestSkippedExcepti... |
jmvrbanac/Specter | specter/expect.py | ExpectAssert.serialize | python | def serialize(self):
converted_dict = {
'success': self.success,
'assertion': str(self),
'required': self.required
}
return converted_dict | Serializes the ExpectAssert object for collection.
Warning, this will only grab the available information.
It is strongly that you only call this once all specs and
tests have completed. | train | https://github.com/jmvrbanac/Specter/blob/1f5a729b0aa16242add8c1c754efa268335e3944/specter/expect.py#L41-L53 | null | class ExpectAssert(object):
def __init__(self, target, required=False, src_params=None,
caller_args=[]):
super(ExpectAssert, self).__init__()
self.prefix = _('expect')
self.target = target
self.src_params = src_params
self.actions = [target]
self.suc... |
beregond/super_state_machine | super_state_machine/utils.py | is_ | python | def is_(self, state):
translator = self._meta['translator']
state = translator.translate(state)
return self.actual_state == state | Check if machine is in given state. | train | https://github.com/beregond/super_state_machine/blob/31ad527f4e6b7a01e315ce865735ca18957c223e/super_state_machine/utils.py#L9-L13 | null | """Utilities for core."""
from enum import Enum, unique
from functools import wraps
from .errors import TransitionError
def can_be_(self, state):
"""Check if machine can transit to given state."""
translator = self._meta['translator']
state = translator.translate(state)
if self._meta['complete']:
... |
beregond/super_state_machine | super_state_machine/utils.py | can_be_ | python | def can_be_(self, state):
translator = self._meta['translator']
state = translator.translate(state)
if self._meta['complete']:
return True
if self.actual_state is None:
return True
transitions = self._meta['transitions'][self.actual_state]
return state in transitions | Check if machine can transit to given state. | train | https://github.com/beregond/super_state_machine/blob/31ad527f4e6b7a01e315ce865735ca18957c223e/super_state_machine/utils.py#L16-L28 | null | """Utilities for core."""
from enum import Enum, unique
from functools import wraps
from .errors import TransitionError
def is_(self, state):
"""Check if machine is in given state."""
translator = self._meta['translator']
state = translator.translate(state)
return self.actual_state == state
def f... |
beregond/super_state_machine | super_state_machine/utils.py | force_set | python | def force_set(self, state):
translator = self._meta['translator']
state = translator.translate(state)
attr = self._meta['state_attribute_name']
setattr(self, attr, state) | Set new state without checking if transition is allowed. | train | https://github.com/beregond/super_state_machine/blob/31ad527f4e6b7a01e315ce865735ca18957c223e/super_state_machine/utils.py#L31-L36 | null | """Utilities for core."""
from enum import Enum, unique
from functools import wraps
from .errors import TransitionError
def is_(self, state):
"""Check if machine is in given state."""
translator = self._meta['translator']
state = translator.translate(state)
return self.actual_state == state
def ca... |
beregond/super_state_machine | super_state_machine/utils.py | set_ | python | def set_(self, state):
if not self.can_be_(state):
state = self._meta['translator'].translate(state)
raise TransitionError(
"Cannot transit from '{actual_value}' to '{value}'."
.format(actual_value=self.actual_state.value, value=state.value)
)
self.force_set(stat... | Set new state for machine. | train | https://github.com/beregond/super_state_machine/blob/31ad527f4e6b7a01e315ce865735ca18957c223e/super_state_machine/utils.py#L39-L48 | null | """Utilities for core."""
from enum import Enum, unique
from functools import wraps
from .errors import TransitionError
def is_(self, state):
"""Check if machine is in given state."""
translator = self._meta['translator']
state = translator.translate(state)
return self.actual_state == state
def ca... |
beregond/super_state_machine | super_state_machine/utils.py | generate_getter | python | def generate_getter(value):
@property
@wraps(is_)
def getter(self):
return self.is_(value)
return getter | Generate getter for given value. | train | https://github.com/beregond/super_state_machine/blob/31ad527f4e6b7a01e315ce865735ca18957c223e/super_state_machine/utils.py#L64-L71 | null | """Utilities for core."""
from enum import Enum, unique
from functools import wraps
from .errors import TransitionError
def is_(self, state):
"""Check if machine is in given state."""
translator = self._meta['translator']
state = translator.translate(state)
return self.actual_state == state
def ca... |
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