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glumpy/glumpy
glumpy/ext/freetype/ft_structs.py
5
35670
#!/usr/bin/env python # -*- coding: utf-8 -*- # ----------------------------------------------------------------------------- # # FreeType high-level python API - Copyright 2011 Nicolas P. Rougier # Distributed under the terms of the new BSD license. # # ---------------------------------------------------------------...
bsd-3-clause
141fde8f26685250a6a27a583865d27b
36.786017
81
0.597869
4.240875
false
false
false
false
glumpy/glumpy
glumpy/geometry/colored_cube.py
3
2467
# ----------------------------------------------------------------------------- # Copyright (c) 2009-2016 Nicolas P. Rougier. All rights reserved. # Distributed under the (new) BSD License. # ----------------------------------------------------------------------------- import numpy as np from glumpy import gloo def c...
bsd-3-clause
6c781461fc6aef49255e108b0de3bcae
31.460526
79
0.38711
2.88538
false
false
false
false
glumpy/glumpy
glumpy/transforms/conic_equal_area.py
3
3901
# ----------------------------------------------------------------------------- # Copyright (c) 2009-2016 Nicolas P. Rougier. All rights reserved. # Distributed under the (new) BSD License. # ----------------------------------------------------------------------------- """ Conic Equal Area projection See: https://gith...
bsd-3-clause
ed2648cffdf10174e7f667c5a1fc85d1
27.268116
79
0.555755
4.203664
false
false
false
false
ihmeuw/vivarium
src/vivarium/framework/artifact/hdf.py
1
13279
""" ============= HDF Interface ============= A convenience wrapper around the `tables <https://www.pytables.org>`_ and :mod:`pandas` HDF interfaces. Public Interface ---------------- The public interface consists of 5 functions: .. list-table:: HDF Public Interface :widths: 20 60 :header-rows: 1 * - Func...
bsd-3-clause
b856d25f5197f4db4cce580e72657dea
29.738426
106
0.59756
3.998494
false
false
false
false
ihmeuw/vivarium
src/vivarium/interface/interactive.py
1
7890
""" ========================== Vivarium Interactive Tools ========================== This module provides an interface for interactive simulation usage. The main part is the :class:`InteractiveContext`, a sub-class of the main simulation object in ``vivarium`` that has been extended to include convenience methods for ...
bsd-3-clause
79ed10e63280f5b7f278809d13604a0e
32.151261
94
0.6
4.555427
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false
false
false
ihmeuw/vivarium
tests/config_tree/test_basic_functionality.py
1
15651
import textwrap import pytest import yaml from vivarium.config_tree import ( ConfigNode, ConfigTree, ConfigurationError, ConfigurationKeyError, DuplicatedConfigurationError, ) @pytest.fixture(params=list(range(1, 5))) def layers(request): return [f"layer_{i}" for i in range(1, request.param ...
bsd-3-clause
e3227d32945fb58b4a4a0f8726fb4afa
30.682186
91
0.609226
3.205858
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true
false
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scrapy/scrapy
tests/test_linkextractors.py
1
25760
import pickle import re import unittest from scrapy.http import HtmlResponse, XmlResponse from scrapy.link import Link from scrapy.linkextractors.lxmlhtml import LxmlLinkExtractor from tests import get_testdata # a hack to skip base class tests in pytest class Base: class LinkExtractorTestCase(unittest.TestCase)...
bsd-3-clause
7029e08f794644e7e3eb63bb250ce366
48.922481
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scrapy/scrapy
scrapy/commands/__init__.py
1
6713
""" Base class for Scrapy commands """ import os import argparse from pathlib import Path from typing import Any, Dict, Optional from twisted.python import failure from scrapy.crawler import CrawlerProcess from scrapy.utils.conf import arglist_to_dict, feed_process_params_from_cli from scrapy.exceptions import UsageE...
bsd-3-clause
02762e61f690d8719f1924bdb4814c5b
39.197605
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scrapy/scrapy
tests/test_utils_signal.py
3
3511
import asyncio from pydispatch import dispatcher from pytest import mark from testfixtures import LogCapture from twisted.internet import defer, reactor from twisted.python.failure import Failure from twisted.trial import unittest from scrapy.utils.signal import send_catch_log, send_catch_log_deferred from scrapy.uti...
bsd-3-clause
586a3c988885ccc2a84e4099af4c3e01
31.211009
78
0.670179
3.837158
false
true
false
false
scrapy/scrapy
scrapy/commands/parse.py
2
10567
import json import logging from typing import Dict from itemadapter import is_item, ItemAdapter from w3lib.url import is_url from twisted.internet.defer import maybeDeferred from scrapy.commands import BaseRunSpiderCommand from scrapy.http import Request from scrapy.utils import display from scrapy.utils.spider impo...
bsd-3-clause
a697ed1dfb2b15d5e024dd2fb85af071
38.137037
117
0.559478
4.27987
false
false
false
false
scrapy/scrapy
scrapy/utils/spider.py
3
2195
import inspect import logging from scrapy.spiders import Spider from scrapy.utils.defer import deferred_from_coro from scrapy.utils.misc import arg_to_iter logger = logging.getLogger(__name__) def iterate_spider_output(result): if inspect.isasyncgen(result): return result elif inspect.iscoroutine(r...
bsd-3-clause
40d2b355788c655eb721399e91790d02
30.811594
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0.651025
4.012797
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false
false
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scrapy/scrapy
scrapy/cmdline.py
2
5706
import sys import os import argparse import cProfile import inspect import pkg_resources import scrapy from scrapy.crawler import CrawlerProcess from scrapy.commands import ScrapyCommand, ScrapyHelpFormatter, BaseRunSpiderCommand from scrapy.exceptions import UsageError from scrapy.utils.misc import walk_modules from ...
bsd-3-clause
3526f97882507aa994f433a6ff393d31
30.180328
97
0.627234
3.763852
false
false
false
false
scrapy/scrapy
scrapy/utils/request.py
1
13713
""" This module provides some useful functions for working with scrapy.http.Request objects """ import hashlib import json import warnings from typing import Dict, Iterable, List, Optional, Tuple, Union from urllib.parse import urlunparse from weakref import WeakKeyDictionary from w3lib.http import basic_auth_header ...
bsd-3-clause
61b5de7a231db9cd8a42780f3225d6af
40.807927
112
0.651426
4.310909
false
false
false
false
moraes/tipfy
tipfy/utils.py
9
4320
#!/usr/bin/env python # # Copyright 2009 Facebook # # Licensed under the Apache License, Version 2.0 (the "License"); you may # not use this file except in compliance with the License. You may obtain # a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or a...
bsd-3-clause
46e7ec1021452299f8a6643d70a6a1eb
26
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false
false
moraes/tipfy
tipfy/appengine/acl.py
9
11435
# -*- coding: utf-8 -*- """ tipfy.appengine.acl ~~~~~~~~~~~~~~~~~~~ Simple Access Control List This module provides utilities to manage permissions for anything that requires some level of restriction, such as datastore models or handlers. Access permissions can be grouped into roles for convenience, so that a...
bsd-3-clause
352701344724e868eaa9fac037f0ca88
27.516209
76
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3.290647
false
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false
false
moraes/tipfy
tipfy/appengine/blobstore.py
9
12717
# -*- coding: utf-8 -*- """ tipfy.appengine.blobstore ~~~~~~~~~~~~~~~~~~~~~~~~~ Handler library for Blobstore API. Contains handler mixins to help with uploading and downloading blobs. BlobstoreDownloadMixin: Has helper method for easily sending blobs to client. BlobstoreUploadMixin: mix...
bsd-3-clause
a788edd8ed971f34b0f6f095a410dd21
32.55409
80
0.595659
4.334356
false
false
false
false
moraes/tipfy
tipfy/auth/twitter.py
9
7220
# -*- coding: utf-8 -*- """ tipfy.auth.twitter ~~~~~~~~~~~~~~~~~~ Implementation of Twitter authentication scheme. Ported from `tornado.auth`_. :copyright: 2009 Facebook. :copyright: 2011 tipfy.org. :license: Apache License Version 2.0, see LICENSE.txt for more details. """ from __future_...
bsd-3-clause
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36.025641
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pika/pika
tests/acceptance/async_adapter_tests.py
1
44865
# too-many-lines # pylint: disable=C0302 # Suppress pylint messages concerning missing class and method docstrings # pylint: disable=C0111 # Suppress pylint warning about attribute defined outside __init__ # pylint: disable=W0201 # Suppress pylint warning about access to protected member # pylint: disable=W0212 # ...
bsd-3-clause
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pika/pika
tests/unit/diagnostic_utils_test.py
2
2715
""" Test of `pika.diagnostic_utils` """ import unittest import logging import pika.compat from pika import diagnostic_utils # Suppress invalid-name, since our test names are descriptive and quite long # pylint: disable=C0103 # Suppress missing-docstring to allow test method names to be printed by our # test runne...
bsd-3-clause
b262f56288382aec158a71abffbbd663
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pika/pika
examples/consumer_simple.py
1
1745
# -*- coding: utf-8 -*- # pylint: disable=C0111,C0103,R0205 import json import logging import pika from pika.exchange_type import ExchangeType print('pika version: %s' % pika.__version__) connection = pika.BlockingConnection( pika.ConnectionParameters(host='localhost')) main_channel = connection.channel() consu...
bsd-3-clause
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pika/pika
pika/adapters/select_connection.py
1
45096
"""A connection adapter that tries to use the best polling method for the platform pika is running on. """ import abc import collections import errno import heapq import logging import select import time import threading import pika.compat from pika.adapters.utils import nbio_interface from pika.adapters.base_connec...
bsd-3-clause
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pika/pika
pika/heartbeat.py
1
8167
"""Handle AMQP Heartbeats""" import logging import pika.exceptions from pika import frame LOGGER = logging.getLogger(__name__) class HeartbeatChecker: """Sends heartbeats to the broker. The provided timeout is used to determine if the connection is stale - no received heartbeats or other activity will c...
bsd-3-clause
d3b6e6badde4571ec0afdd890d0e44b1
38.076555
172
0.639525
4.348775
false
false
false
false
pika/pika
examples/direct_reply_to.py
1
2394
# -*- coding: utf-8 -*- # pylint: disable=C0111,C0103,R0205 """ This example demonstrates RabbitMQ's "Direct reply-to" usage via `pika.BlockingConnection`. See https://www.rabbitmq.com/direct-reply-to.html for more info about this feature. """ import pika SERVER_QUEUE = 'rpc.server.queue' def main(): """ Here,...
bsd-3-clause
8b910da7182b4ff231d5632caabd3cdd
29.303797
82
0.651629
3.855072
false
false
false
false
djc/couchdb-python
couchdb/tests/couchhttp.py
1
3677
# -*- coding: utf-8 -*- # # Copyright (C) 2009 Christopher Lenz # All rights reserved. # # This software is licensed as described in the file COPYING, which # you should have received as part of this distribution. import socket import time import unittest from couchdb import http, util from couchdb.tests import testu...
bsd-3-clause
fdfb03f1b4bc78515d46790d7532c357
33.688679
141
0.608376
3.802482
false
true
false
false
django/channels
tests/security/test_auth.py
3
7021
from importlib import import_module from unittest import mock import pytest from asgiref.sync import sync_to_async from django.conf import settings from django.contrib.auth import ( BACKEND_SESSION_KEY, HASH_SESSION_KEY, SESSION_KEY, get_user_model, user_logged_in, user_logged_out, ) from djang...
bsd-3-clause
16b7975007c96954736a2310a77f0dcd
26.861111
86
0.681242
3.915784
false
true
false
false
jjhelmus/nmrglue
tests/test_spinsolve.py
2
1779
""" Tests for the fileio.spinsolve submodule """ import nmrglue as ng from pathlib import Path from setup import DATA_DIR def test_acqu(): """ read nmr_fid.dx """ dic, data = ng.spinsolve.read(Path(DATA_DIR) / "spinsolve" / "ethanol", "nmr_fid.dx") assert dic["acqu"]["Sample"] == "EtOH" assert dic[...
bsd-3-clause
1db00bb5a30cea72a3d27802eb5a0c9d
30.210526
89
0.600337
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false
jjhelmus/nmrglue
nmrglue/fileio/rnmrtk.py
2
22364
""" Functions for reading and writing Rowland NMR Toolkit (RNMRTK) files """ from __future__ import division __developer_info__ = """ Information of the Rowland NMR Toolkit file format ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ """ import numpy as np from warnings import warn from . import fileiobase ####...
bsd-3-clause
dceda070939f1cfcfb4be35fc2c0fab4
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jjhelmus/nmrglue
tests/test_simpson.py
4
5071
import nmrglue.fileio.simpson as simpson import numpy as np from numpy.testing import assert_allclose, assert_raises import os.path from setup import DATA_DIR DD_1D = os.path.join(DATA_DIR, 'simpson_1d') DD_2D = os.path.join(DATA_DIR, 'simpson_2d') def test_1d_time(): """ reading 1D time domain files """ #...
bsd-3-clause
225388e3f6608dd53f71b9604a1a61ef
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jjhelmus/nmrglue
nmrglue/analysis/analysisbase.py
2
10485
""" analysisbase provides general purpose analysis functions and classes used by several nmrglue.analysis modules """ import numpy as np pi = np.pi # helper functions def neighbors(pt, shape, structure): """ Generate a list of all neighbors to a point. Parameters ---------- pt : tuple of ints ...
bsd-3-clause
d61f09a2111e8bce15066a64de32bcc4
26.093023
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false
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jjhelmus/nmrglue
nmrglue/analysis/linesh.py
2
26044
""" Functions for fitting and simulating arbitrary dimensional lineshapes commonly found in NMR experiments """ from __future__ import print_function import numpy as np from .leastsqbound import leastsqbound from .analysisbase import squish from .lineshapes1d import ls_str2class from ..fileio import table pi = np.p...
bsd-3-clause
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jobovy/galpy
galpy/snapshot/nemo_util.py
1
1972
############################################################################### # nemo_util.py: some utilities for handling NEMO snapshots ############################################################################### import os import subprocess import tempfile import numpy def read(filename,ext=None,swapyz=False):...
bsd-3-clause
6974d077aaf2a1ab9d563f2d4a3e5521
33
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false
false
jobovy/galpy
doc/source/examples/sellwood-jrjp.py
1
4179
import csv import os import os.path import re import sys import cPickle as pickle import numpy as nu from galpy.orbit import Orbit from galpy.potential import LogarithmicHaloPotential, PowerSphericalPotential from galpy.util import plot _degtorad= nu.pi/180. def hms_to_rad(ra): spl= re.split(r' ',ra) return ...
bsd-3-clause
b663729614e7053cf4962f0aa682af27
30.186567
84
0.520699
3.070536
false
false
false
false
jobovy/galpy
galpy/potential/SCFPotential.py
1
40308
import hashlib import numpy from numpy.polynomial.legendre import leggauss from scipy import integrate from scipy.special import gamma, gammaln, lpmn from ..util import conversion, coords from ..util._optional_deps import _APY_LOADED from .Potential import Potential if _APY_LOADED: from astropy import units fro...
bsd-3-clause
2ee7934fa3b4a316640eae3511560519
33.304681
372
0.549916
3.19246
false
false
false
false
jobovy/galpy
tests/test_SpiralArmsPotential.py
1
60567
import numpy from packaging.version import parse as parse_version _NUMPY_VERSION= parse_version(numpy.__version__) _NUMPY_1_23= (_NUMPY_VERSION > parse_version('1.22'))\ *(_NUMPY_VERSION < parse_version('1.24')) # For testing 1.23 precision issues import unittest from numpy.testing import assert_allclose from sci...
bsd-3-clause
a4837d10e8d984b24c1f0731f2042263
77.353169
141
0.559909
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false
true
false
false
jobovy/galpy
galpy/potential/Irrgang13.py
1
3211
# Milky-Way mass models from Irrgang et al. (2013) import numpy from ..potential import (MiyamotoNagaiPotential, NFWPotential, PlummerPotential, SCFPotential, scf_compute_coeffs_spherical) from ..util import conversion # Their mass unit mgal_in_msun= 1e5/conversion._G...
bsd-3-clause
4d6c2c2e8ad1446edcc7169c25371b39
41.25
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false
false
false
pyecore/pyecore
pyecore/ordered_set_patch.py
1
2846
import ordered_set from typing import Iterable SLICE_ALL = ordered_set.SLICE_ALL # monkey patching the OrderedSet implementation def insert(self, index, key): """Adds an element at a dedicated position in an OrderedSet. This implementation is meant for the OrderedSet from the ordered_set package only. ...
bsd-3-clause
8c312f36dc6427c636833f92476239ce
27.46
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false
false
false
false
pyecore/pyecore
tests/test_derived.py
2
1494
import pytest from pyecore.ecore import * def test_default_derived_collection(): collection = EDerivedCollection.create(None, None) with pytest.raises(AttributeError): len(collection) with pytest.raises(AttributeError): collection[0] with pytest.raises(AttributeError): collec...
bsd-3-clause
c4253383e52a5907c68fdf38a884793a
24.322034
71
0.630522
3.6
false
true
false
false
pyecore/pyecore
pyecore/commands.py
1
10554
""" This module introduce the command system which allows to defined various that can be executed onto a commands stack. Each command can also be 'undo' and 'redo'. """ from abc import ABCMeta, abstractmethod from collections import UserList from .ecore import EObject, BadValueError from .resources import ResourceSet ...
bsd-3-clause
09d61ecd48aed2638728dee1860e9aaf
28.154696
79
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false
false
false
lmcinnes/umap
umap/parametric_umap.py
1
39979
import numpy as np from umap import UMAP from warnings import warn, catch_warnings, filterwarnings from numba import TypingError import os from umap.spectral import spectral_layout from sklearn.utils import check_random_state import codecs, pickle from sklearn.neighbors import KDTree import sys try: import tensor...
bsd-3-clause
f0362b8fa23c96703b938f4355b151ec
33.554019
114
0.599165
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false
false
false
lmcinnes/umap
umap/tests/test_umap_nn.py
1
5348
import numpy as np import pytest from numpy.testing import assert_array_almost_equal from sklearn.neighbors import KDTree from sklearn.preprocessing import normalize from umap import distances as dist from umap.umap_ import ( nearest_neighbors, smooth_knn_dist, ) # ===========================================...
bsd-3-clause
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86
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false
true
false
false
lmcinnes/umap
umap/tests/test_composite_models.py
1
3681
from umap import UMAP import pytest try: # works for sklearn>=0.22 from sklearn.manifold import trustworthiness except ImportError: # this is to comply with requirements (scikit-learn>=0.20) # More recent versions of sklearn have exposed trustworthiness # in top level module API # see: https://...
bsd-3-clause
814e68f001cc5d9ce04b955023e159a9
30.461538
88
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false
lmcinnes/umap
umap/utils.py
1
6662
# Author: Leland McInnes <leland.mcinnes@gmail.com> # # License: BSD 3 clause import time from warnings import warn import numpy as np import numba from sklearn.utils.validation import check_is_fitted import scipy.sparse @numba.njit(parallel=True) def fast_knn_indices(X, n_neighbors): """A fast computation of k...
bsd-3-clause
2a0639b2de18bb39f13025c044bc11ae
29.281818
117
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false
false
false
false
machinalis/iepy
iepy/webui/corpus/admin.py
2
3787
from django.contrib import admin from django.core import urlresolvers from django.db.models import Q from relatedwidget import RelatedWidgetWrapperBase from corpus.models import ( IEDocument, IEDocumentMetadata, Entity, EntityKind, Relation, EntityOccurrence, GazetteItem ) admin.site.site_header = 'IEPY admi...
bsd-3-clause
c16b3c29703fc2fdf57cb30320165117
33.743119
89
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3.723697
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false
false
false
machinalis/iepy
tests/test_relations.py
2
18064
from unittest import mock from iepy.data.models import EvidenceLabel from .factories import ( RelationFactory, EntityFactory, EntityKindFactory, TextSegmentFactory, EntityOccurrenceFactory, IEDocFactory, ) from .manager_case import ManagerTestCase class TestRelations(ManagerTestCase): def test_cant_...
bsd-3-clause
649915c17297402510d045b076710ed6
46.915119
98
0.654728
3.3923
false
true
false
false
machinalis/iepy
iepy/webui/corpus/migrations/0011_data_migration_moving_relation_from_candiates_to_labels.py
2
2630
# -*- coding: utf-8 -*- from __future__ import unicode_literals import logging from django.db import models, migrations logging.basicConfig(format="%(asctime)-15s %(message)s") logger = logging.getLogger(__file__) logger.setLevel(logging.INFO) def get_key(evidence): return ( evidence.left_entity_occurr...
bsd-3-clause
6152d92bb4a27e9777f939d67ca68961
35.027397
88
0.651711
3.587995
false
false
false
false
machinalis/iepy
iepy/preprocess/corenlp.py
1
8725
import subprocess import xmltodict import os import sys import logging import stat from functools import lru_cache import iepy from iepy.utils import DIRS, unzip_from_url logger = logging.getLogger(__name__) def detect_java_version(): java_cmd = os.getenv('JAVAHOME') if not java_cmd: print('Environ...
bsd-3-clause
0d5eb377392ede30dc4c62f977b30d40
38.659091
94
0.597479
3.41621
false
false
false
false
machinalis/iepy
iepy/__init__.py
2
3647
import os import sys from importlib import import_module import django from django.conf import settings # Version number reading ... fname = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'version.txt') with open(fname, encoding='utf-8') as filehandler: __version__ = filehandler.read().strip().replace(...
bsd-3-clause
229c070f99df3baee2a7f331ca3f1252
36.214286
101
0.618042
4.125566
false
false
false
false
machinalis/iepy
setup.py
1
3267
from setuptools import setup, find_packages # Always prefer setuptools over distutils from os import path import sys assert sys.version_info >= (3, 4, 0), "Python 3.4 or newer is required" HERE = path.abspath(path.dirname(__file__)) # Get the long description from the relevant file with open(path.join(HERE, 'READM...
bsd-3-clause
b64164c78822b1e7f9da6a72175a0ddb
30.699029
98
0.662787
3.583974
false
false
false
false
machinalis/iepy
iepy/metrics.py
2
1212
# -*- coding: utf-8 -*- import time def result_dict_from_predictions(evidences, real_labels, predictions): correct = [] incorrect = [] tp, fp, tn, fn = 0.0, 0.0, 0.0, 0.0 for evidence, real, predicted in zip(evidences, real_labels, predictions): if real == predicted: correct.appen...
bsd-3-clause
3a62a7fa2ad3c0298836d8a4bc582c68
24.25
78
0.491749
3.775701
false
false
false
false
machinalis/iepy
iepy/webui/corpus/migrations/0003_auto_20140922_1547.py
2
1063
# -*- coding: utf-8 -*- from __future__ import unicode_literals from django.db import models, migrations class Migration(migrations.Migration): dependencies = [ ('corpus', '0002_auto_20140918_1733'), ] operations = [ migrations.AlterModelOptions( name='labeledrelationevidenc...
bsd-3-clause
31a170afae3b9c16f4e8519748a6226a
38.37037
277
0.614299
4.072797
false
false
false
false
biolink/ontobio
bin/materialize.py
1
6455
import click import json import os import yaml import requests import gzip import urllib import shutil import re import glob import logging import copy import yamldown from functools import wraps # from ontobio.util.user_agent import get_user_agent from ontobio.ontol_factory import OntologyFactory from ontobio impor...
bsd-3-clause
90264a496bd3b81a07db2fcb892e2d2e
33.704301
139
0.669404
3.476037
false
false
false
false
biolink/ontobio
ontobio/bin/phenolog.py
1
4423
#!/usr/bin/env python """ Command line wrapper to obographs library. Example: (venv) ~/repos/biolink-api(master) $ python obographs/bin/phenolog.py -vvv -r obo:mp -R go 'abnormal cardiovascular system physiology' With background: python obographs/bin/phenolog.py -b 'nervous system phenotype' -v -r cache/ontologies/m...
bsd-3-clause
afcc4ca6646d5e7c96809286cd9238b4
36.168067
141
0.570653
3.883231
false
false
false
false
biolink/ontobio
tests/test_phenosim_engine.py
1
5390
from ontobio.sim.phenosim_engine import PhenoSimEngine from ontobio.sim.api.owlsim2 import OwlSim2Api from ontobio.vocabulary.similarity import SimAlgorithm from ontobio.model.similarity import IcStatistic from unittest.mock import patch import os import json MONDO_0008199 = ['HP:0000751', 'HP:0000738', 'HP:0000726'...
bsd-3-clause
b11d261d5555f15d70f329b7d0d580ec
35.174497
93
0.598145
3.424396
false
false
false
false
biolink/ontobio
ontobio/slimmer.py
1
2961
import networkx as nx import logging logger = logging.getLogger(__name__) def get_minimal_subgraph(g, nodes): """ given a set of nodes, extract a subgraph that excludes non-informative nodes - i.e. those that are not MRCAs of pairs of existing nodes. Note: no property chain reasoning is performe...
bsd-3-clause
9f4b36c01d61aedda6989c62e0753828
29.214286
87
0.515366
3.5
false
false
false
false
biolink/ontobio
ontobio/model/bbop_graph.py
1
3211
""" BBOP Graph class created in the original biolink-api before ontobio was stripped out, it is still used in the scigraph-util TODO Merge this with OBOGraph """ from typing import Dict class BBOPGraph: """ BBOPGraph Graph object model https://github.com/berkeleybop/bbop-graph """ nodemap = {} ...
bsd-3-clause
ac889d75fafeb15ccb4ab41332a38bf7
23.891473
69
0.515416
3.712139
false
false
false
false
biolink/ontobio
ontobio/sparql/sparql_ontology.py
1
8756
""" Classes for representing ontologies backed by a SPARQL endpoint ``` Ontology RemoteSparqlOntology EagerRemoteSparqlOntology LazyRemoteSparqlOntology ``` """ import networkx as nx import logging import ontobio.ontol from ontobio.ontol import Ontology, Synonym, TextDefinition from ontobio.sparql.sparql_o...
bsd-3-clause
9439ce84c046efff2908f7edfb7943d5
32.80695
177
0.565555
3.759553
false
false
false
false
biolink/ontobio
ontobio/golr/golr_query.py
1
68763
""" A query wrapper for a Golr instance Intended to work with: * Monarch golr instance * AmiGO/GO golr instance (including both GO and Planteome) Conventions ----------- Documents follow either entity or association patterns. Associations ------------ Connects some kind of *subject* to an *object* via a *relation...
bsd-3-clause
c092aee93625f6104c3356d5de4e7c0d
34.907572
163
0.557393
3.906545
false
false
false
false
biolink/ontobio
ontobio/sparql/skos.py
1
4073
import logging import requests import rdflib from rdflib import Namespace from rdflib.namespace import RDF from rdflib.namespace import SKOS from prefixcommons.curie_util import contract_uri from ontobio.ontol import Ontology, Synonym # TODO: make configurable GEMET = Namespace('http://www.eionet.europa.eu/gemet/200...
bsd-3-clause
37d26e9a3b64dfc6a5787c9cac244c18
32.113821
86
0.544071
3.860664
false
false
false
false
biolink/ontobio
ontobio/util/go_utils.py
1
2826
from ontobio.ontol_factory import OntologyFactory class GoAspector: def __init__(self, go_ontology): if go_ontology: self.ontology = go_ontology else: self.ontology = OntologyFactory().create("go") def get_ancestors_through_subont(self, go_term, relations): """...
bsd-3-clause
37599b01a06cba87d57140b75c5f4a55
33.888889
120
0.591649
3.897931
false
false
false
false
shadow-robot/sr_common
sr_description/test/test_compatibility.py
1
8589
#!/usr/bin/env python # -*- coding: utf-8 -*- ###################################################################### # Software License Agreement (BSD License) # # Copyright (c) 2021, Bielefeld University # All rights reserved. # # Redistribution and use in source and binary forms, with or without # modification, ...
bsd-3-clause
28534e391de1c68de6a893dad78788a4
37.004425
108
0.608453
3.898774
false
false
false
false
encode/uvicorn
tools/cli_usage.py
1
1998
""" Look for a marker comment in docs pages, and place the output of `$ uvicorn --help` there. Pass `--check` to ensure the content is in sync. """ import argparse import subprocess import sys import typing from pathlib import Path def _get_usage_lines() -> typing.List[str]: res = subprocess.run(["uvicorn", "--he...
bsd-3-clause
dd0d4aeffed28d3fb7ffc96f3cbdd040
27.542857
85
0.587588
3.438898
false
false
false
false
encode/uvicorn
uvicorn/protocols/websockets/websockets_impl.py
1
13536
import asyncio import http import logging import sys from typing import TYPE_CHECKING, Any, List, Optional, Sequence, Tuple, Union, cast from urllib.parse import unquote import websockets from websockets.datastructures import Headers from websockets.exceptions import ConnectionClosed from websockets.extensions.permess...
bsd-3-clause
05a37a7c16dc54cf14a7ccba204db46c
35.882834
87
0.583629
4.263307
false
false
false
false
encode/uvicorn
uvicorn/protocols/http/h11_impl.py
1
20152
import asyncio import http import logging import sys from typing import TYPE_CHECKING, Callable, List, Optional, Tuple, Union, cast from urllib.parse import unquote import h11 from uvicorn.config import Config from uvicorn.logging import TRACE_LOG_LEVEL from uvicorn.protocols.http.flow_control import ( CLOSE_HEAD...
bsd-3-clause
deb929d8382be1c8851a7e35ff225e59
34.985714
169
0.560639
4.217664
false
false
false
false
encode/uvicorn
uvicorn/supervisors/watchgodreload.py
1
5491
import logging import warnings from pathlib import Path from socket import socket from typing import TYPE_CHECKING, Callable, Dict, List, Optional from watchgod import DefaultWatcher from uvicorn.config import Config from uvicorn.supervisors.basereload import BaseReload if TYPE_CHECKING: import os DirEntry ...
bsd-3-clause
cf78c8df3ec4b1a5d6518c10216fec60
33.753165
84
0.562193
4.263199
false
true
false
false
quantmind/lux
lux/ext/content/contents.py
1
7180
import os import stat from datetime import datetime, date from collections import Mapping from itertools import chain from dateutil.parser import parse as parse_date from pulsar.api import Unsupported from pulsar.utils.slugify import slugify from pulsar.utils.structures import mapping_iterator from lux.utils.date im...
bsd-3-clause
8a4a5ddbe939150ddba090cd36c33290
28.792531
78
0.597493
3.936404
false
false
false
false
quantmind/lux
lux/ext/sessions/browser.py
1
5814
"""Backends for Browser based Authentication """ import time from functools import wraps from pulsar.api import ( Http401, PermissionDenied, Http404, HttpRedirect, BadRequest ) from pulsar.apps.wsgi import Route from lux.utils.date import to_timestamp, date_from_now, iso8601 from lux.utils.context import app_attr...
bsd-3-clause
544f76583adc5dfafb183e777b3796d2
32.222857
74
0.602511
4.284451
false
false
false
false
quantmind/lux
tests/web/test_signup.py
1
5683
from tests import web class AuthTest(web.WebsiteTest): def _get_code(self, message): url = '/reset-password/' idx = message.find(url) self.assertTrue(idx) msg = message[idx+len(url):] idx = msg.find(' ') return msg[:idx] async def test_html_signup(self): ...
bsd-3-clause
fe370a5af9a01050420d1409d9a621d0
40.181159
72
0.554989
4.175606
false
true
false
false
quantmind/lux
lux/ext/smtp/log.py
1
3013
import logging import json from inspect import isawaitable from pulsar.api import ensure_future MESSAGE = 'Exception while posting message to Slack' def context_text_formatter(context): res = "" maxlen = max([len(key) for key in context]) for key, val in context.items(): space = " " * (maxlen -...
bsd-3-clause
ed0695a4573aa7d33a566e1e44b9d31f
31.75
77
0.557252
3.892765
false
false
false
false
quantmind/lux
tests/sockjs/test_rest.py
1
10210
import json import asyncio from lux.utils import test from lux.utils.crypt import create_uuid class TestSockJSRestApp(test.AppTestCase): config_file = 'tests.sockjs' @classmethod async def beforeAll(cls): cls.super_token, cls.pippo_token = await asyncio.gather( cls.user_token('testus...
bsd-3-clause
3091e47f82135c9c8da9ffe2123f9b2e
40.504065
79
0.597747
4.000784
false
true
false
false
quantmind/lux
lux/utils/crypt/arc4.py
1
2165
'''RC4, ARC4, ARCFOUR algorithm for encryption. Adapted from # # RC4, ARC4, ARCFOUR algorithm # # Copyright (c) 2009 joonis new media # Author: Thimo Kraemer <thimo.kraemer@joonis.de> # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU ...
bsd-3-clause
9b9cecfb8792a66c56c30e6deccadddb
27.486842
76
0.611085
3.341049
false
false
false
false
quantmind/lux
lux/ext/auth/rest/registrations.py
1
5326
from datetime import datetime from pulsar.api import PermissionDenied, Http404 from lux.core import http_assert from lux.ext.rest import RestRouter, route from lux.models import Schema, fields, ValidationError from lux.ext.odm import Model from . import ensure_service_user, IdSchema URI = 'registrations' email_t...
bsd-3-clause
6e0fd230fb81118194cab93d866c7737
29.786127
73
0.616786
4.277912
false
false
false
false
quantmind/lux
tests/auth/groups.py
1
2785
class GroupsMixin: """Groups CRUD views """ async def test_group_validation(self): payload = {'name': 'abc'} request = await self.client.post(self.api_url('groups'), json=payload, token=self.super_token) ...
bsd-3-clause
33a8e0613ca8faeddc7facde6b133a8c
38.225352
78
0.504129
4.427663
false
false
false
false
quantmind/lux
lux/core/commands/stop.py
1
1680
import os import time import signal from pulsar.utils.tools import Pidfile from lux.core import LuxCommand, Setting, CommandError class Command(LuxCommand): help = "Stop a running server" option_list = ( Setting('timeout', ('--timeout',), default=10, type=int, desc=(...
bsd-3-clause
084051d9634903092153db1079fbafcb
30.111111
78
0.542857
4.148148
false
false
false
false
quantmind/lux
tests/odm/test_postgresql.py
1
12869
from dateutil.parser import parse from lux.utils import test from tests.odm.utils import OdmUtils class TestPostgreSql(OdmUtils, test.AppTestCase): @classmethod async def beforeAll(cls): cls.super_token = await cls.user_token('testuser', jwt=cls.admin_jwt) async def test_odm(self): tab...
bsd-3-clause
9707494daa9c10fd09c7c90a370ad54b
39.724684
77
0.571062
4.132627
false
true
false
false
quantmind/lux
lux/ext/auth/rest/authorization.py
1
4160
from pulsar.api import Http401, BadRequest, UnprocessableEntity from lux.models import Schema, fields, ValidationError from lux.utils.date import date_from_now from lux.ext.rest import RestRouter, route from lux.ext.odm import Model from ..backend import AuthenticationError from .tokens import TokenSchema from . impo...
bsd-3-clause
5b0bdf08b9247bc09a4682b21302011c
30.755725
78
0.609375
4.526659
false
false
false
false
quantmind/lux
lux/ext/sockjs/socketio.py
1
2441
import sys import hashlib from random import randint from pulsar.api import HttpException from pulsar.apps.wsgi import Router, route from pulsar.utils.httpurl import CacheControl from .transports.websocket import WebSocket from .utils import IFRAME_TEXT class SocketIO(Router): """A Router for sockjs requests ...
bsd-3-clause
5a7979b920e81cb25cc7e1dc55a185e5
31.118421
70
0.612044
4.054817
false
false
false
false
morepath/morepath
morepath/request.py
1
11760
"""Morepath request implementation. Entirely documented in :class:`morepath.Request` and :class:`morepath.Response` in the public API. """ from webob import BaseRequest, Response as BaseResponse from dectate import Sentinel from .reify import reify from .traject import create_path, parse_path from .error import Link...
bsd-3-clause
4b4aa869b42a40e22426bff6dc388484
34.421687
80
0.619133
4.379888
false
false
false
false
morepath/morepath
morepath/tests/test_mount_directive.py
1
29067
import morepath from morepath.error import LinkError, ConflictError from webtest import TestApp as Client import pytest def test_model_mount_conflict(): class app(morepath.App): pass class app2(morepath.App): pass class A: pass @app.path(model=A, path="a") def get_a(): ...
bsd-3-clause
8914695fb497493536a78f40b404b24f
23.262938
80
0.586885
3.487343
false
false
false
false
cornell-brg/pymtl
pclib/fl/QueuePortProxy.py
8
3091
#========================================================================= # QueuePortProxy #========================================================================= # These classes provide part of a standard Python deque interface, but # the implementation essentially turns the popleft() and append() methods # into a...
bsd-3-clause
86fb7384171a13da08f3af452c8b3105
27.357798
74
0.359107
5.630237
false
false
false
false
cornell-brg/pymtl
pclib/cl/pipelines_test.py
8
3436
#========================================================================= # pipelines_test.py #========================================================================= import pytest from pymtl import * from pclib.ifcs import InValRdyBundle, OutValRdyBundle from pclib.test import TestSrcSinkSim from pclib.cl ...
bsd-3-clause
3a67ad6da9ae9866fba8726b1dd76c87
31.415094
83
0.467113
3.152294
false
true
false
false
cornell-brg/pymtl
pclib/ifcs/XcelMsg.py
8
2581
#========================================================================= # XcelMsg #========================================================================= # Accelerator request and response messages. from pymtl import * #------------------------------------------------------------------------- # XcelReqMsg #----...
bsd-3-clause
9aa3bae2765d24eaf10cba5f64b325c5
22.898148
74
0.469198
3.762391
false
false
false
false
cornell-brg/pymtl
pymtl/tools/integration/verilog_parser_test_todo.py
8
6172
#======================================================================= # verilog_parser #======================================================================= import pytest import os from verilog_parser import header_parser #----------------------------------------------------------------------- # test cases #--...
bsd-3-clause
6a3e5d1a7e57bd0b8da2c5157081e3b4
22.290566
78
0.542126
3.217935
false
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false
false
cornell-brg/pymtl
pymtl/datatypes/helpers.py
8
3100
#======================================================================= # helpers.py #======================================================================= 'Collection of built-in helpers functions for the PyMTL framework.' import math import operator # NOTE: circular imports between Bits and helpers, using 'impor...
bsd-3-clause
809f8249273a05703ab01bd73a6d4b4a
35.470588
77
0.389355
5.354059
false
false
false
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cornell-brg/pymtl
pclib/rtl/arith.py
8
6880
#======================================================================= # arith.py #======================================================================= '''Collection of translatable arithmetic components.''' from pymtl import * #----------------------------------------------------------------------- # Adder #---...
bsd-3-clause
cf3bff154323127f2c114006484173f3
25.360153
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cornell-brg/pymtl
pclib/rtl/RegisterFile.py
1
3447
#======================================================================= # RegisterFile.py #======================================================================= from pymtl import * #----------------------------------------------------------------------- # RegisterFile #---------------------------------------------...
bsd-3-clause
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32.144231
76
0.380621
4.07929
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cornell-brg/pymtl
pymtl/tools/deprecated/ast_typer.py
8
9396
#========================================================================= # ast_typer.py #========================================================================= # Create a simplified representation of the Python AST for help with # source to source translation. from __future__ import print_function import ast, _a...
bsd-3-clause
826b4d053eab4458b4818f6e44da1d62
36.13834
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4.532562
false
false
false
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flutter/buildroot
build/linux/unbundle/remove_bundled_libraries.py
1
3226
#!/usr/bin/env python3 # # Copyright 2013 The Chromium Authors. All rights reserved. # Use of this source code is governed by a BSD-style license that can be # found in the LICENSE file. """ Removes bundled libraries to make sure they are not used. See README for more details. """ import optparse import os.path imp...
bsd-3-clause
4b4cbac56cb431234a98014f6c403e20
30.320388
80
0.648481
3.915049
false
false
false
false
flutter/buildroot
build/download_nacl_toolchains.py
1
2159
#!/usr/bin/env python3 # # Copyright (c) 2012 The Chromium Authors. All rights reserved. # Use of this source code is governed by a BSD-style license that can be # found in the LICENSE file. """Shim to run nacl toolchain download script only if there is a nacl dir.""" import os import shutil import sys def Main(arg...
bsd-3-clause
407a36dca2b91adf4dac8cc950e7bca7
34.983333
77
0.685503
3.373438
false
false
false
false
flutter/buildroot
build/linux/install-chromeos-fonts.py
1
2238
#!/usr/bin/env python3 # # Copyright 2013 The Chromium Authors. All rights reserved. # Use of this source code is governed by a BSD-style license that can be # found in the LICENSE file. # Script to install the Chrome OS fonts on Linux. # This script can be run manually (as root), but is also run as part # install-bui...
bsd-3-clause
8e32e69a442e7940292e70f2a38c08ad
29.243243
75
0.6479
3.116992
false
false
false
false
flutter/buildroot
build/toolchain/win/tool_wrapper.py
1
7391
# Copyright (c) 2012 The Chromium Authors. All rights reserved. # Use of this source code is governed by a BSD-style license that can be # found in the LICENSE file. """Utility functions for Windows builds. This file is copied to the build directory as part of toolchain setup and is used to set up calls to tools used ...
bsd-3-clause
0cbd4136239549e2bf05c8fe158f811d
37.295337
81
0.647544
3.727181
false
false
false
false
flutter/buildroot
build/toolchain/wrapper_utils.py
1
2854
# Copyright (c) 2016 The Chromium Authors. All rights reserved. # Use of this source code is governed by a BSD-style license that can be # found in the LICENSE file. """Helper functions for gcc_toolchain.gni wrappers.""" import gzip import os import re import subprocess import shlex import shutil import sys import thre...
bsd-3-clause
78bbcfd87095446c613161065a4283bd
38.638889
80
0.713385
3.589937
false
false
false
false
flutter/buildroot
build/android/gyp/util/build_utils.py
1
11762
# Copyright 2013 The Chromium Authors. All rights reserved. # Use of this source code is governed by a BSD-style license that can be # found in the LICENSE file. import ast import contextlib import fnmatch import json import os import pipes import re import shlex import shutil import subprocess import sys import tempf...
bsd-3-clause
86f8d12958b2767c27ec6d3a2daadb1c
28.331671
88
0.667148
3.541704
false
false
false
false
flutter/buildroot
build/download_sdk_extras.py
1
2631
#!/usr/bin/env python3 # # Copyright 2014 The Chromium Authors. All rights reserved. # Use of this source code is governed by a BSD-style license that can be # found in the LICENSE file. """Script to download sdk/extras packages on the bots from google storage. The script expects arguments that specify zips file in t...
bsd-3-clause
e6201e5953f575de22883a2e407ff41a
35.541667
80
0.68339
3.292866
false
false
false
false
matllubos/django-is-core
is_core/generic_views/inlines/inline_form_views.py
1
10444
from django.forms.formsets import DELETION_FIELD_NAME from django.utils.translation import ugettext_lazy as _ from django.utils.functional import cached_property from chamber.utils.forms import formset_has_file_field from is_core.forms.models import BaseInlineFormSet, smartinlineformset_factory, SmartModelForm from i...
bsd-3-clause
acade4552327122c27f1853ae356bc41
34.40339
118
0.599196
3.963567
false
false
false
false
matllubos/django-is-core
is_core/utils/__init__.py
1
14970
import re import json import types import datetime from django.core.exceptions import ImproperlyConfigured from django.contrib.admin.utils import display_for_value as admin_display_for_value from django.core.serializers.json import DjangoJSONEncoder from django.db.models import QuerySet from django.core.exceptions imp...
bsd-3-clause
81ac81018e0d317b511e587e71d2e45e
35.601467
118
0.633801
4.000534
false
false
false
false
matllubos/django-is-core
is_core/forms/generic.py
1
2883
from django.db import models from django.contrib.contenttypes.models import ContentType from django.forms.models import ModelForm from django.contrib.contenttypes.forms import BaseGenericInlineFormSet as OriginBaseGenericInlineFormSet from is_core.forms.models import smartmodelformset_factory from is_core.forms.formse...
bsd-3-clause
75548f85149b9644c1b209e97d9c4e33
43.353846
119
0.63753
4.154179
false
false
false
false
niwinz/django-jinja
django_jinja/views/generic/base.py
1
1148
from ...base import get_match_extension class Jinja2TemplateResponseMixin: jinja2_template_extension = None def get_template_names(self): """ Return a list of template names to be used for the request. This calls the super class's get_template_names and appends the Jinja2 matc...
bsd-3-clause
d5aec7d98198208156cac1db6006ad9a
30.888889
83
0.622822
4.647773
false
false
false
false
dask/dask-ml
tests/test_utils.py
1
6640
from collections import namedtuple import dask.array as da import dask.dataframe as dd import numpy as np import pandas as pd import pandas.testing as tm import pytest from dask.array.utils import assert_eq as assert_eq_ar from dask.dataframe.utils import assert_eq as assert_eq_df from dask_ml.datasets import make_cl...
bsd-3-clause
a9cd60224d6e75e0ccdaef61f650f10e
27.135593
85
0.595633
3.079777
false
true
false
false
andialbrecht/sqlparse
sqlparse/filters/reindent.py
1
9549
# # Copyright (C) 2009-2020 the sqlparse authors and contributors # <see AUTHORS file> # # This module is part of python-sqlparse and is released under # the BSD License: https://opensource.org/licenses/BSD-3-Clause from sqlparse import sql, tokens as T from sqlparse.utils import offset, indent class ReindentFilter:...
bsd-3-clause
ee489a4f7827f01d33bf625a5f518c7b
38.458678
77
0.512619
3.919951
false
false
false
false
andialbrecht/sqlparse
sqlparse/filters/right_margin.py
1
1543
# # Copyright (C) 2009-2020 the sqlparse authors and contributors # <see AUTHORS file> # # This module is part of python-sqlparse and is released under # the BSD License: https://opensource.org/licenses/BSD-3-Clause import re from sqlparse import sql, tokens as T # FIXME: Doesn't work class RightMarginFilter: k...
bsd-3-clause
c57fa319940abe657f9447cefdcba6df
31.145833
74
0.527544
4.262431
false
false
false
false