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"""
Parser module specific to EPC-Map predictions
"""
__author__ = "Felix Simkovic"
__date__ = "12 Dec 2016"
__version__ = "0.1"
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFile
class... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/io/epcmap.py",
"copies": "1",
"size": "4167",
"license": "bsd-3-clause",
"hash": -8979474324407762000,
"line_mean": 36.2053571429,
"line_max": 116,
"alpha_frac": 0.6537077034,
"autogenerated": false,
"ratio": 4.2607361963190185,
"config_test": f... |
"""
Parser module specific to EVfold predictions
"""
__author__ = "Felix Simkovic"
__date__ = "12 Oct 2016"
__version__ = "0.1"
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFi... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/io/evfold.py",
"copies": "1",
"size": "4156",
"license": "bsd-3-clause",
"hash": -3661594621295571500,
"line_mean": 35.4561403509,
"line_max": 106,
"alpha_frac": 0.6443695861,
"autogenerated": false,
"ratio": 4.271325796505653,
"config_test": fa... |
"""
Parser module specific to FASTA sequence files
"""
__author__ = "Felix Simkovic"
__date__ = "09 Sep 2016"
__version__ = "0.1"
from conkit.io._parser import SequenceFileParser
from conkit.core.sequence import Sequence
from conkit.core.sequencefile import SequenceFile
class FastaParser(SequenceFileParser):
""... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/io/fasta.py",
"copies": "1",
"size": "4450",
"license": "bsd-3-clause",
"hash": 4259607130748509700,
"line_mean": 33.2307692308,
"line_max": 104,
"alpha_frac": 0.6179775281,
"autogenerated": false,
"ratio": 4.550102249488752,
"config_test": fals... |
"""
Parser module specific to FreeContact predictions
"""
__author__ = "Felix Simkovic"
__date__ = "12 Oct 2016"
__version__ = "0.1"
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import Cont... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/io/freecontact.py",
"copies": "1",
"size": "4186",
"license": "bsd-3-clause",
"hash": 3129629044810457600,
"line_mean": 35.7192982456,
"line_max": 106,
"alpha_frac": 0.6469182991,
"autogenerated": false,
"ratio": 4.293333333333333,
"config_test"... |
"""
Parser module specific to Gremlin predictions
"""
__author__ = "Felix Simkovic"
__date__ = "04 Oct 2016"
__version__ = "0.1"
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactF... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/io/gremlin.py",
"copies": "1",
"size": "7360",
"license": "bsd-3-clause",
"hash": -38301427400860110,
"line_mean": 38.1489361702,
"line_max": 118,
"alpha_frac": 0.5581521739,
"autogenerated": false,
"ratio": 3.7608584568216656,
"config_test": fa... |
"""
Parser module specific to HH-suite A2M sequence files
"""
__author__ = "Felix Simkovic"
__date__ = "30 Jul 2018"
__version__ = "1.0"
from conkit.io._parser import SequenceFileParser
from conkit.core.sequence import Sequence
from conkit.core.sequencefile import SequenceFile
class A2mParser(SequenceFileParser):
... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/io/a2m.py",
"copies": "1",
"size": "3566",
"license": "bsd-3-clause",
"hash": -3303602189953627000,
"line_mean": 35.7628865979,
"line_max": 106,
"alpha_frac": 0.6469433539,
"autogenerated": false,
"ratio": 4.435323383084577,
"config_test": false... |
"""
Parser module specific to HH-suite A3M sequence files
Credits
-------
Stefan Seemayer and his A3MIO project [https://github.com/sseemayer/BioPython-A3MIO]
"""
__author__ = "Felix Simkovic"
__credits__ = "Stefan Seemayer"
__date__ = "11 Sep 2016"
__version__ = "0.1"
import numpy as np
import re
from conkit.io._... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/io/a3m.py",
"copies": "1",
"size": "6265",
"license": "bsd-3-clause",
"hash": -1591318723693994000,
"line_mean": 36.0710059172,
"line_max": 120,
"alpha_frac": 0.6140462889,
"autogenerated": false,
"ratio": 4.3088033012379645,
"config_test": fals... |
"""
Parser module specific to ncont contact comparison
"""
__author__ = "Felix Simkovic"
__date__ = "16 Nov 2017"
__version__ = "0.1"
import re
import warnings
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contac... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/io/ncont.py",
"copies": "1",
"size": "4565",
"license": "bsd-3-clause",
"hash": 3963971610757674500,
"line_mean": 35.814516129,
"line_max": 106,
"alpha_frac": 0.6416210296,
"autogenerated": false,
"ratio": 4.1880733944954125,
"config_test": fals... |
"""
Parser module specific to Pcons predictions
This module can be used to parse all versions
of the Pcons programs, i.e. PconsC, PconsC2,
and PconsC3.
"""
__author__ = "Felix Simkovic"
__date__ = "26 Oct 2016"
__version__ = "0.1"
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact im... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/io/pcons.py",
"copies": "1",
"size": "6785",
"license": "bsd-3-clause",
"hash": -7904654690708648000,
"line_mean": 35.875,
"line_max": 106,
"alpha_frac": 0.5943994105,
"autogenerated": false,
"ratio": 4.134673979280926,
"config_test": false,
"... |
"""
Parser module specific to Pdb files
"""
from __future__ import division
__author__ = "Felix Simkovic"
__date__ = "27 Sep 2016"
__version__ = "0.1"
import collections
import itertools
import sys
import warnings
if sys.version_info.major < 3:
from itertools import izip as zip
from Bio.PDB import MMCIFParser
... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/io/pdb.py",
"copies": "1",
"size": "11524",
"license": "bsd-3-clause",
"hash": 3603039680332189700,
"line_mean": 35.3533123028,
"line_max": 116,
"alpha_frac": 0.5917216244,
"autogenerated": false,
"ratio": 4.2760667903525045,
"config_test": fals... |
"""
Parser module specific to plmDCA predictions
"""
__author__ = "Felix Simkovic"
__date__ = "03 Aug 2016"
__version__ = "0.1"
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFile
class ... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/io/plmdca.py",
"copies": "1",
"size": "3872",
"license": "bsd-3-clause",
"hash": 4917243146322076000,
"line_mean": 34.5229357798,
"line_max": 106,
"alpha_frac": 0.6624483471,
"autogenerated": false,
"ratio": 4.287929125138428,
"config_test": fal... |
"""
Parser module specific to PSICOV predictions
"""
__author__ = "Felix Simkovic"
__date__ = "03 Aug 2016"
__version__ = "0.1"
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFile
class ... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/io/psicov.py",
"copies": "1",
"size": "4051",
"license": "bsd-3-clause",
"hash": -3837706351210893300,
"line_mean": 36.1651376147,
"line_max": 113,
"alpha_frac": 0.6576154036,
"autogenerated": false,
"ratio": 4.332620320855615,
"config_test": fa... |
"""
Parser module specific to Stockholm sequence files
"""
__author__ = "Felix Simkovic"
__date__ = "09 Sep 2016"
__version__ = "0.1"
import re
from conkit.io._parser import SequenceFileParser
from conkit.core.sequence import Sequence
from conkit.core.sequencefile import SequenceFile
V_RECORD = re.compile(r'^#(\s+S... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/io/stockholm.py",
"copies": "1",
"size": "5227",
"license": "bsd-3-clause",
"hash": 8467493372253689000,
"line_mean": 38.5984848485,
"line_max": 106,
"alpha_frac": 0.6137363689,
"autogenerated": false,
"ratio": 3.993124522536287,
"config_test": ... |
"""Various miscellaneous code required by ConKit"""
__author__ = "Felix Simkovic"
__date__ = "18 May 2018"
__version__ = "2.0"
import numpy as np
import warnings
def fAND(a, b):
"""Function AND operator for two arguments"""
return a and b
def fOR(a, b):
"""Function OR operator for two arguments"""
... | {
"repo_name": "fsimkovic/conkit",
"path": "conkit/misc/__init__.py",
"copies": "1",
"size": "5801",
"license": "bsd-3-clause",
"hash": 8301286259590702000,
"line_mean": 31.2277777778,
"line_max": 155,
"alpha_frac": 0.6507498707,
"autogenerated": false,
"ratio": 4.131766381766382,
"config_test":... |
"""A collection of bandwidth estimators for Kernel Density Estimation"""
from __future__ import division
from __future__ import print_function
__author__ = "Felix Simkovic"
__date__ = "31 Mar 2018"
__version__ = "1.0.1"
import abc
import numpy as np
ABC = abc.ABCMeta("ABC", (object,), {})
class BandwidthBase(ABC)... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/misc/bandwidth.py",
"copies": "2",
"size": "5949",
"license": "bsd-3-clause",
"hash": 2063239215858332700,
"line_mean": 29.984375,
"line_max": 120,
"alpha_frac": 0.633047571,
"autogenerated": false,
"ratio": 3.634086744043983,
"config_test": fal... |
"""A module containing generic Figure related objects"""
__author__ = "Felix Simkovic"
__date__ = "08 Jan 2018"
__version__ = "0.2"
import matplotlib.collections as mcoll
import matplotlib.pyplot as plt
import os
import warnings
class Figure(object):
"""A Figure class to store common features"""
def __init... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/plot/figure.py",
"copies": "2",
"size": "6022",
"license": "bsd-3-clause",
"hash": 6742312867316725000,
"line_mean": 38.1038961039,
"line_max": 127,
"alpha_frac": 0.6104284291,
"autogenerated": false,
"ratio": 4.187760778859527,
"config_test": f... |
"""A module to produce a domain boundary plot"""
from __future__ import division
from __future__ import print_function
__author__ = "Felix Simkovic"
__date__ = "23 Feb 2017"
__version__ = "0.1"
import matplotlib.pyplot as plt
import numpy as np
from conkit.misc import deprecate
from conkit.plot.figure import Figure... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/plot/contactdensity.py",
"copies": "2",
"size": "5851",
"license": "bsd-3-clause",
"hash": -3758635661216307700,
"line_mean": 34.6768292683,
"line_max": 120,
"alpha_frac": 0.6593744659,
"autogenerated": false,
"ratio": 3.972165648336728,
"config... |
"""Energy function templates for restraint generation"""
__author__ = "Felix Simkovic"
__date__ = "13 Aug 2018"
__version__ = "1.0"
import inspect
import numpy as np
class SubselectionAlgorithm(object):
"""A class to collect all subselection algorithms"""
@classmethod
def _numpify(cls, data):
"... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/misc/selectalg.py",
"copies": "2",
"size": "4920",
"license": "bsd-3-clause",
"hash": -1975311546420301800,
"line_mean": 30.1392405063,
"line_max": 108,
"alpha_frac": 0.6355691057,
"autogenerated": false,
"ratio": 4.46866485013624,
"config_test"... |
"""Internal utility functions"""
__author__ = "Felix Simkovic"
__date__ = "16 Feb 2017"
__version__ = "0.1"
import numpy as np
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFile
from conkit.core.sequence import Sequence
from conkit.co... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/plot/tools.py",
"copies": "2",
"size": "6286",
"license": "bsd-3-clause",
"hash": -693627950164279800,
"line_mean": 28.2372093023,
"line_max": 108,
"alpha_frac": 0.6306076997,
"autogenerated": false,
"ratio": 3.737217598097503,
"config_test": fa... |
"""Internal utility functions"""
__author__ = "Felix Simkovic"
__date__ = "20 Nov 2016"
__version__ = "0.1"
import io
import sys
import tempfile
def create_tmp_f(content=None, mode="w"):
"""Create a temporary file
Parameters
----------
mode : str, optional
Write-mode [default: 'w']
conte... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/_iotools.py",
"copies": "2",
"size": "3667",
"license": "bsd-3-clause",
"hash": 5738524363494228000,
"line_mean": 27.874015748,
"line_max": 80,
"alpha_frac": 0.6634851377,
"autogenerated": false,
"ratio": 4.229527104959631,
"config_test": fal... |
"""
Parent classes for all parser classes
"""
__author__ = "Felix Simkovic"
__date__ = "04 Oct 2016"
__version__ = "0.1"
import abc
ABC = abc.ABCMeta("ABC", (object,), {})
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFile
from conki... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/_parser.py",
"copies": "2",
"size": "3072",
"license": "bsd-3-clause",
"hash": -3339861248142050000,
"line_mean": 32.3913043478,
"line_max": 80,
"alpha_frac": 0.7109375,
"autogenerated": false,
"ratio": 4.478134110787172,
"config_test": false... |
"""
Parser module specific to bbcontacts predictions
"""
__author__ = "Felix Simkovic"
__date__ = "23 Jul 2018"
__version__ = "0.2"
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import Conta... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/bbcontacts.py",
"copies": "2",
"size": "4310",
"license": "bsd-3-clause",
"hash": 3260847587475627000,
"line_mean": 35.218487395,
"line_max": 106,
"alpha_frac": 0.6535962877,
"autogenerated": false,
"ratio": 4.371196754563894,
"config_test": ... |
"""
Parser module specific to BCL::Contact predictions
"""
__author__ = "Felix Simkovic"
__date__ = "12 Dec 2016"
__version__ = "0.1"
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import Con... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/bclcontact.py",
"copies": "2",
"size": "3606",
"license": "bsd-3-clause",
"hash": -720209512395820300,
"line_mean": 34.0097087379,
"line_max": 106,
"alpha_frac": 0.6713810316,
"autogenerated": false,
"ratio": 4.349819059107358,
"config_test":... |
"""
Parser module specific to CASP-RR predictions
"""
__author__ = "Felix Simkovic"
__date__ = "03 Aug 2016"
__version__ = "1.0"
import collections
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactf... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/casp.py",
"copies": "2",
"size": "9019",
"license": "bsd-3-clause",
"hash": 7598386063491845000,
"line_mean": 42.1531100478,
"line_max": 118,
"alpha_frac": 0.5600399157,
"autogenerated": false,
"ratio": 3.9661389621811787,
"config_test": fals... |
"""
Parser module specific to CCMpred predictions
"""
from __future__ import division
__author__ = "Felix Simkovic"
__date__ = "03 Aug 2016"
__version__ = "0.1"
import numpy as np
import sys
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import Co... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/ccmpred.py",
"copies": "2",
"size": "5272",
"license": "bsd-3-clause",
"hash": -397028043059552600,
"line_mean": 34.8639455782,
"line_max": 115,
"alpha_frac": 0.6437784522,
"autogenerated": false,
"ratio": 4.138147566718995,
"config_test": fa... |
"""
Parser module specific to ComsatIO predictions
"""
__author__ = "Felix Simkovic"
__date__ = "12 Oct 2016"
__version__ = "0.1"
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import Contact... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/membrain.py",
"copies": "2",
"size": "4546",
"license": "bsd-3-clause",
"hash": 1228823388059338200,
"line_mean": 34.2403100775,
"line_max": 112,
"alpha_frac": 0.6326440827,
"autogenerated": false,
"ratio": 4.163003663003663,
"config_test": f... |
"""
Parser module specific to COMSAT predictions
"""
__author__ = "Felix Simkovic"
__date__ = "03 Aug 2016"
__version__ = "0.1"
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFi... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/comsat.py",
"copies": "2",
"size": "4125",
"license": "bsd-3-clause",
"hash": -1323071427415659000,
"line_mean": 33.375,
"line_max": 120,
"alpha_frac": 0.6475151515,
"autogenerated": false,
"ratio": 4.196337741607325,
"config_test": false,
... |
"""
Parser module specific to EVfold predictions
"""
__author__ = "Felix Simkovic"
__date__ = "12 Oct 2016"
__version__ = "0.1"
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFi... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/evfold.py",
"copies": "2",
"size": "4174",
"license": "bsd-3-clause",
"hash": -4277767885461485000,
"line_mean": 35.2956521739,
"line_max": 106,
"alpha_frac": 0.6415908002,
"autogenerated": false,
"ratio": 4.281025641025641,
"config_test": fa... |
"""
Parser module specific to Gremlin predictions
"""
__author__ = "Felix Simkovic"
__date__ = "04 Oct 2016"
__version__ = "0.1"
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactF... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/gremlin.py",
"copies": "2",
"size": "7588",
"license": "bsd-3-clause",
"hash": 9132490941670831000,
"line_mean": 36.5643564356,
"line_max": 106,
"alpha_frac": 0.5413811281,
"autogenerated": false,
"ratio": 3.847870182555781,
"config_test": fa... |
"""
Parser module specific to HH-suite A3M sequence files
Credits
-------
Stefan Seemayer and his A3MIO project [https://github.com/sseemayer/BioPython-A3MIO]
"""
__author__ = "Felix Simkovic"
__credits__ = "Stefan Seemayer"
__date__ = "11 Sep 2016"
__version__ = "0.1"
import numpy as np
import re
from conkit.io._... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/a3m.py",
"copies": "2",
"size": "6265",
"license": "bsd-3-clause",
"hash": 3348055704799542300,
"line_mean": 36.0710059172,
"line_max": 120,
"alpha_frac": 0.6140462889,
"autogenerated": false,
"ratio": 4.302884615384615,
"config_test": false,... |
"""
Parser module specific to Pcons predictions
This module can be used to parse all versions
of the Pcons programs, i.e. PconsC, PconsC2,
and PconsC3.
"""
__author__ = "Felix Simkovic"
__date__ = "26 Oct 2016"
__version__ = "0.1"
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact im... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/pcons.py",
"copies": "2",
"size": "6785",
"license": "bsd-3-clause",
"hash": -8978421239601861000,
"line_mean": 35.875,
"line_max": 106,
"alpha_frac": 0.5943994105,
"autogenerated": false,
"ratio": 4.134673979280926,
"config_test": false,
"... |
"""
Parser module specific to Pdb files
"""
from __future__ import division
__author__ = "Felix Simkovic"
__date__ = "27 Sep 2016"
__version__ = "0.1"
import collections
import itertools
import sys
import warnings
from Bio.PDB import MMCIFParser
from Bio.PDB import PDBParser
from conkit.io._parser import ContactFi... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/pdb.py",
"copies": "2",
"size": "11276",
"license": "bsd-3-clause",
"hash": -829118641154207500,
"line_mean": 35.8496732026,
"line_max": 116,
"alpha_frac": 0.6003902093,
"autogenerated": false,
"ratio": 4.231144465290806,
"config_test": false... |
"""
Parser module specific to PSICOV predictions
"""
__author__ = "Felix Simkovic"
__date__ = "03 Aug 2016"
__version__ = "0.1"
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFile
class ... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/psicov.py",
"copies": "2",
"size": "4068",
"license": "bsd-3-clause",
"hash": -5337778236020167000,
"line_mean": 35.9818181818,
"line_max": 113,
"alpha_frac": 0.6548672566,
"autogenerated": false,
"ratio": 4.341515474919957,
"config_test": fa... |
"""
Parser module specific to Stockholm sequence files
"""
__author__ = "Felix Simkovic"
__date__ = "09 Sep 2016"
__version__ = "0.1"
import re
from conkit.io._parser import SequenceFileParser
from conkit.core.sequence import Sequence
from conkit.core.sequencefile import SequenceFile
V_RECORD = re.compile(r"^#(\s+S... | {
"repo_name": "rigdenlab/conkit",
"path": "conkit/io/stockholm.py",
"copies": "2",
"size": "5229",
"license": "bsd-3-clause",
"hash": -6799347814635260000,
"line_mean": 38.6136363636,
"line_max": 106,
"alpha_frac": 0.6135016255,
"autogenerated": false,
"ratio": 3.9916030534351146,
"config_test"... |
import argparse
import csv
from pyproj import Proj, transform
def argparser():
parser = argparse.ArgumentParser(description="Convert coordiantes with pyproj")
parser.add_argument("-p", "--path",
help="Path to csv file with coordinates")
parser.add_argument("-c", "--coordinate",
... | {
"repo_name": "andrewyushkevich/projconverter",
"path": "projconverter/projconverter.py",
"copies": "1",
"size": "3405",
"license": "bsd-3-clause",
"hash": 3413172690285213000,
"line_mean": 36.8333333333,
"line_max": 84,
"alpha_frac": 0.6631424376,
"autogenerated": false,
"ratio": 4.2722710163111... |
#import pytest
import shutil
import numpy as np
import os
from cloudvolume import Storage, CloudVolume
from cloudvolume.lib import Bbox, Vec, min2, max2, find_closest_divisor
TEST_NUMBER = np.random.randint(0, 999999)
CLOUD_BUCKET = 'seunglab-test'
layer_path = '/tmp/removeme/'
def create_storage(layer_name='lay... | {
"repo_name": "jhuapl-boss/ingest-client",
"path": "ingestclient/test/layer_harness.py",
"copies": "1",
"size": "2736",
"license": "apache-2.0",
"hash": -2568585337072889000,
"line_mean": 29.4,
"line_max": 90,
"alpha_frac": 0.6736111111,
"autogenerated": false,
"ratio": 3.2075029308323564,
"con... |
'''Fortran Code Analyser 0.2. This version provides filters to allow
the user to specify the directories and files. It then parses and
analyses these files building up an internal hierarchy of
subroutines and calls. The analysis provides some basic
information about the code in terms of number of subrou... | {
"repo_name": "rupertford/fanalyser",
"path": "src/CodeAnalysis.py",
"copies": "1",
"size": "20527",
"license": "bsd-3-clause",
"hash": -5580394189727176000,
"line_mean": 35.524911032,
"line_max": 79,
"alpha_frac": 0.5491791299,
"autogenerated": false,
"ratio": 4.474062772449869,
"config_test":... |
from CodeAnalysis import CodeAnalysis, Stats, Link
try:
c = CodeAnalysis()
#c.add_directory("/home/rupert/proj/isenes2/N512_endgame_ppsrc",
#included_files=['*.f90','*.f'])
c.add_directory(
"/home/rupert/proj/isenes2/code_analysis/ppsrc-nemo",
included_files=['*.f90', '*.f'])
#c.add_... | {
"repo_name": "rupertford/fanalyser",
"path": "src/example.py",
"copies": "1",
"size": "2778",
"license": "bsd-3-clause",
"hash": -9150827244256993000,
"line_mean": 43.0952380952,
"line_max": 79,
"alpha_frac": 0.7210223182,
"autogenerated": false,
"ratio": 3.556978233034571,
"config_test": fals... |
import os
import argparse
import sys
import mx
import mx_sulong
import mx_testsuites
_suite = mx.suite('irbuilder')
class Tool(object):
def supports(self, language):
return language in self.supportedLanguages
def runTool(self, args, errorMsg=None, verbose=None, **kwargs):
try:
i... | {
"repo_name": "pointhi/java-llvm-ir-builder",
"path": "mx.irbuilder/mx_irbuilder.py",
"copies": "1",
"size": "15945",
"license": "bsd-3-clause",
"hash": 564018677672945200,
"line_mean": 39.8846153846,
"line_max": 171,
"alpha_frac": 0.6476638445,
"autogenerated": false,
"ratio": 3.657949070887818,... |
"""BSD 3-Clause License
Copyright (c) 2017, Zach
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice,
this list of cond... | {
"repo_name": "craymichael/News",
"path": "News/CreateDataSet.py",
"copies": "1",
"size": "4979",
"license": "bsd-3-clause",
"hash": 8606164863336298000,
"line_mean": 34.0633802817,
"line_max": 77,
"alpha_frac": 0.6356698132,
"autogenerated": false,
"ratio": 3.6826923076923075,
"config_test": f... |
import argparse
import datetime
from enum import Enum
import getopt
import glob
import logging
from typing import Any, Dict, List
import numpy as np
import os
import sys
from time import sleep
from . import arimage
from . import env
from . import jobs
from . import log
logger = log.get_logger()
CURRENT_DATE_TIME = ... | {
"repo_name": "zstuartp/AstroReduce",
"path": "astroreduce/flatfield.py",
"copies": "1",
"size": "16290",
"license": "bsd-3-clause",
"hash": -2925336448701211000,
"line_mean": 32.7267080745,
"line_max": 106,
"alpha_frac": 0.614732965,
"autogenerated": false,
"ratio": 3.5668929275235386,
"config... |
import multiprocessing
from queue import Queue
from threading import Thread
from time import sleep
from typing import Callable, Tuple
from . import env
from . import progress
_job_queue = Queue() # FIFO job queue
_cpu_count = multiprocessing.cpu_count() # Max threads = _cpu_count
class Job:
... | {
"repo_name": "zstuartp/AstroReduce",
"path": "astroreduce/jobs.py",
"copies": "1",
"size": "3424",
"license": "bsd-3-clause",
"hash": 962184919488713900,
"line_mean": 33.9387755102,
"line_max": 80,
"alpha_frac": 0.6889602804,
"autogenerated": false,
"ratio": 4.061684460260973,
"config_test": f... |
import os
from typing import Callable, Dict, List, Tuple
_vars = {}
_var_hooks = {}
_VAR_DEFAULT_VAL = False
def _run_var_hooks(key: str, run_global_hooks: bool=False):
""" Run all of the update hooks for the specified variable """
if run_global_hooks:
hook_key = ""
else:
hook_key = ke... | {
"repo_name": "zstuartp/AstroReduce",
"path": "astroreduce/env.py",
"copies": "1",
"size": "3224",
"license": "bsd-3-clause",
"hash": 3615226628838383600,
"line_mean": 30.9207920792,
"line_max": 80,
"alpha_frac": 0.6771091811,
"autogenerated": false,
"ratio": 3.8380952380952382,
"config_test": ... |
"""
This module contains methods to find the closest positive semidefinite matrix
with fixed trace by the method in arXiv 1707.01022v1 and
N.J. Higham, Linear Algebra and Its Applications 103, 103 (1998)
"""
from itertools import product
import numpy as np
@np.vectorize
def heaviside(x, bias=0) -> int:
"""
H... | {
"repo_name": "quantumlib/OpenFermion",
"path": "src/openfermion/third_party/representability/_higham.py",
"copies": "2",
"size": "5540",
"license": "apache-2.0",
"hash": 5094349292868071000,
"line_mean": 34.2866242038,
"line_max": 80,
"alpha_frac": 0.6649819495,
"autogenerated": false,
"ratio": ... |
from itertools import product
import numpy as np
import pytest
from openfermion.third_party.representability._higham import (
heaviside, higham_polynomial, higham_root, map_to_tensor, map_to_matrix,
fixed_trace_positive_projection)
def test_heaviside():
assert np.isclose(heaviside(0), 1.0)
assert np.i... | {
"repo_name": "kevinsung/OpenFermion",
"path": "src/openfermion/third_party/representability/_higham_test.py",
"copies": "2",
"size": "4784",
"license": "apache-2.0",
"hash": 3296942784024123400,
"line_mean": 36.0852713178,
"line_max": 80,
"alpha_frac": 0.6699414716,
"autogenerated": false,
"rati... |
import time
import mock
from elasticapm.utils.threading import IntervalTimer
def test_interval_timer():
func = mock.Mock()
timer = IntervalTimer(function=func, interval=0.1, args=(1,), kwargs={"a": "b"})
timer.start()
time.sleep(0.25)
try:
assert func.call_count == 2
for call in... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/utils/threading_tests.py",
"copies": "1",
"size": "2733",
"license": "bsd-3-clause",
"hash": 5737748071281400000,
"line_mean": 34.4935064935,
"line_max": 87,
"alpha_frac": 0.7072813758,
"autogenerated": false,
"ratio": 3.9267241379310347,... |
from __future__ import absolute_import
import os
import threading
from timeit import default_timer
class IntervalTimer(threading.Thread):
"""
A timer that runs a function repeatedly. In contrast to threading.Timer,
IntervalTimer runs the given function in perpetuity or until it is cancelled.
When r... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/utils/threading.py",
"copies": "1",
"size": "4219",
"license": "bsd-3-clause",
"hash": 3820652462879717000,
"line_mean": 38.8018867925,
"line_max": 117,
"alpha_frac": 0.6736193411,
"autogenerated": false,
"ratio": 4.585869565217391,
... |
from __future__ import absolute_import
from elasticapm.instrumentation.packages.dbapi2 import (
ConnectionProxy,
CursorProxy,
DbApi2Instrumentation,
extract_signature,
)
from elasticapm.traces import capture_span
from elasticapm.utils import compat, default_ports
class PGCursorProxy(CursorProxy):
... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/psycopg2.py",
"copies": "1",
"size": "5917",
"license": "bsd-3-clause",
"hash": 8090356849414829000,
"line_mean": 40.3776223776,
"line_max": 108,
"alpha_frac": 0.6516815954,
"autogenerated": false,
"ratio": 4... |
from typing import Union
from aiohttp.web import HTTPException, Request, Response
from elasticapm.conf import Config
from elasticapm.utils import compat, get_url_dict
def get_data_from_request(request: Request, config: Config, event_type: str):
result = {
"method": request.method,
"socket": {"re... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/contrib/aiohttp/utils.py",
"copies": "1",
"size": "2711",
"license": "bsd-3-clause",
"hash": 7344600517105543000,
"line_mean": 43.4426229508,
"line_max": 102,
"alpha_frac": 0.7358908152,
"autogenerated": false,
"ratio": 4.2359375,
... |
import itertools
import os
import pytest
from pytest_bdd import given, parsers, scenario, scenarios, then, when
pytestmark = pytest.mark.bdd
version_counter = itertools.count(0)
scenarios(os.path.join("features", "api_key.feature"))
@given("an agent")
def an_agent(elasticapm_client):
return elasticapm_client
... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/bdd/api_key_tests.py",
"copies": "1",
"size": "3492",
"license": "bsd-3-clause",
"hash": -1323404933014292200,
"line_mean": 37.3736263736,
"line_max": 81,
"alpha_frac": 0.7488545246,
"autogenerated": false,
"ratio": 3.816393442622951,
"... |
# BSD 3-Clause License
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
#
#
#
import mock
from elasticapm.conf.constants import ERROR
def test_chained_cause_exception(elasticapm_client):
try:
try:... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/client/py3_exception_tests.py",
"copies": "1",
"size": "3737",
"license": "bsd-3-clause",
"hash": 2088771209682477300,
"line_mean": 36.37,
"line_max": 81,
"alpha_frac": 0.6831683168,
"autogenerated": false,
"ratio": 4.325231481481482,
"... |
"""
Framework integration for Tornado
Note that transaction creation is actually done in the tornado
instrumentation. This module only creates the client for later use by the
that instrumentation, and triggers the global instrumentation itself.
"""
import tornado
import elasticapm
from elasticapm import Client
clas... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/contrib/tornado/__init__.py",
"copies": "1",
"size": "3097",
"license": "bsd-3-clause",
"hash": 9001081031123442000,
"line_mean": 42.6197183099,
"line_max": 91,
"alpha_frac": 0.7148853729,
"autogenerated": false,
"ratio": 4.488405797... |
from elasticapm.conf import constants
from elasticapm.contrib.asyncio.traces import async_capture_span
from elasticapm.instrumentation.packages.asyncio.base import AsyncAbstractInstrumentedModule
from elasticapm.traces import DroppedSpan, execution_context
from elasticapm.utils import default_ports, url_to_destination... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/asyncio/httpcore.py",
"copies": "1",
"size": "6561",
"license": "bsd-3-clause",
"hash": -4350760711749811700,
"line_mean": 45.2042253521,
"line_max": 120,
"alpha_frac": 0.6486816034,
"autogenerated": false,
"... |
from elasticapm.conf import constants
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.traces import DroppedSpan, capture_span, execution_context
from elasticapm.utils import default_ports, url_to_destination
from elasticapm.utils.disttracing import TracingOptions
class... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/httpcore.py",
"copies": "1",
"size": "5947",
"license": "bsd-3-clause",
"hash": -5159531544515076000,
"line_mean": 44.053030303,
"line_max": 120,
"alpha_frac": 0.6381368757,
"autogenerated": false,
"ratio": 4... |
from elasticapm.contrib.asyncio.traces import async_capture_span
from elasticapm.instrumentation.packages.asyncio.base import AsyncAbstractInstrumentedModule
from elasticapm.instrumentation.packages.dbapi2 import extract_signature
class AioPGInstrumentation(AsyncAbstractInstrumentedModule):
name = "aiopg"
i... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/asyncio/aiopg.py",
"copies": "1",
"size": "3081",
"license": "bsd-3-clause",
"hash": -1927148410315851000,
"line_mean": 45.6818181818,
"line_max": 103,
"alpha_frac": 0.7078870497,
"autogenerated": false,
"rat... |
from elasticapm.contrib.asyncio.traces import async_capture_span
from elasticapm.instrumentation.packages.asyncio.base import AsyncAbstractInstrumentedModule
from elasticapm.utils import get_host_from_url, sanitize_url, url_to_destination
class HttpxAsyncClientInstrumentation(AsyncAbstractInstrumentedModule):
na... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/asyncio/httpx.py",
"copies": "1",
"size": "2927",
"license": "bsd-3-clause",
"hash": 1302667277549686300,
"line_mean": 46.2096774194,
"line_max": 107,
"alpha_frac": 0.7109668603,
"autogenerated": false,
"rati... |
from elasticapm.contrib.asyncio.traces import async_capture_span
from elasticapm.instrumentation.packages.asyncio.base import AsyncAbstractInstrumentedModule
class AsyncIOSleepInstrumentation(AsyncAbstractInstrumentedModule):
name = "asyncio_sleep"
instrument_list = [("asyncio.tasks", "sleep")]
async d... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/asyncio/sleep.py",
"copies": "1",
"size": "2132",
"license": "bsd-3-clause",
"hash": 7123617368978146000,
"line_mean": 49.7619047619,
"line_max": 106,
"alpha_frac": 0.7668855535,
"autogenerated": false,
"rati... |
from elasticapm import async_capture_span
from elasticapm.conf import constants
from elasticapm.instrumentation.packages.asyncio.base import AsyncAbstractInstrumentedModule
from elasticapm.traces import DroppedSpan, execution_context
from elasticapm.utils import get_host_from_url, sanitize_url, url_to_destination
from... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/asyncio/aiohttp_client.py",
"copies": "1",
"size": "4615",
"license": "bsd-3-clause",
"hash": 611172715110196100,
"line_mean": 47.0729166667,
"line_max": 103,
"alpha_frac": 0.6936078007,
"autogenerated": false,... |
from elasticapm import set_transaction_name
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.traces import capture_span
class GraphQLExecutorInstrumentation(AbstractInstrumentedModule):
name = "graphql"
instrument_list = [
("graphql.execution.executors.... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/graphql.py",
"copies": "1",
"size": "4455",
"license": "bsd-3-clause",
"hash": -2902518067008229000,
"line_mean": 40.25,
"line_max": 117,
"alpha_frac": 0.6505050505,
"autogenerated": false,
"ratio": 4.2067988... |
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.instrumentation.packages.dbapi2 import extract_signature
from elasticapm.traces import capture_span
from elasticapm.utils import compat
class CassandraInstrumentation(AbstractInstrumentedModule):
name = "cassandra"
... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/cassandra.py",
"copies": "1",
"size": "3899",
"license": "bsd-3-clause",
"hash": -911572380112124300,
"line_mean": 46.5487804878,
"line_max": 114,
"alpha_frac": 0.6609387022,
"autogenerated": false,
"ratio": ... |
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.traces import capture_span
from elasticapm.utils.compat import urlparse
class BotocoreInstrumentation(AbstractInstrumentedModule):
name = "botocore"
instrument_list = [("botocore.client", "BaseClient._make_api_ca... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/botocore.py",
"copies": "1",
"size": "2604",
"license": "bsd-3-clause",
"hash": 5000728283754540000,
"line_mean": 44.6842105263,
"line_max": 105,
"alpha_frac": 0.7319508449,
"autogenerated": false,
"ratio": 4... |
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.traces import capture_span
from elasticapm.utils import get_host_from_url, sanitize_url, url_to_destination
class HttpxClientInstrumentation(AbstractInstrumentedModule):
name = "httpx"
instrument_list = [("httpx"... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/httpx.py",
"copies": "1",
"size": "2853",
"license": "bsd-3-clause",
"hash": 8467349541368355000,
"line_mean": 45.0161290323,
"line_max": 107,
"alpha_frac": 0.7062740974,
"autogenerated": false,
"ratio": 4.32... |
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.traces import capture_span
class DjangoTemplateInstrumentation(AbstractInstrumentedModule):
name = "django_template"
instrument_list = [("django.template", "Template.render")]
def call(self, module, method, ... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/django/template.py",
"copies": "1",
"size": "2926",
"license": "bsd-3-clause",
"hash": -8041358861252520000,
"line_mean": 39.0821917808,
"line_max": 99,
"alpha_frac": 0.7026657553,
"autogenerated": false,
"ra... |
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.traces import capture_span
class Jinja2Instrumentation(AbstractInstrumentedModule):
name = "jinja2"
instrument_list = [("jinja2", "Template.render")]
def call(self, module, method, wrapped, instance, args, k... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/jinja2.py",
"copies": "1",
"size": "2123",
"license": "bsd-3-clause",
"hash": 8958381773305217000,
"line_mean": 48.3720930233,
"line_max": 104,
"alpha_frac": 0.7626000942,
"autogenerated": false,
"ratio": 4.4... |
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.traces import capture_span
class PyMemcacheInstrumentation(AbstractInstrumentedModule):
name = "pymemcache"
method_list = [
"add",
"append",
"cas",
"decr",
"delete",
... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/pymemcache.py",
"copies": "1",
"size": "4195",
"license": "bsd-3-clause",
"hash": 5547005771008261000,
"line_mean": 37.1363636364,
"line_max": 99,
"alpha_frac": 0.6133492253,
"autogenerated": false,
"ratio": ... |
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.traces import capture_span
class PyMongoInstrumentation(AbstractInstrumentedModule):
name = "pymongo"
instrument_list = [
("pymongo.collection", "Collection.aggregate"),
("pymongo.collection", "Co... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/pymongo.py",
"copies": "1",
"size": "6008",
"license": "bsd-3-clause",
"hash": 5854874139761133000,
"line_mean": 43.1764705882,
"line_max": 105,
"alpha_frac": 0.6439747004,
"autogenerated": false,
"ratio": 4.... |
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.traces import capture_span
class PythonMemcachedInstrumentation(AbstractInstrumentedModule):
name = "python_memcached"
method_list = [
"add",
"append",
"cas",
"decr",
"dele... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/python_memcached.py",
"copies": "1",
"size": "3082",
"license": "bsd-3-clause",
"hash": 5845111186083285000,
"line_mean": 38.5128205128,
"line_max": 118,
"alpha_frac": 0.6726151849,
"autogenerated": false,
"r... |
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.traces import capture_span
class ZLibInstrumentation(AbstractInstrumentedModule):
name = "zlib"
instrument_list = [("zlib", "compress"), ("zlib", "decompress")]
def call(self, module, method, wrapped, instanc... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/zlib.py",
"copies": "1",
"size": "2105",
"license": "bsd-3-clause",
"hash": -8844335162627404000,
"line_mean": 49.119047619,
"line_max": 86,
"alpha_frac": 0.7562945368,
"autogenerated": false,
"ratio": 4.4037... |
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.traces import capture_span
try:
from functools import lru_cache
except ImportError:
from cachetools.func import lru_cache
class PyLibMcInstrumentation(AbstractInstrumentedModule):
name = "pylibmc"
instru... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/pylibmc.py",
"copies": "1",
"size": "3572",
"license": "bsd-3-clause",
"hash": -5838370599033900000,
"line_mean": 38.2527472527,
"line_max": 87,
"alpha_frac": 0.6595744681,
"autogenerated": false,
"ratio": 4.... |
from elasticapm.instrumentation.packages.dbapi2 import (
ConnectionProxy,
CursorProxy,
DbApi2Instrumentation,
extract_signature,
)
from elasticapm.traces import capture_span
from elasticapm.utils.encoding import shorten
class SQLiteCursorProxy(CursorProxy):
provider_name = "sqlite"
def extra... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/sqlite.py",
"copies": "1",
"size": "3450",
"license": "bsd-3-clause",
"hash": 5145880143301188000,
"line_mean": 38.2045454545,
"line_max": 110,
"alpha_frac": 0.7005797101,
"autogenerated": false,
"ratio": 4.3... |
from elasticapm.instrumentation.packages.dbapi2 import (
ConnectionProxy,
CursorProxy,
DbApi2Instrumentation,
extract_signature,
)
from elasticapm.utils import default_ports
class MySQLCursorProxy(CursorProxy):
provider_name = "mysql"
def extract_signature(self, sql):
return extract_... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/mysql.py",
"copies": "1",
"size": "2597",
"license": "bsd-3-clause",
"hash": 4303306986499664000,
"line_mean": 40.8870967742,
"line_max": 102,
"alpha_frac": 0.7339237582,
"autogenerated": false,
"ratio": 4.25... |
from elasticapm.instrumentation.packages.dbapi2 import (
ConnectionProxy,
CursorProxy,
DbApi2Instrumentation,
extract_signature,
)
from elasticapm.utils import default_ports
class PyMSSQLCursorProxy(CursorProxy):
provider_name = "pymssql"
def extract_signature(self, sql):
return extr... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/pymssql.py",
"copies": "1",
"size": "2967",
"license": "bsd-3-clause",
"hash": 1985983942527879700,
"line_mean": 37.0384615385,
"line_max": 98,
"alpha_frac": 0.7020559488,
"autogenerated": false,
"ratio": 4.1... |
from elasticapm.metrics.base_metrics import MetricsSet
try:
import psutil
except ImportError:
raise ImportError("psutil not found. Install it to get system and process metrics")
class CPUMetricSet(MetricsSet):
def __init__(self, registry):
psutil.cpu_percent(interval=None)
self._process ... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/metrics/sets/cpu_psutil.py",
"copies": "1",
"size": "2902",
"license": "bsd-3-clause",
"hash": -4205775372601300000,
"line_mean": 47.3666666667,
"line_max": 102,
"alpha_frac": 0.7150241213,
"autogenerated": false,
"ratio": 4.10466760... |
from __future__ import absolute_import
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.traces import capture_span, execution_context
class Redis3CheckMixin(object):
instrument_list_3 = []
instrument_list = []
def get_instrument_list(self):
try:
... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/redis.py",
"copies": "1",
"size": "4327",
"license": "bsd-3-clause",
"hash": 1807489818456486000,
"line_mean": 41.4215686275,
"line_max": 114,
"alpha_frac": 0.7053385718,
"autogenerated": false,
"ratio": 4.22... |
from __future__ import absolute_import
from elasticapm.utils.wsgi import get_environ, get_headers, get_host
def test_get_headers_tuple_as_key():
result = dict(get_headers({("a", "tuple"): "foo"}))
assert result == {}
def test_get_headers_coerces_http_name():
result = dict(get_headers({"HTTP_ACCEPT": "... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/utils/wsgi/tests.py",
"copies": "1",
"size": "3867",
"license": "bsd-3-clause",
"hash": -4679328028833868000,
"line_mean": 36.1826923077,
"line_max": 103,
"alpha_frac": 0.7015774502,
"autogenerated": false,
"ratio": 3.5838739573679335,
... |
from __future__ import absolute_import
import django
from django.conf import settings
from django.conf.urls import url
from django.http import HttpResponse
from tests.contrib.django.testapp import views
def handler500(request):
if getattr(settings, "BREAK_THAT_500", False):
raise ValueError("handler500... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/contrib/django/testapp/urls.py",
"copies": "1",
"size": "3635",
"license": "bsd-3-clause",
"hash": 1219591392277866000,
"line_mean": 48.7945205479,
"line_max": 115,
"alpha_frac": 0.7339752407,
"autogenerated": false,
"ratio": 3.7167689161... |
from __future__ import absolute_import
import logging
import os
import platform
import stat
import mock
import pytest
from elasticapm.conf import (
Config,
ConfigurationError,
EnumerationValidator,
FileIsReadableValidator,
PrecisionValidator,
RegexValidator,
VersionedConfig,
_BoolCon... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/config/tests.py",
"copies": "1",
"size": "13988",
"license": "bsd-3-clause",
"hash": -5779659436168238000,
"line_mean": 32.5443645084,
"line_max": 118,
"alpha_frac": 0.6362596511,
"autogenerated": false,
"ratio": 3.5547649301143585,
"co... |
from __future__ import absolute_import
import logging
import os
get_logger = logging.getLogger
if os.environ.get("ELASTIC_APM_USE_STRUCTLOG", "").lower() == "true":
try:
import structlog
get_logger = structlog.get_logger
except ImportError:
# use stdlib logger to log warning
... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/utils/logging.py",
"copies": "1",
"size": "2038",
"license": "bsd-3-clause",
"hash": -1130278349705736400,
"line_mean": 42.3617021277,
"line_max": 90,
"alpha_frac": 0.7512266928,
"autogenerated": false,
"ratio": 4.308668076109937,
... |
from __future__ import absolute_import
import logging
import time
from django.contrib.auth.models import User
from django.http import HttpResponse, StreamingHttpResponse
from django.shortcuts import get_object_or_404, render
import elasticapm
from elasticapm.utils import compat
class MyException(Exception):
p... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/contrib/django/testapp/views.py",
"copies": "1",
"size": "4295",
"license": "bsd-3-clause",
"hash": -3006038600940299300,
"line_mean": 28.8263888889,
"line_max": 81,
"alpha_frac": 0.7164144354,
"autogenerated": false,
"ratio": 4.059546313... |
from __future__ import absolute_import
import pytest
import webob
from elasticapm.conf.constants import ERROR
from elasticapm.middleware import ElasticAPM
def example_app(environ, start_response):
raise ValueError("hello world")
def test_error_handler(elasticapm_client):
middleware = ElasticAPM(example_a... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/middleware/tests.py",
"copies": "1",
"size": "2934",
"license": "bsd-3-clause",
"hash": 236789748418234430,
"line_mean": 39.1917808219,
"line_max": 81,
"alpha_frac": 0.7280163599,
"autogenerated": false,
"ratio": 4.120786516853933,
"con... |
from __future__ import absolute_import
import pytest
from elasticapm.utils.disttracing import TraceParent
from tests.utils import assert_any_record_contains
@pytest.mark.parametrize("tracing_bits,expected", [("00", {"recorded": 0}), ("01", {"recorded": 1})])
def test_tracing_options(tracing_bits, expected):
he... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/utils/test_disttracing_header.py",
"copies": "1",
"size": "6623",
"license": "bsd-3-clause",
"hash": -9051808977670244000,
"line_mean": 43.75,
"line_max": 101,
"alpha_frac": 0.7387890684,
"autogenerated": false,
"ratio": 3.275469831849654... |
from __future__ import absolute_import
import re
import elasticapm
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.utils.logging import get_logger
logger = get_logger("elasticapm.instrument")
should_capture_body_re = re.compile("/(_search|_msearch|_count|_async_searc... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/elasticsearch.py",
"copies": "1",
"size": "4576",
"license": "bsd-3-clause",
"hash": 676845082113319300,
"line_mean": 41.7663551402,
"line_max": 103,
"alpha_frac": 0.6643356643,
"autogenerated": false,
"ratio... |
from opentracing.span import Span as OTSpanBase
from opentracing.span import SpanContext as OTSpanContextBase
from elasticapm import traces
from elasticapm.utils import compat, get_url_dict
from elasticapm.utils.logging import get_logger
try:
# opentracing-python 2.1+
from opentracing import logs as ot_logs
... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/contrib/opentracing/span.py",
"copies": "1",
"size": "5900",
"license": "bsd-3-clause",
"hash": 210392333603895000,
"line_mean": 42.3823529412,
"line_max": 92,
"alpha_frac": 0.6303389831,
"autogenerated": false,
"ratio": 3.9517749497... |
import aiohttp
from aiohttp.web import HTTPException, Response, middleware
import elasticapm
from elasticapm import get_client
from elasticapm.conf import constants
from elasticapm.contrib.aiohttp.utils import get_data_from_request, get_data_from_response
from elasticapm.utils.disttracing import TraceParent
class A... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/contrib/aiohttp/middleware.py",
"copies": "1",
"size": "4968",
"license": "bsd-3-clause",
"hash": -1617843311633864000,
"line_mean": 47.2330097087,
"line_max": 117,
"alpha_frac": 0.6612318841,
"autogenerated": false,
"ratio": 4.47567... |
import ctypes
import itertools
import re
from elasticapm.conf import constants
from elasticapm.utils import compat
from elasticapm.utils.logging import get_logger
logger = get_logger("elasticapm.utils")
class TraceParent(object):
__slots__ = ("version", "trace_id", "span_id", "trace_options", "tracestate", "tr... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/utils/disttracing.py",
"copies": "1",
"size": "9931",
"license": "bsd-3-clause",
"hash": 4277756320746965000,
"line_mean": 40.3791666667,
"line_max": 119,
"alpha_frac": 0.6460577988,
"autogenerated": false,
"ratio": 4.190295358649789... |
import datetime
import os
import pytest
from elasticapm.conf.constants import TRANSACTION
pymongo = pytest.importorskip("pymongo")
pytestmark = [pytest.mark.mongodb]
if "MONGODB_HOST" not in os.environ:
pytestmark.append(pytest.mark.skip("Skipping mongodb tests, no MONGODB_HOST environment variable set"))
... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/instrumentation/pymongo_tests.py",
"copies": "1",
"size": "14842",
"license": "bsd-3-clause",
"hash": 3343020686450965500,
"line_mean": 44.9504643963,
"line_max": 107,
"alpha_frac": 0.6964694785,
"autogenerated": false,
"ratio": 3.5054322... |
import decimal
import re
from collections import namedtuple
def _starmatch_to_regex(pattern):
"""
This is a duplicate of starmatch_to_regex() in utils/__init__.py
Duplication to avoid circular imports
"""
options = re.DOTALL
# check if we are case sensitive
if pattern.startswith("(?-i)")... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/conf/constants.py",
"copies": "1",
"size": "3542",
"license": "bsd-3-clause",
"hash": -1720855541045945300,
"line_mean": 30.0701754386,
"line_max": 99,
"alpha_frac": 0.6905702993,
"autogenerated": false,
"ratio": 3.595939086294416,
... |
import elasticapm
from elasticapm.instrumentation.packages.asyncio.base import AsyncAbstractInstrumentedModule
from elasticapm.instrumentation.packages.elasticsearch import ElasticSearchConnectionMixin
class ElasticSearchAsyncConnection(ElasticSearchConnectionMixin, AsyncAbstractInstrumentedModule):
name = "elas... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/asyncio/elasticsearch.py",
"copies": "1",
"size": "2632",
"license": "bsd-3-clause",
"hash": -5275752525711098000,
"line_mean": 45.1754385965,
"line_max": 98,
"alpha_frac": 0.7393617021,
"autogenerated": false,... |
import functools
import os
from elasticapm.traces import execution_context
from elasticapm.utils import wrapt
from elasticapm.utils.logging import get_logger
logger = get_logger("elasticapm.instrument")
class ElasticAPMFunctionWrapper(wrapt.FunctionWrapper):
# used to differentiate between our own function wra... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/base.py",
"copies": "1",
"size": "11103",
"license": "bsd-3-clause",
"hash": 3385802258409999400,
"line_mean": 43.951417004,
"line_max": 120,
"alpha_frac": 0.6544177249,
"autogenerated": false,
"ratio": 4.612... |
import functools
import warnings
# https://wiki.python.org/moin/PythonDecoratorLibrary#Smart_deprecation_warnings_.28with_valid_filenames.2C_line_numbers.2C_etc..29
# Updated to work with 2.6 and 3+.
from elasticapm.utils import compat
def deprecated(alternative=None):
"""This is a decorator which can be used t... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/utils/deprecation.py",
"copies": "1",
"size": "2641",
"license": "bsd-3-clause",
"hash": -6443496107023444000,
"line_mean": 43.0166666667,
"line_max": 131,
"alpha_frac": 0.7171525937,
"autogenerated": false,
"ratio": 4.39434276206322... |
import functools
from elasticapm.conf.constants import LABEL_RE
from elasticapm.traces import DroppedSpan, capture_span, error_logger, execution_context
from elasticapm.utils import get_name_from_func
class async_capture_span(capture_span):
def __call__(self, func):
self.name = self.name or get_name_fro... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/contrib/asyncio/traces.py",
"copies": "1",
"size": "4164",
"license": "bsd-3-clause",
"hash": 3930787670127833600,
"line_mean": 39.427184466,
"line_max": 108,
"alpha_frac": 0.6649855908,
"autogenerated": false,
"ratio": 4.42978723404... |
import gzip
import random
import string
import time
import timeit
import mock
import pytest
from elasticapm.transport.base import Transport, TransportState
from elasticapm.transport.exceptions import TransportException
from elasticapm.utils import compat
from tests.fixtures import DummyTransport, TempStoreClient
fro... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/transports/test_base.py",
"copies": "1",
"size": "10064",
"license": "bsd-3-clause",
"hash": -1988228350080580000,
"line_mean": 38.6220472441,
"line_max": 107,
"alpha_frac": 0.701709062,
"autogenerated": false,
"ratio": 3.7650579872802097... |
import inspect
def get_me_a_test_frame():
a_local_var = 42
return inspect.currentframe()
def get_me_more_test_frames(count, func=None):
if count <= 1:
if func:
func()
return [inspect.currentframe()]
else:
return get_me_more_test_frames(count=count - 1, func=func)... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/utils/stacks/__init__.py",
"copies": "1",
"size": "1939",
"license": "bsd-3-clause",
"hash": -6427777056397832000,
"line_mean": 42.0888888889,
"line_max": 93,
"alpha_frac": 0.7436823105,
"autogenerated": false,
"ratio": 4.25219298245614,
... |
import itertools
from elasticapm.conf import constants
from elasticapm.instrumentation.packages.base import AbstractInstrumentedModule
from elasticapm.traces import DroppedSpan, capture_span, execution_context
from elasticapm.utils import default_ports, url_to_destination
from elasticapm.utils.disttracing import Trac... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/instrumentation/packages/urllib3.py",
"copies": "1",
"size": "6359",
"license": "bsd-3-clause",
"hash": 1786848442810478000,
"line_mean": 43.7816901408,
"line_max": 108,
"alpha_frac": 0.6880012581,
"autogenerated": false,
"ratio": 4.... |
import json
import os
import socket
import urllib3
def aws_metadata():
"""
Fetch AWS metadata from the local metadata server. If metadata server is
not found, return an empty dictionary
"""
http = urllib3.PoolManager()
try:
# This will throw an error if the metadata server isn't ava... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/utils/cloud.py",
"copies": "1",
"size": "6434",
"license": "bsd-3-clause",
"hash": -6161225308610313000,
"line_mean": 37.2976190476,
"line_max": 118,
"alpha_frac": 0.6134597451,
"autogenerated": false,
"ratio": 4.394808743169399,
"... |
import logging
import os
import re
import resource
import threading
from elasticapm.metrics.base_metrics import MetricsSet
SYS_STATS = "/proc/stat"
MEM_STATS = "/proc/meminfo"
PROC_STATS = "/proc/self/stat"
CGROUP1_MEMORY_LIMIT = "memory.limit_in_bytes"
CGROUP1_MEMORY_USAGE = "memory.usage_in_bytes"
CGROUP1_MEMORY_S... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "elasticapm/metrics/sets/cpu_linux.py",
"copies": "1",
"size": "11817",
"license": "bsd-3-clause",
"hash": 5349807994070634000,
"line_mean": 44.45,
"line_max": 117,
"alpha_frac": 0.5814504527,
"autogenerated": false,
"ratio": 3.8756969498196128,... |
import mock
import pytest
from elasticapm.conf import constants
from elasticapm.conf.constants import TRANSACTION
from elasticapm.traces import capture_span
from elasticapm.utils.compat import urlparse
from elasticapm.utils.disttracing import TraceParent
try:
from urllib.error import HTTPError, URLError
from... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/instrumentation/urllib_tests.py",
"copies": "1",
"size": "11524",
"license": "bsd-3-clause",
"hash": -1871823718752377000,
"line_mean": 42.3233082707,
"line_max": 119,
"alpha_frac": 0.7190211732,
"autogenerated": false,
"ratio": 3.7198192... |
import mock
import pytest
from elasticapm.conf import constants
from elasticapm.instrumentation.packages.botocore import BotocoreInstrumentation
boto3 = pytest.importorskip("boto3")
pytestmark = pytest.mark.boto3
@mock.patch("botocore.endpoint.Endpoint.make_request")
def test_botocore_instrumentation(mock_make_r... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/instrumentation/botocore_tests.py",
"copies": "1",
"size": "4858",
"license": "bsd-3-clause",
"hash": -1225714635661801700,
"line_mean": 41.6140350877,
"line_max": 106,
"alpha_frac": 0.7235487855,
"autogenerated": false,
"ratio": 3.745566... |
import mock
import pytest
from elasticapm.utils import compat
try:
from werkzeug.datastructures import MultiDict
has_multidict = True
except ImportError:
has_multidict = False
try:
from django.utils.datastructures import MultiValueDict
has_multivaluedict = True
except ImportError:
has_mult... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/utils/compat_tests.py",
"copies": "1",
"size": "3525",
"license": "bsd-3-clause",
"hash": 5740182162988330000,
"line_mean": 39.0568181818,
"line_max": 92,
"alpha_frac": 0.6703546099,
"autogenerated": false,
"ratio": 3.6190965092402463,
... |
import mock
import urllib3
import elasticapm.utils.cloud
GCP_DATA = b"""{
"instance": {
"id": 4306570268266786072,
"machineType": "projects/513326162531/machineTypes/n1-standard-1",
"name": "basepi-test",
"zone": "projects/513326162531/zones/us-west3-a"
},
"project": {"num... | {
"repo_name": "beniwohli/apm-agent-python",
"path": "tests/utils/cloud_tests.py",
"copies": "1",
"size": "4740",
"license": "bsd-3-clause",
"hash": 8894549616221116000,
"line_mean": 34.6390977444,
"line_max": 90,
"alpha_frac": 0.6622362869,
"autogenerated": false,
"ratio": 3.4076204169662114,
"... |
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