prompt large_stringlengths 72 9.34k | completion large_stringlengths 0 7.61k |
|---|---|
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>import os
class Config(object):
DEBUG = False
TESTING = False
CSRF_ENABLED = True
SECRET_KEY = "super_secret_key"
SQLALCHEMY_DATABASE_URI = os.environ['DATABASE_URL']
class ProductionConfig(Config):
DEBUG = False
SECRET_KEY = os.environ['... | DEVELOPMENT = True
DEBUG = True |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>import os
class Config(object):
DEBUG = False
TESTING = False
CSRF_ENABLED = True
SECRET_KEY = "super_secret_key"
SQLALCHEMY_DATABASE_URI = os.environ['DATABASE_URL']
class ProductionConfig(Config):
DEBUG = False
SECRET_KEY = os.environ['... | TESTING = True |
<|file_name|>test_login.py<|end_file_name|><｜fim▁begin｜><｜fim▁hole｜>@pytest.fixture
def driver(request):
wd = webdriver.Firefox(capabilities={"marionette": True})
#(desired_capabilities={"chromeOptions": {"args": ["--start-fullscreen"]}})
request.addfinalizer(wd.quit)
return wd
def test_example(driver... | import pytest
from selenium import webdriver
|
<|file_name|>test_login.py<|end_file_name|><｜fim▁begin｜>import pytest
from selenium import webdriver
@pytest.fixture
def driver(request):
<|fim_middle|>
def test_example(driver):
driver.get("http://localhost/litecart/admin/")
driver.find_element_by_xpath("//input[@name='username']").send_keys("admin")
... | wd = webdriver.Firefox(capabilities={"marionette": True})
#(desired_capabilities={"chromeOptions": {"args": ["--start-fullscreen"]}})
request.addfinalizer(wd.quit)
return wd |
<|file_name|>test_login.py<|end_file_name|><｜fim▁begin｜>import pytest
from selenium import webdriver
@pytest.fixture
def driver(request):
wd = webdriver.Firefox(capabilities={"marionette": True})
#(desired_capabilities={"chromeOptions": {"args": ["--start-fullscreen"]}})
request.addfinalizer(wd.quit)
... | driver.get("http://localhost/litecart/admin/")
driver.find_element_by_xpath("//input[@name='username']").send_keys("admin")
driver.find_element_by_xpath("//input[@name='password']").send_keys("admin")
driver.find_element_by_xpath("//button[@name='login']").click() |
<|file_name|>test_login.py<|end_file_name|><｜fim▁begin｜>import pytest
from selenium import webdriver
@pytest.fixture
def <|fim_middle|>(request):
wd = webdriver.Firefox(capabilities={"marionette": True})
#(desired_capabilities={"chromeOptions": {"args": ["--start-fullscreen"]}})
request.addfinalizer(wd.qu... | driver |
<|file_name|>test_login.py<|end_file_name|><｜fim▁begin｜>import pytest
from selenium import webdriver
@pytest.fixture
def driver(request):
wd = webdriver.Firefox(capabilities={"marionette": True})
#(desired_capabilities={"chromeOptions": {"args": ["--start-fullscreen"]}})
request.addfinalizer(wd.quit)
... | test_example |
<|file_name|>setup.py<|end_file_name|><｜fim▁begin｜># coding: utf-8
import sys
from setuptools import setup, find_packages
NAME = "pollster"
VERSION = "2.0.2"
# To install the library, run the following
#
# python setup.py install
#
# prerequisite: setuptools
# http://pypi.python.org/pypi/setuptools
<｜fim▁hole｜>REQUI... | |
<|file_name|>split.py<|end_file_name|><｜fim▁begin｜>s="the quick brown fox jumped over the lazy dog"
t = s.split(" ")
for v in t:
print(v)
r = s.split("e")
for v in r:
print(v)
x = s.split()
for v in x:
print(v)
# 2-arg version of split not supported
# y = s.split(" ",7)
# for v in y:<｜fim▁hole｜><｜fim▁e... | # print v |
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | """
|
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | ""Find in files DockWidget"""
CONF_SECTION = 'ipython'
def __init__(self, parent, args, kernel_widget, kernel_name):
super(IPythonPlugin, self).__init__(parent)
self.kernel_widget = kernel_widget
self.kernel_name = kernel_name
self.ipython_widget = create_wi... |
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | uper(IPythonPlugin, self).__init__(parent)
self.kernel_widget = kernel_widget
self.kernel_name = kernel_name
self.ipython_widget = create_widget(argv=args.split())
layout = QHBoxLayout()
layout.addWidget(self.ipython_widget)
self.setLayout(layo... |
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | ""Toggle widget visibility"""
if self.dockwidget:
self.dockwidget.setVisible(state)
|
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | ""Return widget title"""
return "IPython (%s) - Experimental!" % self.kernel_name
|
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | ""
Return the widget to give focus to when
this plugin's dockwidget is raised on top-level
"""
return self.ipython_widget._control
|
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | ""Return a list of actions related to plugin"""
return []
|
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | ""Register plugin in Spyder's main window"""
self.main.add_dockwidget(self)
|
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | ""Refresh widget"""
pass
|
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | ""Perform actions before parent main window is closed"""
return True
|
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | elf.dockwidget.setVisible(state)
|
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | _init__( |
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | oggle( |
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | et_plugin_title( |
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | et_focus_widget( |
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | et_plugin_actions( |
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | egister_plugin( |
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | efresh_plugin( |
<|file_name|>ipython.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
#
# Copyright © 2011 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""IPython v0.11+ Plugin"""
from spyderlib.qt.QtGui import QHBoxLayout
# Local imports
from spyderlib.wid... | losing_plugin( |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | self.client.get(url_for("user.logout"))
|
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
<|fim_middle|>
<｜fim▁end｜> | DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI = "sqlite:///" + DB_FILE[1]
LOGGING = {"version": 1}
TESTING = True
WTF_CSRF_ENABLED = False
USER_ENABLE_LOGIN_WITHOUT_CONFIRM = True
def create_app(self):
ret = iis.create_app(self.__class__)
app = ret[0]
self.use... |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | ret = iis.create_app(self.__class__)
app = ret[0]
self.user_manager = ret[1]
return app |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | db.create_all()
self.create_user("admin", "passW1") |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | db.session.remove()
db.drop_all() |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | username = username or "admin"
password = password or "passW1"
self.client.post(url_for('user.login'), data=dict(
username=username,
password=password
), follow_redirects=False)
return User.query.filter_by(username=username).one() |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | self.client.get(url_for("user.logout")) |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | user = User(username=username,
password=self.user_manager.hash_password(password),
email=username + "@localhost",
confirmed_at=datetime.fromtimestamp(0.0),
active=True)
db.session.add(user)
db.session.commit()
... |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | self.logout()
res = self.client.get(url)
self.assertEqual(302, res.status_code)
self.assertIn(url_for('user.login'), res.headers['Location']) |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | create_app |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | setUp |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | tearDown |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | login |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | logout |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | create_user |
<|file_name|>base.py<|end_file_name|><｜fim▁begin｜>import tempfile
from datetime import datetime
import flask_testing
from flask import url_for
import iis
from iis.models import User
from iis.extensions import db
class BaseTestCase(flask_testing.TestCase):
DB_FILE = tempfile.mkstemp()
SQLALCHEMY_DATABASE_URI... | assertLoginRequired |
<|file_name|>package.py<|end_file_name|><｜fim▁begin｜># Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class XorgServer(AutotoolsPackage, XorgPackage)... | |
<|file_name|>package.py<|end_file_name|><｜fim▁begin｜># Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class XorgServer(AutotoolsPackage, XorgPackage)... | """X.Org Server is the free and open source implementation of the display
server for the X Window System stewarded by the X.Org Foundation."""
homepage = "http://cgit.freedesktop.org/xorg/xserver"
xorg_mirror_path = "xserver/xorg-server-1.18.99.901.tar.gz"
version('1.18.99.901', sha256='c8425163b5... |
<|file_name|>test_exteriorfuelequipment.py<|end_file_name|><｜fim▁begin｜>import os
import tempfile
import unittest
import logging
from pyidf import ValidationLevel
import pyidf
from pyidf.idf import IDF
from pyidf.exterior_equipment import ExteriorFuelEquipment
log = logging.getLogger(__name__)
class TestExteriorFuelE... |
idf = IDF()
idf.add(obj)
idf.save(self.path, check=False) |
<|file_name|>test_exteriorfuelequipment.py<|end_file_name|><｜fim▁begin｜>import os
import tempfile
import unittest
import logging
from pyidf import ValidationLevel
import pyidf
from pyidf.idf import IDF
from pyidf.exterior_equipment import ExteriorFuelEquipment
log = logging.getLogger(__name__)
class TestExteriorFuelE... | def setUp(self):
self.fd, self.path = tempfile.mkstemp()
def tearDown(self):
os.remove(self.path)
def test_create_exteriorfuelequipment(self):
pyidf.validation_level = ValidationLevel.error
obj = ExteriorFuelEquipment()
# alpha
var_name = "Name"
ob... |
<|file_name|>test_exteriorfuelequipment.py<|end_file_name|><｜fim▁begin｜>import os
import tempfile
import unittest
import logging
from pyidf import ValidationLevel
import pyidf
from pyidf.idf import IDF
from pyidf.exterior_equipment import ExteriorFuelEquipment
log = logging.getLogger(__name__)
class TestExteriorFuelE... | self.fd, self.path = tempfile.mkstemp() |
<|file_name|>test_exteriorfuelequipment.py<|end_file_name|><｜fim▁begin｜>import os
import tempfile
import unittest
import logging
from pyidf import ValidationLevel
import pyidf
from pyidf.idf import IDF
from pyidf.exterior_equipment import ExteriorFuelEquipment
log = logging.getLogger(__name__)
class TestExteriorFuelE... | os.remove(self.path) |
<|file_name|>test_exteriorfuelequipment.py<|end_file_name|><｜fim▁begin｜>import os
import tempfile
import unittest
import logging
from pyidf import ValidationLevel
import pyidf
from pyidf.idf import IDF
from pyidf.exterior_equipment import ExteriorFuelEquipment
log = logging.getLogger(__name__)
class TestExteriorFuelE... | pyidf.validation_level = ValidationLevel.error
obj = ExteriorFuelEquipment()
# alpha
var_name = "Name"
obj.name = var_name
# alpha
var_fuel_use_type = "Electricity"
obj.fuel_use_type = var_fuel_use_type
# object-list
var_schedule_name = "o... |
<|file_name|>test_exteriorfuelequipment.py<|end_file_name|><｜fim▁begin｜>import os
import tempfile
import unittest
import logging
from pyidf import ValidationLevel
import pyidf
from pyidf.idf import IDF
from pyidf.exterior_equipment import ExteriorFuelEquipment
log = logging.getLogger(__name__)
class TestExteriorFuelE... | setUp |
<|file_name|>test_exteriorfuelequipment.py<|end_file_name|><｜fim▁begin｜>import os
import tempfile
import unittest
import logging
from pyidf import ValidationLevel
import pyidf
from pyidf.idf import IDF
from pyidf.exterior_equipment import ExteriorFuelEquipment
log = logging.getLogger(__name__)
class TestExteriorFuelE... | tearDown |
<|file_name|>test_exteriorfuelequipment.py<|end_file_name|><｜fim▁begin｜>import os
import tempfile
import unittest
import logging
from pyidf import ValidationLevel
import pyidf
from pyidf.idf import IDF
from pyidf.exterior_equipment import ExteriorFuelEquipment
log = logging.getLogger(__name__)
class TestExteriorFuelE... | test_create_exteriorfuelequipment |
<|file_name|>bowtie2.py<|end_file_name|><｜fim▁begin｜>import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
class Bowtie2Aligner(BaseAligner, IPlugin):
def run(self):
"""
Map READS to CONTIGS a... | if len(reads) == 2:
cmd_args += ['-1', reads[0], '-2', reads[1]] |
<|file_name|>bowtie2.py<|end_file_name|><｜fim▁begin｜>import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
class Bowtie2Aligner(BaseAligner, IPlugin):
<|fim_middle|>
<｜fim▁end｜> | def run(self):
"""
Map READS to CONTIGS and return alignment.
Set MERGED_PAIR to True if reads[1] is a merged
paired end file
"""
contig_file = self.data.contigfiles[0]
reads = self.data.readfiles
## Index contigs
prefix = os.path.join(self.... |
<|file_name|>bowtie2.py<|end_file_name|><｜fim▁begin｜>import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
class Bowtie2Aligner(BaseAligner, IPlugin):
def run(self):
<|fim_middle|>
<｜fim▁end｜> | """
Map READS to CONTIGS and return alignment.
Set MERGED_PAIR to True if reads[1] is a merged
paired end file
"""
contig_file = self.data.contigfiles[0]
reads = self.data.readfiles
## Index contigs
prefix = os.path.join(self.outpath, 'bt2')
... |
<|file_name|>bowtie2.py<|end_file_name|><｜fim▁begin｜>import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
class Bowtie2Aligner(BaseAligner, IPlugin):
def run(self):
"""
Map READS to CONTIGS a... | cmd_args += ['-1', reads[0], '-2', reads[1]] |
<|file_name|>bowtie2.py<|end_file_name|><｜fim▁begin｜>import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
class Bowtie2Aligner(BaseAligner, IPlugin):
def run(self):
"""
Map READS to CONTIGS a... | cmd_args += ['-U', reads[0]] |
<|file_name|>bowtie2.py<|end_file_name|><｜fim▁begin｜>import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
class Bowtie2Aligner(BaseAligner, IPlugin):
def run(self):
"""
Map READS to CONTIGS a... | raise Exception('Bowtie plugin error') |
<|file_name|>bowtie2.py<|end_file_name|><｜fim▁begin｜>import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
class Bowtie2Aligner(BaseAligner, IPlugin):
def run(self):
"""
Map READS to CONTIGS a... | raise Exception('Unable to complete alignment') |
<|file_name|>bowtie2.py<|end_file_name|><｜fim▁begin｜>import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
class Bowtie2Aligner(BaseAligner, IPlugin):
def run(self):
"""
Map READS to CONTIGS a... | bamfile = os.path.join(self.outpath, '{}_{}.bam'.format(os.path.basename(contig_file), i))
self.arast_popen(['samtools', 'merge', bamfile] + bamfiles)
if not os.path.exists(bamfile):
raise Exception('Unable to complete alignment') |
<|file_name|>bowtie2.py<|end_file_name|><｜fim▁begin｜>import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
class Bowtie2Aligner(BaseAligner, IPlugin):
def run(self):
"""
Map READS to CONTIGS a... | raise Exception('Unable to complete alignment') |
<|file_name|>bowtie2.py<|end_file_name|><｜fim▁begin｜>import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
class Bowtie2Aligner(BaseAligner, IPlugin):
def run(self):
"""
Map READS to CONTIGS a... | bamfile = bamfiles[0]
if not os.path.exists(bamfile):
raise Exception('Unable to complete alignment') |
<|file_name|>bowtie2.py<|end_file_name|><｜fim▁begin｜>import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
class Bowtie2Aligner(BaseAligner, IPlugin):
def run(self):
"""
Map READS to CONTIGS a... | raise Exception('Unable to complete alignment') |
<|file_name|>bowtie2.py<|end_file_name|><｜fim▁begin｜>import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
class Bowtie2Aligner(BaseAligner, IPlugin):
def <|fim_middle|>(self):
"""
Map READS t... | run |
<|file_name|>tumblrserv.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
## tumblrserv.py implements a Tumblr (http://www.tumblr.com) markup parsing
## engine and compatible webserver.
##
## Version: 0.2 final
##
## Copyright (C) 2009 Jeremy Herbert
## Contact mailto:jeremy@jeremyherbert.net
##
## ... | |
<|file_name|>tumblrserv.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
## tumblrserv.py implements a Tumblr (http://www.tumblr.com) markup parsing
## engine and compatible webserver.
##
## Version: 0.2 final
##
## Copyright (C) 2009 Jeremy Herbert
## Contact mailto:jeremy@jeremyherbert.net
##
## ... | arguments.pop(0) |
<|file_name|>tumblrserv.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
## tumblrserv.py implements a Tumblr (http://www.tumblr.com) markup parsing
## engine and compatible webserver.
##
## Version: 0.2 final
##
## Copyright (C) 2009 Jeremy Herbert
## Contact mailto:jeremy@jeremyherbert.net
##
## ... | if os.path.exists(next_arg(arguments, '--config')):
config_path = next_arg(arguments, '--config') |
<|file_name|>tumblrserv.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
## tumblrserv.py implements a Tumblr (http://www.tumblr.com) markup parsing
## engine and compatible webserver.
##
## Version: 0.2 final
##
## Copyright (C) 2009 Jeremy Herbert
## Contact mailto:jeremy@jeremyherbert.net
##
## ... | config_path = next_arg(arguments, '--config') |
<|file_name|>tumblrserv.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
## tumblrserv.py implements a Tumblr (http://www.tumblr.com) markup parsing
## engine and compatible webserver.
##
## Version: 0.2 final
##
## Copyright (C) 2009 Jeremy Herbert
## Contact mailto:jeremy@jeremyherbert.net
##
## ... | pull_data( next_arg(arguments, '--pull-data') ) |
<|file_name|>tumblrserv.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
## tumblrserv.py implements a Tumblr (http://www.tumblr.com) markup parsing
## engine and compatible webserver.
##
## Version: 0.2 final
##
## Copyright (C) 2009 Jeremy Herbert
## Contact mailto:jeremy@jeremyherbert.net
##
## ... | if not os.path.exists("themes/" + next_arg(arguments, '--theme') + '.thtml'):
err_exit("The theme file %s.thtml does not exist in the themes\
directory." % next_arg(arguments, '--theme'))
config['defaults']['theme_name'] = next_arg(arguments, '--theme') |
<|file_name|>tumblrserv.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
## tumblrserv.py implements a Tumblr (http://www.tumblr.com) markup parsing
## engine and compatible webserver.
##
## Version: 0.2 final
##
## Copyright (C) 2009 Jeremy Herbert
## Contact mailto:jeremy@jeremyherbert.net
##
## ... | err_exit("The theme file %s.thtml does not exist in the themes\
directory." % next_arg(arguments, '--theme')) |
<|file_name|>tumblrserv.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
## tumblrserv.py implements a Tumblr (http://www.tumblr.com) markup parsing
## engine and compatible webserver.
##
## Version: 0.2 final
##
## Copyright (C) 2009 Jeremy Herbert
## Contact mailto:jeremy@jeremyherbert.net
##
## ... | if not has_keys(config['publishing_info'], \
( 'url', 'username', 'password' )):
err_exit('The configuration file is missing some critical publishing\
information. Please make sure you have specified your url, username and\
password.')
publish_theme(config['publishing_info']['url'],\
con... |
<|file_name|>tumblrserv.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
## tumblrserv.py implements a Tumblr (http://www.tumblr.com) markup parsing
## engine and compatible webserver.
##
## Version: 0.2 final
##
## Copyright (C) 2009 Jeremy Herbert
## Contact mailto:jeremy@jeremyherbert.net
##
## ... | err_exit('The configuration file is missing some critical publishing\
information. Please make sure you have specified your url, username and\
password.') |
<|file_name|>tumblrserv.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
## tumblrserv.py implements a Tumblr (http://www.tumblr.com) markup parsing
## engine and compatible webserver.
##
## Version: 0.2 final
##
## Copyright (C) 2009 Jeremy Herbert
## Contact mailto:jeremy@jeremyherbert.net
##
## ... | config['optimisations']['do_nothing'] = True |
<|file_name|>asyncio_example.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
import time
from nicfit.aio import Application
async def _main(args):
print(args)
print("Sleeping 2...")
time.sleep(2)
print("Sleeping 0...")
return 0<｜fim▁hole｜>def atexit():
print("atexit")
app = Application(... | |
<|file_name|>asyncio_example.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
import time
from nicfit.aio import Application
async def _main(args):
<|fim_middle|>
def atexit():
print("atexit")
app = Application(_main, atexit=atexit)
app.arg_parser.add_argument("--example", help="Example cli")
app.run(... | print(args)
print("Sleeping 2...")
time.sleep(2)
print("Sleeping 0...")
return 0 |
<|file_name|>asyncio_example.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
import time
from nicfit.aio import Application
async def _main(args):
print(args)
print("Sleeping 2...")
time.sleep(2)
print("Sleeping 0...")
return 0
def atexit():
<|fim_middle|>
app = Application(_main, ate... | print("atexit") |
<|file_name|>asyncio_example.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
import time
from nicfit.aio import Application
async def <|fim_middle|>(args):
print(args)
print("Sleeping 2...")
time.sleep(2)
print("Sleeping 0...")
return 0
def atexit():
print("atexit")
app = Application(_... | _main |
<|file_name|>asyncio_example.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
import time
from nicfit.aio import Application
async def _main(args):
print(args)
print("Sleeping 2...")
time.sleep(2)
print("Sleeping 0...")
return 0
def <|fim_middle|>():
print("atexit")
app = Application(_m... | atexit |
<|file_name|>linked_tap.py<|end_file_name|><｜fim▁begin｜>from __future__ import print_function
import numpy as np
from bokeh.client import push_session
from bokeh.io import curdoc
from bokeh.models import (ColumnDataSource, DataRange1d, Plot, Circle, WidgetBox,
Row, Button, TapTool)
N = 9
... | |
<|file_name|>linked_tap.py<|end_file_name|><｜fim▁begin｜>from __future__ import print_function
import numpy as np
from bokeh.client import push_session
from bokeh.io import curdoc
from bokeh.models import (ColumnDataSource, DataRange1d, Plot, Circle, WidgetBox,
Row, Button, TapTool)
N = 9
... | color = ["blue"]*N
if inds['1d']['indices']:
indices = inds['1d']['indices']
for i in indices:
color[i] = "red"
source2.data["color"] = color |
<|file_name|>linked_tap.py<|end_file_name|><｜fim▁begin｜>from __future__ import print_function
import numpy as np
from bokeh.client import push_session
from bokeh.io import curdoc
from bokeh.models import (ColumnDataSource, DataRange1d, Plot, Circle, WidgetBox,
Row, Button, TapTool)
N = 9
... | inds = inds['1d']['indices']
if inds:
[index] = inds
radius = [0.1]*N
radius[index] = 0.2
else:
radius = [0.1]*N
source1.data["radius"] = radius |
<|file_name|>linked_tap.py<|end_file_name|><｜fim▁begin｜>from __future__ import print_function
import numpy as np
from bokeh.client import push_session
from bokeh.io import curdoc
from bokeh.models import (ColumnDataSource, DataRange1d, Plot, Circle, WidgetBox,
Row, Button, TapTool)
N = 9
... | source1.selected = {
'0d': {'flag': False, 'indices': []},
'1d': {'indices': []},
'2d': {'indices': {}}
}
source2.selected = {
'0d': {'flag': False, 'indices': []},
'1d': {'indices': []},
'2d': {'indices': {}}
} |
<|file_name|>linked_tap.py<|end_file_name|><｜fim▁begin｜>from __future__ import print_function
import numpy as np
from bokeh.client import push_session
from bokeh.io import curdoc
from bokeh.models import (ColumnDataSource, DataRange1d, Plot, Circle, WidgetBox,
Row, Button, TapTool)
N = 9
... | indices = inds['1d']['indices']
for i in indices:
color[i] = "red" |
<|file_name|>linked_tap.py<|end_file_name|><｜fim▁begin｜>from __future__ import print_function
import numpy as np
from bokeh.client import push_session
from bokeh.io import curdoc
from bokeh.models import (ColumnDataSource, DataRange1d, Plot, Circle, WidgetBox,
Row, Button, TapTool)
N = 9
... | [index] = inds
radius = [0.1]*N
radius[index] = 0.2 |
<|file_name|>linked_tap.py<|end_file_name|><｜fim▁begin｜>from __future__ import print_function
import numpy as np
from bokeh.client import push_session
from bokeh.io import curdoc
from bokeh.models import (ColumnDataSource, DataRange1d, Plot, Circle, WidgetBox,
Row, Button, TapTool)
N = 9
... | radius = [0.1]*N |
<|file_name|>linked_tap.py<|end_file_name|><｜fim▁begin｜>from __future__ import print_function
import numpy as np
from bokeh.client import push_session
from bokeh.io import curdoc
from bokeh.models import (ColumnDataSource, DataRange1d, Plot, Circle, WidgetBox,
Row, Button, TapTool)
N = 9
... | print("\npress ctrl-C to exit")
session = push_session(document)
session.show()
session.loop_until_closed() |
<|file_name|>linked_tap.py<|end_file_name|><｜fim▁begin｜>from __future__ import print_function
import numpy as np
from bokeh.client import push_session
from bokeh.io import curdoc
from bokeh.models import (ColumnDataSource, DataRange1d, Plot, Circle, WidgetBox,
Row, Button, TapTool)
N = 9
... | on_selection_change1 |
<|file_name|>linked_tap.py<|end_file_name|><｜fim▁begin｜>from __future__ import print_function
import numpy as np
from bokeh.client import push_session
from bokeh.io import curdoc
from bokeh.models import (ColumnDataSource, DataRange1d, Plot, Circle, WidgetBox,
Row, Button, TapTool)
N = 9
... | on_selection_change2 |
<|file_name|>linked_tap.py<|end_file_name|><｜fim▁begin｜>from __future__ import print_function
import numpy as np
from bokeh.client import push_session
from bokeh.io import curdoc
from bokeh.models import (ColumnDataSource, DataRange1d, Plot, Circle, WidgetBox,
Row, Button, TapTool)
N = 9
... | on_reset_click |
<|file_name|>test_add_project.py<|end_file_name|><｜fim▁begin｜>from model.project import Project
def test_add_project(app):
project=Project(name="students_project", description="about Project")
try:
ind = app.project.get_project_list().index(project)<｜fim▁hole｜> app.project.delete_named_project(... | |
<|file_name|>test_add_project.py<|end_file_name|><｜fim▁begin｜>from model.project import Project
def test_add_project(app):
<|fim_middle|>
<｜fim▁end｜> | project=Project(name="students_project", description="about Project")
try:
ind = app.project.get_project_list().index(project)
app.project.delete_named_project(project)
except ValueError:
pass
old_projects = app.project.get_project_list()
app.project.create(project)
new_p... |
<|file_name|>test_add_project.py<|end_file_name|><｜fim▁begin｜>from model.project import Project
def <|fim_middle|>(app):
project=Project(name="students_project", description="about Project")
try:
ind = app.project.get_project_list().index(project)
app.project.delete_named_project(project)
... | test_add_project |
<|file_name|>test_source_notfound.py<|end_file_name|><｜fim▁begin｜>import source_navigation_steps
import functional_test
class TestSourceInterfaceNotFound(<｜fim▁hole｜> self._source_not_found()<｜fim▁end｜> | functional_test.FunctionalTest,
source_navigation_steps.SourceNavigationStepsMixin):
def test_not_found(self): |
<|file_name|>test_source_notfound.py<|end_file_name|><｜fim▁begin｜>import source_navigation_steps
import functional_test
class TestSourceInterfaceNotFound(
functional_test.FunctionalTest,
source_navigation_steps.SourceNavigationStepsMixin):
<|fim_middle|>
<｜fim▁end｜> | def test_not_found(self):
self._source_not_found() |
<|file_name|>test_source_notfound.py<|end_file_name|><｜fim▁begin｜>import source_navigation_steps
import functional_test
class TestSourceInterfaceNotFound(
functional_test.FunctionalTest,
source_navigation_steps.SourceNavigationStepsMixin):
def test_not_found(self):
<|fim_middle|>
<｜fim▁e... | self._source_not_found() |
<|file_name|>test_source_notfound.py<|end_file_name|><｜fim▁begin｜>import source_navigation_steps
import functional_test
class TestSourceInterfaceNotFound(
functional_test.FunctionalTest,
source_navigation_steps.SourceNavigationStepsMixin):
def <|fim_middle|>(self):
self._source_not_found(... | test_not_found |
<|file_name|>runtests.py<|end_file_name|><｜fim▁begin｜>import unittest
import os
from ui import main
print os.getcwd()
class TestMain(unittest.TestCase):
def setUp(self):
self.m = main.MainWindow()
def test_mainWindow(self):
assert(self.m)
def test_dataframe(self):
import ... | datasets = ['iris','Nile','morley','freeny','sleep','mtcars']
for a in datasets:
main.rsession.r('%s=%s' % (a,a)) |
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