Instruction stringlengths 362 7.83k | output_code stringlengths 1 945 |
|---|---|
Continue the code snippet: <|code_start|> self.fast = TssJsStarterThread(self.project)
self.fast.start()
self._wait_for_finish_and_notify_user()
def kill(self):
""" Trigger killing of adapter, tss.js and queue. """
Debug('tss+', "Killing tss.js process and adapter thread (f... | MESSAGE.show('Typescript project intialized for file : %s' % self.project.tsconfigfile, True, with_panel=False) |
Predict the next line after this snippet: <|code_start|> Keeps two tss.js Processes and adapters for each project root.
Process SLOW is for slow commands like tss>errors which can last more than 5s easily.
Process FAST is for fast reacting commands eg. for autocompletion or type.
"""
def... | Debug('notify', 'starting tsserver ' + self.project.tsconfigfile) |
Continue the code snippet: <|code_start|> """
commands_to_remove = []
for possible_duplicate in self.middleware_queue: # from old to new
if possible_duplicate.id == command.id:
commands_to_remove.append(possible_duplicate)
if len(commands_to_remove) > 0:
... | self.stdin.write(encode(async_command.command)) |
Given the following code snippet before the placeholder: <|code_start|> "I have tried this path: %s" % node_path,
"Please install nodejs and/or set node_path in the project or plugin settings to the actual executable.",
"If you are on windows and just have inst... | tss_path = get_tss_path() |
Using the snippet: <|code_start|> self.error = "\n".join(["Could not find nodejs.",
"I have tried this path: %s" % node_path,
"Please install nodejs and/or set node_path in the project or plugin settings to the actual executable.",
"If you are on wi... | node_path = default_node_path(self.project.get_setting('node_path')) |
Here is a snippet: <|code_start|>
return (i, dir)
# ----------------------------------------- THREAD: (tss.js and adapter starter) ------------------------ #
class TssJsStarterThread(Thread):
"""
After starting, this class provides the methods and fields
* send_async_command(...)
... | kwargs = get_kwargs(stderr=False) |
Given the code snippet: <|code_start|> def start_tss_processes(self):
"""
Start tss.js (2 times).
Displays message to user while starting and calls project.on_services_started() afterwards
"""
Debug('notify', 'starting tsserver ' + self.project.tsconfigfile)
se... | set_plugin_temporarily_disabled() |
Predict the next line for this snippet: <|code_start|> return False
return line_text.endswith(".") or partial_completion()
def get_col_after_last_dot(line_text):
return line_text.rfind(".") + 1
class Completion(object):
completion_chars = ['.']#['.',':']
completion_list = []
interface = ... | Debug('error', 'Completion request failed: %s' % tss_result_json) |
Given the following code snippet before the placeholder: <|code_start|> return
Debug('autocomplete', " -> command to sublime to now show autocomplete box with prepared list" )
# this will trigger Listener.on_query_completions
# but on_query_compl... | kindModifiers = get_prefix(entry['kindModifiers']) |
Based on the snippet: <|code_start|> for entry in entries:
if self.interface and entry['kind'] != 'primitive type' and entry['kind'] != 'interface' : continue
key = self._get_list_key(entry)
value = self._get_list_value(entry)
self.completion_list.append((key,value... | is_member = is_member_completion( get_content_of_line_at(view, cursor_pos) ) |
Based on the snippet: <|code_start|> previous_file = filename
text.append("\n%i >" % e['start']['line'])
text.append(re.sub(r'^.*?:\s*', '', e['text'].replace('\r','')))
line += 1
a = (e['start']['line']-1, e['start']['character']-1)
b = (e['end']['line']-1, e['end']... | key = fn2k(file_name) |
Predict the next line after this snippet: <|code_start|>
#{'lineText': ' let total = 0;',
# 'file': '/home/daniel/.config/sublime-text-3/Packages/ArcticTypescript/tests/TDDTesting/main.ts',
# 'min': {'character': 13,
# 'line': 43},
# 'lim': {'character': 18,
# 'line': 43},
# 'ref': {'textSpan': ... | Debug('refactor', self.refs_by_file) |
Based on the snippet: <|code_start|>
class Refactor():
def __init__(self, edit, project, refs, old_name, new_name):
Thread.__init__(self)
self.project = project
self.refs = {r['ref'] for r in refs}
self.old_name = old_name
self.new_name = new_name
self.edit_token = ... | file_ = fn2k(ref['file']) |
Based on the snippet: <|code_start|># coding=utf8
# delete code taken from sublime origami : https://github.com/SublimeText/Origami
XMIN, YMIN, XMAX, YMAX = list(range(4))
class Layout(object):
# CONSTRUCTEUR
def __init__(self):
super(Layout, self).__init__()
# UPDATE
@max_calls(name='Layo... | Debug('layout', 'UPDATE: group: %i' % group) |
Using the snippet: <|code_start|># coding=utf8
# delete code taken from sublime origami : https://github.com/SublimeText/Origami
XMIN, YMIN, XMAX, YMAX = list(range(4))
class Layout(object):
# CONSTRUCTEUR
def __init__(self):
super(Layout, self).__init__()
# UPDATE
<|code_end|>
, determine the... | @max_calls(name='Layout.update') |
Here is a snippet: <|code_start|># coding=utf8
class TsconfigEventListener(sublime_plugin.EventListener):
""" Listen to file events -> Activate TsconfigLinter.
check_tsconfig immediately returns if file is no tsconfig.json """
def on_activated_async(self, view):
<|code_end|>
. Write the next line u... | check_tsconfig(view) |
Predict the next line after this snippet: <|code_start|> """ Listen to file events -> Activate TsconfigLinter.
check_tsconfig immediately returns if file is no tsconfig.json """
def on_activated_async(self, view):
check_tsconfig(view)
def on_load_async(self, view):
check_tsconfig(v... | show_lint_in_status(view) |
Continue the code snippet: <|code_start|># coding=utf8
class TsconfigEventListener(sublime_plugin.EventListener):
""" Listen to file events -> Activate TsconfigLinter.
check_tsconfig immediately returns if file is no tsconfig.json """
def on_activated_async(self, view):
check_tsconfig(view)... | linting_succeeded = expand_filesglob(linter) |
Based on the snippet: <|code_start|># coding=utf8
class TsconfigEventListener(sublime_plugin.EventListener):
""" Listen to file events -> Activate TsconfigLinter.
check_tsconfig immediately returns if file is no tsconfig.json """
def on_activated_async(self, view):
check_tsconfig(view)
... | @catch_CancelCommand |
Using the snippet: <|code_start|># coding=utf8
class TsconfigEventListener(sublime_plugin.EventListener):
""" Listen to file events -> Activate TsconfigLinter.
check_tsconfig immediately returns if file is no tsconfig.json """
def on_activated_async(self, view):
check_tsconfig(view)
d... | project = opened_project_by_tsconfig(linter.file_name) |
Given snippet: <|code_start|># coding=utf8
DEFAULT_DEBOUNCE_DELAY = 0.2 # Will also be used for AsyncCommand debounce
# DEBOUNCE CALL
def debounce(fn, delay=DEFAULT_DEBOUNCE_DELAY, uid=None, *args):
uid = uid if uid else fn
<|code_end|>
, continue by predicting the next line. Consider current file imports:
... | if uid in debounced_timers: |
Given the following code snippet before the placeholder: <|code_start|># coding=utf8
# ----------------------------------- ERROR HIGHTLIGHTER -------------------------------------- #
class ErrorsHighlighter(object):
# Constants
underline = sublime.DRAW_SQUIGGLY_UNDERLINE | sublime.DRAW_NO_FILL | sublime.D... | @max_calls(name='Errors.highlight') |
Continue the code snippet: <|code_start|># coding=utf8
# ----------------------------------- ERROR HIGHTLIGHTER -------------------------------------- #
class ErrorsHighlighter(object):
# Constants
underline = sublime.DRAW_SQUIGGLY_UNDERLINE | sublime.DRAW_NO_FILL | sublime.DRAW_NO_OUTLINE | sublime.DRAW_... | self.error_icon = ".."+os.path.join(package_path.split('Packages')[1], 'icons', 'bright-illegal') |
Predict the next line after this snippet: <|code_start|>
def __init__(self, project):
self.project = project
self._icon_paths()
def _icon_paths(self):
""" defines paths for icons """
if os.name == 'nt':
self.error_icon = ".."+os.path.join(package_path.split('Packag... | self.errors[fn2k(view.file_name())] = error_texts |
Here is a snippet: <|code_start|>class ErrorsHighlighter(object):
# Constants
underline = sublime.DRAW_SQUIGGLY_UNDERLINE | sublime.DRAW_NO_FILL | sublime.DRAW_NO_OUTLINE | sublime.DRAW_EMPTY_AS_OVERWRITE
def __init__(self, project):
self.project = project
self._icon_paths()
def _ic... | if is_ts(view): |
Using the snippet: <|code_start|> return self
def set_callback_kwargs(self, **callback_kwargs):
""" Set additional arguments the callbacks will be called with. """
self.callback_kwargs = callback_kwargs
return self
def set_result_callback(self, result_callback=None):
"""... | Debug('command', "CMD queued @FAST: %s" % self.id) |
Using the snippet: <|code_start|> self.command = command
self.project = project
self.id = "%s-rnd%s" % (command[:6][:-1], uuid.uuid4().hex[0:5])
self.result_callback = None
self.replaced_callback = None
self.executing_callback = None
self.callback_kwargs = {}
... | def activate_debounce(self, delay=DEFAULT_DEBOUNCE_DELAY): |
Predict the next line for this snippet: <|code_start|># coding=utf8
# ------------------------------------- PROJECT WIZZARD ----------------------------------------- #
class ProjectWizzard(object):
def __init__(self, view, finished_callback):
self.finished_callback = finished_callback
self.wi... | Debug('project+', 'Disable ArcticTypescript while in WizzardMode') |
Given the code snippet: <|code_start|> max_lines = 0
for m in self.messages:
max_lines = max(max_lines, len(m))
for m in self.messages:
while len(m) < max_lines:
m.append('')
def on_select(i):
#self.window.run_command("hide_overlay")
... | self.actions.append(lambda: [self.window.open_file(package_path + '/examples/basic_browser_project/tsconfig.json'), self._cleanup()]) |
Next line prediction: <|code_start|># coding=utf8
# ------------------------------------- PROJECT WIZZARD ----------------------------------------- #
class ProjectWizzard(object):
def __init__(self, view, finished_callback):
self.finished_callback = finished_callback
self.window = view.window... | set_plugin_temporarily_disabled() # Disable global until wizzard is cancled or finished |
Using the snippet: <|code_start|>
def _finish(self):
""" make and write tsconfig.json. Call finished_callback """
Debug('project+', 'Wizzard finished: Create and write tsconfig.json')
content = { "compilerOptions" : {}, "files" : {}}
if self.module is None:
content['compi... | set_plugin_temporarily_enabled() |
Using the snippet: <|code_start|># coding=utf8
# ------------------------------------- PROJECT WIZZARD ----------------------------------------- #
class ProjectWizzard(object):
def __init__(self, view, finished_callback):
self.finished_callback = finished_callback
self.window = view.window()
... | assert is_plugin_temporarily_disabled() |
Here is a snippet: <|code_start|> and uses them. If no such view can be found, it creates one and layoutes it to group 1
"""
if self.get_view() is None:
## add next to existing t3s views
## or create layout if not created yet
self.t3sviews.get_window_and_g... | Debug('focus', 'bring_to_top: focus view %i' % self._view_reference.id()) |
Using the snippet: <|code_start|># coding=utf8
class Base(object):
"""
This object represents a special view to display ArcticTypescript information like
the error list or the outline structure
"""
def __init__(self, name, t3sviews):
self.name = name
self.t3sviews = t3svie... | @max_calls() |
Predict the next line after this snippet: <|code_start|># --------------------------------------- ERRORS -------------------------------------- #
class Errors(object):
def __init__(self, project):
self.project = project
self.lasterrors = []
self.message = "" # contains exception message if ... | Debug('error', 'Internal ArcticTypescript error during show_errors: %s (Exception Message: %s)' % (errors, e)) |
Predict the next line after this snippet: <|code_start|># coding=utf8
# --------------------------------------- ERRORS -------------------------------------- #
class Errors(object):
def __init__(self, project):
self.project = project
self.lasterrors = []
self.message = "" # contains exc... | @max_calls() |
Given the code snippet: <|code_start|> self.line_to_file = line_to_file
self.line_to_pos = line_to_pos
self.text = ''.join(text)
def _flatten_errortext(self, text_or_dict):
text = []
if isinstance(text_or_dict, str):
text.append(text_or_dict.replace('\r',''))
... | if fn2k(e['file']) == fn2k(view.file_name()): |
Given the code snippet: <|code_start|>
def kwargs_to_namedtuple(func):
def wrapper(**kwargs):
controls = namedtuple('Controls', list(kwargs.keys()))(**kwargs)
return func(controls)
return wrapper
def namedtuple_to_kwargs(func):
def wrapper(controls):
return func(**(controls._todict... | private.data = GrowableArray(cols=5, length=1000) |
Next line prediction: <|code_start|># Copyright 2008 - 2019 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Fou... | if not _TRY_PYSIDE: |
Predict the next line after this snippet: <|code_start|>
#
# private data shared among functions
#
class Private(object):
pass
private = Private()
#
# functions
#
def initialize(log_text_box, data_chart, **kwargs):
# setup the logger and log display box
# examples of how to use:
# private.logger.d... | private.data = GrowableArray(cols=2, length=1000) |
Continue the code snippet: <|code_start|> pluck = w_pluck.value
monitor = w_monitor.value
N_tfft = w_N_tfft.value
N_tfft_display = w_N_tfft_display.value
drag = w_drag.value
messages.write('\n=== WAVES ===============================\n')
# spatial domain data and initial condition
N_pluck... | data_yt = CircularArray(length=N_tfft, cols=2) |
Based on the snippet: <|code_start|># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Stre... | for i in TSI.layout: |
Given the following code snippet before the placeholder: <|code_start|># Copyright 2013 - 2016, James Humphry
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License,... | layout = [TextField("Station code", 3), |
Using the snippet: <|code_start|># it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without e... | IntegerField("Minimum Interchange Time", 2), |
Given the code snippet: <|code_start|># the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PAR... | VarTextField("Comments", 100)] |
Based on the snippet: <|code_start|># Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
# MA 02110-1301, USA.
#
'''Generate SQL that will create a suitable schema for storing data
from ATOC .ALF additional fixed link files. This is done dynamically to
ensure it keeps in sync with the definitions in nrcif.py... | for i in ALF.layout: |
Given the code snippet: <|code_start|># You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
# MA 02110-1301, USA.
#
'''Generate SQL that will create a suitable schema for storing... | DDL.write(layouts['BS'].generate_sql_ddl()+",\n") |
Here is a snippet: <|code_start|># Copyright 2013 - 2016, James Humphry
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later vers... | layouts = mca_layouts.copy() |
Given the code snippet: <|code_start|>
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distribu... | layouts["HD"] = reduced_hd |
Given the following code snippet before the placeholder: <|code_start|># This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later versio... | layouts["BX"] = corrected_bx |
Predict the next line for this snippet: <|code_start|># You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
# MA 02110-1301, USA.
#
'''Generate SQL that will create a suitable sc... | tablename = layouts[i].name.lower().replace(" ", "_") |
Using the snippet: <|code_start|>
def download_workflow():
utils.download_workflow()
def update_postrun_json_init(input_json, output_json):
utils.update_postrun_json_init(input_json, output_json)
def update_postrun_json_upload_output(input_json, execution_metadata_file, md5file, output_json, language, endpo... | version='%(prog)s ' + __version__) |
Using the snippet: <|code_start|> "MaxAttempts": 10000,
"BackoffRate": 1.0
},
{
"ErrorEquals": ["EC2InstanceLimitWaitException"],
"IntervalSeconds": 600,
"MaxAttempts": 1008, # 1 wk
"BackoffRate": 1.0
},
lambda_error... | region_name=AWS_REGION, |
Given the following code snippet before the placeholder: <|code_start|> "BackoffRate": 1.0
},
{
"ErrorEquals": ["EC2InstanceLimitWaitException"],
"IntervalSeconds": 600,
"MaxAttempts": 1008, # 1 wk
"BackoffRate": 1.0
},
lambda_e... | aws_acc=AWS_ACCOUNT_NUMBER, |
Predict the next line for this snippet: <|code_start|> ]
sfn_check_task_retry_conditions = [
{
"ErrorEquals": ["EC2StartingException"],
"IntervalSeconds": 300,
"MaxAttempts": 25,
"BackoffRate": 1.0
},
{
"ErrorEquals": ["StillRun... | return create_tibanna_suffix(self.dev_suffix, self.usergroup) |
Predict the next line after this snippet: <|code_start|>
config = {
'function_name': 'check_task_awsem',
'function_module': 'service',
'function_handler': 'handler',
'handler': 'service.handler',
'region': AWS_REGION,
'runtime': 'python3.6',
'role': 'tibanna_lambda_init_role',
'descripti... | return check_task(event) |
Given snippet: <|code_start|>
config = {
'function_name': 'check_task_awsem',
'function_module': 'service',
'function_handler': 'handler',
'handler': 'service.handler',
<|code_end|>
, continue by predicting the next line. Consider current file imports:
from tibanna.check_task import check_task
from tib... | 'region': AWS_REGION, |
Based on the snippet: <|code_start|>
class StepFunctionCostUpdater(object):
sfn_type = SFN_TYPE
def __init__(self,
dev_suffix=None,
<|code_end|>
, predict the immediate next line with the help of imports:
from .vars import (
AWS_REGION,
AWS_ACCOUNT_NUMBER,
SFN_TYPE,
UPDATE_CO... | region_name=AWS_REGION, |
Given snippet: <|code_start|>
class StepFunctionCostUpdater(object):
sfn_type = SFN_TYPE
def __init__(self,
dev_suffix=None,
region_name=AWS_REGION,
<|code_end|>
, continue by predicting the next line. Consider current file imports:
from .vars import (
AWS_REGION,
AW... | aws_acc=AWS_ACCOUNT_NUMBER, |
Here is a snippet: <|code_start|> return "arn:aws:lambda:" + self.region_name + ":" + self.aws_acc + ":function:"
@property
def sfn_name(self):
return 'tibanna_' + self.sfn_type + self.lambda_suffix + '_costupdater'
@property
def iam(self):
return IAM(self.usergroup)
@prope... | "Resource": self.lambda_arn_prefix + UPDATE_COST_LAMBDA_NAME + self.lambda_suffix, |
Given the code snippet: <|code_start|>
class StepFunctionCostUpdater(object):
sfn_type = SFN_TYPE
def __init__(self,
dev_suffix=None,
region_name=AWS_REGION,
aws_acc=AWS_ACCOUNT_NUMBER,
usergroup=None):
self.dev_suffix = dev_suffix
... | return create_tibanna_suffix(self.dev_suffix, self.usergroup) |
Given snippet: <|code_start|>
def test_upload():
randomstr = 'test-' + create_jobid()
os.mkdir(randomstr)
filepath = os.path.join(os.path.abspath(randomstr), randomstr)
with open(filepath, 'w') as f:
f.write('haha')
<|code_end|>
, continue by predicting the next line. Consider current file impo... | upload(filepath, 'tibanna-output', 'uploadtest') |
Based on the snippet: <|code_start|>
@pytest.fixture()
def check_task_input():
return {"config": {"log_bucket": "tibanna-output"},
"jobid": "test_job",
"push_error_to_end": True
}
@pytest.fixture()
def s3(check_task_input):
bucket_name = check_task_input['config']['log_buc... | service.handler(check_task_input_modified, '') |
Here is a snippet: <|code_start|>
@pytest.fixture()
def check_task_input():
return {"config": {"log_bucket": "tibanna-output"},
"jobid": "test_job",
"push_error_to_end": True
}
@pytest.fixture()
def s3(check_task_input):
bucket_name = check_task_input['config']['log_bucket... | with pytest.raises(EC2StartingException) as excinfo: |
Using the snippet: <|code_start|> jobid = 'notmyjobid'
check_task_input_modified = check_task_input
check_task_input_modified['jobid'] = jobid
check_task_input_modified['config']['start_time'] = datetime.strftime(datetime.now(tzutc()) - timedelta(minutes=13),
... | with pytest.raises(StillRunningException) as excinfo: |
Based on the snippet: <|code_start|> assert 'aborted' in str(excinfo.value)
# cleanup
s3.delete_objects(Delete={'Objects': [{'Key': job_started}]})
s3.delete_objects(Delete={'Objects': [{'Key': job_aborted}]})
@pytest.mark.webtest
def test_check_task_awsem_throws_exception_if_not_done(check_task_input)... | with pytest.raises(MetricRetrievalException) as excinfo: |
Given the following code snippet before the placeholder: <|code_start|>def s3(check_task_input):
bucket_name = check_task_input['config']['log_bucket']
return boto3.resource('s3').Bucket(bucket_name)
@pytest.mark.webtest
def test_check_task_awsem_fails_if_no_job_started(check_task_input, s3):
# ensure the... | with pytest.raises(EC2IdleException) as excinfo: |
Here is a snippet: <|code_start|> job_started = "%s.job_started" % jobid
s3.delete_objects(Delete={'Objects': [{'Key': job_started}]})
with pytest.raises(EC2StartingException) as excinfo:
service.handler(check_task_input_modified, '')
assert 'Failed to find jobid' in str(excinfo.value)
@pytest.... | with pytest.raises(JobAbortedException) as excinfo: |
Here is a snippet: <|code_start|>
@pytest.fixture()
def check_task_input():
return {"config": {"log_bucket": "tibanna-output"},
"jobid": "test_job",
"push_error_to_end": True
}
@pytest.fixture()
def s3(check_task_input):
bucket_name = check_task_input['config']['log_bucket... | AWSEM_TIME_STAMP_FORMAT) |
Predict the next line for this snippet: <|code_start|>
top_contents = """
Timestamp: 2020-12-18-18:55:37
top - 18:55:37 up 4 days, 3:18, 2 users, load average: 2.00, 2.00, 2.30
Tasks: 344 total, 1 running, 343 sleeping, 0 stopped, 0 zombie
%Cpu(s): 6.6 us, 0.1 sy, 0.0 ni, 93.2 id, 0.0 wa, 0.0 hi, 0.0 si... | top1 = top.Top('') |
Here is a snippet: <|code_start|>
config = {
'function_name': 'run_task_awsem',
'function_module': 'service',
'function_handler': 'handler',
'handler': 'service.handler',
'region': AWS_REGION,
'runtime': 'python3.6',
'role': 'tibanna_lambda_init_role',
'description': 'launch an ec2 inst... | return run_task(event) |
Predict the next line after this snippet: <|code_start|>
config = {
'function_name': 'run_task_awsem',
'function_module': 'service',
'function_handler': 'handler',
'handler': 'service.handler',
<|code_end|>
using the current file's imports:
from tibanna.run_task import run_task
from tibanna.vars impo... | 'region': AWS_REGION, |
Predict the next line for this snippet: <|code_start|>
def test_general_awsem_error_msg():
eh = AWSEMErrorHandler()
res = eh.general_awsem_error_msg('somejobid')
assert res == 'Job encountered an error check log using tibanna log --job-id=somejobid [--sfn=stepfunction]'
def test_general_awsem_check_log_m... | with pytest.raises(AWSEMJobErrorException) as exec_info: |
Next line prediction: <|code_start|>
def test_combine_two():
x = combine_two('a', 'b')
assert x == 'a/b'
x = combine_two(['a1', 'a2'], ['b1', 'b2'])
assert x == ['a1/b1', 'a2/b2']
x = combine_two([['a1', 'a2'], ['b1', 'b2']], [['c1', 'c2'], ['d1', 'd2']])
assert x == [['a1/c1', 'a2/c2'], ['b1/d1... | x = run_on_nested_arrays2(1, 2, sum0) |
Predict the next line after this snippet: <|code_start|> "end_time": "20190531-04:24:55-UTC",
"filesystem": "/dev/nvme1n1",
"instance_id": "i-08d1c54ed1f74ab36",
"status": "0",
"total_input_size": "2.2G",
"total_output_size": "4.2G",
"total_tmp_size": "7.4G",
... | r = awsem.AwsemPostRunJson(**postrun_json) |
Given the code snippet: <|code_start|> assert hasattr(r, 'class_')
assert hasattr(r, 'dir_')
assert hasattr(r, 'path')
assert hasattr(r, 'profile')
assert hasattr(r, 'unzip') # default '' if omitted
assert r.class_ == 'File'
assert r.dir_ == 'somebucket'
assert r.path == 'somefilepath'
... | with pytest.raises(MalFormattedRunJsonException) as ex: |
Next line prediction: <|code_start|>
config = {
'function_name': 'update_cost_awsem',
'function_module': 'service',
'function_handler': 'handler',
'handler': 'service.handler',
'region': AWS_REGION,
'runtime': 'python3.6',
'role': 'tibanna_lambda_init_role',
'description': 'update costs... | return update_cost(event) |
Predict the next line for this snippet: <|code_start|>
config = {
'function_name': 'update_cost_awsem',
'function_module': 'service',
'function_handler': 'handler',
'handler': 'service.handler',
<|code_end|>
with the help of current file imports:
from tibanna.update_cost import update_cost
from tiban... | 'region': AWS_REGION, |
Based on the snippet: <|code_start|> entry = ccpnProject.currentNmrEntryStore.findFirstEntry()
strucGen = entry.findFirstStructureGeneration()
refStructure = strucGen.structureEnsemble.sortedModels()[0]
if outType == "mol2":
mol2Format = Mol2Format.Mol2For... | molecule = ACTopol( |
Given the following code snippet before the placeholder: <|code_start|> )
if not molecule.acExe:
molecule.printError("no 'antechamber' executable... aborting!")
hint1 = "HINT1: is 'AMBERHOME' environment variable set?"
hint2 = (... | msg = elapsedTime(execTime) |
Given snippet: <|code_start|> else:
resTempFile = os.path.join(dirTemp, "%s.pdb" % resName)
entry = ccpnProject.currentNmrEntryStore.findFirstEntry()
strucGen = entry.findFirstStructureGeneration()
refStructure = strucGen.structureEnsemble.sortedModels()[0... | print(header) |
Using the snippet: <|code_start|>
r = "<[<Atom id=3, name=C1, c3>, <Atom id=4, name=H, hc>, <Atom id=5, name=H, hc>, <Atom id=6, name=H, hc>], ang=0.00>"
def test_atom():
atom = Atom("C1", "c3", 3, 5, 12.0, 0.5, (1.0, 0.9, 0.5))
assert str(atom) == "<Atom id=3, name=C1, c3>"
def test_bond():
a1 = Atom("... | angle = Angle([a1, a2, a3], 46.3, 1.91637234) |
Given snippet: <|code_start|>
r = "<[<Atom id=3, name=C1, c3>, <Atom id=4, name=H, hc>, <Atom id=5, name=H, hc>, <Atom id=6, name=H, hc>], ang=0.00>"
def test_atom():
atom = Atom("C1", "c3", 3, 5, 12.0, 0.5, (1.0, 0.9, 0.5))
assert str(atom) == "<Atom id=3, name=C1, c3>"
def test_bond():
a1 = Atom("C1",... | bond = Bond([a1, a2], 330.0, 1.0969) |
Given the code snippet: <|code_start|>
file_types = (
("file_name"),
("em_mdp"),
("AC_frcmod"),
("AC_inpcrd"),
("AC_lib"),
("AC_prmtop"),
("mol2"),
("CHARMM_inp"),
("CHARMM_prm"),
("CHARMM_rtf"),
("CNS_inp"),
("CNS_par"),
("CNS_top"),
("GMX_OPLS_itp"),
("GMX_... | jj = json.loads(acpype_api(inputFile="benzene.pdb", debug=True)) |
Here is a snippet: <|code_start|>"""
Script to get energies from AMBER and GROMACS
for a given system and compare them
"""
def error(v1, v2):
"""percentage relative error"""
if v1 == v2:
return 0
return abs(v1 - v2) / max(abs(v1), abs(v2)) * 100
ff = 4.1840
vv = ["ANGLE", "BOND", "DIHED", "EP... | x.split("=") for x in re.sub(r"\s+=\s+", "=", _getoutput(cmd_amb)).strip().replace("1-4 ", "1-4_").split() |
Given the code snippet: <|code_start|>
def dotproduct(aa, bb):
"""scalar product"""
return sum((a * b) for a, b in zip(aa, bb))
def cross_product(a, b):
"""cross product"""
c = [a[1] * b[2] - a[2] * b[1], a[2] * b[0] - a[0] * b[2], a[0] * b[1] - a[1] * b[0]]
return c
def length(v):
"""distan... | angle = math.acos(dotproduct(n1, n2) / (length(n1) * length(n2))) * 180 / Pi |
Next line prediction: <|code_start|> help="print nothing (not allowed with arg -d)",
)
parser.add_argument(
"-o",
"--outtop",
choices=["all"] + outTopols,
action="store",
default="all",
dest="outtop",
help="output topologies: all (default), gmx, cns... | default=MAXTIME, |
Next line prediction: <|code_start|> "--keyword",
action="store",
dest="keyword",
help="mopac or sqm keyword, inside quotes",
)
parser.add_argument(
"-f",
"--force",
action="store_true",
dest="force",
help="force topologies recalculation ane... | choices=["all"] + outTopols, |
Predict the next line for this snippet: <|code_start|>
allTotal = len(ccpCodes) * 2
jobsOK = [] # list of Mols that have at least a PDB or IDEAL clean: [[both],[pdb,ideal]]
totalTxt = ""
for group in groupResults:
header, subHead, dummy, lista = group
if "Mols clean" == subHead:
jobsOK = lista
subT... | out = _getoutput(cmd) |
Given the following code snippet before the placeholder: <|code_start|>class Bond:
"""
attributes: pair of Atoms, spring constant (kcal/mol), dist. eq. (Ang)
"""
def __init__(self, atoms, kBond, rEq):
self.atoms = atoms
self.kBond = kBond
self.rEq = rEq
def __str__(self):
... | return f"<{self.atoms}, ang={self.thetaEq * 180 / Pi:.2f}>" |
Predict the next line for this snippet: <|code_start|>
def test_no_ac(janitor, capsys):
binaries = {"ac_bin": "no_ac", "obabel_bin": "obabel"}
msg = f"ERROR: no '{binaries['ac_bin']}' executable... aborting!"
inp = "AAA.mol2"
with pytest.raises(SystemExit) as e_info:
<|code_end|>
with the help of cur... | cli.init_main(argv=["-di", inp, "-c", "gas"], binaries=binaries) |
Next line prediction: <|code_start|>
def test_no_ac(janitor, capsys):
binaries = {"ac_bin": "no_ac", "obabel_bin": "obabel"}
msg = f"ERROR: no '{binaries['ac_bin']}' executable... aborting!"
inp = "AAA.mol2"
with pytest.raises(SystemExit) as e_info:
cli.init_main(argv=["-di", inp, "-c", "gas"]... | _getoutput(f"rm -vfr {temp_base}* .*{temp_base}*") |
Given the following code snippet before the placeholder: <|code_start|>
-----------------------------------------
|-----win1------|-----win2-----|---------
-----------------------------------------
To improve efficiency, there are several method to be adopted:
1) The section that have matched, we don't search it... | hanning = hann(DEF_FFT_SIZE, sym=0) |
Here is a snippet: <|code_start|>
ZCR_FALG = False
SIGNAL_START_FLAG = False
EXPECT_ZCR = int(DEF_FFT_SIZE/framerate*base_frq*2)
#data length
data_len = len(wdata)
num = int(data_len/DEF_FFT_SIZE)
frames_num = t*framerate/DEF_FFT_SIZE
print frames_num
if frames_num>num:
frames_num = num
#frequency domai... | hanning = hann(DEF_FFT_SIZE, sym=0) |
Given snippet: <|code_start|> start = Q.pop() # explore a cycle from start node
node = start # current node on cycle
while next_[node] < len(graph[node]): # visit all allowable arcs
neighbor = graph[node][next_[node]] # traverse an arc
... | write_graph(filename, graph, arc_label=weight, directed=directed) |
Using the snippet: <|code_start|># jill-jênn vie et christoph dürr - 2020
# coding=utf8
# pylint: disable=missing-docstring
class TestNextPermutation(unittest.TestCase):
def test_solve_word_addition(self):
self.assertEqual(solve_word_addition(["A", "B", "C"]), 32)
self.assertEqual(solve_word_add... | self.assertEqual(next_permutation(L), True) |
Continue the code snippet: <|code_start|>"""
def _alternate(u, bigraph, visitU, visitV, matchV):
"""extend alternating tree from free vertex u.
visitU, visitV marks all vertices covered by the tree.
"""
visitU[u] = True
for v in bigraph[u]:
if not visitV[v]:
visitV[v] = Tru... | matchV = max_bipartite_matching(bigraph) |
Here is a snippet: <|code_start|># snip{
# pylint: disable=too-many-arguments
def _augment(graph, capacity, flow, val, u, target, visit):
"""Find an augmenting path from u to target with value at most val"""
visit[u] = True
if u == target:
return val
for v in graph[u]:
cuv = capacity[u][... | add_reverse_arcs(graph, capacity) |
Given snippet: <|code_start|>#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""\
Decompose DAG into a minimum number of chains
jill-jenn vie et christoph durr - 2015-2018
"""
# snip{
def dilworth(graph):
"""Decompose a DAG into a minimum number of chains by Dilworth
:param graph: directed graph in listlist ... | match = max_bipartite_matching(graph) # maximum matching |
Using the snippet: <|code_start|># -*- coding: utf-8 -*-
"""\
Largest area rectangle in a binary matrix
plus grand rectangle monochromatique
jill-jenn vie et christoph durr - 2014-2018
"""
# snip{
def rectangles_from_grid(P, black=1):
"""Largest area rectangle in a binary matrix
:param P: matrix
:param ... | (area, left, height, right) = rectangles_from_histogram(t) |
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