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#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import math
import srwl_uti_smp
def set_optics(v=None):
el = []
pp = []
names = ['M1', 'M1_Grating', 'Grating', 'GA', 'GA_M3A', 'M3A', 'M3', 'M3_SSA', 'SSA',... | mkeilman/sirepo | tests/template/srw_generate_data/nsls-ii-esm-beamline.py | Python | apache-2.0 | 34,340 | [
"Gaussian"
] | 190e5af7d9ff833b84526c66f1a2bc09565eb41617c2a74f1532ba27f87ab851 |
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | kobejean/tensorflow | tensorflow/python/autograph/pyct/static_analysis/liveness.py | Python | apache-2.0 | 6,834 | [
"VisIt"
] | 819784f7da68d2d0ee7232831e52004de243c6ccb9fd020997f13edb898b7a0c |
"""Implementation of the WebSocket protocol.
`WebSockets <http://dev.w3.org/html5/websockets/>`_ allow for bidirectional
communication between the browser and server.
WebSockets are supported in the current versions of all major browsers,
although older versions that do not support WebSockets are still in use
(refer ... | bdarnell/tornado | tornado/websocket.py | Python | apache-2.0 | 61,445 | [
"VisIt"
] | b8199ae17902138442004db013c0ba9831c32fde51dce3cd98f5c5eac8b48163 |
# Copyright 2008-2009 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of django-facebookconnect.
#
# django-facebookconnect is free software: you can redistribute it and/or modify
# it under the te... | mapmyfitness/django-facebookconnect | facebookconnect/management/commands/fixemailfieldsize.py | Python | gpl-3.0 | 1,428 | [
"Brian"
] | f47c8655b232f76c36792ee119413489bae8e7939bf985895bcbbf2bde8e1a7f |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jjas0nn/solvem | tensorflow/lib/python2.7/site-packages/tensorflow/contrib/distributions/python/ops/mvn.py | Python | mit | 28,680 | [
"Gaussian"
] | b51dd3d97c1f705ada4dd969a57e8f94f360186ac56d4ba0179b8f22e2c98028 |
import gc
import sys
import unittest
import warnings
import weakref
import inspect
import types
from test import support
class FinalizationTest(unittest.TestCase):
def test_frame_resurrect(self):
# A generator frame can be resurrected by a generator's finalization.
def gen():
nonloca... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.5.0/Lib/test/test_generators.py | Python | mit | 58,546 | [
"VisIt"
] | 3adbe727fcb5dc81ed747ec17dcba8c0bcdf39ff8b5c830cb8078e246e822e75 |
"""
SWORDv2 API implementation for SSS
This provides an implenentation of sss.core.SwordServer and related support classes which implements the features that are used by this
module.
"""
from sss.core import SwordServer, ServiceDocument, SDCollection, SwordError, Authenticator, Auth, DepositResponse, EntryDocument, S... | JiscPER/jper-sword-in | service/sword.py | Python | apache-2.0 | 20,738 | [
"Octopus"
] | a1306ad32a22619edc2fae7819c9648438911b19c8b572e2bbb7b52f54f757de |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# plheatmap.py
#
# Copyright 2016 Cosmo <cosmo@CosmoSpectre>
#
# 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 3 of the Li... | CosmoJG/neural-heatmap | dd-path-length/plheatmap.py | Python | gpl-3.0 | 6,199 | [
"NEURON"
] | 23caa11a472a6f4fe5cc410509ab9d4ee94bf95f8b7412e4e1389b0e12b4ebdf |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requ... | aksmas/rl-glue-ext | projects/codecs/Python/src/tests/test_message_agent.py | Python | apache-2.0 | 1,430 | [
"Brian"
] | da303790a18119ad692d02cc2936489cc45d946bac8d53f026692ec3b28d8000 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Martin Hawlisch, Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2022 Jan Skarvall
# Copyright (C) 2022 Nick Hall
#
# This program i... | gramps-project/gramps | gramps/gen/datehandler/test/datehandler_test.py | Python | gpl-2.0 | 8,243 | [
"Brian"
] | caee6d40862307ffe6b6bf57fe0ea776aca6cc3afbc7f1ff232b6069394534cd |
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 31 13:06:41 2014
@author: samantha
Double-Gaussian fit
"""
import numpy as np
from scipy.optimize import curve_fit
# Two-Gaussian model
def func(x, a0, b0, c0, a1, b1, c1):
return a0 * np.exp(-(x-b0)**2/(2*c0**2))\
+ a1 * np.exp(-(x-b1)**2/(2*c1**2))
... | hkaushalya/LearningSciKit | Exe3_311_OReillySciPyAndNumPy.py | Python | gpl-3.0 | 1,419 | [
"Gaussian"
] | 19c53677c54e60d9d6181750c086817f9babea2f40da016b5105bda9f875a827 |
""":func:`~pandas.eval` parsers
"""
import ast
import tokenize
from functools import partial
import pandas as pd
from pandas import compat
from pandas.compat import StringIO, lmap, zip, reduce, string_types
from pandas.core.base import StringMixin
from pandas.core import common as com
import pandas.formats.printing ... | BigDataforYou/movie_recommendation_workshop_1 | big_data_4_you_demo_1/venv/lib/python2.7/site-packages/pandas/computation/expr.py | Python | mit | 25,528 | [
"VisIt"
] | 29804a56b642f845f3e3080ec7009c4d706543c3ef88cb838f6ab819fa960edb |
#!/usr/bin/env python
'''
Master loader for CANON April (Spring) 2021 Campaign
'''
import os
import sys
from datetime import datetime
parentDir = os.path.join(os.path.dirname(__file__), "../")
sys.path.insert(0, parentDir)
from CANON import CANONLoader
import timing
cl = CANONLoader('stoqs_canon_april2021', 'CANON-... | stoqs/stoqs | stoqs/loaders/CANON/loadCANON_april2021.py | Python | gpl-3.0 | 8,768 | [
"NetCDF"
] | da66a647bd72bd436009b4e1211955ad7c67c4b1037a138e5be8b67370fcf1c3 |
import matplotlib.pyplot as plt
import argparse
'''parser = argparse.ArgumentParser()
parser.add_argument("parameter", type=str,
help="Options : mass, age, radius, lum, velo, long")
parser.add_argument("numberBins", type=int,
help="Set number of bins for histogram")
args = parse... | WillArmentrout/galSims | plotting/ParamHist.py | Python | gpl-2.0 | 3,725 | [
"Galaxy"
] | 18bce6400a80ebf26b42212430a1c33e6a28523dda3de09505e1b8b15c02f19c |
#!/usr/bin/env python
# Copyright 2014-2021 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/fci/direct_spin1.py | Python | apache-2.0 | 38,662 | [
"PySCF"
] | c2ea6295a6c86b4c2838d4ad4ba315e6ab56c18646c2376dcd87d9d89d961217 |
#
# Parse tree nodes for expressions
#
import cython
cython.declare(error=object, warning=object, warn_once=object, InternalError=object,
CompileError=object, UtilityCode=object, StringEncoding=object, operator=object,
Naming=object, Nodes=object, PyrexTypes=object, py_object_type=objec... | hpfem/cython | Cython/Compiler/ExprNodes.py | Python | apache-2.0 | 371,587 | [
"VisIt"
] | 0e9a2408ff9dabd687f401ca1f111fb3d8b2865e286f4b17f4f37dd0eeb0d663 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/bibles/forms/editbibledialog.py | Python | gpl-2.0 | 10,299 | [
"Brian"
] | bc08fd0479ecf8723c5314b40b0f944bbbe98dc13789681c245bd224cbf26306 |
class SWRLObjectVisitor(object):
"""Marker class"""
def visit(self, node):
"""
:param node: an object of one of the following classes:
- owlapy.model.SWRLRule
- owlapy.model.SWRLClassAtom
- owlapy.model.SWRLDataRangeAtom
- owlapy.model.SWRLObjectP... | patrickwestphal/owlapy | owlapy/model/swrlobjectvisitor.py | Python | gpl-3.0 | 1,432 | [
"VisIt"
] | 945075352134a62810c170932c2bc5005c677a92b1f9f1419daaf89ffbb18397 |
#!/usr/bin/env python
# coding: utf-8
#
# Copyright 2007 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | hossamkhader/ns-3 | upload.py | Python | gpl-2.0 | 99,818 | [
"VisIt"
] | 31f1118f9be76ebc6971f9d2ec269d8b3443d4168b5f3fc08bed7e0f3ae02047 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | SamStudio8/scikit-bio | skbio/sequence/tests/test_iupac_sequence.py | Python | bsd-3-clause | 19,961 | [
"scikit-bio"
] | bbc339777bc7d48384fe33bc209c9385c3c669184b2ef972227cdfd1f0ab5e2f |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
# CREATED:2015-02-15 10:06:03 by Brian McFee <brian.mcfee@nyu.edu>
'''Helpful tools for deprecation'''
import warnings
from decorator import decorator
import six
def moved(moved_from, version, version_removed):
'''This is a decorator which can be used to mark funct... | ruohoruotsi/librosa | librosa/util/decorators.py | Python | isc | 2,239 | [
"Brian"
] | dc813b9d71bf5dc6ce08d8f8c49aa6bcb351f2e6a8bdf2201d2c811f0b8aa366 |
#!/usr/bin/env python
# coding:utf-8
from sqlalchemy import *
from base_model import *
class UserVisitLog(Model):
__tablename__ = 'tb_user_visit_log'
id = Column(Integer, primary_key=True)
#for UV(user visit): anonymous:userid=sessionid
uid = Column(String(255), nullable=False)
login_time = Colum... | cshzc/X1Tool | src/server/database/models/use_visity_log.py | Python | gpl-2.0 | 541 | [
"VisIt"
] | 346ba2475289cbe299a14cba854aac12042364608887e7b24851bc202ee3c0db |
# Copyright 2015-2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law... | wklken/yapf | yapf/yapflib/blank_line_calculator.py | Python | apache-2.0 | 6,497 | [
"VisIt"
] | c9d1a464bb52b9fc95b7af39cc40fab4ef23a384128bb89f5e063f39370bdeae |
from collections import OrderedDict
from edc_constants.constants import REQUIRED, NOT_REQUIRED, ADDITIONAL, NOT_ADDITIONAL
from edc_visit_schedule.classes import (
VisitScheduleConfiguration, site_visit_schedules,
CrfTuple, MembershipFormTuple, ScheduleTuple, RequisitionPanelTuple)
from tshilo_dikotla.constan... | botswana-harvard/tshilo-dikotla | td_infant/visit_schedule/infant_birth_visit_schedule.py | Python | gpl-2.0 | 16,178 | [
"VisIt"
] | 4e9992bc28fe8149a44eec86ea71bf25aa29df0f28f581257fb7616235993def |
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
try:
CLAW = os.environ['CLAW']
except:
raise Exception("*** Must first set CLAW enviornment variable")
#... | clawpack/geoclaw_tutorial_csdms2016 | chile2010b/setrun_original.py | Python | bsd-2-clause | 13,572 | [
"NetCDF"
] | f3fbd8fd8d882bd76ac23a2c10268a4ef2a1299aa0346e00eefadabc1b9614fd |
# python3
# pylint: disable=g-bad-file-header
# Copyright 2021 DeepMind Technologies Limited. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org... | deepmind/neural_testbed | neural_testbed/agents/factories/bbb.py | Python | apache-2.0 | 4,315 | [
"Gaussian"
] | 9069f05cbf79b5af55cfe18ece0729d9b883baca8853eb0d6a0351de907682ac |
"""
This file provides a more advanced example of vtkTable access and
manipulation methods.
"""
from vtk import *
#------------------------------------------------------------------------------
# Script Entry Point (i.e., main() )
#------------------------------------------------------------------------------
if __n... | b3c/VTK-5.8 | Examples/Infovis/Python/tables4.py | Python | bsd-3-clause | 1,290 | [
"VTK"
] | b9178b3f2ce5e6744bdab2fc72458888cf87f59ac480213e3448cf2d49fd6d69 |
import numpy as np
import pylab as pl
class SMP():
### this is a soft margin perceptron also supporting kernels
def __init__(self, max_it = 4400, kernel = None, degree=3, disp=1):
self.max_it = max_it
self.disp = disp
if kernel == 'poly':
self.kernel = lambda x, y: (np.inner(x, y) + 1)**degree
elif kerne... | wedgeCountry/SMP | SMP.py | Python | gpl-3.0 | 2,738 | [
"Gaussian"
] | d21e51c8d3c835f1fbac1a792290719af13068caaa415340bc2734699ec3a9d7 |
"""
Copyright (C) 2017 Roberto Bruttomesso <roberto.bruttomesso@gmail.com>
This file is distributed under the terms of the 3-clause BSD License.
A copy of the license can be found in the root directory or at
https://opensource.org/licenses/BSD-3-Clause.
Author: Roberto Bruttomesso <roberto.bruttomesso@gmail.com>
Da... | formalmethods/intrepyd | intrepyd/lustre2py/parser.py | Python | bsd-3-clause | 1,027 | [
"VisIt"
] | 68065409c0ff10646b4f2568b238e00cfa99846e53068d9f49861dcf73fc9146 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/domain/returnedsale.py | Python | gpl-2.0 | 24,066 | [
"VisIt"
] | a7c2ade5243e548487808c56a7f90d8d00d3a3f934d989278d68428f9c233db6 |
'''
Resource handling
Keep track of the names/locations of any static resources we use, file types.
@author: Robert Toomey (retoomey)
'''
import os
def getScriptDir():
""" Get root location this script is running from. Found this example
on google. Basically use the file path of THIS module... | retoomey/WDSS2Python | w2py/resource.py | Python | apache-2.0 | 3,409 | [
"NetCDF"
] | 97237416e422f27c3eb21f601b2065c3f3337da0be2d1e763140af01083456d2 |
"""Sample conformations from clusters
{{header}}
Meta
----
depends:
- ../../top.pdb
- ../../trajs
"""
import mdtraj as md
import os
from msmbuilder.io.sampling import sample_states
from msmbuilder.io import load_trajs, save_generic, preload_top, backup, load_generic
## Load
meta, ttrajs = load_trajs('ttrajs')
... | mpharrigan/mixtape | msmbuilder/project_templates/cluster/sample-clusters.py | Python | lgpl-2.1 | 880 | [
"MDTraj"
] | 09f0237d43388e8239f60f00908864fdef3532dc5b46ae639e38d415241656ff |
###########################################################################
#
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/l... | google/starthinker | dags/cm_user_editor_dag.py | Python | apache-2.0 | 4,129 | [
"VisIt"
] | 00520d38e13f91ac7d36e727268e178bc25a605cc20cc7489abb8607da4d960e |
# this file contains all the string data (inputs and outputs) for tests
# the SD trees were originally produced on SD 3.4.1 but they work up
# to (at least) SD 3.5.2. the UD trees were produced using UD 3.5.2.
# tests now require SD/UD 3.5.2 (and thus Java 1.8). downside of this
# is that we can't test JPype on older ... | dmcc/PyStanfordDependencies | test/data.py | Python | apache-2.0 | 58,776 | [
"MOOSE"
] | 2191705e54c40ccb883382beeb11549d617c8d4ca75b0b8cc43bf5d358acdf61 |
import abc
import numpy as np
import operator
import six
import sys
import uuid
import logging
import warnings
import weakref
from ast import parse
if six.PY2:
from funcsigs import signature, Parameter as SigParameter
else:
from inspect import signature, Parameter as SigParameter
__all__ = ['Nexus', 'NexusEr... | dsavoiu/kafe2 | kafe2/core/fitters/nexus.py | Python | gpl-3.0 | 50,584 | [
"VisIt"
] | 6b2717e8b58e822f9f90a5c5789b115560158b1d71daa5684442cb4f60c14f8f |
"""Define a graph of nodes-links-patches.
Nodes and links are required. If no patches are provided, no patches will
be created.
Examples
--------
>>> from landlab.graph import NetworkGraph, Graph
>>> node_x, node_y = [0, 0, 0, 1, 1, 1, 2, 2, 2], [0, 1, 2, 0, 1, 2, 0, 1, 2]
>>> graph = NetworkGraph((node_y, node_x),... | amandersillinois/landlab | landlab/graph/graph.py | Python | mit | 31,162 | [
"NetCDF"
] | 3a9cdbb0e5711644e0c1a3c8a36c2e6328b85b43d0cf5f138718808bc618c553 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
import collections
import logging
import threading
import itertools
import time
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
FIRST_COMPLETED = 'FIRST_COMPLETED'
FIRST_EXCEPTION = 'FIRST_EXCEPTION'
ALL_COMPLETED... | maxrothman/aws-alfred-workflow | venv/lib/python2.7/site-packages/concurrent/futures/_base.py | Python | mit | 21,072 | [
"Brian"
] | 6a5bed9fe1f805879b4b507d4625f6d2a8bfa5fa74235679c231aaf9807eaf19 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
import iris
# <codecell>
# calculate the current speed using a EPIC NetCDF file
url = 'http://geoport.whoi.edu/thredds/dodsC/usgs/data2/emontgomery/stellwagen/CF-1.6/RCNWR/9541aqd-cal.nc'
# <codecell>
u = iris.load_cube(url,'eastward_sea_water_veloci... | rsignell-usgs/notebook | calc_speed.py | Python | mit | 980 | [
"NetCDF"
] | 7daa7eb1e4145ecd892ea37f8f763ad69d487f497055fc60ef6a287db214936b |
import variants_pb2
import sys
import os
import pysam
from pysam import VariantFile
from pymongo import MongoClient
import json
import google.protobuf.json_format as json_format
import time
import progressbar
import uuid
import google.protobuf.struct_pb2 as struct_pb2
import argparse
parser = argparse.ArgumentParser()... | Arc39/vcf_to_ga | scr.py | Python | apache-2.0 | 8,074 | [
"pysam"
] | 12557a233700fc4c0746cf4ff364f3c7b69d115d666369917edeb8707800afbd |
from __future__ import absolute_import
input_name = '../examples/diffusion/laplace_coupling_lcbcs.py'
output_name = 'test_laplace_coupling_lcbcs.vtk'
from tests_basic import TestInput
class Test(TestInput):
pass
| vlukes/sfepy | tests/test_input_laplace_coupling_lcbcs.py | Python | bsd-3-clause | 217 | [
"VTK"
] | 29a63a47a27f895a3fa37e711c4a1f5864e2d104b1bb315e838c8da7b85af29b |
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 16 19:04:22 2016
@author: tih
"""
import pandas as pd
import glob
import gdal
import osr
import os
import numpy as np
import subprocess
from pyproj import Proj, transform
import scipy.interpolate
def Run_command_window(argument):
"""
This function runs the argume... | wateraccounting/wa | General/raster_conversions.py | Python | apache-2.0 | 30,795 | [
"ADF",
"NetCDF"
] | d7f15783f7a0b4fa0ab999cd2ba1786b75baa8ae3e286d5117e1aabcca5ec1ee |
from nose.tools import *
from pysam import FastaFile
import pysam
import asmvar.variantutil as vutil
from asmvar.variantutil import VariantCandidateReader as vcreader
from asmvar.haplotype import Haplotype as Hap
import asmvar.datum as dm
import asmvar.common as com
from asmvar.read import Read
def setup():
print... | ShujiaHuang/AsmVar2 | tests/asmvar_tests.py | Python | mit | 8,854 | [
"pysam"
] | eeed9411d728951be09cfe8b52e39cd725b2a88d31b47df388ce2d13cb1deba9 |
#!/bin/python
from new-vm.py import *
from libvirt-ks-kvm.conf import *
#Generates a KS file.
#This KS file is just an example and will not work with your environment. You will need to manually edit this config file.
def ks_configurator():
KS = "
install
text
cdrom
lang en_US.UTF-8
keyboard us
network --onboot yes... | brianfarlinger/Quick-Configuration | ks-configurator.py | Python | gpl-3.0 | 1,928 | [
"Brian"
] | 42eae39ddb16cb79ae2e4d403fd6ae4fa6138537bee460fbd74103f8e86e887b |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_aos_libnao.py | Python | apache-2.0 | 1,597 | [
"PySCF"
] | 215c88ddbcd77a44164cba8535ee58a6ef38d7da9201296f0fa04c7c5df1254a |
"""\
@file llmessage.py
@brief Message template parsing and compatiblity
$LicenseInfo:firstyear=2007&license=mit$
Copyright (c) 2007-2009, Linden Research, Inc.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
i... | gabeharms/firestorm | indra/lib/python/indra/ipc/llmessage.py | Python | lgpl-2.1 | 12,631 | [
"GULP"
] | 65c366e5b998f682f4d6fd32562ac7b7588ff09322c2cb55b3626d82c25dba9b |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/r-gcrma/package.py | Python | lgpl-2.1 | 1,898 | [
"Bioconductor"
] | b8193d4a0ff74dd4bbb81a6149f1d628ea7aec125e5a0fb300d9e8276e548a5b |
from __future__ import print_function
import os
import sys
import argparse
import pysam
def convert_sams2bams(sams):
separator = ","
split_sams = sams.split(separator)
bams = list()
for sam in split_sams:
bam = sam.replace(".sam", ".bam")
bams.append(bam)
os.system("samtools ... | Xinglab/rmats2sashimiplot | src/rmats2sashimiplot/rmats2sashimiplot.py | Python | gpl-2.0 | 44,567 | [
"pysam"
] | b6ed489b9d42159885bcef87864018bdfaeaa6870e3235945af1c653ce063d39 |
# ----------------------------------------------------------------------
# Copyright (c) 2016, The Regents of the University of California All
# rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# ... | drichmond/tinker | python/QDR.py | Python | bsd-3-clause | 3,773 | [
"TINKER"
] | a3eaf3efbb037f0f3a10972346dc7ab86668853d17ff61af14c4d9bc83d46692 |
### Script calculates probability as area under a normal gaussian curve,
### given inputs of x1, x2, mu (mean), sigma(standard deviation) and computes
### the probabability using the integral function and the gaussian curve.
from math import sqrt,erf
## If plotting as well
#import matplotlib.pyplot as plt
#import numpy... | ProfessorKazarinoff/staticsite | content/code/statistics/area_under_normal_curve.py | Python | gpl-3.0 | 1,147 | [
"Gaussian"
] | 47c92b165fcf267efd879f63f2a64d6f4e3e8020523f5aa2700df88770abe980 |
#!/usr/bin/env python
# megamapper intersector
# by Nikolaus Obholzer, Jan 2012
import sys, re, tempfile, subprocess
import os, shutil
#import pkg_resources; pkg_resources.require( "bx-python" )
#from bx.cookbook import doc_optparse
from galaxy import eggs
def stop_err(msg):
sys.stderr.write(msg)
sys.exit()
... | maxplanck-ie/Megamapper | candidator.py | Python | bsd-3-clause | 1,163 | [
"Galaxy"
] | e54da51ea92e27d654a558c84d07a80ad334308dd42c3f1da6d0137342cb697f |
import time
import numpy as np
from ase.transport.tools import dagger
from ase.transport.selfenergy import LeadSelfEnergy
from ase.transport.greenfunction import GreenFunction
from ase.parallel import world
class STM:
def __init__(self, h1, s1, h2, s2 ,h10, s10, h20, s20, eta1, eta2, w=0.5, pdos=[], logfile = N... | suttond/MODOI | ase/transport/stm.py | Python | lgpl-3.0 | 7,518 | [
"ASE"
] | 557f4bb7671409d2992177d2629f4584f3b1f64897bfd6c08e21769e8745ef69 |
# (c) 2014, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible 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 3 of the License, or
# (at your option) any later version.... | shakamunyi/ansible | v2/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 3,344 | [
"Brian"
] | e9c8c07c3cf193b8b8d47726e49fa0c355ff44332d2e803522c3535a53c2bba7 |
from unittest import TestCase
from docclass import Classifier
from docclass import getwords
__author__ = 'maria'
class TestGetwords(TestCase):
def testGetFeatures(self):
c = Classifier(getwords)
dict = c.getfeatures("Hello World world world , hello has cats and vervyveryveryveryveryverylon... | stefanseibert/DataMining | experiment03/scripts/test_classifier.py | Python | mit | 3,957 | [
"CASINO"
] | 7a91ece01600c680fcb7ea1a052cf147cec5938f0d919472058480c101cce064 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Using solvent model in the CCSD calculations. When applying solvent model,
this example has convergence issue.
'''
from pyscf import gto, scf, cc
from pyscf import solvent
mol = gto.M(atom='''
C 0.000000 0.000000 -0.54250... | gkc1000/pyscf | examples/solvent/03-ccsd_with_ddcosmo.py | Python | apache-2.0 | 1,201 | [
"PySCF"
] | bebfc1b0de9e4e0ef1b5886b8f795e9109fd14ff29efb7249af52095e4b0bbed |
#! /usr/bin/env python
"""
metaHGT (meta-community Horizontal Gene Transfer tracker):
in-situ and real time HGT tracker for series metagenomes
Copyright(c) 2013 Chengwei Luo (luo.chengwei@gatech.edu)
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Pub... | fw1121/metaHGT | src/calHGT.py | Python | gpl-3.0 | 15,394 | [
"pysam"
] | b0294ebe877da0ba7a71df0548f70fca991a6ba629fccc97fb8fe4eaa87a0f62 |
from __future__ import division, absolute_import, print_function
import os
import sys
import types
import re
from numpy.core.numerictypes import issubclass_, issubsctype, issubdtype
from numpy.core import product, ndarray, ufunc, asarray
__all__ = [
'issubclass_', 'issubsctype', 'issubdtype', 'deprecate',
'd... | techtonik/numpy | numpy/lib/utils.py | Python | bsd-3-clause | 36,391 | [
"VisIt"
] | 37bd6d1e1dc3eb3375d4d7a807d0a14b0ac34d54014ded2c0a4fcffe382d16a0 |
from fractions import Fraction
"""
We want to determine the optimum polynomial OP(k,n) for a given degree k-1:
OP(k,n) = a(0) + a(1) * n + a(2) * n^2 + ... + a(k-1) * n^(k-1)
Plugging values n = 1...k into OP(k, n) must generate the series u(n):
OP(k, 1) = u(1)
OP(k, 2) = u(2)
OP(k, 3) = u(3)
...
O... | brunorijsman/euler-problems-python | euler/problem101.py | Python | bsd-2-clause | 4,006 | [
"Gaussian"
] | 6fbc9d753efeaa1638c0ed25ddfb7f9bad68088d4c0976dc3dd051b69f6dace5 |
"""
Profile Model Access
"""
import logging
from ozpcenter import errors
from ozpcenter import models
from ozpcenter import utils
from django.contrib import auth
import ozpcenter.model_access as generic_model_access
import ozpcenter.api.storefront.model_access as storefront_model_access
from plugins import plugin_man... | aml-development/ozp-backend | ozpcenter/api/profile/model_access.py | Python | apache-2.0 | 7,248 | [
"VisIt"
] | d8d19b9c0724459f5f2122c950c42a00c166d72d2cfeaa32ebfdceab00708410 |
from neuron import h
def shape_3D(self):
self.dend[0].connect(self.soma, 0.5, 0)
for i in range(1, 2):
self.dend[i].connect(self.dend[i-1], 1, 0)
self.dend[3].connect(self.dend[1], 1, 0)
for i in range(4, 6):
self.dend[i].connect(self.dend[i-1], 1, 0)
self.dend[7].connect(self.dend[5], 1, 0)
self.dend[8].conn... | penguinscontrol/Spinal-Cord-Modeling | Python/Mn_geometry_output3.py | Python | gpl-2.0 | 894,622 | [
"NEURON"
] | d1854e182c641a477bacb540fb17c94146a38c41c12bcca86c9dcd6f5795d4f4 |
# tests/test_tensorflow_imagenet_adapter.py - unit test for the tensorflow ImageNet adapter.
#
# Copyright (c) 2017 SingularityNET
#
# Distributed under the MIT software license, see LICENSE file.
#
import logging
import os
from pathlib import Path
import base64
import pytest
from adapters.tensorflow.imagenet import... | jensenbox/singnet | agent/tests/test_tensorflow_imagenet_adapter.py | Python | mit | 5,023 | [
"Bowtie"
] | 5a8989ca72f357edf37d58b70ad608250c2b221d9e9ecac345bf6b712f2f7291 |
#!/usr/bin/env python
"""
Created on Fri Dec 5 10:41:33 2014
Author: Oren Freifeld
Email: freifeld@csail.mit.edu
"""
import numpy as np
from pylab import plt
from cpab.cpa2d.inference.transformation.Register import Register
from of.utils import *
import pylab
from get_data import get_data
if not inside_spyder():
... | freifeld/cpabDiffeo | cpab/cpa2d/apps/register/register_images_MNIST.py | Python | mit | 6,138 | [
"Gaussian"
] | 9ef539668b18ccfb91771beea53908b8e48d6159fa21525ccc15a3bd3c6928b0 |
# Lint as: python2, python3
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
... | mlperf/training_results_v0.7 | Google/benchmarks/transformer/implementations/transformer-research-TF-tpu-v4-512/lingvo/tasks/mt/encoder.py | Python | apache-2.0 | 35,293 | [
"Gaussian"
] | 8b65acdd4dc25dc6b02ddddeb3d9b9dca764e1404daa7da946729a5d0b4b9e65 |
import matplotlib
matplotlib.use('Agg')
import numpy as np
import netCDF4
from datetime import datetime
import pyroms
import pyroms_toolbox
import sys
def create_HYCOM_file(name, time, lon, lat, z, var):
print 'Write with file %s' %name
#create netCDF file
nc = netCDF4.Dataset(name, 'w', format='NETCD... | dcherian/pyroms | examples/Arctic_HYCOM/get_hycom_GLBa0.08_temp_2014.py | Python | bsd-3-clause | 4,746 | [
"NetCDF"
] | 4773f55eeef1ced5e3cc50af7ea8fe91a1b737437f498c735c26e92e18d7f4b4 |
# Copyright 2013-2021 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)
import glob
class Chombo(MakefilePackage):
"""The Chombo package provides a set of tools for implementing finite
... | LLNL/spack | var/spack/repos/builtin/packages/chombo/package.py | Python | lgpl-2.1 | 4,968 | [
"Brian"
] | cae6447d4b81be84f179800ea6333fe90d0eb9be9865d5ae7b381fd340f81da2 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the main LMS Dashboard (aka, Student Dashboard).
"""
from ..helpers import UniqueCourseTest
from ...fixtures.course import CourseFixture
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.dashboard import DashboardPage
class BaseLmsDashboardTest(UniqueCo... | tiagochiavericosta/edx-platform | common/test/acceptance/tests/lms/test_lms_dashboard.py | Python | agpl-3.0 | 3,835 | [
"VisIt"
] | 4ff56920b508317b3fbad2c26f4aadaa5c0c0823d191be23bfe12ac80eca3578 |
#!/usr/bin/env python3
import numpy as np
import matplotlib.pyplot as plt
from LoLIM.utilities import processed_data_dir
from LoLIM.IO.raw_tbb_IO import MultiFile_Dal1, filePaths_by_stationName
from LoLIM.signal_processing import remove_saturation
from LoLIM.findRFI import window_and_filter
from LoLIM.read_pulse_data... | Bhare8972/LOFAR-LIM | LIM_scripts/examples/print_all_antenna_locations.py | Python | mit | 1,184 | [
"Brian"
] | 55ea85a64ca9f7fd466ff5a4612872151a1eeca12dbf171cf865759566f24b83 |
import sys
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
from fitFunctions import gaussian
import mpfit
import scipy.stats
import smooth
from util.ObsFile import ObsFile
from util.FileName import FileName
import Utils.bin as binTools
import os
import struct
def smoothBaseline(baselines,nPtsInMod... | bmazin/SDR | Projects/TestBaseline/compareBaseline.py | Python | gpl-2.0 | 9,678 | [
"Gaussian"
] | 9bcb82ecfe9138e5e210b05d626d67ca6638dc491b41b21669395ab0305533d9 |
import test.support
# Skip tests if _multiprocessing wasn't built.
test.support.import_module('_multiprocessing')
# Skip tests if sem_open implementation is broken.
test.support.import_module('multiprocessing.synchronize')
# import threading after _multiprocessing to raise a more revelant error
# message: "No m... | Orav/kbengine | kbe/src/lib/python/Lib/test/test_concurrent_futures.py | Python | lgpl-3.0 | 24,513 | [
"Brian"
] | de0bf2527611b5f47ea6306ef4bdf5edad3282b7b40ae237ec7007bc241a9352 |
# -*- coding: utf-8 -*-
# Copyright (C) 2012, Almar Klein, Ant1, Marius van Voorden
#
# This code is subject to the (new) BSD license:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of s... | jamesrobb/remo-2016-mongooses | rush_hour/gif/images2gif.py | Python | mit | 36,120 | [
"NEURON"
] | e865ab661431dda627da0141c5ec0ea28c0a7f65c8ad6362855521138c22257d |
###############################################################################
##
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary forms, with or without
## modification, ... | CMUSV-VisTrails/WorkflowRecommendation | vistrails/db/versions/v0_7_0/translate/v0_6_0.py | Python | bsd-3-clause | 10,591 | [
"VTK"
] | d2d358bd63bc6dbf21b3571399deed39de261481ce3ff80cd146b2b0458527f1 |
# 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 RScater(RPackage):
"""Single-Cell Analysis Toolkit for Gene Expression Data in R.
... | rspavel/spack | var/spack/repos/builtin/packages/r-scater/package.py | Python | lgpl-2.1 | 3,379 | [
"Bioconductor"
] | 39981e8bf6aa693dd6798ab558abdaedee8fea10bcd5e4d1ac1a6e7273857bf7 |
#!/usr/bin/env python
# Copyright (c) 2018 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import print_function
import re
import scm
import subprocess2
import sys
try:
import urlparse
except ImportErro... | endlessm/chromium-browser | third_party/depot_tools/metrics_utils.py | Python | bsd-3-clause | 8,811 | [
"VisIt"
] | 530f7574c5010dcdb1dacd0c1e32cc1a0c0223d0242ab1b97545b820f62cb9bd |
#!usr/bin/env python
import sys
from Bio import SeqIO
import networkx as nx
from collections import Counter
import os
from commands import getoutput
# do the core gene find
def manual_print():
print 'This script used reciprocal best hits to identify orthologs between species and a given species, then e... | Rinoahu/fastclust | deprecate/py27/scripts/rbh2phy.py | Python | gpl-3.0 | 7,356 | [
"BLAST",
"VisIt"
] | 4fb657cb137d58ed45759cd718921c41210b0c74b47c772080d254a8b7355b4b |
# pymol -c generate2.py
from chempy import io
from glob import glob
from copy import deepcopy
# backbone-independent rotamers
lines = io.lst.fromFile("bbind02.May.lib")
# skip to the data section
while lines[0][0:3]!='Res':
lines.pop(0)
lines.pop(0)
chi = { 'CYS' :
{ '1': ('N' , 'CA' , 'CB' , 'SG' ) ... | gratefulfrog/lib | python/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py | Python | gpl-2.0 | 3,747 | [
"ChemPy",
"PyMOL"
] | 9ea4958b32980590b486775001125c79b97c2bfb4678345a5365034d0e83cd15 |
import hashlib
import os
import pytest
from Bootstrapper import BootstrapperPlugin
from Bootstrapper.BootstrapperDb import BootstrapperDb
from Peer import Peer
from Crypt import CryptRsa
from util import helper
@pytest.fixture()
def bootstrapper_db(request):
BootstrapperPlugin.db.close()
BootstrapperPlugin.... | OliverCole/ZeroNet | plugins/disabled-Bootstrapper/Test/TestBootstrapper.py | Python | gpl-2.0 | 10,142 | [
"MOE"
] | 25462b20aed278957d189de0bf5c67fc0b33cbe87a10c61b33578890298324d1 |
# Copyright 2001 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
This module provides code to work the NCBI's XML format for Medline.
Functions:
choose_fo... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Medline/NLMMedlineXML.py | Python | apache-2.0 | 9,614 | [
"Biopython"
] | 994b6600ad96fec619fa8359082ba1e0ed16cf5cf3f4ab56aef89a87aa6c724c |
#!/usr/bin/env python
import sys
import os
import cPickle as pickle
import gzip
import pysam
def remove_rRNA(fileInNameBam, fileInNamePickle, fileOutName):
if os.path.exists(fileOutName):
print '%s already exists!' % fileOutName
return
if os.path.exists(fileInNamePickle):
FileIn = gz... | ratschlab/RiboDiff | tools/pipeline/filter_reads/filtering_RNA.py | Python | gpl-3.0 | 1,045 | [
"pysam"
] | e8dca9f0f48485d92a37ef24b7d72fbfed964975e319395722edc5dc9f50b1c6 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Module which defines basic entries for each ion and oxide to compute a
Pourbaix diagram
"""
__author__ = "Sai Jayaraman"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.0"
__maintainer__ = "Sai Jayaraman"
__email__ = "sja... | rousseab/pymatgen | pymatgen/analysis/pourbaix/entry.py | Python | mit | 14,048 | [
"pymatgen"
] | ef3710af96bb4f2bf287ebbe5c8b9f4ed958ab94a10ea86e4420f341b0f58d2b |
#!/usr/bin/env python
# GPL HEADER START
#
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 only,
# as published by the Free Software Foundation.
#
# This program is d... | chaos/lustre-kdmu | lustre/utils/Lustre/cmdline.py | Python | gpl-2.0 | 7,282 | [
"VisIt"
] | 5967a19601686be9da22051e48fbf1e66d6e728fbde819c6b833d07de3093137 |
import pytest
import numpy as np
import xarray as xr
from glotaran import ParameterGroup
from glotaran.builtin.models.doas import DOASModel
from glotaran.builtin.models.doas.doas_matrix import calculate_doas_matrix
class OneOscillation():
sim_model = DOASModel.from_dict({
'oscillation': {
'os... | glotaran/glotaran | glotaran/builtin/models/doas/test/test_doas_model.py | Python | gpl-3.0 | 9,452 | [
"Gaussian"
] | 289edc53cfcee494c8036c85d0e2cf4aa7fcf08373636c1ac8428981ff934a17 |
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2018 Raik Gruenberg & Johan Leckner
##
## 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 v... | graik/biskit | biskit/core/trajparsePDBs.py | Python | gpl-3.0 | 5,946 | [
"Amber",
"NetCDF"
] | e4973a415389e07c31f503f8a5907a3317222b3b06748fef5d29a0758abe1085 |
# Built-in modules #
import subprocess, sys
# Constants #
module_names = {
"biopython": "Bio",
"ipython": "IPython",
"scikit-learn": "sklearn",
"scikit-bio": "skbio",
"biom-formt": "biom",
}
################################################################################
def check_setu... | DC23/plumbing | plumbing/dependencies.py | Python | mit | 1,590 | [
"Biopython",
"scikit-bio"
] | 25539f93a251f16087ddd5c5c9d6763ee10fe67f8cba96fb220379687915b6ff |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
from dj... | RotorWidgets/base-station | config/urls.py | Python | gpl-3.0 | 1,848 | [
"VisIt"
] | cee128320a6a8fba74a2d8e73cb19f4be4f8a41a860bd0ada0e9eaa61b21e9c0 |
from Bio import PDB, SeqIO, AlignIO,pairwise2
from Bio.Seq import Seq
from Bio.SubsMat import MatrixInfo as matlist
import os,sys,csv,cPickle
import numpy as np
import warnings
warnings.filterwarnings("ignore")
f = open('pdb_ids_all').read().splitlines()
pdb_unique_ids = sorted(list(set(f)))
file_pref = "../Data/"
wo... | biocryst/gc | validation/clusters_rmsd.py | Python | mit | 4,413 | [
"CRYSTAL"
] | d3af20a921a40f968be9fce0c32923c1d063fc450f1c60cbdfac44eb2c4915c2 |
# Copyright 2018 Open Source Robotics Foundation, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law... | ros2/launch | launch/test/launch/test_launch_description.py | Python | apache-2.0 | 3,917 | [
"VisIt"
] | bf7457ce9421efd6799c24564672143a80e26ef571dad1406f5af4b276a36bdf |
#!/usr/bin/env python
########################################################################
# File : dirac-dms-replicate-lfn
# Author : Stuart Paterson
########################################################################
"""
Replicate an existing LFN to another Storage Element
Example:
$ dirac-dms-replica... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/scripts/dirac_dms_replicate_lfn.py | Python | gpl-3.0 | 1,980 | [
"DIRAC"
] | 79945027e26eb907630863434a36b3f32cfe6ed892ff10c2011eb7eb894e32ed |
from datetime import datetime
import warnings
import numpy as np
import pandas as pd
from pandas import DataFrame
import matplotlib.pyplot as plt
from statsmodels.stats.diagnostic import acorr_ljungbox
from statsmodels.tsa.stattools import adfuller as ADF
from statsmodels.graphics.tsaplots import plot_acf, plot_pacf
i... | bigdig/vnpy | examples/data_analysis/data_analysis.py | Python | mit | 10,377 | [
"ADF"
] | 9b0647fe7ad64019d5b677093721bd082c8bc1c7c15a3bdf9164a0d7da77ebd6 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/diversity/alpha/tests/test_gini.py | Python | bsd-3-clause | 2,172 | [
"scikit-bio"
] | 0edc1a4e6d43266a00c48a402581b0ce61b0bbed7f17ba59ca2842a63d0f3fff |
from nose.tools import eq_, ok_, raises
import pods
import os
import re
import sys
if sys.version_info >= (3, 0):
from urllib.error import HTTPError, URLError
else:
from urllib2 import URLError as HTTPError
from urllib2 import URLError
# details of a test page
test_url = "http://www.bbc.co.uk/"
store_dir... | sods/ods | pods/testing/util_tests.py | Python | bsd-3-clause | 2,178 | [
"BLAST"
] | 42a00f201d6ac8b90454d04a89d2743fb4568ac491321f2d83570672db71a964 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/vasp/nlep/mpopt.py | Python | gpl-3.0 | 21,833 | [
"CRYSTAL",
"VASP"
] | fa80f46269c065c3d5a4f9919289d04d03c6c6a8aebff59928494cad8cf07adb |
#
# This file is part of the CCP1 Graphical User Interface (ccp1gui)
#
# (C) 2002-2005 CCLRC Daresbury Laboratory
#
# 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 ... | alexei-matveev/ccp1gui | viewer/main.py | Python | gpl-2.0 | 218,187 | [
"CHARMM",
"ChemPy",
"DL_POLY",
"Dalton",
"GAMESS",
"Jaguar",
"MOPAC",
"Molpro",
"PyMOL",
"VTK",
"VisIt"
] | 7f3b64eed225f8f8d18cbd58d85e4ac245289f07a6ddffdf97336aaaf95aa3d8 |
"""
calculate coverage across a list of regions
"""
import os
import os.path as op
import yaml
from argparse import ArgumentParser
# import matplotlib.pyplot as plt
# from matplotlib.backends.backend_pdf import PdfPages
# import matplotlib
# import seaborn as sns
from ichwrapper import cluster, arguments
# import pand... | lpantano/ASMfinder | scripts/asm-pipeline.py | Python | mit | 7,652 | [
"Galaxy"
] | 0c274c87094ddca6edf5e08ccab2383860357ed2b16d81b4649e2a31f136dea6 |
"""
Some classes and functions for analysing chromosome conformations generated with
Hamiltonian Monte Carlo.
"""
import numpy as np
import pylab as plt
from isdhic import utils
from csb.bio.utils import distance_matrix
from collections import OrderedDict
class Ensemble(object):
def __init__(self, samples):
... | michaelhabeck/isdhic | scripts/analyze.py | Python | mit | 3,085 | [
"PyMOL"
] | 7fc73d85fddedd19912879176fc2e27ffb98e5a2bff991dc06b1b1ed52b4e253 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/awidgets/slider.py | Python | gpl-3.0 | 1,189 | [
"Brian"
] | 38141ccc5fc718719db3c9c237d19d3a98b8bca7ed0095405ec966ed089b8235 |
## ENVISIoN
##
## Copyright (c) 2021 Gabriel Anderberg, Didrik Axén, Adam Engman,
## Kristoffer Gubberud Maras, Joakim Stenborg
## All rights reserved.
##
## Redistribution and use in source and binary forms, with or without
## modification, are permitted provided that the following conditions are met:
##
## 1. ... | rartino/ENVISIoN | envisionpy/hdf5parser/ELK/elf_parser_elk.py | Python | bsd-2-clause | 4,287 | [
"Elk"
] | 9cc0ec019770222a0b17f9fd04aa9607ed48e65e9a35172b052794c688a33e35 |
# Generated from java-escape by ANTLR 4.5
from antlr4 import *
# This class defines a complete generic visitor for a parse tree produced by CParser.
class CVisitor(ParseTreeVisitor):
# Visit a parse tree produced by CParser#FunctionExpression.
def visitFunctionExpression(self, ctx):
return self.visit... | smartanthill/plugin-handler-compiler | smartanthill_phc/antlr_parser/CVisitor.py | Python | gpl-2.0 | 11,540 | [
"VisIt"
] | 97746dcc0f6bc8459d4ddf16fb1c980b0985e35afdee753313514d8c53468758 |
import lb_loader
import numpy as np
import pandas as pd
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
pd.set_option('display.width', 1000)
platform = mm.Platform_getPlatformByName("CUDA")
n_steps = 1500
temperature = 300. * u.kelvin
collision_rate = 1.0 / ... | kyleabeauchamp/HMCNotes | code/old/test_ghmc_respa_compare_mixed.py | Python | gpl-2.0 | 1,663 | [
"OpenMM"
] | a6240d9aa42b44a7738a481a0a6809db28723ca5e15de32f60dfb455fc62e843 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/do/eagle/build.py | Python | mit | 10,025 | [
"Galaxy"
] | 378e68f0274516a76c47ebe223e5c8caca2a0d049537c9c7636f9137d01ddd43 |
"""Runs the main game loop and user interface.
"""
import os, sys
from copy import copy, deepcopy
import actions
from Character import Character
from Character import Character
from Weapon import Weapon
from Spell import Spell
EMPTY_LINE = '{}{:>141}'.format('#', '#\n')
BORDER_LINE = "{:#>142}".format("\n")
def ene... | tomhettinger/simplestone | gameboard/loop.py | Python | mit | 11,292 | [
"CRYSTAL"
] | 0ca4343eca48eded8f0d5cd1fe757c20f2b5f1bc8188ee4705a2ce75f0163e4d |
"""Unit tests of MQConsumer interface in the DIRAC.Resources.MessageQueue.MQConsumer
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
from DIRAC import S_OK
from DIRAC.Resources.MessageQueue.MQConsumer import MQConsumer
from DIRAC.Resource... | ic-hep/DIRAC | src/DIRAC/Resources/MessageQueue/test/Test_MQConsumer.py | Python | gpl-3.0 | 4,195 | [
"DIRAC"
] | 0ba199f9219dd116d8710301af0754759ea03c1085aebfb9c82a5378b50aeca5 |
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