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from pymol.wizard import Wizard
from pymol import cmd
import pymol
import copy
default_map = [ '', '', '']
default_level = [ 1.0, 3.0, -3.0]
default_radius = 8.0
default_track = 0
class Density(Wizard):
def __init__(self,_self=cmd):
self.cmd = _self
self.cmd.unpick()
Wizard.__i... | gratefulfrog/lib | python/pymol/wizard/density.py | Python | gpl-2.0 | 10,162 | [
"PyMOL"
] | 34ee3be4c49ac0bd124bd66b1278376562905073c9969e28c8ccaec652ad178b |
from collections import defaultdict, Sized
from functools import partial
import numpy as np
from scipy.stats import rankdata
import sklearn
from sklearn.base import is_classifier, clone
from sklearn.externals.joblib import Parallel, delayed
from sklearn.model_selection._search import BaseSearchCV
from sklearn.utils i... | betatim/BlackBox | skopt/searchcv.py | Python | bsd-3-clause | 27,200 | [
"Gaussian"
] | a56a32c08191820c42956d27df4d1618b6e5cf018fb9f0f0ccd287c86a8bc428 |
import os.path as op
import numpy as nm
from sfepy import data_dir
from sfepy.base.testing import TestCommon
def init_vec(variables):
return nm.random.rand(variables.di.ptr[-1])
def check_vec(self, vec, ii, ok, conds, variables):
from sfepy.discrete.common.dof_info import expand_nodes_to_equations
for... | RexFuzzle/sfepy | tests/test_conditions.py | Python | bsd-3-clause | 9,711 | [
"VTK"
] | feeeb6a5ba2ad93ddaf5035481e28d81c7be2a712f507162a5eaf360b2112b10 |
import re
import sys
import datetime
import AlphaSubstValidation
import AlphaSubstPrep
import AlphaSubstBaseMLBootstrap
import AlphaSubstScoring
import random
def stop_err(msg):
"Write the error message and exit"
sys.stderr.write(msg)
sys.exit()
#Retrieve Data
OutputFile = sys.argv[1]
Method = sys.argv[2]... | jmchilton/galaxy-central | tools/mdea/BaseML.py | Python | mit | 8,690 | [
"Galaxy"
] | eb4591969bba5656ccd95b5a6d8e32d600d946a41972c1eda3001d47c920f3cb |
# 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/ao_log.py | Python | apache-2.0 | 18,300 | [
"GPAW",
"Gaussian",
"PySCF",
"SIESTA"
] | 898d6d779b76bf175dae643315dbeb8da6a80cb2bd43d517542ae3ff7fbf8c4d |
"""Utility routines depending on the finder,
a combination of code by Jack Jansen and erik@letterror.com.
Most events have been captured from
Lasso Capture AE and than translated to python code.
IMPORTANT
Note that the processes() function returns different values
depending on the OS version it is running on. On MacO... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-2.3/Lib/plat-mac/findertools.py | Python | mit | 30,503 | [
"BLAST"
] | d3793bd588c12ec578e81c979ec8c3844e910263d95e0ea4b6a8c956f904b923 |
# ==================================================================================================
# Copyright 2011 Twitter, Inc.
# --------------------------------------------------------------------------------------------------
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... | imsut/commons | src/python/twitter/common/log/__init__.py | Python | apache-2.0 | 2,176 | [
"Brian"
] | 928acb41e14fac221ba2c4a2185f881cba612ad56b2080ef321c46a9bfcba5b7 |
#!/usr/bin/env python
# Python Module to work with ROMS
# Owner: Rafael Soutelino - rsoutelino@gmail.com
# Committers: Andre Lobato - andrefelipelobato@gmail.com
# Last modification: Mar, 2016
#####################################################################
from dateutil.parser import parse
import numpy as np
impo... | rsoutelino/romslab | romslab.py | Python | mit | 76,507 | [
"NetCDF"
] | a3cf0f378c8bc18ab5c9f66e53122cd0b6b6919739578e90e127d8c5515a1ca1 |
# Copyright (c) 2003-2014 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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, o... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/pylint/lint.py | Python | agpl-3.0 | 58,101 | [
"VisIt"
] | d0edc055500d8731999e4f501dd90561da3ca9a0efd8f677ee48fba877cb789c |
#!/usr/bin/env python
"""
list FileCatalog file or directory
"""
import os
from COMDIRAC.Interfaces import critical
from COMDIRAC.Interfaces import DSession
from COMDIRAC.Interfaces import createCatalog
from COMDIRAC.Interfaces import pathFromArguments
if __name__ == "__main__":
import sys
from DIRAC.Core.Base ... | pigay/COMDIRAC | Interfaces/scripts/dls.py | Python | gpl-3.0 | 7,966 | [
"DIRAC"
] | b7516eb1b144baa390626ce2c545be349b8c31630e9b1b975912c2f71fdc0eff |
"""
Tools for the instructor dashboard
"""
import dateutil
import json
from django.conf import settings
from django.contrib.auth.models import User
from django.http import HttpResponseBadRequest
from django.utils.timezone import utc
from django.utils.translation import ugettext as _
from courseware.models import Stud... | ampax/edx-platform | lms/djangoapps/instructor/views/tools.py | Python | agpl-3.0 | 7,903 | [
"VisIt"
] | 6bfcff3d06fc45c04eefa09b6dbc2fe0c146acdb2221cd35b09a346be18c269b |
#!/usr/bin/env python
"""
Fit parameters of classical interatomic potentials using a metaheuristic algorithm.
Because of computational efficiency, optimization of a lot of parameters using
gradient-based approaches is out of focus in this program, and that should be
performed in a Fortran program.
Usage:
{0:s} [opti... | ryokbys/nap | nappy/fitpot/fp.py | Python | mit | 29,415 | [
"ADF",
"VASP"
] | d30587965c5157d70a0d83c7423b5c7e07631d17a22dbddd5a671abc3103e408 |
import sqlite3
import os
import types
import hashlib
import time
import DIRAC
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.FrameworkSystem.private.monitoring.Activity import Activity
from DIRAC.Core.Utilities import Time
class MonitoringCatalog:
def __init__( self, dataPath ):
"""
Initialize monitor... | coberger/DIRAC | FrameworkSystem/private/monitoring/MonitoringCatalog.py | Python | gpl-3.0 | 12,544 | [
"DIRAC"
] | 810276f8f933806ff03edfb28a71901a8e534bab60eacee14b2c65ba2620926a |
###############################################################################
##
## Copyright 2011-2012 Tavendo GmbH
##
## 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:... | cachedout/AutobahnPython | autobahn/autobahn/useragent.py | Python | apache-2.0 | 9,585 | [
"Galaxy"
] | 29705521baddc14dcf0fdc74d1b32c5b66bb129d2537314c459d4cf2b76992e0 |
import os
import copy
import math
import functools
import numpy as np
from ddapp import transformUtils
from ddapp.asynctaskqueue import AsyncTaskQueue
from ddapp import objectmodel as om
from ddapp import visualization as vis
from ddapp import robotstate
from ddapp import segmentation
from ddapp import planplayback
f... | edowson/director | src/python/ddapp/tabledemo.py | Python | bsd-3-clause | 48,436 | [
"VTK"
] | 652c8873d9e58dc5ce92091e982af1dfab8a7f2bf0944c11bc47a12657c0f5e0 |
from itertools import izip_longest
from numpy import array
from numpy.testing import assert_array_almost_equal
import unittest
from periodic.crystal import Crystal
class TestNaCl(unittest.TestCase):
# Test data is from the Navy's Crystal Lattie Structures website:
# http://cst-www.nrl.navy.mil/lattice/stru... | danielsjensen1/crystalpy | tests/test_translate.py | Python | bsd-3-clause | 1,987 | [
"CRYSTAL"
] | 3fc938a0ff6f267b394d25713b29d80307b3f92ed4ec281362fc7559edccf8f2 |
"""
A general-purpose Simulation class for discrete events.
The Simulation object is the central object of a simulation. It
handles the simulation clock time and maintains communication between
the components of the simulation.
A simulation is structured as a directed graph of event-processing
nodes called EventPr... | ioam/svn-history | topo/base/simulation.py | Python | bsd-3-clause | 64,355 | [
"NEURON"
] | 9e785f4aad6ed667e63d89395128e0d378fe2a3985c60b1b612196c2031a3e66 |
#!/usr/bin/env python
# coding: utf-8
# # Neural networks
#
# Artificial neural networks are computational systems that can learn to
# perform tasks by considering examples, generally without being
# programmed with any task-specific rules. It is supposed to mimic a
# biological system, wherein neurons interact by se... | CompPhysics/MachineLearning | doc/LectureNotes/_build/jupyter_execute/chapter9.py | Python | cc0-1.0 | 31,431 | [
"NEURON"
] | 765ad384dc01f1549e50702f979e46c5ad3d964c41a39622054eef37063bb237 |
#
# (C) Copyright 2001/2002 Kai Sterker <kaisterker@linuxgames.com>
# Part of the Adonthell Project http://adonthell.linuxgames.com
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License.
# This program is distributed in the hope that it will... | ksterker/wastesedge | scripts/schedules/mapcharacters/oliver.py | Python | gpl-2.0 | 2,646 | [
"exciting"
] | 3ed3a4e150069a30141ad4e26190fa92ca9c3c6d913cdf47719771828acfa2a5 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import math
from collections import namedtuple
Point = namedtuple("Point", ['x', 'y'])
def length(point1, point2):
return math.sqrt((point1.x - point2.x)**2 + (point1.y - point2.y)**2)
def solve_it(input_data):
# Modify this code to run your optimization algorithm
... | discreteoptimization/assignment | tsp/solver.py | Python | mit | 1,515 | [
"VisIt"
] | aa6e110abe73b9eb80133862d28b6f753f54791615f833c8efadd090d1a96ebc |
# geotecha - A software suite for geotechncial engineering
# Copyright (C) 2018 Rohan T. Walker (rtrwalker@gmail.com)
#
# 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 L... | rtrwalker/geotecha | geotecha/speccon/test/dim1sin_test_data_gen.py | Python | gpl-3.0 | 14,033 | [
"DIRAC"
] | 9b9724e1d02b858dc984315cad058f46ea993341784d17dc762c7d3f506b4c2f |
'''
Created on 07.05.2017
@author: Mr. Jones
'''
'''receive values from a given node and add them to the given dictionary'''
class ExtractValueVisitor():
def __init__(self):
self.optimization = 0
self.values = {}
def visit(self, node,parent):
method = 'visit_%s'... | mrj0n3s/jimplify | Jimplify/jimplify/visitors/extractvaluevisitor.py | Python | mit | 674 | [
"VisIt"
] | e9513bd9727381fe66117c1f074c5d0ec84e2ac8dd672c1aff211b00b4705abd |
from sys import argv
import matplotlib.pyplot as plt
from ase.dft import STM
from gpaw import restart
filename = argv[1]
z0 = 8
bias = 1.0
atoms, calc = restart(filename, txt=None)
stm = STM(atoms, symmetries=[0, 1, 2])
c = stm.get_averaged_current(bias, z0)
print 'Average current at z=%f: %f' % (z0, c)
# Get ... | robwarm/gpaw-symm | doc/exercises/stm/stm.py | Python | gpl-3.0 | 508 | [
"ASE",
"GPAW"
] | 21fffa7ac70c92d42c9c3460f9670650cae9b2f72eaa9583f0eea37242d86bf5 |
#
# Copyright (C) 2009, Jose Antonio Martin H.
#
#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... | okkhoy/mo-rlglue-python-codec | rlglue/utils/TaskSpecVRLGLUE3.py | Python | mit | 10,559 | [
"Brian"
] | 2342da887fbeba0a7acc951291505d5ccaf69cf4831f8fba4fff539daec0a732 |
"""Collection of functions to process mini batches."""
import numpy as np
from sklearn.preprocessing import OneHotEncoder
def invert_full_matrix_np(full_adjacency):
full_adjacency = np.squeeze(full_adjacency)
n_nodes = full_adjacency.shape[1]
full_adjacency = np.append(np.zeros([1, n_nodes]), full_adjace... | tree-gan/BonsaiNet | batch_utils.py | Python | mit | 6,481 | [
"NEURON"
] | 4ef342e179eb0ef1c437faedb2a0adb89a9012ac11ce17d6467271bfefdd1905 |
import cv2
import numpy
import operator
from logger import logger
def watershed(image, grayed, edges, min_ratio, max_count):
""" Applies watershed algorithm to 'image' with markers derived
from 'edges'
Args:
image: original image
grayed: grayed and optionally blurred version of 'image... | xiwenc/cbir-invenio | src/segmentation.py | Python | mit | 5,133 | [
"Gaussian"
] | 1c5e83c375d9129f6f4fa9ed3308df4c0f215aeb414bcd73622fcd4ea0c185c8 |
from __future__ import print_function, division
import os,unittest,numpy as np
from pyscf.nao import gw as gw_c
class KnowValues(unittest.TestCase):
def test_rescf(self):
""" reSCF then G0W0 """
fc = \
"""-1.176137582599898090e+00
-6.697973984258517310e-01
-5.155143130039178123e-01
-4.36544872408... | gkc1000/pyscf | pyscf/nao/test/test_0061_gw_rescf_g0w0_h2o.py | Python | apache-2.0 | 1,273 | [
"PySCF"
] | 7dd219c40469cf1b043a7d387bc7311d390411dd78d7610c408004bd579ec7b5 |
import sys
# Include relative path for mimpy library.
import mimpy.mesh.hexmeshwmsfracs as mesh
import mimpy.mfd.mfd as mfd
import numpy as np
res_mfd = mfd.MFD()
res_mfd.set_compute_diagonality(True)
res_mfd.set_m_e_construction_method(0)
#Define the permeability function
def K(p, i, j, k):
return np.eye(3)
... | ohinai/mimpy | examples/fractures/multi_frac_w_input/hexmesh_example_1.py | Python | bsd-3-clause | 2,579 | [
"VTK"
] | bbde03567cfb35d8e078623c0f5ca6f648b7668a2c47fc013822c0734f431cff |
# coding: utf-8
from __future__ import unicode_literals
import binascii
import collections
import email
import getpass
import io
import optparse
import os
import re
import shlex
import shutil
import socket
import struct
import subprocess
import sys
import itertools
import xml.etree.ElementTree
try:
import urllib... | mxamin/youtube-dl | youtube_dl/compat.py | Python | unlicense | 88,570 | [
"Bowtie"
] | dccf01642ab568b1d3af34b6657bafdea53e385df19a8ff22a85ee0cc8b7aad1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Setup.py for pymatgen."""
import sys
import platform
import os
from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext as _build_ext
class build_ext(_bui... | davidwaroquiers/pymatgen | setup.py | Python | mit | 8,335 | [
"ABINIT",
"ASE",
"CRYSTAL",
"Gaussian",
"NWChem",
"VASP",
"VTK",
"pymatgen"
] | 079a9a073cb95765652a0f48a2d74076aa59984fbecc864b998f178392cf5650 |
""" GraphData encapsulates input data for the DIRAC Graphs plots
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/Phedex Project by ... <to be added>
"""
from __future__ import print_function
__RCSID__ = "$Id$"
import time
import datetime
import numpy
from matplotlib.dates ... | chaen/DIRAC | Core/Utilities/Graphs/GraphData.py | Python | gpl-3.0 | 17,366 | [
"DIRAC"
] | a137ced7e84a91daedc2ebedf0b82790d8d3741ea0f06f81c090ecd70e0f744e |
import cv2
import numpy as np
from matplotlib import pyplot as plt
import matplotlib.patches as mpatches
from skimage.morphology import skeletonize, thin, medial_axis, closing, square
from skimage.util import invert
from skimage.color import rgb2gray, label2rgb
from skimage import data,img_as_ubyte
from skimage.filter... | YubinXie/Computational-Pathology | thresholded.py | Python | gpl-2.0 | 12,038 | [
"Gaussian"
] | d8b632c12e77a93844b80fd35486159da73b97b3ad0113a37536a7558b148035 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
import matplotlib
matplotlib.use('TkAgg')
from matplotlib import pyplot as plt
from data import get_value, draw_sky
import numpy as np
import tensorflow as tf
from edward.models import Normal, Uniform
M = 300 # number of galax... | trungnt13/BAY2-uef17 | 4_generate_artificial_sky.py | Python | gpl-3.0 | 2,534 | [
"Galaxy"
] | a60f699c7d587451ec987b6a89510b55be88c4b7645dbbd93487b70af14f34ac |
# -*- coding: utf-8 -*-
import cPickle, os, time, ConfigParser
import numpy as np
import ROOT, sys
from multiprocessing import Process, Queue
from scale.scale import Scale
sql = True
try:
from temdbWO import Storage
except ImportError:
sql = False
print 'database is unavailable'
class Constants:
c = 2997924... | muchnoi/HPGe | vepp2k/vepp2k.py | Python | gpl-3.0 | 31,813 | [
"Gaussian"
] | e01d51ec07341c62daa5802565bf91da84f80fbf51486cc59079cb641cae0f2a |
##############################################################################
# Copyright (c) 2013-2017, 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... | skosukhin/spack | var/spack/repos/builtin/packages/r-affyqcreport/package.py | Python | lgpl-2.1 | 2,212 | [
"Bioconductor"
] | 69d623acab310fa714d97a65a687be31f832242e333d63750e153a8f18f29e7a |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
from El.core import *
from ctypes import CFUNCTYPE
# S... | justusc/Elemental | python/matrices.py | Python | bsd-3-clause | 84,298 | [
"Gaussian"
] | 0dd3f1796a762fc86701d18229590969837d40634e315efee2d3cb40e676f4fa |
import collections, logging, itertools
import bashlex.parser
import bashlex.ast
from explainshell import errors, util, helpconstants
class matchgroup(object):
'''a class to group matchresults together
we group all shell results in one group and create a new group for every
command'''
def __init__(se... | Mtax/explainshell | explainshell/matcher.py | Python | gpl-3.0 | 26,896 | [
"VisIt"
] | 8cb67a9ae1441f1a4d7f0f6802197b3a50dfea3ba5967894af804bbe17388c22 |
#!/usr/bin/env python
"""
Archive a transformation
"""
from DIRAC.Core.Base.Script import Script
@Script()
def main():
# Registering arguments will automatically add their description to the help menu
Script.registerArgument(["transID: transformation ID"])
_, args = Script.parseCommandLine()
transIDs... | DIRACGrid/DIRAC | src/DIRAC/TransformationSystem/scripts/dirac_transformation_archive.py | Python | gpl-3.0 | 790 | [
"DIRAC"
] | 1506ed5703e693978f95bbba2ae461cc7836205a30b2dda14fa258cf13202e41 |
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 25 17:48:33 2015
@author: timmonen
"""
import sys
import os
import subprocess as sp
import argparse
import pysam
from pipeline.sample import Sample
# Functions
def pre_map(sample, VERBOSE=0,**kwargs):
fn_in = sample.get_read_filenames(gzip=True, trimmed=True)['d... | timmonen/pipeline | pipeline/pre_map.py | Python | mit | 1,789 | [
"pysam"
] | 788fe2346072dff99cf6d67961d6fa1021e19f030ccc293312be8e7bfc8c7cff |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""Tests for computing orbitals, densities and orbital angular momenta."""
import numpy as np
from unittest import TestCase
from exatomic import Universe, nwchem, molcas
from exatomi... | exa-analytics/exatomic | exatomic/algorithms/tests/test_orbital.py | Python | apache-2.0 | 2,362 | [
"ADF",
"MOLCAS",
"NWChem"
] | 328246f8d8b3c5cd52b3816c3d7b82de946c10ac9ccebcd8224ee1a27d1b8437 |
#! /usr/bin/python3 -B
# *************************************************** *
# This file is a part of ccROJ project *
# distributed under GNU General Public License v3.0. *
# Please visit the webpage: github.com/dsp-box/ccROJ *
# for more information. *
# ... | dsp-box/ccROJ | manual/draw-image.py | Python | gpl-3.0 | 7,574 | [
"VisIt"
] | efd8ad8d652dbcffb17de0f53bdce67906d11b82b1b0677effb3dc5bf24e1b9d |
from openmmtools import hmc_integrators, testsystems
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
timestep = 1.0 * u.femtoseconds
target_length = 200 * u.nanoseconds
steps_per_hmc = 12
n_steps = int(target_length / timestep)
output_frequency = 20
#barostat_frequency = 4
barostat... | kyleabeauchamp/HMCNotes | code/old/production_density_amber.py | Python | gpl-2.0 | 1,873 | [
"OpenMM"
] | 24eefe68f040aff9a8b15f9ff3b7277196ea5bc74247023f03fc8ccff89e53e0 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | manuzhang/incubator-beam | sdks/python/apache_beam/pipeline_test.py | Python | apache-2.0 | 15,533 | [
"VisIt"
] | a58ec043225fa3f3bc75de8299f82ce79bacad4da9a32f57a963844df06e9349 |
adjectives = [
'homely',
'rough',
'yellow',
'dry',
'deafening',
'substantial',
'zesty',
'watchful',
'kooky',
'small',
'grown',
'closed',
'offbeat',
'variable',
'specific',
'novel',
'marvelous',
'private',
'bony',
'best',
'hospitable',
... | MatthewJWalls/nomenclature | names.py | Python | mit | 18,679 | [
"Jaguar",
"MOOSE",
"Octopus"
] | dfbde6dbc7403ce2e8c827145f945f08ccf6cfe2a3b07f44c8411b71a8bba523 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020 F5 Networks Inc.
# GNU General Public License v3.0 (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
import os
import semver
import sys
from .lib.common impor... | F5Networks/f5-ansible-modules | tasks/collection.py | Python | mit | 4,203 | [
"Galaxy"
] | 5acca6d995b46eb81e525985a6db8acf5720540f63ed7500fe7e1532674250b5 |
"""generates atoms object from .smc file and views in ase gui
usage: python viewCluster.py smcfile
where smcfile is the full path to .smc file
"""
import sys
from montecarlo import *
from ase.cluster.cubic import FaceCenteredCubic
import ase
from data import fcc
from atommontecarlodata import AtomMonteCarloData
from as... | auag92/n2dm | Asap-3.8.4/Projects/NanoparticleMC/misc/viewCluster.py | Python | mit | 771 | [
"ASE"
] | 41267011b736e66d1d28bea4e1333bd2d6b9e24b8e3c92c00695c33db4b656f7 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | jairideout/scikit-bio | skbio/util/tests/test_testing.py | Python | bsd-3-clause | 9,114 | [
"scikit-bio"
] | 56c63b1d06c6fd3757931ffd594eb8870628bc8db4da40b59626c92fe2d2c85a |
"""rbf - Radial basis functions for interpolation/smoothing scattered Nd data.
Written by John Travers <jtravs@gmail.com>, February 2007
Based closely on Matlab code by Alex Chirokov
Additional, large, improvements by Robert Hetland
Some additional alterations by Travis Oliphant
Permission to use, modify, and distrib... | ales-erjavec/scipy | scipy/interpolate/rbf.py | Python | bsd-3-clause | 9,416 | [
"Gaussian"
] | 7649b5b5d5a58b0ffb205774c8b2988bc92263f4b0af152b5eb1943a2118dcc8 |
# -*- coding: utf-8 -*-
{
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" je opcioni izraz kao sto je "polje1=\'nova vrijednost\'". Ne mozete azurirati ili izbristi rezultati JOIN-a',
'# of Houses Damaged': 'Broj oštećenih kuća',
'# of Houses... | ahaym/eden | languages/bs.py | Python | mit | 538,016 | [
"VisIt"
] | c50f146723cf9bb3e21d9780b36ea338f7bcd4bb002e938c9a8835897dd1b04e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jgonthier/psi4 | psi4/driver/mdi_engine.py | Python | lgpl-3.0 | 15,842 | [
"Psi4"
] | ca6fef0e627a0a5a65cd204fde3f279607a66b1fac05017ecde6a8f0c04092fd |
# -*- coding: utf-8 -*-
# Copyright 2022 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-compute | tests/unit/gapic/compute_v1/test_disk_types.py | Python | apache-2.0 | 66,139 | [
"Octopus"
] | 449f8f03eec2004f932159d71b2e0ea243aa1badd3bc637497acdd02226e52d1 |
""" Composite actions over managers shared between HTTP endpoint (routes.py)
and message queue.
"""
from pulsar.client.setup_handler import build_job_config
from pulsar.managers import status
from pulsar.managers import PULSAR_UNKNOWN_RETURN_CODE
from galaxy.tools.deps import dependencies
import os
def status_dict(ma... | ssorgatem/pulsar | pulsar/manager_endpoint_util.py | Python | apache-2.0 | 3,837 | [
"Galaxy"
] | 7c8e1307d503d2486242bfdd7fee4b08623fe99424d62beccfcd72d058ab349b |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/FixedPairListAdress.py | Python | gpl-3.0 | 2,974 | [
"ESPResSo"
] | 9c831d18e3c9224004919686509564744f311db7b2d052a6cd6f62573a769521 |
"""
Open-source code by @andersenchen and @sbchou at Knewton.
August 2013
Contains class KalmanFilter, an implementation of the hybrid Kalman
filter algorithm), and a Simulator class for testing.
"""
import itertools
import math
import random
import numpy as np
class KalmanFilter:
"""
A class for statistica... | Knewton/Kalman | open_source_kalman.py | Python | mit | 8,086 | [
"Gaussian"
] | a1cf5cdeee154d2c32cb673a21cfcade37a4a6264cd59cca55ce3c779893287d |
# -*- coding: utf-8 -*-
"""
Deal with DER encoding and decoding.
Adapted from python-ecdsa at https://github.com/warner/python-ecdsa
Copyright (c) 2010 Brian Warner
Portions written in 2005 by Peter Pearson and placed in the public domain.
The MIT License (MIT)
Copyright (c) 2013 by Richard Kiss
Permission is here... | zsulocal/pycoin | pycoin/tx/script/der.py | Python | mit | 4,302 | [
"Brian"
] | c4da12a03ef4656b837f9bd52e8b48a2375c4c482bb05a91e23bbd981f5ecb91 |
# Copyright 2010 http://www.collabq.com
import logging
import re
from django.conf import settings
from common import api
from common import clean
from common import exception
from common import patterns
from common import user
from common import util
from common.protocol import base
from common.protocol import sms
H... | CollabQ/CollabQ | common/sms.py | Python | apache-2.0 | 10,292 | [
"VisIt"
] | c2db0ccb3a4139501cf1c20bd07e9d403c36230bc3d4ffb6f09363784f620888 |
# Copyright (C) 2017 Martin Nilsson
# This file is part of the Memtran compiler.
#
# The Memtran compiler 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
# ... | LJMNilsson/memtran | src/type_inference_and_annotation.py | Python | gpl-3.0 | 78,047 | [
"VisIt"
] | 87d48a97d1cb4d78c8c982bf8d02d5a523cf1de6702d03f5802350fd292e661c |
# pylint: disable-msg=I0011,C0301,W0611
# copyright 2003-2010 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
# copyright 2003-2010 Sylvain Thenault, all rights reserved.
# contact mailto:thenault@gmail.com
#
# This file is part of logilab-astng.
#
# logi... | dbbhattacharya/kitsune | vendor/packages/logilab-astng/test/regrtest_data/import_package_subpackage_module.py | Python | bsd-3-clause | 3,147 | [
"VisIt"
] | 445c69c8f20bd2b2e1155108bacbee6d347f89f180776e0231e81d45f318c76e |
#! /usr/bin/env python
from __future__ import unicode_literals
# coding: utf-8
# Use Gzipped files without extractionpyp
import shutil
import logging
import datetime
import os # operation system packages
import ConfigParser as configparser # a package to parse INI file or confige file.
import argparse # a packa... | Attayeb/qanaus | auto-q.py | Python | bsd-3-clause | 36,108 | [
"BLAST"
] | 42a546e4fa444cb24273fb0e725bbabedb47529076602b86d09411b51461e322 |
import os
import time
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
import mdtraj.reporters
import sys
code = "3DMV"
ff_name = "amber99sbnmr"
water_name = 'tip3p'
which_forcefield = "%s.xml" % ff_name
which_water = '%s.xml' % water_name
platform_name = "CUDA"
timestep = 2.0 * u.... | kyleabeauchamp/fah-projects | old/equilibrate_boxes.py | Python | gpl-2.0 | 1,862 | [
"MDTraj",
"OpenMM"
] | d50b7e8e6c824cd2fcb3d131d7621fc3515f0e42d804fb450126f71d518e0a14 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# Stephen Fromm <sfromm@gmail.com>
# Brian Coca <briancoca+dev@gmail.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 publish... | erinn/ansible | lib/ansible/plugins/action/assemble.py | Python | gpl-3.0 | 5,710 | [
"Brian"
] | 31dd594c8741ec8931c058ab7ad923a1092a18a5f29d1e4289909095f59fefa6 |
"""
Internal implementation of a SAT solver, used by L{solver.SATSolver}.
This is not part of the public API.
"""
# Copyright (C) 2010, Thomas Leonard
# See the README file for details, or visit http://0install.net.
# The design of this solver is very heavily based on the one described in
# the MiniSat paper "An Exte... | timdiels/zeroinstall | zeroinstall/injector/sat.py | Python | lgpl-2.1 | 19,298 | [
"VisIt"
] | 4b58bf019576328f1613016aff506be138761dd19b60b8d6d7316237e8defcd8 |
"""
Acceptance tests for course in studio
"""
from nose.plugins.attrib import attr
from common.test.acceptance.tests.studio.base_studio_test import StudioCourseTest
from common.test.acceptance.pages.studio.auto_auth import AutoAuthPage
from common.test.acceptance.pages.studio.users import CourseTeamPage
from common.t... | louyihua/edx-platform | common/test/acceptance/tests/studio/test_studio_course_team.py | Python | agpl-3.0 | 14,318 | [
"VisIt"
] | 42e4da445423aa75c9b26340f183cb89890df0ab966599f63af38c297cdc5c08 |
# -*- coding: utf-8 -*-
# Copyright 2022 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-automl | tests/unit/gapic/automl_v1/test_auto_ml.py | Python | apache-2.0 | 220,732 | [
"Octopus"
] | a79b59ea0c9a8de6061eb5eef5c1244084f1781366ae8c5c6e09094e67905ba7 |
# Copyright (C) 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writi... | googleapis/proto-plus-python | tests/test_json.py | Python | apache-2.0 | 4,319 | [
"Octopus"
] | 0d86e82889329de1dc40d7883e7f8838460e2cc6fc89b7159ce6b157458b98b2 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Created on Nov 10, 2012
@author: shyue
"""
from pymatgen.util.testing import PymatgenTest
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "0.1"
__maint... | mbkumar/pymatgen | pymatgen/core/tests/test_composition.py | Python | mit | 25,224 | [
"pymatgen"
] | ad54531e2ea07096fbd4959f695936ff151034c2a7ea2f5fd53f6ebb0d9f1f09 |
#!/usr/bin/env python
"""
Creates graph of modeled time series from multiple files. See figures
in the "Getting Started" section of the User's Manual.
"""
# example from grid-sequencing example:
# $ ./tsshow.py ice_volume_glacierized ice_volume_glacierized-gridseq.png ts_g20km_10ka_hy.nc '20 km for 10 ka' ts_g10km... | talbrecht/pism_pik | examples/std-greenland/tsshow.py | Python | gpl-3.0 | 2,444 | [
"NetCDF"
] | e19d2ad4e6adff3322241930ac771f508799f444e1191fae42251ea8e1bace40 |
# -*- coding: utf-8 -*-
"""QGIS Unit tests for edit widgets.
.. note:: 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.
"""
__au... | supergis/QGIS | tests/src/python/test_qgsrelationeditwidget.py | Python | gpl-2.0 | 10,897 | [
"Galaxy"
] | 066f5b76e94591ec0801dfbd38049d0089a7c2f419b47b13f29ba7ee5c415d28 |
from django.test import TestCase
from push_notifications.api.rest_framework import APNSDeviceSerializer, GCMDeviceSerializer
from rest_framework.serializers import ValidationError
from tests.mock_responses import GCM_DRF_INVALID_HEX_ERROR, GCM_DRF_OUT_OF_RANGE_ERROR
class APNSDeviceSerializerTestCase(TestCase):
def ... | gkirkpatrick/django-push-notifications | tests/test_rest_framework.py | Python | mit | 4,471 | [
"Galaxy"
] | d7a4f007fb09050a67a180a61579654eb61c1f54d3b5359702a6c0d2594ff1e8 |
""" Test class for agents
"""
# imports
import unittest
import json
import os
from DIRAC.WorkloadManagementSystem.PilotAgent.pilotTools import PilotParams, CommandBase
from DIRAC.WorkloadManagementSystem.PilotAgent.pilotCommands import GetPilotVersion
class PilotTestCase( unittest.TestCase ):
""" Base class for th... | andresailer/DIRAC | WorkloadManagementSystem/PilotAgent/test/Test_Pilot.py | Python | gpl-3.0 | 1,723 | [
"DIRAC"
] | c40ab9aa448afed6d122fba77d2161b9e553d3f4089a97bb99a2e896b612b63c |
from tests.test_helper import *
class TestCreditCard(unittest.TestCase):
def test_create_adds_credit_card_to_existing_customer(self):
customer = Customer.create().customer
result = CreditCard.create({
"customer_id": customer.id,
"number": "4111111111111111",
"exp... | eldarion/braintree_python | tests/integration/test_credit_card.py | Python | mit | 33,947 | [
"COLUMBUS"
] | 7fdd48dce526ac15fb5df42e8f1fb309f7164f113bec6297ec7e209b788c0df3 |
import os
def print_cli_help_message():
x = os.system("clear; clear;")
print "\n\n\n<<<<<-------------------------COMMAND-LINE INTERFACE TO THIS MODULE------------------------->>>>>\n\n\tARGUMENTS LIST:"
args_note="""
-d = database file path
-d_t = table name in database
-g = google domain [make sure i... | ARDivekar/SearchDistribute | other/Legacy/cli_help.py | Python | mit | 16,371 | [
"VisIt"
] | cacff98321389ea9c10e40cc3691683231fbb6982a442bd11a0ad0b11a30077b |
#!/usr/bin/python
"""
Copyright 2012 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | clreinki/GalaxyHarvester | myAlerts.py | Python | agpl-3.0 | 2,715 | [
"Galaxy"
] | 4008741e871a317bcba1be1f358f58abcc3b61dc4cb3f614a767961edd8288f2 |
#!/usr/bin/env python
# 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
#
# U... | gkc1000/pyscf | pyscf/tools/mo_mapping.py | Python | apache-2.0 | 3,885 | [
"PySCF"
] | b95fbf054dbb34b5ca6119e4d960a351b9e513e7b6ee9c918187b8e89dd3cf21 |
"""
Computes putative binding pockets on protein.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2017, Stanford University"
__license__ = "MIT"
import os
import tempfile
import numpy as np
fr... | joegomes/deepchem | deepchem/dock/binding_pocket.py | Python | mit | 11,738 | [
"RDKit"
] | c11246b2483e11913176173725fe3ed296350cf79346db55c52d391c0ff1db20 |
"""
Acceptance tests for Studio related to the container page.
The container page is used both for displaying units, and
for displaying containers within units.
"""
from nose.plugins.attrib import attr
from unittest import skip
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.accep... | louyihua/edx-platform | common/test/acceptance/tests/studio/test_studio_container.py | Python | agpl-3.0 | 53,390 | [
"VisIt"
] | 0ad48ac85c205d38a05c2014f2bfd945f68423229e34541680f9e18aa49294c5 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
#
# The dataset read by this exercise ("combVectors.vtk") has field data
# associated with the pointdata, namely two vector fields. In this exercise,
# you will convert both ... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Programmable/Testing/Python/MultidimensionalSolution.py | Python | bsd-3-clause | 7,335 | [
"VTK"
] | 9baa1239e28cca6aef41c77e571f0d7b538018cfc1b41f31c4247c2a7c142dd1 |
#!/usr/bin/env python
# Script using Biopython objects to import and adapt PDB files
from Bio.PDB import *
import numpy as np
import requests
import argparse
parser=PDBParser(QUIET=True)
#Protocol
# 1) Read in arguments for downloading PDB files
# 2) Read in table of PDB entries and CDR ranges
# 3) Delete atoms in CD... | rtb1c13/scripts | SAXS_MD/Light_delete_CDR.py | Python | gpl-2.0 | 6,763 | [
"Biopython"
] | ffb8f0798a86dddfa654170bac4bbb5a515e5c2a2c7f201c55521d82dc4e4f57 |
import os
import glob
import mdtraj as md
import numpy as np
top = md.load('fs-peptide.pdb')
for fn in glob.glob('trajectory-*.dcd'):
print(fn)
t = md.load(fn, top=top)
# the stride is 10 picoseconds
t.time = np.arange(t.n_frames) * 10
t = t[::5]
t.save(os.path.join('strided', os.path.spl... | msmbuilder/msmb_data | msmb_data/fs_peptide/post-process.py | Python | lgpl-2.1 | 344 | [
"MDTraj"
] | b30c83d16797bfe5dc7e6fd74238788b6300846ae4eabe53af2244b449137eef |
STATES = (
('AK', 'Alaska'),
('AL', 'Alabama'),
('AR', 'Arkansas'),
('AZ', 'Arizona'),
('CA', 'California'),
('CO', 'Colorado'),
('CT', 'Connecticut'),
('DC', 'District of Columbia'),
('DE', 'Delaware'),
('FL', 'Florida'),
('GA', 'Georgia'),
('HI', 'Hawaii'),
('IA', '... | pavel-paulau/perfrunner | spring/dictionary.py | Python | apache-2.0 | 138,828 | [
"COLUMBUS",
"Elk"
] | 5ae2aef1160c1c433ba63bc53290a2d0780f6989d86087ae075ff5d4f6ea6e2d |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/busy_widget.py | Python | gpl-2.0 | 3,415 | [
"VisIt"
] | b90a57dd298d2691f458ea3f6281c351a4809252017278171b9c55ad6665b6e9 |
# The MIT License (MIT)
#
# Copyright (c) 2015 Brian Wray (brian@wrocket.org)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# ... | wrocket/Tulip-Chess | tests/search_tests/test_simple_attacks.py | Python | mit | 2,888 | [
"Brian"
] | c3230108f28e6754b2765bf9482fcda1559eddc262633aa973732b79f34b7e54 |
__author__ = "Mihaela Rosca"
__contact__ = "mihaela.c.rosca@gmail.com"
import numpy as np
import restrictedBoltzmannMachine as rbm
# TODO: use conjugate gradient for backpropagation instead of steepest descent
# see here for a theano example http://deeplearning.net/tutorial/code/logistic_cg.py
# TODO: add weight de... | mihaelacr/pydeeplearn | code/old-version/deepbelief.py | Python | bsd-3-clause | 9,738 | [
"NEURON"
] | c7c23e9c62d3061dd1cc1023b96a7affeb6bb15413846af377387112c807b755 |
'''
Abyssium -
Aluminum - 2.71
Ash - 0.71
Atherite -
Beechwood - 0.82
Brass - 8.47
Bronze - 8.20
Ceramic -
Chainmail -
Copper - 8.94
Cotton -
Diamond - 0.03
Divinum -
Glass -
Gold - 19... | etkirsch/legends-of-erukar | erukar/content/modifiers/material/random/__init__.py | Python | agpl-3.0 | 2,083 | [
"CRYSTAL"
] | 0e90dc992b43a04ac5e34b3514ff2fa9e54e82522bf8f536f070bf0b76e11a82 |
import unittest
from test import support
from itertools import *
from weakref import proxy
from decimal import Decimal
from fractions import Fraction
import sys
import operator
import random
import copy
import pickle
from functools import reduce
maxsize = support.MAX_Py_ssize_t
minsize = -maxsize-1
def lzip(*args):
... | timm/timmnix | pypy3-v5.5.0-linux64/lib-python/3/test/test_itertools.py | Python | mit | 83,293 | [
"GULP"
] | a3f9f271e5c45f672325b49a4fc66dbaf80c9faab657b07b053e3ddd2d809967 |
"""
Adds Skip and Timeout guards
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
# Imports
import threading
import uuid
from pycsp.parallel.const import *
from pycsp.p... | runefriborg/pycsp | pycsp/parallel/guard.py | Python | mit | 7,041 | [
"Brian"
] | 9dadfa8e7a8806042e9e4c8e883cd8efbbcc16e925cceb1c2001a92d92beaa74 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import logging
import time
import traceback
import contextlib
from collections import Mapping
from distutils.version import LooseVersion
from ..conventions import cf_encoder
from ..core.utils... | jhamman/xray | xarray/backends/common.py | Python | apache-2.0 | 9,144 | [
"NetCDF"
] | f2c4e203b62a1ef24e402a489af9d4c1ffeb745a7e2fa39fed8f88afcfc5d4da |
# th.po
val = {" days." : "",
"(all)" : "",
"(any)" : "",
"(anyone)" : "(ไม่มี)",
"(available)" : "",
"(blank)" : "",
"(both)" : "",
"(everyone)" : "",
"(master user, not editable)" : "",
"(no change)" : "",
"(no deduction)" : "",
"(none)" : "(ไม่มี)",
"(unknown)" : "",
"(use system)" : "",
"({0} given, {1} remaining)... | bobintetley/asm3 | src/asm3/locales/locale_th.py | Python | gpl-3.0 | 116,103 | [
"Amber",
"VisIt"
] | a10357f26361f3d3f870deea58cc282789eace3579befc40bf7a695845c19fe8 |
#!/usr/bin/env
"""
GOA_Winds_StormPatterns.py
Compare Gorepoint/globec winds (along shore) to telleconnection indices
GorePoint - 58deg 58min N, 150deg 56min W
and Globec3 59.273701N, 148.9653W
Files are created by GOA_Winds_NARR_model_prep.py
-Filtered NARR winds with a triangular filter (1/4, 1/2, ... | shaunwbell/FOCI_Analysis | ReanalysisRetreival_orig/GOA_Winds/GOA_Winds_StormPatterns.py | Python | mit | 13,331 | [
"NetCDF"
] | 18d9619d28cd7286277d7c7035f8e04ffc634c8ae599237827b86ebe7e21b4b3 |
# $HeadURL$
__RCSID__ = "$Id$"
import threading
class Synchronizer:
""" Class encapsulating a lock
allowing it to be used as a synchronizing
decorator making the call thread-safe"""
def __init__( self, lockName = "", recursive = False ):
from DIRAC.Core.Utilities.LockRing import LockRing
self.__lockN... | Sbalbp/DIRAC | Core/Utilities/ThreadSafe.py | Python | gpl-3.0 | 2,622 | [
"DIRAC"
] | 26b59175bdc992f0100de8eae9153cddcb30255e9384618178e1a6f9d5c0a29e |
# --------------------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# --------------------------------------------------------------------... | yugangw-msft/azure-cli | src/azure-cli/azure/cli/command_modules/appservice/_params.py | Python | mit | 90,609 | [
"ASE"
] | 4711c6cc466c3d5f867754314d05d3b495e97bae1964a525135a5fe7ebc3998a |
# -*- coding: utf-8 -*-
"""
==========================================
Reconstructing a Coulomb occupation ladder
==========================================
Filling of the 2 degenerate orbitals of an atom in function of the chemical
potential
"""
from scipy.special import binom
from scipy.optimize import fsolve
from ... | Titan-C/slaveparticles | examples/spins/plot_deg_2orb_fill.py | Python | gpl-3.0 | 2,126 | [
"DIRAC"
] | 0e6e9611330d5fdbdf4532c9569880bdd0f3a726998ca58bb762f2a54ce6f5e7 |
"""
"""
import os.path
import posixpath
from collections import deque
from glob import glob
from logging import getLogger
from galaxy.util import in_directory
from .util import PathHelper
log = getLogger(__name__)
TYPES_TO_METHOD = dict(
input="inputs_directory",
unstructured="unstructured_files_directory"... | galaxyproject/pulsar | pulsar/client/job_directory.py | Python | apache-2.0 | 6,152 | [
"Galaxy"
] | b4f6f80092203163f2fa1b71ee0fc28d4bb807d2d79dceb24b93ea85d3106a1b |
"""
Author: Thomas G. Close (tclose@oist.jp)
Copyright: 2012-2014 Thomas G. Close.
License: This file is part of the "NineLine" package, which is released under
the MIT Licence, see LICENSE for details.
"""
from __future__ import absolute_import
import pyNN.neuron.standardmodels.synapses
from pype9.sim... | tclose/PyPe9 | pype9/simulate/neuron/network/synapses.py | Python | mit | 803 | [
"NEURON"
] | f9dac28a10028e65ac9d7088a2602262e1cff1fc44ba2e63495daa4bf1c44c88 |
import pylab as pyl
import cPickle as pickle
galaxies = pickle.load(open('./galaxies.pickle','rb'))
galaxies = filter(lambda galaxy: galaxy.ston_I > 30., galaxies)
mergers = pyl.asarray([galaxy.Merger for galaxy in galaxies])
icd = pyl.asarray([galaxy.ICD_IH*100 for galaxy in galaxies])
stack = pyl.column_stack((mer... | boada/ICD | sandbox/shuffle.py | Python | mit | 712 | [
"Galaxy"
] | d0b0482f441989c8a4650d23b995716ed4e64511a23439c60a8d8ca336837449 |
"""Tests for phonon calculation at specific q-points."""
import numpy as np
from phonopy import Phonopy
from phonopy.units import VaspToTHz
def testQpoints(ph_nacl_nofcsym: Phonopy):
"""Test phonon calculation at specific q-points by NaCl."""
phonon = ph_nacl_nofcsym
qpoints = [[0, 0, 0], [0, 0, 0.5]]
... | atztogo/phonopy | test/phonon/test_qpoints.py | Python | bsd-3-clause | 735 | [
"phonopy"
] | 3ed3666f60084fdcec7e217789c9b5c0768284d201b358dbbd9e359b7f6fce3c |
# -*- coding: utf-8 -*-
# Copyright JS Foundation and other contributors, https://js.foundation/
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright
# ... | mp-coder/translate-dev-tools | esprima/esprima.py | Python | mit | 4,382 | [
"VisIt"
] | 61d11acb422994de7b5b2793189375bb853fa8ac2c4b860ea9f6b33ac9ca583f |
""" The list of words used by DPG """
words = [ "and", "ask", "ass", "ape", "ate", "axe", "air", "aim", "ana", "awe", "act", "add", "age", "all", "ant",
"bat", "ban", "bar", "bed", "bee", "bet", "bit", "bug", "bob", "bot", "boy", "bud", "but",
"cab", "can", "cap", "cat", "car", "cog", "con", "cop", "cot", "cow", "coy"... | w8rbt/dpg | python/the_words.py | Python | isc | 1,849 | [
"Elk"
] | 5716d2eca98796cae4b00b0b1bd751e795f194569b0f5d42c778eb8e70f9490e |
"""
Copyright (C) 2014, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Rudolf Streif (rstreif@jaguarlandrover.com)
"""
from __future__ import absolute_import
i... | afan1/rvi_backend | web/devices/tasks.py | Python | mpl-2.0 | 3,005 | [
"Jaguar"
] | 5aaa0789af53f4eefee0c729e1c14a93310af9022689cebb8be04e15675a0c27 |
Python 2.7.5 (default, May 15 2013, 22:43:36) [MSC v.1500 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> f=file('hello.txt')
>>> lines=f.readlines()
>>> for line in lines:
... print (line,)
...
('hello world\n',)
('hello china\n',)
('hello hushupei',)
>>> f.close()... | hushupei/PyCode | b.py | Python | gpl-3.0 | 5,909 | [
"VisIt"
] | c3b8433f1a70732d2fc339379e7685bd4697a3f524432b56df586479c134f2de |
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