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##############################################################################
# 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/py-biopython/package.py | Python | lgpl-2.1 | 1,753 | [
"Biopython"
] | c6265185d86834774ff93fa7c542780ff3298e7ff9ce17f54dd0467b9405c08a |
"""
Provides rolling statistical moments and related descriptive
statistics implemented in Cython
"""
from __future__ import division
import warnings
import numpy as np
from pandas.core.dtypes.common import is_scalar
from pandas.core.api import DataFrame, Series
from pandas.util._decorators import Substitution, Append... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/pandas/stats/moments.py | Python | mit | 31,620 | [
"Gaussian"
] | 1306abd7585ff069b7720910bf076ff560653f2e200af472d1e204f39806fd07 |
from octopus.core import app, initialise, add_configuration
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("-d", "--debug", action="store_true", help="pycharm debug support enable")
parser.add_argument("-c", "--config", help="additional configuration t... | CottageLabs/finance | service/web.py | Python | apache-2.0 | 2,056 | [
"Octopus"
] | 074982963fc68af6b36fd2a8100cfdd8069e636c807f0faaceca84361925113a |
# Package Imports
from ..workspace import Block, Disconnected, Cancelled
from .machines import machine_declaration
# Twisted Imports
from twisted.internet import reactor, defer, task
# Octopus Imports
from octopus import data
from octopus.data.errors import Immutable
from octopus.data.data import BaseVariable
from oc... | richardingham/octopus | octopus/blocktopus/blocks/images.py | Python | mit | 4,698 | [
"Octopus"
] | 5b439205d38dab6e382ad9ff531b26c02098f72bb9b2dc49836d07947ccea65c |
from __future__ import annotations
import inspect
from xia2.Modules.DoseAccumulate import accumulate_dose
class XSample:
"""An object representation of a sample."""
def __init__(self, name, crystal):
"""Create a new sample named name, belonging to XCrystal object crystal."""
# set up this ... | xia2/xia2 | src/xia2/Schema/XSample.py | Python | bsd-3-clause | 3,220 | [
"CRYSTAL"
] | ffbac8d0795bb8ea85b5be626d54544759eee61e33586b9683a9913d45d7b2cb |
#!/usr/bin/env python
# Run
#
# python setup.py build
#
# to build this extension in place.
# To use it, the extension should be copied to the appropriate AlGDock
# subdirectory for extensions.
package_name = "MMTK"
from distutils.core import setup, Command, Extension
from distutils.command.build import build
from d... | CCBatIIT/AlGDock | AlGDock/ForceFields/Pose/setup.py | Python | mit | 12,538 | [
"Amber",
"DIRAC",
"NetCDF"
] | 339dbb3d248a91c35f2339819a725da7fd2e82fbcc410cd7325d93f30972b421 |
dice = {
11111: "a" ,
11112: "a's" ,
11113: "a-1" ,
11114: "a-z" ,
11115: "aa" ,
11116: "aaa" ,
11121: "aaaa" ,
11122: "aaron" ,
11123: "ab" ,
11124: "aback" ,
11125: "abacus" ,
11126: "abase" ,
11131: "abash" ,
11132: "abate" ,
11133: "abbey" ,
11134: "abbot" ,
11135: "abbr" ,
11136: "abby" ,
11141:... | jthomp888999/Diceware | dicts/dice_dict2.py | Python | mit | 133,998 | [
"Amber",
"BLAST",
"Brian",
"Elk",
"GULP",
"Galaxy",
"Jaguar",
"MOE",
"MOOSE",
"SIESTA",
"VisIt"
] | 32dd0ab3d63fe2238d9912fbcf517fb0a1dcdcbd6c72a88c0cb1fbf44037f273 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
"""Helper f... | harterj/moose | python/MooseDocs/common/log.py | Python | lgpl-2.1 | 3,295 | [
"MOOSE"
] | 10fc20638ebc527a78862195d8a298d5d467693f40f37f32bab38fc3fde287fa |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import collections
import numpy as np
import operator
import os
import functools
from math import exp, sqrt
from monty.serialization import loadfn
from pymatgen.core.periodic_table import Element, Specie
fro... | dongsenfo/pymatgen | pymatgen/analysis/bond_valence.py | Python | mit | 21,312 | [
"Gaussian",
"pymatgen"
] | 64b38a4e68d324c643b2da6357e159915c91ab4d03476baab5fc22d5df90d355 |
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/api/access.py | Python | apache-2.0 | 8,206 | [
"Galaxy"
] | 2dabe225b128b49f66181f28b35e45f9ca3f861d19ef5108348a4ca4218c69a5 |
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import pathlib
from setuptools import find_packages, setup
here = pathlib.Path(__file__).parent.resolve()
install_requires = (here / 'requirements.txt').read_text(encoding='utf-8').splitlines()
setup(
install_requires=insta... | sysadmin75/ansible | setup.py | Python | gpl-3.0 | 1,116 | [
"Galaxy"
] | 880b819d96cafe1a2c564030c295a0e83b398fd4cadf79c9af6f27399db0db7d |
__author__ = 'joon'
import sys
sys.path.insert(0, 'src')
sys.path.insert(0, 'lib')
sys.path.insert(0, 'ResearchTools')
from imports.import_caffe import *
from caffetools.netblocks import get_learned_param, get_frozen_param, conv_relu, max_pool, conv
param = (get_frozen_param(), get_learned_param())
def vgg_conv1s... | coallaoh/GuidedLabelling | src/segmentation/networks.py | Python | mit | 3,993 | [
"Gaussian"
] | 934586785699cd5e63f2babe2ae41e0a76fd883edfe8c8cbaedcbc46ccd1086c |
import cherrypy
import SOAPpy
import re
import random
from blast_html import *
server = SOAPpy.SOAPProxy("hatfull12.bio.pitt.edu:31415/")
###########################################################
class orderedList:
###########################################################
def __init__(self,items):
... | byuphamerator/phamerator-dev | phamerator/web-pham.py | Python | gpl-2.0 | 36,182 | [
"BLAST"
] | 989f325b909f784b04ddf9b05dd2f73431fd0d74a8286382117df1ec1b954f24 |
#!/usr/bin/python
"""generate_functions.py
Yo dawg, I heard you like code generation so I wrote a code
generator to write your code generators!
"""
import sys
import os
input_list = """sqrt
exp
log
abs|Abs|-1
floor
ceil|ceiling|3/2
sin
sinh
asin
asinh
cos
cosh
acos
acosh
tan
tanh
atan
atanh||1/2
csc
sec
cot
coth
aco... | maprieto/octsympy | src/generate_functions.py | Python | gpl-3.0 | 5,011 | [
"DIRAC"
] | 3e5ce8db649e86613c20838f3a6bdf80384683c79a10ece4ec3de356ae462685 |
#!/usr/bin/python2.6
import numpy
import sys
from osgeo import gdal
from osgeo.gdalconst import *
"""
.. module:: read_file.py
:synopsis: Module used to read input file, and convert data to numpy array
.. moduleauthor:: Daniel Wild <daniel.wild@ga.gov.au>
"""
def readASC(inputFile):
"""
Reads .asc DEM ... | dynaryu/Wind_multipliers | tests_characterisation/read_file.py | Python | gpl-3.0 | 2,378 | [
"NetCDF"
] | 905ae1fb1f5c5eef3d56fc66b677b74eb7b3ec2d0df58f521701dbb613f058e4 |
"""User-friendly public interface to polynomial functions. """
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple, Rational
)
from sympy.core.mul import _keep_coeff
from sympy.core.sympify import (
sympify, SympifyError,
)
from sympy.core.decorators import (
_sympifyit,
)
from ... | srjoglekar246/sympy | sympy/polys/polytools.py | Python | bsd-3-clause | 150,850 | [
"Gaussian"
] | a6dda0117b0cf532035bbeddef3cfaf97548478a642e7e086c8147c27785e462 |
# $HeadURL$
__RCSID__ = "$Id$"
import time
import select
import cStringIO
try:
from hashlib import md5
except:
from md5 import md5
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Core.Utilities import DEncode
class BaseTransport:
b... | vmendez/DIRAC | Core/DISET/private/Transports/BaseTransport.py | Python | gpl-3.0 | 10,296 | [
"DIRAC"
] | 5d77413e5cf6d2417892e1e7fa980edebfdf44e6117514fece5f52e2b83ca9e1 |
import numpy as np
from astropy.table import Table
from astropy.io import fits
import matplotlib.pyplot as plt
import matplotlib
import pickle
from matplotlib import cm
from numpy.random import randn
# table path
path = "/Users/caojunzhi/Downloads/upload_20170330/red_clump_dr13.fits"
star = fits.open(path)
table =... | peraktong/Cannon-Experiment | DR13/0330_read_table_rc.py | Python | mit | 24,195 | [
"VisIt"
] | 082925b61b69a4b078e790d72816e40eb7d42bdd210378d0b9092538ecb5dfc4 |
"""
Local Laplacian, see e.g. Aubry et al 2011, "Fast and Robust Pyramid-based Image Processing".
"""
from __future__ import print_function
# TODO: This allows you to use "true" div (vs floordiv) in Python2 for the / operator;
# unfortunately it appears to also replace the overloads we've carefully added for Halide.
... | Trass3r/Halide | python_bindings/apps/local_laplacian.py | Python | mit | 9,109 | [
"Gaussian"
] | 39f865aa981d8f559491396cd2960e96cbb2177d23da80fc2e516dd1c0f14c1a |
"""
==================================================
Automatic Relevance Determination Regression (ARD)
==================================================
Fit regression model with Bayesian Ridge Regression.
See :ref:`bayesian_ridge_regression` for more information on the regressor.
Compared to the OLS (ordinary l... | RPGOne/Skynet | scikit-learn-c604ac39ad0e5b066d964df3e8f31ba7ebda1e0e/examples/linear_model/plot_ard.py | Python | bsd-3-clause | 2,622 | [
"Gaussian"
] | 7cbccaf6fd3f03821b409d0e968543731b398ae9387e8a8169bb5d2b9111815d |
#
# @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/procrouting/sapt/fisapt_proc.py | Python | lgpl-3.0 | 7,495 | [
"Psi4"
] | c1834a188b4b5276306b7f3942488db3954099eab6d6db7b0ae154a9c3e1c0c4 |
#!/usr/bin/env python
# -*- coding: Latin-1 -*-
##
def syntax():
print "syntax: python runner.py Win32|x64|all"
##
r"""runner.py - run some tests on the exiv2 build"""
##
import sys
import os.path
##
def Q(path):
return '"' + path + '"'
##
##
def System(cmd):
# print "System ",cmd
... | limbolily/exiv2 | msvc2005/runner.py | Python | gpl-2.0 | 3,296 | [
"VisIt"
] | 5db5c2687b0158a4368736b3beaf297abcb1f01ad7b44a29623b6320a30ea5f5 |
"""Utility commands to cycle active objects in pymol.
Adds cycler types to pymol:
pdbdircycler - Cycles through all pdbs in a given directory.
pdbdircyclerlite - Cycles through all pdbs in a given directory, loading one object at a time.
pdblistfilecycler - Cycles through all pdbs listed ... | weitzner/Dotfiles | pymol_scripts/Cycler.py | Python | mit | 7,155 | [
"PyMOL"
] | 00d4acf223b135dca86c0d0671aafd350ea6f5d194f71c6bb19b4212abec3707 |
###############################
# 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/plotfit.py | Python | gpl-3.0 | 4,199 | [
"CRYSTAL",
"VASP"
] | e2ff38d8482c79a708c38e4603668efd7cec844ee832a3e3e88da592de7f43c4 |
import random
import requests
from helga import log
logger = log.getLogger(__name__)
class XKCDClient(object):
BASE = 'https://xkcd.com'
EXT = 'info.0.json'
def __init__(self):
self._sess = requests.Session()
def _request(self, comic_number=None):
url_args = [str(a) for a in (self... | crlane/helga-xkcd | helga_xkcd/client.py | Python | mit | 1,322 | [
"VisIt"
] | 9c8d6771d5ee091d28eeb47c2dd6a97babd2de2a2701b70692f3f802aa87cc4e |
import subprocess
import tempfile
from pathlib import Path
import numpy as np
from pysisyphus.config import get_cmd
from pysisyphus.constants import BOHR2ANG
from pysisyphus.helpers_pure import interpolate_colors
TPL_BASE = """
{orient}
function _setModelState() {{
select;
Spacefill 0.0;
frank off;
... | eljost/pysisyphus | pysisyphus/wrapper/jmol.py | Python | gpl-3.0 | 2,886 | [
"Jmol"
] | f685a7a9c8e127f71467abeb5d645c3c2a7f74a34db3f9330a2200b165d911ef |
'''
Main file for displaying depth/color/skeleton information and extracting features
'''
import os
import optparse
from time import time
import cPickle as pickle
import numpy as np
import scipy.misc as sm
import scipy.ndimage as nd
import skimage
from skimage import feature, color
from pyKinectTools.utils.Utils impo... | colincsl/pyKinectTools | pyKinectTools/scripts/ExtractAndVisualizeVideo.py | Python | bsd-2-clause | 15,899 | [
"Mayavi"
] | d021dd5c8d6764612bd2aa5bd12fe49cb9964f363f31bc15943690eb66b665f4 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/p4util/p4regex.py | Python | lgpl-3.0 | 1,246 | [
"Psi4"
] | b2d1d109ac69bf16f08cf50775719c7cc342876903bab6f04fe751b6290c40c3 |
"""
Original code by @philopon
https://gist.github.com/philopon/a75a33919d9ae41dbed5bc6a39f5ede2
"""
import sys
import os
import requests
import subprocess
import shutil
from logging import getLogger, StreamHandler, INFO
logger = getLogger(__name__)
logger.addHandler(StreamHandler())
logger.setLevel(INFO)
default_ch... | lilleswing/deepchem | scripts/colab_install.py | Python | mit | 3,490 | [
"MDTraj",
"OpenMM",
"RDKit"
] | 46f9f4c92184131452b5d1294a1d24a03d4295baf062bae10115bf8a2870002b |
from numpy import arange, meshgrid, empty
from abc import ABCMeta, abstractmethod
from pyproj import Proj
class ModelGrid(metaclass=ABCMeta):
"""Creates a spatial grid"""
def __init__(self):
self.var_name = '' # name of the modelled variable
@abstractmethod # flags method that MUST be implemente... | kmunve/APS | aps/aps_io/grid_data.py | Python | mit | 2,564 | [
"NetCDF"
] | ccbd5393a47c83af3b9e2ab97ce5f54575d4a3852e63c1d7e7156e27e0d0a06b |
# Copyright 2000-2002 Brad Chapman.
# Copyright 2004-2005 by M de Hoon.
# Copyright 2007-2010 by Peter Cock.
# 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.
"""Provides objects ... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Seq.py | Python | gpl-2.0 | 84,964 | [
"Biopython"
] | 9f18fdd3ac6e3ccd8f9d47963851fb2f31310b9ca95f029943de47670488b00f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, absolute_import
"""
This module provides conversion between the Atomic Simulation Environment
Atoms object and pymatgen Structure objects.
"""
__author__ = ... | Bismarrck/pymatgen | pymatgen/io/ase.py | Python | mit | 2,331 | [
"ASE",
"pymatgen"
] | d3af72441eb567cac4ac8a947e36aa27190420c60f194de59d92e9df4f625395 |
import numpy
from chainer import cuda
from chainer import initializer
# Original code forked from MIT licensed keras project
# https://github.com/fchollet/keras/blob/master/keras/initializations.py
class Normal(initializer.Initializer):
"""Initializes array with a normal distribution.
Each element of the ... | benob/chainer | chainer/initializers/normal.py | Python | mit | 2,423 | [
"Gaussian"
] | ab94ec3b159761a6f9776b788730d77ff276e826e5dba5db9a6c6080c4ed7403 |
#!/usr/bin/env python
"""
SYNOPSIS
python dataset.py [-h,--help] [-v,--verbose] [-d,--directory DIRECTORY]
DESCRIPTION
Assert the existence of the GeoLife dataset within the specified DIRECTORY.
If the dataset is not present, this script will first see if a ZIP archive
is within that directory and wi... | DrDougPhD/geolife2one | data/dataset.py | Python | mit | 9,564 | [
"VisIt"
] | 3c32737a0f65bd40310b67bf27eff8fec80598f922f12fd56db643c8afcf7a1d |
#!/usr/bin/python
####
# 02/2006 Will Holcomb <wholcomb@gmail.com>
# This library 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 Foundation; either
# version 2.1 of the License, or (at your option) any later ver... | datadesk/python-documentcloud | documentcloud/MultipartPostHandler.py | Python | mit | 8,051 | [
"Brian"
] | d1932bf7956f66d28e0bdf6eca444ad0dc9fc9b319f7ab68e42cf990c48012c7 |
"""
CIS is an open source command-line tool for easy collocation, visualization, analysis, and
comparison of diverse gridded and ungridded datasets used in the atmospheric sciences.
.. note ::
The CIS documentation has detailed usage information, including a :doc:`user guide <../index>`
for new users.
As a c... | zak-k/cis | cis/__init__.py | Python | gpl-3.0 | 4,185 | [
"NetCDF"
] | c3584127df5896f578d6e3f0eeb95125de1ca2f923d3f8f174575187173ff37e |
""" BHMM: A toolkit for Bayesian hidden Markov model analysis of single-molecule trajectories.
This project provides tools for estimating the number of metastable states, rate
constants between the states, equilibrium populations, distributions
characterizing the states, and distributions of these quantities from
sing... | marscher/bhmm | setup.py | Python | lgpl-3.0 | 4,392 | [
"Gaussian"
] | b9df924bd3c0c6f2f7ef944014e6f4af1161f9f0e00e60d81e64806eb839221a |
from urllib import quote_plus
from flask import jsonify, make_response, request, abort, render_template
from app import app
from app.urlshortener import URLShortener
from app.urlshortener.url import decodeURLPath, encodeURL, isValidScheme
from app.urlshortener.name import removeControlCharacters, isValidName
backend... | ollpu/lyli-api | app/views.py | Python | mit | 2,076 | [
"VisIt"
] | c557b1e7044d9c60ee5c7ec892bd8344023dd8b3044e1de04a97c2da9f145b37 |
from __future__ import annotations
import math
from scitbx import matrix
from scitbx.math import r3_rotation_axis_and_angle_from_matrix
def difference_rotation_matrix_axis_angle(crystal_a, crystal_b, target_angle=0):
from cctbx import sgtbx
# assert crystal_a.get_space_group() == crystal_b.get_space_group(... | dials/dials | algorithms/indexing/compare_orientation_matrices.py | Python | bsd-3-clause | 3,522 | [
"CRYSTAL"
] | a199a15e1da4f192b077a09892b03d8e06cccaf54aaa18a87937964c0e6d8bfb |
import unittest
import tempfile
import shutil
import os
from contextlib import closing
from traits.testing.api import UnittestTools
from tvtk.api import tvtk
from mayavi.core.api import NullEngine
from simphony.cuds.particles import Particles
from simphony.cuds.mesh import Mesh
from simphony.cuds.lattice import make_c... | simphony/simphony-mayavi | simphony_mayavi/sources/tests/test_cuds_file_source.py | Python | bsd-2-clause | 5,557 | [
"Mayavi"
] | bc2c89e394708e913f012b648ba6239cfa0a8b35346b787d15ad4a3492f6ed8d |
# $HeadURL$
__RCSID__ = "$Id$"
import sys
import os
import getopt
import types
import DIRAC
from DIRAC import gLogger
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gConfigurationData
from DIRAC.ConfigurationSystem.private.Refresher import gRefresher
from DIRAC.Configu... | avedaee/DIRAC | ConfigurationSystem/Client/LocalConfiguration.py | Python | gpl-3.0 | 17,793 | [
"DIRAC"
] | 251ffc9c0851f7e1bce635a8a685fd90abe5584ed7e25d7c424933aed9eaec53 |
# $HeadURL: $
""" ElementInspectorAgent
This agent inspect Resources, and evaluates policies that apply.
"""
import datetime
import math
import Queue
from DIRAC import S_ERROR, S_OK
from DIRAC.Core.Base.AgentModule import AgentMo... | calancha/DIRAC | ResourceStatusSystem/Agent/ElementInspectorAgent.py | Python | gpl-3.0 | 9,022 | [
"DIRAC"
] | d64e57dcc6570e8e7276cdad010fce350396945b27ac4ee4c5cac71a01d31535 |
data = (
'gwan', # 0x00
'gwanj', # 0x01
'gwanh', # 0x02
'gwad', # 0x03
'gwal', # 0x04
'gwalg', # 0x05
'gwalm', # 0x06
'gwalb', # 0x07
'gwals', # 0x08
'gwalt', # 0x09
'gwalp', # 0x0a
'gwalh', # 0x0b
'gwam', # 0x0c
'gwab', # 0x0d
'gwabs', # 0x0e
'gwas', # 0x... | gquirozbogner/contentbox-master | third_party/unidecode/x0ad.py | Python | apache-2.0 | 5,024 | [
"GULP"
] | b742dee26ff377a1330cf35325e25b6f2a3f7abdb63baca2f1edd2e4a27754d3 |
#
# Copyright 2018 Analytics Zoo Authors.
#
# 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... | intel-analytics/analytics-zoo | pyzoo/test/zoo/orca/automl/model/test_base_keras_model.py | Python | apache-2.0 | 4,523 | [
"ORCA"
] | bb1609a23e613fcb52458a02cb804037841ecc0620c354b6fe8b5680f20a78d4 |
import json
from pathlib import Path
import logging
import click
import tornado.ioloop
import tornado.web
import tornado.websocket
from tornado.log import enable_pretty_logging
import pyqrcode
from .export import data2usd_ascii, data2usdz, data2gltf, data2obj
from . import __version__
handler = logging.StreamHandl... | thomann/plotVR | plotAR-py/plotar/server.py | Python | agpl-3.0 | 8,251 | [
"Gaussian"
] | a0cfdde547d534a8c3b3bd95d88485c026d33445a93fe315d999f414d4e80898 |
import os
import glob
import subprocess
from gpaw.test.big.agts import AGTSQueue
from gpaw.test.big.niflheim import NiflheimCluster
def cmd(c):
x = os.system(c)
assert x == 0, c
os.chdir('agts')
cmd('svn checkout https://svn.fysik.dtu.dk/projects/gpaw/trunk gpaw')
cmd("""echo "\
cd agts/gpaw&& \
source /... | ajylee/gpaw-rtxs | tools/niflheim-agts.py | Python | gpl-3.0 | 2,077 | [
"ASE",
"GPAW"
] | e45e8bd6ef940543c435c046953ead1f47eddab55f98ab5a3688e7075031c900 |
import numpy as np
from math import pi, log
import pylab
from scipy import fft, ifft
from scipy.optimize import curve_fit
i = 10000
x = np.linspace(0, 3.5 * pi, i)
y = (0.3*np.sin(x) + np.sin(1.3 * x) + 0.9 * np.sin(4.2 * x) + 0.06 *
np.random.randn(i))
def _datacheck_peakdetect(x_axis, y_axis):
if x_axis is... | bmazin/SDR | Setup/WideSweep/peakdetect.py | Python | gpl-2.0 | 28,254 | [
"TINKER"
] | f2c9432ae72c463d4e54cb092d43be1c1679784b6ac3c88cfb52990271cc5126 |
'''
Set up a cyclic peptide nanotube and visualise the structure with matplotlib.
@author: Mark Oakley
'''
import numpy as np
import os
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from tubemaker.nanotube import read_amber_coords, orient_coords, build_tube
if __name__ == "__main__":
# ... | marktoakley/PeptideNanoTubes | example/Tubemaker/plot.py | Python | gpl-3.0 | 974 | [
"Amber"
] | 318676abbba8f0aed64773b641a7949341f75ec942f0741b070899ca97140663 |
# This file is part of Jeedom.
#
# Jeedom 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.
#
# Jeedom is distributed in the hope that i... | jeedom/plugin-template | resources/demond/demond.py | Python | gpl-2.0 | 3,838 | [
"Desmond"
] | 45e98175697e5271fb595a07c869bddfbfb0b24526481a6e2d84285aabb363a7 |
import numpy as np
import netCDF4 as nc
from .ncutil import nc_copy
def reduce_kpoints(subset, fname_in, fname_out):
"""
Reduce the number of kpoints by selecting a subset of indices.
Read the file fname_in and write the reduced data in fname_out.
Use the name of fname_in to determine the type of file... | jmbeuken/abinit | scripts/post_processing/ElectronPhononCoupling/ElectronPhononCoupling/util/reduce_kpoints.py | Python | gpl-3.0 | 4,306 | [
"NetCDF"
] | b97046b50408735ab10178cc748841327dc3bcf90cd51187d9b7826cc13b4670 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/topology/PDBParser.py | Python | gpl-2.0 | 15,051 | [
"MDAnalysis",
"VMD"
] | 2065290cf9a2c456017ef89cdd8a1f6d4ec3f8d4c63f467b1810aebe8c673799 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: Simplified BSD
from copy import deepcopy
import re
import numpy as np
from scipy import linalg
from .cov import read_cov, _get_whitener_data
from .io.constants import FIFF
from .io.pi... | alexandrebarachant/mne-python | mne/dipole.py | Python | bsd-3-clause | 41,062 | [
"Mayavi"
] | 4ac8b483b25d7d66f10162934825cbc6487567e1bc91bfcc22c775ec312fb7cc |
#! /usr/bin/python
'''pysam - a python module for reading, manipulating and writing
genomic data sets.
pysam is a lightweight wrapper of the htslib C-API and provides
facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ
files as well as access to the command line functionality of the
samtools and bcft... | kyleabeauchamp/pysam | setup.py | Python | mit | 15,401 | [
"pysam"
] | 83dc9e49bf6309312150fce1dfc8fa15bc45d04656af3fe1f3e930e967681a26 |
from ase import Atoms
from ase.structure import molecule
from ase.parallel import paropen
from gpaw import GPAW, Mixer, MixerDif
from gpaw.utilities.tools import split_formula
cell = [14.4, 14.4, 14.4]
data = paropen('data.txt', 'a')
##Reference from J. Chem. Phys. Vol 120 No. 15, 15 April 2004, page 6898
tpss_de = [... | ajylee/gpaw-rtxs | gpaw/test/big/tpss/tpss.py | Python | gpl-3.0 | 3,230 | [
"ASE",
"GPAW"
] | 4016b52ff720490f3382fdc6dbc45462b27300c1bcabff7f0780e97f2aaebad1 |
#!/usr/bin/env python
# Mesa 3-D graphics library
#
# Copyright (C) 1999-2006 Brian Paul All Rights Reserved.
#
# 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, includ... | CPFDSoftware-Tony/gmv | utils/Mesa/Mesa-7.8.2/src/mesa/es/main/get_gen.py | Python | gpl-3.0 | 33,026 | [
"Brian"
] | 34f5400ed8914738056eedb6c002d64dc9381b4ca08b50c639e3c06f8783d73b |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | mhlechner/psi4 | psi4/driver/qcdb/libmintsbasisset.py | Python | gpl-2.0 | 58,094 | [
"CFOUR",
"Gaussian",
"Psi4"
] | 2f34be413512a902aed8038c04ed9bca9f069fb941c143455525301e35dbc82d |
"""Abstract classes for :class:`fixture.base.Fixture` descendants that load / unload data
See :ref:`Using LoadableFixture<using-loadable-fixture>` for examples.
"""
# from __future__ import with_statement
__all__ = ['LoadableFixture', 'EnvLoadableFixture', 'DBLoadableFixture', 'DeferredStoredObject']
import sys, typ... | patrickod/fixture | fixture/loadable/loadable.py | Python | lgpl-2.1 | 16,777 | [
"VisIt"
] | 6637f85ac3c633d0ce19065982375108c9d4b2b92b2bc65ee0c7d556d1462e3b |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Execute computations asynchronously using threads or processes."""
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
import sys
from concurrent.futures._base import (FIRST_COMPLETED,
... | ms-iot/python | cpython/Lib/concurrent/futures/__init__.py | Python | bsd-3-clause | 842 | [
"Brian"
] | 3482ef1b68eb20484ec35eb9a99c76f416637de5a301472c98692b3cb010ab90 |
import lmfit
import numpy as np
import json
import functools
import operator
import suspect.basis
# this is the underlying function for the GaussianPeak model class
def gaussian(in_data, amplitude, frequency, phase, fwhm):
return amplitude * in_data.inherit(suspect.basis.gaussian(in_data.time_axis(), frequency, ... | openmrslab/suspect | suspect/fitting/singlet.py | Python | mit | 5,453 | [
"Gaussian"
] | 52040d0afb62140ebb0c1fa299c36c01dae37e5c7f050b3396c4b1bf87d5d8ae |
#!/bin/env python
""" Reset failed requests and operations therein """
__RCSID__ = "$Id: $"
import sys
from DIRAC.Core.Base import Script
maxReset = 100
Script.registerSwitch( '', 'Job=', ' jobID: reset requests for jobID' )
Script.registerSwitch( '', 'Failed', ' reset Failed requests' )
Script.registerSwitch( '', ... | avedaee/DIRAC | RequestManagementSystem/scripts/dirac-dms-reset-request.py | Python | gpl-3.0 | 3,325 | [
"DIRAC"
] | d3b49ba5b05dec50012dcfe18be641bc681c3c6d5ce58eb1e042b8ddd1559d17 |
# -*- coding: utf-8 -*-
#
# You can specify the sources you want to read in this file. All sources must
# be placed inside of
# sources = [
# SOURCE1
# SOURCE2
# ...
# ]
# Each source should look like
# {
# 'setting_name': 'setting_value',
# ...
# },
#
# For output* templating... | livibetter/clis | samples/clis.cfg.py | Python | mit | 8,297 | [
"VisIt"
] | da22c3bae89c34b9806142c6d39ac48e3708efc2cb62995b75bde893870eedc9 |
import numpy as np
from numpy.linalg import inv
import os, os.path
### IPR specific stuff ###
class FortranError(Exception):
'''When fortran doesn't keep spaces between numbers so everything goes to
shit because fortran is such a decrepit POS'''
class GulpError(Exception):
'''gulp runtime error'''
class ... | wolverton-research-group/fitpot | fitpot/data.py | Python | mit | 6,057 | [
"GULP"
] | 5d9e690a1e95047f4bc4a02d4f34243338a370ca4925665c1fc003d6e11d0400 |
################################################################################
# Copyright (C) 2011-2013 Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
import numpy as np
import matplotlib.pyplot as plt
import h5py
i... | SalemAmeen/bayespy | bayespy/demos/saving.py | Python | mit | 4,028 | [
"Gaussian"
] | 38dd10e1f179c0ae029e5dcddf6122c41f717064d42981fd3d0d0ca4c61093b3 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License
"""
Module for implementing a CTRL file object class for the Stuttgart
LMTO-ASA code. It will primarily be used to generate a pymatgen
Structure object in the pymatgen.electronic_structure.cohp.py module.
"""
import re
impo... | vorwerkc/pymatgen | pymatgen/io/lmto.py | Python | mit | 15,527 | [
"pymatgen"
] | 0258c11c6f524d7ccdd78a16c744d9ecfa4e0ce3423355d82439bcc504d21b03 |
'''
Run an assimilation cycle using the Kalman Filter; for each assimilation window:
1. observations are obtained (simulated from the truth plus a random realization of R);
2. an analysis is computed;
3. the analysis is integrated using the model to produce the forecast;
4. covariance matrices are propagated usin... | martndj/DaleyMenard1993 | kalmanFilter.py | Python | gpl-3.0 | 4,907 | [
"Gaussian"
] | 3bba166893eab9c52c00681f103062e7fc69555bfa178b7964be279788b977e7 |
# (C) British Crown Copyright 2014, Met Office
#
# This file is part of Iris.
#
# Iris 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 Foundation, either version 3 of the License, or
# (at your option) any later ve... | scollis/iris | lib/iris/tests/experimental/test_raster.py | Python | gpl-3.0 | 4,636 | [
"NetCDF"
] | 2d08e97e8583805161d44f8afda0cca5375ae7638d125b952bfd60258f5fc5c5 |
""" Agent to extend the number of tasks given the Transformation definition
"""
from DIRAC import S_OK, gLogger
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.ConfigurationSystem.Client.Helpers.Operations ... | chaen/DIRAC | TransformationSystem/Agent/MCExtensionAgent.py | Python | gpl-3.0 | 4,845 | [
"DIRAC"
] | 274516cd93a20d2c0e8d64fc4cf3fe039fe1d2965e3e92ec864947b098c12d2b |
from sys import argv
import pylab as plt
from ase.dft import STM
from gpaw import restart
filename = argv[1]
if len(argv) > 2:
z = float(argv[2])
else:
z = 2.5
atoms, calc = restart(filename, txt=None)
stm = STM(atoms, symmetries=[0, 1, 2])
c = stm.get_averaged_current(z)
# Get 2d array of constant c... | qsnake/gpaw | doc/exercises/stm/stm.py | Python | gpl-3.0 | 469 | [
"ASE",
"GPAW"
] | 450ee736f3e42c0e9a81e2c8f167aa09a5259485d222c7758f718a4ca6e43caf |
import common, chess, copy
# patterns/cycles/pw
def check(problem, board, solution):
retval = {}
# patterns/cycles
tb = TrajectoriesBuilder()
tb.visit(solution, [])
traverse_trajectories([], tb.result, retval)
# pw
traverse_for_platzwechsel([], solution.siblings, retval)
re... | tectronics/olive-gui | legacy/trajectories.py | Python | gpl-3.0 | 6,236 | [
"VisIt"
] | f9dbc1cd0d8403b60423661ad100ea2ae8071bf1cebf5fb2db7a206a1da3334d |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""Mirror of :mod:`iris.tests.unit.fileformats.netcdf.test_Saver`, but with lazy arrays."""
# Import iris.tests first so that ... | SciTools/iris | lib/iris/tests/unit/fileformats/netcdf/test_Saver__lazy.py | Python | lgpl-3.0 | 3,694 | [
"NetCDF"
] | 403a88425d09b928cdd7838b590e49a5916cc29f8f1d9a4cac52c9369cd987f7 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-wms-job-delete
# Author : Stuart Paterson
########################################################################
"""
Reschedule the given DIRAC job
"""
from __future__ import print_function
... | chaen/DIRAC | Interfaces/scripts/dirac-wms-job-reschedule.py | Python | gpl-3.0 | 1,297 | [
"DIRAC"
] | 697fac207899a654599828d52e076343a346a65cb9e2061ea8b5f106b1a1e876 |
# -----------------------------------------------------------------------
#
# < pyetree_concert.py >
#
# -----------------------------------------------------------------------
# -----------------------------------------------------------------------
#
# File Name : pyetree_concert.py
#
# ... | josefgrosch/Pyetree | pyetree/PyetreeConcert.py | Python | apache-2.0 | 3,926 | [
"MOOSE"
] | 55dbf252d52cc780fd099b89969f10aee4e99fd4112f37dfc16996f83c992ab2 |
from django.contrib import admin
# Register your models here.
from .models import (
Collaborator,
Harvest,
Route,
Visit,
)
from pmm.admin import PersonAdmin
from core.admin import ContentAdmin
@admin.register(Collaborator)
class CollaboratorAdmin(PersonAdmin):
list_display = PersonAdmin.list_disp... | sauli6692/ibc-server | rte/admin.py | Python | mit | 1,179 | [
"VisIt"
] | 3b919b80e4d9ee716bae8a35a33b4e3e615e6af7add46beec5946a9866e3d986 |
'''
Created on Jul 21, 2011
@author: mkiyer
'''
import logging
import os
import sys
from chimerascan import pysam
from chimerascan.lib import config
from chimerascan.lib.chimera import DiscordantTags, DISCORDANT_TAG_NAME, \
OrientationTags, ORIENTATION_TAG_NAME, DiscordantRead
from chimerascan.lib.gene_to_genome ... | genome-vendor/chimerascan | chimerascan/pipeline/discordant_reads_to_bedpe.py | Python | gpl-3.0 | 3,908 | [
"pysam"
] | 2d8c73adb13d9f361a0530c992189d629f6377184b5b2b9810c5ce3be886c910 |
#!/usr/bin/python
#
# @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... | CDSherrill/psi4 | doc/sphinxman/document_cfour.py | Python | lgpl-3.0 | 2,585 | [
"CFOUR",
"Psi4"
] | b8ac6f269354fe2143f79e145e89a97ce322a073551386a52d67556e65fc58d5 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo 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 ... | KaiSzuttor/espresso | testsuite/python/lb_pressure_tensor_acf.py | Python | gpl-3.0 | 4,387 | [
"ESPResSo"
] | d9ea69d0309f2ab312ba3d579b141efbc334a6443ac45a959969f1f835e683fb |
from __future__ import print_function, absolute_import
import os
import sys
import json
import shutil
import subprocess
import tempfile
import warnings
from setuptools import Extension
from distutils.dep_util import newer_group
from distutils.errors import DistutilsExecError, DistutilsSetupError
from distutils.ccompil... | gph82/mdtraj | basesetup.py | Python | lgpl-2.1 | 15,842 | [
"MDTraj"
] | 45f005df053aa3b9ff1f215e8c96497e6d3b30403a77efdb46660ef3d2b55397 |
#!/usr/bin/python
"""
Classes to read and process MedLine XML record files, for use in processing modules.
They can handle the XML format used by PubMed and MedLine services, for example as returned by eutils online services
>>> xml_records = urllib.urlopen('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi... | hectormartinez/rougexstem | taln2016/icsisumm-primary-sys34_v1/nltk/nltk-0.9.2/nltk_contrib/bioreader/bioreader.py | Python | apache-2.0 | 20,328 | [
"Biopython"
] | 557d06b35c734a239a91fc4718e7e3705208fe1479a63d2a0cbb8cfb18d89093 |
from pypuf.simulation.arbiter_based.ltfarray import LTFArray
from numpy.random import RandomState
from pypuf.learner.base import Learner
from pypuf.learner.liu.partition import getChallenge
from pypuf.learner.liu.chebyshev import findCenter
from pypuf.learner.liu.chebyshev2 import findCenter2
from pypuf.learner.l... | nicostephan/pypuf | pypuf/learner/liu/polytope_algorithm.py | Python | gpl-3.0 | 5,502 | [
"Gaussian"
] | 1e6dccf66152fca0e1c7fe05be32e79df2e8e02a96d659d95134b06a0cb7c3b3 |
# -*- coding: utf-8 -*-
"""
This is a deprecated backend. :mod:`~xrt.backends.raycing` is much more
functional. Module :mod:`~xrt.backends.shadow` works with shadow input files,
starts the ray-tracing and gets its output.
.. warning::
Shadow3 is not supported.
.. warning::
xrtQook and xrtGlow do not work w... | kklmn/xrt | xrt/backends/shadow.py | Python | mit | 16,156 | [
"CRYSTAL"
] | 075973981f72a44d673125f7cdcc262e7ab36969a56982a80041b20517279b04 |
import numpy as np
from cora.signal import corr21cm
from cora.foreground import galaxy
def test_corr_signal():
"""Test that the signal power spectrum is being calculated correctly.
Correct here is referenced to a specific version believed to have no errors.
"""
cr = corr21cm.Corr21cm()
aps1 = ... | radiocosmology/cora | tests/test_corr.py | Python | mit | 1,914 | [
"Galaxy"
] | fe0d9b60748e407463d21658daf1b732b1f724470d266a121a46f683fc157828 |
# -*- coding: utf-8 -*-
import numpy as np
from shapely.geometry.polygon import Polygon
import datetime
import netCDF4 as nc
import itertools
import geojson
from shapely.ops import cascaded_union
from shapely.geometry.multipolygon import MultiPolygon, MultiPolygonAdapter
from shapely import prepared, wkt
from shapely.g... | mapping/OpenClimateGIS | src/openclimategis/util/ncconv/experimental/OLD_experimental/in_memory_oo_multi2.py | Python | bsd-3-clause | 34,083 | [
"NetCDF"
] | 470a251c581d0fa210f9fe13b78a310a5ce96d71fc48297ac36404b2dc63d2c2 |
##
## See COPYING file distributed along with the ncanda-data-integration package
## for the copyright and license terms
##
"""
A collection of utility functions used by aseba_prep.py and aseba_reformat.py
"""
from __future__ import print_function
from __future__ import division
from builtins import str
from builtins... | sibis-platform/ncanda-data-integration | scripts/reporting/aseba_utils.py | Python | bsd-3-clause | 5,978 | [
"VisIt"
] | 3d1d152c468062d067bf81094ab70ed6caed6befa6ed11d792e3bba57984694b |
#!/usr/bin/env python
VERSION='1.00'
import os,sys,time
import optparse
from RecoLuminosity.LumiDB import pileupParser
from RecoLuminosity.LumiDB import selectionParser
from math import exp
from math import sqrt
def parseInputFile(inputfilename):
'''
output ({run:[ls:[inlumi, meanint]]})
'''
selectf=op... | iamjakob/lumiCalc | LumiDB/scripts/pileupCalc.py | Python | apache-2.0 | 10,205 | [
"Gaussian"
] | 758325ee272346eace50f27327f9d437da704fe2a68f67c2512e65445abce5b5 |
# Copyright 2001 by Iddo Friedberg. 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.
from Bio import FSSP
from Bio.FSSP import FSSPTools
import sys
import os
# import pickle
tes... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_FSSP.py | Python | gpl-2.0 | 2,016 | [
"Biopython"
] | 8871ebad586ee094c49bde78ec604327d478418c48b46123680f62f270c3238e |
"""
Instantiate the global Configuration Object
gConfig is used everywhere within DIRAC to access Configuration data
"""
from DIRAC.ConfigurationSystem.private.ConfigurationClient import ConfigurationClient
#: Global gConfig object of type :class:`~DIRAC.ConfigurationSystem.private.ConfigurationClient.Configuratio... | DIRACGrid/DIRAC | src/DIRAC/ConfigurationSystem/Client/Config.py | Python | gpl-3.0 | 524 | [
"DIRAC"
] | 6fc501c4a489dd95d5a480c65573d1f7974fb38440a4488bb6a74dddf0e8db69 |
# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the... | karrtikr/ete | ete3/coretype/tree.py | Python | gpl-3.0 | 91,899 | [
"scikit-bio"
] | 40340d0dc54114da4c26d4e6bd71788c53a669b1c54adc5fc0b2928019d065cc |
import simtk.openmm as openmm
import simtk.unit as unit
import mdtraj as md
import numpy as np
import copy
import enum
InteractionGroup = enum.Enum("InteractionGroup", ['unique_old', 'unique_new', 'core', 'environment'])
#######LOGGING#############################
import logging
logging.basicConfig(level = logging.NO... | choderalab/perses | perses/annihilation/relative.py | Python | mit | 161,386 | [
"Amber",
"MDTraj",
"OpenMM"
] | 82113a28c176cf7b235835602f08722ccc2a0ddb33186fc9e7a9c8354d487f39 |
# -*- encoding: utf-8 -*-
import os
from django.contrib.staticfiles.testing import StaticLiveServerTestCase
from django.urls import reverse
from selenium.common.exceptions import NoSuchElementException
from splinter.driver.webdriver.phantomjs import WebDriver as SplinterWebDriver
from scriptorium.helpers.npm import res... | alex20465/open-scriptorium | scriptorium/base/test/__init__.py | Python | mit | 3,305 | [
"VisIt"
] | 603ffb15757e510824b5ad88057e215deef768c34b782e0eb7ca49e088e309f3 |
#!/usr/bin/env python
'''
GOAL:
- test several models that describe how disks shrink and integrated SFR decreases as a result of outside-in quenching
USAGE
- from within ipython
%run ~/Dropbox/pythonCode/LCSsimulate-infall.py
t = run_sim(tmax=0,drdt_step=0.05,nrandom=1000)
t = run_sim(tmax=1,drdt_step=0.05,nrandom... | rfinn/LCS | python/LCSsimulate-infall-sfrs.py | Python | gpl-3.0 | 39,087 | [
"Galaxy"
] | ee9a68dd8e983e490cc034547f58ffb931ff189eba2581d184ad0e96a73fdd21 |
import bpy
from bpy.props import BoolProperty,IntProperty,FloatProperty,EnumProperty,PointerProperty,FloatVectorProperty,StringProperty
from . import config
# def SetResolution(self, context):
# self.width = max(int(context.scene.blcloudrender.res_p*context.scene.blcloudrender.res_x),1);
# self.height = max(int(c... | jaelpark/droplet-render | addon/panel.py | Python | bsd-3-clause | 18,741 | [
"Gaussian"
] | 6829416b853185246031e05b649edd9b912b0017732a09d359a4807814e66df3 |
#!/usr/local/bin/env python
"""
Various Python utilities for OpenMM.
"""
from openmmtools import testsystems, integrators, alchemy, mcmc, states, cache, utils, constants, forces, forcefactories, storage, multistate
# Handle versioneer
from ._version import get_versions
versions = get_versions()
__version__ = versio... | choderalab/openmmtools | openmmtools/__init__.py | Python | mit | 408 | [
"OpenMM"
] | e281723b60cc5c60362c08b24707c4abf448eb73bb367e9249e64c50a48e7706 |
"""Implementation of Apache VFS schemes and URLs."""
import os
from rasterio.compat import urlparse
# NB: As not to propagate fallacies of distributed computing, Rasterio
# does not support HTTP or FTP URLs via GDAL's vsicurl handler. Only
# the following local filesystem schemes are supported.
SCHEMES = {'gzip': '... | ryfeus/lambda-packs | Rasterio_osgeo_shapely_PIL_pyproj_numpy/source/rasterio/vfs.py | Python | mit | 2,206 | [
"NetCDF"
] | 95ab3e25283d2aaf728705bea3a74ac0501f833e812761c03d6fd20555d00a89 |
'''<h1>Library for surface x-ray diffraction simulations</h1>
<p> The problem of modelling the sample is divided to four
different classes: Sample, Slab, UnitCell and Instrument.
A Slab is the basic unit that builds up a sample and can
be seen as a quasi-unitcell for the sxrd problem.
Stricitly it is a 2D unitcell with... | haozhangphd/genx-py3 | genx/models/sxrd.py | Python | gpl-3.0 | 42,067 | [
"Gaussian"
] | f231b32831298e634121953ec7c611b51ebcc7b8b2ec74188ff1eb6bbba9ecbd |
#!/usr/bin/env python
#
# $File: cppParentChooser.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redist... | BoPeng/simuPOP | docs/cppParentChooser.py | Python | gpl-2.0 | 2,430 | [
"VisIt"
] | 447a025d6060822939b12aed689cdda0bb65f00f4c4dce6b7f497e4399773535 |
#! /usr/bin/python
#coding=utf-8
import pycurl, re, cStringIO #pycurl is better than urllib
from Tkinter import * #import functions only when necessary
url0 = "http://site.baidu.com" #begin from a navigate page
global MAXNUM #the max num of web pages to visit
MAXNUM = 20
global urlnum ... | bookug/study | python/js-counter.py | Python | gpl-3.0 | 7,112 | [
"VisIt"
] | 709bee4f115d4d256e46d6cbca70e192a2ca852fdd65820580effc7b2c8d7a73 |
"""
Test vv.diff module
"""
__author__ = "Dan Gunter <dkgunter@lbl.gov>"
import logging
import random
import unittest
from pymatgen.db.tests.common import MockQueryEngine
from pymatgen.db.vv.diff import Differ, Delta
#
db_config = {
"host": "localhost",
"port": 27017,
"database": "test",
"aliases_co... | materialsproject/pymatgen-db | pymatgen/db/vv/tests/test_diff.py | Python | mit | 8,690 | [
"pymatgen"
] | 1840553a94cdab20ecc479edc09dac96b8467336e9660764eaab1681f1ce5ecf |
"""
Routines for interpolating forcing fields for the 3D solver.
"""
from firedrake import *
import numpy as np
import scipy.spatial.qhull as qhull
import thetis.timezone as timezone
import thetis.interpolation as interpolation
import thetis.coordsys as coordsys
from .log import *
import netCDF4
import thetis.physical_... | tkarna/cofs | thetis/forcing.py | Python | mit | 35,873 | [
"NetCDF"
] | d36e1db5f7cd51cc14478b1dc2dd54d02f2621f7a0892ad5588ec9194533c16a |
""" StorageOccupancy records the Storage Elements occupancy over time
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseAccountingType
class StorageOccupancy(BaseA... | ic-hep/DIRAC | src/DIRAC/AccountingSystem/Client/Types/StorageOccupancy.py | Python | gpl-3.0 | 1,252 | [
"DIRAC"
] | 675a560c40e6adca86960c96e69e16e6c620edde8ce75a26b0aabffac5bfb537 |
##
# Copyright 2015-2018 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | bartoldeman/easybuild-easyblocks | easybuild/easyblocks/m/molpro.py | Python | gpl-2.0 | 11,928 | [
"Molpro"
] | e2155c555f2a01fec33d8e74838b63ac3d23ac0900b08a110c82df960ef23c88 |
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