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#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
from scipy._lib.six import string_types, exec_, PY2
from scipy._lib._util import getargspec_no_self as _getargspec
import sys
import keyword
import r... | jor-/scipy | scipy/stats/_distn_infrastructure.py | Python | bsd-3-clause | 125,438 | [
"Gaussian"
] | 016595588545d26605784d826bf8e635b3606009f9da366a65e6d38909294b12 |
#Standard dependencies
import os
import sys
import inspect
import time
import cPickle as pickle
import re
from copy import copy
from string import Template
#Non-standard dependencies
import numpy as np
from scipy.interpolate import InterpolatedUnivariateSpline as spline
import matplotlib as mpl
mpl.use('Agg')
import p... | starry99/catmap | catmap/__init__.py | Python | gpl-3.0 | 2,096 | [
"ASE"
] | 95a051107eed23217bd39d6fa5d524b0f24549b1604c86494065d0c2c9af8144 |
""" A wrapper to get the needed preferences application wide """
# Copyright (C) 2009-2010, Ecole Polytechnique Federale de Lausanne (EPFL) and
# University Hospital Center and University of Lausanne (UNIL-CHUV)
#
# Modified BSD License
# Standard library imports
from os.path import join
import pkg_resources
# Enthou... | LTS5/connectomeviewer | cviewer/plugins/ui/preference_manager.py | Python | bsd-3-clause | 4,244 | [
"Mayavi"
] | 9961449fb45d1809238d96cffc96948956ceb97f03f8b5b95210b7d896aee200 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Directadmin API - Python implementation of Directadmin Web API
Copyright (C) 2009, Andrés Gattinoni
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, e... | el-barto/python-directadmin | directadmin/api.py | Python | gpl-3.0 | 51,302 | [
"VisIt"
] | bb028b6ab9b37afdf1da9806b5201824ee37ea4a7a4dfeb4174e8cfbd82baafc |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a Composition class to represent compositions,
and a ChemicalPotential class to represent potentials.
"""
import collections
import numbers
import string
from itertools import combin... | fraricci/pymatgen | pymatgen/core/composition.py | Python | mit | 51,187 | [
"pymatgen"
] | 4f4dc51f05d675c77c3eaab519a50afae6825065cb3b1895c1cd84f316e35461 |
import re
from pycp2k import CP2K
from ase.lattice.cubic import Diamond
from ase.visualize import view
#===============================================================================
# Create the Si lattice here
lattice = Diamond(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol='Si',
... | SINGROUP/pycp2k | examples/example_si_cutoff.py | Python | lgpl-3.0 | 2,407 | [
"ASE",
"CP2K"
] | 73ad4aea1d89dea080edd3402fee759be0fdf44e1d408bea5bae780d149505aa |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
import frappe
from frappe import _, throw
from frappe.utils import add_days, cint, cstr, date_diff, formatdate, getdate
from erpnext.hr.doctype.employee.employee import get_holiday_list_for_... | mhbu50/erpnext | erpnext/maintenance/doctype/maintenance_schedule/maintenance_schedule.py | Python | gpl-3.0 | 12,406 | [
"VisIt"
] | 8acc38c23db11086bd7627e0b6fd224ceff152034eb2211e253bede0a89db7c1 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views import defaults as default_views
from django.conf.urls.i18n import i18n_patterns
from... | Uran198/med | config/urls.py | Python | bsd-3-clause | 1,852 | [
"VisIt"
] | dc61dbbe5d5a5797e8f6c81f2bbb8b000286b88f6c1022c722776dce79b790f1 |
import numpy as np
from gym.spaces import Box
from metaworld.envs import reward_utils
from metaworld.envs.asset_path_utils import full_v2_path_for
from metaworld.envs.mujoco.sawyer_xyz.sawyer_xyz_env import SawyerXYZEnv, _assert_task_is_set
class SawyerFaucetCloseEnvV2(SawyerXYZEnv):
def __init__(self):
... | rlworkgroup/metaworld | metaworld/envs/mujoco/sawyer_xyz/v2/sawyer_faucet_close_v2.py | Python | mit | 4,061 | [
"Gaussian"
] | d0026644bf20660f301a2f0778950497e83f03f50d5c358aa5c7cf5b060504d2 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_seproperties.py | Python | bsd-3-clause | 3,509 | [
"VisIt"
] | 7d6728d1b697661c78e165805594ab8350cdb2e044bb2105b1245c4c4d3bce22 |
#Internet Archive ROM Launcher
#Zach Morris
#https://github.com/zach-morris/plugin.program.iarl
from resources.lib.xbmcswift2b import Plugin
from resources.lib.xbmcswift2b import actions
from resources.lib.xbmcswift2b import ListItem as LI
import os, sys, subprocess, xbmc, xbmcgui, xbmcaddon
from resources.lib.util im... | zach-morris/plugin.program.iarl | addon.py | Python | gpl-2.0 | 159,845 | [
"ADF"
] | 3ed386056670924dc1850adc2dd2d5b67c8d20a4534fd1502021e4dced4df5a7 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Final/results/objects/384/test10_cross_validate_objects_1200ms.py | Python | mit | 4,252 | [
"Mayavi"
] | 53db17e15a57dfd741f6e40859dc7bcff4515dc8bffc7c5bfd60a6c9c5a67c3f |
from math import pi, sqrt
import numpy as np
from numpy.fft import fftn
from ase.units import Hartree
from gpaw.lfc import LocalizedFunctionsCollection as LFC
from gpaw.pair_density import PairDensity2 as PairDensity
from gpaw.poisson import PoissonSolver, FFTPoissonSolver
from gpaw.utilities import pack, unpack, pac... | ajylee/gpaw-rtxs | gpaw/coulomb.py | Python | gpl-3.0 | 12,422 | [
"ASE",
"GPAW",
"Gaussian"
] | ec8cf62eff4491c68a0c439c9e6776b43a9b1f3b4384e0b10bfb1208e8bbd3a3 |
from kameleon_mcmc.distribution.Gaussian import Gaussian
from kameleon_mcmc.mcmc.samplers.MCMCSampler import MCMCSampler
from numpy.lib.twodim_base import eye
class StandardMetropolis(MCMCSampler):
'''
Just a plain, old, boring Metropolis Algorithm
with a fixed scale and a fixed covairance matrix
'''
... | karlnapf/kameleon-mcmc | kameleon_mcmc/mcmc/samplers/StandardMetropolis.py | Python | bsd-2-clause | 1,130 | [
"Gaussian"
] | 8e4a48bc377b56968904b0c835c3746933b99c674a4d03272e5fa208e940e12c |
import os
import numpy as np
os.environ['THEANO_FLAGS'] = 'floatX=float32'
import theano
import theano.tensor as tt
import theano.tensor.signal.pool # noqa: 401
# dtype = theano.config.floatX
from run_core import load_network, SoftLIFRate, round_layer
def compute_layer(layer, inputs, data):
assert isinstance(... | hunse/cuda-convnet2 | run_numpy.py | Python | apache-2.0 | 8,487 | [
"NEURON"
] | 8888e4871d55ac993a70e64fc9f63160d42c3a0bdfe3e999c9b171815ccab364 |
"""
Parses an XML feed into a Python representation. You should probably use L{iface_cache.iface_cache} rather than the functions here.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
import os
from logging import debug, info, warn
im... | dabrahams/zeroinstall | zeroinstall/injector/reader.py | Python | lgpl-2.1 | 8,295 | [
"VisIt"
] | f268d809183e404502485bbd0950db4b21ed6871867bdf32b8cb2e456c1618aa |
import pandas as pd
from astropy.io import fits
import astropy.coordinates as cd
from ctc_observ import *
from ctc_arrays import *
from scipy.interpolate import interp1d
#load HSC catalog first
#hsc = pd.read_csv('/cuc36/xxl/multiwavelength/HSC/wide.csv')
def pdf_sep_gen(sep_arcsec,xposerr,opterr,pdf='Rayleigh'):
'''... | CTJChen/ctc_astropylib | lrmatch_old.py | Python | apache-2.0 | 14,519 | [
"Gaussian"
] | f06ef17cd3edd734fcca1fc3ecfba9adfe27a37058fdc806ab67861dd87a836f |
from InputParameters import InputParameters
from Job import Job
import os, sys, subprocess, shutil
class PBSJob(Job):
def validParams():
params = Job.validParams()
params.addRequiredParam('chunks', "The number of PBS chunks.")
# Only one of either of the next two paramteres can be specified
params.... | gleicher27/Tardigrade | moose/framework/scripts/ClusterLauncher/PBSJob.py | Python | lgpl-2.1 | 5,473 | [
"MOOSE"
] | 2c3b7652547ea8dfab18aa60ac8d1b641ea014bdad03642acf3d7c2dca2a972c |
# Written by Bram Cohen
# see LICENSE.txt for license information
# For a description of the algorithm see https://wiki.theory.org/BitTorrentSpecification#Choking_and_Optimistic_Unchoking.
from random import randrange
class Choker:
def __init__(self, max_uploads, schedule, done = lambda: False, min_uploads = Non... | mgp/bittorrent-dissected | Choker.py | Python | mit | 11,757 | [
"VisIt"
] | ad784e1a58e85009360333148fed1994db864632471d53d0f7d3a29413bc9831 |
#
# Honeybee: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Honeybee.
#
# Copyright (c) 2013-2020, Mostapha Sadeghipour Roudsari <mostapha@ladybug.tools>
# Honeybee is free software; you can redistribute it and/or modify
# it under the terms of the GNU G... | mostaphaRoudsari/Honeybee | src/Honeybee_Generate Climate Based Sky.py | Python | gpl-3.0 | 7,388 | [
"EPW"
] | 6000e1c30d3ec37c3c76f4b254d460e7932d401a715070b60026916884147a93 |
import socket
import webbrowser
import httplib2
import oauth2client.clientsecrets as clientsecrets
from six.moves import input
from apiclient.discovery import build
from functools import wraps
from oauth2client.client import FlowExchangeError
from oauth2client.client import AccessTokenRefreshError
from oauth2client.cl... | smeggingsmegger/PyDrive | pydrive/auth.py | Python | apache-2.0 | 15,036 | [
"VisIt"
] | 9e82eddb9f827dccea99b37577a0f39f4d4f5b5403b4f98f08c1cf3fc504d193 |
import numpy as np
import re
class PwxOutput:
def __init__(self, out):
self.outfile = out
def total_energy(self):
"""Parse output file to get total energy
Because this method should also work for relaxation
runs, in which a total energy is printed for every iteration,
... | sroelants/quint | output.py | Python | gpl-2.0 | 4,245 | [
"CRYSTAL"
] | 7b4e8b0b3a819cb9864a74c3d71393269cc38cf035c973a0bb8b78773d5cedd4 |
# EmphysemaViewer by Corine Slagboom & Noeska Smit
#
#
# Based on SkeletonAUIViewer:
# Copyright (c) Charl P. Botha, TU Delft.
# All rights reserved.
# See COPYRIGHT for details.
# skeleton of an AUI-based viewer module
# copy and modify for your own purposes.
# set to False for 3D viewer, True for 2D image viewer
I... | nagyistoce/devide | modules/user/EmphysemaViewer/EmphysemaViewer.py | Python | bsd-3-clause | 22,332 | [
"VTK"
] | 54e37fdf8e8b7fb2c962e5e71502ea91ba6de28f6aa4f1e6fe1b1a8dafeabfb1 |
#!/usr/bin/env python
"""
Copyright 2016 Brian Quach
Licensed under MIT (https://github.com/brianquach/udacity-nano-fullstack-conference/blob/master/LICENSE) # noqa
"""
import endpoints
import json
import webapp2
from google.appengine.api import app_identity
from google.appengine.api import mail
from google.appengine... | brianquach/udacity-nano-fullstack-game | main.py | Python | mit | 7,415 | [
"Brian"
] | 2c4f3bd75260413ab7197a3b78fd47beb15e85a3ad727fe035563f12ec868bf1 |
# coding=utf-8
import logging
import threading
import time
from octopus import err
from octopus import constant
from octopus.service.selector._base import BaseSelector
from octopus.util import tools
log = logging.getLogger(constant.LOGGER_NAME)
class BaseClient(object):
def __init__(self, thrift_mod, selector,... | ideascf/octopus | service/client/_base.py | Python | mit | 3,049 | [
"Octopus"
] | 778108edb1a10d5d39d4f0a491f6586e834642a7b48350a0f8dde4df7fa1be7c |
"""
Generate a toy dataset for the matrix tri-factorisation case, and store it.
We use dimensions 100 by 50 for the dataset, 10 row clusters, and 5 column clusters.
As the prior for F, G we take value 1 for all entries (so exp 1), and for S value 2 (so exp 1/2).
As a result, each value in R has a value of around 25,... | ThomasBrouwer/BNMTF | data_toy/bnmtf/generate_bnmtf.py | Python | apache-2.0 | 3,776 | [
"Gaussian"
] | e039cda0a270c0fa59cb7cd8f6992b8110b5b3c070f9f1dea37c52be558ecead |
"""
`cirrina` - Opinionated web framework
Simple cirrina server example.
:license: LGPL, see LICENSE for details
"""
import logging
import sys
import cirrina
from aiohttp import web
#: Holds the logger for the current example
logger = logging.getLogger(__name__)
#: Create cirrina app.
app = cirrina.Server()
app.e... | neolynx/cirrina | examples/basic/server.py | Python | lgpl-3.0 | 4,986 | [
"VisIt"
] | a7cd129ac9c7e2c25b2191fb5ca4294eabc3330d573e257b3782183f2a2a563b |
#!/usr/bin/env python
# -*- coding:utf-8 -*-
"""
# Author: Hackathon
# Description: I find the code in https://djangosnippets.org/snippets/3046/.
You can visit that site for more inforation.
bug: change mimetype to content_type for django1.7
"""
import datetime
from django.db.models.query import Que... | PegasusWang/Physics_web | physics/excel_response.py | Python | mit | 3,534 | [
"VisIt"
] | d7748c01f54d147238a63abffdca3c893005544782e07857b14578e8106c17d8 |
"""Config flow for Elk-M1 Control integration."""
import asyncio
import logging
from urllib.parse import urlparse
import elkm1_lib as elkm1
import voluptuous as vol
from homeassistant import config_entries, exceptions
from homeassistant.const import (
CONF_ADDRESS,
CONF_HOST,
CONF_PASSWORD,
CONF_PROTO... | tboyce021/home-assistant | homeassistant/components/elkm1/config_flow.py | Python | apache-2.0 | 4,890 | [
"Elk"
] | 2318a06e134eb007d3d1a69919b8860bc74e9c48b5c009c4e593777ec35150ce |
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
# Copyright (C) 2012 Olaf Lenz
#
# 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 L... | KonradBreitsprecher/espresso | src/core/gen_featureconfig.py | Python | gpl-3.0 | 4,430 | [
"ESPResSo"
] | 2cb11611a41cc760151c0bcbbef4b8283d71becdb264aa7ca31786188c1ce885 |
import mdtraj as md
import os
import operator
import numpy as np
from functools import reduce
class TrajReader:
'''
def __init__(self, trajlistName, atomlistName, trajDir, trajExt, File_TOP):
self.trajlistName = trajlistName
self.atomlistName = atomlistName
self.trajDir = trajDir
... | stephenliu1989/HK_DataMiner | hkdataminer/utils/reader_.py | Python | apache-2.0 | 7,594 | [
"MDTraj"
] | 88c75df7025c33269a083bbb6bda4cb383ed2fccb9ab8f3c5a064bb9140ab198 |
#!/usr/bin/env python
"""
:Author: Martin Kircher
:Contact: mkircher@uw.edu
:Date: *13.04.2012
"""
import sys, os
from optparse import OptionParser
from collections import defaultdict
import pysam
parser = OptionParser("%prog [options]")
parser.add_option("-p","--prefix", dest="prefix", help="Prefix for output fil... | shendurelab/cfDNA | BAM_RG_Length.py | Python | mit | 2,686 | [
"pysam"
] | 6c80f8fea1bd25f3c857cc33931d6401ef416dcce040dc103fd65ef9294600a7 |
"""
Copyright (c) 2016 Gianluca Gerard
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
to use, copy, modify, merge, publish, distribute... | glgerard/MDBN | src/dbn.py | Python | apache-2.0 | 25,760 | [
"Gaussian"
] | 2edebaba7f8fce8d0620ddae4fe95491f6fabd2553e9b41ac9ed795546b26de3 |
import pickle
from ase.structure import molecule as mol
from ase import Atoms
from multiasecalc.lammps.charmm import CHARMM
from multiasecalc.lammps.dynamics import LAMMPSOptimizer
from multiasecalc.utils import get_datafile
from energy import Fragmentation
from ase.data.s22 import data as s22_sim_data
from ase.data.... | csmm/multiase | tests/lammps/charmm_energy.py | Python | gpl-2.0 | 5,314 | [
"ASE",
"CHARMM",
"GPAW",
"LAMMPS"
] | 486e35aa636eef7c40526784872b6cd6f550d7d5662944dbfdfca8baf29d8305 |
#!/usr/bin/python
#
# Octopus - IT Automation Tool
# Coded by: Alisson Menezes
# - alisson.copyleft@gmail.com
#
# Date: 29/04/2014
#
# Central Configuration Server
#
# x01 - CRUD
# x02 - RN
# x03 - Sockets
#
import socket
import json
from pymongo import *
import pymongo
import thread
import time
import os
# --- c... | AlissonMMenezes/Octopus | server/octopus/octopus_functions.py | Python | gpl-2.0 | 5,663 | [
"Octopus"
] | 8fa636d60609d8e671696fed83c404cba004b01f7aaeb1a3e7f70f90d06d3c9a |
import numpy as np
import mdtraj as md
from msmbuilder.example_datasets import fetch_alanine_dipeptide
from msmbuilder.featurizer import StrucRMSDFeaturizer
# np.testing.assert_array_almost_equal(array1,array2)
def test_alanine_dipeptide_basic():
# This test takes the rmsd of the 0th set of alanine dipeptide
... | stephenliu1989/msmbuilder | msmbuilder/tests/test_strucrmsdfeaturizer.py | Python | lgpl-2.1 | 5,164 | [
"MDTraj"
] | 4218e4d3f71f5ca08203d0303804d6a213a1f1feb99a99535740ae1c0295633b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Low-level objects providing an abstraction for the objects involved in the calculation.
"""
from __future__ import unicode_literals, division, print_function
import collections
import abc
import six
import ... | sonium0/pymatgen | pymatgen/io/abinitio/abiobjects.py | Python | mit | 42,022 | [
"ABINIT",
"CRYSTAL",
"Gaussian",
"pymatgen"
] | e8f962b18411750e5b74cb174b1e1404965c9fef2bc86a1f0baeb90e94a120d6 |
""" This is the customize script for GPAW on Sherlock
Compiling gpaw with this customize.py (which you should keep in the
directory where you've cloned the repository to) can be done by
python setup.py --remove-default-flags --customize=../sherlock.stanford.edu.customize.py build_ext
"""
#careful here:
# mpiicc is i... | RKBK/gpaw-customize-files | sherlock.stanford.edu.customize.py | Python | mit | 3,589 | [
"GPAW"
] | 81dfa426749cee270e67189255c3a715c3b95d1435f30e3ddf2e0f12dae85e26 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ =... | sonium0/pymatgen | pymatgen/io/gaussianio.py | Python | mit | 589 | [
"Gaussian",
"pymatgen"
] | ddeb75eddae3593863748eb4b68f4e9e7cc994a333611eb1d78d192e075f7975 |
import tensorflow as tf
from kentf.scoping import adapt_name
class DiagonalCovarianceGaussian:
def __init__(self, means, log_variances, name=None):
name = adapt_name(name, "gaussian")
with tf.name_scope(name):
self.name = name
self.N = tf.identity(tf.shape(means)[0], "N")
... | kkleidal/kentf | gaussian.py | Python | mit | 2,860 | [
"Gaussian"
] | dac680ecea605a7f8441d64caf784ba84bec1aa4224d740ec2f7535a46405933 |
"""Contains the parent class for MPF's Language module."""
# language.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
import re
from mpf.sy... | jabdoa2/mpf | mpf/media_controller/core/language.py | Python | mit | 6,008 | [
"Brian"
] | 5cb34fe9a20828434b89af9ea1408fdb46d48a3ed99dac71de7e7366305ddac2 |
from __future__ import print_function, division
import time
import warnings
from mdtraj.utils.delay_import import import_
from mdtraj.utils.validation import ensure_type, cast_indices, check_random_state
from mdtraj.utils.unit import in_units_of
from mdtraj.utils.rotation import rotation_matrix_from_quaternion, uniform... | kyleabeauchamp/mdtraj | mdtraj/utils/__init__.py | Python | lgpl-2.1 | 3,720 | [
"MDTraj"
] | c349c6eef34cb71e7f8e793f72f1986c967aee9f22a14a193068ee4aae96334a |
from __future__ import unicode_literals
from django.conf import settings
import six.moves.urllib.parse as urlparse
from horizon.utils.memoized import memoized # noqa
import requests
import json
@memoized
def get_token(request):
return request.user.token.id
# ----------------------------------------------------... | Crystal-SDS/dashboard | crystal_dashboard/api/projects.py | Python | gpl-3.0 | 3,910 | [
"CRYSTAL"
] | 84f76d13b586580df2026ecfea7200c625a49e707892ca01f43e8a96c34e26f2 |
#!/usr/bin/env python
r"""
Constructing workflows (:mod:`skbio.workflow`)
==============================================
.. currentmodule:: skbio.workflow
Construct arbitrarily complex workflows in which the specific methods run are
determined at runtime. This module supports short circuiting a workflow if an
item fa... | Kleptobismol/scikit-bio | skbio/workflow.py | Python | bsd-3-clause | 18,613 | [
"exciting",
"scikit-bio"
] | 154978bc5cdfcef5b08f6c9d4bed5d14325f942ee6b42104bdbda281451443e8 |
from dnfpy.core.map2D import Map2D
import dnfpy.core.utils as utils
import numpy as np
class OnOffFilter(Map2D):
"""
One on cell in the center and two off cells
Parameters :
on cell stdXY, intXY
off cells stdXY, intXY
shift distance ( distance between center on ... | bchappet/dnfpy | src/dnfpy/model/onOffFilter.py | Python | gpl-2.0 | 1,085 | [
"Gaussian"
] | 5c84880744c06396a3bb9200ca094cc7cda92815b4719602c12ba3da352f55aa |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import logging
import numpy as np
from monty.json import MSONable
from scipy.spatial import HalfspaceIntersection
from scipy.optimize import bisect
from itertools import chain
from pymatgen.electronic_structur... | blondegeek/pymatgen | pymatgen/analysis/defects/thermodynamics.py | Python | mit | 30,426 | [
"pymatgen"
] | eadb2cb2d00faa4aa79e8c06ac9a02f4c50f4898bd706f80d1687b38d0be0920 |
#!/usr/bin/python
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
""" Module: gitim
=============
"""
from __future__ import print_function
import platform
import numpy as np
from scipy.spatial import distance
from . import utilities
f... | Marcello-Sega/pytim | pytim/gitim.py | Python | gpl-3.0 | 13,525 | [
"GROMOS",
"MDAnalysis",
"MDTraj",
"OpenMM"
] | f6e35ba21b7b9147fecbcab2e3583111fa71d97e9a38b4a3be47fb9f209647a3 |
#!/usr/bin/env python
from utilities import filesFromList, vtkWriteDataStructured2d, vtkWriteHeaderAndGridStructured2d
from utilities import vtkWritePointDataHeader, vtkWritePointDataStructured2D
from utilities import writeLog
from plotTools import addContourf, addToPlot
from footprintTools import *
from mapTools impor... | saskartt/P4UL | pyFootprint/footprintGather.py | Python | mit | 7,807 | [
"Gaussian",
"VTK"
] | abb826f06c3c4c3a836afb17e53a06d0fdbd20b5f6671a7d559b7122121acc75 |
import copy
from hearthbreaker.cards.base import SpellCard
from hearthbreaker.tags.action import AddCard
from hearthbreaker.tags.base import Effect, BuffUntil, Buff, AuraUntil, ActionTag
from hearthbreaker.tags.condition import IsSpell
from hearthbreaker.tags.event import TurnStarted, TurnEnded, SpellCast
from hearthbr... | Ragowit/hearthbreaker | hearthbreaker/cards/spells/rogue.py | Python | mit | 9,707 | [
"TINKER"
] | eb820743bfaf84d9f2dc06e345aefcc6849a7682c74ced7c635066705e76e239 |
##
# Copyright 2013-2021 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... | boegel/easybuild-easyblocks | easybuild/easyblocks/e/esmf.py | Python | gpl-2.0 | 5,444 | [
"NetCDF"
] | 5d7133f8ca3bb4f7cd46e6a21e7340078b4a7fdad80b6faec655866836a92ef4 |
##############################################################
## Brian P. Kent
## cd_tree.py
## Created: 20130417
## Updated: 20130417
##############################################################
##############
### SET UP ###
##############
"""
Main functions and classes for construction and use of Chaudhuri-Dasgup... | nicolasfauchereau/DeBaCl | debacl/cd_tree.py | Python | bsd-3-clause | 25,521 | [
"Brian"
] | 4c11c570a3b6e2b996fd10a66bcb0dad924ee143266480f00e5af767f725af43 |
import mock
import unittest
import tempfile
import os
import shutil
import errno
from DIRAC import S_OK, S_ERROR, gLogger
# gLogger.setLevel( 'DEBUG' )
from DIRAC.Resources.Storage.StorageElement import StorageElementItem
def mock_StorageFactory_getConfigStorageName( storageName, referenceType ):
resolvedName = ... | vmendez/DIRAC | Resources/Storage/test/TestFilePlugin.py | Python | gpl-3.0 | 16,320 | [
"DIRAC"
] | 108540873e4994b5802df13af2931c1e8143d327813cf8cfad1acf815e03434b |
import numpy as np
import numpy.linalg as la
from scipy import sparse as sp
from scipy.sparse import linalg as spla
from pysal.model.spreg.utils import spdot, spmultiply
from .family import Binomial, Poisson
def _compute_betas(y, x):
"""
compute MLE coefficients using iwls routine
Methods: p189, Iterativ... | lixun910/pysal | pysal/model/spglm/iwls.py | Python | bsd-3-clause | 4,241 | [
"Gaussian"
] | ac3b6c578739b757457074cac5095dc2026666ed33bb12d7c55f21a9a689983d |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | Rositsazz/hack33 | config/urls.py | Python | mit | 1,599 | [
"VisIt"
] | 7704662bc6c35ff37360ccad2e69fc0a6066b0e30a8949bced61c44598c5b815 |
#!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
"""
This module provides a set of teachers that deal with dialog.
``FixedDialogTeacher(Teacher)``
Base class for... | facebookresearch/ParlAI | parlai/core/teachers.py | Python | mit | 99,105 | [
"VisIt"
] | 6514023d33d948ae80e0bef4a87d77a1b23868abbf27d899a90836de5f612605 |
# Copyright (c) 2020 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... | luotao1/Paddle | python/paddle/fluid/dygraph/dygraph_to_static/loop_transformer.py | Python | apache-2.0 | 29,117 | [
"VisIt"
] | e6db81d944f84fd1f35eef78c807bb9b1b5adbada35cfa5029360fbbc8ffbe22 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | ashutoshvt/psi4 | psi4/share/psi4/databases/S22by5.py | Python | lgpl-3.0 | 176,348 | [
"Psi4"
] | 18888a04b1e12fd8a6d57153067d107dd368df7f6bd105d2c401f70b19008945 |
#!/usr/bin/python2
#
# Copyright (c) 2012 The Native Client Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
#
"""
The core object model for the Decoder Generator. The dg_input and
dg_output modules both operate in terms of these class... | Lind-Project/native_client | src/trusted/validator_arm/dgen_core.py | Python | bsd-3-clause | 80,167 | [
"ASE"
] | 0c9ee8f2d4e43df5aac8843c639d477adc3f57478a563738d9a5b5c0cbe27778 |
#!/usr/bin/env python
#=======================================================================================================================
# Created on 2014-08-11
# @author: Yi Li
#
# PyLOH
# Copyright (c) 2014 Yi Li <yil8@uci.edu>
#
# This code is free software; you can redistribute it and/or modify it
# under th... | uros-sipetic/PyLOH | bin/bam2DNAcopy.py | Python | gpl-2.0 | 3,083 | [
"pysam"
] | 0d53d47f5afb0bb51a84d92c9bbc7f5ff61144cab3ad42a4ea5ad27935f4e71b |
# -*- coding: utf-8 -*-
# Copyright 2013 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
import os
import unittest
import sys
from splinter import Browser
from .base import BaseBrowserTests
from .fake_webapp import EXAMPLE_A... | bmcculley/splinter | tests/test_zopetestbrowser.py | Python | bsd-3-clause | 5,355 | [
"VisIt"
] | 37fb6e7867c4e6586212474351e1d01151af270c59fae69e29b826466d289972 |
# Orca
#
# Copyright 2009 Eitan Isaacson
#
# 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 version.
#
# This library is ... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/notify-osd/__init__.py | Python | gpl-3.0 | 838 | [
"ORCA"
] | 608cd593124afb8f0c7cb15e9a2cfa220c509fbf602f6fc51eaa7ad2afc8e5d0 |
#!/usr/bin/env python
# ***** BEGIN LICENSE BLOCK *****
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this file,
# You can obtain one at http://mozilla.org/MPL/2.0/.
# ***** END LICENSE BLOCK *****
import copy
import os
import pla... | mrrrgn/build-mozharness | mozharness/mozilla/testing/testbase.py | Python | mpl-2.0 | 26,922 | [
"VisIt"
] | 485014c6ebb07a01f4e9fd14ab1efabcaaca5479b984ac1c1ece4b87e502c538 |
"""
Definitions of the various forms used
"""
from wtforms import validators, widgets, Form, Field, FormField, FieldList, TextField, TextAreaField, BooleanField, DecimalField, IntegerField, SelectField, SelectMultipleField, FileField, PasswordField, StringField, SubmitField, HiddenField, compat
from flask import g
fro... | twschum/mix-mind | mixmind/forms.py | Python | apache-2.0 | 15,031 | [
"Amber"
] | 5281bea9d94aab4127edd3a38967f751f5370d32b7445d4b7ad656afa0175eb5 |
from ovito import *
from ovito.io import *
from ovito.modifiers import *
import numpy
node = import_file("../../files/LAMMPS/animation.dump.gz")
modifier = ColorCodingModifier()
node.modifiers.append(modifier)
print("Parameter defaults:")
print(" start_value: {}".format(modifier.start_value))
print(" end_value: ... | srinath-chakravarthy/ovito | tests/scripts/test_suite/color_coding_modifier.py | Python | gpl-3.0 | 1,160 | [
"LAMMPS",
"OVITO"
] | 9e480c336b3a0e31e538be127871cdd3ea52efa8c389bd055126ec8488d40b32 |
import os
from mpp.models import SQLTestCase
from mpp.lib.config import GPDBConfig
from mpp.lib.gpfilespace import Gpfilespace
from mpp.lib.gpfilespace import HAWQGpfilespace
def setUpFilespaceForCTAS(isForHawq):
config = GPDBConfig()
if isForHawq:
filespace = HAWQGpfilespace()
else:
... | cjcjameson/gpdb | src/test/tinc/tincrepo/ddl/create_table_as/test_ctas.py | Python | apache-2.0 | 2,141 | [
"ORCA"
] | 06a848f26b0b7bb58814f43881955922c8c737f12b7ef0a85eeed1fe974bc395 |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/nek5000/package.py | Python | lgpl-2.1 | 10,813 | [
"VisIt"
] | 26c8aa1c4ada66b124bee5c52cdfd13eec14a38f0a35525da580dea0c886fdf8 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2014-2016, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This p... | scottpurdy/nupic | src/nupic/algorithms/anomaly_likelihood.py | Python | agpl-3.0 | 28,330 | [
"Gaussian"
] | 479befa6640ebf35a8d73b087266fad1af93203464a3ab4b0831950fd6c80d2a |
import os
import sys
from ase import Atoms, Atom, QuasiNewton, PickleTrajectory
from gpaw import *
from gpaw.cluster import Cluster
from gpaw.utilities.viewmol import ViewmolTrajectory, write_viewmol
s = Cluster([Atom('H'), Atom('H',(0,0,3))])
s.minimal_box(2)
c = GPAW(h=0.3, nbands=2)
s.set_calculator(c)
vfname='t... | robwarm/gpaw-symm | oldtest/viewmol_trajectory.py | Python | gpl-3.0 | 674 | [
"ASE",
"GPAW"
] | 44d87955409a5eac6432a4c3cc33abc910f4a6b419095b18d0c6f1915c55c70c |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
pick random sample
generate random permutation
distributions on the real line:
------------------------------
uniform
... | trivoldus28/pulsarch-verilog | tools/local/bas-release/bas,3.9/lib/python/lib/python2.3/random.py | Python | gpl-2.0 | 29,339 | [
"Gaussian"
] | 71e2e04d1bfd07bbacd00482d059cee3f1f8d5e409153d55632055729bf26022 |
from __future__ import print_function
##################################################
# Data utilities package
#
# Generic routines, useful for all data
##################################################
import sys
print("Loading data utilities")
# Load routines from separate files
#try:
# from plot... | kevinpetersavage/BOUT-dev | tools/pylib/boututils/__init__.py | Python | gpl-3.0 | 3,195 | [
"Mayavi",
"VTK"
] | eb563c8e828705a552e7c06a61b79d071de3a20ed481c1d5a0280d66a4187701 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes for non-standard space-group settings
"""
import re
from fractions import Fraction
from typing import List, Tuple, Union
import numpy as np
from pymatgen.core import Lattice
from pymatgen.co... | materialsproject/pymatgen | pymatgen/symmetry/settings.py | Python | mit | 7,555 | [
"pymatgen"
] | 6d469786151f9907ac0403bce7dd212ec2ffc437b4893a15362ee8907f6f9e70 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | cxxgtxy/tensorflow | tensorflow/python/ops/image_ops_test.py | Python | apache-2.0 | 240,446 | [
"Gaussian"
] | ccced6757f958347e5ef3d728109587eeb1a3a76ee5a8f9d37476367bd0fe42b |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software ... | veger/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 32,900 | [
"Galaxy"
] | cf9d210a177f34cdddd683d75e67ac129ef3ec4e60077997e04f9efca9774075 |
#
# Copyright (C) 2009 Niek Linnenbank
#
# 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 License, or
# (at your option) any later version.
#
# This program is distribute... | dalmemail/AmayaOS-English | site_scons/dist.py | Python | gpl-3.0 | 6,941 | [
"VisIt"
] | 09738ad8e3a1e06ddf88941efab13e80fa3a2928b73d9f53ba795a7bc56b017d |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | ghchinoy/tensorflow | tensorflow/python/autograph/pyct/qual_names.py | Python | apache-2.0 | 8,125 | [
"VisIt"
] | 95d77da66dfb59087a196a8cf191d6f07cb17559dea6e50b6ebb89de03245244 |
# -*- coding: utf-8 -*-
import numpy as np
import cv2
import os
from matplotlib import pyplot as plt
def test1():
img = cv2.imread('./../img/human.jpg', 0)
ret, thresh1 = cv2.threshold(img, 127, 255, cv2.THRESH_BINARY)
ret, thresh2 = cv2.threshold(img, 127, 255, cv2.THRESH_BINARY_INV)
ret, thresh3 = ... | KaoruNasuno/opencv_tutorials | image_processing_in_opencv/image_thresholding.py | Python | mit | 1,574 | [
"Gaussian"
] | d628a1d1bb0da7cc5617e1e14c7bb6db9b3b8ef1d555a2b2c6670b5d607db0f9 |
#!/usr/bin/python
from multiprocessing import Pool
import time
import os
import sys
import simplejson as json
import argparse
from Bio import SeqIO
from Bio.SeqUtils import GC
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
# Copyright(C) 2014 David Ream
# Released under GPL version 3 licence. http://www.... | reamdc1/gene_block_evolution_old | cdhit_operons.py | Python | gpl-3.0 | 29,487 | [
"BLAST"
] | dd8fcb71d198e4a091254c79915972765a1629227f0b82d14a14720a9d8f747e |
#!/usr/bin/env python
"""
dirac-rss-set-token
Script that helps setting the token of the elements in RSS. It can acquire or
release the token. If the releaseToken switch is used, no matter what was the
previous token, it will be set to rs_svc ( RSS owns it ). If not set, the token
will be set to w... | vmendez/DIRAC | ResourceStatusSystem/scripts/dirac-rss-set-token.py | Python | gpl-3.0 | 7,075 | [
"DIRAC"
] | 7547568ccdd3bc1fb2e6ee218017dc3b28d80cbba7b52b336dafd6d0a7c3508f |
#!/usr/bin/env python
import os
import discogs_client as dc
USER_AGENT = "discogs-banner +http://github.com/jesseward"
class DiscogsWrapper(object):
"""
Returns an OAuth authentication handle for requests against the
Discogs API.
"""
def __init__(self, config):
self.token_file = os.path... | jesseward/discogs-banner | discogs_banner/discogs_wrapper.py | Python | mit | 2,835 | [
"VisIt"
] | 6ec2cab4374654aac9419b4356ea0457ea478d8e4d6f06d8310a8d04e1ac695f |
# Taken from: https://raw.githubusercontent.com/lennax/biopython/f_loc5/Bio/SeqUtils/Mapper/MapPositions.py
# Copyright 2012 Lenna X. Peterson <arklenna@gmail.com>
# 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... | kantale/MutationInfo | biopython_mapper/MapPositions.py | Python | mit | 13,008 | [
"Biopython"
] | 917378c4de14541210d214d9220de58f26e1d78a18fc7d4ad19bd1be2b45234c |
#
# pynestml_frontend.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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... | kperun/nestml | pynestml/frontend/pynestml_frontend.py | Python | gpl-2.0 | 5,775 | [
"NEURON"
] | fbf20ef14c8eda55100010a40ec8c5126cb02e7428b7a9e5e1007db8733f2229 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
'''
freeseer - vga/presentation capture software
Copyright (C) 2013 Free and Open Source Software Learning Centre
http://fosslc.org
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 ... | Freeseer/freeseer | src/freeseer/plugins/audiomixer/audiopassthrough/widget.py | Python | gpl-3.0 | 2,366 | [
"VisIt"
] | a72defc90ba5f1488e6c147aff2d48ba4355be7edc32e3792878f95d0ce5dd1f |
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
import os
from setuptools import setup, find_packages
version = '0.0.9'
description = "CP2K tools & scripts"
cur_dir = os.path.dirname(__file__)
try:
long_description = open(os.path.join(cur_dir, 'README.md')).read()
except:
long_description = description... | dev-zero/cp2k-tools | setup.py | Python | apache-2.0 | 1,640 | [
"CP2K"
] | 7982f4dd1a29917088de2436c9f26804ea1ebd089b5092a388d52bc0ac4243da |
#!/usr/bin/env python
""" update local cfg
"""
import os
from DIRAC.Core.Base.Script import Script
Script.setUsageMessage("\n".join([__doc__.split("\n")[1], "Usage:", " %s [options] ... DB ..." % Script.scriptName]))
Script.parseCommandLine()
args = Script.getPositionalArgs()
setupName = args[0]
# Where to store ... | DIRACGrid/DIRAC | tests/Jenkins/dirac-cfg-update-server.py | Python | gpl-3.0 | 15,704 | [
"DIRAC"
] | 4350d8a380bed56e21a8bc0b4da46627633e0e5b1b32cbf4219e6e514e4b6173 |
import numpy as np
from scipy.stats import gaussian_kde, mvn
from .model_GP import normal_pdf, GP_K, Geweke_Z
def logistic(y, C=2):
"""logistic function: transfer y to psi
"""
return np.exp(y) / (C - 1.0 + np.exp(y))
def logit(psi, C=2):
"""logistic function: transfer psi to y
"""
return np.lo... | huangyh09/diceseq | diceseq/models/bayes_factor.py | Python | apache-2.0 | 12,071 | [
"Gaussian"
] | d233ee2e90a80b5b8cb75ba637b9b88c857565bba14061ef7c1df8d4cee61ebc |
# -*- coding: utf-8 -*-
"""
@namespace Area
Tools and events manipulation
Copyright 2007, NATE-LSI-EPUSP
Oficina is developed in Brazil at Escola Politécnica of
Universidade de São Paulo. NATE is part of LSI (Integrable
Systems Laboratory) and stands for Learning, Work and Entertainment
Research Group. Visit o... | samdroid-apps/paint-activity | Area.py | Python | gpl-2.0 | 72,770 | [
"FLEUR",
"VisIt"
] | f569199b6405ee5f280ef2503cd0f2d455f3b03de2486400153c049d0707a44b |
from tools.load import LoadMatrix
from numpy import where
lm=LoadMatrix()
traindat = lm.load_numbers('../data/fm_train_real.dat')
testdat = lm.load_numbers('../data/fm_test_real.dat')
parameter_list=[[traindat,testdat, 1.3],[traindat,testdat, 1.4]]
def kernel_gaussian_modular (fm_train_real=traindat,fm_test_real=tes... | ratschlab/ASP | examples/undocumented/python_modular/kernel_gaussian_modular.py | Python | gpl-2.0 | 795 | [
"Gaussian"
] | edee5982048b7f3408be7a7dd866314f6f7fe3b7bbaa85ecbeca328f11749d4f |
import ast
from unittest import (
TestCase,
)
from darglint.analysis.yield_visitor import (
YieldVisitor,
)
from .utils import (
reindent,
)
class YieldsVisitorTests(TestCase):
def assertFound(self, program):
"""Assert that the yield was found.
Args:
program: The program ... | terrencepreilly/darglint | tests/test_yield_visitor.py | Python | mit | 2,964 | [
"VisIt"
] | be91769e8e18c1835566b58a9f8878eeeb41a1ec6ca5d9a30716bd4f85ab934b |
# convcmd - convert extension commands definition
#
# Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from common import NoRepo, MissingTool, SKIPREV, mapfile
from cvs import conv... | jordigh/mercurial-crew | hgext/convert/convcmd.py | Python | gpl-2.0 | 18,870 | [
"VisIt"
] | 8d2cfa03202ab59547d1f1b249b7f28f6586e70e280a4ae4985224b411e5a791 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
"""Superimpose two structures."""
import numpy
from Bio.SVDSuperimposer import SVDSuperi... | bryback/quickseq | genescript/Bio/PDB/Superimposer.py | Python | mit | 2,351 | [
"Biopython"
] | a8a210a5a80cc971b5e1028eb01454b103136cd1531cccbcf10fb937e9de33ae |
import tyre.utils
import re
import pandas as pd
##
## normalizeXXX
##
## input: item
## outout item
def normalize_brand(item):
if "brand" in item:
s=item["brand"]
s.replace("-", " ").replace("_", " ")
item["brand"] = s
return item
def normalize_load_index(item):
if "load_index" ... | matteoredaelli/scrapy_tyres | tyre/item.py | Python | gpl-3.0 | 8,288 | [
"MOE"
] | 85043b4a0d70cfb8ab8c5ab3570cc8feb6fcd4675a7792e07ce573b24e000e00 |
""" push new fasta files to EW
Conducts a scan of a directory for fasta files, and pushes those that don't exist into the EW server
THIS ASSUMES THERE IS A CONFIG FILE CONTAINING A DICTIONARY CONFIG, with keys 'IP' AND 'PORT' PASSED AS sys.argv[1]
i.e. the first and only argument.
An example of such a file would rea... | davidhwyllie/findNeighbour2 | testScripts/push_new_samples.py | Python | lgpl-3.0 | 3,251 | [
"Biopython"
] | 6eef7a360ae0755178ea28d4bda698b572a04c85afe15e8144e30d15dbf04c6a |
# -*- coding: utf-8 -*-
# Orca
#
# Copyright 2004-2008 Sun Microsystems Inc.
#
# 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... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/chnames.py | Python | gpl-3.0 | 25,110 | [
"ORCA"
] | ccec3316816d8b6fa7d37464243f601a3a4a47c6369b64b67456fa465a7ef870 |
from __future__ import absolute_import
from __future__ import print_function
import sys,os
import pandas as pd
#import get_compounds_from_wikidata as wd
sys.path.append('/global/project/projectdirs/openmsi/jupyterhub_libs/anaconda/lib/python2.7/site-packages')
from rdkit import Chem
import numpy as np
from rdkit.Chem i... | biorack/metatlas | metatlas/interfaces/compounds/not_used/get_compounds_each_provider.py | Python | bsd-3-clause | 11,717 | [
"RDKit"
] | 9d0c51f707a9019c09b0505ce503cf5193f952368f603234540574cc8e8fcb11 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/
from __future__ import division, absolute_import, with_statement, print_function, unicode_literals
import requests
import ... | mitre/multiscanner | multiscanner/modules/Detonation/VxStream.py | Python | mpl-2.0 | 8,242 | [
"VisIt"
] | ef8ce46037179240cf9001ac8209f59791ca7fb02702059a88e414277c66d6c4 |
#!/usr/bin/env python
import vtk
def pine_root_connectivity(fileName, noConnectivity):
def NumberOfTriangles(pd):
"""
Count the number of triangles.
:param pd: vtkPolyData.
:return: The number of triangles.
"""
cells = pd.GetPolys()
numOfTriangles = 0
... | lorensen/VTKExamples | src/Python/VisualizationAlgorithms/PineRootConnectivity.py | Python | apache-2.0 | 3,904 | [
"VTK"
] | 7632866f78ac7a7e94fcccd96e4df31348c222967f2fb6852d55ab94e9eb1b96 |
from hic import *
import networkx as nx
import datetime as dt
import os.path
import argparse
import logging
import pysam
import vcf
import sys
# log config
logging.basicConfig(filename='split-network.log', level=logging.DEBUG)
#
# Read base and quality
#
def read_base_and_quality(alignedRead, pos):
return aligne... | koadman/proxigenomics | graph/src/splitNetwork.py | Python | gpl-2.0 | 9,668 | [
"pysam"
] | 1831c6c47537c6b076dc737e579e5b3977cb2dec91be88923eb3d4705df6b697 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2013 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-... | GoogleCloudPlatform/gsutil | gslib/__main__.py | Python | apache-2.0 | 34,238 | [
"VisIt"
] | 6f607a5c21fcf75808e8261f9a3f053e08979c0e01e54f0378b21c009ec5d322 |
"""this is python equivalent of ./Wrapping/Tcl/vtktesting/backdrop.tcl
This script is used while running python tests translated from Tcl."""
import vtk
basePlane = None
baseMapper = None
base = None
backPlane = None
backMapper = None
back = None
leftPlane = None
leftMapper = None
left = None
def BuildBackdrop (mi... | b3c/VTK-5.8 | Utilities/vtkTclTest2Py/backdrop.py | Python | bsd-3-clause | 1,885 | [
"VTK"
] | 2ab6e5c454743977a9cdcbf2633665b335fd9fedd6641b1dcef7f50f7a4d5e6e |
from __future__ import unicode_literals
from django.test import TestCase
from django.utils import six
from .models import (Building, Child, Device, Port, Item, Country, Connection,
ClientStatus, State, Client, SpecialClient, TUser, Person, Student,
Organizer, Class, Enrollment, Hen, Chick, A, B, C)
class Se... | liavkoren/djangoDev | tests/select_related_regress/tests.py | Python | bsd-3-clause | 9,045 | [
"Brian"
] | cdb411c140f006695b0093340e0635236dc8158becc00d64b2622af0538ea29c |
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