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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Spectrassembler main program
@author: Antoine Recanati
"""
from __future__ import print_function
from time import time
import sys
import argparse
from functools import partial
from multiprocessing import Pool
import numpy as np
from Bio import SeqIO
from scipy.sparse ... | antrec/spectrassembler | spectrassembler.py | Python | mit | 8,727 | [
"BWA"
] | 67c8500c35ceca80b4f900187e0d4c6912ea6ade296ec200b8b8f1fc64429771 |
#
# Copyright (c) 2001-2014, Scott D. Peckham
#
#
#-----------------------------------------------------------------------
# NOTES: This file defines a "base class" for permafrost
# components as well as functions used by most or
# all permafrost methods. The methods of this class
# shoul... | permamodel/permamodel | permamodel/components/perma_base.py | Python | mit | 30,289 | [
"NetCDF"
] | f6921329fd8abf0fa27aa759b945261f727dbab6d441f9bb24dfa9d73a12a10d |
#!/usr/bin/env python
## This is call back script which will be executed after created the grib2 files.
##
## Hycom Model Input requires analysis of 06, 09, 12, 15, 18, 21-hours from
## yesterday and 00 & 03-hours from today date. All 3-hourly forecasts from
## today date.
##
## While creating tar ball, all files m... | arulalant/UMRider | bsubScripts/ncum_india_gnc/create_pres_nc.py | Python | gpl-2.0 | 2,473 | [
"NetCDF"
] | 170e8912b28fdc1ed6d34a5bc7a01b39cdd330640154b2e4038f92cadd8a0c0a |
from sim import Sim
class TransportManager(object):
def __init__(self, planets=[]):
self.planets = planets
self.sim = Sim()
self.dest_planet = None
self.building = None
self.resources_needed = {
'metal': 0,
'crystal': 0,
'deuterium': 0
}
self.resources_sent = self.resources_needed
self.buildi... | r4fek/ogame-bot | transport_manager.py | Python | bsd-2-clause | 6,106 | [
"CRYSTAL"
] | 0394e4fc7b74353d58de21fde33b6a92b9e8b065ca7be7a83298a0625e2402c3 |
# -*- coding: utf-8 -*-
#
# gif_pop_psc_exp.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... | stinebuu/nest-simulator | pynest/examples/gif_pop_psc_exp.py | Python | gpl-2.0 | 14,318 | [
"NEURON"
] | 03f160475edf6b913dd64be13bbf45fd2a3b2b856caacb00ed4645baef20d508 |
#########################################################################################
# LSF.py
# 10.11.2014
# Author: A.T.
#########################################################################################
""" LSF.py is a DIRAC independent class representing LSF batch system.
LSF objects are used as bac... | yujikato/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/LSF.py | Python | gpl-3.0 | 5,907 | [
"DIRAC"
] | d1a43f0e7c381b6237c0e0e27a81590ac7d4c7e8213348a985162e1c04504c12 |
#!/usr/bin/env python
#
# Copyright (c) 2001 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
#
# A module containing user-configuration utilities, debug stuff and
# many other functions. This... | zooko/egtp | common/mojostd.py | Python | agpl-3.0 | 77,571 | [
"Amber",
"VisIt"
] | 06f4fc8d78bb16789a136ff07cf284ccb9c5d919ff01a92d1f1216b68873629a |
from scipy import stats
import numpy as np
from numpy.testing import assert_almost_equal, assert_, assert_raises, \
assert_array_almost_equal, assert_array_almost_equal_nulp
def test_kde_1d():
#some basic tests comparing to normal distribution
np.random.seed(8765678)
n_basesample = 500
xn = np.ran... | teoliphant/scipy | scipy/stats/tests/test_kdeoth.py | Python | bsd-3-clause | 5,881 | [
"Gaussian"
] | edf51ceaf7c0ed5b8410f7c14ba5fa640bf2e19df323bd310140182e4333576a |
from datetime import date
import json
from collections import OrderedDict
from ..geodis_decoder_rest_ws import GeodisDecoderRestWs
from ..geodis_encoder_rest_ws import GeodisEncoderRestWs
from ..geodis_transport_rest_ws import GeodisTransportRestWs
from ..geodis_api_rest_ws import GeodisApiTrackingListOut
def test_e... | akretion/roulier | roulier/carriers/geodis/tests/wip_test_rest.py | Python | agpl-3.0 | 10,375 | [
"VisIt"
] | 4893c0aa70c8668a21350c03d59823770fb921abf3340ee83baea5966ff8ee88 |
import ast
import logging
logger = logging.getLogger(__name__)
def capitalize_first_letter(string):
return string[0].capitalize() + string[1:]
BOOLOP_SYMBOLS = {
ast.And: 'and',
ast.Or: 'or'
}
CMPOP_SYMBOLS = {
ast.Eq: '==',
ast.Gt: '>',
ast.GtE: '>=',
ast.In: 'in',... | socialdevices/manager | core/parsers.py | Python | bsd-3-clause | 25,592 | [
"VisIt"
] | 6e6a598963bf591864cadd3e48be4a9af65759b820dfc84cda9c3ba965a4914f |
#!/usr/bin/env python
"""
.. py:currentmodule:: FileFormat.Results.Spectra
.. moduleauthor:: Hendrix Demers <hendrix.demers@mail.mcgill.ca>
MCXRay spectra result file.
"""
# Script information for the file.
__author__ = "Hendrix Demers (hendrix.demers@mail.mcgill.ca)"
__version__ = ""
__date__ = ""
__copy... | drix00/pymcxray | pymcxray/FileFormat/Results/Spectra.py | Python | apache-2.0 | 10,999 | [
"CRYSTAL"
] | 78f7589eaaf5b21861ac45847569ce10d8cabc22cdebc0808c22f66bb42e44f2 |
import logging
import os
import re
import test_db_util
import time
import galaxy.model as model
import galaxy.model.tool_shed_install as install_model
import galaxy.util
from galaxy.web import security
from base.twilltestcase import TwillTestCase
from base.tool_shed_util import repository_installation_timeout
from g... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/install_and_test_tool_shed_repositories/base/twilltestcase.py | Python | gpl-3.0 | 10,930 | [
"Galaxy"
] | 1efde427c01ab41568a351c88657e41096b5df9747fa67126ee8aa64eeaf1f07 |
#* 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
from TestHa... | harterj/moose | python/TestHarness/testers/RunException.py | Python | lgpl-2.1 | 2,543 | [
"MOOSE"
] | ff53501c70fe2ac03f0ba654090959a795155dc52ee5ef5ae36d600623b7f615 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2019 Chris Caron <lead2gold@gmail.com>
# All rights reserved.
#
# This code is licensed under the MIT License.
#
# 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 th... | SickGear/SickGear | lib/apprise/plugins/NotifySlack.py | Python | gpl-3.0 | 27,621 | [
"VisIt"
] | 3afc3607ccbd60a3bb78af2a18d66d4e8c6b5979324f8ef216778c862c9d1518 |
"""
Distributions
-------------
A widget for plotting attribute distributions.
"""
from math import sqrt
import sys
import collections
from xml.sax.saxutils import escape
from PyQt4 import QtGui, QtCore
from PyQt4.QtCore import Qt
from PyQt4.QtGui import QToolTip
import numpy
import pyqtgraph as pg
import Orange.da... | marinkaz/orange3 | Orange/widgets/visualize/owdistributions.py | Python | bsd-2-clause | 27,882 | [
"Gaussian"
] | 2377a0c387a5e85772396a2d8d20661dcb97509ab499ff8f1242ac78b2b16e47 |
from django.db import models
from django.utils.translation import ugettext, ugettext_lazy as _
from apps.patients.models import Patient
from apps.human_resources.models import Employee
from medserver.middlewares.current_user import get_employee
class VisitReason(models.Model):
name = models.CharField(_('visit rea... | kirillmakhonin/med | MED.Server/apps/visit_planning/models.py | Python | mit | 3,722 | [
"VisIt"
] | 282a385e094a9918f6662ae718d9aeb2b860f7979b0a575f4c2ada08b5eb158a |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may ... | MJJoyce/climate | examples/configuration_file_examples/run_RCMES.py | Python | apache-2.0 | 11,491 | [
"NetCDF"
] | 3d01a4be1ef5d3c60b4ffd226f99e03bf1293046e03392381789651b912d261b |
"""Performs a linear transformation to input data using a
tvtk.BoxWidget. This does not work with
ImageData/StructuredPoints/RectilinearGrid.
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2006-2015, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
try:
import cPickl... | dmsurti/mayavi | mayavi/filters/transform_data.py | Python | bsd-3-clause | 7,621 | [
"Mayavi"
] | da6e075cfb055c29fe1de473860b5ce52f87f0f0fc5b24f5775dc8e1ab4e0c9c |
from jasp import *
from ase.io import read
from ase.io.vasp import write_vasp
from ase.calculators.vasp import Vasp
"""
code for running NEB calculations in jasp
here is typical code to set up the band:
with jasp('../surfaces/Pt-slab-O-fcc') as calc:
initial_atoms = calc.get_atoms()
with jasp('../surfaces/Pt-sl... | jboes/jasp | jasp/jasp_neb.py | Python | gpl-2.0 | 14,334 | [
"ASE",
"VASP"
] | 38cf9ce6edd2df2aea0890fab69cac08906ee02169a693daaf8662cded73a087 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/web/deviceinfo.py | Python | gpl-2.0 | 9,020 | [
"VisIt"
] | a0d129b3557df6122cf6c65567e68ea44ca96d9b970ce43e092206266b55cb82 |
"""0MQ authentication related functions and classes."""
#-----------------------------------------------------------------------------
# Copyright (C) 2013 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYI... | ellisonbg/pyzmq | zmq/auth/certs.py | Python | lgpl-3.0 | 4,382 | [
"Brian"
] | 6a3b74b24311de5a8950043df788841b824de60f38e15b8f1b378cf6c96132fb |
#!/Users/student/anaconda/bin/python
'''
.. module:: Driver
:platform: Unix, Windows
:synopsis: A sample driver class to analyze an epitope.
.. moduleauthor:: Amelia F. Antrim <amelia.f.antrim@gmail.com>
'''
from collections import defaultdict
import sys
import math
import os
from ASAParse import ASAParse
fr... | afantrim/epitope_mapping | src/SequentialPairs/Driver.py | Python | gpl-2.0 | 3,743 | [
"PyMOL"
] | d843d8e4e92742b752286cacf8134a9a0e34bfe3a8701ffe611bee3f1cfe42d8 |
"""
Extended docstrings for functions.py
"""
pi = r"""
`\pi`, roughly equal to 3.141592654, represents the area of the unit
circle, the half-period of trigonometric functions, and many other
things in mathematics.
Mpmath can evaluate `\pi` to arbitrary precision::
>>> from mpmath import *
>>> mp.dps = 50; m... | fredrik-johansson/mpmath | mpmath/function_docs.py | Python | bsd-3-clause | 280,580 | [
"Gaussian"
] | d19f2ff839e61f3f7792446492ee8ac1456cf9f84fb7bfb8b64f5f9bde618c80 |
###############################################################################
##
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary forms, with or without
## modification, ... | CMUSV-VisTrails/WorkflowRecommendation | vistrails/packages/spreadsheet/spreadsheet_sheet.py | Python | bsd-3-clause | 22,475 | [
"VTK"
] | f95f078c12ce115c72e3dfe0e330e9dfc2313e7ffd1b189a7f5ae9f9675942db |
from toontown.coghq.SpecImports import *
GlobalEntities = {1000: {'type': 'levelMgr',
'name': 'LevelMgr',
'comment': '',
'parentEntId': 0,
'cogLevel': 0,
'farPlaneDistance': 1500,
'modelFilename': 'phase_10/models/cashbotHQ/ZONE07a',
'wantDoors': 1},
1001: {'type... | ksmit799/Toontown-Source | toontown/coghq/CashbotMintGearRoom_Action00.py | Python | mit | 7,931 | [
"Bowtie"
] | de4acc6dc3639c1cdea98df69ae48d56734c530bacaebd9d491ddc4502a6613b |
#implementation of probabilty function
#Maximum Likelihood function
#Gaussian Distridution
from scipy.weave.c_spec import num_to_c_types
__author__ = 'Schmidtz'
import matplotlib.pyplot as plt
import matplotlib as mpl
import numpy as np
from numpy import matlib
from numpy import *
from numpy.random import *
import py... | jminyu/PatternRecognition_library | Prob_function.py | Python | gpl-3.0 | 981 | [
"Gaussian"
] | 9d8f25736ec45fe2b55555238b328f3cb03733ae6f9a7dd2e0cfb6925a3f2bb2 |
"""An example (for the galaxy zoo dataset)
"""
__author__ = 'georgeoblapenko'
__license__ = "GPL"
__maintainer__ = "George Oblapenko"
__email__ = "kunstmord@kunstmord.com"
from os import path
from skimage.io import imread
import skimage.filter
from src.dataset import UnlabeledDataSet, LabeledDataSet
def otsu(fpath):... | Kunstmord/datalib | src/example.py | Python | gpl-3.0 | 1,990 | [
"Galaxy"
] | cf4c056d8304e3270229afea5dfb0099f7156dcda62cc1c913a85f70bf5d2123 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | shepdelacreme/ansible | lib/ansible/modules/files/acl.py | Python | gpl-3.0 | 11,844 | [
"Brian"
] | a125e3df46b2ae1ef475cf12b768fdfeff768cfb2129ed3ee693eebcf066b4af |
'''
Created on 24 Dec 2016
@author: dusted-ipro
'''
import numpy as np
from environment import world
from environment.sensing import closestStar, dist
from agents.base import baseAgent
from data.tradableTypes import allTradables
class explorer(baseAgent):
'''
Explorer Agent
- Gets a star the clan has ... | nicholac/universe_abm | agents/explorer.py | Python | mit | 6,912 | [
"VisIt"
] | 412cd41770327039183ea964ae4a6f9a0b12689986543f09587bbf17ceba564c |
#!/usr/bin/env python
__author__ = "Will Van Treuren"
__copyright__ = "Copyright 2013, The QIIME Project"
__credits__ = ["Will Van Treuren, Julia Goodrich"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "Will Van Treuren"
__email__ = "wdwvt1@gmail.com"
from numpy import asarray
from qiime.parse impor... | adamrp/qiime | qiime/make_bipartite_network.py | Python | gpl-2.0 | 11,260 | [
"Cytoscape"
] | ba83b3cf9862b194e0baf6558c561a22b2511d8f9579f14cf84d9b706350e2fe |
import ast, collections, dis, types, sys
from functools import reduce
from itertools import chain
from check_subset import check_conformity
def assemble(assembly):
return bytes(iter(assembly.encode(0, dict(assembly.resolve(0)))))
def plumb_depths(assembly):
depths = [0]
assembly.plumb(depths)
return ma... | darius/tailbiter | article-code/tailbiter2.py | Python | mit | 17,936 | [
"VisIt"
] | ce843f57bd59e8b624a46b18ccf34e5e79f32adfcd8b694424d76499b3b192e8 |
import os
import cv2
import h5py
import parmap
import argparse
import numpy as np
try:
import cPickle as pickle
except ImportError:
import pickle
from skimage import color
from tqdm import tqdm as tqdm
import sklearn.neighbors as nn
import matplotlib.pylab as plt
from matplotlib.colors import LogNorm
import mat... | tdeboissiere/DeepLearningImplementations | Colorful/src/data/make_dataset.py | Python | mit | 10,034 | [
"Gaussian"
] | bb2b4d72ec4904594c36dae95e2364854f3372f04eb5759fc1796da527d711b3 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# ... | SKIRT/PTS | magic/config/list_ned.py | Python | agpl-3.0 | 973 | [
"Galaxy"
] | 12afadf4057a6602391fb4b681ef18fcf55999de3bcada962680eb865a4c6049 |
#!/usr/bin/env python
from scipy import stats
from scipy.special import gamma,digamma,polygamma
from numpy import log,mean,var,exp,array
from math import sqrt
__all__ = ["derive_informed_priors"]
__doc__ = """Routines to derive informed priors for quasi-simultaneous bayesian inference
These routines are described in... | esc/Psignifit-3.x | pypsignifit/psigsimultaneous.py | Python | mit | 6,909 | [
"Gaussian"
] | 05df46f934f50b690dd18749312d1c3e1ba22c78b926befcff182881266e611a |
#pylint: disable=missing-docstring
#* 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/... | nuclear-wizard/moose | python/chigger/observers/ChiggerObserver.py | Python | lgpl-2.1 | 2,252 | [
"MOOSE",
"VTK"
] | e3cb637395d69daff10d75568966c87efff0b82772d671475c36d9fe71e3ee92 |
"""
Combine parsed data from a set of batch processing output files and write to a
single CSV file.
"""
import logging
import os
import re
import csv
import pandas as pd
from .. import io
from .. import parsing
from .. import util
logger = logging.getLogger(__name__)
class OutputStitcher(object):
"""
Given... | BenaroyaResearch/bripipetools | bripipetools/postprocessing/stitching.py | Python | mit | 10,439 | [
"HTSeq"
] | 57b23e3948340c2a92cde0339b778e8e8966c8dd126041a5a1e85aa06006a404 |
import os
import unittest
from adaptivemd import File, WorkerScheduler, Worker
from adaptivemd import OpenMMEngine
from adaptivemd import Project
from adaptivemd import PyEMMAAnalysis
def start_local_worker(proj_name):
import subprocess, sys, os
path = os.path.dirname(sys.executable) + ':' + os.environ['PAT... | markovmodel/adaptivemd | adaptivemd/tests/test_simple_strategy.py | Python | lgpl-2.1 | 5,240 | [
"OpenMM"
] | 436f9f0860c74c81189f59dd396918a3eed0c9c28b8f16439bffda389b5ca7ca |
# Copyright 2014 Uri Laserson
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... | churchlab/ulutil | ulutil/blast.py | Python | apache-2.0 | 1,846 | [
"BLAST"
] | fd06c813a25f1826141a7cb9db31deafbe15265d60a884369eb8f65cb6c363ba |
from sqlalchemy import exceptions, schema, topological, util
from sqlalchemy.sql import expression, operators, visitors
from itertools import chain
"""Utility functions that build upon SQL and Schema constructs."""
def sort_tables(tables, reverse=False):
tuples = []
class TVisitor(schema.SchemaVisitor):
... | santisiri/popego | envs/ALPHA-POPEGO/lib/python2.5/site-packages/SQLAlchemy-0.4.3-py2.5.egg/sqlalchemy/sql/util.py | Python | bsd-3-clause | 10,524 | [
"VisIt"
] | a34a698ae1a90aaef87aedc4610f33ff46ac894f53e3a19444695ecee932e17e |
"""
create or use a client-side cookie storing username;
there is no input form data to parse in this example
"""
import http.cookies, os
cookstr = os.environ.get("HTTP_COOKIE")
cookies = http.cookies.SimpleCookie(cookstr)
usercook = cookies.get("user") # fetch if sent
if usercook == N... | simontakite/sysadmin | pythonscripts/programmingpython/Internet/Web/cgi-bin/cookies.py | Python | gpl-2.0 | 786 | [
"Brian"
] | ebf340d1f4130241a104018bad8ef9d8e5204caa88096b58dedd554ef48a3cea |
#!/home/paulk/software/bin/python
from __future__ import division
import sys,os,time,gzip
import cPickle,pysam,random,math
import pylab
from multiprocessing import Process,Queue
import numpy
"""
Synopsis
Given a GTF file of genes, txs and exons prints to stdout the union of genes'
exons over all txs.
"""
def usage():... | polarise/RP-python | gene2exons.py | Python | gpl-2.0 | 2,496 | [
"pysam"
] | 3e588df946a8dc74a97f6acae18f35a6049a2c0f3f988e2550fbc0213d235a4b |
# CS669 - Assignment 2 (Group-2)
# Last edit: 28/10/17
# About:
# This program is for testing text data of the color histogram feature vectors extracted from images and given GMM.
import numpy as np
import math
import os
import random
dimension=24 # Dimension of data vectors.
K=3 # Value of K ... | aayushm107/Bayes-Classifier-GMM- | src/py/test_images_non_overlapping_color_histogram.py | Python | gpl-3.0 | 8,500 | [
"Gaussian"
] | f06fe37fb7de82e4514a94c8fa6a934c0d1ed30118ce1d00c4b90d9fcd75437b |
# Orca
#
# Copyright 2006-2008 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 later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/gnome-search-tool/script.py | Python | gpl-3.0 | 6,924 | [
"ORCA"
] | b53459eb69a49b1ae689c1d95787f1d93da5ab0e3cbb6fad3f115e27ce7c1212 |
# coding=utf-8
r"""
This code was generated by
\ / _ _ _| _ _
| (_)\/(_)(_|\/| |(/_ v1.0.0
/ /
"""
from tests import IntegrationTestCase
from tests.holodeck import Request
from twilio.base.exceptions import TwilioException
from twilio.http.response import Response
class ConversationTestCase(Inte... | twilio/twilio-python | tests/integration/conversations/v1/test_conversation.py | Python | mit | 11,582 | [
"VisIt"
] | 0762d6d9885cec74ecdda2645eae717235df635c9643473e438fe670542c1544 |
"""
md-cookbook: Get cookin' with MD simulations!
md-cookbook is a python script library that allows users to easily
setup molecular dynamics (MD) trajectories using OpenMM.
"""
from setuptools import setup, find_packages
from glob import glob
classifiers = """\
Development Status :: 3 - Alpha
Intended A... | cxhernandez/md-cookbook | setup.py | Python | mit | 1,211 | [
"OpenMM"
] | 059240250c87eb31598df98fb22324f7c5bf25cdeecb1f26eee6363982706a88 |
import os
import sys
path_to_scripts = os.path.dirname(os.path.realpath(__file__))
assert not path_to_scripts.endswith('/')
##
## the directories db/ and external/ do not live in the github repository
## They will hopefully get created when you run the setup.py script.
##
path_to_db = path_to_scripts+'/db'
assert os... | phbradley/tcr-dist | paths.py | Python | mit | 875 | [
"BLAST"
] | 57996af9e4dde2ef04e399d540aed03f75befdf36915fb23b9487a6f92df00cb |
import heapq
def a_star(G, start, goal, heuristic, varname, exclude_group=[]):
"""shortest path using basic a_star"""
# The queue stores priority, node, cost to reach, and parent.
queue = [(0, start, 0, None)]
# This dictionary maps enqueued nodes to distance of discovered paths
# and the computed heuristics t... | sfcta/BikeRouter | route_model/traversal/a_star.py | Python | gpl-3.0 | 2,573 | [
"VisIt"
] | 608434ba576374a5671757b5c00b8b663b8bb85e012d59844afcd0d72d9c3e33 |
"""
Heisenberg: CC mapping with convolutive FFT
STA using SVD
"""
import numpy as np
#np.__config__.show() # make sure we are on mkl
import sys
import tables
import matplotlib.pyplot as plt
#plt.interactive(1)
#from ipdb import set_trace as trace
#import cProfile # profile the code with cProfile.run('self.learn(sti... | ursk/heise | heise.py | Python | gpl-2.0 | 13,193 | [
"Gaussian"
] | f20eebfd0fb9c27c784a794413806345ab4b82d6a588d356b75cc3dfb997c73e |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | kkreis/espressopp | src/interaction/AngularPotential.py | Python | gpl-3.0 | 2,654 | [
"ESPResSo"
] | 87e556661a12bb4bfcf4e5dd5cd02c5fed09a2a6950efae3b624b90248e5cad8 |
# coding=utf-8
# Copyright 2014 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
from __future__ import (absolute_import, division, generators, nested_scopes, print_function,
unicode_literals, with_statement)
from textwrap import... | kslundberg/pants | tests/python/pants_test/targets/test_wiki_page.py | Python | apache-2.0 | 3,051 | [
"exciting"
] | e795dac201aec876bf8415d914743b1e017bc9a96f2cc8ec9d01b50521a4d430 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
DIRAC and GridPP: perform a query on the CERN@school frames.
"""
#...for the operating system stuff.
import os
#...for parsing the arguments.
import argparse
#...for the logging.
import logging as lg
# Import the JSON library.
import json
# The DIRAC import stat... | gridpp/dirac-getting-started | perform_frame_query.py | Python | mit | 3,626 | [
"DIRAC"
] | 1d7533f714748ae7be18c0a14e827bf4c78d127230a449b11f723efaa9a6da71 |
from ase import Atoms
from ase.constraints import FixAtoms
from ase.io import Trajectory
from ase.optimize import QuasiNewton
from ase.calculators.morse import MorsePotential
atoms = Atoms('H7',
positions=[(0, 0, 0),
(1, 0, 0),
(0, 1, 0),
... | miroi/open-collection | theoretical_chemistry/software_runs/ase/runs/geopt_h7/h7_geopt.py | Python | mit | 779 | [
"ASE"
] | cc178ea463e5eb560654c4690aff6db98af14eee15e8373c26e3799a65a97a4f |
# Copyright 2012, SIL International
# All rights reserved.
#
# 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 License, or
# (at your option) any lat... | silnrsi/graide | lib/graide/filetabs.py | Python | lgpl-2.1 | 20,102 | [
"VisIt"
] | 48fc26df1d0f982e6e163994d89d5c704463127c381e6aac5ce68482a8ced57d |
import crosscat.cython_code.CyclicComponentModel as ccm
import math
import random
import numpy
import six
from scipy.stats import vonmises
from crosscat.utils.general_utils import logmeanexp
import pdb
pi = math.pi
next_seed = lambda rng: rng.randrange(2147483647)
default_hyperparameters = dict(a=1.0, b=pi, kappa... | mit-probabilistic-computing-project/crosscat | src/tests/component_model_extensions/CyclicComponentModel.py | Python | apache-2.0 | 13,854 | [
"Gaussian"
] | fbe3771229384259bd8792b93df57a6af033e7cc07c337c8f4b4db1c2a718ede |
#!/usr/bin/python
#coding=utf8
##----------------------------------------------------------------------------##
## █ █ ##
## ████████ ##
## ██ ██ ... | AmazingCow/ImageOrganizer | imgorg.py | Python | gpl-3.0 | 15,530 | [
"VisIt"
] | d4436453f84fdea6eda8570b743851692359277b0f34c8c14ab51383654ae230 |
import astropy.io.fits as pyfits
import astropy.wcs as pywcs
import os
import numpy as np
import montage_wrapper as montage
import shutil
import sys
import glob
import time
from matplotlib.path import Path
from scipy.ndimage import zoom
from pdb import set_trace
_TOP_DIR = '/data/tycho/0/leroy.42/allsky/'
_INDEX_DIR ... | arlewis/galaxy_cutouts | versions/extract_stamp_v4.py | Python | mit | 22,185 | [
"Galaxy"
] | b012d180f1f9e64da3a0edf72b74e9e2f8b62c7af8365ef2c588afd6678aae85 |
from __future__ import (
absolute_import, unicode_literals, print_function, division,
)
import functools
import time
import warnings
import inspect
import collections
from itertools import count
__metaclass__ = type
try:
from functools import lru_cache
except ImportError:
try:
from backports.functools_lru_cach... | EternityForest/KaithemAutomation | kaithem/src/thirdparty/lowpriority/jaraco/functools.py | Python | gpl-3.0 | 11,074 | [
"CRYSTAL"
] | 6af1fe75cb050dd063202415ad3d86ea6ee759e99fbccae670645b7d119436ef |
#!/usr/bin/env python
##
## @file printAnnotation.py
## @brief Prints annotation strings for each element
## @author Akiya Jouraku
##
## This file is part of libSBML. Please visit http://sbml.org for more
## information about SBML, and the latest version of libSBML.
##
import sys
import os.path
from libsbml... | dilawar/moose-full | dependencies/libsbml-5.9.0/examples/python/printAnnotation.py | Python | gpl-2.0 | 4,052 | [
"VisIt"
] | c8b4fd9cc552b5c2722c428ee9f8b48bd0cdd0eb1f8d1c64c494b2c4f43d02cd |
from six import PY2, PY3
from syn.five import xrange
from syn.types.a import Type, String, Unicode, \
hashable, serialize, deserialize, estr, rstr, generate, visit, find_ne, \
DifferentLength, DiffersAtIndex, Basestring, primitive_form
from syn.types.a import enumerate as enumerate_
from syn.base_utils import i... | mbodenhamer/syn | syn/types/a/tests/test_string.py | Python | mit | 3,867 | [
"VisIt"
] | c6ccfbdaf887ff9d3e35bee1d28b875e6fe7ddeb85ccee04313054c1e4412554 |
#!/usr/bin/env python3
import sys, argparse, os, re
import logging
import uuid
import math
from copy import copy
from shutil import move
from datetime import datetime
FORMAT = '%(levelname)s %(asctime)-15s %(name)-20s %(message)s'
logger = logging.getLogger('Alignment_Workflow')
logger.setLevel(logging.DEBUG)
loggin... | bioinform/somaticseq | somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py | Python | bsd-2-clause | 12,564 | [
"BWA"
] | 2bfbdddf78170c0d78db5b8e829ba40f7fab901569ffb7280f62c7da2027ad9d |
# -*- coding: utf-8 -*-
##
##
## This file is part of Indico.
## Copyright (C) 2002 - 2014 European Organization for Nuclear Research (CERN).
##
## Indico 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; eith... | pferreir/indico-backup | indico/MaKaC/plugins/Collaboration/RecordingManager/micala.py | Python | gpl-3.0 | 24,360 | [
"TINKER"
] | d3a642ff84be379ff1748e32c6c7d66dfa26fda225623916e8b5e19c3e5eb4bb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# File: InfoGAN-mnist.py
# Author: Yuxin Wu
import argparse
import numpy as np
import os
import cv2
import tensorflow as tf
from tensorpack import *
from tensorpack.dataflow import dataset
from tensorpack.tfutils import gradproc, optimizer, summary
from tensorpack.tfutils... | ppwwyyxx/tensorpack | examples/GAN/InfoGAN-mnist.py | Python | apache-2.0 | 10,694 | [
"Gaussian"
] | 6a715342893050907ff20ff2e3b28753a4db44537b4f6eb62ff7ce54911dbe2b |
# derived from
# http://downloads.majestic.com/majestic_million.csv
# fetched 2018-05-22
#
# see also
#
# https://majestic.com/reports/majestic-million
#
# The Majestic Million is a list of the top 1 million website in the
# world, ordered by the number of referring subnets. A subnet is a bit
# complex – but to a l... | sebastian-nagel/cc-crawl-statistics | stats/tld_majestic_top_1m.py | Python | apache-2.0 | 10,710 | [
"CASINO",
"MOE"
] | ee05e33eabf96d1355bae94111f4a7bdbfd954cc7ae51f607715a6405c4a2ad4 |
#!/usr/bin/python
# coding: utf-8
"""
_____ __ __ __
/ ___/ ______ __________ ___ / / / /___ _____/ /_
\__ \ | /| / / __ `/ ___/ __ `__ \/ /_/ / __ \/ ___/ __/
___/ / |/ |/ / /_/ / / / / / / / / __ / /_/ (__ ) /_
/____/|__/|__/\__,_/_/ /_/ /_/ /_/_/ /_/\____... | behollan/SwarmBot | src/SwarmHost.py | Python | mit | 23,351 | [
"VisIt"
] | d670f605ee541c35268a080c41df3f3e44b2c531f174743dfba3c9ca4e549aa3 |
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/adc/test/test_radc/test_dfadc_N2.py | Python | apache-2.0 | 3,766 | [
"PySCF"
] | acb49cbf71314ef536eb4aa155cfa2e578553afbd4f3eb0c7ae0208a4da754c5 |
# Placeholder because parallel moved
# Remove this in version 1.0
from __future__ import absolute_import
import warnings
with warnings.catch_warnings():
warnings.simplefilter('always', DeprecationWarning)
warnings.warn(("qcprot has moved to MDAnalysis.lib.qcprot "
"and will be removed from h... | kain88-de/mdanalysis | package/MDAnalysis/core/qcprot.py | Python | gpl-2.0 | 408 | [
"MDAnalysis"
] | 34e9def303b6cc22ffaa5efcdbe554e6d4e14d029d541cafdca02807426471d5 |
"""
Example of an elaborate dialog showing a multiple views on the same data, with
3 cuts synchronized.
This example shows how to have multiple views on the same data, how to
embedded multiple scenes in a dialog, and the caveat in populating them
with data, as well as how to add some interaction logic on an
ImagePlane... | dmsurti/mayavi | examples/mayavi/interactive/volume_slicer.py | Python | bsd-3-clause | 8,669 | [
"Mayavi",
"VTK"
] | 65205cfd06473be21eeaf62d75f2b6cc65dce85cb3cd9e209c6549e75f67b5f1 |
import unittest
import pysam
import os
import sys
import re
import copy
import gzip
from TestUtils import load_and_convert, make_data_files, TABIX_DATADIR, IS_PYTHON3
def setUpModule():
make_data_files(TABIX_DATADIR)
@unittest.skipUnless(IS_PYTHON3, "Requires Python 3 Extended Iterable Unpacking")
class TestBED... | pysam-developers/pysam | tests/tabixproxies_test.py | Python | mit | 13,463 | [
"pysam"
] | ab48401f29c57ca6cbdc501f170db8233d64b618a428b0195da8d3eda9d786b6 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | ravibhure/ansible | lib/ansible/modules/network/avi/avi_poolgroupdeploymentpolicy.py | Python | gpl-3.0 | 5,842 | [
"VisIt"
] | 1897188f48b7d754b49d44e4ff91e943553cf42593527f804524e798f58aaaf9 |
"""
Acceptance tests for course in studio
"""
from nose.plugins.attrib import attr
from .base_studio_test import StudioCourseTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.users import CourseTeamPage
from ...pages.studio.index import DashboardPage
@attr('shard_2')
class CourseTeamPageT... | beni55/edx-platform | common/test/acceptance/tests/studio/test_studio_course_team.py | Python | agpl-3.0 | 14,146 | [
"VisIt"
] | ac74a48113ad522e7056ab61a86a8452116c7ac2db74dbfd979c65d7dae3b9da |
__author__ = "waroquiers"
import numpy as np
from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode
from pymatgen.analysis.chemenv.utils.graph_utils import (
MultiGraphCycle,
SimpleGraphCycle,
get_delta,
)
from pymatgen.util.testing import PymatgenTest
class FakeNode(object... | gmatteo/pymatgen | pymatgen/analysis/chemenv/utils/tests/test_graph_utils.py | Python | mit | 29,253 | [
"pymatgen"
] | c1a41e1bb64b9ab727a20d32b0f38a2fd3dbde3a8ce7c0e143a27aa91b5e737d |
#!/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... | kbrebanov/ansible | lib/ansible/modules/network/avi/avi_authprofile.py | Python | gpl-3.0 | 4,650 | [
"VisIt"
] | 6909e45f9f078320b18768f83116c661dec3ad6e5dfd70919434ec755675a275 |
"""Acceptance tests for LMS-hosted Programs pages"""
from common.test.acceptance.fixtures.catalog import CatalogFixture, CatalogIntegrationMixin
from common.test.acceptance.fixtures.course import CourseFixture
from common.test.acceptance.fixtures.programs import ProgramsConfigMixin
from common.test.acceptance.pages.c... | edx-solutions/edx-platform | common/test/acceptance/tests/lms/test_programs.py | Python | agpl-3.0 | 6,263 | [
"VisIt"
] | 72e556f364737488861644390e6704521adcc40cde45fc9618cd500c6dc842a9 |
# Issue #93 on moose-core
import numpy as np
import pylab as pl
import moose
import sys
dt = 10e-6
def loadAndRun(solver=True):
simtime = 500e-3
model = moose.loadModel('../data/h10.CNG.swc', '/cell')
comp = moose.element('/cell/apical_e_177_0')
soma = moose.element('/cell/soma')
for i in range(... | rahulgayatri23/moose-core | tests/issues/issue_93.py | Python | gpl-3.0 | 1,510 | [
"MOOSE"
] | ecabc9dcc30c591aa048c789dceda3b70b5e18e9752b147813947e4b208ef66a |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('atados_core', '0024_subscription_postal_code'),
]
operations = [
migrations.AddField(
model_name='nonprofit',
... | atados/api | atados_core/migrations/0025_nonprofit_visit_status.py | Python | mit | 606 | [
"VisIt"
] | 091ea597d45ce59c47fcb93550afe6815621a2a0f3d61bd8fe296d1bef625aca |
MAIL_FROM_ADDRESS = "none@example.com"
MAIL_SUBJECT_PREFIX = "[octopus] "
# Settings for Flask-Mail. Set in app.cfg
MAIL_SERVER = None # default localhost
MAIL_PORT = 25 # default 25
#MAIL_USE_TLS # default False
#MAIL_USE_SSL # default False
#MAIL_DEBUG ... | JiscPER/magnificent-octopus | octopus/config/mail.py | Python | apache-2.0 | 564 | [
"Octopus"
] | 118f559794c61f648a4839fc380fc0a09d892da5d134eba8cb73406a8fa63d14 |
import lb_loader
import pandas as pd
import simtk.openmm.app as app
import numpy as np
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems, integrators
precision = "mixed"
sysname = "switchedljbox"
system, positions, groups, temperature, timestep, langevin_times... | kyleabeauchamp/HMCNotes | code/misc/test_mjhmc.py | Python | gpl-2.0 | 1,360 | [
"OpenMM"
] | 20287993b51fa835ccb7511178ca68115285d4a12cf7a2e7a9e9d685651f1c5e |
#coding: utf-8
from splinter.browser import Browser
from time import sleep, time
import logging
logger = logging.getLogger(__name__)
TIMEOUT=5
class Struct:
def __init__(self, **entries):
self.__dict__.update(entries)
def paradinha(time=0.4):
sleep(time)
# sleep(2)
def _build_browser():
#... | bankonme/www.freedomsponsors.org | djangoproject/core_splinter_tests/tests/helpers/appdriver.py | Python | agpl-3.0 | 15,808 | [
"VisIt"
] | e34a80bb551362e84c4d8b2600f88eb2aa98ed7d7e9aa2cdceb53eb131b2df9b |
########################################################################
# File : JobWrapper.py
# Author : Stuart Paterson
########################################################################
""" The Job Wrapper Class is instantiated with arguments tailored for running
a particular job. The JobWrapper starts ... | petricm/DIRAC | WorkloadManagementSystem/JobWrapper/JobWrapper.py | Python | gpl-3.0 | 62,887 | [
"DIRAC"
] | 2920fbde3619cca3bac5aaea38cc05e2c275789731d6a8e7ca7a28d91cd7b0ed |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | bauruine/ansible | v2/ansible/playbook/role.py | Python | gpl-3.0 | 12,013 | [
"Galaxy"
] | f87c4ba0baffa3c6a20b142f57a82f63262f3f0a7028590f3c26fc0f783cea80 |
from django import forms
from edc_constants.constants import NO, NOT_EVALUATED, YES
from td_maternal.models import MaternalConsent
from ..models import InfantFuPhysical
from .base_infant_model_form import BaseInfantModelForm
class InfantFuPhysicalForm(BaseInfantModelForm):
def clean(self):
cleaned_da... | TshepangRas/tshilo-dikotla | td_infant/forms/infant_fu_physical_form.py | Python | gpl-2.0 | 8,983 | [
"VisIt"
] | d33220a66837661891f48430844f6f156d00ef78fddd80a64a696a25af64099a |
"""Force constants calculation."""
# Copyright (C) 2011 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must r... | atztogo/phonopy | phonopy/harmonic/force_constants.py | Python | bsd-3-clause | 27,237 | [
"CRYSTAL",
"phonopy"
] | 37487db57993c21a2f9eebd816678863822e2a548f17b839b7540e5b4f0c37e0 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RXmapbridge(RPackage):
"""Export plotting files to the xmapBridge for visualisation in X:M... | rspavel/spack | var/spack/repos/builtin/packages/r-xmapbridge/package.py | Python | lgpl-2.1 | 1,004 | [
"Bioconductor"
] | 93e0d52bdcbf301035c72c3cbbd6bd1912ec4791e214c0feb7a627e671482df2 |
import os
from unittest import TestCase
from unittest.mock import patch
import requests
from singleinbox import find_users_without, get_username_password
from pycuc.japi import UnityAPI
def fetch_http_test_file(file):
"""
Fetches a test file of the HTTP Content and returns in bytes
:param file: A properl... | shepherdjay/cisco-unified-scripts | tests/test_functional.py | Python | mit | 2,642 | [
"Brian"
] | c1cf04d2e58f2279652e51958a80542f0ca9b9ca6e1db929f10efb51f79347a7 |
# -*- coding: utf-8 -*-
""" Tests for student account views. """
import re
from unittest import skipUnless
from urllib import urlencode
import json
import mock
import ddt
import markupsafe
from django.conf import settings
from django.core.urlresolvers import reverse
from django.core import mail
from django.contrib im... | dkarakats/edx-platform | lms/djangoapps/student_account/test/test_views.py | Python | agpl-3.0 | 22,617 | [
"VisIt"
] | 6c6d87f453dbdd705d0b9935ee477183e989f623919e8550f5e100d0da9ee199 |
from . import core, utils
import cgt
import ctypes, os.path as osp, hashlib, numpy as np, sys, subprocess, string, os, time, traceback, cPickle
from collections import defaultdict, namedtuple
from StringIO import StringIO
import logging
def function(inputs, outputs, dbg=None, updates=None, givens=None):
assert isi... | dementrock/cgt | cgt/compilation.py | Python | mit | 36,755 | [
"VisIt"
] | adbc1591bde2f3e9479d468f5603b67cecd3b7cd562eb921f6bea6263f54a698 |
# Copyright 2020 Google Research. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law... | tensorflow/examples | tensorflow_examples/lite/model_maker/third_party/efficientdet/nms_np.py | Python | apache-2.0 | 8,364 | [
"Gaussian"
] | 0deede0828419ac8cc9fd750b73b846baa4ec74bbcae11162a2e805c97417dfa |
#
# co_co_vector_variable_in_non_vector_declaration.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... | kperun/nestml | pynestml/cocos/co_co_vector_variable_in_non_vector_declaration.py | Python | gpl-2.0 | 3,368 | [
"NEURON"
] | 8bacc12fa2d9c71f87a76e4d7df27cc1a60eca2fa7652625774af9f45f93f0b5 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import numpy as np
from pymatgen.core.operations import MagSymmOp, SymmOp
from pymatgen.electronic_structure.core import Magmom
from pymatgen.util.testing import PymatgenTest
class SymmOpTestCase(PymatgenTest):
def set... | vorwerkc/pymatgen | pymatgen/core/tests/test_operations.py | Python | mit | 9,855 | [
"pymatgen"
] | 72e7e887055db73bf265290ea94114f2f876f1f317a1f3c116f173c511312c65 |
# -*- coding:utf-8 -*-
# Created by xupingmao on 2017/05/29
# @since 2017/08/04
# @modified 2022/02/19 16:23:09
"""短消息处理，比如任务、备忘、临时文件等等
tag: 短消息的类型
key/keyword: 短消息关键字
"""
import time
import re
import math
import web
import xutils
import xtables
import xauth
import xconfig
import xmanager
import xtemplate
from xut... | xupingmao/xnote | handlers/message/message.py | Python | gpl-3.0 | 31,784 | [
"VisIt"
] | 93e299f8967fe8ba485c876eb4053ae8b717dd555118bff9f6b262c58c036ed7 |
#!/usr/bin/env python
# coding: utf-8
#
# Copyright 2007 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | Neozaru/depot_tools | third_party/upload.py | Python | bsd-3-clause | 99,460 | [
"VisIt"
] | bddca28002ea442aeb6ecb50367374d3491febc5841859e7c4b3c4e2e16b3759 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010 Radim Rehurek <radimrehurek@seznam.cz>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Module for Latent Semantic Analysis (aka Latent Semantic Indexing) in Python.
Implements scalable truncated Singular Value Decompo... | ccri/gensim | gensim/models/lsimodel.py | Python | gpl-3.0 | 34,863 | [
"Gaussian"
] | c14e1a6eb10bb49bb84e869b44257123a90f814ff568cc24190d3f5bae06d313 |
"""Ultra-liberal feed finder
http://diveintomark.org/projects/feed_finder/
Usage:
getFeeds(uri) - returns list of feeds associated with this address
Example:
>>> import feedfinder
>>> feedfinder.getFeeds('http://diveintomark.org/')
['http://diveintomark.org/xml/atom.xml']
>>> feedfinder.getFeeds('macnn.com')
['http:... | marguerite/susews-planet | rawdoglib/feedfinder.py | Python | gpl-2.0 | 11,917 | [
"Brian"
] | 3ff6680357e1b4bc91a0784a9a6aee941d294fa79d78de02d217aa5d7b5f2f25 |
pci_vendor = {0L: 'Gammagraphx, Inc.',
26L: 'Ascend Communications, Inc.',
51L: 'Paradyne Corp.',
61L: 'Lockheed Martin Corp',
112L: 'Hauppauge Computer Works Inc.',
256L: 'Ncipher Corp. Ltd',
291L: 'General Dynamics',
352L: 'us robotics',
1653L: 'Dynalink',
2161L: 'Berkom',
2697L: 'BREA Technologies Inc.'... | sogeti-esec-lab/LKD | example/pci_vendor.py | Python | bsd-3-clause | 46,571 | [
"BWA",
"CRYSTAL"
] | 057f9c6c40aa547b99f5a7613c2142167397ad7ea9a976517c135fe4affe1b89 |
import time
import numpy as np
from scipy.special import erfinv
from scipy.interpolate import interp1d
# --- local ---
from . import util as UT
import corner as DFM
import matplotlib.pyplot as plt
def logSFR_initiate(SHsnaps, indices, theta_sfh=None, theta_sfms=None, testing=False):
''' initiate log SFR funct... | changhoonhahn/centralMS | centralms/sfh.py | Python | mit | 20,377 | [
"Galaxy",
"Gaussian"
] | 2cd83c0fd411c45123ce6bc89fe69c3b3d7d7791d51303052fdc5fcffd54801c |
__author__ = 'Tom'
'''TB Animation Tools is a toolset for animators
*******************************************************************************
License and Copyright
Copyright 2015-Tom Bailey
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser G... | tb-animator/tbtools | apps/tb_playback.py | Python | mit | 3,904 | [
"VisIt"
] | b6e82de0c93e6e87659b69850776367c0051dec5cf26872fa0a858622143e3a8 |
"""Null object for the assemblers."""
from .base import BaseAssembler
from .. import db_atram, util
class NoneAssembler(BaseAssembler):
"""Null object for the assemblers."""
def __init__(self, args, cxn, log):
"""Build the assembler."""
super().__init__(args, cxn, log)
self.steps = [... | juliema/aTRAM | lib/assemblers/none.py | Python | bsd-3-clause | 909 | [
"BLAST"
] | 0124f94472080240750ba88d3dd72e6052a5cf0aba259143540513bd966c5b06 |
from pylab import *
from brian import *
from util import *
def simpleaxis(ax):
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.get_xaxis().tick_bottom()
ax.get_yaxis().tick_left()
def plot_ISI_histogram(ISI_monitor, spike_monitor, rate_monitor, xy, xytext, **plotargs):... | blennon/MLI_PKJ_net | MLI_PKJ_net/plotting_util.py | Python | mit | 5,810 | [
"Brian"
] | f79c37593434eda4c6a7624414938e5f54d027a11bcddae745cda39551507e91 |
"""
Numerical python functions written for compatability with MATLAB
commands with the same names.
MATLAB compatible functions
-------------------------------
:func:`cohere`
Coherence (normalized cross spectral density)
:func:`csd`
Cross spectral density uing Welch's average periodogram
:func:`detrend`
Remov... | SpaceKatt/CSPLN | apps/scaffolding/mac/web2py/web2py.app/Contents/Resources/lib/python2.7/matplotlib/mlab.py | Python | gpl-3.0 | 100,604 | [
"Gaussian"
] | 4805f92eebe8c797f01247c4b80c5b6c99e36b4d845aad99463159cf8561f4ab |
import transitemcee
from transitemcee import get_ar
import numpy as np
from copy import deepcopy
from scipy.stats import truncnorm
from claretquadpy import claretquad
from claret4ppy import claretlimb4p
from numpy import random
import time as thetime
import emcee
import tmodtom as tmod
import sys
from scipy import opt... | mrtommyb/redgiantGP | old_code/transitemcee_rv.py | Python | mit | 54,341 | [
"Gaussian"
] | b8e4012ba90b15111b5e75478ae166495ccc0660169606825dc4e20611f55cc9 |
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