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|---|---|---|---|---|---|---|---|
'''
Created : Jan 16, 2017
Last major update : June 29, 2017
@author: Alexandre Day
Purpose:
Fast density clustering
'''
import numpy as np
import time
from numpy.random import random
import sys, os
from .density_estimation import KDE
import pickle
from collections import OrderedDict as OD
from sklearn.n... | alexandreday/fast_density_clustering | build/lib/fdc/fdc.py | Python | bsd-3-clause | 23,059 | [
"Gaussian"
] | edd8fbc860f516658337868398fc5cc0dfd04078c807072111cfe9662feb7f4f |
# to understand whot is done here and why, look at myGayss.md
# about the root of random numbers in Python
# https://github.com/python/cpython/blob/master/Lib/random.py
import os
import random as r
import math
import commonVar as common
#import urllib.request
import zipfile, requests, io
# the myGauss calculation is... | terna/SLAPP3 | 6 objectSwarmObserverAgents_AESOP_turtleLib_NetworkX/oligopoly/myGauss.py | Python | cc0-1.0 | 5,913 | [
"Gaussian"
] | 415810dcc5bab419613056ca55c67edbea4a10093f3193db20570233fbfbd61e |
#!/usr/bin/python
import bvpl_octree_batch;
import multiprocessing
import Queue
import time
import os;
import optparse;
from xml.etree.ElementTree import ElementTree
import sys
class dbvalue:
def __init__(self, index, type):
self.id = index # unsigned integer
self.type = type # string
class gauss_job... | mirestrepo/voxels-at-lems | pmvs/gauss_smoothing_batch.py | Python | bsd-2-clause | 9,060 | [
"Gaussian"
] | cab273433283780a8e6c5a7ba5f282e53b8d58e95680fac10ed641b6550a5a58 |
import numpy as np
import matplotlib.pyplot as plt
import scipy.io
def getPlotLog(d,log,dmax=200):
d = np.array(d, dtype=float)
log = np.array(log, dtype=float)
dplot = np.kron(d,np.ones(2))
logplot = np.kron(log,np.ones(2))
# dplot = dplot[1:]
dplot = np.append(dplot[1:],dmax)
ret... | jaabell/Seismogram | syntheticSeismogram.py | Python | mit | 14,041 | [
"Gaussian"
] | 66be24d192560f10066eadbc34edb86a9ce8316cae77703bca960ee0f5d9052f |
"""Copyright 2008 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.4'
__date__ = 'May 02 2008'
from threading import *
from ... | jantman/tuxostat | fs_backup/home/tuxostat/devel/PhidgetsPython/Phidgets/Devices/TextLCD.py | Python | gpl-3.0 | 11,021 | [
"VisIt"
] | 9cfc73f220dd9a8f03893cf2f7d914db850efea3ead1d3b2f379ca22f29bdd02 |
from ase import Atom, Atoms
from gpaw import GPAW
from gpaw.test import equal
a = 4.00
d = a / 2**0.5
z = 1.1
b = 1.5
slab = Atoms([Atom('Al', (0, 0, 0)),
Atom('Al', (a, 0, 0)),
Atom('Al', (a/2, d/2, -d/2)),
Atom('Al', (3*a/2, d/2, -d/2)),
... | robwarm/gpaw-symm | gpaw/test/big/miscellaneous/H2Al110.py | Python | gpl-3.0 | 1,200 | [
"ASE",
"GPAW"
] | 9bc4b11431354565200e87bf85446f07f712d5f617ebf7fea8fc28dd905e989b |
#!/usr/bin/env python
#
# SchoolTool - common information systems platform for school administration
# Copyright (c) 2003 Shuttleworth Foundation
#
# 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... | gorakhargosh/select_backport | runtests.py | Python | mit | 42,181 | [
"VisIt"
] | 573ebdfe2df116b739241422221cfd69b7b642833b2e12f309c966e6b78b3637 |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | thomasaarholt/hyperspy | hyperspy/tests/model/test_model.py | Python | gpl-3.0 | 30,297 | [
"Gaussian"
] | 6a4e44a3c960f59a988aac46f5e9b2c043d0f15e335438ef8697ac79d2529b79 |
import numpy as np
import tensorflow as tf
from tensorflow.contrib import rnn
def _print_success_message():
print('Tests Passed')
def test_create_lookup_tables(create_lookup_tables):
with tf.Graph().as_default():
test_text = '''
Moe_Szyslak Moe's Tavern Where the elite meet to dr... | d-k-b/udacity-deep-learning | tv-script-generation/problem_unittests.py | Python | mit | 13,365 | [
"MOE"
] | b0987ede237f7413276b10a00969c15bdcd582983cf439b6557bbdaed3c995ce |
"""
Functions to extract trajectory from a perses relative calculation
"""
import numpy as np
import mdtraj as md
from perses.analysis.utils import open_netcdf
def get_hybrid_topology(file):
""" Extracts hybrid_topology object from the .npy file generated by relative calculations
Parameters
----------... | choderalab/perses | perses/analysis/extract_trajectory.py | Python | mit | 1,648 | [
"MDTraj"
] | ad52eaaf77ea27e17f4f0484d4f58237f8aff78b1aca964993a6b5bf69db17ba |
try:
visits = int(open(counter_file).read())
except IOError:
# first visit : the file does not exist
visits = 0
if not hasattr(Session(),"user"):
visits += 1
out = open(counter_file,'w')
out.write(str(visits))
out.close()
Session().user = None # create attribute user
print "... | jhjguxin/PyCDC | Karrigell-2.3.5/webapps/demo/counter.py | Python | gpl-3.0 | 340 | [
"VisIt"
] | 988395175023477d05d7e2f34a6a40affa0959abf1ed7651a2a2fb8bb72827c8 |
from ScriptingLanguage.Interpreter import Interpreter, UndefinedVariable
__author__ = 'chronium'
def visit_expression(expression):
left = expression.value[0].visit()
if expression.value[1]:
right = expression.value[2].visit()
try:
return {
'+': left + right,
... | chronium/ChronoScript | ScriptingLanguage/Visitors/ExpressionVisitor.py | Python | gpl-2.0 | 820 | [
"VisIt"
] | 83a77cb6d6d4d023f67c152fe836cbe505f0215eb343b93a579f72a2645bc80f |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2015-2019 Bitergia
#
# 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 ... | valeriocos/perceval | perceval/backends/core/stackexchange.py | Python | gpl-3.0 | 10,898 | [
"VisIt"
] | 1717aba5de58093a7cf1e003c490a92ce7fad78f6be6be14320ca1a7ea1a4bc5 |
#!/usr/bin/env python
import sys
import os
import subprocess
import pysam
import textwrap
import argparse
def print_header():
print textwrap.dedent("""\
##fileformat=VCFv4.1
##phasing=none
##INDIVIDUAL=TRUTH
##SAMPLE=<ID=TRUTH,Individual="TRUTH",Description="bamsurgeon spike-in">
##INFO=<ID=CI... | chaelir/bamsurgeon | etc/makevcf_sv.py | Python | mit | 4,073 | [
"pysam"
] | e58ad491aaa04415ee07aeef58dd4c915bb67de346770a4d4dc2b75ffb130810 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | ujenmr/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 44,052 | [
"VisIt"
] | 25dac55812d002e164c32033ee594e48b086010dfed7032042466886c1bb9708 |
import numpy as np
import astropy.units as u
from astropy.coordinates import SkyCoord
import pandas as pd
import pymc3 as pm
import seaborn as sns
import numba
from scipy import integrate
from .binaries import make_systems
from wisps.utils.tools import get_distance
from tqdm import tqdm
import wisps
import wis... | caganze/wisps | wisps/simulations/euclid.py | Python | mit | 3,455 | [
"Galaxy"
] | e3ee3958182bfdf2a6b14ff2f6d088663a612f1845727873b042e9518de6751b |
"""
In this program we study the Lax-Wendroff method and its convergence.
Marina von Steinkirch, spring/2013
Based on Mike Zingale's code 2nd-order accurate finite-volume implementation
of linear advection with piecewise linear slope reconstruction
"""
import numpy
import pylab
import... | bt3gl/Numerical-Methods-for-Physics | homework4_advection_hyperbolic_PDEs/lax_wendroff/lax_method.py | Python | apache-2.0 | 5,600 | [
"Gaussian"
] | c645e7068c20460ea7c04eddb5150f348a0141f6f87a83f6adbeb21e86a48283 |
# -*- coding: utf-8 -*-
"""
===============================================================================
Atom classes for crystal structures (:mod:`sknano.core.atoms._basis_atoms`)
===============================================================================
.. currentmodule:: sknano.core.atoms._basis_atoms
"""
... | scikit-nano/scikit-nano | sknano/core/atoms/_basis_atoms.py | Python | bsd-2-clause | 1,432 | [
"CRYSTAL"
] | 56707c2aa1fe05893ab72f409ca76a5178fdb922e36bafdfe549e2b1d678421d |
#! /usr/bin/env python
import macrodensity as md
import math
import numpy as np
import matplotlib.pyplot as plt
import csv
from itertools import izip
potential_file = 'LOCPOT' # The file with VASP output for potential
coordinate_file = 'POSCAR' # The coordinates file NOTE NOTE This must be in vasp 4 format
species =... | WMD-group/MacroDensity | examples/OnSitePotential.py | Python | mit | 2,829 | [
"ASE",
"VASP"
] | db6b6a68d156df98f53a27cc69b74dbf1b2b01bdf4e7c239fe70c23dad1bd69b |
#!/usr/bin/env python3
# This file is part of the LSLTools package.
# Copyright 2014
# Jari Torniainen <jari.torniainen@ttl.fi>,
# Andreas Henelius <andreas.henelius@ttl.fi>
# Finnish Institute of Occupational Health
#
# This code is released under the MIT license
# http://opensource.org/licenses/mit-license.php
#
# P... | bwrc/lsltools | lsltools/sim.py | Python | mit | 25,614 | [
"Gaussian"
] | 1df286255c80c54cf972157326c8950929a2ba14a82c0e1287fcad03c850b843 |
"""
fitness v0.01
- implements a fitness function base class
Copyright 2011 Brian Monkaba
This file is part of ga-bitbot.
ga-bitbot 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 ... | OndroNR/ga-bitbot | libs/fitness.py | Python | gpl-3.0 | 9,169 | [
"Brian"
] | e728219028f96d817ced77a947b3309348dd938efbf15def37b032da4653ee61 |
from .fgir import *
from .optimize import FlowgraphOptimization
from .error import Warn
import asyncio
class PCodeOp(object):
'''A class interface for creating coroutines.
This helps us keep track of valid computational elements. Every coroutine in
a PCode object should be an method of PCodeOp.'''
@staticmet... | Planet-Nine/cs207project | pype/pcode.py | Python | mit | 5,058 | [
"VisIt"
] | 02abecc112e32357192d692dbc4d121b81d1886a4438e0eccfa0468f4f8f13d9 |
import pickle
import gzip
import os, sys, errno
import time
import math
# numpy & theano imports need to be done in this order (only for some numpy installations, not sure why)
import numpy
#import gnumpy as gnp
# we need to explicitly import this in some cases, not sure why this doesn't get imported with numpy itse... | bajibabu/merlin | src/work_in_progress/run_merlin_v2.py | Python | apache-2.0 | 58,040 | [
"NEURON"
] | ac97443739432a8473ba697444d27c264c134a56611224c5c6e07aacef882b37 |
import vtk
from math import sqrt
from vtk.test import Testing
plane = vtk.vtkPlane()
plane.SetOrigin(5,5,9.8)
plane.SetNormal(0,0,1)
coords = [(0,0,0),(10,0,0),(10,10,0),(0,10,0),
(0,0,10),(10,0,10),(10,10,10),(0,10,10),
(5,0,0),(10,5,0),(5,10,0),(0,5,0),
(5,0,9.5),(10,5,9.3),... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Core/Testing/Python/cutPolygons.py | Python | bsd-3-clause | 2,949 | [
"VTK"
] | a8e92b2189be7cbb51b1e82cec1ae6a2aff51af6f080230245da246ca95c9762 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Lee-Ping Wang
# Contributors: Robert McGibbon
#
# MDTraj is fr... | marscher/mdtraj | MDTraj/formats/arc.py | Python | lgpl-2.1 | 9,800 | [
"MDTraj",
"TINKER"
] | 10a37f3107c6eab0c8ea857cfbefa8560f66399fd9276cbaf0271f0497f9fceb |
# -*- coding: utf-8 -*-
# @Author: LC
# @Date: 2016-03-26 22:42:39
# @Last modified by: LC
# @Last Modified time: 2016-04-11 15:22:41
# @Email: liangchaowu5@gmail.com
# 功能：单线程下载搜狗输入法的词库，使用时把主函数中的baseDir改成自己的下载目录即可，注意baseDir末尾不能有/
import urllib2
import Queue
import re
import os
import time
import downloadSingleFil... | ltf/lab | plab/thesaurus/spider/SougouThesaurusSpider/singleThreadDownload.py | Python | gpl-3.0 | 3,214 | [
"VisIt"
] | e851fd9408ba1f87e7b0c8a2b5bb6fb6661765fb2425776d9bcbec136d0580b5 |
# -*- coding: utf-8 -*-
"""
Jinja2
~~~~~~
Jinja2 is a template engine written in pure Python. It provides a
`Django`_ inspired non-XML syntax but supports inline expressions and
an optional `sandboxed`_ environment.
Nutshell
--------
Here a small example of a Jinja template::
{% extends 'base.html' %}
{% b... | patricmutwiri/jinja2 | setup.py | Python | bsd-3-clause | 2,614 | [
"VisIt"
] | 1db89241e6f21af26ff16089bc7d1d8f3d992274b21125b47f6929fc62a59900 |
# encoding: utf-8
"""
filters.py -- Custom signal filtering functions
Exported namespace: amplitude_envelope, halfwave, quick_boxcar, circular_blur
Created by Joe Monaco on 2007-11-15. Updated 2009-09-11.
Copyright (c) 2007-2009 Columbia University. All rights reserved.
Copyright (c) 2009-2011 Johns Hopkins Universit... | jdmonaco/vmo-feedback-model | src/tools/filters.py | Python | mit | 2,661 | [
"Gaussian"
] | 61d18dd539766b125fd1a96e7dfbfc64ca81c17ab75bab80d57bdca617c4ddb8 |
general_midi = {
1: "Acoustic Grand Piano",
2: "Bright Acoustic Piano",
3: "Electric Grand Piano",
4: "Honky-tonk Piano",
5: "Electric Piano 1",
6: "Electric Piano 2",
7: "Harpsichord",
8: "Clavinet",
9: "Celesta",
10: "Glockenspiel",
11: "Music Box",
12: "Vibraphone",
... | JasonFruit/abcviewer | abcv/general_midi.py | Python | mit | 3,121 | [
"CRYSTAL"
] | 1a71adebfca2315446382bc61de99f5769d9f3642ca9db8f7327f70b4c960baa |
###############################################################################
##
## Copyright (C) 2014-2015, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | hjanime/VisTrails | scripts/dist/mac/setup.py | Python | bsd-3-clause | 4,169 | [
"VTK"
] | f63c18875adde9a8b723783640b25632363a6839572aecf52d09994cab6940e0 |
import moose
from IPython import embed
# Try to connect pool to species
pool = moose.Pool('/pool')
species = moose.Species('/species')
embed()
species.pool = pool
| rahulgayatri23/moose-core | python/libmumbl/test/test1.py | Python | gpl-3.0 | 163 | [
"MOOSE"
] | 75df22b10383b5b901f539ef18d1112a9eb95552115dee828bfefda94094a2fc |
#!/usr/bin/env python
import sys
import logging
import argparse
from Bio import SeqIO
from Bio.Data import CodonTable
logging.basicConfig(level=logging.INFO)
log = logging.getLogger()
def translate(fasta_file, target="protein", table=11, strip_stops=False, met=False):
records = list(SeqIO.parse(fasta_file, "fast... | TAMU-CPT/galaxy-tools | tools/fasta/fasta_translate.py | Python | gpl-3.0 | 2,495 | [
"Biopython"
] | 5a8e73d43002f9384222b5ea5cb23acbeb2a93616a7d525353d9fa317ec71486 |
"""
========================================
Special functions (:mod:`scipy.special`)
========================================
.. module:: scipy.special
Nearly all of the functions below are universal functions and follow
broadcasting and automatic array-looping rules. Exceptions are
noted.
.. seealso::
`scipy.s... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/scipy/special/__init__.py | Python | gpl-3.0 | 27,475 | [
"Gaussian"
] | f1aaad7dc887dd88a14850633fff595bf5b56738645381afd683be596cb59699 |
import numpy as np
import matplotlib.pyplot as plt
import emcee
import batman
def _gaus(x, a, b, x0, sigma):
"""
Simple Gaussian function
Parameters
----------
x : float or 1-d numpy array
The data to evaluate the Gaussian over
a : float
the amplitude
b : float
the... | jradavenport/ThirdWay | thirdway/thirdway.py | Python | mit | 1,017 | [
"Gaussian"
] | 1fa4a53b1bd98b2d08c03bb1c86adcf1d6171a037db1581339e0d1414129f3e7 |
# Copyright 2000 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""This provides useful general math tools.
Functions:
fcmp Compare two floating point ... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/mathfns.py | Python | apache-2.0 | 2,452 | [
"Biopython"
] | 51ce17408ea06e5c3afe6397219926dc8a1c6ef9ad2523f1aa8686eb8b26f04a |
######################################################################
#
# Functions to calculate integration points and weights for Gaussian
# quadrature
#
# x,w = gaussxw(N) returns integration points x and integration
# weights w such that sum_i w[i]*f(x[i]) is the Nth-order
# Gaussian approximat... | KiMiralles/Python-Learning | Computational Physics Newman/Book Resources/gaussxw.py | Python | gpl-3.0 | 1,896 | [
"Gaussian"
] | 9b3a2fef5f94dbaf193ce52ef65f1474d3d2dd1858d4e5747b44ccca497860be |
################################################################################
# Copyright (C) 2014 Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
"""
Demonstrate categorical Markov chain with hidden Markov model (HMM... | SalemAmeen/bayespy | bayespy/demos/hmm.py | Python | mit | 4,839 | [
"Gaussian"
] | e37dca3820568745f853fef5adce5decb7bb12d195701f3ec2bb240c13f5d283 |
# -*- coding: utf-8 -*-
"""
***************************************************************************
translate.py
---------------------
Date : August 2012
Copyright : (C) 2012 by Victor Olaya
Email : volayaf at gmail dot com
*****************************... | pblottiere/QGIS | python/plugins/processing/algs/gdal/gdaladdo.py | Python | gpl-2.0 | 6,874 | [
"Gaussian"
] | 5f3ec163a1953ca80418be20363f6ec64f7db0358b1b320b432cdf57e2357d96 |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | jonathonwalz/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 104,709 | [
"VisIt"
] | 1d58b4f33a49cd69bb5b11948628bb2d719869f7f6897b44c5a4ab3b16bf35e2 |
#!/usr/bin/env python
################################################################################
# hapClassifier.py is script to classify sickle cell haplotypes
# Copyright (c) [2017] [Elmutaz Shaikho Elhaj Mohammed]
################################################################################
#!/usr/local/bi... | eshaikho/haplotypeClassifier | hapClassifier.py | Python | mit | 6,003 | [
"pysam"
] | 42dc6da4d695706e89ffe2be63cfb1d400d4e8ac503f9c5c3f12b203c95f64f9 |
#
#@BEGIN LICENSE
#
# cctransort by Psi4 Developer, a plugin to:
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of t... | lothian/cctransort | __init__.py | Python | gpl-2.0 | 1,151 | [
"Psi4"
] | 8c1b73889f2af4f030a41176318b9ab8fa285c0940b9475fc9b9c8b608360a61 |
# Copyright (C) 2012,2013,2016,2018
# 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 term... | espressopp/espressopp | src/interaction/Cosine.py | Python | gpl-3.0 | 3,359 | [
"ESPResSo"
] | 7191bad3f202be6a30fa898cf9f6728ba3ff690ef7367961fb8420677fec8f18 |
import unittest
import configparser
import os
import tempfile
import socket
from IPy import IP
from kagent_utils import KConfig
class TestKConfig(unittest.TestCase):
# server section
url = 'http://localhost:1337/'
path_login = 'login/path'
path_register = 'register/path'
path_ca_host = 'ca/host... | karamelchef/kagent-chef | files/default/kagent_utils/tests/test_kagent_config.py | Python | gpl-3.0 | 10,234 | [
"Elk"
] | 9d0e019fe698cfd74770757ce4d1e115e4f3be6d47af942e452399d02e153c66 |
# -*- coding: utf-8 -*-
#
# Author: Sam Rushing <rushing@nightmare.com>
#
# Copyright (C) 2013 Alexander Shorin
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution.
#
"""
.. module:: astm.asynclib
:synopsis: Forked vers... | Alwnikrotikz/python-astm | astm/asynclib.py | Python | bsd-3-clause | 32,183 | [
"Amber"
] | 017b63522d347a9b9c7192d0b7d71f80bac5ff21b69960ace2a88c7c2bc836fe |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
import numpy as np
from CrystalField import ... | mganeva/mantid | scripts/Inelastic/CrystalField/CrystalFieldMultiSite.py | Python | gpl-3.0 | 25,091 | [
"CRYSTAL",
"Gaussian"
] | 6bbcf219e1ffed37247f16de0babb4eef5990ae75e9a8e348bbcfe934b252feb |
# -*- coding: utf-8 -*-
# Copyright (c) 2006-2016 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2010 Daniel Harding <dharding@gmail.com>
# Copyright (c) 2012-2014 Google, Inc.
# Copyright (c) 2013-2017 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 Brett Cannon <brett@python.org>
# Copyri... | lucidmotifs/auto-aoc | .venv/lib/python3.5/site-packages/pylint/checkers/base.py | Python | mit | 78,705 | [
"VisIt"
] | e2c39f726b2a242d137da94f8d56f3623d77bed0ad23085dd3bd34b0e3da76bc |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
A simple example to run CASCI calculation.
'''
import pyscf
mol = pyscf.M(
atom = 'O 0 0 0; O 0 0 1.2',
basis = 'ccpvdz',
spin = 2)
myhf = mol.RHF().run()
# 6 orbitals, 8 electrons
mycas = myhf.CASCI(6, 8).run()
#
# Note this myc... | sunqm/pyscf | examples/mcscf/00-simple_casci.py | Python | apache-2.0 | 3,014 | [
"PySCF"
] | a792b775e367e5ed9651a6522064cfc0fe8e0725c64297c895da1950234991b6 |
"""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-SunOS-i386/lib/python/lib/python2.4/random.py | Python | gpl-2.0 | 29,814 | [
"Gaussian"
] | 8e16a071fb83b96a4a186a8c29a477eee2273c4dfcb14966f792e2e8579c4674 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# 2015-04-13T21:56+08:00
import json
import time
entry = {}
entry['title'] = 'Dive into history, 2009 edition'
entry['article_link'] = 'http://diveintomark.org/archives/2009/03/27/dive-into-history-2009'
entry['comments_link'] = None
entry['internal_id'] = b'\xDE\xD5\x... | myd7349/DiveIntoPython3Practices | chapter_13_SerializingPythonObjects/serializing_datatypes_unsupported_by_json.py | Python | lgpl-3.0 | 2,466 | [
"CRYSTAL"
] | 0d33c9a022f19591ce6cfc30cdaa4a9b0951f8c075654e57fbd531cfd6a7e990 |
"""
A simple VTK widget for PyQt or PySide.
See http://www.trolltech.com for Qt documentation,
http://www.riverbankcomputing.co.uk for PyQt, and
http://pyside.github.io for PySide.
This class is based on the vtkGenericRenderWindowInteractor and is
therefore fairly powerful. It should also play nicely with the
... | hlzz/dotfiles | graphics/VTK-7.0.0/Wrapping/Python/vtk/qt/QVTKRenderWindowInteractor.py | Python | bsd-3-clause | 19,228 | [
"CRYSTAL",
"VTK"
] | 99bb68443e59dfaf7b9b457697607d8ce712969603911b7981e5c801f59c89a9 |
#!/usr/bin/env python2
desc="""Report sites with differences between bam files.
"""
epilog="""AUTHOR:
l.p.pryszcz+git@gmail.com
Mizerow, 25/02/2014
"""
import argparse, os, sys
import pysam, subprocess
from datetime import datetime
from bam2snps import _remove_indels
def get_allele_frequency(bases, alphabet="ACGT")... | lpryszcz/bin | bam2difference.py | Python | gpl-3.0 | 3,445 | [
"pysam"
] | b3c6ffa4f484c0f1d85b2f0bc80d09f394eb707992f57c2201b446c10301d7a6 |
"""
This module contains fileIO operations and file conversion for the image
processing tool kit in the NSLS-II data analysis software package.
The functions included in this module focus on reading and writing
netCDF files. This is the file format used by Mark Rivers for
x-ray computed microtomography data collected a... | licode/scikit-xray | skbeam/io/net_cdf_io.py | Python | bsd-3-clause | 3,187 | [
"NetCDF"
] | 71787a1fdf66a43c9f10834624bb4927f4f588df1ac6b38140fe4463e51d8923 |
import numpy
from matplotlib import pyplot as plt
class Model:
def __init__(self, train):
self._train = train
def fit(self, beta, grad=True):
return self(self._train, beta, grad=grad)
class MultiModel(Model):
def __init__(self, train, terms):
"""
Arguments:
train {*} - The training data ... | bauerca/BikeShareDemand_Carl | models.py | Python | gpl-2.0 | 4,087 | [
"Gaussian"
] | 27a0d8ebe205679fc187b960454bfd6b9a60cd78540295939f650c264884d436 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2013, Jeroen Hoekx <jeroen.hoekx@dsquare.be>, Alexander Bulimov <lazywolf0@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 So... | milad-soufastai/ansible-modules-extras | system/lvol.py | Python | gpl-3.0 | 14,624 | [
"Firefly"
] | 62cf2714a9f00a2c9a8e5093db98f999b1003790d528cfd1a856012c60f8e0be |
"""
Default Django settings. Override these with settings in the module pointed to
by the DJANGO_SETTINGS_MODULE environment variable.
"""
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
def gettext_noop(s):
return s
####... | kaedroho/django | django/conf/global_settings.py | Python | bsd-3-clause | 22,212 | [
"VisIt"
] | cf88a291528d17b86a5645ddecdc25096ef9d50721f46c3de00df526cc9bdc7f |
#!@PYTHON_EXECUTABLE@
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
#... | mhlechner/psi4 | psi4/run_psi4.py | Python | gpl-2.0 | 10,262 | [
"Psi4"
] | 693033d3a479b51988b8a9403e2b14afaf98be806c434b87f9796ecbbf04b8af |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | moto-timo/robotframework | src/robot/model/itemlist.py | Python | apache-2.0 | 2,798 | [
"VisIt"
] | fb7dfbf0348217c2db21d5161af88d532ccdc408eb0a91626b553e5597c3514c |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-datacatalog | tests/unit/gapic/datacatalog_v1beta1/test_data_catalog.py | Python | apache-2.0 | 296,123 | [
"Octopus"
] | b7c1ea950232098b9e067aaff2465052fc909d1b9e6fb12f59e5f1cc7c9f99c7 |
#!/usr/bin/env python3
# Copyright (C) 2013,2014,2018-2019 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, ei... | KaiSzuttor/espresso | src/config/gen_sampleconfig.py | Python | gpl-3.0 | 1,753 | [
"ESPResSo"
] | faccec11a25c7578940527465a5b6ce15c36e2f830de869dd2d49d622fde70b8 |
from pyml.cluster.base import ClusterBase
from pyml.utils import set_seed
import warnings
class KMeans(ClusterBase):
def __init__(self, k=3, initialisation='Forgy', max_iterations=100, min_change=1,
seed=None, norm='l1'):
"""
KMeans implementation
:type k: int
:t... | gf712/PyML | pyml/cluster/kmeans.py | Python | mit | 6,082 | [
"Gaussian"
] | e44c3e8cb17cede9c3654c218801d4200f3af16971222eb16b2cd0cc6496bf66 |
import os
from ase import Atom, Atoms
from ase.io import PickleTrajectory
co = Atoms([Atom('C', (0, 0, 0)),
Atom('O', (0, 0, 1.2))])
traj = PickleTrajectory('1.traj', 'w', co)
for i in range(5):
co.positions[:, 2] += 0.1
traj.write()
del traj
traj = PickleTrajectory('1.traj', 'a')
co = traj[-1]
pri... | slabanja/ase | ase/test/trajectory.py | Python | gpl-2.0 | 1,075 | [
"ASE"
] | ff0063bd6714448cbaa1e4719030891c41b6f69742128a74f70211251b65b567 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Remove cullers so single vertex will render
ren1 = vtk.vtkRenderer()
ren1.GetCullers().RemoveAllItems()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderW... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Common/DataModel/Testing/Python/TestStructuredGrid.py | Python | gpl-3.0 | 5,545 | [
"VTK"
] | 4f20940f0c79be310040e4b97038a8475bec3e19a7c327a0ae8091a08fa75183 |
# Andrew Miller <amiller@cs.ucf.edu> 2011
#
# BlockPlayer - 3D model reconstruction using the Lattice-First algorithm
# See:
# "Interactive 3D Model Acquisition and Tracking of Building Block Structures"
# Andrew Miller, Brandyn White, Emiko Charbonneau, Zach Kanzler, and Joseph J. LaViola Jr.
# IEEE VR 2012,... | amiller/blockplayer | blockplayer/grid.py | Python | mpl-2.0 | 9,344 | [
"Mayavi"
] | 68e1f5d23ea86fe8b96f88e2327bcc41bab4d773b6f3c8572fa45906b1326bc8 |
"""
========================================================
Gaussian process regression (GPR) on Mauna Loa CO2 data.
========================================================
This example is based on Section 5.4.3 of "Gaussian Processes for Machine
Learning" [RW2006]. It illustrates an example of complex kernel engine... | glemaitre/scikit-learn | examples/gaussian_process/plot_gpr_co2.py | Python | bsd-3-clause | 6,373 | [
"Gaussian"
] | 434fb758ab358afed3acfe0697cfa89f6c00bdf750c7a718e3ba7ecadd10ce4b |
from coalib.bearlib.abstractions.Linter import linter
from dependency_management.requirements.DistributionRequirement import (
DistributionRequirement)
@linter(executable='verilator',
output_format='regex',
use_stderr=True,
output_regex=r'\%(?:(?P<severity>Error|Warning.*?).*?):'
... | gs0510/coala-bears | bears/verilog/VerilogLintBear.py | Python | agpl-3.0 | 1,483 | [
"VisIt"
] | 0006f720ed89ba5d97fcbe4a766be75817cb3acfd5c5b9bc4c16808cdf3b3878 |
#!/usr/bin/env python
"""\
py.cleanup [PATH] ...
Delete typical python development related files recursively under the specified PATH (which defaults to the current working directory). Don't follow links and don't recurse into directories with a dot. Optionally remove setup.py related files and empty
directories.
"... | blindroot/pycmd | pycmd/pycleanup.py | Python | mit | 3,617 | [
"VisIt"
] | e7d41b8190179ae1b0e1f533c65d8c74dfdb54b13ac907e8a5bd74fc9f66ed6d |
#!/usr/bin/env python
#
# Copyright (C) 2011-2012 ABINIT Group (Yann Pouillon)
#
# This file is part of the ABINIT software package. For license information,
# please see the COPYING file in the top-level directory of the ABINIT source
# distribution.
#
from time import gmtime,strftime
import commands
import os
impor... | qsnake/abinit | util/maintainers/check-build-refs.py | Python | gpl-3.0 | 1,788 | [
"ABINIT"
] | 8ec0513bfa0c5a36825a69e837fa8fbcd017965f00dd430b9b3f44e93ea8f75b |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-spanner | scripts/fixup_spanner_admin_instance_v1_keywords.py | Python | apache-2.0 | 6,522 | [
"VisIt"
] | 0bdbb8ac2427cc89c9325eb17cef90fd23c6847f55ec6c2f731454f38f64b668 |
# Copyright 2017 Canonical Ltd.
# Licensed under the LGPLv3, see LICENCE file for details.
from unittest import TestCase
import macaroonbakery.httpbakery as httpbakery
import requests
from mock import patch
from httmock import HTTMock, response, urlmatch
ID_PATH = 'http://example.com/someprotecteurl'
json_macaroon ... | go-macaroon-bakery/py-macaroon-bakery | macaroonbakery/tests/test_bakery.py | Python | lgpl-3.0 | 9,725 | [
"VisIt"
] | a8705dd2dc7408d3a54218fae91ca944d3996d0fa86f72e78d351ba002157d81 |
#!/usr/bin/env python
"""
This script drives an NWChem calculation given a generic QM specification
"""
import json
import os
import pint
from run import *
CRDPARAMS = "nwchem.crdparams"
class QMMMRunner(QMRunner):
def _geom_block(self):
if not os.path.isfile(CRDPARAMS):
raise IOError('Requi... | molecular-toolkit/chemistry-docker-images | makefiles/buildfiles/nwchem/runqmmm.py | Python | apache-2.0 | 650 | [
"NWChem"
] | 4d6c7dfedbf4c2f39f428cd684b94399347d64d7a0d86cce9f33c9365c5f9196 |
#
# -*- coding: utf-8 -*-
#
# (C) Copyright 2016 Karellen, Inc. (http://karellen.co/)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | karellen/karellen-sqlite | build.py | Python | apache-2.0 | 2,363 | [
"VisIt"
] | 31f5e0b8b9efc74d35009f5e1ce5e8e4df7de56580bd48cda052a4490606765f |
# -*- coding: utf-8 -*-
"""
Subraph centrality and communicability betweenness.
"""
# Copyright (C) 2011 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
import networkx as nx
from networkx.utils import *
__au... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/networkx/algorithms/centrality/subgraph_alg.py | Python | gpl-3.0 | 9,596 | [
"Desmond"
] | 4c7980c1647f02359a0452f8d1e0611451e23d415ebb8646485858c83cc70242 |
""" ProxyRenewalAgent keeps the proxy repository clean.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN ProxyRenewalAgent
:end-before: ##END
:dedent: 2
:caption: ProxyRenewalAgent options
"""
import concurrent.futures
from DIRAC import S_OK
from DIRAC.Core.Base.AgentModul... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/Agent/ProxyRenewalAgent.py | Python | gpl-3.0 | 3,325 | [
"DIRAC"
] | cb49654656f23b6953953deeebd2aceacd6a0298495914fa7a5ea4ff5f7f342c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from pymatgen.io.cif import CifParser
from pymatgen.analysis.magnetism.jahnteller import *
import unittest
test_dir = os.path.join(os.path.dirname(__file__), ... | nisse3000/pymatgen | pymatgen/analysis/magnetism/tests/test_jahnteller.py | Python | mit | 5,117 | [
"pymatgen"
] | 63b4533ebb5f4f89abc08abcdd9d4d4f46ac62d97e2d98d1ac4703d88583f5d9 |
import time
#from telegramFormat import *
from api_definitions import *
import itertools
import struct
import io
import logging
logging.basicConfig(level=logging.DEBUG)
logger = logging.getLogger(__name__)
# #file handler for logs
# handler = logging.FileHandler('commands.log')
# handler.setLevel(logging.INFO)
# # c... | bojandjukic1/SAP_CORK | Coffee_Machine/CGI Call and Script - New/commands.py | Python | gpl-3.0 | 24,743 | [
"ESPResSo"
] | a14c5cab31ed48904defeef916769f5b0e8693fe71facd168696e5657102e213 |
import tweepy
import json
import cPickle
import zmq
# Authentication details. To obtain these visit dev.twitter.com
consumer_key = 'PUpKEozSrCV5x06mc1uNDMgMN'
consumer_secret = 'q0W7N8wDCD41O9pPu8yej42BnJ138Gwpl2wQsB5wvxLqvciKQy'
access_token = '1315274378-RxFpa0iNmDucPaxMCENLaeeky9k4rL9JN0Zjn60'
access_token_secret ... | lnhubbell/Quarium | twitter_stream.py | Python | mit | 2,221 | [
"VisIt"
] | 2bd98c6d96fb2c12e097b3b3b7546aa01bd0e78d7acf0050ff62b19fe73a2d13 |
# -*- coding: utf-8 -*-
"""This module contains the controller classes of the application."""
# symbols which are imported by "from mse.controllers import *"
__all__ = ['Root']
# standard library imports
import os.path
# import logging
# log = logging.getLogger('mse.controllers')
# third-party imports
from cherrypy... | jinmingda/MicroorganismSearchEngine | mse/controllers.py | Python | mit | 10,790 | [
"VisIt"
] | d119bb7db289c137eeee9a90632f14cdee783d326139d5858517465746f71044 |
# -*- coding:utf-8 -*-
#
# Compute the normal and the gaussian curvature of a mesh
#
# Based on :
# Discrete Differential-Geometry Operators for Triangulated 2-Manifolds
# Mark Meyer, Mathieu Desbrun, Peter Schröder, Alan H. Barr
# VisMath '02, Berlin (Germany)
# External dependencies
import math
import nu... | microy/PyMeshToolkit | MeshToolkit/Core/Curvature.py | Python | mit | 8,082 | [
"Gaussian"
] | e95a779d0a3747f8ed1b9e5f028fbae51297037d695aa287a6ceebd16261789b |
#!/usr/bin/env python
#JSON {"lot": "UKS/6-31G*",
#JSON "scf": "ODASCFSolver",
#JSON "linalg": "CholeskyLinalgFactory",
#JSON "difficulty": 3,
#JSON "description": "Basic UKS DFT example with LDA exhange-correlation functional (Dirac+VWN)"}
from horton import *
# Load the coordinates from file.
# Use the XYZ file... | eustislab/horton | data/examples/hf_dft/uks_methyl_lda.py | Python | gpl-3.0 | 2,833 | [
"DIRAC",
"Gaussian"
] | 75590f6323cf066ea4efafe86698f69b6f594a21176b754db054e338a6426736 |
#### PATTERN | WEB #################################################################################
# Copyright (c) 2010 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
# http://www.clips.ua.ac.be/pages/pattern
####################################... | decebel/dataAtom_alpha | bin/plug/py/external/pattern/web/__init__.py | Python | apache-2.0 | 115,157 | [
"VisIt"
] | 1053a318d34d19587cab39fc03032149511425bb8547a284dcd77c3b67c9e640 |
from dnfpy.cellular.hardlib import HardLib
from dnfpy.core.map2D import Map2D
from dnfpy.cellular.nSpikeConvolution import normalizeIntensity,normalizeProba
import numpy as np
import random
import sys
class Rsdnf2LayerConvolution(Map2D):
class Params:
#enum CellRsdnf_Params {NB_SPIKE=0,PROBA=1,PRECISIO... | bchappet/dnfpy | src/dnfpy/cellular/rsdnf2LayerConvolution.py | Python | gpl-2.0 | 5,576 | [
"NEURON"
] | 955a848a56a1ac255a3654018963a7bc28c37c2b645efe237f49b08e35cef50c |
#!/usr/bin/env python
# Python example script that uses the vtkMatlabEngineInterface to perform
# a calculation (sin(x)^2 + cos(x)^2 = 1) on VTK array data, and pass the
# result back to VTK.
# VTK must be built with VTK_USE_MATLAB_MEX turned on for this example to work!
from __future__ import print_function
from vtk... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/Infovis/Python/Matlab_engine_interface.py | Python | gpl-3.0 | 1,277 | [
"VTK"
] | b857d2a54e38263c7fd53aba1f6a012ce856a2fb72926ccbb9327b9848241535 |
#!/usr/bin/env python
################################################################################
# Copyright (C) 2014, 2015 GenAP, McGill University and Genome Quebec Innovation Centre
#
# This file is part of MUGQIC Pipelines.
#
# MUGQIC Pipelines is free software: you can redistribute it and/or modify
# it und... | ccmbioinfo/mugqic_pipelines | pipelines/illumina_run_processing/illumina_run_processing.py | Python | lgpl-3.0 | 46,253 | [
"BLAST"
] | 22a76e5f34c0e4e9d9daac29b09f46b791cd9f84af2170da6dfc6cebda5314c5 |
# 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/Time_Window/test10_cross_validate_objects_800ms.py | Python | mit | 4,257 | [
"Mayavi"
] | e8158ce12cf51ffd0f7e026c4081d57189b89751320c9cbce5eb1791c89e61b8 |
from __future__ import division
import numpy as np
import matplotlib.pyplot as plt
Vth = 15 # mV
w = 2 # ms
tau = 10 # ms
def calc_error(isi):
"""
Calculate approximation error for a given target inter-spike interval.
"""
# input current required for LIF to spike at t = isi
current = Vth/(... | achilleas-k/brian-scripts | thesis_stuff/reldiff.py | Python | apache-2.0 | 2,203 | [
"NEURON"
] | 2133384385e55a405966ad99a0bc75c421bcd2b4a3659bcc680f992855d86c9d |
#!/usr/bin/env python
"""
A linting tool to check if templates are safe
"""
from __future__ import print_function
import argparse
import ast
from enum import Enum
import os
import re
import sys
import textwrap
class StringLines(object):
"""
StringLines provides utility methods to work with a string in terms o... | Learningtribes/edx-platform | scripts/safe_template_linter.py | Python | agpl-3.0 | 101,020 | [
"VisIt"
] | 1b6f1111fce8bb6cefbcc3d3f94c341a16bbeebcf70d0bb59948ab4b0c6ec37d |
#*******************************************************************
# * File: merge.py
# * Description:
# * Author: HarshaRani
# * E-mail: hrani@ncbs.res.in
# ********************************************************************/
# ***********************************************************... | subhacom/moose-core | python/moose/merge/merge.py | Python | gpl-3.0 | 28,816 | [
"MOOSE"
] | 7cf8fccedd6519f0fc0434901d1de5ebbae4ab7333977699c17b1a1a888d9ac8 |
# Copyright (c) 2014. Mount Sinai School of Medicine
#
# 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 o... | cpcloud/pepdata | setup.py | Python | apache-2.0 | 2,182 | [
"Biopython"
] | 0b5dbbd2d97b3afd07373dc5f18b6bbeac5941542b28204687aeeeca9d23ffbb |
#!/usr/bin/env python3
# INSert membrANE
# A simple, versatile tool for building coarse-grained simulation systems
# Copyright (C) 2017 Tsjerk A. Wassenaar and contributors
#
# 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 ... | Tsjerk/Insane | tests/utils.py | Python | gpl-2.0 | 12,460 | [
"MDAnalysis"
] | 905a0dd31bc13a0e32969c491ed11f62c254921c2ae46964e660baa587c2a9d3 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | zhouyao1994/incubator-superset | superset/viz.py | Python | apache-2.0 | 91,799 | [
"VisIt"
] | 0bb53b189dda45c4c4c74b10a21c0234d50515ee980e6a6a28009812711d5f71 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright 2012 The Plaso Project Authors.
# Please see the AUTHORS file for details on individual authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the Lic... | iwm911/plaso | plaso/parsers/sqlite_plugins/chrome_cookies.py | Python | apache-2.0 | 5,703 | [
"VisIt"
] | f9f05c4acb89a831fd24a9c2b0fe3bf34fd254280d57c0ef4fca7df5b5db10dd |
"""Contains the base class for the Snux driver overlay.
This class overlays an existing WPC-compatible platform interface to work with
Mark Sunnucks's System 11 interface board.
"""
# snux.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the ... | spierepf/mpf | mpf/platform/snux.py | Python | mit | 14,196 | [
"Brian"
] | 4c65c5f8082fbaa3a7893b47d7f444e41b0d9a1cf9889d558de7c217f1df9831 |
###############################################################################
# Copyright 2017-2021 - Climate Research Division
# Environment and Climate Change Canada
#
# This file is part of the "fstd2nc" package.
#
# "fstd2nc" is free software: you can redistribute it and/or modify
# it under... | neishm/fstd2nc | fstd2nc/mixins/netcdf.py | Python | lgpl-3.0 | 18,945 | [
"NetCDF"
] | 44129eddd74e4aa92c2f813d63c7c82fd3188e06d5b4cc3a4826ed176f2b643e |
"""
There are two kinds of Repositories in PyChemia
Structure Repositories where many structures are stored
Execution Repositories where the out of every calculation
is stored
Each structure contains some metadata that is accessible with
the StructureEntry object
Also each calculation has it own metadata accessible ... | MaterialsDiscovery/PyChemia | pychemia/db/repo.py | Python | mit | 16,947 | [
"pymatgen"
] | eb549a37fb5921231e8655e063ab0d05a7c2a27302c9a03db052f12e79805fb0 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkIVWriter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkIV... | nagyistoce/devide | modules/vtk_basic/vtkIVWriter.py | Python | bsd-3-clause | 460 | [
"VTK"
] | d3a0abf956db319dbb422dc6294cc0215d54b786b16b70cda735ea8b4ced13ab |
import random
from main import Game
import game
import objects
import libtcodpy as libtcod
import items
from main import game_instance
class Monster(object):
def init(self,*a): pass
def take_turn(self): pass
def load_data(self, data):
for k,v in data.items():
setattr(self, k,v)
return self
class BasicMonst... | fiddlerwoaroof/yinjar | monsters.py | Python | bsd-3-clause | 7,779 | [
"Amber"
] | 3a0c3ab5226eb569b40985f048a5ceac88937520e5f4d2a794d9ce387d7ec756 |
#!/usr/bin/env python
# Copyright 2014-2021 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/pbc/x2c/sfx2c1e.py | Python | apache-2.0 | 11,486 | [
"PySCF"
] | 31043fff7ad310df88742821b7b8bb6bc5635b99288afe3f54c878300ff68c86 |
# -*- coding: utf-8 -*-
# @author: Thomas Anderson
###################
# run_expt.py #
###################
# Thomas Anderson #
###################
# 29/01/2014 #
###################
# Last updated: #
# 11/03/2014 #
###################
##########################
# Python QR Code Project #
# ----------... | Driminary/python-qr-project | source/run_expt.py | Python | mit | 5,005 | [
"Gaussian"
] | a48053c02cc7bda1a158c5f91d3ee01254bd78336ec9408effef9d0c3933eca2 |
#!/usr/bin/python
import os, sys, inspect, subprocess, tempfile
# Include the parent directory in the search path.
cmd_folder = os.path.abspath(os.path.split(inspect.getfile( inspect.currentframe() ))[0])
if cmd_folder not in sys.path:
sys.path.insert(0, cmd_folder)
from common import dbConn, DEFAULT_TAG, BACKUP... | eldering/autoanalyst | code_analyzer/analyzer.py | Python | mit | 26,667 | [
"VisIt"
] | 90e18d26a5658cdc46915932ac301a41141c26565401e9bf003afe020ebfc00d |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/driver/procrouting/response/scf_products.py | Python | lgpl-3.0 | 21,923 | [
"Psi4"
] | d06634059cddc309e2a976f03130fe6eeff93d7b708c364697f6636d9f09790b |
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