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# vi: ts=4 sw=4
'''
:mod:`ophyd.control.areadetector.plugins` - areaDetector plugins
======================================================
.. module:: ophyd.control.areadetector.plugins
:synopsis: `areaDetector`_ plugin abstractions
.. _areaDetector: http://cars.uchicago.edu/software/epics/areaDetector.html
'''
... | dchabot/ophyd | ophyd/areadetector/plugins.py | Python | bsd-3-clause | 27,534 | [
"NetCDF"
] | 184db27f6b69bebe25ec4dd90baab88a72e1684ae9349318f5a9dcec9e1dcf2c |
# This file is part of MSMAccelerator.
#
# Copyright 2011 Stanford University
#
# MSMAccelerator 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... | pandegroup/msmaccelerator | drivers/GROMACS/gromacs_driver.py | Python | gpl-3.0 | 12,666 | [
"Gromacs"
] | 593cbf733e2083ebd6ea4ae9cb6350c78b5a46dbf5e0cf3eb4785d6ceac5090d |
from net import NeuralNet
import numpy as np
#TODO(Wesley) More tests
class TestNeuralNet(object):
def test_zero_system(self):
net = NeuralNet(3, 2, 4, 1, seed=0)
net.weights = [ np.zeros((3,4)),
np.zeros((4,4)),
np.zeros((4,4)),
... | WesleyAC/toybox | neuralnets/net_test.py | Python | mit | 526 | [
"NEURON"
] | d5d5e0bf1751021420aed2024f45167db89be9efb1f81423922e66bf18ff2234 |
# -*- coding: utf-8 -*-
# Copyright (C) 2010-2016 Bastian Kleineidam
#
# 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.
#... | wummel/patool | patoolib/__init__.py | Python | gpl-3.0 | 31,283 | [
"ADF"
] | 681bda0d66e98394d55906e5bb8fb9bae13fef8365b02bf8bdf68f33e89c952d |
from bs4 import BeautifulSoup
from collections import defaultdict
from operator import itemgetter
import urllib
import urllib2
import cookielib
import re
import time
import requests
import sys
class RepReader:
def __init__(self, username, password):
self.username = username
self.password = passwor... | rbonick/care-tags_scripts | care_tags_repmeter/repreader.py | Python | mit | 8,433 | [
"VisIt"
] | 68c0558cdf687c163b309a0dceec59e864fa840dd50e4d89164024441dfa1606 |
#!/usr/bin/env python
#coding=utf-8
# modifyDate: 20120808 ~ 20120810
# 原作者为：bones7456, http://li2z.cn/
# 修改者为：decli@qq.com
# v1.2，changeLog：
# +: 文件日期/时间/颜色显示、多线程支持、主页跳转
# -: 解决不同浏览器下上传文件名乱码问题：仅IE，其它浏览器暂时没处理。
# -: 一些路径显示的bug，主要是 cgi.escape() 转义问题
# ?: notepad++ 下直接编译的server路径问题
"""
简介：这是一个 python 写的轻量级的文件共享服务器（基于... | yuuagh/pywork | testserver/1.py | Python | gpl-3.0 | 14,241 | [
"VisIt"
] | 6e4f2f0e5869f4395d2238913b0e2313fbfccdaf6db6fc3e037d824663f06426 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
'''Pychemqt, Chemical Engineering Process simulator
Copyright (C) 2009-2017, Juan José Gómez Romera <jjgomera@gmail.com>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Softwar... | jjgomera/pychemqt | UI/viewComponents.py | Python | gpl-3.0 | 85,199 | [
"Pybel"
] | 3c5a66b251b1b2be8f991e6e4da210ea89953328d2deab683507b6326141bc2e |
import glob
import pandas as pd
import numpy as np
pd.set_option('display.max_columns', 50) # print all rows
import os
os.chdir("/gpfs/commons/home/biederstedte-934/evan_projects/correct_phylo_files")
normalB = glob.glob("binary_position_RRBS_normal_B_cell*")
mcell = glob.glob("binary_position_RRBS_NormalBCD19pCD27... | evanbiederstedt/RRBSfun | trees/chrom_scripts/normal_chr08.py | Python | mit | 25,843 | [
"MCell"
] | abfa30a3815bae8b68095ec3bd346d9c7b0b23da055b057ebd67fa60f7c30b90 |
# -*- coding: utf-8 -*-
import time
import numpy as np
from pyodesys import ODESys as _ODESys
from pyodesys.results import Result
from chempy.units import get_derived_unit, unitless_in_registry, uniform, patched_numpy as pnp
from .integrate import run
from ._chemreac import cvode_predefined_durations_fields
class ODE... | chemreac/chemreac | chemreac/_odesys.py | Python | bsd-2-clause | 4,778 | [
"ChemPy"
] | 2050c77ebf6f818559bcdbf1120f51a52a2cce76e6db2dfcfd2dade309e0eb4a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module implements more advanced transformations.
"""
__author__ = "Shyue Ping Ong, Stephen Dacek"
__copyright__ = "Copyright 2012, The Materials Pro... | sonium0/pymatgen | pymatgen/transformations/advanced_transformations.py | Python | mit | 24,299 | [
"pymatgen"
] | decdfc3ff8c585a94d0d0fe4d31f64bbea09b07d4aada38af56098078f317335 |
#!/usr/bin/python3
########################################################################
# Solves problem 183 from projectEuler.net.
# Calculates the sum of the results of a special function from 5 to
# 10000.
# Copyright (C) 2011 Santiago Alessandri
#
# This program is free software: you can redistribut... | sanSS/programming-contests | project-euler/problem183.py | Python | gpl-3.0 | 1,641 | [
"VisIt"
] | d854c6f28cd1636d089dabf281218bd0b9d399c90ccce87426b4a5e1e1897858 |
#!/usr/bin/env python
# Processes uploads from the user.
# WARNING: Changes in this tool (particularly as related to parsing) may need
# to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools
import codecs
import gzip
import os
import shutil
import sys
import tempfile
import urllib
import zipfile
fro... | lappsgrid-incubator/docker-galaxy-lappsgrid | tools/data_source/upload.py | Python | apache-2.0 | 20,474 | [
"Galaxy"
] | e483f4cd430ad80dad0216025277c15c1327a696929abd335fe687fb680fb52d |
#!/usr/bin/python
"""
Created on Tue Apr 19 19:30:34 2016
@author: noel
"""
import sys
# For debugging in spyder
sys_path = '/home/noel/Projects/Protein_design/EntropyMaxima/src'
charmmdir = '/home/noel/Projects/Protein_design/EntropyMaxima/params/charmm27.ff/'
is_in_path = False
for i in sys.path:
if i == sys_pat... | noelcjr/EntropyMaxima | em/in_development/join_insulin_linker.py | Python | gpl-3.0 | 17,414 | [
"CHARMM"
] | 25c3f1d063c91420b0ff5ff1515f476a849cb5692ef38654d388efc822dddfde |
# coding: utf-8
# In[4]:
from __future__ import division
from sys import stdout
import numpy as np
import networkx as nx
from sklearn.metrics.pairwise import euclidean_distances
from sklearn.metrics import pairwise_distances_argmin_min
import matplotlib.pyplot as plt
from itertools import repeat
from Queue imp... | DavidMcDonald1993/ghsom | ghsom_paralleI_signal_frequency.py | Python | gpl-2.0 | 20,000 | [
"NEURON",
"VisIt"
] | df5a7ad0d094f99287755d1abe2c84def512d2d099422bead0df418db12b0363 |
"""
ltdexec.processor.validator
===========================
Validator classes verify that the raw source code or abstract syntax tree is
permissible before it is finally compiled to Python byte code. They signal
errors through exceptions, which may be used to provide an error message.
"""
import ast
import re
from... | dpwhite2/limitedexec | ltdexec/processor/validator.py | Python | bsd-2-clause | 10,093 | [
"VisIt"
] | d5882c15de09abac6facd70fe26e1bf189f8629bb3e1286aff03a7b24421e47e |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
# Disable the "wildcard import" warning so we can bring in all methods from
# course helpers and ui helpers
# pylint: disable=wildcard-import
# Disable the "Unused import %s from wildcard import" warning
# pylint: disable=unused-wildcard-impor... | Stanford-Online/edx-platform | common/djangoapps/terrain/steps.py | Python | agpl-3.0 | 7,378 | [
"VisIt"
] | ebf591951e010979a4d52e447a6f40c9354f71d72841a76b8c20eeb82d84ed89 |
__auther__='Jorgen Grimnes, Sudhanshu Patel'
from sklearn import datasets
import numpy as np
from activation_functions import sigmoid_function, tanh_function, linear_function,\
LReLU_function, ReLU_function, symmetric_elliot_function, elliot_function
from neuralnet import NeuralNet
... | sudhanshuptl/python-neural-network | Iris_Data_Backprop/main.py | Python | bsd-2-clause | 2,498 | [
"NEURON"
] | 04d9abfc7a2bf588392ac431dc0d0080e7a4474857e08151ea6a30ff5cb78a11 |
"""Interactive Dashboard Toolkit."""
__version__ = '0.11.1-dev'
from bowtie._app import App, View
from bowtie._command import command
from bowtie.pager import Pager
from bowtie._cache import cache
def load_ipython_extension(ipython):
"""Enable IPython extension."""
from bowtie._magic import BowtieMagic
... | jwkvam/bowtie | bowtie/__init__.py | Python | mit | 358 | [
"Bowtie"
] | c1fdaa28e9d9dd715a842bf847013d45e60b9103da6df13f5eb101a203666c40 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Jerome Rapinat, B. Malengier
# Copyright (C) 2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public ... | prculley/gramps | gramps/plugins/quickview/lineage.py | Python | gpl-2.0 | 8,503 | [
"Brian"
] | 0ea2263f1a72e53a4abc53fd69062658fdac1add5dd44767a5915170172a8c12 |
"""
ioHub
.. file: ioHub/examples/simple/simpleTest.py
Copyright (C) 2012 Sol Simpson
Distributed under the terms of the GNU General Public License (GPL version 3 or any later version).
.. moduleauthor:: Sol Simpson <sol@isolver-software.com> + contributors, please see credits section of documentation.
.. fileauthor:... | peteristhegreat/ioHub | examples/simpleEyeTracker/simpleTrackerTest.py | Python | gpl-3.0 | 11,713 | [
"Gaussian"
] | 0b666148658abf548a5d28bcc5388bb5aaaf1923daac3f175fc4a4569cbe7cc1 |
"""
Provides rolling statistical moments and related descriptive
statistics implemented in Cython
"""
from __future__ import division
import warnings
import numpy as np
from pandas import lib
from pandas.core.api import DataFrame, Series
from pandas.util.decorators import Substitution, Appender
__all__ = ['rolling_co... | pjryan126/solid-start-careers | store/api/zillow/venv/lib/python2.7/site-packages/pandas/stats/moments.py | Python | gpl-2.0 | 30,509 | [
"Gaussian"
] | d7265e05b69370e0fc0dcb131d05c4b50c71205b4272dc6a181444a57e532850 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015, imageio contributors
# imageio is distributed under the terms of the (new) BSD License.
# flake8: noqa
"""
Imagio is plugin-based. Every supported format is provided with a
plugin. You can write your own plugins to make imageio support
additional formats. And we would be... | kerimlcr/ab2017-dpyo | ornek/imageio/imageio-2.1.2/imageio/plugins/__init__.py | Python | gpl-3.0 | 3,665 | [
"ASE"
] | bce19275ba8aa00dc24f45b14cd6fe4b3ba8a854320cb1530f83fab83a843c1e |
import sys
import argparse
import logging
import os
from Bio import SeqIO, AlignIO
from Bio.SeqRecord import SeqRecord
import subprocess
import time
import math
from mypyli import samparser
logging.basicConfig()
LOG = logging.getLogger()
LOG.setLevel("DEBUG")
class QueryMapper(object):
def __init__(self, query... | hunter-cameron/Bioinformatics | job_scripts/omri/find_conserved_regions.py | Python | mit | 36,800 | [
"BWA"
] | 5c0a5f7435416573241088b446ce48778f81670f82679fadb147d891785556dd |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-delete
# Author : Stuart Paterson
########################################################################
"""
Peek StdOut of the given DIRAC job
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Cor... | andresailer/DIRAC | Interfaces/scripts/dirac-wms-job-peek.py | Python | gpl-3.0 | 1,119 | [
"DIRAC"
] | 23c134c0c3e84a894bfd75dcd230ab249f86476140ae3110a6621c2dea7fa52c |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# read in a Chaco file
chReader = vtk.vtkChacoReader()
chReader.SetBaseName(VTK_DATA_ROOT + "/Data/vwgt")
chReader.SetGenerateGlobalElementIdArray(1)
chReader.SetGenerateGlobalNodeIdA... | collects/VTK | IO/Geometry/Testing/Python/TestChacoReader.py | Python | bsd-3-clause | 1,163 | [
"VTK"
] | a12a0dd515e4ed7811168abc7ab77f4c1d3485fde86fa8a3c1faad7d1785e6a5 |
"""
:mod:`pyffi.formats.nif` --- NetImmerse/Gamebryo (.nif and .kf)
===============================================================
Implementation
--------------
.. autoclass:: NifFormat
:show-inheritance:
:members:
:undoc-members:
Regression tests
----------------
These tests are used to check for functio... | griest024/PokyrimTools | pyffi-develop/pyffi/formats/nif/__init__.py | Python | mit | 310,538 | [
"VisIt"
] | 8420a1433cac51f3b0c47011dea0193c84de22df2ddd891b5c6d8b5f58ebf91e |
#!/usr/bin/env python3
#
# Copyright (C) 2018-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | KaiSzuttor/espresso | maintainer/gh_post_style_patch.py | Python | gpl-3.0 | 3,237 | [
"ESPResSo"
] | 0a2a07990666f4430c0fbffab26c2644a7d206e7c88e88e950702a656bbeba53 |
from galaxy.web.base.controller import *
from galaxy.web.framework.helpers import time_ago, iff, grids
from galaxy import util
from galaxy.model.mapping import desc
from galaxy.model.orm import *
from galaxy.util.json import *
from galaxy.util.odict import odict
from galaxy.tags.tag_handler import TagHandler
from sqlal... | volpino/Yeps-EURAC | lib/galaxy/web/controllers/history.py | Python | mit | 51,819 | [
"Galaxy"
] | ae3a2dedec834eee8f0a45cd79dd95bbe00b48984094f1d22973ef7fe165d5dd |
# author: brian dillmann
# for rcsc
import RPi.GPIO as GPIO
class Output:
def __init__(self, name, loc, invert = False):
if not isinstance(loc, (int, long)):
raise TypeError('Output Location must be an integer')
if not name.replace(' ', '').isalnum():
raise ValueError('Device names mu... | dillmann/rscs | lib/Devices/Output.py | Python | mit | 648 | [
"Brian"
] | 0d743842b267d6c96a72e5074316dd63dd994f1746bb4c83bb2da9e1320170e7 |
#!/usr/local/bin/python
import numpy as np
import scipy.signal
import matplotlib
render = True
if render:
matplotlib.use('pgf')
import matplotlib.pyplot as plt
def gaussian(t, o):
return np.exp(-np.square(t) / (2.0 * np.square(o)))
def sin_modulated_gaussian(t, o):
return -gaussian(t, o) * np.sin(t / o... | reuk/waveguide | scripts/python/kernels/kernels.py | Python | gpl-2.0 | 4,812 | [
"Gaussian"
] | 22c20f153813d301adde033232eb5d6af615e8698a89ca71a5b3d3d60b669b36 |
#
# Copyright (C) 2007, Mark Lee
#
#http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required... | steckdenis/rlglue-py3 | rlglue/environment/EnvironmentLoaderScript.py | Python | apache-2.0 | 1,728 | [
"Brian"
] | f19f91367da1e8a4c5b72d9cc0c8e16a9177f063cdf12e6de1274d4a84ec3d69 |
"""
This example shows how to plot data on rectangular 2D grids
(grids that are not rectlinear in geographic or native map projection
coordinates).
An example of such a grid is the 'POP' grid which is used in
the ocean component NCAR Community Climate System Model (CCSM).
"POP" stands for "Parallel Ocean Program", whi... | raincoatrun/basemap | examples/ccsm_popgrid.py | Python | gpl-2.0 | 2,812 | [
"NetCDF"
] | 23de13ee69bb75a875f5648be5ad498b8fb0af1ef0880ceaee468605f9de6fca |
import vtk
import math
import numpy as np
from core.settings import Settings
class UPoint:
def __init__(self, p, dist_to_closest_point):
self.p = p
self.dist_to_closest_point = dist_to_closest_point
def compute_energy(self):
diff = self.dist_to_closest_point - Settings.inter_neuron_distance
if... | zibneuro/brainvispy | generators/uniformpointcloud.py | Python | bsd-3-clause | 2,947 | [
"VTK"
] | c1c23b389814d30d4b2b16b0aa8e0e47e84634dbd8d3d44859379991be3cfff0 |
# -*- coding: utf-8 -*-
"""
Created on Mon Feb 17 18:23:40 2014
@author: fbaraba
"""
import numpy as np
from scipy.special import erf
from scipy.optimize import minimize
from scipy.ndimage import label
from scipy.ndimage.filters import convolve, maximum_filter
from scipy.ndimage.measurements import maximum_position,... | fedebarabas/tormenta | tormenta/analysis/maxima.py | Python | gpl-3.0 | 21,514 | [
"Gaussian"
] | 2814f13ff2635024833723828a229b04c5363df15c69a154e048a3a6cc623bc4 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Read some Fluent GAMBIT in ASCII form
reader = vtk.vtkGAMBITReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/prism.neu")
mapper = vtk.vtkDataSetMapper()
mapper.SetInputC... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/IO/Geometry/Testing/Python/TestGAMBITReader.py | Python | gpl-3.0 | 836 | [
"VTK"
] | 1cbefc356c077cd898e2e195452b6d34448ed8370596ac3b1d54966a44fce06a |
import argparse
import sys,logging,shutil
from rdkit import Chem
from rdkit.Chem import AllChem
import magma
def main():
"Entry point for magma script"
magmacommand = MagmaCommand()
return magmacommand.run()
class MagmaCommand(object):
"""Console script with multiple sub-commands to perform MAGMa calc... | NLeSC/MAGMa | job/magma/script/__init__.py | Python | apache-2.0 | 23,554 | [
"RDKit"
] | 721b32f017623c16283b49023e7d8cc75f67b6ae68e8c1db91c3e1e05b6f058e |
"""
Computational Neurodynamics
Exercise 1
Simulates the Hodgkin-Huxley neuron model using the RK4 method,
assuming a resting potential of 0mV, as in the 1952 paper. To get a
realistic resting potential of -65mV, refer to HHNeuronDemo.py
(C) Murray Shanahan et al, 2015
"""
import numpy as np
import matplotlib.pyplot... | pmediano/ComputationalNeurodynamics | Fall2016/Exercise_1/Solutions/HHNeuronRK4.py | Python | gpl-3.0 | 1,675 | [
"NEURON"
] | 1ce1cc856967f47a9bf243da6fdfa2485647ab14fe92d4acba4dc47901b70c92 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/common/views/common.py | Python | gpl-3.0 | 5,855 | [
"Brian"
] | ca2b27df976f17b1c84da27bf637b502c15af62f728744b60a465adcdf863c9f |
import logging
logger = logging.getLogger()
import itertools
import numpy as np
import scipy.stats
from fastkde import fastKDE
##======================================================================
##
# A domain which has a size and can be split, also can be checked
# for insideness
class Domain(object):
def i... | velezj/ml-chats | bayes_error_rate/code/bayes_error_rate.py | Python | apache-2.0 | 16,710 | [
"Gaussian"
] | 41c34700df64c53d3b8927613fbcd6602c7aa2cba9519a5c94795c508626f5ae |
#! A test of the basis specification. A benzene atom is defined using a ZMatrix containing dummy atoms
#! and various basis sets are assigned to different atoms. The symmetry of the molecule is automatically
#! lowered to account for the different basis sets.
import psi4
psi4.set_output_file("output.dat", False)
re... | lothian/psi4 | tests/python/mints2/input.py | Python | lgpl-3.0 | 4,186 | [
"Psi4"
] | d49941fc2e896c1709a3a602fbe9a087d071c5a27c1f0e80db78efce362b55f9 |
# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from .model import Model
from .parameterization.variational import VariationalPosterior
from .mapping import Mapping
from .. import likelihoods
from .. import kern
from ..inference.l... | SheffieldML/GPy | GPy/core/gp.py | Python | bsd-3-clause | 34,986 | [
"Gaussian"
] | 21afc1ee742b2e9341b479a2a46e0a05f3b182243743dfdfedcff31f95769031 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/vasp/test_lsorbit.py | Python | gpl-3.0 | 2,556 | [
"CRYSTAL",
"VASP"
] | 2c8b65a0b8b1de142c38f68a732a4373bcb807cea65a64126fefbf1e594baf81 |
"""
Created on Dec 27, 2017
@author: tjoneslo
"""
import logging
import argparse
import os
from .Galaxy import Galaxy
from .WikiReview import WikiReview
from wikitools.page import Page
logger = logging.getLogger('WikiCreateWorlds')
class WikiCreateWorld(object):
"""
classdocs
"""
page_template = ''... | makhidkarun/traveller_pyroute | PyRoute/WikiCreateWorlds.py | Python | mit | 11,445 | [
"Galaxy"
] | 8253f67039559939390b72b1da38222e2e5474fb8bf9a2f205984dce23fb062c |
import time
from typing import Callable, Dict, List, Tuple
import GPy
import nearestPD
import numpy as np
import scipy.linalg as la
from GPy.inference.latent_function_inference.expectation_propagation import posteriorParams # , gaussianApproximation
from GPy.inference.latent_function_inference.posterior import Poster... | EmuKit/emukit | emukit/examples/preferential_batch_bayesian_optimization/pbbo/inferences/ep_batch_comparison.py | Python | apache-2.0 | 23,757 | [
"Gaussian"
] | fc9c21c05962a676c61d357fb813ab46fb32a3e7a9f21408bef6face7e614fb4 |
from slimscat import generate_screen,run_slimscat
import matplotlib.pyplot as plt
import numpy as np
import os
# gaussian source
nx,ny = 220,256
yy,xx = np.meshgrid(np.arange(ny)-ny/2,np.arange(nx)-nx/2,indexing='ij')
isrc = np.exp(-0.5*(xx**2 + yy**2) / (0.07*np.min([nx,ny]))**2)
# generate screen
if not os.path.isf... | krosenfeld/slimscat | examples/gaussian.py | Python | mit | 739 | [
"Gaussian"
] | 2a00dfb15cc6081e92ef3340596ed76fdbe1171e874c4c86003bae7493a04de7 |
import os
import sys
from pathlib import Path
from setuptools import find_packages, setup
from setuptools.command.install import install
VERSION = Path(Path(__file__).parent, "quilt3", "VERSION").read_text().strip()
def readme():
return """\
Quilt manages data like code (with packages, repositories, browsing an... | quiltdata/quilt | api/python/setup.py | Python | apache-2.0 | 3,090 | [
"VisIt"
] | 77044a750a7444fca898312d31e60b6313f3cad23af97530182ee247be32729e |
# tests 19958 weighted paths of log-transformed Wnt pathway
plRead = open("Wnt-weighted-paths-pathlinker.txt", "r")
csRead = open("Wnt-weighted-paths-cytoscape.txt", "r")
# dict that stores path: weight
pl = {}
epsilon = 0.0001
def sameFloat(a, b):
return abs(a - b) <= epsilon
for line in plRead:
if line[0] == '... | tmmurali/PathLinker | data/Wnt/test-files/Wnt-weighted-paths-comparison.py | Python | gpl-3.0 | 705 | [
"Cytoscape"
] | 207099135306259094862812ced4d5990634a24431c9326398ac79a4553c323a |
from galaxy.web.base.controller import *
class Mobile( BaseController ):
@web.expose
def index( self, trans, **kwargs ):
return trans.fill_template( "mobile/index.mako" )
@web.expose
def history_list( self, trans ):
return trans.fill_template( "mobile/history/list.mako" )
... | dbcls/dbcls-galaxy | lib/galaxy/web/controllers/mobile.py | Python | mit | 2,461 | [
"Galaxy"
] | ecb43d57508c84cfdb3d2d7889ccacfe9f0bc3ab950b3791ac225b0b2dee265b |
# -*- coding: utf-8 -*-
#############################################################################
# SRWLIB Example: Virtual Beamline: a set of utilities and functions allowing to simulate
# operation of an SR Beamline.
# The standard use of this script is from command line, with some optional arguments,
# e.g. for ... | mrakitin/sirepo | tests/template/srw_import_data/srx.py | Python | apache-2.0 | 35,268 | [
"CRYSTAL"
] | 5e372a20c6250116394fa5ec543497edb2f9acf7f81b7a6cae9fe4d23a90720c |
""" This module contains various functions that are special cases
of incomplete gamma functions. It should probably be renamed. """
from __future__ import print_function, division
from sympy.core import Add, S, C, sympify, cacheit, pi, I
from sympy.core.function import Function, ArgumentIndexError
from sympy.func... | wolfram74/numerical_methods_iserles_notes | venv/lib/python2.7/site-packages/sympy/functions/special/error_functions.py | Python | mit | 66,870 | [
"Gaussian"
] | 60eced4168730a28708ee02d411cc6b85cadd2f1b2429ed2c9e9794653fca5db |
#!/usr/bin/env python
import IMP
import IMP.core
import IMP.atom
import IMP.algebra
import IMP.test
import numpy as np
import numpy.random
from math import cos, sin, pi, sqrt, exp, log
def create_test_points(mu, radii):
testers = [[mu[0], mu[1], mu[2]]]
for i in range(3):
t = mu[:]
t[i] += ra... | shanot/imp | modules/core/test/test_gaussian.py | Python | gpl-3.0 | 5,497 | [
"Gaussian"
] | 88b71b609762815e65d5dcd4b1930817d0a6efcf72ac1c04b844c89260c5c63a |
# 31.05.2007, c
# last revision: 25.02.2008
from __future__ import absolute_import
from sfepy import data_dir
filename_mesh = data_dir + '/meshes/2d/circle_sym.mesh'
material_1 = {
'name' : 'coef',
'values' : {
'val' : 1.0,
},
}
material_2 = {
'name' : 'm',
'values' : {
'K' : [[1.0... | vlukes/sfepy | tests/test_laplace_unit_disk.py | Python | bsd-3-clause | 3,356 | [
"VTK"
] | f983bdfbcb907badcb7270ae93c4e00be63ef1d520f5b08f172bb44a9bd0c6fc |
#!/usr/bin/env python
################################################################################
#
# qnex_combine.py
#
# QE NEXAFS post-processor.
#
################################################################################
#
# Copyright 2015 Kane O'Donnell
#
# This library is free software: you can red... | HSINWEI/physics | python/qnex_combine.py | Python | gpl-3.0 | 20,473 | [
"CRYSTAL",
"Quantum ESPRESSO"
] | 941ac61b759da86d304299e369d87d81990c70c2f77510913b99884a0c79988b |
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpatterns = [
url(r'^$', TemplateView.as_view(template_name='page... | kamilski81/cookie_cutter_sample | config/urls.py | Python | mit | 1,560 | [
"VisIt"
] | 2dcabe47fb2f29cb4b3207dc331054a53e18eb168a10ea2134b35b7c77f0d108 |
"""
(This script is independent from lfc_dfc_copy)
This script is used to migrate the content of the LFC DB to the DFC DB when used with Stored procedure and Foreign keys.
It won't work with the other schema. It is the central component of the migration.
* Please read the doc of each method in this script, there are... | vmendez/DIRAC | DataManagementSystem/Utilities/lfc_dfc_db_copy.py | Python | gpl-3.0 | 40,792 | [
"DIRAC"
] | 317a8fa42fec301b337093d0c21ab4ad6f108a41741a6d9f40f73a7627d7f4ab |
# -*- coding: utf-8 -*-
#
# gap_junctions_inhibitory_network.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... | alberto-antonietti/nest-simulator | pynest/examples/gap_junctions_inhibitory_network.py | Python | gpl-2.0 | 5,989 | [
"NEURON"
] | a8d6b6a59b5c01717bf48dcfc08613ff27b5e4c68d2155020e10e77dafa131f5 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
from math import pi
import sys
import numpy as np
from numpy.fft import fftn, ifftn, fft2, ifft2
from ase.parallel import parprint
from gpaw.transformers import Transformer
from gpaw.fd_operators import Laplace, LaplaceA,... | robwarm/gpaw-symm | gpaw/poisson.py | Python | gpl-3.0 | 19,920 | [
"ASE",
"GPAW",
"Gaussian"
] | cf1b959fc60fc9fa4b78ecc9e091dc7841c27c01437e34261235106e9baa04d1 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Routines to get corrected p-values estimates, based on the observations.
It implements 3 approaches:
- Benjamini-Hochberg FDR: http://en.wikipedia.org/wiki/False_discovery_rate
- a class that fits a G... | bthirion/nipy | nipy/algorithms/statistics/empirical_pvalue.py | Python | bsd-3-clause | 19,083 | [
"Gaussian"
] | 868b6dfba6be9fef4142580ce4ece3011896894749bfb818db3843b463c8c5b9 |
# -*- coding: utf-8 -*-
# Copyright 2019-2022 Mike Fährmann
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 as
# published by the Free Software Foundation.
"""Extractors for 4chan archives based on FoolFuuka"""
from .common imp... | mikf/gallery-dl | gallery_dl/extractor/foolfuuka.py | Python | gpl-2.0 | 10,807 | [
"MOE"
] | fc0b291589456b7be612b22010e4a005dcac77f88b2e56f22e61ce0cec017807 |
#!/usr/bin/env python
# CREATED:2013-03-08 15:25:18 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa.feature (feature.py)
#
# Run me as follows:
# cd tests/
# nosetests -v
#
# This test suite verifies that librosa core routines match (numerically) the output
# of various DPWE matlab implementations o... | yunque/librosa | tests/test_filters.py | Python | isc | 10,114 | [
"Brian"
] | fb010be5cb0f22b84c074bacbba78dcb0770849d16eded1e6c730e4874ce262f |
'''
Individual stages of the pipeline implemented as functions from
input files to output files.
The run_stage function knows everything about submitting jobs and, given
the state parameter, has full access to the state of the pipeline, such
as config, options, DRMAA and the logger.
'''
from utils import safe_make_di... | bjpop/fampipeline | src/stages.py | Python | bsd-3-clause | 18,097 | [
"BWA"
] | cffe5ade2a11a41c4a18ac96896ec67fe2e77d2f252cfd774ab421cc686772c1 |
#########################################################################################
# OAR.py
# 10.11.2014
# Author: Matvey Sapunov, A.T.
#########################################################################################
""" OAR.py is a DIRAC independent class representing OAR batch system.
OAR objects... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/OAR.py | Python | gpl-3.0 | 8,866 | [
"DIRAC"
] | 8db26282cfb7ddae2f279b8581e974fbbb36c2df75d31e854fe71a5ac791eee4 |
#!/usr/bin/python
# Copyright 2017 Giorgia Fenoglio
#
# This file is part of NNsTaxonomicResponding.
#
# NNsTaxonomicResponding 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,... | gfbfenoglio/NNsTaxonomicResponding | DCNN/ExtractActivations.py | Python | gpl-3.0 | 14,260 | [
"NEURON"
] | f2f6cd742b4ac60a6025f6c3aea46a35cbffef9919348c816f5602975aa717ce |
# -*- coding: utf-8 -*-
# test ASE3 eos vs ASE2' on EMT Al bulk
import numpy as np
from ase.test import NotAvailable
try:
import scipy
except ImportError:
raise NotAvailable('This needs scipy module.')
from ase.lattice import bulk
from ase.io.trajectory import Trajectory
from ase.calculators.emt import EM... | suttond/MODOI | ase/test/eos.py | Python | lgpl-3.0 | 6,183 | [
"ASE"
] | 9851bf570673e2e54ebc0aad4d07059305426102806b01ef3031454b8c53e2ef |
#! /usr/bin/env python
# VTK polydata file format. References?
import tempfile
import struct
import logging
modeR = 'rb'
modeW = 'wb'
def reader(file):
raise ValueError, "Module "+`__name__`+" does not define a reader method"
def writer(file, reader):
if not reader.indexed:
reader = generic.soup2indexed(reade... | rassouldmb/meshconvert | src/meshconvert/vtk.py | Python | gpl-3.0 | 2,175 | [
"VTK"
] | e310aea06f036a440fb41073e6bc37cca078db40e7c1752870b3d81641d31ac2 |
# sql/compiler.py
# Copyright (C) 2005-2011 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`~sql... | jokajak/itweb | data/env/lib/python2.6/site-packages/SQLAlchemy-0.6.7-py2.6.egg/sqlalchemy/sql/compiler.py | Python | gpl-3.0 | 60,679 | [
"VisIt"
] | cf41ac0e66d3bd80041de17c306f8a8299c8bae0ac486940834ef7363709757a |
import os
from markdown.util import etree
import logging
log = logging.getLogger(__name__)
import MooseDocs
from markdown.inlinepatterns import Pattern
from MooseCommonExtension import MooseCommonExtension
class MooseImageFile(MooseCommonExtension, Pattern):
"""
Markdown extension for handling images.
Usage:
... | paulthulstrup/moose | python/MooseDocs/extensions/MooseImageFile.py | Python | lgpl-2.1 | 2,356 | [
"MOOSE"
] | 78bc325c304bc129d7b17b2ac77265ba35d7639e601d2264796713975ab13fc9 |
# -*- coding: utf-8 -*-
# (c) 2016, Adrian Likins <alikins@redhat.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 you... | ilpianista/ansible | test/units/cli/test_galaxy.py | Python | gpl-3.0 | 52,341 | [
"Galaxy"
] | ceb3668a106f700b425cd8db8a9d98a96d32d30008e57c49b82190a5b65be82d |
# 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 Kassiopeia(CMakePackage):
"""Simulation of electric and magnetic fields and particle track... | iulian787/spack | var/spack/repos/builtin/packages/kassiopeia/package.py | Python | lgpl-2.1 | 2,937 | [
"VTK"
] | d5389c6f5686d125d672611642cebe737f661a6b23465e70aaa61bc29c3fb2f1 |
################################################################################################################
# Tool for mapping primers and annotating fasta and fastq sequences #
# ... | Ambuj-UF/PrimerCheck | PrimerCheck.py | Python | gpl-3.0 | 26,714 | [
"BLAST"
] | f09b1604a5b6d2608ea24228ace673114cd7553bad6eb678241af3cea28999e8 |
r"""
Ordination results format (:mod:`skbio.io.ordination`)
======================================================
.. currentmodule:: skbio.io.ordination
The ordination results file format (``ordination``) stores the results of an
ordination method in a human-readable, text-based format. The format supports
storing t... | Achuth17/scikit-bio | skbio/io/ordination.py | Python | bsd-3-clause | 14,460 | [
"scikit-bio"
] | 49171d97b54bdfaea60ce796a34372bede99ed0208fd26845351ea48c72c3a33 |
maxCorner = (10,10,10)
center = (5,5,5)
normal = (1,1,1)
from yade import pack, export
pred = pack.inAlignedBox(Vector3.Zero,maxCorner)
O.bodies.append(pack.randomDensePack(pred,radius=1.,rRelFuzz=.5,spheresInCell=500))
export.text('/tmp/test.txt')
# text2vtk and text2vtkSection function can be copy-pasted from yade/... | yade/trunk | examples/test/paraview-spheres-solid-section/export_text.py | Python | gpl-2.0 | 715 | [
"ParaView",
"VTK"
] | 9a53d95f08a145e09b7f6591065acc2b82662db70a8f1678327b775e20802716 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import time
from translate.storage import po
from translate.storage import poxliff
from translate.storage import poheader
from translate.misc.dictutils import ordereddict
from translate.misc import wStringIO
from translate.lang.team import guess_language
def t... | lehmannro/translate | storage/test_poheader.py | Python | gpl-2.0 | 10,219 | [
"MOE"
] | 2ec5b361e018e4940c6d23e45e5acccb5b889dac05dd37c6610ef5288482ac89 |
#!/usr/bin/env python
# This file is part of ppnc.
# ppnc Copyright (C) 2015 University of Cambridge
# Ppnc is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at y... | rcurr/ppnc | config/global_attrs.py | Python | gpl-3.0 | 6,733 | [
"NetCDF"
] | af5b667072e83f97f446f4c856fc3faffdc9ee69f9a1e3b6e804f98a362739d4 |
# -*- coding: utf-8 -*-
from setuptools import setup, find_packages
from subprocess import check_output, CalledProcessError
install_requires = [
"argparse>=1.2.1",
"texttable>=0.8.1",
"lxml",
"python-dateutil",
"pytz"
]
version = "1.1.11"
setup(
name='uws-client',
version=version,
url... | aipescience/uws-client | setup.py | Python | apache-2.0 | 1,487 | [
"VisIt"
] | 077948fe988498270e964c04106b31578e2c97a7f8692e2701285e3bd6d9fb41 |
# -*- coding: utf-8 -*-
''' Plots used probabilities for step and spiral growth. '''
import numpy as np
import matplotlib.pyplot as plt
from crystal import *
e = Crystal(100, 100, mode="step")
f = Crystal(100, 100, mode="spin")
x = np.linspace(0, 4, 1000)
y = np.zeros(x.size)
y2 = np.zeros(x.size)
for i in range(x.... | roesel/growth | plot_probabilities.py | Python | cc0-1.0 | 817 | [
"CRYSTAL"
] | 68a9dcf46545436607c3c9b5610cb1073ac4669b10bb64bcaf50c53e027e2618 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/people/lookups.py | Python | gpl-3.0 | 3,699 | [
"Brian"
] | 112ec87020601bad5f8b74d5eff2fb28c76c3bd470febf57731ac4d772a1c16a |
"""Simple molecular dynamics.
A block of 27 cubic unit cells of Cu is set up, a single atom is given
a significant momentum, and constant energy molecular dynamics is
performed.
"""
from numpy import *
from asap3 import Atoms, EMT, units
from ase.visualize.primiplotter import *
from ase.lattice.cubic import FaceCent... | auag92/n2dm | Asap-3.8.4/Examples/PlottingMD.py | Python | mit | 1,071 | [
"ASE",
"NetCDF"
] | ca6355a1c2d8855583c51d2df5fa7684c49cdc47fd64459bfa6476aa5ec47004 |
# -*- coding: utf-8 -*-
#
# Emit documentation build configuration file, created by
# sphinx-quickstart on Thu Jan 3 19:10:48 2013.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All co... | BrianHicks/emit | docs/conf.py | Python | mit | 7,776 | [
"Brian"
] | 88be6664e7463116ce9e966cd4b9ce06da600f2e777cba3b74cd38acfa4e13e6 |
import math
from utils import functionalTesting
from utils import loadData
# read - https://web.stanford.edu/~jurafsky/slp3/9.pdf
# Dataset - https://archive.ics.uci.edu/ml/datasets/Breast+Cancer+Wisconsin+(Diagnostic)
loadDataInstance = loadData()
functionalTestingInstance = functionalTesting()
# load data
datasetI... | snlpatel001213/algorithmia | bayesian/naiveBayes/naiveBayes.py | Python | gpl-3.0 | 7,269 | [
"Gaussian"
] | f03c43b38d1585d33f79ab226a7cf73ac62b04f88b1d2edd73dd4addc674f847 |
from behave import *
import json
import server as server
@given(u'the following customers')
def step_impl(context):
server.data_reset()
for row in context.table:
server.data_load({"first_name": row['first_name'],"last_name": row['last_name'], "id":row['id'],
"gender":row['gender'], "age":row['... | devops-alpha-s17/customers | features/steps/customer_steps.py | Python | apache-2.0 | 3,262 | [
"VisIt"
] | d6a1928094a0393b82135303eb9bf24e8e591eab3e554b2ceacbd3bac710f27b |
#
# Brian C. Lane <bcl@redhat.com>
#
# Copyright 2012 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use, modify,
# copy, or redistribute it subject to the terms and conditions of the GNU
# General Public License v.2. This program is distributed in the hope that it
# will be useful,... | atodorov/pykickstart | pykickstart/commands/unsupported_hardware.py | Python | gpl-2.0 | 1,968 | [
"Brian"
] | b88b2e27d343d2ff83b8e5e55207a87d5b2fb7c5dfece196aa2e9eec985ec00e |
import matplotlib.pyplot as plt
import numpy as np
import scipy.stats as stats
import scipy.misc
import cv2
import functools32
def pipeline(baseVoxel, neighborhood=1, lowerBound=1, upperBound=1):
pMap2DVox = generatepMap2D(generateForegroundVoxel(baseVoxel), neighborhood=neighborhood)
return generate3DPunctaMa... | NeuroDataDesign/pan-synapse | pipeline_1/code/functions/plosLib.py | Python | apache-2.0 | 3,094 | [
"Gaussian"
] | 3dbb78e6a4a5bf5614f27a7afd183eb0e93d3e527df4c42d6c4818e8580494d2 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2013, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | elkingtonmcb/nupic | src/regions/ImageSensorExplorers/Jiggle.py | Python | agpl-3.0 | 5,887 | [
"VisIt"
] | bf06fa50ad96f0abb3dd3dead2e92d09b20260316a2ab61dd782bb30072bb999 |
__author__ = 'Allison MacLeay'
import pandas as pd
import numpy as np
import os
import random
# import CS6140_A_MacLeay.utils
# import CS6140_A_MacLeay.utils.Stats as mystats
# import Stats as mystats
import sys
def load_and_normalize_housing_set_preserve_result_col():
path = '../data/housing'
test_file = "h... | alliemacleay/MachineLearning_CS6140 | utils/__init__.py | Python | mit | 11,402 | [
"Gaussian"
] | 4568c8b2d5b6b56a7c191949673777e81c892d5027d992c5fcbeec1a4d4a2cc3 |
#!/usr/bin/python -u
__version__ = '3.0.8'
"""Data collector/processor for Brultech monitoring devices.
Collect data from Brultech ECM-1240, ECM-1220, and GEM power monitors. Print
the data, save the data to database, or upload the data to a server.
Includes support for uploading to the following services:
* MyEne... | marclennox/btmon-docker | btmon.py | Python | apache-2.0 | 173,845 | [
"Brian"
] | 80d9a597f8e7218516e54f2fd1165bcbe80a8a360bed84f8e05172318ddbfa2e |
#
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option)... | Smiljanic/espresso | testsuite/python/particle.py | Python | gpl-3.0 | 5,617 | [
"ESPResSo"
] | 6717b84743746f77f06019bff850682cf3feefdb19b12f6b27850900bba20276 |
from plugin import Plugin
from glfw import *
from OpenGL.GL import *
from pyglui.cygl.utils import RGBA
from pyglui.cygl import utils as glutils
from pyglui.pyfontstash import fontstash as fs
from pyglui.ui import get_opensans_font_path
from collections import deque
import Image
import math
import numpy as np
import l... | GorkTheOrk/smooth_pursuit | Smooth_Pursuit_Test.py | Python | mit | 25,392 | [
"ORCA"
] | 6e7bfad7055434770e70cfc2d98857255fd5aa894704e05bee4f8c8de8409547 |
#
# Copyright (C) 2007, Mark Lee
#
# http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... | evenmarbles/rlglued | rlglued/agent/client.py | Python | bsd-3-clause | 5,383 | [
"Brian"
] | 10afa5c4c60d8bb489339ceaa89efd9c3fdc235cd8d463dd88ad56e21589be4e |
from __future__ import division, print_function, unicode_literals
# This code is so you can run the samples without installing the package
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
#
testinfo = "f 10 0.033, s, f 20 0.033, s, f 30 0.033, s, f 30 0.033, s, q"
tags = "particl... | google-code-export/los-cocos | test/test_particle_spiral.py | Python | bsd-3-clause | 978 | [
"Galaxy"
] | 3e85bc02ef47273861c2fd9bd3bd388a0c4591ded5571b912e85c7ba014b91ee |
import os
import re
from docutils import nodes
from sphinx import addnodes
from sphinx.errors import SphinxError
from sphinx.util import logging
import aplus_nodes
import directives.meta
import lib.yaml_writer as yaml_writer
import lib.html_tools as html_tools
import lib.toc_languages as toc_languages
from lib.revea... | Aalto-LeTech/a-plus-rst-tools | toc_config.py | Python | mit | 20,652 | [
"VisIt"
] | e4d1c1df2d7b84991ace897d824c7dd5959aa50265a6974c73a3f05e42424b95 |
"""Test lineshapes."""
# --- import --------------------------------------------------------------------------------------
import numpy as np
import WrightTools as wt
# --- test ----------------------------------------------------------------------------------------
def test_gaussian():
x = np.linspace(-2,... | wright-group/WrightTools | tests/kit/lineshapes.py | Python | mit | 1,668 | [
"Gaussian"
] | ce2655287dc692ddaf396eda90ab42081a5e844bf9c14a12bd83713a1ab3d8ab |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkPruneTreeFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vt... | chrisidefix/devide | modules/vtk_basic/vtkPruneTreeFilter.py | Python | bsd-3-clause | 483 | [
"VTK"
] | c44c7dc114dd9763a66f98108d4c1826250271a8dbf2aa566ed9028b05ed7f0f |
"""
Test helper functions and base classes.
"""
import inspect
import json
import unittest
import functools
import operator
import pprint
import requests
import os
import urlparse
from contextlib import contextmanager
from datetime import datetime
from path import Path as path
from bok_choy.javascript import js_defined... | tanmaykm/edx-platform | common/test/acceptance/tests/helpers.py | Python | agpl-3.0 | 31,347 | [
"VisIt"
] | 226362e07d9050e81841dad79dcea5724337cc1fed7ac679f6b707a4287ae144 |
"""
Linear dynamical system model for the AP text dataset.
Each document is modeled as a draw from an LDS with
categorical observations.
"""
import os
import re
import gzip
import time
import pickle
import operator
import collections
import numpy as np
from scipy.misc import logsumexp
from sklearn.feature_extraction.t... | HIPS/pgmult | experiments/ap_lds.py | Python | mit | 17,131 | [
"Gaussian"
] | 5ae2b367c8c7b60240c5462d0421c954bbe81ea391101a24d08cd5df34575370 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
from .periodic_table import Element, Specie, DummySpecie
from .composition import Composition
from .structure import Structure, IStructure, Molecule, IMolecule
from .lat... | matk86/pymatgen | pymatgen/core/__init__.py | Python | mit | 640 | [
"pymatgen"
] | 63a20780a8343ba25c14bb9c18c67c372ce0561e8d6a74934b7f1133a59a707d |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | mfwarren/CrewBank | config/urls.py | Python | mit | 1,601 | [
"VisIt"
] | 70c434bd9a9ed7a991c51b08752a4b7478dc8d20fa8f17594cba3e6e7f39ad65 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <headingcell level=1>
# Learning Programming Through Examples
# <rawcell>
# This is the IPython notebook. You access it through the browser window however it is actually a program running on the super-computer on Will's desk. I have done some work to make sure th... | JudoWill/ResearchNotebooks | LearningPython.py | Python | mit | 25,230 | [
"VisIt"
] | 46651b2dcabef43a4dae3e2ff4102e1436331366d31e4f17654d794d95047f9c |
import itertools
from ..error import GraphQLError
from ..language import ast
from ..language.printer import print_ast
from ..language.visitor import Visitor, visit
from ..type.definition import (
GraphQLInterfaceType,
GraphQLList,
GraphQLNonNull,
GraphQLObjectType,
GraphQLUnionType,
get_named_ty... | gabriel-laet/graphql-py | graphql/core/validation/rules.py | Python | mit | 36,028 | [
"VisIt"
] | 71c571a3e6077dc728419a6cbfac7b395f18ac88fa9d65bc79e24e7876de1d1c |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Feb 25 08:14:31 2020
@author: deborahkhider
Functions concerning wavelet analysis
"""
__all__ = [
#'cwt',
'wwz',
'xwc',
]
import numpy as np
import statsmodels.api as sm
from scipy import signal
from pathos.multiprocessing import Process... | LinkedEarth/Pyleoclim_util | pyleoclim/utils/wavelet.py | Python | gpl-3.0 | 93,806 | [
"Gaussian"
] | 91c090fc533292de100c1b109a5a9e3fb3658cb149dec477c1a5673577869408 |
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