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# -*- coding=utf-8 -*-
from __future__ import absolute_import, print_function, unicode_literals
import unittest
import numpy as np
import os
from chemfiles import Trajectory, MemoryTrajectory, Topology, Frame, UnitCell, Atom
from chemfiles import ChemfilesError
from _utils import remove_warnings
EXPECTED_XYZ_TRAJECT... | Luthaf/Chemharp-python | tests/trajectory.py | Python | mpl-2.0 | 4,929 | [
"Chemfiles"
] | 615b1493636443c3384c2083b04a451304e417a47b2e349e50024809cd81cb64 |
# ----------------------------------------------------------------------
# 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... | david-ragazzi/nupic | nupic/data/generators/distributions.py | Python | gpl-3.0 | 4,452 | [
"Gaussian"
] | a8bf1e8ef800d52258ce389bdec9b0d060297c975f31df3dace648df13207ec4 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Alexander Yang
#
# MDTraj is free software: you can redistribu... | rmcgibbo/mdtraj | mdtraj/formats/gsd.py | Python | lgpl-2.1 | 11,184 | [
"MDTraj"
] | fa65872b1869e79cdc30a5968eff32ea705de6f1835e20e5d20cda16bb62822d |
#! /usr/bin/python
'''
require install of ImcSdk (0.7.1)the script is to login CIMC server, and get the details of common & enabled hardware components, & health brief
[ CIMC hostname, Firmware, CPU, MEM, Server Model, Serial number, NIC card, storage controller and physical disks or onbroad SATA disks]
syntax: python ... | brucelok/ucs | cimc/get_cimc_hardware.py | Python | apache-2.0 | 8,669 | [
"Amber"
] | 3ee62e0c41c9fdaf6e362829ac92b313f454ec3eb2ff6919dbb42129b65b7b05 |
#
# Hailiang Zhang
# NIST & UTK
#
import sys
import os
import locale
import glob
import shutil
import h5py
import random
import numpy as np
import re
import sasmol.sasmol as sasmol
def process_preprocessor_yaml(file_yaml, mvars, scvars):
'''
'''
pdbfile = mvars.pdbfile
dcdfile = mvars.dcdfile
if ... | madscatt/zazzie_1.5 | trunk/sassie/calculate/capriqorn/capriqorn_utils.py | Python | gpl-3.0 | 5,574 | [
"VMD"
] | a3490a5051d7097c26b37e1138f824f5daebfba1a26850cb682fd1eda94abed5 |
#coverage:ignore
""" Compute lambda for double low rank factoriz. method of von Burg, et al """
import numpy as np
from openfermion.resource_estimates.molecule import pyscf_to_cas
def compute_lambda(pyscf_mf, df_factors):
""" Compute lambda for Hamiltonian using DF method of von Burg, et al.
Args:
py... | kevinsung/OpenFermion | src/openfermion/resource_estimates/df/compute_lambda_df.py | Python | apache-2.0 | 1,145 | [
"PySCF"
] | 3fd4723a32b1c702e81ebf436f9e471752d390b6867b0d889e712c696e0e525b |
__all__ = ['data', 'dirac','kernels']
| JohnCEarls/GPUDirac | gpudirac/device/__init__.py | Python | agpl-3.0 | 38 | [
"DIRAC"
] | d36a9cbc8269a5284cdbe3e08c5cf62400db7276be7dc78f2cce93c4f4ca0ace |
'''
Contains generic methods and information (musical keys, MIDI instrument names) to be used by all
MusicAgents in generation of their music.
'''
import pyknon, operator, numpy, random, nltk, math, re
from os import listdir
from os.path import isfile, join
from pyknon.music import NoteSeq, Rest
class MusicHelper:
... | Cabrill/CCMAS16 | music_util.py | Python | mit | 22,781 | [
"CRYSTAL"
] | 58e4aae65d5de95fbb715f130f8377d57b5747dbbd643251a596bad4a8e63784 |
# -*- coding:utf-8 -*-
#
# Copyright 2014 Hewlett-Packard Development Company, L.P.
#
# 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
#
# Unl... | austin987/bandit | bandit/core/node_visitor.py | Python | apache-2.0 | 11,638 | [
"VisIt"
] | cbacd997625eca08b5920b6f829727c7e73423244492d4775a33df706c465ac3 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/songs/forms/__init__.py | Python | gpl-2.0 | 3,331 | [
"Brian"
] | 63a094d2c4cedbc1a3709a7d7dd7620c9c0c2ab1b47dd2f302898acaa9822b4c |
"""
Motion correction of image sequences by 'efficient subpixel image registration
by cross correlation'. A reference image is iteratively computed by aligning
and averaging a subset of images/frames.
2015 Lloyd Russell, Christoph Schmidt-Hieber
*************************************************************************... | jzaremba/sima | sima/motion/dftreg.py | Python | gpl-2.0 | 31,079 | [
"Gaussian"
] | 569546ceae62cd0abebc6dc263e3dd1a697cf51af157002bf86d4f0cf79836ff |
""" Callbacks that handle view creation/deletion/modification functionality.
"""
from typing import List, Tuple
import dash
from dash.dependencies import ALL, Input, Output
from dash.exceptions import PreventUpdate
from .. import constants, id_constants, utils
from ..dash_app import app
@app.callback(
[
... | googleinterns/userjourneytool | ujt/callbacks/view_callbacks.py | Python | apache-2.0 | 4,984 | [
"Cytoscape"
] | 7a7f1fbd024838ce63cd0302904a273bbace0315e2f1f5b6bc88127a49ec9c4d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import numpy as np
from fractions import Fraction
from math import gcd
from itertools import groupby, product
from string import ascii_lowercase
from warnings import warn
import logging
import math
import war... | blondegeek/pymatgen | pymatgen/transformations/advanced_transformations.py | Python | mit | 58,389 | [
"CRYSTAL",
"pymatgen"
] | 89b9b283ec3bfb2f6354aef14ae33e8f870b12c4ea1ca50415cad5e812a0336b |
from setuptools import setup
from os import environ
def readme():
with open('README.rst') as f:
return f.read()
setup(
name='h5cube',
version='0.3',
provides=['h5cube'],
requires=['h5py (>=2.4)', 'numpy (>=1.8)'],
packages=['h5cube'],
url='https://www.github.com/bskinn/h5cube',
... | bskinn/h5cube | setup.py | Python | mit | 1,339 | [
"Brian",
"Gaussian"
] | ec349fa49c8f876ae36f48bbd06640fe8a1efb9be86d57a4575f18e219547d8c |
# -*- coding: UTF-8 -*-
''' Модуль для работы с нечеткими множествами
Модуль реализует функциональность аппарата нечеткой логики в части работы с
нечеткими множествами. Он включает:
- абстрактный класс нечеткого множества,
- шаблоны для создания классификаторов различных видов.
В основном, модуль предназнач... | sejros/FuzzyCalcPy | fuzzycalc/set.py | Python | gpl-3.0 | 18,845 | [
"Gaussian"
] | 43718393164ff3be38f50a3da197a8d3d2fe2accf381669448f3c4a8ab30fb16 |
#!/usr/bin/env python2.7
import pysam, os, argparse, json, subprocess
parser = argparse.ArgumentParser(description='Maps reads to contigs on biotite.',
formatter_class=argparse.ArgumentDefaultsHelpFormatter, add_help=False)
#Required arguments
required = parser.add_argument_group('REQUIRED')
required.add_argument('... | alexherns/biotite-scripts | borehole_map_biotite.py | Python | mit | 3,010 | [
"Bowtie",
"pysam"
] | 8160a824943a12f0c0a058c888fad3a8d95543214292eca355b779b18c4730a4 |
"""
To do:
points outside a contour line (or a polygon)
contour line width
"""
import matplotlib.pyplot as plt
import scipy.stats as stats
import numpy as np
# Test Data
# mean = [0,0]; cov = [[1,0.6],[0.6,1]]
# x,y = np.random.multivariate_normal(mean,cov,5000).T
# xbin = [-4,4]; ybin = [-3,3]
# import quicklook
# qu... | guangtunbenzhu/BGT-Cosmology | Spectroscopy/quicklook.py | Python | mit | 4,305 | [
"Gaussian"
] | 3dfe0dc0ddd26d525ebad539223c58074b9b1b43f8f51a76bbf9f5af4648debe |
#!/usr/bin/env python3
import os
import argparse
import h5py
import statistics
import sys
def main():
args = get_arguments()
print('\nLooking for fast5 files in: ' + args.dir, file=sys.stderr)
fast5_files = find_all_fast5s(args.dir)
print(' Found ' + int_to_str(len(fast5_files)) + ' reads\n', file=... | rrwick/Fast5-to-Fastq | fast5_to_fastq.py | Python | gpl-3.0 | 9,562 | [
"VisIt"
] | 8248615efa28885a084f2b840876e6431d653c7526eea6ea76053430a023ebc6 |
"""File like interface for reading gromacs gro files."""
import os
import numpy as np
import topology as t
STDOPEN=open
class GroError(Exception):
pass
class GroFile(object):
resnum_form = '%5d'
resname_form = '%5s'
atom_name_form = '%5s'
atom_num_form = '%5d'
position_form = '%8.3f'
v... | plediii/coord_util | gro.py | Python | bsd-3-clause | 4,325 | [
"Gromacs"
] | 97409d5a9ace3e41f7b60fbb73097cdf5edf8c360d9acd2972ad79a7b95eb94d |
# Copyright 2007-2016 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 your option) any later ... | sem-geologist/hyperspy | hyperspy/tests/signal/test_eds_tem.py | Python | gpl-3.0 | 14,977 | [
"Gaussian"
] | a651f7513be8d024c13bf810a309034ae574cc4b2c5a6a8afff0599eaea91217 |
"""
Train a neural network on breast cancer data
"""
from decimal import Decimal
import matplotlib.pyplot as plt
import numpy as np
from numpy import genfromtxt
class NeuralNetwork:
"""
Neural network implementation using Numpy
"""
def __init__(self):
self.dataset = genfromtxt('res/breast-c... | kaas3000/exercise-breast-cancer | breast_cancer.py | Python | mit | 8,057 | [
"NEURON"
] | 3a66aa3824731e4111e18629ea42d60e51798553f5bd377e8564154f7f2b7726 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2012-2013 Esteban Tovagliari, Jupiter Jazz Limited
# Copyright (c) 2014-2017 Esteban Tovagliari, The appleseedhq Organization
#
# P... | aytekaman/appleseed | src/appleseed.python/logtarget.py | Python | mit | 2,651 | [
"VisIt"
] | 1190b8f82b8cff4e7db0996381992c7742a3136a2dc3862aaa728c84e9971840 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/plan_pricing_medicare.py | Python | apache-2.0 | 17,606 | [
"VisIt"
] | 11fbe86bbec92e49a0c2ab1ba5b5640fd91de36a0dfa68a9e79061e8fe9f71a0 |
"""
Views for the verification flow
"""
import json
import logging
import decimal
import datetime
from collections import namedtuple
from pytz import UTC
from ipware.ip import get_ip
from django.conf import settings
from django.core.urlresolvers import reverse
from django.http import (
HttpResponse, HttpResponseB... | DefyVentures/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 52,672 | [
"VisIt"
] | cd437758cf685524ef4cbc86a52dfa2c5efc0fa5b5c092bc06c1691a241f86e8 |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import functools
import glob
import itertools
import jinja2
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import sys
import time
import urllib2
import zlib
from xml.etree import ElementTree
from cStringIO ... | pedrobaeza/odoo | addons/web/controllers/main.py | Python | agpl-3.0 | 68,898 | [
"VisIt"
] | bc23c2a574ce0d28107bee3a05c37dbaa9a3a51c0548c8387efb4ae04f64bcfd |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Copyright (c), 2016-2017, Quantum Espresso Foundation and SISSA (Scuola
# Internazionale Superiore di Studi Avanzati). All rights reserved.
# This file is distributed under the terms of the LGPL-2.1 license. See the
# file 'LICENSE' in the root directory of the present... | QEF/postqe | postqe/ase/io.py | Python | lgpl-2.1 | 2,921 | [
"ASE",
"ESPResSo",
"Quantum ESPRESSO"
] | a83e88f1101089acbb595f871a4eb055b9246f499674b401c2f691e7fee7886a |
#!/usr/bin/env @PYTHON_EXECUTABLE@
"""
Description: Viewer and exporter for Siconos mechanics-IO HDF5 files based on VTK.
"""
# Lighter imports before command line parsing
from __future__ import print_function
import sys
import os
import json
import getopt
import math
import traceback
import vtk
from vtk.util.vtkAlgor... | fperignon/siconos | io/swig/io/vview.py | Python | apache-2.0 | 94,827 | [
"VTK"
] | 131cca6729c353f3c88fd4a3321a857dee26cd1e5501cc4112d16b62341b0d35 |
#!/usr/bin/env python
'''
brozzler/cli.py - brozzler command line executables
Copyright (C) 2014-2019 Internet Archive
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/lic... | internetarchive/brozzler | brozzler/cli.py | Python | apache-2.0 | 33,403 | [
"VisIt"
] | 03d4780ea04c60696534d25726e7936061eb9f59fd69e06f48ab96e9cc775ac7 |
"""
Various bayesian regression
"""
from __future__ import print_function
# Authors: V. Michel, F. Pedregosa, A. Gramfort
# License: BSD 3 clause
from math import log
import numpy as np
from scipy import linalg
from scipy.linalg import pinvh
from .base import LinearModel, _rescale_data
from ..base import RegressorMi... | vortex-ape/scikit-learn | sklearn/linear_model/bayes.py | Python | bsd-3-clause | 21,171 | [
"Gaussian"
] | 205d847c8ad23c7bb44bc3f70c70be9b457c7ac7d48be1e3433184b338ed1829 |
# -*- coding: utf-8 -*-
#
# Moonstone is platform for processing of medical images (DICOM).
# Copyright (C) 2009-2011 by Neppo Tecnologia da Informação LTDA
# and Aevum Softwares LTDA
#
# This file is part of Moonstone.
#
# Moonstone is free software: you can redistribute it and/or modify
# it under the terms of the GN... | aevum/moonstone | src/moonstone/bloodstone/scenes/gui/qt/component/tests.py | Python | lgpl-3.0 | 5,961 | [
"VTK"
] | f8cd199fd9e669fb2ad373e1df44a09d4f06cba01f455df5804fa2981fb18a15 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# lsvgridowners - list vgrid owners
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as... | heromod/migrid | mig/cgi-bin/lsvgridowners.py | Python | gpl-2.0 | 1,076 | [
"Brian"
] | 0e1aac8cb43cf3395657660772dc28df58c840b4d3c150d44ed2b8de45f66257 |
#!/usr/bin/env python
import pycurl
import urllib
import cStringIO
import base64
import argparse
import sys
import string
import pygeoip
version = "0.1-http_bots-PoC"
def PrintHelp():
global version
print "usage: dexter.PoC.py [-h] [action] [gateway url]"
print ""
print "Dexter CasinoLoader BAMF PoC ... | bwall/BAMF | IntegrationQueue/http/dexter.PoC.py | Python | mit | 8,178 | [
"Brian"
] | 3d0fb663f4f3308038a7488276fee65c6f43d3e432082cab5c8f15457616d8b3 |
""" Test class for plugins
"""
# pylint: disable=protected-access, missing-docstring, invalid-name,
# line-too-long
# imports
import unittest
import importlib
from mock import MagicMock
from DIRAC.DataManagementSystem.Client.test.mock_DM import dm_mock
from DIRAC.Resources.Catalog.test.mock_FC import fc_mock
from D... | arrabito/DIRAC | TransformationSystem/Agent/test/Test_Plugins.py | Python | gpl-3.0 | 5,265 | [
"DIRAC"
] | 6ae4c8b04f37622fda72156cdca76890fce41b638dfc7cc4a17979437bd2e06e |
#-------------------------------------------------------------------------------
# Name: utils.decorate
# Purpose: Submodule containing custom decorators for Open Anharmonic
#
# Author: Brian Skinn
# bskinn@alum.mit.edu
#
# Created: 30 Oct 2015
# Copyright: (c) Brian Skinn 2016
# Li... | bskinn/opan | opan/utils/decorate.py | Python | mit | 12,754 | [
"Brian"
] | c8da52b5d9abda929b25b2db923f17c94fdc229412e2475be82fe1120a9d5037 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jart/tensorflow | tensorflow/contrib/distributions/python/ops/autoregressive.py | Python | apache-2.0 | 8,421 | [
"Gaussian"
] | fece3480dd9b59a81ff3355bf798ae53ea3f7d0d7f3b78e14fa6ab6ce19f4154 |
from __future__ import absolute_import
import logging
import six
from django.core.urlresolvers import reverse
from django.utils.translation import ugettext as _
from sentry import features
from sentry.integrations import (
IntegrationInstallation,
IntegrationFeatures,
IntegrationProvider,
Integration... | mvaled/sentry | src/sentry/integrations/jira/integration.py | Python | bsd-3-clause | 33,720 | [
"VisIt"
] | fa19ef952fc8a3808383958aa0e730c64ee86f24bada76ced983d8ebc44a48d8 |
#!/usr/bin/env python
'''Remove largest pieces of unused data from gaussian_mbis.h5 files, and repack them.
All gaussian_mbis.h5 files were first generated with the following bash loop:
for d in */; do (cd $d; horton-wpart.py gaussian.fchk gaussian_mbis.h5 mbis
--grid=ultrafine --lmax=1 --ove... | molmod/QuickFF | quickff/data/systems/clean_h5.py | Python | gpl-3.0 | 743 | [
"Gaussian"
] | 5f9df76c8dbfb53cca453f405af73a36354bff82c4976ffab06d4b0f1d14473b |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# License: BSD 3 clause
from itertools import chain, combina... | ningchi/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 42,960 | [
"Gaussian"
] | 3928033fbc9038c733b765e697bf0a8c32c3659a7b4f606d4211720b056775dd |
#!/usr/bin/python
########################################################################
# 15 May 2014
# Patrick Lombard, Centre for Stem Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import subproce... | pdl30/pyrnatools | pyrnatools/bamtoucsc.py | Python | gpl-2.0 | 6,945 | [
"pysam"
] | 9e5bbae74f562d98212b2952c249f2f21aa434d254cbcdf9984e1e1f893c564c |
import os
import sys
import subprocess
import threading
import errno
import unittest
from pysam import AlignmentFile
from TestUtils import make_data_files, BAM_DATADIR
IS_PYTHON2 = sys.version_info[0] == 2
def setUpModule():
make_data_files(BAM_DATADIR)
def alignmentfile_writer_thread(infile, outfile):
def... | pysam-developers/pysam | tests/StreamFiledescriptors_test.py | Python | mit | 3,095 | [
"pysam"
] | 808917aeb59e9fe296f35083ce5eb8e84fedaedf04aef26e870bd6500644d01b |
import os
import vtkAll as vtk
import math
import time
import numpy as np
from ddapp import transformUtils
from ddapp import lcmUtils
from ddapp.timercallback import TimerCallback
from ddapp import objectmodel as om
from ddapp import visualization as vis
from ddapp import applogic as app
from ddapp.debugVis import Deb... | edowson/director | src/python/ddapp/handdriver.py | Python | bsd-3-clause | 5,783 | [
"VTK"
] | ccc03b3d36f9fb2fc810f15c0fe2162598cb25a8fff50a3f88b4175ad84f73f8 |
from __future__ import absolute_import
from __future__ import print_function
import sys, os, yaml, glob
from yaml import YAMLError
import subprocess
import argparse
import itertools
import re
import shutil
from nougat import common, align, pdf
from nougat.pdf.theme import colors, DefaultTheme
from nougat.pdf.peakdetect... | senthil10/NouGAT | sciLifeLab_utils/run_QC_report.py | Python | mit | 21,422 | [
"BWA",
"Gaussian"
] | 60f298d153803a197e532c2b9f7ef858f3d6da8a5c0482c8f50d72b37270693b |
""".. module:: Test_Mail
Test cases for DIRAC.Core.Utilities.DAG module.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC.Core.Utilities.Mail import Mail
__RCSID__ = "$Id $"
def test_createEmail():
m = Mail()
res = m._create("addre... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/test/Test_Mail.py | Python | gpl-3.0 | 1,762 | [
"DIRAC"
] | 90113146bdbdf11f343d9f259d69772a68c248d2510144c9c660d1d2368c7efe |
# -*- coding: iso-8859-1 -*-
#
# Markov Logic Networks
#
# (C) 2006-2010 by Dominik Jain (jain@cs.tum.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# ... | opcode81/ProbCog | src/main/python/MLN/learning/AbstractLearner.py | Python | gpl-3.0 | 13,113 | [
"Gaussian"
] | d6a2cc5f0db715536bface578521ad824cdf1d93a9dc5447d5e4568674467d62 |
# coding: utf8
{
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" é uma expressão opcional como "field1=\'newvalue\'". Não é possível atualizar ou excluir os resultados de uma junção',
'# of International Staff': '# De equipe internacional',
'... | flavour/helios | languages/pt-br.py | Python | mit | 297,683 | [
"VisIt"
] | af3a7adbbeedffca826e04c32be9019563ca95781c3c0f01f32a420a8d3c5714 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | Xeralux/tensorflow | tensorflow/contrib/bayesflow/python/ops/hmc_impl.py | Python | apache-2.0 | 37,626 | [
"Gaussian"
] | 7204b22c735e0e7f700e3c26dfcec50f8eb0cdae4a0804e0e892d8886d09bf4e |
# (C) British Crown Copyright 2018, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any later ve... | dkillick/iris | lib/iris/tests/unit/fileformats/netcdf/test__get_cf_var_data.py | Python | lgpl-3.0 | 3,196 | [
"NetCDF"
] | 1907d527ad987e97c0748bdc105784d691d06ee6a3342ed7a6f70702f17b05aa |
# An experimental script to export a TrakEM2 project's annotations
# directly to the CATMAID database. This is based on Albert Cardona's
# TrakEM2 helper scripts here: https://github.com/acardona/Fiji-TrakEM2-scripts
# Mark Longair 2010
import os
import re
from ini.trakem2 import Project
from ini.trakem2.display im... | aschampion/CATMAID | scripts/export/export_from_trakem2.py | Python | gpl-3.0 | 23,382 | [
"NEURON"
] | 81a435ba45e8d0de6298fa6663249b492c6e2cceaa9a44646cb091f75c2898f7 |
from __future__ import print_function, division
import pandas as pd
import numpy as np
import re
import fastparquet
import logging
import dask.dataframe as dd
import dask.array as da
import dask
import time
import inspect
from .utils import result
class Functor(object):
"""Base class for computations performed o... | timothydmorton/qa_explorer | explorer/functors.py | Python | mit | 16,342 | [
"Galaxy"
] | 60b4f60f2d722e78acf871184eaf6f9a3c6cd38e5dc1dbcb8215f77ef779fdd8 |
#!/usr/bin/env python
# Copyright 2014->future! Mikko Korpela
#
# 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 ... | hirsivaja/pabot | pabot/pabot.py | Python | apache-2.0 | 14,297 | [
"VisIt"
] | ee753eda326d63bedeb76e0f82c5ad7dd063a45b61c625bc75c96a1b816f5943 |
# Copyright 2013-2021 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 Exawind(CMakePackage):
"""Multi-application driver for Exawind project."""
homepage =... | LLNL/spack | var/spack/repos/builtin/packages/exawind/package.py | Python | lgpl-2.1 | 1,279 | [
"NetCDF"
] | 38cdff34cf99d6141e557f62892b826a039b1b1bd83b2f19aa00a7ef73b1aa3a |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import S_OK
from DIRAC.AccountingSystem.Client.Types.DataOperation import DataOperation
from DIRAC.AccountingSystem.private.Plotters.BaseReporter import BaseReporter
class DataOperationPlotter(Base... | yujikato/DIRAC | src/DIRAC/AccountingSystem/private/Plotters/DataOperationPlotter.py | Python | gpl-3.0 | 10,965 | [
"DIRAC"
] | 05bfe83876ba71d4aeead00485035bb2f0e6f6ac0e2b808a323ee9f9123483e3 |
"""
Handling the download of the shifter Proxy
"""
import os
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.File import mkDir
from DIRAC.FrameworkSystem.Client.ProxyManagerClient import gProxyManager
from DIRAC.ConfigurationSystem.Client.Helpers.Op... | arrabito/DIRAC | Core/Utilities/Shifter.py | Python | gpl-3.0 | 2,945 | [
"DIRAC"
] | 19523e8cd86b2b4954fa9001b7ece3d6a9ab92cbfb796fff6ead43f2028752de |
from distutils.core import setup
DESCRIPTION = "General tools for Astronomical Time Series in Python"
LONG_DESCRIPTION = """
gatspy: General tools for Astronomical Time Series in Python
============================================================
Gatspy (pronounced as F. Scott Fitzgerald might pronounce it) is a coll... | bsipocz/gatspy | setup.py | Python | bsd-2-clause | 1,726 | [
"VisIt"
] | cf07ad360a6d36ae9d7b50bd4360dbac5ca20ba11e1e91cadf1dcff108f9761f |
"""
.. module:: compute_season_mean.py
:synopsis: This module do the calculating the mean analysis and forecast
systematic error for every season and store it as nc files in
the appropriate directories.
Finally it should create xml files by cdscaning all the nc files
... | arulalant/mmDiagnosis | diagnosis1/diagnosis/compute_season_mean.py | Python | gpl-3.0 | 20,048 | [
"NetCDF"
] | db0efc77420489f7685c11eb2c8b829cc2ee298c8d2ac4d4f640eb3888c72c90 |
#!/usr/bin/env python
import numpy as np
import chiesa_correction as chc
def gauss1d(x):
return np.exp(-x**2/2.)
def check_int1d():
lbox = 10.
xmin = -lbox/2.
xmax = lbox/2.
print('integrate 1D standard Gaussian')
for nx in [4, 16, 32, 64]:
myx = np.linspace(xmin, xmax, nx)
myy = gauss1d(myx)
... | Paul-St-Young/solid_hydrogen | test/test_quad3d.py | Python | mit | 788 | [
"Gaussian"
] | 877675325ee2e95f60be076f1035d3d016593b985912f9509ff8f88bfd392253 |
import collections
import functools
import operator
import os
import re
from time import time
from ase.atoms import Atoms, symbols2numbers
from ase.db.row import atoms2dict, AtomsRow
from ase.calculators.calculator import all_properties, all_changes
from ase.data import atomic_numbers
from ase.parallel import world, b... | suttond/MODOI | ase/db/core.py | Python | lgpl-3.0 | 15,226 | [
"ASE"
] | 372d51e11ec4e7f115020f7539d677569511c8d0f098a894c05fcc01d7b1d11a |
#!/usr/bin/env python
r"""Liu protocol endpoint implementation.
This module implements a Liu protocol endpoint, including signal
generation. In particular, it implements the exchange
:math:`M_{k+1} = Z_{k+1} + \alpha M_k` ,
where :math:`{M_k}` are the messages sent across the wire, :math:`\alpha` is
the ref... | MrMavs/LiuCipher | src/liuproto/endpoint.py | Python | bsd-2-clause | 5,807 | [
"Gaussian"
] | 476fc8b3de07f1616c52871697709d253deafca87810cfc7ffe65650a3fa369c |
#
# Copyright (C) 2006-2007 Cooper Street Innovations Inc.
# Charles Eidsness <charles@cooper-street.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 Software Foundation; either version 2
# of the License, ... | charleseidsness/eispice | module/device.py | Python | gpl-2.0 | 32,820 | [
"xTB"
] | dec3416f2ad63736935fedd4dec50431d62047a155872940cbde0986fd9d3096 |
"""
CompareNgrid.py
Code for checking the convergence of the grid-based
maximum likelihood calculation.
BJK - 23/06/2017
"""
import sys
import matplotlib.pyplot as pl
from scipy.stats import chi2, norm
import CalcParamPoint as CPP
from CalcLikelihood import *
from WIMpy.Experiment import Experiment
print " "
print ... | bradkav/AntiparticleDM | calc/CompareNgrid.py | Python | mit | 4,661 | [
"DIRAC"
] | 2f81460ec5e258e7189f8a13892180b0bd790b0759a712688ba16cca7283f3d5 |
#
# NAME
# problem_set2_solutions.py
#
# DESCRIPTION
# Open, view, and analyze action potentials recorded during a behavioral
# task. In Problem Set 2, you will write create and test your own code to
# create tuning curves.
#
#Helper code to import some functions we will use
import numpy as n... | h-mayorquin/coursera | neural_data/02_exercise/problem_set2.py | Python | bsd-2-clause | 9,235 | [
"NEURON"
] | 1e534e65dcd26fbd3a10557fdcfd92d6315eda49cc0cdfb3c3469a676252d1c7 |
import numpy as np
import tensorflow as tf
import util
from conditional_dist import ConditionalDistribution
from parameterization import unconstrained, positive_exp, simplex_constrained, unit_interval, psd_matrix_small, psd_diagonal
from transforms import Logit, Simplex1, Simplex, Exp, TransformedDistribution, RowNor... | davmre/bayesflow | elbow/elementary.py | Python | bsd-3-clause | 12,333 | [
"Gaussian"
] | 48f52e17b425d67f79dd61af8bf2fcd7686c0000d91ac57071489a03a9ce2d73 |
#!/usr/bin/env python
# Copyright 2014-2020 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/tools/chgcar.py | Python | apache-2.0 | 9,578 | [
"PySCF",
"VASP",
"VMD"
] | d0134d3b9635d750595aee1b946911c72cc227e7d17c6d86ebe2d4c85021c604 |
import numpy
class Gaussian(object):
"""
Represents a single Gaussian probability
density function.
WARNING: some methods of this class may accept either one vector, as a (d,)
shaped array, or many, as a (n, d) shaped array. For d = 1, do NOT use (n,)
shaped array instead of (n, 1). The last ... | jgrizou/explauto | explauto/models/gaussian.py | Python | gpl-3.0 | 4,081 | [
"Gaussian"
] | 5deeaf9a500c0f667b3546352bea0fbc89609e902c58252b31d26d65d288452e |
"""Factor Analysis.
A latent linear variable model, similar to ProbabilisticPCA.
This implementation is based on David Barber's Book,
Bayesian Reasoning and Machine Learning,
http://www.cs.ucl.ac.uk/staff/d.barber/brml,
Algorithm 21.1
"""
# Author: Christian Osendorfer <osendorf@gmail.com>
# Alexandre Gramfor... | lucidfrontier45/scikit-learn | sklearn/decomposition/factor_analysis.py | Python | bsd-3-clause | 7,592 | [
"Gaussian"
] | 31a4fd75e7c860104917eb7ac59e93b98a00c1109f95c85e673f48373717ce20 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import numpy as np
import unittest2 as unittest
import os
from pymatgen.analysis.structure_analyzer import VoronoiCoordFinder, \
solid_angle, contains_peroxide, Rel... | aykol/pymatgen | pymatgen/analysis/tests/test_structure_analyzer.py | Python | mit | 18,062 | [
"VASP",
"pymatgen"
] | f9dcd81b38cf22d8330f036f217504105020b75b0e6f3d35af7ecf90b7820da7 |
#!/usr/bin/env python
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2018 Raik Gruenberg & Johan Leckner
##
## 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... | graik/biskit | archive_biskit2/scripts/analysis/random_complexes.py | Python | gpl-3.0 | 3,171 | [
"Amber"
] | 1e29fce98c15edb1a3b5b55345debeed180e0fe825351da36bb5bcdfc1d8829d |
# Test case for the code. Calculate few well-known crystals
from __future__ import print_function, division
import os
import sys
from numpy import linspace, array, arange
import numpy
from math import pow
from matplotlib.pyplot import plot, show, figure, draw, axvline, axhline
from pylab import *
from ase.lattice.s... | jochym/Elastic | tests/test_01.py | Python | gpl-3.0 | 7,656 | [
"ASE",
"CRYSTAL",
"VASP"
] | d535b03a62c4e8be53243b9ab9f9119adebcc2573969e452270d967c22fba6f5 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-organismdbi/package.py | Python | lgpl-2.1 | 2,432 | [
"Bioconductor"
] | 57a632cc29b21bd5879e63f1844bb601ce5e08eca74c9c0a47b976c17b2a0b44 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/awidgets/__init__.py | Python | gpl-3.0 | 1,569 | [
"Brian"
] | 4bf63701421cff4843b5b884cc7776c1a7ac07601e9b0b8bb1ffbc648ed2362d |
"""
Plotting whitened data
======================
This tutorial demonstrates how to plot :term:`whitened <whitening>`
evoked data.
Data are whitened for many processes, including dipole fitting, source
localization and some decoding algorithms. Viewing whitened data thus gives
a different perspective on the data that... | wmvanvliet/mne-python | tutorials/evoked/40_whitened.py | Python | bsd-3-clause | 2,291 | [
"Gaussian"
] | 63152a46902f45c172fb17c17a09ed060775615ed7b295f186049c09c7c0f642 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/__init__.py | Python | apache-2.0 | 1,291 | [
"ORCA"
] | f103ecbbbf8d32e3808f4ba44199d1fb9c8a808cacb5dbe18f4ccb74a094cf5b |
# Maintained in full by:
# Catalyst Team <catalyst@gentoo.org>
# Release Engineering Team <releng@gentoo.org>
# Copyright: 2011 Brian Harring <ferringb@gmail.com>
# License: BSD/GPL2
# Copied & edited by: Brian Dolbec <dolsen@gentoo.org>
'''Version information and/or git version information
'''
import os
from snakeo... | proneetv/catalyst | catalyst/version.py | Python | gpl-2.0 | 1,471 | [
"Brian"
] | 22a6289b8321eee87f04f8491529a97b552d83a9aa4cc8f672211eac83a9b679 |
from meowth import checks, command, group, Cog
from meowth.utils.formatters import ask
from meowth.exts.users import Team
from discord.ext import commands
import discord
from timezonefinder import TimezoneFinder
import re
import pickle
from typing import Union
def do_template(message, author, guild):
not_found = ... | FoglyOgly/Meowth | meowth/exts/admin/admin_cog.py | Python | gpl-3.0 | 43,377 | [
"VisIt"
] | 2ced536cdc10695094be1f6043176c6d787a7839541ed2613f70445d4c55af72 |
"""Deals with the attributes (variable parameters) of genes"""
from random import choice, gauss, random, uniform
from neat.config import ConfigParameter
from neat.six_util import iterkeys, iteritems
# TODO: There is probably a lot of room for simplification of these classes using metaprogramming.
class BaseAttribute... | drallensmith/neat-python | neat/attributes.py | Python | bsd-3-clause | 6,011 | [
"Gaussian"
] | bfc257b7c62976427c8b0bd729644be172a0b56d73826e01dc65d82cfde94035 |
__author__ = 'nzhang-dev'
import ast
from ctree.transforms import DeclarationFiller
from ctree.transformations import PyBasicConversions
from ctree.frontend import *
from ctree.c.nodes import MultiNode
code = [
"a = 1",
"a,b = 1,1",
"a = b = 1",
"""a,b = 1,1 \na,b = b,a"""
]
def fib(n):
a,b = 0... | ucb-sejits/ctree | test/test_transformations.py | Python | bsd-2-clause | 617 | [
"VisIt"
] | f9b7a96df66b8c3ed8fa578665444d8a3f34a0fd55ead50d51064f82eb87e336 |
# SimpleCV Cameras & Devices
#load system libraries
from SimpleCV.base import *
from SimpleCV.ImageClass import Image, ImageSet, ColorSpace
from SimpleCV import Display
from SimpleCV.Color import Color
from collections import deque
import time
import ctypes as ct
import subprocess
_index = []
_cameras = []
class Fr... | jayrambhia/SimpleCV2 | SimpleCV/Camera.py | Python | bsd-3-clause | 107,351 | [
"VisIt"
] | ecae5f5bac3e5fe9a597fab653704c1ed54e6a0304c45f32b78ada7e9941e073 |
#!/usr/bin/env python
#Copyright (c) 2013, The Children's Hospital of Philadelphia
#All rights reserved.
#
#Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
#following conditions are met:
#
#1. Redistributions of source code must retain the above copyright... | sgithens/dicom-anon | dicom_anon.py | Python | bsd-2-clause | 50,901 | [
"VisIt"
] | d50ccd1a242512ebdd3dbf798dcedd6ecf197808f9eae7e13cd46a57bac9cf45 |
# shelve.py - save/restore working directory state
#
# Copyright 2013 Facebook, Inc.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
"""save and restore changes to the working directory
The "hg shelve" command saves changes made ... | seewindcn/tortoisehg | src/hgext/shelve.py | Python | gpl-2.0 | 32,615 | [
"VisIt"
] | 40760ec6203cd0f95ee4eb23329d8e1711a8c24eaf4441243b496fdbde4205dd |
import theano
import theano.tensor as T
from theano.sandbox.rng_mrg import MRG_RandomStreams
from mozi.layers.template import Template
floatX = theano.config.floatX
theano_rand = MRG_RandomStreams()
class Noise(Template):
def _test_fprop(self, state_below):
return state_below
def _train_fprop(self... | dksahuji/Mozi | mozi/layers/noise.py | Python | mit | 3,331 | [
"Gaussian"
] | fd30c513288d129758312ac530fe566645aeb804df07cd24ef498a1641a49c2a |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','license','co... | shad/odin_module | build.py | Python | mit | 5,852 | [
"VisIt"
] | a6f737f1ae73f5b51faf0918913f7b9243ea9e749c4fba690086a69417130ee8 |
# -*- coding: utf-8 -*-
import time, datetime
import os
from django.contrib.auth.models import Permission
from django.conf import settings
from django.core import mail
from django.core.urlresolvers import reverse
from django.core.exceptions import ValidationError
from django.test import TestCase
from django.test.clie... | orlenko/bccf | src/pybb/tests.py | Python | unlicense | 72,539 | [
"VisIt"
] | 209180c6275e6ca06c9333ad220a8c0be9f6fd977e81f5493983757a338f32c0 |
from __future__ import annotations
import json
import os
import pathlib
import pytest
import pytest_mock
import iotbx.mtz
from dials.array_family import flex
from dials.command_line.slice_sequence import slice_experiments, slice_reflections
from dials.util.multi_dataset_handling import (
assign_unique_identifier... | xia2/xia2 | tests/regression/test_multiplex.py | Python | bsd-3-clause | 11,435 | [
"CRYSTAL"
] | c5c0b7646d19aff8140eb6a68b4dd9e2efd293a1d1d6dc0b650016e7c310a681 |
import numpy as np
import scipy.sparse as sp
import properties
from ...utils.code_utils import deprecate_class, deprecate_property
from ...simulation import BaseSimulation
from ... import props
from ... import maps
from ...utils import mkvc
from .survey import SurveyVRM
from .receivers import Point, SquareLoop
####... | simpeg/simpeg | SimPEG/electromagnetics/viscous_remanent_magnetization/simulation.py | Python | mit | 40,135 | [
"Gaussian"
] | d773992da08d060f3925de79aea469c920d0061c1c5bf9e32973c14e946ee09e |
#!/usr/bin/env python
import argparse
import shutil
import operator
import icqsol_utils
# Parse Command Line.
parser = argparse.ArgumentParser()
parser.add_argument('--input', dest='input', help='Shape dataset selected from history')
parser.add_argument('--input_file_format_and_type', dest='input_file_format_and_type... | pletzer/galaxy-csg | tools/icqsol_scale_shape/icqsol_scale_shape.py | Python | mit | 2,042 | [
"Galaxy",
"VTK"
] | 1209ac50c692dfd2d6975f31e23235a2ab64089f75973e2290ed566d1fd938bb |
#import ddapp
from ddapp import cameraview
from ddapp import transformUtils
from ddapp import visualization as vis
from ddapp import objectmodel as om
from ddapp import ik
from ddapp.ikparameters import IkParameters
from ddapp.ikplanner import ConstraintSet
from ddapp import polarisplatformplanner
from ddapp import ro... | gizatt/director | src/python/ddapp/coursemodel.py | Python | bsd-3-clause | 5,196 | [
"VTK"
] | 188598c6ef31f3ed4f2aedba21b3583163cddea1bd849390ea806fcc46a6fd3b |
# Copyright (C) 2015, Carlo de Franchis <carlo.de-franchis@ens-cachan.fr>
# Copyright (C) 2015, Gabriele Facciolo <facciolo@cmla.ens-cachan.fr>
# Copyright (C) 2015, Enric Meinhardt <enric.meinhardt@cmla.ens-cachan.fr>
# Copyright (C) 2015, Julien Michel <julien.michel@cnes.fr>
import os
import numpy as np
from s2p i... | mnhrdt/s2p | s2p/block_matching.py | Python | agpl-3.0 | 13,678 | [
"Gaussian"
] | c2d9c3ab633d285d8e4e8bf3b9228e8fa5c4caba2713236080c71968961daea0 |
# -*- coding: utf-8 -*-
# Modified by Allard de Wit (allard.dewit@wur.nl), April 2014
"""
A lightweight Traits like module.
This is designed to provide a lightweight, simple, pure Python version of
many of the capabilities of enthought.traits. This includes:
* Validation
* Type specification with defaults
... | jajberni/pcse_web | main/pcse/traitlets.py | Python | apache-2.0 | 48,908 | [
"Brian"
] | eab3d1fdc109921aeb949a903687c74fb1643bcb399bd3c678e3475c4ad167ce |
# Copyright 2022 The Brax Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wri... | google/brax | brax/experimental/composer/components/__init__.py | Python | apache-2.0 | 2,698 | [
"Octopus"
] | 9527977cd947483d684fb84957c31ff806ca1cf3aa96815b4b488adea4982da2 |
"""Custom script for gdm-simple-greeter"""
import orca.scripts.default as default
class Script(default.Script):
def __init__(self, app):
"""Creates a new script for the given application
Arguments:
- app: the application to create the script for
"""
default.Script.__init__(... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/gdm-simple-greeter/script.py | Python | gpl-3.0 | 411 | [
"ORCA"
] | 4abdc7cf68416484fbf4381729aa96aaca0d78c669a34eae0a1dc30f2a151b91 |
"""Diffusion by an exchange process"""
from __future__ import print_function
from math import sqrt
from ase import Atoms, Atom
from ase.io import write
from ase.visualize import view
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton, MDMin
from ase.neb import NEB
from ase.calculators.emt impor... | misdoro/python-ase | doc/tutorials/selfdiffusion/neb3.py | Python | gpl-2.0 | 1,800 | [
"ASE"
] | bbc567e3552df509c5c080ff008841f352a1e253d0f411b45f8c636bc6a7b1f5 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | rabipanda/tensorflow | tensorflow/contrib/py2tf/pyct/static_analysis/access.py | Python | apache-2.0 | 8,251 | [
"VisIt"
] | a16466102f87e79609fdedf2d5b950a40539cd4ecfe043a2a75929a190712a8c |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-reset-job
# Author : Stuart Paterson
########################################################################
"""
Reset a job or list of jobs in the WMS
"""
__RCSID__ = "$Id$"
import DIR... | Sbalbp/DIRAC | Interfaces/scripts/dirac-admin-reset-job.py | Python | gpl-3.0 | 1,361 | [
"DIRAC"
] | f75f9de9930629049180c32a12182dfdd0ffca27ed7d7f80f87ead535b25bb60 |
#!/usr/bin/env python
# Copyright 2014-2020 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... | gkc1000/pyscf | pyscf/cc/ccsd_rdm.py | Python | apache-2.0 | 21,046 | [
"PySCF"
] | 43dc89b481a3ee81ecd167eb059cecf75f80ac2f1d16120461bd01932bd648e1 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import json
import os
import pytest
import ... | nitzmahone/ansible | test/units/galaxy/test_collection.py | Python | gpl-3.0 | 39,910 | [
"Galaxy"
] | b25377e34ed8ece537eca021a24082a175ca15839f65a8332f550c2717202f29 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | SamStudio8/scikit-bio | skbio/tree/tests/test_tree.py | Python | bsd-3-clause | 45,644 | [
"scikit-bio"
] | 2430e784c0b9ff11104d197998d92ad40a05d5da784601b65188eb5acb975e19 |
#!@TARGET_PYTHON@
# info mostly taken from looking at files. See also
# http://lilypond.org/wiki/?EnigmaTransportFormat
# This supports
#
# * notes
# * rests
# * ties
# * slurs
# * lyrics
# * articulation
# * grace notes
# * tuplets
#
# todo:
# * slur/stem directions
# * voices (2nd half of frame?)
# * mo... | drewm1980/lilypond-an | scripts/etf2ly.py | Python | gpl-2.0 | 32,820 | [
"GULP"
] | 93f2dad12f85ecf2048aaabbd4bae02a3348d00c8f1b1a12f6174487571cdd2a |
#!/usr/bin/env python
'''
PYROMS_TOOLBOX is a toolbox for working with ROMS
ocean models input/output files based on PYROMS
pyroms and pyroms_toolbox are based on the
python/numpy/matplotlib scientific python suite.
NetCDF I/O is based on the NetCDF4-python package.
'''
from iview import iview
from jview import j... | kshedstrom/pyroms | pyroms_toolbox/pyroms_toolbox/__init__.py | Python | bsd-3-clause | 2,522 | [
"NetCDF"
] | a1f14438e4d9ca698953ffc86e2dd6f49076b85a197398069de8a197e3b3cc39 |
__author__ = 'bptripp'
from cnn_stimuli import get_image_file_list
import cPickle as pickle
import time
import numpy as np
import matplotlib.pyplot as plt
from alexnet import preprocess, load_net, load_vgg
def excess_kurtosis(columns):
m = np.mean(columns, axis=0)
sd = np.std(columns, axis=0)
result = np... | bptripp/it-cnn | tuning/selectivity.py | Python | mit | 13,980 | [
"Gaussian",
"NEURON"
] | d09b460f4958b2ae9b336f6e1f76220170f4a19e53d2da84bf3606e05b687fae |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# ... | misko/neon | examples/mnist_merge.py | Python | apache-2.0 | 2,875 | [
"Gaussian"
] | dc69cbe6939af06b6205a34da30b312b270efbfe309fa7dc29418ef43a5502c2 |
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