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#!/usr/bin/env python
#
# 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 distribution, or
# https... | QEF/postqe | postqe/__main__.py | Python | lgpl-2.1 | 1,093 | [
"Quantum ESPRESSO"
] | 5a75617629f5b566c36bd23e9a9f45a5a7d3dc19bc10666f6046bf15a7dcf4b7 |
# 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... | jendap/tensorflow | tensorflow/python/autograph/pyct/static_analysis/live_values.py | Python | apache-2.0 | 5,241 | [
"VisIt"
] | 89d0a597b1d21310c613b8efd5127cea499b02254e66a375ecd194edcbe77a30 |
import glob, os, shutil
from astropy.io import fits
import astropy.io.fits as pyfits # for compatibility...
from multiprocessing import Pool
import argparse
import shutil
import numpy as np
import numpy.ma
import wfc3tools
from datetime import datetime
def parse_args():
"""Parse command line arguements.
Param... | gbrammer/pabeta | driz_tools/ir_data_fixes.py | Python | mit | 6,164 | [
"VisIt"
] | cb43851cff7f2c8d23ac3ddb9e9c49f24fac1da3ea4601b75e4da2f0c14a07d7 |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Math... | sknepneklab/SAMoS | analysis/batch_polar/batch_defects_J1_v0.01.py | Python | gpl-3.0 | 3,268 | [
"VTK"
] | f7c859ac79f4dd735013311544086c86ec5ecbae611e6768e93dc4d8afd69a95 |
# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
import tempfile
import time
import re
import sys
import os
from contextlib import contextmanager
from selenium.common.exceptions import... | maximmaxim345/Sheep-it-blender-plugin | splinter/driver/webdriver/__init__.py | Python | gpl-3.0 | 22,326 | [
"VisIt"
] | 7c56743d01083256c1f5e8ef13a5c11ac823d0b087ba2c50128038b1162a2fa7 |
""" converted from Matlab code
source: http://www.robots.ox.ac.uk/~fwood/teaching/AIMS_CDT_ML_2015/homework/HW_2_em/
% This main file is used to execute the em algorithm for gaussian mixture
% modeling. The data is the fisher iris data where each row of data are
% four measurements taken from the pedal of an iris flo... | leonardbj/AIMS | src/ML_Algorithms/ExpectationMaximization/main_gaussian_mixture.py | Python | mit | 2,633 | [
"Gaussian"
] | ebfa4f81b5c45ef3ff15df5f1db199013b4b00e05941fe8f19b8c817dea573a7 |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | jaidevd/scikit-learn | sklearn/cluster/k_means_.py | Python | bsd-3-clause | 59,631 | [
"Gaussian"
] | 3abcd15904180a0b8bfbacb67c57071a94600de2bd57a44404b9b1661959d46a |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'pyxpad_main.ui'
#
# Created: Fri Oct 7 15:25:29 2016
# by: pyside-uic 0.2.15 running on PySide 1.2.4
#
# WARNING! All changes made in this file will be lost!
# Hand-edited to make it work with Qt4 & Qt5
from Qt import QtCore, __qt_ver... | bendudson/pyxpad | pyxpad/pyxpad_main.py | Python | gpl-3.0 | 24,180 | [
"NetCDF"
] | 92aaa3bd6713b1d9b6784c5ca1221a171980e0c54b9dcb7ba6cf87d9253e216d |
from netconfig.drivers import Prompt, Port, Ports, Config, Model, Firmware, Layer1, Vlan, SpanningTree, MacAddress, Layer2, Routes, Arps, Layer3, Transceiver, FRU, Password, Users, System, Device, PortChannels, Module, Stats, Rfc2863
from slac_utils.net import prefixlen_to_netmask, truncate_physical_port, netmask_to_p... | SLAC-OCIO/net-config | lib/netconfig/drivers/cisco_ios.py | Python | gpl-2.0 | 85,292 | [
"ASE"
] | 18afc1a93c5632bbb4575f4275148b131edcd604a119bfde65e65ed26f9c9af5 |
#!/usr/bin/env python3.5
# -*- coding: utf-8 -*-
"""Script to call modules that generate the blog's content, then posts that
content to the ulyssesredux.tumblr.com.
Each chapter is written by a different script that resides in the
chapter_scripts/ directory. Each of these scripts then draw from
texts in the corpora/ d... | patrick-brian-mooney/UlyssesRedux | daily_script.py | Python | gpl-3.0 | 5,413 | [
"Brian"
] | 10e1d9362639262357c871d70aad5efa6b6aeae7137e317383ffb630c3bd1f25 |
# Copyright (C) 2015 OLogN Technologies AG
#
# This source file 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.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY W... | smartanthill/smartanthill-zepto-compiler | smartanthill_zc/parse_js.py | Python | gpl-2.0 | 21,223 | [
"VisIt"
] | 12af1c38b9d7f7650e1421aaa3f7b8013f6169191528c2bcac5cb0c1f76eff7c |
#!/usr/bin/python
import httplib
import httplib2
import os
import random
import sys
import time
import tempfile
import subprocess
import json
from apiclient.discovery import build
from apiclient.errors import HttpError
from apiclient.http import MediaFileUpload
from oauth2client.client import flow_from_clientsecrets
... | sometallgit/AutoUploader | upload_video.py | Python | mit | 7,700 | [
"VisIt"
] | 883d082dbe5fa462fe4912e8f1406a250315c4759b06e1f305a04fab56a20911 |
# -*- coding: utf-8 -*-
"""Mayavi/traits GUI for setting MRI fiducials."""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
from mayavi.core.ui.mayavi_scene import MayaviScene
from mayavi.tools.mlab_scene_model import MlabSceneModel
import numpy as np
from pyface.api im... | Teekuningas/mne-python | mne/gui/_fiducials_gui.py | Python | bsd-3-clause | 20,158 | [
"Mayavi"
] | a2c0b00df501659930f36c15b8e7a983e9ba5605683a909d715318d81f63aab3 |
#
# Copyright 2017 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googlefonts/glyphsLib | tests/builder/designspace_gen_test.py | Python | apache-2.0 | 17,982 | [
"VisIt"
] | 66f28c27794fcda74798e4599bbaa36fb5b10b4efd876d1e24375d822e70f4b3 |
"""
Given two words (beginWord and endWord), and a dictionary's word list, find all shortest transformation sequence(s) from beginWord to endWord, such that:
Only one letter can be changed at a time
Each intermediate word must exist in the word list
For example,
Given:
beginWord = "hit"
endWord = "cog"
wordList = ["... | Ahmed--Mohsen/leetcode | word_ladder_2.py | Python | mit | 2,853 | [
"VisIt"
] | 29a835255d6eeda4973b73d6ca895310cb7aa5edf7d915f5b00c13a79b0ab068 |
#!/usr/bin/env python3
#
# Copyright (C) 2015 INRA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is... | geraldinepascal/FROGS | libexec/biom2tsv.py | Python | gpl-3.0 | 12,058 | [
"BLAST"
] | 3c706e199b39eeaa3bca60cbd2d85f2c72dfaf2e89d8eb8f244e1535aee0a648 |
# -*- coding: utf-8 -*-
import os
from PIL import Image
import os.path
import time
import torch
import torchvision.datasets as dset
import torchvision.transforms as trn
import torch.utils.data as data
import numpy as np
from PIL import Image
# /////////////// Distortion Helpers ///////////////
import skimage as sk... | hendrycks/robustness | ImageNet-C/create_c/make_cifar_c.py | Python | apache-2.0 | 15,767 | [
"Gaussian"
] | f865ae91dffb2b4834292ce05c876bf3d77f36417f70075a2b5259348b0c83a5 |
import os, re
from subprocess import *
from time import strftime, gmtime, ctime, localtime, asctime
TERM_COLS = 110
LIBMESH_OPTIONS = {
'mesh_mode' : { 're_option' : r'#define\s+LIBMESH_ENABLE_PARMESH\s+(\d+)',
'default' : 'SERIAL',
'options' :
... | amburan/moose | framework/scripts/TestHarness/util.py | Python | lgpl-2.1 | 13,238 | [
"MOOSE",
"VTK"
] | 4a8daf036dfff14a6e933431e0516a064e88528edde1c020c721a773a7b75d50 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
# Credit to Dr. Shyue Ping Ong for the template of the calculator
"""
This module implements a TEM pattern calculator.
"""
import json
import os
from collections import namedtuple
from fractions import Fractio... | davidwaroquiers/pymatgen | pymatgen/analysis/diffraction/tem.py | Python | mit | 27,148 | [
"CRYSTAL",
"pymatgen"
] | 15859085a2b7902491590660630d36607b354cf735048b895fdb9c17bd243c11 |
# -*- coding: utf-8 -*-
# Copyright (C) Duncan Macleod (2016-2020)
#
# This file is part of GWpy.
#
# GWpy 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)... | areeda/gwpy | gwpy/signal/qtransform.py | Python | gpl-3.0 | 24,431 | [
"Gaussian"
] | 9bd76be55ca96e8f3c06f820ddefc7e67fe210c2c4be9e4391670c57e14f581e |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/easy_install.html
""... | bjornlevi/5thpower | nefndaralit/env/lib/python3.6/site-packages/setuptools/command/easy_install.py | Python | mit | 89,413 | [
"VisIt"
] | bd19ca7c02768604f2b7838e2d29dae01144c927e3f7e283e201880337c2ea2f |
"""
Main functions for interacting with LAtools.
(c) Oscar Branson : https://github.com/oscarbranson
"""
import configparser
import itertools
import inspect
import json
import os
import re
import time
import warnings
import dateutil
import textwrap
import matplotlib.pyplot as plt
import matplotlib as mpl
import nump... | oscarbranson/latools | latools/latools.py | Python | mit | 178,184 | [
"Gaussian"
] | db6e65c9de3a40fa34f14d67146204359ada04eb5ca52bdb4888b007ff79bf5b |
#
# Copyright (c) 2010 Brian E. Granger
#
# This file is part of pyzmq.
#
# pyzmq is free software; you can redistribute it and/or modify it under
# the terms of the Lesser GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option)... | svpcom/pyzmq-ctypes | zmq/tests/test_pubsub.py | Python | lgpl-3.0 | 2,007 | [
"Brian"
] | 3432f494fcf295044a7140b5eb0d19dfd4e03b72f02852d7e98691bd3aad882f |
# sql/compiler.py
# Copyright (C) 2005-2017 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:`.c... | Haynie-Research-and-Development/jarvis | deps/lib/python3.4/site-packages/sqlalchemy/sql/compiler.py | Python | gpl-2.0 | 113,402 | [
"VisIt"
] | e4e803bab48211590ad062ea20655cf6b5616dee9224dfd0333731199f2c956b |
#
# LAMMPS.py
#
# Interface to LAMMPS (http://lammps.sandia.gov)
#
# Copyright (c) 2017 Terumasa Tadano
#
# This file is distributed under the terms of the MIT license.
# Please see the file 'LICENCE.txt' in the root directory
# or http://opensource.org/licenses/mit-license.php for information.
#
import numpy as np
... | ttadano/ALM | tools/interface/LAMMPS.py | Python | mit | 11,171 | [
"LAMMPS"
] | 7a180d028e54c9b9d90dba6a9b9e10ca687e152676ec24501791d446fcd98526 |
from flask import Flask, render_template, session, request, redirect
import random
app = Flask(__name__)
app.secret_key = 'my_secret_key'
@app.route('/')
def index():
if not 'gold' in session:
session['gold'] = 0
if not 'activities' in session:
session['activities'] = []
return render_temp... | jiobert/python | Nelson_Alvarez/Assignments/flask_fund/ninja_gold/server.py | Python | mit | 1,138 | [
"CASINO"
] | 84ae50afbf21248879a4c3545998622f015dba6315f83b93443394665943b237 |
""" NotificationDB class is a front-end to the Notifications database
"""
import time
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.Mail import Mail
from DIRAC.Core.Base.DB import DB
from DIRAC.Core.Utilities import DEncode
from DIRAC.ConfigurationSystem.Client.Helpers import Registry
c... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/DB/NotificationDB.py | Python | gpl-3.0 | 35,664 | [
"DIRAC"
] | 6bb3e8d29d98c4b753a739c7912b4d98eb4dcc8125053175b01b8c5bdc1a28e5 |
# -*- coding: utf-8 -*-
# @Author: twankim
# @Date: 2017-02-24 17:46:51
# @Last Modified by: twankim
# @Last Modified time: 2018-03-09 22:15:51
import numpy as np
import time
import sys
import os
import argparse
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from ssac import weakSSAC
from... | twankim/weaksemi | compare_global.py | Python | mit | 10,611 | [
"Gaussian"
] | a8178fc5276cf3c79481db9938a30f9f602fbe38266c387ba5dceb3aa76e39c1 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | frechet_audio_distance/gen_test_files.py | Python | apache-2.0 | 3,034 | [
"Gaussian"
] | c174ddb3a91f04ecb959114343a16c96adee87ad110e0f3dfe8f82984413cb46 |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
from torch.distributions import constraints
from torch.nn import Parameter
import pyro
import pyro.distributions as dist
import pyro.poutine as poutine
from pyro.contrib.gp.models.model import GPModel
from pyro.contri... | uber/pyro | pyro/contrib/gp/models/vsgp.py | Python | apache-2.0 | 7,988 | [
"Gaussian"
] | 1d90aebf1f8ca7777d8a390c6f53b4229b56c9fa52e27a76b9b9eb01dc1f12c7 |
# -*- coding: utf-8 -*-
"""Factories for the OSF models, including an abstract ModularOdmFactory.
Example usage: ::
>>> from tests.factories import UserFactory
>>> user1 = UserFactory()
>>> user1.username
fred0@example.com
>>> user2 = UserFactory()
fred1@example.com
Factory boy docs: http://f... | fabianvf/osf.io | tests/factories.py | Python | apache-2.0 | 14,122 | [
"Brian"
] | fa5d4c16b73bd11312c1be249e7bd29b0a52f03d15bc5f96e32a0d5f5c466318 |
# A library of things to help with simple symmetry operation stuff.
#
# FIXED 17/NOV/06 add a method in here to give a list of likely, and then
# less likely, spacegroups based on an input spacegroup.
# For instance, if the input spacegroup is P 41 21 2 then
# another lik... | xia2/xia2 | src/xia2/lib/SymmetryLib.py | Python | bsd-3-clause | 4,740 | [
"CRYSTAL"
] | 46d38c89729e309f5e903a89a6fe41bbb11eac9866ebab06dffc259ab1bd69b7 |
#!/usr/bin/env python
"""NeutronPy: Neutron scattering tools for scientific data analysis in python
NeutronPy is a collection of commonly used tools aimed at facilitating the
analysis of neutron scattering data. NeutronPy is built primarily using the
numpy and scipy python libraries, with a translation of ResLib 3.4c ... | granrothge/neutronpy | setup.py | Python | mit | 4,445 | [
"CRYSTAL"
] | 097c5a1f7485d2c1cbf4bd4b9eeeb731bd58210968e56d2f2fba412c84fcdfe1 |
#!/usr/bin/env python
import sys
import math
import simtk.openmm.app.element as element
import simtk.unit as unit
import subprocess
import datetime
from six.moves import cStringIO
import mdtraj as md
import logging
logger = logging.getLogger(__name__)
def fix(atomClass):
if atomClass == 'X':
return ''
... | Clyde-fare/openmoltools | openmoltools/amber_parser.py | Python | gpl-2.0 | 22,160 | [
"Amber",
"MDTraj",
"OpenMM"
] | 1a112a72d0074aeccafd4d8443ca578cc17e48893444b8f7daccadd2e1b23c9f |
import random
import math
import hashlib
import datetime
import time
import numpy as np
import btcanalysis as btc
layers=[4,10,3]
layern=len(layers)
randn=0
def rand():
a=time.time()
global randn
b=hashlib.sha256(str(a)+str(randn)).hexdigest()
c=int(b,16)
randn=randn+math.pow(c,0.5)
d=floa... | barisser/perceptron | perceptron.py | Python | mit | 5,632 | [
"NEURON"
] | 213526d539da665a473265342d075a4963328278c0b89ee5bca11b0deb786e58 |
import enum
import json
import logging
import os
import platform
import sys
import textwrap
import uuid
import click
try:
from pybigquery.parse_url import parse_url as parse_bigquery_url
except (ImportError, ModuleNotFoundError):
parse_bigquery_url = None
import great_expectations.exceptions as ge_exceptions... | great-expectations/great_expectations | great_expectations/cli/v012/datasource.py | Python | apache-2.0 | 61,560 | [
"VisIt"
] | 988ae5dcfc251dc2323a306c26486e4a1627a8c6642e290ecc87215a77c748a0 |
# coding: utf-8
# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
from __future__ import division, unicode_literals, print_function
import os
import six
import abc
from functools import partial
import traceback
import shutil
import re
import numpy as np
from monty.dev import de... | Bismarrck/pymatgen | pymatgen/io/vasp/sets_deprecated.py | Python | mit | 63,194 | [
"VASP",
"pymatgen"
] | 39dfac4b6b3d256e65c65a2fcca7cdaf69dc71485b2ab95c4fc67df7c57439f9 |
# Copyright 2016 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... | tongwang01/tensorflow | tensorflow/contrib/distributions/python/ops/distribution.py | Python | apache-2.0 | 33,841 | [
"Gaussian"
] | 218a7a23696e46a01b6e44c2dc7cf4a9681c5df7510ec41b1a0a48b88756e532 |
from __future__ import print_function
import sys
import mdtraj as md
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit
if len(sys.argv) != 4:
print('usage %s <cuda device index> <trajectory index (for output file)> <model index of starting conformation>')
exit(1)
pdb = md.load('100... | msmbuilder/msmb_data | msmb_data/fs_peptide/simulate_fs.py | Python | lgpl-2.1 | 1,685 | [
"MDTraj",
"OpenMM"
] | 20ac657e49ed743ad56597c72ff6e8f7f5c6a44a52293ec445031589190a2287 |
from __future__ import print_function, division
import random
from sympy import Derivative
from sympy.core.basic import Basic
from sympy.core.compatibility import is_sequence, as_int, range
from sympy.core.function import count_ops
from sympy.core.decorators import call_highest_priority
from sympy.core.singleton impo... | kaichogami/sympy | sympy/matrices/dense.py | Python | bsd-3-clause | 44,238 | [
"DIRAC"
] | a09a1e5309c88f4caacf4eca616d3c8501806563ad77cbcc68c77c39ee19c863 |
writePdbAA = {'A' : {
'Res_name': 'ALA',
'atoms':['N','CA','C','O','CB'],
'atom_type':['N','C','C','O','C']},
'R' : {
'Res_name': 'ARG',
'atoms':['N','CA','C','O','CB','CG','CD','NE','CZ','NH1','NH2'],
'atom_type':['N','C','C','O','C','C','C','N','C','N','N']},
... | rspencer27/Mass-Spec-App | main/PDB_coord_old.py | Python | apache-2.0 | 16,056 | [
"NAMD"
] | 512a3199f4d43fcb905f76af845bec3563f341254feae3b638e2a979f0a001e3 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | dilawar/moose-full | moose-examples/tutorials/ChemicalOscillators/TuringOneDim.py | Python | gpl-2.0 | 5,380 | [
"MOOSE"
] | 244771bfe757d1d1485c6428252be4340a4550b73462de7f405a7430c242f0ef |
from numpy import *
import inspect
from operator import itemgetter
def procdf(function,allvars,procaxis,dimidx=0):
iterate = False
if (dimidx <= len(shape(allvars[0]))):
if (procaxis[dimidx] == False):
iterate = True
if iterate:
#procaxis[dimidx] == False !!!
#so the ... | hendrikwout/sciproc | sciproc/scimulti.py | Python | gpl-3.0 | 9,619 | [
"NetCDF"
] | d987d959c49caa3572907ae3b50c6f313c2c427d2dfd259f92921436b84e93f9 |
from askbot.conf.settings_wrapper import settings
from askbot.conf.super_groups import LOGIN_USERS_COMMUNICATION
from askbot.deps import livesettings
from django.utils.translation import ugettext_lazy as _
EMAIL_TEXT = livesettings.ConfigurationGroup(
'EMAIL_TEXT',
_('Email template phrases'),
... | knowledgepoint-devs/askbot-devel | askbot/conf/email_text.py | Python | gpl-3.0 | 1,588 | [
"VisIt"
] | 41ab31ff780fc43ea9c4fc75947fa3945934100ae2713c4c0ccaa6c756a1e5b4 |
# Copyright 2014 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from recipe_engine.types import freeze
DEPS = [
'build/adb',
'build/chromium',
'build/chromium_android',
'build/chromium_tests',
'build... | geminy/aidear | oss/qt/qt-everywhere-opensource-src-5.9.0/qtwebengine/src/3rdparty/chromium/infra/recipes/android/perf.py | Python | gpl-3.0 | 14,074 | [
"Galaxy"
] | 343abefa40aea95c2336c0373c797e1a94e90e17951b75f57ee39c24a87c5f32 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/test_imports.py | Python | gpl-2.0 | 2,473 | [
"MDAnalysis"
] | 8dfa2201985a147ddddd253dfc823d158db564fab169db0d2a34bc7a23197243 |
#!/usr/bin/env python2
# vim:fileencoding=utf-8
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2013, Kovid Goyal <kovid at kovidgoyal.net>'
import sys
from functools import partial
from PyQt5.Qt import (
QMainWi... | jeanlinux/calibre | src/calibre/gui2/tweak_book/editor/image.py | Python | gpl-3.0 | 11,317 | [
"Gaussian"
] | 13df68ea54bc5a84fe1ddd0a18b1d136b980a8c2f4d8b4959598443039edb923 |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'experiment'
tab.settings['Output file name'] = 'fpsq.exp'
#
# Handle the special case of the first scenario
#
self.notebook.switchScenario(0,scenarioType="Single crystal")
#
#
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'experiment'
tab.se... | JohnKendrick/PDielec | Examples/Experiment/fpsq/script.py | Python | mit | 5,416 | [
"CRYSTAL"
] | 045f233d626fecfff365a807285e886154b41df4cc71f674c5dab1c27df1ea1a |
# -*- coding: utf-8 -*-
#
# conncomp.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# ... | sdiazpier/nest-simulator | pynest/examples/spatial/conncomp.py | Python | gpl-2.0 | 3,879 | [
"NEURON"
] | d67bc5b0c0260e2b4290211f5e904b065854cee1278a95ea6fafca8b93b203d4 |
##############################################################################
# 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/p4est/package.py | Python | lgpl-2.1 | 2,340 | [
"VTK"
] | 49c8a49006ad3bff43f555fd32608e11fdbf410cfa4af62e52e82581d0fda895 |
# Copyright (c) 2013-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2013-2014 Google, Inc.
# Copyright (c) 2014-2020 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 Cosmin Poieana <cmin@ropython.org>
# Copyright (c) 2014 Vlad Temian <vladtemian@gmail.com>
# Copyright (c) 2014 Arun Pers... | PyCQA/pylint | pylint/checkers/stdlib.py | Python | gpl-2.0 | 30,910 | [
"VisIt"
] | 12ac907bc8bbc2c4ab418fb104a92a734de8e3938c8cffd88f501c353791bae0 |
""" :mod: DMSRequestOperationsBase
====================
Just a collector of common functions
"""
__RCSID__ = "$Id $"
from DIRAC import S_OK, S_ERROR
from DIRAC.RequestManagementSystem.Client.Operation import Operation
from DIRAC.ConfigurationSystem.Client.Helpers.Resources import getRegi... | fibbo/DIRAC | DataManagementSystem/Agent/RequestOperations/DMSRequestOperationsBase.py | Python | gpl-3.0 | 2,815 | [
"DIRAC"
] | 134759014fd88e28b0defea24b045d45e16403ab82971a0ec7ec128b97c01289 |
# coding: utf-8
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 o... | NAMD/pypln.backend | tests/test_worker_tokenizer.py | Python | gpl-3.0 | 1,683 | [
"NAMD"
] | 13136765f43f86c2ecd2fbf3ae8f01c1219f98195a2b094b66ae43daae3ed11a |
"""Testing the IQ stanzas.
IQ stanzas are described at http://xmpp.org/rfcs/rfc6120.html#stanzas-semantics-iq
type attribute must be one of get, set, result, or error.
id attribute is mandatory.
The exciting parts are in the <query> sub element.
Example:
<iq from="alice@wo... | andrewdied/chupycabra | tests/test_iq.py | Python | lgpl-3.0 | 3,602 | [
"exciting"
] | 9947c702a98453fb13d04a09295a6e13a6b722ed2ab6cbd2c50773caa86d296f |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (gregory_r_warnes@groton.pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
###################... | intip/da-apps | plugins/da_centrallogin/modules/soappy/SOAPpy/Client.py | Python | gpl-2.0 | 15,379 | [
"Brian"
] | ec0d4f3d91ff2d04cd817fd62d9774ea2365f97423382847f066544985eebf8b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from rdkit.Chem import rdMolDescriptors
from rdkit import DataStructs
__license__ = "X11"
METADATA = {
"id": "method_rdkit_hashap_1024_tanimoto",
"representation": "hashap_1024",
"similarity": "tanimoto"
}
def _compute_fingerprint(molecule):
return rdMo... | skodapetr/lbvs-environment | methods/ap/hashap_1024_tanimoto.py | Python | mit | 1,417 | [
"RDKit"
] | 19a9266d3b37c4cac829ef60bfb14a5b5f071e7e2f745c617d153a9b2d1136fc |
from __future__ import print_function, division
from os.path import join
import tempfile
import shutil
import io
from io import BytesIO
try:
from subprocess import STDOUT, CalledProcessError
from sympy.core.compatibility import check_output
except ImportError:
pass
from sympy.core.compatibility import u
... | atreyv/sympy | sympy/printing/preview.py | Python | bsd-3-clause | 12,227 | [
"VisIt"
] | 56e579ab0d6815ef0cf7d0f9f18ed0ab6a1bf96be4b4dce70e54b21964c78343 |
def build_models(process_only_these_targets=None, process_only_these_templates=None, verbose=False):
r'''Uses the build_model method to build homology models for a given set of
targets and templates.
MPI-enabled.
'''
import os
import Bio.SeqIO
import mpi4py.MPI
comm = mpi4py.MPI.COMM_WO... | choderalab/Ensembler2 | MSMSeeder/attic/modelling.py | Python | gpl-2.0 | 13,563 | [
"Biopython",
"MDTraj"
] | fdf02f6ed81f87849b50cd8a279e03285556600772b726e2f95544f667cd3047 |
# symcompartment.py ---
#
# Filename: symcompartment.py
# Description:
# Author:
# Maintainer:
# Created: Thu Jun 20 17:47:10 2013 (+0530)
# Version:
# Last-Updated: Fri Jul 12 12:10:52 2013 (+0530)
# By: subha
# Update #: 71
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
... | dilawar/moose-full | moose-examples/snippets/symcompartment.py | Python | gpl-2.0 | 3,137 | [
"MOOSE"
] | 3e38383d3e7561473d89e7505a56371b1bdb17c0c0be055059841f93475861e6 |
#
# Copyright (c) 2014-2015, Continuum Analytics, Inc. and contributors
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# Redistributions of source code must retain the above copyright notice,... | ibab/datapipe | datapipe/dask.py | Python | mit | 12,777 | [
"VisIt"
] | d4c465cdc19b5e17178512a219a249c5462935f53ad548554c6f06c2e29c1eec |
"""
Created on Thu Feb 9 21:30:03 2012
Test script to play around with the single pulse single qubit Clifford gates achieved via phase-ramping.
"""
from __future__ import division
import numpy as np
from scipy.constants import pi
from scipy.linalg import expm
import matplotlib.pyplot as plt
from PySim.SystemPara... | BBN-Q/PySimulator | scripts/AtomicCliffords.py | Python | apache-2.0 | 4,760 | [
"Gaussian"
] | f198d11e223e2e2dcd8e94d42e54b144220b74223bd46a13051eeb2dc21b47b1 |
import json
import time
import logging
import msgpack
import traceback
import collections
import synapse.link as s_link
import synapse.async as s_async
import synapse.daemon as s_daemon
import synapse.aspects as s_aspects
import synapse.dyndeps as s_dyndeps
import synapse.eventbus as s_eventbus
import synapse.telepath... | imjonsnooow/synapse | synapse/neuron.py | Python | apache-2.0 | 17,207 | [
"NEURON"
] | 9969585a2633bd8ab31361e2c716b9bd6c4dd383409e23a25b4bf8c1b76afcf5 |
# The test code for Le Troter's sulcus pruning algorithm based on path probability
import cPickle
import pyvtk
def load_fundi(Filename):
'''Load fundi from a VTK file
Returns
==========
Fundi : list of 2-tuples of integers
Each element is a line segment in fundi, could b... | binarybottle/mindboggle_sidelined | fundi_from_pits/letroter.py | Python | apache-2.0 | 17,309 | [
"VTK"
] | 53ce04785b9bb0a48634f1be259dfd7495232bab9e2ea4c76c1623cc96732e36 |
######################################################################################
# fitn2dgauss.py
# V.1.0.2 19 May 2015 - Typo fixed on residuals
# V.1.0.1 - 13 March 2015 - Emsellem
# Changed a few lines to simplify the functions and variables
# V.1.0.0 - 12 Mai 2014 - Emsellem
# Adding s... | emsellem/pygme | pygme/fitting/fitn2dgauss.py | Python | bsd-3-clause | 49,600 | [
"Gaussian"
] | c311786b9f32e73c709079cf8afec545cbf24543a620565ef7946cc33dc7e93c |
# import aeropy.CST_lib as cst
import aeropy.CST_3D as cst
import aeropy.CST_3D.mesh_tools as meshtools
import panairwrapper
from aeropy.filehandling.vtk import generate_surface
import numpy as np
import matplotlib.pyplot as plt
# wing_points = stl_processing.points_from_stl('./wing_right.stl')
# wing_points = np.ge... | leal26/pyXFOIL | examples/3D_fitting/full/test.py | Python | mit | 13,211 | [
"VTK"
] | 005d0d1fa50707df1116dffca20f4eec414736bcf921873ddc53b2b7a289e1e8 |
"""Exploration Simulation
Simulation of a spacecraft exploring an asteroid
States are chosen to minimize a cost function tied to the uncertainty of the
shape. Full SE(3) dynamics and the polyhedron potential model is used
Author
------
Shankar Kulumani GWU skulumani@gwu.edu
"""
from __future__ import absolute_imp... | skulumani/asteroid_dumbbell | exploration_sim.py | Python | gpl-3.0 | 100,130 | [
"Mayavi"
] | be5689020962d326d04b19dbb54512d3cbd9d25504b36e260ff03b803cac58c2 |
#!/usr/bin/env python
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the... | MDAnalysis/mdanalysis | package/setup.py | Python | gpl-2.0 | 29,101 | [
"Amber",
"Biopython",
"CHARMM",
"Gromacs",
"LAMMPS",
"MDAnalysis",
"NAMD"
] | 93cc1314520b388aca1bd78397974ccf3011ffb0aa6f94d61ee483091c0520d9 |
# tuftedRS.py ---
#
# Filename: tuftedRS.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Fri Oct 16 13:42:14 2009 (+0530)
# Version:
# Last-Updated: Fri Oct 21 17:16:30 2011 (+0530)
# By: Subhasis Ray
# Update #: 49
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
... | BhallaLab/moose-thalamocortical | DEMOS/pymoose/traub2005/py/tuftedRS.py | Python | lgpl-2.1 | 5,796 | [
"MOOSE",
"NEURON"
] | f6b74909539f2b6189a62641221346cc122abac0f131ce61c4692ead3d5c6681 |
#!/usr/bin/env python
# Copyright (C) Duncan Macleod (2014)
#
# This file is part of GWpy.
#
# GWpy 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 l... | andrew-lundgren/gwpy | examples/table/rate.py | Python | gpl-3.0 | 2,074 | [
"Gaussian"
] | 9d4c2502ce568569f8b6969ce63400200bc8c094cfb9f78054b4248d927faa65 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | anksp21/Community-Zenpacks | ZenPacks.community.mib_utils/setup.py | Python | gpl-2.0 | 3,276 | [
"VisIt"
] | 83dd70b3383630e86282db7afa2840924e07eab27af684a8d203846a89f4f271 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 versi... | gph82/PyEMMA | pyemma/coordinates/data/featurization/misc.py | Python | lgpl-3.0 | 7,202 | [
"MDTraj"
] | bc277eb21a3f4c0cfd37fb2dec1a2341c42aece5f086146eadbf9a662e948557 |
# -*- coding: utf-8 -*-
#
# gif_pop_psc_exp.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License... | SepehrMN/nest-simulator | pynest/examples/gif_pop_psc_exp.py | Python | gpl-2.0 | 14,482 | [
"NEURON"
] | 2f4cf2a2b33f3c91f420853ac502137bc4e8f7bc1d47f909f4be3bec52113502 |
"""
bct v0.01
Bitcoin Trade Simulator
Copyright 2011 Brian Monkaba
This file is part of ga-bitbot.
ga-bitbot is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
... | enikesha/ga-bitbot | bct.py | Python | gpl-3.0 | 35,986 | [
"Brian"
] | 0b50d8bb2cfa5f9d00f2120365650a814ead40e7940f1752c23cde0c7b721429 |
import openvoronoi as ovd
import ovdvtk
import time
import vtk
import datetime
import math
import random
import os
def drawLine(myscreen, p1, p2):
myscreen.addActor(ovdvtk.Line(p1=(p1.x, p1.y, 0), p2=(p2.x, p2.y, 0), color=ovdvtk.yellow))
def writeFrame(w2if, lwr, n):
w2if.Modified()
current_dir = os.ge... | aewallin/openvoronoi | python_examples/line-segment/lineseg_animation.py | Python | lgpl-2.1 | 2,294 | [
"VTK"
] | 5800011703c0bb52d8c6a5a3f12540f81d6b1c2c2cd56309696fdc8546a6295c |
#!/usr/bin/env python
# Copyright 2014-2021 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/mp/dfump2_native.py | Python | apache-2.0 | 26,258 | [
"PySCF"
] | 2db960ec1098263013504b6c4a44b7b74370526e63f72719e7780b6a31403198 |
# This file is part of DEAP.
#
# DEAP 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 version.
#
# DEAP is distributed ... | DailyActie/Surrogate-Model | 01-codes/deap-master/examples/pso/multiswarm.py | Python | mit | 9,257 | [
"Gaussian"
] | 58a7cf72310b213223e6afb99f46f4eac19edc6de353b1c4d41c7e7f8f944166 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Top-level presubmit script for Chromium.
See http://dev.chromium.org/developers/how-tos/depottools/presubmit-scripts
for more details about the presu... | danakj/chromium | PRESUBMIT.py | Python | bsd-3-clause | 83,575 | [
"VisIt"
] | 468f6f82e1645ed2389335e749bf7abee24801e72461ef7039a94841303ef886 |
# coding: utf-8
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import random
import re
import socket
import sys
import time
import math
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_etree_fromstring,
compat_getpass,
compat... | valmynd/MediaFetcher | src/plugins/youtube_dl/youtube_dl/extractor/common.py | Python | gpl-3.0 | 110,711 | [
"VisIt"
] | 3220d5906779de864bfc77601946983ab0c52d90297b46e8bbbdd3aa633b3606 |
import os, sys
from shutil import copyfile
# Adds an allele to the DB
# Inputfile: (single or multiple) fasta file with gen and the allele sequence
# Source: Site or origin from where the alleles came from. PS: Must match the same name when adding ST data!!!
class AddAllele:
def __init__(self, inputfile, stfile, sour... | jeezes/Straintracer | AddAllele.py | Python | bsd-3-clause | 623 | [
"Galaxy"
] | 029b8789c2b47eb2ef83ae93d1cc30875a9dc8277129f00c751879b6cbef3c34 |
#!/usr/bin/env python
import os
import os.path
from sys import exit, argv
import json
import oauth2 as oauth
from StringIO import StringIO
from urlparse import parse_qsl
# Please don't use this key and secret if you create a new version of this script.
# You can request your own API key at https://dev.twitter.com/app... | mondalaci/twitter-backup.py | twitter-backup.py | Python | gpl-3.0 | 5,347 | [
"VisIt"
] | 06228e58145f49107858d00681319442e872d02ead5d4e0c9a14a32927f67bfd |
##
# Copyright 2016-2017 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | ULHPC/easybuild-easyblocks | easybuild/easyblocks/a/adf.py | Python | gpl-2.0 | 3,992 | [
"ADF"
] | 82da38304ff24f8bdc44cf303e6869dc90ae94576fa96741ba5ec82515983484 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 ... | sam-m888/gprime | gprime/plug/menu/_number.py | Python | gpl-2.0 | 2,802 | [
"Brian"
] | 8be8c764e7b75fb32f81aaff49309f0a10a0df759e712f907ed94aeb281733af |
# 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 RAffy(RPackage):
"""Methods for Affymetrix Oligonucleotide Arrays
The package cont... | LLNL/spack | var/spack/repos/builtin/packages/r-affy/package.py | Python | lgpl-2.1 | 1,581 | [
"Bioconductor"
] | 8e24abf28de9484693f959fe2241f0ea28327af9643ff811e22c72569c336c5c |
##
# Copyright 2009-2015 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | valtandor/easybuild-easyblocks | easybuild/easyblocks/w/wrf.py | Python | gpl-2.0 | 14,991 | [
"NetCDF"
] | 36230f3f111da17defce539e6144c37af4a12b6b7dd456afefc3a0871aae0286 |
from aces.materials.POSCAR import structure as Material
class structure(Material):
def getPOSCAR(self):
return """ACES POSCAR
1.00000000000000
4.3715553598745540 0.0000000000000000 0.0000000000000000
0.0000000000000000 4.2918241965252291 0.0000000000000000
... | vanceeasleaf/aces | aces/materials/SnSe_monolayer_minimize.py | Python | gpl-2.0 | 878 | [
"ASE"
] | 315380143e6d450c1a6fe07a40b7594ce47a0898b669cbf45e746abb617aa656 |
"""
Stack RAVE spectra from repeat visits.
"""
import cPickle as pickle
import os
import numpy as np
from astropy.table import Table
parent_spectrum_dir = "/data/gaia-eso/arc/rave/pre-normalized-spectra-with-correct-errors"
stacked_spectrum_dir = os.path.join(parent_spectrum_dir, "stacked-spectra")
if not os.path.... | AnnieJumpCannon/RAVE | stack_repeat_visit_spectra.py | Python | mit | 2,369 | [
"VisIt"
] | 4654ef5afa450d13e888b0ddb8809476d6c692d087adaa5c044c390c68e86315 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015, Vispy Development Team.
# Distributed under the (new) BSD License. See LICENSE.txt for more info.
from __future__ import division
import numpy as np
from ..gloo import Texture2D, VertexBuffer
from ..color import get_colormap
from .shaders import Function, FunctionChain
f... | kkuunnddaannkk/vispy | vispy/visuals/image.py | Python | bsd-3-clause | 15,670 | [
"Gaussian"
] | ed6807ab4cd5578cff4e60900e3bdc66dd918cd50d2ecbf898b7c4d89365bb2e |
#!/usr/bin/python3
import re
import os
import copy
import time
import yaml
import logging
import numpy as np
import pandas as pd
import camoco as co
import networkx as nx
from math import isinf
from itertools import chain
from flask import Flask, url_for, jsonify, request, send_from_directory, abort
print('Loading Ca... | schae234/cob | cob/server.py | Python | mit | 33,713 | [
"Cytoscape"
] | 850475e05a5b663f546e229e25e7308947fcdb3974f1902a902fc3ff69d15007 |
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Provides interfaces to various commands provided by FreeSurfer
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.p... | mick-d/nipype | nipype/interfaces/freesurfer/preprocess.py | Python | bsd-3-clause | 113,186 | [
"Gaussian"
] | 2e61d05e532e6b777125d267c1b1678871ac6ae733db766a8508e26dc35bf592 |
from ase import Atoms
from ase.optimize import QuasiNewton
from ase.neb import NEB
from ase.optimize.mdmin import MDMin
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
b = a / 2
initial = Atoms('Cu4',
positions=[(0, 0, 0),
(0, b, ... | grhawk/ASE | tools/ase/test/vacancy.py | Python | gpl-2.0 | 1,121 | [
"ASE"
] | 3d69e3a5c8d7b967e31ddc3ecc693fdcbc746382b24c0196554105be7e08562b |
# Generated by Django 2.1.4 on 2019-01-31 06:26
from django.conf import settings
import django.contrib.postgres.fields
import django.contrib.postgres.fields.jsonb
from django.db import migrations, models
import django.db.models.deletion
import herders.models
import timezone_field.fields
import uuid
class Migration(m... | PeteAndersen/swarfarm | herders/migrations/0001_initial.py | Python | apache-2.0 | 19,862 | [
"CRYSTAL"
] | f3052dc1f476566e2ed79491c2a11248f70f99121f67e850818d4ffbcb08fb9b |
"""
A set of objects representing each file extension recognized by ImageIO. If an
extension is not listed here it is still supported, as long as there exists a
supporting backend.
"""
from typing import List, Dict
class FileExtension:
"""File Extension Metadata
This class holds information about a image f... | imageio/imageio | imageio/config/extensions.py | Python | bsd-2-clause | 22,732 | [
"NetCDF",
"VTK"
] | bd7865b5f791f4a0faa35e3dc6ab1ae79316b8b2ff69028cfc6d4da6535bd09e |
#
# Copyright (C) 2011-2021 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import os
import sys
import tempfile
import unittest
f... | greglandrum/rdkit | rdkit/Chem/Draw/UnitTestDraw.py | Python | bsd-3-clause | 9,926 | [
"RDKit"
] | 813f8af74e47f5f14aa0cc658e6a0c5a9cc776a01a62cf3622984916b3481eae |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2011 - 2015 -- Lars Heuer <heuer[at]semagia.com>
# All rights reserved.
#
# License: BSD, see LICENSE.txt for more details.
#
"""\
Tests subject parsing.
:author: Lars Heuer (heuer[at]semagia.com)
:organization: Semagia - <http://www.semagia.com/>
:license: BSD lice... | heuer/cablemap | cablemap.core/tests/test_reader_subject.py | Python | bsd-3-clause | 13,996 | [
"VisIt"
] | 59d173b740ca684cf3eab6b734fea2304e337222d5fbaf19a6956d5ef0e32388 |
from numpy import (
vstack, where, intersect1d, in1d, unique,
cross, abs, arccos, sign,
dot, array, cov, nan_to_num, inf, pi,
hstack, repeat, bincount, arange
)
from numpy.linalg import norm, solve
class Box2D:
def __init__(self, *args, **kwargs):
if len(args) <= 5:
self._comp... | demianw/tract_querier | tract_querier/tract_math/tract_obb.py | Python | bsd-3-clause | 46,294 | [
"Mayavi"
] | d68c74330a80c4c8d5d21415a4f2523bf8fe3222a8da641992e1ce4040c52df0 |
#!/usr/bin/python
import os, sys # low level handling, such as command line stuff
import string # string methods available
import re # regular expressions
import getopt # comand line argument handling
from low import * # custom functions, written by myself
import anydbm # index databases (file ... | lotharwissler/bioinformatics | python/geneontology/go-from-blastout.py | Python | mit | 2,996 | [
"BLAST",
"Biopython"
] | 01e8d67b42890c5d7520479c1c24dc7a8f45fa509e0d1c76281912a3aa6a7397 |
"""\
PGBF.py Perform basic operations over primitive
gaussian basis functions. The equations herein are based upon
'Gaussian Expansion Methods for Molecular Orbitals.' H. Taketa,
S. Huzinaga, and K. O-ohata. H. Phys. Soc. Japan, 21, 2313, 1966.
[THO paper].
For the purposes of this routine, a gauss... | berquist/PyQuante | PyQuante/PGBF.py | Python | bsd-3-clause | 9,122 | [
"Gaussian"
] | dd0364858cf75e6112e9f246ccaad71a682e90e043f09953dd293f2650fa594a |
# Storage filtering classes
#
# Copyright (C) 2013 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, or (at your option) any later version.
# This program is distributed... | wgwoods/anaconda | pyanaconda/ui/gui/spokes/filter.py | Python | gpl-2.0 | 27,975 | [
"VisIt"
] | 8fe7117ac429c1b4ac7c0e12e635a2d8d1d74302de5ca0953086e6d252998dc4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
=========================================================================
Program: Visualization Toolkit
Module: TestNamedColorsIntegration.py
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or http://www.... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Rendering/Core/Testing/Python/cells.py | Python | gpl-3.0 | 27,469 | [
"VTK"
] | ace6e5aa12af641603004e402ebd88f9839ae8e27b2b1b8e0b3334518a7619f2 |
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar, Evan Feinberg, and Karl Leswing"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "MIT"
import os
import shutil
from warnings import warn
import time
import tempfile
import hashlib
from collecti... | Agent007/deepchem | deepchem/feat/rdkit_grid_featurizer.py | Python | mit | 51,675 | [
"RDKit"
] | 3065817a3d40ba62ffe4979bd3117d1a17756e0170dbf4e9c915c83870648067 |
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