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# (C) British Crown Copyright 2011 - 2020, Met Office
#
# This file is part of cartopy.
#
# cartopy 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)... | ocefpaf/cartopy | setup.py | Python | lgpl-3.0 | 17,000 | [
"NetCDF"
] | 6f3e971832133d3850da88736e9f5f4ece0d09321d2f252be787bcac311d294a |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2013 João Faria
# This file is part of OPEN which is licensed under the MIT license.
# You should have received a copy of the license along with OPEN. See LICENSE.
#
"""
This module defines the commands that are used as magics in OPEN.
"""
# standard library imports
import glo... | j-faria/OPEN | OPEN/commandsOPEN.py | Python | mit | 45,516 | [
"Gaussian"
] | 9c89c1948a774c65a827044458ee1cd40b83c1d5a4e16c1512f83f1f2997cd32 |
import math
import operator
from csg.geom import *
from functools import reduce
class CSG(object):
"""
Constructive Solid Geometry (CSG) is a modeling technique that uses Boolean
operations like union and intersection to combine 3D solids. This library
implements CSG operations on meshes elegantly and ... | timknip/pycsg | csg/core.py | Python | mit | 20,425 | [
"VTK"
] | b6ea4783fa7d9a2abfdad3de7d0f8cff704d567dfe378c05c10343ccbe377b46 |
## minerals.py -- Some tables for ISM abundances and depletion factors
## that are useful for calculating dust mass and dust-to-gas ratios
##
## 2016.01.22 - lia@space.mit.edu
##----------------------------------------------------------------
import numpy as np
amu = {'H':1.008,'He':4.0026,'C':12.011,'N':14.007,'... | eblur/dust | astrodust/distlib/composition/minerals.py | Python | bsd-2-clause | 3,836 | [
"CRYSTAL"
] | b42f24fd9fe711676f66dd736ab4e6b1827286a82d3e1c34211e5ee0bee892b9 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | examples/ex14_pps/mms_spatial.py | Python | lgpl-2.1 | 743 | [
"MOOSE"
] | 1d044ba9ad40c8c129563534feb7cbe8ad96df067cb1fb5a703db90af3fb116e |
#!/usr/bin/env python
"""
fsclean.py
Faraday synthesis using 3D CLEAN deconvolution
*******************************************************************************
Copyright 2012 Michael Bell
This file is part of fsclean.
fsclean is free software: you can redistribute it and/or modify
it under the terms of the GN... | mrbell/fsclean | fsclean.py | Python | gpl-3.0 | 28,709 | [
"Gaussian"
] | 1456c33b4a0ace8b28f0de7b1007127754b8bee06cc5ca11c6b6dbe54a1fe2f6 |
# Copyright 2013-2015 James S Blachly, MD and The Ohio State University
#
# This file is part of Mucor.
#
# Mucor 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,... | blachlylab/mucor | mucorfeature.py | Python | gpl-3.0 | 3,693 | [
"HTSeq"
] | 93b223ba1a1066728c3b38a155b660e9d341c562204a91efd6671db1878d974c |
# Library of simple models.
import moose
def simple_model_a():
compt = moose.CubeMesh( '/compt' )
r = moose.Reac( '/compt/r' )
a = moose.Pool( '/compt/a' )
a.concInit = 1
b = moose.Pool( '/compt/b' )
b.concInit = 2
c = moose.Pool( '/compt/c' )
c.concInit = 0.5
moose.connect( r, 'sub... | upibhalla/moose-core | tests/python/models.py | Python | gpl-3.0 | 798 | [
"MOOSE"
] | 202a080eab7cf9d0328f2129f638a3e095e9a623edf8656536d14841f8dbd26c |
# -*- coding: utf-8 -*-
"""
End-to-end tests related to the cohort management on the LMS Instructor Dashboard
"""
from datetime import datetime
from pymongo import MongoClient
from pytz import UTC, utc
from bok_choy.promise import EmptyPromise
from .helpers import CohortTestMixin
from ..helpers import UniqueCourseTe... | olexiim/edx-platform | common/test/acceptance/tests/discussion/test_cohort_management.py | Python | agpl-3.0 | 31,431 | [
"VisIt"
] | 49c6f70befa75a4d80489261b1a17d7de9e7209912f0b0d37e478e7477c91f03 |
# $HeadURL: $
''' ResourceManagementDB
Module that provides basic methods to access the ResourceManagementDB.
'''
from datetime import datetime
import sys
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.DB import DB
from DIRAC.Res... | coberger/DIRAC | ResourceStatusSystem/DB/ResourceManagementDB.py | Python | gpl-3.0 | 20,405 | [
"DIRAC"
] | ba420e2a57126ed4aee28bc25cefe2ecbea361bfbc2c0c6d9832ebd836dd74b2 |
"""Definitions of the free parameters.
The free parameters are meant to be used for parameters that one wants to optimize. They can be fixed to a certain
value to disable them from being optimized in a given situation, but they remain classified as 'optimizable' parameters.
"""
from mdt import FreeParameterTemplate
f... | cbclab/MDT | mdt/data/components/standard/parameters/free.py | Python | lgpl-3.0 | 6,030 | [
"Gaussian"
] | 93e825e0b6efda01ac83269dc93e6156706c617873e8970dde2092358efc76a1 |
# Copyright (C) 2021 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | espressomd/espresso | testsuite/scripts/tutorials/test_error_analysis_part1.py | Python | gpl-3.0 | 4,252 | [
"ESPResSo"
] | 1d1f662f6da300e7c7bb5196f190ca828c31f0eb1aeed47a3624a767da95d066 |
from Bio.Blast import NCBIXML as nx
import sys
import os
import matplotlib.pyplot as plt
from matplotlib.ticker import ScalarFormatter, FormatStrFormatter
import argparse
parser = argparse.ArgumentParser(description='Parse & plot blast results')
parser.add_argument('--bed', help='bed file of SV regions', type=str)
par... | berguner/svmap | svmap.py | Python | gpl-3.0 | 9,738 | [
"BLAST"
] | de17bf799ddb7659109a4e67a99e147db429bda6b2fa2ba0e1fe7916c015ec13 |
# Version: 0.16
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.3, 3.4, 3.5, and pypy
* [![Latest Version]
(https://py... | jakirkham/dask | versioneer.py | Python | bsd-3-clause | 65,581 | [
"Brian"
] | 2751332cc6684c5de41c4234d1ab9daf08f7705f7f291a6a51eefcde35f7f1d8 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Provides the capability to load netCDF files and interpret them
according to the 'NetCDF Climate and Forecast (CF) Metadata... | pp-mo/iris | lib/iris/fileformats/cf.py | Python | lgpl-3.0 | 45,520 | [
"NetCDF"
] | e235156e7f89f300ee5a7464a16819ccd2fd0f54474ac554664193a3f678d057 |
"""
Acceptance tests for Studio related to the container page.
"""
from ..pages.studio.auto_auth import AutoAuthPage
from ..pages.studio.overview import CourseOutlinePage
from ..fixtures.course import CourseFixture, XBlockFixtureDesc
from .helpers import UniqueCourseTest
class ContainerBase(UniqueCourseTest):
""... | nanolearning/edx-platform | common/test/acceptance/tests/test_studio_container.py | Python | agpl-3.0 | 13,333 | [
"VisIt"
] | 10bf9e54bfbb65523edb41f7418a0eeab6bede6b287e2cbc30b0108014cfc348 |
"""Hyperion config flow."""
from __future__ import annotations
import asyncio
from contextlib import suppress
import logging
from typing import Any
from urllib.parse import urlparse
from hyperion import client, const
import voluptuous as vol
from homeassistant.components.ssdp import ATTR_SSDP_LOCATION, ATTR_UPNP_SER... | sander76/home-assistant | homeassistant/components/hyperion/config_flow.py | Python | apache-2.0 | 20,066 | [
"VisIt"
] | 032059127990749aec641ee9ddc79288de1535b0cc71287ee0984fc838650a22 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# This software (including its Debian packaging) is available to you under the terms of the GPL-3,
# see "/usr/share/common-licenses/GPL-3".
# Software is created and maintained by Laboratory of Biomolecular Systems Simulation at University of Gdansk.
# Contributors:
# - ... | tomaszmakarewicz/Dynamics | pymol_plugin_dynamics.py | Python | gpl-3.0 | 125,074 | [
"Gaussian",
"Gromacs",
"PyMOL"
] | 9ad0a9408313580a5eec2687b9ef86cba2114bc47f13d04a24eaf4fd38fafefc |
"""
Generate samples of synthetic data sets.
"""
# Authors: B. Thirion, G. Varoquaux, A. Gramfort, V. Michel, O. Grisel,
# G. Louppe, J. Nothman
# License: BSD 3 clause
import numbers
import warnings
import array
import numpy as np
from scipy import linalg
import scipy.sparse as sp
from ..preprocessing impo... | soulmachine/scikit-learn | sklearn/datasets/samples_generator.py | Python | bsd-3-clause | 53,169 | [
"Gaussian"
] | 6ae48e4ecee6e5885559ffe28cc77fd1adc02653e79caeae61190dc14de4ab43 |
import argparse
import inspect
import logging
import json
import base64
from docstring_parser import parse
from collections import namedtuple
from flask import Flask, request
from flask_restx import Api, Resource, fields, abort
from flask_cors import CORS
from indra import get_config
from indra.sources import trips, ... | johnbachman/belpy | rest_api/api.py | Python | mit | 43,684 | [
"Cytoscape"
] | a72b131c716da6f6a97b2a0cc9bb8fd616f80f23d466e09846fed5a236c091d3 |
#!/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/Interaction/Style/Testing/Python/TestStyleJoystickActor.py | Python | gpl-3.0 | 2,123 | [
"VTK"
] | 39c738a1dc5854a6115d628bc942d51f39a8c1035ffd9013b382da0903b77fd0 |
# model from Alex's flipflop file
from keras.layers import TimeDistributed, Dense, Activation
from keras.models import Sequential
from keras.constraints import maxnorm
from backend.Networks import leak_recurrent, dense_output_with_mask
def SimpleRecurrentModel(params):
model = Sequential()
# Incorporating ... | ABAtanasov/KerasCog | models/SimpleRecurrent.py | Python | mit | 1,270 | [
"NEURON"
] | 5b037cf0843b6087810006aba8fa7a7e8adf0ba4ee1c35f109601fa0fa2ff1ad |
#!/usr/bin/env python
#########################################################################################
# Register a volume (e.g., EPI from fMRI or DTI scan) to an anatomical image.
#
# See Usage() below for more information.
#
# ----------------------------------------------------------------------------------... | neuropoly/spinalcordtoolbox | spinalcordtoolbox/scripts/sct_register_multimodal.py | Python | mit | 20,460 | [
"Gaussian"
] | be876ac9a526fc8a4b0c826c74d92c1dbb5ed6be55241a0936fd1b5ed333c6b2 |
"""
Copyright (c) 2014 Brian Muller
Copyright (c) 2015 OpenBazaar
"""
import random
from twisted.internet import defer
from zope.interface import implements
import nacl.signing
from dht.node import Node
from dht.routing import RoutingTable
from dht.utils import digest
from log import Logger
from rpcudp import RPCProto... | JimmyMow/OpenBazaar-Server | dht/protocol.py | Python | mit | 7,311 | [
"Brian"
] | f604e8205b831667599a3b30d11e76b299dfc6f3cb09511f68fa5abb10f75c96 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | kubernetes/autoscaler | hack/boilerplate/boilerplate.py | Python | apache-2.0 | 8,389 | [
"VisIt"
] | f0ab66fc97baf78a9e92a98cc9a24af44db0488603864ddd888f17643ee6e266 |
"""An NNTP client class based on RFC 977: Network News Transfer Protocol.
Example:
>>> from nntplib import NNTP
>>> s = NNTP('news')
>>> resp, count, first, last, name = s.group('comp.lang.python')
>>> print 'Group', name, 'has', count, 'articles, range', first, 'to', last
Group comp.lang.python has 51 articl... | nmercier/linux-cross-gcc | win32/bin/Lib/nntplib.py | Python | bsd-3-clause | 22,106 | [
"Brian"
] | 61ddc278f54de75ef4c4d3b7f3cae18e59dfd98836d7ed0c701d24c963d630ca |
"""
Holds user settings and various helper objects.
@since: 0.53
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import support, _, logger
import os
try:
import ConfigParser
except ImportError:
import configparser as ConfigParser
from zero... | AlexanderRyzhko/0install-TUF | zeroinstall/injector/config.py | Python | lgpl-2.1 | 4,768 | [
"VisIt"
] | f7d25b9744ce18a5e0f6452af2889f0afb62da0f6ad1f616df4744dd0c5a613b |
#!/usr/bin/env python
#
# Copyright (c) 2016 Apple Inc. 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
# notice, this list o... | teamfx/openjfx-8u-dev-rt | modules/web/src/main/native/Source/JavaScriptCore/Scripts/builtins/builtins_generate_internals_wrapper_implementation.py | Python | gpl-2.0 | 7,074 | [
"VisIt"
] | a7ee97ff98b75ede14b38b9e281a77828b76bd37593c6be5473681de7e6c883e |
#!/usr/bin/python -u
import datetime, os, sys, stat, subprocess, re, shutil, time
import select
import numpy
import netcdf
import ConfigParser
config = ConfigParser.ConfigParser()
config.readfp(open(r'/home/pi/rpilogger/catnc.conf'))
if (config.has_option('default','LOCATION_IN')):
_LOCATION_IN = config.get('defa... | deguss/rpilogger | development/catnc.py | Python | gpl-2.0 | 19,981 | [
"NetCDF"
] | 7939f053f7a32a7301ac1e5adab6bb7122befd3b612a5bdcb169944ec71229b9 |
# 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>
# Giorgio Patrini <giorgio.patrini@anu.edu.au>
# ... | BiaDarkia/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 117,634 | [
"Gaussian"
] | da78accd317a650daa8bde486b7d6e5b78bb302724004ce6f39d0ac701244c8a |
'''
Utility class for finding, selecting, weighting, and loading observation data
for neighboring stations around a point location.
Copyright 2014, Jared Oyler.
This file is part of TopoWx.
TopoWx is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publishe... | jaredwo/topowx | twx/interp/station_select.py | Python | gpl-3.0 | 6,881 | [
"Gaussian"
] | c88ded832fea13dd2a6d638b64356bd34f8d414da1ccd132748fb6ca3806f249 |
#!/usr/bin/env python
# encoding: utf-8
"""
Functions related to sky subtraction.
high level iraf wrappers: combine_sky_spectra, setairmass_galaxy, skies
sky_subtract_galaxy
low level FITS functions: find_line_peak, find_lines, get_continuum,
get_peak_cont, get_wave... | tungol/mslit | mslit/sky.py | Python | unlicense | 8,187 | [
"Galaxy"
] | f4cef3f38826120f54e50e9182a659aa4a6bf68e655377bcbc52ec33f8981c43 |
from django.shortcuts import render, redirect
from django.core.urlresolvers import reverse
from django.contrib.auth.decorators import login_required
from django.http import HttpResponse
from django.utils.encoding import smart_str
from django.core.servers.basehttp import FileWrapper
from tethys_gizmos.gizmo_options imp... | CI-WATER/tethysapp-ssw_downloader | tethysapp/ssw_downloader/controllers.py | Python | bsd-2-clause | 5,053 | [
"NetCDF"
] | 71d33ebb622b644fd8d19b938829f39d1ade946699c6516b42dd08f117bd99a3 |
"""
Generates protein-ligand docked poses using Autodock Vina.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "GPL"
import numpy as np
import os
impor... | bowenliu16/deepchem | deepchem/dock/pose_generation.py | Python | gpl-3.0 | 6,276 | [
"Pybel"
] | 304307cae65106a8c84dc5bba96ccd55302f8d495c780d60989180db9ff4f5ec |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | harterj/moose | python/chigger/base/ChiggerResult.py | Python | lgpl-2.1 | 5,871 | [
"MOOSE"
] | f003cf845e9b0dbaa895f232c4ba56a1da68a5b36cc8556c4e30a33818fcd051 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides classes for analyzing phase diagrams.
"""
from six.moves import zip
import numpy as np
import itertools
import collections
from mont... | xhqu1981/pymatgen | pymatgen/phasediagram/analyzer.py | Python | mit | 19,907 | [
"pymatgen"
] | 78642eee1dd5cbfa66548493806ea594088cc972d6451b69056299abdd9d2247 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import numpy as np
import warnings
from ..utils.exceptions import AstropyUserWarning
from ..extern.six.moves import range
__all__ = ['sigma_clip... | joergdietrich/astropy | astropy/stats/sigma_clipping.py | Python | bsd-3-clause | 11,671 | [
"Gaussian"
] | 60a2f800b4b40ae6caeb9ddfca63e76bc244efdf72a483ce86d85dbea31691d3 |
""" ConstantExpressions gathers constant expression. """
from pythran.analyses.aliases import Aliases
from pythran.analyses.globals_analysis import Globals
from pythran.analyses.locals_analysis import Locals
from pythran.analyses.pure_expressions import PureExpressions
from pythran.intrinsic import FunctionIntr
from ... | hainm/pythran | pythran/analyses/constant_expressions.py | Python | bsd-3-clause | 3,547 | [
"VisIt"
] | aca06fb83041a331374c958678d2967af177cfb73ea8da1df7f4f04a315e99e0 |
""" Module invoked for finding and loading DIRAC (and extensions) modules
"""
import os
import imp
from DIRAC.Core.Utilities import List
from DIRAC import gConfig, S_ERROR, S_OK, gLogger
from DIRAC.ConfigurationSystem.Client.Helpers import getInstalledExtensions
from DIRAC.ConfigurationSystem.Client import PathFinder
... | arrabito/DIRAC | Core/Base/private/ModuleLoader.py | Python | gpl-3.0 | 9,349 | [
"DIRAC"
] | 70b25cf0a388c6fb633ce0ce6fe0c330890eb2ab77ebbd83b247f8af7afe9a87 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements DefectCompatibility analysis for consideration of
defects
"""
import logging
from monty.json import MSONable
from pymatgen.analysis.defects.core import Vacancy
from pymatgen.analysis.defects.corre... | materialsproject/pymatgen | pymatgen/analysis/defects/defect_compatibility.py | Python | mit | 29,940 | [
"pymatgen"
] | 4ccc82cd886865e1a2ba7eeb0bc90f94d9db0601bdb63fa9863a68646548f2a0 |
# -*- coding: utf-8 -*-
#
# Copyright © 2013-2015 Michael Rabbitt, Roberto Alsina and others.
#
# 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
# without limita... | techdragon/nikola | nikola/plugins/compile/markdown/mdx_podcast.py | Python | mit | 3,699 | [
"Brian"
] | 34d868fcb11f8acb4197fb8a5451516219ded2bba140a18aacafbeb13351cdee |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2012, 2013 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | Freeseer/freeseer | src/freeseer/tests/frontend/reporteditor/test_reporteditor.py | Python | gpl-3.0 | 3,212 | [
"VisIt"
] | 8922249dac9937c6833ebcefb03e5d02a3c447e9a9006231c9fa539b3663977d |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2010 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program 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 F... | tiagocardosos/stoq | stoqlib/gui/search/taxclasssearch.py | Python | gpl-2.0 | 2,078 | [
"VisIt"
] | ce9517d35b5df61de0e8a6e674d0357a4fe55678caa5b2e72e6602603e239800 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
==============================================================================
Gaussian Processes classification example: exploiting the probabilistic output
==============================================================================
A two-dimensional regression exerci... | mrshu/scikit-learn | examples/gaussian_process/plot_gp_probabilistic_classification_after_regression.py | Python | bsd-3-clause | 3,486 | [
"Gaussian"
] | de49ae949ad7b6e0c9cb3cf253265e246864214dfb99c3b2af621e1b0d99b83a |
# =========================================================================
#
# Imports
#
# =========================================================================
import unittest
from .context import constants
from .context import euler_physics
import numpy as np
import numpy.testing as npt
# ======================... | marchdf/dg1d | tests/test_euler_physics.py | Python | apache-2.0 | 7,497 | [
"BLAST"
] | 6b546f7c022aca704f63894503cfffe845f2b25f6bd7e6508dfd411e46eaa410 |
#!/usr/bin/env python2.7
from __future__ import with_statement
import hashlib
import os
import random
import re
import sys
from pprint import pprint
from fabric import api
from fabric import network
from fabric.colors import blue, green, red, white, yellow, magenta
from fabric.api import abort, cd, local, env, settings... | samsath/cpcc_backend | fabfile.py | Python | gpl-3.0 | 14,658 | [
"GULP"
] | bb409607d9da0a2acf86f326e485af92f3b7684f470d3faa09dbcb1f7660151e |
from rdkit import Chem
# match_atom_index can be of type int or a list - otherwise trouble.
#
# Note that atom_type properties can also have been set in hydrogen_transformations():
#
def set_atom_type(match, match_atom_index, mol, atom_type):
try:
this_atom = match[match_atom_index]
try:
... | jlec/coot | pyrogen/atom_types.py | Python | gpl-3.0 | 8,934 | [
"RDKit"
] | 5729294a6fee8630b5077238a0a374680d52c667571040204d0a5840853cb7ba |
"""
I/O for Tecplot ASCII data format, cf.
<https://github.com/su2code/SU2/raw/master/externals/tecio/360_data_format_guide.pdf>,
<http://paulbourke.net/dataformats/tp/>.
"""
import numpy as np
from ..__about__ import __version__ as version
from .._common import warn
from .._exceptions import ReadError, WriteError
fro... | nschloe/meshio | src/meshio/tecplot/_tecplot.py | Python | mit | 15,144 | [
"ParaView",
"VisIt"
] | 971e3b7dec73c45a223e699d295f171802b58e5c4b00dea43c6cf1d769e84132 |
#!/usr/bin/python
# -*- coding: iso8859-2 -*-
#
# qclib - Quantum Computing library for Python
# Copyright (C) 2006 Robert Nowotniak <rnowotniak@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Softwar... | rnowotniak/qclib | qctest.py | Python | gpl-3.0 | 5,888 | [
"DIRAC"
] | 4c4780398f00577132b94451422b5e8f410655407c1c384808861972e42e5137 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Defines parameters for simulation, used by example_parallel_network.py script
Copyright (C) 2018 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publis... | LFPy/LFPy | examples/bioRxiv281717/example_parallel_network_parameters.py | Python | gpl-3.0 | 29,269 | [
"NEURON"
] | 8000c39b23e09856503522c1090b4385120578a43a2eee0680cd64094c451f3d |
#!/usr/bin/env python
"""
==================
ModEM
==================
# Generate data file for ModEM
# by Paul Soeffky 2013
# revised by LK 2014
# revised by JP 2014
# edited by AK 2016
"""
import os
import mtpy.core.z as mtz
import mtpy.core.mt as mt
import numpy as np
import mtpy.utils.latlongutmconversion as utm... | geophysics/mtpy | mtpy/modeling/modem_new.py | Python | gpl-3.0 | 377,608 | [
"ParaView",
"VTK"
] | dd674a64c6b77e6e3d69b737ebf49ae1fcb5f839b8f9b77e0ce890673e082226 |
from nose2.compat import unittest
from nose2.tools import params
import re
class TestBasicReFunction(unittest.TestCase):
def setUp(self):
pass
def tearDown(self):
pass
def test_001_match_something_at_the_beginning(self):
# re.match only works at the beginning of string
mat... | minhhh/wiki | code/regex/test_regex.py | Python | mit | 3,997 | [
"ADF"
] | cc4c89df727e91c5b6d0fa9841054dd66b1690577138d7e4f82fae70647093d4 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkVoxelContoursToSurfaceFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkVoxelContoursToSurfaceFilter.py | Python | bsd-3-clause | 517 | [
"VTK"
] | 9f76cc8e88e1260fe188866d80aef0fb1f3f8df57c427e2a427dc3b5fd769877 |
import vtk
import numpy as np
from glue.external.qt import QtGui
from vtk.qt4.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
from palettable.colorbrewer import get_map
__all__ = ['QtVTKWidget']
class QtVTKWidget(QtGui.QWidget):
def __init__(self, parent=None):
super(QtVTKWidget, self).__... | astrofrog/cube-viewer | cube_viewer/vtk_widget.py | Python | bsd-2-clause | 4,614 | [
"VTK"
] | 50cce984e4947b3b02e57daa8d749f4a60b227c22040e168b4f467818068c2c6 |
#------------------------------------------------------------------------------
# pycparser: c_generator.py
#
# C code generator from pycparser AST nodes.
#
# Copyright (C) 2008-2015, Eli Bendersky
# License: BSD
#------------------------------------------------------------------------------
from . import c_ast... | hipnusleo/laserjet | resource/pypi/pycparser-2.17/pycparser/c_generator.py | Python | apache-2.0 | 14,236 | [
"VisIt"
] | 45918c3df9458ad0dff0b1d592b20a8918f9a55c95d06a0ea2e17c331de8796f |
# geotecha - A software suite for geotechncial engineering
# Copyright (C) 2018 Rohan T. Walker (rtrwalker@gmail.com)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the L... | rtrwalker/geotecha | geotecha/inputoutput/test/test_inputoutput.py | Python | gpl-3.0 | 38,372 | [
"VisIt"
] | db9bf6d0cb800440a7f0d0c5df067711526094f51a03ec0bad00fad911a5865c |
#
# Copyright 2015 Olli Tapaninen, VTT Technical Research Center of Finland
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | ollitapa/MMP-TracerApi | Tests/MeshTests/meshConeTest.py | Python | apache-2.0 | 1,598 | [
"VTK"
] | 22578206ea0cf09f1c97cc9be08e489de0bf368b8acffce13d2c95d1c7570dbd |
import logging
from paste.httpexceptions import HTTPBadRequest, HTTPForbidden
from time import strftime
from galaxy import util
from galaxy import web
from galaxy import exceptions
from galaxy.web import _future_expose_api as expose_api
from galaxy.util import json
from galaxy.web.base.controller import BaseAPIContro... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py | Python | gpl-3.0 | 30,735 | [
"Galaxy"
] | 3d76b4c911175eaf59804bc2b190264eeceea664815f9403e5522a73226089ae |
#!/usr/bin/env python
#===============================================================================
# Copyright (c) 2014 Geoscience Australia
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
... | alex-ip/agdc | agdc/abstract_ingester/mosaic_contents.py | Python | bsd-3-clause | 10,867 | [
"NetCDF"
] | 556ed5302afc84e18c49d281dd78300e0480f8b12661448d193a3fa0a5f4b527 |
farmer = {
'kb': '''
Farmer(Mac)
Rabbit(Pete)
Mother(MrsMac, Mac)
Mother(MrsRabbit, Pete)
(Rabbit(r) & Farmer(f)) ==> Hates(f, r)
(Mother(m, c)) ==> Loves(m, c)
(Mother(m, r) & Rabbit(r)) ==> Rabbit(m)
(Farmer(f)) ==> Human(f)
(Mother(m, h) & Human(h)) ==> Human(m)
''',
# Note that this order of conjuncts
# would r... | WmHHooper/aima-python | submissions/Martinez/myLogic.py | Python | mit | 2,339 | [
"Amber"
] | fdf491b7888a6dd8b11a619dcecf0ec7a7fc92b4636da7e39f342c01ebb14c9c |
"""
Generate samples of synthetic data sets.
"""
# Authors: B. Thirion, G. Varoquaux, A. Gramfort, V. Michel, O. Grisel,
# G. Louppe
# License: BSD 3 clause
from itertools import product
import numbers
import numpy as np
from scipy import linalg
from ..utils import array2d, check_random_state
from ..utils i... | florian-f/sklearn | sklearn/datasets/samples_generator.py | Python | bsd-3-clause | 43,680 | [
"Gaussian"
] | 58f43fa70720e5ad5cd5eca2da52c541e5dbb0497d7c8be9d4e20037c14934ed |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | dwhswenson/mdtraj | tests/test_xml.py | Python | lgpl-2.1 | 1,415 | [
"MDTraj"
] | 0af44a41656138eeee4ce0729098908b190a5459737a661ec9417dcd06c0fbc1 |
"""Base class for mixture models."""
# Author: Wei Xue <xuewei4d@gmail.com>
# Modified by Thierry Guillemot <thierry.guillemot.work@gmail.com>
# License: BSD 3 clause
from __future__ import print_function
import warnings
from abc import ABCMeta, abstractmethod
from time import time
import numpy as np
from .. impor... | zuku1985/scikit-learn | sklearn/mixture/base.py | Python | bsd-3-clause | 16,649 | [
"Gaussian"
] | d6870d0f873669882f70c280cd5134f9f4d97ce82422f2833e8720a099fec6a7 |
#!/usr/bin/env python3
# -*- encoding: utf-8 -*-
import numpy as np
import stripeline.rng as rng
class FlatRNG:
'Random number generator with uniform distribution in the range [0, 1['
def __init__(self, x_init=0, y_init=0, z_init=0, w_init=0):
'''Initialize the random number generator.
The ... | ziotom78/stripeline | stripeline/noisegen.py | Python | mit | 3,655 | [
"Gaussian"
] | da5b40b84c0700a1673d16d3a05577cffa2ccf458ca2f2339b084c875bd2825d |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module provides a class to fit elliptical isophotes.
"""
import warnings
from astropy.utils.exceptions import AstropyUserWarning
import numpy as np
from .fitter import (DEFAULT_CONVERGENCE, DEFAULT_FFLAG, DEFAULT_MAXGERR,
D... | astropy/photutils | photutils/isophote/ellipse.py | Python | bsd-3-clause | 33,805 | [
"Galaxy"
] | 740526071003fb0b94d236451a6687374bac988e6471710eca0eb84f156649ef |
#!/usr/bin/env python
# Copyright 2017 Informatics Matters Ltd.
#
# 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... | InformaticsMatters/pipelines | src/python/pipelines/rdkit/rxn_smarts_filter.py | Python | apache-2.0 | 4,919 | [
"RDKit"
] | ce8a5ee79cce3f2367fc4a40fcb60d9660f5c00dcbc3e1e83f0306bf1c3ef671 |
# coding: utf-8
# Copyright (c) 2013 Jorge Javier Araya Navarro <jorgean@lavabit.org>
#
# This file is free software: you may copy, redistribute 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... | shackra/thomas-aquinas | summa/summanode.py | Python | bsd-3-clause | 28,940 | [
"VisIt"
] | 67eccbcfc188d946c35d11906f345b21776c68b186e061b1140aba87ee24bc37 |
# Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
# 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 copyrigh... | bp-kelley/rdkit | Code/GraphMol/ChemReactions/Wrap/testSanitize.py | Python | bsd-3-clause | 10,894 | [
"RDKit"
] | 4de2a2c50bad3de37dab6016441e318e8914374af7780d52762482abb4d8be20 |
'''
module: utils.py
use: contains functions associated with general functionality that are not unique to any particular part of the project
'''
import numpy as np
#from scipy.stats import mode #this isnt actually used i think
def getDifferenceArray(vector):
'''
Purpose:
Takes an m by n vector and returns a sym... | jvahala/lucid-robotics | code/python-modules/utils.py | Python | apache-2.0 | 21,305 | [
"Gaussian"
] | a85e88e8b70600ff2642543e1a5a0d1a40278c1ea43b7af93596c6420736cd73 |
"""
# Copyright (C) 2007 Nathan Ramella (nar@remix.net)
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# T... | shouldmakemusic/yaas | LiveOSC/UDPServer.py | Python | gpl-2.0 | 6,206 | [
"VisIt"
] | 9d1db32a84d1e8ff6925685c21afa08967e7639b79942177c30dd67d750ea7a7 |
'''
@author Sumedha Ganjoo
@see LICENSE (MIT style license file).
'''
import os.path
import sys
outputfile=open(sys.argv[2],'w')
outputfile.seek(0,0)
outputfile.write('\n Tool added...For independent use, find the tool under Web Service Tools on the left side window, \n and for use in workflows find the tool und... | UGA-WSAG/wsextensions | WebServiceToolWorkflow_REST_SOAP/refreshTool.py | Python | mit | 469 | [
"Galaxy"
] | dff32671e548439627ba6d30c73076cd6c7493d39ac7167f3033a99b64349c71 |
#!/usr/bin/python
#
# Copyright (c) 2012 The Native Client Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
#
"""
Checks (rule) patterns associated with rows in tables, and adds an
additional column to each row (in each table) which cap... | endlessm/chromium-browser | native_client/src/trusted/validator_arm/dgen_add_patterns.py | Python | bsd-3-clause | 11,007 | [
"VisIt"
] | 00c426769d2d34afef37189cb40bdfb7f93970393ad4c9aafb4a9da6b3d85ff2 |
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import norm
from scipy.integrate import cumtrapz
from scipy.interpolate import interp1d
N_ROLLS = 1000
NPTS = 100
# unfair die
Pr12 = 0.25
Pr6 = 0.5
Pr4 = 0.25
m_12 = N_ROLLS / 12.
s_12 = np.sqrt(N_ROLLS*(1/12.)*(11/12.))
m_6 = N_ROLLS / 6.
s_6 = np... | amaggi/bda | chapter_02/ex_04.py | Python | gpl-2.0 | 1,323 | [
"Gaussian"
] | 97ee5ed03c223421c60920c58148a83ef0de6aaff396e818096b6dd16e04baad |
#coding=utf-8
"""This module contains the "Viz" objects
These objects represent the backend of all the visualizations that
Caravel can render.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import copy
import has... | wbsljh/caravel | caravel/viz.py | Python | apache-2.0 | 67,464 | [
"VisIt"
] | dc3ff4ec182a5a641b5cf3bef4eb67e4d1593d243981c419a4abce69b0c8e083 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the Google Chrome History database plugin."""
import unittest
from plaso.lib import definitions
from plaso.parsers.sqlite_plugins import chrome_history
from tests.parsers.sqlite_plugins import test_lib
class GoogleChrome8HistoryPluginTest(test_lib.SQLiteP... | Onager/plaso | tests/parsers/sqlite_plugins/chrome_history.py | Python | apache-2.0 | 8,746 | [
"VisIt"
] | efa2246df9612aba0e1eb77ceda33d1856e5a812d18d43441ca5f49492fd8c0d |
"""
The B{0install add-feed} command-line interface.
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import SafeException, _
from zeroinstall.support import tasks, raw_input
from zeroinstall.cmd import Us... | dsqmoore/0install | zeroinstall/cmd/add_feed.py | Python | lgpl-2.1 | 3,461 | [
"VisIt"
] | 0085138101a82692a54987abe5d6553e94be63893c8093667c824f70be9eed78 |
import re
from pygments.lexers.theorem import IsabelleLexer
from pygments.lexer import RegexLexer, inherit, bygroups, words
from pygments.token import *
import encoding
__all__ = ['IsarLexer']
class IsarLexer(IsabelleLexer):
name = 'Isabelle/Isar'
keyword_cartouche_text = ('text', 'txt', 'text_raw',
'chapter', ... | lohner/Praktomat | src/utilities/isar_lexer.py | Python | gpl-2.0 | 23,943 | [
"Bowtie"
] | 92a7d32658d3c52fcccde55e86f23aa2f3eac24e337efa751701996884a107e3 |
# -*- coding: utf-8 -*-
"""upload_docs
Implements a Distutils 'upload_docs' subcommand (upload documentation to
PyPI's pythonhosted.org).
"""
from base64 import standard_b64encode
from distutils import log
from distutils.errors import DistutilsOptionError
import os
import socket
import zipfile
import tempfile
import ... | RalfBarkow/Zettelkasten | venv/lib/python3.9/site-packages/setuptools/command/upload_docs.py | Python | gpl-3.0 | 7,151 | [
"VisIt"
] | e3cd8177b92c0417f37689318cd42f9d1d00e9d83c5ce391120f700790702ad5 |
r"""protocols is a module that contains a set of VTK Web related
protocols that can be combined together to provide a flexible way to define
very specific web application.
"""
from time import time
import os, sys, logging, types, inspect, traceback, logging, re
from vtkWebCorePython import vtkWebApplication, ... | hlzz/dotfiles | graphics/VTK-7.0.0/Web/Python/vtk/web/protocols.py | Python | bsd-3-clause | 11,521 | [
"VTK"
] | 91892ff4f7b2e4323b8aab2a68380f3d03fb051544a09b8222b2366189fe740c |
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 11 10:08:31 2015
This file is part of pyNLO.
pyNLO 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 optio... | ycasg/PyNLO | src/pynlo/light/high_V_waveguide.py | Python | gpl-3.0 | 3,514 | [
"CRYSTAL"
] | ee4ad13c6ab6d0749a9ee0593b87185330073ddb87fc6a3504cc67b4caef84e4 |
import lb_loader
import pandas as pd
import simtk.openmm.app as app
import numpy as np
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
pd.set_option('display.width', 1000)
sysname = "chargedswitchedaccurateljbox"
system, positions, groups, temperature, timest... | kyleabeauchamp/HMCNotes | code/misc/debugging_xc.py | Python | gpl-2.0 | 1,183 | [
"OpenMM"
] | 2c8d92f6a325385158204527fb1abcd2021b0ad11cc9973d64da980ceff3c0f6 |
#!/usr/bin/python
import music
from mpi4py import MPI
from matplotlib import mlab
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
plt.ion()
class DynamicUpdate():
#Suppose we know the x range
ax_min = -20
ax_max = 20
def on_launch(self):
#Set up plo... | weidel-p/ros_music_adapter | adapters/pca.py | Python | gpl-3.0 | 5,580 | [
"NEURON"
] | 63bd2ef9571a582e0dbb077b8c16f673232f9c6bcdd31187c752461b07f848c6 |
#! /usr/bin/env python
"""Create landlab model grids."""
from ..core import load_params
from ..io import read_esri_ascii
from ..io.netcdf import read_netcdf
from ..values import constant, plane, random, sine
from .hex import HexModelGrid
from .network import NetworkModelGrid
from .radial import RadialModelGrid
from .r... | amandersillinois/landlab | landlab/grid/create.py | Python | mit | 14,648 | [
"NetCDF"
] | a1a4a58ce517dab41e089eba9e427f4b53b0cf2f0fb1ff5fc78d468d3b1d5012 |
# coding: utf-8
# Copyright 2014-2020 Álvaro Justen <https://github.com/turicas/rows/>
# This program 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
# ... | turicas/rows | tests/tests_fields.py | Python | lgpl-3.0 | 24,002 | [
"MOE"
] | f7f8e4d0a69bbeb1b75dd872813603e713b33ca761629f8848d1f615462121ab |
"""
Test courseware search
"""
import json
import uuid
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.common.logout import LogoutPage
from common.test.acceptance.pages.lms.course_home import... | cpennington/edx-platform | common/test/acceptance/tests/lms/test_lms_cohorted_courseware_search.py | Python | agpl-3.0 | 12,205 | [
"VisIt"
] | 4b520fccdb9405a2403afd170e91a3258583233c7a22d4dc9d97b7dec03ad8b8 |
#! /usr/bin/env python
# ----------------------------------------------------------------------------
# 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.
# --------------------... | Jorge-C/bipy | skbio/maths/stats/distance/anosim.py | Python | bsd-3-clause | 2,908 | [
"scikit-bio"
] | 0d25e7b82f1e5f8294dfd6d071e9241dac7c509dfc08b12c170914af209b57f3 |
"""
This migration script adds the history_dataset_association_display_at_authorization table,
which allows 'private' datasets to be displayed at external sites without making them public.
If using mysql, this script will display the following error, which is corrected in the next
migration script:
history_dataset_ass... | volpino/Yeps-EURAC | lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py | Python | mit | 3,090 | [
"Galaxy"
] | b6a366e611c136212b27d58585540ae69ff541ce79b1e54e3d2c03ef9ef7fed3 |
# coding=utf-8
"""**Utilities for storage module**
"""
import os
import re
import copy
import numpy
import math
from ast import literal_eval
from osgeo import ogr
from geometry import Polygon
from safe.common.numerics import ensure_numeric
from safe.common.utilities import verify
from safe.common.exceptions import B... | drayanaindra/inasafe | safe/storage/utilities.py | Python | gpl-3.0 | 36,585 | [
"NetCDF"
] | 70309fdff29a117a94e83608acb8a4a12f1e7c8d11b001500d8cd3133619a2d1 |
"""
picasso.simulate
~~~~~~~~~~~~~~~~
Simulate single molcule fluorescence data
:author: Maximilian Thomas Strauss, 2016-2018
:copyright: Copyright (c) 2016-2018 Jungmann Lab, MPI of Biochemistry
"""
import numpy as _np
from . import io as _io
from numba import njit
magfac = 0.79
@njit
def calc... | jungmannlab/picasso | picasso/simulate.py | Python | mit | 13,389 | [
"Gaussian"
] | cf86ca7025a76084a85e9f3600808e2fe4384cf182f894c02744a71b79643be2 |
import json
import logging
import networkx as nx
import pytz
from itertools import imap
from functools import partial
from collections import defaultdict
from math import sqrt
from datetime import datetime
from django.core.serializers.json import DjangoJSONEncoder
from django.db import connection
from django.http impo... | catsop/CATMAID | django/applications/catmaid/control/skeletonexport.py | Python | gpl-3.0 | 39,451 | [
"NEURON"
] | 5045383d243f7d194fda7038dd4c769c025223984f86a029b93ef22d794acba3 |
import brain_state_calculate_c as bsc
import numpy as np
import copy
import random as rnd
import pickle
import matplotlib.pyplot as plt
from collections import OrderedDict
from cpp_file_tools_c import cpp_file_tools
class ChangeObs:
def __init__(self, l_obs):
rnd.seed(42)
#wich col we should move
... | scauglog/brain_record_toolbox | benchmark_walk_classifier.py | Python | mit | 22,052 | [
"NEURON"
] | 147039419a310093978f273b06c5fdeb6092856f64139db396d48023eb81b5a3 |
#!/usr/bin/env python
from traits.api import \
HasTraits, Str, Int, List, Button, File, Instance, Dict,Enum, \
on_trait_change, Array, Bool, Color, Tuple, Button
from traitsui.api import Group, View, Handler, Item, \
OKButton, CancelButton, EnumEditor, TableEditor, \
CheckListEditor, ObjectColumn
i... | mattcieslak/DSI2 | dsi2/volumes/scalar_volume.py | Python | gpl-3.0 | 4,498 | [
"Mayavi"
] | 3501a0fbff79a75d495f3618e1eb5ab64abee60b230af8e5539c593d82a17848 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''Views tests for the OSF.'''
from __future__ import absolute_import
import unittest
import json
import datetime as dt
import mock
import httplib as http
import math
import time
from nose.tools import * # noqa PEP8 asserts
from tests.test_features import requires_search... | ckc6cz/osf.io | tests/test_views.py | Python | apache-2.0 | 181,349 | [
"Brian"
] | 1441303e85786233e21827dfb469d96dc6dbf8c3ac0bd79a140effd08d8b6fef |
"""
Tools for creating graph inputs from molecule data
"""
import itertools
import os
import sys
from collections import deque
from functools import partial
from multiprocessing import Pool
from typing import Dict, List, Union
import numpy as np
from pymatgen.analysis.local_env import NearNeighbors
from pymatgen.core... | materialsvirtuallab/megnet | megnet/data/molecule.py | Python | bsd-3-clause | 23,634 | [
"Gaussian",
"Open Babel",
"Pybel",
"RDKit",
"pymatgen"
] | bde3adf4635d761d2723bb629cb3f2a8f1b4a398bf533ad34ee5aaa0eda6c50a |
# Copyright 2018 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google/git-patrol | git_patrol_test.py | Python | apache-2.0 | 14,447 | [
"Brian"
] | 5e426d0437e53facdcb467f45df84f6152b1fe01cab1202f13d5b44c747e134d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Interface with command line GULP.
http://projects.ivec.org
WARNING: you need to have GULP installed on your system.
"""
__author__ = "Bharat Medasani, Wenhao Sun"
__copyright__ = "Copyright 2013, The Mate... | gmatteo/pymatgen | pymatgen/command_line/gulp_caller.py | Python | mit | 27,488 | [
"GULP",
"pymatgen"
] | 6bf1b637ceee5eb42e829fb653a25f04f92ec572828df260f63fa684912b8c33 |
import numpy as np
from scipy import integrate
import math
from scipy.integrate import odeint, ode
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation
from scipy import interpolate
from matplotlib.path import Path
import matplotlib.patches as patches
import matplotlib
from matplotlib.patches ... | GitYiheng/reinforcement_learning_test | test00_previous_files/cartpole.py | Python | mit | 19,516 | [
"Octopus"
] | 2a212d34fc5edc8a06898dcaa61b03e125ccac979ada1b5f4356c7138c8206d0 |
import os
from pyjade import Parser, Compiler as _Compiler
from pyjade.runtime import attrs
from pyjade.utils import process
ATTRS_FUNC = '__pyjade_attrs'
ITER_FUNC = '__pyjade_iter'
class Compiler(_Compiler):
useRuntime = True
def compile_top(self):
return '# -*- coding: utf-8 -*-\n<%%! from pyjade.run... | glennyonemitsu/MarkupHiveServer | src/pyjade/ext/mako.py | Python | mit | 3,388 | [
"VisIt"
] | 709ac275c4016b2b94a6ec5a165b7dec8700b1e7fbf580c676eea445df975a4e |
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# TODO - Don't use "from XXX import *"
from __future__ import print_function
try:
from numpy import *
from numpy import dot # missing in old ... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_SVDSuperimposer.py | Python | gpl-2.0 | 2,041 | [
"Biopython"
] | 4ef7d3b5eb7f748bb40fd3f256b18219792a089b2de005e9ec2e0de3133dd66d |
from __future__ import print_function
import sys
import os
import regreg.api as rr
import numpy as np
from selection.reduced_optimization.generative_model import generate_data, generate_data_random
from selection.reduced_optimization.initial_soln import instance
from selection.tests.instance import logistic_instance,... | selective-inference/selective-inference | sandbox/bayesian/lasso_selection.py | Python | bsd-3-clause | 4,485 | [
"Gaussian"
] | 61576dc62233b6b64047ac49b649b42edc9f18aa5f43865730658ed25fe31795 |
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