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"""
Example of running optical and contact cluster stuff on gromacs file
"""
from __future__ import absolute_import, division, print_function
import os.path as op
import numpy as np
import numpy.testing as npt
import pdb
import gsd.hoomd
import sys
import clustering as cl
import random
import scipy
import time
#from co... | ramansbach/cluster_analysis | clustering/scripts/analyze_angspread_martini.py | Python | mit | 2,547 | [
"Gromacs"
] | ff4f871248d9e8633a8ed747e01adc297c89b9786744a71846b6b67c8968ebe8 |
# -*- coding: utf-8 -*-
# This file is part of beets.
# Copyright 2016, Adrian Sampson.
#
# 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 limitation t... | MyTunesFreeMusic/privacy-policy | beetsplug/beatport.py | Python | mit | 18,362 | [
"VisIt"
] | d873c5c58d243d63c2f37da8cbf1fa8371d7e72664a6738813a55a45158cf597 |
import bond
class Dihedral(object):
"""Docstring for Dihedral"""
dihedral_eqib_len = ""
dihedral_force_const = ""
dihedral_master1 = ""
dihedral_master2 = ""
dihedral_slave1 = ""
dihedral_slave2 = ""
k1 = ""
k2 = ""
k3 = ""
k4 = ""
print_type = 0
dft = False
inte... | sipjca/cmlparser_py | dihedral.py | Python | apache-2.0 | 6,904 | [
"LAMMPS"
] | 5ba389fa63116c8de9e96e842adb2da08e8b31e4528316852ba16156091708db |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Mads Jensen <mje.mads@gmail.com>
#
# License: BSD (3-clause)
import os
import copy
from math import ceil
import warnings
impor... | cmoutard/mne-python | mne/source_estimate.py | Python | bsd-3-clause | 110,449 | [
"Mayavi"
] | 894e552b3beb825012e4c9c0c576ede0eb5af23156c1292ea6e2323fe5a166cd |
# from distutils.core import setup
from setuptools import setup
import os
setup(
name="bigsi",
version="0.3.8",
packages=[
"bigsi",
"bigsi.bloom",
"bigsi.cmds",
"bigsi.utils",
"bigsi.graph",
"bigsi.storage",
"bigsi.matrix",
"bigsi.scoring",
... | Phelimb/cbg | setup.py | Python | mit | 1,737 | [
"Biopython"
] | d759e88608f723e636a0b6ebbbd53be5cc1b1c00cd5965c5615fc5db04f060fd |
import collections
from datetime import datetime, timedelta
import json
import logging
import numbers
import threading
from dateutil.tz import tzutc
import requests
from stats import Statistics
from errors import ApiError
from utils import guess_timezone, DatetimeSerializer
import options
logging_enabled = True
lo... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/analytics/client.py | Python | agpl-3.0 | 16,485 | [
"VisIt"
] | 1205d76532adfab8cca8feb74803b575c5e98edc228e33f85d12080274550152 |
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
from wxPython import wx
class VTKtoPRTools(ScriptedConfigModuleMixin, ModuleBase):
"""Module to convert multi-component VTK image data to PRTools-compatible
dataset.
$Revision: 1.1 $
"""
def __init__(self, mod... | nagyistoce/devide | modules/user/VTKtoPRTools.py | Python | bsd-3-clause | 3,048 | [
"VTK"
] | eb3d19422d765f750a6effe226816f734b80445a11afbe8c3e6309038410e567 |
"""
tracker / OffsetTracker is a class which keeps track of which of the slots
defined in a template have already been seen and uses this information to
answer questions about offsets for advanced x expressions.
"""
import copy
import logging
class OffsetTracker(object):
def __init__(self,reduction,term):
... | ieb/timetables | python/lib/tracker.py | Python | agpl-3.0 | 2,399 | [
"BLAST"
] | ec1c040832dffbe705834bc9cb1340bdf6b1794add2babc887e725f628e4196f |
#!/usr/bin/python
#
# Copyright 2015 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 b... | richardfergie/googleads-python-lib | examples/adwords/v201502/remarketing/add_rule_based_user_lists.py | Python | apache-2.0 | 5,714 | [
"VisIt"
] | a9114332a529cd9e9b9de78acfd658a6f429468b00f23335b08d8c0270165eb8 |
"""
@author: JD Chodera
@author: JH Prinz
"""
from openpathsampling.engines import BaseSnapshot, SnapshotFactory
from . import features
@features.base.attach_features([
features.velocities,
features.coordinates,
features.box_vectors,
features.engine
])
class MDSnapshot(BaseSnapshot):
"""
A f... | choderalab/openpathsampling | openpathsampling/engines/openmm/snapshot.py | Python | lgpl-2.1 | 3,134 | [
"OpenMM"
] | bcab9ef1da7e0557532ba1f1fea8f829c8159f9016abd520573177bb41f1b3d7 |
#!/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 | modules/tensor_mechanics/test/tests/tensile/small_deform_hard3.py | Python | lgpl-2.1 | 1,286 | [
"MOOSE"
] | 2d55797f0a376641c6e96a9ad951fd9901069f769f1fae63f168ce2fc42be020 |
from pycp2k.inputsection import InputSection
class _gaussian1(InputSection):
def __init__(self):
InputSection.__init__(self)
self.Ww = None
self.Sigma = None
self._name = "GAUSSIAN"
self._keywords = {'Sigma': 'SIGMA', 'Ww': 'WW'}
| SINGROUP/pycp2k | pycp2k/classes/_gaussian1.py | Python | lgpl-3.0 | 277 | [
"Gaussian"
] | 125c4ec4722ae844ff6ab41c3d200289cd000904789ba2ae061efba7f20e1c93 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-reschedule
# Author : Stuart Paterson
########################################################################
"""
Reschedule the given DIRAC job
Example:
$ dirac-wms-job-reschedule 1
Reschedul... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_job_reschedule.py | Python | gpl-3.0 | 1,157 | [
"DIRAC"
] | 0db1a5a5717cb327a951b59b77de05744d03d7637b31f1fd22270926ef8807b9 |
""" SandboxHandler is the implementation of the Sandbox service
in the DISET framework
"""
__RCSID__ = "$Id$"
import os
import time
import threading
import tempfile
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.File import mkDir
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from... | andresailer/DIRAC | WorkloadManagementSystem/Service/SandboxStoreHandler.py | Python | gpl-3.0 | 19,330 | [
"DIRAC"
] | 250eedfded71af5e1020270cce21aa7d84525e4cc11ab3ee68b7f4c3862cf812 |
# -*- coding: utf-8 -*-
"""
Acceptance tests for Video.
"""
import os
from unittest import skipIf
from ddt import data, ddt, unpack
from mock import patch
from nose.plugins.attrib import attr
from selenium.webdriver.common.action_chains import ActionChains
from selenium.webdriver.common.by import By
from common.test... | Stanford-Online/edx-platform | common/test/acceptance/tests/video/test_video_module.py | Python | agpl-3.0 | 50,719 | [
"VisIt"
] | c1f276f4c6ecd616dc9015002d8beda10a75f45607b27c85375cfa5a92b1755b |
"""
Instructor Dashboard Views
"""
import datetime
import logging
import uuid
from django.conf import settings
import pytz
from openedx.core.lib.xblock_builtin import get_css_dependencies, get_js_dependencies
from django.contrib.auth.decorators import login_required
from django.contrib.auth.models import User
from ... | proversity-org/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 38,981 | [
"VisIt"
] | ec57c02a441cbc24befb06042a5ee0de472d6c1ab4cf77219db9b28ff92e9930 |
#! /usr/bin/python
"""
Python LSTM (Long short term memory)
with OOPS training (Optimal Ordering Problem Solver)
implementation.
OOPS is an alternative training method that avoids some
of the drawbacks in back-propogation (ie: local minima)
training. An OOPS trainer also allows both supervised... | gau-veldt/LSTM_OOPS | lstm_oops.py | Python | gpl-3.0 | 46,930 | [
"Brian"
] | 21cd21f5200ab2343257258410c6b85e46e8e7b43085c780ae43a78eb388f783 |
import sys
#sys.path.append('/home/dskola/workspace/expression_modeling/')
import matplotlib
#matplotlib.use('Agg')
import collections
import contextlib
import csv
import datetime
import math
import multiprocessing
import os
import re
import shutil
import subprocess
import gzip
import numpy
import scipy.ndimage
import ... | phageghost/pg_tools | pgtools/pileups.py | Python | mit | 198,251 | [
"Bowtie",
"Gaussian"
] | 578d1b58443ff34f3c0dc82c89b87d268cf75c7c52286e474481de4d4ec72592 |
"""Get useful information from live Python objects.
This module encapsulates the interface provided by the internal special
attributes (co_*, im_*, tb_*, etc.) in a friendlier fashion.
It also provides some help for examining source code and class layout.
Here are some of the useful functions provided by this module:... | FFMG/myoddweb.piger | monitor/api/python/Python-3.7.2/Lib/inspect.py | Python | gpl-2.0 | 117,615 | [
"VisIt"
] | 5ad6bf302604e4c80e052cdaa22321d16a1a2cef12a0bbceb21ef5334b3c87bd |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import xml.etree.ElementTree
from ..compat import (
compat_cookiejar,
compat_HTTPError,
compat_http_client,
compat_urllib_error,
co... | marado/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 43,875 | [
"VisIt"
] | 55126af7286036adec46b2f452918ad1508ed7b5178aa9e7203cb4866ec5fd03 |
"""Summary of tensorflow basics.
Parag K. Mital, Jan 2016."""
# %% Import tensorflow and pyplot
import tensorflow as tf
import matplotlib.pyplot as plt
# %% tf.Graph represents a collection of tf.Operations
# You can create operations by writing out equations.
# By default, there is a graph: tf.get_default_graph()
# ... | apoorva-sharma/deep-frame-interpolation | tensorflow_tutorials-master/python/01_basics.py | Python | mit | 4,497 | [
"Gaussian"
] | 77671f18e525da8a50129a07bf2f33883acf5ba345b7ef41bd4cd484c5df2642 |
# -*- coding: utf-8 -*-
"""
Created on Wed Sep 16 14:27:37 2015
@author: Jaromir Camphuijsen (6042473) and Eva van Weel(10244743)
"""
import Tkinter, random
import vtk
from vtk.tk.vtkTkRenderWidget import vtkTkRenderWidget
from Tkinter import *
# Create the renderer and the GUI
class Tissue(object):
def __ini... | JaroCamphuijsen/SVVR | Assignment 4/Assignment4.py | Python | gpl-2.0 | 7,185 | [
"VTK"
] | 8e7ad64abde9ec7db9ef9ea55c7050cfd9f6264ff0f5641156939e5faf640795 |
'''
PathwayGenie (c) University of Manchester 2017
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
import sys
from assembly_genie.build import BuildGenieBase
def main(args):
'''main method.'''
genie = ... | synbiochem/PathwayGenie | assembly_genie/order.py | Python | mit | 705 | [
"VisIt"
] | 0cc0be3206bbc40363069bc9652575aa5bdfc9137f87dbea70771d9673a8ffd6 |
'''
matrix.py
Basic operations with matrixes:
- multiply
- transpose
- invert
And a simple linear least squares solver,
performing a linear fit between two vectors
yi = a+b.xi
Revision History
rev Date Description
0.1 2013.02.13 first issue, basic insanity check
Rafael Rossi
RaRossi@external.technip.... | haphaeu/yoshimi | GumbleBootstrap/matrix.py | Python | lgpl-3.0 | 2,495 | [
"Gaussian"
] | ee4f374b31afc8bc0862fafeb7e919e9b17761cdf548c6f5d8b4cf52a6160a7e |
# mako/ast.py
# Copyright (C) 2006-2015 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""utilities for analyzing expressions and blocks of Python
code, as well as generating Python from AS... | znoland3/zachdemo | venvdir/lib/python3.4/site-packages/mako/ast.py | Python | mit | 6,635 | [
"VisIt"
] | 7c2bd362e0239fef1f285a3fff450e92b060e4ddeb5c5241204fb77aeaf8dc23 |
# Copyright 2015 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... | drpngx/tensorflow | tensorflow/python/ops/gradients_impl.py | Python | apache-2.0 | 47,933 | [
"VisIt"
] | 87795aa178bea7f82bc21dc7cf45b0d7b5c3132337b8c866d179c0bf14cd3da4 |
"""
Automatic processing scripts for grizli
"""
import os
import inspect
import traceback
import glob
import time
import warnings
import numpy as np
import astropy.io.fits as pyfits
import astropy.wcs as pywcs
from .. import prep, utils
from .default_params import UV_N_FILTERS, UV_M_FILTERS, UV_W_FILTERS
from .defaul... | gbrammer/grizli | grizli/pipeline/auto_script.py | Python | mit | 183,603 | [
"Gaussian",
"VisIt"
] | 1cc9b180913321bb6450c6fcb72246f789efcdc48e8333d58d249707627652f2 |
#!/usr/bin/env python
#title :distribution_checkX.py
#description :Checks a sample against 80 distributions by applying the Kolmogorov-Smirnov test.
#author :Andre Dietrich
#email :dietrich@ivs.cs.uni-magdeburg.de
#date :07.10.2014
#version :0.1
#usage :pyth... | Kirubaharan/hydrology | stats/distribution_check.py | Python | gpl-3.0 | 11,192 | [
"Gaussian"
] | 87eba6492fe2f06b8309bfc9ae33d5402df690dbabc1e1af86735b96ccf3d0c1 |
'''
GraphQL.js provides a reference implementation for the GraphQL specification
but is also a useful utility for operating on GraphQL files and building
sophisticated tools.
This primary module exports a general purpose function for fulfilling all
steps of the GraphQL specification in a single operation, but also inc... | wandb/client | wandb/vendor/graphql-core-1.1/wandb_graphql/__init__.py | Python | mit | 7,300 | [
"VisIt"
] | c76333382ed88a97450acbc2999575a2069a714c6f7476934e46dd6f8759b8d2 |
## -*- coding: utf-8 -*-
## Copyright (c) 2015-2018, Exa Analytics Development Team
## Distributed under the terms of the Apache License 2.0
#"""
#Parser for ADF's SCF Section
################################
#Parses the 'S C F' section of an ADF block output.
#"""
#from exa import Parser, Matches, Match
#
#
#class SCF... | avmarchenko/exatomic | exatomic/adf/adf/scf.py | Python | apache-2.0 | 793 | [
"ADF"
] | 5be68e21eac438ae3e57a4e30f4a4d8c906647592c273ec7b83dc3c28981ebf5 |
'''
Driver method to run the monte_carlo module using mixed DNA and protein moves
with simple options for a nucleosomecore particle (NCP)
$Id: gui_mimic_simplest_ncp.py 3103 2016-04-26 20:15:12Z schowell $
'''
import sys
import multiprocessing
import sassie.interface.input_filter as input_filter
import sassie.simulate.... | madscatt/zazzie_1.5 | trunk/sassie/simulate/monte_carlo/gui_mimic_simplest_ncp.py | Python | gpl-3.0 | 5,047 | [
"OpenMM"
] | afeedc21e3aec0aded9b62acdfe1ac8edcaecc1ebfc43f7484d41560cf171855 |
# -*- coding: utf-8 -*-
#
# A way to combine vcf files
#
from collections import OrderedDict
from past.builtins import xrange
import multiprocessing
import os
import time
import pysam
from . import exceptions
from . import fasta
from . import g2g
from . import g2g_utils
from . import vcf
LOG = g2g.get_logger()
... | churchill-lab/g2gtools | g2gtools/vcf2vci.py | Python | mit | 22,155 | [
"pysam"
] | 510349f8b539c3fd853bae634c1c4aaf9b5369e93f836ee03312c8fea95de3e1 |
from __future__ import print_function, division
from sympy.core.compatibility import range
"""
Algorithms and classes to support enumerative combinatorics.
Currently just multiset partitions, but more could be added.
Terminology (following Knuth, algorithm 7.1.2.5M TAOCP)
*multiset* aaabbcccc has a *partition* aaabc... | wxgeo/geophar | wxgeometrie/sympy/utilities/enumerative.py | Python | gpl-2.0 | 43,440 | [
"VisIt"
] | 53295876afc43f015b718d2cdf9b1acbb6af3afcdcef43f52fbb2a57f1b7ddc2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
What it does
============
B{This is the fifth step of ZIBgridfree.}
This tool performs the task of L{zgf_mdrun} on HLRN. In addition to the inherited L{zgf_mdrun} options, you can pick several options for the HLRN job script, such as job queue, time limit, and e-mai... | CMD-at-ZIB/ZIBMolPy | tools/zgf_submit_job_HLRN.py | Python | lgpl-3.0 | 4,924 | [
"Gromacs"
] | 6156ed911ca4cd45f31158780144d2e47a917cfe10835adbc3ae72fdbee58179 |
import warnings
import mdtraj as md
import numpy as np
from msmbuilder.featurizer import LigandContactFeaturizer
from msmbuilder.featurizer import BinaryLigandContactFeaturizer
from msmbuilder.featurizer import LigandRMSDFeaturizer
def _random_trajs():
top = md.Topology()
c = top.add_chain()
r = top.add... | msultan/msmbuilder | msmbuilder/tests/test_ligandfeaturizers.py | Python | lgpl-2.1 | 4,822 | [
"MDTraj"
] | 7b83d4796b850ec74d1bc894ae41caa07a3ee511f87c1b61c458ff4f288d59b1 |
from django.http import HttpResponse
from django.shortcuts import render_to_response
from django.contrib.auth.decorators import login_required
import os
import json
import re
from models import Word, ProcessingLog, RedactionEvent
def get_settings():
f = open(os.path.join(os.getcwd(), '../settings.json'))
setti... | policevideorequests/policevideopublisher | webinterface/webinterface/views.py | Python | bsd-3-clause | 30,481 | [
"Gaussian"
] | 8cf8ba9c49434e5f3edd340a167077f6c5327e65a0a5eb7b50a8937f66c71029 |
# -*- coding: utf-8 -*-
"""
Created on Wed Apr 5 12:39:59 2017
@author: Shabaka
"""
import os
import glob
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import numpy as np
from scipy import stats
# from mayavi import mlab
import multiprocessing
import plotly.plotly as py
import plotly.grap... | qalhata/Python-Scripts-Repo-on-Data-Science | CSV_Concatenate_All.py | Python | gpl-3.0 | 3,117 | [
"Mayavi"
] | d24edd83a598a0e2f7d6291e2a031f6ad1ee0bfbb36fe4e7333f4a829ec8a167 |
""" DIRAC Transformation DB
Transformation database is used to collect and serve the necessary information
in order to automate the task of job preparation for high level transformations.
This class is typically used as a base class for more specific data processing
databases
"""
import re, time, thre... | calancha/DIRAC | TransformationSystem/DB/TransformationDB.py | Python | gpl-3.0 | 68,155 | [
"DIRAC"
] | f41f5bca60c1fd90a2f24dfe447b4ff90a04dc0d7e5a0705a21ec9f281160a3b |
""" """
# mode_controller.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
import os
from collections import namedtuple
from mpf.system.uti... | spierepf/mpf | mpf/media_controller/core/mode_controller.py | Python | mit | 8,091 | [
"Brian"
] | 3fc93f167df4db270b5553103b582a8589d368700c35b93da541896dd9a0cc4c |
# 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.
#
import sys
# Add path to Bio
sys.path.append('../..')
from Bio import FSSP
import copy
from Bio.Align import MultipleSeqAlignment
from Bio import Al... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/FSSP/FSSPTools.py | Python | gpl-2.0 | 4,027 | [
"Biopython"
] | 9a5a8007ccbaf1602ca1d599a2e5bfcc66b460817be5c76caa6032ff834f2e25 |
# proxy module
from __future__ import absolute_import
from mayavi.tools.data_wizards.preview_window import *
| enthought/etsproxy | enthought/mayavi/tools/data_wizards/preview_window.py | Python | bsd-3-clause | 109 | [
"Mayavi"
] | 11872d10461109fcd98ae6edd0b3f7cfb43d4418226c11d203154e1b16b606a4 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements Compatibility corrections for mixing runs of different
functionals.
"""
import abc
import os
import warnings
from collections import defaultdict
from typing import List, Optional, Sequence, Type, Uni... | materialsproject/pymatgen | pymatgen/entries/compatibility.py | Python | mit | 61,576 | [
"VASP",
"pymatgen"
] | cb62c13952932217f4b288c72b74708c6322a218f5f689f0286f5ebd9230b424 |
# Author: Brian Kirk
# --------------------------------------------------------------------------------------------------
def ReadDataFromWeb(dataurl,dataurl2, mous_code):
# --------------------------------------------------------------------------------------------------
"""
This function reads the te... | bmarshallk/NAASC | various_scripts/HarvestAOTXML.py | Python | gpl-3.0 | 35,241 | [
"Brian"
] | 20169d9e1c3099f88fe5dcfebaa5336dc1f7fb7595b20a3ef6d4668c0fb51dad |
from rdkit import RDConfig
import unittest
from rdkit import Chem
from rdkit.Chem import rdMMPA
def natoms(tpl):
return tuple(x.GetNumAtoms() if x is not None else 0 for x in tpl)
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test1(self):
m = Chem.MolFromSmiles('c1ccccc1OC')
frag... | bp-kelley/rdkit | Code/GraphMol/MMPA/Wrap/testMMPA.py | Python | bsd-3-clause | 6,407 | [
"RDKit"
] | 975b937d5f460ccc76b6f664d7b47adf58196d0eaff6cfeab15f57c636d2ce00 |
from datetime import datetime
import pytz
import logging
import smtplib
from model_utils.managers import InheritanceManager
from collections import namedtuple
from boto.exception import BotoServerError # this is a super-class of SESError and catches connection errors
from django.dispatch import receiver
from django.... | TsinghuaX/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 23,513 | [
"VisIt"
] | 208305a8a810ed23a1f3e72c57f3fde9dbe5b59703924459e0844a919e008691 |
import numpy as np
import random
import json
import math
neuron_decay=0.9
maxneuronsperunit=64
maxaxonsperunit=128
maxunits=10
binary_io=True
bitsize=8
runtime=20
testsize=20
class neuron:
id=-1
myunit=-1
active=False
can_mutate=True
threshold=999
amount=0
decay=neuron_decay
... | barisser/Neural | neural.py | Python | mit | 16,325 | [
"NEURON"
] | 52c2ada4f94488c441e6036dd6b15bbdf542ec02b4c1fdb4a7a0ea605a41b87a |
#!/usr/bin/python
__author__ = 'mattdevs'
import os
import logging
import threading
from datetime import datetime
import requests
from requests import ConnectionError
from selenium import webdriver
from apscheduler.scheduler import Scheduler, EVENT_JOB_EXECUTED, EVENT_JOB_ERROR
import shepherd_util
LOG_FILE = "sheph... | mattdevs/site-shepherd | shepherd.py | Python | gpl-2.0 | 2,875 | [
"VisIt"
] | 41e4b8b4330108f54d54a9751df3414f44114ca17c300973780ac5481414db1d |
from __future__ import division, print_function, absolute_import
import numpy as np
from numpy.dual import eig
from scipy.misc import comb
from scipy import linspace, pi, exp
from scipy.signal import convolve
__all__ = ['daub', 'qmf', 'cascade', 'morlet', 'ricker', 'cwt']
def daub(p):
"""
The coefficients f... | juliantaylor/scipy | scipy/signal/wavelets.py | Python | bsd-3-clause | 10,246 | [
"Gaussian"
] | b34f3ab40d5335cbaf2a2a9343601e8f01af0b685137d9dd8a30089b79b5a7fd |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Parser for Psi4 output files."""
from collections import namedtuple
import numpy
from cclib.parser impo... | cclib/cclib | cclib/parser/psi4parser.py | Python | bsd-3-clause | 54,010 | [
"Psi4",
"cclib"
] | b7347e0934df28f72f9348716d3424ce77832dd3ee355e5f8fffdf68b0f9fb54 |
# coding: utf-8
"""
Secure JavaScript Login
~~~~~~~~~~~~~~~~~~~~~~~
:copyleft: 2015 by the secure-js-login team, see AUTHORS for more details.
:created: by JensDiemer.de
:license: GNU GPL v3 or above, see LICENSE for more details
"""
from __future__ import unicode_literals, print_function
import... | jedie/django-secure-js-login | tests/test_doctests.py | Python | gpl-3.0 | 2,713 | [
"VisIt"
] | c3fd224c60b6035a365e5af619373cf36d740f7336a847d89001e77a6222a96d |
import numpy as np
import random
class HopfieldNetwork:
"""
(C) Daniel McNeela, 2016
Implements the Hopfield Network, a recurrent neural network developed by John Hopfield
circa 1982.
c.f. https://en.wikipedia.org/wiki/Hopfield_Network
"""
def __init__(self, num_neurons, activation_fn=Non... | robclewley/fovea | examples/hopfield/hopfield_network.py | Python | bsd-3-clause | 6,549 | [
"NEURON"
] | 2a66199c99719c2403526aee5e69bb81a038d6f5de2ffe8903fc768c3af65991 |
import time
def random():
""" Pseudo random number generator for micro python.
I make no claims about its randomness or suitability for use
Adpoted from:
NUMERICAL RECIPIES: THE ART OF SCIENTIFIC COMPUTING
THIRD EDITION
WILLIAM H. PRESS
SAUL A. TEVKOLSKY
WILLIAM T. VETTERLING
BRIAN P. FLANNERY
CAMBRIDG... | ichbinjakes/CodeExamples | random.py | Python | gpl-3.0 | 969 | [
"Brian"
] | e152d478f53bb772988d63b38fdcc34eec452689588d230289abbefd4c8978ef |
###############################################################################
##
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary forms, with or without
## modification, ... | CMUSV-VisTrails/WorkflowRecommendation | vistrails/packages/vtk/vtkviewcell.py | Python | bsd-3-clause | 39,509 | [
"VTK"
] | be43547bc1db115c2af2ec8743bd0a6874e4f152b72b1784248053f3ee730c3b |
from time import time
from collections import defaultdict
from weakref import WeakKeyDictionary
from octopus.dispatcher.model.enums import *
from octopus.dispatcher.model import Task
from . import models
import logging
LOGGER = logging.getLogger("main.dispatcher.dispatchtree")
class NoRenderNodeAvailable(BaseExcep... | mikrosimage/OpenRenderManagement | src/octopus/dispatcher/model/node.py | Python | bsd-3-clause | 27,782 | [
"Octopus"
] | 04d55b91a41018adb7a97b0c0a384bea7eab08b3418c2e142afebb15a18fda82 |
#! /usr/bin/env python
import cv2
import numpy as np
import matplotlib.pyplot as plt
import time
from image_processor import *
print (TCOLORS.PURPLE + "Unit Test: Applying a Gaussian Blure on an image" + TCOLORS.NORMAL)
SIGMA = 1
ENVELOPE_SIZE = 5
img = cv2.imread(FILENAME)
gray = rgb2gray(img)
width = len(gray)
... | CospanDesign/python | image_processor/gaussian_image_test.py | Python | mit | 1,500 | [
"Gaussian"
] | 7e841ddde03b30a1c56e8bdaccda8013a35af7b1b47ac27c8a160ef63289a52c |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Magnetic space groups.
"""
import os
import sqlite3
import textwrap
from array import array
from fractions import Fraction
import numpy as np
from monty.design_patterns import cached_class
from pymatgen.core.operations ... | vorwerkc/pymatgen | pymatgen/symmetry/maggroups.py | Python | mit | 23,391 | [
"CRYSTAL",
"pymatgen"
] | 729dd2ef2a6cc2371b131f378e7e00d05d4f7b50896ec82eb9324f852fe3f284 |
##############################################################################
# Copyright (c) 2013-2018, 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... | mfherbst/spack | var/spack/repos/builtin/packages/r-vsn/package.py | Python | lgpl-2.1 | 2,698 | [
"Bioconductor"
] | 524d884d30b2f8b4c2cc18b8ce84c992a6d9d79b09954fb7603cf10aab6bcc11 |
import os
from os import listdir
from os.path import isfile, join
import sys
import numpy as np
from enum import Enum
import xml.etree.ElementTree as ET
# Get absolute path of package_directory
package_directory = os.path.dirname(os.path.abspath(__file__)).replace('core','')
# Check if sgems is indeed installed
sgem... | lewisli/gemsflowpy | core/workflow.py | Python | mit | 9,477 | [
"Gaussian"
] | b017eae1abb63baa416d1ed85f58275cf29a94efe240c0c5b9fd19edff043963 |
"""Calculate the expected detection rates for apertif."""
import numpy as np
import matplotlib.pyplot as plt
from tqdm import tqdm
from frbpoppy import CosmicPopulation, Survey, SurveyPopulation, hist
from tests.convenience import plot_aa_style, rel_path
from alpha_real import EXPECTED, poisson_interval
N_DAYS = 1 #... | davidgardenier/frbpoppy | tests/rates/apertif_dist.py | Python | mit | 2,026 | [
"Gaussian"
] | b4480d6c0d382af25a74b14cf544eba7c5acf0f2e1e22c40587f57a98b39cbe3 |
import numpy as num
import numpy as np
from matplotlib import pyplot
import matplotlib as mpt
import pickle,glob
import sys,os,inspect
from matplotlib import rc
from matplotlib import pyplot
from scipy.optimize import curve_fit
import matplotlib.pyplot as plt
from color_mate import color_combine_mate as set_color
def ... | jackey-qiu/genx_pc_qiu | supportive_functions/create_plots.py | Python | gpl-3.0 | 99,040 | [
"Gaussian",
"VTK"
] | 49999d1b0bdff355d1991dddd25b058c8fc813bb39c6ef193548e852e855fe0f |
""" FileManagerBase is a base class for all the specific File Managers
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
# pylint: disable=protected-access
import six
import os
import stat
from DIRAC import S_OK, S_ERROR, gLogger
from... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/FileManager/FileManagerBase.py | Python | gpl-3.0 | 48,207 | [
"DIRAC"
] | f5aff59dd7d6ab614c7ac83b06dfedc580f147c206e04660cac7fd854f7f3c8a |
'''
Here we use two different concepts, times and indices:
Time t 0 1 2 3 4 5
| | | | | |
Vector [ 2 3 1 2 1 ]
| | | | |
Index i 0 1 2 3 4
'''
def select_points_before_time(X, t):
# Return points before given time index
return select_first_points(X, t)
def select_points_... | infant-cognition-tampere/saccademodel-py | saccademodel/utils.py | Python | mit | 2,622 | [
"VisIt"
] | 4b2c0c247cd3bf0f3854797250c8f90be5f13abe66ddbea80db20a67f698c5ca |
# cd pySU/pyMultidark/trunk/bin/fortranfile-0.2.1/
import sys
import numpy as n
import os
from os.path import join
from astropy.io import fits
import time
import cPickle
from scipy.interpolate import interp1d
from scipy.optimize import curve_fit
from scipy.stats import scoreatpercentile as sc
from scipy.stats import n... | JohanComparat/nbody-npt-functions | bin/bin_DF/test_scripts/fit_density_field_to-tracers.py | Python | cc0-1.0 | 38,029 | [
"Galaxy",
"Gaussian"
] | 3917de26e7fcbd31180080fa1ff74c441cea03f5a739dc3999a8bc86be120501 |
from collections import OrderedDict
from edc_visit_schedule.classes import (
VisitScheduleConfiguration, MembershipFormTuple, ScheduleTuple)
from ..models import TestVisit, TestVisit2, TestConsentWithMixin, TestAliquotType, TestPanel
from edc_testing.classes.entries import requisition_entries, crf_entries
class... | botswana-harvard/edc-testing | edc_testing/classes/test_visit_schedule.py | Python | gpl-2.0 | 4,221 | [
"VisIt"
] | 547a56ece9921e0f68eb4035353951e1279d97ec6ee6d944ab5ff01b49b0a0cc |
# -*- coding: utf-8 -*-
"""
This example demonstrates a very basic use of flowcharts: filter data,
displaying both the input and output of the filter. The behavior of
he filter can be reprogrammed by the user.
Basic steps are:
- create a flowchart and two plots
- input noisy data to the flowchart
- flowchart con... | UpSea/thirdParty | pyqtgraph-0.9.10/examples/Flowchart.py | Python | mit | 2,561 | [
"Gaussian"
] | d6bd786a4f42dd80d0e879d5a712750e2b47aaac02bf7c513887e960d5833a63 |
print "importing stuff..."
import numpy as np
import pdb
import matplotlib
matplotlib.use('Agg')
import matplotlib.pylab as plt
from scipy import special
from .datautils import step, spiral
from .context import aep
def run_regression_1D():
np.random.seed(42)
print "create dataset ..."
N = 200
X = np.... | thangbui/geepee | examples/gpr_aep_examples.py | Python | mit | 9,893 | [
"Gaussian"
] | 463028c21e88d0723a6b5634cd1a828018f5c61c3ee9ed4cf6c643f1ea171cf6 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Shortbred(Package):
"""ShortBRED is a system for profiling protein families of interest at... | iulian787/spack | var/spack/repos/builtin/packages/shortbred/package.py | Python | lgpl-2.1 | 1,129 | [
"BLAST",
"Biopython"
] | c20b8df5ab29576ade4947a75075014b7ca074b8be5369cdc66d6e237a10d26b |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008-2010, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License ... | NetNow/wmi-samba | pysamba/wbem/Query.py | Python | gpl-2.0 | 9,256 | [
"VisIt"
] | 660165c068ac8883ed63d5240ceed0a4a728e4be0e0dc34aed7661bb91d2a377 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def waterline_time(zheights, diam, length,s,sampling):
t_total = time.time()
for zh in zheights:
cutter = ocl.BallCutter( diam , length )
wl = ocl.Waterline()
wl.setSTL(s)
wl.setCutter(cutter)
w... | JohnyEngine/CNC | opencamlib/scripts/waterline/waterline_6_weave2.py | Python | apache-2.0 | 1,754 | [
"VTK"
] | 87c433fb3a81a315cd28bfc17f88fd4c54e75990eeb338345623216d41ce1351 |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import os
from os.path import join
import json
from zeroinstall import support
from zeroinstall.support import basedir
from repo import cmd
def handle(args):
cmd.find_config()... | bastianeicher/0repo | repo/cmd/register.py | Python | lgpl-2.1 | 1,246 | [
"VisIt"
] | 66f914aa3e8d08c186da569e288e4577918abebe3fd93abf94798514c2dc08be |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# serverfile - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms o... | heromod/migrid | mig/shared/serverfile.py | Python | gpl-2.0 | 2,686 | [
"Brian"
] | d9aa4fdb7d70ac22fa8b08215ff8dfc80f0de263fb6f100e41f423371bf234ea |
'''TB Animation Tools is a toolset for animators
*******************************************************************************
License and Copyright
Copyright 2015-Tom Bailey
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public Licen... | tb-animator/tbtools | apps/tb_keyframe.py | Python | mit | 4,823 | [
"VisIt"
] | 968a7b276fcc26ccc7465fcb55c19ae0dc53dc713bb43d3548a6903839527119 |
import requests
from bears.general.URLHeadBear import URLHeadBear
from coalib.bears.LocalBear import LocalBear
from coalib.results.Result import Result
from coalib.results.RESULT_SEVERITY import RESULT_SEVERITY
from dependency_management.requirements.PipRequirement import PipRequirement
from memento_client import M... | refeed/coala-bears | bears/general/MementoBear.py | Python | agpl-3.0 | 3,680 | [
"VisIt"
] | 4edfa9c68acc1802bcedaf6d2fbcb5ea79fea93ba588a5f37eeab9963c48737d |
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path
here = path.abspa... | hurwitzlab/muscope-18SV4 | setup.py | Python | mit | 3,883 | [
"Biopython"
] | 2517f7de39684b0f80ac7be10db29fe62feaeb9ed392793b9598bdd72a8fc2af |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# demo.py --- Demonstration program and cheap test suite for pythondialog
#
# Copyright (C) 2002-2010, 2013-2016 Florent Rougon
# Copyright (C) 2000 Robb Shecter, Sultanbek Tezadov
#
# This program is in the public domain.
"""Demonstration program for pythondialog.
T... | Morphux/installer | pythondialog/examples/demo.py | Python | apache-2.0 | 71,973 | [
"Galaxy"
] | 689ec84760b8ddbe3384cf6e82bc2515266426fa4b652f47eb3c6775eb2a91a2 |
#!/usr/bin/env python
########################################################################
# File : dirac-info
# Author : Andrei Tsaregorodtsev
########################################################################
"""
Report info about local DIRAC installation
Example:
$ dirac-info
Option ... | yujikato/DIRAC | src/DIRAC/Core/scripts/dirac_info.py | Python | gpl-3.0 | 3,315 | [
"DIRAC"
] | 6a3cba6640124b88f68d67c6ee56692a085c9e58d5c1950151506b8d408e6188 |
import decimal
# ------------------------------- READ THIS -----------------------------------
#
# This file contains the information the code uses to fit the red sequence
# in different band combinations. To add a new band, create a new dictionary
# that holds all the same keys as the ones that already exist. Then ad... | gillenbrown/rsz | rsz_code/core_rsz/config.py | Python | mit | 16,969 | [
"Galaxy"
] | 2b11567dc0947e1b5e459c7ab43d32422ffe518503910dcc539fbe14967112c9 |
class RepQ01(d.Question):
question = 'Did you have one or more of the following symptoms since your last visit?'
type = 'options-multiple'
blank = True
options = (
(0, 'Runny nose'),
(1, 'Stuffy nose'),
(2, 'Hacking cough'),
(3, 'Dry cough'),
(4, 'Sneezing'),
... | chispita/epiwork | data/surveys/survey-spec.py | Python | agpl-3.0 | 4,170 | [
"VisIt"
] | 9053b17a46fe0145109279cefa6fb724d2119db2d9e3417fb94ee12578b8ba04 |
"""
GP Regression Model
"""
import numpy as np
import time
####################################################################################################
def GPRegress(K_s,PrecMatrix,K_ss,y,return_covariance=False):
"""
Given input array of kernel values, precision matrix, etc, get predictive
distribution... | nealegibson/GeePea | src/GPRegression.py | Python | gpl-3.0 | 1,566 | [
"Gaussian"
] | d29fb6ae5a80ee4649eddc4d37bfb57439e21d2a35f3e3d5d5ffd644a6b4ac82 |
'''
@title fwhm
@author: Rebecca Coles
Updated on Nov 15, 2017
Created on Oct 12, 2017
fwhm
This module holds a series of functions that I use to find the
full-well-half-maximum of a given curve.
Modules:
fwhm3D
This function accepts a 3D array and finds the FWHM of the image.
FWHM is the gaussian PSF full wi... | racoles/general_image_processing_functions | fwhm.py | Python | gpl-3.0 | 1,289 | [
"Gaussian"
] | 5f00c00dabd90663cf8fdf49b01e14a258801c913e575c42045cca2a600d43e9 |
"""A more stable successor to TD3.
By default, this uses a near-identical configuration to that reported in the
TD3 paper.
"""
from ray.rllib.agents.ddpg.ddpg import DDPGTrainer, \
DEFAULT_CONFIG as DDPG_CONFIG
from ray.rllib.utils import merge_dicts
TD3_DEFAULT_CONFIG = merge_dicts(
DDPG_CONFIG,
{
... | stephanie-wang/ray | rllib/agents/ddpg/td3.py | Python | apache-2.0 | 1,659 | [
"Gaussian"
] | c3f727bcb91032df880310c086e68af36f51314bae91ebd99fcd001c0fc08cdf |
"""
"""
import os, sys
import py
class Checkers:
_depend_on_existence = 'exists', 'link', 'dir', 'file'
def __init__(self, path):
self.path = path
def dir(self):
raise NotImplementedError
def file(self):
raise NotImplementedError
def dotfile(self):
return self.pa... | pexip/os-codespeak-lib | py/_path/common.py | Python | mit | 12,413 | [
"VisIt"
] | 70f18df9d5e91d992095a5f6dce3ade6b0e9fbbdd181efa853fc63d49ed5b92f |
"""
Module for reading Gaussian cube files, which have become one of the standard file formats
for volumetric data in quantum chemistry and solid state physics software packages
(VASP being an exception).
Some basic info about cube files
(abridged info from http://paulbourke.net/dataformats/cube/ by Paul Bourke)
The ... | richardtran415/pymatgen | pymatgen/io/cube.py | Python | mit | 9,239 | [
"CPMD",
"Gaussian",
"VASP",
"pymatgen"
] | abef95c451712ad3698ee388dad144c1f7e726a44ae8d0c417b19b78cc01f81a |
# -*- coding: utf-8 -*-
'''
Describe test for Django
@author: Laurent GAY
@organization: sd-libre.fr
@contact: info@sd-libre.fr
@copyright: 2015 sd-libre.fr
@license: This file is part of Lucterios.
Lucterios is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License ... | Diacamma2/financial | diacamma/accounting/tests_entries.py | Python | gpl-3.0 | 87,704 | [
"Dalton"
] | 318c1de3e128ee05a30abaa16e57ddda414e66c632a81b54f18dba011b3da324 |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ...util.linalg import pdinv, dpotrs, dpotri, symmetrify, jitchol, dtrtrs, tdot
from GPy.core.parameterization.variational import VariationalPosterior
class Posterior(object):
""... | avehtari/GPy | GPy/inference/latent_function_inference/posterior.py | Python | bsd-3-clause | 10,849 | [
"Gaussian"
] | 43e7b14b2bd67af2124f83bdbba7cc8acf573601534d6c8bdaea23c36fe59ecf |
from matplotlib import rcParams, rc
import numpy as np
import sys
from fitFunctions import gaussian
import scipy.interpolate
import scipy.signal
from baselineIIR import IirFilter
import pickle
# common setup for matplotlib
params = {'savefig.dpi': 300, # save figures to 300 dpi
'axes.labelsize': 14,
... | bmazin/SDR | Projects/SuperMatchedFilters/photonTriggers.py | Python | gpl-2.0 | 9,211 | [
"Gaussian"
] | 47e72fd6c99f826238a1b7add2597359c9ae91caa32ea7ec779073cc4b6bbf9e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/server/server.py
#
# 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, th... | drptbl/king-phisher | king_phisher/server/server.py | Python | bsd-3-clause | 27,595 | [
"VisIt"
] | 4f1a55ec95719b0027f4b0484bcf2932961304c36f8f768059a8036c0daf02f0 |
"""
Use this script for setting the arguments.
(c) May 2017 by Daniel Seita
"""
import argparse
import logz
import os
import pickle
import tensorflow as tf
import utils
from es import ESAgent
if __name__ == "__main__":
""" LOTS of arguments here, but hopefully most are straightforward. Run
`python main.py -... | DanielTakeshi/rl_algorithms | es/main.py | Python | mit | 2,542 | [
"Gaussian"
] | 8d3a32b9f7d777401f16c4b9effb8483a929f38c359298d1296fc0a3866ea40a |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License")
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | shiwalimohan/RLInfiniteMario | system/codecs/Python/src/tests/test_empty_experiment.py | Python | gpl-2.0 | 2,574 | [
"Brian"
] | 65f0c4c84efc4d3b5140500129fbfca4a01c1c7032f57bb0e7f093917c33f111 |
# !/bin/python
# -*- coding: latin-1 -*-
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# 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 opt... | FedoraScientific/salome-hexablock | src/TEST_PY/test_v6/monica.py | Python | lgpl-2.1 | 5,353 | [
"VTK"
] | f1b048d6f8f6a90ee8b123115e8a85d39a2d190cfde9685c1c91372d1537a0bd |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements equivalents of the basic ComputedEntry objects, which
is the basic entity that can be used to perform many analyses. ComputedEntries
contain calculated information, typically from VAS... | gVallverdu/pymatgen | pymatgen/entries/computed_entries.py | Python | mit | 7,871 | [
"VASP",
"pymatgen"
] | ab21271fc18637a6132c6ff836be4bb4b4d45bcc9c43ec1a86ff4e8cd026955a |
import argparse
from director import consoleapp
from director import cameraview
from director import applogic
from director import viewbehaviors
from director import objectmodel as om
from director import vtkAll as vtk
import PythonQt
from PythonQt import QtGui
import bot_core as lcmbotcore
class ImageViewApp(objec... | patmarion/director | src/python/director/imageviewapp.py | Python | bsd-3-clause | 5,008 | [
"VTK"
] | 5ee7ea5466ac95754758477e19a5f6b441970c5b7267e06585a4aff6b1a0e734 |
"""Rewrite assertion AST to produce nice error messages"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import ast
import errno
import imp
import itertools
import marshal
import os
import re
import string
import struct
import sys
import types
import atom... | lmregus/Portfolio | python/design_patterns/env/lib/python3.7/site-packages/_pytest/assertion/rewrite.py | Python | mit | 41,131 | [
"VisIt"
] | bb3e4eb2af604f374286ce29081eda2b73f4739ea8c7a58c931f977e08cc3365 |
from io import StringIO
import sys
import os.path as osp
import pickle
# get the path to this module directory
data_dir = osp.dirname(sys.modules[__name__].__file__)
BEN_file_name = "3ptb_BEN.pdb"
trypsin_file_name = "3ptb_trypsin.pdb"
waters_3ptb_file_name = "3ptb_water.pdb"
BEN_Hs_file_name = "BEN+Hs_3ptb.pdb"
try... | salotz/mast | mastic/tests/data/__init__.py | Python | mit | 3,805 | [
"CRYSTAL",
"RDKit"
] | 9b6f93ac9bedb1ce89472638ad7af90e43f8dc52b32341ea92dc2bb637814563 |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/test/zoo/chronos/forecaster/test_tcmf_forecaster.py | Python | apache-2.0 | 14,337 | [
"ORCA"
] | 05a9b94c77a2ca2dbe9d915bd14bd2b509bbd3c1c28edfab3d70fa6a54631b04 |
# Portions Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2.
# changelog bisection for mercurial
#
# Copyright 2007 Matt Mackall
# Copyright 2005, 2006 Benoit Boissinot <benoit.boissinot@ens-lyon.org>
#... | facebookexperimental/eden | eden/scm/edenscm/mercurial/hbisect.py | Python | gpl-2.0 | 12,464 | [
"VisIt"
] | c09a3faaad317b617bf9a5dda0dab03138c90ae6ee7a72abbf3ee13743d7795b |
"""
Visualization tools for coarse grids, both C/F splittings and aggregation.
Output is either to file (VTK) or to the screen (matplotlib).
vis_splitting: visualize C/F splittings through vertex elements
vis_aggregate_groups: visualize aggregation through groupins of edges, elements
"""
__docformat__ = "res... | huahbo/pyamg | pyamg/vis/vis_coarse.py | Python | mit | 10,031 | [
"ParaView",
"VTK"
] | 17475e6c5b00bd6d0f67bc916dfa05e0ea98701d4be9c9593ba9932af6326ef3 |
# -*- encoding: utf-8 -*-
#
# Copyright 2012 Moritz Schlarb <mail@moritz-schlarb.de>. All rights reserved.
# Copyright 2013 Martin Zimmermann <info@posativ.org>. All rights reserved.
# License: BSD Style, 2 clauses -- see LICENSE.
from __future__ import absolute_import
import os
import io
import re
import ast
import ... | markvl/acrylamid | acrylamid/templates/mako.py | Python | bsd-2-clause | 5,841 | [
"VisIt"
] | b53e2ac6afc3b147dc0080112ade1fad85d2f16ac09532b3a0bea6f9306cad97 |
"""
Procedures for fitting marginal regression models to dependent data
using Generalized Estimating Equations.
References
----------
KY Liang and S Zeger. "Longitudinal data analysis using
generalized linear models". Biometrika (1986) 73 (1): 13-22.
S Zeger and KY Liang. "Longitudinal Data Analysis for Discrete and
... | jseabold/statsmodels | statsmodels/genmod/generalized_estimating_equations.py | Python | bsd-3-clause | 115,703 | [
"Gaussian"
] | 75321e719c37fbb8e2687169d3e332ea6b3e6cd230e27af8a88d3b39fdbae2c5 |
from math import pi
import pickle
import numpy as np
from ase.atoms import Atoms
from ase.parallel import world, rank, distribute_cpus
from ase.utils import opencew
def make_test_dft_calculation():
a = b = 2.0
c = 6.0
atoms = Atoms(positions=[(0, 0, c / 2)],
symbols='H',
... | askhl/ase | ase/calculators/test.py | Python | gpl-2.0 | 3,631 | [
"ASE"
] | b05f0b50bd9eb1fb33a44df5a496db2e96a72a9f9ae15143dfbac120edd6871a |
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