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#
# A file that opens the neuroConstruct project LarkumEtAl2009 and run multiple simulations stimulating ech terminal apical branch with varying number of synapses.
#
# Author: Matteo Farinella
from sys import *
from java.io import File
from java.lang import System
from java.util import ArrayList
from uc... | pgleeson/TestArea | models/LarkumEtAl2009/pythonScripts/PNMDAs_singlebranches.py | Python | gpl-2.0 | 8,519 | [
"NEURON"
] | 65105d5e6a6ed726062aebeae3ad406ee0c9c5fa475a1467162fec955b7b84e1 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | TheTimmy/spack | var/spack/repos/builtin/packages/netcdf-fortran/package.py | Python | lgpl-2.1 | 2,046 | [
"NetCDF"
] | 4d48de2ae946304626e18e2fd7f511cf189f508803fc9f0a2f61c912c80ec896 |
from __future__ import print_function
from pprint import pprint
import sys
sys.path.append( 'external/pycparser' )
from pycparser import c_parser, c_ast, parse_file
# Portable cpp path for Windows and Linux/Unix
CPPPATH = '../utils/cpp.exe' if sys.platform == 'win32' else 'cpp'
class IdVisitor(c_ast.NodeVisitor):
... | arunksaha/casescore | pycparser_id.py | Python | bsd-3-clause | 916 | [
"VisIt"
] | bd7bdc9f0805d908768fbf7de9e3c5d27584d829800239e01f67b92411a2c30a |
"""Accessors for NAMD FEP datasets.
"""
from os.path import dirname, join
from glob import glob
from .. import Bunch
def load_tyr2ala():
"""Load the NAMD tyrosine to alanine mutation dataset.
Returns
-------
data : Bunch
Dictionary-like object, the interesting attributes are:
- 'da... | alchemistry/alchemtest | src/alchemtest/namd/access.py | Python | bsd-3-clause | 2,582 | [
"NAMD"
] | 1b88a67eff778b26c6c9f80e77fc4def5fed5d1ad7b53310fe47114982a70f74 |
"""
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 array
import numpy as np
from scipy import linalg
import scipy.sparse as sp
from ..preprocessing import MultiLabelBin... | RomainBrault/scikit-learn | sklearn/datasets/samples_generator.py | Python | bsd-3-clause | 56,766 | [
"Gaussian"
] | 21a9a21446b5da7145c383581a7ebe99366b3fefe490cc7ded3f332eedc3a2bf |
import tensorflow as tf
import numpy as np
import pickle
import TrainingFeatureNetInf as TFNI
import sklearn.metrics as metrics
def Classifier(layer_num, neuron_num, Input_feature_shape, Input_label_shape, test_dict):
l_input = len(test_dict[Input_feature_shape][0])
hidden_layer_shape = TFNI.Hidden_layer_shape(laye... | PassiveVision/Feature-Net-Learn | FeatureNetInf.py | Python | gpl-3.0 | 2,269 | [
"NEURON"
] | 6b4f7bab6443b228cd13a2651d7b43937220c94e781bed1a61cde60671be0fc4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This file is part of web2py Web Framework (Copyrighted, 2007-2010).
Developed by Massimo Di Pierro <mdipierro@cs.depaul.edu>.
License: GPL v2
CONTENT_TYPE dictionary created against freedesktop.org' shared mime info
database version 0.70.
"""
__all__ = ['contenttype'... | henkelis/sonospy | web2py/gluon/contenttype.py | Python | gpl-3.0 | 25,110 | [
"NetCDF"
] | e6c05d1f3dce61772be8ec38bfce1b82e95360b9a53084513d38af8bb60e5eb9 |
# -*- coding: utf-8 -*-
"""
CreateInflowFileFromLDASRunoff.py
RAPIDpy
Created by Alan D. Snow, 2015
Adapted from CreateInflowFileFromECMWFRunoff.py.
License: BSD-3-Clause
"""
from netCDF4 import Dataset
from .CreateInflowFileFromGriddedRunoff import \
CreateInflowFileFromGriddedRunoff
class Creat... | erdc-cm/RAPIDpy | RAPIDpy/inflow/CreateInflowFileFromLDASRunoff.py | Python | bsd-3-clause | 1,728 | [
"NetCDF"
] | fc67096fe36befc43e22a7bc61f1469a9f64e895b8683c674159b0ac8c7b3bb6 |
"""
FlexGet build and development utilities - unfortunately this file is somewhat messy
"""
from __future__ import print_function
import glob
import os
import shutil
import sys
from paver.easy import environment, task, cmdopts, Bunch, path, call_task, might_call, consume_args
# These 2 packages do magic on import, eve... | tsnoam/Flexget | pavement.py | Python | mit | 11,572 | [
"GULP"
] | 997e5ba2985f9d20c8a8da6e22d24e2f66b400c4fbf58f4a890f1062065a9aac |
"""
Tool Input Translation.
"""
import logging
from galaxy.util.bunch import Bunch
log = logging.getLogger( __name__ )
class ToolInputTranslator( object ):
"""
Handles Tool input translation.
This is used for data source tools
>>> from galaxy.util import Params
>>> from elementtree.ElementT... | volpino/Yeps-EURAC | lib/galaxy/tools/parameters/input_translation.py | Python | mit | 5,691 | [
"Galaxy"
] | a57bea74bf9960b23aedac49aa7a4225cecac3119ef0c8f6fb3cc677c1b370ce |
# Author: David Goodger
# Contact: goodger@users.sourceforge.net
# Revision: $Revision: 21817 $
# Date: $Date: 2005-07-21 13:39:57 -0700 (Thu, 21 Jul 2005) $
# Copyright: This module has been placed in the public domain.
"""
Parser for Python modules. Requires Python 2.2 or higher.
The `parse_module()` function take... | garinh/cs | docs/support/docutils/readers/python/moduleparser.py | Python | lgpl-2.1 | 25,839 | [
"CRYSTAL",
"VisIt"
] | 08d3c62ff75d5f437b09c60f334c59ba346e54c2733d6860865fdf5338b731d0 |
"""
Basic SparseCFProjection with associated sparse CFs and output,
response, and learning function. If sparse component cannot be imported,
SparseCFProjection will fall back to a basic dense CFProjection.
CFSOF and CFSLF Plugin function allow any single CF output function to
be applied to the sparse CFs, but may suff... | ioam/topographica | topo/sparse/sparsecf.py | Python | bsd-3-clause | 34,459 | [
"Gaussian"
] | c66ebad9cfaa1ce11c7c8a36ded2506e9b4798b7ce35cb80e7e0f0a2af0d1bdf |
# DeepCrystal Technologies 2017 - Patrick Hop
# MIT License - have fun!!
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
import os
import numpy as np
np.random.seed(123)
from sklearn.ensemble import RandomForestRegressor
from sklearn import svm
import ten... | Agent007/deepchem | examples/adme/run_benchmarks.py | Python | mit | 4,255 | [
"CRYSTAL"
] | 49f2d33e1cfc0555c0a56bc08821c24e36e048261a2d9992106dba4acb7473ae |
from math import sqrt
from random import random
import itertools
from itertools import chain
import functools as fcn
def generate_graph(cities):
'''
Generates Travelling Salesman's Graph (undirected graph)
given cities salesman needs to visit
cities - [(x1, y1), (x2, y2), ..., (xn, yn)]
... | sglumac/pyislands | pyislands/permutation/tsp/graph.py | Python | mit | 1,943 | [
"VisIt"
] | fd180ec16338965d7df084334873584375a5f605473fddeb1ac8eae3e534f7af |
import os
import configparser
from pyspark import SparkContext, SparkConf
from pyspark.sql import SQLContext
from pyspark.sql.types import *
import Utils
class Cohort:
#
# Filter out users by using values set in
# property files. If no value is set then the
# filter is not applied
#
def __i... | opme/SurgeonScorecard | python/scorecard/Cohort.py | Python | apache-2.0 | 8,735 | [
"VisIt"
] | 072d43448d379d6a268c9b26eb2e5ff1bc0198d4999ebb815f46fc3949a4a069 |
"""Adding icons and menu items using the freedesktop.org system.
(xdg = X Desktop Group)
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
import shutil, os, tempfile
from logging import info, warn
from zeroinstall import SafeException
... | dabrahams/zeroinstall | zeroinstall/gtkui/xdgutils.py | Python | lgpl-2.1 | 2,917 | [
"VisIt"
] | 62f20b69abfea3fc5792d79fa0f6c6f03c1db9024f5e30d380288ef8a19d3f20 |
# -*- coding: utf-8 -*-
##############################################################################
# 2014 E2OpenPlugins #
# #
# This file is open source software; you can redistribute... | HDMU/e2openplugin-OpenWebif | plugin/controllers/models/owibranding.py | Python | gpl-2.0 | 18,232 | [
"Galaxy"
] | b755aad72826f48db65b3f68acde2e801fab1ca4519793ac08154da1598efa20 |
__author__ = 'kpaskov'
import re
from urllib.parse import urlparse
from behave import step
from selenium.common.exceptions import NoSuchElementException
@step('I visit "{url}" for "{obj}"')
def visit_page_for(context, url, obj):
context.browser.get(context.base_url + url.replace('?', obj))
@step('I click the but... | yeastgenome/SGDFrontend | src/sgd/frontend/yeastgenome/tests/features/steps/__init__.py | Python | mit | 5,859 | [
"VisIt"
] | 601b324aab92bcf34a50f35f665551c411eaf113e2f439841edd46737cfa47ee |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# 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;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | src/rmock/config.py | Python | lgpl-3.0 | 946 | [
"VisIt"
] | 7b40acc48edfba784abea4a62c48290452489c39c99dda73cb7cf18aaabac3eb |
#Raspberry Pi, Minecraft Bombs - Turn any block into a bomb!
#import the minecraft.py module from the minecraft directory
import minecraft.minecraft as minecraft
#import minecraft block module
import minecraft.block as block
#import time, so delays can be used
import time
#import threading, so threads can be ... | mohsraspi/mhscs14 | tristan/bomb.py | Python | gpl-2.0 | 3,239 | [
"BLAST"
] | b709fc48e0fcc3360b17fcea135736ab06da154c8449e7339d851ab4dfd313ad |
# gpdm.py: Implementation of GPDM for single sequence
# This can be used as a starting point for further implementations
# Author: Nishanth
# Date: 2017/01/17
# Source: GPflow source code
import numpy as np
import tensorflow as tf
from GPflow.tf_wraps import eye
from GPflow.model import GPModel
from GPflow._settings i... | ShibataLabPrivate/GPyWorkshop | Experiments/gpdm.py | Python | mit | 5,965 | [
"Gaussian"
] | 57eac4f3eec3b4d32d0733e2f23d9fe87bc21103c4d2abbcc0c48bdc83616542 |
# Copyright (C) 2008 CAMd
# Please see the accompanying LICENSE file for further information.
from __future__ import division
import numpy as np
from gpaw.utilities.blas import rk, r2k, gemm
from gpaw.matrix_descriptor import BandMatrixDescriptor, \
BlacsBandMatrixDescriptor
class ... | qsnake/gpaw | gpaw/hs_operators.py | Python | gpl-3.0 | 23,175 | [
"GPAW"
] | bcae24b4486369b21cfa592b802d71539324b7834d62a1640bca8871b63c0422 |
# -*- coding: utf-8 -*-
### THIS IS THE FILE THAT DEALS WITH ASSET.PROGRESS FILES
# It's core idea is to be able to manage checklist of the
# project asset by asset
# in the previous version, the checklist was constructed
# with a limitation of one indentation of a sub-task
# in this one I want to make sure people c... | JYamihud/blender-organizer | py_data/modules/checklist.py | Python | gpl-2.0 | 54,210 | [
"FLEUR"
] | f6b8296ca1950030ba0b8ccf1ba53d14b875f76678bac18bfdaa686f1b14dae8 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/procrouting/__init__.py | Python | gpl-2.0 | 1,150 | [
"Psi4"
] | 714663801f6fdae80c5893a3b8acae7ad81ee261a4f0a7b6898080f56c83217f |
#!/usr/bin/env python2.7
# This version is created at Mon Mar 17 12:54:44 CET 2014
# Author: Asli I. Ozen (asli@cbs.dtu.dk)
# License: GPL 3.0 (http://www.gnu.org/licenses/gpl-3.0.txt)
import sys, gzip
import re, string
import argparse
import os
from Bio.Blast import NCBIStandalone
from operator import itemgetter, attr... | MG-group-tools/MGFunc | mgfunc_v2/blastparse.py | Python | gpl-3.0 | 14,248 | [
"BLAST"
] | d148cc467fe7723362d48adcf3ae456c84006079033eb11c8966cd3ac70ae1ba |
# -*- coding: utf-8 -*-
# Copyright 2007-2020 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | dnjohnstone/hyperspy | hyperspy/_signals/signal1d.py | Python | gpl-3.0 | 60,556 | [
"Gaussian"
] | 706b899a8923a9c9368c852bf5a232e4760620273e9ed302d181cf70564e8d9c |
"""Unit test for roman1.py
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.3 $"
__date__ = "$Date: 2004/05/05 21:57:20 $"
__copyri... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/roman/stage1/romantest1.py | Python | mit | 5,496 | [
"VisIt"
] | 9fbb7d1e6a96a63edb0c0223efbce713a2e74feb42e863f9ec1ac10845a57aab |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/analysis/test_hole.py | Python | gpl-2.0 | 10,067 | [
"MDAnalysis",
"VMD"
] | acfca22b188d142a6dfaabab4b084891531b235d0c2bcc064ade0cff6624d5f5 |
##
# @package RAMS.NXT
# @file NXTMotor.py
# @author Brian Kim
# @date 7/24/14
# @brief a wrapper around a MotorProfileAssembly that defines an interface with an NXTMotor
#
from NXTPort import NXTPort
from Rover import MotorAssembly
class NXTMotor( NXTPort ):
def __init__( self, asm=None ):
NXTPort.__init__(... | briansan/rams | RAMS/nxt/NXTMotor.py | Python | bsd-3-clause | 1,029 | [
"Brian"
] | 37cad6c5320a5f4face183903b69c766ae21e0df1dbac89c6207553820ef2a16 |
# (C) 2013, James Cammarata <jcammarata@ansible.com>
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import collections
import datetime
import fun... | pmarques/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 37,005 | [
"Galaxy"
] | bc3227e0a13dacaee7ddf56953a746c7d5dba812b926f433823758e315bba66d |
#!/usr/bin/env python
import vtk
def main():
pd_fn = get_program_parameters()
colors = vtk.vtkNamedColors()
polyData = ReadPolyData(pd_fn)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(polyData)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetDiffuseCol... | lorensen/VTKExamples | src/Python/Utilities/SaveSceneToFieldData.py | Python | apache-2.0 | 5,461 | [
"VTK"
] | 9e95c537982f596f39fd19d8d89107566ab5d7208c5aab02b8606d493cb45ba5 |
'''
Parses a Python source file into an AST in JSON format. can be viewed
online in a viewer like: http://jsonviewer.stack.hu/
Usage:
python parse_python_to_json.py --pyfile=test.py # pass in code within a file
python parse_python_to_json.py 'print "Hello world"' # pass in code as a string
Try running on its o... | pgbovine/python-parse-to-json | parse_python_to_json.py | Python | mit | 3,059 | [
"VisIt"
] | 7fa045e95b99cb6222fe1eaf6a0be45f8712940af16f6e24755f1de70821eb4c |
#__author__ = 'Jared Streich and Kevin Murray'
#__version__ = '2983474627822723646378273647280.9001.2 and a half'
#__date__ = 'August, 6 2013'
#Citation at bottom, mostly from Phidgets etc.
#Basic imports
from ctypes import *
import sys
from time import sleep
#Phidget specific imports
from Phidgets.Phi... | borevitzlab/plantspin | sps.py | Python | gpl-3.0 | 6,155 | [
"VisIt"
] | c5f633d1fc0a112c4d96950d61b4b18ea33eedd48f4b331c9c183e71c593e3b6 |
##############################################################################
# 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... | casawa/mdtraj | mdtraj/geometry/hbond.py | Python | lgpl-2.1 | 16,393 | [
"MDTraj"
] | 534837ca9096719ec61d7b31643fb94c2fd15b42a68cbb25034d42cc715a582e |
#!/usr/bin/env python
# vim:fileencoding=UTF-8:ts=4:sw=4:sta:et:sts=4:ai
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2011, Kovid Goyal <kovid@kovidgoyal.net>'
__docformat__ = 'restructuredtext en'
import os, ppr... | sss/calibre-at-bzr | src/calibre/web/jsbrowser/browser.py | Python | gpl-3.0 | 17,114 | [
"VisIt"
] | a6eaa0b342a3baf7266ad9bd5ca4f2b7c631f0f468049eba7050c76df46c938f |
#!/usr/bin/env python2
"""
NAME:
CoPAS_python2.py <https://github.com/daviddelene/CoPAS>
PURPOSE:
To facilitate the installation, setup, and integration of open source
software and packages related to cloud physics, in-situ airborne data.
Download/Clone CoPAS Distribution
cd $HOME
git clone https://github.... | daviddelene/CoPAS | CoPAS_python2.py | Python | agpl-3.0 | 26,416 | [
"Brian"
] | 731bc0d1d072e264e5794e7eba7da00190d11094207e503da3939367d8fe8e38 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | MJJoyce/climate | examples/multi_model_evaluation.py | Python | apache-2.0 | 5,315 | [
"NetCDF"
] | 4f60a55c74beb23b5f637fe5938d20411e7ff67b1fde0e84fda6506f498e20ac |
# Copyright 2000-2010 Michael Hudson-Doyle <micahel@gmail.com>
# Antonio Cuni
#
# All Rights Reserved
#
#
# Permission to use, copy, modify, and distribute this software and
# its documentation for any purpose is hereby granted without fee,
# provided that the above copyri... | c0710204/mirrorsBistu | pypi/bandersnatch/lib/python2.7/site-packages/pyrepl/completing_reader.py | Python | mit | 9,444 | [
"Galaxy"
] | f1769a86bf06ce508dad9a4a52b4f172c69839078925bede629493fdc0201ec0 |
import numpy as np
from enable.api import ColorTrait, Container
from pyface.action.api import Action
from traits.api import Callable, Either, Instance, Tuple, on_trait_change
from .color_function_component import ColorNode, ColorComponent
from .function_component import FunctionComponent
from .gaussian_function_compo... | dmsurti/ensemble | ensemble/ctf/editor.py | Python | bsd-3-clause | 9,124 | [
"Gaussian"
] | 280451f3132859f1738b60f695b82f049486b02b5511486c900124bbf5c6f6e4 |
import numpy as np
heading = {}
heading['xyz'] = [0,1,2]
heading['xy' ] = [0,1]
heading['xz' ] = [0,2]
heading['yz' ] = [1,2]
heading['x' ] = [0]
heading['y' ] = [1]
heading['z' ] = [2]
# polarization is complementary to heading
polarization = {}
polarization['xyz'] = [0,1,2]
polarization['xy' ] = [1,0]
polarizat... | sanromd/emclaw | emclaw/utils/sources.py | Python | lgpl-3.0 | 23,123 | [
"Gaussian"
] | 54b193a0a041088dd2164aeb542bc43beff628eb55730484ce8b376509010a5c |
import os
import sys
import sysconfig
from pysam.libchtslib import *
from pysam.libcutils import *
import pysam.libcutils as libcutils
import pysam.libcfaidx as libcfaidx
from pysam.libcfaidx import *
import pysam.libctabix as libctabix
from pysam.libctabix import *
import pysam.libcsamfile as libcsamfile
from pysam.l... | bioinformed/pysam | pysam/__init__.py | Python | mit | 3,041 | [
"pysam"
] | 22f92f654708cdde78ec3383eb61788d2811a61078f962b465df8c16f91891a9 |
#!/usr/bin/env python
import pprint
import re
import os, sys
import unittest
sys.path[0:0] = ['.', '..']
from pycparser import c_parser
from pycparser.c_ast import *
from pycparser.c_parser import CParser, Coord, ParseError
_c_parser = c_parser.CParser(
lex_optimize=False,
yacc_debug... | keulraesik/pycparser | tests/test_c_parser.py | Python | bsd-3-clause | 62,280 | [
"MOE",
"VisIt"
] | 5d5d0f0a2d90a0e53f7f049715df2abd0b5aec233686a5219377fdf4fa88e8df |
#!/usr/bin/python
# vim: et sw=4 ts=4:
# -*- coding: utf-8 -*-
#
# Piwik - free/libre analytics platform
#
# @link http://piwik.org
# @license http://www.gnu.org/licenses/gpl-3.0.html GPL v3 or later
# @version $Id$
#
# For more info see: http://piwik.org/log-analytics/ and http://piwik.org/docs/log-analytics-tool-how-... | oluabbeys/drupzod | piwik/misc/log-analytics/import_logs.py | Python | gpl-2.0 | 90,649 | [
"VisIt"
] | 62ab684ad0661f742637b32f3a7a34a2588df7bb247ffaffc55efd82802fc915 |
#!../../../../virtualenv/bin/python3
# -*- coding: utf-8 -*-
# NB: The shebang line above assumes you've installed a python virtual environment alongside your working copy of the
# <4most-4gp-scripts> git repository. It also only works if you invoke this python script from the directory where it
# is located. If these... | dcf21/4most-4gp-scripts | src/scripts/degrade_spectra/convolve_library.py | Python | mit | 8,999 | [
"Gaussian"
] | cd944badaab119e41e7cbd463109dfcddc9984405f81162243dcb4413ca04980 |
# -*- coding: utf-8 -*-
def VtkDibujaLineas(nmbActor):
# Define el actor a emplear para dibujar elementos.
ugridMapper= vtk.vtkDataSetMapper().SetInput(ugrid)
nmbActor= vtk.vtkActor()
nmbActor.SetMapper(ugridMapper)
nmbActor.GetProperty().SetColor(0,0,0)
nmbActor.GetProperty().SetRepresentationToWireFrame()... | lcpt/xc | python_modules/postprocess/xcVtk/CAD_model/vtk_plot_lines.py | Python | gpl-3.0 | 352 | [
"VTK"
] | 06464ebeb55a0dcb2a282d5739e2dc65c3ed8ce7851b2a1b81a44c0dbd697459 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import open_connect.connect_core.utils.models
import django_extensions.db.fields
import django.utils.timezone
from django.conf import settings
from pytz import common_timezones
from open_connect.connect_core.utils.... | lpatmo/actionify_the_news | open_connect/accounts/migrations/0001_initial.py | Python | mit | 7,323 | [
"VisIt"
] | 9e620ca0ce869fd9d66aa0fdef8bd6c42367296744f73b657b1ff97282207e1c |
"""Collection of DIRAC useful file related modules.
.. warning::
By default on Error they return None.
"""
#pylint: skip-file
## getGlobbedFiles gives "RuntimeError: maximum recursion depth exceeded" in pylint
import os
import hashlib
import random
import glob
import sys
import re
import errno
__RCSID__ = "$Id$"... | Andrew-McNab-UK/DIRAC | Core/Utilities/File.py | Python | gpl-3.0 | 6,776 | [
"DIRAC"
] | baf02942089adeeac09a6882a3c7e1054a427b82970dc3727c0fba7d03a88ae9 |
#!/usr/bin/env python
import numpy as np
# Eigenvalues a, b, c
e_a = 1.0
e_b = 0.6
e_c = 0.4
eigenvalues = [[e_a, e_b, e_c],
[-e_a, e_b, e_c],
[-e_a, -e_b, e_c],
[-e_a, e_b, -e_c],
[e_a, -e_b, e_c],
[e_a, -e_b, -e_c],
[e_a, e_b, -e_c],
[-e_a, -e_b, -e_c]]
with ... | thewtex/VTKSignedTensor | Testing/Data/Input/GenerateStrainFlavors.py | Python | apache-2.0 | 1,940 | [
"VTK"
] | 9513aec63344ae0e56f2c7f810088f4d597dc15d9341d6ebc60c51b515efa2e9 |
# Copyright (c) 2001-2014, Canal TP and/or its affiliates. All rights reserved.
#
# This file is part of Navitia,
# the software to build cool stuff with public transport.
#
# Hope you'll enjoy and contribute to this project,
# powered by Canal TP (www.canaltp.fr).
# Help us simplify mobility and open public tr... | TeXitoi/navitia | source/jormungandr/jormungandr/utils.py | Python | agpl-3.0 | 6,163 | [
"VisIt"
] | e9225d873a164971436af36249beb8a142c71227e03dedbd65aa3c97a7d9f084 |
try:
from ase.optimize.optimize import Optimizer as ase_Optimizer
except ImportError:
# Fall back to old placement
from ase.optimize import Optimizer as ase_Optimizer
from asap3 import parallelpossible as asap_parallel
if asap_parallel:
from asap3.mpi import world
class Optimizer(ase_Optimizer):
d... | auag92/n2dm | Asap-3.8.4/Python/asap3/optimize/__init__.py | Python | mit | 611 | [
"ASE"
] | 91ba330ab0d900f8f2c3002f9fb3d54958969f8b2f1ce87e8c85f5a03549c600 |
"""
This script parses an ENA metadata file in XML format and prints a subset of information.
Usage: python parse_ENA_sampleInfo_XML.py ERP000909.xml > samples.txt
Input: an XML file exported for a list of ERS accession numbers from ENA using the REST URLs API. For example, one can download an XML file
for sample... | wanyuac/BINF_toolkit | parse_ENA_sampleInfo_XML.py | Python | gpl-3.0 | 2,321 | [
"VisIt"
] | 1f2ce62dd48ceb3de7494a706ec501c700d616135604187040fce7f7ca3342d4 |
# -*- 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 option) any later ... | FedoraScientific/salome-hexablock | src/TEST_PY/test_unit/test_transfo.py | Python | lgpl-2.1 | 3,413 | [
"VTK"
] | 3a28e4ac16f9e37f2513af49923a1bb9424d2fff72f09a52dbbafff641bca677 |
# coding: utf-8
"""
================
Superflux onsets
================
This notebook demonstrates how to recover the Superflux onset detection algorithm of
`Boeck and Widmer, 2013 <http://dafx13.nuim.ie/papers/09.dafx2013_submission_12.pdf>`_
from librosa.
This algorithm improves onset detection accuracy in the prese... | bmcfee/librosa | docs/examples/plot_superflux.py | Python | isc | 3,764 | [
"Brian"
] | 432c6c768892ff53e0d2cce7f0651f5c833c4e222e8754c4f8ffc09679a8d97a |
"""
Support code for 0alias scripts.
@since: 0.28
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, SafeException
from zeroinstall import support
_old_template = '''#!/bin/sh
if [ "$*" = "--versions" ]; then
exec 0launch -gd '%s' "$... | rammstein/0install | zeroinstall/alias.py | Python | lgpl-2.1 | 3,280 | [
"VisIt"
] | 8aad941964e457376a6bb688aca07abf1ec3e319fa72af908986c77adb6cc3da |
# encoding: utf-8
# Copyright (c) 2001-2016, Canal TP and/or its affiliates. All rights reserved.
#
# This file is part of Navitia,
# the software to build cool stuff with public transport.
#
# Hope you'll enjoy and contribute to this project,
# powered by Canal TP (www.canaltp.fr).
# Help us simplify mobility... | antoine-de/navitia | source/jormungandr/jormungandr/realtime_schedule/siri.py | Python | agpl-3.0 | 7,891 | [
"VisIt"
] | f4bed81153e629028e3e8e576fe52126e14c58dc8021bbac82465455c6fae1cc |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import pickle
import numpy as np
from pymatgen.core.composition import Composition
from pymatgen.core.lattice import Lattice
from pymatgen.core.periodic_table import Element, Species
from pymatgen.core.sites import Periodic... | materialsproject/pymatgen | pymatgen/core/tests/test_sites.py | Python | mit | 11,467 | [
"pymatgen"
] | cab47e17b33ace8159ca3659c8277e16310612fa435192dcb3ae19ce773d6535 |
##############################################################################
# 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... | leeping/mdtraj | tests/test_hdf5.py | Python | lgpl-2.1 | 10,192 | [
"MDTraj",
"OpenMM"
] | e3f3e0d4c69ceef4d42f903af06391992e0c73498af5b4b2a446af5a4493acf2 |
import nas
import sys
import lib_nas
#import Lib_NAS_Rnas_IA_
# _bias_2_4 v2.0
# estructura Neuronal 2 bits --4 patrones de adaptacion
# @autor:Jose Luis Prado Seoane ---IT Security Researcher & Developer
# Research: Teoria de Sistemas Neuronales (I.A) --TSNB 808565016
# Redes Neuronales y su convergencia hacia ... | ciudadano72/TSNB_redes_neuronales | bias24.py | Python | gpl-3.0 | 4,681 | [
"NEURON"
] | 5df06c625fe497c7fcb7f6de3bdc6a8f4eaf4f5dc7e2aca44d0c225d5bd16d07 |
# This file is part of Buildbot. Buildbot 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, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without eve... | anish/buildbot | master/buildbot/test/unit/test_steps_shell.py | Python | gpl-2.0 | 43,758 | [
"exciting"
] | c96c339b186350e793ecf3480fbc7aee6a0ab1e650f26a99ed6a25db23f08c31 |
#!/usr/bin/env python
"""
Python implementation of common model fitting operations to
analyse protein folding data. Simply automates some fitting
and value calculation. Will be extended to include phi-value
analysis and other common calculations.
Allows for quick model evaluation and plotting.
Also tried to make thi... | quantumjot/PyFolding | pyfolding/core.py | Python | mit | 35,921 | [
"Gaussian"
] | 6c8a4dcb5ca85d5aad638f50ab45af7e19016be3df924dbe97b2377ecdcf252b |
#!/usr/bin/python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Tests for alchemical factory in `alchemy.py`.
"""
# ==============================================================... | choderalab/openmmtools | openmmtools/tests/test_alchemy.py | Python | mit | 122,836 | [
"MDTraj",
"OpenMM"
] | d237d0a3b933053e0ae8c85a3774804d73f074e12c5d087bd7972f1b1724e469 |
# -*- coding: utf-8 -*-
"""Transport functions for `Fraunhofer's OrientDB <http://graphstore.scai.fraunhofer.de>`_.
`Fraunhofer <https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics.html>`_ hosts
an instance of `OrientDB <https://orientdb.com/>`_ that contains BEL in a schema similar to
:mod:`pybe... | pybel/pybel | src/pybel/io/fraunhofer_orientdb.py | Python | mit | 7,079 | [
"Pybel"
] | 8d81c431b5242300713fcc20005836448b71031bf012fbf83bd3b5d74bb82d6d |
# -*- coding: utf-8 -*-
# from matplotlib import pyplot
#
# pyplot.plot([1, 3, 5, 7], [12, 5, 8, 11])
#
# pyplot.show()
import matplotlib.pyplot as plt
import numpy as np
# create some data to use for the plot
dt = 0.001
t = np.arange(0.0, 10.0, dt)
r = np.exp(-t[:1000]/0.05) # impulse response
x = np.... | mocne/PycharmProjects | HanderCode/handerCode/math.py | Python | mit | 979 | [
"Gaussian"
] | c8bd3501778b8e02e82f2a78da2bbbf41268fc2a4e110c19566897c947db70c5 |
#!/usr/bin/python
# Copyright 2012 Aaron S. Joyner <aaron@joyner.ws>
#
# 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 ... | asjoyner/lewis-class-scorer | lewis_class_test.py | Python | apache-2.0 | 5,963 | [
"Brian"
] | 9952456b89ce93114f1f4d618effd1421e3bafc14b48ad03e5659c96711fbc8e |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/core/ui/slidecontroller.py | Python | gpl-2.0 | 64,513 | [
"Brian"
] | 3f4b19330e8439824d0793d3588f0ad99b71aa79a433948893116b7c47f187c5 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# 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.
"""Classes corresponding to Newick trees, also used for Nexus trees.
See classes in `Bi... | bryback/quickseq | genescript/Bio/Phylo/Newick.py | Python | mit | 1,097 | [
"Biopython"
] | 6709a6013a6aa01f66fd72dec5e880b839be87a6826b2a5eebac3e4316422c12 |
#Import packages that will be used
#GUI generation Packages
import wx
import wx.aui
from wx.lib.buttons import GenBitmapButton,GenBitmapToggleButton
#Operational Packages
import subprocess
import traceback
import types
import os
import sys
import errno
import numpy as np
from Bio import Entrez
from xml.dom import mini... | fxb22/BioGUI | plugins/Tools/ImageJgui.py | Python | gpl-2.0 | 15,688 | [
"BLAST"
] | af67588ec7f1ea2265f4e4cf26bcfeb54a296a1a090ff09dad45146707965daf |
''' Copyright (c) 2013 Potential Ventures Ltd
Copyright (c) 2013 SolarFlare Communications 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 c... | stuarthodgson/cocotb | cocotb/generators/__init__.py | Python | bsd-3-clause | 3,358 | [
"Gaussian"
] | 2f1bc6d6fcd9afa1e929ac48f99d25d838d981f9ed3455fee55b448ee8553b7d |
from .AbstractLinker import AbstractLinker
from .utils import common_subprocess, get_input_file_type, get_text, dict_to_csv, eprint
from .normalize import Normalizer
from .OPSIN import OPSIN
from rdkit.Chem import MolFromSmiles, MolToInchi, InchiToInchiKey
from pubchempy import get_compounds, BadRequestError, NotFoun... | gorgitko/molminer | molminer/ChemSpot.py | Python | mit | 34,926 | [
"RDKit"
] | d922d6d969cb5444581555bfd7623f80873024a8e5e63d7d0090b2bbb49c0e74 |
from __future__ import print_function
import sys
import time
import requests
from numpy import pi, sin, cos
import numpy as np
from bokeh.objects import (Plot, DataRange1d, LinearAxis,
ColumnDataSource, Glyph, PanTool, WheelZoomTool)
from bokeh.glyphs import Line
from bokeh import session
from bokeh import docu... | sahat/bokeh | examples/glyphs/line_animate.py | Python | bsd-3-clause | 1,932 | [
"VisIt"
] | cc8d0125a27929f6e120f48ef4fd210ce24ab14102cffd739898071eb59acf6d |
# Copyright 2017 The 'Scalable Private Learning with PATE' 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
#
# ... | cshallue/models | research/differential_privacy/pate/smooth_sensitivity.py | Python | apache-2.0 | 13,739 | [
"Gaussian"
] | e2956d80bf6b77f4d8b0e349098786d376ad17d12632c14c5a637844484982eb |
import numpy as np
import copy as cp
import random
from board import Board
from sklearn.neighbors import BallTree
from globalconsts import \
EMPTY, RED, BLACK, BKING, RKING, \
FORWARD_LEFT, FORWARD_RIGHT, BACKWARD_LEFT, BACKWARD_RIGHT, \
AI_COLOR, THRESHOLD, PLAYER_COLOR, \
LOSE, WIN, CONTINUE,... | zlalvani/checkers-learner | learner.py | Python | mit | 7,702 | [
"Gaussian"
] | 7578f79a7e43cdf4c9672d85fa4055e50b12d863103d8c6bd12fdfdd27d2ab23 |
import numpy as np
from ase.calculators.emt import EMT
from ase import Atoms
a = 3.60
b = a / 2
cu = Atoms('Cu',
positions=[(0, 0, 0)],
cell=[(0, b, b),
(b, 0, b),
(b, b, 0)],
pbc=1,
calculator=EMT())
e0 = cu.get_potential_energy()
print e0
... | grhawk/ASE | tools/ase/test/emt.py | Python | gpl-2.0 | 1,579 | [
"ASE"
] | 39c3b156b7859942c11b0659201f5b5228338adaa149a393c55192ca54193cca |
#!/usr/bin/env python
import roslib
import rospy
import smach
import smach_ros
from smach import StateMachine
import actionlib
import time
import threading
from smach_ros import SimpleActionState
from smach_ros import ActionServerWrapper
from std_msgs.msg import String, Float64, UInt8, Bool
from wm_interpreter.msg imp... | WalkingMachine/sara_commun | wm_robocup2016/src/stage1_speech_recognition_FR.py | Python | apache-2.0 | 17,022 | [
"Galaxy"
] | e42926a1549e1fc74b591796a690d4065f0f669d21077d057c70927e2cfff7bc |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-service-control | scripts/fixup_servicecontrol_v2_keywords.py | Python | apache-2.0 | 6,089 | [
"VisIt"
] | 6d090c0e89dc32e70045734b826b3cb755d0354f60b2543b908839a5a987ed20 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create a rendering window and renderer
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.StereoCapableWindowOn()
iren = vtk.vtkRenderWindowInte... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/IO/EnSight/Testing/Python/EnSightBlow3Bin.py | Python | gpl-3.0 | 1,508 | [
"VTK"
] | 093cbd2eb6aeb22a982318e9be3bbc676f308af099a5e9e427d3a3902b3344bd |
#!/usr/bin/env python
import cookielib
import sys, os, time, argparse, getpass, re
try:
import mechanize
except ImportError:
print 'python-mechanize module not available.\n'
sys.exit(1)
def webBrowser():
# Browser
br = mechanize.Browser()
# Cookie Jar
cj = cookielib.LWPCookieJar()
br.set_cookiejar(cj... | giopastor/moose | scripts/github_traffic.py | Python | lgpl-2.1 | 5,792 | [
"MOOSE"
] | 0a9220cba24c1fcbfe7e4ac82aff1b629f2802a449da2c2ceb2da91b4758206b |
r"""
****************************
Generalised Gaussian Process
****************************
Introduction
^^^^^^^^^^^^
A GP is a statistical distribution :math:`Y_t`, :math:`t\in\mathrm T`, for
which any finite linear combination of samples has a joint Gaussian
distribution `[1]`_ `[2]`_.
An instance of such class of ... | limix/glimix-core | glimix_core/ggp/__init__.py | Python | mit | 1,188 | [
"Gaussian"
] | 4d57fe8cb810937a287602611371e22e8672ce7559789e96ab6bc23439cfb96a |
class System(object):
def __init__(self):
self.molecules = tuple([])
self.atomtypes = []
self.bondtypes = []
self.angletypes= []
self.dihedraltypes = []
self.impropertypes = []
self.cmaptypes = []
self.interactiontypes = []
self... | resal81/PyTopol | pytopol/parsers/blocks.py | Python | gpl-3.0 | 11,684 | [
"CHARMM",
"Gromacs"
] | 68edeed7a27f4b1649297b617d5e1057569b55190531b3019776fdceef329f00 |
"""Each ElkM1 area will be created as a separate alarm_control_panel."""
from elkm1_lib.const import AlarmState, ArmedStatus, ArmLevel, ArmUpState
import voluptuous as vol
from homeassistant.components.alarm_control_panel import (
FORMAT_NUMBER,
AlarmControlPanel,
)
from homeassistant.components.alarm_control_... | leppa/home-assistant | homeassistant/components/elkm1/alarm_control_panel.py | Python | apache-2.0 | 8,138 | [
"Elk"
] | 05b6fc26a14c1ffd17fbf241f47eea29460745566bf499c505aeb504cd3d5c23 |
###AltAnalyze
#Copyright 2005-2008 J. David Gladstone Institutes, San Francisco California
#Author Nathan Salomonis - nsalomonis@gmail.com
#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 with... | wuxue/altanalyze | AltAnalyze.py | Python | apache-2.0 | 493,280 | [
"Cytoscape",
"pysam"
] | 4a0767cbe64ef7020088768d5b6f1d234d93a57240f5a709f279bf1d2dbdfeda |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | checkAlerts.py | Python | gpl-3.0 | 16,340 | [
"Galaxy"
] | d3c1ba0166eeda10e4a760f469ab6683f71691fbea5e34150d7e0980878bf4cb |
#!/usr/bin/env python
# AUTHOR: Shane Gordon
# CREATED: 2015-06-16 21:46:32
import mdtraj as md
import numpy as np
def compute_rg(fname, topname, step=1):
rg = []
for chunk in md.iterload(fname, top=topname, stride=step):
rg.append(md.compute_rg(chunk))
rg = np.concatenate(rg)
retu... | s-gordon/MD-TAT | mdtat/analysis/rg.py | Python | mit | 326 | [
"MDTraj"
] | 504b4c7f5a3279585c96b9788f9f0d5a6a6b3dc6402108f7d3219dd496abc003 |
#!/usr/bin/python
# (C) 2013, Markus Wildi, markus.wildi@bluewin.ch
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
#
# Thi... | RTS2/rts2 | scripts/rts2saf/rts2saf/data.py | Python | lgpl-3.0 | 15,375 | [
"Gaussian",
"VisIt"
] | db4f5f15dff545fa812807c6e021186f89231b33bcc3da40dbb84191ed937507 |
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
"""
This example demostrates how to get host information from a request object.
To test the script, rename the file to report.rpy, and move it to any directory,
let's say /var/www/html/.
Now, start your Twist web server:
$ twistd -n web --pat... | tzewangdorje/SIPserv | Twisted-13.1.0/doc/web/examples/report.rpy.py | Python | gpl-3.0 | 1,191 | [
"VisIt"
] | 28bb925b185609380be2848e9c3e273a39b4008f3948e036e6181782407bd9f3 |
"""
SDSS Images
-----------
This script plots an example quasar, star, and galaxy image for use in
the tutorial.
"""
import os
import urllib2
import pylab as pl
from matplotlib import image
def _fetch(outfile, RA, DEC, scale=0.2, width=400, height=400):
"""Fetch the image at the given RA, DEC from the SDSS serve... | astroML/sklearn_tutorial | examples/plot_sdss_images.py | Python | bsd-3-clause | 2,206 | [
"Galaxy"
] | 63a1d367b4b60eca23812ce17108bbda6302909c44c55403fc860312af685ac4 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/admin/menu.py | Python | gpl-2.0 | 2,452 | [
"VisIt"
] | 3eaa624eecf58f84390f99d1e55f56108c87f34f096ce006612c5c834706d38c |
# #############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Matthew Harrigan
# Contributors: Robert T. McGibbon
#
# MDTraj is fre... | hainm/mdtraj | mdtraj/core/selection.py | Python | lgpl-2.1 | 14,061 | [
"MDTraj",
"VisIt"
] | 949aaf2eebc115ca0de3492f752b2400275ec109cffafc6c54b9168995371c3d |
# Author: Ahmed Hani
# Package: https://github.com/AhmedHani/Neural-Networks-for-ML/tree/master/Implementations
#
# The package is implemented according to the lectures of Toronto University's Neural Networks for Machine Learning ..
# taught by Geoffrey Hinton.
#
# Course link: https://www.coursera.org/learn/neural-net... | AhmedHani/Neural-Networks-for-ML | Implementations/online_linear_regression.py | Python | gpl-3.0 | 2,503 | [
"Gaussian"
] | 51b75b0031af6c5205da005b7545b84e2e0c21c2ade211023b26acbeda9daf2f |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | evanet/tgm_layer.py | Python | apache-2.0 | 7,365 | [
"Gaussian"
] | e7a296051d8f9b427fa1577f038f4add92ce50d644e8561e94574ad6ba016e18 |
'''
Author: Dr. John T. Hwang <hwangjt@umich.edu>
This package is distributed under New BSD license.
'''
from __future__ import print_function, division
import numpy as np
import unittest
from six.moves import range
from smt.problems import CantileverBeam, Sphere, ReducedProblem, RobotArm, Rosenbrock, Branin
from s... | hwangjt/SMT | smt/tests/test_problems.py | Python | bsd-3-clause | 5,293 | [
"Gaussian"
] | 948793fc039d35cf9d3ead1a442a6479b6dfc7afbc44d83a583e1d114cb5bbf0 |
#!/usr/bin/env python
# Copyright 2016 Stanford University
#
# 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 applicabl... | chuckatkins/legion | language/test.py | Python | apache-2.0 | 13,891 | [
"VisIt"
] | a3517a5545598f94256e149f77a5a8115c5f3a92494fb951b9269072aba07ae4 |
#!/usr/bin/env python
#
# draw_gd_all_core.py
#
# (c) The James Hutton Institute 2013
# Author: Leighton Pritchard
#
# Contact:
# leighton.pritchard@hutton.ac.uk
#
# Leighton Pritchard,
# Information and Computing Sciences,
# James Hutton Institute,
# Errol Road,
# Invergowrie,
# Dundee,
# DD6 9LH,
# Scotland,
# UK
#
#... | widdowquinn/scripts | bioinformatics/draw_gd_all_core.py | Python | mit | 9,049 | [
"Biopython"
] | 2870fad33b33a6d6cab1108f8ef6bda15e960b576ea889c485c541eb5ee2f77a |
import numpy as np #from numpy import mgrid, empty, sin, pi
import vtk
import pandas as pd
from scipy import special
def simple_grid():
# Generate some points.
x, y, z = np.mgrid[1:6:11j, 0:4:13j, 0:3:6j]
base = x[..., 0] + y[..., 0]
# Some interesting z values.
for i in range(z.shape[2]):
z[..., i] =... | kayarre/Tools | vtk/test_points.py | Python | bsd-2-clause | 19,971 | [
"VTK"
] | 6362b73612ddb74a469057a04c1efaa70803f8dafb872750a0e03ab82a902e5c |
import scrapelib
import datetime
import os
import re
from collections import defaultdict
from pupa.scrape import Scraper, Bill, VoteEvent
from pupa.utils.generic import convert_pdf
import lxml.html
def action_type(action):
"""
Used to standardise the bill actions to the terms specified
@ https://opencivi... | cliftonmcintosh/openstates | openstates/sc/bills.py | Python | gpl-3.0 | 16,332 | [
"VisIt"
] | 463e9564b91e618ee3d7f19079959e0173709c21405ab3428821bca7169f390d |
#Author: Miguel Molero <miguel.molero@gmail.com>
from PyQt5.QtCore import *
from PyQt5.QtGui import *
from PyQt5.QtWidgets import *
from pcloudpy.gui.graphics.QVTKWidget import QVTKWidget
class QVTKMainWindow(QMainWindow):
def __init__(self, parent = None):
super(QVTKMainWindow, self).__init__(parent)
... | mmolero/pcloudpy | pcloudpy/gui/graphics/QVTKWindow.py | Python | bsd-3-clause | 998 | [
"VTK"
] | 46833b82c471edffb25360740fa5cdad55dafe35d43af7df5a4f46fb8ace9624 |
# Copyright (c) 2010 Howard Hughes Medical Institute.
# All rights reserved.
# Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
# http://license.janelia.org/license/jfrc_copyright_1_1.html
import neuroptikon
import osgUtil
import os
from neuro_object import NeuroObject
class A... | JaneliaSciComp/Neuroptikon | Source/network/arborization.py | Python | bsd-3-clause | 5,522 | [
"NEURON"
] | 7da27f94f360f1f0b7325469030c57026222a861f1656ed8277b71b76f3f57ca |
""" A script for setting each Visit org from its parent Patient.
This is a manage.py command. Run with --help for documentation.
Example usage:
To run on localhost:
> manage.py setvisitorg
To run on production:
> manage.py setvisitorg --remote
NOTE: This should be no longer needed once the first initialization is... | avastjohn/maventy_new | healthdb/management/commands/setvisitorg.py | Python | bsd-3-clause | 3,015 | [
"VisIt"
] | 7dc43e09ad0ae5781acc1d2cfe0b09fa3e328092e5d7d2ab897eea670d86a9eb |
import argparse
from collections import defaultdict
import pysam
def Parser():
the_parser = argparse.ArgumentParser()
the_parser.add_argument(
'--input', action="store", type=str, help="bam alignment file")
the_parser.add_argument(
'--minquery', type=int,
help="Minimum readsize of... | drosofff/tools-artbio | tools/small_rna_signatures/overlapping_reads.py | Python | mit | 6,930 | [
"pysam"
] | 3eb471313209476d4fde2929179b0eaa024b246efe898fad8e12c9e8c987bfed |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | fedepad/espressopp | src/integrator/Isokinetic.py | Python | gpl-3.0 | 1,738 | [
"ESPResSo"
] | 686be5e5b0b0a075e20430ba9787c6c1374867e8fd8e57d610806901aa4461eb |
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