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#
# Lecture 4 - Visualizing Representations
#
# Deep Convolutional Networks
# Deep Dreaming
#
#
# Introduction
#
# So far, we've seen that a deep convolutional network can get very
# high accuracy in classifying the MNIST dataset, a dataset of
# handwritten digits numbered 0 - 9. What happens when the number
# of ... | dariox2/CADL | session-4/l4b01-deepdreaming.py | Python | apache-2.0 | 35,882 | [
"Gaussian",
"NEURON"
] | 84d70c8709b3bce2d52678ccc3c66786aa2b932cd1827d0d2af69a5623db7bd2 |
from __future__ import print_function, division, absolute_import
# Non-std. lib imports
from PySide.QtCore import Signal, QObject
from PySide.QtGui import QTabWidget, QVBoxLayout, QWidget, QLineEdit, \
QDoubleValidator, QLabel, QGridLayout
from numpy import asarray, nan
# Local imports
from ra... | jensengrouppsu/rapid | rapid/gui/peak.py | Python | mit | 10,319 | [
"Gaussian"
] | b177269b220c3ab14646629995f8628f5fe73b96475a250e95005656e6218f25 |
import h5py
import os
import ipdb
import re
import numpy as npexit
from pylayers.antprop.channel import *
from pylayers.util.project import *
import pylayers.util.pyutil as pyu
import ConfigParser
import numpy.linalg as la
from numpy.linalg import svd
from numpy.fft import *
import time
"""
Module to handle scanner d... | buguen/pylayers | pylayers/measures/exploith5.py | Python | lgpl-3.0 | 38,175 | [
"BLAST",
"Gaussian"
] | cb650c760216e57388c9d5e0a6c0c5d72dd5cb6a0f31b9167a14b824087e50d4 |
import copy
from regraph import Rule, NXGraph
from regraph.utils import (valid_attributes,
normalize_attrs)
from regraph.category_utils import identity
from regraph.primitives import *
class TestPrimitives(object):
def __init__(self):
self.graph = NXGraph()
add_node(se... | Kappa-Dev/ReGraph | tests/test_primitives.py | Python | mit | 8,072 | [
"CDK"
] | 1b4a7ee5c5a13ea057aa6ad1839917ac14dc41f12f3302ae7c4eec820aa79947 |
import random
# Liste des objets. Il est possible d'en rajouter en suivant le modele. ATTENTION: Le rapport rate (probabilite) / Modifier (modificateur) influe enormement sur la jouabilite.
items = (
{"name" : "une Fee" , "rate" : 4 , "type" : 0 , "Modifier" : 6 , "liste" : "une Fee-------------+6 "},
{"name" : "un ... | ValentinPearce/The-Shades | Items.py | Python | agpl-3.0 | 2,609 | [
"FLEUR"
] | 8f34715243171b331f1788413da53fb4ca6d5a91e7e2f3993489e3bca9e95f37 |
import COPASI
import sys
dm = COPASI.CRootContainer.addDatamodel()
assert (isinstance(dm, COPASI.CDataModel))
def remove_reaction_by_name(model, reaction_name):
# type: (COPASI.CModel, str) -> None
key = None
for reaction in model.getReactions():
if reaction.getObjectName() == reaction_name:
... | jonasfoe/COPASI | copasi/bindings/python/examples/remove_reaction.py | Python | artistic-2.0 | 1,042 | [
"COPASI"
] | fc97f5ae2fbde7f58789e3691778722cbe5375dec808f76650f9db43e1a6922a |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | src/python/espressomd/io/mpiio.py | Python | gpl-3.0 | 3,838 | [
"ESPResSo"
] | fa9127057e55d1e9133665e5ee302302db783dccb40b3896511935c90381cf71 |
import math
import pandas
from rdkit.Chem import PandasTools, Descriptors, MolFromSmiles
from sqlalchemy.orm import sessionmaker
import compound_db_utils.database as db
from compound_db_utils import settings
def _gather_columns(table, col_list):
columns = []
for col in col_list:
columns.append(getatt... | martin-sicho/MI_ADM | compound_db_utils/data_loaders.py | Python | gpl-3.0 | 2,695 | [
"RDKit"
] | 5f3d21d182c3a73522870cc0a99836e55ee8a87280a3231907127fd63edcc398 |
import numpy as np
import sklearn.naive_bayes
from HPOlibConfigSpace.configuration_space import ConfigurationSpace
from ParamSklearn.components.base import ParamSklearnClassificationAlgorithm
from ParamSklearn.constants import *
class GaussianNB(ParamSklearnClassificationAlgorithm):
def __init__(self, random_s... | automl/paramsklearn | ParamSklearn/components/classification/gaussian_nb.py | Python | bsd-3-clause | 2,818 | [
"Gaussian"
] | a6cba89a718148871d75c5f4ecb8b91d7502448692ef11630a7acdf8516ec6ed |
"""
This module implements the G0W0 approximation on top of `pyscf.tdscf.rhf_slow` TDHF implementation. Unlike `gw.py`, all
integrals are stored in memory. Several variants of GW are available:
* `pyscf.gw_slow`: the molecular implementation;
* (this module) `pyscf.pbc.gw.gw_slow`: single-kpoint PBC (periodic bounda... | gkc1000/pyscf | pyscf/pbc/gw/gw_slow.py | Python | apache-2.0 | 991 | [
"PySCF"
] | c8003293de1914a568bb52ecb0b725ae761bd406e80d4f15f7c386539657e9ce |
"""Version module.
This module simply stores the version and svn revision numbers, as well
as a changelog. The svn revision number will be updated automatically
whenever there is a change to this file. However, if no change is made
to this file, the revision number will get out of sync. Therefore, one
must update this... | jjdmol/LOFAR | CEP/PyBDSM/src/python/_version.py | Python | gpl-3.0 | 26,368 | [
"Gaussian"
] | 6401fe12b9e1ad8d5dd4cb7503cebb6691be0bbc13c73ad32799d728bef540ea |
import ast
from ctree.visitors import NodeVisitor
from ctree.util import enumerate_flatten
def label_for_py_ast_nodes(self):
from ctree.py.dotgen import PyDotLabeller
return PyDotLabeller().visit(self)
def to_dot_outer_for_py_ast_nodes(self):
return "digraph mytree {\n%s}" % self._to_dot()
def to_dot_... | ucb-sejits/ctree | ctree/dotgen.py | Python | bsd-2-clause | 2,158 | [
"VisIt"
] | f3ebdcb594b569a5b3bfb27293a6d151f74ad75b8d41c62f9fd2900e9e862dc7 |
# merge all arraylists to one arraylist in order to remove time info.
# input: x_t is array along time (t1, t2, ...)
# [[x1(t0), x2(t0), x3(t0), ...], [x1(t1), x2(t1), x3(t1)], ...]
# output: [x1(t0), x2(t0), x3(t0), ..., x1(t1), x2(t1), x3(t1), ...]
# Example: number_1d = merge_t_to_1d(number_t_1d)
def merge_t_... | jht0664/Utility_python_gromacs | python/hjung/array.py | Python | mit | 3,540 | [
"Gromacs",
"MDAnalysis",
"OpenMM"
] | 52c7c07b6c51f1b80c27f4b7d51b4c80b176a2c1a2d29748c05482cc229fe442 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2013, Jeroen Hoekx <jeroen.hoekx@dsquare.be>, Alexander Bulimov <lazywolf0@gmail.com>
# 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__ =... | jcpowermac/ansible | lib/ansible/modules/system/lvol.py | Python | gpl-3.0 | 19,488 | [
"Firefly"
] | d50e052735bcfd28c596553aed899ab52ca4fa8a7727cad1c3c845600785b0c6 |
# -*- coding: utf-8 -*-
"""Dependency graph implementation."""
from __future__ import absolute_import, print_function, unicode_literals
from collections import Counter
from textwrap import dedent
from kombu.utils.encoding import safe_str, bytes_to_str
from celery.five import items, python_2_unicode_compatible
__all__ ... | ammarkhann/FinalSeniorCode | lib/python2.7/site-packages/celery/utils/graph.py | Python | mit | 9,246 | [
"VisIt"
] | 4064ee60e3bf1cdf248e505ad3530074e758fb17d001049c0f50218460361770 |
#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2013, The Deblur Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# --------------------------... | ekopylova/deblur | setup.py | Python | bsd-3-clause | 2,123 | [
"scikit-bio"
] | fc07daae284497bbb8f4d40359fc3f325b2ea30041de38992a0ea553509c9016 |
from __future__ import division
from scipy import random, exp, log, sqrt, argmax, array, stats
TINY = 1e-6
class BaseBandit(object):
"""
Baseclass for Bandit Algorithms. This is intended to be inherited by other Bandits to provide core functions.
The BaseBandit takes care of basic initialization, and up... | beegieb/MultiArmedBandits | algorithms.py | Python | mit | 21,530 | [
"Gaussian"
] | 7caf4ff4f7cb463327f2ce65f4932a44f7e4298bcb48150c6b9eec7b7ade4b7f |
#!/usr/bin/python
# (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# most of it copied from AWX's scan_packages module
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': ... | ilpianista/ansible | lib/ansible/modules/packaging/os/package_facts.py | Python | gpl-3.0 | 14,498 | [
"Brian"
] | 1e7860bde55814a0e4567b2ea9e7ccfba025a59c961f9991f14f0e38d54276f3 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | src/commoncode/fetch.py | Python | apache-2.0 | 3,229 | [
"VisIt"
] | 5d8e97891cb17254edda6417deacd187a394e3e59fcfa05f7b8351d64da996af |
#
# Copyright (C) 2007, Mark Lee
#
#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 required... | steckdenis/rlglue-py3 | rlglue/agent/AgentLoaderScript.py | Python | apache-2.0 | 1,641 | [
"Brian"
] | 264159dd0565ae75e50d6ee55afcda02aee64960876211574b2ff667ab36f69a |
#!/usr/bin/env python3
#
# Got Your Back
#
# 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... | crishoj/got-your-back | gyb.py | Python | apache-2.0 | 57,546 | [
"VisIt"
] | 21b622300b6a00dfca554de072e6357057250a27eff60331a084b6d4f4fffa8d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
####################################
#This code is the outcome of the project Innovative Processing of TMT Proteomics. This is a common project of InSyBio LTD and Nestle Institute of Health Sciences.
#This program implements the step 2 code
###############################... | InSyBio/QtI-Tool | step3.py | Python | gpl-3.0 | 65,478 | [
"Gaussian"
] | e9dbf4e2f338df521f4d00980ddaa0b4fc27ce19dcd7ec1e573ea5f59c515e80 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/core/ui/mediadockmanager.py | Python | gpl-2.0 | 4,280 | [
"Brian"
] | 49d22a00703ed89c6b897b821fa54f283d3af786eb4724ef7ad9427ef229230a |
#
# Copyright (C) 2014 Seiji Matsuoka
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from rdkit.Chem.Draw.canvasbase import CanvasBase
try:
f... | bp-kelley/rdkit | rdkit/Chem/Draw/qtCanvas.py | Python | bsd-3-clause | 3,636 | [
"RDKit"
] | 9d8acdc7e8169d2a3c3e5e9471727b6cd83784bd5f2e560e93807b8ac87b2302 |
import __main__
import sys, time, os
import pymol
pymol.finish_launching()
if not os.path.exists(OutDir):
os.mkdir(OutDir)
GetFilename=lambda i,j: PDBDir+"State%d-%d.pdb"%(i,j)
GetName=lambda i,j: "State%d-%d"%(i,j)
time.sleep(.1)
pymol.cmd.load(NativeFilename, "native")
pymol.cmd.util.chainbow("native")
for i... | msmbuilder/msmbuilder-legacy | Extras/TPTdiagrams/KyleGeneratePNG.py | Python | gpl-2.0 | 1,059 | [
"PyMOL"
] | 56ad48892fd5147f40bcf71671258d8345c1ddad8a463474abe040df07d5c380 |
import cvlib
angle = 0
angles = []
center = []
NumImgs = 24
angleAdj = 15
for i in range(NumImgs): #24
img = cvlib.load("findloop_%d.jpg" % angle)
angles.append(angle)
rng = cvlib.inRangeThresh(img, (20,30,20), (200,130,120))
rng = cvlib.bitNot(rng)
cnt = cvlib.findContours(rng, thresh=250)
if... | nextBillyonair/compVision | AMX/Crystal/jeanImg/cystalCent.py | Python | mit | 1,278 | [
"CRYSTAL"
] | ea0368f8959c5d4138baba066960af4d5f0d8986eaebe625117936881845fa3b |
# Draws the probes from the control Dict
# To be run using "Tools -> Python Shell -> Run Script" inside of paraFoam
# assumes that one OpenFOAM-case is opened
from PyFoam.RunDictionary.ParsedParameterFile import ParsedParameterFile
from PyFoam.Basics.DataStructures import DictProxy
from PyFoam.Paraview import case... | mortbauer/openfoam-extend-Breeder-other-scripting-PyFoam | examples/paraview3/probeAndSetDisplay.py | Python | gpl-2.0 | 2,352 | [
"ParaView"
] | b0255ad3099de386382c08cb13d4f34be15cf97202cb1a76847670b65833e726 |
import wx
class MenuToolBarSetup():
def GetIDs(self):
# Create wx IDs for each menu item
self.plugIds = {}
self.menu_OPTIONS = wx.NewId() # File menu items
self.menu_TOOL = wx.NewId() # ALIGN command
self.menu_DNA = wx.NewId() # Alphab... | fxb22/BioGUI | Utils/MenuToolBarSetup.py | Python | gpl-2.0 | 6,528 | [
"BLAST"
] | 3659c70f26c1f784b25add7d221d5e26cbbd9070cd0b64e9b9c48558e2a81840 |
#!/usr/bin/env python3
###############################################################################
# $Id: gdal_merge.py 124baa7f71f15396a661014a81b6c5b0c82c8004 2020-10-14 17:29:39 +0300 Idan Miara $
#
# Project: InSAR Peppers
# Purpose: Module to extract data from many rasters into one output.
# Author: Frank ... | grueni75/GeoDiscoverer | Source/Platform/Target/Android/core/src/main/jni/gdal-3.2.1/swig/python/osgeo/utils/gdal_merge.py | Python | gpl-3.0 | 19,756 | [
"NetCDF"
] | c0ceae5d07d1f328c2b6934eda6a50bb1c0b261906a660ab7e69dabd7dbb9f3f |
# mako/_ast_util.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
"""
ast
~~~
The `ast` module helps Python applications to process trees of the Pyth... | znoland3/zachdemo | venvdir/lib/python3.4/site-packages/mako/_ast_util.py | Python | mit | 25,690 | [
"VisIt"
] | 511b8a536e6507aa109ddc4936e68b1b5b6671d091895af0d9a3541641446878 |
#!/usr/bin/env python
# (C) Copyright IBM Corporation 2004, 2005
# (C) Copyright Apple Inc. 2011
# All Rights Reserved.
#
# 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,... | ayoubg/gem5-graphics | Mesa-7.11.2_GPGPU-Sim/src/mapi/glapi/gen/gl_gentable.py | Python | bsd-3-clause | 4,331 | [
"Brian"
] | 07bd3e0e41b70ec26c668a9c63c03d9344e2a88256a81fdea48a110ddc644aac |
# $HeadURL$
__RCSID__ = "$Id$"
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseAccountingType
class WMSHistory( BaseAccountingType ):
def __init__( self ):
BaseAccountingType.__init__( self )
self.definitionKeyFields = [ ( 'Status', "VARCHAR(128)" ),
... | arrabito/DIRAC | AccountingSystem/Client/Types/WMSHistory.py | Python | gpl-3.0 | 1,456 | [
"DIRAC"
] | 985863ec5b49bb0da9809cce426e693eb77c5a237ccc58c6d94ca48418bced82 |
#!/usr/bin/env python
"""
Framework to start a simulated vehicle and connect it to MAVProxy.
Peter Barker, April 2016
based on sim_vehicle.sh by Andrew Tridgell, October 2011
"""
from __future__ import print_function
import atexit
import getpass
import optparse
import os
import os.path
import re
import signal
import... | bnsgeyer/Copter3_4 | Tools/autotest/sim_vehicle.py | Python | gpl-3.0 | 32,299 | [
"Firefly"
] | 6c703f35165dbb6cf1df742c6670deffc610efd25c35f866f0318be08e51cd25 |
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
# Copyright (C) 2012 Olaf Lenz
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the L... | KonradBreitsprecher/espresso | src/featuredefs.py | Python | gpl-3.0 | 6,633 | [
"ESPResSo"
] | fdff8882d9f1c10b5f19a87552c63d7c31d3c2eaec79b11be9ec31c47234704a |
from __future__ import absolute_import
import base64
import re
import os
import sys
import urllib
PY3 = sys.version_info[0] == 3
if PY3:
from io import StringIO
basestring = str
else:
from StringIO import StringIO
try:
import json
except ImportError:
import simplejson as json
from .rest import ... | fniephaus/alfred-dropbox | src/dropbox/client.py | Python | mit | 67,628 | [
"VisIt"
] | 39c24e057c588f4ce66cb3adbc367b21940d8ae1536560433031be97864d7c04 |
#!/usr/bin/env python2
"""Report queries with no match from blast.
Author:
l.p.pryszcz+git@gmail.com
Dublin, 17/07/2012
"""
import os, sys
from optparse import OptionParser
from datetime import datetime
from genome_annotation import get_contig2size, genome2dict, parse_blast, _get_formatted_seq
from Bio import S... | lpryszcz/bin | blast2nohit.py | Python | gpl-3.0 | 4,146 | [
"BLAST"
] | 8df30f9b571187e15a22100d203c4167f264600c14e35385d70a9349fc301834 |
# Copyright 2017 Xavier Snelgrove
import numpy as np
import os
import keras
from keras.layers import Lambda
from keras.models import Model
from keras.applications import vgg19
from keras.preprocessing.image import load_img, img_to_array
import keras.backend as K
from scipy.ndimage import interpolation
from scipy im... | wxs/subjective-functions | gram.py | Python | mit | 31,185 | [
"Gaussian"
] | 71284554f2400a5ed1b24b060c77e55de99f3c74a55902e0bdbc8bbea83021e2 |
"""
baserawio
======
Classes
-------
BaseRawIO
abstract class which should be overridden to write a RawIO.
RawIO is a low level API in neo that provides fast access to the raw data.
When possible, all IOs should/implement this level following these guidelines:
* internal use of memmap (or hdf5)
* fast reading o... | samuelgarcia/python-neo | neo/rawio/baserawio.py | Python | bsd-3-clause | 35,812 | [
"NEURON"
] | 0ae4a52f96b4a4710e42350b94773eb499f20739aeb080a69876bb76a49cfabe |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2015 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | eustislab/horton | horton/io/molden.py | Python | gpl-3.0 | 22,361 | [
"Gaussian",
"ORCA",
"Psi4"
] | 44415089cc261a754fcedf0c642d87352fb4c9b4bf8cad258cffe7fa22091e37 |
#
# 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 requ... | evenmarbles/rlglued | tests/test_message_environment.py | Python | bsd-3-clause | 1,665 | [
"Brian"
] | 9d67c2c032d43c798e03b11a178ce1fda29394c9a0f5d8a058dc0c67d735bd64 |
# modified mexican hat wavelet test.py
# spectral analysis for RADAR and WRF patterns
import os, shutil
import time
import pickle
import numpy as np
from scipy import signal, ndimage
import matplotlib.pyplot as plt
from armor import defaultParameters as dp
from armor import pattern
from armor import objects4 as ob
... | yaukwankiu/armor | tests/modifiedMexicanHatTest4.py | Python | cc0-1.0 | 4,109 | [
"Gaussian"
] | c1fe45b417cddf2befd4f09a3d7ea24892ef4ebfcd66259c211eaa3a65f0d5c1 |
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but... | coolsvap/sos | sos/plugins/sapnw.py | Python | gpl-2.0 | 5,803 | [
"ASE"
] | 486a010204840e0a46ad22f4ff0dea6a75903ddb4f3b823e1af683557f25e9d3 |
# Author: Travis Oliphant, 2002
#
# Further updates and enhancements by many SciPy developers.
#
from __future__ import division, print_function, absolute_import
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, sum, around, unique, asarray,
... | ortylp/scipy | scipy/stats/morestats.py | Python | bsd-3-clause | 87,710 | [
"Gaussian"
] | 9132a0f6a1d63063649adcb7bd40cd91019d0199ede934c4c6fa73c586aceaea |
#!/usr/bin/env python3
# nsndswap/__main__.py
# copyright 2017 ViKomprenas, 2-clause BSD license (LICENSE.md)
import sys
import requests
import nsndswap.util
import nsndswap.makin_nsnd
import nsndswap.cookie_nsnd
import nsndswap.viko_nsnd
import nsndswap.web
def main():
makin_nsnd = get_nsnd_page('https://homest... | ViKomprenas/nsndswap | nsndswap/__main__.py | Python | bsd-2-clause | 18,852 | [
"CASINO"
] | ab6944454851132119e84d1ec35bbf30b500d31fe4a7b358d754763176645f9f |
# coding: utf-8
from __future__ import unicode_literals
import unittest
import json
import os
from monty.json import MontyDecoder
from pymatgen.analysis.defects.dilute_solution_model import *
try:
import sympy
except ImportError:
sympy = None
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", ... | Dioptas/pymatgen | pymatgen/analysis/defects/tests/test_dilute_solution_model.py | Python | mit | 4,308 | [
"pymatgen"
] | 1b5ecdc5a7b6f84b6c780171c431ae2c18c758a3bbf07a39042a42e4f1ed289e |
import numpy as np
import matplotlib.pyplot as plt
from scipy import stats
import speclines
import ebossspec, ebossanalysis
data = ebossanalysis.unify_emissionline_profile_readin()
absorption = ebossanalysis.unify_absorptionline_profile_readin()
vel = data['VEL']
yabs = 1.-(1.-absorption['UNIFIEDABSORPTION'])*1.25
ya... | guangtunbenzhu/BGT-Cosmology | Spectroscopy/emissioninfill_movie.py | Python | mit | 1,832 | [
"Gaussian"
] | 3e2208e3ab3ff9b7df6bb1ddc708da90c3a2d9f80ec07ba0afd0286306500d43 |
from property import *
# Layer Split on neuromodulation blocks
L2_ratio = ( 2, 2, 0)
L3_ratio = (16, 2, 2)
L4_ratio = (16, 16, 8)
L5_ratio = ( 8, 0, 0)
L6_ratio = (12, 0, 0)
# Neuron number in layer
L2_NN = sum(L2_ratio)
L3_NN = sum(L3_ratio)
L4_NN = sum(L4_ratio)
L5_NN = sum(L5_ratio)
L6_NN = sum(L6_ratio)
# ... | research-team/robot-dream | direct_translation/scripts/step_1 (columns)/data.py | Python | mit | 1,476 | [
"NEURON"
] | 1c32bf9036bb30bc15165866c60aac53f446b428f91f90a9cbab0b8e92b47515 |
"""
class Visualizer(MorphologyViewer):
def __init__(parent = None, callback = None):
self.callback = callback
self.morphology = moogli.Morphology("morph", 1)
desktop = QtGui.QApplication.desktop()
self.visualizer = MorphologyEditor( self.morphology
... | dilawar/moogli | moogli/main.py | Python | gpl-2.0 | 4,881 | [
"MOOSE"
] | 18dc20f6042634379ee31d1d89bfcb607111b37c84f58845cad89d9edb9b81e4 |
import netCDF4 as nc
import ctypes as ct
import numpy as np
import os
import sys
import math
from mpi4py import MPI
import time
remap = ct.cdll.LoadLibrary(os.path.realpath('libmapper.so'))
def from_mpas(filename):
# construct vortex bounds from Mpas grid structure
f = nc.Dataset(filename)
# in this case it is mu... | aymeric-spiga/remap | py/archive/remap_orig.py | Python | gpl-2.0 | 12,695 | [
"NetCDF"
] | 89545239798fb8e56a9612f4ef88e8fce0b7be1842341fddd68b7032f5379b99 |
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2014-2016 Florian Bruhin (The Compiler) <mail@qutebrowser.org>
#
# This file is part of qutebrowser.
#
# qutebrowser 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 S... | bcb/qutebrowser | scripts/dev/pylint_checkers/settrace.py | Python | gpl-3.0 | 1,643 | [
"VisIt"
] | e8ca2b7c675abcdb79c7032937a5f233a64594186e4a0d6a32c59374d38bdd6d |
import json
import math
import os
import re
import time
import warnings
import numpy as np
from collections import namedtuple
from director import objectmodel as om
from director import applogic as app
from director import lcmUtils
from director import transformUtils
from director.debugVis import DebugData
from direct... | patmarion/director | src/python/director/treeviewer.py | Python | bsd-3-clause | 23,357 | [
"VTK"
] | 827182e721d91e03f2554fd09a82a30e897e68ac80c5dd0e577b9de7d7cf1ba8 |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
from scipy._lib.six import string_types, exec_, PY3
from scipy._lib._util import getargspec_no_self as _getargspec
import sys
import keyword
import r... | pyramania/scipy | scipy/stats/_distn_infrastructure.py | Python | bsd-3-clause | 119,483 | [
"Gaussian"
] | 1a45385d70b9e574dc9d04d3fd219e11813973944f709a762435ce90bf0bbdaa |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py | Python | gpl-2.0 | 1,251 | [
"MDAnalysis"
] | 240c48e5b7b8f9512f94e5f320b121234c1a6e90469b9145737f003147fb10e4 |
#!/usr/bin/env python
"""
"""
import sys
import logging
import argparse
from edl.blastm8 import filterM8, add_hit_table_arguments, FilterParams
from edl.util import add_universal_arguments, setup_logging
def main():
description = """
Take a blast result table and output a subset of hits based on the
chos... | jmeppley/py-metagenomics | filter_blast_m8.py | Python | mit | 4,114 | [
"BLAST"
] | ae5b32141b41719845268fed04a6c6918f6fb843968c1da6e9fae3bbf801731c |
#! /usr/bin/env python
"""
Module with detection algorithms.
"""
from __future__ import division
from __future__ import print_function
__author__ = 'C. Gomez @ ULg'
__all__ = ['detection',
'mask_source_centers',
'peak_coordinates']
import numpy as np
from matplotlib import pyplot as plt
from s... | henry-ngo/VIP | vip_hci/phot/detection.py | Python | mit | 22,560 | [
"Gaussian"
] | 144d5fb8efb474471c6f36ac45cc53c283ea02031a70b62d1e54a092baea2e2a |
from metraj.compute.pointwise import *
from metraj.graphics.simple_plots import *
from metraj.smoothing.segment import *
from metraj.smoothing.simple import *
from metraj.trajectory import *
from metraj.shortcuts.filt import *
def repeated_median_filter(data):
ts = TrajectorySet().load_frame(data)\
.filte... | Hezi-Resheff/trajectory-aa-move-ecol | metraj/examples/simple_filters.py | Python | mit | 4,793 | [
"Gaussian"
] | e3eee02b764297279076ec924ce7aada9221b1f275b48b05e259d6024907a85a |
#!/usr/bin/env python
intro = """
Configuration flags and parameters {#config}
=============
[TOC]
\htmlonly
<p style="text-align: right">
With four parameters I can fit an elephant, and with five I can make him wiggle his trunk.<br><br>
John von Neumann
</p>
\endhtmlonly
#### Notes
- These flags and parameters are... | talbrecht/pism_pik07 | doc/browser/config_doc.py | Python | gpl-3.0 | 7,364 | [
"NetCDF"
] | c7d8daba99569dfe8e1e3917c64d0a9f3afdea40bdab194771e9af4624afaccd |
__author__ = "Rick Sherman"
import unittest2 as unittest
from nose.plugins.attrib import attr
from mock import patch
import os
import json
from jnpr.junos import Device
from jnpr.junos.factory.to_json import PyEzJSONEncoder, TableJSONEncoder, TableViewJSONEncoder
from jnpr.junos.op.routes import RouteSummaryTable
fro... | shermdog/py-junos-eznc | tests/unit/factory/test_to_json.py | Python | apache-2.0 | 3,883 | [
"Firefly"
] | aa0ee7327bcdeb7ded1e59abbe21b0357a40e32aa723b1eabc8b3d3f611398c5 |
#!/usr/bin/python2
# #
# pre-processing of raw downloaded CMIP5 data from the PCMDI portal to something that is standardized for
# use in later downscaling to ALFRESCO AK/Canada extent and resolution needs.
# # # # #
def group_input_filenames( prefix, root_dir ):
import fnmatch, functools, itertools, os, glob
imp... | ua-snap/downscale | old/old_bin/hur_ar5_model_data_preprocess.py | Python | mit | 11,345 | [
"NetCDF"
] | 5d9b10deb5baee6bfa68953a64ef395cffa9cdfb38397a7c1ba5a57f82421257 |
#!/usr/bin/env python
"""
gridded module:
This module defines the gridded.Dataset --
The core class that encapsulates the gridded data model
"""
# py2/3 compatibility
from __future__ import absolute_import, division, print_function, unicode_literals
from gridded.grids import Grid
from gridded.variable import Var... | NOAA-ORR-ERD/gridded | gridded/gridded.py | Python | unlicense | 8,402 | [
"NetCDF"
] | c21e055999646c4a5a6faa40ed6c218f944e2e3728c3e42346fcdbd7195fb5b8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2014, Phil Schwartz <schwartzmx@gmail.com>
#
# This file is part of Ansible
#
# Ansible 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 ... | schwartzmx/ansible-module-devel | windows/win_zip.py | Python | mit | 3,249 | [
"VisIt"
] | 30f89ab438ee8dea13e6132d08fc3482ae267f570d40fb8ef397e0662201de3c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Contribution 2009 by Brad Crittenden <brad [AT] bradcrittenden.net>
# Copyright (C) 2008 Benny Malengier
# Copyright (C) 2010 Jakim Friant
#
# This program is free... | sam-m888/gramps | gramps/gui/plug/export/_exportassistant.py | Python | gpl-2.0 | 24,356 | [
"Brian"
] | 54bdb46cd560b887736acc774ef919ac836bc9546b713b902510826c13c51486 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/scf/ucphf.py | Python | apache-2.0 | 5,854 | [
"PySCF"
] | b0d6da08e7eccb5288531b181bbbb47a2a03463455929ddf2205d95897ba2da7 |
import logging
import warnings
# External libs
import numpy as np
import pandas as pd
import xarray as xr
from scipy import stats
# Optional libs
try:
import salem
except ImportError:
pass
# Locals
from oggm import cfg
from oggm import utils
from oggm import entity_task
from oggm.exceptions import MassBalanc... | TimoRoth/oggm | oggm/shop/cru.py | Python | bsd-3-clause | 16,219 | [
"NetCDF"
] | d04cac5aee0bf67f414a66e5184f023ec4e3f70e2f0118153e08b1a789679182 |
# The MIT License (MIT)
# Copyright (c) 2017 Levak Borok <levak92@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 without restriction, including without limitation the
# rights t... | Levak/RoleKeeper | rolekeeper.py | Python | mit | 116,783 | [
"VisIt"
] | 79571be8dc164c3649c4c7ecf350427ce20e7738b126adfff61c22475261207e |
"""Returns tidy3d simulation from gdsfactory Component."""
import warnings
from typing import Dict, Optional
import matplotlib.pyplot as plt
import numpy as np
import tidy3d as td
import gdsfactory as gf
from gdsfactory.component import Component
from gdsfactory.components.extension import move_polar_rad_copy
from gd... | gdsfactory/gdsfactory | gdsfactory/simulation/gtidy3d/get_simulation_grating_coupler.py | Python | mit | 17,680 | [
"Gaussian"
] | 2a0d529f5605d98ab1aa699bda311c239865d3d0149bc34a7a7061712fbaeb1b |
# $HeadURL: $
''' CacheFeederAgent
This agent feeds the Cache tables with the outputs of the cache commands.
'''
from DIRAC import S_OK
from DIRAC.AccountingSystem.Client.ReportsClient import ReportsClient
from DIRAC.Core.Base.AgentModule ... | sposs/DIRAC | ResourceStatusSystem/Agent/CacheFeederAgent.py | Python | gpl-3.0 | 6,320 | [
"DIRAC"
] | 40b42a35f65152d73a76c6cdb19a4df89ef64cdbf52b5fb5068c9b8a6955b18a |
# This file is part of django-doubleoptin-contactform.
# django-doubleoptin-contactform is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your opt... | MyersGer/django-doubleoptin-contactform | doptincf/views.py | Python | gpl-3.0 | 2,783 | [
"VisIt"
] | dba4b32bc2dc0c895f9ae96c043d2ac01d464c8e3349b1a2893dcf181a6ae4a9 |
# -*- coding: utf-8 -*-
"""
=================================
Parallel Random Walks on Networks
=================================
:Author:
Moritz Emanuel Beber
:Date:
2014-02-12
:Copyright:
Copyright |c| 2014, Jacobs University Bremen gGmbH, all rights reserved.
:File:
parallel.py
.. |c| unicode:: U... | Midnighter/foggy-march | foggy/parallel.py | Python | bsd-3-clause | 23,738 | [
"VisIt"
] | 7664749a8acff84bd2cea8356cc66b0616440662b92270705ca43b703f3ad669 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module contains the definition of some objects used in the chemenv package.
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The ... | gpetretto/pymatgen | pymatgen/analysis/chemenv/utils/defs_utils.py | Python | mit | 4,295 | [
"pymatgen"
] | 6d69eded1ec9190a9ef7e27ca661ea40003151886d4d4a793af218c90b37f4fe |
#!/usr/bin/env python
"""Perspective-distorted sinusoidal grating in gaussian window"""
from VisionEgg import *
start_default_logging(); watch_exceptions()
from VisionEgg.Core import *
from VisionEgg.Gratings import *
from VisionEgg.SphereMap import *
from VisionEgg.Text import *
from VisionEgg.Textures import *
impo... | visionegg/visionegg | demo/mouse_gabor_perspective.py | Python | lgpl-2.1 | 11,119 | [
"Gaussian"
] | 2c50a47fd0e010ead600612db1445df54803f64cdfc1eac5d4c1877a57c72a12 |
# Copyright (c) 2000 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
__revision__ = "$Id: MojoMessage.py,v 1.16 2003/03/09 18:54:57 zooko Exp $"
# Python standard library modules
import re, ... | zooko/egtp_new | egtp/MojoMessage.py | Python | lgpl-2.1 | 15,794 | [
"VisIt"
] | ed70c1839d98c6317dd67132b9447ea85b45edf4542328a22e95819e922045ff |
from __future__ import print_function
import matplotlib
matplotlib.use('Agg')
import argparse
import os
import numpy as np
from molecules.model import MoleculeVAE
from molecules.utils import load_dataset
from pylab import figure, axes, scatter, title, show, savefig
from rdkit import Chem
from rdkit.Chem import Dr... | dakoner/keras-molecules | plot.py | Python | mit | 1,565 | [
"RDKit"
] | 91137a0afcb65d39cf9fc9a460bced8a8affe44ef4d1d35bf6fc841df55d9989 |
##
# Copyright 2009-2017 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | ULHPC/easybuild-easyblocks | easybuild/easyblocks/t/tinker.py | Python | gpl-2.0 | 6,438 | [
"TINKER"
] | df8c2f26562cb05899d15ca0aadd8e264cf7a710da676787432fe93e1faacead |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_poolgroup.py | Python | gpl-3.0 | 6,213 | [
"VisIt"
] | dbe05502b11152b9c6b856b15ef002de4c9b87b626f60045dfe4ca9ec69fdbe9 |
#!/bin/py
#
# Integrate exodus II file in space
#
import sys
import numpy as np
import glob
import vtk
# -----------------------------------------------#
# Perform Radial Integration #
# -----------------------------------------------#
def integrate(name, var):
""" given filename and var, gen... | nicholasmalaya/paleologos | disputatio/routines/int.py | Python | mit | 4,572 | [
"VTK"
] | 7bb5e221a65dfd0914a3a7cbb101f696594b9b19f08514f0d2213229e10c88a6 |
import subprocess
# use git branch for version
version = subprocess.Popen('git rev-parse --abbrev-ref HEAD'.split(), stdout=subprocess.PIPE).communicate()[0].rstrip()
if version[0] == 'v':
version = version[1:]
# get remote url
url = subprocess.Popen('git config --get remote.origin.url'.split(), stdout=subprocess.... | jbechtel/CASMcode | python/vasp/make_setup.py | Python | lgpl-2.1 | 672 | [
"VASP"
] | e1bde83d186243357d2fe5ed89300cb95f444851eb01d1e2fbf5aa42a10cdaf4 |
"""Provides some utilities widely used by other modules"""
import bisect
import collections
import collections.abc
import operator
import os.path
import random
import math
import functools
from itertools import chain, combinations
# _______________________________________________________________________... | pblanc5/Artificial-Intelligence- | Homework3/utils.py | Python | mit | 23,059 | [
"Gaussian"
] | bd495881503e6b3af2de204a6e486f1c365c988a6d1181dbfe58cbdfb5db752f |
# -*- coding: utf-8 -*-
#
# Bio-Formats documentation build configuration file, created by
# sphinx-quickstart on Wed Aug 29 15:42:49 2012.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
#... | mtbc/bioformats | docs/sphinx/conf.py | Python | gpl-2.0 | 10,547 | [
"CRYSTAL"
] | 8fde2565246e9b84c38aa22252ad4e8fcc2c38775e6fa6efea6f8ebbd3cc5e96 |
"""Support for control of ElkM1 outputs (relays)."""
from homeassistant.components.elkm1 import (
DOMAIN as ELK_DOMAIN, ElkEntity, create_elk_entities)
from homeassistant.components.switch import SwitchDevice
DEPENDENCIES = [ELK_DOMAIN]
async def async_setup_platform(
hass, config, async_add_entities, di... | HydrelioxGitHub/home-assistant | homeassistant/components/elkm1/switch.py | Python | apache-2.0 | 1,020 | [
"Elk"
] | 377b05f39b36ce8d9ec9d4cd8b9d88c26d7729004807853119a1c49c0a21d057 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import math
from itertools import product
from functools import reduce
class P1():
"""
Store arrays to make the crystal mapping more
effi... | andyofmelbourne/crappy_crystals | utils/symmetry_operations.py | Python | gpl-3.0 | 31,668 | [
"CRYSTAL"
] | 5287279ee7eeeb2ba7a9e834bde6bb57665d21c6a5b814ce7623b8d508253c80 |
from ...online_crowdsourcing import *
from ...util.facility_location import *
import json
import math
import pickle
import os
MIN_WIDTH = 30
COLORS = [ '#FF0000', '#00FF00', '#0000FF', '#FFFF00', '#00FFFF', '#FF00FF', '#FFFFFF', '#FFBF4A', '#000080', '#626200', '#006262', '#620062', '#44200F', '#008000' ]
NUM_COLS = ... | sbranson/online_crowdsourcing | crowdsourcing/annotation_types/bbox/bbox.py | Python | mit | 30,777 | [
"Gaussian"
] | 58146dab480cd01cf27c3ba264334ab8e014b4c70231ae24d76dd3619b346048 |
#* 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/lgpl-2.1.html
import plat... | harterj/moose | python/TestHarness/testers/Tester.py | Python | lgpl-2.1 | 34,144 | [
"MOOSE",
"VTK"
] | e810d211b09d5cc246a71ce7ecd905b05af3bb3310909802cee7038e0d87a635 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Brian Coca <brian.coca+dev@gmail.com>
# 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
DOCUMENTATION = '''
---
module: ge... | indrajitr/ansible | lib/ansible/modules/getent.py | Python | gpl-3.0 | 4,172 | [
"Brian"
] | 0742e6d7efc5199838b2072a6451a25cbecf781a58eaa05e183e8174ec7952a3 |
"""
Module to compute the Equivalent Widths (EW) of a set of lines,
for a given spectrum.
Uses regression methods to fit Gaussian-like profiles to the
absorption lines, and outputs the distribution of EWs
for every line (with a valid fit), based on the fit parameters
and uncertainties.
**Important**
The spectra has to... | msotov/SPECIES | EWComputation.py | Python | mit | 37,822 | [
"Gaussian"
] | 95b602c35c3e4e3a2cf3c2f6a287b7548b857a1880c608d006f9e62c0a5fc2df |
# Copyright (C) 2015-2022 by the RBniCS authors
#
# This file is part of RBniCS.
#
# SPDX-License-Identifier: LGPL-3.0-or-later
import glob
import os
from rbnics.utils.mpi import parallel_io
from rbnics.utils.test import PatchInstanceMethod
def snapshot_links_to_cache(offline_method):
def patched_export_solutio... | mathLab/RBniCS | rbnics/utils/decorators/snapshot_links_to_cache.py | Python | lgpl-3.0 | 4,035 | [
"ParaView"
] | f48e7e6243f3439a88d622e7373e523738cdd8391a453b87e4701bfdff3e4747 |
from Bio.Blast import NCBIXML
with open('../../samples/sampleXblast.xml') as xmlfh:
for record in NCBIXML.parse(xmlfh):
for align in record.alignments:
print(align.title)
| Serulab/Py4Bio | code/ch9/BLASTparser1.py | Python | mit | 195 | [
"BLAST"
] | 6b6d981b62f0ea1eec31d707d64de405b42374ee3ddf81b60b27cdb1c62aef11 |
# Lint as: python3
"""Crowd objects/human controllers module."""
import abc
import collections
from typing import Any, Callable, Dict, Iterable, List, Optional, Union, Sequence, Text
from absl import logging
import dataclasses
import gin
import numpy as np
#import rvo2
from pybullet_envs.minitaur.envs_v2.sensors imp... | nrz/ylikuutio | external/bullet3/examples/pybullet/gym/pybullet_envs/minitaur/robots/crowd_controller.py | Python | agpl-3.0 | 27,753 | [
"ORCA"
] | cdd2f9740c9e9af26d2c74e5b0659efc73bef89fb8b2751c9718817b0c509985 |
from __future__ import print_function
from ase.data import atomic_masses, chemical_symbols
from ase.db.core import float_to_time_string, now
from ase.utils import hill
import numpy as np
class Summary:
def __init__(self, dct, subscript=None):
self.dct = dct
self.cell = [['{0:.3f}'.forma... | suttond/MODOI | ase/db/summary.py | Python | lgpl-3.0 | 4,308 | [
"ASE"
] | 097e699366b42b914c08bbc532cd1f6faafb9f60bfe200739ccf7272c23aa82e |
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.support.ui import WebDriverWait
from selenium.webdriver.support import expected_conditions as EC
from selenium.common.exceptions import MoveTargetOutOfBoundsException
from selenium.common.exceptions import TimeoutException
from selenium.webdriver.c... | Jasonmk47/OpenWPM | automation/Commands/browser_commands.py | Python | gpl-3.0 | 9,807 | [
"VisIt"
] | 1f0b0714ec5529c5a28c8a3c9af7eb0c21fcd2d953ad7f6e62a8f52bbdbe04f6 |
r"""
This module is a ParaViewWeb server application.
The following command line illustrates how to use it::
$ pvpython -dr .../pvw-light-viz.py --data-dir /.../path-to-your-data-directory
--data
Path used to list that directory on the server and let the client choose a
... | Kitware/light-viz | server/pvw-light-viz.py | Python | bsd-3-clause | 10,193 | [
"ParaView",
"VTK"
] | a01d9a1fc465ad96a70a184aae88c73802d8c075fdb1893300c481a98fee56f9 |
#! /usr/bin/python
import os
SCRIPT_PATH = os.path.dirname(os.path.realpath(__file__))
import sys
import uuid
import shutil
import subprocess
import random
sys.path.append(SCRIPT_PATH + '')
sys.path.append(SCRIPT_PATH + '/wrappers')
import setup_realsim
import basicdefines
import wrapper_lastal
import analyze_venn_o... | isovic/realsim | src/realsim.py | Python | mit | 48,174 | [
"BWA"
] | 5bff78164c615a51965d4940e7db0d55cff9b53b64f65437a46882a6d5fdf091 |
# Copyright 1999 by Jeffrey Chang. All rights reserved.
# 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.
"""Code to work with Medline from the NCBI.
Classes:
- Record A dictionary holding... | zjuchenyuan/BioWeb | Lib/Bio/Medline/__init__.py | Python | mit | 5,346 | [
"Biopython"
] | 82e40d2f1c9ce990b4ef7116f3ac7ba271d97a8f0354541db382a20e39100288 |
# -*- coding: utf-8 -*-
#
# This file is part of the python-chess library.
# Copyright (C) 2012-2016 Niklas Fiekas <niklas.fiekas@backscattering.de>
#
# 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 Foundat... | johncheetham/jcchess | chess/pgn.py | Python | gpl-3.0 | 32,586 | [
"VisIt"
] | ff261759628599d7a1f8d685ff6a93ccc023e1473bf154406c49b60e5a6a81ec |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_csphar_talman_libnao.py | Python | apache-2.0 | 1,605 | [
"PySCF"
] | 5ffadc86145df036a294cfa319127004269ddb7c88bb0fd7bdcf1787b73b82b6 |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2017 Francois Beaune, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any ... | aytekaman/appleseed | scripts/updatetestsuiterefimages.py | Python | mit | 3,477 | [
"VisIt"
] | e88e09d289fb3a50cc55fc7e10f68807f245f85ecef0783196790b88b62a6497 |
from __future__ import with_statement
import os
from datetime import datetime
import logging
from fabric.api import *
env.user = 'bhs'
env.now = datetime.now().strftime('%Y%m%d-%H%M')
def deploy(api_server='test'):
local('npm install && bower install')
local('gulp test')
push_dist(api_server)
def push_... | Inna-r/dbs-front | fabfile.py | Python | agpl-3.0 | 682 | [
"GULP"
] | c2ea6908051ff5effcd349e90fba2cc23f5e99edb24de7b314995c5b36b34bbc |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2014, 2015 CERN.
#
# Invenio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your option) any... | zenodo/invenio | invenio/modules/multimedia/restful.py | Python | gpl-2.0 | 4,723 | [
"VisIt"
] | 00f6c1f58a4f753f682c71514d555002dac4f23e829c563cc4f4182805a329aa |
from approvaltests.core.reporter import Reporter
from approvaltests.reporters.python_native_reporter import PythonNativeReporter
class IntroductionReporter(Reporter):
def report(self, received_path: str, approved_path: str) -> bool:
print(self.get_text())
return PythonNativeReporter().report(rece... | approvals/ApprovalTests.Python | approvaltests/reporters/introduction_reporter.py | Python | apache-2.0 | 735 | [
"VisIt"
] | 8dbb9bd8600d8d79b97a942281f6e14e792908fe8ddd398058bdd12342fdc88b |
# -*- 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.
"""Run all unit tests for cclib."""
from __future__ import print_function
import unittest
import test_data
from test_b... | gaursagar/cclib | test/testall.py | Python | bsd-3-clause | 631 | [
"cclib"
] | 544f992f0b9728e48efb517ed29555006952d7b36778548574439d6b04b1a4f4 |
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