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"""test/conftest.py: dynamic testing configuration for pytest
See the pytest documentation for more details:
https://docs.pytest.org/en/latest/contents.html
"""
import logging
import sys
from test.test_data import (
all_modules,
all_parsers,
module_names,
parser_names,
)
version_major = sys.version_... | ATenderholt/cclib | test/conftest.py | Python | bsd-3-clause | 1,965 | [
"cclib"
] | d4ff438c42078c9925a80317b3b4d66cd6ee51c54b9faaf97ed2ed43bffc8b1b |
#!/usr/bin/env python
# encoding: utf-8
"""
fits2itk.py
Convert a fits file to NRRD for use in Slicer3D
Assumes that the order of axes in the FITS file
is RA, Dec, Velocity.
Example Use
-----------
import fits2itk
# convert a FITS file using the default parameters
infile = "ngc1333_co.fits"
outfile = "ngc1333_co.n... | jfoster17/pyfits2itk | fits2itk.py | Python | mit | 6,788 | [
"ParaView"
] | 3c3ccfbc3f7d66c8dd30a424492b4fed0324d896139ca41a44d8318a39aa481a |
"""
This is only meant to add docs to objects defined in C-extension modules.
The purpose is to allow easier editing of the docstrings without
requiring a re-compile.
NOTE: Many of the methods of ndarray have corresponding functions.
If you update these docstrings, please keep also the ones in
core/fromnum... | behzadnouri/numpy | numpy/add_newdocs.py | Python | bsd-3-clause | 227,238 | [
"Brian"
] | 519f1f04c6aeab27a45b52187ae407a9ec1d88246977f239937135b797a2af8f |
"""
Copyright (C) <2010> Autin L.
This file ePMV_git/patch/crystalCommands.py is part of ePMV.
ePMV 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
... | corredD/ePMV | patch/crystalCommands.py | Python | gpl-3.0 | 6,745 | [
"CRYSTAL"
] | 74033727bf59f8b86d8afdbfd1aab64f3a2e6f7349bcb9a52111eecdf8a1a1e9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""tree_cable.py: A depth 10 binary tree like cable with following properties.
Depth Number Length (microns) Diameter (microns)
==========================================================================
0 1 32.0 16.0
1 2 25.4 10.08
2 4 20.16 6.35
3 8 16.0 ... | dharmasam9/moose-core | tests/python/Rallpacks/rallpacks_tree_cable.py | Python | gpl-3.0 | 8,350 | [
"MOOSE"
] | e943f55079601b26978a683a8bf55226d4db02f419e51ccd4dfa3f42c5f002b8 |
""" Mapping the CATMAID datamodel to a graph database
Each project has its own annotation graph.
- Can I point from one graph to the vertex of another graph?
- Classes could be derived from Ontologies
http://bioportal.bioontology.org/
"""
import time
from bulbs.model import Node
from bulbs.property import Property, ... | catsop/CATMAID | scripts/graphdb/old_test_bulbs.py | Python | gpl-3.0 | 2,887 | [
"NEURON"
] | 64facdbdfe37e739c92c7480831f2261a85ff1663b53e3a57c14bc306afe7441 |
"""
This module contains 'classical' methods of calculating a pore size distribution for
pores in the micropore range (<2 nm). These are derived from the Horvath-Kawazoe models.
"""
import math
import numpy
from scipy import constants
from scipy import optimize
from pygaps.characterisation.models_hk import HK_KEYS
f... | pauliacomi/pyGAPS | src/pygaps/characterisation/psd_micro.py | Python | mit | 47,092 | [
"Avogadro"
] | 061a2a32f21252b4ea432b939570ccd6ad84d4dd1ffaeb1731d06bbc7afcfbc3 |
# 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 | bnn_hmc/core/vi.py | Python | apache-2.0 | 4,956 | [
"Gaussian"
] | 245cd2e2494ffeeb5cf1a57e93481893f73f2a0cc21674cc383f5cfb662a1e05 |
""" Class that contains client access to the job monitoring handler. """
__RCSID__ = "$Id$"
from DIRAC.Core.Base.Client import Client
class JobMonitoringClient(Client):
def __init__(self, **kwargs):
super(JobMonitoringClient, self).__init__(**kwargs)
self.setServer('WorkloadManagement/JobMonitoring')
... | andresailer/DIRAC | WorkloadManagementSystem/Client/JobMonitoringClient.py | Python | gpl-3.0 | 696 | [
"DIRAC"
] | 1567e332e130d1830862f4fc3af4a36a1266461df301de2965c4eaadf3f6d705 |
from toee import *
from utilities import *
from toee import anyone
from py00439script_daemon import *
import _include
from co8Util.TimedEvent import *
from combat_standard_routines import *
from py00439script_daemon import get_f, set_f, get_v, set_v, tpsts, record_time_stamp
def san_dialog( attachee, triggerer ):
if... | GrognardsFromHell/TemplePlus | tpdatasrc/co8fixes/scr/py00338Viscount.py | Python | mit | 8,561 | [
"Gaussian"
] | 4029d1989842ae3001fc6bcfb5d959b2f8274d926b9768f985d403299962dc4c |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | harterj/moose | python/chigger/annotations/TimeAnnotationSource.py | Python | lgpl-2.1 | 1,918 | [
"MOOSE"
] | 5c0604b68f364ae29e6955e5b1d67198421b12f1edd53670c8eefe3a3bc4ba6a |
""" This is the Proxy storage element client """
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Resources.Storage.Utilities import checkArgumentFormat
from DIRAC.Resources.Storage.StorageBase import StorageBase
from DIRAC.ConfigurationSystem.Client ... | vmendez/DIRAC | Resources/Storage/ProxyStorage.py | Python | gpl-3.0 | 7,482 | [
"DIRAC"
] | c296ab258f92e9ffd5ed8b1456b3cfe2265961733175f2ca8d4b9a7000169d11 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | volkandkaya/trading | config/urls.py | Python | bsd-3-clause | 1,229 | [
"VisIt"
] | 5c3fc65f2030a4f5b582aac1e5b41c8bcd5eab4830648e4a926211bc36a72505 |
#
# io - Data input and output
#
from info import __doc__
from numpy import deprecate_with_doc
# These are all deprecated (until the end deprecated tag)
from npfile import npfile
from data_store import save, load, create_module, create_shelf
from array_import import read_array, write_array
from pickler import objloa... | stefanv/scipy3 | scipy/io/__init__.py | Python | bsd-3-clause | 2,826 | [
"NetCDF"
] | 858a66b9b2a7a1fc27c269344077c91eb30220e9dc099e5e29712795a5233165 |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/ghNames.py | Python | gpl-3.0 | 2,565 | [
"Galaxy"
] | 785ebdbccf7869ca1a52f1e8922ce6199f10ab8d04e2c683b9c521a5d1792f69 |
# -*- coding: utf-8 -*-
'''====
EZ-Fit
====
Provides an easy to use wrapper to fit common functions to a data set using the
Levenberg–Marquardt algorithm provided by mpfit. A full description of the
supported functions and how to use the wrapper is given in easyfit.fit
------------------------------------------------... | Nablaquabla/ezfit | easyfit.py | Python | gpl-2.0 | 15,570 | [
"Gaussian"
] | febedfaf0fa714255b9f0182497ce7227ac6fe8393b7634899f07635652c640c |
""" This is the main module that interprets DIRAC cfg format
"""
from __future__ import print_function
import types
import copy
import os
import re
import zipfile
__RCSID__ = "$Id$"
try:
from DIRAC.Core.Utilities import List, ThreadSafe
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
... | petricm/DIRAC | Core/Utilities/CFG.py | Python | gpl-3.0 | 32,787 | [
"DIRAC"
] | 588ad2294e83291d4fe37bc6e25c1a3544835d00cb70e78d7847316e2b750691 |
import numpy as NP
"""
A module which implements the continuous wavelet transform
Wavelet classes:
Morlet
MorletReal
MexicanHat
Paul2 : Paul order 2
Paul4 : Paul order 4
DOG1 : 1st Derivative Of Gaussian
DOG4 : 4th Derivative Of Gaussian
Haar : Unnormalised version of continuous Haar trans... | MattNolanLab/ei-attractor | grid_cell_model/analysis/Wavelets.py | Python | gpl-3.0 | 12,300 | [
"Gaussian"
] | 99e989057ac17077580bb9b351b928174eedbd8a50a5df05d41abf7ada660845 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors: Robert McGibbon, Matthew Har... | dwhswenson/mdtraj | tests/test_topology.py | Python | lgpl-2.1 | 11,353 | [
"MDTraj",
"OpenMM"
] | a9a732cfe5cbd52a20afb272506c94c3c981b4dace83cd07d6e3c1237468e3dc |
#!/usr/bin/python
# This script predicts the grid of probabilities
from sklearn.preprocessing import RobustScaler
from sklearn.neighbors import KNeighborsClassifier
from sklearn.kernel_approximation import RBFSampler
import numpy as np
import json
import math
from sklearn.externals import joblib
from geojson import Fe... | alod83/osiris | srp/predict.py | Python | mit | 8,001 | [
"Gaussian"
] | 496710b7c4f74865f99c4335224ef9792b0c9927c6d14de7bb3e53c4dc5a4691 |
import lb_loader
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
from collections import OrderedDict
EXPERIMENTS = OrderedDict()
def load_lj(cutoff=None, dispersion_correction=False, switch_width=None, shift=False, charge=None, ewaldErrorTolerance=None):
... | kyleabeauchamp/HMCNotes | code/experiments.py | Python | gpl-2.0 | 8,143 | [
"OpenMM"
] | e753b4dbe89ed6f43597b4dbe3a052ace247f839a3c597534ce2e7ceb832c441 |
#!/usr/bin/python
"""
This peak-caller script is part of the CLAM pipeline.
It takes input from re-aligner output, and use permutation to call peaks.
Tested under python 2.7.3
"""
__author__ = 'Zijun Zhang'
__version__ = '1.0.0'
__email__ = 'zj.z@ucla.edu'
from optparse import OptionParser
import ... | Xinglab/CLAM | deprecated/CLAM.fdr_peak.MP.py | Python | gpl-3.0 | 19,701 | [
"pysam"
] | 1835b1bd8fecf11b2b0d43e8990a613d6f9a01dc1c33264a08f1378b3abeb9d4 |
# coding: utf8
import webapp2
from requestmodel import *
from google.appengine.api import mail as gae_mail
from google.appengine.api import users
from google.appengine.api.taskqueue import taskqueue
import gig
import member
import assoc
import logging
import re
import pickle
import os
import stats
import cryptoutil
... | SecondLiners/GO2 | goemail.py | Python | gpl-3.0 | 17,363 | [
"exciting"
] | f57a3b1f8700a268a67d73654069793160c18cff17a7219aeb0ac3416837a2ba |
"""Handle disambiguation of reads from a chimeric input, splitting by organism.
Given specification of mixed input samples, splits a sample into multiple
sub-samples for alignment to individual genomes, then runs third-party disambiguation
scripts to reconcile.
Uses disambiguation scripts contributed by AstraZeneca, ... | hjanime/bcbio-nextgen | bcbio/pipeline/disambiguate/__init__.py | Python | mit | 8,568 | [
"BWA"
] | a60fef29db373f538753b70cd525a4bd890c5a75109d5f58f5d3ddb8d7cd7138 |
"""edc_dashboard URL Configuration
The `urlpatterns` list routes URLs to views. For more information please see:
https://docs.djangoproject.com/en/1.10/topics/http/urls/
Examples:
Function views
1. Add an import: from my_app import views
2. Add a URL to urlpatterns: url(r'^$', views.home, name='home')
Cl... | botswana-harvard/edc-dashboard | example/urls.py | Python | gpl-2.0 | 1,427 | [
"VisIt"
] | dacb5318b57e29e1aea5fd0b01acfe4dc140d1697f6720351257b082d0ba6605 |
'''
Created on Jan 20, 2016
@author: rch
'''
from traits.api import \
Float, HasTraits, Property, cached_property, Int, \
Instance, Array, Bool
import numpy as np
from oricreate.api import MappingTask
from oricreate.api import YoshimuraCPFactory, \
fix, link, r_, s_, t_, MapToSurface,\
GuConstantLeng... | simvisage/oricreate | apps/sandbox/christoph/ex04_canopy.py | Python | gpl-3.0 | 19,829 | [
"Mayavi"
] | c4235dc53818bdb6ef48a29202594ca436c5d8a6f59da3fa3b10d7d85b4d88f4 |
'''
@author Akshay Choche
@see LICENSE (MIT style license file).
'''
import jpype
import logging
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
import warnings
import urllib2
import platform
import os,sys
'''
This scriot is responsible for calling the java code... | UGA-WSAG/wsextensions | WebServiceToolWorkflow_REST_SOAP/removestandalonetool.py | Python | mit | 1,426 | [
"Galaxy"
] | 19676363e5d07e3b0554c4c1893a9955d226913335ffda84cc699c39886fb797 |
#!/usr/bin/env python
from pylab import *
import os
from scipy.stats.stats import spearmanr
from scipy.stats import ks_2samp
from scipy.stats import scoreatpercentile
from scipy.stats.mstats import normaltest
from anderson import *
from astropy.stats import bootstrap
import numpy as np
pscale24=2.45#arcsec per pixel
p... | rfinn/LCS | python27/LCScommon.py | Python | gpl-3.0 | 21,672 | [
"Galaxy"
] | d86ae35ba797a258406bd51ee3b2226161b59e59e0308599b4ccbe64524319db |
#!/usr/bin/python
import time
import os
import sys
import argparse
import MySQLdb
from homolog4 import *
# Copyright(C) 2014 David Ream
# Released under GPL version 3 licence. http://www.gnu.org/licenses/lgpl.html
# Do not remove this comment
# This program's purpose is to convert a homolog data element into an entr... | reamdc1/gene_block_evolution_old | homolog_database_conversion.py | Python | gpl-3.0 | 4,163 | [
"BLAST"
] | 9eeae45fb585e9743c65a62913cd921bf1cfc247fc3d71cf3e0077cde2c2a6aa |
# -*- coding: utf-8 -*-
# Copyright 2020 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 required by applicable law or... | googleads/google-ads-python | google/ads/googleads/v10/resources/types/remarketing_action.py | Python | apache-2.0 | 2,279 | [
"VisIt"
] | d9b8106d464534249351ad7380f79709478c14ae7de9c3562caf69b1deb1449f |
from pyjade import Compiler as _Compiler
from pyjade.runtime import attrs, escape, iteration
import tornado.template
from pyjade.utils import process
from pyjade.exceptions import CurrentlyNotSupported
ATTRS_FUNC = '__pyjade_attrs'
ESCAPE_FUNC = '__pyjade_escape'
ITER_FUNC = '__pyjade_iter'
class Compiler(_Compiler):... | glennyonemitsu/MarkupHiveServer | src/pyjade/ext/tornado/__init__.py | Python | mit | 3,275 | [
"VisIt"
] | 97346e0719b632b87779f5762adcfc54e489a5967f2b8d53afd3ba3c50cfdab5 |
from __future__ import division
from __future__ import print_function
import sys
sys.path.insert(1, "../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.gam import H2OGeneralizedAdditiveEstimator
# In this test, we check and make sure that we can do scoring
def test_gam_model_predict():
prin... | michalkurka/h2o-3 | h2o-py/tests/testdir_algos/gam/pyunit_PUBDEV_7181_check_model_scoring.py | Python | apache-2.0 | 4,642 | [
"Gaussian"
] | 680779c681959ae1e2c037d377932daf311c4474df7c7db82fe416826d128b04 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011-2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Softw... | tiagocardosos/stoq | stoqlib/gui/base/messagebar.py | Python | gpl-2.0 | 1,972 | [
"VisIt"
] | 6989be03cb35566158aff4e6ba169a1b09260bd2a1f0545f607499c902fd8140 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'PreviousSurgery.uterine_fibroids'
db.delete_column(u'patient_previoussurgery', 'uterine_fi... | aazhbd/medical_info01 | patient/migrations/0023_auto__del_field_previoussurgery_uterine_fibroids__del_field_previoussu.py | Python | bsd-3-clause | 30,622 | [
"VisIt"
] | b7db1484d183d6f6a39eaf9f8116701b7fad464b79f02a7845d1044faf373ea3 |
# coding: utf-8
# # Session 4: Visualizing Representations
#
# ## Assignment: Deep Dream and Style Net
#
# <p class='lead'>
# Creative Applications of Deep Learning with Google's Tensorflow
# Parag K. Mital
# Kadenze, Inc.
# </p>
#
# # Overview
#
# In this homework, we'll first walk through visualizing the
# gradient... | dariox2/CADL | session-4/s4b01.py | Python | apache-2.0 | 52,997 | [
"Gaussian",
"NEURON"
] | 91b684810c046dfc9ee1ea922ce1febe80d339ab9d2fce8af0bb9f0f67d8ae3e |
#!/usr/bin/env python
#
# Connect4
#
# Just did this for the fun. Have fun like i did. :)
# I did this in Geany, a small and fast IDE. http://www.geany.org/
#
# Copyright 2009 Diogo Nuno dos Santos Silva <promzao@gmail.com>
#
# This program is free software; you can redistribute i... | prom/Python-Connect-4 | connect4.py | Python | gpl-3.0 | 12,610 | [
"VisIt"
] | d265b26b43c4b5d4b19d2be5f4e6e36c8dfb9fa855d077b095868a58243c1026 |
# This file is part of cldoc. cldoc 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 even the ... | jessevdk/cldoc | cldoc/tree.py | Python | gpl-2.0 | 17,804 | [
"VisIt"
] | 2f0d4d442a9c430afd868e4268515f90567bf29185490eb701956faa8bd0f459 |
# Orca
#
# Copyright 2004-2008 Sun Microsystems Inc.
# Copyright 2010 Joanmarie Diggs
#
# 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 op... | h4ck3rm1k3/orca-sonar | src/orca/scripts/apps/pidgin/script.py | Python | lgpl-2.1 | 7,523 | [
"ORCA"
] | fe415c32bbc403ee88e8883dee7bdb96c91f93599a78d17f5b600216a7cd2909 |
import argparse
import json
import os
import pandas as pd
import requests
def get_parser():
parser = argparse.ArgumentParser(description=__doc__)
input_group = parser.add_mutually_exclusive_group(required=True)
input_group.add_argument('-i', "--infile", action='store',
help="""Path... | ENCODE-DCC/pyencoded-tools | pipeline_input_scripts/generate_mint_chip_input_json.py | Python | mit | 31,462 | [
"BWA"
] | e0f15c5a0ff4a0b6e2c38453b3836af9a8e7650cb8d7aaf3d60645366ec4f2e9 |
# Jackie's Map
# CMDR Jackie Silver, DISC
# Kay Johnston 2017 / 3303
# Thanks are due to everyone who's collected data for the various source lists.
# Special thanks to Lucienn and Anthor for beacon data and edsm landmarks.
version = '3t'
# Standard Python imports. Might need to change PIL to pillow on some ... | KayJohnston/jackies-map | jmap3t.py | Python | bsd-3-clause | 82,087 | [
"Galaxy"
] | 641301f00a4499da0ef483fe2534796297708d50df8d8aad1222993f04f2f785 |
"""
Caffe network visualization: draw the NetParameter protobuffer.
.. note::
This requires pydot>=1.0.2, which is not included in requirements.txt since
it requires graphviz and other prerequisites outside the scope of the
Caffe.
"""
from apollocaffe.proto import caffe_pb2
import pydot
# Internal laye... | pcmoritz/Strada.jl | deps/src/caffe/python/apollocaffe/utils/draw.py | Python | bsd-2-clause | 7,124 | [
"NEURON"
] | 64d42afb15a701cc2733582c14a75d66b8520ff1cdc70434af89159f3012ec0e |
#!/usr/bin/env python
"""
@author: Benjamin Chretien
"""
import math
import numpy as np
from mayavi import mlab
j = complex(0,1)
min_x = -10.
max_x = 10.
min_y = -8.
max_y = 8.
root0 = 1.
lamda = 0.01/abs(max_x)
step_size = 0.1
def f_evolution_element(x, y):
root_real = 2.
roots = np.zeros((3,3))
if y < 0:
... | bchretien/Python-sandbox | src/poly_surface_extrema.py | Python | bsd-2-clause | 4,053 | [
"Mayavi"
] | 029db274f15e54bf79cb99f3b34b9730c5b83b7eddb56c6a9a151f79ec2f567a |
# Copyright (C) 2009 LibreSoft
#
# 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 ... | xybai/MininGit | pycvsanaly2/extensions/Jobs.py | Python | gpl-2.0 | 3,250 | [
"Octopus"
] | 583d7dfa7ee77f8516847c99a9801b5ba8f6f373d656555bb8ec793567c004ce |
# -*- coding: utf-8 -*-
# This file is part of beets.
# Copyright 2016, Adrian Sampson.
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation t... | parapente/beets | beetsplug/discogs.py | Python | mit | 14,490 | [
"VisIt"
] | 97ec70e67d22f333ba194407b3bed530931234483850d6f29f3b20ba53c39e26 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2013 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/remindor-qt | remindor_qt/RemindorQtWindow.py | Python | gpl-3.0 | 15,474 | [
"Brian"
] | f4f31d3a7e5033924261d60ad63f7748bd3aad3bb72a06789806e6a60dbf2107 |
# ******************************************************************************
# Copyright 2014-2018 Intel Corporation
#
# 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.apa... | NervanaSystems/neon | tests/test_gru.py | Python | apache-2.0 | 16,736 | [
"Gaussian"
] | 3dcd41d7b0856386c2e5353eda3fef0fdcca0753b5b8e5cd455129dab5112a15 |
#!/usr/bin/python
# File created on 27 Jan 2012.
from __future__ import division
__author__ = "Kishori M Konwar"
__copyright__ = "Copyright 2013, MetaPathways"
__credits__ = ["r"]
__version__ = "1.0"
__maintainer__ = "Kishori M Konwar"
__status__ = "Release"
try:
import os, re
from os import makedirs, sys, ... | kishori82/MetaPathways_Python.3.0 | libs/python_modules/pipeline/MetaPathways_gather_run_stats.py | Python | mit | 15,903 | [
"BLAST"
] | 922a11fd6726b872bd552ac83cacbff4b52390a7b82202a60edbe5b4d0df28eb |
##############################################################################
##############################################################################
# Example 1.1
# Gaussian process regression for ice varve data
#
# Copyright (c) 2016 Johan Dahlin [ johan.dahlin (at) liu.se ]
# Distributed under the MIT licens... | compops/phd-thesis | example-icevarve/ex-icevarve-gp.py | Python | gpl-3.0 | 1,560 | [
"Gaussian"
] | c9cfb0ed9f71797d40423988905deb94c2ac8538a96f81be909f51bbbecdc7cf |
#!/usr/bin/env python
""" segmental_duplication_gene_analyzer
"""
import argparse
import logging
import os
import sys
from SDDetector.version import __version__
from SDDetector.Entities.Region import Region
from SDDetector.Entities.GeneLink import GeneLink
from SDDetector.Parser.Gff.GffDuplicationParser import GffD... | nlapalu/SDDetector | bin/segmental_duplication_gene_analyzer.py | Python | gpl-3.0 | 13,598 | [
"BLAST"
] | f81a6481e693e97bca0a7938153ad26caf63800b1596b098d5d9d0a43744c43f |
# revlog.py - storage back-end for mercurial
#
# Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
"""Storage back-end for Mercurial.
This provides efficient delta storage with O(1... | joewalnes/idea-community | plugins/hg4idea/testData/bin/mercurial/revlog.py | Python | apache-2.0 | 48,667 | [
"VisIt"
] | c7e8eb2771af9d2cdd75c8735440c7bd0b5e47328bf8aca2f852b90a5a0cedba |
#!/usr/bin/python
#
# Copyright (C) 2011, 2012 Google Inc.
#
# 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 p... | sarahn/ganeti | lib/ovf.py | Python | gpl-2.0 | 67,549 | [
"VisIt"
] | a3f00ffd98d66a185aa4d0f514b11ac82e4a107ec59bd55a0cc71d0710fc951a |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2014 CRS4.
#
# This file is part of blast-python.
#
# blast-python 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)
# ... | crs4/blast-python | test/test_sseq_speed.py | Python | gpl-3.0 | 1,817 | [
"BLAST"
] | d5aac2b2119994dbdcdb60aa8aaac55cb4cd8218814aa4418562403202ef9114 |
"""Analyze python import statements."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import ast
import os
from . import types as t
from .util import (
display,
ApplicationError,
is_subdir,
)
from .data import (
data_context,
)
VIRTUAL_PACKAGES = set([
... | Dhivyap/ansible | test/lib/ansible_test/_internal/import_analysis.py | Python | gpl-3.0 | 9,015 | [
"VisIt"
] | 89e5990394d9a8aedc568d77d71a1bb855debc52a019dbd5bdf389108f936723 |
#
# 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... | mguzdial3/MineCode | python-codec/src/rlglue/network/Network.py | Python | apache-2.0 | 7,403 | [
"Brian"
] | 47f7c4ef1bbd0c504e765a95e08fa627b77a4808f1241b7c676548df83beb023 |
# -*- coding: utf-8; -*-
"""
Copyright (C) 2007-2013 Guake authors
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 progra... | Ozzyboshi/guake | guake/palettes.py | Python | gpl-2.0 | 45,484 | [
"ESPResSo",
"Galaxy"
] | 7fe278f1698025524fd7848f18dee03ff0aad3aaf1a7ecd10ba1d74d542812f2 |
"""
Simulate interlaced spectra.
"""
import os
import glob
from pylab import cm
import matplotlib.pyplot as plt
from matplotlib.ticker import MultipleLocator
import numpy as np
#import pyfits
import astropy.io.fits as pyfits
import unicorn
import unicorn.interlace_fit
import unicorn.utils_c as utils_c
import threed... | gbrammer/unicorn | intersim.py | Python | mit | 28,215 | [
"Gaussian"
] | 81f14e2dd08ba1cb074e6ebe0a9687db3c5b9a2af76cbbbfd83c683ee166b6e1 |
import sys
from ase.atoms import string2symbols
from asap3 import EMT
from asap3.Tools.ParameterOptimization import ParameterPerformance
from asap3.Tools.ParameterOptimization.EMT import *
from asap3.Tools.MaterialProperties import MaterialPropertiesData
def get_parameters(file, number=2):
file = open(file)
t... | auag92/n2dm | Asap-3.8.4/Projects/ParameterOptimization/performance.py | Python | mit | 2,770 | [
"ASE"
] | 917ab44796d548e63c68ad4b0c835ab6301fdf881d5adfe5919a121a2bb56808 |
import unittest
from rdkit import Chem
from rdkit.Geometry.rdGeometry import Point3D
from rdkit.Chem.Features.FeatDirUtilsRD import GetDonor2FeatVects
class TestCase(unittest.TestCase):
def assertListAlmostEqual(self, list1, list2, msg, tol=7):
self.assertEqual(len(list1), len(list2), msg)
for a, ... | rdkit/rdkit | rdkit/Chem/Features/UnitTestFeatDirUtilsRD.py | Python | bsd-3-clause | 7,519 | [
"RDKit"
] | 276e6055ca17e7388ed212abba0b76c20bb08949e20b037d539e44a42778649a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Created on Mar 18, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyue@mit.edu"
__date_... | dongsenfo/pymatgen | pymatgen/apps/borg/tests/test_hive.py | Python | mit | 4,722 | [
"pymatgen"
] | 2c178db24cbb230532361bd202942567d06a615ebfac464f66ffc806afc9163b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License
"""
Module for reading Lobster output files. For more information
on LOBSTER see www.cohp.de.
"""
import collections
import fnmatch
import itertools
import os
import re
import warnings
from collections import d... | gVallverdu/pymatgen | pymatgen/io/lobster.py | Python | mit | 79,306 | [
"VASP",
"pymatgen"
] | cdb0a42abc2cb9938c5a2fe7b7fb4ec2f5495286cf7ead7f04ddc022a24c3f7f |
# 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... | BackupTheBerlios/espressopp | src/io/DumpGRO.py | Python | gpl-3.0 | 3,344 | [
"ESPResSo"
] | 63dc128beb24ceac653f28e92c702be4bbd244c10203633a3d4127d9c99ff787 |
#!/usr/bin/env python
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# Written (W) 2013 Evangelos Anagnostopo... | AzamYahya/shogun | applications/classification/random_fourier_classification.py | Python | gpl-3.0 | 3,552 | [
"Gaussian"
] | 751015d28c8988972ed337901949d75bd61f7b30812d892d1aa3cce94ead5404 |
import pytest
from uwg import SimParam, Weather, Forcing
import os
EPW_PATH = \
os.path.join(os.path.dirname(__file__), 'epw', 'SGP_Singapore.486980_IWEC.epw')
def test_forcing():
"""Test for forcing.py"""
# setup_forcing
dtSim = 300 # Sim time step
dtWeather = 3600 # Weather ... | chriswmackey/UWG_Python | tests/test_forcing.py | Python | gpl-3.0 | 954 | [
"EPW"
] | 2116d3005ed2c6c5991444f7db833314c6a160eddac0342c77d16327d7eeb781 |
"""
.. py:module:: mappers
:platform: Unix
Various mapper implementations. Mappers are functions that map possible feature
value's to the interval [-1, 1]. In Creamas, they are used by individual
agent's to represent agent's preferences over features values.
"""
from creamas.math import gaus_pdf, logistic
from cre... | assamite/creamas | creamas/mappers.py | Python | gpl-2.0 | 10,909 | [
"Gaussian"
] | 883a1f52bbeebdd28b06591be49a6948ed4fbb29eb5d655fd325d1c3fcee6b41 |
import sys
sys.path.insert(1, "../../../")
import h2o, tests
def weights_and_distributions():
htable = h2o.upload_file(h2o.locate("smalldata/gbm_test/moppe.csv"))
htable["premiekl"] = htable["premiekl"].asfactor()
htable["moptva"] = htable["moptva"].asfactor()
htable["zon"] = htable["zon"]
# gam... | brightchen/h2o-3 | h2o-py/tests/testdir_algos/deeplearning/pyunit_weights_and_distributionsDeeplearning.py | Python | apache-2.0 | 1,124 | [
"Gaussian"
] | 06058c56ab86c719444461da398bc6c0d67bfc508f8495a8d15851b7c8bcdcde |
# -*- coding: utf-8 -*-
# This script is modified version of GraupnerBrunel2012 model by Aditya Gilra.
# Modification is following:
# - Added global seed.
# - Removed some messages.
# - Added assertion.
#
# NOTE: This script is used for testing random number generators on various
# platform. This should not be use... | BhallaLab/moose-core | tests/core/test_GraupnerBrunel2012_STDPfromCaPlasticity.py | Python | gpl-3.0 | 8,008 | [
"MOOSE",
"NEURON"
] | f79f1602f209b49a5105e24f267c941aa19be807b6968c3d5fb980562865c58c |
from __future__ import absolute_import
from django.utils.functional import cached_property
from parsimonious.exceptions import IncompleteParseError
from sentry.api.event_search import (
event_search_grammar,
InvalidSearchQuery,
SearchFilter,
SearchKey,
SearchValue,
SearchVisitor,
)
from sentry... | mvaled/sentry | src/sentry/api/issue_search.py | Python | bsd-3-clause | 4,681 | [
"VisIt"
] | 3076dd529fee2a5b6f33724e4e72e54426e5b13e6aee845acf392757a8de7e7b |
"""rbf - Radial basis functions for interpolation/smoothing scattered N-D data.
Written by John Travers <jtravs@gmail.com>, February 2007
Based closely on Matlab code by Alex Chirokov
Additional, large, improvements by Robert Hetland
Some additional alterations by Travis Oliphant
Interpolation with multi-dimensional t... | pizzathief/scipy | scipy/interpolate/rbf.py | Python | bsd-3-clause | 11,446 | [
"Gaussian"
] | 28715070a840ecb477da18325bc6b5dedf41de3f678e6ead3df5a04d1d398878 |
# Copyright 2019 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | tensorflow/tensorflow | tensorflow/python/keras/layers/kernelized.py | Python | apache-2.0 | 11,017 | [
"Gaussian"
] | 76e75d282851a1ee995964cdf8e4777800435e70d362921f32f78f15c9b5c243 |
## Copyright 2016 Kurt Cutajar, Edwin V. Bonilla, Pietro Michiardi, Maurizio Filippone
##
## 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... | mauriziofilippone/deep_gp_random_features | code/likelihoods/__init__.py | Python | apache-2.0 | 741 | [
"Gaussian"
] | d89c0000246279422494da9c0a5049b7c9b7b071e0cf39cbe6a9af3f6e739194 |
'''<b>Smooth</b> smooths (i.e., blurs) images.
<hr>
This module allows you to smooth (blur) images, which can be helpful to
remove artifacts of a particular size.
Note that smoothing can be a time-consuming process.
'''
# CellProfiler is distributed under the GNU General Public License.
# See the accompanying file L... | LeeKamentsky/CellProfiler | cellprofiler/modules/smooth.py | Python | gpl-2.0 | 13,433 | [
"Gaussian"
] | 7ecc00c977ff0c426004499023f56eba4c3eddde6c510698d67cd8acdcabf7fd |
########################################################################
# $HeadURL $
# File: GraphTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/09/28 09:02:23
########################################################################
""" :mod: GraphTests
=======================
.. module: Graph... | arrabito/DIRAC | Core/Utilities/test/Test_Graph.py | Python | gpl-3.0 | 10,806 | [
"DIRAC"
] | 99536279796e66733e5831f3e3f213aa909951c80603de8bf8e2cd53da44e1f7 |
# coding: utf-8
from __future__ import unicode_literals
import itertools
import json
import os.path
import random
import re
import time
import traceback
from .common import InfoExtractor, SearchInfoExtractor
from ..jsinterp import JSInterpreter
from ..swfinterp import SWFInterpreter
from ..compat import (
compa... | vinegret/youtube-dl | youtube_dl/extractor/youtube.py | Python | unlicense | 151,125 | [
"ADF"
] | f4926c7b2adebe6e277c09b937a3deb54e39278bee1d95e3deec72a980308224 |
import numpy as np
# ----------
# Class for univariate gaussian
# p(x) = 1/sqrt(2*pi*simga^2) * e ^ - (x-miu)^2/2*sigma^2
# Where miu is the gaussian mean, and sigma^2 is the gaussian variance
# ----------
class Gaussian:
def __init__(self, mean, variance):
self.mean = mean
self.variance = vari... | ramon-astudillo/lxmls-toolkit | lxmls/distributions/gaussian.py | Python | mit | 664 | [
"Gaussian"
] | 1ffc8284600a1eb43ca496c2bea0138f7666b1bcd1eab074a8c38c7bd22eb37b |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/ajax/bouquets.py | Python | gpl-2.0 | 5,534 | [
"VisIt"
] | 06f22f89f705327e34fca045dd9179dcb675aabcd716231cae9006a3e9f64c12 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2012-2018, CRS4
#
# 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 to
# use, copy, modify... | crs4/hl7apy | hl7apy/v2_4/tables.py | Python | mit | 46,671 | [
"BWA",
"VisIt"
] | 62554885479ada4e2fb502f3f9c8954de5c4847cf28fe604274a8b3fb5f79123 |
#
# 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_
import sys
import keyword
import re
import inspect
import types
import warnings
from scipy.misc import... | chaluemwut/fbserver | venv/lib/python2.7/site-packages/scipy/stats/_distn_infrastructure.py | Python | apache-2.0 | 109,496 | [
"Gaussian"
] | 67e77676c32e643dd761e0c2ce1b76006325a0f211d3a62c9ac856668130a5ef |
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ 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.
#
"""Exposes a class for matchin... | ptosco/rdkit | rdkit/Chem/FragmentMatcher.py | Python | bsd-3-clause | 2,268 | [
"RDKit"
] | 78de740eb1a7e0a7546cf8b9c8f7c534d641d22e0b4656e0cff2024c8a49bed7 |
# Copyright (C) 2012,2013,2016
# 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... | kkreis/espressopp | src/tools/info.py | Python | gpl-3.0 | 2,683 | [
"ESPResSo"
] | 4244ccd870f2baca12ffd9d5849f8be7c9857b75bb6018a1d7ca8b871a1c43f7 |
# (c) 2017, Brian Coca
# (c) 2017 Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
DOCUMENTATION = '''
cache: yaml
short_descriptio... | hryamzik/ansible | lib/ansible/plugins/cache/yaml.py | Python | gpl-3.0 | 1,924 | [
"Brian"
] | 4866089e0a6cb1c1d751a1d4cd5458f581edea96cf9918f03d5dc77fb5bb35b9 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/tests/test_xmlrpc.py | Python | gpl-3.0 | 7,501 | [
"Brian"
] | 8f79c26c10b6fa909cff2682ace2b9c14c9a8889d3c70771a9d0c3ee64f902d6 |
"""Integration with Galaxy nglims.
"""
import collections
import copy
import glob
import gzip
import operator
import os
import subprocess
import joblib
import yaml
from bcbio import utils
from bcbio.distributed.transaction import file_transaction
from bcbio.galaxy.api import GalaxyApiAccess
from bcbio.illumina import... | Cyberbio-Lab/bcbio-nextgen | bcbio/galaxy/nglims.py | Python | mit | 7,932 | [
"BWA",
"Galaxy"
] | 3405687dd80d20a96e73a341433e871d9f623e8162aa06c7b70e5eecdc4e9bf1 |
# 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 in writing, software
# distributed under th... | iskandr/fancyimpute | fancyimpute/simple_fill.py | Python | apache-2.0 | 1,292 | [
"Gaussian"
] | 5abc125902dd6e7a3bf122500ec60119c3ff04cb3d525c6b5358646b1973f62f |
import os
from ase import *
from gpaw import GPAW
from gpaw.mpi import world
O = Atoms([Atom('O')])
O.center(vacuum=2.)
calc = GPAW(nbands=6,
h=.25,
convergence={'eigenstates':1.e-2, 'energy':.1, 'density':.1},
hund=True,
parallel={'domain': world.size})
O.set_calculat... | qsnake/gpaw | oldtest/parallel/domain_only.py | Python | gpl-3.0 | 477 | [
"ASE",
"GPAW"
] | 95f70a61bfaa3fc57da173c13b9ccf8ac322afc271c686b82f6343213e44b946 |
# coding: utf-8
from __future__ import unicode_literals
from __future__ import division
"""
Evaluate the defect concentration based on composition, temperature,
and defect energies using "Dilute Solution Model"
Reference: Phys Rev B, 63, 094103, 2001,
"Density of constitutional and thermal point defects in L12 Al3Sc"... | mbkumar/pydii | pydii/dilute_solution_model.py | Python | mit | 53,799 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | bd68cd12fa00b7dc820b70be6b93adf6d62bffa184ba770ffacf82112cbd08a9 |
"""Simple Python lib for the ISY home automation netapp
This is a Python interface to the ISY rest interface
providomg simple commands to query and control registared Nodes and Scenes
and well as a method of setting or querying vars
"""
__author__ = 'Peter Shipley <peter.shipley@gmail.com>'
__copyright__ = "Copyr... | evilpete/ISYlib-python | ISY/IsyClass.py | Python | bsd-2-clause | 68,214 | [
"Elk"
] | e470a613d0d88b93dc2eff64d9841f7cb130d041475f2ef8e6065506934a0cf3 |
import math
import numpy as np
import matplotlib.pyplot as plt
import skimage.transform as sktr
from unsharp import *
def get_points(im1, im2):
print('Please select 2 points in each image for alignment.')
plt.imshow(im1)
p1, p2 = plt.ginput(2)
plt.close()
plt.imshow(im2)
p3, p4 = plt.ginput(2)... | rachelalbert/CS294-26_code | project3_code/part_1/align_images.py | Python | mit | 2,363 | [
"Gaussian"
] | e3f8d595c6d915f37dcb6e34245792556dbe0568ce2c8af5582e366ee385cd8d |
import ast
import os
import sys
from .python.ast import Visitor
from .python.debug import dump
def transpile(input, prefix='.', outdir=None, namespace='python', verbosity=0):
transpiler = Transpiler(namespace=namespace, verbosity=verbosity)
for file_or_dir in input:
if os.path.isfile(file_or_dir):
... | Felix5721/voc | voc/transpiler.py | Python | bsd-3-clause | 3,397 | [
"VisIt"
] | fb58dba365d6d82ec9beb3b9a27b0721c0085207dd5573c175f5dd3911efe0d9 |
#!/usr/bin/env python
# encoding: utf-8
import inspect
from functools import wraps
from decorator import decorator
import pytest
def use_bintypes(*bintypes):
"""Decorate test to run only for the given bintypes."""
def check_bintype(f):
@wraps(f)
def decorated_function(self, *args, **kwargs)... | sdss/marvin | tests/__init__.py | Python | bsd-3-clause | 6,457 | [
"Galaxy"
] | e94b459b8aa847b2c6c5326f6b1424f5ea94eb4c157eaa2f637a75773b5501cf |
from __main__ import vtk, qt, ctk, slicer
import string
import numpy
import collections
class NodeInformation:
def __init__(self, dataNode, labelNode, allKeys):
self.nodeInformation = collections.OrderedDict()
self.nodeInformation["Node"] = "self.nodeName(self.dataNode)"
self.dataNode = dataNode
... | vnarayan13/Slicer-OpenCAD | HeterogeneityCAD/FeatureExtractionLib/NodeInformation.py | Python | mit | 803 | [
"VTK"
] | 20f020261beacbc62b8290e2a7f5688e8ebe79e39111688b1df943e16bc35d77 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen.core.libxcfunc import LibxcFunc
from pymatgen.util.testing import PymatgenTest
class LibxcFuncTest(PymatgenTest):
def test_libxcfunc_api(self):
"""Testing libxcfunc_api."""
# LDA correlatio... | vorwerkc/pymatgen | pymatgen/core/tests/test_libxcfunc.py | Python | mit | 859 | [
"pymatgen"
] | 65b6924ba278f3327bcbe1eafc3fb7ccdfb44c9e6e209cf7c1d779b6e4b48b67 |
from __future__ import (absolute_import, division, print_function)
import sys
import unittest
import numpy as np
from mantid.simpleapi import *
from mantid.api import *
from testhelpers import run_algorithm
class MatchPeaksTest(unittest.TestCase):
_args = {}
def setUp(self):
func0 = "name=Gaussian... | wdzhou/mantid | Framework/PythonInterface/test/python/plugins/algorithms/MatchPeaksTest.py | Python | gpl-3.0 | 14,834 | [
"Gaussian"
] | bec514bd51f3b3bc83de3dedb60a54feb73ed5372987ca04051e17d89a94c0f2 |
#!/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... | kbrebanov/ansible | lib/ansible/modules/network/avi/avi_certificatemanagementprofile.py | Python | gpl-3.0 | 3,654 | [
"VisIt"
] | 41d747838fc8e73de5dff2fb1202db3e60538781ecdbbef37f71da40828f9a15 |
#!/usr/bin/env python2
# Copyright (C) 2016, 2017(H)
# Max Planck Institute for Polymer Research
#
# 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 Foundatio... | kkreis/espressopp | examples/adress/fadress_selfadjusting/peptide-adres-selfadjusting.py | Python | gpl-3.0 | 21,548 | [
"ESPResSo",
"Gromacs"
] | b19fd9c4e9ca8fef93a95bf15c41f07e3ddc04ee40b02b23cbacf6c64b486ffb |
import unittest
import os
from core.data import DataReader
class DataReaderTest(unittest.TestCase):
def setUp(self):
self.reader = DataReader()
def tearDown(self):
del self.reader
def testDataReader(self):
path = os.path.dirname(os.path.abspath(__file__))
fileName = path + "/data/hi-3.mhd"
imageData ... | berendkleinhaneveld/Registrationshop | tests/test_DataReader.py | Python | mit | 2,084 | [
"VTK"
] | 5333f28d237428e141f0f444f768831e26c205cab2759d4d4341134892980ecc |
from pylab import *
from plotly.tools import FigureFactory as FF
import plotly.graph_objs as go
from scipy.spatial.distance import pdist, squareform, cdist
from .riemannian_manifold import RManifold
from ..data_attachment.measures import Measures, Measure
class Landmarks(RManifold) :
"""
Encodes a Landmarks manifo... | jeanfeydy/lddmm-ot | LDDMM_Python/lddmm_python/modules/manifolds/landmarks.py | Python | mit | 11,202 | [
"DIRAC",
"Gaussian"
] | 3417d3981e4383ee8cb554396d75bbc05d2dde4378190ce3ab9d8095d28034ed |
"""
dip CLI tool main entrypoint
"""
import json
import subprocess
import click
import docker
from dip import __version__
from dip import colors
from dip import errors
from dip import options
from dip import settings
from dip import utils
def clickerr(func):
""" Decorator to catch errors and re-raise as ClickExc... | amancevice/dip | dip/main.py | Python | mit | 9,032 | [
"Amber"
] | 5412cc5655c95f3c3327724591c1b3d5335e0dd0f524386f71ce20d12bb63059 |
###############################################################################
# ilastik: interactive learning and segmentation toolkit
#
# Copyright (C) 2011-2014, the ilastik developers
# <team@ilastik.org>
#
# This program is free software; you can redistribute it and/or
# mod... | nielsbuwen/ilastik | ilastik/applets/thresholdTwoLevels/thresholdingTools.py | Python | gpl-3.0 | 16,113 | [
"Gaussian"
] | cc7b992b3ff6a467b5baec277785cc02ea65a0044f80d383170ed95804c7bb65 |
#
# Copyright (C) 2010-2019 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... | fweik/espresso | doc/tutorials/active_matter/exercises/flow_field.py | Python | gpl-3.0 | 4,424 | [
"ESPResSo",
"ParaView",
"VTK"
] | ce6870e681b489c054c6ad4c1e44439ec875f46c518672d1366bdb8cb375f457 |
#!/usr/bin/python
# encoding: utf-8
"""
colors.py
A list of predefined PyMOL colors.
Created by Shane O'Connor 2014.
"""
import traceback
import colorsys
import matplotlib.colors as mpl_colors
from klab.gfx.colors import ggplot_color_wheel
# How to update this list:
#
# Go to http://pymolwiki.org/index.php/Color_V... | Kortemme-Lab/klab | klab/bio/pymolmod/colors.py | Python | mit | 19,019 | [
"PyMOL"
] | cd524f4a8533b1cb64f5d784a43776ab36b687c17e4e47c9149a5740b1577d09 |
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