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"""
Tests related to the cohorting feature.
"""
from uuid import uuid4
from .helpers import BaseDiscussionMixin, BaseDiscussionTestCase
from .helpers import CohortTestMixin
from ..helpers import UniqueCourseTest
from ...pages.lms.auto_auth import AutoAuthPage
from ...fixtures.course import (CourseFixture, XBlockFixtur... | beni55/edx-platform | common/test/acceptance/tests/discussion/test_cohorts.py | Python | agpl-3.0 | 5,623 | [
"VisIt"
] | 7791d1198bda17bf6ac4855a937e569c014c2c1fa192c71d241bf7b1e56638ba |
"""Function-like objects creating orthorhombic lattices.
The following lattice creators are defined:
SimleOrthorhombic
BaseCenteredOrthorhombic
BodyCenteredOrthorhombic
FaceCenteredOrthorhombic
"""
from ase.lattice.bravais import Bravais
import numpy as np
from ase.data import reference_states as _ref... | slabanja/ase | ase/lattice/orthorhombic.py | Python | gpl-2.0 | 5,431 | [
"ASE",
"CRYSTAL"
] | adf12bb3d19cefbf1a107e98782a261c07ac18e2854e4909993c9a91bf3c67f6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines the abstract base classes for battery-related classes.
Regardless of the kind of electrode, conversion or insertion, there are many
common definitions and properties, e.g., average volt... | gVallverdu/pymatgen | pymatgen/apps/battery/battery_abc.py | Python | mit | 12,906 | [
"pymatgen"
] | d4c0e8a4ae45fc4b534e6e8623ba1d09b8b999ea82b05383473cbe5f26014ad5 |
import numpy as np
from sklearn import preprocessing
import matplotlib
matplotlib.use('TKAgg')
import matplotlib.pyplot as plt
import pycasso
from sklearn.linear_model import lasso_path
from sklearn.linear_model import lars_path
from sklearn import linear_model
import time
import pdb
def generate_sim_lognet(n, d, c,... | jasonge27/picasso | profiling/benchmark.py | Python | gpl-3.0 | 5,287 | [
"Gaussian"
] | 0608fc575aeb7cedbe2b9d4b3cdaf647530fd90840a4c99d00c2d82e7aa1dfc3 |
#!/usr/bin/env python
from functools import partial
from math import sqrt
from netCDF4 import Dataset
import sys
import optparse
import rtree
optparse.OptionParser.format_epilog = lambda self, formatter: self.epilog
class NcFiller:
def __init__(self, options ):
self.options = options
... | rsmz/ncFillMissing | ncFillMissing.py | Python | gpl-3.0 | 9,811 | [
"NetCDF"
] | de2e976fec3ffe85d440e351f9e537d5e88b2ecb353fe636724bccefd58123d4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Count number of reads overlapping each SNP in a sam/bam file.
============================================================================
AUTHOR: Carlo Artieri
MAINTAINER: Michael D Dacre, mike.dacre@gmail.com
ORGANIZATION: Stanford University
LI... | TheFraserLab/ASEr | bin/CountSNPASE.py | Python | mit | 27,444 | [
"pysam"
] | f3a5311a101f5a00c4cd3de183791fe5e7b6894d66b4b2ae7c59504e3e87cc37 |
#!/usr/bin/env python
"""
Uses pysam to bgzip a vcf file as-is.
Headers, which are important, are kept.
Original ordering, which may be specifically needed by tools or external display applications, is also maintained.
usage: %prog in_file out_file
"""
from galaxy import eggs
import pkg_resources; pkg_resources.req... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py | Python | gpl-3.0 | 620 | [
"Galaxy",
"pysam"
] | a63f6469cc28aa48ed034684cb054e04a97232b24fe292b4a9b911aedff0fe2d |
# pymol -c generate1.py
# NOTE: obsolete -- PyMOL now uses Dunbrack rotamers by default
from chempy import io
from glob import glob
sys.path.append(".")
from pymol import cmd
import pymol
from pymol import cmd
def find_torsions(res_sele):
# this routine gets a list of atom ids which correspond to the
# free... | gratefulfrog/lib | python/pymol/pymol_path/data/chempy/sidechains/generate1.py | Python | gpl-2.0 | 4,963 | [
"ChemPy",
"PyMOL"
] | e6464d98485b777b556872fb721189c90a1d4d2d9cc6d929a6d2a5c39cd1e89c |
"""
The ternary module enables plotting of ternary isobaric phase diagrams.
"""
import numpy as np
from pycalphad import equilibrium
import pycalphad.variables as v
from pycalphad.plot.eqplot import eqplot
def ternplot(dbf, comps, phases, conds, x=None, y=None, eq_kwargs=None, **plot_kwargs):
"""
Calculate t... | tkphd/pycalphad | pycalphad/plot/ternary.py | Python | mit | 2,161 | [
"pycalphad"
] | 22f49d95bcbffe5a52be3ffe5aecc4e3367beed7ded66ede6231752b36a15988 |
""" Base Storage Class provides the base interface for all storage plug-ins
exists()
These are the methods for manipulating files:
isFile()
getFile()
putFile()
removeFile()
getFileMetadata()
getFileSize()
prestageFile()
getTransportURL()
These are the methods for... | Andrew-McNab-UK/DIRAC | Resources/Storage/StorageBase.py | Python | gpl-3.0 | 13,178 | [
"DIRAC"
] | 62288ebdcfdd65c2126d27b44970a12ca80a6b8efbf9c8920528a14d94f7789b |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/sequence/tests/test_distance.py | Python | bsd-3-clause | 7,215 | [
"scikit-bio"
] | 28f4a4a6be94be2ecbbf2c56d91ac56117d3d73d18d3553edfa4972bed50ea13 |
from flask import Flask, redirect, request, render_template, session
import random, datetime
app = Flask(__name__)
app.secret_key = '@#$%#&%**%^%^%^#%^*(*'
@app.route('/')
def index():
if (not 'gold_count' in session) or (not 'activities' in session):
session['gold_count'] = 0
session['activities'] = []
return... | jiobert/python | Woodall_Robert/Assignments/ninja_gold/server.py | Python | mit | 1,500 | [
"CASINO"
] | 461a0ef910fe4b4b611d778858762077884c3526b97cb108e1f9f36ef7fb7244 |
import difflib
from test.support import run_unittest, findfile
import unittest
import doctest
import sys
class TestWithAscii(unittest.TestCase):
def test_one_insert(self):
sm = difflib.SequenceMatcher(None, 'b' * 100, 'a' + 'b' * 100)
self.assertAlmostEqual(sm.ratio(), 0.995, places=3)
sel... | brython-dev/brython | www/src/Lib/test/test_difflib.py | Python | bsd-3-clause | 22,094 | [
"MOOSE"
] | 0d6434db7e8bf28e3e92dfee9b77fb58e1055b803ca8975a50197c2562d87c30 |
# -*- coding: utf-8 -*-
"""Copyright 2015 Roger R Labbe Jr.
Code supporting the book
Kalman and Bayesian Filters in Python
https://github.com/rlabbe/Kalman-and-Bayesian-Filters-in-Python
This is licensed under an MIT license. See the LICENSE.txt file
for more information.
"""
from __future__ import (absolute_imp... | zaqwes8811/micro-apps | self_driving/deps/Kalman_and_Bayesian_Filters_in_Python_master/kf_book/kf_internal.py | Python | mit | 2,662 | [
"Gaussian"
] | 8add8cad773090529e2bdea1232984e4f558a27dec6999e2f22c77da2e1fd507 |
import numpy as np
from signal_likelihood import SignalLikelihood
import unittest
from numpy.testing import assert_array_almost_equal,assert_almost_equal, assert_equal
import math
"""
Models the ambient audio scenery with a multivariate
Gaussian distributions. Based on that model we can distinguish
between the ambien... | rfcx/defunct | sound-localization/localization/multivariate_gaussian.py | Python | apache-2.0 | 4,307 | [
"Gaussian"
] | b2c9e711a1e8e8e4fd82dc7099c605862d45a49b914fc5c904d8698fe20679e9 |
# coding=utf-8
#*********************************************************************
# PROGRAM NAME: CoheDegree.py *
# *
#*********************************************************************
# AUTHOR: David Aleja... | davofis/Optical_Coherence_Wavelets | CoherenceDegree.py | Python | gpl-3.0 | 4,451 | [
"Gaussian"
] | c05db8b82a434756b1eb08efeebccc2fd57163fb57b58a3c9768fd0802c5e389 |
"""
Cost layers.
TODO: write more documentation
"""
__docformat__ = 'restructedtext en'
__authors__ = ("Razvan Pascanu "
"KyungHyun Cho "
"Caglar Gulcehre ")
__contact__ = "Razvan Pascanu <r.pascanu@gmail>"
import numpy
import copy
import logging
import theano
import theano.tensor as TT... | lisa-groundhog/GroundHog | groundhog/layers/cost_layers.py | Python | bsd-3-clause | 54,554 | [
"Gaussian"
] | 250392d09f8ac8398cb4832b8ed16dfb14c193d17b6a5ea732b42cb4f5182e05 |
#!/usr/bin/env python
""" A unittest script for the individual importation of cutlass modules. """
import unittest
# pylint: disable=W0703, C1801
class ImportTest(unittest.TestCase):
"""
Test the various imports of the cutlass package.
"""
def testImport16SDnaPrep(self):
""" Test the import... | ihmpdcc/cutlass | tests/test_import.py | Python | mit | 12,506 | [
"VisIt"
] | bf3a13c57ead8acfceaedfe0b9085d4785b9e3679eb3245a3c214d4e830f8a0c |
import os
from yade import mpy as mp
numThreads = 4
O.periodic = True;
O.cell.setBox(0.1000005,0.100005, 0.100005)
numspheres=1000
young = 5e6; density = 1000;
NSTEPS = 5000
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(15),density=density,label='spheremat'))
O.materials.append(Fri... | cosurgi/trunk | examples/openfoam/example_icoFoamYade/scriptMPI.py | Python | gpl-2.0 | 3,195 | [
"VTK"
] | 0b8f176d96c6a06bbfec8ec674f1964b757b0ae99d116fa672ed6cf80d8fb26d |
#!/usr/bin/env python
from keras.models import Sequential, load_model, model_from_json, \
model_from_yaml
from keras.layers import Dense, Dropout, Activation, Merge, Flatten, \
Convolution2D, MaxPooling2D, ZeroPadding2D, Reshape, \
UpSampling2D
from keras.layers.normalization import BatchNormalization
... | waynezv/ANN | ANN_large_v23.py | Python | mit | 25,511 | [
"VisIt"
] | 97d9deecdaba90cfef8d0183a46c75069dacab4dfc46b661bf660989fefecc8f |
# Copyright 2016 Michael J Maurer
#
# 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 writ... | maurermj08/efetch | efetch_server/utils/pathspec_helper.py | Python | apache-2.0 | 42,810 | [
"NetCDF"
] | 1566fc0b9fd06d0d9a4aad2657590f85d8b988f0002b779d5a04a4ab6b8e9742 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# this example tests the warping of PolyData using thin plate splines
# and with grid transforms using different interpolation modes
# create a rendering window
renWin = vtk.vtkRender... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Hybrid/Testing/Python/WarpPolyData.py | Python | gpl-3.0 | 6,369 | [
"VTK"
] | eae20e8edfbced21bd7b51c95eec94fa45891c25374aa03f70a36f03b558a669 |
# 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/tools/convert/gromacs.py | Python | gpl-3.0 | 34,493 | [
"ESPResSo",
"Gromacs"
] | 0ec6063ade012c2719d07f4a8a84310446fdce4e63381af649327ba859c9f1c8 |
# This file is part of the Fluggo Media Library for high-quality
# video and audio processing.
#
# Copyright 2010-2 Brian J. Crowell <brian@fluggo.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foun... | fluggo/Canvas | fluggo/editor/model/commands.py | Python | gpl-3.0 | 38,160 | [
"Brian"
] | b2d5ce4d60c3e8ddf945848d27b6cfea2aa0874571eab6f149ce1d9f73f6b87f |
from hidparser.DeviceBuilder import DeviceBuilder
from hidparser.Item import Item, ItemType, ValueItem
class UsageItem(ValueItem):
def __init__(self, *args, **kwargs):
kwargs["signed"] = False
super(UsageItem, self).__init__(*args, **kwargs)
def visit(self, descriptor: DeviceBuilder):
... | NZSmartie/PyHIDParser | hidparser/ItemLocal.py | Python | mit | 2,905 | [
"VisIt"
] | d12620059d29c55945c729c8dcf85c224795ba3f866347f439162c2f5fcd5676 |
from ..molecule import Molecule
from .formatter import Formatter
class Psi4JobFormatter(Formatter):
def __init__(self, molecule, basis_set=None, memory=250, memory_units="mb"):
self.molecule = molecule
self.basis_set = basis_set
if self.basis_set is None:
self.basis_set = "cc-... | jasonrig/molecule-utils | molutils/util/job_formatters/psi4.py | Python | mit | 1,706 | [
"Psi4"
] | 4c0ac3e663dc93292b01063314efde6f1d810a62b666b518f4669a69efb0c035 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Pism(CMakePackage):
"""Parallel Ice Sheet Model"""
homepage = "http://pism-docs.org/w... | LLNL/spack | var/spack/repos/builtin/packages/pism/package.py | Python | lgpl-2.1 | 5,733 | [
"NetCDF"
] | 905709a63e255206cdcabdd2774ce5f6121c3a4915b9ddbfad71e65a9aa71ef4 |
# Default Django settings. Override these with settings in the module
# pointed-to by the DJANGO_SETTINGS_MODULE environment variable.
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
gettext_noop = lambda s: s
#################... | WillGuan105/django | django/conf/global_settings.py | Python | bsd-3-clause | 21,393 | [
"VisIt"
] | 8d5f2d5100199a2a83c37ea7ea8a6deaeb75c823dfc343c6c522443bb5f54fa3 |
"""
DIRAC.WorkloadManagementSystem.Client package
"""
| DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/__init__.py | Python | gpl-3.0 | 57 | [
"DIRAC"
] | e202f99c01836990dd2f4c254c505083a8c2190036c474f7803fa0a58e4c7c7d |
import yaml
from twisted.internet.defer import inlineCallbacks, Deferred
from juju.environment.tests.test_config import (
EnvironmentsConfigTestBase, SAMPLE_ENV)
from juju.state.errors import EnvironmentStateNotFound
from juju.state.environment import (
EnvironmentStateManager, GlobalSettingsStateManager, SET... | mcclurmc/juju | juju/state/tests/test_environment.py | Python | agpl-3.0 | 9,025 | [
"MOOSE"
] | a471ae20ab25fa42222add9958b2295cb54decc28a41fc350de3a4a4533f5578 |
# Copyright (C) 2018 Henrique Pereira Coutada Miranda
# All rights reserved.
#
# This file is part of yambopy
#
#
from __future__ import print_function, absolute_import
import os
import subprocess
import json
from copy import deepcopy
class Scheduler(object):
"""
Generic scheduler class
Initialize the cla... | alexmoratalla/yambopy | schedulerpy/scheduler.py | Python | bsd-3-clause | 9,582 | [
"ABINIT"
] | 1134935fbc39ae59b19e5bf099e6a5131bd4a330431549d28df2412716300970 |
from __future__ import division
from bs4 import BeautifulSoup
import general
import math
from scraper import *
class Fleet(Scraper):
def __init__(self, browser, config):
super(Fleet, self).__init__(browser, config)
self.general_client = general.General(browser, config)
def spy_planet(self, ... | winiciuscota/OG-Bot | ogbot/scraping/fleet.py | Python | mit | 9,074 | [
"CRYSTAL",
"Galaxy"
] | f05d4b85474af90a41f1aac20cb518cc09670784aa5f8397634959666a6997b1 |
import vtk
from vtk.util import vtkAlgorithm as vta
from vtk.test import Testing
class TestPythonAlgorithm(Testing.vtkTest):
def testSource(self):
class MyAlgorithm(vta.VTKAlgorithm):
def __init__(self):
vta.VTKAlgorithm.__init__(self, nInputPorts=0, outputType='vtkImageData')
... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Python/Testing/Python/TestPythonAlgorithm.py | Python | gpl-3.0 | 4,659 | [
"VTK"
] | 34a49968ca7947af77f639545e4d1413a01dff6b68b5b0a611553a9ec623d41b |
"""
Kernel Density Estimation
-------------------------
"""
# Author: Jake Vanderplas <jakevdp@cs.washington.edu>
import numpy as np
from scipy.special import gammainc
from ..base import BaseEstimator
from ..utils import check_array, check_random_state, check_consistent_length
from ..utils.extmath import row_norms
fr... | chrsrds/scikit-learn | sklearn/neighbors/kde.py | Python | bsd-3-clause | 9,707 | [
"Gaussian"
] | e15618f4f57d74461105aab1a98b2e29c1bbe4eae5c0e318dcf0d11b96096d58 |
#!/usr/bin/env python3
import networkx
import psycopg2
import sys
import json
import random
import itertools
# TODO: cardinal-position map drawing works very well. Figure out how to split
# into subgraphs that don't need explicit positioning, OR, draw as completely
# separate graphs (losing connecting edges maybe, bu... | lotheac/bcproxy | area_to_json.py | Python | isc | 5,459 | [
"VisIt"
] | b3975d9a30b10d966271195763ec08c8159576a29d8bf360f1ecf97ce53255f8 |
"""
This migration script adds a user actions table to Galaxy.
"""
from sqlalchemy import *
from migrate import *
import datetime
now = datetime.datetime.utcnow
import logging
log = logging.getLogger( __name__ )
metadata = MetaData( migrate_engine )
def display_migration_details():
print ""
print "This mig... | volpino/Yeps-EURAC | lib/galaxy/model/migrate/versions/0029_user_actions.py | Python | mit | 1,288 | [
"Galaxy"
] | 61624c119e658d564783ae9a3bfea90eb5e8d1a03980b58f7ab5201ac1365f49 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2005-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012 Gary Burton
# Copyright (C) 2... | jralls/gramps | gramps/gui/viewmanager.py | Python | gpl-2.0 | 73,928 | [
"Brian"
] | 0bc79ffa31edad4533e1110ca15756777dcc9c7f34ec9821a23af3d27ce9063a |
"""Multivariate Gaussian contour classifier.
"""
import numpy as np
from scipy.stats import boxcox
from scipy.stats import multivariate_normal
from motif.core import ContourClassifier
EPS = 1.0
MAX_SCORE = 10000.0
class MvGaussian(ContourClassifier):
'''Multivariate Gaussian contour classifier.
Attributes
... | rabitt/motif | motif/contour_classifiers/mv_gaussian.py | Python | mit | 4,697 | [
"Gaussian"
] | 989554e579c5b9290b9f1ad6de411871f11221343e6e0fd081752d76e22fbcb7 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import pango
import pangocairo
from object import Object
from objects import *
from control import Control
import gtk
class Table(Object):
"""This class represents a table"""
__name__ = "Table"
def __init__(self, rows=5, columns="0", titles=_("Col... | jaliste/sanaviron | sanaviron/objects/table.py | Python | apache-2.0 | 3,884 | [
"FLEUR"
] | 36558687049eac8a46a9a97390267d9167a7b15518b07d58ed46a20cd2c276b5 |
import numpy as np
from gpaw.grid_descriptor import GridDescriptor
from gpaw.fd_operators import Laplace
from gpaw.mpi import rank, size, world
G = 40
N = 2 * 3 * 2 * 5 * 7 * 8 * 3 * 11
B = 2
h = 0.2
a = h * R
M = N // B
assert M * B == N
D = size // B
assert D * B == size
r = rank // B * B
domain_comm = mpi.world.ne... | qsnake/gpaw | oldtest/parallel/poisson10.py | Python | gpl-3.0 | 812 | [
"GPAW"
] | 8918d1adac66dfe145c354ac23241b827d38e14397b22e5aa7d43fc242fd2d95 |
# coding=utf-8
import ladybug.futil as futil
import pytest
import os
def test_unzip_file():
"""Test the unzip file capability"""
folder = "./tests/assets/zip/extracted"
wf_path = "./tests/assets/zip/test.zip"
futil.unzip_file(wf_path, folder)
extracted_epw = os.path.join(folder, "AUS_NSW.Sydney.9... | ladybug-analysis-tools/ladybug-core | tests/futil_test.py | Python | gpl-3.0 | 1,148 | [
"EPW"
] | ba4b554158b6432c826d6d5255a8e60d07face8a46ff265ea9cd7c3b4865db87 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Christoph Klein
# Contributors: Robert T. McGibbon
#
# MDTraj ... | rmcgibbo/mdtraj | mdtraj/formats/lammpstrj.py | Python | lgpl-2.1 | 23,510 | [
"LAMMPS",
"MDTraj"
] | 70129e67b585a44b402a3200a20a2bf9a10f16dc6c30abad7dae230d98665386 |
# Copyright Hybrid Logic Ltd. See LICENSE file for details.
"""
Tests for L{machinist}.
"""
from zope.interface import Attribute, Interface, implementer
from zope.interface.exceptions import DoesNotImplement
from zope.interface.verify import verifyObject, verifyClass
from twisted.python.util import FancyStrMixin
fr... | ClusterHQ/machinist | machinist/test/test_fsm.py | Python | apache-2.0 | 32,930 | [
"Amber"
] | 78d20d41e7a36802c0903d64b783b98fd570ee1311ab846fbd3d8440618ad525 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2014, Nicolas P. Rougier. All Rights Reserved.
# Distributed under the (new) BSD License.
# -----------------------------------------------------------------------------
import ... | duyuan11/glumpy | examples/filter-blur.py | Python | bsd-3-clause | 3,026 | [
"Gaussian"
] | d033ccd36ebecae657ef5de30fa4eab1c1332a27879a633118d4226fb0ee049c |
import datetime
import os
from django.shortcuts import render, get_object_or_404, redirect
from django.http import HttpResponseRedirect, HttpResponse, HttpRequest
from django.urls import reverse
from django.views import generic
from .models import *
from django.utils import timezone
from django.template import Reque... | PrefPy/opra | compsocsite/polls/email.py | Python | mit | 8,409 | [
"VisIt"
] | ff4921125582839605074b5f51855f546287dfd57190a984e3767267b789d906 |
class Mage:
def __init__(self):
self.name = "Minerva"
self.health = 50
self.attack = 25
self.defense = 15
self.speed = 10
self.element = "Ice"
self.spells = [
"Frostbite",
"Glacier",
"Ice Cage",
... | munnellg/OfMagesAndMagic | teams/mystic_marvels/minerva.py | Python | mit | 4,557 | [
"BLAST"
] | 0c935f88395bd10e8c8042370475e6d364866af8269733210914376dab6c1fe9 |
#!/usr/bin/env python
# coding: utf-8
#
# Copyright 2007 Google Inc.
#
# 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 ... | ostree/plaso | utils/upload.py | Python | apache-2.0 | 97,856 | [
"VisIt"
] | dcc6efeaedd489dbcf4c6873a4a7b3b0cf9c0db9695722c34f3b52c8e16e68e6 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. ... | Clyde-fare/cclib | src/cclib/parser/utils.py | Python | lgpl-2.1 | 4,530 | [
"GAMESS",
"cclib"
] | 8c5e2e12900a86f885bd7862443be52f326138b4e3507ac34c693886fc1372b2 |
import requests
import random
from urllib import parse
from bs4 import BeautifulSoup
from cloudbot import hook
search_url = "http://dogpile.com/search"
HEADERS = {'User-Agent': 'Mozilla/5.0 (Linux; Android 4.0.4; Galaxy Nexus Build/IMM76B) AppleWebKit/535.19 (KHTML, like Gecko) Chrome/18.0.1025.133 Mobile Safari/535... | thebestgirl123/CloudBot | plugins/dogpile.py | Python | gpl-3.0 | 1,592 | [
"Galaxy"
] | b9e736776c3f665f523cdc2f0481de66c0a235a78959fd782191bc01929b0ef5 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | lothian/psi4 | psi4/driver/p4util/fcidump.py | Python | lgpl-3.0 | 17,412 | [
"Psi4"
] | 9e238073f1741ec954d8870e6196037caf145cabdfea5e29ccc3412eb613c8e2 |
import sys, json, uuid, os, time, datetime
from misp2cybox import *
from misp2ciq import *
from dateutil.tz import tzutc
from stix.indicator import Indicator
from stix.indicator.valid_time import ValidTime
from stix.ttp import TTP, Behavior
from stix.ttp.malware_instance import MalwareInstance
from stix.incident import... | RichieB2B/MISP | app/files/scripts/misp2stix.py | Python | agpl-3.0 | 19,296 | [
"Amber"
] | e9399923b262ad24f85a1daca73ac2a730c98de51c0e33e1889734c7105e7b51 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <markdowncell>
# This HTML version of is provided for convenience, but it is not the best
# format for the book. In particular, some of the symbols are not rendered
# correctly.
#
# You might prefer to read the [PDF
# version](http://thinkstats.com/thinkstats.pdf)... | chappers/Data-Science | Think-Stats/5 Probability.py | Python | mit | 31,385 | [
"CASINO"
] | 6d74617c926fc3e85d7b72956d2a790ec98d9009114e33685de03299a6c21126 |
"""
ConnectionField and associated classes.
This module defines some basic classes of objects used to create
simulations of cortical sheets that take input through connection
fields that project from other cortical sheets (or laterally from
themselves).
ConnectionField: Holds a single connection field within a
CFProj... | Tasignotas/topographica_mirror | topo/base/cf.py | Python | bsd-3-clause | 47,216 | [
"NEURON"
] | 752ac577c971ae293e07c18c4db1201d0ee90fe88c0a78d685fb6c8eed9f906c |
import datetime
from django.template import Context
from django.test import TestCase, RequestFactory
from cl.custom_filters.templatetags.extras import get_full_host, granular_date
from cl.custom_filters.templatetags.text_filters import naturalduration
from cl.people_db.models import GRANULARITY_DAY, GRANULARITY_MONTH,... | voutilad/courtlistener | cl/custom_filters/tests.py | Python | agpl-3.0 | 5,169 | [
"CRYSTAL"
] | 8d224a55d211d728955249c1652c9035b999be36fd00c50b4790062c6efa9785 |
#!/usr/bin/env python
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2018 Raik Gruenberg & Johan Leckner
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Softwar... | graik/biskit | archive_biskit2/scripts/Mod/search_sequences.py | Python | gpl-3.0 | 5,220 | [
"BLAST"
] | cbb1ef0f6691f8608a260aa3d6886bf0f15a0fb3684458e62d0d7fc98f124399 |
import os
from typing import Tuple
from acme import specs
from acme import types
from acme.wrappers import base as wrapper_base
from acme.wrappers import single_precision
import bsuite
import dm_env
import numpy as np
import sonnet as snt
from src.utils import bsuite_offline_dataset
from src.utils import dm_control_su... | liyuan9988/IVOPEwithACME | src/utils/acme_utils.py | Python | mit | 6,169 | [
"Gaussian"
] | 9ded559436871d840441b7042eb70c1f021450815b80c7f948e1d45faa4ddfd2 |
#
# Brian C. Lane <bcl@redhat.com>
#
# Copyright 2014 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use, modify,
# copy, or redistribute it subject to the terms and conditions of the GNU
# General Public License v.2. This program is distributed in the hope that it
# will be useful,... | vpodzime/pykickstart | pykickstart/commands/sshkey.py | Python | gpl-2.0 | 3,227 | [
"Brian"
] | 58eb2a0913fb402a5717657c5daea351de47ec1d69313ed0a42ae8f25ec68334 |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016-2019 Esteban Tovagliari, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaini... | appleseedhq/appleseed-maya | scripts/appleseedMaya/util.py | Python | mit | 1,635 | [
"VisIt"
] | 69cbea793c759d714a7d13ba5458d7af0e6c83cfac4c111764f358a74efffe7b |
from octopus.sequence.runtime import *
v = variable(0, "variable", "variable")
run(
sequence( #23
once(v > 4, log("v > 4")), #2 #1
wait("2s"), #3
loop_while(v < 2, #7
sequence( #6
increment(v), #4
wait("1 s"), #5
)
),
parallel( #15
loop_un... | richardingham/octopus | examples/variables1.py | Python | mit | 675 | [
"Octopus"
] | a88d8211202ae2fb9e6fbc689ac0424182e135b6b6c24f53ae3d28f5f076edd9 |
from .metadata import METADATA, AUTHOR, TITLE
from Firefly import logging, scheduler
from Firefly.helpers.automation import Automation
from uuid import uuid4
from Firefly.helpers.events import Event, Request, Command
# TODO(zpriddy): These should be in const file
LABEL_TRIGGERS = 'triggers'
def Setup(firefly, package... | Firefly-Automation/Firefly | Firefly/automation/door_alert/door_alert.py | Python | apache-2.0 | 5,117 | [
"Firefly"
] | 6156d6d8251dce2e86d6dc0078e53c2223cf404372b3c5d21e803c8524d56bee |
# $Id$
#
# Copyright (C) 2001-2006 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.
#
""" unit testing code f... | rvianello/rdkit | rdkit/DataStructs/UnitTestcBitVect.py | Python | bsd-3-clause | 11,059 | [
"RDKit"
] | f5e8db18d5943a72fd1dc1ca0f7b98f0a7d46cd230b78645fff6d32a30654e95 |
#!/usr/bin/python
# 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 License, or
# (at your option) any later version.
#
# Ansible is distributed... | willthames/ansible-modules-core | cloud/amazon/elasticache.py | Python | gpl-3.0 | 21,282 | [
"Dalton"
] | 0d15bbc6cf8c313ee4da4419ab8d1736fc6fb2c80fb5f703affaedf24df16589 |
# Natural Language Toolkit: Maximum Entropy Classifiers
#
# Copyright (C) 2001-2013 NLTK Project
# Author: Edward Loper <edloper@gmail.com>
# Dmitry Chichkov <dchichkov@gmail.com> (TypedMaxentFeatureEncoding)
# URL: <http://nltk.org/>
# For license information, see LICENSE.TXT
"""
A classifier model based on m... | TeamSPoon/logicmoo_workspace | packs_sys/logicmoo_nlu/ext/pldata/nltk_3.0a3/nltk/classify/maxent.py | Python | mit | 59,289 | [
"Gaussian"
] | 564426020b68790f1596a887b04051860a5ca5413fd9bbc567641fe6c7afc91c |
"""A VTK file reader object.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2015, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import basename
# Enthought library imports.
from traits.api import Instance
from tvtk.api import tvtk
# Local imports.
fro... | dmsurti/mayavi | mayavi/sources/vtk_file_reader.py | Python | bsd-3-clause | 3,661 | [
"Mayavi",
"VTK"
] | 97a18423f576718fb1da633c6713b22d8c6f01a2da6f3d43f584cbff3e5e63fa |
#
# This is Seisflows
#
# See LICENCE file
#
###############################################################################
# Import system modules
import subprocess
import sys
from functools import partial
from glob import glob
from importlib import import_module
from os.path import basename, join
# Import Numpy
im... | PrincetonUniversity/seisflows | seisflows/solver/base.py | Python | bsd-2-clause | 22,037 | [
"Gaussian"
] | 0710f918272f2fbae70a9be5c0d0578a038904ef8bee3871b62623f0d54d8b70 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: Simplified BSD
import numpy as np
from scipy import linalg
from copy import deepcopy
import re
from .cov import read_cov, _get_whitener_data
from .io.constants import FIFF
from .io.pic... | dimkal/mne-python | mne/dipole.py | Python | bsd-3-clause | 23,401 | [
"Mayavi"
] | b68d3f284db3f42bca0bdc9feab25262b2962b88cc029d85b2884bf1bcad777b |
'''
Choose a set of genomes with highly expressed proteins, and write just those ORFs to a file so we can build a codon adaptation index from them.
The files you probably want are:
bacteria_taxid.txt
highly_expressed_proteins.completegenomes.blastp
/lustre/usr/data/NCBI/RefSeq/bacteria/refseq_orfs.faa
'''... | linsalrob/PhageHosts | code/choose_genomes_with_highly_expressed_proteins.py | Python | mit | 2,256 | [
"BLAST"
] | d68118be0ee77d6df9fe348bcfba47d9a71365753dc580b8064447200512a228 |
## This file is part of PyANTLR. See LICENSE.txt for license
## details..........Copyright (C) Wolfgang Haefelinger, 2004.
## get sys module
import sys
version = sys.version.split()[0]
if version < '2.2.1':
False = 0
if version < '2.3':
True = not False
###xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... | mewbak/idc | antlr.py | Python | lgpl-2.1 | 83,038 | [
"VisIt"
] | 8872ba0a07629f1224316abc67505163f63126cade42564a4ad8c7ad9d600af9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# *********************************************************************
# random forest regression
# read csv file (including feature and label) and use random forest to get the top k similar
# networks for each query network
# *************************************... | zhangjiaobxy/ToBio | sourceCode/rfRegression.py | Python | mit | 9,287 | [
"BLAST"
] | 912d691a4f1373b29278f07037acc943adcae5c4fb9b376cacbd9b08baa378a8 |
######################################################################
# Copyright (C) 2011,2012 Jaakko Luttinen
#
# This file is licensed under Version 3.0 of the GNU General Public
# License. See LICENSE for a text of the license.
######################################################################
###############... | nipunbatra/bayespy | bayespy/inference/vmp/tests/gp.py | Python | gpl-3.0 | 24,073 | [
"Gaussian"
] | d91cb7706b89fa6be5402c2cc025f0bceebe3d3617010f997d3a9d736db156db |
import networkx as nx
import os.path
import json
import random
from collections import OrderedDict
SIMNET_DATA = os.environ["SIMNETDATA"]
CONFIG_FILEPATH = os.path.join(SIMNET_DATA, "config.json")
DETAIL_CONFIG_FILEPATH = os.path.join(SIMNET_DATA, "details.json")
class DetailConfigGenerator:
def __init__(self, c... | BitfuryLightning/lnd-simnet-env | detalize.py | Python | mit | 4,142 | [
"Gaussian"
] | 9dc0ebc0e6d432c96c4e0c69cd5107fe25a622afe5fd983a66a2cac8763977ff |
#
# QAPI command marshaller generator
#
# Copyright IBM, Corp. 2011
# Copyright (C) 2014-2016 Red Hat, Inc.
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
# Michael Roth <mdroth@linux.vnet.ibm.com>
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
#... | gongleiarei/qemu | scripts/qapi-commands.py | Python | gpl-2.0 | 7,383 | [
"VisIt"
] | f4bfccd1f884affb6222cd2e06bf9b5c3ac154d3dab1e6d4b87a12c033bcf9f1 |
from django.db import models
from django.utils import timezone
from django.utils.functional import cached_property
from dateutil.relativedelta import relativedelta
class Membership(models.Model):
created_at = models.DateTimeField(auto_now_add=True)
modified_at = models.DateTimeField(auto_now=True)
renewe... | BridgeCityBicycleCoop/workstand | core/models.py | Python | mit | 2,527 | [
"VisIt"
] | e3ea067b0236ed227eacdd1effdcea14274522ec291fef4c0ac00c512a5963a7 |
# -*- coding: utf-8 -*-
# Unit tests for cache framework
# Uses whatever cache backend is set in the test settings file.
from __future__ import unicode_literals
import copy
import os
import re
import shutil
import tempfile
import threading
import time
import unittest
import warnings
from django.conf import settings
... | Endika/django | tests/cache/tests.py | Python | bsd-3-clause | 85,960 | [
"Brian"
] | 8400c4115425ee1a9fe0e6caa723299c81d24f1033856769a4396775a90d318f |
#*******************************************************************
#* File: RandNumTest.py
#* Description: Common utility functions for testing rngs.
#* Author: Subhasis Ray
#* E-mail: ray dot subhasis at gmail dot com
#* Created: 2008-09-19 14:22:13
#*************************... | BhallaLab/moose-thalamocortical | pymoose/tests/randnum/RandNumTestCase.py | Python | lgpl-2.1 | 1,801 | [
"MOOSE"
] | 59ff145901068320bfc59048f4554e2044abbc146509e30be20aba1871422f09 |
# 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... | hmenke/espresso | src/python/object_in_fluid/__init__.py | Python | gpl-3.0 | 1,355 | [
"ESPResSo"
] | 8d361c238d5159e25350413a0e737d3c44bb5e838ad26b0245f566e968dda209 |
# -*- coding: utf-8 -*-
# Copyright (c) 2008, Armin Ronacher
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# Redistributions of source code must retain the above copyright notice,
# this l... | walterbender/turtleflags | TurtleArt/util/codegen.py | Python | mit | 18,799 | [
"VisIt"
] | 060a22dedfd943232eb53ce193bf6c7ddef903ca4e8d4135ed9d76f6e601d071 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# Copyright 2022 The NiPreps Developers <nipreps@gmail.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... | oesteban/fmriprep | fmriprep/workflows/bold/confounds.py | Python | bsd-3-clause | 40,329 | [
"Gaussian"
] | 2fb369fd87dcd1b5ab666f982c9cadf0564cb3ee22d7ecb34cffafd0f8e70c2d |
#! /usr/bin/env python
#
# Copyright (C) 2015-2016 Rich Lewis <rl403@cam.ac.uk>
# License: 3-clause BSD
import pytest
import numpy as np
import pandas as pd
from ...core import atom, Mol
from . import example_mol # provides m fixture
@pytest.fixture(name='plat')
def plat_mol():
return Mol.from_smiles('[Pt]')
... | richlewis42/scikit-chem | skchem/test/test_core/test_atom.py | Python | bsd-3-clause | 10,497 | [
"RDKit"
] | e98b229f382deda6ae46d9f1a840f7058ac7c8841ca3aa6e2701075fbe9c3c03 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides so-called "strategies" to determine the coordination environments of an atom in a structure.
Some strategies can favour larger or smal... | setten/pymatgen | pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py | Python | mit | 98,567 | [
"pymatgen"
] | 6d794ce4b82354280844e0459c0d559c96fb496555be1ff5525ff236cd4647ea |
import os, sys
import vtk
from vtk.test import Testing
if sys.hexversion < 0x03000000:
# for Python2
import Tkinter as tkinter
from Tkinter import Pack
else:
# for Python3
import tkinter
from tkinter import Pack
from vtk.tk.vtkTkRenderWindowInteractor import vtkTkRenderWindowInteractor
class... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Rendering/Tk/Testing/Python/TestTkRenderWindowInteractor.py | Python | gpl-3.0 | 2,083 | [
"VTK"
] | d0110ef4d988df4eba87e654cce3e419dc05703979d1110afe16f305b04dfbb3 |
# -*- coding: utf-8 -*-
# This program is free software; you can redistribute it and/or modify it under
# the terms of the (LGPL) GNU Lesser General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distri... | andersinno/suds-jurko | tests/test_cache.py | Python | lgpl-3.0 | 39,749 | [
"Firefly"
] | f2f4e92545463d6a5cae17e87d1415162da3a92800b02bbc90da417222af6e62 |
import unittest
import sys
sys.path=['..'] + sys.path
from Exceptions import *
from Parser import Parser,ProgramParser # code from module you're testing
class SimpleTests(unittest.TestCase):
def setUp(self):
"""Call before every test case."""
self.parser = Parser()
def t... | nevillegrech/stdl | src/STDL/Tests/ParserTest.py | Python | epl-1.0 | 7,349 | [
"ADF"
] | 79bba114fc493865b32fa2367bb70a00149c6b2c9e0d64c9e2e986ca4ef26497 |
from base import *
from atom import *
from quilt import *
import runtime
import vat
CFGFuncState = DT('CFGFuncState',
('pendingExits', {int: ['*Block']}),
('gcVars', ['*Var']),
('pastBlocks', [Block]))
CFGFUNC = new_env('CFGFUNC', CFGFuncState)
CFGScopeState = DT('CFGScopeState',
('bl... | pshc/archipelago | flatten.py | Python | mit | 34,669 | [
"VisIt"
] | 0ac7a5796c5981b44859ef53e9e6427ff3d8da81ea962ca8d38c420eaed19b87 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2010 Prof. William H. Green (whgreen@mit.edu) and the
# RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of c... | nickvandewiele/RMG-Py | rmgpy/data/thermo.py | Python | mit | 64,446 | [
"VisIt"
] | dd649d8d68957aecebad5015d770b57f31936b621daf5e9594266b8e27a5a99a |
import numpy as np
import tensorflow as tf
from tensorflow.examples.tutorials.mnist import input_data
import matplotlib.pyplot as plt
def xavier_init(fan_in, fan_out, constant=1):
""" Xavier initialization of network weights"""
# https://stackoverflow.com/questions/33640581/how-to-do-xavier-initialization-on-t... | thaihungle/deepexp | gan/vae.py | Python | mit | 11,214 | [
"Gaussian"
] | 5684b0823004524fd32d3da9a52c511ff445ff15e50b39abb4cf9d033a38761a |
# -----------------------------------------------------------------------
# Copyright: 2010-2018, imec Vision Lab, University of Antwerp
# 2013-2018, CWI, Amsterdam
#
# Contact: astra@astra-toolbox.com
# Website: http://www.astra-toolbox.com/
#
# This file is part of the ASTRA Toolbox.
#
#
# The ASTRA Toolbo... | kohr-h/astra-toolbox | samples/python/s014_FBP.py | Python | gpl-3.0 | 2,476 | [
"Gaussian"
] | 6c5f801065a9b633ee1d5726f472156820c5f9a5362a5959cc67c55dbde09cb8 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkXMLTreeReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.... | chrisidefix/devide | modules/vtk_basic/vtkXMLTreeReader.py | Python | bsd-3-clause | 480 | [
"VTK"
] | 5a8f9be8779f87f9bb88eb9ec2254be0650246b9c6f1333ef49fb11fcca635d5 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'feedIO.ui'
#
# Created: Wed Sep 28 00:29:14 2011
# by: PyQt4 UI code generator 4.7.4
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
class Ui_feedIO(object):
def setupUi(self, feedIO):
... | seejay/feedIO | feedio/UI/feedIO_ui.py | Python | gpl-3.0 | 27,339 | [
"VisIt"
] | bb316892f245c18ad7b26620405fd25e4240ac13f2af8ad67b7dad51d1ef25cb |
from __future__ import print_function
import numpy as np
from . import interpolation
def smoothed(spectrum, **kwargs):
sp = spectrum.copy()
sp.smooth(**kwargs)
return sp
def smooth(data, smooth, smoothtype='gaussian', downsample=True,
downsample_factor=None, convmode='same'):
"""
Smooth... | vlas-sokolov/pyspeckit | pyspeckit/spectrum/smooth.py | Python | mit | 3,104 | [
"Gaussian"
] | c37b8657964f894ef12c1054f9bb390a19ff7424edff001f7d08e606122059cd |
try:
from paraview import vtk
except:
import vtk
try:
from paraview import numpy_support
except:
from vtk.util import numpy_support
try:
from paraview.vtk import vtkFiltersGeneral
except:
pass
import numpy
import copy
from fonctions_basiques import *
from objets import Ob... | aurmarsan/pyturbo | calculs.py | Python | mit | 62,423 | [
"ParaView",
"VTK"
] | 4fc635e774b25e242d78249d61175d229e6ae2c08a6b4836a90734b8e4833079 |
"""@namespace IMP.EMageFit.domino_model
Classes to manage a model using DOMINO.
"""
import sys
import time
import csv
import logging
log = logging.getLogger("DominoModel")
import IMP
import IMP.domino as domino
import IMP.core as core
import IMP.container as container
import IMP.display as display
import IMP.atom ... | shanot/imp | modules/EMageFit/pyext/src/domino_model.py | Python | gpl-3.0 | 51,066 | [
"Gaussian"
] | a682d1b77c95b4592d7f3ae414a7bbf52109ca1658252a75c545081d463abc0d |
import warnings
warnings.warn("pymatgen.serializers.json_coders has been moved to "
"pymatgen.util.serialization. This stub will be removed in pmg "
"2018.01.01.")
from pymatgen.util.serialization import *
| matk86/pymatgen | pymatgen/serializers/json_coders.py | Python | mit | 236 | [
"pymatgen"
] | f80004a7ecd214fd4423f694b6c7abaa820c00989031654e352d39dfa21393cd |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2009, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.community.SuSE | ZenPacks/community/SuSE/modeler/plugins/zenoss/cmd/linux/suse_uname_a.py | Python | gpl-2.0 | 1,622 | [
"VisIt"
] | 94e152738632b0a8af6d7bb333454235b783a58e53c900037c82b7092ccd3eaf |
import contextlib
import datetime
import os
import time
import threading
try:
# If galaxy-lib or Galaxy 19.05 present.
from galaxy.tools.deps.dependencies import DependenciesDescription
except ImportError:
# If galaxy-tool-util or Galaxy 19.09 present.
from galaxy.tool_util.deps.dependencies import Dep... | galaxyproject/pulsar | pulsar/managers/stateful.py | Python | apache-2.0 | 17,983 | [
"Galaxy"
] | f51e6c1baf436e0f220753de2bc838f64363a9401edcb6c1079db2e20a7c70e6 |
#!/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 (C) 2012-2013 Heiko Strathmann
#
from ... | AzamYahya/shogun | examples/undocumented/python_modular/statistics_mmd_kernel_selection_single.py | Python | gpl-3.0 | 4,227 | [
"Gaussian"
] | e6dd70ba4e674a7d1255401e3540952d1678360efaf6eb985eb95f6c8bbfd463 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#This module calculates statistics and saves it to a file
import numpy as np
from scipy import stats as scstats
from tkinter import font as tkfont
import tkinter as tk
import stat_functions as stat
import functions as fu
import model_parser
import time
STANDARD_LENGTH=8
... | espensirnes/paneltime | paneltime/output.py | Python | gpl-3.0 | 20,136 | [
"ADF"
] | 7dd2b61870555d92fd37837089c32ad2ffe27ecd60e4bfedb6b27a2e142d4a09 |
"""Fork of urllib2.
When reading this, don't assume that all code in here is reachable. Code in
the rest of mechanize may be used instead.
Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Python
Software Foundation; All Rights Reserved
Copyright 2002-2009 John J Lee <jjl@pobox.com>
This code is f... | amohanta/yalih | mechanize/_urllib2_fork.py | Python | apache-2.0 | 49,460 | [
"VisIt"
] | 2aade67cdd296bb125939d0f03d3ce23bc341290e0007b3198491d51fe180149 |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | social/urls.py | Python | gpl-3.0 | 1,693 | [
"Brian"
] | 5e658890ec22ca17f866beb6cadba74cbe391c0294606458a83ddd5f625c050d |
""""
scTDA. Library for topological data analysis of high-throughput single-cell RNA-seq data.
Copyright 2017, Pablo G. Camara, Columbia University. All rights reserved.
"""
__author__ = "Pablo G. Camara"
__maintainer__ = "Pablo G. Camara"
__email__ = "pablo.g.camara@gmail.com"
__credits__ = "Patrick van Nieuwenhuiz... | pcamara/scTDA | scTDA/main.py | Python | gpl-3.0 | 97,795 | [
"HTSeq"
] | 065d4687352bec4d21cfe04b1f28a17e221064991f5bb20287c97f280d4c3890 |
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