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# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/core/ui/filerenamedialog.py | Python | gpl-2.0 | 3,645 | [
"Brian"
] | a96b744ba41a1af08d083a1d200a30dce560d3c56add7b59565e158135320c05 |
from __future__ import annotations
from xia2.Experts.LatticeExpert import ApplyLattice
def _parse_idxref_lp_distance_etc(lp_file_lines):
"""Parse the LP file for refined distance, beam centre and so on..."""
beam = None
distance = None
for line in lp_file_lines:
if "DETECTOR COORDINATES" in... | xia2/xia2 | src/xia2/Wrappers/XDS/XDSIdxrefHelpers.py | Python | bsd-3-clause | 4,484 | [
"CRYSTAL"
] | f929f606009d7a4a51b8ed74115d6e6de1d16217e719f58debacddbfeaa38910 |
"""
Support for netcdftime axis in matplotlib.
"""
from __future__ import (absolute_import, division, print_function)
from six.moves import (filter, input, map, range, zip) # noqa
from collections import namedtuple
import matplotlib.dates as mdates
import matplotlib.ticker as mticker
import matplotlib.transforms a... | lbdreyer/nc-time-axis | nc_time_axis/__init__.py | Python | bsd-3-clause | 10,445 | [
"NetCDF"
] | 8a001fdb04cd962e02d5dfa971e24f0ed2c8d189a7c5c4a12a581ea24f3e8e6e |
#Time series example: generate series, visualize, regression
import numpy as np
from statsmodels.tsa.stattools import acf,pacf
from statsmodels.tsa import ar_model
import matplotlib.pyplot as plt
import pandas as pd
def ar1(phi,n):
"""
Generates an instance of an AR(1) process with Gaussian white noise
phi... | tobanw/py-econ-examples | timeseries.py | Python | mit | 2,106 | [
"Gaussian"
] | e53da215fb60324a8320a29426151ab2cc5afb042947c251866354b972b9a012 |
from __future__ import division, print_function, absolute_import
import warnings
import numpy as np
from numpy import array
from numpy.testing import (assert_array_almost_equal, assert_array_equal,
run_module_suite, assert_raises, assert_allclose)
from scipy import signal
window_funcs = [
... | mortonjt/scipy | scipy/signal/tests/test_windows.py | Python | bsd-3-clause | 7,808 | [
"Gaussian"
] | c10c4ca6abdd45dc5ecc4078df915231884c5a294ad126e71c4a742bb03fd413 |
#!/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... | dustymabe/ansible-modules-core | cloud/amazon/ec2_elb_lb.py | Python | gpl-3.0 | 52,548 | [
"Dalton"
] | 17d44f53174008b6a16aabef08aae248f795e16803e92cc9e1c2f7d1b2fbe716 |
#
# Copyright 2020-2021 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# 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 F... | libAtoms/matscipy | scripts/fracture_mechanics/sinclair_continuation.py | Python | lgpl-2.1 | 6,825 | [
"ASE",
"Matscipy"
] | 579b76e1be7217b9c9edfb9b2cbda3d150da0296486d8e9a7a88400862cb471d |
import random
from vtk import *
n = 10000
qinit = vtkQtInitialization()
pd = vtkPolyData()
pts = vtkPoints()
verts = vtkCellArray()
orient = vtkDoubleArray()
orient.SetName('orientation')
label = vtkStringArray()
label.SetName('label')
for i in range(n):
pts.InsertNextPoint(random.random(), random.random(), rando... | berendkleinhaneveld/VTK | Examples/Infovis/Python/labels.py | Python | bsd-3-clause | 1,411 | [
"VTK"
] | 997e37bc697a2993236d9b7d8d085a68fbb791d134f97d0f5aaccb6dc147236e |
# -*- mode: python; -*-
##
## Check if all the necessary modules to run MISO are available
##
import time
import os
import misopy
import misopy.misc_utils as utils
def check_module_availability(required_modules):
unavailable_mods = 0
print "Checking availability of Python modules for MISO"
print "Looking ... | kdaily/altanalyze | misopy/module_availability.py | Python | apache-2.0 | 2,478 | [
"pysam"
] | 77d565cff55ec3e23c03fd3e4f57d525a3ec36ce0455eacb2b0f091d24f215a9 |
#!/opt/local/bin/python
"""
Calculate elastic constants, C11, C12, C44,
Young's modulus, poison's ratio, and shear modulus,
by static method which measures energy differences
w.r.t. given strains.
Usage:
elastic_constants.py [options]
Options:
-h, --help Show this help message and exit.
-n NITER Number of p... | ryokbys/nap | nappy/vasp/elastic_constants.py | Python | mit | 8,539 | [
"VASP"
] | bb55acbf6dde469bc9e8f00ec10b7d2e1b77c37fab53774b4baef48a38e4f1f0 |
# Orca
#
# Copyright 2013 The Orca Team.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library is ... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/evince/__init__.py | Python | gpl-3.0 | 831 | [
"ORCA"
] | fb686a67611c3d15e12c7ae48778751d0a6a606ca1935f5bf6495ab326e521e7 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | wdwvt1/scikit-bio | skbio/sequence/tests/test_sequence.py | Python | bsd-3-clause | 104,848 | [
"scikit-bio"
] | f4567ac868c8070ba5c6393b8670206f6f3a8735388c4f03ff588c5937fdd628 |
import os
import netCDF4 as nc
from .base_grid import BaseGrid
class OasisGrid(BaseGrid):
"""
Python representation of OASIS grid including:
- grid cell centre and corners
- grid cell area
- grid cell masking
"""
def __init__(self, grid_name, model_grid):
# OASIS want... | DoublePrecision/esmgrids | esmgrids/oasis_grid.py | Python | apache-2.0 | 9,345 | [
"NetCDF"
] | 867a08f08254210a4b4797188d6d0eb19fa23a3074862f1f761a195e795329ec |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# @author: Li Li (lili@bnl.g... | ericdill/scikit-beam-examples | demos/xrf/demo_xrf_spectrum.py | Python | bsd-3-clause | 5,373 | [
"Gaussian"
] | 12eedbb9af7a629181896bd0b76bd1f563e71fce939e09e8732ced95ae0ce48c |
# -*- coding: utf-8 -*-
"""
This module calculates a linear system by Gaussian elimination with pivoting.
Almost a copy of on Mike Zingale's code, spring 2013.
"""
import numpy as npy
import os
def gaussElim(A, b):
""" perform gaussian elimination with pivoting, solving A x = b A
is an NxN matri... | NicovincX2/Python-3.5 | Analyse (mathématiques)/Analyse numérique/Conditionnement/gaussElimination.py | Python | gpl-3.0 | 2,193 | [
"Gaussian"
] | 4ad580a86da44729fc4714f8ced8c43b1675b1fb323ae48ccfdc7c9663742f69 |
##
# Copyright 2009-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | akesandgren/easybuild-easyblocks | easybuild/easyblocks/n/neuron.py | Python | gpl-2.0 | 8,950 | [
"NEURON"
] | 727c840c3ccd81cd16d87e627b306a5f3c0442689fd9fbe14904463fcffc4c4e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""fitting.py -- Default posterior probability function and high-level fitting
methods for prospector
"""
import time
from functools import partial as argfix
import numpy as np
from scipy.optimize import minimize, least_squares
import warnings
from .minimizer import mi... | bd-j/prospector | prospect/fitting/fitting.py | Python | mit | 19,433 | [
"Gaussian"
] | bd5a9522f15f8d2ed80dc77aa95a173201dcc72a3bc535ab941bf419f224b91c |
from urllib.parse import urlparse
from bears.general.URLHeadBear import URLHeadBear
from coalib.bears.LocalBear import LocalBear
from coalib.results.Result import Result
from coalib.results.RESULT_SEVERITY import RESULT_SEVERITY
from coalib.results.Diff import Diff
from coalib.settings.Setting import typed_dict
cla... | coala/coala-bears | bears/general/HTTPSBear.py | Python | agpl-3.0 | 3,682 | [
"VisIt"
] | 8b046cfc630464f65b9ffdf41bf4791a641d21cf77079f479485127c2635fe23 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/songs/lib/openlyricsimport.py | Python | gpl-2.0 | 4,131 | [
"Brian"
] | e5fcd2c1ffe5dc54e16a053cad12c2edac2ef412508cbf50b90e7479584f2524 |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# 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 ver... | spring01/libPSI | lib/python/qcdb/exceptions.py | Python | gpl-2.0 | 1,949 | [
"Psi4"
] | c9fe730dfc09f6d5de1a55065df36fe87b28755e2a214c5e36dabf1a2200d039 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | mcsalgado/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 17,328 | [
"Galaxy"
] | 60d8770d7a26d1230d54cb36e1d50b5aa6dffa7211d4721c9343a151af645677 |
# -*- coding: utf-8 -*-
"""
Created on Tue May 20 08:48:44 2014
@author: B Poon (demure) v2
Worksheet: Interpreting Galaxy Redshift Survey Data: Sky Coordinates
"""
#import modules
import numpy as np
from matplotlib import pyplot as plt
from math import *
def plotter(filepath, color, x, y, xname, yname,find=-1,
... | brupoon/nextTwilight | glx_skycoord2.py | Python | mit | 1,975 | [
"Galaxy"
] | 400071ba44287db5a3f7a127b9b4f8b2943aeac1a3edd2942bff0b81c4abee9d |
# -*- coding: utf-8 -*-
"""pyfttt.py - Send IFTTT Webhooks Channel Events"""
import argparse
import os
import sys
import requests
import pyfttt
def parse_arguments():
"""Parse command line arguments"""
parser = argparse.ArgumentParser(prog=sys.argv[0],
description='Sen... | briandconnelly/pyfttt | pyfttt/cmd_script.py | Python | bsd-2-clause | 2,635 | [
"VisIt"
] | 8949367eb766794d4b97a014ee3e17d37fd7aa6ec1f0fd2d9d0306aa3813f7b8 |
import Base
import VS
import gettext
shipsize = VS.getPlayer().rSize()/35
#print "Ship Size: " + str(shipsize) #debug
# rooms
landing = Base.Room ('Landing Pad')
Base.Texture (landing, 'tex', 'bases/forest/landing.sprite', 0, 0)
Base.Ship (landing, 'ship_l', (-0.3, -0.3, 5/shipsize), (0.20, 1, -0.20), (-1, 0, -1))
l... | costalfy/Vega-Strike | data/bases/forest.py | Python | gpl-2.0 | 2,602 | [
"VisIt"
] | 2a030d871fd8c20684e105264311676cea59cc5e760e26c4dc43ea86c54e5b45 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | photoninger/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 42,383 | [
"VisIt"
] | 8d7750fa3de59f196fe85507f0e822ca27cacaf9d6907148a60bccd8357d0fe9 |
"""
@author: thom
"""
import math
from rdkit.Chem import AllChem as Chem
import pymunk as pm
from kinetics_2D import Kinetics2D
from molecule import Molecule
class KineticMolecule(Molecule):
"""A base representation of a Molecule with potential, kinetic and internal energy.
* Potential energy is the ener... | th0mmeke/toyworld | kinetic_molecule.py | Python | gpl-3.0 | 6,929 | [
"RDKit"
] | afac30a16de251b85051b9b6f5e0b8c12fb1ca3af03d30cbfe2921601c878044 |
"""
A collection of functions to find the weights and abscissas for
Gaussian Quadrature.
These calculations are done by finding the eigenvalues of a
tridiagonal matrix whose entries are dependent on the coefficients
in the recursion formula for the orthogonal polynomials with the
corresponding weighting function over ... | e-q/scipy | scipy/special/orthogonal.py | Python | bsd-3-clause | 63,520 | [
"Gaussian"
] | 0c5da8d1e2a1a8613dddb6ad828c043005ff606b337a1d000f80b736a867e225 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import sys
class Xsdk(BundlePackage):
"""Xsdk is a suite of Department of Energy (DOE) packages... | rspavel/spack | var/spack/repos/builtin/packages/xsdk/package.py | Python | lgpl-2.1 | 9,658 | [
"NetCDF"
] | 2cfbe546f559adf5677947096637c4eaf2724a71c915e26beb5c92a0bbd9f966 |
from .compat import with_metaclass
class GenericMeta(type):
def __repr__(cls):
return cls.__name__
def accept(self, visitor):
raise NotImplementedError
class BoolTypeMeta(GenericMeta):
def __repr__(cls):
return 'bool'
def accept(cls, visitor):
return visitor.visit... | vmagamedov/kinko | kinko/types.py | Python | bsd-3-clause | 8,583 | [
"VisIt"
] | 732d523473217addb83a8eaeab4a8328a0de707d0226d276de62d56ae3993748 |
"""Define the public 'draw' function to be used to draw morphology using plotly."""
from __future__ import absolute_import # prevents name clash with local plotly module
from itertools import chain
import numpy as np
try:
import plotly.graph_objs as go
from plotly.offline import plot, iplot, init_notebook_mo... | wizmer/NeuroM | neurom/view/plotly.py | Python | bsd-3-clause | 4,951 | [
"NEURON"
] | 7dbba40af5954482396996ea5d200ab23f9a13d772d45ea9db2a1f166c2b343a |
#!/usr/bin/env python
"""
A VCHILL archive server for NetCDF files that uses threads to handle multiple clients at a time.
Last modified: 2007-07-13
"""
import array
import fpconst
import gzip
import os
import pycdf
import select
import socket
import struct
import sys
import threading
config = {}
exec open("vchill_n... | CSU-RADAR-GROUP/VCHILL | netcdf_server/vchill_netcdf_server.py | Python | gpl-3.0 | 25,691 | [
"NetCDF"
] | 22bb8ba6dc2ec996cc3425b51c050bf120fe6ef3986018986ec5f8de6bb7ada6 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/crystal/test_splitconfigs.py | Python | gpl-3.0 | 2,864 | [
"CRYSTAL",
"VASP"
] | 9572e7dc0d9075a0e5096df144ff47b9e842aa29bf8755f86a88305d1ca9a7f8 |
#-*- coding:utf-8 -*-
'''
Normal Distribution, also called Gaussian Distribution
'''
import numpy as np
import matplotlib.pyplot as plt
def simple_plot():
x = np.linspace(0, 10, 10000)
y = np.random.normal(0, x)
z = np.cos(x**2)
plt.figure(figsize = (8, 4))
plt.plot(x, y, label = "sin(x)", color ... | Justontheway/data-science | python/distribution/Gaussian.py | Python | apache-2.0 | 1,404 | [
"Gaussian"
] | 86ea7e3576b7ec9c711b098faa41ecddeb4c2b2be2148dbb05bc0db9c8c5a497 |
import unittest
import uuid
from datetime import datetime, timedelta
import pybrightcove
import mock
# httplib.HTTPConnection
# httplib.HTTPSConnection
# urllib2.urlopen
# tempfile.mkstemp
# ftplib.FTP
class APIConnectionTest(unittest.TestCase):
def setUp(self):
self.api = pybrightcove.connection.APIConn... | kingcons/pybrightcove | tests/test_connection.py | Python | mit | 3,246 | [
"exciting"
] | de59d97efa4262e7fd91107ed51229e008ed8b7c12a5c69391376e1365b349cf |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/procrouting/dft_funcs/double_hyb_superfuncs.py | Python | lgpl-3.0 | 10,523 | [
"Psi4"
] | a3da9c1006452736a9b5274fdac1695f821e0598b37d5d9575c348e479a5a1d5 |
"""
Acceptance tests for the Import and Export pages
"""
from __future__ import absolute_import
from abc import abstractmethod
from datetime import datetime
from common.test.acceptance.pages.studio.import_export import (
ExportCoursePage,
ExportLibraryPage,
ImportCoursePage,
ImportLibraryPage
)
from c... | ESOedX/edx-platform | common/test/acceptance/tests/studio/test_import_export.py | Python | agpl-3.0 | 7,883 | [
"VisIt"
] | 937fbff2f21242647ba8c2a26cd8dc8e3df28ed3b14f3e74b54e5353d0e4d900 |
# -*- coding: utf-8 -*-
"""
We expect XML file with cluster defined by one algo.
For each Page:
We tabulate the clusters (build a table where each cluster is a cell)
We compute the row, col, row_span, col_span attributes of each cluster
Overwrite the input XML files, adding attributes to the cluster definiti... | Transkribus/TranskribusDU | TranskribusDU/tasks/tabulate_cell_cluster.py | Python | bsd-3-clause | 25,014 | [
"VisIt"
] | 26d067d9c7c8026fc17b95cd0855ae3c0bda7edb224d0bd09f217f3352589b8b |
#
# Copyright (C) 2013-2019 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... | psci2195/espresso-ffans | samples/lj_liquid_distribution.py | Python | gpl-3.0 | 6,052 | [
"ESPResSo"
] | 9f5e0e524a30a7c1082c02a82c0165814304037a75bc7b5988ddbd4e9697e7e2 |
"""
blast related classes and functions
"""
from .RestLib import print_rest_table_contents
from .LatexLib import LatexReportCreator
from .ExpressionLib import read_RSEM_counts_files,read_matrix,read_de_results
from .Heatmap import Heatmap
| ajrichards/htsint | htsint/tools/__init__.py | Python | bsd-3-clause | 241 | [
"BLAST"
] | f0a51182bc120595ada88fdaa6ef14df5b847518378340f07fb61711fe0d8362 |
import os
import signal
from toga.interface.app import App as AppInterface
from .libs import *
from .window import Window
from .widgets.icon import Icon, TIBERIUS_ICON
class MainWindow(Window):
def __init__(self, title=None, position=(100, 100), size=(640, 480)):
super(MainWindow, self).__init__(title, ... | pybee/toga-cocoa | toga_cocoa/app.py | Python | bsd-3-clause | 5,088 | [
"VisIt"
] | 03763a2d91cf42bffe8fd12c30699f170bbee6f649863e0dede40354bcf7f69f |
#!/usr/bin/python
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | google/fplutil | bin/setup_all_prereqs.py | Python | apache-2.0 | 19,014 | [
"VisIt"
] | fb77ca74042dc32aca0404625dd1da4bea725aaea11d730c9182fca4edfe6b30 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from spark.node import Input, Output
from spark.simulation import Simulation, SimulationError
from .neuron import RbfNeuron
from .accumulator import Accumulator
class RbfSimulation(Simulation):
'''
A radial basis function simulation.
'''
... | CtrlC-Root/cse5526 | spark/rbf/simulation.py | Python | mit | 2,636 | [
"NEURON"
] | f35f491399ad0f175bd92750370d85abbd935104686da8cb8728e32751087e89 |
import configparser
import logging
import tkinter as tk
from pathlib import Path
class OutputParameters(object):
def __init__(self, master):
self.config = configparser.ConfigParser()
self.logger = logging.getLogger(__name__)
self.absolute_intensity = tk.IntVar()
self.relative_inte... | Tarskin/HappyTools | HappyTools/bin/output_parameters.py | Python | apache-2.0 | 3,658 | [
"Gaussian"
] | 5358951a7f50bc904bd1c0bdbd82ed2f06656288f60500cf1efdf93e6ba303eb |
""" The gateway service is used for forwarding service calls to the appropriate services.
For this to be used, the following CS option is required::
DIRAC
{
Gateways
{
my.site.org = dips://thisIsAn.url.org:9159/Framework/Gateway
}
}
At the same time, this s... | ic-hep/DIRAC | src/DIRAC/Core/DISET/private/GatewayService.py | Python | gpl-3.0 | 21,104 | [
"DIRAC"
] | 56f97b3b05447b8c0b2e8efafe4e5dd6ffdefc38aeb7b60a3d44a776812d6d6a |
"""
See the PyMOL Sessions processed with this code here <https://github.com/mmagnus/PyMOL4Spliceosome>
"""
from pymol import cmd
from rna_tools.tools.PyMOL4RNA import code_for_color_spl
from rna_tools.tools.PyMOL4RNA import code_for_spl
try:
from pymol import cmd
except ImportError:
print("PyMOL Python lib is... | m4rx9/rna-pdb-tools | rna_tools/tools/PyMOL4RNA/PyMOL4Spliceosome.py | Python | mit | 13,336 | [
"PyMOL"
] | 3507247a491bc7536b57018a0c1f5b36989c2570e0e33e52ecf07c8753cb3fa8 |
# $Id$
'''
C0-C1-N2-C3-C4-N5-C6-C7-N8-C9
|| || ||
O O O
Problem:
known all bond length and bond angles, fix torsion angle between C(=O)
and N, known coordinates of C0, C1, N8, C9, calculate all other
coordinates.
Solution:
detect circle of N2
for each N2 on the circle of N2
calc... | lidaobing/itcc | itcc/ccs2/mezeipro2.py | Python | gpl-3.0 | 9,857 | [
"TINKER"
] | 2d42f2192653431690113b50c94f9a912fa597603cfc7ec824e8e9adadb0d49d |
# -*- coding: utf-8 -*-
import ast
import json
import os
import re
import time
import python_minifier
import git
class Visitor(ast.NodeVisitor):
"""Used to list all the modules imported by a script."""
def __init__(self, lib_path, package):
self.imports = set()
self.lib_path = lib_path
... | kikocorreoso/brython | scripts/make_VFS.py | Python | bsd-3-clause | 5,593 | [
"VisIt"
] | 230fce17a6f5af7b025b3ac3b9e9fa42ea55c0895c3acede40d23afd5958183c |
#!/usr/bin/env python
#
# $File: vspSelector.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribut... | BoPeng/simuPOP | docs/vspSelector.py | Python | gpl-2.0 | 1,848 | [
"VisIt"
] | 036cf04442668c1111b68960efa28d5d1742528df5f0e29edbaec3ff2673c7eb |
'''
Task Coach - Your friendly task manager
Copyright (C) 2004-2010 Task Coach developers <developers@taskcoach.org>
Task Coach 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
... | wdmchaft/taskcoach | taskcoachlib/help/tips.py | Python | gpl-3.0 | 4,343 | [
"VisIt"
] | c2450e4f71c04f294a2a0dbd70ed05e2c15ce312c5dfe61f553e6f23d2f56b21 |
# 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)
import os
from spack import *
class Ferret(Package):
"""Ferret is an interactive computer visualization and analys... | LLNL/spack | var/spack/repos/builtin/packages/ferret/package.py | Python | lgpl-2.1 | 8,752 | [
"NetCDF"
] | 1911c7822ffc8b34e69ceda8342e7e09fe89a7e6683480ce7118a0dd61269d09 |
# coding: utf-8
"""tornado IOLoop API with zmq compatibility
If you have tornado ≥ 3.0, this is a subclass of tornado's IOLoop,
otherwise we ship a minimal subset of tornado in zmq.eventloop.minitornado.
The minimal shipped version of tornado's IOLoop does not include
support for concurrent futures - this will only b... | skycucumber/Messaging-Gateway | webapp/venv/lib/python2.7/site-packages/zmq/eventloop/ioloop.py | Python | gpl-2.0 | 6,416 | [
"Brian"
] | 241e05c584207ada130f6ca3c4af0c8472c561248b911126631fcc1f389ef85a |
#!/usr/bin/env python
# Initial author: Solaiappan Manimaran
# Gets alignment file (currently support sam or BLAST-m8 format (.bl8)) and runs EM algorithm.
# Outputs the pathogens rank in the sample as a report that can be opened in Excel.
# Optionally outputs an updated alignment file (sam/bl8)
#usage information: pa... | PathoScope/PathoScope | pathoscope/pathoid/pathoscope_id.py | Python | gpl-3.0 | 3,202 | [
"BLAST"
] | 803402fe92449d1563d1ee27ac77475fa45576240d142312c7c477d955b8a2e6 |
"""
Update the transformation files of active transformations,
given an InputDataQuery fetched from the Transformation Service.
Possibility to speedup the query time by only fetching files that were added since the last iteration.
Use the CS option RefreshOnly (False by default) and set the DateKey (empty by default) ... | ic-hep/DIRAC | src/DIRAC/TransformationSystem/Agent/InputDataAgent.py | Python | gpl-3.0 | 8,056 | [
"DIRAC"
] | 22d63b68d21b40baae14afe47b9f5c968bc92917ddb9613a629563b7f0e12c7e |
"""
=============================================
Integration and ODEs (:mod:`scipy.integrate`)
=============================================
.. currentmodule:: scipy.integrate
Integrating functions, given function object
============================================
.. autosummary::
:toctree: generated... | beiko-lab/gengis | bin/Lib/site-packages/scipy/integrate/__init__.py | Python | gpl-3.0 | 1,957 | [
"Gaussian"
] | a448d12fd7c7191f1bf8ab10497fa451d7218fb2017d3587539bba7333c88265 |
"""Tests for user-friendly public interface to polynomial functions. """
from sympy.polys.polytools import (
Poly, PurePoly, poly,
parallel_poly_from_expr,
degree, degree_list,
LC, LM, LT,
pdiv, prem, pquo, pexquo,
div, rem, quo, exquo,
half_gcdex, gcdex, invert,
subresultants,
resu... | AunShiLord/sympy | sympy/polys/tests/test_polytools.py | Python | bsd-3-clause | 105,739 | [
"Gaussian"
] | 9cff8b3ab0f4fc2e803798e55fb90f5445ea14dcc3f1ebea71192d2775cbb06a |
# Author: Brian Kirk
#This is a coded version of the directions in https://safe.nrao.edu/wiki/bin/view/ALMA/NAASC/Cycle2ImagingWorkflow
# The purpose of this is to get rid of the menial pre-imaging tasks outlined in the Cycle2 Imaging workflow; essentially, you'll "press for cheese"
import os
import urllib2
import s... | bmarshallk/NAASC | staging_scripts/StagingPipelineCalibration.py | Python | gpl-3.0 | 17,207 | [
"Brian"
] | a351e94411a6eb93c858f3a3797939554827fc3967c2985912688152dbe57646 |
import pele.amber.read_amber as amber
import networkx as nx
import playground.group_rotation.chirality as chirality
import playground.group_rotation.transforms as transforms
from playground.rotamer.measure_dihedral import dihedral_with_symmetry, symmetric_atoms
class Dihedral(object):
def __init__(self, dihedral_a... | khs26/pele | playground/rotamer/find_dihedrals.py | Python | gpl-3.0 | 4,822 | [
"Amber"
] | 0077f8791b3f46b00be0ecf8e2c537067fecf2877a3257b2fae49aaea81a69cd |
from ase.io import write
from gpaw import GPAW
calc = GPAW('anti.gpw')
atoms = calc.get_atoms()
up = calc.get_pseudo_density(0)
down = calc.get_pseudo_density(1)
zeta = (up - down) / (up + down)
write('magnetization.cube', atoms, data=zeta)
| robwarm/gpaw-symm | doc/exercises/dos/magnetization.py | Python | gpl-3.0 | 241 | [
"ASE",
"GPAW"
] | cd4c98b01030fe37a6cd517434b3e4e2662a6f73a050aa9a4e60a1ebd0a5a5bd |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it
# u... | dougxc/mx | mx_compat.py | Python | gpl-2.0 | 5,331 | [
"VisIt"
] | 8c9466160bac28f36c91e41101fdd0be8e4f55cdd2dc3bf5e151b9f2a60271df |
# -*- coding: utf-8 -*-
"""SQLite parser plugin for Mozilla Firefox history database files."""
from __future__ import unicode_literals
from dfdatetime import posix_time as dfdatetime_posix_time
from plaso.containers import events
from plaso.containers import time_events
from plaso.lib import definitions
from plaso.p... | rgayon/plaso | plaso/parsers/sqlite_plugins/firefox_history.py | Python | apache-2.0 | 18,595 | [
"VisIt"
] | beb0dfa90050cd8f4b67e3b907a90b837be6f14d53b7a5962d0d9f0cca6a7064 |
"""
Sample from Gaussian Processes
==============================
Helper functions to sample from a Gaussian process"""
import scipy as SP
def GP_sample_prior(covar,X,logtheta,ns=1):
"""
Create samples form a GP prior
**Parameters:**
X : [double]
inputs to sample from.
covar : :py:c... | PMBio/pygp | misc/gp_sample.py | Python | gpl-2.0 | 1,240 | [
"Gaussian"
] | f2a486841a71c0a9282d8519d445d2d6d10e5ce81740292b12d48d304a9d1469 |
"""
Author: Nicolas Cantale - n.cantale@gmail.com
Small module wrapping sextractor.
The idea is to have a single function taking an image and returning a
sextractor catalog.
Dependencies:
- sextractor (mandatory)
- astroasciidata (mandatory)
- numpy (optional, needed for the array support)
- pyfits (optional, ne... | japs/alipy | alipy/pysex.py | Python | gpl-3.0 | 7,717 | [
"Galaxy"
] | 780588cbd6690677ebcfff308cf5b17a0858615b2664b839c546dfd100a4121d |
from logging import INFO, getLogger, Formatter
from logging.handlers import TimedRotatingFileHandler
from gevent.wsgi import WSGIServer
import os
from octopus.app import create_app
from octopus.settings import ProdConfig
def main():
# Init the app
app = create_app(ProdConfig)
if not os.path.exists(os.path.dir... | quaintm/octopus | run_prod.py | Python | bsd-3-clause | 1,362 | [
"Octopus"
] | bb5e23e40c428678e1cf864c367f9081f39f314dfc3dc68fb568c5e8acea11f3 |
#!/usr/bin/python
"""
Copyright 2012 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 of th... | clreinki/GalaxyHarvester | feedback.py | Python | agpl-3.0 | 2,764 | [
"Galaxy"
] | 941bdb607172225feae44429aaeb3eec030af964f6b027f5deb20dc2f5cad5b9 |
# 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/emails/urls.py | Python | gpl-3.0 | 884 | [
"Brian"
] | 9365b66eb23de92672d96eb4cb83dea5b70af8ae77b8463017460924452349da |
from ase.dft.kpoints import get_bandpath
from qharv.inspect import axes_pos, volumetric, crystal
def cmca4_kpath(axes, npt=16):
G = [0.0, 0.0, 0.0]
Y = [0.5, -0.5, 0.0]
S = [0.5, 0.0, 0.0]
Z = [0.0, 0.0, 0.5]
kpts_reduced, kpath, sp_points = get_bandpath([G, Y, S, G, Z],
axes, npoints=npt)
return kp... | Paul-St-Young/solid_hydrogen | hsolid/dft/bands.py | Python | mit | 349 | [
"ASE",
"CRYSTAL"
] | d2d179f386ef5db45e01abe954b22aaa7504adf71492d023a8dc54bd4d2eebd3 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import os
import warnings
import numpy as np
from pymatgen.io.cif import CifParser, CifWriter, CifBlock
from pymatgen.io.vasp.inputs import Poscar
from... | migueldiascosta/pymatgen | pymatgen/io/tests/test_cif.py | Python | mit | 26,681 | [
"VASP",
"pymatgen"
] | 8257f5a8e5434d9c5c99530179022ece3786b009c8451c11aa18adf61e0bf60e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from __future__ import absolute_import, print_function
"""
This module provides classes used to enumerate surface sites
and to find adsorption sites on slabs
"... | matk86/pymatgen | pymatgen/analysis/adsorption.py | Python | mit | 30,056 | [
"Jmol",
"pymatgen"
] | 19ddb0bc6c9b9bff55ff509ac43902974cb0f25576b786f310c8127ba6dd7980 |
# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is... | sn-amber/mylpp | src/ensight.py | Python | gpl-2.0 | 16,419 | [
"LAMMPS"
] | c9768ce8d8e51ff5049206b702735d7abc269e3b78337dde3002541dbb6d5f91 |
#!/usr/bin/env python
#import genetic
from GEN.gene import gene
from GEN.indi import indi
from GEN import GEN
# GEN, indi, gene
import os
import sys
def gaussian(x, mu, sig):
import numpy as np
gaus = np.exp(-np.power((float(x) - float(mu))/float(sig), 2.) / 2.)
gaus /= ( 2. * np.pi * np.sqrt(float(sig)) )
return... | iljabek/genetic | Evol.py | Python | gpl-2.0 | 5,308 | [
"Gaussian"
] | 05f564aa2f34978f6343707730eca29cfd5d2bad5526ea3a537a07f935741fd5 |
"""
A set of functions to test out self supervised rotated coin image models
"""
import cPickle as pickle
import glob
import numpy as np
import operator
import os
import random
import shutil
import subprocess
import sys
import time
from itertools import islice
from subprocess import Popen
from multiprocessing import P... | GemHunt/sail | rotational/rotational.py | Python | mit | 42,978 | [
"Gaussian"
] | 508cbd88cc7cad88401cb3c241d66f7ff1014d1aa519af928fbf06ed551bc168 |
import isdhic
import random
import numpy as np
import pylab as plt
from isdhic.rex import Swaps, swap_rate
from csb.numeric import log_sum_exp
from test_mcmc import Gaussian
from collections import OrderedDict
def print_rex(states, swaps=[]):
s = []
for i, j in zip(states,states[1:]):
s.append(str(i)... | michaelhabeck/isdhic | tests/test_rex.py | Python | mit | 3,760 | [
"Gaussian"
] | 58d569983c1bde1e9d46fbce7e50a3e6664d4c9d58abb27d7187c5e0564a8130 |
import numpy as np
from scipy.signal import find_peaks_cwt
from scipy.optimize import curve_fit, minimize_scalar
# PEAKHUNT RANGE
peakhunt_range = 0.40
# HELPER FUNCTIONS
def default():
return labspec_fit
def methods():
return {'gauss_fit': {'function': gauss_fit,
'nam... | Baharis/pRuby | methods/peakhunt.py | Python | mit | 21,313 | [
"Gaussian"
] | 95e119145c4385d4d0cc4d3f01f75d0a82b55cc137685fc82b249e8cc1dd8d30 |
#!/usr/bin/env python
################################################################################
#
# This file is part of ghmm
#
# file: HMMEd.py
# author: Janne Grunau
#
# Copyright (C) 1998-2002, Alexander Schliep
#
# Contact: schliep@molgen.mpg... | lukefrasera/fatigueBSN | scripts/include/ghmm-0.9-rc3/HMMEd/HMMEditor.py | Python | gpl-3.0 | 23,318 | [
"Gaussian"
] | cae90278e2b314ca127d96d7b2aa78d095e5b1690819c0ed2282fb970a2b97ca |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pathlib import Path
import warnings
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.periodic_table import Element, Specie
from pymatgen.core.composition import Composition
from pymatgen.c... | montoyjh/pymatgen | pymatgen/core/tests/test_structure.py | Python | mit | 60,409 | [
"pymatgen"
] | 816b1aa03b2bdaff11ed3ad966d6d2b22751b40ada12a2e28ba0d36d48cc9471 |
import numpy as np
from ase.units import Bohr, Hartree
from ase.structure import bulk
from gpaw import GPAW
from gpaw.response.df import DF
from gpaw.response.bse import BSE
GS = 1
df = 1
bse = 1
check_spectrum = 1
if GS:
a = 4.043
atoms = bulk('Al', 'fcc', a=a)
atoms.center()
calc = GPAW(h=0.2,
... | qsnake/gpaw | gpaw/test/bse_aluminum.py | Python | gpl-3.0 | 1,539 | [
"ASE",
"GPAW"
] | a783cd491a47ac8994b5f8ca8dd5505fb964082ffbea7f8c27ba4c99bdbbd63b |
"""translate.py: translate DNA
Usage:
translate -d FILE [-p OUTFILE]
translate -h|--help
translate --version
Options:
-h|--help Show this screen.
--version Show version.
"""
from docopt import docopt
from mgescan.biopython import read_file, translate
from Bio.SeqRecord import SeqRecord
# Des... | MGEScan/mgescan | mgescan/nonltr/translate.py | Python | gpl-3.0 | 2,235 | [
"Biopython"
] | 7f9a611c1e13b1940c78a1af908dafbe464c1d53d7c3fc0d8ff51a4acb454b8e |
#!/usr/bin/env python
import numpy as np
from astropy.io import fits
class sdss_parse:
"""
The class is to parse sdss spectra.
It provides wavelength, flux, sigma_error, mask (valid pixels) arrays.
"""
def __init__(self, path_to_fits,flux_calib=False,off_set=0.0):
shift = 1. + off_se... | ezavarygin/specplot | specplot_tools/sdss_parse.py | Python | mit | 1,824 | [
"Gaussian"
] | 6e620309bdd13759629586f3278f4cee5f8b6963c486c36d8143cf0d42090576 |
"""A thorough test of polling REQ/REP sockets."""
#-----------------------------------------------------------------------------
# Copyright (c) 2010 Brian Granger
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING.BSD, distributed as part of this software.
#---------... | mgadi/naemonbox | sources/psdash/pyzmq-13.1.0/examples/poll/reqrep.py | Python | gpl-2.0 | 1,776 | [
"Brian"
] | 9fc37175af3874b7ff247c81e283384a0622b0fe4ba710f90751119d2dda5998 |
"""
Implementation of a language model class.
TODO: write more documentation
"""
__docformat__ = 'restructedtext en'
__authors__ = ("Razvan Pascanu "
"KyungHyun Cho "
"Caglar Gulcehre ")
__contact__ = "Razvan Pascanu <r.pascanu@gmail>"
import numpy
import itertools
import logging
impo... | vseledkin/LV_groundhog | groundhog/models/LM_model.py | Python | bsd-3-clause | 11,649 | [
"Gaussian"
] | 8ecf7bef43ed15504f88a1236577a6559e915a5d980642a436f7e526c6517a59 |
from unittest import TestCase
import pytest
from rdkit import Chem
import deepchem as dc
from deepchem.data import DiskDataset
from deepchem.feat.one_hot import zinc_charset
from deepchem.models.autoencoder_models.autoencoder import TensorflowMoleculeEncoder, TensorflowMoleculeDecoder
class TestTensorflowEncoders(T... | deepchem/deepchem | contrib/autoencoder_models/test_tensorflowEncoders.py | Python | mit | 1,443 | [
"RDKit"
] | e6e6d069595f3167206b3aca24b1d4d6e12e272158c0a4feab59461c13b298c2 |
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... | elhoim/MISP | app/files/scripts/misp2stix.py | Python | agpl-3.0 | 18,949 | [
"Amber"
] | d9808fb75a6374f6e97ff9e2e2714ac4260a822fe3cfba738753a0ef3c1ecf0d |
# * *************************************************************
# *
# * Soft Active Mater on Surfaces (SAMoS)
# *
# * Author: Rastko Sknepnek
# *
# * Division of Physics
# * School of Engineering, Physics and Mathematics
# * University of Dundee
# *
# * (c) 2013, 2014
# *
# * School of Scienc... | sknepneklab/SAMoS | utils/RastkoVisu/msd.py | Python | gpl-3.0 | 3,559 | [
"VTK"
] | 111f2c5ca36da0b5c83cb1ba2bc81a3a1ac4c2f28930feccea2ce918b668a12f |
# -*- coding: utf-8 -*-
#
# YANK documentation build configuration file, created by templating the MDTraj config file from
# sphinx-quickstart on Tue Jun 11 21:23:28 2013.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present i... | choderalab/yank | docs/conf.py | Python | mit | 9,349 | [
"MDTraj"
] | d78d2e617f4b882eecb5d978fa56add18507618cf7f81e5cac2b069c58bc4dbb |
import os, requests, json, string, datetime, logging, time, csv
from os.path import join, dirname
# __file__ refers to the file settings.py
APP_PROFILE_API = os.path.dirname(os.path.abspath(__file__))
logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')
logging_comp_name ... | WASdev/sample.voice.gateway | soe/python/callerProfileAPI/callerProfileAPI.py | Python | apache-2.0 | 8,882 | [
"Brian"
] | 34c6cfc742f87a46b85d502ce192b4c58dc3791942b67a23d99d56d88c5f6082 |
class Room(object):
def __init__(self, name, description):
self.name = name
self.description = description
self.paths = {}
def go(self, direction):
return self.paths.get(direction, None)
def add_paths(self, paths):
self.paths.update(paths)
central_corridor = Ro... | zedshaw/learn-python3-thw-code | ex52/gothonweb/gothonweb/planisphere.py | Python | mit | 4,537 | [
"BLAST"
] | eeb477f8aeb61550defeeaba01b61acb26d64ea48d0bbb989da57d551b23ecb6 |
# Natural Language Toolkit: Conditional Random Fields
#
# Copyright (C) 2001-2012 NLTK Project
# Author: Edward Loper <edloper@gradient.cis.upenn.edu>
# URL: <http://www.nltk.org/>
# For license information, see LICENSE.TXT
"""
An interface to Mallet <http://mallet.cs.umass.edu/>'s Linear Chain
Conditional Random Fiel... | abad623/verbalucce | verbalucce/nltk/tag/crf.py | Python | apache-2.0 | 31,150 | [
"Gaussian"
] | f409897efde419aa7e159073cd1526e0ea43047219dfd05896a06d6f58a1253b |
# 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 Rsem(MakefilePackage):
"""RSEM is a software package for estimating gene and isoform expre... | LLNL/spack | var/spack/repos/builtin/packages/rsem/package.py | Python | lgpl-2.1 | 986 | [
"Bowtie"
] | 12a7adf6d9dccf94781816ec3a8936efbdb8a711effd0ed8a22b5af84848a321 |
#!/usr/bin/python
#
# Copyright 2012 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required b... | nearlyfreeapps/python-googleadwords | examples/adspygoogle/adwords/v201206/campaign_management/validate_text_ad.py | Python | apache-2.0 | 2,932 | [
"VisIt"
] | 8ed1410cc1bc350610863bcf9953ee104c3f6c67b96e627b0ec75cb8ebb40c48 |
from galaxy.util.json import dumps, loads
from galaxy.util.template import fill_template
import logging
log = logging.getLogger( __name__ )
class ExternalServiceActionResultHandler( object ):
""" Basic Class for External Service Actions Result Handlers"""
type = 'display'
@classmethod
def from_elem... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/external_services/result_handlers/basic.py | Python | gpl-3.0 | 2,652 | [
"Galaxy"
] | 293427b14b2ff2d73eb8a337f080e108351d8b253292215132dbc602ddf89dc1 |
"""
This file is part of the KnownSourceMatcher.
KnownSourceMatcher 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.
KnownSourceMatcher is d... | scienceguyrob/KnownSourceMatcher | KnownSourceMatcher/src/Match/ProfileOperations.py | Python | gpl-2.0 | 76,410 | [
"Gaussian"
] | 60f1043bc3b3dfd6406d285c7e4f51ab53465c71c7c03b4e88c469c6de0437cb |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-ampliqueso/package.py | Python | lgpl-2.1 | 2,435 | [
"Bioconductor"
] | 76dbbd6c33b2bc7bba42c0eef28be6defa9160aa0df01cdfe179f54edf41933e |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/lib/vhf/test/test_nr_direct.py | Python | apache-2.0 | 11,658 | [
"PySCF"
] | 93742d69630aa842653522d0ac00640c4f4f572fe30255f6965880daea6ca99c |
""" Test for WMS clients
"""
# pylint: disable=protected-access, missing-docstring, invalid-name, line-too-long
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import os
import unittest
import importlib
from six import BytesIO
from mock import MagicMock
... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/test/Test_Client_WorkloadManagementSystem.py | Python | gpl-3.0 | 4,000 | [
"DIRAC"
] | 4e25d2e87092a7dd0c4f891608f5153149341bda84392bec80fe5f6c4e24684b |
# A consolidation of the data sources for the project
# includes:
# NetworkX!
# RDFlib!
# Other things!
#
# Works like Configure:
# Inherit from the Data class to access data of all kinds (listed above)
import sqlite3
import networkx as nx
import PyOpenWorm
from PyOpenWorm import Configureable, Configure, ConfigValue... | mwatts15/PyOpenWorm | PyOpenWorm/data.py | Python | mit | 8,854 | [
"NEURON"
] | a6f2208bf631b498ffd4a729043485a201bd062dac6df64c00d98c82992c0bed |
#!/usr/bin/python
import os
import re
import vcf
import glob
import numpy as np
import json
import requests
import pickle
#GENE FORMAT
##chr start stop name
#3 178866311 178952497 PIK3CA
from optparse import OptionParser
# -------------------------------------------------
parser = OptionParser()
pa... | CuppenResearch/SmallTools | Make_Somatic_Mutation_Overview.py | Python | gpl-3.0 | 22,045 | [
"Bioconductor"
] | 4e94ab36a54f3b0747d6b0657a63e28194f18d87eb2333f72bcee68e92446377 |
import numpy as np
import theano
import theano.tensor as T
from itertools import combinations
from keras.layers.core import MaskedLayer, Layer, Dense
from keras.utils.theano_utils import ndim_tensor
from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams
floatX = theano.config.floatX
class Lambda(Mask... | berleon/seya | seya/layers/base.py | Python | bsd-3-clause | 5,370 | [
"Gaussian"
] | e5a3f055fa8c68b104ce3fc2b135007d876f9a7f82619076418fb34e5e7a9bc8 |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | uglyboxer/linear_neuron | net-p3/lib/python3.5/site-packages/sklearn/ensemble/forest.py | Python | mit | 59,682 | [
"Brian"
] | 2dc721ed7bcf8db089001f0c9dee1fd2645d930e122dd9f6e9b75c06c73d06aa |
import os
import sys
import numpy as np
from sklearn.utils import check_random_state
################################################################################
### Simple toy problems
def sample_SG(n, dim, rs=None):
rs = check_random_state(rs)
mu = np.zeros(dim)
sigma = np.eye(dim)
X = rs.mult... | dougalsutherland/opt-mmd | two_sample/generate.py | Python | bsd-3-clause | 9,349 | [
"Gaussian"
] | bf1d127c334fc844a42792805ddccb7a4c6b1e004e70d14dc75ead9af049936c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# @Author: Brian Cherinka, José Sánchez-Gallego, and Brett Andrews
# @Date: 2017-10-25
# @Filename: base.py
# @License: BSD 3-clause (http://www.opensource.org/licenses/BSD-3-Clause)
#
# @Last modified by: José Sánchez-Gallego (gallegoj@uw.edu)
# @Last modified time: 2018... | albireox/marvin | python/marvin/utils/datamodel/drp/base.py | Python | bsd-3-clause | 24,021 | [
"Brian"
] | fa36d0f542e73cef6562e19426381fdd3ec8eab71d45116933b38298ff9c9ffd |
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