text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
"""
@name: Modules/Core/Mqtt/_test/test_mqtt_client.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Jun 5, 2015
@Summary:
Passed all 7 tests - DBK - 2019-08-15
"""
__updated__ = '2019-11-23'
# Import... | DBrianKimmel/PyHouse | Project/src/Modules/Core/Mqtt/_test/test_mqtt_client.py | Python | mit | 5,911 | [
"Brian"
] | 91b735bc755c9ee0a158d57eee83e6a536d890e491e25ad2e651f69c00574d99 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from vector import vectors
# Does not handle pawns moves (en-passant, double advance, promotion) and castle
class Movement:
def __init__(self):
self.vectors = []
self.is_sliding = False
rook_movement = Movement()
rook_movement.vectors.append(vec... | victor-rene/chess-intuition | chess/movement.py | Python | mit | 1,770 | [
"Octopus"
] | 5b536b6ad4b7bf6afe537ccafbbe7266142dd86f23b9b9cb4b5f03a3c83c2f73 |
from __future__ import division, absolute_import, print_function
import os
import sys
import types
import re
import warnings
from numpy.core.numerictypes import issubclass_, issubsctype, issubdtype
from numpy.core import ndarray, ufunc, asarray
__all__ = [
'issubclass_', 'issubsctype', 'issubdtype', 'deprecate',... | jankoslavic/numpy | numpy/lib/utils.py | Python | bsd-3-clause | 34,950 | [
"VisIt"
] | 4fbf2fe289c300cfbba7a022375e95d6f73ac0f9c1423a03274a7b7edf180e6a |
""" Module to perform a trapezoid model fit to flux time seres data
Author: Christopher J Burke
"""
import numpy as np
import matplotlib.pyplot as plt
import scipy.optimize as opt
import sys
def phaseData(t, per, to):
"""Phase the data at period per and centered at to
INPUT:
t - time of data
... | barentsen/dave | trapezoidFit/trapfit.py | Python | mit | 28,177 | [
"Gaussian"
] | b8f962b2c9c158dd9061b71130d4a1e0e30c61330bc2d9c261f4b7eae41081a9 |
#
# -*- coding: utf-8 -*-
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2008 Raphael Ackermann
# 2002-2003 Donald A. Peterson
# 2003 Alex Roitman
# 2009 ... | sam-m888/gprime | gprime/plugins/docgen/latexdoc.py | Python | gpl-2.0 | 49,156 | [
"Brian"
] | e591469584b95e7c5824ce12248a158b1b167202bc939194cf06f0fc766cd216 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Replacement code for the Pyke rules.
For now, we are still emulating various aspects of how our original Pyke-based
code u... | rcomer/iris | lib/iris/fileformats/_nc_load_rules/actions.py | Python | lgpl-3.0 | 21,897 | [
"NetCDF"
] | dc21ed5811c49fb917b6e0c3a7947b920b5e1c31c92b071d2b09d13e64ef9a87 |
"""
Convenience functions for the construction of spatial weights based on
contiguity and distance criteria.
"""
__author__ = "Sergio J. Rey <srey@asu.edu> "
import pysal
from Contiguity import buildContiguity
from Distance import knnW, Kernel, DistanceBand
from util import get_ids, get_points_array_from_shapefile, m... | jlaura/pysal | pysal/weights/user.py | Python | bsd-3-clause | 34,513 | [
"COLUMBUS",
"Gaussian"
] | 0141594bb49f37cdada2a54866e3c3491169c2ab65f5f9f78024c561f95cc362 |
#
# 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... | KaiSzuttor/espresso | samples/lj_liquid.py | Python | gpl-3.0 | 4,979 | [
"ESPResSo"
] | c7a0ed224cb7e80cfb38f01eb75b92ec0fe0864faef0af7ed5188637c774b11f |
from django.conf.urls import url
from crystal_dashboard.dashboards.crystal.rings.storage_policies import views
urlpatterns = [
url(r'^create_storage_policy', views.CreateStoragePolicy.as_view(),
name='create_storage_policy'),
url(r'^update_storage_policy/(?P<id>[^/]+)/$', views.UpdateStoragePolicy.as_v... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/rings/storage_policies/urls.py | Python | gpl-3.0 | 688 | [
"CRYSTAL"
] | ae37c1749f9b3072b138688ceca677c0963ab068010e5117dd0e2545cd8971a6 |
#! CCSD dipole with user-specified basis set
import psi4
psi4.set_output_file("output.dat", False)
h2o = psi4.geometry("""
0 1
H
O 1 0.957
H 2 0.957 1 104.5
""")
psi4.set_options({'freeze_core': 'false'})
psi4.basis_helper("""
# Sadlej-pVTZ
spherical
****
H 0
S 4 1.00
33.8650140000 0.00606... | amjames/psi4 | tests/python/cc54/input.py | Python | lgpl-3.0 | 3,948 | [
"Psi4"
] | af7df7a44ec2071ab828fca3559d3b26639d121dad0def4282635ac97010e2ba |
# SONA imports
from .generators.noise import PulseGenerator
from .generators.noise import NoiseGenerator
from .generators.noise import SineOscillator
from .generators.noise import ColoredNoise
from .generators.operators import Product
from .interface import play
from .interface import Player
from . import macros
# Num... | gpenazzi/sona | src/sona/__init__.py | Python | bsd-3-clause | 371 | [
"Gaussian"
] | 1c385891d8cf87a1b2ff36b205fa956c0729625c060e58b179d181b4c035ef85 |
#!/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/data/radii.py | Python | apache-2.0 | 13,757 | [
"ASE",
"Dalton",
"PySCF"
] | d663e77db9530056e0af426970ee6324025851aff3d200d4b751ca7d1a278971 |
#! /usr/bin/env python
#
# Copyright (C) 2011, 2012, 2014, 2015, 2016, 2017 David Maxwell and Constantine Khroulev
#
# This file is part of PISM.
#
# PISM 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... | talbrecht/pism_pik | examples/python/sia_forward.py | Python | gpl-3.0 | 3,653 | [
"NetCDF"
] | caa60b888f506ca7342401bad1cfa40e603d48409e6725252be6f1c6700bc15e |
"""
Test course update
"""
from uuid import uuid4
from regression.pages.studio.login_studio import StudioLogin
from regression.pages.studio.course_info_studio import (
CourseUpdatesPageExtended
)
from regression.tests.studio.studio_base_test import StudioBaseTestClass
from regression.tests.helpers import LoginHelp... | raeeschachar/edx-e2e-mirror | regression/tests/studio/test_course_update.py | Python | agpl-3.0 | 4,480 | [
"VisIt"
] | 7094656145490e54cd1b86ff63239a6bf914b757e62466c00e9b23b3e7ed08bb |
from __future__ import unicode_literals
import base64
import datetime
import json
import logging
# For Python 3.0 and later
from urllib.request import Request, urlopen
from django.db.models import Max
from django.utils import safestring
import numpy as np
import re
from django.contrib.auth.models import User
from dj... | alexandrovteam/curatr | mcf_standard_browser/standards_review/models.py | Python | apache-2.0 | 13,487 | [
"Pybel"
] | 352d569232469b290857636513dfe77b56813130635a216906ce31a615483e0e |
# -*- coding: utf-8 -*-
import fedmsg.tests.test_meta
import arrow
class TestPagureConglomeratorByIssueAndPR(
fedmsg.tests.test_meta.ConglomerateBase):
expected = [
{
'categories': set(['pagure']),
'end_time': 1458308863.0,
'human_time': arrow.get(1458307676).huma... | fedora-infra/fedmsg_meta_fedora_infrastructure | fedmsg_meta_fedora_infrastructure/tests/conglomerate/pagure/test_pagure.py | Python | lgpl-2.1 | 218,531 | [
"VisIt"
] | e26ea89d957a068c29dbad9f5ed93a61d4c643796d9d8a47e017d0c6db727313 |
""" Runs few integrity checks
"""
__RCSID__ = "$Id$"
import re
import ast
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.ConfigurationSystem.Client.Helpers.Operations impor... | marcelovilaca/DIRAC | TransformationSystem/Agent/ValidateOutputDataAgent.py | Python | gpl-3.0 | 9,685 | [
"DIRAC"
] | c250a570e4c6538239d0099f06061d6ec9f356fde35309cf06ee16a2582e870c |
#
# Copyright (C) 2010-2018 The ESPResSo project
# Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
# Max-Planck-Institute for Polymer Research, Theory Group
#
# 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... | mkuron/espresso | doc/tutorials/02-charged_system/scripts/nacl.py | Python | gpl-3.0 | 5,469 | [
"ESPResSo"
] | 88b0aecdcc0a77528f2babc89b84ba4af2e817cf0d13cada7eb529698ac6e1cf |
from wofrysrw.propagator.wavefront2D.srw_wavefront import WavefrontParameters, SRWWavefront
from wofrysrw.storage_ring.srw_light_source import SRWLightSource
from wofrysrw.storage_ring.srw_electron_beam import SRWElectronBeam
from oasys_srw.srwlib import *
'''
x = 0.0, #Transverse Coordinates of Gaussian Beam Center ... | lucarebuffi/wofrysrw | wofrysrw/storage_ring/light_sources/srw_gaussian_light_source.py | Python | mit | 8,130 | [
"Gaussian"
] | 194e20e72d9d335e33da48f7ba05ea4bdd37376fa6739719ef8fe76c06b9bd8f |
"""Functions for performing the individual processing steps.
- "nfo": Prepare meta-information for each trajectory
- "cnv1": Run trjconv for pbc imaging (gromacs runs only)
- "cnv2": Convert files to netcdf
"""
import subprocess
import os
import glob
import re
import json
import logging
from operator import itemg... | mpharrigan/trajprocess | trajprocess/process.py | Python | mit | 8,629 | [
"Gromacs",
"MDTraj",
"NetCDF"
] | bf2aa040e70cc1617ab687da10444b39037a773b4817635368254cac344d130c |
"""
================================================
Segmenting the picture of greek coins in regions
================================================
This example uses :ref:`spectral_clustering` on a graph created from
voxel-to-voxel difference on an image to break this image into multiple
partly-homogeneous regions.... | glemaitre/scikit-learn | examples/cluster/plot_coin_segmentation.py | Python | bsd-3-clause | 2,948 | [
"Brian",
"Gaussian"
] | 01b7cb5460ca35cccad0e25f02fafacc5007407aed5c136337423cd509f34a41 |
'''
High level interface to Orbkit reading functions
'''
import re
from .native import read_native
from orbkit.read.molden import read_molden
from orbkit.read.gamess import read_gamess
from orbkit.read.gaussian_fchk import read_gaussian_fchk
from orbkit.read.gaussian_log import read_gaussian_log
from orbkit.read.aomi... | orbkit/orbkit | orbkit/read/high_level.py | Python | lgpl-3.0 | 2,531 | [
"GAMESS",
"Gaussian",
"cclib"
] | 3a1d16bbd9f511e646287891cf55d12f607b1878b6fee98d9472e6f542d44c7e |
#!/usr/bin/python
#
# Copyright 2015 John Kendrick
#
# This file is part of PDielec
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the MIT License
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied wa... | JohnKendrick/PDielec | PDielec/AbinitOutputReader.py | Python | mit | 10,508 | [
"ABINIT"
] | a98139b48a95fd660bd9b28087bca87ac6dea5f5a124461cacd7194dda2b1fc8 |
import ocl as cam
import camvtk
import time
import vtk
import datetime
if __name__ == "__main__":
myscreen = camvtk.VTKScreen()
myscreen.setAmbient(20,20,20)
#stl = camvtk.STLSurf(filename="demo.stl")
stl = camvtk.STLSurf(filename="demo2.stl")
print "STL surface read"
myscreen.addActor(s... | AlanZatarain/opencamlib | scripts/kdtree_movie1.py | Python | gpl-3.0 | 5,347 | [
"VTK"
] | 5a150bdd4e598d60eed8fd5e2d2bea80b18b0ef666595d9afaf89f7ccd621ab0 |
from __future__ import print_function
import os
from .abinittask import AbinitTask
__all__ = ['AbinitScfTask']
class AbinitScfTask(AbinitTask):
"""Charge density calculation."""
_TASK_NAME = 'SCF task'
_input_fname = 'scf.in'
_output_fname = 'scf.out'
def __init__(self, dirname, **kwargs):
... | trangel/OPTpy | OPTpy/Abinit/scftask.py | Python | gpl-3.0 | 2,767 | [
"ABINIT",
"pymatgen"
] | 76b546fc1c69709d0c5f48fcf2aae003153a4a5daa3f0c6237aca9c040b8297c |
from __future__ import print_function
"""
Module for read saint raw files from bruker integration
"""
import numpy
from ImageD11 import columnfile
docsheader = """
...from the file sairefl._tp...
Copyright Bruker
ITEM FORMAT DESCRIPTION
---- ------ -----------
COMMENT ... | jonwright/ImageD11 | ImageD11/saintraw.py | Python | gpl-2.0 | 11,924 | [
"CRYSTAL"
] | 8122cfe8e8b3116126a33de7ace9c0977807476cd7cbe62d6ce3b3559f3e2f6e |
from builtins import range
import numpy as np
def affine_forward(x, w, b):
"""
Computes the forward pass for an affine (fully-connected) layer.
The input x has shape (N, d_1, ..., d_k) and contains a minibatch of N
examples, where each example x[i] has shape (d_1, ..., d_k). We will
reshape each ... | YeEmrick/learning | cs231/assignment/assignment2/cs231n/layers.py | Python | apache-2.0 | 29,281 | [
"NEURON"
] | ec67cb9e62caa0d2e847f34922024c0aa291956af5afa2721af653dbec4fab20 |
"""
This module implements modified nodal analysis (MNA).
Copyright 2014--2022 Michael Hayes, UCECE
"""
from __future__ import division
from .assumptions import Assumptions
from .vector import Vector
from .matrix import Matrix, matrix_inverse
from .sym import symsimplify
from .expr import ExprDict, expr
from .voltage... | mph-/lcapy | lcapy/mna.py | Python | lgpl-2.1 | 10,744 | [
"Gaussian"
] | 7bf58d4f604d2e0c8a9d9edcb4e15c2e9712f92a41708df25f7658abc919f0d7 |
#
# Copyright (C) 2003-2013 Greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
""" This is a rough coverage test of the python wrapper
it's intended to be shallow, but broad
"""
from __future__ import print_function
import os,sys,tempfile,gzip
import unittest, doctest
from rdkit import RDConfig... | adalke/rdkit | Code/GraphMol/Wrap/rough_test.py | Python | bsd-3-clause | 138,790 | [
"RDKit"
] | 8a2f4186f38c6d5fba0138e5acbd276fe41cda867a1e420709377b6549d93491 |
#!/usr/local/bin/env python
"""
Test YANK using simple models.
DESCRIPTION
This test suite generates a number of simple models to test the 'Yank' facility.
COPYRIGHT
Written by John D. Chodera <jchodera@gmail.com> while at the University of California Berkeley.
LICENSE
This code is licensed under the latest avai... | andrrizzi/yank | Yank/tests/test_yank.py | Python | mit | 9,253 | [
"MDTraj",
"NetCDF",
"OpenMM"
] | c109d213b1c018d10668fd7ab2f12b8541f935692fc9d7ba615b9f6cd2c98cf5 |
# -*- coding: utf-8 -*-
"""
Unit tests for the statistics module.
:copyright: Copyright 2014-2016 by the Elephant team, see `doc/authors.rst`.
:license: Modified BSD, see LICENSE.txt for details.
"""
from __future__ import division
import itertools
import math
import sys
import unittest
import neo
import numpy as np... | JuliaSprenger/elephant | elephant/test/test_statistics.py | Python | bsd-3-clause | 42,632 | [
"Gaussian"
] | 66f9d021dd48574ea7bc29c88a2bd2a290280e607f620158fc2f2cbaa6fecd81 |
import time
import random
import numpy as np
import pypolyagamma as pypolyagamma
def calculate_C_w(S, w_i):
w_mat = np.diag(w_i)
return np.dot(S.T, np.dot(w_mat, S))
def sample_w_i(S, J_i):
"""
:param S: observation matrix
:param J_i: neuron i's couplings
:return: samples for w_i from a p... | noashin/Ising_model_gibbs_sampler | sampler.py | Python | mit | 6,253 | [
"NEURON"
] | cd55b48281ce401b60ae9caf7c1118b3d114e31a0ec829cfcac169291e7df6f6 |
# -*- coding: utf-8 -*-
"""
A replication of
Chaudhuri, Rishidev, et al.
"A large-scale circuit mechanism for hierarchical dynamical processing in the primate cortex."
Neuron 88.2 (2015): 419-431.
Figure 7D can not be reproduced exactly because the parameters used to generate
the figure in original paper is of higher ... | xjwanglab/book | chaudhuri2015/chaudhuri2015_nonlinear.py | Python | mit | 8,160 | [
"NEURON"
] | 83ecde166a62e794bb3f5c32b65ceea92000a6a098426e716937a46d540ffc19 |
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
Custom_0028_vtk = GetActiveSource()
Threshold1 = Threshold()
Threshold1.Scalars = ['POINTS', 'pressure']
Threshold1.ThresholdRange = [-0.81475600000000004, 0.91933500000000001]
Threshold1.Scalars = ['POINTS', ... | kel85uk/NuSiF_CFD | skeleton/Parameter_files/post_process.py | Python | gpl-2.0 | 5,435 | [
"ParaView"
] | cfc87af5aaefe68d209a206315826464a9ee583d3adafe70d2e4dc7610204b7b |
import logging
from celery import task
from mkt.feed.models import FeedApp, FeedCollection
log = logging.getLogger('z.feed')
@task
def _migrate_collection_colors(ids, model):
"""Migrate deprecated background color (hex) to color (name)."""
cls = FeedApp
if model == 'collection':
cls = FeedCollec... | ingenioustechie/zamboni | mkt/feed/tasks.py | Python | bsd-3-clause | 1,037 | [
"Amber"
] | 08a09a4fb00d574f6a11b84810b13ad130f0473003fd0b3acbd92e657a172e30 |
# -*- coding: utf-8 -*-
"""
functions.py - Miscellaneous functions with no other home
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more infomation.
"""
from __future__ import division
import warnings
import numpy as np
import decimal, re
import ctypes
import sys, struct
from ... | mpvismer/pyqtgraph | pyqtgraph/functions.py | Python | mit | 88,140 | [
"Gaussian"
] | 52fcea0d0fd60005be9db11230a39776293788a243308dbc97bb72a81de536b6 |
"""
=============================
Generic SpectralModel wrapper
=============================
.. moduleauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com>
"""
import numpy as np
from pyspeckit.mpfit import mpfit,mpfitException
from pyspeckit.spectrum.parinfo import ParinfoList,Parinfo
import copy
from astropy import lo... | mikelum/pyspeckit | pyspeckit/spectrum/models/model.py | Python | mit | 43,935 | [
"Gaussian"
] | 35b90e7c00ba35130f5f3db4bc1f22732ff8584b75499481713d724ba98822fd |
from ase.data.molecules import molecule
from ase.parallel import paropen
from gpaw import GPAW
from gpaw.utilities.tools import split_formula
from gpaw.test import equal
cell = [10.,10.,10.]
data = paropen('data.txt', 'w')
##Reference from J. Chem. Phys. Vol 120 No. 15, 15 April 2004, page 6898
tpss_de = {
'Li2': 22.... | qsnake/gpaw | gpaw/test/tpss.py | Python | gpl-3.0 | 2,734 | [
"ASE",
"GPAW"
] | 567636927c4c3d7c5b4c2ca2418715bd79415aebb370e02fa1f84e27d86c299e |
# Copyright 2008-2012 Nokia Siemens Networks Oyj
#
# 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... | Senseg/robotframework | src/robot/model/stats.py | Python | apache-2.0 | 3,540 | [
"VisIt"
] | 7012fee869ee357c1d6039fa272e0623722efab1fc51570a7e40789325d1ce16 |
########################################################################
# $HeadURL$
########################################################################
""" DIRAC FileCatalog component representing a directory tree with
enumerated paths
"""
__RCSID__ = "$Id$"
import os
from types import ListType, StringTy... | marcelovilaca/DIRAC | DataManagementSystem/DB/FileCatalogComponents/DirectoryLevelTree.py | Python | gpl-3.0 | 18,112 | [
"DIRAC"
] | 1c74c04b459db143adf63c111909323cb5dee66ec514689a7c7ffd1a5ff14c8f |
"""
===============================
Ordinary Least Squares with SGD
===============================
Simple Ordinary Least Squares example with stochastic
gradient descent, we draw the linear least
squares solution for a random set of points in the plane.
"""
print __doc__
import pylab as pl
from sklearn.linear_model... | mrshu/scikit-learn | examples/linear_model/plot_sgd_ols.py | Python | bsd-3-clause | 796 | [
"Gaussian"
] | d08a0442e3a113d14bdbc24dfdd476146dcd44d2a430db60c44a25966ad4d46c |
tests=[
("python","UnitTestTrainer.py",{}),
]
longTests=[
]
if __name__=='__main__':
import sys
from rdkit import TestRunner
failed,tests = TestRunner.RunScript('test_list.py',0,1)
sys.exit(len(failed))
| rdkit/rdkit-orig | rdkit/ML/Neural/test_list.py | Python | bsd-3-clause | 221 | [
"RDKit"
] | fdb65de0274467e3a53852cda5dc41ac9b7a51c99eb93bd2b6a7044d6b5346f1 |
#!/usr/bin/env python
"""
Extracts data from reference files or calculates FF data.
Takes a sequence of keywords corresponding to various
datatypes (ex. mb = MacroModel bond lengths) followed by filenames,
and extracts that particular data type from the file.
Note that the order of filenames IS IMPORTANT!
Used to ma... | ericchansen/q2mm | q2mm/calculate.py | Python | mit | 100,623 | [
"Amber",
"Gaussian",
"Jaguar",
"MacroModel",
"TINKER"
] | bcbecab89f96548890f5675461e23d67f336d5ed5657a6ede3360f21d7789850 |
import os
import py
from click.testing import CliRunner
from logstapo.cli import main
TEST_MAIL_BODY = '''
Logstapo results for 'syslog'
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Unusual lines
-------------
Dec 28 01:30:12 hydra login[3728]: pam_unix(login:session): session opened for user root by LOGIN(uid=0)
Dec 28 01:30:12... | ThiefMaster/logstapo | tests/test_logstapo.py | Python | mit | 3,208 | [
"VisIt"
] | f7e5219d271cd0b7819f298c183b0a55cace86476286e234e23dd20c5d51cdc2 |
from __future__ import absolute_import
import sys
from subprocess import call, check_output
sys.path.append("../lib")
sys.path.append("../workers")
from flask import Flask, request, jsonify, send_file
import idigbio
import uuid
from database import Database, Sequence, Result
from align.align import pipeline
app = F... | mjcollin/idigphylo | api/api.py | Python | mit | 4,984 | [
"BioPerl"
] | 592fc2c39bcaf1796a00de6b96ec78a833c17de375715ee2523e150cb33b9f8c |
../../../../share/pyshared/orca/eventsynthesizer.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/eventsynthesizer.py | Python | gpl-3.0 | 51 | [
"ORCA"
] | 0a51ed17367e8f0b93dd283c2ba70a66aa2c2d0cc958dec14ed0c7846e2f25ca |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/mcscf/test/test_mc1step.py | Python | apache-2.0 | 11,340 | [
"PySCF"
] | b974fe42691916db17fe5cb0a969b888a02853f45d6cf503119fafb729ce4374 |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=True) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=True) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfi... | prefetchnta/questlab | bin/x64bin/python/37/Lib/mimetypes.py | Python | lgpl-2.1 | 22,104 | [
"NetCDF"
] | 18e587ef03dde8214610f57bb07e5a0f2ab3a794eee927a9b6b32265cfcb9007 |
# proxy module
from __future__ import absolute_import
from mayavi.sources.ui.parametric_surface import *
| enthought/etsproxy | enthought/mayavi/sources/ui/parametric_surface.py | Python | bsd-3-clause | 105 | [
"Mayavi"
] | 531105091eeed44d3cadd2d16eec9ee8d7263608114a58f3e7f9e9d4a2642510 |
"""
bct active v0.01
- implements an alternative market classification and scoring algo
Bitcoin Trade Simulator
Copyright 2011 Brian Monkaba
This file is part of ga-bitbot.
ga-bitbot is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published b... | stahn/ga-bitbot | bct_active.py | Python | gpl-3.0 | 39,122 | [
"Brian"
] | de35590bb4baec8f4feb45b43cf8288278fb467e8d3d9ae579492327558aa8bc |
#!/usr/bin/env python
"""Writer for FASTA sequence format"""
# ----------------------------------------------------------------------------
# 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... | JWDebelius/scikit-bio | skbio/format/sequences/fasta.py | Python | bsd-3-clause | 4,987 | [
"scikit-bio"
] | 2916660f294c0d3c984b2264742fb3025ba21cb564002799b90b39ae88401e55 |
"""
==================================================
Plot different SVM classifiers in the iris dataset
==================================================
Comparison of different linear SVM classifiers on a 2D projection of the iris
dataset. We only consider the first 2 features of this dataset:
- Sepal length
- Se... | RPGOne/Skynet | scikit-learn-c604ac39ad0e5b066d964df3e8f31ba7ebda1e0e/examples/svm/plot_iris.py | Python | bsd-3-clause | 3,251 | [
"Gaussian"
] | f2fa4ce1edd6c255cc66907a6cb2a7917c228f9f54c4294e26d738f0e3732037 |
import matplotlib.pyplot as plt
import netCDF4
import os
import pandas
def read_netcdf(nc_full_name,variable_list=[]):
"""
Purpose:
Read an OzFlux netCDF file and return the data in an Pandas data frame.
Usage:
df = qcio.nc_read_todf(nc_full_name,variable_list=variable_list)
where nc_full_n... | OzFlux/OzFluxQC | utilities/read_example.py | Python | gpl-3.0 | 4,619 | [
"NetCDF"
] | 5f09de4109ba1a7d46fee6702a0fe264359ee51fb0ef4b90f8e21f073af1a377 |
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
__author__ = 'anton'
import getopt
import os
import sys
... | INNUENDOWEB/INNUca | src/SPAdes-3.9.0-Linux/share/spades/spades_pipeline/truspades/launch_options.py | Python | gpl-3.0 | 6,476 | [
"BWA"
] | b7a312a17b24fe6249a5ba9ac3f4e77978e19af8e84dc3d9cc781b75f12725e7 |
#!/usr/bin/env python2
"""
Creates various combinations of latitude and longitude lines
to demonstrate different grid types for globes. (This requires
the MayaVi visualization library).
The last scene crudely shows what SpaceX's satellite constellation
*may* look like. Altitudes are to scale, but satellite bodies are
... | jnez71/demos | geometry/globe_grids.py | Python | mit | 5,276 | [
"Mayavi"
] | 4e870fb93df8c2755bdfcd0797bfbd546f803e03e9b994946a6fd128a5e80264 |
#!/usr/bin/env python
import roslib,rospy,sys,cv2,time
import numpy as np
roslib.load_manifest('lane_follower')
from std_msgs.msg import Int32
from sensor_msgs.msg import CompressedImage, Image
from cv_bridge import CvBridge, CvBridgeError
bridge = CvBridge()
pub = rospy.Publisher('lane_detection', Int32, queue_size=1... | isarlab-department-engineering/ros_dt_lane_follower | src/lane_detection.py | Python | bsd-3-clause | 5,227 | [
"Gaussian"
] | 603e4afb4f01e9701d369868aab8150378d9c68883908f67dd0996f3f76d62b0 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""rna_clanstix - a tool for visualizing RNA 3D structures based on pairwise structural similarity with Clans.
We hacked Clans thus instead of BLAST-based distances between sequences, you can analyze distances between structures described as p-values of rmsd (based on the meth... | mmagnus/rna-pdb-tools | rna_tools/tools/clanstix/rna_clanstix.py | Python | gpl-3.0 | 21,529 | [
"BLAST"
] | 6d5e250d8eb968fba1a4ac92fec858f34c66ed19c0fec1027542c65837b9ae58 |
#!/usr/bin/env python
"""
Functions that use FreeSurfer commands.
Authors:
- Arno Klein, 2012-2013 (arno@mindboggle.info) http://binarybottle.com
Copyright 2013, Mindboggle team (http://mindboggle.info), Apache v2.0 License
"""
def label_with_classifier(subject, hemi, left_classifier='',
... | binarybottle/mindboggle_sidelined | freesurfer.py | Python | apache-2.0 | 26,053 | [
"Gaussian",
"VTK"
] | 7356e034788d73f0e8c7a98177681e34f1ae812db6fcc8862ec1c12650612185 |
# -*- coding: utf-8 -*-
"""
Kay framework.
:Copyright: (c) 2009 Accense Technology, Inc.
Takashi Matsuo <tmatsuo@candit.jp>,
Ian Lewis <IanMLewis@gmail.com>
All rights reserved.
:license: BSD, see LICENSE for more details.
"""
import os
import sys
impor... | IanLewis/kay | kay/__init__.py | Python | bsd-3-clause | 6,818 | [
"VisIt"
] | 785436d2d727b96b80434942c4b05640c03d82294e9f3ad6f7d5db48c4b28b8a |
"""locate.py - determine architecture and find Java
python-javabridge is licensed under the BSD license. See the
accompanying file LICENSE for details.
Copyright (c) 2003-2009 Massachusetts Institute of Technology
Copyright (c) 2009-2013 Broad Institute
All rights reserved.lo
"""
import ctypes
import os
import sys... | jakirkham/python-javabridge | javabridge/locate.py | Python | bsd-3-clause | 6,661 | [
"VisIt"
] | 5e3039f4875d65a2dc7fdb7856e6a822bccc88e73d629937f8d8d44b1dce8ff2 |
# Copyright 2020 Google Research. 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 applicable law... | tensorflow/examples | tensorflow_examples/lite/model_maker/third_party/efficientdet/hparams_config.py | Python | apache-2.0 | 15,188 | [
"Gaussian"
] | 1af52ddcb0e51570089d331daaf8bd2dc2a67121a4f967b002d01215f88a5266 |
#!/usr/bin/env python
"""Compartment.py:
A compartment in moose.
Last modified: Tue May 13, 2014 06:03PM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__license__ = "GPL"
__version__ ... | subhacom/moose-core | tests/python/Rallpacks/compartment.py | Python | gpl-3.0 | 3,980 | [
"MOOSE"
] | 3c7832873f9d2cb2453e62b9bf597a59b986fb62e4d7525be51ebd6c5605bf94 |
# -*- coding: utf-8 -*-
from __future__ import division, print_function
__all__ = ["multivariate_gaussian_samples", "nd_sort_samples"]
import numpy as np
from scipy.spatial import cKDTree
def multivariate_gaussian_samples(matrix, N, mean=None):
"""
Generate samples from a multidimensional Gaussian with a g... | andres-jordan/george | george/utils.py | Python | mit | 1,691 | [
"Gaussian"
] | 03e6de2344a48b0f4d6c7a0f10bd4485a7662d92fe3ac71d00663e1e2adc85ed |
# Author: Travis Oliphant
# 1999 -- 2002
import operator
import math
import timeit
from scipy.spatial import cKDTree
from . import _sigtools, dlti
from ._upfirdn import upfirdn, _output_len, _upfirdn_modes
from scipy import linalg, fft as sp_fft
from scipy.fft._helper import _init_nd_shape_and_axes
from scipy._lib._ut... | matthew-brett/scipy | scipy/signal/_signaltools.py | Python | bsd-3-clause | 153,038 | [
"Gaussian"
] | a147e9d78527ac627bb4a2d3d474218c7507f6d9a08b023b78212d6e9936fd33 |
# IPython log file
x = np.array([[0.0, 1.5, 2.7],
[1.5, 0.0, 0.0],
[2.7, 0.0, 0.0]])
y = sparse.csr_matrix(x)
y
import networkx as nx
g = nx.from_scipy_sparse_matrix(y)
g[0][1]
get_ipython().run_line_magic('cd', '~/Dropbox/data1/drosophila-embryo/')
get_ipython().run_line_ma... | jni/useful-histories | smoothing-paths.py | Python | bsd-3-clause | 2,475 | [
"Gaussian"
] | 38abc69765a57fc85e3aa00e3a79dd502f158bdfc3a13234095151f1bad7c135 |
##
# title: BreadInterface.Lifecycle
# by: Brian Kim
# description: the set of methods that define
# the stages of existence for a BreadInterface object
#
##
# an interface that defines the life cycle of a breadinterface component
#
class Lifecycle():
def __init__( self ):
pass
def start( self ):
pass
... | briansan/BreadInterface | py/BreadInterface/Lifecycle.py | Python | bsd-2-clause | 450 | [
"Brian"
] | 40cc0fa20a72f98fb1b0c2e5d578fab52ac4b19b40f1d4bdabf5c0408c159425 |
import numpy as np
import os
import sys
import traceback
import pyneb as pn
#from scipy.linalg import solve as solve_sc
from numpy.linalg import solve as solve_np
try:
import cvxopt
cvxopt_ok = True
except:
cvxopt_ok = False
"""
from scipy.sparse.linalg import spsolve as solve_sp
try:
from num... | Morisset/PyNeb_devel | pyneb/utils/misc.py | Python | gpl-3.0 | 15,313 | [
"Gaussian"
] | 08bf82a0d21963c19d7577c5b1dc4754b1f4fcf5a830bd2a0d9c8116339d67c5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines tools to generate and analyze phase diagrams.
"""
import re
import collections
import itertools
import math
import logging
from monty.json import MSONable, MontyDecoder
from functools ... | gVallverdu/pymatgen | pymatgen/analysis/phase_diagram.py | Python | mit | 84,336 | [
"pymatgen"
] | d595e60fa9e70862449fec485201669bc9773bb4e8ff576ecd6259451ea84444 |
#!/usr/bin/env python
# coding: utf-8
from datetime import datetime
from distutils import spawn
import argparse
import json
import os
import platform
import shutil
import socket
import sys
import time
import urllib
import urllib2
import main
from main import config
##################################################... | ssxenon01/contact-sharing | run.py | Python | mit | 18,639 | [
"GULP"
] | d86e53c9f43c555f5c95dba8d9e086899aeb559a1bda0c30afaa509a7fd1ca23 |
###############################
# 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 | src/pylada/config/general.py | Python | gpl-3.0 | 2,387 | [
"CRYSTAL",
"VASP"
] | 06657e9e708bd3851ad56fc7a86b74930caef24d6bf1a80d4623e3b6e8333716 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkMaskPoints(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtk... | nagyistoce/devide | modules/vtk_basic/vtkMaskPoints.py | Python | bsd-3-clause | 480 | [
"VTK"
] | bc6fc89ae0569df7a1a680d95533192455bba3ce47a038ff737e3f4d1f97f047 |
import functools
import warnings
from collections import Mapping, Sequence
from numbers import Number
import numpy as np
import pandas as pd
from . import ops
from . import utils
from . import common
from . import groupby
from . import indexing
from . import alignment
from . import formatting
from .. import conventio... | kjordahl/xray | xray/core/dataset.py | Python | apache-2.0 | 72,806 | [
"NetCDF"
] | c0c0f63e6cbdaedca173959e6ee74a6252b60c1b64855d1a310821fa1798c5a2 |
# -*- coding: utf-8 -*-
from django.test import TestCase
from django.contrib.auth.models import User
from django.urls import reverse
from django.db import transaction
from django.template import Template, RequestContext
from django.http import HttpRequest
from publications.models import Publication, Type, CustomLink, L... | lucastheis/django-publications | publications/tests/tests.py | Python | mit | 12,057 | [
"Galaxy",
"NEURON"
] | fe9fe213b1c7604b475162e1ac91481bc6cc9311980a16f87d0c92779facddc6 |
#!/usr/bin/env python
#**************************************************************************
# Tintwizard
#
# Copyright (C) 2009 Euan Freeman <euan04@gmail.com>
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License version 3
# as published ... | giresun28/malfs-milis | bin/tintwizard.py | Python | mit | 110,544 | [
"VisIt"
] | ec7ec29dd6fe183b5bc8006d673944f8dbf32121de5c9ec0120474d2e1245a38 |
"""Gaussian processes regression. """
# Authors: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
#
# License: BSD 3 clause
import warnings
from operator import itemgetter
import numpy as np
from scipy.linalg import cholesky, cho_solve, solve_triangular
from scipy.optimize import fmin_l_bfgs_b
from sklearn.base im... | jmschrei/scikit-learn | sklearn/gaussian_process/gpr.py | Python | bsd-3-clause | 18,634 | [
"Gaussian"
] | 176bb9396b57c2a1c4dd05098419c5fa8eb440ac03bd6ea86228ca22e30aff9a |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this file,
# You can obtain one at http://mozilla.org/MPL/2.0/.
from auto_nag.bzcleaner import BzCleaner
class SurveySecurityBugs(BzCleaner):
def __init__(self):
super(Su... | mozilla/bztools | auto_nag/scripts/survey_sec_bugs.py | Python | bsd-3-clause | 3,177 | [
"VisIt"
] | 2e960419b8eae82e025da0ffc12a49f48d8bc7809a8312d1f1483026124742a0 |
# -*- coding: utf-8 -*-
# Copyright 2015-2016 LasLabs Inc.
# License AGPL-3.0 or later (http://www.gnu.org/licenses/agpl.html).
import logging
from odoo import models, fields
from odoo.addons.connector.unit.mapper import mapping
from ..unit.backend_adapter import CarepointCRUDAdapter
from ..unit.mapper import Carepoin... | laslabs/odoo-connector-carepoint | connector_carepoint/models/fdb_pem_mogc.py | Python | agpl-3.0 | 3,143 | [
"MOE"
] | 528f0069ccafa763abd36cd0254de0790d29014e976d9174264ce32d98e3810f |
"""
Testing the FileCatalog logic
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import sys
import unittest
import mock
import DIRAC
from DIRAC.Resources.Catalog.FileCatalog import FileCatalog
from DIRAC import S_OK, S_ERROR
__RCSID__ = "$Id $"
c... | yujikato/DIRAC | src/DIRAC/Resources/Catalog/test/Test_FileCatalog.py | Python | gpl-3.0 | 15,775 | [
"DIRAC"
] | 2f9465032ef51495eb87493f0abf359a6133d8ef38488b490031a7751da6a144 |
import pathlib
import numpy as np
import pytest
from util import full
from loprop.core import penalty_function, AU2ANG, pairs
from loprop.dalton import MolFragDalton
from . import h2o_beta_trans_data as ref
from .common import LoPropTestCase
thisdir = pathlib.Path(__file__).parent
case = "h2o_beta_trans"
tmpdir = t... | vahtras/loprop | tests/test_h2o_beta_trans.py | Python | gpl-3.0 | 19,452 | [
"Dalton"
] | 301b30964c8e8e8d9456953b16b2c21ce1c17750512c08684bd104661f4960aa |
# 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 *
class RMulttest(RPackage):
"""Resampling-based multiple hypothesis testing.
Non-parametr... | rspavel/spack | var/spack/repos/builtin/packages/r-multtest/package.py | Python | lgpl-2.1 | 2,298 | [
"Bioconductor"
] | a86dfad2bf3b3242c65f8d819210f568d9e6d16253a8244bcdc2e35f6e6f7a5b |
# codegen.py
# Copyright (C) 2006, 2007, 2008 Michael Bayer mike_mp@zzzcomputing.com
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""provides functionality for rendering a parsetree constructing into module source code."""
import time
impo... | gabriel/shrub | lib/mako/codegen.py | Python | mit | 32,514 | [
"VisIt"
] | 2780dd04068fc3bcc62f62e76dd2e3e05d36f6e69750062bc74ac8cb1fe22f83 |
#Standard dependencies
import os
import sys
import inspect
import time
import cPickle as pickle
import re
from copy import copy
from string import Template
#Non-standard dependencies
import numpy as np
from scipy.interpolate import InterpolatedUnivariateSpline as spline
import matplotlib as mpl
mpl.use('Agg')
import p... | ajmedford/catmap | catmap/__init__.py | Python | gpl-3.0 | 2,369 | [
"ASE"
] | 6767de79b2ec4670502cd44f26c264cac86e7fd4ec92cc62a89a3adb6f6f2f76 |
# * fb.py main module for pythons fbpy package. Draws stuff in the
# * Linux framebuffer.
# * Copyright (C) 2014 Marcell Marosvolgyi aka noisegate
# *
# * 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... | noisegate/fbpy | build/lib.linux-x86_64-2.7/fbpy/fb.py | Python | gpl-2.0 | 33,713 | [
"VisIt"
] | e987213d737dff4bd7e4a55d4aace4cab771dd48ae2c388779b68ee4dda9e97c |
"""
Flask server used for the registration page for **COMEX** app
Context:
- templates-based input form validated fields and checked if all were present
(base_form.html + static/js/comex_reg_form_controllers.js)
- Doors already validated and recorded the (email, password) combination
- labels of SOU... | moma/comex2 | services/main.py | Python | agpl-3.0 | 52,289 | [
"VisIt"
] | a26bbceb1012fa3331a92f508193dd7b6e660078e7fcc53572c72d1d0ce42f3e |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------... | gratefulfrog/lib | python/pymol/wizarding.py | Python | gpl-2.0 | 6,104 | [
"PyMOL"
] | 067207b8ba948ace4af8b9ab48a160ef9f14b9a98bb317554b77d750d291a07a |
"""Notifications for Android TV notification service."""
import base64
import io
import logging
import requests
from requests.auth import HTTPBasicAuth, HTTPDigestAuth
import voluptuous as vol
from homeassistant.components.notify import (
ATTR_DATA,
ATTR_TITLE,
ATTR_TITLE_DEFAULT,
PLATFORM_SCHEMA,
... | kennedyshead/home-assistant | homeassistant/components/nfandroidtv/notify.py | Python | apache-2.0 | 9,929 | [
"Amber"
] | 71211b4f765c02b38d06c6a54346f4f022f648dab82664dda33fccc249e18ee0 |
#!/usr/bin/env python
"""Tests of code for OTU picking"""
__author__ = "Kyle Bittinger, Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
# remember to add yourself if you make changes
__credits__ = [
"Kyle Bittinger",
"Greg Caporaso",
"Rob Knight",
"Jens Reeder",
"William Walters... | josenavas/qiime | tests/test_pick_otus.py | Python | gpl-2.0 | 215,332 | [
"BLAST"
] | f2e0c89ebb384df66718dc70e665192f2e57c7c6afbaad39716624e4abe111d7 |
######################################
#
# Nikolai Rozanov (C) 2017-Present
#
# nikolai.rozanov@gmail.com
#
#####################################
#
# the bottom part of this file is not by me (as is indicated below)
#
import numpy as np
from sklearn.utils import check_random_state
def circle(n,var,rs=1):
rs ... | Kolyan-1/MSc-Thesis-Code | Data/synthetic2.py | Python | bsd-3-clause | 1,526 | [
"Gaussian"
] | b405cf9ec902d9252c1a88e6c71d089e0ca7e19e7c58e9ae28ddad30e420bd79 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# signup - Handle user input from external sign up
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Pu... | heromod/migrid | mig/cgi-bin/signup.py | Python | gpl-2.0 | 1,166 | [
"Brian"
] | 497cc59df066845a05a2ad12178a319631edbbe6a6813d0f7c732cdd981e59d7 |
#!/usr/bin/python
import sys,re
samfile = open(sys.argv[1],'r')
# Second arguments deals with paired reads specification. Add a tag to precise if it's the forward or the reverse strand.
# The tag can be found as the second field of the first line of a fastq file, ususally (illumina) in the form of:
# Forward: 1:N:0:0 ... | loire/bac2ass | Scripts/extract_BAC_reads.py | Python | gpl-2.0 | 4,439 | [
"BWA"
] | a843ad275129580c1289d8a4872899824d28a2482563cbc757c0f3a324a33f35 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | h3biomed/ansible | lib/ansible/modules/cloud/kubevirt/kubevirt_vm.py | Python | gpl-3.0 | 15,788 | [
"Galaxy"
] | 8b88a9fde7b571c9815673675122970d31204164c3c79f9a9a01586b64e574b6 |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2014 CRS4.
#
# This file is part of hadoop-galaxy, released under the terms of the BSD
# 3-Clause License <http://opensource.org/licenses/BSD-3-Clause>.
#
# END_COPYRIGHT
import argparse
import copy
import logging
import os
import subprocess
import sys
import yaml
import pydoop.hdf... | crs4/hadoop-galaxy | hadoop_galaxy/__init__.py | Python | bsd-3-clause | 14,205 | [
"Galaxy"
] | 193cb271b4e815f969aadba0a98acdb10882ef53f1fdf0364c0afa8f979ad167 |
import os
import collections
import copy
import subprocess
import functools
import datetime
import operator
import re
import numpy as np
import netCDF4
import cf_units
from giss import memoize,ioutil,ncutil,giutil,xaccess,gidate,checksum
from giss.functional import *
from giss import functional
from giss.xaccess impo... | citibeth/modele-control | lib/modele/io.py | Python | lgpl-2.1 | 16,915 | [
"NetCDF"
] | 00bba4abb90218478e498b50396cc551c8208c90f6796795499bbcf6b06bd27e |
from splinter.browser import Browser
from time import sleep
#traceback模块 跟踪异常返回信息
import traceback
#ConfigParser模块 读取配置文件
import configparser
import string, os, sys
import notify
# 读取配置文件
cf = configparser.ConfigParser()
cf.read("app.conf")
# 读取12306账户名，密码
uname = cf.get("user", "name")
upasswd=cf.get("user", "pass... | lnO4X/rush_train_py | rush_train.py | Python | apache-2.0 | 3,764 | [
"VisIt"
] | 15fbcf6ff08f9ee4e9b72675f13193096ef9e492b7322f4eea02b032423cfbef |
#
# Copyright (c) 2003-2006 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.
#
""" utility functionality for clustering molec... | greglandrum/rdkit | rdkit/Chem/Fingerprints/ClusterMols.py | Python | bsd-3-clause | 5,671 | [
"RDKit"
] | 5bf9e16ed73f8c3435f5a2259d7c63380b1e6b42af53a2bc4774be1589a60b82 |
#!/afs/crc.nd.edu/x86_64_linux/python/3.4.0/gcc-4.8.0/bin/python3
# umbrella.py - set up umbrella sampling runs from a single steered MD run in GROMACS.
__author__ = "Ken Newcomb"
import os
import sys
import numpy
import shutil
### Inputs ###
num_frames = int(input("Number of frames to analyze: "))
distances = numpy... | hsidky/MolSimScripts | umbrella.py | Python | mit | 3,022 | [
"Gromacs"
] | c4d736d837886441ce79f29a14298726956c254c21ccc15df74ce7e7f1b3d471 |
# -*- coding: utf-8 -*-
import sys
import random
import math
import random
import pylab
N=50
dt=0.4
as0=[45,105,-0.05,-0.01]
a0=[50,100,-0.06,-0.02]
Rv=25
f0=[[16,0,0,0],[0,16,0,0],[0,0,0.04,0],[0,0,0,0.04]]
H=lambda t,a:a[0]*math.sin(a[2]*t)+a[1]*math.sin(a[3]*t)
ir=range(4)
#tk=[i*dt for i in k]
fek=f0
def aS(k... | drewdru/AOI | roadLaneFinding/khalman.py | Python | gpl-3.0 | 1,124 | [
"ASE"
] | d878261754096dd4ab490594611aa74a64637b33cd9d84b79f1cb6d66bc90edb |
import collections
from PyQt5 import QtCore, QtWidgets
from LineSettingsWidget import LineSettingsWidget
import peacock
import mooseutils
class LineGroupWidget(peacock.base.MooseWidget, QtWidgets.QGroupBox):
"""
A GroupBox containing the artist toggles for each postprocessor in the supplied data object.
... | Chuban/moose | python/peacock/PostprocessorViewer/plugins/LineGroupWidget.py | Python | lgpl-2.1 | 12,247 | [
"MOOSE"
] | d154e7e1247bef903674b53e6d4a2c77ecfc78dd062f63854e6faf5366b370fc |
import sys, os, inspect
import os, sys, inspect, inviwopy
path_to_current_folder = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
sys.path.append(path_to_current_folder + "/../")
import envisionpy
import envisionpy.hdf5parser
from envisionpy.network import VisualisationManager
# Path to the ... | rartino/ENVISIoN | demo/elf.py | Python | bsd-2-clause | 807 | [
"VASP"
] | 9ae5646403ffd56aeb90b6b4d992c49413f12e833aa50cb0f92608a178b22fd1 |
# Copyright 2009 by Cymon J. Cox. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Command line wrapper for the multiple alignment program PROBCONS.
"""
from __future__ imp... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Align/Applications/_Probcons.py | Python | gpl-2.0 | 5,281 | [
"Biopython"
] | ddd66d418bd222f3d57343b94b2ce05418a892b3080d4a6bf302ca3852e9955c |
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