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# coding=utf-8
"""
models.py
==========
Core classes for machine-generated equations.
Copyright 2016 Brian Romanchuk
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/lic... | brianr747/SFC_models | sfc_models/models.py | Python | apache-2.0 | 32,199 | [
"Brian"
] | 7bff1c774b36244e92df2956f90f596f103914e3240f81abeb16a309fc03fbbe |
# -*- coding: utf-8 -*-
# @Author: YangZhou
# @Date: 2015-12-10 12:50:49
# @Last Modified by: YangZhou
# @Last Modified time: 2017-06-19 12:27:03
import aces.tools as tl
import aces.config as config
from aces.runners.vdos import vdos
from aces.runners import Runner
from aces.lammpsdata import lammpsdata
# from a... | vanceeasleaf/aces | aces/runners/correlation.py | Python | gpl-2.0 | 6,749 | [
"Gaussian",
"LAMMPS"
] | 260ce21e6b4d1f76abae4537776337ce00aa7e8c440c4d24fc990f0a5b35d7d7 |
# -*- coding: utf-8 -*-
from __future__ import division
import numpy as np
from pgmpy.factors.continuous import ContinuousFactor
from pgmpy.factors.continuous import JointGaussianDistribution
class CanonicalFactor(ContinuousFactor):
u"""
The intermediate factors in a Gaussian network can be described
c... | abinashpanda/pgmpy | pgmpy/factors/continuous/CanonicalFactor.py | Python | mit | 15,135 | [
"Gaussian"
] | 18e293c552555b3f3dab6d550c444d998d6c9ccd0ed49a88258fcce7731f9c63 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from six.moves import filter, zip
import numpy as np
import six
import collections
from numbers import Number
import numbers
from functools import partial
im... | aykol/pymatgen | pymatgen/core/units.py | Python | mit | 27,826 | [
"pymatgen"
] | 89aa345e6b9cba1622a79c4fd92b6e34a13fcb3c0c7141e15ba0fa12cdeb5225 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016 Haggi Krey, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of... | haggi/appleseed-maya | module/scripts/appleseed_maya/aetemplate/aeubershadertemplate.py | Python | mit | 7,943 | [
"VisIt"
] | 904fb2df0c9775e3e9e361a585073683e836945e7c163070389fc22f912896cf |
"""
Projection and related classes.
"""
from collections import OrderedDict
import numpy
from numpy import array,asarray,ones,sometrue, logical_and, logical_or
import param
from param.parameterized import overridable_property
from holoviews import Image, Layout
from holoviews.interface.collector import AttrDict
fr... | mjabri/topographica | topo/base/projection.py | Python | bsd-3-clause | 26,417 | [
"NEURON"
] | 2e25c61a45155b1420de1b088658066110a290d26b2493bf105803876f312c8c |
'''plotting functions for Validation
input -- one or more Single_TractorCat() objects
-- ref is reference Single_TractorCat()
test is test ...
'''
import matplotlib
matplotlib.use('Agg') #display backend
import matplotlib.pyplot as plt
import os
import sys
import numpy as np
from scipy import stats as sp... | legacysurvey/pipeline | py/legacyanalysis/validation/common_plots.py | Python | gpl-2.0 | 11,948 | [
"Gaussian"
] | ec5419ad54acaa6cfb70f5f5cf0487a9fbdb0d65e0ed260c40ab486578d1f952 |
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2016-2020 Florian Bruhin (The Compiler) <mail@qutebrowser.org>
#
# This file is part of qutebrowser.
#
# qutebrowser is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free S... | t-wissmann/qutebrowser | qutebrowser/browser/webengine/webenginetab.py | Python | gpl-3.0 | 63,250 | [
"VisIt"
] | d96c45bb1e5c16d3b82e639ab9137966bab74fa375e82b5e5358301cfc9ebdc9 |
#!/usr/bin/env python3
import os
import sys
import time
import http.server
import platform
from socketserver import ThreadingMixIn
from io import StringIO
import re
__version__ = "0.1"
__all__ = ["SimpleHTTPRequestHandler"]
__author__ = "philokey"
__home_page__ = ""
def init_server():
print("init server")
t... | philokey/AnnotationTool | FrameServer/frameServer.py | Python | bsd-3-clause | 4,626 | [
"VisIt"
] | 5f8ba714d9284137aefbda28c70b1c2434ad0d7bd303f6598bd1e5ccb6f49049 |
###################################################################################
# SNAPSHOT STUFF
###################################################################################
import inspect
import __main__
from param.parameterized import Parameterized, Parameter
# CEBALERT: Can't this stuff move to the P... | Tasignotas/topographica_mirror | topo/misc/snapshots.py | Python | bsd-3-clause | 9,345 | [
"Gaussian"
] | 6e2e19d3eae633fa70a8c05432a14e7d17f9dc011422312a90d91f912a8115cd |
# encoding: utf-8
"""
swatch, a parser for adobe swatch exchange files
Copyright (c) 2014 Marcos A Ojeda http://generic.cx/
With notes from
http://iamacamera.org/default.aspx?id=109 and
http://www.colourlovers.com/ase.phps
All Rights Reserved
MIT Licensed, see LICENSE.TXT for details
"""
import logging
import struct
... | nsfmc/swatch | swatch/writer.py | Python | mit | 4,463 | [
"ASE"
] | 352e71bc95b25be97d26129bb6882f559b01c7f6ceda8744d1f6c4f2cb8b7d72 |
#!/usr/bin/env python
#=============================================================================#
# #
# NAME: do_QUfit_1D_emcee.py #
# ... | crpurcell/RM-tools | RMtools_1D/deprecated/do_QUfit_1D_emcee.py | Python | mit | 40,707 | [
"Gaussian"
] | 5afee3d8991c9b95494a37e5b848b1e89798775559831ff71cfe3f1a14ea6ce2 |
#!/usr/bin/env python
'''
File name: main_ripp_mod.py
Author: Guillaume Viejo
Date created: 16/08/2017
Python Version: 3.5.2
'''
import sys
import numpy as np
import pandas as pd
import scipy.io
from functions import *
# from pylab import *
# import ipyparallel
from multiprocessing import Pool
imp... | gviejo/ThalamusPhysio | python/main_make_ISOMAP_NO_HD.py | Python | gpl-3.0 | 6,593 | [
"Gaussian"
] | aa06355116a79caf53413b2d5e6eb915a6e35595620c7498aea8432eb8a0eff6 |
#!/usr/bin/env python3
# Copyright 2017 Krzysztof Stopa (stopa.krzysztof.k@gmail.com)
# This file is part of Copernicus Atmosphere Monitoring Service (CAMS) downloading and
# processing tools (CAMS tools).
# CAMS tools is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser Gen... | kstopa/cams-tools | cams/cli.py | Python | lgpl-3.0 | 4,854 | [
"NetCDF"
] | c6fb57c01f07cd7d8e5bcf189308783c611e8a02ffd2a036d71247c36ad6fbba |
"""
==========================================
Author: Tyler Brockett
Username: /u/tylerbrockett
Description: Alert Bot (Formerly sales__bot)
Date Created: 11/13/2015
Date Last Edited: 04/02/2017
Version: v2.0
==========================================
"""
from accounts ... | tylerbrockett/reddit-bot-buildapcsales | src/utils/inbox.py | Python | mit | 11,914 | [
"VisIt"
] | 3fa65f42589e3ce890916cde4e361eedb45d10ed4e1a4267408f3488d5cc37c8 |
from tcga_encoder.utils.helpers import *
from tcga_encoder.data.data import *
from tcga_encoder.definitions.tcga import *
#from tcga_encoder.definitions.nn import *
from tcga_encoder.definitions.locations import *
#from tcga_encoder.algorithms import *
import seaborn as sns
from sklearn.manifold import TSNE, locally_li... | tedmeeds/tcga_encoder | tcga_encoder/analyses/kmeans_from_z_space_global_learn_survival.py | Python | mit | 17,736 | [
"Amber"
] | 937a1b98a42a753a8f22276b9977c0bba2da04ef63066673fd87f99e44bf064a |
"""
@name: PyHouse/src/Modules/Computer/_test/test_Internet.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2017 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 29, 2015
@Summary:
"""
__updated__ = '2017-01-11'
# Import system type stuff
from twiste... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/_test/test_Internet.py | Python | mit | 827 | [
"Brian"
] | cb09fc9d0b9a9f5e0afaa9027788fbb835bd5db15749a2d82a222af359ae8104 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
"""Tool for... | harterj/moose | python/mooseutils/eval_path.py | Python | lgpl-2.1 | 765 | [
"MOOSE"
] | 5531dc913b12d5fb1054ad3b2769e02656bc7258fa18992cefe3a6eb5bfbc798 |
from __future__ import print_function
import numpy as np
from shapely import geometry
import scipy.integrate
import pdb
from . import basic
from stompy import utils
class ParticlesKGS(basic.UgridParticles):
"""
Extension of basic particle tracking to (1) use the method
of Ketefian, Gross and Stelling f... | rustychris/stompy | stompy/model/pypart/ketefian.py | Python | mit | 22,813 | [
"NetCDF"
] | 581a50cb66a0e55adf38ea7afac4eac644a015105ba0e47547873bdc67bc9120 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
"""The structure class, representing a macromolecular structure."""
from Bio.PDB.Entity i... | zjuchenyuan/BioWeb | Lib/Bio/PDB/Structure.py | Python | mit | 1,457 | [
"Biopython"
] | fdb61461f3318140657a70431a408a50daed6a9b197e6736404097ea9a503440 |
__author__ = 'Zhouhao Zeng'
import HTSeq
import sys
from optparse import OptionParser
import numpy
import collections
def getSummitProfile(ga, summit_pos_set, window_size, resolution, upstream_extension, downstream_extension):
upstream_num_points = upstream_extension / resolution
downstream_num_points = down... | zhouhaozeng/bioinformatics-codebase | profile/generate_profile_matrix_around_summits.py | Python | gpl-3.0 | 6,877 | [
"HTSeq"
] | 1bf505de3282712eb66b329aae2a4ab09e6af749cc3b823206128d749dafa899 |
"""
muphyspy.io.write_netcdf
=========================
A grouping of scripts designed to create a NetCDF file (NetCDF4).
Created by Nick Guy.
"""
# HISTORY::
# 19 May 2014 - Nick Guy. NRC, NOAA/NSSL (nick.guy@noaa.gov)
# FUNCTIONS::
# rab_netcdf_vars - Pulls out a number of variables from NetCDF file created
# ... | nguy/pyparticleprobe | pyparticleprobe/io/write_netcdf.py | Python | lgpl-2.1 | 1,664 | [
"NetCDF"
] | 4a4c28648940828ae4c75ded6e63e42f734ba1738dbd9565fe91bed4f67b3244 |
import argparse, os, requests, math, threading, webbrowser, random, sys # , pdfkit
from StringIO import StringIO
from bson.errors import InvalidId
import matplotlib.tri as tri
if __name__ == "__main__":
from pymatgen.matproj.rest import MPRester
from pymatgen.phasediagram.pdmaker import PhaseDiagram
from ... | materialsproject/MPContribs | mpcontribs-portal/mpcontribs/users/als_beamline/scripts/post_submission.py | Python | mit | 6,832 | [
"pymatgen"
] | d70fee908923dd3ef4f0ffdfebcb423b878e02a82703ed4f5c508635096ead30 |
#!/usr/bin/env python
# Copyright 2014-2019 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/prop/zfs/uhf.py | Python | apache-2.0 | 13,644 | [
"DIRAC",
"PySCF"
] | 255120063f05a001666e3916047f75d37845afc2d01cd47c429eafbe92e37efe |
import unittest
from test.support import (verbose, refcount_test, run_unittest,
strip_python_stderr, cpython_only)
from test.script_helper import assert_python_ok, make_script, temp_dir
import sys
import time
import gc
import weakref
try:
import threading
except ImportError:
thread... | mancoast/CPythonPyc_test | fail/340_test_gc.py | Python | gpl-3.0 | 32,448 | [
"VisIt"
] | bd99523bb27fc56659888693e50070d7e0fcd4b53c409c62dce216597fb3e69c |
##############################################################################
# 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-aneufinderdata/package.py | Python | lgpl-2.1 | 1,722 | [
"Bioconductor"
] | 3533c1c53a464cc38a412412757e08a353dbc3dc2260ae4d776f36e70d391239 |
#!/usr/bin/env python
# This file is part of OpenDrift.
#
# OpenDrift is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, version 2
#
# OpenDrift is distributed in the hope that it will be useful,
# but WITHOUT AN... | knutfrode/opendrift | opendrift/readers/reader_cmems.py | Python | gpl-2.0 | 2,228 | [
"NetCDF"
] | 81d10f62739d7f9ae77075d65a9441e9eab46326597c847d05291d18cb8066b0 |
from plotly.offline import iplot
from random import sample
from scipy.optimize import curve_fit
import plotly.graph_objs as go
import numpy as np
import glob
import json
import pickle
import sys
import zmq
## internal functions
def _gauss(x, A, μ, σ):
return A * np.exp(- (x-μ)**2 / (2.0 * σ**2)... | tarnap/CalibRaTe | api/calc.py | Python | unlicense | 6,337 | [
"Gaussian"
] | 0b5fe577c95d8184c86a7d164e6ae809e12a2760dabe01c2359781cace832a81 |
#
# QAPI visitor generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
# Michael Roth <mdroth@linux.vnet.ibm.com>
#
# This work is licensed under the terms of the GNU GPLv2.
# See the COPYING.LIB file in the top-level directory.
from ordereddict import OrderedDict
from qapi ... | emonty/vhd-util | tools/qemu-xen/scripts/qapi-visit.py | Python | gpl-2.0 | 13,526 | [
"VisIt"
] | e4238c5b83c6588f67341aba6dd470a38c1b60f73b59619248d347b0dbf013d4 |
""" Test functions for stats module
"""
from __future__ import division, print_function, absolute_import
import warnings
import re
import sys
import pickle
import os
from numpy.testing import (assert_equal, assert_array_equal,
assert_almost_equal, assert_array_almost_equal,
... | jamestwebber/scipy | scipy/stats/tests/test_distributions.py | Python | bsd-3-clause | 159,223 | [
"Gaussian"
] | 7bb50b1084c0bb426e011c76eba3219a177fd53badd42819567f6e3caf9a71f7 |
#Copyright 2009 Brian Meeker
#
#This file is part of pyFish.
#
#pyFish 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.
#
#pyFish is distri... | palebluedot2/pyfish | src/RandomBot.py | Python | gpl-3.0 | 4,883 | [
"Brian"
] | 2d07a1ace12ba6999c4d7c6feb04b7565cdf31a15cb3876eb0e42c04599c4de8 |
###############################################################################
# import Python modules
# import 3rd party modules
from numpy import *
#from pylab import *
# import user modules
from .acalc import *
###############################################################################
"""
20070202 HI: Thi... | kernsuite-debian/lofar | CEP/Calibration/ExpIon/src/mpfit.py | Python | gpl-3.0 | 100,852 | [
"Gaussian"
] | 14f8ad8431bd74986f7c21452fb5d53931d2811580700f1a8c93e09f565a4649 |
from basic_utils.layers import ConcatFixedStd, Add_One, Softplus
from basic_utils.utils import *
from models.optimizers import Target_Updater
class StochPolicy:
def __init__(self, net, probtype, updater, target_net=None, tau=0.01, update_target_every=None):
self.net = net
self.target_net = target_... | hzxsnczpku/banrinochoujou | models/policies.py | Python | mit | 9,017 | [
"Gaussian"
] | 4abc27f612eb6dca959a98c35daa57feae276dee8a775235f5dc08904abc44d9 |
__version__ = '0.1.0'
__release__ = __version__ + '-dev'
__authors__ = 'Dereje Jima'
__authoremails__ = 'ddjima2015@gmail.com'
__description__ = 'Map unmapped contigs from pathdiscov to the ref genome using blastx and tblast'
__projectname__ = 'runtblastx'
__keywords__ = "tblastx, blastx, pathdiscov, blast"
| demis001/runtblastx | runtblastx/__init__.py | Python | gpl-2.0 | 309 | [
"BLAST"
] | 41b65d3687301426b1bdbbde1f5dbbfef9c771f2235df152bafee53e371775bf |
"""
Unit cell stacker
=================
This code can be used for stacking the unit cells of different content and
dimension to a single cell. This is intended to be helpful for constructing
complex super cell structures.
The unit cells should be given in Gaussian format, where the lattice vectors
are input in the sa... | tschijnmo/CellStacker | CellStacker.py | Python | mit | 14,455 | [
"Gaussian"
] | cf8a0d5aa758e0e2bd05ed40aa869f39ed8e868fac53279bd3e0e9a709506839 |
"""An explicit representation of a routing tree in a machine.
This representation of a route explicitly describes a tree-structure and the
complete path taken by a route. This is used during place and route in
preference to a set of RoutingTableEntry tuples since it is more easily
verified and more accurately represen... | project-rig/rig | rig/place_and_route/routing_tree.py | Python | gpl-2.0 | 5,120 | [
"VisIt"
] | ec52b277033dc1e93b37f5d139a7182913de64f6b46aaa0d97228682f028c708 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'Clinic.type'
db.add_column(u'clinics_clinic', 'type',
... | myvoice-nigeria/myvoice | myvoice/clinics/migrations/0045_auto__add_field_clinic_type.py | Python | bsd-2-clause | 13,421 | [
"VisIt"
] | 038bf5b7e7ff738a6ccd289d381e7f1dddea2ba87731e56dc9393de25e7c1c06 |
"""
Default Django settings. Override these with settings in the module pointed to
by the DJANGO_SETTINGS_MODULE environment variable.
"""
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
def gettext_noop(s):
return s
####... | piquadrat/django | django/conf/global_settings.py | Python | bsd-3-clause | 21,772 | [
"VisIt"
] | afe7a7acd886508cc06f89d619aa14f47d3303b3f71d9729a25463ba7aa46342 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Christoph Klein
# Contributors:
#
# MDTraj is free software: y... | kyleabeauchamp/mdtraj | mdtraj/formats/lammpstrj.py | Python | lgpl-2.1 | 20,166 | [
"LAMMPS",
"MDTraj"
] | 6eb7b52bab16aca33f255a0cff2bef4939575e320533c06aa6e602b2206f8874 |
# (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... | alxgu/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 49,181 | [
"VisIt"
] | 961b36fc8aecaba593dbc54ef7fb23c2c232a4b36c8dfd987210ab085c566e9d |
""" Python 'utf-7' Codec
Written by Brian Quinlan (brian@sweetapp.com).
"""
import codecs
# ## Codec APIs
encode = codecs.utf_7_encode
def decode(input, errors='strict'):
return codecs.utf_7_decode(input, errors, True)
class IncrementalEncoder(codecs.IncrementalEncoder):
def encode(self, input, final=Fal... | ppyordanov/HCI_4_Future_Cities | Server/src/virtualenv/Lib/encodings/utf_7.py | Python | mit | 953 | [
"Brian"
] | 34bf3ba0988d693582a7a440ccaa6fcb3e16d5866fc2c9857094cc62ecf1c4f1 |
#!/usr/bin/env python
##
## @file run.py
## @brief Unit test runner for libSBML Python doc converter
## @author Mike Hucka
##
## <!--------------------------------------------------------------------------
## This file is part of libSBML. Please visit http://sbml.org for more
## information about SBML, and the ... | mgaldzic/antimony | src/bindings/python/doc-converter/test/run.py | Python | bsd-3-clause | 1,977 | [
"VisIt"
] | 01a87c829fed2da9e1528b07c8876be5d300e65ea2b0798307b9bc4ce93aa2b5 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py | Python | gpl-2.0 | 19,617 | [
"MDAnalysis"
] | a8767e89ac9d81e9f8f347fca21950ec6b4412f8a29c02c27cb6cf5a21d908da |
import imp
import os
import marshal
import struct
import sys
from cStringIO import StringIO
from compiler import ast, parse, walk, syntax
from compiler import pyassem, misc, future, symbols
from compiler.consts import SC_LOCAL, SC_GLOBAL, SC_FREE, SC_CELL
from compiler.consts import (CO_VARARGS, CO_VARKEYWORDS, CO_NEW... | 2ndy/RaspIM | usr/lib/python2.6/compiler/pycodegen.py | Python | gpl-2.0 | 47,101 | [
"VisIt"
] | 853e205eb981b7a155232437ce30b3029c00b58bd993e4be0349ae3c68d0755b |
from ase import Atoms
from gpaw import GPAW
from gpaw.xc.noncollinear import NonCollinearFunctional, \
NonCollinearLCAOEigensolver, NonCollinearMixer
from gpaw.xc import XC
h = Atoms('H', magmoms=[1])
h.center(vacuum=2)
h.calc = GPAW(txt='c.txt', mode='lcao', basis='dz(dzp)', h=0.25)
e0 = h.get_potential_energy()... | robwarm/gpaw-symm | gpaw/test/noncollinear/h.py | Python | gpl-3.0 | 687 | [
"ASE",
"GPAW"
] | 3b6fa50c1862a7492e00229e3656ed309b14919e1dba457f7e1b22bab33a32d8 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/utils/test_failure.py | Python | gpl-2.0 | 1,417 | [
"MDAnalysis"
] | 87fe2739b5e31887ecc5894cdc8a70c87938b6f51f080264d32e5c6d8faf7584 |
#!/usr/bin/env python
'''
Created on Jan 5, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
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 Founda... | genome-vendor/chimerascan | chimerascan/chimerascan_run.py | Python | gpl-3.0 | 51,648 | [
"Bowtie",
"pysam"
] | 87a714b075f6a07518e61549e35a2c44723ac3a20556c4fd22178a503919c447 |
def read(filename):
import numpy as np
from numpy import ma
# from Scientific.IO.NetCDF import NetCDFFile
from scipy.io.netcdf import netcdf_file as NetCDFFile
"""
read a netcdf file and return a dictionnary with
key: name of the variables: value (array)
array is masked is missing_value... | nicolasfauchereau/ICU | lib/netcdf/read.py | Python | bsd-3-clause | 1,539 | [
"NetCDF"
] | 97852cf1eb38de38d6a61ffc24d27b60fb82bbe89ca5a14bcf72d556abeb5097 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | AsimmHirani/ISpyPi | tensorflow/contrib/tensorflow-master/tensorflow/contrib/factorization/python/ops/gmm.py | Python | apache-2.0 | 5,883 | [
"Gaussian"
] | b5556ff1648d140cdd926b73cd025ac6b81b54f31dbd37e361c1d70d5a497183 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-delete
# Author : Stuart Paterson
########################################################################
"""
Reschedule the given DIRAC job
"""
from __future__ import print_function
__RCSID__ = ... | fstagni/DIRAC | Interfaces/scripts/dirac-wms-job-reschedule.py | Python | gpl-3.0 | 1,220 | [
"DIRAC"
] | c7ffb875f55469ac3b21fe7a1a62fca3ae6db6a3e8a6ae8db59843cea401e8a9 |
"""This is a test to test the paraview proxy manager API."""
import paraview
paraview.compatibility.major = 3
paraview.compatibility.minor = 4
from paraview import servermanager
def Error(message):
raise "ERROR: %s" % message
servermanager.Connect()
pxm = servermanager.ProxyManager()
p1 = servermanager.sources.... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/ParaViewCore/ServerManager/Default/Testing/Python/ProxyManager.py | Python | gpl-3.0 | 1,508 | [
"ParaView"
] | e90838c978add907f424fc550d2cc54f9b80267e0d6854445cc996e9d0118b94 |
r"""OS routines for Mac, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, or ce, e.g. unlink, stat, etc.
- os.path is either posixpath or ntpath
- os.name is either 'posix', 'nt', 'os2' or 'ce'.
- os.curdir is a string representing the current directory ('.' or... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.1/Lib/os.py | Python | mit | 21,463 | [
"VisIt"
] | 2544a46ba25c3ddbddfbf65092695dfe1b6a0cce3262450b32bc63dd5fa62c77 |
# -*- coding: utf-8 -*-
"""
The module contains the Somoclu class that trains and visualizes
self-organizing maps and emergent self-organizing maps.
Created on Sun July 26 15:07:47 2015
@author: Peter Wittek
"""
from __future__ import division, print_function
import sys
import matplotlib.cm as cm
import matplotlib.py... | peterwittek/somoclu | src/Python/somoclu/train.py | Python | gpl-3.0 | 34,266 | [
"Gaussian"
] | bd33036fe4a4f92a50b4f965594cba54fc01afb5d9aea82f0c14aea2fd44c10c |
from windb2.model.wrf import heightinterp
__author__ = 'Mike Dvorak'
"""Vertically interpolates a WRF netCDF output file to eta-half levels."""
import numpy
import numpy.ma
from netCDF4 import Dataset
from windb2.model.wrf import config
import windb2.model.wrf.constants as constants
import logging
logger = logging.... | sailorsenergy/windb2 | windb2/model/wrf/heightinterpfile.py | Python | gpl-3.0 | 20,882 | [
"NetCDF"
] | ad9a8a6b680701ae33861038c6b29bd8abbaeb419f6d4ada7bed7b02bf54aedb |
import unittest
import time
from rdkit import Chem
from rdkit.Chem import rdFMCS
def load_smiles(text):
mols = []
for line in text.strip().splitlines():
smiles = line.split()[0]
mol = Chem.MolFromSmiles(smiles)
assert mol is not None, smiles
mols.append(mol)
return mols
_ignore = object()
c... | rvianello/rdkit | rdkit/Chem/UnitTestMCS.py | Python | bsd-3-clause | 10,979 | [
"RDKit"
] | 51e65c24f541eb9ca67950bbab3b56363ab05d8dcf6cd4fb64ca87cb58eb71d8 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | btabibian/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 30,798 | [
"Gaussian"
] | 2f6752bfaa47d33f5b8d11ae1a3f6343d9b6bd9e11810f0b8c88202b808e8c4c |
# Author: Travis Oliphant, 2002
#
# Further updates and enhancements by many SciPy developers.
#
from __future__ import division, print_function, absolute_import
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, around, unique, asarray,
... | mgaitan/scipy | scipy/stats/morestats.py | Python | bsd-3-clause | 91,460 | [
"Gaussian"
] | d45892d9549cf6a5f6e2ac93036f57833b800bcc64c9a6a794aac62ada6bc35b |
import matplotlib
matplotlib.use('Agg')
from msmbuilder.dataset import dataset
from msmbuilder import msm, featurizer, utils, decomposition
import numpy as np
import mdtraj as md
import matplotlib.pyplot as plt
from glob import glob
import os
# Source directory for MEK simulations
source_directory = '/cbio/jclab/pr... | choderalab/MSMs | shanson/mek-10488/msmbuilder-finding4/msmbuilder-finding4-mek.py | Python | gpl-2.0 | 2,134 | [
"MDTraj"
] | 72f9baaa2e50e7ff0e107547ea8f7df00c899b2b210a92d3ed1c5d47439f55a9 |
#!/usr/bin/env python3 -B -tt
import urllib.request, urllib.parse, time
class APIquery(object):
"""USGS Earthquake API Python3 Wrapper
KEYWORD ARGUMENTS
params** -- any USGS earthquake query parameter, for a list and
description of parameters, visit:
h... | abshinn/usgs | code/usgs.py | Python | mit | 5,241 | [
"VisIt"
] | b58cc6f7d8aa4093c39dbdb2379dbc5561b601597d80d97a18d9745c5bd6b36c |
# -*- coding: utf-8 -*-
import sys
sys.path[0:0] = [""]
import bson
import os
import pickle
import unittest
import uuid
from datetime import datetime
from bson import DBRef, ObjectId
from tests import fixtures
from tests.fixtures import (PickleEmbedded, PickleTest, PickleSignalsTest,
Pickl... | starsirius/mongoengine | tests/document/instance.py | Python | mit | 94,238 | [
"exciting"
] | c3aa423c54c16e503657506c0670d4c6c46b4f27721dc1da4f8d4c825112fe59 |
'''
Conversion of basis sets to Dalton format
'''
from .. import lut, manip, sort, misc, printing
def write_dalton(basis):
'''Converts a basis set to Dalton format
'''
s = '! Basis = {}\n\n'.format(basis['name'])
basis = manip.make_general(basis, False, True)
basis = sort.sort_basis(basis, Fals... | MOLSSI-BSE/basis_set_exchange | basis_set_exchange/writers/dalton.py | Python | bsd-3-clause | 2,999 | [
"Dalton"
] | eb3c40269b7f98c8b77170a8fbf495e8a2b1f41ea4aab97449fff72576f15619 |
__author__ = 'fahadadeel'
import jpype
class HelloWorld:
def __init__(self, dataDir):
self.dataDir = dataDir
def main(self):
"""
: The path to the documents directory. :
"""
Document = jpype.JClass("com.aspose.words.Document")
DocumentBuilder = jpype.JCla... | asposewords/Aspose_Words_Java | Plugins/Aspose_Words_Java_for_Python/quickstart/__init__.py | Python | mit | 7,795 | [
"VisIt"
] | da2e00901ef9fe869fa0e2d103a5c0e46b7c405b843b18f112df998fd559f588 |
"""Support for Ecobee sensors."""
from pyecobee.const import ECOBEE_STATE_CALIBRATING, ECOBEE_STATE_UNKNOWN
from homeassistant.const import (
DEVICE_CLASS_HUMIDITY,
DEVICE_CLASS_TEMPERATURE,
PERCENTAGE,
TEMP_FAHRENHEIT,
)
from homeassistant.helpers.entity import Entity
from .const import _LOGGER, DOMA... | tboyce021/home-assistant | homeassistant/components/ecobee/sensor.py | Python | apache-2.0 | 4,808 | [
"VisIt"
] | 8b6a20e77b5674a77a523202f928ef3e18f84527505058e4818cc5bf8d786450 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | nburn42/tensorflow | tensorflow/contrib/autograph/converters/side_effect_guards.py | Python | apache-2.0 | 7,026 | [
"VisIt"
] | 955334460aa96cd3ef862b7b1940a96697ef30e2221c45c1d465b064d5571363 |
# encoding: utf-8
"""
Job and task components for writing .xml files that the Windows HPC Server
2008 can use to start jobs.
Authors:
* Brian Granger
* MinRK
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed u... | mattvonrocketstein/smash | smashlib/ipy3x/parallel/apps/winhpcjob.py | Python | mit | 11,856 | [
"Brian"
] | 8411bf49b32a307f351b02246cc4e2885a31eca3ad65bacccd3f1470df512657 |
from common import Modules, data_strings, load_yara_rules, PEParseModule, ModuleMetadata, is_ip_or_domain, RC4
from string import ascii_uppercase, ascii_lowercase, digits, punctuation
from pefile import PE
class maazben(PEParseModule):
def __init__(self):
md = ModuleMetadata(
module_name="maaz... | bwall/bamfdetect | BAMF_Detect/modules/maazben.py | Python | mit | 2,292 | [
"Brian"
] | 72f2357487fe7ba535c1ed62ceedf8ee0b93725cb844b076218aaeb1cc3c23a4 |
from rest_framework import generics
from .models import Visit
from .serializers import VisitSerializer
class VisitList(generics.ListCreateAPIView):
queryset = Visit.objects.all()
serializer_class = VisitSerializer
class VisitDetail(generics.RetrieveUpdateDestroyAPIView):
queryset = Visit.objects.all()
... | dwagon/Scheduler | scheduler/visit/restviews.py | Python | gpl-2.0 | 365 | [
"VisIt"
] | 35ea2bce51511ad14262b4c50d1381b48b43ea93398f90db8bdc81c50567688f |
from setuptools import setup
from setuptools.command.develop import develop
from setuptools.command.install import install
from setuptools.command.bdist_egg import bdist_egg
from setuptools.command.easy_install import easy_install
import subprocess
import os
SETUP_DIR = os.path.dirname(os.path.abspath(__file__))
def ... | GillesPy/gillespy | setup.py | Python | gpl-3.0 | 3,332 | [
"Brian"
] | c40962dc8575f9606277ae278c52d0c192eae9d32906036b508eba32752e1f93 |
# -*- coding: utf-8 -*-
r'''This module contains classes for different types of network layers.
.. image:: _static/feedforward_neuron.svg
In a standard feedforward neural network layer, each node :math:`i` in layer
:math:`k` receives inputs from all nodes in layer :math:`k-1`, then transforms
the weighted sum of the... | masterkeywikz/seq2graph | src/theanets-0.6.1/theanets/layers/base.py | Python | mit | 15,948 | [
"Gaussian"
] | 9c867740a739e510355f78196b7284b5bed0b623910a3a221ca5f09753bd1605 |
#!/usr/env/python
import numpy as np
import matplotlib.pyplot as plt
# from scipy.ndimage import filters
from scipy.misc import logsumexp
# from scipy.stats import describe
from sklearn.decomposition import TruncatedSVD
from ..datasets import datasets
from ..datasets import synthetic as synth
from ..utils import arr... | dblalock/flock | python/algo/misc.py | Python | mit | 19,976 | [
"Gaussian"
] | 74292b7a4c340a7dcd3d22a612b63d74d7783c062f5e855164023b84f4a3a921 |
import sys
import urllib
import re
import os
import xbmc
import xbmcaddon
############################################################################
# ADDON INFO
############################################################################
ADDON = xbmcaddon.Addon()
ADDON_ID = ADDON.getAddonInfo('id')
ADDON_VERSION... | dannyellis/plugin.video.nhl-gamecenter | resources/lib/globals.py | Python | gpl-2.0 | 5,486 | [
"COLUMBUS"
] | 4cb98389c95dc9e9ddf2bcc928cbb0d458584ddcdeb080f968c8566acfe5cc81 |
from __future__ import absolute_import
import numpy as np
from skimage._shared import testing
from skimage._shared.testing import assert_array_almost_equal
from skimage.filters import threshold_local, gaussian
from skimage.util.apply_parallel import apply_parallel, dask_available
@testing.skipif(not dask_available,... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/skimage/util/tests/test_apply_parallel.py | Python | gpl-3.0 | 2,117 | [
"Gaussian"
] | e85862b19cbe173d36617259584bca5d62f7ac12353511859847f00794a15a67 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'NeuronArticleMap.added_by'
db.add_column('neuroelectro_neuronarticlemap', 'added_by',
... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0044_auto__add_field_neuronarticlemap_added_by.py | Python | gpl-2.0 | 25,758 | [
"NEURON"
] | e919cb719a332097b2fde577acec86837bc36fdf03dc5beffc0abf1f843e76ea |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/delegates/coloredfloatdelegate.py | Python | gpl-2.0 | 5,101 | [
"VisIt"
] | 6e0efe297353f1125d7f47c5e901ea86ff869d74f5a1a8fe1286023d96e6cc18 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import numpy as np
import matplotlib.pyplot as plt
import shtns
import sys
from mayavi import mlab
def get_grid(theta, phi):
th2D, p2D = np.meshgrid(theta, phi, indexing='ij')
x = np.sin(th2D) * np.cos(p2D)
y = np.sin(th2D) * np.sin(p2D)
z = np.cos(t... | AnkitBarik/inermodz | rossby.py | Python | gpl-3.0 | 1,471 | [
"Mayavi"
] | 366e023f86467edb8890d8866ea2a9bbf693c09a920bc7952b1c7c0b4f61ec49 |
'''
Created on 2013-12-04
This module contains common meta data and access functions for CESM model output.
@author: Andre R. Erler, GPL v3
'''
# external imports
import numpy as np
import os
try: import pickle as pickle
except: import pickle
# from atmdyn.properties import variablePlotatts
from geodata.base impor... | aerler/GeoPy | src/datasets/CESM.py | Python | gpl-3.0 | 55,702 | [
"NetCDF"
] | 6067bbec63feb172654e14f09cca7a0710ff72846dc7e7cc466246f49da79370 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/test_persistence.py | Python | gpl-2.0 | 6,450 | [
"MDAnalysis"
] | 534151da82846913ba463114b10515bbdd7a1ec5800380983053b3be7bf60a64 |
import os
import numpy as np
'''
input validation module
provides functions to validate all input variables to the Jacapo calculator.
'''
###########################################3
### Validation functions
##########################################
def valid_int(x):
if (isinstance(x, int) or isinstance(x,np.int... | slabanja/ase | ase/calculators/jacapo/validate.py | Python | gpl-2.0 | 9,130 | [
"ASE"
] | b76a9c869ec1b2063845ce49a1ce6f39f1628812aca46e525192817136ff7b44 |
import pylab as pyl
import cPickle as pickle
galaxies = pickle.load(open('galaxies.pickle','rb'))
galaxies = filter(lambda galaxy: galaxy.ston_I > 30., galaxies)
f1 = pyl.figure(1,figsize=(5,5))
f1s1 = f1.add_subplot(111)
#Upper and Lower limit arrow verts
arrowup_verts = [[0.,0.], [-1., -1], [0.,0.],
... | boada/ICD | sandbox/legacy_plot_code/plot_icd_vs_color.py | Python | mit | 706 | [
"Galaxy"
] | 503561a8f0f47e6f7ce2c1b25e8d3212b92939f12a284c3a55e6c48018b79071 |
# Copyright 2020,2021 Sony Corporation.
# Copyright 2021 Sony Group Corporation.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | sony/nnabla | python/src/nnabla/utils/get_file_handle.py | Python | apache-2.0 | 16,496 | [
"VisIt"
] | 7d6fe7d0227cfc6677d981425f9c15a6ccb5d7b1ba318dd4c5ec722168f4e658 |
import os
from os.path import dirname, join
from collections import OrderedDict
import pandas as pd
import numpy as np
import json
from bokeh.io import curdoc
from bokeh.layouts import row, widgetbox, column, gridplot, layout
from bokeh.models import Select, Div, Column, \
HoverTool, ColumnDataSource, Button, RadioB... | joshgabriel/dft-crossfilter | CompleteApp/crossfilter_app/main.py | Python | mit | 25,701 | [
"DMol3",
"VASP"
] | e0b1b2fd143b86ebcb9a637862436efa107420b5b4a521b155e5ee5eecd6e8e7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module implements symmetry-related structure forms.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__vers... | aykol/pymatgen | pymatgen/symmetry/structure.py | Python | mit | 2,612 | [
"pymatgen"
] | 75daec6536494c76f9644805102e2cdb37af914ec9f3f171ad82692f85ab4d26 |
#!/usr/bin/env python3
"""Cheap and simple API helper
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.3 $"
__date__ = "$Date: 2004... | jtraver/dev | python3/docker/apihelper.py | Python | mit | 1,806 | [
"VisIt"
] | 1319d2241dc996bc3f4bfe9a7f4535c22a84f2ef18ad6003e28a603b88123d1a |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import re
f... | harterj/moose | python/MooseDocs/extensions/special.py | Python | lgpl-2.1 | 1,411 | [
"MOOSE"
] | 43d12b714b5f6e8f02e051504ff12833f592064205c5d3fa9955128cf9dd471a |
# coding: utf-8
import unittest
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.util.testing import PymatgenTest
from pymatgen.util.coord import in_coord_list
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.analysis.wulff import WulffShape
... | dongsenfo/pymatgen | pymatgen/analysis/tests/test_wulff.py | Python | mit | 7,673 | [
"pymatgen"
] | 75e8928801424062d748ed86e7af04c415b45933e5239c26e54a418ab59795e2 |
"""
Tools for the instructor dashboard
"""
import json
import operator
import dateutil
from django.contrib.auth.models import User
from django.http import HttpResponseBadRequest
from django.utils.translation import ugettext as _
from opaque_keys.edx.keys import UsageKey
from pytz import UTC
from six import string_type... | jolyonb/edx-platform | lms/djangoapps/instructor/views/tools.py | Python | agpl-3.0 | 7,067 | [
"VisIt"
] | 0f9fa0e32147cd329ec5f06a9b3fd9512384cfb1354a5113d7e1cd2df6986694 |
#!/usr/bin/env python
## A function to generate an d-dimensional Gaussian data
import numpy as np
from numpy import random
import matplotlib.pyplot as plt
##Function to generate the gaussian data with the required mean and variance
## Inputs: mean(d-dimensional row vector)\
## S(d*d symmetric and positive definite... | WyoARCC/arcc-106-python | Examples/gaussian_generator.py | Python | mit | 841 | [
"Gaussian"
] | ea1c362f9c7da6afc9d8c1e26d4b41b6d37a18d31ac0bf8721f5ce5e72e4754f |
from pathlib import Path
import shutil
import tempfile
import pytest
# from pysisyphus.helpers import geom_loader, align_geoms
from pysisyphus.benchmarks import Benchmark
from pysisyphus.run import run_from_dict
from pysisyphus.testing import using
from pysisyphus.xyzloader import write_geoms_to_trj
ZmXTB = Benchma... | eljost/pysisyphus | tests/test_zimmerman_xtb/test_zimmerman_xtb.py | Python | gpl-3.0 | 3,009 | [
"xTB"
] | dbd10972ac43a64123312bec7e5b6ffc4881c49d2e8d6bea5d1bde47ae9b5dd3 |
#!/usr/bin/env python
"""
DragonPy - sbc09 memory info
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:created: 2013 by Jens Diemer - www.jensdiemer.de
:copyleft: 2013 by the DragonPy team, see AUTHORS for more details.
:license: GNU GPL v3 or above, see LICENSE for more details.
"""
import logging
from MC6809.co... | jedie/DragonPy | dragonpy/sbc09/mem_info.py | Python | gpl-3.0 | 28,292 | [
"VisIt"
] | 3cb4cc93bff464359f78a569f58bb8c916db5537136701e66d46df77a4626bb3 |
#!/usr/bin/env python
# Copyright 2019-2020 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... | gkc1000/pyscf | pyscf/solvent/pol_embed.py | Python | apache-2.0 | 13,515 | [
"PySCF"
] | 4265d8976524476d1c94fc39a2e190b851d9fbf3cdd35031eabfa21bb3b69e71 |
#!/usr/bin/python
import os.path
import sys
import os, time, subprocess
import textwrap
import argparse
import glob
install_dir = os.path.dirname(__file__)
print os.getcwd()
print install_dir
#os.chdir("/home/kaymazy/test/")
#os.mkdir('%s' %fastq[:-6])
#os.chdir('/home/kaymazy/test/%s' %fastq[:-6])
#outDir=os.getcwd(... | yasinkaymaz/endSeqTools | endSeq_tools.py | Python | gpl-3.0 | 25,738 | [
"BWA",
"Bowtie"
] | e42dcb00bc15023987f3cc9ff3295e02d89abdcceb38ba2ba55000b199626751 |
#!/usr/bin/env python2
# Script to analyze code and arrange ld sections.
#
# Copyright (C) 2008-2014 Kevin O'Connor <kevin@koconnor.net>
#
# This file may be distributed under the terms of the GNU GPLv3 license.
import operator
import sys
# LD script headers/trailers
COMMONHEADER = """
/* DO NOT EDIT! This is an au... | lynxis/seabios | scripts/layoutrom.py | Python | gpl-3.0 | 27,114 | [
"VisIt"
] | 5659e3f3650c8000f128df49bd9c83b2f333e5e6c59c2b6a645b6fe2600f51ad |
__author__ = 'Victoria'
from src.game.Creature import *
from src.game.Monsters import *
from src.game.Attributes import *
from src.game.StatePattern3 import *
from random import*
class Hero(Creatures, Observable, Observer, GameAttributes, HeroState):
attackState = None
roamState = None
runState = None
... | victorianorton/SimpleRPGGame | src/game/Heros.py | Python | mit | 5,717 | [
"VisIt"
] | 6d8ae604f60dcd77ac5d259237855a0703a0d1f08efc9f311aac89f35b317865 |
"""
Support for Google - Calendar Event Devices.
For more details about this platform, please refer to the documentation at
https://home-assistant.io/components/google/
NOTE TO OTHER DEVELOPERS: IF YOU ADD MORE SCOPES TO THE OAUTH THAN JUST
CALENDAR THEN USERS WILL NEED TO DELETE THEIR TOKEN_FILE. THEY WILL LOSE THEI... | Duoxilian/home-assistant | homeassistant/components/google.py | Python | mit | 9,710 | [
"VisIt"
] | 542e0abb2d42549caa4bc98ab72c422f1a239f05c262807a681fd7cd3ccfb370 |
#!/usr/bin/python3
try:
import smbus
except ImportError:
raise ImportError("python3-smbus not found. Install with 'sudo apt-get install python3-smbus'")
try:
import spidev
except ImportError:
raise ImportError("spidev not found. Visit https://www.abelectronics.co.uk/kb/article/2/spi-and-raspbian-linux-o... | abelectronicsuk/ABElectronics_Python3_Libraries | ExpanderPi/ABE_ExpanderPi.py | Python | mit | 29,372 | [
"TINKER",
"VisIt"
] | a8d807ec426a78480e611608daa943b589339ee5b6c00b64ba5864d22819179c |
# coding: utf-8
import datetime
import shutil
import tempfile
import zipfile
import os
from django.conf import settings
from django.contrib import messages
from django.contrib.auth.models import Group
from django.core.urlresolvers import reverse
from django.test import TestCase
from django.test.utils import override_s... | DevHugo/zds-site | zds/tutorialv2/tests/tests_views.py | Python | gpl-3.0 | 203,631 | [
"VisIt"
] | 05cdea94bd5137a8fa189f9bef94d6c597126809c53105a94e9c4d34af7730c1 |
# This plugin is adapted from the Python Console plugin and the IPython
# cookbook at:
# http://ipython.scipy.org/moin/Cookbook/EmbeddingInGTK
# Copyright (C) 2009-2010 Brian Parma
# Updated 2012 Brian Parma
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU... | sjohannes/exaile | plugins/ipconsole/__init__.py | Python | gpl-2.0 | 8,658 | [
"Brian"
] | f8095d00f7f1c6b4fc6ac10fd4a6715380e774eef15d9d1e4a8335ec5e0fa78e |
""" Python Obit SkyModel class
This class contains a sky model and can Fourier transform it
and subtract from or divide into a UV data..
Both FITS and AIPS cataloged files are supported.
SkyModel Members with python interfaces:
List - used to pass instructions to processing
Mosaic - ImageMosaic
"""
# $Id$
#-... | kernsuite-debian/obit | python/SkyModel.py | Python | gpl-2.0 | 37,357 | [
"Gaussian"
] | 95a2bd66e4dc715f8da007a6dc98284946e6aaabb1b4135f9665011098b38e9e |
## Copyright 2022 Google LLC
##
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
##
## https://www.apache.org/licenses/LICENSE-2.0
##
## Unless required by applicable law or agreed to in ... | google-business-communications/bm-snippets-python | send-message-authentication-request-suggestion.py | Python | apache-2.0 | 3,702 | [
"VisIt"
] | 7e31f37e08c549766f7fe03b3461f27c9fc78e7574370f0426c6a9762b31ebe9 |
#!/usr/bin/env python
"""Download PMIDs for references related to pubmed journals
Example:
$ python download_pmids.py outputfile
"""
from Bio import SeqIO
from Bio.Blast import NCBIWWW, NCBIXML
import re
import logging
__author__ = "Matthew Whiteside"
__copyright__ = "Copyright Government of Canada 2012-2... | superphy/insilico-subtyping | phylotyper/data/download/blast.py | Python | apache-2.0 | 3,757 | [
"BLAST"
] | 6c620a04c0d61b46d976795d37d8e094d4361ebe590ca636fce4255139d3a589 |
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