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from .model import Model
import numpy as np
import astropy.units as u
__all__ = ['Gaussian']
class Gaussian(Model):
def __init__(self, norm=1.e-5, ecenter=6.7, sigma=0.1,
lims=[(0, 1.e10), (0.0, 200.0), (0.0,100.0)],
units=['s^-1 cm^-2', 'keV', 'keV'],
name='Gaus... | eblur/xpysis | pyxsis/models/gaussian.py | Python | lgpl-3.0 | 1,815 | [
"Gaussian"
] | 95a2e02c18fd3e475269c1310f8c26245a435c24465a3f46f7b34fcbc1cc945e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright 2014, Dennis Drescher
# All rights reserved.
#
# This library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation; either version 2.1 of ... | thresherdj/shrinkypic | lib/shrinkypic/process/tools.py | Python | mit | 1,707 | [
"VisIt"
] | c0b019c94d71fa2df04b436e14b5f82dbc5d576d5c5d48137ba1c12c63c7ac89 |
'''
Created on Jun 20, 2012
@author: mkiyer
'''
import logging
import argparse
import sys
import os
import collections
import shelve
import pysam
from chimerascan.bx.cluster import ClusterTree
from chimerascan.lib import config
from chimerascan.lib.sam import get_aligned_intervals
from chimerascan.lib.chimera import... | tectronics/chimerascan | chimerascan/pipeline/cluster_discordant_reads.py | Python | gpl-3.0 | 8,905 | [
"pysam"
] | 8b974eabc14be2d8b6288755f613ad99c2425cf8569278aca946ccaa77f237aa |
"""
Standard GAN implemented on top of keras/tensorflow.
"""
import os
import pickle
import sys
from keras import applications
from keras import layers
from keras import models
from keras import optimizers
from keras.preprocessing import image
import numpy as np
from PIL import Image
from dlutils import plot_image_... | wayaai/GAN-Sandbox | gan.py | Python | mit | 9,658 | [
"Gaussian"
] | 6591f59c715d580144db7ba35f1ad29b9c1af6f94679100d4407fb1b4a530048 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | fedepad/espressopp | src/interaction/LennardJonesCapped.py | Python | gpl-3.0 | 12,810 | [
"ESPResSo"
] | eb7cdcc39a7a0fbac7a654831e3a681116efb04c7fcaf2b4848b420daf01fd4e |
"""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:
knownfiles -- list ... | lfcnassif/MultiContentViewer | release/modules/ext/libreoffice/program/python-core-3.3.0/lib/mimetypes.py | Python | lgpl-3.0 | 20,483 | [
"NetCDF"
] | d204b84f09c0e77b01a1279ee459f7bd0fcc13b2ce31a5e5ba61cf3ab04bbe6f |
"""
GLM connected by a sparse network and Gaussian weights.
"""
import numpy as np
SbmWeightedModel = \
{
# Number of neurons (parametric model!)
'N' : 1,
# Parameters of the nonlinearity
'nonlinearity' :
{
'type' : 'explinear'
},
# Parameters of the bias
... | slinderman/theano_pyglm | pyglm/models/sbm_weighted_model.py | Python | mit | 2,306 | [
"Gaussian"
] | e471dfcb812e9c268afd5812543bd5edddbaa4c9e60e815ff63ece679d8a902e |
from __future__ import print_function, division, absolute_import #, unicode_literals
import sys
import os
import imp
import platform
import re
from tests.pymods.termcolor import cprint
# Handle py2, py3k differences.
py2 = sys.version_info[0] <= 2
if py2:
import cPickle as pickle
from cStringIO import String... | abinit/abinit | tests/__init__.py | Python | gpl-3.0 | 35,051 | [
"ABINIT",
"NetCDF",
"VASP",
"Wannier90"
] | 50b4eb47c456792bd91532e224f4b04775373396aa1b16faa5ac9ae682edc56a |
from ResoFit.calibration import Calibration
from ResoFit.fitresonance import FitResonance
from ResoFit.experiment import Experiment
import matplotlib.pyplot as plt
import numpy as np
import pprint
from ResoFit._utilities import get_foil_density_gcm3
from ResoFit._utilities import Layer
# Global parameters
energy_min =... | ornlneutronimaging/ResoFit | ResoFit/data/IPTS_19558/ipts_19558_UGd.py | Python | bsd-3-clause | 3,938 | [
"Gaussian"
] | 7a5674e358447d6400fda85828c67db0dbc551675f2c21c01a2bd7ad7398f8de |
# Test export module
import os
import flopy
pth = os.path.join('..', 'examples', 'data', 'mf2005_test')
namfiles = [namfile for namfile in os.listdir(pth) if namfile.endswith('.nam')]
#skip = ["MNW2-Fig28.nam", "testsfr2.nam", "testsfr2_tab.nam"]
skip = []
def export_netcdf(namfile):
if namfile in skip:
r... | mrustl/flopy | autotest/t007_test.py | Python | bsd-3-clause | 9,916 | [
"NetCDF"
] | 63f1d53f98fbfb6fb20e46720f47f9856327ec7320d6f900d5206d85dd58ce46 |
import sys
sys.path.insert(1, "../../../")
import h2o
def offsets_and_distributions(ip,port):
# cars
cars = h2o.upload_file(h2o.locate("smalldata/junit/cars_20mpg.csv"))
cars = cars[cars["economy_20mpg"].isna() == 0]
cars["economy_20mpg"] = cars["economy_20mpg"].asfactor()
offset = h2o.H2OFrame(py... | weaver-viii/h2o-3 | h2o-py/tests/testdir_algos/deeplearning/pyunit_offsets_and_distributionsDeeplearning.py | Python | apache-2.0 | 1,609 | [
"Gaussian"
] | 60a506a3bc0c71db99eb812ab247b88d955f8b0085faac86c594068bbff9195b |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | Laurawly/tvm-1 | tests/micro/arduino/test_arduino_rpc_server.py | Python | apache-2.0 | 13,580 | [
"VisIt"
] | 9abfd8929686e22840b511ca33a5cfc0e929ee198b32dfb9ad339cb5301b972c |
"""
Utils for working with ReferenceGenome maker.
"""
import os
import tempfile
from Bio import SeqIO
from django.conf import settings
from reference_genome_maker import reference_genome_maker
# from debug.debug_util import FakeException
from main.exceptions import ValidationException
from main.model_utils import cl... | woodymit/millstone | genome_designer/utils/reference_genome_maker_util.py | Python | mit | 4,642 | [
"Biopython"
] | 27796914995c5bd2387f23fdd387c8d6c51afeb9674bcc4c5d453fa7b16def10 |
# -*- coding: utf-8 -*-
"""
pyxs.client
~~~~~~~~~~~
This module implements XenStore client, which can communicate with
XenStore either via: :class:`~pyxs.connection.UnixSocketConnection`
or :class:`~pyxs.connection.XenBusConnection`.
:copyright: (c) 2011 by Selectel.
:copyright: (c) 2016 b... | selectel/pyxs | pyxs/client.py | Python | lgpl-3.0 | 23,703 | [
"TINKER"
] | a97c64a1dfc4709dbcf4952e0a28f2abd045500a8cb8452ecdafb1626d03a431 |
#!/usr/bin/env python3
import json
import random
import string
import resource
from ast import parse
from logging import getLogger
from traceback import print_exc
from xml.etree.ElementTree import Element
from xml.etree.ElementTree import tostring
import html5lib
from webob import Request
from webob import Response
fr... | rcarmo/pythonium | web-console/wsgi.py | Python | lgpl-2.1 | 4,900 | [
"VisIt"
] | 09471c517bdd3638133c44755d9cb8290836a760d12e2b3405d0678d0bab3a97 |
# coding: utf-8
# # Test out standardized ADCIRC, SELFE and FVCOM datasets
#
# The datasets being accessed here are NetCDF files from ADCIRC, SELFE and FVCOM, with attributes added or modified virtually using NcML to meet the [UGRID conevntions standard for unstructured grid models](https://github.com/ugrid-conv... | NOAA-ORR-ERD/gridded | examples/UGRID_plotting_COMT.py | Python | unlicense | 4,515 | [
"NetCDF"
] | 9c8990823b4ae8eb567d34163a1f955cacb461d8d2f68df1e6217c2df70df749 |
import os
import unittest
from monty.serialization import loadfn
from pymatgen.util.testing import PymatgenTest
class IRDielectricTensorTest(PymatgenTest):
def setUp(self):
self.ir_spectra = loadfn(os.path.join(PymatgenTest.TEST_FILES_DIR, "ir_spectra_mp-991652_DDB.json"))
def test_basic(self):
... | vorwerkc/pymatgen | pymatgen/phonon/tests/test_ir_spectra.py | Python | mit | 666 | [
"pymatgen"
] | 3b77b4318fe9dac48bd89b6beeea4fa358fe810ff1054ebc505cddf8c9ee81d3 |
#-------------------------------------------------------------------------------------------------------------------#
#
# IB2d is an Immersed Boundary Code (IB) for solving fully coupled
# fluid-structure interaction models. This version of the code is based off of
# Peskin's Immersed Boundary Method Paper in Acta N... | nickabattista/IB2d | data_analysis/analysis_in_python/Example_For_Data_Analysis/Example_Channel_Flow_Analysis.py | Python | gpl-3.0 | 10,244 | [
"VTK"
] | 8b31566817c97011a18bf70c9da4a1a116e1cb3779e22f2ecbbb50177aefd9fc |
# ============================================================================
#
# 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/one2manydelegate.py | Python | gpl-2.0 | 2,483 | [
"VisIt"
] | fd3ce251d057acba31057b18b6caad3738c3acc410f31cde1402fc5901cfbdcb |
""" ModuleBase - contains the base class for workflow modules. Defines several common utility methods.
The modules defined within this package are developed in a way to be executed by a DIRAC.Core.Worfklow.Worfklow.
In particular, a DIRAC.Core.Workflow.Worfklow object will only call the "execute" function, tha... | yujikato/DIRAC | src/DIRAC/Workflow/Modules/ModuleBase.py | Python | gpl-3.0 | 21,527 | [
"DIRAC"
] | 5fdb415cfc2460487785311c4adc18527e63d18a92342530b676b092288f24c6 |
#!/usr/bin/env python2
# -*- coding: utf8 -*-
"""Pipeline for Goodman High Troughput Spectrograph spectra Extraction.
This program finds reduced images, i.e. trimmed, bias subtracted, flat fielded,
etc. that match the ``<pattern>`` in the source folder, then classify them in
two groups: Science or Lamps. For science i... | soar-telescope/goodman | goodman_pipeline/spectroscopy/redspec.py | Python | bsd-3-clause | 22,879 | [
"Gaussian"
] | 4dc41fb01d10da40a542976175b15b838e9568819c8901c7b31529f709dc6f4d |
""" PlotBase is a base class for various Graphs plots
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/Phedex Project by ... <to be added>
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from DIRAC.Core.Utilitie... | yujikato/DIRAC | src/DIRAC/Core/Utilities/Graphs/PlotBase.py | Python | gpl-3.0 | 9,056 | [
"DIRAC"
] | 26e358205ae878967882edbf6949b103f1fb026a72a1c83481e8d592e228e837 |
# Copyright (C) 2014 Olaf Lenz
#
# 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 version.
#
# ESPR... | jdegraaf/espresso | src/python/espressomd/__init__.py | Python | gpl-3.0 | 1,170 | [
"ESPResSo"
] | ec1d91be650200662a03b257802192e5cfc6c211145b556ff2836ec40764a6d1 |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core import GP
from .. import likelihoods
from ..util.input_warping_functions import KumarWarping
from .. import kern
class InputWarpedGP(GP):
"""Input Warped GP
This d... | SheffieldML/GPy | GPy/models/input_warped_gp.py | Python | bsd-3-clause | 5,297 | [
"Gaussian"
] | 75b54e776711f600ca1e006b07c437154699935a98a65b26a356136de86937e7 |
# -*- 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/lib/test_pkdtree.py | Python | gpl-2.0 | 6,303 | [
"MDAnalysis"
] | 82386e07db0f064c43b6eabcb95b47cde6ef21eccb3b61f30c5c86bcab327169 |
import numpy as np
import histomicstk as htk
import histomicstk.filters.shape as htk_shape_filters
def detect_nuclei_kofahi(im_nuclei_stain, im_nuclei_fgnd_mask, min_radius,
max_radius, min_nucleus_area, local_max_search_radius):
"""Performs a nuclear segmentation using kofahi's method.... | DigitalSlideArchive/HistomicsTK | histomicstk/segmentation/nuclear/detect_nuclei_kofahi.py | Python | apache-2.0 | 3,114 | [
"Gaussian"
] | 64b4d498a467189c4c6a1b58934190b7e9cd92ae47b8ebd8e77525931d955d70 |
#=============================================================================
# gpx_layer_routes.py
# Copyright 2013--2016, Trinity College
# Last modified: 31 March 2016
#=============================================================================
import gtk
import math
import pykarta.geometry
import pykarta.draw
... | david672orford/GPX_Trip_Planner | Code/gpx_layer_routes.py | Python | gpl-2.0 | 13,152 | [
"FLEUR"
] | b188a74016853d4d02bb1d6e75ebd0219fa7e62f8ff272726dcac03e04399e2c |
# -*- coding: utf-8 -*-
# (c) 2016-2021 Andreas Motl <andreas.motl@elmyra.de>
import tempfile
from pprint import pprint
from string import Template
from pkg_resources import resource_string
from twisted.web.template import renderElement
from twisted.logger import Logger
from kotori.io.export.html import DygraphsPage
fr... | daq-tools/kotori | kotori/io/export/plot.py | Python | agpl-3.0 | 14,561 | [
"NetCDF"
] | ab313b8d9752deb1e2b890ea6ec8b0288d6c92e4c647568f85382e769166ce80 |
#!/usr/bin/env python3
from uiautomator import device as d
import os
import random
# from shapely.geometry import polygon
def get_ui_object(string_id_name):
return d(resourceId="com.facebook.orca:id/" + string_id_name)
# nexus 4
# rim size 184
# width 768
# height 1184
# max possible rim right x 676 (768 -1/... | Tanapruk/fb_emoji_basketball | auto_shoot.py | Python | mit | 11,087 | [
"ORCA"
] | 08283cbdf69db0e8ba445bcc90df45ab8e798b0ebdad9f96f9cc8189cab3b26f |
#!/usr/bin/python
#
# ThotKeeper -- a personal daily journal application.
#
# Copyright (c) 2004-2008 C. Michael Pilato. All rights reserved.
#
# By using this file, you agree to the terms and conditions set forth in
# the LICENSE file which can be found at the top level of the ThotKeeper
# distribution.
#
# Website: ... | Isendir/thotkeeper | lib/tk_main.py | Python | bsd-2-clause | 65,243 | [
"VisIt"
] | 9740f2ec5f8de1ddbfaef00fdafa06c2edc20a3533447ee5f1a6b3a9f698e40d |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Allow Sz value to be changed during the SCF iteration.
'''
from pyscf import gto, scf
mol = gto.M(atom='O 0 0 0; O 0 0 1')
mf = scf.UHF(mol)
mf.verbose = 4
mf = scf.addons.dynamic_sz_(mf)
mf.kernel()
| gkc1000/pyscf | examples/scf/53-dynamic_sz.py | Python | apache-2.0 | 277 | [
"PySCF"
] | 1396bd0a7c19e69e011e9f3a18a68c3984bf0a199980b2765e9619cc80e2eb21 |
#/*
# *
# * SimilarTracks for Kodi.
# *
# * Copyright (C) 2015 Brian Hornsby
# *
# * This program is free software: you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation, either version 3 of the License, or
# * (at your option) an... | brianhornsby/script.similartracks | resources/lib/kodisettings.py | Python | gpl-3.0 | 2,008 | [
"Brian"
] | c8b868eab473af13bedb896fd48b7a5f6956e36e6f2e2854fb232b8bbdbc9f66 |
# -*- coding: utf-8 -*-
"""
Created on Mon Sep 29 22:53:20 2014
@author: warrenmorningstar
"""
# ======================================================================
from astropy import units, constants
from astropy.cosmology import FlatLambdaCDM
import numpy as np
import evillens as evil
from scipy.interpolate im... | wmorning/EvilLens | evillens/exponentialdiskLens.py | Python | gpl-2.0 | 3,575 | [
"Galaxy"
] | 5dfa3f47baffba7b854baafba2193eac4bbc9ee77c6462ea36c0e55175b83636 |
from gpaw import GPAW, restart, FermiDirac, PoissonSolver
from ase import Atoms
from gpaw.test import equal, gen
import os
from gpaw.mpi import world
gen('Si', xcname='GLLBSC')
e = {}
niter = {}
energy_tolerance = 0.0001
niter_tolerance = 0
e_ref = {'LDA': {'restart': -5.5728768784094758},
'GLLBSC': {'rest... | ajylee/gpaw-rtxs | gpaw/test/restart_band_structure.py | Python | gpl-3.0 | 1,885 | [
"ASE",
"GPAW"
] | 1e11bebcef71949e2f4b9edb02cb36d497756e56dcbe2433fc4ce3f8f30e87b7 |
"""
Contains the user interface in the Universe class
"""
import logging, common, os, string
from random import choice
from galaxy import web, config
log = logging.getLogger( __name__ )
class User( common.Root ):
@web.expose
def index( self, trans, **kwd ):
if trans.get_user():
trans.respo... | jmchilton/galaxy-central | galaxy/interfaces/user.py | Python | mit | 8,575 | [
"Galaxy"
] | 053a4d2fa4c343638364b46b7b596ee558d19374928a6abba3769d5a8b25c2c2 |
# ImportDataLibraries/ImportDataLibraries.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py
# to make a new Galaxy tool called ImportDataLibraries
# User admin@galaxy.org at 04/05/2015 11:45:42
# rgToolFactory.py
# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# co... | myoshimura080822/tools_of_preanalysis_on_docker_galaxy | ImportDataLibraries/ImportDataLibraries.py | Python | mit | 32,545 | [
"Galaxy"
] | 8f5220c61c49e7099367516162f2d5150f30508573d3eadad2c1d3ce501ce73c |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements an interface to the VAMPIRE code for atomistic
simulations of magnetic materials.
This module depends on a compiled vampire executable available in the path.
Please download at https://vampire.york.... | materialsproject/pymatgen | pymatgen/command_line/vampire_caller.py | Python | mit | 15,042 | [
"pymatgen"
] | d437f1f4c583a7733e937ac44e5aaf8ca1df44e7dfbceb5af897f3bd3fd042dc |
import numpy
from scipy.signal import detrend
from statsmodels.tsa import tsatools
from numpy import linalg
from statsmodels.tsa.stattools import adfuller
__author__ = 'Christophe'
def is_not_stationary(v, significance='5%', max_d=6, reg='nc', autolag='AIC'):
""" Augmented Dickey Fuller test for a unit root in a... | chris-ch/cointeg | src/statsext/cointeg.py | Python | gpl-3.0 | 9,098 | [
"ADF"
] | 37684a5efa08abb4ffa95c11e5e07c21abf79f2f629858a97e9d6a468fe93b51 |
"""Data models to store and process data. """
from django.db import models
class Transcript(models.Model):
"""A class for storing Transcript data. """
transcript_id = models.CharField(primary_key=True, max_length=100)
gene_id = models.CharField(max_length=100)
sequence = models.TextField(null=False)... | michal-stuglik/newtbase | newtbase/models.py | Python | gpl-2.0 | 3,504 | [
"BLAST"
] | c40b1cbd9cc69f7747cfc945504573c5342b1696b5578e2d7500a1bbd3c7fbe5 |
"""Some kind of template matching -- looking for temporal shapes in a
sequence"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from six.moves import xrange
import tensorflow as tf
def online_saw_tensors(batch_size, sequence_length, block_size, stddev=1... | PFCM/datasets | rnndatasets/synthetic/template/template.py | Python | bsd-3-clause | 6,819 | [
"Gaussian"
] | 240d96d4b40c9330f39e773d175c92bb5f96c342153feada9885f560f638060c |
#!/usr/bin/env python
# This code extracts the phonon DOS information from total_dos.dat generated by Phonopy code
# It then finds the last two peaks in DOS so that the frequency at which those peaks occured
# are assumed to be longitudinal optiocal (LO) and transverse optical (TO) phonon frequencies
# Please contact ... | albalu/Handy-VASP-DFT-Calculations-Scripts | find_DOS_peaks.py | Python | gpl-3.0 | 1,744 | [
"phonopy"
] | 217334c480e33ff3df76c3553aeb1b406263658c1a9cc758443e4b3e5731f883 |
#! /usr/local/bioinfo/python/3.4.3_build2/bin/python
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC
import pandas as pd
import argparse
def importBlastOutput():
'''
Import Blast output using pandas read_csv.
Pandas dataframe will used to make a lis... | 3nrique0/Tools_for_Bioinformatics | blast_and_extract/4_extract_genomic_sequences.py | Python | gpl-3.0 | 8,475 | [
"BLAST"
] | 90ef517f1b06571f8ff21d9074d9a74f481195cde2614a1e654ec5d6cc57f62b |
#
# When publishing work that uses these basis sets, please use the following citation:
#
# K.G. Dyall, Theor. Chem. Acc. (1998) 99:366; addendum Theor. Chem. Acc. (2002) 108:365;
# revision Theor. Chem. Acc. (2006) 115:441. Basis sets available from the Dirac web site,
# http://dirac.chem.sdu.dk.
Pt = [[0, -1, [623... | gkc1000/pyscf | pyscf/gto/basis/dyall_tz.py | Python | apache-2.0 | 13,036 | [
"DIRAC"
] | e906c9f475786dde8531ce1422b59864b5d0da45cd5909463cb983c11325fcb0 |
import io
import json
import re
import os
import sys
import click
from subprocess import CalledProcessError, Popen, PIPE
from httpie.context import Environment
from httpie.core import main as httpie_main
from parsimonious.exceptions import ParseError, VisitationError
from parsimonious.grammar import Grammar
from par... | eliangcs/http-prompt | http_prompt/execution.py | Python | mit | 20,120 | [
"VisIt"
] | 27f43a6dd6bc101f3932a4084758dc5a739187ce0ba2d94cd4c6fdf34884dd21 |
# -*- coding: utf-8 -*-
"""
General utilities and exceptions.
"""
from collections import defaultdict, namedtuple, OrderedDict
try:
from collections.abc import ItemsView, Mapping
except ImportError: # Python 2
ItemsView = list
from collections import Mapping
from functools import wraps
from itertools imp... | bjodah/chempy | chempy/util/pyutil.py | Python | bsd-2-clause | 8,881 | [
"ChemPy"
] | ce3af5cfd8d369d44dc59adf1073e62eca0c6f93c3ee652d48364a7cac8b1636 |
# Copyright 2015 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... | hfp/tensorflow-xsmm | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 119,847 | [
"Gaussian"
] | d8ac7698022555bbcf8d2a53d257729258b610b2a9a44ffefcf955adff5d6922 |
#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import math
import srwl_uti_smp
def set_optics(v, names=None, want_final_propagation=True):
el = []
pp = []
if not names:
names = ['S0', 'S0_HDM', 'H... | radiasoft/sirepo | tests/template/srw_generate_data/nsls-ii-chx-beamline.py | Python | apache-2.0 | 32,074 | [
"Gaussian"
] | 80acf77648ae84cc6deba173b5b1e9291b442e6383b9881c69799d08f938f462 |
# This file is part of Androguard.
#
# Copyright (c) 2012 Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# 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://... | reox/androguard | androguard/decompiler/dad/writer.py | Python | apache-2.0 | 26,467 | [
"VisIt"
] | 83d5ca8d634eb159cd0faeae0dceb909cbc97775d977ec8ad2c517dd2d8ee4ba |
# OpenFermion plugin to interface with Psi4
# Copyright 2017 The OpenFermion Developers.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at ... | quantumlib/OpenFermion-Psi4 | examples/plotter.py | Python | lgpl-3.0 | 3,307 | [
"Psi4"
] | 8d555d90226edf3248916f73e0f9fc6b2120a215aa1b765ebc259d40a7f757e2 |
"""
Estimate Functional Connectivity using an estimator for Sparse Inverse Covariances
==================================================================================
This example constructs a functional connectome using the sparse penalized MLE
estimator implemented using QUIC.
This function extracts time-series f... | skggm/skggm | examples/plot_functional_brain_networks.py | Python | mit | 3,539 | [
"NEURON"
] | 9453dc8e751933f7cfc015af789651e47c5a8f2dd2bfcbf2a14d741b6bc97762 |
# coding: utf8
{
'': '',
' Quotas: %(quotas)s x%(quota_amount).2f': ' Cuotas: %(quotas)s x%(quota_amount).2f',
' Transaction number: %s': ' Número de transacción: %s',
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" es una expresión opcional ... | reingart/erplibre | languages/es-ar.py | Python | agpl-3.0 | 43,217 | [
"VisIt"
] | 5294ff38ae5e3b3c348dcf2173e9bff09bd18188a4ddf27107279b874c57595c |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You s... | Clyde-fare/cclib | src/cclib/bridge/cclib2openbabel.py | Python | lgpl-2.1 | 1,577 | [
"Open Babel",
"cclib"
] | addf9f68019edfba11fe18293cc906b4377ae34c06fe9881b46365e3b3563c42 |
# -*- coding: utf-8 -*-
"""
Created on Fri May 04 10:26:49 2018
@author: Mostafa Meliani <melimostafa@gmail.com>
Multi-Fidelity co-Kriging: recursive formulation with autoregressive model of
order 1 (AR1)
Adapted on January 2021 by Andres Lopez-Lopera to the new SMT version
"""
from copy import deepcopy
import numpy... | relf/smt | smt/applications/mfk.py | Python | bsd-3-clause | 27,354 | [
"Gaussian"
] | b8d5f7d61dad2ec0a38a8daa4c0eda99182ea09cea01c89eb1b28e4082b5ec44 |
# created by Chirath R, chirath.02@gmail.com
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import datetime
from smtplib import SMTPException
from django.contrib.auth.models import User
from django import forms
from django.contrib.sites.shortcuts import get_current_site
from django.forms.utils import... | akshayharidas/fosswebsite | promotion/views.py | Python | mit | 12,308 | [
"VisIt"
] | ec3c1a4c72ef04ecb2541f7b17e255b6c827b795e45fc756d503ef9ee6758177 |
import os
import Rappture
from Rappture.tools import executeCommand as RapptureExec
import shutil
import math
import numpy as np
import scipy.spatial.distance as scdistance
from tempfile import mkstemp
import sys
import re
def log(msg):
try:
driver.put('output.log(output_log)', msg, append=True)
dr... | NanoBioNode/nanoDDSCATplus | rappture/ddaconvert/ddaconvert.py | Python | gpl-3.0 | 48,072 | [
"VTK"
] | 9b2a17d10b648e3adcd398e30f1724bb90bfd9b4415308aeb6ab382af05b8b5a |
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/main/search_indexes.py | Python | apache-2.0 | 5,696 | [
"Galaxy"
] | a6f1625f9186b9de3b185cddd9b742662c70503a50d15c8bb1faabd675a86640 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/ajax/workinprogress.py | Python | gpl-2.0 | 4,803 | [
"VisIt"
] | b178f0725d85f25f6bd77fad7ac7a18ce58e8ffd3f05429a2d56b9d4f49e9b0b |
# $Id$
#
# Copyright (C) 2009 Greg Landrum
# All Rights Reserved
#
from __future__ import print_function
from rdkit.six.moves import cPickle
from rdkit.six import iterkeys
from rdkit import DataStructs,Chem
from rdkit import Chem
similarityMethods={'RDK':DataStructs.ExplicitBitVect,
'AtomPairs':Dat... | soerendip42/rdkit | rdkit/Chem/MolDb/FingerprintUtils.py | Python | bsd-3-clause | 3,481 | [
"RDKit"
] | d8e6af500e52fa75b444498b336266e8c39fd7c2a5a923ba407b04398f6cb11d |
from __future__ import print_function, division
import os
import tempfile
import h5py
import numpy as np
from numpy.testing import assert_array_almost_equal_nulp
from ...dust import IsotropicDust
from .. import Model
from ...util.functions import random_id
def get_test_dust():
dust = IsotropicDust([3.e9, 3.e16... | bluescarni/hyperion | hyperion/model/tests/test_helpers.py | Python | bsd-2-clause | 3,671 | [
"VisIt"
] | 33525f4c0ad714035e0b7c403b3d0cf54aba9a3d50eba319390dc11fb2344756 |
# Copyright (c) Charl P. Botha, TU Delft.
# All rights reserved.
# See COPYRIGHT for details.
# Hello there person reading this source!
# At the moment, I'm trying to get a fully-functioning DICOM browser
# out the door as fast as possible. As soon as the first version is
# out there and my one user can start giving ... | nagyistoce/devide | modules/viewers/DICOMBrowser.py | Python | bsd-3-clause | 44,972 | [
"VTK"
] | 621f05756f97b3fe7055dbe4343854fa3957bb8e543a8fd9e61733af9aad6f13 |
"""Contains a class for custom particle filters in Python."""
from abc import abstractmethod
from collections.abc import Hashable, Callable
class CustomFilter(Hashable, Callable):
"""Abstract base class for custom particle filters.
The class allows the definition of particle filters in Python (see
`hoomd... | joaander/hoomd-blue | hoomd/filter/custom.py | Python | bsd-3-clause | 3,688 | [
"HOOMD-blue"
] | a2fde33c00e040aecd1aababb81c0b400543c972fe5a3d23c0f8a4c2efc5b439 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
=============================================================
Compare the effect of different scalers on data with outliers
=============================================================
Feature 0 (median income in a block) and feature 5 (number of households) of
the `... | BiaDarkia/scikit-learn | examples/preprocessing/plot_all_scaling.py | Python | bsd-3-clause | 13,982 | [
"Gaussian"
] | 171ec00ca5520ab8b3c317d5fc06fe58f5d79abae96c75f5fff41464416482e9 |
import pytest
import smartsheet
@pytest.mark.usefixtures("smart_setup")
class TestGroups:
group = None
members = None
def test_create_group(self, smart_setup):
smart = smart_setup['smart']
group = smart.models.Group({
'name': 'Knuckleheads',
'description': 'Why, I o... | smartsheet-platform/smartsheet-python-sdk | tests/integration/test_groups.py | Python | apache-2.0 | 2,846 | [
"MOE"
] | bd6c2b797822bb194ea250f432034a1e7d803531f76afb8b1fb53ac59964bd44 |
#!/usr/bin/python
# -------------------------------------------------------------------------
# Hygrosens Support Library
# Copyright 2005 by Brian C. Lane
# All rights Reserved
# Licensed under GPL v2, see the COPYRIGHT and COPYING files
# =========================================================================
# 06... | bcl/hygrosens | hygrosens/__init__.py | Python | gpl-2.0 | 7,413 | [
"Brian"
] | 627fc7e2366a59f04ba8d16674925035f32ba060274b7f6f1b3efdc632c2fccb |
"""
Service class implements the server side part of the DISET protocol
There are 2 main parts in this class:
- All useful functions for initialization
- All useful functions to handle the requests
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function... | ic-hep/DIRAC | src/DIRAC/Core/DISET/private/Service.py | Python | gpl-3.0 | 30,426 | [
"DIRAC"
] | 9651b879461eb6437339240ba6eb932fd781d510ed29ea7b5dcdf29b56ed220a |
# Class to handle the notification email.
from irrigator_pro.settings import NOTIFICATION_SMTP, NOTIFICATION_HOST, NOTIFICATION_PORT
import smtplib
from tabulate import tabulate # Still needed?
from datetime import date
from email.mime.text import MIMEText
from email.mime.multipart import MIMEMultipart
class EmailL... | warnes/irrigatorpro | irrigator_pro/notifications/notification_email.py | Python | mit | 3,301 | [
"VisIt"
] | 87d2262a6ea384da322b0c054610d0133f638f65b0618c74275cf513d80c4041 |
"""
Type Abstract Domain
====================
Non-relational abstract domain to be used for **input data assumption analysis**.
The set of possible values of a program variable in a state is represented as a type.
:Authors: Caterina Urban and Madelin Schumacher
"""
from collections import defaultdict
from copy import... | caterinaurban/Lyra | src/lyra/abstract_domains/assumption/type_domain.py | Python | mpl-2.0 | 50,970 | [
"VisIt"
] | 34b221628fabc1823f6148877c8fca105f1afad850a31add7e1588c595291035 |
#!/usr/bin/env python
from ROOT import gRandom, TH1, TH1D, gROOT, cout, TMath, gStyle
gROOT.LoadMacro( "$HOME/Downloads/RooUnfold/libRooUnfold.so" )
from ROOT import RooUnfoldResponse
from ROOT import RooUnfoldBayes
from ROOT import RooUnfoldSvd
from ROOT import RooUnfoldTUnfold
from ROOT import RooUnfoldInvert
from... | skluth/RooUnfold | examples/RooUnfoldTest.py | Python | apache-2.0 | 16,544 | [
"Gaussian"
] | c646fdb0c511ae0c3fb276676ffa8b995cd9a19266ab2a51249720cef9372ef4 |
# -*- coding: utf-8 -*-
# This file is part of Shuup.
#
# Copyright (c) 2012-2016, Shoop Commerce Ltd. All rights reserved.
#
# This source code is licensed under the AGPLv3 license found in the
# LICENSE file in the root directory of this source tree.
import os
import pytest
from django.core.urlresolvers import reve... | suutari/shoop | shuup_tests/browser/front/test_category_view.py | Python | agpl-3.0 | 15,273 | [
"VisIt"
] | 78326573492719d8ed35692e0cf34872b9a99cee9a7e01e7fe4fa4676d3ab315 |
# -*- coding: utf-8 -*-
"""Top-level display functions for displaying object in different formats.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2013 The IPython Development Team
#
# Distributed under the terms of the BSD License. ... | mattvonrocketstein/smash | smashlib/ipy3x/core/display.py | Python | mit | 32,493 | [
"Brian"
] | 49fcdfb73a2c351021f7454b43c6132132f89c5f6b2c6c6d9aaa26907d9ae6ee |
# converted to java and then to python by p.j.leonard
# based on C++ code found at
# http://www.codeproject.com/KB/recipes/BP.aspx?msg=2809798#xx2809798xx
import math
import random
import copy
import pickle
"""
multilayer neural network
"""
def sigmoid(x):
if x < -100.0: # avoid... | pauljohnleonard/pod-world | CI_2015/demos/brains/feedforwardbrain.py | Python | gpl-2.0 | 6,562 | [
"NEURON"
] | 44740db3274b4e0967a3cbf10d39412851534e97e31d3c14b9f0826805485ced |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import xml.etree.ElementTree
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_HTTPError,
compat_http_client,
compat_... | puckipedia/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 55,659 | [
"VisIt"
] | ebd0b5ee24ac0a2c9ff5d98fe061e3603e92f0802d852a4c465419ff90a356bc |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2011 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the Licens... | andrebellafronte/stoq | stoqlib/gui/stockicons.py | Python | gpl-2.0 | 8,754 | [
"VisIt"
] | 9df04608941633486d7303d5a296b24fd3341300848932e83909a82917a854e8 |
#
# libtcod 1.5.2 python wrapper
# Copyright (c) 2008,2009,2010 Jice & Mingos
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright... | brycepg/cave-dweller | cave_dweller/libtcodpy.py | Python | gpl-3.0 | 61,662 | [
"Amber"
] | d9bc6a08683c4dda40f808cb11cc9597349669d1b39f716eec5e2c6cb959d2cf |
''' Synchronizer
Module that keeps the database synchronized with the CS
Module that updates the RSS database ( ResourceStatusDB ) with the information
in the Resources section. If there are additions in the CS, those are incorporated
to the DB. If there are deletions, entries in RSS tables for those elements ... | marcelovilaca/DIRAC | ResourceStatusSystem/Utilities/Synchronizer.py | Python | gpl-3.0 | 21,652 | [
"DIRAC"
] | 9b31d0d80716f1b9cae21c96ac84e9c4fb04afc81648c172be13184343f335a8 |
# -*- coding: utf-8 -*-
try:
# Python 2.7
from collections import OrderedDict
except:
# Python 2.6
from gluon.contrib.simplejson.ordered_dict import OrderedDict
from gluon import current
from gluon.html import *
from gluon.storage import Storage
from gluon.validators import IS_NOT_EMPTY
from s3 impor... | sahana/Turkey | modules/templates/Philippines/config.py | Python | mit | 139,396 | [
"Amber"
] | 2adfbbee3586969b5302c259cdbc9bd9db3b48d05543cfb7c2950dd03f819a13 |
"""
=========================
Bayesian Ridge Regression
=========================
Computes a Bayesian Ridge Regression on a synthetic dataset.
See :ref:`bayesian_ridge_regression` for more information on the regressor.
Compared to the OLS (ordinary least squares) estimator, the coefficient
weights are slightly shift... | ldirer/scikit-learn | examples/linear_model/plot_bayesian_ridge.py | Python | bsd-3-clause | 3,875 | [
"Gaussian"
] | b86e0761b7baa717d33d8c299613a36cbbb623b60626fc762cf27368e1c2cccc |
# This file is part of COFFEE
#
# COFFEE is Copyright (c) 2014, Imperial College London.
# Please see the AUTHORS file in the main source directory for
# a full list of copyright holders. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided ... | gmarkall/COFFEE | coffee/loop_scheduler.py | Python | bsd-3-clause | 39,807 | [
"VisIt"
] | 19c0b4030dcf9ae57fc005d3862d951b6ae311b5d5406d9a112f765b9fbcb573 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
This module implements various transmuter classes.
Transmuters are essentially classes that generate TransformedStructures from
various data sources. They enable the... | matk86/pymatgen | pymatgen/alchemy/transmuters.py | Python | mit | 15,774 | [
"VASP",
"pymatgen"
] | 4691f98b8b858483d30d4f9b641fac3dc9c246c14fb05793be9344939886729c |
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit import DataStructs
import os
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from sklearn import linear_model, externals
from IPython.display import display
# This is James Sungjin Kim's library
impor... | jskDr/jamespy_py3 | jpandas.py | Python | mit | 76,236 | [
"RDKit"
] | 45cd55eca9284b9f61a18a62938920a36f86c290a920687b92ea6bfd77519220 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: LiangTing
2021/12/18 16:06:31
"""
import numpy as np
import os
def get_frequency_eigen_info(num_basis, eig_file='eigenvector.out', directory=None):
if not directory:
eig_path = os.path.join(os.getcwd(), eig_file)
else:
eig_path = os.... | brucefan1983/GPUMD | examples/empirical_potentials/phonon_vibration_viewer/view_eigen_gpumd.py | Python | gpl-3.0 | 5,260 | [
"LAMMPS"
] | 75b203c9285b267f4729a1ac8f771964ff2e9e3f0e7d09003042f2a111203867 |
#!/usr/bin/env python
# GoodFET Client Library
#
# (C) 2009 Travis Goodspeed <travis at radiantmachines.com>
#
# This code is being rewritten and refactored. You've been warned!
import sys, time, string, cStringIO, struct, glob, os;
import sqlite3;
fmt = ("B", "<H", None, "<L")
def getClient(name="GoodFET"):
i... | EastL/killerbee | killerbee/GoodFET.py | Python | bsd-3-clause | 30,147 | [
"Firefly"
] | 6d8ca24d547b7219dae675461abf94230cf02f3880d91639476063b47e084ae0 |
"""
@name: PyHouse/src/Modules/Core/_test/test_setup_logging.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com>
@copyright: (c) 2014-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Aug 30, 2014
@Summary:
Passed all 4 tests - DBK - 2019-01-03
"""
__updated__ = '2019-01-03'
... | DBrianKimmel/PyHouse | Project/src/Modules/Core/_test/test_setup_logging.py | Python | mit | 1,979 | [
"Brian"
] | 639402609b38c4a7c488cb167c3cdd3bd1d9ec74111269d0a49b4522a9f7e668 |
# (c) 2019 Open Source Geospatial Foundation - all rights reserved
# (c) 2014 - 2015 Centre for Maritime Research and Experimentation (CMRE)
# (c) 2013 - 2014 German Aerospace Center (DLR)
# This code is licensed under the GPL 2.0 license, available at the root
# application directory.
import unittest
import os
import... | geoserver/wps-remote | test/test_computation_job_outputs.py | Python | gpl-2.0 | 24,150 | [
"NetCDF"
] | 42301d129df0786e59e4d2e81294e11c7e729ae31d791f9f24b081d33caccc03 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | src/python/espressomd/shapes.py | Python | gpl-3.0 | 7,500 | [
"ESPResSo"
] | 1d00e057139f5f0a86de82871b168256b9ac5732a574e88f88baab2e13503de8 |
# Zulip Settings intended to be set by a system administrator.
#
# See http://zulip.readthedocs.io/en/latest/settings.html for
# detailed technical documentation on the Zulip settings system.
#
### MANDATORY SETTINGS
#
# These settings MUST be set in production. In a development environment,
# sensible default values w... | calvinleenyc/zulip | zproject/prod_settings_template.py | Python | apache-2.0 | 16,864 | [
"VisIt"
] | 2cd6c6ccfeaf99de01208b245355b62fe88ff73801aa9aeb8fae78e37eb9c6e4 |
# encoding: 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 model 'ArticleFullText'
db.create_table('neuroelectro_articlefulltext', (
... | lessc0de/neuroelectro_org | neuroelectro/south_migrations/0006_auto__add_articlefulltext.py | Python | gpl-2.0 | 7,932 | [
"NEURON"
] | 47e630c343fd001cf009b254cede0d514e88b264f18d79a29543eff171ec2daf |
#!/usr/bin/env python
import json
import optparse
import os
import subprocess
import sys
import tempfile
CHUNK_SIZE = 2**20
DEFAULT_DATA_TABLE_NAME = "bowtie_indexes"
def get_id_name( params, dbkey, fasta_description=None):
# TODO: ensure sequence_id is unique and does not already appear in location file
se... | ASaiM/tools-iuc | data_managers/data_manager_bowtie_index_builder/data_manager/bowtie_index_builder.py | Python | mit | 4,124 | [
"Bowtie"
] | a2c9663fa6d1bf174706bb076512cf2c938edde12669138e28320013f0bccdf3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2011, 2012, 2013, 2014.
# Author(s):
# Esben S. Nielsen <esn@dmi.dk>
# Adam Dybbroe <adam.dybbroe@smhi.se>
# Martin Raspaud <martin.raspaud@smhi.se>
# This program is free software: you can redistribute it and/or modify
# it under the terms of the ... | silenteddie/modisTrackL1L2 | pyorbital/orbital.py | Python | gpl-2.0 | 28,725 | [
"EPW"
] | c17819f418592773f8b427c9c23f9adaef5eb6f90ce1e45320455825dd62546f |
# -*- coding: utf-8 -*-
from skued import kinematicsim, bragg_peaks
from crystals import Crystal
from scipy.ndimage import gaussian_filter
import numpy as np
import itertools as it
import pytest
DIFF_PATTERN_SIZE = 256
MAX_INV_ANG = 5.5
def diff_pattern_sc():
"""Simulate a single-crystal diffraction pattern"""
... | LaurentRDC/scikit-ued | skued/image/tests/test_indexing.py | Python | gpl-3.0 | 1,429 | [
"CRYSTAL"
] | 427f6088626659f1f42b59660b77d49405d6d3f31a0d91668478b963e4ec5c58 |
"""
tools for dealing with frozen atoms. Especially in relation to neighbor lists
.. currentmodule:: pele.utils.frozen_atoms
.. autosummary::
:toctree: generated/
FreezePot
makeBLJNeighborListPotFreeze
"""
import numpy as np
import pele.potentials.ljpshift as ljpshift
from pele.potentials.pote... | js850/pele | pele/utils/frozen_atoms.py | Python | gpl-3.0 | 17,704 | [
"PyMOL"
] | cb504e244a9f6eb33fe334482c5d1a86708d860db54453300b0b919bbfbc728a |
import os
from ase import Atoms
from ase.units import Hartree
from gpaw import GPAW
from gpaw.test import equal, gen
import gpaw.mpi as mpi
# Generate non-scalar-relativistic setup for Cu:
gen('Cu', scalarrel=False)
a = 8.0
c = a / 2
Cu = Atoms('Cu', [(c, c, c)], magmoms=[1],
cell=(a, a, a), pbc=0)
calc =... | robwarm/gpaw-symm | gpaw/test/Cu.py | Python | gpl-3.0 | 968 | [
"ASE",
"GPAW"
] | 20b48b2d61ce5daa9282be47c032f8932f0ad7d9d55e6cc6a4dac18fa2acffca |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
from arakawac import Arakawa1D
from shallowwater import Model
class ShallowWater1D(Arakawa1D, Model):
"""The Shallow Water Equations on the Arakawa-C grid."""
def __init__(self, nx, Lx=1.0e7, nu=1.0e3, nu_phi=None, dt=1000.0):
super(Sha... | jamesp/shallowwater | beta_plane/shallow1d.py | Python | mit | 4,346 | [
"Gaussian"
] | 4607b336f38dca6b5768f14fa0ba610fff268faab7014596d4813b8fd121eae5 |
#!/usr/bin/env python
from __future__ import print_function
import sdm
import numpy as np
import progressbar as pbar
import random
neg = [np.random.normal(0, 1, (12, 4)) for _ in range(50)]
pos = [np.random.normal(1, .2, (12, 4)) for _ in range(50)]
bags = neg + pos
labels = [0] * len(neg) + [1] * len(pos)
widgets =... | dougalsutherland/sdm | python/test_python.py | Python | bsd-3-clause | 2,276 | [
"Gaussian"
] | 695fc76cb97d78111282eb1bf719d391de58e92f8035d1effb97005ac5549109 |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | giorgiop/scikit-learn | sklearn/cluster/k_means_.py | Python | bsd-3-clause | 59,414 | [
"Gaussian"
] | 446d1039e6051194d1fb38f162fb4562897d6752abd3e6664851174a97c6c3d9 |
#===============================================================================
#
# PopulationGenerator.py
#
# This file is part of ANNarchy.
#
# Copyright (C) 2016-2018 Julien Vitay <julien.vitay@gmail.com>,
# Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
#
# This program is free software: y... | ANNarchy/ANNarchy | ANNarchy/generator/Population/PopulationGenerator.py | Python | gpl-2.0 | 19,907 | [
"NEURON"
] | 27df87661d68ce7385aaddfb0d0e632b394ede29e7cdc3f212d1bda6866acc8b |
# http://www.bionicbunny.org/
#
# Copyright (c) 2014 Oleksandr Sviridenko
#
# 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 requi... | robionica/b3 | src/main/python/b3/tools/compilers/propgcc.py | Python | apache-2.0 | 4,525 | [
"VisIt"
] | e9345a3723ed08170878581876e4b51486261d16cc3814864501d08e247cba25 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Writing FCIDUMP file for given integrals or SCF orbitals
'''
from functools import reduce
import numpy
from pyscf import gto, scf, ao2mo
from pyscf import tools
from pyscf import symm
mol = gto.M(
atom = [['H', 0, 0, i] for i in range(6)],... | gkc1000/pyscf | examples/tools/01-fcidump.py | Python | apache-2.0 | 2,462 | [
"PySCF"
] | 6d88b4359d9e57147495618abe5359c0c7f3ebf70c3d76c9c61627f10f6e6012 |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | treycausey/scikit-learn | sklearn/cluster/k_means_.py | Python | bsd-3-clause | 50,102 | [
"Gaussian"
] | 13fcb823499ad169042069ee927bbf3b7deeeec6b91abcc273447920eb762ebf |
from enum import Enum
from datetime import datetime, date
from dateutil.relativedelta import relativedelta, MO
import argparse
import holidays
import pandas as pd
class BGEHolidays(holidays.HolidayBase):
def _populate(self, year):
holidays.UnitedStates._populate(self, year)
# Remove Martin Luther... | e2thenegpii/EnergyCalc | src/TOU.py | Python | mit | 4,729 | [
"COLUMBUS"
] | 9bb3554431d48dd4ef392393a8c17e1ff19c736db5e31f62891daf139ee9e18f |
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