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# ! /usr/bin/python
# -*- coding: utf-8 -*-
# import numerical module numpy
import numpy as np
# import plotting module matplotlib
import matplotlib.pyplot as plt
# import operation system module os
import os
# import curve fitting model
from lmfit.models import GaussianModel, LinearModel
# Description: Read the p... | geosharma/ruland_analysis | saxs_ruland_analysis_gaussian.py | Python | gpl-3.0 | 10,502 | [
"Gaussian"
] | 9ca2ba0e1b12825e1dd41737389ed52f6d487e2f910b11b1078492d5a43dcbb8 |
#!/usr/bin/env python
"""
Contains the SignalModel class definition
SignalModel - a class that represents the signal fit model
"""
from ROOT import RooGaussian, RooCBShape, RooRealVar, RooArgList, RooAddPdf
class SignalModel(object):
"""
A class that represents a signal model
The model ... | semkiv/fcc-reconstruction | utility/SignalModel.py | Python | gpl-3.0 | 3,118 | [
"CRYSTAL",
"Gaussian"
] | 1089748e98b3c9e685f9e85de6ab17aa18292e9b739c9e2129cb0095f54b716c |
# Copyright 2017 Battelle Energy Alliance, 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | idaholab/raven | framework/SupervisedLearning/GaussPolynomialRom.py | Python | apache-2.0 | 31,881 | [
"Gaussian"
] | 4f31420dfddc5bb82fada2b6733b20241ff4f1c96c581ecb4b8084d2041ca04f |
#!/usr/bin/env python
########################################################################
# File : dirac_admin_add_shifter
# Author : Federico Stagni
########################################################################
"""
Adds or modify a shifter, in the operations section of the CS
"""
from __future__ impo... | ic-hep/DIRAC | src/DIRAC/ConfigurationSystem/scripts/dirac_admin_add_shifter.py | Python | gpl-3.0 | 1,618 | [
"DIRAC"
] | 1300e25a55a02b62720e11af1d4963c1549004f267587740c0cc919b3e0d1201 |
from __future__ import (absolute_import, division, print_function)
from .Instrument import Instrument
from AbinsModules import AbinsParameters
from AbinsModules import AbinsConstants
from AbinsModules.FrequencyPowderGenerator import FrequencyPowderGenerator
class ToscaInstrument(Instrument, FrequencyPowderGenerator)... | wdzhou/mantid | scripts/AbinsModules/Instruments/ToscaInstrument.py | Python | gpl-3.0 | 2,568 | [
"Gaussian"
] | b3823c25e4fe1f73c7da7199db891198c177b9dc1c6990343b63167e843dca0f |
# 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... | strint/tensorflow | tensorflow/contrib/distributions/python/ops/mvn_tril.py | Python | apache-2.0 | 7,520 | [
"Gaussian"
] | f2a96fc9a651f527d585e388ea11b96e861b0853678d9e4b54775aa7fce34067 |
# Encoding = utf-8
import numpy as np
import pymatgen.io.nwchem as nw
"""
A collection of utility methods for other modules.
"""
def distance(coord1, coord2):
"""
Calculate the distance between two coordinates, defined by arrays.
:param coord1:
:param coord2:
:return:
"""
return np.lina... | mbercx/cage | cage/utils.py | Python | mit | 1,134 | [
"NWChem",
"pymatgen"
] | 68ddaa197598a417ee216bfac2061ae57bf6d83988d3eed0e3d39911c6e6a247 |
from xml.etree import ElementTree as ET
import string
import os, sys
from math import *
import moose
from neuroml_utils import *
class ChannelML():
def __init__(self,nml_params):
self.cml='http://morphml.org/channelml/schema'
self.context = moose.PyMooseBase.getContext()
self.nml_params =... | BhallaLab/moose-thalamocortical | python/moose/neuroml/ChannelML.py | Python | lgpl-2.1 | 19,772 | [
"MOOSE"
] | 54434112aabcac153c1f45cd1fa33111115e350067a926e125f506d99fbf8e75 |
# -*- coding: utf-8 -*-
"""Pre-defined predicates for nodes."""
from ..utils import part_has_modifier
from ...graph import BELGraph
from ....constants import (
ACTIVITY,
DEGRADATION,
SOURCE_MODIFIER,
TARGET_MODIFIER,
TRANSLOCATION,
)
from ....dsl import BaseEntity
__all__ = [
"has_edge_modifi... | pybel/pybel | src/pybel/struct/filters/node_predicates/activities.py | Python | mit | 1,800 | [
"Pybel"
] | 3b63845551e4c5873401e7fe9e25bcc88a5a6c44773e5f61812bd8e9eda97717 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Contribution 2009 by Reinhard Mueller <reinhard.mueller@bytewise.at>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2013-2014 Paul Franklin
#
# This program is free software... | SNoiraud/gramps | gramps/plugins/textreport/kinshipreport.py | Python | gpl-2.0 | 17,399 | [
"Brian"
] | 6299c19de7332bbd6f549b4ff99e70f56495be474d28d4f13a7720732d60aede |
#!/usr/bin/env python
from __future__ import absolute_import
import re
from markdown import Markdown
from markdown.util import AMP_SUBSTITUTE, HTML_PLACEHOLDER_RE
from markdown.odict import OrderedDict
from docutils import nodes
from docutils import parsers
try:
from html import entities
except ImportError:
... | tk0miya/sphinxcontrib-markdown | sphinxcontrib/markdown.py | Python | bsd-2-clause | 7,231 | [
"VisIt"
] | 83634cb5f40f2545cf29d5eb11cf33dfdf1ffb251eb05ffc9486f57b9617f69a |
import numpy as np
from deepchem.utils.typing import RDKitMol
from deepchem.utils.data_utils import pad_array
from deepchem.feat.base_classes import MolecularFeaturizer
from deepchem.feat.molecule_featurizers.atomic_coordinates import AtomicCoordinates
class BPSymmetryFunctionInput(MolecularFeaturizer):
"""Calcula... | deepchem/deepchem | deepchem/feat/molecule_featurizers/bp_symmetry_function_input.py | Python | mit | 2,185 | [
"RDKit"
] | 0d5780bc5600b03d302d5c039adc8553bf1b81298c9e8381b82fb002275e9728 |
#
# ANNarchy - Short-term plasticity network
#
# Implementation of the recurrent network proposed in:
#
# Tsodyks, Uziel and Markram (2000). Synchrony Generation in Recurrent Networks with Frequency-Dependent Synapses, The Journal of Neuroscience, 20(50).
#
# authors: Julien Vitay, Helge Uelo Dinkelbach
#
from ... | vitay/ANNarchy | examples/tsodyks_markram/TsodyksMarkram.py | Python | gpl-2.0 | 3,872 | [
"NEURON"
] | 65cdcf6ffe575c1b3dd1c9946c5a26ec6a76ab6f2295bdeb395071a097bc678b |
# iCraft is Copyright 2010 both
#
# The Archives team:
# <Adam Guy> adam@adam-guy.com AKA "Adam01"
# <Andrew Godwin> andrew@aeracode.org AKA "Aera"
# <Dylan Lukes> lukes.dylan@gmail.com AKA "revenant"
# <Gareth Coles> colesgareth2@hotmail.com... | TheArchives/Nexus | core/entities/giant_create.py | Python | bsd-2-clause | 2,092 | [
"VisIt"
] | 9c2c1f3987cae2a8ce686ab5cefea8b7dfefdd34866be211c7da42d5de451e81 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/share/psi4/databases/S22by5.py | Python | lgpl-3.0 | 176,348 | [
"Psi4"
] | 0b995982aa9ab63be51add49601fbace97ab54ed4435553bb3bcee9a0e5c562c |
# yellowbrick.contrib.statsmodels.base
# A basic wrapper for statsmodels that emulates a scikit-learn estimator.
#
# Author: Ian Ozsvald
# Created: Wed Jan 10 12:47:00 2018 -0500
#
# ID: base.py [] benjamin@bengfort.com $
"""
A basic wrapper for statsmodels that emulates a scikit-learn estimator.
"""
###############... | pdamodaran/yellowbrick | yellowbrick/contrib/statsmodels/base.py | Python | apache-2.0 | 2,626 | [
"Gaussian"
] | c0ecd1b2c5d7faf9d223671e00b0d447a92eb2106e602a8655f20d049a8aa71c |
"""
This python module provides functionality to parse the methods of a
VTK object.
Created by Prabhu Ramachandran. Committed in Apr, 2002.
"""
import string, re, sys
import types
# set this to 1 if you want to see debugging messages - very useful if
# you have problems
DEBUG=0
def debug (msg):
if DEBUG:
... | collects/VTK | Wrapping/Python/vtk/util/vtkMethodParser.py | Python | bsd-3-clause | 13,426 | [
"VTK"
] | f695a050fbc0d00352b64e1c3772ba5972cfda70700c0ed435105fb9ea71c080 |
#!/usr/bin/python
import subprocess
import sys
def install(package):
subprocess.check_call([sys.executable, "-m", "pip", "install", package])
install("netCDF4")
from scipy.stats import cauchy
import random
import math
import csv
import numpy as np
import netCDF4 as nc
import argparse
'''parser = argparse.Argument... | WillArmentrout/galSims | simulate/Simulate.py | Python | gpl-2.0 | 15,568 | [
"Galaxy",
"Gaussian"
] | 15950308defbb8a763ea50394e4c087677a998d2cb32203aa0ea32a94fbeb50b |
## This code computes the time-evolution of an initial state in presence of a harmonic interaction
## given by the potential energy function V(x) = (m * omega**2 * x**2)/2
## Length coordinate is in units of l0 = sqrt(hbar/(m*omega)) and energy is measured in units of E0 = hbar*omega/2. In these
## units, the eigenva... | deadbeatfour/notebooks | SWE_wavepacket/Time_Evolution.py | Python | mit | 3,547 | [
"Gaussian"
] | 92df694399067639c32a366e5292f3fe23f7ebf172ecbff7a6feb21f6fda4a9e |
import pandas as pd
import numpy as np
import re #regular expression
import itertools
import matplotlib.pyplot as plt
from mpltools import color
from collections import OrderedDict
from rdkit import Chem
#The following libraries are generated by Sungjin Kim
from . import jchem
from . import jutil
def gen_14BQ_OH()... | jskDr/jamespy | j3/jquinone.py | Python | mit | 26,743 | [
"RDKit"
] | 64abd9cc4e86b436b13f6128e1aafbece3f2a6f734e13bd07c3ae9fe6eae824e |
import lb_loader
import pandas as pd
import simtk.openmm.app as app
import numpy as np
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
sysname = "ljbox"
system, positions, groups, temperature, timestep = lb_loader.load(sysname)
system.addForce(mm.AndersenTher... | kyleabeauchamp/HMCNotes | code/correctness/old/test_verlet_anderson.py | Python | gpl-2.0 | 1,303 | [
"OpenMM"
] | d06d8f55eeac6fdf757e1038f71bdf7c6765bb5b38eb7b7facb3faa95b933ff7 |
# Author: Travis Oliphant
# 1999 -- 2002
import operator
import math
import timeit
from scipy.spatial import cKDTree
from . import _sigtools
from ._ltisys import dlti
from ._upfirdn import upfirdn, _output_len, _upfirdn_modes
from scipy import linalg, fft as sp_fft
from scipy.fft._helper import _init_nd_shape_and_axes... | perimosocordiae/scipy | scipy/signal/_signaltools.py | Python | bsd-3-clause | 153,046 | [
"Gaussian"
] | 6f3851ab1f04998d5679df904d1bd8771cd2e0155813ea7f1121e76a5445fe40 |
school_infos = []
# convert each character to lower case, convert space to _, ignore commas
def normalize(name):
name = name.lower()
new_name = ""
for c in name:
if c.isalpha():
new_name += c
elif c.isspace():
new_name += '_'
return new_name
class SchoolInfo:
... | ducalpha/SOP_Generator | school_infos.py | Python | mit | 3,150 | [
"exciting"
] | fd718a994fa80e03d4451921beaa89088eca693d11c17cded29ae8bdfec83874 |
from __future__ import print_function
import numpy as np
from numpy import exp, sin, degrees, radians, pi, sqrt
from sasmodels.weights import Dispersion as BaseDispersion
class Dispersion(BaseDispersion):
r"""
Maier-Saupe dispersion on orientation.
.. math:
w(\theta) = e^{a{\cos^2 \theta}}
... | SasView/sasmodels | example/weights/maier_saupe.py | Python | bsd-3-clause | 4,591 | [
"Gaussian"
] | 58088e7db3dd9ad3c02dceafd11c249979cdb2bdb9ed08052fc7f05b224169b3 |
#-----------------------------------------------------------------
# gen_stub.py -- genenrate stub code
#
from __future__ import print_function
import sys, os
from pycparser import parse_file, c_generator, c_parser, c_ast, preprocess_file
# This is not required if you've installed pycparser into
# your site-packages... | songjiguo/interface-code-generator | stub_generator/gen_stub.py | Python | bsd-3-clause | 5,618 | [
"VisIt"
] | 822766030ee1af8fb94dadc16c26ee4f7e3a78d9da03811bd501afa2761dcbb3 |
# Written by Lauri Lehtovaara, 2008
"""This module defines CSCG-class, which implements conjugate gradient
for complex symmetric matrices. Requires Numpy and GPAW's own BLAS."""
import numpy as np
from gpaw.utilities.blas import axpy
from gpaw.utilities.blas import dotu
from gpaw.utilities.blas import dotc
from gpaw... | qsnake/gpaw | gpaw/tddft/cscg.py | Python | gpl-3.0 | 6,483 | [
"GPAW"
] | be5ae8a31e6c9107cd6228c229be9ae8217fada0ff94f01b92e4f1be45ce0afe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License... | sparkslabs/kamaelia_ | Sketches/RJL/IRC/KambotIRC.py | Python | apache-2.0 | 13,785 | [
"DIRAC"
] | 02f1e7b17cd0f0d0ce2b815984aea4fe5ea0960c4955e1875af9e68d537c07d0 |
"""
Instructor Dashboard Views
"""
import logging
import datetime
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation import ugettext as _
from django_future.csrf import ensure_csrf_cookie
from django.vie... | LearnEra/LearnEraPlaftform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 19,664 | [
"VisIt"
] | b93ff1720774cea21b53775c7a486cbe9c92f0c487b079624540979d5456fede |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2008-2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Softw... | andrebellafronte/stoq | stoqlib/domain/payment/category.py | Python | gpl-2.0 | 2,282 | [
"VisIt"
] | daff38971313320b83cc5d01dd8c5ef4d4de1619ee28824b86ac9cd2d7749885 |
class Entity():
def __init__(self, dialect=None, document=None, parent=None):
self.dialect = dialect
self.document = document
self.parent = parent
self.children = []
self._start_index = None
self._end_index = None
@property
def parent_section(self):
n... | delins/tweakmark | tweakmark/entities/entity.py | Python | lgpl-3.0 | 3,149 | [
"VisIt"
] | 774f0a5649f74a7020d63b4ef6470d93ebbcf30f226b0eebe92abdc62edda417 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RGraph(RPackage):
"""graph: A package to handle graph data structures
A package th... | LLNL/spack | var/spack/repos/builtin/packages/r-graph/package.py | Python | lgpl-2.1 | 1,055 | [
"Bioconductor"
] | f0661318e8aad8580dcba8f59798e3acb995e3e4632c2c6653df790a41034494 |
# media.py
#
#
# Copyright 2010 alex arsenovic <arsenovic@virginia.edu>
#
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 o... | tectronics/mwavepy | mwavepy/media/media.py | Python | gpl-3.0 | 23,902 | [
"Gaussian"
] | ee5bc9104d23e636c9f8077f202e253eb4b78bede38d934c4ae655875d630c3f |
# -*- coding: utf-8 -*-
##
## CreateInflowFileFromLDASRunoff.py
## spt_lsm_autorapid_process
##
## Created by Alan D. Snow (adapted from CreateInflowFileFromECMWFRunoff.py).
## Copyright © 2015-2016 Alan D Snow. All rights reserved.
## License: BSD-3 Clause
import csv
import netCDF4 as NET
import numpy as NUM
imp... | erdc-cm/spt_erai_autorapid_process | imports/CreateInflowFileFromLDASRunoff.py | Python | mit | 11,792 | [
"NetCDF"
] | a6b68c0e3eb4420de8c11c7b74a8649d6f2b49d6bf88e39531cbd1b5e7a538c8 |
"""Bayesian Gaussian Mixture Models and
Dirichlet Process Gaussian Mixture Models"""
# Author: Alexandre Passos (alexandre.tp@gmail.com)
# Bertrand Thirion <bertrand.thirion@inria.fr>
#
# Based on mixture.py by:
# Ron Weiss <ronweiss@gmail.com>
# Fabian Pedregosa <fabian.pedregosa@inria.fr>
#
... | lucidfrontier45/scikit-learn | sklearn/mixture/dpgmm.py | Python | bsd-3-clause | 30,523 | [
"Gaussian"
] | 87a9443e3d1b486c2b912ab02d369b72dcffb693ea5a6e841a620912c19af388 |
"""The base Controller API
Provides the BaseController class for subclassing, and other objects
utilized by Controllers.
"""
from pylons import c, cache, config, g, request, response, session
from pylons.controllers import WSGIController
from pylons.controllers.util import abort, etag_cache, redirect_to
from pylons.de... | DIRACGrid/DIRACWeb | dirac/lib/base.py | Python | gpl-3.0 | 1,350 | [
"DIRAC"
] | eff4abe67c744783205f82facb749708d580c6758403cfaf7bdd620fa7b14a0a |
# coding: utf-8
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import random
import re
import socket
import sys
import time
import math
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_etree_Element,
compat_etree_f... | ping/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 138,357 | [
"VisIt"
] | 6a1a0a64c2ad3edb6fcf2670b800a1eac059ec2c6a10a54df35f6a790538edc2 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Python Scripts documentation build configuration file.
This file is execfile()d with the current directory set to its
containing dir.
Note that not all possible configuration values are present in this
autogenerated file.
All configuration values have a default; val... | kallimachos/python | doc/conf.py | Python | gpl-3.0 | 7,446 | [
"Brian"
] | 466d91afd8c60c3dc74c364abc4186e3a13ce66006746ca6842737dffe187e55 |
#!/usr/bin/python
"""
# Created on Aug 12, 2016
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com) GitHub ID: grastogi23
#
# module_check: not supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
"... | andmos/ansible | lib/ansible/modules/network/avi/avi_api_session.py | Python | gpl-3.0 | 8,328 | [
"VisIt"
] | 7b53685fe3ec3a226133ed7f94aa3999e08cfd8b3f5cf9fec6bbada774d610b3 |
import math
import numpy
import random
import operator
import types
import numpy as np
class Transform(object):
"""
Rotation and translation represented as 4 x 4 matrix
"""
def __init__(self, matrix):
self.matrix = numpy.array(matrix)
self.matrix_inv = None
self.zRot = False
... | rll/lfd | lfd/rapprentice/util.py | Python | bsd-2-clause | 23,718 | [
"Gaussian"
] | be2c72ea251ca2234904a7fe78c9aa8386e1e7b24f315f451dfc96f58c384d64 |
# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
import itertools
from ..core.model import Model
from ..core.parameterization.variational import VariationalPosterior
from ..core.mapping import Mapping
from .. import likelihoods
fro... | SheffieldML/GPy | GPy/models/multioutput_gp.py | Python | bsd-3-clause | 7,500 | [
"Gaussian"
] | a1e8eb7467aeba8997be5272e65d82b8a9ba268867780904bc63106b75c8a897 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import tempfile
from monty.json import MontyDecoder
from monty.serialization import loadfn
from pymatgen.io.vasp.sets import *
from pymatgen.io.vasp.inp... | nisse3000/pymatgen | pymatgen/io/vasp/tests/test_sets.py | Python | mit | 34,925 | [
"VASP",
"pymatgen"
] | f22aa2bbf15cef145fb2b90e6fc4679173b37a82205126811fe7fee4159272b7 |
# Copyright 2012 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of ngs_crumbs.
# ngs_crumbs 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, ... | JoseBlanca/ngs_crumbs | crumbs/bam/statistics.py | Python | gpl-3.0 | 24,423 | [
"pysam"
] | 03d1141e2418f2b224aa17ef2774466d1e6052b4ae7f86d814c7c6591cc96b60 |
"""Handle disambiguation of reads from a chimeric input, splitting by organism.
Given specification of mixed input samples, splits a sample into multiple
sub-samples for alignment to individual genomes, then runs third-party disambiguation
scripts to reconcile.
Uses disambiguation scripts contributed by AstraZeneca, ... | Cyberbio-Lab/bcbio-nextgen | bcbio/pipeline/disambiguate/__init__.py | Python | mit | 8,526 | [
"BWA"
] | a0087f593f43cae65863e0b37b91f4bd8b43721fe3b10d03bf50e75012dd78d0 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | src/python/espressomd/__cinit__.py | Python | gpl-3.0 | 710 | [
"ESPResSo"
] | 9022bd866123063c871fa3dfac7ea1076c2689ffcab56c433f1f94b2a178acdb |
"""Testing for kernels for Gaussian processes."""
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# Licence: BSD 3 clause
from collections import Hashable
import inspect
import numpy as np
from scipy.optimize import approx_fprime
from sklearn.metrics.pairwise \
import PAIRWISE_KERNEL_FUNCTIONS, euc... | arjoly/scikit-learn | sklearn/gaussian_process/tests/test_kernels.py | Python | bsd-3-clause | 11,736 | [
"Gaussian"
] | 47d4b00b02daa0d29d8b1807dd0eed07fc28b346271d375d98491d48f31977d3 |
# Copyright (c) 2014 ETH Zurich, Institute of Astronomy, Lukas Gamper <lukas.gamper@usystems.ch>
from __future__ import print_function, division, absolute_import, unicode_literals
from hope._ast import *
class Dumper(NodeVisitor):
"""
Generates a human readable string representation of a HOPE AST.
Can ... | cosmo-ethz/hope | hope/_dump.py | Python | gpl-3.0 | 6,959 | [
"VisIt"
] | f457168e67fb0dcb886e0f9fbcee61c1b0632ef2d647fbf3f526172c00a59493 |
# -*- coding: utf-8 -*-
# ------------------------------------------------------------
# streamondemand.- XBMC Plugin
# Canal para asiansubita
# http://blog.tvalacarta.info/plugin-xbmc/streamondemand.
# ------------------------------------------------------------
import re
import sys
import urlparse
from core import l... | orione7/Italorione | channels/asiansubita.py | Python | gpl-3.0 | 5,774 | [
"ADF"
] | 2c4d0f21de95e0a13e7a772a9d8358eddc1dd0bbef025d569cc5ba70001a753f |
'''
Created on 29.04.2017
@author: Mr. Jones
'''
import slimit.ast
class CFGVisitor():
def __init__(self):
self.indent = 0
self.temp_dict = {}
def visit(self, node, flow_node):
#print node
method = 'visit_%s' % node.__class__.__name__
return ge... | mrj0n3s/jimplify | Jimplify/jimplify/visitors/cfgvisitor.py | Python | mit | 3,199 | [
"VisIt"
] | d2179a69507980cb2e17a1a7b7cff7980a6608c9fbe442fc3fc81d1e5d68693c |
#!/usr/bin/env python
#===============================================================================
# Copyright (c) 2014 Geoscience Australia
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions ar... | alex-ip/agdc | agdc/modis_ingester/modis_dataset.py | Python | bsd-3-clause | 16,759 | [
"NetCDF"
] | 12426d36d1177d6e7c51e5ed27538d06b3f3a824f5ec7e497cfc0fe1176ae837 |
#!/usr/bin/python3
from subprocess import call
import os, sys
DIRECTORIO_EXTRACCION_LISTADOS="codigo_extraido"
DIRECTORIO_WORKSPACE="workspace"
DIRECTORIO_CODIGO_FUENTE="src"
EXTRAER_CLASE = "class"
EXTRAER_METODO= "method"
lista_extractor=["java", "-jar", "Extractor.jar"]
class Extraccion(object):
def __init__(s... | OscarMaestre/servicios | extraer_listados.py | Python | cc0-1.0 | 5,369 | [
"CASINO"
] | 017ed2154b62886a9252d34d91c0afe64ba8cb58bd0752f40077bae48f3a1873 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from glob import glob
from spack import *
class Liggghts(MakefilePackage):
"""Discrete element method par... | LLNL/spack | var/spack/repos/builtin/packages/liggghts/package.py | Python | lgpl-2.1 | 4,053 | [
"VTK"
] | b2d015d9084ff7f62e022eef5c798381341be57fbaaee6c4fb2f4fe6625077bf |
#!/usr/bin/env python
#
# Copyright (c) 2016 Matt Davis, <mdavis@ansible.com>
# Chris Houseknecht, <house@redhat.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 ... | simonwydooghe/ansible | contrib/inventory/azure_rm.py | Python | gpl-3.0 | 41,171 | [
"Galaxy"
] | ebc6e03869b33b1264f6904a22e6a6e2e78ee0a714af90445f74cb3c46c324d8 |
#!/usr/bin/env python
# encoding: utf-8
#
# Copyright (c) 2008 Doug Hellmann All rights reserved.
#
"""Traverse a directory tree.
"""
__version__ = "$Id$"
#end_pymotw_header
import os
import os.path
import pprint
def visit(arg, dirname, names):
print dirname, arg
for name in names:
subname = os.path.... | qilicun/python | python2/PyMOTW-1.132/PyMOTW/ospath/ospath_walk.py | Python | gpl-3.0 | 687 | [
"VisIt"
] | dedea47f073d9337fdc6439022d8fe8900283240d9f793d4507004755f0fd8a9 |
from octopus.runtime import *
from octopus.sequence.control import StateMonitor
v = variable(0, "i", "i")
test = (((v >= 4) & (v <= 6)) | ((v >= 9) & (v <= 14))) == False
d = StateMonitor()
d.add(test)
d.trigger_step = sequence(
log("Triggered"),
wait(4),
log("Still Triggered"),
)
d.reset_step = sequence(
log("Re... | rasata/octopus | examples/test_statemonitor.py | Python | mit | 535 | [
"Octopus"
] | 3140e569d397a1bf59023f1f36b5c2f31436793a16556a4c91dd5b4d07236fcf |
"""DIRAC Administrator API Class
All administrative functionality is exposed through the DIRAC Admin API. Examples include
site banning and unbanning, WMS proxy uploading etc.
"""
import os
import DIRAC
from DIRAC.Core.Utilities.PromptUser import promptUser
from DIRAC.Core.Base.API ... | hgiemza/DIRAC | Interfaces/API/DiracAdmin.py | Python | gpl-3.0 | 40,032 | [
"DIRAC"
] | b8b9478e07c43596dd83641d2eb2b6dc25f7b37b9fa26a95baddc7ce5d7b4a8f |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Read an alignment from stdin and for each block print the result of
evaluating `template_string` (in cheetah template format). The alignment
block will be placed in the template context as `a` and the list of components
as `c`.
usage: %prog template [options]
-f, --fo... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/align_print_template.py | Python | bsd-3-clause | 1,101 | [
"Galaxy"
] | 9d99ef656d6c25ef07b59ee7dea39e0cdd997fa29d1d4416ee50c9961256def0 |
# -*- coding: utf-8 -*-
# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry
# and reaction kinetics.
# Copyright (C) 2008-2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, An Ghysels
# <An.Ghysels@UGent.be> and Matthias Vandichel <Matthias.Vandichel@UGent.be>
# Center for Molecular Modeling... | molmod/tamkin | tamkin/io/vasp.py | Python | gpl-3.0 | 9,371 | [
"VASP"
] | 4ab72aee65b0c08e4318f65e444fbc3c667157337ffdf7baa70a7df0a1633296 |
#!/usr/bin/env python
"""
dirac-rss-list-status
Script that dumps the DB information for the elements into the standard output.
If returns information concerning the StatusType and Status attributes.
Usage:
dirac-rss-list-status
--element= Element family to be Synchronized ( Sit... | andresailer/DIRAC | ResourceStatusSystem/scripts/dirac-rss-list-status.py | Python | gpl-3.0 | 5,951 | [
"DIRAC"
] | 213b14cc7c8d2a0d9c08007775dc1b4294fc20d86c3f2de26703db7089e98667 |
##############################################################################
# Copyright (c) 2013-2018, 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... | EmreAtes/spack | var/spack/repos/builtin/packages/transposome/package.py | Python | lgpl-2.1 | 1,624 | [
"BLAST"
] | 9bd5d67173cec5a65dc604a83b8101cd1bac3b3161c3b1ced073aede7368ff1b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import json
import random
from collections import namedtuple
import pytest
from marshmallow import Schema, fields, utils, MarshalResult, UnmarshalResult
from marshmallow.exceptions import ValidationError
from marshmallow.compat import unicode, OrderedDict
from tests.bas... | etataurov/marshmallow | tests/test_schema.py | Python | mit | 74,275 | [
"Brian"
] | 7fa839f3e979cc6f5fec8ab79b48ffc10e076fbd51073bc9bf13a31a5564082c |
r"""
=======================================
Robust vs Empirical covariance estimate
=======================================
The usual covariance maximum likelihood estimate is very sensitive to the
presence of outliers in the data set. In such a case, it would be better to
use a robust estimator of covariance to guar... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/examples/covariance/plot_robust_vs_empirical_covariance.py | Python | mit | 6,463 | [
"Gaussian"
] | 5cea40ba8680a02d07515b1b25d71e3d95e21dc9037c53182f24c4ea0e73642a |
#!/usr/bin/python
# Copyright (c) 2016-2021 Julien Peloton, Giulio Fabbian.
#
# This file is part of s4cmb
#
# 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
#... | JulienPeloton/s4cmb | s4cmb/instrument.py | Python | gpl-3.0 | 39,278 | [
"Gaussian"
] | a9c7b0490eb266fc12642780b0b7ab7b2be2d787ca4307c5beba8326c3d78116 |
# -*- coding: utf-8 -*-
import re
from easydict import EasyDict as edict
from django.test import SimpleTestCase
from rando.core.tests import NavigationTest
from rando.trekking.models import Trek
class TrekFulltextTest(SimpleTestCase):
def setUp(self):
self.trek = Trek()
self.trek.properties = e... | camillemonchicourt/Geotrek-rando | rando/trekking/tests/__init__.py | Python | bsd-2-clause | 2,749 | [
"FLEUR"
] | 0365f4d8e1961b4cdf6bb1c13dfae87d24a86144cf2c01cf333387a228d4e3e9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
Created on Jan 25, 2012
"""
__author__ = "Anubhav Jain, Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ =... | aykol/pymatgen | pymatgen/apps/battery/tests/test_insertion_battery.py | Python | mit | 4,805 | [
"pymatgen"
] | 9d8a2f451f20fbb27d8f84e4936429b2e76e64998fa502f77beaf6de268c579f |
from orchestration.service import Service
from orchestration.config import config as file_treat
from orchestration import config
from orchestration.exception import ConfigError
from orchestration.exception import DependencyError
from orchestration.database import database_update
from orchestration.container_api.volum... | icsnju/nap-core | nap_rest/orchestration/project.py | Python | apache-2.0 | 9,972 | [
"VisIt"
] | 57876bf9ad1981f736e66eab30de53832d93611c2adde0a6874624a5b39f716a |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
#
# 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; ... | SNoiraud/gramps | gramps/gui/plug/quick/_textbufdoc.py | Python | gpl-2.0 | 12,642 | [
"Brian"
] | f2ff8f71f2419d227297359e6804f8d39984f34b6c8a32e42cb42dc13bc05beb |
dictionary = '''the
of
and
to
a
in
for
is
on
that
by
this
with
i
you
it
not
or
be
are
from
at
as
your
all
have
new
more
an
was
we
will
home
can
us
about
if
page
my
has
search
free
but
our
one
other
do
no
information
time
they
site
he
up
may
what
which
their
news
out
use
any
there
see
only
so
his
when
contact
here
busin... | Emigna/05AB1E | lib/dictionary.py | Python | mit | 77,329 | [
"Amber",
"BLAST",
"Brian",
"CASINO",
"COLUMBUS",
"CRYSTAL",
"Galaxy",
"Jaguar",
"VisIt",
"exciting"
] | c6e0596456ca3a44e2958ec1139326428bc351f6987a1de33e835c90d855f90c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import json
import functools
import pickle
from pymatgen.core.periodic_table import Element
"""
Most features of this module has been moved t... | Bismarrck/pymatgen | pymatgen/util/serialization.py | Python | mit | 4,111 | [
"pymatgen"
] | fbd29e0a39df4029c8acdb05d9661dec971862cb9c4bcf4c717d5ea7d79fa20d |
#!/usr/bin/env python
import sys
import os
import subprocess
#Local imports
from chemistry import elementdata, io
'''Usage: python make_dispersion_files.py'''
description='''
This program takes, as input, a generic template file, and creates
input files using geometries from all .gxyz files that are
located in the p... | mvanvleet/workflow-for-force-fields | scripts/make_dmapol_files.py | Python | gpl-3.0 | 4,475 | [
"GAMESS"
] | 43540524434de59249fd11b9e23669fcba14f830b256a9c264b2c804442bcc1d |
# supLTS.py ---
#
# Filename: supLTS.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Mon Sep 23 00:18:00 2009 (+0530)
# Version:
# Last-Updated: Fri Oct 21 17:02:07 2011 (+0530)
# By: Subhasis Ray
# Update #: 72
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#... | BhallaLab/moose-thalamocortical | DEMOS/pymoose/traub2005/py/supLTS.py | Python | lgpl-2.1 | 7,947 | [
"MOOSE",
"NEURON"
] | ade137c0470e44ff015d4dd6e5ec3a22c22cce0a875d31b9b1e062010ae81c21 |
"""
Copyright (c) 2013-2014 Heiko Strathmann, Dino Sejdinovic
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
*
1. Redistributions of source code must retain the above copyright notice, this
list of ... | karlnapf/kameleon-mcmc | kameleon_mcmc/tests/GibbsGaussianFullConditionalTest.py | Python | bsd-2-clause | 2,963 | [
"Gaussian"
] | 8b278c15897728359fab7af7c9eb6918389fc8586570e421d34058968050b280 |
# Copyright (C) 2017 Alexandre Morlet, Fulvio Paleari, Henrique Pereira Coutada Miranda
# All rights reserved.
#
# This file is part of yambopy
#
#
from yamboparser import *
from os import *
import argparse
from operator import itemgetter
def add_qp(output,add=[],substract=[],addimg=[],verbose=False):
# Define fil... | alexandremorlet/yambopy | scripts/add_qp.py | Python | bsd-3-clause | 7,296 | [
"NetCDF",
"Yambo"
] | 8af3430b7b38176dae0ce6b269734e5f7ceed839603338a37b03e587e985ca99 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Enable Breit Gaunt interaction for Dirac-Hartree-Fock solver
'''
from pyscf import gto, scf
mol = gto.M(
verbose = 5,
atom = '''
Cl 0 0 0
H 0 1.9 0''',
basis = {'Cl': gto.uncontract_basis(gto.basis.load('ccpvdz', 'Cl')),
... | gkc1000/pyscf | examples/scf/05-breit_gaunt.py | Python | apache-2.0 | 644 | [
"DIRAC",
"PySCF"
] | 0ed29a59d5b3f40eadbbdd942ec31b2166884f9a263f3b1b94298aa5ef263d2b |
#!/usr/bin/env python
from distutils.core import setup
from glob import glob
from os.path import join
import os
import sys
long_description = """\
Jacapo is a python package providing an interface to Dacapo that
is compatible with the open source Atomic Simulation
Environment in the python scripting language."""
if... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/calculators/jacapo/setup.py | Python | gpl-2.0 | 1,000 | [
"ASE"
] | 79edd943678c7f28439397b78f1944059edb9fe29821e7bf4ad1971247601065 |
""" Class for the LCG File Catalog Client
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
__RCSID__ = "$Id"
from past.builtins import long
import six
from stat import *
import os
import re
import time
import DIRAC
from DIRAC import S_OK, S_ERROR, gLog... | yujikato/DIRAC | src/DIRAC/Resources/Catalog/LcgFileCatalogClient.py | Python | gpl-3.0 | 64,863 | [
"DIRAC"
] | a353d0c2314d1e715b6096924df7eb2df71605da611336244006e07bcec3a591 |
#! /usr/bin/env python
"""Static analysis tool for checking docstring conventions and style.
Implemented checks cover PEP257:
http://www.python.org/dev/peps/pep-0257/
Other checks can be added, e.g. NumPy docstring conventions:
https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt
The repository is l... | bartvm/pep257 | pep257.py | Python | mit | 30,649 | [
"VisIt"
] | 1c1da0dee6150711fa098bb65c02f2d1d381d961fc11360eecb5694ee6d371a5 |
# -*- coding: utf-8 -*-
"""
This script can be used to extract data from a netcdf file, and put this into an
tvtk.unstructuredGrid, saved as xml file.
Created on Thu Jan 22 11:26:05 2015
@author: rongen
"""
# coding: utf-8
import netCDF4
import numpy as np
from tvtk.api import tvtk
import mayavi.mlab as mlab
from ... | grongen/point-cloud-visualization | netcdf_to_tvtk_ug.py | Python | gpl-3.0 | 3,005 | [
"Mayavi",
"NetCDF"
] | 7347c4f61f7a45c7b39de4ea0120009303ad469eda223d8abe5f0cbfe71e308b |
""" core implementation of testing process: init, session, runtest loop. """
from __future__ import absolute_import, division, print_function
import functools
import os
import six
import sys
import _pytest
from _pytest import nodes
import _pytest._code
import py
try:
from collections import MutableMapping as Mapp... | anthgur/servo | tests/wpt/web-platform-tests/tools/third_party/pytest/_pytest/main.py | Python | mpl-2.0 | 29,612 | [
"VisIt"
] | ef2223765c23bc3aec56107cbfef6cda1ef0982e46d26d89d33b812c2289b803 |
# -*- coding: utf-8 -*-
""" Discrete temperature thermodynamic Monte Carlo algorithms. """
import theano as th
import theano.tensor as tt
import theano.sandbox.rng_mrg as mrg_rand
from thermomc.hmc import HamiltonianSampler
class AnnealedImportanceSampler(HamiltonianSampler):
"""Annealed Importance Sampler (Neal... | matt-graham/thermodynamic-monte-carlo | thermomc/discrete_temp.py | Python | mit | 8,402 | [
"Gaussian"
] | 909356238d3bce54a4e3eded0598a434f418fdb3eaf53540ef282d3682d42a5b |
# ----------------------------------------------------------------------------
# Copyright 2014 Nervana Systems Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.o... | lihuanghai/neon | neon/backends/cc2.py | Python | apache-2.0 | 82,581 | [
"Gaussian"
] | 8846dd63dbd4f423ae51ddec61d729a169414287bdfd6ed4932aef888d2a212f |
import numpy as np
from numpy import clip, floor, zeros, empty, r_, sqrt
import numba
from numba import jit
from skimage import feature
from skimage import color
from . import Util, Canny, IO
import pynutmeg
import time
def linear_interpolate(im, x):
x = np.asarray(x)
x0 = floor(x).astype(int)
x1 = x... | kitizz/edge3d-paper | src/tools/Image.py | Python | gpl-3.0 | 19,319 | [
"Gaussian"
] | 8daf57da47588a79ec5f2b89113396f09747034e2537b1cedace4da813fdc736 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# 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 applicab... | google-research/google-research | musiq/model/preprocessing.py | Python | apache-2.0 | 12,009 | [
"Gaussian"
] | 0f6dba5f3f644818aaa5915392ed314499ee0f25eeb5fa5e0c8636c748ced3a6 |
from rdkit.Chem import MolFromSmiles
from rdkit.Chem import Draw
import numpy as np
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
def one_of_k_encoding(x, allowable_set):
if x not in allowable_set:
raise Exception("input {0} not in allowable set{1}:".format(x, allowable_set))
retur... | debbiemarkslab/neural-fingerprint-theano | code/rdkit_preprocessing/neuralFingerprintUtils.py | Python | mit | 2,311 | [
"RDKit"
] | 83fcded27c6361706938376140f4ffec1c0a07f02d24923e74a67bc43ddf4e70 |
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
from scipy.ndimage.filters import gaussian_filter
from neupy.utils import tensorflow_session
from neupy.exceptions import InvalidConnection
from neupy.algorithms.gd.base import BaseOptimizer
__all__ = ('saliency_map', 'saliency_map_graph')
... | itdxer/neupy | neupy/plots/saliency_map.py | Python | mit | 4,391 | [
"Gaussian"
] | 40825820a4b0d8fc1f283c811e775d2f2934f10264bfc1730129913f5fbf5f7f |
#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2009-2011 by the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of thi... | chatelak/RMG-Py | rmgpy/molecule/symmetry.py | Python | mit | 19,203 | [
"RDKit"
] | 202899114d44329a7dec2e38baae082716595454cf7ae071d2807e8f74e7a917 |
#!/usr/bin/env python3
"""
Created on Wed Sep 18 03:29:24 2019.
@author: mtageld
"""
import cv2
import numpy as np
from PIL import Image
from histomicstk.annotations_and_masks.annotation_and_mask_utils import \
get_image_from_htk_response
from histomicstk.annotations_and_masks.masks_to_annotations_handler import... | DigitalSlideArchive/HistomicsTK | histomicstk/saliency/tissue_detection.py | Python | apache-2.0 | 9,364 | [
"Gaussian"
] | 7468be7878b2460568b4fca3132e9ec0459698fa1d328087ae97cf3c1958e9d0 |
#!/usr/local/bin/python
#Dirac.py
import sympy.galgebra.GA as GA
import sympy.galgebra.latex_ex as tex
import sys
GA.set_main(sys.modules[__name__])
if __name__ == '__main__':
metric = '1 0 0 0,'+\
'0 -1 0 0,'+\
'0 0 -1 0,'+\
'0 0 0 -1'
vars = GA.make_symbols... | gnulinooks/sympy | sympy/galgebra/examples/Dirac.py | Python | bsd-3-clause | 1,306 | [
"DIRAC"
] | 083e9d9cdf3529823ccd1c6c66112b74790851a124969d8adf8ac142d9ef3039 |
#
# Copyright (C) 2004 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import rdBase
try:
import rdSimDivPickers
from rdSimDivPickers import *
except ImportError:
rdSimDivPickers=None
| rdkit/rdkit-orig | rdkit/SimDivFilters/__init__.py | Python | bsd-3-clause | 205 | [
"RDKit"
] | 8c36fceb76b3bd1fe2360b7e71186c0b12e5e173fa4fe7f562f2ceddd92f727c |
__docformat__ = 'reStructuredText'
'''
Accumulated energy last 24h.
============================
Neglecting horizontal energy transfers as well as effects due to blowing snow
or vegetation, the balance for an open and flat snow cover is given in units
W m-2 by:
net change rate of internal energy per unit... | kmunve/pysenorge | pysenorge/themes/energy_balance_daily.py | Python | gpl-3.0 | 1,910 | [
"NetCDF"
] | f5bc385af3942bd7f028d1b32bfb0cde4c607a17157cfdf2f3d646fc3af367d4 |
# Copyright 2017 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... | rabipanda/tensorflow | tensorflow/contrib/py2tf/pyct/static_analysis/live_values.py | Python | apache-2.0 | 4,422 | [
"VisIt"
] | 92cfe2d3583dccad0cd263eec1748ff78ee9da22b351ed08c75403d123ed997e |
""" FileReport class encapsulates methods to report file status to the transformation DB """
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import DEncode
from DIRAC.TransformationSystem.Client.TransformationClient import TransformationClient
from DIRAC.RequestManagemen... | avedaee/DIRAC | TransformationSystem/Client/FileReport.py | Python | gpl-3.0 | 2,181 | [
"DIRAC"
] | 236232d53f065abddecde3ec56f8bb9da369f0425f7458785404d69850642fb9 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
from pyscf import gto, scf, mcscf
'''
Tune CASSCF parameters to reduce the FCI solver cost.
The default CASSCF settings are optimized for large system so that the cost of
IO and integral transformation are minimal. But they are not optimal for
sm... | gkc1000/pyscf | examples/mcscf/01-for_expensive_fci.py | Python | apache-2.0 | 1,177 | [
"PySCF"
] | 9d265b2e2fa4209c268ecf8fb79fbcff465a2cae2e3e454752670b9d9d6b328b |
# Copyright 2014 Alistair Muldal <alistair.muldal@pharm.ox.ac.uk>
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# Th... | orlandi/connectomicsPerspectivesPaper | participants_codes/konnectomics/basic_workflow.py | Python | mit | 6,560 | [
"NEURON"
] | 91ef41ee00412977d10e799bd0d2011d1c7e7f49692e111cc7bfba58c14523e4 |
import json
import logging
import os
import tarfile
import tempfile
from time import strftime
from galaxy import util
from galaxy import web
from galaxy.model.orm import and_
from galaxy.web.base.controller import BaseAPIController
from galaxy.web.base.controller import HTTPBadRequest
from galaxy.web.framework.helpers... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/tool_shed/api/repositories.py | Python | gpl-3.0 | 32,758 | [
"Galaxy"
] | e05b3f731bd41b04c81c835d2f3823b7e574def8346354e187aa3601d31c1e9c |
# Copyright (c) 2012, Siu Kwan Lam
# All rights reserved.
#
# Contains the CodeGenerationBase class.
import logging
import ast
import types, dialect
from pymothoa.util.descriptor import Descriptor, instanceof
from compiler_errors import *
logger = logging.getLogger(__name__)
class CodeGenerationBase(ast.NodeVisito... | sklam/pymothoa | pymothoa/backend.py | Python | bsd-2-clause | 19,070 | [
"VisIt"
] | b60e97904d539756382f966a5e584b7c47f96a6afe5f937ae95c8f76bd876ae1 |
# Copyright (C) 2015 Atsushi Togo
# All rights reserved.
#
# This file is part of spglib.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyright
# notice... | sauliusg/cod-tools | src/externals/spglib/python/spglib/spglib.py | Python | gpl-2.0 | 27,046 | [
"CRYSTAL"
] | 65bbb79277e16782d72da106c7fd8990c72e8650f8c97469252d93ef66a80547 |
#
# 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 us... | brad-kaiser/spark | python/pyspark/ml/regression.py | Python | apache-2.0 | 64,602 | [
"Gaussian"
] | e34cacedb8bc957f142b4b268a024d335c7dc46e90e33e4f40d39d5b6d4129a8 |
from skimage import exposure
from skimage.transform import rescale
from scipy.ndimage.interpolation import map_coordinates
from scipy.ndimage.filters import gaussian_filter
from scipy.misc import imread
from sklearn import preprocessing
import cv2
from skimage.transform import rotate
import numpy as np
import random
im... | vherman3/AxonSegmentation | AxonDeepSeg/learning/input_data.py | Python | mit | 11,605 | [
"Gaussian"
] | 95896e3c18dfbb6551a27d2cedb532db98a5102fa49233a1910a383e0946b10e |
""" :mod: GFAL2_SRM2Storage
=================
.. module: python
:synopsis: SRM2 module based on the GFAL2_StorageBase class.
"""
from types import StringType, ListType
# from DIRAC
from DIRAC.Resources.Storage.GFAL2_StorageBase import GFAL2_StorageBase
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
fro... | marcelovilaca/DIRAC | Resources/Storage/GFAL2_SRM2Storage.py | Python | gpl-3.0 | 6,907 | [
"DIRAC"
] | da8c38e5c214cc2c75b18e4595adc3bdbad8daae357c231025b1b06cd41374c9 |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/udPassword.py | Python | gpl-3.0 | 2,716 | [
"Galaxy"
] | e00015a21d77b90640ea4edea0f7b59bf52886e292184fe3e642a1898908029b |
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