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# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to perform analyses of
the local environments (e.g., finding near neighbors)
of single sites in molecules and structures.
"""
import json
import math
import os
import warnings
... | richardtran415/pymatgen | pymatgen/analysis/local_env.py | Python | mit | 171,647 | [
"Gaussian",
"Jmol",
"VASP",
"pymatgen"
] | d212a21e20d699b0e91f5799e5cdfb5967f22a5868f0e5c4d4b9390f8edc0f7e |
"""
Building candidate models
"""
import itertools
from pycalphad.core.cache import cacheit
import symengine
from espei.sublattice_tools import interaction_test
def make_successive(xs):
"""
Return a list of successive combinations
Parameters
----------
xs : list
List of elements, e.g. [X,... | PhasesResearchLab/ESPEI | espei/parameter_selection/model_building.py | Python | mit | 7,017 | [
"pycalphad"
] | d28866d42cf72ab372c89da1c645169b712a27820ce4e03be8416fa01e28d44d |
#! /usr/bin/env python
########################################################################
# File : dirac-admin-set-site-protocols
# Author : Stuart Paterson
########################################################################
"""
Defined protocols for each SE for a given site.
Example:
$ dirac-admin-se... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_set_site_protocols.py | Python | gpl-3.0 | 1,310 | [
"DIRAC"
] | 6eacb145bab78334ef9e77221576ce579c947cc1b218576b99034a5633580ee8 |
import os, sys, math
import numpy as np
import scipy
import pylab
import scipy.optimize
import lib.LammpsIO as lmp_io
import lib.DataAnalysis as da
import lib.DataMorphing as dm
def generate_interaction_list(num_of_types):
int_set = []
for ii in xrange(1, num_of_types+1):
for iii in xrange(ii, num_of_types+1)... | uschille/FabSim | python/IBI.py | Python | lgpl-3.0 | 24,218 | [
"LAMMPS"
] | b08465ae35718c13eef4489ff2d9dad69e0b08388dede45abbc05002968cef1a |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ---------------------... | JWDebelius/scikit-bio | setup.py | Python | bsd-3-clause | 2,965 | [
"scikit-bio"
] | 53247b553149d82b99f3eccc321bf6e536969a5fe0c71f3797b33cdeb5e653df |
# -*- coding: utf-8 -*-
#
# recording_demo.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License,... | sanjayankur31/nest-simulator | pynest/examples/recording_demo.py | Python | gpl-2.0 | 2,196 | [
"NEURON"
] | 70683a197ce2dd4bc31086f3dc50102b30fd3cac6bc0954bf73ed665c9adf625 |
#!/usr/bin/python3
# encoding: utf-8
# Berreman4x4 example
# Authors: O. Castany, C. Molinaro
# Example of a cholesteric liquid crystal
import numpy, Berreman4x4
from numpy import sin, sqrt, abs
from Berreman4x4 import c, pi, e_y
import matplotlib.pyplot as pyplot
# Materials
glass = Berreman4x4.IsotropicNonDispers... | Berreman4x4/Berreman4x4 | examples/cholesteric-example.py | Python | gpl-3.0 | 4,607 | [
"CRYSTAL"
] | cfb8a12536ad029966b98b5bb16906d01b61b6ab672d183c17ade64aba95aaff |
# $HeadURL: $
''' Command
Base class for all commands.
'''
from DIRAC import gLogger, S_OK
__RCSID__ = '$Id: $'
class Command( object ):
'''
The Command class is a simple base class for all the commands
for interacting with the clients
'''
def __init__( self, args = None, clients = None ):
... | Sbalbp/DIRAC | ResourceStatusSystem/Command/Command.py | Python | gpl-3.0 | 2,153 | [
"DIRAC"
] | f88ddbc7fee5c99e22d6848b25b99bb1886c7f7626c9ec79459cf8bc3ce6002e |
#!/usr/bin/env python
#-------------------------------------------------------------
# Author: Thomas Schwarzl <schwarzl@embl.de>
# With the help of: Christian Hauer <chauer@embl.de>
# Licenced under MIT Creative Licence
# Last change: 21 October 2014
#-------------------------------------------------------------
#---... | Distue/iclipper | lib/iCLIP.py | Python | mit | 41,846 | [
"HTSeq"
] | f7d25259f783d2e4f013c5939d868c7993e88eaaf6adfb46399f64116ebaf1fe |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
datatypes_repository_name = 'emboss_datatypes_0020'
datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This reposi... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_1300_reset_all_metadata.py | Python | gpl-3.0 | 34,892 | [
"Galaxy"
] | 8853862d046f71c6710258074f7b985a56132afbd318e9e9211433f296a414f5 |
"""uwg simulation running commands."""
import sys
import json
import logging
try:
import click
except ImportError:
raise ImportError(
'click is not installed. Try `pip install . [cli]` command.'
)
from uwg import UWG
_logger = logging.getLogger(__name__)
@click.group(help='Commands for simulatin... | chriswmackey/UWG_Python | uwg/cli/simulate.py | Python | gpl-3.0 | 3,213 | [
"EPW"
] | 2dab0cc0358c3f92b6ae1376db2d53e2f0361ff6f438a867d000eba9326a48c0 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""
Ref. to Kresse-paper ... XXX
"""
import numpy as np
from gpaw.utilities.blas import axpy
from gpaw.fd_operators import FDOperator
class BaseMixer:
"""Pulay density mixer."""
def __init__(self, beta=0.1, ... | qsnake/gpaw | gpaw/dfpt/mixer.py | Python | gpl-3.0 | 17,948 | [
"GPAW"
] | bff834d4984661fda881e414868be81f9892be0f552d1ab5319c8bf240949508 |
#
# Copyright 2014 Flytxt
#
# 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 ... | himanshu14/GMM | GMMModel.py | Python | apache-2.0 | 3,380 | [
"Gaussian"
] | d82bc14b1b6ad1ffcac0b906300a7ea779de551bd27cd68de278cb98c6d0bbf3 |
import sys
import struct
import traceback
import envi
import envi.bits as e_bits
from envi.bits import binary
from envi.archs.arm.const import *
from envi.archs.arm.regs import *
# Universal opcode things:
# len
# mode
#FIXME: TODO
# * Thumb Extension Parser
# * Jazelle Extension Parser
# * Emulators
#######... | joxeankoret/nightmare | lib/interfaces/envi/archs/arm/armdisasm.py | Python | gpl-2.0 | 61,423 | [
"xTB"
] | 3b9b43b49b347051ad20e6ef955b5f6c203e31e44bdaf2255bc2027c331cee52 |
from PyQt4 import Qt
import sys
import matplotlib.pyplot as plt
import numpy as np
from collections import OrderedDict
import sys
import csv
class Window(Qt.QWidget):
def __init__(self):
Qt.QWidget.__init__(self)
global global_results
from OneStopTrack import global_results
self.c... | mzie/RATRACTION | animal_movement_heatmap.py | Python | gpl-3.0 | 5,243 | [
"Gaussian"
] | d37587cf3d84c3c3a6fa747e247b35118c1d535d7b01804d442e75dcf545b50e |
from __future__ import division
from __future__ import print_function
import sys
sys.path.insert(1, "../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.gam import H2OGeneralizedAdditiveEstimator
# In this test, we check and make sure Gam can run without predictor columns as long as gam column is... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/gam/pyunit_PUBDEV_7931_gam_null_predictors.py | Python | apache-2.0 | 2,490 | [
"Gaussian"
] | cfad1eb486ce22ec5e47a65a8410423fa7014c66c152549181e815a4f839e431 |
#!/usr/bin/env python
# encoding: utf-8
"""
Analyze multiple periods and starspot evolution
"""
from __future__ import print_function, division, absolute_import
import datetime
import os
import sys
from scipy.ndimage import gaussian_filter
from scipy import signal
import numpy as np
import pandas as pd
import matplot... | jlurie/decatur | decatur/mulitperiodic.py | Python | mit | 14,463 | [
"Gaussian"
] | 5a168c02462291bb2b631f956d7e18c0b039d7632f77ac265d6dd8b77cb84aaf |
from __future__ import absolute_import, division, print_function
import unicodedata
import numpy as np
from .. import Variable, coding
from ..core.pycompat import OrderedDict, basestring, unicode_type
# Special characters that are permitted in netCDF names except in the
# 0th position of the string
_specialchars = ... | jcmgray/xarray | xarray/backends/netcdf3.py | Python | apache-2.0 | 4,111 | [
"NetCDF"
] | ac9172674d5b96ca996290e956d677e9db76527e3d2e4ec896e2ab48b94ebfd2 |
#!/usr/bin/env python
"""
Copyright (c) 2006-2014 sqlmap developers (http://sqlmap.org/)
See the file 'doc/COPYING' for copying permission
"""
import cookielib
import glob
import inspect
import logging
import os
import random
import re
import socket
import string
import sys
import threading
import time
import urllib2... | Snifer/BurpSuite-Plugins | Sqlmap/lib/core/option.py | Python | gpl-2.0 | 82,251 | [
"VisIt"
] | e78a17c8acf9f790152a3dfb4b021618bd2b36890b3aee68d6c5aadf8e83677f |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
"""
Module ... | nuclear-wizard/moose | python/MooseDocs/common/__init__.py | Python | lgpl-2.1 | 1,172 | [
"MOOSE"
] | 1f2f75f2d6c4158527b6e3aa61ae559d56761b4bea7eea893e7d590bd243e2a9 |
# 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... | mkuron/espresso | testsuite/python/scafacos_dipoles_1d_2d.py | Python | gpl-3.0 | 5,604 | [
"ESPResSo"
] | 87ff1676c783b46f3057f1cee42e45d9cfb40da241313a3cabf4018326191b17 |
#!/usr/bin/python
import math
import argparse
from string import maketrans
#Script used in order to obtain primers.
parser = argparse.ArgumentParser()
parser.add_argument('-file', action="store", dest = 'File', required = "True")
parser.add_argument('-fasta', action = "store", dest = "genome", required = "True")
parse... | davidwilson-85/easymap | primers/primer-generation-old.py | Python | gpl-3.0 | 10,749 | [
"Biopython"
] | 47d5fbf56395905bbddbcbf2345fefee24c9f4c5ad80ee53d75680dc4f78bcd9 |
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, print_function, unicode_literals, division)
class BaseNode:
def accept(self, visitor):
visitor.visit(self)
class TopLevelQuery(BaseNode):
def __init__(self, query, q_size=None, q_from=None, aggs=None, sort=None):
self.query = ... | BrandKarma/elasticsearch_dsl | elasticsearch_dsl/ast.py | Python | bsd-3-clause | 4,718 | [
"VisIt"
] | 3d2f104498d8de867bb3114793e208c71cac48e0bb60e1eea27926a518cba76f |
# Copyright (C) 2009 Google Inc. 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
# notice, this list of conditions and the f... | windyuuy/opera | chromium/src/third_party/WebKit/Tools/Scripts/webkitpy/common/config/committers_unittest.py | Python | bsd-3-clause | 20,632 | [
"Brian"
] | 2687431fc9e226bfdf4ecfcc5489d86c25966ea1a52b1ebc9a98cf9c6aa436fc |
import cPickle as pickle
import copy
import os
import menpo.io as mio
import numpy as np
from menpo.feature import no_op
from menpo.landmark import labeller, face_ibug_68_to_face_ibug_66_trimesh
from menpo.math import as_matrix
from menpo.model import PCAModel
from menpo.transform import PiecewiseAffine
from menpofit.... | azinasg/AAM_TL | Instance_Gaussian_WithoutLog.py | Python | bsd-3-clause | 19,070 | [
"Gaussian"
] | 61eadc95e246d8e279cde355680cd667eabbb407b19630458722911fd02732fa |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
The basic photometry class for the TASOC Photometry pipeline.
All other specific photometric algorithms will inherit from BasePhotometry.
.. codeauthor:: Rasmus Handberg <rasmush@phys.au.dk>
"""
import numpy as np
import h5py
import sqlite3
import logging
import date... | tasoc/photometry | photometry/BasePhotometry.py | Python | gpl-3.0 | 72,934 | [
"Gaussian"
] | b2b39baa52c65a0f6850223347e0c0409f76e2dfb43443389d1c661e69428336 |
#!/usr/bin/python
#
# Counts the bases for each sequence in a FASTA file and spits them out along with the sequence record id, tab separated.
#
# Requires: BioPython
import sys
from Bio import SeqIO
def main():
if len(sys.argv)!=2:
print "countbases.py <fasta-file>"
sys.exit(0)
for seq_recor... | carnegie-dpb/biotools | countbases.py | Python | gpl-2.0 | 453 | [
"Biopython"
] | 34345028e5d405dccba48f2e8e0ad1771b0640fc69ef4318273953a4dfacc3fa |
##
# Copyright 2009-2018 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | bartoldeman/easybuild-easyblocks | easybuild/easyblocks/t/tinker.py | Python | gpl-2.0 | 6,443 | [
"TINKER"
] | e0c6627d20d0de69b9a13df787ceaf6d91ec04ac4b543e52c54846fe44a07b81 |
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
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 Softw... | thica/ORCA-Remote | src/interfaces/remoteghost/Evenghost_Plugin/ORCA/__init__.py | Python | gpl-3.0 | 11,936 | [
"ORCA"
] | 3ae4bf25ecd6723742c0be26a20d46c3445cd7db473144c10c328c240f2ed300 |
#!/usr/bin/env python
#TODO: the above hash bang sould work on any Unix/Linux system. Anyway, check
#your path to env or your Python interpreter
#PPM from RC transmitters Calibrate Version 2.0
#
#PPMRC - PPM interpreter, calibrator and remapper
#Copyright (C) 2017 Francesco Antonetti Lamorgese Passeri
#https://github... | antlampas/ppmrc | Example/FlightGear/Linux/ppmrc.py | Python | gpl-3.0 | 10,863 | [
"VisIt"
] | d3ad2154892f8abda675f8e33846fa06c69202157233363a546a2dd374749c81 |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
#
# Impressive, a fancy presentation tool
# Copyright (C) 2005-2014 Martin J. Fiedler <martin.fiedler@gmx.net>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License, version 2, as
# published by ... | bcousson/impressive | impressive.py | Python | gpl-2.0 | 244,069 | [
"VisIt"
] | 74287b42cbab3de537008a78d453abd29b9534b4d30dbe53046676c3f139310d |
"""
This module starts with an aterm graph and finds suitable executors for the
subgraphs that can be handled by that executor.
"""
import blaze
from blaze.engine import pipeline
from blaze.engine import llvm_execution
from blaze.engine import dispatch
class ExecutionPipeline(object):
def __init__(self):
... | davidcoallier/blaze | blaze/engine/execution_pipeline.py | Python | bsd-2-clause | 1,595 | [
"VisIt"
] | f5025c26bada9c7f6a9598b156ef24c7b178beddb563166f5618da16019b95cc |
""" Unit tests for pipelines expressed via arlexecute
"""
import logging
import sys
import unittest
import numpy
from astropy import units as u
from astropy.coordinates import SkyCoord
from data_models.polarisation import PolarisationFrame
from data_models.memory_data_models import BlockVisibility, Visibility
from p... | SKA-ScienceDataProcessor/algorithm-reference-library | tests/workflows/test_imaging_arlexecute.py | Python | apache-2.0 | 25,025 | [
"Gaussian"
] | 2abb25253bf4f8dabd7c672a6ab0a1a79ec1f62cbd88d95926082f2ccf78cbaf |
# Author: Robert McGibbon <rmcgibbo@gmail.com>
# Contributors: Matthew Harrigan <matthew.harrigan@outlook.com>
# Copyright (c) 2015, Stanford University
# All rights reserved.
from __future__ import absolute_import, print_function, division
import sys
import os
import re
import glob
from os.path import join, exists, ... | stephenliu1989/msmbuilder | msmbuilder/dataset.py | Python | lgpl-2.1 | 15,521 | [
"MDTraj"
] | c5492ca8ab66579c294333342e5e1d6ff42fc2b79b632aa916a7618707e0df7b |
#!/usr/bin/env python
"""
TextureCoordinates
"""
"""
Copyright 2001 Pearu Peterson all rights reserved,
Pearu Peterson <pearu@ioc.ee>
Permission to use, modify, and distribute this software is given under the
terms of the LGPL. See http://www.fsf.org
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RI... | chunshen1987/iSS | utilities/for_paraview/lib/TextureCoordinates.py | Python | mit | 1,968 | [
"VTK"
] | 2508ba1b4bd66f6160df48534a962ba7955ea494696ef56b1db90d01754bcae3 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module implements an interface to enumlib, Gus Hart"s excellent Fortran
code for enumerating derivative structures.
This module depends on a compiled enumlib with the executables multienum.x and
makestr.x available in the path. Please downloa... | rousseab/pymatgen | pymatgen/command_line/enumlib_caller.py | Python | mit | 15,703 | [
"VASP",
"pymatgen"
] | 3856bd60bedee48eee613f75ba3a8aa373501fc96146a37f9dffda6df38d4496 |
#!/usr/bin/env python2.7
# This version is created at Mon Mar 17 12:54:44 CET 2014
# Author: Asli I. Ozen (asli@cbs.dtu.dk)
# License: GPL 3.0 (http://www.gnu.org/licenses/gpl-3.0.txt)
import sys, gzip
import re, string
import argparse
import os
from Bio.Blast import NCBIStandalone
from operator import itemgetter, attr... | MG-group-tools/MGFunc | mgfunc_v2/bldecide.py | Python | gpl-3.0 | 14,596 | [
"BLAST"
] | ecc48efd4a22cad1444640b1e9bda6c7d90ebf0fcb6e1a2f9a2ff5e420b6c99e |
# -*- coding: utf-8 -*-
"""
Copyright (C) 2014-2020 OSMC (KodeKarnage)
This file is part of script.module.osmcsetting.pi
SPDX-License-Identifier: GPL-2.0-or-later
See LICENSES/GPL-2.0-or-later for more information.
"""
import os
import subprocess
import traceback
import xbmcaddon
import xbmcgui
from... | osmc/osmc | package/mediacenter-addon-osmc/src/script.module.osmcsetting.pi/resources/lib/osmcpi/osmc/osmc_setting.py | Python | gpl-2.0 | 5,950 | [
"VisIt"
] | 4a8e4c86dd6a5c4fc49468a5298bb9e2544c177f395d94f20b189cc26c2d7543 |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
pick random sample
pick weighted random sample
generate random permutation
distributions on the real line:
---------------------... | kenshay/ImageScript | Script_Runner/PYTHON/Lib/random.py | Python | gpl-3.0 | 27,484 | [
"Gaussian"
] | c83be042e9a868d29d7db05e68dd8e10b567a44697a76b702e6dae2d5ba5591e |
from ase.dft.kpoints import monkhorst_pack
assert [0, 0, 0] in monkhorst_pack((1, 3, 5)).tolist()
assert [0, 0, 0] not in monkhorst_pack((1, 3, 6)).tolist()
assert len(monkhorst_pack((3, 4, 6))) == 3 * 4 * 6
from ase.units import Hartree, Bohr, kJ, mol, kcal, kB, fs
print Hartree, Bohr, kJ/mol, kcal/mol, kB*300, fs... | grhawk/ASE | tools/ase/test/things.py | Python | gpl-2.0 | 568 | [
"ASE"
] | 369f8022bca68d3f2357ea7eaf3949ed32b858c88daed152063c7e21ea6b773d |
#! /usr/bin/env python
from StringIO import StringIO
import numpy as np
###
def loadstate(logfn, dumpfn):
f = open(logfn)
l = f.readline()
while len(l.split()) == 0 or l.split()[0] != 'Step':
l = f.readline()
l = f.readline().split()
ect, ecoul, elong, lx = map(float, [l[4]... | Atomistica/lammps-bsct | tests/TEST_NaCl/eval.py | Python | gpl-2.0 | 2,001 | [
"LAMMPS"
] | 11d47cdc3ddc85c18c8d5753a37868c446196045fd5c6136244858bc54121c0d |
# cell.py ---
#
# Filename: cell.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Fri Mar 9 23:17:17 2012 (+0530)
# Version:
# Last-Updated: Fri Jul 10 15:56:23 2015 (+0530)
# By: subha
# Update #: 692
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Chang... | dilawar/moose-full | moose-examples/traub_2005/py/cells.py | Python | gpl-2.0 | 15,472 | [
"MOOSE",
"NEURON"
] | 0b7e127598697b75c3745ebe7ec6965699b0cdc279e29611edbc34508abacf9d |
"""network2.py
~~~~~~~~~~~~~~
An improved version of network.py, implementing the stochastic
gradient descent learning algorithm for a feedforward neural network.
Improvements include the addition of the cross-entropy cost function,
regularization, and better initialization of network weights. Note
that I have focuse... | haphaeu/yoshimi | neural_networks/mnist/network2.py | Python | lgpl-3.0 | 14,535 | [
"Gaussian",
"NEURON"
] | 752a1ce561192cd8f9ee6c53defb463420c20d9388312d368fc81974a2333ed7 |
import re
import numpy as np
import scipy.sparse
import pytest
from sklearn.datasets import load_digits, load_iris
from sklearn.model_selection import train_test_split
from sklearn.model_selection import cross_val_score
from sklearn.utils._testing import assert_almost_equal
from sklearn.utils._testing import assert... | glemaitre/scikit-learn | sklearn/tests/test_naive_bayes.py | Python | bsd-3-clause | 35,392 | [
"Gaussian"
] | 87a61ce688e515e1431cb005839a0f3d350ac2b796f37a418a73976181c6b255 |
import os
import random
import scipy.integrate
import scipy.interpolate
import scipy.signal
import string
import numpy
import astropy.io.fits as pyfits
class SpectrumError( Exception ):
def __init__(self, value, errmsg):
'''
SpectrumError
Raised on execptions within Spectrum object... | JNMcLane/MoogPy | MoogTools/SpectralTools.py | Python | mit | 79,066 | [
"Gaussian"
] | 1229b3a86120260b26b1a84fa39c95ad6de94aeab27214f9eac86d0b53f767de |
###
# Copyright 2008-2011 Diamond Light Source Ltd.
# This file is part of Diffcalc.
#
# Diffcalc 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 late... | DiamondLightSource/diffcalc | test/diffcalc/ub/test_crystal.py | Python | gpl-3.0 | 2,172 | [
"CRYSTAL"
] | a9dfa683bd6864072b19ad28a7796bd24ca90cb654cc79e97727b21e65d50226 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
It merges the reports from BOWTIE-method with BLAT-method.
Author: Daniel Nicorici, Daniel.Nicorici@gmail.com
Copyright (c) 2009-2021 Daniel Nicorici
This file is part of FusionCatcher.
FusionCatcher is free software: you can redistribute it and/or modify
it under... | ndaniel/fusioncatcher | bin/merge_reports.py | Python | gpl-3.0 | 19,594 | [
"BWA",
"Bowtie",
"Elk"
] | 1281e355a3f7f26606d6091a63a110cce3b1ab68ccfd7f04d3d455277a79d076 |
#!/usr/bin/env python
__author__ = 'arulalant'
__version__ = 'v2.0.1'
__long_name__ = 'NCUM Parallel Rider by targetting creation of TIGGE Grib2 files'
"""
Inputs: NCUM fieldsfile / pp format files
Outputs: WMO-NCEP Grib2 format files
This script produce output files as multiple 6 hourly forecasts data from
differe... | arulalant/UMRider | g2utils/um2grb2tigge.py | Python | gpl-2.0 | 143,069 | [
"NetCDF"
] | 395275c50d6f0083ce2d9a8fe5af00a1c1f57d324147cad386048fc66b7024ca |
from __future__ import print_function
import os
import tempfile
import numpy as np
import fitsio
from astrometry.util.fits import fits_table, merge_tables
from astrometry.util.file import trymakedirs
from tractor.ellipses import EllipseESoft, EllipseE
from tractor.galaxy import ExpGalaxy
from tractor import PointS... | legacysurvey/pipeline | py/legacypipe/survey.py | Python | gpl-2.0 | 64,528 | [
"Galaxy",
"Gaussian"
] | 0c751d43ef9e3d0f5076283bcea2313627cb751702667d562e45c9efeabc2c96 |
#!/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... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/main.py | Python | gpl-2.0 | 36,828 | [
"VisIt"
] | d2f2e62701ef6ef1e309870c97319e11cdf3297a59b6f3485109e7e82790f3f8 |
# Copyright 2017 Codas Lab
#
# 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 to in writing, softwa... | CoDaS-Lab/image_analysis | demo/obliquevr.py | Python | apache-2.0 | 2,088 | [
"Bowtie"
] | 9fc45bdf4bf24c32bd996e64cd119d4b2a671e21d4da4e968a59c009d1af2dd7 |
from matplotlib import patches
import numpy as np
import pickle
from pybrain.datasets import SupervisedDataSet
from pybrain.structure import RecurrentNetwork, FeedForwardNetwork
from pybrain.structure.connections.full import FullConnection
from pybrain.structure.modules.linearlayer import LinearLayer
from pybrain.struc... | vitaliykomarov/NEUCOGAR | old/main.py | Python | gpl-2.0 | 22,609 | [
"NEURON"
] | ebdc76bd68873a5af8558d49609ee457b10bb4e9ac2d3b93e8267d2949884edf |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB ... | vinodpanicker/scancode-toolkit | tests/cluecode/test_copyrights.py | Python | apache-2.0 | 180,672 | [
"Brian",
"VisIt"
] | 2fd6fcbe4cefc1e8ebb0f068357d3269606bf3487c6d1e3dc493767eea371ed0 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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)
#
# Released under ... | MDAnalysis/mdanalysis | package/MDAnalysis/topology/GROParser.py | Python | gpl-2.0 | 4,984 | [
"GROMOS",
"Gromacs",
"MDAnalysis"
] | c0d8d8222907cdae0dd2c8396a5c79cdbbb454dce5260de1325ad4c3a9affe68 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/songs/forms/editversedialog.py | Python | gpl-2.0 | 5,909 | [
"Brian"
] | 0113fe3bfbb50fa5874851549d8514d066d56da892ce2d816b6690b5bb822681 |
#!/usr/bin/env python
import numpy as np
from horton import *
# Load the Gaussian output from file
fn_fchk = context.get_fn('test/water_sto3g_hf_g03.fchk')
# Replace the previous line with any other fchk file, e.g. fn_fchk = 'yourfile.fchk'.
mol = IOData.from_file(fn_fchk)
# Partition the density with the Becke sche... | eustislab/horton | data/examples/wpart/becke.py | Python | gpl-3.0 | 672 | [
"Gaussian"
] | eeeb897504fbcdb9e0227f6a25a09fd9f5d17c995ec1e137328eb975b483a0d5 |
import os,csv
folder = "/home8/kanika/moose/mat_files/"
output = '/home8/kanika/petsc2/src/ksp/ksp/examples/tutorials/moose_features/tutorials/properties_script.sh'
target = open(output,'w')
target.write("clear \n")
feat_file = open('/home8/kanika/petsc2/src/ksp/ksp/examples/tutorials/moose_features/tutorials/propert... | LighthouseHPC/lighthouse | sandbox/petsc/moose-petsc-features/compute_32_feat.py | Python | mit | 1,480 | [
"MOOSE"
] | 2981632c5a1ad025dcce0dc9ce68823e80c8efd7b21afb23952db2de895fcfb3 |
from typing import List, Dict
import numpy
from allennlp.common.util import JsonDict
from allennlp.data import DatasetReader, Instance
from allennlp.data.fields import FlagField, TextField, SequenceLabelField
from allennlp.data.tokenizers.spacy_tokenizer import SpacyTokenizer
from allennlp.models import Model
from a... | allenai/allennlp | allennlp/predictors/sentence_tagger.py | Python | apache-2.0 | 4,294 | [
"VisIt"
] | f22e151003fbb1dc3226653ab77b588ff59f93dc01e930feaef21c2440ecc391 |
"""Unit test for util.py"""
import pysal
from pysal.common import *
import pysal.weights
import numpy as np
from scipy import sparse, float32
from scipy.spatial import KDTree
import os
import gc
class Testutil(unittest.TestCase):
def setUp(self):
self.w = pysal.rook_from_shapefile(
pysal.examp... | spreg-git/pysal | pysal/weights/tests/test_util.py | Python | bsd-3-clause | 7,381 | [
"COLUMBUS"
] | c841ba4b1532b16bde65e0488d0face386ab3e9df0af18ce2bc74a099601598f |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | francisco-dlp/hyperspy | hyperspy/_components/expression.py | Python | gpl-3.0 | 12,316 | [
"Gaussian"
] | 61860bdd91b7c1e4539119ac210f1e477e74aa5b1dbf78827420d84a8bbcd0f8 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import math
import numpy as np
from .core import Kernel1D, Kernel2D, Kernel
from .utils import has_even_axis, raise_even_kernel_exception, KernelSizeError
from astropy.modeling import models
from astropy.modeling.core import Fittable1DModel, Fittable2DM... | lpsinger/astropy | astropy/convolution/kernels.py | Python | bsd-3-clause | 33,934 | [
"Gaussian"
] | 28b1175fa902264d61a0a5b67cfb5ae4b6a529e3d93eae9f80ad949e61df1ebf |
# Copyright (C) 2011-2019 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... | pkreissl/espresso | testsuite/python/ek_eof_one_species.py | Python | gpl-3.0 | 19,793 | [
"ESPResSo",
"VTK"
] | 703b80211f00478658fc13094cb203f3f5f0666daa57e7b50ae96db8a387081f |
"""LAMMPS calculator for preparing and parsing single-point LAMMPS \
calculations."""
import subprocess
import numpy as np
# TODO: split LAMMPS input and data files into separate classes
def run_lammps(lammps_executable, input_file, output_file):
"""Runs a single point LAMMPS calculation.
:param lammps_exec... | mir-group/flare | flare/lammps/lammps_calculator.py | Python | mit | 6,652 | [
"LAMMPS"
] | 5ff906e2cf757ca02c28963a1ea54dbb8c48ad9308e56f0a9444d1dcf856bcab |
""" The Bdii2CSAgent performs checking BDII for availability of CE
resources for a given or any configured VO. It detects resources not yet
present in the CS and notifies the administrators.
For the CEs already present in the CS, the agent is updating
if necessary settings which were changed in the BDII recently
The f... | DIRACGrid/DIRAC | src/DIRAC/ConfigurationSystem/Agent/Bdii2CSAgent.py | Python | gpl-3.0 | 13,250 | [
"DIRAC"
] | bca330d0d8a32ba6011c8fd7220f9244fd05044980a6672deeeea5d45f920c7c |
import autograd.numpy as npa
import numpy as np
import matplotlib.pylab as plt
from autograd.extend import defjvp, defvjp
from scipy.linalg import dft
import sys
sys.path.append('../ceviche')
from ceviche import fdtd, jacobian
from ceviche.utils import my_fft
""" Autograd through spectrum computation """
Nx = 50
N... | fancompute/ceviche | examples/autograd_fft.py | Python | mit | 2,151 | [
"Gaussian"
] | 72d2d0f150d914b755fb0ec3a434c8ae48475d709c716263ec3598363b688c90 |
# encoding: utf-8
import copy
import collections
from lkbutils import nodemodel, yamllib
class RedundantRelation(ValueError):
def __init__(self, src, dest, link=None, encoding=u'utf-8'):
self.src = src
self.dest = dest
self.link = link
msg = self.mkmsg(src, dest, link)
sup... | drowse314-dev-ymat/lexical-knowledge-base-for-japanese-civil-law | lkbutils/relationprovider/__init__.py | Python | mit | 7,314 | [
"VisIt"
] | c34f5bfcbe843b7059d39b4cfcbfcc77e35f621879011cc3463f29aab8cce746 |
import gzip
import sys
# the location of the taxonomy files
defaultdir = '/home2/db/taxonomy/current/'
'''
From nodes.dmp
tax_id -- node id in GenBank taxonomy database
parent tax_id -- parent node id in GenBank taxonomy database
rank ... | dacuevas/bioinformatics | ncbi_taxonomy/taxon.py | Python | mit | 6,722 | [
"BLAST"
] | 5468878954cd8636a68a482329917f8acd62c92850dc12d5c7f522f0ebd7a381 |
import sys
import numpy as np
import gzip
import pysam
import operator
import util
NUCLEOTIDES = set(['A', 'C', 'T', 'G'])
SNP_UNDEF = -1
# codes for CIGAR string
BAM_CMATCH = 0 # M - match/mismatch to ref M
BAM_CINS = 1 # I - insertion in read relative to ref
BAM_CDEL = 2 # D - deletion in r... | smozaffari/WASP | mapping/snptable.py | Python | apache-2.0 | 16,983 | [
"pysam"
] | 2716d9802150925f41c2389e9a31afe6d4712b59a55fbb4d91ca84c886d20fb1 |
#!/usr/bin/env python
# @package adjust_timeline
# \author Andy Aschwanden, University of Alaska Fairbanks, USA
# \brief Script adjusts a time axis of a file.
# \details Script adjusts the time axis of a file.
# Say you have monthly climate forcing from 1980-1-1 through 2001-1-1 in
# the forcing file foo_1980-1999.nc... | talbrecht/pism_pik | util/adjust_timeline.py | Python | gpl-3.0 | 5,497 | [
"NetCDF"
] | babff84294a0bf39f8a9fbfd2e3a69612ff995257c2ac719d7c2c89b2e43b2e3 |
# -*- coding: utf-8 -*-
"""Test grounding."""
import unittest
from unittest import mock
import bioregistry
import pyobo
from pyobo.mocks import get_mock_id_name_mapping
from pybel.constants import (
ANNOTATIONS,
CONCEPT,
GMOD,
IDENTIFIER,
KIND,
MEMBERS,
NAME,
NAMESPACE,
PMOD,
... | pybel/pybel | tests/test_grounding.py | Python | mit | 20,364 | [
"Pybel"
] | eb6e14ce4f26aa0701399ba676a228488df767fa6a85b43edd1ca3eeef21f05c |
from __future__ import unicode_literals
from ..person import Provider as PersonProvider
class Provider(PersonProvider):
formats = (
'{{first_name}} {{last_name}}',
'{{first_name}} {{last_name}}',
'{{first_name}} {{last_name}}',
'{{first_name}} {{last_name}}',
'{{first_name}... | ShaguptaS/faker | faker/providers/en_US/person.py | Python | mit | 38,668 | [
"Amber",
"Brian",
"COLUMBUS",
"CRYSTAL",
"Dalton",
"Desmond"
] | 9a6e95450c3ad359267f2e8ee83fe824c2ebfe4c5bed4eacca1ab642b176aa4a |
"""
=================================
Gaussian Mixture Model Ellipsoids
=================================
Plot the confidence ellipsoids of a mixture of two Gaussians with EM
and variational Dirichlet process.
Both models have access to five components with which to fit the
data. Note that the EM model will necessari... | vermouthmjl/scikit-learn | examples/mixture/plot_gmm.py | Python | bsd-3-clause | 2,875 | [
"Gaussian"
] | 198df19b49d8383b2a4da91ee28d3854bbf55231b0e518b0956e77543a1ed34c |
import matplotlib.pyplot as plt
import numpy as np
from scipy.integrate import odeint
gamma = 4.4983169634398596e-06
def derivs(solarray, t, M, S):
"""Computes the derivatives of the equations dictating the behavior of the stars orbiting galaxy M and the
disrupting galaxy, S
Parameters
----------... | bjshaw/phys202-project | galaxy_project/DE_solver.py | Python | mit | 2,258 | [
"Galaxy"
] | 7ab5b67dd4a4074dbd8cbd3507935a1312deca206ec3ba2f870cd9a4a4c438fd |
#
# Copyright (C) 2000 greg Landrum
#
""" unit tests for the ID3 implementation """
from rdkit import RDConfig
import unittest
from rdkit.ML.DecTree import ID3,DecTree
import cPickle
from rdkit.ML.Data import MLData
class ID3TestCase(unittest.TestCase):
def setUp(self):
print '\n%s: '%self.shortDescription(),... | rdkit/rdkit-orig | rdkit/ML/DecTree/UnitTestID3.py | Python | bsd-3-clause | 5,726 | [
"RDKit"
] | 7f506a07cd8487db6965888cc9454956f3447e87a1e65a2ff635202bf7d7b1f0 |
"""Support for Z-Wave lights."""
from __future__ import annotations
import logging
from typing import Any
from zwave_js_server.client import Client as ZwaveClient
from zwave_js_server.const import ColorComponent, CommandClass
from homeassistant.components.light import (
ATTR_BRIGHTNESS,
ATTR_COLOR_TEMP,
... | sander76/home-assistant | homeassistant/components/zwave_js/light.py | Python | apache-2.0 | 14,879 | [
"Amber"
] | 3f3c9830d5af2c75bdf8516db167c392faa506f44bfa7785d5a244928a2fc20c |
"""
==================================================
Automatic Relevance Determination Regression (ARD)
==================================================
Fit regression model with Bayesian Ridge Regression.
See :ref:`bayesian_ridge_regression` for more information on the regressor.
Compared to the OLS (ordinary l... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/examples/linear_model/plot_ard.py | Python | mit | 2,827 | [
"Gaussian"
] | 1f3a112006523e716bde70f79e3a904150d6e8756a78c63df95ed13c215befba |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/driver/p4util/spectrum.py | Python | lgpl-3.0 | 13,818 | [
"Avogadro",
"Gaussian",
"Psi4"
] | 80af72b4e042ab4305b2e4b1ac1104191677c59b872f061a931e3aa18ca2874a |
import matplotlib as mpl
mpl.use('Agg')
import numpy as np
import moose
import rdesigneur as rd
def test_current_pulse_squid():
"""Test current pulse.
>>> test_current_pulse_squid()
Rdesigneur: Elec model has 1 compartments and 0 spines on 0 compartments.
[array([-0.065 , -0.06525877, -0.06549723, ... | dilawar/moose-core | tests/rdesigneur/test_30_squid_currentPulse.py | Python | gpl-3.0 | 1,098 | [
"MOOSE"
] | faf99a6bf2461fb3a320ae2be4ae0309d73c121231027f9ed2150d8b3f165e50 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-dialogflow | tests/unit/gapic/dialogflow_v2/test_participants.py | Python | apache-2.0 | 127,239 | [
"Octopus"
] | 1590517dc135bd5eacb39afa46f132400cbaf235662b14aa5fb6d373e37d9a9b |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/prop/hfc/uks.py | Python | apache-2.0 | 4,256 | [
"PySCF"
] | 70382740c36309dab8bb55baa34dd806654c106d87ee7b049ad48c75b96e146f |
#!/usr/bin/env python
# -- coding:utf-8 --
# Last-modified: 12 June 2020 10:48:53 PM
#
# Module/Scripts Description
#
# Copyright (c) 2020 Rowan University
#
# This code is free software; you can redistribute it and/or modify it
# under the terms of the BSD License (see the file COPYING included with
# the di... | YONGCHENUTD/C3S | bin/runC3S.py | Python | gpl-3.0 | 6,466 | [
"pysam"
] | edf82d108902705d5abf061ee7d0165d08fd0d9162d3da5782164fa5f9d30d00 |
import tensorflow as tf # neural network for function approximation
import gym # environment
import numpy as np # matrix operation and math functions
from gym import wrappers
import gym_morph # customized environment for cart-pole
import matplotlib
# matplotlib.use('Agg')
import matplotlib.pyplot as plt
import time
st... | GitYiheng/reinforcement_learning_test | test03_monte_carlo/t50_plot_at_200.py | Python | mit | 8,063 | [
"NEURON"
] | 355c8dcd1de18cf8e3a574c66d2cb05d56f37c19011b0b992205914c85f0c88b |
import unittest
import numpy as np
import pysal
from pysal.contrib.handler import Model
from functools import partial
from pysal.spreg import diagnostics
#from pysal.spreg.ols import OLS as OLS
OLS = Model
#from pysal.spreg.twosls import TSLS as TSLS
TSLS = partial(Model, mtype='TSLS')
#from pysal.spreg.twosls_sp impor... | TaylorOshan/pysal | pysal/contrib/handler/tests/test_diagnostics_sp.py | Python | bsd-3-clause | 6,254 | [
"COLUMBUS"
] | 737e5f1316b99dadbd27c57322883a03460683b0125e6bc94270337d8b31438e |
# 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... | govarguz/espressopp | testsuite/interaction_potentials/unittest/PTestLennardJones.py | Python | gpl-3.0 | 2,370 | [
"ESPResSo"
] | 8d1a3ddcabeddc3952b5b745be2c97eef9f898b139ee500e200b5afa35deba4a |
import ast
import json
import pycodestyle
from gql_checker.__about__ import (
__author__, __copyright__, __email__, __license__, __summary__, __title__,
__uri__, __version__
)
from gql_checker.stdlib_list import STDLIB_NAMES
from graphql import Source, validate, parse, build_client_schema
__all__ = [
"_... | graphql-python/gql | gql-checker/gql_checker/__init__.py | Python | mit | 3,483 | [
"VisIt"
] | 287cf40a45e6cf82e184f877e3d7bb698907221f4cb217d4d9cc142a980f9562 |
# excepthook1.py#
#
# If the root frame contains a method __ExceptHook__, then this is automagically
# set as the exception hook for/by the Application.
#
# (If you want to remove or replace it, you can always tinker around with
# sys.excepthook.)
import sys
sys.path.append("../..")
from wax import *
from wax.tools.e... | MSMBA/msmba-workflow | msmba-workflow/srclib/wax/examples/excepthook1.py | Python | gpl-2.0 | 779 | [
"TINKER"
] | 325c231c935b9ef40f14e1b1e839911922858e8b70703db0c143687fe41dab08 |
"""
==========================================
Statistical functions (:mod:`scipy.stats`)
==========================================
.. module:: scipy.stats
This module contains a large number of probability distributions as
well as a growing library of statistical functions.
Each univariate distribution is an insta... | ales-erjavec/scipy | scipy/stats/__init__.py | Python | bsd-3-clause | 8,924 | [
"Gaussian"
] | 11a5683900849340eb4c1176ada871f21ffa673436b58552860b8533454e1599 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RSseq(RPackage):
"""Shrinkage estimation of dispersion in Negative Binomial models for RNA... | rspavel/spack | var/spack/repos/builtin/packages/r-sseq/package.py | Python | lgpl-2.1 | 1,773 | [
"Bioconductor"
] | 3e4d4eb64565ddb1697739492a933178cfb38e3c99a37aeb8e3924cd9d4a5bc9 |
#!/usr/bin/env python2
# This script checks and can optionally update Zapdos source files.
# You should always run this script without the "-u" option
# first to make sure there is a clean dry run of the files that should
# be updated
# This is based on a script of the same name in the MOOSE Framework:
# https://githu... | lindsayad/zapdos | scripts/fixup_headers.py | Python | lgpl-2.1 | 5,929 | [
"MOOSE"
] | fa731d85c223f73d614d2891afaf2fad764d99af4920222a18449df3747ebb3d |
from __future__ import absolute_import
import sys, os, yaml, glob
import subprocess
import argparse
import re
from sciLifeLab_utils import submit_job
def main(args):
projectFolder = os.getcwd()
samples_data_dir = args.sample_data_dir
projectName = os.path.basename(os.path.normpath(samples_data_dir)... | SciLifeLab/NouGAT | sciLifeLab_utils/run_QC_analysis.py | Python | mit | 6,886 | [
"BWA"
] | ced956ecc12be8db561dc6a7cea3178d911cb75f40bcb8a1fca02ed5be76cd83 |
from flask import Flask, render_template, session, request, redirect
import random
app = Flask(__name__)
app.secret_key = 'gold123'
@app.route('/')
def index():
if not 'gold' in session:
session['gold'] = 0
if not 'activities' in session:
session['activities'] = []
return render_template('ninja1.html', )
@app... | jiobert/python | Smith_Ben/Assignments/ninja_gold copy/ninjagold.py | Python | mit | 1,032 | [
"CASINO"
] | bf45bef3198391f126aa87b05015aaac9840760734d5896b7e59318e03d9bc53 |
import astropy.io.fits as fits
import numpy as np
import os
import astropy.constants as c
import astropy.units as u
import glob
from scipy.ndimage import binary_opening
import aplpy
from . import catalogs
import matplotlib as mpl
mpl.rcParams['xtick.direction'] = 'in'
mpl.rcParams['ytick.direction'] = 'in'
from confi... | rfriesen/GAS | GAS/columnDensities.py | Python | mit | 15,569 | [
"Gaussian"
] | 9a94935a4f93ae80aab37d1c673613277e53ec0c54e9b1d5d9d0dedf4bbd9e10 |
from __future__ import print_function
from collections import defaultdict
from functools import partial
import gc, inspect, os, sys
import numpy as np
from sklearn.datasets import make_regression
from sklearn.metrics import r2_score
from sklearn.model_selection import train_test_split
import h2o
from h2o.sklearn.wrap... | h2oai/h2o-3 | h2o-py/tests/testdir_sklearn/pyunit_sklearn_regression_all_estimators.py | Python | apache-2.0 | 5,468 | [
"Gaussian"
] | 5abbe2ea74e1dfb23adbb7bcc90e036f8dbbe43d9de321a26656aa10ee89fe6c |
import numpy as np
import glob
filename2 = 'data.GPCSH1.65r1-Eq-300K' #data.GP2.0w0r2-Compacted-Eq' # xyz file was given gy Roland E Pellenq
flist2 = glob.glob(filename2)
natoms_GBP = 103231
rotation = (90.00*np.pi)/180.00
c=np.cos(rotation)
s=np.sin(rotation)
#the 1st col. is string so its loaded seperately
fo... | msadat/python-scripts | rotate_lammps_data.py | Python | gpl-3.0 | 5,902 | [
"LAMMPS"
] | 5fba9db4b1d662a51061ba822d0789ab5a2b9fbd9da9757380cf04fc33d9b180 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | yaxinlx/apiserver-builder | cmd/vendor/k8s.io/kubernetes/cluster/juju/layers/kubernetes-worker/reactive/kubernetes_worker.py | Python | apache-2.0 | 31,640 | [
"CDK"
] | 4fc7cd8549303214e382f9c3cf7e9cd0d5c7189dc39d3996666710d1214464f6 |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris 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 your option) any l... | ghislainp/iris | lib/iris/fileformats/netcdf.py | Python | gpl-3.0 | 69,416 | [
"NetCDF"
] | bf06403d42f34a27bab8d5abfab7cfe31157c84dc82590b947e5e6e2b7d6b6a3 |
# This file is part of the Fluggo Media Library for high-quality
# video and audio processing.
#
# Copyright 2010 Brian J. Crowell <brian@fluggo.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Founda... | fluggo/Canvas | fluggo/editor/ui/canvas/view.py | Python | gpl-3.0 | 11,571 | [
"Brian"
] | f64c3dcf87446568cd76992c9777f8811daf395655c7e1c033942b24c8ec0dea |
# Copyright 2021 DeepMind Technologies Limited
#
# 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 agree... | deepmind/brave | brave/datasets/augmentations.py | Python | apache-2.0 | 8,591 | [
"Gaussian"
] | 9dbda54fa56d0542ccaa4927809984436221c240116a86203e736dff961d4a76 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import zeroinstall
import os
from zeroinstall.support import tasks
from zeroinstall.injector.model import Interface, Feed, stable, testing, developer, stability_levels
from zeroinstall.injector import writer, namespac... | pombredanne/zero-install | zeroinstall/0launch-gui/properties.py | Python | lgpl-2.1 | 18,674 | [
"VisIt"
] | 5a7eea2406467b02da416444763fa734a8ad2aa04b41a3d57d45403af954e207 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements equivalents of the basic ComputedEntry objects, which
is the basic entity that can be used to perform many analyses. ComputedEntries
contain calculated information, typically from VAS... | richardtran415/pymatgen | pymatgen/entries/computed_entries.py | Python | mit | 36,654 | [
"VASP",
"pymatgen"
] | 0337d9d27218593918a30ec1a57ae48df7d1d45da1493cea20573e3f2e2874ac |
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