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""" Bokeh is a Python interactive visualization library that targets modern
web browsers for presentation.
Its goal is to provide elegant, concise construction of novel graphics in the
style of d3.js, but also deliver this capability with high-performance
interactivity over very large or streaming datasets. Bokeh can ... | phobson/bokeh | bokeh/__init__.py | Python | bsd-3-clause | 1,891 | [
"VisIt"
] | 92e08e6edbcef08a10d87d029d228f68b61bc866c1d0b80f13df779ed5a34d69 |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | fabio-otsuka/invesalius3 | invesalius/data/mask.py | Python | gpl-2.0 | 14,213 | [
"VTK"
] | bca50e9602d800c68c8a651e73acf1137289da0322165483e0c56d8b695ca462 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2007 Donald N. Allingham
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012-2016 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of th... | beernarrd/gramps | gramps/plugins/drawreport/timeline.py | Python | gpl-2.0 | 21,796 | [
"Brian"
] | 868ef00f0e88c1df8442470ddc4ae67fde64da9221133c407d71efb62fcc2a4b |
# -*- coding: utf-8 -*-
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""This module defines a density class."""
from math import pi, sqrt
import numpy as np
from gpaw import debug, extra_parameters
from gpaw.mixer import BaseMixer, Mixer, MixerSum
from gpaw.transfor... | robwarm/gpaw-symm | gpaw/density.py | Python | gpl-3.0 | 21,933 | [
"GPAW"
] | a4c2408e36d17b29e4750ca3dcc38b0c017bf9b9026347b922ada6cfa7aa23a1 |
#! /usr/bin/env python
# Copyright 2014 Uri Laserson
#
# 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 o... | churchlab/ulutil | bin/fasta2tiles.py | Python | apache-2.0 | 2,908 | [
"BLAST",
"Biopython"
] | bba80ca583deb088248a3329a614b4100b06f942ca2cd5ec9e282fb68e9e23f4 |
from numpy import *
from enthought.mayavi import mlab
polar = linspace(0,pi,100)
azimuth = linspace(0, 2*pi,100)
phi,th = meshgrid(polar, azimuth)
r = 0.25 * sqrt(5.0/pi) * (3 * cos(phi) ** 2 - 1) #Ylm(0,2)
x = r*sin(phi)*cos(th)
y = r*cos(phi)
z = r*sin(phi)*sin(th)
mlab.mesh(x, y, z)
mlab.show()
| wavicles/pycode-browser | Code/PythonBook/chap4/ylm20.py | Python | gpl-3.0 | 304 | [
"Mayavi"
] | c2099275b23593134ba0ee1b9c531563e003b943697e9614186cf5d090ffc24d |
# optional dependency
try:
# noinspection PyPackageRequirements
import vtk
# noinspection PyPackageRequirements
from vtk.util import numpy_support as nps
except ImportError:
vtk = None
nps = None
import numpy as np
import six
from .colormaps import matplotlib_color_maps
from .helpers import c... | K3D-tools/K3D-jupyter | k3d/factory.py | Python | mit | 59,018 | [
"VTK"
] | 15072edc224796c670006af3362d2b1ac6eebcc205d0249f100e61fe7dd03532 |
import Gears as gears
from .. import *
class BigDog(Component, gears.SpatialFilter) :
def __init__(self, **args):
gears.SpatialFilter.__init__(self)
Component.__init__(self, **args)
def applyWithArgs(
self,
stimulus,
*,
sigma1 : 'Standard devi... | szecsi/Gears | GearsPy/Project/Components/Spatial/BigDog.py | Python | gpl-2.0 | 2,933 | [
"Gaussian"
] | 2bde526899b9205ec3f766c12b55ede38c059a7f8a5f8c5f2b9bb26beab5c91b |
"""
================
DPDF Monte Carlo
================
Routines for handling EMAF DPDF's. Citation: Ellsworth-Bowers et al. (2013).
"""
# TODO read DPDFs
# create functions for:
# dust masses
# sizes / radius
# bolometric luminosity
# isotropic water maser luminosity
import os as _os
import numpy as _np
impo... | autocorr/besl | besl/dpdf_calc.py | Python | gpl-3.0 | 21,410 | [
"Gaussian"
] | 5d7b6d745b919526ff83e07a148b866e74ce0be1a60e00f69b14f422e515f3ef |
"""
Output support for X3D and X3DOM file types.
See http://www.web3d.org/x3d/specifications/
X3DOM outputs to html pages that should display 3-d manipulatable atoms in
modern web browsers.
"""
from ase.parallel import paropen
from ase.data import covalent_radii
from ase.data.colors import jmol_colors
def write_x3d(... | grhawk/ASE | tools/ase/io/x3d.py | Python | gpl-2.0 | 4,225 | [
"ASE"
] | f79e830416cc0c51274fe8d94c5417574294bd8d5fdb25590ac817cd00dad50d |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure that all files contain proper licensing information."""
import json
import optparse
import os.path
import subproces... | danakj/chromium | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 24,584 | [
"Galaxy"
] | 998acd962e78cbd2a2119aea26ddd20ea913dc6b60b6771318788cae70c45ff7 |
from __future__ import (print_function, absolute_import, division, unicode_literals)
import inspect
import numpy as np
from matplotlib import gridspec
from matplotlib import pyplot as plt
import scipy
from astropy.stats import sigma_clipped_stats, sigma_clip
from pypeit import debugger
from pypeit import msgs
fro... | PYPIT/PYPIT | pypeit/core/arc.py | Python | gpl-3.0 | 56,216 | [
"Gaussian"
] | 14bd83121989bd52cdf65f20bf4e213a65aca2d0a9301c4f62923ce160df6b9b |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Consumer class that builds a Structure object.
This is used by the PDBParser and MMCIF... | zjuchenyuan/BioWeb | Lib/Bio/PDB/StructureBuilder.py | Python | mit | 10,881 | [
"Biopython"
] | cf0ecaa8a6f68469d42518541d4699c1a9ed3a29c14bd865303c3b32fd227ac6 |
#! /usr/bin/env python
# coding=utf-8
# Copyright (c) 2019 Uber Technologies, 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.org/licenses/LICENSE-2.0
#
# Unles... | uber/ludwig | ludwig/models/trainer.py | Python | apache-2.0 | 55,436 | [
"NEURON"
] | 599d594f23704b7e6eb65eb930656fb114ed04e1b9f55756a951c95bc38fdee0 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | bearstech/ansible | lib/ansible/modules/network/avi/avi_applicationpersistenceprofile.py | Python | gpl-3.0 | 6,497 | [
"VisIt"
] | 8cd67fdff72351c83edcec5b01c4f8ea261e11c05d25a8c517e9cfa0b1196769 |
# mako/codegen.py
# Copyright (C) 2006-2011 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""provides functionality for rendering a parsetree constructing into module source code."""
impo... | hobbe/notifry-o | appengine/mako/codegen.py | Python | apache-2.0 | 40,108 | [
"VisIt"
] | 9a7239819f24524636f10886df81864f1942d1719e6a0e567dd131f3962170d0 |
import unittest
import numpy as np
from numpy.testing import assert_array_almost_equal
from skgstat import Variogram, OrdinaryKriging
class TestKrigingInstantiation(unittest.TestCase):
def setUp(self):
np.random.seed(42)
self.c = np.random.gamma(10, 4, size=(50, 2))
np.random.seed(42)
... | mmaelicke/scikit-gstat | skgstat/tests/test_kriging.py | Python | mit | 6,723 | [
"Gaussian"
] | 2e4a2081b7972e76b9cbc6815ac323f3229ce77f4785640b5163ce37c0989ff7 |
from ase import *
from hotbit import *
from numpy import *
from box.systems import nanotube
# testing chiral
atoms = nanotube('C',1.42,5,0)
atoms = Atoms(atoms,container='Chiral')
atoms.set_container(angle=0.0)
traj=PickleTrajectory('tmp.trj','w',atoms)
for angle in concatenate( (linspace(0,pi/2,50),linspace(pi/2,0,50... | pekkosk/hotbit | hotbit/test/test_containers.py | Python | gpl-2.0 | 1,399 | [
"ASE"
] | 5cc15418ca63626cee01de568cd99c791f126375952633c8de42b68b7fcad197 |
# 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... | cg31/tensorflow | tensorflow/contrib/distributions/python/ops/normal.py | Python | apache-2.0 | 8,362 | [
"Gaussian"
] | da66a01ed3b12d2eecb62e03c1473ff28c835ec5ff76111bfbc9a6277790dc17 |
"""
Data utitlities
"""
from typing import Tuple
import numpy as np
from pymatgen.core import Molecule, Structure
from pymatgen.optimization.neighbors import find_points_in_spheres
from megnet.config import DataType
from megnet.utils.typing import StructureOrMolecule
def get_graphs_within_cutoff(
structure: Str... | materialsvirtuallab/megnet | megnet/utils/data.py | Python | bsd-3-clause | 1,900 | [
"pymatgen"
] | fa9fe0f0e1c7ea13959ce171d899154ad9dd20d4ded57624968b35870e2e4ce0 |
#
# commands.py - the GraalVM specific commands
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free ... | mur47x111/GraalVM | mx.graal/mx_graal.py | Python | gpl-2.0 | 101,799 | [
"VisIt"
] | e30e4a15e0e481b7704e69e6d8385cb91a58b07e5c82e46e68321dd38c359461 |
#!/usr/bin/env python
"""Check configuration options against the defaults in the ConfigTemplate.cfg files.
This script can help to discover discrepancies in the configuration:
- Typos in option names
- Removed options
- Missing authorization settings
This script should be run by dirac administrators after majo... | chaen/DIRAC | ConfigurationSystem/scripts/dirac-admin-check-config-options.py | Python | gpl-3.0 | 7,064 | [
"DIRAC"
] | 27aa04bc48c7eaa8b598eeefaa4e24239a97fb85f3df4f3eb5d936ba0217c74e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# updateresconfig - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the te... | heromod/migrid | mig/cgi-bin/updateresconfig.py | Python | gpl-2.0 | 1,118 | [
"Brian"
] | 3771e6427d2474d8db95ac04eb669207024c90b8e21e2d91d9b71bc8d8e06400 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/evolve/Mutators.py | Python | mit | 41,424 | [
"Gaussian"
] | b4ed9c479a4e5b43316ea955ecdd6a604a7aa2a4b2fd76ecb65a73675043022c |
# coding: utf-8
# # Machine Learning Engineer Nanodegree
# ## Supervised Learning
# ## Project: Building a Student Intervention System
# Welcome to the second project of the Machine Learning Engineer Nanodegree! In this notebook, some template code has already been provided for you, and it will be your job to implem... | armandosrz/UdacityNanoMachine | student_intervention/student_intervention.py | Python | apache-2.0 | 27,641 | [
"Gaussian"
] | 982878db792984b939fe9f12937cb082ee88969cfbd6e0c09df720bedac0ae4d |
#!/usr/bin/env python
##
## See COPYING file distributed along with the ncanda-data-integration package
## for the copyright and license terms
##
"""
Report: Baseline and Year 1 Cases with Scans
============================================
Creates a csv files containing all cases that are included in the study. Using... | sibis-platform/ncanda-datacore | scripts/reporting/create_cases_include_list.py | Python | bsd-3-clause | 5,343 | [
"VisIt"
] | c956c7485f4507db58434324853d005797fdecb19b66d504499fafb786d804c5 |
#Author : Lewis Mervin lhm30@cam.ac.uk
#Supervisor : Dr. A. Bender
#All rights reserved 2016
#Protein Target Prediction Tool trained on SARs from PubChem (Mined 21/06/16) and ChEMBL21
#Molecular Descriptors : 2048bit Morgan Binary Fingerprints (Rdkit) - ECFP4
#Dependencies : rdkit, sklearn, numpy
#libraries
from rdkit... | lhm30/PIDGINv2 | predict_enriched_two_libraries.py | Python | mit | 11,819 | [
"RDKit"
] | cc94777c321bdc09b92a00f5d6cd435feb0b9b38b340dc8c207e1dd2db512cb2 |
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for SearchIO BlastIO plain text parsers."""
import os
import unittest
from Bio ... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_SearchIO_blast_text.py | Python | gpl-2.0 | 104,809 | [
"BLAST",
"Biopython"
] | a0cfe266e0474158588a02190e2cc8f560cef9197c2177f022a9fe748be6a368 |
"""
This script adds the filename_override_metadata column to the JobExternalOutputMetadata table,
allowing existing metadata files to be written when using external metadata and a cluster
set up with read-only access to database/files
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from sqlalchemy.exceptio... | volpino/Yeps-EURAC | lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py | Python | mit | 1,968 | [
"Galaxy"
] | 5cc79f70d94cde432b00769a2e9cd9cbaf16b96ffd311a9a0dd6d5f1981e0a11 |
''' Test_RSS_Policy_JobEfficiencyPolicy
'''
import unittest
import DIRAC.ResourceStatusSystem.Policy.JobEfficiencyPolicy as moduleTested
################################################################################
class JobEfficiencyPolicy_TestCase( unittest.TestCase ):
def setUp( self ):
'''
Setup
... | andresailer/DIRAC | ResourceStatusSystem/Policy/test/Test_RSS_Policy_JobEfficiencyPolicy.py | Python | gpl-3.0 | 3,796 | [
"DIRAC"
] | d8cd80fde14fadb2c768d56f073d971ccf6e9de88d21d2da5bdc5cceb70b8ec0 |
AREACODES = {
"201": {
"areaCode": "201",
"cities": "Jersey City",
"countryAbbrev": "US",
"countryCode": "840",
"stateProvinceDistrictAbbrev": "NJ",
"stateProvinceDistrictName": "Ne... | usc-isi-i2/dig-extract | dig/extract/entity/telephone/areacode.py | Python | apache-2.0 | 120,329 | [
"COLUMBUS"
] | c8004a89efb8159b70f4bceaca45d5bc9ebfb73398c53b2b19fdc20faaca0f5f |
import os
from ase.test import NotAvailable
try:
nwchem_command = os.getenv('NWCHEM_COMMAND')
if nwchem_command == None:
raise NotAvailable('NWCHEM_COMMAND not defined')
except NotAvailable:
raise NotAvailable('Nwchem required')
import numpy as np
from ase.tasks.main import run
atoms, task = ru... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/test/nwchem/nwchem_cmdline.py | Python | gpl-2.0 | 503 | [
"ASE",
"NWChem"
] | f288913035c75024cb2683a646012c336bf1a63363627305b796fd0cd5b2c300 |
# -*- coding: utf-8 -*-
"""The database manager for PyBEL.
Under the hood, PyBEL caches namespace and annotation files for quick recall on later use. The user doesn't need to
enable this option, but can specify a database location if they choose.
"""
import logging
import time
from typing import Iterable, List, Mapp... | pybel/pybel | src/pybel/manager/cache_manager.py | Python | mit | 40,663 | [
"Pybel"
] | 916ef3208db253b8ce973a079e186fbc746676b003f70782e61277d757ee3325 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import itertools
import pytest
import numpy as np
from numpy.testing import assert_allclose
from astropy.convolution.utils import discretize_model
from astropy.modeling.functional_models import (
Gaussian1D, Box1D, RickerWavelet1D, Gaussian2D, Box2D... | stargaser/astropy | astropy/convolution/tests/test_discretize.py | Python | bsd-3-clause | 7,108 | [
"Gaussian"
] | 96cdc47be3383b1a45a13c932e4d788b2788514dc256c39975af38c8aa447e51 |
import lmfit
import numpy
import sympy
from nose.tools import *
from numpy.testing import *
from scipy_data_fitting import Data
from scipy_data_fitting import Model
from scipy_data_fitting import Fit
class TestFit():
def get_model(self):
model = Model('exponential_model')
symbols = ('f', 'a', 'k... | razor-x/scipy-data_fitting | test/test_fit.py | Python | mit | 10,288 | [
"Avogadro"
] | 37ef3f951d8a492e4e5b438fdb99983e2f7a690d5c055b5e78fa2b5b3d365b7b |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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
#... | rmcgibbo/psi4public | psi4/driver/procrouting/proc_table.py | Python | lgpl-3.0 | 10,390 | [
"CFOUR",
"Psi4"
] | 0fd6076005af8e4891a354c936d6d7036b97b8b0cc079d9ae1cabd235175f020 |
# 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/CodeInterfaces/MooseBasedApp/MooseData.py | Python | apache-2.0 | 4,655 | [
"MOOSE"
] | 63180b7f782f8a3e6ffff01f2e54eddc018b9524e74828792ca8ace4583f8b7b |
"""
author
"""
import abc
import logging
import os.path
from collections import OrderedDict
from uuid import UUID
import netCDF4
import numpy as np
from .dictify import UUIDObjectJSON
from .stores import NamedObjectStore, ObjectStore, PseudoAttributeStore
from .proxy import LoaderProxy
import sys
if sys.version_info... | jhprinz/openpathsampling | openpathsampling/netcdfplus/netcdfplus.py | Python | lgpl-2.1 | 42,699 | [
"NetCDF"
] | 168e49b03a1c8cf96f3940ec0643185798a5698e1f1d18fdb7d73b6df1bde93b |
#!/usr/bin/env python3
# -*- coding: UTF-8 -*-
"""Death by Captcha HTTP and socket API clients.
There are two types of Death by Captcha (DBC hereinafter) API: HTTP and
socket ones. Both offer the same functionalily, with the socket API
sporting faster responses and using way less connections.
To access the socket A... | oczkers/gdown | gdown/deathbycaptcha.py | Python | gpl-3.0 | 16,208 | [
"VisIt"
] | 75fbb25b96bbeaf11acd5e273148d4ced5a534e14378ac69dfdb69c15fd20050 |
"""
@package medpy.io.load
Provides functionality connected with image loading.
The supplied methods hide more complex usage of a number of third party modules.
@author Oskar Maier
@version r0.2.1
@since 2012-05-28
@status Release
"""
# build-in modules
import os
# third-party modules
import scipy
# own module... | kleinfeld/medpy | medpy/io/load.py | Python | gpl-3.0 | 11,304 | [
"VTK"
] | c1d1d4211d5e3aa8b06bbbd02c5d9e91e8d1c3d0775144077b7b805652134eb5 |
#!/usr/bin/env python3
from gaussian import GaussianCom, GaussianLog
print("Trying to read qm_modred_gen.com, a simple gassian.com file")
gaussian_file_name = "qm_modred_gen.com"
gaussian_com = GaussianCom(gaussian_file_name)
print("List of atoms:\n", gaussian_com.atoms_list)
print("Everything seems ok\n\n")
print(... | eduardoftoliveira/oniomMacGyver | tests/TODO/test1.py | Python | gpl-3.0 | 1,222 | [
"Gaussian"
] | 7dc0aaf344f2022305d3be557f3eae04c8f50962f0a1f8f5f2d3a4b98e0bf78b |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/machines/urls/machines.py | Python | gpl-3.0 | 1,480 | [
"Brian"
] | 90c915df3196ad531ab37c64c57e4646609911c241754588620181ab8a1ab18e |
import networkx as nx
import numpy as np
import collections
from pymatgen.analysis.chemenv.coordination_environments.structure_environments import LightStructureEnvironments
from pymatgen.analysis.chemenv.connectivity.environment_nodes import get_environment_node
from pymatgen.analysis.chemenv.connectivity.connected_co... | fraricci/pymatgen | pymatgen/analysis/chemenv/connectivity/structure_connectivity.py | Python | mit | 14,247 | [
"pymatgen"
] | 3d5ee949bd46b4f1785dc482029853713974f4f1e89f9e5c90a955641ed2bc1f |
import py
import subprocess
import sys
import pytest
import _pytest
MODSET = [
x
for x in py.path.local(_pytest.__file__).dirpath().visit("*.py")
if x.purebasename != "__init__"
]
@pytest.mark.parametrize("modfile", MODSET, ids=lambda x: x.purebasename)
def test_fileimport(modfile):
# this test ensur... | paulrouget/servo | tests/wpt/web-platform-tests/tools/third_party/pytest/testing/test_modimport.py | Python | mpl-2.0 | 721 | [
"VisIt"
] | d696a8c3cb3f102c6ade20d516909b76a2b7c292a4e101212c543188a2799bdc |
import unittest
from test import support
from itertools import *
import weakref
from decimal import Decimal
from fractions import Fraction
import operator
import random
import copy
import pickle
from functools import reduce
import sys
import struct
maxsize = support.MAX_Py_ssize_t
minsize = -maxsize-1
def lzip(*args):... | yotchang4s/cafebabepy | src/main/python/test/test_itertools.py | Python | bsd-3-clause | 95,088 | [
"GULP"
] | bea6db865af1120c6cd2307f642318dea4f2bf4caf8af0f71bc47320192fffe1 |
#!/usr/bin/env python
###############################################################################
##
## Copyright (C) 2014-2016, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is par... | VisTrails/VisTrails | scripts/dist/mac/fix_qtplugin_libs.py | Python | bsd-3-clause | 6,588 | [
"ParaView"
] | f46b947c3b277c16173b89f4559bd57913e9281e373c1ff777babf5f85d4c5c6 |
# -*- coding: utf-8 -*-
"""A simple tool to document how to control AWS resources.
AWS AUTHENTICATION
-------------------
In order to run any of the code below, you need a profile with AWS credentials
set up on your computer. It's very easy to do this. Google how to configure
your profile with boto3, or visit the do... | borkit/scriptdump | AWS/amazonctrl.py | Python | mit | 37,380 | [
"VisIt"
] | 8daa686573cd25dcd56639077a8a9746b092b27b90841da516451c21de34c60d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import math
import numpy as np
from pymatgen.core.periodic_table import Element
"""
Utilities for generating nicer plots.
"""
__author__ = "Shyue Ping Ong"
... | czhengsci/pymatgen | pymatgen/util/plotting.py | Python | mit | 14,181 | [
"pymatgen"
] | de04e0a7e3948f3ac4d31d2aa749dc8843604da09dc7f0e2346c3ceb8a79e410 |
import numpy as np
import matplotlib.pyplot as plt
import uncertainties
from scipy.signal import find_peaks
from scipy.optimize import curve_fit
import scipy.constants as sc
import scipy.integrate as integrate
from uncertainties import ufloat
from uncertainties import unumpy as unp
from uncertainties.unumpy import nomi... | smjhnits/Praktikum_TU_D_16-17 | Fortgeschrittenenpraktikum/Protokolle/V18_Germaniumdetektor/Python/Caesium.py | Python | mit | 9,404 | [
"Gaussian"
] | d7f1a983d73d6658279eec0559c58fc11ec385a8f5f20966d82c47233f956112 |
#!/usr/bin/python
__author__="Brian Hone"
import sys, os, string, pprint
import gdb
sym_types = {
gdb.SYMBOL_LOC_UNDEF : "undefined",
gdb.SYMBOL_LOC_CONST : "constant_int",
gdb.SYMBOL_LOC_STATIC : "fixed_address",
gdb.SYMBOL_LOC_REGISTER : "register",
gdb.SYMBOL_LOC_ARG : "argument",
gdb.SYM... | bthcode/cmake_scipy_ctypes_example | gdb-plot/show_frame.py | Python | bsd-3-clause | 2,333 | [
"Brian"
] | c061cc42ed2307bea9763e39881263e86b1bff1c76266e5071a8dfe9d36c685f |
__docformat__ = 'reStructuredText'
'''
Wind-transported snow
:Author: kmu
:Created: 11. may 2011
:Updated by RL 12. Sep. 2013
'''
# Built-in
import os
from optparse import OptionParser
# Adds folder containing the "pysenorge" package to the PYTHONPATH
execfile(os.path.join(os.path.dirname(__file__), "s... | kmunve/pysenorge | pysenorge/themes/additional_snow_depth_wind_varexp.py | Python | gpl-3.0 | 10,620 | [
"NetCDF"
] | 588b0d91b961a231be40e809c1ec3482c1ddc60c93a38603873db89b93247eb7 |
# -*- 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-vm-migration | tests/unit/gapic/vmmigration_v1/test_vm_migration.py | Python | apache-2.0 | 466,381 | [
"Octopus"
] | 3946e8ff7aa36ff2ba6e1b24c552a2ce4bae7aee5ba62d6df4cef4353fe5c489 |
import os
import lan
debug = False
class CGenerator(object):
""" Uses the same visitor pattern as the NodeVisitor, but modified to
return a value from each visit method, using string accumulation in
generic_visit.
"""
def __init__(self):
self.output = ''
self.quotes = '\... | dikujepsen/OpenTran | v2.0/framework/Matmul/cgen.py | Python | mit | 9,212 | [
"VisIt"
] | 2ee9dfcc02277607d452c22b522f76f85d78947127b6379dae89bb115dd8c093 |
"""
Methods for aligning raw fastq reads to a reference genome.
"""
import copy
from datetime import datetime
import os
import subprocess
from subprocess import PIPE
from subprocess import Popen
from celery import task
from django.conf import settings
from main.models import AlignmentGroup
from main.models import Da... | churchlab/millstone | genome_designer/pipeline/read_alignment.py | Python | mit | 26,857 | [
"BWA"
] | 23e9b9162698a994089309802aa4e46aa5bdf2f8b6f19dd49bf2e21577831983 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
'''
Miscellaneous algorithms for 2D contours and 3D triangularized meshes handling
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.... | mick-d/nipype_source | nipype/algorithms/mesh.py | Python | bsd-3-clause | 3,597 | [
"VTK"
] | a049587bb82f55145c514bf196a5993873bf99fabe278e96543b69b00599bd84 |
# Default Django settings. Override these with settings in the module
# pointed-to by the DJANGO_SETTINGS_MODULE environment variable.
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
gettext_noop = lambda s: s
#################... | jamespacileo/django-france | django/conf/global_settings.py | Python | bsd-3-clause | 20,910 | [
"VisIt"
] | 20184a4009ecbf04bbd3758a066207643a0cd92d3cbd4e48e89a278eb0323531 |
"""
Compare speed and fit quality for a few cases using mpfit and scipy.optimize.leastsq
"""
from __future__ import division,absolute_import
from agpy.mpfit import mpfit
from agpy.timer import print_timing
from scipy.optimize import leastsq
import scipy.optimize
import numpy as np
import timeit
def gaussian(x,A,dx,w,... | scienceopen/gaussfitter | gaussfitter/mpfit/tests/mpfit_vs_scipy.py | Python | bsd-3-clause | 5,299 | [
"Gaussian"
] | c0851c2eeda306c3994c439219e868a578cae7fe91d8742a0c90e8cb6e0a8cff |
# -*- coding: utf-8 -*-
"""
Created on Fri Mar 27 09:06:18 2015
@author: Diogo Silva
"""
import numpy as np
from K_Means2 import *
from sklearn import datasets # generate gaussian mixture
from timeit import default_timer as timer # timing
##generate data
n = 1e6
d = 2
k = 20
n = np.int(n)
total_bytes = np.float(... | Chiroptera/QCThesis | experiments/CUDA/test_K_Means.py | Python | mit | 1,391 | [
"Gaussian"
] | ff18046fbfd99d751f6d87e00e153de73055165ac5eb5ac90f14149aa312d4c7 |
# 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
#
# Unless required by appl... | sunqm/pyscf | pyscf/adc/test/test_radc/test_N2_radc_ea.py | Python | apache-2.0 | 3,435 | [
"PySCF"
] | 10fcc007b66797c1b05772ab5b5577f280019d47f24f2647820d316aeda619be |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2012 onwards University of Deusto
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution.
#
# This software consists of contributions made by many individuals,
# list... | zstars/weblabdeusto | server/src/weblab/admin/deploy.py | Python | bsd-2-clause | 48,598 | [
"CDK"
] | 97bc36430f1892b7c4471e4003881142a1ce11d5c01d6f3f91dc671ffeb1ae72 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Stefan Siegel
# Copyright (C) 2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Genera... | beernarrd/gramps | gramps/plugins/rel/rel_de.py | Python | gpl-2.0 | 11,304 | [
"Brian"
] | f63b59445abc076aaa64b5bd3fae7fd39f74cb0131e14373437dfb37c7133306 |
# Dual Annealing implementation.
# Copyright (c) 2018 Sylvain Gubian <sylvain.gubian@pmi.com>,
# Yang Xiang <yang.xiang@pmi.com>
# Author: Sylvain Gubian, Yang Xiang, PMP S.A.
"""
A Dual Annealing global optimization algorithm
"""
from __future__ import division, print_function, absolute_import
import numpy as np
fr... | Eric89GXL/scipy | scipy/optimize/_dual_annealing.py | Python | bsd-3-clause | 28,866 | [
"VisIt"
] | 108696235750fcb526a03b8a0d58f0695b1fa75e0c4481a7338e45e30c1fa76e |
#!/usr/bin/env python
import struct, getopt, sys, fftfit, psr_utils, os.path, sinc_interp, Pgplot
import numpy as Num
from infodata import infodata
from prepfold import pfd
from polycos import polycos
from psr_constants import *
from types import StringType, FloatType, IntType
scopes = {'GBT':'1', 'Arecibo':'3', 'Park... | pscholz/presto | bin/sum_profiles.py | Python | gpl-2.0 | 14,958 | [
"Gaussian"
] | 583ef9e7dc8fdab2d58a6bccb44295bde4709f76bdf093c5a9f1d741caa00eae |
#!/usr/bin/env python
########################################################################
# File : dirac-proxy-init.py
# Author : Adrian Casajus
########################################################################
import os
import sys
import glob
import time
import datetime
import DIRAC
from DIRAC import ... | petricm/DIRAC | FrameworkSystem/scripts/dirac-proxy-init.py | Python | gpl-3.0 | 10,806 | [
"DIRAC"
] | 61686b51580cd5cff29555b92b51282c511026d5c1a1607e1e8cae11729e0438 |
# Copyright 2008-2011 by Peter Cock. All rights reserved.
# Revisions copyright 2012 by Christian Brueffer. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from Bio import Mi... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_ClustalOmega_tool.py | Python | gpl-2.0 | 8,776 | [
"Biopython"
] | 6b75b7f629e5fe84139febbd9a294ff699d29d0109ef700e20747cbc693f4d7d |
#!/usr/bin/env python3
### VERY MUCH PYTHON 3 !!!
"""
Example for aiohttp.web basic async service
Uses a background timer to print to a logger
exposes an obvious REST endpoint
It's a template!
Made available under the MIT license as follows:
Copyright 2017 Brian Bulkowski brian@bulkowski.org
Permission is hereby ... | bbulkow/MagnusFlora | rest/template.py | Python | mit | 5,576 | [
"Brian"
] | 23aed2e20ae7ea0530aec7857a60c96107e332bd5295fb629d6a463ef7ee5c37 |
#!/usr/bin/env python
# Install.py tool to download, unpack, build, and link to the plumed2 library
# used to automate the steps described in the README file in this dir
from __future__ import print_function
import sys,os,re,subprocess,hashlib
# help message
help = """
Syntax from src dir: make lib-plumed args="-b"... | quang-ha/lammps | lib/plumed/Install.py | Python | gpl-2.0 | 6,412 | [
"LAMMPS"
] | 281af03a45ffbc78d9f5b6fac9258b0aed24718f8d0d0925ec934577d0a2c0f6 |
"""
Contains the mechanism to evaluate whether to use or not a catalog
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id $"
from pyparsing import infixNotation, opAssoc, Word, printables, Literal, Suppress
from DIRAC import S_OK, gLog... | yujikato/DIRAC | src/DIRAC/Resources/Catalog/FCConditionParser.py | Python | gpl-3.0 | 10,605 | [
"DIRAC"
] | 2e537b64c95a798efce44c9f15ef019fccbee55a56dacec1e93c9743c7543fdc |
#!/usr/bin/env/ python3
"""
Convert NetCDF4 files to ASCII (plain text)
"""
import sys
import argparse
import numpy as np
import netCDF4
args = []
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='convert file from netCDF to ASCII format',
formatter_cla... | guilindner/VortexFitting | vortexfitting/convertToASCII.py | Python | mit | 2,212 | [
"NetCDF"
] | a35a35bacc23669326f05bbff42aaa961d7eb10fdb115e2a0efabf526619aaaf |
#Import all nessesary classes
import random
import math
import time
import webbrowser
import pickle
import os
import getpass
class player: #Define Player class
'the Player'
def __init__(self,name):
self.name = name #Make the name of player
self.money = 500 #Set money to 500g
self.a =... | KitsuneUdon/Fortify | src/Fortify.py | Python | gpl-3.0 | 27,439 | [
"VisIt"
] | f7c8f9b659df5ef3a68499ad0313fe4c99b2e509f9be0bc16eeca48859f3e3b9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes to represent all xas and stitching methods
"""
import math
from typing import List
from scipy.interpolate import interp1d
import numpy as np
from pymatgen.analysis.structure_matc... | mbkumar/pymatgen | pymatgen/analysis/xas/spectrum.py | Python | mit | 10,813 | [
"pymatgen"
] | 909ff9cb4240d8e4cb1c1e51dd0f81d71ed6a3fec64b9236847e095a9045674a |
import sys
import os
import warnings
import ruamel.yaml as yaml
from fnmatch import fnmatch
__author__ = "Pymatgen Development Team"
__email__ ="pymatgen@googlegroups.com"
__maintainer__ = "Shyue Ping Ong"
__maintainer_email__ ="shyuep@gmail.com"
__version__ = "2019.3.27"
SETTINGS_FILE = os.path.join(os.path.expand... | montoyjh/pymatgen | pymatgen/__init__.py | Python | mit | 3,204 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | 6bc423015b2ab1b5c55e77024a90ef4e3f98f72735e8536f8cb86201c8c5e36a |
########################################################################
# $HeadURL: $
# File : JobSchedulingAgent.py
# Author : Stuart Paterson
########################################################################
""" The Job Scheduling Agent takes the information gained from all previous
optimizers and ... | Sbalbp/DIRAC | WorkloadManagementSystem/Agent/JobSchedulingAgent.py | Python | gpl-3.0 | 25,769 | [
"DIRAC"
] | 77740bddc508616955a25391c8b9dbc3bca2705a6dc5042700585b28448976ab |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# glumpy is an OpenGL framework for the fast visualization of numpy arrays.
# Copyright (C) 2009-2011 Nicolas P. Rougier. All rights reserved.
#
# Redistribution and use in source and binary fo... | duyuan11/glumpy | glumpy/data/build-spatial-filters.py | Python | bsd-3-clause | 18,863 | [
"Gaussian"
] | 1c1d14ae007c90441b3d69627828fe2bdf5a025612207f03a3a051d8022ff8c1 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
import time
m = 2000
n = 4000
testMehrotra = ... | justusc/Elemental | examples/interface/QPDirect.py | Python | bsd-3-clause | 4,271 | [
"Gaussian"
] | 12e234ba50a12256857807996615daf829f1731b2df7da416d764b79d1b798cf |
import os
import urlparse
import datetime
import time
import zlib
import hashlib
import redis
import re
import mongoengine as mongo
import random
import requests
import HTMLParser
import tweepy
from collections import defaultdict
from BeautifulSoup import BeautifulSoup
from mongoengine.queryset import Q
from django.con... | manderson23/NewsBlur | apps/social/models.py | Python | mit | 149,068 | [
"BLAST"
] | f0353b7cafac08bf6111b49f7212757c36bf8e872464d8c4e44f35dea986555f |
""" DIRAC Basic MySQL Class
It provides access to the basic MySQL methods in a multithread-safe mode
keeping used connections in a python Queue for further reuse.
These are the coded methods:
__init__( host, user, passwd, name, [maxConnsInQueue=10] )
Initializes the Queue and tries to connect to... | yujikato/DIRAC | src/DIRAC/Core/Utilities/MySQL.py | Python | gpl-3.0 | 52,838 | [
"DIRAC"
] | 32b81acaf6ad810b13c360818c2639fae764242c8e0b502fa3831094cc131202 |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from io import BytesIO
from xml.dom import Node
def format_node(node, indent):
"""Ensure that every element is indented by the string 'indent'."""
doc = node.ownerDocument
elems = []
for child in node.childNo... | 0install/0repo | repo/formatting.py | Python | lgpl-2.1 | 1,050 | [
"VisIt"
] | 3025c48abe285f03887bd55c455fff5213df0148ffb583c42dd0a5192cdc3a55 |
# 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... | BackupTheBerlios/espressopp | src/analysis/AnalysisBase.py | Python | gpl-3.0 | 3,279 | [
"ESPResSo"
] | b19e006ba13ca75315dcdf54156e8e551a9f0a98169e99f67e1ef22d01b64df4 |
# $Id$
#
# Copyright (C) 2016 Novartis Institute of BioMedical Research
# 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 co... | rvianello/rdkit | Code/GraphMol/StructChecker/Wrap/rough_test.py | Python | bsd-3-clause | 7,469 | [
"RDKit"
] | d0ac203390408f6e82afafa32e83b1a24726e9f4ed69f7bc5c94680f2de5a234 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# chksum - checksum one or more files
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License ... | heromod/migrid | mig/cgi-bin/chksum.py | Python | gpl-2.0 | 1,071 | [
"Brian"
] | cdc2717d9be36e778c593eea1fc0a2e42d78e138a18b7168316948cded88ee7f |
"""
LAADS (Level 1 Atmosphere Archive and Distribution System)
NASA's LAADS hosts petabytes of land and atmospheric data obtained from a
wide array of different sources
--------------------------------------------------------------------------------------------
MODIS (Moderate Resolution Imaging Spectroradiomete... | mathnathan/OpenTiles | dataSources.py | Python | mit | 19,675 | [
"CRYSTAL"
] | c97221a00d5561a670fb07cb5770d40d5a1e2a23a8e22b4404d922b30b51bb05 |
#!/usr/bin/env python
#
# $File: combinedSampling.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redist... | BoPeng/simuPOP | docs/combinedSampling.py | Python | gpl-2.0 | 1,450 | [
"VisIt"
] | 33941591ac36828b9b63dc85a322e268e6e4dddb9e04f050d14a5e0df28c1dab |
"""Collection of functions to process mini batches."""
import numpy as np
from sklearn.preprocessing import OneHotEncoder
def invert_full_matrix_np(full_adjacency):
full_adjacency = np.squeeze(full_adjacency)
n_nodes = full_adjacency.shape[1]
full_adjacency = np.append(np.zeros([1, n_nodes]), full_adjace... | RoozbehFarhoodi/McNeuron | batch_utils.py | Python | mit | 8,917 | [
"NEURON"
] | 42fec6fa01fe5b07a254a22114c99f9c5ed74b5e86fb8e8f12c44f57d27acbbb |
#!/usr/bin/env python
from __future__ import division
'''
Created on Mar 14, 2012
'''
__author__ = "Anubhav Jain"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Anubhav Jain"
__email__ = "ajain@lbl.gov"
__date__ = "Mar 14, 2012"
import pymongo
from collections import ... | mp-interns/ga_optimization_ternary | ga_optimization_ternary/database.py | Python | mit | 7,527 | [
"pymatgen"
] | e38252b54e8a08d7d276a6e907d4c856e7e1b7016c7c1a2c43e0bf627c4e708e |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011, 2012, 2013 CERN.
##
## Invenio 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, or ... | kaplun/invenio | modules/bibupload/lib/batchuploader_engine.py | Python | gpl-2.0 | 29,420 | [
"VisIt"
] | 2ed59174cc2d0475a15f6404e749c8d58d1772964073460f23ba65883e8a2732 |
#!/usr/bin/env python
# Copyright (c) 2011-2020, wradlib developers.
# Distributed under the MIT License. See LICENSE.txt for more info.
"""
NetCDF Data I/O
^^^^^^^^^^^^^^^
.. autosummary::
:nosignatures:
:toctree: generated/
{}
"""
__all__ = [
"open_cfradial1_dataset",
"open_cfradial1_mfdataset",
... | wradlib/wradlib | wradlib/io/netcdf.py | Python | mit | 12,254 | [
"NetCDF"
] | 80f195107e21bc0ae2b083f20ea074c82cd2757f4c2940418fb8771124171276 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-limma/package.py | Python | lgpl-2.1 | 1,755 | [
"Bioconductor"
] | ddf36078461bd37733046b7f6caedd0fa2763399e28e122c78096f1a90464ed7 |
""" gpr_fit_2d.py
An example that uses functionality from the GPR module
to regress a 2-Dimensional Function
"""
# ------------------------------------------------------------
# Imports
# ------------------------------------------------------------
import time, os, sys, copy
import numpy as np
... | aerialhedgehog/VyPy | examples/gpr_fit_2d.py | Python | bsd-3-clause | 8,849 | [
"Gaussian"
] | 6d90c7ca68e892c2d352032223775216093153481170324eb2722899bedea34b |
#!/usr/bin/env python
'''
RMP2
'''
import time
from functools import reduce
import copy
import numpy
from pyscf import gto
from pyscf import lib
from pyscf import ao2mo
from pyscf.ao2mo import _ao2mo
from pyscf.mp import mp2
from pyscf import __config__
from mpi4pyscf.lib import logger
from mpi4pyscf.tools import mpi... | sunqm/mpi4pyscf | mpi4pyscf/mp/mp2.py | Python | gpl-3.0 | 8,320 | [
"PySCF"
] | 0782ccfde38072d2aaa3e1276b1e0deaa2043e1ae5b5f52f311eb5178b7568e0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import itertools
import numpy as np
from pymatgen.core.lattice import Lattice, get_points_in_spheres
from pymatgen.core.operations import SymmOp
from pymatgen.util.testing import PymatgenTest
class Lattice... | gmatteo/pymatgen | pymatgen/core/tests/test_lattice.py | Python | mit | 24,635 | [
"pymatgen"
] | 9d11c302e8627a50b8880e07d712ed0cd0168baf7baca2ce33eaff4c64c35ed8 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/mobile/bouquets.py | Python | gpl-2.0 | 6,829 | [
"VisIt"
] | e925b0ecd832d03c5f19ce822b2697e0c3fe8578d97b579ffd3fe036d3bed29c |
#!/usr/local/bin/python
"""
setup_serial.py file for LAMMPS with dummy serial MPI library
"""
from distutils.core import setup, Extension
import os, glob
path = os.path.dirname(os.getcwd())
# list of src files for LAMMPS and MPI STUBS
libfiles = glob.glob("%s/src/*.cpp" % path) + \
glob.glob("%s/src/STU... | gladk/LIGGGHTS-PUBLIC | python/setup_serial.py | Python | gpl-2.0 | 1,109 | [
"LAMMPS"
] | fea6b541334fa3bfff350526deac6f43b4a0957b043bc94f9703ac61ddc2d6ee |
#!/usr/bin/env python
"""
Pulls sources from a set of input data (tracts/patches or visits/ccds)
and dumps it a subset of the source table columns into a single fits file
The output columns include the number of children and the calibrated Kron magnitude
as well as ra/dec/id/parent_id.
This is meant as more of a temp... | HSC-Users/hscTools | clackner/python/sourceTable.py | Python | gpl-3.0 | 3,329 | [
"VisIt"
] | de4726c95e33b0129c22b4757514f4e89f2aa86a636ee90eb12c31754328839e |
"""
Build a density map out of a list of coordinates
(easier to just use np.histogram2d)
"""
try:
import pyfits
import pyregion
except ImportError:
print "densitymap requires pyfits and pyregion"
import numpy
from agpy import gaussfitter
def dmregion(header,region,outfits=None,smoothpix=2,clobber=True):
... | ufoym/agpy | agpy/densitymap.py | Python | mit | 2,824 | [
"Gaussian"
] | 56aad0960606af9f75b7a5d2ef0b2043c97142936b7dd21ddfe87787690918de |
#!C:\OSGEO4~1\bin\python.exe
# ******************************************************************************
# $Id: pct2rgb.py 2cd032b5169300975d137226eb99944340ac8c31 2018-05-10 19:33:02 +1000 Ben Elliston $
#
# Name: pct2rgb
# Project: GDAL Python Interface
# Purpose: Utility to convert paletted imag... | kubaszostak/gdal-dragndrop | osgeo/apps/Python27/Scripts/pct2rgb.py | Python | mit | 7,415 | [
"NetCDF"
] | 2fb119ef617742e68b8216f461509d90348fd530e64b466cc2fa9341597fddc7 |
# coding=utf-8
# Copyright 2022 The Mesh TensorFlow 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... | tensorflow/mesh | mesh_tensorflow/transformer/utils.py | Python | apache-2.0 | 126,154 | [
"MOE"
] | 263e5b53a04ceb0ee25a0f0b9ca0bf50cef403707ace843eb5ceb194d94297dc |
"""
genetic v0.01
Copyright 2011 Brian Monkaba
This file is part of ga-bitbot.
ga-bitbot is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any... | Pascal66/ga-bitbot | libs/genetic.py | Python | gpl-3.0 | 24,917 | [
"Brian"
] | 5c3b1bc9beeec15d5655f7872c5018bb18dff22d8374d7e24ea2631b0becc101 |
# Copyright 2019 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... | frreiss/tensorflow-fred | tensorflow/python/keras/layers/preprocessing/image_preprocessing.py | Python | apache-2.0 | 52,428 | [
"Gaussian"
] | ab40e8390cd43459f3ce0e45e887a67ea38dc086eaef4ca595910fcc71a5bab3 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | setup.py | Python | apache-2.0 | 5,777 | [
"PySCF"
] | 94b6151544215795a54dbc72b5ae94c8e5bb6b1c58ceffd65afcd0302a59fd00 |
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