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from resources.common import RadialOptions
from services.sui.SUIService import MessageBoxType
import time
from services.sui.SUIWindow import Trigger
from java.util import Vector
import main.NGECore
import sys
def createRadial(core, owner, target, radials):
radials.clear()
radials.add(RadialOptions(0, 7, 0, 'Examin... | ProjectSWGCore/NGECore2 | scripts/radial/item/tunable.py | Python | lgpl-3.0 | 2,359 | [
"CRYSTAL"
] | 3044a4feba91d94399cfa0bd122e1e2b51fa0267479c8677488f45ed95084a5a |
# --------------------------------Import----------------------------------------#
import csv
max_bq_num = 95
atoms_num = 18
ix = []
iy = []
iz = []
br = 0.5291772083
def d_range(start, stop, step):
r = start
while r < stop:
yield r
r += step
# return R
def chunks(l, n):
"""Yield suc... | elekezem/Bq_atoms_gen | grid-2d-g09.py | Python | mit | 5,519 | [
"Dalton"
] | 4274f8f650fe8245855ea12e31f6f66e2f6a174da79f9eda223363db219ab1c6 |
from operator import *
# Define decorator/wrapper for mutation operators to filter out duplicate mutants
def remove_duplicates(func):
def rm_dub(*args, **kwargs):
res = list()
result = func(*args, **kwargs)
if result is not None:
for x in result:
if x ... | STLInspector/STLInspector | STLInspector/core/temporallogic/clause.py | Python | apache-2.0 | 19,465 | [
"ASE"
] | f8c9a442ae5f80ce010ee517d77067d12e4e872cf3268f25faaa301d4a235075 |
#!/usr/bin/env python
"""Dongle.py: a class interfacing a physical S-CRIB Scramble device accessible
through pylibftdi library - project sCribManager - Python."""
'''
@author: Dan Cvrcek, George French
@copyright: Copyright 2013-14, Smart Crib Ltd
@credits: George French, Dan Cvrcek
@license: GPL version 3 (e.g., htt... | smartcrib/password-scrambler-ws | sCribManager/Dongle.py | Python | gpl-3.0 | 24,144 | [
"VisIt"
] | a5e16047deb07c083c1adfefd8baff2a51ed0aa6b58bfb20ffa15e7416922b45 |
# This snakemake file performs the following actions on one biosample.
# This biosample may contain multiple subsamples and be sequenced multiple times.
# Further, each sequencing run can be missing some subsamples.
# This snakemake file does not perform optimization of thresholding perameters.
#
# 1. quality trimming
... | brianyu2010/Mini-Metagenomic_Analyses | Snakefile_toplevel1.py | Python | gpl-3.0 | 5,441 | [
"BLAST",
"Brian"
] | 6dc5070202f9c58b34adaed3ce22eb3fa1d7e1f34dee524508c3214b3d4a6916 |
# Copyright 2013 Cloudbase Solutions SRL
# Copyright 2013 Pedro Navarro Perez
# 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... | costingalan/networking-hyperv-7.0.3-1.0.2 | hyperv/neutron/hyperv_neutron_agent.py | Python | apache-2.0 | 18,405 | [
"VisIt"
] | f2c04dd0e77b497362cc0a2e60ccbf5c1ad141b779ab61a89ac62a96632fb82b |
# 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 *
import os
class Orca(Package):
"""An ab initio, DFT and semiempirical SCF-MO package
Not... | rspavel/spack | var/spack/repos/builtin/packages/orca/package.py | Python | lgpl-2.1 | 1,728 | [
"ORCA"
] | 80afe3e0ca9c511de28431053fec96686eefe2f2c5e8ca128c8b6157e3dd6735 |
"""MayaVi test related utilities.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2008, Enthought, Inc.
# License: BSD Style.
# Standard library imports
import gc
import os
import os.path
import sys
import logging
import traceback
from optparse import OptionParser
# Enthought library im... | liulion/mayavi | integrationtests/mayavi/common.py | Python | bsd-3-clause | 25,008 | [
"Mayavi",
"VTK"
] | ca12138a2448e9eed5f9ee1fa91240a465e40efb69ff953fbf84447b90b007b2 |
"""
A registry for engines, sources, filters and modules.
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import splitext
import logging
# Enthought library imports.
from traits.api import HasTraits, List,... | liulion/mayavi | mayavi/core/registry.py | Python | bsd-3-clause | 5,174 | [
"Mayavi"
] | f87fd491eb18033723ba8c48037140d5de60cb747d04f712d1ae2f23a5554c31 |
import json
import os
import unittest
from pymatgen.phonon.bandstructure import (
PhononBandStructure,
PhononBandStructureSymmLine,
)
from pymatgen.util.testing import PymatgenTest
class PhononBandStructureSymmLineTest(PymatgenTest):
def setUp(self):
with open(
os.path.join(PymatgenTe... | vorwerkc/pymatgen | pymatgen/phonon/tests/test_bandstructure.py | Python | mit | 3,570 | [
"pymatgen"
] | cfad8b7ebf52abab9a07ecf30aef4c9c59ffcb0f61c1d7fda3c3c9ffd2849901 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2011 Yesudeep Mangalapilly <yesudeep@gmail.com>
# Copyright 2012 Google Inc. 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 ... | gorakhargosh/mom | mom/tests/test_mom_functional.py | Python | apache-2.0 | 30,591 | [
"MOE"
] | 3db746119bfd6a9e24c25ea5b9fc32ea22b3444142c7dd74cd17b839e8eda72e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#
# pylint: disable=no-member, chained-comparison, unnecessary-comprehension, not-callable
"""
This module provides objects to inspect the status of the Abinit tasks at run-time.
by extracting information from t... | richardtran415/pymatgen | pymatgen/io/abinit/abiinspect.py | Python | mit | 23,273 | [
"ABINIT",
"CRYSTAL",
"pymatgen"
] | d48ba97251aac98ef9bed30b24a67539646d32c42d6718086961d39ad0bc4fce |
from ase import *
# XXX This cannot be converted to ase 3, since we lack ANEB
raise NotImplementedError
#from ASE.Calculators.PairPotential import PairPotential
#from ASE.Filters.Subset import Subset
#from ASE.Dynamics.AdaptiveNudgedElasticBand import AdaptiveNudgedElasticBand
#from ASE.IO.NetCDF import ReadNetCDF
im... | conwayje/ase-python | tutorials/N2Ru-Dissociation2-ANEB.py | Python | gpl-2.0 | 1,415 | [
"ASE",
"NetCDF"
] | b4be5f731717d5ac02bbdedf75ba07b479f546d3dc83cf7af44080a2bba3bfc7 |
# -*- coding: utf-8 -*-
"""Contains tests for the AggregatingDataSource."""
from contextlib import contextmanager
from cStringIO import StringIO
import json
import mock
import urllib2
import urlparse
import testify as T
from firefly.data_sources.aggregating_data_source import AggregatingDataSource
from firefly import... | Yelp/firefly | tests/data_sources/aggregating_data_source_test.py | Python | isc | 20,112 | [
"Firefly"
] | 7c5bbea35a4937d4d833656b10531d0366243128bf6faa2b6cdbc90e9d6ace67 |
"""Mission Pinball Framework example machine files."""
import os
from os.path import join, dirname
from setuptools import setup
from _version import version
PACKAGE_FILES_EXCLUDED_EXT = ['pyc']
data_files = list()
for root, subFolders, files in os.walk('.'):
for fn in files:
ext = fn.split('.')[-1].lo... | missionpinball/mpf-examples | setup.py | Python | mit | 1,530 | [
"Brian"
] | 035a48eb19f8842d6b394c91fed35feb4762b8f1cbba6240c097da15a2992ac4 |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
from __future__ import unicode_literals
import bindings as bi
import re
import sys
PY3 = sys.version_info[0] == 3
str_type = str if PY3 else (str, unicode)
# We specify these not as real types, but as parameter annotations in the docstrings
class PythonTypeTranslatorFor... | jangorecki/h2o-3 | h2o-bindings/bin/gen_python.py | Python | apache-2.0 | 19,852 | [
"Gaussian"
] | 08e7e983e7851f3cc6cce5cf895da4c6e4d095bdb1e38ce694ad9e7a4f57ca15 |
# Copyright (c) 2001-2014, Canal TP and/or its affiliates. All rights reserved.
#
# This file is part of Navitia,
# the software to build cool stuff with public transport.
#
# Hope you'll enjoy and contribute to this project,
# powered by Canal TP (www.canaltp.fr).
# Help us simplify mobility and open public tr... | xlqian/navitia | source/jormungandr/jormungandr/utils.py | Python | agpl-3.0 | 19,521 | [
"VisIt"
] | 3e47ce68f034bf549008535d42797294d07d421f723f710565e5c31d1bb8e77f |
# -*- coding: utf-8 -*-
"""photometr.py - Simple Aperture photometry. Very old code, superceded by
astropy affiliated package `photutils.`
"""
# FIXME: kind of a stupid class dependence.
# Ideally a photometer object should take an image and a region object
# as arguments, where the region object is an instance of a... | bd-j/sedpy | sedpy/boneyard/photometer.py | Python | mit | 10,160 | [
"Gaussian"
] | adc85b1c97994f49bed49904b70f0feb709b67b41e95af625a8011862c414280 |
from galaxy.test.base.twilltestcase import TwillTestCase
#from twilltestcase import TwillTestCase
class UcscTests(TwillTestCase):
def test_00_first(self): # will run first due to its name
"""3A_GetData: Clearing history"""
self.clear_history()
def test_10_upload(self):
"""3A_GetDa... | jmchilton/galaxy-central | galaxy/test/functional/test_3A_GetData.py | Python | mit | 1,657 | [
"Galaxy"
] | 32c62c9a35043d765056c7d12b7d8d8c266fd13465c73549296d4926e5ae33e2 |
# -*- coding: utf-8 -*-
#
# test_spatial_distributions.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 ... | SepehrMN/nest-simulator | pynest/nest/tests/test_spatial/test_spatial_distributions.py | Python | gpl-2.0 | 28,395 | [
"Gaussian",
"NEURON"
] | a75e0453fc3f820189bea06050e370c131b9c4eadc64d645af88c1bd974bcfef |
'''
Copyright 2014 Travel Modelling Group, Department of Civil Engineering, University of Toronto
This file is part of the TMG Toolbox.
The TMG Toolbox 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 Fou... | TravelModellingGroup/TMGToolbox | TMGToolbox/src/license.py | Python | gpl-3.0 | 35,746 | [
"VisIt"
] | 8b5639964bf06587edf796512bff27996fbdefe1ac5e1aeb80a510c6f8ad3065 |
"""moose_to_neuron.py:
Convert moose model to NEURON.
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2015, Dilawar Singh and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer__ = "Dilawar Sin... | BhallaLab/benchmarks | moose_nrn_equivalence_testing/comparision_with_simple_HH_model/moose_to_neuron.py | Python | gpl-2.0 | 6,713 | [
"MOOSE",
"NEURON"
] | 3c8e42a24b5daef00eb55f1aa96cf3337ad7c0cc35a5dd8284e85809fb4f7ce8 |
#!/usr/bin/env python
# Do some basic imports, and set up logging to catch ImportError.
import inspect
import locale
import logging
import os
import sys
if (__name__ == "__main__"):
global dir_self
locale.setlocale(locale.LC_ALL, "")
# Tkinter chokes on non-US locales with commas for decimal points.
... | Grognak/Grognaks-Mod-Manager | main.py | Python | gpl-3.0 | 71,326 | [
"VisIt"
] | 728d64fee120ff5a1351341d6be79cd5108b3870bbef62b6a772bc76f12c29c3 |
#!/usr/bin/env python
'''
File name: main_make_mucleus_TSNE.py
Author: Guillaume Viejo
Date created: 28/09/2017
Python Version: 3.5.2
'''
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
from functions import *
from pylab import *
from sklearn.decomposit... | gviejo/ThalamusPhysio | python/main_make_AUTOCORR_CORRELATION_SHANKS.py | Python | gpl-3.0 | 6,122 | [
"Gaussian"
] | db90dffce12189b0c7cc998526fa81f86c5ddab6c2616f87991e60ed0befd090 |
# Copyright 2001 by Katharine Lindner. All rights reserved.
# Copyright 2006 by PeterC. All rights reserved.
# Copyright 2007 by Michiel de Hoon. 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... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Geo/__init__.py | Python | gpl-2.0 | 1,980 | [
"Biopython"
] | 0289ef0bc19a2000ddebed6e5b01f4e929d0c892ac65d9557ff585388445e242 |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | naslanidis/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 98,711 | [
"VisIt"
] | 6fa1a351b7fe743720560ea3acc5e67ee52f7de0a74575861f98b03337eb78d9 |
#!/usr/bin/env python
##
## Compute RPKM from SAM/BAM files
##
import os
import time
import scipy
import numpy
from scipy import *
from numpy import *
import misopy
import misopy.sam_utils as sam_utils
from misopy.Gene import load_genes_from_gff
from misopy.parse_csv import *
import pysam
def rpkm_per_region(reg... | Xinglab/rmats2sashimiplot | src/MISO/misopy/sam_rpkm.py | Python | gpl-2.0 | 7,002 | [
"pysam"
] | 50c957037ef138f0873c325c9a1eadf4648a3f6fc002b6f6e3c020a5295eb238 |
#!/usr/bin/env python
'''
A small O2 CASSCF calculation, in which spin and spatial symmetry should be
carefully chosen.
'''
from pyscf import gto, scf, mcscf, fci
#
# Starting from a triplet SCF calculation
#
mol = gto.M(atom='O; O 1 1.2', basis='ccpvdz', spin=2, symmetry=1)
mf = scf.RHF(mol).run()
norb = 4
nelec = ... | gkc1000/pyscf | examples/mcscf/18-o2_spatial_spin_symmetry.py | Python | apache-2.0 | 1,326 | [
"PySCF"
] | bd83fd081e075b7eef111f51f22ba656a251e5f9efcc234b39337ea1d644e0ef |
#
# 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
m = 6000
n = 4000
rho = 10
display = True
wo... | birm/Elemental | examples/interface/RNNLS.py | Python | bsd-3-clause | 2,354 | [
"Gaussian"
] | a2474df13733b90efb9bdc0a221239a0f3367df264364815d7bb9293271a2c25 |
import os
import glob
import click
from netCDF4 import Dataset
from trefoil.netcdf.utilities import copy_variable
from trefoil.cli import cli
@cli.command(short_help='Extract variables from files into new datasets in a new directory')
@click.argument('files')
@click.argument('variables')
@click.argument('o... | consbio/clover | trefoil/cli/extract.py | Python | bsd-3-clause | 1,406 | [
"NetCDF"
] | 2705877816d2cd3fa85b9ceb422cbc82b4a0ff1f18eb95960ba1c64c142b8a0a |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2017 Łukasz Rogalski <rogalski.91@gmail.com>
# Licensed under the GPL: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html
# For details: https://github.com/PyCQA/pylint/blob/master/COPYING
"""
Visitor doing some... | lucidmotifs/auto-aoc | .venv/lib/python3.5/site-packages/pylint/pyreverse/inspector.py | Python | mit | 12,396 | [
"VisIt"
] | 7f7bd42f31f48351a29b91d6b0f534f20f166f24b178f8b68b23842976b3b755 |
import pytest
from pysisyphus.calculators.Rastrigin import Rastrigin
from pysisyphus.calculators.PySCF import PySCF
from pysisyphus.helpers import geom_loader
from pysisyphus.stocastic import *
from pysisyphus.testing import using
def test_get_fragments():
geom = geom_loader("lib:benzene_and_chlorine.xyz")
#... | eljost/pysisyphus | tests/test_stocastic/test_stocastic.py | Python | gpl-3.0 | 4,629 | [
"PySCF",
"xTB"
] | ccedf0a4cc4386684f67e6cf7d2856c348f872f8b23e388ca2d2e4f3a99337ce |
# Copyright 2008-2014 Nokia Solutions and Networks
#
# 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 l... | userzimmermann/robotframework-python3 | src/robot/model/message.py | Python | apache-2.0 | 2,195 | [
"VisIt"
] | 0bd679078fc4c071e172ee2d7de65a073608708549f979f7a46359033579b15d |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | frreiss/tensorflow-fred | tensorflow/python/autograph/converters/functions.py | Python | apache-2.0 | 5,355 | [
"VisIt"
] | 2512763018166b34f83edc908acee1174f5e9ff932ffc53b5a11d0ead492b4d0 |
# 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... | Karaage-Cluster/karaage | karaage/projects/forms.py | Python | gpl-3.0 | 3,730 | [
"Brian"
] | b5151acb7ad0717a80acf7391194ca39d0a7eea91cafa1bce08a2f83a41dc3e8 |
"""Kernels for Gaussian process regression and classification.
The kernels in this module allow kernel-engineering, i.e., they can be
combined via the "+" and "*" operators or be exponentiated with a scalar
via "**". These sum and product expressions can also contain scalar values,
which are automatically converted to... | aabadie/scikit-learn | sklearn/gaussian_process/kernels.py | Python | bsd-3-clause | 66,652 | [
"Gaussian"
] | eed1e3ece83529e70f26428c5608e6116d7aae0fef2f0cf894993707f472d482 |
import moose
import numpy as np
from collections import Counter
def xyPosition(objInfo,xory):
try:
return(float(moose.element(objInfo).getField(xory)))
except ValueError:
return (float(0))
def setupMeshObj(modelRoot):
''' Setup compartment and its members pool,reaction,enz cplx under self.... | subhacom/moose-core | python/moose/chemUtil/chemConnectUtil.py | Python | gpl-3.0 | 7,761 | [
"MOOSE"
] | d658c67f3ff4db74dd5ca4fa50d79d104dd8678b542fe9bf09e67b686c9d272a |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import os
import subprocess
import sys
from setuptools import find_packages, setup
PROJECT_PATH = os.path.dirname(os.path.abspath(__file__))
VERSION = """
# This file is auto-generated with the version information during setup.py... | uber/pyro | setup.py | Python | apache-2.0 | 4,812 | [
"Biopython"
] | 776d1b0a71af986f9afb1e6f815eddaf88bc52704417f2179e5f1d1afb553447 |
"""In-memory representation of interfaces and other data structures.
The objects in this module are used to build a representation of an XML interface
file in memory.
@see: L{reader} constructs these data-structures
@see: U{http://0install.net/interface-spec.html} description of the domain model
@var defaults: Defau... | res2k/0install | zeroinstall/injector/model.py | Python | lgpl-2.1 | 56,135 | [
"VisIt"
] | 48c509c55e58409910a377fcec2434e738545ffff9d2e151b881b466d3bc632d |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.2
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_gslbgeodbprofile.py | Python | bsd-3-clause | 4,055 | [
"VisIt"
] | 928574ce93188fbb193345d2a0905f74c3f41121d66a92df4284b45fd24fbb2e |
import numpy as np
def create_perturb_params(countsmat):
'''
Computes transition probabilities and standard errors of the transition probabilities due to
finite sampling using the MSM counts matrix. First, the transition probabilities are computed
by dividing the each element c_ij by the row-sumemd ... | msultan/msmbuilder | msmbuilder/msm/validation/transmat_errorbar.py | Python | lgpl-2.1 | 2,227 | [
"Gaussian"
] | bd20542db73bde6ab88ca710a7cbb83af60c3a207523a714318254347918170e |
from __future__ import division, unicode_literals
import unittest
import os
import warnings
import json
from sympy import Number, Symbol
from pymatgen.analysis.surface_analysis import SlabEntry, SurfaceEnergyPlotter, NanoscaleStability
from pymatgen.util.testing import PymatgenTest
from pymatgen.entries.computed_entr... | johnson1228/pymatgen | pymatgen/analysis/tests/test_surface_analysis.py | Python | mit | 21,330 | [
"pymatgen"
] | 0af82238818fb15dc4f4163f3065ce0884e98948bfe988eb53fe6a26140921cc |
from __future__ import print_function
# https://en.wikipedia.org/wiki/Red%E2%80%93black_tree
# Invariants:
# 1. A node is either red or black.
# 2. The root is black.
# 3. All leaves are black.
# 4. If a node is red, then both its children are black.
# 5. Every path from a given node to a leaf node has the same no. of... | noporpoise/pyRBT | pyrbt.py | Python | mit | 21,259 | [
"VisIt"
] | 99aacb400e9e76065d784facf7f6217015c02f34e35d3f2802fb1b94c6bdedba |
# -*- coding: utf-8 -*-
# YAFF is yet another force-field code.
# Copyright (C) 2011 Toon Verstraelen <Toon.Verstraelen@UGent.be>,
# Louis Vanduyfhuys <Louis.Vanduyfhuys@UGent.be>, Center for Molecular Modeling
# (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise
# stated.
#
# This file is pa... | molmod/yaff | yaff/sampling/utils.py | Python | gpl-3.0 | 14,776 | [
"LAMMPS"
] | 8227f3e182445e86660d0036e2a9e6f099989045fdc47b8d0123ecef1c9e5054 |
# -*- coding: utf-8 -*-
"""
==========================================
Brainstorm Elekta phantom dataset tutorial
==========================================
Here we compute the evoked from raw for the Brainstorm Elekta phantom
tutorial dataset. For comparison, see [1]_ and:
http://neuroimage.usc.edu/brainstorm/Tu... | teonlamont/mne-python | tutorials/plot_brainstorm_phantom_elekta.py | Python | bsd-3-clause | 6,070 | [
"Mayavi"
] | 3425f62b89e004f12c338c271ddbde98459b4fb16685a29b0ac94b8f5fa80405 |
import sys, re, time, unicodedata, hashlib, types, os, inspect, datetime, string, urllib
import common, tvdb, anidb, scudlee, logging, functions, constants
from functions import XMLFromURL
#from Common import CommonStart, XMLFromURL, SaveFile, MapSeries, GetElementText
from dateutil.parser import parse as dateParse
fr... | Dingmatt/AMSA | Plug-ins/Amsa.bundle/Contents/Code/__init__.py | Python | gpl-3.0 | 8,849 | [
"MOE"
] | d9e8a8c59a5c3f21630851dc027cb1b2c7c49a9406e7ac6fac171add47632099 |
#!/usr/bin/python -u
import os, sys, fnmatch
import common
# do a basic check to see if pylint is even installed
try:
import pylint
except ImportError:
print "Unable to import pylint, it may need to be installed"
sys.exit(1)
pylintrc_path = os.path.expanduser('~/.pylintrc')
if not os.path.exists(pylintrc... | yochow/autotest | utils/run_pylint.py | Python | gpl-2.0 | 2,592 | [
"VisIt"
] | 85aeaeb0c0e19b7549c0b58323c92dd56c355b9c052da7455279dfd83954a2c2 |
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, s... | googleinterns/audio_synthesis | utils/distortion_helper.py | Python | apache-2.0 | 3,743 | [
"Gaussian"
] | c0c8a4534a7f8fda25909f69f97b06bd688c59fff7503956469b3c04e1f20df8 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
import numpy as np
# Import sile objects
from .sile import SileVASP
from ..sile import add_sile, sile_fh_open
from sis... | zerothi/sisl | sisl/io/vasp/out.py | Python | mpl-2.0 | 4,667 | [
"VASP"
] | 00d0b3f77908203e83b387739077cbd9f6970c87f4cfc9a58c340e15463f3000 |
#!/usr/bin/env python
"""
Logout
Example:
$ dirac-logout
"""
import os
import sys
import DIRAC
from DIRAC import gLogger, S_OK, S_ERROR, gConfig
from DIRAC.Core.Security import Locations
from DIRAC.Core.Utilities.DIRACScript import DIRACScript as Script
from DIRAC.Resources.IdProvider.IdProviderFactory import IdPro... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_logout.py | Python | gpl-3.0 | 3,695 | [
"DIRAC"
] | bc22a896b6a0a7893cb29194cbc173429c8fb7be47da6577ba0513a714b58e80 |
# 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 (t... | apache/allura | Allura/allura/lib/helpers.py | Python | apache-2.0 | 42,357 | [
"VisIt"
] | 8a5b3f5670a4fec2128983e550fb355a2826411e999621887bec85f1e748b8b1 |
from django.contrib import messages
from django.contrib.messages import get_messages
from django.http import HttpResponseRedirect
from mezzanine.pages.page_processors import processor_for
from hs_core import page_processors
from hs_core.views import add_generic_context
from .models import CompositeResource
@processo... | hydroshare/hydroshare | hs_composite_resource/page_processors.py | Python | bsd-3-clause | 2,881 | [
"NetCDF"
] | 68501c3fce41af78efdc4070a9d85566de7f7a5273de285452a90872739b0d38 |
#!/usr/bin/python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Test command-line interface.
"""
#===================================================... | jchodera/yank | Yank/tests/test_cli.py | Python | lgpl-3.0 | 3,821 | [
"Amber"
] | b939c2d9014dfd34a3230dc067d8bc25ceb2f929daaa27231d788f3f49cd5509 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | graph_sampler/tests/molecule_sampler_test.py | Python | apache-2.0 | 7,324 | [
"RDKit"
] | a2a6f6f972c58293773f698dc56099cf96a6d2f49855cba527c08fd4b3c9b4ea |
"""
:class:`Devirtualizer` performs method resolution at
compile time.
Devirtualization is implemented using a lattice
with three states: unknown → assigned once → diverges.
The lattice is computed individually for every
variable in scope as well as every
(instance type, field name) pair.
"""
from pythonparser import... | JQIamo/artiq | artiq/compiler/analyses/devirtualization.py | Python | lgpl-3.0 | 3,878 | [
"VisIt"
] | c390347d95be3e6e38d4300fca151d94cd3be79e4099b35e86e347cf9e7f31a4 |
"""
===================================================================
UTILITIES
This toolbox contains many useful functions, which are not related
to solving the inverse problem itself.
Marta Martinez-Camara, EPFL
===================================================================
"""
# take the division operator fr... | LCAV/linvpy | tests/regularizedtau/toolboxutilities.py | Python | bsd-2-clause | 12,452 | [
"Gaussian"
] | ca2f19bb4d7386a32f1b718e0391eaba9de04ccb95e92fb6f78de100af36e497 |
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space 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 t... | mozts2005/OuterSpace | client-pygame/lib/osci/dialog/MainGameDlg.py | Python | gpl-2.0 | 14,374 | [
"Galaxy"
] | b3fd0111593c3bc23c0b5aae267b454e8d48f1f54fb8e5a9a459c5cc57ab3411 |
""" This integration test only need the TaskQueueDB
(which should of course be properly defined also in the configuration),
and connects directly to it
Run this test with::
"python -m pytest tests/Integration/WorkloadManagementSystem/Test_TaskQueueDB.py"
Suggestion: for local testing, run th... | andresailer/DIRAC | tests/Integration/WorkloadManagementSystem/Test_TaskQueueDB.py | Python | gpl-3.0 | 38,712 | [
"DIRAC"
] | 668223d57a5efe314a7143c39a2b65054ea8abce4eb889e945a156e0a21333fd |
## BRIE model
import time
import numpy as np
from scipy.sparse import issparse
import tensorflow as tf
import tensorflow_probability as tfp
from tensorflow_probability import distributions as tfd
class BRIE2():
"""
Ng : number of genes
Nc : number of cells
Kg : number of gene features
Kc : numb... | huangyh09/brie | brie/models/model_TFProb_dev.py | Python | apache-2.0 | 9,656 | [
"Gaussian"
] | e02a337ed7fb0e7577996dcdf453f96dafdf1354fb2986a83ac8c914d98eba2c |
import PythonQt
from PythonQt import QtCore, QtGui, QtUiTools
import director.applogic as app
import director.objectmodel as om
from director.timercallback import TimerCallback
from director import robotstate
from director import visualization as vis
from director import transformUtils
from director import ikconstraint... | patmarion/director | src/python/director/teleoppanel.py | Python | bsd-3-clause | 60,437 | [
"VTK"
] | 47caf203913f2ff9c3981f1b09aea0a7836b5b96a5cf4022e6067d684b3c0b43 |
from pyramid.response import Response
from pyramid.view import view_config, view_defaults
import beepaste.pasteFunctions as func
from beepaste.selectOptions import languagesList
from beepaste.models.api import API
import json
import base64
from beepaste.models.pastes import Pastes
def verifyKey(apikey, request):
a... | beepaste/beepaste | beepaste/views/api/views.py | Python | gpl-3.0 | 4,715 | [
"VisIt"
] | 0f04935827c88c171563c88dcfd486f3ceb0b197f4d42d23cb73e371884d48dc |
# Example_CZTS-AntisiteDefects.py by J. M. Skelton
# -------
# Imports
# -------
# Import routines from Transformer.
from Transformer.IO.StructureIO import ReadStructure;
from Transformer.Framework.BatchIO import ExportResultSet;
from Transformer.Framework.Convenience import AntisiteDefects;
# ----
# Main
# ----... | JMSkelton/Transformer | Examples/Example_CZTS-AntisiteDefects.py | Python | gpl-3.0 | 1,182 | [
"VASP"
] | 173687d186b70639f120c8e810fef4f1bb942c94d39ad61709c13ba9e04122bb |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
from __future__ import with_statement
import functools
import logging
import threading
import time
try:
from collections import namedtuple
except ImportError:
from concurrent.futures._compat import namedtuple... | santegoeds/pythonfutures | concurrent/futures/_base.py | Python | bsd-2-clause | 19,614 | [
"Brian"
] | e048c6ab30542e438c45798f67cf477c7370b2fe5abdc1d59cee146dd8c8f351 |
# 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, software
# distributed under t... | scrapinghub/keystone | keystone/hacking/checks.py | Python | apache-2.0 | 9,999 | [
"VisIt"
] | e512db51458a9a6eee948cfdc90016d20b71c597b2856c7e02e109b73dcd9d4c |
"""Unit test for plural6.py
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.1 $"
__date__ = "$Date: 2004/03/17 14:34:40 $"
__copyr... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/plural/stage6/pluraltest6.py | Python | mit | 2,153 | [
"VisIt"
] | 521cd9e8388685904f628b70722b553722fbe23223fd5f7645b3f14c648f21e5 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | witgo/spark | python/pyspark/ml/clustering.py | Python | apache-2.0 | 62,508 | [
"Gaussian"
] | 7dc75e442744cf593e321f80555ca8243d0ddb077f6d92c4846657a023e81c08 |
#-------------------------------------------------------------------------------
# . File : GAMESSOutputFile.py
# . Program : MolarisTools
# . Copyright : USC, Mikolaj Feliks (2015-2018)
# . License : GNU GPL v3.0 (http://www.gnu.org/licenses/gpl-3.0.en.html)
#--------------------------------------------... | mfx9/MolarisTools | MolarisTools/Parser/GAMESSOutputFile.py | Python | gpl-3.0 | 7,302 | [
"GAMESS",
"Gaussian"
] | 6f05731320fe0cdbb657a1450d3445f51cee51b40eb0142c49ccf20056a502f8 |
from nwchem import *
from math import *
def geom_get_coords(name):
#
# This routine returns a list with the cartesian
# coordinates in user input units for the geometry
# of given name
#
try:
actualname = rtdb_get(name)
if (actualname == None):
actualname = name
except NWChemError:
actu... | rangsimanketkaew/NWChem | contrib/python/nwgeom.py | Python | mit | 8,121 | [
"NWChem"
] | 7fc0e967c5c4bcaa5d1d609dd0a2bbf017f5a5da31faaf8e482cbe25090ad4db |
# Copyright 2009-2014 Lee Harr
#
# This file is part of pybotwar.
# http://pybotwar.googlecode.com/
#
# Pybotwar 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 yo... | YMIndustries/pybotwar | world.py | Python | gpl-3.0 | 19,911 | [
"BLAST"
] | 0b0d93c02173c4c82c3709fe643a332e8a0ec5dd13cb7cc7c1c784fe5a5dc2ec |
# This is for spawned PyRosetta processes that do the Rosetta intensive computations
# Why is a new process being spawned -> because Python's Global Interpreter Lock only let's one thread
# perform computations at any time
# Every time a Rosetta job needs to be run, it has to be run in a thread to prevent the GUI from ... | schenc3/InteractiveROSETTA | InteractiveROSETTA/server/daemon_server.py | Python | gpl-2.0 | 54,483 | [
"PyMOL"
] | 48d39841e1c8d1b11b78199556ed5ad4ddc0f5f602aee5787bf7c413ced9dac2 |
import pickle
# mathtext fails to create labels with matplotlib 0.99 on el6
import matplotlib
matplotlib.rc('text', usetex=True)
import matplotlib.pyplot as plt
from ase.units import Hartree
plt.figure(1)
plt.figure(figsize=(6.5, 4.5))
plt.figure(2)
plt.figure(figsize=(6.5, 4.5))
for wlin in [25.,50.,75.,100.]:
... | robwarm/gpaw-symm | doc/tutorials/gw_tutorial/plot_frequency.py | Python | gpl-3.0 | 997 | [
"ASE"
] | c88ca2317c3e12fb495a94cf130e09e5240583d4a0b91c34b1fa38c8746dbf5d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen.core.spectrum import Spectrum
import numpy as np
"""
This module defines classes to represent all xas
"""
__author__ = "Chen Zheng"
__copyright__ = "Copyright 2012, The Materials Project"
__vers... | dongsenfo/pymatgen | pymatgen/analysis/xas/spectrum.py | Python | mit | 1,559 | [
"pymatgen"
] | 6e8319ffe0c4baa2acd1a12ac13d77684d7e71fb086b9a6a3b07f470eceb6711 |
#
# This program is free software you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation either version 3 of the License, or
# (at your option) any later version.
#
# Written (C) 2012-2013 Heiko Strathmann
#
from numpy import *
from py... | JingheZ/shogun | examples/undocumented/python_modular/graphical/statistics_linear_time_mmd.py | Python | gpl-3.0 | 6,353 | [
"Gaussian"
] | 9f26918ab20888f5871350bcffa324974a5c0e65a51de94d187e7f5155696854 |
#!/usr/bin/env python
"""
Change libtetrabz source file so that they are compatible with the Abinit build system.
"""
from __future__ import unicode_literals, division, print_function, absolute_import
import os
here = os.path.dirname(__file__)
f90_files = [f for f in os.listdir(here) if f.startswith("libtetrabz") and... | abinit/abinit | shared/common/src/17_libtetra_ext/libtetrabz2abi.py | Python | gpl-3.0 | 949 | [
"ABINIT"
] | 3a7a14348cb5684467cc57d06da1df9f05a949df80e62dcf20981005db990985 |
#!python
#############################################################################
# cubit2specfem3d.py #
# this file is part of GEOCUBIT #
# #... | vmont/specfem3d | CUBIT_GEOCUBIT/geocubitlib/cubit2specfem3d.py | Python | gpl-3.0 | 62,524 | [
"NetCDF"
] | ab9325bd2dddc44b5edcfd85f78273f91215276a5eb765911df3f7f829cf4ee2 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | caio2k/RIDE | src/robotide/lib/robot/model/filter.py | Python | apache-2.0 | 3,465 | [
"VisIt"
] | e1c8564fb33b36c7995f522acbdd875f3a8fa154f6e58e9eb0e3440b4940f0e4 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/tinker/state.py | Python | gpl-2.0 | 9,373 | [
"ChemPy",
"PyMOL",
"TINKER"
] | 5377cd5446442d8853a6e39a006daabc96dd899f9ad746688969d82c5b09281f |
''' Extractors that operate on AudioStim inputs. '''
from abc import ABCMeta
from os import path
import sys
import logging
import numpy as np
from scipy import fft
import pandas as pd
from pliers.stimuli.audio import AudioStim
from pliers.stimuli.text import ComplexTextStim
from pliers.extractors.base import Extract... | tyarkoni/pliers | pliers/extractors/audio.py | Python | bsd-3-clause | 23,156 | [
"VisIt"
] | 34f65290684277601a847b93b38cd922af4db66477241f50688f796a956abd25 |
#
# Copyright (c) 2001 - 2015 The SCons Foundation
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, merge... | Uli1/mapnik | scons/scons-local-2.4.0/SCons/Taskmaster.py | Python | lgpl-2.1 | 40,565 | [
"VisIt"
] | bd2d26f55f083c6351fe6f017f57ce366535394f0eb6b30b93cf06230e1fcb50 |
'''
phretrieve.py - a collection of methods used for phase processing and retrieval.
21/12/2015 - LNT - first.
'''
# useful imports
import numpy as np
import scipy.ndimage as ndi
from scipy.signal import correlate2d
from skimage.restoration import unwrap_phase
# for testing purposes
import phplot
# subtract a referen... | taylo589/phproc | phretrieve.py | Python | gpl-2.0 | 15,513 | [
"Gaussian"
] | 0defde1b250f55422bcaa35495796179a61d4adb7ea8bc24f783e969ddb59a5f |
#!/usr/bin/env python
# import egads package
import egads
# import thermodynamic module and rename to simplify usage
import egads.algorithms.thermodynamics as thermo
# get list of all NetCDF files in 'data' directory
filenames = egads.get_file_list('data/*.nc')
f = egads.input.EgadsNetCdf() # create EgadsNetCdf... | eufarn7sp/egads-eufar | Documentation/EGADS Algorithm Handbook - LATEX/example.py | Python | bsd-3-clause | 798 | [
"NetCDF"
] | 551b6f3c2c845be0b62e0615f67f68f0ad1cbe07bd3c33c235d7c2497f1a80e0 |
########################################################################
# $HeadURL$
########################################################################
""" FutureHandler is the implementation of a future
service in the DISET framework
"""
__RCSID__ = "$Id$"
from types import *
from DIRAC.Core.DISET.Reques... | avedaee/DIRAC | WorkloadManagementSystem/Service/FutureHandler.py | Python | gpl-3.0 | 695 | [
"DIRAC"
] | 2a68f2449b4fa16cb16a0c965ca6268b4935c5caff6230923a7f2d3b8b1f7cc9 |
# -*- coding: utf-8 -*-
# Copyright (c) 2008-2010, 2013 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2014 Google, Inc.
# Copyright (c) 2014 Arun Persaud <arun@nubati.net>
# Copyright (c) 2015-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2015 Ionel Cristian Maries <contact@ionelmc.ro>
... | axbaretto/beam | sdks/python/.tox/lint/lib/python2.7/site-packages/pylint/test/unittest_pyreverse_diadefs.py | Python | apache-2.0 | 7,080 | [
"VisIt"
] | 870a4e365422b0377cc4a3cef3ad532b7783f91f7b88049b443bee6c847cd104 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/server/database/models.py
#
# 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
# n... | 0x0mar/king-phisher | king_phisher/server/database/models.py | Python | bsd-3-clause | 9,986 | [
"VisIt"
] | 722725f2f7dd75d482a14c57f8923b4161b6b20cbb94c357720a2b328e2bee0f |
from WebAppDIRAC.Lib.WebHandler import WebHandler, asyncGen
from DIRAC.Core.DISET.RPCClient import RPCClient
class DataLoggingHandler(WebHandler):
AUTH_PROPS = "authenticated"
@asyncGen
def web_getData(self):
sData = self.getSessionData()
result = {}
user = sData["user"]["username"]
if user == ... | zmathe/WebAppDIRAC | WebApp/handler/DataLoggingHandler.py | Python | gpl-3.0 | 1,000 | [
"DIRAC"
] | 98a0667eb7329b011889018ac3d285c52ce3e323b731a1511ecf431c59a6925b |
# -*- coding: utf-8 -*-
r"""
.. _disc-filtering:
===================================
Background information on filtering
===================================
Here we give some background information on filtering in general, and
how it is done in MNE-Python in particular.
Recommended reading for practical applications ... | mne-tools/mne-tools.github.io | 0.20/_downloads/68dbe405ac02c372b6167f7e86b7e3e0/plot_background_filtering.py | Python | bsd-3-clause | 49,887 | [
"Gaussian"
] | 448e0a5909498322bb743e21e9cd24447e6e06cd9e1865bf2bf41bfce27ff161 |
#!/usr/bin/python2.4
# Copyright (c) 2006-2008 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.
"""The 'grit android2grd' tool."""
import getopt
import os.path
import re
import StringIO
import types
from xml.dom import Nod... | paul99/clank | tools/grit/grit/tool/android2grd.py | Python | bsd-3-clause | 19,185 | [
"xTB"
] | 067a5f27f38aeb71d5c61c073132cca539ccd96ae9824d3c1913b2d01c70783a |
# Orca
#
# Copyright 2004-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/Thunderbird/__init__.py | Python | gpl-3.0 | 1,015 | [
"ORCA"
] | 079b19649d8da4e039c69cde7f3e9a807e032b062a16c505ef76bf3af0e3bd42 |
########################################################################
# $HeadURL$
# File : InputDataByProtocol.py
# Author : Stuart Paterson
########################################################################
""" The Input Data By Protocol module wraps around the Replica Management
components to provid... | sposs/DIRAC | WorkloadManagementSystem/Client/InputDataByProtocol.py | Python | gpl-3.0 | 11,475 | [
"DIRAC"
] | f5b733c296d2fcfcd059702024215894cdbdd0572aa451e1721e5322f1b8b245 |
#
# Copyright (C) 2019 Greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import time
import gzip
import rdkit
from rdkit import Chem
f... | ptosco/rdkit | Regress/Scripts/fingerprint_screenout.py | Python | bsd-3-clause | 4,158 | [
"RDKit"
] | 93dcc264e34a483887003a53b8abada9f92ec7e1ab17f34307b0282b39a8c507 |
#!/usr/bin/env python
import os
import math
import obspy
import numpy as np
import matplotlib.pyplot as plt
from scipy import signal
class SyntheticSeismogram(object):
def __init__(self, file_name):
"""
Reads in an ascii seismogram, in the specfem3d_globe format. Returns a
synthetic seis... | michael-afanasiev/specfem_control_room | components/classes/seismogram.py | Python | gpl-2.0 | 6,561 | [
"Gaussian"
] | f3b7b8732146a60104884a58fde6efd947095d4dc5b0725002ed692f4ff42398 |
# Hop --- a framework to analyze solvation dynamics from MD simulations
# Copyright (c) 2007-2010 Oliver Beckstein <orbeckst@gmail.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 Foundation, either v... | iwelland/hop | hop/sitemap.py | Python | lgpl-3.0 | 114,583 | [
"CHARMM",
"CRYSTAL",
"Gaussian",
"MDAnalysis",
"VMD"
] | 68c42045c3d842490520b90cc58ae7ef63a333c8d21b44243baa8a2566be9a2e |
#
# Copyright 2011-2021 Universidad Complutense de Madrid
#
# This file is part of Megara DRP
#
# SPDX-License-Identifier: GPL-3.0+
# License-Filename: LICENSE.txt
#
"""LCB Standard Star Image Recipe for Megara"""
from astropy import constants as const
import astropy.io.fits as fits
import astropy.units as u
import ... | sergiopasra/megaradrp | megaradrp/recipes/calibration/lcbstdstar.py | Python | gpl-3.0 | 10,115 | [
"Gaussian"
] | 8d2edcf572a9b4d2e08374c45d5250682911419669ce05d4496a4190a6a74682 |
# -*- coding: utf-8 -*-
# SyConn - Synaptic connectivity inference toolkit
#
# Copyright (c) 2016 - now
# Max-Planck-Institute of Neurobiology, Munich, Germany
# Authors: Philipp Schubert, Joergen Kornfeld
import glob
import os
from collections import defaultdict
from typing import TYPE_CHECKING, Dict, Optional, Tuple,... | StructuralNeurobiologyLab/SyConn | syconn/reps/segmentation_helper.py | Python | gpl-2.0 | 22,791 | [
"NEURON"
] | 318d837cd95c3b63f13b20983f0ea8955c9bea02cbd37f0fa13715fb1d34e84b |
#!/usr/bin/env python
import vtk
import numpy as np
from vmtk import vmtkscripts
from vmtk import vtkvmtk
import argparse
import itertools
import os
def close_cell(section):
#assume the cell array of lines
section.BuildCells()
section.BuildLinks()
numberOfLinePoints = section.GetNumberOfPoints()
... | kayarre/Tools | vmtk/evaluate_segments.py | Python | bsd-2-clause | 28,113 | [
"VTK"
] | e420c62b897d239be7bbd34dff7cf5c03318116d001a30e790eac03654f33d5a |
import unittest
import os
from os.path import dirname
import sys
import json
from mrjob.job import MRJob
import Geohash
root = dirname(dirname(dirname(dirname(os.path.abspath(__file__)))))
sys.path.append(root)
GEOTWEET_DIR = root
DATA_DIR = os.path.join(root, 'data', 'geo')
COUNTIES_GEOJSON_LOCAL = os.path.join(DAT... | meyersj/geotweet | geotweet/tests/integration/mapreduce/state-county_tests.py | Python | mit | 1,827 | [
"Galaxy"
] | 22c8823be09392ce6f90e812ec2a7f06756c5c8152dc42ad474adbd84c940f53 |
import os, os.path, shutil, logging
import time, datetime, zipfile
import catcher
def overrides(interface_class):
def overrider(method):
assert(method.__name__ in dir(interface_class))
return method
return overrider
#TODO: GC, restore and history view
class FileSystem:
"""an abstract base ... | lihuiba/SoftSAN | filesystem.py | Python | apache-2.0 | 17,250 | [
"ADF"
] | ead4f06feb5a7c1534235b2fcdc1c9317ad1a1871732a02ac6c4d4a70ba7e439 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2010 Prof. William H. Green (whgreen@mit.edu) and the
# RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of c... | faribas/RMG-Py | rmgpy/data/solvation.py | Python | mit | 33,912 | [
"VisIt"
] | 189c50e9970beab09fc8229f46110d982d7e62dfa4462ff3953d30abe23ac71c |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | Inspq/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 29,867 | [
"Galaxy",
"MOOSE"
] | 21a75a50ae59fb58abd5267acd9c037ff6446ac58bde16608a9eb4f8993f00c7 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to
# make it easier to submit large numbers of jobs on supercomputers. It
# provides a python interface to physical input, ... | pylada/pylada-light | src/pylada/ipython/goto.py | Python | gpl-3.0 | 6,348 | [
"CRYSTAL",
"VASP"
] | 8e95721a235c8aa3a6f5c68257114f593e8a198e70a569ae449aa98a868bc954 |
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