text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
'''
sbclearn (c) University of Manchester 2017
sbclearn is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=invalid-name
# pylint: disable=no-member
# pylint: disable=wrong-import-order
import unittest
from ker... | synbiochem/synbiochem-learn | gg_learn/keras/test/test_utils.py | Python | mit | 2,824 | [
"VisIt"
] | 9cbb38deabcd79ace4e3fdede01a6647ee93237ce11577523a02a5cb128b9425 |
from disco.test import TestCase, TestJob
class RawJob(TestJob):
@staticmethod
def map(e, params):
yield 'raw://%s' % e, ''
class RawTestCase(TestCase):
def runTest(self):
input = ['raw://eeny', 'raw://meeny', 'raw://miny', 'raw://moe']
self.job = RawJob().run(input=input)
s... | scrapinghub/disco | tests/test_raw.py | Python | bsd-3-clause | 426 | [
"MOE"
] | f02662e8fecee4f5ff16d3154701bc6cf39f14d304541f7f755412216d1a9f14 |
# encoding: utf-8
#
# Copyright (C) 2013-2015 RoboIME
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This ... | roboime/pyroboime | roboime/options.py | Python | agpl-3.0 | 1,335 | [
"Gaussian"
] | 962174babc3b9ebb750f89abdd7a099e4ee9e945a98ba0405d7cb60f53618ea1 |
# To run this, install Python and make sure it is in your path
# environment variable, and then run it from the command line
# as
#
# python vs3tovtk.py input.vs3 output.vtk
#
# This script should work with Python 2.7+ and 3+
#
import sys
import os
import vs3
fperr = sys.stderr
if not len(sys.argv) in [2,3]: # Re... | jasondegraw/View3D-Resources | scripts/vs3tovtk.py | Python | gpl-3.0 | 1,318 | [
"VTK"
] | 02e156d93d7c20abaad00ce9d08c64d82a0cedca324e241e98b6a9179f85d72a |
"""
Linear Least-Squares Inversion
==============================
Here we demonstrate the basics of inverting data with SimPEG by considering a
linear inverse problem. We formulate the inverse problem as a least-squares
optimization problem. For this tutorial, we focus on the following:
- Defining the forward pro... | simpeg/simpeg | tutorials/02-linear_inversion/plot_inv_1_inversion_lsq.py | Python | mit | 6,216 | [
"Gaussian"
] | 98ac15079bb8fc70123a8d7d4f2df6fe9b0590232c4bb63fc817b5078c810075 |
#!/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 optparse
import os.path
import subprocess
import sys... | loopCM/chromium | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 15,806 | [
"Galaxy"
] | d260e72713c00c693d688b63a5c3c76400b5ba15edab89fc3b907c7c7f4e8be2 |
"""
Utilities to create replication transformations
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import six
from DIRAC.TransformationSystem.Client.Transformation import Transformation
from DIRAC import gLogger, S_OK, S_ERROR
def createDataTransforma... | yujikato/DIRAC | src/DIRAC/TransformationSystem/Utilities/ReplicationTransformation.py | Python | gpl-3.0 | 3,762 | [
"DIRAC"
] | b31e8b60bb6ba6b65486e67934a788330e20b617b71a37313f4bb7d613ebe69c |
#!/usr/bin/env python
"""[License: GNU General Public License v3 (GPLv3)]
This file is part of FuMa.
FuMa 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 opti... | ErasmusMC-Bioinformatics/fuma | fuma/CLI.py | Python | gpl-3.0 | 7,199 | [
"VisIt"
] | 700cca22b00a9f33cf54a0ce73a72d40e5fa474566e757505260c69ed627b4f6 |
from __future__ import absolute_import
import fluent.syntax.ast as FTL
from fluent.migrate.helpers import transforms_from
from fluent.migrate.helpers import VARIABLE_REFERENCE, TERM_REFERENCE
from fluent.migrate import REPLACE, COPY
privacy_hub = "firefox/privacy-hub.lang"
def migrate(ctx):
"""Migrate bedrock/fir... | hoosteeno/bedrock | lib/fluent_migrations/firefox/privacy.py | Python | mpl-2.0 | 18,195 | [
"VisIt"
] | 21b7be8dfd5d2f8cbad7c9cc50727951f2f2cb952740776c863474777fc4e379 |
#!/usr/bin/env python
import click
import os
import sh
@click.command()
@click.argument('omz_network')
@click.option('-s', '--skip', is_flag=True, help='skip downloading / optimizing')
@click.option('-bs', '--batch_size', default=1, help='minibatch size')
@click.option('-nt',
'--num_threads',
... | plaidml/plaidml | tools/benchmarking/benchmark_ov.py | Python | apache-2.0 | 2,429 | [
"Brian"
] | f29a9aecd4a9ea03856278c0c20c539861e2061f3be5e25d2e2f91dd1d7fe4f1 |
#!/usr/bin/env python
"""
Script to convert catalogs from VizieR to index files using
astrometry.net. See
https://confluence.lsstcorp.org/display/LSWUG/Building+Astrometry.net+Index+Files
for more information, especially running at lsst-dev.ncsa.illinois.edu
using the ready-built LSST stack (bash --rcfile ~lsstsw/e... | DarkEnergyScienceCollaboration/Recipes | python/utensils/make_index_files.py | Python | gpl-2.0 | 3,384 | [
"Galaxy"
] | d7cdc8b1be6e7968d2c5ad16c17af53db73b74a0a9f355c60ad3ef117aad51d1 |
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import json
import os
import os.path
import re
import sys
import warnings
from collections import defaultdict
try:
from setuptools import setup, find_packages
from setuptools.command.build_py import build_py as BuildPy
... | computersalat/ansible | setup.py | Python | gpl-3.0 | 15,054 | [
"Galaxy"
] | 9be703630a4118b97b012ebe6dcdce2abfe9a08a7b393f42d8292d6eabaccbaa |
import sys
from collections import defaultdict, OrderedDict
from copy import deepcopy
from operator import itemgetter, attrgetter
import numpy as np
from pythomics.proteomics.config import CARBON_NEUTRON
from scipy import optimize
from scipy.signal import convolve, kaiser
from .cpeaks_wrapper import (
bigauss_fu... | Chris7/pyquant | pyquant/peaks.py | Python | mit | 35,651 | [
"Gaussian"
] | daedcae349be75eed27398153aeb989e6f333c45094916fffa1ba568f000a08d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License, Ve... | sparkslabs/kamaelia | Sketches/MPS/BugReports/FixTests/Kamaelia/Examples/UsingChassis/PAR/par_shutdown.py | Python | apache-2.0 | 3,471 | [
"DIRAC"
] | 1fbdc471886b027606f7cdbf79ef6371c9a7119ac8cbf72cf2ce404df2ff87d1 |
"""
Interactive kinetics app with sliders (with units).
Start by runing:
$ bokeh serve interactive.py
Add --show argument or navigate to:
http://localhost:5006/interactive
"""
from collections import defaultdict
import sys
from chempy.util.bkh import integration_with_sliders
from chempy.units import SI_base_re... | bjodah/aqchem | examples/bokeh_interactive_arrhenius_units.py | Python | bsd-2-clause | 1,400 | [
"ChemPy"
] | 36bacc5786bd8959e989271bbb653cbcef3e6f0a070a36ae71944699a838d4c6 |
from datetime import timedelta
import functools
import itertools
import numpy as np
import pandas as pd
from . import common
from . import indexing
from . import ops
from . import utils
from .pycompat import basestring, OrderedDict, zip, reduce, dask_array_type
from .indexing import (PandasIndexAdapter, LazilyIndexed... | hetland/xray | xray/core/variable.py | Python | apache-2.0 | 34,824 | [
"NetCDF"
] | 531681871002b4354dcf242df4483704cb98bcc00b74090d5343071ef11eb3c7 |
# -*- coding: utf-8 -*-
# Generated by Django 1.10.7 on 2017-07-19 14:36
from django.db import migrations, models
forward = """
CREATE INDEX treenode__history_skeleton_id_index ON treenode__history (skeleton_id);
CREATE INDEX treenode_connector__history_skeleton_id_index ON treenode_connector__history (skelet... | tomka/CATMAID | django/applications/catmaid/migrations/0024_add_neuron_history_indices.py | Python | gpl-3.0 | 1,787 | [
"NEURON"
] | f2c47b9e8617f15034cdf3d3fd67c226396195d13a72a5328190a539a6c436b8 |
"""Null statistical model.
Stat model that always returns 0. This is the null model used to compare
results with and without a statistical model.
"""
from typing import Any, Callable
import dataclasses
from epi_forecast_stat_mech.statistical_models import base
@dataclasses.dataclass
class Null(base.StatisticalModel... | HopkinsIDD/EpiForecastStatMech | epi_forecast_stat_mech/statistical_models/no_stat_model.py | Python | apache-2.0 | 2,024 | [
"Gaussian"
] | e3a181cc188faaf23490feb313efe67e0cfa93dcb76fedd29da1c77c291f903d |
import director.objectmodel as om
import director.applogic as app
from shallowCopy import shallowCopy
import director.vtkAll as vtk
from director import transformUtils
from director import callbacks
from director import frameupdater
from PythonQt import QtCore, QtGui
import os
import colorsys
import weakref
import ite... | mitdrc/director | src/python/director/visualization.py | Python | bsd-3-clause | 39,111 | [
"VTK"
] | 16d101cec27805d7033d112846c8514e6712609a5aad326bb0775a2dfd50fddf |
"""
UKS via SGM
"""
import numpy as np
from frankenstein.tools.tensor_utils import get_unitary_matrix_ov
from pyscf import scf
from frankenstein.sgscf import uks, sguhf
def update_sghf(mf):
pass
class SGUKS(uks.UKS):
# methods for output
print_info = sguhf.print_info
# methods for SCF
upda... | hongzhouye/frankenstein | sgscf/sguks.py | Python | bsd-3-clause | 2,061 | [
"PyMOL",
"PySCF"
] | 75b433a219b2a3950b0a2d1bffdf900b57911fe6434167478cdc34ecf15f61e4 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RQvalue(RPackage):
"""Q-value estimation for false discovery rate control.
This pa... | rspavel/spack | var/spack/repos/builtin/packages/r-qvalue/package.py | Python | lgpl-2.1 | 1,762 | [
"Bioconductor"
] | e9fd8eb7e32a3217314dd441cdf8af49c6c4baf0ef67cc7afcbc28c305fcff44 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Zsolt Foldvari
# 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 General Public License as published by
# the Free Software Foundation; either version 2 ... | Forage/Gramps | gramps/plugins/docgen/pdfdoc.py | Python | gpl-2.0 | 9,784 | [
"Brian"
] | 8a27c0e0990a6b162a5d9d96765d9f5e117e97d8ac85cb635819a5366bc153d5 |
#!/usr/bin/env python
'''
File name: main_make_map.py
Author: Guillaume Viejo
Date created: 28/09/2017
Python Version: 3.5.2
To make shank mapping
'''
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 sklear... | gviejo/ThalamusPhysio | python/main_make_map_pos_neg.py | Python | gpl-3.0 | 16,953 | [
"NEURON"
] | 3fe47c92c72fa1abbff62c5afda7e6ad1ff54c762d967311a530014d29398c40 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import subp... | nuclear-wizard/moose | python/TestHarness/tests/test_DuplicateTestNames.py | Python | lgpl-2.1 | 981 | [
"MOOSE"
] | ed5207065e2971a0cda91db02d57765e796b6d2391562531490da13ac882ca71 |
from __future__ import print_function
import argparse
import mdtraj as md
import multiprocessing as mp
import AdaptivePELE.analysis.trajectory_processing as tp
def parseArguments():
desc = "Program that extracts residue coordinates for a posterior MSM analysis."
parser = argparse.ArgumentParser(description=de... | AdaptivePELE/AdaptivePELE | AdaptivePELE/analysis/dehidratate_and_align.py | Python | mit | 2,438 | [
"MDTraj"
] | 1f51aaf596b9efaaa6532ca4b360d278c300d11005fef858649812305abc50a3 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/ajax/multiepg2.py | Python | gpl-2.0 | 15,057 | [
"VisIt"
] | e665a8acecd0a4ab78f2ebe377e86e9c26eb7d68920e42d3ae76441ba86f70ac |
# ScummVM - Graphic Adventure Engine
#
# ScummVM is the legal property of its developers, whose names
# are too numerous to list here. Please refer to the COPYRIGHT
# file distributed with this source distribution.
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU ... | vanfanel/scummvm | devtools/tasmrecover/tasm/proc.py | Python | gpl-2.0 | 5,172 | [
"VisIt"
] | 7a8da207a2065c3a38c8abf70f6809c5d002842add2ce316b728c8719adc1ea6 |
# -*- coding: utf-8 -*-
#
# Copyright 2008 - 2013 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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, e... | LunarLanding/Pythics | pythics/lib.py | Python | gpl-3.0 | 11,469 | [
"Brian"
] | e27b18d3be6083ebef9f8f7fd4a5ccfd3e4a021ac34b4bab7324a6e526f9ffb5 |
"""
A context manager for managing things injected into :mod:`__builtin__`.
Authors:
* Brian Granger
* Fernando Perez
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2010-2011 The IPython Development Team.
#
# Distributed under the terms of the BSD License.
#
# C... | boompieman/iim_project | project_python2/lib/python2.7/site-packages/IPython/core/builtin_trap.py | Python | gpl-3.0 | 4,283 | [
"Brian"
] | 1537e44a1f54dcf1c149f0fa994d3ab3f06fe2e9e0bcdc6a9ef71447e603131a |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-get-queue-cpu-time.py
# Author : Federico Stagni
########################################################################
"""
Report CPU length of queue, in seconds
This script is used by the dirac-pilo... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/scripts/dirac_wms_get_queue_cpu_time.py | Python | gpl-3.0 | 1,242 | [
"DIRAC"
] | 0c3754ec10aa4110302668b2f58ff7c1d850055db57120f0a4260a1507da0e8e |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | thomasaarholt/hyperspy | hyperspy/utils/peakfinders2D.py | Python | gpl-3.0 | 20,090 | [
"Gaussian"
] | ed57635893ff8dac9623521d97c81d8dd86908662407699fd888b2bc2ee14563 |
import menu
import newgame
import galaxy
import planet
import star
import research
| jespino/GalaxduS | libs/screens/__init__.py | Python | gpl-3.0 | 83 | [
"Galaxy"
] | 0aff78a4e9362f84eb1aeed459267b8e5eb6314560713924dac258bdea36695a |
#
# MRChem, a numerical real-space code for molecular electronic structure
# calculations within the self-consistent field (SCF) approximations of quantum
# chemistry (Hartree-Fock and Density Functional Theory).
# Copyright (C) 2021 Stig Rune Jensen, Luca Frediani, Peter Wind and contributors.
#
# This file is part of... | MRChemSoft/mrchem | python/mrchem/periodictable.py | Python | lgpl-3.0 | 27,216 | [
"CRYSTAL"
] | a90a3a0d7624c196f0e9707499cdf3bdde2ed030346ba6f5723f38f5aafceed9 |
########################################################################
# File : ResourcesDefaults.py
# Author : Ricardo Graciani
########################################################################
"""
Some Helper class to access Default options for Different Resources (CEs, SEs, Catalags,...)
"""
from __futur... | yujikato/DIRAC | src/DIRAC/ConfigurationSystem/Client/Helpers/ResourcesDefaults.py | Python | gpl-3.0 | 3,129 | [
"DIRAC"
] | 98b38ce9dcfc2daecaf9c14416e351406261a66aca8665c61da4405bbc67200a |
# Copyright 2014 by Saket Choudhary. Based on test_Clustalw_tool.py by Peter
# Cock .
#
# 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.
# Last Checked with samtools [0.1.18 (r982:295)]
from Bio imp... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_samtools_tool.py | Python | gpl-2.0 | 9,966 | [
"BWA",
"Biopython"
] | 3949e0682985a8c7d108543101be47b5fc375b595ac29574a202e9b06812d080 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | jwdebelius/Machiavellian | machivellian/tests/test_power.py | Python | bsd-3-clause | 10,523 | [
"scikit-bio"
] | f7fc9e151e58fe9f7249a7eaab8fc79bdfd9e11ea9f6c30e8664688eb1515511 |
from __future__ import unicode_literals
from .common import InfoExtractor
class EngadgetIE(InfoExtractor):
_VALID_URL = r'https?://(?:www\.)?engadget\.com/video/(?P<id>[^/?#]+)'
_TESTS = [{
# video with 5min ID
'url': 'http://www.engadget.com/video/518153925/',
'md5': 'c6820d4828a506... | remitamine/youtube-dl | youtube_dl/extractor/engadget.py | Python | unlicense | 807 | [
"Galaxy"
] | 179764d4fd38a4d27502ec70cde35dd4dfcf9b480ddfa9f89f0a4d8993963195 |
import theano
import theano.tensor as T
from crop import LocallySoftRectangularCropper
from crop import Gaussian
import numpy as np
from datasets import get_cooking_streams
from datasets import get_bmnist_streams
import matplotlib
# Force matplotlib to not use any Xwindows backend.
matplotlib.use('Agg')
import matplotl... | negar-rostamzadeh/rna | test_crop.py | Python | mit | 3,244 | [
"Gaussian"
] | 332dc11a6480f2110477ebca7ac47d287cf5aee32448fb86e7df16b141ab5192 |
from ..core import Mul
from ..core.compatibility import default_sort_key
from ..functions import DiracDelta, Heaviside
def change_mul(node, x):
"""change_mul(node, x)
Rearranges the operands of a product, bringing to front any simple
DiracDelta expression.
If no simple DiracDelta expression was foun... | skirpichev/omg | diofant/integrals/deltafunctions.py | Python | bsd-3-clause | 5,793 | [
"DIRAC"
] | 5abd52c7cdece50c7f2a29f50a05dd792ec6bd639a63da6a64d19c4b3fb50fa3 |
#
# 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... | ssorj/qtools | subrepos/plano/python/plano_tests.py | Python | apache-2.0 | 31,950 | [
"Amber"
] | 1e7afbb5e8d69b83e96402b83fd2322988c63de0e6a2bcd18e1986ec4c774c60 |
"""
===========================================
Common Integral transforms and applications
===========================================
"""
from __future__ import division
from .mcfit import mcfit
from . import kernels
import numpy
from scipy.special import gamma
__all__ = ['Hankel', 'SphericalBessel', 'FourierSine'... | nickhand/pyRSD | pyRSD/extern/mcfit/transforms.py | Python | gpl-3.0 | 2,159 | [
"Gaussian"
] | e799d7c242bf1a8550dafcb34d469d5ca81fc4d4cb6e58b89effad6c300de427 |
#!/usr/bin/env python3
# -*- coding: utf8 -*-
import requests
import argparse
import pprint
import json
import sys
import re
import hmac
import time
from datetime import datetime
import os
import base64
from requests.adapters import HTTPAdapter
from requests.packages.urllib3.util.retry import Retry
HEADERS = { 'Acce... | mozilla/foundation-security-advisories | update_hof.py | Python | mpl-2.0 | 46,500 | [
"Brian"
] | c2fe1fe65e5c110feca6bbde2e9bd4e049a1b507061e934fc53ab65df9194e68 |
# pylint: disable=redefined-outer-name
"""
Tests contour.
"""
import os
from itertools import product
import numpy as np
import pytest
from pygmt import Figure
from pygmt.exceptions import GMTInvalidInput
TEST_DATA_DIR = os.path.join(os.path.dirname(__file__), "data")
POINTS_DATA = os.path.join(TEST_DATA_DIR, "points... | GenericMappingTools/gmt-python | pygmt/tests/test_contour.py | Python | bsd-3-clause | 3,786 | [
"Gaussian"
] | 20fbff94d773ca97e3890934f4457c75723257d04beab2c3e4f08582819fd13d |
'''
Created on 07/31/2014
@Ronak Shah
'''
import argparse
import sys
import time
import os.path
import stat
from subprocess import Popen
import shlex
import shutil
from datetime import date
def main():
parser = argparse.ArgumentParser(prog='Run_FreeBayes.py', description='Run FreeBayes for Long Indels & MNPS (32b... | rhshah/Exome-Pipeline | bin/Run_FreeBayes.py | Python | apache-2.0 | 5,474 | [
"BWA"
] | 986cc00a861e64de259e7d618ffc628598b7b1ffd7cb79811a94cb2e9a1ff97f |
from __future__ import print_function
import sys
import cv2
import os
import numpy as np
import cPickle as pickle
import timeit
import time
from argparse import ArgumentParser
try:
import PIL.Image as Image
except ImportError:
import Image
import chainer
from chainer import cuda, Function, gradient_check, V... | corochann/SeRanet | src/pretrain_crbm.py | Python | mit | 12,398 | [
"Gaussian"
] | 9c83df9abb82e1aa55c7b708bb38f45f89a782b081fae80ef649236b9f10593e |
from functools import *
import pandas as pd
import itertools
try:
from Bio import SeqIO, pairwise2, Phylo
except ImportError:
pass
try:
import dendropy
from dendropy import treecalc
except ImportError:
pass
from copy import deepcopy
from HLAPredCache import *
import subprocess
import tempfile
impo... | agartland/utils | seqtools.py | Python | mit | 37,732 | [
"Cytoscape"
] | c5130d73a43b444a3cf7176e2b3d7f8062ab379a8bd09858533b91135dd370f4 |
# Copyright 2020 DeepMind Technologies Limited. 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 a... | deepmind/deepmind-research | counterfactual_fairness/adult_pscf.py | Python | apache-2.0 | 23,095 | [
"Gaussian"
] | 9507a1daaad4f2f0b052187f7f693d5dd96deb304e493dc462abaf91e8676ce7 |
#!/usr/bin/env python
# encoding: utf-8
import os
import sys
from modularodm import Q
from modularodm.exceptions import ModularOdmException
from framework.auth.core import User
from website import settings
from website.app import init_app
from website.conferences.model import Conference
from datetime import datetim... | zamattiac/osf.io | scripts/populate_conferences.py | Python | apache-2.0 | 32,271 | [
"COLUMBUS"
] | cc9efed33d9390137ddd7895974dedee1c2eed14889d15a7928a8da5807b0e05 |
# -*- coding: utf-8 -*-
# MolMod is a collection of molecular modelling tools for python.
# Copyright (C) 2007 - 2019 Toon Verstraelen <Toon.Verstraelen@UGent.be>, Center
# for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights
# reserved unless otherwise stated.
#
# This file is part of MolMod.
#
#... | molmod/molmod | molmod/constants.py | Python | gpl-3.0 | 1,646 | [
"Avogadro"
] | 4ec56567745f835a1c6166e9c69ff6e326fd39e7c5d3889ec376e81bcba8621d |
from build.management.commands.base_build import Command as BaseBuild
from django.db.models import Q
from django.conf import settings
from protein.models import Protein, ProteinConformation, ProteinAnomaly, ProteinState, ProteinSegment
from residue.models import Residue
from residue.functions import dgn, ggn
from stru... | fosfataza/protwis | build_gpcr/management/commands/build_homology_models.py | Python | apache-2.0 | 254,326 | [
"CRYSTAL"
] | 8539c147f5f4184231280dab921bea1be52864ce32681f4d5fb45a5efa6319f7 |
__license__ = """
MathCaptchaByPass.py is a free script to test the bypassing of a text-based math CAPTCHA. Along with
this script you will find an ASP .NET Web Forms site to test the script against.
Author: Rich Grimes
Twitter: @saltyCoder
Copyright (C) 2014 by Rich Grimes
This ... | saltycoder/MathCaptchaByPass | MathCaptchaByPass.py | Python | gpl-3.0 | 4,607 | [
"VisIt"
] | 7ad2488d35dc5c943cd2b1230af84483ca8700f77a38244b3f0f660d28cccf64 |
"""
Tests for the Abinit workflows classes.
The tests require abipy's factories to run, so abipy should be configured and abinit available.
"""
from __future__ import print_function, division, unicode_literals, absolute_import
import os
import unittest
import abipy.data as abidata
import abipy.abilab as abilab
from a... | davidwaroquiers/abiflows | abiflows/fireworks/workflows/tests/test_abinit_workflows.py | Python | gpl-2.0 | 6,666 | [
"ABINIT"
] | aa8fd94d05b5a6aa969fd33b5faab66049fa0d952ad01ff62a762b042c861a70 |
# -*- coding: utf-8 -*-
import json
from catmaid.models import ClassInstance
from .common import CatmaidApiTestCase
class SearchApiTests(CatmaidApiTestCase):
def test_search_with_no_nodes(self):
self.fake_authentication()
response = self.client.get(
'/%d/search' % self.test_pro... | catmaid/CATMAID | django/applications/catmaid/tests/apis/test_search.py | Python | gpl-3.0 | 7,309 | [
"NEURON"
] | 9e39811a7bb91c67b8a5a227aac53ac0d598a9883db7c9792b0e1fd45aae3dc8 |
# Python3 code
# An example
import galevo
print("\n ================================\n"
" === example_galaxy_evolution ===\n"
" ================================\n")
print(" This test code serves as an example, "
"explaining (see comments in the code) the input parameters of the galaxy ... | Azeret/galIMF | example_galaxy_evolution.py | Python | gpl-3.0 | 2,473 | [
"Galaxy"
] | 963c61ecda0473055cef80c99289b460ef90436534265434a5e24de50feebbb9 |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
pick random sample
generate random permutation
distributions on the real line:
------------------------------
uniform
... | HiSPARC/station-software | user/python/Lib/random.py | Python | gpl-3.0 | 32,457 | [
"Gaussian"
] | 789798fe4bdca163ecbabb49f79ba82aa0aa0c83c05a6b84b3cf86c35b3abc92 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | dwhswenson/mdtraj | tests/test_mdconvert.py | Python | lgpl-2.1 | 7,326 | [
"MDTraj",
"NetCDF"
] | c45db8aaffaaf35af89d9b1ed70189f37a97531831225946efee3829c587d658 |
#!/usr/bin/python
#
# Copyright (C) 2015, Jaguar Land Rover
#
# This program is licensed under the terms and conditions of the
# Mozilla Public License, version 2.0. The full text of the
# Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
#
#
# Register a service specified by command line with an RVI nod... | arod155/rvi-front-end | python/fob.py | Python | mpl-2.0 | 4,294 | [
"Jaguar"
] | c523b68d0bc2e169b0671108ca2e9097a4e4b348a0347adba56d292dd3aa4917 |
import shell
import prints
import collections
import os
import re
import time
### BEGIN CONFIGURATION OPTIONS ###
# location of your itunes library
# (or whatever directory you want to recursively transfer)
ITUNES_LIBRARY = "/Users/chris/Music/iTunes/iTunes Media/Music/"
GALAXY_LIBRARY = "/sdcard/Music/" # use "adb -... | bluquar/itunes_android_nofluff | sync_music.py | Python | mit | 6,489 | [
"Galaxy"
] | a54227c5a918869355d232543af0e3c67d0318b0c78af24b7ffd708c112b77dc |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/MooseDocs/test/tree/test_page.py | Python | lgpl-2.1 | 1,142 | [
"MOOSE"
] | 56b9a8385d96477d8a9fcb4207441f93f1e251731ee6cb8a3d3a945b4d3afa88 |
# Copyright (c) 2012 - 2014 the GPy Austhors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core import GP
from .. import likelihoods
from .. import kern
from .. import util
class GPCoregionalizedRegression(GP):
"""
Gaussian Process model for heterosced... | avehtari/GPy | GPy/models/gp_coregionalized_regression.py | Python | bsd-3-clause | 1,917 | [
"Gaussian"
] | 94f44f0fcb4c8e7d075f6316f6130a2f6305de1fa310a38c4b1b156932e5380e |
#! API access to CCSD amplitudes
import numpy as np
import psi4
Ne = psi4.geometry("""
0 1
Ne 0.0 0.0 0.0
symmetry c1
""")
psi4.set_options({'basis': 'cc-pvdz', 'freeze_core': 'false'})
_, wfn = psi4.energy('ccsd', return_wfn=True, molecule=Ne)
amps = wfn.get_amplitudes()
TIjAb = amps['tIjAb'].to_array()
TIA = amp... | CDSherrill/psi4 | samples/python/cc_amps/test.py | Python | lgpl-3.0 | 3,907 | [
"Psi4"
] | 9eed00e131ba098285281c10702ac9dc98df1b866f047f48b04738c7d0a0d254 |
"""
Functions to operate on polynomials.
"""
from __future__ import division, absolute_import, print_function
__all__ = ['poly', 'roots', 'polyint', 'polyder', 'polyadd',
'polysub', 'polymul', 'polydiv', 'polyval', 'poly1d',
'polyfit', 'RankWarning']
import re
import warnings
import numpy.core.... | AustereCuriosity/numpy | numpy/lib/polynomial.py | Python | bsd-3-clause | 37,980 | [
"Gaussian"
] | 822aaa1cbbda9d8c530778bd25b5818a7bab547209d954a48137371cabf8abed |
import discord
import asyncio
import aiohttp
import os
import random
import traceback
import sys
from datetime import datetime, timedelta
from io import BytesIO, StringIO
from config import *
from settings import *
import json
import urllib.request
################## START INIT #####################
client = discord.C... | Luc1fer666/Discord_project | bot.py | Python | mit | 176,146 | [
"VisIt"
] | 5baa61d2c7ed5a1e3effb411af4cf3a5c62fae324c11a2a603a44ec999301779 |
# -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
... | vlegoff/tsunami | src/primaires/communication/editeurs/socedit/__init__.py | Python | bsd-3-clause | 6,968 | [
"ADF"
] | a7237db14125dfc52ab0ad0c50a56b6d7526891f9011625cec8f2a2373a40180 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module defines classes representing non-periodic and periodic sites.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.co... | Dioptas/pymatgen | pymatgen/core/sites.py | Python | mit | 18,056 | [
"pymatgen"
] | 2b9b39302e474fa717789a48e58ad3fc67e16faf45fecc6e787097cbcb360ee6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
==============================================================================
FusionCatcher
==============================================================================
FusionCatcher searches for novel somatic fusion genes in RNA-seq paired/single-end
reads data prod... | ndaniel/fusioncatcher | bin/fusioncatcher.py | Python | gpl-3.0 | 801,064 | [
"BWA",
"Biopython",
"Bowtie"
] | 14fa4cc51324b66c4d847e53fe92024b011e5c1230eda33bea09a6cbbc931048 |
../../../../../../../share/pyshared/orca/scripts/toolkits/Gecko/script.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/toolkits/Gecko/script.py | Python | gpl-3.0 | 73 | [
"ORCA"
] | 56637d5b6e63b71a6c44d99e51896d00eac50df6f6053ffb4fee30f323436763 |
# -*- coding: utf-8 -*-
"""
=================================
Plot graphs' barycenter using FGW
=================================
This example illustrates the computation barycenter of labeled graphs using FGW
Requires networkx >=2
.. [18] Vayer Titouan, Chapel Laetitia, Flamary R{\'e}mi, Tavenard Romain
and C... | rflamary/POT | examples/plot_barycenter_fgw.py | Python | mit | 6,357 | [
"Gaussian"
] | efd33d1bee93cb577a4f40b0e3dd15fb170faff252e522c9a3597da9f6dd9bdd |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import os
import tempfile
import shutil
from pymatgen.util.testing import PymatgenTest
from monty.functools import lazy_property
from pymatgen.... | aykol/pymatgen | pymatgen/io/abinit/tests/test_flows.py | Python | mit | 10,970 | [
"ABINIT",
"pymatgen"
] | ee8e5b849a2a5c6d6155fb2a2e456ee5dfd98af675b8890941f6662b23b31d1e |
# -*- coding: utf-8 -*-
# This file is part of Shoop.
#
# Copyright (c) 2012-2016, Shoop Ltd. All rights reserved.
#
# This source code is licensed under the AGPLv3 license found in the
# LICENSE file in the root directory of this source tree.
import re
from ast import BinOp, Mod, parse
from six import text_type
impo... | akx/shoop | _misc/ensure_unicode_literals.py | Python | agpl-3.0 | 3,600 | [
"VisIt"
] | 4ab03fb022ee855296d6d4284ba25bded95a82c7d185751236a201d8c77f3a05 |
import sys
import numpy as np
import numpy.linalg as npl
from eric.molecule import Molecule
from eric.utils import print_mat
np.set_printoptions(precision=8, linewidth=200, suppress=True)
def getargs():
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--stub', default="h2o_sto... | berquist/programming_party | eric/project3/project3.py | Python | mpl-2.0 | 10,708 | [
"Q-Chem"
] | 618e75ebcf5b806ac440c2f04f36f27440c7a759d72839cf99969d6585101fd0 |
# creates: a1.png a2.png a3.png cnt1.png cnt2.png gnr1.png gnr2.png
from ase.io import write
from ase.lattice import bulk
from ase.structure import nanotube, graphene_nanoribbon
import numpy as np
for i, a in enumerate([
bulk('Cu', 'fcc', a=3.6),
bulk('Cu', 'fcc', a=3.6, orthorhombic=True),
bulk('Cu', 'fcc... | grhawk/ASE | tools/doc/ase/structure.py | Python | gpl-2.0 | 1,298 | [
"ASE"
] | 7cad5537c40432e00f5cc6ddf0096c4d13f9cd3fce36b92d674e02632dc3087c |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-get-proxy
# Author : Stuart Paterson
########################################################################
"""
Retrieve a delegated proxy for the given user and group
"""
from __future__ import p... | petricm/DIRAC | FrameworkSystem/scripts/dirac-admin-get-proxy.py | Python | gpl-3.0 | 4,433 | [
"DIRAC"
] | 3d706458477e411fddf682efee54810601b853d9df8bc56a8876b3ffc7e47d03 |
"""
Load and save a set of chosen implementations.
@since: 0.27
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import os
from zeroinstall import _, zerostore
from zeroinstall.injector import model
from zeroinstall.injector.policy import get_deprecated_singlet... | res2k/0install | zeroinstall/injector/selections.py | Python | lgpl-2.1 | 16,010 | [
"VisIt"
] | 08383e725e0028e904c3567b2dfa61020eff9ec377359f6a5b66ab0475affc94 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... | GoogleCloudPlatform/k8s-multicluster-ingress | vendor/k8s.io/kubernetes/cluster/juju/layers/kubernetes-worker/reactive/kubernetes_worker.py | Python | apache-2.0 | 38,495 | [
"CDK"
] | 519b3bc78c8b1bdd5bc3c3f0e83671d38e7565a61ac3254849bad27e4ebde834 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A. Beauchamp, TJ Lane, Jo... | swails/mdtraj | mdtraj/core/trajectory.py | Python | lgpl-2.1 | 78,389 | [
"Amber",
"CHARMM",
"Desmond",
"Gromacs",
"LAMMPS",
"MDTraj",
"NAMD",
"NetCDF",
"OpenMM"
] | 6db7d284468f5255fbf6ef8843e34d9d1a83c8d8900263553abe1f4c3c158c82 |
"""
(c) RIKEN 2017. All rights reserved.
Author: Keitaro Yamashita
This software is released under the new BSD License; see LICENSE.
"""
from yamtbx.dataproc.auto.multi_merging.resolve_reindex import KabschSelectiveBreeding
from yamtbx.util import read_path_list
from libtbx.utils import multi_out
import iotbx.phil
i... | keitaroyam/yamtbx | yamtbx/dataproc/auto/command_line/multi_determine_symmetry.py | Python | bsd-3-clause | 4,678 | [
"CRYSTAL"
] | 8fd004b42a9f1a1f6a1326803491993b032001f3672ca78d197d81a418a2f294 |
### FEATURE VECTORS ###
"""
From Wei's paper, we know natural log of volume (lnV), energy per atom (Ec),
elemental weighted average of atomic number (AlnZ), and elemental weighted
std deviation of electronegativity (SX) correlate relatively strongly to
bulk modulus (K).
Feature vectors that utilize these ... | mp-interns/eratosthenes | neigh/featurevectors.py | Python | bsd-2-clause | 2,684 | [
"pymatgen"
] | 68ad110b47c55c9d7e1bd6255e25d347ce42c266a2895c8015e9c263a18ebb29 |
#
#
# File to generate network for execution on parallel NEURON
# Note this script has only been tested with UCL's cluster!
#
# Author: Padraig Gleeson
#
# This file has been developed as part of the neuroConstruct project
# This work has been funded by the Medical Research Council and the
# Wellco... | pgleeson/TestArea | models/Parallel/pythonScripts/Big_Data.py | Python | gpl-2.0 | 6,552 | [
"NEURON"
] | e6a660044e70823e468ebdcfaa180d0cc3fb708a1222e98d48304400b5d00095 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# Stephen Fromm <sfromm@gmail.com>
# Brian Coca <briancoca+dev@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 publish... | ramondelafuente/ansible | lib/ansible/plugins/action/assemble.py | Python | gpl-3.0 | 6,337 | [
"Brian"
] | 261b1bc376a65de30503fbd75bcfb6a869127063b5f71878148f1ff70b2ecc0d |
import src
class GlassCrystal(src.items.Item):
"""
"""
type = "GlassCrystal"
name = "glass crystal"
description = "a fraction of something bigger"
walkable = True
bolted = False
def __init__(self):
"""
set up internal state
"""
super().__init__(display... | MarxMustermann/OfMiceAndMechs | src/itemFolder/resources/glassCrystal.py | Python | gpl-3.0 | 579 | [
"CRYSTAL"
] | 47732277a161aaaa1021a1d8be8d1604b2083d5e045132361d40250574d7b3e8 |
#!/usr/bin/python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Tools for constructing OpenMM System objects from various convenient input file formats... | luirink/yank | Yank/systembuilder.py | Python | lgpl-3.0 | 44,764 | [
"MDTraj",
"OpenMM"
] | 98e90d9c73f510e8c1454119a7a741170373441a3c96662822249bd93fc60be6 |
import ast
import os
import pathlib
import pytest
from vulture import utils
class TestFormatPath:
@pytest.fixture
def tmp_cwd(self, tmp_path, monkeypatch):
cwd = tmp_path / "workingdir"
cwd.mkdir()
monkeypatch.chdir(cwd)
return cwd
def test_relative_inside(self):
... | jendrikseipp/vulture | tests/test_utils.py | Python | mit | 2,812 | [
"VisIt"
] | 40cba9d51bd2e35c1dfe79a0586bc276ca17aaa4f4817e2ec4bd3198dfc7d0f1 |
"""Quality control and summary metrics for next-gen alignments and analysis.
"""
import collections
import copy
import csv
import os
import yaml
from datetime import datetime
import pandas as pd
import glob
import toolz as tz
from bcbio import bam
from bcbio import utils
from bcbio.cwl import cwlutils
from bcbio.log... | lbeltrame/bcbio-nextgen | bcbio/pipeline/qcsummary.py | Python | mit | 17,471 | [
"Galaxy"
] | ec974f5b9105a0bb834264f2210837ef8955ee76fdee6b36eeead3ef1b5ee70f |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | ghislainp/iris | lib/iris/tests/test_io_init.py | Python | gpl-3.0 | 5,591 | [
"NetCDF"
] | 6d393c40c89bb47eb46330e51a47cdeee582cf933658473694329ba668dc84aa |
"""
Class for outlier detection.
This class provides a framework for outlier detection. It consists in
several methods that can be added to a covariance estimator in order to
assess the outlying-ness of the observations of a data set.
Such a "outlier detector" object is proposed constructed from a robust
covariance es... | shikhardb/scikit-learn | sklearn/covariance/outlier_detection.py | Python | bsd-3-clause | 6,856 | [
"Gaussian"
] | 63f02484b5c19293512c35e0d988a822d8a5bef8bbb24b8cb2dfb5586a03ecca |
##
# Copyright 2009-2015 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | ULHPC/modules | easybuild/easybuild-easyblocks/easybuild/easyblocks/o/openfoam.py | Python | mit | 12,010 | [
"ParaView"
] | 194c9774bc16e9211bf35a6857b74320dc5133a0879031462a46dbf5fc927d4d |
#!/usr/bin/env python
# This example shows how to apply an vtkImageData texture to an plane
# vtkPolyData object.
# Note: Input jpg file can be located in the VTKData repository.
#
# @author JBallesteros
##
import vtk
jpegfile = "earth_display.jpg"
# Create a render window
ren = vtk.vtkRenderer()
renWin = vtk.vtkRe... | nicjhan/mom-particles | vtk/plane.py | Python | gpl-2.0 | 1,219 | [
"VTK"
] | d766e8d7c7c0dca5bbe6e53d9125661e30dc6188c35613ac5348ac6f0c2935fa |
#!/home/epicardi/bin/python27/bin/python
# Copyright (c) 2013-2014 Ernesto Picardi <ernesto.picardi@uniba.it>
#
# 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 ... | RNAEDITINGPLUS/main | node/reditools-1.0.4/reditools/FilterTable.py | Python | apache-2.0 | 5,006 | [
"pysam"
] | 0444e190b0137f9ad8aa2763ddc5f6c5673ff482cb9a2fa8f73e7d4eb80fd6a8 |
#! /usr/bin/env python
#
# raster_plot.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
... | gewaltig/cython-neuron | pynest/nest/raster_plot.py | Python | gpl-2.0 | 6,848 | [
"NEURON"
] | 4db8c520071fbf036d9b24a73b76aa934c77887c0b14c7b16fe91e05c7e3dc95 |
from PLC.Faults import *
from PLC.Method import Method
from PLC.Parameter import Parameter, Mixed
from PLC.Auth import Auth
from PLC.Table import Row
from PLC.Persons import Person, Persons
from PLC.sendmail import sendmail
from PLC.TagTypes import TagTypes
from PLC.PersonTags import PersonTags, PersonTag
from PLC.Name... | dreibh/planetlab-lxc-plcapi | PLC/Methods/UpdatePerson.py | Python | bsd-3-clause | 5,165 | [
"VisIt"
] | 01c146db508ac8857d8dc563dcd023932c3e47a827bb061574735aa9d3d5424b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vtk
def main():
# Create five points.
origin = [0.0, 0.0, 0.0]
p0 = [1.0, 0.0, 0.0]
p1 = [0.0, 1.0, 0.0]
p2 = [0.0, 1.0, 2.0]
p3 = [1.0, 2.0, 3.0]
# Create a vtkPoints object and store the points in it
points = vtk.vtkPoints()
... | lorensen/VTKExamples | src/Python/GeometricObjects/LongLine.py | Python | apache-2.0 | 1,952 | [
"VTK"
] | 77f23998ca10788900172e9e3c4e1d1a6044058293a875a5d89324d8b8b69d78 |
"""
Some basic routines to fit models
"""
from pyosci import tools
from pyosci import plotting as plt
from pyevsel.fitting import gauss, Model
from functools import reduce
import pylab as p
import numpy as np
import dashi as d
import seaborn.apionly as sb
d.visual()
from collections import namedtuple
from . impo... | achim1/pmttools | pmttools/fit_routines.py | Python | gpl-3.0 | 8,148 | [
"Gaussian"
] | b7e7d67ec2b7a4f7a7d9d990c9313a6aff4963904df82ca64a45fbce5d6d0d00 |
import os
import sys
from os.path import basename
from tarfile import is_tarfile
from zipfile import is_zipfile
from ase.atoms import Atoms
from ase.units import Bohr
from ase.io.trajectory import PickleTrajectory
from ase.io.bundletrajectory import BundleTrajectory
__all__ = ['read', 'write', 'PickleTrajectory', 'Bu... | slabanja/ase | ase/io/__init__.py | Python | gpl-2.0 | 15,788 | [
"ASE",
"CRYSTAL",
"FHI-aims",
"GPAW",
"Mayavi",
"NetCDF",
"TURBOMOLE",
"VASP",
"VTK",
"WIEN2k",
"exciting"
] | 5e49e86cfcab7defe4b108ac8f4254b00e61601c71096e04593055937208b670 |
from verce.processing import *
import socket
import traceback
import os
import json
class specfemGlobeRunSolverMov(SeismoPreprocessingActivity):
def compute(self):
stdoutdata = None
stderrdata = None
if self.parameters["mpi_invoke"] == 'mpiexec.hydra' or self.parameters["mpi_invoke"] =... | KNMI/VERCE | verce-hpc-pe/src/specfemGlobeRunSolverMov.py | Python | mit | 7,287 | [
"VTK"
] | 576c1a6b60114328496dcd99a8a07af731f46565cebec1c648f6f8d795e846a8 |
#!/usr/bin/python
import argparse
import ConfigParser
import os
import sys
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] )
sys.path = new_path
from galaxy import eggs
eggs.require( "SQLAlchemy >= 0.4" )
import galaxy.webapps.tool_shed.model.mapping as tool_shed_model
from sqlalchemy.... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py | Python | gpl-3.0 | 4,745 | [
"Galaxy"
] | f6f1071aefb9d18f37722285ce10df369adb84dfa21078f78b158c73a4f226f2 |
#!/usr/bin/env python3
# -*-coding:Utf-8 -*
"""Use MCMC to find the stellar mass halo mass relation.
Based on the Behroozi et al 2010 paper.
Use a parametrization of the SHMR, plus a given HMF to find the expected SMF and compare it
to the observed SMF with its uncertainties using a likelihod maximisation.
Started o... | Gorbagzog/StageIAP | MCMC_SHMR.py | Python | gpl-3.0 | 7,470 | [
"Gaussian"
] | 9ff273a0903f01a5dba0fbdb39cc2bee49c828cdae1d7f4e1188584bdd4a69c0 |
# -*- coding: utf-8 -*-
{
"'Cancel' will indicate an asset log entry did not occur": "'Hủy' sẽ chỉ dẫn một lệnh nhập không thực hiện được",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that has a boundary for ... | gallifrey17/eden | languages/vi.py | Python | mit | 373,313 | [
"VisIt"
] | 1cdc7c0136ecca5506795f641172dee39567a824eb92f0b87c8357c3bb46d6de |
#!/usr/bin/env python
import pylab as pyl
import cPickle as pickle
from astLib import astCalc
def plot_icd_vs_mass():
galaxies = pickle.load(open('galaxies.pickle','rb'))
galaxies = filter(lambda galaxy: 0.06 * galaxy.halflight *\
astCalc.da(galaxy.z)*1000/206265. > 2, galaxies)
# Make figure
... | boada/ICD | sandbox/plot_icd_mass_box_width.py | Python | mit | 6,289 | [
"Galaxy"
] | 18bcc6401644d408d4c9fef2bbde7e3b9d7971f20facbf5905f5fa876a9814cc |
from ase import Atoms, Atom
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize.test import run_test
name = 'N2Cu'
def get_atoms_surf():
a = 2.70
c = 1.59 * a
h = 1.85
d = 1.10
slab = Atoms('2Cu', [(0., 0., 0.), (1/3., 1/3., -0.5*c)],
tags=... | grhawk/ASE | tools/ase/optimize/test/N2Cu_relax.py | Python | gpl-2.0 | 4,291 | [
"ASE"
] | 60650b9ecb43fee91f8000d43098a050b585f0e903161718761dfcba068cffa1 |
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