text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
An LFPy example file showing how cells can be run in parallel using MPI.
To run using MPI with 4 cpu cores, issue in terminal
openmpirun -np 4 python example_mpi.py
The example uses mpi4py with openmpi, and do not rely on NEURON's MPI
implementation.
Execution:
<... | LFPy/LFPy | examples/example_mpi.py | Python | gpl-3.0 | 14,433 | [
"NEURON"
] | de24824f581a604cd20c5f906bca0a27454a4e159e64929b775694604d200395 |
"""
CIS is an open source command-line tool and Python library for easy collocation, visualization, analysis, and
comparison of diverse gridded and ungridded datasets used in the atmospheric sciences.
.. note ::
The CIS documentation has detailed usage information, including a :doc:`user guide <../index>`
for... | cedadev/jasmin_cis | cis/__init__.py | Python | gpl-3.0 | 5,022 | [
"NetCDF"
] | 297fdeb6d00b49a2cfa5efee9f6fa4b820f3824aacff1309edb8ede4cc7ad732 |
# creates: Al_phonon.png Al_mode.gif Al_mode.pdf
from ase.lattice import bulk
from ase.calculators.emt import EMT
from ase.dft.kpoints import ibz_points, get_bandpath
from ase.phonons import Phonons
# Setup crystal and EMT calculator
atoms = bulk('Al', a=4.05)
calc = EMT()
# Phonon calculator
N = 6
ph = Phonons(atom... | grhawk/ASE | tools/doc/ase/phonons.py | Python | gpl-2.0 | 2,330 | [
"ASE",
"CRYSTAL"
] | 75547e62e211c7f46bfeb5249c352ff33efb6a971d9b4ef5dd5f0a340bafd7ed |
# 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/.
"""
Sile object for reading/writing Wannier90 in/output
"""
from pathlib import Path
import numpy as np
from scipy.spars... | zerothi/sisl | sisl/io/wannier90/seedname.py | Python | mpl-2.0 | 11,524 | [
"Wannier90"
] | 0e81dfc15dbb41d508899429c09a95e458dbe5c06a2e60c623c370c3cde5dc3d |
"""Bandstructure exercise
Calculate the band structure of Na along the Gamma-X direction.
"""
from gpaw import GPAW, FermiDirac
from ase import Atoms
a = 4.23
atoms = Atoms('Na2',
[(0, 0, 0),
(0.5 * a, 0.5 * a, 0.5 * a)],
pbc=True, cell=(a, a, a))
# Make self-consistent cal... | qsnake/gpaw | doc/tutorials/bandstructures/bandstructure.py | Python | gpl-3.0 | 1,286 | [
"ASE",
"GPAW"
] | 7fde78204b1733b9cd6eed270bc74b58b48a411508cf3f5c74f125b8d82389fe |
import ujson as json
import requests
import time
import logging
import sys
import os
import os.path
import yaml
import logging
import traceback
import select
from pprint import pprint
from cifsdk.format import factory
from argparse import ArgumentParser
from argparse import RawDescriptionHelpFormatter
import textwrap... | aeppert/py-cifsdk | cifsdk/client.py | Python | lgpl-3.0 | 9,982 | [
"Amber"
] | 0c896819e196836f3a84a9994cd63277e35150567447b48294cf3ae7d9283b99 |
'''test methods related to Red Hat Enterprise Linux, e.g. entitlement'''
from behave import *
import ConfigParser
import re
from distutils.version import LooseVersion
config = ConfigParser.ConfigParser()
config.read('config/uat.cfg')
rh_gpg_fingerprint = '567E 347A D004 4ADE 55BA 8A5F 199E 2F91 FD43 1D51'
rh_gpg_fin... | miabbott/UATFramework | steps/redhat.py | Python | gpl-2.0 | 13,774 | [
"VisIt"
] | bf4edadd9fce97785a644a734c207719fd73fdd68f1f15280e1f755aef5865e6 |
#
# @BEGIN LICENSE
#
# QCDB: quantum chemistry common driver and databases
#
# Copyright (c) 2011-2017 The QCDB Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of QCDB.
#
# QCDB is free software; you can redistribute it and/or modify
# it ... | loriab/qcdb | qcdb/libmintsbasissetparser.py | Python | lgpl-3.0 | 12,757 | [
"Gaussian",
"Psi4"
] | ccd10f8737d764cc5a773a6a89792c6b2b0014be54960cd3d274537fd81af4e8 |
"""
wc_server v0.01
web client server
Copyright 2011 Brian Monkaba
This file is part of ga-bitbot.
ga-bitbot is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
... | matthusby/ga-bitbot | wc_server.py | Python | gpl-3.0 | 5,062 | [
"Brian"
] | a7ae12fbbf261237443b04772042493b547961d3c8011e37811350fd0bd2e3b9 |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | devel/external/test_cf/test_cf_convolution_detailed.py | Python | gpl-3.0 | 28,995 | [
"Galaxy"
] | 3b8e54bf4ea211ee3313426ccbb97b430f72f86cc2e94682b66b3adedccf7976 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/movielisthtml.py | Python | gpl-2.0 | 6,726 | [
"VisIt"
] | 2018437741252d6ff27c81bda2dd29ecdaf481c10a678c7c8de95fd685bcc1f3 |
""" Test functions for stats module
"""
from __future__ import division, print_function, absolute_import
import warnings
import re
import sys
from numpy.testing import (TestCase, run_module_suite, assert_equal,
assert_array_equal, assert_almost_equal, assert_array_almost_equal,
assert_allclose, assert_, asse... | mortonjt/scipy | scipy/stats/tests/test_distributions.py | Python | bsd-3-clause | 83,633 | [
"Gaussian"
] | 86cfdceec6325cae2f5b345425f0f3deeb8eb0187aaeb1a0764a8fc5cb6537e9 |
#!/usr/bin/python
"""Test of learn mode."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
sequence.append(KeyPressAction(0, None, "KP_Insert"))
sequence.append(KeyComboAction("h"))
sequence.append(KeyReleaseAction(0, None, "KP_Insert"))
sequence.append(utils.StartRecordingAction())
sequen... | h4ck3rm1k3/orca-sonar | test/keystrokes/gtk-demo/learn_mode.py | Python | lgpl-2.1 | 2,871 | [
"ORCA"
] | 75b4f35316ecb3147ac5b2b637941c792764268b1f899bef4c96e0666bab176b |
"""
Viewing Stanford 3D Scanning Repository lucy model
"""
# Copyright (c) 2014-2015, Enthought, Inc.
# Standard library imports
import os
from os.path import join
# Enthought library imports
from mayavi import mlab
### Download the lucy data, if not already on disk ############################
if not os.path.exists(... | dmsurti/mayavi | examples/mayavi/mlab/lucy.py | Python | bsd-3-clause | 1,073 | [
"Mayavi"
] | 906944e6f55233653199b987311aaa66bdb986610e32d4be2827537c7f996a00 |
# -*- coding: utf-8 -*-
"""
Generate centreline and write it out as .vtk legacy format.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Import path for the CentrelineGenerator script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__), '../... | BlueFern/DBiharMesher | meshes/c8000/Generate8000Centreline.py | Python | gpl-2.0 | 978 | [
"VTK"
] | f7c529e6b129546eb4d4c290fe5300e249ca12cadf145bbf563faa156e37c39a |
# $Id$
# Hop --- a framework to analyze solvation dynamics from MD simulations
# Copyright (c) 2009 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... | iwelland/hop | hop/utilities.py | Python | lgpl-3.0 | 31,715 | [
"MDAnalysis"
] | c6b13669a7b82782602c6f1cff1c0e2f405af7458b32414f34656dcfdb1f2daf |
import os
import sys
import time
import click
import pkg_resources
from livereload import Server, shell
from . import Yass, publisher
from .yass import PAGE_FORMAT
from .__about__ import *
CWD = os.getcwd()
TPL_HEADER = """
---
title: Page Title
description: Page Description
meta:
key: value
---
"""
TPL_BODY ... | mardix/yass | yass/cli.py | Python | mit | 10,078 | [
"VisIt"
] | 0e7921b47c4e6a97e979d2076f11351d267cd2dbd0ed0e76e518912c98c9f873 |
# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
import tempfile
import time
import re
import sys
from contextlib import contextmanager
from selenium.common.exceptions import NoSuchEle... | myself659/splinter | splinter/driver/webdriver/__init__.py | Python | bsd-3-clause | 22,042 | [
"VisIt"
] | ee3a57c4500b60ffe5e4db3d65185937c490230ef97a77775b5c90d47287247b |
#!/usr/bin/env python
"""
Created on Tue Jul 22 16:18:21 2014
@author: Bodangles
"""
from __future__ import print_function
import sys
import warnings
import pickle
import yaml
from six.moves.configparser import ConfigParser
import tables
import scipy as sp
import scipy.fftpack as scfft
import scipy.signal as scisig
im... | jswoboda/SimISR | SimISR/utilFunctions.py | Python | mit | 32,608 | [
"Gaussian"
] | f214dc6104a2ab9be61a6ce096025245782ef19adabcc427cb005abde8cd34f5 |
#!/usr/local/bin/env python
"""
Test replica-exchange facility repex.py using analytically soluble models.
DESCRIPTION
This test suite generates a number of analytically soluble harmonic oscillator models to test
the simulation algorithms defined in the 'repex' replica exchange facility.
COPYRIGHT
Written by John ... | choderalab/brokenyank | tests/repex-tests.py | Python | lgpl-3.0 | 9,960 | [
"NetCDF",
"OpenMM"
] | fa05fc60df11212720c86a8a6798cad8ecc983de1e25adff36a086118e998a58 |
from __future__ import print_function
from __future__ import absolute_import
from .DataTestTemplate import _DataTest
from owmeta.muscle import Muscle
from owmeta.neuron import Neuron
class MuscleTest(_DataTest):
ctx_classes = (Muscle, Neuron)
def test_muscle(self):
self.assertTrue(isinstance(Muscle... | openworm/PyOpenWorm | tests/MuscleTest.py | Python | mit | 960 | [
"NEURON"
] | 0dfadacdba2de60dd72fba27edf12098c164b84635a317723a5730ad03f444a4 |
from src.constant.Number import Number
from src.modifier.Modifier import Modifier
from src.operator.Operator import Operator
from src.roll.Diceroll import Diceroll
from src.roll.Keep import Keep
from src.roll.Reroll import Reroll
from src.visitor.NodeVisitor import NodeVisitor
class ValueCheckVisitor(NodeVisitor):
... | charleshamel73/diceroller | src/visitor/ValueCheckVisitor.py | Python | mit | 1,338 | [
"VisIt"
] | 8a7ae484e4cd11f74fa2fc22b40be6908d9585a6b060cb2905640c1f7983668b |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | psci2195/espresso-ffans | testsuite/scripts/samples/test_electrophoresis.py | Python | gpl-3.0 | 1,729 | [
"ESPResSo"
] | 78a0b57ef835914e45f748634f37c4e22f5b940080820a2e4ff4fd96c956c663 |
from .distribution import Distribution
from .gaussian import GaussianDistribution, GaussianDiagonalDistribution, \
GaussianCholeskyDistribution
__all__ = ['Distribution',
'GaussianDistribution', 'GaussianDiagonalDistribution',
'GaussianCholeskyDistribution']
| carloderamo/mushroom | mushroom_rl/distributions/__init__.py | Python | mit | 286 | [
"Gaussian"
] | fc7e5f3e02cc369c3d0419c19d066faffea15bc1cc03eb9065cf3cd18e2557a3 |
# -*- coding: utf-8 -*-
# Copyright (C) 2014-present Taiga Agile LLC
#
# 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 ver... | taigaio/taiga-back | tests/integration/test_users.py | Python | agpl-3.0 | 43,273 | [
"VisIt"
] | e1301b24a0136c99f7ac5c330556e7dd215b282abc1cec4ad6ca4aee68e31f44 |
"""
soap1.py
A wrapper script for SOAP1
Copyright Peter Li peter@gigasciencejournal.com
"""
import sys, optparse, os, tempfile, shutil, subprocess
def stop_err(msg):
sys.stderr.write('%s\n' % msg)
sys.exit()
def cleanup_before_exit(tmp_dir):
if tmp_dir and os.path.exists(tmp_dir):
shutil.rmtree(t... | gigascience/galaxy-bgisoap | tools/soap1/soap1_wrapper.py | Python | gpl-3.0 | 5,209 | [
"Galaxy"
] | ccd7dd46ac8ffb3940f07adc256b1f8a38b282a77162943d4a460b17c865f859 |
from __future__ import print_function
from .mtuple import *
import re
import csv
import operator
import sys
import itertools
#### Function definitions ####
def make_ignores_list(ic):
"""Make a list from a string of read positions that are to be ignored. Input should be 1-based co-ordinates and these are converted... | PeteHaitch/methtuple | methtuple/funcs.py | Python | mit | 36,645 | [
"BWA",
"pysam"
] | 7450875a697706d05636ebfa485a802177e83381f26aad0893594229e2c5f403 |
"""Test the dirac-transformation-replication script and helper"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
from mock import MagicMock as Mock, patch
from DIRAC import S_OK, S_ERROR
from DIRAC.TransformationSystem.Utilities.Replicati... | ic-hep/DIRAC | src/DIRAC/TransformationSystem/test/Test_replicationTransformation.py | Python | gpl-3.0 | 10,957 | [
"DIRAC"
] | b50922c0fb4215efd591c744aea0ff34d40744bf43a4bf0dc12ed820af675847 |
# (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... | fossilet/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 19,533 | [
"Galaxy",
"MOOSE"
] | 5c9eadab2470d2e2cc83a3d79e638057a1234de58f55fd975340bc68681f4aa6 |
"""
Plotting utilities for Bayesian hidden Markov models.
"""
import matplotlib
# Force matplotlib to not use any Xwindows backend.
matplotlib.use('Agg')
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from bhmm import GaussianOutputModel
__author__ = "John D. Chodera, Frank Noe"
__copyrigh... | bhmm/legacy-bhmm-force-spectroscopy-manuscript | examples/plots.py | Python | lgpl-3.0 | 7,013 | [
"Gaussian"
] | 359b9098435e6d15544f46c74f5348425e17185d059940cbbd1d8333a76faf5e |
import numpy as np
import numpy.testing as npt
from dipy.data import get_fnames
from dipy.sims.voxel import add_noise
from dipy.segment.mrf import (ConstantObservationModel,
IteratedConditionalModes)
from dipy.segment.tissue import (TissueClassifierHMRF)
# Load a coronal slice from a T1-... | FrancoisRheaultUS/dipy | dipy/segment/tests/test_mrf.py | Python | bsd-3-clause | 16,036 | [
"Gaussian"
] | 79ef03e8dc95cf42086304a6cee9fc864a8f31d77d30dad7a47aaeb51f9dbc59 |
#!/usr/bin/env python
"""
Default--uses the Gaussian Naive Bayes classifier
"""
from api import State, util
import random, os
from sklearn.externals import joblib
DEFAULT_MODEL = os.path.dirname(os.path.realpath(__file__)) + '/gnb-rand-model.pkl'
# DEFAULT_MODEL = os.path.dirname(os.path.realpath(__file__)) + '/gnb... | GreenGear5/planet-wars | bots/ml-gnb/ml-gnb.py | Python | mit | 4,388 | [
"Gaussian"
] | 16d7c305699c6751a0856d3c72c1c3e5295834f37597aaac85daaec37e379c96 |
"""Receives Android tablet input data transmitted via UDP
by the GfxTablet Android app and pushes it to WebSocket client.
GfxTablet: https://github.com/rfc2822/GfxTablet
"""
import logging
import socket
from tornado.websocket import WebSocketHandler
from tornado.ioloop import IOLoop
from tornado.web import Applicatio... | jzitelli/GfxTablet.js | GfxTablet.py | Python | mit | 2,603 | [
"Galaxy"
] | fbe8925debb6437a3b36e230877853cd178e292f923b63ccfd0846a379136c0d |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Test a markdown source for ISMRM abstracts submission constraints.
This is optimized for 2019 abstracts.
Note: only Python is required, but optional features may be unavailable.
For colored messages, install the `blessed` or `blessings` Python package
(both are avail... | norok2/honolulu_abstract | ismrm_abstract/ismrm_abstract.py | Python | gpl-3.0 | 41,524 | [
"ASE"
] | 9d280682f04042e864e4a5bd7226fe43a925ae0c8b8a7e71ca5198c778cdf6bf |
# sql/elements.py
# Copyright (C) 2005-2021 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: https://www.opensource.org/licenses/mit-license.php
"""Core SQL expression elements, including :class:`_expression.ClauseElement`,
:cla... | zzzeek/sqlalchemy | lib/sqlalchemy/sql/elements.py | Python | mit | 180,066 | [
"VisIt"
] | 4ce865353be5cc515bbf35b0e4b2b9359efaa97bf8d0081e47a1a63e1760ce9f |
#!/usr/bin/python
#-*- coding: utf-8 -*-
# Copyright (C) 2015, Nikolai Chernikov <nikolai.chernikov.ru@gmail.com>
#
# "convert2ugrid" is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License v3+. "convert2ugrid" is distributed in the
# hope that it will be use... | cdd1969/convert2ugrid | lib/create_uGrid_netcdf.py | Python | gpl-3.0 | 19,968 | [
"NetCDF"
] | a4d30409537b0a1cac9649c761627eb9706ad6081aeb460e31e244d8cc76bb6b |
#!/usr/bin/python
#
# Copyright (c) 2017 Ansible Project
#
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
ANSIBLE_METADATA = {'metadata_version': '1.1',
'status': ['preview'],
'supported_by': 'community'}
DOCUMENTATION = """
---
mod... | photoninger/ansible | lib/ansible/modules/cloud/amazon/elasticache.py | Python | gpl-3.0 | 20,791 | [
"Dalton"
] | 788f6816c0c031e57eaf5f5056250b3d57e8b461a7ae9d30f8fcd49abbedb908 |
import unittest
import numpy as np
import matplotlib.pylab as plt
import sys
sys.path.append('../ceviche')
from ceviche import fdtd
class TestFields_FDTD(unittest.TestCase):
""" Tests the field patterns by inspection """
def setUp(self):
# basic simulation parameters
self.Nx = 80
se... | fancompute/ceviche | tests/test_fields_fdtd.py | Python | mit | 2,320 | [
"Gaussian"
] | 0562b2c5566dcd3f984e5ae1d3afdc07e6fdb9436b81de385f137cfc026aea5b |
from cdo import Cdo
from tempfile import mkstemp
import os
from flyingpigeon.utils import drs_filename, get_variable, calc_grouping , sort_by_filename
from flyingpigeon import config
import logging
logger = logging.getLogger(__name__)
DIR_MASKS = config.masks_dir()
DIR_SHP = config.shapefiles_dir()
def countries():... | sradanov/flyingpigeon | flyingpigeon/subset.py | Python | apache-2.0 | 10,305 | [
"NetCDF"
] | c0bc323c4305527fc11733cd8174d705665e63de1e74b6def30a756ac790a033 |
"""
Course Outline page in Studio.
"""
import datetime
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise
from selenium.webdriver.support.ui import Select
from selenium.webdriver.common.keys import Keys
from .course_page import CoursePage
from .container import ContainerPage
from .... | xuxiao19910803/edx | common/test/acceptance/pages/studio/overview.py | Python | agpl-3.0 | 25,466 | [
"VisIt"
] | aa77de4d32e845a026709fdcde1a7a7f3e1eb9a67ec513e0afb100c2fdfff079 |
# pylint: disable=C0111
# pylint: disable=W0621
import urllib
from lettuce import world
from django.contrib.auth.models import User
from student.models import CourseEnrollment
from xmodule.modulestore.django import modulestore, clear_existing_modulestores
from xmodule.contentstore.django import _CONTENTSTORE
@world.... | c0710204/edx-platform | common/djangoapps/terrain/course_helpers.py | Python | agpl-3.0 | 2,494 | [
"VisIt"
] | 6db65e89b9b1fd8948230cb5f81f2acf84fd65c8a90248a6a5c9981a98f3bb3f |
# """Honeybee PointGroup and TestPointGroup."""
from __future__ import division
from ..vectormath.euclid import Point3, Vector3
from ..schedule import Schedule
from collections import defaultdict, OrderedDict
try:
from itertools import izip as zip
except ImportError:
# python 3
pass
import types
import copy... | ladybug-tools/honeybee | honeybee_plus/radiance/analysispoint.py | Python | gpl-3.0 | 37,750 | [
"ASE"
] | c2ce8c4fe3e60e2f4b464ca5d408526d01304abf1b89a54eae58de73f38a6152 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""This package implements basic input and output capabilities for Abinit."""
from .netcdf import * # noqa
from .pseudos import * # noqa
| gmatteo/pymatgen | pymatgen/io/abinit/__init__.py | Python | mit | 249 | [
"ABINIT",
"NetCDF",
"pymatgen"
] | 38c3edce0afe41132adc374e1fb08e909ff4d26b3366f9ec5aec5c31d43318d1 |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
import warnings
from scipy.special import comb
from scipy.misc.doccer import inherit_docstring_from
from scipy import special
from scipy import optim... | piyush0609/scipy | scipy/stats/_continuous_distns.py | Python | bsd-3-clause | 119,431 | [
"Gaussian"
] | 6de7ac7cd449dc3708fae2be59b833a01a196c008fd6bf75663db7d7f4020cf9 |
from ase.test import cli, require
from ase.db import connect
from ase.db.jsondb import read_json
from ase.calculators.gaussian import Gaussian
require('gaussian')
cli("""\
ase-build O | ase-run gaussian -d gaussian_cmdline.json &&
ase-build O2 | ase-run gaussian -d gaussian_cmdline.json""")
c = connect('gaussian_cmdli... | askhl/ase | ase/test/gaussian/gaussian_cmdline.py | Python | gpl-2.0 | 732 | [
"ASE",
"Gaussian"
] | d133dd40472a0641e4a4360c2737d6b057ad2e5c0e44e9d9a91b9e119e5b475f |
import numpy as np
from alis import almsgs
from alis import alfunc_base
from scipy.special import wofz
msgs=almsgs.msgs()
class VoigtConv(alfunc_base.Base) :
"""
Convolves the spectrum with a Voigt profile:
p[0] = sigma
p[1] = damping
"""
def __init__(self, prgname="", getinst=False, atomic=Non... | rcooke-ast/ALIS | alis/alfunc_voigtconv.py | Python | gpl-3.0 | 16,032 | [
"Gaussian"
] | 94b97d5e8cd29a7239c810860fbef799b847a2a8787dcdd6c26f07d2347cd768 |
import numpy as np
import pylab as plt
import tractor
from legacypipe.survey import RexGalaxy, LogRadius
from astrometry.util.util import Tan
'''
An example of rendering a Rex galaxy in an image.
'''
if __name__ == '__main__':
H,W = 100,100
pixscale = 0.262
ra,dec = 40., 10.
psf_sigma = 1.4 # pixels... | legacysurvey/pipeline | py/legacyanalysis/model.py | Python | gpl-2.0 | 1,649 | [
"Galaxy"
] | 9c69e708ccb2a07436bd22293a7bb80fec38101674c70d6cba6f36990954ba36 |
# -*- coding: utf-8 -*-
# @Author: Zachary Priddy
# @Date: 2016-04-11 09:01:35
# @Last Modified by: Zachary Priddy
# @Last Modified time: 2016-10-16 22:04:15
import logging
class FireflyZwave(object):
def __init__(self):
self.zwave = None
ff_zwave = FireflyZwave()
## Import and setup mongo
## Monogo Set... | zpriddy/Firefly | Firefly/core/__init__.py | Python | apache-2.0 | 2,162 | [
"Firefly"
] | e63c4edea84568b0423a2e577b78644b0322c4bc1f302cf8b65c3a69718b7b3a |
import cv2
import scipy.ndimage.filters as filter
import numpy as np
import scipy.signal as signal
from scipy.special import erf
import copy
import sys
#import numba
#Utilitary functions
#TODO try with cython
#@numba.autojit
def generateWrappedDistance(size,center,wrap):
"""Compute the oriented distance (real) b... | bchappet/dnfpy | src/dnfpy/core/utils.py | Python | gpl-2.0 | 8,840 | [
"Gaussian"
] | e573319e87f87cbd9e1bc03ab75ad25e67e0c6cc9e2718f2342e4b5ef08711e5 |
from sklearn.datasets import make_classification
from sklearn.model_selection import train_test_split
from itertools import product
import numpy as np
import pandas as pd
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.animation
class NeuralNetwork:
g = np.vec... | ijkilchenko/numpy_or_bust | neural_network.py | Python | mit | 9,494 | [
"NEURON"
] | 6d99c962ff479d7f5381dabf06fdbe6cf461aee38dc33375c874abba359b752b |
import tempfile
from pathlib import Path
from pywps import Process, LiteralInput, FORMATS
from pywps.inout.outputs import MetaFile, MetaLink4
from flyingpigeon.subset_base import Subsetter
from flyingpigeon.processes.wpsio import resource, variable, start, end, output, metalink
import ocgis
import ocgis.exc
class S... | bird-house/flyingpigeon | flyingpigeon/processes/wps_subset_wfs_polygon.py | Python | apache-2.0 | 3,342 | [
"NetCDF"
] | ed996c5b8f13179c75d8c9cfda9dd78f0a7a0d2f162e1b052bcaf4c4d0092b6c |
"""
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
from pycsp_import import *
import check
import time
import random
@choice
def action(assertCheck, id, channel_input=... | runefriborg/pycsp | test/buffertest.py | Python | mit | 6,429 | [
"Brian"
] | e02a2b9ec8db126bb8f4e6f54eaef5fc6284173f07040cb2ad827f29a6a133a6 |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy, ... | alexholcombe/dot-jump | dataRaw/Fixed Cue/test_dot-jump21Nov2016_14-21.py | Python | gpl-3.0 | 26,446 | [
"Gaussian"
] | 2e3f5616370bdf7b2f2a248b42de05d4733b343820f4422eb00e4d166ff3cb4c |
""" Topological sort can be applyed on DAGs graphs.
DAGs grpah means Directed acyclic graphs.
Any ordering of all nodes that satisfy all relationships is:
topological sort. It means we start from one node and visit all only once,
and we visited them all in one path.
"""
from Queue import Queue
def to... | jtomasevic/graphs_in_python | graphs/topological_sort.py | Python | unlicense | 1,204 | [
"VisIt"
] | f49d258d038a8a6e2385596805cbe0aa2a889d9d031254889ed6ca71fb139c07 |
import pickle
import gzip
import os, sys, errno
import time
import math
# numpy & theano imports need to be done in this order (only for some numpy installations, not sure why)
import numpy
#import gnumpy as gnp
# we need to explicitly import this in some cases, not sure why this doesn't get imported with numpy itse... | bajibabu/merlin | misc/recipes/MGE/run_mge_dnn.py | Python | apache-2.0 | 43,353 | [
"NEURON"
] | d2d113e41acbdc9de86e49262c535a4e58582aa92b6293e2012b179caa9fefc1 |
# Copyright 2020 DeepMind Technologies Limited.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# https://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed t... | deepmind/active_ops | gp_models.py | Python | apache-2.0 | 12,000 | [
"Gaussian"
] | 0f7b98c46e04721f9fe435671007fbccbd605d2d7678d8135787bfedb6b1bff8 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/actions/GuiStatusPictures.py | Python | gpl-3.0 | 9,688 | [
"ORCA"
] | af14bdde9bee8727e9202b301f9006b02c28d19c8097c236aed93070ad62ad73 |
#!/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/mobile/timeradded.py | Python | gpl-2.0 | 9,130 | [
"VisIt"
] | cbdaa55ad87627bb06dea02bd583ec3f130a12d5e4a369df4263b99e5d610010 |
from statsmodels.sandbox.predict_functional import predict_functional
import numpy as np
import pandas as pd
import pytest
import statsmodels.api as sm
# If true, the output is written to a multi-page pdf file.
pdf_output = False
try:
import matplotlib.pyplot as plt
except ImportError:
pass
def pctl(q):
... | statsmodels/statsmodels | statsmodels/sandbox/tests/test_predict_functional.py | Python | bsd-3-clause | 12,778 | [
"Gaussian"
] | 25a5a813cd160df3b0180b7e3a988ee51ac58cd471485c977e005ca0e0f7f203 |
import os
import subprocess
def run(cmd, shell=True):
"""
Run a command and check the return code.
"""
pipe = subprocess.Popen(cmd, stdout=subprocess.PIPE,
stderr=subprocess.STDOUT, shell=shell)
out = pipe.stdout.read()
retcode = pipe.wait()
if retcode != 0:
... | abhishekgahlot/compbio | test/test_codequality.py | Python | mit | 4,081 | [
"BLAST"
] | 74b16ac87c58465fb8f95c1bc43f9aec1f77400bbbd789d4818ab01873870569 |
import openvoronoi as ovd
import ovdvtk
import time
import vtk
import datetime
import math
import random
import os
import sys
import pickle
import gzip
if __name__ == "__main__":
# w=2500
# h=1500
# w=1920
# h=1080
w = 1024
h = 1024
myscreen = ovdvtk.VTKScreen(width=w, height=h)
ovdvt... | aewallin/openvoronoi | python_examples/chain_5_collinear2.py | Python | lgpl-2.1 | 3,863 | [
"VTK"
] | 560cdda9d1d84255dfd918e2b09727e9ad7e98c9cd151f629b89504570bc1202 |
"""
Copyright (C) 2015-2019 Jakub Krajniak <jkrajniak@gmail.com>
This file is part of bakery.
This file is distributed under free software licence:
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, ... | MrTheodor/bakery | src/structures.py | Python | gpl-3.0 | 63,585 | [
"Gromacs"
] | d756c3027870046654ef8a40a6706b23bcdd3905f773bce95b561f107afab540 |
# -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Tests for the SkyCoord class. Note that there are also SkyCoord tests in
test_api_ape5.py
"""
import copy
import pytest
import numpy as np
import numpy.testing as npt
from astropy import units as u
from astropy.tests.helper... | bsipocz/astropy | astropy/coordinates/tests/test_sky_coord.py | Python | bsd-3-clause | 60,131 | [
"Galaxy"
] | b4fe8582df53fbba4e142080a3cafd7abaf0ab90dcf6c04dafb5f9458cadafda |
from asyncio import gather, Lock, Semaphore, sleep, CancelledError
from collections import deque
from time import time, monotonic
from queue import Empty
from itertools import cycle
from sys import exit
from distutils.version import StrictVersion
from aiopogo import PGoApi, HashServer, json_loads, exceptions as ex
fro... | RobTwoThree/Monocle | monocle/worker.py | Python | mit | 57,986 | [
"VisIt"
] | b7f9d71a67110142560657e9b03dafc30576a1aa711349c94c143022602b4ccd |
# Copyright 2006-2016 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# Nice link:
# http://www.ebi.ac.uk/help/formats_frame.html
r"""Sequence input/output as S... | zjuchenyuan/BioWeb | Lib/Bio/SeqIO/__init__.py | Python | mit | 41,691 | [
"BioPerl",
"Biopython"
] | f0ee5699f0c3cd29f2505506625e1478743a280587c584632ea9b7c6daba9aa2 |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin, urlsplit, parse_qs, urlunsplit
from django.views.generic import TemplateView
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
i... | mbareta/edx-platform-ft | common/djangoapps/student/views.py | Python | agpl-3.0 | 109,714 | [
"VisIt"
] | c4cf92e3e36cd876310ad7d5f7f5b2f83c944c20b3ae2a0a30336f3aa304db8b |
#!/usr/bin/python
import os
import signal
import sys
import time
import json
import threading
from node import Node
from interfaces.telegram import Telegram
interface = None
nodes = []
conf = {}
def quit(signum, frame):
print 'quit'
interface.stop()
sys.exit(0)
if __name__ == '__main__':
signal.si... | GustavoKatel/octopus | main.py | Python | gpl-3.0 | 1,058 | [
"Octopus"
] | df6c16da6bd4f11a1a701a5e66fec270cbed2105276c303eb09844b94f6387ba |
#!/usr/bin/env python3
import pandas as pd
import numpy as np
from path import Path # pip install --user path.py
import re
import netCDF4
from collections import namedtuple
from typing import Iterable, Any, Dict
# This program can only work with data results with following properties
MSG_LEN_START = 0
MSG_LEN_END =... | philip-bl/HPC-latencies-prediction | predict.py | Python | mit | 7,392 | [
"NetCDF"
] | 5d7c2850fb397bb0acc1542ecbb26fcf402a61cd2b10762d9391f3f3c7fff3fb |
# Copyright 2014-2016 The ODL development group
#
# This file is part of ODL.
#
# ODL 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.
... | bgris/ODL_bgris | lib/python3.5/site-packages/odl/phantom/noise.py | Python | gpl-3.0 | 6,986 | [
"Gaussian"
] | 5dd85297dceb48b691a630532137ba2285c590d4f79c799773f9c2306128406e |
###############################################################################
# Copyright Keith Butler(2014) #
# #
# This file MacroDensity.density_tools.py is free software: you can #
... | WMD-group/MacroDensity | macrodensity/density_tools.py | Python | mit | 25,379 | [
"GULP",
"VASP"
] | 6d70573b0cb1f512519265a3cb74bbd234fe48f25ae65183c0ef81eb2c9b90ef |
from __future__ import print_function
import os
import unittest
from six import iteritems
import numpy as np
from numpy import dot, array_equal
try:
import pandas
is_pandas = True
except ImportError:
is_pandas = False
import pyNastran
from pyNastran.bdf.bdf import BDF
from pyNastran.op2.op2 import OP2, F... | saullocastro/pyNastran | pyNastran/op2/test/op2_unit_tests.py | Python | lgpl-3.0 | 90,642 | [
"VTK"
] | edfb57bf8b9eae5199c51ca2f08ec417109775fbf2c39824ef1224c923a2122c |
"""
#;+
#; NAME:
#; abs_line
#; Version 1.0
#;
#; PURPOSE:
#; Module for individual absorption lines
#; 01-Nov-2014 by JXP
#;-
#;------------------------------------------------------------------------------
"""
from __future__ import print_function, absolute_import, division, unicode_literals
import numpy as... | profxj/xastropy | xastropy/spec/abs_line.py | Python | bsd-3-clause | 12,318 | [
"Galaxy"
] | c14ddcbfec4940d15c196aeeda99b4cc429610712df404a6fbf1132a68a9280b |
import netCDF4 as netcdf
from pymc.database import base
from pymc import six
import pymc
import numpy as np
import os
import sys
import warnings
import traceback
import pickle
import codecs
__all__ = ['Trace', 'Database']
class Trace(base.Trace):
"""netCDF4 Trace class"""
def _initialize(self):
if... | jchodera/torsionfit | torsionfit/netcdf4.py | Python | gpl-2.0 | 10,075 | [
"NetCDF"
] | 802a2a17fb31c116d574babf82c4b9fe882875cf4e3ff811e4bc93e0e0b6b92e |
#!/usr/bin/env python
#
# Copyright (c) 2001 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
#
# standard modules
import modval
import xdrlib
from xdrlib import Packer,Unpacker
import tripled... | zooko/egtp | common/mesgen.py | Python | agpl-3.0 | 48,972 | [
"VisIt"
] | b0f4fb6f9a53878a7666f3894aa0ae330d1dbfab0fc7dd66b46575cfb587bb18 |
#!/usr/bin/env python3
"""Chemistry example from https://github.com/Qiskit/qiskit-aqua/blob/master/README.md
"""
from qiskit.chemistry import FermionicOperator
from qiskit.chemistry.drivers import PySCFDriver, UnitsType
from qiskit.aqua.operators import Z2Symmetries
# Use PySCF, a classical computational chemistry s... | dlyongemallo/quantum-computation | qiskit/aqua-chemistry-example.py | Python | apache-2.0 | 1,793 | [
"PySCF"
] | d366f2985d13dd46c0de531dafda300026795b8eac0940b2e61e75a33a281bf2 |
print "Hello, World!"
print "Se Min Park."
print "NHD IS COMING 'ROUND THE CORNER TIME TO WRITE THE ESSAY..."
print "ONLY 22 DAYS LEFT."
print True
print False
print 2
print 0.2354678436575432
print (22, "DAYS. SEND HELP.")
print ("Mr. Brian Haynes", "NHD", "Annexations", "GO HOME", 23)
print ("Mr. David Craig", "Engli... | semin2346-cmis/semin2346-cmis-cs2 | hello.py | Python | cc0-1.0 | 754 | [
"Brian"
] | 063d9263a9ce3d91caa0b2cd8af878d53241f39287515163659d471b27f7e621 |
from __future__ import with_statement
import hashlib
import os
import posixpath
import stat
import re
from fnmatch import filter as fnfilter
from fabric.state import output, connections, env
from fabric.utils import warn
from fabric.context_managers import settings
# TODO: use self.sftp.listdir_iter on Paramiko 1.1... | jaraco/fabric | fabric/sftp.py | Python | bsd-2-clause | 13,013 | [
"VisIt"
] | 2e5ea8e3cef2edeb17819ee0de3571d2c44ff45cdb8f64889e2cf2b9eafcfde2 |
#!/usr/bin/env python3
import itertools
from collections import defaultdict
import logging
from operator import mul
import networkx as nx
import numpy as np
import pandas as pd
from pgmpy.base import DirectedGraph
from pgmpy.factors import TabularCPD, JointProbabilityDistribution, Factor
from pgmpy.independencies im... | liquidmetal/pgmpy | pgmpy/models/BayesianModel.py | Python | mit | 27,579 | [
"VisIt"
] | 3fcb445c52cdcba069c12f95ffc9b21c425f05c78b12fb6293f34f5ac6a30c5e |
import os, sys
sys.path.insert(0, os.path.join("..",".."))
from nodebox.graphics.context import *
from nodebox.graphics import *
from nodebox.graphics.shader import *
# This example will make more sense after you've seen the examples in /07-filter
# NodeBox for OpenGL has a range of commands for filtering images.
#... | pepsipepsi/nodebox_opengl_python3 | examples/03-image/03-filter.py | Python | bsd-3-clause | 1,608 | [
"Gaussian"
] | 31cbeeb1b7e7d348ec125dd7ca61ccbd6c4bf93ef67f521cd81bd27def8ed812 |
#!/usr/bin/python
import sys
from xml.dom.minidom import parse, parseString
import xml.dom.ext
infileName=sys.argv[1]
endTime=sys.argv[2]
stepNumber=sys.argv[3]
resultFilename=sys.argv[4]
tempDirectory=sys.argv[5]
speciesNames=sys.argv[6:]
domTree=parse(infileName)
def getModelName(CopasiNode):
modelName=... | jonasfoe/COPASI | semantic-test-suite/addTestSuiteInfo.py | Python | artistic-2.0 | 8,571 | [
"COPASI"
] | 11dbb02acce3b0b82c5d381d6e4ae86277af6eaa72fa3eeba4bd05372bfedd81 |
"""
==========
Model Grid
==========
Fit a line based on parameters output from a grid of models
Module API
^^^^^^^^^^
"""
import numpy as np
from pyspeckit.mpfit import mpfit
import matplotlib.cbook as mpcb
import copy
try:
import scipy.interpolate
import scipy.ndimage
scipyOK = True
except ImportError:
... | jpinedaf/pyspeckit | pyspeckit/spectrum/models/modelgrid.py | Python | mit | 2,036 | [
"Gaussian"
] | 3c130d9159fb8369a5d34cb021c77bef619a445107f19f809c8514317b546e79 |
# Copyright 2018 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | GoogleCloudPlatform/python-docs-samples | bigquery/datalab-migration/samples_test.py | Python | apache-2.0 | 11,636 | [
"Brian"
] | 2afdca9a3acb09ff90d2fd2f39aedf6e049f5d251f22e14bcc4a3273b7822964 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2017 The Chromium OS Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Autosuspend udev rule generator
This script is executed at build time to generate udev rules. The
resu... | darkcircle/systemd | tools/chromiumos/gen_autosuspend_rules.py | Python | gpl-2.0 | 7,221 | [
"Octopus"
] | 85a9537c2a18e0b94821982f3ae822991c1b75c509ca1041083492684cddbe12 |
import pytest
import psi4
import itertools
from .utils import compare_integers, compare_values
pytestmark = pytest.mark.quick
def test_no_screening_schwarz():
"""Checks the number of shell quartets screened with Schwarz screening.
No shell quartets should be screened with a threshold of 0.0"""
mol = psi... | jturney/psi4 | tests/pytests/test_erisieve.py | Python | lgpl-3.0 | 10,949 | [
"Psi4"
] | bc8a18ae94c118074e17ff2669a709a78a6beb01e2161fde1a884663cb983213 |
#!/usr/bin/env python
"""
map_locations.py
Generate and save a map of locations visited, based on GPS logs.
Copyright (C) 2014-2018, 2020 George C. Privon
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Founda... | privong/magellan | map_locations.py | Python | gpl-3.0 | 8,529 | [
"Gaussian"
] | cfb2e947e80ce8d515fdbe783329d1fab40595abd4ec37508aa8628589534d48 |
import astropy.wcs
import ephem
import astropy.units as u
import astropy.coordinates as astroCoords
import numpy as np
import matplotlib.mlab as mlab
import astropy.convolution as conv
import matplotlib.pyplot as plt
from astropy.io import fits
from scipy.spatial.distance import euclidean
class createImage(object):
... | PWhiddy/kbmod | analysis/createImage.py | Python | bsd-2-clause | 44,943 | [
"Gaussian"
] | 11f564b669d8754a46da03e2474c5a7ea34335e1f06433f172b51b903642a946 |
# Tests the MoleculeMatcher functionality by readin in the
# mae and str file, and matching up atoms
import os
import logging
logging.basicConfig()
dir = os.path.dirname(__file__) + "/"
#==============================================================================
#def test_read_str(capfd, tmpdir):
# """
# Tes... | drorlab/dabble | test/graph_ligand/test_graph_ligand.py | Python | gpl-2.0 | 3,389 | [
"VMD"
] | 16b0a626658902a8582a0eee9d526d133b6c23389843030be35d23e8d8b55081 |
# pylint: skip-file
### This file is generated do not edit it by hand!
def configuration():
""" Overview of Configuration Parameters
------------------------------------
``display``
This parameter determines the amount of output of you see at the
screen: The larger its value is, th... | liquidSVM/liquidSVM | bindings/python/liquidSVM/doc.py | Python | agpl-3.0 | 30,003 | [
"Gaussian"
] | 1e2929e3f1d8bbce1ef07de6853190140bfbb35bf7365d1f842b7c932628fd12 |
import hetnetpy.abbreviation
def test__get_duplicates():
get_duplicates = hetnetpy.abbreviation.get_duplicates
assert get_duplicates(range(5)) == set()
assert get_duplicates("abcd") == set()
assert get_duplicates("abbccd") == {"b", "c"}
def test__find_abbrevs():
"""For a list of strings (kinds),... | dhimmel/hetio | test/abbreviation_test.py | Python | cc0-1.0 | 1,467 | [
"BLAST"
] | fcbd91c89ed7f2726e0ecc78e7b4f12d5036a8f8d48c0e7750ce559a096eb762 |
"""A client for the ClassyFire API which enables efficient querying with
chemical database files"""
import csv
import io
import json
import os
import time
import requests
url = "http://classyfire.wishartlab.com"
chunk_size = 1000
sleep_interval = 60
def structure_query(compound, label='pyclassyfire'):
"""Subm... | JamesJeffryes/pyclassyfire | pyclassyfire/client.py | Python | mit | 8,963 | [
"RDKit"
] | 484811d55f2119b5b35b3883120c9620fbadfa001cf6aa628ac3444f84a30962 |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2009 Jan Decaluwe
#
# The myhdl 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 t... | DeadBugEngineering/myHDL_shenanigans | ssd1306_8x64bit_driver/myhdl_10dev/lib/python2.7/site-packages/myhdl-1.0.dev0-py2.7.egg/myhdl/_Waiter.py | Python | lgpl-2.1 | 8,324 | [
"VisIt"
] | 9594c6e3572c87e5f47223f9607090ab05f565c76d64f5671fd432be27d8c038 |
# -*- coding: utf-8 -*-
"""
This script creates the plot with the data downloaded by 'get_data.py'
"""
import numpy as np
import yt.mods as ytm
from tvtk.api import tvtk
from mayavi import mlab
from tvtk.util.ctf import PiecewiseFunction
from tvtk.util.ctf import ColorTransferFunction
from astropy.io import fits
# py... | Cadair/scipy2014plotting | create_plot.py | Python | bsd-2-clause | 5,546 | [
"Mayavi",
"VTK"
] | 311a42b3ecd2c14f7354b484eb961cafd8ce8ad2013a5f243c264aaf9c826108 |
import ftl.dbgtim as dbgtim
class TarjanSCC:
""" Tarjan's strongly connected components algorithm
http://en.wikipedia.org/wiki/Tarjan%E2%80%99s_strongly_connected_components_algorithm
"""
def __init__(self):
# INPUT: list of all nodes in the graph
self.nodes = []
# OUTPUT:... | jsyk/spnsyn-demo | ftl/tarjan.py | Python | gpl-2.0 | 3,409 | [
"VisIt"
] | 46dad5ae76341c3a63fe2be2fb2f63b96e59e5cec4350c4f388bddbb62cf9be0 |
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__license__ = "GPL"
__version__ = "1.0.0"
__maintainer__ ... | upibhalla/moose-core | python/moose/plot_utils.py | Python | gpl-3.0 | 9,624 | [
"MOOSE"
] | 25bdc61685f8be409dd7439ae3b19856516a420fe7ea28b00f99f6a075c36f55 |
import copy
import numpy as np
import math
from hartmann.asr import HMMSet
from hartmann.asr import HMM
from hartmann.asr import MOG
from hartmann.asr import Gaussian
def load_gmm_hmm(ctxfile, modelfile):
model = HMMSet()
with open(ctxfile, 'r') as fin:
for line in fin:
# Prepare as if new ... | hartmannw/research | hartmann/kaldi/model.py | Python | unlicense | 4,683 | [
"Gaussian"
] | 372c6ea2eb2ad532af0e5ae67cf1cfdfc2e9858d64108d733525d56a07322237 |
########################################################################
# $HeadURL$
########################################################################
""" DIRAC FileCatalog Security Manager mix-in class
"""
__RCSID__ = "$Id$"
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Security.Properties import ... | calancha/DIRAC | DataManagementSystem/DB/FileCatalogComponents/SecurityManager.py | Python | gpl-3.0 | 8,389 | [
"DIRAC"
] | 73d7c7e432d3db05ceb7b9c1c9d163b2c2ad16a695b9eeacd685f1b8eeb95e4c |
"""
I/O for VTK <https://vtk.org/wp-content/uploads/2015/04/file-formats.pdf>.
"""
from functools import reduce
import numpy as np
from ..__about__ import __version__
from .._common import warn
from .._exceptions import ReadError, WriteError
from .._files import open_file
from .._mesh import Mesh
from .._vtk_common i... | nschloe/meshio | src/meshio/vtk/_vtk_42.py | Python | mit | 24,679 | [
"VTK"
] | 8375bbae0ff444539d53c37d81a0833b394e1ffe6851b688fb23dfb73ed7e816 |
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
import sys
sys.path.append("../")
from functions import *
from pylab import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import matplotlib.cm as cm
import os
#####################################... | gviejo/ThalamusPhysio | python/figure_article_v3/main_article_v3_fig_3.py | Python | gpl-3.0 | 14,944 | [
"Gaussian"
] | 424d96376d07987f63145fb106559e468928099a66a28a95a761c60a557eb620 |
# Author: Prabhu Ramachandran <prabhu [at] aero . iitb . ac . in>
# Copyright (c) 2008, Prabhu Ramachandran
# License: BSD Style.
# Enthought library imports.
from traits.api import HasTraits, List, Str, Instance
from apptools.preferences.api import PreferencesHelper
################################################... | dmsurti/mayavi | mayavi/tools/preferences_mirror.py | Python | bsd-3-clause | 2,098 | [
"Mayavi"
] | 5a2f4f7010e3f92960e8c11e5ec443b6220f6a434d887fcb2f67b8e57869649b |
#!/usr/bin/env python
import os,re
SettingsList={}
#SettingsList["PREFIX"]="";
#SettingsList["GROUPLBL"]="";
#SettingsList["SJM_FILE"]="";
#REST ARE OK FOR NOW
SettingsList["HANDLER_SCRIPT"]="perl /UCHC/HPC/Everson_HPC/SimpleJobManager/bin/run_with_env --verbose --module /UCHC/HPC/Everson_HPC/cluster_scripts/modulefile... | kotoroshinoto/Cluster_SimpleJob_Generator | pybin/Pipeline/settings/BiotoolsSettings.py | Python | unlicense | 4,051 | [
"BWA",
"Bowtie"
] | 80b88e388f9c45acdaff17a64d64d8999d5dfd1c1a97c5bbdd385e4c500eda4b |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.