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# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Parser for Q-Chem output files"""
import itertools
import math
import re
import datetime
import numpy
from packaging.... | berquist/cclib | cclib/parser/qchemparser.py | Python | bsd-3-clause | 81,907 | [
"Gaussian",
"Q-Chem",
"cclib"
] | 9af65cf8f57a4d6427829b4abc53b41d172397c519a2565aacc1c546c3e38dd2 |
# -*- coding: iso-8859-1 -*-
from array import array
import sys
# Tant qu'à faire vu qu'ici le nombre de caractères par noeud est complètement
# dynamique, on peut se lâcher, mettre 1024 caractère ou plus
CHARS_PER_NODE = 1024
class tst_node(object):
""" classe représentant un noeud du TST """
# __slots__ es... | nlehuen/pytst | python/compacttst.py | Python | mit | 28,991 | [
"VisIt"
] | 0c18f50308a7bfd04df8ef961feb022399e46511d4241b861ba765e5243cf42a |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
repository_name = 'bismark_0070'
repository_description = "Galaxy's bismark wrapper"
repository_long_description = "Long description of Galaxy's bismark wrapper"
category_name = 'Test 0070 Invalid Tool Revisions'
category_description = 'Tests for a ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_0070_invalid_tool.py | Python | gpl-3.0 | 4,650 | [
"Galaxy"
] | 02461af13a42013a6a3074da279a39f4cfe151d6cbee0c9e37383f7e55408b41 |
from __future__ import division, print_function, unicode_literals
# This code is so you can run the samples without installing the package
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
#
testinfo = "f 10 0.033, s, f 20 0.033, s, f 30 0.033, s, f 30 0.033, s, q"
tags = "particl... | google-code-export/los-cocos | test/test_particle_meteor.py | Python | bsd-3-clause | 978 | [
"Galaxy"
] | 8ca50d106ca877ab67362bf0a5c5d03ca4ed76b64562e474a5a502fc431bd14f |
# force floating point division. Can still use integer with //
from __future__ import division
# This file is used for importing the common utilities classes.
import numpy as np
import matplotlib.pyplot as plt
import sys
from GeneralUtil.python import PlotUtilities
import IWT_Util
from Research.Perkins.AnalysisUtil.Fo... | prheenan/Research | Perkins/AnalysisUtil/EnergyLandscapes/IWT_Plot.py | Python | gpl-3.0 | 7,873 | [
"FoldX"
] | 8b4c57c4e4aa0d847477f7284c7d4148ae63e05e490c3d4f718bf00fa53f10a6 |
""" Module containing the environment to run experiments.
An :class:`~pypet.environment.Environment` provides an interface to run experiments based on
parameter exploration.
The environment contains and might even create a :class:`~pypet.trajectory.Trajectory`
container which can be filled with parameters and results... | nigroup/pypet | pypet/environment.py | Python | bsd-3-clause | 148,936 | [
"Brian"
] | 71c281975617c32464bc375f839001fc4acbed4993cbd536dc6eacc3eda39bd0 |
#!/usr/bin/env python3
from setuptools import setup
setup(
name='mir.msmtpq',
version='1.0.1',
description='Message queue for msmtp',
long_description='',
keywords='',
url='https://github.com/darkfeline/mir.msmtpq',
author='Allen Li',
author_email='darkfeline@felesatra.moe',
classi... | darkfeline/pymsmtpq | setup.py | Python | apache-2.0 | 732 | [
"MOE"
] | 33d9668604944ef89ade23820ff54626f3c0ba564cf6326fbbd84b0dfaca31bc |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | alexanderturner/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 98,799 | [
"VisIt"
] | a5bdc87705e568bdd11360fcac89b092fc91c335a51dd17d6aaee90fd0f5b8d6 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2014, 2015 CERN.
#
# Invenio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your option) any... | drjova/invenio-search | invenio_search/walkers/facets.py | Python | gpl-2.0 | 3,896 | [
"VisIt"
] | 682e00ffb5c00100871ac70a7a04163e0d097ed84e98f5fe1f4c4601b69758f1 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import S_OK, S_ERROR, gLogger
class FilterExecutor(object):
ALLKW = "all"
def __init__(self):
self.__filters = {}
self.__globalFilters = []
def applyFilters(self, iD, credDict, con... | yujikato/DIRAC | src/DIRAC/AccountingSystem/private/Policies/FilterExecutor.py | Python | gpl-3.0 | 1,421 | [
"DIRAC"
] | ee664f4019b8ca22f580d6103db640ac1107e250bd076b1f689bc11d97a2a110 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | Mistobaan/tensorflow | tensorflow/python/ops/linalg/linear_operator_test_util.py | Python | apache-2.0 | 25,949 | [
"Gaussian"
] | 6f94f815bdd6a736b95139c646f11305f535a57a7691064d691b5d90bdd6dcfb |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | nchammas/spark | python/pyspark/pandas/tests/test_series.py | Python | apache-2.0 | 128,270 | [
"Elk"
] | 204e1ca3a09dff986a57d66575dfd3ecb6bfad80b09d7aebc4e2f1585fb4c6e4 |
"""a prototype multiobjective opt under uncertainty algorithm
"""
import os
import numpy as np
import pandas as pd
import pyemu
from .ensemble_method import EnsembleMethod
class ParetoObjFunc(object):
"""multiobjective function calculator."""
def __init__(self, pst, obj_function_dict, logger):
self... | jtwhite79/pyemu | pyemu/prototypes/moouu.py | Python | bsd-3-clause | 36,825 | [
"Gaussian"
] | 6d7b2e6122b9f2d8dbb0ff5324922b486944300e3f6e1a30ad9676d040d4c76e |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-get-jdl
# Author : Stuart Paterson
########################################################################
"""
Retrieve the current JDL of a DIRAC job
Usage:
dirac-wms-job-get-jdl [options] ... ... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_job_get_jdl.py | Python | gpl-3.0 | 2,000 | [
"DIRAC"
] | 02445484f1586e8df2dc9c2738ef11497bef560c6968734166ebf4227c8e12cf |
import sys
import os
import re
import datetime
import shutil
import gzip
import glob
from collections import namedtuple
import tempfile
import traceback
import Bio.SeqUtils
import simtk.openmm
import yaml
import msmbuilder
import warnings
import ensembler
import ensembler.version
import Bio
import Bio.SeqIO
import Bio.... | choderalab/ensembler | ensembler/modeling.py | Python | gpl-2.0 | 42,150 | [
"Biopython",
"MDTraj",
"OpenMM"
] | 7017d4b6d1b48774f9440a54f80d7e957158cfdb417ae4d302f3f90bb24cefcb |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | greglandrum/rdkit | rdkit/Chem/EState/UnitTestEState.py | Python | bsd-3-clause | 5,360 | [
"RDKit"
] | 2ad31ef1147bde8fa1b3d23b03b9eb043d39883aa7dfc9282158530a9e1aa9e0 |
#!/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/providers.py | Python | gpl-2.0 | 5,501 | [
"VisIt"
] | cdbbeea5d15ab9e6e4641da1ce4b74d81126f9f7e412d0de0b6e9586f1266d4b |
import copy
import os
from collections import OrderedDict
import numpy as np
import robosuite.utils.transform_utils as T
from robosuite.controllers import controller_factory, load_controller_config
from robosuite.models.grippers import gripper_factory
from robosuite.robots.manipulator import Manipulator
from robosuit... | ARISE-Initiative/robosuite | robosuite/robots/bimanual.py | Python | mit | 26,392 | [
"Gaussian"
] | 6b1fa7f9c30ebb60cfc58ff66a0e03feed57c1df0449ee9665aa6ba1c9f37b58 |
# This file is part of xrayutilities.
#
# xrayutilities 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
# (at your option) any later version.
#
# This program is distributed... | dkriegner/xrayutilities | examples/xrayutilities_io_cif_parser.py | Python | gpl-2.0 | 1,102 | [
"CRYSTAL"
] | f14044ac8551e8ae4cfad85800f75418954fdaf9e344a05a5a19d2c2dbc0baff |
# $Id$
import operator
from itcc.Torsionfit import cmpmol
from itcc.Tinker import tinker
from itcc.Tools import tools
__revision__ = '$Rev$'
optimize = tinker.batchoptimize
energy = tinker.batchenergy
class Meritresult(dict):
pass
def chkdeform(flist1, flist2):
numdeformstru = 0
data = cmpmol.batchc... | lidaobing/itcc | itcc/torsionfit/merit.py | Python | gpl-3.0 | 3,096 | [
"TINKER"
] | fe5ed7461cc39958851e926ea523e7ca6b3a0a78840a1d6020a47bb3a824d712 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# 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 Fre... | arunkgupta/gramps | gramps/gen/filters/rules/place/_hasgallery.py | Python | gpl-2.0 | 1,787 | [
"Brian"
] | 334803477fad4e1c37a797a94893b1a3011ce60b8cfc9ef286146af13ce2f1bc |
"""
This migration script adds the tables necessary to support tagging of histories,
datasets, and history-dataset associations (user views of datasets).
If using mysql, this script will display the following error, which is corrected in the next
migration script:
history_dataset_association_tag_association table fai... | volpino/Yeps-EURAC | lib/galaxy/model/migrate/versions/0015_tagging.py | Python | mit | 4,565 | [
"Galaxy"
] | d8edc73f1fc66d65b3802edd49dde2e85cde40608ea93e9af680c6cedf4ec72e |
'''
-------------------------------------------------------------------------------
This script is an example of making changes on a CUCME/CUBE box, which is
just a router with special options enabled.
-------------------------------------------------------------------------------
'''
#Global imports
from netmiko impo... | admiralspark/NetSpark-Scripts | Example_Scripts/Cisco/ephoneChange.py | Python | gpl-3.0 | 2,977 | [
"Elk"
] | 6971f9472384c19271b03446be11f1497ec71a1000a47b92b578314ab239bc42 |
from typing import Optional
################################################################
# Zulip Server settings.
#
# This file controls settings that affect the whole Zulip server.
# See our documentation at:
# https://zulip.readthedocs.io/en/latest/production/settings.html
#
# For developer documentation on th... | dhcrzf/zulip | zproject/prod_settings_template.py | Python | apache-2.0 | 22,300 | [
"VisIt"
] | 7710154914accace1c18b74963507d0f4255849fa5f72a8644cafff9ab7a4f55 |
"""
A collection of functions to find the weights and abscissas for
Gaussian Quadrature.
These calculations are done by finding the eigenvalues of a
tridiagonal matrix whose entries are dependent on the coefficients
in the recursion formula for the orthogonal polynomials with the
corresponding weighting function over ... | pizzathief/scipy | scipy/special/orthogonal.py | Python | bsd-3-clause | 62,286 | [
"Gaussian"
] | f45c119e59ab0afaed57c765417107bb97a693f77259c0090a4651a8e4fc593d |
import numpy as np
import _RandomNumberGenerator as RNG
def add(projections, Gaussian=None, Poisson=None):
if Poisson is not None:
if not np.isscalar(Poisson):
raise ValueError(
"Poisson value should be an scalar, is " + str(type(Poisson)) + " instead."
)
else:
... | CERN/TIGRE | Python/tigre/utilities/CTnoise.py | Python | bsd-3-clause | 1,041 | [
"Gaussian"
] | beceb94e1643db13c7d1fcb96296eaf46d40ab489226c360d8312650730583fe |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import json
import os
import pytest
import ... | thaim/ansible | test/units/galaxy/test_collection.py | Python | mit | 21,643 | [
"Galaxy"
] | 4bc15f17a234a6b40068cad70c30523c0aef81cffd126fffb2bbdf9f640eb5cd |
# Copyright 2022 The T5 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 applicable law or agreed to in writi... | google-research/text-to-text-transfer-transformer | t5/evaluation/metrics_test.py | Python | apache-2.0 | 19,933 | [
"MOOSE"
] | 7d527d6def8b7a66b9a74fa2703e49d44bc5bf7b65dd15d631ba8c09e998016c |
import numpy as np
def cnn_setup(params):
"""
Defining convolutional architecture.
Arguments: Parameters defining the entire model.
"""
class cnn_layer():
def __init__(self, layerType, dimFilters, nFilters, stride, border='valid', doNoise = True, doBN = True):
self.type = lay... | bigaidream-projects/drmad | gpu_ver/refcode/setup.py | Python | mit | 13,270 | [
"Gaussian"
] | cadd85567df2939aa67d38d38bdac6a85acff35ee6c90af9cd96c9a29030a855 |
#coding=utf8
from __future__ import unicode_literals
import sys
import os
import shutil
import re
import xlrd
import yaml
import alias
import typedef
import lseri
reload(sys)
sys.setdefaultencoding("utf8")
import codecs
def cp65001(name):
if name.lower() == "cp65001":
return codecs.lookup("utf8")
codecs.re... | bttscut/xls-converter | converter/xlsparse.py | Python | mit | 14,562 | [
"VisIt"
] | 960d84cb3b28d7fe7b0beb3cd71d3c8bb45ca0aabc5e643b6ca2f4f48b582dc0 |
""" Tornado-based HTTPs JobStateUpdate service.
"""
from DIRAC import gLogger
from DIRAC.Core.Tornado.Server.TornadoService import TornadoService
from DIRAC.WorkloadManagementSystem.Service.JobStateUpdateHandler import JobStateUpdateHandlerMixin
sLog = gLogger.getSubLogger(__name__)
class TornadoJobStateUpdateHandl... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Service/TornadoJobStateUpdateHandler.py | Python | gpl-3.0 | 383 | [
"DIRAC"
] | 0afe3465e82c5f0f98fe5429d894d7d1dd40836a5da6cee5b11baf6c646ae1ad |
from collections import deque
def tarjan(g):
"""
Tarjan's algo for finding strongly connected components in a directed graph
Uses two main attributes of each node to track reachability, the index of that node
within a component(index), and the lowest index reachable from that node(lowlink).
We t... | TheAlgorithms/Python | graphs/tarjans_scc.py | Python | mit | 2,652 | [
"VisIt"
] | fed4391976988dd4fed5ebc76eb46637fd2afe5a8a9116d7b27a66706d32a611 |
''' The application programming interface for Pyleoclim
@author: fengzhu
Created on Jan 31, 2020
'''
from ..utils import tsutils, plotting, mapping, lipdutils, tsmodel, tsbase
from ..utils import wavelet as waveutils
from ..utils import spectral as specutils
from ..utils import correlation as corrutils
from ..utils i... | LinkedEarth/Pyleoclim_util | pyleoclim/core/ui.py | Python | gpl-3.0 | 339,387 | [
"CRYSTAL",
"Gaussian",
"TINKER"
] | 3b15d6bb98a8b096f6c280019d70ecb32d7a408fb60b179ccf00f1c6e11ddcac |
"""Support the ElkM1 Gold and ElkM1 EZ8 alarm/integration panels."""
import logging
import re
import voluptuous as vol
from homeassistant.const import (
CONF_EXCLUDE, CONF_HOST, CONF_INCLUDE, CONF_PASSWORD,
CONF_TEMPERATURE_UNIT, CONF_USERNAME)
from homeassistant.core import HomeAssistant, callback # noqa
fro... | jamespcole/home-assistant | homeassistant/components/elkm1/__init__.py | Python | apache-2.0 | 8,007 | [
"Elk"
] | 3ddf12470f3aef6dd752a0e6d331a70cbcf194234d7730e6c251870fe91b7261 |
import imp
import os
import marshal
import struct
import sys
from cStringIO import StringIO
is_jython = sys.platform.startswith('java')
from compiler import ast, parse, walk, syntax
from compiler import misc, future, symbols
from compiler.consts import SC_LOCAL, SC_GLOBAL_IMPLICIT, SC_GLOBAL_EXPLICT, \
SC_FREE, S... | adaussy/eclipse-monkey-revival | plugins/python/org.eclipse.eclipsemonkey.lang.python/Lib/compiler/pycodegen.py | Python | epl-1.0 | 47,712 | [
"VisIt"
] | 3f3189105c565e550fc435ed6257a0a3c453d2c3b7bfbbca4b516dbab8a945de |
#!/usr/bin/python
"""
Copyright 2010 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester 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 th... | clreinki/GalaxyHarvester | udEmail.py | Python | agpl-3.0 | 2,533 | [
"Galaxy"
] | da61fd5a08de6af42fd858f8f17464760f9aaf1eca373d2113ed94b031ec10a7 |
# -*- coding: utf8
"""Random Projection transformers
Random Projections are a simple and computationally efficient way to
reduce the dimensionality of the data by trading a controlled amount
of accuracy (as additional variance) for faster processing times and
smaller model sizes.
The dimensions and distribution of Ra... | bnaul/scikit-learn | sklearn/random_projection.py | Python | bsd-3-clause | 22,989 | [
"Gaussian"
] | 0dae8e4f8aacf5190cd9a541a95fb89fc7276f34884535f457ef7dd67ed504aa |
#!/usr/bin/env python
"""Copyright 2010 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.8'
__date__ = 'May 17 2010'
#Basi... | dborrero/Reed-Taylor-Couette | PhidgetPythonSamples/Stepper-simple.py | Python | gpl-2.0 | 5,280 | [
"VisIt"
] | a225f64aceb1b3696b6a139e9d7fd891533d15a1389e6568a716096fffe51d0b |
#!/usr/bin/env python
import pysam
import numpy
import os,sys,re
from optparse import *
from logging import error
COMPLEMENT = {
'a' : 't',
't' : 'a',
'c' : 'g',
'g' : 'c',
'k' : 'm',
'm' : 'k',
'r' : 'y',
'y' : 'r',
's' : 's',
'w' : 'w',
'b' : 'v',
'v' : 'b',
'h' : ... | marvin-jens/find_circ | unmapped2anchors.py | Python | gpl-3.0 | 6,014 | [
"pysam"
] | 3eacbba71253487c1a7400b97720b281cac83a7008c5090d6e827f65990c600f |
# Generated by Django 3.1.8 on 2021-04-19 10:39
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("foirequest", "0049_auto_20210203_1237"),
]
operations = [
migrations.AddField(
model_name="foimessage",
name="conten... | fin/froide | froide/foirequest/migrations/0050_auto_20210419_1239.py | Python | mit | 1,114 | [
"VisIt"
] | c2dc808a59a3e8384420b854674a1a80eb2ecb2ac70c3ac26e37c5ae84fa6c86 |
# 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.
# Autocompletion config for YouCompleteMe in Chromium.
#
# USAGE:
#
# 1. Install YCM [https://github.com/Valloric/YouCompleteMe]
# (Googlers s... | danakj/chromium | tools/vim/chromium.ycm_extra_conf.py | Python | bsd-3-clause | 12,768 | [
"VisIt"
] | cc340a532248c82993b990ba3d6d198550462e1c49aebe66563a830c211f9f9a |
"""
The ansible action handles generating a custom inventory file
and running the supplied playbook on the stack instances. This also
includes cloning the playbook down from a remote url if supplied instead
of a path and installing the requirements from a requirements.yml file if
one is found in the playbook directory.... | invenia/shepherd | shepherd/actions/ansible.py | Python | mpl-2.0 | 7,481 | [
"Galaxy"
] | cbdf55b666cb21ccbc33df7ee59335720a8c8ae58138d1a1467e38cad19000a7 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# 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 Fr... | SNoiraud/gramps | gramps/plugins/rel/rel_pl.py | Python | gpl-2.0 | 32,097 | [
"Brian"
] | 6126e26e1f50d4e1441e273158e90137e6b86c000e6b55df02b677d6bb07e2dc |
'''
Steps for problem.feature lettuce tests
'''
# pylint: disable=C0111
# pylint: disable=W0621
from lettuce import world, step
from lettuce.django import django_url
from common import i_am_registered_for_the_course, TEST_SECTION_NAME
from problems_setup import PROBLEM_DICT, answer_problem, problem_has_answer, add_pr... | abhinavp13/IITBX-edx-platform-dev | lms/djangoapps/courseware/features/problems.py | Python | agpl-3.0 | 5,877 | [
"VisIt"
] | c274430d38d660297ba39fb58ad9033469444fb98ce1f65b43c5c6773fe61b2f |
s = '''
=====
gback
=====
This package provides an simpler interface to Google calendars using
the google-api-python-client python package and OAuth.
Examples
--------
Note: See the "Setting up the project on Google" section below before trying
the examples.
List calendar names::
>>> from gback import GCalSes... | Schwarzschild/gback | gback/readme.py | Python | mit | 4,544 | [
"VisIt"
] | 2222be0026d9b8a8ea7435ba3d77198b4ce22d7f6ce095339c496ced0b97192f |
import signal
from contextlib import ExitStack
from functools import lru_cache
from pathlib import Path
from shutil import rmtree
from subprocess import Popen
from tempfile import NamedTemporaryFile
import os
from typing import Mapping, Tuple
from pandas import DataFrame
from rpy2.robjects import r, NULL as null, Str... | reimandlab/ActiveDriverDB | website/analyses/gene_sets.py | Python | lgpl-2.1 | 6,995 | [
"Cytoscape"
] | a524628ed528ad348345ca5a7e65aad1f9c2e56731f390d83bd94a2434524d36 |
"Yang/Wu's OEP implementation, in PyQuante."
from math import sqrt
import settings
from PyQuante.NumWrap import zeros,matrixmultiply,transpose,dot,identity,\
array,solve
from PyQuante.Ints import getbasis, getints, getJ,get2JmK,getK
from PyQuante.LA2 import geigh,mkdens,trace2,simx
from PyQuante.hartree_fock impo... | berquist/PyQuante | PyQuante/OEP.py | Python | bsd-3-clause | 25,427 | [
"Gaussian"
] | 4f798bafe39e1af47c1912f458204f3567a219816356b4639ebb8bc0d5b39828 |
# -*- coding: utf-8 -*-
#
# Google Genomics documentation build configuration file, created by
# sphinx-quickstart on Wed Apr 30 15:58:16 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated fil... | deflaux/start-here | docs/source/conf.py | Python | apache-2.0 | 18,947 | [
"BLAST",
"Bioconductor"
] | d74d69ea9016df3588951c7d7413ece1f079ba96ed363b53137910119295d6b3 |
"""
The B{0install download} command-line interface.
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import sys
from zeroinstall import _
from zeroinstall.cmd import UsageError, select
from zeroinstall.injector import model
from zeroinstall.support import tas... | slovenwd/0install | zeroinstall/cmd/download.py | Python | lgpl-2.1 | 1,483 | [
"VisIt"
] | 5579b4966c0fefa72498edd17512f740dc699e49c57342c46388671372a329ec |
#!/usr/bin/env python2
# createLinearModel.py
###############################################################################
# ------------------------- Description ---------------------------------------
###############################################################################
# This script will be used to c... | stevenjoelbrey/PMFutures | Python/createLinearModel.py | Python | mit | 8,965 | [
"NetCDF"
] | 7cfe5f2f93c0baa791e96078fcfb35883faf94d1ea9fb9648dc20f4247c44ed7 |
# Changes:
#
# can now specify 'zipfile = None', in this case the Python module
# library archive is appended to the exe.
# Todo:
#
# Make 'unbuffered' a per-target option
from distutils.core import Command
from distutils.spawn import spawn
from distutils.errors import *
import sys, os, imp, types, stat
import ... | mollstam/UnrealPy | UnrealPyEmbed/Development/Python/2015.08.07-Python2710-x64-Source-vs2015/Python27/Source/py2exe-0.6.8/py2exe/build_exe.py | Python | mit | 65,585 | [
"VisIt"
] | bbb981ffc8db6df0069a32cff7570a3e1702ef21264d2eb5478e0ca3ad2d9bb9 |
'''
========================================================================
count - Count reads per gene from BAM using UMIs and mapping coordinates
========================================================================
*Count the number of reads per gene based on the mapping co-ordinate and the UMI attached to the... | CGATOxford/UMI-tools | umi_tools/count.py | Python | mit | 7,483 | [
"HTSeq",
"pysam"
] | 5a0b5a1b51b84ccdc4761cb9a86c28d780e6634a1e0de6fd736a74a949e81ed2 |
from sympy.core.basic import Basic, S, C, sympify
from sympy.core.function import Function
from sympy.ntheory import sieve
from math import sqrt
from sympy.utilities.decorator import deprecated
###############################################################################
######################## FACTORIAL and MULT... | hazelnusse/sympy-old | sympy/functions/combinatorial/factorials.py | Python | bsd-3-clause | 12,446 | [
"VisIt"
] | 2755d8f6fdecaa898aa5c1441b565ede4a83ba391451dee3dde9fb6334e5ac5a |
# copies.py - copy detection for Mercurial
#
# Copyright 2008 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
import util
import heapq
def _nonoverlap(d1, d2, d3):
"Return list of elements in d1... | joewalnes/idea-community | plugins/hg4idea/testData/bin/mercurial/copies.py | Python | apache-2.0 | 8,242 | [
"VisIt"
] | 04efba43bee6927732e632a95c90bb0b34a26658145f9265eb9b2ce45c0e37ee |
"""
Migration script to create the migrate_tools table.
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
import datetime
now = datetime.datetime.utcnow
# Need our custom types, but don't import anything else from model
from galaxy.model.custom_types impor... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py | Python | gpl-3.0 | 1,469 | [
"Galaxy"
] | 2ed4bccf9d2f802a616ee80c26769d9fb545070e92999c815b8952801f1091ee |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import os
from unittest import TestCase
import unittest2 as unittest
from pymatgen.analysis.molecule_structure_comparator import \
MoleculeStructureComparator
from p... | aykol/pymatgen | pymatgen/analysis/tests/test_molecule_structure_comparator.py | Python | mit | 4,991 | [
"pymatgen"
] | 13f327786f581c5f029cbe4f7e9f54df3fe7fea77ec1bb854917164d4ed45d7e |
import numpy
from sandbox.kernel.AbstractKernel import AbstractKernel
from sandbox.util.Parameter import Parameter
class GaussianKernel(AbstractKernel):
"""
A class to find gaussian kernel evaluations k(x, y) = exp (-||x - y||^2/2 sigma^2)
"""
def __init__(self, sigma=1.0):
"""
Init... | charanpald/sandbox | sandbox/kernel/GaussianKernel.py | Python | gpl-3.0 | 1,829 | [
"Gaussian"
] | b39d3bc03a1a3383993e1303009e4c172326e4502e4fd01a8f3ce0f264ec3f10 |
"""
Miscellaneous code to run benchmarks and operate on mpsrime files.
"""
from __future__ import print_function
from __future__ import division
import argparse
import os.path
import tempfile
import time
import msprime
import Bio
from Bio import Phylo
import dendropy
import ete2
import numpy as np
def run_compress(... | jeromekelleher/msprime-paper | examples/examples.py | Python | gpl-3.0 | 8,175 | [
"Biopython"
] | 57c7a1990a7a9919c0eaea44674488798712244fb463d3c0345be2c4e27d931b |
import os, sys, re
import urllib2
from bs4 import BeautifulSoup
class mineApps:
def __init__(self, pagePath):
self.page = pagePath
#read the page provided during object creation
@staticmethod
def set_buffer(pageURL):
soup = BeautifulSoup(urllib2.urlopen(pageURL).read())
return soup
#set an object for ... | bharathkallurs/appsminer | appMiner.py | Python | bsd-3-clause | 5,373 | [
"CASINO"
] | 766a201ad43f4286b868e9ed88a08c30c80490881ed184e2247f6ea41b919062 |
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
# we need to explicitly import this in some cases, not sure why this doesn't get imported with numpy itself
import numpy.distut... | bajibabu/merlin | src/work_in_progress/oliver/run_tpdnn.py | Python | apache-2.0 | 101,142 | [
"NEURON"
] | 087e7da80b5ac49449bb00d916da04b79ef7442f56983f99f2bf14047ea04588 |
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# Licence: BSD 3 clause
from __future__ import print_function
import numpy as np
from scipy import linalg, optimize
from ..base import BaseEstimator, RegressorMixin
from ..metrics... | jmetzen/scikit-learn | sklearn/gaussian_process/gaussian_process.py | Python | bsd-3-clause | 34,896 | [
"Gaussian"
] | a9867c3a33cb4b53a41fc44ef1fd7b424176290c7575f490903dcbd61b5fb011 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | Xeralux/tensorflow | tensorflow/python/keras/_impl/keras/layers/noise.py | Python | apache-2.0 | 6,255 | [
"Gaussian"
] | befdbff6f747ef3b2f3829366d68354a25e1dd7785448c41327b94149bc2c7b8 |
#!/usr/bin/env python
import os, sys
from ConfigParser import ConfigParser
from optparse import OptionParser
default_config = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..', 'config/galaxy.ini') )
parser = OptionParser()
parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy confi... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/scripts/set_dataset_sizes.py | Python | gpl-3.0 | 1,878 | [
"Galaxy"
] | 2b638787c2ccba9315a741fd2f7610212782f98fa74ef09e301e01683d5bde39 |
## INFO ########################################################################
## ##
## COUBLET ##
## ======= ... | petervaro/coublet | presenters/post.py | Python | mit | 2,820 | [
"VisIt"
] | 3f8c36ea03658c45ae841161c59592e579eaedcd58212c3095653c229463e095 |
from autonomous import Autonomous
from mecanum_drive import MecanumDrive
from intake import Intake
from shooter import Shooter
from shooter_service import ShooterService
try:
import wpilib
except ImportError:
from pyfrc import wpilib
class Aimbot(wpilib.SimpleRobot):
def __init__(self):
super().__init__()
... | eshsrobotics/aimbot | robot.py | Python | mit | 2,293 | [
"Jaguar"
] | cf98b863968959a7b9cc1791428b34f85e158ddb5c60161733ee97f9c4c0e7a2 |
from __future__ import absolute_import
from __future__ import print_function
import sys, os, yaml, glob
import subprocess
import string
import sys
from nougat import common
def run(global_config, sample_config):
sorted_libraries_by_insert = common._sort_libraries_by_insert(sample_config)
#Check if the user ha... | senthil10/NouGAT | nougat/assemble.py | Python | mit | 36,060 | [
"Bowtie"
] | af473e5b8ba0b91d19831ee485692a1897fb3690af6bcc9df48e8980ab0cef09 |
# -*- coding: utf-8 -*-
#
#Created on Fri Apr 14 15:21:17 2017
#
#author: Elina Thibeau-Sutre
#
from .initializations import initialize_log_assignements,initialize_mcw
from .base import _full_covariance_matrices
from .base import _log_normal_matrix
from .base import BaseMixture
from .base import _log_B
import numpy a... | 14thibea/megamix | megamix/batch/DPGMM.py | Python | apache-2.0 | 20,644 | [
"Gaussian"
] | f4654df2a44bad67b3215e2cfc5bc2c9c8c7bc43e829ac60432b692daa60fbbc |
# -*- coding: utf-8 -*-
#
# mpitest_issue_578_sp.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 Li... | lekshmideepu/nest-simulator | testsuite/pytests/test_sp/mpitest_issue_578_sp.py | Python | gpl-2.0 | 3,178 | [
"Gaussian"
] | b9e91947f2d9637ee63ae667ba830a9bd3400a6f7f0591b3b7dc073c76b299ff |
import os
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging
#
# DeveloperToolsForExtensions
#
class DeveloperToolsForExtensions(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/master/Bas... | lassoan/SlicerDeveloperToolsForExtensions | DeveloperToolsForExtensions/DeveloperToolsForExtensions.py | Python | apache-2.0 | 20,653 | [
"VTK"
] | fab1a583ad772ea06e044addcd570d246a156b3b80bc0196be2f26a83bf91393 |
# Copyright 2011 Nicholas Bray
#
# 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... | ncbray/pystream | bin/util/typedispatch.py | Python | apache-2.0 | 3,787 | [
"VisIt"
] | cef3a4ed03cd03d188ea5633194738c9ca102df22ea2b01a2fe08030532161ce |
import os
import shutil
import pytest
from eppy import modeleditor
from eppy.modeleditor import IDF
from eppy.runner.run_functions import paths_from_version, EnergyPlusRunError
THIS_DIR = os.path.dirname(os.path.abspath(__file__))
RESOURCES_DIR = os.path.join(THIS_DIR, os.pardir, 'resources')
IDD_FILES = os.path.j... | jamiebull1/eppy | eppy/tests/test_reproduce_bugs.py | Python | mit | 1,615 | [
"EPW"
] | 21b6069c21bfe721c3e9e1788a5e2d7dda3cc73775c8133cc73d65975283d8e8 |
#!/usr/bin/env python
"""Module to create concatemer per genome of orthologs, create a phylogenetic tree and deduce taxa from that tree."""
from Bio import AlignIO, Phylo, SeqIO
from shared import create_directory, parse_options, extract_archive_of_files, create_archive_of_files
from select_taxa import select_genomes_... | ODoSE/odose.nl | concatemer_tree.py | Python | mit | 12,074 | [
"Biopython"
] | 07f963cebd5dd7269a96e2fcd8c81534fbb261be5dd0569bc92e1df50b0d1bdb |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2013, 2014 CERN.
#
# Invenio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your option) any... | kasioumis/invenio | invenio/modules/workflows/testsuite/test_workflows.py | Python | gpl-2.0 | 31,935 | [
"Galaxy"
] | b6956f4cd0f835ce603181f9b524cbc30152fcde318cb35c64f22175f76847d0 |
""" Helper functions for accessing Paraview functionality
.. moduleauthor:: Zenotech Ltd
"""
from paraview.simple import *
# from paraview.vtk.util import numpy_support
try:
from paraview.vtk.dataset_adapter import numpyTovtkDataArray
from paraview.vtk.dataset_adapter import Table
from paraview.vtk.dataset_... | zenotech/zPost | python/zutil/post.py | Python | bsd-3-clause | 41,409 | [
"ParaView",
"VTK"
] | e0436282299ee2b988ed97d690fa581513625e28f9dce1bf415fc62fda87d5b5 |
import numpy as nm
from sfepy.base.base import output, assert_
from sfepy.base.ioutils import ensure_path
from sfepy.linalg import cycle
from sfepy.discrete.fem.mesh import Mesh
from sfepy.mesh.mesh_tools import elems_q2t
def get_tensor_product_conn(shape):
"""
Generate vertex connectivity for cells of a tens... | RexFuzzle/sfepy | sfepy/mesh/mesh_generators.py | Python | bsd-3-clause | 35,893 | [
"ParaView",
"VTK"
] | c0e94ee428f35dbdbc93f88e99d327895fb9abbb6eb751542ef28ccb04b4bf8a |
#!/usr/bin/env python2.7
"""
@author Frank Austin Nothaft fnothaft@berkeley.edu
@date 12/30/2015
Pipeline to go from FASTQ to VCF using both the ADAM+HaplotypeCaller pipeline
as well as the GATK best practices pipeline.
0 --> ... --> 4 --> 5
| |++(6)
| 7 --> 9 --> ... --> 12 ... | jpfeil/toil-scripts | src/toil_scripts/adam_gatk_pipeline/align_and_call.py | Python | apache-2.0 | 20,325 | [
"BWA"
] | 7885da6e18c43cc6baf5fcab64c1b1d113ba2ed077077f59c573512030e0b015 |
# -*- coding: utf-8 -*-
"""
ASSET is a statistical method :cite:`asset-Torre16_e1004939` for the detection
of repeating sequences of synchronous spiking events in parallel spike trains.
ASSET analysis class object of finding patterns
-----------------------------------------------
.. autosummary::
:toctree: toct... | JuliaSprenger/elephant | elephant/asset.py | Python | bsd-3-clause | 72,742 | [
"NEURON"
] | 07f47335d2ef7ed6549fd79a03d9f60e2d737267373e4f3c1becb451468e7676 |
#!/usr/bin/env python
import unittest
import mlbgame
from datetime import datetime
class TestGame(unittest.TestCase):
def test_day(self):
games = mlbgame.day(2016, 8, 2)
for game in games:
if game.home_team == 'Mets':
g = game
self.assertIsInstance(game.... | panzarino/mlbgame | tests/test_game.py | Python | mit | 20,130 | [
"Brian"
] | a103e9843cf7ec88d4ac97abda116fc2a17a8ad7f44f667580baa70efa730a7f |
# encoding: utf-8
"""
Export (not only) geometry to various formats.
"""
from __future__ import print_function
from builtins import zip
from builtins import range
from builtins import object
from yade.wrapper import *
from yade import utils,Matrix3,Vector3
#textExt====================================================... | yade/trunk | py/export.py | Python | gpl-2.0 | 44,375 | [
"ParaView",
"VTK"
] | a0f388e8ca6fd38200c8fcffaf25114aff506dbd797d7b8f5b14db2531b01ae4 |
"""
Workaround for a bug introduced in 1.5.2 where all units got converted to lower case....
"""
from cis.data_io.products import AProduct
from cf_units import Unit
import logging
class flight_track(AProduct):
def get_file_signature(self):
return [r'.*\.nc']
def create_coords(self, filenames, usr_va... | duncanwp/cis_plugins | ukca_flight_track.py | Python | lgpl-3.0 | 2,942 | [
"NetCDF"
] | fd15d8cfb9c557e9feb893120368fb84db00d6e4795cd70dc817769c374a153f |
#!/usr/bin/env python
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the Free
# Software Foundation; either version 3 of the License, or (at your option)
# any later version.
# This program is distributed in the hope that i... | netceteragroup/esa-beam | beam-3dveglab-vlab/src/main/scripts/mk_microsite.py | Python | gpl-3.0 | 26,138 | [
"VisIt"
] | 33da724e6c5b4643e69762eeb59ff6f3341868eac6a16c7ec792fefdb6ff71cc |
#!/usr/bin/env python
import ujson as json
import logging
import zmq
import cif.hunter
from cifsdk.msg import Msg
from cifsdk.client.zeromq import ZMQ as Client
from cif.constants import HUNTER_ADDR, HUNTER_SINK_ADDR
from csirtg_indicator import Indicator
from csirtg_indicator.exceptions import InvalidIndicator
import... | csirtgadgets/bearded-avenger | cif/hunter/__init__.py | Python | mpl-2.0 | 4,715 | [
"Amber"
] | da3ee61fd64eba19e1864444c52700839f73bcc13f1e9fc48be48f4f666e40b9 |
#!/usr/bin/env python
import random
import itertools
import rospy
from visualization_msgs.msg import MarkerArray, Marker
from geometry_msgs.msg import Point, Quaternion
from std_msgs.msg import UInt8, Float64
import numpy as np
import math
from sklearn.cluster import KMeans, DBSCAN
from sklearn import svm
from sklearn.... | phamngtuananh/Singaboat_RobotX2016 | robotx_nav/nodes/pinger_planner.py | Python | gpl-3.0 | 16,399 | [
"Gaussian"
] | 8edde7be48d905a37035ca8d1d06f731fa2f43042106b853bbcbc5b874f996a8 |
# Lint as: python3
"""A high level modeling interface for jax-based statistical + mechanistic models."""
import collections
import dataclasses
import functools
import itertools
from typing import Callable
import jax
import jax.numpy as jnp
import numpy as np
import xarray
import tensorflow_probability
tfp = tensorflo... | HopkinsIDD/EpiForecastStatMech | epi_forecast_stat_mech/stat_mech_estimator.py | Python | apache-2.0 | 17,310 | [
"Gaussian"
] | f0eb45855845fc0ee2fac10ce0e9ed908be8f923c8a08c429d596692dc4c1d92 |
#! /usr/bin/env python3
import os
import sys
import stat
class default_params:
mode_res = 256
output_timestep_size = -1
f_sphere = 0
timestepping_method = 'l_erk'
timestepping_order = 1
verbosity=0
timestep_size = 0.001
max_timesteps = 1
normal_mode_analysis = 0
rexi_m = 256
rexi_h = 0.15
rexi_hal... | schreiberx/sweet | benchmarks_sphere/paper_jrn_nla_rexi_linear/sph_rexi_paper_time_to_solution_timestepping_methods/jobs_create.py | Python | mit | 5,995 | [
"Gaussian"
] | cce15948e094b1c116053b0e881ccf077d331100d4584101eb9bf9f59aeaa8d8 |
import copy
import json
import subprocess
from os import system
import pyrebase
import requests
import collections
from Firefly import aliases, logging, scheduler
from Firefly.const import API_ALEXA_VIEW, API_FIREBASE_VIEW, FIREFLY_SECURITY_MONITORING, SOURCE_LOCATION, SOURCE_TIME, TYPE_DEVICE, TYPE_ROUTINE
from Fire... | Firefly-Automation/Firefly | Firefly/services/firebase/firebase.py | Python | apache-2.0 | 29,353 | [
"Firefly"
] | f0d7a92c3c9d25d78f5de65a4e51700b4859d1becc0ad0e40b7e01f4a0813f19 |
# -*- coding: utf-8 -*-
"""
Gaussians model: Inferring a mean and standard deviation.
Chapter 4.1, Bayesian Cognitive Modeling.
Created Aug/2015 by Johannes Keyser <j.keyser@donders.ru.nl>
"""
import pymc3 as pm
import numpy as np
import pandas as pd
x = np.array([1.1, 1.9, 2.3, 1.8])
model = pm.Model()
with model:... | JoKeyser/BCMinPyMC3 | ch4-1_Gaussian.py | Python | gpl-3.0 | 1,114 | [
"Gaussian"
] | 36838bd0027a7816f48709c4410a623cbf86fa4904730201b9808fe4fffd6ad7 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | src/python/espressomd/MDA_ESP/__init__.py | Python | gpl-3.0 | 8,024 | [
"ESPResSo",
"MDAnalysis"
] | 6f1b87830da875ef9887519adad49e656e7b0dca3b81e7db57b48920b2ca43bc |
# -*- coding: utf-8 -*-
#MIT License
#Copyright (c) 2017 Marton Kelemen
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the "Software"), to deal
#in the Software without restriction, including without limitation the rights
#to use, c... | mkelcb/knet | knet/com/application/logic/knet/knet_manager.py | Python | mit | 32,687 | [
"NEURON"
] | 0f1e47fc6d2a64d1b9313dbd4030e2a1d552c84b26af930107ce343e8ecc8cb9 |
# This code is so you can run the samples without installing the package
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
#
testinfo = "f 10 0.033, s, f 20 0.033, s, f 30 0.033, s, f 30 0.033, s, q"
tags = "particles, Galaxy"
import pyglet
import cocos
from cocos.director import ... | eevee/cocos2d-mirror | test/test_particle_galaxy.py | Python | bsd-3-clause | 911 | [
"Galaxy"
] | b6fcb1d08f1f47b2c4c9089369ee9a3fb9d1e9bd2dd6af353b8dbdea3be07b36 |
import os
import tempfile
from ase.io import write
import ase.parallel as parallel
from ase.old import OldASEListOfAtomsWrapper
def view(atoms, data=None, viewer='ag', repeat=None, block=False):
# Ignore for parallel calculations:
if parallel.size != 1:
return
if hasattr(atoms, 'GetUnitCell'):
... | slabanja/ase | ase/visualize/__init__.py | Python | gpl-2.0 | 1,574 | [
"ASE",
"Avogadro",
"RasMol",
"VMD"
] | 43875aac58a66ed75f72aad8b3fdf35edc4075e10423a0118eaf0fc2359651a3 |
import os
import re
import sys
from string import *
import commands
import subprocess
try: import cPickle as pickle
except: import pickle
from copy import copy, deepcopy
from math import log as math_log, sqrt
import random
NUMBERS='0123456789'
DNA_LETT='ACGT'
SS_LETT='0SETBH'
AA_LETT='ACDEFGHIKLMNPQRSTVWYUOB' ... | marco-mariotti/selenoprofiles | MMlib.py | Python | gpl-2.0 | 341,845 | [
"BLAST"
] | fd7a1f4d9455d46706449c4a1aa9c9e05d9a95b937734530d37b09e2255b268f |
# Licensed under GPL version 3 - see LICENSE.rst
import numpy as np
from astropy.table import Column
import astropy.units as u
from astropy.coordinates import SkyCoord
from ..base import SimulationSequenceElement
from ..math.rotations import axangle2mat
from ..math.utils import norm_vector, h2e, e2h
class PointingMo... | hamogu/marxs | marxs/source/pointing.py | Python | gpl-3.0 | 9,206 | [
"Gaussian"
] | 9d3d233f873cdc30c6e7eb468519fabb40a0b1c36a4c327f18b53ac2ef751e0f |
"""
homeassistant.components.isy994
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Connects to an ISY-994 controller and loads relevant components to control its
devices. Also contains the base classes for ISY Sensors, Lights, and Switches.
For configuration details please visit the documentation for this component at
https://home-a... | CCOSTAN/home-assistant | homeassistant/components/isy994.py | Python | mit | 7,012 | [
"VisIt"
] | 998dcfb9656667b70124a2929cdc798a75fe6d11326d25eb91e9c051dd48a3b5 |
# Author: Felix Wiemann
# Contact: Felix_Wiemann@ososo.de
# Revision: $Revision: 21817 $
# Date: $Date: 2005-07-21 13:39:57 -0700 (Thu, 21 Jul 2005) $
# Copyright: This file has been placed in the public domain.
# This is a mapping of Unicode characters to LaTeX equivalents.
# The information has been extracted from
#... | garinh/cs | docs/support/docutils/writers/unicode_latex.py | Python | lgpl-2.1 | 73,667 | [
"Bowtie"
] | fd96364111c87e34b32acac74798fa861fff08b9f371c85715a55d252f35350b |
from builtins import range, str
import numpy as np
from scipy.special import erf
try:
from scipy.weave import inline
except ImportError as e:
try:
from weave import inline
except ImportError as e:
pass
from peri.special import functions
from peri.comp import Component
from peri.util impor... | peri-source/peri | peri/comp/objs.py | Python | mit | 32,566 | [
"Gaussian"
] | 500ed0ba99858f54fc73d6489d23791e404eff2cd67467e899a6b6b54a247c69 |
"""
Certificate HTML webview.
"""
import logging
from datetime import datetime
from uuid import uuid4
import pytz
import six
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.http import Http404, HttpResponse
from django.template import RequestContext
from django.... | stvstnfrd/edx-platform | lms/djangoapps/certificates/views/webview.py | Python | agpl-3.0 | 32,627 | [
"VisIt"
] | 3113dda81e8c1e485a135d47a4a5edf518b9223bbbc7107f233725e504d716e9 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
A unified data anlaysis and visualization platform for computational and
theoretical chemists, physicists, etc. Support for molecular geometry and
orbital visualization is provid... | exa-analytics/exatomic | exatomic/__init__.py | Python | apache-2.0 | 2,551 | [
"ADF",
"ESPResSo",
"Gaussian",
"MOLCAS",
"NWChem",
"OpenMolcas",
"Quantum ESPRESSO"
] | 84eec5ff50fd3e6aeda6bbe18a5dc8ae39dae0959591178246fefd5af1eb360b |
"""
General Numerical Solver for the 1D Time-Dependent Schrodinger's equation.
author: Jake Vanderplas
email: vanderplas@astro.washington.edu
website: http://jakevdp.github.com
license: BSD
Please feel free to use and modify this, but keep the above information. Thanks!
"""
import numpy as np
from matplotlib import p... | ingelectronicadj/FisicaConPython | FisicaCuantica/Soluciones de la ecuacion de Schrodinger/schrodinger.py | Python | gpl-3.0 | 9,290 | [
"Gaussian"
] | 62936ef26a28cb0f738613c72fa1d62330c2d6599bc50c9b35d6adf21ad0c88d |
#########################################
# Polly.py
# categories: speech
# more info @: http://myrobotlab.org/service/Polly
#########################################
# start the service
polly = Runtime.start('polly','Polly')
polly.setKey("YOUR_KEY_ID","YOUR_KEY_SECRET")
polly.setLanguage("en")
polly.setVoice(u"Brian"... | MyRobotLab/pyrobotlab | service/Polly.py | Python | apache-2.0 | 491 | [
"Brian"
] | 8b4a8139b35d5d05b1d2cb805e2613dc45889a99a2be3919dc316d8e7b3fb496 |
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