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# Functions to implement several important functions for
# various Continous and Discrete Probability Distributions
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
import math
import warnings
from copy import copy
from scipy.misc import comb, derivative
from s... | jasonmccampbell/scipy-refactor | scipy/stats/distributions.py | Python | bsd-3-clause | 207,806 | [
"Gaussian"
] | ba488592958de538a4effb2be13498fcde15017d1ff58de19b2b9b33589efe7c |
"""Definitions of Celery tasks in Askbot
in this module there are two types of functions:
* those wrapped with a @task decorator and a ``_celery_task`` suffix - celery tasks
* those with the same base name, but without the decorator and the name suffix
the actual work units run by the task
Celery tasks are special ... | jesonyang001/qarepo | askbot/tasks.py | Python | gpl-3.0 | 9,694 | [
"VisIt"
] | 0c5626305b0942af933660035af3760104b8caff272046937018a4d0334f9411 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# ProxyAgentHandler - An Mip server
#
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Lice... | heromod/migrid | mig/vm-proxy/proxyagenthandler.py | Python | gpl-2.0 | 6,437 | [
"Brian"
] | 18fc5c2e165ee0eac11a7ef88a72e4453b42788403c897ee5eef3f0ef19d40a3 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/mp/mp2.py | Python | apache-2.0 | 3,539 | [
"PySCF"
] | ac9f3e8c02faaee2a302f887536738a805f70b04ca809931267e3428fa6b638f |
"""
gmagoon 07/06/09: new class for MOPAC parsing, based on gaussianparser.py from cclib, described below:
cclib (http://cclib.sf.net) is (c) 2006, the cclib development team
and licensed under the LGPL (http://www.gnu.org/copyleft/lgpl.html).
"""
__revision__ = "$Revision: 814 $"
#import re
import numpy... | connie/RMG-Java | source/cclib/parser/mopacparser.py | Python | mit | 10,487 | [
"MOPAC",
"cclib"
] | 7c546479bb43349ffa3502f481803eccf339ea57f68ba7381d9eb823d9024b2d |
# --------------------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# --------------------------------------------------------------------... | yugangw-msft/azure-cli | src/azure-cli/azure/cli/command_modules/acr/_params.py | Python | mit | 45,359 | [
"VisIt"
] | 6737052661c62ed4a14f3fa700e7bdce3329c26a0fd59ca0e9e1b316028c4dc7 |
"""
Backend wrapper
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC.FrameworkSystem.private.standardLogging.LogLevels import LogLevels
class AbstractBackend(object):
"""
AbstractBackend is used to create an abstractio... | yujikato/DIRAC | src/DIRAC/Resources/LogBackends/AbstractBackend.py | Python | gpl-3.0 | 4,578 | [
"DIRAC"
] | af460c8e83a555965b8176e2d3392450a14030effe59084d7d99d100044d092d |
from datetime import datetime
from urllib import urlencode
from jinja2 import Environment, FileSystemLoader
import cherrypy
from libbe import storage
from libbe import bugdir
from libbe.command.depend import get_blocked_by, get_blocks
from libbe.command.target import add_target, remove_target
from libbe.command.targe... | aaiyer/bugseverywhere | libbe/interfaces/web/web.py | Python | gpl-2.0 | 8,323 | [
"VisIt"
] | b12dd5d9abee93e8fcd32d70bdc6dc6031050d401d790f5c15ac8311e83da114 |
""" DIRAC FileCatalog Security Manager mix-in class with no access checks
"""
from DIRAC import S_OK
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.SecurityManager.SecurityManagerBase import SecurityManagerBase
class NoSecurityManager(SecurityManagerBase):
def getPathPermissions(self, paths, credDict):
... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/SecurityManager/NoSecurityManager.py | Python | gpl-3.0 | 868 | [
"DIRAC"
] | 5df2e1c5be785c8ee30a3fec8a2fe4cfc034e618a7f0aa83d9ea2e6833bcef20 |
#! /usr/bin/env python
"""
Routines to create front file removing md.1.last solutions.
So, in this front file contains solution from CASP11 stage2
These routines were developed by:
Rodrigo Antonio Faccioli - rodrigo.faccioli@usp.br / rodrigo.faccioli@gmail.com
Leandro Oliveira Bortot - leandro.b... | rodrigofaccioli/2pg_cartesian | scripts/analysis/CASP/creating_front_removing_md.py | Python | apache-2.0 | 2,406 | [
"Gromacs"
] | 6f7cdf2ef47daae03791ef5307e9c99cfa2727868f88a8f98a75f68bf7257a12 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/ipython/listfolders.py | Python | gpl-3.0 | 2,518 | [
"CRYSTAL",
"VASP"
] | f70cf5144cc1fded358599f61f44f1a971c2e5bbf23c57724227ccb35f1eaa77 |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2020 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Johann Rohwer (jrohwer@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permission to use... | bgoli/pysces | pysces/PyscesParScan.py | Python | bsd-3-clause | 13,323 | [
"PySCeS"
] | 62bcb559f431c381ac546efee3ff9b49b407b89a9b95ea21c8da672950d916b6 |
#!/usr/bin/env python
"""
dirac-rss-set-status
Script that facilitates the modification of a element through the command line.
However, the usage of this script will set the element token to the command
issuer with a duration of 1 day.
"""
from datetime import datetime, timedelta
from DIRAC ... | marcelovilaca/DIRAC | ResourceStatusSystem/scripts/dirac-rss-set-status.py | Python | gpl-3.0 | 8,786 | [
"DIRAC"
] | eb00f8dfa47a6a31822aadc536931ae53cb8342d278b7bb4f92b6736409dac47 |
Oatmeal_rasin_cookies = 42 # these are the assigned ingredients and their values
#ingredients needed with quantity
Cups_of_sugar_per42_cookies = .75
Cups_of_Brownsugar_per42_cookies = .25
Cups_of_Butter_per42_cookies = .5
Tspoon_of_vanilla_per42_cookies = .5
Eggs_per42_cookies = 1
Cups_of_flour_per42_cookies ... | FPU-CIS-312/MiniProject2 | CIS312_Project2_DeLaCruz.py | Python | mit | 6,584 | [
"VisIt"
] | 42114d59514f9fc7d2ae5025c07901bf286311f145cd5840bf08f16a446a19ef |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | demis001/scikit-bio | skbio/sequence/tests/test_dna.py | Python | bsd-3-clause | 1,674 | [
"scikit-bio"
] | bc743e268d35ad7637700a130ca76d2496973af78b811c8193cab27e45996740 |
#
# Copyright 2016 The BigDL 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 ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/tfpark/text/keras/text_model.py | Python | apache-2.0 | 1,856 | [
"ORCA"
] | 51185afe17071f277dd5fa28c1d0b8bb790086e3f462e3c0a6d81f59b3d315d9 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/images/lib/imagetab.py | Python | gpl-2.0 | 5,196 | [
"Brian"
] | daae3a305949a2169e2cfda8c3a2cc83e595d3ac4abe8d875e8b64d6dc6f70f9 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | to266/hyperspy | hyperspy/model.py | Python | gpl-3.0 | 60,233 | [
"Gaussian"
] | c1f42ef1837447913907674bced6e4792c1c9030e2abed96908b5ce40f28a318 |
"""
Routines for generating and sampling a Wigner vibrational distribution.
"""
import numpy as np
import scipy.linalg as sp_linalg
import nomad.math.constants as constants
import nomad.core.glbl as glbl
import nomad.core.log as log
import nomad.core.trajectory as trajectory
def set_initial_coords(wfn):
"""Sample... | mschuurman/FMSpy | nomad/initconds/wigner.py | Python | lgpl-3.0 | 6,068 | [
"Gaussian"
] | 8f3118d945a6e6ac88c7d4402fc8868eec2aff87b5b0a6b7d0c3b3874a15995a |
#!/usr/bin/env python
import unittest
class TestFusion(unittest.TestCase):
def test_01(self):
import HTSeq
self.assertTrue(len(str(HTSeq.__version__)) > 0)
def main():
unittest.main()
if __name__ == '__main__':
main()
| simon-anders/htseq | python2/tests/test_loading.py | Python | gpl-3.0 | 253 | [
"HTSeq"
] | 595477532923f25c706b9b21d48020e9d365aef90e3919d8222467b07811597e |
import netCDF4 as nc
import numpy as np
from rasterio.crs import CRS
from affine import Affine
# import os
# from datetime import date
from pprint import pprint
file1 = '/home/ldutrieux/sandbox/test_data/nc/test.nc'
meta = {'width': 3000,
'height': 2000,
'crs': CRS({u'lon_0': 0, u'ellps': u'WGS84', u... | loicdtx/blog | sandbox/test_geo_ncdf.py | Python | mit | 3,137 | [
"NetCDF"
] | 2333719e07e1eac21a29a5d20330be63b7c5b0f97abd5cf41ea093fe0bd2bec2 |
"""
Logging Root
"""
from __future__ import print_function
__RCSID__ = "$Id$"
import logging
import time
import sys
from DIRAC.FrameworkSystem.private.standardLogging.LogLevels import LogLevels
from DIRAC.FrameworkSystem.private.standardLogging.Logging import Logging
from DIRAC.Resources.LogBackends.StdoutBackend im... | fstagni/DIRAC | FrameworkSystem/private/standardLogging/LoggingRoot.py | Python | gpl-3.0 | 10,297 | [
"DIRAC"
] | 76f3c81c6e56abaff6edd1ec4df318e2ae364a8cbc9f1265e0724329d91b0070 |
import matplotlib
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
from scipy import polyfit, polyval, stats
import pandas as pd
from mytext import textTL, textTR
import statsmodels.api as sm
from patsy import dmatrices, ModelDesc, Term, LookupFactor
from copy import ... | agartland/utils | corrplots.py | Python | mit | 31,054 | [
"Gaussian"
] | 2f6c824f5fee30566ce76a89fc179ab6a71030cb000fd9c10410a4c6cee3a0dc |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/bin/__init__.py | Python | gpl-2.0 | 1,151 | [
"VisIt"
] | d3398a5be3954c16cf5f9696760bdba57111079233db38ce37c313f22bf7103d |
# -*- coding: iso-8859-1 -*-
# Copyright (C) 2007 Maryland Robotics Club
# Copyright (C) 2007 Joseph Lisee <jlisee@umd.edu>
# All rights reserved.
#
# Author: Joseph Lisee <jlisee@umd.edu>
#
# modified for pybert's vtk import to fit python-2.9@linux
# Standard python imports
import ctypes as __ctypes
import os.p... | florian-wagner/gimli | python/pygimli/gui/vtk/getHandleHack.py | Python | gpl-3.0 | 1,162 | [
"VTK"
] | 54ac5c4bf3a7d06ecbfcc5e2d8db661c14ffbe5b4b923feb5c6025e471eb0c55 |
# Copyright 2015 Docker, 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 agree... | kireledan/molecule | test/unit/test_interpolation.py | Python | mit | 3,418 | [
"Galaxy"
] | 2c6bd8a38782ea661bcd37500bc9b2afac901629946770f3b36d36770e25ee9f |
"""
Human cortical neuron using A-current model in reduced, 2D version of Hodgkin-Huxley model
Section 9.5
"""
from __future__ import division
from PyDSTool import *
from PyDSTool.Toolbox.phaseplane import *
from PyDSTool.Toolbox.PRCtools import *
from common_lib import *
from Ch9_HH_red import *
gentype='dopri' # d... | robclewley/compneuro | Ch9_HH_humanPRC.py | Python | bsd-3-clause | 1,394 | [
"NEURON"
] | 1de45d9c4142ed999aa64cdc6b8ae58e2ae70b64929803c77c73806c76fbd6ba |
# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from .gp import GP
from .parameterization.param import Param
from ..inference.latent_function_inference import var_dtc
from .. import likelihoods
from .parameterization.variational i... | beckdaniel/GPy | GPy/core/sparse_gp.py | Python | bsd-3-clause | 8,908 | [
"Gaussian"
] | 77b47ea7a19b667f90f916f35035c2076373c079389623c0842a5d788aac0e01 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | demis001/scikit-bio | skbio/tree/tests/test_nj.py | Python | bsd-3-clause | 8,963 | [
"scikit-bio"
] | 5914b3971a74ad1778cbdb6179d1c4f817054cfa8f3d71d596d63094fd318ce8 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 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 Gen... | sam-m888/gprime | gprime/filters/rules/_hassourcecountbase.py | Python | gpl-2.0 | 2,621 | [
"Brian"
] | a19482c45d474c6bd8a5af521e82af038d36c21e7cd19a5b79a8dc2c22c05f5f |
import sys, os, re
import pickle, json
import shelve
import pkgutil, pyclbr, inspect, ast
import traceback
from importlib import import_module
from collections import OrderedDict
from itertools import groupby
import zlib
import numpy as np
from pymake import ExpDesign, ExpeFormat
from pymake import get_pymake_settings... | dtrckd/pymake | pymake/frontend/io.py | Python | gpl-3.0 | 25,337 | [
"VisIt"
] | 5dddebd7c259852cb581a2a4320908743780d110dd613457c73705e2edd0667e |
#!/usr/bin/env python
"""
Submit a DRMAA job given a user id and a job template file (in JSON format)
defining any or all of the following: args, remoteCommand, outputPath,
errorPath, nativeSpecification, name, email, project
"""
import os
import sys
import errno
import pwd
import json
#import drmaa
new_path = [ os.... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/scripts/drmaa_external_runner.py | Python | gpl-3.0 | 4,091 | [
"Galaxy"
] | c6462c27986e01d87e95bd95f32642b325dac3f9ddf062625ab055eb51b2be4c |
# Copyright 2015 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
import ast
import re
import unittest
from dataclasses import dataclass
from enum import Enum
from pathlib import Path
from textwrap import dedent
from typing import Callable, List, Optiona... | jsirois/pants | src/python/pants/engine/rules_test.py | Python | apache-2.0 | 36,272 | [
"VisIt"
] | 9d690edaa04da8b5ecde3f105f395c1af06bc55a1a7469f19cb42e056c343319 |
"""
Classes for generating HTML forms
"""
import logging, sys, os, time
from operator import itemgetter
from cgi import escape
from galaxy.util import restore_text, relpath, nice_size, unicodify
from galaxy.util.json import dumps
from galaxy.web import url_for
from binascii import hexlify
log = logging.getLogger(__n... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/web/form_builder.py | Python | gpl-3.0 | 38,961 | [
"Galaxy"
] | 9c857e2ec4c8a777db569389d62a0bc51f74355ad7436dc5e3ca2a0cbc566106 |
################################################################################
# ________ ________ ________ ________ ___ _____ ______
# |\ __ \|\ __ \|\ ___ \|\ ____\|\ \|\ _ \ _ \
# \ \ \|\ \ \ \|\ \ \ \_|\ \ \ \___|\ \ \ \ \\\__\ \ \
# \ \ __ \ \ ____\ \ \ \\ \... | azov3902/linguinesim | __init__.py | Python | gpl-3.0 | 2,051 | [
"Galaxy"
] | 1127ac1e6e93472a26994cd9a088a65250fb68288bb3f368ffd47c79a8cb31fd |
# Copyright (c) 2012, 2013 Ricardo Andrade
# Copyright (c) 2015 James Hensman
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from scipy.special import ndtr as std_norm_cdf
#define a standard normal pdf
_sqrt_2pi = np.sqrt(2*np.pi)
def std_norm_pdf(x):
x = np.clip(x,-1e150,1e150)
... | mikecroucher/GPy | GPy/util/univariate_Gaussian.py | Python | bsd-3-clause | 5,982 | [
"Gaussian"
] | 844b84800ecfe553a4960ead8a32584590b56381b676a610f84b6bd1938cf1e9 |
"""
=================
django-geckoboard
=================
Geckoboard_ is a hosted, real-time status board serving up indicators
from web analytics, CRM, support, infrastructure, project management,
sales, etc. It can be connected to virtually any source of quantitative
data. This Django_ application provides view de... | jcassee/django-geckoboard | django_geckoboard/__init__.py | Python | mit | 13,255 | [
"Amber"
] | b88b5beedcc114b8c411ac29454098f83d84b212080f15d78c460d57b3531380 |
from octopus.core import app
from octopus.modules.epmc import client as epmc
from octopus.modules.doaj import client as doaj
from octopus.modules.crossref import client as crossref
from octopus.modules.identifiers import pmid, doi, pmcid
from octopus.lib import mail
from service import models, sheets, licences
import o... | CottageLabs/oacwellcome | service/workflow.py | Python | apache-2.0 | 44,828 | [
"Octopus"
] | 4f4f5b2967837c3d75709767ff6595c30b76a3fa5822caeebc3a6ec87cb04165 |
# Copyright 2021 Open Source Robotics Foundation, 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... | ros2/launch | launch_xml/test/launch_xml/test_reset.py | Python | apache-2.0 | 2,224 | [
"VisIt"
] | 669ae9942595b4ddd573814d0185ccf25b78d801e5da05c4c69230e0a999ff05 |
import pandas as pd
import ujson
from textwrap import indent
from ..client import inject_client
from ..neuroncriteria import neuroncriteria_args
from ..utils import compile_columns
# Core set of columns
CORE_NEURON_COLS = ['bodyId', 'instance', 'type',
'pre', 'post', 'downstream', 'upstream', 'mit... | connectome-neuprint/neuprint-python | neuprint/queries/neurons.py | Python | bsd-3-clause | 11,449 | [
"NEURON"
] | 03fb718e33ff638807eed8cd34f6ee01faf697d8b2bf378077ac8a57c08f02fd |
# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | GoogleCloudPlatform/functions-framework-python | tests/test_decorator_functions.py | Python | apache-2.0 | 2,134 | [
"Galaxy"
] | 1c50b3519bb6b4900e9dc0633135347c1160c54a76883a0eea3631ad083c9661 |
'''
Flickr Search API miner
Text search is happening in the following way (from: https://www.flickr.com/services/api/flickr.photos.search.html):
Photos who's title, description or tags contain the text will be returned.
You can exclude results that match a term by prepending it with a - character.
'''
import ... | douwekiela/mmfeat | mmfeat/miner/flickr.py | Python | bsd-3-clause | 6,397 | [
"VisIt"
] | af6d9db2f06654a0b2241ba6316e495ec22d9a25662ed4cdea24ca623f98bd0a |
"""
===================
Module: bbcflib.snp
===================
From a set of BAM files produced by an alignement on the genome, calls snps and annotates them
with respect to a set of coding genes on the same genome.
"""
# Built-in modules #
import sys, tarfile
from itertools import product
import math
# Internal mod... | bbcf/bbcflib | bbcflib/snp.py | Python | gpl-3.0 | 23,704 | [
"pysam"
] | 58b2099bb24563cffff581a5514915a61b2ae18281fced881fad371450530227 |
"""
Test command line program dials.two_theta_refine by running a job with saved
data and comparing with expected output.
"""
from __future__ import annotations
from pathlib import Path
import procrunner
import pytest
from dxtbx.model.experiment_list import ExperimentListFactory
def test(dials_data, tmpdir):
... | dials/dials | tests/command_line/test_two_theta_refine.py | Python | bsd-3-clause | 3,234 | [
"CRYSTAL"
] | 2a51061f582585cc18b740a7b7fc2849f58d56f5f075f0926f8636c141fb5500 |
import os
import sys
import json
from datamanagerpkg import ProtonCommunication_data_manager
from datamanagerpkg import GalaxyCommunication_data_manager
from sequencer.models import Experiments, GalaxyUsers
from sequencer.models import GalaxyJobs, ExperimentRawData
from sequencer.models import UserCommonJobs,Supported... | CARPEM/GalaxyDocker | data-manager-hegp/analysisManager/analysismanager/STARTUP_Add_Workflows_Information.py | Python | mit | 8,085 | [
"Galaxy"
] | 94da49d94753042b51c5f07058d02e1ad37d33f5718bb3d84ac3c508402bf20a |
#
# 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... | dhalperi/beam | sdks/python/apache_beam/examples/snippets/snippets.py | Python | apache-2.0 | 40,432 | [
"VisIt"
] | 03421fde5c5dd26b490be9bd1514592d94478bf103585c6e4e9c214cc899dd10 |
"""
==========================================
Symmetric Diffeomorphic Registration in 2D
==========================================
This example explains how to register 2D images using the Symmetric Normalization
(SyN) algorithm proposed by Avants et al. [Avants09]_ (also implemented in
the ANTS software [Avants11]_... | nilgoyyou/dipy | doc/examples/syn_registration_2d.py | Python | bsd-3-clause | 7,053 | [
"Gaussian"
] | 57ec5408027c81101cc09f6b054f254a5e8568a4fee362d64a0011d069119522 |
# (C) British Crown Copyright 2010 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | davidnmurray/iris | lib/iris/__init__.py | Python | gpl-3.0 | 13,779 | [
"NetCDF"
] | 7eff6c532e44a62addd5e57afe5d813b45164847232ac141a9e38390bd4012ad |
#!/usr/bin/python2.7
# Copyright 2010 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | saicheems/discovery-artifact-manager | google-api-client-generator/src/googleapis/codegen/api.py | Python | apache-2.0 | 36,860 | [
"VisIt"
] | 95ec99d02bf882b4723d83dbbea941d70c13b2b404ee558651341f968827b8d4 |
"""
Title: RandAugment for Image Classification for Improved Robustness
Author: [Sayak Paul](https://twitter.com/RisingSayak)
Date created: 2021/03/13
Last modified: 2021/03/17
Description: RandAugment for training an image classification model with improved robustness.
"""
"""
Data augmentation is a very useful techni... | keras-team/keras-io | examples/vision/randaugment.py | Python | apache-2.0 | 11,421 | [
"Gaussian"
] | 0eebebd92af956e6435f91aa1b0faa13fcbaf9aa1bbd92e8fb5e2a5103e73ab2 |
"""
FCKeditor - The text editor for internet
Copyright (C) 2003-2006 Frederico Caldeira Knabben
Licensed under the terms of the GNU Lesser General Public License:
http://www.opensource.org/licenses/lgpl-license.php
For further information visit:
http://www.fckeditor.net/
"Support Open Source software. ... | 7421121176/docvert | core/lib/fckeditor/fckeditor.py | Python | gpl-3.0 | 3,896 | [
"VisIt"
] | 6f0d194eb8c34814b601a1347ecb3951469037005499e313e07cb2b5648d3223 |
#!/usr/bin/env python
from vtk import *
import os.path
data_dir = "../../../../VTKData/Data/Infovis/SQLite/"
if not os.path.exists(data_dir):
data_dir = "../../../../../VTKData/Data/Infovis/SQLite/"
if not os.path.exists(data_dir):
data_dir = "../../../../../../VTKData/Data/Infovis/SQLite/"
sqlite_file = data_dir ... | jmerkow/VTK | Examples/Infovis/Python/streaming_statistics.py | Python | bsd-3-clause | 3,140 | [
"VTK"
] | a9ca1f882bcbbc157ed27c8bfb9975b35c385ab12d5769f48812ae88635c066f |
# -*- coding: utf-8 -*-
####################################################################################################
#
# PySpice - A Spice Package for Python
# Copyright (C) 2014 Fabrice Salvaire
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Pu... | FabriceSalvaire/PySpice | PySpice/Spice/HighLevelElement.py | Python | gpl-3.0 | 31,274 | [
"Gaussian"
] | 2ca8ac0dc44dc4c2624f3d2b040df2986b67c0fbe6f7a83dbd3747cce27996b6 |
#! /usr/bin/env python
"""
Module with cube cosmetic functions for SDI datasets.
"""
from __future__ import division
from __future__ import print_function
__author__ = 'V. Christiaens @ UChile/ULg, C. Gomez @ ULg'
__all__ = ['cube_correct_nan',
'approx_stellar_position']
import copy
import numpy as np
fr... | henry-ngo/VIP | vip_hci/preproc/cosmetics_ifs.py | Python | mit | 7,298 | [
"Gaussian"
] | 1af50a0a09bbba0e021917904551389c04d36ae74c1680717714b70284bd8b04 |
#!/usr/local/bin/env python
# =============================================================================================
# MODULE DOCSTRING
# =============================================================================================
"""
Run YANK self tests after installation.
"""
# ===========================... | choderalab/yank | Yank/commands/selftest.py | Python | mit | 8,985 | [
"OpenMM"
] | 5f2cc05661f38a4c697b98d891f9e1bce0cbc83780c22dc6276d08722eec8b6a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides classes to perform topological analyses of structures.
"""
__author__ = "Shyue Ping Ong, Geoffroy Hautier, Sai Jayaraman"
__copyright... | aykol/pymatgen | pymatgen/analysis/structure_analyzer.py | Python | mit | 65,115 | [
"CRYSTAL",
"Gaussian",
"pymatgen"
] | 89a8631f78f4061372e21e065adc88f1d4c49bbd377a3267035e25822ff1eab8 |
#!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# 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,... | govarguz/espressopp | testsuite/ljcos/test_ljcos.py | Python | gpl-3.0 | 2,338 | [
"ESPResSo"
] | 4c406c20c5fa80b617a2a7094381a737ed85473cbcd798803b944622c974205e |
"""Visits API views."""
from dry_rest_permissions.generics import DRYPermissions
from rest_framework import mixins, status, viewsets
from rest_framework.decorators import action
from rest_framework.response import Response
from .models import Participation, Place, Visit
from .serializers import (ParticipationCancell... | oser-cs/oser-website | visits/views.py | Python | gpl-3.0 | 6,803 | [
"VisIt"
] | ad9fbd20f04c789ad4270c0f19e15bed9410bd72e4dd951bafd55d307b07c57c |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkEnSightGoldReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkEnSightGoldReader.py | Python | bsd-3-clause | 496 | [
"VTK"
] | a86a1034699c9b9dff8ea5cfab6173ef845f198cd9f07b2df081e62d25fdc4d2 |
usage="""a module to compute basic statistics of skymaps"""
import healpy as hp
import numpy as np
#=================================================
#
# general helper methods
#
#=================================================
def cos_dtheta(theta1, phi1, theta2, phi2, safe=False):
"""
computes the angular separ... | reedessick/skymap_statistics | skymap_statistics/stats.py | Python | gpl-2.0 | 21,174 | [
"Gaussian"
] | a72b16e696f7b616d39770f0dc79c38b3402b24a50a6208df88a8a2ffe934739 |
from __future__ import print_function as _print_function
from __future__ import absolute_import as _absolute_import
import os
import unittest
import tempfile
import numpy as np
import debacl as dcl
from numpy.testing import assert_array_equal
class TestLSTConstructors(unittest.TestCase):
"""
Test that the v... | CoAxLab/DeBaCl | debacl/test/test_lst.py | Python | bsd-3-clause | 19,190 | [
"Gaussian"
] | 9e761d3ef6f7d7c0d2b1da0c105efc81e6eb2cd6afe160da5bf889205188247c |
from llts.models import *
from llts.serializers import *
from llts import permissions as localpermissions
from django.contrib.auth.models import User
from django.contrib.auth import get_user_model
from django.db import transaction
from rest_framework import generics, permissions, views, status, mixins
from rest_framewo... | ryanrborn/lds-leader-tool-suite-backend | llts/views.py | Python | mit | 6,074 | [
"VisIt"
] | 8b450f4e64035c092a67c1a0f57850a0220c033ffb55c36014a3f2fa7ddbf9bb |
#
# Copyright 2014-2015, 2017, 2021 Lars Pastewka (U. Freiburg)
# 2018-2021 Jan Griesser (U. Freiburg)
# 2020 Jonas Oldenstaedt (U. Freiburg)
# 2015 Adrien Gola (KIT)
# 2014 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://gith... | libAtoms/matscipy | matscipy/calculators/__init__.py | Python | lgpl-2.1 | 1,292 | [
"Matscipy"
] | 7e45b0de201c20d11ca4cdbd817fbdc0c9dcedc4a8941e7c0ac666f0c414bd0a |
"""
New version of bioconductor? This script goes through each current Bioconductor
recipe, finds the corresponding dependencies that are also in this repo, and
reports the [reverse toplogically sorted] set of Bioconductor packages that
should be updated using bioconductor-scraper.py.
In other words, the first items i... | jasper1918/bioconda-recipes | scripts/bioconductor/update_bioconductor_packages.py | Python | mit | 1,989 | [
"Bioconda",
"Bioconductor"
] | f90ba68594b055cd8c6d2acc60fe43704cf4a7735a34e1b6e55779128abde462 |
from cytoscape_helper import ViewStyle
node_shapes = ('ellipse', 'triangle', 'rectangle', 'roundrectangle', 'cutrectangle', 'bottomroundrectangle', 'barrel',
'rhomboid', 'diamond', 'pentagon', 'hexagon', 'concavehexagon', 'heptagon', 'octagon', 'star', 'vee')
node_background = ('background-color', 'back... | danielkupco/viewX-vscode | src/python/cytoscape_rule_engine.py | Python | mit | 11,194 | [
"Cytoscape",
"VisIt"
] | 2f057f6195a486f460fcf0cf83a3a16112eb40d797aecafcc13004a6be8872a0 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
import random
def drawVertex(myscreen, p, vertexColor, rad=1):
myscreen.addActor( camvtk.Sphere( center=(p.x,p.y,p.z), radius=rad, color=vertexColor ) )
def drawEdge(myscreen, e, edgeColor=camvtk.yellow):
p1 = e[0]
p2 = e[1]
m... | AlanZatarain/opencamlib | scripts/voronoi/voronoi_9_graphviz.py | Python | gpl-3.0 | 9,367 | [
"VTK"
] | e6e2028edf11db3ee481e9c3995b8a790b0956509d3235e19f2e890e22558836 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RAgdex(RPackage):
"""Agreement of Differential Expression Analysis.
A tool to eval... | iulian787/spack | var/spack/repos/builtin/packages/r-agdex/package.py | Python | lgpl-2.1 | 1,042 | [
"Bioconductor"
] | 8a67b39762e7a41a78095dafb09e25f1b41202df8d961d8e9495a75f5a49db08 |
#!/usr/bin/python3.4
# Copyright 2015 Dalton Nikitas
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... | rhiw/yggdrasil | scripts/python/volume_resizer.py | Python | apache-2.0 | 4,090 | [
"Dalton"
] | 9d2144eb63ae33337381013960fccac64b52010471f2430267b5a8a7de6e9f10 |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | paulojamorim/invesalius3 | invesalius/data/surface.py | Python | gpl-2.0 | 37,383 | [
"VTK"
] | 9576509ff280a13a2ed27431ba7c4eeba9a6583935d67babb8046e110c52c10b |
from galaxy import config, tools, jobs, web
import galaxy.model.mapping
class UniverseApplication( object ):
"""Encapsulates the state of a Universe application"""
def __init__( self, **kwargs ):
# Read config file and check for errors
self.config = config.Configuration( **kwargs )
self... | jmchilton/galaxy-central | galaxy/app.py | Python | mit | 1,636 | [
"Galaxy"
] | 8fc1ce85a367becfc33d42253a87b8efb2168f53127f795e406666e3a6ec5336 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Foundati... | tiagocardosos/stoq | stoqlib/gui/test/test_payment_editor.py | Python | gpl-2.0 | 9,904 | [
"VisIt"
] | a84d4444d68f63f2cb64597ea38ce076dc94dce21f7ad48f3897f3f3e912db3c |
from .utilsTest import (cp2k_available, remove_files)
from nac.common import read_cell_parameters_as_array
from nac.workflows.input_validation import process_input
from qmflows import (cp2k, run)
from scm import plams
import pytest
def test_input_validation():
"""
test the templates and keywords completion
... | felipeZ/nonAdiabaticCoupling | test/test_input_validation.py | Python | mit | 1,685 | [
"CP2K"
] | f33205a7ddafb088d636e68dcd23641dcef9bc2827564cdec155298e8c613e4a |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | imaculate/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 64,632 | [
"Brian"
] | 5af31f5f2c6a6692f42c3dd0159a29456c7af4159cd83d5925a1533546f6fdb1 |
#! /usr/bin/env python
from openturns import *
import math
TESTPREAMBLE()
RandomGenerator.SetSeed(0)
try:
# for fft, the best implementation is given for N = 2^p
size = 16
# collection for test
collection = NumericalComplexCollection(size)
# Fill the data with artificial values
# Create a... | sofianehaddad/ot-svn | python/test/t_KissFFT_std.py | Python | mit | 2,038 | [
"Gaussian"
] | de0623c424008ba508d578d2f1b14505abfcae7642b1257b37df81f8fe03ca8a |
import logging
import httplib2
import json
import os
import hashlib
# This module performs authentication based on the tokens
# issued by Globus Online's Nexus service, see this URL for
# details:
# http://globusonline.github.com/nexus-docs/api.html
#
# Import the Globus Online client libraries, originally
# sourced f... | PATRIC3/auth | python-libs/oauth.py | Python | mit | 8,832 | [
"VisIt"
] | f153f3fa13619c4574c79f80a18d2ee3e97677c1f21cb72b0badfcb02323c089 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2006 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/gui/editors/stationeditor.py | Python | gpl-2.0 | 2,747 | [
"VisIt"
] | 7cf5d973cd7eecfb375c3386debeffcc8738273a33ee15cb3d86b6a848e981d1 |
# -*- coding: utf-8 -*-
"""Production example script that averages repeated tranects, resolving and visualizing secondary circulation
Driver script that is designed to average repeated ADCP transect observations
in an effort of reduce measurement error and better resolve non-steamwise and
velocities and secondary circ... | esatel/ADCPy | adcpy/transect_average.py | Python | mit | 12,135 | [
"NetCDF"
] | 68eda5f14239bedf8d02bb016f2b94ab54e262859555ebe519cdc7376eeceaa2 |
#!/usr/bin/env python3
#
# A PyMol extension script template
#
def main():
"""main"""
raise RuntimeError('This module should not be executed as a script')
if __name__ =='__main__':
main()
in_pymol = False
try:
import pymol
in_pymol = True
except ImportError as ie:
main()
... | joy13975/elfin | pymol_scripts/extensions/extension_template.py | Python | mit | 403 | [
"PyMOL"
] | 95d52a912643f9971d5e29357bacfbbdf8fc02961e781ce193c5a70c0bb7b2d6 |
""" :mod: RequestTaskTests
=======================
.. module: RequestTaskTests
:synopsis: test cases for RequestTask class
test cases for RequestTask class
"""
__RCSID__ = "$Id $"
# #
# @file RequestTaskTests.py
# @author Krzysztof.Ciba@NOSPAMgmail.com
# @date 2013/03/27 15:59:40
# @brief Definition ... | andresailer/DIRAC | RequestManagementSystem/private/test/RequestTaskTests.py | Python | gpl-3.0 | 3,127 | [
"DIRAC"
] | 514da6d039c9d8dee2d13ae0cdd2d54482d4be9778f68b733e3a26cacbee8b65 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import numpy as np
import unittest
import os
from pymatgen.analysis.local_env import ValenceIonicRadiusEvaluator, \
VoronoiNN, VoronoiNN_modified, JMolNN, \
... | gpetretto/pymatgen | pymatgen/analysis/tests/test_local_env.py | Python | mit | 36,366 | [
"Jmol",
"pymatgen"
] | d07ac06d5d69402989e60b3cf1f73adf0d52eb074c0c9b598d0124a2362c271b |
info = {
"name": "ln",
"date_order": "DMY",
"january": [
"sánzá ya yambo",
"yan"
],
"february": [
"fbl",
"sánzá ya míbalé"
],
"march": [
"msi",
"sánzá ya mísáto"
],
"april": [
"apl",
"sánzá ya mínei"
],
"may": [
... | scrapinghub/dateparser | dateparser/data/date_translation_data/ln.py | Python | bsd-3-clause | 3,004 | [
"Yambo"
] | cb8f2d4927b8cfd6cbe83faa44c99e694119b7f89da2021a271dbeb1f6917e75 |
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distribu... | quantumlib/OpenFermion-PySCF | openfermionpyscf/_pyscf_molecular_data.py | Python | apache-2.0 | 10,620 | [
"PySCF"
] | bca280c6b38d88385ea3d47f26a01aee04210f1f68abd7e852a2ec9e2d10240b |
# Copyright 2002 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from Bio.config.DBRegistry import CGIDB, DBGroup
prodoc_expasy_cgi = CGIDB(
name="prodoc-... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/dbdefs/prodoc.py | Python | apache-2.0 | 589 | [
"Biopython"
] | 569f08dd93126727d9dee9e709495a9260342fd58d7404fd699de7258a194f52 |
from __future__ import division #brings in Python 3.0 mixed type calculation rules
import logging
import numpy as np
import pandas as pd
class ScreenipFunctions(object):
"""
Function class for screenip.
"""
def __init__(self):
"""Class representing the functions for screenip"""
super(... | puruckertom/ubertool | ubertool/screenip/screenip_functions.py | Python | unlicense | 16,439 | [
"VisIt"
] | 8e7588fc67f46ad1173fbd7533a5bd9eddbb20116da913b67e366b9ea699bdca |
# Orca
#
# Copyright 2004-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | h4ck3rm1k3/orca-sonar | src/orca/scripts/apps/gedit/script.py | Python | lgpl-2.1 | 5,782 | [
"ORCA"
] | 0da08e03150b8dadd3af4b28be18d58b254c21a23f3631e24c8ad4ae4a6efd13 |
#!/usr/bin/env python
"""
Convert an e-value to a bit score.
Example usage:
$ e-value-to-bit-score.py --dbSize 168142520 --dbSequenceCount 5660 \
--queryLength 111 --lengthAdjustment 26 --eValue 0.0813077725194
37.3537
"""
from __future__ import print_function
import argparse
from dark.blast.score import eValue... | acorg/dark-matter | bin/e-value-to-bit-score.py | Python | mit | 1,259 | [
"BLAST"
] | 2c1a894c88a90889c93b881f56b8fc8fedc85aec23b1bde79b65099031096563 |
#!/usr/bin/python
#
# Open SoundControl for Python
# Copyright (C) 2002 Daniel Holth, Clinton McChesney
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the Licen... | nuigroup/pymt-widgets | pymt/lib/osc/OSC.py | Python | lgpl-3.0 | 10,856 | [
"VisIt"
] | cbe2c1cdb20b474a322fb26b1f1f8844031b41aca826987f50e058025ee11907 |
###################################################################################################
# Facade to Apache Commons Math
###################################################################################################
import sys
import math
import operator
import java.util.List
import java.lang.reflect... | paulscherrerinstitute/pshell | src/main/assembly/script/Lib/mathutils.py | Python | gpl-3.0 | 29,683 | [
"Gaussian"
] | 65d3734e8b851c4c2b4e81e7f5656fa7adf607c2e863bc6e7b6689467483a48e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Views tests for the OSF."""
from __future__ import absolute_import
import datetime as dt
import httplib as http
import json
import time
import unittest
import urllib
from flask import request
import mock
import pytest
from nose.tools import * # noqa PEP8 asserts
from... | icereval/osf.io | tests/test_views.py | Python | apache-2.0 | 209,983 | [
"Brian",
"VisIt"
] | 3740e7a39d49f07936cb21e686db4424f2d356a9695666994ca0313b54a27ea5 |
"""An example of how to generate a 3D structured points dataset
using numpy arrays. Also shown is a way to visualize this data with
the mayavi2 application.
The script can be run like so::
$ mayavi2 -x structured_points3d.py
Alternatively, it can be run as::
$ python structured_points3d.py
"""
# Author: Prabh... | dmsurti/mayavi | examples/mayavi/advanced_visualization/structured_points3d.py | Python | bsd-3-clause | 2,276 | [
"Mayavi",
"VTK"
] | 5335d0704b852d326bb239f0635d3ec613264f317978e507dfdb9e2e5e5988c6 |
# -*- python -*-
# vim:set ft=python:
# @@PLEAC@@_NAME
# @@SKIP@@ Python
# @@PLEAC@@_WEB
# @@SKIP@@ http://www.python.org
# @@PLEAC@@_INTRO
# @@SKIP@@ The latest version of Python is 2.4 but users of 2.3 and 2.2 (and
# @@SKIP@@ in some cases earlier versions) can use the code herein.
# @@SKIP@@ Users of 2.2 and 2.3 ... | agoncal/core | text/src/test/resources/examples/python/pleac.in.py | Python | epl-1.0 | 304,306 | [
"MOE"
] | 9464fc8290756e73920cba264379f1b92834c90ef9a1e4828e824b4d361d751d |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors: Robert McGibbon, John D. Cho... | ctk3b/mdtraj | mdtraj/formats/mol2.py | Python | lgpl-2.1 | 7,931 | [
"MDTraj",
"OpenMM"
] | 5e458aa227f439c5c8f61fe50be2139ec69b7bc1e1de3bafc1d7664c90dbdbc6 |
#!/usr/bin/env python
# Processes uploads from the user.
# WARNING: Changes in this tool (particularly as related to parsing) may need
# to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools
from __future__ import print_function
import codecs
import errno
import gzip
import os
import shutil
import sy... | MGEScan/mgescan | galaxy-modified/tools/mgescan/upload.py | Python | gpl-3.0 | 20,266 | [
"Galaxy"
] | 6a3504d03a1ac391f489ed0c28b6edde52ced9f7ed8f8eacbba76c3986eaaa75 |
# Helper script for understanding stencils and convolutions
from scipy import signal
from scipy import ndimage
import numpy as np
def format1dforcplusplus(arr):
return '{' + ','.join(str(round(e)) for e in arr) + '}'
def format2dforcplusplus(arr):
return '{' + ','.join(format1dforcplusplus(e) for e in arr) +... | GollyGang/ready | Scripts/Python/convolve.py | Python | gpl-3.0 | 3,429 | [
"Gaussian"
] | 6f1c11b439e9de997a323924c7c3354fb401a86da607229316005ccc84759b5f |
"""
To know more or get code samples, please visit my website:
https://morvanzhou.github.io/tutorials/
Or search: 莫烦Python
Thank you for supporting!
"""
# please note, all tutorial code are running under python3.5.
# If you use the version like python2.7, please modify the code accordingly
# 9 - Autoencoder example
... | MediffRobotics/DeepRobotics | DeepLearnMaterials/tutorials/kerasTUT/9-Autoencoder_example.py | Python | gpl-3.0 | 2,216 | [
"VisIt"
] | 669f78abef6f7f2677074e0e90b837554bc2133833ca702f36a64edad41389e5 |
#!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# 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,... | kkreis/espressopp | testsuite/DPDThermostat/test_DPDThermostat.py | Python | gpl-3.0 | 6,256 | [
"ESPResSo"
] | b4f362f7d418f1758774a8cc230e125892b34e2f5b178aaf866daedc3895a7ce |
#!/usr/bin/env python
"""
Manage DFT calculations on the cluster computer via some scheduler.
- Search directories under given directory whether there are directories
in which a DFT calculation should be done.
- Compute nodes required to compute those DFT calculations.
- Create job scripts for each submission.
Usage... | ryokbys/nap | nappy/clutil/clmgr.py | Python | mit | 24,257 | [
"VASP"
] | 3c6e24656f6cd5007610d61dfc7e0ea6acfde05e4f945beb37dbaa8c7a1e76d9 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
from bi... | DJMedhaug/BizSprint | config/urls.py | Python | bsd-3-clause | 2,605 | [
"VisIt"
] | f7ed44317455898bf1819439ea75dca95883cea852b4df2b4d3faa850eaf3277 |
import numpy as np
def doublebar(i,j,k,l, Vee):
return Vee[i,j,k,l] - Vee[i,j,l,k]
def Dir2Mul(p,q,r,s, Vee):
#Dirac to Mulliken notation
return Vee[p,r,q,s]
def MP2(occ, F, C, VeeMO):
#Get MO orbital energies
CT = np.transpose(C)
eps = np.dot(np.dot(CT, F),C)
#Calc... | Melisius/SlowQuant | slowquant/mollerplesset/MPn.py | Python | bsd-3-clause | 3,418 | [
"DIRAC"
] | 134563050f8d2cb18201913549c0f76742d3fa3d7e1543d2c27671588edbadf4 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
""" Generator for C style prototypes and definitions """
import glob
import os
import re
import sys
from idl_log import ErrOut, I... | zcbenz/cefode-chromium | ppapi/generators/idl_c_header.py | Python | bsd-3-clause | 9,704 | [
"VisIt"
] | 25e4c5989b692c61c24a54d24e29d073ef82741655233b11a5d8ccd91fbef07e |
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