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#!/usr/bin/env python3
"""
Module with implementation of the daemon part of lgogwebui.
"""
import os
import re
import json
from fcntl import fcntl, F_GETFL, F_SETFL
from subprocess import Popen, PIPE
from threading import Timer
from queue import Queue
from time import sleep
from datetime import datetime
from sqlalchem... | graag/lgogwebui | lgogdaemon.py | Python | bsd-2-clause | 17,816 | [
"Galaxy"
] | 1a516c9fdfc083cb765ded813e4a0bbbff46d18b0512989ece33a3695db38a17 |
#!/usr/bin/env python
import numpy as np
import argparse
import json
import os
import random
import ray
from ray import tune
from ray.tune.schedulers import PopulationBasedTraining
def pbt_function(config, checkpoint_dir=None):
"""Toy PBT problem for benchmarking adaptive learning rate.
The goal is to opti... | richardliaw/ray | python/ray/tune/examples/pbt_function.py | Python | apache-2.0 | 3,953 | [
"Gaussian"
] | 59e35212a60eddefcacf9e70d6da285461357c6d71524f4c3346fe51e2427de5 |
# FIXME: to bring back to life
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from DIRAC.Resources.Catalog.FileCatalogClient import FileCatalogClient
import cmd
import sys
from DIRAC.DataManagementSystem.Client.CmdDirCompletion.AbstractFileSystem import D... | ic-hep/DIRAC | tests/Integration/DataManagementSystem/FIXME_dfc_dir_completion.py | Python | gpl-3.0 | 1,436 | [
"DIRAC"
] | 95302d7f4211e8c61a78f972ab31fa2613828e76e61fd64c248225c4a644230f |
# Compiled by Charles Harris, dated October 3, 2002
# updated to 2002 values by BasSw, 2006
# Updated to 2006 values by Vincent Davis June 2010
# Updated to 2014 values by Joseph Booker, 2015
# Updated to 2018 values by Jakob Jakobson, 2019
"""
Fundamental Physical Constants
------------------------------
These const... | arokem/scipy | scipy/constants/codata.py | Python | bsd-3-clause | 155,289 | [
"Avogadro",
"VisIt"
] | 53c9eb3f0c63a1165685fb7feeba889423211584bccee1216da09c2a659f0317 |
#
# Copyright (C) 2000 greg Landrum
#
""" handles doing cross validation with decision trees
This is, perhaps, a little misleading. For the purposes of this module,
cross validation == evaluating the accuracy of a tree.
"""
from __future__ import print_function
import numpy
from rdkit.ML.Data import SplitData
f... | rvianello/rdkit | rdkit/ML/DecTree/CrossValidate.py | Python | bsd-3-clause | 6,981 | [
"RDKit"
] | 3f51b74b73b78df5d46ee96f3ae2859c6b44371e96b2ea72e9b9ebc6fec1efcd |
# Sample module in the public domain. Feel free to use this as a template
# for your modules (and you can remove this header and take complete credit
# and liability)
#
# Contact: Brian Carrier [carrier <at> sleuthkit [dot] org]
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is f... | dgrove727/autopsy | pythonExamples/Aug2015DataSourceTutorial/FindContactsDb.py | Python | apache-2.0 | 9,071 | [
"Brian"
] | f14f81796fd98ecde012b73c3aead115ee1a534861417a9798e0c5596496066f |
import unittest
from test import test_support
from itertools import *
import weakref
from decimal import Decimal
from fractions import Fraction
import sys
import operator
import random
import copy
import pickle
from functools import reduce
maxsize = test_support.MAX_Py_ssize_t
minsize = -maxsize-1
def onearg(x):
'... | HiSPARC/station-software | user/python/Lib/test/test_itertools.py | Python | gpl-3.0 | 74,270 | [
"GULP"
] | 0ec8c213705260504b0a2bed92a24c7a84247ddc3e4c466e16c48bc07e82d15e |
'''
Created on Jul 1, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
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... | genome-vendor/chimerascan | chimerascan/pipeline/write_output.py | Python | gpl-3.0 | 8,182 | [
"pysam"
] | 205e02f9cc7d61459f943e757dcf66c837335c76e03a64778f6df51cabee25d1 |
""" FileCatalogFactory class to create file catalog client objects according to the
configuration description
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.Help... | ic-hep/DIRAC | src/DIRAC/Resources/Catalog/FileCatalogFactory.py | Python | gpl-3.0 | 2,823 | [
"DIRAC"
] | 747aefe3e36abdaed17843ec4d556b329ec2214a1e38812d8892cfcb177657f5 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | allenlavoie/tensorflow | tensorflow/contrib/timeseries/python/timeseries/math_utils.py | Python | apache-2.0 | 43,090 | [
"Gaussian"
] | 487601e604a495025d38af7473be5c57b3b3a2b9b66c2d28ab58a5f363b790d9 |
"""
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 ... | stefanv/scipy3 | scipy/special/orthogonal.py | Python | bsd-3-clause | 19,797 | [
"Gaussian"
] | 5dfa1efbacf328ced9dde72ed31a75b6a38a11c46fcb70718f1aebb0c4cfedf5 |
from __future__ import division
from nose import SkipTest
from nose.plugins.attrib import attr
import numpy as np
import scipy.stats as st
import numpy.random as nr
import pymc3 as pm
from .helpers import SeededTest
from .test_distributions import (build_model, Domain, product, R, Rplus, Rplusbig, Unit, Nat,
... | wanderer2/pymc3 | pymc3/tests/test_distributions_random.py | Python | apache-2.0 | 19,553 | [
"exciting"
] | 145622a3a974e98dd36fa08f02f5d411c9dc402b98c9fb603e07cdf59c8f6418 |
"""Read genome build configurations from Galaxy *.loc and bcbio-nextgen resource files.
"""
from six.moves import configparser
import glob
import os
import sys
from xml.etree import ElementTree
import toolz as tz
import yaml
from six import iteritems
from bcbio import utils
from bcbio.distributed import objectstore
f... | brainstorm/bcbio-nextgen | bcbio/pipeline/genome.py | Python | mit | 14,481 | [
"Galaxy"
] | 046e8076e8dfc4c1cf7ba66581e5b54586467eb5fd5ee501515c37113d3389c4 |
"""Tests for the Amber Electric Data Coordinator."""
from __future__ import annotations
from typing import Generator
from unittest.mock import Mock, patch
from amberelectric import ApiException
from amberelectric.model.channel import Channel, ChannelType
from amberelectric.model.current_interval import CurrentInterva... | jawilson/home-assistant | tests/components/amberelectric/test_coordinator.py | Python | apache-2.0 | 9,038 | [
"Amber"
] | 9cba6259a9b8790aba3bf6f4e5102e7ec9603dc9ca4b6748d4f3f2903c05a242 |
# dirwalk.py
# Try out the directory-walking functionality in Python.
# Acknowledgement - The first part of this code (to the end of the
# first for-loop) comes from the Python docs for os.walk() here -
# http://docs.python.org/library/os.html
import os
from os.path import join, getsize
for root, dirs, fil... | mooseman/teagit | dirwalk.py | Python | unlicense | 907 | [
"VisIt"
] | 5125701e1468f450af1b0bfd4f9dadd14abcde5bdca294faab5a985b731eccfe |
# -*- coding: utf-8 -*-
# Copyright (C) 2017-2018 CIRCL Computer Incident Response Center Luxembourg (smile gie)
# Copyright (C) 2017-2018 Christian Studer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published... | MISP/MISP | app/files/scripts/stix2misp.py | Python | agpl-3.0 | 79,612 | [
"Galaxy"
] | c47cd85481d1ad6822a719c04afc52ffbc33f29b0a9a6c8e841a17d6c4861d7e |
from module_base import ModuleBase
from module_mixins import NoConfigModuleMixin
import module_utils
import vtk
IMAGE_DATA = 0
POLY_DATA = 1
class StreamerVTK(NoConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._image_data_streamer ... | nagyistoce/devide | modules/filters/StreamerVTK.py | Python | bsd-3-clause | 2,309 | [
"VTK"
] | e15b40786a2da5ef5d78d1d08dbfe03982dae726b16ff1c7736110c47633ce00 |
#!/usr/bin/python
# sfcdumper
# a utility to extract information from Creatures 1/2 SFC (world save)/EXP (creature export) files
# reverse-engineered by fuzzie and nornagon
# TODO: a lot of reads probably need to be changed to signed reads
# eg, room CA sources
# TODO: lots of unknown values :)
identifiers = {}
try:
... | bdonlan/openc2e | src/tools/sfcdumper.py | Python | lgpl-2.1 | 29,925 | [
"NEURON"
] | a45e2b067084de7364cf64efb80119b9d0ae60812bf2a06100872c60c49e420e |
import unittest
from random import shuffle
from bizdays import *
from bizdays import isseq, Date, DateIndex, load_holidays, DateOutOfRange
from datetime import datetime, timedelta
set_option('mode', 'python')
def asDate(dt):
if isseq(dt):
return [Date(d).date for d in dt]
return Date(dt).date
def... | wilsonfreitas/python-bizdays | test_bizdays.py | Python | mit | 37,186 | [
"COLUMBUS"
] | e6a46cbd882319754a9a43e0751e6b420f0896d4239f4cc026aff39dd8b78eb8 |
import os
import urllib
from thredds_crawler.crawl import Crawl
import logging
import logging.handlers
logger = logging.getLogger('thredds_crawler')
fh = logging.handlers.RotatingFileHandler('/home/testbed/iso/logs/iso_harvest.log', maxBytes=1024*1024*10, backupCount=5)
fh.setLevel(logging.DEBUG)
ch = logging.StreamHa... | rsignell-usgs/comt_pycsw | get_iso.py | Python | cc0-1.0 | 5,720 | [
"ESPResSo"
] | 8cb646f4b47632f1ab8182dce7c72b382e37fb682d50948f44a66d62dc1dae88 |
from typing import Optional, Union, Dict
import os
import os.path as osp
import shutil
from ogb.utils import smiles2graph
from ogb.utils.url import decide_download, download_url, extract_zip
import pandas as pd
import numpy as np
from tqdm import tqdm
import torch
class PCQM4MDataset(object):
def __init__(self,... | snap-stanford/ogb | ogb/lsc/pcqm4m.py | Python | mit | 8,331 | [
"RDKit"
] | 7e38c3eb03355db12b857993d96384010fed761c2f89c78c7f49ed3e774d135c |
#!/usr/bin/env python
import os,sys
import getopt
(opts, args) = getopt.getopt(sys.argv[1:],
"n:",
[
"numframes=",
],
)
numframes = None
for option, arg in opts:
if option in ('-n', '--numframes'):
numframes = int(arg)
if numframes is None:
raise ValueError, "You must supply the maximum number of fram... | paultcochrane/pyvisi | special_vis/steffen/make_frames_loop.py | Python | gpl-2.0 | 887 | [
"VTK"
] | 10387daa5166f74975980cff10c32441fc83f76f7492b9647619fc7091f0c3d7 |
"""remove file, not used functions"""
from utils import file_transaction
import os
import pysam
import gzip
from collections import defaultdict, Counter
from tailseq import do
from tailseq import logger
from tailseq.detect import tune
def counts(data, args):
logger.my_logger.info("Counting sample %s:" % data['... | lpantano/seqcluster-helper | sqhelper/annotate.py | Python | mit | 6,236 | [
"pysam"
] | d41125b702c4a30dc85fcc10e8537afd36a5a057886a1e71f3cb7b9d368bf1a2 |
# Copyright 2015 Isotoma Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing... | mitchellrj/touchdown | touchdown/core/goals.py | Python | apache-2.0 | 3,341 | [
"VisIt"
] | 80b7d6326e5bd57029592bd52634a155a8727dd36a3ebb1311c62a33d3d9bc10 |
import new
import sys
from base.twilltestcase import TwillTestCase
from base.interactor import build_interactor, stage_data_in_history
from galaxy.tools import DataManagerTool
from galaxy.util import bunch
import logging
log = logging.getLogger( __name__ )
toolbox = None
#Do not test Data Managers as part of the stan... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/functional/test_toolbox.py | Python | gpl-3.0 | 5,526 | [
"Galaxy"
] | aeb6c92a38892d98e0a0fba3f96025eb525cac80afcb87fa80d7e6ce4f962f9f |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | kkreis/espressopp | src/interaction/StillingerWeberTripleTerm.py | Python | gpl-3.0 | 7,323 | [
"ESPResSo"
] | 3d19b7061794e7699fcaf9b4156cec5771441d450602f95dd746ecc0728ea6f2 |
#!/usr/bin/env python
# @file kmer_repeat_counter.py
# @author Esko Kautto (esko.kautto@osumc.edu)
# @updated 2017-12-18
import os
import argparse
import functools
import subprocess
import time
from datetime import datetime, timedelta
from multiprocessing import Process, Queue, BoundedSemaphore, Semaphore
import pysa... | OSU-SRLab/MANTIS | kmer_repeat_counter.py | Python | gpl-3.0 | 31,101 | [
"pysam"
] | e144f57932a23ac45d1fa410e3b01a2340017e0d635a874a11762a193b456b3d |
"""
Command Line Parameters for creating the Replication transformations Script
"""
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Security.ProxyInfo import getProxyInfo
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import getVOMSVOForGroup
class Params:
"""Parameter Object"""
def __init__... | DIRACGrid/DIRAC | src/DIRAC/TransformationSystem/Utilities/ReplicationCLIParameters.py | Python | gpl-3.0 | 6,120 | [
"DIRAC"
] | 704baaf7ca14ec5872deecb5074b347ee8c8ae595fb3a20d401c77967e32fc81 |
"""
The class is for fitting a grid function by a set of gaussian functions
"""
from wf import WF
from IPython.core.debugger import Tracer
import glob
import os
import sys
import numpy as np
from scipy.optimize import curve_fit
from scipy.interpolate import Rbf
import math
# ---------------------------------------... | freude/mb_project | g_fit3d.py | Python | gpl-2.0 | 22,807 | [
"Gaussian"
] | 35dc7286a447f4644488431000c6daee45248c4d658af87ad22ee5074dbad597 |
# Copyright 2013 OpenStack Foundation
# 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 requ... | SUSE-Cloud/glance | glance/api/v2/image_members.py | Python | apache-2.0 | 10,501 | [
"Brian"
] | 794ac947f535355ae0e77ee8b3f4a4a91206383b42072160e5e5342c00def566 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | fweik/espresso | testsuite/python/domain_decomposition.py | Python | gpl-3.0 | 2,800 | [
"ESPResSo"
] | 2d868cb328ab6656bf14ad3e2edce3cdc562442658b92db60dae847369cf86f0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Usage: extract_junc.py [options] <bam>
Options:
-h --help Show help message.
--version Show version.
-o output_dir Output file directory [default: ./].
--url Extract from remote url.
--bb Convert to BigW... | kepbod/seqlib | bin/extract_junc.py | Python | mit | 2,044 | [
"pysam"
] | 6b114dd2a8b08f78281fa789b024a206ba4e910a7cb2a510e1bfaa9e1c610657 |
#! /usr/bin/env python
import re
import math
import collections
import numpy as np
import time
import operator
from scipy.io import mmread, mmwrite
from random import randint
from sklearn import cross_validation
from sklearn import linear_model
from sklearn.grid_search import GridSearchCV
from sklearn import preproces... | Goodideax/CS249 | predict_gp_5000.py | Python | bsd-3-clause | 14,600 | [
"Gaussian"
] | caa51cd26144cff85dde54d2631d95c8e9d520c24c3803bb15518facff5dedb5 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2013 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published ... | Freeseer/freeseer | src/freeseer/tests/framework/test_database.py | Python | gpl-3.0 | 4,528 | [
"VisIt"
] | e377f50ab3e82a963bc95db43f9f2bd054370c20decdd0b88c6f95180fdf9715 |
../../../../../../../share/pyshared/orca/scripts/toolkits/Gecko/structural_navigation.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/toolkits/Gecko/structural_navigation.py | Python | gpl-3.0 | 88 | [
"ORCA"
] | ecea8de48ebd8fab3570d939eb604383c56da18dae6be875839a308fcbedee3d |
# Minimal support for git commands on an hg repository
#
# Copyright 2005, 2006 Chris Mason <mason@suse.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
'''browse the repository in a graphical way
The hgk extension allows bro... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg/hgext/hgk.py | Python | gpl-3.0 | 11,735 | [
"VisIt"
] | 9d2d60b3310aa6b85f6fe939452325d5c0cf7138677bcd5fd8594ee9aa729483 |
__name__ = '__main__'
import os
import sys
import time
import datetime
import glob
import pickle
from functools import wraps
## NB parseCommandLine first then import Dirac!!
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
from LHCbDIRAC.Interfaces.API.DiracLHCb import DiracLHCb
from DIRAC.Interfa... | ganga-devs/ganga | ganga/GangaLHCb/Lib/Server/DiracLHCbDefinition.py | Python | gpl-3.0 | 2,006 | [
"DIRAC"
] | 3e4c23263d60b2a7ca373ac672a0eafc7398051368bbb5f64aded35e96a92a8c |
""" Class that contains client access to the job monitoring handler. """
from DIRAC.Core.Base.Client import Client, createClient
from DIRAC.Core.Utilities.DEncode import ignoreEncodeWarning
from DIRAC.Core.Utilities.JEncode import strToIntDict
from DIRAC.Core.Utilities.Decorators import deprecated
@createClient("Wor... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/JobMonitoringClient.py | Python | gpl-3.0 | 2,585 | [
"DIRAC"
] | 90874406e2ecf95ca20f965007d78910bdae8660d0b48637f5e68f3bac546bc4 |
"""Shared acceptance test functions."""
from random import choice
from time import sleep
import requests
import json
from splinter.driver.webdriver import WebDriverElement
from adhocracy_core.testing import god_login
from adhocracy_core.testing import god_password
from adhocracy_core.testing import participant_passwo... | xs2maverick/adhocracy3.mercator | src/adhocracy_frontend/adhocracy_frontend/tests/acceptance/shared.py | Python | agpl-3.0 | 5,414 | [
"VisIt"
] | a90a3d414a9cfce3a01909b2eced3191eee9fda1dbfd1df04993a072f7c75408 |
#
# Copyright (C) 2007-2008 by Greg Landrum
# All rights reserved
#
from __future__ import print_function
import numpy
from rdkit import Chem, Geometry
from rdkit import RDLogger
from rdkit.Chem.Subshape import SubshapeObjects
from rdkit.Numerics import Alignment
logger = RDLogger.logger()
class SubshapeAlignment... | rvianello/rdkit | rdkit/Chem/Subshape/SubshapeAligner.py | Python | bsd-3-clause | 13,435 | [
"PyMOL",
"RDKit"
] | 61bbef586ec0005b9c54118450ad8cdcfd7c868c114f7fdc16af42fa9eac9803 |
import numpy as np
class Tri6:
"""Class for a six noded quadratic triangular element.
Provides methods for the calculation of section properties based on the finite element method.
:param int el_id: Unique element id
:param coords: A 2 x 6 array of the coordinates of the tri-6 nodes. The first three... | ebrahimraeyat/civilTools | section/sectionproperties/analysis/fea.py | Python | gpl-3.0 | 27,892 | [
"Gaussian"
] | 551a40d33b7098f8fb6643c35c257b3617497a927daf38dc5d26df6a0f67de2a |
"""
Created on 21 Feb 2013
@author: jmht
"""
# Python modules
import copy
import glob
import logging
import os
import random
import shutil
# Our modules
from ample.modelling import energy_functions, octopus_predict, multimer_definitions
from ample.parsers import psipred_parser
from ample.util import ample_util, pdb_... | linucks/ample | ample/modelling/rosetta_model.py | Python | bsd-3-clause | 56,227 | [
"BLAST",
"Gaussian",
"Octopus"
] | e1627b290a870adfcb381e2a618786e23a8e1fa645e604becfd26788bdfb3478 |
#!/usr/bin/python
#
# Copyright 2015 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 required by... | tgracchus/spinnaker | dev/build_release.py | Python | apache-2.0 | 24,397 | [
"ORCA"
] | 10ef3cadadebbbcbe89e8870e8e1d59b29abf9479b6f01d303516899e6007a3d |
# -*- coding: utf-8 -*-
"""
/***************************************************************************
MeshNetCDFDialog
A QGIS plugin
Create Gmsh mesh from NetCDF (.nc) file where the z-coordinate is a metric for the mesh size.
-------------------
... | janhui/test_engine | release/mesh_netcdf/meshnetcdfdialog.py | Python | lgpl-2.1 | 1,488 | [
"NetCDF"
] | 3cd4174c6d3b9572780b000eb76b60d295852304cb833863b18dd53612ab0d58 |
import argparse
from pele.gui import run_gui
from pele.amber.amberSystem import AMBERSystem
from pele.utils.optim_compatibility import OptimDBConverter
desc="""Start a pele gui from a PATHSAMPLE database for an amber system.
The following files must be present. min.data, ts.data, points.min, points.ts, coords.prmto... | marktoakley/LamarckiAnt | SCRIPTS/PATHSAMPLE/pele_gui_amber.py | Python | gpl-3.0 | 2,025 | [
"Amber"
] | f6dceb9f21ab922751cb416443e53bafadce66a6d8a3983c99ca86f9b1449a4f |
import os
import mock
import unittest
import DIRAC
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Resources.ProxyProvider.ProxyProviderFactory import ProxyProviderFactory
certsPath = os.path.join(os.path.dirname(DIRAC.__file__), "Core/Security/test/certs")
def sf_getInfoAboutProviders(of, providerName, option... | DIRACGrid/DIRAC | src/DIRAC/Resources/ProxyProvider/test/Test_ProxyProviderFactory.py | Python | gpl-3.0 | 2,824 | [
"DIRAC"
] | 03c081afc5340ecf6b510a3be8dcbb095f7ca4305fd44c6b00edbc7bf7c17097 |
# Copyright (C) 2008 NSC Jyvaskyla
# Please see the accompanying LICENSE file for further information.
from __future__ import print_function
import numpy as np
from ase.units import Hartree, Bohr
from weakref import proxy
def ij2s(i,j):
return '%04i%04i' %(i,j)
class PairPotential:
def __init__(se... | pekkosk/hotbit | hotbit/pairpotential.py | Python | gpl-2.0 | 5,890 | [
"ASE"
] | a6326ad66e86bdae30cb37211a318b45fca2f7bcdaf53feabd34f67638796ef0 |
#--------------------------------------------------------------------------
# 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 ... | dfelinto/invesalius3 | invesalius/reader/analyze_reader.py | Python | gpl-2.0 | 1,620 | [
"VTK"
] | d99e660ec27ed6064744e6b1ea4e0d5694b58db90f81d5bd955278598ebaa57e |
#!/usr/bin/env python
import os
import sys
import glob
import pysam
import argparse
import multiprocessing
def get_args():
'''Parse sys.argv'''
parser = argparse.ArgumentParser()
parser.add_argument('-i','--input', required=True,
help='The input bam file.')
parser.add_argument('... | JoshDaly/scriptShed | GenerateRGTags.py | Python | gpl-2.0 | 5,700 | [
"pysam"
] | 50e9009f454a4803de727019d6b1c7b327fec152aa9daa16d4dc9e23f5fd9b76 |
"""
Tests for user authorization password-related functionality.
"""
import json
import logging
import re
from datetime import datetime, timedelta
from unittest.mock import Mock, patch
import pytest
import ddt
from django.conf import settings
from django.contrib.auth import get_user_model
from django.core import mail
... | eduNEXT/edunext-platform | openedx/core/djangoapps/user_authn/views/tests/test_password.py | Python | agpl-3.0 | 13,061 | [
"VisIt"
] | 94d756552ac1da3c73738709ba6e4fd38eedbe5707c82997e0bacf8855c33f69 |
# This file is part of turbulucid
# (c) 2018 Timofey Mukha
# The code is released under the GNU GPL Version 3 licence.
# See LICENCE.txt and the Legal section in the README for more information
"""
ASSMPTIONS
* The averaging direction is the z axis
* The geometry is "fit in" between to x-y planes.
"""
from __... | timofeymukha/turbulucid | turbulucid/bin/averageAlongAxis.py | Python | gpl-3.0 | 28,843 | [
"VTK"
] | c9eccbbfc3c5bfce6f46f98b03d939f68ac9d6a444ceed7c98fc1f1207e36887 |
"""
The :mod:`sklearn.metrics.pairwise` submodule implements utilities to evaluate
pairwise distances or affinity of sets of samples.
This module contains both distance metrics and kernels. A brief summary is
given on the two here.
Distance metrics are a function d(a, b) such that d(a, b) < d(a, c) if objects
a and b... | mrshu/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 27,296 | [
"Gaussian"
] | 69b44b095df8cf10b875c3dc72c30c09f4d77adf8314608fdb9206a621f7ff65 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | tszym/ansible | lib/ansible/modules/network/avi/avi_gslbapplicationpersistenceprofile.py | Python | gpl-3.0 | 3,659 | [
"VisIt"
] | f9b23c1d50eec8554ef2c70601cab3c766be67831b755183863bb29dd7646082 |
#!/usr/bin/env python3
# -*-coding:UTF-8 -*
import os
import sys
import redis
import datetime
sys.path.append(os.path.join(os.environ['AIL_BIN'], 'packages/'))
import Date
sys.path.append(os.path.join(os.environ['AIL_BIN'], 'lib/'))
import ConfigLoader
import item_basic
from pytaxonomies import Taxonomies
from pymi... | CIRCL/AIL-framework | bin/packages/Tag.py | Python | agpl-3.0 | 24,436 | [
"Galaxy"
] | bc0b1efab1fdad4dbe24b7e1bb59a633e2598ee650d2e7dd32b8d98f0284477f |
from consensus import *
import pandas as pd
import csv
import operator
from ast import literal_eval
import numpy as np
import matplotlib.pyplot as plt
'''
Some very quick and dirty analysis on the outputs of the RGZ consensus code and testing the effect
of various weighting schemes. --- Kyle Willett (UMN), 25 May 20... | willettk/rgz-analysis | python/weighting_analysis.py | Python | mit | 11,905 | [
"Galaxy"
] | 2a6ad441c8cca762c849c8c726361ce303dca527cc8dbe3e65e69fab8d3d2e81 |
# -*- coding: utf-8 -*-
"""Utitility functions."""
import os
import tempfile
import tarfile
import requests
import shutil
from re import search
from urllib.parse import urlparse
from zipfile import ZipFile
import flyingpigeon as fp
from .config import Paths
import logging
LOGGER = logging.getLogger("PYWPS")
paths ... | bird-house/flyingpigeon | flyingpigeon/utils.py | Python | apache-2.0 | 7,986 | [
"NetCDF"
] | a3d16ea1b42537cababbae8d91e53f09493df39aa69abb6de8a8bbe90292ab29 |
#! /usr/bin/env python
import matplotlib
matplotlib.use('agg')
import matplotlib.pyplot as plt
import sys
import argparse
import os
import numpy
from ptp.ptpllh import species_setting, showTree
class pnode:
def __init__(self, newpartition, lastpnode, all_taxa, pmap, all_partitions, bound, taxa_order, numtrees):
... | zhangjiajie/PTP | bin/summary.py | Python | gpl-3.0 | 20,082 | [
"VisIt"
] | 8dfe1df8644bc38d41aaa5056153d04dde528fec41e364c2a846c17567e70488 |
# Lint as: python3
# Copyright 2020 The TensorFlow Probability 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 ... | tensorflow/probability | spinoffs/inference_gym/inference_gym/internal/data.py | Python | apache-2.0 | 31,463 | [
"Gaussian"
] | 4fdd9fe9d345871fb1c7f9db17ca1f91a49aa6329a4832d77a69b684a22a5407 |
from ase import Atoms
from gpaw import GPAW
import numpy as np
# spin paired H2
d = 0.75
h2 = Atoms('H2', [[0, 0, 0], [0, 0, d]])
h2.center(vacuum=2.)
e = np.array([])
f = np.array([])
for XC in ['pyPBE', 'pyRPBE']:
e = np.array([])
f = np.array([])
for i in [2, 0]:
xc = XC[i:]
calc = GPA... | robwarm/gpaw-symm | gpaw/test/pygga.py | Python | gpl-3.0 | 1,084 | [
"ASE",
"GPAW"
] | 4e1fecfc11c91953eb93d033602696131d8efd40e1f7d20c1c71ace00ed5b2d3 |
import sys
from optparse import OptionParser
import numpy as np
from gpaw.atom.atompaw import AtomPAW
from gpaw.atom.basis import rsplit_by_norm, QuasiGaussian,\
get_gaussianlike_basis_function
from gpaw.basis_data import BasisFunction, Basis
from gpaw.hgh import setups as hgh_setups, sc_setups as hgh_sc_setups,... | robwarm/gpaw-symm | gpaw/atom/apawbasis.py | Python | gpl-3.0 | 7,257 | [
"GPAW"
] | 3585417a41f5ee8da784f2e31e2bea99b222ad0c8473bbd029e7529b7a6a83d7 |
#!/usr/bin/env python3
#
# Copyright (c) Bo Peng and the University of Texas MD Anderson Cancer Center
# Distributed under the terms of the 3-clause BSD License.
import os
import subprocess
import pytest
from sos.targets import file_target
from sos import execute_workflow
has_docker = True
try:
subprocess.check_... | BoPeng/SOS | test/test_remote.py | Python | gpl-3.0 | 12,302 | [
"ADF"
] | 57f67f586ba747c905aacbb2cef9bfd53e92eb0ceeaef71429c122428998d850 |
from mayavi import mlab
import numpy as np
import matplotlib.pyplot as plt
mlab.options.offscreen = True
if __name__ == '__main__':
n = 23
fdragz = np.zeros(n)
f0z = np.zeros(n)
fdragz2 = np.zeros(n)
f0z2 = np.zeros(n)
factors = np.arange(0.1,2.4,0.1)
for i,factor in zip(range(n),factors):
... | martinjrobins/paper_SPHDEMvariational | post_process.py | Python | gpl-2.0 | 2,177 | [
"Mayavi"
] | 7169b23a6f3a6448d19213deb35d3dce057069549d1cbeebab207048a85d793b |
#
# Post-processing script QE --> EPW
# 14/07/2015 - Samuel Ponce
#
import numpy as np
import os
# Enter the number of irr. q-points
user_input = raw_input('Enter the prefix used for PH calculations (e.g. diam)\n')
prefix = str(user_input)
# Enter the number of irr. q-points
user_input = raw_input('Enter the numb... | mmdg-oxford/papers | Ponce-PRB-2018/phonons/pp.py | Python | gpl-3.0 | 929 | [
"EPW"
] | 96df878fa218ccfefaa4f803134c4836eaf23766253ed8bbf3022e348ac884ca |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import mock
import time
from django.contrib.auth.models import User
from sentry.models import Project
from sentry.coreapi import project_from_id, project_from_api_key_and_id, \
extract_auth_vars, project_from_auth_vars, validate_hmac, APIUnauthorized,... | Kronuz/django-sentry | tests/api/tests.py | Python | bsd-3-clause | 5,021 | [
"ADF"
] | 2b3fbe85ffba5984d8d3e4ea36fe2039a29f161075b0d72ce966c67560e60981 |
import os
from ase.test import NotAvailable
try:
fleur = os.getenv('FLEUR')
if fleur == None:
raise NotAvailable('FLEUR not defined')
except NotAvailable:
raise NotAvailable('Fleur required')
import numpy as np
from ase.tasks.main import run
atoms, task = run("fleur bulk Al -x fcc -a 4.04 --k-p... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/test/fleur/fleur_cmdline.py | Python | gpl-2.0 | 387 | [
"ASE",
"FLEUR"
] | f16127315a125d9d99267b7a317beeeb1d141ed336ee402798cc97f40f1e1ac3 |
"""
A module to compute kernel based representations.
The methods in this module are intended to be used directly as kernels for
kernel methods (e.g. SVMs or KRR). This results in features that are dependent
on the number of molecules used to fit the transformers. These should then
give single vectors that have length... | crcollins/molml | molml/kernel.py | Python | mit | 11,175 | [
"Gaussian"
] | 2d706b64e5884175fd0019fb7f7c7eee6c702c7a84dc3f9965336464ddd01a63 |
# Copyright DataStax, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, softwa... | datastax/python-driver | tests/integration/advanced/test_adv_metadata.py | Python | apache-2.0 | 17,207 | [
"TINKER"
] | 8a728f7bf7d5b9ba894ca7c1990a1aee3a7620e61fba58a25c6a5635fbebcdf6 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | allenlavoie/tensorflow | tensorflow/contrib/autograph/pyct/qual_names.py | Python | apache-2.0 | 7,157 | [
"VisIt"
] | 31b146f88d736f1e73f5b2b788078bba3d93fbccc7415e7851b8d619134b3ee5 |
#!/usr/bin/env python
import sys
from ase import *
from gpaw import GPAW
from gpaw.mpi import rank
gpw = '/tmp/H-par.gpw'
a = 4.0
def f(n, magmom, periodic, dd):
H = Atoms('H', positions=[(a/2, a/2, a/2)], magmoms=[magmom],
pbc=periodic,
cell=(a, a, a))
H.set_calculator(GPAW(n... | qsnake/gpaw | oldtest/parallel/par6.py | Python | gpl-3.0 | 1,573 | [
"ASE",
"GPAW"
] | 32ad9ea4fa49f70316dac5efe78eb82c1d2f2d989d3eeca57baaa8b35ed498c6 |
__author__ = 'Jiashun'
import re
import time
import os
import string
from collections import Counter
starts = time.clock()
def s(si_, sj_):
if qu[si_] == seq2[sj_]:
return 2
else:
return -1
def alignment(seq1, seq2):
m = len(seq1)
n = len(seq2)
g = -3
ma... | JiaShun-Xiao/python-implement-fast-BLAST-Basic-Local-Alignment-Search-Tool | blast.py | Python | mit | 5,890 | [
"BLAST"
] | 81eea98d5d4cd1d67ffdaa1661d7019724f451938408475a461c51462f9741f9 |
# Transformer/IO/StructureSetIO.py
# -------
# Imports
# -------
import fractions;
import io;
import os;
import re;
import sys;
import tarfile;
import time;
import warnings;
from Transformer.IO import StructureIO;
from Transformer.StructureSet import StructureSet;
from Transformer.Utilities import Multiprocessing... | JMSkelton/Transformer | Transformer/IO/StructureSetIO.py | Python | gpl-3.0 | 12,191 | [
"VASP"
] | 01b2934e4215470bba5b0879fedfdf48cbda5155419a400da70fb51fc48bb1af |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
import sys
import pysam
import string
rule = string.maketrans("ATCGN", "TAGCN")
def aln_stat(read):
flag = 1
if read.is_read2:
flag = 2
if read.is_reverse:
seq = read.seq.translate(rule)[::-1]
qual = read.qual[::-1]
return "@%s/%... | longrw/mypython | bam2fastq_1.py | Python | gpl-3.0 | 5,002 | [
"pysam"
] | c3af326d7700d34b6c744d6a7ab118c38e08850a4b85b3fcd1983ab44be81928 |
"""
Module for testing code
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
from __future__ import absolute_import
from builtins import str
try:
basestring
except NameError:
basestring = str
from future import standard_library
standard_library... | Neurosim-lab/netpyne | netpyne/tests/tests.py | Python | mit | 171,950 | [
"Gaussian",
"NEURON"
] | b537168728dbac1c30c8b460ddd07f04d83eab026b6da677139cb05ef035a8d7 |
#!/usr/bin/env python
from ase.io.xyz import read_xyz
from ase.io import read
from collections import OrderedDict
from ase import Atoms
from ase_utils import symbol_number
import numpy as np
import numpy.linalg as nl
import itertools
def read_win(filename='wannier90.up.win', poscar=None):
# read cell
cell = ... | mailhexu/pyDFTutils | pyDFTutils/wannier90/xyz_read.py | Python | lgpl-3.0 | 4,850 | [
"ASE",
"Wannier90"
] | 4393aaba603bcdf8e2ca126e1a2b29dbc486e5231090ccd85784e3593750f02e |
#!/usr/bin/python
# coding: utf-8
# #################################################################################
# Copyright (C) 2014 Francesco Giovannini, Neurosys - INRIA CR Nancy - Grand Est
# Authors: Francesco Giovannini
# email: francesco.giovannini@inria.fr
# website: http://neurosys.loria.fr/
# Permission... | JoErNanO/brianmodel | brianmodel/neuron/ioniccurrent/__init__.py | Python | gpl-3.0 | 1,264 | [
"Brian"
] | c13d682686ab5d022394421b588d157323426825d13d2f044d8e001701d7c162 |
#!/usr/bin/env python3
"""
Jackson Labs Firefly-II and ULN-2550 GPS logger
that allows logging every N seconds,
even when GPS is giving data every second.
This is NOT an NMEA logger, it uses SCPI over serial port
Note: Jackson Labs default baud rate is 115200
"""
from serial import Serial
from pathlib import Path
fro... | scienceopen/nmeautils | SCPIlogger.py | Python | gpl-3.0 | 3,281 | [
"Firefly"
] | ef16c809661616a3cff5cf87ba6cc2452c55bae6948ac5597d053a1a076dee7c |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | supertom/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 23,537 | [
"Galaxy",
"MOOSE"
] | 4cd9805cbe8ef62c07acf1294f9425f83e0c04169b6ec9cbd07dfe22c4238f21 |
#!/usr/bin/env python
import gtk
from gettext import gettext as _
import gobject
from ase.gui.widgets import pack
class Movie(gtk.Window):
def __init__(self, gui):
gtk.Window.__init__(self)
self.set_position(gtk.WIN_POS_NONE)
self.connect('destroy', self.close)
#self.connect('delet... | conwayje/ase-python | ase/gui/movie.py | Python | gpl-2.0 | 4,578 | [
"ASE"
] | 91f820a4de5e4e39a4950ba02e933383bdf170a94854e21e4ddce3f05ca4dec4 |
""" Command module contains the base "Command" class, base for all RSS commands
"""
__RCSID__ = '$Id$'
from DIRAC import gLogger, S_OK
class Command(object):
"""
The Command class is a simple base class for all the commands
for interacting with the clients
"""
def __init__(self, args=None, clients=N... | arrabito/DIRAC | ResourceStatusSystem/Command/Command.py | Python | gpl-3.0 | 2,432 | [
"DIRAC"
] | 536ed3b66895a1462dc65305afdf958d613be64faf4474e744599125d53b7cd0 |
"""
A Tkinter based backend for piddle.
Perry A. Stoll
Created: February 15, 1999
Requires PIL for rotated string support.
Known Problems:
- Doesn't handle the interactive commands yet.
- PIL based canvas inherits lack of underlining strings from piddlePIL
You can find the latest version of this file:
... | ptosco/rdkit | rdkit/sping/TK/pidTK.py | Python | bsd-3-clause | 16,438 | [
"RDKit"
] | 8b7d99cf999ece8155171b0533ac2c86186d875098433ad9a5b4ea4287fe5839 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/interfaces/Interfaces.py | Python | gpl-3.0 | 8,757 | [
"ORCA"
] | 7f664ac44a1fdbaf326096f034e0b5da7de208c2d57c13da82b705ea45fbcafb |
#!/usr/bin/env python
"""compares BSR values between two groups in a BSR matrix
Numpy and BioPython need to be installed. Python version must be at
least 2.7 to use collections"""
from optparse import OptionParser
import subprocess
from ls_bsr.util import prune_matrix
from ls_bsr.util import compare_values
from ls_b... | jasonsahl/LS-BSR | tools/compare_BSR.py | Python | gpl-3.0 | 3,059 | [
"Biopython"
] | 1ccc993af8fccc83a03a297d3720dbbd9da467e66309158f4f46e5daae1c3bd7 |
import numpy as np
from ase.structure import bulk
from ase.units import Hartree, Bohr
from gpaw import GPAW, FermiDirac
from ase.dft import monkhorst_pack
for kpt in (3, 4):
kpts = (kpt, kpt, kpt)
bzk_kc = monkhorst_pack(kpts)
shift_c = []
for Nk in kpts:
if Nk % 2 == 0:
shift_c.ap... | ajylee/gpaw-rtxs | gpaw/test/test_ibzqpt.py | Python | gpl-3.0 | 799 | [
"ASE",
"GPAW"
] | 151d6953c7ef16809f596d9534adb5b76074088eae34b13cb19741f79bffe2f6 |
"""
pplacer.py Placing reads on the phylogenetic tree
"""
import sys,os
import os, shutil, subprocess, sys, optparse, fnmatch, glob
def stop_err(msg):
sys.stderr.write("%s\n" % msg)
sys.exit()
def main():
usage = """%prog [options]
options (listed below) default to 'None' if omitted
"""
parser ... | Rothamsted/AppliedBioinformatics | galaxyMetaomics/pplacer.py | Python | mit | 2,529 | [
"Galaxy"
] | 43d8ea4f7e50e10a455aa5a976ec3d5e913ab296a952f1fa75c9a7b65e47b91c |
# -*- coding: utf-8 -*-
"""
ramlient
~~~~~~~~
Access to a RAML API done right, in Python.
:copyright: (c) 2017 by Timo Furrer <tuxtimo@gmail.com>
:license: MIT, see LICENSE for more details.
"""
import ast
import os
import sys
import codecs
from setuptools import setup, find_packages
# These py... | timofurrer/ramlient | setup.py | Python | mit | 3,627 | [
"VisIt"
] | 4b31c8fcf66f0e4e84b8e1edd089419ba83746f762aa2188b6a9513c26eb6072 |
from setuptools import setup, find_packages # Always prefer setuptools over distutils
from codecs import open # To use a consistent encoding
from os import path
here = path.abspath(path.dirname(__file__))
# Get the long description from the relevant file
with open(path.join(here, 'DESCRIPTION.rst'), encoding='utf-8... | openearth/vtkanim | setup.py | Python | gpl-3.0 | 2,888 | [
"VTK"
] | 36547abe132e33f9f72ec025b13b742156565c8a4b3b562a06a9993307aefd2e |
# nsdf.py ---
#
# Filename: nsdf.py
# Description:
# Author: subha
# Maintainer:
# Created: Fri Jun 26 12:23:07 2015 (-0400)
# Version:
# Last-Updated:
# By:
# Update #: 0
# URL:
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# This program is free soft... | dilawar/moose-full | moose-examples/snippets/nsdf.py | Python | gpl-2.0 | 5,664 | [
"MOOSE"
] | 1adbe188bd12eb1da2ed92d7b7e3b987828eb39f5511ec24398a6e8e524cb655 |
"""Test out creating and plotting a geodesic waypoint (great circle) on the
sphere
"""
from point_cloud import wavefront
from kinematics import sphere
from visualization import graphics
from lib import geodesic, surface_mesh
import numpy as np
# generate a sphere for plotting
sphere_mesh = surface_mesh.SurfMesh(1, ... | skulumani/asteroid_dumbbell | integration/geodesic_waypoint.py | Python | gpl-3.0 | 1,044 | [
"Mayavi"
] | d2b71c794fd8662ae667b564ab9d1383bd26e510d760abfdd24af3b55e5a8335 |
import os
import sys
from ase.io import read
from ase.constraints import *
if len(sys.argv) < 1:
print "Usage: python replace_with_fixed_cluster.py file.traj"
exit()
atoms = read(sys.argv[1])
metals = atoms.get_chemical_symbols()[:2]
if len(set(metals)) < 2:
del metals[1]
hostname = os.environ.get('HOST... | brohr/brohr.github.io | ASE/Adsorption/replace_with_fixed_cluster.py | Python | gpl-2.0 | 1,055 | [
"ASE"
] | 6f706a1d03490f1c58c60ab1e8fcb87dc1cbeed5bc4cdef6958b799b1ca73809 |
from os.path import abspath, basename, join, exists
from os.path import dirname
from os.path import relpath
from os import listdir, sep
from re import findall
from io import open
from ..staging import COMMAND_VERSION_FILENAME
from ..action_mapper import FileActionMapper
from ..action_mapper import path_type
from ..act... | ssorgatem/pulsar | pulsar/client/staging/up.py | Python | apache-2.0 | 17,587 | [
"Galaxy"
] | d784c920699d9af47da4b04e7fbf95042c8e4ccd113debfdc946bb9777704a28 |
# -*- coding: utf-8 -*
' Get real-links from tudou.com '
__author__ = "piratf"
import urllib2
import string
import sys
import time
import re
import webbrowser
from sgmllib import SGMLParser
Website = 'tudou'
# get wordtype of current machine with Windows OS
type = sys.getfilesystemencoding()
# headers = {
# 'U... | piratf/python | tudouSpider/tudouSpider.py | Python | mpl-2.0 | 10,103 | [
"VisIt"
] | 0d0ff7a24e985d4c3f17f4ad53df8c2303abc8721686f92b69ec216120370f50 |
"""
RMSMonitoring type is used to monitor behaviour pattern of requests executed by RequestManagementSystem
inside DataManagementSystem/Agent/RequestOperations.
Understanding the key fields:
'objectType': This field describes the type of object which can be Request, Operation, or File.
'operationType': This field cont... | yujikato/DIRAC | src/DIRAC/MonitoringSystem/Client/Types/RMSMonitoring.py | Python | gpl-3.0 | 1,988 | [
"DIRAC"
] | 07a178add61dfa1bfe2c127e320747c3c82de5b3a7407cd7a40d967e7c971731 |
# third-party modules
import pandas as pd
class LogFile(object):
def _skip_header(self):
""" Set the internal cursor to the beginning of the MD run.
In CP2K Quickstep output, the part before "GO, CP2K, GO" is not of general interest and consists of preparatory
information that is currently not parsed.
"""
... | ferchault/iago | src/iago/cp2k.py | Python | mit | 5,526 | [
"CP2K"
] | c7f6558c7c65139e321cff510f57dfe6bf6c25e128d86f715346432ea10dde14 |
import math
import takktile
from time import sleep
from ddapp import lcmUtils
from ddapp.debugVis import DebugData
from ddapp import roboturdf
from ddapp import transformUtils
from ddapp import visualization as vis
from ddapp import vtkAll as vtk
sensorLocationLeft = {}
# This finger is colloquially called the "thum... | gizatt/director | src/python/ddapp/takktilevis.py | Python | bsd-3-clause | 7,646 | [
"VTK"
] | 755452e46fb124a1c2792d688cdde57e7f035b7af579ff056591952996682523 |
"""
Module containing functions interacting with the CS and useful for the RSS
modules.
"""
from DIRAC import gConfig, gLogger, S_OK
from DIRAC.Core.Utilities.SiteSEMapping import getSEParameters
from DIRAC.ConfigurationSystem.Client.Helpers.Resources import getQueues, getCESiteMapping
from DIRAC.DataManagementSystem.... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Utilities/CSHelpers.py | Python | gpl-3.0 | 4,472 | [
"DIRAC"
] | 11f2c7ca678bfc0609e19fa18e506ffd753d3eb95ecf02a9dec86040b8969daf |
import os, sys, math
import numpy as np
import scipy
import pylab
import lib.LammpsIO as lmp_io
import mpl_toolkits.mplot3d.axes3d as p3
def smooth_data(x,window_len=13,window='flat'):
"""smooth the data using a window with requested size. courtesy of the scipy cookbook.
This method is based on the convolution of... | uschille/FabSim | python/plot_lammps.py | Python | lgpl-3.0 | 11,585 | [
"LAMMPS"
] | 77b41b6aa873c67396363957189ac5485e5059115ae9cc7c8e3ee7f1028ea73f |
# -*- coding: utf-8 -*-
""" Sahana Eden Incident Reporting Model
@copyright: 2009-2013 (c) Sahana Software Foundation
@license: MIT
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 Sof... | sahildua2305/eden | modules/s3db/irs.py | Python | mit | 59,082 | [
"VisIt"
] | ef01503c139c32300dee2e1d089eb348ba3aa03cc3d7aff85ecb11572a9c9c5d |
import numpy as np
import decimal
import echidna.core.spectra as spectra
class Smear(object):
""" This class smears the energy and radius of a spectra.
The class can recieve energy and radius as individual data points or a
1 dimensional numpy array to smear which is then returned. 2d and 3d
arrays wi... | drjeannewilson/echidna | echidna/core/smear.py | Python | mit | 18,727 | [
"Gaussian"
] | baf7d544814d6cdd286f8efdd127149a5643bc694d823ea47f04ba60f2a9890f |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/request_plan_find.py | Python | apache-2.0 | 22,043 | [
"VisIt"
] | f990a4f1aecc17c4dc4f34c2d8aa3db97f18de848d1d3a6bb667c03a54fe16e8 |
# -*- coding: utf-8 -*-
#
# HeroesAIWinter2016 documentation build configuration file, created by
# sphinx-quickstart on Sat Jan 9 10:57:37 2016.
#
# 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 ... | Heroes-Academy/AI_Winter_2016 | docs/source/conf.py | Python | mit | 8,272 | [
"Brian"
] | f7d04878637e4177c3e65b7248f6befeb175ac3255512cb613fcca28d3ef6955 |
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