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import unittest2
import datetime
from google.appengine.api import urlfetch
from google.appengine.ext import db
from google.appengine.ext import testbed
from google.appengine.ext.webapp import Response
# from controllers.datafeed_controller import UsfirstEventDetailsGet
from models.event import Event
from models.team... | synth3tk/the-blue-alliance | tests/test_datafeed_controller.py | Python | mit | 1,758 | [
"COLUMBUS"
] | 3838900e3fe88739c68a611bc373b55f8c305577718ce540a65e2c20e20a0e62 |
#!/usr/bin/env python
import numpy as np
from numpy.linalg import eigh
from tran import fourier_hr2hk
import sys
class HR():
"""
The Wannier tight-binding (TB) Hamiltonian in real space.
"""
def __init__(self, nwann, nrpt, irpt0, rpts, deg_rpt, hr):
self.nwann=nwann
self.nrpt = nrpt... | quanshengwu/wannier_tools | utility/wannhr_symm/lib/read_hamr.py | Python | gpl-3.0 | 6,682 | [
"Wannier90"
] | 79e85e2c01a59025339c7e7c79dad30de216503035c144ee04cc42dc95d3276a |
from prettytable import PrettyTable
from splinter import Browser
import time
from settings import *
SAVE_SCREENSHOT_AT_LOCATION = BASE_PATH + '1.png'
SAVE_TEXT_AT_LOCATION = BASE_PATH + 't.txt'
def search_flight():
try:
browser = Browser('chrome', headless=True)
browser.visit(SITE_NAME)
... | sachs7/Flight-Finder | site_visit.py | Python | gpl-3.0 | 2,122 | [
"VisIt"
] | 2d0374b7fca8749194dd5b6bee5d8714638a38524cd93f28572caffc8e3b3678 |
# !/usr/bin/env python
# -*- coding: utf-8 -*-
import vtk
def main():
colors = vtk.vtkNamedColors()
colors.SetColor("BkgColor", [26, 51, 102, 255])
parametricObjects = list()
parametricObjects.append(vtk.vtkParametricBoy())
parametricObjects.append(vtk.vtkParametricConicSpiral())
parametric... | lorensen/VTKExamples | src/Python/Deprecated/GeometricObjects/ParametricObjectsDemo.py | Python | apache-2.0 | 5,485 | [
"VTK"
] | e4bf7a034af1477fd8551550f89ddf70f47ef0d329e9de990591a202fa989e00 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import requests
"""
This module provides an interface to the MaterialsVirtualLab's MEGNet REST API
for rapid property prediction.
"""
__author__ = "Shyue Ping Ong"
__version__ = "1.0"
__maintainer__ = "Shyu... | dongsenfo/pymatgen | pymatgen/ext/crystalsai.py | Python | mit | 4,319 | [
"CRYSTAL",
"pymatgen"
] | 205e16bd6de3416cb72936830eda6bb3471507aa530be67da6554eba8e176d4b |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Utilities often used by cclib parsers and scripts"""
import importlib
import re
from itertools import accumulate
impo... | berquist/cclib | cclib/parser/utils.py | Python | bsd-3-clause | 8,712 | [
"GAMESS",
"cclib"
] | e08ffe1a4e4ee5197f05d7d1429fe4948f99e991bbf60c244d1f6295bfbaeeb6 |
# -*- coding: utf-8 -*-
import base64
import datetime
import time
import traceback
import re
from lxml import etree
from dateutil.relativedelta import relativedelta
import sys
import random
from Queue import Queue
from threading import Thread
reload(sys)
sys.setdefaultencoding("utf8")
if __name__ == '__main__':
... | Svolcano/python_exercise | dianhua/worker/crawler/china_mobile/guangxi/main.py | Python | mit | 33,176 | [
"VisIt"
] | c0713f44d1d0ba2ac7e13d8f3b990ed98b407a51f39faf51ff2368adefab4bb1 |
from __future__ import (absolute_import, division, print_function)
import numpy as np
import re
import AbinsModules
from mantid.kernel import Atom
class LoadCASTEP(AbinsModules.GeneralAbInitioProgram):
"""
Class which handles loading files from foo.phonon output CASTEP files.
Functions to read phonon fil... | ScreamingUdder/mantid | scripts/AbinsModules/LoadCASTEP.py | Python | gpl-3.0 | 11,122 | [
"CASTEP"
] | 8518668d46b6906aa66238595c1791588d0ff8f140dbad35c2f9034978c010a9 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/mooseutils/tests/test_find_moose_executable.py | Python | lgpl-2.1 | 2,209 | [
"MOOSE"
] | be39987a51ff46d306ea37f37012320e64417eadb3b45606e7ae80810ec11309 |
class Error (Exception): pass
import os
import re
import tarfile
import pyfastaq
import json
import subprocess
import sys
from ariba import common, card_record, vfdb_parser, megares_data_finder, megares_zip_parser
allowed_ref_dbs = {
'argannot',
'card',
'megares',
'plasmidfinder',
'resfinder',
... | sanger-pathogens/ariba | ariba/ref_genes_getter.py | Python | gpl-3.0 | 30,576 | [
"Biopython"
] | 521ef0444d2aff3b3509ed1e34c0b6473428047fa51eb095d6faa8f464aacbf8 |
#!/usr/bin/env python
#
# Copyright 2012 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio 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, or (at your option)
# ... | manojgudi/sandhi | modules/gr36/gr-filter/python/qa_firdes.py | Python | gpl-3.0 | 10,446 | [
"Gaussian"
] | 7be3bd301df421ce53fc15b4eeb72bdec8bb41bdaffc5a1e0040387ebdd5af45 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes used to define a non-periodic molecule and a
periodic structure.
"""
import math
import os
import json
import collections
import itertools
from abc import ABCMeta, abstractmeth... | fraricci/pymatgen | pymatgen/core/structure.py | Python | mit | 162,106 | [
"ABINIT",
"CRYSTAL",
"Gaussian",
"NetCDF",
"VASP",
"exciting",
"pymatgen"
] | 013fa8bc369c0e04980ecd58e6f15ac07d1cbced52401d173a68178926d6fb9e |
#!/usr/bin/env python
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the fol... | BlueBrain/NeuroM | examples/section_ids.py | Python | bsd-3-clause | 2,451 | [
"NEURON"
] | 57dfcf367dbc9fbce6b81345e4148655b259a3418c93dde1ad6fc5e447a46d07 |
#!/usr/bin/env python
#
# -*- coding: utf-8 -*-
#
# PID_fan_control.py
#
# Simple PID loop to control fan speed.
#
#
# Copyright (C) 2015-2016 Brian Rudy (Setarcos)
#
# PID_fan_control is free software; you can redistribute it
# and/or modify it under the terms of the GNU General Public License
# as published by the ... | rudybrian/PID_Fan_Control | PID_fan_control.py | Python | gpl-2.0 | 7,110 | [
"Brian"
] | a55e6419251cc90f08ca3851e0b2fe130ce4915a794e4508ad1b770a3e522d7f |
import bpy
from io_scene_cs.utilities import rnaType, rnaOperator
from io_scene_cs.utilities import HasSetProperty, RemoveSetPropertySet
from io_scene_cs.utilities import RemovePanels, RestorePanels
class csShaderVarContextPanel():
bl_space_type = "PROPERTIES"
bl_region_type = "WINDOW"
bl_context... | baoboa/Crystal-Space | scripts/blender/io_scene_cs/ui/shadervarcontext.py | Python | lgpl-2.1 | 1,110 | [
"CRYSTAL"
] | 225b64ba280a410f02707a33ec00ce28e4e7ed095dc895993c45f86bb28e638d |
# .. coding: utf-8
# $Id: __init__.py 8058 2017-04-19 16:45:32Z milde $
# Author: Engelbert Gruber, Günter Milde
# Maintainer: docutils-develop@lists.sourceforge.net
# Copyright: This module has been placed in the public domain.
"""LaTeX2e document tree Writer."""
__docformat__ = 'reStructuredText'
# code contributi... | burzillibus/RobHome | venv/lib/python2.7/site-packages/docutils/writers/latex2e/__init__.py | Python | mit | 128,523 | [
"VisIt"
] | eee1fe50c8cced36c6e0862e5ac09c27c692009479c24f4b7f9de9585b67b54c |
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 12 19:19:32 2016
@author: Radu
"""
from neuron import h
h.load_file('stdgui.hoc')
from matplotlib import pyplot
from neuronpy.graphics import spikeplot
from Network import ClarkeNetwork
import simrun
def tweak_leak(cells, Ncells):
for a in range(Ncells):
ce... | penguinscontrol/Spinal-Cord-Modeling | ClarkesNetwork/test2.py | Python | gpl-2.0 | 1,380 | [
"NEURON"
] | 23fe0795fefb0c8b148ce2b2ebd83c02a8c28b1840a68b1f6a205aaec2c3e65c |
#!/usr/bin/env python
"""
Framework to start a simulated vehicle and connect it to MAVProxy.
Peter Barker, April 2016
based on sim_vehicle.sh by Andrew Tridgell, October 2011
"""
import atexit
import getpass
import optparse
import os
import os.path
import signal
import subprocess
import sys
import tempfile
import ti... | hsteinhaus/ardupilot | Tools/autotest/sim_vehicle.py | Python | gpl-3.0 | 31,053 | [
"Firefly"
] | faa35dd326b93afa1f593c0f4b07f0155ec44d6ce6f650bfd1d973851c74510a |
r"""*Nonlocal CLI tests for* ``sphobjinv``.
``sphobjinv`` is a toolkit for manipulation and inspection of
Sphinx |objects.inv| files.
**Author**
Brian Skinn (bskinn@alum.mit.edu)
**File Created**
20 Mar 2019
**Copyright**
\(c) Brian Skinn 2016-2022
**Source Repository**
http://www.github.com/bskinn... | bskinn/sphobjinv | tests/test_cli_nonlocal.py | Python | mit | 6,998 | [
"Brian"
] | 6a45e0106684b9b637efc82bb937326d5d7881effa2d6167b594e3dea7b2a12d |
#!/usr/bin/env python
""" Illustrates texturing on a glyph and also illustrates how easy it
is to change that texture when you treat it as a numpy array. You can
change the numpy array in-place and have TVTK re-render the scene.
TVTK sees a view of this array without doing any data transfers.
"""
# Authors: Prabhu R... | dmsurti/mayavi | examples/tvtk/animated_texture.py | Python | bsd-3-clause | 4,371 | [
"VTK"
] | af7ecf2b2182b4ea54396b3aaf9747a48aff51dd757719e9b310dac9af2d2d2e |
"""
.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
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.... | Multiscale-Genomics/mg-process-fastq | tests/test_tb_generate_tads.py | Python | apache-2.0 | 4,007 | [
"BWA"
] | 36282a6682bd2a7664a6361811b9c50c0ab486618304f66b2edbd2c28d1bb86e |
import pylab
import numpy
import string
def chi_sq(fit,y,err):
'''
Returns chi_sq estimate for the fit.
'''
X_sq=numpy.sum(((y-fit)/err)**2)
nu=len(y)-2.0
sigma=numpy.sum(y-fit)/nu
return X_sq
def fit(x,y,err,which):
'''
Performs fit to input data. Computes function (gauss or lore... | justincely/classwork | UMD/AST615/HW3/fit.py | Python | bsd-3-clause | 3,157 | [
"Gaussian"
] | c07bbfd5d67df8365b8559cd22a4ae38d9ea9613a10540fedec489af22043053 |
import matplotlib.pyplot as plt
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
from utils import gauss_2d_anisotropic, uv_to_ed
def scatter_3d(x1, x2, y, xlabel='u', ylabel='v', zlabel='flux', xlim3d=None,
ylim3d=None, zlim3d=None):
"""
Do 3d scatter plot.
... | ipashchenko/ra_survey | ra_survey/plotting.py | Python | mit | 6,863 | [
"Gaussian"
] | 39f0063ec719620dd0b7e262710a983cc5f60ea97499e3423d79393094fd44e4 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2008 B. Malengier
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012 Nick Hall
#
# This program is free software; you can redistribute it ... | arunkgupta/gramps | gramps/plugins/tool/mediamanager.py | Python | gpl-2.0 | 25,419 | [
"Brian",
"VisIt"
] | 28101ca879a5a03b7751fcba774baf746a31a2fb6b3f62b22ecaa04c1113bacb |
# coding: utf-8
from __future__ import unicode_literals
import hmac
import hashlib
import base64
from .common import InfoExtractor
from ..utils import (
determine_ext,
float_or_none,
int_or_none,
js_to_json,
mimetype2ext,
parse_iso8601,
remove_start,
)
class NYTimesBaseIE(InfoExtractor):... | Orochimarufan/youtube-dl | youtube_dl/extractor/nytimes.py | Python | unlicense | 8,904 | [
"Octopus"
] | f97dbe5bb685003c48109d30d5219cc09496666d0a5404c38339026e0a414647 |
"""
This module is for hemodynamic reponse function (hrf) specification.
Here we provide for SPM, Glover hrfs and finite timpulse response (FIR) models.
This module closely follows SPM implementation
Author: Bertrand Thirion, 2011--2015
"""
import warnings
import numpy as np
def _gamma_difference_hrf(tr, oversampli... | INCF/pybids | bids/analysis/hrf.py | Python | mit | 16,570 | [
"DIRAC"
] | 29946065f30e2046dd9af1fb287e77d2bc2716ce8cc95269d5df91ce7482c591 |
#!/usr/bin/env python
# Copyright 2014-2016 OpenMarket Ltd
#
# 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 applicabl... | matrix-org/synapse | contrib/cmdclient/console.py | Python | apache-2.0 | 30,085 | [
"VisIt"
] | 67b7f58bd394675f201df287b69bb8fc797df2f71bf98e7a0d60b09c81792310 |
# $Id$
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Atom-based calculat... | greglandrum/rdkit | rdkit/Chem/Crippen.py | Python | bsd-3-clause | 6,112 | [
"RDKit"
] | f00542121567ba8fd78b8dd752797b12348c0cde46db2e4442b8634d55d19d76 |
"""
[1] Gene H. Golub and John H. Welsch,
Calculation of Gauss Quadrature Rules,
Mathematics of Computation,
Vol. 23, No. 106 (Apr., 1969), pp. 221-230+s1-s10,
<https://doi.org/10.1090/S0025-5718-69-99647-1>,
<https://www.semanticscholar.org/paper/Calculation-of-Gauss-Quadrature-Rules-%2A-By-Gene-Go... | nschloe/quadpy | src/quadpy/tools/main.py | Python | mit | 5,223 | [
"Gaussian"
] | ed350eaba73ba560f7cfd761b7a4cfa1900ce23ed0da9cd4311371328ade14e7 |
# -*- coding: utf-8 -*-
# Copyright 2022 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... | googleapis/python-dialogflow | tests/unit/gapic/dialogflow_v2beta1/test_conversation_profiles.py | Python | apache-2.0 | 108,999 | [
"Octopus"
] | 8b896579be7c8c180299001853a26c512ea3337cde8986999634c032349661a8 |
"""Test the Elk-M1 Control config flow."""
from homeassistant import config_entries, setup
from homeassistant.components.elkm1.const import DOMAIN
from tests.async_mock import AsyncMock, MagicMock, PropertyMock, patch
def mock_elk(invalid_auth=None, sync_complete=None):
"""Mock m1lib Elk."""
mocked_elk = Ma... | GenericStudent/home-assistant | tests/components/elkm1/test_config_flow.py | Python | apache-2.0 | 9,878 | [
"Elk"
] | 739d3d906c9fb004b9903c3a95fb1f30a434290528c3198406d271d7771ca4c2 |
import vapoursynth as vs
import numpy as np
core = vs.get_core()
clip = video_in
def mat(dim=3, mid=1, rest=0):
a = np.ones((dim, dim), np.int16) * rest
a[len(a)//2,len(a)//2] = mid
return a
def mat5x5(mid=1, rest=0):
return mat(5, mid, rest)
def mat3x3(mid=1, rest=0):
return mat(3, mid, rest)
... | ahjolinna/mpv-conf | mpv/etc/vs-scripts/conv-tests.py | Python | gpl-2.0 | 2,565 | [
"Gaussian"
] | 4ea6b074cb5021369743594b54390f0848a2486d2f9e46f8252bc8b521c61adc |
#!python
# coding=utf-8
import os
import time
import shutil
from glob import glob
from pyinotify import (
IN_CLOSE_WRITE,
IN_MOVED_TO,
ThreadedNotifier,
WatchManager
)
from gutils import safe_makedirs
from gutils.slocum import SlocumMerger
from gutils.watch.binary import Slocum2AsciiProcessor
from gut... | SECOORA/GUTILS | gutils/tests/test_watch.py | Python | mit | 5,050 | [
"NetCDF"
] | dd21950194c1a9f9f64b6b7b13edcc77a784ceaed38384bf9d8fc7dc1839093a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import datetime
import unittest
import numpy as np
from pymatgen import Structure, Molecule
from pymatgen.util.provenance import StructureNL, HistoryNode, Author
"""
Unit tests for StructureNL (SNL) format
""... | gVallverdu/pymatgen | pymatgen/util/tests/test_provenance.py | Python | mit | 10,114 | [
"pymatgen"
] | 22cd935ed1189241bf7a199f353181b481e0ff9dbb2f790db7fc3d6bd19b3cc5 |
import sys
import os
import xmlrpclib
import cPickle
import subprocess
from time import sleep
from optparse import OptionParser
from numpy import zeros
import visit_writer
usage = "usage: %prog [options]"
description = """\
Magnetohydrodynamics (MHD) simulation software.
This package does MHD simulations using the H... | certik/mhd-hermes | utils.py | Python | bsd-3-clause | 3,717 | [
"Mayavi",
"VTK"
] | 1c264de6277bab33dee59df1224d637d505036c3a074addabf03902901e6d995 |
from math import sqrt, pi, exp
from mpmath import gamma, gammainc
import sys
#-------------------------------------------------------------------------------
class X2:
"""The parent class for two-center integrals.
Keyword arguments:
scale -- The multiplicative scaling factor for the non-zero term contri... | berquist/obarasaika | obarasaika/obara_saika.py | Python | bsd-3-clause | 27,826 | [
"Gaussian"
] | c4a7b1cc80ff1fc7a57ec623faa78a9361025e1bd7f09f3ef6aaaad60bb5ba66 |
# Copyright (c) 2014-2019. Mount Sinai School of Medicine
#
# 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 ... | hammerlab/varcode | setup.py | Python | apache-2.0 | 2,683 | [
"Biopython"
] | c019d5f58896e8eff12878c6b445e189f1e099f5d0238d68cabb69b8d630e2f3 |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Merge any overlapping regions of bed files. Bed files can be provided on the
command line or on stdin. Merged regions are always reported on the '+'
strand, and any fields beyond chrom/start/stop are lost.
usage: %prog bed files ...
"""
import psyco_full
import sys
fro... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/bed_merge_overlapping.py | Python | bsd-3-clause | 812 | [
"Galaxy"
] | 62af6f992d917f5d6fe3796c249b85a7fe774a1133a83bb69cd8f79e33166ec3 |
# Copyright 2020 The HuggingFace Team. 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 applicabl... | huggingface/pytorch-transformers | src/transformers/activations_tf.py | Python | apache-2.0 | 2,766 | [
"Gaussian"
] | 89cb2ec9fd77ed75cb4cc52ad1c4da279d2c3e0d2eae15b919c2581f7ec5e1f3 |
# ---Libraries---
# Standard library
import math
# Third-party libraries
import cv2
import numpy as np
from scipy import stats
from skimage import transform as tf
from sklearn.preprocessing import normalize
# Private libraries
# Return the image after Gaussian filtering and Otsu's thresholding
def image_binarizati... | avicorp/firstLook | src/utils.py | Python | apache-2.0 | 3,976 | [
"Gaussian"
] | 16c4605b4ad63e228dad901faa885ccfb8e284ae292f3e7ecbabd8c49f7c4768 |
# 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
#
from __future__ import division, print_function, absolute_import
import math
import warnings
fro... | sargas/scipy | scipy/stats/distributions.py | Python | bsd-3-clause | 222,099 | [
"Gaussian"
] | cbef1cb9b7eec9f4f7a30380aa97d6dd554cbde76be37a52b036ce99c8b91d5d |
#!/usr/bin/env python
import gzip
import json
import optparse # using optparse as hydra still python 2.6
import os.path
import shutil
def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
data_manager_d... | Christian-B/galaxy_shedtools | directory_data_manager/data_manager/directory_data_manager.py | Python | gpl-2.0 | 3,686 | [
"Galaxy"
] | cee2c717a8bf871012d51a684ce732633427687ad19d54e2fbfcd5acc3e42c64 |
'''
* Created by Zhenia Syryanyy (Yevgen Syryanyy)
* e-mail: yuginboy@gmail.com
* License: this code is under GPL license
* Last modified: 2017-07-12
'''
from feff.libs.class_Spectrum import Spectrum, GraphElement, TableData, BaseData
import os
import datetime
from time import sleep
from collections import OrderedDict ... | yuginboy/from_GULP_to_FEFF | feff/libs/class_for_parallel_comparison.py | Python | gpl-3.0 | 114,615 | [
"FEFF"
] | d860406ee85139a0cf60249eedb7a0854e199768d4a5425e75fa222dfcc2ee56 |
import os
import unittest
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging
#
# NodeInfo
#
class NodeInfo(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py... | SlicerRt/SlicerDebuggingTools | NodeInfo/NodeInfo.py | Python | bsd-3-clause | 13,550 | [
"VTK"
] | f4cc154e4a5580af2f2f8bfa2530a77f58f4402c6d5b07422abf7adf736347e8 |
########################################################################
# $HeadURL$
# File : CPUNormalization.py
# Author : Ricardo Graciani
########################################################################
""" DIRAC Workload Management System Client module that encapsulates all the
methods necessary t... | avedaee/DIRAC | WorkloadManagementSystem/Client/CPUNormalization.py | Python | gpl-3.0 | 3,163 | [
"DIRAC"
] | d77202fbf02829e548afb53cb456d86eb4eb559ffcb8f6570ecaff07bae057f5 |
# Copyright 2018 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 by applicable law o... | tensorflow/probability | tensorflow_probability/python/sts/components/local_linear_trend.py | Python | apache-2.0 | 17,805 | [
"Gaussian"
] | 214349455be1ead6a2e8e4b3676a15410e18dc5308af231d660362d5f8a3e64d |
import random
from ase import Atoms
from ase.ga.data import PrepareDB
metals = ['Al', 'Au', 'Cu', 'Ag', 'Pd', 'Pt', 'Ni']
population_size = 10
# Create database
db = PrepareDB('fcc_alloys.db',
population_size=population_size,
metals=metals)
# Create starting population
for i in xrange... | PHOTOX/fuase | ase/doc/tutorials/ga/ga_fcc_alloys_start.py | Python | gpl-2.0 | 520 | [
"ASE"
] | 7a861bfbab9bcf2aa0c3bd2c57c9d99af1a310b2d7f956125a5804972cf6ade4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# startstore - [insert a few words of module description on this line]
# 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 o... | heromod/migrid | mig/cgi-bin/startstore.py | Python | gpl-2.0 | 1,108 | [
"Brian"
] | ee92289175137e19b8709de5b01ca0c7e0feba25f303c33d68436d2f3e155b8c |
#
# Copyright (C) 2007, Mark Lee
#
#http://rl-glue-ext.googlecode.com/
#
# 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... | okkhoy/mo-rlglue-python-codec | rlglue/agent/ClientAgent.py | Python | mit | 5,108 | [
"Brian"
] | 67bcb696e7e5ff7051997293799da51bc620c2771a5563326e701cefa6b2d2ea |
# cell.py ---
#
# Filename: cell.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Fri Mar 9 23:17:17 2012 (+0530)
# Version:
# Last-Updated: Sun Jun 25 10:08:16 2017 (-0400)
# By: subha
# Update #: 699
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Chang... | BhallaLab/moose-examples | traub_2005/py/cells.py | Python | gpl-2.0 | 15,686 | [
"MOOSE",
"NEURON"
] | 45519c390e71513faa7a4ce9248232c6db6d161db750f28a1885a5591f4354cd |
# mako/_ast_util.py
# Copyright 2006-2020 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""
ast
~~~
This is a stripped down version of Armin Ronacher's ast module.
:copyr... | scheib/chromium | third_party/mako/mako/_ast_util.py | Python | bsd-3-clause | 20,414 | [
"VisIt"
] | 40a5d90b40dba5879f2a14eb4198cb82370d5e54e0637f2c6c1faf9814761e95 |
import ocl
import pyocl
import camvtk
import time
import vtk
import datetime
import math
if __name__ == "__main__":
print ocl.revision()
myscreen = camvtk.VTKScreen()
a=ocl.Point(1,0.6,0.1)
myscreen.addActor(camvtk.Point(center=(a.x,a.y,a.z), color=(1,0,1)))
b=ocl.Point(0,1,0)
myscre... | AlanZatarain/opencamlib | scripts/drop-cutter/drop_cutter_one-triangle_3_compoundcutter.py | Python | gpl-3.0 | 2,219 | [
"VTK"
] | 4d1aa9c22db92c58d22404ff54bb2c8aec19222fa63c37f1e2503db92ba02a86 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageNormalize(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk... | chrisidefix/devide | modules/vtk_basic/vtkImageNormalize.py | Python | bsd-3-clause | 491 | [
"VTK"
] | 9b58d89e11b035c8f3e6dee6f27fbefde258dc81a66b761432ae1de6e8ebe002 |
import sys
import random
from math import log, exp
import csv
from itertools import product
def create_aa_dict():
aa_dict = {"L": "leu",
"P": "pro",
"H": "his",
"Q": "gln",
"R": "arg",
"I": "ile",
"M": "met",
"... | rjorton/ortools | ortools.py | Python | gpl-3.0 | 47,852 | [
"Biopython"
] | 16bebb33a02e01f0016cce9dde47500d76786b1fe9358b1a9cec5604fcdd6166 |
# coding: utf-8
# Copyright (c) Materials Virtual Lab
# Distributed under the terms of the BSD License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
import unittest
import tempfile
import os
import shutil
import random
import json
import numpy as np
from monty.os.path impo... | materialsvirtuallab/veidt | veidt/potential/tests/test_mt.py | Python | bsd-3-clause | 4,115 | [
"LAMMPS",
"pymatgen"
] | ec94ee8f6e61146d76d46e0819a092fd3e28911c311ad2e515cd731a811b97e1 |
"""
Source finding
==============
Simple source finder that can be used to find objects from astronomical images.
:reqiures: NumPy
:requires: SciPy
:requires: matplotlib
:author: Sami-Matias Niemi
:contact: s.niemi@ucl.ac.uk
:version: 0.6
"""
import matplotlib
matplotlib.use('PDF')
import datetime, sys
from optpars... | sniemi/EuclidVisibleInstrument | analysis/sourceFinder.py | Python | bsd-2-clause | 18,368 | [
"Gaussian"
] | 8d01240664cdf5f4db808f6258ba1eccfb940fce3bd967f817608b109fd55fac |
"""
Test the MousePickDispatcher.
"""
import unittest
from traits.api import HasTraits, Instance
from mayavi.core.null_engine import NullEngine, DummyViewer
from tvtk.api import tvtk
from mayavi.tools.engine_manager import engine_manager
from mayavi.core.registry import registry
from mayavi.core.mouse_pick_dispatche... | dmsurti/mayavi | mayavi/tests/test_mouse_pick_dispatcher.py | Python | bsd-3-clause | 3,001 | [
"Mayavi",
"VTK"
] | 5c6cc70a39fc36ec9270b8ee69b45f706e82b00238d9f63d9d7f83f17eeeef92 |
# Copyright (c) 2018 PaddlePaddle 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 appli... | QiJune/Paddle | python/paddle/fluid/layers/nn.py | Python | apache-2.0 | 220,572 | [
"NEURON"
] | bff211d7d2aeadcdd3893f6fb2cb58bf9204bb35018aeb9ff703c2128dd85ae7 |
# coding: utf-8
from __future__ import unicode_literals, division, print_function
import os
import tempfile
import shutil
from pymatgen.util.testing import PymatgenTest
from monty.functools import lazy_property
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.io.a... | rousseab/pymatgen | pymatgen/io/abinitio/tests/test_flows.py | Python | mit | 10,583 | [
"ABINIT",
"pymatgen"
] | b8ad3aa2194d43544b88b23b98a44eb70ed6772d65a79685daae706ebabb5138 |
#
# Copyright 2018 Analytics Zoo 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... | intel-analytics/analytics-zoo | pyzoo/test/zoo/orca/automl/search/test_ray_tune_search_engine.py | Python | apache-2.0 | 9,299 | [
"ORCA"
] | 3ccb68bde6409bf12753a932258202281eb2785cf942929dde1af4d883be605b |
"""
Acceptance tests for Studio related to the asset index page.
"""
from flaky import flaky
from ...pages.studio.asset_index import AssetIndexPage
from .base_studio_test import StudioCourseTest
from ...fixtures.base import StudioApiLoginError
from ..helpers import skip_if_browser
class AssetIndexTest(StudioCourse... | devs1991/test_edx_docmode | common/test/acceptance/tests/studio/test_studio_asset.py | Python | agpl-3.0 | 1,900 | [
"VisIt"
] | 31930d42cdb72594b2e5c07731f6efc264ce8cc5dfeebf64b29398ff6630dc40 |
"""=================================================="""
""" HELP """
"""=================================================="""
""" AUTHOR: Brady Hammond """
""" CREATED: 12/17/16 """
""" EDITED BY: Brady Hammond ... | BradyHammond/Topic_Modeler | help.py | Python | gpl-3.0 | 21,235 | [
"VisIt"
] | 3ea8bbc06bcca50cb60d6608c28ab45e7be3468dcf48ef5dda50c7d38356391f |
import os
import shutil
import unittest
from custodian.vasp.validators import (
VaspAECCARValidator,
VaspFilesValidator,
VaspNpTMDValidator,
VasprunXMLValidator,
)
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "test_files")
cwd = os.getcwd()
class VasprunXMLValidatorTest(unitt... | materialsproject/custodian | custodian/vasp/tests/test_validators.py | Python | mit | 2,741 | [
"VASP"
] | 7834328cd32c459e9349a7c6f7c978374c2a77cc03b90cfbce46c3e69a02e408 |
from __future__ import print_function
import numpy as np
import sys
import regreg.api as rr
from selection.tests.instance import logistic_instance, gaussian_instance
from selection.approx_ci.selection_map import threshold_score_map
from selection.approx_ci.ci_approx_density import approximate_conditional_density
from ... | selective-inference/selective-inference | selectinf/sandbox/approx_ci/tests/test_threshold_score.py | Python | bsd-3-clause | 4,582 | [
"Gaussian"
] | 35fcb38d569f295dc52f06cb783376971284cbf9648dd42eb0f59b34dc5a7911 |
"""Ops and optimizations for using BLAS calls
BLAS = Basic Linear Algebra Subroutines
Learn more about BLAS here:
http://www.netlib.org/blas/blast-forum/
The standard BLAS libraries implement what is called "legacy BLAS" in that
document.
This documentation describes Theano's BLAS optimization pipeline.
Where th... | JazzeYoung/VeryDeepAutoEncoder | theano/tensor/blas.py | Python | bsd-3-clause | 92,596 | [
"BLAST"
] | 0b8d32ae7dc1ef64d4dc04555efd968dafc1d26d30364896291595834cd7bc4d |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Implement Snapshot."""
import hoomd
from hoomd import _hoomd
class _ConfigurationData:
def __init__(self, cpp_obj):
self._cpp_obj = cpp_obj
... | joaander/hoomd-blue | hoomd/snapshot.py | Python | bsd-3-clause | 11,904 | [
"HOOMD-blue"
] | edfe98d26e0d16680b8ea1fb7ec912b780b3fb11421b862dbd2140a16d8f0282 |
# Copyright (C) 2015, Carlo de Franchis <carlo.de-franchis@cmla.ens-cachan.fr>
# Copyright (C) 2015, Gabriele Facciolo <facciolo@cmla.ens-cachan.fr>
# Copyright (C) 2015, Enric Meinhardt <enric.meinhardt@cmla.ens-cachan.fr>
# Copyright (C) 2019, Julien Michel (CNES) <julien.michel@cnes.fr>
from __future__ import print... | dyoussef/s2p | s2plib/sift.py | Python | agpl-3.0 | 9,426 | [
"Gaussian"
] | 6d49049e6b71366b20dc4fca67a5db935baabd893f4b74ea9a0c64060259e79e |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | pmghalvorsen/gramps_branch | gramps/plugins/webreport/narrativeweb.py | Python | gpl-2.0 | 374,796 | [
"Brian"
] | c031c11f78f84a5d9f40aba97d2a46f5dde19558b31a7b4462c5b3aef5e919ea |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
# Modified to print out atom serial_number instead of sequentially, RTB 22-Apr-16
"""Outp... | rtb1c13/scripts | SAXS_MD/_PDBIO_edit.py | Python | gpl-2.0 | 8,517 | [
"Biopython"
] | 27f5c70eea6cfbe2e1b7972c1a1602df360d4f73db1d1e305420358a2312b4db |
"""
The MIT License
Copyright (c) 2008 Vijay Ganesh
2014 Jurriaan Bremer, jurriaanbremer@gmail.com
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
wit... | guorendong/iridium-browser-ubuntu | third_party/stp/src/bindings/python/stp/stp.py | Python | bsd-3-clause | 21,484 | [
"VisIt"
] | 8c7785ee17fbad2f950498d5e726a596ea4ef3468cdc5d8c695d13291c5236fe |
import sys
from distutils.version import LooseVersion
from ariba import external_progs
from ariba import __version__ as ariba_version
package_min_versions = {
'bs4': '4.1.0',
'dendropy': '4.1.0',
'pyfastaq': '3.12.0',
'pysam': '0.8.1',
'pymummer' : '0.7.1',
}
package_max_versions = {
#'pysam'... | martinghunt/ariba | ariba/versions.py | Python | gpl-3.0 | 2,213 | [
"pysam"
] | 536d93df1094a1f47048eb3a0b0e93832a5fea546a4f8e69790e55842b7a3a5a |
#! /usr/bin/python
import sys
import math
from solid import *
from solid.utils import * # Not required, but the utils module is useful
from plate import *
hex_clearance = 0.2
mount_hex_r = hex_r1 - hex_clearance
sys.stderr.write ("mount_hex_r: %g\n" % mount_hex_r)
hex_mount = cylinder (r2 = mount_hex_r,
r... | chertykov/Tripod | phone-mount.py | Python | gpl-2.0 | 2,328 | [
"Galaxy"
] | 94bdcdbdd9796445583637f4929604259c305d25e0881436ce7bf560c5e16570 |
# coding=utf-8
# Copyright 2022 RigL 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 agree... | google-research/rigl | rigl/experimental/jax/pruning/symmetry_test.py | Python | apache-2.0 | 23,548 | [
"NEURON"
] | 0b53ea27ba8ad017ea00837c06fcf4d48ce4cea57e7aa3eb828f2c6ee04f1ded |
# -*- coding: utf-8 -*-
u"""
NetCDF reader/writer module.
This module is used to read and create NetCDF files. NetCDF files are
accessed through the `netcdf_file` object. Data written to and from NetCDF
files are contained in `netcdf_variable` objects. Attributes are given
as member variables of the `netcdf_file` and ... | altMITgcm/MITgcm66h | utils/python/MITgcmutils/MITgcmutils/pupynere.py | Python | mit | 39,520 | [
"NetCDF"
] | 29e0f54387f92fe2cb974648a8d1bdb888b3b45367271f4b7d9beac69106b1e4 |
"""
==========================================================
Comparison of kernel ridge and Gaussian process regression
==========================================================
This example illustrates differences between a kernel ridge regression and a
Gaussian process regression.
Both kernel ridge regression an... | manhhomienbienthuy/scikit-learn | examples/gaussian_process/plot_compare_gpr_krr.py | Python | bsd-3-clause | 13,335 | [
"Gaussian"
] | 74b47a2800d5e8a56a2b8b5114d7df874d1ae2ae85f22cd80c5a6f405b6f78c8 |
# Copyright (c) 2015-2018 Cisco Systems, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge... | metacloud/molecule | molecule/command/init/scenario.py | Python | mit | 6,722 | [
"Galaxy"
] | 33371877908d713d62c465bd8345a78a9f36e375d53825a49f20c855df414489 |
#!/usr/bin/python3
import warnings
warnings.simplefilter(action="ignore", category=FutureWarning)
import camoco.PCCUP as PCCUP
from .Camoco import Camoco
from .RefGen import RefGen
from .Locus import Locus, Gene
from .Expr import Expr
from .Tools import memoize, available_datasets
from .Term import Term
from .Onto... | schae234/Camoco | camoco/COB.py | Python | mit | 95,136 | [
"Cytoscape"
] | c72a483857d5d1de97965c60b9d399c4785b553a5f97d37bd3751e0dbec3eaba |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-gdsfmt/package.py | Python | lgpl-2.1 | 2,401 | [
"Bioconductor"
] | 9ed973da45fd95d076e52d5fe494bdd8bb273807ff3e45de54cd7336c4d6b10f |
"""Sphinx configuration."""
import sys
import os
import sphinx
sphinx_ver = tuple(map(int, sphinx.__version__.split('.')))
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.ab... | joaander/hoomd-blue | sphinx-doc/conf.py | Python | bsd-3-clause | 1,827 | [
"HOOMD-blue"
] | cd090e2c43d6e28b2236fcba9c38091278259625889eff4fed72571ab0b2f60e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ =... | migueldiascosta/pymatgen | pymatgen/io/xyzio.py | Python | mit | 574 | [
"pymatgen"
] | d3f3d6ef7300f5a259a48b269d81b59013ee5e1a39c1705c644d779d757958c7 |
""" The SGE TimeLeft utility interrogates the SGE batch system for the
current CPU consumed, as well as its limit.
"""
from __future__ import print_function
__RCSID__ = "$Id$"
import os
import re
import time
import socket
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.TimeLeft.TimeLeft import... | fstagni/DIRAC | Core/Utilities/TimeLeft/SGETimeLeft.py | Python | gpl-3.0 | 6,703 | [
"DIRAC"
] | 3dc27f28a463f7628b763ce5acf0e577a654541d9870f5d9638200e2ce2e6635 |
# -*- coding: utf-8 -*-
# Copyright 2022 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... | googleapis/python-service-usage | tests/unit/gapic/service_usage_v1/test_service_usage.py | Python | apache-2.0 | 85,305 | [
"Octopus"
] | d0d2b2824c98c7e0a411a61d1c27495a5046c50f2e214e260cecaaef0509f1cc |
# -*- coding: UTF-8 -*-
from conference import cachef
from conference import models
from pages.models import Page
from collections import defaultdict
from datetime import datetime, timedelta
from django.conf import settings
from django.contrib import comments
from django.contrib.auth.models import User
from django.co... | pythonitalia/conference | conference/dataaccess.py | Python | bsd-2-clause | 25,323 | [
"ESPResSo"
] | 635a6811967c32fd609ce5c9ed6ca7e242b320c01cec467db2c7b4db667757e8 |
#!/usr/bin/env python
"""The X12.map.SQL module emits SQL table definitions from an :mod:`X12.parse` structure.
These table definitions are minimized by flattening Segments into their
parent Loop structures.
See :ref:`traversal` for notes on the **Visitor** design pattern.
.. autoclass:: SQLDetailsVisitor
:memb... | sbuss/TigerShark | tigershark/X12/map/SQL.py | Python | bsd-3-clause | 5,653 | [
"VisIt"
] | 814b8fd180995f781a728f167377d60dd2013e552505911b98b00a4af27b58ac |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Created on Apr 30, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "S... | sonium0/pymatgen | pymatgen/serializers/tests/test_json_coders.py | Python | mit | 4,504 | [
"pymatgen"
] | ba26123c44f75e95ac002e2eccf3c893f1b0421d98cbc3cd579affbd1de67ca9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
""" Munch is a subclass of dict with attribute-style access.
>>> b = Munch()
>>> b.hello = 'world'
>>> b.hello
'world'
>>> b['hello'] += "!"
>>> b.hello
'world!'
>>> b.foo = Munch(lol=True)
>>> b.foo.lol
True
>>> b.foo is b['foo'... | georgestarcher/TA-SyncKVStore | bin/ta_synckvstore/munch/__init__.py | Python | mit | 12,940 | [
"Brian"
] | ef37c85670568fbc604b34fd2e97e02cd62af74feada9cfd789e70ee58d29ea4 |
#!/usr/bin/env python
#
"""
Author: Bas van der Vlies
Date : 1 June 2012
Desc. : Standard python module to parse accounting files for TORQUE
SVN Info:
$Id$
$URL$
Torque Info:
abort Job has been aborted by the server
C checkpoint Job has been checkpointed and held
D delete Job has been delete... | ehiggs/pbs-python | src/PBSacct.py | Python | gpl-3.0 | 6,294 | [
"ADF"
] | 98611a2c426e6853aeef3f867c7c5bba4e75f7d0839b6c2adb412348d8b42f24 |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# @author: Li Li (lili@bnl.g... | danielballan/scikit-xray | skbeam/core/fitting/tests/test_lineshapes.py | Python | bsd-3-clause | 13,271 | [
"Gaussian"
] | 49a3a2d7ddaacf88013be8007240325b823e62dfb928dbcf60c4f47cae1a0956 |
#!/usr/bin/python
# Usage example:
# python captions.py --videoid='<video_id>' --name='<name>' --file='<file>' --language='<language>' --action='action'
import httplib2
import os
import sys
from apiclient.discovery import build_from_document
from apiclient.errors import HttpError
from oauth2client.client ... | JacobChrist/YouTube-Caption | youtube-caption.py | Python | bsd-3-clause | 8,156 | [
"VisIt"
] | 0fca687860814b426573c5560dc8bceb6645a82ae21c421d698bbaaf279a84b4 |
# -*- coding: utf-8 -*-
"""
pygments.lexers._asybuiltins
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This file contains the asy-function names and asy-variable names of
Asymptote.
Do not edit the ASYFUNCNAME and ASYVARNAME sets by hand.
TODO: perl/python script in Asymptote SVN similar to asy-list.pl but onl... | sysbot/pastedown | vendor/pygments/pygments/lexers/_asybuiltins.py | Python | mit | 27,319 | [
"Gaussian"
] | 2e3cfceb3da9462ca4dcd8fa8df132e0ec5f3cc40044903d722e59b05de7dada |
"""
Connected components.
"""
import itertools
import logging
import networkx as nx
import numpy as np
from matplotlib.patches import Circle, FancyArrowPatch
from monty.json import MSONable, jsanitize
from networkx.algorithms.components import is_connected
from networkx.algorithms.traversal import bfs_tree
from pyma... | materialsproject/pymatgen | pymatgen/analysis/chemenv/connectivity/connected_components.py | Python | mit | 42,289 | [
"pymatgen"
] | 960173af2a40eca3d688194f8ee6892cbaaf5bbae4ee8052282154a3585a2e28 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | samples/rigid_body.py | Python | gpl-3.0 | 3,363 | [
"ESPResSo"
] | 173ecb6137848b549ceb48f1949b61ea44a7140e6f2796597167b6a870ad2688 |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008-2012 Daniel Moisset, Ricardo Quesada, Rayentray Tappa,
# Lucio Torre
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided t... | shadowmint/nwidget | lib/cocos2d-0.5.5/cocos/skeleton.py | Python | apache-2.0 | 15,167 | [
"VisIt"
] | 46ce20d8365ae4fdd5ad8c4c3e856fa8982ae858f6eb1ce2d79a234498c714de |
#PBS -l nodes=1:ppn=1:xeon8
#PBS -q verylong
#PBS -N E_plot_data_gen
#PBS -m ae
import sys
import os
from atommontecarlodata import AtomMonteCarloData
import numpy as np
from ase import units #used to get kB in eV/K
import cPickle as pickle
fdir = sys.argv[1] #Directory of .amc files to join
#e_filter = float(sys.argv... | auag92/n2dm | Asap-3.8.4/Projects/NanoparticleMC/misc/saveenergiesamc_end.py | Python | mit | 970 | [
"ASE"
] | 0f476069669fd00746528c0ee017a91c7a430f67edcf4aea9a25a56c89cdaf89 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from itertools import product
import numpy as np
from pymatgen.analysis.elasticity.strain import Deformation
from pymatgen.core.surface import (SlabGenerator,
get_symmetrical... | blondegeek/pymatgen | pymatgen/analysis/substrate_analyzer.py | Python | mit | 17,529 | [
"pymatgen"
] | a4bce78266c10feab03a81b7265143689e8b96746c0430ada4692f673ebd2036 |
"""Tests for the ArchiveFiles Operation"""
from functools import partial
import logging
import os
import pytest
from mock import MagicMock as Mock
from DIRAC import S_ERROR, S_OK
from DIRAC.Core.Utilities import DEncode
from DIRAC.RequestManagementSystem.Client.File import File
from DIRAC.RequestManagementSystem.Cli... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/Agent/RequestOperations/test/Test_ArchiveFiles.py | Python | gpl-3.0 | 13,933 | [
"DIRAC"
] | dae7f9985f8cd801239ba55053ac048fac2f1feed2dc40348c5296952d5e1439 |
import rdkit.Chem as Chem
from rdkit.Chem import AllChem
import autograd.numpy as np
def smiles_to_fps(data, fp_length, fp_radius):
return stringlist2intarray(np.array([smile_to_fp(s, fp_length, fp_radius) for s in data]))
def smile_to_fp(s, fp_length, fp_radius):
m = Chem.MolFromSmiles(s)
return (AllChem... | HIPS/neural-fingerprint | neuralfingerprint/rdkit_utils.py | Python | mit | 588 | [
"RDKit"
] | 4a77068bf7f443c310308bf462526fd1d0444afb567df0f903f78fffbed5dfd2 |
# Copyright 2006-2014 by Peter Cock. All rights reserved.
# Revisions copyright 2011 Brandon Invergo. 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.
"""Tests for Bio.AlignIO.Ph... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_AlignIO_PhylipIO.py | Python | gpl-2.0 | 8,602 | [
"Biopython"
] | ca690a096cd611f0602927344870f2e00a29066e9345e7ecf32c0351432cde27 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# PMDA
# Copyright (c) 2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher ve... | MDAnalysis/pmda | pmda/test/test_contacts.py | Python | gpl-2.0 | 10,048 | [
"MDAnalysis"
] | bc7adbcf63cab125f4b25b1e8fcdcb02efbeb3e7d99aae49238d8682d5a8b1b5 |
import logging
from numpy.lib.twodim_base import diag, eye
from numpy.ma.core import asarray
import os
from os.path import expanduser
from pickle import dump
from independent_jobs.engines.BatchClusterParameters import BatchClusterParameters
from independent_jobs.engines.SGEComputationEngine import SGEComputationEngi... | karlnapf/ozone-roulette | ozone/scripts/sample_ozone_posterior_average_sge.py | Python | bsd-2-clause | 2,849 | [
"Gaussian"
] | ddee84652063d0c021005acde83dce294206d2bf78a59c05988c7ae158772bab |
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